#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
RBM23	55147	hgsc.bcm.edu	37	14	23371265	23371266	+	In_Frame_Ins	INS	-	-	GCA	rs376457710|rs568447355	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23371265_23371266insGCA	ENST00000359890.3	-	12	1364_1365	c.1169_1170insTGC	c.(1168-1170)gcc>gcTGCc	p.390_390A>AA	RBM23_ENST00000346528.5_In_Frame_Ins_p.356_356A>AA|RBM23_ENST00000399922.2_In_Frame_Ins_p.374_374A>AA|RBM23_ENST00000542016.2_In_Frame_Ins_p.220_220A>AA|RBM23_ENST00000555209.1_In_Frame_Ins_p.140_140A>AA	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23	390	Ala-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)		GGgcggcggcggcagcagcagc	0.554																																					p.A390delinsAA		Pindel,Atlas-Indel	.											.	RBM23	44	.	0			c.1170_1171insTGC						PASS	.																																			SO:0001652	inframe_insertion	55147	exon12			.	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.1167_1169dupTGC	14.37:g.23371272_23371274dupGCA	ENSP00000352956:p.Ala393dup	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	45	17	0.378	NM_001077351	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	In_Frame_Ins	INS	ENST00000359890.3	37	CCDS41921.1																																																																																			.	.	weak		0.554	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		
CCDC180	100499483	hgsc.bcm.edu	37	9	100092968	100092969	+	In_Frame_Ins	INS	-	-	GAGGAG	rs71369506|rs9696736|rs113264216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100092968_100092969insGAGGAG	ENST00000357054.1	+	32	3677_3678	c.2742_2743insGAGGAG	c.(2743-2745)gag>GAGGAGgag	p.915_915E>EEE	CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000411667.2_In_Frame_Ins_p.773_773E>EEE|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_In_Frame_Ins_p.776_776E>EEE|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_In_Frame_Ins_p.776_776E>EEE			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	915	Glu-rich.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											agaaggaggaagaggaggagga	0.5														2962	0.591454	0.7443	0.6614	5008	,	,		17231	0.5813		0.3907	False		,,,				2504	0.5521				p.E775delinsEEE		Pindel,Atlas-Indel	.											.	.	.	.	0			c.2325_2326insGAGGAG						PASS	.																																			SO:0001652	inframe_insertion	0	exon18			.	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.2749_2754dupGAGGAG	9.37:g.100092969_100092974dupGAGGAG	ENSP00000349562:p.GluGlu919dup	Somatic	19	.	.		WXS	Illumina HiSeq	Phase_I	32	17	0.531	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	In_Frame_Ins	INS	ENST00000357054.1	37																																																																																				-|0.500;GAGGAG|0.500	0.500	strong		0.500	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
MZT2A	653784	hgsc.bcm.edu	37	2	132248330	132248331	+	Intron	INS	-	-	GC	rs59442386|rs111311763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:132248330_132248331insGC	ENST00000309451.6	-	2	365				MZT2A_ENST00000410036.2_Intron|MIR4784_ENST00000579560.1_RNA|AC093838.4_ENST00000438378.2_RNA	NM_001085365.1	NP_001078834.1	Q6P582	MZT2A_HUMAN	mitotic spindle organizing protein 2A							centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				breast(1)|lung(1)	2						GAGGGAACCCGGGGGGCCTGGA	0.589														583	0.116414	0.2776	0.085	5008	,	,		18369	0.004		0.0915	False		,,,				2504	0.0624				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																			SO:0001627	intron_variant	100873780	.			.	BC018206	CCDS42758.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000173272	ENSG00000173272			33187	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2A"""	613449	"""family with sequence similarity 128, member A"""	FAM128A		20360068	Standard	NM_001085365		Approved	MOZART2A	uc002tsw.4	Q6P582	OTTHUMG00000153606	ENST00000309451.6:c.319+1117->GC	2.37:g.132248330_132248331insGC		Somatic	238	.	.		WXS	Illumina HiSeq	Phase_I	230	45	0.196	.	Q3SWV8|Q8WVB2	RNA	INS	ENST00000309451.6	37	CCDS42758.1																																																																																			-|0.500;GC|0.500	0.500	strong		0.589	MZT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331811.2		
NUCB2	4925	hgsc.bcm.edu	37	11	17352478	17352480	+	In_Frame_Del	DEL	ACA	ACA	-	rs189362726|rs535406012|rs3842269	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	177	.	.		WXS	Illumina HiSeq	Phase_I	136	45	0.331	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	
ETFB	2109	hgsc.bcm.edu	37	19	51857614	51857615	+	Intron	INS	-	-	G	rs55874945|rs141529162|rs74357706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51857614_51857615insG	ENST00000309244.4	-	2	149				CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.11_ENST00000600067.1_Intron|ETFB_ENST00000354232.4_Frame_Shift_Ins_p.P93fs	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						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)		GGCAAGAAGGTGGGGGCCTCAG	0.639													GGGGG|GGGGG|GGGGGG|insertion	119	0.023762	0.003	0.0231	5008	,	,		18043	0.0		0.0547	False		,,,				2504	0.045				p.P93fs		Pindel,Atlas-Indel	.											.	ETFB	46	.	0			c.279_280insC						PASS	.		,	34,4230		0,34,2098					,	-1.4	0.0		dbSNP_129	57	372,7882		10,352,3765	no	intron,frameshift	ETFB	NM_001985.2,NM_001014763.1	,	10,386,5863	A1A1,A1R,RR		4.5069,0.7974,3.2433	,	,		406,12112				SO:0001627	intron_variant	2109	exon1			.	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.58-52->C	19.37:g.51857619_51857619dupG		Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	44	13	0.295	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Frame_Shift_Ins	INS	ENST00000309244.4	37	CCDS12828.1																																																																																			-|0.980;G|0.020	0.020	strong		0.639	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
HOXB1	3211	hgsc.bcm.edu	37	17	46608184	46608185	+	In_Frame_Ins	INS	-	-	GGGCGCTGT	rs534792734|rs145570960	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	62	.	.		WXS	Illumina HiSeq	Phase_I	27	13	0.481	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		
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249503	71249532	+	In_Frame_Del	DEL	CCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	CCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	-	rs376694979|rs200517331|rs540274094|rs11234084|rs200162819|rs532438179|rs369043826|rs574564297	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	CCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:71249503_71249532delCCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	ENST00000398534.3	+	1	433_462	c.402_431delCCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	c.(400-432)tgccagtccagctgctgcaagccctgctgttcc>tgc	p.QSSCCKPCCS135del		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	135	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)	p.C143Y(1)		cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						CATCCTGCTGCCAGTCCAGCTGCTGCAAGCCCTGCTGTTCCCAGTCCAGC	0.617														167	0.0333466	0.0522	0.0245	5008	,	,		25774	0.0288		0.0348	False		,,,				2504	0.0174				p.134_144del		Atlas-Indel	.											.	KRTAP5-8	28	.	1	Substitution - Missense(1)	stomach(1)	c.401_430del						PASS	.																																			SO:0001651	inframe_deletion	57830	exon1			.	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.402_431delCCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	11.37:g.71249503_71249532delCCAGTCCAGCTGCTGCAAGCCCTGCTGTTC	ENSP00000420723:p.Gln135_Ser144del	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	157	13	0.0828025	NM_021046	Q6L8G7|Q6UTX6	In_Frame_Del	DEL	ENST00000398534.3	37	CCDS41683.1																																																																																			.	.	none		0.617	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
BPNT1	10380	hgsc.bcm.edu	37	1	220231181	220231181	+	3'UTR	DEL	T	T	-	rs34887640	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:220231181delT	ENST00000469520.2	-	0	2381				BPNT1_ENST00000354807.3_3'UTR|BPNT1_ENST00000322067.7_3'UTR			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		TTAAAATTACTGTGAAAAACA	0.318													T|T|-|deletion	1037	0.207069	0.0197	0.2305	5008	,	,		15564	0.2093		0.3588	False		,,,				2504	0.2853				.		Pindel,Atlas-Indel	.											.	BPNT1	29	.	0			.						PASS	.			49,665		19,11,327	1.0	1.0	1.0			1.2	0.0	1	dbSNP_126	1	439,805		197,45,380	no	utr-3	BPNT1	NM_006085.4		216,56,707	A1A1,A1R,RR		35.2894,6.8627,24.9234			220231181	488,1470	244	349	593	SO:0001624	3_prime_UTR_variant	10380	.			.	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.*1005A>-	1.37:g.220231181delT		Somatic	133	.	.		WXS	Illumina HiSeq	Phase_I	163	77	0.472	.	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	RNA	DEL	ENST00000469520.2	37	CCDS41469.1																																																																																			T|0.776;-|0.224	0.224	strong		0.318	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085	
OR8B3	390271	hgsc.bcm.edu	37	11	124266697	124266698	+	Frame_Shift_Ins	INS	-	-	G	rs201661436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:124266697_124266698insG	ENST00000354597.3	-	1	566_567	c.550_551insC	c.(550-552)ctcfs	p.L184fs		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	184						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)		AAGCTGGAGGAGGGGGAGTATG	0.49													ggggg|GGGGG|GGGGGG|insertion	176	0.0351438	0.0008	0.0288	5008	,	,		20997	0.0079		0.0477	False		,,,				2504	0.1012				p.L184fs		Atlas-Indel	.											.	OR8B3	36	.	0			c.551_552insC						PASS	.			41,4223		0,41,2091						3.6	1.0			43	431,7821		14,403,3709	no	frameshift	OR8B3	NM_001005467.1		14,444,5800	A1A1,A1R,RR		5.223,0.9615,3.7712				472,12044				SO:0001589	frameshift_variant	390271	exon1			.	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.551dupC	11.37:g.124266702_124266702dupG	ENSP00000346611:p.Leu184fs	Somatic	588	0	0		WXS	Illumina HiSeq	Phase_I	999	198	0.198198	NM_001005467	Q6IFQ8|Q8NGH1	Frame_Shift_Ins	INS	ENST00000354597.3	37	CCDS31709.1																																																																																			-|0.977;G|0.023	0.023	strong		0.490	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577707	90577707	+	RNA	DEL	G	G	-	rs527250207|rs202116886	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	107	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_012115		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	alt		0.378	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
ZFHX4	79776	hgsc.bcm.edu	37	8	77765299	77765301	+	In_Frame_Del	DEL	CCT	CCT	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:77765299_77765301delCCT	ENST00000521891.2	+	10	6590_6592	c.6142_6144delCCT	c.(6142-6144)cctdel	p.P2061del	ZFHX4_ENST00000518282.1_In_Frame_Del_p.P2035del|ZFHX4_ENST00000050961.6_In_Frame_Del_p.P2016del|ZFHX4_ENST00000455469.2_In_Frame_Del_p.P2016del	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2016					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(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			accaccaccacctcctcctcctc	0.601										HNSCC(33;0.089)																											p.2047_2048del		Atlas-Indel	.											.	ZFHX4	878	.	0			c.6141_6143del						PASS	.																																			SO:0001651	inframe_deletion	79776	exon10			.		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6142_6144delCCT	8.37:g.77765308_77765310delCCT	ENSP00000430497:p.Pro2061del	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	97	25	0.257732	NM_024721	G3V138|Q18PS0|Q6ZN20	In_Frame_Del	DEL	ENST00000521891.2	37	CCDS47878.2																																																																																			.	.	none		0.601	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
FZD2	2535	hgsc.bcm.edu	37	17	42636477	42636477	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:42636477delC	ENST00000315323.3	+	1	1553	c.1421delC	c.(1420-1422)accfs	p.T474fs		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	474					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cell-cell signaling (GO:0007267)|cochlea morphogenesis (GO:0090103)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|inner ear receptor cell development (GO:0060119)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of cGMP metabolic process (GO:0030825)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|sensory perception of smell (GO:0007608)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	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(2)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(8)	33		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.189)		GTGCCCGCCACCATCGTCATC	0.632																																					p.T474fs		Pindel,Atlas-Indel	.											.	FZD2	81	.	0			c.1420delA						PASS	.						73.0	59.0	64.0					17																	42636477		2203	4300	6503	SO:0001589	frameshift_variant	2535	exon1			.	L37882	CCDS11484.1	17q21.1	2014-01-29	2014-01-29			ENSG00000180340		"""GPCR / Class F : Frizzled receptors"""	4040	protein-coding gene	gene with protein product		600667	"""frizzled (Drosophila) homolog 2"", ""frizzled homolog 2 (Drosophila)"", ""frizzled 2, seven transmembrane spanning receptor"", ""frizzled family receptor 2"""			7558010, 9813155	Standard	NM_001466		Approved		uc002igx.2	Q14332		ENST00000315323.3:c.1421delC	17.37:g.42636477delC	ENSP00000323901:p.Thr474fs	Somatic	96	.	.		WXS	Illumina HiSeq	Phase_I	90	19	0.211	NM_001466	Q0VG82	Frame_Shift_Del	DEL	ENST00000315323.3	37	CCDS11484.1																																																																																			.	.	none		0.632	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111500816	111500817	+	Splice_Site	INS	-	-	TAAAA	rs145708081|rs369027426		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:111500816_111500817insTAAAA	ENST00000261486.5	-	23	2209		c.e23-1		EPB41L4A-AS1_ENST00000413221.2_lincRNA|EPB41L4A_ENST00000507810.1_Intron	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	117	43	0.367521	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
MICA	100507436	hgsc.bcm.edu	37	6	31380161	31380161	+	Frame_Shift_Del	DEL	G	G	-	rs41293539|rs547446871|rs138201170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31380161delG	ENST00000449934.2	+	5	1006	c.952delG	c.(952-954)ggcfs	p.G318fs	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)				TGTTGCTGCTGGCTGCTGCTA	0.453													?|GG|G|unsure	1026	0.204872	0.0537	0.2824	5008	,	,		19280	0.3869		0.1272	False		,,,				2504	0.2464				p.A317fs		Atlas-Indel	.											.	MICA	21	.	0			c.951delT						PASS	.						218.0	178.0	190.0					6																	31380161		692	1576	2268	SO:0001589	frameshift_variant	100507436	exon5			.	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.952delG	6.37:g.31380161delG	ENSP00000413079:p.Gly318fs	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	151	12	0.0794702	NM_001177519		Frame_Shift_Del	DEL	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	strong		0.453	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
AUTS2	26053	hgsc.bcm.edu	37	7	70255576	70255577	+	In_Frame_Ins	INS	-	-	CCA	rs538005366|rs35604576|rs375018695		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:70255576_70255577insCCA	ENST00000342771.4	+	19	3695_3696	c.3374_3375insCCA	c.(3373-3378)agccac>agCCAccac	p.1133_1134insH	AUTS2_ENST00000406775.2_In_Frame_Ins_p.1109_1110insH	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	1133	His-rich.									breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CACGACTACAGccaccaccacc	0.678																																					p.S1125delinsSH		Pindel,Atlas-Indel	.											.	AUTS2	173	.	0			c.3374_3375insCCA						PASS	.																																			SO:0001652	inframe_insertion	26053	exon19			.	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.3396_3398dupCCA	7.37:g.70255583_70255585dupCCA	ENSP00000344087:p.His1133_His1133dup	Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	71	13	0.183	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	In_Frame_Ins	INS	ENST00000342771.4	37	CCDS5539.1																																																																																			.	.	none		0.678	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
CELA1	1990	hgsc.bcm.edu	37	12	51723598	51723599	+	Frame_Shift_Ins	INS	-	-	G	rs398102298|rs76813052|rs17860363|rs75442020	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	83	.	.		WXS	Illumina HiSeq	Phase_I	55	19	0.345	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	
SYT14	255928	hgsc.bcm.edu	37	1	210267894	210267896	+	In_Frame_Del	DEL	GAA	GAA	-	rs144713062|rs200839898|rs2307890	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:210267894_210267896delGAA	ENST00000472886.1	+	5	684_686	c.670_672delGAA	c.(670-672)gaadel	p.E225del	SYT14_ENST00000399639.2_In_Frame_Del_p.E225del|SYT14_ENST00000422431.1_In_Frame_Del_p.E270del|SYT14_ENST00000534859.1_In_Frame_Del_p.E225del|SYT14_ENST00000537238.1_In_Frame_Del_p.E187del|SYT14_ENST00000367019.1_In_Frame_Del_p.E225del|SYT14_ENST00000367015.1_In_Frame_Del_p.E187del|SYT14_ENST00000271745.7_3'UTR			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	225					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)		TAAAGGATATGAAGAAGATGTTC	0.384														399	0.0796725	0.0098	0.0677	5008	,	,		16957	0.0655		0.1421	False		,,,				2504	0.1329				p.268_269del		Pindel,Atlas-Indel	.											.	SYT14	89	.	0			c.804_806del						PASS	.		,,,	107,4159		4,99,2030					,,,	2.2	1.0		dbSNP_134	76	1145,7109		84,977,3066	no	coding,coding,coding,coding	SYT14	NM_153262.2,NM_001146264.1,NM_001146262.1,NM_001146261.1	,,,	88,1076,5096	A1A1,A1R,RR		13.8721,2.5082,10.0	,,,	,,,		1252,11268				SO:0001651	inframe_deletion	255928	exon6			.	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.670_672delGAA	1.37:g.210267897_210267899delGAA	ENSP00000418901:p.Glu225del	Somatic	182	.	.		WXS	Illumina HiSeq	Phase_I	219	51	0.233	NM_001146264	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	In_Frame_Del	DEL	ENST00000472886.1	37	CCDS31014.1																																																																																			GAA|0.912;-|0.088	0.088	strong		0.384	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262	
PRDM2	7799	hgsc.bcm.edu	37	1	14106394	14106395	+	In_Frame_Ins	INS	-	-	CTC	rs2308040|rs148293494|rs59028030		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:14106394_14106395insCTC	ENST00000235372.7	+	8	2960_2961	c.2104_2105insCTC	c.(2104-2106)act>aCTCct	p.703_704insP	PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000311066.5_In_Frame_Ins_p.703_704insP|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000413440.1_In_Frame_Ins_p.502_503insP|PRDM2_ENST00000343137.4_In_Frame_Ins_p.502_503insP	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	703				P -> PP (in Ref. 1 and 7). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P703_A704insP(1)		endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		AGATAAACTAACTCCTGCAGGG	0.401																																					p.T702delinsTP		Pindel,Atlas-Indel	.											.	PRDM2	147	.	1	Insertion - In frame(1)	ovary(1)	c.2104_2105insCTC						PASS	.		,,,	2438,1826		699,1040,393					,,,	0.5	0.2		dbSNP_100	80	3443,4811		676,2091,1360	no	coding,coding,intron,coding	PRDM2	NM_015866.4,NM_012231.4,NM_001135610.1,NM_001007257.2	,,,	1375,3131,1753	A1A1,A1R,RR		41.7131,42.8236,46.9803	,,,	,,,		5881,6637				SO:0001652	inframe_insertion	7799	exon8			.	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.2105_2107dupCTC	1.37:g.14106395_14106397dupCTC	ENSP00000235372:p.Pro703_Pro703dup	Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	67	12	0.179	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	In_Frame_Ins	INS	ENST00000235372.7	37	CCDS150.1																																																																																			-|0.492;CTC|0.508	0.508	strong		0.401	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
CD33	945	hgsc.bcm.edu	37	19	51729104	51729107	+	Frame_Shift_Del	DEL	CCGG	CCGG	-	rs546468173|rs201074739|rs571957160|rs201342074	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCGG	CCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51729104_51729107delCCGG	ENST00000262262.4	+	3	485_488	c.464_467delCCGG	c.(463-468)cccggcfs	p.PG155fs	CD33_ENST00000391796.3_Frame_Shift_Del_p.PG155fs|CD33_ENST00000421133.2_Frame_Shift_Del_p.PG28fs|CD33_ENST00000436584.2_Frame_Shift_Del_p.PG28fs	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	155	Ig-like C2-type.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|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)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.G156C(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	ACTCTAGAACCCGGCCACTCCAAA	0.613														29	0.00579073	0.0015	0.0115	5008	,	,		18806	0.0		0.0189	False		,,,				2504	0.0				p.155_156del		Pindel,Atlas-Indel	.											.	CD33	55	.	1	Substitution - Missense(1)	lung(1)	c.463_466del						PASS	.		,,	24,4240		1,22,2109					,,	-6.1	0.0		dbSNP_131	84	233,8017		5,223,3897	no	frameshift,frameshift,frameshift	CD33	NM_001772.3,NM_001177608.1,NM_001082618.1	,,	6,245,6006	A1A1,A1R,RR		2.8242,0.5629,2.0537	,,	,,		257,12257				SO:0001589	frameshift_variant	945	exon3			.	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.464_467delCCGG	19.37:g.51729104_51729107delCCGG	ENSP00000262262:p.Pro155fs	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	92	28	0.304	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Frame_Shift_Del	DEL	ENST00000262262.4	37	CCDS33084.1																																																																																			CCGG|0.992;-|0.008	0.008	strong		0.613	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
MAGI1	9223	hgsc.bcm.edu	37	3	65425560	65425561	+	In_Frame_Ins	INS	-	-	CTG	rs113903140|rs35698502|rs142043619|rs377562449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:65425560_65425561insCTG	ENST00000497477.2	-	9	1262_1263	c.1263_1264insCAG	c.(1261-1266)cagaca>cagCAGaca	p.421_422insQ	MAGI1_ENST00000483466.1_In_Frame_Ins_p.421_422insQ|MAGI1_ENST00000402939.2_In_Frame_Ins_p.421_422insQ|MAGI1_ENST00000330909.8_In_Frame_Ins_p.421_422insQ|MAGI1_ENST00000470990.1_5'UTR			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	421	Poly-Gln.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|neuron death (GO:0070997)|protein complex assembly (GO:0006461)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	alpha-actinin binding (GO:0051393)|ATP binding (GO:0005524)|protein C-terminus binding (GO:0008022)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|liver(1)|lung(21)|pancreas(1)|skin(5)	51		Lung NSC(201;0.0016)		BRCA - Breast invasive adenocarcinoma(55;0.00138)|KIRC - Kidney renal clear cell carcinoma(15;0.0988)|Kidney(15;0.133)		CAACCTTCTGTctgctgctgct	0.559											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T422delinsQT		Pindel,Atlas-Indel	.											.	MAGI1	481	.	0			c.1264_1265insCAG						PASS	.																																			SO:0001652	inframe_insertion	9223	exon9			.	AB010894	CCDS33780.1, CCDS33781.1, CCDS2904.1	3p14.1	2009-10-06	2005-05-10	2005-05-10	ENSG00000151276	ENSG00000151276			946	protein-coding gene	gene with protein product		602625	"""BAI1-associated protein 1"""	BAIAP1		9647739, 9225980	Standard	XM_005265563		Approved	BAP1, MAGI-1, TNRC19, AIP3, WWP3	uc003dmn.3	Q96QZ7	OTTHUMG00000157554	ENST00000497477.2:c.1261_1263dupCAG	3.37:g.65425567_65425569dupCTG	ENSP00000424369:p.Gln421_Gln421dup	Somatic	73	.	.	1084	WXS	Illumina HiSeq	Phase_I	59	13	0.220	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	In_Frame_Ins	INS	ENST00000497477.2	37																																																																																				.	.	strong		0.559	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742	
OR2C1	4993	hgsc.bcm.edu	37	16	3406757	3406757	+	Frame_Shift_Del	DEL	T	T	-	rs142397376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3406757delT	ENST00000304936.2	+	1	869	c.817delT	c.(817-819)ttcfs	p.F273fs		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	273					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						CCAGGGCAAGTTCATTTCCCT	0.552													TT|TT|T|deletion	158	0.0315495	0.003	0.0403	5008	,	,		20105	0.0179		0.0716	False		,,,				2504	0.0368				p.K272fs		Pindel,Atlas-Indel	.											.	OR2C1	38	.	0			c.816delG						PASS	.			43,4215		0,43,2086	99.0	79.0	86.0			-5.8	0.7	16	dbSNP_134	91	496,7756		11,474,3641	no	frameshift	OR2C1	NM_012368.2		11,517,5727	A1A1,A1R,RR		6.0107,1.0099,4.3086			3406757	539,11971	2197	4299	6496	SO:0001589	frameshift_variant	4993	exon1			.	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.817delT	16.37:g.3406757delT	ENSP00000307726:p.Phe273fs	Somatic	154	.	.		WXS	Illumina HiSeq	Phase_I	162	51	0.315	NM_012368	A0AVA4|Q6IF34|Q6IF55	Frame_Shift_Del	DEL	ENST00000304936.2	37	CCDS10502.1																																																																																			T|0.962;-|0.038	0.038	strong		0.552	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3		
C19orf33	64073	hgsc.bcm.edu	37	19	38795547	38795549	+	In_Frame_Del	DEL	GAA	GAA	-	rs139805446	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38795547_38795549delGAA	ENST00000301246.5	+	4	365_367	c.264_266delGAA	c.(262-267)gtgaag>gtg	p.K91del	C19orf33_ENST00000588605.1_3'UTR|CTB-102L5.4_ENST00000591889.1_3'UTR	NM_033520.1	NP_277055.1	Q9GZP8	IMUP_HUMAN	chromosome 19 open reading frame 33	91						nucleus (GO:0005634)						all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			AGCCCAAAGTgaagaagaaggag	0.596														771	0.153954	0.0386	0.2349	5008	,	,		18940	0.1478		0.1839	False		,,,				2504	0.228				p.88_89del		Pindel,Atlas-Indel	.											.	C19orf33	9	.	0			c.263_265del						PASS	.		,,,,,,,	367,3897		16,335,1781					,,,,,,,	0.9	0.4		dbSNP_130	84	1288,6966		99,1090,2938	no	utr-3,coding,utr-3,utr-3,utr-3,utr-3,utr-3,utr-3	C19orf33,YIF1B	NM_033557.3,NM_033520.1,NM_001145463.1,NM_001145462.1,NM_001145461.1,NM_001039673.2,NM_001039672.2,NM_001039671.2	,,,,,,,	115,1425,4719	A1A1,A1R,RR		15.6046,8.6069,13.221	,,,,,,,	,,,,,,,		1655,10863				SO:0001651	inframe_deletion	64073	exon4			.	AF213678	CCDS12511.1	19q13.2	2012-10-26			ENSG00000167644	ENSG00000167644			16668	protein-coding gene	gene with protein product	"""immortalization-upregulated protein"", ""HAI-2 related small protein"", ""hepatocyte growth factor activator inhibitor type 2-related small protein"""					11080599	Standard	NM_033520		Approved	IMUP-1, IMUP-2, H2RSP, IMUP	uc002ohu.1	Q9GZP8	OTTHUMG00000181894	ENST00000301246.5:c.264_266delGAA	19.37:g.38795553_38795555delGAA	ENSP00000301246:p.Lys91del	Somatic	321	.	.		WXS	Illumina HiSeq	Phase_I	266	65	0.244	NM_033520	Q0P6G2|Q96H58|Q9HCR4	In_Frame_Del	DEL	ENST00000301246.5	37	CCDS12511.1																																																																																			GAA|0.847;-|0.153	0.153	strong		0.596	C19orf33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458168.1	NM_033520	
C20orf202	400831	hgsc.bcm.edu	37	20	1187535	1187536	+	Frame_Shift_Del	DEL	AG	AG	-	rs375391788|rs529757520		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1187535_1187536delAG	ENST00000400633.1	+	2	221_222	c.158_159delAG	c.(157-159)cagfs	p.Q53fs		NM_001009612.2	NP_001009612.1	A1L168	CT202_HUMAN	chromosome 20 open reading frame 202	53										endometrium(1)	1						ATTCAAGATCAGAGTCTCCTGC	0.604																																					p.53_53del		Pindel,Atlas-Indel	.											.	C20orf202	12	.	0			c.157_158del						PASS	.			2,2824		1,0,1412						3.5	1.0			37	19,5057		3,13,2522	no	frameshift	C20orf202	NM_001009612.2		4,13,3934	A1A1,A1R,RR		0.3743,0.0708,0.2658				21,7881				SO:0001589	frameshift_variant	400831	exon2			.		CCDS46567.1	20p13	2009-09-10			ENSG00000215595	ENSG00000215595			37254	protein-coding gene	gene with protein product							Standard	NM_001009612		Approved		uc002wer.4	A1L168	OTTHUMG00000129375	ENST00000400633.1:c.158_159delAG	20.37:g.1187537_1187538delAG	ENSP00000383474:p.Gln53fs	Somatic	135	.	.		WXS	Illumina HiSeq	Phase_I	107	37	0.346	NM_001009612		Frame_Shift_Del	DEL	ENST00000400633.1	37	CCDS46567.1																																																																																			.	.	none		0.604	C20orf202-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251531.1	NM_001009612	
CARD8	22900	hgsc.bcm.edu	37	19	48735017	48735018	+	Frame_Shift_Ins	INS	-	-	TT	rs146319637|rs140826611	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48735017_48735018insTT	ENST00000359009.4	-	4	438_439	c.126_127insAA	c.(124-129)aaagtcfs	p.V43fs	CARD8_ENST00000520753.1_Frame_Shift_Ins_p.V148fs|CARD8_ENST00000520015.1_Frame_Shift_Ins_p.V148fs|CARD8_ENST00000357778.5_5'UTR|CARD8_ENST00000520153.1_Frame_Shift_Ins_p.V98fs|CARD8_ENST00000447740.2_Frame_Shift_Ins_p.V98fs|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000519940.1_Frame_Shift_Ins_p.V148fs|CARD8_ENST00000391898.3_Frame_Shift_Ins_p.V148fs|CARD8_ENST00000521613.1_Frame_Shift_Ins_p.V98fs			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	43					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)		TCAAAACAGACTTTAGAAGCAT	0.376														211	0.0421326	0.0023	0.0274	5008	,	,		21883	0.0575		0.0527	False		,,,				2504	0.0798				p.V148fs		Pindel,Atlas-Indel	.											.	CARD8	53	.	0			c.442_443insAA						PASS	.		,,,,	47,4217		0,47,2085					,,,,	-0.7	0.0		dbSNP_134	104	487,7767		16,455,3656	yes	frameshift,frameshift,frameshift,frameshift,frameshift	CARD8	NM_014959.3,NM_001184903.1,NM_001184902.1,NM_001184901.1,NM_001184900.1	,,,,	16,502,5741	A1A1,A1R,RR		5.9002,1.1023,4.2659	,,,,	,,,,		534,11984				SO:0001589	frameshift_variant	22900	exon5			.	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.125_126dupAA	19.37:g.48735018_48735019dupTT	ENSP00000351901:p.Val43fs	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	109	38	0.349	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Frame_Shift_Ins	INS	ENST00000359009.4	37																																																																																				-|0.962;TT|0.038	0.038	strong		0.376	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
OR51F1	256892	hgsc.bcm.edu	37	11	4790874	4790874	+	Frame_Shift_Del	DEL	G	G	-	rs563980182|rs34672924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790874delG	ENST00000380383.1	-	1	294	c.295delC	c.(295-297)cgtfs	p.R99fs	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Frame_Shift_Del_p.R92fs|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	99						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)		CTGATTTCACGTGCCTCAAAC	0.423													G|G|-|deletion	1081	0.215855	0.4569	0.2017	5008	,	,		22520	0.0		0.2714	False		,,,				2504	0.0654				p.R92fs		Pindel,Atlas-Indel	.											OR51F1,NS,carcinoma,-1,1	OR51F1	60	1	0			c.275delG	GRCh37	CD035870	OR51F1	D	rs34672924	PASS	.			1902,2362		424,1054,654	57.0	62.0	60.0			-0.4	0.0	11	dbSNP_126	75	2098,6156		281,1536,2310	no	frameshift	OR51F1	NM_001004752.1		705,2590,2964	A1A1,A1R,RR		25.418,44.606,31.954			4790874	4000,8518	1817	4059	5876	SO:0001589	frameshift_variant	256892	exon1			.	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.295delC	11.37:g.4790874delG	ENSP00000369744:p.Arg99fs	Somatic	137	.	.		WXS	Illumina HiSeq	Phase_I	118	37	0.314	NM_001004752		Frame_Shift_Del	DEL	ENST00000380383.1	37																																																																																				G|0.772;-|0.228	0.228	strong		0.423	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
PGGT1B	5229	hgsc.bcm.edu	37	5	114557642	114557643	+	Frame_Shift_Ins	INS	-	-	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:114557642_114557643insA	ENST00000419445.1	-	7	741_742	c.721_722insT	c.(721-723)tcafs	p.S241fs	PGGT1B_ENST00000379615.3_Intron|PGGT1B_ENST00000514178.1_5'UTR	NM_005023.3	NP_005014.2	P53609	PGTB1_HUMAN	protein geranylgeranyltransferase type I, beta subunit	241					negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|protein geranylgeranylation (GO:0018344)|response to cytokine (GO:0034097)	CAAX-protein geranylgeranyltransferase complex (GO:0005953)	CAAX-protein geranylgeranyltransferase activity (GO:0004662)|protein geranylgeranyltransferase activity (GO:0004661)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6		all_cancers(142;0.000523)|all_epithelial(76;6.45e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		Epithelial(69;2.95e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.98e-08)|all cancers(49;3.1e-06)		TTCTTTTTCTGAAAAAACTTCT	0.351																																					p.S241fs		Pindel,Atlas-Indel	.											.	PGGT1B	26	.	0			c.722_723insT						PASS	.																																			SO:0001589	frameshift_variant	5229	exon7			.		CCDS4116.1	5q23.1	2008-02-05			ENSG00000164219	ENSG00000164219			8895	protein-coding gene	gene with protein product		602031				8106351	Standard	NM_005023		Approved	GGTI, BGGI	uc003kqw.4	P53609	OTTHUMG00000128893	ENST00000419445.1:c.722dupT	5.37:g.114557648_114557648dupA	ENSP00000404676:p.Ser241fs	Somatic	475	.	.		WXS	Illumina HiSeq	Phase_I	423	73	0.173	NM_005023	Q5MJP9	Frame_Shift_Ins	INS	ENST00000419445.1	37	CCDS4116.1																																																																																			.	.	none		0.351	PGGT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250855.2	NM_005023	
CLSPN	63967	hgsc.bcm.edu	37	1	36203660	36203662	+	In_Frame_Del	DEL	TTC	TTC	-	rs200760879	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:36203660_36203662delTTC	ENST00000318121.3	-	22	3652_3654	c.3595_3597delGAA	c.(3595-3597)gaadel	p.E1199del	CLSPN_ENST00000251195.5_In_Frame_Del_p.E1199del|RP11-435D7.3_ENST00000373226.2_RNA|CLSPN_ENST00000466308.1_5'Flank|CLSPN_ENST00000373220.3_In_Frame_Del_p.E1135del|CLSPN_ENST00000520551.1_In_Frame_Del_p.E1146del	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	1199					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				CCTCCCCAATTTCTTCTTCTTCT	0.365														141	0.028155	0.0015	0.0346	5008	,	,		11091	0.001		0.0676	False		,,,				2504	0.047				p.1199_1200del		Pindel,Atlas-Indel	.											.	CLSPN	248	.	0			c.3596_3598del						PASS	.		,	42,4224		0,42,2091					,	1.1	1.0			153	536,7718		22,492,3613	no	coding,coding	CLSPN	NM_022111.3,NM_001190481.1	,	22,534,5704	A1A1,A1R,RR		6.4938,0.9845,4.6166	,	,		578,11942				SO:0001651	inframe_deletion	63967	exon22			.	AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"""claspin homolog (Xenopus laevis)"""			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.3595_3597delGAA	1.37:g.36203669_36203671delTTC	ENSP00000312995:p.Glu1199del	Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	49	14	0.286	NM_022111	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	In_Frame_Del	DEL	ENST00000318121.3	37	CCDS396.1																																																																																			TTC|0.962;-|0.038	0.038	strong		0.365	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111	
COL6A3	1293	hgsc.bcm.edu	37	2	238244864	238244866	+	In_Frame_Del	DEL	GCA	GCA	-	rs35879189	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000353578.4_In_Frame_Del_p.2753_2754AA>A|COL6A3_ENST00000347401.3_In_Frame_Del_p.2758_2759AA>A|COL6A3_ENST00000346358.4_In_Frame_Del_p.2759_2760AA>A|COL6A3_ENST00000409809.1_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,Atlas-Indel	.											.	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	53	.	.		WXS	Illumina HiSeq	Phase_I	52	16	0.308	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	
KRTAP9-8	83901	hgsc.bcm.edu	37	17	39394711	39394725	+	In_Frame_Del	DEL	GACCACCTGCTGCAG	GACCACCTGCTGCAG	-	rs550091794|rs374427254|rs373648251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GACCACCTGCTGCAG	GACCACCTGCTGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39394711_39394725delGACCACCTGCTGCAG	ENST00000254072.6	+	1	415_429	c.408_422delGACCACCTGCTGCAG	c.(406-423)gagaccacctgctgcagg>gag	p.TTCCR137del		NM_031963.2	NP_114169.2	Q9BYQ0	KRA98_HUMAN	keratin associated protein 9-8	137	15 X 5 AA repeats of C-C-[RQVSGE]- [SPSNQ]-[TASPI].					keratin filament (GO:0045095)				lung(8)|ovary(1)|prostate(1)	10		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCTGCTGTGAGACCACCTGCTGCAGGACCACTTGC	0.591																																					p.136_141del		Atlas-Indel	.											.	KRTAP9-8	29	.	0			c.407_421del						PASS	.																																			SO:0001651	inframe_deletion	83901	exon1			.	AJ406950	CCDS42334.1	17q21.2	2013-06-25			ENSG00000187272	ENSG00000187272		"""Keratin associated proteins"""	17231	protein-coding gene	gene with protein product						11279113	Standard	NM_031963		Approved	KAP9.8	uc002hwh.4	Q9BYQ0	OTTHUMG00000133604	ENST00000254072.6:c.408_422delGACCACCTGCTGCAG	17.37:g.39394711_39394725delGACCACCTGCTGCAG	ENSP00000254072:p.Thr137_Arg141del	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	220	26	0.118182	NM_031963		In_Frame_Del	DEL	ENST00000254072.6	37	CCDS42334.1																																																																																			.	.	weak		0.591	KRTAP9-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257712.1		
TRAK1	22906	hgsc.bcm.edu	37	3	42251577	42251578	+	Intron	INS	-	-	GGA	rs10634555|rs35624871		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:42251577_42251578insGGA	ENST00000327628.5	+	14	2363				TRAK1_ENST00000341421.3_In_Frame_Ins_p.640_641insE|TRAK1_ENST00000396175.1_Intron|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						CCAGCGGCCACggaggaggagg	0.629																																					p.T688delinsTE	GBM(44;195 884 22595 31865 41850)	Pindel,Atlas-Indel	.											TRAK1,caecum,carcinoma,0,1	TRAK1	188	1	1	Deletion - In frame(1)	kidney(1)	c.2063_2064insGGA						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+100->GGA	3.37:g.42251584_42251586dupGGA		Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	72	11	0.153	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	In_Frame_Ins	INS	ENST00000327628.5	37	CCDS43072.1																																																																																			.	.	strong		0.629	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
AKAP9	10142	hgsc.bcm.edu	37	7	91652178	91652179	+	In_Frame_Ins	INS	-	-	AAC	rs111673064|rs10644111|rs397825978|rs34756483	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91652178_91652179insAAC	ENST00000359028.2	+	15	4264_4265	c.4039_4040insAAC	c.(4039-4041)aaa>aAACaa	p.1347_1348insQ	AKAP9_ENST00000356239.3_In_Frame_Ins_p.1335_1336insQ|AKAP9_ENST00000358100.2_In_Frame_Ins_p.1347_1348insQ			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1347			K -> KQ. {ECO:0000269|PubMed:10202149}.		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)	p.K1335_L1336insQ(1)|p.K1347_L1348insQ(1)		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)			TGAAAAAACTAAACTTGAAGAA	0.312			T	BRAF	papillary thyroid									2127	0.42472	0.6657	0.3689	5008	,	,		15358	0.1825		0.3867	False		,,,				2504	0.4274				p.K1335delinsKQ		Pindel,Atlas-Indel	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	2	Insertion - In frame(2)	ovary(2)	c.4003_4004insAAC						PASS	.		,	2670,1594		824,1022,286					,	2.2	0.0		dbSNP_119	46	3327,4927		650,2027,1450	no	coding,coding	AKAP9	NM_147185.2,NM_005751.4	,	1474,3049,1736	A1A1,A1R,RR		40.3077,37.3827,47.907	,	,		5997,6521				SO:0001652	inframe_insertion	10142	exon14			.	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.4040_4042dupAAC	7.37:g.91652179_91652181dupAAC	ENSP00000351922:p.Lys1347_Leu1348insGln	Somatic	58	.	.		WXS	Illumina HiSeq	Phase_I	52	38	0.731	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	In_Frame_Ins	INS	ENST00000359028.2	37																																																																																				-|0.604;AAC|0.396	0.396	strong		0.312	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
ZNF681	148213	hgsc.bcm.edu	37	19	23927742	23927743	+	Frame_Shift_Del	DEL	CA	CA	-	rs61397759	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	73	.	.		WXS	Illumina HiSeq	Phase_I	54	19	0.352	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	
PRSS48	345062	hgsc.bcm.edu	37	4	152201018	152201019	+	Frame_Shift_Ins	INS	-	-	CAGGT	rs148861921|rs71901196|rs77216366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	194	.	.		WXS	Illumina HiSeq	Phase_I	141	25	0.177	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	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388375	1388376	+	Frame_Shift_Ins	INS	-	-	CA	rs533172496|rs530731346|rs373032956	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1388375_1388376insCA	ENST00000324803.4	+	1	3036_3037	c.76_77insCA	c.(76-78)tcafs	p.S26fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	26					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)			GCCCGCCTGCTCATGTGCCCAT	0.639														782	0.15615	0.1952	0.1412	5008	,	,		17889	0.0278		0.2286	False		,,,				2504	0.1718				p.S26fs		Atlas-Indel	.											.	CRIPAK	185	.	0			c.76_77insCA						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.77_78dupCA	4.37:g.1388376_1388377dupCA	ENSP00000323978:p.Ser26fs	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	191	30	0.157068	NM_175918	Q8NB03	Frame_Shift_Ins	INS	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.639	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
HACE1	57531	hgsc.bcm.edu	37	6	105192108	105192110	+	Intron	DEL	AAC	AAC	-	rs72218235|rs374160571	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:105192108_105192110delAAC	ENST00000262903.4	-	22	2719				HACE1_ENST00000517995.1_Intron|HACE1_ENST00000369125.2_Intron	NM_020771.3	NP_065822.2	Q8IYU2	HACE1_HUMAN	HECT domain and ankyrin repeat containing E3 ubiquitin protein ligase 1						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)	p.?(1)		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)		CAGAACCACTAACAACAAGAACA	0.335														967	0.193091	0.4402	0.1441	5008	,	,		17448	0.003		0.1481	False		,,,				2504	0.136				.		Pindel,Atlas-Indel	.											.	HACE1	96	.	1	Unknown(1)	pancreas(1)	.						PASS	.			1754,2510		344,1066,722						4.5	0.9		dbSNP_120	64	1339,6909		107,1125,2892	no	intron	HACE1	NM_020771.3		451,2191,3614	A1A1,A1R,RR		16.2342,41.1351,24.7203				3093,9419				SO:0001627	intron_variant	57531	.			.	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.2443-3GTT>-	6.37:g.105192111_105192113delAAC		Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	120	35	0.292	.	A8K6U5|B3KY89|B4DFM6|B4DTQ4|B7Z9X6|E9PGP0|Q5VU99|Q5VUA0|Q8ND12|Q9P2M6	Splice_Site	DEL	ENST00000262903.4	37	CCDS5050.1																																																																																			AAC|0.835;-|0.165	0.165	strong		0.335	HACE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041643.2	XM_045095	
SLC22A1	6580	hgsc.bcm.edu	37	6	160560898	160560905	+	Splice_Site	DEL	TGGTAAGT	TGGTAAGT	-	rs36056065|rs35854239|rs200234072|rs77297078|rs113569197	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TGGTAAGT	TGGTAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160560898_160560905delTGGTAAGT	ENST00000366963.4	+	7	1422_1423	c.1275_1276delTGGTAAGT	c.(1273-1278)cctggt>ccgt	p.G426fs	SLC22A1_ENST00000324965.4_Splice_Site_p.G426fs|SLC22A1_ENST00000457470.2_Splice_Site_p.G426fs	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	426					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)	TTATCTCACCTGGTAAGTTGGTAAGTTG	0.495														3453	0.689497	0.7413	0.7839	5008	,	,		15006	0.7411		0.5825	False		,,,				2504	0.6094				p.425_426del		Pindel,Atlas-Indel	.											.	SLC22A1	69	.	0			c.1274_1276del						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+1TGGTAAGT>-	6.37:g.160560906_160560913delTGGTAAGT		Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	35	24	0.686	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	In_Frame_Del	DEL	ENST00000366963.4	37	CCDS5274.1																																																																																			TGGTAAGT|0.311;-|0.689	0.689	strong		0.495	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		Frame_Shift_Del
SHKBP1	92799	hgsc.bcm.edu	37	19	41095087	41095112	+	Intron	DEL	GAGGACAGTCCTGTCCAACAGGGAGG	GAGGACAGTCCTGTCCAACAGGGAGG	-	rs528660073|rs547185289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGGACAGTCCTGTCCAACAGGGAGG	GAGGACAGTCCTGTCCAACAGGGAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41095087_41095112delGAGGACAGTCCTGTCCAACAGGGAGG	ENST00000291842.5	+	15	1638				SHKBP1_ENST00000600733.1_Intron|SHKBP1_ENST00000597649.1_Intron	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1						protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGGCAGCGGTGAGGACAGTCCTGTCCAACAGGGAGGGAGGACAGTC	0.606														1576	0.314696	0.3275	0.3242	5008	,	,		11236	0.3155		0.3231	False		,,,				2504	0.2812				.		Pindel,Atlas-Indel	.											.	SHKBP1	68	.	0			.						PASS	.																																			SO:0001627	intron_variant	92799	.			.	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"""WD repeat domain containing"""	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.1589+3GAGGACAGTCCTGTCCAACAGGGAGG>-	19.37:g.41095087_41095112delGAGGACAGTCCTGTCCAACAGGGAGG		Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	58	29	0.500	.	Q8N2I6|Q8WY93|Q96IB8	Splice_Site	DEL	ENST00000291842.5	37	CCDS12560.1																																																																																			.	.	none		0.606	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392	
REXO1	57455	hgsc.bcm.edu	37	19	1825928	1825930	+	In_Frame_Del	DEL	CTC	CTC	-	rs149465929|rs75443592|rs199696044	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1825928_1825930delCTC	ENST00000170168.4	-	3	2018_2020	c.1924_1926delGAG	c.(1924-1926)gagdel	p.E642del	REXO1_ENST00000587524.1_5'Flank|CTB-31O20.4_ENST00000590531.1_RNA|CTB-31O20.4_ENST00000587741.1_RNA|CTB-31O20.4_ENST00000593201.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	642						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		CCTCACTCTTCTCTTCCTTGGGG	0.606														1503	0.30012	0.2844	0.4135	5008	,	,		15520	0.3829		0.2087	False		,,,				2504	0.2495				p.642_643del		Pindel,Atlas-Indel	.											.	REXO1	55	.	0			c.1925_1927del						PASS	.			1300,2964		203,894,1035						3.2	0.0		dbSNP_106	100	1727,6527		175,1377,2575	no	coding	REXO1	NM_020695.3		378,2271,3610	A1A1,A1R,RR		20.9232,30.4878,24.1812				3027,9491				SO:0001651	inframe_deletion	57455	exon3			.	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1924_1926delGAG	19.37:g.1825928_1825930delCTC	ENSP00000170168:p.Glu642del	Somatic	189	.	.		WXS	Illumina HiSeq	Phase_I	186	56	0.301	NM_020695	Q9ULT2	In_Frame_Del	DEL	ENST00000170168.4	37	CCDS32866.1																																																																																			CTC|0.704;-|0.296	0.296	strong		0.606	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
SIRPA	140885	hgsc.bcm.edu	37	20	1896052	1896054	+	In_Frame_Del	DEL	CGA	CGA	-	rs139878822|rs202172737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1896052_1896054delCGA	ENST00000358771.4	+	2	539_541	c.387_389delCGA	c.(385-390)cccgat>cct	p.D131del	SIRPA_ENST00000356025.3_In_Frame_Del_p.D131del|SIRPA_ENST00000400068.3_In_Frame_Del_p.D131del	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	131	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.D131delD(2)|p.D130A(1)|p.P129P(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		AAGGGAGCCCCGATGACGTGGAG	0.527														1950	0.389377	0.264	0.4063	5008	,	,		16040	0.5933		0.2932	False		,,,				2504	0.4356				p.129_130del	GBM(155;1668 1920 5945 42733 48121)	Atlas-Indel	.											SIRPA,NS,carcinoma,-1,1	SIRPA	83	1	4	Deletion - In frame(2)|Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)|upper_aerodigestive_tract(1)|large_intestine(1)	c.386_388del						PASS	.		,,	1147,3105		167,813,1146					,,	2.0	0.0		dbSNP_134	106	2654,5494		452,1750,1872	no	coding,coding,coding	SIRPA	NM_080792.2,NM_001040023.1,NM_001040022.1	,,	619,2563,3018	A1A1,A1R,RR		32.5724,26.9755,30.6532	,,	,,		3801,8599				SO:0001651	inframe_deletion	140885	exon3			.	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.387_389delCGA	20.37:g.1896052_1896054delCGA	ENSP00000351621:p.Asp131del	Somatic	464	0	0		WXS	Illumina HiSeq	Phase_I	253	26	0.102767	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	In_Frame_Del	DEL	ENST00000358771.4	37	CCDS13022.1																																																																																			.	.	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
FERD3L	222894	hgsc.bcm.edu	37	7	19184746	19184747	+	In_Frame_Ins	INS	-	-	TCT	rs34966908|rs199985178|rs71017023	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	39	.	.		WXS	Illumina HiSeq	Phase_I	58	14	0.241	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		
ODF1	4956	hgsc.bcm.edu	37	8	103573011	103573037	+	In_Frame_Del	DEL	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	-	rs143802899|rs111689913|rs568456031|rs372688769|rs369192995|rs377699584|rs62523271|rs62523272|rs62523273|rs386728348|rs58232162|rs386728346|rs150771034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:103573011_103573037delTGCAACCCCTGCAGCCCCTGCAACCCG	ENST00000285402.3	+	2	808_834	c.652_678delTGCAACCCCTGCAGCCCCTGCAACCCG	c.(652-678)tgcaacccctgcagcccctgcaacccgdel	p.CNPCSPCNP218del	ODF1_ENST00000518835.1_In_Frame_Del_p.CNPCSPCNP11del	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	218	C-X-P repeat region.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			ctgcagcccctgcaacccctgcagcccctgcaacccgtgcagcccAT	0.542														1567	0.312899	0.2731	0.4193	5008	,	,		21683	0.3244		0.2614	False		,,,				2504	0.3323				p.217_226del		Pindel,Atlas-Indel	.											.	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.651_677del						PASS	.																																			SO:0001651	inframe_deletion	4956	exon2			.	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.652_678delTGCAACCCCTGCAGCCCCTGCAACCCG	8.37:g.103573011_103573037delTGCAACCCCTGCAGCCCCTGCAACCCG	ENSP00000285402:p.Cys218_Pro226del	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	198	49	0.247	NM_024410	Q3SX72	In_Frame_Del	DEL	ENST00000285402.3	37	CCDS6293.1																																																																																			.	.	none		0.542	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1		
CPS1	1373	hgsc.bcm.edu	37	2	211421452	211421453	+	5'UTR	INS	-	-	TCT	rs61509952|rs3835047|rs34778124|rs201874641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:211421452_211421453insTCT	ENST00000233072.5	+	0	191_192				CPS1_ENST00000430249.2_In_Frame_Ins_p.5_6insF	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial						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)	GCCACAAATCATCAAAATGACG	0.347														2389	0.477037	0.5968	0.5086	5008	,	,		19934	0.3492		0.4175	False		,,,				2504	0.4857				p.I5delinsIF		Atlas-Indel	.											.	CPS1	485	.	0			c.13_14insTCT						PASS	.		,	2464,1802		707,1050,376					,	3.0	1.0		dbSNP_107	63	3312,4938		646,2020,1459	no	utr-5,coding	CPS1	NM_001875.4,NM_001122633.2	,	1353,3070,1835	A1A1,A1R,RR		40.1455,42.241,46.1489	,	,		5776,6740				SO:0001623	5_prime_UTR_variant	1373	exon2			.	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.-5->TCT	2.37:g.211421452_211421453insTCT		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	84	14	0.166667	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	In_Frame_Ins	INS	ENST00000233072.5	37	CCDS2393.1																																																																																			-|0.556;TCT|0.444	0.444	strong		0.347	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
KANK3	256949	hgsc.bcm.edu	37	19	8389893	8389895	+	In_Frame_Del	DEL	TCC	TCC	-	rs367746100|rs111905975	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:8389893_8389895delTCC	ENST00000593649.1	-	8	2087_2089	c.2022_2024delGGA	c.(2020-2025)gaggac>gac	p.E674del	KANK3_ENST00000330915.3_In_Frame_Del_p.E674del			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	674										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						CACAGCCATGTCCTCCTCTTCCT	0.626														770	0.153754	0.2958	0.1383	5008	,	,		19550	0.0655		0.1223	False		,,,				2504	0.0961				p.675_675del		Pindel,Atlas-Indel	.											.	KANK3	35	.	0			c.2023_2025del						PASS	.			1092,3172		142,808,1182						3.3	1.0		dbSNP_132	62	1089,7165		100,889,3138	no	coding	KANK3	NM_198471.2		242,1697,4320	A1A1,A1R,RR		13.1936,25.6098,17.4229				2181,10337				SO:0001651	inframe_deletion	256949	exon8			.	AK128815	CCDS12199.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000186994		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	24796	protein-coding gene	gene with protein product		614611	"""ankyrin repeat domain 47"""	ANKRD47		17996375, 19554261	Standard	NM_198471		Approved	FLJ46061	uc010dwa.3	Q6NY19		ENST00000593649.1:c.2022_2024delGGA	19.37:g.8389896_8389898delTCC	ENSP00000470728:p.Glu674del	Somatic	89	.	.		WXS	Illumina HiSeq	Phase_I	96	38	0.396	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	In_Frame_Del	DEL	ENST00000593649.1	37																																																																																				TCC|0.852;-|0.148	0.148	strong		0.626	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144915624	144915624	+	Frame_Shift_Del	DEL	G	G	-	rs66512216|rs1778112	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:144915624delG	ENST00000369354.3	-	14	1990	c.1801delC	c.(1801-1803)ctgfs	p.L602fs	PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.L668fs|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.L602fs|PDE4DIP_ENST00000529945.1_Frame_Shift_Del_p.L765fs|PDE4DIP_ENST00000313431.9_Frame_Shift_Del_p.L765fs|PDE4DIP_ENST00000369351.3_Frame_Shift_Del_p.L602fs|PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.L739fs|PDE4DIP_ENST00000479408.2_Frame_Shift_Del_p.L389fs|PDE4DIP_ENST00000530740.1_Frame_Shift_Del_p.L739fs|PDE4DIP_ENST00000369349.3_Frame_Shift_Del_p.L602fs			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	602					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)		TTGCAGAGCAGTGTTGCACTA	0.463			T	PDGFRB	MPD																																p.L764fs		Pindel,Atlas-Indel	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.2291delT						PASS	.		,,,,	205,4061		0,205,1928	117.0	102.0	107.0		,,,,	5.2	0.9	1	dbSNP_130	115	1400,6846		0,1400,2723	no	frameshift,frameshift,frameshift,frameshift,frameshift	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1,NM_001002812.1,NM_001002811.1	,,,,	0,1605,4651	A1A1,A1R,RR		16.9779,4.8054,12.8277	,,,,	,,,,	144915624	1605,10907	2203	4296	6499	SO:0001589	frameshift_variant	9659	exon10			.	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.1801delC	1.37:g.144915624delG	ENSP00000358360:p.Leu602fs	Somatic	159	.	.		WXS	Illumina HiSeq	Phase_I	177	30	0.169	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Frame_Shift_Del	DEL	ENST00000369354.3	37	CCDS30824.1																																																																																			G|0.808;-|0.192	0.192	strong		0.463	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305776	+	In_Frame_Ins	INS	-	-	GGCAGCAGCTGGGGC	rs535144703|rs141265645|rs58117746|rs146438235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39305775_39305776insGGCAGCAGCTGGGGC	ENST00000343246.4	-	1	278_279	c.244_245insGCCCCAGCTGCTGCC	c.(244-246)cag>cGCCCCAGCTGCTGCCag	p.81_82insRPSCC		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	81	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcaggtggtctggcagcagcag	0.653														2119	0.423123	0.5401	0.4236	5008	,	,		17097	0.3065		0.3897	False		,,,				2504	0.4192				p.Q82delinsRPSCCQ		Atlas-Indel	.											KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	0			c.245_246insGCCCCAGCTGCTGCC						PASS	.																																			SO:0001652	inframe_insertion	85289	exon1			.	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.244_245insGCCCCAGCTGCTGCC	17.37:g.39305775_39305776insGGCAGCAGCTGGGGC	ENSP00000340546:p.Cys81_Gln82insArgProSerCysCys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	52	34	0.653846	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																			.	.	none		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
VSIG10	54621	hgsc.bcm.edu	37	12	118506328	118506333	+	In_Frame_Del	DEL	TCCTCC	TCCTCC	-	rs67582641|rs199991783|rs72125532	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCCTCC	TCCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:118506328_118506333delTCCTCC	ENST00000359236.5	-	8	1692_1697	c.1416_1421delGGAGGA	c.(1414-1422)gaggaggaa>gaa	p.472_474EEE>E		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	472	Glu-rich.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						TGCAGCAtcttcctcctcctcctcct	0.485														1628	0.32508	0.3737	0.2939	5008	,	,		23177	0.5248		0.1829	False		,,,				2504	0.2219				p.473_474del		Atlas-Indel	.											.	VSIG10	41	.	0			c.1417_1422del						PASS	.																																			SO:0001651	inframe_deletion	54621	exon8			.		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1416_1421delGGAGGA	12.37:g.118506334_118506339delTCCTCC	ENSP00000352172:p.Glu472_Glu473del	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	232	45	0.193966	NM_019086	Q9NWQ7	In_Frame_Del	DEL	ENST00000359236.5	37	CCDS44992.1																																																																																			.	.	strong		0.485	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744801	23744803	+	In_Frame_Del	DEL	CAT	CAT	-	rs148005528		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23744801_23744803delCAT	ENST00000357460.5	-	2	1798_1800	c.1634_1636delATG	c.(1633-1638)gatgtg>gtg	p.D545del	HOMEZ_ENST00000431326.2_In_Frame_Del_p.D547del|HOMEZ_ENST00000561013.1_In_Frame_Del_p.D547del	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	545					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		TGTATGatcacatcatcatcatc	0.438																																					p.545_546del		Pindel,Atlas-Indel	.											.	HOMEZ	80	.	0			c.1635_1637del						PASS	.																																			SO:0001651	inframe_deletion	57594	exon2			.	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1634_1636delATG	14.37:g.23744810_23744812delCAT	ENSP00000350049:p.Asp545del	Somatic	145	.	.		WXS	Illumina HiSeq	Phase_I	215	40	0.186	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	In_Frame_Del	DEL	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	strong		0.438	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
SULT2B1	6820	hgsc.bcm.edu	37	19	49102605	49102610	+	In_Frame_Del	DEL	CCAGCC	CCAGCC	-	rs16989366|rs535907004		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCAGCC	CCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49102605_49102610delCCAGCC	ENST00000201586.2	+	7	1218_1223	c.1040_1045delCCAGCC	c.(1039-1047)tccagcccc>tcc	p.SP352del	SULT2B1_ENST00000323090.4_In_Frame_Del_p.SP337del	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	352	Pro/Ser-rich.				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)		agacccaactccagccccagccccag	0.66																																					p.347_348del		Pindel,Atlas-Indel	.											.	SULT2B1	72	.	0			c.1039_1044del						PASS	.		,	1,4133		0,1,2066					,	-3.9	0.0		dbSNP_126	21	16,8050		0,16,4017	no	coding,coding	SULT2B1	NM_177973.1,NM_004605.2	,	0,17,6083	A1A1,A1R,RR		0.1984,0.0242,0.1393	,	,		17,12183				SO:0001651	inframe_deletion	6820	exon7			.	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.1040_1045delCCAGCC	19.37:g.49102611_49102616delCCAGCC	ENSP00000201586:p.Ser352_Pro353del	Somatic	244	.	.		WXS	Illumina HiSeq	Phase_I	203	38	0.187	NM_177973	O00205|O75814	In_Frame_Del	DEL	ENST00000201586.2	37	CCDS12723.1																																																																																			.	.	none		0.660	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
TRDN	10345	hgsc.bcm.edu	37	6	123594510	123594511	+	Splice_Site	INS	-	-	A	rs147062785|rs386359375	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:123594510_123594511insA	ENST00000398178.3	-	28	1619		c.e28-2		TRDN_ENST00000334268.4_Splice_Site	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin						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)		CAGATATAGCTAAAATAAATAA	0.238													AAAAA|AAAA|AAAAA|deletion	1317	0.262979	0.0946	0.2104	5008	,	,		12974	0.5069		0.1859	False		,,,				2504	0.3558				.		Pindel,Atlas-Indel	.											.	TRDN	88	.	0			c.1598-2->T						PASS	.			198,1964		33,132,916						4.2	0.0		dbSNP_130	5	764,4058		183,398,1830	no	splice-3	TRDN	NM_006073.2		216,530,2746	A1A1,A1R,RR		15.844,9.1582,13.7743				962,6022				SO:0001630	splice_region_variant	10345	exon29			.	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.1598-2->T	6.37:g.123594514_123594514dupA		Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	62	21	0.339	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Splice_Site	INS	ENST00000398178.3	37	CCDS55053.1																																																																																			-|0.740;A|0.260	0.260	strong		0.238	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Intron
THAP2	83591	hgsc.bcm.edu	37	12	72070506	72070508	+	In_Frame_Del	DEL	GTT	GTT	-	rs140783391	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GTT	GTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:72070506_72070508delGTT	ENST00000308086.2	+	3	1806_1808	c.305_307delGTT	c.(304-309)agttgt>agt	p.C103del	RP11-293I14.2_ENST00000548802.1_Intron	NM_031435.3	NP_113623.1	Q9H0W7	THAP2_HUMAN	THAP domain containing, apoptosis associated protein 2	103						nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	10						AAAAACAACAGTTGTTCTCCAGC	0.34														202	0.0403355	0.0113	0.0591	5008	,	,		19109	0.003		0.0507	False		,,,				2504	0.0941				p.102_102del		Pindel,Atlas-Indel	.											.	THAP2	29	.	0			c.304_306del						PASS	.			82,4182		2,78,2052						2.0	1.0		dbSNP_134	46	567,7685		14,539,3573	no	coding	THAP2	NM_031435.3		16,617,5625	A1A1,A1R,RR		6.8711,1.9231,5.1854				649,11867				SO:0001651	inframe_deletion	83591	exon3			.	BC008358	CCDS9001.1	12q21.1	2013-01-25				ENSG00000173451		"""THAP (C2CH-type zinc finger) domain containing"""	20854	protein-coding gene	gene with protein product		612531				12575992	Standard	NM_031435		Approved	DKFZP564I0422	uc001swq.3	Q9H0W7	OTTHUMG00000169556	ENST00000308086.2:c.305_307delGTT	12.37:g.72070509_72070511delGTT	ENSP00000310796:p.Cys103del	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	108	37	0.343	NM_031435	B2R8P3	In_Frame_Del	DEL	ENST00000308086.2	37	CCDS9001.1																																																																																			GTT|0.969;-|0.031	0.031	strong		0.340	THAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404796.1	NM_031435	
RP1L1	94137	hgsc.bcm.edu	37	8	10467569	10467571	+	In_Frame_Del	DEL	CTC	CTC	-	rs200175359		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:10467569_10467571delCTC	ENST00000382483.3	-	4	4260_4262	c.4037_4039delGAG	c.(4036-4041)ggagaa>gaa	p.G1346del		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)		tgctgtccttctccttctgtttc	0.483																																					p.1346_1347del		Atlas-Indel	.											.	RP1L1	453	.	0			c.4038_4040del						PASS	.																																			SO:0001651	inframe_deletion	94137	exon4			.	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.4037_4039delGAG	8.37:g.10467569_10467571delCTC	ENSP00000371923:p.Gly1346del	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	208	13	0.0625	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	none		0.483	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
C1orf86	199990	hgsc.bcm.edu	37	1	2124345	2124346	+	Intron	INS	-	-	TTG	rs142041547	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:2124345_2124346insTTG	ENST00000378546.4	-	3	495				C1orf86_ENST00000400919.3_5'UTR|C1orf86_ENST00000378545.3_Intron|C1orf86_ENST00000487186.1_Intron	NM_182533.2	NP_872339	Q6NZ36	FAP20_HUMAN	chromosome 1 open reading frame 86						cellular response to DNA damage stimulus (GO:0006974)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	cell junction (GO:0030054)|chromosome (GO:0005694)|Fanconi anaemia nuclear complex (GO:0043240)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)			central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-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;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		ggccTTTTCTTTTGTTGTTGTT	0.569														52	0.0103834	0.0015	0.013	5008	,	,		20221	0.001		0.0348	False		,,,				2504	0.0051				p.K180delinsNK		Atlas-Indel	.											.	C1orf86	20	.	0			c.540_541insCAA						PASS	.																																			SO:0001627	intron_variant	199990	exon4			.	AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585			26428	protein-coding gene	gene with protein product		615183				14702039	Standard	NM_182533		Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000378546.4:c.470+731->CAA	1.37:g.2124352_2124354dupTTG		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	11	0.22	NM_001256946	A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	In_Frame_Ins	INS	ENST00000378546.4	37	CCDS38.2																																																																																			.	.	strong		0.569	C1orf86-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316541.1	NM_182533	
OR1B1	347169	hgsc.bcm.edu	37	9	125391770	125391771	+	Frame_Shift_Ins	INS	-	-	A	rs398102330|rs78126045|rs11421222	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:125391770_125391771insA	ENST00000304833.3	-	1	81_82	c.44_45insT	c.(43-45)ttgfs	p.L15fs	RP11-64P14.7_ENST00000431442.1_RNA|RP11-64P14.7_ENST00000419604.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	15						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)|lung(6)|prostate(1)	16						ACCCAAGGAGCAAAAAAACCGG	0.475													?|AAAAAAA|AAAAAAAA|unsure	2046	0.408546	0.3888	0.2954	5008	,	,		22113	0.3383		0.504	False		,,,				2504	0.4898				p.L15fs		Pindel,Atlas-Indel	.											.	OR1B1	48	.	0			c.45_46insT						PASS	.			1831,2421		393,1045,688						-0.3	0.5		dbSNP_134	87	4104,4128		1026,2052,1038	no	frameshift	OR1B1	NM_001004450.1		1419,3097,1726	A1A1,A1R,RR		49.8542,43.0621,47.5409				5935,6549				SO:0001589	frameshift_variant	347169	exon1			.	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.45dupT	9.37:g.125391777_125391777dupA	ENSP00000303151:p.Leu15fs	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	78	21	0.269	NM_001004450	Q6IFN3	Frame_Shift_Ins	INS	ENST00000304833.3	37	CCDS35126.1																																																																																			-|0.589;A|0.411	0.411	strong		0.475	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
ACAA1	30	hgsc.bcm.edu	37	3	38162039	38162042	+	IGR	DEL	GAGA	GAGA	-	rs140494598		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGA	GAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38162039_38162042delGAGA	ENST00000333167.8	-	0	1785				ACAA1_ENST00000480865.1_5'Flank|DLEC1_ENST00000346219.3_Frame_Shift_Del_p.GE1602fs|DLEC1_ENST00000452631.2_Frame_Shift_Del_p.GE1605fs|DLEC1_ENST00000308059.6_Frame_Shift_Del_p.GE1602fs	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		AGTGCGAGTGGAGAGAGAGAGATG	0.578																																					p.1602_1603del		Pindel,Atlas-Indel	.											.	DLEC1	278	.	0			c.4804_4807del						PASS	.																																			SO:0001628	intergenic_variant	9940	exon34			.	X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"""peroxisomal 3-oxoacyl-Coenzyme A thiolase"""	604054	"""acetyl-Coenzyme A acyltransferase 1"""				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087		3.37:g.38162047_38162050delGAGA		Somatic	322	.	.		WXS	Illumina HiSeq	Phase_I	301	66	0.219	NM_007335	G5E935|Q96CA6	Frame_Shift_Del	DEL	ENST00000333167.8	37	CCDS2673.1																																																																																			.	.	alt		0.578	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607	
MEF2B	100271849	hgsc.bcm.edu	37	19	19257101	19257102	+	Intron	INS	-	-	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19257101_19257102insG	ENST00000602424.2	-	9	1496				MEF2B_ENST00000410050.1_Frame_Shift_Ins_p.A295fs|MEF2B_ENST00000409224.1_Frame_Shift_Ins_p.A291fs|MEF2B_ENST00000409447.2_Intron|MEF2BNB-MEF2B_ENST00000444486.3_Intron|MEF2B_ENST00000424583.2_Frame_Shift_Ins_p.A288fs|MEF2BNB-MEF2B_ENST00000514819.3_Intron|MEF2BNB-MEF2B_ENST00000602276.1_5'Flank|MEF2B_ENST00000162023.5_Frame_Shift_Ins_p.A288fs	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B						muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell junction (GO:0030054)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|haematopoietic_and_lymphoid_tissue(21)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)			GAGGACACGGCGGGGGGCCCAT	0.703											OREG0025379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A288fs		Atlas-Indel	.											.	MEF2B	41	.	0			c.862_863insC						PASS	.																																			SO:0001627	intron_variant	100271849	exon8			.	X63380	CCDS12394.1, CCDS46024.1	19p13.11	2010-05-12	2007-04-24					"""Myocyte enhancer factors"""	6995	protein-coding gene	gene with protein product		600661				1516833, 8575763	Standard	NM_001145785		Approved	RSRFR2	uc002nll.2	Q02080		ENST00000602424.2:c.769+261->C	19.37:g.19257107_19257107dupG		Somatic	21	0	0	731	WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_001145785	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Frame_Shift_Ins	INS	ENST00000602424.2	37	CCDS12394.1																																																																																			.	.	none		0.703	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144923729	144923729	+	Frame_Shift_Del	DEL	T	T	-	rs3215779|rs369106087	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:144923729delT	ENST00000369354.3	-	6	918	c.729delA	c.(727-729)gaafs	p.E243fs	PDE4DIP_ENST00000313382.9_Frame_Shift_Del_p.E309fs|PDE4DIP_ENST00000369356.4_Frame_Shift_Del_p.E243fs|PDE4DIP_ENST00000529945.1_Frame_Shift_Del_p.E406fs|PDE4DIP_ENST00000313431.9_Frame_Shift_Del_p.E406fs|PDE4DIP_ENST00000369351.3_Frame_Shift_Del_p.E243fs|PDE4DIP_ENST00000369359.4_Frame_Shift_Del_p.E380fs|PDE4DIP_ENST00000479408.2_Frame_Shift_Del_p.E30fs|PDE4DIP_ENST00000530740.1_Frame_Shift_Del_p.E380fs|PDE4DIP_ENST00000369349.3_Frame_Shift_Del_p.E243fs			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	243					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)		TTTCCTGGAGTTCTGCCAAGT	0.448			T	PDGFRB	MPD								TT|TT|T|deletion	928	0.185304	0.0113	0.2205	5008	,	,		39069	0.3988		0.1799	False		,,,				2504	0.181				p.L407fs		Pindel,Atlas-Indel	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.1219delC						PASS	.						364.0	305.0	325.0					1																	144923729		2203	4300	6503	SO:0001589	frameshift_variant	9659	exon2			.	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.729delA	1.37:g.144923729delT	ENSP00000358360:p.Glu243fs	Somatic	468	.	.		WXS	Illumina HiSeq	Phase_I	612	94	0.154	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Frame_Shift_Del	DEL	ENST00000369354.3	37	CCDS30824.1																																																																																			.	.	weak		0.448	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
GOLGA2P5	55592	hgsc.bcm.edu	37	12	100550838	100550839	+	RNA	INS	-	-	GGAG	rs150871002|rs375559149	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:100550838_100550839insGGAG	ENST00000397112.4	-	0	1985				RN7SL176P_ENST00000580352.1_RNA|AC010203.1_ENST00000408843.1_RNA	NR_036632.1		Q9HBQ8	GGA2B_HUMAN								Golgi apparatus (GO:0005794)				large_intestine(1)|lung(3)	4						CAGCTTCACCTGGAGGGAGGGG	0.624														170	0.0339457	0.0015	0.0504	5008	,	,		11181	0.004		0.0686	False		,,,				2504	0.0613				.		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1670-2->CTCC						PASS	.			42,4222		2,38,2092						1.7	0.0		dbSNP_134	50	526,7728		21,484,3622	no	intergenic				23,522,5714	A1A1,A1R,RR		6.3727,0.985,4.5375				568,11950						55592	exon11			.																													12.37:g.100550843_100550846dupGGAG		Somatic	84	.	.		WXS	Illumina HiSeq	Phase_I	71	16	0.225	NR_036632	Q9NSV2	RNA	INS	ENST00000397112.4	37																																																																																				-|0.969;GGAG|0.031	0.031	strong		0.624	GOLGA2B-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000396439.2		
WDR87	83889	hgsc.bcm.edu	37	19	38377392	38377409	+	In_Frame_Del	DEL	CCTCCTCCTCCTCCCTTA	CCTCCTCCTCCTCCCTTA	-	rs7252765|rs201328117		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCTCCTCCTCCTCCCTTA	CCTCCTCCTCCTCCCTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38377392_38377409delCCTCCTCCTCCTCCCTTA	ENST00000303868.5	-	6	7009_7026	c.6785_6802delTAAGGGAGGAGGAGGAGG	c.(6784-6804)gtaagggaggaggaggaggaa>gaa	p.VREEEE2262del	WDR87_ENST00000447313.2_In_Frame_Del_p.VREEEE2301del	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2262	Glu-rich.									NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						tccttcctttcctcctcctcctcccttacctcctcctc	0.486																																					p.2262_2268del		Pindel,Atlas-Indel	.											.	WDR87	191	.	0			c.6786_6803del						PASS	.			1388,1236		603,182,527						0.2	0.0		dbSNP_134	64	2355,3029		947,461,1284	no	coding	WDR87	NM_031951.3		1550,643,1811	A1A1,A1R,RR		43.7407,47.1037,46.7408				3743,4265				SO:0001651	inframe_deletion	83889	exon6			.	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.6785_6802delTAAGGGAGGAGGAGGAGG	19.37:g.38377392_38377409delCCTCCTCCTCCTCCCTTA	ENSP00000368025:p.Val2262_Glu2267del	Somatic	42	.	.		WXS	Illumina HiSeq	Phase_I	50	10	0.200	NM_031951	Q9BWV9	In_Frame_Del	DEL	ENST00000303868.5	37	CCDS46063.1																																																																																			.	.	none		0.486	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
DOK3	79930	hgsc.bcm.edu	37	5	176930172	176930174	+	IGR	DEL	GAG	GAG	-	rs376911686|rs370427653|rs79945738|rs138153794	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:176930172_176930174delGAG	ENST00000357198.4	-	0	1729				DOK3_ENST00000377112.4_In_Frame_Del_p.L187del|RP11-1334A24.6_ENST00000506025.1_RNA|DOK3_ENST00000312943.6_In_Frame_Del_p.L289del	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3						Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	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)|Epithelial(233;0.191)			AGCAGGAGCAGAGGAGGGAACGC	0.631														2674	0.533946	0.4425	0.4741	5008	,	,		19022	0.6121		0.5318	False		,,,				2504	0.6217				p.289_290del		Pindel,Atlas-Indel	.											.	DOK3	41	.	0			c.866_868del						PASS	.		,	1477,1699		465,547,576					,	1.2	0.0		dbSNP_126	47	2974,2754		1007,960,897	no	coding,coding	DOK3	NM_001144876.1,NM_001144875.1	,	1472,1507,1473	A1A1,A1R,RR		48.0796,46.505,49.9888	,	,		4451,4453				SO:0001628	intergenic_variant	79930	exon6			.	AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850		5.37:g.176930175_176930177delGAG		Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	98	29	0.296	NM_001144875	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	In_Frame_Del	DEL	ENST00000357198.4	37	CCDS4426.1																																																																																			GAG|0.466;-|0.534	0.534	strong		0.631	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872	
MICA	100507436	hgsc.bcm.edu	37	6	31380158	31380161	+	Frame_Shift_Del	DEL	GCTG	GCTG	-	rs41293539|rs547446871|rs138201170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GCTG	GCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31380158_31380161delGCTG	ENST00000449934.2	+	5	1003_1006	c.949_952delGCTG	c.(949-954)gctggcfs	p.AG317fs	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)				TGCTGTTGCTGCTGGCTGCTGCTA	0.456														480	0.0958466	0.0976	0.0692	5008	,	,		20271	0.121		0.1203	False		,,,				2504	0.0613				p.316_317del		Pindel,Atlas-Indel	.											.	MICA	21	.	0			c.948_951del						PASS	.			1009,2901		76,857,1022						0.3	0.0		dbSNP_127	255	1985,6023		143,1699,2162	no	frameshift	MICA	NM_001177519.1		219,2556,3184	A1A1,A1R,RR		24.7877,25.8056,25.1217				2994,8924				SO:0001589	frameshift_variant	100507436	exon5			.	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.949_952delGCTG	6.37:g.31380162_31380165delGCTG	ENSP00000413079:p.Ala317fs	Somatic	167	.	.		WXS	Illumina HiSeq	Phase_I	155	30	0.194	NM_001177519		Frame_Shift_Del	DEL	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	strong		0.456	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
CD200R1L	344807	hgsc.bcm.edu	37	3	112545911	112545911	+	Frame_Shift_Del	DEL	T	T	-	rs58161637|rs200703227	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	162	.	.		WXS	Illumina HiSeq	Phase_I	167	89	0.533	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	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24470690	24470691	+	Frame_Shift_Ins	INS	-	-	A	rs368539076|rs374759434	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24470690_24470691insA	ENST00000335125.6	+	6	755_756	c.629_630insA	c.(628-633)ctgcacfs	p.H211fs	DHRS4L2_ENST00000545240.1_Intron|DHRS4L2_ENST00000382755.4_Frame_Shift_Ins_p.H209fs|DHRS4L2_ENST00000543805.1_Intron|DHRS4L2_ENST00000397071.1_Intron|DHRS4L2_ENST00000537912.1_Frame_Shift_Ins_p.H136fs|DHRS4L2_ENST00000534993.1_Intron|DHRS4L2_ENST00000558753.1_Frame_Shift_Ins_p.H136fs	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	209						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		GTGAACTGCCTGCACCTGGACT	0.525													A|-|A|deletion	178	0.0355431	0.0076	0.0187	5008	,	,		17571	0.1022		0.0139	False		,,,				2504	0.0389				p.L210fs		Pindel,Atlas-Indel	.											.	DHRS4L2	29	.	0			c.629_630insA						PASS	.		,,,	146,4000		28,90,1955					,,,	2.5	1.0			148	336,7912		30,276,3818	no	frameshift,frameshift,frameshift,frameshift	DHRS4L2	NM_198083.3,NM_001193637.1,NM_001193636.1,NM_001193635.1	,,,	58,366,5773	A1A1,A1R,RR		4.0737,3.5215,3.889	,,,	,,,		482,11912				SO:0001589	frameshift_variant	317749	exon6			.		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	Exception_encountered	14.37:g.24470690_24470691insA	ENSP00000334801:p.His211fs	Somatic	936	.	.		WXS	Illumina HiSeq	Phase_I	144	73	0.507	NM_198083	Q3YLD4	Frame_Shift_Ins	INS	ENST00000335125.6	37	CCDS9606.2																																																																																			.	.	weak		0.525	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
GGA3	23163	hgsc.bcm.edu	37	17	73234805	73234806	+	Frame_Shift_Ins	INS	-	-	TCTG			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73234805_73234806insTCTG	ENST00000245541.6	-	16	2204_2205	c.1988_1989insCAGA	c.(1987-1989)gaafs	p.E663fs	GGA3_ENST00000582717.1_Frame_Shift_Ins_p.E591fs|GGA3_ENST00000538886.1_Frame_Shift_Ins_p.E541fs|GGA3_ENST00000578348.1_Frame_Shift_Ins_p.E541fs|GGA3_ENST00000582486.1_Frame_Shift_Ins_p.E591fs|GGA3_ENST00000351904.7_Frame_Shift_Ins_p.E630fs	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	663	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			ATGGAGAGAGTTCTGTCCCAGA	0.535											OREG0024729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E663fs		Pindel,Atlas-Indel	.											GGA3,NS,carcinoma,0,1	GGA3	54	1	0			c.1989_1990insCAGA						PASS	.																																			SO:0001589	frameshift_variant	23163	exon16			.	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.1985_1988dupCAGA	17.37:g.73234806_73234809dupTCTG	ENSP00000245541:p.Glu663fs	Somatic	203	.	.	1143	WXS	Illumina HiSeq	Phase_I	205	45	0.220	NM_138619	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Frame_Shift_Ins	INS	ENST00000245541.6	37	CCDS11717.1																																																																																			.	.	none		0.535	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619	
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-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTTTGCCCAGACATGGA	CTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	104	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_012115		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	none		0.378	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129946	175129946	+	Frame_Shift_Del	DEL	C	C	-	rs386636937|rs542219168|rs71563271|rs2072035	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:175129946delC	ENST00000423313.1	-	4	740	c.204delG	c.(202-204)aagfs	p.K75fs	KIAA0040_ENST00000545251.2_Frame_Shift_Del_p.K75fs|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_Frame_Shift_Del_p.K75fs	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tcttcttcttcttcttcttgt	0.498																																					p.K69fs		Atlas-Indel	.											.	KIAA0040	2	.	0			c.205delA						PASS	.						82.0	69.0	73.0					1																	175129946		692	1591	2283	SO:0001589	frameshift_variant	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.204delG	1.37:g.175129946delC	ENSP00000462172:p.Lys75fs	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	132	25	0.189394	NM_001162893	A8K9H6|Q2NKQ0	Frame_Shift_Del	DEL	ENST00000423313.1	37																																																																																				-|1.000	.	weak		0.498	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
CFAP74	85452	hgsc.bcm.edu	37	1	1900106	1900107	+	IGR	INS	-	-	CTC	rs61233860|rs145742571|rs72634902	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1900106_1900107insCTC								TMEM52 (49394 upstream) : C1orf222 (19455 downstream)																							ACTGTGGTCTTCTTGCAAAAGT	0.569														997	0.199081	0.1324	0.1945	5008	,	,		21168	0.3284		0.2376	False		,,,				2504	0.1196				p.K405delinsEK		Pindel,Atlas-Indel	.											.	KIAA1751	92	.	0			c.1213_1214insGAG						PASS	.			643,3311		79,485,1413						-3.9	0.0		dbSNP_129	188	1999,6033		265,1469,2282	no	coding	KIAA1751	NM_001080484.1		344,1954,3695	A1A1,A1R,RR		24.8879,16.262,22.0424				2642,9344				SO:0001628	intergenic_variant	85452	exon11			.																													1.37:g.1900106_1900107insCTC		Somatic	205	.	.		WXS	Illumina HiSeq	Phase_I	119	58	0.487	NM_001080484		In_Frame_Ins	INS		37																																																																																				.	.	strong	0	0.569								
CACNA1A	773	hgsc.bcm.edu	37	19	13395957	13395959	+	In_Frame_Del	DEL	TCC	TCC	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13395957_13395959delTCC	ENST00000360228.5	-	21	3614_3616	c.3615_3617delGGA	c.(3613-3618)gaggaa>gaa	p.1205_1206EE>E	CACNA1A_ENST00000573710.2_In_Frame_Del_p.1206_1207EE>E	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	1206	Poly-Glu.				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)	ACGGtcgtcttcctcctcctcct	0.552																																					p.1207_1207del		Pindel,Atlas-Indel	.											.	CACNA1A	715	.	0			c.3619_3621del						PASS	.		,,,,	3,3657		1,1,1828					,,,,	-3.5	0.6			103	12,7868		0,12,3928	no	coding,coding,coding,coding,coding	CACNA1A	NM_023035.2,NM_001174080.1,NM_001127222.1,NM_001127221.1,NM_000068.3	,,,,	1,13,5756	A1A1,A1R,RR		0.1523,0.082,0.13	,,,,	,,,,		15,11525				SO:0001651	inframe_deletion	773	exon21			.	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.3615_3617delGGA	19.37:g.13395966_13395968delTCC	ENSP00000353362:p.Glu1206del	Somatic	170	.	.		WXS	Illumina HiSeq	Phase_I	172	45	0.262	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	In_Frame_Del	DEL	ENST00000360228.5	37	CCDS45998.1																																																																																			.	.	none		0.552	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
CCL27	10850	hgsc.bcm.edu	37	9	34661945	34661945	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34661945delC	ENST00000259631.4	-	3	393	c.335delG	c.(334-336)ggcfs	p.G112fs	CCL27_ENST00000557161.1_5'UTR|RP11-195F19.30_ENST00000564224.1_RNA	NM_006664.2	NP_006655.1	Q9Y4X3	CCL27_HUMAN	chemokine (C-C motif) ligand 27	112					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)		GGGGCTTCAGCCCATTTTCCT	0.448																																					p.G112fs		Pindel,Atlas-Indel	.											.	CCL27	6	.	0			c.336delC						PASS	.						88.0	97.0	94.0					9																	34661945		2203	4300	6503	SO:0001589	frameshift_variant	10850	exon3			.	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.335delG	9.37:g.34661945delC	ENSP00000259631:p.Gly112fs	Somatic	122	.	.		WXS	Illumina HiSeq	Phase_I	107	32	0.299	NM_006664		Frame_Shift_Del	DEL	ENST00000259631.4	37	CCDS6569.1																																																																																			.	.	none		0.448	CCL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052228.1	NM_006664	
BPTF	2186	hgsc.bcm.edu	37	17	65955758	65955759	+	In_Frame_Ins	INS	-	-	CCTCCAGCC	rs139709271|rs202116659		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:65955758_65955759insCCTCCAGCC	ENST00000321892.4	+	26	8467_8468	c.8406_8407insCCTCCAGCC	c.(8407-8409)cct>CCTCCAGCCcct	p.2803_2803P>PPAP	BPTF_ENST00000424123.3_In_Frame_Ins_p.2521_2521P>PPAP|BPTF_ENST00000335221.5_In_Frame_Ins_p.2660_2660P>PPAP|BPTF_ENST00000306378.6_In_Frame_Ins_p.2677_2677P>PPAP			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2803	Pro-rich.			AP -> VL (in Ref. 1; BAA89208). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.A2676A(1)|p.A2659A(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGACAccagctcctccagcccc	0.579																																					p.A2676delinsAPPA		Pindel,Atlas-Indel	.											BPTF_ENST00000335221,rectum,carcinoma,0,2	BPTF	415	2	2	Substitution - coding silent(2)	large_intestine(2)	c.8028_8029insCCTCCAGCC						PASS	.																																			SO:0001652	inframe_insertion	2186	exon24			.	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8416_8424dupCCTCCAGCC	17.37:g.65955759_65955767dupCCTCCAGCC	ENSP00000315454:p.ProAlaPro2809dup	Somatic	207	.	.		WXS	Illumina HiSeq	Phase_I	106	46	0.434	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	In_Frame_Ins	INS	ENST00000321892.4	37																																																																																				-|0.707;CCTCCAGCC|0.293	0.293	strong		0.579	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
ARSD	414	hgsc.bcm.edu	37	X	2835999	2836007	+	In_Frame_Del	DEL	CCACGCCGG	CCACGCCGG	-	rs113556864|rs190767292		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCACGCCGG	CCACGCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	148	0	0		WXS	Illumina HiSeq	Phase_I	85	24	0.282353	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		
ATF7IP2	80063	hgsc.bcm.edu	37	16	10524657	10524659	+	In_Frame_Del	DEL	GAC	GAC	-	rs56252625|rs75627261|rs571414967|rs113642662	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAC	GAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	278	.	.		WXS	Illumina HiSeq	Phase_I	202	98	0.485	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	
DLGAP2	9228	hgsc.bcm.edu	37	8	1626460	1626461	+	In_Frame_Ins	INS	-	-	CAC	rs200151488	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:1626460_1626461insCAC	ENST00000421627.2	+	9	2263_2264	c.2129_2130insCAC	c.(2128-2133)atcacc>atCACcacc	p.712_713insT		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	791					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				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)		CCAGGCCACATCACCACGGAGG	0.609														107	0.0213658	0.0053	0.0331	5008	,	,		18378	0.001		0.0497	False		,,,				2504	0.0266				p.I710delinsIT		Pindel,Atlas-Indel	.											.	DLGAP2	292	.	0			c.2129_2130insCAC						PASS	.			36,4032		1,34,1999						3.9	0.0			63	413,7659		18,377,3641	no	coding	DLGAP2	NM_004745.3		19,411,5640	A1A1,A1R,RR		5.1165,0.885,3.6985				449,11691				SO:0001652	inframe_insertion	9228	exon9			.	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.2133_2135dupCAC	8.37:g.1626464_1626466dupCAC	ENSP00000400258:p.Thr712_Thr712dup	Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	157	43	0.274	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	In_Frame_Ins	INS	ENST00000421627.2	37	CCDS47760.1																																																																																			-|0.982;CAC|0.018	0.018	strong		0.609	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
C1orf141	400757	hgsc.bcm.edu	37	1	67558870	67558874	+	Frame_Shift_Del	DEL	TCATT	TCATT	-	rs200104842|rs373816272|rs577736835	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCATT	TCATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:67558870_67558874delTCATT	ENST00000371007.2	-	8	1126_1130	c.1017_1021delAATGA	c.(1015-1023)gaaatgagtfs	p.MS340fs	C1orf141_ENST00000371006.1_Frame_Shift_Del_p.MS340fs|C1orf141_ENST00000544837.1_Frame_Shift_Del_p.MS340fs	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	340										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						GTTTGGGCACTCATTTCATGAATAA	0.361														19	0.00379393	0.0023	0.0072	5008	,	,		16889	0.0		0.0109	False		,,,				2504	0.0				p.340_341del		Atlas-Indel	.											.	C1orf141	58	.	0			c.1018_1022del						PASS	.			10,4244		0,10,2117						-2.1	0.0			110	69,8177		2,65,4056	no	frameshift	C1orf141	NM_001013674.1		2,75,6173	A1A1,A1R,RR		0.8368,0.2351,0.632				79,12421				SO:0001589	frameshift_variant	400757	exon8			.	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.1017_1021delAATGA	1.37:g.67558870_67558874delTCATT	ENSP00000360046:p.Met340fs	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	125	14	0.112	NM_001276351	Q0P5P5|Q5JVX5	Frame_Shift_Del	DEL	ENST00000371007.2	37	CCDS30745.1																																																																																			TCATT|0.994;-|0.006	0.006	strong		0.361	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674	
CELA1	1990	hgsc.bcm.edu	37	12	51740415	51740416	+	Frame_Shift_Del	DEL	AC	AC	-	rs370927847|rs386762976|rs61761206|rs55827519|rs148235680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:51740415_51740416delAC	ENST00000293636.1	-	1	47_48	c.7_8delGT	c.(7-9)gtcfs	p.V3fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	3					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.V3fs*21(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						ACCATAAAGGACCAGCATGTTG	0.515														1840	0.367412	0.2988	0.451	5008	,	,		16016	0.5546		0.3211	False		,,,				2504	0.2556				p.3_3del		Atlas-Indel	.											.	CELA1	39	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.8_9del						PASS	.																																			SO:0001589	frameshift_variant	1990	exon1			.		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.7_8delGT	12.37:g.51740415_51740416delAC	ENSP00000293636:p.Val3fs	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	131	14	0.10687	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Frame_Shift_Del	DEL	ENST00000293636.1	37	CCDS8812.1																																																																																			.	.	weak		0.515	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
ACIN1	22985	hgsc.bcm.edu	37	14	23548783	23548784	+	In_Frame_Ins	INS	-	-	GAACGT	rs78164858|rs148403158|rs61741621|rs5807202|rs3077646	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23548783_23548784insGAACGT	ENST00000262710.1	-	6	2261_2262	c.1934_1935insACGTTC	c.(1933-1935)tct>tcACGTTCt	p.645_645S>SRS	ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000605057.1_In_Frame_Ins_p.587_587S>SRS|ACIN1_ENST00000555053.1_In_Frame_Ins_p.645_645S>SRS|ACIN1_ENST00000457657.1_In_Frame_Ins_p.605_605S>SRS	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	645	Ser-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		ATGCTGAACGAGAACGTGAACG	0.485														1942	0.38778	0.5318	0.2637	5008	,	,		21370	0.4226		0.2664	False		,,,				2504	0.3701				p.S645delinsSRS		Atlas-Indel	.											.	ACIN1	147	.	0			c.1935_1936insACGTTC						PASS	.		,,	2635,143,113,3,1370		775,98,106,3,878,1,1,0,42,0,0,6,0,0,222					,,	-4.2	0.3		dbSNP_126	219	3073,1,288,0,4892		417,1,253,0,1985,0,0,0,0,0,0,35,0,0,1436	no	codingComplex,codingComplex,codingComplex	ACIN1	NM_014977.3,NM_001164815.1,NM_001164814.1	,,	1192,99,359,3,2863,1,1,0,42,0,0,41,0,0,1658	A1A1,A1A2,A1A3,A1A4,A1R,A2A2,A2A3,A2A4,A2R,A3A3,A3A4,A3R,A4A4,A4R,RR		40.7318,38.2036,49.976	,,	,,		5708,144,401,3,6262				SO:0001652	inframe_insertion	22985	exon6			.	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1929_1934dupACGTTC	14.37:g.23548784_23548789dupGAACGT	ENSP00000262710:p.ArgSer647dup	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	294	53	0.180272	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	In_Frame_Ins	INS	ENST00000262710.1	37	CCDS9587.1																																																																																			.	.	strong		0.485	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
EIF3A	8661	hgsc.bcm.edu	37	10	120819176	120819187	+	In_Frame_Del	DEL	AAGGAACCAAAG	AAGGAACCAAAG	-	rs374628063		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AAGGAACCAAAG	AAGGAACCAAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:120819176_120819187delAAGGAACCAAAG	ENST00000369144.3	-	10	1497_1508	c.1370_1381delCTTTGGTTCCTT	c.(1369-1383)tctttggttcctttt>ttt	p.SLVP457del	SNORA19_ENST00000384737.1_RNA|EIF3A_ENST00000541549.1_In_Frame_Del_p.SLVP423del|SNORA19_ENST00000410656.1_RNA	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)	p.P460F(1)		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)		GCATCAACAAAAGGAACCAAAGAAGTCAAACG	0.434																																					p.457_461del		Atlas-Indel	.											.	EIF3A	142	.	1	Substitution - Missense(1)	skin(1)	c.1371_1382del						PASS	.																																			SO:0001651	inframe_deletion	8661	exon10			.	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.1370_1381delCTTTGGTTCCTT	10.37:g.120819176_120819187delAAGGAACCAAAG	ENSP00000358140:p.Ser457_Pro460del	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	176	25	0.142045	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	In_Frame_Del	DEL	ENST00000369144.3	37	CCDS7608.1																																																																																			.	.	none		0.434	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750	
CHD8	57680	hgsc.bcm.edu	37	14	21862616	21862616	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21862616delA	ENST00000557364.1	-	31	5682	c.5419delT	c.(5419-5421)tatfs	p.Y1807fs	CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000399982.2_Frame_Shift_Del_p.Y1807fs|SNORD9_ENST00000362566.1_RNA|SNORD8_ENST00000363915.1_RNA|CHD8_ENST00000430710.3_Frame_Shift_Del_p.Y1528fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1807					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		ACCACTCGATAAAAATCAGTT	0.413																																					p.Y1807fs		Pindel,Atlas-Indel	.											.	CHD8	339	.	0			c.5420delA						PASS	.						53.0	52.0	52.0					14																	21862616		1958	4159	6117	SO:0001589	frameshift_variant	57680	exon30			.	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.5419delT	14.37:g.21862616delA	ENSP00000451601:p.Tyr1807fs	Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	156	30	0.192	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	37	CCDS53885.1																																																																																			.	.	none		0.413	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
CDKN2AIP	55602	hgsc.bcm.edu	37	4	184367559	184367561	+	In_Frame_Del	DEL	CTG	CTG	-	rs398108445|rs147291711|rs10533201|rs201501817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:184367559_184367561delCTG	ENST00000504169.1	+	3	929_931	c.722_724delCTG	c.(721-726)tctgca>tca	p.A242del	CDKN2AIP_ENST00000506835.1_3'UTR|CDKN2AIP_ENST00000302350.4_3'UTR	NM_017632.2	NP_060102.1	Q9NXV6	CARF_HUMAN	CDKN2A interacting protein	242	Ser-rich.			Missing (in Ref. 3; EAX04691 and 4; AAH22270). {ECO:0000305}.	negative regulation of cell growth (GO:0030308)|positive regulation of signal transduction (GO:0009967)|regulation of protein stability (GO:0031647)	cytoplasm (GO:0005737)|granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	p53 binding (GO:0002039)|RNA binding (GO:0003723)			endometrium(1)|kidney(2)|large_intestine(2)|lung(1)	6		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;1.15e-26)|Epithelial(43;2.98e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|GBM - Glioblastoma multiforme(59;4.22e-06)|Colorectal(24;5.87e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		AAACACGGTTCTGCATCATTTGT	0.458														1818	0.363019	0.1203	0.4164	5008	,	,		22238	0.244		0.7247	False		,,,				2504	0.4039				p.241_241del		Pindel,Atlas-Indel	.											.	CDKN2AIP	31	.	0			c.721_723del						PASS	.			915,3351		96,723,1314						1.2	0.8		dbSNP_134	82	6064,2190		2233,1598,296	no	coding	CDKN2AIP	NM_017632.2		2329,2321,1610	A1A1,A1R,RR		26.5326,21.4487,44.2572				6979,5541				SO:0001651	inframe_deletion	55602	exon3			.	AK000043	CCDS34110.1	4q35.1	2008-02-05			ENSG00000168564	ENSG00000168564			24325	protein-coding gene	gene with protein product	"""collaborates/cooperates with ARF (alternate reading frame) protein"""	615914				12154087, 16803988	Standard	NM_017632		Approved	FLJ20036, CARF	uc003ivp.1	Q9NXV6	OTTHUMG00000160626	ENST00000504169.1:c.722_724delCTG	4.37:g.184367559_184367561delCTG	ENSP00000427108:p.Ala242del	Somatic	64	.	.		WXS	Illumina HiSeq	Phase_I	54	11	0.204	NM_017632	Q8TBM5|Q9NYH0	In_Frame_Del	DEL	ENST00000504169.1	37	CCDS34110.1																																																																																			CTG|0.559;-|0.441	0.441	strong		0.458	CDKN2AIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361488.1	NM_017632	
TDG	6996	hgsc.bcm.edu	37	12	104373728	104373729	+	Frame_Shift_Ins	INS	-	-	A	rs151041931	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:104373728_104373729insA	ENST00000392872.3	+	3	520_521	c.286_287insA	c.(286-288)gaafs	p.E96fs	TDG_ENST00000542036.1_5'Flank|TDG_ENST00000266775.9_Frame_Shift_Ins_p.E92fs|TDG_ENST00000544861.1_5'UTR	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	96					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.I98fs*6(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		AGAAAAACAAGAAAAAATTACA	0.356								Base excision repair (BER), DNA glycosylases					AAAAAA|AAAAAA|AAAAAAA|insertion	2365	0.472244	0.4947	0.4597	5008	,	,		24291	0.4802		0.4324	False		,,,				2504	0.4836				p.E96fs		Atlas-Indel	.											.	TDG	43	.	1	Insertion - Frameshift(1)	ovary(1)	c.286_287insA						PASS	.			2087,2177		2,2083,47						5.2	1.0		dbSNP_130	68	3484,4770		1,3482,644	yes	frameshift	TDG	NM_003211.4		3,5565,691	A1A1,A1R,RR		42.2098,48.9447,44.5039				5571,6947				SO:0001589	frameshift_variant	6996	exon3			.	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.292dupA	12.37:g.104373734_104373734dupA	ENSP00000376611:p.Glu96fs	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	136	35	0.257353	NM_003211	Q8IUZ6|Q8IZM3	Frame_Shift_Ins	INS	ENST00000392872.3	37	CCDS9095.1																																																																																			.	.	strong		0.356	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
OR2T8	343172	hgsc.bcm.edu	37	1	248084470	248084471	+	Frame_Shift_Ins	INS	-	-	G	rs140846339|rs149623571|rs547311711	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248084470_248084471insG	ENST00000319968.4	+	1	151_152	c.151_152insG	c.(151-153)cacfs	p.H51fs		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H51D(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	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)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCACTGGGACCACCGGCTCCAC	0.535																																					p.H51fs		Atlas-Indel	.											OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	1	Substitution - Missense(1)	large_intestine(1)	c.151_152insG						PASS	.																																			SO:0001589	frameshift_variant	343172	exon1			.		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	Exception_encountered	1.37:g.248084470_248084471insG	ENSP00000326225:p.His51fs	Somatic	726	0	0		WXS	Illumina HiSeq	Phase_I	441	69	0.156463	NM_001005522		Frame_Shift_Ins	INS	ENST00000319968.4	37	CCDS31100.1																																																																																			.	.	none		0.535	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
OR1J2	26740	hgsc.bcm.edu	37	9	125273385	125273386	+	Frame_Shift_Ins	INS	-	-	T	rs145911830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:125273385_125273386insT	ENST00000335302.5	+	1	305_306	c.305_306insT	c.(304-309)tattttfs	p.YF102fs		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	102						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(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						TCTCAGATGTATTTTTTTATAT	0.401													TTTTTTT|TTTTTTT|TTTTTTTT|insertion	273	0.0545128	0.0681	0.0591	5008	,	,		23759	0.002		0.0974	False		,,,				2504	0.0429				p.Y102fs		Pindel,Atlas-Indel	.											.	OR1J2	64	.	0			c.305_306insT						PASS	.																																			SO:0001589	frameshift_variant	26740	exon1			.		CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"""GPCR / Class A : Olfactory receptors"""	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.312dupT	9.37:g.125273392_125273392dupT	ENSP00000335575:p.Tyr102fs	Somatic	135	.	.		WXS	Illumina HiSeq	Phase_I	140	36	0.257	NM_054107	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Frame_Shift_Ins	INS	ENST00000335302.5	37	CCDS35121.1																																																																																			-|0.940;T|0.060	0.060	strong		0.401	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1		
RHBG	57127	hgsc.bcm.edu	37	1	156354348	156354348	+	Frame_Shift_Del	DEL	C	C	-	rs11303415	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156354348delC	ENST00000368249.1	+	9	1303	c.1265delC	c.(1264-1266)tccfs	p.S422fs	RHBG_ENST00000368246.2_Splice_Site|RHBG_ENST00000494874.1_Intron|RHBG_ENST00000255013.3_Frame_Shift_Del_p.S353fs|RHBG_ENST00000400992.2_Frame_Shift_Del_p.S390fs	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	422	Interaction with ANK3.				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)	p.R425fs*>17(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					TTTCTGGACTCCCCCCCCAGA	0.632											OREG0013871	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		2118	0.422923	0.6059	0.2925	5008	,	,		18146	0.5446		0.2396	False		,,,				2504	0.3313				p.S422fs		Pindel,Atlas-Indel	.											.	RHBG	133	.	1	Deletion - Frameshift(1)	ovary(1)	c.1264delT						PASS	.						38.0	63.0	55.0					1																	156354348		1930	4140	6070	SO:0001589	frameshift_variant	57127	exon9			.	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.1265delC	1.37:g.156354348delC	ENSP00000357232:p.Ser422fs	Somatic	170	.	.	1777	WXS	Illumina HiSeq	Phase_I	187	66	0.353	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Frame_Shift_Del	DEL	ENST00000368249.1	37																																																																																				-|1.000;|0.000	1.000	strong		0.632	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37465386	37465390	+	Splice_Site	DEL	TGGGG	TGGGG	-	rs188283136|rs200434923	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TGGGG	TGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:37465386_37465390delTGGGG	ENST00000346753.3	-	16	1985		c.e16-2		TMPRSS6_ENST00000406725.1_Splice_Site|TMPRSS6_ENST00000381792.2_Splice_Site|TMPRSS6_ENST00000406856.1_Splice_Site	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6						angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						GAGGCCATGCtggggtggggtgggg	0.668														2248	0.448882	0.7504	0.2435	5008	,	,		11865	0.4266		0.4036	False		,,,				2504	0.2566				.		Atlas-Indel	.											.	TMPRSS6	99	.	0			.						PASS	.			1238,890		571,96,397						5.1	1.0			10	2211,3145		918,375,1385	no	splice-3	TMPRSS6	NM_153609.2		1489,471,1782	A1A1,A1R,RR		41.2808,41.8233,46.085				3449,4035				SO:0001630	splice_region_variant	164656	.			.	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.1869-2CCCCA>-	22.37:g.37465396_37465400delTGGGG		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	97	22	0.226804	.	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Splice_Site	DEL	ENST00000346753.3	37	CCDS13941.1																																																																																			TGGGG|0.528;-|0.472	0.472	strong		0.668	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	Intron
FOXD4L2	100036519	hgsc.bcm.edu	37	9	42719280	42719280	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:42719280delC	ENST00000377590.1	+	1	2047	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_001099279.1	NP_001092749.1	Q6VB85	FX4L2_HUMAN	forkhead box D4-like 2	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.W406fs*>11(1)		haematopoietic_and_lymphoid_tissue(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		GGGCGCGGTGCTGGGCGGGCA	0.677																																					p.C405fs		Pindel,Atlas-Indel	.											.	FOXD4L4	5	.	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.1214delG						PASS	.																																			SO:0001589	frameshift_variant	349334	exon1			.			9p12	2008-07-21			ENSG00000204828				24813	protein-coding gene	gene with protein product						12421752	Standard			Approved	OTTHUMG00000066752	uc004acn.3	Q6VB85	OTTHUMG00000066752	ENST00000377590.1:c.1215delC	9.37:g.42719280delC	ENSP00000366814:p.Cys405fs	Somatic	308	.	.		WXS	Illumina HiSeq	Phase_I	138	26	0.188	NM_199244		Frame_Shift_Del	DEL	ENST00000377590.1	37	CCDS43817.1																																																																																			.	.	weak		0.677	FOXD4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143077.1	NM_001099279	
CELA1	1990	hgsc.bcm.edu	37	12	51740413	51740414	+	Frame_Shift_Ins	INS	-	-	C	rs573952082|rs386762976|rs377599213|rs370927847	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:51740413_51740414insC	ENST00000293636.1	-	1	49_50	c.9_10insG	c.(7-12)gtccttfs	p.L4fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	4					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						TTACCATAAAGGACCAGCATGT	0.515													?|-|C|unsure	1840	0.367412	0.2988	0.451	5008	,	,		13831	0.5546		0.3211	False		,,,				2504	0.2556				p.L4fs		Atlas-Indel	.											CELA1,NS,carcinoma,+1,1	CELA1	39	1	0			c.10_11insG						PASS	.																																			SO:0001589	frameshift_variant	1990	exon1			.		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.9_10insG	12.37:g.51740413_51740414insC	ENSP00000293636:p.Leu4fs	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	134	14	0.104478	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Frame_Shift_Ins	INS	ENST00000293636.1	37	CCDS8812.1																																																																																			-|0.426;TGGACCATATCCACTTACCATAAAGGAC|0.574	.	alt		0.515	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
EP400	57634	hgsc.bcm.edu	37	12	132547093	132547094	+	In_Frame_Ins	INS	-	-	CAG	rs10902490|rs113304321|rs528214697	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:132547093_132547094insCAG	ENST00000333577.4	+	48	8398_8399	c.8289_8290insCAG	c.(8290-8292)cag>CAGcag	p.2764_2764Q>QQ	EP400_ENST00000389562.2_In_Frame_Ins_p.2727_2727Q>QQ|EP400_ENST00000332482.4_In_Frame_Ins_p.2691_2691Q>QQ|EP400_ENST00000330386.6_In_Frame_Ins_p.2647_2647Q>QQ|EP400_ENST00000389561.2_In_Frame_Ins_p.2728_2728Q>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	89	0	0		WXS	Illumina HiSeq	Phase_I	139	43	0.309353	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	
C2orf71	388939	hgsc.bcm.edu	37	2	29287926	29287927	+	In_Frame_Ins	INS	-	-	GCT	rs139768554|rs72122505|rs201781577|rs35753661	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:29287926_29287927insGCT	ENST00000331664.5	-	2	3674_3675	c.3675_3676insAGC	c.(3673-3678)agcgag>agcAGCgag	p.1225_1226insS	C2orf71_ENST00000602958.1_5'Flank	NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1225			S -> SS. {ECO:0000269|PubMed:21412943}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)		p.S1225_E1226insS(2)		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						GGGCTCTCCTCGCTGCTGCTGC	0.624														1871	0.373602	0.5257	0.2637	5008	,	,		17644	0.4931		0.2545	False		,,,				2504	0.2454				p.E1226delinsSE		Pindel,Atlas-Indel	.											.	C2orf71	146	.	2	Insertion - In frame(2)	ovary(1)|breast(1)	c.3676_3677insAGC						PASS	.			1580,1994		462,656,669						5.2	1.0		dbSNP_130	16	1923,5511		406,1111,2200	no	coding	C2orf71	NM_001029883.1		868,1767,2869	A1A1,A1R,RR		25.8676,44.2082,31.8223				3503,7505				SO:0001652	inframe_insertion	388939	exon2			.		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.3673_3675dupAGC	2.37:g.29287933_29287935dupGCT	ENSP00000332809:p.Ser1225_Ser1225dup	Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	43	15	0.349	NM_001029883		In_Frame_Ins	INS	ENST00000331664.5	37	CCDS42669.1																																																																																			.	.	strong		0.624	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
SPAG16	79582	hgsc.bcm.edu	37	2	215013915	215013915	+	Frame_Shift_Del	DEL	T	T	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:215013915delT	ENST00000331683.5	+	15	1740	c.1645delT	c.(1645-1647)tttfs	p.F549fs	SPAG16_ENST00000374309.3_Frame_Shift_Del_p.F455fs	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	549					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)		GCTGTGGGACTTTCGGAAGCT	0.368																																					p.D548fs		Pindel,Atlas-Indel	.											.	SPAG16	134	.	0			c.1644delC						PASS	.						166.0	165.0	165.0					2																	215013915		2203	4300	6503	SO:0001589	frameshift_variant	79582	exon15			.	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.1645delT	2.37:g.215013915delT	ENSP00000332592:p.Phe549fs	Somatic	307	.	.		WXS	Illumina HiSeq	Phase_I	179	55	0.307	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Frame_Shift_Del	DEL	ENST00000331683.5	37	CCDS2396.1																																																																																			.	.	none		0.368	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129948	175129955	+	Frame_Shift_Del	DEL	TCTTCTTG	TCTTCTTG	-	rs3208835|rs542219168|rs71563271|rs202239690|rs386636937|rs57794404		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCTTCTTG	TCTTCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:175129948_175129955delTCTTCTTG	ENST00000423313.1	-	4	731_738	c.195_202delCAAGAAGA	c.(193-204)aacaagaagaagfs	p.NKK65fs	KIAA0040_ENST00000545251.2_Frame_Shift_Del_p.NKK65fs|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_Frame_Shift_Del_p.NKK65fs	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	ttcttcttcttcttcttgttcttctCTG	0.51																																					p.66_68del		Atlas-Indel	.											.	KIAA0040	2	.	0			c.196_203del						PASS	.																																			SO:0001589	frameshift_variant	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.195_202delCAAGAAGA	1.37:g.175129948_175129955delTCTTCTTG	ENSP00000462172:p.Asn65fs	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	131	25	0.19084	NM_001162893	A8K9H6|Q2NKQ0	Frame_Shift_Del	DEL	ENST00000423313.1	37																																																																																				.	.	none		0.510	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
ANKRD34C	390616	hgsc.bcm.edu	37	15	79586693	79586695	+	In_Frame_Del	DEL	GTG	GTG	-	rs536236949	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GTG	GTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:79586693_79586695delGTG	ENST00000558647.2	+	1	1067_1069	c.1067_1069delGTG	c.(1066-1071)tgtggt>tgt	p.G357del	ANKRD34C_ENST00000421388.2_In_Frame_Del_p.G357del			P0C6C1	AN34C_HUMAN	ankyrin repeat domain 34C	357										endometrium(3)|kidney(1)|skin(1)	5						CAAGAGAAATGTGGTATGGGTCC	0.542														6	0.00119808	0.0	0.0029	5008	,	,		19452	0.0		0.004	False		,,,				2504	0.0				p.356_356del		Pindel,Atlas-Indel	.											.	ANKRD34C	29	.	0			c.1066_1068del						PASS	.			7,2311		2,3,1154						-3.8	0.0			34	15,4489		2,11,2239	no	coding	ANKRD34C	NM_001146341.1		4,14,3393	A1A1,A1R,RR		0.333,0.302,0.3225				22,6800				SO:0001651	inframe_deletion	390616	exon2			.		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.1067_1069delGTG	15.37:g.79586693_79586695delGTG	ENSP00000454921:p.Gly357del	Somatic	57	.	.		WXS	Illumina HiSeq	Phase_I	39	22	0.564	NM_001146341	H3BNM1	In_Frame_Del	DEL	ENST00000558647.2	37	CCDS53965.1																																																																																			.	.	none		0.542	ANKRD34C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416713.2	NM_001146341	
SH3BGR	6450	hgsc.bcm.edu	37	21	40883671	40883672	+	In_Frame_Ins	INS	-	-	AGA	rs111921581|rs397694871|rs3831201|rs77389080	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:40883671_40883672insAGA	ENST00000333634.4	+	6	767_768	c.689_690insAGA	c.(688-693)ggagaa>ggAGAagaa	p.232_233insE	SH3BGR_ENST00000380634.1_In_Frame_Ins_p.121_122insE|SH3BGR_ENST00000380637.3_In_Frame_Ins_p.121_122insE|SH3BGR_ENST00000380631.1_In_Frame_Ins_p.121_122insE|SH3BGR_ENST00000458295.1_In_Frame_Ins_p.90_91insE	NM_007341.2	NP_031367	P55822	SH3BG_HUMAN	SH3 domain binding glutamate-rich protein	232	Glu-rich (acidic).			E -> EE (in Ref. 4; BM474020). {ECO:0000305}.	positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)		ACTGCAGAAGGAGAAGAGCCTG	0.46																																					p.G230delinsGE		Pindel,Atlas-Indel	.											SH3BGR,colon,carcinoma,0,1	SH3BGR	29	1	0			c.689_690insAGA						PASS	.		,	2200,2064		562,1076,494					,	-5.7	0.0		dbSNP_131	112	4701,3553		1343,2015,769	no	coding,coding	SH3BGR	NM_007341.2,NM_001001713.1	,	1905,3091,1263	A1A1,A1R,RR		43.0458,48.4053,44.8714	,	,		6901,5617				SO:0001652	inframe_insertion	6450	exon6			.		CCDS13666.1, CCDS33560.1	21q22.3	2014-02-19	2014-02-19		ENSG00000185437	ENSG00000185437			10822	protein-coding gene	gene with protein product	"""21-glutamic acid-rich protein"""	602230	"""SH3 domain binding glutamic acid-rich protein"""			9050928	Standard	NM_007341		Approved	21-GARP	uc002yya.3	P55822	OTTHUMG00000074113	ENST00000333634.4:c.693_695dupAGA	21.37:g.40883675_40883677dupAGA	ENSP00000332513:p.Glu232_Glu232dup	Somatic	86	.	.		WXS	Illumina HiSeq	Phase_I	98	41	0.418	NM_007341	A6ND59|D3DSI2|Q9BRB8	In_Frame_Ins	INS	ENST00000333634.4	37	CCDS13666.1																																																																																			.	.	strong		0.460	SH3BGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157377.6	NM_007341	
CELA1	1990	hgsc.bcm.edu	37	12	51740388	51740416	+	Splice_Site	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs150350903|rs573952082|rs532961697|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs3059200|rs148235680|rs370927847|rs907354|rs148270827|rs116944010|rs57614420|rs386762976|rs55827519	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:51740388_51740416delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	1	47_57	c.7_17delGTCCTTTATGGTAAGTGGATATGGTCCAG	c.(7-18)gtcctttatggt>t	p.VLYG3fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	3					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.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						AGGGTTGCGACTGGACCATATCCACTTACCATAAAGGACCAGCATGTTG	0.511																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						PASS	.																																			SO:0001630	splice_region_variant	1990	exon1			.		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.16+1GTCCTTTATGGTAAGTGGATATGGTCCAG>-	12.37:g.51740388_51740416delCTGGACCATATCCACTTACCATAAAGGAC		Somatic	204	.	.		WXS	Illumina HiSeq	Phase_I	138	21	0.152	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	37	CCDS8812.1																																																																																			-|0.574;CACCAGGAAGCG|0.426	0.574	alt		0.511	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	Frame_Shift_Del
SCNN1G	6340	hgsc.bcm.edu	37	16	23226618	23226619	+	In_Frame_Ins	INS	-	-	TCC			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:23226618_23226619insTCC	ENST00000300061.2	+	13	1921_1922	c.1778_1779insTCC	c.(1777-1782)aatcca>aaTCCtcca	p.594_595insP	CTC-391G2.1_ENST00000563471.1_RNA	NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	594					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)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	GGCCAGGACAATCCAGCCCTGG	0.609																																					p.N593delinsNP		Pindel	.											.	SCNN1G	82	.	0			c.1778_1779insTCC						PASS	.			0,4264		0,0,2132						4.3	0.8			103	3,8251		0,3,4124	no	coding	SCNN1G	NM_001039.3		0,3,6256	A1A1,A1R,RR		0.0363,0.0,0.024				3,12515				SO:0001652	inframe_insertion	6340	exon13			.	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10602	protein-coding gene	gene with protein product		600761	"""sodium channel, nonvoltage-gated 1, gamma"", ""sodium channel, non-voltage-gated 1, gamma"""			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.1779_1781dupTCC	16.37:g.23226619_23226621dupTCC	ENSP00000300061:p.Pro594_Pro594dup	Somatic	91	.	.		WXS	Illumina HiSeq	Phase_I	94	36	0.383	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	In_Frame_Ins	INS	ENST00000300061.2	37	CCDS10608.1																																																																																			.	.	none		0.609	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039	
HSP90B1	7184	hgsc.bcm.edu	37	12	104332202	104332204	+	In_Frame_Del	DEL	GAA	GAA	-	rs546630977		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:104332202_104332204delGAA	ENST00000299767.5	+	7	1122_1124	c.940_942delGAA	c.(940-942)gaadel	p.E318del		NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	318					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)	tgcagtagaggaagaagaagaag	0.379																																					p.313_314del		Pindel	.											.	HSP90B1	72	.	0			c.939_941del						PASS	.			45,4219		0,45,2087						-0.2	1.0			44	116,8138		0,116,4011	no	coding	HSP90B1	NM_003299.1		0,161,6098	A1A1,A1R,RR		1.4054,1.0553,1.2861				161,12357				SO:0001651	inframe_deletion	7184	exon7			.	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.940_942delGAA	12.37:g.104332211_104332213delGAA	ENSP00000299767:p.Glu318del	Somatic	185	.	.		WXS	Illumina HiSeq	Phase_I	153	41	0.268	NM_003299	Q96A97	In_Frame_Del	DEL	ENST00000299767.5	37	CCDS9094.1																																																																																			.	.	none		0.379	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
ZCCHC6	79670	hgsc.bcm.edu	37	9	88937852	88937854	+	In_Frame_Del	DEL	TTT	TTT	-	rs58050565|rs77621374|rs200402481|rs397759922	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:88937852_88937854delTTT	ENST00000375963.3	-	13	2983_2985	c.2811_2813delAAA	c.(2809-2814)aaaaat>aat	p.K937del	ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000375961.2_In_Frame_Del_p.K937del|ZCCHC6_ENST00000277141.6_In_Frame_Del_p.K226del|ZCCHC6_ENST00000375960.2_In_Frame_Del_p.K814del	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	937				Missing (in Ref. 1; CAI45944/CAH56219). {ECO:0000305}.	RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.N938delN(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						CACAGGTGAATTTTTTTCTTCAC	0.345														2624	0.523962	0.562	0.4899	5008	,	,		19309	0.4792		0.5417	False		,,,				2504	0.5245				p.938_938del		Pindel	.											.	ZCCHC6	105	.	1	Deletion - In frame(1)	large_intestine(1)	c.2812_2814del						PASS	.		,,	2377,1887		665,1047,420					,,	4.1	1.0		dbSNP_129	62	4461,3793		1183,2095,849	no	coding,coding,coding	ZCCHC6	NM_024617.3,NM_001185074.1,NM_001185059.1	,,	1848,3142,1269	A1A1,A1R,RR		45.9535,44.2542,45.3747	,,	,,		6838,5680				SO:0001651	inframe_deletion	79670	exon13			.	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"""Zinc fingers, CCHC domain containing"""	25817	protein-coding gene	gene with protein product	"""TUTase7"""					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.2811_2813delAAA	9.37:g.88937855_88937857delTTT	ENSP00000365130:p.Lys937del	Somatic	227	.	.		WXS	Illumina HiSeq	Phase_I	244	75	0.307	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	In_Frame_Del	DEL	ENST00000375963.3	37	CCDS35057.1																																																																																			.	.	weak		0.345	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617	
HSPBAP1	79663	hgsc.bcm.edu	37	3	122459290	122459291	+	In_Frame_Ins	INS	-	-	AGA	rs71270423|rs370465518|rs34964328|rs16338	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122459290_122459291insAGA	ENST00000306103.2	-	8	1511_1512	c.1368_1369insTCT	c.(1366-1371)cctcaa>cctTCTcaa	p.456_457PQ>PSQ	HSPBAP1_ENST00000383659.1_3'UTR	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	456				P -> PS (in Ref. 3; AAH17763). {ECO:0000305}.		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)		ATGAATGTTTGAGGAGTCGTAG	0.386														759	0.151558	0.2277	0.1671	5008	,	,		16998	0.126		0.1382	False		,,,				2504	0.0777				p.Q457delinsSQ		Pindel	.											HSPBAP1,NS,carcinoma,+1,1	HSPBAP1	32	1	0			c.1369_1370insTCT						PASS	.			830,3436		82,666,1385						1.2	0.0		dbSNP_54	189	1244,7010		94,1056,2977	no	coding	HSPBAP1	NM_024610.5		176,1722,4362	A1A1,A1R,RR		15.0715,19.4562,16.5655				2074,10446				SO:0001652	inframe_insertion	79663	exon8			.	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.1368_1369insTCT	3.37:g.122459290_122459291insAGA	ENSP00000302562:p.Pro456_Gln457insSer	Somatic	394	.	.		WXS	Illumina HiSeq	Phase_I	384	93	0.242	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	In_Frame_Ins	INS	ENST00000306103.2	37	CCDS3017.1																																																																																			-|0.847;AGA|0.153	0.153	strong		0.386	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610	
NELFA	7469	hgsc.bcm.edu	37	4	1988188	1988189	+	Intron	INS	-	-	CT	rs35401110|rs3034718	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1988188_1988189insCT	ENST00000411638.2	-	5	650				NELFA_ENST00000382882.3_Intron|NELFA_ENST00000542778.1_Intron|MIR943_ENST00000401286.1_RNA	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A						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)										TCCCCCACCCCGAGCTCAGAAC	0.678														1385	0.276558	0.4629	0.255	5008	,	,		14126	0.2778		0.1928	False		,,,				2504	0.1247				.		Pindel	.											.	.	.	.	0			.						PASS	.			1739,0,2511		377,0,985,0,0,763						1.7	0.0		dbSNP_126	28	1828,4,6416		208,1,1411,0,3,2501	no	intron	WHSC2	NM_005663.4		585,1,2396,0,3,3264	A1A1,A1A2,A1R,A2A2,A2R,RR		22.2114,40.9176,28.5726				3567,4,8927				SO:0001627	intron_variant	100126332	.			.	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.635-59->AG	4.37:g.1988188_1988189insCT		Somatic	192	.	.		WXS	Illumina HiSeq	Phase_I	151	42	0.278	.	A2A2T1|O95392	RNA	INS	ENST00000411638.2	37																																																																																				CT|1.000;|0.000	1.000	strong		0.678	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663	
LRRC49	54839	hgsc.bcm.edu	37	15	71276481	71276483	+	In_Frame_Del	DEL	CAA	CAA	-	rs3834543|rs398027832|rs201509714|rs56720495	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:71276481_71276483delCAA	ENST00000260382.5	+	11	1314_1316	c.1054_1056delCAA	c.(1054-1056)caadel	p.Q354del	LRRC49_ENST00000560369.1_In_Frame_Del_p.Q359del|LRRC49_ENST00000443425.2_In_Frame_Del_p.Q310del|LRRC49_ENST00000436542.2_3'UTR|LRRC49_ENST00000560158.2_In_Frame_Del_p.Q42del|LRRC49_ENST00000560691.1_In_Frame_Del_p.Q60del|LRRC49_ENST00000544974.2_In_Frame_Del_p.Q344del	NM_001199017.1|NM_017691.3	NP_001185946.1|NP_060161.2	Q8IUZ0	LRC49_HUMAN	leucine rich repeat containing 49	354				Missing (in Ref. 1; BAA90984 and 4; AAH37982). {ECO:0000305}.		cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(3)|skin(3)	34						GTGGGACTTGCAACAACAACGAG	0.389														2183	0.435903	0.2383	0.4539	5008	,	,		14780	0.6032		0.4742	False		,,,				2504	0.4785				p.356_357del		Pindel	.											.	LRRC49	73	.	0			c.1068_1070del						PASS	.		,,	1217,3047		165,887,1080					,,	3.4	1.0		dbSNP_107	101	3897,4357		922,2053,1152	no	coding,coding,coding	LRRC49	NM_017691.3,NM_001199018.1,NM_001199017.1	,,	1087,2940,2232	A1A1,A1R,RR		47.2135,28.5413,40.8532	,,	,,		5114,7404				SO:0001651	inframe_deletion	54839	exon11			.		CCDS32282.1, CCDS55971.1, CCDS58376.1, CCDS61694.1	15q23	2005-08-09				ENSG00000137821			25965	protein-coding gene	gene with protein product						12477932	Standard	NM_001199017		Approved	FLJ20156	uc010ukf.2	Q8IUZ0		ENST00000260382.5:c.1054_1056delCAA	15.37:g.71276487_71276489delCAA	ENSP00000260382:p.Gln354del	Somatic	216	.	.		WXS	Illumina HiSeq	Phase_I	110	55	0.500	NM_001199017	B3KVX1|B7Z366|F5H1J4|G5E9T5|H0YLN4|Q9NXM6	In_Frame_Del	DEL	ENST00000260382.5	37	CCDS32282.1																																																																																			CAA|0.500;-|0.500	0.500	strong		0.389	LRRC49-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417209.3	NM_017691	
PLD1	5337	hgsc.bcm.edu	37	3	171455452	171455452	+	Intron	DEL	A	A	-	rs545683379		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:171455452delA	ENST00000351298.4	-	3	287				PLD1_ENST00000342215.6_Intron|PLD1_ENST00000356327.5_Intron|PLD1_ENST00000340989.4_Intron	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific						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)	GATATACACTAAAAAAAAAAG	0.323																																					.	NSCLC(149;2174 3517 34058)	Pindel	.											.	PLD1	134	.	0			c.161-2T>-						PASS	.		,	25,150,4089		0,0,25,0,150,1957	43.0	44.0	44.0		,	5.4	0.9	3	dbSNP_130	48	26,282,7944		0,0,26,1,280,3819	no	intron,intron	PLD1	NM_002662.4,NM_001130081.2	,	0,0,51,1,430,5776	A1A1,A1A2,A1R,A2A2,A2R,RR		3.7324,4.1041,3.8591	,	,	171455452	51,432,12033	2203	4299	6502	SO:0001627	intron_variant	5337	exon4			.	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.161-3T>-	3.37:g.171455452delA		Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	80	33	0.412	NM_001130081		Splice_Site	DEL	ENST00000351298.4	37	CCDS3216.1																																																																																			.	.	none		0.323	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
RIMBP3B	440804	hgsc.bcm.edu	37	22	21739333	21739335	+	In_Frame_Del	DEL	GAG	GAG	-	rs201364657		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:21739333_21739335delGAG	ENST00000434111.1	+	1	1671_1673	c.1186_1188delGAG	c.(1186-1188)gagdel	p.E397del		NM_001128635.1	NP_001122107.1	A6NNM3	RIM3B_HUMAN	RIMS binding protein 3B	397																	TACCCTGCAAGAGGAGAACAAGC	0.665																																					p.395_396del		Pindel	.											.	RIMBP3C	6	.	0			c.1185_1187del						PASS	.																																			SO:0001651	inframe_deletion	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.1186_1188delGAG	22.37:g.21739336_21739338delGAG	ENSP00000407925:p.Glu397del	Somatic	211	.	.		WXS	Illumina HiSeq	Phase_I	181	74	0.409	NM_001128633		In_Frame_Del	DEL	ENST00000434111.1	37	CCDS46668.1																																																																																			GAG|0.990;-|0.010	0.010	strong		0.665	RIMBP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320196.2	XM_036936	
KIAA1841	84542	hgsc.bcm.edu	37	2	61361326	61361326	+	Frame_Shift_Del	DEL	G	G	-	rs142269591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	.											.	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	178	.	.		WXS	Illumina HiSeq	Phase_I	170	57	0.335	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	
CFAP74	85452	hgsc.bcm.edu	37	1	1887092	1887112	+	IGR	DEL	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	-	rs3838976|rs199780644|rs3838975|rs562842260|rs139735565	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1887092_1887112delGCCCGCCCACCCTGGCTTGGC								TMEM52 (36380 upstream) : C1orf222 (32450 downstream)														p.W736R(1)|p.K733N(1)									GGCCCTCACCGCCCGCCCACCCTGGCTTGGCCTGGCAGCCT	0.643																																					p.732_739del		Pindel	.											.	KIAA1751	92	.	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.2195_2215del						PASS	.																																			SO:0001628	intergenic_variant	85452	exon18			.																													1.37:g.1887092_1887112delGCCCGCCCACCCTGGCTTGGC		Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	61	24	0.393	NM_001080484		In_Frame_Del	DEL		37																																																																																				-|0.223;G|0.777	0.223	alt	0	0.643								
TPSD1	23430	hgsc.bcm.edu	37	16	1306560	1306560	+	Frame_Shift_Del	DEL	G	G	-	rs3830782|rs397840555	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1306560delG	ENST00000211076.3	+	2	274	c.126delG	c.(124-126)cagfs	p.Q42fs	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Frame_Shift_Del_p.Q35fs	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	42	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				TTGGGGGGCAGGAGGCCCCCA	0.697													|||unknown(ALL_OTHER_Ns)	1341	0.267772	0.4191	0.3401	5008	,	,		17418	0.1528		0.2217	False		,,,				2504	0.1779				p.Q42fs		Pindel	.											.	TPSD1	47	.	0			c.125delA						PASS	.			1594,2670		311,972,849	32.0	48.0	43.0			-2.8	0.0	16	dbSNP_114	55	1800,6452		185,1430,2511	no	frameshift	TPSD1	NM_012217.2		496,2402,3360	A1A1,A1R,RR		21.8129,37.3827,27.1173			1306560	3394,9122	2038	4218	6256	SO:0001589	frameshift_variant	23430	exon2			.	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.126delG	16.37:g.1306560delG	ENSP00000211076:p.Gln42fs	Somatic	234	.	.		WXS	Illumina HiSeq	Phase_I	182	90	0.495	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Frame_Shift_Del	DEL	ENST00000211076.3	37	CCDS10432.1																																																																																			G|0.731;-|0.269	0.269	strong		0.697	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
INF2	64423	hgsc.bcm.edu	37	14	105173863	105173868	+	In_Frame_Del	DEL	CCCCAC	CCCCAC	-	rs573567814	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCCCAC	CCCCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105173863_105173868delCCCCAC	ENST00000392634.4	+	8	1371_1376	c.1259_1264delCCCCAC	c.(1258-1266)accccaccc>acc	p.PP427del	INF2_ENST00000330634.7_In_Frame_Del_p.PP427del	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	427	Pro-rich.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.P427_P428delPP(1)		large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CAGGCGTCCAccccacccccaccccc	0.718																																					p.420_421del		Pindel	.											.	INF2	148	.	1	Deletion - In frame(1)	skin(1)	c.1258_1263del						PASS	.																																			SO:0001651	inframe_deletion	64423	exon8			.	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.1259_1264delCCCCAC	14.37:g.105173869_105173874delCCCCAC	ENSP00000376410:p.Pro427_Pro428del	Somatic	83	.	.		WXS	Illumina HiSeq	Phase_I	92	19	0.207	NM_001031714	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	In_Frame_Del	DEL	ENST00000392634.4	37	CCDS9989.2																																																																																			.	.	alt		0.718	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129925	175129933	+	In_Frame_Del	DEL	CTTCTTCTT	CTTCTTCTT	-	rs567102553|rs150137790|rs374766108	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTTCTTCTT	CTTCTTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:175129925_175129933delCTTCTTCTT	ENST00000423313.1	-	4	753_761	c.217_225delAAGAAGAAG	c.(217-225)aagaagaagdel	p.KKK73del	KIAA0040_ENST00000545251.2_In_Frame_Del_p.KKK73del|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000444639.1_In_Frame_Del_p.KKK73del	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	cttcttcatccttcttcttcttcttcttc	0.502																																					p.73_76del		Pindel	.											.	KIAA0040	2	.	0			c.218_226del						PASS	.																																			SO:0001651	inframe_deletion	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.217_225delAAGAAGAAG	1.37:g.175129934_175129942delCTTCTTCTT	ENSP00000462172:p.Lys73_Lys75del	Somatic	116	.	.		WXS	Illumina HiSeq	Phase_I	131	39	0.298	NM_001162893	A8K9H6|Q2NKQ0	In_Frame_Del	DEL	ENST00000423313.1	37																																																																																				.	.	strong		0.502	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
C16orf96	342346	hgsc.bcm.edu	37	16	4644390	4644392	+	In_Frame_Del	DEL	AGG	AGG	-	rs139232890|rs59955859	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4644390_4644392delAGG	ENST00000444310.4	+	13	2906_2908	c.2906_2908delAGG	c.(2905-2910)caggag>cag	p.E970del		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						CTCGGTATCCAGGAGGATTGTCA	0.631														371	0.0740815	0.2247	0.0331	5008	,	,		17641	0.003		0.0457	False		,,,				2504	0.002				p.969_969del		Pindel	.											.	C16orf96	28	.	0			c.2905_2907del						PASS	.			407,2191		81,245,973						1.8	0.0		dbSNP_129	48	160,4518		20,120,2199	no	coding	C16orf96	NM_001145011.1		101,365,3172	A1A1,A1R,RR		3.4203,15.6659,7.7927				567,6709				SO:0001651	inframe_deletion	342346	exon13			.		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.2906_2908delAGG	16.37:g.4644393_4644395delAGG	ENSP00000415027:p.Glu970del	Somatic	133	.	.		WXS	Illumina HiSeq	Phase_I	160	46	0.287	NM_001145011		In_Frame_Del	DEL	ENST00000444310.4	37	CCDS53986.1																																																																																			AGG|0.931;-|0.069	0.069	strong		0.631	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
ANKRD36	375248	hgsc.bcm.edu	37	2	97779488	97779488	+	Frame_Shift_Del	DEL	C	C	-	rs141447363	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:97779488delC	ENST00000461153.2	+	1	256	c.12delC	c.(10-12)ggcfs	p.G4fs	ANKRD36_ENST00000420699.2_Frame_Shift_Del_p.G4fs			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	4										endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						TGGAAGACGGCAAGCGGGAGA	0.562													?|C|-|unsure	121	0.0241613	0.0023	0.0389	5008	,	,		10528	0.0		0.0845	False		,,,				2504	0.0061				p.G4fs		Pindel	.											ANKRD36_ENST00000420699,right_lower_lobe,carcinoma,0,2	ANKRD36	170	2	0			c.11delG						PASS	.			57,3647		4,49,1799	69.0	65.0	66.0			-0.9	0.0	2	dbSNP_134	69	690,7198		41,608,3295	no	frameshift	ANKRD36	NM_001164315.1		45,657,5094	A1A1,A1R,RR		8.7475,1.5389,6.4441			97779488	747,10845	1923	4101	6024	SO:0001589	frameshift_variant	375248	exon1			.	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.12delC	2.37:g.97779488delC	ENSP00000419530:p.Gly4fs	Somatic	178	.	.		WXS	Illumina HiSeq	Phase_I	149	43	0.289	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Frame_Shift_Del	DEL	ENST00000461153.2	37	CCDS54379.1																																																																																			C|0.967;-|0.033	0.033	strong		0.562	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
HCG17	414778	hgsc.bcm.edu	37	6	30229034	30229035	+	lincRNA	INS	-	-	T	rs11393606|rs568184983	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:30229034_30229035insT	ENST00000453558.1	-	0	126				HLA-L_ENST00000463348.1_RNA					HLA complex group 17 (non-protein coding)																		TGAGGCCACCCTGAGGTGCTGG	0.599													T|T|TT|insertion	1991	0.397564	0.3003	0.4496	5008	,	,		19996	0.5308		0.2465	False		,,,				2504	0.5102				.		Pindel	.											.	.	.	.	0			.						PASS	.			1185,3073		160,865,1104						4.0	1.0		dbSNP_120	97	1988,6262		247,1494,2384	no	intergenic				407,2359,3488	A1A1,A1R,RR		24.097,27.83,25.3678				3173,9335						3139	.			.	AB023055		6p21	2012-11-02	2008-08-13		ENSG00000241701	ENSG00000270604		"""Long non-coding RNAs"""	31339	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 46"", ""long intergenic non-protein coding RNA 46"""						Standard	NR_052012		Approved	NCRNA00046, LINC00046	uc031snc.1		OTTHUMG00000031114		6.37:g.30229035_30229035dupT		Somatic	177	.	.		WXS	Illumina HiSeq	Phase_I	186	54	0.290	.		RNA	INS	ENST00000453558.1	37																																																																																				-|0.500;T|0.500	0.500	strong		0.599	HCG17-002	KNOWN	basic|exp_conf	lincRNA	lincRNA	OTTHUMT00000256054.1	NR_052012	
BTBD10	84280	hgsc.bcm.edu	37	11	13410691	13410694	+	Intron	DEL	GAAA	GAAA	-	rs375824034|rs3833472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAAA	GAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:13410691_13410694delGAAA	ENST00000278174.5	-	9	1363				BTBD10_ENST00000528120.1_Intron|BTBD10_ENST00000530907.1_Intron	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10							nucleus (GO:0005634)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		AGGATAACCTGAAAGAAAGAAAGA	0.392														407	0.08127	0.0772	0.0764	5008	,	,		19335	0.0675		0.1233	False		,,,				2504	0.0613				.		Pindel	.											.	BTBD10	43	.	0			.						PASS	.			358,3904		23,312,1796						4.1	1.0		dbSNP_107	46	1001,7253		58,885,3184	no	intron	BTBD10	NM_032320.5		81,1197,4980	A1A1,A1R,RR		12.1275,8.3998,10.8581				1359,11157				SO:0001627	intron_variant	84280	.			.	AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"""BTB/POZ domain containing"""	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.1118-3TTTC>-	11.37:g.13410699_13410702delGAAA		Somatic	41	.	.		WXS	Illumina HiSeq	Phase_I	52	14	0.269	.	B7Z228|Q86WG1	Splice_Site	DEL	ENST00000278174.5	37	CCDS7811.1																																																																																			GAAA|0.908;-|0.092	0.092	strong		0.392	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
DICER1	23405	hgsc.bcm.edu	37	14	95562995	95562997	+	In_Frame_Del	DEL	TCC	TCC	-	rs544960260		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:95562995_95562997delTCC	ENST00000526495.1	-	25	4551_4553	c.4260_4262delGGA	c.(4258-4263)gaggat>gat	p.E1420del	DICER1_ENST00000527414.1_In_Frame_Del_p.E1420del|DICER1_ENST00000393063.1_In_Frame_Del_p.E1420del|DICER1_ENST00000541352.1_In_Frame_Del_p.E1420del|DICER1_ENST00000343455.3_In_Frame_Del_p.E1420del|DICER1_ENST00000556045.1_In_Frame_Del_p.E318del			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	1420					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		ctcctcctcatcctcctcctcGT	0.488			"""Mis F, N"""		"""sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"""	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome																												p.1421_1421del		Pindel	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"""dicer 1, ribonuclease type III """		"""E, M, O"""	.	DICER1	181	.	0			c.4261_4263del						PASS	.		,,	2,4262		0,2,2130					,,	-8.1	0.8			54	27,8227		0,27,4100	no	coding,coding,coding	DICER1	NM_177438.2,NM_030621.3,NM_001195573.1	,,	0,29,6230	A1A1,A1R,RR		0.3271,0.0469,0.2317	,,	,,		29,12489				SO:0001651	inframe_deletion	23405	exon23	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	.	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"""dicer 1, double-stranded RNA-specific endoribonuclease"""	606241	"""Dicer1, Dcr-1 homolog (Drosophila)"", ""multinodular goitre 1"""	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.4260_4262delGGA	14.37:g.95563001_95563003delTCC	ENSP00000437256:p.Glu1420del	Somatic	156	.	.		WXS	Illumina HiSeq	Phase_I	242	75	0.310	NM_001271282	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	In_Frame_Del	DEL	ENST00000526495.1	37	CCDS9931.1																																																																																			.	.	none		0.488	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		
VWDE	221806	hgsc.bcm.edu	37	7	12391268	12391269	+	Frame_Shift_Ins	INS	-	-	A	rs11454536|rs398094831	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:12391268_12391269insA	ENST00000275358.3	-	19	4004_4005	c.3816_3817insT	c.(3814-3819)aataaafs	p.K1273fs		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1273						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TCCTCTTCTTTATTTACACTTT	0.337													A|A|AA|insertion	697	0.139177	0.1505	0.0937	5008	,	,		16921	0.1905		0.1014	False		,,,				2504	0.1421				p.K1273_E1274delinsX		Pindel	.											.	VWDE	123	.	0			c.3817_3818insT						PASS	.			310,1762		51,208,777						1.9	0.0		dbSNP_120	217	402,3750		45,312,1719	no	frameshift	VWDE	NM_001135924.1		96,520,2496	A1A1,A1R,RR		9.6821,14.9614,11.4396				712,5512				SO:0001589	frameshift_variant	221806	exon19			.		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.3817dupT	7.37:g.12391269_12391269dupA	ENSP00000275358:p.Lys1273fs	Somatic	170	.	.		WXS	Illumina HiSeq	Phase_I	199	67	0.337	NM_001135924	B7ZM77|Q96SQ3	Frame_Shift_Ins	INS	ENST00000275358.3	37	CCDS47544.1																																																																																			-|0.844;A|0.156	0.156	strong		0.337	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
MUC5B	727897	hgsc.bcm.edu	37	11	1271219	1271221	+	In_Frame_Del	DEL	CCA	CCA	-	rs61430934|rs199629887	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1271219_1271221delCCA	ENST00000529681.1	+	31	13167_13169	c.13109_13111delCCA	c.(13108-13113)gccacc>gcc	p.T4373del	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_In_Frame_Del_p.T4376del	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4373	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.			Missing (in Ref. 4; CAA96577). {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)		ACCACGAAGGCCACCACGACAAG	0.635														328	0.0654952	0.0242	0.1095	5008	,	,		19711	0.0496		0.0805	False		,,,				2504	0.091				p.4370_4370del		Pindel	.											.	MUC5B	473	.	0			c.13108_13110del						PASS	.			85,4011		5,75,1968						-0.1	0.0		dbSNP_129	110	576,7474		25,526,3474	no	coding	MUC5B	NM_002458.2		30,601,5442	A1A1,A1R,RR		7.1553,2.0752,5.4421				661,11485				SO:0001651	inframe_deletion	727897	exon31			.	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.13109_13111delCCA	11.37:g.1271222_1271224delCCA	ENSP00000436812:p.Thr4373del	Somatic	323	.	.		WXS	Illumina HiSeq	Phase_I	293	64	0.218	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	In_Frame_Del	DEL	ENST00000529681.1	37	CCDS44515.2																																																																																			CCA|0.926;-|0.074	0.074	strong		0.635	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MCMBP	79892	hgsc.bcm.edu	37	10	121587063	121587065	+	IGR	DEL	CTT	CTT	-	rs201053908|rs148162878	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:121587063_121587065delCTT	ENST00000360003.3	-	0	4113				INPP5F_ENST00000369080.3_In_Frame_Del_p.S448del|INPP5F_ENST00000361976.2_In_Frame_Del_p.S1058del	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)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						CATGTAACTCCTTCTCCTTCAGA	0.493														25	0.00499201	0.0	0.0144	5008	,	,		18792	0.002		0.0099	False		,,,				2504	0.0031				p.1057_1057del		Pindel	.											.	INPP5F	112	.	0			c.3169_3171del						PASS	.			5,4255		1,3,2126						5.9	1.0			106	70,8176		4,62,4057	no	coding	INPP5F	NM_014937.3		5,65,6183	A1A1,A1R,RR		0.8489,0.1174,0.5997				75,12431				SO:0001628	intergenic_variant	22876	exon20			.	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.121587063_121587065delCTT		Somatic	157	.	.		WXS	Illumina HiSeq	Phase_I	129	37	0.287	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	In_Frame_Del	DEL	ENST00000360003.3	37	CCDS7617.1																																																																																			CTT|0.994;-|0.006	0.006	strong		0.493	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
SLC28A1	9154	hgsc.bcm.edu	37	15	85438311	85438312	+	In_Frame_Ins	INS	-	-	TTG	rs17215836|rs151038463	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000394573.1_In_Frame_Ins_p.140_141insV|SLC28A1_ENST00000537703.1_In_Frame_Ins_p.62_63insV|SLC28A1_ENST00000537216.1_In_Frame_Ins_p.140_141insV|SLC28A1_ENST00000538177.1_In_Frame_Ins_p.140_141insV|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	.											.	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	121	.	.		WXS	Illumina HiSeq	Phase_I	58	29	0.500	NM_201651	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		
PI4KAP2	375133	hgsc.bcm.edu	37	22	21829514	21829517	+	RNA	DEL	TGTC	TGTC	-	rs113567369|rs57294418	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:21829514_21829517delTGTC	ENST00000450651.1	-	0	1821_1824							A4QPH2	PI4P2_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha pseudogene 2						phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(3)|urinary_tract(1)	4						AGAGCTTGATTGTCTGGCCGCGAA	0.564														3270	0.652955	0.8162	0.5865	5008	,	,		11476	0.4454		0.8708	False		,,,				2504	0.4693				.		Pindel	.											.	PI4KAP2	11	.	0			.						PASS	.			3028,976		1236,556,210						2.4	1.0		dbSNP_132	21	6139,1303		2723,693,305	no	intergenic				3959,1249,515	A1A1,A1R,RR		17.5087,24.3756,19.9109				9167,2279						375133	.			.			22q11.21	2014-03-20	2007-08-14		ENSG00000183506	ENSG00000183506			33577	pseudogene	pseudogene							Standard	NR_003700		Approved		uc011aie.1	A4QPH2	OTTHUMG00000150827		22.37:g.21829514_21829517delTGTC		Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	118	36	0.305	.	Q6ICJ0|Q6ZT68|Q8WUK7	RNA	DEL	ENST00000450651.1	37																																																																																				TGTC|0.500;-|0.500	0.500	strong		0.564	PI4KAP2-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000334908.1		
SF3A2	8175	hgsc.bcm.edu	37	19	2248152	2248153	+	In_Frame_Ins	INS	-	-	GGAGTCCACCCTCCAGCCCCC	rs59267791|rs539335935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2248152_2248153insGGAGTCCACCCTCCAGCCCCC	ENST00000221494.5	+	9	1420_1421	c.1002_1003insGGAGTCCACCCTCCAGCCCCC	c.(1003-1005)gga>GGAGTCCACCCTCCAGCCCCCgga	p.335_335G>GVHPPAPG	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	335	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		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)		CCCCAGCTCCTGGAGTCCACCC	0.733																																					p.P334delinsPGVHPPAP		Pindel	.											SF3A2,colon,carcinoma,0,1	SF3A2	22	1	0			c.1002_1003insGGAGTCCACCCTCCAGCCCCC						PASS	.																																			SO:0001652	inframe_insertion	8175	exon9			.	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1003_1023dupGGAGTCCACCCTCCAGCCCCC	19.37:g.2248152_2248153insGGAGTCCACCCTCCAGCCCCC	ENSP00000221494:p.ValHisProProAlaProGly363dup	Somatic	28	.	.		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_007165	B2RBU1|D6W605|O75245	In_Frame_Ins	INS	ENST00000221494.5	37	CCDS12084.1																																																																																			.	.	none		0.733	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3		
CDCP2	200008	hgsc.bcm.edu	37	1	54605319	54605320	+	Frame_Shift_Ins	INS	-	-	C	rs77544356|rs66812916|rs36013100|rs66537746|rs75306471|rs549857682	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:54605319_54605320insC	ENST00000371330.1	-	4	2070_2071	c.1223_1224insG	c.(1222-1224)cccfs	p.P408fs	CDCP2_ENST00000530059.1_Intron|RP11-446E24.4_ENST00000525949.1_5'Flank	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	408						extracellular region (GO:0005576)		p.M409fs*>42(1)		kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						GACCATTCATGGGGGGGGCAGG	0.594													?|-|C|unsure	2403	0.479832	0.3631	0.6614	5008	,	,		16583	0.3889		0.6521	False		,,,				2504	0.4254				p.P408fs		Pindel	.											.	CDCP2	52	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1224_1225insG						PASS	.																																			SO:0001589	frameshift_variant	200008	exon4			.		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.1223_1224insG	1.37:g.54605319_54605320insC	ENSP00000360381:p.Pro408fs	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	76	44	0.579	NM_201546	Q6ZWJ3	Frame_Shift_Ins	INS	ENST00000371330.1	37	CCDS588.2																																																																																			.	.	strong		0.594	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
OR2B11	127623	hgsc.bcm.edu	37	1	247615262	247615262	+	Frame_Shift_Del	DEL	A	A	-	rs35305980|rs397733455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247615262delA	ENST00000318749.6	-	1	46	c.23delT	c.(22-24)ttcfs	p.F8fs		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	8						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)			GTCCCCTAAGAAGCTATGGTT	0.473													AA|AA|A|deletion	2249	0.449081	0.2852	0.5274	5008	,	,		21865	0.4762		0.4563	False		,,,				2504	0.5798				p.F8fs		Pindel	.											.	OR2B11	102	.	0			c.24delC						PASS	.			1318,2948		196,926,1011	74.0	72.0	73.0			0.0	0.0	1	dbSNP_131	112	3624,4628		809,2006,1311	no	frameshift	OR2B11	NM_001004492.1		1005,2932,2322	A1A1,A1R,RR		43.9166,30.8955,39.4792			247615262	4942,7576	2167	4183	6350	SO:0001589	frameshift_variant	127623	exon1			.		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.23delT	1.37:g.247615262delA	ENSP00000325682:p.Phe8fs	Somatic	138	.	.		WXS	Illumina HiSeq	Phase_I	155	90	0.581	NM_001004492	B2RP03	Frame_Shift_Del	DEL	ENST00000318749.6	37	CCDS31090.1																																																																																			A|0.570;-|0.430	0.430	strong		0.473	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
FAM171B	165215	hgsc.bcm.edu	37	2	187559047	187559048	+	In_Frame_Ins	INS	-	-	CAA	rs73979342|rs144403657|rs71017336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187559047_187559048insCAA	ENST00000304698.5	+	1	350_351	c.147_148insCAA	c.(148-150)caa>CAAcaa	p.50_50Q>QQ	AC017101.10_ENST00000453665.1_RNA	NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	50	Gln-rich.					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						agcagcagcagcaacaacaaca	0.634														2602	0.519569	0.5106	0.5216	5008	,	,		14904	0.7183		0.4404	False		,,,				2504	0.407				p.Q49delinsQQ		Pindel	.											FAM171B,NS,carcinoma,0,1	FAM171B	146	1	0			c.147_148insCAA						PASS	.																																			SO:0001652	inframe_insertion	165215	exon1			.	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.160_162dupCAA	2.37:g.187559054_187559056dupCAA	ENSP00000304108:p.Gln56dup	Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	70	30	0.429	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	In_Frame_Ins	INS	ENST00000304698.5	37	CCDS33347.1																																																																																			-|0.371;CAA|0.629	0.629	strong		0.634	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
NPL	80896	hgsc.bcm.edu	37	1	182763576	182763576	+	Splice_Site	DEL	T	T	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:182763576delT	ENST00000367553.1	+	2	112		c.e2+2		NPL_ENST00000367554.3_Intron|NPL_ENST00000463899.1_Splice_Site|NPL_ENST00000367552.2_Splice_Site|NPL_ENST00000258317.2_Splice_Site|NPL_ENST00000367550.2_Splice_Site|NPL_ENST00000367555.1_Splice_Site	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)						carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						TGAGAATGGGTAACTATCATT	0.458																																					.		Pindel	.											.	NPL	55	.	0			c.68+1T>-						PASS	.		,,,,	1,4265		0,1,2132	118.0	118.0	118.0		,,,,	5.3	1.0	1		118	1,8253		0,1,4126	no	splice-5,splice-5,splice-5,splice-5,intron	NPL	NM_030769.2,NM_001200056.1,NM_001200052.1,NM_001200051.1,NM_001200050.1	,,,,	0,2,6258	A1A1,A1R,RR		0.0121,0.0234,0.016	,,,,	,,,,	182763576	2,12518	2203	4300	6503	SO:0001630	splice_region_variant	80896	exon3			.	AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"""dihydrodipicolinate synthetase homolog 1 (E. coli)"""	611412	"""chromosome 1 open reading frame 13"""	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.68+2T>-	1.37:g.182763576delT		Somatic	140	.	.		WXS	Illumina HiSeq	Phase_I	168	61	0.363	NM_001200051	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Splice_Site	DEL	ENST00000367553.1	37	CCDS1350.1																																																																																			.	.	none		0.458	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769	Intron
TPTE	7179	hgsc.bcm.edu	37	21	10942925	10942927	+	In_Frame_Del	DEL	CTT	CTT	-	rs113444703|rs386816290|rs3047743|rs558478158		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:10942925_10942927delCTT	ENST00000361285.4	-	12	989_991	c.660_662delAAG	c.(658-663)agaagg>agg	p.220_221RR>R	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_In_Frame_Del_p.182_183RR>R|TPTE_ENST00000298232.7_In_Frame_Del_p.202_203RR>R	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		Pindel	.											.	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	536	.	.		WXS	Illumina HiSeq	Phase_I	816	129	0.158	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		
CHD1	1105	hgsc.bcm.edu	37	5	98192165	98192167	+	In_Frame_Del	DEL	AGG	AGG	-	rs398102328|rs79267787|rs138635992|rs61749618	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:98192165_98192167delAGG	ENST00000284049.3	-	35	5199_5201	c.5050_5052delCCT	c.(5050-5052)cctdel	p.P1684del		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1684					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)	p.P1684delP(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TGGAGCCATAAGGAGATCTCTGA	0.453														1065	0.21266	0.3411	0.2262	5008	,	,		18993	0.0427		0.2763	False		,,,				2504	0.1391				p.1684_1685del		Pindel	.											.	CHD1	137	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.5051_5053del						PASS	.			1429,2837		256,917,960						5.8	1.0		dbSNP_130	90	2258,5994		309,1640,2177	no	coding	CHD1	NM_001270.2		565,2557,3137	A1A1,A1R,RR		27.3631,33.4974,29.4536				3687,8831				SO:0001651	inframe_deletion	1105	exon35			.	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.5050_5052delCCT	5.37:g.98192165_98192167delAGG	ENSP00000284049:p.Pro1684del	Somatic	296	.	.		WXS	Illumina HiSeq	Phase_I	255	69	0.271	NM_001270	Q17RZ3	In_Frame_Del	DEL	ENST00000284049.3	37	CCDS34204.1																																																																																			AGG|0.775;-|0.225	0.225	strong		0.453	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
ZNF772	400720	hgsc.bcm.edu	37	19	57988666	57988667	+	In_Frame_Ins	INS	-	-	GCC	rs77164240|rs528587884|rs34678661|rs193920834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57988666_57988667insGCC	ENST00000343280.4	-	1	271_272	c.11_12insGGC	c.(10-12)gct>gcGGCt	p.4_4A>AA	AC003005.2_ENST00000595422.1_lincRNA|ZNF772_ENST00000425074.3_In_Frame_Ins_p.4_4A>AA|ZNF772_ENST00000601768.1_In_Frame_Ins_p.4_4A>AA|AC004076.9_ENST00000596831.1_In_Frame_Ins_p.4_4A>AA|ZNF772_ENST00000427512.2_5'UTR|ZNF772_ENST00000356584.3_In_Frame_Ins_p.4_4A>AA|ZNF772_ENST00000600175.1_In_Frame_Ins_p.4_4A>AA|AC004076.9_ENST00000415705.3_5'UTR	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	4					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)		CCATCGGCTCAGCCGCCGCCAT	0.644											OREG0025695	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		2037	0.406749	0.3124	0.4481	5008	,	,		16965	0.5823		0.2753	False		,,,				2504	0.4591				p.A4delinsAA	Melanoma(5;289 436 14293 15924 30817)	Pindel	.											ZNF772,colon,carcinoma,0,1	ZNF772	42	1	0			c.12_13insGGC						PASS	.		,	1273,2975		195,883,1046					,	-4.0	0.0		dbSNP_126	62	2294,5946		320,1654,2146	no	coding,coding	ZNF772	NM_001144068.1,NM_001024596.2	,	515,2537,3192	A1A1,A1R,RR		27.8398,29.967,28.5634	,	,		3567,8921				SO:0001652	inframe_insertion	400720	exon1			.	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.9_11dupGGC	19.37:g.57988673_57988675dupGCC	ENSP00000341165:p.Ala4dup	Somatic	286	.	.	1027	WXS	Illumina HiSeq	Phase_I	196	51	0.260	NM_001144068	A6NJK9|B4DH56|B4DYS0	In_Frame_Ins	INS	ENST00000343280.4	37	CCDS33133.1																																																																																			GCC|1.000;|0.000	1.000	strong		0.644	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
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-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GGGCCGCGGAGG	GGGCCGCGGAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140186979_140186990delGGGCCGCGGAGG	ENST00000530339.1	+	1	207_218	c.207_218delGGGCCGCGGAGG	c.(205-219)aagggccgcggaggc>aac	p.69_73KGRGG>N	PCDHA4_ENST00000356878.4_In_Frame_Del_p.69_73KGRGG>N|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_In_Frame_Del_p.69_73KGRGG>N	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	73	.	.		WXS	Illumina HiSeq	Phase_I	29	13	0.448	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	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388594	1388622	+	Frame_Shift_Del	DEL	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	-	rs76374232|rs151313714|rs540461234|rs75969203|rs558358960|rs79704405|rs200174708	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CACGTGCCCATGTGGAGTGCCCGCCTGCT	CACGTGCCCATGTGGAGTGCCCGCCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	184	.	.		WXS	Illumina HiSeq	Phase_I	157	47	0.299	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	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119755	38119757	+	In_Frame_Del	DEL	CAA	CAA	-	rs201160789|rs71322688|rs55745992|rs67890459|rs77530465|rs199535040	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	.											.	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	128	.	.		WXS	Illumina HiSeq	Phase_I	118	35	0.297	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		
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427685	70427685	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:70427685delG	ENST00000377413.1	-	1	2046	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_199244.2	NP_954714.2	Q8WXT5	FX4L4_HUMAN	forkhead box D4-like 4	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)								GBM - Glioblastoma multiforme(29;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TGCCCGCCCAGCACCGCGCCC	0.677																																					p.W406fs		Pindel	.											.	FOXD4L4	5	.	0			c.1216delT						PASS	.																																			SO:0001589	frameshift_variant	349334	exon1			.		CCDS75845.1	9q13	2007-03-19			ENSG00000184659	ENSG00000184659			23762	protein-coding gene	gene with protein product		611085					Standard	NM_199244		Approved	bA460E7.2, OTTHUMG00000013337		Q8WXT5	OTTHUMG00000013337	ENST00000377413.1:c.1215delC	9.37:g.70427685delG	ENSP00000366630:p.Cys405fs	Somatic	310	.	.		WXS	Illumina HiSeq	Phase_I	131	26	0.198	NM_199244	Q5RIB4	Frame_Shift_Del	DEL	ENST00000377413.1	37	CCDS6621.1																																																																																			.	.	weak		0.677	FOXD4L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037143.2		
KIAA0754	643314	hgsc.bcm.edu	37	1	39879397	39879435	+	In_Frame_Del	DEL	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	-	rs371382486|rs55976345|rs541496808|rs199726261|rs548996855|rs112569629|rs201613510	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879397_39879435delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	ENST00000530275.1	+	1	3247_3285	c.3052_3090delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	c.(3052-3090)gaggaatccgcctccgcagctgttgcagtgcccacccccdel	p.EESASAAVAVPTP1018del	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1018	Ala-rich.									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)			GCCCACCCCAGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCCGAGGAATCTG	0.682																																					p.1153_1166del		Pindel	.											.	KIAA0754	93	.	0			c.3459_3497del						PASS	.		,,	832,2850		248,336,1257					,,	0.0	0.0			18	1888,6000		448,992,2504	no	intron,coding,intron	MACF1,KIAA0754	NM_033044.3,NM_015038.1,NM_012090.4	,,	696,1328,3761	A1A1,A1R,RR		23.9351,22.5964,23.5091	,,	,,		2720,8850				SO:0001651	inframe_deletion	643314	exon1			.			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.3052_3090delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	1.37:g.39879397_39879435delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	ENSP00000431179:p.Glu1018_Pro1030del	Somatic	197	.	.		WXS	Illumina HiSeq	Phase_I	65	19	0.292	NM_015038	E9PMC2|Q6ZSB2	In_Frame_Del	DEL	ENST00000530275.1	37																																																																																				.	.	none		0.682	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176769	70176769	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:70176769delG	ENST00000377420.1	-	1	2046	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_001126334.1	NP_001119806.1	Q5VV16	FX4L5_HUMAN	forkhead box D4-like 5	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|lung(2)	7						TGCCCGCCCAGCACCGCGCCC	0.677																																					p.W406fs		Pindel	.											.	FOXD4L5	27	.	0			c.1216delT						PASS	.			10,4		5,0,2	0.0	1.0	1.0			1.1	0.1	9		1	16,8		8,0,4	no	frameshift	FOXD4L5	NM_001126334.1		13,0,6	A1A1,A1R,RR		33.3333,28.5714,31.5789			70176769	26,12	0	3	3	SO:0001589	frameshift_variant	653427	exon1			.		CCDS47977.1	9q13	2008-07-21			ENSG00000204779	ENSG00000204779			18522	protein-coding gene	gene with protein product						12234674	Standard	NM_001126334		Approved	bA15J10.2, OTTHUMG00000013332	uc010moc.3	Q5VV16	OTTHUMG00000013332	ENST00000377420.1:c.1215delC	9.37:g.70176769delG	ENSP00000366637:p.Cys405fs	Somatic	322	.	.		WXS	Illumina HiSeq	Phase_I	136	24	0.176	NM_001126334		Frame_Shift_Del	DEL	ENST00000377420.1	37	CCDS47977.1																																																																																			.	.	weak		0.677	FOXD4L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037122.1	NM_001126334	
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-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GACATCTTTGCCCAGACATGGA	GACATCTTTGCCCAGACATGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	103	.	.		WXS	Illumina HiSeq	Phase_I	73	32	0.438	NM_001137668		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																				.	.	alt		0.374	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
MDP1	145553	hgsc.bcm.edu	37	14	24683267	24683267	+	Frame_Shift_Del	DEL	A	A	-	rs3215610|rs398102305	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24683267delA	ENST00000288087.7	-	6	605	c.494delT	c.(493-495)ttgfs	p.L165fs	TM9SF1_ENST00000530611.1_5'Flank|CHMP4A_ENST00000347519.6_5'Flank|NEDD8-MDP1_ENST00000604306.1_5'Flank|CHMP4A_ENST00000542700.2_5'Flank|TM9SF1_ENST00000556387.1_5'Flank|MDP1_ENST00000396833.2_Frame_Shift_Del_p.F118fs|CHMP4A_ENST00000530996.1_5'Flank|AL136419.6_ENST00000565988.1_RNA|CHMP4A_ENST00000609024.1_5'Flank|MDP1_ENST00000532557.1_5'UTR	NM_001199822.1|NM_138476.3	NP_001186751.1|NP_612485.2	Q86V88	MGDP1_HUMAN	magnesium-dependent phosphatase 1	165						extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)			breast(2)|large_intestine(2)|lung(3)	7						GCTGGACCTCAAAGGCCCAGT	0.418													AA|AAA|AA|insertion	1020	0.203674	0.4342	0.0807	5008	,	,		23163	0.2123		0.0686	False		,,,				2504	0.1094				p.L182fs		Pindel	.											.	.	.	.	0			c.546delG						PASS	.		,,,	1728,2536		344,1040,748	42.0	63.0	56.0		,,,	2.4	0.9	14	dbSNP_134	68	579,7675		25,529,3573	no	frameshift,frameshift,utr-3,frameshift	MDP1,NEDD8-MDP1	NM_138476.3,NM_001199823.1,NM_001199822.1,NM_001199821.1	,,,	369,1569,4321	A1A1,A1R,RR		7.0148,40.5253,18.4295	,,,	,,,	24683267	2307,10211	2162	4299	6461	SO:0001589	frameshift_variant	100528064	exon7			.	BC046912	CCDS9620.1, CCDS55908.1	14q12	2009-07-09			ENSG00000213920	ENSG00000213920			28781	protein-coding gene	gene with protein product	"""fructosamine-6-phosphatase"""					10889041, 16670083	Standard	NM_138476		Approved	MGC5987, FN6Pase		Q86V88	OTTHUMG00000133477	ENST00000288087.7:c.494delT	14.37:g.24683267delA	ENSP00000288087:p.Leu165fs	Somatic	151	.	.		WXS	Illumina HiSeq	Phase_I	207	83	0.401	NM_001199823	Q86Y84|Q8NAD9	Frame_Shift_Del	DEL	ENST00000288087.7	37	CCDS9620.1																																																																																			A|0.812;-|0.188	0.188	strong		0.418	MDP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257367.1	NM_138476	
PEBP4	157310	hgsc.bcm.edu	37	8	22570908	22570908	+	Frame_Shift_Del	DEL	T	T	-	rs35121552|rs398102329	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:22570908delT	ENST00000256404.6	-	7	750	c.659delA	c.(658-660)aacfs	p.N220fs	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	220						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)		CTCCGCCTGGTTTTTGTGCTT	0.602													TTTT|TTTTT|TTTT|insertion	1434	0.286342	0.2413	0.4582	5008	,	,		16468	0.2996		0.3231	False		,,,				2504	0.1738				p.N220fs		Pindel	.											.	PEBP4	23	.	0			c.660delC						PASS	.			1065,2683		185,695,994	54.0	57.0	56.0			-4.5	0.0	8	dbSNP_130	78	2573,5375		433,1707,1834	no	frameshift	PEBP4	NM_144962.2		618,2402,2828	A1A1,A1R,RR		32.3729,28.4152,31.1047			22570908	3638,8058	1899	4079	5978	SO:0001589	frameshift_variant	157310	exon7			.	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.659delA	8.37:g.22570908delT	ENSP00000256404:p.Asn220fs	Somatic	127	.	.		WXS	Illumina HiSeq	Phase_I	221	69	0.312	NM_144962	Q5EVA1|Q8WW74	Frame_Shift_Del	DEL	ENST00000256404.6	37	CCDS43724.1																																																																																			T|0.680;-|0.320	0.320	strong		0.602	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
TEP1	7011	hgsc.bcm.edu	37	14	20841707	20841707	+	Missense_Mutation	SNP	C	C	T	rs1713449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20841707C>T	ENST00000262715.5	-	46	6680	c.6640G>A	c.(6640-6642)Gtc>Atc	p.V2214I	TEP1_ENST00000556935.1_Missense_Mutation_p.V2106I|TEP1_ENST00000545983.1_Missense_Mutation_p.V552I	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	130	0	0		WXS	Illumina HiSeq	Phase_I	198	75	0.378788	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	
DST	667	hgsc.bcm.edu	37	6	56457044	56457044	+	Missense_Mutation	SNP	T	T	C	rs186813964	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56457044T>C	ENST00000361203.3	-	45	12213	c.12206A>G	c.(12205-12207)aAa>aGa	p.K4069R	DST_ENST00000370769.4_Missense_Mutation_p.K4071R|DST_ENST00000312431.6_Missense_Mutation_p.K4069R|DST_ENST00000370788.2_Missense_Mutation_p.K1983R|DST_ENST00000446842.2_Missense_Mutation_p.K3745R|DST_ENST00000421834.2_Missense_Mutation_p.K1983R|DST_ENST00000244364.6_Missense_Mutation_p.K1657R|DST_ENST00000370754.5_Missense_Mutation_p.K4249R			Q03001	DYST_HUMAN	dystonin	4069					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)			AGATAAGTGTTTGCTCGCTGT	0.428													T|||	12	0.00239617	0.0	0.0029	5008	,	,		16441	0.0		0.004	False		,,,				2504	0.0061				p.K1657R		Atlas-SNP	.											DST_ENST00000370769,NS,lymphoid_neoplasm,0,2	DST	1427	2	0			c.A4970G						PASS	.	T	ARG/LYS	2,3780		0,2,1889	81.0	80.0	81.0		4970	3.2	1.0	6		81	44,8184		0,44,4070	yes	missense	DST	NM_015548.4	26	0,46,5959	CC,CT,TT		0.5348,0.0529,0.383	benign	1657/5172	56457044	46,11964	1891	4114	6005	SO:0001583	missense	667	exon30			AAGTGTTTGCTCG	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.12206A>G	6.37:g.56457044T>C	ENSP00000354508:p.Lys4069Arg	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	12.87	2.068920	0.36470	5.29E-4	0.005348	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T;T	0.51325	1.35;1.35;1.35;1.35;1.35;0.71;1.35;1.35	5.8	3.23	0.37069	.	0.226724	0.30177	N	0.010236	T	0.17492	0.0420	L	0.41710	1.295	0.24732	N	0.993083	B;B;B;B;B	0.15473	0.01;0.011;0.005;0.013;0.004	B;B;B;B;B	0.22880	0.013;0.042;0.011;0.028;0.012	T	0.08722	-1.0708	9	0.15952	T	0.53	.	10.2141	0.43158	0.0:0.1428:0.0:0.8572	.	1983;4071;4249;4069;1657	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	R	1657;4249;4071;1983;3745;4069;1983;4069	ENSP00000244364:K1657R;ENSP00000359790:K4249R;ENSP00000359805:K4071R;ENSP00000400883:K1983R;ENSP00000393645:K3745R;ENSP00000307959:K4069R;ENSP00000359824:K1983R;ENSP00000354508:K4069R	ENSP00000244364:K1657R	K	-	2	0	DST	56565003	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.130000	0.31393	0.376000	0.24707	0.528000	0.53228	AAA	T|0.998;C|0.002	0.002	strong		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
LRRC27	80313	hgsc.bcm.edu	37	10	134161517	134161517	+	Missense_Mutation	SNP	C	C	T	rs2474329	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:134161517C>T	ENST00000368614.3	+	6	688	c.583C>T	c.(583-585)Cgt>Tgt	p.R195C	LRRC27_ENST00000344079.5_Missense_Mutation_p.R195C|LRRC27_ENST00000392638.2_Missense_Mutation_p.R195C|LRRC27_ENST00000368615.3_Missense_Mutation_p.R195C|LRRC27_ENST00000368612.1_Missense_Mutation_p.R133C|LRRC27_ENST00000432555.2_Missense_Mutation_p.R68C|LRRC27_ENST00000368610.3_Missense_Mutation_p.R133C|LRRC27_ENST00000356571.4_3'UTR|LRRC27_ENST00000368613.4_Missense_Mutation_p.R195C	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	136	0	0		WXS	Illumina HiSeq	Phase_I	121	49	0.404959	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	
OAS3	4940	hgsc.bcm.edu	37	12	113403684	113403684	+	Silent	SNP	C	C	T	rs2240188	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113403684C>T	ENST00000228928.7	+	12	2718	c.2539C>T	c.(2539-2541)Ctg>Ttg	p.L847L	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	847	OAS domain 3.				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)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						CCGAGCCCAGCTGGAGGCATG	0.582													C|||	1423	0.284145	0.4221	0.3775	5008	,	,		21311	0.1558		0.2604	False		,,,				2504	0.1881				p.L847L		Atlas-SNP	.											.	OAS3	63	.	0			c.C2539T						PASS	.	C		1461,2543		252,957,793	34.0	38.0	37.0		2539	2.5	1.0	12	dbSNP_98	37	2231,6139		305,1621,2259	no	coding-synonymous	OAS3	NM_006187.2		557,2578,3052	TT,TC,CC		26.6547,36.4885,29.8368		847/1088	113403684	3692,8682	2002	4185	6187	SO:0001819	synonymous_variant	4940	exon12			GCCCAGCTGGAGG	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.2539C>T	12.37:g.113403684C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			C|0.728;T|0.272	0.272	strong		0.582	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
LAMA4	3910	hgsc.bcm.edu	37	6	112480041	112480041	+	Silent	SNP	A	A	G	rs3752577	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:112480041A>G	ENST00000230538.7	-	14	2107	c.1710T>C	c.(1708-1710)agT>agC	p.S570S	RP1-142L7.5_ENST00000585373.1_RNA|LAMA4_ENST00000389463.4_Silent_p.S563S|RP1-142L7.5_ENST00000425503.1_RNA|LAMA4_ENST00000522006.1_Silent_p.S563S|LAMA4_ENST00000424408.2_Silent_p.S563S	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	570	Domain II and I.				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)		CTTGTAGTTCACTTTTGGCTC	0.323													A|||	457	0.091254	0.028	0.1225	5008	,	,		17123	0.13		0.1034	False		,,,				2504	0.1022				p.S570S		Atlas-SNP	.											.	LAMA4	227	.	0			c.T1710C						PASS	.	A	,,	195,4211	122.5+/-159.9	5,185,2013	192.0	168.0	176.0		1710,1689,1689	-0.3	0.9	6	dbSNP_107	176	758,7842	181.9+/-230.5	35,688,3577	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	40,873,5590	GG,GA,AA		8.814,4.4258,7.3274	,,	570/1824,563/1817,563/1817	112480041	953,12053	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon14			TAGTTCACTTTTG		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.1710T>C	6.37:g.112480041A>G		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	201	106	0.527363	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																			A|0.915;G|0.085	0.085	strong		0.323	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
MUC4	4585	hgsc.bcm.edu	37	3	195513411	195513411	+	Silent	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195513411A>T	ENST00000463781.3	-	2	5499	c.5040T>A	c.(5038-5040)ccT>ccA	p.P1680P	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.P1680P	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)		TGACAGGAAGAGGGGTGGCGT	0.612																																					p.P1680P		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,-2,4	MUC4	1505	4	0			c.T5040A						scavenged	.						38.0	36.0	37.0					3																	195513411		690	1583	2273	SO:0001819	synonymous_variant	4585	exon2			AGGAAGAGGGGTG	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.5040T>A	3.37:g.195513411A>T		Somatic	521	7	0.0134357		WXS	Illumina HiSeq	Phase_I	659	19	0.0288316	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																																																																																			.	.	none		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CNNM2	54805	hgsc.bcm.edu	37	10	104836853	104836853	+	Silent	SNP	C	C	T	rs35647154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:104836853C>T	ENST00000369878.4	+	8	2732	c.2544C>T	c.(2542-2544)gaC>gaT	p.D848D	CNNM2_ENST00000433628.2_Silent_p.D826D	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	848					magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		GGTTGCCAGACGAGACAGCCA	0.552													C|||	139	0.0277556	0.0106	0.0461	5008	,	,		17827	0.001		0.0795	False		,,,				2504	0.0123				p.D848D		Atlas-SNP	.											.	CNNM2	119	.	0			c.C2544T						PASS	.	C	,	98,4154		1,96,2029	97.0	104.0	102.0		2544,2478	-9.7	0.2	10	dbSNP_126	102	584,7862		21,542,3660	no	coding-synonymous,coding-synonymous	CNNM2	NM_017649.3,NM_199076.1	,	22,638,5689	TT,TC,CC		6.9145,2.3048,5.3709	,	848/876,826/854	104836853	682,12016	2126	4223	6349	SO:0001819	synonymous_variant	54805	exon8			GCCAGACGAGACA	AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"""cyclin M2"""	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.2544C>T	10.37:g.104836853C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	37	26	0.702703	NM_017649	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	37	CCDS44474.1																																																																																			C|0.952;T|0.048	0.048	strong		0.552	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649	
MUC17	140453	hgsc.bcm.edu	37	7	100677586	100677586	+	Silent	SNP	A	A	G	rs189731103		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677586A>G	ENST00000306151.4	+	3	2953	c.2889A>G	c.(2887-2889)tcA>tcG	p.S963S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	963	59 X approximate tandem repeats.|Ser-rich.				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)					AAGCCACTTCATCTCCTACAA	0.527																																					p.S963S		Atlas-SNP	.											.	MUC17	804	.	0			c.A2889G						PASS	.	A		626,3780		0,626,1577	329.0	308.0	316.0		2889	-0.7	0.0	7	dbSNP_134	316	572,8028		0,572,3728	no	coding-synonymous	MUC17	NM_001040105.1		0,1198,5305	GG,GA,AA		6.6512,14.2079,9.2111		963/4494	100677586	1198,11808	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACTTCATCTCCT	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.2889A>G	7.37:g.100677586A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	527	170	0.322581	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			A|0.999;G|0.001	0.001	weak		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FAM131C	348487	hgsc.bcm.edu	37	1	16385042	16385042	+	Missense_Mutation	SNP	G	G	A	rs77667563	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16385042G>A	ENST00000375662.4	-	7	916	c.733C>T	c.(733-735)Cgg>Tgg	p.R245W	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	245	Pro-rich.									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)		GGCAGCCGCCGCCGATGCTGC	0.741																																					p.R245W		Atlas-SNP	.											FAM131C,NS,other,0,1	FAM131C	21	1	0			c.C733T						PASS	.						2.0	2.0	2.0					1																	16385042		1409	3130	4539	SO:0001583	missense	348487	exon7			GCCGCCGCCGATG		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.733C>T	1.37:g.16385042G>A	ENSP00000364814:p.Arg245Trp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	773	0.35393772893772896	210	0.4268292682926829	106	0.292817679558011	224	0.3916083916083916	233	0.3073878627968338	G	11.88	1.771185	0.31320	.	.	ENSG00000185519	ENST00000375662	T	0.15487	2.42	4.8	-0.971	0.10303	.	2.839240	0.01092	N	0.005214	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.65815	0.995	P	0.46825	0.528	T	0.32428	-0.9907	9	0.54805	T	0.06	-7.4813	4.4045	0.11402	0.1749:0.0:0.3887:0.4365	.	245	Q96AQ9	F131C_HUMAN	W	245	ENSP00000364814:R245W	ENSP00000364814:R245W	R	-	1	2	FAM131C	16257629	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.080000	0.11339	-0.172000	0.10779	0.549000	0.68633	CGG	G|0.646;A|0.354	0.354	strong		0.741	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
MFSD4	148808	hgsc.bcm.edu	37	1	205554085	205554085	+	Missense_Mutation	SNP	G	G	C	rs7526132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:205554085G>C	ENST00000367147.4	+	5	1034	c.941G>C	c.(940-942)gGc>gCc	p.G314A	MFSD4_ENST00000536357.1_Missense_Mutation_p.G227A|MFSD4_ENST00000539267.1_Missense_Mutation_p.G314A	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	314			G -> A (in dbSNP:rs7526132). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			CACATCACGGGCGCCCTGGTA	0.602											OREG0014158	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2133	0.425919	0.708	0.4942	5008	,	,		16679	0.0813		0.4503	False		,,,				2504	0.3262				p.G314A		Atlas-SNP	.											.	MFSD4	46	.	0			c.G941C						PASS	.	C	ALA/GLY	2876,1530	484.2+/-360.0	923,1030,250	119.0	115.0	116.0		941	4.8	0.0	1	dbSNP_116	116	4124,4476	590.4+/-392.7	1005,2114,1181	yes	missense	MFSD4	NM_181644.4	60	1928,3144,1431	CC,CG,GG		47.9535,34.7254,46.1787	benign	314/515	205554085	7000,6006	2203	4300	6503	SO:0001583	missense	148808	exon5			TCACGGGCGCCCT	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.941G>C	1.37:g.205554085G>C	ENSP00000356115:p.Gly314Ala	Somatic	161	1	0.00621118	2153	WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_181644	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Missense_Mutation	SNP	ENST00000367147.4	37	CCDS1455.1	908	0.4157509157509158	325	0.6605691056910569	176	0.4861878453038674	49	0.08566433566433566	358	0.47229551451187335	C	2.834	-0.241878	0.05906	0.652746	0.479535	ENSG00000174514	ENST00000367147;ENST00000539267;ENST00000536357	T;T;T	0.80214	-1.35;-1.35;-1.35	5.77	4.8	0.61643	Major facilitator superfamily domain, general substrate transporter (1);	0.098253	0.64402	N	0.000001	T	0.00012	0.0000	N	0.26042	0.785	0.44221	P	0.002947000000000033	B;B;B	0.20164	0.0;0.001;0.042	B;B;B	0.21546	0.002;0.006;0.035	T	0.42430	-0.9452	9	0.16420	T	0.52	-20.5692	15.5649	0.76284	0.0:0.6577:0.3423:0.0	rs7526132;rs17347495;rs17857120;rs52798117;rs7526132	259;227;314	B7Z8X0;B7Z8X3;Q8N468	.;.;MFSD4_HUMAN	A	314;314;227	ENSP00000356115:G314A;ENSP00000445329:G314A;ENSP00000440183:G227A	ENSP00000356115:G314A	G	+	2	0	MFSD4	203820708	1.000000	0.71417	0.040000	0.18447	0.709000	0.40893	4.195000	0.58400	1.594000	0.50039	-0.120000	0.15030	GGC	G|0.514;C|0.486	0.486	strong		0.602	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090391.1	NM_181644	
C10orf10	11067	hgsc.bcm.edu	37	10	45473317	45473317	+	Silent	SNP	C	C	T	rs3740094	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:45473317C>T	ENST00000298295.3	-	2	379	c.162G>A	c.(160-162)ctG>ctA	p.L54L	RASSF4_ENST00000472561.1_Intron|C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000374417.2_Intron|RASSF4_ENST00000340258.5_Intron|RASSF4_ENST00000334940.6_Intron	NM_007021.3	NP_008952.1	Q9NTK1	DEPP_HUMAN	chromosome 10 open reading frame 10	54						mitochondrion (GO:0005739)				lung(1)	1						TGGCCTTGTCCAGCACAGAGG	0.667													C|||	739	0.147564	0.0083	0.1167	5008	,	,		16950	0.3056		0.1581	False		,,,				2504	0.184				p.L54L		Atlas-SNP	.											.	C10orf10	6	.	0			c.G162A						PASS	.	C	,	162,4242		5,152,2045	44.0	44.0	44.0		162,	-2.9	0.0	10	dbSNP_107	44	1406,7192		120,1166,3013	no	coding-synonymous,intron	C10orf10,RASSF4	NM_007021.3,NM_032023.3	,	125,1318,5058	TT,TC,CC		16.3526,3.6785,12.0597	,	54/213,	45473317	1568,11434	2202	4299	6501	SO:0001819	synonymous_variant	11067	exon2			CTTGTCCAGCACA	AB022718	CCDS7210.1	10q11.21	2014-07-31			ENSG00000165507	ENSG00000165507			23355	protein-coding gene	gene with protein product	"""decidual protein induced by progesterone"", ""fasting induced"", ""fat-specific expressed gene"""	611309				24530860, 19937567, 16123073	Standard	NM_007021		Approved	DEPP, FIG, Fseg	uc001jbr.4	Q9NTK1	OTTHUMG00000018063	ENST00000298295.3:c.162G>A	10.37:g.45473317C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	34	28	0.823529	NM_007021	B2R6A1|O94997|Q5T735|Q76MX8	Silent	SNP	ENST00000298295.3	37	CCDS7210.1																																																																																			C|0.872;T|0.128	0.128	strong		0.667	C10orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047758.1	NM_007021	
GATA2	2624	hgsc.bcm.edu	37	3	128204951	128204951	+	Missense_Mutation	SNP	C	C	T	rs2335052	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:128204951C>T	ENST00000341105.2	-	3	821	c.490G>A	c.(490-492)Gcc>Acc	p.A164T	GATA2_ENST00000430265.2_Missense_Mutation_p.A164T|GATA2_ENST00000487848.1_Missense_Mutation_p.A164T	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	164			A -> T (in dbSNP:rs2335052). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|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)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		CCAGAGTGGGCTGCTGTAGGG	0.672			Mis		AML(CML blast transformation)								C|||	1166	0.232827	0.2156	0.2406	5008	,	,		13545	0.378		0.1829	False		,,,				2504	0.1524				p.A164T		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	GATA2,colon,carcinoma,0,2	GATA2	122	2	0			c.G490A	GRCh37	CM066570	GATA2	M	rs2335052	PASS	.	C	THR/ALA,THR/ALA,THR/ALA	736,3670	293.0+/-282.3	66,604,1533	41.0	39.0	40.0		490,490,490	1.8	0.9	3	dbSNP_100	40	1395,7205	258.7+/-282.2	122,1151,3027	yes	missense,missense,missense	GATA2	NM_001145661.1,NM_001145662.1,NM_032638.4	58,58,58	188,1755,4560	TT,TC,CC		16.2209,16.7045,16.3847	benign,benign,benign	164/481,164/467,164/481	128204951	2131,10875	2203	4300	6503	SO:0001583	missense	2624	exon3			AGTGGGCTGCTGT	AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"""GATA zinc finger domain containing"""	4171	protein-coding gene	gene with protein product		137295	"""GATA-binding protein 2"""			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.490G>A	3.37:g.128204951C>T	ENSP00000345681:p.Ala164Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	150	62	0.413333	NM_001145662	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	529	0.24221611721611722	101	0.20528455284552846	81	0.22375690607734808	212	0.3706293706293706	135	0.17810026385224276	C	11.98	1.801096	0.31869	0.167045	0.162209	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.97303	-4.32;-4.33;-4.32	3.9	1.83	0.25207	.	0.333921	0.33875	N	0.004464	T	0.00012	0.0000	N	0.04724	-0.175	0.34725	P	0.270903	B;B	0.15473	0.013;0.001	B;B	0.19391	0.025;0.002	T	0.10086	-1.0645	9	0.21540	T	0.41	-13.4507	9.5554	0.39334	0.0:0.5805:0.4195:0.0	rs2335052;rs4343643;rs17465403;rs60980469;rs2335052	164;164	P23769-2;P23769	.;GATA2_HUMAN	T	164	ENSP00000345681:A164T;ENSP00000400259:A164T;ENSP00000417074:A164T	ENSP00000345681:A164T	A	-	1	0	GATA2	129687641	0.824000	0.29247	0.899000	0.35326	0.973000	0.67179	0.622000	0.24433	0.911000	0.36747	0.484000	0.47621	GCC	C|0.800;T|0.200	0.200	strong		0.672	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638	
TTC38	55020	hgsc.bcm.edu	37	22	46685380	46685380	+	Silent	SNP	C	C	T	rs11705624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46685380C>T	ENST00000381031.3	+	12	1240	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	TTC38_ENST00000445282.2_Silent_p.D330D	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	388						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						AGGCTGAGGACGGGAACCCTG	0.692													C|||	204	0.0407348	0.0083	0.0576	5008	,	,		14688	0.001		0.1193	False		,,,				2504	0.0327				p.D388D		Atlas-SNP	.											.	TTC38	40	.	0			c.C1164T						PASS	.	C		82,4088		1,80,2004	28.0	36.0	33.0		1164	-6.7	0.0	22	dbSNP_120	33	867,7541		48,771,3385	no	coding-synonymous	TTC38	NM_017931.2		49,851,5389	TT,TC,CC		10.3116,1.9664,7.5449		388/470	46685380	949,11629	2085	4204	6289	SO:0001819	synonymous_variant	55020	exon12			TGAGGACGGGAAC		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.1164C>T	22.37:g.46685380C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_017931	Q8WV27|Q9NWP8	Silent	SNP	ENST00000381031.3	37	CCDS43030.1																																																																																			C|0.932;T|0.068	0.068	strong		0.692	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140773812	140773812	+	Missense_Mutation	SNP	G	G	A	rs144796076	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140773812G>A	ENST00000398604.2	+	1	1432	c.1432G>A	c.(1432-1434)Gac>Aac	p.D478N	PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	478	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)			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)			GACTGCACACGACCCCGACAG	0.547													.|||	10	0.00199681	0.0	0.0029	5008	,	,		17412	0.0		0.007	False		,,,				2504	0.001				p.D478N		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G1432A						PASS	.	G	,ASN/ASP,,,,,,,,,,,ASN/ASP	4,4204		0,4,2100	51.0	55.0	53.0		,1432,,,,,,,,,,,1432	5.1	0.4	5	dbSNP_134	53	26,8436		0,26,4205	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	,23,,,,,,,,,,,23	0,30,6305	AA,AG,GG		0.3073,0.0951,0.2368	,,,,,,,,,,,,	,478/821,,,,,,,,,,,478/933	140773812	30,12640	2104	4231	6335	SO:0001583	missense	9708	exon1			GCACACGACCCCG	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.1432G>A	5.37:g.140773812G>A	ENSP00000381605:p.Asp478Asn	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	182	78	0.428571	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	.	16.62	3.173397	0.57584	9.51E-4	0.003073	ENSG00000253767	ENST00000398604	T	0.74526	-0.85	5.06	5.06	0.68205	Cadherin (4);Cadherin-like (1);	0.000000	0.32273	U	0.006322	D	0.91958	0.7453	H	0.99970	5.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95745	0.8787	10	0.87932	D	0	.	18.0785	0.89435	0.0:0.0:1.0:0.0	.	478;478	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	N	478	ENSP00000381605:D478N	ENSP00000381605:D478N	D	+	1	0	PCDHGA8	140753996	1.000000	0.71417	0.373000	0.26003	0.201000	0.24016	9.595000	0.98260	2.366000	0.80165	0.655000	0.94253	GAC	G|0.996;A|0.004	0.004	strong		0.547	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
GBE1	2632	hgsc.bcm.edu	37	3	81720086	81720086	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:81720086G>A	ENST00000429644.2	-	3	975	c.332C>T	c.(331-333)tCg>tTg	p.S111L	GBE1_ENST00000477426.1_5'UTR|GBE1_ENST00000489715.1_Missense_Mutation_p.S70L	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	111					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.S111L(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		GTATGGGTACGAAAATGGATT	0.338									Glycogen Storage Disease, type IV																												p.S111L		Atlas-SNP	.											GBE1_ENST00000429644,colon,carcinoma,0,1	GBE1	111	1	1	Substitution - Missense(1)	large_intestine(1)	c.C332T						PASS	.						64.0	60.0	61.0					3																	81720086		1816	4085	5901	SO:0001583	missense	2632	exon3	Familial Cancer Database	Andersen Disease, Brancher deficiency	GGGTACGAAAATG		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"""glycogen branching enzyme"", ""Andersen disease"", ""glycogen storage disease type IV"""	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.332C>T	3.37:g.81720086G>A	ENSP00000410833:p.Ser111Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	35	0.336538	NM_000158	B3KWV3|Q96EN0	Missense_Mutation	SNP	ENST00000429644.2	37	CCDS54612.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.802766	0.70682	.	.	ENSG00000114480	ENST00000429644;ENST00000264326;ENST00000489715	T;T	0.18657	2.2;2.21	5.5	3.72	0.42706	Immunoglobulin E-set (1);Glycoside hydrolase, family 13, N-terminal (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.30386	0.0763	L	0.57536	1.79	0.38321	D	0.943534	P;D	0.54207	0.888;0.965	B;P	0.51055	0.3;0.657	T	0.14309	-1.0477	10	0.66056	D	0.02	-3.5779	11.1977	0.48722	0.1509:0.0:0.8491:0.0	.	70;111	E9PGM4;Q04446	.;GLGB_HUMAN	L	111;162;70	ENSP00000410833:S111L;ENSP00000419638:S70L	ENSP00000264326:S162L	S	-	2	0	GBE1	81802776	1.000000	0.71417	0.699000	0.30290	0.813000	0.45954	5.642000	0.67888	0.694000	0.31654	0.650000	0.86243	TCG	.	.	none		0.338	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
OR5H15	403274	hgsc.bcm.edu	37	3	97888337	97888337	+	Missense_Mutation	SNP	C	C	T	rs13082608	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	314	0	0		WXS	Illumina HiSeq	Phase_I	225	113	0.502222	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		
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73932560	73932560	+	Silent	SNP	A	A	G	rs17851629	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:73932560A>G	ENST00000265755.3	+	5	906	c.513A>G	c.(511-513)gaA>gaG	p.E171E	GTF2IRD1_ENST00000455841.2_Silent_p.E203E|GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000424337.2_Silent_p.E171E|GTF2IRD1_ENST00000476977.1_Silent_p.E171E	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	171					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						GGCTGCCCGAAGGCCTGGCCT	0.662													G|||	1186	0.236821	0.4682	0.196	5008	,	,		14985	0.0952		0.16	False		,,,				2504	0.1779				p.E203E		Atlas-SNP	.											.	GTF2IRD1	91	.	0			c.A609G						PASS	.	G	,,	1791,2611		358,1075,768	24.0	24.0	24.0		609,513,513	1.6	1.0	7	dbSNP_123	24	1707,6893		165,1377,2758	no	coding-synonymous,coding-synonymous,coding-synonymous	GTF2IRD1	NM_001199207.1,NM_005685.3,NM_016328.2	,,	523,2452,3526	GG,GA,AA		19.8488,40.6861,26.9036	,,	203/977,171/945,171/960	73932560	3498,9504	2201	4300	6501	SO:0001819	synonymous_variant	9569	exon5			GCCCGAAGGCCTG	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.513A>G	7.37:g.73932560A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	306	71	0.232026	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Silent	SNP	ENST00000265755.3	37	CCDS5571.1																																																																																			A|0.744;G|0.256	0.256	strong		0.662	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
SRCAP	10847	hgsc.bcm.edu	37	16	30732558	30732558	+	Missense_Mutation	SNP	C	C	A	rs149248373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:30732558C>A	ENST00000262518.4	+	21	3687	c.3302C>A	c.(3301-3303)aCg>aAg	p.T1101K	SRCAP_ENST00000344771.4_Intron|SRCAP_ENST00000395059.2_Missense_Mutation_p.T1101K	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1101	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			CGGCCTCCCACGCCAACCTTG	0.602													C|||	9	0.00179712	0.0	0.0014	5008	,	,		17448	0.0		0.006	False		,,,				2504	0.002				p.T1101K		Atlas-SNP	.											.	SRCAP	298	.	0			c.C3302A						PASS	.	C	LYS/THR	5,4389	9.9+/-24.2	0,5,2192	109.0	118.0	115.0		3302	4.4	0.9	16	dbSNP_134	115	75,8525	44.0+/-102.2	0,75,4225	yes	missense	SRCAP	NM_006662.2	78	0,80,6417	AA,AC,CC		0.8721,0.1138,0.6157	possibly-damaging	1101/3231	30732558	80,12914	2197	4300	6497	SO:0001583	missense	10847	exon21			CTCCCACGCCAAC	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.3302C>A	16.37:g.30732558C>A	ENSP00000262518:p.Thr1101Lys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	11.98	1.799401	0.31869	0.001138	0.008721	ENSG00000080603	ENST00000262518;ENST00000395059	D;D	0.91351	-2.83;-2.72	5.36	4.41	0.53225	.	.	.	.	.	T	0.75759	0.3893	N	0.14661	0.345	0.80722	D	1	P;P	0.38020	0.615;0.481	B;B	0.38954	0.286;0.149	T	0.74940	-0.3493	9	0.28530	T	0.3	-1.5386	7.321	0.26528	0.0:0.7419:0.17:0.0881	.	1101;1101	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	K	1101	ENSP00000262518:T1101K;ENSP00000378499:T1101K	ENSP00000262518:T1101K	T	+	2	0	SRCAP	30640059	0.102000	0.21896	0.924000	0.36721	0.955000	0.61496	1.191000	0.32138	1.499000	0.48617	0.557000	0.71058	ACG	C|0.996;A|0.004	0.004	strong		0.602	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
LAMA1	284217	hgsc.bcm.edu	37	18	7023371	7023371	+	Silent	SNP	A	A	G	rs684634	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:7023371A>G	ENST00000389658.3	-	19	2586	c.2493T>C	c.(2491-2493)tgT>tgC	p.C831C		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	831	Laminin EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)				AACCATCTGCACATCTGTATC	0.502													G|||	2190	0.4373	0.8533	0.389	5008	,	,		20795	0.1429		0.3807	False		,,,				2504	0.271				p.C831C		Atlas-SNP	.											LAMA1,NS,adenoma,0,1	LAMA1	458	1	0			c.T2493C						scavenged	.	G		3319,1087	389.8+/-327.4	1257,805,141	77.0	75.0	75.0		2493	-6.0	0.9	18	dbSNP_83	75	3267,5333	645.7+/-400.2	603,2061,1636	no	coding-synonymous	LAMA1	NM_005559.3		1860,2866,1777	GG,GA,AA		37.9884,24.6709,49.3618		831/3076	7023371	6586,6420	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon19			ATCTGCACATCTG	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.2493T>C	18.37:g.7023371A>G		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			A|0.524;G|0.476	0.476	strong		0.502	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
WDR46	9277	hgsc.bcm.edu	37	6	33256653	33256653	+	Silent	SNP	G	G	A	rs34931270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:33256653G>A	ENST00000374617.4	-	2	563	c.207C>T	c.(205-207)atC>atT	p.I69I	PFDN6_ENST00000374610.2_5'Flank|PFDN6_ENST00000463584.1_5'Flank|WDR46_ENST00000477718.1_5'UTR|PFDN6_ENST00000374607.1_5'Flank|RGL2_ENST00000437840.2_5'Flank|PFDN6_ENST00000374606.5_5'Flank|PFDN6_ENST00000395131.1_5'Flank	NM_001164267.1|NM_005452.5	NP_001157739.1|NP_005443.3	O15213	WDR46_HUMAN	WD repeat domain 46	69							poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	20						GCTTCTTAGAGATCCGAGACT	0.577													G|||	67	0.0133786	0.0015	0.0144	5008	,	,		16163	0.002		0.0249	False		,,,				2504	0.0286				p.I69I		Atlas-SNP	.											.	WDR46	43	.	0			c.C207T						PASS	.	G	,	25,4381	29.0+/-57.7	0,25,2178	43.0	47.0	46.0		,207	3.1	0.8	6	dbSNP_126	46	334,8266	113.1+/-173.2	6,322,3972	no	intron,coding-synonymous	WDR46	NM_001164267.1,NM_005452.5	,	6,347,6150	AA,AG,GG		3.8837,0.5674,2.7603	,	,69/611	33256653	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	9277	exon2			CTTAGAGATCCGA	Z97184	CCDS4772.1	6p21.3	2013-01-09	2005-05-31	2005-05-31	ENSG00000227057	ENSG00000227057		"""WD repeat domain containing"""	13923	protein-coding gene	gene with protein product		611440	"""chromosome 6 open reading frame 11"""	C6orf11		9545376, 9521053	Standard	NM_005452		Approved	BING4, UTP7	uc003ods.3	O15213	OTTHUMG00000031192	ENST00000374617.4:c.207C>T	6.37:g.33256653G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_005452	A6NDP5|Q5HYZ0|Q5STK5|Q5STR3	Silent	SNP	ENST00000374617.4	37	CCDS4772.1																																																																																			G|0.977;A|0.023	0.023	strong		0.577	WDR46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076382.2	NM_005452	
FASTKD2	22868	hgsc.bcm.edu	37	2	207631461	207631461	+	Missense_Mutation	SNP	G	G	A	rs3762568	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:207631461G>A	ENST00000236980.6	+	2	392	c.44G>A	c.(43-45)aGc>aAc	p.S15N	MDH1B_ENST00000392214.2_5'Flank|MDH1B_ENST00000454776.2_5'Flank|MDH1B_ENST00000449792.1_5'Flank|FASTKD2_ENST00000403094.3_Missense_Mutation_p.S15N|MDH1B_ENST00000374412.3_5'Flank|FASTKD2_ENST00000402774.3_Missense_Mutation_p.S15N	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	15			S -> N (in dbSNP:rs3762568).		cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(2)	21				LUSC - Lung squamous cell carcinoma(261;0.0718)|Epithelial(149;0.119)|Lung(261;0.138)		TCAGTGGAGAGCAAAATGAAT	0.403													G|||	579	0.115615	0.264	0.0562	5008	,	,		16349	0.0516		0.0586	False		,,,				2504	0.0818				p.S15N		Atlas-SNP	.											.	FASTKD2	49	.	0			c.G44A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	1075,3331	379.9+/-323.5	136,803,1264	63.0	68.0	66.0		44,44,44	1.0	0.2	2	dbSNP_107	66	652,7948	164.2+/-216.6	31,590,3679	yes	missense,missense,missense	FASTKD2	NM_001136193.1,NM_001136194.1,NM_014929.3	46,46,46	167,1393,4943	AA,AG,GG		7.5814,24.3985,13.2785	possibly-damaging,possibly-damaging,possibly-damaging	15/711,15/711,15/711	207631461	1727,11279	2203	4300	6503	SO:0001583	missense	22868	exon2			TGGAGAGCAAAAT	BC001544	CCDS2371.1	2q33.3	2008-02-05	2006-07-07	2006-07-07	ENSG00000118246	ENSG00000118246			29160	protein-coding gene	gene with protein product		612322	"""KIAA0971"""	KIAA0971			Standard	NM_014929		Approved		uc002vbx.3	Q9NYY8	OTTHUMG00000132917	ENST00000236980.6:c.44G>A	2.37:g.207631461G>A	ENSP00000236980:p.Ser15Asn	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	128	34	0.265625	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	211	0.09661172161172162	121	0.2459349593495935	23	0.06353591160220995	27	0.0472027972027972	40	0.052770448548812667	G	11.96	1.794198	0.31777	0.243985	0.075814	ENSG00000118246	ENST00000236980;ENST00000418289;ENST00000402774;ENST00000403094	T;T;T;T	0.51325	2.38;0.71;2.38;2.38	4.85	0.971	0.19698	.	0.242367	0.29233	N	0.012757	T	0.00012	0.0000	L	0.46157	1.445	0.48135	P	4.0200000000001346E-4	B;B	0.13594	0.008;0.005	B;B	0.16289	0.015;0.006	T	0.10132	-1.0643	9	0.87932	D	0	-0.4365	4.75	0.13056	0.252:0.0:0.5982:0.1498	rs3762568;rs52824953;rs3762568	15;15	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	N	15	ENSP00000236980:S15N;ENSP00000409927:S15N;ENSP00000385990:S15N;ENSP00000384929:S15N	ENSP00000236980:S15N	S	+	2	0	FASTKD2	207339706	0.686000	0.27661	0.194000	0.23346	0.831000	0.47069	-0.204000	0.09425	-0.001000	0.14495	0.491000	0.48974	AGC	G|0.885;A|0.115	0.115	strong		0.403	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929	
SPEG	10290	hgsc.bcm.edu	37	2	220353013	220353013	+	Silent	SNP	G	G	A	rs875098	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220353013G>A	ENST00000312358.7	+	32	7971	c.7839G>A	c.(7837-7839)ccG>ccA	p.P2613P	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2613	Ig-like 9.				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)		GCCCTGCACCGCACATCTCCT	0.642													G|||	1434	0.286342	0.2905	0.2709	5008	,	,		19669	0.1468		0.2724	False		,,,				2504	0.4499				p.P2613P		Atlas-SNP	.											.	SPEG	272	.	0			c.G7839A						PASS	.	G		1078,3026		146,786,1120	43.0	46.0	45.0		7839	1.3	1.0	2	dbSNP_86	45	2129,6277		274,1581,2348	no	coding-synonymous	SPEG	NM_005876.4		420,2367,3468	AA,AG,GG		25.3271,26.2671,25.6355		2613/3268	220353013	3207,9303	2052	4203	6255	SO:0001819	synonymous_variant	10290	exon32			TGCACCGCACATC	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.7839G>A	2.37:g.220353013G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	51	14	0.27451	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			G|0.747;A|0.253	0.253	strong		0.642	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
ELP2	55250	hgsc.bcm.edu	37	18	33709898	33709898	+	Start_Codon_SNP	SNP	T	T	A	rs370904237		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:33709898T>A	ENST00000358232.6	+	1	65	c.2T>A	c.(1-3)aTg>aAg	p.M1K	SLC39A6_ENST00000590986.1_5'Flank|ELP2_ENST00000351393.6_Start_Codon_SNP_p.M1K|ELP2_ENST00000350494.6_Start_Codon_SNP_p.M1K|ELP2_ENST00000542824.1_Start_Codon_SNP_p.M1K|ELP2_ENST00000442325.2_Start_Codon_SNP_p.M1K|ELP2_ENST00000423854.2_Start_Codon_SNP_p.M1K|SLC39A6_ENST00000440549.2_5'Flank|SLC39A6_ENST00000269187.5_5'Flank	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	1					chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						GTTGGCGACATGGTGGCACCC	0.607																																					p.M1K		Atlas-SNP	.											.	ELP2	70	.	0			c.T2A						PASS	.						75.0	68.0	71.0					18																	33709898		2203	4300	6503	SO:0001582	initiator_codon_variant	55250	exon1			GCGACATGGTGGC	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"""Elongator acetyltransferase complex subunits"", ""WD repeat domain containing"""	18248	protein-coding gene	gene with protein product			"""signal transducer and activator of transcription 3 interacting protein 1"", ""elongation protein 2 homolog (S. cerevisiae)"""	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.2T>A	18.37:g.33709898T>A	ENSP00000350967:p.Met1Lys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_001242879	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Missense_Mutation	SNP	ENST00000358232.6	37	CCDS11918.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022524	0.75275	.	.	ENSG00000134759	ENST00000358232;ENST00000351393;ENST00000442325;ENST00000423854;ENST00000350494;ENST00000542824	T;T;T;T;T;T	0.60299	0.2;0.36;0.67;0.84;0.43;0.35	5.61	5.61	0.85477	.	0.038317	0.85682	D	0.000000	T	0.75228	0.3821	.	.	.	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;0.992;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.996;0.996;0.972;0.997;0.998;0.996	T	0.78620	-0.2133	9	0.87932	D	0	-22.5353	12.1884	0.54254	0.0:0.0:0.0:1.0	.	1;1;1;1;1;1	B4DTG0;E7EP23;E9PCX0;Q6IA86-2;Q6IA86-3;Q6IA86	.;.;.;.;.;ELP2_HUMAN	K	1	ENSP00000350967:M1K;ENSP00000257191:M1K;ENSP00000414851:M1K;ENSP00000391202:M1K;ENSP00000316051:M1K;ENSP00000443800:M1K	ENSP00000316051:M1K	M	+	2	0	ELP2	31963896	1.000000	0.71417	0.998000	0.56505	0.466000	0.32739	3.835000	0.55805	2.136000	0.66102	0.477000	0.44152	ATG	.	.	alt		0.607	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255	Missense_Mutation
DVL2	1856	hgsc.bcm.edu	37	17	7133609	7133609	+	Silent	SNP	G	G	A	rs2074216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7133609G>A	ENST00000005340.5	-	3	687	c.405C>T	c.(403-405)tcC>tcT	p.S135S	DVL2_ENST00000574642.1_5'UTR|DVL2_ENST00000575458.1_Silent_p.S135S	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	135					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						CTCACTGGAAGGATGGAGGCC	0.622													G|||	1666	0.332668	0.267	0.268	5008	,	,		17320	0.3859		0.3777	False		,,,				2504	0.3661				p.S135S		Atlas-SNP	.											.	DVL2	49	.	0			c.C405T						PASS	.	G		1167,3239	403.3+/-332.7	152,863,1188	88.0	97.0	94.0		405	-0.9	1.0	17	dbSNP_96	94	3061,5539	463.4+/-366.0	548,1965,1787	no	coding-synonymous	DVL2	NM_004422.2		700,2828,2975	AA,AG,GG		35.593,26.4866,32.5081		135/737	7133609	4228,8778	2203	4300	6503	SO:0001819	synonymous_variant	1856	exon3			CTGGAAGGATGGA	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.405C>T	17.37:g.7133609G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	37	CCDS11091.1																																																																																			G|0.674;A|0.326	0.326	strong		0.622	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
ANAPC1	64682	hgsc.bcm.edu	37	2	112608394	112608394	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:112608394T>C	ENST00000341068.3	-	14	2381	c.1609A>G	c.(1609-1611)Act>Gct	p.T537A		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	537					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|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)|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)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.T537A(5)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						GGCTTTGGAGTACTAACGCCA	0.433																																					p.T537A		Atlas-SNP	.											ANAPC1,NS,carcinoma,0,9	ANAPC1	116	9	5	Substitution - Missense(5)	lung(3)|kidney(1)|endometrium(1)	c.A1609G						scavenged	.						109.0	106.0	107.0					2																	112608394		2203	4300	6503	SO:0001583	missense	64682	exon14			TTGGAGTACTAAC	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.1609A>G	2.37:g.112608394T>C	ENSP00000339109:p.Thr537Ala	Somatic	834	6	0.00719424		WXS	Illumina HiSeq	Phase_I	672	14	0.0208333	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	CCDS2093.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.716|4.716	0.133071|0.133071	0.09032|0.09032	.|.	.|.	ENSG00000153107|ENSG00000153107	ENST00000341068|ENST00000427997	.|.	.|.	.|.	4.57|4.57	3.37|3.37	0.38596|0.38596	.|.	0.273018|.	0.23039|.	U|.	0.052629|.	T|T	0.55305|0.55305	0.1912|0.1912	L|L	0.45352|0.45352	1.415|1.415	0.37887|0.37887	D|D	0.930579|0.930579	B|.	0.14438|.	0.01|.	B|.	0.18263|.	0.021|.	T|T	0.53535|0.53535	-0.8425|-0.8425	9|5	0.08837|.	T|.	0.75|.	-8.0757|-8.0757	10.3103|10.3103	0.43704|0.43704	0.1479:0.0:0.0:0.8521|0.1479:0.0:0.0:0.8521	.|.	537|.	Q9H1A4|.	APC1_HUMAN|.	A|C	537|71	.|.	ENSP00000339109:T537A|.	T|Y	-|-	1|2	0|0	ANAPC1|ANAPC1	112324865|112324865	1.000000|1.000000	0.71417|0.71417	0.138000|0.138000	0.22173|0.22173	0.127000|0.127000	0.20565|0.20565	3.555000|3.555000	0.53727|0.53727	0.570000|0.570000	0.29347|0.29347	0.369000|0.369000	0.22263|0.22263	ACT|TAC	T|0.500;C|0.500	0.500	strong		0.433	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	
LOR	4014	hgsc.bcm.edu	37	1	153234295	153234295	+	Silent	SNP	G	G	A	rs12043009	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:153234295G>A	ENST00000368742.3	+	2	927	c.870G>A	c.(868-870)ggG>ggA	p.G290G		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	290					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GTGGCTCCGGGAGTGGCAAGG	0.692													G|||	973	0.194289	0.3828	0.1542	5008	,	,		9988	0.0685		0.2326	False		,,,				2504	0.0583				p.G290G		Atlas-SNP	.											.	LOR	19	.	0			c.G870A						PASS	.	G		953,2271		129,695,788	6.0	8.0	7.0		870	-1.5	0.0	1	dbSNP_120	7	1211,5851		114,983,2434	no	coding-synonymous	LOR	NM_000427.2		243,1678,3222	AA,AG,GG		17.1481,29.5596,21.0383		290/313	153234295	2164,8122	1612	3531	5143	SO:0001819	synonymous_variant	4014	exon2			CTCCGGGAGTGGC	M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.870G>A	1.37:g.153234295G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	74	25	0.337838	NM_000427	Q5T869|Q5XKF8	Silent	SNP	ENST00000368742.3	37	CCDS30870.1	490	0.22435897435897437	195	0.39634146341463417	66	0.18232044198895028	47	0.08216783216783216	182	0.24010554089709762	G	8.025	0.760514	0.15914	0.295596	0.171481	ENSG00000203782	ENST00000392652	.	.	.	4.24	-1.45	0.08828	.	.	.	.	.	T	0.25158	0.0611	.	.	.	0.43613	P	0.0040120000000000156	.	.	.	.	.	.	T	0.25710	-1.0124	4	0.87932	D	0	1.8651	4.3283	0.11051	0.3272:0.3631:0.3097:0.0	rs12043009;rs12043009	.	.	.	K	290	.	ENSP00000376422:E290K	E	+	1	0	LOR	151500919	0.019000	0.18553	0.010000	0.14722	0.844000	0.47949	-0.788000	0.04614	-0.548000	0.06199	0.563000	0.77884	GAG	G|0.777;A|0.223	0.223	strong		0.692	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1	NM_000427	
C10orf35	219738	hgsc.bcm.edu	37	10	71391538	71391538	+	Silent	SNP	T	T	C	rs1381932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:71391538T>C	ENST00000373279.4	+	3	198	c.39T>C	c.(37-39)gaT>gaC	p.D13D	C10orf35_ENST00000491890.1_3'UTR	NM_145306.2	NP_660349.1	Q96D05	CJ035_HUMAN	chromosome 10 open reading frame 35	13						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5						TCGTGCAGGATGACGACCCCC	0.602													T|||	973	0.194289	0.2821	0.1513	5008	,	,		17823	0.0407		0.2087	False		,,,				2504	0.2495				p.D13D		Atlas-SNP	.											.	C10orf35	22	.	0			c.T39C						PASS	.	T		1296,3110	428.7+/-342.0	200,896,1107	165.0	122.0	137.0		39	-5.1	1.0	10	dbSNP_88	137	1916,6684	335.1+/-321.3	216,1484,2600	no	coding-synonymous	C10orf35	NM_145306.2		416,2380,3707	CC,CT,TT		22.2791,29.4144,24.6963		13/122	71391538	3212,9794	2203	4300	6503	SO:0001819	synonymous_variant	219738	exon3			GCAGGATGACGAC	BC013587	CCDS7295.1	10q22.2	2003-11-21			ENSG00000171224	ENSG00000171224			23519	protein-coding gene	gene with protein product						12477932	Standard	NM_145306		Approved		uc001jpq.4	Q96D05	OTTHUMG00000018383	ENST00000373279.4:c.39T>C	10.37:g.71391538T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	68	47	0.691176	NM_145306		Silent	SNP	ENST00000373279.4	37	CCDS7295.1																																																																																			T|0.773;C|0.227	0.227	strong		0.602	C10orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048454.1	NM_145306	
ABCB5	340273	hgsc.bcm.edu	37	7	20666195	20666195	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:20666195G>A	ENST00000404938.2	+	3	721	c.69G>A	c.(67-69)caG>caA	p.Q23Q		NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	23					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)	p.Q23H(1)		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						CAGAAGAACAGCCAAAACTGA	0.333																																					p.Q23Q		Atlas-SNP	.											ABCB5_ENST00000404938,NS,carcinoma,0,1	ABCB5	357	1	1	Substitution - Missense(1)	lung(1)	c.G69A						scavenged	.						77.0	67.0	70.0					7																	20666195		1568	3581	5149	SO:0001819	synonymous_variant	340273	exon3			AGAACAGCCAAAA	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.69G>A	7.37:g.20666195G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	146	4	0.0273973	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	37	CCDS55090.1																																																																																			.	.	none		0.333	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
ZNF641	121274	hgsc.bcm.edu	37	12	48736985	48736985	+	Missense_Mutation	SNP	T	T	G	rs2732481	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:48736985T>G	ENST00000544117.2	-	6	1796	c.1088A>C	c.(1087-1089)cAg>cCg	p.Q363P	ZNF641_ENST00000301042.3_Missense_Mutation_p.Q363P|ZNF641_ENST00000448928.3_Missense_Mutation_p.Q340P|ZNF641_ENST00000547026.1_Missense_Mutation_p.Q349P			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	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	219	218	0.995434	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	
PITRM1	10531	hgsc.bcm.edu	37	10	3191823	3191823	+	Missense_Mutation	SNP	C	C	T	rs2388556	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:3191823C>T	ENST00000224949.4	-	16	1895	c.1861G>A	c.(1861-1863)Gtc>Atc	p.V621I	PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380994.1_Missense_Mutation_p.V179I|PITRM1_ENST00000380989.2_Missense_Mutation_p.V621I|PITRM1_ENST00000464395.1_5'Flank|PITRM1_ENST00000451104.2_Missense_Mutation_p.V589I|PITRM1-AS1_ENST00000598280.1_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	102	0	0		WXS	Illumina HiSeq	Phase_I	63	49	0.777778	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		
MYH13	8735	hgsc.bcm.edu	37	17	10219113	10219113	+	Missense_Mutation	SNP	C	C	T	rs17690195	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:10219113C>T	ENST00000418404.3	-	28	4044	c.3881G>A	c.(3880-3882)cGa>cAa	p.R1294Q	RP11-401O9.4_ENST00000609088.1_RNA|MYH13_ENST00000252172.4_Missense_Mutation_p.R1294Q			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1294			R -> Q (in dbSNP:rs17690195).		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						CTCTTCCACTCGGTGGCTCAG	0.577													C|||	717	0.143171	0.0492	0.1513	5008	,	,		18444	0.1567		0.166	False		,,,				2504	0.227				p.R1294Q		Atlas-SNP	.											.	MYH13	533	.	0			c.G3881A						PASS	.	C	GLN/ARG	236,3744		7,222,1761	100.0	99.0	99.0		3881	3.0	1.0	17	dbSNP_123	99	1276,7066		91,1094,2986	yes	missense	MYH13	NM_003802.2	43	98,1316,4747	TT,TC,CC		15.2961,5.9296,12.2707	benign	1294/1939	10219113	1512,10810	1990	4171	6161	SO:0001583	missense	8735	exon29			TCCACTCGGTGGC	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.3881G>A	17.37:g.10219113C>T	ENSP00000404570:p.Arg1294Gln	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	176	87	0.494318	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	294	0.1346153846153846	25	0.0508130081300813	59	0.16298342541436464	96	0.16783216783216784	114	0.1503957783641161	C	3.961	-0.010351	0.07727	0.059296	0.152961	ENSG00000006788	ENST00000252172	T	0.74947	-0.89	4.1	3.02	0.34903	Myosin tail (1);	.	.	.	.	T	0.00109	0.0003	N	0.00599	-1.345	0.45342	P	0.0016690000000000316	B	0.02656	0.0	B	0.04013	0.001	T	0.09143	-1.0688	8	0.02654	T	1	.	9.3419	0.38085	0.0:0.0864:0.0:0.9136	rs17690195;rs52795546;rs56637558;rs17690195	1294	Q9UKX3	MYH13_HUMAN	Q	1294	ENSP00000252172:R1294Q	ENSP00000252172:R1294Q	R	-	2	0	MYH13	10159838	1.000000	0.71417	0.999000	0.59377	0.800000	0.45204	4.757000	0.62213	0.634000	0.30469	-0.517000	0.04412	CGA	C|0.857;T|0.143	0.143	strong		0.577	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	
DAG1	1605	hgsc.bcm.edu	37	3	49570200	49570200	+	Silent	SNP	C	C	T	rs1801143	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49570200C>T	ENST00000539901.1	+	3	2814	c.2256C>T	c.(2254-2256)caC>caT	p.H752H	DAG1_ENST00000515359.2_Silent_p.H752H|DAG1_ENST00000545947.1_Silent_p.H752H|DAG1_ENST00000541308.1_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	117	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	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		
MAP9	79884	hgsc.bcm.edu	37	4	156276289	156276289	+	Silent	SNP	C	C	T	rs2341894	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:156276289C>T	ENST00000311277.4	-	10	1577	c.1314G>A	c.(1312-1314)gtG>gtA	p.V438V	AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000596165.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000600928.1_RNA|AC097467.2_ENST00000594492.1_RNA|AC097467.2_ENST00000594666.1_RNA|AC097467.2_ENST00000597831.1_RNA|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000593387.2_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000601977.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000608406.1_RNA|AC097467.2_ENST00000596754.1_RNA|MAP9_ENST00000515654.1_Silent_p.V414V|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000609254.1_RNA|AC097467.2_ENST00000598890.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	438					cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		CATGTAAATACACATTTTTCT	0.244													T|||	3705	0.739816	0.9546	0.5533	5008	,	,		13242	0.9266		0.5616	False		,,,				2504	0.5726				p.V438V		Atlas-SNP	.											.	MAP9	79	.	0			c.G1314A						PASS	.	T		3899,469		1752,395,37	56.0	60.0	59.0		1314	-10.3	0.1	4	dbSNP_100	59	4588,3938		1248,2092,923	no	coding-synonymous	MAP9	NM_001039580.1		3000,2487,960	TT,TC,CC		46.1881,10.7372,34.1787		438/648	156276289	8487,4407	2184	4263	6447	SO:0001819	synonymous_variant	79884	exon10			TAAATACACATTT	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.1314G>A	4.37:g.156276289C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	75	47	0.626667	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Silent	SNP	ENST00000311277.4	37	CCDS35493.1																																																																																			C|0.324;T|0.676	0.676	strong		0.244	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
GLI3	2737	hgsc.bcm.edu	37	7	42005836	42005836	+	Silent	SNP	C	C	G	rs61758978	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:42005836C>G	ENST00000395925.3	-	15	2919	c.2835G>C	c.(2833-2835)ctG>ctC	p.L945L	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	945					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|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)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CCATGTTGGGCAGGGGCGTCG	0.716									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				C|||	42	0.00838658	0.0023	0.0216	5008	,	,		14107	0.0		0.0189	False		,,,				2504	0.0051				p.L945L		Atlas-SNP	.											.	GLI3	312	.	0			c.G2835C						PASS	.	C		14,4322		0,14,2154	11.0	15.0	14.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2835	4.1	1.0	7	dbSNP_129	14	162,8342		4,154,4094	no	coding-synonymous	GLI3	NM_000168.5		4,168,6248	GG,GC,CC		1.905,0.3229,1.3707		945/1581	42005836	176,12664	2168	4252	6420	SO:0001819	synonymous_variant	2737	exon15	Familial Cancer Database	;	GTTGGGCAGGGGC		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.2835G>C	7.37:g.42005836C>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																			C|0.986;G|0.014	0.014	strong		0.716	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197176	39197176	+	Silent	SNP	G	G	A	rs3815561	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39197176G>A	ENST00000306271.4	-	1	537	c.474C>T	c.(472-474)taC>taT	p.Y158Y		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	158						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)			ACTGTCCACAGTAGGATGGGC	0.627													g|||	1112	0.222045	0.1967	0.2622	5008	,	,		17623	0.2817		0.1332	False		,,,				2504	0.2577				p.Y158Y		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.C474T						PASS	.	G		725,3381		53,619,1381	31.0	35.0	34.0		474	5.1	1.0	17	dbSNP_107	34	1275,7081		98,1079,3001	no	coding-synonymous	KRTAP1-1	NM_030967.2		151,1698,4382	AA,AG,GG		15.2585,17.6571,16.0488		158/178	39197176	2000,10462	2053	4178	6231	SO:0001819	synonymous_variant	81851	exon1			TCCACAGTAGGAT	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.474C>T	17.37:g.39197176G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	239	130	0.543933	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			G|1.000;|0.000	.	weak		0.627	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
TAF4B	6875	hgsc.bcm.edu	37	18	23866185	23866185	+	Missense_Mutation	SNP	G	G	C	rs74947492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:23866185G>C	ENST00000269142.5	+	7	2310	c.1312G>C	c.(1312-1314)Gtg>Ctg	p.V438L	TAF4B_ENST00000578121.1_Missense_Mutation_p.V438L|TAF4B_ENST00000400466.2_Missense_Mutation_p.V438L	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	438					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)			AAAACCACTTGTGACATCTGT	0.488													G|||	223	0.0445288	0.0151	0.0663	5008	,	,		22685	0.0089		0.0954	False		,,,				2504	0.0532				p.V438L		Atlas-SNP	.											.	TAF4B	71	.	0			c.G1312C						PASS	.	G	LEU/VAL	130,3784		5,120,1832	58.0	57.0	57.0		1312	2.9	1.0	18	dbSNP_131	57	863,7455		35,793,3331	yes	missense	TAF4B	NM_005640.1	32	40,913,5163	CC,CG,GG		10.3751,3.3214,8.1181	benign	438/863	23866185	993,11239	1957	4159	6116	SO:0001583	missense	6875	exon7			CCACTTGTGACAT	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.1312G>C	18.37:g.23866185G>C	ENSP00000269142:p.Val438Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	115	0.052655677655677656	9	0.018292682926829267	34	0.09392265193370165	5	0.008741258741258742	67	0.08839050131926121	G	10.51	1.371004	0.24771	0.033214	0.103751	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.23552	1.9;1.91;1.9	5.72	2.91	0.33838	.	0.207171	0.32459	N	0.006066	T	0.00271	0.0008	N	0.11560	0.145	0.58432	P	1.999999999946489E-6	B;B	0.30406	0.278;0.117	B;B	0.24974	0.057;0.035	T	0.23190	-1.0195	9	0.18710	T	0.47	-0.654	4.4493	0.11612	0.2542:0.0:0.5562:0.1896	.	438;438	Q92750;A4PBF7	TAF4B_HUMAN;.	L	438	ENSP00000389365:V438L;ENSP00000269142:V438L;ENSP00000383314:V438L	ENSP00000269142:V438L	V	+	1	0	TAF4B	22120183	0.001000	0.12720	0.990000	0.47175	0.937000	0.57800	0.138000	0.16016	0.753000	0.32945	0.557000	0.71058	GTG	G|0.926;C|0.074	0.074	strong		0.488	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792003	8792003	+	Silent	SNP	C	C	T	rs9915880	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8792003C>T	ENST00000447110.1	-	10	1225	c.1101G>A	c.(1099-1101)tcG>tcA	p.S367S	PIK3R5_ENST00000584803.1_Silent_p.S367S|PIK3R5_ENST00000581552.1_Silent_p.S367S	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	367				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						GGGCCGGCCCCGAGGCCTGGG	0.627													c|||	1017	0.203075	0.2995	0.2853	5008	,	,		18342	0.001		0.2833	False		,,,				2504	0.1401				p.S367S	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.G1101A						PASS	.	C	,	1297,3109	432.8+/-343.4	203,891,1109	72.0	75.0	74.0		1101,1101	-9.0	0.1	17	dbSNP_119	74	2686,5914	427.5+/-355.6	414,1858,2028	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	617,2749,3137	TT,TC,CC		31.2326,29.4371,30.6243	,	367/881,367/881	8792003	3983,9023	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			CGGCCCCGAGGCC	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.1101G>A	17.37:g.8792003C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			C|0.736;T|0.264	0.264	strong		0.627	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
ZC3H3	23144	hgsc.bcm.edu	37	8	144522457	144522457	+	Missense_Mutation	SNP	G	G	A	rs36083358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144522457G>A	ENST00000262577.5	-	11	2600	c.2569C>T	c.(2569-2571)Cct>Tct	p.P857S		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	857					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)			CAGTGGGGAGGTGCAGCCACG	0.687													G|||	54	0.0107827	0.0008	0.013	5008	,	,		14818	0.0		0.0417	False		,,,				2504	0.002				p.P857S		Atlas-SNP	.											.	ZC3H3	75	.	0			c.C2569T						PASS	.	G	SER/PRO	44,4338		0,44,2147	14.0	17.0	16.0		2569	-2.6	0.0	8	dbSNP_126	16	430,8154		9,412,3871	yes	missense	ZC3H3	NM_015117.2	74	9,456,6018	AA,AG,GG		5.0093,1.0041,3.6557	probably-damaging	857/949	144522457	474,12492	2191	4292	6483	SO:0001583	missense	23144	exon11			GGGGAGGTGCAGC	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.2569C>T	8.37:g.144522457G>A	ENSP00000262577:p.Pro857Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	113	38	0.336283	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	38	0.0173992673992674	0	0.0	6	0.016574585635359115	0	0.0	32	0.04221635883905013	G	11.73	1.724598	0.30593	0.010041	0.050093	ENSG00000014164	ENST00000262577	T	0.46063	0.88	3.56	-2.63	0.06133	.	1.990810	0.02478	N	0.088190	T	0.03695	0.0105	N	0.20986	0.625	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.03829	-1.1000	10	0.11794	T	0.64	.	1.6498	0.02769	0.1968:0.2918:0.3632:0.1482	rs36083358	857	Q8IXZ2	ZC3H3_HUMAN	S	857	ENSP00000262577:P857S	ENSP00000262577:P857S	P	-	1	0	ZC3H3	144593600	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.560000	0.23500	-0.308000	0.08792	0.467000	0.42956	CCT	G|0.973;A|0.027	0.027	strong		0.687	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
CBR3	874	hgsc.bcm.edu	37	21	37507501	37507501	+	Missense_Mutation	SNP	G	G	A	rs8133052	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:37507501G>A	ENST00000290354.5	+	1	292	c.11G>A	c.(10-12)tGc>tAc	p.C4Y	CBR3-AS1_ENST00000608622.1_RNA|CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000453159.1_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	26	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	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		
C17orf78	284099	hgsc.bcm.edu	37	17	35743010	35743010	+	Missense_Mutation	SNP	C	C	G	rs1714987	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:35743010C>G	ENST00000300618.4	+	4	505	c.455C>G	c.(454-456)aCt>aGt	p.T152S	ACACA_ENST00000416895.1_Intron|C17orf78_ENST00000586700.1_Intron|ACACA_ENST00000353139.5_Intron|ACACA_ENST00000589665.1_5'Flank|RP11-378E13.3_ENST00000592238.1_RNA	NM_173625.3	NP_775896.3	Q8N4C9	CQ078_HUMAN	chromosome 17 open reading frame 78	152			T -> S (in dbSNP:rs1714987). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)		p.T152S(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(1)	6		Breast(25;0.00295)|Ovarian(249;0.15)				TTTCCCACCACTGCCCCTTCT	0.388													C|||	1584	0.316294	0.2526	0.2493	5008	,	,		15541	0.5377		0.1918	False		,,,				2504	0.3497				p.T152S		Atlas-SNP	.											C17orf78,NS,carcinoma,0,1	C17orf78	23	1	1	Substitution - Missense(1)	stomach(1)	c.C455G						PASS	.	C	SER/THR,,	875,2713		118,639,1037	54.0	49.0	51.0		455,,	1.9	0.0	17	dbSNP_89	51	1471,6647		146,1179,2734	yes	missense,intron,intron	ACACA,C17orf78	NM_173625.3,NM_198834.1,NM_198839.1	58,,	264,1818,3771	GG,GC,CC		18.1202,24.3868,20.041	possibly-damaging,,	152/276,,	35743010	2346,9360	1794	4059	5853	SO:0001583	missense	284099	exon4			CCACCACTGCCCC	BC034672	CCDS45655.1	17q12	2014-05-06			ENSG00000167230	ENSG00000278505			26831	protein-coding gene	gene with protein product						14702039	Standard	NM_173625		Approved	FLJ39647	uc002hns.3	Q8N4C9	OTTHUMG00000188467	ENST00000300618.4:c.455C>G	17.37:g.35743010C>G	ENSP00000300618:p.Thr152Ser	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_173625	Q8N8D2	Missense_Mutation	SNP	ENST00000300618.4	37	CCDS45655.1	695	0.3182234432234432	145	0.29471544715447157	91	0.2513812154696133	316	0.5524475524475524	143	0.18865435356200527	C	8.831	0.940004	0.18281	0.243868	0.181202	ENSG00000167230	ENST00000300618	T	0.48201	0.82	4.94	1.87	0.25490	.	0.660665	0.13966	N	0.350483	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.15930	0.015	B	0.16289	0.015	T	0.46775	-0.9167	9	0.26408	T	0.33	-1.6736	7.1964	0.25855	0.0:0.7231:0.0:0.2769	rs1714987;rs17846097;rs17859100;rs52823794;rs57014482;rs1714987	152	Q8N4C9	CQ078_HUMAN	S	152	ENSP00000300618:T152S	ENSP00000300618:T152S	T	+	2	0	C17orf78	32817123	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.114000	0.10757	0.375000	0.24679	0.655000	0.94253	ACT	C|0.700;G|0.300	0.300	strong		0.388	C17orf78-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451570.2	NM_173625	
OR52E2	119678	hgsc.bcm.edu	37	11	5080337	5080337	+	Missense_Mutation	SNP	T	T	C	rs61746343	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5080337T>C	ENST00000321522.2	-	1	520	c.521A>G	c.(520-522)cAt>cGt	p.H174R		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	174						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(13)|ovary(2)|skin(3)	20		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)		GGGAATTACATGATTCCCACA	0.398													T|||	1048	0.209265	0.2746	0.3559	5008	,	,		22989	0.0873		0.2237	False		,,,				2504	0.1278				p.H174R		Atlas-SNP	.											.	OR52E2	63	.	0			c.A521G						PASS	.	T	ARG/HIS	1160,3242	409.5+/-335.0	154,852,1195	86.0	80.0	82.0		521	-1.2	0.1	11	dbSNP_129	82	1773,6823	320.7+/-314.7	174,1425,2699	yes	missense	OR52E2	NM_001005164.2	29	328,2277,3894	CC,CT,TT		20.6259,26.3517,22.565	benign	174/326	5080337	2933,10065	2201	4298	6499	SO:0001583	missense	119678	exon1			ATTACATGATTCC	AB065800	CCDS31371.1	11p15.4	2012-08-09			ENSG00000176787	ENSG00000176787		"""GPCR / Class A : Olfactory receptors"""	14769	protein-coding gene	gene with protein product							Standard	NM_001005164		Approved		uc010qyw.2	Q8NGJ4	OTTHUMG00000066608	ENST00000321522.2:c.521A>G	11.37:g.5080337T>C	ENSP00000322088:p.His174Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	466	0.21336996336996336	136	0.2764227642276423	104	0.287292817679558	62	0.10839160839160839	164	0.21635883905013192	T	0.098	-1.156324	0.01686	0.263517	0.206259	ENSG00000176787	ENST00000321522	T	0.00063	8.78	3.76	-1.16	0.09678	GPCR, rhodopsin-like superfamily (1);	1.067990	0.07299	N	0.873832	T	0.00012	0.0000	L	0.33189	0.99	0.58432	P	1.0000000000287557E-6	B	0.09022	0.002	B	0.15484	0.013	T	0.00330	-1.1812	9	0.10111	T	0.7	.	8.6192	0.33851	0.0:0.3152:0.0:0.6848	rs61746343	174	Q8NGJ4	O52E2_HUMAN	R	174	ENSP00000322088:H174R	ENSP00000322088:H174R	H	-	2	0	OR52E2	5036913	0.000000	0.05858	0.149000	0.22428	0.832000	0.47134	-0.595000	0.05727	-0.211000	0.10124	-0.262000	0.10625	CAT	T|0.770;C|0.230	0.230	strong		0.398	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
PCSK7	9159	hgsc.bcm.edu	37	11	117078702	117078702	+	Silent	SNP	A	A	C	rs200068220		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117078702A>C	ENST00000320934.3	-	14	2400	c.1770T>G	c.(1768-1770)ctT>ctG	p.L590L	PCSK7_ENST00000529458.1_5'UTR|PCSK7_ENST00000540028.1_Silent_p.L231L	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	590					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.L590L(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCCTGATGACAAGCCTGTAGG	0.567			T	IGH@	MLCLS																																p.L590L		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	PCSK7,NS,carcinoma,0,1	PCSK7	59	1	1	Substitution - coding silent(1)	ovary(1)	c.T1770G						scavenged	.						2.0	2.0	2.0					11																	117078702		1345	2817	4162	SO:0001819	synonymous_variant	9159	exon14			GATGACAAGCCTG	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1770T>G	11.37:g.117078702A>C		Somatic	819	176	0.214896		WXS	Illumina HiSeq	Phase_I	1188	984	0.828283	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			.	.	weak		0.567	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
KLHL31	401265	hgsc.bcm.edu	37	6	53519062	53519062	+	Silent	SNP	A	A	G	rs10948758	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:53519062A>G	ENST00000407079.1	-	1	1008	c.1009T>C	c.(1009-1011)Ttg>Ctg	p.L337L	KLHL31_ENST00000370905.3_Silent_p.L337L			Q9H511	KLH31_HUMAN	kelch-like family member 31	337					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)					TCTCTATACAAGATGTCTCTG	0.488													A|||	3417	0.682308	0.5272	0.7723	5008	,	,		20054	0.6994		0.7366	False		,,,				2504	0.7546				p.L337L		Atlas-SNP	.											.	KLHL31	48	.	0			c.T1009C						PASS	.	A		2523,1883	630.0+/-395.4	710,1103,390	93.0	89.0	91.0		1009	2.9	0.8	6	dbSNP_120	91	6461,2139	713.9+/-406.0	2443,1575,282	no	coding-synonymous	KLHL31	NM_001003760.4		3153,2678,672	GG,GA,AA		24.8721,42.7372,30.9242		337/635	53519062	8984,4022	2203	4300	6503	SO:0001819	synonymous_variant	401265	exon2			TATACAAGATGTC		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.1009T>C	6.37:g.53519062A>G		Somatic	245	2	0.00816326		WXS	Illumina HiSeq	Phase_I	215	213	0.990698	NM_001003760	A6N9J2|B2RP49	Silent	SNP	ENST00000407079.1	37	CCDS34478.1																																																																																			A|0.316;G|0.684	0.684	strong		0.488	KLHL31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040965.1	NM_001003760	
AIFM3	150209	hgsc.bcm.edu	37	22	21330787	21330787	+	Silent	SNP	C	C	T	rs7285694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:21330787C>T	ENST00000399167.2	+	11	1230	c.990C>T	c.(988-990)gcC>gcT	p.A330A	AIFM3_ENST00000465606.1_3'UTR|AIFM3_ENST00000333607.6_Silent_p.A330A|AIFM3_ENST00000335375.5_Silent_p.A318A|AIFM3_ENST00000399163.2_Silent_p.A330A|AIFM3_ENST00000405089.1_Silent_p.A336A|AIFM3_ENST00000440238.2_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	70	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	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	
SURF2	6835	hgsc.bcm.edu	37	9	136228006	136228006	+	Silent	SNP	G	G	A	rs34939258	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	71	0	0		WXS	Illumina HiSeq	Phase_I	53	17	0.320755	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	
PSMB6	5694	hgsc.bcm.edu	37	17	4699552	4699552	+	Silent	SNP	G	G	A	rs3169950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	38	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	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	
CD79B	974	hgsc.bcm.edu	37	17	62007498	62007498	+	Silent	SNP	A	A	G	rs2070776	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:62007498A>G	ENST00000006750.3	-	3	458	c.366T>C	c.(364-366)tgT>tgC	p.C122C	CD79B_ENST00000349817.2_Intron|CD79B_ENST00000392795.3_Silent_p.C123C	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	122	Ig-like V-type.				B cell receptor signaling pathway (GO:0050853)|immune response (GO:0006955)|signal transduction (GO:0007165)	B cell receptor complex (GO:0019815)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.C122C(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						ACTTCTGCTGACAGAAGTAGA	0.577			"""Mis, O"""		DLBCL								G|||	2813	0.561701	0.6974	0.4841	5008	,	,		21845	0.4881		0.6531	False		,,,				2504	0.4151				p.C123C		Atlas-SNP	.		Dom	yes		17	17q23	974	"""CD79b molecule, immunoglobulin-associated beta"""		L	CD79B,NS,carcinoma,0,1	CD79B	38	1	1	Substitution - coding silent(1)	stomach(1)	c.T369C						scavenged	.	G	,,	2967,1439	466.2+/-354.4	996,975,232	127.0	102.0	111.0		366,369,	0.6	0.1	17	dbSNP_96	111	5612,2988	462.5+/-365.7	1846,1920,534	no	coding-synonymous,coding-synonymous,intron	CD79B	NM_000626.2,NM_001039933.1,NM_021602.2	,,	2842,2895,766	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	34.7442,32.66,34.0381	,,	122/230,123/231,	62007498	8579,4427	2203	4300	6503	SO:0001819	synonymous_variant	974	exon3			CTGCTGACAGAAG	L27587	CCDS11655.1, CCDS11656.1, CCDS42372.1	17q23	2014-09-17	2006-03-28			ENSG00000007312		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1699	protein-coding gene	gene with protein product		147245	"""CD79B antigen (immunoglobulin-associated beta)"""	IGB		9545642	Standard	XM_005257858		Approved	B29	uc002jdp.1	P40259		ENST00000006750.3:c.366T>C	17.37:g.62007498A>G		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	151	66	0.437086	NM_001039933	Q53FS2|Q9BU06	Silent	SNP	ENST00000006750.3	37	CCDS11655.1																																																																																			A|0.371;G|0.629	0.629	strong		0.577	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1		
CEP41	95681	hgsc.bcm.edu	37	7	130051013	130051013	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:130051013A>G	ENST00000223208.5	-	5	497	c.227T>C	c.(226-228)cTc>cCc	p.L76P	CEP41_ENST00000343969.5_Missense_Mutation_p.L76P|CEP41_ENST00000541543.1_Missense_Mutation_p.L60P	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	76					cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein polyglutamylation (GO:0018095)|protein transport (GO:0015031)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|membrane (GO:0016020)|primary cilium (GO:0072372)											TTGATCAGAGAGGGAAGCAAC	0.403																																					p.L76P		Atlas-SNP	.											TSGA14,NS,carcinoma,+1,1	.	.	1	0			c.T227C						PASS	.						167.0	153.0	157.0					7																	130051013		2203	4300	6503	SO:0001583	missense	95681	exon5			TCAGAGAGGGAAG	AJ278890	CCDS5821.1, CCDS59078.1, CCDS59079.1, CCDS59080.1	7q32	2014-02-20	2011-10-04	2011-10-04	ENSG00000106477	ENSG00000106477			12370	protein-coding gene	gene with protein product		610523	"""testis specific, 14"""	TSGA14		14654843, 22246503	Standard	NM_018718		Approved	DKFZp762H1311, FLJ22445, JBTS15	uc003vpz.4	Q9BYV8	OTTHUMG00000157823	ENST00000223208.5:c.227T>C	7.37:g.130051013A>G	ENSP00000223208:p.Leu76Pro	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	71	54	0.760563	NM_018718	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.350277	0.82132	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969;ENST00000492389;ENST00000472739;ENST00000477003;ENST00000475282;ENST00000469826	D;D;D;D;D;D;D;D	0.90620	-2.7;-2.33;-2.66;-2.35;-2.34;-2.36;-1.84;-1.5	5.93	5.93	0.95920	Rhodanese-like (1);	0.242522	0.36409	N	0.002614	D	0.94371	0.8190	M	0.67953	2.075	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.71656	0.974;0.916;0.909	D	0.94745	0.7922	10	0.72032	D	0.01	-10.3632	15.1976	0.73104	1.0:0.0:0.0:0.0	.	60;76;76	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	P	76;60;76;41;41;73;41;63	ENSP00000223208:L76P;ENSP00000445888:L60P;ENSP00000342738:L76P;ENSP00000419192:L41P;ENSP00000417593:L41P;ENSP00000420670:L73P;ENSP00000418363:L41P;ENSP00000418712:L63P	ENSP00000223208:L76P	L	-	2	0	TSGA14	129838249	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.635000	0.67841	2.273000	0.75805	0.482000	0.46254	CTC	.	.	none		0.403	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718	
SCLT1	132320	hgsc.bcm.edu	37	4	129867280	129867280	+	Missense_Mutation	SNP	T	T	A	rs10028124	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:129867280T>A	ENST00000281142.5	-	16	1824	c.1321A>T	c.(1321-1323)Agt>Tgt	p.S441C	SCLT1_ENST00000439369.2_Intron|SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000503215.1_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	441			S -> C (in dbSNP:rs10028124). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						CTGTAATCACTCTCATTTCCT	0.348													T|||	3807	0.760184	0.9599	0.7637	5008	,	,		14832	0.7044		0.673	False		,,,				2504	0.635				p.S441C		Atlas-SNP	.											.	SCLT1	136	.	0			c.A1321T						PASS	.	T	CYS/SER	4025,379	788.6+/-414.9	1839,347,16	98.0	91.0	93.0		1321	1.5	1.0	4	dbSNP_119	93	5628,2968	665.6+/-402.3	1866,1896,536	yes	missense	SCLT1	NM_144643.2	112	3705,2243,552	AA,AT,TT		34.5277,8.6058,25.7462	possibly-damaging	441/689	129867280	9653,3347	2202	4298	6500	SO:0001583	missense	132320	exon16			AATCACTCTCATT	AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.1321A>T	4.37:g.129867280T>A	ENSP00000281142:p.Ser441Cys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Missense_Mutation	SNP	ENST00000281142.5	37	CCDS3740.1	1619	0.7413003663003663	465	0.9451219512195121	270	0.7458563535911602	387	0.6765734265734266	497	0.6556728232189973	T	15.55	2.867699	0.51588	0.913942	0.654723	ENSG00000151466	ENST00000281142	T	0.30981	1.51	4.39	1.5	0.22942	.	0.681258	0.15234	N	0.273277	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.9999999618503	D	0.55800	0.973	P	0.53360	0.724	T	0.23048	-1.0199	8	.	.	.	-0.2858	6.1918	0.20528	0.0:0.3324:0.0:0.6676	rs10028124;rs52819094	441	Q96NL6	SCLT1_HUMAN	C	441	ENSP00000281142:S441C	.	S	-	1	0	SCLT1	130086730	0.035000	0.19736	0.999000	0.59377	0.710000	0.40934	0.010000	0.13242	0.594000	0.29761	0.454000	0.30748	AGT	T|0.257;A|0.743	0.743	strong		0.348	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643	
CSTA	1475	hgsc.bcm.edu	37	3	122060404	122060404	+	Missense_Mutation	SNP	C	C	T	rs34173813	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122060404C>T	ENST00000264474.3	+	3	336	c.287C>T	c.(286-288)aCg>aTg	p.T96M		NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	96			T -> M (in dbSNP:rs34173813).		keratinocyte differentiation (GO:0030216)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|peptide cross-linking (GO:0018149)|single organismal cell-cell adhesion (GO:0016337)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			large_intestine(2)|lung(2)	4				GBM - Glioblastoma multiforme(114;0.155)		GACGAGCTGACGGGCTTTTAG	0.398													C|||	474	0.0946486	0.0189	0.1124	5008	,	,		18573	0.0407		0.1561	False		,,,				2504	0.1769				p.T96M	Pancreas(26;157 1503 12440)	Atlas-SNP	.											.	CSTA	11	.	0			c.C287T	GRCh37	CM076131	CSTA	M	rs34173813	PASS	.	C	MET/THR	212,4194	129.0+/-165.8	1,210,1992	119.0	117.0	118.0		287	-7.3	0.0	3	dbSNP_126	118	1277,7323	255.2+/-280.2	110,1057,3133	yes	missense	CSTA	NM_005213.3	81	111,1267,5125	TT,TC,CC		14.8488,4.8116,11.4486	probably-damaging	96/99	122060404	1489,11517	2203	4300	6503	SO:0001583	missense	1475	exon3			AGCTGACGGGCTT		CCDS3011.1	3q21	2008-04-15			ENSG00000121552	ENSG00000121552			2481	protein-coding gene	gene with protein product		184600		STF1, STFA		1674139	Standard	NM_005213		Approved		uc003eex.3	P01040	OTTHUMG00000159488	ENST00000264474.3:c.287C>T	3.37:g.122060404C>T	ENSP00000264474:p.Thr96Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_005213	Q6IB90	Missense_Mutation	SNP	ENST00000264474.3	37	CCDS3011.1	168	0.07692307692307693	3	0.006097560975609756	50	0.13812154696132597	8	0.013986013986013986	107	0.14116094986807387	C	13.20	2.165243	0.38217	0.048116	0.148488	ENSG00000121552	ENST00000264474	T	0.78126	-1.15	5.34	-7.34	0.01427	Proteinase inhibitor I25, cystatin (1);	1.232960	0.05253	N	0.514252	T	0.00468	0.0015	.	.	.	0.80722	P	0.0	P	0.45715	0.865	B	0.36504	0.226	T	0.33137	-0.9880	8	0.72032	D	0.01	0.7508	2.1125	0.03706	0.5059:0.1369:0.1003:0.2569	rs34173813	96	P01040	CYTA_HUMAN	M	96	ENSP00000264474:T96M	ENSP00000264474:T96M	T	+	2	0	CSTA	123543094	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.161000	0.01278	-1.034000	0.03295	0.655000	0.94253	ACG	T|0.104;G|0.000;C|0.895	0.104	strong		0.398	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213	
SPEG	10290	hgsc.bcm.edu	37	2	220354365	220354365	+	Silent	SNP	C	C	T	rs56132883	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220354365C>T	ENST00000312358.7	+	36	8757	c.8625C>T	c.(8623-8625)ttC>ttT	p.F2875F	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2875	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)		CCAAGCCTTTCGTCCTTGACA	0.607													C|||	1435	0.286542	0.2905	0.2723	5008	,	,		10793	0.1468		0.2734	False		,,,				2504	0.4489				p.F2875F		Atlas-SNP	.											.	SPEG	272	.	0			c.C8625T						PASS	.	C		1047,2959		145,757,1101	133.0	142.0	139.0		8625	-3.5	0.4	2	dbSNP_129	139	2113,6187		273,1567,2310	no	coding-synonymous	SPEG	NM_005876.4		418,2324,3411	TT,TC,CC		25.4578,26.1358,25.6785		2875/3268	220354365	3160,9146	2003	4150	6153	SO:0001819	synonymous_variant	10290	exon36			GCCTTTCGTCCTT	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.8625C>T	2.37:g.220354365C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	106	25	0.235849	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			C|0.748;T|0.252	0.252	strong		0.607	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
CHD7	55636	hgsc.bcm.edu	37	8	61765419	61765419	+	Silent	SNP	G	G	A	rs6999971	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:61765419G>A	ENST00000423902.2	+	31	6614	c.6135G>A	c.(6133-6135)ccG>ccA	p.P2045P	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2045					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TAATTGAGCCGATCACAGAGG	0.517													G|||	79	0.0157748	0.0061	0.0187	5008	,	,		17725	0.0		0.0487	False		,,,				2504	0.0092				p.P2045P		Atlas-SNP	.											.	CHD7	534	.	0			c.G6135A						PASS	.	G		26,3774		0,26,1874	104.0	107.0	106.0		6135	-7.4	0.6	8	dbSNP_116	106	315,7921		10,295,3813	no	coding-synonymous	CHD7	NM_017780.3		10,321,5687	AA,AG,GG		3.8247,0.6842,2.8332		2045/2998	61765419	341,11695	1900	4118	6018	SO:0001819	synonymous_variant	55636	exon31			TGAGCCGATCACA	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.6135G>A	8.37:g.61765419G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	25	23	0.92	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																			G|0.976;A|0.024	0.024	strong		0.517	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
METTL25	84190	hgsc.bcm.edu	37	12	82752543	82752543	+	Missense_Mutation	SNP	T	T	G	rs112592060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:82752543T>G	ENST00000248306.3	+	1	268	c.199T>G	c.(199-201)Tcg>Gcg	p.S67A	METTL25_ENST00000547357.1_3'UTR|CCDC59_ENST00000256151.7_5'UTR|CCDC59_ENST00000548126.1_5'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	67							methyltransferase activity (GO:0008168)										GAAGTCAGCGTCGGAGACGGA	0.642											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	212	0.0423323	0.0182	0.0591	5008	,	,		14159	0.002		0.0805	False		,,,				2504	0.0654				p.S67A		Atlas-SNP	.											.	.	.	.	0			c.T199G						PASS	.	T	ALA/SER	140,4266	94.8+/-133.5	3,134,2066	55.0	51.0	52.0		199	0.6	0.0	12	dbSNP_132	52	811,7789	183.9+/-232.0	43,725,3532	yes	missense	C12orf26	NM_032230.2	99	46,859,5598	GG,GT,TT		9.4302,3.1775,7.312	benign	67/604	82752543	951,12055	2203	4300	6503	SO:0001583	missense	84190	exon1			TCAGCGTCGGAGA	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.199T>G	12.37:g.82752543T>G	ENSP00000248306:p.Ser67Ala	Somatic	278	0	0	1216	WXS	Illumina HiSeq	Phase_I	224	80	0.357143	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	89	0.04075091575091575	11	0.022357723577235773	22	0.06077348066298342	1	0.0017482517482517483	55	0.07255936675461741	T	0.966	-0.701842	0.03255	0.031775	0.094302	ENSG00000127720	ENST00000248306;ENST00000548200	T	0.29655	1.56	3.86	0.59	0.17458	.	1.506270	0.05197	N	0.504215	T	0.00412	0.0013	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19160	-1.0314	10	0.07813	T	0.8	0.4847	6.1071	0.20079	0.0:0.1738:0.4342:0.3919	.	67	Q8N6Q8	CL026_HUMAN	A	67	ENSP00000248306:S67A	ENSP00000248306:S67A	S	+	1	0	C12orf26	81276674	0.016000	0.18221	0.014000	0.15608	0.116000	0.19942	0.707000	0.25704	0.280000	0.22209	-0.219000	0.12488	TCG	T|0.938;G|0.062	0.062	strong		0.642	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
PLCD1	5333	hgsc.bcm.edu	37	3	38051941	38051941	+	Silent	SNP	T	T	C	rs9857730	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38051941T>C	ENST00000334661.4	-	6	1125	c.903A>G	c.(901-903)ccA>ccG	p.P301P	PLCD1_ENST00000479619.1_5'Flank|PLCD1_ENST00000463876.1_Silent_p.P322P	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	301	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		AGTGGCTAAGTGGCTGGCCCA	0.612													C|||	1336	0.266773	0.5053	0.1657	5008	,	,		19691	0.0863		0.1769	False		,,,				2504	0.2945				p.P322P		Atlas-SNP	.											PLCD1_ENST00000463876,NS,carcinoma,0,2	PLCD1	87	2	0			c.A966G						PASS	.	C	,	2062,2344	607.3+/-390.9	479,1104,620	55.0	56.0	56.0		966,903	-5.7	0.8	3	dbSNP_119	56	1808,6792	731.9+/-406.8	181,1446,2673	no	coding-synonymous,coding-synonymous	PLCD1	NM_001130964.1,NM_006225.3	,	660,2550,3293	CC,CT,TT		21.0233,46.7998,29.7555	,	322/778,301/757	38051941	3870,9136	2203	4300	6503	SO:0001819	synonymous_variant	5333	exon6			GCTAAGTGGCTGG		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"""EF-hand domain containing"""	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.903A>G	3.37:g.38051941T>C		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_001130964	B3KR14|Q86VN8	Silent	SNP	ENST00000334661.4	37	CCDS2671.1																																																																																			T|0.725;C|0.275	0.275	strong		0.612	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2		
F5	2153	hgsc.bcm.edu	37	1	169511755	169511755	+	Missense_Mutation	SNP	T	T	C	rs4524	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:169511755T>C	ENST00000367797.3	-	13	2774	c.2573A>G	c.(2572-2574)aAa>aGa	p.K858R	F5_ENST00000367796.3_Missense_Mutation_p.K863R	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	858	B.		K -> R (in dbSNP:rs4524). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:11758222, ECO:0000269|PubMed:2827731, ECO:0000269|PubMed:3110773, 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)	TTCTTGACTTTTGAATTCTCC	0.453													T|||	1336	0.266773	0.1679	0.3948	5008	,	,		21468	0.248		0.2535	False		,,,				2504	0.3425				p.K858R		Atlas-SNP	.											.	F5	301	.	0			c.A2573G						PASS	.	T	ARG/LYS	813,3593	321.3+/-297.0	68,677,1458	187.0	175.0	179.0		2573	-1.7	0.0	1	dbSNP_52	179	2355,6245	393.6+/-344.4	300,1755,2245	yes	missense	F5	NM_000130.4	26	368,2432,3703	CC,CT,TT		27.3837,18.4521,24.358	benign	858/2225	169511755	3168,9838	2203	4300	6503	SO:0001583	missense	2153	exon13			TGACTTTTGAATT	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.2573A>G	1.37:g.169511755T>C	ENSP00000356771:p.Lys858Arg	Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	361	352	0.975069	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	532	0.24358974358974358	96	0.1951219512195122	130	0.35911602209944754	113	0.19755244755244755	193	0.2546174142480211	T	0.281	-0.986145	0.02180	0.184521	0.273837	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.19105	2.17;2.17	5.34	-1.7	0.08159	.	0.830320	0.10778	N	0.635169	T	0.01523	0.0049	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47711	-0.9096	9	0.15499	T	0.54	-3.9453	5.1617	0.15064	0.0:0.3402:0.1552:0.5046	rs4524;rs52817149;rs59950571;rs4524	858	P12259	FA5_HUMAN	R	858;863	ENSP00000356771:K858R;ENSP00000356770:K863R	ENSP00000356770:K863R	K	-	2	0	F5	167778379	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.454000	0.06770	-0.097000	0.12307	-1.534000	0.00916	AAA	T|0.760;C|0.240	0.240	strong		0.453	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
FAM170A	340069	hgsc.bcm.edu	37	5	118969960	118969960	+	Missense_Mutation	SNP	C	C	T	rs328694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	170	0	0		WXS	Illumina HiSeq	Phase_I	134	58	0.432836	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	
HGFAC	3083	hgsc.bcm.edu	37	4	3444593	3444593	+	Silent	SNP	G	G	A	rs2073504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:3444593G>A	ENST00000382774.3	+	2	367	c.252G>A	c.(250-252)ccG>ccA	p.P84P	HGFAC_ENST00000511533.1_Silent_p.P84P	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	84					proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGGGGCTCCCGCCCCCGCCCA	0.672													G|||	1155	0.230631	0.2057	0.2291	5008	,	,		15322	0.372		0.175	False		,,,				2504	0.1769				p.P84P		Atlas-SNP	.											HGFAC,NS,carcinoma,0,1	HGFAC	69	1	0			c.G252A						PASS	.	G		927,3473	330.4+/-301.5	90,747,1363	43.0	51.0	48.0		252	-1.1	0.0	4	dbSNP_96	48	1407,7191	265.7+/-286.3	119,1169,3011	yes	coding-synonymous	HGFAC	NM_001528.2		209,1916,4374	AA,AG,GG		16.3643,21.0682,17.9566		84/656	3444593	2334,10664	2200	4299	6499	SO:0001819	synonymous_variant	3083	exon2			GCTCCCGCCCCCG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.252G>A	4.37:g.3444593G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	37	CCDS3369.1																																																																																			G|0.806;A|0.194	0.194	strong		0.672	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
PIEZO1	9780	hgsc.bcm.edu	37	16	88780090	88780090	+	IGR	SNP	G	G	A	rs2290904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88780090G>A	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Silent_p.V303V|CTU2_ENST00000378384.3_Silent_p.V216V|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Silent_p.V303V|CTU2_ENST00000567949.1_Silent_p.V374V	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						ACGTGGTGGTGGTGCGGCCCA	0.652													G|||	723	0.144369	0.2322	0.0865	5008	,	,		18261	0.0625		0.1372	False		,,,				2504	0.1585				p.V303V		Atlas-SNP	.											CTU2_ENST00000453996,NS,carcinoma,0,4	CTU2	66	4	0			c.G909A						PASS	.	G	,	981,3399	364.4+/-316.9	95,791,1304	74.0	71.0	72.0		909,909	3.7	1.0	16	dbSNP_100	72	1236,7352	246.5+/-274.9	82,1072,3140	no	coding-synonymous,coding-synonymous	CTU2	NM_001012759.1,NM_001012762.1	,	177,1863,4444	AA,AG,GG		14.3922,22.3973,17.0959	,	303/516,303/486	88780090	2217,10751	2190	4294	6484	SO:0001628	intergenic_variant	348180	exon9			GGTGGTGGTGCGG	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.88780090G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	20	0.15748	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1																																																																																			G|0.834;A|0.166	0.166	strong		0.652	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
GOLGA3	2802	hgsc.bcm.edu	37	12	133357412	133357412	+	Missense_Mutation	SNP	T	T	C	rs2291260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:133357412T>C	ENST00000450791.2	-	17	3737	c.3554A>G	c.(3553-3555)aAg>aGg	p.K1185R	GOLGA3_ENST00000456883.2_Missense_Mutation_p.K1185R|GOLGA3_ENST00000204726.3_Missense_Mutation_p.K1185R			Q08378	GOGA3_HUMAN	golgin A3	1185			K -> R (in dbSNP:rs2291260).		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)	p.K1185R(1)		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)		CACCTTCTCCTTCTCCTTCTC	0.557													T|||	1536	0.306709	0.3328	0.2493	5008	,	,		21709	0.2877		0.2187	False		,,,				2504	0.4223				p.K1185R		Atlas-SNP	.											GOLGA3,NS,carcinoma,0,1	GOLGA3	234	1	1	Substitution - Missense(1)	prostate(1)	c.A3554G						PASS	.	T	ARG/LYS	1452,2954	469.6+/-355.5	232,988,983	148.0	136.0	140.0		3554	5.6	0.2	12	dbSNP_100	140	2095,6505	361.9+/-332.5	266,1563,2471	yes	missense	GOLGA3	NM_005895.3	26	498,2551,3454	CC,CT,TT		24.3605,32.9551,27.272	probably-damaging	1185/1499	133357412	3547,9459	2203	4300	6503	SO:0001583	missense	2802	exon18			TTCTCCTTCTCCT	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.3554A>G	12.37:g.133357412T>C	ENSP00000410378:p.Lys1185Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_005895	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	588	0.2692307692307692	177	0.3597560975609756	95	0.26243093922651933	160	0.27972027972027974	156	0.20580474934036938	T	16.05	3.011940	0.54468	0.329551	0.243605	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883	T;T;T	0.32023	1.47;1.47;1.48	5.61	5.61	0.85477	.	0.042054	0.85682	D	0.000000	T	0.00012	0.0000	L	0.54323	1.7	0.09310	P	1.0	D;D	0.89917	0.998;1.0	D;D	0.91635	0.994;0.999	T	0.33954	-0.9848	9	0.36615	T	0.2	.	15.4487	0.75257	0.0:0.0:0.0:1.0	rs2291260;rs52837892;rs56863919;rs2291260	1185;1185	Q08378-2;Q08378	.;GOGA3_HUMAN	R	1185	ENSP00000204726:K1185R;ENSP00000410378:K1185R;ENSP00000409303:K1185R	ENSP00000204726:K1185R	K	-	2	0	GOLGA3	131867485	1.000000	0.71417	0.219000	0.23793	0.016000	0.09150	3.103000	0.50298	2.123000	0.65237	0.523000	0.50628	AAG	T|0.724;C|0.276	0.276	strong		0.557	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
TTC7A	57217	hgsc.bcm.edu	37	2	47301029	47301029	+	Silent	SNP	A	A	G	rs3739099	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:47301029A>G	ENST00000319190.5	+	20	2912	c.2544A>G	c.(2542-2544)gtA>gtG	p.V848V	RP11-761B3.1_ENST00000422269.1_Intron|C2orf61_ENST00000464527.2_Intron|TTC7A_ENST00000394850.2_Silent_p.V872V|TTC7A_ENST00000263737.6_Silent_p.V494V|TTC7A_ENST00000409245.1_Silent_p.V814V|AC073283.7_ENST00000421759.1_RNA	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	848					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)			GCAGCCCTGTACTGCCCTTCT	0.687													G|||	1665	0.332468	0.3064	0.2507	5008	,	,		17841	0.6577		0.0885	False		,,,				2504	0.3415				p.V848V		Atlas-SNP	.											TTC7A,NS,carcinoma,0,1	TTC7A	80	1	0			c.A2544G						PASS	.	G		1221,3183	692.2+/-405.5	177,867,1158	41.0	35.0	37.0		2544	1.0	1.0	2	dbSNP_107	37	641,7959	780.6+/-407.7	30,581,3689	no	coding-synonymous	TTC7A	NM_020458.2		207,1448,4847	GG,GA,AA		7.4535,27.7248,14.3187		848/859	47301029	1862,11142	2202	4300	6502	SO:0001819	synonymous_variant	57217	exon20			CCCTGTACTGCCC	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.2544A>G	2.37:g.47301029A>G		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	307	136	0.442997	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			A|0.774;G|0.226	0.226	strong		0.687	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
IQCE	23288	hgsc.bcm.edu	37	7	2645526	2645526	+	Missense_Mutation	SNP	G	G	A	rs10950797	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:2645526G>A	ENST00000402050.2	+	20	1944	c.1760G>A	c.(1759-1761)cGc>cAc	p.R587H	IQCE_ENST00000438376.2_Missense_Mutation_p.R571H|IQCE_ENST00000325979.7_Missense_Mutation_p.R522H|IQCE_ENST00000404984.1_Missense_Mutation_p.R536H	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	587			R -> H (in dbSNP:rs10950797).			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)		CCTGTGCCCCGCGTTCCGAGC	0.701													G|||	1277	0.254992	0.1135	0.2882	5008	,	,		11500	0.4415		0.1531	False		,,,				2504	0.3354				p.R587H		Atlas-SNP	.											IQCE,NS,carcinoma,+1,1	IQCE	66	1	0			c.G1760A						scavenged	.	G	HIS/ARG,HIS/ARG	447,3701		27,393,1654	26.0	32.0	30.0		1712,1760	-0.4	0.0	7	dbSNP_120	30	1087,7303		60,967,3168	no	missense,missense	IQCE	NM_001100390.1,NM_152558.3	29,29	87,1360,4822	AA,AG,GG		12.9559,10.7763,12.2348	benign,benign	571/680,587/696	2645526	1534,11004	2074	4195	6269	SO:0001583	missense	23288	exon20			TGCCCCGCGTTCC	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.1760G>A	7.37:g.2645526G>A	ENSP00000385597:p.Arg587His	Somatic	266	2	0.0075188		WXS	Illumina HiSeq	Phase_I	313	89	0.284345	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	527	0.2413003663003663	64	0.13008130081300814	90	0.24861878453038674	257	0.4493006993006993	116	0.15303430079155672	G	7.761	0.705496	0.15172	0.107763	0.129559	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979;ENST00000423196	T;T;T;T;T	0.25579	2.65;2.64;2.65;2.65;1.79	4.79	-0.411	0.12370	.	1.266030	0.05323	N	0.527013	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B;B;B	0.12630	0.004;0.006;0.004;0.003	B;B;B;B	0.08055	0.001;0.001;0.002;0.003	T	0.43294	-0.9400	9	0.06891	T	0.86	1.1401	4.4147	0.11450	0.277:0.3155:0.4075:0.0	rs10950797;rs58914059;rs10950797	522;571;587;571	B4DXN1;B4DDX4;Q6IPM2;Q6IPM2-4	.;.;IQCE_HUMAN;.	H	587;536;571;522;167	ENSP00000385597:R587H;ENSP00000385945:R536H;ENSP00000396178:R571H;ENSP00000313772:R522H;ENSP00000405982:R167H	ENSP00000313772:R522H	R	+	2	0	IQCE	2612052	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.250000	0.02885	-0.075000	0.12798	-0.254000	0.11334	CGC	G|0.768;A|0.232	0.232	strong		0.701	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
TTN	7273	hgsc.bcm.edu	37	2	179395555	179395555	+	Missense_Mutation	SNP	C	C	A	rs67254537	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179395555C>A	ENST00000591111.1	-	308	101088	c.100864G>T	c.(100864-100866)Gcc>Tcc	p.A33622S	TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A35263S|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A32695S|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A26198S|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A26323S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A26390S|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33622					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)			GGTGATACGGCTTTCGGGTGA	0.498													C|||	26	0.00519169	0.0	0.0043	5008	,	,		17482	0.0		0.0229	False		,,,				2504	0.0				p.A35263S		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+2,5	TTN	18412	5	0			c.G105787T						scavenged	.	C	SER/ALA,SER/ALA,SER/ALA,SER/ALA	8,3810		0,8,1901	126.0	126.0	126.0		79168,78967,98083,78592	1.7	1.0	2	dbSNP_130	126	118,8112		0,118,3997	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	99,99,99,99	0,126,5898	AA,AC,CC		1.4338,0.2095,1.0458	benign,benign,benign,benign	26390/27119,26323/27052,32695/33424,26198/26927	179395555	126,11922	1909	4115	6024	SO:0001583	missense	7273	exon358			ATACGGCTTTCGG	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.100864G>T	2.37:g.179395555C>A	ENSP00000465570:p.Ala33622Ser	Somatic	391	2	0.00511509		WXS	Illumina HiSeq	Phase_I	331	130	0.392749	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		11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	C	14.13	2.444064	0.43429	0.002095	0.014338	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.63580	-0.05;0.2;0.18;0.19	4.99	1.67	0.24075	Ribonuclease H-like (1);	.	.	.	.	T	0.34774	0.0909	N	0.14661	0.345	0.25422	N	0.988263	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	T	0.34976	-0.9807	9	0.87932	D	0	.	8.5875	0.33666	0.1266:0.7197:0.0:0.1537	.	26198;26323;26390;33622	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	32695;26198;26390;26323;26195	ENSP00000343764:A32695S;ENSP00000434586:A26198S;ENSP00000340554:A26390S;ENSP00000352154:A26323S	ENSP00000340554:A26390S	A	-	1	0	TTN	179103801	1.000000	0.71417	0.988000	0.46212	0.766000	0.43426	2.644000	0.46613	0.509000	0.28195	0.455000	0.32223	GCC	C|0.993;A|0.007	0.007	strong		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
LRRC4B	94030	hgsc.bcm.edu	37	19	51051935	51051935	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51051935G>A	ENST00000599957.1	-	2	358	c.161C>T	c.(160-162)gCc>gTc	p.A54V	LRRC4B_ENST00000389201.3_Missense_Mutation_p.A54V			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	54	LRRNT.				positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		GCAGGAGGTGGCCGGCGGGGA	0.716																																					p.A54V		Atlas-SNP	.											.	LRRC4B	89	.	0			c.C161T						PASS	.						5.0	7.0	6.0					19																	51051935		1891	4047	5938	SO:0001583	missense	94030	exon2			GAGGTGGCCGGCG	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"""Immunoglobulin superfamily / I-set domain containing"", ""Endogenous ligands"""	25042	protein-coding gene	gene with protein product	"""netrin-G3 ligand"""		"""leucine-rich repeats and immunoglobulin-like domains 4"""	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.161C>T	19.37:g.51051935G>A	ENSP00000471502:p.Ala54Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_001080457	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	37	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.724144	0.68959	.	.	ENSG00000131409	ENST00000389201;ENST00000535879	T	0.44083	0.93	3.66	2.57	0.30868	.	0.000000	0.56097	U	0.000023	T	0.35393	0.0930	M	0.68317	2.08	0.40088	D	0.976213	B	0.29432	0.244	B	0.18871	0.023	T	0.19224	-1.0312	10	0.33940	T	0.23	.	8.9339	0.35688	0.0:0.229:0.771:0.0	.	54	Q9NT99	LRC4B_HUMAN	V	54	ENSP00000373853:A54V	ENSP00000373853:A54V	A	-	2	0	LRRC4B	55743747	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.242000	0.58714	0.830000	0.34757	0.544000	0.68410	GCC	.	.	none		0.716	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457	
ATP13A5	344905	hgsc.bcm.edu	37	3	193052769	193052769	+	Nonsense_Mutation	SNP	G	G	A	rs74437357	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:193052769G>A	ENST00000342358.4	-	10	1180	c.1063C>T	c.(1063-1065)Cag>Tag	p.Q355*		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	355						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GGCTTGACCTGGATAACTTCT	0.458													g|||	48	0.00958466	0.0008	0.0072	5008	,	,		18680	0.0		0.0328	False		,,,				2504	0.0092				p.Q355X		Atlas-SNP	.											.	ATP13A5	171	.	0			c.C1063T						PASS	.	G	stop/GLN	24,4382	32.6+/-62.9	0,24,2179	130.0	128.0	129.0		1063	5.9	1.0	3	dbSNP_131	129	256,8344	99.5+/-161.0	5,246,4049	yes	stop-gained	ATP13A5	NM_198505.2		5,270,6228	AA,AG,GG		2.9767,0.5447,2.1529		355/1219	193052769	280,12726	2203	4300	6503	SO:0001587	stop_gained	344905	exon10			TGACCTGGATAAC	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.1063C>T	3.37:g.193052769G>A	ENSP00000341942:p.Gln355*	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_198505	Q6UWS4|Q6ZWL0	Nonsense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	31	0.014194139194139194	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	27	0.03562005277044855	g	39	7.502010	0.98322	0.005447	0.029767	ENSG00000187527	ENST00000342358	.	.	.	5.87	5.87	0.94306	.	0.423339	0.22770	N	0.055850	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-2.2837	18.7725	0.91898	0.0:0.0:1.0:0.0	.	.	.	.	X	355	.	ENSP00000341942:Q355X	Q	-	1	0	ATP13A5	194535463	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	9.518000	0.98022	2.791000	0.96007	0.655000	0.94253	CAG	G|0.979;A|0.021	0.021	strong		0.458	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
ANKDD1A	348094	hgsc.bcm.edu	37	15	65235776	65235776	+	Missense_Mutation	SNP	A	A	G	rs34988193	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65235776A>G	ENST00000380230.3	+	11	1092	c.1063A>G	c.(1063-1065)Aag>Gag	p.K355E	ANKDD1A_ENST00000395723.1_Missense_Mutation_p.K264E|ANKDD1A_ENST00000357698.3_Missense_Mutation_p.K355E|ANKDD1A_ENST00000395720.1_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	183	0	0		WXS	Illumina HiSeq	Phase_I	102	69	0.676471	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	
DSG1	1828	hgsc.bcm.edu	37	18	28919763	28919763	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:28919763A>C	ENST00000257192.4	+	11	1674	c.1462A>C	c.(1462-1464)Aat>Cat	p.N488H		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	488	Cadherin 4. {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)			AAGTTTTGGTAATGACGACAG	0.328																																					p.N488H		Atlas-SNP	.											DSG1,NS,carcinoma,-2,1	DSG1	176	1	0			c.A1462C						PASS	.						80.0	81.0	81.0					18																	28919763		2203	4300	6503	SO:0001583	missense	1828	exon11			TTTGGTAATGACG	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.1462A>C	18.37:g.28919763A>C	ENSP00000257192:p.Asn488His	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	138	52	0.376812	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	A	4.359	0.066056	0.08388	.	.	ENSG00000134760	ENST00000257192	T	0.58210	0.35	3.05	-5.83	0.02325	Cadherin (2);	3.162780	0.00531	N	0.000201	T	0.32675	0.0837	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.16689	-1.0394	10	0.72032	D	0.01	.	0.9696	0.01413	0.2735:0.1294:0.3832:0.2139	.	488	Q02413	DSG1_HUMAN	H	488	ENSP00000257192:N488H	ENSP00000257192:N488H	N	+	1	0	DSG1	27173761	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.215000	0.09279	-0.831000	0.04256	-0.574000	0.04147	AAT	.	.	none		0.328	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
FAM200A	221786	hgsc.bcm.edu	37	7	99145845	99145845	+	Silent	SNP	C	C	T	rs10238965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99145845C>T	ENST00000449309.1	-	2	565	c.186G>A	c.(184-186)ttG>ttA	p.L62L		NM_145111.3	NP_659802.1	Q8TCP9	F200A_HUMAN	family with sequence similarity 200, member A	62						integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			endometrium(1)|kidney(5)|large_intestine(2)|ovary(2)|skin(1)	11						aatacgatgacaataaggctc	0.403													T|||	2314	0.462061	0.9342	0.2853	5008	,	,		22164	0.3353		0.165	False		,,,				2504	0.3855				p.L62L		Atlas-SNP	.											.	FAM200A	27	.	0			c.G186A						PASS	.	T		3473,929		1369,735,97	117.0	111.0	113.0		186	-4.1	0.0	7	dbSNP_119	113	1235,7361		102,1031,3165	no	coding-synonymous	FAM200A	NM_145111.3		1471,1766,3262	TT,TC,CC		14.3671,21.104,36.221		62/574	99145845	4708,8290	2201	4298	6499	SO:0001819	synonymous_variant	221786	exon2			CGATGACAATAAG		CCDS5668.1	7q22.1	2010-02-22	2010-02-22	2010-02-22	ENSG00000221909	ENSG00000221909			25401	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 38"""	C7orf38		10607616	Standard	NM_145111		Approved	FLJ36794, DKFZp727G131	uc003ura.3	Q8TCP9	OTTHUMG00000156723	ENST00000449309.1:c.186G>A	7.37:g.99145845C>T		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	384	135	0.351562	NM_145111	A4D293|A8K3V9|B2RD92|C9J6A8|D6W5T2|Q8N9P3	Silent	SNP	ENST00000449309.1	37	CCDS5668.1																																																																																			C|0.566;T|0.434	0.434	strong		0.403	FAM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345467.1	NM_145111	
HSD17B13	345275	hgsc.bcm.edu	37	4	88231429	88231429	+	Missense_Mutation	SNP	G	G	A	rs62305723	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	365	1	0.00273973		WXS	Illumina HiSeq	Phase_I	265	130	0.490566	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	
PRDM5	11107	hgsc.bcm.edu	37	4	121737704	121737704	+	Missense_Mutation	SNP	G	G	A	rs190835070		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:121737704G>A	ENST00000264808.3	-	7	1009	c.769C>T	c.(769-771)Cgg>Tgg	p.R257W	PRDM5_ENST00000515109.1_Missense_Mutation_p.R226W|PRDM5_ENST00000428209.2_Missense_Mutation_p.R226W	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	257					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						GCATCCCCCCGGCAAGTCTCC	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		18108	0.0		0.001	False		,,,				2504	0.0				p.R257W		Atlas-SNP	.											PRDM5,NS,carcinoma,+1,1	PRDM5	76	1	0			c.C769T						scavenged	.	G	TRP/ARG	0,4406		0,0,2203	55.0	51.0	52.0		769	4.2	0.9	4		52	2,8598	2.2+/-6.3	0,2,4298	no	missense	PRDM5	NM_018699.2	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	257/631	121737704	2,13004	2203	4300	6503	SO:0001583	missense	11107	exon7			CCCCCCGGCAAGT	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.769C>T	4.37:g.121737704G>A	ENSP00000264808:p.Arg257Trp	Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	78	24	0.307692	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Missense_Mutation	SNP	ENST00000264808.3	37	CCDS3716.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	23.5	4.419624	0.83559	0.0	2.33E-4	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	T;T;T	0.15372	2.43;2.43;2.43	6.07	4.24	0.50183	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.270689	0.41396	D	0.000900	T	0.29321	0.0730	L	0.48362	1.52	0.80722	D	1	D;D;D	0.76494	0.978;0.999;0.978	B;P;B	0.56916	0.425;0.809;0.306	T	0.04635	-1.0937	10	0.87932	D	0	-1.8067	14.4681	0.67497	0.0:0.0:0.5912:0.4088	.	226;226;257	Q0VAI9;Q9NQX1-2;Q9NQX1	.;.;PRDM5_HUMAN	W	257;226;226	ENSP00000264808:R257W;ENSP00000422309:R226W;ENSP00000404832:R226W	ENSP00000264808:R257W	R	-	1	2	PRDM5	121957154	1.000000	0.71417	0.861000	0.33841	0.998000	0.95712	3.119000	0.50422	1.546000	0.49388	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	strong		0.493	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
MYH14	79784	hgsc.bcm.edu	37	19	50760716	50760716	+	Silent	SNP	C	C	G	rs378811	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50760716C>G	ENST00000596571.1	+	15	2082	c.2082C>G	c.(2080-2082)cgC>cgG	p.R694R	MYH14_ENST00000598205.1_Silent_p.R702R|MYH14_ENST00000262269.8_Silent_p.R735R|MYH14_ENST00000425460.1_Silent_p.R702R|MYH14_ENST00000376970.2_Silent_p.R727R|MYH14_ENST00000440075.2_Silent_p.R735R|MYH14_ENST00000601313.1_Silent_p.R735R			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	694	Myosin motor.				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)		GTTTTGTCCGCTGCATTGTCC	0.612													C|||	1792	0.357827	0.3374	0.3026	5008	,	,		19529	0.374		0.4026	False		,,,				2504	0.362				p.R735R		Atlas-SNP	.											MYH14_ENST00000262269,NS,carcinoma,0,4	MYH14	261	4	0			c.C2205G						PASS	.	C	,,	1336,2946		217,902,1022	31.0	34.0	33.0		2106,2205,2082	4.5	1.0	19	dbSNP_80	33	3603,4903		771,2061,1421	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	988,2963,2443	GG,GC,CC		42.3583,31.2004,38.6221	,,	702/2004,735/2037,694/1996	50760716	4939,7849	2141	4253	6394	SO:0001819	synonymous_variant	79784	exon18			TGTCCGCTGCATT	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.2082C>G	19.37:g.50760716C>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.617;G|0.383	0.383	strong		0.612	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
CLEC3A	10143	hgsc.bcm.edu	37	16	78064733	78064733	+	Missense_Mutation	SNP	C	C	A	rs2072663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:78064733C>A	ENST00000575655.1	+	3	670	c.589C>A	c.(589-591)Caa>Aaa	p.Q197K	CLEC3A_ENST00000565808.1_3'UTR|CLEC3A_ENST00000299642.4_Missense_Mutation_p.Q206K|RP11-281J9.2_ENST00000563114.1_RNA	NM_005752.4	NP_005743.4	O75596	CLC3A_HUMAN	C-type lectin domain family 3, member A	197			Q -> K (in dbSNP:rs2072663). {ECO:0000269|PubMed:12975309}.		skeletal system development (GO:0001501)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	18						CACCATCCCTCAATAGGTCTT	0.413													C|||	658	0.13139	0.0719	0.1441	5008	,	,		20795	0.245		0.1223	False		,,,				2504	0.0951				p.Q206K		Atlas-SNP	.											.	CLEC3A	39	.	0			c.C616A						PASS	.	C	LYS/GLN	363,4033	170.1+/-200.6	15,333,1850	67.0	69.0	69.0		589	3.8	0.3	16	dbSNP_96	69	1147,7451	227.5+/-262.8	82,983,3234	yes	missense	CLEC3A	NM_005752.4	53	97,1316,5084	AA,AC,CC		13.3403,8.2575,11.6207	benign	197/198	78064733	1510,11484	2198	4299	6497	SO:0001583	missense	10143	exon3			ATCCCTCAATAGG	AF077345	CCDS10927.1, CCDS10927.2	16q23	2008-02-05	2005-02-09	2005-02-11	ENSG00000166509	ENSG00000166509		"""C-type lectin domain containing"""	2052	protein-coding gene	gene with protein product		613588	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 1 (cartilage-derived)"""	CLECSF1		10524194	Standard	NM_001244755		Approved		uc002ffh.5	O75596	OTTHUMG00000137620	ENST00000575655.1:c.589C>A	16.37:g.78064733C>A	ENSP00000460682:p.Gln197Lys	Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	97	84	0.865979	NM_005752	B2R8C4|Q3SX91|Q6UXF5	Missense_Mutation	SNP	ENST00000575655.1	37		329	0.15064102564102563	49	0.09959349593495935	45	0.12430939226519337	143	0.25	92	0.12137203166226913	C	10.14	1.268501	0.23136	0.082575	0.133403	ENSG00000166509	ENST00000299642	.	.	.	6.07	3.85	0.44370	.	21.172100	0.01519	N	0.018298	T	0.00012	0.0000	N	0.08118	0	0.50813	P	1.020000000000465E-4	B	0.06786	0.001	B	0.01281	0.0	T	0.21109	-1.0255	8	0.21540	T	0.41	.	10.2292	0.43245	0.0:0.1348:0.0:0.8652	rs2072663;rs2234867;rs60748914;rs2072663	197	O75596	CLC3A_HUMAN	K	197	.	ENSP00000299642:Q197K	Q	+	1	0	CLEC3A	76622234	0.904000	0.30761	0.264000	0.24511	0.032000	0.12392	3.057000	0.49931	0.547000	0.28938	-0.238000	0.12139	CAA	C|0.867;A|0.133	0.133	strong		0.413	CLEC3A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005752	
OSBPL1A	114876	hgsc.bcm.edu	37	18	21739725	21739725	+	IGR	SNP	T	T	C	rs1049684	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:21739725T>C	ENST00000319481.3	-	0	4195				CABYR_ENST00000399496.3_Silent_p.P277P|CABYR_ENST00000399499.1_Silent_p.P277P|CABYR_ENST00000581397.1_Silent_p.P277P|RP11-799B12.4_ENST00000583267.1_lincRNA|CABYR_ENST00000415309.2_Intron|CABYR_ENST00000327201.6_Silent_p.P179P	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	119	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	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	
OR51F2	119694	hgsc.bcm.edu	37	11	4843164	4843164	+	Silent	SNP	C	C	T	rs113211514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4843164C>T	ENST00000322110.5	+	1	614	c.549C>T	c.(547-549)tgC>tgT	p.C183C	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2	183						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(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGTCCTTCTGCAGTTCTATGG	0.453													C|||	82	0.0163738	0.0008	0.0403	5008	,	,		25828	0.0		0.0527	False		,,,				2504	0.0				p.C183C		Atlas-SNP	.											.	OR51F2	72	.	0			c.C549T						PASS	.	C		38,4364	42.3+/-75.8	1,36,2164	303.0	267.0	279.0		549	2.7	0.7	11	dbSNP_132	279	350,8246	118.8+/-178.2	10,330,3958	no	coding-synonymous	OR51F2	NM_001004753.1		11,366,6122	TT,TC,CC		4.0717,0.8632,2.9851		183/343	4843164	388,12610	2201	4298	6499	SO:0001819	synonymous_variant	119694	exon1			CTTCTGCAGTTCT	BK004281	CCDS31361.1	11p15.4	2012-08-09			ENSG00000176925	ENSG00000176925		"""GPCR / Class A : Olfactory receptors"""	15197	protein-coding gene	gene with protein product							Standard	NM_001004753		Approved		uc010qyn.2	Q8NH61	OTTHUMG00000066508	ENST00000322110.5:c.549C>T	11.37:g.4843164C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	NM_001004753	Q6IFI1	Silent	SNP	ENST00000322110.5	37	CCDS31361.1																																																																																			C|0.971;T|0.029	0.029	strong		0.453	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753	
RNF151	146310	hgsc.bcm.edu	37	16	2018912	2018912	+	Missense_Mutation	SNP	A	A	G	rs62617079	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2018912A>G	ENST00000569714.1	+	4	732	c.724A>G	c.(724-726)Ata>Gta	p.I242V	RNF151_ENST00000569210.2_3'UTR|RNF151_ENST00000321392.3_Missense_Mutation_p.I241V	NM_174903.4	NP_777563.2	Q2KHN1	RN151_HUMAN	ring finger protein 151	242					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2						CAGGGCCAACATACCTTGTAA	0.637													G|||	194	0.038738	0.0991	0.0187	5008	,	,		15844	0.0		0.0149	False		,,,				2504	0.0358				p.I242V		Atlas-SNP	.											.	RNF151	12	.	0			c.A724G						PASS	.	G	VAL/ILE	323,3613		10,303,1655	9.0	13.0	12.0		724	-0.8	0.0	16	dbSNP_129	12	185,8081		2,181,3950	yes	missense	RNF151	NM_174903.4	29	12,484,5605	GG,GA,AA		2.2381,8.2063,4.1633	benign	242/246	2018912	508,11694	1968	4133	6101	SO:0001583	missense	146310	exon4			GCCAACATACCTT	BC029501	CCDS58405.1	16p13.3	2013-01-09			ENSG00000179580	ENSG00000179580		"""RING-type (C3HC4) zinc fingers"""	23235	protein-coding gene	gene with protein product						12477932	Standard	NM_174903		Approved		uc002cnt.1	Q2KHN1	OTTHUMG00000176852	ENST00000569714.1:c.724A>G	16.37:g.2018912A>G	ENSP00000456566:p.Ile242Val	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_174903	Q8NHS5	Missense_Mutation	SNP	ENST00000569714.1	37	CCDS58405.1	72	0.03296703296703297	56	0.11382113821138211	5	0.013812154696132596	0	0.0	11	0.014511873350923483	N	0.013	-1.609973	0.00842	0.082063	0.022381	ENSG00000179580	ENST00000321392	D	0.84516	-1.86	3.61	-0.751	0.11076	.	.	.	.	.	T	0.02230	0.0069	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23154	-1.0196	8	0.02654	T	1	4.8474	4.768	0.13141	0.2615:0.3335:0.405:0.0	rs62617079	242	Q2KHN1	RN151_HUMAN	V	241	ENSP00000325794:I241V	ENSP00000325794:I241V	I	+	1	0	RNF151	1958913	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	-0.301000	0.08232	-0.339000	0.08401	-0.166000	0.13349	ATA	A|0.963;G|0.037	0.037	strong		0.637	RNF151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434030.1	NM_174903	
GAS8	2622	hgsc.bcm.edu	37	16	90103659	90103659	+	Missense_Mutation	SNP	G	G	A	rs17178299	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:90103659G>A	ENST00000268699.4	+	7	898	c.776G>A	c.(775-777)cGg>cAg	p.R259Q	GAS8_ENST00000540721.1_3'UTR|GAS8_ENST00000536122.1_Missense_Mutation_p.R234Q	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	259			R -> Q (in dbSNP:rs17178299).		cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		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;0.029)		GAGGACATGCGGAAGAAGGAG	0.637													G|||	240	0.0479233	0.0038	0.013	5008	,	,		21050	0.1488		0.0507	False		,,,				2504	0.0256				p.R259Q		Atlas-SNP	.											.	GAS8	29	.	0			c.G776A						PASS	.	G	GLN/ARG	50,4346	50.2+/-85.5	0,50,2148	58.0	56.0	57.0		776	4.4	1.0	16	dbSNP_123	57	516,8084	144.7+/-200.5	15,486,3799	yes	missense	GAS8	NM_001481.2	43	15,536,5947	AA,AG,GG		6.0,1.1374,4.3552	possibly-damaging	259/479	90103659	566,12430	2198	4300	6498	SO:0001583	missense	2622	exon7			ACATGCGGAAGAA	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.776G>A	16.37:g.90103659G>A	ENSP00000268699:p.Arg259Gln	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	234	30	0.128205	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	100	0.045787545787545784	3	0.006097560975609756	7	0.019337016574585635	47	0.08216783216783216	43	0.05672823218997362	G	19.36	3.812005	0.70797	0.011374	0.06	ENSG00000141013	ENST00000536122;ENST00000268699;ENST00000540721	T;T	0.46451	0.87;0.87	5.49	4.44	0.53790	.	0.258952	0.37955	N	0.001866	T	0.01558	0.0050	L	0.45352	1.415	0.22918	P	0.99856096	P;P	0.46656	0.882;0.774	B;B	0.40228	0.323;0.126	T	0.15321	-1.0441	8	.	.	.	-37.1049	3.5798	0.07947	0.3568:0.0:0.6432:0.0	rs17178299;rs17178299	230;259	B7Z1X3;O95995	.;GAS8_HUMAN	Q	234;259;230	ENSP00000440977:R234Q;ENSP00000268699:R259Q	.	R	+	2	0	GAS8	88631160	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.732000	0.68563	2.578000	0.87016	0.563000	0.77884	CGG	G|0.958;A|0.042	0.042	strong		0.637	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
CARNS1	57571	hgsc.bcm.edu	37	11	67191346	67191346	+	Silent	SNP	C	C	T	rs3741180	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:67191346C>T	ENST00000307823.3	+	9	2210	c.1758C>T	c.(1756-1758)gcC>gcT	p.A586A	CARNS1_ENST00000531040.1_Silent_p.A683A|CARNS1_ENST00000423745.2_Silent_p.A586A|CARNS1_ENST00000445895.2_Silent_p.A709A	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	586	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						AGGGCGAGGCCGACCACCCAG	0.632													C|||	61	0.0121805	0.0015	0.0086	5008	,	,		20290	0.0308		0.0169	False		,,,				2504	0.0051				p.A709A		Atlas-SNP	.											.	CARNS1	60	.	0			c.C2127T						PASS	.	C	,	26,4250		0,26,2112	82.0	92.0	88.0		2127,1758	-10.1	0.6	11	dbSNP_107	88	212,8250		5,202,4024	no	coding-synonymous,coding-synonymous	CARNS1	NM_001166222.1,NM_020811.1	,	5,228,6136	TT,TC,CC		2.5053,0.608,1.8684	,	709/951,586/828	67191346	238,12500	2138	4231	6369	SO:0001819	synonymous_variant	57571	exon10			CGAGGCCGACCAC		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.1758C>T	11.37:g.67191346C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Silent	SNP	ENST00000307823.3	37	CCDS44658.1																																																																																			C|0.981;T|0.019	0.019	strong		0.632	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110447512	110447512	+	Missense_Mutation	SNP	G	G	C	rs142972518	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:110447512G>C	ENST00000378402.5	+	29	3538	c.3434G>C	c.(3433-3435)gGg>gCg	p.G1145A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1145	IPT/TIG 4.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CAGAATGTAGGGGGTGAAGAG	0.443										HNSCC(38;0.096)			G|||	58	0.0115815	0.0015	0.0101	5008	,	,		18338	0.0		0.0268	False		,,,				2504	0.0225				p.G1145A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3434C						PASS	.	G	ALA/GLY	15,3743		0,15,1864	197.0	197.0	197.0		3434	-2.3	0.0	8	dbSNP_134	197	167,8083		3,161,3961	yes	missense	PKHD1L1	NM_177531.4	60	3,176,5825	CC,CG,GG		2.0242,0.3991,1.5157	benign	1145/4244	110447512	182,11826	1879	4125	6004	SO:0001583	missense	93035	exon29			ATGTAGGGGGTGA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.3434G>C	8.37:g.110447512G>C	ENSP00000367655:p.Gly1145Ala	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	251	97	0.386454	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	27	0.012362637362637362	0	0.0	5	0.013812154696132596	0	0.0	22	0.029023746701846966	G	2.585	-0.296544	0.05532	0.003991	0.020242	ENSG00000205038	ENST00000378402	D	0.85702	-2.02	6.07	-2.3	0.06785	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.912531	0.09435	N	0.802529	T	0.53142	0.1778	L	0.34521	1.04	0.09310	N	1	B	0.16396	0.017	B	0.21360	0.034	T	0.50074	-0.8870	10	0.12103	T	0.63	.	12.0147	0.53307	0.3405:0.0:0.6595:0.0	.	1145	Q86WI1	PKHL1_HUMAN	A	1145	ENSP00000367655:G1145A	ENSP00000367655:G1145A	G	+	2	0	PKHD1L1	110516688	0.005000	0.15991	0.000000	0.03702	0.004000	0.04260	0.643000	0.24750	-0.303000	0.08856	-0.768000	0.03414	GGG	G|0.986;C|0.014	0.014	strong		0.443	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
NLRP10	338322	hgsc.bcm.edu	37	11	7981822	7981822	+	Missense_Mutation	SNP	A	A	G	rs143403695	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:7981822A>G	ENST00000328600.2	-	2	1498	c.1337T>C	c.(1336-1338)tTc>tCc	p.F446S		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	446	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)		ACTACTCAGGAAAGCGGCAAG	0.488																																					p.F446S		Atlas-SNP	.											.	NLRP10	146	.	0			c.T1337C						PASS	.	A	SER/PHE	1,4401		0,1,2200	99.0	109.0	106.0		1337	3.7	0.2	11	dbSNP_134	106	1,8591		0,1,4295	yes	missense	NLRP10	NM_176821.3	155	0,2,6495	GG,GA,AA		0.0116,0.0227,0.0154	possibly-damaging	446/656	7981822	2,12992	2201	4296	6497	SO:0001583	missense	338322	exon2			CTCAGGAAAGCGG	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.1337T>C	11.37:g.7981822A>G	ENSP00000327763:p.Phe446Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	53	34	0.641509	NM_176821	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	37	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	A	10.78	1.446070	0.25987	2.27E-4	1.16E-4	ENSG00000182261	ENST00000328600	D	0.87103	-2.21	4.86	3.73	0.42828	.	0.000000	0.42548	D	0.000691	D	0.92205	0.7528	M	0.83012	2.62	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	D	0.84554	0.0646	10	0.87932	D	0	.	7.3185	0.26513	0.8987:0.0:0.1013:0.0	.	446	Q86W26	NAL10_HUMAN	S	446	ENSP00000327763:F446S	ENSP00000327763:F446S	F	-	2	0	NLRP10	7938398	0.997000	0.39634	0.178000	0.23040	0.011000	0.07611	6.425000	0.73370	0.828000	0.34709	0.533000	0.62120	TTC	A|0.999;G|0.001	0.001	strong		0.488	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821	
ANO7	50636	hgsc.bcm.edu	37	2	242157241	242157241	+	Missense_Mutation	SNP	G	G	A	rs76832527	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242157241G>A	ENST00000274979.8	+	20	2378	c.2275G>A	c.(2275-2277)Gcc>Acc	p.A759T	ANO7_ENST00000402430.3_Missense_Mutation_p.A758T	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	759					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						GGCCGAGCGCGCCCAGGACAT	0.721													g|||	555	0.110823	0.0174	0.1758	5008	,	,		7845	0.1131		0.172	False		,,,				2504	0.1258				p.A759T		Atlas-SNP	.											ANO7,colon,carcinoma,-2,1	ANO7	136	1	0			c.G2275A						scavenged	.		THR/ALA	215,4153		9,197,1978	16.0	17.0	17.0		2275	2.8	1.0	2	dbSNP_131	17	1483,7097		131,1221,2938	yes	missense	ANO7	NM_001001891.3	58	140,1418,4916	AA,AG,GG		17.2844,4.9222,13.114	possibly-damaging	759/934	242157241	1698,11250	2184	4290	6474	SO:0001583	missense	50636	exon20			GAGCGCGCCCAGG	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.2275G>A	2.37:g.242157241G>A	ENSP00000274979:p.Ala759Thr	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_001001891	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	255|255	0.11675824175824176|0.11675824175824176	10|10	0.02032520325203252|0.02032520325203252	68|68	0.1878453038674033|0.1878453038674033	61|61	0.10664335664335664|0.10664335664335664	116|116	0.15303430079155672|0.15303430079155672	g|g	22.8|22.8	4.333562|4.333562	0.81801|0.81801	0.049222|0.049222	0.172844|0.172844	ENSG00000146205|ENSG00000146205	ENST00000274979;ENST00000402430|ENST00000451047	T;T|T	0.67171|0.69806	-0.25;-0.25|-0.43	2.84|2.84	2.84|2.84	0.33178|0.33178	.|.	0.152058|.	0.42821|.	N|.	0.000643|.	T|T	0.00241|0.00241	0.0007|0.0007	L|L	0.52011|0.52011	1.625|1.625	0.21499|0.21499	P|P	0.9996691|0.9996691	P|.	0.41673|.	0.759|.	B|.	0.38378|.	0.272|.	T|T	0.26087|0.26087	-1.0113|-1.0113	9|6	0.56958|0.87932	D|D	0.05|0	.|.	13.5641|13.5641	0.61807|0.61807	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	759|.	Q6IWH7|.	ANO7_HUMAN|.	T|H	759;758|71	ENSP00000274979:A759T;ENSP00000385418:A758T|ENSP00000403625:R71H	ENSP00000274979:A759T|ENSP00000403625:R71H	A|R	+|+	1|2	0|0	ANO7|ANO7	241805914|241805914	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	8.276000|8.276000	0.89894|0.89894	1.305000|1.305000	0.44909|0.44909	0.298000|0.298000	0.19748|0.19748	GCC|CGC	G|0.874;A|0.126	0.126	strong		0.721	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
BCL9L	283149	hgsc.bcm.edu	37	11	118772413	118772413	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118772413C>T	ENST00000334801.3	-	6	3003	c.2039G>A	c.(2038-2040)cGg>cAg	p.R680Q	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	680					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		CAGCTGGTGCCGCAGCAGCTC	0.652																																					p.R680Q		Atlas-SNP	.											BCL9L_ENST00000392849,colon,carcinoma,-1,3	BCL9L	254	3	0			c.G2039A						scavenged	.						36.0	36.0	36.0					11																	118772413		2199	4295	6494	SO:0001583	missense	283149	exon6			TGGTGCCGCAGCA	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.2039G>A	11.37:g.118772413C>T	ENSP00000335320:p.Arg680Gln	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	197	2	0.0101523	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.555908	0.65425	.	.	ENSG00000186174	ENST00000334801;ENST00000526143;ENST00000392849;ENST00000431085	T	0.63744	-0.06	4.67	4.67	0.58626	.	0.000000	0.40640	N	0.001044	T	0.66809	0.2827	L	0.31664	0.95	0.50171	D	0.999857	D;D	0.89917	1.0;0.999	D;P	0.66847	0.947;0.886	T	0.61113	-0.7128	10	0.17369	T	0.5	-21.2041	17.3498	0.87320	0.0:1.0:0.0:0.0	.	675;680	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	Q	680;643;680;680	ENSP00000335320:R680Q	ENSP00000335320:R680Q	R	-	2	0	BCL9L	118277623	1.000000	0.71417	1.000000	0.80357	0.802000	0.45316	4.470000	0.60175	2.419000	0.82065	0.313000	0.20887	CGG	.	.	none		0.652	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
ZNF568	374900	hgsc.bcm.edu	37	19	37487975	37487975	+	Missense_Mutation	SNP	G	G	A	rs16971886	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:37487975G>A	ENST00000455427.2	+	9	1519	c.1190G>A	c.(1189-1191)cGt>cAt	p.R397H		NM_001204839.1	NP_001191768.1	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	428					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAGGCTTTTCGTTATGACACA	0.468													G|||	1381	0.275759	0.2905	0.379	5008	,	,		23245	0.0942		0.3608	False		,,,				2504	0.2822				p.R461H		Atlas-SNP	.											ZNF568_ENST00000455427,NS,carcinoma,0,1	ZNF568	106	1	0			c.G1382A						scavenged	.																																			SO:0001583	missense	374900	exon10			CTTTTCGTTATGA	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000455427.2:c.1190G>A	19.37:g.37487975G>A	ENSP00000413396:p.Arg397His	Somatic	5	1	0.2		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_001204838	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000455427.2	37	CCDS56093.1	601	0.2751831501831502	143	0.29065040650406504	123	0.3397790055248619	47	0.08216783216783216	288	0.37994722955145116	G	15.42	2.827593	0.50845	.	.	ENSG00000198453	ENST00000444991;ENST00000455427;ENST00000433993	T;T;T	0.08102	3.13;3.13;3.13	3.74	0.101	0.14517	.	.	.	.	.	T	0.00012	0.0000	L	0.28694	0.88	0.80722	P	0.0	D;D	0.54207	0.965;0.965	P;P	0.49561	0.615;0.615	T	0.47799	-0.9089	8	0.33940	T	0.23	.	2.1824	0.03878	0.1023:0.1688:0.3836:0.3453	rs16971886;rs52819337;rs16971886	397;397	E7ER33;B4DS92	.;.	H	461;397;329	ENSP00000389794:R461H;ENSP00000413396:R397H;ENSP00000399643:R329H	ENSP00000399643:R329H	R	+	2	0	ZNF568	42179815	0.000000	0.05858	0.000000	0.03702	0.993000	0.82548	-4.985000	0.00163	0.027000	0.15297	0.597000	0.82753	CGT	G|0.732;A|0.267	0.267	strong		0.468	ZNF568-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000457465.1	NM_198539	
SSPO	23145	hgsc.bcm.edu	37	7	149523277	149523277	+	RNA	SNP	A	A	G	rs1004200	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149523277A>G	ENST00000378016.2	+	0	14363							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)			ATGGAGCGACATCGGACTTGT	0.652													A|||	2248	0.448882	0.7027	0.3732	5008	,	,		19271	0.4286		0.3052	False		,,,				2504	0.3282				p.H4787R		Atlas-SNP	.											.	.	.	.	0			c.A14360G						PASS	.	A	ARG/HIS	2525,1401		843,839,281	37.0	46.0	43.0		14379	1.6	0.0	7	dbSNP_86	43	2714,5562		449,1816,1873	no	missense	SSPO	NM_198455.2	29	1292,2655,2154	GG,GA,AA		32.7936,35.6852,42.9356	benign	4787/5148	149523277	5239,6963	1963	4138	6101			23145	exon101			AGCGACATCGGAC	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.149523277A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	32	6	0.1875	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				A|0.586;G|0.414	0.414	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
GSDMD	79792	hgsc.bcm.edu	37	8	144642854	144642854	+	Silent	SNP	G	G	A	rs11551202	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144642854G>A	ENST00000526406.1	+	7	1375	c.492G>A	c.(490-492)ctG>ctA	p.L164L	GSDMD_ENST00000262580.4_Silent_p.L164L|GSDMD_ENST00000533063.1_Silent_p.L212L	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	191	0	0		WXS	Illumina HiSeq	Phase_I	251	77	0.306773	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	
BPIFA1	51297	hgsc.bcm.edu	37	20	31825568	31825568	+	Silent	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:31825568C>A	ENST00000354297.4	+	2	122	c.51C>A	c.(49-51)acC>acA	p.T17T	BPIFA1_ENST00000375413.4_Silent_p.T17T|BPIFA1_ENST00000375422.2_Silent_p.T17T	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	17					antibacterial humoral response (GO:0019731)|innate immune response (GO:0045087)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|regulation of liquid surface tension (GO:0050828)|regulation of sodium ion transmembrane transport (GO:1902305)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	lipid binding (GO:0008289)										TAGCCCAGACCATGGCCCAGT	0.562																																					p.T17T		Atlas-SNP	.											PLUNC,NS,carcinoma,+1,1	.	.	1	0			c.C51A						scavenged	.						84.0	82.0	82.0					20																	31825568		2203	4300	6503	SO:0001819	synonymous_variant	51297	exon2			CCAGACCATGGCC	AB024937	CCDS13217.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000198183	ENSG00000198183		"""BPI fold containing"""	15749	protein-coding gene	gene with protein product		607412	"""palate, lung and nasal epithelium carcinoma associated"", ""palate, lung and nasal epithelium associated"""	PLUNC		11018263, 11251963, 21787333	Standard	NM_130852		Approved	LUNX, bA49G10.5, SPLUNC1	uc002wyv.3	Q9NP55	OTTHUMG00000032243	ENST00000354297.4:c.51C>A	20.37:g.31825568C>A		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	107	3	0.0280374	NM_016583	A8K9R3|E1P5M9|Q9NZT0	Silent	SNP	ENST00000354297.4	37	CCDS13217.1																																																																																			.	.	none		0.562	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852	
FLG	2312	hgsc.bcm.edu	37	1	152276377	152276377	+	Missense_Mutation	SNP	C	C	G	rs139284720	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152276377C>G	ENST00000368799.1	-	3	11020	c.10985G>C	c.(10984-10986)aGt>aCt	p.S3662T	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3662	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S3662T(2)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACTGGCCTGACTACCACTGGA	0.587									Ichthyosis																												p.S3662T		Atlas-SNP	.											FLG,extremity,malignant_melanoma,0,2	FLG	900	2	2	Substitution - Missense(2)	skin(2)	c.G10985C						scavenged	.						34.0	36.0	35.0					1																	152276377		2199	4266	6465	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCCTGACTACCAC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10985G>C	1.37:g.152276377C>G	ENSP00000357789:p.Ser3662Thr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	272	45	0.165441	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.330609	0.24167	.	.	ENSG00000143631	ENST00000368799	T	0.20598	2.06	4.62	-2.36	0.06663	.	.	.	.	.	T	0.14874	0.0359	M	0.69823	2.125	0.09310	N	1	P	0.40211	0.707	P	0.54889	0.763	T	0.26883	-1.0090	9	0.25751	T	0.34	.	3.5688	0.07909	0.4266:0.3171:0.0:0.2564	.	3662	P20930	FILA_HUMAN	T	3662	ENSP00000357789:S3662T	ENSP00000357789:S3662T	S	-	2	0	FLG	150543001	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.742000	0.04850	-0.547000	0.06207	-0.240000	0.12126	AGT	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
IGSF10	285313	hgsc.bcm.edu	37	3	151171542	151171542	+	Silent	SNP	A	A	G	rs7621591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151171542A>G	ENST00000282466.3	-	3	344	c.345T>C	c.(343-345)aaT>aaC	p.N115N		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	115					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)			TTCGGACTTTATTATAGCTCA	0.323													G|||	4065	0.811701	0.8926	0.781	5008	,	,		15197	0.7649		0.7714	False		,,,				2504	0.8139				p.N115N		Atlas-SNP	.											.	IGSF10	279	.	0			c.T345C						PASS	.	G		3682,600		1589,504,48	72.0	80.0	77.0		345	1.7	1.0	3	dbSNP_116	77	6604,1968		2570,1464,252	no	coding-synonymous	IGSF10	NM_178822.4		4159,1968,300	GG,GA,AA		22.9585,14.0121,19.9782		115/2624	151171542	10286,2568	2141	4286	6427	SO:0001819	synonymous_variant	285313	exon3			GACTTTATTATAG	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.345T>C	3.37:g.151171542A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			A|0.195;G|0.805	0.805	strong		0.323	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777196	18777196	+	Missense_Mutation	SNP	A	A	C	rs41268983	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:18777196A>C	ENST00000380548.4	+	19	3308	c.2969A>C	c.(2968-2970)gAg>gCg	p.E990A		NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	990						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)		GGCCCGAAGGAGGCCCTGCAG	0.662													A|||	457	0.091254	0.0113	0.0749	5008	,	,		15776	0.122		0.1431	False		,,,				2504	0.1258				p.E990A		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.A2969C						PASS	.	A	ALA/GLU	143,3647		5,133,1757	24.0	28.0	27.0		2969	5.8	1.0	9	dbSNP_127	27	1265,6929		95,1075,2927	yes	missense	ADAMTSL1	NM_001040272.5	107	100,1208,4684	CC,CA,AA		15.4381,3.7731,11.749	benign	990/1763	18777196	1408,10576	1895	4097	5992	SO:0001583	missense	92949	exon19			CGAAGGAGGCCCT	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.2969A>C	9.37:g.18777196A>C	ENSP00000369921:p.Glu990Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_001040272	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	208	0.09523809523809523	7	0.014227642276422764	30	0.08287292817679558	60	0.1048951048951049	111	0.14643799472295516	A	12.05	1.821260	0.32237	0.037731	0.154381	ENSG00000178031	ENST00000380548	T	0.63417	-0.04	5.75	5.75	0.90469	.	2.098050	0.05591	N	0.574590	T	0.00440	0.0014	N	0.14661	0.345	0.09310	P	1.0	P	0.52316	0.952	P	0.46885	0.53	T	0.11817	-1.0572	9	0.18276	T	0.48	.	16.0488	0.80740	1.0:0.0:0.0:0.0	rs41268983	990	Q8N6G6	ATL1_HUMAN	A	990	ENSP00000369921:E990A	ENSP00000369921:E990A	E	+	2	0	ADAMTSL1	18767196	1.000000	0.71417	0.999000	0.59377	0.909000	0.53808	4.474000	0.60203	2.199000	0.70637	0.374000	0.22700	GAG	A|0.895;C|0.105	0.105	strong		0.662	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
DNHD1	144132	hgsc.bcm.edu	37	11	6585838	6585838	+	Silent	SNP	G	G	A	rs11825255	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6585838G>A	ENST00000527990.2	+	30	10560	c.10560G>A	c.(10558-10560)caG>caA	p.Q3520Q	DNHD1_ENST00000254579.6_Silent_p.Q3520Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3520					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)		AATCGGAGCAGTACCAGTGGG	0.552													G|||	991	0.197883	0.5484	0.1254	5008	,	,		19760	0.0149		0.0417	False		,,,				2504	0.1247				p.Q3520Q		Atlas-SNP	.											.	DNHD1	198	.	0			c.G10560A						PASS	.	G		681,703		168,345,179	124.0	119.0	120.0		10560	4.7	0.9	11	dbSNP_120	120	153,3029		3,147,1441	no	coding-synonymous	DNHD1	NM_144666.2		171,492,1620	AA,AG,GG		4.8083,49.2052,18.2654		3520/4754	6585838	834,3732	692	1591	2283	SO:0001819	synonymous_variant	144132	exon32			GGAGCAGTACCAG	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.10560G>A	11.37:g.6585838G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.816;A|0.184	0.184	strong		0.552	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
HTR2A	3356	hgsc.bcm.edu	37	13	47469939	47469939	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:47469939C>T	ENST00000378688.4	-	1	234	c.103G>A	c.(103-105)Gga>Aga	p.G35R	HTR2A_ENST00000543956.1_Intron|HTR2A_ENST00000542664.1_Missense_Mutation_p.G35R			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	35					activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|behavioral response to cocaine (GO:0048148)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|memory (GO:0007613)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of vasoconstriction (GO:0045907)|protein localization to cytoskeleton (GO:0044380)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|regulation of hormone secretion (GO:0046883)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|sleep (GO:0030431)|synaptic transmission (GO:0007268)|temperature homeostasis (GO:0001659)|urinary bladder smooth muscle contraction (GO:0014832)	cell body fiber (GO:0070852)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(10)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_lung(13;7.2e-10)|Lung NSC(96;3.77e-07)|Breast(56;2.06e-05)|Prostate(109;0.00116)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|Myeloproliferative disorder(33;0.0333)		GBM - Glioblastoma multiforme(144;4.67e-05)|COAD - Colon adenocarcinoma(199;0.224)	Acepromazine(DB01614)|Amisulpride(DB06288)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinitapride(DB08810)|Cisapride(DB00604)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyclobenzaprine(DB00924)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Donepezil(DB00843)|Doxepin(DB01142)|Epinastine(DB00751)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Flupentixol(DB00875)|Fluspirilene(DB04842)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mesoridazine(DB00933)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Molindone(DB01618)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Paroxetine(DB00715)|Pergolide(DB01186)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Remoxipride(DB00409)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	TTAGCTTCTCCGGAGTTAAAG	0.428																																					p.G35R		Atlas-SNP	.											.	HTR2A	98	.	0			c.G103A						PASS	.						102.0	100.0	101.0					13																	47469939		2203	4300	6503	SO:0001583	missense	3356	exon2			CTTCTCCGGAGTT	X57830	CCDS9405.1, CCDS53867.1	13q14-q21	2012-08-08	2012-02-03		ENSG00000102468	ENSG00000102468		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5293	protein-coding gene	gene with protein product		182135	"""5-hydroxytryptamine (serotonin) receptor 2A"""	HTR2		8035173	Standard	NM_000621		Approved	5-HT2A	uc010acr.4	P28223	OTTHUMG00000016881	ENST00000378688.4:c.103G>A	13.37:g.47469939C>T	ENSP00000367959:p.Gly35Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_000621	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Missense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1	.	.	.	.	.	.	.	.	.	.	C	1.837	-0.468315	0.04445	.	.	ENSG00000102468	ENST00000378688;ENST00000542664	T;T	0.54866	0.55;0.55	5.49	1.83	0.25207	.	0.180503	0.39407	N	0.001371	T	0.29588	0.0738	N	0.17082	0.46	0.23309	N	0.997934	B	0.15473	0.013	B	0.08055	0.003	T	0.18272	-1.0342	10	0.13853	T	0.58	.	8.1078	0.30896	0.0:0.6054:0.0:0.3946	.	35	P28223	5HT2A_HUMAN	R	35	ENSP00000367959:G35R;ENSP00000437737:G35R	ENSP00000367959:G35R	G	-	1	0	HTR2A	46367940	0.018000	0.18449	0.035000	0.18076	0.996000	0.88848	0.190000	0.17057	0.028000	0.15324	0.585000	0.79938	GGA	.	.	none		0.428	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621	
ANK1	286	hgsc.bcm.edu	37	8	41563685	41563685	+	Silent	SNP	G	G	A	rs1137177	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:41563685G>A	ENST00000347528.4	-	18	2156	c.2073C>T	c.(2071-2073)ggC>ggT	p.G691G	ANK1_ENST00000379758.2_Silent_p.G691G|ANK1_ENST00000289734.7_Silent_p.G691G|ANK1_ENST00000352337.4_Silent_p.G691G|ANK1_ENST00000396945.1_Silent_p.G691G|ANK1_ENST00000265709.8_Silent_p.G724G|ANK1_ENST00000396942.1_Silent_p.G691G	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	691	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CCACCATGACGCCGTGTTTGA	0.542													G|||	906	0.180911	0.0159	0.2954	5008	,	,		17858	0.0794		0.2823	False		,,,				2504	0.3231				p.G724G		Atlas-SNP	.											.	ANK1	497	.	0			c.C2172T						PASS	.	G	,,,,	250,4156	145.4+/-180.2	7,236,1960	82.0	73.0	76.0		2073,2172,2073,2073,2073	-10.6	0.0	8	dbSNP_86	76	2304,6296	387.5+/-342.2	320,1664,2316	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	327,1900,4276	AA,AG,GG		26.7907,5.6741,19.6371	,,,,	691/1881,724/1898,691/1857,691/1882,691/1720	41563685	2554,10452	2203	4300	6503	SO:0001819	synonymous_variant	286	exon18			CATGACGCCGTGT	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2073C>T	8.37:g.41563685G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	111	76	0.684685	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	369	0.16895604395604397	11	0.022357723577235773	100	0.27624309392265195	37	0.06468531468531469	221	0.29155672823219	G	0.494	-0.874159	0.02550	0.056741	0.267907	ENSG00000029534	ENST00000520299	.	.	.	5.32	-10.6	0.00265	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999952	.	.	.	.	.	.	T	0.17228	-1.0376	3	.	.	.	.	1.3955	0.02260	0.2645:0.2406:0.3132:0.1818	rs1137177;rs2304878;rs3200981;rs17424473;rs17602822;rs1137177	.	.	.	C	5	.	.	R	-	1	0	ANK1	41682842	0.002000	0.14202	0.002000	0.10522	0.035000	0.12851	-1.576000	0.02129	-3.094000	0.00246	-1.075000	0.02238	CGT	G|0.832;N|0.000	.	strong		0.542	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
DGCR6L	85359	hgsc.bcm.edu	37	22	20307256	20307256	+	Silent	SNP	G	G	A	rs7235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	320	2	0.00625		WXS	Illumina HiSeq	Phase_I	291	129	0.443299	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	
PCM1	5108	hgsc.bcm.edu	37	8	17817553	17817553	+	Missense_Mutation	SNP	G	G	T	rs17635381	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17817553G>T	ENST00000519253.1	+	14	2322	c.2071G>T	c.(2071-2073)Gcc>Tcc	p.A691S	PCM1_ENST00000325083.8_Missense_Mutation_p.A691S|PCM1_ENST00000524226.1_Missense_Mutation_p.A692S			Q15154	PCM1_HUMAN	pericentriolar material 1	691			A -> S (in dbSNP:rs17635381).		centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		AGTTATCTCTGCCAGTGCATC	0.358			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""								G|||	723	0.144369	0.0227	0.1268	5008	,	,		17835	0.3661		0.1272	False		,,,				2504	0.1104				p.A691S		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.G2071T						PASS	.	G	SER/ALA	128,3638		5,118,1760	73.0	68.0	70.0		2071	5.2	1.0	8	dbSNP_123	70	1192,7040		77,1038,3001	yes	missense	PCM1	NM_006197.3	99	82,1156,4761	TT,TG,GG		14.4801,3.3988,11.0018	probably-damaging	691/2025	17817553	1320,10678	1883	4116	5999	SO:0001583	missense	5108	exon14			ATCTCTGCCAGTG		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.2071G>T	8.37:g.17817553G>T	ENSP00000431099:p.Ala691Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	203	63	0.310345	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		379	0.17353479853479853	13	0.026422764227642278	48	0.13259668508287292	214	0.3741258741258741	104	0.13720316622691292	G	12.27	1.886862	0.33348	0.033988	0.144801	ENSG00000078674	ENST00000325083;ENST00000517730;ENST00000519253;ENST00000524226	T;T;T;T	0.28454	3.5;2.55;1.61;1.61	5.17	5.17	0.71159	.	0.268940	0.35903	N	0.002912	T	0.00012	0.0000	L	0.44542	1.39	0.09310	P	1.0	B;B;P;B	0.40534	0.144;0.044;0.72;0.031	B;B;B;B	0.43536	0.082;0.082;0.423;0.017	T	0.50591	-0.8810	9	0.25106	T	0.35	-0.1599	16.7078	0.85377	0.0:0.0:1.0:0.0	rs17635381;rs17635381	691;730;692;691	E7ETA6;E7EV93;E7EV56;Q15154	.;.;.;PCM1_HUMAN	S	691;730;691;692	ENSP00000327077:A691S;ENSP00000428131:A730S;ENSP00000431099:A691S;ENSP00000430521:A692S	ENSP00000327077:A691S	A	+	1	0	PCM1	17861833	1.000000	0.71417	0.992000	0.48379	0.161000	0.22273	3.715000	0.54897	2.791000	0.96007	0.637000	0.83480	GCC	G|0.834;N|0.000	.	strong		0.358	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
LY75	4065	hgsc.bcm.edu	37	2	160697271	160697271	+	Missense_Mutation	SNP	G	G	A	rs147904044	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160697271G>A	ENST00000263636.4	-	25	3503	c.3476C>T	c.(3475-3477)tCt>tTt	p.S1159F	LY75_ENST00000554112.1_Missense_Mutation_p.S1159F|LY75_ENST00000553424.1_Missense_Mutation_p.S1159F|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.S1159F|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.S1159F	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1159	C-type lectin 7. {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)		CCATAAGGAAGAGTTGTGAAG	0.483													G|||	6	0.00119808	0.0	0.0043	5008	,	,		18429	0.0		0.003	False		,,,				2504	0.0				p.S1159F		Atlas-SNP	.											.	LY75	151	.	0			c.C3476T						PASS	.	G	PHE/SER,PHE/SER,PHE/SER	8,4398	14.3+/-33.2	0,8,2195	150.0	143.0	145.0		3476,3476,3476	3.5	0.0	2	dbSNP_134	145	45,8555	27.9+/-77.7	0,45,4255	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	155,155,155	0,53,6450	AA,AG,GG		0.5233,0.1816,0.4075	benign,benign,benign	1159/1874,1159/1818,1159/1723	160697271	53,12953	2203	4300	6503	SO:0001583	missense	4065	exon25			AAGGAAGAGTTGT	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.3476C>T	2.37:g.160697271G>A	ENSP00000263636:p.Ser1159Phe	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	132	61	0.462121	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	8.582	0.882464	0.17467	0.001816	0.005233	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	5.35	3.48	0.39840	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.24392	0.0591	L	0.50919	1.6	0.18873	N	0.999983	P;P;D	0.57571	0.899;0.952;0.98	P;P;P	0.56700	0.509;0.642;0.804	T	0.05194	-1.0900	9	0.44086	T	0.13	-0.8422	10.0198	0.42035	0.0:0.1485:0.6974:0.1541	.	1159;1159;1159	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	F	1159	ENSP00000451511:S1159F;ENSP00000451446:S1159F;ENSP00000263636:S1159F;ENSP00000423463:S1159F;ENSP00000421035:S1159F	ENSP00000423463:S1159F	S	-	2	0	LY75;LY75-CD302	160405517	0.933000	0.31639	0.011000	0.14972	0.281000	0.26958	1.035000	0.30216	0.570000	0.29347	0.655000	0.94253	TCT	G|0.996;A|0.004	0.004	strong		0.483	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
MPC2	25874	hgsc.bcm.edu	37	1	167893759	167893759	+	Silent	SNP	G	G	A	rs9618	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:167893759G>A	ENST00000367846.4	-	2	324	c.126C>T	c.(124-126)ttC>ttT	p.F42F	MPC2_ENST00000271373.4_Silent_p.F42F	NM_015415.3	NP_056230.1	O95563	MPC2_HUMAN	mitochondrial pyruvate carrier 2	42					cellular metabolic process (GO:0044237)|mitochondrial pyruvate transport (GO:0006850)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate transmembrane transporter activity (GO:0050833)										GAGCCCAGAAGAAAACTGTTC	0.299													A|||	2036	0.40655	0.6823	0.5202	5008	,	,		16494	0.1806		0.3519	False		,,,				2504	0.2423				p.F42F		Atlas-SNP	.											BRP44,caecum,carcinoma,0,1	.	.	1	0			c.C126T						scavenged	.	A	,	2624,1772		794,1036,368	17.0	19.0	18.0		126,126	2.1	1.0	1	dbSNP_79	18	2851,5725		507,1837,1944	no	coding-synonymous,coding-synonymous	BRP44	NM_001143674.2,NM_015415.3	,	1301,2873,2312	AA,AG,GG		33.2439,40.3094,42.2063	,	42/128,42/128	167893759	5475,7497	2198	4288	6486	SO:0001819	synonymous_variant	25874	exon3			CCAGAAGAAAACT		CCDS1266.1	1q24	2012-07-30	2012-07-30	2012-07-30	ENSG00000143158	ENSG00000143158			24515	protein-coding gene	gene with protein product		614737	"""brain protein 44"""	BRP44		3022128, 22628558	Standard	NM_015415		Approved	DKFZP564B167	uc001get.3	O95563	OTTHUMG00000034570	ENST00000367846.4:c.126C>T	1.37:g.167893759G>A		Somatic	170	2	0.0117647		WXS	Illumina HiSeq	Phase_I	153	89	0.581699	NM_001143674	A8K261|Q3SXR6|Q6FIF3	Silent	SNP	ENST00000367846.4	37	CCDS1266.1																																																																																			G|0.609;A|0.391	0.391	strong		0.299	MPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083652.1	NM_015415	
FAM189A1	23359	hgsc.bcm.edu	37	15	29544656	29544656	+	Silent	SNP	T	T	C	rs4583203	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	241	0	0		WXS	Illumina HiSeq	Phase_I	133	93	0.699248	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	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49376582	49376582	+	Missense_Mutation	SNP	G	G	A	rs564196	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49376582G>A	ENST00000200453.5	+	2	361	c.92G>A	c.(91-93)cGc>cAc	p.R31H		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	31	Required for localization in the endoplasmic reticulum.		R -> H (in dbSNP:rs564196).		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)		CTCCTCAGCCGCGCCTGGAGC	0.652													G|||	1372	0.273962	0.5325	0.2262	5008	,	,		16179	0.0873		0.1501	False		,,,				2504	0.2781				p.R31H		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G92A						PASS	.	G	HIS/ARG	2111,2289		524,1063,613	25.0	28.0	27.0		92	2.2	0.9	19	dbSNP_83	27	1232,7358		75,1082,3138	yes	missense	PPP1R15A	NM_014330.3	29	599,2145,3751	AA,AG,GG		14.3423,47.9773,25.7352	probably-damaging	31/675	49376582	3343,9647	2200	4295	6495	SO:0001583	missense	23645	exon2			TCAGCCGCGCCTG	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.92G>A	19.37:g.49376582G>A	ENSP00000200453:p.Arg31His	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	499	0.22847985347985347	249	0.5060975609756098	82	0.2265193370165746	54	0.0944055944055944	114	0.1503957783641161	G	17.76	3.468799	0.63625	0.479773	0.143423	ENSG00000087074	ENST00000200453	T	0.05996	3.36	4.28	2.16	0.27623	.	0.226254	0.28606	N	0.014748	T	0.00012	0.0000	L	0.43923	1.385	0.33266	P	0.43964800000000004	D	0.76494	0.999	P	0.57846	0.828	T	0.45264	-0.9273	9	0.72032	D	0.01	-4.0888	6.5741	0.22555	0.2149:0.0:0.7851:0.0	rs564196;rs564196	31	O75807	PR15A_HUMAN	H	31	ENSP00000200453:R31H	ENSP00000200453:R31H	R	+	2	0	PPP1R15A	54068394	0.865000	0.29922	0.897000	0.35233	0.378000	0.30076	1.188000	0.32102	0.758000	0.33059	0.561000	0.74099	CGC	G|0.729;A|0.271	0.271	strong		0.652	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
AMT	275	hgsc.bcm.edu	37	3	49455330	49455330	+	Silent	SNP	C	C	T	rs11715915	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49455330C>T	ENST00000273588.3	-	8	1256	c.954G>A	c.(952-954)cgG>cgA	p.R318R	AMT_ENST00000476226.1_5'UTR|AMT_ENST00000538581.1_Silent_p.R262R|AMT_ENST00000395338.2_Silent_p.R318R|AMT_ENST00000546031.1_Silent_p.R221R|AMT_ENST00000458307.2_Silent_p.R274R	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	84	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	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	
C8orf31	286122	hgsc.bcm.edu	37	8	144124609	144124609	+	Missense_Mutation	SNP	T	T	C	rs11136300	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144124609T>C	ENST00000395172.1	+	3	468	c.116T>C	c.(115-117)cTg>cCg	p.L39P	C8orf31_ENST00000517653.1_3'UTR	NM_173687.2	NP_775958.1	Q8N9H6	CH031_HUMAN	chromosome 8 open reading frame 31	39			L -> P (in dbSNP:rs11136300).							breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CAGGGGCTGCTGGCTGCCAGG	0.647													c|||	3532	0.705272	0.7428	0.6873	5008	,	,		16665	0.7282		0.6392	False		,,,				2504	0.7117				p.L39P		Atlas-SNP	.											.	C8orf31	18	.	0			c.T116C						PASS	.	C	PRO/LEU	3182,1224	417.6+/-338.0	1161,860,182	34.0	38.0	37.0		116	-4.4	0.0	8	dbSNP_120	37	5494,3106	464.9+/-366.4	1740,2014,546	yes	missense	C8orf31	NM_173687.2	98	2901,2874,728	CC,CT,TT		36.1163,27.7803,33.2923	probably-damaging	39/133	144124609	8676,4330	2203	4300	6503	SO:0001583	missense	286122	exon3			GGCTGCTGGCTGC		CCDS6395.1	8q24.3	2012-04-11			ENSG00000177335	ENSG00000177335			26731	protein-coding gene	gene with protein product							Standard	NM_173687		Approved	FLJ37131	uc003yxp.1	Q8N9H6	OTTHUMG00000164771	ENST00000395172.1:c.116T>C	8.37:g.144124609T>C	ENSP00000378601:p.Leu39Pro	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	130	53	0.407692	NM_173687	Q6GMU7	Missense_Mutation	SNP	ENST00000395172.1	37	CCDS6395.1	1547	0.7083333333333334	368	0.7479674796747967	241	0.6657458563535912	453	0.791958041958042	485	0.6398416886543535	c	1.232	-0.623858	0.03636	0.722197	0.638837	ENSG00000177335	ENST00000395172	T	0.58358	0.34	2.38	-4.36	0.03645	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.34700	-0.9818	8	0.28530	T	0.3	.	1.0046	0.01484	0.1367:0.2771:0.2283:0.3579	rs11136300;rs61189848;rs11136300	39	Q8N9H6	CH031_HUMAN	P	39	ENSP00000378601:L39P	ENSP00000378601:L39P	L	+	2	0	C8orf31	144195984	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.651000	0.00857	-1.757000	0.01316	-2.048000	0.00412	CTG	T|0.317;C|0.683	0.683	strong		0.647	C8orf31-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380167.1	NM_173687	
MUC4	4585	hgsc.bcm.edu	37	3	195506917	195506917	+	Missense_Mutation	SNP	A	A	C	rs150128295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195506917A>C	ENST00000463781.3	-	2	11993	c.11534T>G	c.(11533-11535)aTc>aGc	p.I3845S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.I3845S	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)		TGAGGAAGGGATGGTGACAGG	0.582													.|||	733	0.146366	0.4009	0.0821	5008	,	,		7906	0.0169		0.0915	False		,,,				2504	0.0378				p.I3845S		Atlas-SNP	.											MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	0			c.T11534G						scavenged	.						7.0	8.0	8.0					3																	195506917		360	1219	1579	SO:0001583	missense	4585	exon2			GAAGGGATGGTGA	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.11534T>G	3.37:g.195506917A>C	ENSP00000417498:p.Ile3845Ser	Somatic	95	4	0.0421053		WXS	Illumina HiSeq	Phase_I	40	23	0.575	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	366	0.16758241758241757	88	0.17886178861788618	53	0.1464088397790055	106	0.1853146853146853	119	0.15699208443271767	N	0.005	-2.179133	0.00308	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.46819	1.31;0.86	.	.	.	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	P	0.42993	0.797	B	0.37550	0.253	T	0.03095	-1.1073	6	.	.	.	.	3.3668	0.07206	0.6523:0.0:0.0:0.3476	.	3717	E7ESK3	.	S	3845	ENSP00000417498:I3845S;ENSP00000420243:I3845S	.	I	-	2	0	MUC4	196991696	0.000000	0.05858	0.052000	0.19188	0.052000	0.14988	-1.321000	0.02697	-2.393000	0.00584	-2.525000	0.00183	ATC	A|0.832;C|0.168	0.168	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAT4	79633	hgsc.bcm.edu	37	4	126237971	126237971	+	Silent	SNP	C	C	T	rs72928772	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:126237971C>T	ENST00000394329.3	+	1	418	c.405C>T	c.(403-405)ttC>ttT	p.F135F		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	135	Cadherin 1. {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						CCCCCGTTTTCCCGGACCCCT	0.607											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	653	0.130391	0.0696	0.1354	5008	,	,		17170	0.0982		0.2197	False		,,,				2504	0.1503				p.F135F		Atlas-SNP	.											.	FAT4	1752	.	0			c.C405T						PASS	.	C		353,3723		14,325,1699	33.0	38.0	36.0		405	5.4	1.0	4	dbSNP_130	36	1818,6592		193,1432,2580	no	coding-synonymous	FAT4	NM_024582.4		207,1757,4279	TT,TC,CC		21.6171,8.6605,17.3875		135/4982	126237971	2171,10315	2038	4205	6243	SO:0001819	synonymous_variant	79633	exon1			CGTTTTCCCGGAC	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.405C>T	4.37:g.126237971C>T		Somatic	78	0	0	1548	WXS	Illumina HiSeq	Phase_I	45	6	0.133333	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			C|0.831;T|0.169	0.169	strong		0.607	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
ANKRD33	341405	hgsc.bcm.edu	37	12	52285086	52285086	+	Missense_Mutation	SNP	G	G	A	rs3180417	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52285086G>A	ENST00000340970.4	+	6	1152	c.781G>A	c.(781-783)Gta>Ata	p.V261I	ANKRD33_ENST00000301190.6_Silent_p.K452K|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Missense_Mutation_p.V192I			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	60	0	0		WXS	Illumina HiSeq	Phase_I	48	45	0.9375	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	
CEP170B	283638	hgsc.bcm.edu	37	14	105344823	105344823	+	Silent	SNP	G	G	A	rs41314519	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105344823G>A	ENST00000414716.3	+	5	546	c.318G>A	c.(316-318)ccG>ccA	p.P106P	CEP170B_ENST00000453495.1_Silent_p.P106P|CEP170B_ENST00000556508.1_Silent_p.P36P|CEP170B_ENST00000418279.1_Silent_p.P36P	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	106						cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.P106P(1)									ACCGAGTCCCGGAGGAGGCAC	0.627													G|||	150	0.0299521	0.0015	0.0259	5008	,	,		18718	0.0367		0.0447	False		,,,				2504	0.0491				p.P106P		Atlas-SNP	.											KIAA0284_ENST00000414716,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.G318A						scavenged	.	G	,	31,4161		0,31,2065	95.0	102.0	100.0		318,108	-8.3	0.0	14	dbSNP_127	100	285,8149		3,279,3935	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	3,310,6000	AA,AG,GG		3.3792,0.7395,2.5028	,	106/1555,36/1520	105344823	316,12310	2096	4217	6313	SO:0001819	synonymous_variant	283638	exon5			AGTCCCGGAGGAG	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.318G>A	14.37:g.105344823G>A		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	129	47	0.364341	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																			G|0.969;A|0.031	0.031	strong		0.627	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
TRRAP	8295	hgsc.bcm.edu	37	7	98602800	98602800	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:98602800C>T	ENST00000359863.4	+	68	10749	c.10540C>T	c.(10540-10542)Cgg>Tgg	p.R3514W	TRRAP_ENST00000446306.3_Missense_Mutation_p.R3503W|TRRAP_ENST00000355540.3_Missense_Mutation_p.R3485W	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3514					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)			CACCGCAGCCCGGCGGCTGTA	0.587																																					p.R3514W		Atlas-SNP	.											TRRAP_ENST00000359863,NS,carcinoma,0,2	TRRAP	863	2	0			c.C10540T						scavenged	.						80.0	74.0	76.0					7																	98602800		2203	4300	6503	SO:0001583	missense	8295	exon68			GCAGCCCGGCGGC	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.10540C>T	7.37:g.98602800C>T	ENSP00000352925:p.Arg3514Trp	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	123	3	0.0243902	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405411	0.62288	.	.	ENSG00000196367	ENST00000359863;ENST00000355540;ENST00000446306	D;D	0.82526	-1.62;-1.62	5.53	-2.83	0.05769	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.92133	0.7506	M	0.91196	3.185	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	0.92976	0.6402	10	0.87932	D	0	.	20.0014	0.97409	0.6346:0.3654:0.0:0.0	.	3485;3242;3514	Q9Y4A5-2;Q59FH1;Q9Y4A5	.;.;TRRAP_HUMAN	W	3514;3485;3502	ENSP00000352925:R3514W;ENSP00000347733:R3485W	ENSP00000347733:R3485W	R	+	1	2	TRRAP	98440736	0.006000	0.16342	0.938000	0.37757	0.449000	0.32228	0.151000	0.16283	-0.322000	0.08615	0.491000	0.48974	CGG	.	.	none		0.587	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
RREB1	6239	hgsc.bcm.edu	37	6	7189437	7189437	+	Missense_Mutation	SNP	G	G	A	rs201588284		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:7189437G>A	ENST00000349384.6	+	6	621	c.307G>A	c.(307-309)Gga>Aga	p.G103R	Y_RNA_ENST00000364613.1_RNA|RREB1_ENST00000379938.2_Missense_Mutation_p.G103R|RREB1_ENST00000334984.6_Missense_Mutation_p.G103R|RREB1_ENST00000379933.3_Missense_Mutation_p.G103R	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	103					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)				CAGCATCTGCGGAAAGTCACT	0.557													G|||	1	0.000199681	0.0	0.0	5008	,	,		18775	0.001		0.0	False		,,,				2504	0.0				p.G103R		Atlas-SNP	.											RREB1_ENST00000379938,NS,carcinoma,-2,2	RREB1	242	2	0			c.G307A						PASS	.						67.0	53.0	57.0					6																	7189437		2203	4300	6503	SO:0001583	missense	6239	exon6			ATCTGCGGAAAGT	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.307G>A	6.37:g.7189437G>A	ENSP00000305560:p.Gly103Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	32	5.181977	0.94885	.	.	ENSG00000124782	ENST00000379933;ENST00000491191;ENST00000379938;ENST00000471433;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T;T;T	0.66460	3.19;-0.21;3.19;3.19;3.19;3.19;3.19	5.65	5.65	0.86999	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000016	T	0.80177	0.4575	M	0.75447	2.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.962	T	0.80759	-0.1239	10	0.62326	D	0.03	-55.3388	19.7284	0.96174	0.0:0.0:1.0:0.0	.	103;103;103	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	R	103	ENSP00000369265:G103R;ENSP00000420519:G103R;ENSP00000369270:G103R;ENSP00000420299:G103R;ENSP00000305560:G103R;ENSP00000335574:G103R;ENSP00000419511:G103R	ENSP00000335574:G103R	G	+	1	0	RREB1	7134436	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.304000	0.78882	2.668000	0.90789	0.591000	0.81541	GGA	G|0.999;A|0.001	0.001	strong		0.557	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
DHRS4L2	317749	hgsc.bcm.edu	37	14	24459520	24459520	+	Silent	SNP	T	T	C	rs45583341	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24459520T>C	ENST00000335125.6	+	2	384	c.258T>C	c.(256-258)acT>acC	p.T86T	DHRS4L2_ENST00000545240.1_Silent_p.T86T|DHRS4L2_ENST00000382755.4_Silent_p.T84T|DHRS4L2_ENST00000543805.1_5'UTR|DHRS4L2_ENST00000397071.1_Silent_p.T86T|DHRS4L2_ENST00000537912.1_Silent_p.T86T|DHRS4L2_ENST00000534993.1_5'UTR|DHRS4L2_ENST00000558753.1_Silent_p.T86T	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	84						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		TGACGGGCACTGTGTGCCATG	0.677													N|||	815	0.16274	0.0968	0.1499	5008	,	,		14725	0.2262		0.1223	False		,,,				2504	0.2372				p.T86T		Atlas-SNP	.											DHRS4L2,colon,carcinoma,0,1	DHRS4L2	29	1	0			c.T258C						PASS	.	C	,,,	340,4060	773.1+/-413.9	24,292,1884	37.0	40.0	39.0		174,,,258	0.2	1.0	14	dbSNP_127	39	850,7746	759.3+/-407.5	63,724,3511	no	coding-synonymous,utr-5,utr-5,coding-synonymous	DHRS4L2	NM_001193635.1,NM_001193636.1,NM_001193637.1,NM_198083.3	,,,	87,1016,5395	CC,CT,TT		9.8883,7.7273,9.1567	,,,	58/171,,,86/233	24459520	1190,11806	2200	4298	6498	SO:0001819	synonymous_variant	317749	exon2			GGGCACTGTGTGC		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.258T>C	14.37:g.24459520T>C		Somatic	299	1	0.00334448		WXS	Illumina HiSeq	Phase_I	244	237	0.971311	NM_198083	Q3YLD4	Silent	SNP	ENST00000335125.6	37	CCDS9606.2																																																																																			T|0.868;C|0.132	0.132	strong		0.677	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
C1orf105	92346	hgsc.bcm.edu	37	1	172431386	172431386	+	Splice_Site	SNP	G	G	A	rs41310899	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:172431386G>A	ENST00000367727.4	+	5	539		c.e5+1		C1orf105_ENST00000367725.4_Splice_Site|C1orf105_ENST00000367726.1_Splice_Site	NM_139240.3	NP_640333.3	O95561	CA105_HUMAN	chromosome 1 open reading frame 105											large_intestine(1)|lung(12)|prostate(1)|skin(1)	15						TGAGTTATAGGTAAGTCAACA	0.368													G|||	220	0.0439297	0.0272	0.049	5008	,	,		18977	0.0		0.0875	False		,,,				2504	0.0634				.		Atlas-SNP	.											.	C1orf105	24	.	0			c.341+1G>A						PASS	.	G		137,4269	98.5+/-137.1	2,133,2068	88.0	82.0	84.0			4.3	0.9	1	dbSNP_127	84	516,8084	144.7+/-200.5	19,478,3803	yes	splice-5	C1orf105	NM_139240.3		21,611,5871	AA,AG,GG		6.0,3.1094,5.0208			172431386	653,12353	2203	4300	6503	SO:0001630	splice_region_variant	92346	exon5			TTATAGGTAAGTC	AL035295	CCDS1301.1, CCDS72983.1	1q24.3	2012-06-26			ENSG00000180999	ENSG00000180999			29591	protein-coding gene	gene with protein product						12477932	Standard	NM_139240		Approved		uc001gik.3	O95561	OTTHUMG00000034750	ENST00000367727.4:c.341+1G>A	1.37:g.172431386G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	255	76	0.298039	NM_139240	Q8IY02	Splice_Site	SNP	ENST00000367727.4	37	CCDS1301.1	102	0.046703296703296704	14	0.028455284552845527	17	0.04696132596685083	0	0.0	71	0.09366754617414248	G	13.48	2.249473	0.39797	0.031094	0.06	ENSG00000180999	ENST00000367727;ENST00000488100;ENST00000367725	.	.	.	4.26	4.26	0.50523	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4933	0.55912	0.0:0.0:1.0:0.0	rs41310899	.	.	.	.	-1	.	.	.	+	.	.	C1orf105	170698009	1.000000	0.71417	0.872000	0.34217	0.510000	0.34073	3.673000	0.54591	2.659000	0.90383	0.655000	0.94253	.	G|0.948;A|0.052	0.052	strong		0.368	C1orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084062.2	NM_139240	Intron
KCTD17	79734	hgsc.bcm.edu	37	22	37458586	37458586	+	Silent	SNP	C	C	T	rs116956945	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	92	0	0		WXS	Illumina HiSeq	Phase_I	78	46	0.589744	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	
ARMC4	55130	hgsc.bcm.edu	37	10	28257852	28257852	+	Splice_Site	SNP	C	C	T	rs199740026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:28257852C>T	ENST00000305242.5	-	9	1330	c.1238G>A	c.(1237-1239)cGg>cAg	p.R413Q	ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000239715.3_Splice_Site_p.R270Q|ARMC4_ENST00000545014.1_Intron|ARMC4_ENST00000537576.1_Splice_Site_p.R105Q	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	413					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						AGAAACATACCGAAGTAATTG	0.458													C|||	557	0.111222	0.1884	0.0836	5008	,	,		18036	0.003		0.1213	False		,,,				2504	0.1278				p.R413Q		Atlas-SNP	.											ARMC4,rectum,NS,-1,1	ARMC4	177	1	0			c.G1238A						scavenged	.						4.0	3.0	3.0					10																	28257852		1459	3081	4540	SO:0001630	splice_region_variant	55130	exon9			ACATACCGAAGTA	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.1238+1G>A	10.37:g.28257852C>T		Somatic	1045	1	0.000956938		WXS	Illumina HiSeq	Phase_I	697	233	0.33429	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	261	0.11950549450549451	136	0.2764227642276423	36	0.09944751381215469	3	0.005244755244755245	86	0.11345646437994723	C	7.770	0.707261	0.15239	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.35605	1.3;1.3;1.3;1.3	3.89	2.05	0.26809	.	1.074070	0.07060	N	0.833582	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.35628	0.513	B	0.21360	0.034	T	0.26052	-1.0114	8	.	.	.	-2.5181	6.1142	0.20117	0.0:0.7713:0.0:0.2287	.	413	Q5T2S8	ARMC4_HUMAN	Q	105;413;105;307;270	ENSP00000443208:R105Q;ENSP00000306410:R413Q;ENSP00000398155:R307Q;ENSP00000239715:R270Q	.	R	-	2	0	ARMC4	28297858	0.423000	0.25482	0.063000	0.19743	0.008000	0.06430	0.554000	0.23407	0.620000	0.30215	0.557000	0.71058	CGG	C|0.500;T|0.500	0.500	weak		0.458	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	Missense_Mutation
HEBP2	23593	hgsc.bcm.edu	37	6	138734029	138734029	+	Silent	SNP	A	A	C	rs2076279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:138734029A>C	ENST00000607197.1	+	4	709	c.432A>C	c.(430-432)ggA>ggC	p.G144G	HEBP2_ENST00000367697.3_Missense_Mutation_p.D105A|HEBP2_ENST00000448741.1_Missense_Mutation_p.D116A	NM_014320.2	NP_055135.1	Q9Y5Z4	HEBP2_HUMAN	heme binding protein 2	144					negative regulation of mitochondrial membrane potential (GO:0010917)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of necrotic cell death (GO:0010940)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(3)	5	Breast(32;0.0933)			GBM - Glioblastoma multiforme(68;0.000732)|OV - Ovarian serous cystadenocarcinoma(155;0.00171)		CTTTCGATGGATTTTCTAGTG	0.388													A|||	247	0.0493211	0.0514	0.0591	5008	,	,		21332	0.0982		0.0308	False		,,,				2504	0.0082				p.G144G		Atlas-SNP	.											.	HEBP2	12	.	0			c.A432C						PASS	.	A		150,4256	103.0+/-141.5	2,146,2055	152.0	144.0	147.0		432	2.0	1.0	6	dbSNP_96	147	183,8417	81.8+/-144.4	3,177,4120	no	coding-synonymous	HEBP2	NM_014320.2		5,323,6175	CC,CA,AA		2.1279,3.4044,2.5604		144/206	138734029	333,12673	2203	4300	6503	SO:0001819	synonymous_variant	23593	exon4			CGATGGATTTTCT	AF117616	CCDS5191.1	6q24	2008-08-29	2002-09-23	2002-09-27	ENSG00000051620	ENSG00000051620			15716	protein-coding gene	gene with protein product		605825	"""chromosome 6 open reading frame 34"""	C6orf34		10640688, 17098234	Standard	NM_014320		Approved	SOUL	uc003qhw.1	Q9Y5Z4	OTTHUMG00000015671	ENST00000607197.1:c.432A>C	6.37:g.138734029A>C		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	178	76	0.426966	NM_014320	Q96P57	Silent	SNP	ENST00000607197.1	37	CCDS5191.1	128	0.05860805860805861	23	0.046747967479674794	22	0.06077348066298342	66	0.11538461538461539	17	0.022427440633245383	A	13.17	2.156608	0.38119	0.034044	0.021279	ENSG00000051620	ENST00000448741;ENST00000367697	T;T	0.20463	2.07;2.07	5.75	2.03	0.26663	.	.	.	.	.	T	0.14270	0.0345	.	.	.	0.41933	P	0.009422000000000041	.	.	.	.	.	.	T	0.04930	-1.0917	5	0.56958	D	0.05	.	8.3223	0.32136	0.7686:0.0:0.2314:0.0	rs2076279;rs2076279	.	.	.	A	116;105	ENSP00000392101:D116A;ENSP00000356670:D105A	ENSP00000356670:D105A	D	+	2	0	HEBP2	138775722	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.028000	0.30128	0.458000	0.26988	-0.370000	0.07254	GAT	A|0.961;C|0.039	0.039	strong		0.388	HEBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042426.2		
PCNT	5116	hgsc.bcm.edu	37	21	47808679	47808679	+	Missense_Mutation	SNP	C	C	T	rs7279204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:47808679C>T	ENST00000359568.5	+	18	3594	c.3487C>T	c.(3487-3489)Cgc>Tgc	p.R1163C	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1163			R -> C (in dbSNP:rs7279204).		brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GGACGCCCTGCGCAGGCTGCT	0.677													C|||	762	0.152157	0.0711	0.1816	5008	,	,		16098	0.1984		0.1312	False		,,,				2504	0.2147				p.R1163C		Atlas-SNP	.											PCNT,face,carcinoma,-1,1	PCNT	283	1	0			c.C3487T						scavenged	.	C	CYS/ARG	288,4118	152.9+/-186.6	13,262,1928	55.0	57.0	56.0		3487	-3.1	0.1	21	dbSNP_116	56	1110,7490	226.8+/-262.4	71,968,3261	yes	missense	PCNT	NM_006031.5	180	84,1230,5189	TT,TC,CC		12.907,6.5365,10.7489	probably-damaging	1163/3337	47808679	1398,11608	2203	4300	6503	SO:0001583	missense	5116	exon18			GCCCTGCGCAGGC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.3487C>T	21.37:g.47808679C>T	ENSP00000352572:p.Arg1163Cys	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	135	80	0.592593	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	303	0.13873626373626374	36	0.07317073170731707	49	0.13535911602209943	114	0.1993006993006993	104	0.13720316622691292	C	12.00	1.806265	0.31961	0.065365	0.12907	ENSG00000160299	ENST00000359568	T	0.01685	4.69	4.57	-3.08	0.05347	.	0.246216	0.19223	N	0.119601	T	0.00012	0.0000	M	0.62723	1.935	0.58432	P	1.0000000000287557E-6	D;D	0.89917	1.0;1.0	D;D	0.83275	0.981;0.996	T	0.04128	-1.0975	9	0.72032	D	0.01	.	15.9319	0.79668	0.2121:0.7879:0.0:0.0	rs7279204	1045;1163	O95613-2;O95613	.;PCNT_HUMAN	C	1163	ENSP00000352572:R1163C	ENSP00000352572:R1163C	R	+	1	0	PCNT	46633107	0.095000	0.21747	0.091000	0.20842	0.071000	0.16799	0.207000	0.17395	-0.233000	0.09797	-0.274000	0.10170	CGC	C|0.883;T|0.117	0.117	strong		0.677	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
SEMG2	6407	hgsc.bcm.edu	37	20	43850400	43850400	+	Missense_Mutation	SNP	C	C	A	rs2233896	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	265	0	0		WXS	Illumina HiSeq	Phase_I	198	79	0.39899	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	
AP3D1	8943	hgsc.bcm.edu	37	19	2116649	2116649	+	Silent	SNP	A	A	G	rs2074960	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2116649A>G	ENST00000345016.5	-	17	2187	c.1956T>C	c.(1954-1956)cgT>cgC	p.R652R	AP3D1_ENST00000356926.4_Silent_p.R561R|AP3D1_ENST00000350812.6_Silent_p.R483R|AP3D1_ENST00000355272.6_Silent_p.R652R	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	652					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)		GGTGCTTGGGACGCCGCTGCT	0.692													G|||	818	0.163339	0.1301	0.1311	5008	,	,		16167	0.1944		0.17	False		,,,				2504	0.1922				p.R652R		Atlas-SNP	.											AP3D1,NS,carcinoma,-1,1	AP3D1	81	1	0			c.T1956C						scavenged	.	G	,	566,3642		35,496,1573	23.0	25.0	24.0		1683,1956	-10.3	0.0	19	dbSNP_96	24	1647,6805		167,1313,2746	no	coding-synonymous,coding-synonymous	AP3D1	NM_001077523.1,NM_003938.5	,	202,1809,4319	GG,GA,AA		19.4865,13.4506,17.4803	,	561/1113,652/1154	2116649	2213,10447	2104	4226	6330	SO:0001819	synonymous_variant	8943	exon17			CTTGGGACGCCGC	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.1956T>C	19.37:g.2116649A>G		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																			A|0.834;G|0.166	0.166	strong		0.692	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
ZNF622	90441	hgsc.bcm.edu	37	5	16465442	16465442	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:16465442T>C	ENST00000308683.2	-	1	459	c.333A>G	c.(331-333)gaA>gaG	p.E111E		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	111					intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of kinase activity (GO:0033674)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						CCAAGTTCTTTTCATTCATCA	0.562																																					p.E111E		Atlas-SNP	.											ZNF622,NS,carcinoma,-2,1	ZNF622	49	1	0			c.A333G						PASS	.						167.0	152.0	157.0					5																	16465442		2203	4300	6503	SO:0001819	synonymous_variant	90441	exon1			GTTCTTTTCATTC	AY046059	CCDS3886.1	5p15.1	2012-10-05			ENSG00000173545	ENSG00000173545			30958	protein-coding gene	gene with protein product		608694				11802789, 12645566	Standard	NM_033414		Approved	MGC2485, MGC17552, ZPR9	uc003jfq.3	Q969S3	OTTHUMG00000090567	ENST00000308683.2:c.333A>G	5.37:g.16465442T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_033414		Silent	SNP	ENST00000308683.2	37	CCDS3886.1																																																																																			.	.	none		0.562	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414	
MANEA	79694	hgsc.bcm.edu	37	6	96053922	96053922	+	Missense_Mutation	SNP	T	T	A	rs35772543	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:96053922T>A	ENST00000358812.4	+	5	1164	c.1030T>A	c.(1030-1032)Ttt>Att	p.F344I		NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	344	Catalytic. {ECO:0000305}.			F -> I (in Ref. 2; AAQ75077, 3; BAB14298 and 4; CAE45927). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		CCTAAAATTATTTTGTGATAA	0.378													T|||	226	0.0451278	0.0038	0.0605	5008	,	,		18638	0.0595		0.0765	False		,,,				2504	0.0429				p.F344I		Atlas-SNP	.											.	MANEA	58	.	0			c.T1030A						PASS	.	T	ILE/PHE	84,4322	68.1+/-105.8	2,80,2121	59.0	64.0	62.0		1030	6.2	0.9	6	dbSNP_126	62	740,7858	177.2+/-226.9	39,662,3598	yes	missense	MANEA	NM_024641.3	21	41,742,5719	AA,AT,TT		8.6067,1.9065,6.3365	probably-damaging	344/463	96053922	824,12180	2203	4299	6502	SO:0001583	missense	79694	exon5			AAATTATTTTGTG	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.1030T>A	6.37:g.96053922T>A	ENSP00000351669:p.Phe344Ile	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	37	CCDS5032.1	136	0.06227106227106227	2	0.0040650406504065045	29	0.08011049723756906	37	0.06468531468531469	68	0.08970976253298153	T	29.1	4.981294	0.93044	0.019065	0.086067	ENSG00000172469	ENST00000358812	D	0.92647	-3.08	6.17	6.17	0.99709	.	0.086298	0.85682	N	0.000000	D	0.95990	0.8694	M	0.86740	2.835	0.09310	P	0.9999999800898	D	0.89917	1.0	D	0.87578	0.998	D	0.95687	0.8737	9	0.46703	T	0.11	-24.0744	16.0034	0.80327	0.0:0.0:0.0:1.0	rs35772543	344	Q5SRI9	MANEA_HUMAN	I	344	ENSP00000351669:F344I	ENSP00000351669:F344I	F	+	1	0	MANEA	96160643	1.000000	0.71417	0.915000	0.36163	0.910000	0.53928	7.603000	0.82811	2.371000	0.80710	0.533000	0.62120	TTT	T|0.936;A|0.064	0.064	strong		0.378	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641	
SYNE1	23345	hgsc.bcm.edu	37	6	152712440	152712440	+	Missense_Mutation	SNP	G	G	T	rs117480635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:152712440G>T	ENST00000367255.5	-	52	8577	c.7976C>A	c.(7975-7977)aCc>aAc	p.T2659N	SYNE1_ENST00000341594.5_Missense_Mutation_p.T2698N|SYNE1_ENST00000265368.4_Missense_Mutation_p.T2659N|SYNE1_ENST00000448038.1_Missense_Mutation_p.T2666N|SYNE1_ENST00000423061.1_Missense_Mutation_p.T2666N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2659					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)		TTTCTCCAGGGTGTCTTTGCT	0.507										HNSCC(10;0.0054)			G|||	8	0.00159744	0.0	0.0	5008	,	,		15514	0.0		0.006	False		,,,				2504	0.002				p.T2666N		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C7997A						PASS	.	G	ASN/THR,ASN/THR	4,4402	8.1+/-20.4	0,4,2199	109.0	104.0	106.0		7997,7976	5.0	0.0	6	dbSNP_132	106	30,8570	20.4+/-63.3	0,30,4270	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	65,65	0,34,6469	TT,TG,GG		0.3488,0.0908,0.2614	possibly-damaging,possibly-damaging	2666/8750,2659/8798	152712440	34,12972	2203	4300	6503	SO:0001583	missense	23345	exon52			TCCAGGGTGTCTT	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.7976C>A	6.37:g.152712440G>T	ENSP00000356224:p.Thr2659Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	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	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.754	1.168155	0.21621	9.08E-4	0.003488	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.54279	0.67;0.67;0.58;0.67;0.79	5.91	5.04	0.67666	.	0.341353	0.25419	N	0.030816	T	0.31638	0.0803	M	0.62723	1.935	0.24214	N	0.995468	P;B;B;P	0.39696	0.612;0.413;0.413;0.683	B;B;B;B	0.40602	0.203;0.179;0.179;0.334	T	0.19095	-1.0316	10	0.17832	T	0.49	.	11.5958	0.50972	0.1855:0.0:0.8145:0.0	.	2642;2659;2659;2666	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	N	2659;2666;2659;2666;2698	ENSP00000356224:T2659N;ENSP00000396024:T2666N;ENSP00000265368:T2659N;ENSP00000390975:T2666N;ENSP00000341887:T2698N	ENSP00000265368:T2659N	T	-	2	0	SYNE1	152754133	0.997000	0.39634	0.010000	0.14722	0.702000	0.40608	3.098000	0.50259	1.500000	0.48636	0.655000	0.94253	ACC	G|0.998;T|0.002	0.002	strong		0.507	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
MLLT4	4301	hgsc.bcm.edu	37	6	168317816	168317816	+	Silent	SNP	A	A	C	rs6906754	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168317816A>C	ENST00000447894.2	+	19	2592	c.2592A>C	c.(2590-2592)ccA>ccC	p.P864P	MLLT4_ENST00000366806.2_Silent_p.P864P|MLLT4_ENST00000344191.4_Silent_p.P864P|MLLT4_ENST00000351017.4_Silent_p.P871P|MLLT4_ENST00000400822.3_Silent_p.P863P|MLLT4_ENST00000392108.3_Silent_p.P864P|MLLT4_ENST00000392112.1_Silent_p.P848P			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	864	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ATGACATTCCAAATATAAACA	0.348			T	MLL	AL								A|||	964	0.192492	0.2247	0.2118	5008	,	,		16930	0.1935		0.0775	False		,,,				2504	0.2526				p.P864P		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	.	MLLT4	351	.	0			c.A2592C						PASS	.	A	,	798,3608	317.7+/-295.3	65,668,1470	136.0	129.0	131.0		2592,2544	-11.0	0.0	6	dbSNP_116	131	680,7920	169.0+/-220.4	26,628,3646	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	91,1296,5116	CC,CA,AA		7.907,18.1117,11.364	,	864/1652,848/1744	168317816	1478,11528	2203	4300	6503	SO:0001819	synonymous_variant	4301	exon19			CATTCCAAATATA	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.2592A>C	6.37:g.168317816A>C		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	179	98	0.547486	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				A|0.869;C|0.131	0.131	strong		0.348	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
FLG	2312	hgsc.bcm.edu	37	1	152286367	152286367	+	Missense_Mutation	SNP	C	C	A	rs41267154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152286367C>A	ENST00000368799.1	-	3	1030	c.995G>T	c.(994-996)gGc>gTc	p.G332V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	332	Ser-rich.		G -> V (in dbSNP:rs41267154).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGTCTGGAGCCATCTCTTGA	0.567									Ichthyosis				-|||	1706	0.340655	0.115	0.4193	5008	,	,		19207	0.6062		0.171	False		,,,				2504	0.4908				p.G332V		Atlas-SNP	.											.	FLG	900	.	0			c.G995T						PASS	.	C	VAL/GLY	582,3824		39,504,1660	195.0	196.0	196.0		995	1.2	0.0	1	dbSNP_127	196	1444,7156		124,1196,2980	no	missense	FLG	NM_002016.1	109	163,1700,4640	AA,AC,CC		16.7907,13.2093,15.5774	probably-damaging	332/4062	152286367	2026,10980	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGGAGCCATCTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.995G>T	1.37:g.152286367C>A	ENSP00000357789:p.Gly332Val	Somatic	383	1	0.00261097		WXS	Illumina HiSeq	Phase_I	538	180	0.334572	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	676	0.30952380952380953	64	0.13008130081300814	125	0.3453038674033149	355	0.6206293706293706	132	0.1741424802110818	-	9.095	1.002721	0.19121	0.132093	0.167907	ENSG00000143631	ENST00000368799	T	0.01685	4.69	3.14	1.2	0.21068	.	.	.	.	.	T	0.02571	0.0078	M	0.70595	2.14	0.80722	P	0.0	D	0.89917	1.0	D	0.81914	0.995	T	0.46247	-0.9205	8	0.33141	T	0.24	0.3437	5.3802	0.16187	0.0:0.7225:0.0:0.2775	rs41267154	332	P20930	FILA_HUMAN	V	332	ENSP00000357789:G332V	ENSP00000357789:G332V	G	-	2	0	FLG	150552991	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.020000	0.03618	0.200000	0.20447	0.400000	0.26472	GGC	C|0.793;A|0.207	0.207	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
POM121L12	285877	hgsc.bcm.edu	37	7	53103794	53103794	+	Missense_Mutation	SNP	C	C	T	rs73357087	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:53103794C>T	ENST00000408890.4	+	1	446	c.430C>T	c.(430-432)Cct>Tct	p.P144S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	144				P -> S (in Ref. 3; CAD38744). {ECO:0000305}.						endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GATCGCGCCCCCTGAGCGTCA	0.711													C|||	720	0.14377	0.2073	0.2133	5008	,	,		11532	0.0982		0.1451	False		,,,				2504	0.0542				p.P144S		Atlas-SNP	.											POM121L12,NS,carcinoma,-1,1	POM121L12	146	1	0			c.C430T						PASS	.	C	SER/PRO	741,3127		76,589,1269	20.0	24.0	23.0		430	0.7	0.0	7	dbSNP_130	23	1083,7119		55,973,3073	yes	missense	POM121L12	NM_182595.3	74	131,1562,4342	TT,TC,CC		13.2041,19.1572,15.1118	probably-damaging	144/297	53103794	1824,10246	1934	4101	6035	SO:0001583	missense	285877	exon1			GCGCCCCCTGAGC		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.430C>T	7.37:g.53103794C>T	ENSP00000386133:p.Pro144Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	42	29	0.690476	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	363	0.1662087912087912	105	0.21341463414634146	72	0.19889502762430938	63	0.11013986013986014	123	0.16226912928759896	C	12.14	1.849414	0.32699	0.191572	0.132041	ENSG00000221900	ENST00000408890	T	0.75477	-0.94	1.76	0.674	0.17946	.	.	.	.	.	T	0.00144	0.0004	L	0.49126	1.545	0.80722	P	0.0	D	0.71674	0.998	P	0.51833	0.681	T	0.04593	-1.0940	8	0.56958	D	0.05	.	6.4991	0.22158	0.0:0.5256:0.4744:0.0	.	144	Q8N7R1	P1L12_HUMAN	S	144	ENSP00000386133:P144S	ENSP00000386133:P144S	P	+	1	0	POM121L12	53071288	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	2.258000	0.43249	0.171000	0.19730	0.455000	0.32223	CCT	C|0.843;T|0.157	0.157	strong		0.711	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
TRAPPC11	60684	hgsc.bcm.edu	37	4	184600571	184600571	+	Silent	SNP	C	C	A	rs62357990	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:184600571C>A	ENST00000334690.6	+	9	1099	c.897C>A	c.(895-897)atC>atA	p.I299I	TRAPPC11_ENST00000357207.4_Silent_p.I299I	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	299					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											GAAAACACATCGACTTGTGTA	0.363													C|||	310	0.061901	0.056	0.0389	5008	,	,		17834	0.1319		0.0537	False		,,,				2504	0.0225				p.I299I		Atlas-SNP	.											.	.	.	.	0			c.C897A						PASS	.	C	,	232,4174	138.8+/-174.5	8,216,1979	92.0	93.0	93.0		897,897	-9.0	0.1	4	dbSNP_129	93	573,8027	154.2+/-208.4	22,529,3749	no	coding-synonymous,coding-synonymous	C4orf41	NM_021942.4,NM_199053.1	,	30,745,5728	AA,AC,CC		6.6628,5.2655,6.1895	,	299/1134,299/1087	184600571	805,12201	2203	4300	6503	SO:0001819	synonymous_variant	60684	exon9			ACACATCGACTTG		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.897C>A	4.37:g.184600571C>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	8	0.140351	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Silent	SNP	ENST00000334690.6	37	CCDS34112.1																																																																																			C|0.939;A|0.061	0.061	strong		0.363	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
FTH1P18	441490	hgsc.bcm.edu	37	X	37061389	37061389	+	IGR	SNP	C	C	T	rs28675922		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:37061389C>T								FAM47C (31650 upstream) : PRRG1 (147138 downstream)																							TCTGGCTTCCCGACGTCATGA	0.622													t|||	1160	0.307285	0.5545	0.2262	3775	,	,		12980	0.0734		0.0726	False		,,,				2504	0.1258				p.G125R		Atlas-SNP	.											.	.	.	.	0			c.G373A						PASS	.																																			SO:0001628	intergenic_variant	441490	exon1			GCTTCCCGACGTC																													X.37:g.37061389C>T		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_001271682		Missense_Mutation	SNP		37																																																																																				C|0.736;T|0.264	0.264	strong	0	0.622								
DDC	1644	hgsc.bcm.edu	37	7	50607649	50607649	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:50607649C>T	ENST00000444124.2	-	3	479	c.279G>A	c.(277-279)atG>atA	p.M93I	DDC_ENST00000426377.1_Intron|DDC_ENST00000380984.4_Missense_Mutation_p.M93I|AC018705.5_ENST00000454521.1_RNA|DDC_ENST00000489162.1_5'UTR|DDC_ENST00000357936.5_Missense_Mutation_p.M93I|DDC_ENST00000431062.1_Missense_Mutation_p.M93I	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	93	2 X approximate tandem repeats.				catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	CCCCGCACAGCATGTCCGCAA	0.657																																					p.M93I		Atlas-SNP	.											DDC_ENST00000380984,NS,carcinoma,-2,2	DDC	100	2	0			c.G279A						scavenged	.						90.0	74.0	80.0					7																	50607649		2202	4300	6502	SO:0001583	missense	1644	exon3			GCACAGCATGTCC		CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.279G>A	7.37:g.50607649C>T	ENSP00000403644:p.Met93Ile	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	183	2	0.010929	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Missense_Mutation	SNP	ENST00000444124.2	37	CCDS5511.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.48|15.48	2.846608|2.846608	0.51164|0.51164	.|.	.|.	ENSG00000132437|ENSG00000132437	ENST00000430300|ENST00000357936;ENST00000431062;ENST00000444124;ENST00000380984	.|T;T;T;T	.|0.41065	.|1.01;1.13;1.01;1.01	5.5|5.5	4.61|4.61	0.57282|0.57282	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.073190	.|0.85682	.|N	.|0.000000	T|T	0.41143|0.41143	0.1146|0.1146	L|L	0.48986|0.48986	1.54|1.54	0.58432|0.58432	D|D	0.999997|0.999997	.|B;B	.|0.09022	.|0.002;0.002	.|B;B	.|0.18871	.|0.023;0.017	T|T	0.24977|0.24977	-1.0145|-1.0145	5|10	.|0.48119	.|T;T	.|0.1;0.1	-22.6585|-22.6585	16.2655|16.2655	0.82577|0.82577	0.0:0.867:0.133:0.0|0.0:0.867:0.133:0.0	.|.	.|93;93	.|Q53Y41;P20711	.|.;DDC_HUMAN	Y|I	59|93	.|ENSP00000350616:M93I;ENSP00000399184:M93I;ENSP00000403644:M93I;ENSP00000370371:M93I	.|ENSP00000350616:M93I;ENSP00000350616:M93I	C|M	-|-	2|3	0|0	DDC|DDC	50575143|50575143	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.726000|0.726000	0.41606|0.41606	2.611000|2.611000	0.46334|0.46334	1.287000|1.287000	0.44583|0.44583	0.655000|0.655000	0.94253|0.94253	TGC|ATG	.	.	none		0.657	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		
ZNF543	125919	hgsc.bcm.edu	37	19	57839567	57839567	+	Missense_Mutation	SNP	T	T	A	rs1968090	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57839567T>A	ENST00000321545.4	+	4	1082	c.737T>A	c.(736-738)cTc>cAc	p.L246H		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	246			L -> H (in dbSNP:rs1968090). {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)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		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;0.0257)		CTTCAGCACCTCATCATCCAC	0.507													a|||	3414	0.681709	0.7716	0.7133	5008	,	,		21232	0.5843		0.7197	False		,,,				2504	0.5992				p.L246H		Atlas-SNP	.											.	ZNF543	61	.	0			c.T737A						PASS	.	A	HIS/LEU	3295,1111	397.0+/-330.2	1223,849,131	70.0	70.0	70.0		737	2.3	0.6	19	dbSNP_92	70	6414,2186	373.1+/-336.9	2402,1610,288	yes	missense	ZNF543	NM_213598.3	99	3625,2459,419	AA,AT,TT		25.4186,25.2156,25.3498	benign	246/601	57839567	9709,3297	2203	4300	6503	SO:0001583	missense	125919	exon4			AGCACCTCATCAT	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.737T>A	19.37:g.57839567T>A	ENSP00000322545:p.Leu246His	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	1508	0.6904761904761905	356	0.7235772357723578	261	0.7209944751381215	338	0.5909090909090909	553	0.7295514511873351	A	0.092	-1.165669	0.01673	0.747844	0.745814	ENSG00000178229	ENST00000321545	T	0.22336	1.96	2.33	2.33	0.28932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.73319	2.225	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15780	-1.0425	8	0.31617	T	0.26	.	7.18	0.25768	0.7995:0.0:0.0:0.2005	rs1968090;rs16987824;rs52796659;rs1968090	246	Q08ER8	ZN543_HUMAN	H	246	ENSP00000322545:L246H	ENSP00000322545:L246H	L	+	2	0	ZNF543	62531379	0.000000	0.05858	0.576000	0.28549	0.816000	0.46133	-0.576000	0.05854	0.328000	0.23435	-0.364000	0.07487	CTC	T|0.268;A|0.732	0.732	strong		0.507	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
FFAR4	338557	hgsc.bcm.edu	37	10	95326676	95326676	+	Missense_Mutation	SNP	C	C	T	rs61866610	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	113	0	0		WXS	Illumina HiSeq	Phase_I	82	72	0.878049	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	
TMEM199	147007	hgsc.bcm.edu	37	17	26684707	26684707	+	Nonsense_Mutation	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:26684707T>A	ENST00000292114.3	+	1	104	c.14T>A	c.(13-15)tTg>tAg	p.L5*	TMEM199_ENST00000581386.1_3'UTR|TMEM199_ENST00000395404.3_5'Flank|POLDIP2_ENST00000540200.1_5'Flank|MIR4723_ENST00000585070.1_RNA|TMEM199_ENST00000509083.1_Nonsense_Mutation_p.L5*|CTB-96E2.3_ENST00000591482.1_RNA|POLDIP2_ENST00000003607.4_5'Flank	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199	5						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		GCGTCCTCTTTGCTTGCGGGC	0.692																																					p.L5X		Atlas-SNP	.											.	TMEM199	15	.	0			c.T14A						PASS	.						46.0	53.0	50.0					17																	26684707		2203	4299	6502	SO:0001587	stop_gained	147007	exon1			CCTCTTTGCTTGC	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498	ENST00000292114.3:c.14T>A	17.37:g.26684707T>A	ENSP00000292114:p.Leu5*	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	41	16	0.390244	NM_152464		Nonsense_Mutation	SNP	ENST00000292114.3	37	CCDS11228.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.715363	0.68844	.	.	ENSG00000244045	ENST00000292114;ENST00000509083	.	.	.	4.87	3.78	0.43462	.	0.423693	0.22233	N	0.062791	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.4721	9.6131	0.39674	0.0:0.0:0.1765:0.8235	.	.	.	.	X	5	.	ENSP00000292114:L5X	L	+	2	0	TMEM199	23708834	0.068000	0.21057	0.001000	0.08648	0.003000	0.03518	2.583000	0.46094	0.861000	0.35504	-0.313000	0.08912	TTG	.	.	none		0.692	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37462926	37462926	+	Silent	SNP	G	G	A	rs2235321	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:37462926G>A	ENST00000346753.3	-	17	2333	c.2217C>T	c.(2215-2217)taC>taT	p.Y739Y	TMPRSS6_ENST00000406725.1_Silent_p.Y730Y|TMPRSS6_ENST00000381792.2_Silent_p.Y752Y|TMPRSS6_ENST00000406856.1_Silent_p.Y752Y	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	739	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.Y739Y(1)		breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						GCGTCACCTGGTAGCGATAGA	0.607													G|||	1783	0.35603	0.41	0.2118	5008	,	,		20113	0.4087		0.4245	False		,,,				2504	0.2607				p.Y739Y		Atlas-SNP	.											TMPRSS6,NS,carcinoma,0,1	TMPRSS6	99	1	1	Substitution - coding silent(1)	stomach(1)	c.C2217T						PASS	.	G		1850,2556	536.1+/-374.4	378,1094,731	133.0	98.0	110.0		2217	3.7	1.0	22	dbSNP_98	110	3223,5377	485.3+/-371.6	616,1991,1693	yes	coding-synonymous	TMPRSS6	NM_153609.2		994,3085,2424	AA,AG,GG		37.4767,41.9882,39.0051		739/812	37462926	5073,7933	2203	4300	6503	SO:0001819	synonymous_variant	164656	exon17			CACCTGGTAGCGA	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.2217C>T	22.37:g.37462926G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	201	99	0.492537	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			G|0.622;A|0.377	0.377	strong		0.607	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
GAA	2548	hgsc.bcm.edu	37	17	78084769	78084769	+	Silent	SNP	G	G	A	rs1042396	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78084769G>A	ENST00000302262.3	+	11	1800	c.1581G>A	c.(1579-1581)agG>agA	p.R527R	GAA_ENST00000390015.3_Silent_p.R527R	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	527					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)	p.R527R(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	ACTTCATCAGGGGCTCTGAGG	0.597													G|||	799	0.159545	0.034	0.2579	5008	,	,		17055	0.1091		0.2724	False		,,,				2504	0.1953				p.R527R		Atlas-SNP	.											GAA,NS,carcinoma,0,1	GAA	66	1	1	Substitution - coding silent(1)	stomach(1)	c.G1581A						PASS	.	G	,,	301,4105	164.0+/-195.7	13,275,1915	90.0	79.0	83.0		1581,1581,1581	0.7	0.6	17	dbSNP_86	83	2422,6178	400.5+/-346.8	334,1754,2212	no	coding-synonymous,coding-synonymous,coding-synonymous	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	,,	347,2029,4127	AA,AG,GG		28.1628,6.8316,20.9365	,,	527/953,527/953,527/953	78084769	2723,10283	2203	4300	6503	SO:0001819	synonymous_variant	2548	exon12			CATCAGGGGCTCT		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"""Pompe disease"", ""glycogen storage disease type II"""	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.1581G>A	17.37:g.78084769G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	131	62	0.473282	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	37	CCDS32760.1																																																																																			G|0.800;A|0.200	0.200	strong		0.597	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		
PLEKHH2	130271	hgsc.bcm.edu	37	2	43926943	43926943	+	Silent	SNP	T	T	A	rs7606783	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:43926943T>A	ENST00000282406.4	+	8	956	c.846T>A	c.(844-846)ccT>ccA	p.P282P		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	282					negative regulation of actin filament depolymerization (GO:0030835)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(24)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	56		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CTGGGGCTCCTGTGAGTGACT	0.517													A|||	2640	0.527157	0.7935	0.4741	5008	,	,		18637	0.1647		0.5467	False		,,,				2504	0.5583				p.P282P		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.T846A						PASS	.	A		3296,1110	399.7+/-331.3	1235,826,142	71.0	73.0	72.0		846	-11.7	0.0	2	dbSNP_116	72	4606,3994	554.4+/-386.5	1246,2114,940	no	coding-synonymous	PLEKHH2	NM_172069.3		2481,2940,1082	AA,AT,TT		46.4419,25.1929,39.2434		282/1494	43926943	7902,5104	2203	4300	6503	SO:0001819	synonymous_variant	130271	exon8			GGCTCCTGTGAGT	AB095948	CCDS1812.1	2p22	2013-01-10			ENSG00000152527	ENSG00000152527		"""Pleckstrin homology (PH) domain containing"""	30506	protein-coding gene	gene with protein product		612723					Standard	NM_172069		Approved	KIAA2028, PLEKHH1L	uc010yny.2	Q8IVE3	OTTHUMG00000128657	ENST00000282406.4:c.846T>A	2.37:g.43926943T>A		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	218	101	0.463303	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Silent	SNP	ENST00000282406.4	37	CCDS1812.1																																																																																			T|0.440;A|0.560	0.560	strong		0.517	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069	
TTN	7273	hgsc.bcm.edu	37	2	179400718	179400718	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179400718C>T	ENST00000591111.1	-	307	96057	c.95833G>A	c.(95833-95835)Gaa>Aaa	p.E31945K	TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E33586K|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E31018K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E24521K|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E24646K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E24713K|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA			Q8WZ42	TITIN_HUMAN	titin	31945	Ig-like 141.				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)			CCTTCCACTTCCAAGGAGGCA	0.428																																					p.E33586K		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+2,5	TTN	18412	5	0			c.G100756A						scavenged	.						68.0	63.0	65.0					2																	179400718		1896	4132	6028	SO:0001583	missense	7273	exon357			CCACTTCCAAGGA	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.95833G>A	2.37:g.179400718C>T	ENSP00000465570:p.Glu31945Lys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	101	2	0.019802	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	17.25	3.341260	0.60963	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18	5.6	5.6	0.85130	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	0.52240	0.1722	N	0.20574	0.59	0.54753	D	0.999984	B;B;B;B	0.25272	0.122;0.061;0.061;0.122	B;B;B;B	0.22601	0.04;0.01;0.01;0.04	T	0.51679	-0.8675	9	0.87932	D	0	.	19.9756	0.97304	0.0:1.0:0.0:0.0	.	24521;24646;24713;31945	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	31018;24521;24713;24646;24518	ENSP00000343764:E31018K;ENSP00000434586:E24521K;ENSP00000340554:E24713K;ENSP00000352154:E24646K	ENSP00000340554:E24713K	E	-	1	0	TTN	179108964	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.793000	0.96121	0.563000	0.77884	GAA	.	.	none		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CASP8	841	hgsc.bcm.edu	37	2	202137432	202137432	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:202137432A>G	ENST00000432109.2	+	5	672	c.483A>G	c.(481-483)aaA>aaG	p.K161K	CASP8_ENST00000323492.7_Silent_p.K161K|CASP8_ENST00000358485.4_Silent_p.K220K|CASP8_ENST00000264274.9_Silent_p.K161K|CASP8_ENST00000392259.2_Silent_p.K161K|CASP8_ENST00000392266.3_Silent_p.K161K|CASP8_ENST00000392258.3_Silent_p.K161K|CASP8_ENST00000264275.5_Silent_p.K193K	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	161	DED 2. {ECO:0000255|PROSITE- ProRule:PRU00065}.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|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)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						ACATCCTGAAAAGAGTCTGTG	0.438										HNSCC(4;0.00038)																											p.K220K	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											.	CASP8	272	.	0			c.A660G						PASS	.						154.0	157.0	156.0					2																	202137432		2203	4300	6503	SO:0001819	synonymous_variant	841	exon4			CCTGAAAAGAGTC	U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"""Caspases"""	1509	protein-coding gene	gene with protein product		601763	"""caspase 8, apoptosis-related cysteine protease"""			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.483A>G	2.37:g.202137432A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	107	71	0.663551	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Silent	SNP	ENST00000432109.2	37	CCDS2342.1																																																																																			.	.	none		0.438	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228	
ZNF534	147658	hgsc.bcm.edu	37	19	52937339	52937339	+	Silent	SNP	G	G	A	rs17780173	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52937339G>A	ENST00000332323.6	+	2	208	c.147G>A	c.(145-147)gaG>gaA	p.E49E	ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000433050.1_Intron|ZNF534_ENST00000432303.2_Intron	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	49	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)			central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						CCCTAGGTGAGGATAATGTCC	0.488													G|||	1248	0.249201	0.1165	0.2579	5008	,	,		18246	0.4772		0.1282	False		,,,				2504	0.3119				p.E49E		Atlas-SNP	.											.	ZNF534	105	.	0			c.G147A						PASS	.	G	,	422,2714		28,366,1174	103.0	99.0	100.0		,147	1.0	0.4	19	dbSNP_123	100	795,6369		40,715,2827	no	intron,coding-synonymous	ZNF534	NM_001143938.1,NM_001143939.1	,	68,1081,4001	AA,AG,GG		11.0972,13.4566,11.8155	,	,49/675	52937339	1217,9083	1568	3582	5150	SO:0001819	synonymous_variant	147658	exon2			AGGTGAGGATAAT	AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"""Zinc fingers, C2H2-type"", ""-"""	26337	protein-coding gene	gene with protein product			"""KRAB domain only 3"""	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.147G>A	19.37:g.52937339G>A		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	243	96	0.395062	NM_001143939	Q76KX9	Silent	SNP	ENST00000332323.6	37	CCDS46165.1																																																																																			G|0.765;A|0.235	0.235	strong		0.488	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512	
TLN1	7094	hgsc.bcm.edu	37	9	35712003	35712003	+	Splice_Site	SNP	G	G	A	rs2295795	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:35712003G>A	ENST00000314888.9	-	28	4033	c.3680C>T	c.(3679-3681)tCg>tTg	p.S1227L	TLN1_ENST00000540444.1_Splice_Site_p.S1227L	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1227			S -> L (in dbSNP:rs2295795). {ECO:0000269|Ref.1}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCCTCCTACCGAGTCACTCAG	0.597													G|||	1009	0.201478	0.0197	0.268	5008	,	,		18282	0.3383		0.2704	False		,,,				2504	0.1881				p.S1227L		Atlas-SNP	.											.	TLN1	185	.	0			c.C3680T						PASS	.	G	LEU/SER	280,4126	155.5+/-188.7	14,252,1937	54.0	49.0	51.0		3680	4.9	1.0	9	dbSNP_100	51	2408,6192	398.5+/-346.1	332,1744,2224	yes	missense-near-splice	TLN1	NM_006289.3	145	346,1996,4161	AA,AG,GG		28.0,6.355,20.6674	benign	1227/2542	35712003	2688,10318	2203	4300	6503	SO:0001630	splice_region_variant	7094	exon28			CCTACCGAGTCAC	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.3681+1C>T	9.37:g.35712003G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	521	0.23855311355311357	12	0.024390243902439025	100	0.27624309392265195	213	0.3723776223776224	196	0.25857519788918204	G	16.00	2.999336	0.54147	0.06355	0.28	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.12147	2.71;2.71	5.82	4.92	0.64577	.	0.356696	0.30492	N	0.009506	T	0.00012	0.0000	L	0.54323	1.7	0.20403	P	0.9999095468	B	0.09022	0.002	B	0.04013	0.001	T	0.46978	-0.9152	9	0.32370	T	0.25	-0.5518	16.3893	0.83528	0.0:0.0:0.8673:0.1327	rs2295795;rs17260374;rs60567288;rs2295795	1227	Q9Y490	TLN1_HUMAN	L	1227	ENSP00000316029:S1227L;ENSP00000442981:S1227L	ENSP00000316029:S1227L	S	-	2	0	TLN1	35702003	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	7.695000	0.84257	1.466000	0.48025	-0.169000	0.13324	TCG	G|0.785;A|0.215	0.215	strong		0.597	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Missense_Mutation
TCP10L2	401285	hgsc.bcm.edu	37	6	167592606	167592606	+	Silent	SNP	T	T	A	rs201866116	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	75	0	0		WXS	Illumina HiSeq	Phase_I	131	44	0.335878	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	
CLK2	1196	hgsc.bcm.edu	37	1	155235736	155235736	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:155235736T>C	ENST00000368361.4	-	8	1163	c.848A>G	c.(847-849)gAt>gGt	p.D283G	CLK2_ENST00000355560.4_Missense_Mutation_p.D281G|CLK2_ENST00000497188.1_5'UTR|CLK2_ENST00000361168.5_Missense_Mutation_p.D282G|CLK2_ENST00000536801.1_Missense_Mutation_p.D283G			P49760	CLK2_HUMAN	CDC-like kinase 2	283	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CAGCTTGTTATCATGGAGGAC	0.502								Other conserved DNA damage response genes																													p.D282G		Atlas-SNP	.											CLK2,NS,carcinoma,-1,1	CLK2	55	1	0			c.A845G						scavenged	.						136.0	126.0	129.0					1																	155235736		2203	4300	6503	SO:0001583	missense	1196	exon8			TTGTTATCATGGA	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"""CDC-like kinases"""	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.848A>G	1.37:g.155235736T>C	ENSP00000357345:p.Asp283Gly	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	185	2	0.0108108	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Missense_Mutation	SNP	ENST00000368361.4	37		.	.	.	.	.	.	.	.	.	.	.	26.3	4.721785	0.89298	.	.	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000424156;ENST00000536801	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.045544	0.85682	D	0.000000	T	0.13841	0.0335	L	0.46741	1.465	0.80722	D	1	B;B	0.16603	0.018;0.015	B;B	0.31016	0.123;0.075	T	0.04053	-1.0981	10	0.87932	D	0	.	14.0981	0.65037	0.0:0.0:0.0:1.0	.	283;282	P49760;P49760-3	CLK2_HUMAN;.	G	282;283;281;55;283	ENSP00000354856:D282G;ENSP00000357345:D283G;ENSP00000347759:D281G;ENSP00000441023:D283G	ENSP00000347759:D281G	D	-	2	0	CLK2	153502360	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.825000	0.86693	2.264000	0.75181	0.533000	0.62120	GAT	.	.	none		0.502	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993	
XIRP2	129446	hgsc.bcm.edu	37	2	168115769	168115769	+	Missense_Mutation	SNP	G	G	C	rs16853344	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168115769G>C	ENST00000409728.1	+	11	2901	c.2812G>C	c.(2812-2814)Gaa>Caa	p.E938Q	XIRP2_ENST00000409605.1_Missense_Mutation_p.E683Q|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.E905Q|XIRP2_ENST00000409043.1_Missense_Mutation_p.E905Q|XIRP2_ENST00000420519.1_Missense_Mutation_p.E938Q|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409195.1_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					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						TCTGAGCCATGAATGTACAGC	0.438													G|||	904	0.180511	0.3154	0.1239	5008	,	,		19064	0.12		0.1123	False		,,,				2504	0.1708				p.E938Q		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2812C						PASS	.	G	GLN/GLU,GLN/GLU,,GLN/GLU,	1076,2764		155,766,999	91.0	84.0	86.0		2713,2812,,2047,	4.0	0.0	2	dbSNP_123	86	808,7474		43,722,3376	yes	missense,missense,utr-3,missense,utr-3	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	29,29,,29,	198,1488,4375	CC,CG,GG		9.7561,28.0208,15.542	,,,,	905/939,938/972,,683/717,	168115769	1884,10238	1920	4141	6061	SO:0001583	missense	129446	exon11			AGCCATGAATGTA	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	ENST00000409728.1:c.2812G>C	2.37:g.168115769G>C	ENSP00000386619:p.Glu938Gln	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	378	0.17307692307692307	175	0.3556910569105691	43	0.11878453038674033	72	0.1258741258741259	88	0.11609498680738786	G	15.51	2.855789	0.51376	0.280208	0.097561	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.78707	-1.19;-1.2;-1.19;-1.2;-1.19	5.91	3.97	0.46021	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P;P	0.43287	0.454;0.802	B;B	0.36719	0.117;0.231	T	0.22521	-1.0214	7	0.25751	T	0.34	.	5.0051	0.14284	0.0883:0.16:0.6078:0.1439	rs16853344;rs52807647;rs57534200;rs16853344	905;938	A4UGR9-4;A4UGR9-6	.;.	Q	905;938;905;938;683	ENSP00000386454:E905Q;ENSP00000386619:E938Q;ENSP00000386724:E905Q;ENSP00000415541:E938Q;ENSP00000386981:E683Q	ENSP00000386454:E905Q	E	+	1	0	XIRP2	167824015	0.033000	0.19621	0.004000	0.12327	0.148000	0.21650	1.778000	0.38614	1.466000	0.48025	0.650000	0.86243	GAA	G|0.841;C|0.159	0.159	strong		0.438	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
LURAP1L	286343	hgsc.bcm.edu	37	9	12775855	12775855	+	Silent	SNP	T	T	C	rs572021640		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:12775855T>C	ENST00000319264.3	+	1	836	c.141T>C	c.(139-141)ggT>ggC	p.G47G	LURAP1L_ENST00000489107.1_3'UTR|RP11-3L8.3_ENST00000417638.1_RNA	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	50	Gly-rich.		Missing.														GGGGGAgcggtggtggtggcg	0.677																																					p.G47G		Atlas-SNP	.											.	.	.	.	0			c.T141C						PASS	.						5.0	6.0	5.0					9																	12775855		2076	4056	6132	SO:0001819	synonymous_variant	286343	exon1			GAGCGGTGGTGGT	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.141T>C	9.37:g.12775855T>C		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	17	7	0.411765	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Silent	SNP	ENST00000319264.3	37	CCDS6473.1																																																																																			.	.	none		0.677	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
PLIN4	729359	hgsc.bcm.edu	37	19	4511354	4511354	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4511354G>A	ENST00000301286.3	-	3	2575	c.2576C>T	c.(2575-2577)gCg>gTg	p.A859V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	859	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						GGCCACTTTCGCAGCACCGGT	0.587																																					p.A859V		Atlas-SNP	.											PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	0			c.C2576T						scavenged	.						68.0	78.0	75.0					19																	4511354		1926	4130	6056	SO:0001583	missense	729359	exon3			ACTTTCGCAGCAC	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.2576C>T	19.37:g.4511354G>A	ENSP00000301286:p.Ala859Val	Somatic	302	3	0.00993378		WXS	Illumina HiSeq	Phase_I	336	12	0.0357143	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	G	3.131	-0.178501	0.06380	.	.	ENSG00000167676	ENST00000301286	T	0.02863	4.13	4.78	-1.01	0.10169	.	0.874251	0.09537	N	0.788765	T	0.01189	0.0039	N	0.03948	-0.315	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.48525	-0.9028	10	0.07644	T	0.81	-5.1453	5.6638	0.17684	0.3615:0.0:0.4823:0.1562	.	859	Q96Q06	PLIN4_HUMAN	V	859	ENSP00000301286:A859V	ENSP00000301286:A859V	A	-	2	0	PLIN4	4462354	0.065000	0.20965	0.000000	0.03702	0.002000	0.02628	-0.241000	0.08940	-0.050000	0.13356	-0.379000	0.06801	GCG	.	.	none		0.587	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
SYT2	127833	hgsc.bcm.edu	37	1	202574784	202574784	+	Silent	SNP	G	G	A	rs1968583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:202574784G>A	ENST00000367267.1	-	2	309	c.117C>T	c.(115-117)agC>agT	p.S39S	SYT2_ENST00000367268.4_Silent_p.S39S|RP11-569A11.1_ENST00000428573.1_RNA	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	39					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	TGTCCTCCTGGCTCTCCCCAG	0.557													G|||	1797	0.358826	0.0794	0.4597	5008	,	,		17852	0.3621		0.5746	False		,,,				2504	0.4397				p.S39S		Atlas-SNP	.											.	SYT2	51	.	0			c.C117T						PASS	.	G	,	693,3713	291.3+/-281.4	65,563,1575	70.0	67.0	68.0		117,117	2.1	1.0	1	dbSNP_92	68	4549,4051	595.3+/-393.4	1191,2167,942	no	coding-synonymous,coding-synonymous	SYT2	NM_001136504.1,NM_177402.4	,	1256,2730,2517	AA,AG,GG		47.1047,15.7286,40.3045	,	39/420,39/420	202574784	5242,7764	2203	4300	6503	SO:0001819	synonymous_variant	127833	exon2			CTCCTGGCTCTCC	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"""Synaptotagmins"""	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.117C>T	1.37:g.202574784G>A		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	338	331	0.97929	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	37	CCDS1427.1																																																																																			G|0.596;A|0.404	0.404	strong		0.557	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318821	21318821	+	Missense_Mutation	SNP	A	A	C	rs1714865	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:21318821A>C	ENST00000583088.1	+	3	1062	c.167A>C	c.(166-168)gAg>gCg	p.E56A	KCNJ12_ENST00000331718.5_Missense_Mutation_p.E56A	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	56					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)	p.E56A(1)		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)	TGCAACATTGAGTTCGCCAAC	0.597										Prostate(3;0.18)																											p.E56A		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,3	.	.	3	1	Substitution - Missense(1)	stomach(1)	c.A167C						scavenged	.	A	ALA/GLU	1553,2853		0,1553,650	194.0	130.0	152.0		167	5.3	1.0	17	dbSNP_89	152	2888,5712		0,2888,1412	yes	missense	KCNJ12	NM_021012.4	107	0,4441,2062	CC,CA,AA		33.5814,35.2474,34.1458	benign	56/434	21318821	4441,8565	2203	4300	6503	SO:0001583	missense	100134444	exon3			ACATTGAGTTCGC	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.167A>C	17.37:g.21318821A>C	ENSP00000463778:p.Glu56Ala	Somatic	306	2	0.00653595		WXS	Illumina HiSeq	Phase_I	223	32	0.143498	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	A	7.891	0.732400	0.15507	0.352474	0.335814	ENSG00000184185	ENST00000331718	D	0.93811	-3.29	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.057699	0.64402	D	0.000001	T	0.00012	0.0000	N	0.16130	0.375	0.52099	D	0.999949	B	0.12013	0.005	B	0.22880	0.042	T	0.03840	-1.0999	10	0.09843	T	0.71	.	15.3028	0.73966	1.0:0.0:0.0:0.0	rs1714865;rs3752035;rs1714865	56	Q14500	IRK12_HUMAN	A	56	ENSP00000328150:E56A	ENSP00000328150:E56A	E	+	2	0	KCNJ12	21259414	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.171000	0.94802	2.027000	0.59764	0.482000	0.46254	GAG	A|0.988;C|0.012	0.012	strong		0.597	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
CDC6	990	hgsc.bcm.edu	37	17	38457151	38457151	+	Missense_Mutation	SNP	G	G	A	rs13706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38457151G>A	ENST00000209728.4	+	10	1792	c.1321G>A	c.(1321-1323)Gtt>Att	p.V441I	CTD-2267D19.6_ENST00000602403.1_lincRNA	NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	441			V -> I (in dbSNP:rs13706). {ECO:0000269|PubMed:15489334, 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						CATCTCAGAAGTTGATGGTAA	0.428													G|||	1402	0.279952	0.5348	0.183	5008	,	,		21220	0.3482		0.1113	False		,,,				2504	0.1074				p.V441I		Atlas-SNP	.											.	CDC6	53	.	0			c.G1321A	GRCh37	CM065057	CDC6	M	rs13706	PASS	.	G	ILE/VAL	2014,2392	561.4+/-380.7	479,1056,668	217.0	194.0	202.0		1321	3.8	1.0	17	dbSNP_52	202	950,7650	208.7+/-250.1	57,836,3407	yes	missense	CDC6	NM_001254.3	29	536,1892,4075	AA,AG,GG		11.0465,45.7104,22.7895	possibly-damaging	441/561	38457151	2964,10042	2203	4300	6503	SO:0001583	missense	990	exon10			TCAGAAGTTGATG	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.1321G>A	17.37:g.38457151G>A	ENSP00000209728:p.Val441Ile	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	235	119	0.506383	NM_001254	Q8TB30	Missense_Mutation	SNP	ENST00000209728.4	37	CCDS11365.1	608	0.2783882783882784	255	0.5182926829268293	62	0.1712707182320442	215	0.3758741258741259	76	0.10026385224274406	G	19.42	3.823558	0.71143	0.457104	0.110465	ENSG00000094804	ENST00000209728	T	0.52983	0.64	5.96	3.82	0.43975	.	0.185081	0.46442	N	0.000289	T	0.00012	0.0000	L	0.54908	1.71	0.24597	P	0.99379435	P	0.44578	0.838	B	0.44224	0.444	T	0.49670	-0.8915	9	0.17369	T	0.5	-11.9661	10.4299	0.44400	0.204:0.0:0.796:0.0	rs13706;rs1048815;rs2230629;rs3188865;rs17852245;rs57349852;rs13706	441	Q99741	CDC6_HUMAN	I	441	ENSP00000209728:V441I	ENSP00000209728:V441I	V	+	1	0	CDC6	35710677	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	4.003000	0.57061	1.539000	0.49286	0.655000	0.94253	GTT	G|0.734;A|0.266	0.266	strong		0.428	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1		
QRICH1	54870	hgsc.bcm.edu	37	3	49067904	49067904	+	Missense_Mutation	SNP	T	T	C	rs61729488	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49067904T>C	ENST00000395443.2	-	10	2784	c.2312A>G	c.(2311-2313)aAt>aGt	p.N771S	QRICH1_ENST00000479449.1_5'Flank|IMPDH2_ENST00000326739.4_5'Flank|QRICH1_ENST00000357496.2_Missense_Mutation_p.N771S|QRICH1_ENST00000424300.1_Missense_Mutation_p.N771S|RP13-131K19.6_ENST00000607245.1_RNA	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	88	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	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	
DNAH9	1770	hgsc.bcm.edu	37	17	11757556	11757556	+	Silent	SNP	C	C	G	rs12449553	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	139	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	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	
NACA2	342538	hgsc.bcm.edu	37	17	59668517	59668517	+	Missense_Mutation	SNP	C	C	A	rs61748812	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:59668517C>A	ENST00000521764.1	-	1	46	c.25G>T	c.(25-27)Gtc>Ttc	p.V9F		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	9					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)					GTAGCAGGGACGGTTTCTGTG	0.582													C|||	47	0.00938498	0.0	0.0144	5008	,	,		20219	0.001		0.0229	False		,,,				2504	0.0133				p.V9F		Atlas-SNP	.											.	NACA2	33	.	0			c.G25T						PASS	.	C	PHE/VAL	26,4380	34.3+/-65.2	0,26,2177	65.0	59.0	61.0		25	0.8	0.9	17	dbSNP_129	61	239,8361	96.6+/-158.3	4,231,4065	yes	missense	NACA2	NM_199290.3	50	4,257,6242	AA,AC,CC		2.7791,0.5901,2.0375	benign	9/216	59668517	265,12741	2203	4300	6503	SO:0001583	missense	342538	exon1			CAGGGACGGTTTC	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.25G>T	17.37:g.59668517C>A	ENSP00000427802:p.Val9Phe	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_199290	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	24	0.01098901098901099	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	15	0.01978891820580475	C	12.65	2.001431	0.35320	0.005901	0.027791	ENSG00000253506	ENST00000521764	T	0.49139	0.79	0.753	0.753	0.18404	.	0.000000	0.50627	U	0.000103	T	0.16981	0.0408	L	0.60455	1.87	0.37959	D	0.93291	B	0.02656	0.0	B	0.06405	0.002	T	0.23261	-1.0193	8	.	.	.	.	.	.	.	.	9	Q9H009	NACA2_HUMAN	F	9	ENSP00000427802:V9F	.	V	-	1	0	NACA2	57023299	1.000000	0.71417	0.943000	0.38184	0.139000	0.21198	2.662000	0.46766	0.702000	0.31825	0.411000	0.27672	GTC	C|0.980;A|0.020	0.020	strong		0.582	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
GRAMD1B	57476	hgsc.bcm.edu	37	11	123480981	123480981	+	Silent	SNP	T	T	C	rs10893053	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:123480981T>C	ENST00000529750.1	+	13	1752	c.1425T>C	c.(1423-1425)caT>caC	p.H475H	GRAMD1B_ENST00000322282.7_Silent_p.H475H|GRAMD1B_ENST00000456860.2_Silent_p.H482H|GRAMD1B_ENST00000450171.2_Silent_p.H166H	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	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	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	
LAMA1	284217	hgsc.bcm.edu	37	18	7080048	7080048	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:7080048T>C	ENST00000389658.3	-	3	364	c.271A>G	c.(271-273)Aac>Gac	p.N91D	RP11-76K13.3_ENST00000581502.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	91	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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)				TGCCACCAGTTATTGGTGCCA	0.418																																					p.N91D		Atlas-SNP	.											.	LAMA1	458	.	0			c.A271G						PASS	.						167.0	135.0	146.0					18																	7080048		2203	4300	6503	SO:0001583	missense	284217	exon3			ACCAGTTATTGGT	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.271A>G	18.37:g.7080048T>C	ENSP00000374309:p.Asn91Asp	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	246	116	0.471545	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.140937	0.56936	.	.	ENSG00000101680	ENST00000389658	T	0.75821	-0.97	5.61	4.45	0.53987	Laminin, N-terminal (3);	0.245554	0.40908	D	0.000990	T	0.60495	0.2273	L	0.31526	0.94	0.29065	N	0.883622	B	0.19200	0.034	B	0.16289	0.015	T	0.57911	-0.7729	10	0.72032	D	0.01	.	7.2768	0.26290	0.0:0.0731:0.157:0.7699	.	91	P25391	LAMA1_HUMAN	D	91	ENSP00000374309:N91D	ENSP00000374309:N91D	N	-	1	0	LAMA1	7070048	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.279000	0.43435	0.964000	0.38108	0.533000	0.62120	AAC	.	.	none		0.418	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
GPR146	115330	hgsc.bcm.edu	37	7	1097895	1097895	+	Silent	SNP	A	A	G	rs61910751	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:1097895A>G	ENST00000397095.1	+	2	967	c.744A>G	c.(742-744)ccA>ccG	p.P248P	GPR146_ENST00000297468.3_Silent_p.P248P|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	248						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)		TCTGGACGCCACACTATCTGA	0.647													G|||	345	0.0688898	0.0204	0.0821	5008	,	,		17834	0.0		0.1262	False		,,,				2504	0.137				p.P248P		Atlas-SNP	.											.	GPR146	20	.	0			c.A744G						PASS	.		,,,	206,4198	800.2+/-415.6	2,202,1998	59.0	48.0	52.0		,,,744	-10.2	0.0	7	dbSNP_129	52	1354,7244	751.8+/-407.4	106,1142,3051	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	108,1344,5049	GG,GA,AA		15.7478,4.6776,11.9982	,,,	,,,248/334	1097895	1560,11442	2202	4299	6501	SO:0001819	synonymous_variant	115330	exon1			GACGCCACACTAT	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.744A>G	7.37:g.1097895A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	41	26	0.634146	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			A|0.893;G|0.106;T|0.000	0.106	strong		0.647	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
MUC17	140453	hgsc.bcm.edu	37	7	100678421	100678421	+	Missense_Mutation	SNP	T	T	A	rs200902631|rs10265276	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678421T>A	ENST00000306151.4	+	3	3788	c.3724T>A	c.(3724-3726)Tct>Act	p.S1242T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1242	59 X approximate tandem repeats.|Ser-rich.		S -> T (in dbSNP:rs10265276).		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)					CCTTTCAACATCTCCCGTTGA	0.517													A|||	1177	0.235024	0.3389	0.1009	5008	,	,		29246	0.253		0.1213	False		,,,				2504	0.2883				p.S1242T		Atlas-SNP	.											MUC17,NS,carcinoma,-1,1	MUC17	804	1	0			c.T3724A						scavenged	.	A	THR/SER	1322,3084	695.6+/-406.0	206,910,1087	288.0	284.0	286.0		3724	-1.7	0.0	7	dbSNP_119	286	999,7601	773.2+/-407.7	57,885,3358	no	missense	MUC17	NM_001040105.1	58	263,1795,4445	AA,AT,TT		11.6163,30.0045,17.8456	benign	1242/4494	100678421	2321,10685	2203	4300	6503	SO:0001583	missense	140453	exon3			TCAACATCTCCCG	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.3724T>A	7.37:g.100678421T>A	ENSP00000302716:p.Ser1242Thr	Somatic	137	2	0.0145985		WXS	Illumina HiSeq	Phase_I	249	244	0.97992	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	471	0.21565934065934067	160	0.3252032520325203	46	0.1270718232044199	161	0.28146853146853146	104	0.13720316622691292	A	1.120	-0.655521	0.03480	0.300045	0.116163	ENSG00000169876	ENST00000306151	T	0.02498	4.27	0.838	-1.68	0.08212	.	.	.	.	.	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	0.35871	-0.9771	8	0.09084	T	0.74	.	2.3789	0.04349	0.3049:0.2132:0.0:0.4819	rs10265276;rs59394740	1242	Q685J3	MUC17_HUMAN	T	1242	ENSP00000302716:S1242T	ENSP00000302716:S1242T	S	+	1	0	MUC17	100465141	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.179000	0.03090	-2.874000	0.00322	-1.617000	0.00794	TCT	T|0.819;A|0.181	0.181	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CPAMD8	27151	hgsc.bcm.edu	37	19	17017878	17017878	+	Missense_Mutation	SNP	G	G	A	rs56408444	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	212	0	0		WXS	Illumina HiSeq	Phase_I	195	89	0.45641	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	
NIPAL3	57185	hgsc.bcm.edu	37	1	24785393	24785393	+	Silent	SNP	C	C	T	rs2272935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:24785393C>T	ENST00000374399.4	+	9	1157	c.789C>T	c.(787-789)gcC>gcT	p.A263A	NIPAL3_ENST00000339255.2_Silent_p.A263A|NIPAL3_ENST00000003912.3_Silent_p.A181A	NM_020448.4	NP_065181.1	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3	263						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(1)	14						TGAGTCAAGCCTCACAGATGT	0.463													C|||	1534	0.30631	0.1589	0.4409	5008	,	,		20800	0.4534		0.2773	False		,,,				2504	0.2883				p.A263A		Atlas-SNP	.											NIPAL3,NS,carcinoma,+1,1	NIPAL3	36	1	0			c.C789T						scavenged	.	C		704,3702	295.0+/-283.4	49,606,1548	215.0	176.0	189.0		789	1.6	1.0	1	dbSNP_100	189	2253,6347	382.3+/-340.3	281,1691,2328	no	coding-synonymous	NIPAL3	NM_020448.4		330,2297,3876	TT,TC,CC		26.1977,15.9782,22.7357		263/407	24785393	2957,10049	2203	4300	6503	SO:0001819	synonymous_variant	57185	exon9			TCAAGCCTCACAG	BX640883	CCDS30631.1	1p36.12-p35.1	2009-03-24		2009-03-24	ENSG00000001461	ENSG00000001461			25233	protein-coding gene	gene with protein product				NPAL3		8619474, 9110174	Standard	NM_020448		Approved	DJ462O23.2	uc001bjh.3	Q6P499	OTTHUMG00000003299	ENST00000374399.4:c.789C>T	1.37:g.24785393C>T		Somatic	188	2	0.0106383		WXS	Illumina HiSeq	Phase_I	124	95	0.766129	NM_020448	A2A298|Q6MZT9|Q9BVE6	Silent	SNP	ENST00000374399.4	37	CCDS30631.1	697	0.3191391941391941	77	0.1565040650406504	148	0.4088397790055249	260	0.45454545454545453	212	0.2796833773087071	C	16.35	3.098373	0.56183	0.159782	0.261977	ENSG00000001461	ENST00000432012	.	.	.	5.86	1.62	0.23740	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45862	-0.9232	3	.	.	.	-24.4414	1.4986	0.02471	0.2365:0.43:0.1193:0.2142	rs2272935;rs52791624;rs58306533;rs2272935	.	.	.	L	75	.	.	P	+	2	0	NIPAL3	24657980	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.530000	0.23036	0.366000	0.24427	0.563000	0.77884	CCT	C|0.732;T|0.268	0.268	strong		0.463	NIPAL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276996.1	NM_020448	
PCSK7	9159	hgsc.bcm.edu	37	11	117079654	117079654	+	Missense_Mutation	SNP	A	A	T	rs471009		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117079654A>T	ENST00000320934.3	-	13	2280	c.1650T>A	c.(1648-1650)agT>agA	p.S550R	PCSK7_ENST00000529458.1_5'Flank|PCSK7_ENST00000540028.1_Missense_Mutation_p.S191R	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	550					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		ACATCATGCCACTGGGGCAGA	0.607			T	IGH@	MLCLS																																p.S550R		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	PCSK7,NS,carcinoma,0,2	PCSK7	59	2	0			c.T1650A						scavenged	.						59.0	60.0	59.0					11																	117079654		2201	4296	6497	SO:0001583	missense	9159	exon13			CATGCCACTGGGG	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1650T>A	11.37:g.117079654A>T	ENSP00000325917:p.Ser550Arg	Somatic	422	3	0.007109		WXS	Illumina HiSeq	Phase_I	424	23	0.0542453	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	37	CCDS8382.1	14	0.00641025641025641	4	0.008130081300813009	0	0.0	5	0.008741258741258742	5	0.006596306068601583	G	13.99	2.403210	0.42613	.	.	ENSG00000160613	ENST00000320934;ENST00000540028;ENST00000543900	T;T	0.78364	-1.17;-1.17	4.68	-1.84	0.07809	Proprotein convertase, P (1);Galactose-binding domain-like (1);	0.043659	0.85682	D	0.000000	T	0.79227	0.4410	M	0.66378	2.025	0.53005	D	0.999965	D	0.69078	0.997	D	0.73380	0.98	T	0.78984	-0.1988	10	0.59425	D	0.04	-16.1089	12.2196	0.54428	0.5973:0.0:0.4027:0.0	rs471009;rs3741289	550	Q16549	PCSK7_HUMAN	R	550;191;550	ENSP00000325917:S550R;ENSP00000441944:S191R	ENSP00000325917:S550R	S	-	3	2	PCSK7	116584864	0.024000	0.19004	0.958000	0.39756	0.007000	0.05969	-0.746000	0.04829	-0.944000	0.03686	-2.386000	0.00229	AGT	A|0.994;T|0.006	0.006	strong		0.607	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
SSUH2	51066	hgsc.bcm.edu	37	3	8675539	8675539	+	Missense_Mutation	SNP	G	G	A	rs2276800	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:8675539G>A	ENST00000317371.4	-	11	1311	c.86C>T	c.(85-87)cCg>cTg	p.P29L	SSUH2_ENST00000341795.3_Missense_Mutation_p.P29L|SSUH2_ENST00000415132.1_Missense_Mutation_p.P29L|SSUH2_ENST00000544814.1_Intron			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	29			P -> L (in dbSNP:rs2276800).			cytoplasm (GO:0005737)											GGACTCACGCGGGCCAGCCAG	0.657													A|||	1671	0.333666	0.6838	0.2651	5008	,	,		10609	0.1984		0.1829	False		,,,				2504	0.2035				p.P29L		Atlas-SNP	.											C3orf32,NS,carcinoma,0,2	.	.	2	0			c.C86T						PASS	.	A	LEU/PRO	2615,1791	503.9+/-365.7	793,1029,381	27.0	30.0	29.0		86	-4.0	0.0	3	dbSNP_100	29	1528,7072	728.5+/-406.7	120,1288,2892	yes	missense	C3orf32	NM_015931.1	98	913,2317,3273	AA,AG,GG		17.7674,40.6491,31.8545	probably-damaging	29/354	8675539	4143,8863	2203	4300	6503	SO:0001583	missense	51066	exon4			TCACGCGGGCCAG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.86C>T	3.37:g.8675539G>A	ENSP00000324551:p.Pro29Leu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_015931	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	636	0.29120879120879123	323	0.6565040650406504	89	0.24585635359116023	86	0.15034965034965034	138	0.1820580474934037	A	6.834	0.522996	0.13066	0.593509	0.177674	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132	T;T;T	0.51817	0.74;0.74;0.69	3.97	-4.02	0.04034	.	0.656465	0.14884	N	0.292819	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	0.33085	-0.9882	9	0.07813	T	0.8	0.3753	6.2471	0.20825	0.3373:0.0:0.5156:0.147	rs2276800;rs57482921;rs2276800	29	Q9Y2M2	CC032_HUMAN	L	29	ENSP00000339150:P29L;ENSP00000324551:P29L;ENSP00000410757:P29L	ENSP00000324551:P29L	P	-	2	0	C3orf32	8650539	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.643000	0.05421	-1.368000	0.02149	-0.893000	0.02921	CCG	G|0.689;A|0.311	0.311	strong		0.657	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931	
ZNF106	64397	hgsc.bcm.edu	37	15	42744094	42744094	+	Missense_Mutation	SNP	A	A	G	rs12440118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42744094A>G	ENST00000263805.4	-	2	633	c.307T>C	c.(307-309)Tgg>Cgg	p.W103R	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_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	103			W -> R (in dbSNP:rs12440118).		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)										TCTCGTCTCCATTGGGGTCGT	0.438													A|||	295	0.0589058	0.0068	0.1037	5008	,	,		18656	0.006		0.1362	False		,,,				2504	0.0726				p.W103R		Atlas-SNP	.											.	ZFP106	117	.	0			c.T307C						PASS	.	A	ARG/TRP	165,4241	109.9+/-148.2	1,163,2039	215.0	195.0	202.0		307	-4.6	0.2	15	dbSNP_120	202	1288,7310	256.1+/-280.7	103,1082,3114	yes	missense	ZFP106	NM_022473.1	101	104,1245,5153	GG,GA,AA		14.9802,3.7449,11.1735	benign	103/1884	42744094	1453,11551	2203	4299	6502	SO:0001583	missense	64397	exon2			GTCTCCATTGGGG	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.307T>C	15.37:g.42744094A>G	ENSP00000263805:p.Trp103Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	142	0.06501831501831502	4	0.008130081300813009	42	0.11602209944751381	0	0.0	96	0.1266490765171504	A	1.982	-0.433843	0.04669	0.037449	0.149802	ENSG00000103994	ENST00000263805	T	0.13420	2.59	5.44	-4.57	0.03421	.	0.644100	0.15631	N	0.252384	T	0.00039	0.0001	N	0.12746	0.255	0.22591	P	0.99895191	B	0.02656	0.0	B	0.01281	0.0	T	0.37056	-0.9722	9	0.06099	T	0.92	0.8154	6.0782	0.19927	0.2285:0.0:0.2073:0.5642	rs12440118;rs17709157;rs52810470;rs61196539;rs12440118	103	Q9H2Y7	ZF106_HUMAN	R	103	ENSP00000263805:W103R	ENSP00000263805:W103R	W	-	1	0	ZFP106	40531386	0.001000	0.12720	0.165000	0.22776	0.988000	0.76386	-0.349000	0.07731	-1.037000	0.03283	-0.282000	0.10007	TGG	A|0.907;G|0.093	0.093	strong		0.438	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
ALOX12B	242	hgsc.bcm.edu	37	17	7989492	7989492	+	Missense_Mutation	SNP	A	A	G	rs542947562		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7989492A>G	ENST00000319144.4	-	2	454	c.194T>C	c.(193-195)aTc>aCc	p.I65T	MIR4314_ENST00000583321.1_RNA	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	65	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|oxidation-reduction process (GO:0055114)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|protein lipidation (GO:0006497)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)	arachidonate 12-lipoxygenase activity (GO:0004052)|iron ion binding (GO:0005506)|linoleate 9S-lipoxygenase activity (GO:1990136)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	16						GCGGATGATGATGAGCTCACC	0.612										Multiple Myeloma(8;0.094)			A|||	1	0.000199681	0.0	0.0	5008	,	,		19749	0.0		0.001	False		,,,				2504	0.0				p.I65T		Atlas-SNP	.											.	ALOX12B	61	.	0			c.T194C						PASS	.						111.0	90.0	97.0					17																	7989492		2203	4300	6503	SO:0001583	missense	242	exon2			ATGATGATGAGCT	AF038461	CCDS11129.1	17p13.1	2008-03-18			ENSG00000179477	ENSG00000179477	1.13.11.-	"""Arachidonate lipoxygenases"""	430	protein-coding gene	gene with protein product		603741				9618483	Standard	NM_001139		Approved	12R-LOX	uc002gjy.1	O75342	OTTHUMG00000108180	ENST00000319144.4:c.194T>C	17.37:g.7989492A>G	ENSP00000315167:p.Ile65Thr	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	266	130	0.488722	NM_001139		Missense_Mutation	SNP	ENST00000319144.4	37	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.595105	0.46318	.	.	ENSG00000179477	ENST00000319144	T	0.63417	-0.04	4.58	3.48	0.39840	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.253600	0.39909	N	0.001228	T	0.46502	0.1396	N	0.21142	0.635	0.29604	N	0.847425	B	0.29955	0.263	B	0.29440	0.102	T	0.49504	-0.8933	10	0.62326	D	0.03	-23.0942	10.4946	0.44770	0.8365:0.1635:0.0:0.0	.	65	O75342	LX12B_HUMAN	T	65	ENSP00000315167:I65T	ENSP00000315167:I65T	I	-	2	0	ALOX12B	7930217	0.990000	0.36364	0.952000	0.39060	0.922000	0.55478	7.844000	0.86867	0.765000	0.33221	0.529000	0.55759	ATC	.	.	none		0.612	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3		
TOX4	9878	hgsc.bcm.edu	37	14	21960816	21960816	+	Silent	SNP	T	T	C	rs1060722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21960816T>C	ENST00000405508.1	+	8	1317	c.1041T>C	c.(1039-1041)ctT>ctC	p.L347L	TOX4_ENST00000262709.3_Silent_p.L347L|TOX4_ENST00000448790.2_Silent_p.L324L			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	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	146	144	0.986301	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	
CR1	1378	hgsc.bcm.edu	37	1	207741312	207741312	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:207741312A>G	ENST00000367049.4	+	25	4096	c.4096A>G	c.(4096-4098)Agc>Ggc	p.S1366G	RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367052.1_Intron|CR1_ENST00000400960.2_Missense_Mutation_p.S916G|RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367053.1_Missense_Mutation_p.S916G|CR1_ENST00000367051.1_Missense_Mutation_p.S916G	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	916	Sushi 21. {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						CATTGGAGAGAGCACCATCCG	0.547																																					p.S1366G		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,-2,2	CR1	354	2	0			c.A4096G						scavenged	.						86.0	105.0	99.0					1																	207741312		1816	4082	5898	SO:0001583	missense	1378	exon25			GGAGAGAGCACCA	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.4096A>G	1.37:g.207741312A>G	ENSP00000356016:p.Ser1366Gly	Somatic	368	2	0.00543478		WXS	Illumina HiSeq	Phase_I	514	5	0.00972763	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	a	16.47	3.131842	0.56828	.	.	ENSG00000203710	ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	2.73	1.55	0.23275	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.73682	0.3618	M	0.77103	2.36	0.22745	N	0.998781	D;D;D;D	0.64830	0.994;0.99;0.993;0.994	D;D;D;D	0.79108	0.963;0.982;0.919;0.992	T	0.58983	-0.7539	9	0.33141	T	0.24	.	5.9694	0.19342	0.7324:0.2675:0.0:0.0	.	916;466;916;1366	Q5SR44;E9PQN4;P17927;E9PDY4	.;.;CR1_HUMAN;.	G	916;916;916;1366	ENSP00000356018:S916G;ENSP00000356020:S916G;ENSP00000383744:S916G;ENSP00000356016:S1366G	ENSP00000356016:S1366G	S	+	1	0	CR1	205807935	0.940000	0.31905	0.979000	0.43373	0.756000	0.42949	0.034000	0.13776	0.440000	0.26502	0.402000	0.26972	AGC	.	.	none		0.547	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
CLCF1	23529	hgsc.bcm.edu	37	11	67135006	67135006	+	Silent	SNP	A	A	T	rs867193	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:67135006A>T	ENST00000312438.7	-	2	305	c.108T>A	c.(106-108)ccT>ccA	p.P36P	CLCF1_ENST00000528474.1_Silent_p.P26P|CLCF1_ENST00000533438.1_Silent_p.P26P|AP003419.11_ENST00000543494.1_RNA	NM_013246.2	NP_037378.1	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1	36					B cell differentiation (GO:0030183)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immunoglobulin production (GO:0002639)|positive regulation of isotype switching to IgE isotypes (GO:0048295)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)	CNTFR-CLCF1 complex (GO:0097059)|CRLF-CLCF1 complex (GO:0097058)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	ciliary neurotrophic factor receptor binding (GO:0005127)|cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)			endometrium(1)|urinary_tract(1)	2			BRCA - Breast invasive adenocarcinoma(15;2.39e-06)			TGGAGGGGCCAGGCCCTGGGT	0.622													A|||	391	0.0780751	0.1422	0.0519	5008	,	,		16418	0.1141		0.0358	False		,,,				2504	0.0164				p.P36P		Atlas-SNP	.											.	CLCF1	15	.	0			c.T108A						PASS	.	A	,	591,3809	260.4+/-263.7	47,497,1656	123.0	103.0	110.0		78,108	-4.2	1.0	11	dbSNP_86	110	290,8300	107.2+/-168.0	7,276,4012	no	coding-synonymous,coding-synonymous	CLCF1	NM_001166212.1,NM_013246.2	,	54,773,5668	TT,TA,AA		3.376,13.4318,6.7821	,	26/216,36/226	67135006	881,12109	2200	4295	6495	SO:0001819	synonymous_variant	23529	exon2			GGGGCCAGGCCCT	BC012939	CCDS31617.1, CCDS53666.1	11q13.3	2014-01-28	2006-07-03		ENSG00000175505	ENSG00000175505			17412	protein-coding gene	gene with protein product	"""B-cell stimulating factor 3"", ""cold-induced sweating syndrome 2"", ""novel neurotrophin-1"""	607672	"""CRLF1 associated cytokine-like factor 1"""			10500198, 10448081, 16782820	Standard	NM_001166212		Approved	NNT1, BSF3, CLC, NR6, CISS2, BSF-3, NNT-1	uc010rpp.2	Q9UBD9	OTTHUMG00000167669	ENST00000312438.7:c.108T>A	11.37:g.67135006A>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	174	91	0.522988	NM_013246	B4DNT4|Q6NZA4	Silent	SNP	ENST00000312438.7	37	CCDS31617.1																																																																																			A|0.928;T|0.072	0.072	strong		0.622	CLCF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395478.1	NM_013246	
MYH14	79784	hgsc.bcm.edu	37	19	50726570	50726570	+	Silent	SNP	G	G	A	rs4801822	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50726570G>A	ENST00000596571.1	+	4	657	c.657G>A	c.(655-657)gcG>gcA	p.A219A	MYH14_ENST00000598205.1_Silent_p.A219A|MYH14_ENST00000262269.8_Silent_p.A219A|MYH14_ENST00000425460.1_Silent_p.A219A|MYH14_ENST00000376970.2_Silent_p.A219A|MYH14_ENST00000440075.2_Silent_p.A219A|MYH14_ENST00000601313.1_Silent_p.A219A			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	219	Myosin motor.				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)	p.A219A(2)		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)		CCCACGTGGCGTCGTCTCCAA	0.632													A|||	2368	0.472843	0.1573	0.4942	5008	,	,		17994	0.5804		0.6123	False		,,,				2504	0.6299				p.A219A		Atlas-SNP	.											MYH14_ENST00000262269,NS,carcinoma,0,2	MYH14	261	2	2	Substitution - coding silent(2)	prostate(2)	c.G657A						scavenged	.	A	,,	987,3349		132,723,1313	44.0	51.0	49.0		657,657,657	-6.1	0.1	19	dbSNP_111	49	5380,3192		1712,1956,618	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	1844,2679,1931	AA,AG,GG		37.2375,22.7629,49.326	,,	219/2004,219/2037,219/1996	50726570	6367,6541	2168	4286	6454	SO:0001819	synonymous_variant	79784	exon5			CGTGGCGTCGTCT	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.657G>A	19.37:g.50726570G>A		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	158	62	0.392405	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			G|0.507;A|0.494	0.494	strong		0.632	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
CPT1A	1374	hgsc.bcm.edu	37	11	68560787	68560787	+	Silent	SNP	C	C	T	rs2229737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68560787C>T	ENST00000265641.5	-	9	1117	c.963G>A	c.(961-963)gaG>gaA	p.E321E	CPT1A_ENST00000538994.1_Silent_p.E73E|CPT1A_ENST00000539743.1_Silent_p.E321E|CPT1A_ENST00000540367.1_Silent_p.E321E|CPT1A_ENST00000376618.2_Silent_p.E321E	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	321					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	ACTCACCTGTCTCCTCTCCTG	0.483													C|||	255	0.0509185	0.0318	0.0663	5008	,	,		16444	0.0198		0.1233	False		,,,				2504	0.0235				p.E321E		Atlas-SNP	.											.	CPT1A	89	.	0			c.G963A						PASS	.	C	,	167,4233	106.9+/-145.3	4,159,2037	52.0	45.0	48.0		963,963	1.1	1.0	11	dbSNP_120	48	910,7678	198.9+/-243.1	56,798,3440	no	coding-synonymous,coding-synonymous	CPT1A	NM_001031847.2,NM_001876.3	,	60,957,5477	TT,TC,CC		10.5962,3.7955,8.2923	,	321/757,321/774	68560787	1077,11911	2200	4294	6494	SO:0001819	synonymous_variant	1374	exon9			ACCTGTCTCCTCT	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.963G>A	11.37:g.68560787C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	116	45	0.387931	NM_001876	Q8TCU0|Q9BWK0	Silent	SNP	ENST00000265641.5	37	CCDS8185.1																																																																																			C|0.914;T|0.086	0.086	strong		0.483	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	
LRTM1	57408	hgsc.bcm.edu	37	3	54958968	54958968	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:54958968G>A	ENST00000273286.5	-	2	444	c.282C>T	c.(280-282)ttC>ttT	p.F94F	CACNA2D3_ENST00000474759.1_Intron|CACNA2D3_ENST00000288197.5_Intron|CACNA2D3_ENST00000490478.1_Intron|LRTM1_ENST00000493075.1_Silent_p.F18F|CACNA2D3_ENST00000415676.2_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	94						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		GAAGCCCATGGAAAGCTCCAG	0.473																																					p.F94F		Atlas-SNP	.											LRTM1,NS,carcinoma,-1,1	LRTM1	52	1	0			c.C282T						scavenged	.						54.0	54.0	54.0					3																	54958968		2203	4300	6503	SO:0001819	synonymous_variant	57408	exon2			CCCATGGAAAGCT	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.282C>T	3.37:g.54958968G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_020678	Q8IUU2	Silent	SNP	ENST00000273286.5	37	CCDS2876.1																																																																																			.	.	none		0.473	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678	
PF4V1	5197	hgsc.bcm.edu	37	4	74719624	74719624	+	Silent	SNP	C	C	G	rs34446485	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:74719624C>G	ENST00000226524.3	+	2	399	c.225C>G	c.(223-225)ctC>ctG	p.L75L		NM_002620.2	NP_002611.1	P10720	PF4V_HUMAN	platelet factor 4 variant 1	75					cell chemotaxis (GO:0060326)|immune response (GO:0006955)	extracellular space (GO:0005615)	heparin binding (GO:0008201)			endometrium(1)|liver(2)	3	Breast(15;0.00102)		all cancers(17;0.00176)|Lung(101;0.128)|LUSC - Lung squamous cell carcinoma(112;0.187)			CTGCCCAACTCATGTGAGTCC	0.602																																					p.L75L		Atlas-SNP	.											PF4V1,NS,carcinoma,0,1	PF4V1	8	1	0			c.C225G						scavenged	.	C		81,4307	17.9+/-39.9	7,67,2120	66.0	74.0	71.0		225	-2.3	0.1	4	dbSNP_126	71	31,8565	1.2+/-3.3	3,25,4270	no	coding-synonymous	PF4V1	NM_002620.2		10,92,6390	GG,GC,CC		0.3606,1.8459,0.8626		75/105	74719624	112,12872	2194	4298	6492	SO:0001819	synonymous_variant	5197	exon2			CCAACTCATGTGA	M26167	CCDS3561.1	4q12-q21	2008-08-15			ENSG00000109272	ENSG00000109272			8862	protein-coding gene	gene with protein product		173461				2725510	Standard	NM_002620		Approved	SCYB4V1, CXCL4V1, CXCL4L1	uc003hhg.1	P10720	OTTHUMG00000130177	ENST00000226524.3:c.225C>G	4.37:g.74719624C>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	123	25	0.203252	NM_002620	A1L4S0	Silent	SNP	ENST00000226524.3	37	CCDS3561.1																																																																																			C|0.981;G|0.019	0.019	strong		0.602	PF4V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252495.1		
SERPINB8	5271	hgsc.bcm.edu	37	18	61654463	61654463	+	Missense_Mutation	SNP	A	A	G	rs3826616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:61654463A>G	ENST00000397985.2	+	7	1332	c.1076A>G	c.(1075-1077)cAc>cGc	p.H359R	SERPINB8_ENST00000493661.1_Intron|SERPINB8_ENST00000542677.1_Missense_Mutation_p.H177R|SERPINB8_ENST00000353706.2_Missense_Mutation_p.H359R	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	359			H -> R (in dbSNP:rs3826616). {ECO:0000269|PubMed:8530382}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				TTCATCAGGCACCACAAAACC	0.502													A|||	2747	0.548522	0.3782	0.6744	5008	,	,		19698	0.5446		0.5427	False		,,,				2504	0.6994				p.H359R		Atlas-SNP	.											.	SERPINB8	42	.	0			c.A1076G						PASS	.	A	ARG/HIS,ARG/HIS	1874,2532	539.1+/-375.2	403,1068,732	100.0	99.0	99.0		1076,1076	5.7	0.1	18	dbSNP_107	99	4989,3611	625.4+/-397.7	1452,2085,763	yes	missense,missense	SERPINB8	NM_002640.3,NM_198833.1	29,29	1855,3153,1495	GG,GA,AA		41.9884,42.5329,47.232	probably-damaging,probably-damaging	359/375,359/375	61654463	6863,6143	2203	4300	6503	SO:0001583	missense	5271	exon7			TCAGGCACCACAA	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"""Serine (or cysteine) peptidase inhibitors"""	8952	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase 2"""	601697	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"""	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.1076A>G	18.37:g.61654463A>G	ENSP00000381072:p.His359Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	137	73	0.532847	NM_198833	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	37	CCDS11991.1	1199	0.548992673992674	218	0.44308943089430897	233	0.643646408839779	318	0.5559440559440559	430	0.5672823218997362	A	16.85	3.236928	0.58886	0.425329	0.580116	ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000542677	D;D;T	0.82984	-1.67;-1.67;2.72	5.65	5.65	0.86999	Serpin domain (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.88640	2.97	0.09310	P	0.9999999695095	D	0.71674	0.998	D	0.73380	0.98	T	0.49808	-0.8900	9	0.87932	D	0	.	15.2098	0.73214	1.0:0.0:0.0:0.0	rs3826616;rs52836834;rs3826616	359	P50452	SPB8_HUMAN	R	359;359;177	ENSP00000381072:H359R;ENSP00000331368:H359R;ENSP00000438328:H177R	ENSP00000331368:H359R	H	+	2	0	SERPINB8	59805443	1.000000	0.71417	0.130000	0.21974	0.163000	0.22366	9.044000	0.93805	2.371000	0.80710	0.533000	0.62120	CAC	A|0.466;G|0.534	0.534	strong		0.502	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848	
TTN	7273	hgsc.bcm.edu	37	2	179621184	179621184	+	Intron	SNP	G	G	A	rs72955212	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179621184G>A	ENST00000591111.1	-	44	10528				TTN_ENST00000589042.1_Silent_p.C3673C|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000342175.6_Silent_p.C3502C|TTN_ENST00000360870.5_Intron|TTN-AS1_ENST00000590773.1_RNA			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)			CCGTGTCACCGCACTTTACAG	0.453													g|||	26	0.00519169	0.0	0.0043	5008	,	,		21646	0.0		0.0229	False		,,,				2504	0.0				p.C3673C		Atlas-SNP	.											TTN_ENST00000342175,NS,carcinoma,-2,1	TTN	18412	1	0			c.C11019T						scavenged	.	A	,,,,	10,3856		0,10,1923	90.0	86.0	87.0		,,,,10506	-10.3	0.0	2	dbSNP_130	87	120,8124		0,120,4002	no	intron,intron,intron,intron,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,130,5925	AA,AG,GG		1.4556,0.2587,1.0735	,,,,	,,,,3502/27119	179621184	130,11980	1933	4122	6055	SO:0001627	intron_variant	7273	exon46			GTCACCGCACTTT	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.10303+2526C>T	2.37:g.179621184G>A		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	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|0.990;A|0.010	0.010	strong		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PEX11G	92960	hgsc.bcm.edu	37	19	7550844	7550844	+	Silent	SNP	G	G	A	rs34970001	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:7550844G>A	ENST00000221480.1	-	2	137	c.129C>T	c.(127-129)tcC>tcT	p.S43S	PEX11G_ENST00000593942.1_5'UTR|PEX11G_ENST00000599519.1_5'Flank	NM_001270539.1|NM_080662.3	NP_001257468.1|NP_542393.1	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	43					peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						TCCCCACTTCGGACCTGGCGG	0.572													G|||	1278	0.255192	0.2572	0.255	5008	,	,		16452	0.2083		0.3032	False		,,,				2504	0.2515				p.S43S		Atlas-SNP	.											.	PEX11G	16	.	0			c.C129T						PASS	.	G		1083,3323	392.1+/-328.4	131,821,1251	86.0	67.0	73.0		129	-6.1	0.1	19	dbSNP_126	73	2458,6142	406.1+/-348.7	360,1738,2202	no	coding-synonymous	PEX11G	NM_080662.2		491,2559,3453	AA,AG,GG		28.5814,24.5801,27.2259		43/242	7550844	3541,9465	2203	4300	6503	SO:0001819	synonymous_variant	92960	exon2			CACTTCGGACCTG	BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883			20208	protein-coding gene	gene with protein product		607583				12417726	Standard	NM_080662		Approved		uc002mgk.2	Q96HA9		ENST00000221480.1:c.129C>T	19.37:g.7550844G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_001270539	Q8NDM0	Silent	SNP	ENST00000221480.1	37	CCDS12178.1																																																																																			G|0.725;A|0.275	0.275	strong		0.572	PEX11G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458965.1	NM_080662	
OCM2	4951	hgsc.bcm.edu	37	7	97617822	97617822	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:97617822A>G	ENST00000257627.4	-	2	191	c.100T>C	c.(100-102)Tca>Cca	p.S34P	OCM2_ENST00000473987.2_5'UTR	NM_006188.3	NP_006179.2	P0CE71	OCM2_HUMAN	oncomodulin 2	34							calcium ion binding (GO:0005509)			lung(4)	4						GAGAGGCCTGACGTCTGGAAG	0.468																																					p.S34P		Atlas-SNP	.											OCM2,NS,malignant_melanoma,+1,1	OCM2	19	1	0			c.T100C						scavenged	.						166.0	158.0	161.0					7																	97617822		2203	4300	6503	SO:0001583	missense	4951	exon2			GGCCTGACGTCTG	BC156841	CCDS5653.1	7q21.2	2014-04-01			ENSG00000135175	ENSG00000135175		"""EF-hand domain containing"""	34396	protein-coding gene	gene with protein product							Standard	NM_006188		Approved		uc003upc.3	P0CE71	OTTHUMG00000154162	ENST00000257627.4:c.100T>C	7.37:g.97617822A>G	ENSP00000257627:p.Ser34Pro	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	194	2	0.0103093	NM_006188	P32930|Q6ISI5|Q75MW0	Missense_Mutation	SNP	ENST00000257627.4	37	CCDS5653.1	.	.	.	.	.	.	.	.	.	.	a	14.70	2.615069	0.46631	.	.	ENSG00000135175	ENST00000257627	T	0.72615	-0.67	3.98	3.98	0.46160	.	0.128899	0.52532	D	0.000075	T	0.60907	0.2305	L	0.56280	1.765	0.26955	N	0.965939	P	0.51147	0.942	B	0.38985	0.287	T	0.62506	-0.6840	10	0.72032	D	0.01	-3.2324	8.1641	0.31215	0.8203:0.0:0.0:0.1797	.	34	P0CE71	OCM2_HUMAN	P	34	ENSP00000257627:S34P	ENSP00000257627:S34P	S	-	1	0	OCM2	97455758	0.722000	0.28017	0.999000	0.59377	0.991000	0.79684	3.463000	0.53050	1.685000	0.51034	0.386000	0.25728	TCA	.	.	none		0.468	OCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334188.1	NM_006188	
GTF2A1	2957	hgsc.bcm.edu	37	14	81686832	81686832	+	Splice_Site	SNP	C	C	G	rs201410281		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:81686832C>G	ENST00000553612.1	-	1	434		c.e1+1		GTF2A1_ENST00000434192.2_Intron	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa						gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(234;0.0287)		CACGTCCTTACCACGGTGTTT	0.577																																					.		Atlas-SNP	.											.	GTF2A1	34	.	0			c.30+1G>C						PASS	.						39.0	40.0	40.0					14																	81686832		2202	4293	6495	SO:0001630	splice_region_variant	2957	exon2			TCCTTACCACGGT	X75383	CCDS9873.1, CCDS9874.1	14q31	2010-03-23	2002-08-29					"""General transcription factors"""	4646	protein-coding gene	gene with protein product		600520	"""glucose regulated protein, 58kD pseudogene"""			8224848	Standard	NM_015859		Approved	TFIIA	uc001xvf.2	P52655		ENST00000553612.1:c.30+1G>C	14.37:g.81686832C>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	74	21	0.283784	NM_015859	Q3KNQ9	Splice_Site	SNP	ENST00000553612.1	37	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.205504	0.58234	.	.	ENSG00000165417	ENST00000553612	.	.	.	3.35	3.35	0.38373	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2408	0.59995	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTF2A1	80756585	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	5.468000	0.66743	1.400000	0.46741	0.305000	0.20034	.	C|1.000;T|0.000	.	alt		0.577	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859	Intron
TBC1D2	55357	hgsc.bcm.edu	37	9	100961704	100961704	+	Missense_Mutation	SNP	C	C	T	rs34769888	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100961704C>T	ENST00000375066.5	-	13	2804	c.2713G>A	c.(2713-2715)Gag>Aag	p.E905K	TBC1D2_ENST00000375063.1_Missense_Mutation_p.E456K|TBC1D2_ENST00000342112.5_Missense_Mutation_p.E698K|TBC1D2_ENST00000375064.1_3'UTR	NM_018421.3	NP_060891.3	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	916					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GCACAGCCCTCGGACACAGCT	0.682													C|||	20	0.00399361	0.0	0.0043	5008	,	,		15710	0.0		0.006	False		,,,				2504	0.0112				p.E916K		Atlas-SNP	.											.	TBC1D2	70	.	0			c.G2746A						PASS	.	C	LYS/GLU	11,4395	16.8+/-37.8	0,11,2192	62.0	64.0	63.0		2713	3.5	0.0	9	dbSNP_126	63	80,8518	45.8+/-104.6	1,78,4220	yes	missense	TBC1D2	NM_018421.3	56	1,89,6412	TT,TC,CC		0.9304,0.2497,0.6998	benign	905/918	100961704	91,12913	2203	4299	6502	SO:0001583	missense	55357	exon13			AGCCCTCGGACAC	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375066.5:c.2713G>A	9.37:g.100961704C>T	ENSP00000364207:p.Glu905Lys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375066.5	37	CCDS35080.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	16.15	3.041987	0.55003	0.002497	0.009304	ENSG00000095383	ENST00000375066;ENST00000342112;ENST00000375063	T;T;T	0.08896	3.04;3.5;3.11	5.34	3.5	0.40072	.	0.512441	0.20582	N	0.089520	T	0.04907	0.0132	L	0.57536	1.79	0.09310	N	0.999999	B;B	0.33919	0.306;0.432	B;B	0.22386	0.017;0.039	T	0.33317	-0.9873	10	0.13470	T	0.59	.	9.2808	0.37727	0.0:0.8294:0.0:0.1706	rs34769888	916;905	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	K	905;698;456	ENSP00000364207:E905K;ENSP00000341567:E698K;ENSP00000364203:E456K	ENSP00000341567:E698K	E	-	1	0	TBC1D2	100001525	0.612000	0.27000	0.033000	0.17914	0.033000	0.12548	1.029000	0.30140	0.641000	0.30601	0.511000	0.50034	GAG	C|0.994;T|0.006	0.006	strong		0.682	TBC1D2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053367.1	NM_018421	
SLC2A14	144195	hgsc.bcm.edu	37	12	7967076	7967076	+	Silent	SNP	A	A	G	rs10845983	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7967076A>G	ENST00000543909.1	-	16	2158	c.1399T>C	c.(1399-1401)Ttg>Ctg	p.L467L	SLC2A14_ENST00000539924.1_Silent_p.L482L|SLC2A14_ENST00000431042.2_Silent_p.L444L|SLC2A14_ENST00000535295.1_Silent_p.L358L|SLC2A14_ENST00000542546.1_Silent_p.L358L|SLC2A14_ENST00000396589.2_Silent_p.L467L|SLC2A14_ENST00000542505.1_Silent_p.L108L|SLC2A14_ENST00000340749.5_Silent_p.L444L			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						PASS	.	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	131	0	0		WXS	Illumina HiSeq	Phase_I	124	65	0.524194	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	
SEC31B	25956	hgsc.bcm.edu	37	10	102265183	102265183	+	Missense_Mutation	SNP	G	G	A	rs2295772	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102265183G>A	ENST00000370345.3	-	10	1211	c.1114C>T	c.(1114-1116)Cca>Tca	p.P372S	SEC31B_ENST00000451524.1_Missense_Mutation_p.P372S	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	372			P -> S (in dbSNP:rs2295772).		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GGTATCAGTGGTGCTTGTGCC	0.512													A|||	927	0.185104	0.1997	0.1844	5008	,	,		20023	0.1319		0.1909	False		,,,				2504	0.2147				p.P372S		Atlas-SNP	.											.	SEC31B	84	.	0			c.C1114T						PASS	.	A	SER/PRO	858,3548	744.3+/-411.5	86,686,1431	182.0	190.0	187.0		1114	3.5	0.4	10	dbSNP_100	187	1893,6707	728.3+/-406.7	216,1461,2623	yes	missense	SEC31B	NM_015490.3	74	302,2147,4054	AA,AG,GG		22.0116,19.4734,21.1518	benign	372/1180	102265183	2751,10255	2203	4300	6503	SO:0001583	missense	25956	exon10			TCAGTGGTGCTTG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.1114C>T	10.37:g.102265183G>A	ENSP00000359370:p.Pro372Ser	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	106	68	0.641509	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	395	0.18086080586080586	71	0.1443089430894309	71	0.19613259668508287	94	0.16433566433566432	159	0.20976253298153033	A	4.865	0.160694	0.09287	0.194734	0.220116	ENSG00000075826	ENST00000370345;ENST00000451524	T;T	0.58358	0.74;0.34	5.82	3.47	0.39725	.	0.219047	0.46758	N	0.000273	T	0.00012	0.0000	N	0.00729	-1.24	0.09310	P	0.999999999998951	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21724	-1.0237	9	0.02654	T	1	-0.5132	1.7084	0.02887	0.3605:0.1058:0.093:0.4407	rs2295772;rs17672591;rs52801527;rs59297200;rs2295772	371;372	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	S	372	ENSP00000359370:P372S;ENSP00000391178:P372S	ENSP00000359370:P372S	P	-	1	0	SEC31B	102255173	1.000000	0.71417	0.368000	0.25939	0.978000	0.69477	2.770000	0.47662	0.123000	0.18342	-0.361000	0.07541	CCA	G|0.808;A|0.192	0.192	strong		0.512	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
ABCA5	23461	hgsc.bcm.edu	37	17	67290840	67290840	+	Missense_Mutation	SNP	T	T	C	rs17686569	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:67290840T>C	ENST00000392676.3	-	11	1515	c.1451A>G	c.(1450-1452)cAg>cGg	p.Q484R	ABCA5_ENST00000392677.2_Missense_Mutation_p.Q484R|ABCA5_ENST00000588877.1_Missense_Mutation_p.Q484R			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	484	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		Q -> R (in dbSNP:rs17686569). {ECO:0000269|PubMed:12504089}.		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)	GTATGTCTTCTGAATACCACT	0.274													T|||	720	0.14377	0.2375	0.1945	5008	,	,		13946	0.0456		0.1412	False		,,,				2504	0.0849				p.Q484R		Atlas-SNP	.											.	ABCA5	162	.	0			c.A1451G						PASS	.	T	ARG/GLN,ARG/GLN	1040,3366	382.1+/-324.3	127,786,1290	77.0	80.0	79.0		1451,1451	4.8	1.0	17	dbSNP_123	79	1232,7364	246.8+/-275.1	83,1066,3149	yes	missense,missense	ABCA5	NM_018672.3,NM_172232.2	43,43	210,1852,4439	CC,CT,TT		14.3322,23.6042,17.4742	benign,benign	484/1643,484/1643	67290840	2272,10730	2203	4298	6501	SO:0001583	missense	23461	exon10			GTCTTCTGAATAC	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.1451A>G	17.37:g.67290840T>C	ENSP00000376443:p.Gln484Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	304	0.1391941391941392	120	0.24390243902439024	60	0.16574585635359115	16	0.027972027972027972	108	0.1424802110817942	T	11.71	1.719576	0.30503	0.236042	0.143322	ENSG00000154265	ENST00000392677;ENST00000392676	T;T	0.38240	1.15;1.15	4.83	4.83	0.62350	ABC transporter-like (1);	0.231149	0.31145	N	0.008171	T	0.00012	0.0000	N	0.01679	-0.765	0.25480	P	0.9877487	B;B	0.25850	0.136;0.101	B;B	0.20184	0.028;0.017	T	0.28870	-1.0030	8	.	.	.	.	13.2667	0.60137	0.0:0.0:0.0:1.0	rs17686569;rs56415964;rs17686569	484;484	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	R	484	ENSP00000376444:Q484R;ENSP00000376443:Q484R	.	Q	-	2	0	ABCA5	64802435	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	2.539000	0.45718	1.919000	0.55581	0.460000	0.39030	CAG	T|0.839;C|0.161	0.161	strong		0.274	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
ST6GALNAC1	55808	hgsc.bcm.edu	37	17	74625517	74625517	+	Silent	SNP	T	T	C	rs139045542	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:74625517T>C	ENST00000156626.7	-	2	607	c.408A>G	c.(406-408)acA>acG	p.T136T	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	136					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						TGGGTGACAGTGTGTTCACCA	0.587													T|||	9	0.00179712	0.0	0.0072	5008	,	,		19622	0.0		0.004	False		,,,				2504	0.0				p.T136T		Atlas-SNP	.											.	ST6GALNAC1	42	.	0			c.A408G						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	177.0	162.0	167.0		408	-7.6	0.0	17	dbSNP_134	167	49,8551	31.7+/-84.0	0,49,4251	no	coding-synonymous	ST6GALNAC1	NM_018414.3		0,52,6451	CC,CT,TT		0.5698,0.0681,0.3998		136/601	74625517	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	55808	exon2			TGACAGTGTGTTC	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.408A>G	17.37:g.74625517T>C		Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	395	204	0.516456	NM_018414	Q6UW90|Q9NSC6	Silent	SNP	ENST00000156626.7	37	CCDS11748.1																																																																																			T|0.996;C|0.004	0.004	strong		0.587	ST6GALNAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450974.1	NM_018414	
ANK1	286	hgsc.bcm.edu	37	8	41583294	41583294	+	Silent	SNP	C	C	T	rs2304873	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:41583294C>T	ENST00000347528.4	-	6	680	c.597G>A	c.(595-597)ccG>ccA	p.P199P	ANK1_ENST00000379758.2_Silent_p.P199P|ANK1_ENST00000289734.7_Silent_p.P199P|ANK1_ENST00000352337.4_Silent_p.P199P|ANK1_ENST00000396945.1_Silent_p.P199P|ANK1_ENST00000265709.8_Silent_p.P232P|ANK1_ENST00000396942.1_Silent_p.P199P	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	199	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			AAAGCACGTCCGGGTTGGGGT	0.726													C|||	526	0.105032	0.0151	0.0893	5008	,	,		16267	0.1577		0.1213	False		,,,				2504	0.1667				p.P232P		Atlas-SNP	.											.	ANK1	497	.	0			c.G696A						PASS	.	C	,,,,	151,4251	95.7+/-134.4	2,147,2052	61.0	38.0	46.0		597,696,597,597,597	-11.8	0.2	8	dbSNP_100	46	1176,7422	226.2+/-262.0	85,1006,3208	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	87,1153,5260	TT,TC,CC		13.6776,3.4303,10.2077	,,,,	199/1881,232/1898,199/1857,199/1882,199/1720	41583294	1327,11673	2201	4299	6500	SO:0001819	synonymous_variant	286	exon6			CACGTCCGGGTTG	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.597G>A	8.37:g.41583294C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	27	9	0.333333	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1																																																																																			C|0.900;T|0.100	0.100	strong		0.726	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
SMAD3	4088	hgsc.bcm.edu	37	15	67473790	67473790	+	Splice_Site	SNP	C	C	T	rs117185005	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:67473790C>T	ENST00000327367.4	+	6	1180	c.870C>T	c.(868-870)atC>atT	p.I290I	SMAD3_ENST00000537194.2_Splice_Site_p.I95I|SMAD3_ENST00000439724.3_Splice_Site_p.I246I|SMAD3_ENST00000540846.2_Splice_Site_p.I185I	NM_005902.3	NP_005893.1	P84022	SMAD3_HUMAN	SMAD family member 3	290	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.|Sufficient for interaction with XPO4.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activin receptor signaling pathway (GO:0032924)|cell cycle arrest (GO:0007050)|cell-cell junction organization (GO:0045216)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|embryonic pattern specification (GO:0009880)|endoderm development (GO:0007492)|evasion or tolerance of host defenses by virus (GO:0019049)|extrinsic apoptotic signaling pathway (GO:0097191)|gene expression (GO:0010467)|heart looping (GO:0001947)|immune response (GO:0006955)|immune system development (GO:0002520)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|lens fiber cell differentiation (GO:0070306)|liver development (GO:0001889)|mesoderm formation (GO:0001707)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein phosphorylation (GO:0001933)|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 wound healing (GO:0061045)|nodal signaling pathway (GO:0038092)|osteoblast development (GO:0002076)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription factor import into nucleus (GO:0042993)|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 beta3 production (GO:0032916)|primary miRNA processing (GO:0031053)|protein stabilization (GO:0050821)|regulation of binding (GO:0051098)|regulation of epithelial cell proliferation (GO:0050678)|regulation of immune response (GO:0050776)|regulation of striated muscle tissue development (GO:0016202)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|somitogenesis (GO:0001756)|T cell activation (GO:0042110)|thyroid gland development (GO:0030878)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transdifferentiation (GO:0060290)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transport (GO:0006810)|ureteric bud development (GO:0001657)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nuclear inner membrane (GO:0005637)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|bHLH transcription factor binding (GO:0043425)|chromatin DNA binding (GO:0031490)|co-SMAD binding (GO:0070410)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(11)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(7;0.125)		GGAGACACATCGGTATGGGGT	0.622													C|||	42	0.00838658	0.0008	0.0043	5008	,	,		9014	0.0		0.0239	False		,,,				2504	0.0143				p.I290I		Atlas-SNP	.											.	SMAD3	119	.	0			c.C870T						PASS	.	C	,,,	22,4380	29.0+/-57.7	0,22,2179	41.0	39.0	40.0		555,738,285,870	-0.9	1.0	15	dbSNP_132	40	175,8423	78.9+/-141.6	4,167,4128	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SMAD3	NM_001145102.1,NM_001145103.1,NM_001145104.1,NM_005902.3	,,,	4,189,6307	TT,TC,CC		2.0354,0.4998,1.5154	,,,	185/321,246/382,95/231,290/426	67473790	197,12803	2201	4299	6500	SO:0001630	splice_region_variant	4088	exon6			ACACATCGGTATG	BC050743	CCDS10222.1, CCDS45288.1, CCDS53950.1, CCDS53951.1	15q21-q22	2006-11-06	2006-11-06	2004-05-26	ENSG00000166949	ENSG00000166949		"""SMADs"""	6769	protein-coding gene	gene with protein product		603109	"""MAD, mothers against decapentaplegic homolog 3 (Drosophila)"", ""SMAD, mothers against DPP homolog 3 (Drosophila)"""	MADH3		8774881, 8673135	Standard	NM_001145102		Approved	JV15-2, HsT17436	uc002aqj.3	P84022	OTTHUMG00000133230	ENST00000327367.4:c.871+1C>T	15.37:g.67473790C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	35	25	0.714286	NM_005902	A8K4B6|B7Z4Z5|B7Z6M9|B7Z9Q2|F5H383|O09064|O09144|O14510|O35273|Q92940|Q93002|Q9GKR4	Silent	SNP	ENST00000327367.4	37	CCDS10222.1																																																																																			.	.	weak		0.622	SMAD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256967.2	NM_005902	Silent
NCAPD3	23310	hgsc.bcm.edu	37	11	134062764	134062764	+	Missense_Mutation	SNP	C	C	T	rs12292394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:134062764C>T	ENST00000534548.2	-	16	1929	c.1865G>A	c.(1864-1866)cGg>cAg	p.R622Q		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	622			R -> Q (in dbSNP:rs12292394).		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GACCACCCCCCGCAACCAGGC	0.547													C|||	130	0.0259585	0.0008	0.0231	5008	,	,		16262	0.0149		0.0537	False		,,,				2504	0.045				p.R622Q		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G1865A						PASS	.	C	GLN/ARG	39,4363	42.3+/-75.8	0,39,2162	76.0	74.0	75.0		1865	-11.8	0.0	11	dbSNP_120	75	508,8086	144.5+/-200.4	17,474,3806	yes	missense	NCAPD3	NM_015261.2	43	17,513,5968	TT,TC,CC		5.9111,0.886,4.209	benign	622/1499	134062764	547,12449	2201	4297	6498	SO:0001583	missense	23310	exon16			ACCCCCCGCAACC	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1865G>A	11.37:g.134062764C>T	ENSP00000433681:p.Arg622Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	142	29	0.204225	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	59	0.027014652014652016	1	0.0020325203252032522	11	0.03038674033149171	8	0.013986013986013986	39	0.051451187335092345	C	1.884	-0.457079	0.04540	0.00886	0.059111	ENSG00000151503	ENST00000534548	T	0.64260	-0.09	5.88	-11.8	0.00035	Armadillo-like helical (1);Armadillo-type fold (1);	0.776444	0.12953	N	0.425681	T	0.02610	0.0079	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04427	-1.0952	10	0.13470	T	0.59	-0.2737	3.2744	0.06893	0.135:0.157:0.3922:0.3158	rs12292394;rs12292394	622	P42695	CNDD3_HUMAN	Q	622	ENSP00000433681:R622Q	ENSP00000431612:R622Q	R	-	2	0	NCAPD3	133567974	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.370000	0.02575	-2.799000	0.00353	-2.351000	0.00242	CGG	C|0.962;T|0.038	0.038	strong		0.547	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	
VWA5B1	127731	hgsc.bcm.edu	37	1	20650001	20650001	+	Silent	SNP	C	C	T	rs146423282	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:20650001C>T	ENST00000375079.2	+	8	1315	c.1119C>T	c.(1117-1119)agC>agT	p.S373S	VWA5B1_ENST00000289825.4_Silent_p.S90S|VWA5B1_ENST00000375083.4_Silent_p.S373S|RP4-745E8.2_ENST00000444923.1_RNA|VWA5B1_ENST00000289815.8_Silent_p.S373S	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	373	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GCAGCATGAGCGGGATCAGCA	0.602													C|||	9	0.00179712	0.0008	0.0	5008	,	,		17207	0.0		0.007	False		,,,				2504	0.001				p.S373S		Atlas-SNP	.											.	VWA5B1	44	.	0			c.C1119T						PASS	.	C		5,1379		0,5,687	53.0	47.0	49.0		1119	-0.9	1.0	1	dbSNP_134	49	23,3159		0,23,1568	no	coding-synonymous	VWA5B1	NM_001039500.2		0,28,2255	TT,TC,CC		0.7228,0.3613,0.6132		373/1216	20650001	28,4538	692	1591	2283	SO:0001819	synonymous_variant	127731	exon8			CATGAGCGGGATC	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.1119C>T	1.37:g.20650001C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	47	8	0.170213	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Silent	SNP	ENST00000375079.2	37																																																																																				C|0.995;T|0.005	0.005	strong		0.602	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
RASAL1	8437	hgsc.bcm.edu	37	12	113573237	113573237	+	Missense_Mutation	SNP	C	C	G	rs7960087	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113573237C>G	ENST00000261729.5	-	2	346	c.31G>C	c.(31-33)Gtg>Ctg	p.V11L	RASAL1_ENST00000446861.3_Missense_Mutation_p.V11L|RASAL1_ENST00000546530.1_Missense_Mutation_p.V11L|RASAL1_ENST00000548055.1_Missense_Mutation_p.V11L|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	11	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.		V -> L (in dbSNP:rs7960087). {ECO:0000269|PubMed:15489334}.		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)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)	p.V11L(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						CCCTCCACCACGCGAACATTC	0.677													C|||	97	0.019369	0.0144	0.0317	5008	,	,		11792	0.0		0.0457	False		,,,				2504	0.0102				p.V11L		Atlas-SNP	.											RASAL1,NS,carcinoma,0,2	RASAL1	89	2	2	Substitution - Missense(2)	prostate(2)	c.G31C						scavenged	.	C	LEU/VAL,LEU/VAL,LEU/VAL	90,4306		2,86,2110	34.0	30.0	31.0		31,31,31	3.4	1.0	12	dbSNP_116	31	309,8285		5,299,3993	yes	missense,missense,missense	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	32,32,32	7,385,6103	GG,GC,CC		3.5955,2.0473,3.0716	benign,benign,benign	11/807,11/777,11/805	113573237	399,12591	2198	4297	6495	SO:0001583	missense	8437	exon2			CCACCACGCGAAC	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.31G>C	12.37:g.113573237C>G	ENSP00000261729:p.Val11Leu	Somatic	240	2	0.00833333		WXS	Illumina HiSeq	Phase_I	199	96	0.482412	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	37	CCDS9165.1	45	0.020604395604395604	5	0.01016260162601626	7	0.019337016574585635	0	0.0	33	0.04353562005277045	C	9.955	1.221292	0.22457	0.020473	0.035955	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.12465	2.68;2.68;2.68;2.68	3.44	3.44	0.39384	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.301944	0.26362	N	0.024816	T	0.01454	0.0047	N	0.10760	0.04	0.26908	N	0.966964	B;B;B;B;B;B	0.14805	0.011;0.009;0.011;0.005;0.003;0.009	B;B;B;B;B;B	0.14578	0.011;0.006;0.011;0.009;0.01;0.006	T	0.22765	-1.0207	10	0.49607	T	0.09	.	10.5931	0.45321	0.0:1.0:0.0:0.0	rs7960087;rs7960087	11;11;23;11;11;11	B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;RASL1_HUMAN;.	L	11	ENSP00000450244:V11L;ENSP00000261729:V11L;ENSP00000395920:V11L;ENSP00000448510:V11L	ENSP00000261729:V11L	V	-	1	0	RASAL1	112057620	1.000000	0.71417	1.000000	0.80357	0.053000	0.15095	1.663000	0.37429	1.946000	0.56461	0.484000	0.47621	GTG	C|0.974;G|0.026	0.026	strong		0.677	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
EEF1A2	1917	hgsc.bcm.edu	37	20	62126185	62126185	+	Silent	SNP	A	A	G	rs310617	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62126185A>G	ENST00000298049.7	-	3	664	c.594T>C	c.(592-594)ggT>ggC	p.G198G	EEF1A2_ENST00000217182.3_Silent_p.G198G			Q05639	EF1A2_HUMAN	eukaryotic translation elongation factor 1 alpha 2	198	tr-type G.				positive regulation of apoptotic process (GO:0043065)|response to inorganic substance (GO:0010035)	eukaryotic translation elongation factor 1 complex (GO:0005853)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(14)|stomach(1)	20	all_cancers(38;9.45e-12)		BRCA - Breast invasive adenocarcinoma(10;1.22e-05)			GCATGTTGTCACCGTGCCAGC	0.672													G|||	2963	0.591653	0.59	0.5029	5008	,	,		14466	0.6181		0.5934	False		,,,				2504	0.6278				p.G198G		Atlas-SNP	.											EEF1A2,NS,carcinoma,0,3	EEF1A2	60	3	0			c.T594C						PASS	.	G		2603,1785	624.9+/-394.4	770,1063,361	37.0	31.0	33.0		594	-7.8	0.1	20	dbSNP_79	33	4849,3747	606.6+/-395.1	1394,2061,843	no	coding-synonymous	EEF1A2	NM_001958.2		2164,3124,1204	GG,GA,AA		43.59,40.6791,42.6063		198/464	62126185	7452,5532	2194	4298	6492	SO:0001819	synonymous_variant	1917	exon4			GTTGTCACCGTGC	AF163763	CCDS13522.1	20q13.3	2010-06-03			ENSG00000101210	ENSG00000101210			3192	protein-coding gene	gene with protein product		602959	"""statin-like"", ""statin"""	STNL, STN		8354261, 8812466	Standard	NM_001958		Approved	EEF1AL, HS1	uc002yfe.2	Q05639	OTTHUMG00000033076	ENST00000298049.7:c.594T>C	20.37:g.62126185A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_001958	B5BUF3|E1P5J1|P54266|Q0VGC7	Silent	SNP	ENST00000298049.7	37	CCDS13522.1																																																																																			A|0.419;G|0.581	0.581	strong		0.672	EEF1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080495.1	NM_001958	
AAK1	22848	hgsc.bcm.edu	37	2	69709919	69709919	+	Silent	SNP	A	A	G	rs6721259	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:69709919A>G	ENST00000409085.4	-	18	2767	c.2391T>C	c.(2389-2391)tcT>tcC	p.S797S	AAK1_ENST00000406297.3_Silent_p.S797S|AAK1_ENST00000409068.1_Intron	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	797					endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						AAGTGTCAGGAGATTTGAGTC	0.398													A|||	715	0.142772	0.2141	0.1023	5008	,	,		21839	0.0407		0.1938	False		,,,				2504	0.1278				p.S797S		Atlas-SNP	.											.	AAK1	121	.	0			c.T2391C						PASS	.	A		705,3121		69,567,1277	138.0	142.0	141.0		2391	4.8	1.0	2	dbSNP_116	141	1410,6856		128,1154,2851	no	coding-synonymous	AAK1	NM_014911.3		197,1721,4128	GG,GA,AA		17.0578,18.4266,17.4909		797/962	69709919	2115,9977	1913	4133	6046	SO:0001819	synonymous_variant	22848	exon18			GTCAGGAGATTTG	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.2391T>C	2.37:g.69709919A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																			A|0.862;G|0.138	0.138	strong		0.398	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
ARSD	414	hgsc.bcm.edu	37	X	2835985	2835985	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	176	0	0		WXS	Illumina HiSeq	Phase_I	107	40	0.373832	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		
PSG2	5670	hgsc.bcm.edu	37	19	43575982	43575982	+	Silent	SNP	C	C	T	rs150568950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43575982C>T	ENST00000406487.1	-	4	932	c.834G>A	c.(832-834)aaG>aaA	p.K278K		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	278	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				ATTGCTGAAACTTCCCATTAA	0.448													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		20458	0.0		0.001	False		,,,				2504	0.0				p.K278K		Atlas-SNP	.											PSG2,NS,carcinoma,-1,1	PSG2	84	1	0			c.G834A						PASS	.	C		6,4398	825.3+/-416.5	0,6,2196	190.0	199.0	196.0		834	-1.7	0.0	19	dbSNP_134	196	32,8566	817.7+/-406.9	0,32,4267	no	coding-synonymous	PSG2	NM_031246.3		0,38,6463	TT,TC,CC		0.3722,0.1362,0.2923		278/336	43575982	38,12964	2202	4299	6501	SO:0001819	synonymous_variant	5670	exon4			CTGAAACTTCCCA		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.834G>A	19.37:g.43575982C>T		Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	234	108	0.461538	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			C|0.998;T|0.002	0.002	strong		0.448	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
CCDC40	55036	hgsc.bcm.edu	37	17	78071052	78071052	+	Silent	SNP	T	T	C	rs12952612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78071052T>C	ENST00000397545.4	+	19	3057	c.3030T>C	c.(3028-3030)gaT>gaC	p.D1010D		NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	1010					axonemal dynein complex assembly (GO:0070286)|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 (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			AGGCCACCGATGAGTGCACCA	0.572													C|||	3577	0.714257	0.7088	0.5663	5008	,	,		21540	0.6567		0.7614	False		,,,				2504	0.8374				p.D1010D		Atlas-SNP	.											CCDC40,NS,carcinoma,0,1	CCDC40	198	1	0			c.T3030C						PASS	.	C		2864,1182		1015,834,174	68.0	74.0	72.0		3030	-1.2	0.0	17	dbSNP_121	72	6261,2071		2345,1571,250	no	coding-synonymous	CCDC40	NM_017950.3		3360,2405,424	CC,CT,TT		24.856,29.214,26.2805		1010/1143	78071052	9125,3253	2023	4166	6189	SO:0001819	synonymous_variant	55036	exon19			CACCGATGAGTGC	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.3030T>C	17.37:g.78071052T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			T|0.282;C|0.718	0.718	strong		0.572	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
PLRG1	5356	hgsc.bcm.edu	37	4	155459194	155459194	+	Silent	SNP	A	A	T	rs7668818	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	258	2	0.00775194		WXS	Illumina HiSeq	Phase_I	154	120	0.779221	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	
DOCK1	1793	hgsc.bcm.edu	37	10	129046371	129046371	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129046371G>A	ENST00000280333.6	+	28	2993	c.2884G>A	c.(2884-2886)Gta>Ata	p.V962I	DOCK1_ENST00000484400.1_3'UTR	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	962					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)		GACTGATGTGGTAGTAAGTGT	0.388																																					p.V962I		Atlas-SNP	.											.	DOCK1	188	.	0			c.G2884A						PASS	.						112.0	103.0	106.0					10																	129046371		1898	4109	6007	SO:0001583	missense	1793	exon28			GATGTGGTAGTAA	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.2884G>A	10.37:g.129046371G>A	ENSP00000280333:p.Val962Ile	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	186	85	0.456989	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	11.06	1.528362	0.27299	.	.	ENSG00000150760	ENST00000280333	T	0.21734	1.99	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.11495	0.0280	N	0.10733	0.035	0.80722	D	1	B;B	0.24426	0.01;0.103	B;B	0.18871	0.015;0.023	T	0.11084	-1.0602	10	0.07030	T	0.85	.	19.1025	0.93279	0.0:0.0:1.0:0.0	.	962;962	B2RUU3;Q14185	.;DOCK1_HUMAN	I	962	ENSP00000280333:V962I	ENSP00000280333:V962I	V	+	1	0	DOCK1	128936361	1.000000	0.71417	0.997000	0.53966	0.630000	0.37929	6.639000	0.74314	2.491000	0.84063	0.563000	0.77884	GTA	.	.	none		0.388	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103124135	103124135	+	Silent	SNP	T	T	G	rs11225634	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:103124135T>G	ENST00000375735.2	+	66	10308	c.10164T>G	c.(10162-10164)acT>acG	p.T3388T	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.T3395T	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3388	AAA 5. {ECO:0000250}.				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)		CCATTGTTACTGAGGTTAACT	0.348													T|||	907	0.18111	0.3752	0.1254	5008	,	,		15809	0.0933		0.1252	False		,,,				2504	0.1063				p.T3395T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10185G						PASS	.	T	,	1168,2482		189,790,846	109.0	105.0	106.0		10185,10164	0.5	1.0	11	dbSNP_120	106	955,7229		63,829,3200	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	252,1619,4046	GG,GT,TT		11.6691,32.0,17.9398	,	3395/4315,3388/4308	103124135	2123,9711	1825	4092	5917	SO:0001819	synonymous_variant	79659	exon67			TGTTACTGAGGTT	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.10164T>G	11.37:g.103124135T>G		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	432	294	0.680556	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			T|0.824;G|0.176	0.176	strong		0.348	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
PLXNA1	5361	hgsc.bcm.edu	37	3	126741041	126741041	+	Silent	SNP	C	C	T	rs150052583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126741041C>T	ENST00000393409.2	+	21	4152	c.4152C>T	c.(4150-4152)cgC>cgT	p.R1384R	PLXNA1_ENST00000251772.4_Silent_p.R1361R	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1384					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)		TCTCCATGCGCGACCGCGGGA	0.612													C|||	28	0.00559105	0.0038	0.0101	5008	,	,		22692	0.001		0.0129	False		,,,				2504	0.002				p.R1384R		Atlas-SNP	.											PLXNA1,colon,carcinoma,+2,1	PLXNA1	185	1	0			c.C4152T						PASS	.	C		11,4393	17.9+/-39.9	0,11,2191	62.0	54.0	56.0		4152	-5.4	0.9	3	dbSNP_134	56	93,8505	53.1+/-113.8	0,93,4206	no	coding-synonymous	PLXNA1	NM_032242.3		0,104,6397	TT,TC,CC		1.0816,0.2498,0.7999		1384/1897	126741041	104,12898	2202	4299	6501	SO:0001819	synonymous_variant	5361	exon21			CATGCGCGACCGC	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.4152C>T	3.37:g.126741041C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																			C|0.992;T|0.008	0.008	strong		0.612	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242	
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441478	39441478	+	Missense_Mutation	SNP	C	C	A	rs138934952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:39441478C>A	ENST00000308521.5	+	4	854	c.497C>A	c.(496-498)cCa>cAa	p.P166Q	APOBEC3G_ENST00000452957.2_Intron	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	166					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|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)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|skin(2)	16	Melanoma(58;0.04)					GAAGGTCAGCCATTCATGCCT	0.527													C|||	9	0.00179712	0.0	0.0	5008	,	,		22581	0.0		0.0089	False		,,,				2504	0.0				p.P166Q		Atlas-SNP	.											.	APOBEC3F	37	.	0			c.C497A						PASS	.	C	GLN/PRO	1,4405		0,1,2202	363.0	299.0	321.0		497	-1.4	0.0	22	dbSNP_134	321	13,8587		0,13,4287	no	missense	APOBEC3F	NM_145298.5	76	0,14,6489	AA,AC,CC		0.1512,0.0227,0.1076	benign	166/374	39441478	14,12992	2203	4300	6503	SO:0001583	missense	200316	exon4			GTCAGCCATTCAT	BC038808	CCDS33648.1, CCDS33649.1	22q13.1-q13.2	2008-05-15			ENSG00000128394	ENSG00000128394		"""Apolipoprotein B mRNA editing enzymes"""	17356	protein-coding gene	gene with protein product		608993				11863358, 17121840	Standard	NM_145298		Approved	ARP8, BK150C2.4.MRNA, KA6	uc003aww.3	Q8IUX4	OTTHUMG00000151080	ENST00000308521.5:c.497C>A	22.37:g.39441478C>A	ENSP00000309749:p.Pro166Gln	Somatic	455	0	0		WXS	Illumina HiSeq	Phase_I	425	197	0.463529	NM_145298	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Missense_Mutation	SNP	ENST00000308521.5	37	CCDS33648.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	.	5.006	0.186780	0.09547	2.27E-4	0.001512	ENSG00000128394	ENST00000308521	T	0.63096	-0.02	2.27	-1.43	0.08884	APOBEC-like, C-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.30386	0.0763	N	0.25825	0.765	0.09310	N	1	B	0.18741	0.03	B	0.17433	0.018	T	0.15292	-1.0442	9	0.20519	T	0.43	.	1.0452	0.01568	0.2303:0.3935:0.226:0.1502	.	166	Q8IUX4	ABC3F_HUMAN	Q	166	ENSP00000309749:P166Q	ENSP00000309749:P166Q	P	+	2	0	APOBEC3F	37771424	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.825000	0.04433	-0.226000	0.09899	0.400000	0.26472	CCA	C|0.998;A|0.002	0.002	strong		0.527	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298	
RNF151	146310	hgsc.bcm.edu	37	16	2018578	2018578	+	Missense_Mutation	SNP	C	C	G	rs45488492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2018578C>G	ENST00000569714.1	+	4	398	c.390C>G	c.(388-390)caC>caG	p.H130Q	RNF151_ENST00000569210.2_3'UTR|RNF151_ENST00000321392.3_Missense_Mutation_p.H129Q	NM_174903.4	NP_777563.2	Q2KHN1	RN151_HUMAN	ring finger protein 151	130					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2						TGGCAGAGCACCGGCAGCATT	0.711													C|||	252	0.0503195	0.0991	0.0245	5008	,	,		15086	0.0		0.0239	False		,,,				2504	0.0818				p.H130Q		Atlas-SNP	.											.	RNF151	12	.	0			c.C390G						PASS	.	C	GLN/HIS	316,3654		12,292,1681	10.0	11.0	11.0		390	0.6	0.1	16	dbSNP_127	11	240,8028		2,236,3896	no	missense	RNF151	NM_174903.4	24	14,528,5577	GG,GC,CC		2.9028,7.9597,4.5432	probably-damaging	130/246	2018578	556,11682	1985	4134	6119	SO:0001583	missense	146310	exon4			AGAGCACCGGCAG	BC029501	CCDS58405.1	16p13.3	2013-01-09			ENSG00000179580	ENSG00000179580		"""RING-type (C3HC4) zinc fingers"""	23235	protein-coding gene	gene with protein product						12477932	Standard	NM_174903		Approved		uc002cnt.1	Q2KHN1	OTTHUMG00000176852	ENST00000569714.1:c.390C>G	16.37:g.2018578C>G	ENSP00000456566:p.His130Gln	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	93	50	0.537634	NM_174903	Q8NHS5	Missense_Mutation	SNP	ENST00000569714.1	37	CCDS58405.1	83	0.038003663003663	56	0.11382113821138211	8	0.022099447513812154	0	0.0	19	0.025065963060686015	c	11.37	1.619320	0.28801	0.079597	0.029028	ENSG00000179580	ENST00000321392	D	0.92752	-3.1	5.25	0.546	0.17196	Zinc finger, TRAF-type (1);TRAF-like (1);Seven In Absentia Homolog-type (1);Zinc finger, SIAH-type (1);	0.141153	0.45867	D	0.000326	T	0.40272	0.1110	M	0.87180	2.865	0.39718	P	0.028576000000000046	D	0.89917	1.0	D	0.91635	0.999	T	0.75294	-0.3368	9	0.87932	D	0	-27.2691	7.805	0.29198	0.0:0.5926:0.0:0.4074	rs45488492	130	Q2KHN1	RN151_HUMAN	Q	129	ENSP00000325794:H129Q	ENSP00000325794:H129Q	H	+	3	2	RNF151	1958579	0.009000	0.17119	0.100000	0.21137	0.019000	0.09904	-0.044000	0.12023	0.235000	0.21160	0.655000	0.94253	CAC	C|0.963;G|0.037	0.037	strong		0.711	RNF151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434030.1	NM_174903	
PPM1F	9647	hgsc.bcm.edu	37	22	22287862	22287862	+	Silent	SNP	G	G	A	rs2027789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:22287862G>A	ENST00000263212.5	-	5	753	c.648C>T	c.(646-648)aaC>aaT	p.N216N	PPM1F_ENST00000407142.1_Silent_p.N48N|PPM1F_ENST00000397495.4_Silent_p.N216N|PPM1F_ENST00000538191.1_Silent_p.N112N	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	216					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		GGCGGGCAGCGTTGGTGTGCA	0.632													G|||	1237	0.247005	0.2874	0.2939	5008	,	,		17553	0.0863		0.4006	False		,,,				2504	0.1667				p.N216N		Atlas-SNP	.											.	PPM1F	34	.	0			c.C648T						PASS	.	G		1232,3174	425.1+/-340.7	161,910,1132	69.0	59.0	63.0		648	-8.1	0.0	22	dbSNP_94	63	3386,5214	501.0+/-375.3	671,2044,1585	no	coding-synonymous	PPM1F	NM_014634.3		832,2954,2717	AA,AG,GG		39.3721,27.9619,35.5067		216/455	22287862	4618,8388	2203	4300	6503	SO:0001819	synonymous_variant	9647	exon5			GGCAGCGTTGGTG	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19388	protein-coding gene	gene with protein product	"""partner of PIX 2"", ""Ca(2+)/calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1F (PP2C domain containing)"""			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.648C>T	22.37:g.22287862G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	80	29	0.3625	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Silent	SNP	ENST00000263212.5	37	CCDS13796.1																																																																																			G|0.665;A|0.335	0.335	strong		0.632	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634	
FNDC1	84624	hgsc.bcm.edu	37	6	159667961	159667961	+	Silent	SNP	T	T	G	rs294911	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159667961T>G	ENST00000297267.9	+	15	4850	c.4650T>G	c.(4648-4650)acT>acG	p.T1550T	FNDC1_ENST00000340366.6_Silent_p.T1487T	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1550					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)		AGACTGACACTGCAGTACCTA	0.458													T|||	803	0.160343	0.0363	0.317	5008	,	,		18776	0.0982		0.2396	False		,,,				2504	0.1994				p.T1550T		Atlas-SNP	.											.	FNDC1	250	.	0			c.T4650G						PASS	.	T		255,3601		12,231,1685	131.0	127.0	128.0		4650	-10.2	0.0	6	dbSNP_79	128	1962,6328		218,1526,2401	no	coding-synonymous	FNDC1	NM_032532.2		230,1757,4086	GG,GT,TT		23.6671,6.6131,18.2529		1550/1895	159667961	2217,9929	1928	4145	6073	SO:0001819	synonymous_variant	84624	exon15			TGACACTGCAGTA	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.4650T>G	6.37:g.159667961T>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	103	63	0.61165	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	384	0.17582417582417584	30	0.06097560975609756	111	0.30662983425414364	55	0.09615384615384616	188	0.24802110817941952	T	3.832	-0.035489	0.07497	0.066131	0.236671	ENSG00000164694	ENST00000329629	.	.	.	5.12	-10.2	0.00374	.	.	.	.	.	T	0.02929	0.0087	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.21280	-1.0250	3	.	.	.	-0.3529	1.6692	0.02808	0.3931:0.0817:0.1885:0.3367	rs294911;rs17218437;rs59174672;rs294911	.	.	.	G	1446	.	.	C	+	1	0	FNDC1	159587951	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.140000	0.03210	-1.951000	0.01029	-1.433000	0.01084	TGC	T|0.835;G|0.165	0.165	strong		0.458	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
PHPT1	29085	hgsc.bcm.edu	37	9	139744524	139744524	+	Silent	SNP	C	C	T	rs8666	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139744524C>T	ENST00000247665.10	+	2	557	c.220C>T	c.(220-222)Ctg>Ttg	p.L74L	MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000492540.1_3'UTR|MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000371661.1_Silent_p.L74L|PHPT1_ENST00000545326.1_Silent_p.L74L	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	74					negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CTGTGAGTGTCTGGGCGGCGG	0.662													C|||	214	0.0427316	0.0015	0.0202	5008	,	,		14400	0.0089		0.0318	False		,,,				2504	0.1605				p.L74L		Atlas-SNP	.											.	PHPT1	14	.	0			c.C220T						PASS	.	C	,	33,4373		0,33,2170	104.0	100.0	101.0		220,220	4.6	1.0	9	dbSNP_52	101	283,8317		5,273,4022	no	coding-synonymous,coding-synonymous	PHPT1	NM_001135861.1,NM_014172.4	,	5,306,6192	TT,TC,CC		3.2907,0.749,2.4296	,	74/125,74/126	139744524	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	29085	exon2			GAGTGTCTGGGCG	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"""phosphohistidine phosphatase 14kDa"", "" sex-regulated protein janus-a"""	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950	ENST00000247665.10:c.220C>T	9.37:g.139744524C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	176	82	0.465909	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Silent	SNP	ENST00000247665.10	37	CCDS7009.1																																																																																			C|0.972;T|0.028	0.028	strong		0.662	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461074	141461074	+	Silent	SNP	A	A	G	rs61739560	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:141461074A>G	ENST00000438773.2	-	2	532	c.399T>C	c.(397-399)gcT>gcC	p.A133A	TRAPPC9_ENST00000389327.3_Silent_p.A133A|TRAPPC9_ENST00000389328.4_Silent_p.A231A	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	133					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						TGGGGTAGAAAGCCACGTCGG	0.582													G|||	321	0.0640974	0.1036	0.072	5008	,	,		19685	0.004		0.0785	False		,,,				2504	0.0521				p.A231A		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.T693C						PASS	.	G	,	494,3912	782.0+/-414.5	28,438,1737	69.0	60.0	63.0		399,693	4.5	1.0	8	dbSNP_129	63	727,7873	786.2+/-407.6	34,659,3607	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	62,1097,5344	GG,GA,AA		8.4535,11.212,9.388	,	133/1149,231/1247	141461074	1221,11785	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon2			GTAGAAAGCCACG	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.399T>C	8.37:g.141461074A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	128	50	0.390625	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1																																																																																			A|0.913;G|0.087	0.087	strong		0.582	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
CLEC11A	6320	hgsc.bcm.edu	37	19	51228634	51228634	+	Silent	SNP	G	G	A	rs11084024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51228634G>A	ENST00000250340.4	+	4	1079	c.882G>A	c.(880-882)gaG>gaA	p.E294E	CLEC11A_ENST00000599973.1_Missense_Mutation_p.E311K	NM_002975.2	NP_002966.1	Q9Y240	CLC11_HUMAN	C-type lectin domain family 11, member A	294	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|growth factor activity (GO:0008083)			kidney(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	7		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GCACGCTCGAGAACTGCGTGG	0.711													G|||	759	0.151558	0.1853	0.1182	5008	,	,		13732	0.0506		0.2505	False		,,,				2504	0.1319				p.E294E		Atlas-SNP	.											.	CLEC11A	23	.	0			c.G882A						PASS	.	G		796,3586		69,658,1464	17.0	16.0	17.0		882	3.5	1.0	19	dbSNP_120	17	1859,6691		212,1435,2628	no	coding-synonymous	CLEC11A	NM_002975.2		281,2093,4092	AA,AG,GG		21.7427,18.1652,20.5305		294/324	51228634	2655,10277	2191	4275	6466	SO:0001819	synonymous_variant	6320	exon4			GCTCGAGAACTGC	AF087658	CCDS12800.1	19q13.3	2010-04-27	2005-02-09	2005-02-11		ENSG00000105472		"""C-type lectin domain containing"""	10576	protein-coding gene	gene with protein product		604713	"""stem cell growth factor; lymphocyte secreted C-type lectin"""	SCGF		9207134, 9442024	Standard	NM_002975		Approved	P47, LSLCL, CLECSF3	uc002psy.3	Q9Y240		ENST00000250340.4:c.882G>A	19.37:g.51228634G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_002975	B2RAD4	Silent	SNP	ENST00000250340.4	37	CCDS12800.1																																																																																			G|0.808;A|0.192	0.192	strong		0.711	CLEC11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464062.1	NM_002975	
TONSL	4796	hgsc.bcm.edu	37	8	145661320	145661320	+	Silent	SNP	G	G	A	rs2721140	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145661320G>A	ENST00000409379.3	-	17	2525	c.2496C>T	c.(2494-2496)gcC>gcT	p.A832A	AC084125.4_ENST00000442850.1_RNA|AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	832					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						GCCAGTCCCCGGCCAGGCACT	0.741													g|||	2347	0.46865	0.4115	0.438	5008	,	,		13786	0.4246		0.4662	False		,,,				2504	0.6155				p.A832A		Atlas-SNP	.											TONSL_ENST00000409379,rectum,carcinoma,0,2	TONSL	128	2	0			c.C2496T						PASS	.			1747,2459		402,943,758	8.0	11.0	10.0		2496	-8.9	0.0	8	dbSNP_100	10	3725,4593		923,1879,1357	no	coding-synonymous	TONSL	NM_013432.4		1325,2822,2115	AA,AG,GG		44.7824,41.5359,43.6921		832/1379	145661320	5472,7052	2103	4159	6262	SO:0001819	synonymous_variant	4796	exon17			GTCCCCGGCCAGG		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"""Ankyrin repeat domain containing"""	7801	protein-coding gene	gene with protein product		604546	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"""	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.2496C>T	8.37:g.145661320G>A		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Silent	SNP	ENST00000409379.3	37	CCDS34968.2																																																																																			G|0.603;A|0.397	0.397	strong		0.741	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432	
IPO9	55705	hgsc.bcm.edu	37	1	201798367	201798367	+	Silent	SNP	C	C	T	rs537589191		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201798367C>T	ENST00000361565.4	+	1	99	c.30C>T	c.(28-30)gcC>gcT	p.A10A	IPO9_ENST00000464348.1_3'UTR|IPO9-AS1_ENST00000421449.1_RNA|IPO9-AS1_ENST00000421159.1_RNA|IPO9-AS1_ENST00000413035.1_RNA	NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	10					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone binding (GO:0042393)|protein transporter activity (GO:0008565)			cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	38						CTGGTGCGGCCTCCGGGCTGC	0.711													C|||	1	0.000199681	0.0	0.0	5008	,	,		9698	0.0		0.0	False		,,,				2504	0.001				p.A10A		Atlas-SNP	.											.	IPO9	98	.	0			c.C30T						PASS	.						10.0	12.0	12.0					1																	201798367		2164	4234	6398	SO:0001819	synonymous_variant	55705	exon1			TGCGGCCTCCGGG	AF410465	CCDS1415.1	1q31.3	2008-02-05			ENSG00000198700	ENSG00000198700		"""Importins"""	19425	protein-coding gene	gene with protein product						11823430, 10574461	Standard	NM_018085		Approved	Imp9, FLJ10402	uc001gwz.3	Q96P70	OTTHUMG00000035805	ENST00000361565.4:c.30C>T	1.37:g.201798367C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	60	19	0.316667	NM_018085	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Silent	SNP	ENST00000361565.4	37	CCDS1415.1																																																																																			.	.	none		0.711	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085	
OTX1	5013	hgsc.bcm.edu	37	2	63283178	63283178	+	Silent	SNP	C	C	G	rs17850223	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	268	0	0		WXS	Illumina HiSeq	Phase_I	275	136	0.494545	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		
FGF3	2248	hgsc.bcm.edu	37	11	69625385	69625385	+	Silent	SNP	C	C	T	rs35420992	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:69625385C>T	ENST00000334134.2	-	3	498	c.408G>A	c.(406-408)acG>acA	p.T136T		NM_005247.2	NP_005238.1	P11487	FGF3_HUMAN	fibroblast growth factor 3	136					anatomical structure morphogenesis (GO:0009653)|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)|insulin receptor signaling pathway (GO:0008286)|negative regulation of cardiac muscle tissue development (GO:0055026)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|post-anal tail morphogenesis (GO:0036342)|semicircular canal morphogenesis (GO:0048752)|signal transduction (GO:0007165)|thymus development (GO:0048538)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	growth factor activity (GO:0008083)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	13			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)			TACTAGACACCGTCCGGTACA	0.647													C|||	261	0.0521166	0.0386	0.0274	5008	,	,		15484	0.0159		0.0954	False		,,,				2504	0.0808				p.T136T		Atlas-SNP	.											.	FGF3	27	.	0			c.G408A						PASS	.	C		196,4200		4,188,2006	32.0	39.0	36.0		408	-2.8	0.0	11	dbSNP_126	36	895,7689		56,783,3453	no	coding-synonymous	FGF3	NM_005247.2		60,971,5459	TT,TC,CC		10.4264,4.4586,8.4052		136/240	69625385	1091,11889	2198	4292	6490	SO:0001819	synonymous_variant	2248	exon3			AGACACCGTCCGG		CCDS8195.1	11q13	2010-06-25	2010-06-25		ENSG00000186895	ENSG00000186895			3681	protein-coding gene	gene with protein product	"""INT-2 proto-oncogene protein"", ""oncogene INT2"", ""V-INT2 murine mammary tumor virus integration site oncogene homolog"", ""murine mammary tumor virus integration site 2, mouse"""	164950	"""fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)"""	INT2			Standard	NM_005247		Approved	HBGF-3	uc001oph.3	P11487	OTTHUMG00000167888	ENST00000334134.2:c.408G>A	11.37:g.69625385C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	184	75	0.407609	NM_005247	Q0VG69	Silent	SNP	ENST00000334134.2	37	CCDS8195.1																																																																																			C|0.931;T|0.069	0.069	strong		0.647	FGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396835.1	NM_005247	
DSCAML1	57453	hgsc.bcm.edu	37	11	117395707	117395707	+	Silent	SNP	C	C	T	rs142205484	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117395707C>T	ENST00000321322.6	-	5	931	c.930G>A	c.(928-930)tcG>tcA	p.S310S	DSCAML1_ENST00000527706.1_Silent_p.S40S	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	250					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.S310S(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TAGGGTAGCCCGAGGCGGTGC	0.677																																					p.S310S		Atlas-SNP	.											DSCAML1,colon,carcinoma,0,1	DSCAML1	286	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G930A						scavenged	.	C		0,4400		0,0,2200	21.0	21.0	21.0		930	-9.9	0.2	11	dbSNP_134	21	2,8584		0,2,4291	no	coding-synonymous	DSCAML1	NM_020693.2		0,2,6491	TT,TC,CC		0.0233,0.0,0.0154		310/2114	117395707	2,12984	2200	4293	6493	SO:0001819	synonymous_variant	57453	exon5			GTAGCCCGAGGCG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.930G>A	11.37:g.117395707C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	2	0.0206186	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			C|0.999;T|0.001	0.001	strong		0.677	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
ACPT	93650	hgsc.bcm.edu	37	19	51297826	51297826	+	Missense_Mutation	SNP	C	C	A	rs55735528|rs386810263	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51297826C>A	ENST00000270593.1	+	9	974	c.974C>A	c.(973-975)gCc>gAc	p.A325D	ACPT_ENST00000270594.3_Missense_Mutation_p.A232D|CTD-2568A17.8_ENST00000594114.1_RNA	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	325						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GGGAATCCCGCCAAAGATGGA	0.617													A|||	1652	0.329872	0.1309	0.2161	5008	,	,		17428	0.6538		0.3012	False		,,,				2504	0.3753				p.A325D		Atlas-SNP	.											.	ACPT	43	.	0			c.C974A						PASS	.	C	ASP/ALA	673,3733		44,585,1574	39.0	39.0	39.0		974	2.9	0.0	19	dbSNP_129	39	2383,6217		348,1687,2265	yes	missense	ACPT	NM_033068.2	126	392,2272,3839	AA,AC,CC		27.7093,15.2746,23.4968	benign	325/427	51297826	3056,9950	2203	4300	6503	SO:0001583	missense	93650	exon9			ATCCCGCCAAAGA	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.974C>A	19.37:g.51297826C>A	ENSP00000270593:p.Ala325Asp	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	37	CCDS12802.1	640	0.29304029304029305	50	0.1016260162601626	71	0.19613259668508287	329	0.5751748251748252	190	0.25065963060686014	N	3.945	-0.013485	0.07727	0.152746	0.277093	ENSG00000142513	ENST00000270593;ENST00000270594	T;T	0.76709	2.97;-1.04	3.9	2.88	0.33553	.	0.642945	0.14811	N	0.297051	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	0.46638	-0.9177	9	0.14656	T	0.56	-10.0341	8.9577	0.35827	0.8111:0.1889:0.0:0.0	rs55735528;rs61505895	325	Q9BZG2	PPAT_HUMAN	D	325;232	ENSP00000270593:A325D;ENSP00000270594:A232D	ENSP00000270593:A325D	A	+	2	0	ACPT	55989638	0.004000	0.15560	0.017000	0.16124	0.002000	0.02628	1.783000	0.38664	0.688000	0.31529	-0.367000	0.07326	GCC	C|0.752;A|0.248	0.248	strong		0.617	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102508056	102508056	+	Missense_Mutation	SNP	C	C	A	rs10129889	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102508056C>A	ENST00000360184.4	+	65	12251	c.12087C>A	c.(12085-12087)caC>caA	p.H4029Q	RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557551.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4029	AAA 6. {ECO:0000250}.		H -> Q (in dbSNP:rs10129889). {ECO:0000269|PubMed:9205841, ECO:0000269|Ref.4}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						ACCTGACCCACATTGTGGGCA	0.602													C|||	496	0.0990415	0.2784	0.0519	5008	,	,		19868	0.002		0.0696	False		,,,				2504	0.0204				p.H4029Q		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C12087A						PASS	.	C	GLN/HIS	1199,3207	418.7+/-338.4	164,871,1168	59.0	61.0	60.0		12087	4.6	1.0	14	dbSNP_119	60	534,8066	148.8+/-204.0	20,494,3786	yes	missense	DYNC1H1	NM_001376.4	24	184,1365,4954	AA,AC,CC		6.2093,27.2129,13.3246	benign	4029/4647	102508056	1733,11273	2203	4300	6503	SO:0001583	missense	1778	exon65			GACCCACATTGTG	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.12087C>A	14.37:g.102508056C>A	ENSP00000348965:p.His4029Gln	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	143	48	0.335664	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	203	0.09294871794871795	138	0.2804878048780488	20	0.055248618784530384	0	0.0	45	0.059366754617414245	C	7.360	0.624576	0.14193	0.272129	0.062093	ENSG00000197102	ENST00000360184	T	0.07908	3.15	5.61	4.59	0.56863	Dynein heavy chain (1);	0.094690	0.64402	D	0.000001	T	0.00012	0.0000	N	0.03154	-0.405	0.22112	P	0.999354976	B	0.06786	0.001	B	0.04013	0.001	T	0.48570	-0.9024	9	0.18710	T	0.47	.	8.1177	0.30953	0.0:0.7299:0.0:0.2701	rs10129889;rs17292699;rs17292706;rs17541554;rs57501843;rs10129889	4029	Q14204	DYHC1_HUMAN	Q	4029	ENSP00000348965:H4029Q	ENSP00000348965:H4029Q	H	+	3	2	DYNC1H1	101577809	0.995000	0.38212	0.984000	0.44739	0.984000	0.73092	0.450000	0.21762	1.256000	0.44068	0.655000	0.94253	CAC	C|0.882;A|0.118	0.118	strong		0.602	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
SH3TC2	79628	hgsc.bcm.edu	37	5	148407893	148407893	+	Missense_Mutation	SNP	C	C	A	rs6875902	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:148407893C>A	ENST00000515425.1	-	11	1503	c.1402G>T	c.(1402-1404)Gcc>Tcc	p.A468S	SH3TC2_ENST00000513340.1_5'Flank|SH3TC2_ENST00000538184.1_Missense_Mutation_p.A15S|SH3TC2_ENST00000512049.1_Missense_Mutation_p.A461S|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	53	30	0.566038	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	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435194	7435194	+	Silent	SNP	G	G	A	rs12498567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:7435194G>A	ENST00000319098.4	-	1	1506	c.1413C>T	c.(1411-1413)ggC>ggT	p.G471G	SORCS2_ENST00000507866.2_Intron|SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	471	Saposin B-type 4. {ECO:0000255|PROSITE- ProRule:PRU00415}.				sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						GGGTCCTGGGGCCGTGGCAGG	0.642													G|||	577	0.115216	0.1036	0.1138	5008	,	,		17473	0.1111		0.1839	False		,,,				2504	0.0654				p.G471G		Atlas-SNP	.											PSAPL1_ENST00000319098,NS,carcinoma,-1,2	PSAPL1	51	2	0			c.C1413T						PASS	.	G	,	490,3460		32,426,1517	19.0	22.0	21.0		1413,	-1.3	0.0	4	dbSNP_120	21	1450,6834		121,1208,2813	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	153,1634,4330	AA,AG,GG		17.5036,12.4051,15.8574	,	471/522,	7435194	1940,10294	1975	4142	6117	SO:0001819	synonymous_variant	768239	exon1			CCTGGGGCCGTGG	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.1413C>T	4.37:g.7435194G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			G|0.868;A|0.132	0.132	strong		0.642	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
ABHD17A	81926	hgsc.bcm.edu	37	19	1880950	1880950	+	Intron	SNP	T	T	C	rs4807160	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1880950T>C	ENST00000292577.7	-	2	766				ABHD17A_ENST00000590661.1_Intron|ABHD17A_ENST00000250974.9_Missense_Mutation_p.K144E	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A							extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										CCCCAGCTCTTGCCCAGCAGG	0.657													N|||	3160	0.63099	0.6241	0.6686	5008	,	,		16727	0.5913		0.6243	False		,,,				2504	0.6616				p.K144E		Atlas-SNP	.											FAM108A1,NS,carcinoma,0,1	FAM108A1	29	1	0			c.A430G						PASS	.	C	,GLU/LYS	2846,1556		908,1030,263	31.0	37.0	35.0		,430	-4.9	0.0	19	dbSNP_111	35	5388,3210		1692,2004,603	yes	intron,missense	FAM108A1	NM_001130111.1,NM_031213.3	,56	2600,3034,866	CC,CT,TT		37.3343,35.3476,36.6615	,	,144/362	1880950	8234,4766	2201	4299	6500	SO:0001627	intron_variant	81926	exon3			AGCTCTTGCCCAG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"""Abhydrolase domain containing"""	28756	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 27"", ""family with sequence similarity 108, member A1"""	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.332+283A>G	19.37:g.1880950T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_031213	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Missense_Mutation	SNP	ENST00000292577.7	37	CCDS45902.1	1370	0.6272893772893773	311	0.6321138211382114	246	0.6795580110497238	348	0.6083916083916084	465	0.6134564643799473	-	0.034	-1.315169	0.01331	0.646524	0.626657	ENSG00000129968	ENST00000250974	T	0.30448	1.53	2.47	-4.94	0.03057	.	9.963510	0.00357	N	0.000036	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35450	-0.9788	8	0.06236	T	0.91	.	6.6701	0.23064	0.0:0.2997:0.1519:0.5483	rs4807160;rs17856603;rs56812054	144	Q96GS6-2	.	E	144	ENSP00000250974:K144E	ENSP00000250974:K144E	K	-	1	0	FAM108A1	1831950	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	-0.878000	0.04192	-1.995000	0.00971	-0.231000	0.12243	AAG	T|0.372;C|0.628	0.628	strong		0.657	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213	
AHNAK2	113146	hgsc.bcm.edu	37	14	105413649	105413649	+	Silent	SNP	A	A	G	rs201545349	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105413649A>G	ENST00000333244.5	-	7	8258	c.8139T>C	c.(8137-8139)gaT>gaC	p.D2713D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2713						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)			GGAGTTTCACATCCACCTGGC	0.612													.|||	29	0.00579073	0.0174	0.0	5008	,	,		17337	0.0		0.0	False		,,,				2504	0.0061				p.D2713D		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-2,1	AHNAK2	719	1	0			c.T8139C						scavenged	.						130.0	144.0	139.0					14																	105413649		1936	4121	6057	SO:0001819	synonymous_variant	113146	exon7			TTTCACATCCACC	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.8139T>C	14.37:g.105413649A>G		Somatic	239	2	0.0083682		WXS	Illumina HiSeq	Phase_I	281	13	0.0462633	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.998;G|0.002	0.002	weak		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
DOK7	285489	hgsc.bcm.edu	37	4	3494847	3494847	+	Silent	SNP	G	G	A	rs6831659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:3494847G>A	ENST00000340083.5	+	7	1199	c.1134G>A	c.(1132-1134)gcG>gcA	p.A378A	DOK7_ENST00000389653.2_Silent_p.A378A|DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR	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	92	0	0		WXS	Illumina HiSeq	Phase_I	65	38	0.584615	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	
TMEM8A	58986	hgsc.bcm.edu	37	16	427452	427452	+	Missense_Mutation	SNP	C	C	T	rs146645376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:427452C>T	ENST00000431232.2	-	3	593	c.433G>A	c.(433-435)Gtt>Att	p.V145I	TMEM8A_ENST00000250930.3_5'UTR|TMEM8A_ENST00000476735.1_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	145					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						GGGTGGGAAACGTTGACGGAG	0.692											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	3	0.000599042	0.0	0.0014	5008	,	,		15162	0.0		0.002	False		,,,				2504	0.0				p.V145I		Atlas-SNP	.											.	TMEM8A	49	.	0			c.G433A						PASS	.	C	ILE/VAL	1,4383		0,1,2191	20.0	21.0	21.0		433	-2.8	0.7	16	dbSNP_134	21	21,8571		0,21,4275	yes	missense	TMEM8A	NM_021259.2	29	0,22,6466	TT,TC,CC		0.2444,0.0228,0.1695	benign	145/772	427452	22,12954	2192	4296	6488	SO:0001583	missense	58986	exon3			GGGAAACGTTGAC	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.433G>A	16.37:g.427452C>T	ENSP00000401338:p.Val145Ile	Somatic	124	0	0	588	WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	2.751	-0.260131	0.05791	2.28E-4	0.002444	ENSG00000129925	ENST00000431232	T	0.22945	1.93	4.59	-2.78	0.05859	.	0.629806	0.14558	N	0.312254	T	0.09158	0.0226	N	0.16833	0.445	0.80722	D	1	B	0.16396	0.017	B	0.06405	0.002	T	0.28364	-1.0046	10	0.15066	T	0.55	-0.0054	12.862	0.57918	0.0:0.1718:0.0:0.8282	.	145	Q9HCN3	TMM8A_HUMAN	I	145	ENSP00000401338:V145I	ENSP00000401338:V145I	V	-	1	0	TMEM8A	367453	0.069000	0.21087	0.699000	0.30290	0.293000	0.27360	-0.831000	0.04405	-0.760000	0.04677	0.563000	0.77884	GTT	C|0.998;T|0.002	0.002	strong		0.692	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
TSSC1	7260	hgsc.bcm.edu	37	2	3261173	3261173	+	Silent	SNP	A	A	G	rs10188932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:3261173A>G	ENST00000382125.4	-	4	505	c.313T>C	c.(313-315)Ttg>Ctg	p.L105L	TSSC1_ENST00000443925.2_Silent_p.L105L|TSSC1_ENST00000478754.1_5'UTR|TSSC1_ENST00000398659.4_Silent_p.L132L	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	105										breast(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	18	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.212)		OV - Ovarian serous cystadenocarcinoma(76;0.00877)|Epithelial(75;0.0283)|all cancers(51;0.0464)		CCTGATTCCAATTCCTTCGGC	0.542													A|||	199	0.0397364	0.0635	0.0115	5008	,	,		18120	0.0079		0.0338	False		,,,				2504	0.0665				p.L105L	Colon(140;1261 1762 4183 34270 49743)	Atlas-SNP	.											.	TSSC1	39	.	0			c.T313C						PASS	.	A		270,4136	151.4+/-185.3	10,250,1943	109.0	96.0	100.0		313	-0.5	0.4	2	dbSNP_119	100	289,8311	106.2+/-167.1	5,279,4016	no	coding-synonymous	TSSC1	NM_003310.2		15,529,5959	GG,GA,AA		3.3605,6.128,4.298		105/388	3261173	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	7260	exon4			ATTCCAATTCCTT	AF019952	CCDS1651.1	2p25.3	2013-01-10			ENSG00000032389	ENSG00000032389		"""WD repeat domain containing"""	12383	protein-coding gene	gene with protein product		608998				9403053, 9925925	Standard	NM_003310		Approved		uc002qxj.2	Q53HC9	OTTHUMG00000090329	ENST00000382125.4:c.313T>C	2.37:g.3261173A>G		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	192	92	0.479167	NM_003310	D6W4Y1|O43179|Q53S19|Q53SG2	Silent	SNP	ENST00000382125.4	37	CCDS1651.1																																																																																			A|0.960;G|0.040	0.040	strong		0.542	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310	
MUC17	140453	hgsc.bcm.edu	37	7	100678405	100678405	+	Silent	SNP	T	T	C	rs4729648	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678405T>C	ENST00000306151.4	+	3	3772	c.3708T>C	c.(3706-3708)gcT>gcC	p.A1236A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1236	59 X approximate tandem repeats.|Ser-rich.				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)					GTTCTGAGGCTAGCACCCTTT	0.522													T|||	989	0.197484	0.2663	0.0893	5008	,	,		30674	0.2212		0.1083	False		,,,				2504	0.2485				p.A1236A		Atlas-SNP	.											MUC17,caecum,carcinoma,0,1	MUC17	804	1	0			c.T3708C						scavenged	.	T		340,4066	144.2+/-179.2	0,340,1863	305.0	293.0	297.0		3708	-0.9	0.0	7	dbSNP_111	297	209,8391	66.0+/-128.3	0,209,4091	no	coding-synonymous	MUC17	NM_001040105.1		0,549,5954	CC,CT,TT		2.4302,7.7167,4.2211		1236/4494	100678405	549,12457	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TGAGGCTAGCACC	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.3708T>C	7.37:g.100678405T>C		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	253	72	0.284585	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.936;C|0.064	0.064	strong		0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552090	178552090	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:178552090C>T	ENST00000251582.7	-	19	2943	c.2842G>A	c.(2842-2844)Gac>Aac	p.D948N		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	948	TSP type-1 3. {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)		GTGGTGTTGTCGTGTAGCGGC	0.692																																					p.D948N		Atlas-SNP	.											ADAMTS2,caecum,carcinoma,0,2	ADAMTS2	190	2	0			c.G2842A						scavenged	.						112.0	113.0	113.0					5																	178552090		2203	4300	6503	SO:0001583	missense	9509	exon19			TGTTGTCGTGTAG	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.2842G>A	5.37:g.178552090C>T	ENSP00000251582:p.Asp948Asn	Somatic	223	3	0.0134529		WXS	Illumina HiSeq	Phase_I	176	3	0.0170455	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	0.743	-0.775731	0.02951	.	.	ENSG00000087116	ENST00000251582	T	0.53857	0.6	5.31	2.0	0.26442	.	0.301971	0.27792	N	0.017833	T	0.26774	0.0655	N	0.12422	0.21	0.80722	D	1	B	0.24317	0.101	B	0.22601	0.04	T	0.10730	-1.0617	10	0.06757	T	0.87	.	8.4694	0.32975	0.0:0.7177:0.0:0.2823	.	948	O95450	ATS2_HUMAN	N	948	ENSP00000251582:D948N	ENSP00000251582:D948N	D	-	1	0	ADAMTS2	178484696	0.966000	0.33281	0.957000	0.39632	0.030000	0.12068	1.550000	0.36223	0.026000	0.15269	-1.140000	0.01884	GAC	.	.	none		0.692	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
PLEKHM2	23207	hgsc.bcm.edu	37	1	16044401	16044401	+	Silent	SNP	G	G	A	rs16851970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16044401G>A	ENST00000375799.3	+	4	518	c.291G>A	c.(289-291)ctG>ctA	p.L97L	PLEKHM2_ENST00000375793.2_Silent_p.L97L	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	97	Interaction with KIF5B.|RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GTGCCTGGCTGTACCTGGCCC	0.547													G|||	932	0.186102	0.3676	0.1527	5008	,	,		21735	0.0337		0.1889	False		,,,				2504	0.1186				p.L97L		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.G291A						PASS	.	G		1185,2735		177,831,952	62.0	64.0	63.0		291	2.0	1.0	1	dbSNP_123	63	1573,6729		144,1285,2722	no	coding-synonymous	PLEKHM2	NM_015164.2		321,2116,3674	AA,AG,GG		18.9472,30.2296,22.5659		97/1020	16044401	2758,9464	1960	4151	6111	SO:0001819	synonymous_variant	23207	exon4			CTGGCTGTACCTG	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.291G>A	1.37:g.16044401G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	64	17	0.265625	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	37	CCDS44063.1																																																																																			G|0.797;A|0.203	0.203	strong		0.547	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164	
HEXB	3074	hgsc.bcm.edu	37	5	73985215	73985215	+	Missense_Mutation	SNP	A	A	G	rs11556045	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:73985215A>G	ENST00000261416.7	+	2	479	c.362A>G	c.(361-363)aAa>aGa	p.K121R	HEXB_ENST00000511181.1_5'UTR	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	121			K -> R (in dbSNP:rs11556045).		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)	p.K121R(1)		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)		TTCCAGGCTAAAACCCAGGTT	0.383													G|||	1115	0.222644	0.2693	0.2421	5008	,	,		20059	0.1667		0.1809	False		,,,				2504	0.2464				p.K121R	Melanoma(66;841 1270 13391 18706 27225)	Atlas-SNP	.											HEXB,NS,carcinoma,0,1	HEXB	34	1	1	Substitution - Missense(1)	stomach(1)	c.A362G						PASS	.	G	ARG/LYS	1141,3265	716.3+/-408.6	153,835,1215	175.0	174.0	174.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	362	-7.6	0.0	5	dbSNP_120	174	1452,7148	751.3+/-407.4	142,1168,2990	yes	missense	HEXB	NM_000521.3	26	295,2003,4205	GG,GA,AA		16.8837,25.8965,19.937	benign	121/557	73985215	2593,10413	2203	4300	6503	SO:0001583	missense	3074	exon2			AGGCTAAAACCCA	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.362A>G	5.37:g.73985215A>G	ENSP00000261416:p.Lys121Arg	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	210	95	0.452381	NM_000521		Missense_Mutation	SNP	ENST00000261416.7	37	CCDS4022.1	453	0.20741758241758243	136	0.2764227642276423	83	0.2292817679558011	96	0.16783216783216784	138	0.1820580474934037	G	3.616	-0.078595	0.07141	0.258965	0.168837	ENSG00000049860	ENST00000261416	D	0.88664	-2.41	5.83	-7.58	0.01313	Acetylhexosaminidase, subunit a/b (1);	1.785790	0.02227	N	0.064526	T	0.00012	0.0000	N	0.16708	0.43	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48525	-0.9028	9	0.12103	T	0.63	2.2681	11.1512	0.48460	0.4827:0.2908:0.2265:0.0	rs11556045;rs56932933;rs11556045	121	P07686	HEXB_HUMAN	R	121	ENSP00000261416:K121R	ENSP00000261416:K121R	K	+	2	0	HEXB	74020971	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.913000	0.04042	-3.763000	0.00110	-3.424000	0.00037	AAA	A|0.792;G|0.208	0.208	strong		0.383	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521	
TICRR	90381	hgsc.bcm.edu	37	15	90168693	90168693	+	Missense_Mutation	SNP	T	T	A	rs1866928	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:90168693T>A	ENST00000268138.7	+	20	5257	c.5152T>A	c.(5152-5154)Tca>Aca	p.S1718T	TICRR_ENST00000560985.1_Missense_Mutation_p.S1717T|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1718			S -> T (in dbSNP:rs1866928). {ECO:0000269|PubMed:14702039}.		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)										ACTGCTTGAGTCAGAGGGCAA	0.652													T|||	1933	0.385982	0.466	0.3285	5008	,	,		16768	0.3968		0.335	False		,,,				2504	0.3599				p.S1718T		Atlas-SNP	.											.	.	.	.	0			c.T5152A						PASS	.	T	THR/SER	1793,2607	515.5+/-368.9	343,1107,750	47.0	51.0	49.0		5152	0.7	0.0	15	dbSNP_92	49	2896,5702	442.5+/-360.1	484,1928,1887	yes	missense	C15orf42	NM_152259.3	58	827,3035,2637	AA,AT,TT		33.6823,40.75,36.0748	benign	1718/1911	90168693	4689,8309	2200	4299	6499	SO:0001583	missense	90381	exon20			CTTGAGTCAGAGG	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.5152T>A	15.37:g.90168693T>A	ENSP00000268138:p.Ser1718Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	69	52	0.753623	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	781	0.3576007326007326	214	0.4349593495934959	111	0.30662983425414364	200	0.34965034965034963	256	0.33773087071240104	T	9.772	1.173020	0.21704	0.4075	0.336823	ENSG00000140534	ENST00000268138	T	0.08102	3.13	5.51	0.722	0.18225	.	1.173460	0.06260	N	0.693698	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.18013	0.025	B	0.06405	0.002	T	0.46512	-0.9186	9	0.44086	T	0.13	-0.2223	5.1564	0.15036	0.0:0.3823:0.3545:0.2632	rs1866928;rs3825997;rs1866928	1718	Q7Z2Z1	TICRR_HUMAN	T	1718	ENSP00000268138:S1718T	ENSP00000268138:S1718T	S	+	1	0	C15orf42	87969697	0.007000	0.16637	0.002000	0.10522	0.028000	0.11728	0.220000	0.17660	0.356000	0.24157	-1.055000	0.02315	TCA	T|0.635;A|0.365	0.365	strong		0.652	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
PHLDB3	653583	hgsc.bcm.edu	37	19	44001345	44001345	+	Silent	SNP	C	C	T	rs7257767	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44001345C>T	ENST00000292140.5	-	6	1110	c.750G>A	c.(748-750)gaG>gaA	p.E250E	PHLDB3_ENST00000599242.1_Silent_p.E250E	NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	250							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				TGTCCCGATCCTCCTCCTCCT	0.632													C|||	892	0.178115	0.3321	0.1066	5008	,	,		16847	0.1131		0.1113	False		,,,				2504	0.1564				p.E250E		Atlas-SNP	.											.	PHLDB3	30	.	0			c.G750A						PASS	.	C		1146,3260	401.5+/-332.0	143,860,1200	59.0	58.0	58.0		750	1.0	1.0	19	dbSNP_116	58	891,7709	197.9+/-242.4	48,795,3457	no	coding-synonymous	PHLDB3	NM_198850.3		191,1655,4657	TT,TC,CC		10.3605,26.01,15.662		250/641	44001345	2037,10969	2203	4300	6503	SO:0001819	synonymous_variant	653583	exon6			CCGATCCTCCTCC		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.750G>A	19.37:g.44001345C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_198850	Q8N7Z4	Silent	SNP	ENST00000292140.5	37	CCDS12621.2																																																																																			C|0.843;T|0.157	0.157	strong		0.632	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
ANO7	50636	hgsc.bcm.edu	37	2	242157228	242157228	+	Silent	SNP	G	G	T	rs78605785	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242157228G>T	ENST00000274979.8	+	20	2365	c.2262G>T	c.(2260-2262)ccG>ccT	p.P754P	ANO7_ENST00000402430.3_Silent_p.P753P	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	754					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						ACCGGCGCCCGGTGGCCGAGC	0.706													g|||	615	0.122804	0.1573	0.183	5008	,	,		8027	0.0		0.2356	False		,,,				2504	0.044				p.P754P		Atlas-SNP	.											.	ANO7	136	.	0			c.G2262T						PASS	.			646,3732		49,548,1592	16.0	18.0	18.0		2262	-5.3	1.0	2	dbSNP_131	18	1869,6707		204,1461,2623	no	coding-synonymous	ANO7	NM_001001891.3		253,2009,4215	TT,TG,GG		21.7934,14.7556,19.4149		754/934	242157228	2515,10439	2189	4288	6477	SO:0001819	synonymous_variant	50636	exon20			GCGCCCGGTGGCC	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.2262G>T	2.37:g.242157228G>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	g	12.25	1.883025	0.33255	0.147556	0.217934	ENSG00000146205	ENST00000451047	.	.	.	2.69	-5.26	0.02772	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31024	-0.9958	4	.	.	.	.	5.1019	0.14764	0.1079:0.4916:0.289:0.1115	.	.	.	.	C	67	.	.	G	+	1	0	ANO7	241805901	0.000000	0.05858	0.983000	0.44433	0.985000	0.73830	-4.591000	0.00211	-0.621000	0.05633	0.298000	0.19748	GGT	C|0.028;G|0.842;T|0.131	0.131	strong		0.706	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
SKAP1	8631	hgsc.bcm.edu	37	17	46266849	46266849	+	Silent	SNP	G	G	A	rs66753385	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	105	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	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	
BRD1	23774	hgsc.bcm.edu	37	22	50187853	50187853	+	Missense_Mutation	SNP	C	C	T	rs35331092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50187853C>T	ENST00000216267.8	-	6	2674	c.2188G>A	c.(2188-2190)Gct>Act	p.A730T	BRD1_ENST00000542442.1_Missense_Mutation_p.A418T|BRD1_ENST00000404034.1_Missense_Mutation_p.A730T|BRD1_ENST00000457780.2_Missense_Mutation_p.A730T|BRD1_ENST00000404760.1_Missense_Mutation_p.A730T|BRD1_ENST00000342989.5_Missense_Mutation_p.A325T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	730			A -> T (in dbSNP:rs35331092).		histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GACTTCATAGCGCAGGTGAGG	0.607													C|||	342	0.0682907	0.0825	0.0317	5008	,	,		18559	0.003		0.0596	False		,,,				2504	0.1513				p.A730T		Atlas-SNP	.											.	BRD1	144	.	0			c.G2188A						PASS	.	C	THR/ALA	422,3984	206.5+/-228.1	21,380,1802	59.0	63.0	62.0		2188	-0.9	0.4	22	dbSNP_126	62	590,8010	156.4+/-210.3	24,542,3734	yes	missense	BRD1	NM_014577.1	58	45,922,5536	TT,TC,CC		6.8605,9.5778,7.781	benign	730/1059	50187853	1012,11994	2203	4300	6503	SO:0001583	missense	23774	exon6			TCATAGCGCAGGT	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2188G>A	22.37:g.50187853C>T	ENSP00000216267:p.Ala730Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	59	0.59	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	96	0.04395604395604396	41	0.08333333333333333	12	0.03314917127071823	0	0.0	43	0.05672823218997362	C	14.17	2.456934	0.43634	0.095778	0.068605	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T;T	0.28255	2.57;2.57;2.58;2.44;1.62;2.01	5.4	-0.94	0.10405	.	0.418477	0.26248	N	0.025479	T	0.00754	0.0025	L	0.39898	1.24	0.28355	P	0.9207138	P;P;P;D	0.54964	0.948;0.63;0.788;0.969	B;B;B;B	0.43728	0.247;0.12;0.169;0.429	T	0.07654	-1.0761	9	0.31617	T	0.26	.	21.7236	0.99959	0.1644:0.8356:0.0:0.0	rs35331092	730;325;730;730	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	T	730;730;730;730;418;325;190	ENSP00000216267:A730T;ENSP00000384076:A730T;ENSP00000385858:A730T;ENSP00000410042:A730T;ENSP00000437514:A418T;ENSP00000345886:A325T	ENSP00000216267:A730T	A	-	1	0	BRD1	48573857	0.065000	0.20965	0.369000	0.25952	0.980000	0.70556	0.428000	0.21395	-0.460000	0.07003	0.655000	0.94253	GCT	C|0.936;T|0.064	0.064	strong		0.607	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
SLC4A11	83959	hgsc.bcm.edu	37	20	3214895	3214895	+	Silent	SNP	C	C	T	rs34460295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:3214895C>T	ENST00000380056.3	-	4	452	c.405G>A	c.(403-405)gcG>gcA	p.A135A	SLC4A11_ENST00000380059.3_Silent_p.A162A|SLC4A11_ENST00000539553.2_Silent_p.A119A	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	135					bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TGCTGGCCTGCGCCAGGAAGC	0.612													C|||	117	0.0233626	0.0333	0.0086	5008	,	,		16337	0.0198		0.0249	False		,,,				2504	0.0225				p.A162A	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G486A						PASS	.	C	,,	181,4225	117.1+/-155.0	4,173,2026	118.0	107.0	111.0		357,486,405	-10.4	0.5	20	dbSNP_126	111	174,8426	79.8+/-142.4	2,170,4128	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	6,343,6154	TT,TC,CC		2.0233,4.108,2.7295	,,	119/876,162/919,135/892	3214895	355,12651	2203	4300	6503	SO:0001819	synonymous_variant	83959	exon5			GGCCTGCGCCAGG	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.405G>A	20.37:g.3214895C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																			C|0.974;T|0.026	0.026	strong		0.612	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
MYLK	4638	hgsc.bcm.edu	37	3	123512627	123512627	+	Missense_Mutation	SNP	G	G	T	rs28497577	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:123512627G>T	ENST00000475616.1	-	1	61	c.62C>A	c.(61-63)cCc>cAc	p.P21H	MYLK_ENST00000360772.3_Missense_Mutation_p.P21H|MYLK_ENST00000360304.3_Missense_Mutation_p.P21H|MYLK_ENST00000346322.5_Missense_Mutation_p.P21H|MYLK_ENST00000359169.1_Missense_Mutation_p.P21H			Q15746	MYLK_HUMAN	myosin light chain kinase	21			P -> H (in dbSNP:rs28497577).		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)		AACTCTTGAGGGATCCACACT	0.542													G|||	988	0.197284	0.4183	0.1052	5008	,	,		19509	0.0556		0.0855	False		,,,				2504	0.2249				p.P21H		Atlas-SNP	.											.	MYLK	224	.	0			c.C62A						PASS	.	G	HIS/PRO,HIS/PRO,HIS/PRO,HIS/PRO	1598,2808	496.2+/-363.5	283,1032,888	67.0	69.0	68.0		62,62,62,62	0.2	0.5	3	dbSNP_125	68	807,7793	188.3+/-235.3	32,743,3525	yes	missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	77,77,77,77	315,1775,4413	TT,TG,GG		9.3837,36.2687,18.4915	benign,benign,benign,benign	21/1915,21/1846,21/1864,21/1795	123512627	2405,10601	2203	4300	6503	SO:0001583	missense	4638	exon4			CTTGAGGGATCCA	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.62C>A	3.37:g.123512627G>T	ENSP00000418335:p.Pro21His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	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	341	0.15613553113553114	207	0.42073170731707316	44	0.12154696132596685	26	0.045454545454545456	64	0.08443271767810026	G	4.655	0.121816	0.08931	0.362687	0.093837	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616;ENST00000360367	T;T;T;T;T	0.68331	-0.32;-0.27;-0.32;-0.3;-0.27	5.91	0.146	0.14833	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B;B;B	0.12630	0.006;0.006;0.001;0.0;0.002;0.0;0.003	B;B;B;B;B;B;B	0.15870	0.014;0.014;0.003;0.002;0.007;0.002;0.006	T	0.39121	-0.9629	8	0.26408	T	0.33	.	20.3305	0.98715	0.0:0.0:0.8627:0.1373	rs28497577;rs59516889;rs28497577	21;21;21;21;21;21;21	Q15746-6;Q15746-5;D3DN97;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;.;MYLK_HUMAN	H	21	ENSP00000354004:P21H;ENSP00000353452:P21H;ENSP00000352088:P21H;ENSP00000320622:P21H;ENSP00000418335:P21H	ENSP00000320622:P21H	P	-	2	0	MYLK	124995317	0.886000	0.30341	0.528000	0.27938	0.337000	0.28794	-0.203000	0.09438	0.013000	0.14918	0.655000	0.94253	CCC	G|0.819;T|0.181	0.181	strong		0.542	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
MTTP	4547	hgsc.bcm.edu	37	4	100504575	100504575	+	Missense_Mutation	SNP	G	G	C	rs2306986	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:100504575G>C	ENST00000265517.5	+	3	497	c.294G>C	c.(292-294)gaG>gaC	p.E98D	MTTP_ENST00000422897.2_Missense_Mutation_p.E98D|MTTP_ENST00000457717.1_Missense_Mutation_p.E98D|MTTP_ENST00000511045.1_Missense_Mutation_p.E125D			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	98	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		E -> D (in dbSNP:rs2306986).		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)	AGAGAGGAGAGAAGAGCATCT	0.383													G|||	592	0.118211	0.205	0.072	5008	,	,		16968	0.2143		0.0159	False		,,,				2504	0.0399				p.E98D		Atlas-SNP	.											.	MTTP	127	.	0			c.G294C						PASS	.	G	ASP/GLU	818,3586	319.3+/-296.1	78,662,1462	112.0	121.0	118.0		294	2.7	1.0	4	dbSNP_100	118	351,8249	117.6+/-177.1	5,341,3954	yes	missense	MTTP	NM_000253.2	45	83,1003,5416	CC,CG,GG		4.0814,18.574,8.9895	benign	98/895	100504575	1169,11835	2202	4300	6502	SO:0001583	missense	4547	exon4			AGGAGAGAAGAGC		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.294G>C	4.37:g.100504575G>C	ENSP00000265517:p.Glu98Asp	Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	283	136	0.480565	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	276	0.12637362637362637	98	0.1991869918699187	21	0.058011049723756904	142	0.24825174825174826	15	0.01978891820580475	G	11.36	1.614497	0.28712	0.18574	0.040814	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000422897;ENST00000538053	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	5.71	2.66	0.31614	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.311546	0.39687	N	0.001285	T	0.00012	0.0000	N	0.08118	0	0.46167	P	0.0010970000000000146	B;P;P	0.40302	0.202;0.712;0.712	B;B;B	0.39617	0.183;0.159;0.305	T	0.24764	-1.0151	8	.	.	.	-2.4524	4.55	0.12107	0.303:0.0:0.5391:0.1579	rs2306986;rs52838208;rs2306986	125;98;98	E9PBP6;P55157;Q6P5T3	.;MTP_HUMAN;.	D	108;125;98;98;98;98	ENSP00000426755:E108D;ENSP00000427679:E125D;ENSP00000400821:E98D;ENSP00000265517:E98D;ENSP00000407350:E98D	.	E	+	3	2	MTTP	100723598	0.683000	0.27633	1.000000	0.80357	0.921000	0.55340	0.170000	0.16663	0.771000	0.33359	-0.140000	0.14226	GAG	G|0.897;C|0.103	0.103	strong		0.383	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
MDGA1	266727	hgsc.bcm.edu	37	6	37626142	37626142	+	Silent	SNP	C	C	T	rs2273110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:37626142C>T	ENST00000434837.3	-	3	1439	c.261G>A	c.(259-261)tcG>tcA	p.S87S	MDGA1_ENST00000297153.7_Silent_p.S87S|MDGA1_ENST00000505425.1_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	83	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	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		
MATN2	4147	hgsc.bcm.edu	37	8	98943545	98943545	+	Silent	SNP	A	A	G	rs2290471	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:98943545A>G	ENST00000520016.1	+	2	631	c.507A>G	c.(505-507)acA>acG	p.T169T	MATN2_ENST00000524308.1_Silent_p.T169T|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000254898.5_Silent_p.T169T|MATN2_ENST00000521689.1_Silent_p.T169T			O00339	MATN2_HUMAN	matrilin 2	169	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)			TGATCGTGACAGATGGGAGAC	0.592													G|||	1390	0.277556	0.5023	0.2565	5008	,	,		21133	0.0804		0.2883	False		,,,				2504	0.181				p.T169T		Atlas-SNP	.											MATN2_ENST00000520016,NS,carcinoma,+1,2	MATN2	165	2	0			c.A507G						PASS	.	G	,	1825,2387		422,981,703	38.0	44.0	42.0		507,507	-11.6	0.0	8	dbSNP_100	42	2405,6067		366,1673,2197	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	788,2654,2900	GG,GA,AA		28.3876,43.3286,33.3491	,	169/957,169/938	98943545	4230,8454	2106	4236	6342	SO:0001819	synonymous_variant	4147	exon3			CGTGACAGATGGG	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.507A>G	8.37:g.98943545A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1																																																																																			A|0.787;G|0.213	0.213	strong		0.592	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
DFNA5	1687	hgsc.bcm.edu	37	7	24742436	24742436	+	Silent	SNP	T	T	C	rs17149912	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:24742436T>C	ENST00000342947.3	-	9	1625	c.1200A>G	c.(1198-1200)gcA>gcG	p.A400A	DFNA5_ENST00000409775.3_Silent_p.A400A|DFNA5_ENST00000419307.1_Silent_p.A236A|DFNA5_ENST00000409970.1_Silent_p.A236A|DFNA5_ENST00000545231.1_Silent_p.A236A	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	400					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)		p.A400A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						GCAGAGCTGCTGCGCTATCTG	0.507													T|||	1011	0.201877	0.1384	0.2637	5008	,	,		20265	0.2798		0.1501	False		,,,				2504	0.2168				p.A400A	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											DFNA5,NS,carcinoma,-2,2	DFNA5	51	2	1	Substitution - coding silent(1)	stomach(1)	c.A1200G						PASS	.	T	,,	584,3822	255.8+/-260.9	44,496,1663	95.0	90.0	91.0		1200,708,1200	-5.8	0.0	7	dbSNP_123	91	1341,7259	255.7+/-280.4	107,1127,3066	no	coding-synonymous,coding-synonymous,coding-synonymous	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	,,	151,1623,4729	CC,CT,TT		15.593,13.2547,14.8009	,,	400/497,236/333,400/497	24742436	1925,11081	2203	4300	6503	SO:0001819	synonymous_variant	1687	exon9			AGCTGCTGCGCTA	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.1200A>G	7.37:g.24742436T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	98	72	0.734694	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	37	CCDS5389.1																																																																																			T|0.828;C|0.172	0.172	strong		0.507	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
PRB3	5544	hgsc.bcm.edu	37	12	11420773	11420773	+	Missense_Mutation	SNP	C	C	T	rs200940772		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:11420773C>T	ENST00000279573.7	-	3	545	c.410G>A	c.(409-411)cGt>cAt	p.R137H	PRB3_ENST00000381842.3_Missense_Mutation_p.R137H|PRB3_ENST00000538488.1_Intron|PRB3_ENST00000440870.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	137	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.			R -> H (in Ref. 1; CAA30728). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			CTTTCCCGGACGAGGCGGGGG	0.642																																					p.R137H		Atlas-SNP	.											PRB3,NS,carcinoma,0,2	PRB3	84	2	0			c.G410A						scavenged	.						26.0	28.0	27.0					12																	11420773		1477	3379	4856	SO:0001583	missense	5544	exon3			CCCGGACGAGGCG			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.410G>A	12.37:g.11420773C>T	ENSP00000279573:p.Arg137His	Somatic	116	6	0.0517241		WXS	Illumina HiSeq	Phase_I	108	7	0.0648148	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		.	.	.	.	.	.	.	.	.	.	.	0.011	-1.697568	0.00725	.	.	ENSG00000197870	ENST00000381842	T	0.04917	3.53	0.707	-1.41	0.08941	.	21.670500	0.01603	N	0.022149	T	0.05547	0.0146	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38650	-0.9651	9	0.41790	T	0.15	.	4.061	0.09839	0.0:0.1851:0.2048:0.6101	.	137	Q04118	PRB3_HUMAN	H	137	ENSP00000371264:R137H	ENSP00000279573:R137H	R	-	2	0	PRB3	11312040	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.782000	0.04643	-2.300000	0.00658	-1.404000	0.01136	CGT	C|0.998;T|0.002	0.002	weak		0.642	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626529	140626529	+	Silent	SNP	C	C	T	rs17844564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140626529C>T	ENST00000231173.3	+	1	1383	c.1383C>T	c.(1381-1383)cgC>cgT	p.R461R		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	461	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)			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)			TGTTCGTCCGCGAGAACAACA	0.637													C|||	584	0.116613	0.1263	0.1787	5008	,	,		16065	0.0397		0.1551	False		,,,				2504	0.0992				p.R461R		Atlas-SNP	.											.	PCDHB15	138	.	0			c.C1383T						PASS	.	C		557,3849		70,417,1716	78.0	83.0	82.0		1383	-1.1	0.7	5	dbSNP_123	82	1414,7174		126,1162,3006	no	coding-synonymous	PCDHB15	NM_018935.2		196,1579,4722	TT,TC,CC		16.4648,12.6419,15.1685		461/788	140626529	1971,11023	2203	4294	6497	SO:0001819	synonymous_variant	56121	exon1			CGTCCGCGAGAAC	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.1383C>T	5.37:g.140626529C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	110	43	0.390909	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			C|0.029;G|0.971	.	alt		0.637	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
APOB	338	hgsc.bcm.edu	37	2	21225753	21225753	+	Missense_Mutation	SNP	C	C	T	rs1042031	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:21225753C>T	ENST00000233242.1	-	29	12668	c.12541G>A	c.(12541-12543)Gaa>Aaa	p.E4181K	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4181			E -> K (in dbSNP:rs1042031). {ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:2994225, ECO:0000269|PubMed:3030729, ECO:0000269|PubMed:3464946, ECO:0000269|PubMed:3763409, ECO:0000269|PubMed:3841481}.		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)					ATATGGAATTCTTGAGTAACT	0.463													C|||	640	0.127796	0.1611	0.1196	5008	,	,		19930	0.0446		0.2127	False		,,,				2504	0.0869				p.E4181K		Atlas-SNP	.											.	APOB	761	.	0			c.G12541A						PASS	.	C	LYS/GLU	652,3754	277.5+/-273.7	34,584,1585	66.0	64.0	64.0		12541	0.2	0.0	2	dbSNP_86	64	1508,7092	283.9+/-296.4	137,1234,2929	yes	missense	APOB	NM_000384.2	56	171,1818,4514	TT,TC,CC		17.5349,14.798,16.6077	benign	4181/4564	21225753	2160,10846	2203	4300	6503	SO:0001583	missense	338	exon29			GGAATTCTTGAGT	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.12541G>A	2.37:g.21225753C>T	ENSP00000233242:p.Glu4181Lys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	333	0.15247252747252749	97	0.19715447154471544	58	0.16022099447513813	21	0.03671328671328671	157	0.20712401055408972	C	13.89	2.373145	0.42105	0.14798	0.175349	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00737	5.76	5.99	0.147	0.14838	.	0.748815	0.12158	N	0.494257	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	8.000000000008E-6	B	0.15141	0.012	B	0.13407	0.009	T	0.33085	-0.9882	9	0.27082	T	0.32	.	5.4344	0.16472	0.0:0.5218:0.1308:0.3473	rs1042031;rs3181511;rs17247312;rs17398356;rs52807383;rs60017641;rs1042031	4181	P04114	APOB_HUMAN	K	4181	ENSP00000233242:E4181K	ENSP00000233242:E4181K	E	-	1	0	APOB	21079258	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.080000	0.11339	-0.260000	0.09418	-0.140000	0.14226	GAA	C|0.848;T|0.152	0.152	strong		0.463	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
CTRC	11330	hgsc.bcm.edu	37	1	15772212	15772212	+	Missense_Mutation	SNP	C	C	T	rs121909293	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15772212C>T	ENST00000375949.4	+	7	786	c.760C>T	c.(760-762)Cgg>Tgg	p.R254W	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_3'UTR	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	254	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		Missing (in PCTT; associated with disease susceptibility; results in reduced protein secretion and loss of activity). {ECO:0000269|PubMed:18172691}.|R -> Q (found in a patient with chronic pancreatitis; unknown pathological significance; mutant protein secretion, activity and trypsin-mediated degradation are comparable to those of wild-type). {ECO:0000269|PubMed:19407484}.|R -> W (in PCTT; associated with susceptibility to disease; results in reduced secretion; normal activity; the mutant undergoes proteolytic degradation during trypsin-mediated activation; dbSNP:rs121909293). {ECO:0000269|PubMed:18059268, ECO:0000269|PubMed:18172691, ECO:0000269|PubMed:22580415, ECO:0000269|PubMed:23135764}.		proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGTCTACACCCGGGTGTCCGC	0.632													C|||	8	0.00159744	0.0	0.0	5008	,	,		15935	0.0		0.008	False		,,,				2504	0.0				p.R254W		Atlas-SNP	.											.	CTRC	28	.	0			c.C760T	GRCh37	CM080169	CTRC	M	rs121909293	PASS	.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	81.0	82.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	760	4.7	1.0	1	dbSNP_133	82	33,8567	22.8+/-68.1	0,33,4267	yes	missense	CTRC	NM_007272.2	101	0,34,6469	TT,TC,CC		0.3837,0.0227,0.2614	probably-damaging	254/269	15772212	34,12972	2203	4300	6503	SO:0001583	missense	11330	exon7			TACACCCGGGTGT	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"""elastase 4"""	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.760C>T	1.37:g.15772212C>T	ENSP00000365116:p.Arg254Trp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	37	10	0.27027	NM_007272	A8K082|O00765|Q9NUH5	Missense_Mutation	SNP	ENST00000375949.4	37	CCDS156.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	C	19.97	3.925157	0.73213	2.27E-4	0.003837	ENSG00000162438	ENST00000375949	D	0.94793	-3.52	4.68	4.68	0.58851	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.053971	0.85682	D	0.000000	D	0.97244	0.9099	H	0.94808	3.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96153	0.9109	10	0.87932	D	0	-43.8301	16.7021	0.85357	0.0:1.0:0.0:0.0	.	254	Q99895	CTRC_HUMAN	W	254	ENSP00000365116:R254W	ENSP00000365116:R254W	R	+	1	2	CTRC	15644799	0.930000	0.31532	1.000000	0.80357	0.586000	0.36452	1.189000	0.32114	2.606000	0.88127	0.650000	0.86243	CGG	C|0.997;T|0.003	0.003	strong		0.632	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272	
ITIH2	3698	hgsc.bcm.edu	37	10	7774358	7774358	+	Missense_Mutation	SNP	C	C	G	rs7084817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:7774358C>G	ENST00000358415.4	+	14	1871	c.1705C>G	c.(1705-1707)Cta>Gta	p.L569V	ITIH2_ENST00000379587.4_Missense_Mutation_p.L558V	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	569			L -> V (in dbSNP:rs7084817).		hyaluronan metabolic process (GO:0030212)|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)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						GCAGGATTTTCTATCGAAAGA	0.478													C|||	100	0.0199681	0.0045	0.0144	5008	,	,		17716	0.003		0.0497	False		,,,				2504	0.0317				p.L569V		Atlas-SNP	.											.	ITIH2	144	.	0			c.C1705G						PASS	.	C	VAL/LEU	56,4350	56.2+/-92.4	0,56,2147	98.0	87.0	91.0		1705	3.5	0.9	10	dbSNP_116	91	427,8173	131.7+/-189.4	13,401,3886	yes	missense	ITIH2	NM_002216.2	32	13,457,6033	GG,GC,CC		4.9651,1.271,3.7137	probably-damaging	569/947	7774358	483,12523	2203	4300	6503	SO:0001583	missense	3698	exon14			GATTTTCTATCGA	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1705C>G	10.37:g.7774358C>G	ENSP00000351190:p.Leu569Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	78	26	0.333333	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	51	0.023351648351648352	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	42	0.055408970976253295	C	16.74	3.206606	0.58343	0.01271	0.049651	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.13778	2.56;2.56	5.32	3.45	0.39498	.	0.079977	0.52532	D	0.000069	T	0.01765	0.0056	M	0.67953	2.075	0.37530	D	0.917889	D	0.56968	0.978	P	0.47744	0.556	T	0.03231	-1.1058	10	0.42905	T	0.14	-13.7079	5.7545	0.18164	0.1441:0.633:0.0:0.2229	rs7084817	569	P19823	ITIH2_HUMAN	V	569;558	ENSP00000351190:L569V;ENSP00000368906:L558V	ENSP00000351190:L569V	L	+	1	2	ITIH2	7814364	0.794000	0.28838	0.903000	0.35520	0.956000	0.61745	1.323000	0.33701	1.252000	0.44001	0.643000	0.83706	CTA	C|0.965;G|0.035	0.035	strong		0.478	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
LGALS14	56891	hgsc.bcm.edu	37	19	40196611	40196611	+	Intron	SNP	C	C	T	rs35541195	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40196611C>T	ENST00000392052.3	+	2	238				LGALS14_ENST00000360675.3_Missense_Mutation_p.R22C	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14						apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			TAATGTGTGCCGCTTCTGGGA	0.493													C|||	252	0.0503195	0.0356	0.0648	5008	,	,		19968	0.0		0.1451	False		,,,				2504	0.0143				p.R22C		Atlas-SNP	.											.	LGALS14	38	.	0			c.C64T						PASS	.	C	,CYS/ARG	239,4167		9,221,1973	202.0	150.0	168.0		,64	-0.5	0.0	19	dbSNP_126	168	1098,7502		66,966,3268	yes	intron,missense	LGALS14	NM_020129.2,NM_203471.1	,180	75,1187,5241	TT,TC,CC		12.7674,5.4244,10.2799	,	,22/169	40196611	1337,11669	2203	4300	6503	SO:0001627	intron_variant	56891	exon2			GTGTGCCGCTTCT	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.16-626C>T	19.37:g.40196611C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	232	124	0.534483	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	159	0.07280219780219781	26	0.052845528455284556	31	0.0856353591160221	0	0.0	102	0.1345646437994723	.	5.101	0.204247	0.09704	0.054244	0.127674	ENSG00000006659	ENST00000360675	T	0.09163	3.01	0.906	-0.462	0.12168	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.30937	0.301	B	0.04013	0.001	T	0.41910	-0.9482	8	0.56958	D	0.05	.	3.7318	0.08496	0.5522:0.4478:0.0:0.0	rs35541195;rs60146906	22	A8MPV8	.	C	22	ENSP00000353893:R22C	ENSP00000353893:R22C	R	+	1	0	LGALS14	44888451	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.305000	0.08188	-0.197000	0.10350	0.313000	0.20887	CGC	C|0.907;T|0.093	0.093	strong		0.493	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	
SLC30A8	169026	hgsc.bcm.edu	37	8	118184783	118184783	+	Missense_Mutation	SNP	C	C	T	rs13266634	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:118184783C>T	ENST00000456015.2	+	8	973	c.973C>T	c.(973-975)Cgg>Tgg	p.R325W	SLC30A8_ENST00000521243.1_Missense_Mutation_p.R276W|SLC30A8_ENST00000519688.1_Missense_Mutation_p.R276W|SLC30A8_ENST00000427715.2_Missense_Mutation_p.R276W	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	325			R -> Q (in dbSNP:rs16889462).|R -> W (in dbSNP:rs13266634). {ECO:0000269|PubMed:17293876}.		cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			AGCAGCCAGCCGGGACAGCCA	0.488													C|||	1278	0.255192	0.0741	0.2666	5008	,	,		19655	0.4573		0.2833	False		,,,				2504	0.2546				p.R325W	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											.	SLC30A8	102	.	0			c.C973T	GRCh37	CM072050	SLC30A8	M	rs13266634	PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	426,3980	206.2+/-227.9	18,390,1795	85.0	83.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	826,826,826,826,973	-1.8	0.9	8	dbSNP_121	84	2564,6036	418.7+/-352.8	398,1768,2134	yes	missense,missense,missense,missense,missense	SLC30A8	NM_001172811.1,NM_001172813.1,NM_001172814.1,NM_001172815.1,NM_173851.2	101,101,101,101,101	416,2158,3929	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	29.814,9.6686,22.9894	benign,benign,benign,benign,benign	276/321,276/321,276/321,276/321,325/370	118184783	2990,10016	2203	4300	6503	SO:0001583	missense	169026	exon8			GCCAGCCGGGACA		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"""Solute carriers"""	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.973C>T	8.37:g.118184783C>T	ENSP00000415011:p.Arg325Trp	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	159	62	0.389937	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	37	CCDS6322.1	616	0.28205128205128205	41	0.08333333333333333	95	0.26243093922651933	263	0.4597902097902098	217	0.2862796833773087	C	11.92	1.783088	0.31593	0.096686	0.29814	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.15	-1.75	0.08031	.	1.130630	0.06487	N	0.733902	T	0.00012	0.0000	L	0.49778	1.585	0.54753	P	1.2000000000012001E-5	B	0.09022	0.002	B	0.04013	0.001	T	0.42982	-0.9419	9	0.62326	D	0.03	0.3986	0.8731	0.01218	0.2334:0.3419:0.1149:0.3098	rs13266634;rs17813302;rs57876063;rs13266634	325	Q8IWU4	ZNT8_HUMAN	W	276;276;276;325	ENSP00000428545:R276W;ENSP00000407505:R276W;ENSP00000431069:R276W;ENSP00000415011:R325W	ENSP00000407505:R276W	R	+	1	2	SLC30A8	118253964	0.000000	0.05858	0.922000	0.36590	0.584000	0.36387	-0.403000	0.07214	-0.224000	0.09928	0.650000	0.86243	CGG	C|0.758;T|0.242	0.242	strong		0.488	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851	
TUBB1	81027	hgsc.bcm.edu	37	20	57599402	57599402	+	Missense_Mutation	SNP	G	G	A	rs6070697	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	48	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	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	
HRNR	388697	hgsc.bcm.edu	37	1	152191225	152191225	+	Silent	SNP	G	G	A	rs147277587	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152191225G>A	ENST00000368801.2	-	3	2955	c.2880C>T	c.(2878-2880)caC>caT	p.H960H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	960					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)			ACCTAGAGCCGTGTTGTTCGT	0.542													G|||	2	0.000399361	0.0	0.0	5008	,	,		24128	0.0		0.001	False		,,,				2504	0.001				p.H960H		Atlas-SNP	.											.	HRNR	403	.	0			c.C2880T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	285.0	276.0	279.0		2880	-7.5	0.0	1	dbSNP_134	279	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	HRNR	NM_001009931.1		0,8,6495	AA,AG,GG		0.0698,0.0454,0.0615		960/2851	152191225	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			AGAGCCGTGTTGT	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.2880C>T	1.37:g.152191225G>A		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	367	148	0.40327	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			G|0.999;A|0.001	0.001	strong		0.542	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
AKAP9	10142	hgsc.bcm.edu	37	7	91630620	91630620	+	Missense_Mutation	SNP	G	G	T	rs6964587	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91630620G>T	ENST00000359028.2	+	9	1650	c.1425G>T	c.(1423-1425)atG>atT	p.M475I	AKAP9_ENST00000356239.3_Missense_Mutation_p.M463I|AKAP9_ENST00000358100.2_Missense_Mutation_p.M475I			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	475	Glu-rich.		M -> I (in dbSNP:rs6964587). {ECO:0000269|PubMed:10358086}.		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)			TGGAGGAAATGAAAACACGGC	0.373			T	BRAF	papillary thyroid								T|||	1864	0.372204	0.5023	0.3573	5008	,	,		21441	0.1617		0.3867	False		,,,				2504	0.409				p.M463I		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.G1389T	GRCh37	CM064968	AKAP9	M	rs6964587	PASS	.	T	ILE/MET,ILE/MET	2261,2141	566.4+/-381.9	576,1109,516	93.0	100.0	98.0		1389,1389	-3.5	0.1	7	dbSNP_116	98	3466,5134	618.5+/-396.8	680,2106,1514	yes	missense,missense	AKAP9	NM_005751.4,NM_147185.2	10,10	1256,3215,2030	TT,TG,GG		40.3023,48.637,44.0471	benign,benign	463/3908,463/3900	91630620	5727,7275	2201	4300	6501	SO:0001583	missense	10142	exon8			GGAAATGAAAACA	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.1425G>T	7.37:g.91630620G>T	ENSP00000351922:p.Met475Ile	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		786	0.3598901098901099	255	0.5182926829268293	136	0.3756906077348066	100	0.17482517482517482	295	0.3891820580474934	T	0.019	-1.456513	0.01071	0.51363	0.403023	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.03441	3.93;3.93;3.93	5.61	-3.46	0.04767	.	0.420625	0.17659	N	0.166392	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.09022	0.002;0.002;0.002;0.0	B;B;B;B	0.08055	0.002;0.003;0.003;0.0	T	0.38757	-0.9646	9	0.36615	T	0.2	.	13.89	0.63733	0.0:0.0588:0.6372:0.304	rs6964587;rs59973703;rs6964587	475;463;463;475	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	I	463;475;475;475;475	ENSP00000348573:M463I;ENSP00000351922:M475I;ENSP00000350813:M475I	ENSP00000348573:M463I	M	+	3	0	AKAP9	91468556	0.310000	0.24527	0.116000	0.21606	0.002000	0.02628	0.234000	0.17930	-0.686000	0.05170	-1.050000	0.02344	ATG	G|0.608;T|0.392	0.392	strong		0.373	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
OR6Q1	219952	hgsc.bcm.edu	37	11	57798723	57798723	+	Missense_Mutation	SNP	A	A	G	rs921135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:57798723A>G	ENST00000302622.3	+	1	322	c.299A>G	c.(298-300)gAt>gGt	p.D100G	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	100				D -> G (in Ref. 1; BAC05958, 3; AAI51148 and 4; AAK95094). {ECO:0000305}.		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)				TCTTATGCTGATTGCCTATCC	0.478													G|||	2044	0.408147	0.3238	0.2651	5008	,	,		22105	0.6825		0.2913	False		,,,				2504	0.4611				p.D100G		Atlas-SNP	.											.	OR6Q1	58	.	0			c.A299G						PASS	.	G	GLY/ASP	1482,2920	677.5+/-403.4	247,988,966	173.0	163.0	166.0		299	3.8	1.0	11	dbSNP_86	166	2565,6027	690.1+/-404.4	395,1775,2126	yes	missense	OR6Q1	NM_001005186.2	94	642,2763,3092	GG,GA,AA		29.8534,33.6665,31.1451	benign	100/318	57798723	4047,8947	2201	4296	6497	SO:0001583	missense	219952	exon1			ATGCTGATTGCCT	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.299A>G	11.37:g.57798723A>G	ENSP00000307734:p.Asp100Gly	Somatic	441	2	0.00453515		WXS	Illumina HiSeq	Phase_I	390	197	0.505128	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Missense_Mutation	SNP	ENST00000302622.3	37	CCDS31541.1	840	0.38461538461538464	154	0.3130081300813008	96	0.26519337016574585	376	0.6573426573426573	214	0.28232189973614774	G	0.593	-0.832308	0.02713	0.336665	0.298534	ENSG00000172381	ENST00000302622	T	0.01172	5.23	4.76	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39210	N	0.001437	T	0.00012	0.0000	N	0.00080	-2.225	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16630	-1.0396	9	0.02654	T	1	.	7.9273	0.29883	0.0878:0.2843:0.6279:0.0	rs921135;rs52804731;rs57644368;rs921135	100	Q8NGQ2	OR6Q1_HUMAN	G	100	ENSP00000307734:D100G	ENSP00000307734:D100G	D	+	2	0	OR6Q1	57555299	0.027000	0.19231	0.992000	0.48379	0.888000	0.51559	0.808000	0.27154	1.036000	0.39998	-0.136000	0.14681	GAT	A|0.655;G|0.345	0.345	strong		0.478	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
DCST1	149095	hgsc.bcm.edu	37	1	155019710	155019710	+	Missense_Mutation	SNP	A	A	C	rs11264300	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:155019710A>C	ENST00000295542.1	+	14	1630	c.1534A>C	c.(1534-1536)Atg>Ctg	p.M512L	RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000392480.1_Missense_Mutation_p.M512L|DCST1_ENST00000368419.2_Missense_Mutation_p.M512L|DCST1_ENST00000423025.2_Missense_Mutation_p.M487L	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	512			M -> L (in dbSNP:rs11264300). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	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)			GGGAGACTCCATGCTAGCCCG	0.532													A|||	2777	0.554513	0.3858	0.5865	5008	,	,		18637	0.8849		0.3569	False		,,,				2504	0.6227				p.M512L		Atlas-SNP	.											DCST1,rectum,carcinoma,0,1	DCST1	69	1	0			c.A1534C						scavenged	.	A	LEU/MET,LEU/MET	1798,2608	527.6+/-372.2	350,1098,755	88.0	86.0	87.0		1459,1534	3.7	1.0	1	dbSNP_120	87	2984,5616	462.0+/-365.6	524,1936,1840	yes	missense,missense	DCST1	NM_001143687.2,NM_152494.3	15,15	874,3034,2595	CC,CA,AA		34.6977,40.808,36.7676	benign,benign	487/682,512/707	155019710	4782,8224	2203	4300	6503	SO:0001583	missense	149095	exon14			GACTCCATGCTAG	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1534A>C	1.37:g.155019710A>C	ENSP00000295542:p.Met512Leu	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	266	6	0.0225564	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	37	CCDS1083.1	1163	0.5325091575091575	179	0.3638211382113821	193	0.5331491712707183	517	0.9038461538461539	274	0.36147757255936674	A	11.83	1.756878	0.31137	0.40808	0.346977	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	4.88	3.73	0.42828	Dendritic cell-specific transmembrane protein-like (1);	0.190127	0.51477	N	0.000086	T	0.06416	0.0165	L	0.31420	0.93	0.36215	P	0.148416	B;B	0.16166	0.016;0.016	B;B	0.18561	0.022;0.022	T	0.24048	-1.0171	9	0.06494	T	0.89	-31.4022	8.753	0.34629	0.8085:0.1915:0.0:0.0	rs11264300;rs52800761;rs60521342;rs11264300	487;512	E9PHV3;Q5T197	.;DCST1_HUMAN	L	512;512;487;512	ENSP00000295542:M512L;ENSP00000376271:M512L;ENSP00000387369:M487L;ENSP00000357404:M512L	ENSP00000295542:M512L	M	+	1	0	DCST1	153286334	1.000000	0.71417	1.000000	0.80357	0.492000	0.33523	3.293000	0.51779	0.960000	0.38005	0.533000	0.62120	ATG	A|0.559;C|0.441	0.441	strong		0.532	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
MUC4	4585	hgsc.bcm.edu	37	3	195512742	195512742	+	Silent	SNP	G	G	A	rs113755990	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195512742G>A	ENST00000463781.3	-	2	6168	c.5709C>T	c.(5707-5709)acC>acT	p.T1903T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T1903T	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)	p.T1903T(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)		CATGAAGAGGGGTGGTGTCAC	0.572																																					p.T1903T		Atlas-SNP	.											MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,6	MUC4	1505	6	6	Substitution - coding silent(6)	haematopoietic_and_lymphoid_tissue(6)	c.C5709T						PASS	.						41.0	36.0	38.0					3																	195512742		689	1590	2279	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.5709C>T	3.37:g.195512742G>A		Somatic	390	0	0		WXS	Illumina HiSeq	Phase_I	615	80	0.130081	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|0.992;A|0.008	0.008	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF721	170960	hgsc.bcm.edu	37	4	437221	437221	+	Silent	SNP	G	G	A	rs114734668	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:437221G>A	ENST00000338977.5	-	2	1047	c.999C>T	c.(997-999)tcC>tcT	p.S333S	ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000511833.2_Silent_p.S345S|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	333					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(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						AAAGGTTTGCGGACTGTCTAA	0.438													g|||	96	0.0191693	0.0197	0.0317	5008	,	,		20834	0.0		0.0348	False		,,,				2504	0.0133				p.R345S		Atlas-SNP	.											.	ZNF721	205	.	0			c.A1035T						PASS	.	G		95,4205		4,87,2059	97.0	105.0	102.0		1035	-1.4	0.0	4	dbSNP_132	102	313,8221		2,309,3956	no	coding-synonymous	ZNF721	NM_133474.2		6,396,6015	AA,AG,GG		3.6677,2.2093,3.1791		345/924	437221	408,12426	2150	4267	6417	SO:0001819	synonymous_variant	170960	exon3			GTTTGCGGACTGT	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.999C>T	4.37:g.437221G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37																																																																																				G|0.977;A|0.023	0.023	strong		0.438	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
ZNF333	84449	hgsc.bcm.edu	37	19	14829749	14829749	+	Missense_Mutation	SNP	C	C	T	rs3764626	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14829749C>T	ENST00000292530.6	+	12	1701	c.1610C>T	c.(1609-1611)gCg>gTg	p.A537V	ZNF333_ENST00000536363.1_Missense_Mutation_p.A428V|ZNF333_ENST00000540689.2_Intron	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	537			A -> V (in dbSNP:rs3764626).		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						TATGAGTGCGCGACTTGCGGT	0.532													G|||	2410	0.48123	0.438	0.4914	5008	,	,		22164	0.619		0.3022	False		,,,				2504	0.5746				p.A537V	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.C1610T						PASS	.	G	VAL/ALA	1769,2637		362,1045,796	103.0	81.0	89.0		1610	0.3	0.0	19	dbSNP_107	89	2553,6047		394,1765,2141	yes	missense	ZNF333	NM_032433.2	64	756,2810,2937	TT,TC,CC		29.686,40.1498,33.2308	possibly-damaging	537/666	14829749	4322,8684	2203	4300	6503	SO:0001583	missense	84449	exon12			AGTGCGCGACTTG		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"""Zinc fingers, C2H2-type"", ""-"""	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.1610C>T	19.37:g.14829749C>T	ENSP00000292530:p.Ala537Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	129	55	0.426357	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Missense_Mutation	SNP	ENST00000292530.6	37	CCDS12316.1	944	0.43223443223443225	212	0.43089430894308944	149	0.4116022099447514	338	0.5909090909090909	245	0.3232189973614776	G	16.10	3.028610	0.54790	0.401498	0.29686	ENSG00000160961	ENST00000536363;ENST00000292530	T;T	0.07688	3.17;3.17	2.54	0.305	0.15801	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	B	0.32507	0.373	B	0.26094	0.066	T	0.16988	-1.0384	8	0.36615	T	0.2	.	12.1716	0.54161	0.0:0.5749:0.4251:0.0	rs3764626;rs59099264;rs3764626	537	Q96JL9	ZN333_HUMAN	V	428;537	ENSP00000439749:A428V;ENSP00000292530:A537V	ENSP00000292530:A537V	A	+	2	0	ZNF333	14690749	0.000000	0.05858	0.000000	0.03702	0.889000	0.51656	-0.446000	0.06837	-0.096000	0.12329	-0.120000	0.15030	GCG	C|0.613;T|0.387	0.387	strong		0.532	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433	
SGOL2	151246	hgsc.bcm.edu	37	2	201437328	201437328	+	Silent	SNP	C	C	A	rs35987478	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:201437328C>A	ENST00000357799.4	+	7	2357	c.2259C>A	c.(2257-2259)atC>atA	p.I753I		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)	753					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						ATAAGGAAATCATCCCTGGAA	0.338													C|||	1058	0.211262	0.1581	0.2017	5008	,	,		17672	0.2917		0.2535	False		,,,				2504	0.1636				p.I753I		Atlas-SNP	.											.	SGOL2	126	.	0			c.C2259A						PASS	.	C	,,	495,3137		25,445,1346	56.0	52.0	53.0		2259,2259,2259	0.8	0.0	2	dbSNP_126	53	2025,6103		238,1549,2277	no	coding-synonymous,coding-synonymous,coding-synonymous	SGOL2	NM_001160033.1,NM_001160046.1,NM_152524.5	,,	263,1994,3623	AA,AC,CC		24.9139,13.6289,21.4286	,,	753/1261,753/1262,753/1266	201437328	2520,9240	1816	4064	5880	SO:0001819	synonymous_variant	151246	exon7			GGAAATCATCCCT	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.2259C>A	2.37:g.201437328C>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	83	65	0.783133	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Silent	SNP	ENST00000357799.4	37	CCDS42796.1																																																																																			C|0.760;A|0.240	0.240	strong		0.338	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
LVRN	206338	hgsc.bcm.edu	37	5	115338958	115338958	+	Missense_Mutation	SNP	G	G	T	rs17138632	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:115338958G>T	ENST00000357872.4	+	12	2042	c.1918G>T	c.(1918-1920)Gtt>Ttt	p.V640F	AQPEP_ENST00000395528.2_Missense_Mutation_p.V157F	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		640			V -> F (in dbSNP:rs17138632).			integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AGAAATGCAAGTTTCAGATTC	0.289													G|||	130	0.0259585	0.0015	0.0836	5008	,	,		14198	0.001		0.0298	False		,,,				2504	0.0399				p.V640F		Atlas-SNP	.											FLJ90650,NS,carcinoma,0,1	.	.	1	0			c.G1918T						PASS	.	G	PHE/VAL	25,4377	31.7+/-61.6	0,25,2176	51.0	56.0	55.0		1918	-0.9	1.0	5	dbSNP_123	55	272,8304	100.1+/-161.6	4,264,4020	yes	missense	AQPEP	NM_173800.4	50	4,289,6196	TT,TG,GG		3.1716,0.5679,2.2885	benign	640/991	115338958	297,12681	2201	4288	6489	SO:0001583	missense	0	exon12			ATGCAAGTTTCAG																												ENST00000357872.4:c.1918G>T	5.37:g.115338958G>T	ENSP00000350541:p.Val640Phe	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	59	0.027014652014652016	3	0.006097560975609756	31	0.0856353591160221	1	0.0017482517482517483	24	0.0316622691292876	G	11.64	1.698549	0.30142	0.005679	0.031716	ENSG00000172901	ENST00000395528;ENST00000357872;ENST00000379578	T;T	0.23552	1.9;1.9	5.03	-0.942	0.10398	.	0.861260	0.10039	N	0.723709	T	0.00580	0.0019	L	0.57536	1.79	0.24475	N	0.994371	P	0.39282	0.666	B	0.33521	0.165	T	0.14144	-1.0483	10	0.09843	T	0.71	.	4.9292	0.13909	0.4644:0.3211:0.2146:0.0	rs17138632;rs52805082;rs17138632	640	Q6Q4G3	AMPQ_HUMAN	F	157;640;629	ENSP00000378899:V157F;ENSP00000350541:V640F	ENSP00000350541:V640F	V	+	1	0	AC010282.1	115366857	0.986000	0.35501	0.999000	0.59377	0.995000	0.86356	0.095000	0.15127	0.102000	0.17638	0.460000	0.39030	GTT	G|0.972;T|0.028	0.028	strong		0.289	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
LRP2	4036	hgsc.bcm.edu	37	2	170070172	170070172	+	Missense_Mutation	SNP	C	C	T	rs4667596	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:170070172C>T	ENST00000263816.3	-	36	6320	c.6035G>A	c.(6034-6036)aGa>aAa	p.R2012K		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2012			R -> K (in dbSNP:rs4667596).		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)"""	CTTACTGCGTCTGTGATAAAC	0.398													C|||	135	0.0269569	0.0	0.0793	5008	,	,		18951	0.0536		0.0189	False		,,,				2504	0.0072				p.R2012K		Atlas-SNP	.											.	LRP2	751	.	0			c.G6035A						PASS	.	C	LYS/ARG	16,4390	23.3+/-48.9	0,16,2187	134.0	132.0	132.0		6035	2.2	0.7	2	dbSNP_111	132	175,8425	80.4+/-143.0	1,173,4126	yes	missense	LRP2	NM_004525.2	26	1,189,6313	TT,TC,CC		2.0349,0.3631,1.4686	benign	2012/4656	170070172	191,12815	2203	4300	6503	SO:0001583	missense	4036	exon36			CTGCGTCTGTGAT		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.6035G>A	2.37:g.170070172C>T	ENSP00000263816:p.Arg2012Lys	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	186	81	0.435484	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	83	0.038003663003663	0	0.0	20	0.055248618784530384	47	0.08216783216783216	16	0.021108179419525065	C	11.76	1.735572	0.30774	0.003631	0.020349	ENSG00000081479	ENST00000263816	D	0.90788	-2.73	5.96	2.19	0.27852	Six-bladed beta-propeller, TolB-like (1);	0.205916	0.48767	N	0.000163	T	0.25005	0.0607	L	0.41906	1.305	0.80722	D	1	B	0.16166	0.016	B	0.10450	0.005	T	0.56896	-0.7903	10	0.05351	T	0.99	.	10.6121	0.45427	0.0:0.7417:0.0:0.2583	rs4667596;rs17848167;rs52819452;rs4667596	2012	P98164	LRP2_HUMAN	K	2012	ENSP00000263816:R2012K	ENSP00000263816:R2012K	R	-	2	0	LRP2	169778418	1.000000	0.71417	0.654000	0.29608	0.973000	0.67179	2.600000	0.46240	0.128000	0.18479	0.650000	0.86243	AGA	C|0.980;T|0.020	0.020	strong		0.398	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
ZAK	51776	hgsc.bcm.edu	37	2	174128513	174128513	+	Missense_Mutation	SNP	C	C	T	rs3769148	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:174128513C>T	ENST00000375213.3	+	19	1670	c.1592C>T	c.(1591-1593)tCg>tTg	p.S531L	MLK7-AS1_ENST00000423106.2_RNA|MLTK_ENST00000409176.2_Missense_Mutation_p.S531L|MLK7-AS1_ENST00000422703.1_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	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	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		
SMCHD1	23347	hgsc.bcm.edu	37	18	2750477	2750477	+	Silent	SNP	A	A	G	rs2304859	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:2750477A>G	ENST00000320876.6	+	32	4475	c.4137A>G	c.(4135-4137)gcA>gcG	p.A1379A	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.A1379A	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1379					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						ACAAAGATGCATCCTTCTTAG	0.313													G|||	1933	0.385982	0.2685	0.4467	5008	,	,		17899	0.5218		0.2634	False		,,,				2504	0.4877				p.A1379A		Atlas-SNP	.											SMCHD1,colon,carcinoma,+1,3	SMCHD1	88	3	0			c.A4137G						PASS	.	G		955,2687		126,703,992	45.0	42.0	43.0		4137	0.8	1.0	18	dbSNP_100	43	2297,5879		311,1675,2102	no	coding-synonymous	SMCHD1	NM_015295.2		437,2378,3094	GG,GA,AA		28.0944,26.2219,27.5173		1379/2006	2750477	3252,8566	1821	4088	5909	SO:0001819	synonymous_variant	23347	exon32			AGATGCATCCTTC	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.4137A>G	18.37:g.2750477A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	116	73	0.62931	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			G|0.336;N|0.000	0.336	strong		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
ZC3H11A	9877	hgsc.bcm.edu	37	1	203818973	203818973	+	Silent	SNP	C	C	A	rs41299639	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:203818973C>A	ENST00000545588.1	+	14	5585	c.1758C>A	c.(1756-1758)gcC>gcA	p.A586A	ZC3H11A_ENST00000332127.4_Silent_p.A586A|ZC3H11A_ENST00000367212.3_Silent_p.A586A|ZC3H11A_ENST00000367214.1_Silent_p.A586A|ZC3H11A_ENST00000367210.1_Silent_p.A586A	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	586					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GAGATGTAGCCTCTTGCAATA	0.507													C|||	877	0.17512	0.1112	0.183	5008	,	,		18937	0.1558		0.2197	False		,,,				2504	0.2301				p.A586A		Atlas-SNP	.											.	ZC3H11A	71	.	0			c.C1758A						PASS	.	C		569,3837	253.0+/-259.1	23,523,1657	94.0	88.0	90.0		1758	0.5	0.0	1	dbSNP_127	90	1796,6804	323.2+/-315.9	196,1404,2700	no	coding-synonymous	ZC3H11A	NM_014827.4		219,1927,4357	AA,AC,CC		20.8837,12.9142,18.1839		586/811	203818973	2365,10641	2203	4300	6503	SO:0001819	synonymous_variant	9877	exon17			TGTAGCCTCTTGC		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"""Zinc fingers, CCCH-type domain containing"""	29093	protein-coding gene	gene with protein product		613513	"""zinc finger CCCH-type domain containing 11A"""	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.1758C>A	1.37:g.203818973C>A		Somatic	341	1	0.00293255		WXS	Illumina HiSeq	Phase_I	492	486	0.987805	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Silent	SNP	ENST00000545588.1	37	CCDS30978.1																																																																																			C|0.815;A|0.185	0.185	strong		0.507	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17158120	17158120	+	Missense_Mutation	SNP	C	C	T	rs61733866	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:17158120C>T	ENST00000265970.7	-	8	1756	c.1757G>A	c.(1756-1758)aGt>aAt	p.S586N	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.S206N	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	586					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						ATCTAAAGCACTACAGATTTT	0.328													C|||	32	0.00638978	0.0	0.0043	5008	,	,		16548	0.0		0.005	False		,,,				2504	0.0245				p.S586N		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.G1757A						PASS	.	C	ASN/SER	8,4390	15.5+/-35.6	0,8,2191	114.0	109.0	111.0		1757	4.6	1.0	11	dbSNP_129	111	97,8489	53.1+/-113.8	0,97,4196	yes	missense	PIK3C2A	NM_002645.2	46	0,105,6387	TT,TC,CC		1.1297,0.1819,0.8087	benign	586/1687	17158120	105,12879	2199	4293	6492	SO:0001583	missense	5286	exon8			AAAGCACTACAGA	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.1757G>A	11.37:g.17158120C>T	ENSP00000265970:p.Ser586Asn	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	9	0.004120879120879121	0	0.0	4	0.011049723756906077	0	0.0	5	0.006596306068601583	C	11.39	1.626054	0.28978	0.001819	0.011297	ENSG00000011405	ENST00000265970;ENST00000540361;ENST00000544896	T;T	0.62788	0.0;0.38	5.5	4.58	0.56647	.	0.440892	0.29995	N	0.010680	T	0.36908	0.0984	L	0.35723	1.085	0.32142	N	0.585417	B	0.23735	0.09	B	0.21360	0.034	T	0.43393	-0.9394	10	0.10377	T	0.69	-8.3308	7.5542	0.27814	0.0:0.7019:0.1477:0.1504	.	586	O00443	P3C2A_HUMAN	N	586;206;586	ENSP00000265970:S586N;ENSP00000438687:S206N	ENSP00000265970:S586N	S	-	2	0	PIK3C2A	17114696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.729000	0.47327	1.459000	0.47892	0.561000	0.74099	AGT	C|0.992;T|0.008	0.008	strong		0.328	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
ZNF234	10780	hgsc.bcm.edu	37	19	44660967	44660967	+	Silent	SNP	A	A	G	rs12609635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44660967A>G	ENST00000426739.2	+	6	1056	c.798A>G	c.(796-798)ggA>ggG	p.G266G	ZNF234_ENST00000592437.1_Silent_p.G266G	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	266					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)				AGGAATGTGGAAGGGCCTTCA	0.418													G|||	2851	0.569289	0.9418	0.4726	5008	,	,		23488	0.4931		0.3668	False		,,,				2504	0.4213				p.G266G		Atlas-SNP	.											.	ZNF234	132	.	0			c.A798G						PASS	.	G	,	3702,704	272.5+/-270.8	1568,566,69	136.0	144.0	142.0		798,798	-4.3	0.0	19	dbSNP_120	142	3162,5438	643.0+/-399.9	577,2008,1715	no	coding-synonymous,coding-synonymous	ZNF234	NM_001144824.1,NM_006630.2	,	2145,2574,1784	GG,GA,AA		36.7674,15.9782,47.2244	,	266/701,266/701	44660967	6864,6142	2203	4300	6503	SO:0001819	synonymous_variant	10780	exon6			ATGTGGAAGGGCC	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.798A>G	19.37:g.44660967A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Silent	SNP	ENST00000426739.2	37	CCDS46101.1																																																																																			A|0.448;G|0.552	0.552	strong		0.418	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2		
PLCL1	5334	hgsc.bcm.edu	37	2	198950029	198950029	+	Silent	SNP	A	A	G	rs2228135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:198950029A>G	ENST00000428675.1	+	2	2186	c.1788A>G	c.(1786-1788)caA>caG	p.Q596Q	PLCL1_ENST00000437704.2_Silent_p.Q498Q	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	596	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|inositol 1,4,5 trisphosphate binding (GO:0070679)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(14)|lung(44)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	80					Quinacrine(DB01103)	AATCTGTTCAATACAGGGATT	0.413													G|||	1162	0.232029	0.3578	0.1931	5008	,	,		18872	0.248		0.1909	False		,,,				2504	0.1155				p.Q596Q		Atlas-SNP	.											.	PLCL1	358	.	0			c.A1788G						PASS	.	G		1430,2976	654.7+/-399.8	238,954,1011	69.0	72.0	71.0		1788	1.5	1.0	2	dbSNP_98	71	1539,7061	741.3+/-407.1	127,1285,2888	no	coding-synonymous	PLCL1	NM_006226.3		365,2239,3899	GG,GA,AA		17.8953,32.4557,22.8279		596/1096	198950029	2969,10037	2203	4300	6503	SO:0001819	synonymous_variant	5334	exon2			TGTTCAATACAGG	D42108	CCDS2326.1, CCDS2326.2	2q33	2014-06-13	2002-02-18	2002-02-22	ENSG00000115896	ENSG00000115896			9063	protein-coding gene	gene with protein product	"""phospholipase C related, but catalytically inactive protein"", ""protein phosphatase 1, regulatory subunit 127"""	600597	"""phospholipase C, epsilon"""	PLCE		7633416	Standard	NM_006226		Approved	PLC-L, PLCL, PRIP, PPP1R127	uc010fsp.3	Q15111	OTTHUMG00000132750	ENST00000428675.1:c.1788A>G	2.37:g.198950029A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Silent	SNP	ENST00000428675.1	37	CCDS2326.2																																																																																			A|0.767;G|0.233	0.233	strong		0.413	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226	
FAM83E	54854	hgsc.bcm.edu	37	19	49106995	49106995	+	Missense_Mutation	SNP	G	G	A	rs3745728	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49106995G>A	ENST00000263266.3	-	4	1121	c.932C>T	c.(931-933)cCg>cTg	p.P311L		NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	311			P -> L (in dbSNP:rs3745728). {ECO:0000269|PubMed:14702039}.					p.P311L(1)		NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		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;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CACGCGGTGCGGGCTGCGGCC	0.776													G|||	914	0.182508	0.1316	0.1484	5008	,	,		6380	0.3333		0.1233	False		,,,				2504	0.181				p.P311L		Atlas-SNP	.											FAM83E,NS,NS,0,1	FAM83E	34	1	1	Substitution - Missense(1)	NS(1)	c.C932T						scavenged	.	G	LEU/PRO	319,3115		18,283,1416	4.0	4.0	4.0		932	2.7	0.5	19	dbSNP_107	4	790,6694		40,710,2992	no	missense	FAM83E	NM_017708.3	98	58,993,4408	AA,AG,GG		10.5559,9.2895,10.1575	probably-damaging	311/479	49106995	1109,9809	1717	3742	5459	SO:0001583	missense	54854	exon4			CGGTGCGGGCTGC	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.932C>T	19.37:g.49106995G>A	ENSP00000263266:p.Pro311Leu	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	7	2	0.285714	NM_017708	Q9NXK1	Missense_Mutation	SNP	ENST00000263266.3	37	CCDS42587.1	405	0.18543956043956045	68	0.13821138211382114	52	0.143646408839779	194	0.33916083916083917	91	0.12005277044854881	G	18.13	3.555078	0.65425	0.092895	0.105559	ENSG00000105523	ENST00000263266	T	0.11277	2.79	3.79	2.65	0.31530	.	11.390300	0.00166	N	0.000000	T	0.00012	0.0000	L	0.32530	0.975	0.29073	P	0.883177	D	0.69078	0.997	P	0.53035	0.716	T	0.36939	-0.9727	9	0.35671	T	0.21	-5.1491	9.7456	0.40444	0.0:0.2122:0.7878:0.0	rs3745728	311	Q2M2I3	FA83E_HUMAN	L	311	ENSP00000263266:P311L	ENSP00000263266:P311L	P	-	2	0	FAM83E	53798807	1.000000	0.71417	0.455000	0.27031	0.142000	0.21351	4.236000	0.58675	1.845000	0.53610	0.549000	0.68633	CCG	G|0.814;A|0.186	0.186	strong		0.776	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
TARM1	441864	hgsc.bcm.edu	37	19	54577419	54577419	+	Silent	SNP	G	G	A	rs145288894	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54577419G>A	ENST00000432826.1	-	4	435	c.411C>T	c.(409-411)acC>acT	p.T137T	TARM1_ENST00000446034.2_Silent_p.T145T	NM_001135686.1	NP_001129158.2	B6A8C7	TARM1_HUMAN	T cell-interacting, activating receptor on myeloid cells 1	137	Ig-like C2-type 2.					integral component of membrane (GO:0016021)				endometrium(1)|stomach(2)	3						TTCCACCTGCGGTCACTGTAC	0.532													G|||	32	0.00638978	0.0008	0.0072	5008	,	,		20007	0.0		0.0169	False		,,,				2504	0.0092				p.T137T		Atlas-SNP	.											.	TARM1	10	.	0			c.C411T						PASS	.	G		3,1381		0,3,689	105.0	105.0	105.0		411	-7.7	0.0	19	dbSNP_134	105	48,3134		2,44,1545	yes	coding-synonymous	TARM1	NM_001135686.1		2,47,2234	AA,AG,GG		1.5085,0.2168,1.117		137/272	54577419	51,4515	692	1591	2283	SO:0001819	synonymous_variant	441864	exon4			ACCTGCGGTCACT		CCDS46173.1	19q13.42	2013-01-29			ENSG00000248385	ENSG00000248385		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	37250	protein-coding gene	gene with protein product							Standard	XM_005258952		Approved		uc010yei.1	B6A8C7		ENST00000432826.1:c.411C>T	19.37:g.54577419G>A		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	227	97	0.427313	NM_001135686	B4DWY4	Silent	SNP	ENST00000432826.1	37	CCDS46173.1																																																																																			G|0.993;A|0.007	0.007	strong		0.532	TARM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465679.1	NM_001135686	
AK4	205	hgsc.bcm.edu	37	1	65690461	65690461	+	Silent	SNP	G	G	A	rs4915685	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:65690461G>A	ENST00000327299.7	+	4	670	c.465G>A	c.(463-465)ccG>ccA	p.P155P	AK4_ENST00000395334.2_Silent_p.P155P|AK4_ENST00000470888.2_3'UTR|AK4_ENST00000545314.1_Silent_p.P155P|AK4_ENST00000546702.1_Silent_p.P103P	NM_013410.3	NP_037542.1			adenylate kinase 4											breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	9						CTGGTGAACCGTTAGTCCAGC	0.413													A|||	1853	0.370008	0.3298	0.3314	5008	,	,		20813	0.6726		0.1769	False		,,,				2504	0.3384				p.P155P		Atlas-SNP	.											.	AK4	22	.	0			c.G465A						PASS	.	A	,,	1379,3027	689.8+/-405.2	220,939,1044	134.0	130.0	131.0		465,465,465	-9.7	0.0	1	dbSNP_111	131	1801,6799	732.9+/-406.9	187,1427,2686	no	coding-synonymous,coding-synonymous,coding-synonymous	AK4	NM_001005353.2,NM_013410.3,NM_203464.2	,,	407,2366,3730	AA,AG,GG		20.9419,31.2982,24.4503	,,	155/224,155/224,155/224	65690461	3180,9826	2203	4300	6503	SO:0001819	synonymous_variant	205	exon5			TGAACCGTTAGTC	AK025926	CCDS629.1	1p31.3	2012-10-02	2010-06-15	2010-06-15	ENSG00000162433	ENSG00000162433	2.7.4.3	"""Adenylate kinases"""	363	protein-coding gene	gene with protein product		103030	"""adenylate kinase 3"", ""adenylate kinase 3-like 1"""	AK3, AK3L1		11485571	Standard	NM_203464		Approved		uc001dby.3	P27144	OTTHUMG00000009033	ENST00000327299.7:c.465G>A	1.37:g.65690461G>A		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	149	110	0.738255	NM_203464		Silent	SNP	ENST00000327299.7	37	CCDS629.1																																																																																			G|0.726;A|0.274	0.274	strong		0.413	AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025040.2	NM_013410	
ELL2	22936	hgsc.bcm.edu	37	5	95234377	95234377	+	Silent	SNP	C	C	T	rs3777203	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:95234377C>T	ENST00000237853.4	-	8	1441	c.1092G>A	c.(1090-1092)ccG>ccA	p.P364P	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	364					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)		CAGGGGGCAGCGGGAGGCCTG	0.507													C|||	1826	0.364617	0.4531	0.245	5008	,	,		15044	0.4325		0.2803	False		,,,				2504	0.3466				p.P364P		Atlas-SNP	.											.	ELL2	63	.	0			c.G1092A						PASS	.	C		1841,2561		401,1039,761	67.0	84.0	78.0		1092	-6.1	0.8	5	dbSNP_107	78	2233,6367		291,1651,2358	no	coding-synonymous	ELL2	NM_012081.5		692,2690,3119	TT,TC,CC		25.9651,41.8219,31.3336		364/641	95234377	4074,8928	2201	4300	6501	SO:0001819	synonymous_variant	22936	exon8			GGGCAGCGGGAGG	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.1092G>A	5.37:g.95234377C>T		Somatic	392	1	0.00255102		WXS	Illumina HiSeq	Phase_I	293	287	0.979522	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			C|0.691;T|0.309	0.309	strong		0.507	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
AMDHD2	51005	hgsc.bcm.edu	37	16	2577943	2577943	+	Missense_Mutation	SNP	A	A	C	rs182580356	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2577943A>C	ENST00000293971.6	+	5	679	c.585A>C	c.(583-585)gaA>gaC	p.E195D	ATP6C_ENST00000569317.1_Missense_Mutation_p.E148D|AMDHD2_ENST00000413459.3_Missense_Mutation_p.E195D|AMDHD2_ENST00000302956.4_Missense_Mutation_p.E195D|AMDHD2_ENST00000565570.1_Intron|CEMP1_ENST00000382350.1_Intron	NM_015944.3	NP_057028.2	Q9Y303	NAGA_HUMAN	amidohydrolase domain containing 2	195					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylneuraminate catabolic process (GO:0019262)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-phosphate deacetylase activity (GO:0008448)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)|skin(2)|urinary_tract(2)	19						GTAGCCACGAAGTGATCCGGG	0.682													G|||	5	0.000998403	0.0	0.0043	5008	,	,		13543	0.0		0.002	False		,,,				2504	0.0				p.E195D		Atlas-SNP	.											.	AMDHD2	33	.	0			c.A585C						PASS	.	A	ASP/GLU,ASP/GLU	2,4356		0,2,2177	11.0	15.0	13.0		585,585	-1.5	0.9	16		13	22,8546		0,22,4262	yes	missense,missense	AMDHD2	NM_001145815.1,NM_015944.3	45,45	0,24,6439	CC,CA,AA		0.2568,0.0459,0.1857	benign,benign	195/595,195/440	2577943	24,12902	2179	4284	6463	SO:0001583	missense	51005	exon5			CCACGAAGTGATC	AF132948	CCDS10471.1, CCDS53984.1	16p13.3	2008-02-05			ENSG00000162066	ENSG00000162066			24262	protein-coding gene	gene with protein product						10810093	Standard	NM_001145815		Approved	CGI-14	uc010uwc.2	Q9Y303	OTTHUMG00000128866	ENST00000293971.6:c.585A>C	16.37:g.2577943A>C	ENSP00000293971:p.Glu195Asp	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	NM_001145815	B4DL77|Q8WV54	Missense_Mutation	SNP	ENST00000293971.6	37		3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	A	11.47	1.647305	0.29246	4.59E-4	0.002568	ENSG00000162066	ENST00000413459;ENST00000302956;ENST00000293971	D;D;D	0.99948	-8.65;-8.65;-8.65	5.32	-1.49	0.08718	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.163396	0.52532	D	0.000061	D	0.99420	0.9795	L	0.35414	1.06	0.80722	D	1	B;B;B	0.19706	0.038;0.002;0.002	B;B;B	0.28553	0.091;0.029;0.017	D	0.99978	1.2301	10	0.27082	T	0.32	-22.327	10.5895	0.45302	0.3942:0.0:0.6058:0.0	.	195;195;195	Q9Y303-3;Q9Y303;Q9Y303-2	.;NAGA_HUMAN;.	D	195	ENSP00000391596:E195D;ENSP00000307481:E195D;ENSP00000293971:E195D	ENSP00000293971:E195D	E	+	3	2	AMDHD2	2517944	1.000000	0.71417	0.855000	0.33649	0.188000	0.23474	0.819000	0.27308	-0.235000	0.09767	-0.146000	0.13790	GAA	A|0.999;C|0.001	0.001	strong		0.682	AMDHD2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000435652.1	NM_015944	
NOLC1	9221	hgsc.bcm.edu	37	10	103919738	103919738	+	Silent	SNP	G	G	A	rs143372447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:103919738G>A	ENST00000605788.1	+	8	1180	c.945G>A	c.(943-945)aaG>aaA	p.K315K	NOLC1_ENST00000603742.1_Silent_p.K34K|NOLC1_ENST00000488254.2_Silent_p.K316K|NOLC1_ENST00000405356.1_Silent_p.K325K	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	315	11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		CTGTGGAGAAGCAGCAGCCTG	0.572													G|||	15	0.00299521	0.0	0.0014	5008	,	,		18044	0.0		0.004	False		,,,				2504	0.0102				p.K315K		Atlas-SNP	.											.	NOLC1	61	.	0			c.G945A						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	38.0	40.0	39.0		945	4.7	1.0	10	dbSNP_134	39	30,8570	19.8+/-62.0	0,30,4270	no	coding-synonymous	NOLC1	NM_004741.3		0,37,6466	AA,AG,GG		0.3488,0.1589,0.2845		315/700	103919738	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon8			GGAGAAGCAGCAG	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.945G>A	10.37:g.103919738G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	16	0.219178	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			G|0.998;A|0.002	0.002	strong		0.572	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
EPHB1	2047	hgsc.bcm.edu	37	3	134898742	134898742	+	Silent	SNP	C	C	T	rs1042787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:134898742C>T	ENST00000398015.3	+	10	2170	c.1800C>T	c.(1798-1800)taC>taT	p.Y600Y	EPHB1_ENST00000493838.1_Silent_p.Y161Y	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	600					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CCTTCACTTACGAGGATCCCA	0.488													T|||	2694	0.537939	0.5166	0.5	5008	,	,		22244	0.7282		0.3797	False		,,,				2504	0.5603				p.Y600Y		Atlas-SNP	.											.	EPHB1	519	.	0			c.C1800T						PASS	.	T		1879,2053		457,965,544	217.0	203.0	208.0		1800	-0.7	1.0	3	dbSNP_107	208	3256,5138		643,1970,1584	yes	coding-synonymous	EPHB1	NM_004441.4		1100,2935,2128	TT,TC,CC		38.7896,47.7874,41.6599		600/985	134898742	5135,7191	1966	4197	6163	SO:0001819	synonymous_variant	2047	exon10			CACTTACGAGGAT	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1800C>T	3.37:g.134898742C>T		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	277	110	0.397112	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																			C|0.508;T|0.492	0.492	strong		0.488	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
PHACTR4	65979	hgsc.bcm.edu	37	1	28800380	28800380	+	Missense_Mutation	SNP	C	C	A	rs61785974	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:28800380C>A	ENST00000373839.3	+	7	1399	c.1138C>A	c.(1138-1140)Cta>Ata	p.L380I	PHACTR4_ENST00000373836.3_Missense_Mutation_p.L390I|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	380	Pro-rich.				actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		ATCCTTAGATCTACACCAGGA	0.507													C|||	1127	0.22504	0.3048	0.2666	5008	,	,		14282	0.0704		0.3111	False		,,,				2504	0.1585				p.L390I		Atlas-SNP	.											.	PHACTR4	64	.	0			c.C1168A						PASS	.	C	ILE/LEU,ILE/LEU	1153,2617		192,769,924	81.0	81.0	81.0		1138,1168	3.3	0.2	1	dbSNP_129	81	2233,5989		282,1669,2160	yes	missense,missense	PHACTR4	NM_001048183.1,NM_023923.3	5,5	474,2438,3084	AA,AC,CC		27.1588,30.5836,28.2355	possibly-damaging,possibly-damaging	380/703,390/713	28800380	3386,8606	1885	4111	5996	SO:0001583	missense	65979	exon6			TTAGATCTACACC	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.1138C>A	1.37:g.28800380C>A	ENSP00000362945:p.Leu380Ile	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	55	48	0.872727	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Missense_Mutation	SNP	ENST00000373839.3	37	CCDS41293.1	560	0.2564102564102564	168	0.34146341463414637	100	0.27624309392265195	54	0.0944055944055944	238	0.31398416886543534	C	5.460	0.270018	0.10349	0.305836	0.271588	ENSG00000204138	ENST00000373839;ENST00000373836;ENST00000373838	T;T	0.24908	1.84;1.83	5.22	3.3	0.37823	.	1.100460	0.06835	N	0.794600	T	0.00012	0.0000	L	0.54323	1.7	0.38745	P	0.04601200000000005	B;B	0.31548	0.328;0.22	B;B	0.28011	0.085;0.024	T	0.41980	-0.9478	9	0.19590	T	0.45	-5.1431	5.4783	0.16708	0.1624:0.676:0.0:0.1616	rs61785974	390;380	Q8IZ21-2;Q8IZ21	.;PHAR4_HUMAN	I	380;390;379	ENSP00000362945:L380I;ENSP00000362942:L390I	ENSP00000362942:L390I	L	+	1	2	PHACTR4	28672967	0.235000	0.23794	0.237000	0.24090	0.250000	0.25880	1.307000	0.33516	0.731000	0.32448	0.655000	0.94253	CTA	C|0.726;A|0.274	0.274	strong		0.507	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923	
DAPK1	1612	hgsc.bcm.edu	37	9	90322238	90322238	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:90322238G>A	ENST00000408954.3	+	26	4587	c.4252G>A	c.(4252-4254)Ggc>Agc	p.G1418S	DAPK1_ENST00000469640.2_Missense_Mutation_p.G1443S|DAPK1_ENST00000491893.1_Missense_Mutation_p.G1352S|DAPK1_ENST00000358077.5_Missense_Mutation_p.G1418S|DAPK1_ENST00000472284.1_Missense_Mutation_p.G1418S	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1418					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						CTGCAACAGCGGCACCTCTTA	0.557									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.G1418S		Atlas-SNP	.											DAPK1_ENST00000408954,colon,carcinoma,0,2	DAPK1	329	2	0			c.G4252A						scavenged	.						37.0	40.0	39.0					9																	90322238		1949	4144	6093	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	AACAGCGGCACCT	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.4252G>A	9.37:g.90322238G>A	ENSP00000386135:p.Gly1418Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	178	4	0.0224719	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.603292	0.87157	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.76060	-0.77;-0.77;-0.91;-0.77;-0.99	5.94	5.94	0.96194	.	0.000000	0.52532	D	0.000063	T	0.77805	0.4185	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.998	P;D;D	0.66497	0.883;0.944;0.912	T	0.72590	-0.4247	10	0.21014	T	0.42	.	20.3594	0.98849	0.0:0.0:1.0:0.0	.	1352;1418;1418	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	S	1418;1418;1443;1418;1352	ENSP00000350785:G1418S;ENSP00000417076:G1418S;ENSP00000418885:G1443S;ENSP00000386135:G1418S;ENSP00000419026:G1352S	ENSP00000350785:G1418S	G	+	1	0	DAPK1	89512058	1.000000	0.71417	0.985000	0.45067	0.974000	0.67602	9.845000	0.99498	2.816000	0.96949	0.563000	0.77884	GGC	.	.	none		0.557	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
SLC7A14	57709	hgsc.bcm.edu	37	3	170198898	170198898	+	Silent	SNP	C	C	T	rs3732449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:170198898C>T	ENST00000231706.5	-	7	1488	c.1173G>A	c.(1171-1173)tcG>tcA	p.S391S	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	391			S -> L (in RP68; uncertain pathological significance). {ECO:0000269|PubMed:24670872}.		negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			CCAGGAACCCCGACACGATGC	0.587													c|||	1690	0.33746	0.5212	0.2608	5008	,	,		18123	0.3849		0.1968	False		,,,				2504	0.2393				p.S391S		Atlas-SNP	.											.	SLC7A14	110	.	0			c.G1173A						PASS	.	T		2131,2275	578.2+/-384.6	503,1125,575	54.0	47.0	50.0		1173	-10.6	0.1	3	dbSNP_107	50	1557,7043	293.4+/-301.3	134,1289,2877	no	coding-synonymous	SLC7A14	NM_020949.2		637,2414,3452	TT,TC,CC		18.1047,48.3659,28.3561		391/772	170198898	3688,9318	2203	4300	6503	SO:0001819	synonymous_variant	57709	exon7			GAACCCCGACACG	BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"""Solute carriers"""	29326	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 142"""	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1173G>A	3.37:g.170198898C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_020949	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	37	CCDS33892.1																																																																																			C|0.688;T|0.312	0.312	strong		0.587	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949	
BACH2	60468	hgsc.bcm.edu	37	6	90642358	90642358	+	Silent	SNP	G	G	A	rs3798789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:90642358G>A	ENST00000257749.4	-	9	3002	c.2295C>T	c.(2293-2295)aaC>aaT	p.N765N	BACH2_ENST00000343122.3_Silent_p.N765N|BACH2_ENST00000537989.1_Silent_p.N765N	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	765						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		AGCAGGGCACGTTTTCCCCCA	0.637													A|||	518	0.103435	0.152	0.0692	5008	,	,		16614	0.0704		0.1074	False		,,,				2504	0.092				p.N765N		Atlas-SNP	.											.	BACH2	224	.	0			c.C2295T						PASS	.	A	,	593,3813	769.3+/-413.7	42,509,1652	42.0	44.0	44.0		2295,2295	-5.0	0.0	6	dbSNP_107	44	1029,7571	770.4+/-407.7	51,927,3322	no	coding-synonymous,coding-synonymous	BACH2	NM_001170794.1,NM_021813.2	,	93,1436,4974	AA,AG,GG		11.9651,13.4589,12.4712	,	765/842,765/842	90642358	1622,11384	2203	4300	6503	SO:0001819	synonymous_variant	60468	exon7			GGGCACGTTTTCC	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.2295C>T	6.37:g.90642358G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	37	CCDS5026.1																																																																																			G|0.877;A|0.123	0.123	strong		0.637	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813	
MAP3K4	4216	hgsc.bcm.edu	37	6	161508880	161508880	+	Missense_Mutation	SNP	A	A	C	rs35533223	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:161508880A>C	ENST00000392142.4	+	10	2865	c.2717A>C	c.(2716-2718)cAc>cCc	p.H906P	MAP3K4_ENST00000366919.2_Missense_Mutation_p.H906P|MAP3K4_ENST00000366920.2_Missense_Mutation_p.H906P|MAP3K4_ENST00000348824.7_Missense_Mutation_p.H906P	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	906			H -> P (in dbSNP:rs35533223). {ECO:0000269|PubMed:17344846}.		activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		CTGACCAAGCACGGTGATCGA	0.512													A|||	57	0.0113818	0.0023	0.0159	5008	,	,		20328	0.0		0.0278	False		,,,				2504	0.0153				p.H906P		Atlas-SNP	.											.	MAP3K4	364	.	0			c.A2717C						PASS	.	A	PRO/HIS,PRO/HIS	36,4370	40.8+/-73.8	0,36,2167	139.0	112.0	121.0		2717,2717	2.0	0.0	6	dbSNP_126	121	344,8256	117.7+/-177.3	5,334,3961	yes	missense,missense	MAP3K4	NM_005922.2,NM_006724.2	77,77	5,370,6128	CC,CA,AA		4.0,0.8171,2.9217	possibly-damaging,possibly-damaging	906/1609,906/1559	161508880	380,12626	2203	4300	6503	SO:0001583	missense	4216	exon10			CCAAGCACGGTGA	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2717A>C	6.37:g.161508880A>C	ENSP00000375986:p.His906Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	32	0.014652014652014652	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	22	0.029023746701846966	A	13.59	2.282961	0.40394	0.008171	0.04	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.70749	-0.5;-0.49;-0.49;-0.51	5.73	1.95	0.26073	.	0.192782	0.44483	D	0.000443	T	0.48696	0.1514	L	0.60455	1.87	0.33817	D	0.628597	B;P;P	0.42993	0.305;0.797;0.472	B;B;B	0.43623	0.245;0.425;0.261	T	0.40059	-0.9583	10	0.33141	T	0.24	-6.8869	6.1099	0.20094	0.7457:0.0:0.1333:0.121	rs35533223	906;906;906	F5H538;Q9Y6R4-2;Q9Y6R4	.;.;M3K4_HUMAN	P	906	ENSP00000355886:H906P;ENSP00000375986:H906P;ENSP00000355887:H906P;ENSP00000297332:H906P	ENSP00000297332:H906P	H	+	2	0	MAP3K4	161428870	1.000000	0.71417	0.000000	0.03702	0.003000	0.03518	4.880000	0.63107	0.483000	0.27608	0.533000	0.62120	CAC	A|0.976;C|0.024	0.024	strong		0.512	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
GLS2	27165	hgsc.bcm.edu	37	12	56865338	56865338	+	Missense_Mutation	SNP	A	A	G	rs2657879	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:56865338A>G	ENST00000311966.4	-	18	2020	c.1742T>C	c.(1741-1743)cTc>cCc	p.L581P	MIP_ENST00000555551.1_5'Flank|GLS2_ENST00000476991.1_5'Flank	NM_013267.2	NP_037399.2	Q9UI32	GLSL_HUMAN	glutaminase 2 (liver, mitochondrial)	581			L -> P (in dbSNP:rs2657879). {ECO:0000269|Ref.3}.		cellular amino acid biosynthetic process (GO:0008652)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate secretion (GO:0014047)|glutamine metabolic process (GO:0006541)|neurotransmitter secretion (GO:0007269)|reactive oxygen species metabolic process (GO:0072593)|regulation of apoptotic process (GO:0042981)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13					L-Glutamine(DB00130)	AGTTTCAGAGAGTGTGTAGGA	0.512													A|||	643	0.128395	0.0371	0.2392	5008	,	,		21065	0.0823		0.2127	False		,,,				2504	0.1339				p.L581P		Atlas-SNP	.											.	GLS2	42	.	0			c.T1742C						PASS	.	A	PRO/LEU	289,4117	159.2+/-191.8	8,273,1922	74.0	66.0	69.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1742	3.1	0.9	12	dbSNP_100	69	1601,6999	297.9+/-303.7	147,1307,2846	yes	missense	GLS2	NM_013267.2	98	155,1580,4768	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	18.6163,6.5592,14.5318	benign	581/603	56865338	1890,11116	2203	4300	6503	SO:0001583	missense	27165	exon18			TCAGAGAGTGTGT		CCDS8921.1, CCDS73482.1	12q13	2013-01-10			ENSG00000135423	ENSG00000135423		"""Ankyrin repeat domain containing"""	29570	protein-coding gene	gene with protein product		606365				11130979, 10620514	Standard	NM_013267		Approved	GA, GLS, LGA, hLGA	uc001slj.3	Q9UI32	OTTHUMG00000140379	ENST00000311966.4:c.1742T>C	12.37:g.56865338A>G	ENSP00000310447:p.Leu581Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	NM_013267	B7Z8Q9|Q8IX91|Q9NYY2|Q9UI31	Missense_Mutation	SNP	ENST00000311966.4	37	CCDS8921.1	299	0.13690476190476192	21	0.042682926829268296	77	0.212707182320442	48	0.08391608391608392	153	0.20184696569920843	A	2.497	-0.316008	0.05422	0.065592	0.186163	ENSG00000135423	ENST00000311966	T	0.30182	1.54	5.6	3.08	0.35506	.	0.387987	0.25590	N	0.029624	T	0.00012	0.0000	L	0.37630	1.12	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.23190	-1.0195	9	0.28530	T	0.3	-19.7846	6.3142	0.21180	0.7659:0.0:0.2341:0.0	rs2657879;rs17442734;rs2657879	581	Q9UI32	GLSL_HUMAN	P	581	ENSP00000310447:L581P	ENSP00000310447:L581P	L	-	2	0	GLS2	55151605	0.286000	0.24305	0.897000	0.35233	0.041000	0.13682	1.374000	0.34283	0.678000	0.31325	0.533000	0.62120	CTC	A|0.864;G|0.136	0.136	strong		0.512	GLS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277113.1	NM_013267	
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987528	154987528	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154987528C>T	ENST00000368426.3	+	3	529	c.392C>T	c.(391-393)cCg>cTg	p.P131L	ZBTB7B_ENST00000535420.1_Missense_Mutation_p.P131L|ZBTB7B_ENST00000417934.2_Missense_Mutation_p.P165L|ZBTB7B_ENST00000292176.2_Missense_Mutation_p.P131L|ZBTB7B_ENST00000487542.1_3'UTR	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	131					cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|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)	p.P131L(1)		endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			CTGGAGATCCCGTGTGTCATC	0.617																																					p.P165L		Atlas-SNP	.											ZBTB7B,NS,carcinoma,0,1	ZBTB7B	69	1	1	Substitution - Missense(1)	endometrium(1)	c.C494T						scavenged	.						41.0	45.0	44.0					1																	154987528		2203	4300	6503	SO:0001583	missense	51043	exon4			AGATCCCGTGTGT	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18668	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 15"""	607646	"""zinc finger protein 67 homolog (mouse)"""	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.392C>T	1.37:g.154987528C>T	ENSP00000357411:p.Pro131Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	37	CCDS1081.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.441574	0.63067	.	.	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43	3.74	3.74	0.42951	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.228496	0.36591	N	0.002506	T	0.63474	0.2514	L	0.46670	1.46	0.44985	D	0.998006	D;D;D	0.71674	0.998;0.998;0.998	P;P;P	0.56916	0.809;0.809;0.809	T	0.68420	-0.5413	10	0.62326	D	0.03	.	13.0548	0.58973	0.0:1.0:0.0:0.0	.	131;131;165	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	L	131;131;165;131	ENSP00000438647:P131L;ENSP00000357411:P131L;ENSP00000406286:P165L;ENSP00000292176:P131L	ENSP00000292176:P131L	P	+	2	0	ZBTB7B	153254152	0.047000	0.20315	0.831000	0.32960	0.985000	0.73830	0.371000	0.20450	1.909000	0.55274	0.462000	0.41574	CCG	.	.	none		0.617	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
PABPC4L	132430	hgsc.bcm.edu	37	4	135121066	135121066	+	Missense_Mutation	SNP	T	T	G	rs11099273	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	63	0	0		WXS	Illumina HiSeq	Phase_I	62	45	0.725806	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	
SLFN12	55106	hgsc.bcm.edu	37	17	33749758	33749758	+	Missense_Mutation	SNP	A	A	G	rs138003670	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33749758A>G	ENST00000394562.1	-	4	813	c.290T>C	c.(289-291)aTg>aCg	p.M97T	SLFN12_ENST00000304905.5_Missense_Mutation_p.M97T|SLFN12_ENST00000452764.3_Missense_Mutation_p.M97T|SLFN12_ENST00000460530.1_5'Flank			Q8IYM2	SLN12_HUMAN	schlafen family member 12	97							ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACCATTCTGCATGAAGTCTAA	0.358													A|||	8	0.00159744	0.0	0.0	5008	,	,		20665	0.0		0.006	False		,,,				2504	0.002				p.M97T		Atlas-SNP	.											.	SLFN12	56	.	0			c.T290C						PASS	.	A	THR/MET	3,4403	6.2+/-15.9	0,3,2200	70.0	70.0	70.0		290	0.7	0.1	17	dbSNP_134	70	31,8569	21.6+/-65.8	0,31,4269	yes	missense	SLFN12	NM_018042.3	81	0,34,6469	GG,GA,AA		0.3605,0.0681,0.2614	benign	97/579	33749758	34,12972	2203	4300	6503	SO:0001583	missense	55106	exon2			TTCTGCATGAAGT	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.290T>C	17.37:g.33749758A>G	ENSP00000378063:p.Met97Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	a	12.33	1.906264	0.33628	6.81E-4	0.003605	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764;ENST00000447040	T;T;T;T	0.22945	3.79;3.79;3.79;1.93	3.27	0.658	0.17855	.	.	.	.	.	T	0.19406	0.0466	L	0.58583	1.82	0.09310	N	1	P	0.51791	0.948	P	0.46362	0.514	T	0.09975	-1.0650	9	0.46703	T	0.11	.	5.5093	0.16872	0.5168:0.0:0.0:0.4831	.	97	Q8IYM2	SLN12_HUMAN	T	97	ENSP00000378063:M97T;ENSP00000302077:M97T;ENSP00000394903:M97T;ENSP00000398315:M97T	ENSP00000302077:M97T	M	-	2	0	SLFN12	30773871	0.062000	0.20869	0.071000	0.20095	0.053000	0.15095	0.162000	0.16501	-0.026000	0.13895	0.358000	0.22013	ATG	A|0.998;G|0.002	0.002	strong		0.358	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
TECRL	253017	hgsc.bcm.edu	37	4	65180425	65180425	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:65180425C>T	ENST00000381210.3	-	5	602	c.492G>A	c.(490-492)agG>agA	p.R164R	TECRL_ENST00000507440.1_Silent_p.R164R|TECRL_ENST00000513125.1_5'UTR	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	164					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						TACATGGGATCCTCAAATAAA	0.378																																					p.R164R		Atlas-SNP	.											TECRL,NS,carcinoma,-2,1	TECRL	106	1	0			c.G492A						scavenged	.						115.0	111.0	112.0					4																	65180425		2203	4300	6503	SO:0001819	synonymous_variant	253017	exon5			TGGGATCCTCAAA	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.492G>A	4.37:g.65180425C>T		Somatic	459	0	0		WXS	Illumina HiSeq	Phase_I	440	5	0.0113636	NM_001010874		Silent	SNP	ENST00000381210.3	37	CCDS33990.1																																																																																			.	.	none		0.378	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874	
ZNF879	345462	hgsc.bcm.edu	37	5	178459283	178459283	+	Missense_Mutation	SNP	A	A	G	rs17078988	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:178459283A>G	ENST00000444149.2	+	5	522	c.334A>G	c.(334-336)Aca>Gca	p.T112A	ZNF879_ENST00000519896.1_3'UTR	NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	112					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)|pancreas(1)|stomach(1)	7						AATTGATGGCACATTTGACTT	0.333													G|||	1824	0.364217	0.5182	0.255	5008	,	,		18690	0.4276		0.2237	False		,,,				2504	0.3129				p.T112A		Atlas-SNP	.											.	ZNF879	41	.	0			c.A334G						PASS	.	G	ALA/THR	618,766		138,342,212	98.0	83.0	87.0		334	-2.4	0.0	5	dbSNP_123	87	706,2476		76,554,961	yes	missense	ZNF879	NM_001136116.1	58	214,896,1173	GG,GA,AA		22.1873,44.6532,28.9969	benign	112/564	178459283	1324,3242	692	1591	2283	SO:0001583	missense	345462	exon5			GATGGCACATTTG	AK300504	CCDS47352.1	5q35.3	2013-01-08			ENSG00000234284	ENSG00000234284		"""Zinc fingers, C2H2-type"", ""-"""	37273	protein-coding gene	gene with protein product							Standard	NM_001136116		Approved	DKFZp686E2433	uc003mjt.4	B4DU55	OTTHUMG00000163596	ENST00000444149.2:c.334A>G	5.37:g.178459283A>G	ENSP00000414887:p.Thr112Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_001136116		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	768	0.3516483516483517	243	0.49390243902439024	100	0.27624309392265195	244	0.42657342657342656	181	0.23878627968337732	G	0	-2.590623	0.00126	0.446532	0.221873	ENSG00000234284	ENST00000444149;ENST00000522442	T;T	0.06142	3.34;5.87	4.32	-2.37	0.06643	.	.	.	.	.	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	0.42137	-0.9469	8	0.07030	T	0.85	0.427	1.2422	0.01965	0.3576:0.2448:0.2425:0.1551	rs17078988;rs52795425;rs17078988	112	B4DU55	ZN879_HUMAN	A	112	ENSP00000414887:T112A;ENSP00000428477:T112A	ENSP00000414887:T112A	T	+	1	0	ZNF879	178391889	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.139000	0.01302	-1.063000	0.03177	-4.156000	0.00010	ACA	A|0.634;G|0.366	0.366	strong		0.333	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1	NM_001136116	
ELK3	2004	hgsc.bcm.edu	37	12	96641452	96641452	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:96641452C>T	ENST00000228741.3	+	3	1268	c.942C>T	c.(940-942)atC>atT	p.I314I	ELK3_ENST00000552142.1_Intron	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	314					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|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)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					TCGGCTCCATCGCCCTCAACA	0.592																																					p.I314I		Atlas-SNP	.											.	ELK3	36	.	0			c.C942T						PASS	.						37.0	35.0	36.0					12																	96641452		2203	4299	6502	SO:0001819	synonymous_variant	2004	exon3			CTCCATCGCCCTC	BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.942C>T	12.37:g.96641452C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Silent	SNP	ENST00000228741.3	37	CCDS9060.1																																																																																			.	.	none		0.592	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230	
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959773	45959773	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:45959773C>T	ENST00000400375.1	-	1	305	c.261G>A	c.(259-261)ccG>ccA	p.P87P	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_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	118	3	0.0254237		WXS	Illumina HiSeq	Phase_I	146	15	0.10274	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		
SERAC1	84947	hgsc.bcm.edu	37	6	158571611	158571611	+	Missense_Mutation	SNP	A	A	T	rs112780453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:158571611A>T	ENST00000367104.3	-	4	270	c.139T>A	c.(139-141)Ttt>Att	p.F47I	SERAC1_ENST00000367102.2_Missense_Mutation_p.F47I|SERAC1_ENST00000367101.1_Missense_Mutation_p.F47I|SERAC1_ENST00000607000.1_Missense_Mutation_p.F47I	NM_032861.3	NP_116250.3	Q96JX3	SRAC1_HUMAN	serine active site containing 1	47				F -> L (in Ref. 3; AAH28594). {ECO:0000305}.	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)		TATGTAAGAAATAAAGAACCT	0.328													A|||	55	0.0109824	0.0113	0.0317	5008	,	,		18723	0.0		0.0119	False		,,,				2504	0.0061				p.F47I		Atlas-SNP	.											.	SERAC1	31	.	0			c.T139A						PASS	.	A	ILE/PHE	91,4315	68.1+/-105.8	2,87,2114	74.0	80.0	78.0		139	5.9	1.0	6	dbSNP_132	78	182,8408	75.7+/-138.4	2,178,4115	yes	missense	SERAC1	NM_032861.3	21	4,265,6229	TT,TA,AA		2.1187,2.0654,2.1006	probably-damaging	47/655	158571611	273,12723	2203	4295	6498	SO:0001583	missense	84947	exon4			TAAGAAATAAAGA	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.139T>A	6.37:g.158571611A>T	ENSP00000356071:p.Phe47Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_032861	Q49AT1|Q5VTX3|Q6PKF3	Missense_Mutation	SNP	ENST00000367104.3	37	CCDS5255.1	23	0.010531135531135532	7	0.014227642276422764	10	0.027624309392265192	0	0.0	6	0.0079155672823219	A	31	5.070022	0.93950	0.020654	0.021187	ENSG00000122335	ENST00000367102;ENST00000367104;ENST00000367101	T;T;T	0.41065	1.01;1.01;1.01	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.49012	0.1532	M	0.73598	2.24	0.53688	D	0.999972	D	0.61080	0.989	P	0.57009	0.811	T	0.53767	-0.8392	10	0.56958	D	0.05	-25.755	15.3295	0.74196	1.0:0.0:0.0:0.0	.	47	Q96JX3	SRAC1_HUMAN	I	47	ENSP00000356069:F47I;ENSP00000356071:F47I;ENSP00000356068:F47I	ENSP00000356068:F47I	F	-	1	0	SERAC1	158491599	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.614000	0.82996	0.488000	0.27723	-0.263000	0.10527	TTT	A|0.981;T|0.019	0.019	strong		0.328	SERAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042862.1	NM_032861	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43822171	43822171	+	Missense_Mutation	SNP	G	G	A	rs7310011	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:43822171G>A	ENST00000389420.3	-	26	3817	c.3818C>T	c.(3817-3819)tCc>tTc	p.S1273F	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.S391F|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.S1273F	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1273			S -> F (in dbSNP:rs7310011).		extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		CTGCACAGGGGAACTAGGAAA	0.458													G|||	183	0.0365415	0.0015	0.0086	5008	,	,		13663	0.0694		0.0348	False		,,,				2504	0.0716				p.S1273F		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.C3818T						PASS	.	G	PHE/SER	26,4380	31.7+/-61.6	0,26,2177	86.0	83.0	84.0		3818	4.9	0.8	12	dbSNP_116	84	242,8358	97.2+/-158.9	6,230,4064	yes	missense	ADAMTS20	NM_025003.3	155	6,256,6241	AA,AG,GG		2.814,0.5901,2.0606	benign	1273/1911	43822171	268,12738	2203	4300	6503	SO:0001583	missense	80070	exon26			ACAGGGGAACTAG	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3818C>T	12.37:g.43822171G>A	ENSP00000374071:p.Ser1273Phe	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	208	96	0.461538	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	78	0.03571428571428571	0	0.0	5	0.013812154696132596	44	0.07692307692307693	29	0.03825857519788918	G	0.596	-0.830847	0.02713	0.005901	0.02814	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.61859	0.24;0.09;0.09;0.07	4.94	4.94	0.65067	.	0.000000	0.44285	D	0.000470	T	0.04497	0.0123	N	0.24115	0.695	0.09310	N	1	B;D	0.62365	0.105;0.991	B;P	0.52424	0.016;0.698	T	0.03344	-1.1046	10	0.48119	T	0.1	.	8.9011	0.35495	0.081:0.0:0.7667:0.1522	rs7310011	1273;391	P59510;E9PBD5	ATS20_HUMAN;.	F	1273;403;391;1273;1273	ENSP00000374071:S1273F;ENSP00000447427:S403F;ENSP00000378911:S391F;ENSP00000448341:S1273F	ENSP00000374068:S1273F	S	-	2	0	ADAMTS20	42108438	0.994000	0.37717	0.778000	0.31720	0.002000	0.02628	1.179000	0.31993	2.675000	0.91044	0.585000	0.79938	TCC	G|0.974;A|0.026	0.026	strong		0.458	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
DHRS4	10901	hgsc.bcm.edu	37	14	24423090	24423090	+	Silent	SNP	A	A	G	rs2273944	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24423090A>G	ENST00000313250.5	+	1	296	c.93A>G	c.(91-93)gcA>gcG	p.A31A	DHRS4_ENST00000397075.3_Silent_p.A31A|DHRS4_ENST00000558581.1_Silent_p.A31A|DHRS4_ENST00000421831.1_Silent_p.A13A|DHRS4_ENST00000397073.2_Silent_p.A13A|DHRS4_ENST00000308178.8_Silent_p.A13A|DHRS4_ENST00000559632.1_Silent_p.A31A|DHRS4_ENST00000543741.2_Silent_p.A31A|DHRS4_ENST00000558263.1_Silent_p.A31A|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000382761.3_Silent_p.A13A|DHRS4_ENST00000397074.3_Silent_p.A31A	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	31			A -> T (in dbSNP:rs1043442).		alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	ACCCGCTCGCAAATAAGGTGG	0.662													.|||	1415	0.282548	0.7973	0.1254	5008	,	,		15599	0.1359		0.0875	False		,,,				2504	0.0501				p.A31A		Atlas-SNP	.											.	DHRS4	22	.	0			c.A93G						PASS	.	G		3004,1398		1049,906,246	28.0	36.0	33.0		93	0.5	0.5	14	dbSNP_100	33	810,7782		36,738,3522	no	coding-synonymous	DHRS4	NM_021004.2		1085,1644,3768	GG,GA,AA		9.4274,31.7583,29.352		31/279	24423090	3814,9180	2201	4296	6497	SO:0001819	synonymous_variant	10901	exon1			GCTCGCAAATAAG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.93A>G	14.37:g.24423090A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	74	72	0.972973	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Silent	SNP	ENST00000313250.5	37	CCDS9605.1																																																																																			A|0.694;G|0.306	0.306	strong		0.662	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
F5	2153	hgsc.bcm.edu	37	1	169512093	169512093	+	Silent	SNP	A	A	G	rs6017	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:169512093A>G	ENST00000367797.3	-	13	2436	c.2235T>C	c.(2233-2235)aaT>aaC	p.N745N	F5_ENST00000367796.3_Silent_p.N750N	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	745	B.				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)	CTTCTTCCTGATTCAATGATG	0.393													A|||	1316	0.26278	0.1679	0.3948	5008	,	,		21864	0.248		0.2535	False		,,,				2504	0.3221				p.N745N		Atlas-SNP	.											.	F5	301	.	0			c.T2235C						PASS	.	A		812,3594	320.7+/-296.8	68,676,1459	216.0	202.0	206.0		2235	-1.3	0.0	1	dbSNP_52	206	2355,6245	393.9+/-344.5	299,1757,2244	no	coding-synonymous	F5	NM_000130.4		367,2433,3703	GG,GA,AA		27.3837,18.4294,24.3503		745/2225	169512093	3167,9839	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			TTCCTGATTCAAT	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.2235T>C	1.37:g.169512093A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	202	202	1	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			A|0.760;G|0.240	0.240	strong		0.393	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
CPM	1368	hgsc.bcm.edu	37	12	69260779	69260779	+	Silent	SNP	C	C	T	rs33925480	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:69260779C>T	ENST00000551568.1	-	7	897	c.837G>A	c.(835-837)acG>acA	p.T279T	CPM_ENST00000546373.1_Silent_p.T279T|CPM_ENST00000338356.3_Silent_p.T279T	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	279					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			ACAGCTCCAACGTAATTTCAA	0.383													C|||	334	0.0666933	0.0129	0.0807	5008	,	,		19671	0.0159		0.1342	False		,,,				2504	0.1125				p.T279T		Atlas-SNP	.											.	CPM	30	.	0			c.G837A						PASS	.	C	,,	145,4261	100.7+/-139.4	2,141,2060	105.0	101.0	102.0		837,837,837	-11.1	0.0	12	dbSNP_126	102	1174,7426	240.1+/-271.0	81,1012,3207	no	coding-synonymous,coding-synonymous,coding-synonymous	CPM	NM_001005502.2,NM_001874.4,NM_198320.3	,,	83,1153,5267	TT,TC,CC		13.6512,3.291,10.1415	,,	279/444,279/444,279/444	69260779	1319,11687	2203	4300	6503	SO:0001819	synonymous_variant	1368	exon7			CTCCAACGTAATT	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"""renal carboxypeptidase"", ""urinary carboxypeptidase B"""	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.837G>A	12.37:g.69260779C>T		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	253	139	0.549407	NM_001005502	B2R800|Q9H2K9	Silent	SNP	ENST00000551568.1	37	CCDS8987.1	142	0.06501831501831502	4	0.008130081300813009	37	0.10220994475138122	6	0.01048951048951049	95	0.12532981530343007	C	6.995	0.553768	0.13374	0.03291	0.136512	ENSG00000135678	ENST00000551897	.	.	.	5.54	-11.1	0.00147	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999999961	.	.	.	.	.	.	T	0.05869	-1.0859	3	.	.	.	-16.4712	9.2735	0.37686	0.1531:0.0757:0.0795:0.6918	rs33925480	.	.	.	H	82	.	.	R	-	2	0	CPM	67547046	0.000000	0.05858	0.019000	0.16419	0.860000	0.49131	-3.148000	0.00583	-2.582000	0.00461	-0.890000	0.02929	CGT	C|0.903;T|0.097	0.097	strong		0.383	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489791	32489791	+	Silent	SNP	A	A	G	rs41550412		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489791A>G	ENST00000374975.3	-	2	323	c.261T>C	c.(259-261)gcT>gcC	p.A87A		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						TCCAGTACTCAGCGTCAGGCC	0.612																																					p.A87A		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.T261C						PASS	.						41.0	38.0	39.0					6																	32489791		2167	4233	6400	SO:0001819	synonymous_variant	3127	exon2			GTACTCAGCGTCA		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.261T>C	6.37:g.32489791A>G		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	16	12	0.75	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			G|0.633;A|0.367	0.633	strong		0.612	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
PFKFB2	5208	hgsc.bcm.edu	37	1	207238419	207238419	+	Silent	SNP	C	C	T	rs72741390	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:207238419C>T	ENST00000367080.3	+	8	670	c.546C>T	c.(544-546)aaC>aaT	p.N182N	PFKFB2_ENST00000541914.1_5'UTR|PFKFB2_ENST00000545806.1_Silent_p.N149N|PFKFB2_ENST00000367079.2_Silent_p.N182N|PFKFB2_ENST00000411990.2_Silent_p.N84N	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	175	0	0		WXS	Illumina HiSeq	Phase_I	207	75	0.362319	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		
TRIM56	81844	hgsc.bcm.edu	37	7	100730707	100730707	+	Silent	SNP	T	T	C	rs372702476		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100730707T>C	ENST00000306085.6	+	3	411	c.114T>C	c.(112-114)caT>caC	p.H38H		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	38					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					CCTGCCTGCATACCTACTGCC	0.687																																					p.H38H	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.T114C						PASS	.	T		0,4242		0,0,2121	51.0	62.0	58.0		114	-1.4	1.0	7		58	2,8486		0,2,4242	no	coding-synonymous	TRIM56	NM_030961.1		0,2,6363	CC,CT,TT		0.0236,0.0,0.0157		38/756	100730707	2,12728	2121	4244	6365	SO:0001819	synonymous_variant	81844	exon3			CCTGCATACCTAC	BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19028	protein-coding gene	gene with protein product			"""tripartite motif-containing 56"""				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.114T>C	7.37:g.100730707T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	20	0.298507	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			.	.	weak		0.687	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
APOB	338	hgsc.bcm.edu	37	2	21232195	21232195	+	Silent	SNP	G	G	A	rs693	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	202	99	0.490099	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		
NOP58	51602	hgsc.bcm.edu	37	2	203155936	203155936	+	Silent	SNP	A	A	C	rs3731700	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:203155936A>C	ENST00000264279.5	+	8	949	c.723A>C	c.(721-723)tcA>tcC	p.S241S	SNORD11B_ENST00000607707.1_RNA|SNORD11_ENST00000459124.1_RNA	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	241				KAAAEISMGTEVSEEDICNILHLCTQ -> EGSCRDIHGNR GFRRRYLQYSASLHP (in Ref. 6; AAF29084). {ECO:0000305}.	cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						CAGAGATATCAATGGGAACAG	0.428													A|||	623	0.124401	0.0053	0.1427	5008	,	,		17596	0.123		0.1402	False		,,,				2504	0.2577				p.S241S		Atlas-SNP	.											.	NOP58	41	.	0			c.A723C						PASS	.	A		109,4297	82.9+/-121.4	4,101,2098	116.0	119.0	118.0		723	-11.3	0.8	2	dbSNP_107	118	1046,7554	221.5+/-258.9	59,928,3313	no	coding-synonymous	NOP58	NM_015934.3		63,1029,5411	CC,CA,AA		12.1628,2.4739,8.8805		241/530	203155936	1155,11851	2203	4300	6503	SO:0001819	synonymous_variant	51602	exon8			GATATCAATGGGA		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"""NOP58 ribonucleoprotein homolog (yeast)"""			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.723A>C	2.37:g.203155936A>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	95	63	0.663158	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	37	CCDS2353.1																																																																																			A|0.904;C|0.096	0.096	strong		0.428	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934	
TRPA1	8989	hgsc.bcm.edu	37	8	72967973	72967973	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:72967973A>G	ENST00000262209.4	-	11	1519	c.1312T>C	c.(1312-1314)Tcc>Ccc	p.S438P	RP11-383H13.1_ENST00000457356.4_3'UTR	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	438					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)	GAATGAATGGACACATTAAAG	0.418																																					p.S438P		Atlas-SNP	.											TRPA1,NS,carcinoma,+2,2	TRPA1	256	2	0			c.T1312C						scavenged	.						35.0	34.0	34.0					8																	72967973		2203	4293	6496	SO:0001583	missense	8989	exon11			GAATGGACACATT	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.1312T>C	8.37:g.72967973A>G	ENSP00000262209:p.Ser438Pro	Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	461	5	0.010846	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	A	18.24	3.580185	0.65992	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.71934	-0.61;-0.61	5.1	5.1	0.69264	Ankyrin repeat-containing domain (4);	0.099950	0.64402	D	0.000001	T	0.75889	0.3911	L	0.38531	1.155	0.58432	D	0.999991	D	0.54207	0.965	D	0.63877	0.919	T	0.75508	-0.3293	10	0.39692	T	0.17	-13.5501	15.1562	0.72743	1.0:0.0:0.0:0.0	.	438	O75762	TRPA1_HUMAN	P	290;438	ENSP00000428151:S290P;ENSP00000262209:S438P	ENSP00000262209:S438P	S	-	1	0	TRPA1	73130527	1.000000	0.71417	1.000000	0.80357	0.633000	0.38033	4.823000	0.62694	2.038000	0.60285	0.528000	0.53228	TCC	.	.	none		0.418	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24459493	24459493	+	Silent	SNP	G	G	A	rs60865462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24459493G>A	ENST00000335125.6	+	2	357	c.231G>A	c.(229-231)caG>caA	p.Q77Q	DHRS4L2_ENST00000545240.1_Silent_p.Q77Q|DHRS4L2_ENST00000382755.4_Silent_p.Q75Q|DHRS4L2_ENST00000543805.1_5'UTR|DHRS4L2_ENST00000397071.1_Silent_p.Q77Q|DHRS4L2_ENST00000537912.1_Silent_p.Q77Q|DHRS4L2_ENST00000534993.1_5'UTR|DHRS4L2_ENST00000558753.1_Silent_p.Q77Q	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	75						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)	p.Q77Q(1)		breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		CCACGCTGCAGGGGGAGGGGC	0.692													g|||	757	0.151158	0.093	0.1354	5008	,	,		15450	0.2252		0.0885	False		,,,				2504	0.229				p.Q77Q		Atlas-SNP	.											DHRS4L2,NS,carcinoma,0,1	DHRS4L2	29	1	1	Substitution - coding silent(1)	stomach(1)	c.G231A						scavenged	.	G	,,,	319,4085	126.1+/-163.2	22,275,1905	36.0	39.0	38.0		147,,,231	0.6	0.0	14	dbSNP_129	38	653,7945	137.9+/-194.8	40,573,3686	no	coding-synonymous,utr-5,utr-5,coding-synonymous	DHRS4L2	NM_001193635.1,NM_001193636.1,NM_001193637.1,NM_198083.3	,,,	62,848,5591	AA,AG,GG		7.5948,7.2434,7.4758	,,,	49/171,,,77/233	24459493	972,12030	2202	4299	6501	SO:0001819	synonymous_variant	317749	exon2			GCTGCAGGGGGAG		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.231G>A	14.37:g.24459493G>A		Somatic	324	3	0.00925926		WXS	Illumina HiSeq	Phase_I	274	267	0.974453	NM_198083	Q3YLD4	Silent	SNP	ENST00000335125.6	37	CCDS9606.2																																																																																			G|0.911;A|0.089	0.089	strong		0.692	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
PCNXL4	64430	hgsc.bcm.edu	37	14	60581863	60581863	+	Silent	SNP	G	G	A	rs219314	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:60581863G>A	ENST00000406854.1	+	4	1595	c.1041G>A	c.(1039-1041)ccG>ccA	p.P347P	PCNXL4_ENST00000317623.4_Silent_p.P113P|PCNXL4_ENST00000406949.1_Silent_p.P113P|PCNXL4_ENST00000404681.2_Silent_p.P347P			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	347						integral component of membrane (GO:0016021)											CCAGTGGTCCGGAAAAACATT	0.383													A|||	3467	0.692292	0.4244	0.8775	5008	,	,		16929	0.7232		0.9016	False		,,,				2504	0.6759				p.P113P		Atlas-SNP	.											.	.	.	.	0			c.G339A						PASS	.	A		1858,1810		465,928,441	138.0	121.0	127.0		339	-10.8	0.0	14	dbSNP_79	127	7352,820		3309,734,43	no	coding-synonymous	C14orf135	NM_022495.5		3774,1662,484	AA,AG,GG		10.0343,49.3457,22.2128		113/939	60581863	9210,2630	1834	4086	5920	SO:0001819	synonymous_variant	64430	exon3			TGGTCCGGAAAAA	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1041G>A	14.37:g.60581863G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	248	247	0.995968	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Silent	SNP	ENST00000406854.1	37																																																																																				G|0.258;A|0.742	0.742	strong		0.383	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
POLR3D	661	hgsc.bcm.edu	37	8	22107986	22107986	+	Silent	SNP	A	A	G	rs75142930	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:22107986A>G	ENST00000397802.4	+	8	1367	c.1152A>G	c.(1150-1152)gtA>gtG	p.V384V	POLR3D_ENST00000306433.4_Silent_p.V384V			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	384					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)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)	p.V384V(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	13				Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		ACAAACTTGTATGTTCCCCTG	0.552													A|||	158	0.0315495	0.0038	0.1124	5008	,	,		19379	0.006		0.0507	False		,,,				2504	0.0184				p.V384V		Atlas-SNP	.											POLR3D,NS,adenoma,0,2	POLR3D	26	2	1	Substitution - coding silent(1)	stomach(1)	c.A1152G						PASS	.	A		52,4354	52.9+/-88.7	0,52,2151	213.0	183.0	193.0		1152	-4.8	1.0	8	dbSNP_132	193	454,8146	136.7+/-193.7	6,442,3852	no	coding-synonymous	POLR3D	NM_001722.2		6,494,6003	GG,GA,AA		5.2791,1.1802,3.8905		384/399	22107986	506,12500	2203	4300	6503	SO:0001819	synonymous_variant	661	exon9			ACTTGTATGTTCC	M17754	CCDS34858.1	8q21	2013-01-21	2003-04-01	2003-04-04	ENSG00000168495	ENSG00000168495		"""RNA polymerase subunits"""	1080	protein-coding gene	gene with protein product		187280	"""BN51 (BHK21) temperature sensitivity complementing"""	BN51T		12391170, 11279001	Standard	NM_001722		Approved	TSBN51, RPC4	uc003xbl.3	P05423	OTTHUMG00000163778	ENST00000397802.4:c.1152A>G	8.37:g.22107986A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	186	53	0.284946	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Silent	SNP	ENST00000397802.4	37	CCDS34858.1																																																																																			A|0.958;G|0.042	0.042	strong		0.552	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722	
IGDCC3	9543	hgsc.bcm.edu	37	15	65621441	65621441	+	Missense_Mutation	SNP	C	C	A	rs12907128	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65621441C>A	ENST00000327987.4	-	14	2502	c.2251G>T	c.(2251-2253)Gtg>Ttg	p.V751L	IGDCC3_ENST00000559231.1_5'Flank	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	751			V -> L (in dbSNP:rs12907128). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9922388}.		neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AGTGGCAGCACGGAGAGCTGG	0.706													C|||	3078	0.614617	0.3744	0.4841	5008	,	,		15867	0.8482		0.5974	False		,,,				2504	0.8088				p.V751L		Atlas-SNP	.											IGDCC3,NS,carcinoma,0,1	IGDCC3	82	1	0			c.G2251T						scavenged	.	C	LEU/VAL	1879,2519		420,1039,740	14.0	18.0	17.0		2251	-5.2	0.0	15	dbSNP_121	17	4960,3636		1438,2084,776	yes	missense	IGDCC3	NM_004884.3	32	1858,3123,1516	AA,AC,CC		42.2987,42.724,47.368	benign	751/815	65621441	6839,6155	2199	4298	6497	SO:0001583	missense	9543	exon14			GCAGCACGGAGAG	AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9700	protein-coding gene	gene with protein product		604184	"""putative neuronal cell adhesion molecule"""	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.2251G>T	15.37:g.65621441C>A	ENSP00000332773:p.Val751Leu	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	81	13	0.160494	NM_004884	O95215	Missense_Mutation	SNP	ENST00000327987.4	37	CCDS10205.1	1281	0.5865384615384616	174	0.35365853658536583	183	0.505524861878453	473	0.8269230769230769	451	0.5949868073878628	C	10.92	1.488150	0.26686	0.42724	0.577013	ENSG00000174498	ENST00000327987;ENST00000443278	T	0.64618	-0.11	5.69	-5.23	0.02798	.	0.954563	0.08665	N	0.911846	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12013	0.005	B	0.04013	0.001	T	0.39210	-0.9625	9	0.22706	T	0.39	-4.3374	0.4385	0.00483	0.3463:0.2056:0.1194:0.3287	rs12907128;rs17854187;rs60161490;rs12907128	751	Q8IVU1	IGDC3_HUMAN	L	751;574	ENSP00000332773:V751L	ENSP00000332773:V751L	V	-	1	0	IGDCC3	63408494	0.638000	0.27225	0.000000	0.03702	0.005000	0.04900	-0.442000	0.06871	-0.789000	0.04498	-1.181000	0.01715	GTG	C|0.461;A|0.539	0.539	strong		0.706	IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	
MAPK8IP1	9479	hgsc.bcm.edu	37	11	45924057	45924057	+	Missense_Mutation	SNP	C	C	T	rs117665789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:45924057C>T	ENST00000241014.2	+	5	909	c.739C>T	c.(739-741)Cct>Tct	p.P247S	MAPK8IP1_ENST00000395629.2_Missense_Mutation_p.P237S	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	247	JNK-binding domain (JBD).				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		CCAGATGGCACCTCCGGGTGG	0.706													C|||	16	0.00319489	0.0	0.0029	5008	,	,		13357	0.0		0.0109	False		,,,				2504	0.0031				p.P247S		Atlas-SNP	.											.	MAPK8IP1	51	.	0			c.C739T						PASS	.	C	SER/PRO	7,4359		0,7,2176	11.0	14.0	13.0		739	4.5	0.9	11	dbSNP_132	13	88,8478		0,88,4195	yes	missense	MAPK8IP1	NM_005456.3	74	0,95,6371	TT,TC,CC		1.0273,0.1603,0.7346	possibly-damaging	247/712	45924057	95,12837	2183	4283	6466	SO:0001583	missense	9479	exon5			ATGGCACCTCCGG		CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.739C>T	11.37:g.45924057C>T	ENSP00000241014:p.Pro247Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_005456	D3DQP4|O43407	Missense_Mutation	SNP	ENST00000241014.2	37	CCDS7916.1	10	0.004578754578754579	0	0.0	0	0.0	2	0.0034965034965034965	8	0.010554089709762533	C	13.85	2.358998	0.41801	0.001603	0.010273	ENSG00000121653	ENST00000241014;ENST00000395629	T;T	0.36699	1.24;1.25	4.51	4.51	0.55191	.	0.065445	0.64402	D	0.000011	T	0.18551	0.0445	N	0.24115	0.695	0.45541	D	0.998496	P	0.43750	0.816	B	0.37267	0.245	T	0.03514	-1.1029	10	0.27785	T	0.31	-3.6985	17.7712	0.88493	0.0:1.0:0.0:0.0	.	247	Q9UQF2	JIP1_HUMAN	S	247;237	ENSP00000241014:P247S;ENSP00000378991:P237S	ENSP00000241014:P247S	P	+	1	0	MAPK8IP1	45880633	0.428000	0.25522	0.877000	0.34402	0.627000	0.37826	3.856000	0.55964	2.504000	0.84457	0.561000	0.74099	CCT	C|0.993;T|0.007	0.007	strong		0.706	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456	
ZKSCAN5	23660	hgsc.bcm.edu	37	7	99129744	99129744	+	Missense_Mutation	SNP	G	G	C	rs150395462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99129744G>C	ENST00000394170.2	+	7	2643	c.2392G>C	c.(2392-2394)Gag>Cag	p.E798Q	ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.E798Q|ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.E798Q	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	798					regulation of transcription, DNA-templated (GO:0006355)|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(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CCATACTGGTGAGAAACCTTT	0.398													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20675	0.0		0.003	False		,,,				2504	0.0				p.E798Q		Atlas-SNP	.											.	ZKSCAN5	63	.	0			c.G2392C						PASS	.	G	GLN/GLU,GLN/GLU	5,4401	11.4+/-27.6	0,5,2198	85.0	91.0	89.0		2392,2392	5.0	1.0	7	dbSNP_134	89	61,8539	38.8+/-94.9	1,59,4240	yes	missense,missense	ZKSCAN5	NM_014569.3,NM_145102.2	29,29	1,64,6438	CC,CG,GG		0.7093,0.1135,0.5075	probably-damaging,probably-damaging	798/840,798/840	99129744	66,12940	2203	4300	6503	SO:0001583	missense	23660	exon7			ACTGGTGAGAAAC	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12867	protein-coding gene	gene with protein product		611272	"""zinc finger protein homologous to Zfp95 in mouse"", ""zinc finger protein 95 homolog (mouse)"""	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.2392G>C	7.37:g.99129744G>C	ENSP00000377725:p.Glu798Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_145102	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.411517	0.83340	0.001135	0.007093	ENSG00000196652	ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.25912	1.77;1.77;1.77	5.03	5.03	0.67393	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.116325	0.38720	N	0.001586	T	0.42177	0.1191	M	0.70595	2.14	0.50171	D	0.99985	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.45556	-0.9253	10	0.72032	D	0.01	.	16.2692	0.82607	0.0:0.0:1.0:0.0	.	798;798	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	Q	798	ENSP00000322872:E798Q;ENSP00000392104:E798Q;ENSP00000377725:E798Q	ENSP00000322872:E798Q	E	+	1	0	ZKSCAN5	98967680	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.485000	0.66850	2.782000	0.95742	0.655000	0.94253	GAG	G|0.996;C|0.004	0.004	strong		0.398	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569	
REPS1	85021	hgsc.bcm.edu	37	6	139266402	139266402	+	Silent	SNP	G	G	A	rs1569238	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:139266402G>A	ENST00000450536.2	-	4	1156	c.582C>T	c.(580-582)ctC>ctT	p.L194L	REPS1_ENST00000531675.1_5'Flank|REPS1_ENST00000258062.5_Silent_p.L194L|REPS1_ENST00000367663.4_Silent_p.L194L|REPS1_ENST00000409812.2_Silent_p.L194L|REPS1_ENST00000415951.2_Silent_p.L194L			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	194					receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		CAGGTCCCGCGAGAGGCCTCT	0.527													A|||	683	0.136382	0.2784	0.036	5008	,	,		15158	0.2183		0.0209	False		,,,				2504	0.0501				p.L194L		Atlas-SNP	.											REPS1,NS,carcinoma,0,1	REPS1	58	1	0			c.C582T						scavenged	.	A	,	907,3499	733.6+/-410.5	79,749,1375	56.0	54.0	54.0		582,582	2.1	1.0	6	dbSNP_88	54	174,8426	806.8+/-407.2	0,174,4126	no	coding-synonymous,coding-synonymous	REPS1	NM_001128617.1,NM_031922.3	,	79,923,5501	AA,AG,GG		2.0233,20.5856,8.3115	,	194/770,194/796	139266402	1081,11925	2203	4300	6503	SO:0001819	synonymous_variant	85021	exon4			TCCCGCGAGAGGC		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"""EF-hand domain containing"""	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.582C>T	6.37:g.139266402G>A		Somatic	110	3	0.0272727		WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_001128617	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Silent	SNP	ENST00000450536.2	37																																																																																				G|0.897;A|0.103	0.103	strong		0.527	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3		
SEPT14	346288	hgsc.bcm.edu	37	7	55902230	55902230	+	Missense_Mutation	SNP	T	T	C	rs146004414	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	136	0	0		WXS	Illumina HiSeq	Phase_I	164	67	0.408537	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	
NCAPD2	9918	hgsc.bcm.edu	37	12	6635274	6635274	+	Missense_Mutation	SNP	G	G	A	rs10849482	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6635274G>A	ENST00000315579.5	+	19	3188	c.2389G>A	c.(2389-2391)Gtg>Atg	p.V797M	NCAPD2_ENST00000545962.1_Missense_Mutation_p.V752M|NCAPD2_ENST00000542492.1_3'UTR	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	797			V -> M (in dbSNP:rs10849482).		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						AGACACACTGGTGAGCATAGG	0.517													G|||	540	0.107827	0.0242	0.1354	5008	,	,		20967	0.0089		0.2107	False		,,,				2504	0.1973				p.V797M		Atlas-SNP	.											.	NCAPD2	99	.	0			c.G2389A						PASS	.	G	MET/VAL	249,4157	143.8+/-178.8	9,231,1963	87.0	83.0	85.0		2389	5.6	1.0	12	dbSNP_120	85	2030,6570	354.8+/-329.6	236,1558,2506	yes	missense	NCAPD2	NM_014865.3	21	245,1789,4469	AA,AG,GG		23.6047,5.6514,17.5227	possibly-damaging	797/1402	6635274	2279,10727	2203	4300	6503	SO:0001583	missense	9918	exon19			ACACTGGTGAGCA	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"""chromosome condensation related SMC associated protein 1"""	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.2389G>A	12.37:g.6635274G>A	ENSP00000325017:p.Val797Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	37	CCDS8548.1	250	0.11446886446886446	20	0.04065040650406504	64	0.17679558011049723	5	0.008741258741258742	161	0.21240105540897097	G	20.6	4.010233	0.75046	0.056514	0.236047	ENSG00000010292	ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602	T;T;T	0.56444	0.46;0.46;0.46	5.62	5.62	0.85841	Armadillo-type fold (1);	0.106954	0.64402	D	0.000007	T	0.00039	0.0001	L	0.55743	1.74	0.30658	P	0.754738	P;P;P	0.51653	0.927;0.801;0.947	P;B;P	0.51135	0.66;0.387;0.536	T	0.01988	-1.1234	9	0.46703	T	0.11	-26.7934	13.8923	0.63747	0.0728:0.0:0.9272:0.0	rs10849482;rs17725920;rs60278952;rs10849482	752;758;797	F5GZJ1;B3KY03;Q15021	.;.;CND1_HUMAN	M	797;669;752;669	ENSP00000325017:V797M;ENSP00000371895:V669M;ENSP00000444417:V752M	ENSP00000325017:V797M	V	+	1	0	NCAPD2	6505535	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.367000	0.44213	2.653000	0.90120	0.655000	0.94253	GTG	G|0.854;A|0.146	0.146	strong		0.517	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
TMEM176A	55365	hgsc.bcm.edu	37	7	150501455	150501455	+	Missense_Mutation	SNP	G	G	T	rs10378	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:150501455G>T	ENST00000484928.1	+	6	1142	c.561G>T	c.(559-561)ttG>ttT	p.L187F	TMEM176A_ENST00000004103.3_Missense_Mutation_p.L187F|TMEM176A_ENST00000461345.1_Missense_Mutation_p.L128F			Q96HP8	T176A_HUMAN	transmembrane protein 176A	187			L -> F (in dbSNP:rs10378).		negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				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)		CCCAGGCCTTGTTCAGAACCC	0.557													G|||	640	0.127796	0.1694	0.1354	5008	,	,		20904	0.0397		0.172	False		,,,				2504	0.1115				p.L187F		Atlas-SNP	.											.	TMEM176A	35	.	0			c.G561T						PASS	.	G	PHE/LEU	721,3685	298.1+/-285.1	63,595,1545	141.0	116.0	125.0		561	2.7	0.2	7	dbSNP_52	125	1471,7129	280.2+/-294.4	137,1197,2966	yes	missense	TMEM176A	NM_018487.2	22	200,1792,4511	TT,TG,GG		17.1047,16.364,16.8538	probably-damaging	187/236	150501455	2192,10814	2203	4300	6503	SO:0001583	missense	55365	exon6			GGCCTTGTTCAGA	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.561G>T	7.37:g.150501455G>T	ENSP00000417626:p.Leu187Phe	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_018487	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	37	CCDS5909.1	291	0.13324175824175824	96	0.1951219512195122	60	0.16574585635359115	20	0.03496503496503497	115	0.1517150395778364	G	7.483	0.649161	0.14516	0.16364	0.171047	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536	T;T;T;T	0.03124	4.04;4.04;4.04;4.04	4.51	2.65	0.31530	.	0.126159	0.32231	U	0.006381	T	0.00012	0.0000	M	0.73962	2.25	0.40538	P	0.019001000000000046	D	0.89917	1.0	D	0.91635	0.999	T	0.09143	-1.0688	9	0.72032	D	0.01	-13.187	8.4204	0.32696	0.0912:0.0:0.7562:0.1526	rs10378;rs3177203;rs3184409;rs11537895;rs17295692;rs17350117;rs10378	187	Q96HP8	T176A_HUMAN	F	187;187;128;139	ENSP00000417626:L187F;ENSP00000004103:L187F;ENSP00000420818:L128F;ENSP00000417834:L139F	ENSP00000004103:L187F	L	+	3	2	TMEM176A	150132388	0.192000	0.23301	0.154000	0.22540	0.002000	0.02628	0.701000	0.25616	0.110000	0.17919	-2.086000	0.00376	TTG	G|0.847;T|0.153	0.153	strong		0.557	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	
FAT3	120114	hgsc.bcm.edu	37	11	92600266	92600266	+	Silent	SNP	G	G	A	rs75649640	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:92600266G>A	ENST00000298047.6	+	21	12035	c.12018G>A	c.(12016-12018)gcG>gcA	p.A4006A	FAT3_ENST00000525166.1_Silent_p.A3856A|FAT3_ENST00000533797.1_Silent_p.A341A|FAT3_ENST00000409404.2_Silent_p.A4006A			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4006	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)				GCAGCTTCGCGGAGGTGGTGG	0.667										TCGA Ovarian(4;0.039)			G|||	329	0.0656949	0.0492	0.0418	5008	,	,		17013	0.0139		0.0716	False		,,,				2504	0.1524				p.A4006A		Atlas-SNP	.											FAT3_ENST00000409404,colon,carcinoma,0,7	FAT3	1822	7	0			c.G12018A						PASS	.	G		175,3883		6,163,1860	10.0	12.0	11.0		12018	-6.6	0.9	11	dbSNP_132	11	630,7706		26,578,3564	no	coding-synonymous	FAT3	NM_001008781.2		32,741,5424	AA,AG,GG		7.5576,4.3125,6.4951		4006/4558	92600266	805,11589	2029	4168	6197	SO:0001819	synonymous_variant	120114	exon21			CTTCGCGGAGGTG	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.12018G>A	11.37:g.92600266G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	167	136	0.814371	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				A|0.048;G|0.952	0.048	strong		0.667	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
FBN3	84467	hgsc.bcm.edu	37	19	8160334	8160334	+	Missense_Mutation	SNP	G	G	A	rs12608849	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	222	0	0		WXS	Illumina HiSeq	Phase_I	166	81	0.487952	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	
FAM25A	643161	hgsc.bcm.edu	37	10	88782100	88782100	+	Missense_Mutation	SNP	G	G	C	rs7079587	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:88782100G>C	ENST00000343959.4	+	2	122	c.103G>C	c.(103-105)Gtg>Ctg	p.V35L	RP11-96C23.14_ENST00000444180.3_RNA	NM_001146157.2	NP_001139629.1	B3EWG3	FM25A_HUMAN	family with sequence similarity 25, member A	35			V -> L (in dbSNP:rs7079587).							stomach(1)	1						GGTGAAGGAGGTGGTGGGACA	0.622													.|||	189	0.0377396	0.0855	0.036	5008	,	,		20449	0.0		0.0388	False		,,,				2504	0.0123				p.V35L		Atlas-SNP	.											.	FAM25A	4	.	0			c.G103C						PASS	.	G	LEU/VAL	100,1284		2,96,594	42.0	39.0	40.0		103	3.9	1.0	10	dbSNP_116	40	117,3065		3,111,1477	no	missense	FAM25A	NM_001146157.2	32	5,207,2071	CC,CG,GG		3.6769,7.2254,4.7525	probably-damaging	35/90	88782100	217,4349	692	1591	2283	SO:0001583	missense	643161	exon2			AAGGAGGTGGTGG		CCDS44451.1	10q23.2	2008-08-13			ENSG00000188100	ENSG00000188100			23436	protein-coding gene	gene with protein product							Standard	NM_001146157		Approved	bA96C23.5	uc010qmo.2	B3EWG3	OTTHUMG00000018664	ENST00000343959.4:c.103G>C	10.37:g.88782100G>C	ENSP00000342790:p.Val35Leu	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	11	6	0.545455	NM_001146157	B2RV02|Q5VTM1	Missense_Mutation	SNP	ENST00000343959.4	37	CCDS44451.1	91|91	0.041666666666666664|0.041666666666666664	48|48	0.0975609756097561|0.0975609756097561	15|15	0.04143646408839779|0.04143646408839779	2|2	0.0034965034965034965|0.0034965034965034965	26|26	0.03430079155672823|0.03430079155672823	G|G	12.56|12.56	1.974538|1.974538	0.34848|0.34848	0.072254|0.072254	0.036769|0.036769	ENSG00000188100|ENSG00000188100	ENST00000343959|ENST00000444180	.|.	.|.	.|.	3.93|3.93	3.93|3.93	0.45458|0.45458	.|.	.|0.000000	.|0.49305	.|D	.|0.000156	T|T	0.03390|0.03390	0.0098|0.0098	.|.	.|.	.|.	0.32906|0.32906	D|D	0.51392|0.51392	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49021|0.49021	-0.8982|-0.8982	4|6	.|0.59425	.|D	.|0.04	-18.7332|-18.7332	13.1877|13.1877	0.59691|0.59691	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs7079587;rs52814476;rs7079587|rs7079587;rs52814476;rs7079587	.|.	.|.	.|.	A|L	41|35	.|.	.|ENSP00000417034:V35L	G|V	+|+	2|1	0|0	FAM25A|FAM25A	88772080|88772080	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.148000|0.148000	0.21650|0.21650	4.172000|4.172000	0.58243|0.58243	2.216000|2.216000	0.71823|0.71823	0.478000|0.478000	0.44815|0.44815	GGT|GTG	G|0.964;C|0.036	0.036	strong		0.622	FAM25A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049182.2		
ZNF445	353274	hgsc.bcm.edu	37	3	44489880	44489880	+	Missense_Mutation	SNP	T	T	C	rs11710965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:44489880T>C	ENST00000396077.2	-	8	1630	c.1283A>G	c.(1282-1284)tAt>tGt	p.Y428C	ZNF445_ENST00000425708.2_Missense_Mutation_p.Y428C	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	428			Y -> C (in dbSNP:rs11710965).		transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|skin(3)	31				KIRC - Kidney renal clear cell carcinoma(197;0.0514)|Kidney(197;0.0646)		CTTGTAGTCATAGTGGTGTGA	0.418													T|||	243	0.0485224	0.0121	0.0648	5008	,	,		22516	0.0		0.171	False		,,,				2504	0.0102				p.Y428C		Atlas-SNP	.											.	ZNF445	91	.	0			c.A1283G						PASS	.	T	CYS/TYR	165,4241	109.5+/-147.8	2,161,2040	123.0	124.0	124.0		1283	-3.7	0.0	3	dbSNP_120	124	1322,7278	260.6+/-283.4	98,1126,3076	yes	missense	ZNF445	NM_181489.5	194	100,1287,5116	CC,CT,TT		15.3721,3.7449,11.4332	benign	428/1032	44489880	1487,11519	2203	4300	6503	SO:0001583	missense	353274	exon8			TAGTCATAGTGGT	AY262260	CCDS2713.1	3p21.32	2013-01-09	2003-10-07		ENSG00000185219	ENSG00000185219		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21018	protein-coding gene	gene with protein product			"""zinc finger protein 168"""	ZNF168		7814019	Standard	NM_181489		Approved	ZKSCAN15, ZSCAN47	uc003cnf.2	P59923	OTTHUMG00000133042	ENST00000396077.2:c.1283A>G	3.37:g.44489880T>C	ENSP00000379387:p.Tyr428Cys	Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	231	106	0.458874	NM_181489	Q3MJD1	Missense_Mutation	SNP	ENST00000396077.2	37	CCDS2713.1	152	0.0695970695970696	5	0.01016260162601626	18	0.049723756906077346	0	0.0	129	0.17018469656992086	T	11.93	1.786117	0.31593	0.037449	0.153721	ENSG00000185219	ENST00000425708;ENST00000396077	T;T	0.05717	3.4;3.4	3.81	-3.72	0.04411	.	0.863253	0.09860	N	0.746305	T	0.00039	0.0001	M	0.81942	2.565	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.06405	0.002;0.002	T	0.32798	-0.9893	9	0.52906	T	0.07	.	5.022	0.14365	0.1326:0.329:0.0:0.5384	rs11710965;rs52799416;rs56621940;rs59518590;rs11710965	416;428	B7ZKX2;P59923	.;ZN445_HUMAN	C	428	ENSP00000413073:Y428C;ENSP00000379387:Y428C	ENSP00000379387:Y428C	Y	-	2	0	ZNF445	44464884	0.398000	0.25279	0.008000	0.14137	0.631000	0.37964	0.903000	0.28475	-0.657000	0.05373	-0.468000	0.05107	TAT	T|0.903;C|0.097	0.097	strong		0.418	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256647.2	NM_181489	
USP19	10869	hgsc.bcm.edu	37	3	49156473	49156473	+	Missense_Mutation	SNP	C	C	G	rs11552724	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49156473C>G	ENST00000398888.2	-	2	424	c.106G>C	c.(106-108)Gat>Cat	p.D36H	USP19_ENST00000488993.1_5'UTR|USP19_ENST00000398898.2_Missense_Mutation_p.D36H|USP19_ENST00000453664.1_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	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	192	0	0		WXS	Illumina HiSeq	Phase_I	187	79	0.42246	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	
MFI2	4241	hgsc.bcm.edu	37	3	196742290	196742290	+	Silent	SNP	T	T	C	rs9855410	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:196742290T>C	ENST00000296350.5	-	9	1292	c.1179A>G	c.(1177-1179)ccA>ccG	p.P393P		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	393	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-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;0.00536)		ACTGGATCTCTGGCTTGAGCC	0.672													t|||	1389	0.277356	0.3956	0.1931	5008	,	,		17562	0.2827		0.2217	False		,,,				2504	0.229				p.P393P		Atlas-SNP	.											.	MFI2	88	.	0			c.A1179G						PASS	.	C		1625,2775		299,1027,874	33.0	27.0	29.0		1179	-11.4	0.0	3	dbSNP_119	29	1892,6706		218,1456,2625	no	coding-synonymous	MFI2	NM_005929.5		517,2483,3499	CC,CT,TT		22.0051,36.9318,27.058		393/739	196742290	3517,9481	2200	4299	6499	SO:0001819	synonymous_variant	4241	exon9			GATCTCTGGCTTG		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.1179A>G	3.37:g.196742290T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	140	65	0.464286	NM_005929	Q9BQE2	Silent	SNP	ENST00000296350.5	37	CCDS3325.1																																																																																			T|0.712;C|0.288	0.288	strong		0.672	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
KLHL33	123103	hgsc.bcm.edu	37	14	20897676	20897676	+	Missense_Mutation	SNP	T	T	C	rs1953225	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20897676T>C	ENST00000344581.4	-	3	1256	c.1034A>G	c.(1033-1035)gAg>gGg	p.E345G		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	345			E -> G (in dbSNP:rs1953225).									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)		GACATTGAGCTCAGGGTTGTA	0.498													T|||	1298	0.259185	0.3812	0.134	5008	,	,		20948	0.2718		0.2097	False		,,,				2504	0.2209				p.E345G		Atlas-SNP	.											.	KLHL33	37	.	0			c.A1034G						PASS	.	T	GLY/GLU	448,936		84,280,328	187.0	163.0	170.0		1034	5.3	1.0	14	dbSNP_92	170	605,2577		57,491,1043	yes	missense	KLHL33	NM_001109997.2	98	141,771,1371	CC,CT,TT		19.0132,32.3699,23.0618	probably-damaging	345/534	20897676	1053,3513	692	1591	2283	SO:0001583	missense	123103	exon3			TTGAGCTCAGGGT		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.1034A>G	14.37:g.20897676T>C	ENSP00000341549:p.Glu345Gly	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	37	CCDS53882.1	526	0.24084249084249085	173	0.3516260162601626	50	0.13812154696132597	153	0.2674825174825175	150	0.19788918205804748	T	8.186	0.795008	0.16327	0.323699	0.190132	ENSG00000185271	ENST00000344581	T	0.79554	-1.28	5.34	5.34	0.76211	Kelch-type beta propeller (1);	0.269175	0.36034	N	0.002825	T	0.00012	0.0000	L	0.39085	1.19	0.80722	P	0.0	B	0.16603	0.018	B	0.18871	0.023	T	0.05115	-1.0905	9	0.56958	D	0.05	.	12.9404	0.58340	0.0:0.0:0.0:1.0	rs1953225;rs17242641;rs57704167;rs1953225	345	A6NCF5	KLH33_HUMAN	G	345	ENSP00000341549:E345G	ENSP00000341549:E345G	E	-	2	0	KLHL33	19967516	0.003000	0.15002	0.986000	0.45419	0.965000	0.64279	1.324000	0.33712	2.242000	0.73789	0.533000	0.62120	GAG	T|0.747;C|0.253	0.253	strong		0.498	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
IGDCC4	57722	hgsc.bcm.edu	37	15	65676617	65676617	+	Silent	SNP	T	T	C	rs2292933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65676617T>C	ENST00000352385.2	-	20	3692	c.3483A>G	c.(3481-3483)ccA>ccG	p.P1161P	IGDCC4_ENST00000558048.1_5'UTR	NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	1161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						CAGGAGCCTCTGGAGGCAGGG	0.627													C|||	2605	0.520168	0.5976	0.5994	5008	,	,		19120	0.6687		0.3926	False		,,,				2504	0.3374				p.P1161P		Atlas-SNP	.											IGDCC4,caecum,carcinoma,-1,1	IGDCC4	95	1	0			c.A3483G						PASS	.	C		2490,1912	520.4+/-370.3	709,1072,420	34.0	37.0	36.0		3483	-2.3	0.0	15	dbSNP_100	36	3477,5121	611.3+/-395.8	690,2097,1512	no	coding-synonymous	IGDCC4	NM_020962.1		1399,3169,1932	CC,CT,TT		40.4396,43.4348,45.9		1161/1251	65676617	5967,7033	2201	4299	6500	SO:0001819	synonymous_variant	57722	exon20			AGCCTCTGGAGGC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.3483A>G	15.37:g.65676617T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	61	45	0.737705	NM_020962	Q9HCE4	Silent	SNP	ENST00000352385.2	37	CCDS10206.1																																																																																			T|0.516;C|0.484	0.484	strong		0.627	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
ANKRD13A	88455	hgsc.bcm.edu	37	12	110474070	110474070	+	Missense_Mutation	SNP	T	T	C	rs2287174	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:110474070T>C	ENST00000261739.4	+	14	1680	c.1514T>C	c.(1513-1515)cTt>cCt	p.L505P	C12orf76_ENST00000546651.2_Intron	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	505			L -> P (in dbSNP:rs2287174).			endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						TGCCAGGAACTTTCAGGACCA	0.453													T|||	415	0.0828674	0.1543	0.0389	5008	,	,		21033	0.119		0.0378	False		,,,				2504	0.0266				p.L505P		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.T1514C						PASS	.	T	PRO/LEU	676,3730	284.3+/-277.5	45,586,1572	189.0	175.0	180.0		1514	3.2	0.9	12	dbSNP_100	180	285,8315	105.2+/-166.2	6,273,4021	yes	missense	ANKRD13A	NM_033121.1	98	51,859,5593	CC,CT,TT		3.314,15.3427,7.3889	benign	505/591	110474070	961,12045	2203	4300	6503	SO:0001583	missense	88455	exon14			AGGAACTTTCAGG	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"""Ankyrin repeat domain containing"""	21268	protein-coding gene	gene with protein product		615123	"""ankyrin repeat domain 13"""	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.1514T>C	12.37:g.110474070T>C	ENSP00000261739:p.Leu505Pro	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	215	120	0.55814	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	37	CCDS9140.1	155	0.07097069597069597	65	0.13211382113821138	16	0.04419889502762431	43	0.07517482517482517	31	0.040897097625329816	T	10.08	1.251222	0.22880	0.153427	0.03314	ENSG00000076513	ENST00000261738;ENST00000261739;ENST00000553251;ENST00000549826;ENST00000551491	T	0.57752	0.38	5.65	3.2	0.36748	.	0.979102	0.08412	N	0.949650	T	0.00271	0.0008	L	0.49778	1.585	0.22918	N	0.998563	B;B;B	0.30281	0.105;0.275;0.229	B;B;B	0.23574	0.029;0.04;0.047	T	0.02070	-1.1219	10	0.33141	T	0.24	-0.6484	5.3529	0.16045	0.0:0.0902:0.179:0.7308	rs2287174;rs11541842;rs52792823;rs2287174	504;251;505	B4DYP5;E9PGV0;Q8IZ07	.;.;AN13A_HUMAN	P	251;505;143;143;32	ENSP00000261739:L505P	ENSP00000261738:L251P	L	+	2	0	ANKRD13A	108958453	0.306000	0.24490	0.879000	0.34478	0.454000	0.32378	0.874000	0.28065	2.149000	0.67028	0.529000	0.55759	CTT	T|0.923;C|0.077	0.077	strong		0.453	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121	
MICA	100507436	hgsc.bcm.edu	37	6	31379752	31379752	+	Silent	SNP	C	C	T	rs17206680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31379752C>T	ENST00000449934.2	+	4	696	c.642C>T	c.(640-642)agC>agT	p.S214S	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)				TCACCCGCAGCGAGGCCTCAG	0.582													c|||	149	0.0297524	0.0106	0.013	5008	,	,		20941	0.0536		0.0477	False		,,,				2504	0.0245				p.S214S		Atlas-SNP	.											.	MICA	21	.	0			c.C642T						PASS	.	T		9,1375		0,9,683	32.0	36.0	35.0		642	-2.0	0.0	6	dbSNP_123	35	128,3054		3,122,1466	no	coding-synonymous	MICA	NM_001177519.1		3,131,2149	TT,TC,CC		4.0226,0.6503,3.0004		214/333	31379752	137,4429	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon4			CCGCAGCGAGGCC	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.642C>T	6.37:g.31379752C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.967;T|0.033	0.033	strong		0.582	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
PCNT	5116	hgsc.bcm.edu	37	21	47855876	47855876	+	Silent	SNP	A	A	G	rs17371795	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:47855876A>G	ENST00000359568.5	+	39	8918	c.8811A>G	c.(8809-8811)acA>acG	p.T2937T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2937					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TTCAGCAGACAGTGAGAGACC	0.567													A|||	736	0.146965	0.0666	0.1801	5008	,	,		17570	0.1994		0.1252	False		,,,				2504	0.2004				p.T2937T		Atlas-SNP	.											.	PCNT	283	.	0			c.A8811G						PASS	.	A		280,4126	155.5+/-188.7	11,258,1934	91.0	96.0	95.0		8811	-6.5	0.0	21	dbSNP_123	95	1056,7544	223.0+/-259.9	63,930,3307	no	coding-synonymous	PCNT	NM_006031.5		74,1188,5241	GG,GA,AA		12.2791,6.355,10.2722		2937/3337	47855876	1336,11670	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon39			GCAGACAGTGAGA	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.8811A>G	21.37:g.47855876A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	130	78	0.6	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			A|0.881;G|0.119	0.119	strong		0.567	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
RASSF4	83937	hgsc.bcm.edu	37	10	45480313	45480313	+	Missense_Mutation	SNP	C	C	T	rs35521977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:45480313C>T	ENST00000374417.2	+	5	468	c.334C>T	c.(334-336)Cgc>Tgc	p.R112C	RASSF4_ENST00000472561.1_3'UTR|RASSF4_ENST00000340258.5_Silent_p.D142D|RASSF4_ENST00000334940.6_Silent_p.D151D			Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	0	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						CCAAGAGCGACGCCAGTTGCA	0.642													.|||	28	0.00559105	0.0	0.0072	5008	,	,		17923	0.001		0.0209	False		,,,				2504	0.001				p.D142D		Atlas-SNP	.											.	RASSF4	33	.	0			c.C426T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	80.0	98.0	92.0		426	-2.9	0.0	10	dbSNP_126	92	186,8414	84.2+/-146.7	2,182,4116	no	coding-synonymous	RASSF4	NM_032023.3		2,192,6309	TT,TC,CC		2.1628,0.227,1.507		142/322	45480313	196,12810	2203	4300	6503	SO:0001583	missense	83937	exon6			GAGCGACGCCAGT	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000374417.2:c.334C>T	10.37:g.45480313C>T	ENSP00000363538:p.Arg112Cys	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	160	49	0.30625	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000374417.2	37		20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	C	15.83	2.947848	0.53186	0.00227	0.021628	ENSG00000107551	ENST00000374417	T	0.32272	1.46	5.82	-2.88	0.05682	.	.	.	.	.	T	0.16727	0.0402	.	.	.	0.27314	N	0.957236	.	.	.	.	.	.	T	0.31558	-0.9939	6	0.41790	T	0.15	-33.1761	11.8796	0.52566	0.0:0.3216:0.0:0.6784	rs35521977	.	.	.	C	112	ENSP00000363538:R112C	ENSP00000363538:R112C	R	+	1	0	RASSF4	44800319	0.014000	0.17966	0.047000	0.18901	0.264000	0.26372	-1.171000	0.03115	-0.807000	0.04393	-0.742000	0.03525	CGC	C|0.987;T|0.013	0.013	strong		0.642	RASSF4-202	KNOWN	basic	protein_coding	protein_coding		NM_032023	
RFTN1	23180	hgsc.bcm.edu	37	3	16419238	16419238	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:16419238C>G	ENST00000334133.4	-	5	1085	c.813G>C	c.(811-813)gaG>gaC	p.E271D	RFTN1_ENST00000432519.1_Missense_Mutation_p.E235D	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	271					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						CTGAGAGTGGCTCTTCATGCA	0.512																																					p.E271D		Atlas-SNP	.											.	RFTN1	79	.	0			c.G813C						PASS	.						64.0	68.0	67.0					3																	16419238		2203	4300	6503	SO:0001583	missense	23180	exon5			GAGTGGCTCTTCA	D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"""raft-linking protein"""					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.813G>C	3.37:g.16419238C>G	ENSP00000334153:p.Glu271Asp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	135	37	0.274074	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	37	CCDS33712.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.443891	0.43429	.	.	ENSG00000131378	ENST00000432519;ENST00000334133;ENST00000451036	T;T;T	0.49139	1.5;1.5;0.79	4.67	-0.787	0.10943	.	0.907323	0.09628	N	0.776624	T	0.33527	0.0866	L	0.36672	1.1	0.21290	N	0.999731	B;B	0.18461	0.028;0.028	B;B	0.16722	0.016;0.016	T	0.27971	-1.0058	10	0.44086	T	0.13	-34.4945	5.6878	0.17813	0.0:0.4135:0.1371:0.4494	.	235;271	G3XAJ6;Q14699	.;RFTN1_HUMAN	D	235;271;271	ENSP00000403926:E235D;ENSP00000334153:E271D;ENSP00000403997:E271D	ENSP00000334153:E271D	E	-	3	2	RFTN1	16394242	0.002000	0.14202	0.103000	0.21229	0.791000	0.44710	-0.043000	0.12043	-0.073000	0.12842	0.561000	0.74099	GAG	.	.	none		0.512	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150	
CCDC79	283847	hgsc.bcm.edu	37	16	66792714	66792714	+	Missense_Mutation	SNP	T	T	C	rs363156	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:66792714T>C	ENST00000558713.2	-	17	2030	c.1958A>G	c.(1957-1959)cAa>cGa	p.Q653R	CCDC79_ENST00000432602.1_Missense_Mutation_p.Q606R|CCDC79_ENST00000415744.1_3'UTR|CCDC79_ENST00000433574.1_3'UTR|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	79	0	0		WXS	Illumina HiSeq	Phase_I	56	5	0.0892857	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		
RADIL	55698	hgsc.bcm.edu	37	7	4876057	4876057	+	Missense_Mutation	SNP	C	C	T	rs3763384	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:4876057C>T	ENST00000399583.3	-	3	902	c.715G>A	c.(715-717)Gac>Aac	p.D239N	RADIL_ENST00000538469.1_5'UTR|RADIL_ENST00000536091.1_Missense_Mutation_p.D239N	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	239			D -> N (in dbSNP:rs3763384). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:19690332}.		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)		CGCATGGCGTCGGGGCCGGGC	0.706													C|||	1257	0.250998	0.0401	0.2853	5008	,	,		13192	0.3264		0.2873	False		,,,				2504	0.3967				p.D239N		Atlas-SNP	.											.	RADIL	110	.	0			c.G715A						PASS	.	C	ASN/ASP	305,3815		19,267,1774	13.0	20.0	18.0		715	4.8	0.1	7	dbSNP_107	18	2586,5772		412,1762,2005	yes	missense	RADIL	NM_018059.4	23	431,2029,3779	TT,TC,CC		30.9404,7.4029,23.1688	benign	239/1076	4876057	2891,9587	2060	4179	6239	SO:0001583	missense	55698	exon3			TGGCGTCGGGGCC	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.715G>A	7.37:g.4876057C>T	ENSP00000382492:p.Asp239Asn	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	524	0.23992673992673993	22	0.044715447154471545	94	0.2596685082872928	195	0.3409090909090909	213	0.28100263852242746	C	10.16	1.274597	0.23307	0.074029	0.309404	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091	T;T	0.24538	3.27;1.85	4.85	4.85	0.62838	.	0.607882	0.16897	N	0.195056	T	0.00012	0.0000	L	0.35414	1.06	0.80722	P	0.0	P	0.39782	0.688	B	0.25291	0.059	T	0.45411	-0.9263	9	0.14252	T	0.57	-25.6462	10.7848	0.46398	0.0:0.9079:0.0:0.0921	rs3763384;rs58768759;rs3763384	239	Q96JH8	RADIL_HUMAN	N	239;213;239	ENSP00000382492:D239N;ENSP00000442533:D239N	ENSP00000320946:D213N	D	-	1	0	RADIL	4842583	0.018000	0.18449	0.055000	0.19348	0.004000	0.04260	0.996000	0.29719	2.243000	0.73865	0.462000	0.41574	GAC	C|0.745;T|0.255	0.255	strong		0.706	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
FURIN	5045	hgsc.bcm.edu	37	15	91424029	91424029	+	Silent	SNP	C	C	T	rs142489043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:91424029C>T	ENST00000268171.3	+	14	1944	c.1665C>T	c.(1663-1665)agC>agT	p.S555S		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	555					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			AAAACACCAGCGAAGCCAACA	0.557													C|||	4	0.000798722	0.0	0.0	5008	,	,		19315	0.0		0.004	False		,,,				2504	0.0				p.S555S		Atlas-SNP	.											.	FURIN	85	.	0			c.C1665T						PASS	.	C		0,4396		0,0,2198	85.0	83.0	84.0		1665	-7.6	0.8	15	dbSNP_134	84	36,8560	25.1+/-72.6	0,36,4262	no	coding-synonymous	FURIN	NM_002569.2		0,36,6460	TT,TC,CC		0.4188,0.0,0.2771		555/795	91424029	36,12956	2198	4298	6496	SO:0001819	synonymous_variant	5045	exon14			CACCAGCGAAGCC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.1665C>T	15.37:g.91424029C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	143	30	0.20979	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	37	CCDS10364.1																																																																																			C|0.997;T|0.003	0.003	strong		0.557	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
KCNT1	57582	hgsc.bcm.edu	37	9	138662273	138662273	+	Silent	SNP	G	G	A	rs17038714	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:138662273G>A	ENST00000263604.3	+	17	1692	c.1692G>A	c.(1690-1692)gcG>gcA	p.A564A	KCNT1_ENST00000488444.2_Silent_p.A564A|KCNT1_ENST00000486577.2_Silent_p.A544A|KCNT1_ENST00000490355.2_Silent_p.A564A|KCNT1_ENST00000491806.2_Silent_p.A550A|KCNT1_ENST00000487664.1_Silent_p.A538A|KCNT1_ENST00000298480.5_Silent_p.A583A|KCNT1_ENST00000371757.2_Silent_p.A583A			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	564	RCK N-terminal.				potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		TCACCTACGCGGCCTTCCACG	0.647													G|||	1780	0.355431	0.4924	0.1772	5008	,	,		15769	0.4147		0.2217	False		,,,				2504	0.3732				p.A583A		Atlas-SNP	.											.	KCNT1	139	.	0			c.G1749A						PASS	.	G		2074,2330	558.6+/-380.0	487,1100,615	86.0	66.0	73.0		1749	-3.1	1.0	9	dbSNP_123	73	1784,6816	317.8+/-313.4	193,1398,2709	no	coding-synonymous	KCNT1	NM_020822.2		680,2498,3324	AA,AG,GG		20.7442,47.0936,29.6678		583/1236	138662273	3858,9146	2202	4300	6502	SO:0001819	synonymous_variant	57582	exon17			CTACGCGGCCTTC	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.1692G>A	9.37:g.138662273G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	37																																																																																				G|0.695;A|0.305	0.305	strong		0.647	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822	
SCEL	8796	hgsc.bcm.edu	37	13	78216915	78216915	+	Silent	SNP	C	C	T	rs2813739	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:78216915C>T	ENST00000349847.3	+	32	2106	c.2022C>T	c.(2020-2022)caC>caT	p.H674H	SCEL_ENST00000535157.1_Silent_p.H632H|SCEL_ENST00000377246.3_Silent_p.H654H	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	155	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	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	
OAS3	4940	hgsc.bcm.edu	37	12	113386779	113386779	+	Missense_Mutation	SNP	C	C	G	rs2285933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113386779C>G	ENST00000228928.7	+	6	1322	c.1143C>G	c.(1141-1143)agC>agG	p.S381R	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	381	Linker.		S -> R (in dbSNP:rs2285933). {ECO:0000269|PubMed:15489334}.		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)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						GAGCAGGGAGCAAACCTCCCT	0.607													C|||	1405	0.280551	0.4092	0.379	5008	,	,		19978	0.1577		0.2565	False		,,,				2504	0.1881				p.S381R		Atlas-SNP	.											OAS3,brain,glioma,0,1	OAS3	63	1	0			c.C1143G						PASS	.	C	ARG/SER	1450,2514		249,952,781	37.0	41.0	40.0		1143	0.0	0.0	12	dbSNP_100	40	2178,6156		291,1596,2280	yes	missense	OAS3	NM_006187.2	110	540,2548,3061	GG,GC,CC		26.1339,36.5792,29.5007	benign	381/1088	113386779	3628,8670	1982	4167	6149	SO:0001583	missense	4940	exon6			AGGGAGCAAACCT	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.1143C>G	12.37:g.113386779C>G	ENSP00000228928:p.Ser381Arg	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	196	85	0.433673	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	621	0.28434065934065933	194	0.3943089430894309	117	0.32320441988950277	105	0.18356643356643357	205	0.2704485488126649	C	2.291	-0.362396	0.05103	0.365792	0.261339	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.06687	3.27	3.0	0.0313	0.14170	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.26002	0.139	B	0.12156	0.007	T	0.47623	-0.9103	8	0.51188	T	0.08	.	3.3881	0.07278	0.0:0.52:0.2178:0.2622	rs2285933;rs2285933	381	Q9Y6K5	OAS3_HUMAN	R	381	ENSP00000228928:S381R	ENSP00000228928:S381R	S	+	3	2	OAS3	111871162	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.993000	0.03720	-0.002000	0.14469	-0.145000	0.13849	AGC	C|0.724;G|0.276	0.276	strong		0.607	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
ADAM15	8751	hgsc.bcm.edu	37	1	155033308	155033308	+	Splice_Site	SNP	G	G	A	rs11589479	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:155033308G>A	ENST00000356955.2	+	19	2378	c.2277G>A	c.(2275-2277)aaG>aaA	p.K759K	ADAM15_ENST00000368412.3_Intron|EFNA4_ENST00000427683.2_5'Flank|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000355956.2_Splice_Site_p.K759K|EFNA4_ENST00000359751.4_5'Flank|EFNA3_ENST00000505139.1_5'Flank|ADAM15_ENST00000368413.1_Splice_Site_p.K465K|ADAM15_ENST00000271836.6_Splice_Site_p.K759K|EFNA4_ENST00000368409.3_5'Flank|EFNA3_ENST00000556931.1_5'Flank|ADAM15_ENST00000359280.4_Splice_Site_p.K759K|ADAM15_ENST00000449910.2_Splice_Site_p.K759K|ADAM15_ENST00000368410.2_Splice_Site_p.K465K|ADAM15_ENST00000360674.4_Intron|ADAM15_ENST00000531455.1_Splice_Site_p.K769K	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	759					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)			GAGGCACTAAGGTGAGTCCTG	0.627													G|||	376	0.0750799	0.0045	0.0951	5008	,	,		18530	0.0089		0.1819	False		,,,				2504	0.1145				p.K769K		Atlas-SNP	.											.	ADAM15	92	.	0			c.G2307A						PASS	.	G	,,,,,	141,4265	93.4+/-132.2	1,139,2063	56.0	57.0	57.0		2277,,2277,2277,2277,2277	4.8	1.0	1	dbSNP_120	57	1456,7144	267.9+/-287.5	118,1220,2962	yes	coding-synonymous-near-splice,intron,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ADAM15	NM_003815.3,NM_207191.1,NM_207194.1,NM_207195.1,NM_207196.1,NM_207197.1	,,,,,	119,1359,5025	AA,AG,GG		16.9302,3.2002,12.2789	,,,,,	759/815,,759/840,759/839,759/863,759/864	155033308	1597,11409	2203	4300	6503	SO:0001630	splice_region_variant	8751	exon19			CACTAAGGTGAGT	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.2277+1G>A	1.37:g.155033308G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	NM_001261464	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Silent	SNP	ENST00000356955.2	37	CCDS1087.1																																																																																			G|0.889;A|0.111	0.111	strong		0.627	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	Silent
ZFR2	23217	hgsc.bcm.edu	37	19	3831765	3831765	+	Missense_Mutation	SNP	G	G	A	rs2240235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3831765G>A	ENST00000262961.4	-	4	501	c.491C>T	c.(490-492)tCg>tTg	p.S164L	ZFR2_ENST00000591965.1_5'UTR	NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	164			S -> L (in dbSNP:rs2240235).				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		GGTGTATCCCGAGGACAAGGT	0.692													G|||	1839	0.367212	0.3858	0.4193	5008	,	,		12850	0.4196		0.4195	False		,,,				2504	0.1973				p.S164L		Atlas-SNP	.											ZFR2,NS,carcinoma,0,1	ZFR2	63	1	0			c.C491T						PASS	.	G	LEU/SER	1712,2580		351,1010,785	26.0	30.0	29.0		491	2.1	0.0	19	dbSNP_98	29	3327,5161		682,1963,1599	yes	missense	ZFR2	NM_015174.1	145	1033,2973,2384	AA,AG,GG		39.1965,39.8882,39.4288	benign	164/940	3831765	5039,7741	2146	4244	6390	SO:0001583	missense	23217	exon4			TATCCCGAGGACA	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"""KIAA1086"""	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.491C>T	19.37:g.3831765G>A	ENSP00000262961:p.Ser164Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_015174		Missense_Mutation	SNP	ENST00000262961.4	37	CCDS45921.1	896	0.41025641025641024	196	0.3983739837398374	155	0.4281767955801105	236	0.4125874125874126	309	0.4076517150395778	G	15.46	2.839235	0.51057	0.398882	0.391965	ENSG00000105278	ENST00000262961;ENST00000438164	T;T	0.15256	3.18;2.44	3.19	2.14	0.27477	.	0.417428	0.19101	N	0.122696	T	0.00012	0.0000	L	0.46157	1.445	0.43036	P	0.005380999999999969	B	0.19331	0.035	B	0.08055	0.003	T	0.47129	-0.9141	9	0.13470	T	0.59	.	6.2186	0.20669	0.1443:0.0:0.8557:0.0	rs2240235;rs60998694;rs2240235	164	Q9UPR6	ZFR2_HUMAN	L	164	ENSP00000262961:S164L;ENSP00000388974:S164L	ENSP00000262961:S164L	S	-	2	0	ZFR2	3782765	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.516000	0.22817	0.552000	0.29026	0.561000	0.74099	TCG	G|0.600;A|0.400	0.400	strong		0.692	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174	
ZNF217	7764	hgsc.bcm.edu	37	20	52192595	52192595	+	Missense_Mutation	SNP	C	C	T	rs61748378	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:52192595C>T	ENST00000371471.2	-	4	3133	c.2708G>A	c.(2707-2709)cGg>cAg	p.R903Q	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.R903Q			O75362	ZN217_HUMAN	zinc finger protein 217	903					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GCTGGCACTCCGATTACAGAA	0.562													C|||	57	0.0113818	0.0008	0.0231	5008	,	,		18605	0.0		0.0368	False		,,,				2504	0.0031				p.R903Q		Atlas-SNP	.											.	ZNF217	227	.	0			c.G2708A						PASS	.	C	GLN/ARG	36,4370	40.8+/-73.8	0,36,2167	63.0	61.0	62.0		2708	5.3	0.1	20	dbSNP_129	62	340,8260	117.6+/-177.1	6,328,3966	yes	missense	ZNF217	NM_006526.2	43	6,364,6133	TT,TC,CC		3.9535,0.8171,2.891	probably-damaging	903/1049	52192595	376,12630	2203	4300	6503	SO:0001583	missense	7764	exon3			GCACTCCGATTAC	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2708G>A	20.37:g.52192595C>T	ENSP00000360526:p.Arg903Gln	Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	40	0.018315018315018316	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	29	0.03825857519788918	C	15.18	2.755994	0.49362	0.008171	0.039535	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.13196	2.61;2.61	5.26	5.26	0.73747	.	0.510022	0.19366	N	0.116007	T	0.02267	0.0070	L	0.39147	1.195	0.09310	N	0.999997	P	0.43938	0.822	B	0.32342	0.144	T	0.17531	-1.0366	10	0.87932	D	0	-20.7069	13.2311	0.59945	0.0:0.9214:0.0:0.0786	rs61748378	903	O75362	ZN217_HUMAN	Q	903;903;63	ENSP00000360526:R903Q;ENSP00000304308:R903Q	ENSP00000304308:R903Q	R	-	2	0	ZNF217	51626002	0.953000	0.32496	0.078000	0.20375	0.006000	0.05464	2.935000	0.48963	2.450000	0.82876	0.650000	0.86243	CGG	C|0.976;T|0.024	0.024	strong		0.562	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
SMG1	23049	hgsc.bcm.edu	37	16	18846429	18846429	+	Silent	SNP	G	G	A	rs56079655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:18846429G>A	ENST00000446231.2	-	49	8527	c.8115C>T	c.(8113-8115)gcC>gcT	p.A2705A	SMG1_ENST00000389467.3_Silent_p.A2705A			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2705					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						TCATTTCAGTGGCAGTGATGA	0.458													G|||	89	0.0177716	0.0008	0.0303	5008	,	,		18948	0.001		0.0477	False		,,,				2504	0.0184				p.A2705A		Atlas-SNP	.											.	SMG1	401	.	0			c.C8115T						PASS	.	G		33,3825		1,31,1897	119.0	115.0	116.0		8115	4.6	1.0	16	dbSNP_129	116	336,7966		5,326,3820	no	coding-synonymous	SMG1	NM_015092.4		6,357,5717	AA,AG,GG		4.0472,0.8554,3.0345		2705/3662	18846429	369,11791	1929	4151	6080	SO:0001819	synonymous_variant	23049	exon49			TTCAGTGGCAGTG	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.8115C>T	16.37:g.18846429G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Silent	SNP	ENST00000446231.2	37	CCDS45430.1																																																																																			G|0.972;A|0.028	0.028	strong		0.458	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
TMEM183A	92703	hgsc.bcm.edu	37	1	202977809	202977809	+	Missense_Mutation	SNP	G	G	A	rs6678040	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:202977809G>A	ENST00000367242.3	+	3	318	c.238G>A	c.(238-240)Gca>Aca	p.A80T	TMEM183A_ENST00000468449.1_3'UTR	NM_001079809.1|NM_138391.4	NP_001073277.1|NP_612400.3	Q8IXX5	T183A_HUMAN	transmembrane protein 183A	80			A -> T (in dbSNP:rs6678040). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)|skin(3)	7			BRCA - Breast invasive adenocarcinoma(75;0.18)			TCAGGTTCCTGCAGAGGAAGC	0.478													G|||	659	0.131589	0.0696	0.2089	5008	,	,		13818	0.1756		0.1093	False		,,,				2504	0.138				p.A80T		Atlas-SNP	.											.	.	.	.	0			c.G238A						PASS	.	G	THR/ALA	378,4028	170.5+/-200.9	16,346,1841	43.0	48.0	46.0		238	3.7	1.0	1	dbSNP_116	46	929,7669	198.7+/-243.0	49,831,3419	yes	missense	TMEM183A	NM_138391.4	58	65,1177,5260	AA,AG,GG		10.8048,8.5792,10.0508	benign	80/377	202977809	1307,11697	2203	4299	6502	SO:0001583	missense	653659	exon3			GTTCCTGCAGAGG	BC013073	CCDS1432.1	1q31.1	2008-09-09	2006-12-18	2006-12-18	ENSG00000163444	ENSG00000163444			20173	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 37"""	C1orf37			Standard	NM_138391		Approved		uc001gyu.1	Q8IXX5	OTTHUMG00000042051	ENST00000367242.3:c.238G>A	1.37:g.202977809G>A	ENSP00000356211:p.Ala80Thr	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	278	172	0.618705	NM_001079809	A8K5W1|Q6NW15|Q96E06	Missense_Mutation	SNP	ENST00000367242.3	37	CCDS1432.1	276	0.12637362637362637	27	0.054878048780487805	77	0.212707182320442	93	0.16258741258741258	79	0.10422163588390501	G	10.56	1.384488	0.25031	0.085792	0.108048	ENSG00000163444	ENST00000367242	T	0.22336	1.96	4.84	3.7	0.42460	.	0.267365	0.36778	N	0.002409	T	0.00012	0.0000	N	0.12182	0.205	0.33821	P	0.370915	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.38866	-0.9641	9	0.07030	T	0.85	-6.7407	3.9794	0.09489	0.2285:0.0:0.569:0.2025	rs6678040;rs6678040	80;80;80;80	A8K5W1;Q8IXX5-2;Q1AE95;Q8IXX5	.;.;T183B_HUMAN;T183A_HUMAN	T	80	ENSP00000356211:A80T	ENSP00000356211:A80T	A	+	1	0	TMEM183A	201244432	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.172000	0.31908	2.223000	0.72356	0.462000	0.41574	GCA	G|0.897;A|0.103	0.103	strong		0.478	TMEM183A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100129.1	NM_138391	
TEKT1	83659	hgsc.bcm.edu	37	17	6704121	6704121	+	Missense_Mutation	SNP	C	C	T	rs2271233	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	232	0	0	636	WXS	Illumina HiSeq	Phase_I	287	148	0.515679	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	
FLG	2312	hgsc.bcm.edu	37	1	152276149	152276149	+	Missense_Mutation	SNP	C	C	T	rs77422831	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152276149C>T	ENST00000368799.1	-	3	11248	c.11213G>A	c.(11212-11214)cGc>cAc	p.R3738H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3738	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGCTCGTGGCGGGATCCTTG	0.607									Ichthyosis				C|||	1437	0.286941	0.0113	0.3919	5008	,	,		20123	0.5804		0.1421	False		,,,				2504	0.4315				p.R3738H		Atlas-SNP	.											.	FLG	900	.	0			c.G11213A						PASS	.	C	HIS/ARG	163,4243	109.1+/-147.4	2,159,2042	235.0	236.0	236.0		11213	-2.2	0.0	1	dbSNP_131	236	1240,7360	249.0+/-276.5	97,1046,3157	no	missense	FLG	NM_002016.1	29	99,1205,5199	TT,TC,CC		14.4186,3.6995,10.7873	possibly-damaging	3738/4062	152276149	1403,11603	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCGTGGCGGGATC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11213G>A	1.37:g.152276149C>T	ENSP00000357789:p.Arg3738His	Somatic	353	1	0.00283286		WXS	Illumina HiSeq	Phase_I	444	170	0.382883	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	568	0.2600732600732601	10	0.02032520325203252	117	0.32320441988950277	330	0.5769230769230769	111	0.14643799472295516	C	11.18	1.563264	0.27915	0.036995	0.144186	ENSG00000143631	ENST00000368799	T	0.01705	4.68	3.5	-2.2	0.06994	.	.	.	.	.	T	0.00210	0.0006	N	0.02751	-0.505	0.80722	P	0.0	P	0.41475	0.751	B	0.25987	0.065	T	0.42068	-0.9473	8	0.30854	T	0.27	.	4.1707	0.10327	0.0:0.343:0.2091:0.448	rs3126080	3738	P20930	FILA_HUMAN	H	3738	ENSP00000357789:R3738H	ENSP00000357789:R3738H	R	-	2	0	FLG	150542773	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.253000	0.01184	-0.570000	0.06022	-0.267000	0.10333	CGC	C|0.841;T|0.159	0.159	strong		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CARD16	114769	hgsc.bcm.edu	37	11	104912221	104912221	+	Missense_Mutation	SNP	T	T	A	rs542571	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:104912221T>A	ENST00000375706.2	-	3	517	c.500A>T	c.(499-501)aAc>aTc	p.N167I	CASP1_ENST00000598974.1_Intron|CASP1_ENST00000415981.2_Intron|CASP1_ENST00000593315.1_Intron|CASP1_ENST00000594519.1_Intron	NM_001017534.1	NP_001017534.1	Q5EG05	CAR16_HUMAN	caspase recruitment domain family, member 16	167			N -> I (in dbSNP:rs542571).		regulation of apoptotic process (GO:0042981)		cysteine-type endopeptidase inhibitor activity (GO:0004869)			endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	11						CAGAAGTATGTTCCTCCAGAA	0.368													.|||	1095	0.21865	0.4244	0.2939	5008	,	,		20036	0.0069		0.1799	False		,,,				2504	0.1452				p.N167I		Atlas-SNP	.											.	CARD16	29	.	0			c.A500T						PASS	.	A	,ILE/ASN	1699,2705		340,1019,843	81.0	83.0	82.0		,500	0.2	0.0	11	dbSNP_83	82	1428,7170		130,1168,3001	yes	utr-3,missense	CARD16	NM_052889.2,NM_001017534.1	,149	470,2187,3844	AA,AT,TT		16.6085,38.5786,24.0501	,benign	,167/198	104912221	3127,9875	2202	4299	6501	SO:0001583	missense	114769	exon3			AGTATGTTCCTCC		CCDS31661.1, CCDS41705.1	11q23	2008-09-15				ENSG00000204397			33701	protein-coding gene	gene with protein product		615680				11432859, 11536016	Standard	NM_052889		Approved	COP1, COP, PSEUDO-ICE		Q5EG05		ENST00000375706.2:c.500A>T	11.37:g.104912221T>A	ENSP00000364858:p.Asn167Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	158	46	0.291139	NM_001017534	Q96RJ9	Missense_Mutation	SNP	ENST00000375706.2	37	CCDS31661.1	433	0.19826007326007325	205	0.4166666666666667	100	0.27624309392265195	2	0.0034965034965034965	126	0.1662269129287599	.	0.003	-2.417365	0.00188	0.385786	0.166085	ENSG00000204397	ENST00000375706	T	0.19394	2.15	1.36	0.171	0.15026	.	0.975408	0.08410	N	0.949995	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	0.45160	-0.9280	9	0.07482	T	0.82	.	1.5094	0.02493	0.4768:0.0:0.2154:0.3078	rs542571;rs542571	167	Q5EG05	CAR16_HUMAN	I	167	ENSP00000364858:N167I	ENSP00000364858:N167I	N	-	2	0	CARD16	104417431	0.001000	0.12720	0.003000	0.11579	0.021000	0.10359	-0.047000	0.11963	-0.424000	0.07382	-0.827000	0.03088	AAC	T|0.776;A|0.224	0.224	strong		0.368	CARD16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000388147.1		
FUT2	2524	hgsc.bcm.edu	37	19	49206603	49206603	+	Silent	SNP	C	C	T	rs281377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49206603C>T	ENST00000425340.2	+	2	507	c.390C>T	c.(388-390)aaC>aaT	p.N130N	FUT2_ENST00000391876.4_Silent_p.N130N	NM_000511.5|NM_001097638.2	NP_000502.4|NP_001091107.1	Q10981	FUT2_HUMAN	fucosyltransferase 2 (secretor status included)	130					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)	7		all_lung(116;4.89e-06)|all_epithelial(76;7.04e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.00011)|all cancers(93;0.000238)|GBM - Glioblastoma multiforme(486;0.0164)|Epithelial(262;0.017)		ACCACCTGAACGACTGGATGG	0.642													C|||	2484	0.496006	0.2678	0.5115	5008	,	,		16532	0.8452		0.4722	False		,,,				2504	0.4581				p.N130N		Atlas-SNP	.											.	FUT2	30	.	0			c.C390T						PASS	.	C	,	1152,3252		158,836,1208	38.0	38.0	38.0	http://www.ncbi.nlm.nih.gov/pubmed?term	390,390	1.4	1.0	19	dbSNP_79	38	3767,4831		839,2089,1371	no	coding-synonymous,coding-synonymous	FUT2	NM_000511.5,NM_001097638.2	,	997,2925,2579	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	43.8125,26.158,37.8326	,	130/344,130/344	49206603	4919,8083	2202	4299	6501	SO:0001819	synonymous_variant	2524	exon2			CCTGAACGACTGG		CCDS33069.1	19q13.33	2014-07-19			ENSG00000176920	ENSG00000176920		"""Fucosyltransferases"""	4013	protein-coding gene	gene with protein product	"""alpha (1,2) fucosyltransferase"", ""galactoside 2-alpha-L-fucosyltransferase 2"", ""GDP-L-fucose:beta-D-galactoside 2-alpha-L-fucosyltransferase 2"", ""alpha(1,2)FT2"", ""secretor factor"", ""secretor blood group alpha-2-fucosyltransferase"""	182100		SE		1763885	Standard	NM_000511		Approved	sej, Se2, SEC2	uc010emc.3	Q10981	OTTHUMG00000164427	ENST00000425340.2:c.390C>T	19.37:g.49206603C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_001097638	Q0VAG5|Q14338|Q5D0G2	Silent	SNP	ENST00000425340.2	37	CCDS33069.1																																																																																			C|0.559;T|0.441	0.441	strong		0.642	FUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378731.2	NM_000511	
DGCR6	8214	hgsc.bcm.edu	37	22	18893902	18893902	+	Silent	SNP	G	G	C	rs408469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:18893902G>C	ENST00000331444.6	+	1	167	c.15G>C	c.(13-15)gcG>gcC	p.A5A	DGCR6_ENST00000608842.1_Silent_p.A5A|DGCR6_ENST00000413981.1_Intron	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6	5				MERYAGALEEVA -> PKGAKAGYQPRG (in Ref. 3). {ECO:0000305}.	cell adhesion (GO:0007155)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|upper_aerodigestive_tract(1)	3						AGCGCTACGCGGGCGCCTTGG	0.711													G|||	222	0.0443291	0.0325	0.0173	5008	,	,		10985	0.0367		0.0358	False		,,,				2504	0.0961				p.A5A		Atlas-SNP	.											.	DGCR6	12	.	0			c.G15C						PASS	.	G		105,4237		1,103,2067	9.0	10.0	10.0		15	-5.2	0.0	22	dbSNP_80	10	242,8254		2,238,4008	no	coding-synonymous	DGCR6	NM_005675.4		3,341,6075	CC,CG,GG		2.8484,2.4182,2.7029		5/221	18893902	347,12491	2171	4248	6419	SO:0001819	synonymous_variant	8214	exon1			CTACGCGGGCGCC	X96484	CCDS13753.1	22q11.21	2008-06-12			ENSG00000183628	ENSG00000183628			2846	protein-coding gene	gene with protein product		601279				8733130	Standard	NM_005675		Approved		uc002zoh.4	Q14129	OTTHUMG00000150162	ENST00000331444.6:c.15G>C	22.37:g.18893902G>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	27	8	0.296296	NM_005675	B2RCH5|D3DX15|G5E9J8|Q9BY28	Silent	SNP	ENST00000331444.6	37	CCDS13753.1																																																																																			G|0.967;C|0.033	0.033	strong		0.711	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316631.2	NM_005675	
GPR146	115330	hgsc.bcm.edu	37	7	1097394	1097394	+	Silent	SNP	T	T	C	rs11767527	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:1097394T>C	ENST00000397095.1	+	2	466	c.243T>C	c.(241-243)ccT>ccC	p.P81P	GPR146_ENST00000297468.3_Silent_p.P81P|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	81						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P81P(2)		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)		CCCTGGCCCCTGTGCACCTGC	0.652													t|||	345	0.0688898	0.0204	0.0821	5008	,	,		18317	0.0		0.1262	False		,,,				2504	0.137				p.P81P		Atlas-SNP	.											GPR146,NS,carcinoma,0,3	GPR146	20	3	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.T243C						scavenged	.		,,,	200,4200	116.3+/-154.2	3,194,2003	34.0	31.0	32.0		,,,243	-7.6	0.0	7	dbSNP_120	32	1339,7259	240.0+/-270.9	102,1135,3062	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	105,1329,5065	CC,CT,TT		15.5734,4.5455,11.8403	,,,	,,,81/334	1097394	1539,11459	2200	4299	6499	SO:0001819	synonymous_variant	115330	exon1			GGCCCCTGTGCAC	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.243T>C	7.37:g.1097394T>C		Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			T|0.898;C|0.102	0.102	strong		0.652	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
CEP250	11190	hgsc.bcm.edu	37	20	34092076	34092076	+	Missense_Mutation	SNP	G	G	A	rs56259282	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	43	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	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	
MROH2B	133558	hgsc.bcm.edu	37	5	41033163	41033163	+	Missense_Mutation	SNP	T	T	C	rs10067611	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:41033163T>C	ENST00000399564.4	-	23	2791	c.2341A>G	c.(2341-2343)Atg>Gtg	p.M781V	MROH2B_ENST00000506092.2_Missense_Mutation_p.M336V	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	781			M -> V (in dbSNP:rs10067611).														CCAATCAGCATCTCCTTGTAG	0.443													T|||	154	0.0307508	0.0303	0.0115	5008	,	,		21483	0.0536		0.0368	False		,,,				2504	0.0153				p.M781V		Atlas-SNP	.											.	.	.	.	0			c.A2341G						PASS	.	T	VAL/MET	131,3905		4,123,1891	122.0	113.0	116.0		2341	-0.3	0.1	5	dbSNP_119	116	246,8104		4,238,3933	yes	missense	HEATR7B2	NM_173489.4	21	8,361,5824	CC,CT,TT		2.9461,3.2458,3.0438	benign	781/1586	41033163	377,12009	2018	4175	6193	SO:0001583	missense	133558	exon23			TCAGCATCTCCTT		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.2341A>G	5.37:g.41033163T>C	ENSP00000382476:p.Met781Val	Somatic	393	1	0.00254453		WXS	Illumina HiSeq	Phase_I	364	155	0.425824	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	81	0.03708791208791209	19	0.03861788617886179	5	0.013812154696132596	31	0.05419580419580419	26	0.03430079155672823	T	0.028	-1.353425	0.01256	0.032458	0.029461	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.05199	3.48;3.48	5.55	-0.28	0.12886	Armadillo-type fold (1);	1.162530	0.06333	N	0.706578	T	0.00384	0.0012	N	0.02011	-0.69	0.19300	N	0.999978	B	0.02656	0.0	B	0.01281	0.0	T	0.44922	-0.9296	10	0.30854	T	0.27	.	0.1565	0.00098	0.3332:0.2446:0.1654:0.2568	rs10067611;rs52811327;rs60860203;rs10067611	781	Q7Z745	HTRB2_HUMAN	V	336;486;781	ENSP00000441504:M336V;ENSP00000382476:M781V	ENSP00000296803:M486V	M	-	1	0	HEATR7B2	41068920	0.851000	0.29673	0.131000	0.22000	0.099000	0.18886	0.119000	0.15626	-0.087000	0.12528	-0.333000	0.08304	ATG	T|0.963;C|0.037	0.037	strong		0.443	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
CCDC180	100499483	hgsc.bcm.edu	37	9	100139161	100139161	+	Silent	SNP	A	A	G	rs11581	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100139161A>G	ENST00000357054.1	+	49	5861	c.4926A>G	c.(4924-4926)caA>caG	p.Q1642Q	CCDC180_ENST00000395220.1_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Silent_p.Q1697Q|CCDC180_ENST00000375202.2_Silent_p.Q1697Q			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1642						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.Q1642Q(1)									ACACTATCCAAGGCCTGTATG	0.517													G|||	2100	0.419329	0.5726	0.4582	5008	,	,		21290	0.5248		0.1958	False		,,,				2504	0.3057				p.Q1697Q		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.A5091G						PASS	.	G		2343,2063	566.4+/-381.9	643,1057,503	127.0	104.0	112.0		5091	2.1	0.6	9	dbSNP_52	112	1624,6976	739.4+/-407.1	146,1332,2822	no	coding-synonymous	C9orf174	NM_020893.2		789,2389,3325	GG,GA,AA		18.8837,46.8225,30.5013		1697/1702	100139161	3967,9039	2203	4300	6503	SO:0001819	synonymous_variant	0	exon37			TATCCAAGGCCTG	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.4926A>G	9.37:g.100139161A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				A|0.654;G|0.346	0.346	strong		0.517	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
FERMT1	55612	hgsc.bcm.edu	37	20	6078246	6078246	+	Silent	SNP	C	C	T	rs149893089		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:6078246C>T	ENST00000217289.4	-	7	1670	c.882G>A	c.(880-882)gaG>gaA	p.E294E	FERMT1_ENST00000536936.1_Silent_p.E37E	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	294	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						ACCTGGCTTGCTCATAGAGTT	0.393													T|||	1	0.000199681	0.0	0.0	5008	,	,		15796	0.0		0.0	False		,,,				2504	0.001				p.E294E		Atlas-SNP	.											.	FERMT1	106	.	0			c.G882A						PASS	.	T		1,4405	826.1+/-416.6	0,1,2202	143.0	135.0	138.0		882	0.8	1.0	20	dbSNP_134	138	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	FERMT1	NM_017671.4		0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461		294/678	6078246	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon7			GGCTTGCTCATAG	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.882G>A	20.37:g.6078246C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			C|0.999;T|0.001	0.001	strong		0.393	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68053807	68053807	+	Missense_Mutation	SNP	T	T	G	rs118013098	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:68053807T>G	ENST00000329153.5	+	29	4082	c.3950T>G	c.(3949-3951)tTc>tGc	p.F1317C	PLEKHH1_ENST00000417684.2_Silent_p.L258L	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	1317	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)		GAAGCTACCTTCATCATGGCC	0.498													T|||	7	0.00139776	0.0	0.0	5008	,	,		18391	0.0		0.007	False		,,,				2504	0.0				p.F1317C		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.T3950G						PASS	.	T	CYS/PHE	4,3938		0,4,1967	61.0	66.0	64.0		3950	5.5	0.9	14	dbSNP_132	64	38,8266		0,38,4114	yes	missense	PLEKHH1	NM_020715.2	205	0,42,6081	GG,GT,TT		0.4576,0.1015,0.343	benign	1317/1365	68053807	42,12204	1971	4152	6123	SO:0001583	missense	57475	exon29			CTACCTTCATCAT	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.3950T>G	14.37:g.68053807T>G	ENSP00000330278:p.Phe1317Cys	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	255	159	0.623529	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	21.5	4.152327	0.78001	0.001015	0.004576	ENSG00000054690	ENST00000329153	T	0.71461	-0.57	5.54	5.54	0.83059	FERM domain (1);	0.398053	0.28989	N	0.013497	T	0.49508	0.1561	N	0.19112	0.55	0.80722	D	1	B	0.14012	0.009	B	0.12156	0.007	T	0.52351	-0.8587	10	0.48119	T	0.1	.	14.4073	0.67090	0.0:0.0:0.0:1.0	.	1317	Q9ULM0	PKHH1_HUMAN	C	1317	ENSP00000330278:F1317C	ENSP00000330278:F1317C	F	+	2	0	PLEKHH1	67123560	0.960000	0.32886	0.910000	0.35882	0.977000	0.68977	4.841000	0.62824	2.326000	0.78906	0.533000	0.62120	TTC	T|0.997;G|0.003	0.003	strong		0.498	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
CPXCR1	53336	hgsc.bcm.edu	37	X	88008807	88008807	+	Missense_Mutation	SNP	G	G	A	rs5984611	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	151	0	0		WXS	Illumina HiSeq	Phase_I	57	57	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	
PSMD8	5714	hgsc.bcm.edu	37	19	38872778	38872778	+	Silent	SNP	C	C	T	rs1131182	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38872778C>T	ENST00000215071.4	+	6	891	c.825C>T	c.(823-825)atC>atT	p.I275I	PSMD8_ENST00000592035.1_Silent_p.I108I|GGN_ENST00000591809.1_5'Flank|PSMD8_ENST00000602911.1_Silent_p.I212I	NM_002812.4	NP_002803.2	P48556	PSMD8_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	275					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 accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)				central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(1)	6	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTGGGTGCATCGAGAAGGCCT	0.542													C|||	318	0.0634984	0.0053	0.1657	5008	,	,		19668	0.0437		0.1014	False		,,,				2504	0.0511				p.I275I		Atlas-SNP	.											.	PSMD8	31	.	0			c.C825T						PASS	.	C		54,2600		0,54,1273	73.0	56.0	62.0		825	-5.0	0.9	19	dbSNP_86	62	419,4199		18,383,1908	no	coding-synonymous	PSMD8	NM_002812.4		18,437,3181	TT,TC,CC		9.0732,2.0347,6.5044		275/351	38872778	473,6799	1327	2309	3636	SO:0001819	synonymous_variant	5714	exon6			GTGCATCGAGAAG	D38047	CCDS12515.2	19q13.2	2009-05-07			ENSG00000099341	ENSG00000099341		"""Proteasome (prosome, macropain) subunits"""	9566	protein-coding gene	gene with protein product						7621825	Standard	NM_002812		Approved	S14, Nin1p, p31, HIP6, HYPF, Rpn12	uc002oii.4	P48556	OTTHUMG00000150691	ENST00000215071.4:c.825C>T	19.37:g.38872778C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_002812	B4DX18|Q6P1L7	Silent	SNP	ENST00000215071.4	37	CCDS12515.2																																																																																			C|0.918;T|0.082	0.082	strong		0.542	PSMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319627.1	NM_002812	
MDN1	23195	hgsc.bcm.edu	37	6	90372574	90372574	+	Missense_Mutation	SNP	A	A	C	rs36040566	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	332	0	0		WXS	Illumina HiSeq	Phase_I	309	150	0.485437	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		
MYO1G	64005	hgsc.bcm.edu	37	7	45016621	45016621	+	Missense_Mutation	SNP	C	C	T	rs61739531	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	132	0	0		WXS	Illumina HiSeq	Phase_I	172	101	0.587209	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		
STKLD1	169436	hgsc.bcm.edu	37	9	136270538	136270538	+	Missense_Mutation	SNP	T	T	G	rs41302673	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136270538T>G	ENST00000371957.3	+	18	2143	c.2036T>G	c.(2035-2037)cTg>cGg	p.L679R	C9orf96_ENST00000371955.1_Missense_Mutation_p.L212R	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		679							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)		TCTGGGGGACTGGAATAGATG	0.557													T|||	187	0.0373403	0.0023	0.0677	5008	,	,		18018	0.0		0.1014	False		,,,				2504	0.0358				p.L679R		Atlas-SNP	.											C9orf96_ENST00000371957,NS,carcinoma,0,1	C9orf96	77	1	0			c.T2036G						PASS	.	T	ARG/LEU	68,4338	61.1+/-98.1	0,68,2135	35.0	37.0	36.0		2036	-5.6	0.0	9	dbSNP_127	36	851,7749	191.4+/-237.6	51,749,3500	yes	missense	C9orf96	NM_153710.3	102	51,817,5635	GG,GT,TT		9.8953,1.5433,7.066	possibly-damaging	679/681	136270538	919,12087	2203	4300	6503	SO:0001583	missense	169436	exon18			GGGGACTGGAATA																												ENST00000371957.3:c.2036T>G	9.37:g.136270538T>G	ENSP00000361025:p.Leu679Arg	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Missense_Mutation	SNP	ENST00000371957.3	37	CCDS35169.1	105	0.04807692307692308	3	0.006097560975609756	24	0.06629834254143646	0	0.0	78	0.10290237467018469	T	10.74	1.435227	0.25813	0.015433	0.098953	ENSG00000198870	ENST00000371957;ENST00000371955	T;T	0.71222	-0.55;0.56	3.37	-5.58	0.02512	.	6.515760	0.00960	U	0.003081	T	0.01454	0.0047	N	0.08118	0	0.09310	N	1	P	0.40476	0.718	B	0.32864	0.154	T	0.26360	-1.0105	10	0.87932	D	0	12.8738	5.8566	0.18722	0.0:0.529:0.1608:0.3103	rs41302673	679	Q8NE28	SGK71_HUMAN	R	679;212	ENSP00000361025:L679R;ENSP00000361023:L212R	ENSP00000361023:L212R	L	+	2	0	C9orf96	135260359	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-1.438000	0.02416	-0.816000	0.04340	0.379000	0.24179	CTG	T|0.932;G|0.068	0.068	strong		0.557	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077765	19077765	+	Missense_Mutation	SNP	T	T	C	rs10833049	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:19077765T>C	ENST00000329773.2	-	2	272	c.185A>G	c.(184-186)aAc>aGc	p.N62S		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	62			N -> S (in dbSNP:rs10833049). {ECO:0000269|PubMed:15862286, ECO:0000269|Ref.5}.		positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)	p.N62S(1)		NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						AGAGAAGGCGTTCCTGCGCAT	0.562													T|||	1595	0.31849	0.5265	0.2781	5008	,	,		17944	0.2659		0.2614	False		,,,				2504	0.1789				p.N62S	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											MRGPRX2,NS,carcinoma,0,1	MRGPRX2	42	1	1	Substitution - Missense(1)	stomach(1)	c.A185G						PASS	.	T	SER/ASN	2074,2324		504,1066,629	82.0	90.0	87.0		185	1.4	0.0	11	dbSNP_120	87	2283,6303		301,1681,2311	yes	missense	MRGPRX2	NM_054030.2	46	805,2747,2940	CC,CT,TT		26.5898,47.1578,33.5567	probably-damaging	62/331	19077765	4357,8627	2199	4293	6492	SO:0001583	missense	117194	exon2			AAGGCGTTCCTGC		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"""GPCR / Class A : Orphans"""	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.185A>G	11.37:g.19077765T>C	ENSP00000333800:p.Asn62Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	37	CCDS7847.1	690	0.3159340659340659	257	0.5223577235772358	102	0.281767955801105	142	0.24825174825174826	189	0.24934036939313983	.	14.37	2.515471	0.44763	0.471578	0.265898	ENSG00000183695	ENST00000329773	T	0.09073	3.02	5.14	1.41	0.22369	GPCR, rhodopsin-like superfamily (1);	0.079983	0.52532	D	0.000064	T	0.00012	0.0000	L	0.58428	1.81	0.80722	P	0.0	D	0.56521	0.976	P	0.57283	0.817	T	0.48570	-0.9024	9	0.66056	D	0.02	.	2.9449	0.05842	0.1426:0.0803:0.1486:0.6285	rs10833049;rs52795288;rs60268974;rs10833049	62	Q96LB1	MRGX2_HUMAN	S	62	ENSP00000333800:N62S	ENSP00000333800:N62S	N	-	2	0	MRGPRX2	19034341	0.172000	0.23043	0.001000	0.08648	0.447000	0.32167	0.390000	0.20768	0.130000	0.18549	0.533000	0.62120	AAC	C|0.329;G|0.000;T|0.671	0.329	strong		0.562	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188401	140188401	+	Silent	SNP	A	A	G	rs2879086	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188401A>G	ENST00000530339.1	+	1	1629	c.1629A>G	c.(1627-1629)ccA>ccG	p.P543P	PCDHA4_ENST00000356878.4_Silent_p.P543P|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.P543P	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	543	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(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)			CCGGCGTGCCACCTCTGGGCA	0.667													.|||	2961	0.591254	0.7194	0.6052	5008	,	,		17420	0.5317		0.5388	False		,,,				2504	0.5235				p.P543P		Atlas-SNP	.											.	PCDHA4	419	.	0			c.A1629G						PASS	.	G	,,,,,	3098,1308	689.7+/-405.2	1100,898,205	62.0	69.0	66.0		,,,1629,,1629	-5.7	0.0	5	dbSNP_101	66	4535,4063	589.2+/-392.5	1193,2149,957	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	2293,3047,1162	GG,GA,AA		47.2552,29.6868,41.3027	,,,,,	,,,543/948,,543/799	140188401	7633,5371	2203	4299	6502	SO:0001819	synonymous_variant	56144	exon1			CGTGCCACCTCTG	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.1629A>G	5.37:g.140188401A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	26	5	0.192308	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			A|0.414;G|0.586	0.586	strong		0.667	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
RNASE1	6035	hgsc.bcm.edu	37	14	21269990	21269990	+	Missense_Mutation	SNP	C	C	G	rs142457376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21269990C>G	ENST00000397967.4	-	2	744	c.238G>C	c.(238-240)Gta>Cta	p.V80L	RNASE1_ENST00000555698.1_Missense_Mutation_p.V40L|RNASE1_ENST00000340900.3_Missense_Mutation_p.V80L|RNASE1_ENST00000412779.2_Missense_Mutation_p.V80L|RNASE1_ENST00000397970.4_Missense_Mutation_p.V80L	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	80					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	TGGACATCTACCAGGGGCTCG	0.552													C|||	5	0.000998403	0.0008	0.0029	5008	,	,		19291	0.0		0.002	False		,,,				2504	0.0				p.V80L		Atlas-SNP	.											.	RNASE1	14	.	0			c.G238C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	2,4404	4.2+/-10.8	0,2,2201	150.0	135.0	140.0		238,238,238,238	0.8	0.0	14	dbSNP_134	140	13,8587	9.1+/-34.3	0,13,4287	yes	missense,missense,missense,missense	RNASE1	NM_002933.4,NM_198232.2,NM_198234.2,NM_198235.2	32,32,32,32	0,15,6488	GG,GC,CC		0.1512,0.0454,0.1153	benign,benign,benign,benign	80/157,80/157,80/157,80/157	21269990	15,12991	2203	4300	6503	SO:0001583	missense	6035	exon3			CATCTACCAGGGG	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"""Ribonucleases, RNase A"""	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.238G>C	14.37:g.21269990C>G	ENSP00000381057:p.Val80Leu	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	274	105	0.383212	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Missense_Mutation	SNP	ENST00000397967.4	37	CCDS9559.1	4	0.0018315018315018315	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	13.62	2.292413	0.40594	4.54E-4	0.001512	ENSG00000129538	ENST00000397967;ENST00000340900;ENST00000412779;ENST00000555698;ENST00000397970	T;T;T;T;T	0.72394	-0.65;-0.65;-0.65;-0.65;-0.65	5.16	0.835	0.18886	Ribonuclease A, domain (4);	1.935630	0.02411	N	0.081637	T	0.73976	0.3656	M	0.70275	2.135	0.09310	N	1	P	0.36125	0.538	P	0.53912	0.737	T	0.54833	-0.8234	10	0.31617	T	0.26	0.5203	3.9548	0.09385	0.1528:0.4635:0.2973:0.0864	.	80	P07998	RNAS1_HUMAN	L	80;80;80;40;80	ENSP00000381057:V80L;ENSP00000344193:V80L;ENSP00000399493:V80L;ENSP00000451058:V40L;ENSP00000381060:V80L	ENSP00000344193:V80L	V	-	1	0	RNASE1	20339830	0.000000	0.05858	0.016000	0.15963	0.470000	0.32858	-0.294000	0.08309	0.282000	0.22254	0.655000	0.94253	GTA	C|0.998;G|0.002	0.002	strong		0.552	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3		
ARID3C	138715	hgsc.bcm.edu	37	9	34622389	34622389	+	Missense_Mutation	SNP	A	A	C	rs3808869	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34622389A>C	ENST00000378909.2	-	5	1095	c.1003T>G	c.(1003-1005)Tgc>Ggc	p.C335G	DCTN3_ENST00000477738.2_5'Flank|DCTN3_ENST00000447983.2_5'Flank|DCTN3_ENST00000378916.4_5'Flank|DCTN3_ENST00000378913.2_5'Flank|DCTN3_ENST00000259632.7_5'Flank|DCTN3_ENST00000341694.2_5'Flank	NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	335	Pro-rich.|REKLES. {ECO:0000255|PROSITE- ProRule:PRU00819}.		C -> G (in dbSNP:rs3808869).		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)		GGGGGCATGCAAGGTCGAGGT	0.627													C|||	3017	0.602436	0.7723	0.598	5008	,	,		16667	0.4802		0.4692	False		,,,				2504	0.6391				p.C335G		Atlas-SNP	.											.	ARID3C	33	.	0			c.T1003G						PASS	.	C	GLY/CYS	3203,1203	415.9+/-337.4	1171,861,171	45.0	47.0	46.0		1003	0.3	0.0	9	dbSNP_107	46	4398,4202	567.4+/-388.8	1127,2144,1029	yes	missense	ARID3C	NM_001017363.1	159	2298,3005,1200	CC,CA,AA		48.8605,27.3037,41.5577	benign	335/413	34622389	7601,5405	2203	4300	6503	SO:0001583	missense	138715	exon5			GCATGCAAGGTCG		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.1003T>G	9.37:g.34622389A>C	ENSP00000368189:p.Cys335Gly	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_001017363		Missense_Mutation	SNP	ENST00000378909.2	37	CCDS35006.1	1233	0.5645604395604396	369	0.75	206	0.569060773480663	294	0.513986013986014	364	0.48021108179419525	C	0.022	-1.413812	0.01145	0.726963	0.511395	ENSG00000205143	ENST00000378909	T	0.38401	1.14	4.61	0.293	0.15742	REKLES domain (1);	0.347888	0.21170	N	0.078986	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	0.27157	-1.0082	9	0.09084	T	0.74	0.5687	4.0924	0.09975	0.2786:0.4597:0.0:0.2617	rs3808869;rs52800005;rs58670080;rs3808869	335	A6NKF2	ARI3C_HUMAN	G	335	ENSP00000368189:C335G	ENSP00000368189:C335G	C	-	1	0	ARID3C	34612389	0.000000	0.05858	0.003000	0.11579	0.980000	0.70556	-0.178000	0.09782	-0.044000	0.13491	-0.232000	0.12228	TGC	A|0.428;C|0.572	0.572	strong		0.627	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061	
OR51I1	390063	hgsc.bcm.edu	37	11	5461861	5461861	+	Missense_Mutation	SNP	C	C	G	rs76233016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5461861C>G	ENST00000380211.1	-	1	883	c.884G>C	c.(883-885)aGt>aCt	p.S295T	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	295					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)		GGTTTTCACACTGTAGATGAT	0.478													C|||	18	0.00359425	0.0	0.0086	5008	,	,		19623	0.0		0.0119	False		,,,				2504	0.0				p.S295T		Atlas-SNP	.											.	OR51I1	66	.	0			c.G884C						PASS	.	C	THR/SER	11,4391	17.9+/-39.9	0,11,2190	120.0	114.0	116.0		884	4.5	1.0	11	dbSNP_132	116	50,8544	31.7+/-84.0	0,50,4247	yes	missense	OR51I1	NM_001005288.2	58	0,61,6437	GG,GC,CC		0.5818,0.2499,0.4694	benign	295/315	5461861	61,12935	2201	4297	6498	SO:0001583	missense	390063	exon1			TTCACACTGTAGA	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.884G>C	11.37:g.5461861C>G	ENSP00000369559:p.Ser295Thr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	125	75	0.6	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	10.13	1.265693	0.23136	0.002499	0.005818	ENSG00000167359	ENST00000321307;ENST00000380211	T	0.37752	1.18	5.47	4.54	0.55810	.	0.096735	0.47093	D	0.000243	T	0.26774	0.0655	M	0.75884	2.315	0.25867	N	0.983753	P	0.48764	0.915	B	0.32677	0.15	T	0.37526	-0.9702	10	0.51188	T	0.08	.	14.2494	0.66009	0.0:0.7161:0.2839:0.0	.	295	Q9H343	O51I1_HUMAN	T	292;295	ENSP00000369559:S295T	ENSP00000439622:S292T	S	-	2	0	OR51I1	5418437	0.045000	0.20229	0.998000	0.56505	0.339000	0.28857	2.449000	0.44935	1.289000	0.44618	0.551000	0.68910	AGT	C|0.994;G|0.006	0.006	strong		0.478	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288	
ATP8B3	148229	hgsc.bcm.edu	37	19	1811603	1811603	+	Missense_Mutation	SNP	C	C	T	rs7250872	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1811603C>T	ENST00000310127.6	-	2	371	c.133G>A	c.(133-135)Gga>Aga	p.G45R	ATP8B3_ENST00000539485.1_Missense_Mutation_p.G45R|ATP8B3_ENST00000525591.1_5'UTR|ATP8B3_ENST00000526092.2_5'UTR	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	45			G -> R (in dbSNP:rs7250872).		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)		GTCTCACCTCCGCGGATGCCA	0.657													c|||	1984	0.396166	0.5068	0.4481	5008	,	,		14880	0.374		0.3141	False		,,,				2504	0.317				p.G45R		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G133A						PASS	.	C	,ARG/GLY	1898,2254		457,984,635	53.0	61.0	58.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,133	1.4	0.0	19	dbSNP_116	58	2506,5894		375,1756,2069	yes	utr-5,missense	ATP8B3	NM_001178002.1,NM_138813.2	,125	832,2740,2704	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	29.8333,45.7129,35.086	,probably-damaging	,45/1301	1811603	4404,8148	2076	4200	6276	SO:0001583	missense	148229	exon2			CACCTCCGCGGAT	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.133G>A	19.37:g.1811603C>T	ENSP00000311336:p.Gly45Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	56	35	0.625	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	859	0.3933150183150183	246	0.5	149	0.4116022099447514	221	0.38636363636363635	243	0.32058047493403696	c	13.83	2.353566	0.41700	0.457129	0.298333	ENSG00000130270	ENST00000310127;ENST00000539485	T;T	0.74421	-0.84;-0.84	2.42	1.37	0.22104	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15473	0.013	B	0.08055	0.003	T	0.40869	-0.9540	8	0.51188	T	0.08	.	5.1659	0.15084	0.0:0.8303:0.0:0.1697	rs7250872;rs12985801;rs16990936;rs58934279;rs7250872	45	O60423	AT8B3_HUMAN	R	45	ENSP00000311336:G45R;ENSP00000443574:G45R	ENSP00000311336:G45R	G	-	1	0	ATP8B3	1762603	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-0.497000	0.06428	0.589000	0.29677	-0.258000	0.10820	GGA	C|0.614;T|0.386	0.386	strong		0.657	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
DMXL2	23312	hgsc.bcm.edu	37	15	51792232	51792232	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:51792232A>G	ENST00000251076.5	-	18	3476	c.3189T>C	c.(3187-3189)agT>agC	p.S1063S	DMXL2_ENST00000543779.2_Silent_p.S1063S|DMXL2_ENST00000449909.3_Intron|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	1063						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)		TGCTCACTGTACTGCTATTAT	0.413																																					p.S1063S		Atlas-SNP	.											DMXL2,NS,carcinoma,-1,2	DMXL2	262	2	0			c.T3189C						scavenged	.						132.0	116.0	122.0					15																	51792232		2195	4293	6488	SO:0001819	synonymous_variant	23312	exon18			CACTGTACTGCTA	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.3189T>C	15.37:g.51792232A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	153	2	0.0130719	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Silent	SNP	ENST00000251076.5	37	CCDS10141.1																																																																																			.	.	none		0.413	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
GRIN1	2902	hgsc.bcm.edu	37	9	140051376	140051376	+	Silent	SNP	G	G	A	rs1126442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:140051376G>A	ENST00000371561.3	+	6	1952	c.855G>A	c.(853-855)gtG>gtA	p.V285V	GRIN1_ENST00000471122.1_3'UTR|GRIN1_ENST00000315048.3_Silent_p.V285V|GRIN1_ENST00000371555.4_Silent_p.V306V|GRIN1_ENST00000350902.5_Silent_p.V285V|GRIN1_ENST00000371553.3_Silent_p.V306V|GRIN1_ENST00000371559.4_Silent_p.V285V|GRIN1_ENST00000371546.4_Silent_p.V306V|GRIN1_ENST00000371550.4_Silent_p.V285V|GRIN1_ENST00000371560.3_Silent_p.V306V	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	285					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|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 density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCGACGCCGTGGGCGTGGTGG	0.677													G|||	699	0.139577	0.0265	0.2017	5008	,	,		11686	0.002		0.336	False		,,,				2504	0.1881				p.V306V	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											.	GRIN1	51	.	0			c.G918A						PASS	.	G	,,,,	288,4106		12,264,1921	29.0	31.0	30.0		855,918,918,855,855	2.7	1.0	9	dbSNP_86	30	2741,5845		447,1847,1999	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRIN1	NM_000832.6,NM_001185090.1,NM_001185091.1,NM_007327.3,NM_021569.3	,,,,	459,2111,3920	AA,AG,GG		31.9241,6.5544,23.3359	,,,,	285/886,306/944,306/907,285/939,285/902	140051376	3029,9951	2197	4293	6490	SO:0001819	synonymous_variant	2902	exon7			CGCCGTGGGCGTG		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4584	protein-coding gene	gene with protein product		138249	"""N-methyl-D-aspartate receptor subunit NR1"""	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.855G>A	9.37:g.140051376G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	149	85	0.57047	NM_001185091	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Silent	SNP	ENST00000371561.3	37	CCDS7031.1																																																																																			G|0.800;A|0.200	0.200	strong		0.677	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487169	32487169	+	Silent	SNP	C	C	T	rs143127183	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32487169C>T	ENST00000374975.3	-	3	692	c.630G>A	c.(628-630)acG>acA	p.T210T		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						TGAGAGGGCTCGTCACGCTTG	0.493													C|||	233	0.0465256	0.059	0.0389	5008	,	,		12789	0.0685		0.0368	False		,,,				2504	0.0225				p.T210T		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	0			c.G630A						scavenged	.						73.0	83.0	80.0					6																	32487169		1886	3734	5620	SO:0001819	synonymous_variant	3127	exon3			AGGGCTCGTCACG		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.630G>A	6.37:g.32487169C>T		Somatic	81	2	0.0246914		WXS	Illumina HiSeq	Phase_I	89	5	0.0561798	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			C|0.100;T|0.900	0.900	weak		0.493	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
GSDMC	56169	hgsc.bcm.edu	37	8	130789767	130789767	+	Missense_Mutation	SNP	G	G	A	rs10090835	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	70	0	0		WXS	Illumina HiSeq	Phase_I	112	72	0.642857	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		
TRPC3	7222	hgsc.bcm.edu	37	4	122824052	122824052	+	Silent	SNP	C	C	T	rs11732666	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:122824052C>T	ENST00000379645.3	-	9	2491	c.2418G>A	c.(2416-2418)agG>agA	p.R806R	TRPC3_ENST00000264811.5_Silent_p.R733R|TRPC3_ENST00000513531.1_Silent_p.R678R	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	721					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CCTTCTGAAGCCTTCTCCTTC	0.358													C|||	1399	0.279353	0.0961	0.4049	5008	,	,		17706	0.4137		0.3121	False		,,,				2504	0.2658				p.R806R		Atlas-SNP	.											.	TRPC3	201	.	0			c.G2418A						PASS	.	C	,	586,3820	257.7+/-262.0	40,506,1657	123.0	114.0	117.0		2418,2199	2.7	1.0	4	dbSNP_120	117	2851,5749	448.1+/-361.7	499,1853,1948	no	coding-synonymous,coding-synonymous	TRPC3	NM_001130698.1,NM_003305.2	,	539,2359,3605	TT,TC,CC		33.1512,13.3,26.4263	,	806/922,733/849	122824052	3437,9569	2203	4300	6503	SO:0001819	synonymous_variant	7222	exon9			CTGAAGCCTTCTC	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.2418G>A	4.37:g.122824052C>T		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Silent	SNP	ENST00000379645.3	37	CCDS47130.1																																																																																			C|0.721;T|0.279	0.279	strong		0.358	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
ZNF705A	440077	hgsc.bcm.edu	37	12	8329700	8329700	+	Missense_Mutation	SNP	A	A	C	rs10743253	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:8329700A>C	ENST00000359286.4	+	5	513	c.424A>C	c.(424-426)Aaa>Caa	p.K142Q		NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	142			K -> Q (in dbSNP:rs10743253).		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.K142Q(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		CAGTGGAAAGAAACCCTATGT	0.373													a|||	2152	0.429712	0.2882	0.4683	5008	,	,		-128	0.5198		0.5616	False		,,,				2504	0.365				p.K142Q		Atlas-SNP	.											ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	1	Substitution - Missense(1)	stomach(1)	c.A424C						scavenged	.	A	GLN/LYS	1390,3016		224,942,1037	125.0	128.0	127.0		424	1.4	0.1	12	dbSNP_120	127	4659,3941		1319,2021,960	no	missense	ZNF705A	NM_001004328.2	53	1543,2963,1997	CC,CA,AA		45.8256,31.5479,46.5093	probably-damaging	142/301	8329700	6049,6957	2203	4300	6503	SO:0001583	missense	440077	exon5			GGAAAGAAACCCT	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.424A>C	12.37:g.8329700A>C	ENSP00000352233:p.Lys142Gln	Somatic	374	4	0.0106952		WXS	Illumina HiSeq	Phase_I	329	155	0.471125	NM_001004328		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	1021	0.4674908424908425	136	0.2764227642276423	170	0.4696132596685083	300	0.5244755244755245	415	0.5474934036939314	.	16.40	3.111296	0.56398	0.315479	0.541744	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.02280	4.36;4.36	1.35	1.35	0.21983	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.88450	2.955	0.44309	P	0.0028200000000000447	D	0.57899	0.981	P	0.59221	0.854	T	0.39860	-0.9593	8	0.87932	D	0	.	6.8118	0.23809	1.0:0.0:0.0:0.0	rs10743253;rs17801815	142	Q6ZN79	Z705A_HUMAN	Q	142	ENSP00000379816:K142Q;ENSP00000352233:K142Q	ENSP00000352233:K142Q	K	+	1	0	ZNF705A	8220967	0.311000	0.24536	0.078000	0.20375	0.253000	0.25986	3.275000	0.51639	0.891000	0.36235	0.329000	0.21502	AAA	A|0.528;C|0.471	0.471	strong		0.373	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
ABCA1	19	hgsc.bcm.edu	37	9	107602666	107602666	+	Silent	SNP	C	C	T	rs2246841	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:107602666C>T	ENST00000374736.3	-	9	1342	c.948G>A	c.(946-948)ggG>ggA	p.G316G		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	316					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)	TGATCTTCAGCCCCCCTCCCT	0.512													C|||	764	0.152556	0.2685	0.1859	5008	,	,		19626	0.0377		0.0944	False		,,,				2504	0.1503				p.G316G		Atlas-SNP	.											.	ABCA1	244	.	0			c.G948A						PASS	.	C		978,3428	367.1+/-318.1	121,736,1346	117.0	89.0	98.0		948	-3.4	1.0	9	dbSNP_100	98	965,7635	210.4+/-251.3	49,867,3384	no	coding-synonymous	ABCA1	NM_005502.3		170,1603,4730	TT,TC,CC		11.2209,22.197,14.9393		316/2262	107602666	1943,11063	2203	4300	6503	SO:0001819	synonymous_variant	19	exon9			CTTCAGCCCCCCT	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.948G>A	9.37:g.107602666C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	241	115	0.477178	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			C|0.866;T|0.134	0.134	strong		0.512	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
MUC4	4585	hgsc.bcm.edu	37	3	195508722	195508722	+	Silent	SNP	G	G	T	rs201248411	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195508722G>T	ENST00000463781.3	-	2	10188	c.9729C>A	c.(9727-9729)acC>acA	p.T3243T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T3243T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	992					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.T3243T(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)		TGGCATGACCGGTGGATGCTG	0.577													.|||	14	0.00279553	0.0083	0.0014	5008	,	,		10446	0.001		0.001	False		,,,				2504	0.0				p.T3243T		Atlas-SNP	.											MUC4_ENST00000463781,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C9729A						scavenged	.						2.0	2.0	2.0					3																	195508722		481	1089	1570	SO:0001819	synonymous_variant	4585	exon2			ATGACCGGTGGAT	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.9729C>A	3.37:g.195508722G>T		Somatic	147	2	0.0136054		WXS	Illumina HiSeq	Phase_I	170	11	0.0647059	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		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CSHL1	1444	hgsc.bcm.edu	37	17	61987570	61987570	+	Missense_Mutation	SNP	G	G	T	rs2727307	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:61987570G>T	ENST00000309894.5	-	4	422	c.423C>A	c.(421-423)gaC>gaA	p.D141E	CSHL1_ENST00000346606.6_Missense_Mutation_p.D47E|CSHL1_ENST00000438387.2_Missense_Mutation_p.D58E|CSHL1_ENST00000450719.3_Missense_Mutation_p.D47E|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000259003.10_Missense_Mutation_p.D79E|CSHL1_ENST00000392824.4_3'UTR|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						scavenged	.	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	600	5	0.00833333		WXS	Illumina HiSeq	Phase_I	440	163	0.370455	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	
SLC12A3	6559	hgsc.bcm.edu	37	16	56933519	56933519	+	Missense_Mutation	SNP	G	G	A	rs11643718	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:56933519G>A	ENST00000563236.1	+	23	2736	c.2711G>A	c.(2710-2712)cGg>cAg	p.R904Q	SLC12A3_ENST00000262502.5_Missense_Mutation_p.R903Q|SLC12A3_ENST00000438926.2_Missense_Mutation_p.R913Q|SLC12A3_ENST00000566786.1_Missense_Mutation_p.R912Q			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	904			R -> Q (in dbSNP:rs11643718). {ECO:0000269|PubMed:10988270, ECO:0000269|PubMed:12112667, ECO:0000269|PubMed:17885550, ECO:0000269|PubMed:9734597}.		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)	CAGAACCCTCGGGCTGAGCAG	0.547													G|||	400	0.0798722	0.0061	0.1369	5008	,	,		20913	0.0744		0.1392	False		,,,				2504	0.0838				p.R913Q		Atlas-SNP	.											SLC12A3,NS,carcinoma,+1,1	SLC12A3	99	1	0			c.G2738A	GRCh37	CM981835	SLC12A3	M	rs11643718	PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	95,4301	76.2+/-114.5	1,93,2104	116.0	107.0	110.0		2738,2735,2711	1.7	0.2	16	dbSNP_120	110	894,7706	202.1+/-245.5	42,810,3448	yes	missense,missense,missense	SLC12A3	NM_000339.2,NM_001126107.1,NM_001126108.1	43,43,43	43,903,5552	AA,AG,GG		10.3953,2.1611,7.61	benign,benign,benign	913/1031,912/1030,904/1022	56933519	989,12007	2198	4300	6498	SO:0001583	missense	6559	exon23			ACCCTCGGGCTGA		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.2711G>A	16.37:g.56933519G>A	ENSP00000456149:p.Arg904Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	80	0.792079	NM_000339	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	37	CCDS58464.1	203	0.09294871794871795	0	0.0	60	0.16574585635359115	50	0.08741258741258741	93	0.12269129287598944	G	3.616	-0.078648	0.07141	0.021611	0.103953	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	4.9	1.7	0.24286	.	0.307617	0.36591	N	0.002511	T	0.00039	0.0001	N	0.02129	-0.67	0.43065	P	0.005303999999999975	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.30909	-0.9962	8	0.02654	T	1	.	8.3737	0.32430	0.2824:0.0:0.7176:0.0	rs11643718;rs17360804;rs52810200;rs61353958;rs11643718	912;904;913	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	Q	912;913	.	ENSP00000262502:R913Q	R	+	2	0	SLC12A3	55491020	0.961000	0.32948	0.158000	0.22627	0.787000	0.44495	1.550000	0.36223	0.079000	0.16929	0.561000	0.74099	CGG	G|0.914;A|0.086	0.086	strong		0.547	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		
WNK1	65125	hgsc.bcm.edu	37	12	994014	994014	+	Silent	SNP	C	C	T	rs10849577	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:994014C>T	ENST00000315939.6	+	19	4687	c.4044C>T	c.(4042-4044)acC>acT	p.T1348T	WNK1_ENST00000340908.4_Silent_p.T941T|WNK1_ENST00000537687.1_Silent_p.T1608T|WNK1_ENST00000535572.1_Silent_p.T1101T|WNK1_ENST00000530271.2_Silent_p.T1846T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1348					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)			GAGTCCCAACCACAGCAGCAG	0.493													C|||	580	0.115815	0.0363	0.1052	5008	,	,		19854	0.1825		0.1531	False		,,,				2504	0.1237				p.T1608T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C4824T						PASS	.	C	,,,	232,4174	138.0+/-173.8	9,214,1980	87.0	82.0	84.0		4824,3303,4044,4800	0.4	0.0	12	dbSNP_120	84	1222,7378	246.2+/-274.8	90,1042,3168	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	,,,	99,1256,5148	TT,TC,CC		14.2093,5.2655,11.1795	,,,	1608/2643,1101/2135,1348/2383,1600/2635	994014	1454,11552	2203	4300	6503	SO:0001819	synonymous_variant	65125	exon19			CCCAACCACAGCA	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.4044C>T	12.37:g.994014C>T		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	305	142	0.465574	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			C|0.885;T|0.115	0.115	strong		0.493	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
AGBL1	123624	hgsc.bcm.edu	37	15	86790936	86790936	+	Silent	SNP	C	C	T	rs371409529		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:86790936C>T	ENST00000441037.2	+	6	518	c.423C>T	c.(421-423)taC>taT	p.Y141Y	AGBL1_ENST00000421325.2_Silent_p.Y141Y	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	141					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						ACCGAGGCTACGTCACCAGCC	0.597																																					p.Y141Y		Atlas-SNP	.											AGBL1,bladder,carcinoma,0,1	AGBL1	151	1	0			c.C423T						PASS	.						25.0	27.0	26.0					15																	86790936		2139	4253	6392	SO:0001819	synonymous_variant	123624	exon6			AGGCTACGTCACC	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.423C>T	15.37:g.86790936C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	105	80	0.761905	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			.	.	alt		0.597	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
OR1A2	26189	hgsc.bcm.edu	37	17	3101691	3101691	+	Missense_Mutation	SNP	G	G	T	rs12150427	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	107	107	1	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	
TSSK2	23617	hgsc.bcm.edu	37	22	19119686	19119686	+	Silent	SNP	C	C	T	rs1052756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	89	0	0		WXS	Illumina HiSeq	Phase_I	104	43	0.413462	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		
BAI2	576	hgsc.bcm.edu	37	1	32193185	32193185	+	Missense_Mutation	SNP	G	G	A	rs41263977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32193185G>A	ENST00000373658.3	-	33	4935	c.4594C>T	c.(4594-4596)Cgc>Tgc	p.R1532C	BAI2_ENST00000398542.1_Missense_Mutation_p.R1413C|BAI2_ENST00000398547.1_Missense_Mutation_p.R1446C|BAI2_ENST00000398538.1_Missense_Mutation_p.R1501C|BAI2_ENST00000373655.2_Missense_Mutation_p.R1531C|BAI2_ENST00000257070.4_Missense_Mutation_p.R1498C|BAI2_ENST00000440175.2_Missense_Mutation_p.R1122C|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000527361.1_Missense_Mutation_p.R1498C|BAI2_ENST00000398556.3_Missense_Mutation_p.R1447C	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1532					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		AAGCTGGGGCGCTCCCCAGGG	0.612													G|||	12	0.00239617	0.0	0.0	5008	,	,		14744	0.0		0.0089	False		,,,				2504	0.0031				p.R1532C		Atlas-SNP	.											.	BAI2	128	.	0			c.C4594T						PASS	.	G	CYS/ARG	7,4399	12.9+/-30.5	0,7,2196	20.0	20.0	20.0		4594	3.3	1.0	1	dbSNP_127	20	77,8523	44.9+/-103.4	0,77,4223	yes	missense	BAI2	NM_001703.2	180	0,84,6419	AA,AG,GG		0.8953,0.1589,0.6459	probably-damaging	1532/1586	32193185	84,12922	2203	4300	6503	SO:0001583	missense	576	exon33			TGGGGCGCTCCCC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4594C>T	1.37:g.32193185G>A	ENSP00000362762:p.Arg1532Cys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	78	58	0.74359	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	14.71	2.616398	0.46736	0.001589	0.008953	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.48201	3.33;1.62;3.33;3.33;1.8;3.33;3.33;1.46;0.82	4.29	3.3	0.37823	.	0.412552	0.18103	N	0.151610	T	0.47911	0.1471	L	0.52011	1.625	0.39636	D	0.970247	P;D;D;P;D;D	0.76494	0.95;0.999;0.981;0.95;0.999;0.988	B;P;P;B;P;B	0.59825	0.409;0.864;0.608;0.409;0.735;0.295	T	0.58267	-0.7666	10	0.87932	D	0	.	11.0708	0.48002	0.0:0.0:0.8153:0.1847	rs41263977	1498;1520;1122;1531;1532;1501	O60241-4;O60241-3;B4DKC3;O60241-2;O60241;A2A3C2	.;.;.;.;BAI2_HUMAN;.	C	1447;1446;1532;1531;1413;1498;1498;1122;1501	ENSP00000381564:R1447C;ENSP00000381555:R1446C;ENSP00000362762:R1532C;ENSP00000362759:R1531C;ENSP00000381550:R1413C;ENSP00000257070:R1498C;ENSP00000435397:R1498C;ENSP00000391071:R1122C;ENSP00000381548:R1501C	ENSP00000257070:R1498C	R	-	1	0	BAI2	31965772	0.999000	0.42202	0.997000	0.53966	0.941000	0.58515	4.208000	0.58486	2.401000	0.81631	0.561000	0.74099	CGC	G|0.994;A|0.006	0.006	strong		0.612	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
ZNF492	57615	hgsc.bcm.edu	37	19	22848028	22848028	+	Missense_Mutation	SNP	G	G	C	rs3745115	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22848028G>C	ENST00000456783.2	+	4	1801	c.1557G>C	c.(1555-1557)aaG>aaC	p.K519N	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	519					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.K519N(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				ACATTGCAAAGATTTCCAAAT	0.323													N|||	980	0.195687	0.354	0.1268	5008	,	,		20410	0.1667		0.1302	False		,,,				2504	0.1278				p.K519N		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	1	Substitution - Missense(1)	stomach(1)	c.G1557C						scavenged	.						18.0	18.0	18.0					19																	22848028		1781	4025	5806	SO:0001583	missense	57615	exon4			TGCAAAGATTTCC	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1557G>C	19.37:g.22848028G>C	ENSP00000413660:p.Lys519Asn	Somatic	836	0	0		WXS	Illumina HiSeq	Phase_I	793	200	0.252207	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.565994	0.00134	.	.	ENSG00000229676	ENST00000456783	T	0.07688	3.17	1.03	-2.06	0.07298	.	.	.	.	.	T	0.02156	0.0067	N	0.03000	-0.44	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40924	-0.9537	8	0.07482	T	0.82	.	0.2809	0.00244	0.2469:0.289:0.2459:0.2181	rs3745115;rs7259827;rs59664756	519	Q9P255	ZN492_HUMAN	N	519	ENSP00000413660:K519N	ENSP00000413660:K519N	K	+	3	2	ZNF492	22639868	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-0.195000	0.09546	-1.287000	0.02381	-1.858000	0.00562	AAG	G|0.500;C|0.500	0.500	weak		0.323	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
DRC7	84229	hgsc.bcm.edu	37	16	57758732	57758732	+	Missense_Mutation	SNP	C	C	A	rs2923144	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57758732C>A	ENST00000360716.3	+	13	1964	c.1743C>A	c.(1741-1743)aaC>aaA	p.N581K	CCDC135_ENST00000394337.4_Missense_Mutation_p.N581K|CCDC135_ENST00000336825.8_Missense_Mutation_p.N516K			Q8IY82	CC135_HUMAN		581			N -> K (in dbSNP:rs2923144).		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						CAGAGTCAAACCCCCGGCCCA	0.602													.|||	450	0.0898562	0.1815	0.0634	5008	,	,		18037	0.001		0.1004	False		,,,				2504	0.0654				p.N581K		Atlas-SNP	.											.	CCDC135	97	.	0			c.C1743A						PASS	.	C	LYS/ASN	725,3669		62,601,1534	47.0	41.0	43.0		1743	-0.1	0.9	16	dbSNP_101	43	842,7756		36,770,3493	yes	missense	CCDC135	NM_032269.5	94	98,1371,5027	AA,AC,CC		9.793,16.4998,12.0613	probably-damaging	581/875	57758732	1567,11425	2197	4299	6496	SO:0001583	missense	84229	exon12			GTCAAACCCCCGG																												ENST00000360716.3:c.1743C>A	16.37:g.57758732C>A	ENSP00000353942:p.Asn581Lys	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	63	49	0.777778	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	173	0.07921245421245421	73	0.1483739837398374	26	0.0718232044198895	1	0.0017482517482517483	73	0.09630606860158311	.	16.68	3.189813	0.57909	0.164998	0.09793	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.09445	3.14;2.98;3.14	5.2	-0.106	0.13596	.	0.296489	0.37715	N	0.001979	T	0.00109	0.0003	M	0.80183	2.485	0.24037	P	0.9960909	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.977	T	0.12167	-1.0558	9	0.18276	T	0.48	-47.579	9.4754	0.38869	0.0:0.6228:0.0:0.3772	rs2923144;rs52829900;rs59847143;rs2923144	516;581	Q8IY82-2;Q8IY82	.;CC135_HUMAN	K	581;516;581	ENSP00000377869:N581K;ENSP00000338938:N516K;ENSP00000353942:N581K	ENSP00000338938:N516K	N	+	3	2	CCDC135	56316233	0.251000	0.23961	0.949000	0.38748	0.883000	0.51084	-0.202000	0.09451	0.222000	0.20900	-0.218000	0.12543	AAC	C|0.891;A|0.109	0.109	strong		0.602	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
TOR2A	27433	hgsc.bcm.edu	37	9	130495633	130495633	+	Intron	SNP	C	C	G	rs564754	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:130495633C>G	ENST00000373284.5	-	3	640				TOR2A_ENST00000458505.3_3'UTR|TOR2A_ENST00000336067.6_Intron|TOR2A_ENST00000373281.5_Missense_Mutation_p.W208C|TOR2A_ENST00000472723.1_5'UTR	NM_001085347.2	NP_001078816	Q5JU69	TOR2A_HUMAN	torsin family 2, member A						chaperone mediated protein folding requiring cofactor (GO:0051085)|protein homooligomerization (GO:0051260)	endoplasmic reticulum lumen (GO:0005788)	ATP binding (GO:0005524)			NS(1)|endometrium(2)	3						AGTGGCCCCCCCACTGTGCCC	0.602													C|||	3124	0.623802	0.7844	0.6081	5008	,	,		17651	0.371		0.6332	False		,,,				2504	0.6687				p.W208C		Atlas-SNP	.											.	TOR2A	26	.	0			c.G624C						PASS	.	C	,,,CYS/TRP	3267,1139	711.3+/-408.0	1215,837,151	50.0	49.0	49.0		,,,624	-1.4	0.0	9	dbSNP_83	49	5087,3513	627.7+/-398.0	1505,2077,718	yes	intron,intron,utr-3,missense	TOR2A	NM_001085347.1,NM_001134430.1,NM_001134431.1,NM_130459.2	,,,215	2720,2914,869	GG,GC,CC		40.8488,25.8511,35.7681	,,,	,,,208/254	130495633	8354,4652	2203	4300	6503	SO:0001627	intron_variant	27433	exon3			GCCCCCCCACTGT	AA873275	CCDS6876.1, CCDS43879.1, CCDS48024.1	9q34.11	2010-08-20			ENSG00000160404	ENSG00000160404			11996	protein-coding gene	gene with protein product		608052				10644435	Standard	NM_001085347		Approved	FLJ14771, TORP1	uc004brs.4	Q5JU69	OTTHUMG00000020706	ENST00000373284.5:c.593+30G>C	9.37:g.130495633C>G		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_130459	A4FU12|A4FU13|Q3ZCN9|Q3ZCP0|Q5JU68|Q66K87|Q6UXW6|Q8NAN5|Q96SL7	Missense_Mutation	SNP	ENST00000373284.5	37	CCDS43879.1	1311	0.6002747252747253	382	0.7764227642276422	219	0.6049723756906077	220	0.38461538461538464	490	0.6464379947229552	C	10.73	1.432873	0.25813	0.741489	0.591512	ENSG00000160404	ENST00000373281	T	0.69040	-0.37	5.39	-1.4	0.08968	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.35475	-0.9787	7	0.38643	T	0.18	.	5.8881	0.18892	0.137:0.2686:0.5145:0.0798	rs564754;rs1755665;rs3739813;rs57276118;rs564754	208	Q5JU69-2	.	C	208	ENSP00000362378:W208C	ENSP00000362378:W208C	W	-	3	0	TOR2A	129535454	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.060000	0.03475	-0.643000	0.05473	-0.311000	0.09066	TGG	C|0.370;G|0.630	0.630	strong		0.602	TOR2A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054205.1	NM_130459	
EFTUD1	79631	hgsc.bcm.edu	37	15	82444437	82444437	+	Silent	SNP	A	A	G	rs905450	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:82444437A>G	ENST00000268206.7	-	18	2526	c.2358T>C	c.(2356-2358)ggT>ggC	p.G786G	EFTUD1_ENST00000359445.3_Silent_p.G735G	NM_024580.5	NP_078856.4	Q7Z2Z2	ETUD1_HUMAN	elongation factor Tu GTP binding domain containing 1	786					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						GAGTATTTTCACCCTCATTCA	0.423													G|||	3934	0.785543	0.8714	0.853	5008	,	,		19640	0.8353		0.7624	False		,,,				2504	0.5941				p.G786G		Atlas-SNP	.											.	EFTUD1	74	.	0			c.T2358C						PASS	.	G	,	3165,545		1354,457,44	98.0	90.0	93.0		2205,2358	-0.3	0.1	15	dbSNP_86	93	6458,1752		2550,1358,197	no	coding-synonymous,coding-synonymous	EFTUD1	NM_001040610.2,NM_024580.5	,	3904,1815,241	GG,GA,AA		21.3398,14.69,19.2701	,	735/1070,786/1121	82444437	9623,2297	1855	4105	5960	SO:0001819	synonymous_variant	79631	exon18			ATTTTCACCCTCA	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.2358T>C	15.37:g.82444437A>G		Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_024580	A6NKY5|B7Z6I0|Q9H8Z6	Silent	SNP	ENST00000268206.7	37	CCDS42071.1																																																																																			A|0.199;G|0.801	0.801	strong		0.423	EFTUD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419252.1	NM_024580	
OBSCN	84033	hgsc.bcm.edu	37	1	228479642	228479642	+	Silent	SNP	C	C	T	rs371392180	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:228479642C>T	ENST00000422127.1	+	39	10427	c.10383C>T	c.(10381-10383)gcC>gcT	p.A3461A	OBSCN_ENST00000366707.4_Silent_p.A580A|OBSCN_ENST00000359599.6_Silent_p.A2308A|OBSCN_ENST00000570156.2_Silent_p.A3890A|OBSCN_ENST00000366709.4_Silent_p.A580A|OBSCN_ENST00000284548.11_Silent_p.A3461A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3461	Ig-like 35.				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)				ATGAAGAGGCCGTGGAAGGGG	0.582													C|||	6	0.00119808	0.0	0.0	5008	,	,		18976	0.006		0.0	False		,,,				2504	0.0				p.A3890A		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,+1,4	OBSCN	2142	4	0			c.C11670T						scavenged	.	C	,	1,3869		0,1,1934	47.0	46.0	46.0		10383,10383	0.9	0.0	1		46	0,8270		0,0,4135	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,1,6069	TT,TC,CC		0.0,0.0258,0.0082	,	3461/7969,3461/6621	228479642	1,12139	1935	4135	6070	SO:0001819	synonymous_variant	84033	exon44			AGAGGCCGTGGAA	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.10383C>T	1.37:g.228479642C>T		Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	381	5	0.0131234	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																																																																																			.	.	none		0.582	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
LYZL2	119180	hgsc.bcm.edu	37	10	30918597	30918597	+	Missense_Mutation	SNP	T	T	C	rs74551644		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:30918597T>C	ENST00000375318.2	-	1	94	c.38A>G	c.(37-39)aAg>aGg	p.K13R		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	0					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)	p.K13R(1)		NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				ACTGCTCCACTTAGTCGGTGA	0.498																																					p.K13R		Atlas-SNP	.											LYZL2,NS,carcinoma,0,1	LYZL2	33	1	1	Substitution - Missense(1)	prostate(1)	c.A38G						scavenged	.						75.0	68.0	71.0					10																	30918597		2203	4298	6501	SO:0001583	missense	119180	exon1			CTCCACTTAGTCG	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.38A>G	10.37:g.30918597T>C	ENSP00000364467:p.Lys13Arg	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	119	11	0.092437	NM_183058	Q6NZ69	Missense_Mutation	SNP	ENST00000375318.2	37	CCDS7167.2	.	.	.	.	.	.	.	.	.	.	T	7.959	0.746565	0.15710	.	.	ENSG00000151033	ENST00000375318	T	0.67865	-0.29	2.18	2.18	0.27775	.	6.432820	0.00541	N	0.000231	T	0.73999	0.3659	.	.	.	0.21719	N	0.999579	D	0.60575	0.988	D	0.73708	0.981	T	0.59306	-0.7479	9	0.19147	T	0.46	-9.5578	6.3337	0.21285	0.0:0.0:0.0:1.0	rs2532753;rs3736977;rs10826590;rs2532753	13	Q7Z4W2-2	.	R	13	ENSP00000364467:K13R	ENSP00000364467:K13R	K	-	2	0	LYZL2	30958603	0.998000	0.40836	0.964000	0.40570	0.029000	0.11900	1.416000	0.34759	1.241000	0.43820	0.377000	0.23210	AAG	.	.	weak		0.498	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058	
PCDHB2	56133	hgsc.bcm.edu	37	5	140475763	140475763	+	Silent	SNP	C	C	G	rs142417694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140475763C>G	ENST00000194155.4	+	1	1537	c.1389C>G	c.(1387-1389)cgC>cgG	p.R463R		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	463	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)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTTCGTCCGCGAGAACAACA	0.637																																					p.R463R		Atlas-SNP	.											PCDHB2,NS,carcinoma,+2,2	PCDHB2	163	2	0			c.C1389G						scavenged	.						78.0	79.0	79.0					5																	140475763		2203	4296	6499	SO:0001819	synonymous_variant	56133	exon1			CGTCCGCGAGAAC	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1389C>G	5.37:g.140475763C>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	123	26	0.211382	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																			C|0.029;G|0.971	0.971	strong		0.637	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
ZIM3	114026	hgsc.bcm.edu	37	19	57649884	57649884	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57649884T>C	ENST00000269834.1	-	3	483	c.98A>G	c.(97-99)tAc>tGc	p.Y33C		NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	33	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(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)		CACATCCCTGTACAAGTTTCT	0.532																																					p.Y33C		Atlas-SNP	.											ZIM3,NS,carcinoma,-1,1	ZIM3	107	1	0			c.A98G						scavenged	.						109.0	95.0	100.0					19																	57649884		2203	4300	6503	SO:0001583	missense	114026	exon3			TCCCTGTACAAGT	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.98A>G	19.37:g.57649884T>C	ENSP00000269834:p.Tyr33Cys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	136	5	0.0367647	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	T	11.46	1.644026	0.29246	.	.	ENSG00000141946	ENST00000269834	T	0.07021	3.23	3.07	2.0	0.26442	Krueppel-associated box (4);	.	.	.	.	T	0.15565	0.0375	M	0.93106	3.38	0.22066	N	0.999387	P	0.45986	0.87	B	0.38562	0.276	T	0.19976	-1.0289	9	0.87932	D	0	.	6.4192	0.21734	0.0:0.1331:0.0:0.8669	.	33	Q96PE6	ZIM3_HUMAN	C	33	ENSP00000269834:Y33C	ENSP00000269834:Y33C	Y	-	2	0	ZIM3	62341696	0.810000	0.29049	0.193000	0.23327	0.404000	0.30871	2.363000	0.44178	0.250000	0.21479	0.172000	0.16884	TAC	.	.	none		0.532	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
TEP1	7011	hgsc.bcm.edu	37	14	20850093	20850093	+	Missense_Mutation	SNP	C	C	T	rs1713456	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20850093C>T	ENST00000262715.5	-	30	4443	c.4403G>A	c.(4402-4404)tGc>tAc	p.C1468Y	TEP1_ENST00000556935.1_Missense_Mutation_p.C1360Y|TEP1_ENST00000545983.1_5'UTR	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1468	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		C -> Y (in dbSNP:rs1713456).		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)		CTGGACGAGGCAGGCAAACGG	0.612													T|||	1198	0.239217	0.4448	0.1888	5008	,	,		17667	0.0992		0.1889	False		,,,				2504	0.1933				p.C1468Y		Atlas-SNP	.											TEP1,NS,carcinoma,+1,1	TEP1	224	1	0			c.G4403A						scavenged	.	T	TYR/CYS	1672,2734	655.1+/-399.9	327,1018,858	147.0	132.0	137.0		4403	3.8	1.0	14	dbSNP_89	137	1579,7021	744.7+/-407.2	141,1297,2862	yes	missense	TEP1	NM_007110.4	194	468,2315,3720	TT,TC,CC		18.3605,37.9483,24.9962	benign	1468/2628	20850093	3251,9755	2203	4300	6503	SO:0001583	missense	7011	exon30			ACGAGGCAGGCAA		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.4403G>A	14.37:g.20850093C>T	ENSP00000262715:p.Cys1468Tyr	Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	120	116	0.966667	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	486	0.22252747252747251	213	0.4329268292682927	73	0.20165745856353592	50	0.08741258741258741	150	0.19788918205804748	T	0.800	-0.755646	0.03019	0.379483	0.183605	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.43688	1.01;0.94	4.98	3.82	0.43975	.	0.431628	0.25302	N	0.031653	T	0.00012	0.0000	N	0.00170	-1.935	0.09310	P	0.999999999813782	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.45175	-0.9279	9	0.02654	T	1	-6.2294	4.6463	0.12574	0.1671:0.0917:0.0:0.7411	rs1713456;rs2228029;rs52817703;rs60076485;rs1713456	1360;811;1468	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	Y	1468;1468;1360	ENSP00000262715:C1468Y;ENSP00000452574:C1360Y	ENSP00000262715:C1468Y	C	-	2	0	TEP1	19919933	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.613000	0.24299	0.325000	0.23359	-0.521000	0.04368	TGC	C|0.754;A|0.001	.	strong		0.612	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
ANKRD6	22881	hgsc.bcm.edu	37	6	90340446	90340446	+	Missense_Mutation	SNP	C	C	T	rs61739327	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:90340446C>T	ENST00000522441.1	+	16	2548	c.1907C>T	c.(1906-1908)cCc>cTc	p.P636L	ANKRD6_ENST00000369408.5_Missense_Mutation_p.P601L|ANKRD6_ENST00000339746.4_Missense_Mutation_p.P636L|ANKRD6_ENST00000520793.1_Missense_Mutation_p.P572L|LYRM2_ENST00000520441.1_Intron|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	54	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	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		
ITGB1	3688	hgsc.bcm.edu	37	10	33214802	33214802	+	Silent	SNP	A	A	G	rs2298141	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:33214802A>G	ENST00000396033.2	-	6	918	c.783T>C	c.(781-783)tgT>tgC	p.C261C	ITGB1_ENST00000302278.3_Silent_p.C261C|ITGB1_ENST00000374956.4_Silent_p.C261C|ITGB1_ENST00000423113.1_Silent_p.C261C|ITGB1_ENST00000484088.1_5'Flank	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	261	VWFA.			CGSLI -> VWMLL (in Ref. 6; AAI13902). {ECO:0000305}.	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)	CGCTTACTCCACAAACTGCAA	0.348													A|||	784	0.15655	0.0401	0.1859	5008	,	,		18818	0.245		0.172	False		,,,				2504	0.1861				p.C261C		Atlas-SNP	.											.	ITGB1	156	.	0			c.T783C						PASS	.	A	,,	250,4156	143.8+/-178.8	9,232,1962	96.0	89.0	92.0		783,783,783	4.6	1.0	10	dbSNP_100	92	1510,7090	285.7+/-297.3	139,1232,2929	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB1	NM_002211.3,NM_033668.2,NM_133376.2	,,	148,1464,4891	GG,GA,AA		17.5581,5.6741,13.5322	,,	261/799,261/802,261/799	33214802	1760,11246	2203	4300	6503	SO:0001819	synonymous_variant	3688	exon6			TACTCCACAAACT	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.783T>C	10.37:g.33214802A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	54	42	0.777778	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																																																																																			A|0.852;G|0.148	0.148	strong		0.348	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211	
MCPH1	79648	hgsc.bcm.edu	37	8	6500544	6500544	+	Missense_Mutation	SNP	C	C	T	rs1057091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:6500544C>T	ENST00000344683.5	+	14	2558	c.2482C>T	c.(2482-2484)Cct>Tct	p.P828S	CTD-2541M15.1_ENST00000527490.1_RNA|CTD-2541M15.1_ENST00000522897.1_RNA|CTD-2541M15.1_ENST00000525186.1_RNA|CTD-2541M15.1_ENST00000515608.1_RNA|MCPH1_ENST00000521175.1_3'UTR	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	828	BRCT 3. {ECO:0000255|PROSITE- ProRule:PRU00033}.		P -> S (in dbSNP:rs1057091). {ECO:0000269|PubMed:18204051}.		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)		GGTCTGTGCCCCTGAAAACTA	0.448													T|||	1220	0.24361	0.174	0.183	5008	,	,		18018	0.2103		0.2972	False		,,,				2504	0.3599				p.P828S	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.C2482T						PASS	.	T	SER/PRO	730,3194		68,594,1300	107.0	102.0	104.0		2482	-1.4	0.0	8	dbSNP_86	104	2508,5792		390,1728,2032	yes	missense	MCPH1	NM_024596.3	74	458,2322,3332	TT,TC,CC		30.2169,18.6035,26.4889	benign	828/836	6500544	3238,8986	1962	4150	6112	SO:0001583	missense	79648	exon14			TGTGCCCCTGAAA	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.2482C>T	8.37:g.6500544C>T	ENSP00000342924:p.Pro828Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	183	47	0.256831	NM_024596	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Missense_Mutation	SNP	ENST00000344683.5	37	CCDS43689.1	492	0.22527472527472528	77	0.1565040650406504	81	0.22375690607734808	112	0.1958041958041958	222	0.2928759894459103	T	0.007	-1.987825	0.00443	0.186035	0.302169	ENSG00000147316	ENST00000344683	D	0.89681	-2.55	4.82	-1.42	0.08913	BRCT (2);	0.437392	0.22979	N	0.053330	T	0.00012	0.0000	N	0.02736	-0.51	0.54753	P	1.0999999999983245E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.18178	-1.0345	9	0.38643	T	0.18	-0.9738	1.0083	0.01492	0.1455:0.178:0.2993:0.3772	rs1057091;rs3197703;rs52793579;rs57739761;rs1057091	828	Q8NEM0	MCPH1_HUMAN	S	828	ENSP00000342924:P828S	ENSP00000342924:P828S	P	+	1	0	MCPH1	6487952	0.017000	0.18338	0.043000	0.18650	0.233000	0.25261	0.291000	0.18994	-0.340000	0.08388	-1.776000	0.00657	CCT	C|0.750;T|0.250	0.250	strong		0.448	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
KLRC4	8302	hgsc.bcm.edu	37	12	10560957	10560957	+	Missense_Mutation	SNP	T	T	C	rs2617170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	194	192	0.989691	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	
MUC16	94025	hgsc.bcm.edu	37	19	9065510	9065510	+	Silent	SNP	G	G	A	rs1867692	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9065510G>A	ENST00000397910.4	-	3	22139	c.21936C>T	c.(21934-21936)ttC>ttT	p.F7312F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7314	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						GGGAAGTAGGGAACTTAATGA	0.453													N|||	906	0.180911	0.2458	0.1196	5008	,	,		22237	0.2679		0.0895	False		,,,				2504	0.1411				p.F7312F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C21936T						PASS	.	G		844,3010		94,656,1177	143.0	138.0	140.0		21936	-0.8	0.0	19	dbSNP_92	140	642,7584		27,588,3498	no	coding-synonymous	MUC16	NM_024690.2		121,1244,4675	AA,AG,GG		7.8045,21.8993,12.3013		7312/14508	9065510	1486,10594	1927	4113	6040	SO:0001819	synonymous_variant	94025	exon3			AGTAGGGAACTTA	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.21936C>T	19.37:g.9065510G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.825;A|0.175	0.175	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
BEST1	7439	hgsc.bcm.edu	37	11	61730553	61730553	+	Intron	SNP	T	T	C	rs17185413	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:61730553T>C	ENST00000378043.4	+	10	2382				BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000449131.2_Missense_Mutation_p.S583P|BEST1_ENST00000378042.3_Intron|BEST1_ENST00000301774.9_Missense_Mutation_p.S271P|FTH1_ENST00000529191.1_Intron|FTH1_ENST00000529631.1_Intron	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						scavenged	.	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	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	167	78	0.467066	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	
L3MBTL4	91133	hgsc.bcm.edu	37	18	5956238	5956238	+	Missense_Mutation	SNP	C	C	T	rs3737353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:5956238C>T	ENST00000284898.6	-	20	2053	c.1853G>A	c.(1852-1854)gGc>gAc	p.G618D	L3MBTL4_ENST00000535782.1_Missense_Mutation_p.G422D|L3MBTL4_ENST00000400105.2_Missense_Mutation_p.G618D|L3MBTL4_ENST00000317931.7_Missense_Mutation_p.G609D|RP11-793A3.1_ENST00000577704.1_RNA	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						scavenged	.	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	178	2	0.011236		WXS	Illumina HiSeq	Phase_I	181	179	0.98895	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	
MICA	100507436	hgsc.bcm.edu	37	6	31379807	31379807	+	Missense_Mutation	SNP	C	C	T	rs1051798	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31379807C>T	ENST00000449934.2	+	4	751	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	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)				CTTCTATCCCCGGAATATCAT	0.582													t|||	1823	0.364018	0.4773	0.4063	5008	,	,		19217	0.2996		0.3141	False		,,,				2504	0.2986				p.R233W		Atlas-SNP	.											.	MICA	21	.	0			c.C697T						PASS	.						16.0	20.0	18.0					6																	31379807		692	1589	2281	SO:0001583	missense	100507436	exon4			TATCCCCGGAATA	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.697C>T	6.37:g.31379807C>T	ENSP00000413079:p.Arg233Trp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	38	0.319328	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	688	0.315018315018315	200	0.4065040650406504	150	0.4143646408839779	136	0.23776223776223776	202	0.26649076517150394	N	3.279	-0.147379	0.06627	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.15017	2.46;2.46	2.52	-5.05	0.02955	.	1.658740	0.04364	N	0.357915	T	0.02304	0.0071	.	.	.	0.80722	P	0.0	B;B	0.18310	0.027;0.008	B;B	0.09377	0.004;0.002	T	0.28681	-1.0036	8	0.39692	T	0.17	.	1.8464	0.03160	0.1203:0.2683:0.332:0.2794	rs1051798;rs3192174;rs17200323;rs17845521;rs17858411;rs17883108;rs52816780;rs1051798	95;233	Q5SS58;Q96QC4	.;.	W	95;233;190;233;124	ENSP00000413079:R233W;ENSP00000402410:R124W	ENSP00000365394:R233W	R	+	1	2	MICA	31487786	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-9.749000	0.00009	-2.258000	0.00694	-3.922000	0.00016	CGG	C|0.730;T|0.270	0.270	strong		0.582	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
SCN7A	6332	hgsc.bcm.edu	37	2	167319011	167319011	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:167319011T>A	ENST00000409855.1	-	9	1097	c.971A>T	c.(970-972)aAa>aTa	p.K324I		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	324					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TATGCCAGCTTTTACACACAC	0.373																																					p.K324I		Atlas-SNP	.											.	SCN7A	410	.	0			c.A971T						PASS	.						71.0	63.0	66.0					2																	167319011		1845	4102	5947	SO:0001583	missense	6332	exon9			CCAGCTTTTACAC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.971A>T	2.37:g.167319011T>A	ENSP00000386796:p.Lys324Ile	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.598912	0.87055	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98717	-5.09;-5.09;-5.09	4.43	4.43	0.53597	Ion transport (1);	0.000000	0.52532	D	0.000071	D	0.99010	0.9662	M	0.83603	2.65	0.42436	D	0.992693	D	0.89917	1.0	D	0.91635	0.999	D	0.99839	1.1060	10	0.87932	D	0	.	12.8081	0.57626	0.0:0.0:0.0:1.0	.	324	Q01118	SCN7A_HUMAN	I	324	ENSP00000386796:K324I;ENSP00000413699:K324I;ENSP00000403846:K324I	ENSP00000259060:K324I	K	-	2	0	SCN7A	167027257	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.043000	0.64208	1.747000	0.51819	0.477000	0.44152	AAA	.	.	none		0.373	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
CEACAM20	125931	hgsc.bcm.edu	37	19	45016116	45016116	+	RNA	SNP	A	A	G	rs8100718	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45016116A>G	ENST00000454753.1	-	0	1813							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)		p.C511R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				GATATATTGCAATACTCAGGA	0.507													A|||	1925	0.384385	0.1679	0.4078	5008	,	,		18720	0.3919		0.4612	False		,,,				2504	0.5736				p.C512R		Atlas-SNP	.											CEACAM20,NS,carcinoma,0,1	CEACAM20	31	1	1	Substitution - Missense(1)	prostate(1)	c.T1534C						scavenged	.	A	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	917,3079		106,705,1187	46.0	46.0	46.0		1535,1256,1256,1535	0.9	0.0	19	dbSNP_116	46	4182,4158		1069,2044,1057	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	180,180,180,180	1175,2749,2244	GG,GA,AA		49.8561,22.9479,41.3343	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	512/597,419/492,419/504,512/585	45016116	5099,7237	1998	4170	6168			125931	exon10			TATTGCAATACTC	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.45016116A>G		Somatic	222	2	0.00900901		WXS	Illumina HiSeq	Phase_I	167	87	0.520958	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				A|0.633;G|0.366	0.366	strong		0.507	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
ADAM12	8038	hgsc.bcm.edu	37	10	127753388	127753388	+	Silent	SNP	C	C	T	rs2279091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	82	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	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		
SLC43A2	124935	hgsc.bcm.edu	37	17	1494567	1494567	+	Silent	SNP	G	G	A	rs12953268	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:1494567G>A	ENST00000301335.5	-	8	1015	c.927C>T	c.(925-927)gcC>gcT	p.A309A	SLC43A2_ENST00000382147.4_Silent_p.A309A|SLC43A2_ENST00000574274.1_5'UTR|SLC43A2_ENST00000412517.3_Silent_p.A172A|SLC43A2_ENST00000571650.1_Silent_p.A309A	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	309					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		GGGTACCTGCGGCATCCGGCT	0.682													G|||	1399	0.279353	0.0832	0.3127	5008	,	,		11580	0.1508		0.5388	False		,,,				2504	0.3865				p.A309A		Atlas-SNP	.											SLC43A2,NS,carcinoma,0,1	SLC43A2	37	1	0			c.C927T						PASS	.	G		726,3680	287.2+/-279.2	55,616,1532	42.0	43.0	43.0		927	-5.5	0.1	17	dbSNP_121	43	4715,3885	595.2+/-393.4	1297,2121,882	no	coding-synonymous	SLC43A2	NM_152346.1		1352,2737,2414	AA,AG,GG		45.1744,16.4775,41.8345		309/570	1494567	5441,7565	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon8			ACCTGCGGCATCC	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.927C>T	17.37:g.1494567G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	53	34	0.641509	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			A|0.422;C|0.000;G|0.578	0.422	strong		0.682	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
PNP	4860	hgsc.bcm.edu	37	14	20940626	20940626	+	Silent	SNP	C	C	T	rs1130650	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20940626C>T	ENST00000361505.5	+	2	317	c.171C>T	c.(169-171)ccC>ccT	p.P57P	RP11-203M5.8_ENST00000554678.1_lincRNA	NM_000270.3	NP_000261.2	P01298	PAHO_HUMAN	purine nucleoside phosphorylase	0					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.P57P(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(2)	10						CCAACTTTCCCCGAAGTACAG	0.468													C|||	1024	0.204473	0.2451	0.2104	5008	,	,		20251	0.2083		0.1998	False		,,,				2504	0.1462				p.P57P		Atlas-SNP	.											PNP,NS,carcinoma,+2,2	PNP	21	2	1	Substitution - coding silent(1)	stomach(1)	c.C171T						PASS	.	C		1058,3348	386.3+/-326.1	119,820,1264	63.0	56.0	58.0		171	0.1	0.3	14	dbSNP_86	58	1521,7079	284.4+/-296.6	143,1235,2922	no	coding-synonymous	PNP	NM_000270.3		262,2055,4186	TT,TC,CC		17.686,24.0127,19.8293		57/290	20940626	2579,10427	2203	4300	6503	SO:0001819	synonymous_variant	4860	exon2			CTTTCCCCGAAGT		CCDS9552.1	14q11.2	2014-09-17	2009-12-02	2009-12-02	ENSG00000198805	ENSG00000198805	2.4.2.1		7892	protein-coding gene	gene with protein product		164050	"""nucleoside phosphorylase"""	NP		6087295	Standard	NM_000270		Approved	PUNP	uc001vxo.4	P00491	OTTHUMG00000029546	ENST00000361505.5:c.171C>T	14.37:g.20940626C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	144	49	0.340278	NM_000270		Silent	SNP	ENST00000361505.5	37	CCDS9552.1																																																																																			C|0.786;T|0.214	0.214	strong		0.468	PNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073646.2	NM_000270.2	
SLC22A11	55867	hgsc.bcm.edu	37	11	64336209	64336209	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:64336209C>T	ENST00000301891.4	+	8	1715	c.1341C>T	c.(1339-1341)tgC>tgT	p.C447C	SLC22A11_ENST00000377581.3_Silent_p.C447C|SLC22A11_ENST00000377585.3_Intron	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	447					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)	p.C447*(1)		breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	GCCTAACCTGCCTCACCATCT	0.597																																					p.C447C		Atlas-SNP	.											SLC22A11,colon,carcinoma,0,1	SLC22A11	54	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1341T						scavenged	.						210.0	166.0	181.0					11																	64336209		2201	4297	6498	SO:0001819	synonymous_variant	55867	exon8			AACCTGCCTCACC	AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"""Solute carriers"""	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.1341C>T	11.37:g.64336209C>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	226	3	0.0132743	NM_018484	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Silent	SNP	ENST00000301891.4	37	CCDS8074.1																																																																																			.	.	none		0.597	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484	
CELA1	1990	hgsc.bcm.edu	37	12	51737562	51737562	+	Missense_Mutation	SNP	T	T	C	rs17860300	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	137	53	0.386861	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	
USP32	84669	hgsc.bcm.edu	37	17	58288421	58288421	+	Missense_Mutation	SNP	C	C	T	rs146577219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	418	1	0.00239234		WXS	Illumina HiSeq	Phase_I	650	108	0.166154	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	
FAM47A	158724	hgsc.bcm.edu	37	X	34148877	34148877	+	Missense_Mutation	SNP	C	C	G	rs5973088		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	145	0	0		WXS	Illumina HiSeq	Phase_I	53	14	0.264151	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	
HEATR1	55127	hgsc.bcm.edu	37	1	236748397	236748397	+	Silent	SNP	A	A	G	rs41304149	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:236748397A>G	ENST00000366582.3	-	17	2283	c.2169T>C	c.(2167-2169)ttT>ttC	p.F723F	HEATR1_ENST00000366581.2_Silent_p.F723F	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	723					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)			TCGCAAATGGAAAGTGGGTTT	0.403													A|||	38	0.00758786	0.0061	0.0072	5008	,	,		19516	0.0		0.0149	False		,,,				2504	0.0102				p.F723F		Atlas-SNP	.											.	HEATR1	197	.	0			c.T2169C						PASS	.	A		40,4366	43.1+/-76.7	0,40,2163	110.0	110.0	110.0		2169	-0.1	1.0	1	dbSNP_127	110	226,8374	92.6+/-154.6	1,224,4075	no	coding-synonymous	HEATR1	NM_018072.5		1,264,6238	GG,GA,AA		2.6279,0.9079,2.0452		723/2145	236748397	266,12740	2203	4300	6503	SO:0001819	synonymous_variant	55127	exon17			AAATGGAAAGTGG	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.2169T>C	1.37:g.236748397A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	212	86	0.40566	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Silent	SNP	ENST00000366582.3	37	CCDS31066.1																																																																																			A|0.984;G|0.016	0.016	strong		0.403	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
APOB	338	hgsc.bcm.edu	37	2	21245813	21245813	+	Silent	SNP	G	G	A	rs1801700	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:21245813G>A	ENST00000233242.1	-	18	2833	c.2706C>T	c.(2704-2706)aaC>aaT	p.N902N		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	902	Heparin-binding.				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)					AGAAGTTGGTGTTCATCTGGA	0.517													G|||	81	0.0161741	0.0008	0.0231	5008	,	,		18975	0.0		0.0467	False		,,,				2504	0.0174				p.N902N		Atlas-SNP	.											.	APOB	761	.	0			c.C2706T						PASS	.	G		47,4359	48.2+/-83.0	0,47,2156	101.0	96.0	98.0		2706	2.7	1.0	2	dbSNP_89	98	416,8184	129.2+/-187.3	11,394,3895	no	coding-synonymous	APOB	NM_000384.2		11,441,6051	AA,AG,GG		4.8372,1.0667,3.5599		902/4564	21245813	463,12543	2203	4300	6503	SO:0001819	synonymous_variant	338	exon18			GTTGGTGTTCATC	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.2706C>T	2.37:g.21245813G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	209	100	0.478469	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			G|0.970;A|0.030	0.030	strong		0.517	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
TECPR2	9895	hgsc.bcm.edu	37	14	102901201	102901201	+	Missense_Mutation	SNP	A	A	G	rs10149146	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	40	0	0		WXS	Illumina HiSeq	Phase_I	51	32	0.627451	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	
CLVS1	157807	hgsc.bcm.edu	37	8	62370916	62370916	+	Silent	SNP	T	T	G	rs72657068	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:62370916T>G	ENST00000519846.1	+	6	1264	c.792T>G	c.(790-792)ccT>ccG	p.P264P	CLVS1_ENST00000518592.1_5'UTR|CLVS1_ENST00000325897.4_Silent_p.P264P			Q8IUQ0	CLVS1_HUMAN	clavesin 1	264	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						TAATACACCCTGAATTTTTGC	0.408													T|||	8	0.00159744	0.0	0.0029	5008	,	,		18914	0.0		0.002	False		,,,				2504	0.0041				p.P264P		Atlas-SNP	.											.	CLVS1	74	.	0			c.T792G						PASS	.	T		0,4406		0,0,2203	128.0	121.0	123.0		792	-0.0	1.0	8	dbSNP_130	123	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	CLVS1	NM_173519.2		0,28,6475	GG,GT,TT		0.3256,0.0,0.2153		264/355	62370916	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	157807	exon5			ACACCCTGAATTT	AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"""retinaldehyde binding protein 1-like 1"""	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.792T>G	8.37:g.62370916T>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	24	8	0.333333	NM_173519	B2R7M5|C8UZT3|Q8NB32	Silent	SNP	ENST00000519846.1	37	CCDS6176.1																																																																																			T|0.998;G|0.002	0.002	strong		0.408	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519	
ACADSB	36	hgsc.bcm.edu	37	10	124800853	124800853	+	Silent	SNP	C	C	T	rs1140591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124800853C>T	ENST00000358776.4	+	5	653	c.639C>T	c.(637-639)caC>caT	p.H213H	ACADSB_ENST00000368869.4_Silent_p.H111H|ACADSB_ENST00000496730.2_3'UTR	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	213					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	GTGCTGAGCACGCAGGGCTCT	0.413													C|||	1141	0.227835	0.2163	0.2176	5008	,	,		17755	0.1419		0.2296	False		,,,				2504	0.3374				p.H213H		Atlas-SNP	.											.	ACADSB	45	.	0			c.C639T						PASS	.	C		950,3456	362.1+/-316.0	103,744,1356	143.0	138.0	139.0		639	-9.7	0.0	10	dbSNP_86	139	2017,6583	353.4+/-329.1	222,1573,2505	no	coding-synonymous	ACADSB	NM_001609.3		325,2317,3861	TT,TC,CC		23.4535,21.5615,22.8125		213/433	124800853	2967,10039	2203	4300	6503	SO:0001819	synonymous_variant	36	exon5			TGAGCACGCAGGG	U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"""acyl-Coenzyme A dehydrogenase, short/branched chain"""			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.639C>T	10.37:g.124800853C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	128	76	0.59375	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Silent	SNP	ENST00000358776.4	37	CCDS7634.1																																																																																			A|0.000;C|0.783;G|0.000;T|0.217	0.217	strong		0.413	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609	
LILRA4	23547	hgsc.bcm.edu	37	19	54849481	54849481	+	Silent	SNP	T	T	G	rs7256494	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54849481T>G	ENST00000291759.4	-	4	437	c.381A>C	c.(379-381)gcA>gcC	p.A127A	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	127	Ig-like C2-type 2.				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)		GGCTTGGCAGTGCGGACAGGG	0.572													G|||	1951	0.389577	0.4554	0.4251	5008	,	,		18707	0.2589		0.3638	False		,,,				2504	0.4366				p.A127A		Atlas-SNP	.											LILRA4,colon,carcinoma,0,4	LILRA4	91	4	0			c.A381C						scavenged	.	G		1958,2448		426,1106,671	49.0	52.0	51.0		381	0.3	0.1	19	dbSNP_116	51	3240,5360		604,2032,1664	no	coding-synonymous	LILRA4	NM_012276.3		1030,3138,2335	GG,GT,TT		37.6744,44.4394,39.9662		127/500	54849481	5198,7808	2203	4300	6503	SO:0001819	synonymous_variant	23547	exon4			TGGCAGTGCGGAC	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.381A>C	19.37:g.54849481T>G		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	146	54	0.369863	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			T|0.611;G|0.389	0.389	strong		0.572	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
KIAA0391	9692	hgsc.bcm.edu	37	14	35735967	35735967	+	Missense_Mutation	SNP	A	A	G	rs11156878	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:35735967A>G	ENST00000557565.1	+	6	1691	c.1310A>G	c.(1309-1311)aAt>aGt	p.N437S	KIAA0391_ENST00000321130.10_Missense_Mutation_p.N421S|KIAA0391_ENST00000605870.1_Missense_Mutation_p.N65S|KIAA0391_ENST00000603544.1_Missense_Mutation_p.N421S|KIAA0391_ENST00000250377.7_Missense_Mutation_p.N342S|KIAA0391_ENST00000604948.1_Missense_Mutation_p.N342S|KIAA0391_ENST00000534898.4_Missense_Mutation_p.N437S	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	437			N -> S (in dbSNP:rs11156878). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		GCCAAACGGAATCTGCGACTG	0.473													A|||	488	0.0974441	0.0318	0.1268	5008	,	,		19353	0.0595		0.1879	False		,,,				2504	0.1115				p.N437S		Atlas-SNP	.											.	KIAA0391	35	.	0			c.A1310G						PASS	.	A	SER/ASN	268,4138	151.4+/-185.3	9,250,1944	210.0	201.0	204.0		1310	5.6	1.0	14	dbSNP_120	204	1446,7154	277.5+/-292.9	124,1198,2978	yes	missense	KIAA0391	NM_014672.2	46	133,1448,4922	GG,GA,AA		16.814,6.0826,13.1785	benign	437/584	35735967	1714,11292	2203	4300	6503	SO:0001583	missense	9692	exon6			AACGGAATCTGCG	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.1310A>G	14.37:g.35735967A>G	ENSP00000454657:p.Asn437Ser	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	272	158	0.580882	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Missense_Mutation	SNP	ENST00000557565.1	37	CCDS32063.1	227	0.10393772893772894	18	0.036585365853658534	52	0.143646408839779	26	0.045454545454545456	131	0.17282321899736147	A	14.91	2.675032	0.47781	0.060826	0.16814	ENSG00000100890	ENST00000554896;ENST00000250377;ENST00000321130;ENST00000534898;ENST00000556121;ENST00000556912;ENST00000557404	T;T;T;T	0.46451	0.9;0.9;0.87;1.0	5.62	5.62	0.85841	.	0.166808	0.53938	D	0.000048	T	0.00144	0.0004	L	0.46885	1.475	0.32908	P	0.485866	B;B	0.25772	0.134;0.134	B;B	0.29862	0.108;0.108	T	0.08617	-1.0713	9	0.24483	T	0.36	-13.9399	14.8151	0.70028	1.0:0.0:0.0:0.0	rs11156878;rs60527017;rs11156878	421;437	O15091-2;O15091	.;MRRP3_HUMAN	S	342;342;421;437;421;65;65	ENSP00000250377:N342S;ENSP00000324697:N421S;ENSP00000440915:N437S;ENSP00000450898:N65S	ENSP00000250377:N342S	N	+	2	0	KIAA0391	34805718	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.276000	0.65580	2.142000	0.66516	0.528000	0.53228	AAT	A|0.882;G|0.118	0.118	strong		0.473	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672	
HTR3B	9177	hgsc.bcm.edu	37	11	113803666	113803666	+	Missense_Mutation	SNP	G	G	A	rs17116138	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:113803666G>A	ENST00000260191.2	+	6	804	c.547G>A	c.(547-549)Gta>Ata	p.V183I	HTR3B_ENST00000537778.1_Missense_Mutation_p.V172I	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	183			V -> I (in dbSNP:rs17116138). {ECO:0000269|PubMed:15293096, ECO:0000269|PubMed:15389765, ECO:0000269|PubMed:16487942}.		cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	AGTGGAAGACGTAGACCTGGC	0.463													G|||	227	0.0453275	0.0734	0.0663	5008	,	,		18515	0.0		0.0408	False		,,,				2504	0.044				p.V183I		Atlas-SNP	.											.	HTR3B	50	.	0			c.G547A	GRCh37	CM083529	HTR3B	M	rs17116138	PASS	.	G	ILE/VAL	350,4052	182.6+/-210.3	17,316,1868	135.0	122.0	126.0		547	-0.4	0.7	11	dbSNP_123	126	272,8320	104.2+/-165.2	5,262,4029	yes	missense	HTR3B	NM_006028.4	29	22,578,5897	AA,AG,GG		3.1657,7.9509,4.7868	benign	183/442	113803666	622,12372	2201	4296	6497	SO:0001583	missense	9177	exon6			GAAGACGTAGACC	AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5298	protein-coding gene	gene with protein product		604654	"""5-hydroxytryptamine (serotonin) receptor 3B"""			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.547G>A	11.37:g.113803666G>A	ENSP00000260191:p.Val183Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	172	42	0.244186	NM_006028	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	CCDS8364.1	99	0.04532967032967033	37	0.07520325203252033	26	0.0718232044198895	0	0.0	36	0.047493403693931395	G	3.018	-0.202429	0.06219	0.079509	0.031657	ENSG00000149305	ENST00000260191;ENST00000537778	T;T	0.78364	-1.17;-1.17	6.17	-0.444	0.12245	Neurotransmitter-gated ion-channel ligand-binding (3);	0.384737	0.27609	N	0.018613	T	0.02610	0.0079	N	0.02973	-0.45	0.58432	P	8.000000000008E-6	B;B	0.18610	0.007;0.029	B;B	0.11329	0.006;0.005	T	0.14337	-1.0476	9	0.02654	T	1	-2.9447	1.6523	0.02774	0.3414:0.0995:0.3786:0.1805	rs17116138;rs56490832;rs17116138	172;183	O95264-2;O95264	.;5HT3B_HUMAN	I	183;172	ENSP00000260191:V183I;ENSP00000443118:V172I	ENSP00000260191:V183I	V	+	1	0	HTR3B	113308876	0.350000	0.24878	0.692000	0.30179	0.931000	0.56810	0.417000	0.21214	0.039000	0.15632	0.655000	0.94253	GTA	G|0.955;A|0.045	0.045	strong		0.463	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028	
FLNB	2317	hgsc.bcm.edu	37	3	58081888	58081888	+	Silent	SNP	T	T	C	rs1522384	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000357272.4_Silent_p.S309S|FLNB_ENST00000358537.3_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	105	0	0		WXS	Illumina HiSeq	Phase_I	75	73	0.973333	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	
HIST1H4G	8369	hgsc.bcm.edu	37	6	26247198	26247198	+	Missense_Mutation	SNP	A	A	G	rs41266821	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26247198A>G	ENST00000244537.4	-	1	61	c.8T>C	c.(7-9)gTt>gCt	p.V3A		NM_003547.2	NP_003538.1	Q99525	H4G_HUMAN	histone cluster 1, H4g	3						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				CTTGCCCCGAACAGACATGAT	0.458													a|||	420	0.0838658	0.028	0.0951	5008	,	,		6130	0.0337		0.1491	False		,,,				2504	0.136				p.V3A		Atlas-SNP	.											.	HIST1H4G	18	.	0			c.T8C						PASS	.	A	ALA/VAL	217,4189		5,207,1991	39.0	37.0	37.0		8	2.5	0.2	6	dbSNP_127	37	1120,7480		63,994,3243	yes	missense	HIST1H4G	NM_003547.2	64	68,1201,5234	GG,GA,AA		13.0233,4.9251,10.2799	benign	3/99	26247198	1337,11669	2203	4300	6503	SO:0001583	missense	8369	exon1			CCCCGAACAGACA	Z80788	CCDS4599.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124578	ENSG00000275663		"""Histones / Replication-dependent"""	4792	protein-coding gene	gene with protein product		602832	"""H4 histone family, member L"", ""histone 1, H4g"""	H4FL		9119399, 12408966	Standard	NM_003547		Approved	H4/l	uc003nhf.3	Q99525	OTTHUMG00000014444	ENST00000244537.4:c.8T>C	6.37:g.26247198A>G	ENSP00000244537:p.Val3Ala	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_003547		Missense_Mutation	SNP	ENST00000244537.4	37	CCDS4599.1	177	0.08104395604395605	13	0.026422764227642278	43	0.11878453038674033	15	0.026223776223776224	106	0.13984168865435356	.	10.77	1.445080	0.25987	0.049251	0.130233	ENSG00000124578	ENST00000244537	.	.	.	3.34	2.46	0.29980	Histone-fold (2);	.	.	.	.	T	0.26304	0.0642	.	.	.	0.35467	P	0.203009	B	0.02656	0.0	B	0.01281	0.0	T	0.14811	-1.0459	6	0.62326	D	0.03	.	11.7724	0.51967	0.1786:0.8214:0.0:0.0	rs41266821;rs52800328	3	Q99525	H4G_HUMAN	A	3	.	ENSP00000244537:V3A	V	-	2	0	HIST1H4G	26355177	0.998000	0.40836	0.181000	0.23098	0.001000	0.01503	4.149000	0.58091	0.726000	0.32339	-0.318000	0.08688	GTT	A|0.903;G|0.097	0.097	strong		0.458	HIST1H4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040107.1	NM_003547	
MUC17	140453	hgsc.bcm.edu	37	7	100680490	100680490	+	Missense_Mutation	SNP	A	A	G	rs199605653		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680490A>G	ENST00000306151.4	+	3	5857	c.5793A>G	c.(5791-5793)atA>atG	p.I1931M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1931	59 X approximate tandem repeats.|Ser-rich.				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)					TAACAAGTATACCTGTCAGCA	0.483																																					p.I1931M		Atlas-SNP	.											.	MUC17	804	.	0			c.A5793G						PASS	.						242.0	240.0	241.0					7																	100680490		2203	4300	6503	SO:0001583	missense	140453	exon3			AAGTATACCTGTC	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.5793A>G	7.37:g.100680490A>G	ENSP00000302716:p.Ile1931Met	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	200	17	0.085	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.052456	0.00394	.	.	ENSG00000169876	ENST00000306151	T	0.02631	4.22	0.579	-1.16	0.09678	.	.	.	.	.	T	0.01592	0.0051	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46911	-0.9157	8	0.33940	T	0.23	.	.	.	.	.	1931	Q685J3	MUC17_HUMAN	M	1931	ENSP00000302716:I1931M	ENSP00000302716:I1931M	I	+	3	3	MUC17	100467210	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-2.112000	0.01332	-3.327000	0.00186	-1.981000	0.00455	ATA	A|0.999;G|0.001	0.001	weak		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
HLA-A	3105	hgsc.bcm.edu	37	6	29913037	29913037	+	Missense_Mutation	SNP	G	G	A	rs1137631	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.V358M			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	246	0	0		WXS	Illumina HiSeq	Phase_I	158	49	0.310127	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	
DNMT3B	1789	hgsc.bcm.edu	37	20	31386449	31386449	+	Splice_Site	SNP	T	T	C	rs2424922	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:31386449T>C	ENST00000328111.2	+	15	1995	c.1674T>C	c.(1672-1674)taT>taC	p.Y558Y	DNMT3B_ENST00000443239.3_Splice_Site_p.Y496Y|DNMT3B_ENST00000201963.3_Splice_Site_p.Y550Y|DNMT3B_ENST00000353855.2_Splice_Site_p.Y538Y|DNMT3B_ENST00000348286.2_Splice_Site_p.Y538Y|DNMT3B_ENST00000344505.4_Splice_Site_p.Y538Y|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000456297.2_Splice_Site_p.Y462Y	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	558					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGCTTGAATATGTAAGCCACA	0.572													C|||	3785	0.755791	0.913	0.6599	5008	,	,		14182	0.9931		0.4205	False		,,,				2504	0.7117				p.Y558Y		Atlas-SNP	.											.	DNMT3B	196	.	0			c.T1674C						PASS	.	C	,,,,,	3664,742		1540,584,79	25.0	30.0	28.0		1488,1386,1674,1614,1614,1650	-6.2	0.5	20	dbSNP_100	28	3850,4750		886,2078,1336	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	DNMT3B	NM_001207055.1,NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1,NM_175850.2	,,,,,	2426,2662,1415	CC,CT,TT		44.7674,16.8407,42.2267	,,,,,	496/729,462/695,558/854,538/834,538/771,550/846	31386449	7514,5492	2203	4300	6503	SO:0001630	splice_region_variant	1789	exon15			TGAATATGTAAGC		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.1674+1T>C	20.37:g.31386449T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_006892	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	37	CCDS13205.1																																																																																			T|0.354;C|0.646	0.646	strong		0.572	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892	Silent
IKBKAP	8518	hgsc.bcm.edu	37	9	111665215	111665215	+	Silent	SNP	A	A	C	rs35054425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:111665215A>C	ENST00000374647.5	-	16	2065	c.1758T>G	c.(1756-1758)ccT>ccG	p.P586P	IKBKAP_ENST00000537196.1_Silent_p.P237P	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	586					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						TAGCCAGAGAAGGTGACTCTG	0.423													A|||	73	0.0145767	0.0015	0.0058	5008	,	,		15642	0.0		0.0089	False		,,,				2504	0.0593				p.P586P		Atlas-SNP	.											.	IKBKAP	122	.	0			c.T1758G						PASS	.	A		8,4398	12.9+/-30.5	0,8,2195	84.0	84.0	84.0		1758	-1.3	1.0	9	dbSNP_126	84	131,8469	67.0+/-129.4	1,129,4170	no	coding-synonymous	IKBKAP	NM_003640.3		1,137,6365	CC,CA,AA		1.5233,0.1816,1.0687		586/1333	111665215	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon16			CAGAGAAGGTGAC	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.1758T>G	9.37:g.111665215A>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	118	50	0.423729	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			A|0.990;C|0.010	0.010	strong		0.423	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
FAM209B	388799	hgsc.bcm.edu	37	20	55111371	55111371	+	Silent	SNP	G	G	A	rs2296130	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:55111371G>A	ENST00000371325.1	+	2	489	c.393G>A	c.(391-393)caG>caA	p.Q131Q		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	131						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											CCGAAGTGCAGAATCTTAAAG	0.398													G|||	1873	0.374002	0.5461	0.3473	5008	,	,		20008	0.0466		0.4483	False		,,,				2504	0.4213				p.Q131Q		Atlas-SNP	.											.	.	.	.	0			c.G393A						PASS	.	G		2376,2030	612.7+/-392.0	639,1098,466	99.0	99.0	99.0		393	1.5	0.2	20	dbSNP_100	99	3934,4666	549.6+/-385.6	869,2196,1235	no	coding-synonymous	C20orf107	NM_001013646.2		1508,3294,1701	AA,AG,GG		45.7442,46.0735,48.5161		131/172	55111371	6310,6696	2203	4300	6503	SO:0001819	synonymous_variant	388799	exon2			AGTGCAGAATCTT	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.393G>A	20.37:g.55111371G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	160	71	0.44375	NM_001013646	Q3KRB5	Silent	SNP	ENST00000371325.1	37	CCDS33494.1																																																																																			G|0.585;A|0.415	0.415	strong		0.398	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
ZNF98	148198	hgsc.bcm.edu	37	19	22575488	22575488	+	Silent	SNP	C	C	T	rs7247735	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22575488C>T	ENST00000357774.5	-	4	670	c.549G>A	c.(547-549)aaG>aaA	p.K183K		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	183					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(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				ATTCTTTACACTTGAAAGATT	0.299													t|||	1998	0.398962	0.413	0.4784	5008	,	,		17504	0.4107		0.4642	False		,,,				2504	0.2444				p.K183K		Atlas-SNP	.											.	ZNF98	230	.	0			c.G549A						PASS	.						26.0	26.0	26.0					19																	22575488		2020	4207	6227	SO:0001819	synonymous_variant	148198	exon4			TTTACACTTGAAA		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.549G>A	19.37:g.22575488C>T		Somatic	403	1	0.00248139		WXS	Illumina HiSeq	Phase_I	281	111	0.395018	NM_001098626		Silent	SNP	ENST00000357774.5	37	CCDS46031.1																																																																																			C|0.551;T|0.449	0.449	strong		0.299	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377086	49377086	+	Missense_Mutation	SNP	T	T	C	rs611251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49377086T>C	ENST00000200453.5	+	2	865	c.596T>C	c.(595-597)gTa>gCa	p.V199A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	199	Glu-rich.		V -> A (in dbSNP:rs611251).		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)		GAAGAAGCTGTAAAGAAAGAA	0.532													T|||	1368	0.273163	0.534	0.2262	5008	,	,		18625	0.0933		0.1521	False		,,,				2504	0.2638				p.V199A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.T596C						PASS	.	T	ALA/VAL	2102,2304	573.6+/-383.6	513,1076,614	149.0	161.0	157.0		596	0.4	0.0	19	dbSNP_83	157	1245,7355	249.3+/-276.6	74,1097,3129	yes	missense	PPP1R15A	NM_014330.3	64	587,2173,3743	CC,CT,TT		14.4767,47.7077,25.7343	probably-damaging	199/675	49377086	3347,9659	2203	4300	6503	SO:0001583	missense	23645	exon2			AAGCTGTAAAGAA	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.596T>C	19.37:g.49377086T>C	ENSP00000200453:p.Val199Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	513	0.2348901098901099	259	0.5264227642276422	81	0.22375690607734808	57	0.09965034965034965	116	0.15303430079155672	T	10.91	1.483851	0.26598	0.477077	0.144767	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.04194	3.68	4.06	0.39	0.16275	.	1.686450	0.03645	N	0.240170	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.26363	0.147	B	0.19666	0.026	T	0.44159	-0.9346	9	0.02654	T	1	-1.0388	2.3232	0.04216	0.2168:0.2659:0.0:0.5173	rs611251;rs3177847;rs3826819;rs52819950;rs58000193;rs611251	199	O75807	PR15A_HUMAN	A	199;39;157	ENSP00000200453:V199A	ENSP00000200453:V199A	V	+	2	0	PPP1R15A	54068898	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.145000	0.16157	0.236000	0.21180	0.418000	0.28097	GTA	T|0.735;G|0.004	.	strong		0.532	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
OR5T2	219464	hgsc.bcm.edu	37	11	56000471	56000471	+	Missense_Mutation	SNP	G	G	A	rs11227599	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56000471G>A	ENST00000313264.4	-	1	266	c.191C>T	c.(190-192)aCt>aTt	p.T64I		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	64			T -> I (in dbSNP:rs11227599).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T64I(1)		endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					GAAGAAGATAGTCTGCAGTTC	0.393													a|||	865	0.172724	0.1868	0.1585	5008	,	,		21467	0.124		0.2117	False		,,,				2504	0.1738				p.T64I		Atlas-SNP	.											OR5T2,NS,carcinoma,0,1	OR5T2	107	1	1	Substitution - Missense(1)	stomach(1)	c.C191T						PASS	.	A	ILE/THR	801,3601	749.1+/-412.0	76,649,1476	72.0	64.0	67.0		191	3.6	0.0	11	dbSNP_120	67	1699,6893	737.2+/-407.0	177,1345,2774	yes	missense	OR5T2	NM_001004746.1	89	253,1994,4250	AA,AG,GG		19.7742,18.1963,19.2396	benign	64/360	56000471	2500,10494	2201	4296	6497	SO:0001583	missense	219464	exon1			AAGATAGTCTGCA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.191C>T	11.37:g.56000471G>A	ENSP00000323688:p.Thr64Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	381	0.17445054945054944	87	0.17682926829268292	54	0.14917127071823205	74	0.12937062937062938	166	0.21899736147757257	A	2.652	-0.281757	0.05642	0.181963	0.197742	ENSG00000181718	ENST00000313264	T	0.00231	8.49	4.77	3.64	0.41730	.	0.464406	0.15753	N	0.246309	T	0.00012	0.0000	N	0.00985	-1.075	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.00414	-1.1754	9	0.05959	T	0.93	.	8.8572	0.35236	0.839:0.0:0.161:0.0	rs11227599;rs52813445;rs11227599	64	Q8NGG2	OR5T2_HUMAN	I	64	ENSP00000323688:T64I	ENSP00000323688:T64I	T	-	2	0	OR5T2	55757047	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.030000	0.13688	0.284000	0.22305	-1.324000	0.01287	ACT	G|0.820;A|0.180	0.180	strong		0.393	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
CSDE1	7812	hgsc.bcm.edu	37	1	115269685	115269685	+	Silent	SNP	A	A	G	rs150190370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:115269685A>G	ENST00000358528.4	-	13	1809	c.1383T>C	c.(1381-1383)taT>taC	p.Y461Y	CSDE1_ENST00000369530.1_Silent_p.Y476Y|CSDE1_ENST00000530886.1_Silent_p.Y331Y|CSDE1_ENST00000261443.5_Silent_p.Y430Y|CSDE1_ENST00000438362.2_Silent_p.Y507Y|CSDE1_ENST00000534699.1_Silent_p.Y461Y|Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000339438.6_Silent_p.Y430Y	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	461	CSD 6.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-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)		CACAGTCATCATAAGCAATAA	0.368													A|||	7	0.00139776	0.0	0.0	5008	,	,		18398	0.0069		0.0	False		,,,				2504	0.0				p.Y507Y		Atlas-SNP	.											.	CSDE1	145	.	0			c.T1521C						PASS	.						140.0	122.0	128.0					1																	115269685		2203	4300	6503	SO:0001819	synonymous_variant	7812	exon14			GTCATCATAAGCA		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1383T>C	1.37:g.115269685A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	84	5	0.0595238	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Silent	SNP	ENST00000358528.4	37	CCDS30812.1																																																																																			A|0.997;G|0.003	0.003	strong		0.368	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
UPF3A	65110	hgsc.bcm.edu	37	13	115064423	115064423	+	Missense_Mutation	SNP	G	G	A	rs3752107	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:115064423G>A	ENST00000375299.3	+	8	1011	c.955G>A	c.(955-957)Gca>Aca	p.A319T	UPF3A_ENST00000475218.2_3'UTR|UPF3A_ENST00000351487.5_Missense_Mutation_p.A286T	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	319					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)		TGCCCCCGGTGCAGTCGTAAA	0.547													G|||	273	0.0545128	0.0136	0.0389	5008	,	,		17352	0.0357		0.0746	False		,,,				2504	0.1196				p.A319T		Atlas-SNP	.											UPF3A,colon,carcinoma,0,1	UPF3A	47	1	0			c.G955A						scavenged	.	G	THR/ALA,THR/ALA	93,4313	75.2+/-113.4	1,91,2111	53.0	51.0	52.0		955,856	-1.2	0.0	13	dbSNP_107	52	529,8071	147.1+/-202.6	19,491,3790	no	missense,missense	UPF3A	NM_023011.3,NM_080687.2	58,58	20,582,5901	AA,AG,GG		6.1512,2.1108,4.7824	benign,benign	319/477,286/444	115064423	622,12384	2203	4300	6503	SO:0001583	missense	65110	exon8			CCCGGTGCAGTCG	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.955G>A	13.37:g.115064423G>A	ENSP00000364448:p.Ala319Thr	Somatic	382	3	0.0078534		WXS	Illumina HiSeq	Phase_I	371	158	0.425876	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Missense_Mutation	SNP	ENST00000375299.3	37	CCDS9543.1	110	0.05036630036630037	11	0.022357723577235773	15	0.04143646408839779	26	0.045454545454545456	58	0.07651715039577836	G	4.682	0.126748	0.08931	0.021108	0.061512	ENSG00000169062	ENST00000375299;ENST00000351487;ENST00000543577	T;T	0.80909	-1.43;1.64	4.08	-1.17	0.09648	.	0.751533	0.12508	N	0.462684	T	0.07773	0.0195	N	0.15975	0.35	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.03423	-1.1038	9	.	.	.	-1.1725	10.6354	0.45563	0.2261:0.0:0.7739:0.0	rs3752107;rs9525320	286;319	Q9H1J1-2;Q9H1J1	.;REN3A_HUMAN	T	319;286;118	ENSP00000364448:A319T;ENSP00000329592:A286T	.	A	+	1	0	UPF3A	114082525	0.302000	0.24454	0.000000	0.03702	0.000000	0.00434	2.210000	0.42816	-0.212000	0.10109	-1.000000	0.02509	GCA	G|0.949;A|0.051	0.051	strong		0.547	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		
SMARCA2	6595	hgsc.bcm.edu	37	9	2029199	2029199	+	Silent	SNP	G	G	A	rs10964471	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:2029199G>A	ENST00000382203.1	+	2	386	c.177G>A	c.(175-177)acG>acA	p.T59T	SMARCA2_ENST00000357248.2_Silent_p.T59T|SMARCA2_ENST00000349721.2_Silent_p.T59T|SMARCA2_ENST00000382194.1_Silent_p.T59T			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	59					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)		CTATGCCGACGATGGGGTCCA	0.522													G|||	544	0.108626	0.0219	0.0648	5008	,	,		19187	0.2222		0.0905	False		,,,				2504	0.1585				p.T59T		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G177A						PASS	.	G	,	126,4280	91.1+/-129.8	2,122,2079	41.0	35.0	37.0		177,177	-11.2	0.0	9	dbSNP_120	37	740,7860	176.6+/-226.4	27,686,3587	no	coding-synonymous,coding-synonymous	SMARCA2	NM_003070.3,NM_139045.2	,	29,808,5666	AA,AG,GG		8.6047,2.8597,6.6585	,	59/1591,59/1573	2029199	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	6595	exon2			GCCGACGATGGGG	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.177G>A	9.37:g.2029199G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	152	78	0.513158	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			G|0.913;A|0.086	0.086	strong		0.522	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
ZNF804A	91752	hgsc.bcm.edu	37	2	185801917	185801917	+	Silent	SNP	A	A	G	rs728534	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:185801917A>G	ENST00000302277.6	+	4	2388	c.1794A>G	c.(1792-1794)aaA>aaG	p.K598K		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	598							metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						GAAAGAAAAAAAGAAAAAAGT	0.333													A|||	798	0.159345	0.0076	0.1326	5008	,	,		18012	0.2312		0.2147	False		,,,				2504	0.2526				p.K598K		Atlas-SNP	.											.	ZNF804A	322	.	0			c.A1794G						PASS	.	A		180,4222		5,170,2026	47.0	55.0	52.0		1794	0.1	0.9	2	dbSNP_86	52	1683,6903		182,1319,2792	no	coding-synonymous	ZNF804A	NM_194250.1		187,1489,4818	GG,GA,AA		19.6017,4.0891,14.344		598/1210	185801917	1863,11125	2201	4293	6494	SO:0001819	synonymous_variant	91752	exon4			GAAAAAAAGAAAA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1794A>G	2.37:g.185801917A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																			A|0.840;G|0.160	0.160	strong		0.333	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
SLC2A9	56606	hgsc.bcm.edu	37	4	9922167	9922167	+	Missense_Mutation	SNP	C	C	T	rs16890979	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:9922167C>T	ENST00000264784.3	-	7	897	c.844G>A	c.(844-846)Gtt>Att	p.V282I	RP13-560N11.1_ENST00000504249.1_RNA|SLC2A9_ENST00000309065.3_Missense_Mutation_p.V253I|SLC2A9_ENST00000506583.1_Missense_Mutation_p.V253I	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	282			V -> I (in dbSNP:rs16890979). {ECO:0000269|PubMed:18327256}.		glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	TCTTGGGAAACGTCTGCTTTA	0.577													C|||	1321	0.263778	0.4803	0.3818	5008	,	,		21107	0.0129		0.2137	False		,,,				2504	0.1973				p.V282I		Atlas-SNP	.											.	SLC2A9	158	.	0			c.G844A	GRCh37	CM086145	SLC2A9	M	rs16890979	PASS	.	C	ILE/VAL,ILE/VAL	1826,2580	527.1+/-372.1	389,1048,766	55.0	49.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	757,844	1.6	0.0	4	dbSNP_123	51	1898,6702	333.8+/-320.7	220,1458,2622	yes	missense,missense	SLC2A9	NM_001001290.1,NM_020041.2	29,29	609,2506,3388	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	22.0698,41.4435,28.6329	benign,benign	253/512,282/541	9922167	3724,9282	2203	4300	6503	SO:0001583	missense	56606	exon7			GGGAAACGTCTGC	AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.844G>A	4.37:g.9922167C>T	ENSP00000264784:p.Val282Ile	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	163	59	0.361963	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	CCDS3407.1	487	0.222985347985348	212	0.43089430894308944	120	0.3314917127071823	3	0.005244755244755245	152	0.20052770448548812	C	8.913	0.959077	0.18507	0.414435	0.220698	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065	T;T;T	0.75367	-0.93;-0.93;-0.93	5.2	1.61	0.23674	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.127893	0.52532	N	0.000078	T	0.00012	0.0000	L	0.49455	1.56	0.37213	P	0.09511800000000004	P;P	0.39883	0.693;0.613	B;B	0.35607	0.114;0.206	T	0.35076	-0.9803	8	.	.	.	.	9.6932	0.40141	0.0:0.7308:0.0:0.2692	rs16890979;rs52793226;rs16890979	253;282	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	I	253;282;253	ENSP00000422209:V253I;ENSP00000264784:V282I;ENSP00000311383:V253I	.	V	-	1	0	SLC2A9	9531265	0.855000	0.29742	0.001000	0.08648	0.002000	0.02628	1.648000	0.37271	-0.007000	0.14345	-0.145000	0.13849	GTT	C|0.737;T|0.263	0.263	strong		0.577	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
RIC1	57589	hgsc.bcm.edu	37	9	5774225	5774225	+	Silent	SNP	T	T	G	rs3739648	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:5774225T>G	ENST00000414202.2	+	26	4442	c.4251T>G	c.(4249-4251)acT>acG	p.T1417T	KIAA1432_ENST00000449720.2_Silent_p.T1301T|KIAA1432_ENST00000418622.3_Silent_p.T1338T	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						scavenged	.	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	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	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		
NLRP14	338323	hgsc.bcm.edu	37	11	7091569	7091569	+	Missense_Mutation	SNP	C	C	T	rs17280682	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	180	0	0		WXS	Illumina HiSeq	Phase_I	169	77	0.455621	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	
ATP5F1	515	hgsc.bcm.edu	37	1	111998734	111998734	+	Missense_Mutation	SNP	A	A	G	rs151112830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:111998734A>G	ENST00000369722.3	+	4	856	c.250A>G	c.(250-252)Atc>Gtc	p.I84V	ATP5F1_ENST00000369721.4_3'UTR|ATP5F1_ENST00000483994.1_Missense_Mutation_p.I23V	NM_001688.4	NP_001679.2	P24539	AT5F1_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1	84				I -> V (in Ref. 1; CAA42782). {ECO:0000305}.	ATP catabolic process (GO:0006200)|ATP synthesis coupled proton transport (GO:0015986)|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)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(1)|cervix(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	8		all_cancers(81;8.16e-06)|all_epithelial(167;5.63e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|Colorectal(144;0.0296)|all cancers(265;0.0488)|Epithelial(280;0.0732)|COAD - Colon adenocarcinoma(174;0.114)|LUSC - Lung squamous cell carcinoma(189;0.135)		AACTGGGCTTATCTTGTACGC	0.373													A|||	9	0.00179712	0.0	0.0029	5008	,	,		19966	0.0		0.006	False		,,,				2504	0.001				p.I84V		Atlas-SNP	.											.	ATP5F1	20	.	0			c.A250G						PASS	.	A	VAL/ILE	3,4403	6.2+/-15.9	0,3,2200	167.0	166.0	166.0		250	3.9	1.0	1	dbSNP_134	166	35,8565	23.4+/-69.3	0,35,4265	yes	missense	ATP5F1	NM_001688.4	29	0,38,6465	GG,GA,AA		0.407,0.0681,0.2922	benign	84/257	111998734	38,12968	2203	4300	6503	SO:0001583	missense	515	exon4			GGGCTTATCTTGT	X60221	CCDS836.1	1p13.2	2012-10-12	2010-06-11		ENSG00000116459	ENSG00000116459		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	840	protein-coding gene	gene with protein product		603270	"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit b, isoform 1"", ""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit B1"""			1831354	Standard	XM_005270929		Approved		uc001ebc.3	P24539	OTTHUMG00000011745	ENST00000369722.3:c.250A>G	1.37:g.111998734A>G	ENSP00000358737:p.Ile84Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	38	7	0.184211	NM_001688	Q9BQ68|Q9BRU8	Missense_Mutation	SNP	ENST00000369722.3	37	CCDS836.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	10.49	1.365555	0.24684	6.81E-4	0.00407	ENSG00000116459	ENST00000369722;ENST00000483994	T;T	0.33216	1.42;1.42	5.21	3.91	0.45181	.	0.280632	0.40908	D	0.000985	T	0.07413	0.0187	L	0.38175	1.15	0.25064	N	0.991048	B;B	0.11235	0.004;0.004	B;B	0.14023	0.01;0.01	T	0.21449	-1.0245	10	0.15952	T	0.53	.	5.0056	0.14286	0.4859:0.3811:0.133:0.0	rs11553285	84;84	Q08ET0;P24539	.;AT5F1_HUMAN	V	84;23	ENSP00000358737:I84V;ENSP00000420366:I23V	ENSP00000358737:I84V	I	+	1	0	ATP5F1	111800257	0.964000	0.33143	1.000000	0.80357	0.721000	0.41392	1.653000	0.37323	2.096000	0.63516	0.533000	0.62120	ATC	A|0.998;G|0.002	0.002	strong		0.373	ATP5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032455.1	NM_001688	
RBM11	54033	hgsc.bcm.edu	37	21	15599340	15599340	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:15599340A>G	ENST00000400577.3	+	5	581	c.572A>G	c.(571-573)cAc>cGc	p.H191R	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	191					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)			endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		AAATGGACTCACCAACAACCA	0.453																																					p.H191R		Atlas-SNP	.											RBM11,NS,carcinoma,0,1	RBM11	41	1	0			c.A572G						scavenged	.						271.0	258.0	263.0					21																	15599340		1964	4154	6118	SO:0001583	missense	54033	exon5			GGACTCACCAACA	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"""RNA binding motif (RRM) containing"""	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.572A>G	21.37:g.15599340A>G	ENSP00000383421:p.His191Arg	Somatic	368	6	0.0163043		WXS	Illumina HiSeq	Phase_I	471	21	0.044586	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	.	.	.	.	.	.	.	.	.	.	A	1.477	-0.558202	0.03967	.	.	ENSG00000185272	ENST00000400577	T	0.07216	3.21	1.87	0.568	0.17333	.	1.040610	0.07512	N	0.908963	T	0.03305	0.0096	N	0.08118	0	0.20307	N	0.999915	B	0.16166	0.016	B	0.04013	0.001	T	0.46775	-0.9167	10	0.17832	T	0.49	.	0.217	0.00163	0.3713:0.2386:0.1563:0.2338	.	191	P57052	RBM11_HUMAN	R	191	ENSP00000383421:H191R	ENSP00000383421:H191R	H	+	2	0	RBM11	14521211	0.764000	0.28473	0.756000	0.31282	0.615000	0.37417	0.317000	0.19487	0.130000	0.18549	0.164000	0.16699	CAC	.	.	none		0.453	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770	
SPEN	23013	hgsc.bcm.edu	37	1	16259813	16259813	+	Missense_Mutation	SNP	A	A	G	rs848210	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16259813A>G	ENST00000375759.3	+	11	7282	c.7078A>G	c.(7078-7080)Aac>Gac	p.N2360D		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	2360	Interaction with MSX2. {ECO:0000250}.|RID.		N -> D (in dbSNP:rs848210).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|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)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCCTGAATCCAACCAAGCTCA	0.532													G|||	3250	0.648962	0.9758	0.7118	5008	,	,		17756	0.3214		0.5577	False		,,,				2504	0.5941				p.N2360D		Atlas-SNP	.											.	SPEN	374	.	0			c.A7078G						PASS	.	G	ASP/ASN	4014,392	195.3+/-220.0	1826,362,15	93.0	110.0	104.0		7078	3.1	0.0	1	dbSNP_86	104	4955,3645	524.0+/-380.4	1425,2105,770	yes	missense	SPEN	NM_015001.2	23	3251,2467,785	GG,GA,AA		42.3837,8.897,31.0395	benign	2360/3665	16259813	8969,4037	2203	4300	6503	SO:0001583	missense	23013	exon11			GAATCCAACCAAG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.7078A>G	1.37:g.16259813A>G	ENSP00000364912:p.Asn2360Asp	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	65	16	0.246154	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	1320	0.6043956043956044	469	0.9532520325203252	252	0.6961325966850829	174	0.3041958041958042	425	0.5606860158311345	G	2.912	-0.225237	0.06022	0.91103	0.576163	ENSG00000065526	ENST00000375759	T	0.08102	3.13	5.15	3.1	0.35709	.	.	.	.	.	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	0.16012	-1.0417	8	0.12103	T	0.63	-1.0705	7.596	0.28048	0.1608:0.1321:0.7072:0.0	rs848210;rs1619706;rs61684002;rs848210	2360	Q96T58	MINT_HUMAN	D	2360	ENSP00000364912:N2360D	ENSP00000364912:N2360D	N	+	1	0	SPEN	16132400	0.499000	0.26083	0.003000	0.11579	0.181000	0.23173	2.198000	0.42705	0.110000	0.17919	-0.355000	0.07637	AAC	A|0.346;G|0.654	0.654	strong		0.532	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
GSAP	54103	hgsc.bcm.edu	37	7	76990178	76990178	+	Silent	SNP	C	C	G	rs4727366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76990178C>G	ENST00000257626.7	-	14	1068	c.990G>C	c.(988-990)ggG>ggC	p.G330G		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	330					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										TCATGTGTGACCCAACATTCT	0.458													G|||	1512	0.301917	0.5461	0.219	5008	,	,		22232	0.0873		0.2326	False		,,,				2504	0.3231				p.G330G		Atlas-SNP	.											PION,caecum,carcinoma,0,1	PION	74	1	0			c.G990C						PASS	.	G		2185,2221	590.3+/-387.3	546,1093,564	227.0	187.0	200.0		990	2.1	0.1	7	dbSNP_111	200	2174,6426	712.8+/-405.9	261,1652,2387	no	coding-synonymous	PION	NM_017439.3		807,2745,2951	GG,GC,CC		25.2791,49.5915,33.5153		330/855	76990178	4359,8647	2203	4300	6503	SO:0001819	synonymous_variant	54103	exon14			GTGTGACCCAACA		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.990G>C	7.37:g.76990178C>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	242	81	0.334711	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Silent	SNP	ENST00000257626.7	37	CCDS34672.2																																																																																			C|0.688;G|0.312	0.312	strong		0.458	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
ALDH8A1	64577	hgsc.bcm.edu	37	6	135239758	135239758	+	Missense_Mutation	SNP	G	G	C	rs41286234	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:135239758G>C	ENST00000265605.2	-	7	1327	c.1259C>G	c.(1258-1260)gCg>gGg	p.A420G	ALDH8A1_ENST00000367847.2_Missense_Mutation_p.A370G|ALDH8A1_ENST00000367845.2_Missense_Mutation_p.A366G	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	420					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)		CACGGTAGCCGCCAGCCCATA	0.557													G|||	30	0.00599042	0.0	0.013	5008	,	,		20564	0.0		0.0199	False		,,,				2504	0.001				p.A420G		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.C1259G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	20,4386	28.1+/-56.4	0,20,2183	143.0	94.0	111.0		1109,1259,1097	4.3	0.8	6	dbSNP_127	111	134,8466	67.3+/-129.8	1,132,4167	yes	missense,missense,missense	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	60,60,60	1,152,6350	CC,CG,GG		1.5581,0.4539,1.1841	benign,benign,benign	370/438,420/488,366/434	135239758	154,12852	2203	4300	6503	SO:0001583	missense	64577	exon7			GTAGCCGCCAGCC	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.1259C>G	6.37:g.135239758G>C	ENSP00000265605:p.Ala420Gly	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	278	133	0.478417	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	17	0.007783882783882784	0	0.0	1	0.0027624309392265192	0	0.0	16	0.021108179419525065	G	10.69	1.420932	0.25639	0.004539	0.015581	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847;ENST00000460753	T;T;T;T	0.78364	1.44;1.44;1.44;-1.17	6.07	4.29	0.51040	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.303101	0.40144	N	0.001165	T	0.58075	0.2097	L	0.43701	1.375	0.47276	D	0.999372	B;B;B	0.21071	0.051;0.041;0.051	B;B;B	0.19391	0.025;0.014;0.025	T	0.60182	-0.7313	10	0.62326	D	0.03	.	12.4456	0.55649	0.0639:0.1187:0.8175:0.0	rs41286234;rs61731732	370;366;420	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	G	420;366;370;105	ENSP00000265605:A420G;ENSP00000356819:A366G;ENSP00000356821:A370G;ENSP00000437161:A105G	ENSP00000265605:A420G	A	-	2	0	ALDH8A1	135281451	1.000000	0.71417	0.790000	0.31976	0.072000	0.16883	3.780000	0.55386	0.879000	0.35944	0.655000	0.94253	GCG	G|0.981;C|0.019	0.019	strong		0.557	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1266537	1266537	+	Silent	SNP	G	G	T	rs199659189	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1266537G>T	ENST00000529681.1	+	31	8485	c.8427G>T	c.(8425-8427)ctG>ctT	p.L2809L	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.L2812L	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2809	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)		CTCCAGCCCTGTCCAGCCCTC	0.682													-|||	290	0.0579073	0.0401	0.1167	5008	,	,		17295	0.0387		0.0706	False		,,,				2504	0.047				p.L2809L		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.G8427T						scavenged	.																																			SO:0001819	synonymous_variant	727897	exon31			AGCCCTGTCCAGC	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.8427G>T	11.37:g.1266537G>T		Somatic	572	5	0.00874126		WXS	Illumina HiSeq	Phase_I	322	90	0.279503	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.790;T|0.211	0.211	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
AQP12A	375318	hgsc.bcm.edu	37	2	241631499	241631499	+	Silent	SNP	G	G	A	rs200769008		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241631499G>A	ENST00000337801.4	+	2	201	c.132G>A	c.(130-132)acG>acA	p.T44T	AQP12A_ENST00000429564.1_Silent_p.T56T|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	44						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)		AGATGAGGACGCTGGTCGAGC	0.701													g|||	1	0.000199681	0.0	0.0	5008	,	,		12447	0.0		0.001	False		,,,				2504	0.0				p.T44T		Atlas-SNP	.											AQP12A,NS,carcinoma,+1,1	AQP12A	32	1	0			c.G132A						PASS	.						25.0	37.0	33.0					2																	241631499		2147	4265	6412	SO:0001819	synonymous_variant	375318	exon2			GAGGACGCTGGTC	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.132G>A	2.37:g.241631499G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_198998		Silent	SNP	ENST00000337801.4	37																																																																																				G|0.998;A|0.002	0.002	weak		0.701	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998	
CENPE	1062	hgsc.bcm.edu	37	4	104059542	104059542	+	Missense_Mutation	SNP	G	G	A	rs2243682	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:104059542G>A	ENST00000265148.3	-	39	6358	c.6269C>T	c.(6268-6270)aCg>aTg	p.T2090M	CENPE_ENST00000380026.3_Missense_Mutation_p.T1969M	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2090			T -> M (in dbSNP:rs2243682). {ECO:0000269|PubMed:1406971}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.T2090M(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CAGGCTTTCCGTAAGGTGCTG	0.393													G|||	550	0.109824	0.0197	0.1153	5008	,	,		18082	0.1409		0.2207	False		,,,				2504	0.0818				p.T2090M		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	1	1	Substitution - Missense(1)	stomach(1)	c.C6269T						PASS	.	G	MET/THR	182,4224	118.0+/-155.7	6,170,2027	241.0	231.0	234.0		6269	0.4	0.0	4	dbSNP_100	234	1772,6828	320.0+/-314.4	196,1380,2724	yes	missense	CENPE	NM_001813.2	81	202,1550,4751	AA,AG,GG		20.6047,4.1307,15.0238	probably-damaging	2090/2702	104059542	1954,11052	2203	4300	6503	SO:0001583	missense	1062	exon39			CTTTCCGTAAGGT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.6269C>T	4.37:g.104059542G>A	ENSP00000265148:p.Thr2090Met	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	324	0.14835164835164835	16	0.032520325203252036	51	0.1408839779005525	74	0.12937062937062938	183	0.24142480211081793	G	10.54	1.379672	0.24944	0.041307	0.206047	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.72394	-0.65;-0.61	4.34	0.381	0.16228	.	.	.	.	.	T	0.00039	0.0001	L	0.44542	1.39	0.80722	P	0.0	P;B	0.37398	0.593;0.297	B;B	0.22386	0.039;0.015	T	0.01401	-1.1364	8	0.45353	T	0.12	.	6.5724	0.22545	0.4583:0.0:0.5417:0.0	rs2243682;rs52801440;rs58953735;rs2243682	1969;2090	Q02224-3;Q02224	.;CENPE_HUMAN	M	2090;2090;1969	ENSP00000265148:T2090M;ENSP00000369365:T1969M	ENSP00000265148:T2090M	T	-	2	0	CENPE	104278991	0.000000	0.05858	0.002000	0.10522	0.296000	0.27459	-0.164000	0.09983	0.137000	0.18759	0.544000	0.68410	ACG	G|0.855;A|0.145	0.145	strong		0.393	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
UBR2	23304	hgsc.bcm.edu	37	6	42571346	42571346	+	Silent	SNP	A	A	T	rs16895863	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:42571346A>T	ENST00000372899.1	+	5	810	c.552A>T	c.(550-552)tcA>tcT	p.S184S	UBR2_ENST00000372903.2_Silent_p.S184S|UBR2_ENST00000372901.1_Silent_p.S184S	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	184					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TTCATTTATCAGAAGATGTGA	0.328													A|||	1006	0.200879	0.2352	0.183	5008	,	,		18936	0.0893		0.2366	False		,,,				2504	0.2454				p.S184S		Atlas-SNP	.											.	UBR2	134	.	0			c.A552T						PASS	.	A	,	1026,3380	375.4+/-321.6	116,794,1293	66.0	64.0	65.0		552,552	3.1	1.0	6	dbSNP_123	65	1828,6762	326.6+/-317.4	204,1420,2671	no	coding-synonymous,coding-synonymous	UBR2	NM_001184801.1,NM_015255.2	,	320,2214,3964	TT,TA,AA		21.2806,23.2864,21.9606	,	184/440,184/1756	42571346	2854,10142	2203	4295	6498	SO:0001819	synonymous_variant	23304	exon5			TTTATCAGAAGAT	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.552A>T	6.37:g.42571346A>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			A|0.793;T|0.207	0.207	strong		0.328	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
IL21R	50615	hgsc.bcm.edu	37	16	27460436	27460436	+	Silent	SNP	C	C	T	rs3093408		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:27460436C>T	ENST00000337929.3	+	9	1922	c.1449C>T	c.(1447-1449)gcC>gcT	p.A483A	IL21R_ENST00000395754.4_Silent_p.A483A|IL21R_ENST00000564089.1_Silent_p.A483A|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000395755.1_Silent_p.A483A	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	483					interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						CACCCCTGGCCGGCCTGGATA	0.672			T	BCL6	NHL								C|||	1	0.000199681	0.0	0.0014	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.A505A		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.C1515T						PASS	.	C	,,	0,4394		0,0,2197	41.0	38.0	39.0		1449,1449,1515	-7.6	0.0	16	dbSNP_103	39	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	IL21R	NM_021798.3,NM_181078.2,NM_181079.4	,,	0,3,6494	TT,TC,CC		0.0349,0.0,0.0231	,,	483/539,483/539,505/561	27460436	3,12991	2197	4300	6497	SO:0001819	synonymous_variant	50615	exon10			CCTGGCCGGCCTG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"""Interleukins and interleukin receptors"", ""CD molecules"""	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1449C>T	16.37:g.27460436C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	105	55	0.52381	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Silent	SNP	ENST00000337929.3	37	CCDS10630.1																																																																																			C|0.999;T|0.001	0.001	strong		0.672	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078	
ABCA5	23461	hgsc.bcm.edu	37	17	67304447	67304447	+	Missense_Mutation	SNP	C	C	T	rs11544715	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:67304447C>T	ENST00000392676.3	-	5	596	c.532G>A	c.(532-534)Gca>Aca	p.A178T	ABCA5_ENST00000392677.2_Missense_Mutation_p.A178T|ABCA5_ENST00000588877.1_Missense_Mutation_p.A178T			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	178			A -> T (in dbSNP:rs11544715). {ECO:0000269|PubMed:12504089}.		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)	TCTATGGATGCTTGTAAAACT	0.348													C|||	621	0.124002	0.1672	0.1888	5008	,	,		15784	0.0446		0.1412	False		,,,				2504	0.0838				p.A178T		Atlas-SNP	.											ABCA5,NS,carcinoma,0,1	ABCA5	162	1	0			c.G532A						PASS	.	C	THR/ALA,THR/ALA	743,3663	306.0+/-289.3	55,633,1515	91.0	97.0	95.0		532,532	3.4	1.0	17	dbSNP_120	95	1225,7375	247.1+/-275.3	82,1061,3157	yes	missense,missense	ABCA5	NM_018672.3,NM_172232.2	58,58	137,1694,4672	TT,TC,CC		14.2442,16.8634,15.1315	probably-damaging,probably-damaging	178/1643,178/1643	67304447	1968,11038	2203	4300	6503	SO:0001583	missense	23461	exon4			TGGATGCTTGTAA	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.532G>A	17.37:g.67304447C>T	ENSP00000376443:p.Ala178Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	269	0.12316849816849818	87	0.17682926829268292	58	0.16022099447513813	16	0.027972027972027972	108	0.1424802110817942	C	12.87	2.067960	0.36470	0.168634	0.142442	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.87029	-2.2;-2.2	4.65	3.44	0.39384	.	0.109437	0.39909	N	0.001230	T	0.00496	0.0016	L	0.39020	1.185	0.29930	P	0.82195	B;B	0.12013	0.004;0.005	B;B	0.14578	0.006;0.011	T	0.33574	-0.9863	8	.	.	.	.	11.3468	0.49565	0.0:0.8391:0.0:0.1609	rs11544715;rs52811902;rs57749310;rs11544715	178;178	Q8WWZ7-2;Q8WWZ7	.;ABCA5_HUMAN	T	178	ENSP00000376444:A178T;ENSP00000376443:A178T	.	A	-	1	0	ABCA5	64816042	0.999000	0.42202	0.998000	0.56505	0.992000	0.81027	1.077000	0.30741	2.118000	0.64928	0.460000	0.39030	GCA	C|0.866;T|0.134	0.134	strong		0.348	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
USHBP1	83878	hgsc.bcm.edu	37	19	17366313	17366313	+	Missense_Mutation	SNP	C	C	T	rs12459398	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17366313C>T	ENST00000252597.3	-	10	1746	c.1573G>A	c.(1573-1575)Gtg>Atg	p.V525M	AC010646.3_ENST00000594059.1_5'Flank|USHBP1_ENST00000431146.2_Missense_Mutation_p.V461M	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 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						AGCAGGAGCACGTGAGCTGGA	0.701													C|||	1348	0.269169	0.3132	0.268	5008	,	,		14664	0.2788		0.2197	False		,,,				2504	0.2515				p.V525M		Atlas-SNP	.											.	USHBP1	85	.	0			c.G1573A						PASS	.	C	MET/VAL	1348,3058	434.3+/-343.9	197,954,1052	38.0	40.0	39.0		1573	-5.5	0.0	19	dbSNP_120	39	1750,6850	304.0+/-306.7	165,1420,2715	no	missense	USHBP1	NM_031941.3	21	362,2374,3767	TT,TC,CC		20.3488,30.5946,23.8198	benign	525/704	17366313	3098,9908	2203	4300	6503	SO:0001583	missense	83878	exon10			GGAGCACGTGAGC	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.1573G>A	19.37:g.17366313C>T	ENSP00000252597:p.Val525Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_031941		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	580	0.26556776556776557	178	0.3617886178861789	87	0.24033149171270718	154	0.2692307692307692	161	0.21240105540897097	C	6.299	0.423219	0.11928	0.305946	0.203488	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.17854	2.25;2.25	4.92	-5.46	0.02608	.	2.347010	0.01907	N	0.039582	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.20671	0.019;0.047	B;B	0.09377	0.004;0.004	T	0.40515	-0.9559	9	0.46703	T	0.11	0.1015	8.5648	0.33534	0.0:0.1432:0.4915:0.3653	rs12459398	461;525	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	M	525;461	ENSP00000252597:V525M;ENSP00000407902:V461M	ENSP00000252597:V525M	V	-	1	0	USHBP1	17227313	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.146000	0.03191	-1.191000	0.02695	-0.882000	0.02950	GTG	C|0.765;T|0.235	0.235	strong		0.701	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
OR5D13	390142	hgsc.bcm.edu	37	11	55541284	55541284	+	Missense_Mutation	SNP	G	G	A	rs11230983	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	421	1	0.0023753		WXS	Illumina HiSeq	Phase_I	397	154	0.387909	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	
FAM179B	23116	hgsc.bcm.edu	37	14	45478260	45478260	+	Missense_Mutation	SNP	A	A	G	rs139225809		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:45478260A>G	ENST00000361577.3	+	6	3263	c.3049A>G	c.(3049-3051)Aac>Gac	p.N1017D	FAM179B_ENST00000382233.2_Intron|FAM179B_ENST00000361462.2_Missense_Mutation_p.N1017D|KLHL28_ENST00000553817.1_Intron	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1017	Ser-rich.									endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TTCCTCACCAAACATCAATTC	0.423													A|||	1	0.000199681	0.0	0.0014	5008	,	,		15443	0.0		0.0	False		,,,				2504	0.0				p.N1017D		Atlas-SNP	.											.	FAM179B	115	.	0			c.A3049G						PASS	.	A	ASP/ASN	1,4405	2.1+/-5.4	0,1,2202	119.0	108.0	112.0		3049	5.7	1.0	14	dbSNP_134	112	6,8594	5.0+/-18.6	0,6,4294	yes	missense	FAM179B	NM_015091.2	23	0,7,6496	GG,GA,AA		0.0698,0.0227,0.0538	probably-damaging	1017/1721	45478260	7,12999	2203	4300	6503	SO:0001583	missense	23116	exon6			TCACCAAACATCA	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.3049A>G	14.37:g.45478260A>G	ENSP00000355045:p.Asn1017Asp	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	159	106	0.666667	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.246111	0.80024	2.27E-4	6.98E-4	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462	T;T	0.04275	3.66;3.66	5.72	5.72	0.89469	Armadillo-type fold (1);	0.136815	0.51477	D	0.000095	T	0.08223	0.0205	L	0.29908	0.895	0.80722	D	1	P;P	0.50943	0.94;0.94	P;P	0.50659	0.647;0.57	T	0.36744	-0.9735	10	0.37606	T	0.19	-15.4805	14.9927	0.71401	1.0:0.0:0.0:0.0	.	1017;1017	G3XAE9;Q9Y4F4	.;F179B_HUMAN	D	1017	ENSP00000355045:N1017D;ENSP00000354917:N1017D	ENSP00000354917:N1017D	N	+	1	0	FAM179B	44548010	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.665000	0.46791	2.171000	0.68590	0.533000	0.62120	AAC	A|0.999;G|0.001	0.001	strong		0.423	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	
ETFB	2109	hgsc.bcm.edu	37	19	51857738	51857738	+	Intron	SNP	G	G	A	rs79338777	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51857738G>A	ENST00000309244.4	-	2	149				CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.11_ENST00000600067.1_Intron|ETFB_ENST00000354232.4_Missense_Mutation_p.P52L	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						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)		tgtaggcagGGGCAGGTCACC	0.582													g|||	387	0.0772764	0.0439	0.0403	5008	,	,		16395	0.1181		0.0696	False		,,,				2504	0.1145				p.P52L		Atlas-SNP	.											.	ETFB	46	.	0			c.C155T						PASS	.	G	LEU/PRO,	196,4210	122.5+/-159.9	3,190,2010	79.0	72.0	74.0		155,	-5.5	0.0	19	dbSNP_131	74	591,8009	156.7+/-210.5	22,547,3731	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	98,	25,737,5741	AA,AG,GG		6.8721,4.4485,6.0511	probably-damaging,	52/347,	51857738	787,12219	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			GGCAGGGGCAGGT	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.58-176C>T	19.37:g.51857738G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	156	0.07142857142857142	23	0.046747967479674794	13	0.03591160220994475	69	0.12062937062937062	51	0.06728232189973615	g	12.18	1.860517	0.32884	0.044485	0.068721	ENSG00000105379	ENST00000354232	D	0.85955	-2.05	2.77	-5.53	0.02552	.	.	.	.	.	T	0.01905	0.0060	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.15954	-1.0419	6	.	.	.	.	1.673	0.02816	0.2749:0.125:0.4452:0.1549	.	52	P38117-2	.	L	52	ENSP00000346173:P52L	.	P	-	2	0	ETFB	56549550	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.733000	0.00803	-1.622000	0.01560	-0.290000	0.09829	CCC	G|0.937;A|0.063	0.063	strong		0.582	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
NLRP4	147945	hgsc.bcm.edu	37	19	56373462	56373462	+	Missense_Mutation	SNP	G	G	A	rs12462372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56373462G>A	ENST00000301295.6	+	5	2545	c.2123G>A	c.(2122-2124)cGt>cAt	p.R708H	NLRP4_ENST00000587891.1_Missense_Mutation_p.R633H|NLRP4_ENST00000346986.5_Missense_Mutation_p.R708H	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	708			R -> H (in dbSNP:rs12462372).		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)			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)		AAACTCTCTCGTGATGACATC	0.473													G|||	528	0.105431	0.0038	0.1599	5008	,	,		22235	0.2391		0.0586	False		,,,				2504	0.1145				p.R708H		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,+1,7	NLRP4	331	7	0			c.G2123A						scavenged	.	G	HIS/ARG	59,4347	56.2+/-92.4	0,59,2144	143.0	128.0	133.0		2123	-6.5	0.0	19	dbSNP_120	133	407,8193	128.3+/-186.6	11,385,3904	yes	missense	NLRP4	NM_134444.4	29	11,444,6048	AA,AG,GG		4.7326,1.3391,3.583	benign	708/995	56373462	466,12540	2203	4300	6503	SO:0001583	missense	147945	exon5			TCTCTCGTGATGA	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.2123G>A	19.37:g.56373462G>A	ENSP00000301295:p.Arg708His	Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	163	91	0.558282	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	225	0.10302197802197802	3	0.006097560975609756	32	0.08839779005524862	142	0.24825174825174826	48	0.0633245382585752	G	0.018	-1.476288	0.01035	0.013391	0.047326	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.53206	0.63;0.63	3.26	-6.52	0.01872	.	.	.	.	.	T	0.00012	0.0000	N	0.05487	-0.04	0.80722	P	0.0	B;B;B	0.27882	0.037;0.183;0.192	B;B;B	0.21546	0.019;0.035;0.015	T	0.21518	-1.0243	8	0.23891	T	0.37	.	8.1119	0.30920	0.689:0.1268:0.1842:0.0	rs12462372;rs52792345;rs60975652;rs12462372	708;633;708	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	H	708	ENSP00000301295:R708H;ENSP00000344787:R708H	ENSP00000301295:R708H	R	+	2	0	NLRP4	61065274	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.408000	0.01042	-1.815000	0.01222	-0.251000	0.11542	CGT	G|0.927;A|0.073	0.073	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
ABAT	18	hgsc.bcm.edu	37	16	8844389	8844389	+	Silent	SNP	C	C	T	rs2229157	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000567812.1_Silent_p.V118V|ABAT_ENST00000569156.1_Silent_p.V103V|ABAT_ENST00000268251.8_Silent_p.V103V	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	187	0	0		WXS	Illumina HiSeq	Phase_I	150	76	0.506667	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	
ZCCHC3	85364	hgsc.bcm.edu	37	20	278806	278806	+	Silent	SNP	C	C	T	rs1057189	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	29	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	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		
RPGRIP1	57096	hgsc.bcm.edu	37	14	21792811	21792811	+	Silent	SNP	G	G	A	rs9322965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21792811G>A	ENST00000400017.2	+	14	1797	c.1797G>A	c.(1795-1797)ccG>ccA	p.P599P	RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000307974.4_Missense_Mutation_p.R8H|RPGRIP1_ENST00000557771.1_Silent_p.P561P|RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000206660.6_Silent_p.P599P	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	599					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)		GCACCCGACCGTTGTCGTTAT	0.478													G|||	925	0.184704	0.2421	0.1427	5008	,	,		21117	0.0188		0.2336	False		,,,				2504	0.2577				p.P599P		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.G1797A						PASS	.	G		835,3111		96,643,1234	125.0	117.0	120.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1797	3.2	0.1	14	dbSNP_119	120	1996,6294		228,1540,2377	no	coding-synonymous	RPGRIP1	NM_020366.3		324,2183,3611	AA,AG,GG		24.0772,21.1607,23.1366		599/1287	21792811	2831,9405	1973	4145	6118	SO:0001819	synonymous_variant	57096	exon14			CCGACCGTTGTCG	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.1797G>A	14.37:g.21792811G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1	357	0.16346153846153846	115	0.23373983739837398	56	0.15469613259668508	6	0.01048951048951049	180	0.23746701846965698	G	8.657	0.899673	0.17686	0.211607	0.240772	ENSG00000092200	ENST00000307974	T	0.79454	-1.27	5.28	3.17	0.36434	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.04320	-1.0960	7	0.37606	T	0.19	-0.1041	2.6329	0.04950	0.2604:0.0:0.3544:0.3852	rs9322965;rs59052867;rs9322965	8	Q96KN7-3	.	H	8	ENSP00000309721:R8H	ENSP00000309721:R8H	R	+	2	0	RPGRIP1	20862651	0.000000	0.05858	0.052000	0.19188	0.972000	0.66771	-0.363000	0.07593	0.534000	0.28695	0.655000	0.94253	CGT	G|0.856;A|0.144	0.144	strong		0.478	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
DDI2	84301	hgsc.bcm.edu	37	1	15959977	15959977	+	Silent	SNP	C	C	T	rs3795763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15959977C>T	ENST00000480945.1	+	4	720	c.549C>T	c.(547-549)gcC>gcT	p.A183A		NM_032341.4	NP_115717.3	Q5TDH0	DDI2_HUMAN	DNA-damage inducible 1 homolog 2 (S. cerevisiae)	183							aspartic-type endopeptidase activity (GO:0004190)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|stomach(1)	17		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00327)|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;9.03e-07)|COAD - Colon adenocarcinoma(227;4.48e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AGGACCGAGCCCGGAGAGAGC	0.403													C|||	1257	0.250998	0.4493	0.2176	5008	,	,		18022	0.0317		0.2684	False		,,,				2504	0.2147				p.A183A		Atlas-SNP	.											.	DDI2	38	.	0			c.C549T						PASS	.	C		1831,2575	535.8+/-374.3	406,1019,778	186.0	222.0	210.0		549	2.7	1.0	1	dbSNP_107	210	2428,6172	401.3+/-347.1	326,1776,2198	no	coding-synonymous	DDI2	NM_032341.4		732,2795,2976	TT,TC,CC		28.2326,41.557,32.7464		183/400	15959977	4259,8747	2203	4300	6503	SO:0001819	synonymous_variant	84301	exon4			CCGAGCCCGGAGA		CCDS30607.1	1p36.13	2010-05-04	2010-05-04		ENSG00000197312	ENSG00000197312			24578	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 2 (S. cerevisiae)"""				Standard	NM_032341		Approved	MGC14844	uc001awx.2	Q5TDH0	OTTHUMG00000002381	ENST00000480945.1:c.549C>T	1.37:g.15959977C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	64	17	0.265625	NM_032341	A8KAE1|Q7RTZ0|Q9BRT1	Silent	SNP	ENST00000480945.1	37	CCDS30607.1																																																																																			C|0.707;T|0.293	0.293	strong		0.403	DDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006826.1	NM_032341	
NAV3	89795	hgsc.bcm.edu	37	12	78400884	78400884	+	Silent	SNP	G	G	A	rs34276383	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:78400884G>A	ENST00000397909.2	+	8	1739	c.1566G>A	c.(1564-1566)ccG>ccA	p.P522P	NAV3_ENST00000228327.6_Silent_p.P522P|NAV3_ENST00000266692.7_Silent_p.P522P|NAV3_ENST00000536525.2_Silent_p.P522P			Q8IVL0	NAV3_HUMAN	neuron navigator 3	522						membrane (GO:0016020)|nuclear envelope (GO:0005635)		p.P522P(1)		NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						GCTTAATTCCGTCTTCCAGTG	0.448										HNSCC(70;0.22)			A|||	744	0.148562	0.0908	0.1095	5008	,	,		19238	0.2143		0.1322	False		,,,				2504	0.2035				p.P522P		Atlas-SNP	.											NAV3,NS,carcinoma,0,1	NAV3	506	1	1	Substitution - coding silent(1)	stomach(1)	c.G1566A						PASS	.	A		405,3417		31,343,1537	66.0	66.0	66.0		1566	-5.4	0.7	12	dbSNP_126	66	1037,7193		61,915,3139	no	coding-synonymous	NAV3	NM_014903.4		92,1258,4676	AA,AG,GG		12.6002,10.5965,11.9648		522/2364	78400884	1442,10610	1911	4115	6026	SO:0001819	synonymous_variant	89795	exon8			AATTCCGTCTTCC	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.1566G>A	12.37:g.78400884G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_014903	Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37																																																																																				G|0.867;A|0.133	0.133	strong		0.448	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
JADE1	79960	hgsc.bcm.edu	37	4	129792873	129792873	+	Missense_Mutation	SNP	A	A	G	rs6855813	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:129792873A>G	ENST00000226319.6	+	11	2265	c.1985A>G	c.(1984-1986)aAt>aGt	p.N662S	PHF17_ENST00000512960.1_Missense_Mutation_p.N662S|PHF17_ENST00000452328.2_Missense_Mutation_p.N650S	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						AGAAGAGACAATCGTTTTCAT	0.423													A|||	112	0.0223642	0.0734	0.0144	5008	,	,		21259	0.001		0.002	False		,,,				2504	0.002				p.N662S		Atlas-SNP	.											.	PHF17	63	.	0			c.A1985G						PASS	.	A	SER/ASN	329,4077	170.5+/-200.9	13,303,1887	77.0	76.0	76.0		1985	2.2	1.0	4	dbSNP_116	76	11,8589	8.4+/-32.0	0,11,4289	yes	missense	PHF17	NM_199320.2	46	13,314,6176	GG,GA,AA		0.1279,7.4671,2.6142	benign	662/843	129792873	340,12666	2203	4300	6503	SO:0001583	missense	79960	exon11			GAGACAATCGTTT																												ENST00000226319.6:c.1985A>G	4.37:g.129792873A>G	ENSP00000226319:p.Asn662Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	96	21	0.21875	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	37	CCDS34062.1	50	0.022893772893772892	43	0.08739837398373984	5	0.013812154696132596	0	0.0	2	0.002638522427440633	A	0.959	-0.703925	0.03255	0.074671	0.001279	ENSG00000077684	ENST00000226319;ENST00000452328;ENST00000512960;ENST00000535321	T;T;T	0.38401	1.14;1.15;1.14	4.59	2.25	0.28309	.	0.840784	0.11323	N	0.575875	T	0.00580	0.0019	N	0.04880	-0.145	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17349	-1.0372	9	.	.	.	.	7.662	0.28409	0.7588:0.0:0.2412:0.0	rs6855813;rs6855813	650;662	Q6IE81-2;Q6IE81	.;JADE1_HUMAN	S	662;650;662;662	ENSP00000226319:N662S;ENSP00000388015:N650S;ENSP00000425730:N662S	.	N	+	2	0	PHF17	130012323	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.779000	0.38624	0.910000	0.36722	0.533000	0.62120	AAT	A|0.972;G|0.028	0.028	strong		0.423	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1		
CROCC	9696	hgsc.bcm.edu	37	1	17273444	17273444	+	Silent	SNP	G	G	A	rs7545185	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:17273444G>A	ENST00000375541.5	+	17	2541	c.2472G>A	c.(2470-2472)acG>acA	p.T824T	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)		AGCTCCCCACGCTGCGCCATG	0.701																																					p.T824T		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.G2472A						PASS	.	G		183,4075		0,183,1946	9.0	9.0	9.0		2472	-5.3	0.0	1	dbSNP_116	9	1201,7057		4,1193,2932	no	coding-synonymous	CROCC	NM_014675.3		4,1376,4878	AA,AG,GG		14.5435,4.2978,11.0578		824/2018	17273444	1384,11132	2129	4129	6258	SO:0001819	synonymous_variant	9696	exon17			CCCCACGCTGCGC	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.2472G>A	1.37:g.17273444G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	39	5	0.128205	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			G|0.809;A|0.191	0.191	strong		0.701	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
USP21	27005	hgsc.bcm.edu	37	1	161132777	161132777	+	Missense_Mutation	SNP	G	G	A	rs17356051	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161132777G>A	ENST00000289865.8	+	6	1183	c.962G>A	c.(961-963)gGc>gAc	p.G321D	USP21_ENST00000368002.3_Missense_Mutation_p.G321D|USP21_ENST00000368001.1_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	155	0	0		WXS	Illumina HiSeq	Phase_I	221	91	0.411765	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		
ZNF99	7652	hgsc.bcm.edu	37	19	22952111	22952111	+	Missense_Mutation	SNP	A	A	G	rs34726149	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22952111A>G	ENST00000596209.1	-	2	109	c.19T>C	c.(19-21)Tgg>Cgg	p.W7R	ZNF99_ENST00000397104.3_Missense_Mutation_p.W28R	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	7	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		W -> R (in dbSNP:rs34726149).		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.W28R(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GTCACATCCCAAAATGTCAAC	0.393													G|||	1089	0.217452	0.4198	0.1326	5008	,	,		15615	0.1756		0.1372	False		,,,				2504	0.1299				p.W7R		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	1	1	Substitution - Missense(1)	stomach(1)	c.T19C						PASS	.	G	ARG/TRP	1654,2736		299,1056,840	70.0	76.0	74.0		82	-2.1	0.0	19	dbSNP_126	74	1041,7557		70,901,3328	no	missense	ZNF99	NM_001080409.2	101	369,1957,4168	GG,GA,AA		12.1075,37.6765,20.7499	benign	28/912	22952111	2695,10293	2195	4299	6494	SO:0001583	missense	7652	exon2			CATCCCAAAATGT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.19T>C	19.37:g.22952111A>G	ENSP00000472969:p.Trp7Arg	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	194	85	0.438144	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	460	0.21062271062271062	205	0.4166666666666667	55	0.15193370165745856	105	0.18356643356643357	95	0.12532981530343007	N	0	-2.657345	0.00108	0.376765	0.121075	ENSG00000213973	ENST00000397104	T	0.01527	4.8	1.04	-2.08	0.07254	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	N	0.00018	-2.82	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47262	-0.9131	8	0.05436	T	0.98	.	2.9505	0.05860	0.2153:0.0:0.2594:0.5253	rs34726149;rs62120120	28	A8MXY4	ZNF99_HUMAN	R	28	ENSP00000380293:W28R	ENSP00000380293:W28R	W	-	1	0	ZNF99	22743951	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.162000	0.03141	-4.685000	0.00036	-4.816000	0.00003	TGG	A|0.809;G|0.191	0.191	strong		0.393	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
SPATA2	9825	hgsc.bcm.edu	37	20	48524827	48524827	+	Silent	SNP	A	A	G	rs2769982	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:48524827A>G	ENST00000422556.1	-	2	550	c.201T>C	c.(199-201)taT>taC	p.Y67Y	SPATA2_ENST00000289431.5_Silent_p.Y67Y|SPATA2_ENST00000543716.1_Intron	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	67					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CCACCACCTCATAGAACTGGA	0.622													G|||	2458	0.490815	0.1316	0.585	5008	,	,		19272	0.7738		0.4503	False		,,,				2504	0.6595				p.Y67Y		Atlas-SNP	.											.	SPATA2	36	.	0			c.T201C						PASS	.	G	,	844,3562	745.8+/-411.7	78,688,1437	79.0	67.0	71.0		201,201	-6.8	0.7	20	dbSNP_100	71	3968,4632	600.7+/-394.3	911,2146,1243	no	coding-synonymous,coding-synonymous	SPATA2	NM_001135773.1,NM_006038.3	,	989,2834,2680	GG,GA,AA		46.1395,19.1557,36.9983	,	67/521,67/521	48524827	4812,8194	2203	4300	6503	SO:0001819	synonymous_variant	9825	exon2			CACCTCATAGAAC	AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 145"""	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.201T>C	20.37:g.48524827A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_006038	E1P626|O94857	Silent	SNP	ENST00000422556.1	37	CCDS13422.1																																																																																			A|0.584;G|0.416	0.416	strong		0.622	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038	
HEATR1	55127	hgsc.bcm.edu	37	1	236729965	236729965	+	Missense_Mutation	SNP	G	G	A	rs61736343	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:236729965G>A	ENST00000366582.3	-	30	4403	c.4289C>T	c.(4288-4290)gCg>gTg	p.A1430V	HEATR1_ENST00000366581.2_Missense_Mutation_p.A1349V	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1430					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)			ATAGGCAGCCGCCAGCACTGT	0.433													G|||	31	0.0061901	0.0008	0.0072	5008	,	,		16809	0.0		0.0149	False		,,,				2504	0.0102				p.A1430V		Atlas-SNP	.											HEATR1,caecum,carcinoma,0,1	HEATR1	197	1	0			c.C4289T						PASS	.	G	VAL/ALA	21,4385	27.2+/-55.0	0,21,2182	33.0	33.0	33.0		4289	-1.5	0.7	1	dbSNP_129	33	224,8376	93.1+/-155.1	1,222,4077	yes	missense	HEATR1	NM_018072.5	64	1,243,6259	AA,AG,GG		2.6047,0.4766,1.8837	benign	1430/2145	236729965	245,12761	2203	4300	6503	SO:0001583	missense	55127	exon30			GCAGCCGCCAGCA	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.4289C>T	1.37:g.236729965G>A	ENSP00000355541:p.Ala1430Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	117	38	0.324786	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	G	10.24	1.294369	0.23564	0.004766	0.026047	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.39229	1.09;1.09	5.6	-1.54	0.08584	Armadillo-like helical (1);Armadillo-type fold (1);	1.273310	0.05144	N	0.494798	T	0.05868	0.0153	N	0.01267	-0.92	0.09310	N	0.99999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18116	-1.0347	10	0.18710	T	0.47	.	11.8433	0.52368	0.5277:0.0:0.4723:0.0	.	1349;1430	Q5T3Q7;Q9H583	.;HEAT1_HUMAN	V	1430;1349	ENSP00000355541:A1430V;ENSP00000355540:A1349V	ENSP00000355540:A1349V	A	-	2	0	HEATR1	234796588	0.002000	0.14202	0.731000	0.30826	0.919000	0.55068	-0.017000	0.12590	-0.537000	0.06290	-0.302000	0.09304	GCG	G|0.985;A|0.015	0.015	strong		0.433	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
MUC17	140453	hgsc.bcm.edu	37	7	100677974	100677974	+	Missense_Mutation	SNP	A	A	G	rs113876641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677974A>G	ENST00000306151.4	+	3	3341	c.3277A>G	c.(3277-3279)Acc>Gcc	p.T1093A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1093	59 X approximate tandem repeats.|Ser-rich.				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)					CAGCATGCCAACCTCAACTTA	0.507																																					p.T1093A		Atlas-SNP	.											.	MUC17	804	.	0			c.A3277G						PASS	.						479.0	385.0	417.0					7																	100677974		2203	4300	6503	SO:0001583	missense	140453	exon3			ATGCCAACCTCAA	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.3277A>G	7.37:g.100677974A>G	ENSP00000302716:p.Thr1093Ala	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	890	178	0.2	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	1.073	-0.669248	0.03403	.	.	ENSG00000169876	ENST00000306151	T	0.02258	4.37	0.693	-0.692	0.11301	.	.	.	.	.	T	0.00998	0.0033	N	0.14661	0.345	0.09310	N	1	P	0.37985	0.613	B	0.25140	0.058	T	0.46638	-0.9177	9	0.10902	T	0.67	.	4.0642	0.09852	0.7272:0.0:0.2728:0.0	.	1093	Q685J3	MUC17_HUMAN	A	1093	ENSP00000302716:T1093A	ENSP00000302716:T1093A	T	+	1	0	MUC17	100464694	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.411000	0.07142	-0.284000	0.09102	0.165000	0.16767	ACC	A|0.998;G|0.002	0.002	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ATG12	9140	hgsc.bcm.edu	37	5	115177207	115177207	+	Missense_Mutation	SNP	T	T	C	rs74844425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:115177207T>C	ENST00000509910.1	-	1	348	c.43A>G	c.(43-45)Att>Gtt	p.I15V	ATG12_ENST00000509598.1_5'Flank|AP3S1_ENST00000316788.7_5'UTR|ATG12_ENST00000274459.4_Missense_Mutation_p.I62V|ATG12_ENST00000500945.2_Missense_Mutation_p.I15V			O94817	ATG12_HUMAN	autophagy related 12	15					autophagic vacuole assembly (GO:0000045)|C-terminal protein lipidation (GO:0006501)|cellular response to nitrogen starvation (GO:0006995)|innate immune response (GO:0045087)|mitochondrion degradation (GO:0000422)|negative regulation of type I interferon production (GO:0032480)|nucleophagy (GO:0044804)	Atg12-Atg5-Atg16 complex (GO:0034274)|pre-autophagosomal structure membrane (GO:0034045)	Atg8 ligase activity (GO:0019776)			endometrium(2)|kidney(1)|lung(1)|prostate(1)	5		all_cancers(142;0.00377)|all_epithelial(76;0.000129)|Prostate(80;0.0132)|Ovarian(225;0.0776)|Lung NSC(810;0.245)		OV - Ovarian serous cystadenocarcinoma(64;7.59e-08)|Epithelial(69;7.05e-07)|all cancers(49;3.11e-05)		CCAGCAGCAATTGAAGTAGGA	0.607													T|||	69	0.013778	0.0061	0.0159	5008	,	,		14266	0.002		0.0258	False		,,,				2504	0.0225				p.I15V		Atlas-SNP	.											.	ATG12	14	.	0			c.A43G						PASS	.	T	VAL/ILE	43,4361	45.3+/-79.5	0,43,2159	77.0	85.0	82.0		43	-4.3	0.0	5	dbSNP_131	82	222,8378	91.6+/-153.7	5,212,4083	yes	missense	ATG12	NM_004707.3	29	5,255,6242	CC,CT,TT		2.5814,0.9764,2.0378	benign	15/141	115177207	265,12739	2202	4300	6502	SO:0001583	missense	9140	exon1			CAGCAATTGAAGT	AB017507	CCDS4122.1, CCDS4122.2, CCDS64222.1	5q21-q22	2014-02-12	2012-06-06	2005-09-11	ENSG00000145782	ENSG00000145782			588	protein-coding gene	gene with protein product	"""APG12 autophagy 12-like"""	609608	"""Apg12 (autophagy 12, S. cerevisiae)-like"", ""APG12 autophagy 12-like (S. cerevisiae)"", ""ATG12 autophagy related 12 homolog (S. cerevisiae)"""	APG12L		9852036	Standard	NM_004707		Approved	APG12	uc003krh.3	O94817	OTTHUMG00000128889	ENST00000509910.1:c.43A>G	5.37:g.115177207T>C	ENSP00000425107:p.Ile15Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_004707	Q6PJV2	Missense_Mutation	SNP	ENST00000509910.1	37	CCDS4122.2	28	0.01282051282051282	3	0.006097560975609756	7	0.019337016574585635	2	0.0034965034965034965	16	0.021108179419525065	T	11.03	1.518606	0.27211	0.009764	0.025814	ENSG00000145782	ENST00000274459;ENST00000509910;ENST00000500945	.	.	.	4.88	-4.3	0.03710	.	1.771270	0.02653	N	0.106639	T	0.07954	0.0199	N	0.08118	0	0.25174	N	0.990258	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14090	-1.0485	9	0.25751	T	0.34	-24.0427	9.1821	0.37148	0.0:0.6604:0.1496:0.1899	.	15;62	O94817;C1IDX9	ATG12_HUMAN;.	V	62;15;15	.	ENSP00000274459:I62V	I	-	1	0	ATG12	115205106	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.491000	0.06474	-0.369000	0.08028	-0.250000	0.11733	ATT	A|0.000;C|0.019;T|0.980	0.019	strong		0.607	ATG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250851.3	NM_004707	
SARDH	1757	hgsc.bcm.edu	37	9	136573412	136573412	+	Silent	SNP	G	G	A	rs2073815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136573412G>A	ENST00000371872.4	-	11	1724	c.1467C>T	c.(1465-1467)caC>caT	p.H489H	SARDH_ENST00000422262.2_Silent_p.H321H|SARDH_ENST00000439388.1_Silent_p.H489H	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	489					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)		GCGTTACCTCGTGCAGCGGGT	0.637													G|||	2123	0.423922	0.2254	0.464	5008	,	,		17063	0.4891		0.5577	False		,,,				2504	0.4591				p.H489H		Atlas-SNP	.											SARDH,NS,carcinoma,0,2	SARDH	112	2	0			c.C1467T						PASS	.	G	,	1190,3216	415.0+/-337.0	157,876,1170	73.0	66.0	68.0		1467,1467	0.6	1.0	9	dbSNP_96	68	4982,3618	625.8+/-397.8	1437,2108,755	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	1594,2984,1925	AA,AG,GG		42.0698,27.0086,47.455	,	489/919,489/919	136573412	6172,6834	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon11			TACCTCGTGCAGC		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.1467C>T	9.37:g.136573412G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			G|0.539;A|0.461	0.461	strong		0.637	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
FKBP1A	2280	hgsc.bcm.edu	37	20	1350709	1350709	+	3'UTR	SNP	T	T	C	rs8392	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1350709T>C	ENST00000400137.4	-	0	534				FKBP1A_ENST00000381724.3_3'UTR|FKBP1A_ENST00000460490.1_5'UTR|SDCBP2-AS1_ENST00000609470.1_RNA|SDCBP2-AS1_ENST00000446423.1_RNA|SDCBP2-AS1_ENST00000609285.1_RNA	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	87	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	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		
SLC9C2	284525	hgsc.bcm.edu	37	1	173474429	173474429	+	Silent	SNP	T	T	C	rs12026637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:173474429T>C	ENST00000367714.3	-	26	3689	c.3267A>G	c.(3265-3267)caA>caG	p.Q1089Q	SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	1089					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										GCTCAGATGCTTGGATTATCA	0.398													T|||	1524	0.304313	0.0136	0.3213	5008	,	,		20902	0.6448		0.2087	False		,,,				2504	0.4325				p.Q1089Q		Atlas-SNP	.											.	.	.	.	0			c.A3267G						PASS	.	T		212,4194	127.8+/-164.7	7,198,1998	126.0	115.0	118.0		3267	2.8	0.0	1	dbSNP_120	118	1782,6818	320.8+/-314.8	185,1412,2703	no	coding-synonymous	SLC9A11	NM_178527.3		192,1610,4701	CC,CT,TT		20.7209,4.8116,15.3314		1089/1125	173474429	1994,11012	2203	4300	6503	SO:0001819	synonymous_variant	284525	exon26			AGATGCTTGGATT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.3267A>G	1.37:g.173474429T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	165	51	0.309091	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			T|0.805;C|0.195	0.195	strong		0.398	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
KDM1B	221656	hgsc.bcm.edu	37	6	18161563	18161563	+	Silent	SNP	G	G	A	rs4716224	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	77	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29911317	29911317	+	Missense_Mutation	SNP	A	A	G	rs41557913	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29911317A>G	ENST00000396634.1	+	5	957	c.616A>G	c.(616-618)Acg>Gcg	p.T206A	HLA-A_ENST00000376806.5_Missense_Mutation_p.T206A|HLA-A_ENST00000376802.2_Missense_Mutation_p.T206A|HLA-A_ENST00000376809.5_Missense_Mutation_p.T206A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	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)	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						GCTGCAGCGCACGGGTACCAG	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)																											p.T206A		Atlas-SNP	.											.	HLA-A	89	.	0			c.A616G						PASS	.						46.0	41.0	43.0					6																	29911317		1506	2706	4212	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CAGCGCACGGGTA	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.616A>G	6.37:g.29911317A>G	ENSP00000379873:p.Thr206Ala	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	201	44	0.218905	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.401	0.841969	0.16963	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00672	5.89;5.9;5.89;5.92	3.78	-2.91	0.05631	MHC class I-like antigen recognition (4);	0.687394	0.11659	N	0.542010	T	0.00241	0.0007	N	0.02842	-0.48	0.19945	N	0.999945	B;B;P;B;B;B;B	0.40931	0.0;0.0;0.733;0.0;0.0;0.0;0.0	B;B;P;B;B;B;B	0.58577	0.0;0.0;0.841;0.0;0.001;0.0;0.0	T	0.41787	-0.9489	10	0.02654	T	1	.	5.2393	0.15464	0.5803:0.0:0.2648:0.1549	rs41557913	85;206;206;206;206;206;206	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	A	206	ENSP00000379873:T206A;ENSP00000366002:T206A;ENSP00000366005:T206A;ENSP00000365998:T206A	ENSP00000365998:T206A	T	+	1	0	HLA-A	30019296	0.041000	0.20044	0.912000	0.35992	0.330000	0.28571	0.315000	0.19451	-0.517000	0.06461	-0.366000	0.07423	ACG	A|0.991;G|0.010	0.010	strong		0.642	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
PLXNA2	5362	hgsc.bcm.edu	37	1	208252777	208252777	+	Missense_Mutation	SNP	G	G	C	rs17011882	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:208252777G>C	ENST00000367033.3	-	12	3171	c.2414C>G	c.(2413-2415)gCa>gGa	p.A805G		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	805			A -> G (in dbSNP:rs17011882).		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)		CCGCTGGGCTGCACACTTGTA	0.587													G|||	228	0.0455272	0.0015	0.098	5008	,	,		19890	0.1022		0.0189	False		,,,				2504	0.0368				p.A805G		Atlas-SNP	.											PLXNA2,NS,carcinoma,+1,1	PLXNA2	178	1	0			c.C2414G						PASS	.	G	GLY/ALA	29,4375		0,29,2173	20.0	21.0	21.0		2414	4.7	0.5	1	dbSNP_123	21	149,8451		0,149,4151	yes	missense	PLXNA2	NM_025179.3	60	0,178,6324	CC,CG,GG		1.7326,0.6585,1.3688	benign	805/1895	208252777	178,12826	2202	4300	6502	SO:0001583	missense	5362	exon12			TGGGCTGCACACT	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.2414C>G	1.37:g.208252777G>C	ENSP00000356000:p.Ala805Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	110	63	0.572727	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	103	0.04716117216117216	1	0.0020325203252032522	35	0.09668508287292818	53	0.09265734265734266	14	0.018469656992084433	G	6.591	0.477461	0.12521	0.006585	0.017326	ENSG00000076356	ENST00000367033	T	0.56611	0.45	5.6	4.66	0.58398	.	0.155240	0.56097	D	0.000026	T	0.00998	0.0033	N	0.11892	0.195	0.20873	P	0.999835302	B	0.11235	0.004	B	0.11329	0.006	T	0.04115	-1.0976	9	0.21540	T	0.41	.	16.2292	0.82321	0.0:0.1332:0.8668:0.0	rs17011882;rs52798765;rs17011882	805	O75051	PLXA2_HUMAN	G	805	ENSP00000356000:A805G	ENSP00000356000:A805G	A	-	2	0	PLXNA2	206319400	1.000000	0.71417	0.548000	0.28192	0.994000	0.84299	4.978000	0.63799	1.308000	0.44962	0.655000	0.94253	GCA	G|0.972;C|0.028	0.028	strong		0.587	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
RYR3	6263	hgsc.bcm.edu	37	15	34015013	34015013	+	Silent	SNP	G	G	A	rs2293027	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:34015013G>A	ENST00000389232.4	+	44	6787	c.6717G>A	c.(6715-6717)ggG>ggA	p.G2239G	RYR3_ENST00000415757.3_Silent_p.G2239G|Y_RNA_ENST00000363138.1_RNA	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2239	4 X approximate repeats.				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)		GGGGAAACGGGCTCTTGGCAG	0.572													G|||	807	0.161142	0.0772	0.0965	5008	,	,		17079	0.2351		0.1859	False		,,,				2504	0.2188				p.G2239G		Atlas-SNP	.											RYR3,NS,carcinoma,+2,1	RYR3	760	1	0			c.G6717A						PASS	.	G		341,3615		17,307,1654	84.0	93.0	90.0		6717	-7.1	0.0	15	dbSNP_100	90	1529,6757		153,1223,2767	no	coding-synonymous	RYR3	NM_001036.3		170,1530,4421	AA,AG,GG		18.4528,8.6198,15.2753		2239/4871	34015013	1870,10372	1978	4143	6121	SO:0001819	synonymous_variant	6263	exon44			AAACGGGCTCTTG		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.6717G>A	15.37:g.34015013G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	83	28	0.337349	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.841;A|0.159	0.159	strong		0.572	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
APEH	327	hgsc.bcm.edu	37	3	49721532	49721532	+	IGR	SNP	G	G	A	rs3197999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49721532G>A	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Missense_Mutation_p.R703C	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)	p.R689C(1)		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)		GCTGGCCAGCGGGACCTTGCG	0.567													G|||	961	0.191893	0.2179	0.1686	5008	,	,		20686	0.0565		0.3131	False		,,,				2504	0.1881				p.R703C		Atlas-SNP	.											MST1,NS,carcinoma,0,1	MST1	84	1	1	Substitution - Missense(1)	stomach(1)	c.C2107T						scavenged	.	G	CYS/ARG	1036,3370	380.4+/-323.7	120,796,1287	64.0	61.0	62.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2107	-2.8	0.1	3	dbSNP_105	62	2525,6075	411.6+/-350.5	385,1755,2160	yes	missense	MST1	NM_020998.3	180	505,2551,3447	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	29.3605,23.5134,27.3797	possibly-damaging	703/726	49721532	3561,9445	2203	4300	6503	SO:0001628	intergenic_variant	4485	exon18			GCCAGCGGGACCT	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.49721532G>A		Somatic	480	2	0.00416667		WXS	Illumina HiSeq	Phase_I	441	202	0.45805	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	472|472	0.21611721611721613|0.21611721611721613	119|119	0.241869918699187|0.241869918699187	81|81	0.22375690607734808|0.22375690607734808	37|37	0.06468531468531469|0.06468531468531469	235|235	0.3100263852242744|0.3100263852242744	G|G	17.19|17.19	3.327308|3.327308	0.60743|0.60743	0.235134|0.235134	0.293605|0.293605	ENSG00000173531|ENSG00000173531	ENST00000448220|ENST00000449682	.|D	.|0.89196	.|-2.48	5.59|5.59	-2.82|-2.82	0.05787|0.05787	.|.	.|0.559462	.|0.14941	.|N	.|0.289511	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.74389|0.74389	2.26|2.26	0.46298|0.46298	P|P	0.0010210000000000496|0.0010210000000000496	.|P	.|0.40681	.|0.727	.|B	.|0.40702	.|0.338	T|T	0.21280|0.21280	-1.0250|-1.0250	4|9	.|0.66056	.|D	.|0.02	.|.	12.6939|12.6939	0.56992|0.56992	0.07:0.7015:0.147:0.0815|0.07:0.7015:0.147:0.0815	rs3197999;rs52793577;rs60772290;rs3197999|rs3197999;rs52793577;rs60772290;rs3197999	.|703	.|G3XAK1	.|.	L|C	172|703	.|ENSP00000414287:R703C	.|ENSP00000414287:R703C	P|R	-|-	2|1	0|0	MST1|MST1	49696536|49696536	0.511000|0.511000	0.26179|0.26179	0.123000|0.123000	0.21794|0.21794	0.860000|0.860000	0.49131|0.49131	1.075000|1.075000	0.30716|0.30716	-0.545000|-0.545000	0.06224|0.06224	0.655000|0.655000	0.94253|0.94253	CCG|CGC	G|0.749;A|0.251	0.251	strong		0.567	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
SRRM5	100170229	hgsc.bcm.edu	37	19	44118191	44118191	+	Missense_Mutation	SNP	G	G	A	rs34163641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44118191G>A	ENST00000607544.1	+	3	2240	c.1918G>A	c.(1918-1920)Gac>Aac	p.D640N	ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000526798.1_Missense_Mutation_p.D655N|SRRM5_ENST00000417606.1_Missense_Mutation_p.D640N			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	640	Ser-rich.									endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						CAAGGAGAGCGACCCCAGTCA	0.512													G|||	1179	0.235423	0.2693	0.1628	5008	,	,		17199	0.1498		0.2565	False		,,,				2504	0.3078				p.D640N		Atlas-SNP	.											.	SRRM5	38	.	0			c.G1918A						PASS	.	G	ASN/ASP,	314,1070		32,250,410	78.0	80.0	79.0		1918,	-1.9	0.0	19	dbSNP_126	79	846,2336		112,622,857	yes	missense,intron	ZNF428,SRRM5	NM_001145641.1,NM_182498.3	23,	144,872,1267	AA,AG,GG		26.5871,22.6879,25.4052	possibly-damaging,	640/716,	44118191	1160,3406	692	1591	2283	SO:0001583	missense	100170229	exon1			GAGAGCGACCCCA	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.1918G>A	19.37:g.44118191G>A	ENSP00000476253:p.Asp640Asn	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_001145641	B4DNF0	Missense_Mutation	SNP	ENST00000607544.1	37	CCDS46095.1	470	0.21520146520146521	129	0.2621951219512195	60	0.16574585635359115	86	0.15034965034965034	195	0.25725593667546176	G	10.30	1.312032	0.23821	0.226879	0.265871	ENSG00000226763	ENST00000526798;ENST00000417606	.	.	.	4.28	-1.9	0.07665	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.24618	0.107	B	0.15484	0.013	T	0.37888	-0.9686	7	0.42905	T	0.14	.	5.2613	0.15576	0.4778:0.1513:0.3709:0.0	rs34163641	640	B3KS81	SRRM5_HUMAN	N	655;640	.	ENSP00000414512:D640N	D	+	1	0	SRRM5	48810031	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.560000	0.05964	-0.256000	0.09473	-0.258000	0.10820	GAC	G|0.784;A|0.216	0.216	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	
POLR1D	51082	hgsc.bcm.edu	37	13	28240021	28240021	+	Silent	SNP	C	C	T	rs41291680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:28240021C>T	ENST00000399697.3	+	3	418	c.300C>T	c.(298-300)tcC>tcT	p.S100S	POLR1D_ENST00000465887.1_3'UTR	NM_001206559.1|NM_152705.2	NP_001193488.1|NP_689918.1	Q9Y2S0	RPAC2_HUMAN	polymerase (RNA) I polypeptide D, 16kDa	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)			endometrium(1)|large_intestine(1)|lung(4)|stomach(2)	8		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.0758)|OV - Ovarian serous cystadenocarcinoma(117;0.1)|Epithelial(112;0.213)		CTCGAGGTTCCGCCAGTTACT	0.607													C|||	42	0.00838658	0.0038	0.0043	5008	,	,		14051	0.001		0.0258	False		,,,				2504	0.0072				p.S100S		Atlas-SNP	.											.	POLR1D	31	.	0			c.C300T						PASS	.	C	,	25,4381	31.7+/-61.6	0,25,2178	72.0	78.0	76.0		216,300	-11.7	0.0	13	dbSNP_127	76	225,8375	91.6+/-153.7	3,219,4078	no	coding-synonymous,coding-synonymous	POLR1D	NM_001206559.1,NM_152705.2	,	3,244,6256	TT,TC,CC		2.6163,0.5674,1.9222	,	72/95,100/123	28240021	250,12756	2203	4300	6503	SO:0001819	synonymous_variant	51082	exon3			AGGTTCCGCCAGT	AF077044, BC018528	CCDS9324.1, CCDS9325.1, CCDS73555.1	13q12.2	2013-01-21			ENSG00000186184	ENSG00000186184		"""RNA polymerase subunits"""	20422	protein-coding gene	gene with protein product		613715				11042152, 12391170	Standard	NM_015972		Approved	RPAC2, RPA16, RPO1-3, RPA9, MGC9850	uc001urp.3	Q9Y2S0	OTTHUMG00000016635	ENST00000399697.3:c.300C>T	13.37:g.28240021C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_152705	Q5TBX2|Q96BR3	Silent	SNP	ENST00000399697.3	37	CCDS9324.1																																																																																			A|0.000;C|0.983;T|0.017	0.017	strong		0.607	POLR1D-004	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044306.1	NM_015972, NM_152705	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505179	37505179	+	Silent	SNP	T	T	C	rs57914746	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:37505179T>C	ENST00000602533.1	+	32	2871	c.2772T>C	c.(2770-2772)gaT>gaC	p.D924D	ANKRD30A_ENST00000361713.1_Silent_p.D924D|ANKRD30A_ENST00000374660.1_Silent_p.D1043D			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	980					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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						TTCAAAAAGATCACTGTGAAC	0.328													T|||	795	0.158746	0.2837	0.1095	5008	,	,		15900	0.1161		0.171	False		,,,				2504	0.0562				p.D924D		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.T2772C						PASS	.	T		1060,2562		174,712,925	71.0	67.0	68.0		2772	-5.3	0.0	10	dbSNP_129	68	1418,6720		131,1156,2782	no	coding-synonymous	ANKRD30A	NM_052997.2		305,1868,3707	CC,CT,TT		17.4244,29.2656,21.0714		924/1342	37505179	2478,9282	1811	4069	5880	SO:0001819	synonymous_variant	91074	exon32			AAAAGATCACTGT	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.2772T>C	10.37:g.37505179T>C		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	162	33	0.203704	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																				T|0.822;C|0.178	0.178	strong		0.328	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
GBP4	115361	hgsc.bcm.edu	37	1	89655787	89655787	+	Silent	SNP	T	T	C	rs41305862	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89655787T>C	ENST00000355754.6	-	7	1228	c.1131A>G	c.(1129-1131)gaA>gaG	p.E377E		NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	377						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)		CTGCAATGGCTTCCCTCTCAC	0.532													T|||	109	0.0217652	0.0113	0.0159	5008	,	,		18719	0.0119		0.0278	False		,,,				2504	0.044				p.E377E		Atlas-SNP	.											.	GBP4	89	.	0			c.A1131G						PASS	.	T		52,4354	52.3+/-87.9	0,52,2151	103.0	97.0	99.0		1131	0.2	1.0	1	dbSNP_127	99	216,8384	90.9+/-153.0	1,214,4085	no	coding-synonymous	GBP4	NM_052941.4		1,266,6236	CC,CT,TT		2.5116,1.1802,2.0606		377/641	89655787	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	115361	exon7			AATGGCTTCCCTC	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.1131A>G	1.37:g.89655787T>C		Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	166	158	0.951807	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Silent	SNP	ENST00000355754.6	37	CCDS721.1																																																																																			T|0.977;C|0.023	0.023	strong		0.532	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
TDP1	55775	hgsc.bcm.edu	37	14	90458308	90458308	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:90458308T>C	ENST00000335725.4	+	13	1664	c.1414T>C	c.(1414-1416)Tgg>Cgg	p.W472R	TDP1_ENST00000393454.2_Missense_Mutation_p.W472R|TDP1_ENST00000357382.3_Missense_Mutation_p.W233R|TDP1_ENST00000393452.3_Missense_Mutation_p.W472R|TDP1_ENST00000555880.1_Missense_Mutation_p.W472R	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	472					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		AAAACAGAATTGGCTGCATTC	0.318								Repair of DNA-protein crosslinks																													p.W472R		Atlas-SNP	.											.	TDP1	47	.	0			c.T1414C						PASS	.						120.0	124.0	123.0					14																	90458308		2203	4299	6502	SO:0001583	missense	55775	exon13			CAGAATTGGCTGC	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.1414T>C	14.37:g.90458308T>C	ENSP00000337353:p.Trp472Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	15	0.168539	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	CCDS9888.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.69|17.69	3.452357|3.452357	0.63290|0.63290	.|.	.|.	ENSG00000042088|ENSG00000042088	ENST00000556063|ENST00000393452;ENST00000393454;ENST00000335725;ENST00000357382;ENST00000555880	.|T;T;T;T;T	.|0.44881	.|0.91;0.91;0.91;0.91;0.91	5.94|5.94	4.76|4.76	0.60689|0.60689	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68842|0.68842	0.3045|0.3045	M|M	0.90483|0.90483	3.12|3.12	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999;1.0	.|D;D;D;D;D	.|0.91635	.|0.998;0.998;0.999;0.99;0.999	T|T	0.73789|0.73789	-0.3872|-0.3872	5|10	.|0.66056	.|D	.|0.02	-23.862|-23.862	11.4452|11.4452	0.50118|0.50118	0.1353:0.0:0.0:0.8647|0.1353:0.0:0.0:0.8647	.|.	.|472;472;472;233;472	.|G3V2F4;E7EPD8;B2RDI0;Q86TV8;Q9NUW8	.|.;.;.;.;TYDP1_HUMAN	S|R	112|472;472;472;233;472	.|ENSP00000377098:W472R;ENSP00000377099:W472R;ENSP00000337353:W472R;ENSP00000349952:W233R;ENSP00000450628:W472R	.|ENSP00000337353:W472R	L|W	+|+	2|1	0|0	TDP1|TDP1	89528061|89528061	1.000000|1.000000	0.71417|0.71417	0.926000|0.926000	0.36857|0.36857	0.998000|0.998000	0.95712|0.95712	6.735000|6.735000	0.74806|0.74806	1.015000|1.015000	0.39444|0.39444	0.459000|0.459000	0.35465|0.35465	TTG|TGG	.	.	none		0.318	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
ZMYM5	9205	hgsc.bcm.edu	37	13	20425948	20425948	+	Missense_Mutation	SNP	T	T	C	rs9579718	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:20425948T>C	ENST00000337963.4	-	3	637	c.373A>G	c.(373-375)Ata>Gta	p.I125V	ZMYM5_ENST00000382905.4_Missense_Mutation_p.I125V|ZMYM5_ENST00000382907.4_Missense_Mutation_p.I125V	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	125			I -> V (in dbSNP:rs9579718). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		TTTGTTTCTATGTCCTCTTCA	0.373													T|||	491	0.0980431	0.1717	0.0735	5008	,	,		19623	0.0813		0.0924	False		,,,				2504	0.0389				p.I125V		Atlas-SNP	.											.	ZMYM5	73	.	0			c.A373G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	709,3697	287.8+/-279.5	63,583,1557	68.0	72.0	71.0		373,373,373	0.1	1.0	13	dbSNP_119	71	590,8010	156.0+/-209.9	15,560,3725	yes	missense,missense,missense	ZMYM5	NM_001039649.2,NM_001039650.2,NM_001142684.1	29,29,29	78,1143,5282	CC,CT,TT		6.8605,16.0917,9.9877	benign,benign,benign	125/209,125/383,125/670	20425948	1299,11707	2203	4300	6503	SO:0001583	missense	9205	exon3			TTTCTATGTCCTC	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"""Zinc fingers, MYM type"""	13029	protein-coding gene	gene with protein product			"""zinc finger protein 237"""	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.373A>G	13.37:g.20425948T>C	ENSP00000337034:p.Ile125Val	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	180	74	0.411111	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		193	0.08836996336996338	71	0.1443089430894309	26	0.0718232044198895	35	0.06118881118881119	61	0.08047493403693931	T	5.678	0.309723	0.10733	0.160917	0.068605	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382907;ENST00000382905	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	4.41	0.0975	0.14494	.	.	.	.	.	T	0.00073	0.0002	L	0.39898	1.24	0.50313	P	1.3799999999997148E-4	B;B;B	0.20671	0.005;0.047;0.017	B;B;B	0.17979	0.004;0.02;0.013	T	0.16188	-1.0411	8	0.41790	T	0.15	-0.003	4.8086	0.13331	0.4309:0.0784:0.0:0.4907	rs9579718;rs17850147;rs52817925;rs9579718	125;125;125	Q9UJ78;Q9UJ78-2;Q9UJ78-1	ZMYM5_HUMAN;.;.	V	125;115;125;125	ENSP00000337034:I125V;ENSP00000445779:I115V;ENSP00000372364:I125V;ENSP00000372361:I125V	ENSP00000337034:I125V	I	-	1	0	ZMYM5	19323948	0.858000	0.29795	0.982000	0.44146	0.538000	0.34931	-0.078000	0.11375	-0.036000	0.13669	0.402000	0.26972	ATA	T|0.901;C|0.099	0.099	strong		0.373	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242	
SRRM2	23524	hgsc.bcm.edu	37	16	2819196	2819196	+	Silent	SNP	G	G	C	rs150110237	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2819196G>C	ENST00000301740.8	+	12	8481	c.7932G>C	c.(7930-7932)tcG>tcC	p.S2644S	SRRM2_ENST00000574593.1_3'UTR|AC092117.2_ENST00000581119.1_RNA	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2644	Ser-rich.				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						cctcctcctcgtcgtcttcct	0.597													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18150	0.0		0.0	False		,,,				2504	0.0				p.S2644S		Atlas-SNP	.											.	SRRM2	263	.	0			c.G7932C						PASS	.	C		24,4372	823.0+/-416.5	0,24,2174	112.0	112.0	112.0		7932	-3.7	0.1	16	dbSNP_134	112	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	SRRM2	NM_016333.3		0,29,6469	CC,CG,GG		0.0581,0.546,0.2231		2644/2753	2819196	29,12967	2198	4300	6498	SO:0001819	synonymous_variant	23524	exon12			CTCCTCGTCGTCT	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.7932G>C	16.37:g.2819196G>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	22	0.285714	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																			G|0.998;C|0.002	0.002	strong		0.597	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
FLG	2312	hgsc.bcm.edu	37	1	152276871	152276871	+	Silent	SNP	A	A	G	rs3126066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152276871A>G	ENST00000368799.1	-	3	10526	c.10491T>C	c.(10489-10491)gaT>gaC	p.D3497D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3497	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCTGGAGCCATCTCCTGATT	0.582									Ichthyosis				G|||	2239	0.447085	0.5204	0.4395	5008	,	,		19200	0.6448		0.1471	False		,,,				2504	0.4581				p.D3497D		Atlas-SNP	.											.	FLG	900	.	0			c.T10491C						PASS	.	G		2040,2366	609.3+/-391.3	470,1100,633	267.0	264.0	265.0		10491	-4.6	0.0	1	dbSNP_103	265	1276,7318	759.6+/-407.6	123,1030,3144	no	coding-synonymous	FLG	NM_002016.1		593,2130,3777	GG,GA,AA		14.8476,46.3005,25.5077		3497/4062	152276871	3316,9684	2203	4297	6500	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGAGCCATCTCCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10491T>C	1.37:g.152276871A>G		Somatic	322	1	0.00310559		WXS	Illumina HiSeq	Phase_I	433	136	0.314088	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.703;G|0.297	0.297	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789312	117789312	+	Missense_Mutation	SNP	C	C	A	rs200637340|rs201746372|rs58754377		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789312C>A	ENST00000430170.2	-	2	350	c.263G>T	c.(262-264)cGg>cTg	p.R88L	TMPRSS13_ENST00000445164.2_Missense_Mutation_p.R88L|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.R88L|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.R88L|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.R88L	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	88	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					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)		CGGAGATGCCCGGGCTGGAGA	0.642																																					p.R88L		Atlas-SNP	.											TMPRSS13_ENST00000445164,NS,NS,0,3	TMPRSS13	75	3	0			c.G263T						scavenged	.						51.0	61.0	58.0					11																	117789312		2001	4153	6154	SO:0001583	missense	84000	exon2			GATGCCCGGGCTG	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	ENST00000430170.2:c.263G>T	11.37:g.117789312C>A	ENSP00000387702:p.Arg88Leu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	264	5	0.0189394	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	37	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152681	0.57259	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	D;D;D;D;D	0.89050	-2.46;-2.44;-2.43;-2.45;-2.38	4.21	0.0434	0.14221	.	0.867270	0.09660	N	0.772538	T	0.79516	0.4459	.	.	.	0.09310	N	1	B;B	0.13594	0.008;0.001	B;B	0.13407	0.009;0.002	T	0.62282	-0.6887	9	0.31617	T	0.26	.	4.5554	0.12135	0.154:0.5793:0.0:0.2667	.	83;88	Q9BYE2-4;E9PRA0	.;.	L	88;83;88;88;88;88	ENSP00000435813:R88L;ENSP00000434279:R88L;ENSP00000387702:R88L;ENSP00000394114:R88L;ENSP00000436502:R88L	ENSP00000337113:R83L	R	-	2	0	TMPRSS13	117294522	0.000000	0.05858	0.000000	0.03702	0.204000	0.24138	-1.930000	0.01557	-0.218000	0.10018	0.643000	0.83706	CGG	C|1.000;T|0.000	.	alt		0.642	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
NKX2-2	4821	hgsc.bcm.edu	37	20	21494184	21494184	+	Missense_Mutation	SNP	C	C	T	rs8192562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:21494184C>T	ENST00000377142.4	-	1	480	c.124G>A	c.(124-126)Gcc>Acc	p.A42T	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	42					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						GCCCTCTTGGCTGGCTCGGGC	0.667													C|||	150	0.0299521	0.003	0.0418	5008	,	,		9819	0.0		0.0944	False		,,,				2504	0.0225				p.A42T		Atlas-SNP	.											.	NKX2-2	49	.	0			c.G124A						PASS	.	C	THR/ALA	65,4341	59.3+/-96.0	1,63,2139	26.0	27.0	27.0		124	1.5	1.0	20	dbSNP_117	27	679,7921	164.6+/-216.9	27,625,3648	yes	missense	NKX2-2	NM_002509.3	58	28,688,5787	TT,TC,CC		7.8953,1.4753,5.7204	benign	42/274	21494184	744,12262	2203	4300	6503	SO:0001583	missense	4821	exon1			TCTTGGCTGGCTC	AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"""Homeoboxes / ANTP class : NKL subclass"""	7835	protein-coding gene	gene with protein product		604612	"""NK-2 (Drosophila) homolog B"", ""NK2 transcription factor related, locus 2 (Drosophila)"""	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.124G>A	20.37:g.21494184C>T	ENSP00000366347:p.Ala42Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_002509		Missense_Mutation	SNP	ENST00000377142.4	37	CCDS13145.1	85	0.03891941391941392	4	0.008130081300813009	20	0.055248618784530384	0	0.0	61	0.08047493403693931	C	9.981	1.228068	0.22542	0.014753	0.078953	ENSG00000125820	ENST00000377142	D	0.90676	-2.71	4.9	1.46	0.22682	.	0.218384	0.29021	N	0.013386	T	0.10465	0.0256	N	0.01352	-0.895	0.30555	N	0.765043	B	0.02656	0.0	B	0.04013	0.001	T	0.47873	-0.9083	10	0.13470	T	0.59	.	4.5555	0.12135	0.0:0.3915:0.3003:0.3081	rs8192562	42	O95096	NKX22_HUMAN	T	42	ENSP00000366347:A42T	ENSP00000366347:A42T	A	-	1	0	NKX2-2	21442184	0.887000	0.30362	0.959000	0.39883	0.604000	0.37047	1.396000	0.34531	1.050000	0.40346	-0.252000	0.11476	GCC	C|0.952;T|0.048	0.048	strong		0.667	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9		
C7orf26	79034	hgsc.bcm.edu	37	7	6639953	6639953	+	Silent	SNP	G	G	A	rs34300529	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:6639953G>A	ENST00000344417.5	+	4	1341	c.1074G>A	c.(1072-1074)gtG>gtA	p.V358V	C7orf26_ENST00000359073.5_Silent_p.V261V|C7orf26_ENST00000472693.1_3'UTR	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	358										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		CTCTGCAGGTGGCCATGGCCT	0.662													G|||	380	0.0758786	0.0174	0.134	5008	,	,		13378	0.0278		0.1829	False		,,,				2504	0.0532				p.V358V		Atlas-SNP	.											C7orf26,NS,carcinoma,0,1	C7orf26	33	1	0			c.G1074A						PASS	.	G		177,4229	109.1+/-147.4	6,165,2032	28.0	28.0	28.0		1074	4.3	1.0	7	dbSNP_126	28	1502,7098	266.9+/-287.0	144,1214,2942	no	coding-synonymous	C7orf26	NM_024067.2		150,1379,4974	AA,AG,GG		17.4651,4.0172,12.9094		358/450	6639953	1679,11327	2203	4300	6503	SO:0001819	synonymous_variant	79034	exon4			GCAGGTGGCCATG	BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.1074G>A	7.37:g.6639953G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_024067	Q9BQ43	Silent	SNP	ENST00000344417.5	37	CCDS5353.1	219	0.10027472527472528	12	0.024390243902439025	53	0.1464088397790055	9	0.015734265734265736	145	0.19129287598944592	G	9.926	1.213517	0.22289	0.040172	0.174651	ENSG00000146576	ENST00000445375	.	.	.	5.2	4.32	0.51571	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.13229	-1.0517	3	.	.	.	-33.9265	7.4662	0.27322	0.0865:0.0:0.7487:0.1647	rs34300529	.	.	.	S	96	.	.	G	+	1	0	C7orf26	6606478	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.646000	0.46630	1.515000	0.48885	0.555000	0.69702	GGC	G|0.883;A|0.117	0.117	strong		0.662	C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067	
MUC17	140453	hgsc.bcm.edu	37	7	100679754	100679754	+	Missense_Mutation	SNP	C	C	G	rs4992073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100679754C>G	ENST00000306151.4	+	3	5121	c.5057C>G	c.(5056-5058)aCt>aGt	p.T1686S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1686	59 X approximate tandem repeats.|Ser-rich.				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)					TCAACTTATACTGAAGGAAGA	0.468																																					p.T1686S		Atlas-SNP	.											.	MUC17	804	.	0			c.C5057G						PASS	.						191.0	206.0	201.0					7																	100679754		2203	4300	6503	SO:0001583	missense	140453	exon3			CTTATACTGAAGG	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.5057C>G	7.37:g.100679754C>G	ENSP00000302716:p.Thr1686Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	184	120	0.652174	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.307	-0.970357	0.02232	.	.	ENSG00000169876	ENST00000306151	T	0.01963	4.53	0.932	-1.86	0.07760	.	.	.	.	.	T	0.00845	0.0028	N	0.02539	-0.55	0.09310	N	1	B	0.20261	0.043	B	0.08055	0.003	T	0.46062	-0.9218	9	0.05436	T	0.98	.	6.7353	0.23405	0.0:0.4292:0.5708:0.0	rs4992073	1686	Q685J3	MUC17_HUMAN	S	1686	ENSP00000302716:T1686S	ENSP00000302716:T1686S	T	+	2	0	MUC17	100466474	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.458000	0.06737	-0.486000	0.06744	-3.678000	0.00024	ACT	C|0.973;G|0.027	0.027	strong		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150054	11150054	+	Missense_Mutation	SNP	C	C	T	rs79420812	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:11150054C>T	ENST00000538986.1	-	1	420	c.421G>A	c.(421-423)Gtt>Att	p.V141I	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	141				VCH -> ICQ (in Ref. 3; AAU21140). {ECO:0000305}.	sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V141I(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						AGGTGACAAACCAAAAAGAAC	0.388													C|||	916	0.182907	0.0371	0.1225	5008	,	,		20886	0.3185		0.2227	False		,,,				2504	0.2423				p.V141I		Atlas-SNP	.											TAS2R20,NS,carcinoma,0,1	TAS2R20	17	1	1	Substitution - Missense(1)	ovary(1)	c.G421A						scavenged	.	C	ILE/VAL	239,4167	139.6+/-175.2	7,225,1971	128.0	114.0	118.0		421	-5.9	0.0	12	dbSNP_131	118	1704,6896	311.7+/-310.5	167,1370,2763	yes	missense	TAS2R20	NM_176889.2	29	174,1595,4734	TT,TC,CC		19.814,5.4244,14.9393	benign	141/310	11150054	1943,11063	2203	4300	6503	SO:0001583	missense	259295	exon1			GACAAACCAAAAA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.421G>A	12.37:g.11150054C>T	ENSP00000441624:p.Val141Ile	Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	402	0.18406593406593408	19	0.03861788617886179	50	0.13812154696132597	171	0.29895104895104896	162	0.21372031662269128	C	2.515	-0.312165	0.05422	0.054244	0.19814	ENSG00000255837	ENST00000538986	T	0.36340	1.26	2.93	-5.87	0.02297	.	0.867467	0.09448	U	0.800842	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.12156	0.007	T	0.39078	-0.9631	9	0.25751	T	0.34	.	1.3021	0.02081	0.4189:0.2764:0.1245:0.1802	.	141	P59543	T2R20_HUMAN	I	141	ENSP00000441624:V141I	ENSP00000441624:V141I	V	-	1	0	TAS2R20	11041321	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.252000	0.00539	-1.958000	0.01019	-0.964000	0.02622	GTT	C|0.838;T|0.162	0.162	strong		0.388	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
GSTA2	2939	hgsc.bcm.edu	37	6	52617738	52617738	+	Missense_Mutation	SNP	G	G	A	rs2234951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:52617738G>A	ENST00000493422.1	-	5	483	c.328C>T	c.(328-330)Ccc>Tcc	p.P110S		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	110	GST C-terminal.		P -> S (in dbSNP:rs2234951).		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)	TGACTAAAGGGCAGAAGAAGG	0.383													.|||	354	0.0706869	0.0015	0.0216	5008	,	,		19157	0.13		0.0527	False		,,,				2504	0.1564				p.P110S		Atlas-SNP	.											.	GSTA2	33	.	0			c.C328T	GRCh37	CM040431	GSTA2	M	rs2234951	PASS	.	G	SER/PRO	34,4372		0,34,2169	208.0	195.0	199.0		328	1.3	0.0	6	dbSNP_98	199	298,8302		6,286,4008	yes	missense	GSTA2	NM_000846.4	74	6,320,6177	AA,AG,GG		3.4651,0.7717,2.5527	benign	110/223	52617738	332,12674	2203	4300	6503	SO:0001583	missense	2939	exon5			TAAAGGGCAGAAG	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.328C>T	6.37:g.52617738G>A	ENSP00000420168:p.Pro110Ser	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	207	111	0.536232	NM_000846	Q12759|Q16491|Q9NTY6	Missense_Mutation	SNP	ENST00000493422.1	37	CCDS4944.1	124	0.056776556776556776	2	0.0040650406504065045	7	0.019337016574585635	72	0.1258741258741259	43	0.05672823218997362	N	9.997	1.232425	0.22626	0.007717	0.034651	ENSG00000244067	ENST00000493422	T	0.02015	4.5	2.26	1.34	0.21922	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.01489	0.0048	M	0.83118	2.625	0.80722	P	0.0	B	0.12013	0.005	B	0.15052	0.012	T	0.21861	-1.0233	9	0.45353	T	0.12	.	8.1054	0.30883	0.0:0.0:0.7573:0.2427	rs2234951;rs16882924;rs61371438;rs2234951	110	P09210	GSTA2_HUMAN	S	110	ENSP00000420168:P110S	ENSP00000420168:P110S	P	-	1	0	GSTA2	52725697	0.001000	0.12720	0.001000	0.08648	0.359000	0.29487	0.375000	0.20518	0.498000	0.27948	0.306000	0.20318	CCC	G|0.960;A|0.040	0.040	strong		0.383	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846	
ZNF433	163059	hgsc.bcm.edu	37	19	12126128	12126128	+	Silent	SNP	C	C	T	rs79356451		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:12126128C>T	ENST00000344980.6	-	4	1724	c.1554G>A	c.(1552-1554)tcG>tcA	p.S518S	ZNF433_ENST00000419886.2_Silent_p.S483S|CTD-2006C1.2_ENST00000495324.1_RNA|CTD-2006C1.2_ENST00000406892.2_RNA|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	518					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(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						GAAAGGAGCTCGAACAGTTGA	0.433													C|||	1	0.000199681	0.0	0.0	5008	,	,		23439	0.0		0.001	False		,,,				2504	0.0				p.S518S		Atlas-SNP	.											ZNF433,colon,carcinoma,-1,2	ZNF433	49	2	0			c.G1554A						scavenged	.	C		0,4398		0,0,2199	71.0	76.0	74.0		1554	-2.4	0.0	19	dbSNP_132	74	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	ZNF433	NM_001080411.1		0,4,6494	TT,TC,CC		0.0465,0.0,0.0308		518/674	12126128	4,12992	2199	4299	6498	SO:0001819	synonymous_variant	163059	exon4			GGAGCTCGAACAG	AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"""Zinc fingers, C2H2-type"", ""-"""	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.1554G>A	19.37:g.12126128C>T		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	153	84	0.54902	NM_001080411	Q86VX3	Silent	SNP	ENST00000344980.6	37	CCDS45983.1																																																																																			C|0.999;T|0.001	0.001	strong		0.433	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602	
ZNF460	10794	hgsc.bcm.edu	37	19	57802806	57802806	+	Silent	SNP	C	C	T	rs2041109	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57802806C>T	ENST00000360338.3	+	3	1219	c.897C>T	c.(895-897)aaC>aaT	p.N299N	ZNF460_ENST00000537645.1_Silent_p.N258N	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	299					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(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TCTTGCATAACAAGAGCCACA	0.468													c|||	923	0.184305	0.0908	0.3084	5008	,	,		22596	0.1657		0.2515	False		,,,				2504	0.1728				p.N299N		Atlas-SNP	.											.	ZNF460	59	.	0			c.C897T						PASS	.	C		494,3912	229.4+/-244.0	27,440,1736	95.0	85.0	89.0		897	-0.9	0.0	19	dbSNP_94	89	2199,6401	375.0+/-337.6	295,1609,2396	no	coding-synonymous	ZNF460	NM_006635.3		322,2049,4132	TT,TC,CC		25.5698,11.212,20.7058		299/563	57802806	2693,10313	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			GCATAACAAGAGC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.897C>T	19.37:g.57802806C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			C|0.799;T|0.201	0.201	strong		0.468	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
WDR41	55255	hgsc.bcm.edu	37	5	76728996	76728996	+	Silent	SNP	T	T	C	rs72769029	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:76728996T>C	ENST00000296679.4	-	13	1719	c.1344A>G	c.(1342-1344)aaA>aaG	p.K448K	WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000414719.2_Silent_p.K194K|WDR41_ENST00000507029.1_Silent_p.K393K	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	448						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)		TCTCCTCTAATTTTTGAAATA	0.368													T|||	83	0.0165735	0.0015	0.0245	5008	,	,		17492	0.0		0.0338	False		,,,				2504	0.0307				p.K448K		Atlas-SNP	.											.	WDR41	29	.	0			c.A1344G						PASS	.	T		21,4383	27.2+/-55.0	0,21,2181	118.0	121.0	120.0		1344	-0.2	1.0	5	dbSNP_130	120	238,8362	96.8+/-158.5	5,228,4067	no	coding-synonymous	WDR41	NM_018268.2		5,249,6248	CC,CT,TT		2.7674,0.4768,1.9917		448/460	76728996	259,12745	2202	4300	6502	SO:0001819	synonymous_variant	55255	exon13			CTCTAATTTTTGA	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.1344A>G	5.37:g.76728996T>C		Somatic	218	2	0.00917431		WXS	Illumina HiSeq	Phase_I	221	219	0.99095	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	37	CCDS4038.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
HLA-A	3105	hgsc.bcm.edu	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29910607G>C	ENST00000396634.1	+	4	488	c.147G>C	c.(145-147)gtG>gtC	p.V49V	HLA-A_ENST00000376806.5_Silent_p.V49V|HLA-A_ENST00000376802.2_Silent_p.V49V|HLA-A_ENST00000376809.5_Silent_p.V49V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	49	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)	p.V49V(2)		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						TCATCGCCGTGGGCTACGTGG	0.692									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.V49V		Atlas-SNP	.											HLA-A,NS,carcinoma,0,5	HLA-A	89	5	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G147C						PASS	.																																			SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGCCGTGGGCTAC	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.147G>C	6.37:g.29910607G>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	119	17	0.142857	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	weak		0.692	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
REM2	161253	hgsc.bcm.edu	37	14	23354066	23354066	+	Missense_Mutation	SNP	G	G	C	rs8014119	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23354066G>C	ENST00000267396.4	+	2	410	c.287G>C	c.(286-288)gGc>gCc	p.G96A	REM2_ENST00000536884.1_Missense_Mutation_p.G96A	NM_173527.2	NP_775798.2	Q8IYK8	REM2_HUMAN	RAS (RAD and GEM)-like GTP binding 2	96			G -> A (in dbSNP:rs8014119).		small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|large_intestine(2)|ovary(1)	5	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.012)		TCATCCTCTGGCTCGTCTGAC	0.622													G|||	536	0.107029	0.1755	0.1167	5008	,	,		17859	0.0347		0.1074	False		,,,				2504	0.0818				p.G96A		Atlas-SNP	.											.	REM2	21	.	0			c.G287C						PASS	.	G	ALA/GLY	654,3700		52,550,1575	39.0	45.0	43.0		287	5.1	1.0	14	dbSNP_116	43	713,7841		34,645,3598	yes	missense	REM2	NM_173527.2	60	86,1195,5173	CC,CG,GG		8.3353,15.0207,10.5903	benign	96/341	23354066	1367,11541	2177	4277	6454	SO:0001583	missense	161253	exon2			CCTCTGGCTCGTC		CCDS45082.1	14q11.2	2014-05-09	2006-12-14		ENSG00000139890	ENSG00000139890			20248	protein-coding gene	gene with protein product			"""RAS (RAD and GEM) like GTP binding 2"""			10727423	Standard	NM_173527		Approved	FLJ38964	uc001whf.1	Q8IYK8	OTTHUMG00000170277	ENST00000267396.4:c.287G>C	14.37:g.23354066G>C	ENSP00000267396:p.Gly96Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	112	66	0.589286	NM_173527	B7Z5P1|Q8N8R8	Missense_Mutation	SNP	ENST00000267396.4	37	CCDS45082.1	246	0.11263736263736264	95	0.19308943089430894	43	0.11878453038674033	27	0.0472027972027972	81	0.10686015831134564	G	15.07	2.725068	0.48833	0.150207	0.083353	ENSG00000139890	ENST00000267396;ENST00000536884	T;T	0.66638	-0.22;1.37	6.02	5.07	0.68467	.	0.455510	0.25178	N	0.032546	T	0.00109	0.0003	L	0.29908	0.895	0.25215	P	0.9899493	P;P	0.48503	0.911;0.457	B;B	0.43990	0.438;0.081	T	0.05683	-1.0870	9	0.15499	T	0.54	.	12.652	0.56766	0.0892:0.0:0.9108:0.0	rs8014119;rs52832581;rs8014119	96;96	B7Z5P1;Q8IYK8	.;REM2_HUMAN	A	96	ENSP00000267396:G96A;ENSP00000442774:G96A	ENSP00000267396:G96A	G	+	2	0	REM2	22423906	0.998000	0.40836	0.997000	0.53966	0.887000	0.51463	3.232000	0.51302	1.414000	0.47017	0.655000	0.94253	GGC	G|0.884;C|0.116	0.116	strong		0.622	REM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408290.1	NM_173527	
GCN1L1	10985	hgsc.bcm.edu	37	12	120608031	120608031	+	Silent	SNP	A	A	G	rs2286050	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:120608031A>G	ENST00000300648.6	-	15	1473	c.1461T>C	c.(1459-1461)acT>acC	p.T487T	AC004812.1_ENST00000582675.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	487					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAACCCCTTCAGTGATGGTGG	0.567													A|||	1447	0.288938	0.3101	0.1297	5008	,	,		20192	0.5655		0.1541	False		,,,				2504	0.227				p.T487T		Atlas-SNP	.											.	GCN1L1	207	.	0			c.T1461C						PASS	.	A		1140,3030		166,808,1111	109.0	115.0	113.0		1461	-11.7	0.5	12	dbSNP_100	113	1244,7210		114,1016,3097	no	coding-synonymous	GCN1L1	NM_006836.1		280,1824,4208	GG,GA,AA		14.7149,27.3381,18.8847		487/2672	120608031	2384,10240	2085	4227	6312	SO:0001819	synonymous_variant	10985	exon15			CCCTTCAGTGATG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.1461T>C	12.37:g.120608031A>G		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	167	75	0.449102	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			A|0.709;G|0.291	0.291	strong		0.567	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
TTN	7273	hgsc.bcm.edu	37	2	179395573	179395573	+	Missense_Mutation	SNP	C	C	T	rs56324595	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179395573C>T	ENST00000591111.1	-	308	101070	c.100846G>A	c.(100846-100848)Gaa>Aaa	p.E33616K	TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.E35257K|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E32689K|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.E26192K|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.E26317K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.E26384K|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33616			E -> K. {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)			TGAGAAGGTTCTGGAGATTTC	0.493													C|||	33	0.00658946	0.0	0.0058	5008	,	,		17611	0.0		0.0278	False		,,,				2504	0.001				p.E35257K		Atlas-SNP	.											.	TTN	18412	.	0			c.G105769A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	9,3781		0,9,1886	133.0	131.0	132.0		78574,98065,78949,79150	5.0	1.0	2	dbSNP_129	132	144,8066		0,144,3961	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	56,56,56,56	0,153,5847	TT,TC,CC		1.754,0.2375,1.275	probably-damaging,probably-damaging,probably-damaging,probably-damaging	26192/26927,32689/33424,26317/27052,26384/27119	179395573	153,11847	1895	4105	6000	SO:0001583	missense	7273	exon358			AAGGTTCTGGAGA	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.100846G>A	2.37:g.179395573C>T	ENSP00000465570:p.Glu33616Lys	Somatic	437	1	0.00228833		WXS	Illumina HiSeq	Phase_I	383	158	0.412533	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		24	0.01098901098901099	0	0.0	2	0.0055248618784530384	0	0.0	22	0.029023746701846966	C	18.11	3.551406	0.65311	0.002375	0.01754	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.64085	-0.08;0.18;0.16;0.15	4.99	4.99	0.66335	Ribonuclease H-like (1);	.	.	.	.	T	0.47875	0.1469	L	0.29908	0.895	0.58432	D	0.999999	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	0.68693	-0.5341	9	0.87932	D	0	.	18.2867	0.90117	0.0:1.0:0.0:0.0	rs56324595	26192;26317;26384;33616	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	32689;26192;26384;26317;26189	ENSP00000343764:E32689K;ENSP00000434586:E26192K;ENSP00000340554:E26384K;ENSP00000352154:E26317K	ENSP00000340554:E26384K	E	-	1	0	TTN	179103819	1.000000	0.71417	1.000000	0.80357	0.815000	0.46073	7.818000	0.86416	2.321000	0.78463	0.455000	0.32223	GAA	C|0.988;T|0.012	0.012	strong		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
P2RX3	5024	hgsc.bcm.edu	37	11	57137371	57137371	+	Silent	SNP	G	G	A	rs2276039	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:57137371G>A	ENST00000263314.2	+	12	1129	c.1095G>A	c.(1093-1095)acG>acA	p.T365T		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	365					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						ATGAGACTACGCTGAAAATCG	0.552													G|||	2060	0.411342	0.0756	0.4813	5008	,	,		20321	0.6319		0.3847	False		,,,				2504	0.6155				p.T365T		Atlas-SNP	.											P2RX3,NS,adenoma,0,1	P2RX3	55	1	0			c.G1095A						PASS	.	G		572,3830	250.0+/-257.2	43,486,1672	106.0	88.0	94.0		1095	-7.2	0.0	11	dbSNP_100	94	3200,5392	477.5+/-369.7	605,1990,1701	yes	coding-synonymous	P2RX3	NM_002559.3		648,2476,3373	AA,AG,GG		37.2439,12.9941,29.0288		365/398	57137371	3772,9222	2201	4296	6497	SO:0001819	synonymous_variant	5024	exon12			GACTACGCTGAAA	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.1095G>A	11.37:g.57137371G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	170	69	0.405882	NM_002559	Q6DK37|Q9UQB6	Silent	SNP	ENST00000263314.2	37	CCDS7953.1																																																																																			G|0.664;A|0.336	0.336	strong		0.552	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
HEG1	57493	hgsc.bcm.edu	37	3	124748226	124748226	+	Silent	SNP	G	G	A	rs2860440	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:124748226G>A	ENST00000311127.4	-	2	490	c.423C>T	c.(421-423)ggC>ggT	p.G141G		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	141					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						GAACCATCACGCCCTCTTTGG	0.498													G|||	2448	0.488818	0.3775	0.4697	5008	,	,		20274	0.4792		0.5457	False		,,,				2504	0.6043				p.G141G		Atlas-SNP	.											HEG1,colon,carcinoma,0,1	HEG1	109	1	0			c.C423T						PASS	.	G		1410,2446		251,908,769	102.0	95.0	97.0		423	-10.8	0.0	3	dbSNP_101	97	4179,4093		1041,2097,998	no	coding-synonymous	HEG1	NM_020733.1		1292,3005,1767	AA,AG,GG		49.4802,36.5664,46.0834		141/1382	124748226	5589,6539	1928	4136	6064	SO:0001819	synonymous_variant	57493	exon2			CATCACGCCCTCT	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.423C>T	3.37:g.124748226G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Silent	SNP	ENST00000311127.4	37	CCDS46898.1																																																																																			G|0.528;A|0.472	0.472	strong		0.498	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12887174	12887174	+	Missense_Mutation	SNP	C	C	T	rs61777003		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:12887174C>T	ENST00000535591.1	-	3	878	c.683G>A	c.(682-684)cGc>cAc	p.R228H		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	228					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)			p.R228H(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						TTGGAGGCAGCGCAGCTTGAG	0.527																																					p.R228H		Atlas-SNP	.											PRAMEF11,extremity,malignant_melanoma,0,1	PRAMEF11	72	1	1	Substitution - Missense(1)	skin(1)	c.G683A						scavenged	.																																			SO:0001583	missense	440560	exon3			AGGCAGCGCAGCT	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.683G>A	1.37:g.12887174C>T	ENSP00000439551:p.Arg228His	Somatic	29	2	0.0689655		WXS	Illumina HiSeq	Phase_I	13	3	0.230769	NM_001146344		Missense_Mutation	SNP	ENST00000535591.1	37	CCDS53268.1	.	.	.	.	.	.	.	.	.	.	.	0.026	-1.374502	0.01214	.	.	ENSG00000204513	ENST00000535591;ENST00000331684;ENST00000437584	T;T	0.53206	0.63;0.63	1.48	-1.16	0.09678	.	1.511700	0.03844	N	0.271170	T	0.15349	0.0370	N	0.01134	-0.995	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25012	-1.0144	10	0.05959	T	0.93	.	4.3434	0.11120	0.0:0.4269:0.0:0.5731	rs61777003	228	O60813	PRA11_HUMAN	H	228;269;228	ENSP00000439551:R228H;ENSP00000391839:R228H	ENSP00000328783:R269H	R	-	2	0	PRAMEF11	12809761	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.181000	0.01257	-0.346000	0.08312	-0.939000	0.02691	CGC	C|0.833;T|0.167	0.167	weak		0.527	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
OSMR	9180	hgsc.bcm.edu	37	5	38919158	38919158	+	Missense_Mutation	SNP	G	G	A	rs10941412	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:38919158G>A	ENST00000274276.3	+	11	1981	c.1579G>A	c.(1579-1581)Gaa>Aaa	p.E527K		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	527	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> K (in dbSNP:rs10941412).		cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					TGCAGACCCCGAAAACAGTGA	0.368													G|||	733	0.146366	0.2678	0.0908	5008	,	,		19569	0.0		0.1839	False		,,,				2504	0.1339				p.E527K		Atlas-SNP	.											.	OSMR	133	.	0			c.G1579A						PASS	.	G	LYS/GLU	1058,3348	385.4+/-325.7	130,798,1275	103.0	98.0	100.0		1579	4.0	0.0	5	dbSNP_120	100	1444,7156	276.4+/-292.3	114,1216,2970	yes	missense	OSMR	NM_003999.2	56	244,2014,4245	AA,AG,GG		16.7907,24.0127,19.2373	possibly-damaging	527/980	38919158	2502,10504	2203	4300	6503	SO:0001583	missense	9180	exon11			GACCCCGAAAACA	U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"""Fibronectin type III domain containing"""	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1579G>A	5.37:g.38919158G>A	ENSP00000274276:p.Glu527Lys	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	186	91	0.489247	NM_003999	Q6P4E8|Q96QJ6	Missense_Mutation	SNP	ENST00000274276.3	37	CCDS3928.1	291	0.13324175824175824	118	0.23983739837398374	37	0.10220994475138122	0	0.0	136	0.17941952506596306	G	13.91	2.377555	0.42105	0.240127	0.167907	ENSG00000145623	ENST00000274276;ENST00000513831	T;T	0.43688	0.94;1.26	4.91	4.04	0.47022	Long hematopoietin receptor, Gp130 family 2, conserved site (1);Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.818301	0.11790	N	0.529272	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	D	0.57257	0.979	P	0.46940	0.532	T	0.03761	-1.1006	9	0.07644	T	0.81	.	8.9699	0.35899	0.0998:0.0:0.9002:0.0	rs10941412;rs10941412	527	Q99650	OSMR_HUMAN	K	527;134	ENSP00000274276:E527K;ENSP00000423913:E134K	ENSP00000274276:E527K	E	+	1	0	OSMR	38954915	0.024000	0.19004	0.003000	0.11579	0.018000	0.09664	2.348000	0.44045	1.295000	0.44724	0.591000	0.81541	GAA	G|0.831;A|0.169	0.169	strong		0.368	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999	
TPTE	7179	hgsc.bcm.edu	37	21	10941955	10941955	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:10941955A>G	ENST00000361285.4	-	14	1077	c.748T>C	c.(748-750)Tca>Cca	p.S250P	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.S212P|TPTE_ENST00000298232.7_Missense_Mutation_p.S232P	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	250	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)		GATGGAAATGACATAGCAATA	0.289																																					p.S250P		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,+1,2	TPTE	513	2	0			c.T748C						scavenged	.						212.0	203.0	206.0					21																	10941955		2203	4297	6500	SO:0001583	missense	7179	exon14			GAAATGACATAGC	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.748T>C	21.37:g.10941955A>G	ENSP00000355208:p.Ser250Pro	Somatic	450	0	0		WXS	Illumina HiSeq	Phase_I	698	8	0.0114613	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	10.37	1.332388	0.24167	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.98849	-5.18;-5.18;-5.18	1.8	1.8	0.24995	Phosphatase tensin type (1);	0.000000	0.85682	U	0.000000	D	0.98963	0.9647	M	0.89658	3.05	0.53005	D	0.999961	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.91635	0.998;0.999;0.973	D	0.98773	1.0729	10	0.72032	D	0.01	-6.2679	7.6104	0.28126	1.0:0.0:0.0:0.0	.	212;232;250	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	P	232;250;212	ENSP00000298232:S232P;ENSP00000355208:S250P;ENSP00000344441:S212P	ENSP00000298232:S232P	S	-	1	0	TPTE	9963826	1.000000	0.71417	1.000000	0.80357	0.075000	0.17131	6.862000	0.75484	1.084000	0.41184	0.163000	0.16589	TCA	.	.	none		0.289	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
TCHH	7062	hgsc.bcm.edu	37	1	152082376	152082376	+	Missense_Mutation	SNP	C	C	A	rs200755879	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152082376C>A	ENST00000368804.1	-	2	3316	c.3317G>T	c.(3316-3318)cGg>cTg	p.R1106L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1106	10 X 30 AA tandem repeats.				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)			TTGCCTCTCCCGCTCCTGGCG	0.612													C|||	54	0.0107827	0.0053	0.0	5008	,	,		22224	0.0456		0.0	False		,,,				2504	0.001				p.R1106L		Atlas-SNP	.											TCHH,left_upper_lobe,carcinoma,-1,1	TCHH	275	1	0			c.G3317T						scavenged	.	C	LEU/ARG	26,3924		0,26,1949	92.0	94.0	94.0		3317	-6.1	0.0	1		94	1,8273		0,1,4136	no	missense	TCHH	NM_007113.2	102	0,27,6085	AA,AC,CC		0.0121,0.6582,0.2209	benign	1106/1944	152082376	27,12197	1975	4137	6112	SO:0001583	missense	7062	exon3			CTCTCCCGCTCCT	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.3317G>T	1.37:g.152082376C>A	ENSP00000357794:p.Arg1106Leu	Somatic	143	2	0.013986		WXS	Illumina HiSeq	Phase_I	208	4	0.0192308	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	C	5.178	0.218352	0.09810	0.006582	1.21E-4	ENSG00000159450	ENST00000368804	T	0.12361	2.69	3.07	-6.14	0.02111	.	.	.	.	.	T	0.01387	0.0045	N	0.12746	0.255	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.44528	-0.9322	9	0.26408	T	0.33	.	4.343	0.11119	0.4645:0.2516:0.0:0.2839	.	1106	Q07283	TRHY_HUMAN	L	1106	ENSP00000357794:R1106L	ENSP00000357794:R1106L	R	-	2	0	TCHH	150349000	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.957000	0.01521	-1.861000	0.01153	-1.305000	0.01319	CGG	.	.	weak		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
CHD2	1106	hgsc.bcm.edu	37	15	93552488	93552488	+	Silent	SNP	C	C	T	rs34315566	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:93552488C>T	ENST00000394196.4	+	35	5595	c.4527C>T	c.(4525-4527)atC>atT	p.I1509I	CHD2_ENST00000557381.1_Silent_p.I1509I	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1509					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)			TGCTGAAAATCGGAGACCGGA	0.527													C|||	74	0.0147764	0.0038	0.0086	5008	,	,		18724	0.0		0.0557	False		,,,				2504	0.0072				p.I1509I		Atlas-SNP	.											.	CHD2	280	.	0			c.C4527T						PASS	.	C		42,4352	43.1+/-76.7	2,38,2157	106.0	86.0	93.0		4527	-5.5	1.0	15	dbSNP_126	93	466,8130	137.5+/-194.4	12,442,3844	no	coding-synonymous	CHD2	NM_001271.3		14,480,6001	TT,TC,CC		5.4211,0.9558,3.9107		1509/1829	93552488	508,12482	2197	4298	6495	SO:0001819	synonymous_variant	1106	exon35			GAAAATCGGAGAC	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.4527C>T	15.37:g.93552488C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	66	17	0.257576	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	37	CCDS10374.2																																																																																			C|0.967;T|0.033	0.033	strong		0.527	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
ESYT2	57488	hgsc.bcm.edu	37	7	158534381	158534381	+	Silent	SNP	G	G	C	rs59980573	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:158534381G>C	ENST00000251527.5	-	17	2147	c.2082C>G	c.(2080-2082)ccC>ccG	p.P694P	ESYT2_ENST00000435514.2_Silent_p.P129P	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	722					endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CGGCCTCAGGGGGCTGGGCCT	0.637													G|||	1701	0.339657	0.4085	0.1888	5008	,	,		15915	0.5813		0.171	False		,,,				2504	0.2781				p.P694P		Atlas-SNP	.											.	ESYT2	70	.	0			c.C2082G						PASS	.			1517,2889	475.3+/-357.3	269,979,955	37.0	40.0	39.0		2082	-9.7	0.0	7	dbSNP_129	39	1395,7205	266.0+/-286.5	104,1187,3009	no	coding-synonymous	ESYT2	NM_020728.2		373,2166,3964	CC,CG,GG		16.2209,34.4303,22.3897		694/894	158534381	2912,10094	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon17			CTCAGGGGGCTGG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2082C>G	7.37:g.158534381G>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	78	53	0.679487	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			G|0.740;C|0.260	0.260	strong		0.637	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
PGLS	25796	hgsc.bcm.edu	37	19	17631821	17631821	+	Silent	SNP	G	G	A	rs148164602	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17631821G>A	ENST00000252603.2	+	5	752	c.708G>A	c.(706-708)ctG>ctA	p.L236L	FAM129C_ENST00000332386.5_5'Flank|FAM129C_ENST00000300971.2_5'Flank|CTD-3131K8.3_ENST00000596192.1_RNA|FAM129C_ENST00000352727.3_5'Flank|FAM129C_ENST00000335393.4_5'Flank|FAM129C_ENST00000595684.1_5'Flank	NM_012088.2	NP_036220.1	O95336	6PGL_HUMAN	6-phosphogluconolactonase	236					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	6-phosphogluconolactonase activity (GO:0017057)|monosaccharide binding (GO:0048029)			endometrium(1)|lung(1)	2						CCGGGAAACTGTGCTGGTTCT	0.647													G|||	76	0.0151757	0.0015	0.0202	5008	,	,		12940	0.0		0.0437	False		,,,				2504	0.0164				p.L236L		Atlas-SNP	.											.	PGLS	12	.	0			c.G708A						PASS	.	G		40,4358		0,40,2159	24.0	25.0	24.0		708	-10.6	0.1	19	dbSNP_134	24	382,8212		1,380,3916	no	coding-synonymous	PGLS	NM_012088.2		1,420,6075	AA,AG,GG		4.445,0.9095,3.2482		236/259	17631821	422,12570	2199	4297	6496	SO:0001819	synonymous_variant	25796	exon5			GAAACTGTGCTGG	AJ243972	CCDS12361.1	19p13.2	2008-02-05				ENSG00000130313	3.1.1.31		8903	protein-coding gene	gene with protein product		604951				10518023	Standard	NM_012088		Approved	6PGL	uc002ngw.3	O95336		ENST00000252603.2:c.708G>A	19.37:g.17631821G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	146	64	0.438356	NM_012088		Silent	SNP	ENST00000252603.2	37	CCDS12361.1																																																																																			G|0.977;A|0.023	0.023	strong		0.647	PGLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464154.1		
VCAN	1462	hgsc.bcm.edu	37	5	82834299	82834299	+	Missense_Mutation	SNP	G	G	A	rs188703	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:82834299G>A	ENST00000265077.3	+	8	6042	c.5477G>A	c.(5476-5478)cGt>cAt	p.R1826H	VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.R839H|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1826	GAG-beta.		R -> H (in dbSNP:rs188703).		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)	ACTCTCCCACGTAGTCCTGCC	0.483													G|||	1795	0.358427	0.3449	0.4611	5008	,	,		16825	0.3234		0.4254	False		,,,				2504	0.271				p.R1826H		Atlas-SNP	.											VCAN,NS,carcinoma,-1,1	VCAN	498	1	0			c.G5477A						PASS	.	G	,HIS/ARG,,HIS/ARG	1549,2857	445.5+/-347.7	261,1027,915	69.0	77.0	74.0		,2516,,5477	0.2	0.0	5	dbSNP_79	74	3441,5159	478.3+/-369.9	704,2033,1563	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,29,,29	965,3060,2478	AA,AG,GG		40.0116,35.1566,38.3669	,benign,,benign	,839/2410,,1826/3397	82834299	4990,8016	2203	4300	6503	SO:0001583	missense	1462	exon8			TCCCACGTAGTCC	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.5477G>A	5.37:g.82834299G>A	ENSP00000265077:p.Arg1826His	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	832	0.38095238095238093	139	0.28252032520325204	169	0.46685082872928174	203	0.3548951048951049	321	0.4234828496042216	G	12.50	1.956712	0.34565	0.351566	0.400116	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.84660	-1.85;-1.88;3.27	5.82	0.253	0.15551	.	0.983187	0.08317	N	0.964443	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.31931	0.347;0.235	B;B	0.27170	0.077;0.035	T	0.21415	-1.0246	9	0.49607	T	0.09	.	2.0501	0.03569	0.1803:0.1061:0.4634:0.2501	rs188703;rs309558;rs479344;rs52807291;rs60541692;rs188703	839;1826	P13611-2;P13611	.;CSPG2_HUMAN	H	1826;839;839	ENSP00000265077:R1826H;ENSP00000340062:R839H;ENSP00000426251:R839H	ENSP00000265077:R1826H	R	+	2	0	VCAN	82870055	0.003000	0.15002	0.001000	0.08648	0.027000	0.11550	0.786000	0.26844	0.328000	0.23435	0.655000	0.94253	CGT	G|0.623;A|0.377	0.377	strong		0.483	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
ZCCHC6	79670	hgsc.bcm.edu	37	9	88959938	88959938	+	Silent	SNP	C	C	T	rs791323	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:88959938C>T	ENST00000375963.3	-	5	1123	c.951G>A	c.(949-951)ctG>ctA	p.L317L	ZCCHC6_ENST00000375948.1_5'Flank|ZCCHC6_ENST00000375961.2_Silent_p.L317L|ZCCHC6_ENST00000375947.1_Silent_p.L150L|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000375960.2_Silent_p.L317L	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	317					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						GTTTAATTTCCAGCCTCTGTT	0.383													T|||	3102	0.619409	0.8253	0.5288	5008	,	,		19149	0.5308		0.5447	False		,,,				2504	0.5736				p.L317L		Atlas-SNP	.											ZCCHC6,colon,carcinoma,0,1	ZCCHC6	105	1	0			c.G951A						PASS	.	T	,,	3447,959	362.6+/-316.2	1346,755,102	143.0	130.0	134.0		951,951,951	2.7	1.0	9	dbSNP_86	134	4670,3930	548.2+/-385.3	1249,2172,879	no	coding-synonymous,coding-synonymous,coding-synonymous	ZCCHC6	NM_001185059.1,NM_001185074.1,NM_024617.3	,,	2595,2927,981	TT,TC,CC		45.6977,21.7658,37.5903	,,	317/1496,317/1260,317/1496	88959938	8117,4889	2203	4300	6503	SO:0001819	synonymous_variant	79670	exon5			AATTTCCAGCCTC	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"""Zinc fingers, CCHC domain containing"""	25817	protein-coding gene	gene with protein product	"""TUTase7"""					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.951G>A	9.37:g.88959938C>T		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	213	105	0.492958	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Silent	SNP	ENST00000375963.3	37	CCDS35057.1																																																																																			C|0.379;N|0.000	.	strong		0.383	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617	
MOV10L1	54456	hgsc.bcm.edu	37	22	50528569	50528569	+	Missense_Mutation	SNP	A	A	T	rs12628964	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50528569A>T	ENST00000262794.5	+	1	135	c.52A>T	c.(52-54)Acc>Tcc	p.T18S	MOV10L1_ENST00000545383.1_Missense_Mutation_p.T18S|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000540615.1_5'Flank|MOV10L1_ENST00000395858.3_Missense_Mutation_p.T18S	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	18			T -> S (in dbSNP:rs12628964).		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)		GACGGCGGACACCCCTAGGGA	0.756													A|||	1242	0.248003	0.1218	0.3818	5008	,	,		8047	0.255		0.2356	False		,,,				2504	0.3292				p.T18S		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A52T						PASS	.						6.0	7.0	7.0					22																	50528569		1551	2828	4379	SO:0001583	missense	54456	exon1			GCGGACACCCCTA	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.52A>T	22.37:g.50528569A>T	ENSP00000262794:p.Thr18Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	531	0.24313186813186813	60	0.12195121951219512	122	0.3370165745856354	178	0.3111888111888112	171	0.22559366754617413	A	11.91	1.780956	0.31502	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858	D;D;T	0.83673	-1.75;-1.75;-1.34	4.73	-8.4	0.00965	.	2.671080	0.01827	N	0.034422	T	0.00012	0.0000	N	0.01576	-0.805	0.54753	P	1.0999999999983245E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.07065	-1.0792	9	0.08381	T	0.77	1.5492	0.9037	0.01280	0.4069:0.1189:0.2329:0.2413	rs12628964	18;18	A8MXC6;Q9BXT6	.;M10L1_HUMAN	S	18	ENSP00000438978:T18S;ENSP00000262794:T18S;ENSP00000379199:T18S	ENSP00000262794:T18S	T	+	1	0	MOV10L1	48870696	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.754000	0.01816	-1.708000	0.01401	-1.098000	0.02139	ACC	A|0.756;T|0.244	0.244	strong		0.756	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
CLEC19A	728276	hgsc.bcm.edu	37	16	19297219	19297219	+	Missense_Mutation	SNP	T	T	G	rs179196	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	127	0	0		WXS	Illumina HiSeq	Phase_I	125	52	0.416	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	
ZNF335	63925	hgsc.bcm.edu	37	20	44596545	44596545	+	Silent	SNP	G	G	A	rs3848719	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44596545G>A	ENST00000322927.2	-	5	742	c.642C>T	c.(640-642)agC>agT	p.S214S	ZNF335_ENST00000494955.1_5'UTR|ZNF335_ENST00000426788.1_Silent_p.S59S	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	214					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GCACCGGGGAGCTGGGCCCAC	0.652													G|||	930	0.185703	0.0749	0.3084	5008	,	,		17763	0.0		0.4254	False		,,,				2504	0.1933				p.S214S		Atlas-SNP	.											ZNF335,NS,carcinoma,0,1	ZNF335	115	1	0			c.C642T						PASS	.	G		645,3761		54,537,1612	32.0	35.0	34.0		642	3.4	0.9	20	dbSNP_108	34	3695,4903		789,2117,1393	no	coding-synonymous	ZNF335	NM_022095.3		843,2654,3005	AA,AG,GG		42.9751,14.6391,33.3743		214/1343	44596545	4340,8664	2203	4299	6502	SO:0001819	synonymous_variant	63925	exon5			CGGGGAGCTGGGC	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.642C>T	20.37:g.44596545G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																			G|0.728;A|0.272	0.272	strong		0.652	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43632536	43632536	+	Missense_Mutation	SNP	C	C	T	rs7163	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	104	0	0		WXS	Illumina HiSeq	Phase_I	73	13	0.178082	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		
INTS3	65123	hgsc.bcm.edu	37	1	153736314	153736314	+	Silent	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:153736314G>T	ENST00000318967.2	+	17	2341	c.1773G>T	c.(1771-1773)acG>acT	p.T591T	INTS3_ENST00000512605.1_Silent_p.T385T|INTS3_ENST00000456435.1_Silent_p.T385T|INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000435409.2_Silent_p.T591T	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	592					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GCAGTGATACGGAGGCCCAGT	0.537																																					p.T591T		Atlas-SNP	.											INTS3,NS,carcinoma,+1,1	INTS3	83	1	0			c.G1773T						scavenged	.						124.0	102.0	109.0					1																	153736314		2203	4300	6503	SO:0001819	synonymous_variant	65123	exon17			TGATACGGAGGCC	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.1773G>T	1.37:g.153736314G>T		Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	316	4	0.0126582	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	37	CCDS1052.1																																																																																			.	.	none		0.537	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
OR4C16	219428	hgsc.bcm.edu	37	11	55340379	55340379	+	Missense_Mutation	SNP	T	T	C	rs559449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55340379T>C	ENST00000314634.3	+	1	776	c.776T>C	c.(775-777)cTt>cCt	p.L259P		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	259			L -> P (in dbSNP:rs559449). {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)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				TACACATGCCTTGCAACCGTA	0.403													N|||	2398	0.478834	0.3275	0.5951	5008	,	,		19920	0.5446		0.5547	False		,,,				2504	0.455				p.L259P		Atlas-SNP	.											.	OR4C16	104	.	0			c.T776C						PASS	.	C	PRO/LEU	1536,2866	670.9+/-402.4	274,988,939	159.0	135.0	143.0		776	4.7	0.3	11	dbSNP_83	143	4721,3871	542.3+/-384.2	1321,2079,896	yes	missense	OR4C16	NM_001004701.2	98	1595,3067,1835	CC,CT,TT		45.0535,34.8932,48.153	benign	259/311	55340379	6257,6737	2201	4296	6497	SO:0001583	missense	219428	exon1			CATGCCTTGCAAC	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.776T>C	11.37:g.55340379T>C	ENSP00000324913:p.Leu259Pro	Somatic	400	1	0.0025		WXS	Illumina HiSeq	Phase_I	365	168	0.460274	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	1087	0.4977106227106227	135	0.27439024390243905	219	0.6049723756906077	308	0.5384615384615384	425	0.5606860158311345	C	0.007	-1.951729	0.00470	0.348932	0.549465	ENSG00000181935	ENST00000314634	T	0.00015	9.17	4.68	4.68	0.58851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00007	-3.15	0.35649	P	0.188373	B	0.02656	0.0	B	0.01281	0.0	T	0.25984	-1.0116	9	0.02654	T	1	.	10.8556	0.46798	0.0:0.9081:0.0:0.0919	rs559449;rs56587050;rs56801259;rs559449	259	Q8NGL9	OR4CG_HUMAN	P	259	ENSP00000324913:L259P	ENSP00000324913:L259P	L	+	2	0	OR4C16	55096955	0.002000	0.14202	0.339000	0.25562	0.077000	0.17291	0.668000	0.25127	1.222000	0.43521	-0.231000	0.12243	CTT	T|0.517;C|0.483	0.483	strong		0.403	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121616250	121616250	+	Silent	SNP	G	G	A	rs4629793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:121616250G>A	ENST00000393386.2	+	5	891	c.480G>A	c.(478-480)gcG>gcA	p.A160A	PTPRZ1_ENST00000449182.1_Silent_p.A160A	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	160	Alpha-carbonic anhydrase.				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						GCTTTGATGCGGACCGATTTT	0.313													g|||	1388	0.277157	0.0514	0.353	5008	,	,		15770	0.3323		0.4722	False		,,,				2504	0.271				p.A160A		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G480A						PASS	.	A	,,	488,3918	225.9+/-241.6	36,416,1751	110.0	104.0	106.0		480,480,480	-10.9	0.0	7	dbSNP_111	106	3599,4993	518.5+/-379.3	766,2067,1463	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,	802,2483,3214	AA,AG,GG		41.8878,11.0758,31.4433	,,	160/1456,160/1449,160/2316	121616250	4087,8911	2203	4296	6499	SO:0001819	synonymous_variant	5803	exon5			TGATGCGGACCGA	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.480G>A	7.37:g.121616250G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	68	51	0.75	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			G|0.681;A|0.319	0.319	strong		0.313	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
USP32	84669	hgsc.bcm.edu	37	17	58285542	58285542	+	Missense_Mutation	SNP	G	G	A	rs147413172	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	575	1	0.00173913		WXS	Illumina HiSeq	Phase_I	635	146	0.229921	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	
NOX3	50508	hgsc.bcm.edu	37	6	155761246	155761246	+	Missense_Mutation	SNP	G	G	T	rs3749930	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:155761246G>T	ENST00000159060.2	-	6	614	c.512C>A	c.(511-513)aCa>aAa	p.T171K		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	171	Ferric oxidoreductase.		T -> K (in dbSNP:rs3749930).		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)		GCCTGCTATTGTCCTTAGCAA	0.393													G|||	989	0.197484	0.0734	0.1873	5008	,	,		17556	0.4821		0.0527	False		,,,				2504	0.228				p.T171K		Atlas-SNP	.											.	NOX3	93	.	0			c.C512A						PASS	.	G	LYS/THR	313,4093	165.1+/-196.6	8,297,1898	102.0	100.0	101.0		512	5.8	0.2	6	dbSNP_107	101	367,8233	121.3+/-180.4	3,361,3936	yes	missense	NOX3	NM_015718.2	78	11,658,5834	TT,TG,GG		4.2674,7.1039,5.2284	probably-damaging	171/569	155761246	680,12326	2203	4300	6503	SO:0001583	missense	50508	exon6			GCTATTGTCCTTA	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.512C>A	6.37:g.155761246G>T	ENSP00000159060:p.Thr171Lys	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_015718	Q9HBJ9	Missense_Mutation	SNP	ENST00000159060.2	37	CCDS5250.1	430	0.19688644688644688	28	0.056910569105691054	53	0.1464088397790055	301	0.5262237762237763	48	0.0633245382585752	G	22.4	4.284765	0.80803	0.071039	0.042674	ENSG00000074771	ENST00000159060	D	0.95756	-3.8	5.79	5.79	0.91817	Flavoprotein transmembrane component (1);	0.000000	0.64402	D	0.000004	D	0.95965	0.8686	M	0.74467	2.265	0.25165	P	0.99032905	D	0.58268	0.982	P	0.57620	0.824	D	0.95255	0.8363	9	0.41790	T	0.15	-21.7527	13.3132	0.60393	0.072:0.0:0.928:0.0	rs3749930;rs59445351;rs3749930	171	Q9HBY0	NOX3_HUMAN	K	171	ENSP00000159060:T171K	ENSP00000159060:T171K	T	-	2	0	NOX3	155802938	1.000000	0.71417	0.154000	0.22540	0.132000	0.20833	5.010000	0.64004	2.757000	0.94681	0.644000	0.83932	ACA	G|0.878;T|0.122	0.122	strong		0.393	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
TTC4	7268	hgsc.bcm.edu	37	1	55182300	55182300	+	Missense_Mutation	SNP	T	T	A	rs1147990	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:55182300T>A	ENST00000371281.3	+	2	226	c.139T>A	c.(139-141)Tcg>Acg	p.S47T	MROH7-TTC4_ENST00000414150.2_Nonsense_Mutation_p.C1282*|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	47			S -> T (in dbSNP:rs1147990). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.							breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						CCTATTTATGTCGAGAGCGCC	0.408													A|||	3347	0.668331	0.5038	0.6081	5008	,	,		20068	0.9683		0.5477	False		,,,				2504	0.7485				p.S47T		Atlas-SNP	.											TTC4,NS,carcinoma,-2,1	TTC4	21	1	0			c.T139A						PASS	.	A	THR/SER	2432,1974	555.1+/-379.2	673,1086,444	89.0	89.0	89.0		139	4.9	1.0	1	dbSNP_87	89	4395,4205	570.7+/-389.4	1119,2157,1024	yes	missense	TTC4	NM_004623.4	58	1792,3243,1468	AA,AT,TT		48.8953,44.8025,47.5088	benign	47/388	55182300	6827,6179	2203	4300	6503	SO:0001583	missense	7268	exon2			TTTATGTCGAGAG		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"""Tetratricopeptide (TTC) repeat domain containing"""	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.139T>A	1.37:g.55182300T>A	ENSP00000360329:p.Ser47Thr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	43	0.977273	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	ENST00000371281.3	37	CCDS596.1	1449	0.6634615384615384	277	0.5630081300813008	214	0.5911602209944752	556	0.972027972027972	402	0.5303430079155673	A	10.97	1.502706	0.26949	0.551975	0.511047	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.12569	2.67	4.92	4.92	0.64577	.	.	.	.	.	T	0.00012	0.0000	N	0.03050	-0.425	0.52099	P	5.599999999994498E-5	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.38714	-0.9648	8	0.02654	T	1	-7.8097	9.6171	0.39698	0.8434:0.0:0.0:0.1566	rs1147990;rs1623164;rs17856041;rs56423771;rs56930428;rs1147990	47;58	O95801;Q5TA95	TTC4_HUMAN;.	T	47;58	ENSP00000360329:S47T	ENSP00000360329:S47T	S	+	1	0	TTC4	54954888	1.000000	0.71417	0.996000	0.52242	0.591000	0.36615	5.925000	0.70062	1.011000	0.39340	-0.257000	0.10917	TCG	T|0.395;A|0.605	0.605	strong		0.408	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623	
FLG	2312	hgsc.bcm.edu	37	1	152284505	152284505	+	Missense_Mutation	SNP	C	C	G	rs201137357	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152284505C>G	ENST00000368799.1	-	3	2892	c.2857G>C	c.(2857-2859)Gag>Cag	p.E953Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	953	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAATGTCCCTCACTGTCACTG	0.572									Ichthyosis				-|||	685	0.136781	0.3707	0.0576	5008	,	,		22374	0.0694		0.0258	False		,,,				2504	0.0603				p.E953Q		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.G2857C						scavenged	.	G	GLN/GLU	442,3964		4,434,1765	302.0	283.0	290.0		2857	2.1	0.0	1	dbSNP_134	290	5,8595		0,5,4295	no	missense	FLG	NM_002016.1	29	4,439,6060	GG,GC,CC		0.0581,10.0318,3.4369	probably-damaging	953/4062	152284505	447,12559	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCCCTCACTGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2857G>C	1.37:g.152284505C>G	ENSP00000357789:p.Glu953Gln	Somatic	340	1	0.00294118		WXS	Illumina HiSeq	Phase_I	463	32	0.0691145	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	7.629	0.678402	0.14841	0.100318	5.81E-4	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.08008	3.14	4.22	2.12	0.27331	.	.	.	.	.	T	0.03477	0.0100	N	0.11724	0.165	0.09310	N	1	D	0.61697	0.99	P	0.61201	0.885	T	0.41770	-0.9490	9	0.25751	T	0.34	.	6.5814	0.22596	0.2048:0.5963:0.1989:0.0	.	953	P20930	FILA_HUMAN	Q	953;160	ENSP00000357789:E953Q	ENSP00000357789:E953Q	E	-	1	0	FLG	150551129	0.000000	0.05858	0.004000	0.12327	0.029000	0.11900	-0.312000	0.08113	0.743000	0.32719	0.473000	0.43528	GAG	.	.	weak		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
RAI14	26064	hgsc.bcm.edu	37	5	34757666	34757666	+	Missense_Mutation	SNP	G	G	A	rs17521570	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:34757666G>A	ENST00000265109.3	+	3	417	c.130G>A	c.(130-132)Gcc>Acc	p.A44T	RAI14_ENST00000506376.1_Missense_Mutation_p.A36T|RAI14_ENST00000512629.1_Missense_Mutation_p.A44T|RAI14_ENST00000397449.1_Missense_Mutation_p.A37T|RAI14_ENST00000503673.1_Missense_Mutation_p.A44T|RAI14_ENST00000507276.1_3'UTR|RAI14_ENST00000428746.2_Missense_Mutation_p.A44T|RAI14_ENST00000515799.1_Missense_Mutation_p.A47T	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	44			A -> T (in dbSNP:rs17521570).			actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					CAAGAAGGGGGCCAGTGCCAC	0.542													G|||	495	0.0988419	0.0076	0.1052	5008	,	,		18526	0.1141		0.1262	False		,,,				2504	0.1738				p.A47T		Atlas-SNP	.											.	RAI14	100	.	0			c.G139A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	123,4283	91.1+/-129.8	0,123,2080	75.0	72.0	73.0		130,130,130,106,139,130	3.9	1.0	5	dbSNP_123	73	1052,7548	222.3+/-259.4	46,960,3294	yes	missense,missense,missense,missense,missense,missense	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	58,58,58,58,58,58	46,1083,5374	AA,AG,GG		12.2326,2.7916,9.0343	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	44/981,44/981,44/952,36/973,47/984,44/981	34757666	1175,11831	2203	4300	6503	SO:0001583	missense	26064	exon5			AAGGGGGCCAGTG	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.130G>A	5.37:g.34757666G>A	ENSP00000265109:p.Ala44Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	207	0.09478021978021978	6	0.012195121951219513	33	0.09116022099447514	62	0.10839160839160839	106	0.13984168865435356	G	14.89	2.671784	0.47781	0.027916	0.122326	ENSG00000039560	ENST00000265109;ENST00000514527;ENST00000513974;ENST00000512629;ENST00000428746;ENST00000514873;ENST00000503673;ENST00000504052;ENST00000512305;ENST00000514036;ENST00000515799;ENST00000508315;ENST00000512625;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.70869	-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52;-0.52	5.72	3.89	0.44902	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.01189	0.0039	M	0.74389	2.26	0.25756	P	0.9850026	B;B;B;B	0.21688	0.026;0.059;0.003;0.003	B;B;B;B	0.27170	0.046;0.077;0.009;0.015	T	0.48969	-0.8987	8	0.45353	T	0.12	-7.0983	11.6973	0.51551	0.067:0.1235:0.8095:0.0	rs17521570;rs52832216;rs17521570	36;44;47;44	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	T	44;44;44;44;44;44;44;44;44;44;47;44;44;36;37	ENSP00000265109:A44T;ENSP00000424879:A44T;ENSP00000422112:A44T;ENSP00000422377:A44T;ENSP00000388725:A44T;ENSP00000421424:A44T;ENSP00000422942:A44T;ENSP00000422515:A44T;ENSP00000422114:A44T;ENSP00000424502:A44T;ENSP00000427123:A47T;ENSP00000426770:A44T;ENSP00000425115:A44T;ENSP00000423854:A36T;ENSP00000380591:A37T	ENSP00000265109:A44T	A	+	1	0	RAI14	34793423	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.473000	0.35387	1.443000	0.47586	0.650000	0.86243	GCC	G|0.906;A|0.094	0.094	strong		0.542	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
APEH	327	hgsc.bcm.edu	37	3	49721798	49721798	+	IGR	SNP	C	C	A	rs13085791	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49721798C>A	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Silent_p.R655R	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)		TCTCACTCTCCCGCACACGTC	0.597													C|||	1046	0.208866	0.2632	0.1729	5008	,	,		21198	0.0565		0.3241	False		,,,				2504	0.1994				p.R655R		Atlas-SNP	.											.	MST1	84	.	0			c.G1965T						PASS	.	C		1184,3222	408.9+/-334.8	153,878,1172	55.0	57.0	56.0		1965	-6.0	0.0	3	dbSNP_121	56	2576,6024	406.4+/-348.8	399,1778,2123	no	coding-synonymous	MST1	NM_020998.3		552,2656,3295	AA,AC,CC		29.9535,26.8724,28.9097		655/726	49721798	3760,9246	2203	4300	6503	SO:0001628	intergenic_variant	4485	exon17			ACTCTCCCGCACA	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.49721798C>A		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	349	180	0.515759	NM_020998	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1	515	0.2358058608058608	148	0.3008130081300813	83	0.2292817679558011	37	0.06468531468531469	247	0.3258575197889182	C	5.900	0.350100	0.11182	0.268724	0.299535	ENSG00000173531	ENST00000448220	.	.	.	5.59	-5.99	0.02213	.	.	.	.	.	.	.	.	.	.	.	0.23023	P	0.99841852	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.6906	0.02851	0.1818:0.3582:0.266:0.194	rs13085791;rs13085791	.	.	.	X	125	.	.	G	-	1	0	MST1	49696802	0.000000	0.05858	0.001000	0.08648	0.939000	0.58152	-1.124000	0.03260	-1.376000	0.02126	0.655000	0.94253	GGA	C|0.725;A|0.275	0.275	strong		0.597	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
OR1F1	4992	hgsc.bcm.edu	37	16	3254972	3254972	+	Silent	SNP	T	T	C	rs2075851	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	226	2	0.00884956		WXS	Illumina HiSeq	Phase_I	167	167	1	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		
ABHD16B	140701	hgsc.bcm.edu	37	20	62492922	62492922	+	Missense_Mutation	SNP	T	T	A	rs2281534	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62492922T>A	ENST00000369916.3	+	1	357	c.29T>A	c.(28-30)cTg>cAg	p.L10Q	C20ORF135_ENST00000601296.1_Missense_Mutation_p.Q99L	NM_080622.3	NP_542189.1	Q9H3Z7	ABHGB_HUMAN	abhydrolase domain containing 16B	10			L -> Q (in dbSNP:rs2281534).				hydrolase activity (GO:0016787)			endometrium(2)|kidney(1)|lung(3)	6						GTGAAGGCGCTGGTGCGCGTG	0.677													T|||	329	0.0656949	0.0136	0.0548	5008	,	,		11583	0.129		0.0706	False		,,,				2504	0.0736				p.L10Q		Atlas-SNP	.											.	ABHD16B	22	.	0			c.T29A						PASS	.	T	GLN/LEU	73,4309		0,73,2118	25.0	16.0	19.0		29	3.8	1.0	20	dbSNP_100	19	598,7952		8,582,3685	yes	missense	ABHD16B	NM_080622.3	113	8,655,5803	AA,AT,TT		6.9942,1.6659,5.1887	probably-damaging	10/470	62492922	671,12261	2191	4275	6466	SO:0001583	missense	140701	exon1			AGGCGCTGGTGCG		CCDS13539.1	20q13.33	2013-01-17	2010-12-09	2010-12-09	ENSG00000183260	ENSG00000183260		"""Abhydrolase domain containing"""	16128	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 135"""	C20orf135			Standard	NM_080622		Approved	dJ591C20.1	uc002ygx.1	Q9H3Z7	OTTHUMG00000033010	ENST00000369916.3:c.29T>A	20.37:g.62492922T>A	ENSP00000358932:p.Leu10Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_080622		Missense_Mutation	SNP	ENST00000369916.3	37	CCDS13539.1	154	0.07051282051282051	8	0.016260162601626018	20	0.055248618784530384	72	0.1258741258741259	54	0.0712401055408971	T	19.21	3.784167	0.70222	0.016659	0.069942	ENSG00000183260	ENST00000369916	T	0.54866	0.55	3.77	3.77	0.43336	.	0.612694	0.15192	U	0.275503	T	0.01454	0.0047	M	0.76727	2.345	0.35373	P	0.21074700000000002	D	0.76494	0.999	P	0.61800	0.894	T	0.46317	-0.9200	9	0.87932	D	0	-8.8752	10.7261	0.46068	0.0:0.0:0.0:1.0	rs2281534	10	Q9H3Z7	ABHGB_HUMAN	Q	10	ENSP00000358932:L10Q	ENSP00000358932:L10Q	L	+	2	0	ABHD16B	61963366	0.986000	0.35501	0.987000	0.45799	0.990000	0.78478	4.022000	0.57203	1.476000	0.48215	0.533000	0.62120	CTG	T|0.942;A|0.058	0.058	strong		0.677	ABHD16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080254.1		
KRT10	3858	hgsc.bcm.edu	37	17	38978462	38978462	+	Missense_Mutation	SNP	C	C	T	rs77919366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38978462C>T	ENST00000269576.5	-	1	385	c.376G>A	c.(376-378)Ggc>Agc	p.G126S	TMEM99_ENST00000496847.1_Intron|TMEM99_ENST00000301665.3_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	126	Gly-rich.|Head.		G -> S (in dbSNP:rs77919366). {ECO:0000269|PubMed:7512983}.		cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)	p.G126S(1)		NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				cctccaaagccgcctccaCCA	0.557													C|||	665	0.132788	0.0703	0.1816	5008	,	,		11883	0.0377		0.2296	False		,,,				2504	0.181				p.G126S		Atlas-SNP	.											KRT10,NS,carcinoma,0,1	KRT10	56	1	1	Substitution - Missense(1)	prostate(1)	c.G376A						scavenged	.	C	,,,SER/GLY	440,3964	209.8+/-230.5	29,382,1791	54.0	47.0	50.0		,,,376	-0.9	0.5	17	dbSNP_131	50	1968,6632	336.7+/-322.0	221,1526,2553	yes	intron,intron,intron,missense	KRT10,TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3,NM_000421.3	,,,56	250,1908,4344	TT,TC,CC		22.8837,9.9909,18.5174	,,,benign	,,,126/585	38978462	2408,10596	2202	4300	6502	SO:0001583	missense	3858	exon1			CAAAGCCGCCTCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.376G>A	17.37:g.38978462C>T	ENSP00000269576:p.Gly126Ser	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	37	CCDS11377.1	302	0.1382783882783883	32	0.06504065040650407	71	0.19613259668508287	17	0.02972027972027972	182	0.24010554089709762	C	7.168	0.586981	0.13749	0.099909	0.228837	ENSG00000186395	ENST00000269576	D	0.82433	-1.61	0.445	-0.891	0.10573	.	0.536646	0.15796	N	0.244207	T	0.00039	0.0001	L	0.39898	1.24	0.58432	P	5.999999999950489E-6	B	0.17268	0.021	B	0.04013	0.001	T	0.02484	-1.1152	8	0.39692	T	0.17	.	.	.	.	.	126	P13645	K1C10_HUMAN	S	126	ENSP00000269576:G126S	ENSP00000269576:G126S	G	-	1	0	KRT10	36231988	0.002000	0.14202	0.500000	0.27589	0.782000	0.44232	0.081000	0.14823	-0.330000	0.08514	0.372000	0.22366	GGC	C|0.838;T|0.162	0.162	strong		0.557	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421	
PAPSS1	9061	hgsc.bcm.edu	37	4	108575989	108575989	+	Silent	SNP	G	G	A	rs3733633	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:108575989G>A	ENST00000265174.4	-	8	1235	c.963C>T	c.(961-963)gaC>gaT	p.D321D	PAPSS1_ENST00000511304.1_5'UTR	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	321					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		CTGTACAGCCGTCCAGCCTCT	0.498													A|||	1240	0.247604	0.2466	0.2608	5008	,	,		16353	0.3512		0.2256	False		,,,				2504	0.1554				p.D321D		Atlas-SNP	.											.	PAPSS1	57	.	0			c.C963T						PASS	.	A		1057,3349	724.6+/-409.5	116,825,1262	109.0	112.0	111.0		963	-7.9	0.6	4	dbSNP_107	111	1822,6778	731.7+/-406.8	186,1450,2664	no	coding-synonymous	PAPSS1	NM_005443.4		302,2275,3926	AA,AG,GG		21.186,23.99,22.1359		321/625	108575989	2879,10127	2203	4300	6503	SO:0001819	synonymous_variant	9061	exon8			ACAGCCGTCCAGC	Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.963C>T	4.37:g.108575989G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	233	125	0.536481	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Silent	SNP	ENST00000265174.4	37	CCDS3676.1																																																																																			G|0.759;A|0.241	0.241	strong		0.498	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197499	39197499	+	Nonsense_Mutation	SNP	G	G	A	rs3213755	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39197499G>A	ENST00000306271.4	-	1	214	c.151C>T	c.(151-153)Cag>Tag	p.Q51*		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	51			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)			AAGCTGGTCTGGCAGCAGCTT	0.612																																					p.Q51X		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.C151T	GRCh37	CM067999	KRTAP1-1	M	rs3213755	PASS	.	G	stop/GLN	743,3287		55,633,1327	75.0	86.0	83.0		151	3.6	1.0	17	dbSNP_106	83	1292,7138		100,1092,3023	yes	stop-gained	KRTAP1-1	NM_030967.2		155,1725,4350	AA,AG,GG		15.3262,18.4367,16.3323		51/178	39197499	2035,10425	2015	4215	6230	SO:0001587	stop_gained	81851	exon1			TGGTCTGGCAGCA	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.151C>T	17.37:g.39197499G>A	ENSP00000305975:p.Gln51*	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	188	84	0.446809	NM_030967	A6NC32|Q96S60|Q96S67	Nonsense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	426	0.19505494505494506	87	0.17682926829268292	84	0.23204419889502761	151	0.263986013986014	104	0.13720316622691292	G	21.1	4.100620	0.76983	0.184367	0.153262	ENSG00000188581	ENST00000306271;ENST00000543328	.	.	.	3.6	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999401316	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	7.1567	0.25641	0.1206:0.0:0.8794:0.0	rs3213755	.	.	.	X	51;41	.	ENSP00000305975:Q51X	Q	-	1	0	KRTAP1-1	36451025	0.237000	0.23815	1.000000	0.80357	0.931000	0.56810	-0.153000	0.10144	2.339000	0.79563	0.650000	0.86243	CAG	G|0.804;A|0.196	0.196	strong		0.612	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
ATF5	22809	hgsc.bcm.edu	37	19	50435862	50435862	+	Missense_Mutation	SNP	C	C	T	rs283526	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50435862C>T	ENST00000423777.2	+	3	739	c.362C>T	c.(361-363)cCc>cTc	p.P121L	MIR4751_ENST00000578027.1_RNA|CTC-326K19.6_ENST00000451973.1_Intron|NUP62_ENST00000352066.3_5'Flank|ATF5_ENST00000595125.1_Missense_Mutation_p.P121L|NUP62_ENST00000422090.2_5'Flank	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	121	Interaction with PTP4A1. {ECO:0000250}.		P -> L (in dbSNP:rs283526). {ECO:0000269|PubMed:15221005, ECO:0000269|PubMed:15489334}.		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)	GATGCCCCGCCCCTCccacca	0.657													T|||	3348	0.66853	0.9274	0.6412	5008	,	,		3984	0.6538		0.5169	False		,,,				2504	0.5092				p.P121L	GBM(48;768 989 9196 9511 26329)	Atlas-SNP	.											ATF5,NS,carcinoma,0,1	ATF5	27	1	0			c.C362T						scavenged	.	T	LEU/PRO,LEU/PRO	3791,567		1662,467,50	10.0	8.0	9.0		362,362	2.9	0.6	19	dbSNP_79	9	4462,4004		1225,2012,996	yes	missense,missense	ATF5	NM_001193646.1,NM_012068.5	98,98	2887,2479,1046	TT,TC,CC		47.2951,13.0106,35.6441	benign,benign	121/283,121/283	50435862	8253,4571	2179	4233	6412	SO:0001583	missense	22809	exon4			CCCCGCCCCTCCC	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.362C>T	19.37:g.50435862C>T	ENSP00000396954:p.Pro121Leu	Somatic	105	3	0.0285714		WXS	Illumina HiSeq	Phase_I	119	107	0.89916	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Missense_Mutation	SNP	ENST00000423777.2	37	CCDS12789.1	1316	0.6025641025641025	383	0.7784552845528455	212	0.585635359116022	353	0.6171328671328671	368	0.48548812664907653	T	0.581	-0.837221	0.02692	0.869894	0.527049	ENSG00000169136	ENST00000423777	T	0.40225	1.04	2.87	2.87	0.33458	.	0.770342	0.11118	N	0.597734	T	0.00012	0.0000	N	0.00413	-1.525	0.40654	P	0.01793100000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.28554	-1.0040	9	0.09843	T	0.71	-3.2089	6.5705	0.22535	0.0:0.1248:0.0:0.8752	rs283526;rs3170546;rs3745493;rs17845046;rs17857823;rs60018578;rs283526	121	Q9Y2D1	ATF5_HUMAN	L	121	ENSP00000396954:P121L	ENSP00000396954:P121L	P	+	2	0	ATF5	55127674	0.985000	0.35326	0.614000	0.29051	0.323000	0.28346	1.942000	0.40243	0.499000	0.27970	-0.554000	0.04202	CCC	C|0.351;T|0.649	0.649	strong		0.657	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2		
CHPF2	54480	hgsc.bcm.edu	37	7	150935430	150935430	+	Missense_Mutation	SNP	G	G	C	rs3748098	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:150935430G>C	ENST00000035307.2	+	4	3495	c.1982G>C	c.(1981-1983)gGg>gCg	p.G661A	MIR671_ENST00000390183.1_RNA|CHPF2_ENST00000495645.1_Missense_Mutation_p.G653A|RP4-548D19.3_ENST00000607902.1_RNA	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	661					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						GCTCCTATAGGGGGGAGATTT	0.701													G|||	207	0.0413339	0.0061	0.111	5008	,	,		13688	0.0149		0.0666	False		,,,				2504	0.0409				p.G661A		Atlas-SNP	.											.	CHPF2	52	.	0			c.G1982C						PASS	.	G	ALA/GLY	72,4294		1,70,2112	9.0	12.0	11.0		1982	3.0	0.2	7	dbSNP_107	11	694,7842		27,640,3601	yes	missense	CHPF2	NM_019015.1	60	28,710,5713	CC,CG,GG		8.1303,1.6491,5.9371	possibly-damaging	661/773	150935430	766,12136	2183	4268	6451	SO:0001583	missense	54480	exon4			CTATAGGGGGGAG	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.1982G>C	7.37:g.150935430G>C	ENSP00000035307:p.Gly661Ala	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	39	10	0.25641	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	37	CCDS34779.1	107	0.04899267399267399	6	0.012195121951219513	43	0.11878453038674033	10	0.017482517482517484	48	0.0633245382585752	G	3.215	-0.160799	0.06502	0.016491	0.081303	ENSG00000033100	ENST00000495645;ENST00000035307	T;T	0.24350	1.86;1.86	4.81	3.03	0.35002	.	0.177071	0.50627	N	0.000115	T	0.00109	0.0003	N	0.00347	-1.61	0.38178	D	0.939527	P;P	0.43024	0.798;0.759	B;B	0.43838	0.433;0.306	T	0.30208	-0.9986	10	0.07175	T	0.84	-25.0544	11.6931	0.51527	0.0:0.3371:0.6629:0.0	rs3748098	661;653	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	A	653;661	ENSP00000418914:G653A;ENSP00000035307:G661A	ENSP00000035307:G661A	G	+	2	0	CHPF2	150566363	1.000000	0.71417	0.185000	0.23176	0.116000	0.19942	1.235000	0.32671	0.654000	0.30846	-0.719000	0.03609	GGG	G|0.948;C|0.052	0.052	strong		0.701	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
SEMA7A	8482	hgsc.bcm.edu	37	15	74703022	74703022	+	Silent	SNP	G	G	A	rs2075592	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:74703022G>A	ENST00000261918.4	-	14	2492	c.1944C>T	c.(1942-1944)gcC>gcT	p.A648A	SEMA7A_ENST00000543145.2_Silent_p.A634A|SEMA7A_ENST00000542748.1_Silent_p.A483A	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	648					axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						AGAGGGAGGCGGCCAGGGCAC	0.687													G|||	910	0.181709	0.4002	0.036	5008	,	,		16063	0.1915		0.0467	False		,,,				2504	0.1186				p.A648A		Atlas-SNP	.											.	SEMA7A	58	.	0			c.C1944T						PASS	.	G	,,	1413,2981	431.6+/-343.0	229,955,1013	43.0	45.0	44.0		1902,1449,1944	-9.1	0.0	15	dbSNP_96	44	390,8196	120.6+/-179.8	13,364,3916	no	coding-synonymous,coding-synonymous,coding-synonymous	SEMA7A	NM_001146029.1,NM_001146030.1,NM_003612.3	,,	242,1319,4929	AA,AG,GG		4.5423,32.1575,13.8906	,,	634/653,483/502,648/667	74703022	1803,11177	2197	4293	6490	SO:0001819	synonymous_variant	8482	exon14			GGAGGCGGCCAGG	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"""Semaphorins"", ""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10741	protein-coding gene	gene with protein product	"""John Milton Hagen blood group"", ""H-Sema K1"""	607961	"""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A"", ""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"""	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1944C>T	15.37:g.74703022G>A		Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	111	78	0.702703	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Silent	SNP	ENST00000261918.4	37	CCDS10262.1																																																																																			G|0.857;A|0.143	0.143	strong		0.687	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612	
RP1L1	94137	hgsc.bcm.edu	37	8	10467576	10467576	+	Silent	SNP	T	T	C	rs4840499	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:10467576T>C	ENST00000382483.3	-	4	4255	c.4032A>G	c.(4030-4032)acA>acG	p.T1344T		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1360	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)		cttctccttctgtttctttag	0.483																																					p.T1344T		Atlas-SNP	.											.	RP1L1	453	.	0			c.A4032G						PASS	.						87.0	82.0	84.0					8																	10467576		1932	4125	6057	SO:0001819	synonymous_variant	94137	exon4			TCCTTCTGTTTCT	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.4032A>G	8.37:g.10467576T>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	224	87	0.388393	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			T|0.566;C|0.434	0.434	strong		0.483	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
OR52N4	390072	hgsc.bcm.edu	37	11	5776484	5776484	+	Nonsense_Mutation	SNP	A	A	T	rs4910844	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	187	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	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	
FBN2	2201	hgsc.bcm.edu	37	5	127597518	127597518	+	Silent	SNP	G	G	A	rs10070365	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:127597518G>A	ENST00000508053.1	-	70	9248	c.8274C>T	c.(8272-8274)tcC>tcT	p.S2758S	FBN2_ENST00000262464.4_Silent_p.S2758S			P35556	FBN2_HUMAN	fibrillin 2	2758					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ATGCTTCTGGGGACAGAGCAT	0.453													G|||	565	0.112819	0.1952	0.0865	5008	,	,		20024	0.0476		0.1243	False		,,,				2504	0.0757				p.S2758S		Atlas-SNP	.											.	FBN2	858	.	0			c.C8274T						PASS	.	G		764,3642	310.5+/-291.6	61,642,1500	233.0	198.0	210.0		8274	0.3	1.0	5	dbSNP_119	210	1038,7562	220.2+/-258.0	62,914,3324	no	coding-synonymous	FBN2	NM_001999.3		123,1556,4824	AA,AG,GG		12.0698,17.34,13.8551		2758/2913	127597518	1802,11204	2203	4300	6503	SO:0001819	synonymous_variant	2201	exon64			TTCTGGGGACAGA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.8274C>T	5.37:g.127597518G>A		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	185	93	0.502703	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			G|0.871;A|0.129	0.129	strong		0.453	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
ATE1	11101	hgsc.bcm.edu	37	10	123549691	123549691	+	Silent	SNP	T	T	G	rs35350755	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:123549691T>G	ENST00000224652.6	-	11	1456	c.1371A>C	c.(1369-1371)ccA>ccC	p.P457P	ATE1_ENST00000369040.3_Silent_p.P361P|ATE1_ENST00000369043.3_Silent_p.P457P|ATE1_ENST00000543447.1_Silent_p.P342P|ATE1_ENST00000540606.1_Silent_p.P450P|ATE1_ENST00000535655.1_Silent_p.P158P	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	457					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				TACCTGCTTCTGGGTCCTGGT	0.483													T|||	2512	0.501597	0.4879	0.4813	5008	,	,		20044	0.5387		0.4284	False		,,,				2504	0.5716				p.P457P		Atlas-SNP	.											.	ATE1	67	.	0			c.A1371C						PASS	.	T	,	2112,2294	576.7+/-384.3	511,1090,602	110.0	110.0	110.0		1371,1371	-8.7	0.8	10	dbSNP_126	110	3825,4775	539.9+/-383.7	856,2113,1331	no	coding-synonymous,coding-synonymous	ATE1	NM_001001976.1,NM_007041.2	,	1367,3203,1933	GG,GT,TT		44.4767,47.9346,45.6482	,	457/519,457/519	123549691	5937,7069	2203	4300	6503	SO:0001819	synonymous_variant	11101	exon11			TGCTTCTGGGTCC	AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.1371A>C	10.37:g.123549691T>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_001001976	O95261|Q5SQQ3|Q8WW04	Silent	SNP	ENST00000224652.6	37	CCDS31300.1																																																																																			T|0.544;G|0.456	0.456	strong		0.483	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907275	12907275	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:12907275G>C	ENST00000317869.6	-	2	1093	c.868C>G	c.(868-870)Cag>Gag	p.Q290E		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	290						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						GAGTCATCCTGGCCATTGGTG	0.443																																					p.Q290E		Atlas-SNP	.											HNRNPCL1,NS,neuroblastoma,0,1	HNRNPCL1	68	1	0			c.C868G						scavenged	.						125.0	135.0	132.0					1																	12907275		2203	4299	6502	SO:0001583	missense	343069	exon2			CATCCTGGCCATT	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.868C>G	1.37:g.12907275G>C	ENSP00000365370:p.Gln290Glu	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	144	2	0.0138889	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-4.135616	0.00001	.	.	ENSG00000179172	ENST00000317869	T	0.07216	3.21	1.09	-2.18	0.07037	.	0.420350	0.20880	N	0.084017	T	0.01353	0.0044	N	0.00583	-1.355	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.31971	-0.9924	10	0.02654	T	1	.	2.6632	0.05032	0.0:0.3331:0.2756:0.3913	.	290	O60812	HNRCL_HUMAN	E	290	ENSP00000365370:Q290E	ENSP00000365370:Q290E	Q	-	1	0	HNRNPCL1	12829862	0.994000	0.37717	0.016000	0.15963	0.063000	0.16089	-0.019000	0.12546	-1.068000	0.03156	-0.786000	0.03341	CAG	.	.	none		0.443	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
SBSN	374897	hgsc.bcm.edu	37	19	36015652	36015652	+	Silent	SNP	C	C	T	rs17705633	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36015652C>T	ENST00000452271.2	-	3	1738	c.1710G>A	c.(1708-1710)tcG>tcA	p.S570S	SBSN_ENST00000518157.1_Silent_p.S227S	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	570						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)			GCGTGTTGACCGAGGCCTGCA	0.597													C|||	500	0.0998403	0.0825	0.0951	5008	,	,		18374	0.0248		0.1581	False		,,,				2504	0.1442				p.S570S		Atlas-SNP	.											.	SBSN	58	.	0			c.G1710A						PASS	.	C	,,	458,3948	216.1+/-234.9	22,414,1767	131.0	106.0	115.0		1710,447,681	2.0	1.0	19	dbSNP_123	115	1478,7122	280.8+/-294.7	137,1204,2959	no	coding-synonymous,coding-synonymous,coding-synonymous	SBSN	NM_001166034.1,NM_001166035.1,NM_198538.3	,,	159,1618,4726	TT,TC,CC		17.186,10.3949,14.8854	,,	570/591,149/170,227/248	36015652	1936,11070	2203	4300	6503	SO:0001819	synonymous_variant	374897	exon3			GTTGACCGAGGCC	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.1710G>A	19.37:g.36015652C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_001166034	A8K5J0|E9PBV3	Silent	SNP	ENST00000452271.2	37	CCDS54253.1																																																																																			C|0.874;T|0.126	0.126	strong		0.597	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538	
EMC3	55831	hgsc.bcm.edu	37	3	10028294	10028294	+	Silent	SNP	G	G	A	rs11551739	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:10028294G>A	ENST00000245046.2	-	1	510	c.52C>T	c.(52-54)Cta>Tta	p.L18L	AC034193.5_ENST00000326237.3_RNA|EMC3_ENST00000429759.1_Silent_p.L18L	NM_018447.2	NP_060917.1	Q9P0I2	EMC3_HUMAN	ER membrane protein complex subunit 3	18						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											ACGATGGGTAGGACCACCCAG	0.537													G|||	182	0.0363419	0.0053	0.0476	5008	,	,		19680	0.0		0.1163	False		,,,				2504	0.0256				p.L18L		Atlas-SNP	.											.	EMC3	2	.	0			c.C52T						PASS	.	G		49,4357		1,47,2155	143.0	118.0	127.0		52	4.8	1.0	3	dbSNP_120	127	756,7844		33,690,3577	no	coding-synonymous	TMEM111	NM_018447.2		34,737,5732	AA,AG,GG		8.7907,1.1121,6.1895		18/262	10028294	805,12201	2203	4300	6503	SO:0001819	synonymous_variant	55831	exon1			TGGGTAGGACCAC	AF157321	CCDS2594.1	3p25.3	2012-05-23	2012-05-23	2012-05-23	ENSG00000125037	ENSG00000125037			23999	protein-coding gene	gene with protein product			"""transmembrane protein 111"""	TMEM111		19797678, 22119785	Standard	NM_018447		Approved		uc003bun.3	Q9P0I2	OTTHUMG00000128652	ENST00000245046.2:c.52C>T	3.37:g.10028294G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_018447	B2R4Z9|Q53GH8|Q6ZMC2	Silent	SNP	ENST00000245046.2	37	CCDS2594.1																																																																																			G|0.941;A|0.059	0.059	strong		0.537	EMC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250532.1	NM_018447	
MPDZ	8777	hgsc.bcm.edu	37	9	13176312	13176312	+	Silent	SNP	C	C	T	rs2274856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:13176312C>T	ENST00000319217.7	-	20	3001	c.2754G>A	c.(2752-2754)tcG>tcA	p.S918S	MPDZ_ENST00000447879.1_Silent_p.S918S|MPDZ_ENST00000536827.1_Silent_p.S918S|MPDZ_ENST00000541718.1_Silent_p.S918S|MPDZ_ENST00000381022.2_Silent_p.S918S|MPDZ_ENST00000381015.4_Silent_p.S918S|MPDZ_ENST00000546205.1_Silent_p.S918S	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	918					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)		TTATGTCCACCGAAGGTGTAT	0.388													C|||	1969	0.393171	0.5257	0.3012	5008	,	,		18249	0.495		0.2594	False		,,,				2504	0.3119				p.S918S		Atlas-SNP	.											.	MPDZ	324	.	0			c.G2754A						PASS	.	C		1657,2057		373,911,573	92.0	79.0	83.0		2754	-11.6	0.0	9	dbSNP_100	83	2132,6068		295,1542,2263	no	coding-synonymous	MPDZ	NM_003829.3		668,2453,2836	TT,TC,CC		26.0,44.615,31.8029		918/2042	13176312	3789,8125	1857	4100	5957	SO:0001819	synonymous_variant	8777	exon20			GTCCACCGAAGGT	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.2754G>A	9.37:g.13176312C>T		Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	256	138	0.539062	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				C|0.613;T|0.387	0.387	strong		0.388	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
MUC17	140453	hgsc.bcm.edu	37	7	100680370	100680370	+	Silent	SNP	C	C	T	rs201762013|rs10257974	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680370C>T	ENST00000306151.4	+	3	5737	c.5673C>T	c.(5671-5673)ccC>ccT	p.P1891P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1891	59 X approximate tandem repeats.|Ser-rich.				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)					CAACAACTCCCGCTGTCACCA	0.502													-|||	800	0.159744	0.2814	0.0879	5008	,	,		24145	0.0972		0.1193	False		,,,				2504	0.1524				p.P1891P		Atlas-SNP	.											.	MUC17	804	.	0			c.C5673T						PASS	.	T		1063,3333		193,677,1328	237.0	251.0	246.0		5673	-0.2	0.0	7	dbSNP_119	246	987,7613		56,875,3369	no	coding-synonymous	MUC17	NM_001040105.1		249,1552,4697	TT,TC,CC		11.4767,24.1811,15.7741		1891/4494	100680370	2050,10946	2198	4300	6498	SO:0001819	synonymous_variant	140453	exon3			AACTCCCGCTGTC	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.5673C>T	7.37:g.100680370C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	233	228	0.978541	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.861;T|0.139	0.139	strong		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
COL6A3	1293	hgsc.bcm.edu	37	2	238283605	238283605	+	Silent	SNP	G	G	A	rs12622093	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238283605G>A	ENST00000295550.4	-	8	3581	c.3129C>T	c.(3127-3129)ggC>ggT	p.G1043G	COL6A3_ENST00000392004.3_Silent_p.G837G|COL6A3_ENST00000392003.2_Silent_p.G636G|COL6A3_ENST00000472056.1_Silent_p.G436G|COL6A3_ENST00000353578.4_Silent_p.G837G|COL6A3_ENST00000347401.3_Silent_p.G842G|COL6A3_ENST00000346358.4_Silent_p.G843G|COL6A3_ENST00000409809.1_Silent_p.G837G	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1043	Nonhelical region.|VWFA 6. {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)		ACAGAGGGAAGCCGCTCCTGA	0.587													G|||	1081	0.215855	0.1082	0.2536	5008	,	,		19171	0.2698		0.2465	False		,,,				2504	0.2474				p.G1043G		Atlas-SNP	.											COL6A3_ENST00000392004,NS,carcinoma,0,2	COL6A3	608	2	0			c.C3129T						PASS	.	G	,,,,	568,3838	248.7+/-256.4	42,484,1677	46.0	49.0	48.0		3129,1908,2511,1308,2511	1.2	0.9	2	dbSNP_120	48	2008,6592	348.4+/-327.0	244,1520,2536	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	286,2004,4213	AA,AG,GG		23.3488,12.8915,19.8062	,,,,	1043/3178,636/1037,837/1238,436/2571,837/2972	238283605	2576,10430	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon8			AGGGAAGCCGCTC	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.3129C>T	2.37:g.238283605G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	27	0.36	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.795;A|0.205	0.205	strong		0.587	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
KRT75	9119	hgsc.bcm.edu	37	12	52827740	52827740	+	Missense_Mutation	SNP	G	G	C	rs2232386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52827740G>C	ENST00000252245.5	-	1	569	c.349C>G	c.(349-351)Ccc>Gcc	p.P117A		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	117	Gly-rich.|Head.		P -> A (in dbSNP:rs2232386).		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)		CCTCCAGGGGGACACACGGGG	0.612													G|||	647	0.129193	0.0726	0.2262	5008	,	,		15852	0.1548		0.1213	False		,,,				2504	0.1186				p.P117A		Atlas-SNP	.											.	KRT75	75	.	0			c.C349G						PASS	.	G	ALA/PRO	388,4018	195.3+/-220.0	18,352,1833	116.0	119.0	118.0		349	2.9	0.0	12	dbSNP_98	118	935,7665	204.9+/-247.5	54,827,3419	yes	missense	KRT75	NM_004693.2	27	72,1179,5252	CC,CG,GG		10.8721,8.8062,10.1722	possibly-damaging	117/552	52827740	1323,11683	2203	4300	6503	SO:0001583	missense	9119	exon1			CAGGGGGACACAC	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.349C>G	12.37:g.52827740G>C	ENSP00000252245:p.Pro117Ala	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	238	118	0.495798	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	286	0.13095238095238096	36	0.07317073170731707	65	0.17955801104972377	95	0.1660839160839161	90	0.11873350923482849	G	5.471	0.271891	0.10349	0.088062	0.108721	ENSG00000170454	ENST00000252245	T	0.74106	-0.81	5.74	2.87	0.33458	.	0.116168	0.38778	N	0.001573	T	0.00356	0.0011	M	0.61703	1.905	0.80722	P	0.0	P	0.41498	0.752	P	0.46208	0.507	T	0.14727	-1.0462	9	0.54805	T	0.06	.	7.8082	0.29215	0.1445:0.0:0.7251:0.1304	rs2232386;rs17716647;rs52833224;rs2232386	117	O95678	K2C75_HUMAN	A	117	ENSP00000252245:P117A	ENSP00000252245:P117A	P	-	1	0	KRT75	51114007	0.000000	0.05858	0.007000	0.13788	0.094000	0.18550	0.052000	0.14163	0.322000	0.23283	-0.152000	0.13540	CCC	G|0.888;C|0.112	0.112	strong		0.612	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
ZNF235	9310	hgsc.bcm.edu	37	19	44793278	44793278	+	Missense_Mutation	SNP	A	A	G	rs141976678	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44793278A>G	ENST00000291182.4	-	5	412	c.310T>C	c.(310-312)Tca>Cca	p.S104P	ZNF235_ENST00000589248.1_Intron|ZNF235_ENST00000589799.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	104					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(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				TGCCAGCATGAAAGCTCTCCC	0.418																																					p.S104P		Atlas-SNP	.											.	ZNF235	60	.	0			c.T310C						PASS	.	A	PRO/SER	3,4403	4.2+/-10.8	0,3,2200	56.0	58.0	57.0		310	0.9	0.6	19	dbSNP_134	57	8,8592	4.3+/-15.6	0,8,4292	yes	missense	ZNF235	NM_004234.4	74	0,11,6492	GG,GA,AA		0.093,0.0681,0.0846	benign	104/739	44793278	11,12995	2203	4300	6503	SO:0001583	missense	9310	exon5			AGCATGAAAGCTC	X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"""Zinc fingers, C2H2-type"", ""-"""	12866	protein-coding gene	gene with protein product		604749	"""zinc finger protein homologous to Zfp93 in mouse"""	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.310T>C	19.37:g.44793278A>G	ENSP00000291182:p.Ser104Pro	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Missense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.706086	0.30232	6.81E-4	9.3E-4	ENSG00000159917	ENST00000433015;ENST00000391957;ENST00000291182;ENST00000359844	T	0.05855	3.38	4.18	0.951	0.19579	.	0.487586	0.15465	N	0.260936	T	0.03695	0.0105	N	0.13003	0.285	0.20074	N	0.999938	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.42068	-0.9473	10	0.33940	T	0.23	.	7.7635	0.28965	0.7099:0.0:0.2901:0.0	.	100;104	Q14590-2;Q14590	.;ZN235_HUMAN	P	100;104;104;26	ENSP00000291182:S104P	ENSP00000291182:S104P	S	-	1	0	ZNF235	49485118	0.001000	0.12720	0.635000	0.29338	0.938000	0.57974	0.195000	0.17155	0.279000	0.22186	0.379000	0.24179	TCA	A|0.999;G|0.001	0.001	strong		0.418	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1		
KRT24	192666	hgsc.bcm.edu	37	17	38855721	38855721	+	Missense_Mutation	SNP	G	G	A	rs148215930		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38855721G>A	ENST00000264651.2	-	6	1392	c.1336C>T	c.(1336-1338)Cgc>Tgc	p.R446C		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	446	Coil 2.|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)				AGCAGGCGGCGGTAGGTCTCG	0.473													g|||	1	0.000199681	0.0008	0.0	5008	,	,		17677	0.0		0.0	False		,,,				2504	0.0				p.R446C	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											KRT24,NS,carcinoma,+1,1	KRT24	60	1	0			c.C1336T						scavenged	.	A	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	148.0	147.0	147.0		1336	3.6	1.0	17	dbSNP_134	147	0,8600	1.2+/-3.3	0,0,4300	yes	missense	KRT24	NM_019016.2	180	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging	446/526	38855721	2,13004	2203	4300	6503	SO:0001583	missense	192666	exon6			GGCGGCGGTAGGT		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.1336C>T	17.37:g.38855721G>A	ENSP00000264651:p.Arg446Cys	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	197	2	0.0101523	NM_019016	Q9NXG7	Missense_Mutation	SNP	ENST00000264651.2	37	CCDS11372.1	.	.	.	.	.	.	.	.	.	.	g	14.00	2.406008	0.42715	4.54E-4	0.0	ENSG00000167916	ENST00000264651	D	0.94828	-3.53	5.62	3.61	0.41365	Filament (1);Intermediate filament protein, conserved site (1);	.	.	.	.	D	0.89434	0.6714	L	0.49126	1.545	0.44595	D	0.997566	P	0.37276	0.589	B	0.30105	0.111	D	0.84520	0.0627	9	0.29301	T	0.29	.	8.3607	0.32357	0.135:0.0:0.7387:0.1263	.	446	Q2M2I5	K1C24_HUMAN	C	446	ENSP00000264651:R446C	ENSP00000264651:R446C	R	-	1	0	KRT24	36109247	0.999000	0.42202	0.999000	0.59377	0.889000	0.51656	0.807000	0.27140	0.723000	0.32274	-0.185000	0.12909	CGC	G|1.000;A|0.000	0.000	weak		0.473	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
BLVRA	644	hgsc.bcm.edu	37	7	43843423	43843423	+	Silent	SNP	G	G	A	rs1131372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:43843423G>A	ENST00000402924.1	+	8	772	c.609G>A	c.(607-609)gtG>gtA	p.V203V	BLVRA_ENST00000265523.4_Silent_p.V203V	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	203					heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)	p.V203V(1)		endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						AAATGACAGTGTGTCTGGAGA	0.468													G|||	450	0.0898562	0.053	0.1657	5008	,	,		20684	0.0804		0.1223	False		,,,				2504	0.0624				p.V203V		Atlas-SNP	.											BLVRA,NS,carcinoma,0,1	BLVRA	26	1	1	Substitution - coding silent(1)	stomach(1)	c.G609A						PASS	.	G		241,4165	140.4+/-175.9	8,225,1970	114.0	116.0	115.0		609	1.7	1.0	7	dbSNP_86	115	949,7651	207.7+/-249.4	52,845,3403	no	coding-synonymous	BLVRA	NM_000712.3		60,1070,5373	AA,AG,GG		11.0349,5.4698,9.1496		203/297	43843423	1190,11816	2203	4300	6503	SO:0001819	synonymous_variant	644	exon8			GACAGTGTGTCTG	BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR			Standard	NM_001253823		Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.609G>A	7.37:g.43843423G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	95	33	0.347368	NM_001253823	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	Silent	SNP	ENST00000402924.1	37	CCDS5472.1																																																																																			G|0.908;A|0.092	0.092	strong		0.468	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	NM_000712	
ZNF471	57573	hgsc.bcm.edu	37	19	57037103	57037103	+	Missense_Mutation	SNP	C	C	G	rs16987303	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57037103C>G	ENST00000308031.5	+	5	1800	c.1667C>G	c.(1666-1668)tCc>tGc	p.S556C	ZNF471_ENST00000593197.1_3'UTR|ZNF471_ENST00000591537.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	556			S -> C (in dbSNP:rs16987303). {ECO:0000269|PubMed:10718198}.		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		AGCCAAACTTCCAATCTTACT	0.408													C|||	414	0.0826677	0.0068	0.0994	5008	,	,		20133	0.004		0.2008	False		,,,				2504	0.1329				p.S556C	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.C1667G						PASS	.	C	CYS/SER	138,4268	99.4+/-138.0	5,128,2070	90.0	93.0	92.0		1667	3.9	0.0	19	dbSNP_123	92	1609,6991	299.5+/-304.5	158,1293,2849	no	missense	ZNF471	NM_020813.2	112	163,1421,4919	GG,GC,CC		18.7093,3.1321,13.4323	probably-damaging	556/627	57037103	1747,11259	2203	4300	6503	SO:0001583	missense	57573	exon5			AAACTTCCAATCT	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1667C>G	19.37:g.57037103C>G	ENSP00000309161:p.Ser556Cys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	198	0.09065934065934066	7	0.014227642276422764	43	0.11878453038674033	1	0.0017482517482517483	147	0.19393139841688653	C	13.46	2.244568	0.39697	0.031321	0.187093	ENSG00000196263	ENST00000308031	T	0.01725	4.67	3.9	3.9	0.45041	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.83312	2.635	0.37354	P	0.08905799999999997	P	0.47350	0.894	B	0.43916	0.436	T	0.33574	-0.9863	8	0.66056	D	0.02	.	10.2455	0.43339	0.1985:0.8015:0.0:0.0	rs16987303;rs52813441;rs16987303	556	Q9BX82	ZN471_HUMAN	C	556	ENSP00000309161:S556C	ENSP00000309161:S556C	S	+	2	0	ZNF471	61728915	0.000000	0.05858	0.009000	0.14445	0.932000	0.56968	-0.046000	0.11983	2.005000	0.58758	0.462000	0.41574	TCC	C|0.882;G|0.118	0.118	strong		0.408	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
PGR	5241	hgsc.bcm.edu	37	11	100922202	100922202	+	Silent	SNP	G	G	A	rs1042839	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	231	0	0		WXS	Illumina HiSeq	Phase_I	399	118	0.295739	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		
RFX4	5992	hgsc.bcm.edu	37	12	107141265	107141265	+	Missense_Mutation	SNP	G	G	A	rs61743416	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:107141265G>A	ENST00000392842.1	+	16	2098	c.1684G>A	c.(1684-1686)Gct>Act	p.A562T	RFX4_ENST00000357881.4_Missense_Mutation_p.A571T|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000229387.5_Missense_Mutation_p.A468T	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	562					cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						GACGACGGCTGCTGGGTCCCC	0.498													G|||	54	0.0107827	0.0023	0.0202	5008	,	,		19904	0.0099		0.0109	False		,,,				2504	0.0164				p.A571T		Atlas-SNP	.											.	RFX4	218	.	0			c.G1711A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	22,4384	29.9+/-59.1	0,22,2181	104.0	94.0	97.0		1711,1402,1684	5.4	1.0	12	dbSNP_129	97	101,8499	55.2+/-116.2	0,101,4199	yes	missense,missense,missense	RFX4	NM_001206691.1,NM_032491.5,NM_213594.2	58,58,58	0,123,6380	AA,AG,GG		1.1744,0.4993,0.9457	benign,benign,benign	571/745,468/642,562/736	107141265	123,12883	2203	4300	6503	SO:0001583	missense	5992	exon16			ACGGCTGCTGGGT	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1684G>A	12.37:g.107141265G>A	ENSP00000376585:p.Ala562Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Missense_Mutation	SNP	ENST00000392842.1	37	CCDS9106.1	24	0.01098901098901099	2	0.0040650406504065045	10	0.027624309392265192	2	0.0034965034965034965	10	0.013192612137203167	G	20.7	4.034562	0.75617	0.004993	0.011744	ENSG00000111783	ENST00000392842;ENST00000357881;ENST00000229387	T;T;T	0.64618	-0.1;-0.11;0.89	5.45	5.45	0.79879	.	0.101606	0.64402	D	0.000002	T	0.26557	0.0649	N	0.14661	0.345	0.58432	D	0.999996	P;P;P	0.41313	0.634;0.745;0.487	B;B;B	0.40444	0.298;0.329;0.124	T	0.45789	-0.9237	10	0.45353	T	0.12	-13.2519	19.3053	0.94158	0.0:0.0:1.0:0.0	rs61743416	468;571;562	B2RDW4;Q33E94-2;Q33E94	.;.;RFX4_HUMAN	T	562;571;468	ENSP00000376585:A562T;ENSP00000350552:A571T;ENSP00000229387:A468T	ENSP00000229387:A468T	A	+	1	0	RFX4	105665395	1.000000	0.71417	0.952000	0.39060	0.981000	0.71138	9.098000	0.94202	2.562000	0.86427	0.655000	0.94253	GCT	G|0.990;A|0.010	0.010	strong		0.498	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
DNPEP	23549	hgsc.bcm.edu	37	2	220251685	220251685	+	Missense_Mutation	SNP	T	T	G	rs11539909	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220251685T>G	ENST00000273075.4	-	3	368	c.148A>C	c.(148-150)Aac>Cac	p.N50H	AC053503.4_ENST00000420563.1_RNA|DNPEP_ENST00000373972.1_Intron|DNPEP_ENST00000523282.1_Missense_Mutation_p.N58H	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	40					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAAGGCGGTTGCGGCATTCA	0.597													T|||	61	0.0121805	0.0008	0.0058	5008	,	,		18233	0.0		0.0338	False		,,,				2504	0.0225				p.N50H		Atlas-SNP	.											.	DNPEP	40	.	0			c.A148C						PASS	.	T	HIS/ASN	22,3906		0,22,1942	81.0	83.0	82.0		148	2.5	1.0	2	dbSNP_120	82	243,8037		6,231,3903	yes	missense	DNPEP	NM_012100.2	68	6,253,5845	GG,GT,TT		2.9348,0.5601,2.1707	benign	50/486	220251685	265,11943	1964	4140	6104	SO:0001583	missense	23549	exon3			GGCGGTTGCGGCA		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.148A>C	2.37:g.220251685T>G	ENSP00000273075:p.Asn50His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	72	57	0.791667	NM_012100	Q9BW44|Q9NUV5	Missense_Mutation	SNP	ENST00000273075.4	37	CCDS42823.1	34	0.015567765567765568	0	0.0	3	0.008287292817679558	0	0.0	31	0.040897097625329816	T	9.734	1.163043	0.21538	0.005601	0.029348	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000523282;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000519905	.	.	.	5.07	2.45	0.29901	.	0.631746	0.17163	N	0.184599	T	0.14442	0.0349	L	0.55481	1.735	0.09310	N	1	B;P;B	0.37122	0.355;0.583;0.355	B;B;B	0.43155	0.297;0.41;0.201	T	0.14531	-1.0469	9	0.62326	D	0.03	-9.2171	11.5346	0.50631	0.0:0.0:0.2536:0.7464	rs11539909;rs11539909	58;50;50	E7ETB3;B7Z822;Q53SB6	.;.;.	H	50;50;58;58;36;50;50;36	.	ENSP00000273075:N50H	N	-	1	0	DNPEP	219959929	0.817000	0.29147	0.998000	0.56505	0.058000	0.15608	0.916000	0.28651	1.907000	0.55213	0.459000	0.35465	AAC	T|0.980;G|0.020	0.020	strong		0.597	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100	
CDKL3	51265	hgsc.bcm.edu	37	5	133655067	133655067	+	Silent	SNP	C	C	T	rs373913998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:133655067C>T	ENST00000265334.4	-	6	892	c.774G>A	c.(772-774)ttG>ttA	p.L258L	CDKL3_ENST00000435240.2_5'UTR|CDKL3_ENST00000523832.1_Silent_p.L258L|CDKL3_ENST00000521755.1_Intron|CDKL3_ENST00000609383.1_Intron|CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000435211.1_Silent_p.L258L|CDKL3_ENST00000523054.1_Silent_p.L69L|CDKL3_ENST00000536186.1_Intron|CDKL3_ENST00000522501.1_5'UTR|CDKL3_ENST00000609654.1_Silent_p.L69L|CDKL3_ENST00000521118.1_Silent_p.L258L	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	258	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATCTGCCAACAATCCATTAA	0.428													C|||	3	0.000599042	0.0	0.0014	5008	,	,		15912	0.0		0.002	False		,,,				2504	0.0				p.L258L		Atlas-SNP	.											.	CDKL3	76	.	0			c.G774A						PASS	.	C	,	0,3060		0,0,1530	87.0	84.0	85.0		774,774	1.5	1.0	5		85	13,6839		0,13,3413	no	coding-synonymous,coding-synonymous	CDKL3	NM_001113575.1,NM_016508.3	,	0,13,4943	TT,TC,CC		0.1897,0.0,0.1312	,	258/593,258/456	133655067	13,9899	1530	3426	4956	SO:0001819	synonymous_variant	51265	exon6			TGCCAACAATCCA	AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	2.7.11.22	"""Cyclin-dependent kinases"""	15483	protein-coding gene	gene with protein product	"""serine-threonine protein kinase NKIAMRE"""	608459				10463609	Standard	NM_016508		Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000265334.4:c.774G>A	5.37:g.133655067C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_001113575	D3DQA0|D3DQA1|Q9P114	Silent	SNP	ENST00000265334.4	37	CCDS47264.1																																																																																			.	.	weak		0.428	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377697.1	NM_001113575	
ZMYM1	79830	hgsc.bcm.edu	37	1	35570214	35570214	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:35570214C>T	ENST00000373330.1	+	7	825	c.651C>T	c.(649-651)tgC>tgT	p.C217C	ZMYM1_ENST00000373329.1_3'UTR|ZMYM1_ENST00000359858.4_Silent_p.C217C			Q5SVZ6	ZMYM1_HUMAN	zinc finger, MYM-type 1	217						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(8)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTAATGCCTGCCTTTCAAAGT	0.353																																					p.C217C		Atlas-SNP	.											ZMYM1,NS,carcinoma,+1,1	ZMYM1	86	1	0			c.C651T						scavenged	.						82.0	76.0	78.0					1																	35570214		2043	4234	6277	SO:0001819	synonymous_variant	79830	exon6			TGCCTGCCTTTCA	AK096206	CCDS41302.1	1p34.3	2008-05-02	2005-09-12		ENSG00000197056	ENSG00000197056		"""Zinc fingers, MYM type"""	26253	protein-coding gene	gene with protein product			"""zinc finger, MYM domain containing 1"""			12477932	Standard	XM_005271216		Approved	FLJ23151, MYM	uc001bym.3	Q5SVZ6	OTTHUMG00000004374	ENST00000373330.1:c.651C>T	1.37:g.35570214C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	126	3	0.0238095	NM_024772	D3DPR7|Q7Z3Q4	Silent	SNP	ENST00000373330.1	37	CCDS41302.1																																																																																			.	.	none		0.353	ZMYM1-001	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012705.1	NM_024772	
SPATA13	221178	hgsc.bcm.edu	37	13	24868919	24868919	+	Silent	SNP	T	T	C	rs35793500	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:24868919T>C	ENST00000382095.4	+	9	1655	c.1248T>C	c.(1246-1248)aaT>aaC	p.N416N	SPATA13_ENST00000382108.3_Silent_p.N1041N|SPATA13_ENST00000424834.2_Silent_p.N1041N|SPATA13_ENST00000343003.6_Silent_p.N360N|RP11-307N16.6_ENST00000382141.4_Silent_p.N919N|SPATA13_ENST00000399949.2_Silent_p.N338N|SPATA13_ENST00000409126.1_Silent_p.N276N	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	416	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)		CCATGAAGAATGTGGCCTGTC	0.488													T|||	145	0.0289537	0.0416	0.0548	5008	,	,		19603	0.001		0.0427	False		,,,				2504	0.0082				p.N1041N		Atlas-SNP	.											.	SPATA13	92	.	0			c.T3123C						PASS	.	T	,	138,4268	98.0+/-136.7	3,132,2068	142.0	119.0	127.0		3123,1248	-8.1	0.8	13	dbSNP_126	127	353,8247	119.5+/-178.9	5,343,3952	no	coding-synonymous,coding-synonymous	SPATA13	NM_001166271.1,NM_153023.2	,	8,475,6020	CC,CT,TT		4.1047,3.1321,3.7752	,	1041/1278,416/653	24868919	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	221178	exon10			GAAGAATGTGGCC	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.1248T>C	13.37:g.24868919T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	43	0.398148	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	37	CCDS9305.1	84	0.038461538461538464	18	0.036585365853658534	24	0.06629834254143646	1	0.0017482517482517483	41	0.05408970976253298	T	8.097	0.775766	0.16051	0.031321	0.041047	ENSG00000182957	ENST00000424834	.	.	.	5.42	-8.05	0.01106	.	.	.	.	.	T	0.06462	0.0166	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50575	-0.8812	4	.	.	.	.	9.7411	0.40418	0.0:0.3084:0.0888:0.6028	rs35793500	.	.	.	R	1079	.	.	C	+	1	0	SPATA13	23766919	0.001000	0.12720	0.818000	0.32626	0.668000	0.39293	-1.799000	0.01746	-1.650000	0.01506	-0.366000	0.07423	TGT	T|0.961;C|0.039	0.039	strong		0.488	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
COL4A1	1282	hgsc.bcm.edu	37	13	110850842	110850842	+	Silent	SNP	A	A	G	rs995224	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:110850842A>G	ENST00000375820.4	-	21	1378	c.1257T>C	c.(1255-1257)ccT>ccC	p.P419P	COL4A1_ENST00000543140.1_Silent_p.P419P	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	419	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CAGGGGGCCCAGGGGAACCAG	0.592													a|||	1034	0.20647	0.2073	0.3732	5008	,	,		16322	0.0546		0.2664	False		,,,				2504	0.182				p.P419P		Atlas-SNP	.											.	COL4A1	372	.	0			c.T1257C						PASS	.			950,3456	326.9+/-299.8	107,736,1360	45.0	53.0	50.0		1257	-6.4	0.0	13	dbSNP_86	50	2334,6266	360.6+/-332.0	332,1670,2298	no	coding-synonymous	COL4A1	NM_001845.4		439,2406,3658	GG,GA,AA		27.1395,21.5615,25.2499		419/1670	110850842	3284,9722	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon21			GGGCCCAGGGGAA	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.1257T>C	13.37:g.110850842A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	43	0.413462	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			T|0.000;G|0.240;C|0.000;A|0.760	0.240	strong		0.592	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
EPS15	2060	hgsc.bcm.edu	37	1	51826921	51826921	+	Missense_Mutation	SNP	T	T	C	rs17567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:51826921T>C	ENST00000371733.3	-	24	2562	c.2466A>G	c.(2464-2466)atA>atG	p.I822M	EPS15_ENST00000396122.4_Missense_Mutation_p.I499M|EPS15_ENST00000371730.2_Missense_Mutation_p.I688M	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	822	15 X 3 AA repeats of D-P-F.|Pro-rich.		I -> M (in dbSNP:rs17567). {ECO:0000269|PubMed:8183552}.		cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						GATCACAAAATATTTCAGGAT	0.408			T	MLL	ALL								C|||	1169	0.233427	0.5673	0.1643	5008	,	,		18708	0.0119		0.2038	False		,,,				2504	0.09				p.I822M		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.	EPS15	72	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A2466G						PASS	.	C	MET/ILE,MET/ILE	2266,2140	579.9+/-385.0	583,1100,520	160.0	153.0	155.0		1524,2466	5.8	1.0	1	dbSNP_63	155	1982,6618	723.4+/-406.5	228,1526,2546	yes	missense,missense	EPS15	NM_001159969.1,NM_001981.2	10,10	811,2626,3066	CC,CT,TT		23.0465,48.5701,32.6618	benign,benign	508/583,822/897	51826921	4248,8758	2203	4300	6503	SO:0001583	missense	2060	exon24			ACAAAATATTTCA	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"""EF-hand domain containing"""	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2466A>G	1.37:g.51826921T>C	ENSP00000360798:p.Ile822Met	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	129	89	0.689922	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Missense_Mutation	SNP	ENST00000371733.3	37	CCDS557.1	512	0.23443223443223443	284	0.5772357723577236	57	0.1574585635359116	11	0.019230769230769232	160	0.21108179419525067	C	11.41	1.631297	0.28978	0.514299	0.230465	ENSG00000085832	ENST00000371730;ENST00000371733;ENST00000396122	T;T;T	0.42131	0.98;0.98;0.98	5.85	5.85	0.93711	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.42189	-0.9466	8	0.32370	T	0.25	.	8.8043	0.34927	0.0:0.8244:0.0:0.1756	rs17567;rs12753160;rs17846526;rs17859599;rs52820243;rs58525844;rs17567	688;822;508	B1AUU8;P42566;P42566-2	.;EPS15_HUMAN;.	M	688;822;499	ENSP00000360795:I688M;ENSP00000360798:I822M;ENSP00000379428:I499M	ENSP00000360795:I688M	I	-	3	3	EPS15	51599509	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	0.672000	0.25187	1.492000	0.48499	-0.186000	0.12905	ATA	T|0.702;C|0.298	0.298	strong		0.408	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
LAD1	3898	hgsc.bcm.edu	37	1	201355943	201355943	+	Silent	SNP	C	C	T	rs2799677	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201355943C>T	ENST00000391967.2	-	3	847	c.546G>A	c.(544-546)aaG>aaA	p.K182K	LAD1_ENST00000367313.3_Silent_p.K196K	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	182						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						GCATGGAGGACTTCTCCAAGA	0.562													T|||	2592	0.517572	0.7474	0.3775	5008	,	,		14011	0.5179		0.4622	False		,,,				2504	0.363				p.K182K		Atlas-SNP	.											.	LAD1	42	.	0			c.G546A						PASS	.	T		3042,1364	446.3+/-348.0	1054,934,215	72.0	80.0	77.0		546	-1.2	0.0	1	dbSNP_100	77	4199,4401	573.6+/-389.9	1000,2199,1101	no	coding-synonymous	LAD1	NM_005558.3		2054,3133,1316	TT,TC,CC		48.8256,30.9578,44.3257		182/518	201355943	7241,5765	2203	4300	6503	SO:0001819	synonymous_variant	3898	exon3			GGAGGACTTCTCC	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.546G>A	1.37:g.201355943C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	237	70	0.295359	NM_005558	O95614|Q96GD8	Silent	SNP	ENST00000391967.2	37	CCDS1410.1																																																																																			C|0.459;T|0.541	0.541	strong		0.562	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
FAM135B	51059	hgsc.bcm.edu	37	8	139263158	139263158	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:139263158G>T	ENST00000395297.1	-	6	638	c.468C>A	c.(466-468)ttC>ttA	p.F156L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	156										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GGAAATAGTCGAACATGACCG	0.597										HNSCC(54;0.14)																											p.F156L		Atlas-SNP	.											.	FAM135B	423	.	0			c.C468A						PASS	.						128.0	140.0	136.0					8																	139263158		2096	4217	6313	SO:0001583	missense	51059	exon6			ATAGTCGAACATG	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.468C>A	8.37:g.139263158G>T	ENSP00000378710:p.Phe156Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	G	22.8	4.340691	0.81911	.	.	ENSG00000147724	ENST00000395297	T	0.72282	-0.64	5.47	-3.38	0.04883	.	0.000000	0.85682	D	0.000000	D	0.82449	0.5039	M	0.84585	2.705	0.44652	D	0.99763	D	0.89917	1.0	D	0.91635	0.999	D	0.83531	0.0091	10	0.87932	D	0	-21.2002	14.2536	0.66035	0.5756:0.0:0.4243:0.0	.	156	Q49AJ0	F135B_HUMAN	L	156	ENSP00000378710:F156L	ENSP00000276737:F156L	F	-	3	2	FAM135B	139332340	0.004000	0.15560	0.973000	0.42090	0.969000	0.65631	-0.976000	0.03786	-0.602000	0.05775	-0.254000	0.11334	TTC	.	.	none		0.597	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
BTBD11	121551	hgsc.bcm.edu	37	12	108011971	108011971	+	Silent	SNP	G	G	A	rs56296886	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:108011971G>A	ENST00000280758.5	+	10	2796	c.2268G>A	c.(2266-2268)aaG>aaA	p.K756K	BTBD11_ENST00000357167.4_Silent_p.K293K|BTBD11_ENST00000490090.2_Silent_p.K756K|RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000420571.2_Intron	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	756						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						AGCCAGAGAAGGAGAAGAGTG	0.597													G|||	9	0.00179712	0.0015	0.0043	5008	,	,		20060	0.0		0.003	False		,,,				2504	0.001				p.K756K		Atlas-SNP	.											.	BTBD11	122	.	0			c.G2268A						PASS	.	G	,	6,4400	11.4+/-27.6	0,6,2197	62.0	65.0	64.0		879,2268	4.7	1.0	12	dbSNP_129	64	70,8530	41.7+/-99.0	0,70,4230	no	coding-synonymous,coding-synonymous	BTBD11	NM_001017523.1,NM_001018072.1	,	0,76,6427	AA,AG,GG		0.814,0.1362,0.5843	,	293/642,756/1105	108011971	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	121551	exon10			AGAGAAGGAGAAG	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.2268G>A	12.37:g.108011971G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			G|0.996;A|0.004	0.004	strong		0.597	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
ZNF835	90485	hgsc.bcm.edu	37	19	57176482	57176482	+	Missense_Mutation	SNP	C	C	T	rs12462469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57176482C>T	ENST00000537055.2	-	2	316	c.85G>A	c.(85-87)Gaa>Aaa	p.E29K		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	29			E -> K (in dbSNP:rs12462469). {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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						TCCTGGTTTTCCTGCAGGTCC	0.607													.|||	2065	0.41234	0.4531	0.379	5008	,	,		15832	0.4702		0.3131	False		,,,				2504	0.4233				p.E29K		Atlas-SNP	.											.	ZNF835	106	.	0			c.G85A						PASS	.	C	LYS/GLU	1677,2285		367,943,671	75.0	79.0	78.0		85	1.1	0.0	19	dbSNP_120	78	2491,5819		372,1747,2036	yes	missense	ZNF835	NM_001005850.2	56	739,2690,2707	TT,TC,CC		29.9759,42.3271,33.9635	benign	29/538	57176482	4168,8104	1981	4155	6136	SO:0001583	missense	90485	exon2			GGTTTTCCTGCAG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.85G>A	19.37:g.57176482C>T	ENSP00000444747:p.Glu29Lys	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	865	0.39606227106227104	232	0.4715447154471545	128	0.35359116022099446	264	0.46153846153846156	241	0.3179419525065963	C	8.447	0.852126	0.17034	0.423271	0.299759	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.06142	3.34	2.19	1.09	0.20402	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.26318	0.146	B	0.24974	0.057	T	0.38735	-0.9647	8	0.06236	T	0.91	.	6.5636	0.22499	0.0:0.6963:0.3037:0.0	rs12462469	51	Q9Y2P0	ZN835_HUMAN	K	51;29	ENSP00000444747:E29K	ENSP00000341756:E51K	E	-	1	0	ZNF835	61868294	0.000000	0.05858	0.007000	0.13788	0.062000	0.15995	0.145000	0.16157	0.467000	0.27218	0.491000	0.48974	GAA	C|0.621;T|0.379	0.379	strong		0.607	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
WDR20	91833	hgsc.bcm.edu	37	14	102675350	102675350	+	Silent	SNP	G	G	C	rs6575900	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102675350G>C	ENST00000342702.3	+	3	874	c.843G>C	c.(841-843)ggG>ggC	p.G281G	WDR20_ENST00000335263.5_Silent_p.G281G|WDR20_ENST00000545563.1_Silent_p.G108G|WDR20_ENST00000424963.2_Silent_p.G157G|WDR20_ENST00000499851.2_Silent_p.G24G|WDR20_ENST00000322340.5_Intron|WDR20_ENST00000299135.6_3'UTR|WDR20_ENST00000556807.1_Silent_p.G220G|WDR20_ENST00000556511.2_Silent_p.G220G|WDR20_ENST00000454394.2_Silent_p.G312G	NM_001242418.1|NM_144574.3	NP_001229347.1|NP_653175.2	Q8TBZ3	WDR20_HUMAN	WD repeat domain 20	281										breast(1)|large_intestine(2)|lung(4)|prostate(1)	8						TGACAGGTGGGGAGGACGACT	0.552													C|||	1722	0.34385	0.761	0.2133	5008	,	,		18621	0.0724		0.2078	False		,,,				2504	0.2924				p.G312G		Atlas-SNP	.											.	WDR20	35	.	0			c.G936C						PASS	.	C	,,,,,,,	3010,1396	460.2+/-352.5	1036,938,229	89.0	66.0	74.0		,,660,936,879,843,843,660	-11.7	0.0	14	dbSNP_116	74	1761,6839	734.8+/-406.9	171,1419,2710	no	utr-3,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR20	NM_001242414.1,NM_001242415.1,NM_001242416.1,NM_001242417.1,NM_001242418.1,NM_144574.3,NM_181291.2,NM_181308.2	,,,,,,,	1207,2357,2939	CC,CG,GG		20.4767,31.6841,36.6831	,,,,,,,	,,220/521,312/601,293/582,281/570,281/582,220/509	102675350	4771,8235	2203	4300	6503	SO:0001819	synonymous_variant	91833	exon4			AGGTGGGGAGGAC	BC028387	CCDS9968.1, CCDS9969.1, CCDS9970.1, CCDS55942.1, CCDS55943.1, CCDS55944.1, CCDS55945.1	14q32.31	2013-01-09				ENSG00000140153		"""WD repeat domain containing"""	19667	protein-coding gene	gene with protein product							Standard	NM_181291		Approved	DMR, MGC33177, FLJ33659	uc010txu.2	Q8TBZ3		ENST00000342702.3:c.843G>C	14.37:g.102675350G>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	167	59	0.353293	NM_001242417	B4DN18|E7EUY8|F8W9S4|G3V2F8|G3V5R0|H0YJJ1|Q86TU2|Q8NCN7|Q8WXX2|Q9UF86	Silent	SNP	ENST00000342702.3	37	CCDS9969.1	647	0.29624542124542125	372	0.7560975609756098	92	0.2541436464088398	40	0.06993006993006994	143	0.18865435356200527	C	1.987	-0.432810	0.04669	0.683159	0.204767	ENSG00000140153	ENST00000556511	.	.	.	5.83	-11.7	0.00046	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.11470	-1.0586	4	.	.	.	.	11.658	0.51330	0.2768:0.5269:0.1962:0.0	rs6575900;rs6575900	.	.	.	R	212	.	.	G	+	1	0	WDR20	101745103	0.000000	0.05858	0.017000	0.16124	0.929000	0.56500	-2.301000	0.01137	-2.971000	0.00286	-2.098000	0.00363	GGA	G|0.664;C|0.336	0.336	strong		0.552	WDR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414963.1	NM_181291	
XIRP2	129446	hgsc.bcm.edu	37	2	168041152	168041152	+	Splice_Site	SNP	T	T	C	rs16853169	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168041152T>C	ENST00000409728.1	+	4	750		c.e4+2		XIRP2_ENST00000409605.1_5'Flank|XIRP2_ENST00000409273.1_5'Flank|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Splice_Site|XIRP2_ENST00000295237.9_Intron|XIRP2_ENST00000409195.1_Intron	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2						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						cttatatttgtaaggttctcg	0.433													T|||	514	0.102636	0.1286	0.0735	5008	,	,		19459	0.0665		0.0825	False		,,,				2504	0.1462				.		Atlas-SNP	.											.	XIRP2	914	.	0			c.661+2T>C						PASS	.																																			SO:0001630	splice_region_variant	129446	exon4			TATTTGTAAGGTT	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	ENST00000409728.1:c.661+2T>C	2.37:g.168041152T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	187	91	0.486631	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Splice_Site	SNP	ENST00000409728.1	37	CCDS56143.1																																																																																			T|0.904;C|0.096	0.096	strong		0.433	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	Intron
OR5P3	120066	hgsc.bcm.edu	37	11	7847472	7847472	+	Silent	SNP	C	C	T	rs1482793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:7847472C>T	ENST00000328375.1	-	1	47	c.48G>A	c.(46-48)ggG>ggA	p.G16G	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153445.1	NP_703146.1	Q8WZ94	OR5P3_HUMAN	olfactory receptor, family 5, subfamily P, 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)			autonomic_ganglia(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	15				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCTCAGATAACCCCAAAAGAG	0.348													C|||	2223	0.44389	0.0726	0.5937	5008	,	,		19327	0.4762		0.6292	False		,,,				2504	0.6155				p.G16G		Atlas-SNP	.											.	OR5P3	44	.	0			c.G48A						PASS	.	C		723,3615		122,479,1568	44.0	45.0	45.0		48	-4.9	0.0	11	dbSNP_88	45	5273,3283		1672,1929,677	no	coding-synonymous	OR5P3	NM_153445.1		1794,2408,2245	TT,TC,CC		38.3707,16.6667,46.5022		16/312	7847472	5996,6898	2169	4278	6447	SO:0001819	synonymous_variant	120066	exon1			AGATAACCCCAAA	AF158377	CCDS7783.1	11p15.4	2012-08-09			ENSG00000182334	ENSG00000182334		"""GPCR / Class A : Olfactory receptors"""	14784	protein-coding gene	gene with protein product							Standard	NM_153445		Approved	JCG1	uc010rbg.2	Q8WZ94	OTTHUMG00000165669	ENST00000328375.1:c.48G>A	11.37:g.7847472C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_153445	Q6IFE1|Q8NGM2	Silent	SNP	ENST00000328375.1	37	CCDS7783.1																																																																																			C|0.504;T|0.496	0.496	strong		0.348	OR5P3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385697.1	NM_153445	
DBX2	440097	hgsc.bcm.edu	37	12	45444426	45444426	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:45444426G>A	ENST00000332700.6	-	1	456	c.285C>T	c.(283-285)gcC>gcT	p.A95A	RP11-478B9.1_ENST00000548424.1_RNA	NM_001004329.2	NP_001004329.2	Q6ZNG2	DBX2_HUMAN	developing brain homeobox 2	95					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(3)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	22	Lung SC(27;0.192)	Lung NSC(34;0.142)		GBM - Glioblastoma multiforme(48;0.0515)		AGGGCGCCCCGGCGGGGCTAA	0.721																																					p.A95A		Atlas-SNP	.											.	DBX2	45	.	0			c.C285T						PASS	.						4.0	5.0	5.0					12																	45444426		1972	3943	5915	SO:0001819	synonymous_variant	440097	exon1			CGCCCCGGCGGGG		CCDS31781.1	12q12	2011-06-20				ENSG00000185610		"""Homeoboxes / ANTP class : NKL subclass"""	33186	protein-coding gene	gene with protein product						11239429	Standard	NM_001004329		Approved	FLJ16139	uc001rok.1	Q6ZNG2	OTTHUMG00000169559	ENST00000332700.6:c.285C>T	12.37:g.45444426G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	68	21	0.308824	NM_001004329		Silent	SNP	ENST00000332700.6	37	CCDS31781.1																																																																																			.	.	none		0.721	DBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404810.1	NM_001004329	
CPSF4	10898	hgsc.bcm.edu	37	7	99047978	99047978	+	Silent	SNP	T	T	C	rs883403	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99047978T>C	ENST00000292476.5	+	4	397	c.387T>C	c.(385-387)cgT>cgC	p.R129R	CPSF4_ENST00000441580.1_Silent_p.R76R|CPSF4_ENST00000451876.1_Intron|ATP5J2_ENST00000466753.1_Intron|ATP5J2-PTCD1_ENST00000413834.1_Intron|ATP5J2-PTCD1_ENST00000437572.1_Intron|PTCD1_ENST00000555673.1_Intron|CPSF4_ENST00000436336.2_Silent_p.R129R|CPSF4_ENST00000471455.1_3'UTR			O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4, 30kDa	129					modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA processing (GO:0006397)|viral life cycle (GO:0019058)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(5)	14	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GGTATGACCGTGGCTTCTGCA	0.617													C|||	2277	0.454673	0.9054	0.2824	5008	,	,		19251	0.3403		0.165	False		,,,				2504	0.3834				p.R129R		Atlas-SNP	.											.	CPSF4	24	.	0			c.T387C						PASS	.	C	,,	3396,1010	375.1+/-321.5	1304,788,111	69.0	59.0	62.0		387,,387	-11.7	0.3	7	dbSNP_86	62	1238,7362	761.7+/-407.6	102,1034,3164	no	coding-synonymous,intron,coding-synonymous	CPSF4,ATP5J2-PTCD1	NM_001081559.1,NM_001198879.1,NM_006693.2	,,	1406,1822,3275	CC,CT,TT		14.3953,22.9233,35.6297	,,	129/245,,129/270	99047978	4634,8372	2203	4300	6503	SO:0001819	synonymous_variant	10898	exon4			TGACCGTGGCTTC		CCDS5664.1, CCDS47652.1	7q22	2007-10-18	2002-08-29		ENSG00000160917	ENSG00000160917			2327	protein-coding gene	gene with protein product		603052	"""cleavage and polyadenylation specific factor 4, 30kD subunit"""			9651582, 9224719	Standard	NM_006693		Approved	NAR, CPSF30	uc003uqj.3	O95639	OTTHUMG00000154599	ENST00000292476.5:c.387T>C	7.37:g.99047978T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	160	47	0.29375	NM_001081559	D6W5S8|Q6FGE6|Q86TF8|Q9BTW6	Silent	SNP	ENST00000292476.5	37	CCDS5664.1	858	0.39285714285714285	428	0.8699186991869918	112	0.30939226519337015	192	0.3356643356643357	126	0.1662269129287599	C	9.966	1.224022	0.22457	0.770767	0.143953	ENSG00000160917	ENST00000440514	.	.	.	5.93	-11.7	0.00046	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999811	.	.	.	.	.	.	T	0.23190	-1.0195	3	.	.	.	-8.6058	5.2076	0.15299	0.1613:0.3878:0.0609:0.39	rs883403;rs11539768;rs17854666;rs57853370;rs883403	.	.	.	R	11	.	.	W	+	1	0	CPSF4	98885914	0.000000	0.05858	0.280000	0.24747	0.974000	0.67602	-1.672000	0.01952	-2.308000	0.00652	-0.733000	0.03571	TGG	T|0.639;C|0.361	0.361	strong		0.617	CPSF4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336254.1		
TMEM259	91304	hgsc.bcm.edu	37	19	1014377	1014377	+	Silent	SNP	A	A	G	rs1058506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	125	53	0.424	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	
OR8H2	390151	hgsc.bcm.edu	37	11	55873096	55873096	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55873096A>G	ENST00000313503.1	+	1	578	c.578A>G	c.(577-579)tAc>tGc	p.Y193C		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	193						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)|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)					ACTGATACATACAACACCGAA	0.408										HNSCC(53;0.14)																											p.Y193C		Atlas-SNP	.											OR8H2,larynx,carcinoma,+1,1	OR8H2	117	1	0			c.A578G						scavenged	.						239.0	221.0	227.0					11																	55873096		2201	4296	6497	SO:0001583	missense	390151	exon1			ATACATACAACAC	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.578A>G	11.37:g.55873096A>G	ENSP00000323982:p.Tyr193Cys	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	243	3	0.0123457	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	a	13.03	2.116618	0.37339	.	.	ENSG00000181767	ENST00000313503	T	0.00216	8.53	3.58	-0.829	0.10796	GPCR, rhodopsin-like superfamily (1);	0.517808	0.17993	N	0.155151	T	0.00300	0.0009	M	0.74389	2.26	0.09310	N	1	P	0.46859	0.885	P	0.54544	0.755	T	0.48479	-0.9032	10	0.72032	D	0.01	.	2.0379	0.03544	0.5777:0.1304:0.1648:0.1271	.	193	Q8N162	OR8H2_HUMAN	C	193	ENSP00000323982:Y193C	ENSP00000323982:Y193C	Y	+	2	0	OR8H2	55629672	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.161000	0.10026	0.065000	0.16485	0.362000	0.22060	TAC	.	.	none		0.408	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
SYNRG	11276	hgsc.bcm.edu	37	17	35956391	35956391	+	Splice_Site	SNP	G	G	C	rs12944821	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:35956391G>C	ENST00000339208.6	-	3	259	c.119C>G	c.(118-120)gCa>gGa	p.A40G	SYNRG_ENST00000345615.4_Splice_Site_p.A40G|SYNRG_ENST00000591288.1_Splice_Site_p.A40G|SYNRG_ENST00000585472.1_Intron|SYNRG_ENST00000502449.2_Splice_Site_p.A40G|SYNRG_ENST00000394378.2_Splice_Site_p.A40G|SYNRG_ENST00000346661.4_Splice_Site_p.A40G	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	40			A -> G (in dbSNP:rs12944821).		endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CATCAGGCCTGCTGAAAATAT	0.383													G|||	1009	0.201478	0.1203	0.3372	5008	,	,		21269	0.251		0.1789	False		,,,				2504	0.1871				p.A40G		Atlas-SNP	.											SYNRG,rectum,carcinoma,0,1	SYNRG	101	1	0			c.C119G						scavenged	.	G	GLY/ALA,,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	564,3842	251.8+/-258.4	39,486,1678	83.0	78.0	80.0		119,,119,119,119,119,119	3.7	1.0	17	dbSNP_121	80	1587,7013	295.7+/-302.5	151,1285,2864	yes	missense-near-splice,intron,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	SYNRG	NM_001163544.1,NM_001163545.1,NM_001163546.1,NM_001163547.1,NM_007247.4,NM_080550.3,NM_198882.1	60,,60,60,60,60,60	190,1771,4542	CC,CG,GG		18.4535,12.8007,16.5385	benign,,benign,benign,benign,benign,benign	40/1237,,40/1180,40/1109,40/1315,40/1225,40/1260	35956391	2151,10855	2203	4300	6503	SO:0001630	splice_region_variant	11276	exon3			AGGCCTGCTGAAA	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.119-1C>G	17.37:g.35956391G>C		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	118	49	0.415254	NM_001163544	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	440	0.20146520146520147	55	0.11178861788617886	116	0.32044198895027626	139	0.243006993006993	130	0.17150395778364116	G	13.47	2.246510	0.39697	0.128007	0.184535	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378;ENST00000394379	T;T;T;T;T	0.46451	1.53;1.53;0.87;0.87;0.87	6.07	3.74	0.42951	.	0.470274	0.20873	N	0.084129	T	0.00012	0.0000	L	0.27053	0.805	0.29416	P	0.860872	B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001;0.001	T	0.34477	-0.9827	9	0.24483	T	0.36	.	12.9222	0.58239	0.0721:0.1192:0.8088:0.0	rs12944821;rs12944821	40;40;40;40;40;40;40	A8MYE0;B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;.;SYNRG_HUMAN	G	40	ENSP00000005279:A40G;ENSP00000343610:A40G;ENSP00000315722:A40G;ENSP00000424893:A40G;ENSP00000377903:A40G	ENSP00000343610:A40G	A	-	2	0	SYNRG	33030504	1.000000	0.71417	0.995000	0.50966	0.973000	0.67179	3.224000	0.51238	1.548000	0.49413	0.655000	0.94253	GCA	G|0.825;C|0.175	0.175	strong		0.383	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	Missense_Mutation
LILRA3	11026	hgsc.bcm.edu	37	19	54803750	54803750	+	Missense_Mutation	SNP	G	G	T	rs149807835	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54803750G>T	ENST00000251390.3	-	3	165	c.74C>A	c.(73-75)cCc>cAc	p.P25H	LILRA3_ENST00000391744.3_Missense_Mutation_p.P25H|LILRA3_ENST00000391745.1_Missense_Mutation_p.P42H	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	25					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)		CTTGGGGAGGGGCCCTGGAAG	0.597													.|||	11	0.00219649	0.0008	0.0086	5008	,	,		12025	0.0		0.004	False		,,,				2504	0.0				p.P25H		Atlas-SNP	.											LILRA3,NS,haematopoietic_neoplasm,0,3	LILRA3	65	3	0			c.C74A						scavenged	.	G	HIS/PRO,HIS/PRO	9,4373		0,9,2182	47.0	47.0	47.0		74,74	0.0	0.0	19	dbSNP_134	47	146,8236		8,130,4053	no	missense,missense	LILRA3	NM_001172654.1,NM_006865.3	77,77	8,139,6235	TT,TG,GG		1.7418,0.2054,1.2144	,	25/376,25/440	54803750	155,12609	2191	4191	6382	SO:0001583	missense	11026	exon3			GGGAGGGGCCCTG	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.74C>A	19.37:g.54803750G>T	ENSP00000251390:p.Pro25His	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	103	2	0.0194175	NM_001172654	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	.	.	.	.	.	.	.	.	.	.	G	4.906	0.168293	0.09339	0.002054	0.017418	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.00784	5.7;5.7;5.7	2.5	0.00277	0.14052	Immunoglobulin-like fold (1);	0.651463	0.13424	N	0.388953	T	0.00440	0.0014	L	0.46819	1.47	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.002	T	0.46386	-0.9195	10	0.42905	T	0.14	.	3.0355	0.06121	0.1596:0.0:0.5785:0.2619	.	25;25	E7EU74;Q8N6C8	.;LIRA3_HUMAN	H	25;25;42	ENSP00000251390:P25H;ENSP00000375624:P25H;ENSP00000375625:P42H	ENSP00000251390:P25H	P	-	2	0	LILRA3	59495562	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-0.137000	0.10389	-0.019000	0.14055	-0.343000	0.07986	CCC	G|0.970;T|0.030	0.030	strong		0.597	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
BSN	8927	hgsc.bcm.edu	37	3	49690627	49690627	+	Missense_Mutation	SNP	G	G	A	rs35762866	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49690627G>A	ENST00000296452.4	+	5	3752	c.3638G>A	c.(3637-3639)gGc>gAc	p.G1213D		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1213			G -> D (in dbSNP:rs35762866).		synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GGACCCCATGGCGGCCCCTCT	0.657													G|||	184	0.0367412	0.0015	0.0764	5008	,	,		14865	0.0		0.1064	False		,,,				2504	0.0225				p.G1213D		Atlas-SNP	.											.	BSN	272	.	0			c.G3638A						PASS	.	G	ASP/GLY	94,4272		2,90,2091	12.0	15.0	14.0		3638	1.0	0.0	3	dbSNP_126	14	957,7609		49,859,3375	no	missense	BSN	NM_003458.3	94	51,949,5466	AA,AG,GG		11.1721,2.153,8.1271	probably-damaging	1213/3927	49690627	1051,11881	2183	4283	6466	SO:0001583	missense	8927	exon5			CCCATGGCGGCCC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3638G>A	3.37:g.49690627G>A	ENSP00000296452:p.Gly1213Asp	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	105	0.04807692307692308	3	0.006097560975609756	21	0.058011049723756904	0	0.0	81	0.10686015831134564	G	9.470	1.095325	0.20471	0.02153	0.111721	ENSG00000164061	ENST00000296452	T	0.20200	2.09	5.12	1.05	0.20165	.	0.430079	0.24516	N	0.037853	T	0.00300	0.0009	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31586	-0.9938	10	0.12766	T	0.61	.	10.6173	0.45458	0.0695:0.3747:0.5558:0.0	rs35762866	1213	Q9UPA5	BSN_HUMAN	D	1213	ENSP00000296452:G1213D	ENSP00000296452:G1213D	G	+	2	0	BSN	49665631	0.033000	0.19621	0.001000	0.08648	0.725000	0.41563	2.208000	0.42797	-0.090000	0.12462	0.462000	0.41574	GGC	G|0.940;A|0.060	0.060	strong		0.657	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
PIEZO1	9780	hgsc.bcm.edu	37	16	88787673	88787673	+	Missense_Mutation	SNP	G	G	A	rs35159887	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88787673G>A	ENST00000301015.9	-	39	5815	c.5569C>T	c.(5569-5571)Ccc>Tcc	p.P1857S	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	1857					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						TCCACTTGGGGTTCTGGGGTC	0.652													G|||	832	0.166134	0.0144	0.1787	5008	,	,		17762	0.0764		0.3072	False		,,,				2504	0.3098				p.P1857S		Atlas-SNP	.											PIEZO1,NS,carcinoma,0,1	PIEZO1	79	1	0			c.C5569T						PASS	.	G	SER/PRO	84,1300		3,78,611	58.0	57.0	57.0		5569	-0.4	0.0	16	dbSNP_126	57	1069,2109		167,735,687	yes	missense	PIEZO1	NM_001142864.2	74	170,813,1298	AA,AG,GG		33.6375,6.0694,25.274	benign	1857/2522	88787673	1153,3409	692	1589	2281	SO:0001583	missense	9780	exon39			CTTGGGGTTCTGG	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.5569C>T	16.37:g.88787673G>A	ENSP00000301015:p.Pro1857Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	16	0.213333	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	359|359	0.16437728937728938|0.16437728937728938	13|13	0.026422764227642278|0.026422764227642278	81|81	0.22375690607734808|0.22375690607734808	39|39	0.06818181818181818|0.06818181818181818	226|226	0.29815303430079154|0.29815303430079154	G|G	6.191|6.191	0.403423|0.403423	0.11754|0.11754	0.060694|0.060694	0.336375|0.336375	ENSG00000103335|ENSG00000103335	ENST00000301015|ENST00000451779	T|.	0.71579|.	-0.58|.	4.48|4.48	-0.409|-0.409	0.12378|0.12378	.|.	1.563880|.	0.04107|.	N|.	0.313931|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25890|0.25890	0.77|0.77	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.42965|0.42965	-0.9420|-0.9420	9|4	0.08837|.	T|.	0.75|.	-3.4232|-3.4232	7.7829|7.7829	0.29074|0.29074	0.1446:0.3574:0.498:0.0|0.1446:0.3574:0.498:0.0	rs35159887|rs35159887	1857|.	Q92508|.	PIEZ1_HUMAN|.	S|I	1857|1802	ENSP00000301015:P1857S|.	ENSP00000301015:P1857S|.	P|T	-|-	1|2	0|0	FAM38A|FAM38A	87315174|87315174	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.292000|0.292000	0.27327|0.27327	-0.123000|-0.123000	0.10611|0.10611	0.077000|0.077000	0.16863|0.16863	0.448000|0.448000	0.29417|0.29417	CCC|ACC	G|0.825;A|0.175	0.175	strong		0.652	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
MICAL3	57553	hgsc.bcm.edu	37	22	18301693	18301693	+	Missense_Mutation	SNP	T	T	C	rs8135914	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:18301693T>C	ENST00000441493.2	-	26	4086	c.3734A>G	c.(3733-3735)cAg>cGg	p.Q1245R		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1245	Pro-rich.			Q -> R (in Ref. 5; BAA74842). {ECO:0000305}.	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)		CACGGGTGGCTGGGGCTGCGG	0.682													C|||	1277	0.254992	0.3812	0.2161	5008	,	,		12128	0.0893		0.331	False		,,,				2504	0.2045				p.Q1245R		Atlas-SNP	.											.	MICAL3	53	.	0			c.A3734G						PASS	.	C	ARG/GLN	1292,2596		229,834,881	11.0	15.0	14.0		3734	-4.2	0.0	22	dbSNP_116	14	2684,5550		476,1732,1909	yes	missense	MICAL3	NM_015241.2	43	705,2566,2790	CC,CT,TT		32.5966,33.2305,32.7999	benign	1245/2003	18301693	3976,8146	1944	4117	6061	SO:0001583	missense	57553	exon26			GGTGGCTGGGGCT	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.3734A>G	22.37:g.18301693T>C	ENSP00000416015:p.Gln1245Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	55	20	0.363636	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	548|548	0.2509157509157509|0.2509157509157509	180|180	0.36585365853658536|0.36585365853658536	86|86	0.23756906077348067|0.23756906077348067	45|45	0.07867132867132867|0.07867132867132867	237|237	0.31266490765171506|0.31266490765171506	C|C	5.042|5.042	0.193465|0.193465	0.09599|0.09599	0.332305|0.332305	0.325966|0.325966	ENSG00000093100|ENSG00000093100	ENST00000441493|ENST00000252134	T|.	0.62232|.	0.04|.	4.73|4.73	-4.25|-4.25	0.03766|0.03766	.|.	.|.	.|.	.|.	.|.	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	0.41822|0.41822	-0.9487|-0.9487	8|4	0.10902|.	T|.	0.67|.	.|.	6.364|6.364	0.21445|0.21445	0.1275:0.3101:0.463:0.0994|0.1275:0.3101:0.463:0.0994	rs8135914;rs61587067|rs8135914;rs61587067	1245|.	Q7RTP6|.	MICA3_HUMAN|.	R|G	1245|227	ENSP00000416015:Q1245R|.	ENSP00000416015:Q1245R|.	Q|S	-|-	2|1	0|0	XXbac-B461K10.4|XXbac-B461K10.4	16681693|16681693	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.645000|-1.645000	0.02000|0.02000	-1.684000|-1.684000	0.01443|0.01443	-2.475000|-2.475000	0.00201|0.00201	CAG|AGC	T|0.774;C|0.226	0.226	strong		0.682	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
SRRM5	100170229	hgsc.bcm.edu	37	19	44118353	44118353	+	Missense_Mutation	SNP	G	G	A	rs2302421	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44118353G>A	ENST00000607544.1	+	3	2402	c.2080G>A	c.(2080-2082)Gac>Aac	p.D694N	ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000526798.1_Missense_Mutation_p.D709N|SRRM5_ENST00000417606.1_Missense_Mutation_p.D694N			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	119	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	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	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258336	25258336	+	Missense_Mutation	SNP	C	C	T	rs150756150		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:25258336C>T	ENST00000328086.7	-	5	1984	c.1181G>A	c.(1180-1182)cGa>cAa	p.R394Q		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	394					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		GAACTTGGTTCGACACTGTTC	0.478																																					p.R394Q		Atlas-SNP	.											ZKSCAN2,rectum,carcinoma,-1,1	ZKSCAN2	90	1	0			c.G1181A						scavenged	.	C	GLN/ARG	0,4394		0,0,2197	140.0	129.0	133.0		1181	5.8	1.0	16	dbSNP_134	133	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZKSCAN2	NM_001012981.4	43	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	394/968	25258336	1,12993	2197	4300	6497	SO:0001583	missense	342357	exon5			TTGGTTCGACACT	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.1181G>A	16.37:g.25258336C>T	ENSP00000331626:p.Arg394Gln	Somatic	357	1	0.00280112		WXS	Illumina HiSeq	Phase_I	401	5	0.0124688	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	.	.	.	.	.	.	.	.	.	.	C	31	5.092979	0.94149	0.0	1.16E-4	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.47869	0.83	5.76	5.76	0.90799	SANT domain, DNA binding (1);	0.000000	0.64402	D	0.000019	T	0.69735	0.3144	M	0.78049	2.395	0.36406	D	0.863415	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.998	T	0.75900	-0.3154	10	0.59425	D	0.04	-24.0843	15.8146	0.78589	0.0:1.0:0.0:0.0	.	190;394;394	B4DYF0;Q63HK3-2;Q63HK3	.;.;ZKSC2_HUMAN	Q	394	ENSP00000331626:R394Q	ENSP00000331626:R394Q	R	-	2	0	ZKSCAN2	25165837	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	2.146000	0.42216	2.882000	0.98803	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	weak		0.478	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
PHLPP1	23239	hgsc.bcm.edu	37	18	60645509	60645509	+	Silent	SNP	C	C	T	rs34061095	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:60645509C>T	ENST00000262719.5	+	17	4233	c.3999C>T	c.(3997-3999)aaC>aaT	p.N1333N	PHLPP1_ENST00000400316.4_Silent_p.N821N			O60346	PHLP1_HUMAN	PH domain and leucine rich repeat protein phosphatase 1	1333	PP2C-like.				apoptotic process (GO:0006915)|entrainment of circadian clock (GO:0009649)|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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			endometrium(2)|kidney(2)|lung(13)	17						GCAAGGTGAACGGAGTGACTG	0.602													C|||	145	0.0289537	0.003	0.0389	5008	,	,		23677	0.002		0.1004	False		,,,				2504	0.0112				p.N1333N		Atlas-SNP	.											.	PHLPP1	164	.	0			c.C3999T						PASS	.	C		68,4200		0,68,2066	42.0	47.0	45.0		3999	-0.9	1.0	18	dbSNP_126	45	726,7752		30,666,3543	no	coding-synonymous	PHLPP1	NM_194449.2		30,734,5609	TT,TC,CC		8.5633,1.5933,6.2294		1333/1718	60645509	794,11952	2134	4239	6373	SO:0001819	synonymous_variant	23239	exon17			GGTGAACGGAGTG	AB011178	CCDS45881.1, CCDS45881.2	18q21.32	2013-01-11	2009-05-26	2009-05-26	ENSG00000081913	ENSG00000081913		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"", ""Pleckstrin homology (PH) domain containing"""	20610	protein-coding gene	gene with protein product		609396	"""pleckstrin homology domain containing, family E (with leucine rich repeats) member 1"", ""PH domain and leucine rich repeat protein phosphatase"""	PLEKHE1, PHLPP		10570941, 15808505	Standard	NM_194449		Approved	KIAA0606, SCOP	uc021ule.1	O60346	OTTHUMG00000150629	ENST00000262719.5:c.3999C>T	18.37:g.60645509C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_194449	A1A4F5|Q641Q7|Q6P4C4|Q6PJI6|Q86TN6|Q96FK2|Q9NUY1	Silent	SNP	ENST00000262719.5	37	CCDS45881.2																																																																																			C|0.951;T|0.049	0.049	strong		0.602	PHLPP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319249.2	NM_194449	
MEPE	56955	hgsc.bcm.edu	37	4	88767008	88767008	+	Missense_Mutation	SNP	G	G	A	rs17013285	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:88767008G>A	ENST00000424957.3	+	4	1061	c.988G>A	c.(988-990)Gtt>Att	p.V330I	MEPE_ENST00000560249.1_Missense_Mutation_p.V217I|MEPE_ENST00000361056.3_Missense_Mutation_p.V330I|MEPE_ENST00000395102.4_Missense_Mutation_p.V361I|MEPE_ENST00000497649.2_Missense_Mutation_p.V306I|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000540395.1_Missense_Mutation_p.V217I	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	330			V -> I (in dbSNP:rs17013285).		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)		GGCAGATGCTGTTGATGTCAG	0.458													G|||	863	0.172324	0.0484	0.1801	5008	,	,		20635	0.2827		0.164	False		,,,				2504	0.229				p.V330I		Atlas-SNP	.											.	MEPE	86	.	0			c.G988A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	286,4120	158.1+/-190.9	8,270,1925	65.0	64.0	64.0		988,649,649,649,988	0.4	0.0	4	dbSNP_123	64	1468,7132	274.2+/-291.1	134,1200,2966	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	142,1470,4891	AA,AG,GG		17.0698,6.4911,13.4861	benign,benign,benign,benign,benign	330/526,217/413,217/413,217/413,330/526	88767008	1754,11252	2203	4300	6503	SO:0001583	missense	56955	exon4			GATGCTGTTGATG	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.988G>A	4.37:g.88767008G>A	ENSP00000416984:p.Val330Ile	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_020203	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	385	0.1762820512820513	25	0.0508130081300813	54	0.14917127071823205	171	0.29895104895104896	135	0.17810026385224276	G	9.102	1.004490	0.19199	0.064911	0.170698	ENSG00000152595	ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.43688	0.94;0.94;0.94;0.95;0.94	4.68	0.436	0.16549	.	0.506936	0.16629	N	0.206152	T	0.00012	0.0000	L	0.31207	0.915	0.80722	P	0.0	B	0.15719	0.014	B	0.10450	0.005	T	0.34650	-0.9820	9	0.31617	T	0.26	-0.3551	3.377	0.07241	0.3818:0.2037:0.4145:0.0	rs17013285;rs52799941;rs17013285	330	Q9NQ76	MEPE_HUMAN	I	330;361;306;217;330	ENSP00000416984:V330I;ENSP00000378534:V361I;ENSP00000422747:V306I;ENSP00000443491:V217I;ENSP00000354341:V330I	ENSP00000354341:V330I	V	+	1	0	MEPE	88986032	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.389000	0.20751	0.161000	0.19458	0.655000	0.94253	GTT	G|0.854;A|0.146	0.146	strong		0.458	MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1		
MATN2	4147	hgsc.bcm.edu	37	8	99006748	99006748	+	Silent	SNP	C	C	T	rs11559201	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:99006748C>T	ENST00000520016.1	+	6	1246	c.1122C>T	c.(1120-1122)caC>caT	p.H374H	MATN2_ENST00000521689.1_Silent_p.H374H|MATN2_ENST00000254898.5_Silent_p.H374H|MATN2_ENST00000524308.1_Intron|MATN2_ENST00000522025.2_Silent_p.H90H			O00339	MATN2_HUMAN	matrilin 2	374	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					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)			GATGTCAGCACGAGTGTGTTA	0.423													C|||	610	0.121805	0.1513	0.1052	5008	,	,		18606	0.0774		0.1471	False		,,,				2504	0.1135				p.H374H		Atlas-SNP	.											.	MATN2	165	.	0			c.C1122T						PASS	.	C	,	518,3382		29,460,1461	176.0	173.0	174.0		1122,1122	-11.5	0.0	8	dbSNP_120	174	1436,6846		126,1184,2831	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	155,1644,4292	TT,TC,CC		17.3388,13.2821,16.0401	,	374/957,374/938	99006748	1954,10228	1950	4141	6091	SO:0001819	synonymous_variant	4147	exon7			TCAGCACGAGTGT	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.1122C>T	8.37:g.99006748C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	153	58	0.379085	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	263	0.12042124542124542	74	0.15040650406504066	42	0.11602209944751381	37	0.06468531468531469	110	0.14511873350923482	C	3.537	-0.094593	0.07053	0.132821	0.173388	ENSG00000132561	ENST00000518154;ENST00000521041	.	.	.	5.73	-11.5	0.00074	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999863628	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.0438	8.8597	0.35249	0.0652:0.1537:0.1297:0.6513	rs11559201;rs17850660;rs17858379;rs58845670;rs11559201	.	.	.	X	157;129	.	.	R	+	1	2	MATN2	99075924	0.000000	0.05858	0.048000	0.18961	0.667000	0.39255	-2.725000	0.00808	-3.721000	0.00115	-1.595000	0.00837	CGA	C|0.872;T|0.128	0.128	strong		0.423	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
PDE1C	5137	hgsc.bcm.edu	37	7	31848706	31848706	+	Silent	SNP	A	A	G	rs3213709	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:31848706A>G	ENST00000396191.1	-	16	2285	c.1830T>C	c.(1828-1830)ggT>ggC	p.G610G	PDE1C_ENST00000396193.1_Silent_p.G670G|PDE1C_ENST00000396184.3_Silent_p.G610G|PDE1C_ENST00000321453.7_Silent_p.G610G|PDE1C_ENST00000396182.2_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						scavenged	.	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	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	106	30	0.283019	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		
FLNA	2316	hgsc.bcm.edu	37	X	153581932	153581932	+	Silent	SNP	A	A	G	rs2070825	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:153581932A>G	ENST00000369850.3	-	36	6086	c.5850T>C	c.(5848-5850)gcT>gcC	p.A1950A	FLNA_ENST00000498491.1_5'Flank|FLNA_ENST00000344736.4_Silent_p.A1910A|FLNA_ENST00000360319.4_Silent_p.A1942A|FLNA_ENST00000369856.3_Intron|FLNA_ENST00000422373.1_Silent_p.A1942A	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	1950					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)					CTGTGACCCGAGCAGTGAAGG	0.617													.|||	959	0.25404	0.4259	0.134	3775	,	,		15156	0.0665		0.0626	False		,,,				2504	0.1769				p.A1950A		Atlas-SNP	.											.	FLNA	373	.	0			c.T5850C						PASS	.	G	,	1867,1955		392,795,288,439,282	59.0	65.0	63.0		5850,5826	3.9	1.0	X	dbSNP_96	63	704,6012		21,467,195,1939,1667	no	coding-synonymous,coding-synonymous	FLNA	NM_001110556.1,NM_001456.3	,	413,1262,483,2378,1949	GG,GA,G,AA,A		10.4824,48.8488,24.3974	,	1950/2648,1942/2640	153581932	2571,7967	2196	4289	6485	SO:0001819	synonymous_variant	2316	exon36			GACCCGAGCAGTG	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.5850T>C	X.37:g.153581932A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001110556	E9KL45|Q5HY53|Q5HY55|Q8NF52	Silent	SNP	ENST00000369850.3	37	CCDS48194.1																																																																																			A|0.755;0|0.006	.	strong		0.617	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
GPR98	84059	hgsc.bcm.edu	37	5	89989779	89989779	+	Silent	SNP	G	G	A	rs16876822	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	170	0	0		WXS	Illumina HiSeq	Phase_I	156	154	0.987179	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	
NUP210	23225	hgsc.bcm.edu	37	3	13395475	13395475	+	Missense_Mutation	SNP	G	G	C	rs2280085	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:13395475G>C	ENST00000254508.5	-	17	2543	c.2461C>G	c.(2461-2463)Cct>Gct	p.P821A		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	821			P -> A (in dbSNP:rs2280085).		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)					GGCAGCTCAGGCTCGATGCTG	0.622													G|||	1044	0.208466	0.2126	0.1729	5008	,	,		19709	0.2897		0.165	False		,,,				2504	0.1892				p.P821A		Atlas-SNP	.											.	NUP210	182	.	0			c.C2461G						PASS	.	G	ALA/PRO	929,3477	333.6+/-303.0	108,713,1382	31.0	26.0	27.0		2461	2.3	0.0	3	dbSNP_100	27	1423,7175	252.6+/-278.6	121,1181,2997	yes	missense	NUP210	NM_024923.2	27	229,1894,4379	CC,CG,GG		16.5504,21.0849,18.0867	benign	821/1888	13395475	2352,10652	2203	4299	6502	SO:0001583	missense	23225	exon17			GCTCAGGCTCGAT	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.2461C>G	3.37:g.13395475G>C	ENSP00000254508:p.Pro821Ala	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	226	104	0.460177	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	454	0.2078754578754579	84	0.17073170731707318	59	0.16298342541436464	185	0.32342657342657344	126	0.1662269129287599	G	0.017	-1.499222	0.01001	0.210849	0.165504	ENSG00000132182	ENST00000254508	T	0.49432	0.78	5.23	2.31	0.28768	.	0.560572	0.18343	N	0.144138	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B;B	0.23249	0.082;0.049	B;B	0.25140	0.058;0.039	T	0.33650	-0.9860	9	0.09338	T	0.73	0.0042	4.1682	0.10317	0.1349:0.3424:0.4056:0.1171	rs2280085;rs2280085	821;821	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	A	821	ENSP00000254508:P821A	ENSP00000254508:P821A	P	-	1	0	NUP210	13370475	0.400000	0.25295	0.002000	0.10522	0.072000	0.16883	2.121000	0.41977	0.247000	0.21414	0.563000	0.77884	CCT	G|0.807;C|0.193	0.193	strong		0.622	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
ZDHHC20	253832	hgsc.bcm.edu	37	13	21976996	21976996	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:21976996T>C	ENST00000400590.3	-	5	578	c.380A>G	c.(379-381)tAt>tGt	p.Y127C	ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.Y64C|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.Y127C|ZDHHC20_ENST00000415724.1_Missense_Mutation_p.Y127C|ZDHHC20_ENST00000320220.9_Missense_Mutation_p.Y127C			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	127					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		TTTTTCACAATATCTGATAGC	0.353																																					p.Y127C		Atlas-SNP	.											.	ZDHHC20	36	.	0			c.A380G						PASS	.						65.0	62.0	63.0					13																	21976996		1862	4106	5968	SO:0001583	missense	253832	exon5			TCACAATATCTGA	AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"""Zinc fingers, DHHC-type"""	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.380A>G	13.37:g.21976996T>C	ENSP00000383433:p.Tyr127Cys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	51	32	0.627451	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		.	.	.	.	.	.	.	.	.	.	T	19.89	3.910520	0.72983	.	.	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000542645;ENST00000415724	T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.62270	0.2414	H	0.96489	3.83	0.80722	D	1	D;P	0.63046	0.992;0.812	P;D	0.63381	0.908;0.914	T	0.76348	-0.2992	10	0.87932	D	0	-33.8396	15.3153	0.74069	0.0:0.0:0.0:1.0	.	64;127	B4DRN8;Q5W0Z9-3	.;.	C	127;127;127;64;127	ENSP00000383433:Y127C;ENSP00000313583:Y127C;ENSP00000371905:Y127C;ENSP00000443236:Y64C;ENSP00000401232:Y127C	ENSP00000313583:Y127C	Y	-	2	0	ZDHHC20	20874996	1.000000	0.71417	0.973000	0.42090	0.820000	0.46376	4.578000	0.60929	2.069000	0.61940	0.533000	0.62120	TAT	.	.	none		0.353	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251	
LRRC16A	55604	hgsc.bcm.edu	37	6	25472737	25472737	+	Silent	SNP	C	C	T	rs41271815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:25472737C>T	ENST00000329474.6	+	11	1230	c.862C>T	c.(862-864)Ctg>Ttg	p.L288L	LRRC16A_ENST00000377969.3_Silent_p.L127L	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	288					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						TGGCAACCCACTGGAGGATAG	0.418													C|||	320	0.0638978	0.0061	0.0245	5008	,	,		16628	0.0764		0.0865	False		,,,				2504	0.1339				p.L288L		Atlas-SNP	.											.	LRRC16A	168	.	0			c.C862T						PASS	.	C	,	47,3697		0,47,1825	47.0	43.0	44.0		862,862	5.8	1.0	6	dbSNP_127	44	579,7621		19,541,3540	no	coding-synonymous,coding-synonymous	LRRC16A	NM_001173977.1,NM_017640.5	,	19,588,5365	TT,TC,CC		7.061,1.2553,5.2411	,	288/1366,288/1372	25472737	626,11318	1872	4100	5972	SO:0001819	synonymous_variant	55604	exon11			AACCCACTGGAGG	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.862C>T	6.37:g.25472737C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Silent	SNP	ENST00000329474.6	37	CCDS54973.1																																																																																			C|0.935;T|0.065	0.065	strong		0.418	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
FAM13B	51306	hgsc.bcm.edu	37	5	137278682	137278682	+	Missense_Mutation	SNP	T	T	C	rs33956817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:137278682T>C	ENST00000033079.3	-	21	2855	c.2404A>G	c.(2404-2406)Atg>Gtg	p.M802V	FAM13B_ENST00000425075.2_Missense_Mutation_p.M678V|FAM13B_ENST00000420893.2_Missense_Mutation_p.M774V	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	802			M -> V (in dbSNP:rs33956817).		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						GTTTTCAACATATCACCTAAC	0.383													T|||	140	0.0279553	0.0295	0.0418	5008	,	,		16171	0.0		0.0487	False		,,,				2504	0.0235				p.M802V		Atlas-SNP	.											.	FAM13B	46	.	0			c.A2404G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	119,4287	90.6+/-129.3	0,119,2084	118.0	117.0	118.0		2320,2032,2404	3.7	1.0	5	dbSNP_126	118	384,8216	124.6+/-183.3	9,366,3925	yes	missense,missense,missense	FAM13B	NM_001101800.1,NM_001101801.1,NM_016603.2	21,21,21	9,485,6009	CC,CT,TT		4.4651,2.7009,3.8674	benign,benign,benign	774/888,678/792,802/916	137278682	503,12503	2203	4300	6503	SO:0001583	missense	51306	exon21			TCAACATATCACC	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"""Rho GTPase activating proteins"""	1335	protein-coding gene	gene with protein product		609371	"""chromosome 5 open reading frame 5"", ""family with sequence similarity 13, member B1"""	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.2404A>G	5.37:g.137278682T>C	ENSP00000033079:p.Met802Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_016603	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	76	0.0347985347985348	17	0.034552845528455285	22	0.06077348066298342	0	0.0	37	0.048812664907651716	T	7.885	0.731049	0.15507	0.027009	0.044651	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.21191	3.18;2.02;3.13	6.07	3.66	0.41972	.	0.451157	0.24851	N	0.035084	T	0.00998	0.0033	N	0.14661	0.345	0.22401	N	0.999132	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32375	-0.9909	10	0.15952	T	0.53	-0.2236	7.4229	0.27081	0.0:0.0717:0.1445:0.7837	rs33956817	678;774;802	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	V	802;678;774	ENSP00000033079:M802V;ENSP00000394669:M678V;ENSP00000388521:M774V	ENSP00000033079:M802V	M	-	1	0	FAM13B	137306581	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.931000	0.40134	1.072000	0.40860	0.533000	0.62120	ATG	T|0.960;C|0.040	0.040	strong		0.383	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		
CSMD3	114788	hgsc.bcm.edu	37	8	113363466	113363466	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:113363466G>A	ENST00000297405.5	-	40	6507	c.6263C>T	c.(6262-6264)tCt>tTt	p.S2088F	CSMD3_ENST00000343508.3_Missense_Mutation_p.S2048F|CSMD3_ENST00000352409.3_Missense_Mutation_p.S2018F|CSMD3_ENST00000455883.2_Missense_Mutation_p.S1984F	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2088	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGTAATGTGAGAGTGACCCTA	0.294										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S2088F		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C6263T						PASS	.						120.0	122.0	121.0					8																	113363466		2203	4292	6495	SO:0001583	missense	114788	exon40			ATGTGAGAGTGAC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6263C>T	8.37:g.113363466G>A	ENSP00000297405:p.Ser2088Phe	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	20	0.224719	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.226833	0.79576	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	4.32	4.32	0.51571	Complement control module (2);Sushi/SCR/CCP (3);	0.087525	0.48286	D	0.000186	T	0.79919	0.4529	M	0.81614	2.55	0.54753	D	0.999985	D;P;D	0.89917	0.973;0.921;1.0	P;P;D	0.79784	0.847;0.722;0.993	T	0.82573	-0.0390	10	0.54805	T	0.06	.	17.3411	0.87296	0.0:0.0:1.0:0.0	.	1984;2088;2048	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	F	2048;2088;1358;1984;2018	ENSP00000345799:S2048F;ENSP00000297405:S2088F;ENSP00000341558:S1358F;ENSP00000412263:S1984F;ENSP00000343124:S2018F	ENSP00000297405:S2088F	S	-	2	0	CSMD3	113432642	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.772000	0.85439	2.380000	0.81148	0.650000	0.86243	TCT	.	.	none		0.294	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
RAET1E	135250	hgsc.bcm.edu	37	6	150210681	150210681	+	Missense_Mutation	SNP	G	G	A	rs9371533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:150210681G>A	ENST00000357183.4	-	3	557	c.425C>T	c.(424-426)aCc>aTc	p.T142I	RAET1E-AS1_ENST00000605899.1_RNA|RAET1E_ENST00000529948.1_Missense_Mutation_p.T142I|RAET1E_ENST00000532335.1_Missense_Mutation_p.T142I|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000367363.3_Missense_Mutation_p.T106I	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	142	MHC class I alpha-2 like.		T -> I (in dbSNP:rs9371533).	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)		CTCTCCATTGGTGGCGAACTG	0.468													N|||	3435	0.685903	0.8442	0.5447	5008	,	,		21656	0.8968		0.4324	False		,,,				2504	0.6155				p.T142I		Atlas-SNP	.											RAET1E,NS,carcinoma,+1,2	RAET1E	20	2	0			c.C425T						scavenged	.	A	ILE/THR	3478,928	353.3+/-312.1	1384,710,109	156.0	127.0	137.0		425	-1.8	0.0	6	dbSNP_119	137	3544,5056	631.0+/-398.4	742,2060,1498	yes	missense	RAET1E	NM_139165.2	89	2126,2770,1607	AA,AG,GG		41.2093,21.0622,46.0095	benign	142/264	150210681	7022,5984	2203	4300	6503	SO:0001583	missense	135250	exon3			CCATTGGTGGCGA	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.425C>T	6.37:g.150210681G>A	ENSP00000349709:p.Thr142Ile	Somatic	320	2	0.00625		WXS	Illumina HiSeq	Phase_I	305	137	0.44918	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	37	CCDS5221.1	1415	0.6478937728937729	397	0.806910569105691	200	0.5524861878453039	503	0.8793706293706294	315	0.4155672823218997	A	3.644	-0.072921	0.07228	0.789378	0.412093	ENSG00000164520	ENST00000532335;ENST00000357183;ENST00000367363;ENST00000529948	T;T;T;T	0.06068	3.35;3.35;5.85;3.35	3.68	-1.75	0.08031	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.757356	0.11741	N	0.534006	T	0.00300	0.0009	N	0.00159	-1.955	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	0.35847	-0.9772	9	0.07644	T	0.81	-6.9511	4.4433	0.11584	0.3415:0.3442:0.3142:0.0	rs9371533;rs59091272;rs9371533	142;106;142	Q8TD07;Q8TD07-2;Q8TD07-3	N2DL4_HUMAN;.;.	I	142;142;106;142	ENSP00000437067:T142I;ENSP00000349709:T142I;ENSP00000356332:T106I;ENSP00000432366:T142I	ENSP00000349709:T142I	T	-	2	0	RAET1E	150252374	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.847000	0.27696	-0.637000	0.05516	-1.330000	0.01273	ACC	G|0.403;A|0.597	0.597	strong		0.468	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
ASTN2	23245	hgsc.bcm.edu	37	9	119770495	119770495	+	Silent	SNP	G	G	A	rs61736198	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:119770495G>A	ENST00000313400.4	-	7	1567	c.1467C>T	c.(1465-1467)tcC>tcT	p.S489S	ASTN2_ENST00000373996.3_Silent_p.S489S|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000361209.2_Silent_p.S438S			O75129	ASTN2_HUMAN	astrotactin 2	489					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						TTAACCAGTCGGAGATGTCCA	0.512													G|||	38	0.00758786	0.0008	0.0058	5008	,	,		20493	0.0159		0.0089	False		,,,				2504	0.0082				p.S438S		Atlas-SNP	.											.	ASTN2	307	.	0			c.C1314T						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	112.0	96.0	101.0		1314	-9.3	0.4	9	dbSNP_129	101	42,8558	28.5+/-78.6	1,40,4259	no	coding-synonymous	ASTN2	NM_014010.4		1,48,6454	AA,AG,GG		0.4884,0.1816,0.3844		438/1289	119770495	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	23245	exon6			CCAGTCGGAGATG	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.1467C>T	9.37:g.119770495G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	225	101	0.448889	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37																																																																																				G|0.994;A|0.006	0.006	strong		0.512	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
UBN1	29855	hgsc.bcm.edu	37	16	4925291	4925291	+	Silent	SNP	T	T	G	rs17137364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4925291T>G	ENST00000396658.4	+	14	3583	c.2880T>G	c.(2878-2880)gtT>gtG	p.V960V	UBN1_ENST00000545171.1_Silent_p.V960V|UBN1_ENST00000262376.6_Silent_p.V960V|UBN1_ENST00000590769.1_Silent_p.V960V	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	960	Ser-rich.				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						AAATGCCTGTTTCCCAGAAGT	0.597													T|||	332	0.0662939	0.1467	0.0331	5008	,	,		18402	0.006		0.0785	False		,,,				2504	0.0307				p.V960V		Atlas-SNP	.											.	UBN1	88	.	0			c.T2880G						PASS	.	T	,	543,3851	242.5+/-252.5	26,491,1680	52.0	58.0	56.0		2880,2880	-6.2	0.1	16	dbSNP_123	56	664,7936	166.1+/-218.1	29,606,3665	no	coding-synonymous,coding-synonymous	UBN1	NM_001079514.1,NM_016936.3	,	55,1097,5345	GG,GT,TT		7.7209,12.3578,9.2889	,	960/1135,960/1135	4925291	1207,11787	2197	4300	6497	SO:0001819	synonymous_variant	29855	exon15			GCCTGTTTCCCAG	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.2880T>G	16.37:g.4925291T>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Silent	SNP	ENST00000396658.4	37	CCDS10525.1																																																																																			T|0.912;G|0.088	0.088	strong		0.597	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936	
CAPS2	84698	hgsc.bcm.edu	37	12	75715330	75715330	+	Missense_Mutation	SNP	C	C	A	rs10879901	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:75715330C>A	ENST00000409445.3	-	6	571	c.375G>T	c.(373-375)ttG>ttT	p.L125F	CAPS2_ENST00000409799.1_Missense_Mutation_p.L75F|CAPS2_ENST00000393284.3_5'UTR|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	161	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	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		
IL18R1	8809	hgsc.bcm.edu	37	2	103013177	103013177	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:103013177C>T	ENST00000409599.1	+	12	1813	c.1457C>T	c.(1456-1458)cCc>cTc	p.P486L	IL18R1_ENST00000233957.1_Missense_Mutation_p.P486L			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	486	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)	p.P486H(1)		breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						ACATTCTTGCCCCAATCACTA	0.353																																					p.P486L		Atlas-SNP	.											IL18R1,NS,carcinoma,0,1	IL18R1	72	1	1	Substitution - Missense(1)	lung(1)	c.C1457T						scavenged	.						91.0	96.0	94.0					2																	103013177		2203	4300	6503	SO:0001583	missense	8809	exon10			TCTTGCCCCAATC	U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.1457C>T	2.37:g.103013177C>T	ENSP00000387211:p.Pro486Leu	Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	294	4	0.0136054	NM_003855	B2R9Y5|Q52LC9	Missense_Mutation	SNP	ENST00000409599.1	37	CCDS2060.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.291262	0.80914	.	.	ENSG00000115604	ENST00000410040;ENST00000409599;ENST00000233957	T;T;T	0.02446	4.29;4.29;4.29	5.59	5.59	0.84812	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.64402	D	0.000002	T	0.17662	0.0424	M	0.90650	3.135	0.80722	D	1	D;D	0.57899	0.981;0.981	P;P	0.56514	0.8;0.8	T	0.00609	-1.1646	10	0.56958	D	0.05	.	19.9595	0.97236	0.0:1.0:0.0:0.0	.	485;486	B7ZKV7;Q13478	.;IL18R_HUMAN	L	486	ENSP00000386663:P486L;ENSP00000387211:P486L;ENSP00000233957:P486L	ENSP00000233957:P486L	P	+	2	0	IL18R1	102379609	0.999000	0.42202	0.852000	0.33557	0.913000	0.54294	5.317000	0.65822	2.797000	0.96272	0.563000	0.77884	CCC	.	.	none		0.353	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855	
CYP27C1	339761	hgsc.bcm.edu	37	2	127956964	127956964	+	Silent	SNP	G	G	A	rs149542135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:127956964G>A	ENST00000335247.7	-	4	670	c.540C>T	c.(538-540)gcC>gcT	p.A180A	CYP27C1_ENST00000409327.1_Silent_p.A180A	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	180						membrane (GO:0016020)	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 (GO:0016705)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		TGTCGACGCCGGCCAGCAGCA	0.582													G|||	2	0.000399361	0.0	0.0	5008	,	,		19906	0.0		0.002	False		,,,				2504	0.0				p.A180A		Atlas-SNP	.											.	CYP27C1	52	.	0			c.C540T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	158.0	139.0	145.0		540	-2.6	0.9	2	dbSNP_134	145	16,8584	11.2+/-40.8	1,14,4285	no	coding-synonymous	CYP27C1	NM_001001665.3		1,15,6487	AA,AG,GG		0.186,0.0227,0.1307		180/373	127956964	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	339761	exon4			GACGCCGGCCAGC	AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"""Cytochrome P450s"""	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.540C>T	2.37:g.127956964G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_001001665	Q6ZNI7	Silent	SNP	ENST00000335247.7	37	CCDS33285.1																																																																																			G|0.999;A|0.001	0.001	strong		0.582	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665	
ZAK	51776	hgsc.bcm.edu	37	2	174055646	174055646	+	Silent	SNP	T	T	C	rs35853276	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:174055646T>C	ENST00000375213.3	+	6	517	c.439T>C	c.(439-441)Ttg>Ctg	p.L147L	MLTK_ENST00000539448.1_Silent_p.L147L|MLTK_ENST00000409176.2_Silent_p.L147L|MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000338983.3_Silent_p.L147L|MLTK_ENST00000480606.1_3'UTR|MLTK_ENST00000431503.2_Silent_p.L46L|MLK7-AS1_ENST00000419609.1_RNA	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	97	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	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		
WDR11	55717	hgsc.bcm.edu	37	10	122649482	122649482	+	Silent	SNP	A	A	G	rs2289337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:122649482A>G	ENST00000263461.6	+	18	2550	c.2304A>G	c.(2302-2304)gcA>gcG	p.A768A	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)	p.A768A(1)		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						AATTAATAGCAATGTACAATG	0.398													A|||	987	0.197085	0.2579	0.1628	5008	,	,		15097	0.0962		0.2207	False		,,,				2504	0.2188				p.A768A		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.A2304G						PASS	.	A		1230,3176	420.2+/-338.9	180,870,1153	113.0	107.0	109.0		2304	-2.9	1.0	10	dbSNP_100	109	1909,6691	338.5+/-322.8	216,1477,2607	yes	coding-synonymous	WDR11	NM_018117.11		396,2347,3760	GG,GA,AA		22.1977,27.9165,24.135		768/1225	122649482	3139,9867	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon18			AATAGCAATGTAC	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.2304A>G	10.37:g.122649482A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	63	21	0.333333	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			T|0.005;G|0.229	0.229	strong		0.398	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
ABCG8	64241	hgsc.bcm.edu	37	2	44102491	44102491	+	Silent	SNP	C	C	T	rs4148221	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:44102491C>T	ENST00000272286.2	+	11	1785	c.1695C>T	c.(1693-1695)gcC>gcT	p.A565A		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	565	ABC transmembrane type-2.				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)	TCAGCAATGCCCTCTACAACT	0.617													C|||	639	0.127596	0.1694	0.1556	5008	,	,		18103	0.0188		0.1759	False		,,,				2504	0.1135				p.A565A		Atlas-SNP	.											.	ABCG8	98	.	0			c.C1695T						PASS	.	C		727,3679	299.8+/-286.0	60,607,1536	56.0	58.0	57.0		1695	-3.5	0.1	2	dbSNP_110	57	1524,7076	287.1+/-298.1	128,1268,2904	no	coding-synonymous	ABCG8	NM_022437.2		188,1875,4440	TT,TC,CC		17.7209,16.5002,17.3074		565/674	44102491	2251,10755	2203	4300	6503	SO:0001819	synonymous_variant	64241	exon11			CAATGCCCTCTAC	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.1695C>T	2.37:g.44102491C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	37	CCDS1815.1																																																																																			C|0.850;T|0.150	0.150	strong		0.617	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73179672	73179672	+	Silent	SNP	C	C	T	rs3749645	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:73179672C>T	ENST00000426542.2	+	23	3038	c.3018C>T	c.(3016-3018)taC>taT	p.Y1006Y	ARHGEF28_ENST00000513042.2_Silent_p.Y1006Y|ARHGEF28_ENST00000296799.4_Silent_p.Y693Y|ARHGEF28_ENST00000545377.1_Silent_p.Y1006Y|ARHGEF28_ENST00000287898.5_Silent_p.Y1006Y|ARHGEF28_ENST00000512883.1_5'Flank|ARHGEF28_ENST00000437974.1_Silent_p.Y1006Y|ARHGEF28_ENST00000296794.6_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	74	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	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		
DNAH17	8632	hgsc.bcm.edu	37	17	76472768	76472768	+	Silent	SNP	G	G	A	rs7405830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76472768G>A	ENST00000585328.1	-	52	8149	c.8025C>T	c.(8023-8025)ctC>ctT	p.L2675L	DNAH17_ENST00000586052.1_Intron|DNAH17_ENST00000389840.5_Silent_p.L2666L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2666					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)			AAAGGCGGACGAGGTCCAGTG	0.507													A|||	1881	0.375599	0.761	0.2435	5008	,	,		20560	0.2798		0.1909	False		,,,				2504	0.2372				p.L2680L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C8040T						PASS	.	A		2623,1379		873,877,251	110.0	124.0	119.0		8040	-9.5	0.4	17	dbSNP_116	119	1610,6712		158,1294,2709	no	coding-synonymous	DNAH17	NM_173628.3		1031,2171,2960	AA,AG,GG		19.3463,34.4578,34.3476		2680/4463	76472768	4233,8091	2001	4161	6162	SO:0001819	synonymous_variant	8632	exon52			GCGGACGAGGTCC	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.8025C>T	17.37:g.76472768G>A		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	270	143	0.52963	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.641;A|0.359	0.359	strong		0.507	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
DISP1	84976	hgsc.bcm.edu	37	1	223116474	223116474	+	Missense_Mutation	SNP	G	G	T	rs71583926|rs2789975	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:223116474G>T	ENST00000284476.6	+	2	473	c.309G>T	c.(307-309)gaG>gaT	p.E103D	DISP1_ENST00000360254.2_Missense_Mutation_p.E103D|DISP1_ENST00000495684.1_Intron	NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	103			E -> K (in dbSNP:rs2609383).		determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		GCCATCCCGAGGCTGGCCCTG	0.522													G|||	1060	0.211661	0.1566	0.1715	5008	,	,		23499	0.2907		0.1352	False		,,,				2504	0.3119				p.E103D		Atlas-SNP	.											.	DISP1	145	.	0			c.G309T						PASS	.	G	ASP/GLU	738,3668	304.1+/-288.3	59,620,1524	140.0	120.0	127.0		309	4.5	1.0	1	dbSNP_100	127	1176,7424	239.7+/-270.7	86,1004,3210	yes	missense	DISP1	NM_032890.3	45	145,1624,4734	TT,TG,GG		13.6744,16.7499,14.7163	benign	103/1525	223116474	1914,11092	2203	4300	6503	SO:0001583	missense	84976	exon4			TCCCGAGGCTGGC	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.309G>T	1.37:g.223116474G>T	ENSP00000284476:p.Glu103Asp	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	203	132	0.650246	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	399	0.18269230769230768	70	0.14227642276422764	64	0.17679558011049723	156	0.2727272727272727	109	0.1437994722955145	G	11.48	1.650644	0.29336	0.167499	0.136744	ENSG00000154309	ENST00000360254;ENST00000284476	T;D	0.91843	0.85;-2.92	5.62	4.51	0.55191	.	0.682047	0.14375	N	0.323515	T	0.00073	0.0002	L	0.51422	1.61	0.43982	P	0.003322999999999965	B	0.23937	0.094	B	0.16722	0.016	T	0.27297	-1.0078	9	0.14252	T	0.57	-28.9434	15.411	0.74917	0.0781:0.0:0.9219:0.0	rs2789975;rs3814305	103	Q96F81	DISP1_HUMAN	D	103	ENSP00000355848:E103D;ENSP00000284476:E103D	ENSP00000284476:E103D	E	+	3	2	DISP1	221183097	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.341000	0.52151	2.652000	0.90054	0.650000	0.86243	GAG	G|0.844;T|0.156	0.156	strong		0.522	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
ZNF845	91664	hgsc.bcm.edu	37	19	53856702	53856702	+	Missense_Mutation	SNP	G	G	A	rs200114728	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53856702G>A	ENST00000595091.1	+	5	2993	c.2774G>A	c.(2773-2775)cGt>cAt	p.R925H	ZNF845_ENST00000458035.1_Missense_Mutation_p.R925H			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)	p.R925H(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AAAACCTTCCGTCACAATTCA	0.363													.|||	267	0.0533147	0.0484	0.0562	5008	,	,		21751	0.0466		0.0915	False		,,,				2504	0.0256				p.R925H		Atlas-SNP	.											ZNF845,NS,carcinoma,0,6	ZNF845	101	6	3	Substitution - Missense(3)	kidney(3)	c.G2774A						scavenged	.						33.0	30.0	31.0					19																	53856702		692	1591	2283	SO:0001583	missense	91664	exon4			CCTTCCGTCACAA	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.2774G>A	19.37:g.53856702G>A	ENSP00000470005:p.Arg925His	Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	189	14	0.0740741	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	G	5.812	0.334080	0.11013	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.36157	1.27	2.0	-4.0	0.04057	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42585	0.1209	L	0.58302	1.8	0.09310	N	1	D	0.55800	0.973	P	0.53760	0.734	T	0.43925	-0.9361	9	0.51188	T	0.08	.	10.7803	0.46374	0.0:0.6804:0.1821:0.1375	.	925	Q96IR2	ZN845_HUMAN	H	925;841	ENSP00000388311:R925H	ENSP00000412086:R841H	R	+	2	0	ZNF845	58548514	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.662000	0.00032	-1.603000	0.01597	-0.499000	0.04595	CGT	.	.	weak		0.363	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
TCHH	7062	hgsc.bcm.edu	37	1	152083806	152083806	+	Silent	SNP	C	C	T	rs200947543	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152083806C>T	ENST00000368804.1	-	2	1886	c.1887G>A	c.(1885-1887)agG>agA	p.R629R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	629	9 X 28 AA approximate tandem repeats.				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)			GCTGCTGGCGCCTCTCTTCCT	0.677													c|||	18	0.00359425	0.0008	0.0043	5008	,	,		15925	0.0		0.0129	False		,,,				2504	0.001				p.R629R		Atlas-SNP	.											.	TCHH	275	.	0			c.G1887A						PASS	.			8,3992		0,8,1992	34.0	40.0	38.0		1887	-0.7	0.0	1	dbSNP_134	38	85,8265		1,83,4091	no	coding-synonymous	TCHH	NM_007113.2		1,91,6083	TT,TC,CC		1.018,0.2,0.753		629/1944	152083806	93,12257	2000	4175	6175	SO:0001819	synonymous_variant	7062	exon3			CTGGCGCCTCTCT	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.1887G>A	1.37:g.152083806C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	206	127	0.616505	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	37	CCDS41396.1																																																																																			C|0.993;T|0.007	0.007	strong		0.677	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
MTNR1A	4543	hgsc.bcm.edu	37	4	187455329	187455329	+	Silent	SNP	G	G	A	rs8192549	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187455329G>A	ENST00000307161.5	-	2	768	c.567C>T	c.(565-567)atC>atT	p.I189I	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	189					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	CCACCACGGCGATGGTGTAGG	0.577													G|||	48	0.00958466	0.0015	0.0101	5008	,	,		20839	0.001		0.0298	False		,,,				2504	0.0082				p.I189I		Atlas-SNP	.											.	MTNR1A	46	.	0			c.C567T						PASS	.	G		29,4377	36.0+/-67.5	0,29,2174	136.0	131.0	133.0		567	-9.9	0.0	4	dbSNP_117	133	312,8288	111.0+/-171.3	3,306,3991	no	coding-synonymous	MTNR1A	NM_005958.3		3,335,6165	AA,AG,GG		3.6279,0.6582,2.6219		189/351	187455329	341,12665	2203	4300	6503	SO:0001819	synonymous_variant	4543	exon2			CACGGCGATGGTG		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"""GPCR / Class A : Melatonin receptors"""	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.567C>T	4.37:g.187455329G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	65	13	0.2	NM_005958	A0AVC5|B0M0L2	Silent	SNP	ENST00000307161.5	37	CCDS3848.1																																																																																			G|0.977;A|0.023	0.023	strong		0.577	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1		
ZBED4	9889	hgsc.bcm.edu	37	22	50277968	50277968	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50277968G>T	ENST00000216268.5	+	2	1135	c.658G>T	c.(658-660)Gat>Tat	p.D220Y		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	220						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)		CCCGTCCCCCGATCGAATAAC	0.547																																					p.D220Y		Atlas-SNP	.											ZBED4,NS,carcinoma,0,1	ZBED4	102	1	0			c.G658T						scavenged	.						59.0	57.0	57.0					22																	50277968		2203	4300	6503	SO:0001583	missense	9889	exon2			TCCCCCGATCGAA	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.658G>T	22.37:g.50277968G>T	ENSP00000216268:p.Asp220Tyr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	110	2	0.0181818	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Missense_Mutation	SNP	ENST00000216268.5	37	CCDS33677.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.327698	0.41197	.	.	ENSG00000100426	ENST00000216268	T	0.52057	0.68	5.31	4.29	0.51040	.	0.282737	0.33253	N	0.005105	T	0.40247	0.1109	L	0.27053	0.805	0.52099	D	0.999946	P	0.43826	0.818	B	0.42163	0.378	T	0.46442	-0.9191	10	0.87932	D	0	-8.5986	16.0896	0.81084	0.0:0.1342:0.8658:0.0	.	220	O75132	ZBED4_HUMAN	Y	220	ENSP00000216268:D220Y	ENSP00000216268:D220Y	D	+	1	0	ZBED4	48663972	1.000000	0.71417	0.059000	0.19551	0.017000	0.09413	6.103000	0.71492	1.457000	0.47850	0.650000	0.86243	GAT	.	.	none		0.547	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
HMG20A	10363	hgsc.bcm.edu	37	15	77750802	77750802	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:77750802A>G	ENST00000381714.3	+	3	481	c.53A>G	c.(52-54)gAc>gGc	p.D18G	HMG20A_ENST00000336216.4_Missense_Mutation_p.D18G	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	18					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						GCAGATGAAGACGGTTCCAAG	0.423																																					p.D18G		Atlas-SNP	.											.	HMG20A	48	.	0			c.A53G						PASS	.						94.0	94.0	94.0					15																	77750802		2196	4294	6490	SO:0001583	missense	10363	exon3			ATGAAGACGGTTC	AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"""High mobility group / Non-canonical"""	5001	protein-coding gene	gene with protein product	"""HMG box domain containing 1"""	605534	"""high-mobility group 20A"""			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.53A>G	15.37:g.77750802A>G	ENSP00000371133:p.Asp18Gly	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	63	5	0.0793651	NM_018200	A6NHY3|D3DW78|Q53G31|Q9NSF6	Missense_Mutation	SNP	ENST00000381714.3	37	CCDS10295.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.820448	0.50633	.	.	ENSG00000140382	ENST00000336216;ENST00000381714	T;T	0.70986	-0.53;-0.53	5.76	5.76	0.90799	.	0.067632	0.64402	D	0.000012	T	0.67011	0.2848	N	0.24115	0.695	0.44816	D	0.997829	B;P	0.46395	0.247;0.877	B;P	0.49829	0.053;0.623	T	0.71431	-0.4595	10	0.66056	D	0.02	-17.0189	14.3238	0.66505	1.0:0.0:0.0:0.0	.	18;18	Q9NP66;Q9NP66-2	HM20A_HUMAN;.	G	18	ENSP00000336856:D18G;ENSP00000371133:D18G	ENSP00000336856:D18G	D	+	2	0	HMG20A	75537857	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.672000	0.68102	2.200000	0.70718	0.460000	0.39030	GAC	.	.	none		0.423	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200	
HNF1A	6927	hgsc.bcm.edu	37	12	121437114	121437114	+	Silent	SNP	G	G	A	rs55834942	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	HNF1A_ENST00000544413.1_Silent_p.T515T|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000541395.1_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	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	241	117	0.485477	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	
MUC17	140453	hgsc.bcm.edu	37	7	100679809	100679809	+	Silent	SNP	C	C	T	rs71525815|rs4992074	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100679809C>T	ENST00000306151.4	+	3	5176	c.5112C>T	c.(5110-5112)agC>agT	p.S1704S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1704	59 X approximate tandem repeats.|Ser-rich.				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)					CGGTGGCCAGCTCTGCAATCA	0.483													T|||	1178	0.235224	0.3396	0.1023	5008	,	,		24513	0.253		0.1213	False		,,,				2504	0.2873				p.S1704S		Atlas-SNP	.											.	MUC17	804	.	0			c.C5112T						PASS	.	T		1324,3082	695.5+/-405.9	207,910,1086	188.0	203.0	198.0		5112	-1.2	0.0	7	dbSNP_113	198	999,7601	773.3+/-407.7	57,885,3358	no	coding-synonymous	MUC17	NM_001040105.1		264,1795,4444	TT,TC,CC		11.6163,30.0499,17.861		1704/4494	100679809	2323,10683	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			GGCCAGCTCTGCA	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.5112C>T	7.37:g.100679809C>T		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.823;T|0.177	0.177	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
GUCA1C	9626	hgsc.bcm.edu	37	3	108639384	108639384	+	Missense_Mutation	SNP	T	T	C	rs6804162	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:108639384T>C	ENST00000261047.3	-	2	385	c.253A>G	c.(253-255)Atg>Gtg	p.M85V	GUCA1C_ENST00000393963.3_Missense_Mutation_p.M85V|GUCA1C_ENST00000471108.1_Missense_Mutation_p.M85V	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	85	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		M -> V (in dbSNP:rs6804162).		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						TTTTCTTGCATGATTAGATTT	0.289													C|||	1688	0.337061	0.438	0.2522	5008	,	,		18067	0.25		0.3807	False		,,,				2504	0.3057				p.M85V	NSCLC(157;1360 1999 30631 40189 44208)	Atlas-SNP	.											.	GUCA1C	39	.	0			c.A253G						PASS	.	C	VAL/MET	1844,2562	630.5+/-395.5	393,1058,752	77.0	74.0	75.0		253	3.1	0.0	3	dbSNP_116	75	3062,5534	657.8+/-401.5	548,1966,1784	yes	missense	GUCA1C	NM_005459.3	21	941,3024,2536	CC,CT,TT		35.6212,41.852,37.7327	benign	85/210	108639384	4906,8096	2203	4298	6501	SO:0001583	missense	9626	exon2			CTTGCATGATTAG	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.253A>G	3.37:g.108639384T>C	ENSP00000261047:p.Met85Val	Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	318	315	0.990566	NM_005459	O95844|Q9UNM0	Missense_Mutation	SNP	ENST00000261047.3	37	CCDS2954.1	741	0.3392857142857143	205	0.4166666666666667	93	0.2569060773480663	143	0.25	300	0.39577836411609496	C	6.052	0.377909	0.11466	0.41852	0.356212	ENSG00000138472	ENST00000393963;ENST00000261047;ENST00000471108	T;T;T	0.40476	1.03;1.03;1.03	5.17	3.1	0.35709	EF-hand-like domain (1);	0.215490	0.39909	N	0.001229	T	0.00012	0.0000	N	0.11255	0.115	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44757	-0.9307	9	0.06236	T	0.91	.	2.791	0.05388	0.2015:0.4347:0.0:0.3638	rs6804162;rs52828740;rs56507439;rs56791641;rs6804162	85;85	C9JNI2;O95843	.;GUC1C_HUMAN	V	85	ENSP00000377535:M85V;ENSP00000261047:M85V;ENSP00000417761:M85V	ENSP00000261047:M85V	M	-	1	0	GUCA1C	110122074	0.009000	0.17119	0.005000	0.12908	0.729000	0.41735	-0.034000	0.12225	0.598000	0.29829	-0.186000	0.12905	ATG	T|0.647;C|0.353	0.353	strong		0.289	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459	
CP	1356	hgsc.bcm.edu	37	3	148904434	148904434	+	Silent	SNP	T	T	G	rs1053709	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:148904434T>G	ENST00000264613.6	-	11	2212	c.1950A>C	c.(1948-1950)ggA>ggC	p.G650G	CP_ENST00000462336.1_5'UTR	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	650	F5/8 type A 2.|Plastocyanin-like 4.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CGGCCTCATTTCCGGCGCTGA	0.458													T|||	98	0.0195687	0.0008	0.036	5008	,	,		20261	0.001		0.0457	False		,,,				2504	0.0256				p.G650G		Atlas-SNP	.											.	CP	112	.	0			c.A1950C						PASS	.	T		59,4347	55.5+/-91.7	1,57,2145	154.0	139.0	144.0		1950	2.2	1.0	3	dbSNP_86	144	520,8080	146.2+/-201.8	10,500,3790	no	coding-synonymous	CP	NM_000096.3		11,557,5935	GG,GT,TT		6.0465,1.3391,4.4518		650/1066	148904434	579,12427	2203	4300	6503	SO:0001819	synonymous_variant	1356	exon11			CTCATTTCCGGCG	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1950A>C	3.37:g.148904434T>G		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	263	137	0.520913	NM_000096	Q14063|Q2PP18|Q9UKS4	Silent	SNP	ENST00000264613.6	37	CCDS3141.1																																																																																			T|0.962;G|0.038	0.038	strong		0.458	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	
FAM189A1	23359	hgsc.bcm.edu	37	15	29416901	29416901	+	Missense_Mutation	SNP	A	A	G	rs2279482	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:29416901A>G	ENST00000261275.4	-	10	1291	c.1292T>C	c.(1291-1293)gTg>gCg	p.V431A		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	431			V -> A (in dbSNP:rs2279482).			integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						GCTCCCAGGCACAGCCTCAGA	0.562													a|||	858	0.171326	0.2315	0.1153	5008	,	,		16403	0.2202		0.0775	False		,,,				2504	0.1759				p.V431A		Atlas-SNP	.											.	FAM189A1	20	.	0			c.T1292C						PASS	.	G	ALA/VAL	311,1073		40,231,421	63.0	69.0	67.0		1292	-3.4	0.0	15	dbSNP_100	67	231,2951		9,213,1369	yes	missense	FAM189A1	NM_015307.1	64	49,444,1790	GG,GA,AA		7.2596,22.4711,11.8703	benign	431/540	29416901	542,4024	692	1591	2283	SO:0001583	missense	23359	exon10			CCAGGCACAGCCT		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.1292T>C	15.37:g.29416901A>G	ENSP00000261275:p.Val431Ala	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	32	26	0.8125	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	37	CCDS45198.1	330	0.1510989010989011	113	0.22967479674796748	40	0.11049723756906077	122	0.21328671328671328	55	0.07255936675461741	a	0.012	-1.672619	0.00758	0.224711	0.072596	ENSG00000104059	ENST00000261275	T	0.09630	2.96	4.28	-3.41	0.04839	.	2.367780	0.01632	N	0.023592	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	0.43294	-0.9400	9	0.15066	T	0.55	-18.2153	3.3831	0.07261	0.2555:0.1122:0.508:0.1243	rs2279482;rs59311904;rs2279482	431	O60320	F1891_HUMAN	A	431	ENSP00000261275:V431A	ENSP00000261275:V431A	V	-	2	0	FAM189A1	27204193	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.069000	0.14552	-0.411000	0.07530	-3.557000	0.00030	GTG	A|0.843;G|0.157	0.157	strong		0.562	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
KHSRP	8570	hgsc.bcm.edu	37	19	6416627	6416627	+	Silent	SNP	C	C	T	rs149214856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6416627C>T	ENST00000398148.3	-	14	1454	c.1362G>A	c.(1360-1362)acG>acA	p.T454T	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	454	Gly-rich.|KH 4. {ECO:0000255|PROSITE- ProRule:PRU00117}.				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						CGAAGGCTCCCGTCTGCTGGT	0.587													C|||	8	0.00159744	0.0	0.0043	5008	,	,		17267	0.0		0.005	False		,,,				2504	0.0				p.T454T	Colon(55;593 1006 2067 9135 22980)	Atlas-SNP	.											KHSRP,NS,carcinoma,-1,1	KHSRP	51	1	0			c.G1362A						scavenged	.	C		2,3890		0,2,1944	44.0	48.0	47.0		1362	-10.6	0.4	19	dbSNP_134	47	22,8262		0,22,4120	no	coding-synonymous	KHSRP	NM_003685.2		0,24,6064	TT,TC,CC		0.2656,0.0514,0.1971		454/712	6416627	24,12152	1946	4142	6088	SO:0001819	synonymous_variant	8570	exon14			GGCTCCCGTCTGC	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		ENST00000398148.3:c.1362G>A	19.37:g.6416627C>T		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	126	74	0.587302	NM_003685	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Silent	SNP	ENST00000398148.3	37	CCDS45936.1																																																																																			C|0.998;T|0.002	0.002	strong		0.587	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1		
NPY4R	5540	hgsc.bcm.edu	37	10	47087609	47087609	+	Missense_Mutation	SNP	G	G	A	rs386743380|rs79871698	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	67	0	0		WXS	Illumina HiSeq	Phase_I	74	16	0.216216	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		
ZNF649	65251	hgsc.bcm.edu	37	19	52394736	52394736	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52394736T>C	ENST00000354957.3	-	5	937	c.653A>G	c.(652-654)aAg>aGg	p.K218R	ZNF649_ENST00000600738.1_Splice_Site_p.K218R|CTC-429C10.2_ENST00000600329.1_RNA	NM_023074.3	NP_075562.2	Q9BS31	ZN649_HUMAN	zinc finger protein 649	218					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00152)|OV - Ovarian serous cystadenocarcinoma(262;0.0185)		GAGCCTGTACTTCTTGTAGAA	0.483																																					p.K218R		Atlas-SNP	.											ZNF649,NS,carcinoma,0,2	ZNF649	72	2	0			c.A653G						scavenged	.						119.0	114.0	116.0					19																	52394736		2203	4300	6503	SO:0001583	missense	65251	exon5			CTGTACTTCTTGT	BC005368	CCDS12843.1	19q13.41	2013-01-08				ENSG00000198093		"""Zinc fingers, C2H2-type"", ""-"""	25741	protein-coding gene	gene with protein product		611903				15950191	Standard	NM_023074		Approved	FLJ12644	uc002pxy.3	Q9BS31		ENST00000354957.3:c.653A>G	19.37:g.52394736T>C	ENSP00000347043:p.Lys218Arg	Somatic	354	5	0.0141243		WXS	Illumina HiSeq	Phase_I	354	5	0.0141243	NM_023074	A8MYJ5|B2RDC4|Q9H9N2	Missense_Mutation	SNP	ENST00000354957.3	37	CCDS12843.1	.	.	.	.	.	.	.	.	.	.	T	10.18	1.278977	0.23307	.	.	ENSG00000198093	ENST00000354957	T	0.15834	2.39	2.61	0.223	0.15292	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09818	0.0241	N	0.21583	0.68	0.09310	N	1	B	0.23185	0.081	B	0.15484	0.013	T	0.33059	-0.9883	9	0.31617	T	0.26	.	6.6154	0.22774	0.0:0.2836:0.0:0.7164	.	218	Q9BS31	ZN649_HUMAN	R	218	ENSP00000347043:K218R	ENSP00000347043:K218R	K	-	2	0	ZNF649	57086548	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.478000	0.06575	0.157000	0.19338	0.327000	0.21459	AAG	.	.	none		0.483	ZNF649-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461097.1	NM_023074	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100803982	100803982	+	Silent	SNP	C	C	T	rs79213484	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:100803982C>T	ENST00000298815.8	+	7	696	c.693C>T	c.(691-693)aaC>aaT	p.N231N	ARHGAP42_ENST00000524892.2_Silent_p.N197N|snoU13_ENST00000459511.1_RNA	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	126	0	0		WXS	Illumina HiSeq	Phase_I	211	56	0.265403	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	
RANBP2	5903	hgsc.bcm.edu	37	2	109367844	109367844	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	1915	10	0.00522193		WXS	Illumina HiSeq	Phase_I	1919	20	0.0104221	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	
THADA	63892	hgsc.bcm.edu	37	2	43625184	43625184	+	Missense_Mutation	SNP	T	T	A	rs33979934	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:43625184T>A	ENST00000405006.4	-	29	4504	c.4153A>T	c.(4153-4155)Act>Tct	p.T1385S	THADA_ENST00000485353.1_5'UTR|THADA_ENST00000415080.2_Missense_Mutation_p.T1066S|THADA_ENST00000330266.7_Intron|THADA_ENST00000405975.2_Missense_Mutation_p.T1385S	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1385			T -> S (in dbSNP:rs33979934). {ECO:0000269|PubMed:15489334}.					p.T1385S(1)		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)				GACAACAGAGTTCGAATGGTA	0.493													T|||	1068	0.213259	0.2723	0.1412	5008	,	,		19775	0.0327		0.2704	False		,,,				2504	0.3119				p.T1385S		Atlas-SNP	.											THADA,NS,carcinoma,0,1	THADA	131	1	1	Substitution - Missense(1)	stomach(1)	c.A4153T						scavenged	.	T	SER/THR,SER/THR	981,3127		126,729,1199	158.0	161.0	160.0		4153,4153	-10.3	0.0	2	dbSNP_126	160	2088,6336		268,1552,2392	yes	missense,missense	THADA	NM_001083953.1,NM_022065.4	58,58	394,2281,3591	AA,AT,TT		24.7863,23.8802,24.4893	benign,benign	1385/1954,1385/1954	43625184	3069,9463	2054	4212	6266	SO:0001583	missense	63892	exon29			ACAGAGTTCGAAT	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.4153A>T	2.37:g.43625184T>A	ENSP00000385995:p.Thr1385Ser	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	207	101	0.487923	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	421|421	0.19276556776556777|0.19276556776556777	128|128	0.2601626016260163|0.2601626016260163	54|54	0.14917127071823205|0.14917127071823205	26|26	0.045454545454545456|0.045454545454545456	213|213	0.28100263852242746|0.28100263852242746	T|T	3.520|3.520	-0.097927|-0.097927	0.07010|0.07010	0.238802|0.238802	0.247863|0.247863	ENSG00000115970|ENSG00000115970	ENST00000407351|ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006	.|T;T;T	.|0.64803	.|-0.12;-0.12;-0.12	5.17|5.17	-10.3|-10.3	0.00346|0.00346	.|Armadillo-type fold (1);	.|0.961987	.|0.08558	.|N	.|0.927958	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01576|0.01576	-0.805|-0.805	0.45762|0.45762	P|P	0.0013440000000000119|0.0013440000000000119	.|B;B;B;B	.|0.18968	.|0.004;0.032;0.002;0.001	.|B;B;B;B	.|0.20767	.|0.007;0.031;0.002;0.001	T|T	0.16988|0.16988	-1.0384|-1.0384	4|9	.|0.18710	.|T	.|0.47	.|.	8.8731|8.8731	0.35327|0.35327	0.236:0.5274:0.0:0.2366|0.236:0.5274:0.0:0.2366	rs33979934;rs61143339|rs33979934;rs61143339	.|1064;1312;1066;1385	.|Q6YHU6-2;B6ZDQ0;C9JJB1;Q6YHU6	.|.;.;.;THADA_HUMAN	D|S	624|1385;1312;1066;1385	.|ENSP00000386088:T1385S;ENSP00000416048:T1066S;ENSP00000385995:T1385S	.|ENSP00000349464:T1312S	E|T	-|-	3|1	2|0	THADA|THADA	43478688|43478688	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.014000|0.014000	0.08584|0.08584	-0.358000|-0.358000	0.07641|0.07641	-1.592000|-1.592000	0.01619|0.01619	-0.248000|-0.248000	0.11899|0.11899	GAA|ACT	A|0.209;T|0.791	0.209	strong		0.493	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
CLHC1	130162	hgsc.bcm.edu	37	2	55449464	55449464	+	Silent	SNP	T	T	C	rs17852670	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:55449464T>C	ENST00000401408.1	-	3	429	c.84A>G	c.(82-84)caA>caG	p.Q28Q	CLHC1_ENST00000494539.1_Intron|CLHC1_ENST00000407122.1_Silent_p.Q28Q|CLHC1_ENST00000406437.2_5'UTR|CLHC1_ENST00000406076.1_Intron	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	28																	TTATGTATCTTTGCACACTTT	0.353													T|||	1142	0.228035	0.1324	0.2248	5008	,	,		17106	0.3482		0.2107	False		,,,				2504	0.2536				p.Q28Q		Atlas-SNP	.											.	.	.	.	0			c.A84G						PASS	.	T	,	656,3748	281.9+/-276.2	59,538,1605	200.0	198.0	199.0		,84	1.9	1.0	2	dbSNP_123	199	1862,6738	333.7+/-320.7	206,1450,2644	no	intron,coding-synonymous	C2orf63	NM_001135598.1,NM_152385.2	,	265,1988,4249	CC,CT,TT		21.6512,14.8955,19.3633	,	,28/587	55449464	2518,10486	2202	4300	6502	SO:0001819	synonymous_variant	130162	exon3			GTATCTTTGCACA		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.84A>G	2.37:g.55449464T>C		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	204	198	0.970588	NM_152385	B2RDV1|Q53R93|Q8N403	Silent	SNP	ENST00000401408.1	37	CCDS33201.1																																																																																			T|0.796;C|0.204	0.204	strong		0.353	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
COL4A3	1285	hgsc.bcm.edu	37	2	228135631	228135631	+	Missense_Mutation	SNP	C	C	T	rs28381984	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:228135631C>T	ENST00000396578.3	+	25	1883	c.1721C>T	c.(1720-1722)cCg>cTg	p.P574L	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000439598.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	574	Triple-helical region.		P -> L (in dbSNP:rs28381984). {ECO:0000269|PubMed:8083201}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CCTGGAACTCCGGGAGTGAAA	0.507													C|||	2003	0.39996	0.152	0.4409	5008	,	,		17505	0.4752		0.4732	False		,,,				2504	0.5532				p.P574L		Atlas-SNP	.											COL4A3_ENST00000328380,NS,carcinoma,-1,2	COL4A3	293	2	0			c.C1721T						PASS	.	C	LEU/PRO	782,2936		92,598,1169	54.0	58.0	56.0		1721	5.8	0.1	2	dbSNP_125	56	3848,4336		917,2014,1161	yes	missense	COL4A3	NM_000091.4	98	1009,2612,2330	TT,TC,CC		47.0186,21.0328,38.901	probably-damaging	574/1671	228135631	4630,7272	1859	4092	5951	SO:0001583	missense	1285	exon25			GAACTCCGGGAGT		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.1721C>T	2.37:g.228135631C>T	ENSP00000379823:p.Pro574Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	77	59	0.766234	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	856	0.39194139194139194	81	0.16463414634146342	161	0.4447513812154696	266	0.46503496503496505	348	0.45910290237467016	C	19.26	3.793365	0.70452	0.210328	0.470186	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.93076	-3.16	5.8	5.8	0.92144	.	0.108401	0.41605	D	0.000847	T	0.00012	0.0000	M	0.77103	2.36	0.09310	P	0.999999516562	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.944;0.987;1.0;0.998	T	0.00000	-1.3321	9	0.59425	D	0.04	.	16.9678	0.86290	0.0:1.0:0.0:0.0	rs28381984;rs58545005;rs28381984	574;574;574;574	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	L	574	ENSP00000379823:P574L	ENSP00000323334:P574L	P	+	2	0	COL4A3	227843875	0.367000	0.25023	0.130000	0.21974	0.769000	0.43574	2.193000	0.42658	2.740000	0.93945	0.650000	0.86243	CCG	C|0.604;T|0.396	0.396	strong		0.507	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
MUC17	140453	hgsc.bcm.edu	37	7	100679760	100679760	+	Missense_Mutation	SNP	G	G	A	rs73168394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100679760G>A	ENST00000306151.4	+	3	5127	c.5063G>A	c.(5062-5064)gGa>gAa	p.G1688E		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1688	59 X approximate tandem repeats.|Ser-rich.				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)					TATACTGAAGGAAGAACTCCT	0.478																																					p.G1688E		Atlas-SNP	.											MUC17,caecum,carcinoma,0,2	MUC17	804	2	0			c.G5063A						scavenged	.						187.0	202.0	197.0					7																	100679760		2203	4300	6503	SO:0001583	missense	140453	exon3			CTGAAGGAAGAAC	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.5063G>A	7.37:g.100679760G>A	ENSP00000302716:p.Gly1688Glu	Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	184	52	0.282609	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.044	-1.274900	0.01410	.	.	ENSG00000169876	ENST00000306151	T	0.06068	3.35	0.579	-1.16	0.09678	.	.	.	.	.	T	0.02649	0.0080	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.46062	-0.9218	8	0.02654	T	1	.	.	.	.	.	1688	Q685J3	MUC17_HUMAN	E	1688	ENSP00000302716:G1688E	ENSP00000302716:G1688E	G	+	2	0	MUC17	100466480	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.758000	0.00374	-0.992000	0.03472	-1.407000	0.01130	GGA	G|0.989;A|0.011	0.011	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
COL21A1	81578	hgsc.bcm.edu	37	6	56035495	56035495	+	Silent	SNP	G	G	A	rs41271846	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56035495G>A	ENST00000244728.5	-	5	1375	c.978C>T	c.(976-978)agC>agT	p.S326S	COL21A1_ENST00000535941.1_Silent_p.S326S|COL21A1_ENST00000370819.1_Silent_p.S326S	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	326	Laminin G-like.				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(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			CATTAATTACGCTGGTTGTTG	0.358													G|||	9	0.00179712	0.0	0.0	5008	,	,		17653	0.0		0.005	False		,,,				2504	0.0041				p.S326S		Atlas-SNP	.											.	COL21A1	201	.	0			c.C978T						PASS	.	G		7,3729		0,7,1861	79.0	71.0	74.0		978	1.5	0.6	6	dbSNP_127	74	72,8136		1,70,4033	no	coding-synonymous	COL21A1	NM_030820.3		1,77,5894	AA,AG,GG		0.8772,0.1874,0.6614		326/958	56035495	79,11865	1868	4104	5972	SO:0001819	synonymous_variant	81578	exon5			AATTACGCTGGTT	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.978C>T	6.37:g.56035495G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Silent	SNP	ENST00000244728.5	37	CCDS55025.1																																																																																			G|0.997;A|0.003	0.003	strong		0.358	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
CHRNA2	1135	hgsc.bcm.edu	37	8	27328511	27328511	+	Missense_Mutation	SNP	G	G	A	rs2472553	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:27328511G>A	ENST00000520933.2	-	1	218	c.65C>T	c.(64-66)aCc>aTc	p.T22I	CHRNA2_ENST00000407991.1_Missense_Mutation_p.T22I|CHRNA2_ENST00000240132.2_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	180	0	0		WXS	Illumina HiSeq	Phase_I	210	81	0.385714	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		
ACAD9	28976	hgsc.bcm.edu	37	3	128627933	128627933	+	Silent	SNP	C	C	T	rs876755	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:128627933C>T	ENST00000308982.7	+	14	1557	c.1476C>T	c.(1474-1476)ccC>ccT	p.P492P	ACAD9_ENST00000511526.1_3'UTR	NM_014049.4	NP_054768.2	Q9H845	ACAD9_HUMAN	acyl-CoA dehydrogenase family, member 9	492						dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	30						TTGTGCACCCCAGTCTTGCGG	0.592													C|||	1554	0.310304	0.2852	0.2651	5008	,	,		19974	0.5665		0.1899	False		,,,				2504	0.2362				p.P492P		Atlas-SNP	.											.	ACAD9	51	.	0			c.C1476T						PASS	.	C		1173,3233	413.9+/-336.6	166,841,1196	56.0	50.0	52.0		1476	1.4	0.7	3	dbSNP_86	52	1876,6724	333.6+/-320.6	202,1472,2626	no	coding-synonymous	ACAD9	NM_014049.4		368,2313,3822	TT,TC,CC		21.814,26.6228,23.443		492/622	128627933	3049,9957	2203	4300	6503	SO:0001819	synonymous_variant	28976	exon14			GCACCCCAGTCTT	AF078854	CCDS3053.1	3q21.3	2013-05-24	2010-04-30		ENSG00000177646	ENSG00000177646		"""Mitochondrial respiratory chain complex assembly factors"""	21497	protein-coding gene	gene with protein product		611103	"""acyl-Coenzyme A dehydrogenase family, member 9"""			12359260, 21057504, 20816094	Standard	NM_014049		Approved	NPD002, MGC14452	uc003ela.4	Q9H845	OTTHUMG00000159942	ENST00000308982.7:c.1476C>T	3.37:g.128627933C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_014049	D3DNB8|Q8WXX3	Silent	SNP	ENST00000308982.7	37	CCDS3053.1																																																																																			C|0.723;T|0.277	0.277	strong		0.592	ACAD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358405.1	NM_014049	
KRT76	51350	hgsc.bcm.edu	37	12	53164848	53164848	+	Silent	SNP	G	G	A	rs7313832	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53164848G>A	ENST00000332411.2	-	7	1472	c.1419C>T	c.(1417-1419)aaC>aaT	p.N473N		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	473	Coil 2.|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						CCAGCTTGACGTTCATCAGCT	0.577													G|||	2089	0.417133	0.3555	0.3991	5008	,	,		16564	0.3919		0.5855	False		,,,				2504	0.3661				p.N473N		Atlas-SNP	.											KRT76,NS,adenoma,0,1	KRT76	72	1	0			c.C1419T						scavenged	.	G		1630,2776	502.0+/-365.1	303,1024,876	130.0	118.0	122.0		1419	-7.3	0.1	12	dbSNP_116	122	4790,3810	613.1+/-396.0	1335,2120,845	no	coding-synonymous	KRT76	NM_015848.4		1638,3144,1721	AA,AG,GG		44.3023,36.995,49.3618		473/639	53164848	6420,6586	2203	4300	6503	SO:0001819	synonymous_variant	51350	exon7			CTTGACGTTCATC	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.1419C>T	12.37:g.53164848G>A		Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	159	69	0.433962	NM_015848	B4DRR3|Q7Z795	Silent	SNP	ENST00000332411.2	37	CCDS8838.1																																																																																			G|0.510;A|0.490	0.490	strong		0.577	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
BTNL2	56244	hgsc.bcm.edu	37	6	32363816	32363816	+	Splice_Site	SNP	T	T	C	rs2076530	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32363816T>C	ENST00000374993.1	-	5	1077	c.1078A>G	c.(1078-1080)Agt>Ggt	p.S360G	BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000414363.1_Splice_Site_p.S150G|BTNL2_ENST00000544175.1_Splice_Site_p.S83G|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Splice_Site_p.S266G|BTNL2_ENST00000540315.1_Splice_Site_p.S150G|BTNL2_ENST00000454136.3_Splice_Site_p.S360G	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	61	0	0		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	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
NOD2	64127	hgsc.bcm.edu	37	16	50745583	50745583	+	Silent	SNP	T	T	G	rs1861759	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	106	0	0		WXS	Illumina HiSeq	Phase_I	89	86	0.966292	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	
SYK	6850	hgsc.bcm.edu	37	9	93641175	93641175	+	Silent	SNP	C	C	T	rs2306041	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:93641175C>T	ENST00000375754.4	+	11	1669	c.1521C>T	c.(1519-1521)taC>taT	p.Y507Y	SYK_ENST00000375747.1_Silent_p.Y484Y|SYK_ENST00000375746.1_Silent_p.Y507Y|SYK_ENST00000375751.4_Silent_p.Y484Y	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	507	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|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)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						CCCAACATTACGCCAAGATCA	0.438			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								C|||	993	0.198283	0.2179	0.366	5008	,	,		20099	0.2321		0.1362	False		,,,				2504	0.0818				p.Y507Y		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.C1521T						PASS	.	C	,,,	968,3438	365.4+/-317.4	102,764,1337	181.0	158.0	166.0		1452,1521,1452,1521	-3.4	1.0	9	dbSNP_100	166	1215,7385	245.3+/-274.2	88,1039,3173	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	190,1803,4510	TT,TC,CC		14.1279,21.97,16.7846	,,,	484/613,507/636,484/613,507/636	93641175	2183,10823	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon11			ACATTACGCCAAG	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1521C>T	9.37:g.93641175C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	176	89	0.505682	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			C|0.822;T|0.178	0.178	strong		0.438	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
KIAA0556	23247	hgsc.bcm.edu	37	16	27784497	27784497	+	Missense_Mutation	SNP	G	G	A	rs117316062	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:27784497G>A	ENST00000261588.4	+	23	4295	c.4276G>A	c.(4276-4278)Gag>Aag	p.E1426K		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1426						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						GCTGTATGACGAGCGAGGAGA	0.542													G|||	47	0.00938498	0.0	0.0231	5008	,	,		18339	0.0		0.0278	False		,,,				2504	0.0031				p.E1426K		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G4276A						PASS	.	G	LYS/GLU	32,4362	38.4+/-70.7	1,30,2166	62.0	56.0	58.0		4276	4.9	0.3	16	dbSNP_132	58	253,8347	97.9+/-159.5	1,251,4048	yes	missense	KIAA0556	NM_015202.2	56	2,281,6214	AA,AG,GG		2.9419,0.7283,2.1933	benign	1426/1619	27784497	285,12709	2197	4300	6497	SO:0001583	missense	23247	exon23			TATGACGAGCGAG	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.4276G>A	16.37:g.27784497G>A	ENSP00000261588:p.Glu1426Lys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	59	34	0.576271	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	G	14.66	2.600602	0.46423	0.007283	0.029419	ENSG00000047578	ENST00000261588	T	0.13901	2.55	4.89	4.89	0.63831	.	0.064498	0.64402	D	0.000008	T	0.06600	0.0169	L	0.49350	1.555	0.44816	D	0.99782	P	0.45715	0.865	P	0.45639	0.488	T	0.02646	-1.1129	10	0.23302	T	0.38	-26.6329	17.6554	0.88176	0.0:0.0:1.0:0.0	.	1426	O60303	K0556_HUMAN	K	1426	ENSP00000261588:E1426K	ENSP00000261588:E1426K	E	+	1	0	KIAA0556	27691998	1.000000	0.71417	0.251000	0.24312	0.199000	0.23934	5.062000	0.64326	2.254000	0.74563	0.561000	0.74099	GAG	G|0.983;A|0.017	0.017	strong		0.542	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
CCDC79	283847	hgsc.bcm.edu	37	16	66812797	66812797	+	Silent	SNP	C	C	T	rs363162	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:66812797C>T	ENST00000558713.2	-	9	894	c.822G>A	c.(820-822)acG>acA	p.T274T	CCDC79_ENST00000432602.1_Silent_p.T274T|CCDC79_ENST00000415744.1_Silent_p.T274T|CCDC79_ENST00000433574.1_Silent_p.T274T|CCDC79_ENST00000561333.1_5'UTR|CCDC79_ENST00000433154.1_Silent_p.T274T			Q8NA31	TERB1_HUMAN	coiled-coil domain containing 79	274					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						CCACAGTCTTCGTCACAACCA	0.403													T|||	2896	0.578275	0.677	0.4928	5008	,	,		19836	0.6498		0.4384	False		,,,				2504	0.5757				p.T274T		Atlas-SNP	.											.	CCDC79	32	.	0			c.G822A						PASS	.	T		867,517		271,325,96	165.0	127.0	139.0		822	3.6	1.0	16	dbSNP_79	139	1387,1795		308,771,512	no	coding-synonymous	CCDC79	NM_001136505.1		579,1096,608	TT,TC,CC		43.5889,37.3555,49.3649		274/728	66812797	2254,2312	692	1591	2283	SO:0001819	synonymous_variant	283847	exon10			AGTCTTCGTCACA	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.822G>A	16.37:g.66812797C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	101	17	0.168317	NM_001136505	A0AUW1	Silent	SNP	ENST00000558713.2	37																																																																																				C|0.441;T|0.559	0.559	strong		0.403	CCDC79-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000418864.2		
IGFN1	91156	hgsc.bcm.edu	37	1	201183424	201183424	+	Missense_Mutation	SNP	G	G	A	rs41304263	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201183424G>A	ENST00000335211.4	+	13	8978	c.8848G>A	c.(8848-8850)Gtc>Atc	p.V2950I	IGFN1_ENST00000295591.8_Missense_Mutation_p.V110I|IGFN1_ENST00000451870.2_Missense_Mutation_p.V493I	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	493						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						TAAGGATGGCGTCAAGGTACT	0.577													G|||	97	0.019369	0.0076	0.0389	5008	,	,		17684	0.0		0.0437	False		,,,				2504	0.0164				p.V2950I		Atlas-SNP	.											.	IGFN1	220	.	0			c.G8848A						PASS	.	G	ILE/VAL	80,4326	65.3+/-102.7	0,80,2123	66.0	51.0	56.0		8848	2.8	1.0	1	dbSNP_127	56	522,8078	142.2+/-198.4	16,490,3794	yes	missense	IGFN1	NM_001164586.1	29	16,570,5917	AA,AG,GG		6.0698,1.8157,4.6286	benign	2950/3709	201183424	602,12404	2203	4300	6503	SO:0001583	missense	91156	exon13			GATGGCGTCAAGG	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.8848G>A	1.37:g.201183424G>A	ENSP00000334714:p.Val2950Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	127	84	0.661417	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	57|57	0.0260989010989011|0.0260989010989011	11|11	0.022357723577235773|0.022357723577235773	14|14	0.03867403314917127|0.03867403314917127	0|0	0.0|0.0	32|32	0.04221635883905013|0.04221635883905013	G|G	12.91|12.91	2.079584|2.079584	0.36662|0.36662	0.018157|0.018157	0.060698|0.060698	ENSG00000163395|ENSG00000163395	ENST00000412892|ENST00000335211;ENST00000451870;ENST00000295591	.|T;T;T	.|0.66815	.|-0.23;-0.23;-0.23	3.66|3.66	2.75|2.75	0.32379|0.32379	.|.	.|0.540943	.|0.16807	.|N	.|0.198737	T|T	0.14700|0.14700	0.0355|0.0355	M|M	0.64567|0.64567	1.98|1.98	0.20926|0.20926	N|N	0.999824|0.999824	.|B	.|0.33940	.|0.433	.|B	.|0.38954	.|0.286	T|T	0.38090|0.38090	-0.9677|-0.9677	5|10	.|0.44086	.|T	.|0.13	.|.	2.1086|2.1086	0.03697|0.03697	0.1078:0.1664:0.4439:0.2819|0.1078:0.1664:0.4439:0.2819	rs41304263;rs61739654|rs41304263;rs61739654	.|2950	.|F8WAI1	.|.	H|I	367|2950;493;110	.|ENSP00000334714:V2950I;ENSP00000398386:V493I;ENSP00000295591:V110I	.|ENSP00000295591:V110I	R|V	+|+	2|1	0|0	IGFN1|IGFN1	199450047|199450047	0.136000|0.136000	0.22515|0.22515	0.996000|0.996000	0.52242|0.52242	0.611000|0.611000	0.37282|0.37282	0.563000|0.563000	0.23547|0.23547	0.748000|0.748000	0.32831|0.32831	0.462000|0.462000	0.41574|0.41574	CGT|GTC	G|0.960;A|0.040	0.040	strong		0.577	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
EEPD1	80820	hgsc.bcm.edu	37	7	36327317	36327317	+	Missense_Mutation	SNP	C	C	T	rs196594	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	190	0	0		WXS	Illumina HiSeq	Phase_I	249	154	0.618474	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	
PTPN23	25930	hgsc.bcm.edu	37	3	47453659	47453659	+	Silent	SNP	G	G	T	rs147959396	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:47453659G>T	ENST00000265562.4	+	22	4226	c.4149G>T	c.(4147-4149)ccG>ccT	p.P1383P	PTPN23_ENST00000431726.1_Silent_p.P1257P	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1383	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)		ATCAGCGGCCGCTGCACACGC	0.627													G|||	5	0.000998403	0.0	0.0043	5008	,	,		20941	0.0		0.002	False		,,,				2504	0.0				p.P1383P		Atlas-SNP	.											.	PTPN23	85	.	0			c.G4149T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	53.0	52.0	53.0		4149	-1.4	1.0	3	dbSNP_134	53	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	PTPN23	NM_015466.2		0,41,6462	TT,TG,GG		0.407,0.1362,0.3152		1383/1637	47453659	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	25930	exon22			GCGGCCGCTGCAC	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.4149G>T	3.37:g.47453659G>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	259	140	0.540541	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Silent	SNP	ENST00000265562.4	37	CCDS2754.1																																																																																			G|0.997;T|0.003	0.003	strong		0.627	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
OLFML2B	25903	hgsc.bcm.edu	37	1	161993192	161993192	+	Missense_Mutation	SNP	T	T	C	rs12130792	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161993192T>C	ENST00000294794.3	-	1	452	c.29A>G	c.(28-30)tAc>tGc	p.Y10C	OLFML2B_ENST00000367940.2_Missense_Mutation_p.Y10C	NM_015441.1	NP_056256.1	Q68BL8	OLM2B_HUMAN	olfactomedin-like 2B	10			Y -> C (in dbSNP:rs12130792).		extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(22)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.0172)			CAGAGCGAAGTAGAGAACTAG	0.627													T|||	488	0.0974441	0.1604	0.0375	5008	,	,		17425	0.1419		0.0726	False		,,,				2504	0.0348				p.Y10C		Atlas-SNP	.											.	OLFML2B	114	.	0			c.A29G						PASS	.	T	CYS/TYR	629,3777	269.5+/-269.1	50,529,1624	56.0	56.0	56.0		29	2.8	0.6	1	dbSNP_120	56	648,7952	165.9+/-218.0	23,602,3675	yes	missense	OLFML2B	NM_015441.1	194	73,1131,5299	CC,CT,TT		7.5349,14.276,9.8185	benign	10/751	161993192	1277,11729	2203	4300	6503	SO:0001583	missense	25903	exon1			GCGAAGTAGAGAA	BX648975	CCDS1236.1, CCDS72966.1	1q23.1	2008-02-05			ENSG00000162745	ENSG00000162745			24558	protein-coding gene	gene with protein product							Standard	XM_005245075		Approved	DKFZP586L151	uc001gbu.3	Q68BL8	OTTHUMG00000024047	ENST00000294794.3:c.29A>G	1.37:g.161993192T>C	ENSP00000294794:p.Tyr10Cys	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	230	72	0.313043	NM_015441	B7ZA39|Q5VU96|Q6NX46|Q86X11|Q9Y3X6	Missense_Mutation	SNP	ENST00000294794.3	37	CCDS1236.1	239	0.10943223443223443	84	0.17073170731707318	14	0.03867403314917127	85	0.1486013986013986	56	0.07387862796833773	T	5.529	0.282591	0.10458	0.14276	0.075349	ENSG00000162745	ENST00000294794;ENST00000367940	D;D	0.86432	-2.12;-2.12	4.85	2.76	0.32466	.	.	.	.	.	T	0.37919	0.1021	N	0.01576	-0.805	0.23645	P	0.99722	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10894	-1.0610	8	0.02654	T	1	.	6.6908	0.23169	0.0:0.7575:0.0:0.2425	rs12130792;rs58683497;rs12130792	10;10	F2Z3N3;Q68BL8	.;OLM2B_HUMAN	C	10	ENSP00000294794:Y10C;ENSP00000356917:Y10C	ENSP00000294794:Y10C	Y	-	2	0	OLFML2B	160259816	0.782000	0.28689	0.575000	0.28536	0.084000	0.17831	0.741000	0.26202	0.501000	0.28013	-0.366000	0.07423	TAC	T|0.895;C|0.105	0.105	strong		0.627	OLFML2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060552.2	NM_015441	
USH2A	7399	hgsc.bcm.edu	37	1	215848641	215848641	+	Silent	SNP	T	T	C	rs2797235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:215848641T>C	ENST00000307340.3	-	63	12998	c.12612A>G	c.(12610-12612)acA>acG	p.T4204T	USH2A_ENST00000366943.2_Silent_p.T4204T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4204	Fibronectin type-III 27. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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.T4204T(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)		CGGCCTGGATTGTCTGATTTC	0.413										HNSCC(13;0.011)			T|||	3454	0.689696	0.6127	0.7954	5008	,	,		21060	0.6429		0.8091	False		,,,				2504	0.6442				p.T4204T		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	1	1	Substitution - coding silent(1)	stomach(1)	c.A12612G						PASS	.	T		2812,1594	665.9+/-401.6	894,1024,285	124.0	123.0	123.0		12612	-2.0	0.1	1	dbSNP_100	123	7000,1600	742.9+/-407.2	2845,1310,145	no	coding-synonymous	USH2A	NM_206933.2		3739,2334,430	CC,CT,TT		18.6047,36.1779,24.5579		4204/5203	215848641	9812,3194	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon63			CTGGATTGTCTGA	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.12612A>G	1.37:g.215848641T>C		Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	268	265	0.988806	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			T|0.265;C|0.735	0.735	strong		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
CACNA1A	773	hgsc.bcm.edu	37	19	13445208	13445208	+	Silent	SNP	C	C	T	rs2248069	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13445208C>T	ENST00000360228.5	-	8	1181	c.1182G>A	c.(1180-1182)gaG>gaA	p.E394E	CACNA1A_ENST00000573710.2_Silent_p.E394E	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	394	Binding to the beta subunit. {ECO:0000250}.				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)	TTGAGATCCACTCCATGTACC	0.547													C|||	3211	0.641174	0.4758	0.7767	5008	,	,		15172	0.6339		0.6789	False		,,,				2504	0.7372				p.E394E		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G1182A						PASS	.	C	,,,,	2108,1734		593,922,406	103.0	102.0	102.0		1182,1182,1182,1182,1182	0.6	1.0	19	dbSNP_100	102	5682,2578		1972,1738,420	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	,,,,	2565,2660,826	TT,TC,CC		31.2107,45.1327,35.6305	,,,,	394/2267,394/2262,394/2507,394/2264,394/2513	13445208	7790,4312	1921	4130	6051	SO:0001819	synonymous_variant	773	exon8			GATCCACTCCATG	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.1182G>A	19.37:g.13445208C>T		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.375;T|0.625	0.625	strong		0.547	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
SV2B	9899	hgsc.bcm.edu	37	15	91811749	91811749	+	Silent	SNP	G	G	A	rs3743444	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:91811749G>A	ENST00000394232.1	+	9	1757	c.1287G>A	c.(1285-1287)gtG>gtA	p.V429V	SV2B_ENST00000330276.4_Silent_p.V429V|SV2B_ENST00000545111.2_Silent_p.V278V	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	429					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)			AAATGAAGGTGTTTTTTGGTG	0.413													A|||	697	0.139177	0.2595	0.0937	5008	,	,		21557	0.0893		0.1392	False		,,,				2504	0.0603				p.V429V		Atlas-SNP	.											.	SV2B	98	.	0			c.G1287A						PASS	.	A	,	899,3497	739.9+/-411.1	97,705,1396	172.0	164.0	166.0		834,1287	-7.5	0.7	15	dbSNP_107	166	982,7614	773.8+/-407.7	66,850,3382	no	coding-synonymous,coding-synonymous	SV2B	NM_001167580.1,NM_014848.4	,	163,1555,4778	AA,AG,GG		11.4239,20.4504,14.4781	,	278/533,429/684	91811749	1881,11111	2198	4298	6496	SO:0001819	synonymous_variant	9899	exon10			GAAGGTGTTTTTT	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.1287G>A	15.37:g.91811749G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	95	64	0.673684	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																			G|0.848;A|0.152	0.152	strong		0.413	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
TEPP	374739	hgsc.bcm.edu	37	16	58019396	58019396	+	Missense_Mutation	SNP	G	G	A	rs9934227	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:58019396G>A	ENST00000441824.2	+	6	735	c.698G>A	c.(697-699)aGc>aAc	p.S233N	TEPP_ENST00000569996.1_3'UTR|TEPP_ENST00000290871.5_Missense_Mutation_p.S260N	NM_199456.2	NP_955535.2	Q6URK8	TEPP_HUMAN	testis, prostate and placenta expressed	233				S -> N (in Ref. 1; AAR18688/AAR18689 and 3; AAI04459/AAI04460). {ECO:0000305}.		extracellular region (GO:0005576)				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	8						TACTGCCTCAGCCAGAACCCC	0.682													A|||	3924	0.783546	0.9486	0.585	5008	,	,		12536	0.5595		0.8559	False		,,,				2504	0.8579				p.S260N		Atlas-SNP	.											.	TEPP	30	.	0			c.G779A						PASS	.	A	ASN/SER,ASN/SER	4117,279	151.4+/-185.3	1931,255,12	48.0	49.0	48.0		779,698	1.5	1.0	16	dbSNP_119	48	7296,1304	251.8+/-278.1	3092,1112,96	yes	missense,missense	TEPP	NM_199046.2,NM_199456.2	46,46	5023,1367,108	AA,AG,GG		15.1628,6.3467,12.1807	benign,benign	260/299,233/272	58019396	11413,1583	2198	4300	6498	SO:0001583	missense	374739	exon6			GCCTCAGCCAGAA	BC104458	CCDS10790.1, CCDS45496.1	16q13	2009-04-20			ENSG00000159648	ENSG00000159648			33745	protein-coding gene	gene with protein product		610264				14652002	Standard	NM_199456		Approved		uc002emv.4	Q6URK8	OTTHUMG00000133463	ENST00000441824.2:c.698G>A	16.37:g.58019396G>A	ENSP00000401917:p.Ser233Asn	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	214	212	0.990654	NM_199046	Q6URK7	Missense_Mutation	SNP	ENST00000441824.2	37	CCDS45496.1	1679	0.7687728937728938	467	0.9491869918699187	244	0.6740331491712708	318	0.5559440559440559	650	0.8575197889182058	A	4.918	0.170667	0.09391	0.936533	0.848372	ENSG00000159648	ENST00000290871;ENST00000441824	T;T	0.40756	1.08;1.02	5.1	1.54	0.23209	.	0.169343	0.40728	N	0.001030	T	0.00012	0.0000	N	0.00034	-2.56	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34650	-0.9820	9	0.02654	T	1	-19.9726	7.8965	0.29710	0.6453:0.0:0.3547:0.0	rs9934227;rs58628736;rs9934227	233;260	Q6URK8;Q6URK8-2	TEPP_HUMAN;.	N	260;233	ENSP00000290871:S260N;ENSP00000401917:S233N	ENSP00000290871:S260N	S	+	2	0	TEPP	56576897	0.997000	0.39634	0.997000	0.53966	0.852000	0.48524	0.593000	0.23999	0.085000	0.17107	-0.442000	0.05670	AGC	G|0.164;A|0.836	0.836	strong		0.682	TEPP-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000431966.1	NM_199456	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503155	140503155	+	Silent	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140503155G>T	ENST00000194152.1	+	1	1575	c.1575G>T	c.(1573-1575)gcG>gcT	p.A525A	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	525	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)			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)			CCCTGCAGGCGTTCGAGTTCC	0.682																																					p.A525A		Atlas-SNP	.											PCDHB4,caecum,carcinoma,+1,1	PCDHB4	177	1	0			c.G1575T						scavenged	.						69.0	78.0	75.0					5																	140503155		2203	4298	6501	SO:0001819	synonymous_variant	56131	exon1			GCAGGCGTTCGAG	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.1575G>T	5.37:g.140503155G>T		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	252	4	0.015873	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			.	.	none		0.682	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
OR10X1	128367	hgsc.bcm.edu	37	1	158549264	158549264	+	Silent	SNP	G	G	A	rs863360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158549264G>A	ENST00000368150.1	-	1	425	c.426C>T	c.(424-426)atC>atT	p.I142I		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	142						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)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					GAGGGTTACAGATGGCCAGGA	0.458													G|||	2516	0.502396	0.5741	0.4135	5008	,	,		22554	0.5853		0.4732	False		,,,				2504	0.4131				p.I142I		Atlas-SNP	.											OR10X1,NS,carcinoma,0,1	OR10X1	96	1	0			c.C426T						scavenged	.	G		2499,1907	627.1+/-394.8	679,1141,383	75.0	76.0	75.0		426	2.1	1.0	1	dbSNP_86	75	3826,4774	538.9+/-383.5	877,2072,1351	no	coding-synonymous	OR10X1	NM_001004477.1		1556,3213,1734	AA,AG,GG		44.4884,43.2819,48.6314		142/327	158549264	6325,6681	2203	4300	6503	SO:0001819	synonymous_variant	128367	exon1			GTTACAGATGGCC	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.426C>T	1.37:g.158549264G>A		Somatic	354	3	0.00847458		WXS	Illumina HiSeq	Phase_I	460	247	0.536957	NM_001004477	Q6IFR8	Silent	SNP	ENST00000368150.1	37	CCDS30900.1																																																																																			G|0.489;A|0.511	0.511	strong		0.458	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
ZNF454	285676	hgsc.bcm.edu	37	5	178391860	178391860	+	Missense_Mutation	SNP	G	G	A	rs6867221	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:178391860G>A	ENST00000320129.3	+	5	758	c.455G>A	c.(454-456)tGt>tAt	p.C152Y	ZNF454_ENST00000519564.1_Missense_Mutation_p.C152Y	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	152			C -> Y (in dbSNP:rs6867221). {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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|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;0.234)		TCACAGGAATGTGATGAATCC	0.498													G|||	1359	0.271366	0.1104	0.281	5008	,	,		17861	0.3403		0.3131	False		,,,				2504	0.3681				p.C152Y		Atlas-SNP	.											.	ZNF454	99	.	0			c.G455A						PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS	627,3779	272.8+/-271.0	46,535,1622	86.0	83.0	84.0		455,455,455	1.5	0.0	5	dbSNP_116	84	2728,5872	435.4+/-358.0	421,1886,1993	yes	missense,missense,missense	ZNF454	NM_001178089.1,NM_001178090.1,NM_182594.2	194,194,194	467,2421,3615	AA,AG,GG		31.7209,14.2306,25.7958	benign,benign,benign	152/523,152/523,152/523	178391860	3355,9651	2203	4300	6503	SO:0001583	missense	285676	exon5			AGGAATGTGATGA	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"""Zinc fingers, C2H2-type"", ""-"""	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.455G>A	5.37:g.178391860G>A	ENSP00000326249:p.Cys152Tyr	Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	151	83	0.549669	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	608	0.2783882783882784	63	0.12804878048780488	97	0.26795580110497236	208	0.36363636363636365	240	0.316622691292876	G	8.080	0.772256	0.16051	0.142306	0.317209	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.03951	3.75;3.75	4.61	1.45	0.22620	.	4.329230	0.00789	N	0.001329	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18461	0.028	B	0.14023	0.01	T	0.47861	-0.9084	9	0.39692	T	0.17	7.0408	1.8445	0.03156	0.1253:0.1909:0.4704:0.2134	rs6867221;rs52835898;rs6867221	152	Q8N9F8	ZN454_HUMAN	Y	152	ENSP00000326249:C152Y;ENSP00000430354:C152Y	ENSP00000326249:C152Y	C	+	2	0	ZNF454	178324466	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.406000	0.21032	0.153000	0.19213	0.555000	0.69702	TGT	G|0.733;A|0.267	0.267	strong		0.498	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718	
CDCA2	157313	hgsc.bcm.edu	37	8	25364331	25364331	+	Missense_Mutation	SNP	G	G	A	rs4872318	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:25364331G>A	ENST00000330560.3	+	15	2626	c.2149G>A	c.(2149-2151)Gta>Ata	p.V717I	CDCA2_ENST00000521098.2_3'UTR|CDCA2_ENST00000380665.3_Missense_Mutation_p.V702I	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	60	38	0.633333	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	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249605	71249605	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:71249605C>T	ENST00000398534.3	+	1	535	c.504C>T	c.(502-504)tgC>tgT	p.C168C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	168	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						CCAGCTGCTGCAAGCCCTGCT	0.592																																					p.C168C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C504T						PASS	.						134.0	144.0	141.0					11																	71249605		2200	4294	6494	SO:0001819	synonymous_variant	57830	exon1			CTGCTGCAAGCCC	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.504C>T	11.37:g.71249605C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	136	13	0.0955882	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			.	.	none		0.592	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
PRF1	5551	hgsc.bcm.edu	37	10	72358722	72358722	+	Missense_Mutation	SNP	T	T	C	rs28933375	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72358722T>C	ENST00000441259.1	-	3	915	c.755A>G	c.(754-756)aAc>aGc	p.N252S	PRF1_ENST00000373209.2_Missense_Mutation_p.N252S	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	252	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.		N -> S (in FHL2; dbSNP:rs28933375). {ECO:0000269|PubMed:10583959}.		apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CTCCACCTCGTTGTCCGTGAG	0.632			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				T|||	38	0.00758786	0.0106	0.0058	5008	,	,		18685	0.0		0.0109	False		,,,				2504	0.0092				p.N252S		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.A755G	GRCh37	CM992952	PRF1	M	rs28933375	PASS	.	T	SER/ASN,SER/ASN	40,4366	43.8+/-77.6	0,40,2163	123.0	88.0	100.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	755,755	4.7	0.0	10	dbSNP_125	100	70,8530	41.7+/-99.0	0,70,4230	yes	missense,missense	PRF1	NM_001083116.1,NM_005041.4	46,46	0,110,6393	CC,CT,TT		0.814,0.9079,0.8458	benign,benign	252/556,252/556	72358722	110,12896	2203	4300	6503	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	ACCTCGTTGTCCG	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.755A>G	10.37:g.72358722T>C	ENSP00000398568:p.Asn252Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	77	59	0.766234	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	13	0.005952380952380952	5	0.01016260162601626	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	T	4.521	0.096594	0.08681	0.009079	0.00814	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.82803	-1.65;-1.65	5.83	4.69	0.59074	Membrane attack complex component/perforin (MACPF) domain (3);	0.677027	0.15448	N	0.261829	T	0.50326	0.1609	N	0.01168	-0.975	0.09310	A	8.34466e-13	B	0.02656	0.0	B	0.06405	0.002	T	0.57207	-0.7851	9	0.21540	T	0.41	-13.5412	10.0841	0.42408	0.0:0.0793:0.0:0.9206	rs28933375	252	P14222	PERF_HUMAN	S	252	ENSP00000362305:N252S;ENSP00000398568:N252S	ENSP00000316746:N252S	N	-	2	0	PRF1	72028728	0.000000	0.05858	0.003000	0.11579	0.010000	0.07245	0.743000	0.26231	1.021000	0.39600	0.533000	0.62120	AAC	T|0.994;C|0.006	0.006	strong		0.632	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
CEP162	22832	hgsc.bcm.edu	37	6	84904604	84904604	+	Missense_Mutation	SNP	G	G	C	rs17790493	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:84904604G>C	ENST00000403245.3	-	10	1139	c.1025C>G	c.(1024-1026)tCt>tGt	p.S342C	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Missense_Mutation_p.S266C	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		GTTTTTACCAGATTCCATAGT	0.284													G|||	50	0.00998403	0.0015	0.0173	5008	,	,		17468	0.0		0.0328	False		,,,				2504	0.0031				p.S342C		Atlas-SNP	.											KIAA1009,NS,carcinoma,0,1	KIAA1009	119	1	0			c.C1025G						PASS	.	G	CYS/SER	35,4369	40.0+/-72.8	0,35,2167	114.0	107.0	109.0		1025	5.1	1.0	6	dbSNP_123	109	214,8382	90.4+/-152.6	4,206,4088	yes	missense	KIAA1009	NM_014895.2	112	4,241,6255	CC,CG,GG		2.4895,0.7947,1.9154	probably-damaging	342/1404	84904604	249,12751	2202	4298	6500	SO:0001583	missense	22832	exon10			TTACCAGATTCCA																												ENST00000403245.3:c.1025C>G	6.37:g.84904604G>C	ENSP00000385215:p.Ser342Cys	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_014895		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	39	0.017857142857142856	0	0.0	9	0.024861878453038673	0	0.0	30	0.0395778364116095	G	15.89	2.966270	0.53507	0.007947	0.024895	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.17854	2.25;2.25	5.08	5.08	0.68730	.	0.101115	0.44688	D	0.000429	T	0.37019	0.0988	M	0.77616	2.38	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.31420	-0.9944	10	0.87932	D	0	-20.0543	17.2476	0.87032	0.0:0.0:1.0:0.0	rs17790493;rs52814056;rs17790493	342;342	Q5TB80;C9JFM9	QN1_HUMAN;.	C	266;342	ENSP00000257766:S266C;ENSP00000385215:S342C	ENSP00000257766:S266C	S	-	2	0	KIAA1009	84961323	1.000000	0.71417	1.000000	0.80357	0.448000	0.32197	6.309000	0.72825	2.369000	0.80426	0.557000	0.71058	TCT	G|0.983;C|0.017	0.017	strong		0.284	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
DHRS4L1	728635	hgsc.bcm.edu	37	14	24517940	24517940	+	RNA	SNP	T	T	C	rs200157408	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24517940T>C	ENST00000558293.1	+	0	588					NR_102693.1																						CAACAAGACCTTGGCCATAGA	0.493													C|||	148	0.0295527	0.0106	0.0115	5008	,	,		23427	0.0377		0.0139	False		,,,				2504	0.0757				p.L199L		Atlas-SNP	.											.	.	.	.	0			c.T595C						PASS	.						180.0	181.0	181.0					14																	24517940		2203	4300	6503			728635	exon8			AAGACCTTGGCCA																													14.37:g.24517940T>C		Somatic	1050	0	0		WXS	Illumina HiSeq	Phase_I	1886	474	0.251326	NM_001082488		Silent	SNP	ENST00000558293.1	37																																																																																				.	.	weak		0.493	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1		
MYCBPAP	84073	hgsc.bcm.edu	37	17	48603503	48603503	+	Missense_Mutation	SNP	C	C	T	rs9890721	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48603503C>T	ENST00000323776.5	+	14	2335	c.2173C>T	c.(2173-2175)Cgg>Tgg	p.R725W	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.R688W	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)			GAGTCCTCAGCGGAAGAGCAT	0.622													C|||	2693	0.53774	0.2163	0.5548	5008	,	,		14998	0.8363		0.5507	False		,,,				2504	0.6391				p.R725W		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C2173T						PASS	.	C	TRP/ARG	1145,3261	398.5+/-330.9	158,829,1216	69.0	68.0	68.0		2173	-4.6	0.0	17	dbSNP_119	68	4678,3922	593.9+/-393.2	1282,2114,904	yes	missense	MYCBPAP	NM_032133.4	101	1440,2943,2120	TT,TC,CC		45.6047,25.9873,44.7716	benign	725/985	48603503	5823,7183	2203	4300	6503	SO:0001583	missense	84073	exon14			CCTCAGCGGAAGA	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.2173C>T	17.37:g.48603503C>T	ENSP00000323184:p.Arg725Trp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	1222	0.5595238095238095	117	0.23780487804878048	200	0.5524861878453039	487	0.8513986013986014	418	0.5514511873350924	C	10.55	1.380972	0.24944	0.259873	0.543953	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.26810	1.71;1.71	5.35	-4.59	0.03400	.	1.293160	0.05121	N	0.490681	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.40175	-0.9577	9	0.51188	T	0.08	-1.8414	3.847	0.08939	0.3639:0.273:0.0:0.363	rs9890721;rs17642285;rs17856809;rs59499446;rs9890721	688	Q8TBZ2	MYBPP_HUMAN	W	725;688	ENSP00000323184:R725W;ENSP00000397209:R688W	ENSP00000323184:R725W	R	+	1	2	MYCBPAP	45958502	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.121000	0.01322	-1.075000	0.03129	-2.299000	0.00261	CGG	C|0.507;N|0.000	.	strong		0.622	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
MUC17	140453	hgsc.bcm.edu	37	7	100678740	100678740	+	Missense_Mutation	SNP	T	T	C	rs4269454	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678740T>C	ENST00000306151.4	+	3	4107	c.4043T>C	c.(4042-4044)cTg>cCg	p.L1348P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1348	59 X approximate tandem repeats.|Ser-rich.		L -> P (in dbSNP:rs4269454). {ECO:0000269|PubMed:9299468}.		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)					AACACCACACTGGTGGCCAGT	0.463													N|||	1193	0.238219	0.351	0.1023	5008	,	,		25539	0.252		0.1213	False		,,,				2504	0.2883				p.L1348P		Atlas-SNP	.											.	MUC17	804	.	0			c.T4043C						PASS	.	C	PRO/LEU	1348,3058	693.0+/-405.6	209,930,1064	228.0	227.0	227.0		4043	-1.7	0.0	7	dbSNP_111	227	999,7601	773.3+/-407.7	57,885,3358	no	missense	MUC17	NM_001040105.1	98	266,1815,4422	CC,CT,TT		11.6163,30.5946,18.0455	benign	1348/4494	100678740	2347,10659	2203	4300	6503	SO:0001583	missense	140453	exon3			CCACACTGGTGGC	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.4043T>C	7.37:g.100678740T>C	ENSP00000302716:p.Leu1348Pro	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	234	223	0.952991	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	430	0.19688644688644688	159	0.3231707317073171	42	0.11602209944751381	140	0.24475524475524477	89	0.11741424802110818	c	0.013	-1.645144	0.00792	0.305946	0.116163	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.861	-1.72	0.08107	.	.	.	.	.	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	0.44050	-0.9353	8	0.27785	T	0.31	.	3.1089	0.06351	0.1991:0.2846:0.0:0.5164	rs4269454;rs10374373;rs52835910;rs4269454	1348	Q685J3	MUC17_HUMAN	P	1348	ENSP00000302716:L1348P	ENSP00000302716:L1348P	L	+	2	0	MUC17	100465460	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.110000	0.01334	-3.604000	0.00133	-3.178000	0.00056	CTG	T|0.821;C|0.179	0.179	strong		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MMP27	64066	hgsc.bcm.edu	37	11	102567207	102567207	+	Missense_Mutation	SNP	T	T	A	rs1276286	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102567207T>A	ENST00000260229.4	-	6	888	c.797A>T	c.(796-798)gAa>gTa	p.E266V		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	266			E -> V (in dbSNP:rs1276286). {ECO:0000269|PubMed:12975309}.		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	CTTAGCAGGTTCCTTAGGCAG	0.413													A|||	2191	0.4375	0.1725	0.5043	5008	,	,		18588	0.629		0.4443	False		,,,				2504	0.544				p.E266V		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	0			c.A797T						scavenged	.	A	VAL/GLU	1066,3340	723.7+/-409.4	113,840,1250	151.0	154.0	153.0		797	-1.3	0.0	11	dbSNP_87	153	3904,4694	606.3+/-395.1	863,2178,1258	yes	missense	MMP27	NM_022122.2	121	976,3018,2508	AA,AT,TT		45.4059,24.1943,38.219	benign	266/514	102567207	4970,8034	2203	4299	6502	SO:0001583	missense	64066	exon6			GCAGGTTCCTTAG	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.797A>T	11.37:g.102567207T>A	ENSP00000260229:p.Glu266Val	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	254	67	0.26378	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	931	0.42628205128205127	84	0.17073170731707318	169	0.46685082872928174	336	0.5874125874125874	342	0.45118733509234826	A	0.065	-1.215502	0.01542	0.241943	0.454059	ENSG00000137675	ENST00000260229	T	0.14266	2.52	5.89	-1.3	0.09259	.	3.758110	0.00837	N	0.001700	T	0.00012	0.0000	N	0.02830	-0.485	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44467	-0.9326	9	0.20046	T	0.44	.	5.2352	0.15443	0.4414:0.0:0.2808:0.2778	rs1276286;rs17800318;rs52815827;rs56490119;rs1276286	266	Q9H306	MMP27_HUMAN	V	266	ENSP00000260229:E266V	ENSP00000260229:E266V	E	-	2	0	MMP27	102072417	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.450000	0.06803	-0.348000	0.08286	-1.349000	0.01238	GAA	T|0.600;A|0.400	0.400	strong		0.413	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256920	140256920	+	Silent	SNP	G	G	C	rs115718636	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140256920G>C	ENST00000398631.2	+	1	1863	c.1863G>C	c.(1861-1863)ccG>ccC	p.P621P	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	621	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)			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)			CGCACATCCCGTTCCACGTGG	0.672													.|||	111	0.0221645	0.0129	0.0303	5008	,	,		17234	0.0		0.0656	False		,,,				2504	0.0072				p.P621P	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,colon,carcinoma,0,2	PCDHA12	196	2	0			c.G1863C						PASS	.	G	,,,,,,,,,,,,,,,	117,4289	87.8+/-126.4	0,117,2086	228.0	205.0	213.0		,,,1863,,,,,,,,,,,,1863	-0.7	0.9	5	dbSNP_132	213	437,8161	133.5+/-191.0	11,415,3873	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	,,,,,,,,,,,,,,,	11,532,5959	CC,CG,GG		5.0826,2.6555,4.2602	,,,,,,,,,,,,,,,	,,,621/942,,,,,,,,,,,,621/793	140256920	554,12450	2203	4299	6502	SO:0001819	synonymous_variant	56137	exon1			CATCCCGTTCCAC	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.1863G>C	5.37:g.140256920G>C		Somatic	368	1	0.00271739		WXS	Illumina HiSeq	Phase_I	298	150	0.503356	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.959;C|0.041	0.041	strong		0.672	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
PCNT	5116	hgsc.bcm.edu	37	21	47851796	47851796	+	Silent	SNP	G	G	A	rs9983522	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:47851796G>A	ENST00000359568.5	+	38	8525	c.8418G>A	c.(8416-8418)gcG>gcA	p.A2806A	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2806					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					ACTTGCAAGCGATGCTTGAAA	0.582													G|||	734	0.146565	0.0666	0.1801	5008	,	,		20552	0.1984		0.1252	False		,,,				2504	0.1994				p.A2806A		Atlas-SNP	.											.	PCNT	283	.	0			c.G8418A						PASS	.	G		279,4127	155.2+/-188.4	11,257,1935	59.0	58.0	58.0		8418	-10.6	0.0	21	dbSNP_119	58	1054,7546	221.6+/-259.0	63,928,3309	no	coding-synonymous	PCNT	NM_006031.5		74,1185,5244	AA,AG,GG		12.2558,6.3323,10.2491		2806/3337	47851796	1333,11673	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon38			GCAAGCGATGCTT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.8418G>A	21.37:g.47851796G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	56	38	0.678571	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			G|0.887;A|0.113	0.113	strong		0.582	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
C15orf41	84529	hgsc.bcm.edu	37	15	36989578	36989578	+	Silent	SNP	C	C	T	rs117638434	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:36989578C>T	ENST00000566621.1	+	8	781	c.531C>T	c.(529-531)aaC>aaT	p.N177N	C15orf41_ENST00000567389.1_Silent_p.N79N|C15orf41_ENST00000338183.4_Silent_p.N79N|C15orf41_ENST00000562877.1_Silent_p.N79N|C15orf41_ENST00000565792.1_3'UTR|C15orf41_ENST00000437989.2_Silent_p.N177N|C15orf41_ENST00000569302.1_Silent_p.N177N	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	177										kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		TAGAGAAAAACCTGTCCTTCC	0.408													C|||	22	0.00439297	0.0	0.0014	5008	,	,		15677	0.0		0.0209	False		,,,				2504	0.0				p.N177N		Atlas-SNP	.											.	C15orf41	24	.	0			c.C531T						PASS	.	C	,	17,3791		0,17,1887	183.0	184.0	184.0		531,237	-0.8	1.0	15	dbSNP_132	184	99,8177		1,97,4040	no	coding-synonymous,coding-synonymous	C15orf41	NM_001130010.1,NM_032499.4	,	1,114,5927	TT,TC,CC		1.1962,0.4464,0.9599	,	177/282,79/184	36989578	116,11968	1904	4138	6042	SO:0001819	synonymous_variant	84529	exon8			GAAAAACCTGTCC	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.531C>T	15.37:g.36989578C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	110	84	0.763636	NM_001130010	B2RD87	Silent	SNP	ENST00000566621.1	37	CCDS45215.1																																																																																			C|0.992;T|0.008	0.008	strong		0.408	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062023	64062023	+	Missense_Mutation	SNP	A	A	C	rs10878073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:64062023A>C	ENST00000324472.4	-	1	334	c.151T>G	c.(151-153)Tcc>Gcc	p.S51A	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	51			S -> A (in dbSNP:rs10878073). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GACCTCCAGGAGCCCCTTGGC	0.642													a|||	1979	0.395168	0.4425	0.2565	5008	,	,		15241	0.5714		0.1978	False		,,,				2504	0.4509				p.S51A		Atlas-SNP	.											.	DPY19L2	97	.	0			c.T151G						PASS	.	A	ALA/SER	1708,2698		318,1072,813	43.0	53.0	49.0		151	-2.2	0.0	12	dbSNP_120	49	1715,6881		177,1361,2760	yes	missense	DPY19L2	NM_173812.4	99	495,2433,3573	CC,CA,AA		19.9511,38.7653,26.3267	benign	51/759	64062023	3423,9579	2203	4298	6501	SO:0001583	missense	283417	exon1			TCCAGGAGCCCCT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.151T>G	12.37:g.64062023A>C	ENSP00000315988:p.Ser51Ala	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	155	64	0.412903	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	748	0.3424908424908425	180	0.36585365853658536	98	0.27071823204419887	324	0.5664335664335665	146	0.19261213720316622	a	2.066	-0.414146	0.04766	0.387653	0.199511	ENSG00000177990	ENST00000324472;ENST00000542209	T;T	0.32753	1.44;2.38	1.61	-2.25	0.06888	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.43893	-0.9363	7	.	.	.	.	7.1276	0.25482	0.6882:0.3118:0.0:0.0	rs10878073;rs10878073	51	Q6NUT2	D19L2_HUMAN	A	51	ENSP00000315988:S51A;ENSP00000444932:S51A	.	S	-	1	0	DPY19L2	62348290	0.378000	0.25114	0.010000	0.14722	0.014000	0.08584	-0.429000	0.06982	-0.692000	0.05128	-1.193000	0.01689	TCC	A|0.717;C|0.283	0.283	strong		0.642	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
OR52A5	390054	hgsc.bcm.edu	37	11	5153261	5153261	+	Silent	SNP	A	A	G	rs2472530	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5153261A>G	ENST00000307388.1	-	1	611	c.612T>C	c.(610-612)ttT>ttC	p.F204F		NM_001005160.2	NP_001005160.1	Q9H2C5	O52A5_HUMAN	olfactory receptor, family 52, subfamily A, member 5	204					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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(18)|skin(3)	35		Medulloblastoma(188;0.0049)|all_neural(188;0.0442)|Breast(177;0.0675)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.2)		CAAAGGCAACAAATAGGCCAT	0.423													A|||	995	0.198682	0.0144	0.232	5008	,	,		23011	0.3929		0.2028	False		,,,				2504	0.2198				p.F204F		Atlas-SNP	.											.	OR52A5	80	.	0			c.T612C						PASS	.	A		220,4182	131.0+/-167.6	7,206,1988	108.0	104.0	105.0		612	5.1	1.0	11	dbSNP_100	105	1823,6773	326.6+/-317.4	213,1397,2688	no	coding-synonymous	OR52A5	NM_001005160.2		220,1603,4676	GG,GA,AA		21.2075,4.9977,15.7178		204/317	5153261	2043,10955	2201	4298	6499	SO:0001819	synonymous_variant	390054	exon1			GGCAACAAATAGG	BK004433	CCDS31373.1	11p15.4	2012-08-09			ENSG00000171944	ENSG00000171944		"""GPCR / Class A : Olfactory receptors"""	19580	protein-coding gene	gene with protein product							Standard	NM_001005160		Approved		uc010qyx.2	Q9H2C5	OTTHUMG00000066616	ENST00000307388.1:c.612T>C	11.37:g.5153261A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_001005160		Silent	SNP	ENST00000307388.1	37	CCDS31373.1																																																																																			A|0.815;G|0.185	0.185	strong		0.423	OR52A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142823.1	NM_001005160	
FAM71F2	346653	hgsc.bcm.edu	37	7	128312463	128312463	+	Missense_Mutation	SNP	C	C	G	rs74343948	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:128312463C>G	ENST00000480462.1	+	1	118	c.12C>G	c.(10-12)atC>atG	p.I4M	FAM71F2_ENST00000378704.3_Missense_Mutation_p.I4M|FAM71F2_ENST00000477515.1_Missense_Mutation_p.I4M|FAM71F2_ENST00000460349.1_3'UTR			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	4										NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						TGAGTAAAATCAGGGGCCTCC	0.522													.|||	562	0.11222	0.034	0.1066	5008	,	,		16667	0.1657		0.1322	False		,,,				2504	0.1462				p.I4M		Atlas-SNP	.											.	FAM71F2	19	.	0			c.C12G						PASS	.	C	MET/ILE,MET/ILE	214,3556		11,192,1682	33.0	34.0	33.0		12,12	1.1	1.0	7	dbSNP_132	33	1243,6983		116,1011,2986	yes	missense,missense	FAM71F2	NM_001012454.3,NM_001128926.1	10,10	127,1203,4668	GG,GC,CC		15.1106,5.6764,12.1457	benign,benign	4/310,4/301	128312463	1457,10539	1885	4113	5998	SO:0001583	missense	346653	exon1			TAAAATCAGGGGC	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member B"""	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.12C>G	7.37:g.128312463C>G	ENSP00000420140:p.Ile4Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	54	10	0.185185	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	241	0.11034798534798534	26	0.052845528455284556	37	0.10220994475138122	90	0.15734265734265734	88	0.11609498680738786	C	16.28	3.080033	0.55753	0.056764	0.151106	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001;ENST00000477515	T;T;T;T;T	0.37411	3.01;3.01;3.01;3.01;1.2	4.86	1.13	0.20643	.	0.270429	0.26248	N	0.025467	T	0.00210	0.0006	L	0.57536	1.79	0.40727	P	0.017286000000000024	D;P	0.55385	0.971;0.952	P;P	0.57620	0.824;0.671	T	0.04440	-1.0951	9	0.33940	T	0.23	0.4287	7.1167	0.25421	0.0:0.2398:0.0:0.7602	.	4;4	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	M	4	ENSP00000418907:I4M;ENSP00000420140:I4M;ENSP00000367976:I4M;ENSP00000401654:I4M;ENSP00000419649:I4M	ENSP00000367976:I4M	I	+	3	3	FAM71F2	128099699	0.998000	0.40836	0.974000	0.42286	0.897000	0.52465	0.156000	0.16382	0.092000	0.17331	-0.140000	0.14226	ATC	C|0.884;G|0.116	0.116	strong		0.522	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
ZNF554	115196	hgsc.bcm.edu	37	19	2834808	2834808	+	Silent	SNP	T	T	C	rs8102063	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2834808T>C	ENST00000317243.5	+	5	1773	c.1575T>C	c.(1573-1575)tgT>tgC	p.C525C		NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	525					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)		TCATTGACTGTGGGAAAGCGT	0.428													T|||	1974	0.394169	0.3306	0.3314	5008	,	,		21483	0.3413		0.4463	False		,,,				2504	0.5256				p.C525C		Atlas-SNP	.											.	ZNF554	47	.	0			c.T1575C						PASS	.	T		1349,2851		213,923,964	67.0	68.0	68.0		1575	1.8	0.9	19	dbSNP_116	68	4080,4414		998,2084,1165	no	coding-synonymous	ZNF554	NM_001102651.1		1211,3007,2129	CC,CT,TT		48.0339,32.119,42.7682		525/539	2834808	5429,7265	2100	4247	6347	SO:0001819	synonymous_variant	115196	exon5			TGACTGTGGGAAA	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.1575T>C	19.37:g.2834808T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	NM_001102651	Q8NAT3|Q9BWN3	Silent	SNP	ENST00000317243.5	37	CCDS42462.1																																																																																			C|0.395;N|0.000	0.395	strong		0.428	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
DDX20	11218	hgsc.bcm.edu	37	1	112309230	112309230	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:112309230C>T	ENST00000369702.4	+	11	2804	c.2184C>T	c.(2182-2184)agC>agT	p.S728S	DDX20_ENST00000475700.1_Silent_p.S336S	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	728					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGGGGCTAGCCAGAGAGCTA	0.483																																					p.S728S		Atlas-SNP	.											.	DDX20	50	.	0			c.C2184T						PASS	.						65.0	67.0	66.0					1																	112309230		2203	4300	6503	SO:0001819	synonymous_variant	11218	exon11			GGCTAGCCAGAGA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.2184C>T	1.37:g.112309230C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	87	4	0.045977	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Silent	SNP	ENST00000369702.4	37	CCDS842.1																																																																																			.	.	none		0.483	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
MKI67	4288	hgsc.bcm.edu	37	10	129903465	129903465	+	Silent	SNP	A	A	G	rs2857028	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129903465A>G	ENST00000368654.3	-	13	7014	c.6639T>C	c.(6637-6639)caT>caC	p.H2213H	MKI67_ENST00000368653.3_Silent_p.H1853H	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2213	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)				TAGTTTTCTCATGAGTCGTGG	0.498													A|||	956	0.190895	0.1172	0.3156	5008	,	,		19117	0.12		0.2704	False		,,,				2504	0.1933				p.H2213H		Atlas-SNP	.											.	MKI67	363	.	0			c.T6639C						PASS	.	A	,	578,3828	254.3+/-259.9	37,504,1662	239.0	231.0	233.0		5559,6639	-0.3	0.0	10	dbSNP_100	233	2133,6467	366.7+/-334.4	274,1585,2441	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	311,2089,4103	GG,GA,AA		24.8023,13.1185,20.8442	,	1853/2897,2213/3257	129903465	2711,10295	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			TTTCTCATGAGTC	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.6639T>C	10.37:g.129903465A>G		Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	322	179	0.555901	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			T|0.007;G|0.212	0.212	strong		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
POLD1	5424	hgsc.bcm.edu	37	19	50905042	50905042	+	Silent	SNP	G	G	A	rs20582	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50905042G>A	ENST00000440232.2	+	4	377	c.324G>A	c.(322-324)gcG>gcA	p.A108A	POLD1_ENST00000599857.1_Silent_p.A108A|POLD1_ENST00000595904.1_Silent_p.A108A	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	108					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|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)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CAGGCCCAGCGCAGCCTGTGC	0.672								DNA polymerases (catalytic subunits)					G|||	946	0.188898	0.3245	0.1023	5008	,	,		11288	0.1607		0.0706	False		,,,				2504	0.2178				p.A108A		Atlas-SNP	.											.	POLD1	174	.	0			c.G324A						PASS	.	G		1266,3124		224,818,1153	27.0	34.0	31.0		324	-7.7	0.0	19	dbSNP_67	31	602,7940		24,554,3693	no	coding-synonymous	POLD1	NM_002691.2		248,1372,4846	AA,AG,GG		7.0475,28.8383,14.4448		108/1108	50905042	1868,11064	2195	4271	6466	SO:0001819	synonymous_variant	5424	exon4			CCCAGCGCAGCCT		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.324G>A	19.37:g.50905042G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	48	30	0.625	NM_002691	Q8NER3|Q96H98	Silent	SNP	ENST00000440232.2	37	CCDS12795.1																																																																																			A|0.170;G|0.829;T|0.000	0.170	strong		0.672	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
ZMYM5	9205	hgsc.bcm.edu	37	13	20413021	20413021	+	Missense_Mutation	SNP	T	T	C	rs41292167	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:20413021T>C	ENST00000337963.4	-	5	955	c.691A>G	c.(691-693)Aca>Gca	p.T231A	ZMYM5_ENST00000382905.4_Missense_Mutation_p.T231A|RP11-61K9.2_ENST00000422148.2_RNA|ZMYM5_ENST00000382907.4_Intron	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	231			T -> A (in dbSNP:rs41292167).			nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		TGTTGGGCTGTAGGCTGGAAA	0.438													T|||	487	0.0972444	0.1687	0.0735	5008	,	,		18398	0.0813		0.0924	False		,,,				2504	0.0389				p.T231A		Atlas-SNP	.											.	ZMYM5	73	.	0			c.A691G						PASS	.	T	,ALA/THR,ALA/THR	702,3704	291.3+/-281.4	61,580,1562	204.0	203.0	203.0		,691,691	-0.3	0.2	13	dbSNP_127	203	591,8009	157.6+/-211.2	16,559,3725	yes	intron,missense,missense	ZMYM5	NM_001039649.2,NM_001039650.2,NM_001142684.1	,58,58	77,1139,5287	CC,CT,TT		6.8721,15.9328,9.9416	,benign,benign	,231/383,231/670	20413021	1293,11713	2203	4300	6503	SO:0001583	missense	9205	exon5			GGGCTGTAGGCTG	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"""Zinc fingers, MYM type"""	13029	protein-coding gene	gene with protein product			"""zinc finger protein 237"""	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.691A>G	13.37:g.20413021T>C	ENSP00000337034:p.Thr231Ala	Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	232	96	0.413793	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		192	0.08791208791208792	70	0.14227642276422764	26	0.0718232044198895	35	0.06118881118881119	61	0.08047493403693931	T	12.66	2.004845	0.35415	0.159328	0.068721	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382905	T;T;T	0.41065	1.01;1.01;1.01	4.67	-0.334	0.12666	.	0.324108	0.34386	N	0.004013	T	0.00073	0.0002	N	0.22421	0.69	0.45791	P	0.0013290000000000246	B;B	0.20780	0.048;0.032	B;B	0.15870	0.013;0.014	T	0.07635	-1.0762	9	0.42905	T	0.14	-1.8158	4.8425	0.13498	0.4731:0.0:0.3778:0.1491	rs41292167;rs56860401	231;231	Q9UJ78;Q9UJ78-1	ZMYM5_HUMAN;.	A	231;221;231	ENSP00000337034:T231A;ENSP00000445779:T221A;ENSP00000372361:T231A	ENSP00000337034:T231A	T	-	1	0	ZMYM5	19311021	1.000000	0.71417	0.159000	0.22649	0.918000	0.54935	0.848000	0.27710	0.073000	0.16731	-0.542000	0.04241	ACA	T|0.903;C|0.097	0.097	strong		0.438	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242	
OR51A2	401667	hgsc.bcm.edu	37	11	4976291	4976291	+	Missense_Mutation	SNP	G	G	A	rs55889636	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4976291G>A	ENST00000380371.1	-	1	652	c.653C>T	c.(652-654)tCt>tTt	p.S218F	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_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						scavenged	.		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	38	1	0.0263158		WXS	Illumina HiSeq	Phase_I	521	161	0.309021	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	
OR5L2	26338	hgsc.bcm.edu	37	11	55594868	55594868	+	Silent	SNP	C	C	T	rs150337368		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55594868C>T	ENST00000378397.1	+	1	174	c.174C>T	c.(172-174)ccC>ccT	p.P58P		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, 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)	p.P58>?(1)		breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				TCCACACCCCCGTGTACTTTT	0.468										HNSCC(27;0.073)			N|||	1	0.000199681	0.0	0.0	5008	,	,		20212	0.001		0.0	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											OR5L2,right_upper_lobe,carcinoma,0,1	OR5L2	135	1	1	Complex(1)	lung(1)	c.C174T						scavenged	.	C		1,4399		0,1,2199	250.0	230.0	236.0		174	1.2	1.0	11	dbSNP_134	236	4,8588		0,4,4292	no	coding-synonymous	OR5L2	NM_001004739.1		0,5,6491	TT,TC,CC		0.0466,0.0227,0.0385		58/312	55594868	5,12987	2200	4296	6496	SO:0001819	synonymous_variant	26338	exon1			CACCCCCGTGTAC	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"""GPCR / Class A : Olfactory receptors"""	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.174C>T	11.37:g.55594868C>T		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	253	4	0.0158103	NM_001004739	Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	CCDS31511.1																																																																																			C|1.000;T|0.000	0.000	weak		0.468	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
PKD2L1	9033	hgsc.bcm.edu	37	10	102089663	102089663	+	Silent	SNP	C	C	T	rs569511	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102089663C>T	ENST00000318222.3	-	1	580	c.198G>A	c.(196-198)gtG>gtA	p.V66V	PKD2L1_ENST00000338519.3_Silent_p.V66V|PKD2L1_ENST00000353274.3_Silent_p.V66V	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	66					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		AGCAGCTGGACACCTGGGTCC	0.557													C|||	685	0.136781	0.1021	0.085	5008	,	,		13499	0.0337		0.1153	False		,,,				2504	0.3487				p.C12Y		Atlas-SNP	.											.	PKD2L1	103	.	0			c.G35A						PASS	.	C		485,3921	226.2+/-241.8	30,425,1748	78.0	80.0	79.0		198	0.3	0.4	10	dbSNP_83	79	1145,7455	234.4+/-267.4	76,993,3231	no	coding-synonymous	PKD2L1	NM_016112.2		106,1418,4979	TT,TC,CC		13.314,11.0077,12.5327		66/806	102089663	1630,11376	2203	4300	6503	SO:0001819	synonymous_variant	9033	exon1			GCTGGACACCTGG	AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9011	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 3"""	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.198G>A	10.37:g.102089663C>T		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	162	108	0.666667	NM_001253837	O75972|Q5W039|Q9UP35|Q9UPA2	Missense_Mutation	SNP	ENST00000318222.3	37	CCDS7492.1	203	0.09294871794871795	56	0.11382113821138211	32	0.08839779005524862	22	0.038461538461538464	93	0.12269129287598944	C	2.201	-0.383055	0.04966	0.110077	0.13314	ENSG00000107593	ENST00000465680	T	0.55930	0.49	5.57	0.255	0.15561	.	0.558636	0.17756	N	0.163041	T	0.00524	0.0017	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.08351	-1.0726	6	0.54805	T	0.06	-2.5227	2.1951	0.03909	0.1367:0.4921:0.1331:0.238	rs569511	.	.	.	I	23	ENSP00000434019:V23I	ENSP00000434019:V23I	V	-	1	0	PKD2L1	102079653	0.010000	0.17322	0.355000	0.25773	0.134000	0.20937	-0.344000	0.07780	0.325000	0.23359	-0.143000	0.13931	GTC	C|0.882;T|0.118	0.118	strong		0.557	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049863.2	NM_016112	
VCAN	1462	hgsc.bcm.edu	37	5	82837631	82837631	+	Missense_Mutation	SNP	G	G	T	rs160277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:82837631G>T	ENST00000265077.3	+	8	9374	c.8809G>T	c.(8809-8811)Gat>Tat	p.D2937Y	VCAN_ENST00000502527.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.D1950Y|VCAN_ENST00000342785.4_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2937	GAG-beta.		D -> Y (in dbSNP:rs160277).		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)	AAACAAAACCGATGGTCAAGT	0.398													G|||	1806	0.360623	0.357	0.4597	5008	,	,		18764	0.3234		0.4254	False		,,,				2504	0.2669				p.D2937Y		Atlas-SNP	.											.	VCAN	498	.	0			c.G8809T						PASS	.	G	,TYR/ASP,,TYR/ASP	1625,2781	482.4+/-359.4	296,1033,874	80.0	85.0	83.0		,5848,,8809	0.8	0.0	5	dbSNP_79	83	3433,5167	503.3+/-375.9	700,2033,1567	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,160,,160	996,3066,2441	TT,TG,GG		39.9186,36.8815,38.8897	,possibly-damaging,,possibly-damaging	,1950/2410,,2937/3397	82837631	5058,7948	2203	4300	6503	SO:0001583	missense	1462	exon8			AAAACCGATGGTC	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.8809G>T	5.37:g.82837631G>T	ENSP00000265077:p.Asp2937Tyr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	837	0.38324175824175827	145	0.29471544715447157	168	0.46408839779005523	203	0.3548951048951049	321	0.4234828496042216	G	12.91	2.079124	0.36662	0.368815	0.399186	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.18338	2.22;2.22	5.99	0.819	0.18785	.	1.042050	0.07483	N	0.904317	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D;D	0.60160	0.987;0.979	P;P	0.52672	0.706;0.607	T	0.46748	-0.9169	9	0.59425	D	0.04	.	2.3966	0.04391	0.5352:0.1193:0.2293:0.1161	rs160277;rs310482;rs496670;rs3734093;rs52794243;rs60765899;rs160277	1950;2937	P13611-2;P13611	.;CSPG2_HUMAN	Y	2937;1950	ENSP00000265077:D2937Y;ENSP00000340062:D1950Y	ENSP00000265077:D2937Y	D	+	1	0	VCAN	82873387	0.001000	0.12720	0.001000	0.08648	0.083000	0.17756	0.638000	0.24674	0.540000	0.28808	-0.312000	0.09012	GAT	G|0.618;T|0.382	0.382	strong		0.398	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
LRRN1	57633	hgsc.bcm.edu	37	3	3886721	3886721	+	Silent	SNP	C	C	A	rs3749350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:3886721C>A	ENST00000319331.3	+	2	1157	c.396C>A	c.(394-396)acC>acA	p.T132T	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	132						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)		ATCAGATTACCGAGATGACTG	0.428													A|||	1458	0.291134	0.4047	0.2565	5008	,	,		20305	0.4067		0.1074	False		,,,				2504	0.2321				p.T132T		Atlas-SNP	.											.	LRRN1	82	.	0			c.C396A						PASS	.	A		1584,2822	658.8+/-400.5	301,982,920	70.0	73.0	72.0		396	-11.3	0.0	3	dbSNP_107	72	1090,7510	768.9+/-407.6	67,956,3277	no	coding-synonymous	LRRN1	NM_020873.5		368,1938,4197	AA,AC,CC		12.6744,35.951,20.5597		132/717	3886721	2674,10332	2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			GATTACCGAGATG	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.396C>A	3.37:g.3886721C>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			C|0.758;A|0.242	0.242	strong		0.428	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
ALPL	249	hgsc.bcm.edu	37	1	21894735	21894735	+	Missense_Mutation	SNP	T	T	C	rs3200254	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:21894735T>C	ENST00000374840.3	+	7	1037	c.787T>C	c.(787-789)Tac>Cac	p.Y263H	ALPL_ENST00000374832.1_Missense_Mutation_p.Y263H|ALPL_ENST00000539907.1_Missense_Mutation_p.Y186H|ALPL_ENST00000374830.1_5'Flank|ALPL_ENST00000425315.2_Missense_Mutation_p.Y263H|ALPL_ENST00000540617.1_Missense_Mutation_p.Y208H	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	109	0	0		WXS	Illumina HiSeq	Phase_I	66	48	0.727273	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	
KDM4C	23081	hgsc.bcm.edu	37	9	7170006	7170006	+	Intron	SNP	G	G	A	rs7022348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:7170006G>A	ENST00000381309.3	+	21	3559				KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.S1037N|KDM4C_ENST00000428870.2_Intron	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C						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						TCTAAAAAAAGCCAATGCAAC	0.398													G|||	667	0.133187	0.1876	0.1369	5008	,	,		19592	0.001		0.2366	False		,,,				2504	0.0869				p.S1037N		Atlas-SNP	.											.	KDM4C	186	.	0			c.G3110A						PASS	.	G	ASN/SER,	232,1152		24,184,484	50.0	44.0	46.0		3110,	0.9	0.0	9	dbSNP_116	46	728,2454		83,562,946	yes	missense,intron	KDM4C	NM_001146694.1,NM_015061.3	46,	107,746,1430	AA,AG,GG		22.8787,16.763,21.025	,	1037/1048,	7170006	960,3606	692	1591	2283	SO:0001627	intron_variant	23081	exon21			AAAAAAGCCAATG	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.2994+116G>A	9.37:g.7170006G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	316	0.1446886446886447	87	0.17682926829268292	56	0.15469613259668508	0	0.0	173	0.22823218997361477	G	11.29	1.595464	0.28445	0.16763	0.228787	ENSG00000107077	ENST00000381306	T	0.16196	2.36	4.15	0.896	0.19253	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.50171	P	1.4300000000000423E-4	B	0.06786	0.001	B	0.09377	0.004	T	0.45556	-0.9253	6	.	.	.	.	6.7317	0.23387	0.3685:0.0:0.6315:0.0	rs7022348;rs7022348	1037	Q9H3R0-2	.	N	1037	ENSP00000370707:S1037N	.	S	+	2	0	KDM4C	7160006	0.000000	0.05858	0.011000	0.14972	0.016000	0.09150	-0.100000	0.10990	0.173000	0.19788	0.467000	0.42956	AGC	G|0.846;A|0.154	0.154	strong		0.398	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
TTLL6	284076	hgsc.bcm.edu	37	17	46847364	46847364	+	Missense_Mutation	SNP	C	C	A	rs2032844	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46847364C>A	ENST00000393382.3	-	14	2277	c.2136G>T	c.(2134-2136)gaG>gaT	p.E712D	TTLL6_ENST00000433608.2_Missense_Mutation_p.E405D	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						GGCCACTGTACTCAGAGCTGG	0.517													C|||	1193	0.238219	0.2602	0.3905	5008	,	,		15857	0.1736		0.2445	False		,,,				2504	0.1605				p.E712D		Atlas-SNP	.											.	TTLL6	113	.	0			c.G2136T						PASS	.	C	ASP/GLU,ASP/GLU	1137,3269	402.6+/-332.4	148,841,1214	68.0	72.0	70.0		2136,1215	-3.8	0.0	17	dbSNP_94	70	2144,6456	368.4+/-335.1	262,1620,2418	yes	missense,missense	TTLL6	NM_001130918.1,NM_173623.3	45,45	410,2461,3632	AA,AC,CC		24.9302,25.8057,25.2268	probably-damaging,probably-damaging	712/892,405/585	46847364	3281,9725	2203	4300	6503	SO:0001583	missense	284076	exon14			ACTGTACTCAGAG	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.2136G>T	17.37:g.46847364C>A	ENSP00000377043:p.Glu712Asp	Somatic	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	315	150	0.47619	NM_001130918		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	537	0.24587912087912087	129	0.2621951219512195	133	0.3674033149171271	89	0.1555944055944056	186	0.24538258575197888	C	18.07	3.541315	0.65085	0.258057	0.249302	ENSG00000170703	ENST00000440941;ENST00000305326;ENST00000433608;ENST00000393382	.	.	.	4.36	-3.84	0.04256	.	6.187980	0.00357	N	0.000038	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P;D	0.76494	0.954;0.999	B;D	0.80764	0.437;0.994	T	0.23476	-1.0187	8	0.49607	T	0.09	.	5.6836	0.17790	0.1313:0.5714:0.0:0.2972	rs2032844;rs52819623;rs58091541;rs2032844	664;405	Q8N841;G5E937	TTLL6_HUMAN;.	D	712;405;390;664	.	ENSP00000302547:E405D	E	-	3	2	TTLL6	44202363	0.000000	0.05858	0.002000	0.10522	0.210000	0.24377	-1.741000	0.01837	-0.440000	0.07211	0.655000	0.94253	GAG	C|0.755;A|0.245	0.245	strong		0.517	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
CACNA1C	775	hgsc.bcm.edu	37	12	2558186	2558186	+	Silent	SNP	G	G	A	rs1544514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:2558186G>A	ENST00000347598.4	+	4	522	c.522G>A	c.(520-522)gcG>gcA	p.A174A	CACNA1C_ENST00000399597.1_Silent_p.A174A|CACNA1C_ENST00000399637.1_Silent_p.A174A|CACNA1C_ENST00000480911.1_Silent_p.A174A|CACNA1C_ENST00000399606.1_Silent_p.A174A|CACNA1C_ENST00000344100.3_Silent_p.A174A|CACNA1C_ENST00000399617.1_Silent_p.A174A|CACNA1C_ENST00000399634.1_Silent_p.A174A|CACNA1C_ENST00000399641.1_Silent_p.A174A|CACNA1C_ENST00000399644.1_Silent_p.A174A|CACNA1C_ENST00000399629.1_Silent_p.A174A|CACNA1C_ENST00000399621.1_Silent_p.A174A|CACNA1C_ENST00000399591.1_Silent_p.A174A|CACNA1C_ENST00000399601.1_Silent_p.A174A|CACNA1C_ENST00000406454.3_Silent_p.A174A|CACNA1C_ENST00000399638.1_Silent_p.A174A|CACNA1C_ENST00000327702.7_Silent_p.A174A|CACNA1C_ENST00000335762.5_Silent_p.A174A|CACNA1C_ENST00000402845.3_Silent_p.A174A|CACNA1C_ENST00000399603.1_Silent_p.A174A|CACNA1C_ENST00000399649.1_Silent_p.A174A|CACNA1C_ENST00000399655.1_Silent_p.A174A|CACNA1C_ENST00000399595.1_Silent_p.A174A	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	174					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)	CGGTGGAAGCGTTTTTAAAAG	0.403													G|||	603	0.120407	0.0756	0.147	5008	,	,		17828	0.0655		0.1928	False		,,,				2504	0.1442				p.A174A		Atlas-SNP	.											CACNA1C_ENST00000344100,colon,carcinoma,+1,2	CACNA1C	1023	2	0			c.G522A						PASS	.	G	,,,,,,,,,,,,,,,,,,,,,,	326,3334		21,284,1525	90.0	84.0	86.0		522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522,522	-0.1	1.0	12	dbSNP_88	86	1749,6401		192,1365,2518	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	,,,,,,,,,,,,,,,,,,,,,,	213,1649,4043	AA,AG,GG		21.4601,8.9071,17.5699	,,,,,,,,,,,,,,,,,,,,,,	174/2139,174/2187,174/2180,174/2174,174/2167,174/2159,174/2158,174/2158,174/2158,174/2156,174/2147,174/2147,174/2145,174/2139,174/2139,174/2139,174/2139,174/2136,174/2128,174/2139,174/2174,174/2199,174/2222	2558186	2075,9735	1830	4075	5905	SO:0001819	synonymous_variant	775	exon4			GGAAGCGTTTTTA	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.522G>A	12.37:g.2558186G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	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																																																																																			G|0.860;A|0.140	0.140	strong		0.403	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
OR5K4	403278	hgsc.bcm.edu	37	3	98073313	98073313	+	Missense_Mutation	SNP	A	A	G	rs9822460	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:98073313A>G	ENST00000354924.2	+	1	616	c.616A>G	c.(616-618)Att>Gtt	p.I206V	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	206			I -> V (in dbSNP:rs9822460).			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)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						TTCAATACCAATTCAAATCTT	0.328													A|||	1168	0.233227	0.2451	0.232	5008	,	,		18812	0.1726		0.2217	False		,,,				2504	0.2924				p.I206V		Atlas-SNP	.											.	OR5K4	75	.	0			c.A616G						PASS	.	A	VAL/ILE	1199,3207	415.0+/-337.0	180,839,1184	81.0	82.0	82.0		616	2.7	1.0	3	dbSNP_119	82	1757,6843	317.6+/-313.3	180,1397,2723	yes	missense	OR5K4	NM_001005517.1	29	360,2236,3907	GG,GA,AA		20.4302,27.2129,22.728	benign	206/322	98073313	2956,10050	2203	4300	6503	SO:0001583	missense	403278	exon1			ATACCAATTCAAA		CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"""GPCR / Class A : Olfactory receptors"""	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.616A>G	3.37:g.98073313A>G	ENSP00000347003:p.Ile206Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	157	90	0.573248	NM_001005517		Missense_Mutation	SNP	ENST00000354924.2	37	CCDS33802.1	447	0.20467032967032966	116	0.23577235772357724	78	0.2154696132596685	81	0.14160839160839161	172	0.22691292875989447	A	3.044	-0.196857	0.06259	0.272129	0.204302	ENSG00000196098	ENST00000354924	T	0.00044	8.83	5.06	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33057	U	0.005331	T	0.00012	0.0000	N	0.25094	0.71	0.49687	P	1.8300000000004424E-4	B	0.16603	0.018	B	0.25405	0.06	T	0.04128	-1.0975	9	0.02654	T	1	-10.2086	7.8213	0.29290	0.827:0.0:0.173:0.0	rs9822460;rs52816954;rs9822460	206	A6NMS3	OR5K4_HUMAN	V	206	ENSP00000347003:I206V	ENSP00000347003:I206V	I	+	1	0	OR5K4	99556003	0.000000	0.05858	0.987000	0.45799	0.961000	0.63080	-0.114000	0.10757	0.493000	0.27837	0.491000	0.48974	ATT	A|0.782;G|0.218	0.218	strong		0.328	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1		
RBM48	84060	hgsc.bcm.edu	37	7	92158154	92158154	+	Silent	SNP	G	G	A	rs117787377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:92158154G>A	ENST00000265732.5	+	1	68	c.27G>A	c.(25-27)ggG>ggA	p.G9G	RBM48_ENST00000481551.1_Silent_p.G9G|PEX1_ENST00000438045.1_5'Flank|PEX1_ENST00000248633.4_5'Flank|PEX1_ENST00000428214.1_5'Flank	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	9						nucleus (GO:0005634)	RNA binding (GO:0003723)										GGGAGCTAGGGAGTTTATTTG	0.552													G|||	20	0.00399361	0.0008	0.0029	5008	,	,		17571	0.0		0.0149	False		,,,				2504	0.002				p.G9G		Atlas-SNP	.											.	.	.	.	0			c.G27A						PASS	.	G		18,3950		0,18,1966	70.0	75.0	74.0		27	-4.0	0.0	7	dbSNP_132	74	123,8149		0,123,4013	no	coding-synonymous	C7orf64	NM_032120.2		0,141,5979	AA,AG,GG		1.4869,0.4536,1.152		9/368	92158154	141,12099	1984	4136	6120	SO:0001819	synonymous_variant	84060	exon1			GCTAGGGAGTTTA	AL136619	CCDS43615.1	7q21.2	2013-02-12	2011-12-09	2011-12-09	ENSG00000127993	ENSG00000127993		"""RNA binding motif (RRM) containing"""	21785	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 64"""	C7orf64			Standard	NM_032120		Approved	DKFZp564O0523, HSPC304	uc003ulz.3	Q5RL73	OTTHUMG00000159535	ENST00000265732.5:c.27G>A	7.37:g.92158154G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	266	167	0.62782	NM_032120	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Silent	SNP	ENST00000265732.5	37	CCDS43615.1																																																																																			G|0.992;A|0.008	0.008	strong		0.552	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120	
PLCG2	5336	hgsc.bcm.edu	37	16	81929488	81929488	+	Silent	SNP	C	C	T	rs1143688	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:81929488C>T	ENST00000359376.3	+	13	1363	c.1149C>T	c.(1147-1149)gaC>gaT	p.D383D		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	383	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						TCAAGTTTGACGACGTCGTGC	0.577													C|||	2036	0.40655	0.1029	0.5994	5008	,	,		19362	0.7113		0.3549	False		,,,				2504	0.4192				p.D383D		Atlas-SNP	.											.	PLCG2	276	.	0			c.C1149T						PASS	.	C		616,3574		56,504,1535	159.0	170.0	166.0		1149	-9.9	0.1	16	dbSNP_86	166	3035,5431		557,1921,1755	no	coding-synonymous	PLCG2	NM_002661.3		613,2425,3290	TT,TC,CC		35.8493,14.7017,28.848		383/1266	81929488	3651,9005	2095	4233	6328	SO:0001819	synonymous_variant	5336	exon13			GTTTGACGACGTC		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.1149C>T	16.37:g.81929488C>T		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	121	108	0.892562	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			C|0.594;N|0.000	.	strong		0.577	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
HAPLN3	145864	hgsc.bcm.edu	37	15	89424765	89424765	+	Missense_Mutation	SNP	C	C	T	rs140982817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:89424765C>T	ENST00000359595.3	-	3	530	c.316G>A	c.(316-318)Ggg>Agg	p.G106R	HAPLN3_ENST00000562889.1_Missense_Mutation_p.G168R	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	106	Ig-like V-type. {ECO:0000305}.				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)	TGCCTCAGCCCGATGGCCACC	0.662													C|||	3	0.000599042	0.0	0.0029	5008	,	,		18397	0.0		0.001	False		,,,				2504	0.0				p.G106R		Atlas-SNP	.											HAPLN3,caecum,carcinoma,0,1	HAPLN3	43	1	0			c.G316A						PASS	.	C	ARG/GLY	2,4398	4.2+/-10.8	0,2,2198	95.0	76.0	83.0		316	4.2	0.4	15	dbSNP_134	83	55,8543	34.8+/-89.0	0,55,4244	yes	missense	HAPLN3	NM_178232.2	125	0,57,6442	TT,TC,CC		0.6397,0.0455,0.4385	probably-damaging	106/361	89424765	57,12941	2200	4299	6499	SO:0001583	missense	145864	exon3			TCAGCCCGATGGC	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.316G>A	15.37:g.89424765C>T	ENSP00000352606:p.Gly106Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	70	21	0.3	NM_178232	A8K7P0	Missense_Mutation	SNP	ENST00000359595.3	37	CCDS10346.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.60	3.429872	0.62844	4.55E-4	0.006397	ENSG00000140511	ENST00000359595	T	0.65364	-0.15	4.21	4.21	0.49690	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.77705	0.4170	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85370	0.1113	10	0.87932	D	0	-31.7116	15.5717	0.76345	0.0:1.0:0.0:0.0	.	106;106	A8K7T8;Q96S86	.;HPLN3_HUMAN	R	106	ENSP00000352606:G106R	ENSP00000352606:G106R	G	-	1	0	HAPLN3	87225769	1.000000	0.71417	0.441000	0.26858	0.188000	0.23474	7.032000	0.76498	1.870000	0.54199	0.650000	0.86243	GGG	C|0.998;T|0.002	0.002	strong		0.662	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
SDC3	9672	hgsc.bcm.edu	37	1	31347399	31347399	+	Missense_Mutation	SNP	C	C	T	rs4949184	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:31347399C>T	ENST00000339394.6	-	4	1081	c.907G>A	c.(907-909)Gat>Aat	p.D303N	SDC3_ENST00000336798.7_Missense_Mutation_p.D245N|SDC3_ENST00000471567.1_5'Flank	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	303			D -> N (in dbSNP:rs4949184). {ECO:0000269|PubMed:11527150}.		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)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		TCTGGCTCATCCCGGATTGTG	0.587													C|||	1174	0.234425	0.3782	0.1628	5008	,	,		18096	0.0665		0.1799	False		,,,				2504	0.32				p.D303N		Atlas-SNP	.											.	SDC3	45	.	0			c.G907A						PASS	.	C	ASN/ASP	1367,3039	454.0+/-350.5	217,933,1053	108.0	106.0	107.0		907	4.7	1.0	1	dbSNP_111	107	1565,7035	292.4+/-300.8	137,1291,2872	yes	missense	SDC3	NM_014654.3	23	354,2224,3925	TT,TC,CC		18.1977,31.0259,22.5434	probably-damaging	303/443	31347399	2932,10074	2203	4300	6503	SO:0001583	missense	9672	exon4			GCTCATCCCGGAT	AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"""Proteoglycans / Cell Surface : Syndecans"""	10660	protein-coding gene	gene with protein product	"""syndecan proteoglycan 3"""	186357	"""syndecan 3 (N-syndecan)"""			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.907G>A	1.37:g.31347399C>T	ENSP00000344468:p.Asp303Asn	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	51	37	0.72549	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Missense_Mutation	SNP	ENST00000339394.6	37	CCDS30661.1	385	0.1762820512820513	180	0.36585365853658536	56	0.15469613259668508	24	0.04195804195804196	125	0.16490765171503957	C	19.78	3.890788	0.72524	0.310259	0.181977	ENSG00000162512	ENST00000336798;ENST00000339394	T;T	0.25414	1.81;1.8	4.7	4.7	0.59300	.	0.266144	0.30809	N	0.008833	T	0.00012	0.0000	N	0.12182	0.205	0.48135	P	4.0200000000001346E-4	B;B	0.13594	0.008;0.008	B;B	0.16289	0.015;0.009	T	0.41680	-0.9495	9	0.36615	T	0.2	-1.9576	6.7554	0.23510	0.0:0.8463:0.0:0.1537	rs4949184;rs57147714;rs4949184	303;245	O75056;D3DPN2	SDC3_HUMAN;.	N	245;303	ENSP00000338346:D245N;ENSP00000344468:D303N	ENSP00000338346:D245N	D	-	1	0	SDC3	31119986	0.715000	0.27946	0.967000	0.41034	0.697000	0.40408	3.045000	0.49838	2.454000	0.82982	0.563000	0.77884	GAT	C|0.795;T|0.205	0.205	strong		0.587	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
IFNA21	3452	hgsc.bcm.edu	37	9	21166423	21166423	+	Silent	SNP	C	C	T	rs1053884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:21166423C>T	ENST00000380225.1	-	1	236	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_002175.2	NP_002166.2	P01568	IFN21_HUMAN	interferon, alpha 21	63					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|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)|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)|cytokine receptor binding (GO:0005126)|type I interferon receptor binding (GO:0005132)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)	14				GBM - Glioblastoma multiforme(5;1.93e-187)|Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CAAACTCCTCCTGGGGGAATC	0.502													C|||	25	0.00499201	0.0151	0.0072	5008	,	,		20179	0.0		0.0	False		,,,				2504	0.0				p.Q63Q		Atlas-SNP	.											.	IFNA21	25	.	0			c.G189A						PASS	.	C		49,4357		0,49,2154	135.0	136.0	135.0		189	3.1	0.0	9	dbSNP_86	135	7,8593		0,7,4293	no	coding-synonymous	IFNA21	NM_002175.2		0,56,6447	TT,TC,CC		0.0814,1.1121,0.4306		63/190	21166423	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	3452	exon1			CTCCTCCTGGGGG		CCDS6497.1	9p22	2010-12-10			ENSG00000137080	ENSG00000137080		"""Interferons"""	5424	protein-coding gene	gene with protein product	"""leukocyte interferon protein"""	147584				1385305	Standard	NM_002175		Approved	IFN-alphaI	uc003zom.2	P01568	OTTHUMG00000019653	ENST00000380225.1:c.189G>A	9.37:g.21166423C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	232	121	0.521552	NM_002175	Q14608|Q5VWD1|Q7M4Q4	Silent	SNP	ENST00000380225.1	37	CCDS6497.1																																																																																			C|0.996;T|0.004	0.004	strong		0.502	IFNA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051882.1	NM_002175	
OR52R1	119695	hgsc.bcm.edu	37	11	4825225	4825225	+	Missense_Mutation	SNP	A	A	G	rs7941731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4825225A>G	ENST00000356069.2	-	1	385	c.386T>C	c.(385-387)aTc>aCc	p.I129T	MMP26_ENST00000380390.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.I208T|MMP26_ENST00000477339.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	129			I -> T (in dbSNP:rs7941731). {ECO:0000269|PubMed:14983052, 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)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGGAAGCAGATAGCCACGTA	0.572													A|||	1549	0.309305	0.5582	0.2795	5008	,	,		21992	0.0129		0.3897	False		,,,				2504	0.2168				p.I129T		Atlas-SNP	.											.	OR52R1	81	.	0			c.T386C						PASS	.	A	THR/ILE	2266,2136	598.9+/-389.2	594,1078,529	127.0	112.0	117.0		386	5.4	1.0	11	dbSNP_116	117	3011,5585	465.5+/-366.5	551,1909,1838	yes	missense	OR52R1	NM_001005177.3	89	1145,2987,2367	GG,GA,AA		35.0279,48.5234,40.5986	probably-damaging	129/316	4825225	5277,7721	2201	4298	6499	SO:0001583	missense	119695	exon1			AAGCAGATAGCCA	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.386T>C	11.37:g.4825225A>G	ENSP00000348368:p.Ile129Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	682	0.31227106227106227	270	0.5487804878048781	117	0.32320441988950277	10	0.017482517482517484	285	0.3759894459102902	A	17.17	3.320491	0.60634	0.514766	0.350279	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.59224	0.28;0.28	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000122	T	0.00012	0.0000	H	0.96970	3.915	0.20821	P	0.999840389	D	0.58620	0.983	P	0.51193	0.662	T	0.48175	-0.9058	9	0.72032	D	0.01	.	14.4289	0.67236	1.0:0.0:0.0:0.0	rs7941731;rs52795806;rs7941731	129	Q8NGF1	O52R1_HUMAN	T	129;208	ENSP00000348368:I129T;ENSP00000369742:I208T	ENSP00000348368:I129T	I	-	2	0	OR52R1	4781801	1.000000	0.71417	1.000000	0.80357	0.428000	0.31595	8.942000	0.92970	2.280000	0.76307	0.528000	0.53228	ATC	A|0.629;G|0.371	0.371	strong		0.572	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
SCEL	8796	hgsc.bcm.edu	37	13	78188078	78188078	+	Missense_Mutation	SNP	A	A	G	rs8002725	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:78188078A>G	ENST00000349847.3	+	24	1523	c.1439A>G	c.(1438-1440)aAa>aGa	p.K480R	SCEL_ENST00000535157.1_Missense_Mutation_p.K438R|SCEL_ENST00000469982.1_3'UTR|SCEL_ENST00000377246.3_Missense_Mutation_p.K460R	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	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	213	113	0.530516	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	
GGT5	2687	hgsc.bcm.edu	37	22	24628928	24628928	+	Silent	SNP	G	G	A	rs762276	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:24628928G>A	ENST00000327365.4	-	4	875	c.459C>T	c.(457-459)cgC>cgT	p.R153R	GGT5_ENST00000263112.7_Silent_p.R121R|GGT5_ENST00000418439.2_Missense_Mutation_p.P78S|GGT5_ENST00000398292.3_Silent_p.R153R	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	153					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						GGCGGCCATGGCGGCGGTGGG	0.701													G|||	639	0.127596	0.0197	0.1888	5008	,	,		13019	0.1746		0.1571	False		,,,				2504	0.1513				p.R153R		Atlas-SNP	.											.	GGT5	61	.	0			c.C459T						PASS	.	G	,,	213,4145		9,195,1975	18.0	21.0	20.0		459,363,459	2.4	1.0	22	dbSNP_86	20	1070,7426		54,962,3232	no	coding-synonymous,coding-synonymous,coding-synonymous	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	,,	63,1157,5207	AA,AG,GG		12.5942,4.8876,9.9813	,,	153/588,121/555,153/587	24628928	1283,11571	2179	4248	6427	SO:0001819	synonymous_variant	2687	exon4			GCCATGGCGGCGG	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"""Gamma-glutamyltransferases"""	4260	protein-coding gene	gene with protein product		137168	"""gamma-glutamyltransferase-like activity 1"""	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.459C>T	22.37:g.24628928G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Silent	SNP	ENST00000327365.4	37	CCDS13825.1	294	0.1346153846153846	12	0.024390243902439025	68	0.1878453038674033	103	0.18006993006993008	111	0.14643799472295516	G	15.59	2.879364	0.51801	0.048876	0.125942	ENSG00000099998	ENST00000418439	T	0.19938	2.11	4.51	2.36	0.29203	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.45806	P	0.0013119999999999798	B	0.14438	0.01	B	0.10450	0.005	T	0.24368	-1.0162	7	0.72032	D	0.01	-40.7365	3.3668	0.07206	0.0949:0.1713:0.557:0.1767	rs762276	78	E7EUG3	.	S	78	ENSP00000392146:P78S	ENSP00000392146:P78S	P	-	1	0	GGT5	22958928	0.009000	0.17119	1.000000	0.80357	0.947000	0.59692	-0.683000	0.05179	0.627000	0.30340	0.585000	0.79938	CCA	G|0.864;A|0.136	0.136	strong		0.701	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	
SIM2	6493	hgsc.bcm.edu	37	21	38117040	38117040	+	Silent	SNP	G	G	A	rs2073416	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:38117040G>A	ENST00000290399.6	+	10	1792	c.1179G>A	c.(1177-1179)tcG>tcA	p.S393S	SIM2_ENST00000430056.3_Silent_p.S393S	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	393	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						AATACAGCTCGTTCCAAATGG	0.617													G|||	1377	0.27496	0.3835	0.1787	5008	,	,		17396	0.2292		0.2237	False		,,,				2504	0.2965				p.S393S		Atlas-SNP	.											.	SIM2	55	.	0			c.G1179A						PASS	.	G	,	1605,2799		306,993,903	28.0	27.0	27.0		1179,1179	-8.8	0.5	21	dbSNP_96	27	1829,6771		192,1445,2663	no	coding-synonymous,coding-synonymous	SIM2	NM_005069.3,NM_009586.2	,	498,2438,3566	AA,AG,GG		21.2674,36.4441,26.4073	,	393/668,393/571	38117040	3434,9570	2202	4300	6502	SO:0001819	synonymous_variant	6493	exon10			CAGCTCGTTCCAA		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"""Basic helix-loop-helix proteins"""	10883	protein-coding gene	gene with protein product	"""transcription factor SIM2"""	600892	"""single-minded (Drosophila) homolog 2"", ""single-minded homolog 2 (Drosophila)"""	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.1179G>A	21.37:g.38117040G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	90	31	0.344444	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Silent	SNP	ENST00000290399.6	37	CCDS13646.1	548	0.2509157509157509	178	0.3617886178861789	71	0.19613259668508287	123	0.21503496503496503	176	0.23218997361477572	G	9.051	0.991992	0.18966	0.364441	0.212674	ENSG00000159263	ENST00000431229	.	.	.	5.05	-8.81	0.00813	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999497838	.	.	.	.	.	.	T	0.36939	-0.9727	3	.	.	.	.	2.7046	0.05158	0.2843:0.3866:0.173:0.1561	rs2073416;rs52820127;rs2073416	.	.	.	I	331	.	.	V	+	1	0	SIM2	37038910	0.865000	0.29922	0.459000	0.27081	0.990000	0.78478	-0.257000	0.08745	-1.581000	0.01642	-0.320000	0.08662	GTT	G|0.736;A|0.264	0.264	strong		0.617	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
FAM47E	100129583	hgsc.bcm.edu	37	4	77192868	77192868	+	Missense_Mutation	SNP	G	G	A	rs3733250	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	130	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	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	
DNAH3	55567	hgsc.bcm.edu	37	16	21145648	21145648	+	Silent	SNP	C	C	T	rs11074483	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:21145648C>T	ENST00000261383.3	-	7	1013	c.1014G>A	c.(1012-1014)aaG>aaA	p.K338K	DNAH3_ENST00000415178.1_Silent_p.K338K	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	338	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)|microtubule motor activity (GO:0003777)	p.K338K(2)		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)		CCTCGTTCCACTTCTTGGCGC	0.522													C|||	1251	0.2498	0.1853	0.3646	5008	,	,		18455	0.2946		0.2336	False		,,,				2504	0.226				p.K338K		Atlas-SNP	.											DNAH3_ENST00000261383,NS,carcinoma,0,2	DNAH3	1142	2	2	Substitution - coding silent(2)	stomach(2)	c.G1014A						PASS	.	C		915,3487	351.3+/-311.2	97,721,1383	112.0	106.0	108.0		1014	3.9	1.0	16	dbSNP_120	108	2100,6500	363.6+/-333.2	263,1574,2463	no	coding-synonymous	DNAH3	NM_017539.1		360,2295,3846	TT,TC,CC		24.4186,20.786,23.1887		338/4117	21145648	3015,9987	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon7			GTTCCACTTCTTG	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.1014G>A	16.37:g.21145648C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			C|0.759;T|0.241	0.241	strong		0.522	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ART5	116969	hgsc.bcm.edu	37	11	3659993	3659993	+	Missense_Mutation	SNP	G	G	T	rs2271586	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:3659993G>T	ENST00000397068.3	-	4	1243	c.851C>A	c.(850-852)aCg>aAg	p.T284K	ART5_ENST00000397067.3_3'UTR|TRPC2_ENST00000526541.1_RNA|ART5_ENST00000359918.4_Missense_Mutation_p.T284K	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	284					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		GTGCCTCTTCGTCATATGAAG	0.597													T|||	1500	0.299521	0.587	0.1988	5008	,	,		18352	0.2252		0.1948	False		,,,				2504	0.1667				p.T284K		Atlas-SNP	.											.	ART5	38	.	0			c.C851A						PASS	.	T	LYS/THR,LYS/THR	2312,2090	573.3+/-383.5	595,1122,484	155.0	142.0	146.0		851,851	2.8	0.0	11	dbSNP_100	146	1698,6898	738.4+/-407.1	165,1368,2765	yes	missense,missense	ART5	NM_001079536.1,NM_053017.3	78,78	760,2490,3249	TT,TG,GG		19.7534,47.4784,30.8509	benign,benign	284/292,284/292	3659993	4010,8988	2201	4298	6499	SO:0001583	missense	116969	exon4			CTCTTCGTCATAT	Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.851C>A	11.37:g.3659993G>T	ENSP00000380258:p.Thr284Lys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_053017	C9IYG7|Q6UX84|Q86W02	Missense_Mutation	SNP	ENST00000397068.3	37	CCDS7743.1	687	0.31456043956043955	311	0.6321138211382114	86	0.23756906077348067	148	0.25874125874125875	142	0.18733509234828497	T	0.010	-1.747008	0.00669	0.525216	0.197534	ENSG00000167311	ENST00000397068;ENST00000359918	T;T	0.08370	3.1;3.1	5.17	2.8	0.32819	.	1.639650	0.03152	N	0.168166	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	0.43475	-0.9389	9	0.05833	T	0.94	1.6704	2.0378	0.03543	0.1613:0.087:0.1686:0.5831	rs2271586;rs58181805;rs2271586	284	Q96L15	NAR5_HUMAN	K	284	ENSP00000380258:T284K;ENSP00000352992:T284K	ENSP00000352992:T284K	T	-	2	0	ART5	3616569	0.352000	0.24895	0.027000	0.17364	0.019000	0.09904	0.781000	0.26774	0.154000	0.19237	-0.256000	0.11100	ACG	G|0.689;T|0.311	0.311	strong		0.597	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017	
HACE1	57531	hgsc.bcm.edu	37	6	105198267	105198267	+	Silent	SNP	A	A	G	rs7752614	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	202	2	0.00990099		WXS	Illumina HiSeq	Phase_I	178	78	0.438202	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	
RSPH3	83861	hgsc.bcm.edu	37	6	159398633	159398633	+	Silent	SNP	T	T	C	rs3756988	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159398633T>C	ENST00000252655.1	-	8	1809	c.1620A>G	c.(1618-1620)gaA>gaG	p.E540E	RSPH3_ENST00000297262.3_Silent_p.E444E|RSPH3_ENST00000367069.2_Silent_p.E398E|RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000449822.1_Silent_p.E302E	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	540								p.E540E(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		GCCCTAAGAGTTCTCTCTCTT	0.448													C|||	1064	0.21246	0.0651	0.3746	5008	,	,		18032	0.3919		0.1034	False		,,,				2504	0.2239				p.E540E		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - coding silent(1)	stomach(1)	c.A1620G						PASS	.	C		404,4002	788.9+/-415.0	12,380,1811	261.0	246.0	251.0		1620	-5.7	0.0	6	dbSNP_107	251	926,7674	777.0+/-407.7	61,804,3435	no	coding-synonymous	RSPH3	NM_031924.4		73,1184,5246	CC,CT,TT		10.7674,9.1693,10.226		540/561	159398633	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	83861	exon8			TAAGAGTTCTCTC	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1620A>G	6.37:g.159398633T>C		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	162	76	0.469136	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Silent	SNP	ENST00000252655.1	37	CCDS5260.1																																																																																			T|0.844;C|0.156	0.156	strong		0.448	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
MASP1	5648	hgsc.bcm.edu	37	3	186953808	186953808	+	Intron	SNP	C	C	T	rs850312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	90	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	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	
NIPAL1	152519	hgsc.bcm.edu	37	4	48037926	48037926	+	Missense_Mutation	SNP	A	A	G	rs13116684	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:48037926A>G	ENST00000295461.5	+	6	1036	c.970A>G	c.(970-972)Atc>Gtc	p.I324V		NM_207330.1	NP_997213.1	Q6NVV3	NIPA3_HUMAN	NIPA-like domain containing 1	324			I -> V (in dbSNP:rs13116684).			integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(2)|large_intestine(1)|lung(3)|skin(2)	8						TTGCTCTGCCATCTTATTCCA	0.413													A|||	1022	0.204073	0.2262	0.1916	5008	,	,		9725	0.1637		0.2187	False		,,,				2504	0.2096				p.I324V		Atlas-SNP	.											.	NIPAL1	29	.	0			c.A970G						PASS	.	A	VAL/ILE	898,3508	346.9+/-309.2	84,730,1389	166.0	152.0	157.0		970	2.2	1.0	4	dbSNP_121	157	1867,6733	333.7+/-320.7	208,1451,2641	yes	missense	NIPAL1	NM_207330.1	29	292,2181,4030	GG,GA,AA		21.7093,20.3813,21.2594	probably-damaging	324/411	48037926	2765,10241	2203	4300	6503	SO:0001583	missense	152519	exon6			TCTGCCATCTTAT	BC067881	CCDS3479.1	4p12	2009-03-24		2009-03-24	ENSG00000163293	ENSG00000163293			27194	protein-coding gene	gene with protein product				NPAL1			Standard	NM_207330		Approved	DKFZp686A06115	uc003gxw.3	Q6NVV3	OTTHUMG00000128622	ENST00000295461.5:c.970A>G	4.37:g.48037926A>G	ENSP00000295461:p.Ile324Val	Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	343	172	0.501458	NM_207330	B3KTB0|Q68DA9	Missense_Mutation	SNP	ENST00000295461.5	37	CCDS3479.1	461	0.21108058608058608	119	0.241869918699187	72	0.19889502762430938	110	0.19230769230769232	160	0.21108179419525067	A	13.45	2.240068	0.39598	0.203813	0.217093	ENSG00000163293	ENST00000295461	D	0.92805	-3.11	5.96	2.24	0.28232	.	0.063928	0.64402	N	0.000005	T	0.00412	0.0013	M	0.74258	2.255	0.25630	P	0.9863127	D	0.64830	0.994	D	0.71656	0.974	T	0.00303	-1.1833	8	.	.	.	.	12.2212	0.54435	0.8724:0.0:0.1276:0.0	rs13116684;rs13116684	324	Q6NVV3	NIPA3_HUMAN	V	324	ENSP00000295461:I324V	.	I	+	1	0	NIPAL1	47732683	1.000000	0.71417	0.985000	0.45067	0.095000	0.18619	6.085000	0.71343	0.168000	0.19655	-1.122000	0.02009	ATC	A|0.792;G|0.208	0.208	strong		0.413	NIPAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250491.4	NM_207330	
ZNF679	168417	hgsc.bcm.edu	37	7	63726993	63726993	+	Missense_Mutation	SNP	G	G	A	rs10949885	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:63726993G>A	ENST00000421025.1	+	5	1251	c.982G>A	c.(982-984)Gaa>Aaa	p.E328K	ZNF679_ENST00000255746.4_Missense_Mutation_p.E328K	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	328				E -> K (in Ref. 2; AAH33523). {ECO:0000305}.	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)|lung(11)|skin(1)|stomach(1)	18						CACATGTGAAGAATGTGGCAA	0.403													.|||	511	0.102037	0.0371	0.1268	5008	,	,		21389	0.003		0.2346	False		,,,				2504	0.138				p.E328K		Atlas-SNP	.											.	ZNF679	80	.	0			c.G982A						PASS	.	G	LYS/GLU	101,1283		7,87,598	28.0	29.0	29.0		982	0.8	0.4	7	dbSNP_120	29	718,2464		82,554,955	no	missense	ZNF679	NM_153363.2	56	89,641,1553	AA,AG,GG		22.5644,7.2977,17.9369	probably-damaging	328/412	63726993	819,3747	692	1591	2283	SO:0001583	missense	168417	exon5			TGTGAAGAATGTG	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"""Zinc fingers, C2H2-type"", ""-"""	28650	protein-coding gene	gene with protein product	"""hypothetical protein MGC42415"""					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.982G>A	7.37:g.63726993G>A	ENSP00000416809:p.Glu328Lys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	70	45	0.642857	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	286	0.13095238095238096	32	0.06504065040650407	61	0.1685082872928177	0	0.0	193	0.2546174142480211	G	9.289	1.050110	0.19827	0.072977	0.225644	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.07327	3.2;3.2	0.81	0.81	0.18732	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.37750	1.13	0.80722	P	0.0	D	0.76494	0.999	D	0.76071	0.987	T	0.40156	-0.9578	8	0.62326	D	0.03	.	6.9761	0.24677	0.0:0.0:1.0:0.0	rs10949885;rs17846046;rs17859037	328	Q8IYX0	ZN679_HUMAN	K	328	ENSP00000416809:E328K;ENSP00000255746:E328K	ENSP00000255746:E328K	E	+	1	0	ZNF679	63364428	0.000000	0.05858	0.427000	0.26684	0.430000	0.31655	0.163000	0.16520	0.181000	0.19994	0.184000	0.17185	GAA	G|0.853;A|0.147	0.147	strong		0.403	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363	
RTP2	344892	hgsc.bcm.edu	37	3	187419816	187419816	+	Missense_Mutation	SNP	T	T	C	rs61754877	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:187419816T>C	ENST00000358241.1	-	1	529	c.101A>G	c.(100-102)aAc>aGc	p.N34S	RP11-211G3.3_ENST00000437407.1_5'Flank|RP11-211G3.3_ENST00000449623.1_5'Flank	NM_001004312.2	NP_001004312.2	Q5QGT7	RTP2_HUMAN	receptor (chemosensory) transporter protein 2	34					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			large_intestine(3)|lung(14)|skin(1)	18	all_cancers(143;4.06e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0515)		GGGCTTGAGGTTGGGGTCTAT	0.577													T|||	852	0.170128	0.1581	0.1009	5008	,	,		17659	0.1409		0.1938	False		,,,				2504	0.2413				p.N34S		Atlas-SNP	.											.	RTP2	38	.	0			c.A101G						PASS	.	T	SER/ASN	664,3742	284.6+/-277.7	49,566,1588	131.0	135.0	133.0		101	0.8	1.0	3	dbSNP_129	133	1679,6921	309.0+/-309.2	139,1401,2760	yes	missense	RTP2	NM_001004312.2	46	188,1967,4348	CC,CT,TT		19.5233,15.0704,18.0148	benign	34/226	187419816	2343,10663	2203	4300	6503	SO:0001583	missense	344892	exon1			TTGAGGTTGGGGT	AY562236	CCDS33911.1	3q27.3	2014-02-20	2006-11-21		ENSG00000198471	ENSG00000198471		"""Receptor transporter proteins"""	32486	protein-coding gene	gene with protein product	"""receptor transporting protein 2"", ""zinc finger, 3CxxC-type 2"""	609138	"""receptor transporter protein 2"""			16271481, 15550249, 16720576	Standard	NM_001004312		Approved	MGC78665, Z3CXXC2	uc003fro.1	Q5QGT7	OTTHUMG00000156458	ENST00000358241.1:c.101A>G	3.37:g.187419816T>C	ENSP00000350976:p.Asn34Ser	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	264	124	0.469697	NM_001004312	Q6NVH4	Missense_Mutation	SNP	ENST00000358241.1	37	CCDS33911.1	326	0.14926739926739926	73	0.1483739837398374	37	0.10220994475138122	61	0.10664335664335664	155	0.20448548812664907	T	11.49	1.654110	0.29425	0.150704	0.195233	ENSG00000198471	ENST00000358241	T	0.15952	2.38	4.61	0.746	0.18365	.	0.523691	0.21799	N	0.068950	T	0.00012	0.0000	L	0.28504	0.86	0.45261	P	0.001731000000000038	B	0.06786	0.001	B	0.11329	0.006	T	0.36383	-0.9750	9	0.33940	T	0.23	-29.0332	4.2053	0.10486	0.0:0.1865:0.1736:0.6399	rs61754877	34	Q5QGT7	RTP2_HUMAN	S	34	ENSP00000350976:N34S	ENSP00000350976:N34S	N	-	2	0	RTP2	188902510	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	0.691000	0.25467	0.126000	0.18424	0.528000	0.53228	AAC	T|0.832;C|0.168	0.168	strong		0.577	RTP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344259.1	NM_001004312	
KIAA0226	9711	hgsc.bcm.edu	37	3	197432036	197432036	+	Missense_Mutation	SNP	C	C	T	rs61743568	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:197432036C>T	ENST00000296343.5	-	3	229	c.230G>A	c.(229-231)cGc>cAc	p.R77H	KIAA0226_ENST00000389665.5_Missense_Mutation_p.R77H|KIAA0226_ENST00000449205.1_Missense_Mutation_p.R77H|KIAA0226_ENST00000273582.5_Missense_Mutation_p.R17H|KIAA0226_ENST00000467303.1_5'UTR	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	77	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				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)		ATCCGTCTGGCGGCGGCACGC	0.537													C|||	329	0.0656949	0.1188	0.0403	5008	,	,		20385	0.0		0.0984	False		,,,				2504	0.046				p.R77H	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.G230A						PASS	.	C	HIS/ARG,HIS/ARG	437,3599		26,385,1607	54.0	53.0	53.0		50,230	-1.5	1.0	3	dbSNP_129	53	724,7632		32,660,3486	yes	missense,missense	KIAA0226	NM_001145642.2,NM_014687.1	29,29	58,1045,5093	TT,TC,CC		8.6644,10.8276,9.3689	benign,benign	17/928,77/973	197432036	1161,11231	2018	4178	6196	SO:0001583	missense	9711	exon3			GTCTGGCGGCGGC	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.230G>A	3.37:g.197432036C>T	ENSP00000296343:p.Arg77His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	45	0.661765	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	147	0.0673076923076923	57	0.11585365853658537	15	0.04143646408839779	0	0.0	75	0.09894459102902374	C	14.78	2.637975	0.47153	0.108276	0.086644	ENSG00000145016	ENST00000273582;ENST00000296343;ENST00000389665;ENST00000449205	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	5.63	-1.51	0.08664	RUN (2);	0.482830	0.20874	N	0.084104	T	0.00109	0.0003	N	0.22421	0.69	0.35867	P	0.17206900000000003	B;B;B	0.27140	0.169;0.012;0.015	B;B;B	0.17433	0.018;0.002;0.007	T	0.27673	-1.0067	9	0.41790	T	0.15	.	11.5696	0.50826	0.0:0.3548:0.0:0.6452	.	77;17;77	E9PEM3;Q92622-2;Q92622	.;.;RUBIC_HUMAN	H	17;77;77;77	ENSP00000273582:R17H;ENSP00000296343:R77H;ENSP00000374316:R77H;ENSP00000390962:R77H	ENSP00000273582:R17H	R	-	2	0	KIAA0226	198916433	0.935000	0.31712	0.991000	0.47740	0.824000	0.46624	0.195000	0.17155	-0.170000	0.10816	-0.134000	0.14843	CGC	C|0.929;T|0.071	0.071	strong		0.537	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
ZNF543	125919	hgsc.bcm.edu	37	19	57838018	57838018	+	Missense_Mutation	SNP	C	C	G	rs6510057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57838018C>G	ENST00000321545.4	+	3	508	c.163C>G	c.(163-165)Cca>Gca	p.P55A		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		P -> A (in dbSNP:rs6510057). {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)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		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;0.0257)		TTTGTTCAAACCAGAGCTGAT	0.493													c|||	2264	0.452077	0.5439	0.5043	5008	,	,		16382	0.2798		0.5308	False		,,,				2504	0.3875				p.P55A		Atlas-SNP	.											.	ZNF543	61	.	0			c.C163G						PASS	.	C	ALA/PRO	2399,2007	615.4+/-392.6	649,1101,453	82.0	76.0	78.0		163	0.2	0.1	19	dbSNP_116	78	4776,3824	610.7+/-395.7	1348,2080,872	yes	missense	ZNF543	NM_213598.3	27	1997,3181,1325	GG,GC,CC		44.4651,45.5515,44.8332	benign	55/601	57838018	7175,5831	2203	4300	6503	SO:0001583	missense	125919	exon3			TTCAAACCAGAGC	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.163C>G	19.37:g.57838018C>G	ENSP00000322545:p.Pro55Ala	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	996	0.45604395604395603	246	0.5	177	0.4889502762430939	165	0.28846153846153844	408	0.5382585751978892	C	6.412	0.444210	0.12164	0.544485	0.555349	ENSG00000178229	ENST00000321545	T	0.00995	5.46	2.4	0.225	0.15325	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	B	0.17465	0.022	B	0.14578	0.011	T	0.16100	-1.0414	8	0.51188	T	0.08	.	4.3985	0.11374	0.0:0.6549:0.0:0.3451	rs6510057;rs17373672;rs6510057	55	Q08ER8	ZN543_HUMAN	A	55	ENSP00000322545:P55A	ENSP00000322545:P55A	P	+	1	0	ZNF543	62529830	0.001000	0.12720	0.134000	0.22075	0.064000	0.16182	0.584000	0.23864	0.120000	0.18254	0.467000	0.42956	CCA	C|0.496;G|0.504	0.504	strong		0.493	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
OR6F1	343169	hgsc.bcm.edu	37	1	247875608	247875608	+	Silent	SNP	C	C	G	rs6587382	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247875608C>G	ENST00000302084.2	-	1	497	c.450G>C	c.(448-450)gtG>gtC	p.V150V	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V150V(1)		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)			CGAAACCACACACCCAGGAGC	0.582													G|||	1634	0.326278	0.6067	0.2118	5008	,	,		19859	0.2232		0.2316	False		,,,				2504	0.2321				p.V150V		Atlas-SNP	.											OR6F1,NS,carcinoma,-2,3	OR6F1	88	3	1	Substitution - coding silent(1)	stomach(1)	c.G450C						scavenged	.	G		2357,2049	568.1+/-382.3	602,1153,448	66.0	74.0	71.0		450	-4.0	0.0	1	dbSNP_116	71	2202,6398	710.9+/-405.8	286,1630,2384	no	coding-synonymous	OR6F1	NM_001005286.1		888,2783,2832	GG,GC,CC		25.6047,46.5048,35.0531		150/309	247875608	4559,8447	2203	4300	6503	SO:0001819	synonymous_variant	343169	exon1			ACCACACACCCAG	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.450G>C	1.37:g.247875608C>G		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	133	89	0.669173	NM_001005286	B2RNV6|Q6IF02|Q96R39	Silent	SNP	ENST00000302084.2	37	CCDS31095.1																																																																																			C|0.661;G|0.339	0.339	strong		0.582	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286	
ALG12	79087	hgsc.bcm.edu	37	22	50301476	50301476	+	Silent	SNP	T	T	C	rs8135963	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50301476T>C	ENST00000330817.6	-	7	1158	c.885A>G	c.(883-885)gcA>gcG	p.A295A		NM_024105.3	NP_077010.1	Q9BV10	ALG12_HUMAN	ALG12, alpha-1,6-mannosyltransferase	295					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|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)	alpha-1,6-mannosyltransferase activity (GO:0000009)|dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity (GO:0052917)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(3)	12		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)		BRCA - Breast invasive adenocarcinoma(115;0.199)|LUAD - Lung adenocarcinoma(64;0.247)		TGAAGCCCAGTGCCAGCACCG	0.622													C|||	2014	0.402157	0.8253	0.1902	5008	,	,		18089	0.1806		0.2097	False		,,,				2504	0.407				p.A295A		Atlas-SNP	.											ALG12,NS,carcinoma,0,1	ALG12	35	1	0			c.A885G						PASS	.	C		3136,1270	432.8+/-343.4	1121,894,188	136.0	125.0	129.0		885	-9.6	0.0	22	dbSNP_116	129	1850,6750	730.8+/-406.8	201,1448,2651	yes	coding-synonymous	ALG12	NM_024105.3		1322,2342,2839	CC,CT,TT		21.5116,28.8243,38.3362		295/489	50301476	4986,8020	2203	4300	6503	SO:0001819	synonymous_variant	79087	exon7			GCCCAGTGCCAGC	AJ303120	CCDS14081.1	22q13.33	2013-02-26	2013-02-26		ENSG00000182858	ENSG00000182858	2.4.1.260	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	19358	protein-coding gene	gene with protein product	"""dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichol alpha-1,6-mannosyltransferase"", ""dol-P-Man dependent alpha-1,6-mannosyltransferase"""	607144	"""asparagine-linked glycosylation 12 homolog (yeast, alpha-1,6-mannosyltransferase)"", ""asparagine-linked glycosylation 12, alpha-1,6-mannosyltransferase homolog (S. cerevisiae)"""			11983712	Standard	NM_024105		Approved	ECM39	uc003biy.3	Q9BV10	OTTHUMG00000150289	ENST00000330817.6:c.885A>G	22.37:g.50301476T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	NM_024105	A6PWM1|Q4KMH4|Q8NG10|Q96AA4	Silent	SNP	ENST00000330817.6	37	CCDS14081.1	754	0.34523809523809523	409	0.8313008130081301	74	0.20441988950276244	107	0.18706293706293706	164	0.21635883905013192	C	0.366	-0.936583	0.02340	0.711757	0.215116	ENSG00000182858	ENST00000486602	.	.	.	4.8	-9.6	0.00553	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.14643	-1.0465	3	.	.	.	-9.9376	1.8826	0.03231	0.1691:0.3659:0.1762:0.2889	rs8135963;rs60186810;rs8135963	.	.	.	A	31	.	.	T	-	1	0	ALG12	48687480	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.665000	0.00106	-3.134000	0.00235	-3.324000	0.00044	ACT	T|0.617;C|0.383	0.383	strong		0.622	ALG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317405.2	NM_024105	
ALX4	60529	hgsc.bcm.edu	37	11	44296946	44296946	+	Silent	SNP	C	C	T	rs11037928	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	164	74	0.451219	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		
CAPN3	825	hgsc.bcm.edu	37	15	42702836	42702836	+	Silent	SNP	C	C	T	rs147774793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42702836C>T	ENST00000397163.3	+	21	2454	c.2235C>T	c.(2233-2235)taC>taT	p.Y745Y	CAPN3_ENST00000357568.3_Silent_p.Y739Y|CAPN3_ENST00000397204.4_Silent_p.Y80Y|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000356316.3_Silent_p.Y652Y|CAPN3_ENST00000397200.4_Silent_p.Y233Y|CAPN3_ENST00000562199.1_3'UTR|CAPN3_ENST00000569136.1_Silent_p.Y80Y|CAPN3_ENST00000318023.7_Silent_p.Y739Y|CAPN3_ENST00000337571.4_Silent_p.Y80Y|CAPN3_ENST00000349748.3_Silent_p.Y653Y|CAPN3_ENST00000561817.1_Silent_p.Y80Y	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	745	Domain IV.|EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		TCAACAGCTACGAGATGCGAA	0.517																																					p.Y745Y		Atlas-SNP	.											.	CAPN3	172	.	0			c.C2235T	GRCh37	CM051887	CAPN3	M	rs147774793	PASS	.	C	,,,,,	2,4404	4.2+/-10.8	0,2,2201	65.0	59.0	61.0		2235,2217,1959,699,240,240	-3.8	1.0	15	dbSNP_134	61	9,8589	7.1+/-27.0	0,9,4290	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1,NM_173088.1,NM_173089.1,NM_173090.1	,,,,,	0,11,6491	TT,TC,CC		0.1047,0.0454,0.0846	,,,,,	745/822,739/816,653/730,233/310,80/157,80/157	42702836	11,12993	2203	4299	6502	SO:0001819	synonymous_variant	825	exon21			CAGCTACGAGATG	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.2235C>T	15.37:g.42702836C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	89	20	0.224719	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
FLG	2312	hgsc.bcm.edu	37	1	152284854	152284854	+	Silent	SNP	A	A	G	rs3120653	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152284854A>G	ENST00000368799.1	-	3	2543	c.2508T>C	c.(2506-2508)gaT>gaC	p.D836D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	836	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCCTGACCATCTTGGGATG	0.592									Ichthyosis				-|||	2370	0.473243	0.5567	0.4553	5008	,	,		20739	0.6558		0.173	False		,,,				2504	0.4939				p.D836D		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	0			c.T2508C						PASS	.	C		2208,2198		542,1124,537	320.0	318.0	319.0		2508	-5.9	0.0	1	dbSNP_103	319	1462,7138		126,1210,2964	no	coding-synonymous	FLG	NM_002016.1		668,2334,3501	GG,GA,AA		17.0,49.8865,28.2177		836/4062	152284854	3670,9336	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCATCTTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2508T>C	1.37:g.152284854A>G		Somatic	360	1	0.00277778		WXS	Illumina HiSeq	Phase_I	449	147	0.327394	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.687;G|0.313	0.313	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ZBTB46	140685	hgsc.bcm.edu	37	20	62407104	62407104	+	Silent	SNP	C	C	T	rs3827026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62407104C>T	ENST00000245663.4	-	3	1299	c.1149G>A	c.(1147-1149)ctG>ctA	p.L383L	ZBTB46_ENST00000395104.1_Silent_p.L383L|ZBTB46_ENST00000302995.2_Silent_p.L383L	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	383					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)					CGTCGGCCTTCAGCGACAGCA	0.687											OREG0026130	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	411	0.0820687	0.003	0.0634	5008	,	,		16782	0.0784		0.1272	False		,,,				2504	0.1595				p.L383L		Atlas-SNP	.											.	ZBTB46	72	.	0			c.G1149A						PASS	.	C		103,4303	81.9+/-120.4	0,103,2100	52.0	55.0	54.0		1149	-1.6	0.7	20	dbSNP_107	54	1088,7512	226.2+/-262.0	77,934,3289	no	coding-synonymous	ZBTB46	NM_025224.3		77,1037,5389	TT,TC,CC		12.6512,2.3377,9.1573		383/590	62407104	1191,11815	2203	4300	6503	SO:0001819	synonymous_variant	140685	exon3			GGCCTTCAGCGAC	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.1149G>A	20.37:g.62407104C>T		Somatic	152	0	0	1061	WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.909;T|0.091	0.091	strong		0.687	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
KANK4	163782	hgsc.bcm.edu	37	1	62703977	62703977	+	Missense_Mutation	SNP	G	G	A	rs34591898	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:62703977G>A	ENST00000371153.4	-	10	3338	c.2960C>T	c.(2959-2961)gCg>gTg	p.A987V	KANK4_ENST00000371150.1_Missense_Mutation_p.A343V|KANK4_ENST00000317477.4_Missense_Mutation_p.A125V|KANK4_ENST00000354381.3_Missense_Mutation_p.A359V	NM_181712.4	NP_859063.3	Q5T7N3	KANK4_HUMAN	KN motif and ankyrin repeat domains 4	987			A -> V (in dbSNP:rs34591898).			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						GCCCTGCTCCGCGTGGGCTCT	0.582													G|||	243	0.0485224	0.0038	0.0346	5008	,	,		18776	0.0942		0.0258	False		,,,				2504	0.0951				p.A987V		Atlas-SNP	.											KANK4,bladder,carcinoma,-1,2	KANK4	135	2	0			c.C2960T						PASS	.	G	VAL/ALA	29,4377	35.2+/-66.4	0,29,2174	38.0	41.0	40.0		2960	3.2	0.9	1	dbSNP_126	40	234,8366	94.5+/-156.4	2,230,4068	yes	missense	KANK4	NM_181712.4	64	2,259,6242	AA,AG,GG		2.7209,0.6582,2.0221	benign	987/996	62703977	263,12743	2203	4300	6503	SO:0001583	missense	163782	exon10			TGCTCCGCGTGGG	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.2960C>T	1.37:g.62703977G>A	ENSP00000360195:p.Ala987Val	Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	264	72	0.272727	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	37	CCDS620.1	85	0.03891941391941392	3	0.006097560975609756	14	0.03867403314917127	49	0.08566433566433566	19	0.025065963060686015	G	3.047	-0.196172	0.06259	0.006582	0.027209	ENSG00000132854	ENST00000371153;ENST00000317477;ENST00000354381;ENST00000371150	T;T;T;T	0.52983	0.79;0.64;0.83;0.83	5.02	3.15	0.36227	Ankyrin repeat-containing domain (2);	0.652243	0.12748	N	0.442434	T	0.01061	0.0035	L	0.28274	0.84	0.09310	N	0.999999	B;B	0.31100	0.308;0.109	B;B	0.24155	0.051;0.013	T	0.03086	-1.1074	10	0.28530	T	0.3	-1.9699	6.2608	0.20899	0.2197:0.0:0.6484:0.1319	rs34591898	359;987	Q5T7N3-2;Q5T7N3	.;KANK4_HUMAN	V	987;125;359;343	ENSP00000360195:A987V;ENSP00000321161:A125V;ENSP00000346352:A359V;ENSP00000360192:A343V	ENSP00000321161:A125V	A	-	2	0	KANK4	62476565	0.001000	0.12720	0.861000	0.33841	0.749000	0.42624	0.246000	0.18160	0.717000	0.32145	0.305000	0.20034	GCG	G|0.975;A|0.025	0.025	strong		0.582	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712	
TNFSF11	8600	hgsc.bcm.edu	37	13	43148565	43148565	+	Silent	SNP	T	T	C	rs2296533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:43148565T>C	ENST00000239849.6	+	1	277	c.126T>C	c.(124-126)ccT>ccC	p.P42P	TNFSF11_ENST00000358545.2_Intron|TNFSF11_ENST00000398795.2_5'UTR|TNFSF11_ENST00000544862.1_Intron|TNFSF11_ENST00000405262.2_Intron			O14788	TNF11_HUMAN	tumor necrosis factor (ligand) superfamily, member 11	42					activation of JUN kinase activity (GO:0007257)|bone resorption (GO:0045453)|calcium ion homeostasis (GO:0055074)|cytokine-mediated signaling pathway (GO:0019221)|ERK1 and ERK2 cascade (GO:0070371)|immune response (GO:0006955)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|monocyte chemotaxis (GO:0002548)|organ morphogenesis (GO:0009887)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of bone resorption (GO:0045780)|positive regulation of corticotropin-releasing hormone secretion (GO:0051466)|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 homotypic cell-cell adhesion (GO:0034112)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast development (GO:2001206)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	cytokine activity (GO:0005125)|tumor necrosis factor receptor binding (GO:0005164)|tumor necrosis factor receptor superfamily binding (GO:0032813)			kidney(1)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	10		Lung NSC(96;1.11e-05)|Breast(139;0.00868)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000249)|GBM - Glioblastoma multiforme(144;0.00119)|BRCA - Breast invasive adenocarcinoma(63;0.073)	Denosumab(DB06643)|Lenalidomide(DB00480)	ACCAGCCCCCTGCCGCCTCCC	0.731													C|||	2331	0.465455	0.559	0.4164	5008	,	,		11179	0.4444		0.4712	False		,,,				2504	0.3896				p.P42P		Atlas-SNP	.											.	TNFSF11	43	.	0			c.T126C						PASS	.	C	,	1483,1969		357,769,600	7.0	8.0	8.0		126,	1.9	0.9	13	dbSNP_100	8	2526,4404		528,1470,1467	no	coding-synonymous,intron	TNFSF11	NM_003701.3,NM_033012.3	,	885,2239,2067	CC,CT,TT		36.4502,42.9606,38.6149	,	42/318,	43148565	4009,6373	1726	3465	5191	SO:0001819	synonymous_variant	8600	exon1			GCCCCCTGCCGCC	AF013171	CCDS9384.1, CCDS9385.1	13q14	2008-02-05			ENSG00000120659	ENSG00000120659		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11926	protein-coding gene	gene with protein product		602642				9312132, 9367155	Standard	NM_003701		Approved	TRANCE, RANKL, OPGL, ODF, CD254	uc001uyu.2	O14788	OTTHUMG00000016807	ENST00000239849.6:c.126T>C	13.37:g.43148565T>C		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	NM_003701	O14723|Q96Q17|Q9P2Q3	Silent	SNP	ENST00000239849.6	37	CCDS9384.1																																																																																			T|0.545;C|0.455	0.455	strong		0.731	TNFSF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044702.2		
KRT84	3890	hgsc.bcm.edu	37	12	52777502	52777502	+	Silent	SNP	A	A	G	rs1945297	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52777502A>G	ENST00000257951.3	-	2	693	c.627T>C	c.(625-627)aaT>aaC	p.N209N	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	209	Linker 1.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GTGGCTCCAGATTGCTCCTGA	0.552													G|||	2485	0.496206	0.6475	0.4798	5008	,	,		20714	0.6776		0.2584	False		,,,				2504	0.3609				p.N209N		Atlas-SNP	.											.	KRT84	61	.	0			c.T627C						PASS	.	G		2600,1806	530.4+/-372.9	791,1018,394	77.0	75.0	76.0		627	1.3	0.8	12	dbSNP_92	76	2317,6283	704.6+/-405.4	310,1697,2293	no	coding-synonymous	KRT84	NM_033045.3		1101,2715,2687	GG,GA,AA		26.9419,40.9896,37.8056		209/601	52777502	4917,8089	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			CTCCAGATTGCTC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.627T>C	12.37:g.52777502A>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	183	71	0.387978	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.586;G|0.414	0.414	strong		0.552	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
DES	1674	hgsc.bcm.edu	37	2	220285309	220285309	+	Silent	SNP	C	C	T	rs1058261	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	159	0	0		WXS	Illumina HiSeq	Phase_I	121	95	0.785124	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	
ZNF777	27153	hgsc.bcm.edu	37	7	149129829	149129829	+	Missense_Mutation	SNP	C	C	T	rs17852167	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149129829C>T	ENST00000247930.4	-	6	1857	c.1534G>A	c.(1534-1536)Gca>Aca	p.A512T		NM_015694.2	NP_056509.2	Q9ULD5	ZN777_HUMAN	zinc finger protein 777	512			A -> T (in dbSNP:rs17852167). {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)			large_intestine(5)|lung(17)|ovary(1)|skin(2)|urinary_tract(1)	26	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			CTTTTCACTGCGGGGTTTCCT	0.716													C|||	769	0.153554	0.143	0.0677	5008	,	,		16217	0.1121		0.1034	False		,,,				2504	0.3231				p.A512T		Atlas-SNP	.											.	ZNF777	63	.	0			c.G1534A						PASS	.	C	THR/ALA	475,3405		29,417,1494	17.0	20.0	19.0		1534	0.4	0.0	7	dbSNP_123	19	885,7331		50,785,3273	yes	missense	ZNF777	NM_015694.2	58	79,1202,4767	TT,TC,CC		10.7717,12.2423,11.2434	benign	512/832	149129829	1360,10736	1940	4108	6048	SO:0001583	missense	27153	exon6			TCACTGCGGGGTT	AB033111	CCDS43675.1	7q36.1	2013-01-08			ENSG00000196453	ENSG00000196453		"""Zinc fingers, C2H2-type"", ""-"""	22213	protein-coding gene	gene with protein product							Standard	NM_015694		Approved	KIAA1285	uc003wfv.3	Q9ULD5	OTTHUMG00000158967	ENST00000247930.4:c.1534G>A	7.37:g.149129829C>T	ENSP00000247930:p.Ala512Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_015694	Q8N2R2|Q8N659	Missense_Mutation	SNP	ENST00000247930.4	37	CCDS43675.1	239	0.10943223443223443	66	0.13414634146341464	23	0.06353591160220995	76	0.13286713286713286	74	0.09762532981530343	C	0.082	-1.182113	0.01633	0.122423	0.107717	ENSG00000196453	ENST00000247930;ENST00000314683	T	0.04970	3.52	4.43	0.385	0.16249	.	0.780284	0.11162	N	0.593006	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B	0.15473	0.013	B	0.08055	0.003	T	0.42548	-0.9445	9	0.72032	D	0.01	-4.1052	2.9869	0.05971	0.1937:0.402:0.0:0.4043	rs17852167	512	Q9ULD5-2	.	T	512;255	ENSP00000247930:A512T	ENSP00000247930:A512T	A	-	1	0	ZNF777	148760762	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.112000	0.10791	0.501000	0.28013	0.460000	0.39030	GCA	C|0.898;T|0.102	0.102	strong		0.716	ZNF777-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352708.1	NM_015694	
PSG3	5671	hgsc.bcm.edu	37	19	43237016	43237016	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43237016T>C	ENST00000327495.5	-	3	813	c.629A>G	c.(628-630)tAc>tGc	p.Y210C	PSG3_ENST00000490592.1_5'Flank|PSG3_ENST00000595140.1_Missense_Mutation_p.Y210C	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	210	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				TCCTGCAGTGTACTTTGTGAC	0.502																																					p.Y210C		Atlas-SNP	.											PSG3,caecum,carcinoma,0,1	PSG3	82	1	0			c.A629G						scavenged	.						249.0	253.0	251.0					19																	43237016		2203	4300	6503	SO:0001583	missense	5671	exon3			GCAGTGTACTTTG		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.629A>G	19.37:g.43237016T>C	ENSP00000332215:p.Tyr210Cys	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	162	4	0.0246914	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	.	.	.	.	.	.	.	.	.	.	-	11.52	1.663604	0.29515	.	.	ENSG00000221826	ENST00000327495	T	0.12255	2.7	1.59	1.59	0.23543	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.18383	0.0441	L	0.46157	1.445	0.09310	N	1	P;B	0.45827	0.867;0.015	P;B	0.51918	0.684;0.015	T	0.10753	-1.0616	9	0.72032	D	0.01	.	5.2153	0.15338	0.0:0.0:0.0:1.0	.	188;210	Q08266;Q16557	.;PSG3_HUMAN	C	210	ENSP00000332215:Y210C	ENSP00000332215:Y210C	Y	-	2	0	PSG3	47928856	0.001000	0.12720	0.004000	0.12327	0.001000	0.01503	0.819000	0.27308	0.725000	0.32318	0.324000	0.21423	TAC	.	.	none		0.502	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
AIM1L	55057	hgsc.bcm.edu	37	1	26650661	26650661	+	Silent	SNP	A	A	G	rs41305769	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:26650661A>G	ENST00000308182.5	-	17	2013	c.1584T>C	c.(1582-1584)gaT>gaC	p.D528D	AIM1L_ENST00000527815.1_Silent_p.D699D			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	528	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.						carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-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;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		TCAGCAGCCCATCCTCGTAGT	0.612													A|||	116	0.0231629	0.0023	0.0259	5008	,	,		17087	0.001		0.0388	False		,,,				2504	0.0562				p.D1573D		Atlas-SNP	.											.	AIM1L	98	.	0			c.T4719C						PASS	.	A		33,4373	37.6+/-69.7	0,33,2170	104.0	93.0	97.0		4719	-7.3	0.9	1	dbSNP_127	97	389,8211	124.8+/-183.5	10,369,3921	no	coding-synonymous	AIM1L	NM_001039775.3		10,402,6091	GG,GA,AA		4.5233,0.749,3.2447		1573/1662	26650661	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	55057	exon18			CAGCCCATCCTCG			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490	ENST00000308182.5:c.1584T>C	1.37:g.26650661A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	50	14	0.28	NM_001039775	B2RNG3|Q5T137|Q5T150	Silent	SNP	ENST00000308182.5	37																																																																																				A|0.972;G|0.028	0.028	strong		0.612	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2	
ACSM4	341392	hgsc.bcm.edu	37	12	7463241	7463241	+	Silent	SNP	A	A	T	rs7968241	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7463241A>T	ENST00000399422.4	+	3	567	c.519A>T	c.(517-519)ccA>ccT	p.P173P		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	173					acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						AGGTGGCCCCAGCGGTGGAGT	0.537													A|||	1618	0.323083	0.1997	0.3156	5008	,	,		-128	0.3502		0.5487	False		,,,				2504	0.2352				p.P173P		Atlas-SNP	.											.	ACSM4	98	.	0			c.A519T						PASS	.	A		994,2972		154,686,1143	48.0	48.0	48.0		519	-4.9	0.0	12	dbSNP_116	48	4313,4013		1119,2075,969	no	coding-synonymous	ACSM4	NM_001080454.1		1273,2761,2112	TT,TA,AA		48.1984,25.063,43.1744		173/581	7463241	5307,6985	1983	4163	6146	SO:0001819	synonymous_variant	341392	exon3			GGCCCCAGCGGTG		CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"""Acyl-CoA synthetase family"""	32016	protein-coding gene	gene with protein product	"""similar to olfactory specific medium-chain acyl CoA synthetase"""	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.519A>T	12.37:g.7463241A>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_001080454	A8MTI6	Silent	SNP	ENST00000399422.4	37	CCDS44825.1																																																																																			A|0.570;T|0.430	0.430	strong		0.537	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454	
CIAPIN1	57019	hgsc.bcm.edu	37	16	57464236	57464236	+	Nonsense_Mutation	SNP	G	G	A	rs170358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57464236G>A	ENST00000565961.1	-	6	684	c.565C>T	c.(565-567)Cga>Tga	p.R189*	CIAPIN1_ENST00000568940.1_Nonsense_Mutation_p.R216*|CIAPIN1_ENST00000569370.1_Nonsense_Mutation_p.R216*|CIAPIN1_ENST00000569246.1_5'Flank|CIAPIN1_ENST00000569979.1_Intron|CIAPIN1_ENST00000394391.4_Silent_p.A254A|CIAPIN1_ENST00000567518.1_Silent_p.A241A					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	141	0	0		WXS	Illumina HiSeq	Phase_I	97	82	0.845361	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	
NHSL1	57224	hgsc.bcm.edu	37	6	138745299	138745299	+	Silent	SNP	G	G	A	rs9495082	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:138745299G>A	ENST00000427025.2	-	7	5380	c.4752C>T	c.(4750-4752)ccC>ccT	p.P1584P	NHSL1_ENST00000343505.5_Silent_p.P1580P	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	1584										breast(2)|endometrium(4)|kidney(1)	7						CCACAGGGCCGGGGGCCTGGG	0.682													G|||	632	0.126198	0.3222	0.0865	5008	,	,		15615	0.0139		0.0845	False		,,,				2504	0.0481				p.P1584P		Atlas-SNP	.											.	NHSL1	99	.	0			c.C4752T						PASS	.	G	,	308,1010		41,226,392	5.0	9.0	7.0		4740,4752	-5.0	0.0	6	dbSNP_119	7	218,2872		5,208,1332	no	coding-synonymous,coding-synonymous	NHSL1	NM_001144060.1,NM_020464.1	,	46,434,1724	AA,AG,GG		7.055,23.3687,11.9328	,	1580/1607,1584/1611	138745299	526,3882	659	1545	2204	SO:0001819	synonymous_variant	57224	exon7			AGGGCCGGGGGCC	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.4752C>T	6.37:g.138745299G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	29	17	0.586207	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Silent	SNP	ENST00000427025.2	37	CCDS55063.1																																																																																			G|0.893;A|0.107	0.107	strong		0.682	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
OR4N2	390429	hgsc.bcm.edu	37	14	20296004	20296004	+	Missense_Mutation	SNP	C	C	T	rs2318279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20296004C>T	ENST00000315947.1	+	1	397	c.397C>T	c.(397-399)Cct>Tct	p.P133S	OR4N2_ENST00000568211.1_Missense_Mutation_p.P133S	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	133			P -> S (in dbSNP:rs2318279).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P133S(1)		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)		TCTGCACTATCCTACTGTCAT	0.522																																					p.P133S		Atlas-SNP	.											OR4N2,NS,carcinoma,0,1	OR4N2	125	1	1	Substitution - Missense(1)	stomach(1)	c.C397T						PASS	.	T	SER/PRO	1656,2750		218,1220,765	205.0	218.0	214.0		397	-1.6	0.0	14	dbSNP_100	214	2205,6395		148,1909,2243	yes	missense	OR4N2	NM_001004723.1	74	366,3129,3008	TT,TC,CC		25.6395,37.5851,29.6863	benign	133/308	20296004	3861,9145	2203	4300	6503	SO:0001583	missense	390429	exon1			CACTATCCTACTG		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.397C>T	14.37:g.20296004C>T	ENSP00000319601:p.Pro133Ser	Somatic	876	1	0.00114155		WXS	Illumina HiSeq	Phase_I	467	260	0.556745	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	569	0.26053113553113555	215	0.4369918699186992	77	0.212707182320442	69	0.12062937062937062	208	0.27440633245382584	.	0.188	-1.055704	0.01965	0.375851	0.256395	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.00995	5.46;5.46	4.53	-1.58	0.08479	GPCR, rhodopsin-like superfamily (1);	0.174373	0.27976	N	0.017092	T	0.00012	0.0000	N	0.21373	0.66	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41556	-0.9502	9	0.40728	T	0.16	-1.2504	2.051	0.03571	0.2302:0.0877:0.3897:0.2924	rs2318279;rs52793006;rs2318279	133	Q8NGD1	OR4N2_HUMAN	S	133	ENSP00000452022:P133S;ENSP00000319601:P133S	ENSP00000319601:P133S	P	+	1	0	OR4N2	19365844	0.000000	0.05858	0.006000	0.13384	0.292000	0.27327	-1.373000	0.02568	-0.283000	0.09115	-0.332000	0.08345	CCT	C|0.753;T|0.247	0.247	strong		0.522	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
MYO1G	64005	hgsc.bcm.edu	37	7	45015107	45015107	+	Silent	SNP	G	G	A	rs61738857	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:45015107G>A	ENST00000258787.7	-	4	676	c.540C>T	c.(538-540)caC>caT	p.H180H		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	180	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						AGCTGTGGATGTGTCCTCCGA	0.597													G|||	645	0.128794	0.1006	0.1772	5008	,	,		20162	0.0962		0.2266	False		,,,				2504	0.0654				p.H180H		Atlas-SNP	.											.	MYO1G	86	.	0			c.C540T						PASS	.	G		500,3906	229.4+/-244.0	22,456,1725	106.0	103.0	104.0		540	2.5	1.0	7	dbSNP_129	104	1819,6781	326.4+/-317.4	192,1435,2673	no	coding-synonymous	MYO1G	NM_033054.2		214,1891,4398	AA,AG,GG		21.1512,11.3482,17.8302		180/1019	45015107	2319,10687	2203	4300	6503	SO:0001819	synonymous_variant	64005	exon4			GTGGATGTGTCCT	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.540C>T	7.37:g.45015107G>A		Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	284	164	0.577465	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Silent	SNP	ENST00000258787.7	37	CCDS34629.1																																																																																			G|0.831;A|0.169	0.169	strong		0.597	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
LRRK1	79705	hgsc.bcm.edu	37	15	101567971	101567971	+	Silent	SNP	C	C	T	rs41535348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:101567971C>T	ENST00000388948.3	+	19	3014	c.2655C>T	c.(2653-2655)aaC>aaT	p.N885N	LRRK1_ENST00000284395.5_Silent_p.N882N	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)			CGCCCGACAACGACATCAAGG	0.632													C|||	18	0.00359425	0.0008	0.0029	5008	,	,		18583	0.0		0.008	False		,,,				2504	0.0072				p.N885N		Atlas-SNP	.											.	LRRK1	310	.	0			c.C2655T						PASS	.	C		6,4338		0,6,2166	26.0	37.0	34.0		2655	-8.9	0.0	15	dbSNP_127	34	87,8451		0,87,4182	no	coding-synonymous	LRRK1	NM_024652.3		0,93,6348	TT,TC,CC		1.019,0.1381,0.7219		885/2016	101567971	93,12789	2172	4269	6441	SO:0001819	synonymous_variant	79705	exon19			CGACAACGACATC	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.2655C>T	15.37:g.101567971C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	129	31	0.24031	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			C|0.995;T|0.005	0.005	strong		0.632	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
CACNA1A	773	hgsc.bcm.edu	37	19	13409407	13409407	+	Missense_Mutation	SNP	C	C	T	rs16024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13409407C>T	ENST00000360228.5	-	19	3039	c.3040G>A	c.(3040-3042)Gag>Aag	p.E1014K	CACNA1A_ENST00000573710.2_Missense_Mutation_p.E1015K	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	1015					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)	GCGTCCCCCTCGTACGTGGCT	0.687													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		9081	0.0		0.003	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G3043A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,3196		0,0,1598	22.0	22.0	22.0		3052,3043,3040,3043,3052	3.5	0.0	19	dbSNP_54	22	35,6103		0,35,3034	yes	missense,missense,missense,missense,missense	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	56,56,56,56,56	0,35,4632	TT,TC,CC		0.5702,0.0,0.375	benign,benign,benign,benign,benign	1018/2267,1015/2262,1014/2507,1015/2264,1018/2513	13409407	35,9299	1598	3069	4667	SO:0001583	missense	773	exon19			CCCCCTCGTACGT	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.3040G>A	19.37:g.13409407C>T	ENSP00000353362:p.Glu1014Lys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	8.418	0.845757	0.16963	0.0	0.005702	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.95853	-3.83	3.54	3.54	0.40534	.	2.783830	0.01492	N	0.017126	D	0.89213	0.6651	L	0.36672	1.1	0.34650	D	0.721503	B;B;B	0.31599	0.0;0.33;0.222	B;B;B	0.17098	0.0;0.017;0.015	T	0.74842	-0.3527	10	0.06236	T	0.91	.	13.8911	0.63740	0.0:1.0:0.0:0.0	rs16024;rs16024	1015;1018;1014	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	K	1014;1018;1015;1015	ENSP00000353362:E1014K	ENSP00000317661:E1015K	E	-	1	0	CACNA1A	13270407	0.456000	0.25744	0.039000	0.18376	0.035000	0.12851	1.820000	0.39032	1.541000	0.49316	0.462000	0.41574	GAG	C|0.997;T|0.003	0.003	strong		0.687	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
NTN5	126147	hgsc.bcm.edu	37	19	49168005	49168005	+	Silent	SNP	G	G	A	rs17851884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	116	0	0		WXS	Illumina HiSeq	Phase_I	148	96	0.648649	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	
TENM3	55714	hgsc.bcm.edu	37	4	183713573	183713573	+	Silent	SNP	C	C	T	rs80197208	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:183713573C>T	ENST00000511685.1	+	26	5871	c.5748C>T	c.(5746-5748)aaC>aaT	p.N1916N	TENM3_ENST00000406950.2_Silent_p.N1916N			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1916					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.E1919fs*37(1)									ACATATACAACCCCCCGGAAA	0.532													C|||	22	0.00439297	0.0	0.0058	5008	,	,		18775	0.0		0.0179	False		,,,				2504	0.0				p.N1916N		Atlas-SNP	.											.	.	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.C5748T						PASS	.	C		13,4031		0,13,2009	70.0	73.0	72.0		5748	3.3	1.0	4	dbSNP_131	72	165,8175		1,163,4006	no	coding-synonymous	ODZ3	NM_001080477.1		1,176,6015	TT,TC,CC		1.9784,0.3215,1.4373		1916/2700	183713573	178,12206	2022	4170	6192	SO:0001819	synonymous_variant	55714	exon25			ATACAACCCCCCG	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.5748C>T	4.37:g.183713573C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	104	25	0.240385	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																			C|0.987;T|0.013	0.013	strong		0.532	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
RNF157	114804	hgsc.bcm.edu	37	17	74162548	74162548	+	Missense_Mutation	SNP	C	C	T	rs11539879	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:74162548C>T	ENST00000269391.6	-	6	754	c.622G>A	c.(622-624)Gga>Aga	p.G208R	RNF157_ENST00000319945.6_Missense_Mutation_p.G208R	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	208			G -> R (in dbSNP:rs11539879).				zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	25			LUSC - Lung squamous cell carcinoma(166;0.187)			CTACCGTCTCCTTCATCCACC	0.483													C|||	80	0.0159744	0.0023	0.0086	5008	,	,		20731	0.0		0.0616	False		,,,				2504	0.0092				p.G208R	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.G622A						PASS	.	C	ARG/GLY	45,4361	46.0+/-80.4	0,45,2158	135.0	126.0	129.0		622	5.4	1.0	17	dbSNP_120	129	438,8162	133.8+/-191.2	14,410,3876	yes	missense	RNF157	NM_052916.2	125	14,455,6034	TT,TC,CC		5.093,1.0213,3.7137	probably-damaging	208/680	74162548	483,12523	2203	4300	6503	SO:0001583	missense	114804	exon6			CGTCTCCTTCATC	AK091467	CCDS32740.1	17q25.3	2004-02-27			ENSG00000141576	ENSG00000141576		"""RING-type (C3HC4) zinc fingers"""	29402	protein-coding gene	gene with protein product						11572484	Standard	NM_052916		Approved	KIAA1917	uc002jqz.3	Q96PX1	OTTHUMG00000132627	ENST00000269391.6:c.622G>A	17.37:g.74162548C>T	ENSP00000269391:p.Gly208Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_052916	Q8NB72|Q96N56	Missense_Mutation	SNP	ENST00000269391.6	37	CCDS32740.1	52	0.023809523809523808	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	47	0.06200527704485488	C	31	5.092725	0.94149	0.010213	0.05093	ENSG00000141576	ENST00000269391;ENST00000319945;ENST00000301610	T;T	0.30714	1.52;1.52	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.13030	0.0316	M	0.72118	2.19	0.80722	D	1	D;D	0.89917	1.0;0.984	D;P	0.77004	0.989;0.899	T	0.18618	-1.0331	10	0.56958	D	0.05	-2.3942	19.1467	0.93472	0.0:1.0:0.0:0.0	rs11539879;rs16968649;rs52823252;rs56594131;rs11539879	208;208	Q96PX1-2;Q96PX1	.;RN157_HUMAN	R	208;208;170	ENSP00000269391:G208R;ENSP00000321837:G208R	ENSP00000269391:G208R	G	-	1	0	RNF157	71674143	1.000000	0.71417	1.000000	0.80357	0.814000	0.46013	7.683000	0.84093	2.684000	0.91462	0.655000	0.94253	GGA	C|0.968;T|0.032	0.032	strong		0.483	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732	
TJP3	27134	hgsc.bcm.edu	37	19	3731985	3731985	+	Silent	SNP	G	G	A	rs1879040	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3731985G>A	ENST00000541714.2	+	6	1128	c.666G>A	c.(664-666)tcG>tcA	p.S222S	TJP3_ENST00000539908.2_Silent_p.S186S|TJP3_ENST00000589378.1_Silent_p.S231S|TJP3_ENST00000262968.9_Silent_p.S241S|TJP3_ENST00000587686.1_Silent_p.S241S|TJP3_ENST00000382008.3_Silent_p.S222S	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	222	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)		p.S241S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		TTACAGATTCGGGCCTGGCTG	0.592													g|||	1644	0.328275	0.2179	0.4179	5008	,	,		16720	0.2768		0.3459	False		,,,				2504	0.4489				p.S231S		Atlas-SNP	.											TJP3,colon,carcinoma,0,2	TJP3	79	2	1	Substitution - coding silent(1)	stomach(1)	c.G693A						PASS	.	A		1168,3238	409.5+/-335.0	147,874,1182	50.0	45.0	46.0		723	-5.4	0.2	19	dbSNP_92	46	3001,5599	462.4+/-365.7	548,1905,1847	no	coding-synonymous	TJP3	NM_014428.1		695,2779,3029	AA,AG,GG		34.8953,26.5093,32.0544		241/953	3731985	4169,8837	2203	4300	6503	SO:0001819	synonymous_variant	27134	exon6			AGATTCGGGCCTG	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.666G>A	19.37:g.3731985G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			G|0.686;A|0.314	0.314	strong		0.592	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
POLQ	10721	hgsc.bcm.edu	37	3	121208894	121208894	+	Missense_Mutation	SNP	T	T	C	rs3218636	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:121208894T>C	ENST00000264233.5	-	16	3012	c.2884A>G	c.(2884-2886)Agt>Ggt	p.S962G		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	962					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)		TGCTCTCTACTTTTATTTAAG	0.303								DNA polymerases (catalytic subunits)					T|||	194	0.038738	0.0151	0.2075	5008	,	,		12810	0.003		0.0219	False		,,,				2504	0.0051				p.S962G	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A2884G						PASS	.	T	GLY/SER	64,4340	55.5+/-91.7	0,64,2138	43.0	43.0	43.0		2884	-2.1	0.0	3	dbSNP_106	43	240,8350	88.4+/-150.7	5,230,4060	yes	missense	POLQ	NM_199420.3	56	5,294,6198	CC,CT,TT		2.7939,1.4532,2.3395	benign	962/2591	121208894	304,12690	2202	4295	6497	SO:0001583	missense	10721	exon16			CTCTACTTTTATT	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.2884A>G	3.37:g.121208894T>C	ENSP00000264233:p.Ser962Gly	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	40	0.588235	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	90	0.04120879120879121	11	0.022357723577235773	60	0.16574585635359115	0	0.0	19	0.025065963060686015	T	7.675	0.687849	0.14973	0.014532	0.027939	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.48201	0.82	4.77	-2.06	0.07298	.	1.246270	0.05257	N	0.515060	T	0.00073	0.0002	N	0.24115	0.695	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.09377	0.001;0.004	T	0.11324	-1.0592	9	0.22706	T	0.39	.	0.668	0.00854	0.2686:0.1578:0.131:0.4426	rs3218636;rs17690139	962;134	O75417;O75417-2	DPOLQ_HUMAN;.	G	585;962;1098	ENSP00000264233:S962G	ENSP00000264233:S962G	S	-	1	0	POLQ	122691584	0.002000	0.14202	0.001000	0.08648	0.301000	0.27625	0.402000	0.20965	-0.183000	0.10585	0.455000	0.32223	AGT	T|0.970;C|0.030	0.030	strong		0.303	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
F5	2153	hgsc.bcm.edu	37	1	169512120	169512120	+	Silent	SNP	G	G	A	rs6016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:169512120G>A	ENST00000367797.3	-	13	2409	c.2208C>T	c.(2206-2208)atC>atT	p.I736I	F5_ENST00000367796.3_Silent_p.I741I	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	736	B.				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)	GGAATGACCTGATTCCTAATG	0.428													A|||	1316	0.26278	0.1679	0.3948	5008	,	,		20914	0.248		0.2535	False		,,,				2504	0.3221				p.I736I		Atlas-SNP	.											.	F5	301	.	0			c.C2208T						PASS	.	A		813,3593	750.9+/-412.2	68,677,1458	227.0	210.0	216.0		2208	-2.7	0.9	1	dbSNP_52	216	2355,6245	702.8+/-405.3	299,1757,2244	no	coding-synonymous	F5	NM_000130.4		367,2434,3702	AA,AG,GG		27.3837,18.4521,24.358		736/2225	169512120	3168,9838	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			TGACCTGATTCCT	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.2208C>T	1.37:g.169512120G>A		Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	241	241	1	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.758;A|0.242	0.242	strong		0.428	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
OR4N2	390429	hgsc.bcm.edu	37	14	20295778	20295778	+	Silent	SNP	C	C	A	rs11621883	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	647	2	0.00309119		WXS	Illumina HiSeq	Phase_I	285	156	0.547368	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		
MUC16	94025	hgsc.bcm.edu	37	19	9070402	9070402	+	Missense_Mutation	SNP	G	G	T	rs12150888	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9070402G>T	ENST00000397910.4	-	3	17247	c.17044C>A	c.(17044-17046)Ccc>Acc	p.P5682T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5684	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						CTCGTTACGGGCTCTGGGCTT	0.512													g|||	819	0.163538	0.1142	0.2536	5008	,	,		20669	0.0089		0.2634	False		,,,				2504	0.2229				p.P5682T		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+2,3	MUC16	4315	3	0			c.C17044A						PASS	.	A	THR/PRO	518,3486		33,452,1517	145.0	139.0	141.0		17044	-2.5	0.0	19	dbSNP_120	141	2434,5912		372,1690,2111	yes	missense	MUC16	NM_024690.2	38	405,2142,3628	TT,TG,GG		29.1637,12.9371,23.9028	probably-damaging	5682/14508	9070402	2952,9398	2002	4173	6175	SO:0001583	missense	94025	exon3			TTACGGGCTCTGG	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.17044C>A	19.37:g.9070402G>T	ENSP00000381008:p.Pro5682Thr	Somatic	382	1	0.0026178		WXS	Illumina HiSeq	Phase_I	412	203	0.492718	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	353	0.16163003663003664	53	0.10772357723577236	92	0.2541436464088398	5	0.008741258741258742	203	0.2678100263852243	g	1.261	-0.615735	0.03663	0.129371	0.291637	ENSG00000181143	ENST00000397910	T	0.35048	1.33	1.87	-2.48	0.06423	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	D	0.71674	0.998	P	0.58454	0.839	T	0.08126	-1.0737	7	0.87932	D	0	.	0.9034	0.01279	0.1587:0.2289:0.3795:0.2329	rs12150888;rs52815216;rs12150888	5682	B5ME49	.	T	5682	ENSP00000381008:P5682T	ENSP00000381008:P5682T	P	-	1	0	MUC16	8931402	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.309000	0.01130	-0.422000	0.07405	-1.549000	0.00901	CCC	G|0.815;T|0.185	0.185	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PARP14	54625	hgsc.bcm.edu	37	3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	rs7632072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122419292A>G	ENST00000474629.2	+	6	2157	c.1891A>G	c.(1891-1893)Act>Gct	p.T631A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	631					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)		CTCCCCAAACACTGTAATCAT	0.348													A|||	278	0.0555112	0.1218	0.0576	5008	,	,		21423	0.001		0.0487	False		,,,				2504	0.0276				p.T631A		Atlas-SNP	.											.	PARP14	242	.	0			c.A1891G						PASS	.	A	ALA/THR	342,3342		18,306,1518	31.0	30.0	31.0		1891	2.1	0.0	3	dbSNP_116	31	361,7841		5,351,3745	yes	missense	PARP14	NM_017554.2	58	23,657,5263	GG,GA,AA		4.4014,9.2834,5.9145	probably-damaging	631/1802	122419292	703,11183	1842	4101	5943	SO:0001583	missense	54625	exon6			CCAAACACTGTAA	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.1891A>G	3.37:g.122419292A>G	ENSP00000418194:p.Thr631Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	111	0.050824175824175824	49	0.09959349593495935	22	0.06077348066298342	1	0.0017482517482517483	39	0.051451187335092345	A	13.04	2.119612	0.37436	0.092834	0.044014	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.10099	2.91	6.06	2.12	0.27331	.	0.174182	0.39759	N	0.001269	T	0.00271	0.0008	M	0.66939	2.045	0.09310	N	1	P;B	0.38827	0.649;0.376	B;B	0.33690	0.168;0.055	T	0.30268	-0.9984	10	0.36615	T	0.2	.	3.82	0.08832	0.663:0.1354:0.0717:0.1299	rs7632072;rs52827643;rs7632072	631;631	Q460N5-4;Q460N5	.;PAR14_HUMAN	A	631;550	ENSP00000418194:T631A	ENSP00000381228:T550A	T	+	1	0	PARP14	123901982	0.014000	0.17966	0.001000	0.08648	0.003000	0.03518	1.250000	0.32850	0.497000	0.27926	0.533000	0.62120	ACT	A|0.950;G|0.050	0.050	strong		0.348	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
SAA1	6288	hgsc.bcm.edu	37	11	18290866	18290866	+	Silent	SNP	T	T	C	rs1136745	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18290866T>C	ENST00000405158.2	+	3	400	c.216T>C	c.(214-216)gcT>gcC	p.A72A	SAA1_ENST00000356524.4_Silent_p.A72A|SAA1_ENST00000532858.1_Silent_p.A72A|RNA5SP334_ENST00000364825.1_RNA	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	72					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.A72A(1)		endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	GTGCCTGGGCTGCAGAAGTGA	0.562																																					p.A72A		Atlas-SNP	.											SAA1,NS,carcinoma,0,1	SAA1	14	1	1	Substitution - coding silent(1)	stomach(1)	c.T216C						scavenged	.						20.0	21.0	20.0					11																	18290866		2190	4260	6450	SO:0001819	synonymous_variant	6288	exon3			CTGGGCTGCAGAA	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.216T>C	11.37:g.18290866T>C		Somatic	100	18	0.18		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_199161	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Silent	SNP	ENST00000405158.2	37	CCDS7835.1																																																																																			C|1.000;|0.000	1.000	weak		0.562	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161	
HEATR1	55127	hgsc.bcm.edu	37	1	236719135	236719135	+	Silent	SNP	T	T	C	rs1885532	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:236719135T>C	ENST00000366582.3	-	39	5733	c.5619A>G	c.(5617-5619)gaA>gaG	p.E1873E	HEATR1_ENST00000366581.2_Silent_p.E1792E	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1873					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)			AGTCCAGGGCTTCCAGGAAAA	0.493													C|||	4372	0.873003	0.8775	0.8833	5008	,	,		19133	0.9593		0.8022	False		,,,				2504	0.8436				p.E1873E		Atlas-SNP	.											.	HEATR1	197	.	0			c.A5619G						PASS	.	C		3866,540	243.7+/-253.3	1692,482,29	121.0	113.0	116.0		5619	1.7	1.0	1	dbSNP_92	116	7069,1531	284.0+/-296.4	2902,1265,133	no	coding-synonymous	HEATR1	NM_018072.5		4594,1747,162	CC,CT,TT		17.8023,12.256,15.9234		1873/2145	236719135	10935,2071	2203	4300	6503	SO:0001819	synonymous_variant	55127	exon39			CAGGGCTTCCAGG	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.5619A>G	1.37:g.236719135T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	242	77	0.318182	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Silent	SNP	ENST00000366582.3	37	CCDS31066.1																																																																																			T|0.153;C|0.847	0.847	strong		0.493	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
THEM6	51337	hgsc.bcm.edu	37	8	143816828	143816828	+	Missense_Mutation	SNP	G	G	A	rs11540544	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:143816828G>A	ENST00000336138.3	+	2	742	c.598G>A	c.(598-600)Ggg>Agg	p.G200R		NM_016647.2	NP_057731.1	Q8WUY1	THEM6_HUMAN	thioesterase superfamily member 6	200						extracellular region (GO:0005576)											CATGGAGAGTGGGCTCAGTGA	0.637													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18322	0.0		0.008	False		,,,				2504	0.001				p.G200R		Atlas-SNP	.											.	.	.	.	0			c.G598A						PASS	.	G	ARG/GLY	6,4386		0,6,2190	63.0	44.0	50.0		598	4.1	1.0	8	dbSNP_120	50	109,8471		1,107,4182	yes	missense	C8orf55	NM_016647.2	125	1,113,6372	AA,AG,GG		1.2704,0.1366,0.8865	probably-damaging	200/209	143816828	115,12857	2196	4290	6486	SO:0001583	missense	51337	exon2			GAGAGTGGGCTCA	BC001311	CCDS6386.1	8q24.3	2012-05-03	2012-04-13	2012-04-13	ENSG00000130193	ENSG00000130193			29656	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 55"""	C8orf55		12477932	Standard	XM_005250955		Approved	DSCD75	uc003yww.1	Q8WUY1	OTTHUMG00000164673	ENST00000336138.3:c.598G>A	8.37:g.143816828G>A	ENSP00000338607:p.Gly200Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_016647	B2RDN6|Q8NBN2|Q9NYI2	Missense_Mutation	SNP	ENST00000336138.3	37	CCDS6386.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	10.94	1.491689	0.26774	0.001366	0.012704	ENSG00000130193	ENST00000336138	T	0.44083	0.93	4.07	4.07	0.47477	.	0.000000	0.64402	D	0.000001	T	0.48822	0.1521	L	0.53249	1.67	0.52099	D	0.999946	D;B	0.89917	1.0;0.062	D;B	0.97110	1.0;0.023	T	0.55457	-0.8138	10	0.56958	D	0.05	-30.9737	11.6462	0.51263	0.0:0.0:1.0:0.0	rs11540544	147;200	B4DWJ7;Q8WUY1	.;CH055_HUMAN	R	200	ENSP00000338607:G200R	ENSP00000338607:G200R	G	+	1	0	C8orf55	143813830	0.996000	0.38824	0.962000	0.40283	0.097000	0.18754	2.712000	0.47186	2.104000	0.64026	0.563000	0.77884	GGG	G|0.992;A|0.008	0.008	strong		0.637	THEM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379706.1	NM_016647	
CECR5	27440	hgsc.bcm.edu	37	22	17640045	17640045	+	Missense_Mutation	SNP	G	G	A	rs7287672	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:17640045G>A	ENST00000336737.4	-	1	122	c.97C>T	c.(97-99)Cgc>Tgc	p.R33C	CECR5-AS1_ENST00000329743.3_RNA|CECR5_ENST00000399852.3_Missense_Mutation_p.R33C|CECR5-AS1_ENST00000431923.1_RNA|CECR5_ENST00000480451.1_5'UTR|CECR5_ENST00000155674.5_Intron	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	4	4	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	
CACNA1C	775	hgsc.bcm.edu	37	12	2721137	2721137	+	Silent	SNP	C	C	T	rs216008	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:2721137C>T	ENST00000347598.4	+	30	3846	c.3846C>T	c.(3844-3846)ttC>ttT	p.F1282F	CACNA1C_ENST00000399597.1_Silent_p.F1262F|CACNA1C_ENST00000399637.1_Silent_p.F1262F|CACNA1C_ENST00000480911.1_Silent_p.F1262F|CACNA1C_ENST00000399606.1_Silent_p.F1282F|CACNA1C_ENST00000344100.3_Silent_p.F1262F|CACNA1C_ENST00000399617.1_Silent_p.F1262F|CACNA1C_ENST00000399634.1_Silent_p.F1262F|CACNA1C_ENST00000399641.1_Silent_p.F1262F|CACNA1C_ENST00000399644.1_Silent_p.F1262F|CACNA1C_ENST00000399629.1_Silent_p.F1262F|CACNA1C_ENST00000399621.1_Silent_p.F1262F|CACNA1C_ENST00000399591.1_Silent_p.F1262F|CACNA1C_ENST00000399601.1_Silent_p.F1262F|CACNA1C_ENST00000406454.3_Silent_p.F1262F|CACNA1C_ENST00000399638.1_Silent_p.F1262F|CACNA1C_ENST00000327702.7_Silent_p.F1262F|CACNA1C_ENST00000335762.5_Silent_p.F1287F|CACNA1C_ENST00000402845.3_Silent_p.F1262F|CACNA1C_ENST00000399603.1_Silent_p.F1262F|CACNA1C_ENST00000399649.1_Silent_p.F1262F|CACNA1C_ENST00000399655.1_Silent_p.F1262F|CACNA1C_ENST00000399595.1_Silent_p.F1262F	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1282					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)	CTGGCCTCTTCACCGTGGAGA	0.542													C|||	1298	0.259185	0.2413	0.2262	5008	,	,		21995	0.3512		0.2087	False		,,,				2504	0.2638				p.F1282F		Atlas-SNP	.											Q6YL47_HUMAN,NS,carcinoma,+2,4	CACNA1C	1023	4	0			c.C3846T						PASS	.						117.0	113.0	114.0					12																	2721137		2183	4296	6479	SO:0001819	synonymous_variant	775	exon30			CCTCTTCACCGTG	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.3846C>T	12.37:g.2721137C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	153	64	0.418301	NM_199460	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|0.730;T|0.270	0.270	strong		0.542	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
MYH7	4625	hgsc.bcm.edu	37	14	23902753	23902753	+	Silent	SNP	G	G	A	rs2069540	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23902753G>A	ENST00000355349.3	-	3	351	c.189C>T	c.(187-189)acC>acT	p.T63T		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	63					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)		TGCCATACTCGGTCTCGGCAG	0.562													G|||	2606	0.520367	0.6392	0.4063	5008	,	,		22211	0.4137		0.4851	False		,,,				2504	0.5869				p.T63T		Atlas-SNP	.											.	MYH7	349	.	0			c.C189T						PASS	.	G		2698,1708	651.7+/-399.3	821,1056,326	124.0	96.0	106.0		189	-8.4	0.2	14	dbSNP_96	106	4163,4437	567.2+/-388.8	984,2195,1121	no	coding-synonymous	MYH7	NM_000257.2		1805,3251,1447	AA,AG,GG		48.407,38.7653,47.2474		63/1936	23902753	6861,6145	2203	4300	6503	SO:0001819	synonymous_variant	4625	exon3			ATACTCGGTCTCG	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.189C>T	14.37:g.23902753G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																			G|0.488;A|0.512	0.512	strong		0.562	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
PEAR1	375033	hgsc.bcm.edu	37	1	156884584	156884584	+	Silent	SNP	C	C	T	rs56260937	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156884584C>T	ENST00000338302.3	+	24	3333	c.3108C>T	c.(3106-3108)gaC>gaT	p.D1036D	PEAR1_ENST00000292357.7_Silent_p.D1036D			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	1036					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)					GACGCCAGGACCGTTGAGGAG	0.612													C|||	938	0.1873	0.1573	0.1628	5008	,	,		20931	0.2827		0.173	False		,,,				2504	0.1616				p.D1036D		Atlas-SNP	.											PEAR1,colon,carcinoma,+2,1	PEAR1	118	1	0			c.C3108T						PASS	.	C		729,3677	300.4+/-286.3	71,587,1545	130.0	88.0	102.0		3108	0.7	1.0	1	dbSNP_129	102	1439,7161	276.0+/-292.1	123,1193,2984	no	coding-synonymous	PEAR1	NM_001080471.1		194,1780,4529	TT,TC,CC		16.7326,16.5456,16.6692		1036/1038	156884584	2168,10838	2203	4300	6503	SO:0001819	synonymous_variant	375033	exon23			CCAGGACCGTTGA	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.3108C>T	1.37:g.156884584C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			C|0.824;T|0.176	0.176	strong		0.612	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
DYDC2	84332	hgsc.bcm.edu	37	10	82126541	82126541	+	Missense_Mutation	SNP	C	C	G	rs36027713	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:82126541C>G	ENST00000372199.1	+	6	966	c.368C>G	c.(367-369)cCa>cGa	p.P123R	DYDC2_ENST00000372197.1_Missense_Mutation_p.P123R|DYDC2_ENST00000372198.1_Missense_Mutation_p.P137R|DYDC2_ENST00000256039.2_Missense_Mutation_p.P123R|DYDC2_ENST00000444807.2_Missense_Mutation_p.P123R			Q96IM9	DYDC2_HUMAN	DPY30 domain containing 2	123										breast(1)|large_intestine(3)|lung(6)|skin(1)	11			Colorectal(32;0.229)			GAATTCCTGCCAGGTACTTCC	0.468													C|||	43	0.00858626	0.0	0.0144	5008	,	,		18616	0.0		0.0308	False		,,,				2504	0.002				p.P137R		Atlas-SNP	.											DYDC2,NS,carcinoma,+1,1	DYDC2	18	1	0			c.C410G						PASS	.	C	ARG/PRO	24,4382	31.7+/-61.6	0,24,2179	108.0	111.0	110.0		368	3.8	0.0	10	dbSNP_126	110	215,8385	90.4+/-152.6	2,211,4087	yes	missense	DYDC2	NM_032372.4	103	2,235,6266	GG,GC,CC		2.5,0.5447,1.8376	possibly-damaging	123/178	82126541	239,12767	2203	4300	6503	SO:0001583	missense	84332	exon4			TCCTGCCAGGTAC	BC018606	CCDS7367.1, CCDS58088.1	10q23.1	2006-06-16			ENSG00000133665	ENSG00000133665			23468	protein-coding gene	gene with protein product						12477932	Standard	NM_032372		Approved	bA36D19.6, MGC16186	uc031pwk.1	Q96IM9	OTTHUMG00000018610	ENST00000372199.1:c.368C>G	10.37:g.82126541C>G	ENSP00000361273:p.Pro123Arg	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	77	55	0.714286	NM_001270042	D3DWD6|Q5QP07|Q5QP11	Missense_Mutation	SNP	ENST00000372199.1	37	CCDS7367.1	31	0.014194139194139194	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	25	0.032981530343007916	C	14.26	2.481710	0.44147	0.005447	0.025	ENSG00000133665	ENST00000372199;ENST00000372198;ENST00000372197;ENST00000444807;ENST00000411538;ENST00000256039	T;T;T;T;T	0.67698	-0.17;-0.28;-0.17;-0.17;-0.17	4.68	3.77	0.43336	.	0.122835	0.37623	N	0.002007	T	0.26629	0.0651	L	0.32530	0.975	0.09310	N	1	B	0.34329	0.449	B	0.26864	0.074	T	0.38394	-0.9663	10	0.54805	T	0.06	-9.1269	10.9297	0.47211	0.0:0.7898:0.2102:0.0	rs36027713;rs61859208	123	Q96IM9	DYDC2_HUMAN	R	123;137;123;123;123;123	ENSP00000361273:P123R;ENSP00000361272:P137R;ENSP00000361271:P123R;ENSP00000410285:P123R;ENSP00000256039:P123R	ENSP00000256039:P123R	P	+	2	0	DYDC2	82116521	0.006000	0.16342	0.014000	0.15608	0.001000	0.01503	1.492000	0.35594	1.558000	0.49541	-0.211000	0.12701	CCA	C|0.982;G|0.018	0.018	strong		0.468	DYDC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049063.1	NM_032372	
RTP4	64108	hgsc.bcm.edu	37	3	187088903	187088903	+	Silent	SNP	C	C	A	rs1533595	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:187088903C>A	ENST00000259030.2	+	2	593	c.483C>A	c.(481-483)atC>atA	p.I161I		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	161					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)		CTTTGGGCATCTGTGGACAGG	0.512													C|||	1926	0.384585	0.1407	0.4942	5008	,	,		1612	0.7351		0.3469	False		,,,				2504	0.3139				p.I161I		Atlas-SNP	.											.	RTP4	20	.	0			c.C483A						PASS	.	C		913,3493	349.3+/-310.3	94,725,1384	63.0	55.0	58.0		483	0.2	0.0	3	dbSNP_88	58	3018,5582	466.0+/-366.7	525,1968,1807	no	coding-synonymous	RTP4	NM_022147.2		619,2693,3191	AA,AC,CC		35.093,20.7217,30.2245		161/247	187088903	3931,9075	2203	4300	6503	SO:0001819	synonymous_variant	64108	exon2			GGGCATCTGTGGA	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.483C>A	3.37:g.187088903C>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_022147	Q9H4F3	Silent	SNP	ENST00000259030.2	37	CCDS33910.1																																																																																			C|0.669;A|0.331	0.331	strong		0.512	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388635	1388635	+	Silent	SNP	T	T	C	rs74518227	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	107	80	0.747664	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	
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150167	39150167	+	Silent	SNP	G	G	A	rs12452295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	332	0	0		WXS	Illumina HiSeq	Phase_I	352	186	0.528409	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		
ACAA2	10449	hgsc.bcm.edu	37	18	47318626	47318626	+	Missense_Mutation	SNP	T	T	C	rs11549285	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:47318626T>C	ENST00000285093.10	-	6	1124	c.649A>G	c.(649-651)Atg>Gtg	p.M217V	ACAA2_ENST00000589432.1_Missense_Mutation_p.M162V|ACAA2_ENST00000587994.1_Missense_Mutation_p.M214V	NM_006111.2	NP_006102.2	P42765	THIM_HUMAN	acetyl-CoA acyltransferase 2	217			M -> V (in dbSNP:rs11549285).		cellular response to hypoxia (GO:0071456)|cholesterol biosynthetic process (GO:0006695)|fatty acid metabolic process (GO:0006631)|negative regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902109)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	acetyl-CoA C-acyltransferase activity (GO:0003988)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(7)|ovary(1)	10						TCTACCTGCATTGTCTGTTTT	0.423													T|||	300	0.0599042	0.0015	0.0375	5008	,	,		16355	0.1885		0.0268	False		,,,				2504	0.0562				p.M217V		Atlas-SNP	.											.	ACAA2	29	.	0			c.A649G						PASS	.	T	VAL/MET	13,4393	17.9+/-39.9	0,13,2190	172.0	144.0	153.0		649	1.8	0.7	18	dbSNP_120	153	191,8409	84.5+/-147.0	6,179,4115	yes	missense	ACAA2	NM_006111.2	21	6,192,6305	CC,CT,TT		2.2209,0.2951,1.5685	benign	217/398	47318626	204,12802	2203	4300	6503	SO:0001583	missense	10449	exon6			CCTGCATTGTCTG	D16294	CCDS11939.1	18q21	2010-04-30	2010-04-30		ENSG00000167315	ENSG00000167315	2.3.1.16		83	protein-coding gene	gene with protein product	"""mitochondrial 3-oxoacyl-Coenzyme A thiolase"""	604770	"""acetyl-Coenzyme A acyltransferase 2"""			8241273	Standard	NM_006111		Approved	DSAEC	uc002ldw.4	P42765	OTTHUMG00000132667	ENST00000285093.10:c.649A>G	18.37:g.47318626T>C	ENSP00000285093:p.Met217Val	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	168	87	0.517857	NM_006111	Q9BUT6	Missense_Mutation	SNP	ENST00000285093.10	37	CCDS11939.1	126	0.057692307692307696	2	0.0040650406504065045	14	0.03867403314917127	91	0.1590909090909091	19	0.025065963060686015	T	2.008	-0.427751	0.04701	0.002951	0.022209	ENSG00000167315	ENST00000285093	D	0.87334	-2.24	5.49	1.75	0.24633	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.104157	0.85682	N	0.000000	T	0.00440	0.0014	N	0.01464	-0.85	0.20074	P	0.999936946	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.05550	-1.0878	9	0.15499	T	0.54	-15.6312	9.3216	0.37968	0.0:0.2745:0.0:0.7255	rs11549285;rs52835379;rs11549285	217;217	B2RB23;P42765	.;THIM_HUMAN	V	217	ENSP00000285093:M217V	ENSP00000285093:M217V	M	-	1	0	ACAA2	45572624	0.963000	0.33076	0.699000	0.30290	0.306000	0.27790	1.674000	0.37544	0.063000	0.16370	-0.269000	0.10298	ATG	T|0.970;C|0.030	0.030	strong		0.423	ACAA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255921.2	NM_006111	
CCP110	9738	hgsc.bcm.edu	37	16	19548152	19548152	+	Silent	SNP	T	T	C	rs179050	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:19548152T>C	ENST00000381396.5	+	4	1408	c.1161T>C	c.(1159-1161)caT>caC	p.H387H	CCP110_ENST00000396208.2_Silent_p.H387H|CCP110_ENST00000396212.2_Silent_p.H387H	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	387	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						CAGCGTGTCATATACTTATAA	0.373													T|||	386	0.0770767	0.1641	0.0663	5008	,	,		21213	0.002		0.0964	False		,,,				2504	0.0245				p.H387H		Atlas-SNP	.											CCP110,NS,adenoma,0,1	CCP110	57	1	0			c.T1161C						PASS	.	T	,	675,3715	263.4+/-265.5	45,585,1565	54.0	54.0	54.0		1161,1161	0.7	1.0	16	dbSNP_79	54	836,7764	188.0+/-235.1	37,762,3501	no	coding-synonymous,coding-synonymous	CCP110	NM_001199022.1,NM_014711.4	,	82,1347,5066	CC,CT,TT		9.7209,15.3759,11.632	,	387/1013,387/992	19548152	1511,11479	2195	4300	6495	SO:0001819	synonymous_variant	9738	exon4			GTGTCATATACTT	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.1161T>C	16.37:g.19548152T>C		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	209	106	0.507177	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Silent	SNP	ENST00000381396.5	37	CCDS55992.1																																																																																			T|0.896;C|0.104	0.104	strong		0.373	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711	
NEBL	10529	hgsc.bcm.edu	37	10	21108377	21108377	+	Silent	SNP	C	C	T	rs1006363	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:21108377C>T	ENST00000377122.4	-	20	2427	c.2031G>A	c.(2029-2031)agG>agA	p.R677R	NEBL_ENST00000377159.4_Intron|NEBL_ENST00000417816.2_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	677					cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CCTGGTTTCGCCTCACTCTCT	0.428													C|||	920	0.183706	0.0204	0.219	5008	,	,		17787	0.252		0.2992	False		,,,				2504	0.1902				p.R677R		Atlas-SNP	.											.	NEBL	199	.	0			c.G2031A						PASS	.	C	,,	336,4070	177.3+/-206.3	15,306,1882	180.0	166.0	171.0		,2031,	3.0	0.0	10	dbSNP_86	171	2539,6061	415.0+/-351.6	376,1787,2137	no	intron,coding-synonymous,intron	NEBL	NM_001173484.1,NM_006393.2,NM_213569.2	,,	391,2093,4019	TT,TC,CC		29.5233,7.626,22.1052	,,	,677/1015,	21108377	2875,10131	2203	4300	6503	SO:0001819	synonymous_variant	10529	exon20			GTTTCGCCTCACT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.2031G>A	10.37:g.21108377C>T		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	154	115	0.746753	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Silent	SNP	ENST00000377122.4	37	CCDS7134.1																																																																																			C|0.789;T|0.211	0.211	strong		0.428	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
SSPO	23145	hgsc.bcm.edu	37	7	149515796	149515796	+	RNA	SNP	C	C	T	rs1557956	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149515796C>T	ENST00000378016.2	+	0	11697							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)			GCACGGACCCCGCTCGCCCTG	0.692													c|||	1008	0.201278	0.2474	0.1945	5008	,	,		11954	0.1746		0.1541	False		,,,				2504	0.2198				p.P3899P		Atlas-SNP	.											.	.	.	.	0			c.C11697T						PASS	.	C		785,3175		101,583,1296	17.0	20.0	19.0		11711	-8.3	0.0	7	dbSNP_88	19	1369,6923		100,1169,2877	yes	coding-notMod3	SSPO	NM_198455.2		201,1752,4173	TT,TC,CC		16.5099,19.8232,17.5808			149515796	2154,10098	1980	4146	6126			23145	exon83			GGACCCCGCTCGC	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.149515796C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	37	4	0.108108	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.816;T|0.184	0.184	strong		0.692	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
FRG1	2483	hgsc.bcm.edu	37	4	190878589	190878589	+	Missense_Mutation	SNP	A	A	G	rs561930100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.						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	553	0	0		WXS	Illumina HiSeq	Phase_I	524	46	0.0877863	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	
AKR1C3	8644	hgsc.bcm.edu	37	10	5136651	5136651	+	Missense_Mutation	SNP	C	C	G	rs12529	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:5136651C>G	ENST00000380554.3	+	1	667	c.15C>G	c.(13-15)caC>caG	p.H5Q	U8_ENST00000459536.1_RNA|AKR1C3_ENST00000605149.1_Intron|AKR1C3_ENST00000439082.2_Intron|AKR1C3_ENST00000470862.2_Intron	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	5			H -> Q (in dbSNP:rs12529). {ECO:0000269|PubMed:10557352, ECO:0000269|PubMed:10622721, ECO:0000269|PubMed:7626489, ECO:0000269|PubMed:7650035, ECO:0000269|PubMed:7788527, ECO:0000269|PubMed:8274401, ECO:0000269|PubMed:9415401}.		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)	ATTCCAAACACCAGTGTGTAA	0.448													C|||	2903	0.579673	0.4569	0.5447	5008	,	,		17728	0.8611		0.4046	False		,,,				2504	0.6605				p.H5Q		Atlas-SNP	.											.	AKR1C3	21	.	0			c.C15G	GRCh37	CM045656	AKR1C3	M	rs12529	PASS	.	C	GLN/HIS	2046,2360	566.7+/-382.0	473,1100,630	216.0	187.0	197.0		15	-4.4	0.0	10	dbSNP_52	197	3546,5052	514.7+/-378.5	767,2012,1520	yes	missense	AKR1C3	NM_003739.4	24	1240,3112,2150	GG,GC,CC		41.2421,46.4367,43.0022	benign	5/324	5136651	5592,7412	2203	4299	6502	SO:0001583	missense	8644	exon1			CAAACACCAGTGT	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.15C>G	10.37:g.5136651C>G	ENSP00000369927:p.His5Gln	Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_001253909	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	1250	0.5723443223443223	244	0.4959349593495935	198	0.5469613259668509	500	0.8741258741258742	308	0.40633245382585753	C	6.504	0.461158	0.12342	0.464367	0.412421	ENSG00000196139	ENST00000380554	T	0.47177	0.85	2.18	-4.36	0.03645	NADP-dependent oxidoreductase domain (1);	5.058380	0.00520	N	0.000183	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	4.000000000004E-6	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.31888	-0.9927	9	0.25106	T	0.35	.	6.2662	0.20928	0.0:0.5802:0.1624:0.2574	rs12529;rs1131108;rs3190662;rs52833180;rs60646959;rs12529	5;5	B4DKT3;P42330	.;AK1C3_HUMAN	Q	5	ENSP00000369927:H5Q	ENSP00000369927:H5Q	H	+	3	2	AKR1C3	5126651	0.000000	0.05858	0.000000	0.03702	0.434000	0.31775	-1.565000	0.02150	-1.160000	0.02804	0.313000	0.20887	CAC	C|0.511;G|0.489	0.489	strong		0.448	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
OR51F1	256892	hgsc.bcm.edu	37	11	4790396	4790396	+	Missense_Mutation	SNP	G	G	A	rs17324609	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790396G>A	ENST00000380383.1	-	1	772	c.773C>T	c.(772-774)gCt>gTt	p.A258V	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.A251V|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	258			A -> V (in dbSNP:rs17324609).			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)		GTAGAAGAAAGCAACTGCTCC	0.483													G|||	230	0.0459265	0.0061	0.0951	5008	,	,		20736	0.0		0.1412	False		,,,				2504	0.0143				p.A251V		Atlas-SNP	.											.	OR51F1	60	.	0			c.C752T						PASS	.	G	VAL/ALA	140,4262	98.0+/-136.7	1,138,2062	102.0	90.0	94.0		752	5.2	0.9	11	dbSNP_123	94	1159,7437	238.2+/-269.8	94,971,3233	yes	missense	OR51F1	NM_001004752.1	64	95,1109,5295	AA,AG,GG		13.483,3.1804,9.9938	possibly-damaging	251/313	4790396	1299,11699	2201	4298	6499	SO:0001583	missense	256892	exon1			AAGAAAGCAACTG	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.773C>T	11.37:g.4790396G>A	ENSP00000369744:p.Ala258Val	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	183	95	0.519126	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		157	0.07188644688644688	2	0.0040650406504065045	47	0.1298342541436464	0	0.0	108	0.1424802110817942	G	20.3	3.963905	0.74131	0.031804	0.13483	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.30714	1.52;1.52	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.783599	0.11487	N	0.559083	T	0.00356	0.0011	L	0.35593	1.075	0.80722	P	0.0	D	0.58970	0.984	P	0.61275	0.886	T	0.03641	-1.1017	9	0.72032	D	0.01	.	11.8249	0.52261	0.0839:0.0:0.9161:0.0	rs17324609;rs52817348;rs17324609	258	A6NGY5	O51F1_HUMAN	V	251;258	ENSP00000345163:A251V;ENSP00000369744:A258V	ENSP00000345163:A251V	A	-	2	0	OR51F1	4746972	0.602000	0.26916	0.874000	0.34290	0.923000	0.55619	2.740000	0.47418	2.728000	0.93425	0.655000	0.94253	GCT	G|0.915;A|0.085	0.085	strong		0.483	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
ACP2	53	hgsc.bcm.edu	37	11	47270255	47270255	+	Missense_Mutation	SNP	C	C	T	rs2167079	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47270255C>T	ENST00000256997.3	-	1	202	c.86G>A	c.(85-87)cGg>cAg	p.R29Q	ACP2_ENST00000537863.1_5'UTR|NR1H3_ENST00000395397.3_5'Flank|ACP2_ENST00000444355.2_Missense_Mutation_p.R29Q|ACP2_ENST00000527256.1_Missense_Mutation_p.R29Q|NR1H3_ENST00000407404.1_5'Flank|ACP2_ENST00000533929.1_5'Flank|NR1H3_ENST00000405576.1_5'Flank|NR1H3_ENST00000529540.1_3'UTR|ACP2_ENST00000529444.1_Missense_Mutation_p.R29Q|NR1H3_ENST00000481889.2_5'Flank|ACP2_ENST00000529788.1_Missense_Mutation_p.R29Q|ACP2_ENST00000530453.1_Missense_Mutation_p.R29Q	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	29			R -> Q (in dbSNP:rs2167079). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		dephosphorylation (GO:0016311)|lysosome organization (GO:0007040)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)	acid phosphatase activity (GO:0003993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)	10						ACTCCGGGCCCGGGTGGGCGG	0.622													T|||	2589	0.516973	0.6203	0.3458	5008	,	,		17244	0.7768		0.3002	False		,,,				2504	0.454				p.R29Q	Melanoma(90;262 1440 11488 44828 48531)	Atlas-SNP	.											.	ACP2	36	.	0			c.G86A						PASS	.	T	GLN/ARG,GLN/ARG	2452,1934		672,1108,413	20.0	22.0	22.0		86,86	5.7	1.0	11	dbSNP_96	22	2478,6114		353,1772,2171	yes	missense,missense	ACP2	NM_001131064.1,NM_001610.2	43,43	1025,2880,2584	TT,TC,CC		28.8408,44.0948,37.9874	benign,benign	29/161,29/424	47270255	4930,8048	2193	4296	6489	SO:0001583	missense	53	exon1			CGGGCCCGGGTGG	X15525	CCDS7928.1, CCDS44583.1	11p11.2	2008-02-05			ENSG00000134575	ENSG00000134575	3.1.3.2		123	protein-coding gene	gene with protein product		171650				975882	Standard	NM_001610		Approved		uc001nei.3	P11117	OTTHUMG00000166949	ENST00000256997.3:c.86G>A	11.37:g.47270255C>T	ENSP00000256997:p.Arg29Gln	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_001610	E9PCI1|Q561W5|Q9BTU7	Missense_Mutation	SNP	ENST00000256997.3	37	CCDS7928.1	1078	0.4935897435897436	279	0.5670731707317073	139	0.3839779005524862	425	0.743006993006993	235	0.3100263852242744	T	17.86	3.491528	0.64074	0.559052	0.288408	ENSG00000134575	ENST00000256997;ENST00000529444;ENST00000527256;ENST00000540414;ENST00000529663;ENST00000530453;ENST00000444355;ENST00000529788	T;T;T;T;T;T;T	0.40476	3.19;3.02;3.31;2.82;1.61;1.6;1.03	5.69	5.69	0.88448	.	0.394063	0.27591	N	0.018686	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999999999996	B;B;B;B;B	0.10296	0.003;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.40496	-0.9560	9	0.02654	T	1	.	9.8795	0.41225	0.0:0.0786:0.0:0.9214	rs2167079;rs2228400;rs58523292;rs2167079	29;29;29;29;29	E9PCI1;E9PHY0;B7Z7D2;F5H1S6;P11117	.;.;.;.;PPAL_HUMAN	Q	29	ENSP00000256997:R29Q;ENSP00000436658:R29Q;ENSP00000432205:R29Q;ENSP00000436487:R29Q;ENSP00000434205:R29Q;ENSP00000414911:R29Q;ENSP00000436828:R29Q	ENSP00000256997:R29Q	R	-	2	0	ACP2	47226831	1.000000	0.71417	0.987000	0.45799	0.990000	0.78478	1.370000	0.34238	1.092000	0.41356	-0.254000	0.11334	CGG	C|0.559;T|0.441	0.441	strong		0.622	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610	
KANK1	23189	hgsc.bcm.edu	37	9	712137	712137	+	Silent	SNP	G	G	C	rs912175	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:712137G>C	ENST00000382303.1	+	7	2023	c.1371G>C	c.(1369-1371)ctG>ctC	p.L457L	KANK1_ENST00000382297.2_Silent_p.L457L|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Silent_p.L299L	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						scavenged	.	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	58	3	0.0517241		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	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	
OR4D1	26689	hgsc.bcm.edu	37	17	56232675	56232675	+	Missense_Mutation	SNP	G	G	A	rs12602205	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:56232675G>A	ENST00000268912.5	+	1	182	c.161G>A	c.(160-162)cGg>cAg	p.R54Q		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	54			R -> Q (in dbSNP:rs12602205).		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)			kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						TTTGACTGCCGGCTCCACACA	0.473													G|||	284	0.0567093	0.0499	0.0519	5008	,	,		19979	0.001		0.0924	False		,,,				2504	0.09				p.R54Q		Atlas-SNP	.											.	OR4D1	48	.	0			c.G161A						PASS	.						176.0	174.0	175.0					17																	56232675		2110	4269	6379	SO:0001583	missense	26689	exon1			ACTGCCGGCTCCA	X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"""GPCR / Class A : Olfactory receptors"""	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.161G>A	17.37:g.56232675G>A	ENSP00000365451:p.Arg54Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_012374	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	37	CCDS42365.1	119	0.05448717948717949	24	0.04878048780487805	23	0.06353591160220995	1	0.0017482517482517483	71	0.09366754617414248	g	11.22	1.574058	0.28092	.	.	ENSG00000141194	ENST00000268912	T	0.01119	5.31	5.63	-0.983	0.10263	GPCR, rhodopsin-like superfamily (1);	0.795760	0.10072	N	0.719604	T	0.00073	0.0002	L	0.41573	1.285	0.09310	N	1	B	0.22604	0.072	B	0.17979	0.02	T	0.44406	-0.9330	10	0.37606	T	0.19	-1.8757	10.6281	0.45519	0.4382:0.0:0.5618:0.0	rs12602205;rs52805994;rs12602205	54	Q15615	OR4D1_HUMAN	Q	54	ENSP00000365451:R54Q	ENSP00000365451:R54Q	R	+	2	0	OR4D1	53587674	0.000000	0.05858	0.001000	0.08648	0.840000	0.47671	-0.235000	0.09016	-0.374000	0.07967	-1.490000	0.00973	CGG	G|0.932;A|0.068	0.068	strong		0.473	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1		
ZNF22	7570	hgsc.bcm.edu	37	10	45499272	45499272	+	Silent	SNP	C	C	G	rs3740092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:45499272C>G	ENST00000298299.3	+	2	1049	c.456C>G	c.(454-456)tcC>tcG	p.S152S	CEP164P1_ENST00000456938.2_RNA|C10orf25_ENST00000298298.1_5'Flank	NM_006963.4	NP_008894.2	P17026	ZNF22_HUMAN	zinc finger protein 22	152					odontogenesis (GO:0042476)|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(2)|endometrium(1)|kidney(2)|lung(2)	8		Prostate(175;0.0352)|all_neural(218;0.202)				GCCAGAGCTCCCACCTTATTC	0.483													C|||	187	0.0373403	0.0151	0.0101	5008	,	,		17093	0.0893		0.0427	False		,,,				2504	0.0276				p.S152S		Atlas-SNP	.											ZNF22,colon,carcinoma,0,1	ZNF22	28	1	0			c.C456G						PASS	.	C		63,4343	60.5+/-97.4	0,63,2140	92.0	98.0	96.0		456	1.7	1.0	10	dbSNP_107	96	417,8183	131.3+/-189.1	6,405,3889	no	coding-synonymous	ZNF22	NM_006963.4		6,468,6029	GG,GC,CC		4.8488,1.4299,3.6906		152/225	45499272	480,12526	2203	4300	6503	SO:0001819	synonymous_variant	7570	exon2			GAGCTCCCACCTT	BC041139	CCDS7211.1	10q11	2013-01-08	2012-07-12		ENSG00000165512	ENSG00000165512		"""Zinc fingers, C2H2-type"""	13012	protein-coding gene	gene with protein product		194529					Standard	NM_006963		Approved	KOX15, HKR-T1, ZNF422, Zfp422	uc001jbw.3	P17026	OTTHUMG00000018064	ENST00000298299.3:c.456C>G	10.37:g.45499272C>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	37	12	0.324324	NM_006963	Q5T741|Q96FM4	Silent	SNP	ENST00000298299.3	37	CCDS7211.1																																																																																			C|0.960;G|0.040	0.040	strong		0.483	ZNF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047761.1	NM_006963	
EYA3	2140	hgsc.bcm.edu	37	1	28304899	28304899	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:28304899T>C	ENST00000373871.3	-	17	1867	c.1627A>G	c.(1627-1629)Att>Gtt	p.I543V	EYA3_ENST00000545175.1_Missense_Mutation_p.I490V|EYA3_ENST00000373863.3_Missense_Mutation_p.I497V|EYA3_ENST00000373864.1_Missense_Mutation_p.I386V|EYA3_ENST00000540618.1_Missense_Mutation_p.I497V|EYA3_ENST00000436342.2_Missense_Mutation_p.I417V	NM_001282561.1|NM_001282562.1	NP_001269490.1|NP_001269491.1	Q99504	EYA3_HUMAN	EYA transcriptional coactivator and phosphatase 3	543					anatomical structure morphogenesis (GO:0009653)|double-strand break repair (GO:0006302)|histone dephosphorylation (GO:0016576)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of DNA repair (GO:0045739)|regulation of transcription, DNA-templated (GO:0006355)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		TTGGCTGCAATTTCTTCATCT	0.368																																					p.I543V		Atlas-SNP	.											.	EYA3	38	.	0			c.A1627G						PASS	.						207.0	200.0	202.0					1																	28304899		2203	4300	6503	SO:0001583	missense	2140	exon17			CTGCAATTTCTTC	U81602	CCDS316.1, CCDS60050.1, CCDS60051.1, CCDS60052.1	1p36	2014-06-19	2014-06-19		ENSG00000158161	ENSG00000158161		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3521	protein-coding gene	gene with protein product		601655	"""eyes absent (Drosophila) homolog 3"", ""eyes absent homolog 3 (Drosophila)"""			9020840	Standard	NM_001990		Approved	DKFZp686C132	uc001bpi.2	Q99504	OTTHUMG00000003916	ENST00000373871.3:c.1627A>G	1.37:g.28304899T>C	ENSP00000362978:p.Ile543Val	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	155	40	0.258065	NM_001990	A8K190|B4DIR7|B4DNZ7|O95463|Q8IVX7|Q99813	Missense_Mutation	SNP	ENST00000373871.3	37	CCDS316.1	.	.	.	.	.	.	.	.	.	.	T	8.394	0.840482	0.16891	.	.	ENSG00000158161	ENST00000373871;ENST00000436342;ENST00000373864;ENST00000540618;ENST00000545175;ENST00000373863	D;D;D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33	5.54	5.54	0.83059	EYA (1);Haloacid dehalogenase-like hydrolase (1);	0.254205	0.46145	D	0.000317	T	0.77805	0.4185	N	0.22421	0.69	0.28710	N	0.903603	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.67074	-0.5762	10	0.28530	T	0.3	-12.8991	10.8241	0.46622	0.0:0.0757:0.0:0.9243	.	497;497;543	B4DIR7;Q8IVX7;Q99504	.;.;EYA3_HUMAN	V	543;417;386;497;490;497	ENSP00000362978:I543V;ENSP00000405587:I417V;ENSP00000362971:I386V;ENSP00000442558:I497V;ENSP00000442280:I490V;ENSP00000362970:I497V	ENSP00000362970:I497V	I	-	1	0	EYA3	28177486	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.160000	0.42348	2.107000	0.64212	0.402000	0.26972	ATT	.	.	none		0.368	EYA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011184.1	NM_001990	
PKDREJ	10343	hgsc.bcm.edu	37	22	46652929	46652929	+	Silent	SNP	G	G	A	rs6008365	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46652929G>A	ENST00000253255.5	-	1	6290	c.6291C>T	c.(6289-6291)tcC>tcT	p.S2097S		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	2097					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AGAAATACACGGACACAACAA	0.483													G|||	1213	0.242212	0.6604	0.1297	5008	,	,		21491	0.002		0.16	False		,,,				2504	0.089				p.S2097S		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C6291T						PASS	.	G		2567,1839	627.1+/-394.8	748,1071,384	42.0	42.0	42.0		6291	-3.4	0.0	22	dbSNP_114	42	1257,7343	249.0+/-276.5	88,1081,3131	no	coding-synonymous	PKDREJ	NM_006071.1		836,2152,3515	AA,AG,GG		14.6163,41.7385,29.4018		2097/2254	46652929	3824,9182	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			ATACACGGACACA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.6291C>T	22.37:g.46652929G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.739;A|0.261	0.261	strong		0.483	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
LARS	51520	hgsc.bcm.edu	37	5	145508637	145508637	+	Silent	SNP	A	A	C	rs61732382|rs35977062	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145508637A>C	ENST00000394434.2	-	26	2839	c.2673T>G	c.(2671-2673)gtT>gtG	p.V891V	LARS_ENST00000274562.9_Silent_p.V864V|LARS_ENST00000510191.1_Silent_p.V837V|LARS_ENST00000545646.1_Silent_p.V845V	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	122	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	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	
KANSL2	54934	hgsc.bcm.edu	37	12	49061511	49061511	+	Missense_Mutation	SNP	T	T	C	rs17238800	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:49061511T>C	ENST00000420613.2	-	7	985	c.938A>G	c.(937-939)aAt>aGt	p.N313S	SNORA2B_ENST00000384583.1_RNA|KANSL2_ENST00000553086.1_Missense_Mutation_p.N313S|KANSL2_ENST00000357861.3_Missense_Mutation_p.N118S|KANSL2_ENST00000550347.1_Missense_Mutation_p.N496S	NM_017822.3	NP_060292.3	Q9H9L4	KANL2_HUMAN	KAT8 regulatory NSL complex subunit 2	313			N -> S (in dbSNP:rs17238800). {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)											AAGAGACTGATTGGAACAACG	0.448													T|||	42	0.00838658	0.0	0.0159	5008	,	,		19093	0.0		0.0189	False		,,,				2504	0.0123				p.N313S		Atlas-SNP	.											.	.	.	.	0			c.A938G						PASS	.	T	SER/ASN	12,3964		0,12,1976	170.0	164.0	166.0		938	5.7	1.0	12	dbSNP_123	166	200,8116		2,196,3960	yes	missense	C12orf41	NM_017822.3	46	2,208,5936	CC,CT,TT		2.405,0.3018,1.7247	benign	313/493	49061511	212,12080	1988	4158	6146	SO:0001583	missense	54934	exon7			GACTGATTGGAAC	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.938A>G	12.37:g.49061511T>C	ENSP00000415436:p.Asn313Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_017822	Q8N3B5|Q96CV0|Q9NX51	Missense_Mutation	SNP	ENST00000420613.2	37	CCDS44869.1	28	0.01282051282051282	0	0.0	11	0.03038674033149171	0	0.0	17	0.022427440633245383	T	21.1	4.103553	0.76983	0.003018	0.02405	ENSG00000139620	ENST00000550347;ENST00000420613;ENST00000547087;ENST00000553086;ENST00000357861	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.68	5.68	0.88126	.	0.042292	0.85682	D	0.000000	T	0.31513	0.0799	L	0.45228	1.405	0.50813	D	0.999899	P;D;D;D	0.76494	0.952;0.984;0.999;0.974	P;P;D;P	0.73708	0.626;0.76;0.981;0.647	T	0.36261	-0.9755	10	0.39692	T	0.17	-29.266	15.2035	0.73159	0.0:0.0:0.0:1.0	rs17238800;rs17851070;rs52828281;rs17238800	496;313;118;313	F8VX10;Q9H9L4;Q9H9L4-2;F8VXI8	.;CL041_HUMAN;.;.	S	496;313;61;313;118	ENSP00000449747:N496S;ENSP00000415436:N313S;ENSP00000447608:N61S;ENSP00000448833:N313S;ENSP00000350527:N118S	ENSP00000350527:N118S	N	-	2	0	C12orf41	47347778	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.692000	0.47018	2.289000	0.77006	0.460000	0.39030	AAT	T|0.984;C|0.016	0.016	strong		0.448	KANSL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408841.1	NM_017822	
KRT84	3890	hgsc.bcm.edu	37	12	52777580	52777580	+	Silent	SNP	A	A	C	rs386763043|rs1613929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52777580A>C	ENST00000257951.3	-	2	615	c.549T>G	c.(547-549)gtT>gtG	p.V183V	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	183	Coil 1A.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CTAGGAACCGAACCTAAATCC	0.493													C|||	1664	0.332268	0.6172	0.3199	5008	,	,		22989	0.1954		0.2068	False		,,,				2504	0.226				p.V183V		Atlas-SNP	.											.	KRT84	61	.	0			c.T549G						PASS	.	C		2127,2279		715,697,791	54.0	55.0	55.0		549	1.2	1.0	12	dbSNP_89	55	1290,7310		180,930,3190	yes	coding-synonymous	KRT84	NM_033045.3		895,1627,3981	CC,CA,AA		15.0,48.2751,26.2725		183/601	52777580	3417,9589	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			GAACCGAACCTAA	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.549T>G	12.37:g.52777580A>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.686;C|0.314	0.314	strong		0.493	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58335626	58335626	+	Missense_Mutation	SNP	A	A	T	rs3751325	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	78	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	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	
GGA2	23062	hgsc.bcm.edu	37	16	23489711	23489711	+	Missense_Mutation	SNP	C	C	G	rs1135045	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:23489711C>G	ENST00000309859.4	-	13	1352	c.1270G>C	c.(1270-1272)Gca>Cca	p.A424P	GGA2_ENST00000569182.1_5'UTR|GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	424	Unstructured hinge.		A -> P (in dbSNP:rs1135045). {ECO:0000269|PubMed:10747088, ECO:0000269|PubMed:10749927, ECO:0000269|PubMed:11331584, ECO:0000269|PubMed:15489334}.		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)		GCTGGCTGTGCTGAGAGGAGG	0.582													G|||	3387	0.676318	0.5219	0.7233	5008	,	,		14776	0.6994		0.8111	False		,,,				2504	0.6892				p.A424P		Atlas-SNP	.											.	GGA2	49	.	0			c.G1270C						PASS	.	G	PRO/ALA	2551,1843	537.6+/-374.8	737,1077,383	101.0	91.0	94.0		1270	2.1	0.4	16	dbSNP_86	94	6935,1665	305.8+/-307.6	2788,1359,153	yes	missense	GGA2	NM_015044.4	27	3525,2436,536	GG,GC,CC		19.3605,41.9436,26.9971	benign	424/614	23489711	9486,3508	2197	4300	6497	SO:0001583	missense	23062	exon13			GCTGTGCTGAGAG	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.1270G>C	16.37:g.23489711C>G	ENSP00000311962:p.Ala424Pro	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	37	CCDS10611.1	1539	0.7046703296703297	268	0.5447154471544715	271	0.7486187845303868	387	0.6765734265734266	613	0.8087071240105541	G	0.886	-0.726950	0.03158	0.580564	0.806395	ENSG00000103365	ENST00000309859	T	0.14391	2.51	4.15	2.1	0.27182	.	1.378670	0.05287	N	0.520402	T	0.00012	0.0000	N	0.00197	-1.87	0.36496	P	0.13126899999999997	B	0.02656	0.0	B	0.01281	0.0	T	0.28522	-1.0041	9	0.18276	T	0.48	-0.0054	6.2465	0.20820	0.1025:0.3645:0.533:0.0	rs1135045;rs2301623;rs3197517;rs11540712;rs17422742;rs17855999;rs1135045	424	Q9UJY4	GGA2_HUMAN	P	424	ENSP00000311962:A424P	ENSP00000311962:A424P	A	-	1	0	GGA2	23397212	0.926000	0.31397	0.449000	0.26957	0.013000	0.08279	0.670000	0.25157	0.139000	0.18822	-0.120000	0.15030	GCA	C|0.272;G|0.728	0.728	strong		0.582	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		
ARSB	411	hgsc.bcm.edu	37	5	78135201	78135201	+	Silent	SNP	C	C	T	rs25413	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:78135201C>T	ENST00000264914.4	-	6	1727	c.1191G>A	c.(1189-1191)ccG>ccA	p.P397P	ARSB_ENST00000565165.1_Silent_p.P397P|ARSB_ENST00000396151.3_Silent_p.P397P	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	397					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)		CCACGAAGTTCGGGTCAATAT	0.433													C|||	1298	0.259185	0.5628	0.1513	5008	,	,		19055	0.0486		0.1799	False		,,,				2504	0.2239				p.P397P	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											ARSB,NS,carcinoma,-1,1	ARSB	47	1	0			c.G1191A						PASS	.	C	,	2188,2218	586.5+/-386.5	546,1096,561	139.0	137.0	138.0		1191,1191	-8.9	0.0	5	dbSNP_71	138	1607,6993	298.3+/-303.9	153,1301,2846	no	coding-synonymous,coding-synonymous	ARSB	NM_000046.3,NM_198709.2	,	699,2397,3407	TT,TC,CC		18.686,49.6596,29.1788	,	397/534,397/414	78135201	3795,9211	2203	4300	6503	SO:0001819	synonymous_variant	411	exon7			GAAGTTCGGGTCA	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.1191G>A	5.37:g.78135201C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	182	103	0.565934	NM_198709	B2RC20|Q8N322|Q9UDI9	Silent	SNP	ENST00000264914.4	37	CCDS4043.1																																																																																			C|0.727;T|0.273	0.273	strong		0.433	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046	
C20orf166	128826	hgsc.bcm.edu	37	20	61162267	61162267	+	Missense_Mutation	SNP	T	T	C	rs6062251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:61162267T>C	ENST00000370527.3	+	3	859	c.80T>C	c.(79-81)gTg>gCg	p.V27A	C20orf166_ENST00000370523.1_Intron|MIR133A2_ENST00000347538.2_RNA|C20orf166_ENST00000370524.2_Intron	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)			ACCCAGCAGGTGGCGCGGGGA	0.677													C|||	2888	0.576677	0.7042	0.5605	5008	,	,		12968	0.3284		0.6243	False		,,,				2504	0.6227				p.V27A		Atlas-SNP	.											.	C20orf166	17	.	0			c.T80C						PASS	.	C	ALA/VAL	2917,1443		1016,885,279	11.0	12.0	12.0		80	-7.9	0.0	20	dbSNP_114	12	5233,3313		1652,1929,692	yes	missense	C20orf166	NM_178463.3	64	2668,2814,971	CC,CT,TT		38.7667,33.0963,36.8511	benign	27/118	61162267	8150,4756	2180	4273	6453	SO:0001583	missense	128826	exon3			AGCAGGTGGCGCG	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.80T>C	20.37:g.61162267T>C	ENSP00000359558:p.Val27Ala	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	20	7	0.35	NM_178463		Missense_Mutation	SNP	ENST00000370527.3	37	CCDS46627.1	1208	0.5531135531135531	341	0.693089430894309	211	0.5828729281767956	191	0.3339160839160839	465	0.6134564643799473	C	9.871	1.198845	0.22121	0.669037	0.612333	ENSG00000174407	ENST00000370527	T	0.36520	1.25	3.93	-7.86	0.01187	.	.	.	.	.	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	0.39522	-0.9610	8	0.09084	T	0.74	.	3.8336	0.08885	0.2485:0.1229:0.4735:0.1551	rs6062251;rs7268727	27	Q9H1L0	CT166_HUMAN	A	27	ENSP00000359558:V27A	ENSP00000359558:V27A	V	+	2	0	C20orf166	60572712	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.298000	0.01140	-1.689000	0.01434	-0.320000	0.08662	GTG	T|0.451;C|0.549	0.549	strong		0.677	C20orf166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109262.1	NM_178463	
HLA-A	3105	hgsc.bcm.edu	37	6	29911124	29911124	+	Silent	SNP	C	C	T	rs3173418	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29911124C>T	ENST00000396634.1	+	5	764	c.423C>T	c.(421-423)gcC>gcT	p.A141A	HLA-A_ENST00000376806.5_Silent_p.A141A|HLA-A_ENST00000376802.2_Silent_p.A141A|HLA-A_ENST00000376809.5_Silent_p.A141A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	141	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						GGCAGGACGCCTACGACGGCA	0.667									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|||	294	0.0587061	0.1021	0.0259	5008	,	,		11867	0.0397		0.0477	False		,,,				2504	0.0542				p.A141A		Atlas-SNP	.											.	HLA-A	89	.	0			c.C423T						PASS	.	C		273,2731		32,209,1261	38.0	27.0	31.0		423	0.8	0.0	6	dbSNP_105	31	321,5089		20,281,2404	no	coding-synonymous	HLA-A	NM_002116.7		52,490,3665	TT,TC,CC		5.9335,9.0879,7.0597		141/366	29911124	594,7820	1502	2705	4207	SO:0001819	synonymous_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGACGCCTACGAC	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.423C>T	6.37:g.29911124C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	166	70	0.421687	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.930;T|0.070	0.070	strong		0.667	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
KIAA1586	57691	hgsc.bcm.edu	37	6	56917538	56917538	+	Missense_Mutation	SNP	G	G	A	rs6926980	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56917538G>A	ENST00000370733.4	+	4	448	c.241G>A	c.(241-243)Gtg>Atg	p.V81M	KIAA1586_ENST00000545356.1_Missense_Mutation_p.V54M|KIAA1586_ENST00000488682.1_3'UTR	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	81			V -> M (in dbSNP:rs6926980).				nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TTTTTTAAATGTGAAGAAGGT	0.308													a|||	1089	0.217452	0.3646	0.1844	5008	,	,		18422	0.131		0.2406	False		,,,				2504	0.1074				p.V81M		Atlas-SNP	.											.	KIAA1586	59	.	0			c.G241A						PASS	.	A	MET/VAL	1488,2918	666.8+/-401.8	240,1008,955	51.0	55.0	54.0		241	-2.1	0.7	6	dbSNP_116	54	1960,6640	721.5+/-406.4	217,1526,2557	yes	missense	KIAA1586	NM_020931.2	21	457,2534,3512	AA,AG,GG		22.7907,33.7721,26.5108	benign	81/788	56917538	3448,9558	2203	4300	6503	SO:0001583	missense	57691	exon4			TTAAATGTGAAGA	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.241G>A	6.37:g.56917538G>A	ENSP00000359768:p.Val81Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	475	0.2174908424908425	180	0.36585365853658536	61	0.1685082872928177	59	0.10314685314685315	175	0.23087071240105542	a	2.665	-0.278949	0.05642	0.337721	0.227907	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.38240	1.16;1.15	3.34	-2.07	0.07276	.	.	.	.	.	T	0.05456	0.0144	N	0.08118	0	0.80722	P	0.0	B;B	0.12013	0.005;0.005	B;B	0.16289	0.015;0.015	T	0.40683	-0.9550	8	0.22109	T	0.4	.	9.0375	0.36296	0.516:0.0:0.484:0.0	rs6926980;rs52837012;rs61004014;rs6926980	54;81	F5H2N6;Q9HCI6	.;K1586_HUMAN	M	81;54	ENSP00000359768:V81M;ENSP00000445507:V54M	ENSP00000359768:V81M	V	+	1	0	KIAA1586	57025497	0.974000	0.33945	0.701000	0.30321	0.786000	0.44442	-0.165000	0.09968	-0.806000	0.04398	-1.708000	0.00717	GTG	G|0.762;A|0.238	0.238	strong		0.308	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077904	19077904	+	Missense_Mutation	SNP	T	T	G	rs11024970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:19077904T>G	ENST00000329773.2	-	2	133	c.46A>C	c.(46-48)Aat>Cat	p.N16H		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	16			N -> H (in dbSNP:rs11024970). {ECO:0000269|PubMed:15862286}.		positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)			NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						TCATTTCCATTCACTGTTGTA	0.532													T|||	566	0.113019	0.1944	0.036	5008	,	,		18231	0.1468		0.0656	False		,,,				2504	0.0716				p.N16H	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											.	MRGPRX2	42	.	0			c.A46C						PASS	.	T	HIS/ASN	702,3696		61,580,1558	192.0	208.0	203.0		46	3.9	0.0	11	dbSNP_120	203	428,8158		7,414,3872	yes	missense	MRGPRX2	NM_054030.2	68	68,994,5430	GG,GT,TT		4.9849,15.9618,8.703	probably-damaging	16/331	19077904	1130,11854	2199	4293	6492	SO:0001583	missense	117194	exon2			TTCCATTCACTGT		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"""GPCR / Class A : Orphans"""	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.46A>C	11.37:g.19077904T>G	ENSP00000333800:p.Asn16His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Missense_Mutation	SNP	ENST00000329773.2	37	CCDS7847.1	219	0.10027472527472528	92	0.18699186991869918	14	0.03867403314917127	67	0.11713286713286714	46	0.06068601583113457	.	15.60	2.882651	0.51908	0.159618	0.049849	ENSG00000183695	ENST00000329773	T	0.06687	3.27	5.04	3.91	0.45181	.	1.260630	0.05164	N	0.498462	T	0.00039	0.0001	L	0.54323	1.7	0.80722	P	0.0	P	0.50617	0.937	P	0.58266	0.836	T	0.13150	-1.0520	9	0.72032	D	0.01	.	6.4342	0.21815	0.0:0.1872:0.0:0.8128	rs11024970;rs52815501;rs59607758;rs11024970	16	Q96LB1	MRGX2_HUMAN	H	16	ENSP00000333800:N16H	ENSP00000333800:N16H	N	-	1	0	MRGPRX2	19034480	0.000000	0.05858	0.048000	0.18961	0.032000	0.12392	0.063000	0.14410	1.052000	0.40392	0.533000	0.62120	AAT	T|0.899;G|0.101	0.101	strong		0.532	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030	
TDRD10	126668	hgsc.bcm.edu	37	1	154516578	154516578	+	Missense_Mutation	SNP	G	G	A	rs3811448	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154516578G>A	ENST00000368480.3	+	9	728	c.643G>A	c.(643-645)Gtc>Atc	p.V215I	TDRD10_ENST00000368482.4_Missense_Mutation_p.V215I|TDRD10_ENST00000479937.1_3'UTR			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	215	Tudor.		V -> I (in dbSNP:rs3811448). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.				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)			GGCTATGCACGTCACTGAGGT	0.637													A|||	907	0.18111	0.1384	0.1455	5008	,	,		19371	0.1706		0.2256	False		,,,				2504	0.229				p.V215I		Atlas-SNP	.											.	TDRD10	48	.	0			c.G643A						PASS	.	A	ILE/VAL,ILE/VAL	605,3801	769.5+/-413.7	30,545,1628	123.0	90.0	101.0		643,643	-6.9	0.0	1	dbSNP_107	101	1695,6905	738.2+/-407.0	171,1353,2776	yes	missense,missense	TDRD10	NM_001098475.1,NM_182499.3	29,29	201,1898,4404	AA,AG,GG		19.7093,13.7313,17.6841	benign,benign	215/367,215/352	154516578	2300,10706	2203	4300	6503	SO:0001583	missense	126668	exon9			ATGCACGTCACTG	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.643G>A	1.37:g.154516578G>A	ENSP00000357465:p.Val215Ile	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Missense_Mutation	SNP	ENST00000368480.3	37	CCDS41406.1	392	0.1794871794871795	70	0.14227642276422764	65	0.17955801104972377	82	0.14335664335664336	175	0.23087071240105542	A	0.789	-0.759617	0.03019	0.137313	0.197093	ENSG00000163239	ENST00000368482;ENST00000368480	T;T	0.10099	2.91;2.91	3.46	-6.93	0.01638	Maternal tudor protein (1);	1.376610	0.05645	N	0.584115	T	0.00695	0.0023	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.40117	-0.9580	9	0.02654	T	1	-4.3245	4.8941	0.13742	0.1922:0.1396:0.5422:0.126	rs3811448;rs60656176;rs3811448	215;215	Q5VZ19;Q5VZ19-2	TDR10_HUMAN;.	I	215	ENSP00000357467:V215I;ENSP00000357465:V215I	ENSP00000357465:V215I	V	+	1	0	TDRD10	152783202	0.000000	0.05858	0.004000	0.12327	0.753000	0.42808	-1.526000	0.02229	-2.265000	0.00688	-0.381000	0.06696	GTC	G|0.821;A|0.179	0.179	strong		0.637	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499	
RGPD3	653489	hgsc.bcm.edu	37	2	107049714	107049714	+	Missense_Mutation	SNP	C	C	G	rs62152468		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:107049714C>G	ENST00000409886.3	-	16	2320	c.2233G>C	c.(2233-2235)Gag>Cag	p.E745Q	RGPD3_ENST00000304514.7_Missense_Mutation_p.E745Q	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	745					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTAAGCATCTCTTTTACAGAC	0.343																																					p.E745Q		Atlas-SNP	.											RGPD3_ENST00000304514,right_upper_lobe,carcinoma,0,2	RGPD3	316	2	0			c.G2233C						scavenged	.						15.0	28.0	24.0					2																	107049714		673	1545	2218	SO:0001583	missense	653489	exon16			GCATCTCTTTTAC		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.2233G>C	2.37:g.107049714C>G	ENSP00000386588:p.Glu745Gln	Somatic	751	3	0.00399467		WXS	Illumina HiSeq	Phase_I	845	364	0.430769	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	4.999	0.185488	0.09495	.	.	ENSG00000153165	ENST00000409886;ENST00000452099;ENST00000304514	T;T	0.24908	1.83;1.83	2.34	2.34	0.29019	.	.	.	.	.	T	0.21841	0.0526	M	0.62723	1.935	0.26104	N	0.980775	P	0.35700	0.516	B	0.20955	0.032	T	0.10405	-1.0631	9	0.42905	T	0.14	-11.6791	10.3857	0.44138	0.0:1.0:0.0:0.0	.	745	A6NKT7	RGPD3_HUMAN	Q	745;503;745	ENSP00000386588:E745Q;ENSP00000303659:E745Q	ENSP00000303659:E745Q	E	-	1	0	RGPD3	106416146	1.000000	0.71417	0.998000	0.56505	0.191000	0.23601	5.692000	0.68256	1.308000	0.44962	0.173000	0.16961	GAG	C|0.250;G|0.750	0.750	weak		0.343	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
SYNE1	23345	hgsc.bcm.edu	37	6	152529260	152529260	+	Silent	SNP	G	G	A	rs3798756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:152529260G>A	ENST00000367255.5	-	125	23272	c.22671C>T	c.(22669-22671)atC>atT	p.I7557I	SYNE1_ENST00000356820.4_Silent_p.I2081I|SYNE1_ENST00000341594.5_Silent_p.I7169I|SYNE1_ENST00000265368.4_Silent_p.I7557I|SYNE1_ENST00000448038.1_Silent_p.I7486I|SYNE1_ENST00000423061.1_Silent_p.I7486I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7557					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)		GGCTGTCAATGATCCCCCGCC	0.502										HNSCC(10;0.0054)			G|||	777	0.155152	0.1067	0.2378	5008	,	,		15324	0.2133		0.1272	False		,,,				2504	0.1309				p.I7557I		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C22671T						PASS	.	G	,	524,3882	241.5+/-251.9	22,480,1701	96.0	88.0	91.0		22458,22671	5.6	1.0	6	dbSNP_107	91	1153,7447	237.1+/-269.0	76,1001,3223	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	98,1481,4924	AA,AG,GG		13.407,11.8929,12.894	,	7486/8750,7557/8798	152529260	1677,11329	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon125			GTCAATGATCCCC	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.22671C>T	6.37:g.152529260G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	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|0.854;A|0.146	0.146	strong		0.502	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
XYLT1	64131	hgsc.bcm.edu	37	16	17292074	17292074	+	Silent	SNP	G	G	C	rs28709752	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:17292074G>C	ENST00000261381.6	-	5	1368	c.1284C>G	c.(1282-1284)ccC>ccG	p.P428P		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	428					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						CTTACCTGATGGGGTAGTCGG	0.607													G|||	632	0.126198	0.2209	0.1441	5008	,	,		16424	0.0268		0.1461	False		,,,				2504	0.0675				p.P428P		Atlas-SNP	.											.	XYLT1	147	.	0			c.C1284G						PASS	.	G		956,3438	357.9+/-314.1	110,736,1351	58.0	53.0	55.0		1284	2.1	1.0	16	dbSNP_125	55	1377,7223	264.1+/-285.4	116,1145,3039	no	coding-synonymous	XYLT1	NM_022166.3		226,1881,4390	CC,CG,GG		16.0116,21.7569,17.9544		428/960	17292074	2333,10661	2197	4300	6497	SO:0001819	synonymous_variant	64131	exon5			CCTGATGGGGTAG	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.1284C>G	16.37:g.17292074G>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	37	CCDS10569.1																																																																																			G|0.846;C|0.154	0.154	strong		0.607	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
GATAD2A	54815	hgsc.bcm.edu	37	19	19612027	19612027	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19612027C>T	ENST00000360315.3	+	9	1614	c.1302C>T	c.(1300-1302)ggC>ggT	p.G434G	GATAD2A_ENST00000429563.2_Silent_p.G262G|GATAD2A_ENST00000358713.3_Silent_p.G434G|GATAD2A_ENST00000404158.1_Silent_p.G435G|GATAD2A_ENST00000537887.1_Silent_p.G63G|GATAD2A_ENST00000252577.5_Silent_p.G434G	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	434	CR2; histone tail-binding.				anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						AGAAGAGCGGCGCCATCATGT	0.627																																					p.G434G		Atlas-SNP	.											GATAD2A_ENST00000360315,colon,carcinoma,+2,2	GATAD2A	81	2	0			c.C1302T						PASS	.						49.0	40.0	43.0					19																	19612027		2203	4300	6503	SO:0001819	synonymous_variant	54815	exon9			GAGCGGCGCCATC	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"""GATA zinc finger domain containing"""	29989	protein-coding gene	gene with protein product	"""p66 alpha"""	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1302C>T	19.37:g.19612027C>T		Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	226	108	0.477876	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Silent	SNP	ENST00000360315.3	37	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	C	7.688	0.690376	0.15039	.	.	ENSG00000167491	ENST00000418032	.	.	.	5.76	-11.5	0.00074	.	.	.	.	.	T	0.34279	0.0892	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52087	-0.8622	4	.	.	.	-20.9578	3.2541	0.06826	0.2384:0.4298:0.078:0.2537	.	.	.	.	C	61	.	.	R	+	1	0	GATAD2A	19473027	0.000000	0.05858	0.006000	0.13384	0.808000	0.45660	-5.377000	0.00127	-4.065000	0.00077	-0.158000	0.13435	CGC	.	.	none		0.627	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43816735	43816735	+	Missense_Mutation	SNP	G	G	C	rs200986004	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:43816735G>C	ENST00000377564.3	+	6	1234	c.841G>C	c.(841-843)Gac>Cac	p.D281H	CNTNAP3B_ENST00000276974.6_Missense_Mutation_p.D281H	NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	281	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						CGAGCTCCTCGACACGCAGGT	0.488													g|||	100	0.0199681	0.0166	0.0101	5008	,	,		22562	0.0466		0.008	False		,,,				2504	0.0164				p.D281H		Atlas-SNP	.											CNTNAP3B,right_lower_lobe,carcinoma,-2,1	CNTNAP3B	37	1	0			c.G841C						scavenged	.																																			SO:0001583	missense	728577	exon6			CTCCTCGACACGC	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.841G>C	9.37:g.43816735G>C	ENSP00000366787:p.Asp281His	Somatic	775	0	0		WXS	Illumina HiSeq	Phase_I	660	101	0.15303	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.	.	.	.	.	.	.	.	.	.	g	14.89	2.671567	0.47781	.	.	ENSG00000154529	ENST00000377564;ENST00000276974;ENST00000341990;ENST00000403166	T;T	0.78246	-1.16;-1.16	2.77	-4.35	0.03656	.	.	.	.	.	T	0.60907	0.2305	N	0.14661	0.345	0.09310	N	1	.	.	.	.	.	.	T	0.56492	-0.7970	7	0.62326	D	0.03	.	8.1029	0.30868	0.5769:0.0:0.4231:0.0	.	.	.	.	H	281	ENSP00000366787:D281H;ENSP00000276974:D281H	ENSP00000276974:D281H	D	+	1	0	CNTNAP3B	43756731	0.000000	0.05858	0.000000	0.03702	0.466000	0.32739	0.894000	0.28350	-0.920000	0.03799	-0.506000	0.04501	GAC	A|0.002;C|0.002;G|0.995	0.002	strong		0.488	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
PTPN4	5775	hgsc.bcm.edu	37	2	120734589	120734589	+	Silent	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:120734589T>A	ENST00000263708.2	+	27	3495	c.2724T>A	c.(2722-2724)atT>atA	p.I908I	PTPN4_ENST00000544261.1_Silent_p.I541I	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	908	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)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	GTGAAGCTATTTTGAAAGTTT	0.328																																					p.I908I		Atlas-SNP	.											PTPN4,NS,carcinoma,+2,1	PTPN4	89	1	0			c.T2724A						PASS	.						53.0	54.0	54.0					2																	120734589		2202	4299	6501	SO:0001819	synonymous_variant	5775	exon27			AGCTATTTTGAAA		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.2724T>A	2.37:g.120734589T>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	133	51	0.383459	NM_002830	B2RBV8|Q9UDA7	Silent	SNP	ENST00000263708.2	37	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	T	4.925	0.171834	0.09391	.	.	ENSG00000088179	ENST00000441089	.	.	.	5.12	3.96	0.45880	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50048	-0.8873	4	.	.	.	.	6.0894	0.19985	0.1433:0.0767:0.0:0.78	.	.	.	.	I	201	.	.	F	+	1	0	PTPN4	120451059	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	2.465000	0.45075	0.798000	0.33994	0.528000	0.53228	TTT	.	.	none		0.328	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1269655	1269655	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1269655T>G	ENST00000529681.1	+	31	11603	c.11545T>G	c.(11545-11547)Tct>Gct	p.S3849A	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S3852A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3849	11 X approximate tandem repeats, Ser/Thr- rich.|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)		GGCCACCGGCTCTGTGGCCAC	0.642																																					p.S3849A		Atlas-SNP	.											.	MUC5B	473	.	0			c.T11545G						PASS	.						118.0	137.0	131.0					11																	1269655		2065	4172	6237	SO:0001583	missense	727897	exon31			ACCGGCTCTGTGG	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.11545T>G	11.37:g.1269655T>G	ENSP00000436812:p.Ser3849Ala	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	341	98	0.28739	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	1.973	-0.435940	0.04636	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21031	2.03;2.21	0.58	-1.16	0.09678	.	.	.	.	.	T	0.17152	0.0412	M	0.75264	2.295	0.09310	N	1	P;P	0.40476	0.718;0.718	B;B	0.28385	0.089;0.089	T	0.10154	-1.0642	9	0.87932	D	0	.	4.7328	0.12974	0.0:0.2164:0.0:0.7836	.	4377;3852	A7Y9J9;E9PBJ0	.;.	A	3849;3852;3793;3754	ENSP00000436812:S3849A;ENSP00000415793:S3852A	ENSP00000343037:S3793A	S	+	1	0	MUC5B	1226231	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-5.111000	0.00150	-0.567000	0.06046	0.163000	0.16589	TCT	.	.	none		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ZNF749	388567	hgsc.bcm.edu	37	19	57955885	57955885	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57955885C>G	ENST00000334181.4	+	3	1619	c.1369C>G	c.(1369-1371)Cag>Gag	p.Q457E	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	457					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.Q457E(1)|p.Q370E(1)		breast(1)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		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;0.0264)|Lung(386;0.177)		AGTTCAGCACCAGAAAATCCA	0.423																																					p.Q457E		Atlas-SNP	.											ZNF749,right_upper_lobe,carcinoma,0,14	ZNF749	75	14	2	Substitution - Missense(2)	endometrium(2)	c.C1369G						scavenged	.						92.0	89.0	90.0					19																	57955885		2203	4300	6503	SO:0001583	missense	388567	exon3			CAGCACCAGAAAA	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"""Zinc fingers, C2H2-type"", ""-"""	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.1369C>G	19.37:g.57955885C>G	ENSP00000333980:p.Gln457Glu	Somatic	239	2	0.0083682		WXS	Illumina HiSeq	Phase_I	197	3	0.0152284	NM_001023561		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	.	.	.	.	.	.	.	.	.	.	C	10.65	1.410685	0.25465	.	.	ENSG00000186230	ENST00000334181	T	0.07327	3.2	1.62	0.523	0.17060	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06826	0.0174	L	0.38649	1.16	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.33904	-0.9850	9	0.52906	T	0.07	.	5.9852	0.19430	0.5886:0.4114:0.0:0.0	.	457	O43361	ZN749_HUMAN	E	457	ENSP00000333980:Q457E	ENSP00000333980:Q457E	Q	+	1	0	ZNF749	62647697	.	.	0.001000	0.08648	0.750000	0.42670	.	.	0.202000	0.20498	0.650000	0.86243	CAG	.	.	none		0.423	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
LMAN1L	79748	hgsc.bcm.edu	37	15	75113023	75113023	+	Silent	SNP	G	G	A	rs145422132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75113023G>A	ENST00000309664.5	+	8	961	c.822G>A	c.(820-822)agG>agA	p.R274R	RP11-414J4.2_ENST00000564823.1_RNA|LMAN1L_ENST00000379709.3_Silent_p.R262R	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	274						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCCTGGCGAGGCAGCTGGAAG	0.602													G|||	47	0.00938498	0.0	0.0115	5008	,	,		20497	0.0		0.0298	False		,,,				2504	0.0092				p.R274R		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G822A						PASS	.	G		32,4362	37.6+/-69.7	0,32,2165	71.0	72.0	72.0		822	3.5	0.8	15	dbSNP_134	72	292,8300	107.4+/-168.2	4,284,4008	no	coding-synonymous	LMAN1L	NM_021819.2		4,316,6173	AA,AG,GG		3.3985,0.7283,2.495		274/527	75113023	324,12662	2197	4296	6493	SO:0001819	synonymous_variant	79748	exon8			GGCGAGGCAGCTG	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.822G>A	15.37:g.75113023G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	42	13	0.309524	NM_021819	Q6UWN2	Silent	SNP	ENST00000309664.5	37	CCDS10270.1																																																																																			G|0.980;A|0.020	0.020	strong		0.602	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		
PIK3R5	23533	hgsc.bcm.edu	37	17	8792171	8792171	+	Silent	SNP	T	T	C	rs11650737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	14	0	0		WXS	Illumina HiSeq	Phase_I	10	10	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	
RSC1A1	6248	hgsc.bcm.edu	37	1	15986547	15986547	+	Missense_Mutation	SNP	T	T	C	rs3766163	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15986547T>C	ENST00000345034.1	+	1	184	c.184T>C	c.(184-186)Ttc>Ctc	p.F62L	DDI2_ENST00000480945.1_3'UTR	NM_006511.1	NP_006502.1	Q92681	RSCA1_HUMAN	regulatory solute carrier protein, family 1, member 1	62			F -> L (in dbSNP:rs3766163). {ECO:0000269|PubMed:14702039}.		intestinal absorption (GO:0050892)|negative regulation of transport (GO:0051051)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	brush border (GO:0005903)|cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel inhibitor activity (GO:0008200)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)	11		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00276)|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)		TTCAGCTGAATTCCAGCTAAA	0.458													T|||	1256	0.250799	0.4478	0.2176	5008	,	,		21772	0.0317		0.2694	False		,,,				2504	0.2147				p.F62L		Atlas-SNP	.											.	RSC1A1	29	.	0			c.T184C						PASS	.	T	LEU/PHE,	1830,2576	536.1+/-374.4	405,1020,778	125.0	131.0	129.0		184,	4.5	1.0	1	dbSNP_107	129	2425,6175	400.9+/-346.9	324,1777,2199	yes	missense,utr-3	RSC1A1,DDI2	NM_006511.1,NM_032341.4	22,	729,2797,2977	CC,CT,TT		28.1977,41.5343,32.7157	benign,	62/618,	15986547	4255,8751	2203	4300	6503	SO:0001583	missense	6248	exon1			GCTGAATTCCAGC	BN000122, X82877	CCDS161.1	1p36.1	1998-08-25			ENSG00000215695	ENSG00000215695			10458	protein-coding gene	gene with protein product		601966					Standard	NM_006511		Approved	RS1	uc010obn.2	Q92681	OTTHUMG00000067830	ENST00000345034.1:c.184T>C	1.37:g.15986547T>C	ENSP00000341963:p.Phe62Leu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	62	19	0.306452	NM_006511	B2RBP5	Missense_Mutation	SNP	ENST00000345034.1	37	CCDS161.1	536	0.2454212454212454	211	0.42886178861788615	102	0.281767955801105	23	0.04020979020979021	200	0.2638522427440633	T	3.705	-0.060682	0.07317	0.415343	0.281977	ENSG00000215695	ENST00000345034	T	0.39229	1.09	5.61	4.48	0.54585	.	0.276090	0.25971	N	0.027139	T	0.00012	0.0000	N	0.19112	0.55	0.36160	P	0.15193	B	0.17268	0.021	B	0.15484	0.013	T	0.40040	-0.9584	9	0.02654	T	1	-23.5652	8.289	0.31946	0.0:0.1583:0.0:0.8417	rs3766163;rs59513823;rs3766163	62	Q92681	RSCA1_HUMAN	L	62	ENSP00000341963:F62L	ENSP00000341963:F62L	F	+	1	0	RSC1A1	15859134	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	1.411000	0.34702	0.966000	0.38159	0.459000	0.35465	TTC	T|0.708;C|0.292	0.292	strong		0.458	RSC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145500.1	NM_006511	
ERAP1	51752	hgsc.bcm.edu	37	5	96130836	96130836	+	Missense_Mutation	SNP	T	T	C	rs26618	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:96130836T>C	ENST00000443439.2	-	5	894	c.828A>G	c.(826-828)atA>atG	p.I276M	ERAP1_ENST00000296754.3_Missense_Mutation_p.I276M	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	276			I -> M (in dbSNP:rs26618).		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)		CTGCTTGATTTATCTTGTCTG	0.403													T|||	1135	0.226637	0.1959	0.1441	5008	,	,		20699	0.2857		0.2187	False		,,,				2504	0.274				p.I276M		Atlas-SNP	.											.	ERAP1	59	.	0			c.A828G	GRCh37	CM020527	ERAP1	M	rs26618	PASS	.	T	MET/ILE,MET/ILE,MET/ILE	889,3517	342.8+/-307.3	73,743,1387	72.0	66.0	68.0		828,828,828	-0.2	1.0	5	dbSNP_76	68	1965,6635	344.4+/-325.3	230,1505,2565	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	10,10,10	303,2248,3952	CC,CT,TT		22.8488,20.177,21.9437	possibly-damaging,possibly-damaging,possibly-damaging	276/942,276/942,276/949	96130836	2854,10152	2203	4300	6503	SO:0001583	missense	51752	exon5			TTGATTTATCTTG	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.828A>G	5.37:g.96130836T>C	ENSP00000406304:p.Ile276Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	456	0.2087912087912088	100	0.2032520325203252	55	0.15193370165745856	135	0.23601398601398602	166	0.21899736147757257	T	17.12	3.308085	0.60305	0.20177	0.228488	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.02916	4.11;4.11	5.71	-0.178	0.13303	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.85462	2.755	0.22896	P	0.99859659	P;P;P	0.47106	0.89;0.774;0.732	P;P;P	0.52031	0.593;0.688;0.561	T	0.30736	-0.9968	9	0.51188	T	0.08	.	10.711	0.45984	0.1063:0.0:0.5215:0.3722	rs26618;rs52799291;rs59427621;rs26618	276;276;276	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	M	276	ENSP00000296754:I276M;ENSP00000406304:I276M	ENSP00000296754:I276M	I	-	3	3	ERAP1	96156592	0.074000	0.21230	0.984000	0.44739	0.976000	0.68499	-0.670000	0.05256	0.044000	0.15775	0.528000	0.53228	ATA	T|0.783;C|0.217	0.217	strong		0.403	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
R3HDM4	91300	hgsc.bcm.edu	37	19	899444	899444	+	Silent	SNP	C	C	T	rs2965284	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:899444C>T	ENST00000361574.5	-	7	772	c.699G>A	c.(697-699)tcG>tcA	p.S233S	R3HDM4_ENST00000587975.1_Silent_p.S212S	NM_138774.3	NP_620129.2	Q96D70	R3HD4_HUMAN	R3H domain containing 4	233	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)										ACTTACTGGCCGAGATGAGGT	0.657													C|||	408	0.0814696	0.0159	0.1081	5008	,	,		12934	0.0109		0.1809	False		,,,				2504	0.1217				p.S233S		Atlas-SNP	.											C19orf22,NS,carcinoma,0,1	.	.	1	0			c.G699A						PASS	.	C		177,4229	114.6+/-152.6	5,167,2031	46.0	47.0	47.0		699	-7.7	1.0	19	dbSNP_101	47	1656,6944	300.6+/-305.0	170,1316,2814	no	coding-synonymous	C19orf22	NM_138774.3		175,1483,4845	TT,TC,CC		19.2558,4.0172,14.0935		233/269	899444	1833,11173	2203	4300	6503	SO:0001819	synonymous_variant	91300	exon7			ACTGGCCGAGATG	BC012775	CCDS12048.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000198858	ENSG00000198858			28270	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 22"""	C19orf22		12477932	Standard	NM_138774		Approved	MGC16353	uc002lqg.2	Q96D70		ENST00000361574.5:c.699G>A	19.37:g.899444C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_138774		Silent	SNP	ENST00000361574.5	37	CCDS12048.1																																																																																			C|0.877;T|0.123	0.123	strong		0.657	R3HDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458209.1	NM_138774	
MED12	9968	hgsc.bcm.edu	37	X	70351982	70351982	+	Silent	SNP	A	A	C	rs376058351		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:70351982A>C	ENST00000374080.3	+	30	4211	c.4179A>C	c.(4177-4179)tcA>tcC	p.S1393S	MED12_ENST00000374102.1_Silent_p.S1393S|MED12_ENST00000333646.6_Silent_p.S1393S			Q93074	MED12_HUMAN	mediator complex subunit 12	1393					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)					TCCAACAGTCAGCAGAGACAG	0.512			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.S1393S		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A4179C						PASS	.	A		0,3657		0,0,1543,571	83.0	76.0	78.0		4179	-8.8	0.4	X		78	2,6605		0,2,2395,1813	no	coding-synonymous	MED12	NM_005120.2		0,2,3938,2384	CC,CA,AA,A		0.0303,0.0,0.0195		1393/2178	70351982	2,10262	2114	4210	6324	SO:0001819	synonymous_variant	9968	exon30			ACAGTCAGCAGAG	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.4179A>C	X.37:g.70351982A>C		Somatic	429	0	0		WXS	Illumina HiSeq	Phase_I	213	207	0.971831	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1																																																																																			.	.	weak		0.512	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
TYRO3	7301	hgsc.bcm.edu	37	15	41857303	41857303	+	Silent	SNP	T	T	C	rs2277536	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	67	0	0		WXS	Illumina HiSeq	Phase_I	47	32	0.680851	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		
MICAL2	9645	hgsc.bcm.edu	37	11	12229655	12229655	+	Silent	SNP	T	T	G	rs2279390	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:12229655T>G	ENST00000256194.4	+	5	846	c.558T>G	c.(556-558)gtT>gtG	p.V186V	MICAL2_ENST00000527195.1_3'UTR|MICAL2_ENST00000379612.3_Silent_p.V186V|MICAL2_ENST00000527546.1_Silent_p.V186V|MICAL2_ENST00000342902.5_Silent_p.V186V|MICAL2_ENST00000537344.1_Silent_p.V186V	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	186	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|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)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		TCGTGAAGGTTCTAGAGCCTC	0.423													T|||	2012	0.401757	0.4856	0.245	5008	,	,		20845	0.501		0.2584	False		,,,				2504	0.4448				p.V186V		Atlas-SNP	.											.	MICAL2	114	.	0			c.T558G						PASS	.	T		2029,2373	564.5+/-381.5	461,1107,633	185.0	169.0	174.0		558	-0.9	0.7	11	dbSNP_100	174	2028,6560	354.2+/-329.4	230,1568,2496	no	coding-synonymous	MICAL2	NM_014632.2		691,2675,3129	GG,GT,TT		23.6143,46.0927,31.2317		186/1125	12229655	4057,8933	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon5			GAAGGTTCTAGAG	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.558T>G	11.37:g.12229655T>G		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	211	113	0.535545	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			G|0.341;N|0.000	0.341	strong		0.423	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
FRMD1	79981	hgsc.bcm.edu	37	6	168479568	168479568	+	Silent	SNP	G	G	A	rs78152017	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168479568G>A	ENST00000283309.6	-	1	271	c.207C>T	c.(205-207)gcC>gcT	p.A69A		NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	69	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)		TCACCCCCACGGCCAGCCGCA	0.706													G|||	506	0.101038	0.1051	0.0807	5008	,	,		13489	0.1181		0.0676	False		,,,				2504	0.1268				p.A69A	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C207T						PASS	.	G		389,4015		15,359,1828	47.0	55.0	52.0		207	-5.8	0.1	6	dbSNP_131	52	685,7905		29,627,3639	no	coding-synonymous	FRMD1	NM_024919.3		44,986,5467	AA,AG,GG		7.9744,8.8329,8.2654		69/550	168479568	1074,11920	2202	4295	6497	SO:0001819	synonymous_variant	79981	exon1			CCCCACGGCCAGC		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.207C>T	6.37:g.168479568G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Silent	SNP	ENST00000283309.6	37	CCDS5306.1																																																																																			G|0.913;A|0.087	0.087	strong		0.706	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
TEKT5	146279	hgsc.bcm.edu	37	16	10775855	10775855	+	Silent	SNP	G	G	A	rs71389065|rs12918646	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:10775855G>A	ENST00000283025.2	-	4	929	c.858C>T	c.(856-858)gaC>gaT	p.D286D		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	286						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						CTTACGTGCCGTCAATTTTCT	0.542													G|||	1476	0.294728	0.143	0.4006	5008	,	,		21540	0.5446		0.159	False		,,,				2504	0.3067				p.D286D		Atlas-SNP	.											TEKT5,pharynx,carcinoma,-2,1	TEKT5	66	1	0			c.C858T						scavenged	.	G		720,3674	298.7+/-285.4	72,576,1549	252.0	191.0	212.0		858	-4.4	0.3	16	dbSNP_121	212	1634,6966	298.2+/-303.8	162,1310,2828	no	coding-synonymous	TEKT5	NM_144674.1		234,1886,4377	AA,AG,GG		19.0,16.386,18.1161		286/486	10775855	2354,10640	2197	4300	6497	SO:0001819	synonymous_variant	146279	exon4			CGTGCCGTCAATT		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.858C>T	16.37:g.10775855G>A		Somatic	164	2	0.0121951		WXS	Illumina HiSeq	Phase_I	151	67	0.443709	NM_144674	A1L3Z3	Silent	SNP	ENST00000283025.2	37	CCDS10542.1																																																																																			ATG|0.500;GTC|0.500	.	alt		0.542	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
EVI5	7813	hgsc.bcm.edu	37	1	93073228	93073228	+	Missense_Mutation	SNP	C	C	A	rs11808092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:93073228C>A	ENST00000370331.1	-	15	1845	c.1836G>T	c.(1834-1836)caG>caT	p.Q612H	EVI5_ENST00000543509.1_Missense_Mutation_p.Q623H|EVI5_ENST00000491940.1_5'UTR|EVI5_ENST00000540033.1_Missense_Mutation_p.Q612H	NM_005665.4	NP_005656.4	O60447	EVI5_HUMAN	ecotropic viral integration site 5	612	Dimerization.|Interaction with AURKB and INCENP.|Targeting to the centrosomes.		Q -> H (in dbSNP:rs11808092).		cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|retrograde transport, endosome to Golgi (GO:0042147)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(1)|skin(1)	38		all_lung(203;0.00146)|Lung NSC(277;0.00565)|all_neural(321;0.185)|Melanoma(281;0.193)|Glioma(108;0.203)		Epithelial(280;8.09e-25)|OV - Ovarian serous cystadenocarcinoma(397;1.27e-22)|all cancers(265;1.74e-21)|GBM - Glioblastoma multiforme(16;0.00233)|BRCA - Breast invasive adenocarcinoma(282;0.211)		GCACTTTCTCCTGTAGGCTAA	0.368													C|||	618	0.123403	0.0696	0.1873	5008	,	,		15421	0.0159		0.2744	False		,,,				2504	0.1063				p.Q612H		Atlas-SNP	.											.	EVI5	94	.	0			c.G1836T						PASS	.	C	HIS/GLN	467,3937	219.1+/-236.9	21,425,1756	175.0	155.0	162.0		1836	4.7	1.0	1	dbSNP_120	162	2206,6392	374.7+/-337.5	283,1640,2376	yes	missense	EVI5	NM_005665.4	24	304,2065,4132	AA,AC,CC		25.6571,10.604,20.5584	benign	612/811	93073228	2673,10329	2202	4299	6501	SO:0001583	missense	7813	exon15			TTTCTCCTGTAGG	AF008915	CCDS30774.1	1p22	2013-07-09			ENSG00000067208	ENSG00000067208			3501	protein-coding gene	gene with protein product	"""neuroblastoma stage 4S gene"""	602942				9618176	Standard	XM_005271180		Approved	NB4S	uc001dox.3	O60447	OTTHUMG00000010895	ENST00000370331.1:c.1836G>T	1.37:g.93073228C>A	ENSP00000359356:p.Gln612His	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_005665	A6NKX8|B9A6J0|Q9H1Y9	Missense_Mutation	SNP	ENST00000370331.1	37	CCDS30774.1	322	0.14743589743589744	28	0.056910569105691054	80	0.22099447513812154	13	0.022727272727272728	201	0.26517150395778366	C	16.26	3.071826	0.55646	0.10604	0.256571	ENSG00000067208	ENST00000370331;ENST00000540033;ENST00000543509	T;T;T	0.33654	1.4;1.4;1.4	5.59	4.67	0.58626	.	0.066222	0.64402	N	0.000007	T	0.31420	0.0796	M	0.74258	2.255	0.20873	P	0.999833227	P;B	0.37276	0.589;0.003	B;B	0.44044	0.439;0.008	T	0.34129	-0.9841	9	0.56958	D	0.05	-3.3187	10.7489	0.46198	0.0:0.7959:0.1332:0.0709	rs11808092;rs17380490;rs52824058;rs56783586;rs11808092	623;612	F5H4R0;O60447	.;EVI5_HUMAN	H	612;612;623	ENSP00000359356:Q612H;ENSP00000440826:Q612H;ENSP00000445019:Q623H	ENSP00000359356:Q612H	Q	-	3	2	EVI5	92845816	0.999000	0.42202	1.000000	0.80357	0.971000	0.66376	0.689000	0.25437	1.342000	0.45619	0.655000	0.94253	CAG	C|0.826;A|0.174	0.174	strong		0.368	EVI5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030047.1	NM_005665	
CIB2	10518	hgsc.bcm.edu	37	15	78401620	78401620	+	Silent	SNP	C	C	T	rs77370542	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:78401620C>T	ENST00000258930.3	-	4	631	c.303G>A	c.(301-303)tcG>tcA	p.S101S	CIB2_ENST00000557846.1_Silent_p.S52S|CIB2_ENST00000539011.1_Silent_p.S58S|CIB2_ENST00000560618.1_Silent_p.S58S	NM_006383.2	NP_006374.1	O75838	CIB2_HUMAN	calcium and integrin binding family member 2	101	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion homeostasis (GO:0055074)|photoreceptor cell maintenance (GO:0045494)	blood microparticle (GO:0072562)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|photoreceptor inner segment (GO:0001917)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	11						CTCGGGGAGCCGACTCGCAGA	0.552													C|||	59	0.0117812	0.0015	0.0187	5008	,	,		17572	0.0		0.0417	False		,,,				2504	0.002				p.S101S		Atlas-SNP	.											CIB2,NS,carcinoma,-1,1	CIB2	24	1	0			c.G303A						scavenged	.	C		23,4369	29.9+/-59.1	0,23,2173	99.0	86.0	90.0		303	-6.4	0.2	15	dbSNP_132	90	308,8278	110.8+/-171.2	6,296,3991	no	coding-synonymous	CIB2	NM_006383.2		6,319,6164	TT,TC,CC		3.5872,0.5237,2.5505		101/188	78401620	331,12647	2196	4293	6489	SO:0001819	synonymous_variant	10518	exon4			GGGAGCCGACTCG	BC047381	CCDS10296.1, CCDS61722.1, CCDS61723.1	15q24	2013-01-10			ENSG00000136425	ENSG00000136425		"""EF-hand domain containing"""	24579	protein-coding gene	gene with protein product		605564	"""deafness, autosomal recessive 48"", ""Usher syndrome 1J (autosomal recessive)"""	DFNB48, USH1J		9931475, 23023331	Standard	NM_006383		Approved	KIP2	uc002bdb.2	O75838	OTTHUMG00000143731	ENST00000258930.3:c.303G>A	15.37:g.78401620C>T		Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	86	16	0.186047	NM_006383	B4DDF0|H0YM71|Q05BT6	Silent	SNP	ENST00000258930.3	37	CCDS10296.1																																																																																			C|0.978;T|0.022	0.022	strong		0.552	CIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289798.1	NM_006383	
C1orf43	25912	hgsc.bcm.edu	37	1	154184993	154184993	+	Missense_Mutation	SNP	G	G	A	rs144385115	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154184993G>A	ENST00000368521.5	-	5	646	c.448C>T	c.(448-450)Cgc>Tgc	p.R150C	C1orf43_ENST00000350592.3_Missense_Mutation_p.R116C|C1orf43_ENST00000368519.1_Missense_Mutation_p.R132C|C1orf43_ENST00000368516.1_Missense_Mutation_p.R116C|C1orf43_ENST00000362076.4_Missense_Mutation_p.R98C|C1orf43_ENST00000368518.1_Missense_Mutation_p.R150C	NM_001098616.1	NP_001092086.1	Q9BWL3	CA043_HUMAN	chromosome 1 open reading frame 43	150						integral component of membrane (GO:0016021)	coenzyme binding (GO:0050662)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	10	all_lung(78;1.98e-30)|Lung NSC(65;2.87e-28)|Hepatocellular(266;0.0877)					AGTGCTTTGCGTACACCCTTG	0.498													G|||	22	0.00439297	0.0008	0.0101	5008	,	,		19963	0.0		0.0119	False		,,,				2504	0.002				p.R150C		Atlas-SNP	.											.	C1orf43	36	.	0			c.C448T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	90.0	82.0	85.0		448,346,292	3.5	1.0	1	dbSNP_134	85	70,8530	41.7+/-99.0	0,70,4230	yes	missense,missense,missense	C1orf43	NM_001098616.1,NM_015449.2,NM_138740.2	180,180,180	0,76,6427	AA,AG,GG		0.814,0.1362,0.5843	benign,benign,benign	150/254,116/220,98/202	154184993	76,12930	2203	4300	6503	SO:0001583	missense	25912	exon5			CTTTGCGTACACC	AF077036	CCDS1061.1, CCDS1062.1, CCDS41404.1, CCDS72924.1	1q21.2	2012-06-25			ENSG00000143612	ENSG00000143612			29876	protein-coding gene	gene with protein product						11042152, 11230159	Standard	XM_005245077		Approved	NICE-3, DKFZp586G1722	uc001fei.2	Q9BWL3	OTTHUMG00000035981	ENST00000368521.5:c.448C>T	1.37:g.154184993G>A	ENSP00000357507:p.Arg150Cys	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	156	84	0.538462	NM_001098616	A8K3G8|D3DV72|D3DV74|Q5M801|Q5VU73|Q5VU83|Q96HP7|Q9UFU2|Q9UGL7|Q9UGL8|Q9Y2R6	Missense_Mutation	SNP	ENST00000368521.5	37	CCDS41404.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	G	15.45	2.837975	0.50951	0.001362	0.00814	ENSG00000143612	ENST00000350592;ENST00000368521;ENST00000362076;ENST00000368519;ENST00000368518;ENST00000368516	.	.	.	5.39	3.5	0.40072	Dehydrogenase, multihelical (1);	0.150760	0.64402	D	0.000008	T	0.32466	0.0830	L	0.58101	1.795	0.53005	D	0.999961	B;B;B;B;B	0.14012	0.007;0.007;0.004;0.003;0.009	B;B;B;B;B	0.14023	0.002;0.002;0.01;0.002;0.003	T	0.31503	-0.9941	9	0.54805	T	0.06	-17.9839	5.6172	0.17438	0.0749:0.1395:0.6412:0.1444	.	132;116;150;98;116	Q9BWL3-5;Q9BWL3-2;Q9BWL3;Q9BWL3-4;Q09GN0	.;.;CA043_HUMAN;.;.	C	116;150;98;132;150;116	.	ENSP00000271925:R116C	R	-	1	0	C1orf43	152451617	1.000000	0.71417	0.998000	0.56505	0.792000	0.44763	4.784000	0.62411	0.821000	0.34540	0.585000	0.79938	CGC	G|0.994;A|0.006	0.006	strong		0.498	C1orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087664.2	NM_015449	
TTN	7273	hgsc.bcm.edu	37	2	179432185	179432185	+	Missense_Mutation	SNP	A	A	G	rs12463674	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179432185A>G	ENST00000591111.1	-	276	73975	c.73751T>C	c.(73750-73752)aTt>aCt	p.I24584T	TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I26225T|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I23657T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I17160T|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I17285T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I17352T			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	109	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	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	
CTSW	1521	hgsc.bcm.edu	37	11	65650883	65650883	+	Silent	SNP	A	A	G	rs35841983	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65650883A>G	ENST00000307886.3	+	9	1054	c.1008A>G	c.(1006-1008)caA>caG	p.Q336Q	CTSW_ENST00000528419.1_Silent_p.Q336Q|FIBP_ENST00000426652.2_5'Flank	NM_001335.3	NP_001326	P56202	CATW_HUMAN	cathepsin W	336					immune response (GO:0006955)	membrane (GO:0016020)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)	9				READ - Rectum adenocarcinoma(159;0.168)		GGGGGGCCCAATGGGGAGAGA	0.602													A|||	89	0.0177716	0.0416	0.0159	5008	,	,		14914	0.0		0.0229	False		,,,				2504	0.0				p.Q336Q		Atlas-SNP	.											.	CTSW	18	.	0			c.A1008G						PASS	.	A		125,4277	94.8+/-133.5	3,119,2079	67.0	73.0	71.0		1008	-10.0	0.0	11	dbSNP_126	71	243,8349	97.7+/-159.3	3,237,4056	no	coding-synonymous	CTSW	NM_001335.3		6,356,6135	GG,GA,AA		2.8282,2.8396,2.8321		336/377	65650883	368,12626	2201	4296	6497	SO:0001819	synonymous_variant	1521	exon9			GGCCCAATGGGGA	AF055903	CCDS8117.1	11q13.1	2008-02-01	2006-12-05		ENSG00000172543	ENSG00000172543		"""Cathepsins"""	2546	protein-coding gene	gene with protein product		602364	"""cathepsin W (lymphopain)"""			9108299, 9675123	Standard	NM_001335		Approved		uc001ogc.1	P56202	OTTHUMG00000166663	ENST00000307886.3:c.1008A>G	11.37:g.65650883A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_001335	Q86VT4	Silent	SNP	ENST00000307886.3	37	CCDS8117.1																																																																																			A|0.975;G|0.025	0.025	strong		0.602	CTSW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391042.1	NM_001335	
ZNF831	128611	hgsc.bcm.edu	37	20	57768743	57768743	+	Missense_Mutation	SNP	C	C	T	rs56057707	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:57768743C>T	ENST00000371030.2	+	1	2669	c.2669C>T	c.(2668-2670)gCt>gTt	p.A890V		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	890							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)					TTGGCTGCTGCTTCTGTTGCC	0.677													.|||	881	0.175919	0.0802	0.2378	5008	,	,		14502	0.2728		0.1899	False		,,,				2504	0.1472				p.A890V		Atlas-SNP	.											.	ZNF831	287	.	0			c.C2669T						PASS	.	C	VAL/ALA	332,3604		16,300,1652	26.0	29.0	28.0		2669	2.8	0.0	20	dbSNP_129	28	1543,6783		139,1265,2759	yes	missense	ZNF831	NM_178457.1	64	155,1565,4411	TT,TC,CC		18.5323,8.435,15.2911	benign	890/1678	57768743	1875,10387	1968	4163	6131	SO:0001583	missense	128611	exon1			CTGCTGCTTCTGT	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.2669C>T	20.37:g.57768743C>T	ENSP00000360069:p.Ala890Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	397	0.18177655677655677	42	0.08536585365853659	78	0.2154696132596685	120	0.2097902097902098	157	0.20712401055408972	C	7.450	0.642402	0.14451	0.08435	0.185323	ENSG00000124203	ENST00000371030	T	0.04654	3.58	3.75	2.79	0.32731	.	1.781660	0.02972	N	0.144512	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	0.45963	-0.9225	9	0.02654	T	1	12.0247	11.476	0.50297	0.1814:0.8186:0.0:0.0	rs56057707;rs61742491	890	Q5JPB2	ZN831_HUMAN	V	890	ENSP00000360069:A890V	ENSP00000360069:A890V	A	+	2	0	ZNF831	57202138	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.376000	0.07465	0.210000	0.20664	-0.808000	0.03180	GCT	C|0.821;T|0.179	0.179	strong		0.677	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
RAG1	5896	hgsc.bcm.edu	37	11	36597313	36597313	+	Missense_Mutation	SNP	A	A	G	rs2227973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	114	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	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	
HTR3B	9177	hgsc.bcm.edu	37	11	113803108	113803108	+	Missense_Mutation	SNP	A	A	C	rs72466469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:113803108A>C	ENST00000260191.2	+	5	723	c.466A>C	c.(466-468)Agt>Cgt	p.S156R	HTR3B_ENST00000537778.1_Missense_Mutation_p.S145R	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	156			S -> R (in dbSNP:rs72466469). {ECO:0000269|PubMed:15293096, ECO:0000269|PubMed:15389765, ECO:0000269|PubMed:21179162}.		cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ion channel activity (GO:0005216)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(11)	20		all_cancers(61;6.81e-18)|all_epithelial(67;6.67e-11)|all_hematologic(158;4.67e-05)|Melanoma(852;0.000316)|Acute lymphoblastic leukemia(157;0.000976)|Breast(348;0.0101)|Prostate(24;0.0154)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;3.04e-06)|Epithelial(105;1.98e-05)|all cancers(92;0.000201)|OV - Ovarian serous cystadenocarcinoma(223;0.151)	Ergoloid mesylate(DB01049)	CTCTGCGTGCAGTTTAGAGAC	0.438													A|||	9	0.00179712	0.0	0.0043	5008	,	,		21219	0.0		0.006	False		,,,				2504	0.0				p.S156R		Atlas-SNP	.											.	HTR3B	50	.	0			c.A466C	GRCh37	CM083528	HTR3B	M	rs72466469	PASS	.	A	ARG/SER	2,4400	2.1+/-5.4	0,2,2199	179.0	153.0	162.0		466	0.7	0.2	11	dbSNP_130	162	69,8523	41.7+/-99.0	2,65,4229	yes	missense	HTR3B	NM_006028.4	110	2,67,6428	CC,CA,AA		0.8031,0.0454,0.5464	possibly-damaging	156/442	113803108	71,12923	2201	4296	6497	SO:0001583	missense	9177	exon5			GCGTGCAGTTTAG	AF080582	CCDS8364.1	11q23.1	2012-05-22	2012-02-03		ENSG00000149305	ENSG00000149305		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5298	protein-coding gene	gene with protein product		604654	"""5-hydroxytryptamine (serotonin) receptor 3B"""			9950429, 10521471	Standard	NM_006028		Approved	5-HT3B	uc001pok.3	O95264	OTTHUMG00000168210	ENST00000260191.2:c.466A>C	11.37:g.113803108A>C	ENSP00000260191:p.Ser156Arg	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	345	220	0.637681	NM_006028	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	CCDS8364.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	A	16.36	3.101980	0.56183	4.54E-4	0.008031	ENSG00000149305	ENST00000260191;ENST00000537778	T;T	0.79554	-1.28;-1.28	5.82	0.729	0.18266	Neurotransmitter-gated ion-channel ligand-binding (3);	0.421195	0.29473	N	0.012047	T	0.75317	0.3833	L	0.52905	1.665	0.33014	D	0.527966	D;P	0.56287	0.975;0.934	P;P	0.59643	0.861;0.643	T	0.77107	-0.2710	10	0.37606	T	0.19	-0.5361	4.9411	0.13965	0.6577:0.0:0.2158:0.1265	.	145;156	O95264-2;O95264	.;5HT3B_HUMAN	R	156;145	ENSP00000260191:S156R;ENSP00000443118:S145R	ENSP00000260191:S156R	S	+	1	0	HTR3B	113308318	0.181000	0.23161	0.166000	0.22797	0.877000	0.50540	0.873000	0.28052	0.144000	0.18951	-0.376000	0.06991	AGT	A|0.996;C|0.004	0.004	strong		0.438	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028	
OSGIN1	29948	hgsc.bcm.edu	37	16	83998922	83998922	+	Silent	SNP	G	G	A	rs146347192		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:83998922G>A	ENST00000343939.2	+	7	1376	c.993G>A	c.(991-993)acG>acA	p.T331T	OSGIN1_ENST00000361711.3_Silent_p.T248T|OSGIN1_ENST00000393306.1_Silent_p.T248T			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	331					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						CCACAGGCACGTTCGACAGCC	0.697																																					p.T248T		Atlas-SNP	.											OSGIN1,NS,carcinoma,+2,1	OSGIN1	33	1	0			c.G744A						scavenged	.	G	,,	0,4398		0,0,2199	26.0	31.0	29.0		993,744,744	-8.1	0.0	16	dbSNP_134	29	2,8580		0,2,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	,,	0,2,6488	AA,AG,GG		0.0233,0.0,0.0154	,,	331/561,248/478,248/478	83998922	2,12978	2199	4291	6490	SO:0001819	synonymous_variant	29948	exon6			AGGCACGTTCGAC	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.993G>A	16.37:g.83998922G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	28	4	0.142857	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	37																																																																																				G|1.000;A|0.000	0.000	weak		0.697	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
SEC31B	25956	hgsc.bcm.edu	37	10	102265815	102265815	+	Silent	SNP	A	A	G	rs2295773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102265815A>G	ENST00000370345.3	-	9	1123	c.1026T>C	c.(1024-1026)caT>caC	p.H342H	SEC31B_ENST00000535773.1_Silent_p.H185H|SEC31B_ENST00000370329.5_Silent_p.H345H|SEC31B_ENST00000451524.1_Silent_p.H342H	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	342					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CCTGTCTCATATGCTGGACTT	0.542													G|||	927	0.185104	0.1997	0.1844	5008	,	,		19940	0.1319		0.1909	False		,,,				2504	0.2147				p.H342H		Atlas-SNP	.											SEC31B,colon,carcinoma,-2,1	SEC31B	84	1	0			c.T1026C						PASS	.	G		858,3548	744.3+/-411.5	86,686,1431	183.0	186.0	185.0		1026	3.1	1.0	10	dbSNP_100	185	1893,6707	728.3+/-406.7	216,1461,2623	no	coding-synonymous	SEC31B	NM_015490.3		302,2147,4054	GG,GA,AA		22.0116,19.4734,21.1518		342/1180	102265815	2751,10255	2203	4300	6503	SO:0001819	synonymous_variant	25956	exon9			TCTCATATGCTGG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.1026T>C	10.37:g.102265815A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	104	76	0.730769	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	37	CCDS7495.1																																																																																			A|0.807;G|0.193	0.193	strong		0.542	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188356	140188356	+	Silent	SNP	A	A	G	rs144593807	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA4_ENST00000356878.4_Silent_p.L528L|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.L528L	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	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(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)			ACGAGGAGCTAGAGCTGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17817	0.0		0.0755	False		,,,				2504	0.0082				p.L528L		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	0			c.A1584G						PASS	.	A	,,,,,	11,4395		0,11,2192	70.0	75.0	73.0		,,,1584,,1584	1.3	1.0	5	dbSNP_134	73	57,8543		9,39,4252	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	9,50,6444	GG,GA,AA		0.6628,0.2497,0.5228	,,,,,	,,,528/948,,528/799	140188356	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			GGAGCTAGAGCTG	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.1584A>G	5.37:g.140188356A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	63	11	0.174603	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			A|0.976;G|0.024	0.024	strong		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
TIAM2	26230	hgsc.bcm.edu	37	6	155577823	155577823	+	Silent	SNP	C	C	T	rs1571766	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:155577823C>T	ENST00000461783.3	+	29	5947	c.4674C>T	c.(4672-4674)gcC>gcT	p.A1558A	TIAM2_ENST00000528391.2_Silent_p.A902A|TIAM2_ENST00000318981.5_Silent_p.A1558A|TIAM2_ENST00000360366.4_Silent_p.A1582A|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000456144.1_Silent_p.A1587A|TIAM2_ENST00000529824.2_Silent_p.A1587A|TIAM2_ENST00000456877.2_Silent_p.A870A|TIAM2_ENST00000367174.2_Silent_p.A934A|TIAM2_ENST00000275246.7_Silent_p.A483A			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1558					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)		CAGATTTTGCCGACAATCTCA	0.567													c|||	3748	0.748403	0.7179	0.7522	5008	,	,		18421	0.9851		0.5954	False		,,,				2504	0.7004				p.A1558A		Atlas-SNP	.											.	TIAM2	161	.	0			c.C4674T						PASS	.	T	,,	3127,1279	697.4+/-406.2	1102,923,178	48.0	49.0	49.0		1449,4674,	-11.7	0.0	6	dbSNP_88	49	5116,3484	632.2+/-398.6	1530,2056,714	no	coding-synonymous,coding-synonymous,utr-3	TIAM2,TFB1M	NM_001010927.2,NM_012454.3,NM_016020.3	,,	2632,2979,892	TT,TC,CC		40.5116,29.0286,36.6216	,,	483/627,1558/1702,	155577823	8243,4763	2203	4300	6503	SO:0001819	synonymous_variant	26230	exon26			TTTTGCCGACAAT		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.4674C>T	6.37:g.155577823C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	174	91	0.522988	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																			C|0.328;T|0.672	0.672	strong		0.567	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
OR4D2	124538	hgsc.bcm.edu	37	17	56247306	56247306	+	Missense_Mutation	SNP	G	G	C	rs80043692	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:56247306G>C	ENST00000545221.1	+	1	290	c.290G>C	c.(289-291)tGc>tCc	p.C97S		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	97						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						TACCAGGGCTGCATGGGTCAG	0.527													G|||	439	0.0876597	0.1354	0.0346	5008	,	,		20459	0.002		0.1153	False		,,,				2504	0.1207				p.C97S		Atlas-SNP	.											OR4D2,NS,haematopoietic_neoplasm,0,1	OR4D2	48	1	0			c.G290C						PASS	.	G	SER/CYS	555,3851	252.4+/-258.8	38,479,1686	113.0	103.0	106.0		290	5.7	1.0	17	dbSNP_132	106	964,7636	209.4+/-250.6	53,858,3389	yes	missense	OR4D2	NM_001004707.3	112	91,1337,5075	CC,CG,GG		11.2093,12.5965,11.6792	probably-damaging	97/308	56247306	1519,11487	2203	4300	6503	SO:0001583	missense	124538	exon1			AGGGCTGCATGGG		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.290G>C	17.37:g.56247306G>C	ENSP00000441354:p.Cys97Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	37	CCDS32688.1	172	0.07875457875457875	66	0.13414634146341464	10	0.027624309392265192	1	0.0017482517482517483	95	0.12532981530343007	G	20.4	3.976158	0.74360	0.125965	0.112093	ENSG00000255713	ENST00000545221	T	0.00540	6.7	5.71	5.71	0.89125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000011	T	0.00039	0.0001	H	0.96365	3.81	0.09310	P	0.99999683858	D	0.89917	1.0	D	0.87578	0.998	T	0.02126	-1.1209	9	0.87932	D	0	-25.7473	17.7074	0.88312	0.0:0.0:1.0:0.0	.	97	P58180	OR4D2_HUMAN	S	97	ENSP00000441354:C97S	ENSP00000441354:C97S	C	+	2	0	OR4D2	53602305	1.000000	0.71417	1.000000	0.80357	0.686000	0.39977	7.955000	0.87856	2.860000	0.98153	0.609000	0.83330	TGC	G|0.898;C|0.102	0.102	strong		0.527	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1		
ZNF254	9534	hgsc.bcm.edu	37	19	24310032	24310032	+	Missense_Mutation	SNP	A	A	T	rs61737180	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:24310032A>T	ENST00000357002.4	+	4	1345	c.1230A>T	c.(1228-1230)gaA>gaT	p.E410D	ZNF254_ENST00000342944.6_Missense_Mutation_p.E325D	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	410					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E410D(1)					all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				AATGTGAAGAATGCGGCAAAG	0.343													A|||	734	0.146565	0.1543	0.0965	5008	,	,		21032	0.1677		0.1441	False		,,,				2504	0.1524				p.E410D		Atlas-SNP	.											ZNF254_ENST00000357002,colon,carcinoma,0,1	ZNF254	88	1	1	Substitution - Missense(1)	large_intestine(1)	c.A1230T						PASS	.	A	ASP/GLU	674,3730	273.7+/-271.5	47,580,1575	41.0	44.0	43.0		1230	-0.1	0.3	19	dbSNP_129	43	1274,7326	247.9+/-275.8	94,1086,3120	yes	missense	ZNF254	NM_203282.2	45	141,1666,4695	TT,TA,AA		14.814,15.3043,14.98	benign	410/660	24310032	1948,11056	2202	4300	6502	SO:0001583	missense	9534	exon4			TGAAGAATGCGGC	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"""Zinc fingers, C2H2-type"", ""-"""	13047	protein-coding gene	gene with protein product		604768	"""zinc finger protein 539"""	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1230A>T	19.37:g.24310032A>T	ENSP00000349494:p.Glu410Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	117	65	0.555556	NM_203282	A4QPC0|Q86XL7	Missense_Mutation	SNP	ENST00000357002.4	37	CCDS32983.1	314	0.14377289377289376	78	0.15853658536585366	37	0.10220994475138122	85	0.1486013986013986	114	0.1503957783641161	A	5.698	0.313254	0.10789	0.153043	0.14814	ENSG00000213096	ENST00000342944;ENST00000357002	T;T	0.07567	3.18;3.18	1.07	-0.105	0.13601	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00039	0.0001	L	0.53249	1.67	0.48288	P	3.769999999999607E-4	P	0.39940	0.696	B	0.31614	0.133	T	0.39313	-0.9620	8	0.51188	T	0.08	.	4.0622	0.09844	0.7335:0.0:0.2665:0.0	rs61737180	410	O75437	ZN254_HUMAN	D	325;410	ENSP00000445527:E325D;ENSP00000349494:E410D	ENSP00000445527:E325D	E	+	3	2	ZNF254	24101872	0.008000	0.16893	0.330000	0.25442	0.746000	0.42486	-0.265000	0.08644	0.441000	0.26529	0.248000	0.18094	GAA	A|0.852;T|0.148	0.148	strong		0.343	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744829	23744829	+	Silent	SNP	C	C	T	rs79723196|rs35076736|rs67447855	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23744829C>T	ENST00000357460.5	-	2	1772	c.1608G>A	c.(1606-1608)gaG>gaA	p.E536E	HOMEZ_ENST00000431326.2_Silent_p.E538E|HOMEZ_ENST00000561013.1_Silent_p.E538E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	536	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		catcatcttcctcctcctcct	0.483													C|||	22	0.00439297	0.0045	0.0058	5008	,	,		18800	0.001		0.0099	False		,,,				2504	0.001				p.E536E		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1608A						PASS	.						32.0	32.0	32.0					14																	23744829		2132	4146	6278	SO:0001819	synonymous_variant	57594	exon2			ATCTTCCTCCTCC	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1608G>A	14.37:g.23744829C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	156	26	0.166667	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	weak		0.483	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
CNTROB	116840	hgsc.bcm.edu	37	17	7847955	7847955	+	Splice_Site	SNP	C	C	A	rs11650083	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7847955C>A	ENST00000563694.1	+	12	2658	c.1733C>A	c.(1732-1734)cCa>cAa	p.P578Q	CNTROB_ENST00000380262.3_Splice_Site_p.P578Q|CNTROB_ENST00000380255.3_Intron|CNTROB_ENST00000565740.1_Splice_Site_p.P578Q	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	578	Pro-rich.|Required for centrosome localization.		P -> Q (in dbSNP:rs11650083). {ECO:0000269|PubMed:11984006, ECO:0000269|PubMed:14702039}.		centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CCCAACCCTCCAGTACGCCTT	0.557													C|||	3028	0.604633	0.447	0.6614	5008	,	,		4301	0.8016		0.4493	False		,,,				2504	0.7342				p.P578Q		Atlas-SNP	.											CNTROB,colon,carcinoma,0,1	CNTROB	61	1	0			c.C1733A						scavenged	.	C	GLN/PRO,GLN/PRO	2082,2324	571.4+/-383.1	501,1080,622	99.0	91.0	94.0		1733,1733	-2.4	0.0	17	dbSNP_120	94	3952,4648	547.5+/-385.2	914,2124,1262	yes	missense-near-splice,missense-near-splice	CNTROB	NM_001037144.5,NM_053051.3	76,76	1415,3204,1884	AA,AC,CC		45.9535,47.2537,46.394	benign,benign	578/926,578/904	7847955	6034,6972	2203	4300	6503	SO:0001630	splice_region_variant	116840	exon12			ACCCTCCAGTACG	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.1734+1C>A	17.37:g.7847955C>A		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Missense_Mutation	SNP	ENST00000563694.1	37	CCDS11126.1	1225	0.5608974358974359	234	0.47560975609756095	220	0.6077348066298343	424	0.7412587412587412	347	0.4577836411609499	C	8.908	0.957899	0.18507	0.472537	0.459535	ENSG00000170037	ENST00000380262	T	0.38077	1.16	4.56	-2.37	0.06643	.	1.024840	0.07770	N	0.951533	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B;B	0.12013	0.001;0.001;0.005	B;B;B	0.12156	0.001;0.001;0.007	T	0.40757	-0.9546	9	0.10902	T	0.67	-1.0583	4.5619	0.12165	0.5422:0.2684:0.0:0.1895	rs11650083;rs52795073;rs57150255;rs11650083	578;578;578	Q8N137-3;Q8N137;Q8N137-2	.;CNTRB_HUMAN;.	Q	578	ENSP00000369614:P578Q	ENSP00000369614:P578Q	P	+	2	0	CNTROB	7788680	0.021000	0.18746	0.002000	0.10522	0.010000	0.07245	-0.104000	0.10923	-0.113000	0.11958	0.561000	0.74099	CCA	C|0.491;A|0.509	0.509	strong		0.557	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	Missense_Mutation
MUC16	94025	hgsc.bcm.edu	37	19	9059181	9059181	+	Missense_Mutation	SNP	G	G	A	rs12459532	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9059181G>A	ENST00000397910.4	-	3	28468	c.28265C>T	c.(28264-28266)cCa>cTa	p.P9422L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9424	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						CAGCGGGCTTGGCCATGACAC	0.512													G|||	182	0.0363419	0.0008	0.1153	5008	,	,		20341	0.0099		0.0189	False		,,,				2504	0.0736				p.P9422L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C28265T						PASS	.	G	LEU/PRO	23,4023		0,23,2000	118.0	117.0	117.0		28265	0.8	0.0	19	dbSNP_120	117	177,8189		3,171,4009	yes	missense	MUC16	NM_024690.2	98	3,194,6009	AA,AG,GG		2.1157,0.5685,1.6113	benign	9422/14508	9059181	200,12212	2023	4183	6206	SO:0001583	missense	94025	exon3			GGGCTTGGCCATG	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.28265C>T	19.37:g.9059181G>A	ENSP00000381008:p.Pro9422Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	170	102	0.6	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	53	0.024267399267399268	0	0.0	35	0.09668508287292818	4	0.006993006993006993	14	0.018469656992084433	g	4.312	0.057126	0.08339	0.005685	0.021157	ENSG00000181143	ENST00000397910	T	0.21031	2.03	1.95	0.802	0.18686	.	.	.	.	.	T	0.00328	0.0010	N	0.19112	0.55	.	.	.	B	0.27625	0.183	B	0.30943	0.122	T	0.21999	-1.0229	8	0.87932	D	0	.	5.1883	0.15195	0.0:0.0:0.6334:0.3666	rs12459532;rs12459532	9422	B5ME49	.	L	9422	ENSP00000381008:P9422L	ENSP00000381008:P9422L	P	-	2	0	MUC16	8920181	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.068000	0.11561	0.328000	0.23435	0.306000	0.20318	CCA	G|0.977;A|0.023	0.023	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TRIM55	84675	hgsc.bcm.edu	37	8	67064654	67064654	+	Missense_Mutation	SNP	A	A	G	rs7843605	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:67064654A>G	ENST00000315962.4	+	8	1401	c.1028A>G	c.(1027-1029)aAa>aGa	p.K343R	TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000353317.5_Missense_Mutation_p.K343R|TRIM55_ENST00000276573.7_Missense_Mutation_p.K343R	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	343			K -> R (in dbSNP:rs7843605).		signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)	p.K343R(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	39		Lung NSC(129;0.138)|all_lung(136;0.221)	Epithelial(68;0.0136)|all cancers(69;0.0582)|BRCA - Breast invasive adenocarcinoma(89;0.0628)|OV - Ovarian serous cystadenocarcinoma(28;0.0904)			gaaggagaaaaagaaggagaa	0.413													G|||	1069	0.213458	0.6664	0.0908	5008	,	,		21464	0.0		0.0915	False		,,,				2504	0.0337				p.K343R		Atlas-SNP	.											TRIM55,NS,carcinoma,0,1	TRIM55	91	1	1	Substitution - Missense(1)	prostate(1)	c.A1028G						PASS	.	G	ARG/LYS,ARG/LYS,ARG/LYS,	2573,1833	510.9+/-367.7	761,1051,391	41.0	38.0	39.0		1028,1028,1028,	-1.8	0.0	8	dbSNP_116	39	825,7775	768.5+/-407.6	43,739,3518	no	missense,missense,missense,intron	TRIM55	NM_033058.2,NM_184085.1,NM_184086.1,NM_184087.1	26,26,26,	804,1790,3909	GG,GA,AA		9.593,41.6024,26.1264	benign,benign,benign,	343/541,343/549,343/453,	67064654	3398,9608	2203	4300	6503	SO:0001583	missense	84675	exon8			GAGAAAAAGAAGG	AJ291712	CCDS6184.1, CCDS6185.1, CCDS6186.1, CCDS6187.1	8q13.1	2013-01-09	2011-01-25	2004-11-17	ENSG00000147573	ENSG00000147573		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	14215	protein-coding gene	gene with protein product		606469	"""ring finger protein 29"", ""tripartite motif-containing 55"""	RNF29		11243782	Standard	NM_033058		Approved	MURF-2	uc003xvv.3	Q9BYV6	OTTHUMG00000164473	ENST00000315962.4:c.1028A>G	8.37:g.67064654A>G	ENSP00000323913:p.Lys343Arg	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	15	14	0.933333	NM_184086	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Missense_Mutation	SNP	ENST00000315962.4	37	CCDS6184.1	423	0.1936813186813187	312	0.6341463414634146	35	0.09668508287292818	0	0.0	76	0.10026385224274406	G	0.158	-1.083948	0.01888	0.583976	0.09593	ENSG00000147573	ENST00000315962;ENST00000353317;ENST00000276573	T;T;T	0.27720	1.66;1.66;1.65	3.94	-1.8	0.07907	.	1.469880	0.04195	N	0.329017	T	0.00012	0.0000	N	0.08118	0	0.46901	P	7.540000000000324E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43845	-0.9366	9	0.24483	T	0.36	.	1.822	0.03112	0.5064:0.1493:0.1936:0.1507	rs7843605;rs52811956;rs7843605	343;343;343	Q9BYV6-2;Q9BYV6;Q9BYV6-3	.;TRI55_HUMAN;.	R	343	ENSP00000323913:K343R;ENSP00000297348:K343R;ENSP00000276573:K343R	ENSP00000276573:K343R	K	+	2	0	TRIM55	67227208	0.055000	0.20627	0.000000	0.03702	0.040000	0.13550	-0.476000	0.06591	-0.529000	0.06358	-0.192000	0.12808	AAA	A|0.741;G|0.259	0.259	strong		0.413	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085	
PCSK5	5125	hgsc.bcm.edu	37	9	78853916	78853916	+	Missense_Mutation	SNP	G	G	C	rs17062264	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:78853916G>C	ENST00000545128.1	+	23	3446	c.2908G>C	c.(2908-2910)Gga>Cga	p.G970R		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	970	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						GGGAGAGTGTGGAGATAGCTG	0.537													C|||	687	0.137181	0.2156	0.1282	5008	,	,		18750	0.0099		0.1243	False		,,,				2504	0.182				p.G970R		Atlas-SNP	.											.	PCSK5	329	.	0			c.G2908C						PASS	.	C	ARG/GLY	321,1431		26,269,581	40.0	35.0	36.0		2908	4.5	0.6	9	dbSNP_123	36	475,3507		31,413,1547	yes	missense	PCSK5	NM_001190482.1	125	57,682,2128	CC,CG,GG		11.9287,18.3219,13.8821		970/1861	78853916	796,4938	876	1991	2867	SO:0001583	missense	5125	exon23			GAGTGTGGAGATA		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.2908G>C	9.37:g.78853916G>C	ENSP00000446280:p.Gly970Arg	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	133	50	0.37594	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	240	0.10989010989010989	96	0.1951219512195122	46	0.1270718232044199	3	0.005244755244755245	95	0.12532981530343007	C	0.020	-1.435645	0.01108	0.183219	0.119287	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.28666	1.6;1.6	5.54	4.53	0.55603	.	0.496439	0.19738	N	0.107185	T	0.00012	0.0000	N	0.01431	-0.87	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	T	0.32134	-0.9918	7	0.16420	T	0.52	0.1669	3.0125	0.06048	0.2711:0.4904:0.14:0.0985	rs17062264;rs56482229;rs58574166;rs17062264	.	.	.	R	970;673;643	ENSP00000446280:G970R;ENSP00000411654:G643R	ENSP00000365945:G673R	G	+	1	0	PCSK5	78043736	0.332000	0.24722	0.620000	0.29132	0.123000	0.20343	1.157000	0.31724	0.523000	0.28482	-0.195000	0.12781	GGA	G|0.882;C|0.118	0.118	strong		0.537	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SEC14L4	284904	hgsc.bcm.edu	37	22	30901592	30901592	+	Missense_Mutation	SNP	T	T	C	rs9608956	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:30901592T>C	ENST00000255858.7	-	1	90	c.7A>G	c.(7-9)Agc>Ggc	p.S3G	SEC14L4_ENST00000392772.2_5'UTR|SEC14L4_ENST00000540456.1_5'UTR|SEC14L4_ENST00000381982.3_Missense_Mutation_p.S3G	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	3			S -> G (in dbSNP:rs9608956).			integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CCGACTCGGCTGCTCATGGTG	0.736													C|||	1028	0.205272	0.2716	0.2997	5008	,	,		13779	0.0397		0.2545	False		,,,				2504	0.1687				p.S3G		Atlas-SNP	.											.	SEC14L4	43	.	0			c.A7G						PASS	.	C	GLY/SER,GLY/SER	1010,3322		147,716,1303	8.0	10.0	9.0		7,7	3.7	1.0	22	dbSNP_119	9	1922,6566		248,1426,2570	no	missense,missense	SEC14L4	NM_001161368.1,NM_174977.3	56,56	395,2142,3873	CC,CT,TT		22.6437,23.3149,22.8705	benign,benign	3/361,3/407	30901592	2932,9888	2166	4244	6410	SO:0001583	missense	284904	exon1			CTCGGCTGCTCAT	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.7A>G	22.37:g.30901592T>C	ENSP00000255858:p.Ser3Gly	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	27	24	0.888889	NM_001161368	A5D6W7|A6NCV4	Missense_Mutation	SNP	ENST00000255858.7	37	CCDS13878.1	449	0.20558608058608058	143	0.29065040650406504	90	0.24861878453038674	24	0.04195804195804196	192	0.2532981530343008	C	8.917	0.960179	0.18507	0.233149	0.226437	ENSG00000133488	ENST00000255858;ENST00000381982	T;T	0.26223	1.75;1.75	3.73	3.73	0.42828	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00006	-3.22	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37361	-0.9709	9	0.06365	T	0.9	0.1944	10.3272	0.43801	0.0:0.9033:0.0:0.0967	rs9608956;rs52821308;rs9608956	3	Q9UDX3	S14L4_HUMAN	G	3	ENSP00000255858:S3G;ENSP00000371412:S3G	ENSP00000255858:S3G	S	-	1	0	SEC14L4	29231592	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.927000	0.56499	1.167000	0.42706	-0.320000	0.08662	AGC	T|0.801;C|0.199	0.199	strong		0.736	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
RGSL1	353299	hgsc.bcm.edu	37	1	182496829	182496829	+	Missense_Mutation	SNP	A	A	G	rs7535533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:182496829A>G	ENST00000294854.8	+	11	2067	c.2047A>G	c.(2047-2049)Ata>Gta	p.I683V	RGSL1_ENST00000456971.2_3'UTR|RGSL1_ENST00000542961.1_Missense_Mutation_p.I718V	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	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	232	137	0.590517	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	
MUC17	140453	hgsc.bcm.edu	37	7	100678820	100678820	+	Missense_Mutation	SNP	T	T	C	rs386716198|rs4367469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678820T>C	ENST00000306151.4	+	3	4187	c.4123T>C	c.(4123-4125)Tgt>Cgt	p.C1375R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1375	59 X approximate tandem repeats.|Ser-rich.		C -> R (in dbSNP:rs4367469). {ECO:0000269|PubMed:9299468}.		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)					TACTGAAGCCTGTTCATCTCC	0.483																																					p.C1375R		Atlas-SNP	.											.	MUC17	804	.	0			c.T4123C						PASS	.	C	ARG/CYS	1301,3105		206,889,1108	232.0	241.0	238.0		4123	-0.5	0.0	7	dbSNP_111	238	999,7601		57,885,3358	no	missense	MUC17	NM_001040105.1	180	263,1774,4466	CC,CT,TT		11.6163,29.5279,17.6841	benign	1375/4494	100678820	2300,10706	2203	4300	6503	SO:0001583	missense	140453	exon3			GAAGCCTGTTCAT	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.4123T>C	7.37:g.100678820T>C	ENSP00000302716:p.Cys1375Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	173	170	0.982659	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	350	0.16025641025641027	113	0.22967479674796748	35	0.09668508287292818	125	0.21853146853146854	77	0.10158311345646438	N	0.035	-1.311408	0.01342	0.295279	0.116163	ENSG00000169876	ENST00000306151	T	0.02974	4.09	0.838	-0.487	0.12060	.	.	.	.	.	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	0.43343	-0.9397	8	0.17832	T	0.49	.	2.045	0.03558	0.4021:0.3014:0.0:0.2965	rs4367469;rs10374415	1375	Q685J3	MUC17_HUMAN	R	1375	ENSP00000302716:C1375R	ENSP00000302716:C1375R	C	+	1	0	MUC17	100465540	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.262000	0.08682	-0.774000	0.04590	-4.225000	0.00009	TGT	T|0.834;C|0.166	0.166	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FAM81B	153643	hgsc.bcm.edu	37	5	94749723	94749723	+	Silent	SNP	G	G	A	rs7726891	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	136	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	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	
IARS	3376	hgsc.bcm.edu	37	9	94985637	94985637	+	Missense_Mutation	SNP	T	T	C	rs556155	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:94985637T>C	ENST00000375643.3	-	32	3810	c.3544A>G	c.(3544-3546)Aag>Gag	p.K1182E	IARS_ENST00000375629.3_3'UTR|IARS_ENST00000443024.2_Missense_Mutation_p.K1182E|IARS_ENST00000447699.2_Missense_Mutation_p.K1072E	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	1182			K -> E (in dbSNP:rs556155). {ECO:0000269|PubMed:17974005}.		gene expression (GO:0010467)|isoleucyl-tRNA aminoacylation (GO:0006428)|osteoblast differentiation (GO:0001649)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|isoleucine-tRNA ligase activity (GO:0004822)	p.K1182Q(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	35					L-Isoleucine(DB00167)	CCTTGTGGCTTTGCATTCAGG	0.453													C|||	804	0.160543	0.0537	0.1988	5008	,	,		18188	0.121		0.1461	False		,,,				2504	0.3333				p.K1182E		Atlas-SNP	.											IARS,rectum,carcinoma,0,1	IARS	74	1	1	Substitution - Missense(1)	large_intestine(1)	c.A3544G						PASS	.	C	GLU/LYS,GLU/LYS	321,4085	797.7+/-415.4	12,297,1894	112.0	104.0	107.0		3544,3544	2.6	0.2	9	dbSNP_83	107	1391,7209	754.2+/-407.5	105,1181,3014	yes	missense,missense	IARS	NM_002161.4,NM_013417.2	56,56	117,1478,4908	CC,CT,TT		16.1744,7.2855,13.1632	benign,benign	1182/1263,1182/1263	94985637	1712,11294	2203	4300	6503	SO:0001583	missense	3376	exon32			GTGGCTTTGCATT	AB209234	CCDS6694.1	9q21	2011-07-01	2007-02-26		ENSG00000196305	ENSG00000196305	6.1.1.5	"""Aminoacyl tRNA synthetases / Class I"""	5330	protein-coding gene	gene with protein product	"""isoleucine tRNA ligase 1, cytoplasmic"""	600709				8812440	Standard	NM_002161		Approved	ILRS, IARS1	uc004aru.4	P41252	OTTHUMG00000020219	ENST00000375643.3:c.3544A>G	9.37:g.94985637T>C	ENSP00000364794:p.Lys1182Glu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	153	85	0.555556	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Missense_Mutation	SNP	ENST00000375643.3	37	CCDS6694.1	269	0.12316849816849818	23	0.046747967479674794	63	0.17403314917127072	69	0.12062937062937062	114	0.1503957783641161	C	2.687	-0.274075	0.05679	0.072855	0.161744	ENSG00000196305	ENST00000375643;ENST00000443024;ENST00000543028;ENST00000447699;ENST00000375660;ENST00000421189	T;T;T	0.43688	0.94;0.94;0.94	5.86	2.58	0.30949	.	0.608943	0.19546	N	0.111689	T	0.00039	0.0001	N	0.02802	-0.49	0.53688	P	2.2999999999995246E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.23511	-1.0186	9	0.06625	T	0.88	-1.4842	6.5975	0.22683	0.0:0.5393:0.0:0.4607	rs556155;rs2070054;rs2230406;rs59750466;rs556155	692;1182;975	F5H1M4;P41252;Q6P0M4	.;SYIC_HUMAN;.	E	1182;1182;191;1072;1182;191	ENSP00000364794:K1182E;ENSP00000406448:K1182E;ENSP00000415020:K1072E	ENSP00000364794:K1182E	K	-	1	0	IARS	94025458	0.997000	0.39634	0.173000	0.22940	0.714000	0.41099	0.383000	0.20651	0.499000	0.27970	-0.128000	0.14901	AAG	A|0.007;C|0.130	0.130	strong		0.453	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161	
ZFR	51663	hgsc.bcm.edu	37	5	32400266	32400266	+	Missense_Mutation	SNP	A	A	G	rs1051489	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	134	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	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		
ZNF665	79788	hgsc.bcm.edu	37	19	53668697	53668697	+	Missense_Mutation	SNP	T	T	C	rs45499997	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	140	0	0		WXS	Illumina HiSeq	Phase_I	134	80	0.597015	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	
LY75	4065	hgsc.bcm.edu	37	2	160735174	160735174	+	Missense_Mutation	SNP	C	C	T	rs147820690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160735174C>T	ENST00000263636.4	-	10	1601	c.1574G>A	c.(1573-1575)gGa>gAa	p.G525E	LY75_ENST00000554112.1_Missense_Mutation_p.G525E|LY75_ENST00000553424.1_Missense_Mutation_p.G525E|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.G525E|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.G525E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	525	C-type lectin 3. {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)		GCAGTTTGTTCCAAAAGGGAC	0.388													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20519	0.0		0.002	False		,,,				2504	0.0				p.G525E		Atlas-SNP	.											.	LY75	151	.	0			c.G1574A						PASS	.	C	GLU/GLY,GLU/GLY,GLU/GLY	5,4401	9.9+/-24.2	0,5,2198	173.0	156.0	162.0		1574,1574,1574	4.4	1.0	2	dbSNP_134	162	23,8577	16.6+/-54.9	0,23,4277	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	98,98,98	0,28,6475	TT,TC,CC		0.2674,0.1135,0.2153	probably-damaging,probably-damaging,probably-damaging	525/1874,525/1818,525/1723	160735174	28,12978	2203	4300	6503	SO:0001583	missense	4065	exon10			TTTGTTCCAAAAG	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.1574G>A	2.37:g.160735174C>T	ENSP00000263636:p.Gly525Glu	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	220	125	0.568182	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	19.40	3.820467	0.71028	0.001135	0.002674	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.51817	0.69;2.98;2.96;0.69;2.98	5.31	4.43	0.53597	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.234809	0.21795	N	0.069012	T	0.66877	0.2834	M	0.73598	2.24	0.48901	D	0.999726	B;D;D;D	0.89917	0.41;1.0;1.0;1.0	P;D;D;D	0.97110	0.45;0.999;1.0;1.0	T	0.67313	-0.5702	10	0.41790	T	0.15	-18.7866	13.1585	0.59531	0.0:0.9209:0.0:0.0791	.	143;525;525;525	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	E	525	ENSP00000451511:G525E;ENSP00000451446:G525E;ENSP00000263636:G525E;ENSP00000423463:G525E;ENSP00000421035:G525E	ENSP00000423463:G525E	G	-	2	0	LY75;LY75-CD302	160443420	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.886000	0.56190	1.367000	0.46095	0.650000	0.86243	GGA	C|0.998;T|0.002	0.002	strong		0.388	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
KIAA1755	85449	hgsc.bcm.edu	37	20	36869516	36869516	+	Missense_Mutation	SNP	C	C	A	rs1205434	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	46	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	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	
OSER1	51526	hgsc.bcm.edu	37	20	42826350	42826350	+	Missense_Mutation	SNP	A	A	C	rs9346	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:42826350A>C	ENST00000372970.2	-	6	401	c.221T>G	c.(220-222)gTg>gGg	p.V74G	OSER1_ENST00000255174.2_Missense_Mutation_p.V74G			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	74			V -> G (in dbSNP:rs9346).		cellular response to hydrogen peroxide (GO:0070301)												CTGAGTTCTCACTGCTCCTCG	0.423													A|||	1771	0.353634	0.5862	0.1354	5008	,	,		22691	0.4196		0.1531	False		,,,				2504	0.3323				p.V74G		Atlas-SNP	.											.	C20orf111	28	.	0			c.T221G						PASS	.	A	GLY/VAL	2235,2171	589.5+/-387.1	574,1087,542	59.0	57.0	58.0		221	1.0	1.0	20	dbSNP_52	58	1215,7385	243.9+/-273.3	80,1055,3165	yes	missense	C20orf111	NM_016470.7	109	654,2142,3707	CC,CA,AA		14.1279,49.2737,26.5262	benign	74/293	42826350	3450,9556	2203	4300	6503	SO:0001583	missense	51526	exon4			GTTCTCACTGCTC	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.221T>G	20.37:g.42826350A>C	ENSP00000362061:p.Val74Gly	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Missense_Mutation	SNP	ENST00000372970.2	37	CCDS13327.1	718	0.32875457875457875	294	0.5975609756097561	58	0.16022099447513813	242	0.4230769230769231	124	0.16358839050131926	A	12.62	1.992149	0.35131	0.507263	0.141279	ENSG00000132823	ENST00000255174;ENST00000372970	T;T	0.54479	0.57;0.57	5.72	1.03	0.20045	.	0.636671	0.16840	N	0.197362	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	0.9999999260926	B	0.21905	0.062	B	0.30716	0.119	T	0.43845	-0.9366	9	0.66056	D	0.02	-0.5225	9.1613	0.37023	0.7244:0.0:0.2756:0.0	rs9346;rs1049822;rs3171228;rs52815417;rs58950417;rs9346	74	Q9NX31	CT111_HUMAN	G	74	ENSP00000255174:V74G;ENSP00000362061:V74G	ENSP00000255174:V74G	V	-	2	0	C20orf111	42259764	0.533000	0.26354	0.992000	0.48379	0.919000	0.55068	1.618000	0.36954	0.116000	0.18110	0.383000	0.25322	GTG	T|0.004;G|0.002	.	strong		0.423	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	
DNAJC1	64215	hgsc.bcm.edu	37	10	22048330	22048330	+	Silent	SNP	C	C	T	rs9045	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	137	0	0		WXS	Illumina HiSeq	Phase_I	103	83	0.805825	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	
VPS41	27072	hgsc.bcm.edu	37	7	38829465	38829465	+	Silent	SNP	C	C	T	rs1001476	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	153	0	0		WXS	Illumina HiSeq	Phase_I	188	84	0.446809	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		
LARS	51520	hgsc.bcm.edu	37	5	145519821	145519821	+	Silent	SNP	G	G	A	rs17493851	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145519821G>A	ENST00000394434.2	-	21	2260	c.2094C>T	c.(2092-2094)gaC>gaT	p.D698D	LARS_ENST00000274562.9_Silent_p.D671D|LARS_ENST00000510191.1_Silent_p.D644D|LARS_ENST00000545646.1_Silent_p.D652D	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	255	2	0.00784314		WXS	Illumina HiSeq	Phase_I	195	195	1	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	
MYO3A	53904	hgsc.bcm.edu	37	10	26462790	26462790	+	Silent	SNP	G	G	A	rs3740232	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	110	0	0		WXS	Illumina HiSeq	Phase_I	78	22	0.282051	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	
CCDC66	285331	hgsc.bcm.edu	37	3	56628033	56628033	+	Nonsense_Mutation	SNP	C	C	T	rs150364083	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:56628033C>T	ENST00000394672.3	+	10	1451	c.1381C>T	c.(1381-1383)Cga>Tga	p.R461*	CCDC66_ENST00000326595.7_Nonsense_Mutation_p.R427*|CCDC66_ENST00000436465.2_Nonsense_Mutation_p.R461*	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	461					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)		AGACAGACGACGACAAAAACA	0.373													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20246	0.0		0.002	False		,,,				2504	0.0				p.R461X		Atlas-SNP	.											.	CCDC66	145	.	0			c.C1381T						PASS	.	C	stop/ARG,stop/ARG	4,4402	9.9+/-24.2	0,4,2199	180.0	168.0	172.0		1279,1381	4.9	1.0	3	dbSNP_134	172	66,8534	39.8+/-96.3	0,66,4234	yes	stop-gained,stop-gained	CCDC66	NM_001012506.4,NM_001141947.1	,	0,70,6433	TT,TC,CC		0.7674,0.0908,0.5382	,	427/915,461/949	56628033	70,12936	2203	4300	6503	SO:0001587	stop_gained	285331	exon10			AGACGACGACAAA	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.1381C>T	3.37:g.56628033C>T	ENSP00000378167:p.Arg461*	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	125	51	0.408	NM_001141947	B3KWL8|Q4VC34|Q8N949	Nonsense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	37	6.393245	0.97529	9.08E-4	0.007674	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	.	.	.	5.81	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.6425	15.6712	0.77279	0.1457:0.8543:0.0:0.0	.	.	.	.	X	417;461;427;461	.	ENSP00000326050:R427X	R	+	1	2	CCDC66	56603073	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	3.573000	0.53856	2.739000	0.93911	0.585000	0.79938	CGA	C|0.996;T|0.004	0.004	strong		0.373	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
NLRP13	126204	hgsc.bcm.edu	37	19	56423893	56423893	+	Silent	SNP	G	G	A	rs303998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	115	110	0.956522	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29912108	29912108	+	Missense_Mutation	SNP	G	G	C	rs2231095	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29912108G>C	ENST00000396634.1	+	6	1170	c.829G>C	c.(829-831)Gag>Cag	p.E277Q	HLA-A_ENST00000376806.5_Missense_Mutation_p.E277Q|HLA-A_ENST00000376802.2_Missense_Mutation_p.E277Q|HLA-A_ENST00000376809.5_Missense_Mutation_p.E277Q			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	277	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						GCCTTCTGGAGAGGAGCAGAG	0.617									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|||	2247	0.448682	0.5129	0.4856	5008	,	,		18227	0.4167		0.4344	False		,,,				2504	0.3834				p.E277Q		Atlas-SNP	.											.	HLA-A	89	.	0			c.G829C						PASS	.						41.0	38.0	39.0					6																	29912108		1511	2707	4218	SO:0001583	missense	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TCTGGAGAGGAGC	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.829G>C	6.37:g.29912108G>C	ENSP00000379873:p.Glu277Gln	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	193	55	0.284974	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	1.666	-0.510311	0.04231	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809;ENST00000376802	T;T;T;T	0.02974	4.09;4.09;4.09;4.09	3.69	-1.97	0.07503	Immunoglobulin-like (4);Immunoglobulin C1-set (8);Immunoglobulin-like fold (4);	0.573958	0.13893	U	0.355507	T	0.01695	0.0054	.	.	.	0.53688	P	2.199999999996649E-5	P;B;B;B;B;B;B	0.43633	0.813;0.0;0.041;0.0;0.134;0.0;0.0	P;B;B;B;B;B;B	0.58520	0.84;0.002;0.12;0.002;0.12;0.004;0.001	T	0.36383	-0.9750	8	0.09843	T	0.71	.	7.9497	0.30008	0.103:0.4273:0.4697:0.0	rs2231095;rs9260183;rs16896035;rs41547214	156;277;277;277;277;277;277	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	Q	277;277;65;277;277	ENSP00000379873:E277Q;ENSP00000366002:E277Q;ENSP00000366005:E277Q;ENSP00000365998:E277Q	ENSP00000365998:E277Q	E	+	1	0	HLA-A	30020087	0.001000	0.12720	0.962000	0.40283	0.439000	0.31926	0.112000	0.15479	-0.204000	0.10235	-3.416000	0.00038	GAG	.	.	weak		0.617	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SMCHD1	23347	hgsc.bcm.edu	37	18	2740714	2740714	+	Silent	SNP	A	A	G	rs12327477	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:2740714A>G	ENST00000320876.6	+	28	3866	c.3528A>G	c.(3526-3528)acA>acG	p.T1176T	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.T1176T	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1176					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TAATAATTACAGATCAGTACG	0.284													G|||	1934	0.386182	0.2685	0.4467	5008	,	,		13651	0.5228		0.2634	False		,,,				2504	0.4877				p.T1176T		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A3528G						PASS	.	G		945,2639		127,691,974	86.0	84.0	85.0		3528	-2.0	1.0	18	dbSNP_120	85	2294,5814		315,1664,2075	no	coding-synonymous	SMCHD1	NM_015295.2		442,2355,3049	GG,GA,AA		28.293,26.3672,27.7027		1176/2006	2740714	3239,8453	1792	4054	5846	SO:0001819	synonymous_variant	23347	exon28			AATTACAGATCAG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3528A>G	18.37:g.2740714A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			A|0.701;G|0.299	0.299	strong		0.284	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
MKI67	4288	hgsc.bcm.edu	37	10	129909929	129909929	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129909929T>G	ENST00000368654.3	-	11	2615	c.2240A>C	c.(2239-2241)gAc>gCc	p.D747A	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.D387A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	747					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)				TTCCTTAAAGTCCATTTTTTG	0.348																																					p.D747A		Atlas-SNP	.											.	MKI67	363	.	0			c.A2240C						PASS	.						99.0	97.0	97.0					10																	129909929		2203	4300	6503	SO:0001583	missense	4288	exon11			TTAAAGTCCATTT	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.2240A>C	10.37:g.129909929T>G	ENSP00000357643:p.Asp747Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295801	0.60086	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01584	4.77;4.75	5.18	4.01	0.46588	.	0.000000	0.45867	D	0.000331	T	0.06872	0.0175	M	0.64404	1.975	0.09310	N	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.79784	0.993;0.973;0.976	T	0.09975	-1.0650	10	0.72032	D	0.01	.	7.2985	0.26408	0.0:0.0771:0.1574:0.7655	.	746;387;747	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	A	747;387;746;322	ENSP00000357643:D747A;ENSP00000357642:D387A	ENSP00000357641:D322A	D	-	2	0	MKI67	129799919	0.017000	0.18338	0.150000	0.22450	0.353000	0.29299	1.086000	0.30853	0.937000	0.37394	0.533000	0.62120	GAC	.	.	none		0.348	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
MUC16	94025	hgsc.bcm.edu	37	19	9075346	9075346	+	Missense_Mutation	SNP	T	T	A	rs2591592	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9075346T>A	ENST00000397910.4	-	3	12303	c.12100A>T	c.(12100-12102)Att>Ttt	p.I4034F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4036	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						GAAGAGATAATACTTGTTTGT	0.473													t|||	2195	0.438299	0.4115	0.4683	5008	,	,		21847	0.2579		0.5755	False		,,,				2504	0.498				p.I4034F		Atlas-SNP	.											.	MUC16	4315	.	0			c.A12100T						PASS	.	T	PHE/ILE	1807,2223		407,993,615	119.0	113.0	115.0		12100	-1.0	0.0	19	dbSNP_100	115	4917,3395		1445,2027,684	yes	missense	MUC16	NM_024690.2	21	1852,3020,1299	AA,AT,TT		40.8446,44.8387,45.5194	probably-damaging	4034/14508	9075346	6724,5618	2015	4156	6171	SO:0001583	missense	94025	exon3			AGATAATACTTGT	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.12100A>T	19.37:g.9075346T>A	ENSP00000381008:p.Ile4034Phe	Somatic	325	1	0.00307692		WXS	Illumina HiSeq	Phase_I	336	165	0.491071	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	936	0.42857142857142855	194	0.3943089430894309	180	0.4972375690607735	127	0.22202797202797203	435	0.5738786279683378	-	5.432	0.264864	0.10294	0.448387	0.591554	ENSG00000181143	ENST00000397910	T	0.02709	4.19	2.33	-1.05	0.10036	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	.	.	.	D	0.59767	0.986	P	0.53912	0.737	T	0.43605	-0.9381	8	0.87932	D	0	.	2.0719	0.03615	0.2508:0.3189:0.0:0.4302	rs2591592;rs52799163;rs2591592	4034	B5ME49	.	F	4034	ENSP00000381008:I4034F	ENSP00000381008:I4034F	I	-	1	0	MUC16	8936346	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.602000	0.05680	-0.363000	0.08101	0.260000	0.18958	ATT	T|0.558;A|0.442	0.442	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ACPT	93650	hgsc.bcm.edu	37	19	51297825	51297825	+	Missense_Mutation	SNP	G	G	A	rs55716643|rs386810263	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51297825G>A	ENST00000270593.1	+	9	973	c.973G>A	c.(973-975)Gcc>Acc	p.A325T	ACPT_ENST00000270594.3_Missense_Mutation_p.A232T|CTD-2568A17.8_ENST00000594114.1_RNA	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	325						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GGGGAATCCCGCCAAAGATGG	0.617													g|||	1652	0.329872	0.1309	0.2161	5008	,	,		17338	0.6538		0.3012	False		,,,				2504	0.3753				p.A325T		Atlas-SNP	.											.	ACPT	43	.	0			c.G973A						PASS	.	G	THR/ALA	673,3733	271.6+/-270.3	44,585,1574	40.0	39.0	39.0		973	1.7	0.0	19	dbSNP_129	39	2385,6215	365.6+/-334.0	349,1687,2264	yes	missense	ACPT	NM_033068.2	58	393,2272,3838	AA,AG,GG		27.7326,15.2746,23.5122	benign	325/427	51297825	3058,9948	2203	4300	6503	SO:0001583	missense	93650	exon9			AATCCCGCCAAAG	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.973G>A	19.37:g.51297825G>A	ENSP00000270593:p.Ala325Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	37	CCDS12802.1	641	0.2934981684981685	50	0.1016260162601626	71	0.19613259668508287	330	0.5769230769230769	190	0.25065963060686014	g	6.161	0.397948	0.11696	0.152746	0.277326	ENSG00000142513	ENST00000270593;ENST00000270594	T;T	0.76448	2.98;-1.02	3.9	1.74	0.24563	.	0.642945	0.14811	N	0.297051	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.14805	0.011	B	0.04013	0.001	T	0.45512	-0.9256	9	0.28530	T	0.3	-10.0341	4.3799	0.11288	0.2057:0.1884:0.6059:0.0	rs55716643;rs60842760	325	Q9BZG2	PPAT_HUMAN	T	325;232	ENSP00000270593:A325T;ENSP00000270594:A232T	ENSP00000270593:A325T	A	+	1	0	ACPT	55989637	0.001000	0.12720	0.009000	0.14445	0.000000	0.00434	0.419000	0.21247	0.468000	0.27243	-0.931000	0.02705	GCC	G|0.751;A|0.249	0.249	strong		0.617	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	
FAM170B	170370	hgsc.bcm.edu	37	10	50339754	50339754	+	Missense_Mutation	SNP	G	G	T	rs73302786	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50339754G>T	ENST00000311787.5	-	2	845	c.756C>A	c.(754-756)gaC>gaA	p.D252E	FAM170B-AS1_ENST00000442525.1_RNA|FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000435809.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	252										central_nervous_system(1)|endometrium(1)|skin(1)	3						CCAGCTGTTGGTCATGTGCTT	0.597													G|||	857	0.171126	0.2163	0.1282	5008	,	,		19690	0.0625		0.2018	False		,,,				2504	0.2209				p.D252E		Atlas-SNP	.											.	FAM170B	20	.	0			c.C756A						PASS	.	G	GLU/ASP	340,1044		40,260,392	95.0	85.0	88.0		756	-5.6	0.0	10	dbSNP_130	88	684,2498		77,530,984	yes	missense	FAM170B	NM_001164484.1	45	117,790,1376	TT,TG,GG		21.4959,24.5665,22.4266	benign	252/284	50339754	1024,3542	692	1591	2283	SO:0001583	missense	170370	exon2			CTGTTGGTCATGT		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.756C>A	10.37:g.50339754G>T	ENSP00000308292:p.Asp252Glu	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	100	74	0.74	NM_001164484	Q86WY6|Q8N6K8	Missense_Mutation	SNP	ENST00000311787.5	37	CCDS53536.1	338	0.15476190476190477	106	0.21544715447154472	42	0.11602209944751381	29	0.050699300699300696	161	0.21240105540897097	G	10.97	1.500335	0.26861	0.245665	0.214959	ENSG00000172538	ENST00000311787	T	0.29917	1.55	5.37	-5.56	0.02529	.	2.209180	0.02269	N	0.068289	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.11235	0.004	B	0.13407	0.009	T	0.24764	-1.0151	9	0.02654	T	1	-11.8138	1.0815	0.01644	0.1911:0.2613:0.14:0.4075	.	252	A6NMN3	F170B_HUMAN	E	252	ENSP00000308292:D252E	ENSP00000308292:D252E	D	-	3	2	FAM170B	50009760	0.863000	0.29885	0.003000	0.11579	0.032000	0.12392	-0.061000	0.11693	-0.560000	0.06102	-0.693000	0.03709	GAC	G|0.844;T|0.156	0.156	strong		0.597	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
FLG	2312	hgsc.bcm.edu	37	1	152278555	152278555	+	Missense_Mutation	SNP	T	T	C	rs80221306	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152278555T>C	ENST00000368799.1	-	3	8842	c.8807A>G	c.(8806-8808)gAc>gGc	p.D2936G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2936	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACCAGCTCTGTCTTCTTGATG	0.552									Ichthyosis																												p.D2936G		Atlas-SNP	.											FLG,NS,haematopoietic_neoplasm,0,2	FLG	900	2	0			c.A8807G						scavenged	.	T	GLY/ASP	267,3373		3,261,1556	22.0	34.0	31.0		8807	1.3	0.0	1	dbSNP_131	31	809,7583		0,809,3387	no	missense	FLG	NM_002016.1	94	3,1070,4943	CC,CT,TT		9.6401,7.3352,8.9428	benign	2936/4062	152278555	1076,10956	1820	4196	6016	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTCTGTCTTCTT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.8807A>G	1.37:g.152278555T>C	ENSP00000357789:p.Asp2936Gly	Somatic	843	9	0.0106762		WXS	Illumina HiSeq	Phase_I	1432	193	0.134777	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	7.089	0.571862	0.13623	0.073352	0.096401	ENSG00000143631	ENST00000368799	T	0.01685	4.69	1.29	1.29	0.21616	.	.	.	.	.	T	0.00815	0.0027	M	0.70595	2.14	0.80722	P	0.0	B	0.17852	0.024	B	0.10450	0.005	T	0.39375	-0.9617	8	0.22706	T	0.39	.	4.7721	0.13160	0.0:0.0:0.0:1.0	.	2936	P20930	FILA_HUMAN	G	2936	ENSP00000357789:D2936G	ENSP00000357789:D2936G	D	-	2	0	FLG	150545179	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.386000	0.07370	0.851000	0.35264	0.248000	0.18094	GAC	T|0.972;C|0.028	0.028	strong		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187692908	187692908	+	Silent	SNP	T	T	G	rs17852916	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187692908T>G	ENST00000295131.2	-	9	1744	c.1705A>C	c.(1705-1707)Aga>Cga	p.R569R		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	569					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			AAAGTTGATCTCTTGTTGTCC	0.368													t|||	726	0.144968	0.3154	0.0994	5008	,	,		17199	0.0208		0.1093	False		,,,				2504	0.1115				p.R569R		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A1705C						PASS	.	G		1331,3075	441.8+/-346.5	205,921,1077	114.0	113.0	113.0		1705	4.3	0.0	2	dbSNP_123	113	972,7628	209.8+/-250.9	45,882,3373	no	coding-synonymous	ZSWIM2	NM_182521.2		250,1803,4450	GG,GT,TT		11.3023,30.2088,17.7072		569/634	187692908	2303,10703	2203	4300	6503	SO:0001819	synonymous_variant	151112	exon9			TTGATCTCTTGTT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1705A>C	2.37:g.187692908T>G		Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	265	123	0.464151	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Silent	SNP	ENST00000295131.2	37	CCDS33348.1																																																																																			T|0.838;G|0.162	0.162	strong		0.368	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
MAS1	4142	hgsc.bcm.edu	37	6	160328620	160328620	+	Silent	SNP	C	C	T	rs220721	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160328620C>T	ENST00000252660.4	+	1	647	c.633C>T	c.(631-633)gtC>gtT	p.V211V		NM_002377.2	NP_002368.1	P04201	MAS_HUMAN	MAS1 proto-oncogene, G protein-coupled receptor	211					activation of NF-kappaB-inducing kinase activity (GO:0007250)|anatomical structure morphogenesis (GO:0009653)|cell proliferation (GO:0008283)|cellular response to peptide hormone stimulus (GO:0071375)|G-protein coupled receptor signaling pathway (GO:0007186)|hippocampus development (GO:0021766)|male gonad development (GO:0008584)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|protein kinase C signaling (GO:0070528)|regulation of inflammatory response (GO:0050727)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin receptor activity (GO:0001595)|angiotensin type II receptor activity (GO:0004945)|G-protein coupled receptor activity (GO:0004930)|peptide binding (GO:0042277)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.6e-06)		CCATCTTGGTCGTGAAGATCC	0.502													C|||	1702	0.339856	0.2927	0.3429	5008	,	,		22495	0.6677		0.2386	False		,,,				2504	0.1677				p.V211V		Atlas-SNP	.											.	MAS1	42	.	0			c.C633T						PASS	.	C		1264,3142	432.8+/-343.4	187,890,1126	110.0	106.0	107.0		633	-0.6	0.0	6	dbSNP_79	107	1873,6727	334.6+/-321.1	206,1461,2633	no	coding-synonymous	MAS1	NM_002377.2		393,2351,3759	TT,TC,CC		21.7791,28.6882,24.1196		211/326	160328620	3137,9869	2203	4300	6503	SO:0001819	synonymous_variant	4142	exon1			CTTGGTCGTGAAG	M13150	CCDS5272.1	6q24-q27	2014-06-26	2014-06-26		ENSG00000130368	ENSG00000130368		"""GPCR / Class A : Orphans"""	6899	protein-coding gene	gene with protein product		165180	"""MAS1 oncogene"""				Standard	NM_002377		Approved		uc003qsz.3	P04201	OTTHUMG00000015944	ENST00000252660.4:c.633C>T	6.37:g.160328620C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_002377	E1P5B3|Q2TBC9|Q6FG47	Silent	SNP	ENST00000252660.4	37	CCDS5272.1																																																																																			C|0.695;T|0.305	0.305	strong		0.502	MAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042930.2	NM_002377	
PCSK7	9159	hgsc.bcm.edu	37	11	117076875	117076875	+	Silent	SNP	G	G	A	rs139944026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117076875G>A	ENST00000320934.3	-	17	2826	c.2196C>T	c.(2194-2196)gaC>gaT	p.D732D	PCSK7_ENST00000529458.1_5'UTR|PCSK7_ENST00000540028.1_3'UTR	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	732					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		TTTCCACTTCGTCTGGATCCT	0.612			T	IGH@	MLCLS																																p.D732D		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C2196T						PASS	.	G		150,4252	98.9+/-137.6	0,150,2051	61.0	51.0	55.0		2196	-7.2	0.0	11	dbSNP_134	55	433,8151	129.7+/-187.7	0,433,3859	no	coding-synonymous	PCSK7	NM_004716.2		0,583,5910	AA,AG,GG		5.0443,3.4075,4.4895		732/786	117076875	583,12403	2201	4292	6493	SO:0001819	synonymous_variant	9159	exon17			CACTTCGTCTGGA	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.2196C>T	11.37:g.117076875G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	438	80	0.182648	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			G|0.934;A|0.066	0.066	strong		0.612	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
SRSF1	6426	hgsc.bcm.edu	37	17	56083705	56083705	+	Splice_Site	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:56083705A>G	ENST00000258962.4	-	2	586	c.378T>C	c.(376-378)tcT>tcC	p.S126S	RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000585096.1_Intron|SRSF1_ENST00000582730.2_Splice_Site_p.S126S|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000584773.1_Splice_Site_p.S126S	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	126	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TACACTCACCAGAGACAACCA	0.527																																					p.S126S		Atlas-SNP	.											.	SRSF1	41	.	0			c.T378C						PASS	.						44.0	53.0	50.0					17																	56083705		2125	4165	6290	SO:0001630	splice_region_variant	6426	exon2			CTCACCAGAGACA		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10780	protein-coding gene	gene with protein product	"""splicing factor 2"", ""pre-mRNA-splicing factor SF2, P33 subunit"", ""alternate splicing factor"", ""SR splicing factor 1"""	600812	"""splicing factor, arginine/serine-rich 1"""	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.379+1T>C	17.37:g.56083705A>G		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	174	56	0.321839	NM_006924	B2R6Z7|D3DTZ3|Q13809	Silent	SNP	ENST00000258962.4	37	CCDS11600.1																																																																																			.	.	none		0.527	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924	Silent
COQ9	57017	hgsc.bcm.edu	37	16	57490480	57490480	+	Missense_Mutation	SNP	A	A	C	rs191446011		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57490480A>C	ENST00000262507.6	+	4	512	c.443A>C	c.(442-444)cAt>cCt	p.H148P	COQ9_ENST00000567933.1_Intron|COQ9_ENST00000567072.1_Missense_Mutation_p.H148P	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN	coenzyme Q9	148					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						CTAATACTGCATTTTGTGACC	0.532													A|||	1	0.000199681	0.0	0.0	5008	,	,		22372	0.0		0.001	False		,,,				2504	0.0				p.H148P		Atlas-SNP	.											.	COQ9	30	.	0			c.A443C						PASS	.	A	PRO/HIS	0,4396		0,0,2198	143.0	123.0	130.0		443	5.6	1.0	16		130	2,8598	2.2+/-6.3	0,2,4298	no	missense	COQ9	NM_020312.3	77	0,2,6496	CC,CA,AA		0.0233,0.0,0.0154	probably-damaging	148/319	57490480	2,12994	2198	4300	6498	SO:0001583	missense	57017	exon4			TACTGCATTTTGT	BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682			25302	protein-coding gene	gene with protein product		612837	"""chromosome 16 open reading frame 49"", ""coenzyme Q9 homolog (yeast)"", ""coenzyme Q9 homolog (S. cerevisiae)"""	C16orf49		19375058	Standard	NM_020312		Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000262507.6:c.443A>C	16.37:g.57490480A>C	ENSP00000262507:p.His148Pro	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	175	24	0.137143	NM_020312	A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	Missense_Mutation	SNP	ENST00000262507.6	37	CCDS32459.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	23.2	4.387434	0.82902	0.0	2.33E-4	ENSG00000088682	ENST00000262507	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.84133	0.5405	M	0.88450	2.955	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.996;0.998;0.998	D	0.86577	0.1851	9	0.54805	T	0.06	-11.6483	14.9239	0.70862	1.0:0.0:0.0:0.0	.	148;148;148;148	B4E0U3;B4DIV2;B4DEE3;O75208	.;.;.;COQ9_HUMAN	P	148	.	ENSP00000262507:H148P	H	+	2	0	COQ9	56047981	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	8.700000	0.91322	2.117000	0.64856	0.460000	0.39030	CAT	A|1.000;C|0.000	0.000	strong		0.532	COQ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432598.3	NM_020312	
CHI3L2	1117	hgsc.bcm.edu	37	1	111783982	111783982	+	Silent	SNP	C	C	A	rs13721	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:111783982C>A	ENST00000445067.2	+	11	1723	c.952C>A	c.(952-954)Cgg>Agg	p.R318R	CHI3L2_ENST00000466741.1_Silent_p.R239R|CHI3L2_ENST00000369744.2_Silent_p.R308R|CHI3L2_ENST00000524472.1_Silent_p.R239R|CHI3L2_ENST00000369748.4_Silent_p.R318R|CHI3L2_ENST00000529459.1_3'UTR			Q15782	CH3L2_HUMAN	chitinase 3-like 2	318			R -> W (in dbSNP:rs13721).		carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		CAAGATCACGCGGCTCCAGGA	0.537													A|||	953	0.190296	0.0507	0.1729	5008	,	,		20313	0.1974		0.333	False		,,,				2504	0.2372				p.R318R		Atlas-SNP	.											.	CHI3L2	38	.	0			c.C952A						PASS	.	A	,,	458,3948		30,398,1775	97.0	87.0	90.0		922,715,952	3.6	0.0	1	dbSNP_52	90	2572,6028		536,1500,2264	no	coding-synonymous,coding-synonymous,coding-synonymous	CHI3L2	NM_001025197.1,NM_001025199.1,NM_004000.2	,,	566,1898,4039	AA,AC,CC		29.907,10.3949,23.2969	,,	308/381,239/312,318/391	111783982	3030,9976	2203	4300	6503	SO:0001819	synonymous_variant	1117	exon9			ATCACGCGGCTCC	U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.952C>A	1.37:g.111783982C>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	77	60	0.779221	NM_004000	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Silent	SNP	ENST00000445067.2	37	CCDS30802.1																																																																																			A|0.280;C|0.697;T|0.022	0.280	strong		0.537	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000	
URB1	9875	hgsc.bcm.edu	37	21	33688855	33688855	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:33688855G>A	ENST00000382751.3	-	38	6671	c.6556C>T	c.(6556-6558)Cgg>Tgg	p.R2186W		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	2186						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						CTCCCTGCCCGGCCCTGGGCA	0.627																																					p.R2186W		Atlas-SNP	.											.	URB1	176	.	0			c.C6556T						PASS	.						21.0	25.0	24.0					21																	33688855		692	1590	2282	SO:0001583	missense	9875	exon38			CTGCCCGGCCCTG	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.6556C>T	21.37:g.33688855G>A	ENSP00000372199:p.Arg2186Trp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	114	71	0.622807	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	.	.	.	.	.	.	.	.	.	.	G	6.936	0.542407	0.13250	.	.	ENSG00000142207	ENST00000382751	T	0.32753	1.44	5.31	1.28	0.21552	.	1.121610	0.06416	N	0.721426	T	0.21186	0.0510	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28996	-1.0026	10	0.49607	T	0.09	-6.2552	6.3726	0.21489	0.1371:0.0:0.4702:0.3927	.	2186	O60287	NPA1P_HUMAN	W	2186	ENSP00000372199:R2186W	ENSP00000372199:R2186W	R	-	1	2	URB1	32610726	0.005000	0.15991	0.001000	0.08648	0.137000	0.21094	0.545000	0.23268	-0.048000	0.13401	-1.319000	0.01295	CGG	.	.	none		0.627	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
D2HGDH	728294	hgsc.bcm.edu	37	2	242690745	242690745	+	Missense_Mutation	SNP	C	C	T	rs1105273	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242690745C>T	ENST00000321264.4	+	8	1291	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V	D2HGDH_ENST00000403782.1_Missense_Mutation_p.A227V|D2HGDH_ENST00000486953.1_Intron	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	361			A -> V (in dbSNP:rs1105273).		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)		CTGGAGCACGCGCTGGGCTCC	0.617													C|||	1078	0.215256	0.2882	0.3271	5008	,	,		19217	0.2242		0.1133	False		,,,				2504	0.1329				p.A361V		Atlas-SNP	.											D2HGDH,NS,carcinoma,-1,1	D2HGDH	39	1	0			c.C1082T						PASS	.	T	VAL/ALA	1168,3238	408.0+/-334.4	153,862,1188	54.0	51.0	52.0		1082	-7.9	0.0	2	dbSNP_86	52	912,7680	201.8+/-245.2	50,812,3434	yes	missense	D2HGDH	NM_152783.3	64	203,1674,4622	TT,TC,CC		10.6145,26.5093,16.0025	benign	361/522	242690745	2080,10918	2203	4296	6499	SO:0001583	missense	728294	exon8			AGCACGCGCTGGG	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.1082C>T	2.37:g.242690745C>T	ENSP00000315351:p.Ala361Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	37	CCDS33426.1	468	0.21428571428571427	134	0.27235772357723576	111	0.30662983425414364	132	0.23076923076923078	91	0.12005277044854881	c	0.048	-1.258655	0.01445	0.265093	0.106145	ENSG00000180902	ENST00000321264;ENST00000403782;ENST00000454048	T;T;T	0.78595	-1.19;-1.19;-1.01	5.1	-7.9	0.01169	FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.602385	0.16472	N	0.212932	T	0.00012	0.0000	N	0.20845	0.615	0.27582	P	0.9495508	B	0.13145	0.007	B	0.14023	0.01	T	0.12091	-1.0561	9	0.02654	T	1	-0.5439	16.7058	0.85371	0.0:0.3272:0.0:0.6728	rs1105273	361	Q8N465	D2HDH_HUMAN	V	361;227;62	ENSP00000315351:A361V;ENSP00000384723:A227V;ENSP00000404596:A62V	ENSP00000315351:A361V	A	+	2	0	D2HGDH	242339418	0.045000	0.20229	0.000000	0.03702	0.026000	0.11368	0.251000	0.18257	-1.680000	0.01450	-0.974000	0.02594	GCG	C|0.817;T|0.183	0.183	strong		0.617	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48598785	48598785	+	Missense_Mutation	SNP	G	G	A	rs1380657	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48598785G>A	ENST00000323776.5	+	9	1432	c.1270G>A	c.(1270-1272)Gca>Aca	p.A424T	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.A387T	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)			TGAAGACACAGCATACTTGTG	0.547													A|||	4060	0.810703	0.913	0.6988	5008	,	,		20382	0.8879		0.7336	False		,,,				2504	0.7515				p.A424T		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.G1270A						PASS	.	A	THR/ALA	3921,485		1750,421,32	64.0	65.0	65.0		1270	-4.3	0.0	17	dbSNP_88	65	6246,2354		2285,1676,339	yes	missense	MYCBPAP	NM_032133.4	58	4035,2097,371	AA,AG,GG		27.3721,11.0077,21.8284	benign	424/985	48598785	10167,2839	2203	4300	6503	SO:0001583	missense	84073	exon9			GACACAGCATACT	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.1270G>A	17.37:g.48598785G>A	ENSP00000323184:p.Ala424Thr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	155	153	0.987097	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	1777	0.8136446886446886	453	0.9207317073170732	258	0.712707182320442	510	0.8916083916083916	556	0.7335092348284961	A	5.695	0.312728	0.10789	0.889923	0.726279	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.45276	0.9;0.9	4.68	-4.29	0.03721	.	2.770710	0.01165	N	0.006722	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	0.28808	-1.0032	9	0.11182	T	0.66	1.3766	8.3331	0.32197	0.5198:0.0:0.3793:0.1009	rs1380657;rs17856808;rs58822805;rs1380657	387	Q8TBZ2	MYBPP_HUMAN	T	424;387	ENSP00000323184:A424T;ENSP00000397209:A387T	ENSP00000323184:A424T	A	+	1	0	MYCBPAP	45953784	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.797000	0.04570	-1.013000	0.03383	-1.007000	0.02485	GCA	G|0.199;A|0.801	0.801	strong		0.547	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
KCNG4	93107	hgsc.bcm.edu	37	16	84256410	84256410	+	Missense_Mutation	SNP	C	C	T	rs7196482	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:84256410C>T	ENST00000308251.4	-	3	1041	c.973G>A	c.(973-975)Ggg>Agg	p.G325R		NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	325			G -> R (in dbSNP:rs7196482).		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)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						TAGGAGCTCCCGCTCGGCCTC	0.677													C|||	885	0.176717	0.2156	0.1686	5008	,	,		17359	0.0506		0.2266	False		,,,				2504	0.2086				p.G325R		Atlas-SNP	.											.	KCNG4	71	.	0			c.G973A						PASS	.	C	ARG/GLY	942,3458	340.2+/-306.1	109,724,1367	30.0	33.0	32.0		973	-2.7	0.0	16	dbSNP_116	32	1922,6678	321.7+/-315.2	212,1498,2590	no	missense	KCNG4	NM_172347.2	125	321,2222,3957	TT,TC,CC		22.3488,21.4091,22.0308	probably-damaging	325/520	84256410	2864,10136	2200	4300	6500	SO:0001583	missense	93107	exon3			AGCTCCCGCTCGG	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.973G>A	16.37:g.84256410C>T	ENSP00000312129:p.Gly325Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	90	18	0.2	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	369	0.16895604395604397	101	0.20528455284552846	63	0.17403314917127072	26	0.045454545454545456	179	0.23614775725593667	C	8.185	0.794792	0.16327	0.214091	0.223488	ENSG00000168418	ENST00000308251	D	0.97041	-4.22	5.61	-2.74	0.05932	Ion transport (1);	0.310951	0.34268	N	0.004108	T	0.00552	0.0018	M	0.75085	2.285	0.58432	P	6.999999999979245E-6	D	0.56521	0.976	P	0.51516	0.672	T	0.50642	-0.8804	9	0.72032	D	0.01	.	8.1708	0.31254	0.0:0.3567:0.1088:0.5345	rs7196482;rs59048729;rs7196482	325	Q8TDN1	KCNG4_HUMAN	R	325	ENSP00000312129:G325R	ENSP00000312129:G325R	G	-	1	0	KCNG4	82813911	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.117000	0.10708	-0.433000	0.07286	0.655000	0.94253	GGG	C|0.810;T|0.190	0.190	strong		0.677	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
TMEM45A	55076	hgsc.bcm.edu	37	3	100287764	100287764	+	Silent	SNP	T	T	C	rs28722928	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:100287764T>C	ENST00000323523.4	+	5	1000	c.687T>C	c.(685-687)taT>taC	p.Y229Y	TMEM45A_ENST00000403410.1_Silent_p.Y245Y	NM_018004.1	NP_060474.1	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	229						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)	11						GTTGGCATTATGCAGTAACCA	0.393													T|||	1251	0.2498	0.3835	0.2493	5008	,	,		19660	0.3185		0.1213	False		,,,				2504	0.1309				p.Y229Y		Atlas-SNP	.											.	TMEM45A	35	.	0			c.T687C						PASS	.	T		1506,2900	479.4+/-358.5	266,974,963	261.0	252.0	255.0		687	-2.4	0.1	3	dbSNP_125	255	1044,7556	220.8+/-258.4	63,918,3319	no	coding-synonymous	TMEM45A	NM_018004.1		329,1892,4282	CC,CT,TT		12.1395,34.1807,19.6063		229/276	100287764	2550,10456	2203	4300	6503	SO:0001819	synonymous_variant	55076	exon5			GCATTATGCAGTA	AK000996	CCDS2937.1	3q12.2	2005-02-04			ENSG00000181458	ENSG00000181458			25480	protein-coding gene	gene with protein product						12477932	Standard	XM_005247568		Approved	FLJ10134, DERP7	uc003dtz.1	Q9NWC5	OTTHUMG00000150327	ENST00000323523.4:c.687T>C	3.37:g.100287764T>C		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	232	112	0.482759	NM_018004	Q53YW5	Silent	SNP	ENST00000323523.4	37	CCDS2937.1																																																																																			T|0.783;C|0.217	0.217	strong		0.393	TMEM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317571.1	NM_018004	
TTBK2	146057	hgsc.bcm.edu	37	15	43170793	43170793	+	Missense_Mutation	SNP	A	A	G	rs6493068	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:43170793A>G	ENST00000267890.6	-	2	131	c.23T>C	c.(22-24)cTg>cCg	p.L8P	TTBK2_ENST00000567274.1_Missense_Mutation_p.L8P|TTBK2_ENST00000567840.1_Missense_Mutation_p.L8P|TTBK2_ENST00000567485.1_5'UTR	NM_173500.3	NP_775771.3	Q6IQ55	TTBK2_HUMAN	tau tubulin kinase 2	8			L -> P (in dbSNP:rs6493068). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:19533200}.		cell death (GO:0008219)|cilium assembly (GO:0042384)|peptidyl-serine phosphorylation (GO:0018105)|smoothened signaling pathway (GO:0007224)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	43		all_cancers(109;6.11e-16)|all_epithelial(112;5.5e-14)|Lung NSC(122;1.76e-08)|all_lung(180;6.04e-08)|Melanoma(134;0.0179)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;3.23e-07)		CAGGATATCCAGCTGCTCTCC	0.458													G|||	2578	0.514776	0.9592	0.2867	5008	,	,		15499	0.4157		0.2803	False		,,,				2504	0.4192				p.L8P		Atlas-SNP	.											.	TTBK2	82	.	0			c.T23C						PASS	.	G	PRO/LEU	3271,759		1343,585,87	159.0	179.0	173.0		23	5.3	0.9	15	dbSNP_116	173	2534,5802		356,1822,1990	yes	missense	TTBK2	NM_173500.3	98	1699,2407,2077	GG,GA,AA		30.3983,18.8337,46.9432	benign	8/1245	43170793	5805,6561	2015	4168	6183	SO:0001583	missense	146057	exon2			ATATCCAGCTGCT	AB020654	CCDS42029.1	15q15.2	2014-01-21			ENSG00000128881	ENSG00000128881			19141	protein-coding gene	gene with protein product		611695	"""spinocerebellar ataxia 11"""	SCA11		10048485	Standard	NM_173500		Approved	KIAA0847	uc001zqo.2	Q6IQ55	OTTHUMG00000175802	ENST00000267890.6:c.23T>C	15.37:g.43170793A>G	ENSP00000267890:p.Leu8Pro	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	102	24	0.235294	NM_173500	O94932|Q6ZN52|Q8IVV1	Missense_Mutation	SNP	ENST00000267890.6	37	CCDS42029.1	1047	0.4793956043956044	465	0.9451219512195121	118	0.3259668508287293	242	0.4230769230769231	222	0.2928759894459103	G	14.23	2.474363	0.43942	0.811663	0.303983	ENSG00000128881	ENST00000267890	T	0.37235	1.21	5.29	5.29	0.74685	.	.	.	.	.	T	0.00012	0.0000	N	0.05124	-0.11	0.22330	P	0.999196997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27157	-1.0082	8	0.25106	T	0.35	.	14.2099	0.65756	0.0722:0.0:0.9278:0.0	rs6493068;rs52823398;rs6493068	8;8	Q6IQ55-3;Q6IQ55	.;TTBK2_HUMAN	P	8	ENSP00000267890:L8P	ENSP00000267890:L8P	L	-	2	0	TTBK2	40958085	1.000000	0.71417	0.892000	0.35008	0.883000	0.51084	5.237000	0.65360	1.242000	0.43836	-0.124000	0.14976	CTG	A|0.525;G|0.475	0.475	strong		0.458	TTBK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431106.2	NM_173500	
CDON	50937	hgsc.bcm.edu	37	11	125889526	125889526	+	Missense_Mutation	SNP	C	C	T	rs3740909	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125889526C>T	ENST00000392693.3	-	4	611	c.484G>A	c.(484-486)Gaa>Aaa	p.E162K	CDON_ENST00000263577.7_Missense_Mutation_p.E162K	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	162	Ig-like C2-type 2.		E -> K (in dbSNP:rs3740909).		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)		p.E162K(1)		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)		GTGGAATGTTCCAGCCATTTT	0.463													T|||	561	0.112021	0.1142	0.1225	5008	,	,		16614	0.127		0.0885	False		,,,				2504	0.1104				p.E162K		Atlas-SNP	.											CDON,NS,carcinoma,0,1	CDON	137	1	1	Substitution - Missense(1)	stomach(1)	c.G484A						PASS	.	T	LYS/GLU	545,3857	775.6+/-414.1	39,467,1695	147.0	151.0	149.0		484	4.0	0.9	11	dbSNP_107	149	739,7859	785.5+/-407.6	30,679,3590	yes	missense	CDON	NM_016952.4	56	69,1146,5285	TT,TC,CC		8.595,12.3807,9.8769	benign	162/1265	125889526	1284,11716	2201	4299	6500	SO:0001583	missense	50937	exon4			AATGTTCCAGCCA	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.484G>A	11.37:g.125889526C>T	ENSP00000376458:p.Glu162Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	203	51	0.251232	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	235|235	0.10760073260073261|0.10760073260073261	59|59	0.11991869918699187|0.11991869918699187	42|42	0.11602209944751381|0.11602209944751381	63|63	0.11013986013986014|0.11013986013986014	71|71	0.09366754617414248|0.09366754617414248	T|T	6.637|6.637	0.485978|0.485978	0.12641|0.12641	0.123807|0.123807	0.08595|0.08595	ENSG00000064309|ENSG00000064309	ENST00000392693;ENST00000263577;ENST00000531586|ENST00000534661	T;T;T|.	0.60548|.	2.7;2.7;0.18|.	5.33|5.33	4.03|4.03	0.46877|0.46877	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.362364|.	0.23589|.	N|.	0.046564|.	T|T	0.00552|0.00552	0.0018|0.0018	L|L	0.35793|0.35793	1.09|1.09	0.58432|0.58432	P|P	5.000000000032756E-6|5.000000000032756E-6	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.11329|.	0.0;0.006;0.003|.	T|T	0.12889|0.12889	-1.0530|-1.0530	9|4	0.02654|.	T|.	1|.	-5.3068|-5.3068	4.0763|4.0763	0.09906|0.09906	0.0:0.2693:0.1793:0.5514|0.0:0.2693:0.1793:0.5514	rs3740909;rs58697958;rs3740909|rs3740909;rs58697958;rs3740909	162;162;162|.	E9PRD8;Q4KMG0;Q4KMG0-2|.	.;CDON_HUMAN;.|.	K|E	162|137	ENSP00000376458:E162K;ENSP00000263577:E162K;ENSP00000434212:E162K|.	ENSP00000263577:E162K|.	E|G	-|-	1|2	0|0	CDON|CDON	125394736|125394736	1.000000|1.000000	0.71417|0.71417	0.903000|0.903000	0.35520|0.35520	0.969000|0.969000	0.65631|0.65631	1.933000|1.933000	0.40153|0.40153	0.961000|0.961000	0.38030|0.38030	-0.361000|-0.361000	0.07541|0.07541	GAA|GGA	C|0.896;N|0.000	.	strong		0.463	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
RPL13A	23521	hgsc.bcm.edu	37	19	49993535	49993535	+	Silent	SNP	C	C	G	rs1064257	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49993535C>G	ENST00000391857.4	+	3	211	c.135C>G	c.(133-135)ggC>ggG	p.G45G	RPL13A_ENST00000477613.2_3'UTR|CTD-3148I10.15_ENST00000595815.1_RNA|SNORD34_ENST00000365633.1_RNA|SNORD35A_ENST00000363389.1_RNA|SNORD32A_ENST00000364805.1_RNA|SNORD33_ENST00000362761.1_RNA	NM_001270491.1|NM_012423.3	NP_001257420.1|NP_036555.1	P40429	RL13A_HUMAN	ribosomal protein L13a	45					cellular protein metabolic process (GO:0044267)|cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of formation of translation preinitiation complex (GO:1901194)|negative regulation of translation (GO:0017148)|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)|focal adhesion (GO:0005925)|GAIT complex (GO:0097452)|large ribosomal subunit (GO:0015934)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)	2		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		ACATTTCTGGCAATTTCTACA	0.567													C|||	80	0.0159744	0.0023	0.0331	5008	,	,		18852	0.0		0.0477	False		,,,				2504	0.0061				p.G45G		Atlas-SNP	.											.	RPL13A	13	.	0			c.C135G						PASS	.	C		46,4360	50.2+/-85.5	0,46,2157	52.0	49.0	50.0		135	-0.3	1.0	19	dbSNP_86	50	443,8157	133.9+/-191.4	11,421,3868	no	coding-synonymous	RPL13A	NM_012423.2		11,467,6025	GG,GC,CC		5.1512,1.044,3.7598		45/204	49993535	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	23521	exon3			TTCTGGCAATTTC	X56932	CCDS12768.1, CCDS74421.1	19q13.3	2011-04-06			ENSG00000142541	ENSG00000142541		"""L ribosomal proteins"""	10304	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 1"""	TSTA1			Standard	NM_012423		Approved	L13A	uc031rlt.1	P40429	OTTHUMG00000134289	ENST00000391857.4:c.135C>G	19.37:g.49993535C>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_012423	A8K505	Silent	SNP	ENST00000391857.4	37	CCDS12768.1																																																																																			C|0.964;G|0.036	0.036	strong		0.567	RPL13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258989.1		
WWC1	23286	hgsc.bcm.edu	37	5	167858372	167858372	+	Missense_Mutation	SNP	T	T	G	rs386694705|rs3822659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:167858372T>G	ENST00000265293.4	+	15	2705	c.2203T>G	c.(2203-2205)Tcc>Gcc	p.S735A	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Missense_Mutation_p.S735A	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	735	C2.		S -> A (polymorphism; associated with Ile-734; affects KIBRA lipid-binding specificity showing stronger interactions with PI(4)P and PI(5)P; dbSNP:rs3822659). {ECO:0000269|PubMed:23778582}.		cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|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)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GGTATCCATGTCCTATCCAGC	0.557													T|||	805	0.160743	0.2859	0.0663	5008	,	,		16464	0.2312		0.0736	False		,,,				2504	0.0757				p.S735A		Atlas-SNP	.											.	WWC1	98	.	0			c.T2203G						PASS	.																																			SO:0001583	missense	23286	exon15			TCCATGTCCTATC	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"""WW, C2 and coiled-coil domain containing"""	29435	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 168"""	610533	"""WW, C2 and coiled-coil domain containing 1"""			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2203T>G	5.37:g.167858372T>G	ENSP00000265293:p.Ser735Ala	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	37	CCDS4366.1	279|279	0.12774725274725274|0.12774725274725274	105|105	0.21341463414634146|0.21341463414634146	26|26	0.0718232044198895|0.0718232044198895	104|104	0.18181818181818182|0.18181818181818182	44|44	0.05804749340369393|0.05804749340369393	T|T	11.22|11.22	1.573212|1.573212	0.28092|0.28092	.|.	.|.	ENSG00000113645|ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038|ENST00000393895;ENST00000524228	T;T;T|.	0.26518|.	1.73;1.73;1.73|.	5.24|5.24	5.24|5.24	0.73138|0.73138	C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00073|0.00073	0.0002|0.0002	M|M	0.61703|0.61703	1.905|1.905	0.09310|0.09310	P|P	0.99999281213|0.99999281213	B;B;B;B|.	0.26195|.	0.095;0.144;0.002;0.077|.	B;B;B;B|.	0.34418|.	0.099;0.182;0.022;0.092|.	T|T	0.11179|0.11179	-1.0598|-1.0598	9|4	0.08381|.	T|.	0.77|.	.|.	10.3846|10.3846	0.44132|0.44132	0.0:0.076:0.0:0.924|0.0:0.076:0.0:0.924	rs3822659;rs60429120;rs3822659|rs3822659;rs60429120;rs3822659	735;641;641;735|.	Q8IX03-2;F5H498;B3KX05;Q8IX03|.	.;.;.;KIBRA_HUMAN|.	A|G	735;735;61|696;511	ENSP00000265293:S735A;ENSP00000427772:S735A;ENSP00000428084:S61A|.	ENSP00000265293:S735A|.	S|V	+|+	1|2	0|0	WWC1|WWC1	167790950|167790950	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	4.456000|4.456000	0.60081|0.60081	1.977000|1.977000	0.57605|0.57605	0.533000|0.533000	0.62120|0.62120	TCC|GTC	T|0.868;G|0.132	0.132	strong		0.557	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
ST3GAL5	8869	hgsc.bcm.edu	37	2	86088311	86088311	+	Missense_Mutation	SNP	T	T	C	rs1138484	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:86088311T>C	ENST00000377332.3	-	3	419	c.311A>G	c.(310-312)cAt>cGt	p.H104R	ST3GAL5_ENST00000393808.3_Missense_Mutation_p.H81R|ST3GAL5_ENST00000393805.1_Missense_Mutation_p.H76R|ST3GAL5_ENST00000484728.1_5'UTR|ST3GAL5_ENST00000525834.2_Missense_Mutation_p.H104R	NM_003896.3	NP_003887.3	Q9UNP4	SIAT9_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 5	104			H -> R (in dbSNP:rs3731824). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9822625, ECO:0000269|Ref.2}.		carbohydrate metabolic process (GO:0005975)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid biosynthetic process (GO:0006688)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	lactosylceramide alpha-2,3-sialyltransferase activity (GO:0047291)|neolactotetraosylceramide alpha-2,3-sialyltransferase activity (GO:0004513)|sialyltransferase activity (GO:0008373)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15						AACCTTTACATGGTCAGGGTC	0.338													C|||	1047	0.209065	0.0605	0.1527	5008	,	,		20921	0.2937		0.1968	False		,,,				2504	0.3753				p.H104R		Atlas-SNP	.											.	ST3GAL5	51	.	0			c.A311G						PASS	.	C	ARG/HIS,ARG/HIS	334,4072	795.3+/-415.3	17,300,1886	116.0	109.0	111.0		242,311	5.0	0.7	2	dbSNP_107	111	1705,6895	737.1+/-407.0	173,1359,2768	yes	missense,missense	ST3GAL5	NM_001042437.1,NM_003896.3	29,29	190,1659,4654	CC,CT,TT		19.8256,7.5806,15.6774	benign,benign	81/396,104/419	86088311	2039,10967	2203	4300	6503	SO:0001583	missense	8869	exon3			TTTACATGGTCAG	AB018356	CCDS1986.2, CCDS42705.1	2p11.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000115525	ENSG00000115525	2.4.99.9	"""Sialyltransferases"""	10872	protein-coding gene	gene with protein product		604402	"""sialyltransferase 9 (CMP-NeuAc:lactosylceramide alpha-2,3-sialyltransferase; GM3 synthase)"""	SIAT9		9822625	Standard	NM_003896		Approved	ST3GalV, SIATGM3S	uc002sqq.1	Q9UNP4	OTTHUMG00000130171	ENST00000377332.3:c.311A>G	2.37:g.86088311T>C	ENSP00000366549:p.His104Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_003896	B3KM82|D6W5L9|O94902|Q53QU1|Q6NZX4|Q6YFL1	Missense_Mutation	SNP	ENST00000377332.3	37	CCDS1986.2	405	0.18543956043956045	28	0.056910569105691054	73	0.20165745856353592	169	0.29545454545454547	135	0.17810026385224276	C	0.240	-1.014477	0.02095	0.075806	0.198256	ENSG00000115525	ENST00000393808;ENST00000393805;ENST00000377332;ENST00000455892;ENST00000525834	T;T;T;T;T	0.36878	1.71;1.71;1.72;1.23;1.29	5.84	4.96	0.65561	.	0.494910	0.22557	N	0.058515	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35798	-0.9774	9	0.02654	T	1	-4.2027	9.0708	0.36491	0.0:0.8325:0.0:0.1675	rs3731824;rs52830384;rs60063777;rs3731824	104;104;81	G3V199;Q9UNP4;Q9UNP4-3	.;SIAT9_HUMAN;.	R	81;76;104;76;104	ENSP00000377397:H81R;ENSP00000377394:H76R;ENSP00000366549:H104R;ENSP00000401375:H76R;ENSP00000433607:H104R	ENSP00000306247:H104R	H	-	2	0	ST3GAL5	85941822	0.674000	0.27549	0.655000	0.29622	0.439000	0.31926	0.845000	0.27668	0.821000	0.34540	-0.119000	0.15052	CAT	T|0.829;C|0.171	0.171	strong		0.338	ST3GAL5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252486.1	NM_003896	
ABCC3	8714	hgsc.bcm.edu	37	17	48745035	48745035	+	Silent	SNP	A	A	C	rs11568601	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48745035A>C	ENST00000285238.8	+	12	1632	c.1552A>C	c.(1552-1554)Agg>Cgg	p.R518R	ABCC3_ENST00000427699.1_Silent_p.R518R	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	518	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|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)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	GGAGGGCATCAGGCAGGGTGA	0.622													A|||	26	0.00519169	0.0015	0.0058	5008	,	,		22136	0.0		0.0189	False		,,,				2504	0.001				p.R518R		Atlas-SNP	.											.	ABCC3	138	.	0			c.A1552C						PASS	.	A	,	21,4385	28.1+/-56.4	0,21,2182	72.0	58.0	63.0		1552,1552	1.7	1.0	17	dbSNP_126	63	219,8381	91.1+/-153.3	3,213,4084	no	coding-synonymous,coding-synonymous	ABCC3	NM_001144070.1,NM_003786.3	,	3,234,6266	CC,CA,AA		2.5465,0.4766,1.8453	,	518/573,518/1528	48745035	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon12			GGCATCAGGCAGG	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.1552A>C	17.37:g.48745035A>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			A|0.984;C|0.016	0.016	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
CANT1	124583	hgsc.bcm.edu	37	17	76993546	76993546	+	Silent	SNP	A	A	G	rs8077024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76993546A>G	ENST00000302345.2	-	2	653	c.159T>C	c.(157-159)gcT>gcC	p.A53A	CANT1_ENST00000591732.1_5'Flank|CANT1_ENST00000591773.1_Silent_p.A53A|CANT1_ENST00000392446.5_Silent_p.A53A	NM_001159773.1|NM_138793.3	NP_001153245.1|NP_620148.1	Q8WVQ1	CANT1_HUMAN	calcium activated nucleotidase 1	53					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|proteoglycan biosynthetic process (GO:0030166)|signal transduction (GO:0007165)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|signal transducer activity (GO:0004871)|uridine-diphosphatase activity (GO:0045134)		CANT1/ETV4(3)	cervix(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)	16			BRCA - Breast invasive adenocarcinoma(99;0.0362)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			AGAGGATGGCAGCACCCACAA	0.697			T	ETV4	prostate								G|||	2221	0.44349	0.4062	0.4366	5008	,	,		9965	0.6716		0.2734	False		,,,				2504	0.4387				p.A53A		Atlas-SNP	.		Dom	yes		17	17q25	124583	calcium activated nucleotidase 1		E	.	CANT1	39	.	0			c.T159C						PASS	.	G	,,	1785,2615		370,1045,785	14.0	18.0	17.0		159,159,159	-3.0	0.0	17	dbSNP_116	17	2383,6201		335,1713,2244	no	coding-synonymous,coding-synonymous,coding-synonymous	CANT1	NM_001159772.1,NM_001159773.1,NM_138793.3	,,	705,2758,3029	GG,GA,AA		27.761,40.5682,32.101	,,	53/402,53/402,53/402	76993546	4168,8816	2200	4292	6492	SO:0001819	synonymous_variant	124583	exon4			GATGGCAGCACCC	AJ312208	CCDS11760.1	17q25.3	2008-02-05	2004-10-12	2004-10-15		ENSG00000171302			19721	protein-coding gene	gene with protein product	"""Soluble Ca-Activated Nucleotidase, isozyme 1"""	613165				12167635	Standard	NM_138793		Approved	SHAPY, SCAN-1	uc002jwk.3	Q8WVQ1		ENST00000302345.2:c.159T>C	17.37:g.76993546A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	99	34	0.343434	NM_001159772	B4DJ54|Q7Z2J7|Q8NG05|Q8NHP0|Q9BSD5	Silent	SNP	ENST00000302345.2	37	CCDS11760.1																																																																																			A|0.572;G|0.428	0.428	strong		0.697	CANT1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437723.2	NM_138793	
FLG	2312	hgsc.bcm.edu	37	1	152277184	152277184	+	Missense_Mutation	SNP	T	T	C	rs146234375	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152277184T>C	ENST00000368799.1	-	3	10213	c.10178A>G	c.(10177-10179)cAt>cGt	p.H3393R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3393	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACTGTTCATGAGTGCTCAC	0.622									Ichthyosis				T|||	2	0.000399361	0.0	0.0	5008	,	,		18980	0.0		0.001	False		,,,				2504	0.001				p.H3393R		Atlas-SNP	.											.	FLG	900	.	0			c.A10178G						PASS	.	T	ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	186.0	214.0	205.0		10178	-0.1	0.0	1	dbSNP_134	205	6,8590	5.0+/-18.6	0,6,4292	no	missense	FLG	NM_002016.1	29	0,7,6494	CC,CT,TT		0.0698,0.0227,0.0538	probably-damaging	3393/4062	152277184	7,12995	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGTTCATGAGTGC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10178A>G	1.37:g.152277184T>C	ENSP00000357789:p.His3393Arg	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	415	119	0.286747	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	9.709	1.156448	0.21454	2.27E-4	6.98E-4	ENSG00000143631	ENST00000368799	T	0.00792	5.69	2.54	-0.0744	0.13731	.	.	.	.	.	T	0.00906	0.0030	M	0.81942	2.565	0.09310	N	1	D	0.65815	0.995	D	0.79108	0.992	T	0.46133	-0.9213	9	0.13108	T	0.6	0.0059	3.1875	0.06606	0.0:0.144:0.2438:0.6122	.	3393	P20930	FILA_HUMAN	R	3393	ENSP00000357789:H3393R	ENSP00000357789:H3393R	H	-	2	0	FLG	150543808	0.004000	0.15560	0.001000	0.08648	0.011000	0.07611	0.165000	0.16564	-0.024000	0.13941	0.373000	0.22412	CAT	T|0.999;C|0.001	0.001	strong		0.622	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
POLN	353497	hgsc.bcm.edu	37	4	2175733	2175733	+	Silent	SNP	A	A	G	rs2022302	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:2175733A>G	ENST00000511885.2	-	11	1676	c.1323T>C	c.(1321-1323)caT>caC	p.H441H	POLN_ENST00000382865.1_Silent_p.H441H|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	441					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)			CCTGAATGGCATGGCTTTCCA	0.418								DNA polymerases (catalytic subunits)					G|||	1612	0.321885	0.5703	0.2435	5008	,	,		24761	0.373		0.1243	False		,,,				2504	0.1922				p.H441H		Atlas-SNP	.											.	POLN	82	.	0			c.T1323C						PASS	.	G		2221,2185	586.4+/-386.5	581,1059,563	270.0	231.0	244.0		1323	-0.9	0.0	4	dbSNP_94	244	995,7605	773.9+/-407.7	60,875,3365	no	coding-synonymous	POLN	NM_181808.2		641,1934,3928	GG,GA,AA		11.5698,49.5915,24.727		441/901	2175733	3216,9790	2203	4300	6503	SO:0001819	synonymous_variant	353497	exon9			AATGGCATGGCTT	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.1323T>C	4.37:g.2175733A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	166	99	0.596386	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Silent	SNP	ENST00000511885.2	37	CCDS3360.1	677	0.309981684981685	281	0.5711382113821138	91	0.2513812154696133	210	0.36713286713286714	95	0.12532981530343007	G	0.009	-1.809418	0.00606	0.504085	0.115698	ENSG00000130997	ENST00000511098	.	.	.	4.28	-0.849	0.10723	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.51012	P	9.80000000000425E-5	.	.	.	.	.	.	T	0.46400	-0.9194	3	.	.	.	-3.7462	9.2076	0.37298	0.5601:0.0:0.4399:0.0	rs2022302;rs61574681;rs2022302	.	.	.	T	75	.	.	M	-	2	0	POLN	2145531	0.000000	0.05858	0.007000	0.13788	0.003000	0.03518	-1.618000	0.02049	-0.617000	0.05664	-2.725000	0.00131	ATG	A|0.714;G|0.286	0.286	strong		0.418	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
AXIN1	8312	hgsc.bcm.edu	37	16	347184	347184	+	Silent	SNP	A	A	G	rs214252	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:347184A>G	ENST00000262320.3	-	7	2198	c.1827T>C	c.(1825-1827)gcT>gcC	p.A609A	AXIN1_ENST00000481769.1_5'Flank|AXIN1_ENST00000354866.3_Silent_p.A609A	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	609	Interaction with PPP2CA.|Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				TCCCCGACTCAGCCTTCTTGG	0.612													A|||	1048	0.209265	0.4281	0.17	5008	,	,		14273	0.0546		0.2237	False		,,,				2504	0.0859				p.A609A		Atlas-SNP	.											.	AXIN1	290	.	0			c.T1827C						PASS	.	A	,	1696,2710	513.6+/-368.4	325,1046,832	192.0	187.0	189.0		1827,1827	-10.3	0.0	16	dbSNP_79	189	1958,6642	345.8+/-325.9	232,1494,2574	no	coding-synonymous,coding-synonymous	AXIN1	NM_003502.3,NM_181050.2	,	557,2540,3406	GG,GA,AA		22.7674,38.493,28.0947	,	609/863,609/827	347184	3654,9352	2203	4300	6503	SO:0001819	synonymous_variant	8312	exon7			CGACTCAGCCTTC	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.1827T>C	16.37:g.347184A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	37	CCDS10405.1																																																																																			A|0.746;G|0.254	0.254	strong		0.612	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
QARS	5859	hgsc.bcm.edu	37	3	49141116	49141116	+	Silent	SNP	G	G	A	rs5030795	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49141116G>A	ENST00000306125.6	-	4	736	c.399C>T	c.(397-399)caC>caT	p.H133H	QARS_ENST00000420147.2_Silent_p.H151H|QARS_ENST00000470225.1_5'Flank|QARS_ENST00000414533.1_Silent_p.H122H			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	95	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	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	
CDC23	8697	hgsc.bcm.edu	37	5	137533901	137533901	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:137533901C>T	ENST00000394886.2	-	9	1029	c.999G>A	c.(997-999)acG>acA	p.T333T		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	333					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|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)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of exit from mitosis (GO:0007096)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)			autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(6)|prostate(2)|skin(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTACACAGCACGTTTCTACAC	0.313																																					p.T333T		Atlas-SNP	.											.	CDC23	46	.	0			c.G999A						PASS	.						77.0	81.0	79.0					5																	137533901		2203	4300	6503	SO:0001819	synonymous_variant	8697	exon9			ACAGCACGTTTCT	AF053977	CCDS4200.2	5q31	2013-01-17	2013-01-17		ENSG00000094880	ENSG00000094880		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1724	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 8"""	603462	"""CDC23 (cell division cycle 23, yeast, homolog)"", ""cell division cycle 23 homolog (S. cerevisiae)"""			9790767	Standard	NM_004661		Approved	APC8, ANAPC8, CUT23	uc003lcl.3	Q9UJX2	OTTHUMG00000129198	ENST00000394886.2:c.999G>A	5.37:g.137533901C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Silent	SNP	ENST00000394886.2	37	CCDS4200.2																																																																																			.	.	none		0.313	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2		
TTI2	80185	hgsc.bcm.edu	37	8	33369944	33369944	+	Missense_Mutation	SNP	T	T	C	rs2304748	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:33369944T>C	ENST00000431156.2	-	2	806	c.188A>G	c.(187-189)gAa>gGa	p.E63G	TTI2_ENST00000519356.1_5'Flank|TTI2_ENST00000360742.5_Missense_Mutation_p.E63G|TTI2_ENST00000520636.1_Missense_Mutation_p.E63G|SNORD13_ENST00000459299.1_RNA	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	63			E -> G (in dbSNP:rs2304748). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.														CCTATCAAATTCTGTGGCTTC	0.527													T|||	2538	0.506789	0.4463	0.4654	5008	,	,		16481	0.5556		0.6252	False		,,,				2504	0.4458				p.E63G		Atlas-SNP	.											C8orf41,NS,carcinoma,-1,1	.	.	1	0			c.A188G						PASS	.	T	GLY/GLU,GLY/GLU	2032,2374	563.2+/-381.1	479,1074,650	71.0	74.0	73.0		188,188	3.3	0.0	8	dbSNP_100	73	5312,3288	643.2+/-399.9	1639,2034,627	yes	missense,missense	TTI2	NM_001102401.1,NM_025115.2	98,98	2118,3108,1277	CC,CT,TT		38.2326,46.1189,43.5338	benign,benign	63/509,63/509	33369944	7344,5662	2203	4300	6503	SO:0001583	missense	80185	exon2			TCAAATTCTGTGG	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.188A>G	8.37:g.33369944T>C	ENSP00000411169:p.Glu63Gly	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	169	102	0.60355	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Missense_Mutation	SNP	ENST00000431156.2	37	CCDS6090.1	1176	0.5384615384615384	220	0.44715447154471544	171	0.4723756906077348	319	0.5576923076923077	466	0.6147757255936676	T	14.07	2.425243	0.43020	0.461189	0.617674	ENSG00000129696	ENST00000360742;ENST00000431156;ENST00000522668;ENST00000520636;ENST00000520397;ENST00000523305	T;T;T;T	0.59772	0.26;0.26;0.24;0.6	4.53	3.34	0.38264	.	0.258590	0.29822	N	0.011110	T	0.00012	0.0000	M	0.76838	2.35	0.58432	P	1.0000000000287557E-6	P;B;B	0.39809	0.689;0.437;0.437	B;B;B	0.34590	0.186;0.115;0.115	T	0.45977	-0.9224	9	0.52906	T	0.07	-14.6433	8.882	0.35380	0.0:0.0:0.1894:0.8106	rs2304748;rs17845116;rs17857909;rs52822961;rs59743233;rs2304748	63;63;63	E5RH83;Q6NXR4;E5RIH5	.;TTI2_HUMAN;.	G	63	ENSP00000353971:E63G;ENSP00000411169:E63G;ENSP00000428401:E63G;ENSP00000428569:E63G	ENSP00000353971:E63G	E	-	2	0	C8orf41	33489486	0.126000	0.22350	0.010000	0.14722	0.011000	0.07611	0.768000	0.26590	0.735000	0.32537	0.533000	0.62120	GAA	C|0.548;N|0.000	0.548	strong		0.527	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	
RNF111	54778	hgsc.bcm.edu	37	15	59368167	59368167	+	Silent	SNP	G	G	A	rs7178935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:59368167G>A	ENST00000557998.1	+	7	1988	c.1701G>A	c.(1699-1701)gtG>gtA	p.V567V	RNF111_ENST00000434298.1_Silent_p.V567V|RNF111_ENST00000561186.1_Silent_p.V567V|RNF111_ENST00000559209.1_Silent_p.V567V|RNF111_ENST00000348370.4_Silent_p.V567V	NM_001270530.1	NP_001257459.1	Q6ZNA4	RN111_HUMAN	ring finger protein 111	567					gene expression (GO:0010467)|pattern specification process (GO:0007389)|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 of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein polyubiquitination (GO:0000209)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|SUMO polymer binding (GO:0032184)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35				all cancers(107;0.194)		CATTGCCAGTGGACCTGAGCA	0.393													A|||	2135	0.426318	0.6589	0.451	5008	,	,		16474	0.4563		0.2634	False		,,,				2504	0.2311				p.V567V	NSCLC(72;983 1365 10746 34387 47081)	Atlas-SNP	.											.	RNF111	179	.	0			c.G1701A						PASS	.	A		2650,1734	518.8+/-369.8	824,1002,366	84.0	74.0	77.0		1701	-1.7	1.0	15	dbSNP_116	77	2367,6215	699.6+/-405.1	348,1671,2272	no	coding-synonymous	RNF111	NM_017610.6		1172,2673,2638	AA,AG,GG		27.581,39.5529,38.6935		567/987	59368167	5017,7949	2192	4291	6483	SO:0001819	synonymous_variant	54778	exon7			GCCAGTGGACCTG	AL157474	CCDS10169.1, CCDS58365.1, CCDS58366.1	15q21	2013-01-09			ENSG00000157450	ENSG00000157450		"""RING-type (C3HC4) zinc fingers"""	17384	protein-coding gene	gene with protein product		605840				11298452	Standard	NM_017610		Approved	ARK, Arkadia, FLJ38008, DKFZP761D081	uc002aft.4	Q6ZNA4	OTTHUMG00000132716	ENST00000557998.1:c.1701G>A	15.37:g.59368167G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	46	35	0.76087	NM_017610	C9JUS4|H0YN55|Q6P9A4|Q6ZMU2|Q7L428|Q7Z346|Q8N1P9|Q8WUA3|Q9NSR1	Silent	SNP	ENST00000557998.1	37	CCDS58366.1																																																																																			G|0.595;A|0.405	0.405	strong		0.393	RNF111-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000416012.1	NM_017610	
KCNK10	54207	hgsc.bcm.edu	37	14	88693725	88693725	+	Silent	SNP	G	G	C	rs2277524	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:88693725G>C	ENST00000340700.5	-	4	1111	c.660C>G	c.(658-660)gtC>gtG	p.V220V	KCNK10_ENST00000319231.5_Silent_p.V225V|KCNK10_ENST00000312350.5_Silent_p.V225V	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	220					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						TCACTCGAAAGACCTTCTCCA	0.448													G|||	1713	0.342053	0.4501	0.2032	5008	,	,		18025	0.4405		0.2187	False		,,,				2504	0.32				p.V225V		Atlas-SNP	.											.	KCNK10	273	.	0			c.C675G						PASS	.	G	,,	1783,2623	526.8+/-372.0	353,1077,773	118.0	114.0	115.0		660,675,675	3.3	1.0	14	dbSNP_100	115	2049,6551	356.4+/-330.3	254,1541,2505	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNK10	NM_021161.4,NM_138317.2,NM_138318.2	,,	607,2618,3278	CC,CG,GG		23.8256,40.4675,29.4633	,,	220/539,225/544,225/544	88693725	3832,9174	2203	4300	6503	SO:0001819	synonymous_variant	54207	exon4			TCGAAAGACCTTC	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.660C>G	14.37:g.88693725G>C		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Silent	SNP	ENST00000340700.5	37	CCDS9880.1																																																																																			G|0.690;C|0.310	0.310	strong		0.448	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161	
SPATA22	84690	hgsc.bcm.edu	37	17	3352331	3352331	+	Missense_Mutation	SNP	C	C	T	rs1488690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:3352331C>T	ENST00000573128.1	-	6	925	c.442G>A	c.(442-444)Gtg>Atg	p.V148M	SPATA22_ENST00000575375.1_Missense_Mutation_p.V148M|SPATA22_ENST00000355380.4_Missense_Mutation_p.V105M|SPATA22_ENST00000268981.5_Missense_Mutation_p.V148M|SPATA22_ENST00000541913.1_Missense_Mutation_p.V132M|SPATA22_ENST00000572969.1_Missense_Mutation_p.V148M|SPATA22_ENST00000397168.3_Missense_Mutation_p.V148M			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	148			V -> M (in dbSNP:rs1488690). {ECO:0000269|PubMed:15489334}.		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						CCCGAACTCACTGGACAAGAA	0.353													c|||	1337	0.266973	0.2209	0.3501	5008	,	,		15865	0.4187		0.1809	False		,,,				2504	0.2025				p.V148M		Atlas-SNP	.											.	SPATA22	49	.	0			c.G442A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1087,3319	392.8+/-328.6	136,815,1252	216.0	208.0	211.0		442,313,442,442,442,442	-9.6	0.0	17	dbSNP_88	211	1585,7015	296.6+/-303.0	144,1297,2859	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	21,21,21,21,21,21	280,2112,4111	TT,TC,CC		18.4302,24.6709,20.5444	benign,benign,benign,benign,benign,benign	148/364,105/321,148/364,148/364,148/270,148/364	3352331	2672,10334	2203	4300	6503	SO:0001583	missense	84690	exon6			AACTCACTGGACA	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.442G>A	17.37:g.3352331C>T	ENSP00000459580:p.Val148Met	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	224	103	0.459821	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Missense_Mutation	SNP	ENST00000573128.1	37	CCDS11027.1	593	0.2715201465201465	108	0.21951219512195122	127	0.35082872928176795	219	0.38286713286713286	139	0.18337730870712401	c	4.615	0.114227	0.08831	0.246709	0.184302	ENSG00000141255	ENST00000355380;ENST00000397168;ENST00000268981;ENST00000541913	T;T;T;T	0.18960	2.19;2.2;2.18;2.19	5.07	-9.61	0.00550	.	1.064140	0.07349	N	0.882007	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.12013	0.002;0.001;0.005;0.001	B;B;B;B	0.10450	0.005;0.003;0.005;0.002	T	0.36768	-0.9734	9	0.26408	T	0.33	-26.657	15.7227	0.77724	0.0:0.2877:0.0:0.7123	rs1488690;rs17822669;rs17852662;rs52823975;rs57028597;rs1488690	132;148;105;148	F5GWB9;B4DXB1;Q8NHS9-2;Q8NHS9	.;.;.;SPT22_HUMAN	M	105;148;148;132	ENSP00000347541:V105M;ENSP00000380354:V148M;ENSP00000268981:V148M;ENSP00000441920:V132M	ENSP00000268981:V148M	V	-	1	0	SPATA22	3299081	0.002000	0.14202	0.019000	0.16419	0.059000	0.15707	-1.651000	0.01989	-1.929000	0.01057	-0.417000	0.06048	GTG	C|0.767;T|0.233	0.233	strong		0.353	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
CYP51A1	1595	hgsc.bcm.edu	37	7	91743150	91743150	+	Silent	SNP	A	A	G	rs7797834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91743150A>G	ENST00000003100.8	-	10	1524	c.1359T>C	c.(1357-1359)caT>caC	p.H453H	LRRD1_ENST00000422722.1_5'UTR|CYP51A1_ENST00000450723.1_Silent_p.H348H	NM_000786.3	NP_000777.1	Q16850	CP51A_HUMAN	cytochrome P450, family 51, subfamily A, polypeptide 1	447					cholesterol biosynthetic process (GO:0006695)|cholesterol biosynthetic process via 24,25-dihydrolanosterol (GO:0033488)|demethylation (GO:0070988)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|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)|membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|sterol 14-demethylase activity (GO:0008398)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|skin(1)	10	all_cancers(62;2.16e-09)|all_epithelial(64;3.86e-08)|Breast(17;0.00206)|all_lung(186;0.169)|all_hematologic(106;0.215)|Lung NSC(181;0.227)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)		Itraconazole(DB01167)|Ketoconazole(DB01026)|Sertaconazole(DB01153)|Tioconazole(DB01007)	CAATACAACGATGACGCCCTA	0.323													A|||	1801	0.359625	0.4539	0.3588	5008	,	,		16445	0.1607		0.3867	False		,,,				2504	0.41				p.H453H	GBM(70;1100 1190 11592 25836 51397)	Atlas-SNP	.											.	CYP51A1	30	.	0			c.T1359C						PASS	.	A	,	2077,2329	553.2+/-378.7	487,1103,613	59.0	61.0	61.0		1359,1044	3.7	1.0	7	dbSNP_116	61	3453,5147	503.1+/-375.8	672,2109,1519	no	coding-synonymous,coding-synonymous	CYP51A1	NM_000786.3,NM_001146152.1	,	1159,3212,2132	GG,GA,AA		40.1512,47.1403,42.5188	,	453/510,348/405	91743150	5530,7476	2203	4300	6503	SO:0001819	synonymous_variant	1595	exon10			ACAACGATGACGC	U51685	CCDS5623.1, CCDS55123.1	7q21.2	2012-10-10	2003-02-14	2003-02-28	ENSG00000001630	ENSG00000001630		"""Cytochrome P450s"""	2649	protein-coding gene	gene with protein product		601637	"""cytochrome P450, 51 (lanosterol 14-alpha-demethylase)"""	CYP51		8975714	Standard	NM_000786		Approved	CP51, CYPL1, P450L1, LDM, P450-14DM	uc003ulm.4	Q16850	OTTHUMG00000131131	ENST00000003100.8:c.1359T>C	7.37:g.91743150A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_000786	A4D1F8|B2RAI4|B4DJ55|O00770|O00772|Q16784|Q8N1A8|Q99868	Silent	SNP	ENST00000003100.8	37	CCDS5623.1	775	0.35485347985347987	241	0.4898373983739837	137	0.3784530386740331	100	0.17482517482517482	297	0.391820580474934	A	13.19	2.164343	0.38217	0.471403	0.401512	ENSG00000001630	ENST00000422867	.	.	.	4.88	3.73	0.42828	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.49735	-0.8908	3	.	.	.	.	10.4441	0.44483	0.9233:0.0:0.0767:0.0	rs7797834;rs10360207;rs57944744;rs7797834	.	.	.	P	166	.	.	S	-	1	0	CYP51A1	91581086	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	3.131000	0.50515	0.894000	0.36317	-0.353000	0.07706	TCG	A|0.620;G|0.380	0.380	strong		0.323	CYP51A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253812.4		
ADAM19	8728	hgsc.bcm.edu	37	5	156918850	156918850	+	Missense_Mutation	SNP	C	C	T	rs2287749	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:156918850C>T	ENST00000517905.1	-	17	2023	c.1979G>A	c.(1978-1980)gGc>gAc	p.G660D	ADAM19_ENST00000257527.4_Missense_Mutation_p.G660D|ADAM19_ENST00000394020.1_Missense_Mutation_p.G662D|ADAM19_ENST00000430702.2_Missense_Mutation_p.G393D			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	660	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CACCCCATGGCCATTGCACTT	0.562													C|||	266	0.053115	0.0477	0.0548	5008	,	,		19065	0.004		0.1163	False		,,,				2504	0.045				p.G660D		Atlas-SNP	.											.	ADAM19	216	.	0			c.G1979A						PASS	.	C	ASP/GLY	278,4128	155.2+/-188.4	9,260,1934	130.0	99.0	109.0		1979	5.2	0.9	5	dbSNP_100	109	1093,7507	228.3+/-263.4	72,949,3279	yes	missense	ADAM19	NM_033274.3	94	81,1209,5213	TT,TC,CC		12.7093,6.3096,10.5413	probably-damaging	660/919	156918850	1371,11635	2203	4300	6503	SO:0001583	missense	8728	exon17			CCATGGCCATTGC	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.1979G>A	5.37:g.156918850C>T	ENSP00000428654:p.Gly660Asp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		146|146	0.06684981684981685|0.06684981684981685	25|25	0.0508130081300813|0.0508130081300813	23|23	0.06353591160220995|0.06353591160220995	3|3	0.005244755244755245|0.005244755244755245	95|95	0.12532981530343007|0.12532981530343007	C|C	18.83|18.83	3.706748|3.706748	0.68615|0.68615	0.063096|0.063096	0.127093|0.127093	ENSG00000135074|ENSG00000135074	ENST00000517374|ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	.|D;D;D;D	.|0.97232	.|-4.3;-4.3;-4.3;-4.3	5.23|5.23	5.23|5.23	0.72850|0.72850	.|Epidermal growth factor-like, type 3 (1);	.|0.000000	.|0.64402	.|D	.|0.000004	T|T	0.35008|0.35008	0.0917|0.0917	M|M	0.72118|0.72118	2.19|2.19	0.58432|0.58432	D|D	0.999999|0.999999	.|P;P;P	.|0.49696	.|0.91;0.855;0.927	.|P;B;P	.|0.49561	.|0.48;0.287;0.615	T|T	0.55457|0.55457	-0.8138|-0.8138	5|10	.|0.62326	.|D	.|0.03	.|.	13.1525|13.1525	0.59498|0.59498	0.0:0.9234:0.0:0.0766|0.0:0.9234:0.0:0.0766	rs2287749;rs17600513;rs56991851;rs2287749|rs2287749;rs17600513;rs56991851;rs2287749	.|660;660;393	.|Q9H013-2;Q9H013;E9PD32	.|.;ADA19_HUMAN;.	T|D	231|393;660;662;660	.|ENSP00000414088:G393D;ENSP00000257527:G660D;ENSP00000377588:G662D;ENSP00000428654:G660D	.|ENSP00000257527:G660D	A|G	-|-	1|2	0|0	ADAM19|ADAM19	156851428|156851428	1.000000|1.000000	0.71417|0.71417	0.907000|0.907000	0.35723|0.35723	0.429000|0.429000	0.31625|0.31625	4.977000|4.977000	0.63792|0.63792	2.451000|2.451000	0.82905|0.82905	0.563000|0.563000	0.77884|0.77884	GCC|GGC	C|0.911;T|0.089	0.089	strong		0.562	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
CNPPD1	27013	hgsc.bcm.edu	37	2	220037444	220037444	+	Missense_Mutation	SNP	G	G	A	rs17655123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220037444G>A	ENST00000409789.1	-	9	1524	c.1097C>T	c.(1096-1098)cCc>cTc	p.P366L	CNPPD1_ENST00000360507.5_Missense_Mutation_p.P366L|SLC23A3_ENST00000409878.3_5'Flank|SLC23A3_ENST00000396775.3_5'Flank|SLC23A3_ENST00000295738.7_5'Flank|SLC23A3_ENST00000455516.2_5'Flank			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	366	Pro-rich.		P -> L (in dbSNP:rs17655123).		regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	integral component of membrane (GO:0016021)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	12						ATGGTACCAGGGGCTGGACAG	0.597													G|||	446	0.0890575	0.0144	0.1182	5008	,	,		16743	0.1597		0.1322	False		,,,				2504	0.0521				p.P366L		Atlas-SNP	.											.	CNPPD1	22	.	0			c.C1097T						PASS	.	G	LEU/PRO	149,4257	100.3+/-138.9	4,141,2058	51.0	52.0	52.0		1097	5.0	0.0	2	dbSNP_123	52	1125,7475	232.5+/-266.1	77,971,3252	yes	missense	CNPPD1	NM_015680.4	98	81,1112,5310	AA,AG,GG		13.0814,3.3818,9.7955	benign	366/411	220037444	1274,11732	2203	4300	6503	SO:0001583	missense	27013	exon8			TACCAGGGGCTGG	AF070638	CCDS2433.1	2q36	2011-03-23	2011-03-23	2011-03-23	ENSG00000115649	ENSG00000115649			25220	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 24"""	C2orf24		8619474, 9110174	Standard	NM_015680		Approved	CGI-57	uc002vju.4	Q9BV87	OTTHUMG00000133132	ENST00000409789.1:c.1097C>T	2.37:g.220037444G>A	ENSP00000386277:p.Pro366Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	95	25	0.263158	NM_015680	B2RC77|O75548|Q9H4N0|Q9UQN0	Missense_Mutation	SNP	ENST00000409789.1	37	CCDS2433.1	236	0.10805860805860806	9	0.018292682926829267	41	0.1132596685082873	90	0.15734265734265734	96	0.1266490765171504	G	10.74	1.434915	0.25813	0.033818	0.130814	ENSG00000115649	ENST00000360507;ENST00000409789	T;T	0.38887	1.11;1.11	5.04	5.04	0.67666	.	0.533609	0.20260	N	0.095897	T	0.00144	0.0004	L	0.29908	0.895	0.44762	P	0.0022370000000000445	B	0.20052	0.041	B	0.21917	0.037	T	0.03818	-1.1001	9	0.48119	T	0.1	3.2816	15.2333	0.73407	0.0:0.0:1.0:0.0	rs17655123;rs57490192;rs17655123	366	Q9BV87	CNPD1_HUMAN	L	366	ENSP00000353698:P366L;ENSP00000386277:P366L	ENSP00000353698:P366L	P	-	2	0	CNPPD1	219745688	0.668000	0.27493	0.015000	0.15790	0.404000	0.30871	2.773000	0.47686	2.609000	0.88269	0.655000	0.94253	CCC	A|0.093;G|0.907;T|0.000	0.093	strong		0.597	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680	
POM121C	100101267	hgsc.bcm.edu	37	7	75051375	75051375	+	Silent	SNP	T	T	C	rs398016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:75051375T>C	ENST00000257665.5	-	11	2885	c.2886A>G	c.(2884-2886)ccA>ccG	p.P962P	POM121C_ENST00000453279.2_Silent_p.P720P|POM121C_ENST00000473168.1_5'Flank			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	962	Pore side. {ECO:0000255}.				mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						GGGTAAGGGCTGGCTTGGCGG	0.657													.|||	1448	0.289137	0.152	0.3069	5008	,	,		11153	0.2589		0.4702	False		,,,				2504	0.3067				p.P720P		Atlas-SNP	.											POM121C,NS,carcinoma,0,1	POM121C	46	1	0			c.A2160G						scavenged	.	C		682,3536		76,530,1503	10.0	13.0	12.0		2160	-6.0	0.0	7	dbSNP_80	12	3609,4787		853,1903,1442	no	coding-synonymous	POM121C	NM_001099415.1		929,2433,2945	CC,CT,TT		42.9848,16.1688,34.0178		720/988	75051375	4291,8323	2109	4198	6307	SO:0001819	synonymous_variant	100101267	exon13			AAGGGCTGGCTTG		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238	ENST00000257665.5:c.2886A>G	7.37:g.75051375T>C		Somatic	222	12	0.0540541		WXS	Illumina HiSeq	Phase_I	200	178	0.89	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000257665.5	37																																																																																				T|0.701;C|0.299	0.299	strong		0.657	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
ZNF91	7644	hgsc.bcm.edu	37	19	23544515	23544515	+	Silent	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:23544515A>T	ENST00000300619.7	-	4	1471	c.1266T>A	c.(1264-1266)acT>acA	p.T422T	ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000397082.2_Silent_p.T390T|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	422					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)				ACTTATGTATAGTAAGATTTG	0.338																																					p.T422T		Atlas-SNP	.											ZNF91_ENST00000300619,NS,lymphoid_neoplasm,-1,2	ZNF91	349	2	0			c.T1266A						PASS	.						13.0	13.0	13.0					19																	23544515		1849	4026	5875	SO:0001819	synonymous_variant	7644	exon4			ATGTATAGTAAGA	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.1266T>A	19.37:g.23544515A>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	111	37	0.333333	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			.	.	none		0.338	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
FAT2	2196	hgsc.bcm.edu	37	5	150931082	150931082	+	Silent	SNP	C	C	G	rs55719915	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:150931082C>G	ENST00000261800.5	-	6	4254	c.4242G>C	c.(4240-4242)tcG>tcC	p.S1414S		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1414	Cadherin 12. {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)			AGTTATAGTTCGACCTTCTCC	0.537													C|||	72	0.014377	0.0	0.0159	5008	,	,		19062	0.0		0.0239	False		,,,				2504	0.0378				p.S1414S		Atlas-SNP	.											FAT2,colon,carcinoma,-1,1	FAT2	465	1	0			c.G4242C						PASS	.	C		21,4385	28.1+/-56.4	0,21,2182	175.0	148.0	157.0		4242	-10.9	0.0	5	dbSNP_129	157	151,8449	73.2+/-135.9	0,151,4149	no	coding-synonymous	FAT2	NM_001447.2		0,172,6331	GG,GC,CC		1.7558,0.4766,1.3225		1414/4350	150931082	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon6			ATAGTTCGACCTT	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.4242G>C	5.37:g.150931082C>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	231	105	0.454545	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.987;G|0.013	0.013	strong		0.537	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
CD163L1	283316	hgsc.bcm.edu	37	12	7585971	7585971	+	Splice_Site	SNP	A	A	G	rs10845159	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7585971A>G	ENST00000313599.3	-	3	501	c.444T>C	c.(442-444)taT>taC	p.Y148Y	CD163L1_ENST00000396630.1_Splice_Site_p.Y148Y|CD163L1_ENST00000416109.2_Silent_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	209	0	0		WXS	Illumina HiSeq	Phase_I	195	101	0.517949	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
ESYT2	57488	hgsc.bcm.edu	37	7	158536345	158536345	+	Missense_Mutation	SNP	A	A	G	rs2305475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:158536345A>G	ENST00000251527.5	-	16	1815	c.1750T>C	c.(1750-1752)Tcc>Ccc	p.S584P	ESYT2_ENST00000435514.2_Missense_Mutation_p.S19P	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	612	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						TTCCCCAGGGAACACTGGTGC	0.552													A|||	1682	0.335863	0.3994	0.1801	5008	,	,		17966	0.5843		0.17	False		,,,				2504	0.2751				p.S584P		Atlas-SNP	.											.	ESYT2	70	.	0			c.T1750C						PASS	.		PRO/SER	1486,2920	455.7+/-351.1	265,956,982	74.0	60.0	65.0		1750	4.1	0.2	7	dbSNP_100	65	1421,7179	248.6+/-276.2	125,1171,3004	yes	missense	ESYT2	NM_020728.2	74	390,2127,3986	GG,GA,AA		16.5233,33.7267,22.3512	probably-damaging	584/894	158536345	2907,10099	2203	4300	6503	SO:0001583	missense	57488	exon16			CCAGGGAACACTG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1750T>C	7.37:g.158536345A>G	ENSP00000251527:p.Ser584Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	60	39	0.65	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	701	0.320970695970696	187	0.3800813008130081	63	0.17403314917127072	323	0.5646853146853147	128	0.16886543535620052	A	17.00	3.277386	0.59758	0.337267	0.165233	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000435514;ENST00000377650;ENST00000429474	T;T;T	0.25749	1.78;1.78;1.78	5.28	4.09	0.47781	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.305484	0.36815	N	0.002395	T	0.00012	0.0000	L	0.61387	1.9	0.24527	P	0.994134	D;B	0.62365	0.991;0.089	P;B	0.56700	0.804;0.178	T	0.46830	-0.9163	9	0.66056	D	0.02	-16.699	10.6259	0.45508	0.8561:0.0:0.0:0.1439	rs2305475;rs61453775;rs2305475	584;612	A0FGR8-2;A0FGR8	.;ESYT2_HUMAN	P	584;633;575;19;19;408	ENSP00000251527:S584P;ENSP00000275418:S575P;ENSP00000411488:S19P	ENSP00000251527:S584P	S	-	1	0	ESYT2	158229106	1.000000	0.71417	0.191000	0.23289	0.556000	0.35491	3.699000	0.54778	0.812000	0.34326	0.455000	0.32223	TCC	A|0.737;C|0.000;G|0.262;T|0.000	0.262	strong		0.552	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
STKLD1	169436	hgsc.bcm.edu	37	9	136269143	136269143	+	Missense_Mutation	SNP	G	G	A	rs17150554	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	178	0	0	1624	WXS	Illumina HiSeq	Phase_I	133	58	0.43609	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		
MYH6	4624	hgsc.bcm.edu	37	14	23862710	23862710	+	Silent	SNP	C	C	T	rs145274612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23862710C>T	ENST00000356287.3	-	22	2975	c.2946G>A	c.(2944-2946)gaG>gaA	p.E982E	MYH6_ENST00000405093.3_Silent_p.E982E			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	982					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)		CAGCCATCTCCTCTGTTAGGT	0.537													C|||	21	0.00419329	0.0	0.0101	5008	,	,		22617	0.0		0.0119	False		,,,				2504	0.002				p.E982E		Atlas-SNP	.											.	MYH6	274	.	0			c.G2946A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	181.0	177.0	178.0		2946	3.3	1.0	14	dbSNP_134	178	103,8497	56.0+/-117.1	0,103,4197	no	coding-synonymous	MYH6	NM_002471.3		0,112,6391	TT,TC,CC		1.1977,0.2043,0.8611		982/1940	23862710	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon23			CATCTCCTCTGTT	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.2946G>A	14.37:g.23862710C>T		Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	422	277	0.656398	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			C|0.992;T|0.008	0.008	strong		0.537	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
SRRM5	100170229	hgsc.bcm.edu	37	19	44118188	44118188	+	Missense_Mutation	SNP	A	A	C	rs3815422	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44118188A>C	ENST00000607544.1	+	3	2237	c.1915A>C	c.(1915-1917)Agc>Cgc	p.S639R	ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000526798.1_Missense_Mutation_p.S654R|SRRM5_ENST00000417606.1_Missense_Mutation_p.S639R			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	37	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	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	
ADAM7	8756	hgsc.bcm.edu	37	8	24333985	24333985	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:24333985C>T	ENST00000175238.6	+	8	756	c.673C>T	c.(673-675)Cga>Tga	p.R225*	ADAM7_ENST00000520720.1_5'UTR|ADAM7_ENST00000380789.1_Nonsense_Mutation_p.R225*|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	225	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					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)		ACTAAGGAACCGAATTTGGGG	0.328																																					p.R225X		Atlas-SNP	.											ADAM7,NS,carcinoma,-1,4	ADAM7	165	4	0			c.C673T						PASS	.						114.0	106.0	109.0					8																	24333985		2203	4300	6503	SO:0001587	stop_gained	8756	exon8			AGGAACCGAATTT	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.673C>T	8.37:g.24333985C>T	ENSP00000175238:p.Arg225*	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	103	37	0.359223	NM_003817	A8K8X7|O75959|Q6PEJ6	Nonsense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	C	37	6.589310	0.97688	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000335595	.	.	.	5.38	2.32	0.28847	.	0.000000	0.46145	D	0.000301	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9142	0.47126	0.496:0.504:0.0:0.0	.	.	.	.	X	225;225;40	.	ENSP00000175238:R225X	R	+	1	2	ADAM7	24389875	0.428000	0.25522	0.898000	0.35279	0.991000	0.79684	0.270000	0.18607	0.721000	0.32231	0.591000	0.81541	CGA	.	.	none		0.328	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
LAMA2	3908	hgsc.bcm.edu	37	6	129807714	129807714	+	Silent	SNP	G	G	A	rs2229850	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	195	104	0.533333	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		
KLRG2	346689	hgsc.bcm.edu	37	7	139138950	139138950	+	Missense_Mutation	SNP	C	C	G	rs17160911	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:139138950C>G	ENST00000340940.4	-	4	1085	c.1016G>C	c.(1015-1017)gGc>gCc	p.G339A	KLRG2_ENST00000393039.2_Intron	NM_198508.2	NP_940910.1	A4D1S0	KLRG2_HUMAN	killer cell lectin-like receptor subfamily G, member 2	339	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		G -> A (in dbSNP:rs17160911).			integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|large_intestine(2)|lung(3)	6	Melanoma(164;0.233)					TGGGTATCTGCCCAGGAAGTC	0.667													C|||	877	0.17512	0.2088	0.1311	5008	,	,		14984	0.2113		0.1252	False		,,,				2504	0.1748				p.G339A		Atlas-SNP	.											KLRG2,NS,carcinoma,0,3	KLRG2	22	3	0			c.G1016C						PASS	.						13.0	10.0	11.0					7																	139138950		1870	3571	5441	SO:0001583	missense	346689	exon4			TATCTGCCCAGGA	AK126174	CCDS5854.1	7q34	2011-08-30			ENSG00000188883	ENSG00000188883		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	24778	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member B"""						Standard	XM_005250311		Approved	FLJ44186, CLEC15B	uc003vvb.3	A4D1S0	OTTHUMG00000157705	ENST00000340940.4:c.1016G>C	7.37:g.139138950C>G	ENSP00000339356:p.Gly339Ala	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_198508	Q2NL79|Q6ZTV6	Missense_Mutation	SNP	ENST00000340940.4	37	CCDS5854.1	340	0.15567765567765568	93	0.18902439024390244	46	0.1270718232044199	110	0.19230769230769232	91	0.12005277044854881	C	6.481	0.456958	0.12283	.	.	ENSG00000188883	ENST00000340940	T	0.16897	2.31	4.78	2.9	0.33743	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.692200	0.12721	N	0.444710	T	0.00012	0.0000	N	0.08118	0	0.20764	P	0.999855632	B	0.18166	0.026	B	0.19391	0.025	T	0.40942	-0.9536	9	0.07325	T	0.83	-8.5467	7.5752	0.27931	0.1896:0.6275:0.1829:0.0	rs17160911;rs17160911	339	A4D1S0	KLRG2_HUMAN	A	339	ENSP00000339356:G339A	ENSP00000339356:G339A	G	-	2	0	KLRG2	138789490	0.488000	0.25996	0.542000	0.28115	0.903000	0.53119	0.271000	0.18626	0.578000	0.29487	0.655000	0.94253	GGC	C|0.832;G|0.166	0.166	strong		0.667	KLRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349433.1	NM_198508	
FAM205A	259308	hgsc.bcm.edu	37	9	34723988	34723988	+	Missense_Mutation	SNP	C	C	A	rs147591106	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34723988C>A	ENST00000378788.3	-	4	3288	c.3249G>T	c.(3247-3249)agG>agT	p.R1083S		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	1083						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						TCCCTGCTGGCCTCTGGTCTT	0.597													C|||	564	0.11262	0.0787	0.1254	5008	,	,		18473	0.0595		0.1402	False		,,,				2504	0.1759				p.R1083S		Atlas-SNP	.											.	FAM205A	45	.	0			c.G3249T						PASS	.						21.0	16.0	18.0					9																	34723988		692	1580	2272	SO:0001583	missense	259308	exon4			TGCTGGCCTCTGG		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.3249G>T	9.37:g.34723988C>A	ENSP00000417711:p.Arg1083Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	60	39	0.65	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	223	0.1021062271062271	44	0.08943089430894309	50	0.13812154696132597	24	0.04195804195804196	105	0.13852242744063326	C	17.38	3.374335	0.61735	.	.	ENSG00000205108	ENST00000378788	T	0.21734	1.99	3.87	-0.387	0.12463	.	.	.	.	.	T	0.00109	0.0003	L	0.49350	1.555	0.47476	P	5.669999999999842E-4	P	0.36837	0.571	B	0.38712	0.28	T	0.21999	-1.0229	8	0.23891	T	0.37	.	3.5673	0.07904	0.0:0.4599:0.1942:0.3459	rs62547037	1083	Q6ZU69	F205A_HUMAN	S	1083	ENSP00000417711:R1083S	ENSP00000417711:R1083S	R	-	3	2	RP11-195F19.10	34713988	0.019000	0.18553	0.904000	0.35570	0.394000	0.30568	-0.082000	0.11304	0.038000	0.15604	-0.142000	0.14014	AGG	C|0.886;A|0.114	0.114	strong		0.597	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
SOHLH2	54937	hgsc.bcm.edu	37	13	36744800	36744800	+	Silent	SNP	G	G	A	rs2296967	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:36744800G>A	ENST00000379881.3	-	10	1213	c.1125C>T	c.(1123-1125)taC>taT	p.Y375Y	CCDC169-SOHLH2_ENST00000511166.1_Silent_p.Y452Y|SOHLH2_ENST00000554962.1_Silent_p.Y452Y	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	375					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.Y375Y(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		CAGTTGCATCGTAGGAAGGGG	0.448													G|||	374	0.0746805	0.003	0.085	5008	,	,		19637	0.0794		0.1014	False		,,,				2504	0.1319				p.Y452Y		Atlas-SNP	.											SOHLH2,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C1356T						PASS	.	G	,	114,4292	87.8+/-126.4	0,114,2089	161.0	147.0	152.0		1356,1125	1.0	0.0	13	dbSNP_100	152	1028,7572	218.1+/-256.6	62,904,3334	no	coding-synonymous,coding-synonymous	SOHLH2,CCDC169-SOHLH2	NM_001198910.1,NM_017826.2	,	62,1018,5423	AA,AG,GG		11.9535,2.5874,8.7806	,	452/503,375/426	36744800	1142,11864	2203	4300	6503	SO:0001819	synonymous_variant	100526761	exon15			TGCATCGTAGGAA	AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"""Basic helix-loop-helix proteins"""	26026	protein-coding gene	gene with protein product	"""spermatogenesis associated 28"""					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.1125C>T	13.37:g.36744800G>A		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	223	119	0.533632	NM_001198910	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Silent	SNP	ENST00000379881.3	37	CCDS9355.1																																																																																			G|0.916;A|0.084	0.084	strong		0.448	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826	
CPNE3	8895	hgsc.bcm.edu	37	8	87540872	87540872	+	Silent	SNP	G	G	A	rs10956871	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:87540872G>A	ENST00000521271.1	+	3	261	c.99G>A	c.(97-99)ttG>ttA	p.L33L	CPNE3_ENST00000198765.4_Silent_p.L33L	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	33	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						TATGTGTGTTGTTTTTGAATA	0.373													A|||	825	0.164736	0.2103	0.1383	5008	,	,		19358	0.0496		0.2555	False		,,,				2504	0.1472				p.L33L		Atlas-SNP	.											.	CPNE3	65	.	0			c.G99A						PASS	.	A		1068,3338	722.7+/-409.3	116,836,1251	116.0	115.0	116.0		99	-5.3	0.4	8	dbSNP_120	116	2330,6270	703.9+/-405.4	315,1700,2285	no	coding-synonymous	CPNE3	NM_003909.3		431,2536,3536	AA,AG,GG		27.093,24.2397,26.1264		33/538	87540872	3398,9608	2203	4300	6503	SO:0001819	synonymous_variant	8895	exon3			TGTGTTGTTTTTG	AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.99G>A	8.37:g.87540872G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	163	49	0.300613	NM_003909	A8KA47|Q8IYA1	Silent	SNP	ENST00000521271.1	37	CCDS6243.1																																																																																			G|0.775;A|0.225	0.225	strong		0.373	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1		
SACS	26278	hgsc.bcm.edu	37	13	23904298	23904298	+	Missense_Mutation	SNP	T	T	G	rs34382952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:23904298T>G	ENST00000382292.3	-	9	13990	c.13717A>C	c.(13717-13719)Aat>Cat	p.N4573H	SACS_ENST00000402364.1_Missense_Mutation_p.N3823H|SACS_ENST00000382298.3_Missense_Mutation_p.N4573H			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4573					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)		TGCATAAAATTTTCAAGTTTT	0.348													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		9531	0.0		0.0099	False		,,,				2504	0.0				p.N4573H		Atlas-SNP	.											.	SACS	871	.	0			c.A13717C						PASS	.	T	HIS/ASN	5,4401	9.9+/-24.2	0,5,2198	66.0	67.0	67.0		13717	5.8	1.0	13	dbSNP_126	67	40,8560	26.3+/-74.7	0,40,4260	yes	missense	SACS	NM_014363.4	68	0,45,6458	GG,GT,TT		0.4651,0.1135,0.346	possibly-damaging	4573/4580	23904298	45,12961	2203	4300	6503	SO:0001583	missense	26278	exon10			TAAAATTTTCAAG	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.13717A>C	13.37:g.23904298T>G	ENSP00000371729:p.Asn4573His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	T	18.35	3.603679	0.66445	0.001135	0.004651	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86366	-2.11;-2.11;-2.11	5.85	5.85	0.93711	.	0.089079	0.85682	D	0.000000	T	0.79627	0.4478	N	0.03608	-0.345	0.35519	D	0.801247	D	0.56521	0.976	P	0.59595	0.86	D	0.88793	0.3279	10	0.59425	D	0.04	.	16.2271	0.82306	0.0:0.0:0.0:1.0	rs34382952	4573	Q9NZJ4	SACS_HUMAN	H	4573;3823;4573	ENSP00000371729:N4573H;ENSP00000385844:N3823H;ENSP00000371735:N4573H	ENSP00000371729:N4573H	N	-	1	0	SACS	22802298	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	6.258000	0.72487	2.234000	0.73211	0.460000	0.39030	AAT	T|0.997;G|0.003	0.003	strong		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
TRPM5	29850	hgsc.bcm.edu	37	11	2434799	2434799	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2434799C>A	ENST00000155858.6	-	13	1918	c.1910G>T	c.(1909-1911)tGg>tTg	p.W637L	TRPM5_ENST00000452833.1_Missense_Mutation_p.W639L|TRPM5_ENST00000528453.1_Missense_Mutation_p.W637L|TRPM5_ENST00000533060.1_Missense_Mutation_p.W637L	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)		GTCCCCCCACCAGATCCTGGT	0.642																																					p.W637L	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1910T						PASS	.						54.0	53.0	53.0					11																	2434799		2202	4299	6501	SO:0001583	missense	29850	exon13			CCCCACCAGATCC	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.1910G>T	11.37:g.2434799C>A	ENSP00000155858:p.Trp637Leu	Somatic	388	1	0.00257732		WXS	Illumina HiSeq	Phase_I	392	126	0.321429	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.130183	0.77549	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41	3.97	3.97	0.46021	.	0.000000	0.64402	D	0.000001	D	0.90448	0.7009	M	0.87381	2.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.995	D	0.92548	0.6047	10	0.87932	D	0	-15.2033	15.4027	0.74855	0.0:1.0:0.0:0.0	.	637;639;637	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	L	631;637;639;637;637;637	ENSP00000434383:W631L;ENSP00000155858:W637L;ENSP00000387965:W639L;ENSP00000434121:W637L;ENSP00000436809:W637L	ENSP00000155858:W637L	W	-	2	0	TRPM5	2391375	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	7.383000	0.79741	1.940000	0.56252	0.313000	0.20887	TGG	.	.	none		0.642	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
IKZF1	10320	hgsc.bcm.edu	37	7	50459542	50459542	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:50459542T>C	ENST00000331340.3	+	7	986	c.831T>C	c.(829-831)tcT>tcC	p.S277S	IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000439701.1_Silent_p.S235S|IKZF1_ENST00000357364.4_Intron|IKZF1_ENST00000359197.5_Silent_p.S235S|IKZF1_ENST00000343574.5_Silent_p.S190S|IKZF1_ENST00000438033.1_Silent_p.S190S|IKZF1_ENST00000349824.4_Intron|IKZF1_ENST00000440768.2_3'UTR	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	277					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				GTAAGAGCTCTATGCCTCAGA	0.413			"""D,T"""	BCL6	"""ALL, DLBCL"""																																p.S277S		Atlas-SNP	.		"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	IKZF1	613	.	131	Unknown(131)	haematopoietic_and_lymphoid_tissue(131)	c.T831C						PASS	.						60.0	59.0	59.0					7																	50459542		1858	4109	5967	SO:0001819	synonymous_variant	10320	exon7			GAGCTCTATGCCT	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.831T>C	7.37:g.50459542T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	4	0.05	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	37																																																																																				.	.	none		0.413	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
PHKG1	5260	hgsc.bcm.edu	37	7	56149939	56149939	+	Silent	SNP	G	G	A	rs13238521	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:56149939G>A	ENST00000297373.2	-	7	749	c.555C>T	c.(553-555)tgC>tgT	p.C185C	PHKG1_ENST00000489604.1_5'Flank|PHKG1_ENST00000452681.2_Silent_p.C217C|PHKG1_ENST00000537360.1_Silent_p.C131C	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	185	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)			TGGGGGTCCCGCAGACCTCTG	0.577													G|||	561	0.112021	0.0492	0.111	5008	,	,		17857	0.2282		0.0835	False		,,,				2504	0.1074				p.C217C	Melanoma(184;580 2064 5329 24177 35303)	Atlas-SNP	.											.	PHKG1	38	.	0			c.C651T						PASS	.	G		226,4180	135.7+/-171.8	6,214,1983	54.0	57.0	56.0		555	-4.4	1.0	7	dbSNP_121	56	513,8087	145.7+/-201.4	12,489,3799	no	coding-synonymous	PHKG1	NM_006213.3		18,703,5782	AA,AG,GG		5.9651,5.1294,5.682		185/388	56149939	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	5260	exon8			GGTCCCGCAGACC	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.555C>T	7.37:g.56149939G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	68	44	0.647059	NM_001258459	B7Z1D0|F5H2S1|Q75LP5	Silent	SNP	ENST00000297373.2	37	CCDS5525.1																																																																																			G|0.924;A|0.076	0.076	strong		0.577	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1	NM_006213	
SCNN1D	6339	hgsc.bcm.edu	37	1	1220954	1220954	+	Intron	SNP	G	G	A	rs12751100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1220954G>A	ENST00000338555.2	+	4	1210				SCNN1D_ENST00000379116.5_Silent_p.S156S|SCNN1D_ENST00000325425.8_Silent_p.S58S|SCNN1D_ENST00000467651.2_3'UTR|SCNN1D_ENST00000400928.3_Intron			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit						ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	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;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	TGGGTAGATCGCCTGGGCCTG	0.657													A|||	2217	0.442692	0.7073	0.3386	5008	,	,		18800	0.6498		0.0368	False		,,,				2504	0.363				p.S156S		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G468A						PASS	.			849,535		251,347,94	47.0	52.0	50.0		468	-2.5	0.0	1	dbSNP_121	50	112,3064		1,110,1477	yes	coding-synonymous	SCNN1D	NM_001130413.3		252,457,1571	AA,AG,GG		3.5264,38.6561,21.0746		156/803	1220954	961,3599	692	1588	2280	SO:0001627	intron_variant	6339	exon6			TAGATCGCCTGGG	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10601	protein-coding gene	gene with protein product		601328	"""sodium channel, nonvoltage-gated 1, delta"", ""sodium channel, non-voltage-gated 1, delta"""			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.67-352G>A	1.37:g.1220954G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	97	28	0.28866	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Silent	SNP	ENST00000338555.2	37		851	0.38965201465201466	353	0.717479674796748	103	0.2845303867403315	367	0.6416083916083916	28	0.036939313984168866	a	4.173	0.030685	0.08101	0.613439	0.035264	ENSG00000162572	ENST00000379110	.	.	.	1.93	-2.48	0.06423	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.51767	P	6.899999999998574E-5	.	.	.	.	.	.	T	0.35351	-0.9792	4	0.44086	T	0.13	.	0.2618	0.00219	0.2696:0.1958:0.148:0.3866	rs12751100;rs61637230	.	.	.	T	24	.	ENSP00000368404:A24T	A	+	1	0	SCNN1D	1210817	0.000000	0.05858	0.011000	0.14972	0.014000	0.08584	-1.094000	0.03359	-1.242000	0.02523	-0.809000	0.03173	GCC	G|0.609;A|0.391	0.391	strong		0.657	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998296	72998296	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:72998296T>C	ENST00000580243.1	+	2	1282	c.934T>C	c.(934-936)Tgt>Cgt	p.C312R	TSHZ1_ENST00000322038.5_Missense_Mutation_p.C267R			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	312					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)		GTGCATGTACTGTGGACACTC	0.557																																					p.C267R		Atlas-SNP	.											.	TSHZ1	104	.	0			c.T799C						PASS	.						150.0	122.0	131.0					18																	72998296		2203	4300	6503	SO:0001583	missense	10194	exon2			ATGTACTGTGGAC	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.934T>C	18.37:g.72998296T>C	ENSP00000464391:p.Cys312Arg	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	159	50	0.314465	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	T	10.93	1.490440	0.26686	.	.	ENSG00000179981	ENST00000322038	D	0.83755	-1.76	5.38	5.38	0.77491	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	D	0.89942	0.6861	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.90801	0.4694	10	0.87932	D	0	-17.6812	15.4172	0.74980	0.0:0.0:0.0:1.0	.	312	Q6ZSZ6	TSH1_HUMAN	R	267	ENSP00000323584:C267R	ENSP00000323584:C267R	C	+	1	0	TSHZ1	71127284	1.000000	0.71417	0.989000	0.46669	0.982000	0.71751	7.694000	0.84235	2.512000	0.84698	0.561000	0.74099	TGT	.	.	none		0.557	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
RARB	5915	hgsc.bcm.edu	37	3	25635200	25635200	+	Splice_Site	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:25635200T>C	ENST00000404969.1	+	6	1012		c.e6+2		RARB_ENST00000437042.2_Splice_Site|RARB_ENST00000458646.1_Splice_Site|RARB_ENST00000330688.4_Splice_Site|RARB_ENST00000462272.1_Splice_Site			P10826	RARB_HUMAN	retinoic acid receptor, beta						embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|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)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	TCTGTGGAGGTACCAACTATG	0.408																																					.		Atlas-SNP	.											RARB_ENST00000404969,NS,carcinoma,+2,2	RARB	123	2	0			c.655+2T>C						scavenged	.						83.0	80.0	81.0					3																	25635200		2203	4300	6503	SO:0001630	splice_region_variant	5915	exon6			TGGAGGTACCAAC	Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"""Nuclear hormone receptors"""	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.1012+2T>C	3.37:g.25635200T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	157	2	0.0127389	NM_016152	P12891|Q00989|Q15298|Q9UN48	Splice_Site	SNP	ENST00000404969.1	37		.	.	.	.	.	.	.	.	.	.	T	23.4	4.417098	0.83449	.	.	ENSG00000077092	ENST00000383772;ENST00000404969;ENST00000538226;ENST00000437042;ENST00000330688;ENST00000458646	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3885	0.83524	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RARB	25610204	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	8.017000	0.88712	2.274000	0.75844	0.529000	0.55759	.	.	.	none		0.408	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152	Intron
SIGLEC10	89790	hgsc.bcm.edu	37	19	51914401	51914401	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51914401C>T	ENST00000339313.5	-	11	2162	c.2046G>A	c.(2044-2046)cgG>cgA	p.R682R	SIGLEC10_ENST00000436984.2_Silent_p.R539R|SIGLEC10_ENST00000442846.3_Silent_p.R439R|SIGLEC10_ENST00000439889.2_Silent_p.R624R|SIGLEC10_ENST00000353836.5_Silent_p.R587R|SIGLEC10_ENST00000432469.2_Silent_p.R504R|SIGLEC10_ENST00000441969.3_Silent_p.R529R|SIGLEC10_ENST00000356298.5_Silent_p.R682R|SIGLEC10_ENST00000525998.1_Silent_p.R497R			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	682					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)		CCTTGGGCATCCGGGCCTCAG	0.567																																					p.R682R		Atlas-SNP	.											SIGLEC12_ENST00000439889,bladder,carcinoma,-1,2	SIGLEC10	112	2	0			c.G2046A						scavenged	.						112.0	109.0	110.0					19																	51914401		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon11			GGGCATCCGGGCC	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.2046G>A	19.37:g.51914401C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	193	2	0.0103627	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			.	.	none		0.567	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ZNF468	90333	hgsc.bcm.edu	37	19	53344701	53344701	+	Silent	SNP	A	A	G	rs10420793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53344701A>G	ENST00000595646.1	-	4	966	c.846T>C	c.(844-846)caT>caC	p.H282H	ZNF468_ENST00000390651.4_Silent_p.H229H|ZNF468_ENST00000243639.4_3'UTR|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_Silent_p.H229H			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	282					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.H282H(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)		GGGATGAATTATGACCAAAGG	0.418													-|||	1803	0.360024	0.562	0.2752	5008	,	,		21073	0.1101		0.2674	False		,,,				2504	0.5				p.H282H		Atlas-SNP	.											ZNF468,NS,carcinoma,0,1	ZNF468	46	1	1	Substitution - coding silent(1)	stomach(1)	c.T846C						scavenged	.	G	,	2294,2112		583,1128,492	125.0	116.0	119.0		846,687	-3.5	0.0	19	dbSNP_119	119	2537,6063		380,1777,2143	no	coding-synonymous,coding-synonymous	ZNF468	NM_001008801.1,NM_199132.1	,	963,2905,2635	GG,GA,AA		29.5,47.9346,37.1444	,	282/523,229/470	53344701	4831,8175	2203	4300	6503	SO:0001819	synonymous_variant	90333	exon4			TGAATTATGACCA	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.846T>C	19.37:g.53344701A>G		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Silent	SNP	ENST00000595646.1	37	CCDS33094.1																																																																																			A|0.649;G|0.351	0.351	strong		0.418	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
DISP2	85455	hgsc.bcm.edu	37	15	40655845	40655845	+	Missense_Mutation	SNP	C	C	G	rs1898883	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:40655845C>G	ENST00000267889.3	+	2	226	c.139C>G	c.(139-141)Ccc>Gcc	p.P47A		NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	47			P -> A (in dbSNP:rs1898883). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:15489334}.		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)		CAAGGCTGTGCCCCCTGAGGC	0.607													G|||	3636	0.726038	0.6717	0.7435	5008	,	,		16518	0.8274		0.6292	False		,,,				2504	0.7822				p.P47A		Atlas-SNP	.											.	DISP2	86	.	0			c.C139G						PASS	.	G	ALA/PRO	2942,1464	458.6+/-352.0	995,952,256	87.0	102.0	97.0		139	4.3	1.0	15	dbSNP_92	97	5671,2929	442.1+/-360.0	1882,1907,511	yes	missense	DISP2	NM_033510.1	27	2877,2859,767	GG,GC,CC		34.0581,33.2274,33.7767	benign	47/1402	40655845	8613,4393	2203	4300	6503	SO:0001583	missense	85455	exon2			GCTGTGCCCCCTG	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.139C>G	15.37:g.40655845C>G	ENSP00000267889:p.Pro47Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	41	35	0.853659	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	1598	0.7316849816849816	344	0.6991869918699187	264	0.7292817679558011	492	0.8601398601398601	498	0.6569920844327177	G	1.819	-0.472695	0.04445	0.667726	0.659419	ENSG00000140323	ENST00000267889	T	0.09445	2.98	5.17	4.26	0.50523	.	0.609132	0.17398	N	0.175676	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	8.000000000008E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.28744	-1.0034	9	0.02654	T	1	-16.6771	8.2234	0.31554	0.0839:0.1579:0.7582:0.0	rs1898883;rs1898883	47	A7MBM2	DISP2_HUMAN	A	47	ENSP00000267889:P47A	ENSP00000267889:P47A	P	+	1	0	DISP2	38443137	0.981000	0.34729	1.000000	0.80357	0.991000	0.79684	1.695000	0.37763	0.783000	0.33636	-0.215000	0.12644	CCC	C|0.308;G|0.692	0.692	strong		0.607	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
AKNA	80709	hgsc.bcm.edu	37	9	117124731	117124731	+	Missense_Mutation	SNP	G	G	A	rs3748176	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	56	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	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	
IMPAD1	54928	hgsc.bcm.edu	37	8	57906042	57906042	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:57906042G>A	ENST00000262644.4	-	1	361	c.103C>T	c.(103-105)Cgc>Tgc	p.R35C		NM_017813.4	NP_060283.3	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	35					chondrocyte development (GO:0002063)|chondroitin sulfate metabolic process (GO:0030204)|embryonic digit morphogenesis (GO:0042733)|endochondral ossification (GO:0001958)|inositol biosynthetic process (GO:0006021)|phosphatidylinositol phosphorylation (GO:0046854)|post-embryonic development (GO:0009791)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|3'-nucleotidase activity (GO:0008254)|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)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	7		all_cancers(86;0.175)|all_lung(136;0.0321)|Lung NSC(129;0.0417)|all_epithelial(80;0.0448)				AGGCTGAAGCGGCCGGCCAAG	0.741																																					p.R35C		Atlas-SNP	.											.	IMPAD1	27	.	0			c.C103T						PASS	.						2.0	2.0	2.0					8																	57906042		1082	2103	3185	SO:0001583	missense	54928	exon1			TGAAGCGGCCGGC		CCDS6169.1	8q12.1	2013-05-16			ENSG00000104331	ENSG00000104331			26019	protein-coding gene	gene with protein product		614010				21549340	Standard	NM_017813		Approved	FLJ20421, IMPA3, gPAPP	uc003xte.4	Q9NX62	OTTHUMG00000164415	ENST00000262644.4:c.103C>T	8.37:g.57906042G>A	ENSP00000262644:p.Arg35Cys	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	8	6	0.75	NM_017813	Q6NVY7	Missense_Mutation	SNP	ENST00000262644.4	37	CCDS6169.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.915816	0.52546	.	.	ENSG00000104331	ENST00000262644	T	0.52983	0.64	5.05	4.17	0.49024	.	0.059812	0.64402	D	0.000007	T	0.36771	0.0979	N	0.24115	0.695	0.80722	D	1	D	0.69078	0.997	P	0.47470	0.548	T	0.24512	-1.0158	10	0.72032	D	0.01	-34.6783	7.4777	0.27387	0.0852:0.0:0.7506:0.1642	.	35	Q9NX62	IMPA3_HUMAN	C	35	ENSP00000262644:R35C	ENSP00000262644:R35C	R	-	1	0	IMPAD1	58068596	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	2.643000	0.46604	1.123000	0.41961	-0.266000	0.10368	CGC	.	.	none		0.741	IMPAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378665.1	NM_017813	
BCLAF1	9774	hgsc.bcm.edu	37	6	136589425	136589425	+	Missense_Mutation	SNP	G	G	T	rs77081633	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:136589425G>T	ENST00000531224.1	-	10	2524	c.2272C>A	c.(2272-2274)Cct>Act	p.P758T	BCLAF1_ENST00000353331.4_Missense_Mutation_p.P756T|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000527536.1_Missense_Mutation_p.P758T|BCLAF1_ENST00000527759.1_Missense_Mutation_p.P756T|BCLAF1_ENST00000392348.2_Missense_Mutation_p.P756T|BCLAF1_ENST00000530767.1_Missense_Mutation_p.P585T|BCLAF1_ENST00000031135.9_5'UTR	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	758	Poly-Ser.				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)		GGAGAAGAAGGTGATGCTGAA	0.343													G|||	12	0.00239617	0.0	0.0014	5008	,	,		20171	0.0		0.0099	False		,,,				2504	0.001				p.P758T	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											.	BCLAF1	203	.	0			c.C2272A						PASS	.						134.0	118.0	123.0					6																	136589425		2203	4300	6503	SO:0001583	missense	9774	exon10			AAGAAGGTGATGC	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.2272C>A	6.37:g.136589425G>T	ENSP00000435210:p.Pro758Thr	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	220	40	0.181818	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	44	0.020146520146520148	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	37	0.048812664907651716	G	8.714	0.912737	0.17907	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348	T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22	4.87	3.74	0.42951	.	0.107851	0.41396	D	0.000887	T	0.04318	0.0119	N	0.14661	0.345	0.80722	D	1	B;P;B;B;B	0.36909	0.042;0.573;0.137;0.042;0.042	B;B;B;B;B	0.36666	0.031;0.23;0.031;0.031;0.031	T	0.14476	-1.0471	10	0.66056	D	0.02	-4.4078	6.3907	0.21585	0.2287:0.0:0.7713:0.0	.	756;86;756;758;585	Q9NYF8-2;B7Z8J9;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;.;BCLF1_HUMAN;.	T	758;756;758;585;756;756	ENSP00000435210:P758T;ENSP00000229446:P756T;ENSP00000435441:P758T;ENSP00000436501:P585T;ENSP00000434826:P756T;ENSP00000376159:P756T	ENSP00000229446:P756T	P	-	1	0	BCLAF1	136631118	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	3.955000	0.56715	2.431000	0.82371	0.484000	0.47621	CCT	G|0.976;T|0.024	0.024	strong		0.343	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
ITPA	3704	hgsc.bcm.edu	37	20	3193978	3193978	+	Silent	SNP	G	G	A	rs8362	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:3193978G>A	ENST00000380113.3	+	3	330	c.138G>A	c.(136-138)caG>caA	p.Q46Q	ITPA_ENST00000399838.3_Intron|ITPA_ENST00000483354.1_Intron|ITPA_ENST00000455664.2_Silent_p.Q29Q	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	143	0	0		WXS	Illumina HiSeq	Phase_I	148	66	0.445946	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		
ABCB5	340273	hgsc.bcm.edu	37	7	20698270	20698270	+	Missense_Mutation	SNP	A	A	G	rs2301641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:20698270A>G	ENST00000404938.2	+	14	2330	c.1678A>G	c.(1678-1680)Aag>Gag	p.K560E	ABCB5_ENST00000258738.6_Missense_Mutation_p.K115E|ABCB5_ENST00000443026.2_Missense_Mutation_p.K115E|ABCB5_ENST00000406935.1_Missense_Mutation_p.K115E	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	560	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		K -> E (in dbSNP:rs2301641). {ECO:0000269|PubMed:15760339}.		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						TTCAGAAAGCAAGTCAGCTGT	0.433													G|||	1822	0.363818	0.584	0.3127	5008	,	,		19820	0.2024		0.328	False		,,,				2504	0.3057				p.K560E		Atlas-SNP	.											.	ABCB5	357	.	0			c.A1678G						PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	2460,1946	552.4+/-378.5	699,1062,442	98.0	86.0	90.0		1678,343,343,343	4.7	0.6	7	dbSNP_100	90	2742,5858	680.3+/-403.6	438,1866,1996	yes	missense,missense,missense,missense	ABCB5	NM_001163941.1,NM_001163942.1,NM_001163993.1,NM_178559.5	56,56,56,56	1137,2928,2438	GG,GA,AA		31.8837,44.167,39.9969	benign,benign,benign,benign	560/1258,115/132,115/127,115/813	20698270	5202,7804	2203	4300	6503	SO:0001583	missense	340273	exon14			GAAAGCAAGTCAG	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.1678A>G	7.37:g.20698270A>G	ENSP00000384881:p.Lys560Glu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	130	50	0.384615	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	739	0.3383699633699634	256	0.5203252032520326	114	0.3149171270718232	117	0.20454545454545456	252	0.3324538258575198	G	1.621	-0.521441	0.04171	0.55833	0.318837	ENSG00000004846	ENST00000404938;ENST00000443026;ENST00000406935;ENST00000258738	T;D;D;T	0.86956	-0.33;-2.19;-2.19;-0.33	5.58	4.69	0.59074	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.64402	N	0.000011	T	0.00012	0.0000	N	0.00028	-2.635	0.43994	P	0.003306999999999949	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	0.42799	-0.9430	9	0.02654	T	1	.	12.5024	0.55962	0.143:0.0:0.857:0.0	rs2301641;rs52809626;rs61332247;rs2301641	115;560;115;115	B5MD19;A7BKA4;Q2M3G0;Q2M3G0-2	.;.;ABCB5_HUMAN;.	E	560;115;115;115	ENSP00000384881:K560E;ENSP00000406730:K115E;ENSP00000383899:K115E;ENSP00000258738:K115E	ENSP00000258738:K115E	K	+	1	0	ABCB5	20664795	1.000000	0.71417	0.610000	0.28997	0.006000	0.05464	6.508000	0.73721	1.511000	0.48818	-0.128000	0.14901	AAG	A|0.625;G|0.375	0.375	strong		0.433	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
HECTD2	143279	hgsc.bcm.edu	37	10	93221018	93221018	+	Missense_Mutation	SNP	G	G	A	rs61754655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:93221018G>A	ENST00000298068.5	+	4	509	c.415G>A	c.(415-417)Gta>Ata	p.V139I	HECTD2_ENST00000536715.1_5'Flank|HECTD2_ENST00000371681.4_Missense_Mutation_p.V139I|HECTD2_ENST00000446394.1_Missense_Mutation_p.V139I	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	139					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)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						TAGGGAAGATGTAGAAAAAGT	0.284													G|||	4	0.000798722	0.0	0.0029	5008	,	,		12787	0.0		0.002	False		,,,				2504	0.0				p.V139I	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.G415A						PASS	.	G	ILE/VAL,ILE/VAL	4,4400	8.1+/-20.4	0,4,2198	101.0	114.0	109.0		415,415	-0.3	1.0	10	dbSNP_129	109	54,8530	34.3+/-88.2	0,54,4238	yes	missense,missense	HECTD2	NM_173497.2,NM_182765.3	29,29	0,58,6436	AA,AG,GG		0.6291,0.0908,0.4466	benign,benign	139/208,139/777	93221018	58,12930	2202	4292	6494	SO:0001583	missense	143279	exon4			GAAGATGTAGAAA	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"""HECT domain containing 2"""			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.415G>A	10.37:g.93221018G>A	ENSP00000298068:p.Val139Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	101	76	0.752475	NM_173497	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Missense_Mutation	SNP	ENST00000298068.5	37	CCDS7414.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.46	1.357431	0.24598	9.08E-4	0.006291	ENSG00000165338	ENST00000446394;ENST00000371681;ENST00000298068	T;T;T	0.46819	1.19;0.86;1.2	5.1	-0.347	0.12617	.	0.414930	0.24467	N	0.038276	T	0.18383	0.0441	L	0.27053	0.805	0.80722	D	1	B;B;B	0.16603	0.0;0.0;0.018	B;B;B	0.10450	0.0;0.0;0.005	T	0.05402	-1.0887	10	0.15499	T	0.54	.	4.2595	0.10733	0.4162:0.0:0.3307:0.2531	rs61754655	139;139;139	E7ERR3;Q5U5R9;Q5VZ98	.;HECD2_HUMAN;.	I	139	ENSP00000401023:V139I;ENSP00000360746:V139I;ENSP00000298068:V139I	ENSP00000298068:V139I	V	+	1	0	HECTD2	93210998	0.670000	0.27512	0.997000	0.53966	0.982000	0.71751	-0.199000	0.09491	-0.086000	0.12550	0.467000	0.42956	GTA	G|0.997;A|0.003	0.003	strong		0.284	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		
SSPO	23145	hgsc.bcm.edu	37	7	149522162	149522162	+	RNA	SNP	G	G	T	rs62617122	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149522162G>T	ENST00000378016.2	+	0	13949							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)			GGAGGAGGCTGCCGGGAGCCA	0.652													G|||	843	0.168331	0.1233	0.1931	5008	,	,		15528	0.1746		0.1551	False		,,,				2504	0.2188				p.C4650F		Atlas-SNP	.											.	.	.	.	0			c.G13949T						PASS	.	G		469,3329		33,403,1463	19.0	25.0	23.0		13963	4.4	0.5	7	dbSNP_129	23	1386,6814		110,1166,2824	yes	coding-notMod3	SSPO	NM_198455.2		143,1569,4287	TT,TG,GG		16.9024,12.3486,15.4609			149522162	1855,10143	1899	4100	5999			23145	exon96			GAGGCTGCCGGGA	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.149522162G>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	68	12	0.176471	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.840;T|0.160	0.160	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
XIRP2	129446	hgsc.bcm.edu	37	2	168104627	168104627	+	Missense_Mutation	SNP	G	G	A	rs61750760	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168104627G>A	ENST00000409195.1	+	9	6814	c.6725G>A	c.(6724-6726)cGg>cAg	p.R2242Q	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R2020Q|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R2242Q	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2067					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						AACAAAAAGCGGGAGACTGAT	0.388													A|||	993	0.198283	0.3268	0.1326	5008	,	,		16388	0.12		0.1233	False		,,,				2504	0.229				p.R2242Q		Atlas-SNP	.											XIRP2,NS,carcinoma,+1,1	XIRP2	914	1	0			c.G6725A						PASS	.	A	,,,GLN/ARG,GLN/ARG	1051,2617		157,737,940	69.0	63.0	65.0		,,,6725,6059	5.3	1.0	2	dbSNP_129	65	919,7261		56,807,3227	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,43,43	213,1544,4167	AA,AG,GG		11.2347,28.6532,16.6273	,,,benign,benign	,,,2242/3550,2020/3328	168104627	1970,9878	1834	4090	5924	SO:0001583	missense	129446	exon9			AAAAGCGGGAGAC	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.6725G>A	2.37:g.168104627G>A	ENSP00000386840:p.Arg2242Gln	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	223	110	0.493274	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	386	0.17673992673992675	172	0.34959349593495936	47	0.1298342541436464	72	0.1258741258741259	95	0.12532981530343007	A	0.882	-0.728533	0.03135	0.286532	0.112347	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02197	4.4;4.4;4.41	5.34	5.34	0.76211	.	0.706038	0.13958	N	0.351060	T	0.00012	0.0000	N	0.00138	-2.015	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	0.37663	-0.9696	9	0.02654	T	1	-0.1717	10.4051	0.44252	0.9212:0.0:0.0788:0.0	rs61750760	2067;2067;2020	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	2242;2242;2020	ENSP00000386840:R2242Q;ENSP00000295237:R2242Q;ENSP00000387255:R2020Q	ENSP00000295237:R2242Q	R	+	2	0	XIRP2	167812873	1.000000	0.71417	0.969000	0.41365	0.100000	0.18952	4.128000	0.57951	0.868000	0.35678	-0.254000	0.11334	CGG	G|0.842;A|0.158	0.158	strong		0.388	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
KANK3	256949	hgsc.bcm.edu	37	19	8399272	8399272	+	Silent	SNP	G	G	A	rs8106699	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:8399272G>A	ENST00000593649.1	-	4	1424	c.1359C>T	c.(1357-1359)gaC>gaT	p.D453D	KANK3_ENST00000330915.3_Silent_p.D453D			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	453										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						CAGGTGTGCCGTCTCTCTTCT	0.622													G|||	650	0.129792	0.2413	0.1239	5008	,	,		16175	0.0327		0.1153	False		,,,				2504	0.0982				p.D453D		Atlas-SNP	.											.	KANK3	35	.	0			c.C1359T						PASS	.	G		923,3483	351.3+/-311.2	89,745,1369	55.0	54.0	54.0		1359	-4.9	0.0	19	dbSNP_116	54	972,7626	212.0+/-252.4	67,838,3394	no	coding-synonymous	KANK3	NM_198471.2		156,1583,4763	AA,AG,GG		11.305,20.9487,14.5724		453/822	8399272	1895,11109	2203	4299	6502	SO:0001819	synonymous_variant	256949	exon4			TGTGCCGTCTCTC	AK128815	CCDS12199.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000186994		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	24796	protein-coding gene	gene with protein product		614611	"""ankyrin repeat domain 47"""	ANKRD47		17996375, 19554261	Standard	NM_198471		Approved	FLJ46061	uc010dwa.3	Q6NY19		ENST00000593649.1:c.1359C>T	19.37:g.8399272G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	Silent	SNP	ENST00000593649.1	37																																																																																				G|0.859;A|0.141	0.141	strong		0.622	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
CEP72	55722	hgsc.bcm.edu	37	5	637637	637637	+	Missense_Mutation	SNP	A	A	G	rs62000999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:637637A>G	ENST00000264935.5	+	7	1000	c.910A>G	c.(910-912)Atg>Gtg	p.M304V	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	304					G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			CTCAGACTCCATGGATACCGA	0.527													G|||	22	0.00439297	0.0008	0.0043	5008	,	,		20995	0.0		0.0169	False		,,,				2504	0.001				p.M304V		Atlas-SNP	.											.	CEP72	53	.	0			c.A910G						PASS	.	G	VAL/MET	8,4398	822.5+/-416.5	0,8,2195	64.0	69.0	67.0		910	-9.5	0.0	5	dbSNP_129	67	180,8420	810.6+/-407.1	1,178,4121	yes	missense	CEP72	NM_018140.3	21	1,186,6316	GG,GA,AA		2.093,0.1816,1.4455	benign	304/648	637637	188,12818	2203	4300	6503	SO:0001583	missense	55722	exon7			GACTCCATGGATA	BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.910A>G	5.37:g.637637A>G	ENSP00000264935:p.Met304Val	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	193	91	0.471503	NM_018140	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	G	0.015	-1.560185	0.00910	0.001816	0.02093	ENSG00000112877	ENST00000264935	T	0.06768	3.26	4.76	-9.52	0.00578	.	2.230810	0.01420	N	0.014329	T	0.01029	0.0034	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34104	-0.9842	10	0.02654	T	1	0.5272	10.8012	0.46489	0.691:0.1782:0.1307:0.0	rs62000999	304	Q9P209	CEP72_HUMAN	V	304	ENSP00000264935:M304V	ENSP00000264935:M304V	M	+	1	0	CEP72	690637	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.554000	0.00926	-2.567000	0.00470	-1.050000	0.02344	ATG	A|0.989;G|0.011	0.011	strong		0.527	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140	
NAPSA	9476	hgsc.bcm.edu	37	19	50863023	50863023	+	Silent	SNP	A	A	G	rs638294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	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	
APOL3	80833	hgsc.bcm.edu	37	22	36537671	36537671	+	Silent	SNP	T	T	G	rs132619	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:36537671T>G	ENST00000349314.2	-	3	823	c.786A>C	c.(784-786)cgA>cgC	p.R262R	APOL3_ENST00000397293.2_Silent_p.R191R|APOL3_ENST00000397287.2_Silent_p.R62R|APOL3_ENST00000361710.2_Silent_p.R62R|APOL3_ENST00000424878.2_Silent_p.R62R|APOL3_ENST00000487423.1_5'Flank	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	262					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						ATACCTTCAATCGGTCAATGC	0.468													T|||	15	0.00299521	0.0008	0.0101	5008	,	,		24005	0.0		0.005	False		,,,				2504	0.002				p.R262R		Atlas-SNP	.											APOL3_ENST00000349314,NS,malignant_melanoma,-1,2	APOL3	60	2	0			c.A786C						PASS	.	T	,,	7,4399	12.9+/-30.5	0,7,2196	87.0	79.0	82.0		786,186,186	-0.1	0.0	22	dbSNP_78	82	51,8549	32.3+/-84.9	0,51,4249	no	coding-synonymous,coding-synonymous,coding-synonymous	APOL3	NM_145640.2,NM_145641.2,NM_145642.2	,,	0,58,6445	GG,GT,TT		0.593,0.1589,0.4459	,,	262/403,62/203,62/203	36537671	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	80833	exon3			CTTCAATCGGTCA	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.786A>C	22.37:g.36537671T>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	45	29	0.644444	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Silent	SNP	ENST00000349314.2	37	CCDS13922.1																																																																																			T|0.997;G|0.003	0.003	strong		0.468	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641	
MUC17	140453	hgsc.bcm.edu	37	7	100677502	100677502	+	Silent	SNP	G	G	A	rs10267904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677502G>A	ENST00000306151.4	+	3	2869	c.2805G>A	c.(2803-2805)ccG>ccA	p.P935P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	935	59 X approximate tandem repeats.|Ser-rich.				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)					GCACCACGCCGGTAGTCAGTT	0.517																																					p.P935P		Atlas-SNP	.											MUC17,right_upper_lobe,carcinoma,+2,1	MUC17	804	1	0			c.G2805A						scavenged	.	G		706,3700		0,706,1497	376.0	325.0	342.0		2805	-2.4	0.0	7	dbSNP_119	342	866,7734		0,866,3434	no	coding-synonymous	MUC17	NM_001040105.1		0,1572,4931	AA,AG,GG		10.0698,16.0236,12.0867		935/4494	100677502	1572,11434	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACGCCGGTAGTC	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.2805G>A	7.37:g.100677502G>A		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	563	198	0.351687	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.969;A|0.031	0.031	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ARSD	414	hgsc.bcm.edu	37	X	2833605	2833605	+	Nonsense_Mutation	SNP	C	C	T	rs111939179		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:2833605C>T	ENST00000381154.1	-	6	1067	c.992G>A	c.(991-993)tGg>tAg	p.W331*	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	331					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)				ACCTATGAGCCAGTCCATCTC	0.498																																					p.W331X		Atlas-SNP	.											.	ARSD	47	.	0			c.G992A						PASS	.						242.0	167.0	192.0					X																	2833605		2203	4300	6503	SO:0001587	stop_gained	414	exon6			ATGAGCCAGTCCA	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.992G>A	X.37:g.2833605C>T	ENSP00000370546:p.Trp331*	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	87	17	0.195402	NM_001669	Q9UHJ8	Nonsense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	16.78	3.216389	0.58452	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	.	.	.	3.68	3.68	0.42216	.	0.211852	0.43919	U	0.000517	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.9467	0.35762	0.0:0.8898:0.0:0.1102	.	.	.	.	X	331	.	ENSP00000217890:W331X	W	-	2	0	ARSD	2843605	1.000000	0.71417	0.749000	0.31150	0.169000	0.22640	3.671000	0.54576	1.478000	0.48253	0.508000	0.49915	TGG	C|0.999;T|0.001	0.001	strong		0.498	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
RDH12	145226	hgsc.bcm.edu	37	14	68193731	68193731	+	Missense_Mutation	SNP	G	G	A	rs17852293	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:68193731G>A	ENST00000551171.1	+	7	806	c.482G>A	c.(481-483)cGg>cAg	p.R161Q	RDH12_ENST00000267502.3_Missense_Mutation_p.R161Q|RDH12_ENST00000539142.1_Missense_Mutation_p.R161Q	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	161			R -> Q (in dbSNP:rs17852293). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16269441, ECO:0000269|PubMed:21602930}.		photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)			large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	CTCCTGGAGCGGCTAAAGGTG	0.587													G|||	527	0.105232	0.0885	0.1513	5008	,	,		20733	0.1101		0.1143	False		,,,				2504	0.0808				p.R161Q		Atlas-SNP	.											RDH12,brain,glioma,0,1	RDH12	43	1	0			c.G482A						PASS	.	G	GLN/ARG	421,3985	206.8+/-228.3	17,387,1799	70.0	63.0	65.0		482	0.7	1.0	14	dbSNP_123	65	1135,7465	233.6+/-266.8	76,983,3241	yes	missense	RDH12	NM_152443.2	43	93,1370,5040	AA,AG,GG		13.1977,9.5552,11.9637	benign	161/317	68193731	1556,11450	2203	4300	6503	SO:0001583	missense	145226	exon7			TGGAGCGGCTAAA	AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19977	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 2"""	608830	"""retinol dehydrogenase 12 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.482G>A	14.37:g.68193731G>A	ENSP00000449079:p.Arg161Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	152	52	0.342105	NM_152443	B2RDA2|Q8TAW6	Missense_Mutation	SNP	ENST00000551171.1	37	CCDS9787.1	241	0.11034798534798534	41	0.08333333333333333	47	0.1298342541436464	64	0.11188811188811189	89	0.11741424802110818	G	10.09	1.253769	0.22965	0.095552	0.131977	ENSG00000139988	ENST00000551171;ENST00000267502;ENST00000539142	D;D;D	0.89415	-2.51;-2.51;-2.51	5.66	0.738	0.18319	NAD(P)-binding domain (1);	0.197807	0.44483	N	0.000444	T	0.02342	0.0072	N	0.17901	0.54	0.34473	P	0.297021	B	0.26602	0.154	B	0.21917	0.037	T	0.29119	-1.0022	9	0.25751	T	0.34	.	5.8805	0.18852	0.2948:0.0:0.5847:0.1205	rs17852293	161	Q96NR8	RDH12_HUMAN	Q	161	ENSP00000449079:R161Q;ENSP00000267502:R161Q;ENSP00000438715:R161Q	ENSP00000267502:R161Q	R	+	2	0	RDH12	67263484	1.000000	0.71417	0.984000	0.44739	0.305000	0.27757	2.495000	0.45337	-0.123000	0.11745	-0.895000	0.02911	CGG	G|0.882;A|0.118	0.118	strong		0.587	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1		
PCNT	5116	hgsc.bcm.edu	37	21	47805773	47805773	+	Silent	SNP	T	T	C	rs61735805	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:47805773T>C	ENST00000359568.5	+	17	3446	c.3339T>C	c.(3337-3339)agT>agC	p.S1113S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1113					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TATCCTTAAGTCACGAGATAG	0.493													T|||	78	0.0155751	0.0008	0.0216	5008	,	,		20050	0.003		0.0398	False		,,,				2504	0.0194				p.S1113S		Atlas-SNP	.											.	PCNT	283	.	0			c.T3339C						PASS	.	T		36,4370	41.6+/-74.8	0,36,2167	124.0	130.0	128.0		3339	-5.8	0.0	21	dbSNP_129	128	383,8217	125.0+/-183.6	10,363,3927	no	coding-synonymous	PCNT	NM_006031.5		10,399,6094	CC,CT,TT		4.4535,0.8171,3.2216		1113/3337	47805773	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon17			CTTAAGTCACGAG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.3339T>C	21.37:g.47805773T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	126	42	0.333333	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			T|0.972;C|0.028	0.028	strong		0.493	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
CEP68	23177	hgsc.bcm.edu	37	2	65296798	65296798	+	Missense_Mutation	SNP	G	G	A	rs7572857	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:65296798G>A	ENST00000377990.2	+	2	423	c.220G>A	c.(220-222)Ggc>Agc	p.G74S	CEP68_ENST00000546106.1_Missense_Mutation_p.G74S|CEP68_ENST00000260569.4_Missense_Mutation_p.G74S|CEP68_ENST00000537589.1_Intron|RAB1A_ENST00000494188.1_5'Flank	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						PASS	.	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	97	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	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	
CARF	79800	hgsc.bcm.edu	37	2	203846817	203846817	+	Missense_Mutation	SNP	A	A	T	rs72932557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:203846817A>T	ENST00000402905.3	+	15	2033	c.1712A>T	c.(1711-1713)tAc>tTc	p.Y571F	WDR12_ENST00000477723.1_Intron|CARF_ENST00000414439.1_Missense_Mutation_p.Y469F|CARF_ENST00000320443.8_Missense_Mutation_p.Y571F|CARF_ENST00000428585.1_Missense_Mutation_p.Y495F|CARF_ENST00000438828.2_Missense_Mutation_p.Y571F|CARF_ENST00000545262.1_Missense_Mutation_p.Y495F|CARF_ENST00000545253.1_Missense_Mutation_p.Y483F	NM_001104586.1|NM_001282910.1|NM_001282911.1|NM_001282912.1	NP_001098056.1|NP_001269839.1|NP_001269840.1|NP_001269841.1	Q8N187	CARTF_HUMAN	calcium responsive transcription factor	571					cellular response to calcium ion (GO:0071277)|cellular response to potassium ion (GO:0035865)|positive regulation of transcription from RNA polymerase II promoter in response to calcium ion (GO:0061400)	nucleolus (GO:0005730)|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 positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)										CAACCAAGGTACACCTCTCCT	0.373													T|||	236	0.0471246	0.0174	0.0749	5008	,	,		18007	0.0159		0.1302	False		,,,				2504	0.0143				p.Y571F		Atlas-SNP	.											ALS2CR8,rectum,carcinoma,-1,1	ALS2CR8	56	1	0			c.A1712T						PASS	.	T	PHE/TYR,PHE/TYR	130,3558		2,126,1716	59.0	55.0	56.0		1712,1712	4.3	0.3	2	dbSNP_130	56	1055,7155		68,919,3118	yes	missense,missense	ALS2CR8	NM_001104586.1,NM_024744.14	22,22	70,1045,4834	TT,TA,AA		12.8502,3.5249,9.9597	benign,benign	571/726,571/726	203846817	1185,10713	1844	4105	5949	SO:0001583	missense	79800	exon16			CAAGGTACACCTC	AB053309	CCDS42801.1, CCDS63091.1	2q33.3	2013-06-12	2013-06-12	2013-06-12	ENSG00000138380	ENSG00000138380			14435	protein-coding gene	gene with protein product	"""calcium-response factor"""	607586	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8"""	ALS2CR8		11586298, 11832226	Standard	XM_005246858		Approved	FLJ21579, CaRF, NYD-SP24	uc002uzo.2	Q8N187	OTTHUMG00000154528	ENST00000402905.3:c.1712A>T	2.37:g.203846817A>T	ENSP00000384006:p.Tyr571Phe	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	132	35	0.265152	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	37	CCDS42801.1	160	0.07326007326007326	9	0.018292682926829267	34	0.09392265193370165	13	0.022727272727272728	104	0.13720316622691292	T	3.052	-0.195095	0.06259	0.035249	0.128502	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	5.45	4.26	0.50523	.	0.229295	0.37715	N	0.001971	T	0.00073	0.0002	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	0.24012	-1.0172	8	0.02654	T	1	0.0747	8.9639	0.35865	0.297:0.0:0.0:0.703	.	483;495;571	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	F	571;469;495;483;495;571;571	.	ENSP00000316224:Y571F	Y	+	2	0	ALS2CR8	203555062	0.839000	0.29477	0.278000	0.24718	0.867000	0.49689	0.917000	0.28665	0.341000	0.23771	-0.257000	0.10917	TAC	A|0.910;T|0.090	0.090	strong		0.373	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586	
MMP8	4317	hgsc.bcm.edu	37	11	102593273	102593273	+	Silent	SNP	T	T	G	rs12803000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102593273T>G	ENST00000236826.3	-	2	332	c.234A>C	c.(232-234)ccA>ccC	p.P78P		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	78					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)	TTTCCTCATTTGGCTTCCCCG	0.458													T|||	131	0.0261581	0.0015	0.036	5008	,	,		21789	0.0089		0.0417	False		,,,				2504	0.0542				p.P78P		Atlas-SNP	.											MMP8,face,malignant_melanoma,-2,1	MMP8	68	1	0			c.A234C						PASS	.	T		38,4368	43.1+/-76.7	0,38,2165	179.0	174.0	175.0		234	-5.5	0.0	11	dbSNP_121	175	441,8155	133.6+/-191.1	13,415,3870	no	coding-synonymous	MMP8	NM_002424.2		13,453,6035	GG,GT,TT		5.1303,0.8625,3.684		78/468	102593273	479,12523	2203	4298	6501	SO:0001819	synonymous_variant	4317	exon2			CTCATTTGGCTTC	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.234A>C	11.37:g.102593273T>G		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	579	141	0.243523	NM_002424	Q45F99	Silent	SNP	ENST00000236826.3	37	CCDS8320.1	50	0.022893772893772892	1	0.0020325203252032522	15	0.04143646408839779	3	0.005244755244755245	31	0.040897097625329816	T	9.744	1.165560	0.21538	0.008625	0.051303	ENSG00000118113	ENST00000438475	.	.	.	5.73	-5.47	0.02600	.	.	.	.	.	T	0.02571	0.0078	.	.	.	0.28932	N	0.891481	.	.	.	.	.	.	T	0.28586	-1.0039	4	.	.	.	.	1.8071	0.03083	0.1913:0.251:0.3608:0.1968	rs12803000;rs12803000	.	.	.	Q	54	.	.	K	-	1	0	MMP8	102098483	0.000000	0.05858	0.021000	0.16686	0.916000	0.54674	-2.650000	0.00858	-0.504000	0.06577	0.533000	0.62120	AAA	T|0.966;G|0.034	0.034	strong		0.458	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
HOXD10	3236	hgsc.bcm.edu	37	2	176983923	176983923	+	Silent	SNP	G	G	C	rs33913965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:176983923G>C	ENST00000249501.4	+	2	1242	c.987G>C	c.(985-987)cgG>cgC	p.R329R	HOXD-AS2_ENST00000440016.2_RNA|HOXD10_ENST00000490088.2_3'UTR	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	329					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|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)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GAGAGAACCGGATCCGAGAAC	0.562													G|||	37	0.00738818	0.0015	0.0187	5008	,	,		10062	0.0		0.0209	False		,,,				2504	0.001				p.R329R		Atlas-SNP	.											.	HOXD10	65	.	0			c.G987C						PASS	.	G		18,4388	25.3+/-52.1	0,18,2185	45.0	48.0	47.0		987	3.9	1.0	2	dbSNP_126	47	193,8407	84.8+/-147.2	1,191,4108	no	coding-synonymous	HOXD10	NM_002148.3		1,209,6293	CC,CG,GG		2.2442,0.4085,1.6223		329/341	176983923	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	3236	exon2			GAACCGGATCCGA		CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"""Homeoboxes / ANTP class : HOXL subclass"""	5133	protein-coding gene	gene with protein product		142984	"""homeo box D10"""	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.987G>C	2.37:g.176983923G>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	159	77	0.484277	NM_002148	Q6NT10	Silent	SNP	ENST00000249501.4	37	CCDS2266.1																																																																																			G|0.984;C|0.016	0.016	strong		0.562	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2		
ZNF879	345462	hgsc.bcm.edu	37	5	178459426	178459426	+	Missense_Mutation	SNP	A	A	C	rs17078991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:178459426A>C	ENST00000444149.2	+	5	665	c.477A>C	c.(475-477)gaA>gaC	p.E159D		NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	159					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.E159D(1)		endometrium(3)|kidney(2)|pancreas(1)|stomach(1)	7						AAGGTGTTGAATTTGGGAAAA	0.373													A|||	1824	0.364217	0.5182	0.255	5008	,	,		19198	0.4276		0.2237	False		,,,				2504	0.3129				p.E159D		Atlas-SNP	.											ZNF879,NS,carcinoma,0,2	ZNF879	41	2	1	Substitution - Missense(1)	stomach(1)	c.A477C						PASS	.	A	ASP/GLU	618,766		138,342,212	91.0	77.0	81.0		477	-1.2	0.3	5	dbSNP_123	81	706,2476		75,556,960	yes	missense	ZNF879	NM_001136116.1	45	213,898,1172	CC,CA,AA		22.1873,44.6532,28.9969	benign	159/564	178459426	1324,3242	692	1591	2283	SO:0001583	missense	345462	exon5			TGTTGAATTTGGG	AK300504	CCDS47352.1	5q35.3	2013-01-08			ENSG00000234284	ENSG00000234284		"""Zinc fingers, C2H2-type"", ""-"""	37273	protein-coding gene	gene with protein product							Standard	NM_001136116		Approved	DKFZp686E2433	uc003mjt.4	B4DU55	OTTHUMG00000163596	ENST00000444149.2:c.477A>C	5.37:g.178459426A>C	ENSP00000414887:p.Glu159Asp	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_001136116		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	770	0.3525641025641026	243	0.49390243902439024	100	0.27624309392265195	244	0.42657342657342656	183	0.24142480211081793	A	9.372	1.070780	0.20147	0.446532	0.221873	ENSG00000234284	ENST00000444149	T	0.06933	3.24	4.45	-1.18	0.09617	.	.	.	.	.	T	0.00012	0.0000	L	0.37850	1.14	0.34582	P	0.28547900000000004	B	0.02656	0.0	B	0.04013	0.001	T	0.42120	-0.9470	8	0.42905	T	0.14	-4.0842	4.6168	0.12430	0.4554:0.3309:0.2137:0.0	rs17078991;rs52798739;rs17078991	159	B4DU55	ZN879_HUMAN	D	159	ENSP00000414887:E159D	ENSP00000414887:E159D	E	+	3	2	ZNF879	178392032	0.000000	0.05858	0.286000	0.24833	0.782000	0.44232	-0.068000	0.11561	-0.283000	0.09115	0.482000	0.46254	GAA	A|0.634;C|0.366	0.366	strong		0.373	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1	NM_001136116	
TREX1	11277	hgsc.bcm.edu	37	3	48508585	48508585	+	Silent	SNP	C	C	T	rs11797	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48508585C>T	ENST00000422277.2	+	1	1357	c.696C>T	c.(694-696)taC>taT	p.Y232Y	SHISA5_ENST00000465449.1_5'Flank|TREX1_ENST00000436480.2_Silent_p.Y177Y|TREX1_ENST00000492235.1_3'UTR|TREX1_ENST00000444177.1_Silent_p.Y167Y|TREX1_ENST00000433541.1_Silent_p.Y38Y|TREX1_ENST00000456089.1_Silent_p.Y38Y|TREX1_ENST00000296443.9_Silent_p.Y177Y	NM_016381.4	NP_057465.1	Q9NSU2	TREX1_HUMAN	three prime repair exonuclease 1	232					cell death (GO:0008219)|cellular response to interferon-beta (GO:0035458)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|innate immune response (GO:0045087)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	endoplasmic reticulum membrane (GO:0005789)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|3'-5'-exodeoxyribonuclease activity (GO:0008296)|adenyl deoxyribonucleotide binding (GO:0032558)|double-stranded DNA binding (GO:0003690)|exodeoxyribonuclease III activity (GO:0008853)|metal ion binding (GO:0046872)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein homodimerization activity (GO:0042803)|single-stranded DNA binding (GO:0003697)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|skin(3)	9				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GGAAGAGCTACAGCCTAGGCA	0.607													C|||	1569	0.313299	0.2383	0.2853	5008	,	,		21572	0.3125		0.4433	False		,,,				2504	0.3016				p.Y232Y		Atlas-SNP	.											.	TREX1	17	.	0			c.C696T						PASS	.	C	,	1210,3196	421.9+/-339.5	170,870,1163	62.0	63.0	63.0		696,531	2.7	1.0	3	dbSNP_52	63	3903,4697	544.3+/-384.6	894,2115,1291	no	coding-synonymous,coding-synonymous	TREX1	NM_016381.3,NM_033629.2	,	1064,2985,2454	TT,TC,CC		45.3837,27.4626,39.3126	,	232/370,177/315	48508585	5113,7893	2203	4300	6503	SO:0001819	synonymous_variant	11277	exon1			GAGCTACAGCCTA	AF151105	CCDS2769.1, CCDS59451.1	3p21.31	2014-09-17			ENSG00000213689	ENSG00000213689			12269	protein-coding gene	gene with protein product		606609	"""Aicardi-Goutieres syndrome 1"""	AGS1		10391904, 10393201, 16845398	Standard	NM_033629		Approved	DRN3	uc010hka.4	Q9NSU2	OTTHUMG00000156205	ENST00000422277.2:c.696C>T	3.37:g.48508585C>T		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	141	80	0.567376	NM_016381	B2RCN9|Q8TEU2|Q9BPW1|Q9Y4X2	Silent	SNP	ENST00000422277.2	37	CCDS43086.1																																																																																			C|0.642;T|0.358	0.358	strong		0.607	TREX1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_016381	
ENPP1	5167	hgsc.bcm.edu	37	6	132172368	132172368	+	Missense_Mutation	SNP	A	A	C	rs1044498	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:132172368A>C	ENST00000360971.2	+	4	537	c.517A>C	c.(517-519)Aag>Cag	p.K173Q		NM_006208.2	NP_006199.2	P22413	ENPP1_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 1	173	SMB 2. {ECO:0000255|PROSITE- ProRule:PRU00350}.		K -> Q (associated with NIDDM; dbSNP:rs1044498). {ECO:0000269|PubMed:10453738, ECO:0000269|PubMed:10480624, ECO:0000269|PubMed:16186408, ECO:0000269|PubMed:20034067}.		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|ATP catabolic process (GO:0006200)|biomineral tissue development (GO:0031214)|bone remodeling (GO:0046849)|cellular phosphate ion homeostasis (GO:0030643)|cellular response to insulin stimulus (GO:0032869)|generation of precursor metabolites and energy (GO:0006091)|immune response (GO:0006955)|inorganic diphosphate transport (GO:0030505)|negative regulation of cell growth (GO:0030308)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of ossification (GO:0030279)|negative regulation of protein autophosphorylation (GO:0031953)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)|regulation of bone mineralization (GO:0030500)|riboflavin metabolic process (GO:0006771)|sequestering of triglyceride (GO:0030730)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|insulin receptor binding (GO:0005158)|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)|protein homodimerization activity (GO:0042803)|scavenger receptor activity (GO:0005044)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(22)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	46	Breast(56;0.0505)			GBM - Glioblastoma multiforme(226;0.0216)|OV - Ovarian serous cystadenocarcinoma(155;0.022)	Amifostine(DB01143)|Ribavirin(DB00811)	CTGCAAGGACAAGGGCGACTG	0.493													C|||	1714	0.342252	0.8835	0.196	5008	,	,		15825	0.0962		0.1332	False		,,,				2504	0.183				p.K173Q	Colon(104;336 1535 5856 11019 33782)	Atlas-SNP	.											.	ENPP1	108	.	0			c.A517C	GRCh37	CM993455	ENPP1	M	rs1044498	PASS	.	C	GLN/LYS	3310,1096	393.3+/-328.8	1262,786,155	133.0	127.0	129.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	517	3.4	0.0	6	dbSNP_86	129	1245,7355	761.3+/-407.6	92,1061,3147	yes	missense	ENPP1	NM_006208.2	53	1354,1847,3302	CC,CA,AA		14.4767,24.8752,35.0223	benign	173/926	132172368	4555,8451	2203	4300	6503	SO:0001583	missense	5167	exon4			AAGGACAAGGGCG	M57736	CCDS5150.2	6q22-q23	2008-02-07			ENSG00000197594	ENSG00000197594	3.1.4.1, 3.6.1.9		3356	protein-coding gene	gene with protein product		173335		NPPS, M6S1, PDNP1		1315502	Standard	NM_006208		Approved	PC-1, PCA1	uc011ecf.2	P22413	OTTHUMG00000015572	ENST00000360971.2:c.517A>C	6.37:g.132172368A>C	ENSP00000354238:p.Lys173Gln	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_006208	Q5T9R6|Q9NPZ3|Q9P1P6|Q9UP61|Q9Y6K3	Missense_Mutation	SNP	ENST00000360971.2	37	CCDS5150.2	640	0.29304029304029305	427	0.8678861788617886	59	0.16298342541436464	62	0.10839160839160839	92	0.12137203166226913	C	11.34	1.610895	0.28712	0.751248	0.144767	ENSG00000197594	ENST00000360971	T	0.43294	0.95	5.55	3.39	0.38822	Somatomedin B domain (4);	0.811774	0.11213	N	0.587550	T	0.21186	0.0510	L	0.46885	1.475	0.80722	P	0.0	B	0.22604	0.072	B	0.26310	0.068	T	0.06607	-1.0817	9	0.27785	T	0.31	-0.3225	14.3354	0.66586	0.8272:0.1728:0.0:0.0	rs1044498;rs1801642;rs3184275;rs17847048;rs52820331;rs1044498	173	P22413	ENPP1_HUMAN	Q	173	ENSP00000354238:K173Q	ENSP00000354238:K173Q	K	+	1	0	ENPP1	132214061	0.097000	0.21791	0.001000	0.08648	0.926000	0.56050	1.966000	0.40481	0.174000	0.19809	-0.187000	0.12897	AAG	A|0.655;C|0.345	0.345	strong		0.493	ENPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042238.2		
KIAA1731	85459	hgsc.bcm.edu	37	11	93433289	93433289	+	Silent	SNP	A	A	G	rs374656563		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:93433289A>G	ENST00000325212.6	+	15	5373	c.5211A>G	c.(5209-5211)acA>acG	p.T1737T	KIAA1731_ENST00000411936.1_Silent_p.T1737T|KIAA1731_ENST00000531700.1_Intron|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	1737						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGAGACAAACAGCATTGCAGC	0.368																																					p.T1737T		Atlas-SNP	.											.	KIAA1731	173	.	0			c.A5211G						PASS	.	A		0,1384		0,0,692	64.0	55.0	58.0		5211	0.1	0.0	11		58	2,3180		0,2,1589	no	coding-synonymous	KIAA1731	NM_033395.1		0,2,2281	GG,GA,AA		0.0629,0.0,0.0438		1737/2602	93433289	2,4564	692	1591	2283	SO:0001819	synonymous_variant	85459	exon15			ACAAACAGCATTG	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.5211A>G	11.37:g.93433289A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	236	142	0.601695	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Silent	SNP	ENST00000325212.6	37	CCDS44708.1																																																																																			.	.	weak		0.368	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
EXO5	64789	hgsc.bcm.edu	37	1	40980668	40980668	+	Missense_Mutation	SNP	T	T	C	rs35672330	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:40980668T>C	ENST00000372703.1	+	2	1526	c.452T>C	c.(451-453)cTt>cCt	p.L151P	RP11-656D10.6_ENST00000437060.1_RNA|EXO5_ENST00000296380.4_Missense_Mutation_p.L151P|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000358527.2_Missense_Mutation_p.L151P			Q9H790	EXO5_HUMAN	exonuclease 5	151					DNA catabolic process, exonucleolytic (GO:0000738)|interstrand cross-link repair (GO:0036297)	cytosol (GO:0005829)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)										CTGAACATACTTTTGCTGATT	0.463													T|||	99	0.0197684	0.0045	0.0403	5008	,	,		21040	0.0		0.0596	False		,,,				2504	0.0051				p.L151P		Atlas-SNP	.											.	.	.	.	0			c.T452C						PASS	.	T	PRO/LEU	60,4346	56.8+/-93.2	0,60,2143	76.0	76.0	76.0		452	3.8	0.0	1	dbSNP_126	76	565,8035	148.9+/-204.1	19,527,3754	yes	missense	DEM1	NM_022774.1	98	19,587,5897	CC,CT,TT		6.5698,1.3618,4.8055	probably-damaging	151/374	40980668	625,12381	2203	4300	6503	SO:0001583	missense	64789	exon3			ACATACTTTTGCT	AK024797	CCDS453.1	1p34.2	2012-11-02	2012-10-30	2012-10-30	ENSG00000164002	ENSG00000164002			26115	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 176"", ""defects in morphology 1 homolog (S. cerevisiae)"""	C1orf176, DEM1		23095756	Standard	NM_022774		Approved	FLJ21144	uc001cfp.3	Q9H790	OTTHUMG00000007305	ENST00000372703.1:c.452T>C	1.37:g.40980668T>C	ENSP00000361788:p.Leu151Pro	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	100	71	0.71	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Missense_Mutation	SNP	ENST00000372703.1	37	CCDS453.1	64	0.029304029304029304	3	0.006097560975609756	18	0.049723756906077346	0	0.0	43	0.05672823218997362	T	11.11	1.542557	0.27563	0.013618	0.065698	ENSG00000164002	ENST00000358527;ENST00000372703;ENST00000420209;ENST00000296380;ENST00000418186;ENST00000415550;ENST00000443729;ENST00000419161	T;T;T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32;1.32;1.32;1.32	4.97	3.84	0.44239	.	0.000000	0.43919	D	0.000515	T	0.08403	0.0209	M	0.74258	2.255	0.25531	N	0.987277	D	0.89917	1.0	D	0.91635	0.999	T	0.04767	-1.0928	10	0.87932	D	0	-19.3156	7.4498	0.27231	0.0:0.097:0.0:0.903	rs35672330	151	Q9H790	EXO5_HUMAN	P	151	ENSP00000351328:L151P;ENSP00000361788:L151P;ENSP00000398437:L151P;ENSP00000296380:L151P;ENSP00000391240:L151P;ENSP00000413565:L151P;ENSP00000409715:L151P;ENSP00000392115:L151P	ENSP00000296380:L151P	L	+	2	0	DEM1	40753255	0.057000	0.20700	0.002000	0.10522	0.372000	0.29890	3.024000	0.49674	1.033000	0.39918	0.528000	0.53228	CTT	T|0.958;C|0.042	0.042	strong		0.463	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
KIAA1586	57691	hgsc.bcm.edu	37	6	56911574	56911574	+	Splice_Site	SNP	A	A	G	rs9382680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56911574A>G	ENST00000370733.4	+	1	228	c.21A>G	c.(19-21)gaA>gaG	p.E7E	KIAA1586_ENST00000545356.1_Splice_Site_p.E7E|KIAA1586_ENST00000488682.1_3'UTR	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	7							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			CGGGGTCGGAAGTGAGTAGTC	0.667																																					p.E7E		Atlas-SNP	.											.	KIAA1586	59	.	0			c.A21G						PASS	.						53.0	53.0	53.0					6																	56911574		2202	4300	6502	SO:0001630	splice_region_variant	57691	exon1			GTCGGAAGTGAGT	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.21+1A>G	6.37:g.56911574A>G		Somatic	407	1	0.002457		WXS	Illumina HiSeq	Phase_I	248	90	0.362903	NM_020931	A8K4M3|Q8IW25	Silent	SNP	ENST00000370733.4	37	CCDS34480.1																																																																																			A|0.824;G|0.176	0.176	strong		0.667	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	Silent
CEP350	9857	hgsc.bcm.edu	37	1	179972337	179972337	+	Silent	SNP	A	A	C	rs17371159	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:179972337A>C	ENST00000367607.3	+	7	1465	c.1047A>C	c.(1045-1047)cgA>cgC	p.R349R		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	349					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						CCAAGATTCGAACACCTGATG	0.368													A|||	258	0.0515176	0.0045	0.062	5008	,	,		19022	0.0139		0.1123	False		,,,				2504	0.0838				p.R349R		Atlas-SNP	.											.	CEP350	418	.	0			c.A1047C						PASS	.	A		114,4292	85.3+/-124.0	1,112,2090	85.0	79.0	81.0		1047	1.4	1.0	1	dbSNP_123	81	1035,7565	218.1+/-256.6	80,875,3345	no	coding-synonymous	CEP350	NM_014810.4		81,987,5435	CC,CA,AA		12.0349,2.5874,8.8344		349/3118	179972337	1149,11857	2203	4300	6503	SO:0001819	synonymous_variant	9857	exon7			GATTCGAACACCT	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.1047A>C	1.37:g.179972337A>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	171	108	0.631579	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1																																																																																			A|0.930;C|0.070	0.070	strong		0.368	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
NOP9	161424	hgsc.bcm.edu	37	14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	rs147123517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24772373C>T	ENST00000267425.3	+	6	1330	c.1237C>T	c.(1237-1239)Cgc>Tgc	p.R413C	NOP9_ENST00000396802.3_Missense_Mutation_p.R413C	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	413							poly(A) RNA binding (GO:0044822)										GGGGGCCTGTCGCAGAGTTGG	0.557													C|||	8	0.00159744	0.0	0.0014	5008	,	,		16884	0.0		0.007	False		,,,				2504	0.0				p.R413C		Atlas-SNP	.											.	.	.	.	0			c.C1237T						PASS	.	C	CYS/ARG	4,4402	6.2+/-15.9	0,4,2199	70.0	71.0	71.0		1237	4.2	1.0	14	dbSNP_134	71	45,8555	30.1+/-81.4	0,45,4255	yes	missense	C14orf21	NM_174913.1	180	0,49,6454	TT,TC,CC		0.5233,0.0908,0.3767	probably-damaging	413/637	24772373	49,12957	2203	4300	6503	SO:0001583	missense	161424	exon6			GCCTGTCGCAGAG		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.1237C>T	14.37:g.24772373C>T	ENSP00000267425:p.Arg413Cys	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	281	94	0.33452	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.19	3.567896	0.65651	9.08E-4	0.005233	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.32753	1.48;1.44	5.16	4.25	0.50352	.	0.224065	0.38897	N	0.001525	T	0.35189	0.0923	L	0.54323	1.7	0.43536	D	0.995829	D	0.76494	0.999	P	0.59288	0.855	T	0.23013	-1.0200	10	0.52906	T	0.07	-4.9362	11.1833	0.48642	0.4521:0.5479:0.0:0.0	.	413	Q86U38	CN021_HUMAN	C	413	ENSP00000267425:R413C;ENSP00000380020:R413C	ENSP00000267425:R413C	R	+	1	0	C14orf21	23842213	0.869000	0.29996	1.000000	0.80357	0.909000	0.53808	0.630000	0.24553	1.356000	0.45884	0.563000	0.77884	CGC	C|0.996;T|0.004	0.004	strong		0.557	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
FAM149A	25854	hgsc.bcm.edu	37	4	187088399	187088399	+	Missense_Mutation	SNP	G	G	T	rs111681837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187088399G>T	ENST00000356371.5	+	13	2231	c.2231G>T	c.(2230-2232)gGt>gTt	p.G744V	FAM149A_ENST00000389354.5_Missense_Mutation_p.G453V|FAM149A_ENST00000514153.1_Missense_Mutation_p.G453V|FAM149A_ENST00000502970.1_Missense_Mutation_p.G453V|FAM149A_ENST00000503432.1_Missense_Mutation_p.G453V|FAM149A_ENST00000227065.4_Missense_Mutation_p.G453V			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	744										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		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;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		ACATGGACAGGTCAAAGTATT	0.373													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		20278	0.0		0.006	False		,,,				2504	0.0				p.G453V		Atlas-SNP	.											.	FAM149A	52	.	0			c.G1358T						PASS	.	G	VAL/GLY,VAL/GLY	7,4399	12.9+/-30.5	0,7,2196	126.0	128.0	128.0		1358,1358	4.8	1.0	4	dbSNP_132	128	58,8542	35.9+/-90.5	0,58,4242	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	109,109	0,65,6438	TT,TG,GG		0.6744,0.1589,0.4998	probably-damaging,probably-damaging	453/483,453/483	187088399	65,12941	2203	4300	6503	SO:0001583	missense	25854	exon12			GGACAGGTCAAAG	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.2231G>T	4.37:g.187088399G>T	ENSP00000348732:p.Gly744Val	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	165	48	0.290909	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		6|6|6	0.0027472527472527475|0.0027472527472527475|0.0027472527472527475	0|0|0	0.0|0.0|0.0	1|1|1	0.0027624309392265192|0.0027624309392265192|0.0027624309392265192	0|0|0	0.0|0.0|0.0	5|5|5	0.006596306068601583|0.006596306068601583|0.006596306068601583	G|G|G	20.2|20.2|20.2	3.945034|3.945034|3.945034	0.73672|0.73672|0.73672	0.001589|0.001589|0.001589	0.006744|0.006744|0.006744	ENSG00000109794|ENSG00000109794|ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354|ENST00000512271|ENST00000510843;ENST00000502894	T;T;T;T;T;T|.|.	0.15372|.|.	2.56;2.43;2.56;2.56;2.56;2.56|.|.	5.62|5.62|5.62	4.77|4.77|4.77	0.60923|0.60923|0.60923	.|.|.	0.309873|.|.	0.32518|.|.	N|.|.	0.005996|.|.	T|T|T	0.64360|0.64360|0.64360	0.2591|0.2591|0.2591	M|M|M	0.65975|0.65975|0.65975	2.015|2.015|2.015	0.52501|0.52501|0.52501	D|D|D	0.999951|0.999951|0.999951	D;D|.|.	0.76494|.|.	0.999;0.999|.|.	D;D|.|.	0.74023|.|.	0.982;0.961|.|.	T|T|T	0.67356|0.67356|0.67356	-0.5691|-0.5691|-0.5691	10|5|5	0.87932|.|.	D|.|.	0|.|.	-13.1821|-13.1821|-13.1821	13.7969|13.7969|13.7969	0.63177|0.63177|0.63177	0.0766:0.0:0.9234:0.0|0.0766:0.0:0.9234:0.0|0.0766:0.0:0.9234:0.0	.|.|.	743;744|.|.	A5PLN7-3;A5PLN7|.|.	.;F149A_HUMAN|.|.	V|S|F	453;744;453;453;453;453|129|131;14	ENSP00000426835:G453V;ENSP00000348732:G744V;ENSP00000227065:G453V;ENSP00000427155:G453V;ENSP00000424380:G453V;ENSP00000374005:G453V|.|.	ENSP00000227065:G453V|.|.	G|R|V	+|+|+	2|3|1	0|2|0	FAM149A|FAM149A|FAM149A	187325393|187325393|187325393	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.965000|0.965000|0.965000	0.64279|0.64279|0.64279	4.047000|4.047000|4.047000	0.57383|0.57383|0.57383	2.652000|2.652000|2.652000	0.90054|0.90054|0.90054	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GGT|AGG|GTC	G|0.995;T|0.005	0.005	strong		0.373	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
XIRP2	129446	hgsc.bcm.edu	37	2	168104988	168104988	+	Missense_Mutation	SNP	G	G	T	rs59889092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168104988G>T	ENST00000409195.1	+	9	7175	c.7086G>T	c.(7084-7086)atG>atT	p.M2362I	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.M2140I|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.M2362I	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2187					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						GTTCATCGATGTTTCTGCCGC	0.478													G|||	865	0.172724	0.2882	0.1196	5008	,	,		16686	0.12		0.1123	False		,,,				2504	0.1708				p.M2362I		Atlas-SNP	.											.	XIRP2	914	.	0			c.G7086T						PASS	.	G	,,ILE/MET,,ILE/MET	981,2963		132,717,1123	101.0	109.0	106.0		,,6420,,7086	-0.7	0.0	2	dbSNP_129	106	800,7498		42,716,3391	yes	intron,intron,missense,intron,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,10,,10	174,1433,4514	TT,TG,GG		9.6409,24.8732,14.5483	,,possibly-damaging,,possibly-damaging	,,2140/3328,,2362/3550	168104988	1781,10461	1972	4149	6121	SO:0001583	missense	129446	exon9			ATCGATGTTTCTG	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.7086G>T	2.37:g.168104988G>T	ENSP00000386840:p.Met2362Ile	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	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	353	0.16163003663003664	151	0.30691056910569103	42	0.11602209944751381	72	0.1258741258741259	88	0.11609498680738786	G	7.688	0.690360	0.15039	0.248732	0.096409	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02258	4.37;4.37;4.37	5.95	-0.665	0.11403	.	1.224870	0.05371	N	0.535332	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B;B	0.19817	0.023;0.039;0.019	B;B;B	0.15870	0.006;0.014;0.003	T	0.46414	-0.9193	9	0.41790	T	0.15	2.8744	7.8749	0.29589	0.213:0.3739:0.4131:0.0	rs59889092;rs61750785	2187;2187;2140	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	I	2362;2362;2140	ENSP00000386840:M2362I;ENSP00000295237:M2362I;ENSP00000387255:M2140I	ENSP00000295237:M2362I	M	+	3	0	XIRP2	167813234	0.001000	0.12720	0.000000	0.03702	0.344000	0.29017	0.038000	0.13862	-0.100000	0.12241	0.655000	0.94253	ATG	G|0.860;T|0.140	0.140	strong		0.478	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
ADAM7	8756	hgsc.bcm.edu	37	8	24356818	24356818	+	Missense_Mutation	SNP	A	A	C	rs13259668	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:24356818A>C	ENST00000175238.6	+	17	1995	c.1912A>C	c.(1912-1914)Aat>Cat	p.N638H	RP11-561E1.1_ENST00000519364.1_RNA|ADAM7_ENST00000520720.1_Missense_Mutation_p.N410H|ADAM7_ENST00000380789.1_Missense_Mutation_p.N638H|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	638	Cys-rich.		N -> H (in dbSNP:rs13259668).			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)		CTCTCAGTGCAATGAAAATCC	0.343													C|||	1634	0.326278	0.3185	0.4452	5008	,	,		16940	0.1935		0.3062	False		,,,				2504	0.41				p.N638H		Atlas-SNP	.											.	ADAM7	165	.	0			c.A1912C						PASS	.	C	HIS/ASN	1430,2976	683.4+/-404.3	232,966,1005	130.0	120.0	123.0		1912	-4.4	0.0	8	dbSNP_121	123	2868,5732	671.8+/-402.9	486,1896,1918	yes	missense	ADAM7	NM_003817.2	68	718,2862,2923	CC,CA,AA		33.3488,32.4557,33.0463	benign	638/755	24356818	4298,8708	2203	4300	6503	SO:0001583	missense	8756	exon17			CAGTGCAATGAAA	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.1912A>C	8.37:g.24356818A>C	ENSP00000175238:p.Asn638His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	125	84	0.672	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	653	0.298992673992674	148	0.3008130081300813	156	0.430939226519337	115	0.20104895104895104	234	0.3087071240105541	C	0.278	-0.988090	0.02162	0.324557	0.333488	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.53857	1.48;1.49;0.6	4.92	-4.36	0.03645	.	1.962480	0.02172	N	0.059785	T	0.00012	0.0000	L	0.27944	0.81	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.33163	-0.9879	9	0.11182	T	0.66	.	3.2326	0.06754	0.5961:0.1976:0.113:0.0933	rs13259668;rs52834855;rs59851115;rs13259668	410;638	E5RK87;Q9H2U9	.;ADAM7_HUMAN	H	638;638;410;453	ENSP00000175238:N638H;ENSP00000370166:N638H;ENSP00000430400:N410H	ENSP00000175238:N638H	N	+	1	0	ADAM7	24412708	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.275000	0.02817	-0.866000	0.04068	-1.782000	0.00648	AAT	A|0.694;C|0.306	0.306	strong		0.343	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
OR52R1	119695	hgsc.bcm.edu	37	11	4825010	4825010	+	Missense_Mutation	SNP	T	T	A	rs6578533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4825010T>A	ENST00000356069.2	-	1	600	c.601A>T	c.(601-603)Aat>Tat	p.N201Y	MMP26_ENST00000380390.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.N280Y|MMP26_ENST00000477339.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	201			N -> Y (in dbSNP:rs6578533). {ECO:0000269|PubMed:14983052, 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)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGAGCCCATTCCCACGACTT	0.493													A|||	1551	0.309704	0.559	0.2795	5008	,	,		23742	0.0129		0.3907	False		,,,				2504	0.2168				p.N201Y		Atlas-SNP	.											.	OR52R1	81	.	0			c.A601T						PASS	.	A	TYR/ASN	2267,2135	577.8+/-384.5	595,1077,529	152.0	115.0	128.0		601	4.4	0.8	11	dbSNP_116	128	3013,5583	663.9+/-402.1	551,1911,1836	yes	missense	OR52R1	NM_001005177.3	143	1146,2988,2365	AA,AT,TT		35.0512,48.5007,40.6216	benign	201/316	4825010	5280,7718	2201	4298	6499	SO:0001583	missense	119695	exon1			GCCCATTCCCACG	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.601A>T	11.37:g.4825010T>A	ENSP00000348368:p.Asn201Tyr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	682	0.31227106227106227	270	0.5487804878048781	117	0.32320441988950277	10	0.017482517482517484	285	0.3759894459102902	A	0.009	-1.845698	0.00568	0.514993	0.350512	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.28255	1.62;1.62	5.57	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	N	0.000407	T	0.00012	0.0000	N	0.00002	-3.515	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47586	-0.9106	9	0.02654	T	1	.	10.3189	0.43753	0.739:0.0:0.0:0.261	rs6578533;rs57223245;rs6578533	201	Q8NGF1	O52R1_HUMAN	Y	201;280	ENSP00000348368:N201Y;ENSP00000369742:N280Y	ENSP00000348368:N201Y	N	-	1	0	OR52R1	4781586	0.002000	0.14202	0.753000	0.31225	0.302000	0.27658	1.733000	0.38156	1.130000	0.42092	-0.265000	0.10407	AAT	A|0.369;N|0.000	0.369	strong		0.493	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
IQGAP3	128239	hgsc.bcm.edu	37	1	156518379	156518379	+	Missense_Mutation	SNP	G	G	A	rs744224	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156518379G>A	ENST00000361170.2	-	17	1997	c.1987C>T	c.(1987-1989)Cgt>Tgt	p.R663C		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	663			R -> C (in dbSNP:rs744224). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		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)					TTACCTGGACGCTGTTTCTTT	0.607													G|||	2039	0.407149	0.2958	0.3646	5008	,	,		19167	0.5724		0.2575	False		,,,				2504	0.5716				p.R663C		Atlas-SNP	.											IQGAP3,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	IQGAP3	146	1	0			c.C1987T						PASS	.	G	CYS/ARG	1316,3090	443.9+/-347.2	196,924,1083	143.0	101.0	115.0		1987	1.9	0.0	1	dbSNP_86	115	2370,6230	394.8+/-344.8	341,1688,2271	yes	missense	IQGAP3	NM_178229.4	180	537,2612,3354	AA,AG,GG		27.5581,29.8684,28.3408	benign	663/1632	156518379	3686,9320	2203	4300	6503	SO:0001583	missense	128239	exon17			CTGGACGCTGTTT	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.1987C>T	1.37:g.156518379G>A	ENSP00000354451:p.Arg663Cys	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	181	178	0.983425	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	758	0.34706959706959706	134	0.27235772357723576	123	0.3397790055248619	311	0.5437062937062938	190	0.25065963060686014	G	3.973	-0.007916	0.07773	0.298684	0.275581	ENSG00000183856	ENST00000361170	T	0.06849	3.25	4.85	1.89	0.25635	.	1.156880	0.06169	N	0.677301	T	0.02455	0.0075	L	0.29908	0.895	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.42085	-0.9472	9	0.48119	T	0.1	2.333	9.5002	0.39013	0.2415:0.0:0.7585:0.0	rs744224;rs1774954;rs17391814;rs57842273;rs744224	663	Q86VI3	IQGA3_HUMAN	C	663	ENSP00000354451:R663C	ENSP00000354451:R663C	R	-	1	0	IQGAP3	154785003	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.029000	0.12329	0.108000	0.17862	-0.258000	0.10820	CGT	G|0.683;A|0.317	0.317	strong		0.607	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
G6PC2	57818	hgsc.bcm.edu	37	2	169764176	169764176	+	Missense_Mutation	SNP	G	G	C	rs492594	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:169764176G>C	ENST00000375363.3	+	5	747	c.655G>C	c.(655-657)Gtt>Ctt	p.V219L	SPC25_ENST00000472216.2_Intron|G6PC2_ENST00000421979.1_3'UTR|G6PC2_ENST00000429379.2_3'UTR|G6PC2_ENST00000461586.1_3'UTR	NM_021176.2	NP_066999.1	Q9NQR9	G6PC2_HUMAN	glucose-6-phosphatase, catalytic, 2	219			V -> L (in dbSNP:rs492594).		carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)	p.V219L(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	13						CCTGTTTGCAGTTGGCTTTTA	0.527													C|||	2321	0.463458	0.3101	0.5634	5008	,	,		21028	0.4335		0.4443	False		,,,				2504	0.6503				p.V219L		Atlas-SNP	.											G6PC2,NS,carcinoma,0,1	G6PC2	44	1	1	Substitution - Missense(1)	stomach(1)	c.G655C						scavenged	.	C	,LEU/VAL	1416,2990	685.6+/-404.6	221,974,1008	216.0	171.0	186.0		,655	3.1	0.9	2	dbSNP_83	186	3923,4677	605.1+/-394.9	899,2125,1276	yes	utr-3,missense	G6PC2	NM_001081686.1,NM_021176.2	,32	1120,3099,2284	CC,CG,GG		45.6163,32.138,41.0503	,benign	,219/356	169764176	5339,7667	2203	4300	6503	SO:0001583	missense	57818	exon5			TTTGCAGTTGGCT	AF283575	CCDS2230.1, CCDS46443.1	2q24-q31	2008-02-05			ENSG00000152254	ENSG00000152254			28906	protein-coding gene	gene with protein product	"""islet specific glucose 6 phosphatase catalytic subunit related protein"""	608058				10078553, 10078554	Standard	NM_021176		Approved	IGRP	uc002uem.3	Q9NQR9	OTTHUMG00000132182	ENST00000375363.3:c.655G>C	2.37:g.169764176G>C	ENSP00000364512:p.Val219Leu	Somatic	485	3	0.00618557		WXS	Illumina HiSeq	Phase_I	412	178	0.432039	NM_021176	E9PAX2|Q6AHZ0	Missense_Mutation	SNP	ENST00000375363.3	37	CCDS2230.1	958	0.43864468864468864	166	0.33739837398373984	204	0.56353591160221	249	0.4353146853146853	339	0.4472295514511873	C	2.235	-0.375122	0.05034	0.32138	0.456163	ENSG00000152254	ENST00000375363	T	0.74315	-0.83	5.86	3.06	0.35304	.	0.500214	0.19206	N	0.120047	T	0.00012	0.0000	N	0.01656	-0.775	0.09310	P	0.9999999999999954	B	0.02656	0.0	B	0.01281	0.0	T	0.43814	-0.9368	9	0.02654	T	1	-19.5491	5.6207	0.17455	0.1171:0.6455:0.1129:0.1245	rs492594;rs3732032;rs52825832;rs492594	219	Q9NQR9	G6PC2_HUMAN	L	219	ENSP00000364512:V219L	ENSP00000364512:V219L	V	+	1	0	G6PC2	169472422	0.973000	0.33851	0.882000	0.34594	0.655000	0.38815	2.141000	0.42168	0.398000	0.25338	-0.824000	0.03097	GTT	G|0.584;C|0.416	0.416	strong		0.527	G6PC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255234.2	NM_021176	
FAM110A	83541	hgsc.bcm.edu	37	20	826334	826334	+	Nonstop_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:826334A>G	ENST00000304189.2	+	3	1268	c.887A>G	c.(886-888)tAg>tGg	p.*296W	FAM110A_ENST00000246100.3_Nonstop_Mutation_p.*296W|FAM110A_ENST00000541082.1_Nonstop_Mutation_p.*296W|FAM110A_ENST00000381939.1_Nonstop_Mutation_p.*296W|FAM110A_ENST00000381941.3_Nonstop_Mutation_p.*296W			Q9BQ89	F110A_HUMAN	family with sequence similarity 110, member A	0						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.*296L(1)		breast(1)|lung(2)	3						GCTGAAGGCTAGGCGCCACTG	0.612																																					p.X296W		Atlas-SNP	.											FAM110A,NS,carcinoma,0,1	FAM110A	18	1	1	Nonstop extension(1)	lung(1)	c.A887G						scavenged	.						37.0	43.0	41.0					20																	826334		2203	4300	6503	SO:0001578	stop_lost	83541	exon2			AAGGCTAGGCGCC	BC012800	CCDS13008.1	20p13	2007-06-21	2007-03-21	2007-03-21	ENSG00000125898	ENSG00000125898			16188	protein-coding gene	gene with protein product		611393	"""chromosome 20 open reading frame 55"""	C20orf55		17499476	Standard	NM_001042353		Approved	bA371L19.3	uc002wef.1	Q9BQ89	OTTHUMG00000031649	ENST00000304189.2:c.887A>G	20.37:g.826334A>G	ENSP00000354163:p.*296Trpext*84	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	3	0.0344828	NM_207121	D3DVW2|Q5R1M7	Missense_Mutation	SNP	ENST00000304189.2	37	CCDS13008.1	.	.	.	.	.	.	.	.	.	.	.	12.29	1.893304	0.33442	.	.	ENSG00000125898	ENST00000381941;ENST00000304189;ENST00000381939;ENST00000246100;ENST00000541082	.	.	.	4.5	2.06	0.26882	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8654	0.13606	0.7359:0.0:0.0977:0.1664	.	.	.	.	W	296	.	.	X	+	2	0	FAM110A	774334	0.541000	0.26417	0.853000	0.33588	0.029000	0.11900	1.952000	0.40343	0.871000	0.35750	0.397000	0.26171	TAG	.	.	none		0.612	FAM110A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077489.1	NM_031424	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33805150	33805150	+	Missense_Mutation	SNP	T	T	C	rs2304968	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33805150T>C	ENST00000260908.7	-	3	1265	c.1148A>G	c.(1147-1149)tAt>tGt	p.Y383C	SLFN12L_ENST00000449046.1_Missense_Mutation_p.Y414C|SLFN12L_ENST00000361112.4_Missense_Mutation_p.Y412C|RP11-686D22.9_ENST00000587076.1_RNA	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	383						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)	p.Y414C(2)|p.Y412C(1)		breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						ACGAAGAGGATAACTCTGGGA	0.398													C|||	3780	0.754792	0.9168	0.6383	5008	,	,		20128	0.6587		0.6829	False		,,,				2504	0.7914				p.Y383C		Atlas-SNP	.											SLFN12L_ENST00000449046,NS,carcinoma,0,6	SLFN12L	140	6	3	Substitution - Missense(3)	kidney(3)	c.A1148G						scavenged	.	C	CYS/TYR	1227,157		546,135,11	135.0	121.0	125.0		1148	-1.2	0.0	17	dbSNP_100	125	2115,1067		707,701,183	yes	missense	SLFN12L	NM_001195790.1	194	1253,836,194	CC,CT,TT		33.5324,11.3439,26.8068	benign	383/589	33805150	3342,1224	692	1591	2283	SO:0001583	missense	100506736	exon3			AGAGGATAACTCT	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.1148A>G	17.37:g.33805150T>C	ENSP00000437635:p.Tyr383Cys	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	97	37	0.381443	NM_001195790	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	37	CCDS56026.1	1593	0.7293956043956044	449	0.9126016260162602	254	0.7016574585635359	397	0.6940559440559441	493	0.6503957783641161	C	1.330	-0.597078	0.03771	0.886561	0.664676	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.03689	3.85;3.95;3.84	1.27	-1.22	0.09494	.	.	.	.	.	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	0.04153	-1.0973	8	0.42905	T	0.14	.	5.2941	0.15743	0.0:0.4062:0.0:0.5938	rs2304968;rs17249618;rs52812194;rs56785656;rs2304968	412	Q6IEE8-2	.	C	383;412;414	ENSP00000437635:Y383C;ENSP00000354412:Y412C;ENSP00000389348:Y414C	ENSP00000437635:Y383C	Y	-	2	0	SLFN12L	30829263	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.731000	0.01853	-0.909000	0.03852	-0.971000	0.02607	TAT	T|0.242;C|0.758	0.758	strong		0.398	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
SLC2A14	144195	hgsc.bcm.edu	37	12	7966958	7966958	+	Missense_Mutation	SNP	C	C	T	rs10845981	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7966958C>T	ENST00000543909.1	-	16	2276	c.1517G>A	c.(1516-1518)gGg>gAg	p.G506E	SLC2A14_ENST00000539924.1_Missense_Mutation_p.G521E|SLC2A14_ENST00000431042.2_Missense_Mutation_p.G483E|SLC2A14_ENST00000535295.1_Missense_Mutation_p.G397E|SLC2A14_ENST00000542546.1_Missense_Mutation_p.G397E|SLC2A14_ENST00000396589.2_Missense_Mutation_p.G506E|SLC2A14_ENST00000542505.1_Missense_Mutation_p.G147E|SLC2A14_ENST00000340749.5_Missense_Mutation_p.G483E			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	365	2	0.00547945		WXS	Illumina HiSeq	Phase_I	179	138	0.77095	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	
PSPH	5723	hgsc.bcm.edu	37	7	56088902	56088902	+	Missense_Mutation	SNP	C	C	T	rs77329757	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:56088902C>T	ENST00000395471.3	-	4	809	c.4G>A	c.(4-6)Gtc>Atc	p.V2I	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Missense_Mutation_p.V2I			P78330	SERB_HUMAN	phosphoserine phosphatase	2				V -> I (in Ref. 1; CAA71318). {ECO:0000305}.	cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GAGTGGGAGACCATCGCTGGA	0.403																																					p.V2I		Atlas-SNP	.											PSPH,rectum,carcinoma,0,1	PSPH	23	1	0			c.G4A						PASS	.						59.0	49.0	53.0					7																	56088902		2203	4300	6503	SO:0001583	missense	5723	exon4			GGGAGACCATCGC	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.4G>A	7.37:g.56088902C>T	ENSP00000378854:p.Val2Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	250	50	0.2	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.870338	0.33069	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626;ENST00000419984;ENST00000421312;ENST00000424596;ENST00000413218;ENST00000416592	D;D;D;T;T	0.82619	-1.63;-1.63;-1.63;-1.11;-1.11	5.5	4.62	0.57501	.	0.498508	0.22451	N	0.059892	T	0.76586	0.4008	L	0.43152	1.355	0.25991	N	0.982243	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.004	T	0.62821	-0.6773	10	0.26408	T	0.33	-18.3475	13.3091	0.60370	0.0:0.9237:0.0:0.0763	.	2;2	Q53EY1;P78330	.;SERB_HUMAN	I	2	ENSP00000275605:V2I;ENSP00000378854:V2I;ENSP00000398653:V2I;ENSP00000399660:V2I;ENSP00000390952:V2I	ENSP00000275605:V2I	V	-	1	0	PSPH	56056396	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	1.602000	0.36783	1.325000	0.45301	0.591000	0.81541	GTC	C|0.996;T|0.004	0.004	strong		0.403	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
OR13C2	392376	hgsc.bcm.edu	37	9	107367132	107367132	+	Silent	SNP	G	G	A	rs10820679	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:107367132G>A	ENST00000542196.1	-	1	819	c.777C>T	c.(775-777)taC>taT	p.Y259Y		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	259						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						TGGGCTTCATGTACATGAAGA	0.433													G|||	1212	0.242013	0.1051	0.366	5008	,	,		20427	0.38		0.2445	False		,,,				2504	0.1943				p.Y259Y		Atlas-SNP	.											.	OR13C2	46	.	0			c.C777T						PASS	.	G		582,3820	248.4+/-256.2	66,450,1685	125.0	110.0	115.0		777	0.4	0.9	9	dbSNP_120	115	1950,6650	339.0+/-323.0	234,1482,2584	no	coding-synonymous	OR13C2	NM_001004481.1		300,1932,4269	AA,AG,GG		22.6744,13.2213,19.4739		259/319	107367132	2532,10470	2201	4300	6501	SO:0001819	synonymous_variant	392376	exon1			CTTCATGTACATG		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.777C>T	9.37:g.107367132G>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	242	117	0.483471	NM_001004481	B9EGV8|Q6IF54	Silent	SNP	ENST00000542196.1	37	CCDS35092.1																																																																																			G|0.791;A|0.209	0.209	strong		0.433	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
TSHZ3	57616	hgsc.bcm.edu	37	19	31769293	31769293	+	Missense_Mutation	SNP	T	T	C	rs143453460	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:31769293T>C	ENST00000240587.4	-	2	1733	c.1406A>G	c.(1405-1407)gAg>gGg	p.E469G		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	469			E -> G (in dbSNP:rs143453460). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:19745106}.		in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CTTCTTGACCTCCACATTCAG	0.542													T|||	18	0.00359425	0.0	0.0086	5008	,	,		18888	0.0		0.0099	False		,,,				2504	0.002				p.E469G		Atlas-SNP	.											TSHZ3_ENST00000240587,NS,carcinoma,+1,2	TSHZ3	549	2	0			c.A1406G						PASS	.	T	GLY/GLU	8,4398	12.9+/-30.5	0,8,2195	152.0	154.0	153.0		1406	5.6	1.0	19	dbSNP_134	153	102,8498	54.8+/-115.7	0,102,4198	yes	missense	TSHZ3	NM_020856.2	98	0,110,6393	CC,CT,TT		1.186,0.1816,0.8458	probably-damaging	469/1082	31769293	110,12896	2203	4300	6503	SO:0001583	missense	57616	exon2			TTGACCTCCACAT	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1406A>G	19.37:g.31769293T>C	ENSP00000240587:p.Glu469Gly	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	199	108	0.542714	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	T	18.15	3.560653	0.65538	0.001816	0.01186	ENSG00000121297	ENST00000240587	T	0.38077	1.16	5.55	5.55	0.83447	.	0.052145	0.85682	D	0.000000	T	0.49898	0.1584	M	0.67397	2.05	0.80722	D	1	D	0.71674	0.998	D	0.72982	0.979	T	0.54957	-0.8215	10	0.44086	T	0.13	-30.6092	15.7178	0.77681	0.0:0.0:0.0:1.0	.	469	Q63HK5	TSH3_HUMAN	G	469	ENSP00000240587:E469G	ENSP00000240587:E469G	E	-	2	0	TSHZ3	36461133	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	5.849000	0.69465	2.099000	0.63709	0.533000	0.62120	GAG	T|0.991;C|0.009	0.009	strong		0.542	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
KRT73	319101	hgsc.bcm.edu	37	12	53005051	53005051	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53005051C>T	ENST00000305748.3	-	6	1081	c.1047G>A	c.(1045-1047)gaG>gaA	p.E349E	RP11-641A6.2_ENST00000549180.1_RNA|RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	349	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTCTGAGATCTCATTTTTGG	0.527																																					p.E349E		Atlas-SNP	.											KRT73,neck,malignant_melanoma,-2,1	KRT73	101	1	0			c.G1047A						scavenged	.						166.0	140.0	148.0					12																	53005051		2203	4300	6503	SO:0001819	synonymous_variant	319101	exon6			TGAGATCTCATTT	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.1047G>A	12.37:g.53005051C>T		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	290	3	0.0103448	NM_175068	Q32MB2	Silent	SNP	ENST00000305748.3	37	CCDS8834.1																																																																																			.	.	none		0.527	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
ZNF831	128611	hgsc.bcm.edu	37	20	57767727	57767727	+	Silent	SNP	T	T	A	rs61743785	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:57767727T>A	ENST00000371030.2	+	1	1653	c.1653T>A	c.(1651-1653)acT>acA	p.T551T		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	551							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)					TAAGCTCGACTGACGTTCCCA	0.726													.|||	211	0.0421326	0.0098	0.0533	5008	,	,		13876	0.0		0.1203	False		,,,				2504	0.0409				p.T551T		Atlas-SNP	.											.	ZNF831	287	.	0			c.T1653A						PASS	.	T		59,3507		1,57,1725	5.0	6.0	6.0		1653	-7.7	0.0	20	dbSNP_129	6	791,6985		37,717,3134	no	coding-synonymous	ZNF831	NM_178457.1		38,774,4859	AA,AT,TT		10.1723,1.6545,7.4943		551/1678	57767727	850,10492	1783	3888	5671	SO:0001819	synonymous_variant	128611	exon1			CTCGACTGACGTT	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.1653T>A	20.37:g.57767727T>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																			T|0.939;A|0.061	0.061	strong		0.726	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
SEC31B	25956	hgsc.bcm.edu	37	10	102269085	102269085	+	Missense_Mutation	SNP	C	C	A	rs3793706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102269085C>A	ENST00000370345.3	-	4	484	c.387G>T	c.(385-387)ttG>ttT	p.L129F	SEC31B_ENST00000535773.1_Intron|SEC31B_ENST00000370329.5_Missense_Mutation_p.L129F|SEC31B_ENST00000451524.1_Missense_Mutation_p.L129F|NDUFB8_ENST00000557395.1_Intron|NDUFB8_ENST00000531258.1_Intron	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	129			L -> F (in dbSNP:rs3793706). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		GGAAAGGATTCAAGTCGAGGG	0.493											OREG0020441	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	972	0.194089	0.23	0.1873	5008	,	,		18265	0.1319		0.1928	False		,,,				2504	0.2157				p.L129F		Atlas-SNP	.											.	SEC31B	84	.	0			c.G387T						PASS	.	A	PHE/LEU	1058,3348	723.6+/-409.4	131,796,1276	161.0	169.0	166.0		387	4.8	1.0	10	dbSNP_107	166	1899,6701	727.9+/-406.7	216,1467,2617	yes	missense	SEC31B	NM_015490.3	22	347,2263,3893	AA,AC,CC		22.0814,24.0127,22.7357	benign	129/1180	102269085	2957,10049	2203	4300	6503	SO:0001583	missense	25956	exon4			AGGATTCAAGTCG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.387G>T	10.37:g.102269085C>A	ENSP00000359370:p.Leu129Phe	Somatic	163	1	0.00613497	1365	WXS	Illumina HiSeq	Phase_I	88	71	0.806818	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	415	0.190018315018315	89	0.18089430894308944	72	0.19889502762430938	94	0.16433566433566432	160	0.21108179419525067	A	3.549	-0.092094	0.07053	0.240127	0.220814	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000370329	T;T;T	0.51325	0.71;0.71;0.71	5.9	4.77	0.60923	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.044767	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00053	-2.39	0.38832	P	0.04412700000000003	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.001	T	0.29882	-0.9997	9	0.02654	T	1	-10.7429	1.3668	0.02202	0.5458:0.1513:0.1581:0.1448	rs3793706;rs61612790;rs3793706	129;129;129;129	B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;SC31B_HUMAN	F	129	ENSP00000359370:L129F;ENSP00000391178:L129F;ENSP00000359354:L129F	ENSP00000359354:L129F	L	-	3	2	SEC31B	102259075	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	0.670000	0.25157	0.501000	0.28013	-0.362000	0.07510	TTG	C|0.796;A|0.204	0.204	strong		0.493	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
WDR59	79726	hgsc.bcm.edu	37	16	74942865	74942865	+	Silent	SNP	T	T	C	rs141093453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74942865T>C	ENST00000262144.6	-	17	1783	c.1653A>G	c.(1651-1653)gtA>gtG	p.V551V		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	551										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						TTGTGAAATATACCAGGTAAC	0.547																																					p.V551V		Atlas-SNP	.											.	WDR59	66	.	0			c.A1653G						PASS	.						90.0	79.0	83.0					16																	74942865		2198	4300	6498	SO:0001819	synonymous_variant	79726	exon17			GAAATATACCAGG	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.1653A>G	16.37:g.74942865T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	87	19	0.218391	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Silent	SNP	ENST00000262144.6	37	CCDS32488.1																																																																																			T|0.973;C|0.027	0.027	strong		0.547	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581	
IGFN1	91156	hgsc.bcm.edu	37	1	201174215	201174215	+	Missense_Mutation	SNP	C	C	A	rs11584104	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201174215C>A	ENST00000335211.4	+	11	1052	c.922C>A	c.(922-924)Ccc>Acc	p.P308T	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Missense_Mutation_p.P308T	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	308						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						GGCAGCCATCCCCCCAAGAGT	0.572													C|||	84	0.0167732	0.0023	0.0317	5008	,	,		17748	0.0		0.0427	False		,,,				2504	0.0164				p.P308T		Atlas-SNP	.											.	IGFN1	220	.	0			c.C922A						PASS	.	C	THR/PRO	13,1367		0,13,677	10.0	13.0	12.0		922	4.7	1.0	1	dbSNP_120	12	183,2993		3,177,1408	yes	missense	IGFN1	NM_001164586.1	38	3,190,2085	AA,AC,CC		5.762,0.942,4.302		308/3709	201174215	196,4360	690	1588	2278	SO:0001583	missense	91156	exon11			GCCATCCCCCCAA	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.922C>A	1.37:g.201174215C>A	ENSP00000334714:p.Pro308Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	168	101	0.60119	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	45	0.020604395604395604	3	0.006097560975609756	10	0.027624309392265192	0	0.0	32	0.04221635883905013	C	12.39	1.923564	0.33908	0.00942	0.05762	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.76316	-1.01;-1.01	4.68	4.68	0.58851	.	.	.	.	.	T	0.46908	0.1417	M	0.75085	2.285	0.80722	D	1	.	.	.	.	.	.	T	0.73672	-0.3909	7	0.72032	D	0.01	.	14.8477	0.70272	0.0:1.0:0.0:0.0	rs11584104	.	.	.	T	308	ENSP00000334714:P308T;ENSP00000398386:P308T	ENSP00000334714:P308T	P	+	1	0	IGFN1	199440838	1.000000	0.71417	0.951000	0.38953	0.035000	0.12851	3.120000	0.50430	2.295000	0.77249	0.655000	0.94253	CCC	C|0.971;A|0.029	0.029	strong		0.572	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
TRPM2	7226	hgsc.bcm.edu	37	21	45820196	45820196	+	Missense_Mutation	SNP	C	C	T	rs35288229	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:45820196C>T	ENST00000397928.1	+	15	2708	c.2263C>T	c.(2263-2265)Cgt>Tgt	p.R755C	TRPM2_ENST00000300481.9_Missense_Mutation_p.R735C|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.R755C|TRPM2_ENST00000300482.5_Missense_Mutation_p.R755C	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	755					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						TGGGCTGTGGCGTGTGACCCT	0.687													C|||	65	0.0129792	0.0038	0.0115	5008	,	,		16582	0.0		0.0427	False		,,,				2504	0.0092				p.R755C		Atlas-SNP	.											TRPM2,NS,carcinoma,-1,1	TRPM2	196	1	0			c.C2263T						PASS	.	C	CYS/ARG	49,4357	50.9+/-86.3	1,47,2155	122.0	86.0	98.0		2263	1.7	0.2	21	dbSNP_126	98	471,8127	138.4+/-195.2	16,439,3844	yes	missense	TRPM2	NM_003307.3	180	17,486,5999	TT,TC,CC		5.478,1.1121,3.9988	probably-damaging	755/1504	45820196	520,12484	2203	4299	6502	SO:0001583	missense	7226	exon15			CTGTGGCGTGTGA	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2263C>T	21.37:g.45820196C>T	ENSP00000381023:p.Arg755Cys	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	212	139	0.65566	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	38	0.0173992673992674	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	30	0.0395778364116095	C	14.95	2.687268	0.48097	0.011121	0.05478	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11	4.87	1.73	0.24493	.	0.125185	0.52532	D	0.000068	T	0.50633	0.1627	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	P;P;P	0.60415	0.874;0.8;0.874	T	0.73167	-0.4068	10	0.72032	D	0.01	-20.2901	12.624	0.56620	0.5646:0.4354:0.0:0.0	rs35288229	755;541;755	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	C	755;755;735;755	ENSP00000300482:R755C;ENSP00000381023:R755C;ENSP00000300481:R735C;ENSP00000381026:R755C	ENSP00000300481:R735C	R	+	1	0	TRPM2	44644624	0.016000	0.18221	0.161000	0.22692	0.261000	0.26267	-0.004000	0.12878	0.401000	0.25424	0.609000	0.83330	CGT	C|0.968;T|0.032	0.032	strong		0.687	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
TCP1	6950	hgsc.bcm.edu	37	6	160201577	160201577	+	Missense_Mutation	SNP	G	G	C	rs148556538	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160201577G>C	ENST00000321394.7	-	9	1275	c.995C>G	c.(994-996)gCc>gGc	p.A332G	SNORA20_ENST00000384662.1_RNA|TCP1_ENST00000420894.2_Missense_Mutation_p.A332G|TCP1_ENST00000392168.2_Missense_Mutation_p.A177G|TCP1_ENST00000544255.1_Missense_Mutation_p.A108G	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	332					'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)|tubulin complex assembly (GO:0007021)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|nuclear heterochromatin (GO:0005720)|pericentriolar material (GO:0000242)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(2)	10		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(65;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)		TTCCAAATTGGCCAGGGTTGA	0.388													G|||	9	0.00179712	0.0068	0.0	5008	,	,		19426	0.0		0.0	False		,,,				2504	0.0				p.A332G		Atlas-SNP	.											.	TCP1	37	.	0			c.C995G						PASS	.	G	GLY/ALA,GLY/ALA	13,4393	17.9+/-39.9	0,13,2190	101.0	102.0	102.0		530,995	5.8	1.0	6	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	TCP1	NM_001008897.1,NM_030752.2	60,60	0,14,6489	CC,CG,GG		0.0116,0.2951,0.1076	possibly-damaging,possibly-damaging	177/402,332/557	160201577	14,12992	2203	4300	6503	SO:0001583	missense	6950	exon9			AAATTGGCCAGGG	X52882	CCDS5269.1, CCDS43522.1	6q25-q27	2012-10-02			ENSG00000120438	ENSG00000120438		"""Heat Shock Proteins / Chaperonins"""	11655	protein-coding gene	gene with protein product		186980				3476253, 3653076	Standard	NM_030752		Approved	D6S230E, CCT1, Ccta	uc003qsr.3	P17987	OTTHUMG00000015937	ENST00000321394.7:c.995C>G	6.37:g.160201577G>C	ENSP00000317334:p.Ala332Gly	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	196	101	0.515306	NM_030752	E1P5B2|Q15556|Q5TCM3	Missense_Mutation	SNP	ENST00000321394.7	37	CCDS5269.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.242607	0.79912	0.002951	1.16E-4	ENSG00000120438	ENST00000321394;ENST00000544255;ENST00000420894;ENST00000392168;ENST00000539756	T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1	5.76	5.76	0.90799	.	0.140834	0.64402	D	0.000003	T	0.81683	0.4874	M	0.84683	2.71	0.58432	D	0.999999	P;P	0.43024	0.798;0.53	P;P	0.45538	0.484;0.456	D	0.83565	0.0109	10	0.56958	D	0.05	-13.3037	20.3242	0.98691	0.0:0.0:1.0:0.0	.	332;332	E7ERF2;P17987	.;TCPA_HUMAN	G	332;108;332;177;130	ENSP00000317334:A332G;ENSP00000439447:A108G;ENSP00000390159:A332G;ENSP00000376008:A177G;ENSP00000441345:A130G	ENSP00000317334:A332G	A	-	2	0	TCP1	160121567	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.269000	0.78482	2.882000	0.98803	0.655000	0.94253	GCC	G|0.999;C|0.001	0.001	strong		0.388	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752	
ZNF543	125919	hgsc.bcm.edu	37	19	57839150	57839150	+	Missense_Mutation	SNP	A	A	G	rs8100491	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57839150A>G	ENST00000321545.4	+	4	665	c.320A>G	c.(319-321)cAa>cGa	p.Q107R		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	107			Q -> R (in dbSNP:rs8100491). {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)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		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;0.0257)		CTCCAGGAACAACTGACACAA	0.478													g|||	3418	0.682508	0.7731	0.7133	5008	,	,		19133	0.5863		0.7197	False		,,,				2504	0.5992				p.Q107R		Atlas-SNP	.											ZNF543,NS,lymphoid_neoplasm,+1,2	ZNF543	61	2	0			c.A320G						PASS	.	G	ARG/GLN	3295,1111	397.6+/-330.5	1223,849,131	70.0	70.0	70.0		320	-5.7	0.0	19	dbSNP_116	70	6414,2186	373.7+/-337.1	2402,1610,288	yes	missense	ZNF543	NM_213598.3	43	3625,2459,419	GG,GA,AA		25.4186,25.2156,25.3498	benign	107/601	57839150	9709,3297	2203	4300	6503	SO:0001583	missense	125919	exon4			AGGAACAACTGAC	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.320A>G	19.37:g.57839150A>G	ENSP00000322545:p.Gln107Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	1508	0.6904761904761905	356	0.7235772357723578	261	0.7209944751381215	338	0.5909090909090909	553	0.7295514511873351	G	0.536	-0.855603	0.02630	0.747844	0.745814	ENSG00000178229	ENST00000321545	T	0.23754	1.89	2.87	-5.73	0.02398	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.42565	-0.9444	8	0.02654	T	1	.	6.0897	0.19987	0.4665:0.0:0.4063:0.1272	rs8100491;rs57192148;rs8100491	107	Q08ER8	ZN543_HUMAN	R	107	ENSP00000322545:Q107R	ENSP00000322545:Q107R	Q	+	2	0	ZNF543	62530962	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.431000	0.01023	-1.610000	0.01583	-2.030000	0.00424	CAA	A|0.278;G|0.722	0.722	strong		0.478	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
ANKRD33	341405	hgsc.bcm.edu	37	12	52282060	52282060	+	5'UTR	SNP	C	C	T	rs697634	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52282060C>T	ENST00000340970.4	+	0	60				ANKRD33_ENST00000301190.6_Silent_p.R30R|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_5'UTR			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33						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)		TTGTGCTCCGCGGAGCCTGGG	0.567													C|||	1661	0.331669	0.149	0.451	5008	,	,		16569	0.4117		0.2952	False		,,,				2504	0.4489				p.R30R		Atlas-SNP	.											.	ANKRD33	33	.	0			c.C90T						PASS	.	C	,	681,3725	287.2+/-279.2	55,571,1577	101.0	93.0	95.0		,90	-4.7	0.0	12	dbSNP_86	95	2676,5924	429.8+/-356.3	396,1884,2020	no	utr-5,coding-synonymous	ANKRD33	NM_001130015.1,NM_182608.3	,	451,2455,3597	TT,TC,CC		31.1163,15.4562,25.8112	,	,30/453	52282060	3357,9649	2203	4300	6503	SO:0001623	5_prime_UTR_variant	341405	exon1			GCTCCGCGGAGCC		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.-312C>T	12.37:g.52282060C>T		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Silent	SNP	ENST00000340970.4	37	CCDS44892.1																																																																																			C|0.719;T|0.281	0.281	strong		0.567	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
C2orf71	388939	hgsc.bcm.edu	37	2	29296870	29296870	+	Silent	SNP	C	C	T	rs62132765	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	630	3	0.0047619		WXS	Illumina HiSeq	Phase_I	617	275	0.445705	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	
APBA3	9546	hgsc.bcm.edu	37	19	3753874	3753874	+	Silent	SNP	G	G	A	rs34868972	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3753874G>A	ENST00000316757.3	-	6	1100	c.900C>T	c.(898-900)atC>atT	p.I300I	AC005954.4_ENST00000586503.1_RNA|AC005954.3_ENST00000591962.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	300	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		GCACGCAGCCGATGTCGGCTG	0.697													G|||	460	0.091853	0.0098	0.1369	5008	,	,		12674	0.0089		0.1839	False		,,,				2504	0.1616				p.I300I		Atlas-SNP	.											.	APBA3	28	.	0			c.C900T						PASS	.	G		135,4159		4,127,2016	10.0	12.0	11.0		900	1.9	1.0	19	dbSNP_126	11	1381,7037		89,1203,2917	no	coding-synonymous	APBA3	NM_004886.3		93,1330,4933	AA,AG,GG		16.4053,3.1439,11.9257		300/576	3753874	1516,11196	2147	4209	6356	SO:0001819	synonymous_variant	9546	exon6			GCAGCCGATGTCG	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.900C>T	19.37:g.3753874G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			G|0.908;A|0.092	0.092	strong		0.697	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
Unknown	0	hgsc.bcm.edu	37	7	63680099	63680099	+	IGR	SNP	C	C	A	rs35920205|rs4320434	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	146	0	0		WXS	Illumina HiSeq	Phase_I	196	70	0.357143	NM_001159524		Missense_Mutation	SNP		37																																																																																				C|0.813;A|0.187	0.187	strong	0	0.398								
UBN2	254048	hgsc.bcm.edu	37	7	138967814	138967814	+	Silent	SNP	G	G	A	rs61995684	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:138967814G>A	ENST00000473989.3	+	15	2163	c.2163G>A	c.(2161-2163)gtG>gtA	p.V721V	UBN2_ENST00000288561.8_Silent_p.V638V	NM_173569.3	NP_775840.3	Q6ZU65	UBN2_HUMAN	ubinuclein 2	721						extracellular space (GO:0005615)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	42						CATCCCTGGTGGCTTCGGTTA	0.463													G|||	518	0.103435	0.1029	0.2666	5008	,	,		17571	0.0972		0.0368	False		,,,				2504	0.0634				p.V721V		Atlas-SNP	.											.	UBN2	90	.	0			c.G2163A						PASS	.	G		340,3524		18,304,1610	56.0	55.0	55.0		2163	4.9	1.0	7	dbSNP_129	55	292,7956		5,282,3837	no	coding-synonymous	UBN2	NM_173569.3		23,586,5447	AA,AG,GG		3.5403,8.7992,5.218		721/1348	138967814	632,11480	1932	4124	6056	SO:0001819	synonymous_variant	254048	exon15			CCTGGTGGCTTCG	AK098644	CCDS43655.1, CCDS43655.2	7q34	2008-12-08			ENSG00000157741	ENSG00000157741			21931	protein-coding gene	gene with protein product		613841				19029251	Standard	NM_173569		Approved	FLJ25778, KIAA2030	uc011kqr.2	Q6ZU65	OTTHUMG00000157623	ENST00000473989.3:c.2163G>A	7.37:g.138967814G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	71	12	0.169014	NM_173569	A4D1S2|Q2YDY4|Q6P1K0|Q86XN9|Q8N7D1	Silent	SNP	ENST00000473989.3	37	CCDS43655.2																																																																																			G|0.927;A|0.073	0.073	strong		0.463	UBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349272.3	NM_173569	
COL6A3	1293	hgsc.bcm.edu	37	2	238244923	238244923	+	Silent	SNP	C	C	T	rs11683438	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000353578.4_Silent_p.T2734T|COL6A3_ENST00000347401.3_Silent_p.T2739T|COL6A3_ENST00000346358.4_Silent_p.T2740T|COL6A3_ENST00000409809.1_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	62	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	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	
MMP25	64386	hgsc.bcm.edu	37	16	3100095	3100095	+	Silent	SNP	C	C	T	rs10431961	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3100095C>T	ENST00000336577.4	+	3	555	c.318C>T	c.(316-318)cgC>cgT	p.R106R	RP11-473M20.7_ENST00000576250.1_RNA|MMP25_ENST00000570755.1_3'UTR	NM_022468.4	NP_071913.1	Q9H239	MMP28_HUMAN	matrix metallopeptidase 25	121					negative regulation of macrophage chemotaxis (GO:0010760)	cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	14					Marimastat(DB00786)	GGCGGCGTCGCCGGTACGCTC	0.701													C|||	1263	0.252196	0.1997	0.3458	5008	,	,		15092	0.1905		0.3091	False		,,,				2504	0.2618				p.R106R	NSCLC(147;665 1067 3888 6863 19894 30469 40247 45633 51336)	Atlas-SNP	.											.	MMP25	35	.	0			c.C318T						PASS	.	C		1000,3394	363.1+/-316.4	121,758,1318	55.0	60.0	58.0		318	-2.1	0.1	16	dbSNP_119	58	2803,5793	435.3+/-358.0	460,1883,1955	no	coding-synonymous	MMP25	NM_022468.4		581,2641,3273	TT,TC,CC		32.6082,22.7583,29.2764		106/563	3100095	3803,9187	2197	4298	6495	SO:0001819	synonymous_variant	64386	exon3			GCGTCGCCGGTAC	AF145442	CCDS10492.1	16p13.3	2008-02-05	2005-08-08			ENSG00000008516			14246	protein-coding gene	gene with protein product		608482	"""matrix metalloproteinase 25"", ""matrix metallopeptidase-like 1"""	MMPL1, MMP20		10628838, 10706098	Standard	NM_022468		Approved	MT6-MMP	uc002cth.3	Q9NPA2		ENST00000336577.4:c.318C>T	16.37:g.3100095C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_022468	Q96F04|Q96TE2	Silent	SNP	ENST00000336577.4	37	CCDS10492.1																																																																																			C|0.727;T|0.273	0.273	strong		0.701	MMP25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437116.1	NM_022468	
PMVK	10654	hgsc.bcm.edu	37	1	154904840	154904840	+	Silent	SNP	T	T	C	rs1891805	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154904840T>C	ENST00000368467.3	-	2	452	c.147A>G	c.(145-147)gaA>gaG	p.E49E		NM_006556.3	NP_006547.1	Q15126	PMVK_HUMAN	phosphomevalonate kinase	49					cholesterol biosynthetic process (GO:0006695)|isopentenyl diphosphate biosynthetic process, mevalonate pathway (GO:0019287)|response to cholesterol (GO:0070723)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|phosphomevalonate kinase activity (GO:0004631)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.142)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GAGCATACTGTTCCTTGAGTG	0.577													C|||	1036	0.206869	0.6407	0.0836	5008	,	,		17611	0.0		0.0636	False		,,,				2504	0.0685				p.E49E		Atlas-SNP	.											.	PMVK	17	.	0			c.A147G						PASS	.	C		2511,1895	543.3+/-376.2	746,1019,438	107.0	94.0	99.0		147	0.6	1.0	1	dbSNP_92	99	555,8045	793.4+/-407.5	12,531,3757	no	coding-synonymous	PMVK	NM_006556.3		758,1550,4195	CC,CT,TT		6.4535,43.0095,23.5737		49/193	154904840	3066,9940	2203	4300	6503	SO:0001819	synonymous_variant	10654	exon2			ATACTGTTCCTTG	L77213	CCDS1073.1	1q21.3	2012-09-20			ENSG00000163344	ENSG00000163344	2.7.4.2		9141	protein-coding gene	gene with protein product		607622				8663599, 10191291	Standard	NM_006556		Approved	PMK, PMKA, HUMPMKI	uc001ffq.3	Q15126	OTTHUMG00000037415	ENST00000368467.3:c.147A>G	1.37:g.154904840T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	238	151	0.634454	NM_006556	Q5TZW9	Silent	SNP	ENST00000368467.3	37	CCDS1073.1																																																																																			T|0.769;C|0.231	0.231	strong		0.577	PMVK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091088.1	NM_006556	
CCBL1	883	hgsc.bcm.edu	37	9	131600394	131600394	+	Missense_Mutation	SNP	A	A	G	rs371451324		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:131600394A>G	ENST00000302586.3	-	5	536	c.374T>C	c.(373-375)tTt>tCt	p.F125S	CCBL1_ENST00000436267.2_Missense_Mutation_p.F219S|CCBL1_ENST00000483599.1_5'UTR|CCBL1_ENST00000320665.6_Missense_Mutation_p.F75S	NM_001122671.1|NM_004059.4	NP_001116143.1|NP_004050.3	Q16773	KAT1_HUMAN	cysteine conjugate-beta lyase, cytoplasmic	125					cellular amino acid biosynthetic process (GO:0008652)|cellular modified amino acid metabolic process (GO:0006575)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine catabolic process (GO:0097053)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|glutamine-phenylpyruvate transaminase activity (GO:0047316)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-glutamine:pyruvate aminotransferase activity (GO:0047945)|L-phenylalanine-oxaloacetate transaminase activity (GO:0036141)|L-phenylalanine:pyruvate aminotransferase activity (GO:0047312)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)	18					L-Glutamine(DB00130)	GTAGCAGTCAAAAAAGGGTTC	0.542																																					p.F125S		Atlas-SNP	.											.	CCBL1	36	.	0			c.T374C						PASS	.	A	SER/PHE,SER/PHE,SER/PHE	0,4402		0,0,2201	165.0	174.0	171.0		374,224,374	5.1	1.0	9		171	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense,missense	CCBL1	NM_001122671.1,NM_001122672.1,NM_004059.4	155,155,155	0,1,6493	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	125/423,75/373,125/423	131600394	1,12987	2201	4293	6494	SO:0001583	missense	883	exon5			CAGTCAAAAAAGG	Y17448	CCDS43884.1, CCDS48038.1, CCDS75915.1	9q34.11	2008-03-11	2008-03-11		ENSG00000171097	ENSG00000171097	2.6.1.64		1564	protein-coding gene	gene with protein product	"""glutamine transaminase K"", ""kyneurenine aminotransferase"""	600547	"""cysteine conjugate-beta lyase; cytoplasmic (glutamine transaminase K, kyneurenine aminotransferase)"""			7883047	Standard	NM_001122671		Approved	KATI, GTK	uc004bwh.3	Q16773	OTTHUMG00000020767	ENST00000302586.3:c.374T>C	9.37:g.131600394A>G	ENSP00000302227:p.Phe125Ser	Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	197	99	0.502538	NM_001122671	Q5T275|Q8N191	Missense_Mutation	SNP	ENST00000302586.3	37	CCDS43884.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.698125	0.88830	0.0	1.16E-4	ENSG00000171097	ENST00000302586;ENST00000320665;ENST00000436267;ENST00000451800;ENST00000416084	D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.83	5.12	5.12	0.69794	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.96731	0.8933	H	0.95950	3.745	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;0.999;1.0;1.0	D	0.97818	1.0255	10	0.87932	D	0	-33.2894	13.7717	0.63029	1.0:0.0:0.0:0.0	.	219;125;75;125;125	B7Z4W5;A8K563;Q16773-2;Q16773;Q5T278	.;.;.;KAT1_HUMAN;.	S	125;75;219;125;125	ENSP00000302227:F125S;ENSP00000317342:F75S;ENSP00000399415:F219S;ENSP00000390377:F125S;ENSP00000412402:F125S	ENSP00000302227:F125S	F	-	2	0	CCBL1	130640215	1.000000	0.71417	0.977000	0.42913	0.944000	0.59088	6.220000	0.72237	1.927000	0.55829	0.528000	0.53228	TTT	.	.	weak		0.542	CCBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054521.2		
FMNL2	114793	hgsc.bcm.edu	37	2	153405594	153405594	+	Silent	SNP	G	G	A	rs1155779	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	184	0	0		WXS	Illumina HiSeq	Phase_I	140	55	0.392857	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	
LRRD1	401387	hgsc.bcm.edu	37	7	91779971	91779971	+	Missense_Mutation	SNP	T	T	G	rs6465353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91779971T>G	ENST00000458448.1	-	4	2355	c.2155A>C	c.(2155-2157)Att>Ctt	p.I719L	LRRD1_ENST00000422722.1_5'UTR|LRRD1_ENST00000343318.5_Missense_Mutation_p.I70L|LRRD1_ENST00000454089.2_Missense_Mutation_p.I70L|LRRD1_ENST00000430130.2_Missense_Mutation_p.I719L|CTB-161K23.1_ENST00000453068.1_RNA			A4D1F6	LRRD1_HUMAN	leucine-rich repeats and death domain containing 1	719					signal transduction (GO:0007165)					breast(4)|endometrium(1)	5						AGTGAAAAAATATTGTAGATA	0.323													G|||	2086	0.416534	0.6717	0.3732	5008	,	,		15605	0.1885		0.3926	False		,,,				2504	0.362				p.I719L		Atlas-SNP	.											.	LRRD1	35	.	0			c.A2155C						PASS	.						97.0	79.0	84.0					7																	91779971		692	1591	2283	SO:0001583	missense	401387	exon3			AAAAAATATTGTA	BC026112	CCDS55124.1	7q21.2	2011-05-23			ENSG00000240720	ENSG00000240720			34300	protein-coding gene	gene with protein product							Standard	NM_001161528		Approved	IMAGE:4798971	uc011khp.1	A4D1F6	OTTHUMG00000155861	ENST00000458448.1:c.2155A>C	7.37:g.91779971T>G	ENSP00000405987:p.Ile719Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_001161528	B7ZMM9|Q49AT9	Missense_Mutation	SNP	ENST00000458448.1	37	CCDS55124.1	899	0.4116300366300366	342	0.6951219512195121	144	0.39779005524861877	114	0.1993006993006993	299	0.3944591029023747	G	5.515	0.279899	0.10458	.	.	ENSG00000240720	ENST00000343318;ENST00000458448;ENST00000430130;ENST00000454089	T;T;T;T	0.17054	2.62;2.3;2.3;2.62	5.61	5.61	0.85477	.	.	.	.	.	T	0.00012	0.0000	N	0.00068	-2.285	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	8	0.02654	T	1	.	15.7556	0.78021	0.0:0.0:0.8621:0.1379	rs6465353;rs59146464;rs6465353	719	A4D1F6	LRRD1_HUMAN	L	70;719;719;70	ENSP00000339642:I70L;ENSP00000405987:I719L;ENSP00000411568:I719L;ENSP00000392112:I70L	ENSP00000339642:I70L	I	-	1	0	LRRD1	91617907	1.000000	0.71417	0.510000	0.27712	0.523000	0.34469	4.909000	0.63314	1.386000	0.46466	-0.121000	0.15023	ATT	T|0.575;G|0.425	0.425	strong		0.323	LRRD1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342027.2	NM_001045475	
ANGEL1	23357	hgsc.bcm.edu	37	14	77269788	77269788	+	Missense_Mutation	SNP	A	A	C	rs2075773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77269788A>C	ENST00000251089.2	-	7	1656	c.1544T>G	c.(1543-1545)tTc>tGc	p.F515C	ANGEL1_ENST00000557179.1_Missense_Mutation_p.F80C	NM_015305.3	NP_056120.2	Q9UNK9	ANGE1_HUMAN	angel homolog 1 (Drosophila)	515			F -> C (in dbSNP:rs2075773).					p.F515C(1)		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)		GCAGAAGCGGAAACGTAGCAG	0.478													A|||	646	0.128994	0.1127	0.0663	5008	,	,		20752	0.2381		0.1083	False		,,,				2504	0.1043				p.F515C		Atlas-SNP	.											ANGEL1,NS,carcinoma,0,1	ANGEL1	63	1	1	Substitution - Missense(1)	stomach(1)	c.T1544G						PASS	.	A	CYS/PHE	525,3881	239.6+/-250.7	32,461,1710	121.0	112.0	115.0		1544	5.9	1.0	14	dbSNP_96	115	886,7714	198.7+/-243.0	45,796,3459	yes	missense	ANGEL1	NM_015305.3	205	77,1257,5169	CC,CA,AA		10.3023,11.9156,10.8488	possibly-damaging	515/671	77269788	1411,11595	2203	4300	6503	SO:0001583	missense	23357	exon7			AAGCGGAAACGTA	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.1544T>G	14.37:g.77269788A>C	ENSP00000251089:p.Phe515Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	137	46	0.335766	NM_015305	B4DWL7|O94859|Q8NCS9	Missense_Mutation	SNP	ENST00000251089.2	37	CCDS9852.1	307	0.14056776556776557	60	0.12195121951219512	27	0.07458563535911603	142	0.24825174825174826	78	0.10290237467018469	A	19.81	3.895803	0.72639	0.119156	0.103023	ENSG00000013523	ENST00000251089;ENST00000557179	T;T	0.81078	-1.45;-1.45	5.95	5.95	0.96441	Endonuclease/exonuclease/phosphatase (2);	0.177612	0.51477	D	0.000099	T	0.00073	0.0002	L	0.42245	1.32	0.28690	P	0.9046536000000001	D	0.69078	0.997	D	0.63113	0.911	T	0.00514	-1.1695	9	0.66056	D	0.02	-6.1924	14.9948	0.71421	1.0:0.0:0.0:0.0	rs2075773;rs56917680;rs2075773	515	Q9UNK9	ANGE1_HUMAN	C	515;80	ENSP00000251089:F515C;ENSP00000451534:F80C	ENSP00000251089:F515C	F	-	2	0	ANGEL1	76339541	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	6.629000	0.74267	2.279000	0.76181	0.533000	0.62120	TTC	A|0.875;C|0.125	0.125	strong		0.478	ANGEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413712.2	NM_015305	
GPRC6A	222545	hgsc.bcm.edu	37	6	117113653	117113653	+	Silent	SNP	T	T	C	rs615199	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:117113653T>C	ENST00000310357.3	-	6	2454	c.2433A>G	c.(2431-2433)ccA>ccG	p.P811P	GPRC6A_ENST00000368549.3_Silent_p.P740P|GPRC6A_ENST00000530250.1_Silent_p.P636P	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	811					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)	p.P811P(1)		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)		TCTCCACAGCTGGTACATATT	0.343													T|||	1534	0.30631	0.1452	0.3674	5008	,	,		24347	0.5228		0.3082	False		,,,				2504	0.2556				p.P811P		Atlas-SNP	.											GPRC6A,NS,carcinoma,0,1	GPRC6A	152	1	1	Substitution - coding silent(1)	stomach(1)	c.A2433G						PASS	.	T		744,3662	304.1+/-288.3	65,614,1524	79.0	81.0	81.0		2433	-5.8	0.3	6	dbSNP_83	81	2838,5762	446.6+/-361.3	459,1920,1921	no	coding-synonymous	GPRC6A	NM_148963.2		524,2534,3445	CC,CT,TT		33.0,16.8861,27.5411		811/927	117113653	3582,9424	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon6			CACAGCTGGTACA	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.2433A>G	6.37:g.117113653T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	188	93	0.494681	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			C|0.301;N|0.000	0.301	strong		0.343	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642827	1642827	+	Missense_Mutation	SNP	G	G	C	rs374921824|rs541987207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1642827G>C	ENST00000399682.1	-	1	541	c.497C>G	c.(496-498)tCc>tGc	p.S166C		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				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)		ACCTGAGGAGGAGCAGCAGGG	0.607													g|||	148	0.0295527	0.056	0.0187	5008	,	,		15114	0.0188		0.0229	False		,,,				2504	0.0194				p.S166C		Atlas-SNP	.											KRTAP5-4,colon,carcinoma,0,3	KRTAP5-4	78	3	0			c.C497G						PASS	.						22.0	35.0	31.0					11																	1642827		692	1590	2282	SO:0001583	missense	387267	exon1			GAGGAGGAGCAGC	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.497C>G	11.37:g.1642827G>C	ENSP00000382590:p.Ser166Cys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	173	16	0.0924855	NM_001012709		Missense_Mutation	SNP	ENST00000399682.1	37		.	.	.	.	.	.	.	.	.	.	G	2.402	-0.337333	0.05278	.	.	ENSG00000241598	ENST00000399682	T	0.00792	5.69	0.891	-0.0782	0.13716	.	.	.	.	.	T	0.00468	0.0015	N	0.02960	-0.455	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.45056	-0.9287	9	0.51188	T	0.08	.	6.6433	0.22921	0.0:0.5966:0.4034:0.0	.	226	Q6L8H1	KRA54_HUMAN	C	166	ENSP00000382590:S166C	ENSP00000382590:S166C	S	-	2	0	KRTAP5-4	1599403	0.001000	0.12720	0.007000	0.13788	0.001000	0.01503	-0.354000	0.07681	-0.014000	0.14175	-1.289000	0.01358	TCC	.	.	none		0.607	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
LILRA4	23547	hgsc.bcm.edu	37	19	54848826	54848826	+	Missense_Mutation	SNP	C	C	T	rs145556773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848826C>T	ENST00000291759.4	-	5	853	c.797G>A	c.(796-798)cGc>cAc	p.R266H	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	266	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)		CCGGCCAGGGCGCTGGGGGAG	0.657													C|||	7	0.00139776	0.0	0.0029	5008	,	,		12832	0.0		0.005	False		,,,				2504	0.0				p.R266H		Atlas-SNP	.											.	LILRA4	91	.	0			c.G797A						PASS	.	C	HIS/ARG	1,4403		0,1,2201	22.0	24.0	23.0		797	-5.0	0.0	19	dbSNP_134	23	56,8542		0,56,4243	yes	missense	LILRA4	NM_012276.3	29	0,57,6444	TT,TC,CC		0.6513,0.0227,0.4384	benign	266/500	54848826	57,12945	2202	4299	6501	SO:0001583	missense	23547	exon5			CCAGGGCGCTGGG	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.797G>A	19.37:g.54848826C>T	ENSP00000291759:p.Arg266His	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	175	95	0.542857	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	.	0.012	-1.661083	0.00772	2.27E-4	0.006513	ENSG00000239961	ENST00000291759	T	0.12879	2.64	2.51	-5.02	0.02982	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.356960	0.01819	N	0.033919	T	0.07593	0.0191	L	0.46157	1.445	0.09310	N	1	B	0.12630	0.006	B	0.18561	0.022	T	0.26326	-1.0106	10	0.18710	T	0.47	.	3.0012	0.06015	0.1276:0.1549:0.1272:0.5903	.	266	P59901	LIRA4_HUMAN	H	266	ENSP00000291759:R266H	ENSP00000291759:R266H	R	-	2	0	LILRA4	59540638	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-2.350000	0.01092	-2.651000	0.00424	-0.391000	0.06502	CGC	C|0.997;T|0.003	0.003	strong		0.657	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
C15orf52	388115	hgsc.bcm.edu	37	15	40629995	40629995	+	Missense_Mutation	SNP	G	G	A	rs149438052	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:40629995G>A	ENST00000559313.1	-	6	760	c.745C>T	c.(745-747)Cgc>Tgc	p.R249C	C15orf52_ENST00000397536.2_Missense_Mutation_p.R39C|C15orf52_ENST00000557973.1_5'Flank	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	249							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)		CGGGCGAGGCGGGCTAGGTCG	0.711																																					p.R249C		Atlas-SNP	.											.	C15orf52	47	.	0			c.C745T						PASS	.						23.0	24.0	24.0					15																	40629995		2202	4298	6500	SO:0001583	missense	388115	exon6			CGAGGCGGGCTAG	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.745C>T	15.37:g.40629995G>A	ENSP00000453969:p.Arg249Cys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Missense_Mutation	SNP	ENST00000559313.1	37	CCDS10055.2	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764787	0.90020	.	.	ENSG00000188549	ENST00000382688;ENST00000397536;ENST00000397535	T	0.72942	-0.7	4.63	4.63	0.57726	.	0.092822	0.45867	D	0.000338	D	0.82637	0.5080	M	0.74258	2.255	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.84930	0.0859	10	0.87932	D	0	-13.7074	12.996	0.58646	0.0:0.0:1.0:0.0	.	39;181;249	Q6ZUT6-2;Q6ZUT6-3;Q6ZUT6	.;.;CO052_HUMAN	C	249;39;181	ENSP00000380670:R39C	ENSP00000372135:R249C	R	-	1	0	C15orf52	38417287	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.805000	0.38883	2.097000	0.63578	0.563000	0.77884	CGC	A|0.001;G|0.999	0.001	strong		0.711	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
SRP72	6731	hgsc.bcm.edu	37	4	57333859	57333859	+	Missense_Mutation	SNP	C	C	T	rs111673705	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:57333859C>T	ENST00000342756.5	+	1	779	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	SRP72_ENST00000504757.1_Missense_Mutation_p.R20W|SRP72_ENST00000510663.1_Missense_Mutation_p.R20W	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	20					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					TGAAGTGAACCGGTATGGCCA	0.682													C|||	7	0.00139776	0.0	0.0014	5008	,	,		14363	0.0		0.005	False		,,,				2504	0.001				p.R20W		Atlas-SNP	.											.	SRP72	59	.	0			c.C58T						PASS	.	C	TRP/ARG	7,4399	9.9+/-24.2	0,7,2196	25.0	25.0	25.0		58	5.6	1.0	4	dbSNP_132	25	44,8556	22.8+/-68.1	0,44,4256	yes	missense	SRP72	NM_006947.3	101	0,51,6452	TT,TC,CC		0.5116,0.1589,0.3921	probably-damaging	20/672	57333859	51,12955	2203	4300	6503	SO:0001583	missense	6731	exon1			GTGAACCGGTATG	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"""Tetratricopeptide (TTC) repeat domain containing"""	11303	protein-coding gene	gene with protein product		602122	"""signal recognition particle 72kD"""			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.58C>T	4.37:g.57333859C>T	ENSP00000342181:p.Arg20Trp	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	151	85	0.562914	NM_006947	G5E9Z8|Q7Z3C0	Missense_Mutation	SNP	ENST00000342756.5	37	CCDS3506.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	34	5.353558	0.95830	0.001589	0.005116	ENSG00000174780	ENST00000342756;ENST00000537129;ENST00000510663	T;T	0.38401	1.14;1.14	5.55	5.55	0.83447	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.51907	0.1702	M	0.75777	2.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.73380	0.976;0.98	T	0.59989	-0.7350	10	0.66056	D	0.02	.	15.0181	0.71605	0.0:1.0:0.0:0.0	.	20;20	G5E9Z8;O76094	.;SRP72_HUMAN	W	20;26;20	ENSP00000342181:R20W;ENSP00000424576:R20W	ENSP00000342181:R20W	R	+	1	2	SRP72	57028616	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.536000	0.60636	2.590000	0.87494	0.655000	0.94253	CGG	C|0.997;G|0.000;T|0.003	0.003	strong		0.682	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
LKAAEAR1	198437	hgsc.bcm.edu	37	20	62714783	62714783	+	3'UTR	SNP	C	C	G	rs6010717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62714783C>G	ENST00000302096.4	-	0	729				OPRL1_ENST00000336866.2_Intron|OPRL1_ENST00000349451.3_5'Flank|C20orf201_ENST00000308906.2_Silent_p.A226A|OPRL1_ENST00000355631.4_Intron			Q8TD35	LKAM1_HUMAN																			CACTCTCAGTCGCCGTCACCG	0.647													C|||	3128	0.624601	0.6422	0.6628	5008	,	,		12748	0.7093		0.6531	False		,,,				2504	0.4571				p.A226A		Atlas-SNP	.											C20orf201,NS,carcinoma,0,1	C20orf201	4	1	0			c.G678C						PASS	.	C	,,	2796,1604		875,1046,279	21.0	23.0	22.0		,678,	1.4	0.0	20	dbSNP_114	22	5362,3220		1675,2012,604	no	intron,coding-synonymous,intron	OPRL1,C20orf201	NM_000913.4,NM_001007125.1,NM_182647.2	,,	2550,3058,883	GG,GC,CC		37.5204,36.4545,37.1591	,,	,226/241,	62714783	8158,4824	2200	4291	6491	SO:0001624	3_prime_UTR_variant	198437	exon2			CTCAGTCGCCGTC																												ENST00000302096.4:c.*5G>C	20.37:g.62714783C>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001007125	Q8N419|Q8TD36	Silent	SNP	ENST00000302096.4	37																																																																																				C|0.368;G|0.632	0.632	strong		0.647	C20orf201-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000080270.2		
HEG1	57493	hgsc.bcm.edu	37	3	124732618	124732618	+	Missense_Mutation	SNP	A	A	G	rs6790837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	179	0	0		WXS	Illumina HiSeq	Phase_I	191	95	0.497382	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	
CLDN8	9073	hgsc.bcm.edu	37	21	31587859	31587859	+	Missense_Mutation	SNP	T	T	C	rs685967	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31587859T>C	ENST00000399899.1	-	1	532	c.385A>G	c.(385-387)Acg>Gcg	p.T129A	CLDN8_ENST00000286809.1_Missense_Mutation_p.T129A	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	129			T -> A (in dbSNP:rs685967).		calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						ACCATGCCCGTGATGATGAAG	0.502													T|||	415	0.0828674	0.1997	0.0447	5008	,	,		20250	0.0069		0.0427	False		,,,				2504	0.0716				p.T129A		Atlas-SNP	.											CLDN8,NS,adenocarcinoma,+2,1	CLDN8	40	1	0			c.A385G						PASS	.	T	ALA/THR	690,3716	288.1+/-279.7	52,586,1565	96.0	86.0	90.0		385	3.7	0.8	21	dbSNP_83	90	413,8187	129.0+/-187.1	8,397,3895	yes	missense	CLDN8	NM_199328.2	58	60,983,5460	CC,CT,TT		4.8023,15.6605,8.4807	benign	129/226	31587859	1103,11903	2203	4300	6503	SO:0001583	missense	9073	exon1			TGCCCGTGATGAT	AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"""Claudins"""	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.385A>G	21.37:g.31587859T>C	ENSP00000382783:p.Thr129Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	130	72	0.553846	NM_199328	D3DSE3|Q53EX7	Missense_Mutation	SNP	ENST00000399899.1	37	CCDS13587.1	132	0.06043956043956044	84	0.17073170731707318	17	0.04696132596685083	3	0.005244755244755245	28	0.036939313984168866	T	0.003	-2.413555	0.00191	0.156605	0.048023	ENSG00000156284	ENST00000399899;ENST00000286809;ENST00000536721	D;D	0.86627	-2.15;-2.15	4.84	3.65	0.41850	.	0.365369	0.28521	N	0.015059	T	0.00552	0.0018	N	0.12443	0.215	0.80722	P	0.0	B	0.24576	0.106	B	0.38056	0.264	T	0.30679	-0.9970	9	0.02654	T	1	.	9.126	0.36816	0.3995:0.0:0.0:0.6005	rs685967;rs52813142;rs685967	129	P56748	CLD8_HUMAN	A	129	ENSP00000382783:T129A;ENSP00000286809:T129A	ENSP00000286809:T129A	T	-	1	0	CLDN8	30509730	0.039000	0.19947	0.754000	0.31244	0.273000	0.26683	0.263000	0.18478	0.946000	0.37632	0.528000	0.53228	ACG	T|0.908;C|0.092	0.092	strong		0.502	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328	
LRRC8B	23507	hgsc.bcm.edu	37	1	90048248	90048248	+	Silent	SNP	C	C	T	rs12130207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:90048248C>T	ENST00000330947.2	+	5	399	c.39C>T	c.(37-39)gcC>gcT	p.A13A	LRRC8B_ENST00000358200.4_Silent_p.A13A|LRRC8B_ENST00000439853.1_Silent_p.A13A|RP5-1007M22.2_ENST00000443562.1_RNA	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	196	0	0		WXS	Illumina HiSeq	Phase_I	130	127	0.976923	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	
SYK	6850	hgsc.bcm.edu	37	9	93637015	93637015	+	Silent	SNP	C	C	T	rs2290890	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:93637015C>T	ENST00000375754.4	+	9	1213	c.1065C>T	c.(1063-1065)ccC>ccT	p.P355P	SYK_ENST00000375747.1_Silent_p.P332P|SYK_ENST00000375746.1_Silent_p.P355P|SYK_ENST00000375751.4_Silent_p.P332P	NM_003177.5	NP_003168.2	P43405	KSYK_HUMAN	spleen tyrosine kinase	355	Interdomain B.				activation of JUN kinase activity (GO:0007257)|adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|B cell receptor signaling pathway (GO:0050853)|beta selection (GO:0043366)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|cell proliferation (GO:0008283)|cellular response to molecule of fungal origin (GO:0071226)|defense response to bacterium (GO:0042742)|enzyme linked receptor protein signaling pathway (GO:0007167)|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)|leukocyte activation involved in immune response (GO:0002366)|leukocyte cell-cell adhesion (GO:0007159)|leukotriene biosynthetic process (GO:0019370)|lymph vessel development (GO:0001945)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of bone resorption (GO:0045780)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process (GO:0045425)|positive regulation of interleukin-3 biosynthetic process (GO:0045401)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of arachidonic acid secretion (GO:0090237)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of neutrophil degranulation (GO:0043313)|regulation of phagocytosis (GO:0050764)|regulation of platelet activation (GO:0010543)|regulation of platelet aggregation (GO:0090330)|regulation of superoxide anion generation (GO:0032928)|serotonin secretion by platelet (GO:0002554)|viral process (GO:0016032)	B cell receptor complex (GO:0019815)|cytosol (GO:0005829)|early phagosome (GO:0032009)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	ATP binding (GO:0005524)|integrin binding (GO:0005178)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(3)|skin(2)|stomach(2)	26						ACGCGGACCCCGAGGAGATCA	0.562			T	"""ETV6, ITK"""	"""MDS, peripheral T-cell lymphoma"""								C|||	981	0.195887	0.2088	0.366	5008	,	,		17794	0.2321		0.1362	False		,,,				2504	0.0818				p.P355P		Atlas-SNP	.		Dom	yes		9	9q22	6850	spleen tyrosine kinase		L	.	SYK	132	.	0			c.C1065T						PASS	.	C	,,,	918,3488	352.6+/-311.8	90,738,1375	145.0	159.0	154.0		996,1065,996,1065	-8.3	0.4	9	dbSNP_100	154	1216,7384	245.4+/-274.3	88,1040,3172	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYK	NM_001135052.2,NM_001174167.1,NM_001174168.1,NM_003177.5	,,,	178,1778,4547	TT,TC,CC		14.1395,20.8352,16.4078	,,,	332/613,355/636,332/613,355/636	93637015	2134,10872	2203	4300	6503	SO:0001819	synonymous_variant	6850	exon9			GGACCCCGAGGAG	L28824	CCDS6688.1, CCDS47992.1	9q22	2013-02-14			ENSG00000165025	ENSG00000165025		"""SH2 domain containing"""	11491	protein-coding gene	gene with protein product		600085				8082894, 1423621	Standard	XM_005252147		Approved		uc004aqz.3	P43405	OTTHUMG00000020200	ENST00000375754.4:c.1065C>T	9.37:g.93637015C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_003177		Silent	SNP	ENST00000375754.4	37	CCDS6688.1																																																																																			C|0.825;T|0.175	0.175	strong		0.562	SYK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053018.1		
ASIC4	55515	hgsc.bcm.edu	37	2	220402665	220402665	+	Missense_Mutation	SNP	C	C	A	rs6436153	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220402665C>A	ENST00000347842.3	+	9	1855	c.1841C>A	c.(1840-1842)cCg>cAg	p.P614Q	ASIC4_ENST00000358078.4_Missense_Mutation_p.P633Q	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	614			P -> Q (in dbSNP:rs6436153).		ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										AGTCCCTGCCCGAGCCGGGGC	0.637													C|||	779	0.155551	0.1422	0.2248	5008	,	,		15505	0.0982		0.1968	False		,,,				2504	0.1411				p.P614Q		Atlas-SNP	.											.	.	.	.	0			c.C1841A						PASS	.	C	GLN/PRO,GLN/PRO	684,3720		57,570,1575	21.0	23.0	22.0		1898,1841	1.9	0.3	2	dbSNP_116	22	1618,6982		161,1296,2843	yes	missense,missense	ACCN4	NM_018674.4,NM_182847.2	76,76	218,1866,4418	AA,AC,CC		18.814,15.5313,17.7022	probably-damaging,probably-damaging	633/667,614/648	220402665	2302,10702	2202	4300	6502	SO:0001583	missense	55515	exon9			CCTGCCCGAGCCG	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	21263	protein-coding gene	gene with protein product		606715	"""amiloride-sensitive cation channel 4, pituitary"", ""amiloride-sensitive cation channel family member 4, pituitary"""	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1841C>A	2.37:g.220402665C>A	ENSP00000326627:p.Pro614Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	34	24	0.705882	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Missense_Mutation	SNP	ENST00000347842.3	37	CCDS2442.1	361	0.1652930402930403	80	0.16260162601626016	64	0.17679558011049723	60	0.1048951048951049	157	0.20712401055408972	C	3.940	-0.014423	0.07681	0.155313	0.18814	ENSG00000072182	ENST00000347842;ENST00000358078	T;T	0.61392	0.11;0.12	4.77	1.94	0.25998	.	0.345630	0.21302	N	0.076785	T	0.00039	0.0001	N	0.22421	0.69	0.46564	P	8.920000000000039E-4	B;B	0.20052	0.024;0.041	B;B	0.19391	0.011;0.025	T	0.11421	-1.0588	9	0.17832	T	0.49	-0.4723	4.8445	0.13507	0.4068:0.427:0.0:0.1661	rs6436153;rs6436153	614;633	Q96FT7;Q96FT7-4	ACCN4_HUMAN;.	Q	614;633	ENSP00000326627:P614Q;ENSP00000350786:P633Q	ENSP00000326627:P614Q	P	+	2	0	ACCN4	220110909	0.027000	0.19231	0.315000	0.25238	0.229000	0.25112	0.221000	0.17680	0.308000	0.22923	-0.126000	0.14955	CCG	C|0.841;A|0.159	0.159	strong		0.637	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
ZNF835	90485	hgsc.bcm.edu	37	19	57176096	57176096	+	Missense_Mutation	SNP	C	C	G	rs77114013	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57176096C>G	ENST00000537055.2	-	2	702	c.471G>C	c.(469-471)caG>caC	p.Q157H		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						TGTGCGTGCGCTGGTGCAGGG	0.667													.|||	122	0.024361	0.003	0.013	5008	,	,		12795	0.0675		0.0308	False		,,,				2504	0.0102				p.Q157H		Atlas-SNP	.											.	ZNF835	106	.	0			c.G471C						PASS	.	C	HIS/GLN	31,4375	36.0+/-67.5	0,31,2172	40.0	42.0	41.0		471	2.7	0.6	19	dbSNP_132	41	228,8372	93.1+/-155.1	6,216,4078	no	missense	ZNF835	NM_001005850.2	24	6,247,6250	GG,GC,CC		2.6512,0.7036,1.9914	probably-damaging	157/538	57176096	259,12747	2203	4300	6503	SO:0001583	missense	90485	exon2			CGTGCGCTGGTGC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.471G>C	19.37:g.57176096C>G	ENSP00000444747:p.Gln157His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	63	0.028846153846153848	4	0.008130081300813009	5	0.013812154696132596	29	0.050699300699300696	25	0.032981530343007916	C	16.04	3.008827	0.54361	0.007036	0.026512	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.07567	3.18	2.68	2.68	0.31781	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01523	0.0049	L	0.60957	1.885	0.09310	N	1	D	0.58970	0.984	P	0.45753	0.492	T	0.24225	-1.0166	9	0.56958	D	0.05	.	5.5238	0.16947	0.0:0.8415:0.0:0.1585	.	179	Q9Y2P0	ZN835_HUMAN	H	179;157	ENSP00000444747:Q157H	ENSP00000341756:Q179H	Q	-	3	2	ZNF835	61867908	0.000000	0.05858	0.550000	0.28217	0.993000	0.82548	0.553000	0.23391	1.494000	0.48533	0.561000	0.74099	CAG	C|0.972;G|0.028	0.028	strong		0.667	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
PDIA2	64714	hgsc.bcm.edu	37	16	336396	336396	+	Missense_Mutation	SNP	G	G	A	rs400037	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:336396G>A	ENST00000219406.6	+	8	1181	c.1163G>A	c.(1162-1164)cGg>cAg	p.R388Q	PDIA2_ENST00000404312.1_Missense_Mutation_p.R385Q	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	388	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.		R -> Q (in dbSNP:rs400037).		cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				TGGGATCAGCGGCCAGTTAAG	0.562													g|||	844	0.16853	0.3457	0.1455	5008	,	,		12070	0.0377		0.1899	False		,,,				2504	0.0583				p.R388Q		Atlas-SNP	.											.	PDIA2	51	.	0			c.G1163A						PASS	.		GLN/ARG	1142,2676		163,816,930	58.0	64.0	62.0		1163	-2.3	1.0	16	dbSNP_80	62	1679,6571		183,1313,2629	yes	missense	PDIA2	NM_006849.2	43	346,2129,3559	AA,AG,GG		20.3515,29.9109,23.3759	benign	388/526	336396	2821,9247	1909	4125	6034	SO:0001583	missense	64714	exon8			ATCAGCGGCCAGT	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"""Protein disulfide isomerases"""	14180	protein-coding gene	gene with protein product		608012	"""protein disulfide isomerase, pancreatic"", ""protein disulfide isomerase-associated 2"""	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.1163G>A	16.37:g.336396G>A	ENSP00000219406:p.Arg388Gln	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	230	105	0.456522	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	394	0.1804029304029304	177	0.3597560975609756	51	0.1408839779005525	27	0.0472027972027972	139	0.18337730870712401	g	0.021	-1.423957	0.01126	0.299109	0.203515	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312;ENST00000435833	T;T;T	0.16897	2.31;2.31;3.97	4.04	-2.31	0.06765	Thioredoxin-like fold (3);	1.119980	0.06633	N	0.759534	T	0.00012	0.0000	N	0.01188	-0.97	0.80722	P	0.0	B	0.12013	0.005	B	0.10450	0.005	T	0.46442	-0.9191	9	0.02654	T	1	.	9.7883	0.40690	0.6167:0.0:0.3833:0.0	rs400037;rs58645006;rs400037	388	Q13087	PDIA2_HUMAN	Q	388;357;385;17	ENSP00000219406:R388Q;ENSP00000384410:R385Q;ENSP00000405081:R17Q	ENSP00000219406:R388Q	R	+	2	0	PDIA2	276397	0.000000	0.05858	0.958000	0.39756	0.812000	0.45895	-0.094000	0.11094	-0.251000	0.09542	0.479000	0.44913	CGG	G|0.810;A|0.190	0.190	strong		0.562	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592193	1592193	+	Intron	SNP	C	C	T	rs371465078	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1592193C>T	ENST00000381605.4	-	1	141				SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Silent_p.Q81Q|SIRPB1_ENST00000568365.1_Silent_p.Q81Q|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000381596.1_5'UTR	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GGCCTTCTTTCTGATTGTAGA	0.522													t|||	2823	0.563698	0.68	0.3876	5008	,	,		6072	0.631		0.3748	False		,,,				2504	0.6564				p.Q81Q		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,malignant_melanoma,0,1	SIRPB1	83	1	0			c.G243A						scavenged	.						94.0	111.0	106.0					20																	1592193		447	1317	1764	SO:0001627	intron_variant	10326	exon2			TTCTTTCTGATTG	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8321G>A	20.37:g.1592193C>T		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	618	20	0.0323625	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			.	.	weak		0.522	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573508	140573508	+	Silent	SNP	C	C	G	rs112214830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140573508C>G	ENST00000239446.4	+	1	1567	c.1383C>G	c.(1381-1383)cgC>cgG	p.R461R		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	461	Cadherin 5. {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)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTTCGTCCGCGAGAACAACA	0.632																																					p.R461R		Atlas-SNP	.											PCDHB10,NS,carcinoma,+2,2	PCDHB10	177	2	0			c.C1383G						scavenged	.						42.0	49.0	47.0					5																	140573508		2203	4290	6493	SO:0001819	synonymous_variant	56126	exon1			CGTCCGCGAGAAC	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1383C>G	5.37:g.140573508C>G		Somatic	109	2	0.0183486		WXS	Illumina HiSeq	Phase_I	86	24	0.27907	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.029;G|0.971	0.971	strong		0.632	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
LAMA1	284217	hgsc.bcm.edu	37	18	7034508	7034508	+	Missense_Mutation	SNP	T	T	G	rs566655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	195	0	0		WXS	Illumina HiSeq	Phase_I	186	88	0.473118	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	
TRAP1	10131	hgsc.bcm.edu	37	16	3724365	3724365	+	Missense_Mutation	SNP	C	C	T	rs145715008		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3724365C>T	ENST00000246957.5	-	9	1107	c.1019G>A	c.(1018-1020)cGc>cAc	p.R340H	TRAP1_ENST00000538171.1_Missense_Mutation_p.R287H|TRAP1_ENST00000573872.1_5'UTR|TRAP1_ENST00000575671.1_Missense_Mutation_p.R131H	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	340					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				GAAGATGCTGCGGATGTTGAG	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		20813	0.001		0.0	False		,,,				2504	0.0				p.R340H		Atlas-SNP	.											TRAP1,colon,carcinoma,-1,1	TRAP1	53	1	0			c.G1019A						PASS	.	C	HIS/ARG	2,4392	4.2+/-10.8	0,2,2195	160.0	102.0	122.0		1019	5.8	1.0	16	dbSNP_134	122	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TRAP1	NM_016292.2	29	0,11,6486	TT,TC,CC		0.1047,0.0455,0.0847	possibly-damaging	340/705	3724365	11,12983	2197	4300	6497	SO:0001583	missense	10131	exon9			ATGCTGCGGATGT	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"""Heat shock proteins / HSPC"""	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.1019G>A	16.37:g.3724365C>T	ENSP00000246957:p.Arg340His	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	163	90	0.552147	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	37	CCDS10508.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	21.3	4.131985	0.77662	4.55E-4	0.001047	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.12569	2.67;2.67	5.82	5.82	0.92795	Ribosomal protein S5 domain 2-type fold (1);	0.000000	0.85682	D	0.000000	T	0.18759	0.0450	L	0.49256	1.55	0.80722	D	1	P;P	0.36944	0.518;0.574	B;B	0.36922	0.152;0.236	T	0.00768	-1.1574	10	0.87932	D	0	-32.3858	19.0936	0.93240	0.0:1.0:0.0:0.0	.	287;340	F5H897;Q12931	.;TRAP1_HUMAN	H	340;287	ENSP00000246957:R340H;ENSP00000442070:R287H	ENSP00000246957:R340H	R	-	2	0	TRAP1	3664366	1.000000	0.71417	1.000000	0.80357	0.202000	0.24057	7.424000	0.80242	2.757000	0.94681	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.602	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
SPEG	10290	hgsc.bcm.edu	37	2	220348751	220348751	+	Missense_Mutation	SNP	C	C	T	rs10755037	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220348751C>T	ENST00000312358.7	+	30	6698	c.6566C>T	c.(6565-6567)cCt>cTt	p.P2189L	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2189	Pro-rich.		P -> L (in dbSNP:rs10755037).		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)		CCCAGTACCCCTAAGTCTGCA	0.662													C|||	1430	0.285543	0.289	0.2738	5008	,	,		13041	0.1448		0.2694	False		,,,				2504	0.4509				p.P2189L		Atlas-SNP	.											SPEG,NS,carcinoma,0,2	SPEG	272	2	0			c.C6566T						scavenged	.	C	LEU/PRO	1072,3052		152,768,1142	39.0	49.0	46.0		6566	1.9	0.0	2	dbSNP_120	46	2065,6317		271,1523,2397	yes	missense	SPEG	NM_005876.4	98	423,2291,3539	TT,TC,CC		24.6361,25.9942,25.084	benign	2189/3268	220348751	3137,9369	2062	4191	6253	SO:0001583	missense	10290	exon30			GTACCCCTAAGTC	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.6566C>T	2.37:g.220348751C>T	ENSP00000311684:p.Pro2189Leu	Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	43	9	0.209302	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	529	0.24221611721611722	129	0.2621951219512195	107	0.2955801104972376	92	0.16083916083916083	201	0.26517150395778366	C	0.010	-1.750379	0.00669	0.259942	0.246361	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.64991	-0.13	3.72	1.85	0.25348	.	0.416002	0.17647	N	0.166837	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.16837	-1.0389	9	0.51188	T	0.08	.	10.7058	0.45954	0.0:0.8205:0.0:0.1795	rs10755037	2189	Q15772	SPEG_HUMAN	L	2189	ENSP00000311684:P2189L	ENSP00000265327:P2189L	P	+	2	0	SPEG	220056995	0.482000	0.25948	0.008000	0.14137	0.002000	0.02628	2.969000	0.49232	0.351000	0.24027	-1.901000	0.00528	CCT	A|0.000;C|0.753;G|0.000;T|0.247	0.247	strong		0.662	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
OR8H2	390151	hgsc.bcm.edu	37	11	55872657	55872657	+	Missense_Mutation	SNP	A	A	C	rs28681529	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55872657A>C	ENST00000313503.1	+	1	139	c.139A>C	c.(139-141)Ata>Cta	p.I47L		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I47L(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)					TGTGGGGATGATATTGATAAT	0.433										HNSCC(53;0.14)			a|||	953	0.190296	0.1604	0.1354	5008	,	,		19738	0.2351		0.2187	False		,,,				2504	0.1943				p.I47L		Atlas-SNP	.											OR8H2,NS,carcinoma,0,1	OR8H2	117	1	1	Substitution - Missense(1)	stomach(1)	c.A139C						PASS	.	A	LEU/ILE	621,3781	260.7+/-263.8	56,509,1636	302.0	269.0	280.0		139	2.4	0.5	11	dbSNP_125	280	1710,6880	308.5+/-308.9	167,1376,2752	no	missense	OR8H2	NM_001005200.1	5	223,1885,4388	CC,CA,AA		19.9069,14.1072,17.9418	benign	47/313	55872657	2331,10661	2201	4295	6496	SO:0001583	missense	390151	exon1			GGGATGATATTGA	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.139A>C	11.37:g.55872657A>C	ENSP00000323982:p.Ile47Leu	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	243	106	0.436214	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	363	0.1662087912087912	60	0.12195121951219512	42	0.11602209944751381	119	0.20804195804195805	142	0.18733509234828497	a	6.642	0.486861	0.12641	0.141072	0.199069	ENSG00000181767	ENST00000313503	T	0.00614	6.21	3.58	2.4	0.29515	GPCR, rhodopsin-like superfamily (1);	0.204125	0.35179	N	0.003382	T	0.00012	0.0000	L	0.58583	1.82	0.58432	P	6.999999999979245E-6	B	0.15141	0.012	B	0.15052	0.012	T	0.46555	-0.9183	9	0.62326	D	0.03	.	10.3431	0.43891	0.8341:0.1659:0.0:0.0	rs28681529	47	Q8N162	OR8H2_HUMAN	L	47	ENSP00000323982:I47L	ENSP00000323982:I47L	I	+	1	0	OR8H2	55629233	0.986000	0.35501	0.510000	0.27712	0.017000	0.09413	2.852000	0.48310	0.509000	0.28195	-0.724000	0.03597	ATA	A|0.582;C|0.418	0.418	strong		0.433	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
INSL4	3641	hgsc.bcm.edu	37	9	5231712	5231712	+	Silent	SNP	T	T	A	rs12720	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:5231712T>A	ENST00000239316.4	+	1	294	c.189T>A	c.(187-189)cgT>cgA	p.R63R		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)	63					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	insulin-like growth factor receptor binding (GO:0005159)|receptor binding (GO:0005102)			endometrium(2)|lung(2)|skin(1)|urinary_tract(1)	6	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.14)		AATCTGGACGTCCCAAAGGTG	0.512													A|||	1999	0.399161	0.7337	0.3775	5008	,	,		19844	0.2222		0.2883	False		,,,				2504	0.2587				p.R63R		Atlas-SNP	.											INSL4,bladder,carcinoma,+2,1	INSL4	20	1	0			c.T189A						PASS	.	A		2877,1529	483.3+/-359.7	937,1003,263	46.0	46.0	46.0		189	0.4	0.0	9	dbSNP_52	46	2350,6250	701.5+/-405.2	305,1740,2255	no	coding-synonymous	INSL4	NM_002195.1		1242,2743,2518	AA,AT,TT		27.3256,34.7027,40.1891		63/140	5231712	5227,7779	2203	4300	6503	SO:0001819	synonymous_variant	3641	exon1			TGGACGTCCCAAA		CCDS6459.1	9p24	2008-02-05			ENSG00000120211	ENSG00000120211			6087	protein-coding gene	gene with protein product		600910				8666396, 9730618	Standard	NM_002195		Approved	EPIL	uc003ziy.3	Q14641	OTTHUMG00000019494	ENST00000239316.4:c.189T>A	9.37:g.5231712T>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	45	0.36	NM_002195	A8K678|Q5W127	Silent	SNP	ENST00000239316.4	37	CCDS6459.1																																																																																			T|0.613;A|0.387	0.387	strong		0.512	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	NM_002195	
ZNF595	152687	hgsc.bcm.edu	37	4	59350	59350	+	Missense_Mutation	SNP	A	A	G	rs6834707	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:59350A>G	ENST00000509152.2	+	2	216	c.31A>G	c.(31-33)Ata>Gta	p.I11V	ZNF595_ENST00000526473.2_Missense_Mutation_p.I11V|ZNF595_ENST00000339368.6_3'UTR			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	11	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(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		GGATGTGGCCATAGAATTCTC	0.428																																					p.I11V		Atlas-SNP	.											.	.	.	.	0			c.A31G						PASS	.	A	VAL/ILE	117,4289	69.2+/-107.0	0,117,2086	360.0	388.0	379.0		31	0.1	0.7	4	dbSNP_116	379	165,8435	62.8+/-124.8	0,165,4135	no	missense	ZNF595	NM_182524.2	29	0,282,6221	GG,GA,AA		1.9186,2.6555,2.1682	benign	11/649	59350	282,12724	2203	4300	6503	SO:0001583	missense	255403	exon2			GTGGCCATAGAAT	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"""Zinc fingers, C2H2-type"", ""-"""	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.31A>G	4.37:g.59350A>G	ENSP00000434858:p.Ile11Val	Somatic	659	0	0		WXS	Illumina HiSeq	Phase_I	863	41	0.0475087	NM_001039127		Missense_Mutation	SNP	ENST00000509152.2	37		.	.	.	.	.	.	.	.	.	.	A	11.22	1.574255	0.28092	0.026555	0.019186	ENSG00000197701	ENST00000509152;ENST00000526473	T;T	0.00824	5.65;5.65	1.26	0.0585	0.14328	Krueppel-associated box (8);	.	.	.	.	T	0.00300	0.0009	.	.	.	0.09310	N	0.999993	B;B	0.28026	0.198;0.046	B;B	0.30316	0.114;0.017	T	0.48479	-0.9032	8	0.33940	T	0.23	.	3.5569	0.07867	0.4697:0.0:0.5303:0.0	rs6834707;rs6834707	11;11	Q8IYB9;Q3SXZ3	ZN595_HUMAN;ZN718_HUMAN	V	11	ENSP00000434858:I11V;ENSP00000437878:I11V	ENSP00000434858:I11V	I	+	1	0	ZNF595	49350	0.068000	0.21057	0.711000	0.30485	0.284000	0.27059	0.134000	0.15932	0.549000	0.28973	0.397000	0.26171	ATA	A|0.997;G|0.003	0.003	strong		0.428	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000357817.2	NM_182524	
HELQ	113510	hgsc.bcm.edu	37	4	84374480	84374480	+	Missense_Mutation	SNP	C	C	T	rs1494961	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:84374480C>T	ENST00000295488.3	-	2	1078	c.916G>A	c.(916-918)Gtt>Att	p.V306I	HELQ_ENST00000510985.1_Missense_Mutation_p.V306I|MRPS18C_ENST00000295491.4_5'Flank|HELQ_ENST00000440639.2_5'Flank|MRPS18C_ENST00000507019.1_5'Flank|MRPS18C_ENST00000507349.1_5'Flank	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	306				V -> I (in Ref. 1; AAL85274, 2; BAC87559 and 4; AAH95473). {ECO:0000305}.	double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						GATGACTCAACTGTTTTCTTA	0.373								Other identified genes with known or suspected DNA repair function					T|||	3328	0.664537	0.826	0.6441	5008	,	,		19522	0.6776		0.4901	False		,,,				2504	0.6268				p.V306I		Atlas-SNP	.											.	HELQ	95	.	0			c.G916A						PASS	.	T	ILE/VAL	3420,986	366.8+/-318.0	1321,778,104	98.0	102.0	101.0	http://www.ncbi.nlm.nih.gov/pubmed?term	916	2.3	0.9	4	dbSNP_88	101	4311,4289	576.2+/-390.4	1082,2147,1071	yes	missense	HELQ	NM_133636.2	29	2403,2925,1175	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	49.8721,22.3786,40.5582	benign	306/1102	84374480	7731,5275	2203	4300	6503	SO:0001583	missense	113510	exon2			ACTCAACTGTTTT	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.916G>A	4.37:g.84374480C>T	ENSP00000295488:p.Val306Ile	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	249	130	0.522088	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	1367	0.6259157509157509	401	0.8150406504065041	220	0.6077348066298343	371	0.6486013986013986	375	0.4947229551451187	T	4.651	0.120977	0.08881	0.776214	0.501279	ENSG00000163312	ENST00000295488;ENST00000510985	T;T	0.57595	0.39;1.35	5.92	2.29	0.28610	.	0.284381	0.36234	N	0.002702	T	0.00012	0.0000	N	0.00801	-1.175	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.26326	-1.0106	9	0.25751	T	0.34	-5.3209	5.8264	0.18556	0.0:0.1996:0.2338:0.5666	rs1494961;rs3733332;rs17354958;rs59130103;rs1494961	306;306;269;306	E3W980;E3W982;Q8TDG4-2;Q8TDG4	.;.;.;HELQ_HUMAN	I	306	ENSP00000295488:V306I;ENSP00000424539:V306I	ENSP00000295488:V306I	V	-	1	0	HELQ	84593504	1.000000	0.71417	0.944000	0.38274	0.925000	0.55904	2.390000	0.44416	0.166000	0.19597	-0.254000	0.11334	GTT	C|0.384;N|0.000	.	strong		0.373	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
MYH10	4628	hgsc.bcm.edu	37	17	8381675	8381675	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8381675G>A	ENST00000269243.4	-	39	5732	c.5594C>T	c.(5593-5595)gCg>gTg	p.A1865V	MYH10_ENST00000379980.4_Missense_Mutation_p.A1881V|MYH10_ENST00000360416.3_Missense_Mutation_p.A1896V|MYH10_ENST00000396239.1_Missense_Mutation_p.A1886V|NDEL1_ENST00000299734.7_Intron	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1865					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)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						ATACTGGTCCGCGTGTCGACG	0.542																																					p.A1896V		Atlas-SNP	.											MYH10,colon,carcinoma,+1,2	MYH10	148	2	0			c.C5687T						scavenged	.						143.0	115.0	125.0					17																	8381675		2203	4300	6503	SO:0001583	missense	4628	exon41			TGGTCCGCGTGTC	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.5594C>T	17.37:g.8381675G>A	ENSP00000269243:p.Ala1865Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	122	2	0.0163934	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.055529	0.36277	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	4.78	4.78	0.61160	Myosin tail (1);	0.053927	0.64402	D	0.000001	T	0.71617	0.3361	L	0.56124	1.755	0.58432	D	0.999998	B;B;B	0.31599	0.112;0.33;0.112	B;B;B	0.32465	0.146;0.139;0.146	T	0.68157	-0.5483	10	0.02654	T	1	.	18.3727	0.90412	0.0:0.0:1.0:0.0	.	1874;1896;1865	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	V	1865;1896;1886;1881	ENSP00000269243:A1865V;ENSP00000353590:A1896V;ENSP00000379539:A1886V;ENSP00000369315:A1881V	ENSP00000269243:A1865V	A	-	2	0	MYH10	8322400	1.000000	0.71417	0.203000	0.23512	0.081000	0.17604	6.398000	0.73244	2.657000	0.90304	0.655000	0.94253	GCG	.	.	none		0.542	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
GALNT15	117248	hgsc.bcm.edu	37	3	16268974	16268974	+	Silent	SNP	T	T	A	rs15767	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:16268974T>A	ENST00000339732.5	+	10	2390	c.1887T>A	c.(1885-1887)cgT>cgA	p.R629R	GALNT15_ENST00000437509.1_Intron	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	629	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										AGCAGTGGCGTTTTGACCAGA	0.443													A|||	1808	0.361022	0.5287	0.3876	5008	,	,		18046	0.2034		0.3887	False		,,,				2504	0.2495				p.R629R		Atlas-SNP	.											GALNTL2,colon,carcinoma,0,4	.	.	4	0			c.T1887A						PASS	.	A		2148,2258	596.7+/-388.7	516,1116,571	125.0	123.0	123.0		1887	-2.8	0.5	3	dbSNP_52	123	3240,5360	650.3+/-400.7	610,2020,1670	no	coding-synonymous	GALNTL2	NM_054110.4		1126,3136,2241	AA,AT,TT		37.6744,48.7517,41.427		629/640	16268974	5388,7618	2203	4300	6503	SO:0001819	synonymous_variant	117248	exon10			GTGGCGTTTTGAC	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	21531	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 15"""	615131	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"""	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1887T>A	3.37:g.16268974T>A		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Silent	SNP	ENST00000339732.5	37	CCDS33711.1	850	0.3891941391941392	277	0.5630081300813008	157	0.43370165745856354	129	0.22552447552447552	287	0.3786279683377309	A	2.572	-0.299389	0.05532	0.487517	0.376744	ENSG00000131386	ENST00000543679	.	.	.	5.4	-2.78	0.05859	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19575	P	0.9999670301	.	.	.	.	.	.	T	0.44802	-0.9304	4	0.37606	T	0.19	.	7.3671	0.26779	0.413:0.0:0.4636:0.1233	rs15767;rs712871;rs1394909;rs3188637;rs17356739;rs15767	.	.	.	D	159	.	ENSP00000445852:V159D	V	+	2	0	GALNTL2	16243978	0.001000	0.12720	0.540000	0.28089	0.098000	0.18820	-0.374000	0.07484	-0.719000	0.04942	-0.257000	0.10917	GTT	T|0.600;A|0.400	0.400	strong		0.443	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110	
XPO5	57510	hgsc.bcm.edu	37	6	43496662	43496662	+	Splice_Site	SNP	A	A	C	rs1106841	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43496662A>C	ENST00000265351.7	-	24	2889	c.2679T>G	c.(2677-2679)cgT>cgG	p.R893R	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	893					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			TTACAAAGACACGTGCTGCAA	0.502													C|||	1956	0.390575	0.6354	0.4222	5008	,	,		17759	0.0565		0.3917	False		,,,				2504	0.3804				p.R893R		Atlas-SNP	.											XPO5,colon,carcinoma,0,2	XPO5	79	2	0			c.T2679G						scavenged	.	C		2283,1575		693,897,339	41.0	44.0	43.0		2679	1.9	1.0	6	dbSNP_86	43	3187,5077		606,1975,1551	yes	coding-synonymous-near-splice	XPO5	NM_020750.2		1299,2872,1890	CC,CA,AA		38.5649,40.8243,45.1246		893/1205	43496662	5470,6652	1929	4132	6061	SO:0001630	splice_region_variant	57510	exon24			AAAGACACGTGCT	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2678-1T>G	6.37:g.43496662A>C		Somatic	79	1	0.0126582		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																			A|0.635;C|0.365	0.365	strong		0.502	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	Silent
SIPA1	6494	hgsc.bcm.edu	37	11	65417434	65417434	+	Silent	SNP	G	G	A	rs746429	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65417434G>A	ENST00000394224.3	+	13	3056	c.2760G>A	c.(2758-2760)gcG>gcA	p.A920A	SIPA1_ENST00000394227.3_Silent_p.A818A|SIPA1_ENST00000527525.1_Silent_p.A818A|SIPA1_ENST00000534313.1_Silent_p.A920A|MIR4489_ENST00000578869.1_RNA	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	920					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						TGTCGGAGGCGGGCAGTGGGA	0.642													G|||	1184	0.236422	0.1392	0.1974	5008	,	,		17816	0.2123		0.3569	False		,,,				2504	0.2965				p.A920A		Atlas-SNP	.											.	SIPA1	45	.	0			c.G2760A						PASS	.	G	,	845,3557	333.1+/-302.8	86,673,1442	67.0	72.0	71.0		2760,2760	-8.5	0.3	11	dbSNP_86	71	2995,5599	462.7+/-365.8	514,1967,1816	no	coding-synonymous,coding-synonymous	SIPA1	NM_006747.3,NM_153253.29	,	600,2640,3258	AA,AG,GG		34.8499,19.1958,29.5476	,	920/1043,920/1043	65417434	3840,9156	2201	4297	6498	SO:0001819	synonymous_variant	6494	exon13			GGAGGCGGGCAGT	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.2760G>A	11.37:g.65417434G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_006747	O14518|O60484|O60618|Q2YD83	Silent	SNP	ENST00000394224.3	37	CCDS8108.1																																																																																			G|0.736;A|0.264	0.264	strong		0.642	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747	
PPFIA2	8499	hgsc.bcm.edu	37	12	81769581	81769581	+	Silent	SNP	C	C	T	rs10862301	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:81769581C>T	ENST00000549396.1	-	10	1285	c.1125G>A	c.(1123-1125)ctG>ctA	p.L375L	PPFIA2_ENST00000333447.7_Silent_p.L357L|PPFIA2_ENST00000552948.1_Silent_p.L375L|PPFIA2_ENST00000549325.1_Silent_p.L357L|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000550584.2_Silent_p.L375L|PPFIA2_ENST00000407050.4_Silent_p.L301L|PPFIA2_ENST00000548586.1_Silent_p.L375L|PPFIA2_ENST00000443686.3_Silent_p.L276L|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000550359.2_Silent_p.L222L	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2	375	Glu-rich.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(37)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)	85						GAACCTGCCGCAGGATAGCTT	0.403													T|||	2232	0.445687	0.5673	0.402	5008	,	,		16197	0.5387		0.2724	False		,,,				2504	0.3947				p.L375L		Atlas-SNP	.											.	PPFIA2	207	.	0			c.G1125A						PASS	.	T	,,,,,,	1778,2016		402,974,521	150.0	147.0	148.0		1125,1071,1125,1125,903,828,1125	-5.7	0.8	12	dbSNP_120	148	2059,6149		257,1545,2302	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIA2	NM_001220473.1,NM_001220474.1,NM_001220475.1,NM_001220476.1,NM_001220477.1,NM_001220478.1,NM_003625.3	,,,,,,	659,2519,2823	TT,TC,CC		25.0853,46.8635,31.9697	,,,,,,	375/1248,357/1233,375/1237,375/1252,301/1157,276/1153,375/1258	81769581	3837,8165	1897	4104	6001	SO:0001819	synonymous_variant	8499	exon9			CTGCCGCAGGATA	AF034799	CCDS55850.1, CCDS55851.1, CCDS55852.1, CCDS55853.1, CCDS55854.1, CCDS55855.1, CCDS55856.1, CCDS55857.1, CCDS59236.1, CCDS73503.1	12q21.31	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9246	protein-coding gene	gene with protein product	"""Liprin-alpha2"""	603143				9624153	Standard	NM_003625		Approved		uc031qis.1	O75334		ENST00000549396.1:c.1125G>A	12.37:g.81769581C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Silent	SNP	ENST00000549396.1	37	CCDS55857.1	955	0.43727106227106227	287	0.5833333333333334	138	0.3812154696132597	323	0.5646853146853147	207	0.27308707124010556	T	6.490	0.458611	0.12342	0.468635	0.250853	ENSG00000139220	ENST00000548790	.	.	.	5.45	-5.72	0.02406	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999899829	.	.	.	.	.	.	T	0.44817	-0.9303	3	.	.	.	-3.6027	3.7466	0.08551	0.0904:0.3488:0.2767:0.2841	rs10862301;rs52801936;rs57160712;rs10862301	.	.	.	Y	193	.	.	C	-	2	0	PPFIA2	80293712	0.378000	0.25114	0.806000	0.32338	0.739000	0.42172	-0.501000	0.06398	-1.195000	0.02680	-1.811000	0.00612	TGC	C|0.573;N|0.000	.	strong		0.403	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1		
FPR2	2358	hgsc.bcm.edu	37	19	52272903	52272903	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52272903C>T	ENST00000598776.1	+	2	1764	c.992C>T	c.(991-993)cCa>cTa	p.P331L	FPR2_ENST00000598953.1_Missense_Mutation_p.P331L|FPR2_ENST00000340023.6_Missense_Mutation_p.P331L	NM_001462.3	NP_001453.1	P25090	FPR2_HUMAN	formyl peptide receptor 2	331					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|N-formyl peptide receptor activity (GO:0004982)			endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	33						GACTCAGCCCCAACTAATGAC	0.537																																					p.P331L		Atlas-SNP	.											FPR2,NS,carcinoma,+1,1	FPR2	66	1	0			c.C992T						scavenged	.						69.0	66.0	67.0					19																	52272903		2203	4300	6503	SO:0001583	missense	2358	exon2			CAGCCCCAACTAA	M88107	CCDS12840.1	19q13.3-q13.4	2012-08-10	2008-04-17	2008-04-17		ENSG00000171049		"""GPCR / Class A : Formyl peptide receptors"", ""GPCR / Class A : Leukotriene receptors"""	3827	protein-coding gene	gene with protein product		136538	"""formyl peptide receptor-like 1"""	FPRL1		9054386	Standard	NM_001462		Approved	LXA4R, HM63, FPRH2, FMLPX, FPR2A, FMLP-R-II, ALXR	uc002pxr.3	P25090		ENST00000598776.1:c.992C>T	19.37:g.52272903C>T	ENSP00000468897:p.Pro331Leu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	3	0.0285714	NM_001005738	A8K3E2	Missense_Mutation	SNP	ENST00000598776.1	37	CCDS12840.1	.	.	.	.	.	.	.	.	.	.	.	3.845	-0.032930	0.07543	.	.	ENSG00000171049	ENST00000340023	T	0.36699	1.24	4.49	-6.34	0.01982	.	1.078530	0.07198	U	0.856927	T	0.15739	0.0379	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32188	-0.9916	10	0.23891	T	0.37	.	11.0913	0.48117	0.2813:0.6157:0.0:0.1029	.	331	P25090	FPR2_HUMAN	L	331	ENSP00000340191:P331L	ENSP00000340191:P331L	P	+	2	0	FPR2	56964715	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.196000	0.09532	-0.941000	0.03700	-0.350000	0.07774	CCA	.	.	none		0.537	FPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466912.2	NM_001005738	
SON	6651	hgsc.bcm.edu	37	21	34945721	34945721	+	Silent	SNP	T	T	C	rs3174808	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:34945721T>C	ENST00000356577.4	+	9	7468	c.6993T>C	c.(6991-6993)aaT>aaC	p.N2331N	SON_ENST00000470533.1_3'UTR|SON_ENST00000381692.2_Silent_p.N359N|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	129	0	0		WXS	Illumina HiSeq	Phase_I	165	73	0.442424	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	
CHMP4A	29082	hgsc.bcm.edu	37	14	24679877	24679877	+	Missense_Mutation	SNP	C	C	T	rs2295322	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24679877C>T	ENST00000609024.1	-	4	505	c.457G>A	c.(457-459)Gga>Aga	p.G153R	TM9SF1_ENST00000530611.1_Missense_Mutation_p.G153R|CHMP4A_ENST00000347519.6_Missense_Mutation_p.G196R|CHMP4A_ENST00000542700.2_5'UTR|TM9SF1_ENST00000556387.1_Missense_Mutation_p.G153R|CHMP4A_ENST00000530996.1_Missense_Mutation_p.G48R|AL136419.6_ENST00000565988.1_RNA			Q9BY43	CHM4A_HUMAN	charged multivesicular body protein 4A	153	Intramolecular interaction with N- terminus. {ECO:0000250}.		G -> R (in dbSNP:rs2295322). {ECO:0000269|PubMed:14583093, ECO:0000269|PubMed:15489334}.	FG -> LLE (in Ref. 4; AAF29098). {ECO:0000305}.	endosomal transport (GO:0016197)|membrane budding (GO:0006900)|membrane organization (GO:0061024)|membrane tubulation (GO:0097320)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			NS(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9				GBM - Glioblastoma multiforme(265;0.0181)		ACATCATCTCCAAAGCCCATA	0.517													C|||	1759	0.351238	0.2489	0.6196	5008	,	,		19262	0.2361		0.504	False		,,,				2504	0.2607				p.G196R		Atlas-SNP	.											.	CHMP4A	20	.	0			c.G586A						PASS	.	C	ARG/GLY	1230,3176	426.4+/-341.1	185,860,1158	214.0	170.0	185.0		586	4.3	1.0	14	dbSNP_100	185	4443,4157	587.9+/-392.3	1125,2193,982	yes	missense	CHMP4A	NM_014169.3	125	1310,3053,2140	TT,TC,CC		48.3372,27.9165,43.6183		196/266	24679877	5673,7333	2203	4300	6503	SO:0001583	missense	29082	exon4			CATCTCCAAAGCC	AF212243	CCDS9619.1	14q12	2012-10-04	2011-09-21	2005-04-04	ENSG00000254505	ENSG00000254505		"""Charged multivesicular body proteins"""	20274	protein-coding gene	gene with protein product		610051	"""chromosome 14 open reading frame 123"", ""chromatin modifying protein 4A"""	C14orf123			Standard	NM_014169		Approved	HSPC134, VPS32A		Q9BY43	OTTHUMG00000167036	ENST00000609024.1:c.457G>A	14.37:g.24679877C>T	ENSP00000476412:p.Gly153Arg	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	240	81	0.3375	NM_014169	Q14D22|Q32Q79|Q86SZ8|Q96QJ9|Q9P026	Missense_Mutation	SNP	ENST00000609024.1	37		840	0.38461538461538464	137	0.2784552845528455	223	0.6160220994475138	115	0.20104895104895104	365	0.4815303430079156	C	23.0	4.367327	0.82463	0.279165	0.516628	ENSG00000100926;ENSG00000254692;ENSG00000254505;ENSG00000254505	ENST00000556387;ENST00000530611;ENST00000347519;ENST00000533011	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	5.2	4.3	0.51218	.	0.161135	0.29868	N	0.010999	T	0.00012	0.0000	H	0.95884	3.735	0.32303	P	0.564775	P;D	0.54964	0.872;0.969	P;D	0.67103	0.675;0.949	T	0.47497	-0.9113	9	0.72032	D	0.01	-11.0912	10.6946	0.45892	0.348:0.652:0.0:0.0	rs2295322;rs11546886;rs17693554;rs52790353;rs61392271;rs2295322	153;196	Q9BY43;Q14D22	CHM4A_HUMAN;.	R	153;153;196;163	ENSP00000451949:G153R;ENSP00000433967:G153R;ENSP00000324205:G196R;ENSP00000432575:G163R	ENSP00000324205:G196R	G	-	1	0	TM9SF1;AL096870.1;RP11-468E2.1	23749717	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.529000	0.67135	1.392000	0.46585	0.561000	0.74099	GGA	C|0.594;T|0.406	0.406	strong		0.517	CHMP4A-012	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471846.1	NM_014169	
AMBRA1	55626	hgsc.bcm.edu	37	11	46564235	46564235	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:46564235C>T	ENST00000458649.2	-	7	1750	c.1332G>A	c.(1330-1332)tcG>tcA	p.S444S	AMBRA1_ENST00000298834.3_Silent_p.S444S|AMBRA1_ENST00000314845.3_Silent_p.S354S|AMBRA1_ENST00000534300.1_Silent_p.S444S|AMBRA1_ENST00000528950.1_Silent_p.S444S|AMBRA1_ENST00000426438.1_Silent_p.S444S|AMBRA1_ENST00000533727.1_Silent_p.S354S			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	444					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		GCAAACTCACCGAAGAGGCAC	0.587																																					p.S354S		Atlas-SNP	.											AMBRA1_ENST00000458649,NS,carcinoma,-1,2	AMBRA1	201	2	0			c.G1062A						scavenged	.						71.0	70.0	70.0					11																	46564235		2201	4299	6500	SO:0001819	synonymous_variant	55626	exon8			ACTCACCGAAGAG	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.1332G>A	11.37:g.46564235C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	170	3	0.0176471	NM_001267783	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Silent	SNP	ENST00000458649.2	37																																																																																				.	.	none		0.587	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
NBPF7	343505	hgsc.bcm.edu	37	1	120387120	120387120	+	IGR	SNP	G	G	A	rs12405228	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	63	0	0	1503	WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_001047980		Silent	SNP		37																																																																																				G|0.564;A|0.436	0.436	strong	0	0.488								
ADHFE1	137872	hgsc.bcm.edu	37	8	67380528	67380528	+	Missense_Mutation	SNP	T	T	C	rs1060242	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:67380528T>C	ENST00000396623.3	+	14	1376	c.1345T>C	c.(1345-1347)Tgt>Cgt	p.C449R	C8orf46_ENST00000482608.2_Intron|ADHFE1_ENST00000415254.1_Missense_Mutation_p.C401R|ADHFE1_ENST00000496501.1_3'UTR	NM_144650.2	NP_653251.2	Q8IWW8	HOT_HUMAN	alcohol dehydrogenase, iron containing, 1	449			C -> R (in dbSNP:rs1060242). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15221005}.		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)			GCTTGCACCCTGTCCCCAGTC	0.403													C|||	2902	0.579473	0.7496	0.6614	5008	,	,		20313	0.381		0.502	False		,,,				2504	0.5757				p.C449R		Atlas-SNP	.											.	ADHFE1	83	.	0			c.T1345C						PASS	.	C	ARG/CYS	3164,1242	429.5+/-342.2	1147,870,186	89.0	85.0	86.0		1345	3.7	0.8	8	dbSNP_86	86	4074,4526	593.6+/-393.2	968,2138,1194	yes	missense	ADHFE1	NM_144650.2	180	2115,3008,1380	CC,CT,TT		47.3721,28.1888,44.3488	benign	449/468	67380528	7238,5768	2203	4300	6503	SO:0001583	missense	137872	exon14			GCACCCTGTCCCC	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.1345T>C	8.37:g.67380528T>C	ENSP00000379865:p.Cys449Arg	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	83	24	0.289157	NM_144650	B4DTJ8|Q49A19|Q68CI7|Q6P2B6|Q96MF9	Missense_Mutation	SNP	ENST00000396623.3	37	CCDS6190.2	1210	0.5540293040293041	366	0.7439024390243902	232	0.6408839779005525	233	0.40734265734265734	379	0.5	C	2.114	-0.402972	0.04865	0.718112	0.473721	ENSG00000147576	ENST00000396623;ENST00000415254	T;T	0.35421	1.31;1.31	5.47	3.68	0.42216	Alcohol dehydrogenase, iron-type (1);	0.046699	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00002	-3.515	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47045	-0.9147	9	0.02654	T	1	-19.9151	10.8035	0.46502	0.0:0.7942:0.0:0.2058	rs1060242;rs1801563;rs3201106;rs3739340;rs17321905;rs52836210;rs59046581;rs1060242	449	Q8IWW8	HOT_HUMAN	R	449;401	ENSP00000379865:C449R;ENSP00000407115:C401R	ENSP00000379865:C449R	C	+	1	0	ADHFE1	67543082	0.947000	0.32204	0.818000	0.32626	0.983000	0.72400	1.922000	0.40045	0.295000	0.22570	-0.186000	0.12905	TGT	T|0.441;C|0.559	0.559	strong		0.403	ADHFE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316867.3	NM_144650	
TBC1D28	254272	hgsc.bcm.edu	37	17	18542519	18542519	+	Missense_Mutation	SNP	T	T	G	rs74452761		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:18542519T>G	ENST00000345096.4	-	5	866	c.167A>C	c.(166-168)gAg>gCg	p.E56A	TBC1D28_ENST00000575570.1_5'Flank|TBC1D28_ENST00000405044.1_Missense_Mutation_p.E56A			Q2M2D7	TBC28_HUMAN	TBC1 domain family, member 28	56				E -> A (in Ref. 1; AAI12013). {ECO:0000305}.			Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(5)|lung(2)|ovary(1)	9						GCGGGGCAGCTCCATCTCACT	0.647																																					p.E56A		Atlas-SNP	.											.	TBC1D28	14	.	0			c.A167C						PASS	.						92.0	101.0	98.0					17																	18542519		2192	4297	6489	SO:0001583	missense	254272	exon6			GGCAGCTCCATCT		CCDS42273.1	17p11.2	2008-10-27			ENSG00000189375	ENSG00000189375			26858	protein-coding gene	gene with protein product							Standard	NM_001039397		Approved	FLJ40244	uc002gud.2	Q2M2D7	OTTHUMG00000059054	ENST00000345096.4:c.167A>C	17.37:g.18542519T>G	ENSP00000339973:p.Glu56Ala	Somatic	569	2	0.00351494		WXS	Illumina HiSeq	Phase_I	312	126	0.403846	NM_001039397	Q2M2E1	Missense_Mutation	SNP	ENST00000345096.4	37	CCDS42273.1	1125	0.5151098901098901	248	0.5040650406504065	183	0.505524861878453	377	0.6590909090909091	317	0.4182058047493404	N	7.143	0.582264	0.13749	.	.	ENSG00000189375	ENST00000345096;ENST00000405044	T;T	0.44881	0.91;0.91	0.418	0.418	0.16429	.	0.321547	0.28187	U	0.016280	T	0.00012	0.0000	M	0.78916	2.43	0.80722	P	0.0	B	0.19331	0.035	B	0.08055	0.003	T	0.36578	-0.9742	8	0.59425	D	0.04	.	.	.	.	.	56	Q2M2D7	TBC28_HUMAN	A	56	ENSP00000339973:E56A;ENSP00000385821:E56A	ENSP00000339973:E56A	E	-	2	0	TBC1D28	18483244	0.334000	0.24739	0.001000	0.08648	0.001000	0.01503	0.493000	0.22451	0.402000	0.25451	0.392000	0.25879	GAG	T|0.485;G|0.515	0.515	strong		0.647	TBC1D28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130672.2	NM_001039397	
TPO	7173	hgsc.bcm.edu	37	2	1418192	1418192	+	Silent	SNP	C	C	G	rs9678281	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:1418192C>G	ENST00000345913.4	+	2	103	c.12C>G	c.(10-12)ctC>ctG	p.L4L	TPO_ENST00000382269.3_Silent_p.L4L|TPO_ENST00000382198.1_Silent_p.L4L|TPO_ENST00000346956.3_Silent_p.L4L|TPO_ENST00000382201.3_Silent_p.L4L|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Silent_p.L4L|TPO_ENST00000539820.1_Silent_p.L4L|TPO_ENST00000329066.4_Silent_p.L4L|TPO_ENST00000337415.3_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						PASS	.	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	194	0	0		WXS	Illumina HiSeq	Phase_I	129	122	0.945736	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	
FLG	2312	hgsc.bcm.edu	37	1	152282917	152282917	+	Missense_Mutation	SNP	G	G	T	rs11204978	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152282917G>T	ENST00000368799.1	-	3	4480	c.4445C>A	c.(4444-4446)tCc>tAc	p.S1482Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1482	Ser-rich.		S -> Y (in dbSNP:rs11204978).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACCGTCTTGGGATGCTGAGTG	0.572									Ichthyosis				G|||	1438	0.287141	0.0113	0.3905	5008	,	,		21395	0.5823		0.1421	False		,,,				2504	0.4315				p.S1482Y		Atlas-SNP	.											.	FLG	900	.	0			c.C4445A						PASS	.	G	TYR/SER	161,4245	108.2+/-146.6	2,157,2044	367.0	352.0	357.0		4445	0.7	0.0	1	dbSNP_120	357	1240,7360	249.0+/-276.5	97,1046,3157	no	missense	FLG	NM_002016.1	144	99,1203,5201	TT,TG,GG		14.4186,3.6541,10.772	possibly-damaging	1482/4062	152282917	1401,11605	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCTTGGGATGCTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4445C>A	1.37:g.152282917G>T	ENSP00000357789:p.Ser1482Tyr	Somatic	359	1	0.00278552		WXS	Illumina HiSeq	Phase_I	449	148	0.329621	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	572	0.2619047619047619	9	0.018292682926829267	118	0.3259668508287293	333	0.5821678321678322	112	0.14775725593667546	G	8.364	0.833852	0.16820	0.036541	0.144186	ENSG00000143631	ENST00000368799	T	0.03801	3.8	2.75	0.67	0.17923	.	.	.	.	.	T	0.01800	0.0057	M	0.81682	2.555	0.80722	P	0.0	P	0.41978	0.767	B	0.40825	0.341	T	0.36890	-0.9729	8	0.02654	T	1	.	4.9552	0.14035	0.0:0.24:0.5137:0.2463	rs11204978;rs52811516;rs11204978	1482	P20930	FILA_HUMAN	Y	1482	ENSP00000357789:S1482Y	ENSP00000357789:S1482Y	S	-	2	0	FLG	150549541	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.247000	0.18179	0.192000	0.20272	0.556000	0.70494	TCC	G|0.836;T|0.164	0.164	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ARRB1	408	hgsc.bcm.edu	37	11	74994352	74994352	+	Silent	SNP	G	G	A	rs877711	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:74994352G>A	ENST00000420843.2	-	5	430	c.333C>T	c.(331-333)caC>caT	p.H111H	ARRB1_ENST00000360025.3_Silent_p.H111H|ARRB1_ENST00000393505.4_Silent_p.H111H	NM_004041.4	NP_004032.2	P49407	ARRB1_HUMAN	arrestin, beta 1	111	Interaction with SRC. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|Notch signaling pathway (GO:0007219)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of GTPase activity (GO:0043547)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-Golgi vesicle-mediated transport (GO:0006892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)|transcription from RNA polymerase II promoter (GO:0006366)	basolateral plasma membrane (GO:0016323)|chromatin (GO:0000785)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|pseudopodium (GO:0031143)	angiotensin receptor binding (GO:0031701)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|enzyme inhibitor activity (GO:0004857)|GTPase activator activity (GO:0005096)|insulin-like growth factor receptor binding (GO:0005159)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(4)|large_intestine(2)|lung(4)|prostate(1)	11						AAGGGTAAGCGTGCTCGCCCA	0.612													G|||	824	0.164537	0.1891	0.2651	5008	,	,		17331	0.0982		0.1113	False		,,,				2504	0.183				p.H111H		Atlas-SNP	.											.	ARRB1	37	.	0			c.C333T						PASS	.	G	,	775,3625	311.9+/-292.3	65,645,1490	64.0	63.0	64.0		333,333	-5.7	0.9	11	dbSNP_86	64	959,7627	209.4+/-250.6	53,853,3387	no	coding-synonymous,coding-synonymous	ARRB1	NM_004041.4,NM_020251.3	,	118,1498,4877	AA,AG,GG		11.1693,17.6136,13.3528	,	111/419,111/411	74994352	1734,11252	2200	4293	6493	SO:0001819	synonymous_variant	408	exon5			GTAAGCGTGCTCG	BC003636	CCDS31640.1, CCDS44684.1	11q13	2008-12-11			ENSG00000137486	ENSG00000137486			711	protein-coding gene	gene with protein product	"""arrestin 2"""	107940		ARR1		8486659	Standard	NM_004041		Approved		uc001owe.2	P49407	OTTHUMG00000165444	ENST00000420843.2:c.333C>T	11.37:g.74994352G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_020251	B6V9G8|O75625|O75630|Q2PP20|Q9BTK8	Silent	SNP	ENST00000420843.2	37	CCDS44684.1																																																																																			G|0.862;A|0.138	0.138	strong		0.612	ARRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384092.3	NM_004041	
CRHR1	1394	hgsc.bcm.edu	37	17	43884402	43884402	+	Silent	SNP	C	C	T	rs12936511	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:43884402C>T	ENST00000398285.3	+	2	60	c.60C>T	c.(58-60)ccC>ccT	p.P20P	CRHR1_ENST00000314537.5_Silent_p.P20P|CRHR1_ENST00000339069.5_5'UTR|CRHR1_ENST00000577353.1_Silent_p.P20P|CRHR1_ENST00000352855.5_Silent_p.P20P|RP11-105N13.4_ENST00000587305.1_RNA|CRHR1_ENST00000293493.7_5'UTR	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	20					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		GGCTGAACCCCGTCTCTGCCT	0.612													c|||	84	0.0167732	0.0038	0.0288	5008	,	,		19215	0.0109		0.0427	False		,,,				2504	0.0051				p.P20P	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.C60T						PASS	.	T	,,,	51,4155		1,49,2053	66.0	72.0	70.0		60,60,60,60	-7.3	0.3	17	dbSNP_121	70	359,8125		8,343,3891	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRHR1	NM_001145146.1,NM_001145147.1,NM_001145148.1,NM_004382.4	,,,	9,392,5944	TT,TC,CC		4.2315,1.2126,3.2309	,,,	20/445,20/376,20/402,20/416	43884402	410,12280	2103	4242	6345	SO:0001819	synonymous_variant	1394	exon2			GAACCCCGTCTCT	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2357	protein-coding gene	gene with protein product	"""corticotropin-releasing factor receptor"""	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.60C>T	17.37:g.43884402C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001145148	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Silent	SNP	ENST00000398285.3	37	CCDS45712.1																																																																																			C|0.970;T|0.030	0.030	strong		0.612	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		
XIRP2	129446	hgsc.bcm.edu	37	2	168107155	168107155	+	Missense_Mutation	SNP	G	G	A	rs16853331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168107155G>A	ENST00000409195.1	+	9	9342	c.9253G>A	c.(9253-9255)Gca>Aca	p.A3085T	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.A2863T|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.A3085T	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2910					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						GCACCAAGTAGCAGCTCATCA	0.368													G|||	993	0.198283	0.3268	0.1326	5008	,	,		18672	0.12		0.1233	False		,,,				2504	0.229				p.A3085T		Atlas-SNP	.											.	XIRP2	914	.	0			c.G9253A						PASS	.	G	,,,THR/ALA,THR/ALA	1072,2760		159,754,1003	83.0	80.0	81.0		,,,9253,8587	2.0	1.0	2	dbSNP_123	81	924,7338		56,812,3263	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,58,58	215,1566,4266	AA,AG,GG		11.1837,27.9749,16.5041	,,,benign,benign	,,,3085/3550,2863/3328	168107155	1996,10098	1916	4131	6047	SO:0001583	missense	129446	exon9			CAAGTAGCAGCTC	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.9253G>A	2.37:g.168107155G>A	ENSP00000386840:p.Ala3085Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	142	64	0.450704	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	386	0.17673992673992675	172	0.34959349593495936	47	0.1298342541436464	72	0.1258741258741259	95	0.12532981530343007	G	4.693	0.128944	0.08981	0.279749	0.111837	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02606	4.23;4.23;4.24	5.42	2.03	0.26663	.	0.951003	0.08851	N	0.884486	T	0.00012	0.0000	L	0.31294	0.92	0.43141	P	0.005102000000000051	B;B;B	0.23249	0.049;0.082;0.082	B;B;B	0.23419	0.021;0.046;0.046	T	0.42327	-0.9458	9	0.19590	T	0.45	-2.2472	9.2099	0.37311	0.2839:0.0:0.7161:0.0	rs16853331;rs52790539;rs16853331	2910;2910;2863	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	T	3085;3085;2863;499	ENSP00000386840:A3085T;ENSP00000295237:A3085T;ENSP00000387255:A2863T	ENSP00000295237:A3085T	A	+	1	0	XIRP2	167815401	0.000000	0.05858	0.958000	0.39756	0.411000	0.31082	-0.255000	0.08769	0.188000	0.20168	0.557000	0.71058	GCA	G|0.816;A|0.184	0.184	strong		0.368	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
SBNO2	22904	hgsc.bcm.edu	37	19	1109595	1109595	+	Silent	SNP	G	G	T	rs185032569	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1109595G>T	ENST00000361757.3	-	28	3363	c.3126C>A	c.(3124-3126)atC>atA	p.I1042I	SBNO2_ENST00000438103.2_Silent_p.I985I|SBNO2_ENST00000587024.1_Silent_p.I1032I	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	1042					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		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)		GGTCCACGCTGATCTGCCACG	0.667													G|||	19	0.00379393	0.0023	0.0014	5008	,	,		6312	0.0		0.0149	False		,,,				2504	0.0				p.I1042I		Atlas-SNP	.											.	SBNO2	112	.	0			c.C3126A						PASS	.	G	,	11,3677		0,11,1833	6.0	7.0	6.0		2955,3126	1.8	1.0	19		6	81,7945		0,81,3932	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	0,92,5765	TT,TG,GG		1.0092,0.2983,0.7854	,	985/1310,1042/1367	1109595	92,11622	1844	4013	5857	SO:0001819	synonymous_variant	22904	exon28			CACGCTGATCTGC	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.3126C>A	19.37:g.1109595G>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			G|0.995;T|0.005	0.005	strong		0.667	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
GM2A	2760	hgsc.bcm.edu	37	5	150647012	150647012	+	Silent	SNP	A	A	G	rs1048723	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	155	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	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	
SOAT1	6646	hgsc.bcm.edu	37	1	179319541	179319541	+	Silent	SNP	C	C	G	rs3753526	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:179319541C>G	ENST00000367619.3	+	14	1568	c.1425C>G	c.(1423-1425)ctC>ctG	p.L475L	SOAT1_ENST00000535686.1_Silent_p.L211L|SOAT1_ENST00000540564.1_Silent_p.L417L|SOAT1_ENST00000539888.1_Silent_p.L410L	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	475					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	ATCCCGTGCTCTTCGTGCTCT	0.398													C|||	838	0.167332	0.0734	0.2277	5008	,	,		18150	0.3552		0.0746	False		,,,				2504	0.1534				p.L475L		Atlas-SNP	.											.	SOAT1	53	.	0			c.C1425G						PASS	.	C		316,4090	169.4+/-200.1	10,296,1897	220.0	187.0	199.0		1425	1.5	1.0	1	dbSNP_107	199	635,7965	163.8+/-216.2	22,591,3687	no	coding-synonymous	SOAT1	NM_003101.4		32,887,5584	GG,GC,CC		7.3837,7.172,7.312		475/551	179319541	951,12055	2203	4300	6503	SO:0001819	synonymous_variant	6646	exon14			CGTGCTCTTCGTG	L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	2.3.1.26		11177	protein-coding gene	gene with protein product	"""acyl-Coenzyme A: cholesterol acyltransferase"""	102642	"""sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1"""	SOAT, STAT		8407899	Standard	NM_003101		Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.1425C>G	1.37:g.179319541C>G		Somatic	372	0	0		WXS	Illumina HiSeq	Phase_I	502	498	0.992032	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Silent	SNP	ENST00000367619.3	37	CCDS1330.1																																																																																			C|0.891;G|0.109	0.109	strong		0.398	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101	
HLA-A	3105	hgsc.bcm.edu	37	6	29910602	29910602	+	Missense_Mutation	SNP	G	G	T	rs41552219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29910602G>T	ENST00000396634.1	+	4	483	c.142G>T	c.(142-144)Gcc>Tcc	p.A48S	HLA-A_ENST00000376806.5_Missense_Mutation_p.A48S|HLA-A_ENST00000376802.2_Missense_Mutation_p.A48S|HLA-A_ENST00000376809.5_Missense_Mutation_p.A48S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	48	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						CCGCTTCATCGCCGTGGGCTA	0.697									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.A48S		Atlas-SNP	.											HLA-A,NS,carcinoma,-2,4	HLA-A	89	4	0			c.G142T						PASS	.						32.0	28.0	29.0					6																	29910602		2201	4298	6499	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TTCATCGCCGTGG	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.142G>T	6.37:g.29910602G>T	ENSP00000379873:p.Ala48Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	109	25	0.229358	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.545	0.874078	0.17395	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00012	9.31;9.31;9.31;9.31	3.72	-7.44	0.01379	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	3.134130	0.02442	N	0.084628	T	0.00039	0.0001	N	0.11927	0.2	0.09310	N	1	B;D;B;D;B	0.69078	0.001;0.997;0.001;0.997;0.001	B;D;B;D;B	0.91635	0.069;0.999;0.111;0.999;0.069	T	0.53989	-0.8360	10	0.44086	T	0.13	.	3.4234	0.07401	0.21:0.0831:0.5765:0.1304	rs41552219	48;48;48;48;48	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	S	48	ENSP00000379873:A48S;ENSP00000366002:A48S;ENSP00000366005:A48S;ENSP00000365998:A48S	ENSP00000348012:A48S	A	+	1	0	HLA-A	30018581	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-6.122000	0.00080	-2.883000	0.00318	-1.516000	0.00938	GCC	A|0.043;G|0.955;T|0.002	0.002	strong		0.697	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
UBASH3B	84959	hgsc.bcm.edu	37	11	122646967	122646967	+	Missense_Mutation	SNP	G	G	A	rs12790613	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:122646967G>A	ENST00000284273.5	+	2	577	c.202G>A	c.(202-204)Gca>Aca	p.A68T		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	68	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.		A -> T (in dbSNP:rs12790613). {ECO:0000269|Ref.3}.		negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.A68T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		AAGTGTTCAGGCAGCATGTGA	0.403													G|||	980	0.195687	0.0325	0.3069	5008	,	,		21037	0.1726		0.3111	False		,,,				2504	0.2423				p.A68T		Atlas-SNP	.											UBASH3B,NS,carcinoma,0,1	UBASH3B	73	1	1	Substitution - Missense(1)	stomach(1)	c.G202A						PASS	.	G	THR/ALA	376,4028	191.9+/-217.4	17,342,1843	100.0	99.0	100.0		202	4.2	1.0	11	dbSNP_121	100	2756,5842	439.0+/-359.1	445,1866,1988	yes	missense	UBASH3B	NM_032873.4	58	462,2208,3831	AA,AG,GG		32.054,8.5377,24.0886	possibly-damaging	68/650	122646967	3132,9870	2202	4299	6501	SO:0001583	missense	84959	exon2			GTTCAGGCAGCAT	AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"""SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"""	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.202G>A	11.37:g.122646967G>A	ENSP00000284273:p.Ala68Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	94	73	0.776596	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	37	CCDS31694.1	465	0.2129120879120879	20	0.04065040650406504	114	0.3149171270718232	109	0.19055944055944055	222	0.2928759894459103	G	17.81	3.480055	0.63849	0.085377	0.32054	ENSG00000154127	ENST00000284273	T	0.22743	1.94	5.14	4.23	0.50019	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.100500	0.64402	D	0.000002	T	0.00012	0.0000	L	0.59967	1.855	0.09310	P	0.9999973605	P	0.46277	0.875	P	0.51297	0.665	T	0.45071	-0.9286	9	0.20046	T	0.44	-8.9395	13.6404	0.62246	0.0746:0.0:0.9254:0.0	rs12790613;rs52802139;rs59822329;rs12790613	68	Q8TF42	UBS3B_HUMAN	T	68	ENSP00000284273:A68T	ENSP00000284273:A68T	A	+	1	0	UBASH3B	122152177	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.092000	0.71414	1.176000	0.42840	-0.140000	0.14226	GCA	G|0.779;A|0.221	0.221	strong		0.403	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873	
USP43	124739	hgsc.bcm.edu	37	17	9580092	9580092	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:9580092C>G	ENST00000285199.7	+	5	959	c.863C>G	c.(862-864)tCt>tGt	p.S288C	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Missense_Mutation_p.S288C	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	288	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	26						GTCTTCCCCTCTAAGAGCCAG	0.542																																					p.S288C		Atlas-SNP	.											.	USP43	65	.	0			c.C863G						PASS	.						91.0	93.0	93.0					17																	9580092		2015	4165	6180	SO:0001583	missense	124739	exon5			TCCCCTCTAAGAG	AK055188	CCDS45610.1, CCDS58516.1	17p12	2005-08-08	2005-08-08			ENSG00000154914		"""Ubiquitin-specific peptidases"""	20072	protein-coding gene	gene with protein product			"""ubiquitin specific protease 43"""			12838346	Standard	NM_153210		Approved	FLJ30626	uc010cod.4	Q70EL4		ENST00000285199.7:c.863C>G	17.37:g.9580092C>G	ENSP00000285199:p.Ser288Cys	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	256	28	0.109375	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.041149	0.35989	.	.	ENSG00000154914	ENST00000285199	T	0.10099	2.91	4.62	2.55	0.30701	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.387701	0.24601	N	0.037138	T	0.12475	0.0303	L	0.50847	1.595	0.09310	N	0.999998	B;B	0.12630	0.001;0.006	B;B	0.23852	0.01;0.049	T	0.18999	-1.0319	10	0.52906	T	0.07	-3.9205	12.7709	0.57421	0.0:0.7264:0.2736:0.0	.	288;288	B7ZVX5;Q70EL4	.;UBP43_HUMAN	C	288	ENSP00000285199:S288C	ENSP00000285199:S288C	S	+	2	0	USP43	9520817	0.587000	0.26791	0.707000	0.30419	0.997000	0.91878	2.000000	0.40816	0.537000	0.28751	0.555000	0.69702	TCT	.	.	none		0.542	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210	
LGALS8	3964	hgsc.bcm.edu	37	1	236706300	236706300	+	Intron	SNP	T	T	A	rs2273865	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:236706300T>A	ENST00000366584.4	+	7	1115				RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000527974.1_Nonsense_Mutation_p.L212*|LGALS8_ENST00000323938.6_Intron|LGALS8_ENST00000526589.1_Nonsense_Mutation_p.L212*|LGALS8_ENST00000352231.2_Nonsense_Mutation_p.L212*|LGALS8_ENST00000341872.6_Intron|LGALS8_ENST00000416919.2_Nonsense_Mutation_p.L153*|LGALS8_ENST00000525042.1_Nonsense_Mutation_p.L153*|LGALS8_ENST00000526634.1_Intron|LGALS8_ENST00000450372.2_Nonsense_Mutation_p.L212*	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8						plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			AATCACACTTTGACTTGCACC	0.373													T|||	657	0.13119	0.2209	0.1225	5008	,	,		18448	0.1806		0.0318	False		,,,				2504	0.0675				p.L212X		Atlas-SNP	.											.	LGALS8	42	.	0			c.T635A						PASS	.	T	stop/LEU,,,stop/LEU	854,3552	335.7+/-304.0	79,696,1428	113.0	108.0	110.0		635,,,635	2.6	1.0	1	dbSNP_100	110	338,8262	116.3+/-176.0	2,334,3964	yes	stop-gained,intron,intron,stop-gained	LGALS8	NM_006499.4,NM_201543.2,NM_201544.2,NM_201545.2	,,,	81,1030,5392	AA,AT,TT		3.9302,19.3827,9.165	,,,	212/360,,,212/360	236706300	1192,11814	2203	4300	6503	SO:0001627	intron_variant	3964	exon9			ACACTTTGACTTG	X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"""Lectins, galactoside-binding"""	6569	protein-coding gene	gene with protein product	"""galectin 8"""	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.549+213T>A	1.37:g.236706300T>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	259	73	0.281853	NM_006499	O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Nonsense_Mutation	SNP	ENST00000366584.4	37	CCDS1612.1	249	0.11401098901098901	96	0.1951219512195122	36	0.09944751381215469	97	0.16958041958041958	20	0.026385224274406333	T	25.4	4.634918	0.87760	0.193827	0.039302	ENSG00000116977	ENST00000527974;ENST00000352231;ENST00000526589;ENST00000450372;ENST00000416919;ENST00000525042	.	.	.	3.77	2.59	0.31030	.	0.176865	0.27424	N	0.019423	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.12103	T	0.63	.	7.1016	0.25340	0.0:0.0:0.231:0.769	rs2273865;rs52827811;rs2273865	.	.	.	X	212;212;212;212;153;153	.	ENSP00000309576:L212X	L	+	2	0	LGALS8	234772923	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	1.360000	0.34125	0.768000	0.33290	0.533000	0.62120	TTG	T|0.899;A|0.101	0.101	strong		0.373	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642823	1642823	+	Silent	SNP	G	G	A	rs529692233|rs374921824	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1642823G>A	ENST00000399682.1	-	1	545	c.501C>T	c.(499-501)tcC>tcT	p.S167S		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				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)		CACAACCTGAGGAGGAGCAGC	0.617													g|||	139	0.0277556	0.0522	0.0159	5008	,	,		14834	0.0179		0.0229	False		,,,				2504	0.0184				p.S167S		Atlas-SNP	.											KRTAP5-4,colon,carcinoma,0,1	KRTAP5-4	78	1	0			c.C501T						PASS	.						22.0	34.0	30.0					11																	1642823		692	1590	2282	SO:0001819	synonymous_variant	387267	exon1			ACCTGAGGAGGAG	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.501C>T	11.37:g.1642823G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	173	16	0.0924855	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.617	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
SLC22A16	85413	hgsc.bcm.edu	37	6	110763875	110763875	+	Missense_Mutation	SNP	A	A	G	rs723685	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:110763875A>G	ENST00000368919.3	-	4	821	c.755T>C	c.(754-756)gTt>gCt	p.V252A	SLC22A16_ENST00000456137.2_3'UTR|RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000439654.1_Missense_Mutation_p.V252A|SLC22A16_ENST00000330550.4_Missense_Mutation_p.V218A	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	252			V -> A (in dbSNP:rs723685).		acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	CAGGGTTCCAACTGCAAAAAA	0.498													A|||	441	0.0880591	0.0968	0.1081	5008	,	,		18484	0.0794		0.0944	False		,,,				2504	0.0644				p.V252A		Atlas-SNP	.											.	SLC22A16	81	.	0			c.T755C						PASS	.	A	ALA/VAL	514,3892	236.5+/-248.6	22,470,1711	90.0	88.0	89.0		755	3.7	0.2	6	dbSNP_86	89	758,7842	181.0+/-229.8	33,692,3575	yes	missense	SLC22A16	NM_033125.2	64	55,1162,5286	GG,GA,AA		8.814,11.6659,9.7801	benign	252/578	110763875	1272,11734	2203	4300	6503	SO:0001583	missense	85413	exon4			GTTCCAACTGCAA		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.755T>C	6.37:g.110763875A>G	ENSP00000357915:p.Val252Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	180	0.08241758241758242	43	0.08739837398373984	32	0.08839779005524862	39	0.06818181818181818	66	0.0870712401055409	A	9.846	1.192480	0.21954	0.116659	0.08814	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949;ENST00000437378	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	4.84	3.67	0.42095	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.841724	0.10529	N	0.664036	T	0.33789	0.0875	L	0.52759	1.655	0.09310	P	1.0	B;B	0.10296	0.001;0.003	B;B	0.09377	0.004;0.003	T	0.15665	-1.0429	9	0.51188	T	0.08	.	10.5063	0.44836	0.9225:0.0:0.0775:0.0	rs723685;rs52815010;rs59277963;rs723685	252;218	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	A	252;169;218;252;82;209	ENSP00000357915:V252A;ENSP00000395642:V169A;ENSP00000328583:V218A;ENSP00000408799:V252A;ENSP00000409306:V82A;ENSP00000416310:V209A	ENSP00000328583:V218A	V	-	2	0	SLC22A16	110870568	0.841000	0.29509	0.161000	0.22692	0.030000	0.12068	4.650000	0.61440	0.695000	0.31675	-0.264000	0.10439	GTT	A|0.905;G|0.095	0.095	strong		0.498	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
LAMA4	3910	hgsc.bcm.edu	37	6	112512905	112512905	+	Silent	SNP	G	G	A	rs2072021	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:112512905G>A	ENST00000230538.7	-	6	1048	c.651C>T	c.(649-651)acC>acT	p.T217T	LAMA4_ENST00000524032.1_5'Flank|LAMA4_ENST00000389463.4_Silent_p.T217T|LAMA4_ENST00000522006.1_Silent_p.T217T|LAMA4_ENST00000424408.2_Silent_p.T217T	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	217	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)		ACTTGAATCCGGTGGTGTTGC	0.483													G|||	1587	0.316893	0.6067	0.1816	5008	,	,		18568	0.2619		0.1352	False		,,,				2504	0.2648				p.T217T		Atlas-SNP	.											.	LAMA4	227	.	0			c.C651T						PASS	.	G	,,	2301,2105	602.8+/-390.0	627,1047,529	99.0	84.0	89.0		651,651,651	-11.4	0.0	6	dbSNP_96	89	1048,7552	222.7+/-259.7	55,938,3307	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	682,1985,3836	AA,AG,GG		12.186,47.7758,25.7497	,,	217/1824,217/1817,217/1817	112512905	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon6			GAATCCGGTGGTG		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.651C>T	6.37:g.112512905G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	151	64	0.423841	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1	601|601	0.2751831501831502|0.2751831501831502	271|271	0.5508130081300813|0.5508130081300813	67|67	0.1850828729281768|0.1850828729281768	164|164	0.2867132867132867|0.2867132867132867	99|99	0.13060686015831136|0.13060686015831136	G|G	6.451|6.451	0.451378|0.451378	0.12223|0.12223	0.522242|0.522242	0.12186|0.12186	ENSG00000112769|ENSG00000112769	ENST00000368640|ENST00000521732	.|.	.|.	.|.	5.7|5.7	-11.4|-11.4	0.00090|0.00090	.|.	.|.	.|.	.|.	.|.	T|T	0.02494|0.02494	0.0076|0.0076	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999993|0.9999999999999993	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.09465|0.09465	-1.0673|-1.0673	3|3	.|.	.|.	.|.	.|.	1.8339|1.8339	0.03135|0.03135	0.468:0.1904:0.075:0.2666|0.468:0.1904:0.075:0.2666	rs2072021;rs59269192;rs2072021|rs2072021;rs59269192;rs2072021	.|.	.|.	.|.	L|W	21|37	.|.	.|.	P|R	-|-	2|1	0|2	LAMA4|LAMA4	112619598|112619598	0.000000|0.000000	0.05858|0.05858	0.023000|0.023000	0.16930|0.16930	0.811000|0.811000	0.45836|0.45836	-4.439000|-4.439000	0.00234|0.00234	-4.513000|-4.513000	0.00045|0.00045	-0.982000|-0.982000	0.02568|0.02568	CCG|CGG	G|0.735;A|0.265	0.265	strong		0.483	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
FAT4	79633	hgsc.bcm.edu	37	4	126239986	126239986	+	Missense_Mutation	SNP	C	C	T	rs1039808	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:126239986C>T	ENST00000394329.3	+	1	2433	c.2420C>T	c.(2419-2421)gCg>gTg	p.A807V		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	807	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> V (in dbSNP:rs1039808).		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						GAGAACGTGGCGCTGGGATAT	0.458													C|||	2124	0.424121	0.6142	0.4092	5008	,	,		20537	0.2252		0.4205	False		,,,				2504	0.3865				p.A807V		Atlas-SNP	.											.	FAT4	1752	.	0			c.C2420T						PASS	.	C	VAL/ALA	2195,1853		617,961,446	144.0	139.0	140.0		2420	5.1	1.0	4	dbSNP_86	140	3568,4802		759,2050,1376	yes	missense	FAT4	NM_024582.4	64	1376,3011,1822	TT,TC,CC		42.6284,45.7757,46.4084	benign	807/4982	126239986	5763,6655	2024	4185	6209	SO:0001583	missense	79633	exon1			ACGTGGCGCTGGG	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.2420C>T	4.37:g.126239986C>T	ENSP00000377862:p.Ala807Val	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	142	38	0.267606	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	906	0.41483516483516486	308	0.6260162601626016	150	0.4143646408839779	126	0.2202797202797203	322	0.42480211081794195	C	13.50	2.255592	0.39896	0.542243	0.426284	ENSG00000196159	ENST00000394329	T	0.01804	4.63	5.13	5.13	0.70059	Cadherin (3);Cadherin-like (1);	0.000000	0.34110	U	0.004241	T	0.00012	0.0000	L	0.38838	1.175	0.09310	P	1.0	P	0.36959	0.575	B	0.37550	0.253	T	0.10730	-1.0617	9	0.49607	T	0.09	.	18.603	0.91256	0.0:1.0:0.0:0.0	rs1039808;rs59138655;rs1039808	807	Q6V0I7	FAT4_HUMAN	V	807	ENSP00000377862:A807V	ENSP00000377862:A807V	A	+	2	0	FAT4	126459436	0.997000	0.39634	0.997000	0.53966	0.476000	0.33039	3.596000	0.54024	2.396000	0.81511	0.655000	0.94253	GCG	C|0.580;T|0.420	0.420	strong		0.458	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
DDX60L	91351	hgsc.bcm.edu	37	4	169294859	169294859	+	Silent	SNP	C	C	T	rs13133439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:169294859C>T	ENST00000511577.1	-	35	4981	c.4734G>A	c.(4732-4734)ggG>ggA	p.G1578G	DDX60L_ENST00000260184.7_Silent_p.G1578G			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1578							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)		TATCTGTGTTCCCCGAAAGAC	0.408													C|||	44	0.00878594	0.0008	0.013	5008	,	,		21270	0.0		0.0298	False		,,,				2504	0.0041				p.G1578G		Atlas-SNP	.											DDX60L,NS,carcinoma,-2,1	DDX60L	116	1	0			c.G4734A						PASS	.	C		31,4315	30.8+/-60.4	0,31,2142	266.0	268.0	267.0		4734	-2.0	0.1	4	dbSNP_121	267	333,8255	111.4+/-171.7	8,317,3969	no	coding-synonymous	DDX60L	NM_001012967.1		8,348,6111	TT,TC,CC		3.8775,0.7133,2.8143		1578/1707	169294859	364,12570	2173	4294	6467	SO:0001819	synonymous_variant	91351	exon35			TGTGTTCCCCGAA	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.4734G>A	4.37:g.169294859C>T		Somatic	373	0	0		WXS	Illumina HiSeq	Phase_I	210	51	0.242857	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.979;T|0.021	0.021	strong		0.408	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
PCDH19	57526	hgsc.bcm.edu	37	X	99663194	99663194	+	Silent	SNP	G	G	T	rs41300169	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:99663194G>T	ENST00000373034.4	-	1	2077	c.402C>A	c.(400-402)atC>atA	p.I134I	PCDH19_ENST00000420881.2_Silent_p.I134I|PCDH19_ENST00000255531.7_Silent_p.I134I	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	134	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(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						TCTCCAGCTCGATCTGTGCTG	0.582													G|||	606	0.16053	0.0272	0.1844	3775	,	,		13549	0.2044		0.0368	False		,,,				2504	0.2035				p.I134I		Atlas-SNP	.											.	PCDH19	269	.	0			c.C402A						PASS	.	G	,,	126,3562		2,104,18,1453,552	112.0	107.0	109.0		402,402,402	-11.4	0.0	X	dbSNP_127	109	360,6268		4,235,117,2160,1713	no	coding-synonymous,coding-synonymous,coding-synonymous	PCDH19	NM_001105243.1,NM_001184880.1,NM_020766.2	,,	6,339,135,3613,2265	TT,TG,T,GG,G		5.4315,3.4165,4.7111	,,	134/1102,134/1149,134/1101	99663194	486,9830	2129	4229	6358	SO:0001819	synonymous_variant	57526	exon1			CAGCTCGATCTGT	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.402C>A	X.37:g.99663194G>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Silent	SNP	ENST00000373034.4	37	CCDS55462.1																																																																																			G|0.871;T|0.129	0.129	strong		0.582	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766	
PLXND1	23129	hgsc.bcm.edu	37	3	129324703	129324703	+	Silent	SNP	G	G	C	rs139286065	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:129324703G>C	ENST00000324093.4	-	1	958	c.780C>G	c.(778-780)tcC>tcG	p.S260S	PLXND1_ENST00000393239.1_Silent_p.S260S	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	260	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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						TGTTGTCGTCGGAGGGGTTGA	0.662													g|||	3	0.000599042	0.0	0.0014	5008	,	,		12752	0.0		0.002	False		,,,				2504	0.0				p.S260S	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C780G						PASS	.			0,4404		0,0,2202	40.0	36.0	37.0		780	2.7	1.0	3	dbSNP_134	37	21,8579	14.6+/-50.1	0,21,4279	no	coding-synonymous	PLXND1	NM_015103.2		0,21,6481	CC,CG,GG		0.2442,0.0,0.1615		260/1926	129324703	21,12983	2202	4300	6502	SO:0001819	synonymous_variant	23129	exon1			GTCGTCGGAGGGG	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.780C>G	3.37:g.129324703G>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	173	74	0.427746	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																			G|0.998;C|0.002	0.002	strong		0.662	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
CDR2L	30850	hgsc.bcm.edu	37	17	73000061	73000061	+	Silent	SNP	A	A	G	rs3744203	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73000061A>G	ENST00000337231.5	+	5	1702	c.1290A>G	c.(1288-1290)gaA>gaG	p.E430E		NM_014603.2	NP_055418.2	Q86X02	CDR2L_HUMAN	cerebellar degeneration-related protein 2-like	430												all_lung(278;0.226)					AGCGGCTGGAACAGAGCCAGC	0.612													G|||	2336	0.466454	0.7504	0.513	5008	,	,		15723	0.1935		0.4225	False		,,,				2504	0.3763				p.E430E		Atlas-SNP	.											HUMPPA,NS,carcinoma,0,1	.	.	1	0			c.A1290G						PASS	.	G		3061,1345		1067,927,209	27.0	24.0	25.0		1290	3.0	1.0	17	dbSNP_107	25	3324,5272		636,2052,1610	no	coding-synonymous	CDR2L	NM_014603.2		1703,2979,1819	GG,GA,AA		38.6691,30.5266,49.1078		430/466	73000061	6385,6617	2203	4298	6501	SO:0001819	synonymous_variant	30850	exon5			GCTGGAACAGAGC		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.1290A>G	17.37:g.73000061A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_014603	B4DFA7|Q15175	Silent	SNP	ENST00000337231.5	37	CCDS11710.2																																																																																			A|0.528;G|0.472	0.472	strong		0.612	CDR2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318080.1	NM_014603	
TRIM56	81844	hgsc.bcm.edu	37	7	100732321	100732321	+	Silent	SNP	C	C	T	rs11760747	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100732321C>T	ENST00000306085.6	+	3	2025	c.1728C>T	c.(1726-1728)aaC>aaT	p.N576N		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	576					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of type I interferon production (GO:0032481)|protein K63-linked ubiquitination (GO:0070534)|regulation of type I interferon production (GO:0032479)|response to type I interferon (GO:0034340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	Lung NSC(181;0.136)|all_lung(186;0.182)					TCAACCCCAACGGCGAAGTGC	0.726													C|||	906	0.180911	0.3366	0.1052	5008	,	,		15445	0.1379		0.1312	False		,,,				2504	0.1196				p.N576N	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.C1728T						PASS	.	C		1162,3026		169,824,1101	56.0	62.0	60.0		1728	-7.4	0.0	7	dbSNP_120	60	996,7416		54,888,3264	no	coding-synonymous	TRIM56	NM_030961.1		223,1712,4365	TT,TC,CC		11.8402,27.7459,17.127		576/756	100732321	2158,10442	2094	4206	6300	SO:0001819	synonymous_variant	81844	exon3			CCCCAACGGCGAA	BK000511	CCDS43625.1	7q11.2	2013-01-09	2011-01-25		ENSG00000169871	ENSG00000169871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19028	protein-coding gene	gene with protein product			"""tripartite motif-containing 56"""				Standard	NM_030961		Approved	RNF109	uc003uxq.3	Q9BRZ2	OTTHUMG00000157032	ENST00000306085.6:c.1728C>T	7.37:g.100732321C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			C|0.857;T|0.143	0.143	strong		0.726	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961	
P2RX3	5024	hgsc.bcm.edu	37	11	57137424	57137424	+	Missense_Mutation	SNP	C	C	T	rs2276038	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:57137424C>T	ENST00000263314.2	+	12	1182	c.1148C>T	c.(1147-1149)gCg>gTg	p.A383V		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	383			A -> V (in dbSNP:rs2276038). {ECO:0000269|Ref.2}.		behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CAGACCACAGCGGAGAAGCAG	0.587													C|||	2163	0.431909	0.0696	0.4914	5008	,	,		19306	0.7163		0.3926	False		,,,				2504	0.6268				p.A383V		Atlas-SNP	.											.	P2RX3	55	.	0			c.C1148T						PASS	.	C	VAL/ALA	546,3856	241.8+/-252.1	42,462,1697	102.0	87.0	92.0		1148	0.1	0.1	11	dbSNP_100	92	3319,5273	490.5+/-372.9	657,2005,1634	yes	missense	P2RX3	NM_002559.3	64	699,2467,3331	TT,TC,CC		38.629,12.4035,29.7445	benign	383/398	57137424	3865,9129	2201	4296	6497	SO:0001583	missense	5024	exon12			CCACAGCGGAGAA	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.1148C>T	11.37:g.57137424C>T	ENSP00000263314:p.Ala383Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	135	59	0.437037	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	37	CCDS7953.1	905	0.4143772893772894	42	0.08536585365853659	160	0.4419889502762431	397	0.6940559440559441	306	0.40369393139841686	C	5.453	0.268630	0.10349	0.124035	0.38629	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.04275	3.66	5.4	0.0746	0.14396	.	0.735097	0.13141	N	0.410610	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	0.06232	-1.0838	9	0.28530	T	0.3	-15.7114	2.1232	0.03731	0.4489:0.3135:0.0883:0.1493	rs2276038;rs17574631;rs2276038	383	P56373	P2RX3_HUMAN	V	382;383	ENSP00000263314:A383V	ENSP00000263314:A383V	A	+	2	0	P2RX3	56894000	0.879000	0.30193	0.065000	0.19835	0.101000	0.19017	0.300000	0.19156	-0.241000	0.09681	-0.457000	0.05445	GCG	C|0.650;T|0.349	0.349	strong		0.587	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
RAB8B	51762	hgsc.bcm.edu	37	15	63548787	63548787	+	Silent	SNP	G	G	A	rs10851726	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:63548787G>A	ENST00000321437.4	+	5	564	c.408G>A	c.(406-408)ggG>ggA	p.G136G	RAB8B_ENST00000448330.2_Silent_p.G136G	NM_016530.2	NP_057614.1	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family	136					adherens junction organization (GO:0034332)|antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|positive regulation of cell projection organization (GO:0031346)|positive regulation of corticotropin secretion (GO:0051461)|protein import into peroxisome membrane (GO:0045046)|small GTPase mediated signal transduction (GO:0007264)	cell tip (GO:0051286)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)			kidney(3)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9						AAGAAAGAGGGGAGAAGGTAA	0.333													G|||	1375	0.274561	0.1452	0.2089	5008	,	,		19289	0.4663		0.1521	False		,,,				2504	0.4243				p.G136G		Atlas-SNP	.											.	RAB8B	23	.	0			c.G408A						PASS	.	G		606,3800	263.8+/-265.7	42,522,1639	103.0	97.0	99.0		408	-8.6	0.6	15	dbSNP_120	99	1200,7400	240.7+/-271.3	91,1018,3191	no	coding-synonymous	RAB8B	NM_016530.2		133,1540,4830	AA,AG,GG		13.9535,13.754,13.8859		136/208	63548787	1806,11200	2203	4300	6503	SO:0001819	synonymous_variant	51762	exon5			AAGAGGGGAGAAG	AL833365	CCDS10183.1	15q22	2008-11-18			ENSG00000166128	ENSG00000166128		"""RAB, member RAS oncogene"""	30273	protein-coding gene	gene with protein product		613532				9030196, 18772196	Standard	XM_006720569		Approved		uc002alz.3	Q92930	OTTHUMG00000132862	ENST00000321437.4:c.408G>A	15.37:g.63548787G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	60	16	0.266667	NM_016530	Q5JPC4|Q9P293	Silent	SNP	ENST00000321437.4	37	CCDS10183.1																																																																																			G|0.814;A|0.186	0.186	strong		0.333	RAB8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256336.1	NM_016530	
INADL	10207	hgsc.bcm.edu	37	1	62257036	62257036	+	Missense_Mutation	SNP	A	A	C	rs1286823	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:62257036A>C	ENST00000371158.2	+	9	1199	c.1085A>C	c.(1084-1086)gAa>gCa	p.E362A	INADL_ENST00000316485.6_Missense_Mutation_p.E362A	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	362			E -> A (in dbSNP:rs1286823).		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						TCTCTTTTTGAAACTTATAAT	0.338													A|||	231	0.0461262	0.0061	0.0634	5008	,	,		18379	0.0248		0.1243	False		,,,				2504	0.0297				p.E362A		Atlas-SNP	.											.	INADL	179	.	0			c.A1085C						PASS	.	A	ALA/GLU	96,4310	76.8+/-115.0	1,94,2108	94.0	98.0	97.0		1085	5.2	1.0	1	dbSNP_87	97	989,7611	214.1+/-253.8	57,875,3368	yes	missense	INADL	NM_176877.2	107	58,969,5476	CC,CA,AA		11.5,2.1788,8.3423	possibly-damaging	362/1802	62257036	1085,11921	2203	4300	6503	SO:0001583	missense	10207	exon9			TTTTTGAAACTTA	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.1085A>C	1.37:g.62257036A>C	ENSP00000360200:p.Glu362Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	46	10	0.217391	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	140	0.0641025641025641	7	0.014227642276422764	33	0.09116022099447514	11	0.019230769230769232	89	0.11741424802110818	A	12.41	1.930837	0.34096	0.021788	0.115	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.18960	2.18;2.18	5.17	5.17	0.71159	PDZ/DHR/GLGF (1);	0.066816	0.56097	D	0.000031	T	0.00412	0.0013	L	0.29908	0.895	0.09310	P	1.0	D;P;P	0.55605	0.972;0.72;0.796	D;P;P	0.64506	0.926;0.643;0.826	T	0.05194	-1.0900	9	0.59425	D	0.04	.	10.4154	0.44318	0.8544:0.0:0.0:0.1456	rs1286823;rs1620006;rs52804250;rs1286823	362;362;362	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	A	362	ENSP00000360200:E362A;ENSP00000326199:E362A	ENSP00000255202:E362A	E	+	2	0	INADL	62029624	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	6.050000	0.71063	2.173000	0.68751	0.460000	0.39030	GAA	A|0.923;C|0.077	0.077	strong		0.338	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
DCAF4	26094	hgsc.bcm.edu	37	14	73425462	73425462	+	Silent	SNP	G	G	A	rs12882409	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:73425462G>A	ENST00000358377.2	+	14	1657	c.1437G>A	c.(1435-1437)ccG>ccA	p.P479P	DCAF4_ENST00000394234.2_Silent_p.P379P|DCAF4_ENST00000353777.3_Silent_p.P309P|DCAF4_ENST00000555042.1_Silent_p.P473P|DCAF4_ENST00000509153.1_Silent_p.P419P	NM_001163509.1|NM_015604.3	NP_001156981.1|NP_056419.2	Q8WV16	DCAF4_HUMAN	DDB1 and CUL4 associated factor 4	479					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|skin(1)	22						GGGGCGCGCCGGGGCTGCTCA	0.627													G|||	713	0.142372	0.0847	0.1153	5008	,	,		16333	0.1548		0.175	False		,,,				2504	0.1933				p.P479P		Atlas-SNP	.											.	DCAF4	40	.	0			c.G1437A						PASS	.	G	,,,,	474,3932		35,404,1764	44.0	54.0	51.0		1419,1374,1437,1137,1257	-10.0	0.1	14	dbSNP_121	51	1533,7067		133,1267,2900	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCAF4	NM_001163508.1,NM_001163509.1,NM_015604.3,NM_181340.2,NM_181341.2	,,,,	168,1671,4664	AA,AG,GG		17.8256,10.7581,15.4313	,,,,	473/490,458/475,479/496,379/396,419/436	73425462	2007,10999	2203	4300	6503	SO:0001819	synonymous_variant	26094	exon14			CGCGCCGGGGCTG	BC018979	CCDS9809.1, CCDS9810.1, CCDS41968.1, CCDS41968.2, CCDS55926.1	14q24.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000119599		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20229	protein-coding gene	gene with protein product			"""WD repeat domain 21"", ""WD repeat domain 21A"""	WDR21, WDR21A			Standard	NM_015604		Approved	DKFZp434K114	uc010ttr.2	Q8WV16		ENST00000358377.2:c.1437G>A	14.37:g.73425462G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_015604	B4DUT6|G3V522|Q86U31|Q8IV10|Q96K22|Q9Y4P5	Silent	SNP	ENST00000358377.2	37	CCDS9809.1																																																																																			G|0.844;A|0.156	0.156	strong		0.627	DCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361058.1	NM_015604	
SCN7A	6332	hgsc.bcm.edu	37	2	167262939	167262939	+	Silent	SNP	A	A	G	rs33953730	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:167262939A>G	ENST00000409855.1	-	25	4326	c.4200T>C	c.(4198-4200)taT>taC	p.Y1400Y		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1400					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	AGGCAAAATTATACATTCCAA	0.353													G|||	266	0.053115	0.031	0.0288	5008	,	,		20106	0.0129		0.0775	False		,,,				2504	0.1166				p.Y1400Y		Atlas-SNP	.											SCN7A_ENST00000409855,NS,carcinoma,-1,2	SCN7A	410	2	0			c.T4200C						PASS	.	G		181,3697		3,175,1761	111.0	110.0	110.0		4200	2.2	1.0	2	dbSNP_126	110	821,7515		38,745,3385	no	coding-synonymous	SCN7A	NM_002976.3		41,920,5146	GG,GA,AA		9.8488,4.6674,8.2037		1400/1683	167262939	1002,11212	1939	4168	6107	SO:0001819	synonymous_variant	6332	exon25			AAAATTATACATT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4200T>C	2.37:g.167262939A>G		Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	351	176	0.501424	NM_002976		Silent	SNP	ENST00000409855.1	37	CCDS46442.1																																																																																			A|0.948;G|0.052	0.052	strong		0.353	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
FPGT	8790	hgsc.bcm.edu	37	1	74665493	74665493	+	Silent	SNP	G	G	A	rs792310	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:74665493G>A	ENST00000609362.1	+	2	265	c.228G>A	c.(226-228)gtG>gtA	p.V76V	FPGT_ENST00000482102.2_Silent_p.V98V|FPGT-TNNI3K_ENST00000533006.1_3'UTR|FPGT_ENST00000370898.3_Silent_p.V89V|FPGT_ENST00000467578.2_Silent_p.V89V|FPGT-TNNI3K_ENST00000370893.1_Silent_p.V76V|LRRIQ3_ENST00000354431.4_5'Flank|FPGT_ENST00000370894.5_Silent_p.V76V|FPGT_ENST00000534056.1_Silent_p.V76V|FPGT-TNNI3K_ENST00000370895.1_Silent_p.V76V|TNNI3K_ENST00000370891.2_Silent_p.V76V|LRRIQ3_ENST00000370909.2_5'Flank|FPGT-TNNI3K_ENST00000370899.3_Silent_p.V76V|FPGT-TNNI3K_ENST00000557284.2_Silent_p.V89V|FPGT_ENST00000524915.1_3'UTR|LRRIQ3_ENST00000370911.3_5'Flank	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	76					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						ACGTTTTTGTGGATCCTGCTG	0.403													A|||	2237	0.446685	0.1619	0.389	5008	,	,		16408	0.7391		0.4642	False		,,,				2504	0.5532				p.V76V		Atlas-SNP	.											.	FPGT	77	.	0			c.G228A						PASS	.	A	,,,,	1005,3401	729.6+/-410.1	122,761,1320	141.0	133.0	136.0		228,228,228,228,228	-3.6	1.0	1	dbSNP_86	136	4157,4443	588.2+/-392.3	1018,2121,1161	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FPGT,FPGT-TNNI3K	NM_001112808.2,NM_001199327.1,NM_001199328.1,NM_001199329.1,NM_003838.3	,,,,	1140,2882,2481	AA,AG,GG		48.3372,22.8098,39.6894	,,,,	76/937,76/844,76/341,76/170,76/595	74665493	5162,7844	2203	4300	6503	SO:0001819	synonymous_variant	8790	exon2			TTTTGTGGATCCT	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.228G>A	1.37:g.74665493G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	57	44	0.77193	NM_001199329	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	37	CCDS663.1																																																																																			G|0.577;A|0.423	0.423	strong		0.403	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
POM121L12	285877	hgsc.bcm.edu	37	7	53103425	53103425	+	Missense_Mutation	SNP	C	C	A	rs10229800	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:53103425C>A	ENST00000408890.4	+	1	77	c.61C>A	c.(61-63)Ccc>Acc	p.P21T		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	21			P -> T (in dbSNP:rs10229800).							endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGCGGGAGAACCCCTGCTGCA	0.711													C|||	623	0.124401	0.1354	0.2089	5008	,	,		12664	0.0992		0.1451	False		,,,				2504	0.0542				p.P21T		Atlas-SNP	.											.	POM121L12	146	.	0			c.C61A						PASS	.	C	THR/PRO	482,3566		32,418,1574	14.0	20.0	18.0		61	0.5	0.0	7	dbSNP_119	18	1051,7277		53,945,3166	yes	missense	POM121L12	NM_182595.3	38	85,1363,4740	AA,AC,CC		12.6201,11.9071,12.3869	possibly-damaging	21/297	53103425	1533,10843	2024	4164	6188	SO:0001583	missense	285877	exon1			GGAGAACCCCTGC		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.61C>A	7.37:g.53103425C>A	ENSP00000386133:p.Pro21Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	108	65	0.601852	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	304	0.1391941391941392	69	0.1402439024390244	70	0.19337016574585636	56	0.0979020979020979	109	0.1437994722955145	C	10.16	1.275119	0.23307	0.119071	0.126201	ENSG00000221900	ENST00000408890	T	0.20881	2.04	1.66	0.497	0.16902	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.31174	0.311	B	0.18561	0.022	T	0.32481	-0.9905	8	0.05833	T	0.94	.	3.1558	0.06504	0.0:0.2723:0.0:0.7277	rs10229800;rs10229800	21	Q8N7R1	P1L12_HUMAN	T	21	ENSP00000386133:P21T	ENSP00000386133:P21T	P	+	1	0	POM121L12	53070919	0.001000	0.12720	0.001000	0.08648	0.004000	0.04260	-0.049000	0.11924	0.138000	0.18790	-0.379000	0.06801	CCC	C|0.870;A|0.130	0.130	strong		0.711	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
LGALS16	148003	hgsc.bcm.edu	37	19	40151098	40151098	+	Missense_Mutation	SNP	A	A	C	rs181925874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40151098A>C	ENST00000392051.3	+	4	435	c.367A>C	c.(367-369)Atg>Ctg	p.M123L		NM_001190441.1	NP_001177370.1			lectin, galactoside-binding, soluble, 16																		ATATGTGAAGATGATTCAAGT	0.428													A|||	2	0.000399361	0.0	0.0014	5008	,	,		23434	0.0		0.001	False		,,,				2504	0.0				p.M123L		Atlas-SNP	.											.	LGALS16	6	.	0			c.A367C						PASS	.																																			SO:0001583	missense	148003	exon4			GTGAAGATGATTC		CCDS54267.1	19q13.2	2011-08-04			ENSG00000249861	ENSG00000249861		"""Lectins, galactoside-binding"""	40039	protein-coding gene	gene with protein product						19497882	Standard	NM_001190441		Approved		uc021uun.1	A8MUM7		ENST00000392051.3:c.367A>C	19.37:g.40151098A>C	ENSP00000375904:p.Met123Leu	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	29	9	0.310345	NM_001190441		Missense_Mutation	SNP	ENST00000392051.3	37	CCDS54267.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	11.38	1.621495	0.28889	.	.	ENSG00000249861	ENST00000392051	T	0.15834	2.39	1.21	-0.276	0.12902	.	.	.	.	.	T	0.14657	0.0354	L	0.46670	1.46	0.09310	N	1	P	0.46706	0.883	P	0.44860	0.462	T	0.13150	-1.0520	9	0.38643	T	0.18	.	3.0591	0.06194	0.6127:0.0:0.0:0.3873	.	123	A8MUM7	LEG16_HUMAN	L	123	ENSP00000375904:M123L	ENSP00000375904:M123L	M	+	1	0	LGALS16	44842938	0.014000	0.17966	0.032000	0.17829	0.295000	0.27426	0.444000	0.21661	-0.500000	0.06614	0.163000	0.16589	ATG	A|1.000;C|0.000	0.000	strong		0.428	LGALS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465022.1		
GPR98	84059	hgsc.bcm.edu	37	5	89988504	89988504	+	Missense_Mutation	SNP	A	A	G	rs2366926	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	245	243	0.991837	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	
LPHN1	22859	hgsc.bcm.edu	37	19	14288369	14288369	+	Silent	SNP	C	C	T	rs146417164	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14288369C>T	ENST00000340736.6	-	3	555	c.258G>A	c.(256-258)ccG>ccA	p.P86P	LPHN1_ENST00000361434.3_Silent_p.P86P	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	86	SUEL-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00260}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGAAGGCGTCCGGCAGGTAGC	0.572													C|||	26	0.00519169	0.0	0.0086	5008	,	,		18398	0.002		0.0179	False		,,,				2504	0.0				p.P86P		Atlas-SNP	.											.	LPHN1	107	.	0			c.G258A						PASS	.	C	,	8,4398	14.3+/-33.2	0,8,2195	137.0	114.0	122.0		258,258	-9.7	0.0	19	dbSNP_134	122	104,8496	57.2+/-118.5	1,102,4197	no	coding-synonymous,coding-synonymous	LPHN1	NM_001008701.2,NM_014921.4	,	1,110,6392	TT,TC,CC		1.2093,0.1816,0.8611	,	86/1475,86/1470	14288369	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	22859	exon3			GGCGTCCGGCAGG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.258G>A	19.37:g.14288369C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			C|0.992;T|0.008	0.008	strong		0.572	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
BIRC6	57448	hgsc.bcm.edu	37	2	32713706	32713706	+	Missense_Mutation	SNP	A	A	T	rs2366894	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:32713706A>T	ENST00000421745.2	+	42	8154	c.8020A>T	c.(8020-8022)Act>Tct	p.T2674S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2674				T -> S (in Ref. 2; AAF75772). {ECO:0000305}.	apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.T2674S(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					TTCTAGTTCAACTGGAAACAA	0.308													T|||	2809	0.560903	0.708	0.6398	5008	,	,		15225	0.3433		0.6412	False		,,,				2504	0.4479				p.T2674S	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,0,3	BIRC6	838	3	1	Substitution - Missense(1)	stomach(1)	c.A8020T						scavenged	.	T	SER/THR	2989,1255		1089,811,222	24.0	23.0	23.0		8020	4.5	1.0	2	dbSNP_100	23	5250,3014		1754,1742,636	yes	missense	BIRC6	NM_016252.3	58	2843,2553,858	TT,TA,AA		36.4714,29.5712,34.1302	benign	2674/4858	32713706	8239,4269	2122	4132	6254	SO:0001583	missense	57448	exon42			AGTTCAACTGGAA	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.8020A>T	2.37:g.32713706A>T	ENSP00000393596:p.Thr2674Ser	Somatic	320	3	0.009375		WXS	Illumina HiSeq	Phase_I	309	151	0.488673	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	1262	0.5778388278388278	330	0.6707317073170732	246	0.6795580110497238	209	0.36538461538461536	477	0.6292875989445911	T	3.123	-0.180114	0.06380	0.704288	0.635286	ENSG00000115760	ENST00000421745	T	0.73047	-0.71	5.67	4.48	0.54585	.	0.216003	0.40469	N	0.001086	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	0.46871	-0.9160	9	0.02654	T	1	.	7.3633	0.26758	0.2499:0.0:0.1305:0.6196	rs2366894;rs52828077;rs2366894	2674	Q9NR09	BIRC6_HUMAN	S	2674	ENSP00000393596:T2674S	ENSP00000393596:T2674S	T	+	1	0	BIRC6	32567210	0.994000	0.37717	1.000000	0.80357	0.992000	0.81027	1.242000	0.32755	0.402000	0.25451	-0.257000	0.10917	ACT	A|0.424;T|0.576	0.576	strong		0.308	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
MDH2	4191	hgsc.bcm.edu	37	7	75695613	75695613	+	Missense_Mutation	SNP	A	A	G	rs10256	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:75695613A>G	ENST00000315758.5	+	9	996	c.902A>G	c.(901-903)aAg>aGg	p.K301R	MDH2_ENST00000432020.2_Missense_Mutation_p.K259R|MDH2_ENST00000443006.1_Missense_Mutation_p.K194R	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	301				K -> R (in Ref. 2; BAG56955). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						GGCATCGAGAAGAACCTGGGC	0.507													a|||	103	0.0205671	0.0008	0.0375	5008	,	,		19541	0.0		0.0517	False		,,,				2504	0.0245				p.K301R		Atlas-SNP	.											.	MDH2	35	.	0			c.A902G						PASS	.	A	ARG/LYS	52,4354	52.3+/-87.9	0,52,2151	74.0	72.0	73.0		902	5.4	1.0	7	dbSNP_52	73	416,8184	129.5+/-187.6	9,398,3893	yes	missense	MDH2	NM_005918.2	26	9,450,6044	GG,GA,AA		4.8372,1.1802,3.5983	benign	301/339	75695613	468,12538	2203	4300	6503	SO:0001583	missense	4191	exon9			TCGAGAAGAACCT		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.902A>G	7.37:g.75695613A>G	ENSP00000327070:p.Lys301Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Missense_Mutation	SNP	ENST00000315758.5	37	CCDS5581.1	50	0.022893772893772892	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	36	0.047493403693931395	A	13.61	2.287440	0.40494	0.011802	0.048372	ENSG00000146701	ENST00000315758;ENST00000443006;ENST00000432020	T;T;T	0.68479	-0.33;-0.33;-0.33	5.41	5.41	0.78517	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.000000	0.85682	D	0.000000	T	0.28995	0.0720	L	0.56199	1.76	0.80722	D	1	B;B	0.31581	0.329;0.024	B;B	0.40375	0.327;0.078	T	0.58222	-0.7674	10	0.59425	D	0.04	-13.4249	14.6204	0.68579	1.0:0.0:0.0:0.0	rs10256;rs1133136;rs3178297;rs3194633;rs17350089;rs3178297	259;301	E9PDB2;P40926	.;MDHM_HUMAN	R	301;194;259	ENSP00000327070:K301R;ENSP00000416929:K194R;ENSP00000408649:K259R	ENSP00000327070:K301R	K	+	2	0	MDH2	75533549	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	7.535000	0.82014	2.050000	0.60909	0.533000	0.62120	AAG	A|0.969;G|0.031	0.031	strong		0.507	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1		
XRCC4	7518	hgsc.bcm.edu	37	5	82648977	82648977	+	Silent	SNP	T	T	G	rs1056503	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:82648977T>G	ENST00000511817.1	+	8	1007	c.927T>G	c.(925-927)tcT>tcG	p.S309S	XRCC4_ENST00000396027.4_Silent_p.S307S|XRCC4_ENST00000282268.3_Silent_p.S307S|XRCC4_ENST00000338635.6_Silent_p.S309S			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	309					cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		CTGAGACGTCTAAAAAGGAGC	0.338								Non-homologous end-joining					G|||	1881	0.375599	0.4758	0.3329	5008	,	,		17355	0.7063		0.1402	False		,,,				2504	0.1718				p.S309S		Atlas-SNP	.											.	XRCC4	37	.	0			c.T927G						PASS	.	G	,,	1942,2464	617.9+/-393.1	424,1094,685	113.0	123.0	120.0		921,927,921	1.1	0.0	5	dbSNP_86	120	1055,7543	768.5+/-407.6	63,929,3307	no	coding-synonymous,coding-synonymous,coding-synonymous	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	,,	487,2023,3992	GG,GT,TT		12.2703,44.0763,23.0468	,,	307/335,309/337,307/335	82648977	2997,10007	2203	4299	6502	SO:0001819	synonymous_variant	7518	exon8			GACGTCTAAAAAG	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.927T>G	5.37:g.82648977T>G		Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	252	115	0.456349	NM_022406	A8K3X4|Q9BS72|Q9UP94	Silent	SNP	ENST00000511817.1	37	CCDS4059.1																																																																																			T|0.685;G|0.315	0.315	strong		0.338	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	
KCNU1	157855	hgsc.bcm.edu	37	8	36788597	36788597	+	Missense_Mutation	SNP	G	G	C	rs190224798	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:36788597G>C	ENST00000399881.3	+	25	2902	c.2865G>C	c.(2863-2865)ttG>ttC	p.L955F	KCNU1_ENST00000518904.1_3'UTR	NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	955					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		CGTCGCTCTTGTCTGGAAGAA	0.443													G|||	3	0.000599042	0.0008	0.0014	5008	,	,		17383	0.0		0.0	False		,,,				2504	0.001				p.L955F		Atlas-SNP	.											.	KCNU1	359	.	0			c.G2865C						PASS	.	G	PHE/LEU	4,3820		0,4,1908	137.0	131.0	133.0		2865	0.5	0.0	8		133	18,8248		0,18,4115	yes	missense	KCNU1	NM_001031836.2	22	0,22,6023	CC,CG,GG		0.2178,0.1046,0.182	possibly-damaging	955/1150	36788597	22,12068	1912	4133	6045	SO:0001583	missense	157855	exon25			GCTCTTGTCTGGA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2865G>C	8.37:g.36788597G>C	ENSP00000382770:p.Leu955Phe	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	218	61	0.279817	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.00	1.510137	0.27036	0.001046	0.002178	ENSG00000215262	ENST00000399881	T	0.39229	1.09	5.41	0.468	0.16732	.	2.385820	0.03106	U	0.161774	T	0.44705	0.1306	M	0.73962	2.25	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.34453	-0.9828	10	0.87932	D	0	0.6019	4.979	0.14155	0.0865:0.1259:0.6256:0.162	.	955	A8MYU2	KCNU1_HUMAN	F	955	ENSP00000382770:L955F	ENSP00000382770:L955F	L	+	3	2	KCNU1	36907755	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.833000	0.27504	-0.142000	0.11354	0.650000	0.86243	TTG	G|1.000;C|0.000	0.000	strong		0.443	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
SRP72	6731	hgsc.bcm.edu	37	4	57366826	57366826	+	Silent	SNP	G	G	A	rs143643243	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:57366826G>A	ENST00000342756.5	+	18	2524	c.1803G>A	c.(1801-1803)ggG>ggA	p.G601G	SRP72_ENST00000510663.1_Silent_p.G540G	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	601					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					TTGGAAAAGGGACCCAGGGAG	0.453																																					p.G601G		Atlas-SNP	.											.	SRP72	59	.	0			c.G1803A						PASS	.	G		6,4400	9.9+/-24.2	0,6,2197	51.0	50.0	50.0		1803	3.3	1.0	4	dbSNP_134	50	24,8576	16.6+/-54.9	0,24,4276	no	coding-synonymous	SRP72	NM_006947.3		0,30,6473	AA,AG,GG		0.2791,0.1362,0.2307		601/672	57366826	30,12976	2203	4300	6503	SO:0001819	synonymous_variant	6731	exon18			AAAAGGGACCCAG	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"""Tetratricopeptide (TTC) repeat domain containing"""	11303	protein-coding gene	gene with protein product		602122	"""signal recognition particle 72kD"""			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.1803G>A	4.37:g.57366826G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	118	78	0.661017	NM_006947	G5E9Z8|Q7Z3C0	Silent	SNP	ENST00000342756.5	37	CCDS3506.1																																																																																			G|0.998;A|0.002	0.002	strong		0.453	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
SMCHD1	23347	hgsc.bcm.edu	37	18	2707619	2707619	+	Missense_Mutation	SNP	G	G	A	rs2276092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:2707619G>A	ENST00000320876.6	+	16	2460	c.2122G>A	c.(2122-2124)Gtt>Att	p.V708I	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Missense_Mutation_p.V708I	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	708			V -> I (in dbSNP:rs2276092).		chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						GCCTAATGAGGTTAGGCCTGC	0.363													A|||	3457	0.690296	0.7141	0.7839	5008	,	,		14767	0.6528		0.6909	False		,,,				2504	0.6299				p.V708I		Atlas-SNP	.											.	SMCHD1	88	.	0			c.G2122A						PASS	.	A	ILE/VAL	2659,981		969,721,130	179.0	168.0	171.0		2122	0.4	0.4	18	dbSNP_100	171	5737,2423		2009,1719,352	yes	missense	SMCHD1	NM_015295.2	29	2978,2440,482	AA,AG,GG		29.6936,26.9505,28.8475	benign	708/2006	2707619	8396,3404	1820	4080	5900	SO:0001583	missense	23347	exon16			AATGAGGTTAGGC	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2122G>A	18.37:g.2707619G>A	ENSP00000326603:p.Val708Ile	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	300	141	0.47	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	1490	0.6822344322344323	354	0.7195121951219512	279	0.7707182320441989	348	0.6083916083916084	509	0.6715039577836411	A	11.19	1.566563	0.28003	0.730495	0.703064	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.22539	1.95;1.95	5.46	0.384	0.16244	.	0.723872	0.12914	N	0.428667	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.19031	-1.0318	9	0.18710	T	0.47	-1.9438	11.4814	0.50328	0.4902:0.0:0.5098:0.0	rs2276092;rs61228446;rs2276092	708	A6NHR9	SMHD1_HUMAN	I	708	ENSP00000326603:V708I;ENSP00000261598:V708I	ENSP00000261598:V708I	V	+	1	0	SMCHD1	2697619	0.000000	0.05858	0.397000	0.26308	0.982000	0.71751	0.281000	0.18810	-0.155000	0.11098	-0.360000	0.07572	GTT	G|0.319;A|0.681	0.681	strong		0.363	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
TANGO6	79613	hgsc.bcm.edu	37	16	68893953	68893953	+	Silent	SNP	T	T	C	rs4597312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:68893953T>C	ENST00000261778.1	+	2	273	c.261T>C	c.(259-261)tcT>tcC	p.S87S		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	87						integral component of membrane (GO:0016021)											CACAAAACTCTGTGGATGTCA	0.428													T|||	405	0.0808706	0.0756	0.0663	5008	,	,		20015	0.0883		0.1183	False		,,,				2504	0.0521				p.S87S		Atlas-SNP	.											.	.	.	.	0			c.T261C						PASS	.	T		318,3472		9,300,1586	122.0	115.0	117.0		261	0.3	1.0	16	dbSNP_111	117	1020,7232		65,890,3171	no	coding-synonymous	TMCO7	NM_024562.1		74,1190,4757	CC,CT,TT		12.3606,8.3905,11.1111		87/1095	68893953	1338,10704	1895	4126	6021	SO:0001819	synonymous_variant	79613	exon2			AAACTCTGTGGAT		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 7"""	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.261T>C	16.37:g.68893953T>C		Somatic	301	2	0.00664452		WXS	Illumina HiSeq	Phase_I	249	212	0.851406	NM_024562	Q569F9|Q9H9K1	Silent	SNP	ENST00000261778.1	37	CCDS45516.1																																																																																			T|0.895;C|0.105	0.105	strong		0.428	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2	
SERPINI2	5276	hgsc.bcm.edu	37	3	167184878	167184878	+	Missense_Mutation	SNP	T	T	C	rs9841174	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:167184878T>C	ENST00000476257.1	-	4	741	c.443A>G	c.(442-444)gAg>gGg	p.E148G	SERPINI2_ENST00000264677.4_Missense_Mutation_p.E148G|SERPINI2_ENST00000461846.1_Missense_Mutation_p.E148G|SERPINI2_ENST00000471111.1_Missense_Mutation_p.E148G|SERPINI2_ENST00000465031.1_5'Flank			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	148			E -> G (in dbSNP:rs9841174).		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						ACTTATCATCTCTGCACAAGC	0.338													t|||	2066	0.41254	0.3737	0.379	5008	,	,		14394	0.506		0.4006	False		,,,				2504	0.4049				p.E158G		Atlas-SNP	.											.	SERPINI2	85	.	0			c.A473G						PASS	.	C	GLY/GLU	1610,2796	496.5+/-363.6	307,996,900	93.0	93.0	93.0		443	3.3	1.0	3	dbSNP_119	93	3261,5339	488.2+/-372.3	638,1985,1677	yes	missense	SERPINI2	NM_006217.3	98	945,2981,2577	CC,CT,TT		37.9186,36.5411,37.4519	possibly-damaging	148/406	167184878	4871,8135	2203	4300	6503	SO:0001583	missense	5276	exon4			ATCATCTCTGCAC	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.443A>G	3.37:g.167184878T>C	ENSP00000420621:p.Glu148Gly	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	929	0.42536630036630035	202	0.4105691056910569	144	0.39779005524861877	282	0.493006993006993	301	0.3970976253298153	t	15.95	2.984489	0.53934	0.365411	0.379186	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111;ENST00000466903;ENST00000467583	D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.7	3.34	0.38264	Serpin domain (3);	0.464061	0.24613	N	0.037024	T	0.00012	0.0000	L	0.42632	1.34	0.43683	P	0.003878999999999966	P	0.40578	0.722	B	0.43990	0.438	T	0.30238	-0.9985	9	0.52906	T	0.07	.	10.0587	0.42261	0.0:0.1354:0.0:0.8646	rs9841174;rs52836184;rs61562449;rs9841174	148	O75830	SPI2_HUMAN	G	148;148;148;148;148;133	ENSP00000420621:E148G;ENSP00000417692:E148G;ENSP00000264677:E148G;ENSP00000419407:E148G;ENSP00000417752:E148G;ENSP00000419255:E133G	ENSP00000264677:E148G	E	-	2	0	SERPINI2	168667572	1.000000	0.71417	0.966000	0.40874	0.567000	0.35839	2.515000	0.45512	0.452000	0.26830	-0.253000	0.11424	GAG	C|0.395;N|0.001	0.395	strong		0.338	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
MLLT4	4301	hgsc.bcm.edu	37	6	168315978	168315978	+	Silent	SNP	G	G	C	rs3213590	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168315978G>C	ENST00000447894.2	+	18	2409	c.2409G>C	c.(2407-2409)gtG>gtC	p.V803V	MLLT4_ENST00000366806.2_Silent_p.V803V|MLLT4_ENST00000344191.4_Silent_p.V803V|MLLT4_ENST00000351017.4_Silent_p.V810V|MLLT4_ENST00000400822.3_Silent_p.V802V|MLLT4_ENST00000392108.3_Silent_p.V803V|MLLT4_ENST00000392112.1_Silent_p.V787V			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	803	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		ATAGATTGGTGACCGACCCAG	0.547			T	MLL	AL								G|||	946	0.188898	0.2103	0.2104	5008	,	,		19363	0.1954		0.0775	False		,,,				2504	0.2526				p.V803V		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	.	MLLT4	351	.	0			c.G2409C						PASS	.	G	,	723,3683	300.1+/-286.2	51,621,1531	122.0	96.0	105.0		2409,2361	-1.4	0.7	6	dbSNP_106	105	678,7922	170.7+/-221.8	26,626,3648	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	77,1247,5179	CC,CG,GG		7.8837,16.4094,10.772	,	803/1652,787/1744	168315978	1401,11605	2203	4300	6503	SO:0001819	synonymous_variant	4301	exon18			ATTGGTGACCGAC	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.2409G>C	6.37:g.168315978G>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	200	79	0.395	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				G|0.880;C|0.120	0.120	strong		0.547	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
MMEL1	79258	hgsc.bcm.edu	37	1	2535613	2535613	+	Silent	SNP	C	C	A	rs4648562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:2535613C>A	ENST00000378412.3	-	10	1085	c.924G>T	c.(922-924)gtG>gtT	p.V308V	MMEL1_ENST00000502556.1_Intron|MMEL1_ENST00000288709.6_Silent_p.V299V			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	308						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)		CCAGCTCCAGCACCTGCACCA	0.677													C|||	2484	0.496006	0.6112	0.4481	5008	,	,		12736	0.5288		0.3121	False		,,,				2504	0.5297				p.V308V		Atlas-SNP	.											.	MMEL1	64	.	0			c.G924T						PASS	.	C		2518,1888		728,1062,413	36.0	36.0	36.0		924	3.5	1.0	1	dbSNP_111	36	2731,5867		435,1861,2003	no	coding-synonymous	MMEL1	NM_033467.3		1163,2923,2416	AA,AC,CC		31.7632,42.8507,40.3645		308/780	2535613	5249,7755	2203	4299	6502	SO:0001819	synonymous_variant	79258	exon10			CTCCAGCACCTGC	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.924G>T	1.37:g.2535613C>A		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	140	31	0.221429	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	37	CCDS30569.2	947	0.4336080586080586	289	0.5873983739837398	150	0.4143646408839779	271	0.4737762237762238	237	0.31266490765171506	C	0.350	-0.945647	0.02304	0.571493	0.317632	ENSG00000142606	ENST00000378411	.	.	.	4.43	3.52	0.40303	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999879	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.4639	0.04548	0.1496:0.533:0.1454:0.1719	rs4648562	.	.	.	.	-1	.	.	.	-	.	.	MMEL1	2525473	0.994000	0.37717	0.999000	0.59377	0.089000	0.18198	0.369000	0.20416	0.930000	0.37217	-0.687000	0.03738	.	C|0.594;A|0.406	0.406	strong		0.677	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
CFB	629	hgsc.bcm.edu	37	6	31915614	31915614	+	Missense_Mutation	SNP	G	G	A	rs4151651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31915614G>A	ENST00000425368.2	+	5	1267	c.754G>A	c.(754-756)Ggc>Agc	p.G252S	CFB_ENST00000497841.1_3'UTR|CFB_ENST00000456570.1_Missense_Mutation_p.G754S|CFB_ENST00000477310.1_Missense_Mutation_p.G603S|CFB_ENST00000556679.1_Missense_Mutation_p.G754S	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	252			G -> S (in dbSNP:rs4151651). {ECO:0000269|Ref.7}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						GGATGGGCACGGCCCAGGTTT	0.567													G|||	51	0.0101837	0.0008	0.0274	5008	,	,		19687	0.0		0.0288	False		,,,				2504	0.002				p.G252S		Atlas-SNP	.											.	CFB	33	.	0			c.G754A						PASS	.	G	SER/GLY	27,2995		0,27,1484	149.0	161.0	156.0		754	2.8	1.0	6	dbSNP_110	156	211,5207		6,199,2504	yes	missense	CFB	NM_001710.5	56	6,226,3988	AA,AG,GG		3.8944,0.8934,2.8199	benign	252/765	31915614	238,8202	1511	2709	4220	SO:0001583	missense	629	exon5			GGGCACGGCCCAG	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"""Complement system"""	1037	protein-coding gene	gene with protein product		138470	"""B-factor, properdin"""	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.754G>A	6.37:g.31915614G>A	ENSP00000416561:p.Gly252Ser	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	37	CCDS4729.1	29	0.013278388278388278	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	23	0.030343007915567283	G	4.690	0.128284	0.08981	0.008934	0.038944	ENSG00000243649;ENSG00000243649;ENSG00000244255;ENSG00000244255	ENST00000556679;ENST00000425368;ENST00000456570;ENST00000477310	T;T;T;T	0.80566	-1.39;-1.28;-1.39;-1.37	5.21	2.83	0.33086	.	0.292737	0.30043	N	0.010547	T	0.28267	0.0698	N	0.03608	-0.345	0.22156	N	0.999324	B;B;B	0.15473	0.013;0.0;0.002	B;B;B	0.04013	0.001;0.0;0.0	T	0.36915	-0.9728	10	0.07482	T	0.82	-8.5672	6.7055	0.23248	0.815:0.0:0.185:0.0	rs4151651;rs52792988;rs4151651	754;252;252	B4E1Z4;P00751;P00751-2	.;CFAB_HUMAN;.	S	754;252;754;603	ENSP00000451848:G754S;ENSP00000416561:G252S;ENSP00000410815:G754S;ENSP00000418996:G603S	ENSP00000416561:G252S	G	+	1	0	CFB;XXbac-BPG116M5.17	32023593	0.906000	0.30813	1.000000	0.80357	0.966000	0.64601	1.254000	0.32897	0.445000	0.26639	-0.294000	0.09567	GGC	G|0.978;A|0.022	0.022	strong		0.567	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710	
C10orf53	282966	hgsc.bcm.edu	37	10	50901938	50901938	+	Splice_Site	SNP	C	C	T	rs1133837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50901938C>T	ENST00000374111.3	+	2	228	c.216C>T	c.(214-216)ttC>ttT	p.F72F	C10orf53_ENST00000374112.3_Splice_Site_p.F72F|C10orf53_ENST00000535836.1_Splice_Site_p.F72F|C10orf53_ENST00000374113.3_Silent_p.F72F	NM_001042427.1	NP_001035892.1	Q8N6V4	CJ053_HUMAN	chromosome 10 open reading frame 53	72										endometrium(1)|lung(6)	7		all_neural(218;0.107)				ACTTGGAGTTCGGTAAGCCCT	0.453													C|||	1768	0.353035	0.3707	0.3732	5008	,	,		23180	0.1389		0.4761	False		,,,				2504	0.409				p.F72F		Atlas-SNP	.											.	C10orf53	19	.	0			c.C216T						PASS	.	C	,	1676,2730	508.9+/-367.1	324,1028,851	169.0	155.0	160.0		216,216	-1.3	1.0	10	dbSNP_86	160	4053,4547	559.2+/-387.4	939,2175,1186	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	C10orf53	NM_001042427.1,NM_182554.2	,	1263,3203,2037	TT,TC,CC		47.1279,38.039,44.0489	,	72/94,72/158	50901938	5729,7277	2203	4300	6503	SO:0001630	splice_region_variant	282966	exon2			GGAGTTCGGTAAG	BC028127	CCDS31202.1, CCDS41521.1	10q11.23	2012-05-24			ENSG00000178645	ENSG00000178645			27421	protein-coding gene	gene with protein product						12477932	Standard	NM_182554		Approved	Em:AC069546.1	uc001jid.1	Q8N6V4	OTTHUMG00000018199	ENST00000374111.3:c.217+1C>T	10.37:g.50901938C>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	101	74	0.732673	NM_182554	A6NI81|A6NLE0|B9ZVK6	Silent	SNP	ENST00000374111.3	37	CCDS41521.1																																																																																			C|0.595;T|0.405	0.405	strong		0.453	C10orf53-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048005.1	NM_182554	Silent
ANKRD13C	81573	hgsc.bcm.edu	37	1	70820008	70820008	+	Silent	SNP	C	C	T	rs61782675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:70820008C>T	ENST00000370944.4	-	1	397	c.84G>A	c.(82-84)gaG>gaA	p.E28E	HHLA3_ENST00000361764.4_5'Flank|HHLA3_ENST00000370940.5_5'Flank|HHLA3_ENST00000531950.1_5'Flank|ANKRD13C_ENST00000262346.6_Silent_p.E28E|HHLA3_ENST00000432224.1_5'Flank|HHLA3_ENST00000359875.5_5'Flank	NM_030816.4	NP_110443.3	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C	28					protein retention in ER lumen (GO:0006621)|regulation of anoikis (GO:2000209)|regulation of receptor biosynthetic process (GO:0010869)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	19						CCGCCGCTTCCTCATCCCCGG	0.622													C|||	471	0.0940495	0.0325	0.0908	5008	,	,		16430	0.0645		0.1054	False		,,,				2504	0.1984				p.E28E		Atlas-SNP	.											.	ANKRD13C	36	.	0			c.G84A						PASS	.	C		171,4235		5,161,2037	34.0	41.0	39.0		84	1.8	1.0	1	dbSNP_129	39	763,7833		28,707,3563	no	coding-synonymous	ANKRD13C	NM_030816.4		33,868,5600	TT,TC,CC		8.8762,3.8811,7.1835		28/542	70820008	934,12068	2203	4298	6501	SO:0001819	synonymous_variant	81573	exon1			CGCTTCCTCATCC		CCDS648.2	1p32.3-p31.3	2013-01-10			ENSG00000118454	ENSG00000118454		"""Ankyrin repeat domain containing"""	25374	protein-coding gene	gene with protein product		615125				11230166	Standard	NM_030816		Approved	DKFZP566D1346, dJ677H15.3	uc001dex.4	Q8N6S4	OTTHUMG00000009343	ENST00000370944.4:c.84G>A	1.37:g.70820008C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	29	7	0.241379	NM_030816	B3KQ97|Q5VYH4|Q5VYH5|Q6PJE4|Q9H0N9	Silent	SNP	ENST00000370944.4	37	CCDS648.2																																																																																			C|0.928;T|0.072	0.072	strong		0.622	ANKRD13C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025903.1	NM_030816	
ASPHD1	253982	hgsc.bcm.edu	37	16	29917177	29917177	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:29917177G>A	ENST00000308748.5	+	3	1384	c.1132G>A	c.(1132-1134)Gag>Aag	p.E378K	ASPHD1_ENST00000483405.1_Missense_Mutation_p.E97K	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	378					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						GGCAGGGGCTGAGCGCCAGGC	0.637																																					p.E378K		Atlas-SNP	.											.	ASPHD1	28	.	0			c.G1132A						PASS	.						70.0	60.0	64.0					16																	29917177		2197	4300	6497	SO:0001583	missense	253982	exon3			GGGGCTGAGCGCC	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.1132G>A	16.37:g.29917177G>A	ENSP00000311447:p.Glu378Lys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_181718	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	Missense_Mutation	SNP	ENST00000308748.5	37	CCDS10660.1	.	.	.	.	.	.	.	.	.	.	G	36	5.897740	0.97081	.	.	ENSG00000174939	ENST00000414952;ENST00000308748	T;T	0.59364	0.27;0.27	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.80177	0.4575	M	0.86953	2.85	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.82938	-0.0209	10	0.87932	D	0	-22.1497	18.742	0.91777	0.0:0.0:1.0:0.0	.	378	Q5U4P2	ASPH1_HUMAN	K	378	ENSP00000388036:E378K;ENSP00000311447:E378K	ENSP00000311447:E378K	E	+	1	0	ASPHD1	29824678	1.000000	0.71417	0.923000	0.36655	0.980000	0.70556	9.149000	0.94659	2.728000	0.93425	0.655000	0.94253	GAG	.	.	none		0.637	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718	
MGMT	4255	hgsc.bcm.edu	37	10	131565064	131565064	+	Missense_Mutation	SNP	A	A	G	rs2308321	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:131565064A>G	ENST00000306010.7	+	5	552	c.520A>G	c.(520-522)Atc>Gtc	p.I174V	RP11-109A6.3_ENST00000428273.1_lincRNA	NM_002412.3	NP_002403.2	P16455	MGMT_HUMAN	O-6-methylguanine-DNA methyltransferase	143					cellular response to ionizing radiation (GO:0071479)|cellular response to organic cyclic compound (GO:0071407)|cellular response to oxidative stress (GO:0034599)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA ligation (GO:0006266)|DNA methylation (GO:0006306)|DNA repair (GO:0006281)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to toxic substance (GO:0009636)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methylated-DNA-[protein]-cysteine S-methyltransferase activity (GO:0003908)|methyltransferase activity (GO:0008168)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	10		all_cancers(35;9.44e-09)|all_epithelial(44;6.98e-08)|Lung NSC(174;0.0157)|all_lung(145;0.0201)|all_neural(114;0.0732)|Colorectal(57;0.0792)|Breast(234;0.167)		OV - Ovarian serous cystadenocarcinoma(35;0.00291)	L-Cysteine(DB00151)	CCCCATCCTCATCCCGTGCCA	0.622								Direct reversal of damage					A|||	257	0.0513179	0.0061	0.0519	5008	,	,		18377	0.0139		0.1362	False		,,,				2504	0.0634				p.I174V		Atlas-SNP	.											.	MGMT	32	.	0			c.A520G	GRCh37	CM004820	MGMT	M	rs2308321	PASS	.	A	VAL/ILE	99,4305	74.7+/-112.8	0,99,2103	32.0	30.0	31.0		520	-0.4	1.0	10	dbSNP_100	31	1104,7496	215.5+/-254.8	70,964,3266	yes	missense	MGMT	NM_002412.3	29	70,1063,5369	GG,GA,AA		12.8372,2.248,9.251	benign	174/239	131565064	1203,11801	2202	4300	6502	SO:0001583	missense	4255	exon5			ATCCTCATCCCGT	M29971	CCDS7660.2	10q26	2005-10-06			ENSG00000170430	ENSG00000170430			7059	protein-coding gene	gene with protein product		156569					Standard	NM_002412		Approved		uc001lkh.2	P16455	OTTHUMG00000019261	ENST00000306010.7:c.520A>G	10.37:g.131565064A>G	ENSP00000302111:p.Ile174Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	143	64	0.447552	NM_002412	Q5VY78	Missense_Mutation	SNP	ENST00000306010.7	37	CCDS7660.2	141	0.06456043956043957	5	0.01016260162601626	23	0.06353591160220995	6	0.01048951048951049	107	0.14116094986807387	A	2.658	-0.280507	0.05642	0.02248	0.128372	ENSG00000170430	ENST00000306010	T	0.13657	2.57	4.92	-0.425	0.12317	.	0.273464	0.34338	N	0.004049	T	0.00039	0.0001	N	0.10645	0.015	0.45490	D	0.998456	B	0.19331	0.035	B	0.19391	0.025	T	0.48091	-0.9065	10	0.02654	T	1	.	9.1823	0.37149	0.6831:0.0:0.3169:0.0	rs2308321;rs17406533;rs60279652;rs2308321	174	B4DEE8	.	V	174	ENSP00000302111:I174V	ENSP00000302111:I174V	I	+	1	0	MGMT	131455054	0.964000	0.33143	0.998000	0.56505	0.356000	0.29392	1.655000	0.37345	-0.047000	0.13423	-0.464000	0.05259	ATC	A|0.927;G|0.073	0.073	strong		0.622	MGMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051009.3	NM_002412	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238672703	238672703	+	Missense_Mutation	SNP	C	C	G	rs3739038	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238672703C>G	ENST00000392000.4	+	11	2464	c.2347C>G	c.(2347-2349)Cac>Gac	p.H783D	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000289175.6_Missense_Mutation_p.H727D|LRRFIP1_ENST00000244815.5_Missense_Mutation_p.H759D	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	783			H -> D (in dbSNP:rs3739038).		innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		AGAGCCAGGGCACTTCAATCC	0.512													G|||	1803	0.360024	0.3563	0.3026	5008	,	,		20722	0.505		0.2495	False		,,,				2504	0.3701				p.H783D		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.C2347G						PASS	.	G	,,ASP/HIS,ASP/HIS,ASP/HIS	1635,2771	659.0+/-400.5	319,997,887	78.0	77.0	77.0		,,2347,2179,2275	1.5	0.0	2	dbSNP_107	77	2004,6596	721.6+/-406.4	219,1566,2515	yes	intron,intron,missense,missense,missense	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,81,81,81	538,2563,3402	GG,GC,CC		23.3023,37.1085,27.9794	,,benign,benign,benign	,,783/809,727/753,759/785	238672703	3639,9367	2203	4300	6503	SO:0001583	missense	9208	exon11			CCAGGGCACTTCA	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"""GC-binding factor 2"""	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.2347C>G	2.37:g.238672703C>G	ENSP00000375857:p.His783Asp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_001137552	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000392000.4	37	CCDS46552.1	811	0.37133699633699635	198	0.4024390243902439	115	0.31767955801104975	318	0.5559440559440559	180	0.23746701846965698	G	0.088	-1.172355	0.01646	0.371085	0.233023	ENSG00000124831	ENST00000289175;ENST00000244815;ENST00000392000	T;T;T	0.06768	3.27;3.27;3.26	5.34	1.5	0.22942	.	8.116580	0.00166	N	0.000000	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	0.45629	-0.9248	9	0.02654	T	1	-13.1981	1.2179	0.01918	0.3763:0.1334:0.3364:0.1539	rs3739038;rs52824301;rs58509875;rs3739038	727;783;759	Q32MZ4-3;Q32MZ4;Q32MZ4-2	.;LRRF1_HUMAN;.	D	727;759;783	ENSP00000289175:H727D;ENSP00000244815:H759D;ENSP00000375857:H783D	ENSP00000244815:H759D	H	+	1	0	LRRFIP1	238337442	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.219000	0.17641	0.268000	0.21939	-0.120000	0.15030	CAC	C|0.687;G|0.312	0.312	strong		0.512	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
CCDC180	100499483	hgsc.bcm.edu	37	9	100105782	100105782	+	Missense_Mutation	SNP	C	C	G	rs2061634	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100105782C>G	ENST00000357054.1	+	33	3919	c.2984C>G	c.(2983-2985)tCc>tGc	p.S995C	CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000411667.2_Missense_Mutation_p.S853C|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Missense_Mutation_p.S856C|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_Missense_Mutation_p.S856C			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	995			S -> C (in dbSNP:rs2061634).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											AACGACACTTCCAGTGCCAAG	0.383													C|||	1394	0.278355	0.41	0.304	5008	,	,		19363	0.1835		0.1998	False		,,,				2504	0.2607				p.S856C		Atlas-SNP	.											.	.	.	.	0			c.C2567G						PASS	.	C	CYS/SER	1846,2560	537.6+/-374.8	400,1046,757	100.0	94.0	96.0		2567	1.9	0.0	9	dbSNP_94	96	2349,6251	392.1+/-343.9	320,1709,2271	yes	missense	C9orf174	NM_020893.2	112	720,2755,3028	GG,GC,CC		27.314,41.8974,32.2543	benign	856/1702	100105782	4195,8811	2203	4300	6503	SO:0001583	missense	0	exon19			ACACTTCCAGTGC	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.2984C>G	9.37:g.100105782C>G	ENSP00000349562:p.Ser995Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		542	0.24816849816849818	207	0.42073170731707316	88	0.2430939226519337	106	0.1853146853146853	141	0.18601583113456466	C	15.07	2.723583	0.48728	0.418974	0.27314	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T	0.13307	2.9;2.9;2.6;2.9	5.39	1.93	0.25924	.	1.074820	0.07175	N	0.853079	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B;B	0.17038	0.02;0.012;0.02	B;B;B	0.17098	0.017;0.01;0.017	T	0.47761	-0.9092	9	0.52906	T	0.07	-0.9304	4.218	0.10544	0.0:0.5169:0.2133:0.2698	rs2061634;rs2061634	879;995;995	Q86Y65;B7ZMG3;Q9P1Z9	.;.;CI174_HUMAN	C	995;856;853;879;856	ENSP00000349562:S995C;ENSP00000364348:S856C;ENSP00000414000:S853C;ENSP00000434727:S856C	ENSP00000349562:S995C	S	+	2	0	C9orf174	99145603	0.001000	0.12720	0.002000	0.10522	0.059000	0.15707	0.649000	0.24843	0.490000	0.27771	0.655000	0.94253	TCC	C|0.698;G|0.302	0.302	strong		0.383	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
CPED1	79974	hgsc.bcm.edu	37	7	120737809	120737809	+	Missense_Mutation	SNP	C	C	T	rs144805034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:120737809C>T	ENST00000310396.5	+	6	1140	c.673C>T	c.(673-675)Ccg>Tcg	p.P225S	CPED1_ENST00000450913.2_Missense_Mutation_p.P225S|CPED1_ENST00000423795.1_Missense_Mutation_p.P5S	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	225						endoplasmic reticulum (GO:0005783)											GCAATTAAAGCCGAGTACTTC	0.428													C|||	5	0.000998403	0.0	0.0	5008	,	,		18641	0.0		0.005	False		,,,				2504	0.0				p.P225S		Atlas-SNP	.											.	.	.	.	0			c.C673T						PASS	.	C	SER/PRO,SER/PRO	6,4400	11.4+/-27.6	0,6,2197	148.0	144.0	146.0		673,673	4.8	0.0	7	dbSNP_134	146	58,8542	36.4+/-91.3	0,58,4242	yes	missense,missense	C7orf58	NM_001105533.1,NM_024913.4	74,74	0,64,6439	TT,TC,CC		0.6744,0.1362,0.4921	possibly-damaging,possibly-damaging	225/784,225/1027	120737809	64,12942	2203	4300	6503	SO:0001583	missense	79974	exon5			TTAAAGCCGAGTA		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.673C>T	7.37:g.120737809C>T	ENSP00000309772:p.Pro225Ser	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	89	73	0.820225	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	13.55	2.271428	0.40194	0.001362	0.006744	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000423795;ENST00000443817	T;T;T;T;T	0.43294	0.95;0.95;0.95;2.02;1.61	5.75	4.82	0.62117	.	1.300280	0.04908	N	0.452653	T	0.30324	0.0761	L	0.40543	1.245	0.24671	N	0.993418	P;B;B	0.39216	0.664;0.435;0.116	B;B;B	0.38500	0.275;0.157;0.043	T	0.11767	-1.0574	10	0.18710	T	0.47	-16.7029	11.2559	0.49054	0.1821:0.8179:0.0:0.0	.	5;225;225	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	S	225;225;225;5;5	ENSP00000309772:P225S;ENSP00000398082:P225S;ENSP00000406122:P225S;ENSP00000415573:P5S;ENSP00000391952:P5S	ENSP00000309772:P225S	P	+	1	0	C7orf58	120525045	0.038000	0.19896	0.015000	0.15790	0.699000	0.40488	0.642000	0.24735	2.710000	0.92621	0.557000	0.71058	CCG	C|0.996;T|0.004	0.004	strong		0.428	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
SIRPA	140885	hgsc.bcm.edu	37	20	1895889	1895889	+	Missense_Mutation	SNP	G	G	C	rs72620874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1895889G>C	ENST00000358771.4	+	2	376	c.224G>C	c.(223-225)gGc>gCc	p.G75A	SIRPA_ENST00000356025.3_Missense_Mutation_p.G75A|SIRPA_ENST00000400068.3_Missense_Mutation_p.G75A	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	75	Ig-like V-type.		G -> A (in dbSNP:rs1057114). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.G75A(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GCTGGACCAGGCCGGGAATTA	0.537													G|||	2164	0.432109	0.298	0.4553	5008	,	,		14136	0.6369		0.3588	False		,,,				2504	0.4611				p.G75A	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,right_upper_lobe,carcinoma,+1,3	SIRPA	83	3	1	Substitution - Missense(1)	pancreas(1)	c.G224C						PASS	.						68.0	62.0	64.0					20																	1895889		2203	4297	6500	SO:0001583	missense	140885	exon3			GACCAGGCCGGGA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.224G>C	20.37:g.1895889G>C	ENSP00000351621:p.Gly75Ala	Somatic	377	0	0		WXS	Illumina HiSeq	Phase_I	207	24	0.115942	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	952	0.4358974358974359	153	0.31097560975609756	151	0.4171270718232044	373	0.6520979020979021	275	0.3627968337730871	G	8.882	0.951948	0.18431	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.66995	-0.24;-0.24;-0.24	5.11	-1.44	0.08856	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.281220	0.04967	N	0.463081	T	0.00012	0.0000	L	0.60957	1.885	0.80722	P	0.0	B;B;B	0.22851	0.0;0.076;0.001	B;B;B	0.26416	0.02;0.069;0.012	T	0.48514	-0.9029	9	0.37606	T	0.19	.	8.9336	0.35686	0.7056:0.0:0.2944:0.0	.	55;75;75	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	A	75	ENSP00000382941:G75A;ENSP00000348307:G75A;ENSP00000351621:G75A	ENSP00000348307:G75A	G	+	2	0	SIRPA	1843889	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.791000	0.04599	-0.225000	0.09913	-0.266000	0.10368	GGC	G|0.689;C|0.311	0.311	strong		0.537	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
YTHDC2	64848	hgsc.bcm.edu	37	5	112926755	112926755	+	Silent	SNP	G	G	A	rs2303718	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:112926755G>A	ENST00000161863.4	+	27	4056	c.3843G>A	c.(3841-3843)tcG>tcA	p.S1281S		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	1281	Ser-rich.				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)		AATCTCCTTCGCCAAGACCAA	0.368													G|||	653	0.130391	0.3162	0.0634	5008	,	,		17480	0.1012		0.0497	False		,,,				2504	0.0399				p.S1281S		Atlas-SNP	.											YTHDC2,NS,carcinoma,+1,1	YTHDC2	118	1	0			c.G3843A						PASS	.	G		1164,3240	399.2+/-331.1	161,842,1199	50.0	50.0	50.0		3843	1.6	1.0	5	dbSNP_100	50	452,8148	134.9+/-192.2	14,424,3862	no	coding-synonymous	YTHDC2	NM_022828.3		175,1266,5061	AA,AG,GG		5.2558,26.4305,12.4269		1281/1431	112926755	1616,11388	2202	4300	6502	SO:0001819	synonymous_variant	64848	exon27			TCCTTCGCCAAGA	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.3843G>A	5.37:g.112926755G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			G|0.869;T|0.001	.	strong		0.368	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
NAT16	375607	hgsc.bcm.edu	37	7	100815816	100815816	+	Silent	SNP	C	C	T	rs12540617	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100815816C>T	ENST00000300303.2	-	4	892	c.654G>A	c.(652-654)gaG>gaA	p.E218E	NAT16_ENST00000455377.1_Silent_p.E218E	NM_198571.2	NP_940973.2	Q8N8M0	NAT16_HUMAN	N-acetyltransferase 16 (GCN5-related, putative)	218							N-acetyltransferase activity (GO:0008080)										CGCCGCCTGCCTCGGACACGG	0.731													C|||	314	0.0626997	0.0023	0.3098	5008	,	,		13813	0.0258		0.0378	False		,,,				2504	0.0327				p.E218E		Atlas-SNP	.											.	.	.	.	0			c.G654A						PASS	.	C		50,4010		0,50,1980	7.0	7.0	7.0		654	2.2	0.1	7	dbSNP_120	7	354,7714		11,332,3691	no	coding-synonymous	C7orf52	NM_198571.2		11,382,5671	TT,TC,CC		4.3877,1.2315,3.3311		218/370	100815816	404,11724	2030	4034	6064	SO:0001819	synonymous_variant	375607	exon4			GCCTGCCTCGGAC	AK096556	CCDS5713.1	7q22.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000167011	ENSG00000167011			22030	protein-coding gene	gene with protein product		615783	"""chromosome 7 open reading frame 52"""	C7orf52			Standard	NM_198571		Approved	FLJ39237	uc003uxy.2	Q8N8M0	OTTHUMG00000157110	ENST00000300303.2:c.654G>A	7.37:g.100815816C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	7	4	0.571429	NM_198571	B3KRS2|Q8NDR1	Silent	SNP	ENST00000300303.2	37	CCDS5713.1																																																																																			C|0.940;T|0.060	0.060	strong		0.731	NAT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347465.1	NM_198571	
ESYT2	57488	hgsc.bcm.edu	37	7	158534372	158534372	+	Silent	SNP	G	G	A	rs57686648	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:158534372G>A	ENST00000251527.5	-	17	2156	c.2091C>T	c.(2089-2091)gcC>gcT	p.A697A	ESYT2_ENST00000435514.2_Silent_p.A132A	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	725					endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CCTGAGGGCCGGCCTCAGGGG	0.657													G|||	1602	0.319888	0.3563	0.183	5008	,	,		15920	0.5774		0.166	False		,,,				2504	0.2607				p.A697A		Atlas-SNP	.											ESYT2,NS,malignant_melanoma,-1,1	ESYT2	70	1	0			c.C2091T						scavenged	.			1358,3048	447.1+/-348.2	215,928,1060	34.0	37.0	36.0		2091	2.1	0.7	7	dbSNP_129	36	1344,7256	258.7+/-282.2	100,1144,3056	no	coding-synonymous	ESYT2	NM_020728.2		315,2072,4116	AA,AG,GG		15.6279,30.8216,20.775		697/894	158534372	2702,10304	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon17			AGGGCCGGCCTCA	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2091C>T	7.37:g.158534372G>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	71	47	0.661972	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			G|0.759;A|0.241	0.241	strong		0.657	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
IQCC	55721	hgsc.bcm.edu	37	1	32672908	32672908	+	Missense_Mutation	SNP	T	T	G	rs3903683	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32672908T>G	ENST00000291358.6	+	5	647	c.626T>G	c.(625-627)tTc>tGc	p.F209C	IQCC_ENST00000537469.1_Missense_Mutation_p.F289C|RP4-622L5.7_ENST00000373604.4_RNA|RP4-622L5.7_ENST00000421616.1_RNA|DCDC2B_ENST00000409358.1_5'Flank	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	209			F -> C (in dbSNP:rs3903683). {ECO:0000269|Ref.2}.							endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CCCCGCGTGTTCCTAGAACAT	0.547													G|||	1139	0.227436	0.3056	0.2378	5008	,	,		17838	0.2302		0.0567	False		,,,				2504	0.2873				p.F289C		Atlas-SNP	.											.	IQCC	46	.	0			c.T866G						PASS	.	G	CYS/PHE,CYS/PHE	1285,3121	699.3+/-406.5	211,863,1129	69.0	69.0	69.0		626,866	2.3	0.0	1	dbSNP_108	69	560,8040	794.2+/-407.5	19,522,3759	yes	missense,missense	IQCC	NM_018134.2,NM_001160042.1	205,205	230,1385,4888	GG,GT,TT		6.5116,29.1648,14.1858	benign,benign	209/467,289/547	32672908	1845,11161	2203	4300	6503	SO:0001583	missense	55721	exon5			GCGTGTTCCTAGA	AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.626T>G	1.37:g.32672908T>G	ENSP00000291358:p.Phe209Cys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	110	88	0.8	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Missense_Mutation	SNP	ENST00000291358.6	37	CCDS355.1	379	0.17353479853479853	152	0.3089430894308943	55	0.15193370165745856	127	0.22202797202797203	45	0.059366754617414245	G	0.013	-1.607113	0.00842	0.291648	0.065116	ENSG00000160051	ENST00000537469;ENST00000291358	T;T	0.08282	3.11;3.11	3.46	2.32	0.28847	.	0.368381	0.20522	N	0.090682	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	0.44982	-0.9292	9	0.02654	T	1	-0.5815	2.9321	0.05803	0.187:0.0:0.5649:0.2481	rs3903683;rs61163302;rs3903683	289;209	F5H7T8;Q4KMZ1	.;IQCC_HUMAN	C	289;209	ENSP00000442291:F289C;ENSP00000291358:F209C	ENSP00000291358:F209C	F	+	2	0	IQCC	32445495	0.023000	0.18921	0.001000	0.08648	0.011000	0.07611	1.192000	0.32150	0.305000	0.22832	-0.217000	0.12591	TTC	T|0.842;G|0.158	0.158	strong		0.547	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134	
PEBP4	157310	hgsc.bcm.edu	37	8	22571018	22571018	+	Silent	SNP	A	A	G	rs1047398	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:22571018A>G	ENST00000256404.6	-	7	640	c.549T>C	c.(547-549)cgT>cgC	p.R183R	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	183						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)		CCAGGTGGAAACGGTTCAGAA	0.562													G|||	1437	0.286941	0.2436	0.4582	5008	,	,		16946	0.2996		0.3231	False		,,,				2504	0.1738				p.R183R		Atlas-SNP	.											.	PEBP4	23	.	0			c.T549C						PASS	.	G		1036,2908		136,764,1072	77.0	79.0	79.0		549	-1.4	0.0	8	dbSNP_86	79	2614,5702		402,1810,1946	no	coding-synonymous	PEBP4	NM_144962.2		538,2574,3018	GG,GA,AA		31.4334,26.2677,29.7716		183/228	22571018	3650,8610	1972	4158	6130	SO:0001819	synonymous_variant	157310	exon7			GTGGAAACGGTTC	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.549T>C	8.37:g.22571018A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	203	122	0.600985	NM_144962	Q5EVA1|Q8WW74	Silent	SNP	ENST00000256404.6	37	CCDS43724.1																																																																																			A|0.697;G|0.303	0.303	strong		0.562	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
TEP1	7011	hgsc.bcm.edu	37	14	20845521	20845521	+	Silent	SNP	A	A	C	rs2229101	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20845521A>C	ENST00000262715.5	-	41	6046	c.6006T>G	c.(6004-6006)ctT>ctG	p.L2002L	TEP1_ENST00000556935.1_Silent_p.L1894L|TEP1_ENST00000545983.1_Silent_p.L340L	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2002					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)		AGAGGGACTGAAGGGAGCATT	0.587													A|||	295	0.0589058	0.09	0.036	5008	,	,		14898	0.002		0.0676	False		,,,				2504	0.0828				p.L2002L		Atlas-SNP	.											.	TEP1	224	.	0			c.T6006G						PASS	.	A		370,4036	189.2+/-215.4	17,336,1850	58.0	51.0	53.0		6006	-3.9	0.2	14	dbSNP_98	53	567,8033	153.4+/-207.8	19,529,3752	no	coding-synonymous	TEP1	NM_007110.4		36,865,5602	CC,CA,AA		6.593,8.3976,7.2044		2002/2628	20845521	937,12069	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon41			GGACTGAAGGGAG		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.6006T>G	14.37:g.20845521A>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	144	95	0.659722	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			A|0.936;C|0.064	0.064	strong		0.587	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
NREP	9315	hgsc.bcm.edu	37	5	111066697	111066697	+	Missense_Mutation	SNP	T	T	C	rs11559	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:111066697T>C	ENST00000379671.3	-	5	392	c.128A>G	c.(127-129)gAg>gGg	p.E43G	STARD4-AS1_ENST00000500779.2_RNA|NREP_ENST00000450761.2_Missense_Mutation_p.E43G|NREP_ENST00000515855.1_3'UTR|NREP_ENST00000447165.2_Missense_Mutation_p.E43G|STARD4-AS1_ENST00000513221.1_RNA|NREP_ENST00000257435.7_Missense_Mutation_p.E43G|NREP_ENST00000509427.1_Missense_Mutation_p.E43G|NREP_ENST00000446294.2_Missense_Mutation_p.E43G|NREP_ENST00000419114.2_Missense_Mutation_p.E43G|NREP_ENST00000395634.3_Missense_Mutation_p.E87G|NREP_ENST00000508870.1_Missense_Mutation_p.E43G|NREP_ENST00000453526.2_Missense_Mutation_p.E43G|NREP_ENST00000509025.1_Intron|NREP_ENST00000455559.2_Missense_Mutation_p.E43G|NREP_ENST00000507742.1_5'UTR|NREP_ENST00000509979.1_3'UTR	NM_001142478.1	NP_001135950.1	Q16612	NREP_HUMAN	neuronal regeneration related protein	43			E -> G (in dbSNP:rs11559).		axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											AGCGTTTGTCTCATCGTTCTT	0.478													T|||	345	0.0688898	0.0151	0.036	5008	,	,		17682	0.2123		0.0427	False		,,,				2504	0.044				p.E87G		Atlas-SNP	.											C5orf13_ENST00000395634,brain,glioma,0,2	.	.	2	0			c.A260G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	133,4271	96.7+/-135.4	3,127,2072	173.0	142.0	153.0		230,260,128,128,128,128,128,128,128,128,128	0.3	0.0	5	dbSNP_52	153	477,8123	140.3+/-196.8	10,457,3833	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	C5orf13	NM_001142474.1,NM_001142475.1,NM_001142476.1,NM_001142477.1,NM_001142478.1,NM_001142479.1,NM_001142480.1,NM_001142481.1,NM_001142482.1,NM_001142483.1,NM_004772.2	98,98,98,98,98,98,98,98,98,98,98	13,584,5905	CC,CT,TT		5.5465,3.02,4.6909	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	77/103,87/113,43/69,43/69,43/69,43/69,43/69,43/69,43/69,43/69,43/69	111066697	610,12394	2202	4300	6502	SO:0001583	missense	9315	exon4			TTTGTCTCATCGT	AF119859	CCDS4105.1, CCDS47255.1	5q22.1	2012-12-07	2012-12-07	2012-01-23	ENSG00000134986	ENSG00000134986			16834	protein-coding gene	gene with protein product	"""neuronal protein 3.1"""	607332	"""chromosome 5 open reading frame 13"", ""neuronal regeneration related protein homolog (rat)"""	C5orf13		8261136, 10981724, 15485502	Standard	NM_004772		Approved	P311, D4S114, PRO1873, PTZ17, SEZ17	uc011cvr.2	Q16612	OTTHUMG00000128795	ENST00000379671.3:c.128A>G	5.37:g.111066697T>C	ENSP00000368993:p.Glu43Gly	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_001142475	B2RDN8|B7Z5D2|D3DSZ8	Missense_Mutation	SNP	ENST00000379671.3	37	CCDS4105.1	182	0.08333333333333333	8	0.016260162601626018	14	0.03867403314917127	129	0.22552447552447552	31	0.040897097625329816	T	1.341	-0.594183	0.03771	0.0302	0.055465	ENSG00000134986	ENST00000379671;ENST00000257435;ENST00000447165;ENST00000446294;ENST00000395634;ENST00000450761;ENST00000419114;ENST00000509427;ENST00000453526;ENST00000455559;ENST00000508870;ENST00000513100	T;T;T;T;T;T;T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6	5.81	0.269	0.15631	.	0.487688	0.20424	N	0.092601	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B	0.15141	0.012;0.012;0.004	B;B;B	0.16722	0.016;0.016;0.011	T	0.10291	-1.0636	8	0.39692	T	0.17	-0.6214	3.0237	0.06084	0.1154:0.1293:0.1203:0.635	rs11559;rs3797721	43;87;43	D6RIC9;B7Z5D2;Q16612	.;.;NP311_HUMAN	G	43;43;43;43;87;43;43;43;43;43;43;43	ENSP00000368993:E43G;ENSP00000257435:E43G;ENSP00000408839:E43G;ENSP00000402965:E43G;ENSP00000378996:E87G;ENSP00000416617:E43G;ENSP00000399766:E43G;ENSP00000422630:E43G;ENSP00000403383:E43G;ENSP00000392559:E43G;ENSP00000427149:E43G;ENSP00000427476:E43G	ENSP00000257435:E43G	E	-	2	0	C5orf13	111094596	0.431000	0.25546	0.001000	0.08648	0.019000	0.09904	2.033000	0.41136	0.101000	0.17610	-0.327000	0.08410	GAG	T|0.940;C|0.060	0.060	strong		0.478	NREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250722.1	NM_004772	
MAP3K9	4293	hgsc.bcm.edu	37	14	71204973	71204973	+	Silent	SNP	C	C	T	rs7153601	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:71204973C>T	ENST00000554752.2	-	8	1832	c.1833G>A	c.(1831-1833)tcG>tcA	p.S611S	MAP3K9_ENST00000553414.1_Silent_p.S353S|MAP3K9_ENST00000555993.2_Silent_p.S611S|MAP3K9_ENST00000554146.1_Silent_p.S348S|MAP3K9_ENST00000381250.4_Silent_p.S611S	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	611					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		CTTCATCTCCCGAGGCAAGCT	0.493													C|||	1084	0.216454	0.1573	0.2565	5008	,	,		19782	0.3363		0.167	False		,,,				2504	0.1953				p.S611S	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.G1833A						PASS	.	C		698,3708	293.3+/-282.5	57,584,1562	131.0	118.0	122.0		1833	-6.1	1.0	14	dbSNP_116	122	1399,7201	270.4+/-288.9	109,1181,3010	no	coding-synonymous	MAP3K9	NM_033141.2		166,1765,4572	TT,TC,CC		16.2674,15.842,16.1233		611/1119	71204973	2097,10909	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon8			ATCTCCCGAGGCA	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1833G>A	14.37:g.71204973C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	244	82	0.336066	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				C|0.823;T|0.177	0.177	strong		0.493	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
OR56A4	120793	hgsc.bcm.edu	37	11	6023928	6023928	+	Missense_Mutation	SNP	C	C	T	rs374569889		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6023928C>T	ENST00000330728.4	-	1	496	c.451G>A	c.(451-453)Gcc>Acc	p.A151T		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	99						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)		AGGAAGCAGGCTGGGAAGCTG	0.552																																					p.A151T		Atlas-SNP	.											OR56A4,NS,carcinoma,+2,1	OR56A4	66	1	0			c.G451A						scavenged	.						91.0	83.0	86.0					11																	6023928		2201	4296	6497	SO:0001583	missense	120793	exon1			AGCAGGCTGGGAA	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.451G>A	11.37:g.6023928C>T	ENSP00000328215:p.Ala151Thr	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	157	2	0.0127389	NM_001005179	B9EH17	Missense_Mutation	SNP	ENST00000330728.4	37	CCDS31404.1	.	.	.	.	.	.	.	.	.	.	C	8.853	0.945178	0.18356	.	.	ENSG00000183389	ENST00000330728	T	0.03065	4.06	3.34	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.608817	0.12225	U	0.487973	T	0.05731	0.0150	M	0.72353	2.195	0.09310	N	0.999999	B	0.10296	0.003	B	0.17722	0.019	T	0.30621	-0.9972	10	0.56958	D	0.05	.	5.6081	0.17391	0.3381:0.559:0.0:0.1029	.	99	Q8NGH8	O56A4_HUMAN	T	151	ENSP00000328215:A151T	ENSP00000328215:A151T	A	-	1	0	OR56A4	5980504	0.006000	0.16342	0.415000	0.26534	0.462000	0.32619	1.350000	0.34010	0.214000	0.20742	0.555000	0.69702	GCC	.	.	alt		0.552	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179	
OR9Q1	219956	hgsc.bcm.edu	37	11	57947264	57947264	+	Silent	SNP	C	C	G	rs11229273	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:57947264C>G	ENST00000335397.3	+	3	664	c.348C>G	c.(346-348)gcC>gcG	p.A116A		NM_001005212.3	NP_001005212.1	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q, 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(1)|large_intestine(1)|liver(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Breast(21;0.222)				ACCTCTTGGCCCTCATGGCCT	0.557													C|||	1679	0.335264	0.093	0.2406	5008	,	,		22617	0.5754		0.2684	False		,,,				2504	0.5511				p.A116A		Atlas-SNP	.											.	OR9Q1	60	.	0			c.C348G						PASS	.	C		472,3930	223.3+/-239.8	28,416,1757	120.0	96.0	104.0		348	-2.9	0.9	11	dbSNP_120	104	2372,6220	395.6+/-345.1	319,1734,2243	no	coding-synonymous	OR9Q1	NM_001005212.3		347,2150,4000	GG,GC,CC		27.6071,10.7224,21.887		116/311	57947264	2844,10150	2201	4296	6497	SO:0001819	synonymous_variant	219956	exon3			CTTGGCCCTCATG	AB065734	CCDS31543.1	11q12.1	2012-08-09				ENSG00000186509		"""GPCR / Class A : Olfactory receptors"""	14724	protein-coding gene	gene with protein product							Standard	NM_001005212		Approved		uc001nmj.3	Q8NGQ5		ENST00000335397.3:c.348C>G	11.37:g.57947264C>G		Somatic	364	1	0.00274725		WXS	Illumina HiSeq	Phase_I	354	351	0.991525	NM_001005212	Q2TAN3|Q96RA7	Silent	SNP	ENST00000335397.3	37	CCDS31543.1																																																																																			C|0.747;G|0.253	0.253	strong		0.557	OR9Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394538.2	NM_001005212	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48595988	48595988	+	Missense_Mutation	SNP	G	G	C	rs8064455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	110	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	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	
CDC25C	995	hgsc.bcm.edu	37	5	137665323	137665323	+	Missense_Mutation	SNP	G	G	A	rs3734166	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:137665323G>A	ENST00000323760.6	-	3	486	c.208C>T	c.(208-210)Cgt>Tgt	p.R70C	CDC25C_ENST00000348983.3_Intron|CDC25C_ENST00000415130.2_Intron|CDC25C_ENST00000356505.3_Missense_Mutation_p.R70C|CDC25C_ENST00000357274.3_Intron|CDC25C_ENST00000514555.1_Missense_Mutation_p.R70C|CDC25C_ENST00000513970.1_Missense_Mutation_p.R70C	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	70			R -> C (in dbSNP:rs3734166). {ECO:0000269|PubMed:11139144, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2195549}.		cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|WW domain binding (GO:0050699)			endometrium(2)|kidney(3)|large_intestine(5)|lung(5)|skin(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.004)|Kidney(363;0.00592)			TCGAGGCAACGTTTTGGGGTT	0.398													G|||	1954	0.390176	0.4773	0.2983	5008	,	,		19081	0.6101		0.3072	False		,,,				2504	0.1963				p.R70C		Atlas-SNP	.											.	CDC25C	37	.	0			c.C208T						PASS	.	G	CYS/ARG,	1964,2442	553.9+/-378.9	435,1094,674	124.0	119.0	121.0		208,	-1.0	1.0	5	dbSNP_107	121	2388,6212	396.6+/-345.4	337,1714,2249	yes	missense,intron	CDC25C	NM_001790.3,NM_022809.2	180,	772,2808,2923	AA,AG,GG		27.7674,44.5756,33.4615	benign,	70/474,	137665323	4352,8654	2203	4300	6503	SO:0001583	missense	995	exon3			GGCAACGTTTTGG	M34065	CCDS4202.1, CCDS4203.1	5q31	2013-01-17	2013-01-17		ENSG00000158402	ENSG00000158402		"""Protein tyrosine phosphatases / Class III Cys-based PTPs"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1727	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 60"""	157680	"""cell division cycle 25C"", ""cell division cycle 25 homolog C (S. cerevisiae)"", ""cell division cycle 25 homolog C (S. pombe)"""	CDC25		1703321	Standard	XM_005272145		Approved	PPP1R60	uc003lcp.1	P30307	OTTHUMG00000129203	ENST00000323760.6:c.208C>T	5.37:g.137665323G>A	ENSP00000321656:p.Arg70Cys	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	889	0.40705128205128205	230	0.46747967479674796	96	0.26519337016574585	333	0.5821678321678322	230	0.3034300791556728	G	12.56	1.973598	0.34848	0.445756	0.277674	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022;ENST00000510119	T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64	4.4	-0.963	0.10330	.	0.512067	0.18564	N	0.137526	T	0.00012	0.0000	N	0.04297	-0.235	0.09310	P	0.999999838467	B;B;B;B	0.14012	0.009;0.005;0.001;0.003	B;B;B;B	0.06405	0.002;0.001;0.001;0.001	T	0.42599	-0.9442	9	0.37606	T	0.19	0.0708	7.8092	0.29221	0.6152:0.0:0.3848:0.0	rs3734166;rs17851708;rs57255403;rs3734166	87;87;70;70	G3V1P6;B4DX61;P30307-2;P30307	.;.;.;MPIP3_HUMAN	C	70;70;70;87;70;70;87	ENSP00000321656:R70C;ENSP00000348898:R70C;ENSP00000424795:R70C;ENSP00000425470:R70C;ENSP00000427251:R70C;ENSP00000427105:R87C	ENSP00000321656:R70C	R	-	1	0	CDC25C	137693222	0.513000	0.26194	0.993000	0.49108	0.961000	0.63080	-0.842000	0.04354	-0.138000	0.11434	0.563000	0.77884	CGT	A|0.359;C|0.003	0.359	strong		0.398	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1		
SLC7A13	157724	hgsc.bcm.edu	37	8	87229702	87229702	+	Silent	SNP	A	A	G	rs4546639	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:87229702A>G	ENST00000297524.3	-	3	1279	c.1176T>C	c.(1174-1176)taT>taC	p.Y392Y	SLC7A13_ENST00000419776.2_Silent_p.Y383Y|SLC7A13_ENST00000520624.1_5'Flank	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	123	0	0		WXS	Illumina HiSeq	Phase_I	98	57	0.581633	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29912333	29912333	+	Missense_Mutation	SNP	C	C	T	rs3179982	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29912333C>T	ENST00000396634.1	+	7	1293	c.952C>T	c.(952-954)Ctt>Ttt	p.L318F	HLA-A_ENST00000376806.5_Missense_Mutation_p.L318F|HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.L318F			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	318					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						CCTGGTTCTCCTTGGAGCTGT	0.592									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|||	2681	0.535343	0.6044	0.6023	5008	,	,		19739	0.4881		0.5229	False		,,,				2504	0.456				p.L318F		Atlas-SNP	.											.	HLA-A	89	.	0			c.C952T						PASS	.	C	PHE/LEU	1582,1436		428,726,355	109.0	103.0	105.0		952	-1.0	0.0	6	dbSNP_105	105	2518,2900		666,1186,857	no	missense	HLA-A	NM_002116.7	22	1094,1912,1212	TT,TC,CC		46.4747,47.5812,48.6012	probably-damaging	318/366	29912333	4100,4336	1509	2709	4218	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTTCTCCTTGGAG	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.952C>T	6.37:g.29912333C>T	ENSP00000379873:p.Leu318Phe	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	253	114	0.450593	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	1165	0.5334249084249084	307	0.6239837398373984	196	0.5414364640883977	273	0.4772727272727273	389	0.5131926121372031	.	3.888	-0.024559	0.07589	0.524188	0.464747	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00995	5.49;5.46;5.49	3.13	-0.987	0.10249	.	0.308416	0.17061	U	0.188566	T	0.01353	0.0044	.	.	.	0.80722	P	0.0	B;B;D;B;B	0.71674	0.0;0.0;0.998;0.0;0.0	B;B;D;B;B	0.81914	0.001;0.004;0.995;0.004;0.001	T	0.47222	-0.9134	8	0.87932	D	0	.	6.4125	0.21698	0.0:0.4707:0.0:0.5293	rs3179982;rs3205680;rs17405339;rs17851725;rs41552629	197;318;318;318;318	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	F	318	ENSP00000379873:L318F;ENSP00000366002:L318F;ENSP00000366005:L318F	ENSP00000366002:L318F	L	+	1	0	HLA-A	30020312	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-2.297000	0.01141	-0.224000	0.09928	-0.330000	0.08379	CTT	C|0.487;T|0.513	0.513	strong		0.592	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
TSR1	55720	hgsc.bcm.edu	37	17	2238152	2238152	+	Missense_Mutation	SNP	T	T	C	rs79597880	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:2238152T>C	ENST00000301364.5	-	5	1674	c.595A>G	c.(595-597)Aaa>Gaa	p.K199E	SGSM2_ENST00000268989.3_5'Flank|SGSM2_ENST00000574563.1_5'Flank|SGSM2_ENST00000426855.2_5'Flank|TSR1_ENST00000576112.2_Missense_Mutation_p.K183E	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	199	Bms1-type G.				ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						TCTATTTGTTTCTTCAGTGGG	0.463													T|||	167	0.0333466	0.0061	0.0072	5008	,	,		20986	0.0764		0.008	False		,,,				2504	0.0706				p.K199E		Atlas-SNP	.											.	TSR1	57	.	0			c.A595G						PASS	.	T	GLU/LYS	28,4378	32.6+/-62.9	0,28,2175	106.0	105.0	105.0		595	5.4	0.5	17	dbSNP_131	105	73,8527	38.3+/-94.2	1,71,4228	yes	missense	TSR1	NM_018128.4	56	1,99,6403	CC,CT,TT		0.8488,0.6355,0.7766	possibly-damaging	199/805	2238152	101,12905	2203	4300	6503	SO:0001583	missense	55720	exon5			TTTGTTTCTTCAG	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"""TSR1, 20S rRNA accumulation, homolog (yeast)"""			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.595A>G	17.37:g.2238152T>C	ENSP00000301364:p.Lys199Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Missense_Mutation	SNP	ENST00000301364.5	37	CCDS32525.1	38	0.0173992673992674	5	0.01016260162601626	3	0.008287292817679558	23	0.04020979020979021	7	0.009234828496042216	T	28.5	4.929292	0.92389	0.006355	0.008488	ENSG00000167721	ENST00000301364	T	0.15718	2.4	5.4	5.4	0.78164	.	0.130635	0.64402	D	0.000002	T	0.10637	0.0260	M	0.86740	2.835	0.80722	D	1	P	0.49358	0.923	P	0.49597	0.616	T	0.04509	-1.0946	10	0.39692	T	0.17	-3.0079	14.6065	0.68483	0.0:0.0:0.0:1.0	.	199	Q2NL82	TSR1_HUMAN	E	199	ENSP00000301364:K199E	ENSP00000301364:K199E	K	-	1	0	TSR1	2184902	1.000000	0.71417	0.495000	0.27527	0.956000	0.61745	7.542000	0.82095	2.046000	0.60703	0.533000	0.62120	AAA	T|0.987;C|0.013	0.013	strong		0.463	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128	
HIF3A	64344	hgsc.bcm.edu	37	19	46823803	46823803	+	Missense_Mutation	SNP	C	C	T	rs61755707	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46823803C>T	ENST00000377670.4	+	9	1160	c.1129C>T	c.(1129-1131)Cct>Tct	p.P377S	HIF3A_ENST00000600383.1_Missense_Mutation_p.P308S|HIF3A_ENST00000420102.2_Missense_Mutation_p.P326S|HIF3A_ENST00000339613.2_Missense_Mutation_p.P321S|HIF3A_ENST00000300862.3_Missense_Mutation_p.P375S|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000244303.6_Missense_Mutation_p.P308S|HIF3A_ENST00000472815.1_Missense_Mutation_p.P308S	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	377					cellular response to hypoxia (GO:0071456)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription from RNA polymerase II promoter (GO:0006366)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(14)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	33		Ovarian(192;0.00965)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00204)|all cancers(93;0.0107)|GBM - Glioblastoma multiforme(486;0.0489)|Epithelial(262;0.136)		CACCCCTAACCCTGGGGACAG	0.647													C|||	51	0.0101837	0.0008	0.0072	5008	,	,		16574	0.0		0.0378	False		,,,				2504	0.0072				p.P377S		Atlas-SNP	.											.	HIF3A	154	.	0			c.C1129T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	22,4384	28.1+/-56.4	0,22,2181	54.0	52.0	53.0		922,1123,1129,922	1.0	0.0	19	dbSNP_129	53	245,8355	97.2+/-158.9	4,237,4059	yes	missense,missense,missense,missense	HIF3A	NM_022462.4,NM_152794.3,NM_152795.3,NM_152796.2	74,74,74,74	4,259,6240	TT,TC,CC		2.8488,0.4993,2.0529	benign,benign,benign,benign	308/601,375/668,377/670,308/451	46823803	267,12739	2203	4300	6503	SO:0001583	missense	64344	exon9			CCTAACCCTGGGG	AK027725	CCDS12681.2, CCDS12682.1, CCDS42580.1, CCDS42580.2	19q13	2013-05-21			ENSG00000124440	ENSG00000124440		"""Basic helix-loop-helix proteins"""	15825	protein-coding gene	gene with protein product		609976				11573933, 11734856	Standard	NM_152794		Approved	IPAS, MOP7, PASD7, bHLHe17	uc002peh.3	Q9Y2N7	OTTHUMG00000141296	ENST00000377670.4:c.1129C>T	19.37:g.46823803C>T	ENSP00000366898:p.Pro377Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	37	CCDS12681.2	32|32	0.014652014652014652|0.014652014652014652	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	29|29	0.03825857519788918|0.03825857519788918	C|C	4.392|4.392	0.072291|0.072291	0.08436|0.08436	0.004993|0.004993	0.028488|0.028488	ENSG00000124440|ENSG00000124440	ENST00000472815|ENST00000244302;ENST00000377670;ENST00000244303;ENST00000339613;ENST00000291300;ENST00000300862;ENST00000420102	.|T;T;T;T;T	.|0.66460	.|0.46;-0.19;0.36;0.48;-0.21	4.47|4.47	1.03|1.03	0.20045|0.20045	.|.	1.425250|1.425250	0.04795|0.04795	N|N	0.432421|0.432421	T|T	0.15825|0.15825	0.0381|0.0381	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B	.|0.10296	.|0.0;0.0;0.001;0.0;0.001;0.001;0.003	.|B;B;B;B;B;B;B	.|0.09377	.|0.0;0.001;0.004;0.001;0.002;0.002;0.002	T|T	0.13019|0.13019	-1.0525|-1.0525	6|10	.|0.33141	.|T	.|0.24	.|.	6.6607|6.6607	0.23012|0.23012	0.0:0.7019:0.0:0.2981|0.0:0.7019:0.0:0.2981	rs61755707|rs61755707	.|326;308;375;326;321;377;377	.|F5H884;B4DNA2;Q9Y2N7-2;B4DSD9;A8MPQ1;Q9Y2N7;B0M185	.|.;.;.;.;.;HIF3A_HUMAN;.	L|S	349|377;377;308;321;321;375;326	.|ENSP00000366898:P377S;ENSP00000244303:P308S;ENSP00000341877:P321S;ENSP00000300862:P375S;ENSP00000407771:P326S	.|ENSP00000244302:P377S	P|P	+|+	2|1	0|0	HIF3A|HIF3A	51515643|51515643	0.009000|0.009000	0.17119|0.17119	0.037000|0.037000	0.18230|0.18230	0.299000|0.299000	0.27559|0.27559	0.005000|0.005000	0.13129|0.13129	0.203000|0.203000	0.20529|0.20529	-0.459000|-0.459000	0.05422|0.05422	CCC|CCT	C|0.981;T|0.019	0.019	strong		0.647	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3		
DOCK2	1794	hgsc.bcm.edu	37	5	169435713	169435713	+	Silent	SNP	A	A	C	rs2287727	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:169435713A>C	ENST00000256935.8	+	32	3275	c.3195A>C	c.(3193-3195)ctA>ctC	p.L1065L	DOCK2_ENST00000540750.1_Silent_p.L126L|DOCK2_ENST00000520908.1_Silent_p.L557L|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1065	Interaction with CRKL.				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)			TGAGACGGCTAATTGGCTTCT	0.488													A|||	1217	0.243011	0.0257	0.3026	5008	,	,		19957	0.3909		0.2783	False		,,,				2504	0.3057				p.L1065L		Atlas-SNP	.											.	DOCK2	389	.	0			c.A3195C						PASS	.	A		338,4068	176.6+/-205.7	11,316,1876	232.0	201.0	211.0		3195	-4.4	0.7	5	dbSNP_100	211	2533,6067	414.1+/-351.3	375,1783,2142	no	coding-synonymous	DOCK2	NM_004946.2		386,2099,4018	CC,CA,AA		29.4535,7.6714,22.0744		1065/1831	169435713	2871,10135	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon32			ACGGCTAATTGGC	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.3195A>C	5.37:g.169435713A>C		Somatic	332	0	0		WXS	Illumina HiSeq	Phase_I	283	143	0.5053	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			A|0.770;C|0.230	0.230	strong		0.488	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
VSIG1	340547	hgsc.bcm.edu	37	X	107320447	107320447	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:107320447C>T	ENST00000217957.5	+	7	1117	c.1000C>T	c.(1000-1002)Cca>Tca	p.P334S	VSIG1_ENST00000415430.3_Missense_Mutation_p.P370S	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	334						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17						agagcctgccccagGATCAGA	0.562																																					p.P370S		Atlas-SNP	.											.	VSIG1	126	.	0			c.C1108T						PASS	.						75.0	69.0	71.0					X																	107320447		2203	4300	6503	SO:0001583	missense	340547	exon8			CCTGCCCCAGGAT	BX648658	CCDS14535.1, CCDS55474.1	Xq22.3	2013-01-29			ENSG00000101842	ENSG00000101842		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28675	protein-coding gene	gene with protein product		300620				12477932	Standard	NM_182607		Approved	MGC44287	uc011msk.2	Q86XK7	OTTHUMG00000022175	ENST00000217957.5:c.1000C>T	X.37:g.107320447C>T	ENSP00000217957:p.Pro334Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	71	4	0.056338	NM_001170553	C9J4P2|Q6MZS4	Missense_Mutation	SNP	ENST00000217957.5	37	CCDS14535.1	.	.	.	.	.	.	.	.	.	.	C	4.558	0.103573	0.08731	.	.	ENSG00000101842	ENST00000415430;ENST00000217957	T;T	0.61274	0.12;0.12	3.5	-7.0	0.01599	.	1.931450	0.02302	N	0.071290	T	0.38427	0.1040	L	0.43152	1.355	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48445	-0.9035	10	0.05436	T	0.98	.	3.3355	0.07100	0.1048:0.1372:0.4102:0.3478	.	370;334	C9J4P2;Q86XK7	.;VSIG1_HUMAN	S	370;334	ENSP00000402219:P370S;ENSP00000217957:P334S	ENSP00000217957:P334S	P	+	1	0	VSIG1	107207103	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.489000	0.00226	-2.917000	0.00306	-4.471000	0.00005	CCA	.	.	none		0.562	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057858.1	NM_182607	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798278	55798278	+	Silent	SNP	C	C	T	rs148523609	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55798278C>T	ENST00000313555.1	+	1	384	c.384C>T	c.(382-384)aaC>aaT	p.N128N		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	128						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					CCATCTGCAACCCACTGCTCT	0.468													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		20153	0.0		0.0089	False		,,,				2504	0.0031				p.N128N		Atlas-SNP	.											.	OR5AS1	121	.	0			c.C384T						PASS	.	C		12,4390	21.2+/-45.6	0,12,2189	150.0	122.0	132.0		384	-1.9	0.3	11	dbSNP_134	132	106,8486	57.5+/-118.9	1,104,4191	no	coding-synonymous	OR5AS1	NM_001001921.1		1,116,6380	TT,TC,CC		1.2337,0.2726,0.9081		128/325	55798278	118,12876	2201	4296	6497	SO:0001819	synonymous_variant	219447	exon1			CTGCAACCCACTG	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.384C>T	11.37:g.55798278C>T		Somatic	335	1	0.00298507		WXS	Illumina HiSeq	Phase_I	295	136	0.461017	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																			C|0.993;T|0.007	0.007	strong		0.468	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
MAATS1	89876	hgsc.bcm.edu	37	3	119421963	119421963	+	Silent	SNP	C	C	T	rs7612861	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:119421963C>T	ENST00000273390.5	+	1	95	c.18C>T	c.(16-18)acC>acT	p.T6T	MAATS1_ENST00000463700.1_Silent_p.T6T	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	6						mitochondrion (GO:0005739)											ACGCAGTAACCATCGAGGAGC	0.642													C|||	917	0.183107	0.1672	0.2392	5008	,	,		12639	0.1825		0.1461	False		,,,				2504	0.2035				p.T6T		Atlas-SNP	.											C3orf15,NS,carcinoma,0,1	.	.	1	0			c.C18T						PASS	.	C		780,3598		63,654,1472	27.0	31.0	30.0		18	-0.2	0.3	3	dbSNP_116	30	1036,7524		52,932,3296	no	coding-synonymous	C3orf15	NM_033364.3		115,1586,4768	TT,TC,CC		12.1028,17.8164,14.0362		6/768	119421963	1816,11122	2189	4280	6469	SO:0001819	synonymous_variant	89876	exon1			AGTAACCATCGAG	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.18C>T	3.37:g.119421963C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Silent	SNP	ENST00000273390.5	37	CCDS2994.1																																																																																			C|0.824;T|0.176	0.176	strong		0.642	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
MUC16	94025	hgsc.bcm.edu	37	19	9072296	9072296	+	Silent	SNP	G	G	T	rs7254970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9072296G>T	ENST00000397910.4	-	3	15353	c.15150C>A	c.(15148-15150)acC>acA	p.T5050T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5052	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						GGGAAGGTGTGGTCATTGCAG	0.468													G|||	844	0.16853	0.171	0.1844	5008	,	,		20301	0.0089		0.2634	False		,,,				2504	0.2209				p.T5050T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C15150A						PASS	.			664,3246		60,544,1351	91.0	86.0	88.0		15150	0.5	0.0	19	dbSNP_116	88	2428,5862		370,1688,2087	no	coding-synonymous	MUC16	NM_024690.2		430,2232,3438	TT,TG,GG		29.2883,16.9821,25.3443		5050/14508	9072296	3092,9108	1955	4145	6100	SO:0001819	synonymous_variant	94025	exon3			AGGTGTGGTCATT	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.15150C>A	19.37:g.9072296G>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.815;T|0.185	0.185	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OLFM4	10562	hgsc.bcm.edu	37	13	53608632	53608632	+	Silent	SNP	C	C	T	rs2298231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:53608632C>T	ENST00000219022.2	+	2	432	c.354C>T	c.(352-354)tcC>tcT	p.S118S		NM_006418.4	NP_006409.3	Q6UX06	OLFM4_HUMAN	olfactomedin 4	118					cell adhesion (GO:0007155)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein homooligomerization (GO:0051260)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|specific granule (GO:0042581)	cadherin binding (GO:0045296)|catalytic activity (GO:0003824)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(4)|kidney(4)|large_intestine(5)|lung(20)|skin(3)|urinary_tract(1)	39		Breast(56;0.000776)|Lung NSC(96;0.000814)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.13e-08)		AAGAACTTTCCAAAGTAAGCA	0.358													T|||	2831	0.565296	0.4168	0.6225	5008	,	,		19452	0.7242		0.501	False		,,,				2504	0.6278				p.S118S		Atlas-SNP	.											.	OLFM4	94	.	0			c.C354T						PASS	.	T		1919,2487	625.9+/-394.6	395,1129,679	44.0	39.0	40.0		354	3.0	1.0	13	dbSNP_100	40	4200,4400	581.9+/-391.3	1079,2042,1179	no	coding-synonymous	OLFM4	NM_006418.4		1474,3171,1858	TT,TC,CC		48.8372,43.5542,47.0475		118/511	53608632	6119,6887	2203	4300	6503	SO:0001819	synonymous_variant	10562	exon2			ACTTTCCAAAGTA	AY358567	CCDS9440.1	13q14	2004-06-25			ENSG00000102837	ENSG00000102837			17190	protein-coding gene	gene with protein product		614061					Standard	NM_006418		Approved	OlfD, GW112, GC1	uc001vhl.3	Q6UX06	OTTHUMG00000016981	ENST00000219022.2:c.354C>T	13.37:g.53608632C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_006418	O95362|Q5VWG0|Q86T22	Silent	SNP	ENST00000219022.2	37	CCDS9440.1																																																																																			C|0.494;T|0.506	0.506	strong		0.358	OLFM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045112.2	NM_006418	
FLG	2312	hgsc.bcm.edu	37	1	152280900	152280900	+	Missense_Mutation	SNP	T	T	G	rs74129452	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280900T>G	ENST00000368799.1	-	3	6497	c.6462A>C	c.(6460-6462)caA>caC	p.Q2154H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2154	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCGATTGCTCTTGGTGGGACC	0.592									Ichthyosis				-|||	1722	0.34385	0.3843	0.3487	5008	,	,		25148	0.4444		0.1541	False		,,,				2504	0.3773				p.Q2154H		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	0			c.A6462C						PASS	.						380.0	322.0	342.0					1																	152280900		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTGCTCTTGGTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6462A>C	1.37:g.152280900T>G	ENSP00000357789:p.Gln2154His	Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	561	143	0.254902	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	2.361	-0.346581	0.05208	.	.	ENSG00000143631	ENST00000368799	T	0.03524	3.9	2.59	-5.18	0.02840	.	.	.	.	.	T	0.00178	0.0005	N	0.00074	-2.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49943	-0.8885	9	0.38643	T	0.18	.	0.1659	0.00108	0.2732:0.2266:0.1592:0.341	.	2154	P20930	FILA_HUMAN	H	2154	ENSP00000357789:Q2154H	ENSP00000357789:Q2154H	Q	-	3	2	FLG	150547524	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.334000	0.00508	-3.813000	0.00104	-2.053000	0.00404	CAA	T|0.872;G|0.128	0.128	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SRRM2	23524	hgsc.bcm.edu	37	16	2816519	2816519	+	Missense_Mutation	SNP	G	G	A	rs138447860	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2816519G>A	ENST00000301740.8	+	11	6539	c.5990G>A	c.(5989-5991)cGc>cAc	p.R1997H		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1997	Arg-rich.|Ser-rich.				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						TCTCGATCTCGCACATCTCCA	0.577													G|||	10	0.00199681	0.0	0.0043	5008	,	,		17504	0.0		0.007	False		,,,				2504	0.0				p.R1997H		Atlas-SNP	.											.	SRRM2	263	.	0			c.G5990A						PASS	.	G	HIS/ARG	3,4393	6.2+/-15.9	0,3,2195	71.0	75.0	74.0		5990	5.3	1.0	16	dbSNP_134	74	50,8550	32.3+/-84.9	0,50,4250	yes	missense	SRRM2	NM_016333.3	29	0,53,6445	AA,AG,GG		0.5814,0.0682,0.4078	probably-damaging	1997/2753	2816519	53,12943	2198	4300	6498	SO:0001583	missense	23524	exon11			GATCTCGCACATC	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.5990G>A	16.37:g.2816519G>A	ENSP00000301740:p.Arg1997His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	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	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	11.77	1.736455	0.30774	6.82E-4	0.005814	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.24908	1.83	5.26	5.26	0.73747	.	0.000000	0.53938	D	0.000043	T	0.23572	0.0570	N	0.08118	0	0.35761	D	0.820188	D	0.76494	0.999	D	0.69654	0.965	T	0.48198	-0.9056	10	0.62326	D	0.03	-6.3676	16.354	0.83228	0.0:0.0:1.0:0.0	.	1997	Q9UQ35	SRRM2_HUMAN	H	1997;1997;1249	ENSP00000301740:R1997H	ENSP00000301740:R1997H	R	+	2	0	SRRM2	2756520	0.967000	0.33354	0.988000	0.46212	0.988000	0.76386	3.451000	0.52964	2.466000	0.83321	0.650000	0.86243	CGC	G|0.997;A|0.003	0.003	strong		0.577	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
DOK7	285489	hgsc.bcm.edu	37	4	3494826	3494826	+	Silent	SNP	A	A	C	rs6811856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:3494826A>C	ENST00000340083.5	+	7	1178	c.1113A>C	c.(1111-1113)tcA>tcC	p.S371S	DOK7_ENST00000389653.2_Silent_p.S371S|DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	371					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)		AACTGGGCTCACTGCTCAGCC	0.701													.|||	1086	0.216853	0.028	0.1427	5008	,	,		12459	0.503		0.2237	False		,,,				2504	0.2229				p.S371S		Atlas-SNP	.											.	DOK7	44	.	0			c.A1113C						PASS	.	A	,	231,4095		12,207,1944	8.0	10.0	9.0		,1113	-7.5	0.0	4	dbSNP_116	9	1637,6863		177,1283,2790	no	utr-3,coding-synonymous	DOK7	NM_001164673.1,NM_173660.4	,	189,1490,4734	CC,CA,AA		19.2588,5.3398,14.5642	,	,371/505	3494826	1868,10958	2163	4250	6413	SO:0001819	synonymous_variant	285489	exon7			GGGCTCACTGCTC	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.1113A>C	4.37:g.3494826A>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_173660	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Silent	SNP	ENST00000340083.5	37	CCDS3370.2																																																																																			A|0.734;C|0.266	0.266	strong		0.701	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
MR1	3140	hgsc.bcm.edu	37	1	181021483	181021483	+	Silent	SNP	C	C	T	rs35223984	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:181021483C>T	ENST00000367580.5	+	4	722	c.717C>T	c.(715-717)aaC>aaT	p.N239N	MR1_ENST00000434571.2_Intron|MR1_ENST00000282990.6_Intron|MR1_ENST00000438435.2_Intron|MR1_ENST00000367579.3_Silent_p.N194N	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	239	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)	p.N239N(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	GGATGAAAAACGGGGAAGAAA	0.443													C|||	48	0.00958466	0.0	0.0216	5008	,	,		20538	0.0		0.0318	False		,,,				2504	0.001				p.N239N	Colon(174;1412 1962 45296 46549 47110)	Atlas-SNP	.											MR1,colon,NS,0,2	MR1	46	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C717T						scavenged	.	C	,,,	45,4361	47.5+/-82.1	0,45,2158	63.0	65.0	64.0		582,,,717	-2.3	1.0	1	dbSNP_126	64	308,8292	111.0+/-171.3	5,298,3997	no	coding-synonymous,intron,intron,coding-synonymous	MR1	NM_001194999.1,NM_001195000.1,NM_001195035.1,NM_001531.2	,,,	5,343,6155	TT,TC,CC		3.5814,1.0213,2.7141	,,,	194/297,,,239/342	181021483	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	3140	exon5			GAAAAACGGGGAA	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"""Immunoglobulin superfamily / C1-set domain containing"""	4975	protein-coding gene	gene with protein product		600764	"""major histocompatibility complex, class I-like sequence"""	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.717C>T	1.37:g.181021483C>T		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	175	110	0.628571	NM_001531	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Silent	SNP	ENST00000367580.5	37	CCDS1342.1																																																																																			C|0.978;T|0.022	0.022	strong		0.443	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531	
PLEC	5339	hgsc.bcm.edu	37	8	145006143	145006143	+	Missense_Mutation	SNP	T	T	C	rs189137260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145006143T>C	ENST00000322810.4	-	18	2720	c.2551A>G	c.(2551-2553)Atc>Gtc	p.I851V	PLEC_ENST00000398774.2_Missense_Mutation_p.I682V|PLEC_ENST00000527096.1_Missense_Mutation_p.I737V|PLEC_ENST00000357649.2_Missense_Mutation_p.I718V|PLEC_ENST00000345136.3_Missense_Mutation_p.I714V|PLEC_ENST00000356346.3_Missense_Mutation_p.I700V|PLEC_ENST00000436759.2_Missense_Mutation_p.I741V|PLEC_ENST00000354958.2_Missense_Mutation_p.I692V|PLEC_ENST00000354589.3_Missense_Mutation_p.I714V	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	851	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						TGTGCCTCGATACAGCAGCAC	0.682													T|||	7	0.00139776	0.0	0.0	5008	,	,		12293	0.0069		0.0	False		,,,				2504	0.0				p.I851V		Atlas-SNP	.											.	PLEC	1144	.	0			c.A2551G						PASS	.						18.0	23.0	21.0					8																	145006143		2101	4235	6336	SO:0001583	missense	5339	exon18			CCTCGATACAGCA	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.2551A>G	8.37:g.145006143T>C	ENSP00000323856:p.Ile851Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	154	83	0.538961	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	7	0.012237762237762238	2	0.002638522427440633	T	10.35	1.327031	0.24080	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	D;D;D;D;D;D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45	4.2	0.331	0.15933	.	0.000000	0.64402	U	0.000016	T	0.69949	0.3168	N	0.21545	0.675	0.34771	D	0.73369	B;B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B;B	0.09377	0.004;0.004;0.004;0.002;0.004;0.004;0.004;0.004	T	0.62872	-0.6762	10	0.23302	T	0.38	.	5.975	0.19373	0.0:0.1853:0.1515:0.6631	.	741;700;692;851;682;714;718;714	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	V	714;718;714;682;851;692;700;741;737	ENSP00000344848:I714V;ENSP00000350277:I718V;ENSP00000346602:I714V;ENSP00000381756:I682V;ENSP00000323856:I851V;ENSP00000347044:I692V;ENSP00000348702:I700V;ENSP00000388180:I741V;ENSP00000434583:I737V	ENSP00000323856:I851V	I	-	1	0	PLEC	145078131	0.157000	0.22836	0.190000	0.23270	0.782000	0.44232	0.054000	0.14205	0.208000	0.20626	0.372000	0.22366	ATC	T|0.995;C|0.005	0.005	strong		0.682	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
LRIG3	121227	hgsc.bcm.edu	37	12	59279660	59279660	+	Silent	SNP	A	A	T	rs11172796	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:59279660A>T	ENST00000320743.3	-	10	1483	c.1197T>A	c.(1195-1197)cgT>cgA	p.R399R	LRIG3_ENST00000379141.4_Silent_p.R339R	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	399					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			TAGTAATAGAACGGATCCGAT	0.373			T	ROS1	NSCLC								T|||	964	0.192492	0.3722	0.1816	5008	,	,		16195	0.1567		0.0835	False		,,,				2504	0.1063				p.R399R		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	LRIG3,NS,haematopoietic_neoplasm,-1,1	LRIG3	120	1	0			c.T1197A						PASS	.	T	,	1412,2994	685.2+/-404.5	222,968,1013	161.0	180.0	174.0		1017,1197	-1.0	1.0	12	dbSNP_120	174	715,7885	786.3+/-407.6	27,661,3612	no	coding-synonymous,coding-synonymous	LRIG3	NM_001136051.1,NM_153377.3	,	249,1629,4625	TT,TA,AA		8.314,32.0472,16.354	,	339/1060,399/1120	59279660	2127,10879	2203	4300	6503	SO:0001819	synonymous_variant	121227	exon10			AATAGAACGGATC	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.1197T>A	12.37:g.59279660A>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_153377	Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																			A|0.833;T|0.167	0.167	strong		0.373	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377	
SLC52A1	55065	hgsc.bcm.edu	37	17	4936898	4936898	+	Missense_Mutation	SNP	C	C	T	rs2304445	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4936898C>T	ENST00000424747.1	-	3	1598	c.886G>A	c.(886-888)Gtg>Atg	p.V296M	SLC52A1_ENST00000512825.2_Missense_Mutation_p.V296M|SLC52A1_ENST00000254853.5_Missense_Mutation_p.V296M	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	296			V -> M (riboflavin transport is unaffected; dbSNP:rs2304445). {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)										GAAGGCAGCACGCCATTGGTC	0.637													C|||	1535	0.30651	0.1172	0.2565	5008	,	,		20856	0.506		0.1909	False		,,,				2504	0.5112				p.V296M		Atlas-SNP	.											GPR172B,caecum,carcinoma,0,1	.	.	1	0			c.G886A						PASS	.	C	MET/VAL,MET/VAL	533,3873	237.7+/-249.4	30,473,1700	80.0	61.0	68.0		886,886	-0.1	0.0	17	dbSNP_100	68	1476,7124	276.7+/-292.4	148,1180,2972	yes	missense,missense	GPR172B	NM_001104577.1,NM_017986.3	21,21	178,1653,4672	TT,TC,CC		17.1628,12.0971,15.4467	probably-damaging,probably-damaging	296/449,296/449	4936898	2009,10997	2203	4300	6503	SO:0001583	missense	55065	exon3			GCAGCACGCCATT	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.886G>A	17.37:g.4936898C>T	ENSP00000399979:p.Val296Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Missense_Mutation	SNP	ENST00000424747.1	37	CCDS11066.1	586	0.2683150183150183	63	0.12804878048780488	89	0.24585635359116023	287	0.5017482517482518	147	0.19393139841688653	C	13.01	2.108368	0.37242	0.120971	0.171628	ENSG00000132517	ENST00000254853;ENST00000512825;ENST00000424747	T;T;T	0.75050	-0.9;-0.9;-0.9	0.913	-0.105	0.13601	.	0.140324	0.47455	D	0.000222	T	0.00012	0.0000	L	0.53729	1.69	0.22330	P	0.999199579	D;D	0.89917	0.968;1.0	P;D	0.74348	0.646;0.983	T	0.40289	-0.9571	9	0.56958	D	0.05	.	3.6344	0.08143	0.0:0.4642:0.0:0.5358	rs2304445;rs59882655;rs2304445	296;296	F5H5Y1;Q9NWF4	.;RFT_HUMAN	M	296	ENSP00000254853:V296M;ENSP00000443026:V296M;ENSP00000399979:V296M	ENSP00000254853:V296M	V	-	1	0	GPR172B	4877622	0.120000	0.22244	0.001000	0.08648	0.008000	0.06430	0.399000	0.20916	-0.032000	0.13758	0.655000	0.94253	GTG	C|0.783;T|0.217	0.217	strong		0.637	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
KIAA1683	80726	hgsc.bcm.edu	37	19	18377981	18377981	+	Silent	SNP	C	C	G	rs61740692	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:18377981C>G	ENST00000600328.3	-	3	562	c.369G>C	c.(367-369)ctG>ctC	p.L123L	KIAA1683_ENST00000600359.3_Silent_p.L77L|KIAA1683_ENST00000392413.4_Silent_p.L123L			Q9H0B3	K1683_HUMAN	KIAA1683	123	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.					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						TCTGGGAAATCAGCTTCTGCC	0.562													C|||	9	0.00179712	0.0015	0.0014	5008	,	,		17364	0.0		0.006	False		,,,				2504	0.0				p.L123L		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G369C						PASS	.	C	,,	8,4398	14.3+/-33.2	0,8,2195	57.0	57.0	57.0		369,231,369	-8.1	0.0	19	dbSNP_129	57	112,8488	60.6+/-122.4	0,112,4188	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	0,120,6383	GG,GC,CC		1.3023,0.1816,0.9227	,,	123/1368,77/1135,123/1181	18377981	120,12886	2203	4300	6503	SO:0001819	synonymous_variant	80726	exon3			GGAAATCAGCTTC	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.369G>C	19.37:g.18377981C>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	194	94	0.484536	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			C|0.984;G|0.016	0.016	strong		0.562	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
PEAR1	375033	hgsc.bcm.edu	37	1	156873727	156873727	+	Silent	SNP	G	G	A	rs12407843	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156873727G>A	ENST00000338302.3	+	3	234	c.9G>A	c.(7-9)ccG>ccA	p.P3P	PEAR1_ENST00000292357.7_Silent_p.P3P			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	3					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)					CAATGTCACCGCCTCTGTGTC	0.637													g|||	974	0.194489	0.146	0.1499	5008	,	,		17619	0.3442		0.1113	False		,,,				2504	0.2229				p.P3P		Atlas-SNP	.											.	PEAR1	118	.	0			c.G9A						PASS	.			638,3768	274.3+/-271.8	57,524,1622	112.0	100.0	104.0		9	-4.5	0.0	1	dbSNP_120	104	974,7626	212.1+/-252.5	61,852,3387	no	coding-synonymous	PEAR1	NM_001080471.1		118,1376,5009	AA,AG,GG		11.3256,14.4803,12.3943		3/1038	156873727	1612,11394	2203	4300	6503	SO:0001819	synonymous_variant	375033	exon2			GTCACCGCCTCTG	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.9G>A	1.37:g.156873727G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			G|0.842;A|0.158	0.158	strong		0.637	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
ZC3H11A	9877	hgsc.bcm.edu	37	1	203787702	203787702	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:203787702A>G	ENST00000545588.1	+	3	3886	c.59A>G	c.(58-60)gAc>gGc	p.D20G	ZC3H11A_ENST00000332127.4_Missense_Mutation_p.D20G|ZC3H11A_ENST00000367212.3_Missense_Mutation_p.D20G|ZC3H11A_ENST00000367214.1_Missense_Mutation_p.D20G|ZC3H11A_ENST00000367210.1_Missense_Mutation_p.D20G	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	20					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TTACAGGGTGACAGCTGCCCA	0.423																																					p.D20G		Atlas-SNP	.											ZC3H11A,NS,carcinoma,+1,1	ZC3H11A	71	1	0			c.A59G						scavenged	.						94.0	83.0	87.0					1																	203787702		2203	4300	6503	SO:0001583	missense	9877	exon6			AGGGTGACAGCTG		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"""Zinc fingers, CCCH-type domain containing"""	29093	protein-coding gene	gene with protein product		613513	"""zinc finger CCCH-type domain containing 11A"""	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.59A>G	1.37:g.203787702A>G	ENSP00000438527:p.Asp20Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	106	3	0.0283019	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Missense_Mutation	SNP	ENST00000545588.1	37	CCDS30978.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.612933	0.87258	.	.	ENSG00000058673	ENST00000432282;ENST00000453771;ENST00000367214;ENST00000367212;ENST00000332127;ENST00000545588;ENST00000367210	T;T;T;T;T;T	0.54279	0.83;0.58;0.58;0.58;0.58;0.58	5.42	5.42	0.78866	Zinc finger, CCCH-type (2);	0.000000	0.85682	D	0.000000	T	0.66809	0.2827	L	0.56199	1.76	0.58432	D	0.99999	D	0.76494	0.999	D	0.77557	0.99	T	0.68515	-0.5388	10	0.56958	D	0.05	-13.8875	12.9846	0.58583	1.0:0.0:0.0:0.0	.	20	O75152	ZC11A_HUMAN	G	20	ENSP00000406531:D20G;ENSP00000356183:D20G;ENSP00000356181:D20G;ENSP00000333253:D20G;ENSP00000438527:D20G;ENSP00000356179:D20G	ENSP00000333253:D20G	D	+	2	0	ZC3H11A	202054325	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	8.526000	0.90588	2.062000	0.61559	0.528000	0.53228	GAC	.	.	none		0.423	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827	
STON2	85439	hgsc.bcm.edu	37	14	81743718	81743718	+	Missense_Mutation	SNP	C	C	T	rs34323725	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:81743718C>T	ENST00000267540.2	-	4	2137	c.1937G>A	c.(1936-1938)cGt>cAt	p.R646H	STON2_ENST00000555447.1_Missense_Mutation_p.R646H|STON2_ENST00000556280.1_5'Flank	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	646	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.		R -> H (in dbSNP:rs34323725).		hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		CCCATGGAAACGGCACTCATG	0.507													C|||	344	0.0686901	0.1165	0.0476	5008	,	,		23494	0.006		0.0944	False		,,,				2504	0.0573				p.R646H		Atlas-SNP	.											.	STON2	94	.	0			c.G1937A						PASS	.	C	HIS/ARG	523,3883	236.8+/-248.8	35,453,1715	74.0	60.0	65.0		1937	0.2	0.3	14	dbSNP_126	65	894,7706	200.0+/-243.9	46,802,3452	yes	missense	STON2	NM_033104.2	29	81,1255,5167	TT,TC,CC		10.3953,11.8702,10.895	benign	646/906	81743718	1417,11589	2203	4300	6503	SO:0001583	missense	85439	exon6			TGGAAACGGCACT	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"""stoned B homolog 2 (Drosophila)"""	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.1937G>A	14.37:g.81743718C>T	ENSP00000267540:p.Arg646His	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	179	122	0.681564	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	37	CCDS9875.1	162	0.07417582417582418	74	0.15040650406504066	18	0.049723756906077346	4	0.006993006993006993	66	0.0870712401055409	C	0.256	-1.002835	0.02128	0.118702	0.103953	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.19250	2.16;2.16	6.16	0.185	0.15096	Clathrin adaptor, mu subunit, C-terminal (3);	0.281600	0.35096	N	0.003451	T	0.00039	0.0001	N	0.21194	0.64	0.46260	P	0.001044000000000045	B;B	0.25235	0.121;0.099	B;B	0.19391	0.025;0.014	T	0.39860	-0.9593	9	0.09590	T	0.72	-0.3178	7.1263	0.25473	0.1001:0.5351:0.0:0.3648	rs34323725	646;646	Q8WXE9;G3V2T7	STON2_HUMAN;.	H	646;658;646	ENSP00000450857:R646H;ENSP00000267540:R646H	ENSP00000267540:R646H	R	-	2	0	STON2	80813471	0.000000	0.05858	0.344000	0.25628	0.488000	0.33401	-0.822000	0.04448	-0.008000	0.14320	0.650000	0.86243	CGT	C|0.900;T|0.100	0.100	strong		0.507	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104	
SCN7A	6332	hgsc.bcm.edu	37	2	167269629	167269629	+	Silent	SNP	T	T	G	rs33922582	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:167269629T>G	ENST00000409855.1	-	21	3543	c.3417A>C	c.(3415-3417)gcA>gcC	p.A1139A		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1139					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	CATTAAATGTTGCCTGTAAAA	0.294													T|||	303	0.0605032	0.059	0.0288	5008	,	,		17441	0.0129		0.0775	False		,,,				2504	0.1166				p.A1139A		Atlas-SNP	.											.	SCN7A	410	.	0			c.A3417C						PASS	.	T		183,3423		3,177,1623	39.0	36.0	36.0		3417	1.5	1.0	2	dbSNP_126	36	743,7377		30,683,3347	no	coding-synonymous	SCN7A	NM_002976.3		33,860,4970	GG,GT,TT		9.1502,5.0749,7.897		1139/1683	167269629	926,10800	1803	4060	5863	SO:0001819	synonymous_variant	6332	exon21			AAATGTTGCCTGT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.3417A>C	2.37:g.167269629T>G		Somatic	367	0	0		WXS	Illumina HiSeq	Phase_I	328	137	0.417683	NM_002976		Silent	SNP	ENST00000409855.1	37	CCDS46442.1																																																																																			T|0.945;G|0.055	0.055	strong		0.294	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
TEK	7010	hgsc.bcm.edu	37	9	27190655	27190655	+	Missense_Mutation	SNP	G	G	A	rs1334811	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:27190655G>A	ENST00000380036.4	+	10	1898	c.1456G>A	c.(1456-1458)Gtt>Att	p.V486I	TEK_ENST00000406359.4_Missense_Mutation_p.V443I|TEK_ENST00000519097.1_Missense_Mutation_p.V339I	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	486	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs1334811). {ECO:0000269|PubMed:17344846}.		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)	ATACAAACCCGTTAATCACTA	0.438													G|||	394	0.0786741	0.121	0.0447	5008	,	,		18526	0.0109		0.0497	False		,,,				2504	0.1452				p.V486I		Atlas-SNP	.											.	TEK	250	.	0			c.G1456A						PASS	.	G	ILE/VAL	553,3853	249.6+/-257.0	35,483,1685	110.0	110.0	110.0		1456	4.7	1.0	9	dbSNP_88	110	422,8178	130.5+/-188.4	11,400,3889	yes	missense	TEK	NM_000459.3	29	46,883,5574	AA,AG,GG		4.907,12.5511,7.4965	benign	486/1125	27190655	975,12031	2203	4300	6503	SO:0001583	missense	7010	exon10			AAACCCGTTAATC	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.1456G>A	9.37:g.27190655G>A	ENSP00000369375:p.Val486Ile	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	176	84	0.477273	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	119	0.05448717948717949	66	0.13414634146341464	12	0.03314917127071823	5	0.008741258741258742	36	0.047493403693931395	G	10.66	1.413443	0.25465	0.125511	0.04907	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000346448;ENST00000406359;ENST00000519080	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.73	4.65	0.58169	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.585658	0.14019	N	0.346917	T	0.00468	0.0015	L	0.29908	0.895	0.21499	N	0.999661	B;P;B;B	0.35612	0.329;0.512;0.329;0.424	B;B;B;B	0.33568	0.062;0.166;0.098;0.119	T	0.00363	-1.1788	10	0.38643	T	0.18	.	13.8836	0.63696	0.0828:0.0:0.9172:0.0	rs1334811;rs61594018;rs1334811	339;519;443;486	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	I	339;486;443;443;296	ENSP00000430686:V339I;ENSP00000369375:V486I;ENSP00000383977:V443I;ENSP00000428337:V296I	ENSP00000343716:V443I	V	+	1	0	TEK	27180655	1.000000	0.71417	1.000000	0.80357	0.469000	0.32828	3.253000	0.51469	2.713000	0.92767	0.591000	0.81541	GTT	G|0.928;A|0.072	0.072	strong		0.438	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
YPEL3	83719	hgsc.bcm.edu	37	16	30106716	30106716	+	5'UTR	SNP	C	C	A	rs184524218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:30106716C>A	ENST00000398838.4	-	0	187				YPEL3_ENST00000563788.1_5'UTR|YPEL3_ENST00000398841.1_Missense_Mutation_p.V30L|YPEL3_ENST00000562641.1_Missense_Mutation_p.V30L|RP11-455F5.3_ENST00000515455.2_RNA|YPEL3_ENST00000565479.1_Intron|YPEL3_ENST00000566595.1_5'UTR|YPEL3_ENST00000566134.1_5'UTR	NM_001145524.1	NP_001138996.1	P61236	YPEL3_HUMAN	yippee-like 3 (Drosophila)							nucleus (GO:0005634)				endometrium(1)|lung(2)	3						AGTGGCCCCACGCGGGGAGCG	0.672													C|||	16	0.00319489	0.0	0.0014	5008	,	,		14972	0.0		0.0129	False		,,,				2504	0.002				p.V30L		Atlas-SNP	.											.	YPEL3	5	.	0			c.G88T						PASS	.	C	,LEU/VAL	6,3864		0,6,1929	23.0	26.0	25.0		,88	3.5	1.0	16		25	108,8124		0,108,4008	yes	utr-5,missense	YPEL3	NM_001145524.1,NM_031477.4	,32	0,114,5937	AA,AC,CC		1.312,0.155,0.942	,	,30/158	30106716	114,11988	1935	4116	6051	SO:0001623	5_prime_UTR_variant	83719	exon1			GCCCCACGCGGGG	AF305622	CCDS42147.1, CCDS45459.1	16p11	2008-02-05							18327	protein-coding gene	gene with protein product		609724					Standard	NM_031477		Approved	MGC10500	uc002dwm.3	P61236		ENST00000398838.4:c.-27G>T	16.37:g.30106716C>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	37	24	0.648649	NM_031477	Q65Z99|Q86VK6|Q9BSJ4|Q9CQB6	Missense_Mutation	SNP	ENST00000398838.4	37	CCDS45459.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	13.01	2.110837	0.37242	0.00155	0.01312	ENSG00000090238	ENST00000398841	.	.	.	3.52	3.52	0.40303	.	0.000000	0.30109	N	0.010388	T	0.16128	0.0388	.	.	.	0.21627	N	0.999613	B	0.06786	0.001	B	0.06405	0.002	T	0.11591	-1.0581	8	0.10902	T	0.67	-5.6356	10.7694	0.46314	0.0:0.8051:0.1949:0.0	.	30	P61236-2	.	L	30	.	ENSP00000381821:V30L	V	-	1	0	YPEL3	30014217	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.998000	0.49465	1.811000	0.52892	0.561000	0.74099	GTG	C|0.995;A|0.005	0.005	strong		0.672	YPEL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434043.1	NM_031477	
OR51F1	256892	hgsc.bcm.edu	37	11	4790575	4790575	+	Silent	SNP	A	A	G	rs12788102	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790575A>G	ENST00000380383.1	-	1	593	c.594T>C	c.(592-594)tgT>tgC	p.C198C	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Silent_p.C191C|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	198						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)		GAATGTCTGAACATGCTAATT	0.383													A|||	243	0.0485224	0.0151	0.0965	5008	,	,		24195	0.0		0.1412	False		,,,				2504	0.0143				p.C191C		Atlas-SNP	.											.	OR51F1	60	.	0			c.T573C						PASS	.	A		214,4188	129.8+/-166.5	2,210,1989	146.0	141.0	143.0		573	2.8	1.0	11	dbSNP_121	143	1159,7437	238.5+/-269.9	94,971,3233	no	coding-synonymous	OR51F1	NM_001004752.1		96,1181,5222	GG,GA,AA		13.483,4.8614,10.5632		191/313	4790575	1373,11625	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			GTCTGAACATGCT	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.594T>C	11.37:g.4790575A>G		Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	306	149	0.486928	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.911;G|0.089	0.089	strong		0.383	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
DMBT1	1755	hgsc.bcm.edu	37	10	124358498	124358498	+	Missense_Mutation	SNP	T	T	G	rs144489236	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124358498T>G	ENST00000338354.3	+	26	3271	c.3165T>G	c.(3163-3165)atT>atG	p.I1055M	DMBT1_ENST00000368956.2_Missense_Mutation_p.I556M|DMBT1_ENST00000368955.3_Missense_Mutation_p.I1045M|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000330163.4_Missense_Mutation_p.I556M|DMBT1_ENST00000368909.3_Missense_Mutation_p.I1055M|DMBT1_ENST00000344338.3_Missense_Mutation_p.I1045M			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1055	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CAGGACCCATTGTCCTGGATG	0.597													t|||	100	0.0199681	0.0023	0.0706	5008	,	,		19043	0.001		0.0427	False		,,,				2504	0.0041				p.I1055M	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	3	0			c.T3165G						scavenged	.	T	MET/ILE,MET/ILE,MET/ILE	22,3952		0,22,1965	148.0	145.0	146.0		1668,3165,3135	-0.3	0.0	10	dbSNP_134	146	259,8081		0,259,3911	no	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	10,10,10	0,281,5876	GG,GT,TT		3.1055,0.5536,2.282	probably-damaging,probably-damaging,probably-damaging	556/1786,1055/2414,1045/2404	124358498	281,12033	1987	4170	6157	SO:0001583	missense	1755	exon26			ACCCATTGTCCTG		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.3165T>G	10.37:g.124358498T>G	ENSP00000342210:p.Ile1055Met	Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	110	68	0.618182	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		57	0.0260989010989011	3	0.006097560975609756	18	0.049723756906077346	1	0.0017482517482517483	35	0.04617414248021108	T	15.03	2.713206	0.48517	0.005536	0.031055	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.1;0.1	3.57	-0.309	0.12769	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.35615	U	0.003084	T	0.40595	0.1123	M	0.93638	3.44	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.998;0.999	D;D;D;D;D	0.87578	0.998;0.972;0.998;0.947;0.969	T	0.67337	-0.5696	10	0.72032	D	0.01	.	8.7996	0.34901	0.0:0.3675:0.0:0.6325	.	562;1055;556;1045;1055	Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	M	1055;1055;1055;1055;1055;1055;556;1045;556;556;1055;1045;556	ENSP00000342210:I1055M;ENSP00000343175:I1045M;ENSP00000327747:I556M;ENSP00000357905:I1055M;ENSP00000357951:I1045M;ENSP00000357952:I556M	ENSP00000331522:I556M	I	+	3	3	DMBT1	124348488	0.000000	0.05858	0.006000	0.13384	0.155000	0.21991	-2.933000	0.00687	-0.009000	0.14296	0.456000	0.33151	ATT	T|0.976;G|0.024	0.024	strong		0.597	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
OR51B4	79339	hgsc.bcm.edu	37	11	5322520	5322520	+	Silent	SNP	G	G	A	rs12283334	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5322520G>A	ENST00000380224.1	-	1	706	c.657C>T	c.(655-657)ctC>ctT	p.L219L	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_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	79	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	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	
EML3	256364	hgsc.bcm.edu	37	11	62378660	62378660	+	Silent	SNP	G	G	A	rs12808829	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:62378660G>A	ENST00000394773.2	-	3	658	c.351C>T	c.(349-351)agC>agT	p.S117S	EML3_ENST00000278845.4_Silent_p.S118S|EML3_ENST00000529309.1_Silent_p.S117S|EML3_ENST00000531557.1_5'Flank|EML3_ENST00000494176.2_Silent_p.S89S|ROM1_ENST00000534093.1_5'Flank|ROM1_ENST00000278833.3_5'Flank	NM_153265.2	NP_694997.2	Q32P44	EMAL3_HUMAN	echinoderm microtubule associated protein like 3	117						cytoplasm (GO:0005737)|microtubule (GO:0005874)				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						ATTGGGTCCCGCTAGGCTCTT	0.687													A|||	972	0.194089	0.1936	0.2032	5008	,	,		15245	0.0506		0.3161	False		,,,				2504	0.2106				p.S117S		Atlas-SNP	.											.	EML3	61	.	0			c.C351T						PASS	.	A		926,3418		102,722,1348	11.0	14.0	13.0		351	-5.5	0.1	11	dbSNP_121	13	2990,5538		549,1892,1823	no	coding-synonymous	EML3	NM_153265.2		651,2614,3171	AA,AG,GG		35.061,21.3168,30.4226		117/897	62378660	3916,8956	2172	4264	6436	SO:0001819	synonymous_variant	256364	exon3			GGTCCCGCTAGGC	AK093146	CCDS8023.2	11q12.3	2013-01-10			ENSG00000149499	ENSG00000149499		"""WD repeat domain containing"""	26666	protein-coding gene	gene with protein product						15225882, 14744259	Standard	NM_153265		Approved	FLJ35827, ELP95	uc001ntu.1	Q32P44	OTTHUMG00000149817	ENST00000394773.2:c.351C>T	11.37:g.62378660G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_153265	Q6ZQW7|Q8NA55	Silent	SNP	ENST00000394773.2	37	CCDS8023.2	472	0.21611721611721613	112	0.22764227642276422	91	0.2513812154696133	32	0.055944055944055944	237	0.31266490765171506	A	4.052	0.007268	0.07866	0.213168	0.35061	ENSG00000149499	ENST00000394776	.	.	.	5.05	-5.49	0.02584	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999872094	.	.	.	.	.	.	T	0.37865	-0.9687	3	.	.	.	-0.0522	7.3335	0.26596	0.2996:0.2839:0.4165:0.0	rs12808829	.	.	.	W	112	.	.	R	-	1	2	EML3	62135236	0.008000	0.16893	0.095000	0.20976	0.334000	0.28698	-0.688000	0.05150	-1.005000	0.03417	-0.521000	0.04368	CGG	G|0.761;A|0.239	0.239	strong		0.687	EML3-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313432.1	NM_153265	
VPS13C	54832	hgsc.bcm.edu	37	15	62253954	62253954	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:62253954G>T	ENST00000261517.5	-	35	3815	c.3742C>A	c.(3742-3744)Ccg>Acg	p.P1248T	VPS13C_ENST00000249837.3_Missense_Mutation_p.P1205T|VPS13C_ENST00000395898.3_Missense_Mutation_p.P1205T|VPS13C_ENST00000395896.4_Missense_Mutation_p.P1248T	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						ACTATAACCGGTGCTTTCAAA	0.458																																					p.P1248T		Atlas-SNP	.											.	VPS13C	506	.	0			c.C3742A						PASS	.						111.0	110.0	111.0					15																	62253954		2203	4300	6503	SO:0001583	missense	54832	exon35			TAACCGGTGCTTT	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.3742C>A	15.37:g.62253954G>T	ENSP00000261517:p.Pro1248Thr	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	109	8	0.0733945	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186000	0.78789	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.14893	2.47;2.47;2.47	5.76	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.49474	0.1559	M	0.90309	3.105	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.76071	0.987;0.982;0.974;0.971	T	0.61520	-0.7046	10	0.87932	D	0	.	14.8531	0.70313	0.0689:0.0:0.9311:0.0	.	1205;1248;1205;1248	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	T	1205;1248;1248;1248	ENSP00000249837:P1205T;ENSP00000261517:P1248T;ENSP00000379233:P1248T	ENSP00000249837:P1205T	P	-	1	0	VPS13C	60041246	1.000000	0.71417	0.936000	0.37596	0.978000	0.69477	9.476000	0.97823	1.434000	0.47414	0.563000	0.77884	CCG	.	.	none		0.458	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
MOK	5891	hgsc.bcm.edu	37	14	102729881	102729881	+	Splice_Site	SNP	A	A	G	rs56377169	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102729881A>G	ENST00000361847.2	-	4	515		c.e4+1		MOK_ENST00000522874.1_Splice_Site|MOK_ENST00000524214.1_Splice_Site|MOK_ENST00000193029.6_Splice_Site	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase						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)										TATTCTACGTACCTCGTATTA	0.318													A|||	278	0.0555112	0.0166	0.049	5008	,	,		18341	0.003		0.0785	False		,,,				2504	0.1431				.		Atlas-SNP	.											.	.	.	.	0			c.283+2T>C						PASS	.	A		121,4281	87.3+/-125.9	1,119,2081	108.0	109.0	108.0			5.8	1.0	14	dbSNP_129	108	613,7987	157.7+/-211.4	17,579,3704	yes	splice-5	MOK	NM_014226.1		18,698,5785	GG,GA,AA		7.1279,2.7488,5.6453			102729881	734,12268	2201	4300	6501	SO:0001630	splice_region_variant	5891	exon5			CTACGTACCTCGT	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.283+1T>C	14.37:g.102729881A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	31	0.322917	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Splice_Site	SNP	ENST00000361847.2	37	CCDS9971.1	80	0.03663003663003663	10	0.02032520325203252	20	0.055248618784530384	2	0.0034965034965034965	48	0.0633245382585752	A	19.54	3.847364	0.71603	0.027488	0.071279	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	.	.	.	5.8	5.8	0.92144	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3848	0.66938	1.0:0.0:0.0:0.0	rs56377169	.	.	.	.	-1	.	.	.	-	.	.	RAGE	101799634	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	7.256000	0.78350	2.209000	0.71365	0.533000	0.62120	.	A|0.954;G|0.046	0.046	strong		0.318	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		Intron
SRBD1	55133	hgsc.bcm.edu	37	2	45640374	45640374	+	Missense_Mutation	SNP	C	C	A	rs3755073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:45640374C>A	ENST00000263736.4	-	19	2454	c.2392G>T	c.(2392-2394)Gtt>Ttt	p.V798F	SRBD1_ENST00000535761.1_Missense_Mutation_p.V317F|SRBD1_ENST00000490133.1_5'UTR	NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	798			V -> F (in dbSNP:rs3755073).		nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			GTGACCTCAACGTCTGCTGAA	0.398													C|||	1056	0.210863	0.3495	0.2493	5008	,	,		20683	0.1468		0.1004	False		,,,				2504	0.1759				p.V798F		Atlas-SNP	.											.	SRBD1	107	.	0			c.G2392T						PASS	.	C	PHE/VAL	1403,3003	462.4+/-353.2	236,931,1036	251.0	229.0	237.0		2392	4.0	0.8	2	dbSNP_107	237	773,7827	182.8+/-231.1	37,699,3564	yes	missense	SRBD1	NM_018079.4	50	273,1630,4600	AA,AC,CC		8.9884,31.8429,16.7307	benign	798/996	45640374	2176,10830	2203	4300	6503	SO:0001583	missense	55133	exon19			CCTCAACGTCTGC	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.2392G>T	2.37:g.45640374C>A	ENSP00000263736:p.Val798Phe	Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	184	182	0.98913	NM_018079	Q53T56|Q96TA4|Q9NW11	Missense_Mutation	SNP	ENST00000263736.4	37	CCDS1823.1	420	0.19230769230769232	167	0.3394308943089431	85	0.23480662983425415	95	0.1660839160839161	73	0.09630606860158311	C	1.385	-0.582339	0.03827	0.318429	0.089884	ENSG00000068784	ENST00000263736;ENST00000535761	T;T	0.30714	1.93;1.52	4.9	4.02	0.46733	.	0.979149	0.08391	N	0.952940	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.25351	0.124	B	0.22152	0.038	T	0.38564	-0.9655	9	0.62326	D	0.03	.	12.2312	0.54488	0.0:0.8418:0.0:0.1582	rs3755073;rs52834816;rs58670373;rs3755073	798	Q8N5C6	SRBD1_HUMAN	F	798;317	ENSP00000263736:V798F;ENSP00000441272:V317F	ENSP00000263736:V798F	V	-	1	0	SRBD1	45493878	0.001000	0.12720	0.793000	0.32043	0.038000	0.13279	0.894000	0.28350	0.678000	0.31325	-1.119000	0.02030	GTT	C|0.818;A|0.182	0.182	strong		0.398	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079	
EIF4ENIF1	56478	hgsc.bcm.edu	37	22	31838085	31838085	+	Silent	SNP	G	G	A	rs5997988	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:31838085G>A	ENST00000397525.1	-	17	2449	c.2226C>T	c.(2224-2226)agC>agT	p.S742S	EIF4ENIF1_ENST00000441289.1_5'Flank|EIF4ENIF1_ENST00000397523.1_Silent_p.S718S|EIF4ENIF1_ENST00000382180.2_Silent_p.S397S|EIF4ENIF1_ENST00000344710.5_Silent_p.S568S|EIF4ENIF1_ENST00000330125.5_Silent_p.S742S	NM_001164501.1	NP_001157973.1	Q9NRA8	4ET_HUMAN	eukaryotic translation initiation factor 4E nuclear import factor 1	742						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						TGGGTACAGAGCTGGATGACA	0.478													G|||	1621	0.323682	0.4039	0.3026	5008	,	,		18314	0.0377		0.4583	False		,,,				2504	0.3865				p.S742S		Atlas-SNP	.											.	EIF4ENIF1	80	.	0			c.C2226T						PASS	.	G	,,	1863,2543	539.4+/-375.3	388,1087,728	104.0	109.0	107.0		2226,1704,2226	-0.7	0.3	22	dbSNP_114	107	3953,4647	550.0+/-385.6	907,2139,1254	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4ENIF1	NM_001164501.1,NM_001164502.1,NM_019843.3	,,	1295,3226,1982	AA,AG,GG		45.9651,42.2833,44.7178	,,	742/986,568/812,742/986	31838085	5816,7190	2203	4300	6503	SO:0001819	synonymous_variant	56478	exon17			TACAGAGCTGGAT	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.2226C>T	22.37:g.31838085G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_019843	B1AKL2|B1AKL3|B2RBF1|Q8NCF2|Q9H708	Silent	SNP	ENST00000397525.1	37	CCDS13898.1																																																																																			G|0.611;A|0.389	0.389	strong		0.478	EIF4ENIF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127926.1	NM_019843	
ABI3	51225	hgsc.bcm.edu	37	17	47297633	47297633	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:47297633C>T	ENST00000225941.1	+	6	1245	c.747C>T	c.(745-747)gcC>gcT	p.A249A	ABI3_ENST00000419580.2_Silent_p.A243A	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	249	Pro-rich.				cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			CACCAGCAGCCGTCGAGGTGT	0.692										HNSCC(55;0.14)																											p.A249A		Atlas-SNP	.											ABI3,right_upper_lobe,carcinoma,0,1	ABI3	35	1	0			c.C747T						scavenged	.						37.0	33.0	35.0					17																	47297633		2200	4299	6499	SO:0001819	synonymous_variant	51225	exon6			AGCAGCCGTCGAG	AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.747C>T	17.37:g.47297633C>T		Somatic	324	1	0.00308642		WXS	Illumina HiSeq	Phase_I	269	3	0.0111524	NM_016428	C9IZN8|Q9H0P6	Silent	SNP	ENST00000225941.1	37	CCDS11546.1																																																																																			.	.	none		0.692	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428	
KIAA0226	9711	hgsc.bcm.edu	37	3	197401952	197401952	+	Silent	SNP	T	T	C	rs28562770	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:197401952T>C	ENST00000296343.5	-	20	2855	c.2856A>G	c.(2854-2856)tcA>tcG	p.S952S	MIR922_ENST00000401223.1_RNA|KIAA0226_ENST00000273582.5_Silent_p.S907S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	952					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)		CCTCGTAGTCTGACAGGTAAG	0.677													C|||	1182	0.236022	0.6475	0.0865	5008	,	,		10006	0.0327		0.1173	False		,,,				2504	0.1176				p.S952S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.A2856G						PASS	.	C	,	2052,1830		540,972,429	31.0	38.0	36.0		2721,2856	-5.3	1.0	3	dbSNP_125	36	839,7391		46,747,3322	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	586,1719,3751	CC,CT,TT		10.1944,47.1406,23.8689	,	907/928,952/973	197401952	2891,9221	1941	4115	6056	SO:0001819	synonymous_variant	9711	exon20			GTAGTCTGACAGG	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.2856A>G	3.37:g.197401952T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	464	0.21245421245421245	321	0.6524390243902439	32	0.08839779005524862	24	0.04195804195804196	87	0.11477572559366754	C	5.623	0.299568	0.10622	0.528594	0.101944	ENSG00000145016	ENST00000413360	.	.	.	5.62	-5.35	0.02697	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999889359	.	.	.	.	.	.	T	0.45175	-0.9279	3	.	.	.	.	1.0963	0.01674	0.169:0.2562:0.2651:0.3097	rs28562770	.	.	.	G	914	.	.	R	-	1	2	KIAA0226	198886349	0.000000	0.05858	0.967000	0.41034	0.377000	0.30045	-7.278000	0.00040	-0.833000	0.04245	-2.378000	0.00233	AGA	T|0.811;C|0.189	0.189	strong		0.677	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
SCAF4	57466	hgsc.bcm.edu	37	21	33068937	33068937	+	Missense_Mutation	SNP	C	C	A	rs78537042	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:33068937C>A	ENST00000286835.7	-	8	1286	c.904G>T	c.(904-906)Gtg>Ttg	p.V302L	SCAF4_ENST00000434667.3_Missense_Mutation_p.V287L|SCAF4_ENST00000399804.1_Missense_Mutation_p.V302L	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	302				V -> L (in Ref. 6; BAA86486). {ECO:0000305}.		nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GCAGCAGGCACGGTGGCGGTG	0.532													C|||	131	0.0261581	0.0023	0.049	5008	,	,		12780	0.0		0.0746	False		,,,				2504	0.0194				p.V302L		Atlas-SNP	.											.	SCAF4	142	.	0			c.G904T						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	82,4324	69.2+/-107.0	3,76,2124	66.0	69.0	68.0		904,904,859	-1.0	0.0	21	dbSNP_132	68	699,7901	172.0+/-222.8	37,625,3638	yes	missense,missense,missense	SCAF4	NM_020706.2,NM_001145445.1,NM_001145444.1	32,32,32	40,701,5762	AA,AC,CC		8.1279,1.8611,6.0049	benign,benign,benign	302/1148,302/1126,287/1133	33068937	781,12225	2203	4300	6503	SO:0001583	missense	57466	exon8			CAGGCACGGTGGC	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.904G>T	21.37:g.33068937C>A	ENSP00000286835:p.Val302Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	161	104	0.645963	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Missense_Mutation	SNP	ENST00000286835.7	37	CCDS33537.1	70	0.03205128205128205	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	50	0.06596306068601583	C	4.593	0.110282	0.08780	0.018611	0.081279	ENSG00000156304	ENST00000434667;ENST00000286835;ENST00000399804	T;T;T	0.41400	1.0;1.0;1.02	4.65	-1.02	0.10135	.	1.513160	0.03578	N	0.229706	T	0.01124	0.0037	N	0.08118	0	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.09100	-1.0690	10	0.11485	T	0.65	0.5448	9.2428	0.37506	0.0:0.4045:0.0:0.5955	.	287;302;302	C9JLZ0;O95104-2;O95104	.;.;SFR15_HUMAN	L	287;302;302	ENSP00000402377:V287L;ENSP00000286835:V302L;ENSP00000382703:V302L	ENSP00000286835:V302L	V	-	1	0	SCAF4	31990808	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-1.270000	0.02831	-0.193000	0.10415	0.655000	0.94253	GTG	C|0.947;A|0.053	0.053	strong		0.532	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
MICALCL	84953	hgsc.bcm.edu	37	11	12315848	12315848	+	Silent	SNP	C	C	T	rs1493952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:12315848C>T	ENST00000256186.2	+	3	1161	c.870C>T	c.(868-870)ggC>ggT	p.G290G		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	290					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		ACTCTGAAGGCGGGAAGAAGG	0.567																																					p.G290G		Atlas-SNP	.											.	MICALCL	59	.	0			c.C870T						PASS	.	T		2016,1876		518,980,448	52.0	58.0	56.0		870	-1.6	0.0	11	dbSNP_88	56	2614,5620		424,1766,1927	no	coding-synonymous	MICALCL	NM_032867.2		942,2746,2375	TT,TC,CC		31.7464,48.2014,38.1824		290/696	12315848	4630,7496	1946	4117	6063	SO:0001819	synonymous_variant	84953	exon3			TGAAGGCGGGAAG	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.870C>T	11.37:g.12315848C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_032867	Q7RTP7|Q96JU6	Silent	SNP	ENST00000256186.2	37	CCDS41620.1																																																																																			C|0.576;T|0.424	0.424	strong		0.567	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
SDC1	6382	hgsc.bcm.edu	37	2	20403949	20403949	+	Silent	SNP	C	C	T	rs2230924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000482879.1_5'UTR|SDC1_ENST00000381150.1_Silent_p.E84E	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	24	0	0		WXS	Illumina HiSeq	Phase_I	30	9	0.3	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	
ZXDC	79364	hgsc.bcm.edu	37	3	126191011	126191011	+	Silent	SNP	G	G	A	rs62264721	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126191011G>A	ENST00000389709.3	-	2	1098	c.1045C>T	c.(1045-1047)Ctg>Ttg	p.L349L	ZXDC_ENST00000336332.5_Silent_p.L349L	NM_025112.4	NP_079388.3	Q2QGD7	ZXDC_HUMAN	ZXD family zinc finger C	349					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)		TGGCTCCGCAGGTGAATTTTC	0.468													G|||	105	0.0209665	0.0061	0.0058	5008	,	,		18844	0.0665		0.0119	False		,,,				2504	0.0143				p.L349L		Atlas-SNP	.											.	ZXDC	87	.	0			c.C1045T						PASS	.	G	,	35,4239		0,35,2102	58.0	63.0	62.0		1045,1045	2.4	1.0	3	dbSNP_129	62	88,8460		0,88,4186	yes	coding-synonymous,coding-synonymous	ZXDC	NM_001040653.2,NM_025112.4	,	0,123,6288	AA,AG,GG		1.0295,0.8189,0.9593	,	349/711,349/859	126191011	123,12699	2137	4274	6411	SO:0001819	synonymous_variant	79364	exon2			TCCGCAGGTGAAT	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.1045C>T	3.37:g.126191011G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_025112	C5J0H9|Q6DKI8|Q7L3L1|Q8NAU2	Silent	SNP	ENST00000389709.3	37	CCDS43145.1																																																																																			G|0.982;A|0.018	0.018	strong		0.468	ZXDC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370327.2	NM_025112	
MORN2	729967	hgsc.bcm.edu	37	2	39109558	39109558	+	Missense_Mutation	SNP	G	G	A	rs3099950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:39109558G>A	ENST00000410014.1	+	5	521	c.142G>A	c.(142-144)Gaa>Aaa	p.E48K	MORN2_ENST00000409665.1_Missense_Mutation_p.E48K|MORN2_ENST00000409077.2_Missense_Mutation_p.E15K|MORN2_ENST00000409131.2_Missense_Mutation_p.E26K|MORN2_ENST00000340556.6_Missense_Mutation_p.E48K|RNU6-851P_ENST00000384565.1_RNA			Q502X0	MORN2_HUMAN	MORN repeat containing 2	48			E -> K (in dbSNP:rs3099950). {ECO:0000269|PubMed:15489334}.							breast(1)	1						TTGCAGGGTGGAAGGTGAAGG	0.338													G|||	349	0.0696885	0.0061	0.0865	5008	,	,		17963	0.001		0.1352	False		,,,				2504	0.1472				p.E48K		Atlas-SNP	.											.	MORN2	3	.	0			c.G142A						PASS	.	G	LYS/GLU	36,1348		0,36,656	178.0	158.0	164.0	http://www.ncbi.nlm.nih.gov/pubmed?term	142	5.4	1.0	2	dbSNP_103	164	373,2809		21,331,1239	yes	missense	MORN2	NM_001145450.1	56	21,367,1895	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	11.7222,2.6012,8.9575	probably-damaging	48/80	39109558	409,4157	692	1591	2283	SO:0001583	missense	729967	exon5			AGGGTGGAAGGTG	AY367766	CCDS46262.1	2p22.1	2010-06-04			ENSG00000188010	ENSG00000188010			30166	protein-coding gene	gene with protein product						12477932	Standard	NM_001145450		Approved	MOPT	uc010fak.3	Q502X0	OTTHUMG00000128589	ENST00000410014.1:c.142G>A	2.37:g.39109558G>A	ENSP00000386563:p.Glu48Lys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_001145450	Q6UL00	Missense_Mutation	SNP	ENST00000410014.1	37	CCDS46262.1	139	0.06364468864468864	5	0.01016260162601626	32	0.08839779005524862	1	0.0017482517482517483	101	0.13324538258575197	G	19.36	3.813180	0.70912	0.026012	0.117222	ENSG00000188010	ENST00000340556;ENST00000410014;ENST00000409665;ENST00000409077;ENST00000409131	T;T;T;T;T	0.79653	0.88;0.88;0.88;-1.29;0.87	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000007	T	0.09730	0.0239	.	.	.	0.22728	P	0.99880355	D	0.89917	1.0	D	0.75484	0.986	T	0.56505	-0.7968	8	0.51188	T	0.08	-19.6045	17.9286	0.88991	0.0:0.0:1.0:0.0	rs3099950;rs52822530;rs60772543;rs3099950	48	Q502X0	MORN2_HUMAN	K	48;48;48;15;26	ENSP00000344551:E48K;ENSP00000386563:E48K;ENSP00000386874:E48K;ENSP00000387161:E15K;ENSP00000387181:E26K	ENSP00000344551:E48K	E	+	1	0	MORN2	38963062	1.000000	0.71417	0.982000	0.44146	0.879000	0.50718	6.017000	0.70805	2.504000	0.84457	0.650000	0.86243	GAA	G|0.919;A|0.081	0.081	strong		0.338	MORN2-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331568.1	NM_194270	
XIRP2	129446	hgsc.bcm.edu	37	2	168106246	168106246	+	Missense_Mutation	SNP	G	G	A	rs16853330	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168106246G>A	ENST00000409195.1	+	9	8433	c.8344G>A	c.(8344-8346)Gta>Ata	p.V2782I	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.V2560I|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.V2782I	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2607					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						AAGAGTGACAGTACAATTGCC	0.408													A|||	1181	0.235823	0.3623	0.1686	5008	,	,		20362	0.2173		0.1282	False		,,,				2504	0.2423				p.V2782I		Atlas-SNP	.											XIRP2,NS,carcinoma,-1,1	XIRP2	914	1	0			c.G8344A						PASS	.	A	,,ILE/VAL,,ILE/VAL	1194,2546		201,792,877	62.0	59.0	60.0		,,7678,,8344	-5.0	0.0	2	dbSNP_123	60	926,7296		56,814,3241	yes	intron,intron,missense,intron,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,29,,29	257,1606,4118	AA,AG,GG		11.2625,31.9251,17.7228	,,possibly-damaging,,possibly-damaging	,,2560/3328,,2782/3550	168106246	2120,9842	1870	4111	5981	SO:0001583	missense	129446	exon9			GTGACAGTACAAT	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.8344G>A	2.37:g.168106246G>A	ENSP00000386840:p.Val2782Ile	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	137	64	0.467153	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	480	0.21978021978021978	192	0.3902439024390244	52	0.143646408839779	136	0.23776223776223776	100	0.13192612137203166	A	0.029	-1.350948	0.01256	0.319251	0.112625	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02446	4.29;4.29;4.29	6.17	-5.01	0.02991	.	1.339210	0.04273	N	0.342418	T	0.00012	0.0000	N	0.02736	-0.51	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	0.47849	-0.9085	9	0.05525	T	0.97	-0.4314	12.7259	0.57170	0.2092:0.2213:0.5694:0.0	rs16853330;rs52825904;rs61575660;rs16853330	2607;2607;2560	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	I	2782;2782;2560;196	ENSP00000386840:V2782I;ENSP00000295237:V2782I;ENSP00000387255:V2560I	ENSP00000295237:V2782I	V	+	1	0	XIRP2	167814492	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-0.912000	0.04046	-1.340000	0.02227	-0.254000	0.11334	GTA	G|0.774;A|0.225	0.225	strong		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
HPSE	10855	hgsc.bcm.edu	37	4	84227453	84227453	+	Missense_Mutation	SNP	C	C	T	rs138882001	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:84227453C>T	ENST00000405413.2	-	10	1245	c.1109G>A	c.(1108-1110)gGc>gAc	p.G370D	HPSE_ENST00000513463.1_Missense_Mutation_p.G312D|HPSE_ENST00000311412.5_Missense_Mutation_p.G370D|HPSE_ENST00000512196.1_Intron	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	370					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	GGCTGACAGGCCCAATTTATC	0.423													C|||	2	0.000399361	0.0	0.0	5008	,	,		17899	0.0		0.001	False		,,,				2504	0.001				p.G370D		Atlas-SNP	.											HPSE,right_upper_lobe,carcinoma,0,1	HPSE	55	1	0			c.G1109A						scavenged	.	C	ASP/GLY,,ASP/GLY,ASP/GLY	6,4400	11.4+/-27.6	0,6,2197	105.0	97.0	100.0		1109,,935,1109	5.1	1.0	4	dbSNP_134	100	16,8584	11.9+/-42.8	0,16,4284	yes	missense,intron,missense,missense	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	94,,94,94	0,22,6481	TT,TC,CC		0.186,0.1362,0.1692	probably-damaging,,probably-damaging,probably-damaging	370/544,,312/486,370/544	84227453	22,12984	2203	4300	6503	SO:0001583	missense	10855	exon9			GACAGGCCCAATT	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1109G>A	4.37:g.84227453C>T	ENSP00000384262:p.Gly370Asp	Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	37	CCDS3602.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	25.5	4.639598	0.87760	0.001362	0.00186	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000454730;ENST00000513463	T;T;T	0.56275	0.47;0.47;0.47	5.08	5.08	0.68730	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.049396	0.85682	D	0.000000	T	0.79759	0.4501	M	0.92970	3.365	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.995;0.997	D	0.84676	0.0714	10	0.72032	D	0.01	-12.7363	18.2572	0.90023	0.0:1.0:0.0:0.0	.	312;312;370	A9JIG7;E9PGR1;Q9Y251	.;.;HPSE_HUMAN	D	370;370;84;312	ENSP00000308107:G370D;ENSP00000384262:G370D;ENSP00000421365:G312D	ENSP00000308107:G370D	G	-	2	0	HPSE	84446477	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.760000	0.74939	2.637000	0.89404	0.491000	0.48974	GGC	C|0.999;T|0.001	0.001	strong		0.423	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
OR7A5	26659	hgsc.bcm.edu	37	19	14938616	14938616	+	Silent	SNP	T	T	C	rs2190686	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14938616T>C	ENST00000322301.3	-	2	525	c.438A>G	c.(436-438)ctA>ctG	p.L146L	OR7A5_ENST00000594432.1_Silent_p.L146L|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	146					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(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						TCCAGGATGCTAGAACCAGCA	0.507													.|||	2800	0.559105	0.6218	0.428	5008	,	,		20351	0.6815		0.3917	False		,,,				2504	0.6135				p.L146L		Atlas-SNP	.											.	OR7A5	43	.	0			c.A438G						PASS	.	C		2699,1707	514.1+/-368.5	825,1049,329	74.0	68.0	70.0		438	0.8	0.0	19	dbSNP_96	70	3404,5196	639.0+/-399.4	692,2020,1588	no	coding-synonymous	OR7A5	NM_017506.1		1517,3069,1917	CC,CT,TT		39.5814,38.7426,46.9245		146/320	14938616	6103,6903	2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			GGATGCTAGAACC	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"""GPCR / Class A : Olfactory receptors"""	8368	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily A, member 5 pseudogene"""				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.438A>G	19.37:g.14938616T>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	37	CCDS12318.1																																																																																			T|0.505;C|0.495	0.495	strong		0.507	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
SLFN13	146857	hgsc.bcm.edu	37	17	33768199	33768199	+	Silent	SNP	G	G	A	rs1822403	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33768199G>A	ENST00000285013.6	-	6	2384	c.2109C>T	c.(2107-2109)gaC>gaT	p.D703D	SLFN13_ENST00000533791.1_Silent_p.D703D|SLFN13_ENST00000542635.1_Silent_p.D703D|SLFN13_ENST00000534689.1_Silent_p.D385D|SLFN13_ENST00000360502.2_Silent_p.D385D|SLFN13_ENST00000526861.1_Silent_p.D703D	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	703						intracellular (GO:0005622)	ATP binding (GO:0005524)	p.D703D(1)		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)		TCTGAAAGTAGTCCAGAAAGA	0.478													G|||	1854	0.370208	0.5068	0.3314	5008	,	,		16920	0.3849		0.3688	False		,,,				2504	0.1994				p.D703D		Atlas-SNP	.											SLFN13,NS,carcinoma,0,1	SLFN13	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C2109T						PASS	.	G		2104,2302	565.2+/-381.6	518,1068,617	129.0	136.0	133.0		2109	2.4	1.0	17	dbSNP_92	133	3222,5378	484.4+/-371.4	610,2002,1688	no	coding-synonymous	SLFN13	NM_144682.5		1128,3070,2305	AA,AG,GG		37.4651,47.7531,40.9503		703/898	33768199	5326,7680	2203	4300	6503	SO:0001819	synonymous_variant	146857	exon6			AAAGTAGTCCAGA	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.2109C>T	17.37:g.33768199G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Silent	SNP	ENST00000285013.6	37	CCDS32620.1																																																																																			.	.	weak		0.478	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
TES	26136	hgsc.bcm.edu	37	7	115897392	115897392	+	Silent	SNP	G	G	C	rs4710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:115897392G>C	ENST00000358204.4	+	7	1337	c.1122G>C	c.(1120-1122)cgG>cgC	p.R374R	TES_ENST00000393481.2_Silent_p.R365R|AC002066.1_ENST00000446355.2_RNA|TES_ENST00000537767.1_Silent_p.R132R|AC073130.3_ENST00000444244.1_RNA	NM_015641.3	NP_056456.1	Q9UGI8	TES_HUMAN	testis derived transcript (3 LIM domains)	374	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|protein complex (GO:0043234)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(4)|lung(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	12	Lung NSC(10;0.0137)|all_lung(10;0.0148)	Breast(660;0.0602)	STAD - Stomach adenocarcinoma(10;0.00878)			AAGTGCAGCGGGTGACCTATA	0.463													G|||	1998	0.398962	0.4092	0.3631	5008	,	,		18084	0.5694		0.2952	False		,,,				2504	0.3415				p.R374R		Atlas-SNP	.											TES_ENST00000257721,colon,carcinoma,+1,2	TES	68	2	0			c.G1122C						PASS	.	G	,	1763,2643	524.6+/-371.4	360,1043,800	114.0	103.0	107.0		1122,1095	-3.6	1.0	7	dbSNP_52	107	2242,6358	379.9+/-339.4	284,1674,2342	no	coding-synonymous,coding-synonymous	TES	NM_015641.3,NM_152829.2	,	644,2717,3142	CC,CG,GG		26.0698,40.0136,30.7935	,	374/422,365/413	115897392	4005,9001	2203	4300	6503	SO:0001819	synonymous_variant	26136	exon7			GCAGCGGGTGACC	AJ250865	CCDS5763.1, CCDS5764.1	7q31.2	2004-04-20			ENSG00000135269	ENSG00000135269			14620	protein-coding gene	gene with protein product		606085				10950921	Standard	NM_015641		Approved	DKFZP586B2022, TESS-2, TESTIN	uc003vho.3	Q9UGI8	OTTHUMG00000023092	ENST00000358204.4:c.1122G>C	7.37:g.115897392G>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	234	76	0.324786	NM_015641	A4D0U6|Q9GZQ1|Q9HAJ9	Silent	SNP	ENST00000358204.4	37	CCDS5763.1																																																																																			T|0.000;G|0.669;C|0.331	0.331	strong		0.463	TES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059413.2	NM_015641	
SRRM2	23524	hgsc.bcm.edu	37	16	2812647	2812647	+	Silent	SNP	C	C	T	rs2240142	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2812647C>T	ENST00000301740.8	+	11	2667	c.2118C>T	c.(2116-2118)agC>agT	p.S706S		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	706	Arg-rich.|Ser-rich.				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						GCAGTAGAAGCTTAGTTAGAC	0.517													C|||	876	0.17492	0.2012	0.1311	5008	,	,		19523	0.2589		0.167	False		,,,				2504	0.092				p.S706S		Atlas-SNP	.											SRRM2,NS,lymphoid_neoplasm,0,1	SRRM2	263	1	0			c.C2118T						scavenged	.	C		837,3559	327.2+/-299.9	72,693,1433	72.0	74.0	74.0		2118	2.0	1.0	16	dbSNP_98	74	1348,7252	261.4+/-283.8	106,1136,3058	no	coding-synonymous	SRRM2	NM_016333.3		178,1829,4491	TT,TC,CC		15.6744,19.04,16.8129		706/2753	2812647	2185,10811	2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			TAGAAGCTTAGTT	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.2118C>T	16.37:g.2812647C>T		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																			C|0.826;T|0.174	0.174	strong		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157009	26157009	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26157009C>T	ENST00000304218.3	+	1	451	c.391C>T	c.(391-393)Cca>Tca	p.P131S	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	131					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						GGCCAAGAAGCCAGCAGGAGC	0.642																																					p.P131S		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C391T						PASS	.						16.0	22.0	20.0					6																	26157009		2201	4297	6498	SO:0001583	missense	3008	exon1			AAGAAGCCAGCAG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.391C>T	6.37:g.26157009C>T	ENSP00000307705:p.Pro131Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	109	35	0.321101	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	3.113	-0.182313	0.06340	.	.	ENSG00000168298	ENST00000304218	T	0.25579	1.79	5.51	-0.293	0.12835	.	0.186307	0.47455	N	0.000233	T	0.04634	0.0126	L	0.38175	1.15	0.48975	D	0.999731	B	0.10296	0.003	B	0.08055	0.003	T	0.29731	-1.0002	10	0.11182	T	0.66	0.2785	3.53	0.07773	0.114:0.485:0.2269:0.1741	.	131	P10412	H14_HUMAN	S	131	ENSP00000307705:P131S	ENSP00000307705:P131S	P	+	1	0	HIST1H1E	26264988	0.865000	0.29922	0.579000	0.28588	0.041000	0.13682	0.334000	0.19787	0.052000	0.16007	0.561000	0.74099	CCA	.	.	none		0.642	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
KRT84	3890	hgsc.bcm.edu	37	12	52777513	52777513	+	Missense_Mutation	SNP	T	T	C	rs2245203	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52777513T>C	ENST00000257951.3	-	2	682	c.616A>G	c.(616-618)Atc>Gtc	p.I206V	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	206	Linker 1.|Rod.		I -> V (in dbSNP:rs2245203).		hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TTGCTCCTGATACATTTCTGC	0.537													C|||	1664	0.332268	0.6172	0.3199	5008	,	,		21008	0.1954		0.2068	False		,,,				2504	0.226				p.I206V		Atlas-SNP	.											.	KRT84	61	.	0			c.A616G						PASS	.	C	VAL/ILE	2466,1940	551.8+/-378.4	717,1032,454	77.0	76.0	76.0		616	3.1	1.0	12	dbSNP_100	76	1804,6796	733.1+/-406.9	180,1444,2676	yes	missense	KRT84	NM_033045.3	29	897,2476,3130	CC,CT,TT		20.9767,44.0309,32.831	benign	206/601	52777513	4270,8736	2203	4300	6503	SO:0001583	missense	3890	exon2			TCCTGATACATTT	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.616A>G	12.37:g.52777513T>C	ENSP00000257951:p.Ile206Val	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	186	73	0.392473	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	664	0.304029304029304	288	0.5853658536585366	100	0.27624309392265195	117	0.20454545454545456	159	0.20976253298153033	C	8.846	0.943350	0.18281	0.559691	0.209767	ENSG00000161849	ENST00000257951	D	0.88354	-2.37	5.32	3.07	0.35406	Filament (1);	0.423150	0.20341	N	0.094240	T	0.00012	0.0000	N	0.01515	-0.825	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45381	-0.9265	9	0.14656	T	0.56	.	9.4999	0.39011	0.0:0.735:0.0:0.265	rs2245203;rs58066728;rs2245203	206	Q9NSB2	KRT84_HUMAN	V	206	ENSP00000257951:I206V	ENSP00000257951:I206V	I	-	1	0	KRT84	51063780	0.006000	0.16342	0.989000	0.46669	0.760000	0.43138	0.122000	0.15687	0.440000	0.26502	-0.119000	0.15052	ATC	T|0.684;C|0.316	0.316	strong		0.537	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
CCDC101	112869	hgsc.bcm.edu	37	16	28603012	28603012	+	Silent	SNP	A	A	G	rs3194168	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:28603012A>G	ENST00000317058.3	+	10	1054	c.867A>G	c.(865-867)gaA>gaG	p.E289E		NM_138414.2	NP_612423.1	Q96ES7	SGF29_HUMAN	coiled-coil domain containing 101	289	SGF29 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00851}.				chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|histone H3 acetylation (GO:0043966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|SAGA-type complex (GO:0070461)	methylated histone binding (GO:0035064)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)	10						CTTGTAAGGAACCCAAGAAAA	0.552													.|||	388	0.077476	0.0794	0.1037	5008	,	,		19281	0.004		0.1233	False		,,,				2504	0.0849				p.E289E		Atlas-SNP	.											.	CCDC101	24	.	0			c.A867G						PASS	.	A		371,4023		14,343,1840	114.0	99.0	104.0		867	0.5	1.0	16	dbSNP_105	104	1140,7460		77,986,3237	no	coding-synonymous	CCDC101	NM_138414.2		91,1329,5077	GG,GA,AA		13.2558,8.4433,11.6284		289/294	28603012	1511,11483	2197	4300	6497	SO:0001819	synonymous_variant	112869	exon10			TAAGGAACCCAAG	AK057008	CCDS10635.1	16p11.2	2010-08-03			ENSG00000176476	ENSG00000176476			25156	protein-coding gene	gene with protein product	"""SAGA-associated factor 29 homolog (yeast)"""	613374				17334388	Standard	NM_138414		Approved	FLJ32446, SGF29	uc002dqf.3	Q96ES7	OTTHUMG00000131763	ENST00000317058.3:c.867A>G	16.37:g.28603012A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_138414	Q96MF5	Silent	SNP	ENST00000317058.3	37	CCDS10635.1																																																																																			A|0.894;G|0.106	0.106	strong		0.552	CCDC101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254691.1	NM_138414	
MS4A14	84689	hgsc.bcm.edu	37	11	60183159	60183159	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:60183159T>C	ENST00000300187.6	+	5	995	c.718T>C	c.(718-720)Tct>Cct	p.S240P	MS4A14_ENST00000395005.2_Missense_Mutation_p.S223P|MS4A14_ENST00000531783.1_Missense_Mutation_p.S273P|MS4A14_ENST00000531787.1_Missense_Mutation_p.S128P|MS4A14_ENST00000395001.1_3'UTR	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	240						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						TATCCTTCCATCTCCCAAATT	0.388																																					p.S273P		Atlas-SNP	.											MS4A14,NS,carcinoma,0,1	MS4A14	120	1	0			c.T817C						scavenged	.						79.0	78.0	79.0					11																	60183159		2203	4299	6502	SO:0001583	missense	84689	exon6			CTTCCATCTCCCA	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.718T>C	11.37:g.60183159T>C	ENSP00000300187:p.Ser240Pro	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	203	5	0.0246305	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	T	7.045	0.563257	0.13498	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.36340	1.26;2.52;1.26;2.8	3.63	-3.34	0.04943	.	10.627900	0.00166	N	0.000000	T	0.16214	0.0390	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.06643	-1.0815	10	0.35671	T	0.21	1.8289	0.1354	0.00078	0.3048:0.236:0.1501:0.3091	.	223;240	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	P	128;240;223;273	ENSP00000437222:S128P;ENSP00000300187:S240P;ENSP00000378453:S223P;ENSP00000433761:S273P	ENSP00000300187:S240P	S	+	1	0	MS4A14	59939735	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.159000	0.03150	-0.750000	0.04740	-1.313000	0.01306	TCT	.	.	none		0.388	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
BSPRY	54836	hgsc.bcm.edu	37	9	116132092	116132092	+	Missense_Mutation	SNP	G	G	C	rs818711	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116132092G>C	ENST00000374183.4	+	6	918	c.879G>C	c.(877-879)caG>caC	p.Q293H	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	293	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		Q -> H (in dbSNP:rs818711).		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						TGAATGTCCAGAACAGTTGTG	0.622													G|||	301	0.0601038	0.0045	0.0476	5008	,	,		18997	0.0734		0.0646	False		,,,				2504	0.1258				p.Q293H		Atlas-SNP	.											.	BSPRY	21	.	0			c.G879C						PASS	.	G	HIS/GLN	56,4062		0,56,2003	59.0	62.0	61.0		879	1.5	1.0	9	dbSNP_86	61	485,7871		17,451,3710	yes	missense	BSPRY	NM_017688.2	24	17,507,5713	CC,CG,GG		5.8042,1.3599,4.337	benign	293/403	116132092	541,11933	2059	4178	6237	SO:0001583	missense	54836	exon6			TGTCCAGAACAGT	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.879G>C	9.37:g.116132092G>C	ENSP00000363298:p.Gln293His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	114	40	0.350877	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	37	CCDS43868.1	114	0.0521978021978022	3	0.006097560975609756	18	0.049723756906077346	46	0.08041958041958042	47	0.06200527704485488	G	12.03	1.814651	0.32053	0.013599	0.058042	ENSG00000119411	ENST00000374183	T	0.13901	2.55	5.54	1.49	0.22878	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.273375	0.41938	N	0.000784	T	0.00468	0.0015	L	0.34521	1.04	0.39021	P	0.040259000000000045	B	0.14012	0.009	B	0.11329	0.006	T	0.10706	-1.0618	9	0.72032	D	0.01	-11.3344	4.8002	0.13292	0.3242:0.1496:0.5262:0.0	rs818711;rs3750530;rs17765453;rs52795781;rs818711	293	Q5W0U4	BSPRY_HUMAN	H	293	ENSP00000363298:Q293H	ENSP00000363298:Q293H	Q	+	3	2	BSPRY	115171913	1.000000	0.71417	0.959000	0.39883	0.936000	0.57629	0.918000	0.28678	0.255000	0.21593	0.561000	0.74099	CAG	G|0.930;C|0.070	0.070	strong		0.622	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
NELL1	4745	hgsc.bcm.edu	37	11	20805335	20805335	+	Silent	SNP	C	C	T	rs2280363	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:20805335C>T	ENST00000357134.5	+	3	446	c.294C>T	c.(292-294)tcC>tcT	p.S98S	NELL1_ENST00000298925.5_Silent_p.S126S|NELL1_ENST00000325319.5_Silent_p.S98S|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	124	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	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	
IFNGR1	3459	hgsc.bcm.edu	37	6	137519588	137519588	+	Silent	SNP	A	A	C	rs11914	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	102	0	0		WXS	Illumina HiSeq	Phase_I	105	39	0.371429	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		
MCC	4163	hgsc.bcm.edu	37	5	112823998	112823998	+	Silent	SNP	C	C	T	rs348943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:112823998C>T	ENST00000408903.3	-	1	529	c.114G>A	c.(112-114)gaG>gaA	p.E38E		NM_001085377.1	NP_001078846	P23508	CRCM_HUMAN	mutated in colorectal cancers	0					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)		GCCGCATCCTCTCCTCCTCGC	0.716													C|||	2519	0.502995	0.3298	0.4524	5008	,	,		10097	0.6726		0.494	False		,,,				2504	0.6074				p.E38E		Atlas-SNP	.											.	MCC	234	.	0			c.G114A						PASS	.	C		1293,2851		203,887,982	39.0	45.0	43.0		114	3.5	1.0	5	dbSNP_79	43	4052,4332		972,2108,1112	yes	coding-synonymous	MCC	NM_001085377.1		1175,2995,2094	TT,TC,CC		48.3302,31.2017,42.6644		38/1020	112823998	5345,7183	2072	4192	6264	SO:0001819	synonymous_variant	4163	exon1			CATCCTCTCCTCC		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	ENST00000408903.3:c.114G>A	5.37:g.112823998C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	83	80	0.963855	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000408903.3	37	CCDS43351.1																																																																																			C|0.505;T|0.495	0.495	strong		0.716	MCC-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370839.1	NM_001085377	
MUC16	94025	hgsc.bcm.edu	37	19	9060915	9060915	+	Missense_Mutation	SNP	C	C	T	rs59168469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9060915C>T	ENST00000397910.4	-	3	26734	c.26531G>A	c.(26530-26532)cGc>cAc	p.R8844H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8846	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						CACTGATGGGCGGCTTGGCCA	0.527													-|||	197	0.0393371	0.0098	0.1182	5008	,	,		19779	0.0109		0.0189	False		,,,				2504	0.0736				p.R8844H		Atlas-SNP	.											.	MUC16	4315	.	0			c.G26531A						PASS	.	G	HIS/ARG	34,4036		0,34,2001	144.0	138.0	140.0		26531	-3.5	0.0	19	dbSNP_129	140	176,8198		3,170,4014	yes	missense	MUC16	NM_024690.2	29	3,204,6015	TT,TC,CC		2.1017,0.8354,1.6876	probably-damaging	8844/14508	9060915	210,12234	2035	4187	6222	SO:0001583	missense	94025	exon3			GATGGGCGGCTTG	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.26531G>A	19.37:g.9060915C>T	ENSP00000381008:p.Arg8844His	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	206	104	0.504854	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	56	0.02564102564102564	2	0.0040650406504065045	35	0.09668508287292818	5	0.008741258741258742	14	0.018469656992084433	-	12.50	1.957132	0.34565	0.008354	0.021017	ENSG00000181143	ENST00000397910	T	0.21734	1.99	2.05	-3.49	0.04724	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.31392	-0.9945	8	0.87932	D	0	.	0.8073	0.01086	0.2741:0.3435:0.2095:0.1729	rs59168469	8844	B5ME49	.	H	8844	ENSP00000381008:R8844H	ENSP00000381008:R8844H	R	-	2	0	MUC16	8921915	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.245000	0.08890	-1.368000	0.02149	-1.317000	0.01298	CGC	C|0.974;T|0.026	0.026	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PKD1	5310	hgsc.bcm.edu	37	16	2161796	2161796	+	Silent	SNP	G	G	A	rs75510884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2161796G>A	ENST00000262304.4	-	15	3580	c.3372C>T	c.(3370-3372)gcC>gcT	p.A1124A	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Silent_p.A1124A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1124	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						AGGGCAGGGAGGCGCGCACGC	0.692													a|||	574	0.114617	0.2935	0.111	5008	,	,		15825	0.0		0.0944	False		,,,				2504	0.0143				p.A1124A		Atlas-SNP	.											PKD1,colon,carcinoma,-2,1	PKD1	184	1	0			c.C3372T						PASS	.	G	,	1061,3315		141,779,1268	20.0	21.0	21.0		3372,3372	-10.3	0.0	16	dbSNP_131	21	832,7746		55,722,3512	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	196,1501,4780	AA,AG,GG		9.6992,24.2459,14.6132	,	1124/4303,1124/4304	2161796	1893,11061	2188	4289	6477	SO:0001819	synonymous_variant	5310	exon15			CAGGGAGGCGCGC	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.3372C>T	16.37:g.2161796G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			G|0.854;A|0.146	0.146	strong		0.692	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
FBXO7	25793	hgsc.bcm.edu	37	22	32875190	32875190	+	Missense_Mutation	SNP	G	G	A	rs11107	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:32875190G>A	ENST00000266087.7	+	2	672	c.345G>A	c.(343-345)atG>atA	p.M115I	FBXO7_ENST00000397426.1_Start_Codon_SNP_p.M1I|FBXO7_ENST00000382058.3_Missense_Mutation_p.M36I|FBXO7_ENST00000465418.1_3'UTR	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	115	Important for interaction with PINK1.		M -> I (in dbSNP:rs11107). {ECO:0000269|PubMed:10531035, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18513678}.		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						AGACTAGCATGCAGGATGAAC	0.448													g|||	2441	0.48742	0.4047	0.5663	5008	,	,		17154	0.6915		0.3748	False		,,,				2504	0.4489				p.M115I		Atlas-SNP	.											.	FBXO7	131	.	0			c.G345A						PASS	.	G	ILE/MET,ILE/MET	1640,2766	501.8+/-365.1	307,1026,870	93.0	92.0	92.0		108,345	-3.6	0.0	22	dbSNP_52	92	3202,5398	483.2+/-371.1	572,2058,1670	yes	missense,missense	FBXO7	NM_001033024.1,NM_012179.3	10,10	879,3084,2540	AA,AG,GG		37.2326,37.222,37.229	benign,benign	36/444,115/523	32875190	4842,8164	2203	4300	6503	SO:0001583	missense	25793	exon2			TAGCATGCAGGAT	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.345G>A	22.37:g.32875190G>A	ENSP00000266087:p.Met115Ile	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	169	66	0.390533	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Missense_Mutation	SNP	ENST00000266087.7	37	CCDS13907.1	1067	0.48855311355311354	185	0.37601626016260165	193	0.5331491712707183	396	0.6923076923076923	293	0.3865435356200528	g	0.741	-0.776340	0.02951	0.37222	0.372326	ENSG00000100225	ENST00000266087;ENST00000452138;ENST00000382058;ENST00000397426;ENST00000444207	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	4.53	-3.63	0.04529	.	1.881220	0.01957	N	0.043074	T	0.00012	0.0000	N	0.00138	-2.015	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	0.47368	-0.9123	9	0.37606	T	0.19	0.134	0.4433	0.00489	0.2236:0.1582:0.2575:0.3607	rs11107;rs710174;rs3171628;rs17350295;rs17771677;rs17850310;rs52811518;rs58963810;rs11107	36;115;1	Q9Y3I1-2;Q9Y3I1;Q5TI86	.;FBX7_HUMAN;.	I	115;36;36;1;1	ENSP00000266087:M115I;ENSP00000388547:M36I;ENSP00000371490:M36I;ENSP00000380571:M1I;ENSP00000404388:M1I	ENSP00000266087:M115I	M	+	3	0	FBXO7	31205190	0.000000	0.05858	0.000000	0.03702	0.231000	0.25187	-0.024000	0.12435	-0.629000	0.05575	-0.578000	0.04140	ATG	G|0.577;N|0.000	.	strong		0.448	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
C19orf53	28974	hgsc.bcm.edu	37	19	13885309	13885309	+	Silent	SNP	C	C	T	rs1128749	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13885309C>T	ENST00000588234.1	+	1	328	c.18C>T	c.(16-18)cgC>cgT	p.R6R	C19orf53_ENST00000593274.1_5'Flank|CTB-5E10.3_ENST00000586297.1_RNA|CTB-5E10.3_ENST00000586894.1_RNA|CTB-5E10.3_ENST00000591826.1_RNA	NM_014047.2	NP_054766.1	Q9UNZ5	L10K_HUMAN	chromosome 19 open reading frame 53	6										breast(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	6			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			AGGGGCAGCGCAAGTTTCAGG	0.642													C|||	1884	0.376198	0.4032	0.317	5008	,	,		16423	0.4256		0.2505	False		,,,				2504	0.4601				p.R6R		Atlas-SNP	.											C19orf53,NS,carcinoma,0,1	C19orf53	14	1	0			c.C18T						PASS	.	C		1733,2661		341,1051,805	16.0	19.0	18.0		18	0.3	1.0	19	dbSNP_86	18	2204,6384		303,1598,2393	no	coding-synonymous	C19orf53	NM_014047.2		644,2649,3198	TT,TC,CC		25.6637,39.4401,30.3266		6/100	13885309	3937,9045	2197	4294	6491	SO:0001819	synonymous_variant	28974	exon1			GCAGCGCAAGTTT	AF078852	CCDS12298.1	19p13.2	2011-11-24			ENSG00000104979	ENSG00000104979			24991	protein-coding gene	gene with protein product	"""leydig cell tumor 10 kDa protein homolog"""					11042152	Standard	NM_014047		Approved	HSPC023, LYDG10	uc002mxg.3	Q9UNZ5		ENST00000588234.1:c.18C>T	19.37:g.13885309C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_014047	B2R4J9	Silent	SNP	ENST00000588234.1	37	CCDS12298.1																																																																																			A|0.000;C|0.661;G|0.000;T|0.338	0.338	strong		0.642	C19orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453621.1	NM_014047	
HRCT1	646962	hgsc.bcm.edu	37	9	35906624	35906624	+	Missense_Mutation	SNP	G	G	A	rs75458097	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	40	15	0.375	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	
VAV2	7410	hgsc.bcm.edu	37	9	136643994	136643994	+	Missense_Mutation	SNP	T	T	C	rs602990	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136643994T>C	ENST00000371850.3	-	22	1811	c.1780A>G	c.(1780-1782)Atg>Gtg	p.M594V	VAV2_ENST00000371851.1_Missense_Mutation_p.M584V|VAV2_ENST00000406606.3_Missense_Mutation_p.M584V	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	594	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.		M -> V (in dbSNP:rs602990). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7762982}.		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)	p.M584V(1)		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)		TAATTCTGCATGGCCACCATC	0.632													C|||	2480	0.495208	0.8404	0.4798	5008	,	,		15534	0.0645		0.5189	False		,,,				2504	0.4591				p.M594V		Atlas-SNP	.											VAV2,NS,carcinoma,0,1	VAV2	165	1	1	Substitution - Missense(1)	stomach(1)	c.A1780G						PASS	.	C	VAL/MET,VAL/MET	3543,863	334.9+/-303.7	1426,691,86	61.0	56.0	58.0		1780,1750	1.9	0.3	9	dbSNP_83	58	4549,4051	556.6+/-386.9	1186,2177,937	yes	missense,missense	VAV2	NM_001134398.1,NM_003371.3	21,21	2612,2868,1023	CC,CT,TT		47.1047,19.5869,37.7826	benign,benign	594/879,584/840	136643994	8092,4914	2203	4300	6503	SO:0001583	missense	7410	exon22			TCTGCATGGCCAC		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.1780A>G	9.37:g.136643994T>C	ENSP00000360916:p.Met594Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Missense_Mutation	SNP	ENST00000371850.3	37	CCDS48053.1	1007	0.4610805860805861	413	0.8394308943089431	175	0.48342541436464087	18	0.03146853146853147	401	0.5290237467018469	C	0.795	-0.757601	0.03019	0.804131	0.528953	ENSG00000160293	ENST00000371850;ENST00000371851;ENST00000406606;ENST00000325440	T;T;T	0.06068	3.35;3.35;3.35	4.8	1.91	0.25777	Src homology-3 domain (3);Variant SH3 (1);	0.290997	0.33075	N	0.005314	T	0.00012	0.0000	N	0.02539	-0.55	0.54753	P	1.799999999996249E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.19128	-1.0315	9	0.08179	T	0.78	.	13.6487	0.62297	0.0:0.8398:0.0:0.1602	rs602990;rs61232391;rs602990	584;594;584	P52735-2;P52735;P52735-3	.;VAV2_HUMAN;.	V	594;584;584;584	ENSP00000360916:M594V;ENSP00000360917:M584V;ENSP00000385362:M584V	ENSP00000317258:M584V	M	-	1	0	VAV2	135633815	0.339000	0.24784	0.298000	0.25002	0.741000	0.42261	0.920000	0.28705	0.116000	0.18110	-2.599000	0.00162	ATG	T|0.441;C|0.559	0.559	strong		0.632	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
XKR8	55113	hgsc.bcm.edu	37	1	28290155	28290155	+	Silent	SNP	G	G	A	rs142513353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:28290155G>A	ENST00000373884.5	+	2	1049	c.441G>A	c.(439-441)acG>acA	p.T147T	XKR8_ENST00000481387.1_3'UTR	NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	147					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		CACAGCTCACGCTGGTGCTGG	0.627													G|||	10	0.00199681	0.0	0.0043	5008	,	,		17805	0.0		0.007	False		,,,				2504	0.0				p.T147T		Atlas-SNP	.											.	XKR8	15	.	0			c.G441A						PASS	.	G		3,4403	4.2+/-10.8	0,3,2200	23.0	20.0	21.0		441	-1.9	1.0	1	dbSNP_134	21	31,8569	19.8+/-62.0	0,31,4269	no	coding-synonymous	XKR8	NM_018053.2		0,34,6469	AA,AG,GG		0.3605,0.0681,0.2614		147/396	28290155	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	55113	exon2			GCTCACGCTGGTG	AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 8"""			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.441G>A	1.37:g.28290155G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	128	16	0.125	NM_018053		Silent	SNP	ENST00000373884.5	37	CCDS315.1																																																																																			G|0.997;A|0.003	0.003	strong		0.627	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053	
MCHR1	2847	hgsc.bcm.edu	37	22	41075543	41075543	+	Missense_Mutation	SNP	A	A	G	rs133072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:41075543A>G	ENST00000249016.4	+	1	790	c.94A>G	c.(94-96)Aac>Gac	p.N32D	MCHR1_ENST00000381433.2_Missense_Mutation_p.N32D|MCHR1_ENST00000498400.1_Intron	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	32			N -> D (no significant functional differences; dbSNP:rs133072). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15941924, ECO:0000269|Ref.4, ECO:0000269|Ref.5, ECO:0000269|Ref.8}.		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)			endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						CCCCCTTCCCAACTGCGGGGC	0.682													G|||	3344	0.667732	0.7209	0.4207	5008	,	,		15490	0.9802		0.6352	False		,,,				2504	0.4826				p.N32D		Atlas-SNP	.											.	MCHR1	45	.	0			c.A94G						PASS	.	G	ASP/ASN	3040,1364	417.2+/-337.8	1071,898,233	28.0	33.0	31.0		94	2.0	0.8	22	dbSNP_78	31	5469,3129	451.7+/-362.7	1749,1971,579	no	missense	MCHR1	NM_005297.3	23	2820,2869,812	GG,GA,AA		36.3922,30.9718,34.5562	benign	32/423	41075543	8509,4493	2202	4299	6501	SO:0001583	missense	2847	exon1			CTTCCCAACTGCG		CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"""GPCR / Class A : MCH receptors"""	4479	protein-coding gene	gene with protein product		601751	"""G protein-coupled receptor 24"""	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.94A>G	22.37:g.41075543A>G	ENSP00000249016:p.Asn32Asp	Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	37	CCDS14004.1	1555	0.711996336996337	359	0.7296747967479674	160	0.4419889502762431	565	0.9877622377622378	471	0.6213720316622692	G	2.184	-0.386845	0.04966	0.690282	0.636078	ENSG00000128285	ENST00000249016;ENST00000381433	T;T	0.62498	0.02;0.56	4.54	2.02	0.26589	.	0.162163	0.29307	N	0.012529	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	0.43410	-0.9393	9	0.02654	T	1	.	5.5049	0.16848	0.4112:0.0:0.5888:0.0	rs133072;rs17844921;rs17856632;rs17857645;rs60741563;rs133072	32	Q99705	MCHR1_HUMAN	D	32	ENSP00000249016:N32D;ENSP00000370841:N32D	ENSP00000249016:N32D	N	+	1	0	MCHR1	39405489	0.925000	0.31364	0.778000	0.31720	0.538000	0.34931	2.486000	0.45259	0.487000	0.27698	-0.320000	0.08662	AAC	A|0.330;G|0.670	0.670	strong		0.682	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297	
OR5T2	219464	hgsc.bcm.edu	37	11	55999950	55999950	+	Missense_Mutation	SNP	G	G	C	rs12221615	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55999950G>C	ENST00000313264.4	-	1	787	c.712C>G	c.(712-714)Ctc>Gtc	p.L238V		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	238			L -> V (in dbSNP:rs12221615).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L238V(1)		endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					AAGTAGAAGAGTAGAAGCTGG	0.433													g|||	507	0.101238	0.059	0.1009	5008	,	,		21064	0.125		0.1173	False		,,,				2504	0.1176				p.L238V		Atlas-SNP	.											OR5T2,right_upper_lobe,carcinoma,+2,3	OR5T2	107	3	1	Substitution - Missense(1)	stomach(1)	c.C712G						PASS	.	G	VAL/LEU	272,4130	152.5+/-186.2	9,254,1938	124.0	117.0	119.0		712	1.9	0.1	11	dbSNP_120	119	1003,7589	216.0+/-255.2	54,895,3347	yes	missense	OR5T2	NM_001004746.1	32	63,1149,5285	CC,CG,GG		11.6736,6.179,9.8122	benign	238/360	55999950	1275,11719	2201	4296	6497	SO:0001583	missense	219464	exon1			AGAAGAGTAGAAG	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.712C>G	11.37:g.55999950G>C	ENSP00000323688:p.Leu238Val	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	223	101	0.452915	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	238	0.10897435897435898	34	0.06910569105691057	33	0.09116022099447514	74	0.12937062937062938	97	0.1279683377308707	G	8.300	0.819727	0.16607	0.06179	0.116736	ENSG00000181718	ENST00000313264	T	0.00164	8.64	5.07	1.93	0.25924	GPCR, rhodopsin-like superfamily (1);	0.201650	0.24403	N	0.038822	T	0.00012	0.0000	N	0.11818	0.18	0.80722	P	0.0	B	0.30068	0.267	B	0.37888	0.26	T	0.20739	-1.0266	9	0.38643	T	0.18	.	9.6981	0.40169	0.0769:0.4016:0.5216:0.0	rs12221615;rs52834703;rs12221615	238	Q8NGG2	OR5T2_HUMAN	V	238	ENSP00000323688:L238V	ENSP00000323688:L238V	L	-	1	0	OR5T2	55756526	0.000000	0.05858	0.067000	0.19924	0.132000	0.20833	-0.189000	0.09629	0.633000	0.30452	0.478000	0.44815	CTC	G|0.901;C|0.099	0.099	strong		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
IKBKAP	8518	hgsc.bcm.edu	37	9	111653574	111653574	+	Silent	SNP	C	C	G	rs1063110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	89	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	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		
OR51F1	256892	hgsc.bcm.edu	37	11	4790857	4790857	+	Silent	SNP	A	A	G	rs11033797	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790857A>G	ENST00000380383.1	-	1	311	c.312T>C	c.(310-312)taT>taC	p.Y104Y	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Silent_p.Y97Y|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	104						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)		CAATGCAGCTATATAGACTGA	0.448													A|||	1080	0.215655	0.4569	0.2017	5008	,	,		22329	0.0		0.2704	False		,,,				2504	0.0654				p.Y97Y		Atlas-SNP	.											.	OR51F1	60	.	0			c.T291C						PASS	.	A		1968,2434	554.2+/-379.0	445,1078,678	77.0	74.0	75.0		291	2.6	0.0	11	dbSNP_120	75	2178,6418	371.0+/-336.1	290,1598,2410	no	coding-synonymous	OR51F1	NM_001004752.1		735,2676,3088	GG,GA,AA		25.3374,44.707,31.8972		97/313	4790857	4146,8852	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			GCAGCTATATAGA	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.312T>C	11.37:g.4790857A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.713;G|0.287	0.287	strong		0.448	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
RBMXL2	27288	hgsc.bcm.edu	37	11	7110548	7110548	+	Missense_Mutation	SNP	C	C	T	rs11041170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	79	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	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	
MADD	8567	hgsc.bcm.edu	37	11	47306628	47306628	+	Missense_Mutation	SNP	G	G	A	rs3736101	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47306628G>A	ENST00000311027.5	+	13	2459	c.2294G>A	c.(2293-2295)cGg>cAg	p.R765Q	MADD_ENST00000395344.3_Intron|MADD_ENST00000402799.1_Intron|MADD_ENST00000406482.1_Intron|MADD_ENST00000342922.4_Missense_Mutation_p.R765Q|MADD_ENST00000407859.3_Intron|MADD_ENST00000402192.2_Missense_Mutation_p.R765Q|MADD_ENST00000349238.3_Missense_Mutation_p.R765Q|MADD_ENST00000395336.3_Missense_Mutation_p.R765Q	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)		TCAGTGCGCCGGCGAATCTAT	0.562													G|||	370	0.0738818	0.025	0.0677	5008	,	,		19379	0.0516		0.1163	False		,,,				2504	0.1237				p.R765Q		Atlas-SNP	.											.	MADD	172	.	0			c.G2294A						PASS	.	G	,,GLN/ARG,GLN/ARG,,,GLN/ARG,,GLN/ARG,GLN/ARG	176,4226	115.0+/-153.0	2,172,2027	98.0	92.0	94.0		,,2294,2294,,,2294,,2294,2294	0.7	0.9	11	dbSNP_107	94	900,7696	200.9+/-244.5	43,814,3441	yes	intron,intron,missense,missense,intron,intron,missense,intron,missense,missense	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	,,43,43,,,43,,43,43	45,986,5468	AA,AG,GG		10.47,3.9982,8.2782	,,benign,benign,,,benign,,benign,benign	,,765/1648,765/1589,,,765/1609,,765/1582,765/1588	47306628	1076,11922	2201	4298	6499	SO:0001583	missense	8567	exon13			TGCGCCGGCGAAT	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.2294G>A	11.37:g.47306628G>A	ENSP00000310933:p.Arg765Gln	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	98	37	0.377551	NM_130470		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	158	0.07234432234432235	13	0.026422764227642278	30	0.08287292817679558	33	0.057692307692307696	82	0.10817941952506596	G	11.01	1.511868	0.27036	0.039982	0.1047	ENSG00000110514	ENST00000342922;ENST00000349238;ENST00000311027;ENST00000395336;ENST00000402192	T;T;T;T;T	0.05382	3.45;3.5;3.5;3.5;3.45	5.99	0.696	0.18075	.	0.309294	0.34002	N	0.004345	T	0.00109	0.0003	N	0.24115	0.695	0.80722	P	0.0	B;B;B;B	0.12013	0.001;0.001;0.0;0.005	B;B;B;B	0.08055	0.003;0.002;0.001;0.003	T	0.43556	-0.9384	9	0.24483	T	0.36	-0.2463	10.2559	0.43397	0.5124:0.0:0.4875:0.0	rs3736101;rs3736101	765;765;765;765	Q8WXG6-7;Q8WXG6-2;Q8WXG6;Q8WXG6-3	.;.;MADD_HUMAN;.	Q	765	ENSP00000343902:R765Q;ENSP00000304505:R765Q;ENSP00000310933:R765Q;ENSP00000378745:R765Q;ENSP00000384287:R765Q	ENSP00000310933:R765Q	R	+	2	0	MADD	47263204	0.028000	0.19301	0.890000	0.34922	0.952000	0.60782	0.100000	0.15231	-0.117000	0.11872	0.655000	0.94253	CGG	G|0.922;A|0.078	0.078	strong		0.562	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
MYBPC3	4607	hgsc.bcm.edu	37	11	47354787	47354787	+	Silent	SNP	C	C	T	rs1052373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47354787C>T	ENST00000545968.1	-	30	3342	c.3288G>A	c.(3286-3288)gaG>gaA	p.E1096E	MYBPC3_ENST00000256993.4_Silent_p.E1095E|MYBPC3_ENST00000399249.2_Silent_p.E1096E	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	1096	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		ACCCCCAGAGCTCCGTGTTGC	0.637													C|||	2385	0.476238	0.5083	0.3329	5008	,	,		19715	0.7202		0.3072	False		,,,				2504	0.4571				p.E1096E		Atlas-SNP	.											.	MYBPC3	102	.	0			c.G3288A						PASS	.	C		1833,2133		433,967,583	41.0	47.0	45.0		3288	2.4	0.7	11	dbSNP_86	45	2524,5782		385,1754,2014	yes	coding-synonymous	MYBPC3	NM_000256.3		818,2721,2597	TT,TC,CC		30.3877,46.2179,35.5036		1096/1275	47354787	4357,7915	1983	4153	6136	SO:0001819	synonymous_variant	4607	exon29			CCAGAGCTCCGTG	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.3288G>A	11.37:g.47354787C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	147	143	0.972789	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Silent	SNP	ENST00000545968.1	37	CCDS53621.1																																																																																			C|0.557;T|0.443	0.443	strong		0.637	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
GHSR	2693	hgsc.bcm.edu	37	3	172165757	172165757	+	Silent	SNP	G	G	C	rs2232169	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:172165757G>C	ENST00000241256.2	-	1	489	c.447C>G	c.(445-447)ctC>ctG	p.L149L	GHSR_ENST00000427970.1_Silent_p.L149L	NM_198407.2	NP_940799.1	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor	149					actin polymerization or depolymerization (GO:0008154)|adult feeding behavior (GO:0008343)|cellular response to insulin stimulus (GO:0032869)|decidualization (GO:0046697)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of hindgut contraction (GO:0043134)|regulation of synapse assembly (GO:0051963)|response to food (GO:0032094)|response to hormone (GO:0009725)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|growth hormone secretagogue receptor activity (GO:0001616)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	33	Ovarian(172;0.00143)|Breast(254;0.197)		Lung(28;3.93e-15)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)|STAD - Stomach adenocarcinoma(35;0.235)			CCTTGGCCCGGAGTGGGAAGC	0.622													C|||	158	0.0315495	0.0658	0.0231	5008	,	,		19788	0.0		0.0278	False		,,,				2504	0.0276				p.L149L	Esophageal Squamous(93;641 1401 20883 29581 34638)	Atlas-SNP	.											GHSR_ENST00000427970,NS,carcinoma,-2,1	GHSR	104	1	0			c.C447G						PASS	.	C	,	301,4105	793.5+/-415.2	7,287,1909	56.0	55.0	55.0		447,447	4.7	1.0	3	dbSNP_98	55	252,8348	806.8+/-407.2	5,242,4053	no	coding-synonymous,coding-synonymous	GHSR	NM_004122.2,NM_198407.2	,	12,529,5962	CC,CG,GG		2.9302,6.8316,4.2519	,	149/290,149/367	172165757	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	2693	exon1			GGCCCGGAGTGGG	AY429112	CCDS3218.1, CCDS46959.1	3q26.31	2012-08-08			ENSG00000121853	ENSG00000121853		"""GPCR / Class A : Ghrelin receptors"""	4267	protein-coding gene	gene with protein product		601898				8688086	Standard	NM_198407		Approved		uc003fib.2	Q92847	OTTHUMG00000156946	ENST00000241256.2:c.447C>G	3.37:g.172165757G>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_198407	Q14D12|Q6ISR8|Q92848|Q96RJ7	Silent	SNP	ENST00000241256.2	37	CCDS3218.1																																																																																			G|0.963;C|0.037	0.037	strong		0.622	GHSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346728.1	NM_004122	
TSHZ3	57616	hgsc.bcm.edu	37	19	31770009	31770009	+	Silent	SNP	C	C	T	rs28609894	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:31770009C>T	ENST00000240587.4	-	2	1017	c.690G>A	c.(688-690)acG>acA	p.T230T		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	230					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					TCATGTGCACCGTCAACTCCA	0.597													C|||	1576	0.314696	0.4304	0.2651	5008	,	,		19559	0.2331		0.2187	False		,,,				2504	0.3763				p.T230T		Atlas-SNP	.											.	TSHZ3	549	.	0			c.G690A						PASS	.	C		1793,2613	529.0+/-372.6	385,1023,795	194.0	174.0	181.0		690	-7.6	0.9	19	dbSNP_125	181	1893,6707	336.8+/-322.0	214,1465,2621	no	coding-synonymous	TSHZ3	NM_020856.2		599,2488,3416	TT,TC,CC		22.0116,40.6945,28.3408		230/1082	31770009	3686,9320	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			GTGCACCGTCAAC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.690G>A	19.37:g.31770009C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	66	0.970588	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			C|0.717;T|0.283	0.283	strong		0.597	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
FAM198A	729085	hgsc.bcm.edu	37	3	43074434	43074434	+	Missense_Mutation	SNP	C	C	T	rs2936817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:43074434C>T	ENST00000430121.2	+	2	774	c.679C>T	c.(679-681)Cat>Tat	p.H227Y	KRBOX1_ENST00000443313.1_Intron	NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	227			H -> Y (in dbSNP:rs2936817). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			extracellular region (GO:0005576)				endometrium(1)	1						CTCAGGAGCTCATCAGTGGCC	0.597													C|||	2197	0.438698	0.3419	0.5331	5008	,	,		20734	0.6518		0.4066	False		,,,				2504	0.316				p.H227Y		Atlas-SNP	.											.	FAM198A	23	.	0			c.C679T						PASS	.	C	TYR/HIS	454,930		72,310,310	20.0	24.0	23.0		679	-0.8	0.0	3	dbSNP_101	23	1295,1887		270,755,566	yes	missense	FAM198A	NM_001129908.2	83	342,1065,876	TT,TC,CC		40.6977,32.8035,38.3049	benign	227/576	43074434	1749,2817	692	1591	2283	SO:0001583	missense	729085	exon2			GGAGCTCATCAGT	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.679C>T	3.37:g.43074434C>T	ENSP00000407301:p.His227Tyr	Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_001129908	B3KR48	Missense_Mutation	SNP	ENST00000430121.2	37	CCDS46808.1	1034	0.4734432234432234	184	0.37398373983739835	190	0.5248618784530387	359	0.6276223776223776	301	0.3970976253298153	C	11.00	1.509802	0.27036	0.328035	0.406977	ENSG00000144649	ENST00000430121	T	0.30182	1.54	4.88	-0.785	0.10950	.	1.499980	0.04146	N	0.320400	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P	0.38863	0.65	B	0.34242	0.178	T	0.40869	-0.9540	8	.	.	.	-9.0853	1.5116	0.02497	0.2799:0.4081:0.1372:0.1749	rs2936817;rs3732855;rs57615568;rs2936817	227	Q9UFP1	F198A_HUMAN	Y	227	ENSP00000407301:H227Y	.	H	+	1	0	FAM198A	43049438	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.050000	0.14120	-0.058000	0.13177	-0.218000	0.12543	CAT	C|0.535;T|0.465	0.465	strong		0.597	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
GAPVD1	26130	hgsc.bcm.edu	37	9	128117027	128117027	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:128117027C>T	ENST00000495955.1	+	24	4008	c.3718C>T	c.(3718-3720)Cgg>Tgg	p.R1240W	GAPVD1_ENST00000394105.2_Missense_Mutation_p.R1249W|GAPVD1_ENST00000394104.2_Missense_Mutation_p.R1240W|GAPVD1_ENST00000297933.6_Missense_Mutation_p.R1222W|GAPVD1_ENST00000394083.2_Missense_Mutation_p.R1174W|GAPVD1_ENST00000312123.9_Missense_Mutation_p.R1201W|GAPVD1_ENST00000265956.4_Missense_Mutation_p.R1214W|GAPVD1_ENST00000470056.1_Missense_Mutation_p.R1195W			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	1240					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						AAGAGTTTTGCGGGACAAAGA	0.428																																					p.R1249W		Atlas-SNP	.											GAPVD1,NS,carcinoma,0,2	GAPVD1	124	2	0			c.C3745T						scavenged	.						171.0	172.0	172.0					9																	128117027		2203	4300	6503	SO:0001583	missense	26130	exon23			GTTTTGCGGGACA		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.3718C>T	9.37:g.128117027C>T	ENSP00000419063:p.Arg1240Trp	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	87	3	0.0344828	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		.	.	.	.	.	.	.	.	.	.	C	25.0	4.589767	0.86851	.	.	ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000297933;ENST00000312123	.	.	.	6.08	6.08	0.98989	.	0.049442	0.85682	D	0.000000	T	0.73369	0.3578	L	0.52573	1.65	0.58432	D	0.999997	D;D;D;D;D;D	0.71674	0.997;0.998;0.997;0.998;0.997;0.997	P;P;P;P;P;P	0.58970	0.702;0.849;0.844;0.844;0.844;0.844	T	0.73291	-0.4029	9	0.66056	D	0.02	.	19.6603	0.95864	0.0:1.0:0.0:0.0	.	1240;255;1195;1201;1222;1249	Q14C86;B3KTX2;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6	GAPD1_HUMAN;.;.;.;.;.	W	1195;1249;1240;1214;1174;1240;1222;1201	.	ENSP00000265956:R1214W	R	+	1	2	GAPVD1	127156848	1.000000	0.71417	0.989000	0.46669	0.714000	0.41099	3.125000	0.50469	2.894000	0.99253	0.591000	0.81541	CGG	.	.	none		0.428	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1		
ZNF155	7711	hgsc.bcm.edu	37	19	44501518	44501518	+	Silent	SNP	G	G	A	rs446016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44501518G>A	ENST00000270014.2	+	5	1637	c.1509G>A	c.(1507-1509)ccG>ccA	p.P503P	ZNF155_ENST00000590615.1_Silent_p.P503P|RP11-15A1.7_ENST00000589021.1_RNA|RP11-15A1.7_ENST00000586860.1_RNA|ZNF155_ENST00000407951.2_Silent_p.P514P	NM_001260487.1|NM_198089.2	NP_001247416|NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	503					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(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				AAGACCAGCCGAGAGACTATA	0.418													G|||	1989	0.397165	0.3328	0.5086	5008	,	,		17839	0.6081		0.2763	False		,,,				2504	0.3119				p.P514P	NSCLC(61;554 1277 20909 42067 42312)	Atlas-SNP	.											.	ZNF155	30	.	0			c.G1542A						PASS	.	G	,	1382,3024	454.9+/-350.8	193,996,1014	92.0	95.0	94.0		1509,1509	-4.1	0.0	19	dbSNP_80	94	2406,6194	397.3+/-345.7	312,1782,2206	no	coding-synonymous,coding-synonymous	ZNF155	NM_003445.2,NM_198089.1	,	505,2778,3220	AA,AG,GG		27.9767,31.3663,29.125	,	503/539,503/539	44501518	3788,9218	2203	4300	6503	SO:0001819	synonymous_variant	7711	exon6			CCAGCCGAGAGAC	U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920		"""Zinc fingers, C2H2-type"", ""-"""	12940	protein-coding gene	gene with protein product		604086	"""zinc finger protein 155 (pHZ-96)"""			7557990	Standard	NM_001260486		Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000270014.2:c.1509G>A	19.37:g.44501518G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_001260488	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	Silent	SNP	ENST00000270014.2	37	CCDS12634.1																																																																																			G|0.668;A|0.332	0.332	strong		0.418	ZNF155-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460074.1	NM_003445	
CCDC81	60494	hgsc.bcm.edu	37	11	86123467	86123467	+	Silent	SNP	G	G	A	rs3741006	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	127	0	0		WXS	Illumina HiSeq	Phase_I	212	209	0.985849	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	
FBN1	2200	hgsc.bcm.edu	37	15	48797307	48797307	+	Silent	SNP	A	A	G	rs25458	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:48797307A>G	ENST00000316623.5	-	16	2330	c.1875T>C	c.(1873-1875)aaT>aaC	p.N625N		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	625	EGF-like 10; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		CGCAACGCCCATTCATGCAGA	0.443													A|||	1487	0.296925	0.5106	0.2046	5008	,	,		19066	0.3522		0.1501	False		,,,				2504	0.1677				p.N625N		Atlas-SNP	.											.	FBN1	310	.	0			c.T1875C	GRCh37	CM070116	FBN1	M	rs25458	PASS	.	A		1954,2440	553.3+/-378.7	441,1072,684	151.0	142.0	145.0		1875	-3.3	1.0	15	dbSNP_71	145	1220,7372	246.8+/-275.1	79,1062,3155	no	coding-synonymous	FBN1	NM_000138.4		520,2134,3839	GG,GA,AA		14.1993,44.4697,24.4417		625/2872	48797307	3174,9812	2197	4296	6493	SO:0001819	synonymous_variant	2200	exon16			ACGCCCATTCATG	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.1875T>C	15.37:g.48797307A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	70	49	0.7	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	37	CCDS32232.1																																																																																			A|0.747;G|0.253	0.253	strong		0.443	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
KLHL31	401265	hgsc.bcm.edu	37	6	53519857	53519857	+	Silent	SNP	G	G	A	rs12210809	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	181	0	0		WXS	Illumina HiSeq	Phase_I	208	106	0.509615	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	
HERPUD2	64224	hgsc.bcm.edu	37	7	35709842	35709842	+	Missense_Mutation	SNP	C	C	T	rs3779234	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:35709842C>T	ENST00000396081.1	-	3	1126	c.322G>A	c.(322-324)Gca>Aca	p.A108T	HERPUD2_ENST00000426180.1_5'Flank|HERPUD2_ENST00000311350.3_Missense_Mutation_p.A108T	NM_022373.4	NP_071768.3	Q9BSE4	HERP2_HUMAN	HERPUD family member 2	108	Ser-rich.		A -> T (in dbSNP:rs3779234). {ECO:0000269|PubMed:15489334}.		response to unfolded protein (GO:0006986)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				kidney(3)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)	18						CTGCTGGATGCCAATGCTTCA	0.383													C|||	1339	0.267372	0.1203	0.3156	5008	,	,		19078	0.2649		0.3678	False		,,,				2504	0.3313				p.A108T		Atlas-SNP	.											.	HERPUD2	47	.	0			c.G322A						PASS	.	C	THR/ALA	775,3631	313.0+/-292.9	71,633,1499	144.0	135.0	138.0		322	2.2	0.9	7	dbSNP_107	138	3319,5281	494.2+/-373.8	651,2017,1632	yes	missense	HERPUD2	NM_022373.4	58	722,2650,3131	TT,TC,CC		38.593,17.5897,31.4778	benign	108/407	35709842	4094,8912	2203	4300	6503	SO:0001583	missense	64224	exon4			TGGATGCCAATGC	BC020264	CCDS5446.1	7p14.2	2006-03-20	2006-03-20		ENSG00000122557	ENSG00000122557			21915	protein-coding gene	gene with protein product	"""homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 2"""						Standard	NM_022373		Approved	FLJ22313	uc003tes.4	Q9BSE4	OTTHUMG00000128687	ENST00000396081.1:c.322G>A	7.37:g.35709842C>T	ENSP00000379390:p.Ala108Thr	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	161	158	0.981366	NM_022373	A4D1Y8|Q9H6F9	Missense_Mutation	SNP	ENST00000396081.1	37	CCDS5446.1	605	0.27701465201465203	63	0.12804878048780488	120	0.3314917127071823	141	0.2465034965034965	281	0.370712401055409	C	12.44	1.937260	0.34189	0.175897	0.38593	ENSG00000122557	ENST00000396081;ENST00000311350;ENST00000413517	T;T;T	0.24723	2.81;2.81;1.84	5.57	2.24	0.28232	.	0.600215	0.18491	N	0.139623	T	0.00012	0.0000	N	0.08118	0	0.31015	P	0.718757	B	0.14438	0.01	B	0.12156	0.007	T	0.47995	-0.9073	9	0.28530	T	0.3	-5.4519	8.905	0.35519	0.0:0.6726:0.1285:0.1989	rs3779234;rs17849911;rs17851785;rs59517106;rs3779234	108	Q9BSE4	HERP2_HUMAN	T	108;108;82	ENSP00000379390:A108T;ENSP00000310729:A108T;ENSP00000391015:A82T	ENSP00000310729:A108T	A	-	1	0	HERPUD2	35676367	0.990000	0.36364	0.901000	0.35422	0.891000	0.51852	0.811000	0.27198	0.681000	0.31386	0.460000	0.39030	GCA	C|0.703;T|0.297	0.297	strong		0.383	HERPUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250584.1	NM_022373	
SLC45A1	50651	hgsc.bcm.edu	37	1	8395560	8395560	+	Missense_Mutation	SNP	G	G	T	rs7535752	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:8395560G>T	ENST00000471889.1	+	6	1892	c.1507G>T	c.(1507-1509)Gcg>Tcg	p.A503S	SLC45A1_ENST00000377479.2_Missense_Mutation_p.A537S|SLC45A1_ENST00000481265.1_3'UTR|SLC45A1_ENST00000289877.8_Missense_Mutation_p.A503S			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	503					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CAGCGAGCGCGCGGAGCAGCC	0.647													G|||	773	0.154353	0.0961	0.1859	5008	,	,		16601	0.0228		0.1839	False		,,,				2504	0.316				p.A503S		Atlas-SNP	.											.	SLC45A1	85	.	0			c.G1507T						PASS	.	G	SER/ALA	462,3944	219.1+/-236.9	21,420,1762	55.0	63.0	60.0		1507	-10.2	0.0	1	dbSNP_116	60	1644,6956	302.1+/-305.8	157,1330,2813	yes	missense	SLC45A1	NM_001080397.1	99	178,1750,4575	TT,TG,GG		19.1163,10.4857,16.1925	benign	503/749	8395560	2106,10900	2203	4300	6503	SO:0001583	missense	50651	exon5			GAGCGCGCGGAGC	AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"""Solute carriers"""	17939	protein-coding gene	gene with protein product	"""H+/sugar symporter"""	605763	"""deleted in neuroblastoma 5"""	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.1507G>T	1.37:g.8395560G>T	ENSP00000418096:p.Ala503Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	37	28	0.756757	NM_001080397	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	37	CCDS30577.1	240	0.10989010989010989	40	0.08130081300813008	72	0.19889502762430938	3	0.005244755244755245	125	0.16490765171503957	G	0.061	-1.223735	0.01530	0.104857	0.191163	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	T;T;T	0.78246	-1.16;-1.16;-1.16	5.09	-10.2	0.00374	.	0.826256	0.11218	N	0.587016	T	0.00039	0.0001	N	0.00996	-1.065	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.16689	-1.0394	9	0.08599	T	0.76	-2.1771	13.6969	0.62585	0.0:0.1439:0.1103:0.7457	rs7535752;rs57840924;rs7535752	503	Q9Y2W3	S45A1_HUMAN	S	503;537;503	ENSP00000418096:A503S;ENSP00000366699:A537S;ENSP00000289877:A503S	ENSP00000289877:A503S	A	+	1	0	SLC45A1	8318147	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.306000	0.08178	-1.967000	0.01008	0.561000	0.74099	GCG	G|0.849;T|0.151	0.151	strong		0.647	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5		
CD1B	910	hgsc.bcm.edu	37	1	158299358	158299358	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158299358A>G	ENST00000368168.3	-	4	795	c.688T>C	c.(688-690)Tac>Cac	p.Y230H		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	230	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					GGCTTTGGGTAGAATCCTGAG	0.587																																					p.Y230H		Atlas-SNP	.											CD1B,colon,carcinoma,+1,1	CD1B	78	1	0			c.T688C						PASS	.						91.0	87.0	88.0					1																	158299358		2203	4300	6503	SO:0001583	missense	910	exon4			TTGGGTAGAATCC	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1635	protein-coding gene	gene with protein product		188360	"""CD1B antigen, b polypeptide"", ""CD1b antigen"""	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.688T>C	1.37:g.158299358A>G	ENSP00000357150:p.Tyr230His	Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	396	231	0.583333	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	37	CCDS1176.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.94|12.94	2.086996|2.086996	0.36855|0.36855	.|.	.|.	ENSG00000158485|ENSG00000158485	ENST00000451207|ENST00000368168	.|T	.|0.03920	.|3.76	4.26|4.26	1.9|1.9	0.25705|0.25705	.|Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	.|0.196307	.|0.25509	.|N	.|0.030200	T|T	0.04952|0.04952	0.0133|0.0133	M|M	0.64080|0.64080	1.96|1.96	0.28660|0.28660	N|N	0.9062|0.9062	.|D;P	.|0.54397	.|0.966;0.888	.|P;P	.|0.59546	.|0.859;0.668	T|T	0.22556|0.22556	-1.0213|-1.0213	5|10	.|0.44086	.|T	.|0.13	-8.3888|-8.3888	5.8437|5.8437	0.18647|0.18647	0.7803:0.0:0.2197:0.0|0.7803:0.0:0.2197:0.0	.|.	.|230;230	.|P29016;P29016-2	.|CD1B_HUMAN;.	P|H	197|230	.|ENSP00000357150:Y230H	.|ENSP00000357150:Y230H	L|Y	-|-	2|1	0|0	CD1B|CD1B	156565982|156565982	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	0.587000|0.587000	0.23909|0.23909	0.280000|0.280000	0.22209|0.22209	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.	none		0.587	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764	
MUC17	140453	hgsc.bcm.edu	37	7	100677378	100677378	+	Missense_Mutation	SNP	C	C	A	rs143956720	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677378C>A	ENST00000306151.4	+	3	2745	c.2681C>A	c.(2680-2682)aCa>aAa	p.T894K		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	894	59 X approximate tandem repeats.|Ser-rich.				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)					GACACCAGCACACCTGTGACC	0.498																																					p.T894K		Atlas-SNP	.											MUC17,NS,lymphoid_neoplasm,0,1	MUC17	804	1	0			c.C2681A						PASS	.	C	LYS/THR	350,4056	140.4+/-175.9	0,350,1853	297.0	290.0	292.0		2681	0.3	0.0	7	dbSNP_134	292	167,8433	48.9+/-108.6	0,167,4133	no	missense	MUC17	NM_001040105.1	78	0,517,5986	AA,AC,CC		1.9419,7.9437,3.9751	probably-damaging	894/4494	100677378	517,12489	2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGCACACCTGT	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.2681C>A	7.37:g.100677378C>A	ENSP00000302716:p.Thr894Lys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	291	77	0.264605	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	3.749	-0.052049	0.07362	0.079437	0.019419	ENSG00000169876	ENST00000306151	T	0.02421	4.3	1.25	0.305	0.15801	.	.	.	.	.	T	0.00178	0.0005	N	0.14661	0.345	0.09310	N	1	D	0.69078	0.997	P	0.52267	0.694	T	0.52609	-0.8553	9	0.27082	T	0.32	.	5.4285	0.16440	0.0:0.7817:0.0:0.2183	.	894	Q685J3	MUC17_HUMAN	K	894	ENSP00000302716:T894K	ENSP00000302716:T894K	T	+	2	0	MUC17	100464098	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.259000	0.18405	0.099000	0.17552	0.196000	0.17591	ACA	C|0.958;A|0.042	0.042	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TMPO	7112	hgsc.bcm.edu	37	12	98927830	98927830	+	Intron	SNP	C	C	G	rs17459334	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:98927830C>G	ENST00000556029.1	+	3	921				TMPO_ENST00000266732.4_Missense_Mutation_p.Q599E|TMPO_ENST00000393053.2_Intron|TMPO_ENST00000261210.5_Intron|TMPO_ENST00000343315.5_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	88	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	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	
PROSER1	80209	hgsc.bcm.edu	37	13	39598616	39598616	+	Silent	SNP	G	G	A	rs61945763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:39598616G>A	ENST00000352251.3	-	7	1391	c.558C>T	c.(556-558)tcC>tcT	p.S186S	PROSER1_ENST00000484434.3_5'Flank|PROSER1_ENST00000350125.3_Silent_p.S164S	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	186	Pro-rich.																ATACTGGTTTGGATGGCCCAA	0.333													G|||	312	0.0623003	0.0083	0.2089	5008	,	,		16787	0.001		0.1064	False		,,,				2504	0.0491				p.S186S		Atlas-SNP	.											.	.	.	.	0			c.C558T						PASS	.	G	,	139,4267	98.5+/-137.1	1,137,2065	114.0	99.0	104.0		558,492	0.1	1.0	13	dbSNP_129	104	1088,7512	225.9+/-261.8	65,958,3277	no	coding-synonymous,coding-synonymous	PROSER1	NM_025138.3,NM_170719.2	,	66,1095,5342	AA,AG,GG		12.6512,3.1548,9.4341	,	186/945,164/923	39598616	1227,11779	2203	4300	6503	SO:0001819	synonymous_variant	80209	exon7			TGGTTTGGATGGC	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.558C>T	13.37:g.39598616G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	153	64	0.418301	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	Silent	SNP	ENST00000352251.3	37	CCDS9368.2																																																																																			G|0.909;A|0.091	0.091	strong		0.333	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
SETD8	387893	hgsc.bcm.edu	37	12	123875311	123875311	+	Silent	SNP	C	C	T	rs74356260		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:123875311C>T	ENST00000402868.3	+	3	693	c.267C>T	c.(265-267)gcC>gcT	p.A89A	SETD8_ENST00000330479.4_Silent_p.A89A|SETD8_ENST00000478781.2_3'UTR			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	130					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)	p.A89A(4)		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)		AACCATTAGCCGGAATCTACA	0.498																																					p.A89A		Atlas-SNP	.											SETD8,NS,carcinoma,0,6	SETD8	35	6	4	Substitution - coding silent(4)	prostate(3)|central_nervous_system(1)	c.C267T						scavenged	.						105.0	100.0	101.0					12																	123875311		2203	4300	6503	SO:0001819	synonymous_variant	387893	exon3			ATTAGCCGGAATC	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.267C>T	12.37:g.123875311C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	176	2	0.0113636	NM_020382	A8K9D0|Q86W83|Q8TD09	Silent	SNP	ENST00000402868.3	37	CCDS9247.1																																																																																			.	.	weak		0.498	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	
SLC39A13	91252	hgsc.bcm.edu	37	11	47431764	47431764	+	Missense_Mutation	SNP	G	G	A	rs35741412	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47431764G>A	ENST00000362021.4	+	2	161	c.119G>A	c.(118-120)cGg>cAg	p.R40Q	RP11-750H9.5_ENST00000532340.1_RNA|SLC39A13_ENST00000524928.1_Missense_Mutation_p.R40Q|RP11-750H9.5_ENST00000532943.1_RNA|SLC39A13_ENST00000533076.1_Missense_Mutation_p.R40Q|SLC39A13_ENST00000531974.1_Missense_Mutation_p.R40Q|SLC39A13_ENST00000354884.4_Missense_Mutation_p.R40Q	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	40					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)		CTCCGGAGCCGGGGGACTGCG	0.687													G|||	38	0.00758786	0.0015	0.013	5008	,	,		13659	0.0		0.0258	False		,,,				2504	0.001				p.R40Q		Atlas-SNP	.											.	SLC39A13	18	.	0			c.G119A						PASS	.	G	GLN/ARG,GLN/ARG	15,4387	20.2+/-43.8	0,15,2186	30.0	36.0	34.0		119,119	2.8	0.9	11	dbSNP_126	34	214,8382	84.5+/-147.0	2,210,4086	yes	missense,missense	SLC39A13	NM_001128225.2,NM_152264.4	43,43	2,225,6272	AA,AG,GG		2.4895,0.3408,1.7618	benign,benign	40/372,40/365	47431764	229,12769	2201	4298	6499	SO:0001583	missense	91252	exon2			GGAGCCGGGGGAC		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.119G>A	11.37:g.47431764G>A	ENSP00000354689:p.Arg40Gln	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_152264	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Missense_Mutation	SNP	ENST00000362021.4	37	CCDS44592.1	25	0.011446886446886446	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	17	0.022427440633245383	G	12.31	1.899337	0.33535	0.003408	0.024895	ENSG00000165915	ENST00000533076;ENST00000531974;ENST00000531419;ENST00000531865;ENST00000362021;ENST00000354884;ENST00000526614;ENST00000527091;ENST00000524928	T;T;T;T;T;T;T;T;T	0.70869	-0.49;0.97;0.96;-0.52;-0.38;-0.19;-0.03;0.97;0.91	5.05	2.85	0.33270	.	1.028510	0.07690	N	0.938611	T	0.29850	0.0746	N	0.14661	0.345	0.21527	N	0.999657	B;B;B	0.21688	0.019;0.013;0.059	B;B;B	0.13407	0.001;0.003;0.009	T	0.31194	-0.9952	10	0.07813	T	0.8	-1.9191	2.8954	0.05689	0.0997:0.1541:0.5026:0.2436	rs35741412;rs61897433	40;40;40	Q96H72;Q96H72-2;E9PNE7	S39AD_HUMAN;.;.	Q	40	ENSP00000434290:R40Q;ENSP00000435845:R40Q;ENSP00000432302:R40Q;ENSP00000434684:R40Q;ENSP00000354689:R40Q;ENSP00000346956:R40Q;ENSP00000432499:R40Q;ENSP00000435076:R40Q;ENSP00000437186:R40Q	ENSP00000346956:R40Q	R	+	2	0	SLC39A13	47388340	1.000000	0.71417	0.932000	0.37286	0.500000	0.33767	1.734000	0.38166	0.884000	0.36064	0.491000	0.48974	CGG	G|0.984;A|0.016	0.016	strong		0.687	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264	
EPB41L3	23136	hgsc.bcm.edu	37	18	5416221	5416221	+	Missense_Mutation	SNP	C	C	T	rs9966357	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:5416221C>T	ENST00000341928.2	-	13	2003	c.1663G>A	c.(1663-1665)Gcc>Acc	p.A555T	EPB41L3_ENST00000542652.2_Intron|EPB41L3_ENST00000542146.1_Intron|EPB41L3_ENST00000342933.3_Missense_Mutation_p.A555T|EPB41L3_ENST00000427684.2_Intron|EPB41L3_ENST00000544123.1_Intron|EPB41L3_ENST00000400111.3_Intron|EPB41L3_ENST00000540638.2_Intron	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	555	Spectrin--actin-binding. {ECO:0000255}.		A -> T (in dbSNP:rs9966357).		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						GAGTCCAAGGCGGGCTCTCCA	0.572													c|||	252	0.0503195	0.121	0.0187	5008	,	,		17646	0.0		0.0268	False		,,,				2504	0.0532				p.A555T		Atlas-SNP	.											.	EPB41L3	222	.	0			c.G1663A						PASS	.	T	THR/ALA	470,3936	220.7+/-238.1	25,420,1758	82.0	84.0	84.0		1663	-11.1	0.0	18	dbSNP_119	84	269,8331	103.3+/-164.5	7,255,4038	yes	missense	EPB41L3	NM_012307.2	58	32,675,5796	TT,TC,CC		3.1279,10.6673,5.682	benign	555/1088	5416221	739,12267	2203	4300	6503	SO:0001583	missense	23136	exon13			CCAAGGCGGGCTC	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.1663G>A	18.37:g.5416221C>T	ENSP00000343158:p.Ala555Thr	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	101	0.04624542124542125	72	0.14634146341463414	7	0.019337016574585635	0	0.0	22	0.029023746701846966	c	0.008	-1.930120	0.00488	0.106673	0.031279	ENSG00000082397	ENST00000341928;ENST00000342933	T;T	0.80393	-1.37;-1.37	5.55	-11.1	0.00147	.	.	.	.	.	T	0.00384	0.0012	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.04268	-1.0964	8	0.13470	T	0.59	.	6.6903	0.23167	0.3941:0.1901:0.0:0.4158	rs9966357;rs52812768;rs9966357	555	Q9Y2J2	E41L3_HUMAN	T	555	ENSP00000343158:A555T;ENSP00000341138:A555T	ENSP00000343158:A555T	A	-	1	0	EPB41L3	5406221	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.647000	0.00860	-4.798000	0.00031	-3.942000	0.00015	GCC	C|0.945;T|0.055	0.055	strong		0.572	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
MICA	100507436	hgsc.bcm.edu	37	6	31379773	31379773	+	Silent	SNP	C	C	T	rs1051796	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31379773C>T	ENST00000449934.2	+	4	717	c.663C>T	c.(661-663)atC>atT	p.I221I	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)				AGGGCAACATCACCGTGACAT	0.602													c|||	1821	0.363618	0.4766	0.4049	5008	,	,		20346	0.3006		0.3141	False		,,,				2504	0.2975				p.I221I		Atlas-SNP	.											.	MICA	21	.	0			c.C663T						PASS	.	C		579,805		132,315,245	31.0	34.0	33.0		663	1.6	0.0	6	dbSNP_86	33	913,2269		126,661,804	no	coding-synonymous	MICA	NM_001177519.1		258,976,1049	TT,TC,CC		28.6926,41.8353,32.6763		221/333	31379773	1492,3074	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon4			CAACATCACCGTG	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.663C>T	6.37:g.31379773C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	111	39	0.351351	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	weak		0.602	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
OR5P3	120066	hgsc.bcm.edu	37	11	7847208	7847208	+	Silent	SNP	T	T	C	rs1482791	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:7847208T>C	ENST00000328375.1	-	1	311	c.312A>G	c.(310-312)gtA>gtG	p.V104V	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153445.1	NP_703146.1	Q8WZ94	OR5P3_HUMAN	olfactory receptor, family 5, subfamily P, member 3	104						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(2)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	15				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAAACGTCACTACAGAACAGA	0.547													T|||	2221	0.44349	0.0711	0.5937	5008	,	,		19791	0.4762		0.6292	False		,,,				2504	0.6155				p.V104V		Atlas-SNP	.											.	OR5P3	44	.	0			c.A312G						PASS	.	T		741,3631		119,503,1564	157.0	153.0	155.0		312	-10.6	0.0	11	dbSNP_88	155	5412,3180		1709,1994,593	no	coding-synonymous	OR5P3	NM_153445.1		1828,2497,2157	CC,CT,TT		37.0112,16.9488,47.4622		104/312	7847208	6153,6811	2186	4296	6482	SO:0001819	synonymous_variant	120066	exon1			CGTCACTACAGAA	AF158377	CCDS7783.1	11p15.4	2012-08-09			ENSG00000182334	ENSG00000182334		"""GPCR / Class A : Olfactory receptors"""	14784	protein-coding gene	gene with protein product							Standard	NM_153445		Approved	JCG1	uc010rbg.2	Q8WZ94	OTTHUMG00000165669	ENST00000328375.1:c.312A>G	11.37:g.7847208T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_153445	Q6IFE1|Q8NGM2	Silent	SNP	ENST00000328375.1	37	CCDS7783.1																																																																																			T|0.476;C|0.524	0.524	strong		0.547	OR5P3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385697.1	NM_153445	
ZNF135	7694	hgsc.bcm.edu	37	19	58572959	58572959	+	Silent	SNP	G	G	A	rs2288274	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:58572959G>A	ENST00000313434.5	+	3	146	c.45G>A	c.(43-45)acG>acA	p.T15T	ZNF135_ENST00000439855.2_Silent_p.T15T|ZNF135_ENST00000511556.1_Silent_p.T15T|ZNF135_ENST00000401053.4_Silent_p.T27T|ZNF135_ENST00000506786.1_5'UTR|ZNF135_ENST00000359978.6_Silent_p.T27T	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	15	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|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)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		AGCAAGTGACGTTTGAGGACG	0.602													G|||	1351	0.269768	0.2859	0.2277	5008	,	,		18117	0.2649		0.2992	False		,,,				2504	0.2526				p.T27T		Atlas-SNP	.											ZNF135_ENST00000401053,colon,carcinoma,+1,3	ZNF135	159	3	0			c.G81A						PASS	.	G	,,,,	1289,3117	438.0+/-345.2	185,919,1099	133.0	117.0	122.0		81,81,81,45,81	-1.0	0.9	19	dbSNP_100	122	2345,6255	392.4+/-344.0	308,1729,2263	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF135	NM_001164527.1,NM_001164529.1,NM_001164530.1,NM_003436.3,NM_007134.1	,,,,	493,2648,3362	AA,AG,GG		27.2674,29.2556,27.941	,,,,	27/124,27/116,27/391,15/671,27/683	58572959	3634,9372	2203	4300	6503	SO:0001819	synonymous_variant	7694	exon2			AGTGACGTTTGAG	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"""Zinc fingers, C2H2-type"", ""-"""	12919	protein-coding gene	gene with protein product		604077	"""zinc finger protein 61"", ""zinc finger protein 135 (clone pHZ-17)"""	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.45G>A	19.37:g.58572959G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	245	106	0.432653	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Silent	SNP	ENST00000313434.5	37		625	0.28617216117216115	158	0.32113821138211385	80	0.22099447513812154	158	0.2762237762237762	229	0.3021108179419525	G	7.475	0.647440	0.14516	0.292556	0.272674	ENSG00000176293	ENST00000391699	.	.	.	2.52	-1.02	0.10135	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999899716	.	.	.	.	.	.	T	0.42207	-0.9465	3	.	.	.	.	1.8703	0.03207	0.1896:0.2962:0.3818:0.1323	rs2288274;rs56480989;rs57809788;rs2288274	.	.	.	H	21	.	.	R	+	2	0	ZNF135	63264771	0.000000	0.05858	0.950000	0.38849	0.869000	0.49853	-2.496000	0.00970	-0.105000	0.12132	-1.339000	0.01253	CGT	G|0.716;A|0.284	0.284	strong		0.602	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
ZBTB45	84878	hgsc.bcm.edu	37	19	59028427	59028427	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:59028427T>C	ENST00000594051.1	-	2	1094	c.614A>G	c.(613-615)gAc>gGc	p.D205G	ZBTB45_ENST00000600990.1_Missense_Mutation_p.D205G|ZBTB45_ENST00000354590.3_Missense_Mutation_p.D205G			Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	205					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)|lung(5)|urinary_tract(1)	11		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)		GTCACCTCGGTCATCAGGGGC	0.672											OREG0025700	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D205G	NSCLC(164;1383 2017 5233 27540 46677)	Atlas-SNP	.											ZBTB45,NS,carcinoma,0,1	ZBTB45	37	1	0			c.A614G						scavenged	.						129.0	135.0	133.0					19																	59028427		2203	4300	6503	SO:0001583	missense	84878	exon2			CCTCGGTCATCAG	AK027392	CCDS12984.1	19q13.43	2013-10-10	2006-09-19	2006-09-19	ENSG00000119574	ENSG00000119574		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	23715	protein-coding gene	gene with protein product			"""zinc finger protein 499"""	ZNF499			Standard	NM_032792		Approved	FLJ14486	uc002qtd.3	Q96K62	OTTHUMG00000183545	ENST00000594051.1:c.614A>G	19.37:g.59028427T>C	ENSP00000469089:p.Asp205Gly	Somatic	180	1	0.00555556	1035	WXS	Illumina HiSeq	Phase_I	188	3	0.0159574	NM_032792		Missense_Mutation	SNP	ENST00000594051.1	37	CCDS12984.1	.	.	.	.	.	.	.	.	.	.	t	15.37	2.813194	0.50527	.	.	ENSG00000119574	ENST00000354590	T	0.08458	3.09	3.23	3.23	0.37069	.	0.988962	0.08166	U	0.987761	T	0.12433	0.0302	N	0.19112	0.55	0.35723	D	0.817307	D	0.67145	0.996	P	0.62740	0.906	T	0.21245	-1.0251	10	0.11794	T	0.64	.	10.1253	0.42646	0.0:0.0:0.0:1.0	.	205	Q96K62	ZBT45_HUMAN	G	205	ENSP00000346603:D205G	ENSP00000346603:D205G	D	-	2	0	ZBTB45	63720239	0.857000	0.29778	0.019000	0.16419	0.283000	0.27025	1.572000	0.36461	1.723000	0.51488	0.383000	0.25322	GAC	.	.	none		0.672	ZBTB45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467067.1	NM_032792	
UMODL1	89766	hgsc.bcm.edu	37	21	43510437	43510437	+	Missense_Mutation	SNP	A	A	G	rs17114359	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43510437A>G	ENST00000408910.2	+	6	820	c.820A>G	c.(820-822)Aat>Gat	p.N274D	UMODL1_ENST00000408989.2_Missense_Mutation_p.N274D|UMODL1_ENST00000400427.1_Missense_Mutation_p.N202D|UMODL1_ENST00000400424.2_Missense_Mutation_p.N202D	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	274	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		N -> D (in dbSNP:rs17114359). {ECO:0000269|PubMed:16026467}.|N -> H (in dbSNP:rs17114359). {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						TGAGGAGCTCAATGCCTGCTC	0.557													A|||	396	0.0790735	0.2148	0.0331	5008	,	,		20658	0.0		0.0467	False		,,,				2504	0.0429				p.N274D	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											UMODL1_ENST00000408989,colon,carcinoma,0,2	UMODL1	186	2	0			c.A820G						scavenged	.						133.0	135.0	134.0					21																	43510437		2139	4236	6375	SO:0001583	missense	89766	exon6			GAGCTCAATGCCT		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.820A>G	21.37:g.43510437A>G	ENSP00000386147:p.Asn274Asp	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	225	90	0.4	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	A	11.69	1.714101	0.30413	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000380462;ENST00000400417	D;D;D;D	0.92048	-2.96;-2.96;-2.96;-2.96	3.89	1.51	0.23008	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);	0.921215	0.08894	N	0.878228	D	0.90249	0.6951	N	0.24115	0.695	0.80722	P	0.0	D;P	0.58620	0.983;0.833	P;B	0.56042	0.79;0.42	D	0.85632	0.1271	9	0.59425	D	0.04	-5.2933	8.6932	0.34280	0.4946:0.5054:0.0:0.0	rs17114359;rs17114359	274;274	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	D	202;202;274;274;120;120	ENSP00000383279:N202D;ENSP00000383276:N202D;ENSP00000386126:N274D;ENSP00000386147:N274D	ENSP00000369829:N120D	N	+	1	0	UMODL1	42383506	0.925000	0.31364	0.004000	0.12327	0.044000	0.14063	1.864000	0.39469	0.188000	0.20168	0.260000	0.18958	AAT	A|0.735;C|0.140;G|0.124	0.124	strong		0.557	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
MUC17	140453	hgsc.bcm.edu	37	7	100677995	100677995	+	Missense_Mutation	SNP	A	A	G	rs149287079		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677995A>G	ENST00000306151.4	+	3	3362	c.3298A>G	c.(3298-3300)Agc>Ggc	p.S1100G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1100	59 X approximate tandem repeats.|Ser-rich.				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)					TAGTGAAGGAAGCACTCCACT	0.517																																					p.S1100G		Atlas-SNP	.											.	MUC17	804	.	0			c.A3298G						PASS	.						490.0	389.0	423.0					7																	100677995		2203	4300	6503	SO:0001583	missense	140453	exon3			GAAGGAAGCACTC	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.3298A>G	7.37:g.100677995A>G	ENSP00000302716:p.Ser1100Gly	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	909	157	0.172717	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.119	-1.127913	0.01770	.	.	ENSG00000169876	ENST00000306151	T	0.02552	4.25	0.693	-1.39	0.08997	.	.	.	.	.	T	0.01870	0.0059	L	0.29908	0.895	0.09310	N	1	B	0.27192	0.171	B	0.14023	0.01	T	0.46721	-0.9171	9	0.25751	T	0.34	.	2.8064	0.05429	0.5265:0.2609:0.2126:0.0	.	1100	Q685J3	MUC17_HUMAN	G	1100	ENSP00000302716:S1100G	ENSP00000302716:S1100G	S	+	1	0	MUC17	100464715	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-1.232000	0.02936	-1.186000	0.02713	-1.357000	0.01221	AGC	.	.	weak		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CALCOCO2	10241	hgsc.bcm.edu	37	17	46939658	46939658	+	Missense_Mutation	SNP	C	C	G	rs10278	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46939658C>G	ENST00000258947.3	+	12	1266	c.1165C>G	c.(1165-1167)Ccc>Gcc	p.P389A	CALCOCO2_ENST00000416445.2_Missense_Mutation_p.P347A|CALCOCO2_ENST00000448105.2_Missense_Mutation_p.P413A|CALCOCO2_ENST00000508679.1_Missense_Mutation_p.P317A|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	170	0	0		WXS	Illumina HiSeq	Phase_I	202	93	0.460396	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	
SLC6A18	348932	hgsc.bcm.edu	37	5	1225676	1225676	+	Silent	SNP	C	C	T	rs33978774	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:1225676C>T	ENST00000324642.3	+	1	207	c.84C>T	c.(82-84)ctC>ctT	p.L28L	SLC6A18_ENST00000296821.4_Silent_p.L28L	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	28					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CCCAGTACCTCCTGAGCTGCA	0.637													C|||	323	0.0644968	0.0076	0.0749	5008	,	,		18277	0.001		0.16	False		,,,				2504	0.1012				p.L28L		Atlas-SNP	.											.	SLC6A18	84	.	0			c.C84T						PASS	.	C		130,4276	93.4+/-132.2	1,128,2074	118.0	101.0	107.0		84	-7.7	0.8	5	dbSNP_126	107	1463,7137	276.8+/-292.5	137,1189,2974	no	coding-synonymous	SLC6A18	NM_182632.2		138,1317,5048	TT,TC,CC		17.0116,2.9505,12.2482		28/629	1225676	1593,11413	2203	4300	6503	SO:0001819	synonymous_variant	348932	exon1			GTACCTCCTGAGC	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"""Solute carriers"""	26441	protein-coding gene	gene with protein product		610300	"""solute carrier family 6 (neurotransmitter transporter), member 18"", ""solute carrier family 6, member 18"""			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.84C>T	5.37:g.1225676C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	NM_182632		Silent	SNP	ENST00000324642.3	37	CCDS3860.1																																																																																			C|0.893;T|0.107	0.107	strong		0.637	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632	
KRT7	3855	hgsc.bcm.edu	37	12	52635360	52635360	+	Silent	SNP	G	G	A	rs999665	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	130	0	0		WXS	Illumina HiSeq	Phase_I	113	111	0.982301	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	
GLYATL3	389396	hgsc.bcm.edu	37	6	49485266	49485266	+	Missense_Mutation	SNP	C	C	A	rs9367358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:49485266C>A	ENST00000371197.4	+	4	423	c.310C>A	c.(310-312)Caa>Aaa	p.Q104K		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	104				Q -> K (in Ref. 1; AK126371). {ECO:0000305}.		mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						TTTTCAAATACAAGGTGAGGT	0.328													C|||	1292	0.257987	0.0121	0.451	5008	,	,		18212	0.499		0.2018	False		,,,				2504	0.2628				p.Q104K		Atlas-SNP	.											.	GLYATL3	19	.	0			c.C310A						PASS	.	C	LYS/GLN	46,1338		0,46,646	163.0	136.0	144.0		310	6.0	1.0	6	dbSNP_119	144	624,2558		61,502,1028	yes	missense	GLYATL3	NM_001010904.1	53	61,548,1674	AA,AC,CC		19.6103,3.3237,14.6737	possibly-damaging	104/289	49485266	670,3896	692	1591	2283	SO:0001583	missense	389396	exon4			CAAATACAAGGTG		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.310C>A	6.37:g.49485266C>A	ENSP00000360240:p.Gln104Lys	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	193	79	0.409326	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	622	0.2847985347985348	12	0.024390243902439025	151	0.4171270718232044	319	0.5576923076923077	140	0.18469656992084432	C	17.64	3.440813	0.63067	0.033237	0.196103	ENSG00000203972	ENST00000371197;ENST00000545705	T;T	0.22336	1.96;1.96	6.01	6.01	0.97437	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	.	.	.	.	T	0.13372	0.0324	M	0.76574	2.34	0.30797	P	0.740263	B	0.28419	0.211	B	0.31547	0.132	T	0.05818	-1.0862	8	0.07030	T	0.85	-4.5353	16.0184	0.80460	0.0:1.0:0.0:0.0	rs9367358;rs52838191;rs60437869;rs9367358	104	Q5SZD4	GLYL3_HUMAN	K	104	ENSP00000360240:Q104K;ENSP00000440029:Q104K	ENSP00000360240:Q104K	Q	+	1	0	GLYATL3	49593225	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.197000	0.58413	2.860000	0.98153	0.655000	0.94253	CAA	C|0.732;A|0.268	0.268	strong		0.328	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
TKTL2	84076	hgsc.bcm.edu	37	4	164393117	164393117	+	Missense_Mutation	SNP	T	T	A	rs11735477	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:164393117T>A	ENST00000280605.3	-	1	1930	c.1770A>T	c.(1768-1770)caA>caT	p.Q590H		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	590			Q -> H (in dbSNP:rs11735477). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.Q590H(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				ACACTGCCAGTTGATGAACAA	0.488													T|||	856	0.170927	0.1445	0.0778	5008	,	,		19406	0.2867		0.1909	False		,,,				2504	0.1329				p.Q590H		Atlas-SNP	.											TKTL2,NS,carcinoma,0,1	TKTL2	130	1	1	Substitution - Missense(1)	prostate(1)	c.A1770T						PASS	.	T	HIS/GLN	705,3701	294.1+/-283.0	67,571,1565	95.0	85.0	88.0		1770	-1.2	0.2	4	dbSNP_120	88	1588,7012	296.5+/-302.9	156,1276,2868	yes	missense	TKTL2	NM_032136.4	24	223,1847,4433	AA,AT,TT		18.4651,16.0009,17.6303	benign	590/627	164393117	2293,10713	2203	4300	6503	SO:0001583	missense	84076	exon1			TGCCAGTTGATGA	BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"""similar to transketolase"""					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.1770A>T	4.37:g.164393117T>A	ENSP00000280605:p.Gln590His	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	137	36	0.262774	NM_032136	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	37	CCDS3805.1	420	0.19230769230769232	71	0.1443089430894309	32	0.08839779005524862	163	0.28496503496503495	154	0.20316622691292877	T	0.934	-0.711875	0.03206	0.160009	0.184651	ENSG00000151005	ENST00000280605	D	0.90955	-2.76	5.16	-1.18	0.09617	Transketolase, C-terminal (1);Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain II (1);Transketolase-like, C-terminal (1);	0.302904	0.31082	N	0.008282	T	0.00012	0.0000	N	0.17594	0.5	0.80722	P	0.0	B	0.14012	0.009	B	0.15052	0.012	T	0.05289	-1.0894	9	0.08179	T	0.78	-8.7736	2.0063	0.03478	0.1287:0.2479:0.3786:0.2447	rs11735477;rs17656580;rs52837438;rs11735477	590	Q9H0I9	TKTL2_HUMAN	H	590	ENSP00000280605:Q590H	ENSP00000280605:Q590H	Q	-	3	2	TKTL2	164612567	0.003000	0.15002	0.204000	0.23530	0.935000	0.57460	-0.689000	0.05144	-0.076000	0.12775	-0.137000	0.14449	CAA	A|0.186;N|0.000	0.186	strong		0.488	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136	
IL22RA1	58985	hgsc.bcm.edu	37	1	24447943	24447943	+	Silent	SNP	G	G	A	rs34967816	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:24447943G>A	ENST00000270800.1	-	7	1115	c.1077C>T	c.(1075-1077)gtC>gtT	p.V359V		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	359					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)		ATGGGGGCCCGACCTCAGGGG	0.617													G|||	587	0.117212	0.2186	0.062	5008	,	,		17802	0.003		0.0974	False		,,,				2504	0.1575				p.V359V		Atlas-SNP	.											.	IL22RA1	62	.	0			c.C1077T						PASS	.	G		850,3556	335.7+/-304.0	90,670,1443	89.0	98.0	95.0		1077	-0.9	0.0	1	dbSNP_126	95	845,7755	193.4+/-239.1	39,767,3494	no	coding-synonymous	IL22RA1	NM_021258.3		129,1437,4937	AA,AG,GG		9.8256,19.2919,13.0324		359/575	24447943	1695,11311	2203	4300	6503	SO:0001819	synonymous_variant	58985	exon7			GGGCCCGACCTCA	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.1077C>T	1.37:g.24447943G>A		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	85	80	0.941176	NM_021258	A8K839|B2R9Y9|Q9HB22	Silent	SNP	ENST00000270800.1	37	CCDS247.1																																																																																			G|0.880;A|0.120	0.120	strong		0.617	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
NLRC4	58484	hgsc.bcm.edu	37	2	32475109	32475109	+	Silent	SNP	G	G	A	rs455060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:32475109G>A	ENST00000404025.2	-	5	2312	c.1824C>T	c.(1822-1824)gcC>gcT	p.A608A	NLRC4_ENST00000360906.5_Silent_p.A608A|NLRC4_ENST00000402280.1_Silent_p.A608A|NLRC4_ENST00000342905.6_Intron			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	608					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)	p.A608A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TGAAGTCCAGGGCACTTGCAC	0.433													A|||	2966	0.592252	0.7201	0.6556	5008	,	,		19989	0.4633		0.6173	False		,,,				2504	0.4816				p.A608A		Atlas-SNP	.											NLRC4,NS,carcinoma,0,1	NLRC4	165	1	1	Substitution - coding silent(1)	stomach(1)	c.C1824T						scavenged	.	A	,,	2993,1413	462.6+/-353.3	1022,949,232	125.0	135.0	132.0		1824,1824,1824	-5.5	0.8	2	dbSNP_80	132	5197,3403	502.2+/-375.6	1574,2049,677	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	,,	2596,2998,909	AA,AG,GG		39.5698,32.0699,37.0291	,,	608/1025,608/1025,608/1025	32475109	8190,4816	2203	4300	6503	SO:0001819	synonymous_variant	58484	exon4			GTCCAGGGCACTT	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.1824C>T	2.37:g.32475109G>A		Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	196	90	0.459184	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Silent	SNP	ENST00000404025.2	37	CCDS33174.1																																																																																			G|0.383;A|0.617	0.617	strong		0.433	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209	
OR2W5	441932	hgsc.bcm.edu	37	1	247654916	247654916	+	RNA	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247654916A>G	ENST00000522351.1	+	0	547							A6NFC9	OR2W5_HUMAN	olfactory receptor, family 2, subfamily W, member 5							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)|kidney(2)|large_intestine(2)|lung(24)|ovary(1)|skin(4)	39	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;0.222)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GTGTCCTCAGACGATGCAGCT	0.562																																					p.T163A		Atlas-SNP	.											OR2W5,NS,adenocarcinoma,-2,1	OR2W5	97	1	0			c.A487G						scavenged	.						119.0	94.0	103.0					1																	247654916		2203	4300	6503			441932	exon1			CCTCAGACGATGC			1q44	2013-03-27		2004-03-10	ENSG00000203664	ENSG00000203664		"""GPCR / Class A : Olfactory receptors"""	15424	other	unknown				OR2W5P		12213199	Standard	NM_001004698		Approved	OST722	uc001icz.2	A6NFC9	OTTHUMG00000040573		1.37:g.247654916A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	243	4	0.0164609	NM_001004698	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	37																																																																																				.	.	none		0.562	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416784	105416784	+	Silent	SNP	A	A	G	rs59373922	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105416784A>G	ENST00000333244.5	-	7	5123	c.5004T>C	c.(5002-5004)ttT>ttC	p.F1668F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1668						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)			CCGACACCCCAAATGATGGCA	0.602													.|||	1298	0.259185	0.3563	0.1081	5008	,	,		17171	0.3462		0.1044	False		,,,				2504	0.3047				p.F1668F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T5004C						PASS	.	G		1080,2792		259,562,1115	198.0	234.0	223.0		5004	-6.9	0.0	14	dbSNP_129	223	900,7304		141,618,3343	no	coding-synonymous	AHNAK2	NM_138420.2		400,1180,4458	GG,GA,AA		10.9703,27.8926,16.3962		1668/5796	105416784	1980,10096	1936	4102	6038	SO:0001819	synonymous_variant	113146	exon7			CACCCCAAATGAT	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.5004T>C	14.37:g.105416784A>G		Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	380	164	0.431579	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.835;G|0.165	0.165	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
USP2	9099	hgsc.bcm.edu	37	11	119229964	119229964	+	Silent	SNP	G	G	A	rs2241646	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:119229964G>A	ENST00000260187.2	-	5	1332	c.1038C>T	c.(1036-1038)taC>taT	p.Y346Y	USP2_ENST00000525735.1_Silent_p.Y137Y|USP2_ENST00000455332.2_Silent_p.Y103Y	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	346	USP.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		AGCGCGGTGCGTATCTCTGGA	0.498													G|||	3544	0.707668	0.5598	0.6383	5008	,	,		20364	0.8611		0.7247	False		,,,				2504	0.7812				p.Y346Y		Atlas-SNP	.											.	USP2	71	.	0			c.C1038T						PASS	.	G	,	2511,1887	629.0+/-395.2	718,1075,406	90.0	79.0	83.0		1038,411	-8.9	0.4	11	dbSNP_98	83	6069,2521	692.4+/-404.6	2159,1751,385	no	coding-synonymous,coding-synonymous	USP2	NM_004205.4,NM_171997.2	,	2877,2826,791	AA,AG,GG		29.3481,42.9059,33.939	,	346/606,137/397	119229964	8580,4408	2199	4295	6494	SO:0001819	synonymous_variant	9099	exon5			CGGTGCGTATCTC	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.1038C>T	11.37:g.119229964G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	283	203	0.717314	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	37	CCDS8422.1																																																																																			G|0.310;A|0.690	0.690	strong		0.498	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
ARSD	414	hgsc.bcm.edu	37	X	2836060	2836060	+	Silent	SNP	G	G	A	rs113318393		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	82	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	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		
KLC4	89953	hgsc.bcm.edu	37	6	43039340	43039340	+	Missense_Mutation	SNP	C	C	T	rs41274918	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43039340C>T	ENST00000394056.2	+	11	1786	c.1291C>T	c.(1291-1293)Cgg>Tgg	p.R431W	KLC4_ENST00000453940.2_Missense_Mutation_p.R354W|KLC4_ENST00000347162.5_Missense_Mutation_p.R431W|KLC4_ENST00000479388.1_Missense_Mutation_p.R431W|KLC4_ENST00000259708.3_Missense_Mutation_p.R449W|KLC4_ENST00000394058.1_Missense_Mutation_p.R431W|RP11-387M24.5_ENST00000606123.1_RNA			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	431						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)	p.R431W(1)		endometrium(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(4)	23			all cancers(41;0.00169)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0376)|KIRC - Kidney renal clear cell carcinoma(2;0.0453)			TGCAGAGGAGCGGGAGGAAAT	0.587													C|||	3	0.000599042	0.0	0.0	5008	,	,		17649	0.0		0.002	False		,,,				2504	0.001				p.R449W		Atlas-SNP	.											KLC4,colon,carcinoma,0,1	KLC4	89	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1345T						scavenged	.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	59.0	61.0	60.0		1291,1291,1345	5.8	1.0	6	dbSNP_127	60	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	KLC4	NM_201521.1,NM_201522.1,NM_201523.1	101,101,101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging,probably-damaging	431/620,431/620,449/638	43039340	2,13004	2203	4300	6503	SO:0001583	missense	89953	exon10			GAGGAGCGGGAGG	AK055293	CCDS4882.1, CCDS4883.1, CCDS47429.1, CCDS75459.1	6p21.1	2013-01-10	2005-09-13	2005-09-13	ENSG00000137171	ENSG00000137171		"""Tetratricopeptide (TTC) repeat domain containing"""	21624	protein-coding gene	gene with protein product			"""kinesin-like 8"""	KNSL8			Standard	NM_001289034		Approved	bA387M24.3	uc003otw.1	Q9NSK0	OTTHUMG00000014720	ENST00000394056.2:c.1291C>T	6.37:g.43039340C>T	ENSP00000377620:p.Arg431Trp	Somatic	280	2	0.00714286		WXS	Illumina HiSeq	Phase_I	251	134	0.533865	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	37	CCDS4883.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.58	3.423957	0.62733	2.27E-4	1.16E-4	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	T;T;T;T;T;T	0.80824	-1.4;-1.38;-1.42;-1.4;-1.4;-1.4	5.83	5.83	0.93111	.	0.000000	0.56097	D	0.000022	D	0.88381	0.6421	M	0.85859	2.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.937;0.999;0.998	D	0.87053	0.2148	10	0.36615	T	0.2	-22.2004	14.7934	0.69860	0.1783:0.8217:0.0:0.0	rs41274918	354;449;431	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	W	431;354;449;431;431;431	ENSP00000340221:R431W;ENSP00000395806:R354W;ENSP00000259708:R449W;ENSP00000418031:R431W;ENSP00000377620:R431W;ENSP00000377622:R431W	ENSP00000259708:R449W	R	+	1	2	KLC4	43147318	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.659000	0.37387	2.765000	0.95021	0.555000	0.69702	CGG	C|0.999;T|0.001	0.001	strong		0.587	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343	
ZNF521	25925	hgsc.bcm.edu	37	18	22775185	22775185	+	Silent	SNP	C	C	T	rs1140026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:22775185C>T	ENST00000361524.3	-	5	3745	c.3597G>A	c.(3595-3597)aaG>aaA	p.K1199K	ZNF521_ENST00000584787.1_Silent_p.K979K|ZNF521_ENST00000538137.2_Silent_p.K1199K	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1199					cell differentiation (GO:0030154)|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)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CCATCTGACACTTGATGCATT	0.323			T	PAX5	ALL								C|||	1135	0.226637	0.1316	0.2089	5008	,	,		19650	0.2768		0.2535	False		,,,				2504	0.2883				p.K1199K		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.G3597A						PASS	.	C		631,3773	271.6+/-270.3	33,565,1604	145.0	126.0	133.0		3597	5.6	1.0	18	dbSNP_86	133	2084,6516	357.9+/-330.9	254,1576,2470	no	coding-synonymous	ZNF521	NM_015461.2		287,2141,4074	TT,TC,CC		24.2326,14.3279,20.8782		1199/1312	22775185	2715,10289	2202	4300	6502	SO:0001819	synonymous_variant	25925	exon5			CTGACACTTGATG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.3597G>A	18.37:g.22775185C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			C|0.786;T|0.214	0.214	strong		0.323	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
NAT2	10	hgsc.bcm.edu	37	8	18258103	18258103	+	Missense_Mutation	SNP	G	G	A	rs1799930	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	52	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	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	
CD44	960	hgsc.bcm.edu	37	11	35222681	35222681	+	Silent	SNP	C	C	T	rs35356320	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:35222681C>T	ENST00000428726.2	+	8	1098	c.975C>T	c.(973-975)acC>acT	p.T325T	CD44_ENST00000434472.2_Intron|CD44_ENST00000433354.2_Silent_p.T325T|CD44_ENST00000263398.6_Intron|CD44_ENST00000278386.6_Intron|CD44_ENST00000449691.2_Silent_p.T325T|CD44_ENST00000352818.4_Intron|CD44_ENST00000433892.2_Intron|CD44_ENST00000415148.2_Silent_p.T282T|CD44_ENST00000526669.2_Intron|CD44_ENST00000360158.4_Intron|CD44_ENST00000437706.2_Silent_p.T325T	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	94	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	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	
CC2D2A	57545	hgsc.bcm.edu	37	4	15569018	15569018	+	Silent	SNP	G	G	A	rs73125627	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	474	1	0.0021097		WXS	Illumina HiSeq	Phase_I	437	213	0.487414	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	
HRNR	388697	hgsc.bcm.edu	37	1	152192395	152192395	+	Silent	SNP	G	G	A	rs61814946	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152192395G>A	ENST00000368801.2	-	3	1785	c.1710C>T	c.(1708-1710)agC>agT	p.S570S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_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)	p.S570S(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)			ATGGGCCACGGCTTGAAGACC	0.587													g|||	474	0.0946486	0.0045	0.0879	5008	,	,		20660	0.0942		0.1322	False		,,,				2504	0.183				p.S570S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	1	Substitution - coding silent(1)	stomach(1)	c.C1710T						PASS	.	G		125,4281		0,125,2078	175.0	184.0	181.0		1710	-7.4	0.0	1	dbSNP_129	181	1267,7333		107,1053,3140	no	coding-synonymous	HRNR	NM_001009931.1		107,1178,5218	AA,AG,GG		14.7326,2.837,10.7028		570/2851	152192395	1392,11614	2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			GCCACGGCTTGAA	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.1710C>T	1.37:g.152192395G>A		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	332	116	0.349398	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			G|0.895;A|0.105	0.105	strong		0.587	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
ITIH4	3700	hgsc.bcm.edu	37	3	52864635	52864635	+	Silent	SNP	A	A	G	rs2276818	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:52864635A>G	ENST00000266041.4	-	1	120	c.24T>C	c.(22-24)cgT>cgC	p.R8R	ITIH4_ENST00000406595.1_Silent_p.R8R|RP5-966M1.6_ENST00000468472.1_3'UTR|ITIH4_ENST00000434759.3_5'UTR|ITIH4_ENST00000346281.5_Silent_p.R8R|RP5-966M1.6_ENST00000513520.1_5'UTR|ITIH4_ENST00000485816.1_Silent_p.R8R	NM_002218.4	NP_002209.2	Q14624	ITIH4_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 4	8					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)		TGCTGCAGGTACGGACAGGCC	0.567													A|||	418	0.0834665	0.0613	0.1297	5008	,	,		19453	0.0417		0.1441	False		,,,				2504	0.0613				p.R8R		Atlas-SNP	.											ITIH4,NS,adenocarcinoma,-1,1	ITIH4	74	1	0			c.T24C						PASS	.	A	,	343,4063	179.7+/-208.2	17,309,1877	145.0	135.0	138.0		24,24	-0.7	0.0	3	dbSNP_100	138	1271,7329	253.3+/-279.0	99,1073,3128	no	coding-synonymous,coding-synonymous	ITIH4	NM_001166449.1,NM_002218.4	,	116,1382,5005	GG,GA,AA		14.7791,7.7848,12.4097	,	8/901,8/931	52864635	1614,11392	2203	4300	6503	SO:0001819	synonymous_variant	3700	exon1			GCAGGTACGGACA	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.24T>C	3.37:g.52864635A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_001166449	B7Z545|E9PGN5|Q15135|Q9P190|Q9UQ54	Silent	SNP	ENST00000266041.4	37	CCDS2865.1																																																																																			A|0.880;G|0.120	0.120	strong		0.567	ITIH4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317715.1	NM_002218	
WIPF3	644150	hgsc.bcm.edu	37	7	29924072	29924072	+	Missense_Mutation	SNP	A	A	G	rs3750092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:29924072A>G	ENST00000409290.1	+	4	962	c.962A>G	c.(961-963)gAa>gGa	p.E321G	WIPF3_ENST00000409123.1_Missense_Mutation_p.E321G|WIPF3_ENST00000242140.5_Missense_Mutation_p.E321G	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	321			E -> G (in dbSNP:rs3750092).		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						AGCAGCAGTGAAACTCCACCC	0.706													A|||	418	0.0834665	0.003	0.0303	5008	,	,		7900	0.3095		0.0477	False		,,,				2504	0.0337				p.E321G		Atlas-SNP	.											WIPF3,NS,carcinoma,0,1	WIPF3	46	1	0			c.A962G						PASS	.	A	GLY/GLU	31,3497		0,31,1733	6.0	6.0	6.0		962	2.8	0.0	7	dbSNP_107	6	252,7690		2,248,3721	yes	missense	WIPF3	NM_001080529.2	98	2,279,5454	GG,GA,AA		3.173,0.8787,2.4673	benign	321/484	29924072	283,11187	1764	3971	5735	SO:0001583	missense	644150	exon5			GCAGTGAAACTCC	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.962A>G	7.37:g.29924072A>G	ENSP00000386878:p.Glu321Gly	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	256	90	0.351562	NM_001080529	B8ZZV2	Missense_Mutation	SNP	ENST00000409290.1	37	CCDS56472.1	161	0.07371794871794872	2	0.0040650406504065045	7	0.019337016574585635	116	0.20279720279720279	36	0.047493403693931395	A	9.085	1.000328	0.19121	0.008787	0.03173	ENSG00000122574	ENST00000409123;ENST00000409290;ENST00000242140	T;T;T	0.46451	0.87;0.87;0.87	4.02	2.85	0.33270	.	0.272273	0.25753	N	0.028536	T	0.00039	0.0001	L	0.54323	1.7	0.80722	P	0.0	B	0.18013	0.025	B	0.12837	0.008	T	0.07121	-1.0789	9	0.28530	T	0.3	.	5.5458	0.17063	0.8728:0.0:0.1272:0.0	rs3750092;rs52794636;rs3750092	321	A6NGB9	WIPF3_HUMAN	G	321	ENSP00000386790:E321G;ENSP00000386878:E321G;ENSP00000242140:E321G	ENSP00000242140:E321G	E	+	2	0	WIPF3	29890597	0.954000	0.32549	0.020000	0.16555	0.014000	0.08584	3.440000	0.52886	1.591000	0.50007	0.448000	0.29417	GAA	A|0.914;G|0.086	0.086	strong		0.706	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
HOOK2	29911	hgsc.bcm.edu	37	19	12876964	12876964	+	Missense_Mutation	SNP	G	G	C	rs897804	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	41	0	0	683	WXS	Illumina HiSeq	Phase_I	14	12	0.857143	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	
TAGLN	6876	hgsc.bcm.edu	37	11	117074109	117074109	+	Silent	SNP	G	G	A	rs12970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117074109G>A	ENST00000532870.1	+	2	1408	c.267G>A	c.(265-267)aaG>aaA	p.K89K	TAGLN_ENST00000530649.1_Silent_p.K89K|PCSK7_ENST00000529458.1_5'Flank|TAGLN_ENST00000392951.4_Silent_p.K89K			Q01995	TAGL_HUMAN	transgelin	89	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				epithelial cell differentiation (GO:0030855)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(4)|lung(1)|urinary_tract(1)	7	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|Epithelial(105;5.49e-05)|all cancers(92;0.000435)		TGGTCTTCAAGCAGATGGAGC	0.552													G|||	372	0.0742812	0.0507	0.0605	5008	,	,		19640	0.0823		0.0706	False		,,,				2504	0.1115				p.K89K		Atlas-SNP	.											.	TAGLN	17	.	0			c.G267A						PASS	.	G	,	181,4221	115.0+/-153.0	5,171,2025	102.0	96.0	98.0		267,267	4.8	1.0	11	dbSNP_52	98	510,8082	145.6+/-201.3	12,486,3798	no	coding-synonymous,coding-synonymous	TAGLN	NM_001001522.1,NM_003186.3	,	17,657,5823	AA,AG,GG		5.9358,4.1118,5.3178	,	89/202,89/202	117074109	691,12303	2201	4296	6497	SO:0001819	synonymous_variant	6876	exon3			CTTCAAGCAGATG	M95787	CCDS8381.1	11q23.2	2008-07-21				ENSG00000149591			11553	protein-coding gene	gene with protein product	"""SM22-alpha"", ""transgelin variant 2"""	600818				8117285, 1520290	Standard	NM_003186		Approved	SM22, WS3-10, TAGLN1, SMCC, DKFZp686P11128	uc001pqm.3	Q01995		ENST00000532870.1:c.267G>A	11.37:g.117074109G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	305	80	0.262295	NM_001001522	O15542	Silent	SNP	ENST00000532870.1	37	CCDS8381.1	145	0.06639194139194139	25	0.0508130081300813	16	0.04419889502762431	56	0.0979020979020979	48	0.0633245382585752	G	9.991	1.230759	0.22542	0.041118	0.059358	ENSG00000149591	ENST00000529622	.	.	.	4.84	4.84	0.62591	.	.	.	.	.	T	0.07007	0.0178	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27806	-1.0063	4	.	.	.	.	17.4726	0.87650	0.0:0.0:1.0:0.0	rs12970;rs2230697;rs3210002;rs11216314	.	.	.	N	39	.	.	S	+	2	0	TAGLN	116579319	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.647000	0.46639	2.666000	0.90696	0.561000	0.74099	AGC	G|0.941;A|0.059	0.059	strong		0.552	TAGLN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392864.1	NM_001001522	
SORCS1	114815	hgsc.bcm.edu	37	10	108367020	108367020	+	Silent	SNP	C	C	T	rs7082289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:108367020C>T	ENST00000263054.6	-	23	3076	c.3069G>A	c.(3067-3069)gcG>gcA	p.A1023A	SORCS1_ENST00000369698.1_Silent_p.A558A|SORCS1_ENST00000344440.6_Silent_p.A1023A|SORCS1_ENST00000478809.2_5'UTR	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1023					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)		CAGGGAGCACCGCCACCAGGA	0.552													C|||	1187	0.237021	0.323	0.0994	5008	,	,		19392	0.2401		0.0765	False		,,,				2504	0.3804				p.A1023A		Atlas-SNP	.											.	SORCS1	534	.	0			c.G3069A						PASS	.	C	,,,,,	1246,3160	428.5+/-341.9	184,878,1141	70.0	67.0	68.0		3069,3069,3069,3069,3069,3069	-11.8	0.0	10	dbSNP_116	68	721,7879	175.9+/-225.9	31,659,3610	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	,,,,,	215,1537,4751	TT,TC,CC		8.3837,28.2796,15.1238	,,,,,	1023/1199,1023/1180,1023/1131,1023/1160,1023/1180,1023/1169	108367020	1967,11039	2203	4300	6503	SO:0001819	synonymous_variant	114815	exon23			GAGCACCGCCACC	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.3069G>A	10.37:g.108367020C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	55	9	0.163636	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1	358	0.16391941391941392	135	0.27439024390243905	36	0.09944751381215469	125	0.21853146853146854	62	0.08179419525065963	C	5.613	0.297926	0.10622	0.282796	0.083837	ENSG00000108018	ENST00000452214	.	.	.	5.92	-11.8	0.00035	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999955085	.	.	.	.	.	.	T	0.23976	-1.0173	3	.	.	.	-22.0366	9.601	0.39603	0.055:0.1218:0.2746:0.5486	rs7082289;rs60556865;rs7082289	.	.	.	Q	38	.	.	R	-	2	0	SORCS1	108357010	0.000000	0.05858	0.001000	0.08648	0.710000	0.40934	-2.984000	0.00661	-5.598000	0.00012	-0.136000	0.14681	CGG	C|0.839;T|0.161	0.161	strong		0.552	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
BAI2	576	hgsc.bcm.edu	37	1	32196453	32196453	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32196453C>T	ENST00000373658.3	-	29	4669	c.4328G>A	c.(4327-4329)cGg>cAg	p.R1443Q	BAI2_ENST00000398542.1_Missense_Mutation_p.R1343Q|BAI2_ENST00000398547.1_Missense_Mutation_p.R1376Q|BAI2_ENST00000398538.1_Missense_Mutation_p.R1431Q|BAI2_ENST00000373655.2_Missense_Mutation_p.R1443Q|BAI2_ENST00000257070.4_Missense_Mutation_p.R1410Q|BAI2_ENST00000440175.2_Missense_Mutation_p.R1052Q|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000527361.1_Missense_Mutation_p.R1410Q|BAI2_ENST00000398556.3_Missense_Mutation_p.R1358Q	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1443					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R1443Q(1)		breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		AGGCATGGTCCGGCTGCGCTC	0.632																																					p.R1443Q		Atlas-SNP	.											BAI2,colon,carcinoma,0,1	BAI2	128	1	1	Substitution - Missense(1)	large_intestine(1)	c.G4328A						PASS	.						40.0	51.0	47.0					1																	32196453		2202	4299	6501	SO:0001583	missense	576	exon29			ATGGTCCGGCTGC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4328G>A	1.37:g.32196453C>T	ENSP00000362762:p.Arg1443Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	39	4	0.102564	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	26.3	4.729029	0.89390	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.47528	1.52;1.76;0.92;0.92;1.89;0.84;0.84;1.55;0.95	5.74	5.74	0.90152	.	0.000000	0.39274	N	0.001419	T	0.61763	0.2373	L	0.48642	1.525	0.51767	D	0.999934	D;D;D;D;D;D;D	0.89917	0.996;0.996;0.999;1.0;0.996;0.994;1.0	P;P;P;D;P;P;D	0.63957	0.883;0.77;0.743;0.92;0.883;0.594;0.92	T	0.52902	-0.8513	10	0.31617	T	0.26	.	19.9066	0.97010	0.0:1.0:0.0:0.0	.	1410;1431;1052;1358;1443;1443;1431	O60241-4;O60241-3;B4DKC3;A2A3C6;O60241-2;O60241;A2A3C2	.;.;.;.;.;BAI2_HUMAN;.	Q	1358;1376;1443;1443;1343;1410;1410;1052;1431	ENSP00000381564:R1358Q;ENSP00000381555:R1376Q;ENSP00000362762:R1443Q;ENSP00000362759:R1443Q;ENSP00000381550:R1343Q;ENSP00000257070:R1410Q;ENSP00000435397:R1410Q;ENSP00000391071:R1052Q;ENSP00000381548:R1431Q	ENSP00000257070:R1410Q	R	-	2	0	BAI2	31969040	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.447000	0.60020	2.884000	0.98904	0.655000	0.94253	CGG	.	.	none		0.632	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
CCDC138	165055	hgsc.bcm.edu	37	2	109408159	109408159	+	Missense_Mutation	SNP	G	G	T	rs35794776	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:109408159G>T	ENST00000295124.4	+	4	355	c.295G>T	c.(295-297)Gat>Tat	p.D99Y	CCDC138_ENST00000412964.2_Missense_Mutation_p.D99Y|CCDC138_ENST00000470608.1_Intron	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	99			D -> Y (in dbSNP:rs35794776).							endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						TTCTTTCCATGATTTGAAGAA	0.289													G|||	361	0.0720847	0.0582	0.0663	5008	,	,		15869	0.0317		0.0527	False		,,,				2504	0.1564				p.D99Y		Atlas-SNP	.											.	CCDC138	49	.	0			c.G295T						PASS	.	G	TYR/ASP	232,4164	130.2+/-166.9	7,218,1973	85.0	102.0	96.0		295	1.9	1.0	2	dbSNP_126	96	503,8053	140.5+/-197.0	17,469,3792	yes	missense	CCDC138	NM_144978.1	160	24,687,5765	TT,TG,GG		5.8789,5.2775,5.6748	benign	99/666	109408159	735,12217	2198	4278	6476	SO:0001583	missense	165055	exon4			TTCCATGATTTGA	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.295G>T	2.37:g.109408159G>T	ENSP00000295124:p.Asp99Tyr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	119	0.05448717948717949	31	0.06300813008130081	23	0.06353591160220995	26	0.045454545454545456	39	0.051451187335092345	G	9.969	1.225072	0.22457	0.052775	0.058789	ENSG00000163006	ENST00000412964;ENST00000295124	D;D	0.90900	-2.75;-2.75	5.77	1.94	0.25998	.	0.572646	0.16856	N	0.196758	T	0.48021	0.1477	L	0.57536	1.79	0.31858	N	0.621322	B;B	0.10296	0.003;0.003	B;B	0.11329	0.006;0.004	T	0.70270	-0.4918	10	0.56958	D	0.05	0.065	3.7033	0.08391	0.1459:0.1312:0.5869:0.136	rs35794776	99;99	Q96M89-2;Q96M89	.;CC138_HUMAN	Y	99	ENSP00000411800:D99Y;ENSP00000295124:D99Y	ENSP00000295124:D99Y	D	+	1	0	CCDC138	108774591	1.000000	0.71417	0.968000	0.41197	0.490000	0.33462	1.379000	0.34340	0.076000	0.16826	-0.152000	0.13540	GAT	G|0.942;T|0.058	0.058	strong		0.289	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	
TPM1	7168	hgsc.bcm.edu	37	15	63351840	63351840	+	Silent	SNP	C	C	A	rs1071646	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:63351840C>A	ENST00000403994.3	+	4	533	c.453C>A	c.(451-453)gcC>gcA	p.A151A	TPM1_ENST00000317516.7_Silent_p.A115A|TPM1_ENST00000357980.4_Silent_p.A193A|TPM1_ENST00000358278.3_Silent_p.A151A|TPM1_ENST00000559281.1_Silent_p.A115A|TPM1_ENST00000559397.1_Silent_p.A151A|TPM1_ENST00000267996.7_Silent_p.A151A|TPM1_ENST00000334895.5_Silent_p.A115A|TPM1_ENST00000288398.6_Silent_p.A151A|TPM1_ENST00000404484.4_Silent_p.A115A|TPM1_ENST00000560959.1_Silent_p.A115A|TPM1_ENST00000560445.1_Intron|TPM1_ENST00000559556.1_Silent_p.A151A	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	151					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						TGAAAGAGGCCAAGCACATTG	0.483													C|||	3534	0.705671	0.6112	0.5591	5008	,	,		20013	0.9504		0.66	False		,,,				2504	0.7321				p.A151A		Atlas-SNP	.											.	TPM1	59	.	0			c.C453A						PASS	.	C	,,,,,,	2714,1692	653.2+/-399.5	860,994,349	77.0	75.0	76.0		453,453,453,453,453,345,453	3.7	1.0	15	dbSNP_86	76	5554,3046	662.0+/-401.9	1805,1944,551	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPM1	NM_000366.5,NM_001018004.1,NM_001018005.1,NM_001018006.1,NM_001018007.1,NM_001018008.1,NM_001018020.1	,,,,,,	2665,2938,900	AA,AC,CC		35.4186,38.4022,36.4293	,,,,,,	151/285,151/285,151/285,151/285,151/285,115/246,151/285	63351840	8268,4738	2203	4300	6503	SO:0001819	synonymous_variant	7168	exon4			AGAGGCCAAGCAC	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	ENST00000403994.3:c.453C>A	15.37:g.63351840C>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	37	5	0.135135	NM_001018007	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Silent	SNP	ENST00000403994.3	37	CCDS45273.1																																																																																			C|0.339;A|0.661	0.661	strong		0.483	TPM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417083.2	NM_001018004	
PDE6A	5145	hgsc.bcm.edu	37	5	149265875	149265875	+	Silent	SNP	G	G	A	rs61733360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149265875G>A	ENST00000255266.5	-	14	1910	c.1791C>T	c.(1789-1791)ttC>ttT	p.F597F		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	597					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)	p.F597F(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	TGTCATGGCAGAAAGCAGCAG	0.527													G|||	133	0.0265575	0.003	0.0749	5008	,	,		20466	0.0119		0.0308	False		,,,				2504	0.0348				p.F597F		Atlas-SNP	.											PDE6A,NS,carcinoma,0,1	PDE6A	98	1	1	Substitution - coding silent(1)	stomach(1)	c.C1791T						PASS	.	G		37,4369	43.1+/-76.7	0,37,2166	155.0	130.0	138.0		1791	5.7	1.0	5	dbSNP_129	138	325,8275	114.6+/-174.5	8,309,3983	no	coding-synonymous	PDE6A	NM_000440.2		8,346,6149	AA,AG,GG		3.7791,0.8398,2.7833		597/861	149265875	362,12644	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon14			ATGGCAGAAAGCA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.1791C>T	5.37:g.149265875G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	163	79	0.484663	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|0.969;A|0.031	0.031	strong		0.527	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
ADNP	23394	hgsc.bcm.edu	37	20	49509184	49509184	+	Silent	SNP	G	G	A	rs17790938	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:49509184G>A	ENST00000396029.3	-	5	2634	c.2067C>T	c.(2065-2067)ggC>ggT	p.G689G	ADNP_ENST00000396032.3_Silent_p.G689G|ADNP_ENST00000349014.3_Silent_p.G689G|ADNP_ENST00000371602.4_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	200	0	0		WXS	Illumina HiSeq	Phase_I	160	82	0.5125	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	
CDH5	1003	hgsc.bcm.edu	37	16	66432424	66432424	+	Silent	SNP	C	C	T	rs3826229|rs386791725	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:66432424C>T	ENST00000341529.3	+	10	1699	c.1551C>T	c.(1549-1551)atC>atT	p.I517I	CDH5_ENST00000539168.1_5'UTR	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	517	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> T (in dbSNP:rs1049970). {ECO:0000269|PubMed:10861224, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7627717}.		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)	TCAAATTCATCTTGAATACTG	0.473													C|||	2079	0.415136	0.3979	0.4409	5008	,	,		21236	0.5506		0.3678	False		,,,				2504	0.3292				p.I517I		Atlas-SNP	.											CDH5,NS,carcinoma,+1,2	CDH5	111	2	0			c.C1551T						PASS	.	C		96,4306		24,48,2129	150.0	127.0	134.0		1551	3.0	0.9	16	dbSNP_107	134	112,8488		25,62,4213	no	coding-synonymous	CDH5	NM_001795.3		49,110,6342	TT,TC,CC		1.3023,2.1808,1.5998		517/785	66432424	208,12794	2201	4300	6501	SO:0001819	synonymous_variant	1003	exon10			ATTCATCTTGAAT	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.1551C>T	16.37:g.66432424C>T		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001795	Q4VAI5|Q4VAI6	Silent	SNP	ENST00000341529.3	37	CCDS10804.1																																																																																			A|0.000;C|0.632;G|0.000;T|0.368	0.368	strong		0.473	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795	
GRHL2	79977	hgsc.bcm.edu	37	8	102570987	102570987	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:102570987C>T	ENST00000251808.3	+	4	963	c.625C>T	c.(625-627)Cgc>Tgc	p.R209C	GRHL2_ENST00000395927.1_Missense_Mutation_p.R193C	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	209					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)			AGACGACCAGCGCAGCACTCC	0.602																																					p.R209C		Atlas-SNP	.											GRHL2,colon,carcinoma,-1,1	GRHL2	68	1	0			c.C625T						scavenged	.						39.0	34.0	36.0					8																	102570987		2203	4300	6503	SO:0001583	missense	79977	exon4			GACCAGCGCAGCA	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.625C>T	8.37:g.102570987C>T	ENSP00000251808:p.Arg209Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	175	2	0.0114286	NM_024915	A1L303|Q6NT03|Q9H8B8	Missense_Mutation	SNP	ENST00000251808.3	37	CCDS34931.1	.	.	.	.	.	.	.	.	.	.	C	16.38	3.105942	0.56291	.	.	ENSG00000083307	ENST00000251808;ENST00000395927;ENST00000395928	T;T	0.13420	2.59;2.59	5.33	5.33	0.75918	.	0.106801	0.64402	D	0.000003	T	0.33440	0.0863	L	0.47716	1.5	0.80722	D	1	D;P	0.89917	1.0;0.523	D;B	0.87578	0.998;0.344	T	0.01715	-1.1289	10	0.56958	D	0.05	-19.875	19.0278	0.92939	0.0:1.0:0.0:0.0	.	209;209	B4DL28;Q6ISB3	.;GRHL2_HUMAN	C	209;193;209	ENSP00000251808:R209C;ENSP00000379260:R193C	ENSP00000251808:R209C	R	+	1	0	GRHL2	102640163	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	4.979000	0.63806	2.489000	0.83994	0.643000	0.83706	CGC	.	.	none		0.602	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	
OR8J3	81168	hgsc.bcm.edu	37	11	55904382	55904382	+	Missense_Mutation	SNP	A	A	C	rs17150102	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	266	0	0		WXS	Illumina HiSeq	Phase_I	257	124	0.48249	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	
MUL1	79594	hgsc.bcm.edu	37	1	20827216	20827216	+	Silent	SNP	C	C	T	rs595980	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	98	0	0		WXS	Illumina HiSeq	Phase_I	85	24	0.282353	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	
NSUN7	79730	hgsc.bcm.edu	37	4	40810663	40810663	+	Missense_Mutation	SNP	A	A	G	rs4861066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:40810663A>G	ENST00000381782.2	+	12	2359	c.1864A>G	c.(1864-1866)Act>Gct	p.T622A	NSUN7_ENST00000316607.5_3'UTR	NM_024677.4	NP_078953	Q8NE18	NSUN7_HUMAN	NOP2/Sun domain family, member 7	622			T -> A (in dbSNP:rs4861066).				methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|cervix(1)|large_intestine(1)|lung(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	12						TGTGAAGAACACTTGTCCCTC	0.527													A|||	842	0.168131	0.1762	0.2305	5008	,	,		19862	0.0208		0.3022	False		,,,				2504	0.1268				p.T622A		Atlas-SNP	.											.	NSUN7	70	.	0			c.A1864G						PASS	.	A	ALA/THR	314,1070		43,228,421	90.0	81.0	84.0		1864	-3.8	0.0	4	dbSNP_111	84	1071,2111		180,711,700	yes	missense	NSUN7	NM_024677.4	58	223,939,1121	GG,GA,AA		33.6581,22.6879,30.3329	benign	622/719	40810663	1385,3181	692	1591	2283	SO:0001583	missense	79730	exon12			AAGAACACTTGTC	BC036568	CCDS3461.2	4p14	2013-10-11	2009-11-23		ENSG00000179299	ENSG00000179299		"""NOP2/Sun domain containing"""	25857	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family, member 7"""			17442852	Standard	NM_024677		Approved	FLJ14001	uc003gvj.4	Q8NE18	OTTHUMG00000128597	ENST00000381782.2:c.1864A>G	4.37:g.40810663A>G	ENSP00000371201:p.Thr622Ala	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_024677	C9JI19|Q8N9K8|Q9H815	Missense_Mutation	SNP	ENST00000381782.2	37	CCDS3461.2	404	0.184981684981685	86	0.17479674796747968	94	0.2596685082872928	14	0.024475524475524476	210	0.2770448548812665	A	10.54	1.379398	0.24944	0.226879	0.336581	ENSG00000179299	ENST00000381782	T	0.04502	3.61	4.6	-3.78	0.04333	.	0.840408	0.10247	N	0.697595	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.45323	-0.9269	9	0.29301	T	0.29	-0.7001	6.4663	0.21983	0.4011:0.2479:0.351:0.0	rs4861066;rs17441944;rs52820359;rs60259255;rs4861066	622	Q8NE18	NSUN7_HUMAN	A	622	ENSP00000371201:T622A	ENSP00000371201:T622A	T	+	1	0	NSUN7	40505420	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	-0.536000	0.06135	-0.924000	0.03780	-0.353000	0.07706	ACT	A|0.808;G|0.192	0.192	strong		0.527	NSUN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250454.2	NM_024677	
TMPRSS2	7113	hgsc.bcm.edu	37	21	42852497	42852497	+	Missense_Mutation	SNP	C	C	T	rs12329760	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:42852497C>T	ENST00000332149.5	-	6	612	c.478G>A	c.(478-480)Gtg>Atg	p.V160M	TMPRSS2_ENST00000398585.3_Missense_Mutation_p.V197M|TMPRSS2_ENST00000458356.1_Missense_Mutation_p.V160M	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	160	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.		V -> M (in dbSNP:rs12329760). {ECO:0000269|PubMed:11414763, ECO:0000269|PubMed:17918732, ECO:0000269|PubMed:9325052}.		positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.V160M(1)	TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				GATGAGTACACCTGAAGGATG	0.507			T	"""ERG, ETV1, ETV4, ETV5"""	prostate								C|||	1309	0.261382	0.2867	0.1542	5008	,	,		20708	0.3621		0.2356	False		,,,				2504	0.226				p.V197M		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"""transmembrane protease, serine 2"""		E	TMPRSS2_ENST00000332149,NS,carcinoma,0,1	TMPRSS2	148	1	1	Substitution - Missense(1)	stomach(1)	c.G589A						PASS	.	C	MET/VAL,MET/VAL	1279,3127	433.5+/-343.6	183,913,1107	62.0	53.0	56.0		589,478	4.2	1.0	21	dbSNP_120	56	1860,6740	330.6+/-319.3	222,1416,2662	yes	missense,missense	TMPRSS2	NM_001135099.1,NM_005656.3	21,21	405,2329,3769	TT,TC,CC		21.6279,29.0286,24.135	probably-damaging,probably-damaging	197/530,160/493	42852497	3139,9867	2203	4300	6503	SO:0001583	missense	7113	exon6			AGTACACCTGAAG	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"""Serine peptidases / Transmembrane"""	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.478G>A	21.37:g.42852497C>T	ENSP00000330330:p.Val160Met	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	202	133	0.658416	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	37	CCDS33564.1	634	0.2902930402930403	145	0.29471544715447157	69	0.19060773480662985	230	0.4020979020979021	190	0.25065963060686014	C	18.40	3.615593	0.66672	0.290286	0.216279	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499;ENST00000424093	T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75	5.12	4.23	0.50019	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.307523	0.26812	N	0.022371	T	0.00012	0.0000	M	0.85462	2.755	0.28298	P	0.9232503	D;D	0.76494	0.999;0.997	D;D	0.65773	0.938;0.937	T	0.10847	-1.0612	9	0.66056	D	0.02	.	9.9163	0.41436	0.0:0.9025:0.0:0.0975	rs12329760;rs60283747;rs12329760	197;160	F8WES1;O15393	.;TMPS2_HUMAN	M	160;197;160;160;120	ENSP00000330330:V160M;ENSP00000381588:V197M;ENSP00000391216:V160M;ENSP00000389006:V160M;ENSP00000397846:V120M	ENSP00000330330:V160M	V	-	1	0	TMPRSS2	41774367	1.000000	0.71417	0.999000	0.59377	0.756000	0.42949	1.578000	0.36525	2.392000	0.81423	0.561000	0.74099	GTG	C|0.744;T|0.256	0.256	strong		0.507	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1		
C10orf71	118461	hgsc.bcm.edu	37	10	50533841	50533841	+	Missense_Mutation	SNP	G	G	C	rs11101094	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	75	0	0		WXS	Illumina HiSeq	Phase_I	64	7	0.109375	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	
EGF	1950	hgsc.bcm.edu	37	4	110902111	110902111	+	Missense_Mutation	SNP	A	A	T	rs11569017	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:110902111A>T	ENST00000265171.5	+	15	2796	c.2351A>T	c.(2350-2352)gAt>gTt	p.D784V	EGF_ENST00000509793.1_Missense_Mutation_p.D742V|EGF_ENST00000503392.1_Missense_Mutation_p.D784V	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	784			D -> V (in dbSNP:rs11569017). {ECO:0000269|Ref.2}.		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)	CTGGCTCTGGATGGTCATCAG	0.418													A|||	385	0.076877	0.0015	0.0865	5008	,	,		19874	0.1944		0.0517	False		,,,				2504	0.0767				p.D784V		Atlas-SNP	.											EGF,NS,adenoma,0,1	EGF	113	1	0			c.A2351T	GRCh37	CM063963	EGF	M	rs11569017	PASS	.	A	VAL/ASP,VAL/ASP,VAL/ASP	59,4347	56.2+/-92.4	0,59,2144	193.0	188.0	190.0		2351,2225,2351	3.7	0.0	4	dbSNP_120	190	513,8087	146.0+/-201.7	13,487,3800	yes	missense,missense,missense	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	152,152,152	13,546,5944	TT,TA,AA		5.9651,1.3391,4.398	benign,benign,benign	784/1167,742/1166,784/1208	110902111	572,12434	2203	4300	6503	SO:0001583	missense	1950	exon15			CTCTGGATGGTCA	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.2351A>T	4.37:g.110902111A>T	ENSP00000265171:p.Asp784Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	134	64	0.477612	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	37	CCDS3689.1	200	0.09157509157509157	2	0.0040650406504065045	30	0.08287292817679558	123	0.21503496503496503	45	0.059366754617414245	A	12.59	1.982226	0.34942	0.013391	0.059651	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.87809	-2.3;-2.3;-2.3	4.89	3.67	0.42095	.	0.751267	0.12903	N	0.429603	T	0.00210	0.0006	M	0.62723	1.935	0.54753	P	1.6000000000016E-5	B;B;B	0.20550	0.046;0.004;0.016	B;B;B	0.15052	0.005;0.012;0.005	T	0.21586	-1.0241	9	0.44086	T	0.13	.	9.8902	0.41285	0.8282:0.1718:0.0:0.0	rs11569017;rs52808448;rs11569017	784;742;784	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	V	742;784;784	ENSP00000424316:D742V;ENSP00000265171:D784V;ENSP00000421384:D784V	ENSP00000265171:D784V	D	+	2	0	EGF	111121560	0.301000	0.24444	0.001000	0.08648	0.270000	0.26580	1.417000	0.34770	0.790000	0.33803	0.459000	0.35465	GAT	A|0.932;T|0.068	0.068	strong		0.418	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		
OPTC	26254	hgsc.bcm.edu	37	1	203472112	203472112	+	Missense_Mutation	SNP	T	T	C	rs79523790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:203472112T>C	ENST00000367222.2	+	6	919	c.803T>C	c.(802-804)cTg>cCg	p.L268P		NM_014359.3	NP_055174.1	Q9UBM4	OPT_HUMAN	opticin	268					negative regulation of angiogenesis (GO:0016525)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)	p.L268P(1)		breast(1)|cervix(1)|kidney(5)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.109)			CCTTTGCCCCTGAGCCTGCGC	0.552													T|||	620	0.123802	0.1672	0.0692	5008	,	,		19180	0.1935		0.0646	False		,,,				2504	0.093				p.L268P		Atlas-SNP	.											OPTC,NS,carcinoma,0,1	OPTC	50	1	1	Substitution - Missense(1)	stomach(1)	c.T803C						PASS	.	T	PRO/LEU	578,3828	235.8+/-248.2	47,484,1672	55.0	59.0	57.0		803	0.4	0.9	1	dbSNP_131	57	367,8233	115.3+/-175.2	9,349,3942	yes	missense	OPTC	NM_014359.3	98	56,833,5614	CC,CT,TT		4.2674,13.1185,7.2659	benign	268/333	203472112	945,12061	2203	4300	6503	SO:0001583	missense	26254	exon6			TGCCCCTGAGCCT	AF161702	CCDS1439.1	1q31	2008-02-05			ENSG00000188770	ENSG00000188770			8158	protein-coding gene	gene with protein product	"""oculoglycan"""	605127				10636917	Standard	NM_014359		Approved		uc001gzu.1	Q9UBM4	OTTHUMG00000036100	ENST00000367222.2:c.803T>C	1.37:g.203472112T>C	ENSP00000356191:p.Leu268Pro	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	193	115	0.595855	NM_014359	Q5T2G4	Missense_Mutation	SNP	ENST00000367222.2	37	CCDS1439.1	250	0.11446886446886446	72	0.14634146341463414	20	0.055248618784530384	107	0.18706293706293706	51	0.06728232189973615	T	8.543	0.873631	0.17322	0.131185	0.042674	ENSG00000188770	ENST00000367222	T	0.56444	0.46	4.13	0.419	0.16438	.	1.051150	0.07520	N	0.910411	T	0.00039	0.0001	N	0.01809	-0.71	0.22819	P	0.99869356	B	0.09022	0.002	B	0.08055	0.003	T	0.13045	-1.0524	9	0.31617	T	0.26	-4.7971	3.2075	0.06671	0.184:0.3359:0.0:0.48	.	268	Q9UBM4	OPT_HUMAN	P	268	ENSP00000356191:L268P	ENSP00000356191:L268P	L	+	2	0	OPTC	201738735	0.093000	0.21703	0.938000	0.37757	0.602000	0.36980	1.284000	0.33249	0.208000	0.20626	0.421000	0.28195	CTG	T|0.915;C|0.085	0.085	strong		0.552	OPTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087964.1	NM_014359	
OR6C70	390327	hgsc.bcm.edu	37	12	55863381	55863381	+	Missense_Mutation	SNP	A	A	G	rs10747756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:55863381A>G	ENST00000327335.4	-	1	541	c.542T>C	c.(541-543)cTt>cCt	p.L181P	RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA	NM_001005499.1	NP_001005499.1	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C, member 70	181			L -> P (in dbSNP:rs10747756).			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)|cervix(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	18						TTGTAGGATAAGAGAAATGTC	0.338													G|||	4156	0.829872	0.972	0.7723	5008	,	,		22499	0.8929		0.7525	False		,,,				2504	0.6933				p.L181P		Atlas-SNP	.											.	OR6C70	35	.	0			c.T542C						PASS	.	G	PRO/LEU	4102,304	164.4+/-196.0	1913,276,14	102.0	107.0	105.0		542	3.2	0.3	12	dbSNP_120	105	6561,2039	352.4+/-328.6	2506,1549,245	yes	missense	OR6C70	NM_001005499.1	98	4419,1825,259	GG,GA,AA		23.7093,6.8997,18.0148	benign	181/313	55863381	10663,2343	2203	4300	6503	SO:0001583	missense	390327	exon1			AGGATAAGAGAAA		CCDS31825.1	12q13.2	2013-09-23			ENSG00000184954	ENSG00000184954		"""GPCR / Class A : Olfactory receptors"""	31299	protein-coding gene	gene with protein product							Standard	NM_001005499		Approved		uc010spn.2	A6NIJ9	OTTHUMG00000171127	ENST00000327335.4:c.542T>C	12.37:g.55863381A>G	ENSP00000329153:p.Leu181Pro	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_001005499		Missense_Mutation	SNP	ENST00000327335.4	37	CCDS31825.1	1834	0.8397435897435898	476	0.967479674796748	278	0.7679558011049724	520	0.9090909090909091	560	0.7387862796833773	G	0.001	-3.373569	0.00015	0.931003	0.762907	ENSG00000184954	ENST00000327335	T	0.00023	8.99	4.06	3.16	0.36331	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	N	0.000099	T	0.00012	0.0000	N	0.00018	-2.81	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32428	-0.9907	9	0.02654	T	1	.	7.1306	0.25499	0.0866:0.0:0.5601:0.3534	rs10747756;rs59156371;rs10747756	181	A6NIJ9	O6C70_HUMAN	P	181	ENSP00000329153:L181P	ENSP00000329153:L181P	L	-	2	0	OR6C70	54149648	0.001000	0.12720	0.270000	0.24601	0.037000	0.13140	0.828000	0.27435	0.481000	0.27557	-0.119000	0.15052	CTT	A|0.170;G|0.830	0.830	strong		0.338	OR6C70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411820.1		
DYNC2H1	79659	hgsc.bcm.edu	37	11	103082558	103082558	+	Silent	SNP	A	A	G	rs17394217	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:103082558A>G	ENST00000375735.2	+	54	8724	c.8580A>G	c.(8578-8580)gaA>gaG	p.E2860E	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.E2860E	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2860	AAA 4. {ECO:0000250}.				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)		TAATCCATGAATCTTGTAAAG	0.264													A|||	389	0.0776757	0.0023	0.0922	5008	,	,		14624	0.0923		0.1243	False		,,,				2504	0.1063				p.E2860E		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A8580G						PASS	.	A	,	85,3421		2,81,1670	29.0	26.0	27.0		8580,8580	-3.2	1.0	11	dbSNP_123	27	847,7065		40,767,3149	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	42,848,4819	GG,GA,AA		10.7053,2.4244,8.1626	,	2860/4315,2860/4308	103082558	932,10486	1753	3956	5709	SO:0001819	synonymous_variant	79659	exon54			CCATGAATCTTGT	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.8580A>G	11.37:g.103082558A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	157	115	0.732484	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			A|0.913;G|0.087	0.087	strong		0.264	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
HNRNPL	3191	hgsc.bcm.edu	37	19	39331198	39331198	+	Splice_Site	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:39331198A>T	ENST00000221419.5	-	7	1248	c.882T>A	c.(880-882)ggT>ggA	p.G294G	AC104534.3_ENST00000594769.1_5'Flank|HNRNPL_ENST00000600873.1_Splice_Site_p.G161G	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	294					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30	all_cancers(60;6.83e-06)|Ovarian(47;0.0454)		Lung(45;0.00342)|LUSC - Lung squamous cell carcinoma(53;0.00575)			TGCCAGGGTCACCTGTGGAGA	0.602																																					p.G294G		Atlas-SNP	.											.	HNRNPL	67	.	0			c.T882A						PASS	.						27.0	27.0	27.0					19																	39331198		2199	4299	6498	SO:0001630	splice_region_variant	3191	exon7			AGGGTCACCTGTG	X16135	CCDS33015.1, CCDS33016.1	19q13.2	2013-06-12		2007-08-16	ENSG00000104824	ENSG00000104824		"""RNA binding motif (RRM) containing"""	5045	protein-coding gene	gene with protein product		603083		HNRPL		2687284	Standard	NM_001533		Approved		uc021uuh.1	P14866	OTTHUMG00000182612	ENST00000221419.5:c.881-1T>A	19.37:g.39331198A>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	30	0.333333	NM_001533	A6ND69|A6NIT8|Q9H3P3	Silent	SNP	ENST00000221419.5	37	CCDS33015.1																																																																																			.	.	none		0.602	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		Silent
TMPRSS2	7113	hgsc.bcm.edu	37	21	42845374	42845374	+	Silent	SNP	G	G	A	rs2298659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:42845374G>A	ENST00000332149.5	-	9	911	c.777C>T	c.(775-777)ggC>ggT	p.G259G	TMPRSS2_ENST00000398585.3_Silent_p.G296G|TMPRSS2_ENST00000458356.1_Silent_p.G259G	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	259	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)		TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				GCGCGCTCTCGCCGCCCACAA	0.662			T	"""ERG, ETV1, ETV4, ETV5"""	prostate								G|||	1049	0.209465	0.1747	0.2176	5008	,	,		14656	0.249		0.2296	False		,,,				2504	0.1892				p.G296G		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"""transmembrane protease, serine 2"""		E	TMPRSS2_ENST00000454499,NS,carcinoma,0,3	TMPRSS2	148	3	0			c.C888T						PASS	.	G	,	810,3552		75,660,1446	22.0	21.0	21.0		888,777	-10.4	0.0	21	dbSNP_100	21	1861,6697		212,1437,2630	no	coding-synonymous,coding-synonymous	TMPRSS2	NM_001135099.1,NM_005656.3	,	287,2097,4076	AA,AG,GG		21.7457,18.5695,20.6734	,	296/530,259/493	42845374	2671,10249	2181	4279	6460	SO:0001819	synonymous_variant	7113	exon9			GCTCTCGCCGCCC	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"""Serine peptidases / Transmembrane"""	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.777C>T	21.37:g.42845374G>A		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	201	131	0.651741	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Silent	SNP	ENST00000332149.5	37	CCDS33564.1																																																																																			G|0.780;A|0.220	0.220	strong		0.662	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1		
IPPK	64768	hgsc.bcm.edu	37	9	95405048	95405048	+	Silent	SNP	A	A	C	rs35248147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:95405048A>C	ENST00000287996.3	-	7	825	c.549T>G	c.(547-549)ctT>ctG	p.L183L		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	183					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						AGTAGAGATCAAGGGGACAGT	0.557													A|||	148	0.0295527	0.0159	0.0331	5008	,	,		20982	0.001		0.0437	False		,,,				2504	0.0603				p.L183L		Atlas-SNP	.											.	IPPK	34	.	0			c.T549G						PASS	.	A		112,4294	86.8+/-125.4	2,108,2093	194.0	145.0	162.0		549	-9.0	0.8	9	dbSNP_126	162	419,8181	129.3+/-187.4	10,399,3891	no	coding-synonymous	IPPK	NM_022755.5		12,507,5984	CC,CA,AA		4.8721,2.542,4.0827		183/492	95405048	531,12475	2203	4300	6503	SO:0001819	synonymous_variant	64768	exon7			GAGATCAAGGGGA	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.549T>G	9.37:g.95405048A>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_022755	Q5T9F7|Q9H7V8	Silent	SNP	ENST00000287996.3	37	CCDS6699.1																																																																																			A|0.966;C|0.034	0.034	strong		0.557	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755	
ATXN2	6311	hgsc.bcm.edu	37	12	111907956	111907956	+	Nonsense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:111907956G>C	ENST00000377617.3	-	20	3433	c.3272C>G	c.(3271-3273)tCa>tGa	p.S1091*	ATXN2_ENST00000535949.1_Nonsense_Mutation_p.S802*|ATXN2_ENST00000542287.2_Nonsense_Mutation_p.S826*|ATXN2_ENST00000608853.1_Nonsense_Mutation_p.S931*|ATXN2_ENST00000550104.1_3'UTR|ATXN2_ENST00000389153.4_Nonsense_Mutation_p.S828*	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1091					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						CTGAGTTGCTGAAGAAGATAC	0.453																																					p.S1091X		Atlas-SNP	.											.	ATXN2	99	.	0			c.C3272G						PASS	.						218.0	172.0	188.0					12																	111907956		2203	4300	6503	SO:0001587	stop_gained	6311	exon20			GTTGCTGAAGAAG	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.3272C>G	12.37:g.111907956G>C	ENSP00000366843:p.Ser1091*	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	174	54	0.310345	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Nonsense_Mutation	SNP	ENST00000377617.3	37	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	G	41	8.647790	0.98899	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000482777;ENST00000542287;ENST00000535949;ENST00000550844	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-12.4094	19.6783	0.95946	0.0:0.0:1.0:0.0	.	.	.	.	X	146;828;1091;110;826;802;16	.	ENSP00000366843:S1091X	S	-	2	0	ATXN2	110392339	1.000000	0.71417	0.973000	0.42090	0.782000	0.44232	9.301000	0.96167	2.724000	0.93272	0.585000	0.79938	TCA	.	.	none		0.453	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973	
SWT1	54823	hgsc.bcm.edu	37	1	185135745	185135745	+	Silent	SNP	A	A	G	rs950327	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:185135745A>G	ENST00000367500.4	+	3	291	c.126A>G	c.(124-126)tcA>tcG	p.S42S	SWT1_ENST00000367501.3_Silent_p.S42S	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	42	Poly-Ser.									breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						CTACTAGTTCATCTTCTATAA	0.294													A|||	1728	0.345048	0.4221	0.3905	5008	,	,		16373	0.1944		0.3499	False		,,,				2504	0.3589				p.S42S		Atlas-SNP	.											.	SWT1	88	.	0			c.A126G						PASS	.	A	,	1765,2641	502.4+/-365.2	352,1061,790	59.0	65.0	63.0		126,126	1.9	0.3	1	dbSNP_86	63	3112,5470	469.3+/-367.5	578,1956,1757	no	coding-synonymous,coding-synonymous	SWT1	NM_001105518.1,NM_017673.6	,	930,3017,2547	GG,GA,AA		36.2619,40.059,37.55	,	42/901,42/901	185135745	4877,8111	2203	4291	6494	SO:0001819	synonymous_variant	54823	exon3			TAGTTCATCTTCT	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.126A>G	1.37:g.185135745A>G		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	188	185	0.984043	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Silent	SNP	ENST00000367500.4	37	CCDS1367.1																																																																																			A|0.680;G|0.320	0.320	strong		0.294	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
ZP3	7784	hgsc.bcm.edu	37	7	76069902	76069902	+	Missense_Mutation	SNP	G	G	C	rs1804905		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76069902G>C	ENST00000394857.3	+	7	1092	c.1034G>C	c.(1033-1035)aGg>aCg	p.R345T	ZP3_ENST00000336517.4_Missense_Mutation_p.R294T|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Missense_Mutation_p.R169T	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	345				R -> T (in Ref. 2; CAA40095). {ECO:0000305}.	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						CAGTGGTCCAGGTCTGCTTCC	0.537																																					p.R345T		Atlas-SNP	.											.	ZP3	32	.	0			c.G1034C						PASS	.						135.0	127.0	130.0					7																	76069902		2203	4300	6503	SO:0001583	missense	7784	exon7			GGTCCAGGTCTGC	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.1034G>C	7.37:g.76069902G>C	ENSP00000378326:p.Arg345Thr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	350	42	0.12	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	8.608|8.608	0.888351|0.888351	0.17540|0.17540	.|.	.|.	ENSG00000188372|ENSG00000188372	ENST00000394860|ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	.|T;T;T	.|0.25250	.|2.41;2.63;1.81	4.64|4.64	-8.56|-8.56	0.00904|0.00904	.|.	.|0.754812	.|0.12103	.|U	.|0.499355	T|T	0.12518|0.12518	0.0304|0.0304	L|L	0.28115|0.28115	0.83|0.83	0.09310|0.09310	N|N	1|1	.|B;B	.|0.19817	.|0.002;0.039	.|B;B	.|0.17722	.|0.004;0.019	T|T	0.33292|0.33292	-0.9874|-0.9874	5|10	.|0.13108	.|T	.|0.6	-0.2921|-0.2921	12.2107|12.2107	0.54377|0.54377	0.1994:0.1279:0.6727:0.0|0.1994:0.1279:0.6727:0.0	rs1804905|rs1804905	.|294;345	.|P21754-3;P21754	.|.;ZP3_HUMAN	R|T	179|294;345;345;169	.|ENSP00000337310:R294T;ENSP00000378326:R345T;ENSP00000411955:R169T	.|ENSP00000337310:R294T	G|R	+|+	1|2	0|0	ZP3|ZP3	75907838|75907838	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.592000|-0.592000	0.05747|0.05747	-1.616000|-1.616000	0.01572|0.01572	-0.291000|-0.291000	0.09656|0.09656	GGT|AGG	G|0.500;C|0.500	0.500	weak		0.537	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
MACF1	23499	hgsc.bcm.edu	37	1	39835817	39835817	+	Missense_Mutation	SNP	A	A	G	rs2296172	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39835817A>G	ENST00000372915.3	+	50	13156	c.13069A>G	c.(13069-13071)Atg>Gtg	p.M4357V	MACF1_ENST00000289893.4_Missense_Mutation_p.M2792V|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000317713.7_Missense_Mutation_p.M2290V|MACF1_ENST00000361689.2_Missense_Mutation_p.M2290V|MACF1_ENST00000567887.1_Missense_Mutation_p.M4389V|MACF1_ENST00000564288.1_Missense_Mutation_p.M4352V|MACF1_ENST00000539005.1_Missense_Mutation_p.M2290V|MACF1_ENST00000545844.1_Missense_Mutation_p.M2290V			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4357			M -> V (in dbSNP:rs2296172). {ECO:0000269|PubMed:10559237}.		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)			GGAAACTTCTATGAGTGCTAA	0.433													A|||	592	0.118211	0.0121	0.2046	5008	,	,		20675	0.1587		0.1948	False		,,,				2504	0.0798				p.M2290V		Atlas-SNP	.											.	MACF1	909	.	0			c.A6868G						PASS	.	A	VAL/MET,VAL/MET	194,4212	122.1+/-159.5	1,192,2010	69.0	68.0	68.0		6868,8374	0.3	1.0	1	dbSNP_100	68	1919,6681	339.9+/-323.4	231,1457,2612	yes	missense,missense	MACF1	NM_012090.4,NM_033044.3	21,21	232,1649,4622	GG,GA,AA		22.314,4.4031,16.2463	benign,benign	2290/5431,2792/5939	39835817	2113,10893	2203	4300	6503	SO:0001583	missense	23499	exon47			ACTTCTATGAGTG	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.13069A>G	1.37:g.39835817A>G	ENSP00000362006:p.Met4357Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		320|320	0.14652014652014653|0.14652014652014653	8|8	0.016260162601626018|0.016260162601626018	76|76	0.20994475138121546|0.20994475138121546	89|89	0.1555944055944056|0.1555944055944056	147|147	0.19393139841688653|0.19393139841688653	A|A	1.600|1.600	-0.526671|-0.526671	0.04141|0.04141	0.044031|0.044031	0.22314|0.22314	ENSG00000127603|ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893|ENST00000372925	T;T;T;T;T;T|.	0.59364|.	0.3;0.33;0.3;0.27;0.4;1.43|.	5.37|5.37	0.348|0.348	0.16026|0.16026	.|.	0.777656|.	0.11516|.	N|.	0.556259|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	P|P	0.9999999709851|0.9999999709851	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.06405|.	0.002;0.001;0.001;0.002|.	T|T	0.37934|0.37934	-0.9684|-0.9684	9|4	0.06099|.	T|.	0.92|.	.|.	0.2216|0.2216	0.00168|0.00168	0.2976:0.2744:0.1754:0.2526|0.2976:0.2744:0.1754:0.2526	rs2296172;rs57700239;rs2296172|rs2296172;rs57700239;rs2296172	4357;2290;2290;2255|.	Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3|.	MACF1_HUMAN;.;.;.|.	V|C	2290;4357;2290;2290;2290;2792|1423	ENSP00000439537:M2290V;ENSP00000362006:M4357V;ENSP00000354573:M2290V;ENSP00000313438:M2290V;ENSP00000444364:M2290V;ENSP00000289893:M2792V|.	ENSP00000289893:M2792V|.	M|Y	+|+	1|2	0|0	MACF1|MACF1	39608404|39608404	0.850000|0.850000	0.29656|0.29656	0.996000|0.996000	0.52242|0.52242	0.949000|0.949000	0.60115|0.60115	0.193000|0.193000	0.17116|0.17116	0.021000|0.021000	0.15133|0.15133	0.533000|0.533000	0.62120|0.62120	ATG|TAT	A|0.855;G|0.145	0.145	strong		0.433	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
PKD1	5310	hgsc.bcm.edu	37	16	2140010	2140010	+	Silent	SNP	A	A	G	rs7203729	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2140010A>G	ENST00000262304.4	-	46	12838	c.12630T>C	c.(12628-12630)ccT>ccC	p.P4210P	PKD1_ENST00000423118.1_Silent_p.P4209P|MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4210					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						GGGAGGGCTCAGGCTCACACC	0.677													G|||	1392	0.277955	0.7247	0.2104	5008	,	,		12411	0.0		0.2028	False		,,,				2504	0.0859				p.P4210P		Atlas-SNP	.											.	PKD1	184	.	0			c.T12630C						PASS	.	G	,	2652,1718		818,1016,351	23.0	24.0	24.0		12627,12630	-9.8	0.0	16	dbSNP_116	24	1629,6961		158,1313,2824	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	976,2329,3175	GG,GA,AA		18.9639,39.3135,33.0324	,	4209/4303,4210/4304	2140010	4281,8679	2185	4295	6480	SO:0001819	synonymous_variant	5310	exon46			GGGCTCAGGCTCA	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.12630T>C	16.37:g.2140010A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_001009944	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			A|0.688;G|0.312	0.312	strong		0.677	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
SPATA3	130560	hgsc.bcm.edu	37	2	231861057	231861057	+	Missense_Mutation	SNP	C	C	T	rs72362780		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231861057C>T	ENST00000452881.1	+	1	217	c.109C>T	c.(109-111)Cca>Tca	p.P37S	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_Missense_Mutation_p.P37S|SPATA3_ENST00000424440.1_Missense_Mutation_p.P37S|SPATA3_ENST00000455816.1_Missense_Mutation_p.P37S			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	37										endometrium(2)|lung(1)	3						TGAATCCACACCACAGCAGCC	0.577																																					p.P37S		Atlas-SNP	.											SPATA3,NS,carcinoma,-2,4	SPATA3	52	4	0			c.C109T						PASS	.						132.0	138.0	137.0					2																	231861057		692	1590	2282	SO:0001583	missense	130560	exon1			TCCACACCACAGC	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.109C>T	2.37:g.231861057C>T	ENSP00000388895:p.Pro37Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	85	14	0.164706	NM_139073	Q86WX5|Q8N9Y6	Missense_Mutation	SNP	ENST00000452881.1	37	CCDS2481.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.829371	0.32329	.	.	ENSG00000173699	ENST00000424440;ENST00000452881;ENST00000433428;ENST00000455816;ENST00000355662;ENST00000440792	.	.	.	3.0	-0.25	0.13007	.	0.940554	0.08697	N	0.907107	T	0.19248	0.0462	N	0.12746	0.255	0.09310	N	1	.	.	.	.	.	.	T	0.27673	-1.0067	7	0.72032	D	0.01	0.139	2.334	0.04242	0.2359:0.4502:0.0:0.3139	.	.	.	.	S	37;37;37;37;37;3	.	ENSP00000347884:P37S	P	+	1	0	SPATA3	231569301	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.302000	0.08221	-0.061000	0.13110	-0.367000	0.07326	CCA	.	.	none		0.577	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
EPS8L3	79574	hgsc.bcm.edu	37	1	110301260	110301260	+	Missense_Mutation	SNP	C	C	T	rs6693815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:110301260C>T	ENST00000361965.4	-	7	593	c.487G>A	c.(487-489)Ggc>Agc	p.G163S	EPS8L3_ENST00000494151.1_5'UTR|EPS8L3_ENST00000369805.3_Missense_Mutation_p.G164S|EPS8L3_ENST00000361852.4_Missense_Mutation_p.G163S|RP4-735C1.4_ENST00000431955.1_RNA	NM_133181.3	NP_573444.2	Q8TE67	ES8L3_HUMAN	EPS8-like 3	163			G -> S (in dbSNP:rs6693815). {ECO:0000269|PubMed:12620401}.			cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	32		all_epithelial(167;1.95e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)		Lung(183;0.0245)|Colorectal(144;0.0365)|all cancers(265;0.103)|Epithelial(280;0.109)|LUSC - Lung squamous cell carcinoma(189;0.137)|COAD - Colon adenocarcinoma(174;0.141)		CTGTCCTGGCCTGGCTGAAGG	0.607													C|||	1585	0.316494	0.7239	0.2248	5008	,	,		17602	0.0556		0.1918	False		,,,				2504	0.228				p.G164S		Atlas-SNP	.											.	EPS8L3	73	.	0			c.G490A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	2703,1703	649.4+/-398.9	828,1047,328	52.0	52.0	52.0		487,487,490	-2.2	0.0	1	dbSNP_116	52	1891,6709	335.0+/-321.2	194,1503,2603	yes	missense,missense,missense	EPS8L3	NM_024526.3,NM_133181.3,NM_139053.2	56,56,56	1022,2550,2931	TT,TC,CC		21.9884,38.6518,35.3222	benign,benign,benign	163/564,163/594,164/595	110301260	4594,8412	2203	4300	6503	SO:0001583	missense	79574	exon7			CCTGGCCTGGCTG	AK025175	CCDS813.1, CCDS814.1, CCDS815.1	1p13.2	2008-02-05			ENSG00000198758	ENSG00000198758			21297	protein-coding gene	gene with protein product		614989				12620401	Standard	NM_139053		Approved	FLJ21522, MGC16817	uc001dyq.2	Q8TE67	OTTHUMG00000011651	ENST00000361965.4:c.487G>A	1.37:g.110301260C>T	ENSP00000355255:p.Gly163Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	80	16	0.2	NM_139053	A8K833|Q5T8Q6|Q5T8Q7|Q5T8Q8|Q96E47|Q9H719	Missense_Mutation	SNP	ENST00000361965.4	37	CCDS814.1	637	0.2916666666666667	351	0.7134146341463414	85	0.23480662983425415	39	0.06818181818181818	162	0.21372031662269128	C	13.57	2.277964	0.40294	0.613482	0.219884	ENSG00000198758	ENST00000361852;ENST00000369805;ENST00000361965	T;T;T	0.59772	2.6;0.24;0.25	5.51	-2.18	0.07037	.	1.692000	0.02443	N	0.084779	T	0.07188	0.0182	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.15473	0.003;0.013;0.001;0.002	B;B;B;B	0.09377	0.001;0.004;0.001;0.004	T	0.07271	-1.0781	9	0.08837	T	0.75	-0.8016	1.3281	0.02129	0.1439:0.3222:0.1401:0.3938	rs6693815;rs6693815	163;163;163;164	A8K2J6;Q8TE67-2;Q8TE67;Q8TE67-3	.;.;ES8L3_HUMAN;.	S	163;164;163	ENSP00000354551:G163S;ENSP00000358820:G164S;ENSP00000355255:G163S	ENSP00000354551:G163S	G	-	1	0	EPS8L3	110102783	0.000000	0.05858	0.003000	0.11579	0.498000	0.33706	-0.846000	0.04336	-0.055000	0.13244	0.655000	0.94253	GGC	C|0.668;T|0.332	0.332	strong		0.607	EPS8L3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032234.1	NM_024526	
ESRRG	2104	hgsc.bcm.edu	37	1	216692669	216692669	+	Silent	SNP	C	C	T	rs945453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:216692669C>T	ENST00000408911.3	-	6	1110	c.957G>A	c.(955-957)tcG>tcA	p.S319S	ESRRG_ENST00000366940.2_Silent_p.S296S|ESRRG_ENST00000361395.2_Silent_p.S296S|ESRRG_ENST00000360012.3_Silent_p.S296S|ESRRG_ENST00000361525.3_Silent_p.S296S|ESRRG_ENST00000391890.3_Silent_p.S303S|ESRRG_ENST00000463665.1_Silent_p.S257S|ESRRG_ENST00000487276.1_Silent_p.S296S|ESRRG_ENST00000366937.1_Silent_p.S331S|ESRRG_ENST00000366938.2_Silent_p.S296S|ESRRG_ENST00000493603.1_Silent_p.S296S|ESRRG_ENST00000493748.1_Silent_p.S296S|ESRRG_ENST00000359162.2_Silent_p.S296S	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	319					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|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)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	CATCCTCAAACGAAAGAGACC	0.473													C|||	3168	0.632588	0.733	0.6354	5008	,	,		15698	0.7381		0.4344	False		,,,				2504	0.59				p.S331S		Atlas-SNP	.											.	ESRRG	111	.	0			c.G993A						PASS	.	C	,,,	2915,1491	676.3+/-403.2	956,1003,244	89.0	86.0	87.0		888,957,888,888	-11.0	0.5	1	dbSNP_86	87	3563,5037	516.1+/-378.7	742,2079,1479	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRRG	NM_001134285.2,NM_001438.3,NM_206594.2,NM_206595.2	,,,	1698,3082,1723	TT,TC,CC		41.4302,33.8402,49.8078	,,,	296/436,319/459,296/436,296/436	216692669	6478,6528	2203	4300	6503	SO:0001819	synonymous_variant	2104	exon7			CTCAAACGAAAGA	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"""Nuclear hormone receptors"""	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.957G>A	1.37:g.216692669C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	118	81	0.686441	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Silent	SNP	ENST00000408911.3	37	CCDS41468.1																																																																																			C|0.442;T|0.558	0.558	strong		0.473	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595	
HEPH	9843	hgsc.bcm.edu	37	X	65427040	65427040	+	Silent	SNP	T	T	C	rs61746100|rs806607	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:65427040T>C	ENST00000343002.2	+	13	2959	c.2295T>C	c.(2293-2295)taT>taC	p.Y765Y	HEPH_ENST00000374727.3_Silent_p.Y768Y|HEPH_ENST00000336279.5_Silent_p.Y498Y|HEPH_ENST00000519389.1_Silent_p.Y819Y|HEPH_ENST00000419594.1_Silent_p.Y576Y|HEPH_ENST00000441993.2_Silent_p.Y768Y			Q9BQS7	HEPH_HUMAN	hephaestin	765	Plastocyanin-like 5.				cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|iron ion transport (GO:0006826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	copper ion binding (GO:0005507)|ferrous iron binding (GO:0008198)|ferroxidase activity (GO:0004322)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(56)|ovary(5)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	89						CCTCTAGTTATGGTTACATTT	0.448													C|||	1320	0.349669	0.7141	0.1988	3775	,	,		9954	0.001		0.171	False		,,,				2504	0.0665				p.Y819Y		Atlas-SNP	.											.	HEPH	224	.	0			c.T2457C						PASS	.	C	,,	3276,559		1190,402,494,40,77	114.0	98.0	103.0		2304,1494,2457	3.6	1.0	X	dbSNP_86	103	1509,5219		122,788,477,1518,1395	no	coding-synonymous,coding-synonymous,coding-synonymous	HEPH	NM_001130860.2,NM_014799.2,NM_138737.3	,,	1312,1190,971,1558,1472	CC,CT,C,TT,T		22.4287,14.5763,45.2996	,,	768/1161,498/892,819/1213	65427040	4785,5778	2203	4300	6503	SO:0001819	synonymous_variant	9843	exon14			TAGTTATGGTTAC	AB014598	CCDS14384.2, CCDS14385.1, CCDS48133.1, CCDS14384.3, CCDS65277.1	Xq11-q12	2008-02-05			ENSG00000089472	ENSG00000089472			4866	protein-coding gene	gene with protein product		300167				9988272, 9734811	Standard	NM_014799		Approved	KIAA0698, CPL	uc011moz.2	Q9BQS7	OTTHUMG00000021732	ENST00000343002.2:c.2295T>C	X.37:g.65427040T>C		Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Silent	SNP	ENST00000343002.2	37																																																																																				0|0.020;C|0.435	0.435	strong		0.448	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737	
ASTN1	460	hgsc.bcm.edu	37	1	177001896	177001896	+	Silent	SNP	C	C	G	rs2076069	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:177001896C>G	ENST00000367654.3	-	3	772	c.561G>C	c.(559-561)ccG>ccC	p.P187P	ASTN1_ENST00000367657.3_Silent_p.P187P|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000361833.2_Silent_p.P187P|ASTN1_ENST00000424564.2_Silent_p.P187P	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	187					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TCTGGGGCTGCGGGACCCGGC	0.612													G|||	751	0.14996	0.0272	0.2118	5008	,	,		17437	0.2599		0.1471	False		,,,				2504	0.1616				p.P187P		Atlas-SNP	.											.	ASTN1	314	.	0			c.G561C						PASS	.	G	,	228,4178	789.4+/-415.0	3,222,1978	38.0	39.0	38.0		561,561	-1.3	0.9	1	dbSNP_96	38	1418,7182	736.8+/-407.0	119,1180,3001	no	coding-synonymous,coding-synonymous	ASTN1	NM_004319.1,NM_207108.1	,	122,1402,4979	GG,GC,CC		16.4884,5.1748,12.6557	,	187/1295,187/1217	177001896	1646,11360	2203	4300	6503	SO:0001819	synonymous_variant	460	exon3			GGGCTGCGGGACC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.561G>C	1.37:g.177001896C>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																				C|0.864;G|0.136	0.136	strong		0.612	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
MMP9	4318	hgsc.bcm.edu	37	20	44642833	44642833	+	Silent	SNP	A	A	C	rs13969	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44642833A>C	ENST00000372330.3	+	11	1840	c.1821A>C	c.(1819-1821)ggA>ggC	p.G607G	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	607					collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	TGGGCCTGGGAGCCGACGTGG	0.736											OREG0025990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2033	0.40595	0.407	0.4669	5008	,	,		13583	0.2292		0.5855	False		,,,				2504	0.3589				p.G607G		Atlas-SNP	.											.	MMP9	84	.	0			c.A1821C						PASS	.	C		1860,1782		544,772,505	3.0	4.0	4.0		1821	1.9	0.5	20	dbSNP_52	4	4661,2573		1627,1407,583	no	coding-synonymous	MMP9	NM_004994.2		2171,2179,1088	CC,CA,AA		35.5682,48.9292,40.0423		607/708	44642833	6521,4355	1821	3617	5438	SO:0001819	synonymous_variant	4318	exon11			CCTGGGAGCCGAC		CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.1821A>C	20.37:g.44642833A>C		Somatic	45	0	0	925	WXS	Illumina HiSeq	Phase_I	8	8	1	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Silent	SNP	ENST00000372330.3	37	CCDS13390.1																																																																																			A|0.580;C|0.420	0.420	strong		0.736	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1		
RFTN1	23180	hgsc.bcm.edu	37	3	16364919	16364919	+	Silent	SNP	A	A	C	rs690216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:16364919A>C	ENST00000334133.4	-	9	1568	c.1296T>G	c.(1294-1296)ccT>ccG	p.P432P	RFTN1_ENST00000432519.1_Silent_p.P396P|OXNAD1_ENST00000435829.2_Intron|OXNAD1_ENST00000605932.1_Intron|OXNAD1_ENST00000606098.1_Intron|RFTN1_ENST00000483671.1_5'UTR|OXNAD1_ENST00000544043.1_Intron	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	432					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						GAGGTAGACAAGGTCTCTGAA	0.458													C|||	2891	0.577276	0.7375	0.5375	5008	,	,		20763	0.5149		0.5626	False		,,,				2504	0.4683				p.P432P		Atlas-SNP	.											.	RFTN1	79	.	0			c.T1296G						PASS	.	C		3032,1374	453.6+/-350.4	1050,932,221	111.0	98.0	103.0		1296	-10.7	0.4	3	dbSNP_83	103	4818,3782	537.1+/-383.1	1359,2100,841	no	coding-synonymous	RFTN1	NM_015150.1		2409,3032,1062	CC,CA,AA		43.9767,31.1847,39.6432		432/579	16364919	7850,5156	2203	4300	6503	SO:0001819	synonymous_variant	23180	exon9			TAGACAAGGTCTC	D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"""raft-linking protein"""					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.1296T>G	3.37:g.16364919A>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	121	48	0.396694	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Silent	SNP	ENST00000334133.4	37	CCDS33712.1																																																																																			A|0.402;C|0.598	0.598	strong		0.458	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150	
ABCA4	24	hgsc.bcm.edu	37	1	94476388	94476388	+	Silent	SNP	C	C	G	rs1801574	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:94476388C>G	ENST00000370225.3	-	40	5768	c.5682G>C	c.(5680-5682)ctG>ctC	p.L1894L	ABCA4_ENST00000535881.1_Silent_p.L13L|ABCA4_ENST00000465352.1_5'UTR|ABCA4_ENST00000536513.1_Silent_p.L164L	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1894					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.L1894L(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GCTGGACCAGCAGGGTCAGGA	0.582													G|||	1005	0.200679	0.2738	0.2075	5008	,	,		17831	0.12		0.2495	False		,,,				2504	0.1299				p.L1894L		Atlas-SNP	.											ABCA4,NS,carcinoma,0,1	ABCA4	275	1	1	Substitution - coding silent(1)	stomach(1)	c.G5682C						PASS	.	G		1077,3329	722.2+/-409.3	146,785,1272	193.0	146.0	162.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5682	-1.1	1.0	1	dbSNP_89	162	2165,6435	712.8+/-405.9	257,1651,2392	no	coding-synonymous	ABCA4	NM_000350.2		403,2436,3664	GG,GC,CC		25.1744,24.4439,24.927		1894/2274	94476388	3242,9764	2203	4300	6503	SO:0001819	synonymous_variant	24	exon40			GACCAGCAGGGTC	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.5682G>C	1.37:g.94476388C>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	71	14	0.197183	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			C|0.758;G|0.242	0.242	strong		0.582	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
ARF3	377	hgsc.bcm.edu	37	12	49333799	49333799	+	Silent	SNP	G	G	A	rs2228417	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:49333799G>A	ENST00000256682.4	-	3	574	c.240C>T	c.(238-240)caC>caT	p.H80H	ARF3_ENST00000541959.1_Silent_p.H80H|AC073610.5_ENST00000537495.1_5'Flank|RP11-302B13.5_ENST00000398092.4_Silent_p.H80H|ARF3_ENST00000447318.2_Intron|ARF3_ENST00000541967.1_5'Flank	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	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	205	107	0.521951	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	
HOXB1	3211	hgsc.bcm.edu	37	17	46607817	46607817	+	Silent	SNP	C	C	T	rs7207109	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	120	0	0		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	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		
BCAR1	9564	hgsc.bcm.edu	37	16	75263816	75263816	+	Silent	SNP	G	G	A	rs145141523	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:75263816G>A	ENST00000162330.5	-	7	2332	c.2206C>T	c.(2206-2208)Ctg>Ttg	p.L736L	RP11-331F4.4_ENST00000489723.1_RNA|BCAR1_ENST00000420641.3_Silent_p.L754L|BCAR1_ENST00000535626.2_Silent_p.L588L|BCAR1_ENST00000538440.2_Silent_p.L736L|BCAR1_ENST00000393420.6_Silent_p.L754L|BCAR1_ENST00000393422.2_Silent_p.L754L|BCAR1_ENST00000542031.2_Silent_p.L734L|BCAR1_ENST00000546196.1_Silent_p.L707L|BCAR1_ENST00000418647.3_Silent_p.L782L|BCAR1_ENST00000566982.1_5'UTR	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	736					actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GAGGGCCCCAGGCCGCCTGTT	0.657													G|||	25	0.00499201	0.0015	0.0014	5008	,	,		15958	0.0		0.0179	False		,,,				2504	0.0041				p.L782L		Atlas-SNP	.											BCAR1_ENST00000393420,NS,carcinoma,0,2	BCAR1	184	2	0			c.C2344T						PASS	.	G	,,,,,,,,	9,4377		0,9,2184	37.0	42.0	40.0		2344,2260,2260,2260,2206,2200,1762,1576,2206	2.7	1.0	16	dbSNP_134	40	169,8417		3,163,4127	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCAR1	NM_001170714.1,NM_001170715.1,NM_001170716.1,NM_001170717.1,NM_001170718.1,NM_001170719.1,NM_001170720.1,NM_001170721.1,NM_014567.3	,,,,,,,,	3,172,6311	AA,AG,GG		1.9683,0.2052,1.3722	,,,,,,,,	782/917,754/889,754/889,754/889,736/871,734/869,588/723,526/661,736/871	75263816	178,12794	2193	4293	6486	SO:0001819	synonymous_variant	9564	exon8			GCCCCAGGCCGCC	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.2206C>T	16.37:g.75263816G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	41	35	0.853659	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Silent	SNP	ENST00000162330.5	37	CCDS10915.1																																																																																			G|0.993;A|0.007	0.007	strong		0.657	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
ITGA6	3655	hgsc.bcm.edu	37	2	173339808	173339808	+	Missense_Mutation	SNP	G	G	A	rs11895564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:173339808G>A	ENST00000264106.6	+	8	1458	c.1255G>A	c.(1255-1257)Gca>Aca	p.A419T	ITGA6_ENST00000264107.7_Missense_Mutation_p.A380T|ITGA6_ENST00000409080.1_Missense_Mutation_p.A380T|ITGA6_ENST00000343713.4_Missense_Mutation_p.A375T|ITGA6_ENST00000409532.1_Missense_Mutation_p.A261T|ITGA6_ENST00000375221.2_Missense_Mutation_p.A419T			P23229	ITA6_HUMAN	integrin, alpha 6	419				A -> T (in Ref. 4; BAG59130 and 7; AAI36456/AAI36457). {ECO:0000305}.	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)			GTTTGGCATTGCAGTAAAAAA	0.333													G|||	1260	0.251597	0.3253	0.2248	5008	,	,		18864	0.0933		0.2793	False		,,,				2504	0.3057				p.A380T		Atlas-SNP	.											ITGA6,NS,NS,-1,1	ITGA6	171	1	0			c.G1138A						PASS	.	G	THR/ALA,THR/ALA	1505,2901	477.4+/-357.9	250,1005,948	78.0	79.0	78.0		1138,1138	4.5	1.0	2	dbSNP_120	78	2560,6040	415.9+/-351.9	370,1820,2110	yes	missense,missense	ITGA6	NM_000210.2,NM_001079818.1	58,58	620,2825,3058	AA,AG,GG		29.7674,34.158,31.2548	benign,benign	380/1074,380/1092	173339808	4065,8941	2203	4300	6503	SO:0001583	missense	3655	exon7			GGCATTGCAGTAA		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.1255G>A	2.37:g.173339808G>A	ENSP00000264106:p.Ala419Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	37		524	0.23992673992673993	164	0.3333333333333333	97	0.26795580110497236	53	0.09265734265734266	210	0.2770448548812665	G	20.9	4.068903	0.76301	0.34158	0.297674	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358	T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	5.35	4.46	0.54185	.	0.160749	0.56097	D	0.000036	T	0.00012	0.0000	L	0.56396	1.775	0.19775	P	0.9999532777	P;B;P;P	0.45428	0.571;0.042;0.858;0.858	B;B;P;P	0.58172	0.389;0.133;0.834;0.746	T	0.01413	-1.1361	8	.	.	.	.	13.3506	0.60599	0.0:0.0:0.7145:0.2855	rs11895564;rs52804239;rs61334157;rs11895564	375;419;380;380	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	T	261;380;419;419;375;380;419;375	ENSP00000386614:A261T;ENSP00000264107:A380T;ENSP00000264106:A419T;ENSP00000364369:A419T;ENSP00000341078:A375T;ENSP00000386896:A380T;ENSP00000406694:A419T;ENSP00000394169:A375T	.	A	+	1	0	ITGA6	173048054	1.000000	0.71417	0.967000	0.41034	0.946000	0.59487	3.120000	0.50430	1.225000	0.43566	0.650000	0.86243	GCA	G|0.714;A|0.286	0.286	strong		0.333	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
PCDHB11	56125	hgsc.bcm.edu	37	5	140579358	140579358	+	Missense_Mutation	SNP	A	A	G	rs3756323	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140579358A>G	ENST00000354757.3	+	1	11	c.11A>G	c.(10-12)cAa>cGa	p.Q4R	PCDHB11_ENST00000536699.1_5'UTR	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	4			Q -> R (in dbSNP:rs3756323).		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)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGGAGAACCAAGGGACACGC	0.502													G|||	764	0.152556	0.2579	0.1902	5008	,	,		21054	0.0407		0.1581	False		,,,				2504	0.093				p.Q4R		Atlas-SNP	.											.	PCDHB11	162	.	0			c.A11G						PASS	.	G	ARG/GLN	1043,3363	725.1+/-409.6	115,813,1275	79.0	74.0	76.0		11	0.2	0.0	5	dbSNP_107	76	1473,7127	749.9+/-407.4	137,1199,2964	yes	missense	PCDHB11	NM_018931.2	43	252,2012,4239	GG,GA,AA		17.1279,23.6723,19.3449	benign	4/798	140579358	2516,10490	2203	4300	6503	SO:0001583	missense	56125	exon1			AGAACCAAGGGAC	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.11A>G	5.37:g.140579358A>G	ENSP00000346802:p.Gln4Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	333	0.15247252747252749	122	0.24796747967479674	63	0.17403314917127072	26	0.045454545454545456	122	0.16094986807387862	G	2.426	-0.331889	0.05314	0.236723	0.171279	ENSG00000197479	ENST00000354757	T	0.46063	0.88	2.69	0.238	0.15480	.	.	.	.	.	T	0.00012	0.0000	N	0.01482	-0.84	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39375	-0.9617	8	0.09843	T	0.71	.	7.8071	0.29209	0.1035:0.3818:0.5147:0.0	rs3756323;rs52814876;rs58371514;rs3756323	4	Q9Y5F2	PCDBB_HUMAN	R	4	ENSP00000346802:Q4R	ENSP00000346802:Q4R	Q	+	2	0	PCDHB11	140559542	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.201000	0.09464	-0.041000	0.13558	-0.368000	0.07277	CAA	A|0.818;G|0.182	0.182	strong		0.502	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
AHNAK2	113146	hgsc.bcm.edu	37	14	105412363	105412363	+	Missense_Mutation	SNP	T	T	C	rs201377363	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105412363T>C	ENST00000333244.5	-	7	9544	c.9425A>G	c.(9424-9426)aAg>aGg	p.K3142R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3142						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)		p.K3142R(1)		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)			CATTTTGAACTTGCTGTCTTT	0.592																																					p.K3142R		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,NS,0,1	AHNAK2	719	1	1	Substitution - Missense(1)	NS(1)	c.A9425G						scavenged	.						181.0	139.0	152.0					14																	105412363		1912	4076	5988	SO:0001583	missense	113146	exon7			TTGAACTTGCTGT	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.9425A>G	14.37:g.105412363T>C	ENSP00000353114:p.Lys3142Arg	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	148	12	0.0810811	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	11.62	1.694140	0.30052	.	.	ENSG00000185567	ENST00000333244	T	0.00882	5.58	3.45	3.45	0.39498	.	.	.	.	.	T	0.05502	0.0145	M	0.85462	2.755	0.23620	N	0.997271	D	0.71674	0.998	D	0.78314	0.991	T	0.12372	-1.0550	9	0.54805	T	0.06	.	9.5748	0.39450	0.0:0.0:0.1761:0.8239	.	3142	Q8IVF2	AHNK2_HUMAN	R	3142	ENSP00000353114:K3142R	ENSP00000353114:K3142R	K	-	2	0	AHNAK2	104483408	0.794000	0.28838	0.977000	0.42913	0.041000	0.13682	3.435000	0.52849	1.195000	0.43115	0.260000	0.18958	AAG	T|0.760;C|0.240	0.240	strong		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
DNAJC13	23317	hgsc.bcm.edu	37	3	132241682	132241682	+	Missense_Mutation	SNP	C	C	T	rs145242123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:132241682C>T	ENST00000260818.6	+	49	5932	c.5684C>T	c.(5683-5685)aCg>aTg	p.T1895M		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1895					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						GTTCGAATTACGTTAATGAAA	0.333													C|||	3	0.000599042	0.0	0.0029	5008	,	,		18811	0.0		0.001	False		,,,				2504	0.0				p.T1895M		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C5684T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	51.0	51.0	51.0		5684	5.2	1.0	3	dbSNP_134	51	12,8588	8.4+/-32.0	0,12,4288	yes	missense	DNAJC13	NM_015268.3	81	0,13,6490	TT,TC,CC		0.1395,0.0227,0.1	benign	1895/2244	132241682	13,12993	2203	4300	6503	SO:0001583	missense	23317	exon49			GAATTACGTTAAT	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.5684C>T	3.37:g.132241682C>T	ENSP00000260818:p.Thr1895Met	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	125	70	0.56	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	8.466	0.856381	0.17106	2.27E-4	0.001395	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.49720	0.77	6.08	5.2	0.72013	Armadillo-like helical (1);Armadillo-type fold (1);	0.122360	0.56097	N	0.000036	T	0.42720	0.1215	L	0.58810	1.83	0.31740	N	0.635937	B	0.13145	0.007	B	0.06405	0.002	T	0.47156	-0.9139	10	0.33940	T	0.23	.	9.9625	0.41704	0.0:0.7534:0.0:0.2466	.	1895	O75165	DJC13_HUMAN	M	1895;542	ENSP00000260818:T1895M	ENSP00000260818:T1895M	T	+	2	0	DNAJC13	133724372	0.797000	0.28877	0.995000	0.50966	0.605000	0.37080	1.532000	0.36029	0.919000	0.36945	-0.797000	0.03246	ACG	C|0.998;T|0.002	0.002	strong		0.333	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
UBAP2	55833	hgsc.bcm.edu	37	9	34017106	34017106	+	Missense_Mutation	SNP	C	C	T	rs1785506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34017106C>T	ENST00000379238.1	-	2	158	c.41G>A	c.(40-42)cGg>cAg	p.R14Q	RNU7-36P_ENST00000516597.1_RNA|UBAP2_ENST00000480885.1_5'UTR|UBAP2_ENST00000539807.1_5'UTR|UBAP2_ENST00000449054.1_Missense_Mutation_p.R14Q|UBAP2_ENST00000360802.1_Missense_Mutation_p.R14Q|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000418786.2_Missense_Mutation_p.R14Q					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)		TGGTTTTTCCCGAGCACCTCG	0.358													C|||	3150	0.628994	0.4909	0.732	5008	,	,		16265	0.8274		0.6163	False		,,,				2504	0.5511				p.R14Q		Atlas-SNP	.											UBAP2,bladder,carcinoma,-1,2	UBAP2	82	2	0			c.G41A						PASS	.	C	GLN/ARG	2347,2059	607.4+/-390.9	621,1105,477	138.0	117.0	124.0		41	5.8	1.0	9	dbSNP_89	124	5309,3291	646.5+/-400.3	1657,1995,648	yes	missense	UBAP2	NM_018449.2	43	2278,3100,1125	TT,TC,CC		38.2674,46.7317,41.1349	possibly-damaging	14/1120	34017106	7656,5350	2203	4300	6503	SO:0001583	missense	55833	exon2			TTTTCCCGAGCAC	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.41G>A	9.37:g.34017106C>T	ENSP00000368540:p.Arg14Gln	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	145	64	0.441379	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	1406	0.6437728937728938	244	0.4959349593495935	256	0.7071823204419889	458	0.8006993006993007	448	0.5910290237467019	C	17.06	3.292071	0.59976	0.532683	0.617326	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000351580;ENST00000418786;ENST00000412543	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	0.999999816373	D;P	0.76494	0.999;0.902	P;B	0.61477	0.889;0.195	T	0.11155	-1.0599	9	0.25751	T	0.34	-9.2197	20.1001	0.97870	0.0:1.0:0.0:0.0	rs1785506;rs3780506;rs52815908;rs61421888;rs1785506	14;14	E7EWG4;Q5T6F2	.;UBAP2_HUMAN	Q	14	ENSP00000368540:R14Q;ENSP00000416932:R14Q;ENSP00000354039:R14Q;ENSP00000404436:R14Q;ENSP00000414800:R14Q	ENSP00000259602:R14Q	R	-	2	0	UBAP2	34007106	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	6.341000	0.72977	2.760000	0.94817	0.655000	0.94253	CGG	C|0.374;T|0.626	0.626	strong		0.358	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
FLT3	2322	hgsc.bcm.edu	37	13	28623525	28623525	+	Silent	SNP	G	G	A	rs146983744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:28623525G>A	ENST00000241453.7	-	8	1113	c.1032C>T	c.(1030-1032)atC>atT	p.I344I	FLT3_ENST00000537084.1_Silent_p.I344I|FLT3_ENST00000380982.4_Silent_p.I344I	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	344					B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|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 tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|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)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CATTACCTACGATGGTAACCA	0.398			"""Mis, O"""		"""AML, ALL"""																																p.I344I		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.C1032T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	245.0	216.0	226.0		1032	3.8	1.0	13	dbSNP_134	226	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FLT3	NM_004119.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		344/994	28623525	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	2322	exon8			ACCTACGATGGTA	U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.1032C>T	13.37:g.28623525G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	133	74	0.556391	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Silent	SNP	ENST00000241453.7	37	CCDS31953.1																																																																																			G|0.999;A|0.001	0.001	strong		0.398	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2		
VARS2	57176	hgsc.bcm.edu	37	6	30887972	30887972	+	Silent	SNP	C	C	T	rs2285319	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:30887972C>T	ENST00000321897.5	+	12	1904	c.1272C>T	c.(1270-1272)tcC>tcT	p.S424S	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000541562.1_Silent_p.S454S|VARS2_ENST00000416670.2_Silent_p.S424S|VARS2_ENST00000542001.1_Silent_p.S284S			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	424					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						CCATGACCTCCCTCTGCGGGG	0.572													C|||	1973	0.39397	0.2602	0.4222	5008	,	,		16186	0.5942		0.2038	False		,,,				2504	0.544				p.S454S		Atlas-SNP	.											.	VARS2	60	.	0			c.C1362T						PASS	.	C	,,	698,2324		83,532,896	57.0	53.0	55.0		852,1362,1272	-2.3	0.0	6	dbSNP_100	55	879,4539		69,741,1899	no	coding-synonymous,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	152,1273,2795	TT,TC,CC		16.2237,23.0973,18.6848	,,	284/924,454/1094,424/1064	30887972	1577,6863	1511	2709	4220	SO:0001819	synonymous_variant	57176	exon13			GACCTCCCTCTGC	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.1272C>T	6.37:g.30887972C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	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|0.745;T|0.255	0.255	strong		0.572	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
MMP10	4319	hgsc.bcm.edu	37	11	102650389	102650389	+	Missense_Mutation	SNP	C	C	T	rs17293607	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102650389C>T	ENST00000279441.4	-	2	229	c.193G>A	c.(193-195)Gga>Aga	p.G65R		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	65			G -> R (in dbSNP:rs17293607). {ECO:0000269|Ref.5}.		collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	TTCTGCATTCCTTGGATTTTT	0.433													C|||	328	0.0654952	0.0106	0.0922	5008	,	,		18822	0.0228		0.159	False		,,,				2504	0.0685				p.G65R		Atlas-SNP	.											.	MMP10	44	.	0			c.G193A	GRCh37	CM065315	MMP10	M	rs17293607	PASS	.	C	ARG/GLY	139,4267	98.9+/-137.6	3,133,2067	98.0	84.0	89.0		193	3.3	1.0	11	dbSNP_123	89	1250,7348	249.7+/-276.9	99,1052,3148	yes	missense	MMP10	NM_002425.2	125	102,1185,5215	TT,TC,CC		14.5383,3.1548,10.6813	benign	65/477	102650389	1389,11615	2203	4299	6502	SO:0001583	missense	4319	exon2			GCATTCCTTGGAT	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"""matrix metalloproteinase 10 (stromelysin 2)"""	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.193G>A	11.37:g.102650389C>T	ENSP00000279441:p.Gly65Arg	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	251	78	0.310757	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	37	CCDS8321.1	176	0.08058608058608059	5	0.01016260162601626	41	0.1132596685082873	17	0.02972027972027972	113	0.14907651715039577	c	10.32	1.317349	0.23908	0.031548	0.145383	ENSG00000166670	ENST00000279441;ENST00000539681	T;T	0.31769	1.48;1.48	4.25	3.34	0.38264	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.264845	0.26578	N	0.023590	T	0.00073	0.0002	N	0.02916	-0.46	0.45390	P	0.0016239999999999588	B	0.15930	0.015	B	0.17098	0.017	T	0.09185	-1.0686	9	0.66056	D	0.02	.	14.6072	0.68489	0.0:0.8532:0.1468:0.0	rs17293607;rs17860948;rs17293607	65	P09238	MMP10_HUMAN	R	65	ENSP00000279441:G65R;ENSP00000441485:G65R	ENSP00000279441:G65R	G	-	1	0	MMP10	102155599	0.956000	0.32656	0.964000	0.40570	0.019000	0.09904	2.172000	0.42463	1.154000	0.42482	-0.189000	0.12847	GGA	C|0.912;T|0.088	0.088	strong		0.433	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
NPC1	4864	hgsc.bcm.edu	37	18	21123523	21123523	+	Missense_Mutation	SNP	C	C	T	rs375047023		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:21123523C>T	ENST00000269228.5	-	14	2695	c.2141G>A	c.(2140-2142)cGt>cAt	p.R714H	NPC1_ENST00000412552.2_Missense_Mutation_p.R396H|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	714	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)					CCCTTGAAGACGTTCATCTCT	0.403																																					p.R714H		Atlas-SNP	.											.	NPC1	114	.	0			c.G2141A						PASS	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	64.0	66.0	65.0		2141	4.9	1.0	18		65	1,8599	1.2+/-3.3	0,1,4299	no	missense	NPC1	NM_000271.4	29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	714/1279	21123523	2,13004	2203	4300	6503	SO:0001583	missense	4864	exon14			TGAAGACGTTCAT	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.2141G>A	18.37:g.21123523C>T	ENSP00000269228:p.Arg714His	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719159	0.89205	2.27E-4	1.16E-4	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.95949	-3.86;-3.86	5.79	4.93	0.64822	Sterol-sensing domain (1);	0.000000	0.85682	D	0.000000	D	0.95918	0.8671	L	0.60067	1.865	0.80722	D	1	D;D	0.61697	0.99;0.99	P;P	0.54889	0.679;0.763	D	0.95741	0.8783	10	0.56958	D	0.05	-14.1977	14.8323	0.70156	0.0:0.9311:0.0:0.0689	.	725;714	Q59GR1;O15118	.;NPC1_HUMAN	H	714;396;559	ENSP00000269228:R714H;ENSP00000408606:R396H	ENSP00000269228:R714H	R	-	2	0	NPC1	19377521	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.448000	0.80631	1.472000	0.48140	-0.142000	0.14014	CGT	.	.	weak		0.403	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
PIP5K1C	23396	hgsc.bcm.edu	37	19	3633473	3633473	+	Missense_Mutation	SNP	C	C	T	rs35014191	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3633473C>T	ENST00000335312.3	-	17	2054	c.1966G>A	c.(1966-1968)Gcc>Acc	p.A656T	PIP5K1C_ENST00000539785.1_Intron	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	656	Mediates interaction with TLN2.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GGGGCCTGGGCGCTATAGTGG	0.701													C|||	34	0.00678914	0.0129	0.0058	5008	,	,		11951	0.0		0.006	False		,,,				2504	0.0072				p.A656T	Esophageal Squamous(135;99 1744 12852 27186 39851)	Atlas-SNP	.											PIP5K1C_ENST00000335312,NS,carcinoma,+1,1	PIP5K1C	63	1	0			c.G1966A						PASS	.	C	,THR/ALA	21,4373		0,21,2176	17.0	22.0	20.0		,1966	-6.2	0.2	19	dbSNP_126	20	101,8487		0,101,4193	no	intron,missense	PIP5K1C	NM_001195733.1,NM_012398.2	,58	0,122,6369	TT,TC,CC		1.1761,0.4779,0.9398	,benign	,656/669	3633473	122,12860	2197	4294	6491	SO:0001583	missense	23396	exon17			CCTGGGCGCTATA	AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1966G>A	19.37:g.3633473C>T	ENSP00000335333:p.Ala656Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_012398	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Missense_Mutation	SNP	ENST00000335312.3	37	CCDS32872.1	12	0.005494505494505495	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	6.504	0.461201	0.12342	0.004779	0.011761	ENSG00000186111	ENST00000335312	T	0.25912	1.77	3.39	-6.18	0.02085	.	0.500976	0.17660	N	0.166351	T	0.05227	0.0139	N	0.03608	-0.345	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.37979	-0.9682	10	0.07813	T	0.8	-8.2929	12.3675	0.55236	0.0:0.2685:0.0:0.7315	rs35014191	656	O60331	PI51C_HUMAN	T	656	ENSP00000335333:A656T	ENSP00000335333:A656T	A	-	1	0	PIP5K1C	3584473	0.551000	0.26497	0.185000	0.23176	0.746000	0.42486	-0.496000	0.06436	-1.205000	0.02645	-0.657000	0.03884	GCC	C|0.992;T|0.008	0.008	strong		0.701	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398	
FAM188B	84182	hgsc.bcm.edu	37	7	30831181	30831181	+	Missense_Mutation	SNP	C	C	T	rs12672119	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:30831181C>T	ENST00000265299.6	+	5	1141	c.1064C>T	c.(1063-1065)gCa>gTa	p.A355V	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	355			A -> V (in dbSNP:rs12672119).							endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGCCAGCCCGCACCTGTCAGG	0.542													T|||	402	0.0802716	0.031	0.0159	5008	,	,		17715	0.1687		0.0209	False		,,,				2504	0.1626				p.A355V		Atlas-SNP	.											.	FAM188B	62	.	0			c.C1064T						PASS	.	T	VAL/ALA	99,3895		2,95,1900	32.0	39.0	36.0		1064	-4.7	0.0	7	dbSNP_120	36	262,8094		1,260,3917	yes	missense	FAM188B	NM_032222.2	64	3,355,5817	TT,TC,CC		3.1355,2.4787,2.9231	benign	355/758	30831181	361,11989	1997	4178	6175	SO:0001583	missense	84182	exon5			AGCCCGCACCTGT	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1064C>T	7.37:g.30831181C>T	ENSP00000265299:p.Ala355Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	123	50	0.406504	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	154	0.07051282051282051	21	0.042682926829268296	8	0.022099447513812154	108	0.1888111888111888	17	0.022427440633245383	T	0.004	-2.287390	0.00248	0.024787	0.031355	ENSG00000106125	ENST00000265299	T	0.09723	2.95	4.4	-4.66	0.03329	.	1.564730	0.03238	N	0.179881	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	0.43653	-0.9378	9	0.87932	D	0	-17.3691	6.9809	0.24702	0.1174:0.3346:0.0:0.5481	rs12672119;rs12672119	355	Q4G0A6	F188B_HUMAN	V	355	ENSP00000265299:A355V	ENSP00000265299:A355V	A	+	2	0	FAM188B	30797706	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.908000	0.04063	-1.168000	0.02776	-2.780000	0.00118	GCA	C|0.935;T|0.065	0.065	strong		0.542	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
ERMP1	79956	hgsc.bcm.edu	37	9	5801283	5801283	+	Missense_Mutation	SNP	T	T	A	rs147318623	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:5801283T>A	ENST00000339450.5	-	11	2049	c.1960A>T	c.(1960-1962)Act>Tct	p.T654S	ERMP1_ENST00000543230.1_Missense_Mutation_p.T232S|ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_3'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	654						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		AAAGTTAAAGTTAGCATGGTT	0.363													T|||	9	0.00179712	0.0	0.0014	5008	,	,		22068	0.0		0.008	False		,,,				2504	0.0				p.T654S		Atlas-SNP	.											.	ERMP1	63	.	0			c.A1960T						PASS	.	T	SER/THR	15,4391	22.3+/-47.3	0,15,2188	145.0	152.0	149.0		1960	-2.8	0.0	9	dbSNP_134	149	93,8507	51.9+/-112.3	3,87,4210	yes	missense	ERMP1	NM_024896.2	58	3,102,6398	AA,AT,TT		1.0814,0.3404,0.8304	benign	654/905	5801283	108,12898	2203	4300	6503	SO:0001583	missense	79956	exon11			TTAAAGTTAGCAT	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"""Felix-ina"""	611156	"""KIAA1815"""	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.1960A>T	9.37:g.5801283T>A	ENSP00000340427:p.Thr654Ser	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	196	100	0.510204	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	37	CCDS34983.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	5.663	0.306992	0.10733	0.003404	0.010814	ENSG00000099219	ENST00000339450;ENST00000543230	T;T	0.19532	2.14;2.14	5.66	-2.79	0.05841	.	0.615286	0.18988	N	0.125692	T	0.04770	0.0129	N	0.11560	0.145	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.27191	-1.0081	10	0.19590	T	0.45	-0.9539	3.4422	0.07468	0.1017:0.3099:0.1041:0.4843	.	654	Q7Z2K6	ERMP1_HUMAN	S	654;232	ENSP00000340427:T654S;ENSP00000439368:T232S	ENSP00000340427:T654S	T	-	1	0	ERMP1	5791283	0.015000	0.18098	0.000000	0.03702	0.921000	0.55340	0.143000	0.16115	-0.378000	0.07918	0.533000	0.62120	ACT	T|0.993;A|0.007	0.007	strong		0.363	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
POLR2B	5431	hgsc.bcm.edu	37	4	57889677	57889677	+	Silent	SNP	C	C	T	rs1056364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:57889677C>T	ENST00000381227.1	+	20	3110	c.2697C>T	c.(2695-2697)agC>agT	p.S899S	POLR2B_ENST00000441246.2_Silent_p.S892S|POLR2B_ENST00000314595.5_Silent_p.S899S|POLR2B_ENST00000431623.2_Silent_p.S824S			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	899					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)	p.S899S(1)		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)					TCAGAACTAGCGAGACGGGCA	0.393													C|||	2764	0.551917	0.4637	0.6412	5008	,	,		19700	0.6786		0.5845	False		,,,				2504	0.4438				p.S899S		Atlas-SNP	.											POLR2B,NS,carcinoma,0,1	POLR2B	108	1	1	Substitution - coding silent(1)	prostate(1)	c.C2697T						PASS	.	C		2143,2263	580.5+/-385.1	518,1107,578	106.0	104.0	105.0		2697	0.9	1.0	4	dbSNP_86	105	4946,3654	622.5+/-397.3	1418,2110,772	no	coding-synonymous	POLR2B	NM_000938.1		1936,3217,1350	TT,TC,CC		42.4884,48.6382,45.4944		899/1175	57889677	7089,5917	2203	4300	6503	SO:0001819	synonymous_variant	5431	exon19			AACTAGCGAGACG		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.2697C>T	4.37:g.57889677C>T		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			C|0.436;T|0.564	0.564	strong		0.393	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
IGSF22	283284	hgsc.bcm.edu	37	11	18735465	18735465	+	Missense_Mutation	SNP	G	G	A	rs11024769	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18735465G>A	ENST00000513874.1	-	14	2168	c.2029C>T	c.(2029-2031)Ctc>Ttc	p.L677F	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	677	Ig-like 4.		L -> F (in dbSNP:rs11024769).							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						AGCAGGATGAGGCCGCTGTCT	0.627													g|||	193	0.0385383	0.0855	0.0159	5008	,	,		22779	0.0496		0.0159	False		,,,				2504	0.0031				p.L677F		Atlas-SNP	.											.	IGSF22	211	.	0			c.C2029T						PASS	.		PHE/LEU	304,4076	148.0+/-182.4	10,284,1896	74.0	80.0	78.0		2029	-0.9	0.0	11	dbSNP_120	78	89,8477	49.4+/-109.1	1,87,4195	yes	missense	IGSF22	NM_173588.3	22	11,371,6091	AA,AG,GG		1.039,6.9406,3.0357	benign	677/1327	18735465	393,12553	2190	4283	6473	SO:0001583	missense	283284	exon14			GGATGAGGCCGCT	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.2029C>T	11.37:g.18735465G>A	ENSP00000421191:p.Leu677Phe	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	186	86	0.462366	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	90	0.04120879120879121	43	0.08739837398373984	7	0.019337016574585635	31	0.05419580419580419	9	0.011873350923482849	G	11.57	1.678099	0.29783	0.069406	0.01039	ENSG00000179057	ENST00000513874	T	0.67345	-0.26	3.98	-0.847	0.10730	.	0.595612	0.12747	U	0.442523	T	0.03608	0.0103	L	0.46741	1.465	0.09310	N	1	P	0.38335	0.627	B	0.40375	0.327	T	0.07520	-1.0768	10	0.54805	T	0.06	.	3.4011	0.07324	0.1161:0.4819:0.2682:0.1338	rs11024769;rs17495509;rs11024769	677	D6RGV7	.	F	677	ENSP00000421191:L677F	ENSP00000322422:L677F	L	-	1	0	IGSF22	18692041	0.000000	0.05858	0.002000	0.10522	0.211000	0.24417	-0.048000	0.11944	0.000000	0.14550	0.448000	0.29417	CTC	G|0.963;A|0.037	0.037	strong		0.627	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789367	117789367	+	Missense_Mutation	SNP	A	A	G	rs200485169		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789367A>G	ENST00000430170.2	-	2	295	c.208T>C	c.(208-210)Tct>Cct	p.S70P	TMPRSS13_ENST00000445164.2_Missense_Mutation_p.S70P|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.S70P|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.S70P|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.S70P	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	70	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					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)		CGGCCTGGAGATGCCCGGCCT	0.677																																					p.S70P		Atlas-SNP	.											TMPRSS13_ENST00000445164,NS,carcinoma,0,3	TMPRSS13	75	3	0			c.T208C						scavenged	.						46.0	53.0	50.0					11																	117789367		1896	4096	5992	SO:0001583	missense	84000	exon2			CTGGAGATGCCCG	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	ENST00000430170.2:c.208T>C	11.37:g.117789367A>G	ENSP00000387702:p.Ser70Pro	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	221	8	0.0361991	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	37	CCDS58185.1	.	.	.	.	.	.	.	.	.	.	A	8.733	0.917098	0.17907	.	.	ENSG00000137747	ENST00000528626;ENST00000336500;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	D;D;D;D;D	0.88975	-2.42;-2.45;-2.45;-2.45;-2.37	1.16	-2.32	0.06745	.	0.000000	0.45606	D	0.000355	T	0.73791	0.3632	N	0.17082	0.46	0.09310	N	1	B	0.22211	0.066	B	0.24394	0.053	T	0.58912	-0.7552	10	0.44086	T	0.13	.	2.7827	0.05365	0.4867:0.0:0.3126:0.2007	.	70	E9PRA0	.	P	70	ENSP00000435813:S70P;ENSP00000434279:S70P;ENSP00000387702:S70P;ENSP00000394114:S70P;ENSP00000436502:S70P	ENSP00000337113:S70P	S	-	1	0	TMPRSS13	117294577	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.557000	0.05985	-1.472000	0.01883	-1.256000	0.01477	TCT	.	.	weak		0.677	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
MUC17	140453	hgsc.bcm.edu	37	7	100677355	100677355	+	Silent	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677355A>C	ENST00000306151.4	+	3	2722	c.2658A>C	c.(2656-2658)tcA>tcC	p.S886S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	886	59 X approximate tandem repeats.|Ser-rich.				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)					GCACCCTTTCAACAACTCCTG	0.498																																					p.S886S		Atlas-SNP	.											.	MUC17	804	.	0			c.A2658C						PASS	.						292.0	289.0	290.0					7																	100677355		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CCTTTCAACAACT	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.2658A>C	7.37:g.100677355A>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	302	23	0.0761589	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.	.	none		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
GPR63	81491	hgsc.bcm.edu	37	6	97247547	97247547	+	Missense_Mutation	SNP	C	C	T	rs35358396	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:97247547C>T	ENST00000229955.3	-	2	406	c.61G>A	c.(61-63)Gtg>Atg	p.V21M	GPR63_ENST00000417980.1_Missense_Mutation_p.V21M	NM_001143957.2|NM_030784.3	NP_001137429.1|NP_110411.1	Q9BZJ6	GPR63_HUMAN	G protein-coupled receptor 63	21			V -> M (in dbSNP:rs35358396).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(5)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;6.89e-05)|Acute lymphoblastic leukemia(125;7.02e-10)|all_hematologic(75;1.23e-06)|all_epithelial(107;0.0618)|Colorectal(196;0.0721)		BRCA - Breast invasive adenocarcinoma(108;0.0912)		TTTTCATACACGACAAATGTT	0.468													C|||	73	0.0145767	0.0008	0.0259	5008	,	,		21414	0.0		0.0477	False		,,,				2504	0.0061				p.V21M		Atlas-SNP	.											GPR63,right_upper_lobe,carcinoma,+2,1	GPR63	60	1	0			c.G61A						PASS	.	C	MET/VAL,MET/VAL	27,4379	33.5+/-64.1	0,27,2176	133.0	120.0	125.0		61,61	1.3	0.3	6	dbSNP_126	125	365,8235	121.0+/-180.1	11,343,3946	yes	missense,missense	GPR63	NM_001143957.1,NM_030784.2	21,21	11,370,6122	TT,TC,CC		4.2442,0.6128,3.014	benign,benign	21/420,21/420	97247547	392,12614	2203	4300	6503	SO:0001583	missense	81491	exon2			CATACACGACAAA	AF317654	CCDS5036.1	6q16.1-q16.3	2012-08-21			ENSG00000112218	ENSG00000112218		"""GPCR / Class A : Orphans"""	13302	protein-coding gene	gene with protein product		606915					Standard	NM_030784		Approved	PSP24(beta), PSP24B	uc003pou.3	Q9BZJ6	OTTHUMG00000015245	ENST00000229955.3:c.61G>A	6.37:g.97247547C>T	ENSP00000229955:p.Val21Met	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	112	65	0.580357	NM_030784	Q9UJH3	Missense_Mutation	SNP	ENST00000229955.3	37	CCDS5036.1	42	0.019230769230769232	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	32	0.04221635883905013	C	1.757	-0.487707	0.04352	0.006128	0.042442	ENSG00000112218	ENST00000536583;ENST00000417980;ENST00000229955;ENST00000369268	T;T;T	0.62364	0.03;0.03;0.03	5.15	1.33	0.21861	.	0.581476	0.14187	N	0.335586	T	0.16342	0.0393	N	0.14661	0.345	0.19575	N	0.999963	P	0.47910	0.902	B	0.30495	0.116	T	0.04178	-1.0971	10	0.54805	T	0.06	3.6865	6.7606	0.23538	0.0:0.5476:0.1141:0.3383	rs35358396	21	Q9BZJ6	GPR63_HUMAN	M	45;21;21;21	ENSP00000393170:V21M;ENSP00000229955:V21M;ENSP00000358273:V21M	ENSP00000229955:V21M	V	-	1	0	GPR63	97354268	0.038000	0.19896	0.342000	0.25602	0.015000	0.08874	0.083000	0.14871	0.290000	0.22444	-0.769000	0.03391	GTG	C|0.974;T|0.026	0.026	strong		0.468	GPR63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041566.2		
GRIN3B	116444	hgsc.bcm.edu	37	19	1004710	1004710	+	Missense_Mutation	SNP	C	C	T	rs4807399	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1004710C>T	ENST00000234389.3	+	3	1229	c.1210C>T	c.(1210-1212)Cgg>Tgg	p.R404W	GRIN3B_ENST00000588335.1_Intron|AC004528.4_ENST00000588380.1_RNA	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	19	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	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		
NBPF10	100132406	hgsc.bcm.edu	37	1	145323667	145323667	+	Missense_Mutation	SNP	C	C	G	rs199626421		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:145323667C>G	ENST00000342960.5	+	27	3539	c.3504C>G	c.(3502-3504)gaC>gaG	p.D1168E	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	755						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.D1168E(1)		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)		TTAAAAAGGACGAAGAAGAGG	0.468																																					p.D1168E		Atlas-SNP	.											NBPF10,NS,carcinoma,0,6	NBPF10	221	6	1	Substitution - Missense(1)	kidney(1)	c.C3504G						scavenged	.																																			SO:0001583	missense	100132406	exon27			AAAGGACGAAGAA	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.3504C>G	1.37:g.145323667C>G	ENSP00000345684:p.Asp1168Glu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	179	4	0.0223464	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	8.960	0.970347	0.18659	.	.	ENSG00000163386	ENST00000342960	T	0.03272	3.99	.	.	.	.	.	.	.	.	T	0.01905	0.0060	L	0.60455	1.87	0.09310	N	1	.	.	.	.	.	.	T	0.41716	-0.9493	5	0.42905	T	0.14	.	.	.	.	.	.	.	.	E	1168	ENSP00000345684:D1168E	ENSP00000345684:D1168E	D	+	3	2	NBPF10	144035024	0.003000	0.15002	0.002000	0.10522	0.088000	0.18126	0.035000	0.13797	-0.430000	0.07318	0.152000	0.16155	GAC	.	.	weak		0.468	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
PNKP	11284	hgsc.bcm.edu	37	19	50364914	50364914	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50364914C>T	ENST00000322344.3	-	15	1446	c.1337G>A	c.(1336-1338)cGc>cAc	p.R446H	PNKP_ENST00000596014.1_Missense_Mutation_p.R446H|PNKP_ENST00000600910.1_Silent_p.P409P|AC018766.5_ENST00000593654.1_RNA|AC018766.5_ENST00000599259.1_RNA|AC018766.5_ENST00000601893.1_RNA|PNKP_ENST00000600573.1_Missense_Mutation_p.R415H|AC018766.4_ENST00000596624.1_RNA	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	446	Kinase. {ECO:0000250}.				dephosphorylation (GO:0016311)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide phosphorylation (GO:0046939)|nucleotide-excision repair, DNA damage removal (GO:0000718)|polynucleotide 3' dephosphorylation (GO:0098506)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|endonuclease activity (GO:0004519)|nucleotide kinase activity (GO:0019201)|polynucleotide 3'-phosphatase activity (GO:0046403)|purine nucleotide binding (GO:0017076)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|urinary_tract(1)	19		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0118)|OV - Ovarian serous cystadenocarcinoma(262;0.0134)		GAGGAAGCAGCGGCAGGGGAC	0.741								Other BER factors																													p.R446H		Atlas-SNP	.											.	PNKP	71	.	0			c.G1337A						PASS	.						4.0	8.0	7.0					19																	50364914		1965	3897	5862	SO:0001583	missense	11284	exon15			AAGCAGCGGCAGG	AF126486	CCDS12783.1	19q13.3-q13.4	2008-02-05				ENSG00000039650			9154	protein-coding gene	gene with protein product		605610				10446192, 10446193	Standard	NM_007254		Approved	PNK	uc002pqj.3	Q96T60		ENST00000322344.3:c.1337G>A	19.37:g.50364914C>T	ENSP00000323511:p.Arg446His	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	24	4	0.166667	NM_007254	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Missense_Mutation	SNP	ENST00000322344.3	37	CCDS12783.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.885414	0.91814	.	.	ENSG00000039650	ENST00000322344	T	0.48201	0.82	3.96	3.96	0.45880	.	0.000000	0.64402	D	0.000003	T	0.66626	0.2808	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.69435	-0.5146	10	0.54805	T	0.06	-17.9148	11.6883	0.51499	0.0:1.0:0.0:0.0	.	407;446	Q9BUL2;Q96T60	.;PNKP_HUMAN	H	446	ENSP00000323511:R446H	ENSP00000323511:R446H	R	-	2	0	PNKP	55056726	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.989000	0.56958	2.226000	0.72624	0.557000	0.71058	CGC	.	.	none		0.741	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254	
HGFAC	3083	hgsc.bcm.edu	37	4	3446091	3446091	+	Missense_Mutation	SNP	G	G	T	rs3748034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:3446091G>T	ENST00000382774.3	+	6	767	c.652G>T	c.(652-654)Gcc>Tcc	p.A218S	HGFAC_ENST00000511533.1_Missense_Mutation_p.A218S	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	218	Fibronectin type-I. {ECO:0000255|PROSITE- ProRule:PRU00478}.		A -> S (in dbSNP:rs3748034).		proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		CGACCGCTGGGCCCGCGTGCG	0.677													G|||	670	0.133786	0.0159	0.1124	5008	,	,		15900	0.3085		0.1362	False		,,,				2504	0.1258				p.A218S		Atlas-SNP	.											.	HGFAC	69	.	0			c.G652T						PASS	.	G	SER/ALA	150,4202		3,144,2029	13.0	15.0	14.0		652	3.7	1.0	4	dbSNP_107	14	1203,7365		78,1047,3159	yes	missense	HGFAC	NM_001528.2	99	81,1191,5188	TT,TG,GG		14.0406,3.4467,10.4721	benign	218/656	3446091	1353,11567	2176	4284	6460	SO:0001583	missense	3083	exon6			CGCTGGGCCCGCG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.652G>T	4.37:g.3446091G>T	ENSP00000372224:p.Ala218Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	37	0.596774	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	318	0.14560439560439561	9	0.018292682926829267	40	0.11049723756906077	158	0.2762237762237762	111	0.14643799472295516	G	13.29	2.194105	0.38707	0.034467	0.140406	ENSG00000109758	ENST00000382774;ENST00000511533	T;T	0.21031	2.03;2.03	3.74	3.74	0.42951	Fibronectin, type I (4);	0.144554	0.45867	D	0.000328	T	0.00012	0.0000	L	0.45581	1.43	0.38956	P	0.04154599999999997	P;B	0.39094	0.659;0.417	B;B	0.40534	0.332;0.179	T	0.48525	-0.9028	9	0.23302	T	0.38	.	13.0704	0.59057	0.0:0.0:1.0:0.0	rs3748034;rs3748034	218;218	D6RAR4;Q04756	.;HGFA_HUMAN	S	218	ENSP00000372224:A218S;ENSP00000421801:A218S	ENSP00000372224:A218S	A	+	1	0	HGFAC	3415889	0.998000	0.40836	1.000000	0.80357	0.591000	0.36615	2.000000	0.40816	1.925000	0.55765	0.462000	0.41574	GCC	G|0.878;T|0.122	0.122	strong		0.677	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
CHAT	1103	hgsc.bcm.edu	37	10	50854637	50854637	+	Missense_Mutation	SNP	G	G	A	rs8178991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50854637G>A	ENST00000337653.2	+	8	1351	c.1198G>A	c.(1198-1200)Gac>Aac	p.D400N	CHAT_ENST00000351556.3_Missense_Mutation_p.D282N|CHAT_ENST00000455728.2_Missense_Mutation_p.D282N|CHAT_ENST00000339797.1_Missense_Mutation_p.D282N|CHAT_ENST00000395559.2_Missense_Mutation_p.D282N|CHAT_ENST00000395562.2_Missense_Mutation_p.D318N	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	400			D -> N (in dbSNP:rs8178991).		adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	GGAGCTCAGCGACACCCACAG	0.637													G|||	30	0.00599042	0.0015	0.0101	5008	,	,		20906	0.0		0.0199	False		,,,				2504	0.001				p.D400N		Atlas-SNP	.											.	CHAT	162	.	0			c.G1198A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	21,4385	29.0+/-57.7	0,21,2182	92.0	81.0	84.0		844,952,844,1198,844,844,844	4.3	0.9	10	dbSNP_117	84	189,8411	85.0+/-147.5	4,181,4115	yes	missense,missense,missense,missense,missense,missense,missense	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	23,23,23,23,23,23,23	4,202,6297	AA,AG,GG		2.1977,0.4766,1.6146	benign,benign,benign,benign,benign,benign,benign	282/631,318/667,282/631,400/749,282/631,282/631,282/631	50854637	210,12796	2203	4300	6503	SO:0001583	missense	1103	exon8			CTCAGCGACACCC	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.1198G>A	10.37:g.50854637G>A	ENSP00000337103:p.Asp400Asn	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	G	19.11	3.763636	0.69878	0.004766	0.021977	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	T;T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	5.27	4.34	0.51931	.	0.099000	0.64402	D	0.000003	T	0.72277	0.3440	M	0.78223	2.4	0.58432	D	0.999996	B;D	0.56968	0.339;0.978	B;P	0.48524	0.096;0.58	T	0.78738	-0.2087	10	0.51188	T	0.08	-24.4513	10.8728	0.46894	0.0727:0.1312:0.7961:0.0	rs8178991	282;400	F8W8I2;P28329	.;CLAT_HUMAN	N	282;282;282;400;318;282	ENSP00000343486:D282N;ENSP00000345878:D282N;ENSP00000378926:D282N;ENSP00000337103:D400N;ENSP00000378929:D318N;ENSP00000390521:D282N	ENSP00000337103:D400N	D	+	1	0	CHAT	50524643	1.000000	0.71417	0.898000	0.35279	0.926000	0.56050	4.110000	0.57831	1.162000	0.42619	0.655000	0.94253	GAC	G|0.986;A|0.014	0.014	strong		0.637	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
INMT	11185	hgsc.bcm.edu	37	7	30791847	30791847	+	Silent	SNP	C	C	T	rs2240822	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:30791847C>T	ENST00000013222.5	+	1	97	c.81C>T	c.(79-81)ttC>ttT	p.F27F	INMT_ENST00000484180.1_Intron|INMT_ENST00000409539.1_Silent_p.F27F|INMT-FAM188B_ENST00000458257.1_Silent_p.F27F	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	27					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						ACTACAGCTTCGATGGCAGCC	0.572													C|||	151	0.0301518	0.0	0.0	5008	,	,		20032	0.1458		0.001	False		,,,				2504	0.0031				p.F27F		Atlas-SNP	.											.	INMT	38	.	0			c.C81T						PASS	.	C	,	0,4406		0,0,2203	119.0	113.0	115.0		81,81	-2.9	0.0	7	dbSNP_98	115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	INMT	NM_001199219.1,NM_006774.4	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	27/263,27/264	30791847	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11185	exon1			CAGCTTCGATGGC		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.81C>T	7.37:g.30791847C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	137	41	0.29927	NM_001199219	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Silent	SNP	ENST00000013222.5	37	CCDS5430.1																																																																																			C|0.981;T|0.019	0.019	strong		0.572	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
SBDS	51119	hgsc.bcm.edu	37	7	66453460	66453460	+	Silent	SNP	G	G	A	rs73151675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:66453460G>A	ENST00000246868.2	-	5	834	c.651C>T	c.(649-651)ttC>ttT	p.F217F		NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	217					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						CAATTTCTCGGAAGCAGCCCG	0.378			Gene Conversion			"""AML, MDS"""			Shwachman-Diamond syndrome				G|||	91	0.0181709	0.0038	0.0187	5008	,	,		21080	0.001		0.0626	False		,,,				2504	0.0092				p.F217F		Atlas-SNP	.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS	20	.	0			c.C651T						PASS	.	G		40,4366	43.8+/-77.6	0,40,2163	104.0	95.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	651	4.2	1.0	7	dbSNP_130	98	472,8128	139.0+/-195.8	12,448,3840	no	coding-synonymous	SBDS	NM_016038.2		12,488,6003	AA,AG,GG		5.4884,0.9079,3.9366		217/251	66453460	512,12494	2203	4300	6503	SO:0001819	synonymous_variant	51119	exon5	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	TTCTCGGAAGCAG	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.651C>T	7.37:g.66453460G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	149	44	0.295302	NM_016038	A8K0P4|Q96FX0|Q9NV53	Silent	SNP	ENST00000246868.2	37	CCDS5537.1																																																																																			G|0.962;A|0.038	0.038	strong		0.378	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038	
GLTPD2	388323	hgsc.bcm.edu	37	17	4692559	4692559	+	Missense_Mutation	SNP	G	G	T	rs2304969	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4692559G>T	ENST00000331264.7	+	2	198	c.145G>T	c.(145-147)Gtt>Ttt	p.V49F	VMO1_ENST00000354194.4_5'Flank|VMO1_ENST00000328739.5_5'Flank|VMO1_ENST00000416307.2_5'Flank|VMO1_ENST00000441199.2_5'Flank	NM_001014985.2	NP_001014985	A6NH11	GLTD2_HUMAN	glycolipid transfer protein domain containing 2	49						cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4						GCAGCCCTGCGTTCCAGGGGA	0.701													G|||	1370	0.273562	0.1369	0.1715	5008	,	,		13658	0.506		0.159	False		,,,				2504	0.409				p.V49F		Atlas-SNP	.											.	GLTPD2	15	.	0			c.G145T						PASS	.	G	PHE/VAL	630,3756		44,542,1607	10.0	12.0	12.0		145	-0.4	0.0	17	dbSNP_100	12	1217,7343		95,1027,3158	yes	missense	GLTPD2	NM_001014985.2	50	139,1569,4765	TT,TG,GG		14.2173,14.3639,14.267	benign	49/292	4692559	1847,11099	2193	4280	6473	SO:0001583	missense	388323	exon2			CCCTGCGTTCCAG	BC029290	CCDS32534.1	17p13.2	2007-12-19				ENSG00000182327			33756	protein-coding gene	gene with protein product							Standard	NM_001014985		Approved		uc002fza.2	A6NH11		ENST00000331264.7:c.145G>T	17.37:g.4692559G>T	ENSP00000328070:p.Val49Phe	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_001014985	A7E2T2	Missense_Mutation	SNP	ENST00000331264.7	37	CCDS32534.1	535	0.24496336996336995	72	0.14634146341463414	57	0.1574585635359116	276	0.4825174825174825	130	0.17150395778364116	G	15.52	2.857505	0.51376	0.143639	0.142173	ENSG00000182327	ENST00000331264	.	.	.	4.3	-0.367	0.12541	.	1.040650	0.07588	N	0.921514	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P	0.45768	0.866	B	0.41691	0.364	T	0.45469	-0.9259	8	0.59425	D	0.04	-13.4729	7.1891	0.25816	0.5324:0.0:0.4676:0.0	rs2304969;rs2304969	49	A6NH11	GLTD2_HUMAN	F	49	.	ENSP00000328070:V49F	V	+	1	0	GLTPD2	4639299	0.000000	0.05858	0.006000	0.13384	0.016000	0.09150	-0.045000	0.12003	0.013000	0.14918	-0.367000	0.07326	GTT	G|0.753;T|0.247	0.247	strong		0.701	GLTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439781.1	NM_001014985	
AKAP9	10142	hgsc.bcm.edu	37	7	91691601	91691601	+	Silent	SNP	C	C	T	rs10236397	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91691601C>T	ENST00000359028.2	+	25	6039	c.5814C>T	c.(5812-5814)ggC>ggT	p.G1938G	AKAP9_ENST00000356239.3_Silent_p.G1926G|AKAP9_ENST00000491695.1_3'UTR|AKAP9_ENST00000358100.2_Silent_p.G1938G			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1938	Glu-rich.				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)			TCATTGATGGCTATGCAGATG	0.308			T	BRAF	papillary thyroid								C|||	1802	0.359824	0.4561	0.3559	5008	,	,		17846	0.1617		0.3857	False		,,,				2504	0.41				p.G1926G		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C5778T						PASS	.	C	,	2096,2310	554.0+/-378.9	497,1102,604	71.0	79.0	76.0		5778,5778	-1.1	1.0	7	dbSNP_119	76	3467,5133	505.5+/-376.4	678,2111,1511	no	coding-synonymous,coding-synonymous	AKAP9	NM_005751.4,NM_147185.2	,	1175,3213,2115	TT,TC,CC		40.314,47.5715,42.7726	,	1926/3908,1926/3900	91691601	5563,7443	2203	4300	6503	SO:0001819	synonymous_variant	10142	exon24			TGATGGCTATGCA	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.5814C>T	7.37:g.91691601C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	185	185	1	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				C|0.605;T|0.395	0.395	strong		0.308	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
C10orf67	256815	hgsc.bcm.edu	37	10	23633566	23633566	+	Silent	SNP	C	C	A	rs2036917	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:23633566C>A	ENST00000323327.4	-	1	208	c.141G>T	c.(139-141)cgG>cgT	p.R47R	RP11-371A19.2_ENST00000443224.1_RNA	NM_153714.2	NP_714925.2	Q8IYJ2	CJ067_HUMAN	chromosome 10 open reading frame 67	47										central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)	5						CGCAGCAGACCCGCAGCTCGG	0.612													C|||	3379	0.67472	0.7277	0.6599	5008	,	,		14886	0.8562		0.4771	False		,,,				2504	0.6299				p.R47R		Atlas-SNP	.											C10orf67,NS,carcinoma,0,1	C10orf67	21	1	0			c.G141T						PASS	.	C		2741,1125		992,757,184	22.0	24.0	23.0		141	-2.6	0.0	10	dbSNP_94	23	4020,4234		998,2024,1105	no	coding-synonymous	C10orf67	NM_153714.2		1990,2781,1289	AA,AC,CC		48.7037,29.0998,44.2162		47/186	23633566	6761,5359	1933	4127	6060	SO:0001819	synonymous_variant	256815	exon1			GCAGACCCGCAGC	BC035732	CCDS44365.1	10p12.31	2012-05-31			ENSG00000179133	ENSG00000179133			28716	protein-coding gene	gene with protein product						12477932	Standard	NM_153714		Approved	MGC46732	uc010qcx.2	Q8IYJ2	OTTHUMG00000017818	ENST00000323327.4:c.141G>T	10.37:g.23633566C>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	92	56	0.608696	NM_153714	A8MUP9|Q5SWD4	Silent	SNP	ENST00000323327.4	37	CCDS44365.1																																																																																			C|0.343;A|0.657	0.657	strong		0.612	C10orf67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047213.1	NM_153714	
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238453	71238453	+	Missense_Mutation	SNP	G	G	C	rs147685834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:71238453G>C	ENST00000398536.4	+	1	141	c.107G>C	c.(106-108)tGt>tCt	p.C36S		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	36	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						TCCAGCTGCTGTGTGCCCGTC	0.682													g|||	1257	0.250998	0.2088	0.2233	5008	,	,		10723	0.2877		0.1918	False		,,,				2504	0.3507				p.C36S		Atlas-SNP	.											KRTAP5-7,NS,carcinoma,0,1	KRTAP5-7	23	1	0			c.G107C						PASS	.	G	SER/CYS	856,3544		65,726,1409	69.0	90.0	83.0		107	1.8	1.0	11	dbSNP_134	83	1314,7270		110,1094,3088	no	missense	KRTAP5-7	NM_001012503.1	112	175,1820,4497	CC,CG,GG		15.3075,19.4545,16.7129	possibly-damaging	36/166	71238453	2170,10814	2200	4292	6492	SO:0001583	missense	440050	exon1			GCTGCTGTGTGCC	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"""Keratin associated proteins"""	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.107G>C	11.37:g.71238453G>C	ENSP00000417330:p.Cys36Ser	Somatic	277	1	0.00361011		WXS	Illumina HiSeq	Phase_I	252	121	0.480159	NM_001012503	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	37	CCDS41682.1	497	0.22756410256410256	100	0.2032520325203252	86	0.23756906077348067	173	0.30244755244755245	138	0.1820580474934037	N	6.704	0.498625	0.12762	0.194545	0.153075	ENSG00000244411	ENST00000398536	T	0.01397	4.94	1.8	1.8	0.24995	.	.	.	.	.	T	0.00012	0.0000	M	0.89658	3.05	0.43608	P	0.004022999999999999	P	0.47106	0.89	P	0.54965	0.765	T	0.33624	-0.9861	8	0.54805	T	0.06	.	7.1256	0.25469	0.0:0.0:1.0:0.0	.	36	Q6L8G8	KRA57_HUMAN	S	36	ENSP00000417330:C36S	ENSP00000417330:C36S	C	+	2	0	KRTAP5-7	70916101	1.000000	0.71417	0.978000	0.43139	0.179000	0.23085	3.185000	0.50934	1.345000	0.45676	0.281000	0.19383	TGT	G|0.807;C|0.193	0.193	strong		0.682	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1		
ACADM	34	hgsc.bcm.edu	37	1	76227022	76227022	+	Silent	SNP	A	A	G	rs1061337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:76227022A>G	ENST00000370841.4	+	11	1598	c.1161A>G	c.(1159-1161)gtA>gtG	p.V387V	ACADM_ENST00000420607.2_Silent_p.V391V|ACADM_ENST00000541113.1_Silent_p.V351V|ACADM_ENST00000543667.1_Silent_p.V198V|ACADM_ENST00000481374.1_3'UTR|ACADM_ENST00000370834.5_Silent_p.V420V	NM_000016.4|NM_001127328.1	NP_000007.1|NP_001120800.1	P11310	ACADM_HUMAN	acyl-CoA dehydrogenase, C-4 to C-12 straight chain	387					cardiac muscle cell differentiation (GO:0055007)|carnitine biosynthetic process (GO:0045329)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|glycogen biosynthetic process (GO:0005978)|liver development (GO:0001889)|medium-chain fatty acid catabolic process (GO:0051793)|medium-chain fatty acid metabolic process (GO:0051791)|oxidation-reduction process (GO:0055114)|post-embryonic development (GO:0009791)|regulation of gluconeogenesis (GO:0006111)|response to cold (GO:0009409)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|identical protein binding (GO:0042802)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)			breast(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|skin(1)	18					Flavin adenine dinucleotide(DB03147)	AATATCCTGTAGAAAAACTAA	0.358													A|||	873	0.174321	0.1362	0.2522	5008	,	,		16861	0.0228		0.3002	False		,,,				2504	0.1973				p.V391V		Atlas-SNP	.											.	ACADM	50	.	0			c.A1173G						PASS	.	A	,	700,3706	293.6+/-282.7	59,582,1562	116.0	110.0	112.0		1161,1173	-0.3	1.0	1	dbSNP_86	112	2551,6049	416.2+/-352.0	393,1765,2142	no	coding-synonymous,coding-synonymous	ACADM	NM_000016.4,NM_001127328.1	,	452,2347,3704	GG,GA,AA		29.6628,15.8874,24.9962	,	387/422,391/426	76227022	3251,9755	2203	4300	6503	SO:0001819	synonymous_variant	34	exon11			TCCTGTAGAAAAA	M16827	CCDS668.1, CCDS44165.1, CCDS65562.1, CCDS72807.1	1p31	2014-09-17	2010-04-30		ENSG00000117054	ENSG00000117054	1.3.99.3		89	protein-coding gene	gene with protein product		607008	"""acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain"""			3035565	Standard	NM_000016		Approved	MCAD, MCADH, ACAD1	uc009wbp.3	P11310	OTTHUMG00000009784	ENST00000370841.4:c.1161A>G	1.37:g.76227022A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	69	54	0.782609	NM_001127328	Q5T4U4|Q9NYF1	Silent	SNP	ENST00000370841.4	37	CCDS668.1																																																																																			A|0.777;G|0.223	0.223	strong		0.358	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1		
KIAA0226	9711	hgsc.bcm.edu	37	3	197427557	197427557	+	Silent	SNP	A	A	G	rs28394098	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:197427557A>G	ENST00000296343.5	-	7	1187	c.1188T>C	c.(1186-1188)acT>acC	p.T396T	KIAA0226_ENST00000389665.5_Silent_p.T396T|KIAA0226_ENST00000449205.1_Silent_p.T396T|KIAA0226_ENST00000273582.5_Silent_p.T336T|KIAA0226_ENST00000467303.1_5'Flank	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	396	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)		CACTGGTGACAGTGAGTGTCT	0.577													G|||	697	0.139177	0.3169	0.0677	5008	,	,		17652	0.0308		0.1034	False		,,,				2504	0.0982				p.T396T	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.T1188C						PASS	.	G	,	1134,2944		137,860,1042	77.0	80.0	79.0		1008,1188	-2.2	0.0	3	dbSNP_125	79	789,7585		38,713,3436	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	175,1573,4478	GG,GA,AA		9.422,27.8077,15.4433	,	336/928,396/973	197427557	1923,10529	2039	4187	6226	SO:0001819	synonymous_variant	9711	exon7			GGTGACAGTGAGT	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.1188T>C	3.37:g.197427557A>G		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	180	76	0.422222	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	271|271	0.12408424908424909|0.12408424908424909	142|142	0.2886178861788618|0.2886178861788618	27|27	0.07458563535911603|0.07458563535911603	24|24	0.04195804195804196|0.04195804195804196	78|78	0.10290237467018469|0.10290237467018469	G|G	6.290|6.290	0.421625|0.421625	0.11928|0.11928	0.278077|0.278077	0.09422|0.09422	ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000415452	.|.	.|.	.|.	5.85|5.85	-2.21|-2.21	0.06973|0.06973	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.33033|0.33033	-0.9884|-0.9884	3|3	.|.	.|.	.|.	.|.	7.4519|7.4519	0.27244|0.27244	0.411:0.2206:0.3684:0.0|0.411:0.2206:0.3684:0.0	rs28394098|rs28394098	.|.	.|.	.|.	R|P	375|155	.|.	.|.	C|L	-|-	1|2	0|0	KIAA0226|KIAA0226	198911954|198911954	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.820000|0.820000	0.46376|0.46376	-0.445000|-0.445000	0.06845|0.06845	-0.698000|-0.698000	0.05085|0.05085	-1.073000|-1.073000	0.02249|0.02249	TGT|CTG	A|0.885;G|0.115	0.115	strong		0.577	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
STKLD1	169436	hgsc.bcm.edu	37	9	136268912	136268912	+	Silent	SNP	A	A	G	rs28510482	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	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		
ANKDD1A	348094	hgsc.bcm.edu	37	15	65236875	65236875	+	Silent	SNP	T	T	C	rs2414865	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65236875T>C	ENST00000380230.3	+	12	1121	c.1092T>C	c.(1090-1092)gcT>gcC	p.A364A	ANKDD1A_ENST00000395723.1_Intron|ANKDD1A_ENST00000357698.3_Intron|ANKDD1A_ENST00000395720.1_Silent_p.A364A	NM_182703.3	NP_874362.3	Q495B1	AKD1A_HUMAN	ankyrin repeat and death domain containing 1A	364					signal transduction (GO:0007165)					NS(1)|endometrium(1)|large_intestine(10)|liver(2)|lung(4)|ovary(1)|prostate(2)	21						TGGCAGTGGCTGTCCGCAGCA	0.517													C|||	2769	0.552915	0.7489	0.3573	5008	,	,		19859	0.3909		0.4463	False		,,,				2504	0.7035				p.A364A		Atlas-SNP	.											.	ANKDD1A	47	.	0			c.T1092C						PASS	.	C		3150,1254	429.9+/-342.4	1130,890,182	77.0	68.0	71.0		1092	-3.0	0.9	15	dbSNP_100	71	3963,4635	600.8+/-394.3	930,2103,1266	no	coding-synonymous	ANKDD1A	NM_182703.3		2060,2993,1448	CC,CT,TT		46.0921,28.4741,45.293		364/523	65236875	7113,5889	2202	4299	6501	SO:0001819	synonymous_variant	348094	exon12			AGTGGCTGTCCGC		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.1092T>C	15.37:g.65236875T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_182703	Q495B2|Q495B3|Q8N7A0|Q8NBS5	Silent	SNP	ENST00000380230.3	37	CCDS10197.2																																																																																			T|0.460;C|0.540	0.540	strong		0.517	ANKDD1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256705.2	NM_182703	
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T	rs77807247	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31914019C>T	ENST00000334046.5	-	1	164	c.134G>A	c.(133-135)cGc>cAc	p.R45H		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	45						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						GCATGATGGGCGGCAGCAGCC	0.498													c|||	161	0.0321486	0.1135	0.0115	5008	,	,		14661	0.0		0.001	False		,,,				2504	0.002				p.R45H		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.G134A						PASS	.	C	HIS/ARG	371,4035	188.5+/-214.9	13,345,1845	110.0	120.0	116.0		134	-6.1	0.0	21	dbSNP_131	116	12,8588	9.8+/-36.6	0,12,4288	yes	missense	KRTAP19-6	NM_181612.2	29	13,357,6133	TT,TC,CC		0.1395,8.4203,2.9448	benign	45/59	31914019	383,12623	2203	4300	6503	SO:0001583	missense	337973	exon1			GATGGGCGGCAGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.134G>A	21.37:g.31914019C>T	ENSP00000375107:p.Arg45His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	141	47	0.333333	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	64	0.029304029304029304	58	0.11788617886178862	6	0.016574585635359115	0	0.0	0	0.0	c	6.926	0.540492	0.13250	0.084203	0.001395	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.11169	2.8	4.39	-6.09	0.02145	.	0.598882	0.13443	N	0.387478	T	0.00109	0.0003	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.32587	-0.9901	9	0.87932	D	0	-1.818	7.3473	0.26670	0.1168:0.3112:0.0:0.5719	.	45	Q3LI70	KR196_HUMAN	H	45	ENSP00000375107:R45H	ENSP00000375107:R45H	R	-	2	0	KRTAP19-6	30835890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.929000	0.03976	-1.347000	0.02208	-1.903000	0.00527	CGC	C|0.969;T|0.031	0.031	strong		0.498	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
PTK2B	2185	hgsc.bcm.edu	37	8	27301725	27301725	+	Silent	SNP	C	C	G	rs1128435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:27301725C>G	ENST00000397501.1	+	28	2959	c.2151C>G	c.(2149-2151)ccC>ccG	p.P717P	PTK2B_ENST00000397497.4_Silent_p.P463P|PTK2B_ENST00000338238.4_Silent_p.P717P|PTK2B_ENST00000420218.2_Silent_p.P717P|PTK2B_ENST00000517339.1_Silent_p.P717P|PTK2B_ENST00000346049.5_Silent_p.P717P|PTK2B_ENST00000544172.1_Silent_p.P717P	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	717	Pro-rich.				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)	CTCTCCAGCCCAGCCGACCTA	0.532													C|||	520	0.103834	0.0325	0.0648	5008	,	,		20200	0.1419		0.1014	False		,,,				2504	0.1912				p.P717P		Atlas-SNP	.											PTK2B_ENST00000544172,bladder,carcinoma,+1,3	PTK2B	304	3	0			c.C2151G						PASS	.	C	,,,	162,4244	108.6+/-147.0	3,156,2044	128.0	113.0	118.0		2151,2151,2151,2151	4.3	1.0	8	dbSNP_86	118	926,7674	205.2+/-247.7	57,812,3431	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	60,968,5475	GG,GC,CC		10.7674,3.6768,8.3654	,,,	717/1010,717/1010,717/968,717/1010	27301725	1088,11918	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon28			CCAGCCCAGCCGA	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.2151C>G	8.37:g.27301725C>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	147	52	0.353741	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			C|0.913;G|0.087	0.087	strong		0.532	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
MS4A5	64232	hgsc.bcm.edu	37	11	60197299	60197299	+	Splice_Site	SNP	G	G	A	rs34169848	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:60197299G>A	ENST00000300190.2	+	1	238	c.152G>A	c.(151-153)gGg>gAg	p.G51E	MS4A5_ENST00000534071.1_3'UTR	NM_023945.2	NP_076434.2	Q9H3V2	MS4A5_HUMAN	membrane-spanning 4-domains, subfamily A, member 5	51						integral component of membrane (GO:0016021)				large_intestine(7)|lung(7)|ovary(1)|skin(1)	16						AAAATCTTAGGGGTAAGTAAG	0.403													G|||	80	0.0159744	0.0008	0.0259	5008	,	,		19383	0.0		0.0507	False		,,,				2504	0.0102				p.G51E		Atlas-SNP	.											.	MS4A5	35	.	0			c.G152A						PASS	.	G	GLU/GLY	58,4348	53.6+/-89.4	0,58,2145	48.0	53.0	51.0		152	4.7	1.0	11	dbSNP_126	51	508,8092	142.2+/-198.4	10,488,3802	yes	missense-near-splice	MS4A5	NM_023945.2	98	10,546,5947	AA,AG,GG		5.907,1.3164,4.3518	probably-damaging	51/201	60197299	566,12440	2203	4300	6503	SO:0001630	splice_region_variant	64232	exon1			TCTTAGGGGTAAG	AB013103	CCDS7987.1	11q12	2008-03-25			ENSG00000166930	ENSG00000166930			13374	protein-coding gene	gene with protein product		606499				11245982, 11401424	Standard	NM_023945		Approved	CD20L2	uc001npo.3	Q9H3V2	OTTHUMG00000167613	ENST00000300190.2:c.153+1G>A	11.37:g.60197299G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	28	10	0.357143	NM_023945	Q9BZH1	Missense_Mutation	SNP	ENST00000300190.2	37	CCDS7987.1	41	0.018772893772893772	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	14.87	2.665848	0.47677	0.013164	0.05907	ENSG00000166930	ENST00000300190	T	0.10192	2.9	4.66	4.66	0.58398	.	0.118079	0.64402	D	0.000018	T	0.05456	0.0144	M	0.88105	2.93	0.39099	D	0.961245	D	0.89917	1.0	D	0.97110	1.0	T	0.03969	-1.0988	10	0.87932	D	0	-5.9109	13.2445	0.60016	0.0:0.0:1.0:0.0	rs34169848;rs34169848	51	Q9H3V2	MS4A5_HUMAN	E	51	ENSP00000300190:G51E	ENSP00000300190:G51E	G	+	2	0	MS4A5	59953875	1.000000	0.71417	1.000000	0.80357	0.152000	0.21847	3.950000	0.56676	2.578000	0.87016	0.467000	0.42956	GGG	G|0.965;A|0.035	0.035	strong		0.403	MS4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395392.1		Missense_Mutation
UNC13A	23025	hgsc.bcm.edu	37	19	17741047	17741047	+	Silent	SNP	A	A	G	rs10413821	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17741047A>G	ENST00000519716.2	-	30	3575	c.3576T>C	c.(3574-3576)gtT>gtC	p.V1192V	UNC13A_ENST00000428389.2_Silent_p.V1280V|UNC13A_ENST00000552293.1_Silent_p.V1192V|UNC13A_ENST00000252773.7_Silent_p.V1192V|UNC13A_ENST00000551649.1_Silent_p.V1192V|UNC13A_ENST00000550896.1_Silent_p.V1190V	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1192	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						GTTGGGAGAAAACATCCACCA	0.547													G|||	2404	0.480032	0.8517	0.451	5008	,	,		19359	0.2966		0.3459	False		,,,				2504	0.3252				p.V1192V		Atlas-SNP	.											.	UNC13A	299	.	0			c.T3576C						PASS	.			3221,985		1248,725,130	42.0	45.0	44.0		3576	3.5	1.0	19	dbSNP_119	44	2927,5509		560,1807,1851	no	coding-synonymous	UNC13A	NM_001080421.2		1808,2532,1981	GG,GA,AA		34.6965,23.4189,48.6315		1192/1704	17741047	6148,6494	2103	4218	6321	SO:0001819	synonymous_variant	23025	exon29			GGAGAAAACATCC	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.3576T>C	19.37:g.17741047A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	136	67	0.492647	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			A|0.571;G|0.429	0.429	strong		0.547	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
KPNB1	3837	hgsc.bcm.edu	37	17	45734285	45734285	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45734285T>C	ENST00000290158.4	+	4	749	c.342T>C	c.(340-342)gcT>gcC	p.A114A	KPNB1_ENST00000537679.1_5'Flank|KPNB1_ENST00000535458.2_5'UTR|KPNB1_ENST00000540627.1_5'UTR|KPNB1_ENST00000577918.1_3'UTR	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	114					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cytokine-mediated signaling pathway (GO:0019221)|intracellular transport of virus (GO:0075733)|NLS-bearing protein import into nucleus (GO:0006607)|protein import into nucleus (GO:0006606)|protein import into nucleus, translocation (GO:0000060)|ribosomal protein import into nucleus (GO:0006610)|small molecule metabolic process (GO:0044281)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum tubular network (GO:0071782)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|ovary(1)|pancreas(1)|skin(1)	4						AGTGTGTGGCTGGTATTGCTT	0.468																																					p.H114H		Atlas-SNP	.											.	KPNB1	58	.	0			c.C342C						PASS	.						138.0	121.0	127.0					17																	45734285		2203	4300	6503	SO:0001819	synonymous_variant	3837	exon4			TGTGGCTGGTATT	L39793	CCDS11513.1, CCDS62228.1	17q21.32	2013-02-14			ENSG00000108424	ENSG00000108424		"""Importins"", ""Armadillo repeat containing"""	6400	protein-coding gene	gene with protein product	"""importin 1"""	602738				7615630, 7627554	Standard	NM_002265		Approved	NTF97, IPOB, MGC2155, MGC2156, MGC2157, IMB1, Impnb, IPO1	uc002ilt.2	Q14974	OTTHUMG00000036957	ENST00000290158.4:c.342T>C	17.37:g.45734285T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	111	46	0.414414	NM_002265	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Silent	SNP	ENST00000290158.4	37	CCDS11513.1																																																																																			.	.	none		0.468	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265	
TSSK1B	83942	hgsc.bcm.edu	37	5	112769997	112769997	+	Silent	SNP	C	C	T	rs34936289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:112769997C>T	ENST00000390666.3	-	1	731	c.540G>A	c.(538-540)gcG>gcA	p.A180A	CTD-2201G3.1_ENST00000416046.2_RNA|CTD-2201G3.1_ENST00000383058.4_RNA|CTD-2201G3.1_ENST00000510381.2_RNA|MCC_ENST00000408903.3_Intron	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	180	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		GGGCCGCATACGCTGGTGACC	0.572													C|||	657	0.13119	0.3253	0.0634	5008	,	,		20988	0.0962		0.0467	False		,,,				2504	0.0399				p.A180A		Atlas-SNP	.											TSSK1B_ENST00000390666,colon,carcinoma,-1,2	TSSK1B	89	2	0			c.G540A						scavenged	.	C	,	1163,3241	406.6+/-333.9	147,869,1186	60.0	59.0	60.0		,540	-2.5	1.0	5	dbSNP_126	60	453,8147	135.1+/-192.4	13,427,3860	no	intron,coding-synonymous	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,	160,1296,5046	TT,TC,CC		5.2674,26.4078,12.4269	,	,180/368	112769997	1616,11388	2202	4300	6502	SO:0001819	synonymous_variant	83942	exon1			CGCATACGCTGGT	AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"""serine/threonine kinase 22D (spermiogenesis associated)"", ""testis-specific serine kinase 1"""	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.540G>A	5.37:g.112769997C>T		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_032028	B2R8D9	Silent	SNP	ENST00000390666.3	37	CCDS4112.1																																																																																			C|0.896;T|0.104	0.104	strong		0.572	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028	
SLC26A2	1836	hgsc.bcm.edu	37	5	149361221	149361221	+	Missense_Mutation	SNP	A	A	T	rs3776070	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149361221A>T	ENST00000286298.4	+	3	2333	c.2065A>T	c.(2065-2067)Act>Tct	p.T689S		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	689	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.		T -> S (in dbSNP:rs3776070).		3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			GTGCAATCCCACTGTGAGGGA	0.423													T|||	966	0.192891	0.3109	0.2738	5008	,	,		21544	0.1022		0.159	False		,,,				2504	0.1043				p.T689S		Atlas-SNP	.											.	SLC26A2	48	.	0			c.A2065T						PASS	.	T	SER/THR	1270,3136	700.3+/-406.6	175,920,1108	59.0	61.0	60.0		2065	5.7	1.0	5	dbSNP_107	60	1251,7349	760.8+/-407.6	86,1079,3135	yes	missense	SLC26A2	NM_000112.3	58	261,1999,4243	TT,TA,AA		14.5465,28.8243,19.3834	benign	689/740	149361221	2521,10485	2203	4300	6503	SO:0001583	missense	1836	exon3			AATCCCACTGTGA	U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"""Solute carriers"""	10994	protein-coding gene	gene with protein product		606718	"""solute carrier family 26 (sulfate transporter), member 2"""	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.2065A>T	5.37:g.149361221A>T	ENSP00000286298:p.Thr689Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_000112	A8K2U3|B2R6J1|Q6N051	Missense_Mutation	SNP	ENST00000286298.4	37	CCDS4300.1	416	0.19047619047619047	141	0.2865853658536585	89	0.24585635359116023	69	0.12062937062937062	117	0.15435356200527706	T	0.011	-1.700543	0.00725	0.288243	0.145465	ENSG00000155850	ENST00000286298	D	0.87571	-2.27	5.72	5.72	0.89469	Sulphate transporter/antisigma-factor antagonist STAS (4);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00690	-1.25	0.45662	P	0.001415000000000055	B	0.02656	0.0	B	0.06405	0.002	T	0.06356	-1.0831	9	0.06625	T	0.88	.	12.3382	0.55079	0.1268:0.0:0.0:0.8732	rs3776070;rs52815587;rs60210541;rs3776070	689	P50443	S26A2_HUMAN	S	689	ENSP00000286298:T689S	ENSP00000286298:T689S	T	+	1	0	SLC26A2	149341414	0.995000	0.38212	0.977000	0.42913	0.148000	0.21650	2.480000	0.45206	1.001000	0.39076	-0.257000	0.10917	ACT	A|0.811;T|0.190	0.190	strong		0.423	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112	
ZFP69	339559	hgsc.bcm.edu	37	1	40961603	40961603	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:40961603C>A	ENST00000372706.1	+	6	2459	c.1453C>A	c.(1453-1455)Cat>Aat	p.H485N	RP11-656D10.3_ENST00000450713.1_RNA|ZFP69_ENST00000372705.3_Missense_Mutation_p.H485N			Q49AA0	ZFP69_HUMAN	ZFP69 zinc finger protein	485					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CTTTAAAAAACATCAGAGACA	0.388																																					p.H485N		Atlas-SNP	.											ZNF642,NS,carcinoma,0,1	.	.	1	0			c.C1453A						scavenged	.						67.0	66.0	66.0					1																	40961603		2203	4300	6503	SO:0001583	missense	339559	exon6			AAAAAACATCAGA	AK122618	CCDS30686.1	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187815	ENSG00000187815		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	24708	protein-coding gene	gene with protein product	"""ZFP69 zinc finger protein A"""		"""zinc finger protein 642"""	ZNF642			Standard	XM_005270808		Approved	ZKSCAN23A, FLJ16030, ZFP69A, ZSCAN54A	uc001cfo.3	Q49AA0	OTTHUMG00000007303	ENST00000372706.1:c.1453C>A	1.37:g.40961603C>A	ENSP00000361791:p.His485Asn	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	121	3	0.0247934	NM_198494	Q5SWM5|Q6ZWK8	Missense_Mutation	SNP	ENST00000372706.1	37	CCDS30686.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.168280	0.78339	.	.	ENSG00000187815	ENST00000372706;ENST00000372705	D;D	0.86865	-2.18;-2.18	4.51	4.51	0.55191	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42964	D	0.000628	D	0.94761	0.8309	M	0.92880	3.355	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	D	0.95476	0.8556	10	0.87932	D	0	-12.0572	15.5403	0.76039	0.0:1.0:0.0:0.0	.	485	Q49AA0	ZN642_HUMAN	N	485	ENSP00000361791:H485N;ENSP00000361790:H485N	ENSP00000361790:H485N	H	+	1	0	ZNF642	40734190	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.676000	0.68131	2.786000	0.95864	0.561000	0.74099	CAT	.	.	none		0.388	ZFP69-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019082.1	NM_198494	
ZNF395	55893	hgsc.bcm.edu	37	8	28210808	28210808	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:28210808T>G	ENST00000344423.5	-	5	832	c.701A>C	c.(700-702)cAc>cCc	p.H234P	ZNF395_ENST00000523202.1_Missense_Mutation_p.H234P|ZNF395_ENST00000523095.1_Missense_Mutation_p.H234P	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	234					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)	p.H234fs*19(1)|p.H234P(1)		cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GGCCTGGGGGTGGGGGGGCGA	0.607																																					p.H234P		Atlas-SNP	.											ZNF395,rectum,carcinoma,0,1	ZNF395	54	1	2	Substitution - Missense(1)|Insertion - Frameshift(1)	large_intestine(2)	c.A701C						scavenged	.						16.0	21.0	19.0					8																	28210808		2199	4291	6490	SO:0001583	missense	55893	exon5			TGGGGGTGGGGGG	AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"""Zinc fingers, C2H2-type"""	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.701A>C	8.37:g.28210808T>G	ENSP00000340494:p.His234Pro	Somatic	139	11	0.0791367		WXS	Illumina HiSeq	Phase_I	180	11	0.0611111	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Missense_Mutation	SNP	ENST00000344423.5	37	CCDS6067.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.620677	0.46736	.	.	ENSG00000186918	ENST00000344423;ENST00000523202;ENST00000523095	T;T;T	0.54279	0.58;0.58;0.58	5.25	4.11	0.48088	.	0.377447	0.31909	N	0.006861	T	0.58018	0.2093	L	0.39633	1.23	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	T	0.55811	-0.8082	10	0.38643	T	0.18	-24.2445	8.5494	0.33442	0.0:0.0911:0.0:0.9089	.	234	Q9H8N7	ZN395_HUMAN	P	234	ENSP00000340494:H234P;ENSP00000429640:H234P;ENSP00000428452:H234P	ENSP00000340494:H234P	H	-	2	0	ZNF395	28266727	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.683000	0.46943	1.988000	0.58038	0.459000	0.35465	CAC	.	.	none		0.607	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1		
KIAA2018	205717	hgsc.bcm.edu	37	3	113376113	113376113	+	Silent	SNP	C	C	T	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1472Q			Q68DE3	K2018_HUMAN	KIAA2018	1472	Gln-rich.					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						gttgctgttgctgctgctgct	0.502																																					p.Q1472Q		Atlas-SNP	.											KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	0			c.G4416A						scavenged	.						68.0	71.0	70.0					3																	113376113		2188	4274	6462	SO:0001819	synonymous_variant	205717	exon7			CTGTTGCTGCTGC	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.4416G>A	3.37:g.113376113C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	69	3	0.0434783	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	weak		0.502	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
MYEOV	26579	hgsc.bcm.edu	37	11	69063726	69063726	+	Missense_Mutation	SNP	G	G	T	rs142581206	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:69063726G>T	ENST00000308946.3	+	3	1259	c.809G>T	c.(808-810)gGg>gTg	p.G270V	MYEOV_ENST00000535407.1_Missense_Mutation_p.G212V|MYEOV_ENST00000441339.2_Missense_Mutation_p.G270V	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	270										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)		GAGGCCCTGGGGGGGTGGCGC	0.677													G|||	14	0.00279553	0.0053	0.0014	5008	,	,		15577	0.003		0.001	False		,,,				2504	0.002				p.G270V		Atlas-SNP	.											MYEOV,NS,carcinoma,-1,1	MYEOV	42	1	0			c.G809T						PASS	.	G	VAL/GLY	16,4384	21.2+/-45.6	0,16,2184	45.0	48.0	47.0		809	-0.7	0.0	11	dbSNP_134	47	22,8566	14.6+/-50.1	0,22,4272	yes	missense	MYEOV	NM_138768.2	109	0,38,6456	TT,TG,GG		0.2562,0.3636,0.2926	possibly-damaging	270/314	69063726	38,12950	2200	4294	6494	SO:0001583	missense	26579	exon3			CCCTGGGGGGGTG	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.809G>T	11.37:g.69063726G>T	ENSP00000308330:p.Gly270Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	7.338	0.620407	0.14193	0.003636	0.002562	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.28666	1.61;1.61;1.6	1.59	-0.717	0.11208	.	.	.	.	.	T	0.13927	0.0337	N	0.08118	0	0.09310	N	1	P	0.49185	0.92	B	0.39805	0.31	T	0.16600	-1.0397	9	0.87932	D	0	.	7.0401	0.25015	0.0:0.5665:0.4335:0.0	.	270	Q96EZ4	MYEOV_HUMAN	V	270;270;212	ENSP00000412482:G270V;ENSP00000308330:G270V;ENSP00000438100:G212V	ENSP00000308330:G270V	G	+	2	0	MYEOV	68820302	0.031000	0.19500	0.000000	0.03702	0.002000	0.02628	0.630000	0.24553	-0.188000	0.10499	0.491000	0.48974	GGG	G|0.998;T|0.002	0.002	strong		0.677	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
SOCS6	9306	hgsc.bcm.edu	37	18	67992432	67992432	+	Silent	SNP	C	C	T	rs2231563	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:67992432C>T	ENST00000397942.3	+	2	844	c.528C>T	c.(526-528)caC>caT	p.H176H	SOCS6_ENST00000582322.1_Silent_p.H176H	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	176					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				AGGATTTCCACGACCTCCAGT	0.552													C|||	197	0.0393371	0.0113	0.0231	5008	,	,		18705	0.0198		0.0785	False		,,,				2504	0.0685				p.H176H	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											.	SOCS6	54	.	0			c.C528T						PASS	.	C		84,4322	71.4+/-109.4	1,82,2120	68.0	60.0	63.0		528	-7.3	0.0	18	dbSNP_98	63	638,7962	163.2+/-215.8	31,576,3693	no	coding-synonymous	SOCS6	NM_004232.3		32,658,5813	TT,TC,CC		7.4186,1.9065,5.5513		176/536	67992432	722,12284	2203	4300	6503	SO:0001819	synonymous_variant	9306	exon2			TTTCCACGACCTC	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16833	protein-coding gene	gene with protein product		605118	"""suppressor of cytokine signaling 4"""	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.528C>T	18.37:g.67992432C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_004232	Q8WUM3	Silent	SNP	ENST00000397942.3	37	CCDS11998.1																																																																																			C|0.949;T|0.051	0.051	strong		0.552	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2		
MUC16	94025	hgsc.bcm.edu	37	19	9006749	9006749	+	Missense_Mutation	SNP	C	C	T	rs75444444	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	277	276	0.99639	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	
CNTN4	152330	hgsc.bcm.edu	37	3	3067850	3067850	+	Silent	SNP	A	A	G	rs7629924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:3067850A>G	ENST00000397461.1	+	14	1935	c.1551A>G	c.(1549-1551)ttA>ttG	p.L517L	CNTN4_ENST00000397459.2_Silent_p.L189L|CNTN4_ENST00000418658.1_Silent_p.L517L|CNTN4_ENST00000358480.3_Silent_p.L298L|CNTN4_ENST00000427331.1_Silent_p.L517L|CNTN4_ENST00000448906.2_Silent_p.L189L	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	517	Ig-like C2-type 6.				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)		GTATTGTTTTACCGTGCCAGG	0.423													G|||	773	0.154353	0.298	0.1484	5008	,	,		18564	0.1022		0.1034	False		,,,				2504	0.0706				p.L517L		Atlas-SNP	.											.	CNTN4	335	.	0			c.A1551G						PASS	.	G	,,,	1233,3173	705.6+/-407.3	173,887,1143	191.0	161.0	171.0		1551,567,1551,567	0.7	0.9	3	dbSNP_116	171	862,7738	780.0+/-407.7	36,790,3474	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CNTN4	NM_001206955.1,NM_001206956.1,NM_175607.2,NM_175613.2	,,,	209,1677,4617	GG,GA,AA		10.0233,27.9846,16.108	,,,	517/1027,189/698,517/1027,189/699	3067850	2095,10911	2203	4300	6503	SO:0001819	synonymous_variant	152330	exon15			TGTTTTACCGTGC	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.1551A>G	3.37:g.3067850A>G		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	186	93	0.5	NM_175607	B2RAX3|Q8IX14|Q8TC35	Silent	SNP	ENST00000397461.1	37	CCDS43041.1																																																																																			A|0.847;G|0.153	0.153	strong		0.423	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
TAOK1	57551	hgsc.bcm.edu	37	17	27835138	27835138	+	Silent	SNP	C	C	T	rs508706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:27835138C>T	ENST00000261716.3	+	14	2082	c.1563C>T	c.(1561-1563)gcC>gcT	p.A521A	TAOK1_ENST00000536202.1_Silent_p.A521A	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	521					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			ACCAGGCTGCCATGGAGAAAG	0.378													T|||	4156	0.829872	0.8699	0.8674	5008	,	,		19327	0.7768		0.8777	False		,,,				2504	0.7546				p.A521A		Atlas-SNP	.											.	TAOK1	151	.	0			c.C1563T						PASS	.	T	,	3879,527	239.9+/-250.9	1709,461,33	75.0	74.0	74.0		1563,1563	-0.4	1.0	17	dbSNP_83	74	7450,1150	235.4+/-268.0	3224,1002,74	no	coding-synonymous,coding-synonymous	TAOK1	NM_020791.2,NM_025142.1	,	4933,1463,107	TT,TC,CC		13.3721,11.961,12.894	,	521/1002,521/854	27835138	11329,1677	2203	4300	6503	SO:0001819	synonymous_variant	57551	exon14			GGCTGCCATGGAG	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.1563C>T	17.37:g.27835138C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_025142	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Silent	SNP	ENST00000261716.3	37	CCDS32601.1																																																																																			C|0.135;A|0.007	.	strong		0.378	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791	
PIEZO1	9780	hgsc.bcm.edu	37	16	88791458	88791458	+	Missense_Mutation	SNP	G	G	A	rs11645197	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88791458G>A	ENST00000301015.9	-	30	4439	c.4193C>T	c.(4192-4194)cCa>cTa	p.P1398L		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1398					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						CTGCCTCCGTGGCGGGGAGGA	0.701													G|||	878	0.175319	0.0121	0.1643	5008	,	,		17170	0.0873		0.3171	False		,,,				2504	0.3487				p.P1398L		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C4193T						PASS	.						5.0	11.0	9.0					16																	88791458		644	1514	2158	SO:0001583	missense	9780	exon30			CTCCGTGGCGGGG	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.4193C>T	16.37:g.88791458G>A	ENSP00000301015:p.Pro1398Leu	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	142	44	0.309859	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	356	0.163003663003663	12	0.024390243902439025	72	0.19889502762430938	46	0.08041958041958042	226	0.29815303430079154	G	13.18	2.159529	0.38119	.	.	ENSG00000103335	ENST00000301015	T	0.71934	-0.61	4.33	4.33	0.51752	.	0.581104	0.16407	N	0.215765	T	0.00012	0.0000	L	0.54323	1.7	0.53688	P	2.4000000000024002E-5	B	0.29716	0.255	B	0.26614	0.071	T	0.06391	-1.0829	9	0.36615	T	0.2	-9.1253	11.3569	0.49621	0.0:0.0:0.8181:0.1819	rs11645197;rs11645197	1398	Q92508	PIEZ1_HUMAN	L	1398	ENSP00000301015:P1398L	ENSP00000301015:P1398L	P	-	2	0	FAM38A	87318959	.	.	0.902000	0.35471	0.960000	0.62799	.	.	2.406000	0.81754	0.462000	0.41574	CCA	G|0.827;A|0.173	0.173	strong		0.701	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
RIPK4	54101	hgsc.bcm.edu	37	21	43187167	43187167	+	Missense_Mutation	SNP	G	G	C	rs6586239	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43187167G>C	ENST00000352483.2	-	1	99	c.35C>G	c.(34-36)gCg>gGg	p.A12G	RIPK4_ENST00000544709.1_5'Flank|RIPK4_ENST00000332512.3_Missense_Mutation_p.A12G|RIPK4_ENST00000542057.1_5'Flank			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	12			A -> G (in dbSNP:rs6586239).		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						GCGCAGCAGCGCCAGGGCCCA	0.726													C|||	614	0.122604	0.2073	0.1095	5008	,	,		9853	0.0		0.1561	False		,,,				2504	0.1094				p.A12G		Atlas-SNP	.											RIPK4_ENST00000352483,colon,carcinoma,0,2	RIPK4	151	2	0			c.C35G						scavenged	.	C	GLY/ALA	784,3600		74,636,1482	18.0	16.0	17.0		35	3.7	1.0	21	dbSNP_116	17	1356,7224		111,1134,3045	yes	missense	RIPK4	NM_020639.2	60	185,1770,4527	CC,CG,GG		15.8042,17.8832,16.5073	benign	12/785	43187167	2140,10824	2192	4290	6482	SO:0001583	missense	54101	exon1			AGCAGCGCCAGGG	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.35C>G	21.37:g.43187167G>C	ENSP00000330161:p.Ala12Gly	Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	42	28	0.666667	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	37		269	0.12316849816849818	103	0.20934959349593496	43	0.11878453038674033	0	0.0	123	0.16226912928759896	C	9.236	1.037100	0.19669	0.178832	0.158042	ENSG00000183421	ENST00000332512;ENST00000352483	T;T	0.15487	2.42;2.42	3.68	3.68	0.42216	.	0.109881	0.38217	N	0.001775	T	0.00012	0.0000	N	0.00088	-2.19	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42632	-0.9440	9	0.02654	T	1	-21.985	12.1646	0.54123	0.0:0.8259:0.1741:0.0	rs6586239;rs6586239	12	P57078-2	.	G	12	ENSP00000332454:A12G;ENSP00000330161:A12G	ENSP00000332454:A12G	A	-	2	0	RIPK4	42060236	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	4.871000	0.63042	0.548000	0.28955	-0.365000	0.07479	GCG	G|0.846;C|0.154	0.154	strong		0.726	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
TOM1	10043	hgsc.bcm.edu	37	22	35742925	35742925	+	Silent	SNP	T	T	G	rs743810	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:35742925T>G	ENST00000449058.2	+	14	1412	c.1287T>G	c.(1285-1287)ggT>ggG	p.G429G	TOM1_ENST00000447733.1_Silent_p.G396G|TOM1_ENST00000411850.1_Silent_p.G429G|TOM1_ENST00000436462.2_Silent_p.G391G|TOM1_ENST00000382034.5_3'UTR|TOM1_ENST00000425375.1_Silent_p.G384G	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	429					endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)	p.G429G(1)		NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						CTTCCCAGGGTAATGATGCGG	0.662													G|||	1757	0.350839	0.6959	0.3458	5008	,	,		14387	0.12		0.2266	False		,,,				2504	0.2536				p.G429G		Atlas-SNP	.											TOM1,NS,carcinoma,0,1	TOM1	43	1	1	Substitution - coding silent(1)	prostate(1)	c.T1287G						scavenged	.	G	,,,	2618,1788	523.1+/-371.0	783,1052,368	65.0	73.0	70.0		1188,1152,1287,1287	-3.6	0.0	22	dbSNP_86	70	2064,6536	714.8+/-406.0	236,1592,2472	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TOM1	NM_001135729.1,NM_001135730.1,NM_001135732.1,NM_005488.2	,,,	1019,2644,2840	GG,GT,TT		24.0,40.581,35.9988	,,,	396/461,384/448,429/494,429/493	35742925	4682,8324	2203	4300	6503	SO:0001819	synonymous_variant	10043	exon14			CCAGGGTAATGAT	AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284			11982	protein-coding gene	gene with protein product		604700	"""target of myb1 (chicken) homolog"""			10329004, 15047686	Standard	NM_005488		Approved		uc003anp.3	O60784	OTTHUMG00000150958	ENST00000449058.2:c.1287T>G	22.37:g.35742925T>G		Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_001135732	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Silent	SNP	ENST00000449058.2	37	CCDS13913.1																																																																																			T|0.655;G|0.345	0.345	strong		0.662	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72513635	72513635	+	Missense_Mutation	SNP	C	C	A	rs12774070	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72513635C>A	ENST00000373207.1	+	19	2809	c.2809C>A	c.(2809-2811)Ctg>Atg	p.L937M	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.L940M	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	937	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.		L -> M (in dbSNP:rs12774070).		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						ACAGTGCCTGCTGCCCCTCTC	0.682													C|||	802	0.160144	0.0159	0.2046	5008	,	,		16195	0.1637		0.2614	False		,,,				2504	0.2157				p.L940M		Atlas-SNP	.											ADAMTS14,NS,carcinoma,0,2	ADAMTS14	148	2	0			c.C2818A						PASS	.	C	MET/LEU,MET/LEU	265,4135		18,229,1953	20.0	15.0	17.0		2809,2818	3.7	1.0	10	dbSNP_121	17	2270,6322		287,1696,2313	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	15,15	305,1925,4266	AA,AC,CC		26.4199,6.0227,19.512	probably-damaging,probably-damaging	937/1224,940/1227	72513635	2535,10457	2200	4296	6496	SO:0001583	missense	140766	exon19			TGCCTGCTGCCCC	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.2809C>A	10.37:g.72513635C>A	ENSP00000362303:p.Leu937Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	368	0.1684981684981685	9	0.018292682926829267	60	0.16574585635359115	103	0.18006993006993008	196	0.25857519788918204	C	20.1	3.939861	0.73557	0.060227	0.264199	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.61392	0.11;0.11	4.58	3.68	0.42216	.	0.083179	0.49305	D	0.000150	T	0.00039	0.0001	L	0.47016	1.485	0.31497	P	0.665223	D;D	0.64830	0.99;0.994	P;D	0.63033	0.871;0.91	T	0.04165	-1.0972	9	0.72032	D	0.01	.	12.4295	0.55565	0.0:0.9178:0.0:0.0822	rs12774070;rs12774070	937;940	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	M	940;937	ENSP00000362304:L940M;ENSP00000362303:L937M	ENSP00000362303:L937M	L	+	1	2	ADAMTS14	72183641	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.839000	0.62810	1.159000	0.42565	0.563000	0.77884	CTG	A|0.174;C|0.826;G|0.000	0.174	strong		0.682	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
ZNF831	128611	hgsc.bcm.edu	37	20	57769140	57769140	+	Missense_Mutation	SNP	G	G	C	rs55786258	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:57769140G>C	ENST00000371030.2	+	1	3066	c.3066G>C	c.(3064-3066)ttG>ttC	p.L1022F		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1022							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.D1025fs*9(1)		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)					GGGCACAGTTGGGGGGGGACA	0.682													.|||	843	0.168331	0.0477	0.2378	5008	,	,		14918	0.2718		0.1899	False		,,,				2504	0.1534				p.L1022F		Atlas-SNP	.											.	ZNF831	287	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.G3066C						PASS	.	G	PHE/LEU	245,3741		5,235,1753	19.0	23.0	21.0		3066	-2.9	0.0	20	dbSNP_129	21	1545,6789		139,1267,2761	yes	missense	ZNF831	NM_178457.1	22	144,1502,4514	CC,CG,GG		18.5385,6.1465,14.5292	probably-damaging	1022/1678	57769140	1790,10530	1993	4167	6160	SO:0001583	missense	128611	exon1			ACAGTTGGGGGGG	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.3066G>C	20.37:g.57769140G>C	ENSP00000360069:p.Leu1022Phe	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	384	0.17582417582417584	29	0.05894308943089431	78	0.2154696132596685	120	0.2097902097902098	157	0.20712401055408972	G	11.05	1.523625	0.27299	0.061465	0.185385	ENSG00000124203	ENST00000371030	T	0.04454	3.62	3.34	-2.88	0.05682	.	4.175570	0.00751	N	0.001077	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.35821	0.523	B	0.26770	0.073	T	0.39860	-0.9593	9	0.59425	D	0.04	2.511	3.8856	0.09097	0.5657:0.0:0.2608:0.1734	rs55786258	1022	Q5JPB2	ZN831_HUMAN	F	1022	ENSP00000360069:L1022F	ENSP00000360069:L1022F	L	+	3	2	ZNF831	57202535	.	.	0.002000	0.10522	0.002000	0.02628	.	.	-0.261000	0.09405	0.467000	0.42956	TTG	G|0.829;C|0.171	0.171	strong		0.682	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493794	77493794	+	Silent	SNP	T	T	C	rs377151545|rs28718623|rs71125518	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77493794T>C	ENST00000238647.3	-	1	1240	c.342A>G	c.(340-342)caA>caG	p.Q114Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	114	Poly-Gln.				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						gctgctgctgttgctgctgct	0.697													T|||	1146	0.228834	0.1649	0.1758	5008	,	,		5976	0.2659		0.2614	False		,,,				2504	0.2812				p.Q114Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.A342G						PASS	.	-		160,2330		6,148,1091	2.0	2.0	2.0		342	0.6	0.0	14	dbSNP_125	2	324,4012		7,310,1851	no	coding-synonymous	IRF2BPL	NM_024496.2		13,458,2942	CC,CT,TT		7.4723,6.4257,7.0905		114/797	77493794	484,6342	1245	2168	3413	SO:0001819	synonymous_variant	64207	exon1			CTGCTGTTGCTGC	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.342A>G	14.37:g.77493794T>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			.	.	weak		0.697	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496	
SLC9C1	285335	hgsc.bcm.edu	37	3	111983157	111983157	+	Silent	SNP	G	G	A	rs62276974	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	176	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	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	
CHD1	1105	hgsc.bcm.edu	37	5	98199204	98199204	+	Silent	SNP	C	C	T	rs161941	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:98199204C>T	ENST00000284049.3	-	31	4484	c.4335G>A	c.(4333-4335)gaG>gaA	p.E1445E	CHD1_ENST00000511067.1_5'UTR	NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1445					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	GTCTAGTATGCTCTAGTTGTT	0.338													T|||	1484	0.296326	0.6082	0.2363	5008	,	,		15783	0.0427		0.2903	False		,,,				2504	0.1851				p.E1445E		Atlas-SNP	.											.	CHD1	137	.	0			c.G4335A						PASS	.	T		2367,2037	559.5+/-380.2	652,1063,487	96.0	102.0	100.0		4335	-6.7	0.8	5	dbSNP_79	100	2469,6129	692.1+/-404.6	355,1759,2185	no	coding-synonymous	CHD1	NM_001270.2		1007,2822,2672	TT,TC,CC		28.716,46.2534,37.1943		1445/1711	98199204	4836,8166	2202	4299	6501	SO:0001819	synonymous_variant	1105	exon31			AGTATGCTCTAGT	AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.4335G>A	5.37:g.98199204C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_001270	Q17RZ3	Silent	SNP	ENST00000284049.3	37	CCDS34204.1																																																																																			C|0.658;T|0.342	0.342	strong		0.338	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
LILRA6	79168	hgsc.bcm.edu	37	19	54744195	54744195	+	Missense_Mutation	SNP	G	G	A	rs1132604	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54744195G>A	ENST00000396365.2	-	6	1252	c.1213C>T	c.(1213-1215)Cac>Tac	p.H405Y	LILRA6_ENST00000419410.2_Missense_Mutation_p.H405Y|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000245621.5_Missense_Mutation_p.H405Y|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	405	Ig-like C2-type 2.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.H405N(1)		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)		GACAGCAGGTGGGGGTTGGAG	0.612													.|||	491	0.0980431	0.2927	0.049	5008	,	,		26348	0.0		0.0229	False		,,,				2504	0.0481				p.H405Y		Atlas-SNP	.											LILRA6,colon,carcinoma,+1,1	LILRA6	75	1	1	Substitution - Missense(1)	lung(1)	c.C1213T						PASS	.						89.0	125.0	113.0					19																	54744195		2196	4300	6496	SO:0001583	missense	79168	exon6			GCAGGTGGGGGTT	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.1213C>T	19.37:g.54744195G>A	ENSP00000379651:p.His405Tyr	Somatic	319	1	0.0031348		WXS	Illumina HiSeq	Phase_I	360	117	0.325	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	102	0.046703296703296704	85	0.17276422764227642	10	0.027624309392265192	0	0.0	7	0.009234828496042216	G	0	-2.632637	0.00115	.	.	ENSG00000244482	ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T	0.00669	5.9;5.9;5.9	2.71	0.427	0.16489	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.167250	0.06702	N	0.771663	T	0.00012	0.0000	N	0.00413	-1.525	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.38845	-0.9642	10	0.02654	T	1	.	5.898	0.18949	0.7984:0.0:0.2016:0.0	.	405;405;405	C9JFH3;Q6PI73;D3YTC4	.;LIRA6_HUMAN;.	Y	405	ENSP00000411227:H405Y;ENSP00000379651:H405Y;ENSP00000245621:H405Y	ENSP00000245621:H405Y	H	-	1	0	LILRA6	59436007	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.810000	0.01729	-0.152000	0.11156	-2.766000	0.00121	CAC	G|0.954;A|0.046	0.046	strong		0.612	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
OBSCN	84033	hgsc.bcm.edu	37	1	228520973	228520973	+	Missense_Mutation	SNP	C	C	G	rs369909	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:228520973C>G	ENST00000422127.1	+	58	15849	c.15805C>G	c.(15805-15807)Ctc>Gtc	p.L5269V	OBSCN_ENST00000366707.4_Missense_Mutation_p.L2903V|OBSCN_ENST00000570156.2_Missense_Mutation_p.L6226V|OBSCN_ENST00000366709.4_Missense_Mutation_p.L2388V|OBSCN_ENST00000284548.11_Missense_Mutation_p.L5269V	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	90	0	0		WXS	Illumina HiSeq	Phase_I	133	46	0.345865	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	
RGS11	8786	hgsc.bcm.edu	37	16	319511	319511	+	Missense_Mutation	SNP	A	A	G	rs739999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:319511A>G	ENST00000397770.3	-	16	1297	c.1280T>C	c.(1279-1281)aTg>aCg	p.M427T	ARHGDIG_ENST00000464609.1_Intron|RGS11_ENST00000359740.5_Missense_Mutation_p.M416T|ITFG3_ENST00000600536.1_Intron|RGS11_ENST00000316163.5_Missense_Mutation_p.M406T|ITFG3_ENST00000442458.2_Intron			O94810	RGS11_HUMAN	regulator of G-protein signaling 11	427			M -> T (in dbSNP:rs739999).		G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)	8		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				CCGTCTCTTCATCTCCAGCGG	0.657													G|||	1547	0.308906	0.6415	0.2493	5008	,	,		17262	0.3194		0.0785	False		,,,				2504	0.1278				p.M427T		Atlas-SNP	.											RGS11,colon,carcinoma,0,1	RGS11	29	1	0			c.T1280C						scavenged	.	G	THR/MET,THR/MET	2422,1982	554.5+/-379.0	673,1076,453	57.0	55.0	55.0		1217,1280	3.5	0.0	16	dbSNP_86	55	769,7831	782.9+/-407.6	45,679,3576	yes	missense,missense	RGS11	NM_003834.1,NM_183337.1	81,81	718,1755,4029	GG,GA,AA		8.9419,45.0045,24.5386	benign,benign	406/447,427/468	319511	3191,9813	2202	4300	6502	SO:0001583	missense	8786	exon16			CTCTTCATCTCCA	AF035153	CCDS10403.1, CCDS42088.1, CCDS66884.1	16p13.3	2008-07-28	2007-08-14		ENSG00000076344	ENSG00000076344		"""Regulators of G-protein signaling"""	9993	protein-coding gene	gene with protein product		603895	"""regulator of G-protein signalling 11"""			9789084	Standard	NM_001286486		Approved		uc002cgj.1	O94810	OTTHUMG00000064893	ENST00000397770.3:c.1280T>C	16.37:g.319511A>G	ENSP00000380876:p.Met427Thr	Somatic	260	2	0.00769231		WXS	Illumina HiSeq	Phase_I	196	81	0.413265	NM_183337	O75883|Q4TT71|Q4TT72	Missense_Mutation	SNP	ENST00000397770.3	37	CCDS42088.1	644	0.2948717948717949	304	0.6178861788617886	87	0.24033149171270718	195	0.3409090909090909	58	0.07651715039577836	G	4.184	0.032829	0.08101	0.549955	0.089419	ENSG00000076344	ENST00000397770;ENST00000316163;ENST00000359740	T;T;T	0.24538	1.86;1.85;1.86	4.42	3.46	0.39613	.	0.327034	0.31821	N	0.007020	T	0.00012	0.0000	N	0.00152	-1.975	0.09310	P	0.999999999866987	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44697	-0.9311	9	0.05959	T	0.93	-12.3827	9.475	0.38867	0.1772:0.0:0.8228:0.0	rs739999;rs57130699;rs739999	416;427;427	O94810-2;Q4TT70;O94810	.;.;RGS11_HUMAN	T	427;406;416	ENSP00000380876:M427T;ENSP00000319069:M406T;ENSP00000352778:M416T	ENSP00000319069:M406T	M	-	2	0	RGS11	259512	1.000000	0.71417	0.046000	0.18839	0.044000	0.14063	4.897000	0.63231	0.341000	0.23771	-1.212000	0.01626	ATG	A|0.720;G|0.280	0.280	strong		0.657	RGS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139325.2		
ZFR2	23217	hgsc.bcm.edu	37	19	3820191	3820191	+	Missense_Mutation	SNP	C	C	T	rs2301843	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3820191C>T	ENST00000262961.4	-	11	1739	c.1729G>A	c.(1729-1731)Gcc>Acc	p.A577T		NM_015174.1	NP_055989.1	Q9UPR6	ZFR2_HUMAN	zinc finger RNA binding protein 2	577	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.		A -> T (in dbSNP:rs2301843).				nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00514)|STAD - Stomach adenocarcinoma(1328;0.19)		TGGAGTGGGGCGCTGGCGGGT	0.726													C|||	1905	0.380391	0.41	0.4135	5008	,	,		15166	0.4296		0.4225	False		,,,				2504	0.2229				p.A577T		Atlas-SNP	.											.	ZFR2	63	.	0			c.G1729A						PASS	.	C	THR/ALA	1531,2657		311,909,874	12.0	16.0	15.0		1729	-3.1	0.0	19	dbSNP_100	15	2987,5193		660,1667,1763	yes	missense	ZFR2	NM_015174.1	58	971,2576,2637	TT,TC,CC		36.5159,36.5568,36.5298	possibly-damaging	577/940	3820191	4518,7850	2094	4090	6184	SO:0001583	missense	23217	exon11			GTGGGGCGCTGGC	AB029009	CCDS45921.1, CCDS45922.1	19p13.3	2012-10-05	2008-03-25	2008-03-25	ENSG00000105278	ENSG00000105278			29189	protein-coding gene	gene with protein product			"""KIAA1086"""	KIAA1086		10470851	Standard	NM_015174		Approved		uc002lyw.2	Q9UPR6	OTTHUMG00000180918	ENST00000262961.4:c.1729G>A	19.37:g.3820191C>T	ENSP00000262961:p.Ala577Thr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_015174		Missense_Mutation	SNP	ENST00000262961.4	37	CCDS45921.1	916	0.4194139194139194	213	0.4329268292682927	152	0.4198895027624309	240	0.4195804195804196	311	0.4102902374670185	C	2.938	-0.219507	0.06061	0.365568	0.365159	ENSG00000105278	ENST00000262961	T	0.06608	3.28	2.52	-3.12	0.05282	.	0.667620	0.13499	N	0.383395	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.39482	-0.9612	9	0.20046	T	0.44	0.3025	3.8591	0.08988	0.0:0.2789:0.3157:0.4054	rs2301843;rs52795129;rs57356575;rs2301843	577	Q9UPR6	ZFR2_HUMAN	T	577	ENSP00000262961:A577T	ENSP00000262961:A577T	A	-	1	0	ZFR2	3771191	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.761000	0.01805	-0.336000	0.08438	-0.327000	0.08410	GCC	C|0.594;T|0.406	0.406	strong		0.726	ZFR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453648.2	NM_015174	
ACOT4	122970	hgsc.bcm.edu	37	14	74060487	74060487	+	Missense_Mutation	SNP	G	G	C	rs45522539	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:74060487G>C	ENST00000326303.4	+	2	793	c.539G>C	c.(538-540)gGc>gCc	p.G180A		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	180					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		CTCCTTGCTGGCCATGGCTTT	0.473													G|||	176	0.0351438	0.0008	0.0159	5008	,	,		18474	0.0317		0.0249	False		,,,				2504	0.1094				p.G180A		Atlas-SNP	.											.	ACOT4	25	.	0			c.G539C						PASS	.	G	ALA/GLY	16,4390	23.3+/-48.9	0,16,2187	109.0	102.0	104.0		539	3.3	1.0	14	dbSNP_127	104	214,8386	89.4+/-151.6	4,206,4090	no	missense	ACOT4	NM_152331.3	60	4,222,6277	CC,CG,GG		2.4884,0.3631,1.7684	benign	180/422	74060487	230,12776	2203	4300	6503	SO:0001583	missense	122970	exon2			TTGCTGGCCATGG	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.539G>C	14.37:g.74060487G>C	ENSP00000323071:p.Gly180Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	191	72	0.376963	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	37	0.01694139194139194	0	0.0	5	0.013812154696132596	16	0.027972027972027972	16	0.021108179419525065	G	12.96	2.094339	0.36952	0.003631	0.024884	ENSG00000177465	ENST00000326303	T	0.38722	1.12	5.25	3.35	0.38373	.	0.569567	0.20198	N	0.097158	T	0.10594	0.0259	L	0.43923	1.385	0.37406	D	0.913058	B	0.30563	0.285	B	0.21360	0.034	T	0.10567	-1.0624	10	0.34782	T	0.22	5.6437	5.2094	0.15308	0.1675:0.0:0.6475:0.185	rs45522539	180	Q8N9L9	ACOT4_HUMAN	A	180	ENSP00000323071:G180A	ENSP00000323071:G180A	G	+	2	0	ACOT4	73130240	0.462000	0.25791	0.991000	0.47740	0.992000	0.81027	1.662000	0.37418	1.138000	0.42230	0.561000	0.74099	GGC	G|0.983;C|0.017	0.017	strong		0.473	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
TNFRSF14	8764	hgsc.bcm.edu	37	1	2488153	2488153	+	Missense_Mutation	SNP	A	A	G	rs4870	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:2488153A>G	ENST00000355716.4	+	1	349	c.50A>G	c.(49-51)aAa>aGa	p.K17R	RP3-395M20.8_ENST00000452793.1_RNA|RP3-395M20.8_ENST00000416860.2_RNA|TNFRSF14_ENST00000442392.2_3'UTR|TNFRSF14_ENST00000409119.1_Missense_Mutation_p.K17R	NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	17			K -> R (in dbSNP:rs4870). {ECO:0000269|PubMed:11756979, ECO:0000269|PubMed:12975309, ECO:0000269|Ref.8}.		cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell migration (GO:2000406)|T cell costimulation (GO:0031295)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			kidney(1)	1	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|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;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;1.11e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000326)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.199)		TCCACCCCCAAAACCGACGTC	0.647			"""Mis, N, F"""		follicular lymphoma								a|||	3079	0.614816	0.7837	0.5303	5008	,	,		14854	0.5397		0.4682	False		,,,				2504	0.6748				p.K17R		Atlas-SNP	.		Rec	yes		1	1p36.32	8764	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""		L	.	TNFRSF14	89	.	0			c.A50G						PASS	.	A	ARG/LYS	3193,1203		1166,861,171	43.0	47.0	45.0		50	-1.1	0.0	1	dbSNP_52	45	4058,4540		951,2156,1192	yes	missense	TNFRSF14	NM_003820.2	26	2117,3017,1363	GG,GA,AA		47.197,27.3658,44.1973	probably-damaging	17/284	2488153	7251,5743	2198	4299	6497	SO:0001583	missense	8764	exon1			CCCCCAAAACCGA	U70321	CCDS44046.1	1p36.32	2012-02-27	2011-08-11		ENSG00000157873	ENSG00000157873		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11912	protein-coding gene	gene with protein product	"""herpesvirus entry mediator"""	602746	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""			8898196, 9162061	Standard	XM_006711018		Approved	HVEM, ATAR, TR2, LIGHTR, HVEA, CD270	uc001ajt.1	Q92956	OTTHUMG00000000792	ENST00000355716.4:c.50A>G	1.37:g.2488153A>G	ENSP00000347948:p.Lys17Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	71	9	0.126761	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Missense_Mutation	SNP	ENST00000355716.4	37	CCDS44046.1	1191	0.5453296703296703	365	0.741869918699187	193	0.5331491712707183	273	0.4772727272727273	360	0.47493403693931396	a	10.75	1.437826	0.25900	0.726342	0.47197	ENSG00000157873	ENST00000426449;ENST00000434817;ENST00000435221;ENST00000451778;ENST00000409119;ENST00000423768;ENST00000355716	D;D;D;D;D;D	0.88664	-2.37;-2.21;-2.21;-2.21;-2.41;-2.17	2.4	-1.09	0.09904	.	.	.	.	.	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;B	0.37864	0.61;0.388	B;B	0.33196	0.145;0.159	T	0.44757	-0.9307	8	0.20519	T	0.43	-1.9033	7.533	0.27693	0.3838:0.6162:0.0:0.0	.	17;17	B4DU65;Q92956	.;TNR14_HUMAN	R	17	ENSP00000411854:K17R;ENSP00000415254:K17R;ENSP00000399292:K17R;ENSP00000399533:K17R;ENSP00000386859:K17R;ENSP00000347948:K17R	ENSP00000347948:K17R	K	+	2	0	TNFRSF14	2486265	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.251000	0.08818	-0.205000	0.10219	0.247000	0.18012	AAA	A|0.440;G|0.560	0.560	strong		0.647	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1		
KIRREL	55243	hgsc.bcm.edu	37	1	158064439	158064439	+	Silent	SNP	C	C	A	rs41273465	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158064439C>A	ENST00000359209.6	+	15	1870	c.1803C>A	c.(1801-1803)ccC>ccA	p.P601P	KIRREL_ENST00000360089.4_Silent_p.P437P|KIRREL_ENST00000368173.3_Silent_p.P617P|KIRREL_ENST00000368172.1_Silent_p.P415P|KIRREL_ENST00000416935.2_Silent_p.P501P|KIRREL_ENST00000392272.2_Silent_p.P498P			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	601				DTREEYEMKDPTNGY -> ERPRIRGRLNTSYSD (in Ref. 1). {ECO:0000305}.	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)					CCCAGGACCCCACCAATGGCT	0.612													C|||	356	0.0710863	0.1188	0.0418	5008	,	,		17489	0.0218		0.0676	False		,,,				2504	0.0818				p.P601P		Atlas-SNP	.											.	KIRREL	346	.	0			c.C1803A						PASS	.	C		465,3939	206.2+/-227.9	20,425,1757	59.0	63.0	61.0		1803	1.2	1.0	1	dbSNP_127	61	586,8012	149.2+/-204.3	24,538,3737	no	coding-synonymous	KIRREL	NM_018240.5		44,963,5494	AA,AC,CC		6.8155,10.5586,8.0834		601/758	158064439	1051,11951	2202	4299	6501	SO:0001819	synonymous_variant	55243	exon15			GGACCCCACCAAT	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.1803C>A	1.37:g.158064439C>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	45	27	0.6	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Silent	SNP	ENST00000359209.6	37	CCDS1172.2																																																																																			C|0.924;A|0.076	0.076	strong		0.612	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240	
CREBBP	1387	hgsc.bcm.edu	37	16	3808872	3808872	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3808872G>A	ENST00000262367.5	-	17	4161	c.3352C>T	c.(3352-3354)Cag>Tag	p.Q1118*	CREBBP_ENST00000382070.3_Nonsense_Mutation_p.Q1080*	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1118	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|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 negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|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)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CCGAGGAGCTGGGGATCTACA	0.433			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.Q1118X		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C3352T						PASS	.						83.0	81.0	81.0					16																	3808872		2197	4300	6497	SO:0001587	stop_gained	1387	exon17			GGAGCTGGGGATC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.3352C>T	16.37:g.3808872G>A	ENSP00000262367:p.Gln1118*	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	141	44	0.312057	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Nonsense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	49	15.347356	0.99831	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-9.7097	18.7675	0.91879	0.0:0.0:1.0:0.0	.	.	.	.	X	1118;1148;1080	.	ENSP00000262367:Q1118X	Q	-	1	0	CREBBP	3748873	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.034000	0.64152	2.499000	0.84300	0.561000	0.74099	CAG	.	.	none		0.433	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
PCDHA8	56140	hgsc.bcm.edu	37	5	140221139	140221139	+	Missense_Mutation	SNP	G	G	A	rs3756331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140221139G>A	ENST00000531613.1	+	1	233	c.233G>A	c.(232-234)aGt>aAt	p.S78N	PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.S78N|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	78	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> N (in dbSNP:rs3756331).		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.S78N(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)			CTGGAGGTAAGTCTGCAGAAT	0.642													.|||	2981	0.595248	0.7383	0.6009	5008	,	,		18152	0.5337		0.5338	False		,,,				2504	0.5245				p.S78N		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,0,2	PCDHA8	366	2	2	Substitution - Missense(2)	stomach(2)	c.G233A						scavenged	.	A	,,,,,,,ASN/SER,,,ASN/SER	2941,1439		1111,719,360	56.0	82.0	73.0		,,,,,,,233,,,233	2.7	1.0	5	dbSNP_107	73	4120,4444		1149,1822,1311	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	,,,,,,,46,,,46	2260,2541,1671	AA,AG,GG		48.1084,32.8539,45.4496	,,,,,,,,,,	,,,,,,,78/951,,,78/815	140221139	7061,5883	2190	4282	6472	SO:0001583	missense	56140	exon1			AGGTAAGTCTGCA	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.233G>A	5.37:g.140221139G>A	ENSP00000434655:p.Ser78Asn	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	1164	0.532967032967033	319	0.6483739837398373	187	0.5165745856353591	290	0.506993006993007	368	0.48548812664907653	A	0.403	-0.917356	0.02396	0.671461	0.481084	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.34859	1.34;1.34	3.91	2.73	0.32206	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	0.000000	0.39083	N	0.001480	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	0.42882	-0.9425	9	0.02654	T	1	.	4.5167	0.11939	0.6189:0.0:0.2461:0.1351	rs3756331;rs6881677;rs17844315;rs59428168	78;78	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	N	78	ENSP00000434655:S78N;ENSP00000367363:S78N	ENSP00000367363:S78N	S	+	2	0	PCDHA8	140201323	0.478000	0.25917	0.985000	0.45067	0.851000	0.48451	3.070000	0.50033	0.083000	0.17047	-0.389000	0.06534	AGT	G|0.466;A|0.534	0.534	strong		0.642	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
KLHL23	151230	hgsc.bcm.edu	37	2	170606041	170606041	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:170606041T>C	ENST00000392647.2	+	4	1720	c.1476T>C	c.(1474-1476)gcT>gcC	p.A492A	KLHL23_ENST00000272797.4_Silent_p.A492A|KLHL23_ENST00000602521.1_5'UTR	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	492										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						GAGAGATAGCTCCCATGATGG	0.443																																					p.A492A		Atlas-SNP	.											KLHL23,colon,carcinoma,+2,1	KLHL23	52	1	0			c.T1476C						scavenged	.						144.0	129.0	134.0					2																	170606041		2203	4300	6503	SO:0001819	synonymous_variant	151230	exon4			GATAGCTCCCATG	BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"""Kelch-like"", ""BTB/POZ domain containing"""	27506	protein-coding gene	gene with protein product			"""kelch-like 23 (Drosophila)"""				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.1476T>C	2.37:g.170606041T>C		Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	264	4	0.0151515	NM_144711	Q8N9B9|Q96FT8	Silent	SNP	ENST00000392647.2	37	CCDS2236.1																																																																																			.	.	none		0.443	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711	
USP33	23032	hgsc.bcm.edu	37	1	78201745	78201745	+	Silent	SNP	G	G	T	rs2296227	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:78201745G>T	ENST00000370793.1	-	7	889	c.543C>A	c.(541-543)gcC>gcA	p.A181A	USP33_ENST00000357428.1_Silent_p.A181A|USP33_ENST00000370794.3_Silent_p.A150A|USP33_ENST00000370792.3_Silent_p.A181A	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	181					axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|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)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	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)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						ATTTACCTCTGGCCCTAAGTT	0.358													T|||	2451	0.489417	0.7451	0.2608	5008	,	,		15784	0.4077		0.332	False		,,,				2504	0.5521				p.A181A	Melanoma(152;72 1870 11110 26780 42647)	Atlas-SNP	.											.	USP33	87	.	0			c.C543A						PASS	.	T	,,	2980,1426	464.3+/-353.8	1026,928,249	126.0	121.0	123.0		543,450,543	1.3	1.0	1	dbSNP_100	123	2594,6006	688.8+/-404.3	428,1738,2134	no	coding-synonymous,coding-synonymous,coding-synonymous	USP33	NM_015017.3,NM_201624.1,NM_201626.1	,,	1454,2666,2383	TT,TG,GG		30.1628,32.365,42.8571	,,	181/943,150/912,181/829	78201745	5574,7432	2203	4300	6503	SO:0001819	synonymous_variant	23032	exon7			ACCTCTGGCCCTA	AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"""Ubiquitin-specific peptidases"""	20059	protein-coding gene	gene with protein product		615146	"""ubiquitin specific protease 33"""			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.543C>A	1.37:g.78201745G>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	109	107	0.981651	NM_201626	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Silent	SNP	ENST00000370793.1	37	CCDS678.1																																																																																			G|0.550;T|0.450	0.450	strong		0.358	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2	NM_015017	
ZNF543	125919	hgsc.bcm.edu	37	19	57840547	57840547	+	Missense_Mutation	SNP	A	A	G	rs10410649	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57840547A>G	ENST00000321545.4	+	4	2062	c.1717A>G	c.(1717-1719)Atg>Gtg	p.M573V		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	573			M -> V (in dbSNP:rs10410649).		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(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		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;0.0257)		AAGACCTTTTATGACTGCACA	0.413													A|||	989	0.197484	0.3169	0.1816	5008	,	,		20065	0.0317		0.2843	False		,,,				2504	0.1288				p.M573V		Atlas-SNP	.											.	ZNF543	61	.	0			c.A1717G						PASS	.	A	VAL/MET	1351,3055	450.6+/-349.4	200,951,1052	87.0	81.0	84.0		1717	-2.8	0.0	19	dbSNP_119	84	2352,6248	393.0+/-344.2	323,1706,2271	yes	missense	ZNF543	NM_213598.3	21	523,2657,3323	GG,GA,AA		27.3488,30.6627,28.4715	benign	573/601	57840547	3703,9303	2203	4300	6503	SO:0001583	missense	125919	exon4			CCTTTTATGACTG	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1717A>G	19.37:g.57840547A>G	ENSP00000322545:p.Met573Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	146	73	0.5	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	466	0.21336996336996336	152	0.3089430894308943	79	0.21823204419889503	18	0.03146853146853147	217	0.2862796833773087	A	4.434	0.080299	0.08533	0.306627	0.273488	ENSG00000178229	ENST00000321545	T	0.05513	3.43	2.45	-2.81	0.05805	.	.	.	.	.	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	0.47573	-0.9107	8	0.52906	T	0.07	.	5.4467	0.16539	0.323:0.4652:0.2119:0.0	rs10410649;rs52820047;rs10410649	573	Q08ER8	ZN543_HUMAN	V	573	ENSP00000322545:M573V	ENSP00000322545:M573V	M	+	1	0	ZNF543	62532359	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.653000	0.05360	-0.852000	0.04141	0.379000	0.24179	ATG	A|0.737;G|0.263	0.263	strong		0.413	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
TMEM39B	55116	hgsc.bcm.edu	37	1	32557486	32557486	+	Silent	SNP	A	A	G	rs744455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32557486A>G	ENST00000336294.5	+	6	947	c.801A>G	c.(799-801)tcA>tcG	p.S267S	TMEM39B_ENST00000487305.1_3'UTR|TMEM39B_ENST00000373634.4_Silent_p.S68S|TMEM39B_ENST00000427288.1_Silent_p.S152S|TMEM39B_ENST00000456834.2_Missense_Mutation_p.T216A	NM_018056.2	NP_060526.2	Q9GZU3	TM39B_HUMAN	transmembrane protein 39B	267						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(5)|ovary(1)|prostate(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GCTGCCTGTCACCCAGCCTCA	0.602													G|||	1120	0.223642	0.2927	0.232	5008	,	,		20192	0.2351		0.0596	False		,,,				2504	0.2812				p.S267S		Atlas-SNP	.											.	TMEM39B	66	.	0			c.A801G						PASS	.	G		1184,3222	710.3+/-407.9	187,810,1206	87.0	73.0	78.0		801	-10.3	0.5	1	dbSNP_86	78	560,8040	794.2+/-407.5	20,520,3760	no	coding-synonymous	TMEM39B	NM_018056.2		207,1330,4966	GG,GA,AA		6.5116,26.8724,13.4092		267/493	32557486	1744,11262	2203	4300	6503	SO:0001819	synonymous_variant	55116	exon6			CCTGTCACCCAGC	AL136695	CCDS351.2	1p35.1	2008-02-05			ENSG00000121775	ENSG00000121775			25510	protein-coding gene	gene with protein product						12477932	Standard	NM_018056		Approved	FLJ10315	uc010ogv.2	Q9GZU3	OTTHUMG00000004020	ENST00000336294.5:c.801A>G	1.37:g.32557486A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	82	55	0.670732	NM_018056	B4DKN8|B4DQE6|B4DTN8|D3DPP4|Q6IA44	Silent	SNP	ENST00000336294.5	37	CCDS351.2	373	0.1707875457875458	147	0.29878048780487804	50	0.13812154696132597	131	0.229020979020979	45	0.059366754617414245	G	13.14	2.148810	0.37923	0.268724	0.065116	ENSG00000121775	ENST00000456834	.	.	.	5.58	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25710	-1.0124	4	0.87932	D	0	-7.3393	2.6143	0.04900	0.4687:0.2282:0.1626:0.1406	rs744455;rs58248543;rs744455	.	.	.	A	216	.	ENSP00000390889:T188A	T	+	1	0	TMEM39B	32330073	0.002000	0.14202	0.532000	0.27989	0.963000	0.63663	-1.285000	0.02791	-2.042000	0.00914	-0.733000	0.03571	ACC	A|0.849;G|0.151	0.151	strong		0.602	TMEM39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011489.2	NM_018056	
DACT1	51339	hgsc.bcm.edu	37	14	59113537	59113537	+	Silent	SNP	C	C	G	rs61755641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:59113537C>G	ENST00000335867.4	+	4	2220	c.2196C>G	c.(2194-2196)tcC>tcG	p.S732S	DACT1_ENST00000556859.1_Silent_p.S451S|DACT1_ENST00000395153.3_Silent_p.S695S|DACT1_ENST00000541264.2_Silent_p.S451S			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	732					dendrite morphogenesis (GO:0048813)|embryonic hindgut morphogenesis (GO:0048619)|gastrulation with mouth forming second (GO:0001702)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of catenin import into nucleus (GO:0035412)|regulation of protein stability (GO:0031647)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|synapse organization (GO:0050808)|Wnt signaling pathway (GO:0016055)	beta-catenin destruction complex (GO:0030877)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|protein kinase A binding (GO:0051018)|protein kinase C binding (GO:0005080)			endometrium(7)|kidney(3)|large_intestine(11)|lung(27)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	53						AGTGCGAGTCCCTGTTCCACT	0.642													C|||	168	0.0335463	0.0303	0.0375	5008	,	,		11194	0.003		0.0616	False		,,,				2504	0.0378				p.S732S		Atlas-SNP	.											.	DACT1	119	.	0			c.C2196G						PASS	.	C	,	143,4263	99.4+/-138.0	2,139,2062	82.0	78.0	80.0		2085,2196	-1.3	1.0	14	dbSNP_129	80	473,8127	137.8+/-194.7	10,453,3837	no	coding-synonymous,coding-synonymous	DACT1	NM_001079520.1,NM_016651.5	,	12,592,5899	GG,GC,CC		5.5,3.2456,4.7363	,	695/800,732/837	59113537	616,12390	2203	4300	6503	SO:0001819	synonymous_variant	51339	exon4			CGAGTCCCTGTTC	AF251079	CCDS9736.1, CCDS41961.1	14q22.3	2013-05-15	2013-05-15		ENSG00000165617	ENSG00000165617			17748	protein-coding gene	gene with protein product		607861	"""dapper homolog 1, antagonist of beta-catenin (xenopus)"", ""dapper, antagonist of beta-catenin, homolog 1 (Xenopus laevis)"""			11970895	Standard	NM_001079520		Approved	DAPPER1, THYEX3, HDPR1, DAPPER, FRODO	uc001xdw.3	Q9NYF0	OTTHUMG00000140324	ENST00000335867.4:c.2196C>G	14.37:g.59113537C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_016651	A8MYJ2|Q86TY0	Silent	SNP	ENST00000335867.4	37	CCDS9736.1																																																																																			C|0.956;G|0.044	0.044	strong		0.642	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651	
OR1N2	138882	hgsc.bcm.edu	37	9	125316028	125316028	+	Missense_Mutation	SNP	T	T	C	rs41297203	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:125316028T>C	ENST00000373688.2	+	1	638	c.580T>C	c.(580-582)Ttc>Ctc	p.F194L		NM_001004457.1	NP_001004457.1	Q8NGR9	OR1N2_HUMAN	olfactory receptor, family 1, subfamily N, member 2	194						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(3)	26						CATCCCTCATTTCTATTGTGA	0.527													T|||	247	0.0493211	0.0741	0.0562	5008	,	,		18342	0.002		0.0934	False		,,,				2504	0.0143				p.F194L		Atlas-SNP	.											.	OR1N2	51	.	0			c.T580C						PASS	.	T	LEU/PHE	288,4118	160.7+/-193.0	8,272,1923	156.0	144.0	148.0		580	4.4	0.9	9	dbSNP_127	148	833,7767	192.4+/-238.4	39,755,3506	yes	missense	OR1N2	NM_001004457.1	22	47,1027,5429	CC,CT,TT		9.686,6.5365,8.6191	probably-damaging	194/331	125316028	1121,11885	2203	4300	6503	SO:0001583	missense	138882	exon1			CCTCATTTCTATT		CCDS35123.1	9q33.2	2013-09-20			ENSG00000171501	ENSG00000171501		"""GPCR / Class A : Olfactory receptors"""	15111	protein-coding gene	gene with protein product							Standard	NM_001004457		Approved		uc011lyx.2	Q8NGR9	OTTHUMG00000020607	ENST00000373688.2:c.580T>C	9.37:g.125316028T>C	ENSP00000362792:p.Phe194Leu	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_001004457	A3KFM2|B2RNY4|Q6IF17|Q96RA3	Missense_Mutation	SNP	ENST00000373688.2	37	CCDS35123.1	133	0.060897435897435896	41	0.08333333333333333	25	0.06906077348066299	1	0.0017482517482517483	66	0.0870712401055409	T	17.40	3.378882	0.61735	0.065365	0.09686	ENSG00000171501	ENST00000373688	T	0.00346	8.01	4.41	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000143	T	0.00039	0.0001	L	0.60957	1.885	0.36795	P	0.11497299999999999	D	0.89917	1.0	D	0.83275	0.996	T	0.73020	-0.4114	9	0.87932	D	0	.	12.917	0.58211	0.0:0.0:0.0:1.0	rs41297203	194	Q8NGR9	OR1N2_HUMAN	L	194	ENSP00000362792:F194L	ENSP00000362792:F194L	F	+	1	0	OR1N2	124355849	0.001000	0.12720	0.878000	0.34440	0.943000	0.58893	0.634000	0.24614	1.869000	0.54173	0.524000	0.50904	TTC	T|0.920;C|0.080	0.080	strong		0.527	OR1N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053937.2		
PSAPL1	768239	hgsc.bcm.edu	37	4	7435443	7435443	+	Silent	SNP	G	G	A	rs6843370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:7435443G>A	ENST00000319098.4	-	1	1257	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	SORCS2_ENST00000507866.2_Intron|SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	388					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						GGTTCTCCGCGTCCCACTCTG	0.622													G|||	512	0.102236	0.1203	0.1052	5008	,	,		19768	0.0317		0.1362	False		,,,				2504	0.1135				p.D388D		Atlas-SNP	.											.	PSAPL1	51	.	0			c.C1164T						PASS	.	G	,	404,3794		21,362,1716	47.0	51.0	50.0		1164,	-7.1	0.0	4	dbSNP_116	50	1343,7079		115,1113,2983	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	136,1475,4699	AA,AG,GG		15.9463,9.6236,13.8431	,	388/522,	7435443	1747,10873	2099	4211	6310	SO:0001819	synonymous_variant	768239	exon1			CTCCGCGTCCCAC	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.1164C>T	4.37:g.7435443G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			G|0.886;A|0.114	0.114	strong		0.622	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
RPL3	6122	hgsc.bcm.edu	37	22	39714490	39714490	+	Silent	SNP	C	C	T	rs6509	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:39714490C>T	ENST00000216146.4	-	2	284	c.111G>A	c.(109-111)ccG>ccA	p.P37P	SNORD43_ENST00000583861.1_RNA|RPL3_ENST00000465618.1_5'UTR|RPL3_ENST00000401609.1_5'UTR	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	37					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|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)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	CCGGCTTGGACGGGTCATCCT	0.597													C|||	1501	0.29972	0.1884	0.4121	5008	,	,		16002	0.119		0.493	False		,,,				2504	0.3579				p.P37P		Atlas-SNP	.											.	RPL3	29	.	0			c.G111A						PASS	.	C	,	977,3429	366.4+/-317.8	107,763,1333	53.0	49.0	50.0		111,111	-5.6	0.0	22	dbSNP_52	50	4261,4333	569.4+/-389.2	1049,2163,1085	no	coding-synonymous,coding-synonymous	RPL3	NM_000967.3,NM_001033853.1	,	1156,2926,2418	TT,TC,CC		49.5811,22.1743,40.2923	,	37/404,37/355	39714490	5238,7762	2203	4297	6500	SO:0001819	synonymous_variant	6122	exon2			CTTGGACGGGTCA	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"""L ribosomal proteins"""	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.111G>A	22.37:g.39714490C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	91	89	0.978022	NM_001033853	B2RDV9|Q15548|Q5I0G0	Silent	SNP	ENST00000216146.4	37	CCDS13988.1	692	0.31684981684981683	104	0.21138211382113822	152	0.4198895027624309	63	0.11013986013986014	373	0.4920844327176781	C	3.178	-0.168576	0.06461	0.221743	0.495811	ENSG00000100316	ENST00000427905	.	.	.	4.5	-5.55	0.02536	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999876598	.	.	.	.	.	.	T	0.42632	-0.9440	3	.	.	.	.	4.7003	0.12823	0.11:0.4806:0.2906:0.1187	rs6509;rs137624;rs17849573;rs17850289;rs17850961;rs17851086;rs17855216;rs58337650	.	.	.	I	69	.	.	V	-	1	0	RPL3	38044436	0.997000	0.39634	0.000000	0.03702	0.148000	0.21650	0.413000	0.21148	-1.649000	0.01508	-0.493000	0.04662	GTC	C|0.625;T|0.375	0.375	strong		0.597	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967	
KMT2D	8085	hgsc.bcm.edu	37	12	49445028	49445028	+	Missense_Mutation	SNP	G	G	A	rs75226229	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:49445028G>A	ENST00000301067.7	-	10	2437	c.2438C>T	c.(2437-2439)cCg>cTg	p.P813L		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	813	Pro-rich.		P -> L (in dbSNP:rs75226229). {ECO:0000269|PubMed:21280141}.	Missing (in Ref. 1; AAC51734). {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)										AGACAGGTGCGGCTCCTCAGT	0.647													G|||	80	0.0159744	0.0023	0.0274	5008	,	,		15268	0.0		0.0487	False		,,,				2504	0.0092				p.P813L		Atlas-SNP	.											.	MLL2	1173	.	0			c.C2438T						PASS	.	G	LEU/PRO	45,3979		0,45,1967	36.0	40.0	38.0		2438	-1.4	0.0	12	dbSNP_132	38	424,7814		15,394,3710	yes	missense	MLL2	NM_003482.3	98	15,439,5677	AA,AG,GG		5.1469,1.1183,3.8248	probably-damaging	813/5538	49445028	469,11793	2012	4119	6131	SO:0001583	missense	8085	exon10			AGGTGCGGCTCCT	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.2438C>T	12.37:g.49445028G>A	ENSP00000301067:p.Pro813Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	174	81	0.465517	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	56	0.02564102564102564	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	43	0.05672823218997362	G	5.855	0.341913	0.11069	0.011183	0.051469	ENSG00000167548	ENST00000301067	T	0.33216	1.42	3.68	-1.4	0.08968	.	.	.	.	.	T	0.01189	0.0039	N	0.02539	-0.55	0.21386	N	0.999707	B	0.02656	0.0	B	0.01281	0.0	T	0.22730	-1.0208	9	0.87932	D	0	.	8.578	0.33609	0.6006:0.0:0.3994:0.0	.	813	O14686	MLL2_HUMAN	L	813	ENSP00000301067:P813L	ENSP00000301067:P813L	P	-	2	0	MLL2	47731295	0.000000	0.05858	0.028000	0.17463	0.009000	0.06853	-0.587000	0.05780	-0.301000	0.08882	-0.972000	0.02603	CCG	G|0.971;A|0.029	0.029	strong		0.647	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
TRPM6	140803	hgsc.bcm.edu	37	9	77416972	77416972	+	Silent	SNP	C	C	T	rs11144089	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:77416972C>T	ENST00000360774.1	-	16	2088	c.1851G>A	c.(1849-1851)ctG>ctA	p.L617L	TRPM6_ENST00000376864.4_Silent_p.L617L|RN7SKP47_ENST00000365347.1_RNA|TRPM6_ENST00000361255.3_Silent_p.L612L|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Silent_p.L612L|TRPM6_ENST00000451710.3_Silent_p.L617L|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	617					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						GCCTTTTCATCAGCACAGCCC	0.473													C|||	447	0.0892572	0.025	0.1066	5008	,	,		18275	0.1558		0.1074	False		,,,				2504	0.0767				p.L617L		Atlas-SNP	.											.	TRPM6	377	.	0			c.G1851A						PASS	.	C	,,	170,4236	111.2+/-149.4	4,162,2037	124.0	98.0	107.0		1836,1836,1851	-4.8	1.0	9	dbSNP_120	107	798,7802	187.0+/-234.4	36,726,3538	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	40,888,5575	TT,TC,CC		9.2791,3.8584,7.4427	,,	612/2018,612/2018,617/2023	77416972	968,12038	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon16			TTTCATCAGCACA	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.1851G>A	9.37:g.77416972C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	154	63	0.409091	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			C|0.911;T|0.089	0.089	strong		0.473	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
SLC46A2	57864	hgsc.bcm.edu	37	9	115652836	115652836	+	Silent	SNP	G	G	A	rs3802492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:115652836G>A	ENST00000374228.4	-	1	357	c.126C>T	c.(124-126)ctC>ctT	p.L42L		NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	42					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						CCTTCACCACGAGGAGTAGCC	0.677													G|||	1408	0.28115	0.3986	0.2363	5008	,	,		15844	0.0982		0.3191	False		,,,				2504	0.3037				p.L42L		Atlas-SNP	.											.	SLC46A2	30	.	0			c.C126T						PASS	.	G		1716,2690	514.7+/-368.7	349,1018,836	57.0	60.0	59.0		126	-1.1	1.0	9	dbSNP_107	59	2750,5850	437.4+/-358.6	472,1806,2022	no	coding-synonymous	SLC46A2	NM_033051.3		821,2824,2858	AA,AG,GG		31.9767,38.9469,34.338		42/476	115652836	4466,8540	2203	4300	6503	SO:0001819	synonymous_variant	57864	exon1			CACCACGAGGAGT	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.126C>T	9.37:g.115652836G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	55	53	0.963636	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	37	CCDS6786.1																																																																																			G|0.682;A|0.318	0.318	strong		0.677	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051	
COL3A1	1281	hgsc.bcm.edu	37	2	189852846	189852846	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:189852846C>T	ENST00000304636.3	+	6	738	c.568C>T	c.(568-570)Cat>Tat	p.H190Y	COL3A1_ENST00000317840.5_Missense_Mutation_p.H190Y	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	190	Triple-helical region.				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)	TACATCTGGTCATCCTGGTTC	0.403																																					p.H190Y		Atlas-SNP	.											COL3A1,mucosal,malignant_melanoma,0,1	COL3A1	292	1	0			c.C568T						scavenged	.						101.0	106.0	104.0					2																	189852846		2203	4300	6503	SO:0001583	missense	1281	exon6			TCTGGTCATCCTG	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.568C>T	2.37:g.189852846C>T	ENSP00000304408:p.His190Tyr	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	299	3	0.0100334	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	.	.	.	.	.	.	.	.	.	.	C	8.880	0.951521	0.18431	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.95171	-3.63;-3.63	5.43	5.43	0.79202	.	0.155742	0.31177	N	0.008108	D	0.90638	0.7064	N	0.19112	0.55	0.46901	D	0.999243	P	0.48911	0.917	P	0.48166	0.569	D	0.87494	0.2429	10	0.02654	T	1	.	19.0366	0.92982	0.0:1.0:0.0:0.0	.	190	P02461	CO3A1_HUMAN	Y	190	ENSP00000304408:H190Y;ENSP00000315243:H190Y	ENSP00000304408:H190Y	H	+	1	0	COL3A1	189561091	0.976000	0.34144	1.000000	0.80357	0.983000	0.72400	3.171000	0.50824	2.830000	0.97506	0.585000	0.79938	CAT	.	.	none		0.403	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
ZC3H11A	9877	hgsc.bcm.edu	37	1	203821314	203821314	+	Silent	SNP	G	G	A	rs41264265	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:203821314G>A	ENST00000545588.1	+	17	6047	c.2220G>A	c.(2218-2220)ccG>ccA	p.P740P	ZC3H11A_ENST00000332127.4_Silent_p.P740P|ZC3H11A_ENST00000367212.3_Silent_p.P740P|ZC3H11A_ENST00000367214.1_Silent_p.P740P|ZC3H11A_ENST00000367210.1_Silent_p.P740P	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	740					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			CCTCACCCCCGGAGGTGTCTG	0.478													G|||	878	0.175319	0.112	0.183	5008	,	,		16468	0.1558		0.2197	False		,,,				2504	0.2301				p.P740P		Atlas-SNP	.											.	ZC3H11A	71	.	0			c.G2220A						PASS	.	G		524,3858		22,480,1689	29.0	33.0	32.0		2220	-11.1	0.0	1	dbSNP_127	32	1733,6833		192,1349,2742	no	coding-synonymous	ZC3H11A	NM_014827.4		214,1829,4431	AA,AG,GG		20.2311,11.958,17.4313		740/811	203821314	2257,10691	2191	4283	6474	SO:0001819	synonymous_variant	9877	exon20			ACCCCCGGAGGTG		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"""Zinc fingers, CCCH-type domain containing"""	29093	protein-coding gene	gene with protein product		613513	"""zinc finger CCCH-type domain containing 11A"""	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.2220G>A	1.37:g.203821314G>A		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	318	280	0.880503	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Silent	SNP	ENST00000545588.1	37	CCDS30978.1																																																																																			.	.	weak		0.478	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827	
PSG8	440533	hgsc.bcm.edu	37	19	43269699	43269699	+	Missense_Mutation	SNP	C	C	T	rs71337226|rs7260508	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43269699C>T	ENST00000306511.4	-	1	132	c.35G>A	c.(34-36)cGc>cAc	p.R12H	PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.R12H|PSG8_ENST00000406636.3_Missense_Mutation_p.R12H	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	12				TQR -> MQH (in Ref. 2; CAH18672). {ECO:0000305}.		extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				CCAGGTGATGCGCTGTGTGCA	0.592													.|||	1786	0.356629	0.7315	0.2709	5008	,	,		17382	0.0903		0.3091	False		,,,				2504	0.2342				p.R12H		Atlas-SNP	.											PSG8_ENST00000404209,NS,carcinoma,-1,2	PSG8	101	2	0			c.G35A						PASS	.	T	HIS/ARG,HIS/ARG,HIS/ARG	1977,1045		665,647,199	117.0	118.0	118.0		35,35,35	-2.7	0.0	19	dbSNP_116	118	1619,3799		254,1111,1344	no	missense,missense,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	29,29,29	919,1758,1543	TT,TC,CC		29.8819,34.5797,42.6066	benign,benign,benign	12/420,12/298,12/427	43269699	3596,4844	1511	2709	4220	SO:0001583	missense	440533	exon1			GTGATGCGCTGTG	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.35G>A	19.37:g.43269699C>T	ENSP00000305005:p.Arg12His	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	706	0.3232600732600733	323	0.6565040650406504	109	0.3011049723756906	45	0.07867132867132867	229	0.3021108179419525	c	2.839	-0.240996	0.05906	0.654203	0.298819	ENSG00000124467	ENST00000404209;ENST00000406636;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.23348	2.18;1.91;2.19	1.35	-2.7	0.06004	.	.	.	.	.	T	0.00012	0.0000	N	0.01297	-0.9	0.80722	P	0.0	B;B;B	0.10296	0.002;0.003;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.34925	-0.9809	8	0.18710	T	0.47	.	7.3607	0.26745	0.0:0.5348:0.0:0.4652	rs7260508;rs60422632	12;12;12	Q9UQ74-2;Q9UQ74;A5PKV3	.;PSG8_HUMAN;.	H	12	ENSP00000385869:R12H;ENSP00000385081:R12H;ENSP00000305005:R12H	ENSP00000305005:R12H	R	-	2	0	PSG8	47961539	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.718000	0.00813	-1.864000	0.01148	-2.741000	0.00127	CGC	C|0.620;T|0.380	0.380	strong		0.592	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
SYTL1	84958	hgsc.bcm.edu	37	1	27676925	27676925	+	Silent	SNP	G	G	A	rs6702341	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:27676925G>A	ENST00000543823.1	+	9	1416	c.954G>A	c.(952-954)aaG>aaA	p.K318K	SYTL1_ENST00000490170.1_3'UTR|SYTL1_ENST00000318074.5_Silent_p.K306K			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	318	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)			NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GCAAGCGCAAGACGGCGGTGA	0.597													G|||	1226	0.244808	0.1392	0.2089	5008	,	,		15790	0.1786		0.3787	False		,,,				2504	0.3436				p.K318K		Atlas-SNP	.											.	SYTL1	57	.	0			c.G954A						PASS	.	G	,	745,3661	304.6+/-288.6	66,613,1524	115.0	101.0	106.0		954,918	3.9	1.0	1	dbSNP_116	106	3233,5367	488.6+/-372.4	618,1997,1685	no	coding-synonymous,coding-synonymous	SYTL1	NM_001193308.1,NM_032872.2	,	684,2610,3209	AA,AG,GG		37.593,16.9088,30.5859	,	318/563,306/551	27676925	3978,9028	2203	4300	6503	SO:0001819	synonymous_variant	84958	exon10			GCGCAAGACGGCG	AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.954G>A	1.37:g.27676925G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	39	30	0.769231	NM_001193308	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Silent	SNP	ENST00000543823.1	37	CCDS53286.1	546	0.25	72	0.14634146341463414	78	0.2154696132596685	100	0.17482517482517482	296	0.39050131926121373	G	11.12	1.546023	0.27652	0.169088	0.37593	ENSG00000142765	ENST00000496001	.	.	.	3.87	3.87	0.44632	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46789	-0.9166	3	.	.	.	-18.2362	6.0715	0.19891	0.2147:0.0:0.7853:0.0	rs6702341	.	.	.	K	166	.	.	R	+	2	0	SYTL1	27549512	1.000000	0.71417	0.999000	0.59377	0.962000	0.63368	0.998000	0.29744	2.155000	0.67459	0.462000	0.41574	AGA	G|0.711;A|0.289	0.289	strong		0.597	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872	
FMO4	2329	hgsc.bcm.edu	37	1	171303626	171303626	+	Missense_Mutation	SNP	G	G	A	rs573059844		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171303626G>A	ENST00000367749.3	+	8	1234	c.904G>A	c.(904-906)Gtg>Atg	p.V302M		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	302					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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					GAAAACCAGCGTGATTGAATT	0.378																																					p.V302M	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											FMO4,caecum,carcinoma,0,1	FMO4	64	1	0			c.G904A						PASS	.						70.0	73.0	72.0					1																	171303626		2203	4300	6503	SO:0001583	missense	2329	exon8			ACCAGCGTGATTG	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.904G>A	1.37:g.171303626G>A	ENSP00000356723:p.Val302Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	170	51	0.3	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.331649	0.41297	.	.	ENSG00000076258	ENST00000367749	T	0.61040	0.14	5.66	4.76	0.60689	.	0.135375	0.48286	D	0.000184	T	0.74680	0.3748	M	0.92880	3.355	0.46954	D	0.999265	D	0.89917	1.0	D	0.85130	0.997	T	0.80939	-0.1158	10	0.72032	D	0.01	-15.5018	10.7486	0.46196	0.1469:0.0:0.8531:0.0	.	302	P31512	FMO4_HUMAN	M	302	ENSP00000356723:V302M	ENSP00000356723:V302M	V	+	1	0	FMO4	169570250	0.823000	0.29233	0.380000	0.26093	0.043000	0.13939	1.146000	0.31589	1.387000	0.46486	-0.128000	0.14901	GTG	.	.	none		0.378	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022	
KNTC1	9735	hgsc.bcm.edu	37	12	123042027	123042027	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:123042027G>A	ENST00000333479.7	+	17	1546	c.1369G>A	c.(1369-1371)Gac>Aac	p.D457N	KNTC1_ENST00000450485.2_Missense_Mutation_p.D420N	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	457					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)		ACTTGTAGACGACGCTAAGGA	0.393																																					p.D457N		Atlas-SNP	.											KNTC1,NS,carcinoma,-2,1	KNTC1	182	1	0			c.G1369A						scavenged	.						127.0	116.0	120.0					12																	123042027		1889	4121	6010	SO:0001583	missense	9735	exon17			GTAGACGACGCTA		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.1369G>A	12.37:g.123042027G>A	ENSP00000328236:p.Asp457Asn	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	132	4	0.030303	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.457581	0.43634	.	.	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.23552	1.9;2.47	5.74	4.85	0.62838	.	0.051785	0.85682	D	0.000000	T	0.13114	0.0318	N	0.08118	0	0.80722	D	1	B;B	0.27700	0.186;0.012	B;B	0.15870	0.014;0.002	T	0.07309	-1.0779	10	0.62326	D	0.03	-13.1538	11.2416	0.48972	0.0686:0.1278:0.8036:0.0	.	420;457	E7ES84;P50748	.;KNTC1_HUMAN	N	420;457	ENSP00000397992:D420N;ENSP00000328236:D457N	ENSP00000328236:D457N	D	+	1	0	KNTC1	121607980	1.000000	0.71417	0.666000	0.29783	0.092000	0.18411	6.852000	0.75430	1.568000	0.49683	0.563000	0.77884	GAC	.	.	none		0.393	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
C14orf37	145407	hgsc.bcm.edu	37	14	58605734	58605734	+	Missense_Mutation	SNP	T	T	C	rs61741497	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:58605734T>C	ENST00000267485.7	-	2	537	c.343A>G	c.(343-345)Act>Gct	p.T115A	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	115						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						CCTGACTCAGTAGGTGTGGAA	0.478													T|||	8	0.00159744	0.0	0.0029	5008	,	,		21817	0.0		0.006	False		,,,				2504	0.0				p.T115A		Atlas-SNP	.											.	C14orf37	87	.	0			c.A343G						PASS	.	T	ALA/THR	8,4398	15.5+/-35.6	0,8,2195	85.0	81.0	82.0		343	2.1	0.1	14	dbSNP_129	82	62,8538	37.4+/-92.8	3,56,4241	yes	missense	C14orf37	NM_001001872.2	58	3,64,6436	CC,CT,TT		0.7209,0.1816,0.5382	possibly-damaging	115/775	58605734	70,12936	2203	4300	6503	SO:0001583	missense	145407	exon2			ACTCAGTAGGTGT		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.343A>G	14.37:g.58605734T>C	ENSP00000267485:p.Thr115Ala	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	212	140	0.660377	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	9.312	1.055831	0.19907	0.001816	0.007209	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.21734	1.99	5.82	2.06	0.26882	.	0.429079	0.24436	N	0.038557	T	0.13415	0.0325	M	0.62723	1.935	0.19300	N	0.99997	B;P;B;B	0.40970	0.208;0.734;0.208;0.208	B;B;B;B	0.39503	0.084;0.301;0.084;0.084	T	0.09729	-1.0661	10	0.37606	T	0.19	-2.845	4.9334	0.13928	0.0:0.2244:0.1493:0.6264	.	153;115;115;115	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	A	115;153	ENSP00000267485:T115A	ENSP00000267485:T115A	T	-	1	0	C14orf37	57675487	0.014000	0.17966	0.120000	0.21714	0.017000	0.09413	-0.048000	0.11944	0.106000	0.17784	0.533000	0.62120	ACT	T|0.995;C|0.005	0.005	strong		0.478	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
VILL	50853	hgsc.bcm.edu	37	3	38043904	38043904	+	Silent	SNP	T	T	C	rs9843296	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38043904T>C	ENST00000283713.6	+	14	1763	c.1497T>C	c.(1495-1497)caT>caC	p.H499H	VILL_ENST00000383759.2_Silent_p.H499H|VILL_ENST00000465644.1_Silent_p.H217H			O15195	VILL_HUMAN	villin-like	499					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)	p.H499H(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		CTGGGCACCATGGAAAGGGGC	0.612													T|||	971	0.19389	0.3495	0.1268	5008	,	,		19229	0.0853		0.1282	False		,,,				2504	0.2106				p.H499H		Atlas-SNP	.											VILL,NS,carcinoma,0,1	VILL	61	1	1	Substitution - coding silent(1)	stomach(1)	c.T1497C						PASS	.	T		1463,2943	470.5+/-355.8	247,969,987	84.0	69.0	74.0		1497	-9.6	0.0	3	dbSNP_119	74	1321,7279	260.2+/-283.1	100,1121,3079	no	coding-synonymous	VILL	NM_015873.3		347,2090,4066	CC,CT,TT		15.3605,33.2047,21.4055		499/857	38043904	2784,10222	2203	4300	6503	SO:0001819	synonymous_variant	50853	exon13			GCACCATGGAAAG		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.1497T>C	3.37:g.38043904T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	37	CCDS2670.2																																																																																			T|0.803;C|0.197	0.197	strong		0.612	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
CELSR3	1951	hgsc.bcm.edu	37	3	48691316	48691316	+	Missense_Mutation	SNP	T	T	C	rs12107252	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48691316T>C	ENST00000164024.4	-	8	5553	c.5273A>G	c.(5272-5274)cAg>cGg	p.Q1758R	CELSR3_ENST00000544264.1_Missense_Mutation_p.Q1758R	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	1758	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		Q -> R (in dbSNP:rs12107252).		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)		CTTACTAAGCTGACAGTCTTT	0.597													c|||	1049	0.209465	0.5076	0.1254	5008	,	,		19198	0.1181		0.1292	False		,,,				2504	0.0429				p.Q1758R		Atlas-SNP	.											.	CELSR3	237	.	0			c.A5273G						PASS	.		ARG/GLN	1949,2457	595.4+/-388.4	430,1089,684	50.0	64.0	59.0		5273	3.5	1.0	3	dbSNP_120	59	1075,7525	762.9+/-407.6	73,929,3298	yes	missense	CELSR3	NM_001407.2	43	503,2018,3982	CC,CT,TT		12.5,44.2351,23.2508	benign	1758/3313	48691316	3024,9982	2203	4300	6503	SO:0001583	missense	1951	exon8			CTAAGCTGACAGT	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.5273A>G	3.37:g.48691316T>C	ENSP00000164024:p.Gln1758Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	208	108	0.519231	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	37	CCDS2775.1	446	0.2042124542124542	246	0.5	44	0.12154696132596685	60	0.1048951048951049	96	0.1266490765171504	c	6.222	0.409163	0.11812	0.442351	0.125	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.79247	-1.25;-1.25	5.24	3.45	0.39498	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	L	0.55103	1.725	0.18873	P	0.9999837373	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41610	-0.9499	8	0.13853	T	0.58	.	10.6341	0.45554	0.0:0.7918:0.0:0.2082	rs12107252;rs58448451;rs12107252	1758;1828	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	R	1758	ENSP00000164024:Q1758R;ENSP00000445694:Q1758R	ENSP00000164024:Q1758R	Q	-	2	0	CELSR3	48666320	0.038000	0.19896	0.997000	0.53966	0.535000	0.34838	0.600000	0.24104	0.328000	0.23435	-0.751000	0.03497	CAG	T|0.781;C|0.219	0.219	strong		0.597	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
TFAP4	7023	hgsc.bcm.edu	37	16	4310468	4310468	+	Missense_Mutation	SNP	C	C	G	rs251732	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4310468C>G	ENST00000204517.6	-	5	982	c.654G>C	c.(652-654)caG>caC	p.Q218H		NM_003223.2	NP_003214.1	Q01664	TFAP4_HUMAN	transcription factor AP-4 (activating enhancer binding protein 4)	218	Gln-rich.		Q -> H (in dbSNP:rs251732). {ECO:0000269|PubMed:15616553}.		cellular response to dexamethasone stimulus (GO:0071549)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:2001269)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|protein homodimerization activity (GO:0042803)|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)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|endometrium(2)|lung(8)|ovary(1)|prostate(1)|skin(1)	14						GGGTccgcagctgctgctgtt	0.647													G|||	3369	0.672724	0.8336	0.6369	5008	,	,		13091	0.7589		0.506	False		,,,				2504	0.5634				p.Q218H		Atlas-SNP	.											TFAP4,colon,carcinoma,0,1	TFAP4	31	1	0			c.G654C						scavenged	.	G	HIS/GLN	3457,937		1372,713,112	21.0	21.0	21.0		654	2.1	1.0	16	dbSNP_79	21	4293,4307		1081,2131,1088	no	missense	TFAP4	NM_003223.2	24	2453,2844,1200	GG,GC,CC		49.9186,21.3245,40.3571	benign	218/339	4310468	7750,5244	2197	4300	6497	SO:0001583	missense	7023	exon5			CCGCAGCTGCTGC	X57435	CCDS10510.1	16p13	2013-05-21	2001-11-28		ENSG00000090447	ENSG00000090447		"""Basic helix-loop-helix proteins"""	11745	protein-coding gene	gene with protein product		600743	"""transcription factor AP-4 (activating enhancer-binding protein 4)"""			2123466	Standard	NM_003223		Approved	AP-4, bHLHc41	uc010uxg.2	Q01664	OTTHUMG00000129435	ENST00000204517.6:c.654G>C	16.37:g.4310468C>G	ENSP00000204517:p.Gln218His	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	187	82	0.438503	NM_003223	O60409	Missense_Mutation	SNP	ENST00000204517.6	37	CCDS10510.1	1457	0.6671245421245421	405	0.823170731707317	223	0.6160220994475138	440	0.7692307692307693	389	0.5131926121372031	G	11.24	1.579246	0.28180	0.786755	0.499186	ENSG00000090447	ENST00000204517	D	0.98717	-5.09	4.26	2.12	0.27331	.	0.467927	0.21148	N	0.079367	T	0.00012	0.0000	N	0.02011	-0.69	0.54753	P	1.0999999999983245E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.46925	-0.9156	9	0.14252	T	0.57	.	3.1819	0.06587	0.1617:0.1383:0.5578:0.1423	rs251732;rs1126923;rs61656003;rs251732	218	Q01664	TFAP4_HUMAN	H	218	ENSP00000204517:Q218H	ENSP00000204517:Q218H	Q	-	3	2	TFAP4	4250469	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	0.599000	0.24089	0.552000	0.29026	-0.986000	0.02555	CAG	C|0.381;G|0.619	0.619	strong		0.647	TFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251595.2	NM_003223	
HEXIM1	10614	hgsc.bcm.edu	37	17	43226887	43226887	+	Silent	SNP	A	A	G	rs12051846	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:43226887A>G	ENST00000332499.2	+	1	2204	c.330A>G	c.(328-330)gaA>gaG	p.E110E	AC002117.1_ENST00000589950.1_RNA|AC002117.1_ENST00000452741.1_RNA	NM_006460.2	NP_006451.1	O94992	HEXI1_HUMAN	hexamethylene bis-acetamide inducible 1	110					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						CAGAAGTGGAACCGACGCCCG	0.677											OREG0024474	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	996	0.198882	0.0477	0.1945	5008	,	,		13173	0.2183		0.2734	False		,,,				2504	0.3098				p.E110E		Atlas-SNP	.											.	HEXIM1	25	.	0			c.A330G						PASS	.	A		296,3994		6,284,1855	7.0	9.0	8.0		330	-0.4	0.1	17	dbSNP_120	8	1844,6602		199,1446,2578	no	coding-synonymous	HEXIM1	NM_006460.2		205,1730,4433	GG,GA,AA		21.8328,6.8998,16.8028		110/360	43226887	2140,10596	2145	4223	6368	SO:0001819	synonymous_variant	10614	exon1			AGTGGAACCGACG	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.330A>G	17.37:g.43226887A>G		Somatic	85	0	0	914	WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_006460	B2R8Y5	Silent	SNP	ENST00000332499.2	37	CCDS11495.1																																																																																			A|0.803;G|0.197	0.197	strong		0.677	HEXIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449821.2	NM_006460	
NLRP5	126206	hgsc.bcm.edu	37	19	56549510	56549510	+	Missense_Mutation	SNP	T	T	C	rs16986899	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56549510T>C	ENST00000390649.3	+	10	2735	c.2735T>C	c.(2734-2736)aTg>aCg	p.M912T		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	912			M -> T (in dbSNP:rs16986899). {ECO:0000269|PubMed:11925379}.		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.M912T(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)		CAGGGAGTAATGCCTCTCAGT	0.532													C|||	1327	0.264976	0.4486	0.1398	5008	,	,		21362	0.3006		0.1889	False		,,,				2504	0.1472				p.M912T		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - Missense(1)	stomach(1)	c.T2735C						scavenged	.	C	THR/MET	1623,2587		320,983,802	132.0	134.0	133.0		2735	-3.1	0.0	19	dbSNP_123	133	1407,7041		129,1149,2946	yes	missense	NLRP5	NM_153447.4	81	449,2132,3748	CC,CT,TT		16.6548,38.5511,23.9374	benign	912/1201	56549510	3030,9628	2105	4224	6329	SO:0001583	missense	126206	exon10			GAGTAATGCCTCT	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.2735T>C	19.37:g.56549510T>C	ENSP00000375063:p.Met912Thr	Somatic	222	2	0.00900901		WXS	Illumina HiSeq	Phase_I	224	104	0.464286	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	580	0.26556776556776557	208	0.42276422764227645	57	0.1574585635359116	178	0.3111888111888112	137	0.18073878627968337	C	0.711	-0.787261	0.02907	0.385511	0.166548	ENSG00000171487	ENST00000390649	T	0.51817	0.69	3.59	-3.09	0.05331	.	1.126530	0.06995	N	0.822221	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	0.40739	-0.9547	9	0.34782	T	0.22	.	2.2949	0.04147	0.2037:0.4503:0.2034:0.1426	rs16986899;rs52814735;rs60032233;rs16986899	912	P59047	NALP5_HUMAN	T	912	ENSP00000375063:M912T	ENSP00000375063:M912T	M	+	2	0	NLRP5	61241322	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.013000	0.12678	-1.137000	0.02888	-1.292000	0.01352	ATG	T|0.731;C|0.269	0.269	strong		0.532	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
CRISP3	10321	hgsc.bcm.edu	37	6	49701439	49701439	+	Missense_Mutation	SNP	C	C	A	rs1864312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:49701439C>A	ENST00000393666.1	-	4	406	c.400G>T	c.(400-402)Gca>Tca	p.A134S	CRISP3_ENST00000433368.2_Missense_Mutation_p.A157S|CRISP3_ENST00000371159.4_Missense_Mutation_p.A165S|CRISP3_ENST00000423399.2_Missense_Mutation_p.A44S|CRISP3_ENST00000263045.4_Missense_Mutation_p.A147S			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	134	SCP.		A -> S (in dbSNP:rs1864312). {ECO:0000269|PubMed:14702039}.		defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			CCAACCACTGCGTTGGGAGTC	0.403													C|||	1831	0.365615	0.2579	0.5821	5008	,	,		18832	0.3105		0.4682	False		,,,				2504	0.3088				p.A157S		Atlas-SNP	.											.	CRISP3	67	.	0			c.G469T						PASS	.	C	SER/ALA,SER/ALA	1322,3084	443.9+/-347.2	198,926,1079	121.0	114.0	117.0		469,439	3.2	0.0	6	dbSNP_92	117	3754,4846	534.0+/-382.5	806,2142,1352	yes	missense,missense	CRISP3	NM_001190986.1,NM_006061.2	99,99	1004,3068,2431	AA,AC,CC		43.6512,30.0045,39.0281	benign,benign	157/269,147/259	49701439	5076,7930	2203	4300	6503	SO:0001583	missense	10321	exon5			CCACTGCGTTGGG	X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.400G>T	6.37:g.49701439C>A	ENSP00000377274:p.Ala134Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	37		877	0.4015567765567766	130	0.26422764227642276	207	0.5718232044198895	184	0.32167832167832167	356	0.46965699208443273	C	7.197	0.592611	0.13875	0.300045	0.436512	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000423399;ENST00000371159;ENST00000354620	T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23	5.1	3.18	0.36537	CAP domain (3);	1.214940	0.06207	U	0.684266	T	0.01189	0.0039	N	0.04387	-0.21	0.80722	P	0.0	B	0.27380	0.177	B	0.31751	0.135	T	0.39860	-0.9593	9	0.07813	T	0.8	.	7.8096	0.29223	0.0:0.7193:0.1797:0.1009	rs1864312;rs13192472;rs52804712;rs59808203;rs1864312	134	P54108	CRIS3_HUMAN	S	147;157;134;44;165;157	ENSP00000263045:A147S;ENSP00000389026:A157S;ENSP00000377274:A134S;ENSP00000410469:A44S;ENSP00000360201:A165S;ENSP00000346636:A157S	ENSP00000263045:A147S	A	-	1	0	CRISP3	49809398	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	0.738000	0.26158	1.146000	0.42352	0.585000	0.79938	GCA	C|0.618;A|0.382	0.382	strong		0.403	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061	
ZNF177	7730	hgsc.bcm.edu	37	19	9492141	9492141	+	Silent	SNP	C	C	T	rs3826783	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9492141C>T	ENST00000589262.1	+	6	1200	c.1134C>T	c.(1132-1134)atC>atT	p.I378I	ZNF177_ENST00000446085.4_3'UTR|ZNF177_ENST00000602738.1_Silent_p.I218I|ZNF177_ENST00000590616.1_Intron|ZNF177_ENST00000541595.2_Silent_p.I218I|ZNF177_ENST00000434737.2_Silent_p.I378I|ZNF177_ENST00000343499.4_Silent_p.I218I|ZNF177_ENST00000602856.1_3'UTR	NM_001172651.1	NP_001166122.1	Q13360	ZN177_HUMAN	zinc finger protein 177	378					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|stomach(2)	13						AAGCCTTCATCGATCAGTCAT	0.473													C|||	2724	0.54393	0.5908	0.5375	5008	,	,		22704	0.4504		0.5606	False		,,,				2504	0.5644				p.I378I		Atlas-SNP	.											.	ZNF177	57	.	0			c.C1134T						PASS	.	C	,,,	2662,1744	647.5+/-398.6	793,1076,334	170.0	170.0	170.0		654,1134,,654	-0.7	0.1	19	dbSNP_107	170	5011,3589	627.4+/-398.0	1465,2081,754	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous	ZNF177,ZNF559-ZNF177	NM_001172650.2,NM_001172651.1,NM_001202425.1,NM_003451.2	,,,	2258,3157,1088	TT,TC,CC		41.7326,39.5824,41.0042	,,,	218/322,378/482,,218/322	9492141	7673,5333	2203	4300	6503	SO:0001819	synonymous_variant	7730	exon6			CTTCATCGATCAG	U37263, BC012012	CCDS12212.1, CCDS54214.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	12966	protein-coding gene	gene with protein product		601276					Standard	NM_003451		Approved		uc021uon.1	Q13360		ENST00000589262.1:c.1134C>T	19.37:g.9492141C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	157	68	0.433121	NM_001172651	B4DY57|E9PDG0|I3L0I4|Q96ER2	Silent	SNP	ENST00000589262.1	37	CCDS54214.1																																																																																			C|0.431;T|0.569	0.569	strong		0.473	ZNF177-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449028.1	NM_003451	
SVEP1	79987	hgsc.bcm.edu	37	9	113170289	113170289	+	Missense_Mutation	SNP	C	C	T	rs143931457	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:113170289C>T	ENST00000401783.2	-	38	7927	c.7591G>A	c.(7591-7593)Gaa>Aaa	p.E2531K	SVEP1_ENST00000374469.1_Missense_Mutation_p.E2508K|SVEP1_ENST00000297826.5_Missense_Mutation_p.E457K	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2531	Sushi 19. {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						CTGGGACCTTCGAGCCGAAAG	0.493													C|||	15	0.00299521	0.0008	0.0086	5008	,	,		21392	0.0		0.008	False		,,,				2504	0.0				p.E2531K		Atlas-SNP	.											.	SVEP1	326	.	0			c.G7591A						PASS	.	C	LYS/GLU	4,3868		0,4,1932	46.0	46.0	46.0		7591	-0.5	0.0	9	dbSNP_134	46	62,8228		0,62,4083	yes	missense	SVEP1	NM_153366.3	56	0,66,6015	TT,TC,CC		0.7479,0.1033,0.5427	possibly-damaging	2531/3572	113170289	66,12096	1936	4145	6081	SO:0001583	missense	79987	exon38			GACCTTCGAGCCG	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.7591G>A	9.37:g.113170289C>T	ENSP00000384917:p.Glu2531Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	9	0.004120879120879121	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	5	0.006596306068601583	C	2.875	-0.233153	0.05983	0.001033	0.007479	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.63913	-0.07;-0.07;-0.07	6.07	-0.482	0.12078	Complement control module (2);Sushi/SCR/CCP (3);	0.429928	0.28815	N	0.014048	T	0.31918	0.0812	L	0.38838	1.175	0.54753	D	0.999989	B	0.17268	0.021	B	0.10450	0.005	T	0.23261	-1.0193	10	0.06099	T	0.92	.	6.6805	0.23117	0.0:0.4592:0.2109:0.3299	.	2531	Q4LDE5	SVEP1_HUMAN	K	2531;2508;457;203	ENSP00000384917:E2531K;ENSP00000363593:E2508K;ENSP00000297826:E457K	ENSP00000297826:E457K	E	-	1	0	SVEP1	112210110	0.019000	0.18553	0.048000	0.18961	0.204000	0.24138	0.273000	0.18662	-0.095000	0.12351	0.655000	0.94253	GAA	C|0.996;T|0.004	0.004	strong		0.493	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HSPD1	3329	hgsc.bcm.edu	37	2	198363504	198363504	+	Silent	SNP	A	A	G	rs1050347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:198363504A>G	ENST00000388968.3	-	2	336	c.69T>C	c.(67-69)acT>acC	p.T23T	HSPE1_ENST00000409729.1_5'Flank|HSPE1-MOB4_ENST00000604458.1_5'Flank|HSPE1_ENST00000233893.5_5'Flank|HSPD1_ENST00000544407.1_Silent_p.T23T|HSPD1_ENST00000345042.2_Silent_p.T23T|HSPE1_ENST00000409468.1_5'Flank	NM_002156.4	NP_002147.2	P10809	CH60_HUMAN	heat shock 60kDa protein 1 (chaperonin)	23					'de novo' protein folding (GO:0006458)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ATP catabolic process (GO:0006200)|B cell activation (GO:0042113)|B cell cytokine production (GO:0002368)|B cell proliferation (GO:0042100)|chaperone-mediated protein complex assembly (GO:0051131)|isotype switching to IgG isotypes (GO:0048291)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell mediated immune response to tumor cell (GO:0002842)|protein maturation (GO:0051604)|protein refolding (GO:0042026)|protein stabilization (GO:0050821)|response to unfolded protein (GO:0006986)|T cell activation (GO:0042110)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lipopolysaccharide receptor complex (GO:0046696)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|chaperone binding (GO:0051087)|DNA replication origin binding (GO:0003688)|double-stranded RNA binding (GO:0003725)|lipopolysaccharide binding (GO:0001530)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|single-stranded DNA binding (GO:0003697)|unfolded protein binding (GO:0051082)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(7)|skin(1)	17			Epithelial(96;0.225)			CATAAGCCCGAGTGAGATGAG	0.502													A|||	792	0.158147	0.1029	0.1744	5008	,	,		17688	0.2282		0.2117	False		,,,				2504	0.0941				p.T23T		Atlas-SNP	.											.	HSPD1	68	.	0			c.T69C						PASS	.	A	,	492,3914		25,442,1736	57.0	57.0	57.0		69,69	2.4	1.0	2	dbSNP_86	57	1646,6954		104,1438,2758	no	coding-synonymous,coding-synonymous	HSPD1	NM_002156.4,NM_199440.1	,	129,1880,4494	GG,GA,AA		19.1395,11.1666,16.4386	,	23/574,23/574	198363504	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	3329	exon2			AGCCCGAGTGAGA	M34664	CCDS33357.1	2q33.1	2011-09-02	2002-08-29		ENSG00000144381	ENSG00000144381		"""Heat Shock Proteins / Chaperonins"""	5261	protein-coding gene	gene with protein product		118190	"""heat shock 60kD protein 1 (chaperonin)"", ""spastic paraplegia 13 (autosomal dominant)"""	SPG13		1980192, 11898127	Standard	NM_002156		Approved	GROEL, HSP60	uc002uui.3	P10809	OTTHUMG00000154463	ENST00000388968.3:c.69T>C	2.37:g.198363504A>G		Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	290	128	0.441379	NM_002156	B2R5M6|B7Z712|Q38L19|Q9UCR6	Silent	SNP	ENST00000388968.3	37	CCDS33357.1																																																																																			A|0.813;G|0.187	0.187	strong		0.502	HSPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335324.2	NM_002156	
CEACAM20	125931	hgsc.bcm.edu	37	19	45024535	45024535	+	RNA	SNP	T	T	C	rs200961907		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45024535T>C	ENST00000454753.1	-	0	1281							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)				AGGGGCTCACTCCGGGCCCGG	0.592																																					p.S335G		Atlas-SNP	.											.	CEACAM20	31	.	0			c.A1003G						PASS	.		GLY/SER,GLY/SER,GLY/SER,GLY/SER	1,3869		0,1,1934	45.0	47.0	46.0		1003,1003,1003,1003	4.3	0.0	19		46	7,8257		0,7,4125	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	56,56,56,56	0,8,6059	CC,CT,TT		0.0847,0.0258,0.0659	probably-damaging,probably-damaging,probably-damaging,probably-damaging	335/597,335/492,335/504,335/585	45024535	8,12126	1935	4132	6067			125931	exon5			GCTCACTCCGGGC	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.45024535T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				T|0.996;C|0.004	0.004	weak		0.592	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
AGAP6	414189	hgsc.bcm.edu	37	10	51748684	51748684	+	Missense_Mutation	SNP	G	G	A	rs61848260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.																																			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	13	0	0		WXS	Illumina HiSeq	Phase_I	20	17	0.85	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	
SCN3A	6328	hgsc.bcm.edu	37	2	165987772	165987772	+	Silent	SNP	T	T	G	rs62174900	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	207	0	0		WXS	Illumina HiSeq	Phase_I	200	93	0.465	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	
ABCB1	5243	hgsc.bcm.edu	37	7	87229440	87229440	+	Missense_Mutation	SNP	T	T	C	rs9282564|rs9332385	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	157	59	0.375796	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	
C14orf177	283598	hgsc.bcm.edu	37	14	99182626	99182626	+	Missense_Mutation	SNP	T	T	C	rs4905757	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:99182626T>C	ENST00000325812.2	+	3	517	c.98T>C	c.(97-99)gTg>gCg	p.V33A		NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177	33			V -> A (in dbSNP:rs4905757).							endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				CGCCCATCAGTGAGCCAACTT	0.567													T|||	105	0.0209665	0.0023	0.0403	5008	,	,		19576	0.001		0.0636	False		,,,				2504	0.0092				p.V33A		Atlas-SNP	.											.	C14orf177	37	.	0			c.T98C						PASS	.	T	ALA/VAL	33,4373	38.4+/-70.7	0,33,2170	140.0	100.0	114.0		98	-0.5	0.0	14	dbSNP_111	114	463,8137	137.1+/-194.1	18,427,3855	yes	missense	C14orf177	NM_182560.2	64	18,460,6025	CC,CT,TT		5.3837,0.749,3.8136	benign	33/126	99182626	496,12510	2203	4300	6503	SO:0001583	missense	283598	exon3			CATCAGTGAGCCA	AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745	ENST00000325812.2:c.98T>C	14.37:g.99182626T>C	ENSP00000321360:p.Val33Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	192	98	0.510417	NM_182560	Q8N7D2	Missense_Mutation	SNP	ENST00000325812.2	37	CCDS9948.1	68	0.031135531135531136	2	0.0040650406504065045	14	0.03867403314917127	1	0.0017482517482517483	51	0.06728232189973615	T	5.415	0.261821	0.10239	0.00749	0.053837	ENSG00000176605	ENST00000325812;ENST00000541516	T;T	0.40225	1.12;1.04	2.29	-0.466	0.12153	.	.	.	.	.	T	0.01905	0.0060	N	0.08118	0	0.09310	N	1	P	0.35481	0.504	B	0.42030	0.373	T	0.15350	-1.0440	9	0.87932	D	0	.	6.4055	0.21662	0.0:0.0:0.5236:0.4764	rs4905757;rs17531319;rs4905757	33	Q52M58	CN177_HUMAN	A	33	ENSP00000321360:V33A;ENSP00000440687:V33A	ENSP00000321360:V33A	V	+	2	0	C14orf177	98252379	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.060000	0.11712	-0.100000	0.12241	0.454000	0.30748	GTG	T|0.973;C|0.027	0.027	strong		0.567	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1	NM_182560	
KIAA0825	285600	hgsc.bcm.edu	37	5	93753017	93753017	+	Missense_Mutation	SNP	C	C	T	rs29910	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:93753017C>T	ENST00000513200.3	-	14	2623	c.2551G>A	c.(2551-2553)Gcc>Acc	p.A851T	KIAA0825_ENST00000312498.7_Missense_Mutation_p.A856T|KIAA0825_ENST00000427991.2_Missense_Mutation_p.A851T	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	851								p.A851T(1)|p.A856T(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTAAAGATGGCTTCCATCAAG	0.353													C|||	921	0.183906	0.1293	0.1715	5008	,	,		18183	0.0784		0.2863	False		,,,				2504	0.2699				p.A851T		Atlas-SNP	.											KIAA0825_ENST00000513200,NS,carcinoma,0,2	KIAA0825	172	2	2	Substitution - Missense(2)	kidney(2)	c.G2551A						PASS	.	C	THR/ALA	205,1179		23,159,510	207.0	172.0	183.0		2551	3.6	1.0	5	dbSNP_76	183	940,2242		144,652,795	yes	missense	KIAA0825	NM_001145678.1	58	167,811,1305	TT,TC,CC		29.5412,14.8121,25.0767	benign	851/1276	93753017	1145,3421	692	1591	2283	SO:0001583	missense	285600	exon15			AGATGGCTTCCAT	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.2551G>A	5.37:g.93753017C>T	ENSP00000424618:p.Ala851Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001145678	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	37		386	0.17673992673992675	50	0.1016260162601626	72	0.19889502762430938	37	0.06468531468531469	227	0.2994722955145119	C	12.22	1.873335	0.33069	0.148121	0.295412	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498	T;T;T	0.49432	0.79;0.79;0.78	5.39	3.57	0.40892	.	0.000000	0.64402	D	0.000010	T	0.00012	0.0000	L	0.34521	1.04	0.35559	P	0.19545800000000002	B	0.29988	0.264	B	0.31290	0.127	T	0.22730	-1.0208	9	0.06494	T	0.89	.	8.2205	0.31539	0.1549:0.7637:0.0:0.0814	rs29910;rs17378492;rs56725943;rs29910	851	Q8IV33	K0825_HUMAN	T	851;851;856	ENSP00000424618:A851T;ENSP00000400288:A851T;ENSP00000312205:A856T	ENSP00000312205:A856T	A	-	1	0	KIAA0825	93778773	0.994000	0.37717	0.989000	0.46669	0.868000	0.49771	0.084000	0.14891	0.608000	0.30000	0.557000	0.71058	GCC	C|0.811;T|0.189	0.189	strong		0.353	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665	
RTKN2	219790	hgsc.bcm.edu	37	10	63977980	63977980	+	Missense_Mutation	SNP	C	C	T	rs61850830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:63977980C>T	ENST00000373789.3	-	8	958	c.862G>A	c.(862-864)Gca>Aca	p.A288T	RTKN2_ENST00000395265.1_Missense_Mutation_p.A288T|RTKN2_ENST00000315289.2_Missense_Mutation_p.A69T	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	288	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					CCTGCAAATGCATCCTCAGCC	0.408													C|||	535	0.106829	0.0098	0.0735	5008	,	,		15862	0.0982		0.1034	False		,,,				2504	0.274				p.A288T		Atlas-SNP	.											.	RTKN2	68	.	0			c.G862A						PASS	.	C	THR/ALA	101,4305	81.4+/-119.9	2,97,2104	69.0	65.0	66.0		862	5.4	1.0	10	dbSNP_129	66	975,7625	212.5+/-252.8	67,841,3392	yes	missense	RTKN2	NM_145307.2	58	69,938,5496	TT,TC,CC		11.3372,2.2923,8.2731	benign	288/610	63977980	1076,11930	2203	4300	6503	SO:0001583	missense	219790	exon8			CAAATGCATCCTC	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"""Pleckstrin homology (PH) domain containing"""	19364	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family K member 1"""	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.862G>A	10.37:g.63977980C>T	ENSP00000362894:p.Ala288Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	42	5	0.119048	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Missense_Mutation	SNP	ENST00000373789.3	37	CCDS7263.1	160	0.07326007326007326	5	0.01016260162601626	25	0.06906077348066299	51	0.08916083916083917	79	0.10422163588390501	C	15.85	2.956169	0.53293	0.022923	0.113372	ENSG00000182010	ENST00000315289;ENST00000395265;ENST00000373789	T;T;T	0.43294	0.95;1.54;1.54	5.42	5.42	0.78866	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.315023	0.39687	N	0.001297	T	0.00998	0.0033	L	0.44542	1.39	0.29024	P	0.886098	D;P	0.53462	0.96;0.822	P;B	0.52454	0.699;0.393	T	0.05162	-1.0902	9	0.19590	T	0.45	-6.1534	11.1113	0.48235	0.0:0.8823:0.0:0.1177	rs61850830	69;288	Q5SVY4;Q8IZC4	.;RTKN2_HUMAN	T	69;288;288	ENSP00000325379:A69T;ENSP00000378682:A288T;ENSP00000362894:A288T	ENSP00000325379:A69T	A	-	1	0	RTKN2	63647986	1.000000	0.71417	0.998000	0.56505	0.982000	0.71751	2.160000	0.42348	2.711000	0.92665	0.655000	0.94253	GCA	C|0.913;T|0.087	0.087	strong		0.408	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307	
ZNF107	51427	hgsc.bcm.edu	37	7	64166802	64166802	+	Missense_Mutation	SNP	G	G	T	rs73138709	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	193	0	0		WXS	Illumina HiSeq	Phase_I	244	143	0.586066	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	
DHRS4	10901	hgsc.bcm.edu	37	14	24424346	24424346	+	Silent	SNP	G	G	A	rs4981491		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24424346G>A	ENST00000313250.5	+	2	434	c.231G>A	c.(229-231)caG>caA	p.Q77Q	DHRS4_ENST00000397075.3_Silent_p.Q77Q|DHRS4_ENST00000558581.1_Silent_p.Q77Q|DHRS4_ENST00000421831.1_Silent_p.Q59Q|DHRS4_ENST00000397073.2_Silent_p.Q59Q|DHRS4_ENST00000308178.8_Silent_p.Q59Q|DHRS4_ENST00000559632.1_Silent_p.Q77Q|DHRS4_ENST00000543741.2_Silent_p.Q77Q|DHRS4_ENST00000558263.1_Silent_p.Q77Q|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000382761.3_Silent_p.Q59Q|DHRS4_ENST00000397074.3_Silent_p.Q77Q	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	77					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CCACGCTGCAGGGGGAGGGGC	0.701																																					p.Q77Q		Atlas-SNP	.											.	DHRS4	22	.	0			c.G231A						PASS	.						37.0	42.0	40.0					14																	24424346		2203	4299	6502	SO:0001819	synonymous_variant	10901	exon2			GCTGCAGGGGGAG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.231G>A	14.37:g.24424346G>A		Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	432	92	0.212963	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Silent	SNP	ENST00000313250.5	37	CCDS9605.1																																																																																			.	.	weak		0.701	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
AK7	122481	hgsc.bcm.edu	37	14	96871104	96871104	+	Missense_Mutation	SNP	G	G	A	rs2275554	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	95	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	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		
OR6C70	390327	hgsc.bcm.edu	37	12	55863398	55863398	+	Silent	SNP	G	G	A	rs12313730	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:55863398G>A	ENST00000327335.4	-	1	524	c.525C>T	c.(523-525)ttC>ttT	p.F175F	RP11-110A12.2_ENST00000555146.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000554049.1_RNA	NM_001005499.1	NP_001005499.1	A6NIJ9	O6C70_HUMAN	olfactory receptor, family 6, subfamily C, member 70	175						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)|cervix(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	18						TGTCACAAATGAAATGATCAA	0.348													G|||	806	0.160942	0.0189	0.2291	5008	,	,		21963	0.0665		0.3131	False		,,,				2504	0.2454				p.F175F		Atlas-SNP	.											.	OR6C70	35	.	0			c.C525T						PASS	.	G		263,4143	146.1+/-180.8	4,255,1944	94.0	97.0	96.0		525	-1.0	0.1	12	dbSNP_120	96	2551,6049	412.8+/-350.9	384,1783,2133	no	coding-synonymous	OR6C70	NM_001005499.1		388,2038,4077	AA,AG,GG		29.6628,5.9691,21.6362		175/313	55863398	2814,10192	2203	4300	6503	SO:0001819	synonymous_variant	390327	exon1			ACAAATGAAATGA		CCDS31825.1	12q13.2	2013-09-23			ENSG00000184954	ENSG00000184954		"""GPCR / Class A : Olfactory receptors"""	31299	protein-coding gene	gene with protein product							Standard	NM_001005499		Approved		uc010spn.2	A6NIJ9	OTTHUMG00000171127	ENST00000327335.4:c.525C>T	12.37:g.55863398G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_001005499		Silent	SNP	ENST00000327335.4	37	CCDS31825.1																																																																																			G|0.814;A|0.186	0.186	strong		0.348	OR6C70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411820.1		
FAM198A	729085	hgsc.bcm.edu	37	3	43097710	43097710	+	Silent	SNP	A	A	G	rs664628	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:43097710A>G	ENST00000430121.2	+	5	1655	c.1560A>G	c.(1558-1560)ctA>ctG	p.L520L		NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	520						extracellular region (GO:0005576)				endometrium(1)	1						CAGGGTGTCTACAGAACATGC	0.567													A|||	1950	0.389377	0.2685	0.5058	5008	,	,		19848	0.5823		0.3887	False		,,,				2504	0.272				p.L520L		Atlas-SNP	.											.	FAM198A	23	.	0			c.A1560G						PASS	.	A		400,984		56,288,348	43.0	42.0	42.0		1560	-3.7	0.0	3	dbSNP_83	42	1211,1971		234,743,614	no	coding-synonymous	FAM198A	NM_001129908.2		290,1031,962	GG,GA,AA		38.0578,28.9017,35.2825		520/576	43097710	1611,2955	692	1591	2283	SO:0001819	synonymous_variant	729085	exon5			GTGTCTACAGAAC	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.1560A>G	3.37:g.43097710A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	136	131	0.963235	NM_001129908	B3KR48	Silent	SNP	ENST00000430121.2	37	CCDS46808.1																																																																																			A|0.589;G|0.411	0.411	strong		0.567	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
DCHS2	54798	hgsc.bcm.edu	37	4	155256177	155256177	+	Silent	SNP	A	A	G	rs6858157	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:155256177A>G	ENST00000357232.4	-	8	1058	c.1059T>C	c.(1057-1059)ggT>ggC	p.G353G	DCHS2_ENST00000507542.1_5'UTR|DCHS2_ENST00000339452.1_Silent_p.G852G	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	353	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)	p.G353G(2)|p.G852G(1)		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)		CTGTGAGCCCACCACCGTCTT	0.423													A|||	1746	0.348642	0.3396	0.3242	5008	,	,		19216	0.3899		0.3101	False		,,,				2504	0.3753				p.G852G		Atlas-SNP	.											DCHS2_ENST00000339452,NS,carcinoma,0,3	DCHS2	594	3	3	Substitution - coding silent(3)	prostate(2)|stomach(1)	c.T2556C						scavenged	.	A	,	1460,2946	471.8+/-356.2	258,944,1001	103.0	105.0	104.0		2556,1059	-4.3	0.9	4	dbSNP_116	104	2827,5773	446.7+/-361.3	467,1893,1940	no	coding-synonymous,coding-synonymous	DCHS2	NM_001142552.1,NM_017639.3	,	725,2837,2941	GG,GA,AA		32.8721,33.1366,32.9617	,	852/1370,353/2917	155256177	4287,8719	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon4			GAGCCCACCACCG	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.1059T>C	4.37:g.155256177A>G		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	95	17	0.178947	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			A|0.668;G|0.332	0.332	strong		0.423	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
DBH	1621	hgsc.bcm.edu	37	9	136522274	136522274	+	Missense_Mutation	SNP	C	C	T	rs6271	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136522274C>T	ENST00000393056.2	+	11	1657	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	DBH-AS1_ENST00000425189.1_RNA	NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	549			R -> C (in dbSNP:rs6271). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:3443096}.		behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	CTCCTTCAACCGCGACGTACT	0.612													C|||	104	0.0207668	0.0053	0.0447	5008	,	,		16323	0.0		0.0606	False		,,,				2504	0.0051				p.R549C		Atlas-SNP	.											.	DBH	86	.	0			c.C1645T	GRCh37	CM054656	DBH	M	rs6271	PASS	.	C	CYS/ARG	57,4349	56.2+/-92.4	0,57,2146	166.0	120.0	136.0		1645	4.2	0.0	9	dbSNP_52	136	656,7944	166.4+/-218.3	25,606,3669	yes	missense	DBH	NM_000787.3	180	25,663,5815	TT,TC,CC		7.6279,1.2937,5.4821	possibly-damaging	549/618	136522274	713,12293	2203	4300	6503	SO:0001583	missense	1621	exon11			TTCAACCGCGACG	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.1645C>T	9.37:g.136522274C>T	ENSP00000376776:p.Arg549Cys	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	204	98	0.480392	NM_000787	Q5T381|Q96AG2	Missense_Mutation	SNP	ENST00000393056.2	37	CCDS6977.2	71	0.03250915750915751	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	44	0.05804749340369393	C	10.61	1.397932	0.25205	0.012937	0.076279	ENSG00000123454	ENST00000393056	T	0.49432	0.78	5.07	4.16	0.48862	.	0.346260	0.30492	N	0.009514	T	0.04815	0.0130	M	0.78223	2.4	0.19300	N	0.99997	D	0.57899	0.981	P	0.47162	0.54	T	0.07888	-1.0749	10	0.54805	T	0.06	-26.8568	8.555	0.33476	0.3682:0.5038:0.128:0.0	rs6271;rs6271	549	P09172	DOPO_HUMAN	C	549	ENSP00000376776:R549C	ENSP00000376776:R549C	R	+	1	0	DBH	135512095	0.996000	0.38824	0.028000	0.17463	0.046000	0.14306	3.394000	0.52551	1.109000	0.41680	-0.500000	0.04577	CGC	C|0.956;T|0.044	0.044	strong		0.612	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
REV1	51455	hgsc.bcm.edu	37	2	100055506	100055506	+	Missense_Mutation	SNP	A	A	G	rs3087386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:100055506A>G	ENST00000258428.3	-	6	998	c.770T>C	c.(769-771)tTt>tCt	p.F257S	REV1_ENST00000393445.3_Missense_Mutation_p.F257S|REV1_ENST00000465835.1_5'UTR	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	257			F -> S (in dbSNP:rs3087386).		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						CTCCTGGGAAAAGGCTGGAGA	0.498								Direct reversal of damage					.|||	2906	0.580272	0.7315	0.7003	5008	,	,		19504	0.3611		0.5666	False		,,,				2504	0.5307				p.F257S		Atlas-SNP	.											.	REV1	100	.	0			c.T770C						PASS	.	G	SER/PHE,SER/PHE	3115,1291	436.8+/-344.8	1099,917,187	57.0	55.0	56.0		770,770	-0.0	0.0	2	dbSNP_102	56	4708,3892	544.8+/-384.7	1283,2142,875	yes	missense,missense	REV1	NM_001037872.1,NM_016316.2	155,155	2382,3059,1062	GG,GA,AA		45.2558,29.301,39.8508	benign,benign	257/1251,257/1252	100055506	7823,5183	2203	4300	6503	SO:0001583	missense	51455	exon6			TGGGAAAAGGCTG	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.770T>C	2.37:g.100055506A>G	ENSP00000258428:p.Phe257Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	1254	0.5741758241758241	355	0.7215447154471545	253	0.6988950276243094	204	0.35664335664335667	442	0.58311345646438	G	0.727	-0.781505	0.02929	0.70699	0.547442	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.25414	1.8;1.8	5.54	-0.0271	0.13927	.	1.017110	0.07806	N	0.957370	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	0.35450	-0.9788	9	0.08179	T	0.78	.	6.4404	0.21847	0.4589:0.1197:0.4214:0.0	rs3087386;rs3749086;rs58019413;rs3087386	236;257;257	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	S	257	ENSP00000377091:F257S;ENSP00000258428:F257S	ENSP00000258428:F257S	F	-	2	0	REV1	99421938	0.164000	0.22935	0.000000	0.03702	0.074000	0.17049	0.717000	0.25851	-0.622000	0.05626	-1.653000	0.00756	TTT	A|0.422;G|0.578	0.578	strong		0.498	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316	
SPATA3	130560	hgsc.bcm.edu	37	2	231861059	231861059	+	Silent	SNP	A	A	T	rs72362780		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231861059A>T	ENST00000452881.1	+	1	219	c.111A>T	c.(109-111)ccA>ccT	p.P37P	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_Silent_p.P37P|SPATA3_ENST00000424440.1_Silent_p.P37P|SPATA3_ENST00000455816.1_Silent_p.P37P			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	37										endometrium(2)|lung(1)	3						AATCCACACCACAGCAGCCTA	0.572																																					p.P37P		Atlas-SNP	.											SPATA3,NS,carcinoma,0,4	SPATA3	52	4	0			c.A111T						scavenged	.						127.0	133.0	131.0					2																	231861059		692	1591	2283	SO:0001819	synonymous_variant	130560	exon1			CACACCACAGCAG	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.111A>T	2.37:g.231861059A>T		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	88	18	0.204545	NM_139073	Q86WX5|Q8N9Y6	Silent	SNP	ENST00000452881.1	37	CCDS2481.1																																																																																			.	.	none		0.572	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
ZFP36L1	677	hgsc.bcm.edu	37	14	69259662	69259662	+	5'UTR	SNP	C	C	A	rs1051533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:69259662C>A	ENST00000439696.2	-	0	295				ZFP36L1_ENST00000336440.3_5'UTR|ZFP36L1_ENST00000555997.1_5'Flank	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TCATCCTGTGCGTTCGCGCGA	0.602													C|||	1019	0.203474	0.3888	0.1513	5008	,	,		11682	0.0089		0.2127	False		,,,				2504	0.181				p.T67T		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.G201T						PASS	.	C		1583,2823	494.3+/-362.9	296,991,916	121.0	117.0	118.0			1.4	1.0	14	dbSNP_86	118	1916,6684	340.3+/-323.5	215,1486,2599	no	utr-5	ZFP36L1	NM_004926.3		511,2477,3515	AA,AC,CC		22.2791,35.9283,26.903			69259662	3499,9507	2203	4300	6503	SO:0001623	5_prime_UTR_variant	677	exon2			CCTGTGCGTTCGC	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"""RING-type (C3HC4) zinc fingers"""	1107	protein-coding gene	gene with protein product		601064	"""zinc finger protein, C3H type, 36-like 1"", ""zinc finger protein 36, C3H type-like 1"""	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.-7G>T	14.37:g.69259662C>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_001244701	Q13851	Silent	SNP	ENST00000439696.2	37	CCDS9791.1																																																																																			C|0.791;A|0.209	0.209	strong		0.602	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		
FLG	2312	hgsc.bcm.edu	37	1	152276659	152276659	+	Missense_Mutation	SNP	T	T	C	rs7532285	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152276659T>C	ENST00000368799.1	-	3	10738	c.10703A>G	c.(10702-10704)cAg>cGg	p.Q3568R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3568	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGACTGCTCCTGAGCAGATCC	0.567									Ichthyosis				t|||	1035	0.206669	0.2133	0.1916	5008	,	,		18266	0.3403		0.0696	False		,,,				2504	0.2117				p.Q3568R		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.A10703G						PASS	.						148.0	201.0	183.0					1																	152276659		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCTCCTGAGCAG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10703A>G	1.37:g.152276659T>C	ENSP00000357789:p.Gln3568Arg	Somatic	398	0	0		WXS	Illumina HiSeq	Phase_I	376	29	0.0771277	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	t	3.885	-0.025135	0.07589	.	.	ENSG00000143631	ENST00000368799	T	0.01647	4.71	3.16	-6.33	0.01988	.	.	.	.	.	T	0.00210	0.0006	N	0.04508	-0.205	0.09310	N	1	B	0.15719	0.014	B	0.10450	0.005	T	0.45948	-0.9226	9	0.15066	T	0.55	.	1.2756	0.02030	0.1435:0.216:0.1461:0.4945	rs7532285;rs56765845;rs7532285	3568	P20930	FILA_HUMAN	R	3568	ENSP00000357789:Q3568R	ENSP00000357789:Q3568R	Q	-	2	0	FLG	150543283	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.180000	0.03088	-1.526000	0.01760	-1.734000	0.00692	CAG	T|0.993;C|0.007	0.007	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
WDR49	151790	hgsc.bcm.edu	37	3	167217964	167217964	+	Missense_Mutation	SNP	A	A	G	rs13060964	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:167217964A>G	ENST00000308378.3	-	14	2257	c.1952T>C	c.(1951-1953)cTg>cCg	p.L651P	WDR49_ENST00000476376.1_Missense_Mutation_p.L476P|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000453925.2_Missense_Mutation_p.L616P	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	651			L -> P (in dbSNP:rs13060964).							breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	50						CGGGGCCTCCAGAATTTGGGG	0.433													G|||	1807	0.360823	0.2632	0.3429	5008	,	,		16385	0.4812		0.3519	False		,,,				2504	0.3906				p.L651P		Atlas-SNP	.											.	WDR49	188	.	0			c.T1952C						PASS	.	G	PRO/LEU	1191,3215	707.3+/-407.5	165,861,1177	128.0	146.0	140.0		1952	3.3	0.1	3	dbSNP_121	140	2999,5601	664.5+/-402.2	539,1921,1840	yes	missense	WDR49	NM_178824.3	98	704,2782,3017	GG,GA,AA		34.8721,27.0313,32.2159	benign	651/698	167217964	4190,8816	2203	4300	6503	SO:0001583	missense	151790	exon14			GCCTCCAGAATTT	AK097556	CCDS3201.1	3q26.1	2013-01-11			ENSG00000174776	ENSG00000174776		"""WD repeat domain containing"""	26587	protein-coding gene	gene with protein product						12477932	Standard	NM_178824		Approved	FLJ33620	uc003fev.1	Q8IV35	OTTHUMG00000158290	ENST00000308378.3:c.1952T>C	3.37:g.167217964A>G	ENSP00000311343:p.Leu651Pro	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	68	40	0.588235	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	798|798	0.36538461538461536|0.36538461538461536	145|145	0.29471544715447157|0.29471544715447157	122|122	0.3370165745856354|0.3370165745856354	264|264	0.46153846153846156|0.46153846153846156	267|267	0.35224274406332456|0.35224274406332456	G|G	0.623|0.623	-0.820174|-0.820174	0.02755|0.02755	0.270313|0.270313	0.348721|0.348721	ENSG00000174776|ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925|ENST00000472600	T;T;T|.	0.52295|.	0.67;1.97;1.03|.	5.13|5.13	3.29|3.29	0.37713|0.37713	.|.	0.401030|.	0.22481|.	N|.	0.059486|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00170|0.00170	-1.935|-1.935	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	0.45906|0.45906	-0.9229|-0.9229	9|4	0.46703|.	T|.	0.11|.	.|.	6.7493|6.7493	0.23477|0.23477	0.328:0.0:0.672:0.0|0.328:0.0:0.672:0.0	rs13060964;rs52834126;rs58923964;rs13060964|rs13060964;rs52834126;rs58923964;rs13060964	616;651|.	E7EQK3;Q8IV35|.	.;WDR49_HUMAN|.	P|R	651;476;616|628	ENSP00000311343:L651P;ENSP00000420508:L476P;ENSP00000410863:L616P|.	ENSP00000311343:L651P|.	L|W	-|-	2|1	0|0	WDR49|WDR49	168700658|168700658	0.130000|0.130000	0.22417|0.22417	0.090000|0.090000	0.20809|0.20809	0.002000|0.002000	0.02628|0.02628	1.406000|1.406000	0.34646|0.34646	1.165000|1.165000	0.42670|0.42670	-0.349000|-0.349000	0.07799|0.07799	CTG|TGG	A|0.662;G|0.338	0.338	strong		0.433	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824	
C19orf40	91442	hgsc.bcm.edu	37	19	33467576	33467576	+	Silent	SNP	G	G	A	rs7258185	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:33467576G>A	ENST00000588258.1	+	5	746	c.636G>A	c.(634-636)acG>acA	p.T212T	C19orf40_ENST00000589646.1_Silent_p.T117T|C19orf40_ENST00000590281.1_Silent_p.T212T|C19orf40_ENST00000590179.1_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	117	0	0	840	WXS	Illumina HiSeq	Phase_I	88	40	0.454545	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	
HEATR1	55127	hgsc.bcm.edu	37	1	236750709	236750709	+	Missense_Mutation	SNP	C	C	T	rs56242514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:236750709C>T	ENST00000366582.3	-	14	1822	c.1708G>A	c.(1708-1710)Gga>Aga	p.G570R	HEATR1_ENST00000366581.2_Missense_Mutation_p.G570R	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	570					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)			TACCATTCTCCATTCTTTGAA	0.289													C|||	38	0.00758786	0.0061	0.0072	5008	,	,		15898	0.0		0.0149	False		,,,				2504	0.0102				p.G570R		Atlas-SNP	.											.	HEATR1	197	.	0			c.G1708A						PASS	.	C	ARG/GLY	40,4354	41.6+/-74.8	0,40,2157	42.0	41.0	41.0		1708	1.8	0.1	1	dbSNP_129	41	222,8356	87.1+/-149.5	1,220,4068	yes	missense	HEATR1	NM_018072.5	125	1,260,6225	TT,TC,CC		2.588,0.9103,2.0197	benign	570/2145	236750709	262,12710	2197	4289	6486	SO:0001583	missense	55127	exon14			ATTCTCCATTCTT	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.1708G>A	1.37:g.236750709C>T	ENSP00000355541:p.Gly570Arg	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	401	126	0.314214	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	15	0.006868131868131868	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	1.351	-0.591306	0.03799	0.009103	0.02588	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.64991	-0.13;1.12	5.58	1.81	0.25067	Armadillo-like helical (1);Armadillo-type fold (1);	0.780131	0.12467	N	0.466323	T	0.12518	0.0304	N	0.03608	-0.345	0.24886	N	0.9922	B	0.02656	0.0	B	0.04013	0.001	T	0.12400	-1.0549	10	0.11182	T	0.66	.	6.6383	0.22895	0.0:0.4837:0.0:0.5163	rs56242514	570	Q9H583	HEAT1_HUMAN	R	570	ENSP00000355541:G570R;ENSP00000355540:G570R	ENSP00000355540:G570R	G	-	1	0	HEATR1	234817332	0.349000	0.24870	0.140000	0.22221	0.727000	0.41649	1.840000	0.39230	0.364000	0.24374	-0.294000	0.09567	GGA	C|0.985;T|0.015	0.015	strong		0.289	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
MICA	100507436	hgsc.bcm.edu	37	6	31382911	31382911	+	3'UTR	SNP	A	A	G	rs1882	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31382911A>G	ENST00000449934.2	+	0	1205				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)				CACtgagggcacctagactct	0.552													g|||	3622	0.723243	0.6982	0.8112	5008	,	,		14191	0.7778		0.5805	False		,,,				2504	0.7853				p.T383A		Atlas-SNP	.											.	MICA	21	.	0			c.A1147G						PASS	.	A		895,489		295,305,92	107.0	103.0	104.0			-0.9	0.0	6	dbSNP_36	104	1634,1548		435,764,392	yes	utr-3	MICA	NM_001177519.1		730,1069,484	GG,GA,AA		48.6486,35.3324,44.6124			31382911	2529,2037	692	1591	2283	SO:0001624	3_prime_UTR_variant	100507436	exon7			GAGGGCACCTAGA	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.*152A>G	6.37:g.31382911A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	119	39	0.327731	NM_000247		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			A|0.320;G|0.680	0.680	strong		0.552	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
PON1	5444	hgsc.bcm.edu	37	7	94946084	94946084	+	Missense_Mutation	SNP	A	A	T	rs854560	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:94946084A>T	ENST00000222381.3	-	3	394	c.163T>A	c.(163-165)Ttg>Atg	p.L55M	PON1_ENST00000542556.1_Missense_Mutation_p.L55M	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	55			L -> M (in dbSNP:rs854560). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1657140, ECO:0000269|PubMed:7916578, ECO:0000269|PubMed:8393742, ECO:0000269|PubMed:8393745, ECO:0000269|PubMed:8812495}.		aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	AGTATCTCCAAGTCTTCAGAG	0.403													A|||	915	0.182708	0.1498	0.2061	5008	,	,		17849	0.0337		0.3579	False		,,,				2504	0.184				p.L55M	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											.	PON1	55	.	0			c.T163A	GRCh37	CM971236	PON1	M	rs854560	PASS	.	A	MET/LEU	762,3644	308.8+/-290.8	64,634,1505	168.0	161.0	163.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	163	-1.8	1.0	7	dbSNP_86	163	3208,5392	485.5+/-371.6	618,1972,1710	yes	missense	PON1	NM_000446.5	15	682,2606,3215	TT,TA,AA		37.3023,17.2946,30.5244	benign	55/356	94946084	3970,9036	2203	4300	6503	SO:0001583	missense	5444	exon3			TCTCCAAGTCTTC	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.163T>A	7.37:g.94946084A>T	ENSP00000222381:p.Leu55Met	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	151	44	0.291391	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	447	0.20467032967032966	75	0.1524390243902439	88	0.2430939226519337	18	0.03146853146853147	266	0.35092348284960423	A	18.84	3.709500	0.68730	0.172946	0.373023	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.49139	0.79;0.79	5.05	-1.76	0.08006	Six-bladed beta-propeller, TolB-like (1);	0.199502	0.43416	D	0.000561	T	0.00012	0.0000	L	0.59436	1.845	0.32800	P	0.500057	D;B	0.58620	0.983;0.004	D;B	0.64410	0.925;0.04	T	0.19063	-1.0317	9	0.66056	D	0.02	-10.6907	4.2104	0.10509	0.3107:0.0:0.2524:0.4369	rs854560;rs1138340;rs1801051;rs2228157;rs3179555;rs3202100;rs11567862;rs17434839;rs57937067	55;55	F5H4W9;P27169	.;PON1_HUMAN	M	55	ENSP00000222381:L55M;ENSP00000444854:L55M	ENSP00000222381:L55M	L	-	1	2	PON1	94784020	0.991000	0.36638	0.995000	0.50966	0.975000	0.68041	0.196000	0.17176	-0.066000	0.12998	0.528000	0.53228	TTG	A|0.717;T|0.283	0.283	strong		0.403	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
HEATR1	55127	hgsc.bcm.edu	37	1	236723108	236723108	+	Missense_Mutation	SNP	C	C	T	rs6661946	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:236723108C>T	ENST00000366582.3	-	34	4790	c.4676G>A	c.(4675-4677)aGt>aAt	p.S1559N	HEATR1_ENST00000366581.2_Missense_Mutation_p.S1478N	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	1559			S -> N (in dbSNP:rs6661946).		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)			TGCAACTGCACTGATATAGCC	0.502													T|||	860	0.171725	0.3684	0.1398	5008	,	,		17205	0.1766		0.0328	False		,,,				2504	0.0665				p.S1559N		Atlas-SNP	.											.	HEATR1	197	.	0			c.G4676A						PASS	.	T	ASN/SER	1397,3009	687.6+/-404.9	210,977,1016	117.0	96.0	103.0		4676	4.6	0.0	1	dbSNP_116	103	339,8261	804.4+/-407.3	3,333,3964	yes	missense	HEATR1	NM_018072.5	46	213,1310,4980	TT,TC,CC		3.9419,31.7068,13.3477	benign	1559/2145	236723108	1736,11270	2203	4300	6503	SO:0001583	missense	55127	exon34			ACTGCACTGATAT	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.4676G>A	1.37:g.236723108C>T	ENSP00000355541:p.Ser1559Asn	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	183	61	0.333333	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Missense_Mutation	SNP	ENST00000366582.3	37	CCDS31066.1	330	0.1510989010989011	171	0.3475609756097561	45	0.12430939226519337	93	0.16258741258741258	21	0.027704485488126648	T	4.221	0.039925	0.08148	0.317068	0.039419	ENSG00000119285	ENST00000366582;ENST00000366581	T;T	0.30448	1.53;1.53	5.74	4.59	0.56863	Armadillo-like helical (1);Armadillo-type fold (1);	0.326894	0.35708	N	0.003034	T	0.00012	0.0000	N	0.00237	-1.79	0.18873	P	0.9999890781	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41945	-0.9480	9	0.07813	T	0.8	.	7.7065	0.28653	0.1247:0.0683:0.0:0.807	rs6661946;rs56728358;rs6661946	1478;1559	Q5T3Q7;Q9H583	.;HEAT1_HUMAN	N	1559;1478	ENSP00000355541:S1559N;ENSP00000355540:S1478N	ENSP00000355540:S1478N	S	-	2	0	HEATR1	234789731	0.999000	0.42202	0.001000	0.08648	0.012000	0.07955	3.763000	0.55257	0.429000	0.26202	-0.390000	0.06520	AGT	C|0.848;T|0.152	0.152	strong		0.502	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
PSME4	23198	hgsc.bcm.edu	37	2	54120025	54120025	+	Missense_Mutation	SNP	A	A	T	rs805408	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:54120025A>T	ENST00000404125.1	-	36	4166	c.4111T>A	c.(4111-4113)Tca>Aca	p.S1371T	PSME4_ENST00000421748.2_Missense_Mutation_p.S515T	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1371			S -> T (in dbSNP:rs805408).		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)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|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)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CTTTCATGTGAATCTGCAACC	0.373													A|||	1749	0.349241	0.2186	0.2522	5008	,	,		16857	0.4742		0.3002	False		,,,				2504	0.5164				p.S1371T		Atlas-SNP	.											.	PSME4	247	.	0			c.T4111A						PASS	.	A	THR/SER	931,3475	355.9+/-313.2	87,757,1359	102.0	100.0	101.0		4111	5.4	1.0	2	dbSNP_86	101	2595,6005	420.4+/-353.4	385,1825,2090	yes	missense	PSME4	NM_014614.2	58	472,2582,3449	TT,TA,AA		30.1744,21.1303,27.1106	benign	1371/1844	54120025	3526,9480	2203	4300	6503	SO:0001583	missense	23198	exon36			CATGTGAATCTGC	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.4111T>A	2.37:g.54120025A>T	ENSP00000384211:p.Ser1371Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	155	79	0.509677	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	658	0.30128205128205127	102	0.2073170731707317	92	0.2541436464088398	230	0.4020979020979021	234	0.3087071240105541	A	9.975	1.226633	0.22542	0.211303	0.301744	ENSG00000068878	ENST00000421748;ENST00000404125	T;T	0.66280	-0.2;-0.2	5.41	5.41	0.78517	Armadillo-like helical (1);Armadillo-type fold (1);	0.192762	0.47093	D	0.000251	T	0.00012	0.0000	N	0.04746	-0.17	0.21184	P	0.999767317	B;B;B	0.10296	0.003;0.0;0.002	B;B;B	0.11329	0.006;0.001;0.001	T	0.28267	-1.0049	9	0.15952	T	0.53	.	15.4442	0.75216	1.0:0.0:0.0:0.0	rs805408;rs52818353;rs805408	746;515;1371	Q14997-2;Q14997-3;Q14997	.;.;PSME4_HUMAN	T	515;1371	ENSP00000410830:S515T;ENSP00000384211:S1371T	ENSP00000384211:S1371T	S	-	1	0	PSME4	53973529	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.976000	0.63785	2.060000	0.61445	0.454000	0.30748	TCA	A|0.713;T|0.287	0.287	strong		0.373	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
FAT3	120114	hgsc.bcm.edu	37	11	92616452	92616452	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:92616452G>A	ENST00000298047.6	+	23	12847	c.12830G>A	c.(12829-12831)cGg>cAg	p.R4277Q	FAT3_ENST00000525166.1_Missense_Mutation_p.R4127Q|FAT3_ENST00000533797.1_Missense_Mutation_p.R612Q|FAT3_ENST00000409404.2_Missense_Mutation_p.R4277Q			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4277					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)				CTGACAGCCCGGCGGGGCGTG	0.667										TCGA Ovarian(4;0.039)																											p.R4277Q		Atlas-SNP	.											FAT3_ENST00000409404,bladder,carcinoma,-1,3	FAT3	1822	3	0			c.G12830A						scavenged	.						43.0	53.0	50.0					11																	92616452		2091	4197	6288	SO:0001583	missense	120114	exon23			CAGCCCGGCGGGG	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.12830G>A	11.37:g.92616452G>A	ENSP00000298047:p.Arg4277Gln	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	77	2	0.025974	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	29.3	4.998227	0.93227	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166;ENST00000533797	T;T;T;D	0.87179	-0.93;-1.0;-0.94;-2.22	5.85	5.85	0.93711	.	.	.	.	.	D	0.93216	0.7839	M	0.80982	2.52	0.80722	D	1	D;B	0.76494	0.999;0.414	P;B	0.60473	0.875;0.087	D	0.92664	0.6144	9	0.51188	T	0.08	.	20.161	0.98133	0.0:0.0:1.0:0.0	.	4277;4277	Q8TDW7-3;Q8TDW7	.;FAT3_HUMAN	Q	4277;4277;4127;612	ENSP00000298047:R4277Q;ENSP00000387040:R4277Q;ENSP00000432586:R4127Q;ENSP00000436399:R612Q	ENSP00000298047:R4277Q	R	+	2	0	FAT3	92256100	1.000000	0.71417	0.849000	0.33467	0.982000	0.71751	6.012000	0.70767	2.770000	0.95276	0.655000	0.94253	CGG	.	.	none		0.667	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
RFX2	5990	hgsc.bcm.edu	37	19	6013057	6013057	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6013057C>T	ENST00000303657.5	-	8	988	c.839G>A	c.(838-840)cGg>cAg	p.R280Q	RFX2_ENST00000592546.1_Missense_Mutation_p.R255Q|RFX2_ENST00000359161.3_Missense_Mutation_p.R280Q|CTC-232P5.1_ENST00000587836.1_RNA	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	280					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						CTCCTGCAGCCGGTTCAGTGG	0.612																																					p.R280Q	Colon(38;171 817 19800 47433 48051)	Atlas-SNP	.											.	RFX2	60	.	0			c.G839A						PASS	.						126.0	122.0	123.0					19																	6013057		2203	4300	6503	SO:0001583	missense	5990	exon8			TGCAGCCGGTTCA		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.839G>A	19.37:g.6013057C>T	ENSP00000306335:p.Arg280Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_000635	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	37	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	C	19.57	3.851655	0.71719	.	.	ENSG00000087903	ENST00000303657;ENST00000359161;ENST00000537791	T;D	0.92149	-0.1;-2.98	4.99	2.84	0.33178	.	0.059667	0.64402	D	0.000002	D	0.88385	0.6422	M	0.65320	2	0.80722	D	1	P;P	0.41848	0.763;0.651	B;B	0.37387	0.248;0.087	D	0.84345	0.0529	10	0.37606	T	0.19	-48.0962	9.5849	0.39510	0.0:0.7782:0.1427:0.0791	.	255;280	P48378-2;P48378	.;RFX2_HUMAN	Q	280;255;67	ENSP00000306335:R280Q;ENSP00000352076:R255Q	ENSP00000306335:R280Q	R	-	2	0	RFX2	5964057	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.746000	0.62133	0.611000	0.30052	0.557000	0.71058	CGG	.	.	none		0.612	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635	
NEK1	4750	hgsc.bcm.edu	37	4	170398454	170398454	+	Missense_Mutation	SNP	T	T	C	rs34099167	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:170398454T>C	ENST00000439128.2	-	24	2811	c.2171A>G	c.(2170-2172)gAa>gGa	p.E724G	NEK1_ENST00000512193.1_Missense_Mutation_p.E655G|NEK1_ENST00000507142.1_Missense_Mutation_p.E752G|NEK1_ENST00000510533.1_Missense_Mutation_p.E680G|NEK1_ENST00000511633.1_Missense_Mutation_p.E708G	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	724			E -> G (in dbSNP:rs34099167). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:17974005}.		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)	p.E752G(1)		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)		TTTTTCATCTTCTTGAGCTTT	0.299													T|||	526	0.105032	0.0802	0.085	5008	,	,		17322	0.1825		0.0974	False		,,,				2504	0.0808				p.E752G		Atlas-SNP	.											NEK1,NS,carcinoma,0,1	NEK1	203	1	1	Substitution - Missense(1)	stomach(1)	c.A2255G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	271,3353		8,255,1549	63.0	55.0	57.0		2255,2123,1964,2039,2171	5.6	1.0	4	dbSNP_126	57	928,7218		60,808,3205	yes	missense,missense,missense,missense,missense	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	98,98,98,98,98	68,1063,4754	CC,CT,TT		11.3921,7.4779,10.1869	benign,benign,benign,benign,benign	752/1287,708/1243,655/1190,680/1215,724/1259	170398454	1199,10571	1812	4073	5885	SO:0001583	missense	4750	exon26			TCATCTTCTTGAG	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.2171A>G	4.37:g.170398454T>C	ENSP00000408020:p.Glu724Gly	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	86	21	0.244186	NM_001199397	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	249	0.11401098901098901	54	0.10975609756097561	28	0.07734806629834254	104	0.18181818181818182	63	0.08311345646437995	T	18.54	3.645851	0.67358	0.074779	0.113921	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.70282	-0.46;-0.45;-0.47;-0.47;-0.45	5.57	5.57	0.84162	.	0.076612	0.56097	D	0.000037	T	0.00440	0.0014	L	0.52364	1.645	0.23649	P	0.99720098	P;D;P;D;P	0.55385	0.915;0.971;0.915;0.971;0.862	P;P;P;P;P	0.57846	0.72;0.828;0.72;0.828;0.529	T	0.06752	-1.0809	9	0.38643	T	0.18	.	13.7635	0.62981	0.0:0.0:0.0:1.0	rs34099167;rs57148876	655;708;752;680;724	Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;NEK1_HUMAN	G	724;708;680;752;655	ENSP00000408020:E724G;ENSP00000423332:E708G;ENSP00000427653:E680G;ENSP00000424757:E752G;ENSP00000424938:E655G	ENSP00000408020:E724G	E	-	2	0	NEK1	170635029	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.786000	0.62425	2.248000	0.74166	0.533000	0.62120	GAA	T|0.885;C|0.115	0.115	strong		0.299	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
CRISP3	10321	hgsc.bcm.edu	37	6	49698883	49698883	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:49698883T>C	ENST00000393666.1	-	6	609	c.603A>G	c.(601-603)ggA>ggG	p.G201G	CRISP3_ENST00000433368.2_Silent_p.G224G|CRISP3_ENST00000371159.4_Silent_p.G232G|CRISP3_ENST00000423399.2_Silent_p.G111G|CRISP3_ENST00000263045.4_Silent_p.G214G			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	201					defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			TACTGCATAGTCCATCGTCAC	0.343																																					p.G224G		Atlas-SNP	.											CRISP3,colon,carcinoma,0,1	CRISP3	67	1	0			c.A672G						scavenged	.						99.0	91.0	94.0					6																	49698883		2203	4300	6503	SO:0001819	synonymous_variant	10321	exon7			GCATAGTCCATCG	X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.603A>G	6.37:g.49698883T>C		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	229	3	0.0131004	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Silent	SNP	ENST00000393666.1	37																																																																																				.	.	none		0.343	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061	
FMO2	2327	hgsc.bcm.edu	37	1	171154959	171154959	+	Missense_Mutation	SNP	A	A	G	rs2020870	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171154959A>G	ENST00000209929.7	+	2	265	c.107A>G	c.(106-108)gAt>gGt	p.D36G	FMO2_ENST00000441535.1_Missense_Mutation_p.D36G|FMO2_ENST00000529935.1_Intron			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	131	0	0		WXS	Illumina HiSeq	Phase_I	213	77	0.361502	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	
OR10S1	219873	hgsc.bcm.edu	37	11	123847473	123847473	+	Missense_Mutation	SNP	A	A	G	rs55944888	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:123847473A>G	ENST00000531945.1	-	1	1015	c.926T>C	c.(925-927)gTg>gCg	p.V309A		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	309						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(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		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)		AGCATGCTTCACCTCCTTGTT	0.527													A|||	577	0.115216	0.0552	0.1585	5008	,	,		21721	0.1081		0.1829	False		,,,				2504	0.1033				p.V309A		Atlas-SNP	.											.	OR10S1	78	.	0			c.T926C						PASS	.	A	ALA/VAL	332,4072	174.8+/-204.3	17,298,1887	81.0	78.0	79.0		926	4.8	0.9	11	dbSNP_129	79	1454,7144	277.4+/-292.8	120,1214,2965	yes	missense	OR10S1	NM_001004474.1	64	137,1512,4852	GG,GA,AA		16.9109,7.5386,13.7363	possibly-damaging	309/332	123847473	1786,11216	2202	4299	6501	SO:0001583	missense	219873	exon1			TGCTTCACCTCCT	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.926T>C	11.37:g.123847473A>G	ENSP00000431914:p.Val309Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	173	115	0.66474	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	274	0.12545787545787546	16	0.032520325203252036	65	0.17955801104972377	68	0.11888111888111888	125	0.16490765171503957	A	9.610	1.131046	0.21041	0.075386	0.169109	ENSG00000196248	ENST00000531945	T	0.39592	1.07	4.82	4.82	0.62117	.	0.000000	0.31989	U	0.006759	T	0.00109	0.0003	M	0.67569	2.06	0.80722	P	0.0	B	0.20368	0.044	B	0.15870	0.014	T	0.07366	-1.0776	9	0.87932	D	0	-20.1912	14.1878	0.65617	1.0:0.0:0.0:0.0	rs55944888	309	Q8NGN2	O10S1_HUMAN	A	309	ENSP00000431914:V309A	ENSP00000431914:V309A	V	-	2	0	OR10S1	123352683	0.440000	0.25618	0.900000	0.35374	0.282000	0.26991	5.304000	0.65744	2.004000	0.58718	0.460000	0.39030	GTG	A|0.862;G|0.138	0.138	strong		0.527	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
VN1R2	317701	hgsc.bcm.edu	37	19	53761857	53761857	+	Missense_Mutation	SNP	G	G	T	rs112986288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53761857G>T	ENST00000341702.3	+	1	313	c.229G>T	c.(229-231)Gtc>Ttc	p.V77F		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	77					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(134;0.00301)		acactctcttgtctctgcaca	0.483													G|||	37	0.00738818	0.0	0.0072	5008	,	,		16666	0.0		0.0139	False		,,,				2504	0.0184				p.V77F		Atlas-SNP	.											.	VN1R2	71	.	0			c.G229T						PASS	.	G	PHE/VAL	8,4376		0,8,2184	35.0	35.0	35.0		229	0.1	0.0	19	dbSNP_132	35	78,8498		1,76,4211	no	missense	VN1R2	NM_173856.2	50	1,84,6395	TT,TG,GG		0.9095,0.1825,0.6636	benign	77/396	53761857	86,12874	2192	4288	6480	SO:0001583	missense	317701	exon1			TCTCTTGTCTCTG	AF370359	CCDS12862.1	19q13.42	2012-08-22			ENSG00000196131	ENSG00000196131		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19872	protein-coding gene	gene with protein product						12123587	Standard	NM_173856		Approved	V1RL2	uc002qbi.2	Q8NFZ6		ENST00000341702.3:c.229G>T	19.37:g.53761857G>T	ENSP00000351244:p.Val77Phe	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	55	22	0.4	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	G	5.291	0.239112	0.10023	0.001825	0.009095	ENSG00000196131	ENST00000341702	T	0.10192	2.9	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	B	0.25169	0.119	B	0.12837	0.008	T	0.38001	-0.9681	9	0.72032	D	0.01	.	2.6651	0.05041	0.4852:0.0:0.5147:0.0	.	77	Q8NFZ6	VN1R2_HUMAN	F	77	ENSP00000351244:V77F	ENSP00000351244:V77F	V	+	1	0	VN1R2	58453669	0.000000	0.05858	0.022000	0.16811	0.022000	0.10575	-1.105000	0.03323	0.132000	0.18615	0.134000	0.15878	GTC	G|0.994;T|0.006	0.006	strong		0.483	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388724	1388724	+	Missense_Mutation	SNP	C	C	G	rs76728908	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	31	20	0.645161	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1272245	1272245	+	Missense_Mutation	SNP	C	C	T	rs2943511	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1272245C>T	ENST00000529681.1	+	31	14193	c.14135C>T	c.(14134-14136)aCg>aTg	p.T4712M	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T4715M	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4712	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.		T -> M (in dbSNP:rs2943511). {ECO:0000269|PubMed:9013550}.		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)		ctgaccagcacggccaccaca	0.617													c|||	356	0.0710863	0.0295	0.1138	5008	,	,		18081	0.0496		0.0974	False		,,,				2504	0.092				p.T4712M		Atlas-SNP	.											MUC5B,colon,carcinoma,0,2	MUC5B	473	2	0			c.C14135T						PASS	.	C	MET/THR	77,4207		2,73,2067	110.0	141.0	131.0		14135	-3.3	0.0	11	dbSNP_101	131	629,7823		39,551,3636	yes	missense	MUC5B	NM_002458.2	81	41,624,5703	TT,TC,CC		7.442,1.7974,5.5433		4712/5763	1272245	706,12030	2142	4226	6368	SO:0001583	missense	727897	exon31			CCAGCACGGCCAC	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.14135C>T	11.37:g.1272245C>T	ENSP00000436812:p.Thr4712Met	Somatic	471	0	0		WXS	Illumina HiSeq	Phase_I	523	255	0.487572	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	154	0.07051282051282051	9	0.018292682926829267	38	0.10497237569060773	43	0.07517482517482517	64	0.08443271767810026	-	2.685	-0.274526	0.05679	0.017974	0.07442	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000535652	T;T	0.19394	2.15;2.33	1.65	-3.31	0.04988	.	.	.	.	.	T	0.00412	0.0013	M	0.75264	2.295	0.80722	P	0.0	D	0.60160	0.987	B	0.35413	0.202	T	0.06023	-1.0850	8	0.87932	D	0	.	2.2239	0.03979	0.177:0.497:0.176:0.1499	rs2943511	4715	E9PBJ0	.	M	4712;4715;4656;485	ENSP00000436812:T4712M;ENSP00000415793:T4715M	ENSP00000343037:T4656M	T	+	2	0	MUC5B	1228821	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-5.903000	0.00091	-0.636000	0.05524	0.194000	0.17425	ACG	C|0.930;T|0.070	0.070	strong		0.617	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MAN2A2	4122	hgsc.bcm.edu	37	15	91452566	91452566	+	Silent	SNP	G	G	A	rs148266546		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:91452566G>A	ENST00000559717.1	+	9	1665	c.1206G>A	c.(1204-1206)ctG>ctA	p.L402L	MAN2A2_ENST00000360468.3_Silent_p.L402L|MAN2A2_ENST00000430376.2_5'Flank|MAN2A2_ENST00000431652.2_5'UTR			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	402					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GGGCAGCCCTGCTTCTGGACC	0.572													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17474	0.0		0.0	False		,,,				2504	0.0				p.L402L		Atlas-SNP	.											.	MAN2A2	99	.	0			c.G1206A						PASS	.	G		0,4396		0,0,2198	56.0	55.0	55.0		1206	4.8	1.0	15	dbSNP_134	55	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	MAN2A2	NM_006122.2		0,4,6492	AA,AG,GG		0.0465,0.0,0.0308		402/1151	91452566	4,12988	2198	4298	6496	SO:0001819	synonymous_variant	4122	exon8			AGCCCTGCTTCTG	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.1206G>A	15.37:g.91452566G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	62	6	0.0967742	NM_006122	A6NH12|A8K1E8|Q13754	Silent	SNP	ENST00000559717.1	37	CCDS32332.1																																																																																			G|1.000;A|0.000	0.000	strong		0.572	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122	
DBN1	1627	hgsc.bcm.edu	37	5	176893942	176893942	+	Missense_Mutation	SNP	C	C	T	rs146597348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:176893942C>T	ENST00000309007.5	-	7	896	c.677G>A	c.(676-678)cGg>cAg	p.R226Q	DBN1_ENST00000393565.1_Missense_Mutation_p.R226Q|DBN1_ENST00000292385.5_Missense_Mutation_p.R228Q	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	226					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)	p.R226Q(1)		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)			CTCCCGCTCCCGGTAGCGCCG	0.701													C|||	14	0.00279553	0.0	0.0043	5008	,	,		13021	0.0		0.008	False		,,,				2504	0.0031				p.R228Q		Atlas-SNP	.											DBN1,NS,lymphoid_neoplasm,0,1	DBN1	122	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G683A						PASS	.	C	GLN/ARG,GLN/ARG	16,4390	23.3+/-48.9	0,16,2187	49.0	52.0	51.0		677,683	5.0	1.0	5	dbSNP_134	51	104,8496	56.0+/-117.1	0,104,4196	no	missense,missense	DBN1	NM_004395.3,NM_080881.2	43,43	0,120,6383	TT,TC,CC		1.2093,0.3631,0.9227	possibly-damaging,possibly-damaging	226/650,228/652	176893942	120,12886	2203	4300	6503	SO:0001583	missense	1627	exon8			CGCTCCCGGTAGC		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.677G>A	5.37:g.176893942C>T	ENSP00000308532:p.Arg226Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	17.79	3.475458	0.63737	0.003631	0.012093	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000477391	T;T;T	0.41065	1.01;1.01;1.53	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.21550	0.0519	N	0.13043	0.29	0.80722	D	1	D;P;P;P	0.61697	0.99;0.865;0.835;0.897	P;B;B;B	0.46718	0.525;0.13;0.06;0.127	T	0.01504	-1.1338	10	0.19147	T	0.46	-14.8828	11.5492	0.50711	0.0:0.9178:0.0:0.0822	.	176;226;226;228	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	Q	226;228;226;225	ENSP00000308532:R226Q;ENSP00000292385:R228Q;ENSP00000377195:R226Q	ENSP00000292385:R228Q	R	-	2	0	DBN1	176826548	0.999000	0.42202	0.990000	0.47175	0.999000	0.98932	4.101000	0.57769	2.586000	0.87340	0.655000	0.94253	CGG	C|0.990;T|0.010	0.010	strong		0.701	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881	
CCPG1	9236	hgsc.bcm.edu	37	15	55664220	55664220	+	Silent	SNP	G	G	A	rs3203152	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:55664220G>A	ENST00000310958.6	-	6	775	c.477C>T	c.(475-477)gaC>gaT	p.D159D	CCPG1_ENST00000425574.3_Silent_p.D159D|MIR628_ENST00000385229.1_RNA|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000442196.3_Silent_p.D159D|CCPG1_ENST00000569205.1_Silent_p.D159D	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	159	Interaction with MCF2L and SRC. {ECO:0000250}.				cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TTGATTCATCGTCACTAGGCT	0.378													G|||	877	0.17512	0.4811	0.0706	5008	,	,		18918	0.0089		0.0855	False		,,,				2504	0.0992				p.D159D		Atlas-SNP	.											.	CCPG1	74	.	0			c.C477T						PASS	.	G	,,,	1495,2167		307,881,643	64.0	61.0	62.0		477,477,477,477	-11.9	0.0	15	dbSNP_105	62	735,7439		29,677,3381	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CCPG1	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_020739.3	,,,	336,1558,4024	AA,AG,GG		8.9919,40.8247,18.8408	,,,	159/808,159/425,159/758,159/758	55664220	2230,9606	1831	4087	5918	SO:0001819	synonymous_variant	9236	exon6			TTCATCGTCACTA	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.477C>T	15.37:g.55664220G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	41	40	0.97561	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Silent	SNP	ENST00000310958.6	37	CCDS42039.1																																																																																			G|0.852;A|0.148	0.148	strong		0.378	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
VWA8	23078	hgsc.bcm.edu	37	13	42385446	42385446	+	Missense_Mutation	SNP	T	T	C	rs9562353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:42385446T>C	ENST00000379310.3	-	17	2046	c.1978A>G	c.(1978-1980)Aga>Gga	p.R660G	VWA8_ENST00000281496.6_Missense_Mutation_p.R660G	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	660			R -> G (in dbSNP:rs9562353).			extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										AACAGTTGTCTGGTAGAAAGT	0.388													T|||	365	0.0728834	0.0877	0.0476	5008	,	,		7178	0.1349		0.0358	False		,,,				2504	0.045				p.R660G		Atlas-SNP	.											KIAA0564,lymph_node,lymphoid_neoplasm,0,1	.	.	1	0			c.A1978G						PASS	.	T	GLY/ARG,GLY/ARG	508,3898	233.9+/-246.9	28,452,1723	125.0	127.0	126.0		1978,1978	3.1	1.0	13	dbSNP_119	126	367,8233	122.7+/-181.7	11,345,3944	yes	missense,missense	KIAA0564	NM_001009814.1,NM_015058.1	125,125	39,797,5667	CC,CT,TT		4.2674,11.5297,6.7277	probably-damaging,probably-damaging	660/1040,660/1906	42385446	875,12131	2203	4300	6503	SO:0001583	missense	23078	exon17			GTTGTCTGGTAGA	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1978A>G	13.37:g.42385446T>C	ENSP00000368612:p.Arg660Gly	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	105	56	0.533333	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	148	0.06776556776556776	43	0.08739837398373984	16	0.04419889502762431	64	0.11188811188811189	25	0.032981530343007916	T	15.34	2.805700	0.50315	0.115297	0.042674	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.66995	-0.24;-0.24	5.27	3.08	0.35506	.	0.000000	0.85682	D	0.000000	T	0.06325	0.0163	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54503	-0.8284	10	0.87932	D	0	.	12.9555	0.58425	0.0:0.0:0.4004:0.5996	rs9562353;rs52800556;rs9562353	660	A3KMH1	K0564_HUMAN	G	564;660;660	ENSP00000368612:R660G;ENSP00000281496:R660G	ENSP00000251030:R564G	R	-	1	2	KIAA0564	41283446	0.999000	0.42202	1.000000	0.80357	0.501000	0.33797	1.280000	0.33202	0.898000	0.36418	0.477000	0.44152	AGA	T|0.931;C|0.069	0.069	strong		0.388	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
MUC4	4585	hgsc.bcm.edu	37	3	195509722	195509722	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195509722G>T	ENST00000463781.3	-	2	9188	c.8729C>A	c.(8728-8730)aCc>aAc	p.T2910N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2910N	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)		AAGAGGCGTGGTGTCACCTGT	0.587																																					p.T2910N		Atlas-SNP	.											.	MUC4	1505	.	0			c.C8729A						PASS	.						13.0	9.0	10.0					3																	195509722		674	1529	2203	SO:0001583	missense	4585	exon2			GGCGTGGTGTCAC	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.8729C>A	3.37:g.195509722G>T	ENSP00000417498:p.Thr2910Asn	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	520	83	0.159615	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	5.988	0.366151	0.11352	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.42;1.46	.	.	.	.	.	.	.	.	T	0.19167	0.0460	N	0.19112	0.55	0.09310	N	1	P	0.39094	0.659	B	0.42959	0.403	T	0.17930	-1.0353	7	.	.	.	.	4.6597	0.12636	0.0:0.0:1.0:0.0	.	2782	E7ESK3	.	N	2910	ENSP00000417498:T2910N;ENSP00000420243:T2910N	.	T	-	2	0	MUC4	196994501	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-0.816000	0.04477	-0.000000	0.14550	0.000000	0.15137	ACC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956194	18956194	+	Silent	SNP	T	T	C	rs2014931	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18956194T>C	ENST00000302797.3	-	1	362	c.138A>G	c.(136-138)gcA>gcG	p.A46A	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)			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						AGAGCACAACTGCGTTTCCTG	0.587													C|||	1819	0.363219	0.3442	0.3588	5008	,	,		26113	0.3075		0.4026	False		,,,				2504	0.409				p.A46A		Atlas-SNP	.											MRGPRX1,caecum,carcinoma,-2,3	MRGPRX1	84	3	0			c.A138G						PASS	.	C		1481,2907		203,1075,916	169.0	160.0	163.0		138	-2.1	0.0	11	dbSNP_92	163	3341,5233		595,2151,1541	no	coding-synonymous	MRGPRX1	NM_147199.3		798,3226,2457	CC,CT,TT		38.9666,33.7511,37.201		46/323	18956194	4822,8140	2194	4287	6481	SO:0001819	synonymous_variant	259249	exon1			CACAACTGCGTTT		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.138A>G	11.37:g.18956194T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	102	101	0.990196	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	37	CCDS7846.1																																																																																			T|0.636;C|0.364	0.364	strong		0.587	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
WDR88	126248	hgsc.bcm.edu	37	19	33635761	33635761	+	Silent	SNP	C	C	T	rs3848596	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	175	84	0.48	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	
BMP2	650	hgsc.bcm.edu	37	20	6759595	6759595	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:6759595C>T	ENST00000378827.4	+	3	2269	c.1050C>T	c.(1048-1050)aaC>aaT	p.N350N		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	350					activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|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 involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						CGTTGGTCAACTCTGTTAACT	0.468																																					p.N350N		Atlas-SNP	.											BMP2,NS,carcinoma,0,1	BMP2	45	1	0			c.C1050T						scavenged	.						129.0	101.0	111.0					20																	6759595		2203	4300	6503	SO:0001819	synonymous_variant	650	exon3			GGTCAACTCTGTT		CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.1050C>T	20.37:g.6759595C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	174	3	0.0172414	NM_001200		Silent	SNP	ENST00000378827.4	37	CCDS13099.1																																																																																			.	.	none		0.468	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3		
RPTOR	57521	hgsc.bcm.edu	37	17	78599562	78599562	+	Silent	SNP	C	C	G	rs17848685	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78599562C>G	ENST00000306801.3	+	2	596	c.234C>G	c.(232-234)acC>acG	p.T78T	RPTOR_ENST00000537330.1_5'UTR|RPTOR_ENST00000570891.1_Silent_p.T78T|RPTOR_ENST00000544334.2_Silent_p.T78T	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	131	0	0		WXS	Illumina HiSeq	Phase_I	167	81	0.48503	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	
CNGA1	1259	hgsc.bcm.edu	37	4	47945295	47945295	+	Missense_Mutation	SNP	C	C	T	rs28642966	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:47945295C>T	ENST00000514170.1	-	8	671	c.352G>A	c.(352-354)Gat>Aat	p.D118N	CNGA1_ENST00000544810.1_Missense_Mutation_p.D118N|CNGA1_ENST00000358519.4_Missense_Mutation_p.D118N|CNGA1_ENST00000402813.3_Missense_Mutation_p.D187N|CNGA1_ENST00000420489.2_Missense_Mutation_p.D118N			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	118			D -> N (in dbSNP:rs28642966). {ECO:0000269|PubMed:7479749}.		phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						TCGTTTTTATCATCTGACTTG	0.318													C|||	1000	0.199681	0.1785	0.1902	5008	,	,		14907	0.3036		0.1332	False		,,,				2504	0.1963				p.D187N		Atlas-SNP	.											.	CNGA1	74	.	0			c.G559A						PASS	.	C	ASN/ASP,ASN/ASP	522,2994		37,448,1273	32.0	28.0	29.0		559,352	3.8	1.0	4	dbSNP_125	29	864,7092		52,760,3166	yes	missense,missense	CNGA1	NM_001142564.1,NM_000087.3	23,23	89,1208,4439	TT,TC,CC		10.8597,14.8464,12.0816	benign,benign	187/760,118/691	47945295	1386,10086	1758	3978	5736	SO:0001583	missense	1259	exon7			TTTTATCATCTGA	M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.352G>A	4.37:g.47945295C>T	ENSP00000426862:p.Asp118Asn	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_001142564	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Missense_Mutation	SNP	ENST00000514170.1	37	CCDS43226.1	494	0.2261904761904762	106	0.21544715447154472	77	0.212707182320442	203	0.3548951048951049	108	0.1424802110817942	C	10.12	1.262041	0.23051	0.148464	0.108597	ENSG00000198515	ENST00000402813;ENST00000514170;ENST00000544810;ENST00000358519;ENST00000420489;ENST00000504722	T;T;T;T;T;T	0.24723	3.38;3.38;3.38;3.38;3.38;1.84	4.66	3.8	0.43715	.	0.671744	0.15028	N	0.284602	T	0.00012	0.0000	L	0.45581	1.43	0.41375	P	0.012488000000000055	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.41998	-0.9477	9	0.12103	T	0.63	.	6.8529	0.24024	0.0:0.7226:0.1803:0.0971	rs28642966;rs28642966	118;118	Q4W5E3;P29973	.;CNGA1_HUMAN	N	187;118;118;118;118;118	ENSP00000384264:D187N;ENSP00000426862:D118N;ENSP00000443401:D118N;ENSP00000351320:D118N;ENSP00000389881:D118N;ENSP00000423721:D118N	ENSP00000351320:D118N	D	-	1	0	CNGA1	47640052	0.075000	0.21258	1.000000	0.80357	0.434000	0.31775	0.535000	0.23114	1.072000	0.40860	0.655000	0.94253	GAT	C|0.787;T|0.213	0.213	strong		0.318	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2	NM_000087	
FLG	2312	hgsc.bcm.edu	37	1	152281948	152281948	+	Missense_Mutation	SNP	G	G	A	rs12405241	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152281948G>A	ENST00000368799.1	-	3	5449	c.5414C>T	c.(5413-5415)gCg>gTg	p.A1805V	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1805	Ser-rich.		A -> V (in dbSNP:rs12405241).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTTGGGACGCTGAGTGCCT	0.592									Ichthyosis				G|||	1440	0.28754	0.0113	0.3905	5008	,	,		20549	0.5843		0.1421	False		,,,				2504	0.4315				p.A1805V		Atlas-SNP	.											.	FLG	900	.	0			c.C5414T						PASS	.	G	VAL/ALA	161,4245	108.2+/-146.6	2,157,2044	311.0	321.0	317.0		5414	-3.6	0.0	1	dbSNP_120	317	1240,7356	248.9+/-276.4	97,1046,3155	no	missense	FLG	NM_002016.1	64	99,1203,5199	AA,AG,GG		14.4253,3.6541,10.7753	probably-damaging	1805/4062	152281948	1401,11601	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGACGCTGAGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5414C>T	1.37:g.152281948G>A	ENSP00000357789:p.Ala1805Val	Somatic	299	1	0.00334448		WXS	Illumina HiSeq	Phase_I	424	154	0.363208	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	574	0.26282051282051283	9	0.018292682926829267	118	0.3259668508287293	335	0.5856643356643356	112	0.14775725593667546	G	9.606	1.130070	0.21041	0.036541	0.144253	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01821	4.62	2.68	-3.56	0.04626	.	.	.	.	.	T	0.01254	0.0041	L	0.49350	1.555	0.80722	P	0.0	D	0.76494	0.999	D	0.68621	0.959	T	0.36383	-0.9750	8	0.25106	T	0.35	.	0.7622	0.01009	0.3595:0.1924:0.2946:0.1534	rs12405241;rs57429267	1805	P20930	FILA_HUMAN	V	1805;40	ENSP00000357789:A1805V	ENSP00000271820:A40V	A	-	2	0	FLG	150548572	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.623000	0.00109	-0.903000	0.03881	-1.464000	0.01018	GCG	G|0.839;A|0.161	0.161	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FAM205A	259308	hgsc.bcm.edu	37	9	34725116	34725116	+	Silent	SNP	G	G	A	rs62547038	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34725116G>A	ENST00000378788.3	-	4	2160	c.2121C>T	c.(2119-2121)gtC>gtT	p.V707V		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	707						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						CCACTGCCAGGACCCCAGAAA	0.547																																					p.V707V		Atlas-SNP	.											.	FAM205A	45	.	0			c.C2121T						PASS	.						17.0	13.0	14.0					9																	34725116		692	1590	2282	SO:0001819	synonymous_variant	259308	exon4			TGCCAGGACCCCA		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.2121C>T	9.37:g.34725116G>A		Somatic	518	1	0.0019305		WXS	Illumina HiSeq	Phase_I	550	163	0.296364	NM_001141917	A8MVW7	Silent	SNP	ENST00000378788.3	37	CCDS55305.1																																																																																			G|0.858;A|0.142	0.142	strong		0.547	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
CENPQ	55166	hgsc.bcm.edu	37	6	49459978	49459978	+	Missense_Mutation	SNP	A	A	G	rs2501968	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:49459978A>G	ENST00000335783.3	+	9	891	c.797A>G	c.(796-798)gAt>gGt	p.D266G		NM_018132.3	NP_060602.2	Q7L2Z9	CENPQ_HUMAN	centromere protein Q	266			D -> G (in dbSNP:rs2501968).		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)					AAGAAACTGGATGCATCTTAA	0.318													A|||	2399	0.479034	0.4085	0.67	5008	,	,		16849	0.5794		0.4334	False		,,,				2504	0.3824				p.D266G		Atlas-SNP	.											CENPQ,colon,carcinoma,0,2	CENPQ	23	2	0			c.A797G						PASS	.	A	GLY/ASP	1823,2583	529.5+/-372.7	366,1091,746	78.0	77.0	78.0		797	4.2	0.4	6	dbSNP_100	78	3511,5089	508.5+/-377.1	718,2075,1507	yes	missense	CENPQ	NM_018132.3	94	1084,3166,2253	GG,GA,AA		40.8256,41.3754,41.0118	benign	266/269	49459978	5334,7672	2203	4300	6503	SO:0001583	missense	55166	exon9			AACTGGATGCATC	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.797A>G	6.37:g.49459978A>G	ENSP00000337289:p.Asp266Gly	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_018132	A8KAF1|Q6IN61|Q9NVS5	Missense_Mutation	SNP	ENST00000335783.3	37	CCDS4925.1	1090	0.4990842490842491	201	0.40853658536585363	225	0.6215469613259669	361	0.6311188811188811	303	0.3997361477572559	A	11.95	1.790577	0.31685	0.413754	0.408256	ENSG00000031691	ENST00000335783;ENST00000371200	T	0.55413	0.52	5.4	4.24	0.50183	.	0.288766	0.37304	N	0.002153	T	0.33876	0.0878	M	0.67953	2.075	0.39877	P	0.02641199999999999	B	0.20671	0.047	B	0.27796	0.083	T	0.35176	-0.9799	9	0.66056	D	0.02	-10.7583	8.0688	0.30676	0.9099:0.0:0.0901:0.0	rs2501968;rs3209643;rs3823209;rs52825404;rs57701029;rs2501968	266	Q7L2Z9	CENPQ_HUMAN	G	266	ENSP00000337289:D266G	ENSP00000337289:D266G	D	+	2	0	CENPQ	49567937	0.998000	0.40836	0.363000	0.25875	0.417000	0.31264	2.228000	0.42981	1.067000	0.40740	0.524000	0.50904	GAT	A|0.545;C|0.003	.	strong		0.318	CENPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040855.2	NM_018132	
BLVRA	644	hgsc.bcm.edu	37	7	43830888	43830888	+	Silent	SNP	T	T	C	rs1802846	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:43830888T>C	ENST00000402924.1	+	5	338	c.175T>C	c.(175-177)Ttg>Ctg	p.L59L	BLVRA_ENST00000265523.4_Silent_p.L59L	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	59					heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)	p.L59L(1)		endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						GCAGATTTCTTTGGAGGATGC	0.502													T|||	530	0.105831	0.1127	0.1671	5008	,	,		16706	0.0804		0.1213	False		,,,				2504	0.0634				p.L59L		Atlas-SNP	.											BLVRA,NS,carcinoma,0,1	BLVRA	26	1	1	Substitution - coding silent(1)	stomach(1)	c.T175C						PASS	.	T		461,3945	220.0+/-237.6	27,407,1769	127.0	120.0	122.0		175	-2.1	1.0	7	dbSNP_89	122	953,7647	208.4+/-249.9	52,849,3399	no	coding-synonymous	BLVRA	NM_000712.3		79,1256,5168	CC,CT,TT		11.0814,10.463,10.8719		59/297	43830888	1414,11592	2203	4300	6503	SO:0001819	synonymous_variant	644	exon5			ATTTCTTTGGAGG	BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR			Standard	NM_001253823		Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.175T>C	7.37:g.43830888T>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	182	59	0.324176	NM_001253823	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	Silent	SNP	ENST00000402924.1	37	CCDS5472.1																																																																																			T|0.890;C|0.110	0.110	strong		0.502	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	NM_000712	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68701948	68701948	+	Silent	SNP	C	C	T	rs11228413	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68701948C>T	ENST00000255078.3	+	11	1665	c.1554C>T	c.(1552-1554)gtC>gtT	p.V518V	IGHMBP2_ENST00000541229.1_3'UTR	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	518					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)			TCCGCCTCGTCAGTTTGCACA	0.582													C|||	665	0.132788	0.1483	0.1902	5008	,	,		18535	0.0208		0.2644	False		,,,				2504	0.0511				p.V518V		Atlas-SNP	.											IGHMBP2,colon,carcinoma,+2,3	IGHMBP2	83	3	0			c.C1554T						PASS	.	C		765,3635	305.5+/-289.0	68,629,1503	118.0	97.0	104.0		1554	3.0	0.5	11	dbSNP_120	104	2127,6461	352.2+/-328.6	258,1611,2425	no	coding-synonymous	IGHMBP2	NM_002180.2		326,2240,3928	TT,TC,CC		24.7671,17.3864,22.2667		518/994	68701948	2892,10096	2200	4294	6494	SO:0001819	synonymous_variant	3508	exon11			CCTCGTCAGTTTG	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.1554C>T	11.37:g.68701948C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	182	88	0.483516	NM_002180	A0PJD2|Q00443|Q14177	Silent	SNP	ENST00000255078.3	37	CCDS8187.1																																																																																			C|0.805;T|0.195	0.195	strong		0.582	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
FAM151B	167555	hgsc.bcm.edu	37	5	79817898	79817898	+	Silent	SNP	A	A	G	rs2431224	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79817898A>G	ENST00000282226.4	+	5	767	c.612A>G	c.(610-612)agA>agG	p.R204R	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	204										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	7		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		TCCCTGTCAGAGCAGCATTAG	0.348													A|||	152	0.0303514	0.0038	0.0461	5008	,	,		18692	0.003		0.0636	False		,,,				2504	0.0491				p.R204R		Atlas-SNP	.											.	FAM151B	25	.	0			c.A612G						PASS	.	A		82,4324	70.3+/-108.2	1,80,2122	163.0	144.0	150.0		612	-0.0	1.0	5	dbSNP_100	150	673,7927	168.7+/-220.2	24,625,3651	no	coding-synonymous	FAM151B	NM_205548.2		25,705,5773	GG,GA,AA		7.8256,1.8611,5.805		204/277	79817898	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	167555	exon5			TGTCAGAGCAGCA		CCDS4051.1	5q14.1	2007-12-18	2007-12-18		ENSG00000152380	ENSG00000152380			33716	protein-coding gene	gene with protein product							Standard	NM_205548		Approved	UNQ9217	uc003kgv.2	Q6UXP7	OTTHUMG00000131303	ENST00000282226.4:c.612A>G	5.37:g.79817898A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_205548	A2RRE4	Silent	SNP	ENST00000282226.4	37	CCDS4051.1																																																																																			A|0.954;G|0.046	0.046	strong		0.348	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548	
SLC12A6	9990	hgsc.bcm.edu	37	15	34542872	34542872	+	Silent	SNP	C	C	G	rs17236798	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:34542872C>G	ENST00000354181.3	-	12	2043	c.1551G>C	c.(1549-1551)ccG>ccC	p.P517P	SLC12A6_ENST00000558589.1_Silent_p.P508P|SLC12A6_ENST00000560164.1_Silent_p.P329P|SLC12A6_ENST00000451844.2_Silent_p.P329P|SLC12A6_ENST00000397707.2_Silent_p.P502P|SLC12A6_ENST00000558667.1_Silent_p.P517P|SLC12A6_ENST00000458406.2_Silent_p.P458P|SLC12A6_ENST00000397702.2_Silent_p.P458P|SLC12A6_ENST00000560611.1_Silent_p.P517P|SLC12A6_ENST00000290209.5_Silent_p.P466P			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	326	0	0		WXS	Illumina HiSeq	Phase_I	211	154	0.729858	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	
GPR98	84059	hgsc.bcm.edu	37	5	89990324	89990324	+	Missense_Mutation	SNP	A	A	G	rs1878878	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:89990324A>G	ENST00000405460.2	+	33	7847	c.7751A>G	c.(7750-7752)aAt>aGt	p.N2584S		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2584	Calx-beta 18. {ECO:0000255}.		N -> S (in dbSNP:rs1878878). {ECO:0000269|PubMed:11230166, 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)			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)		GTGATCTACAATATTAGTCCC	0.438													G|||	4049	0.808506	0.9546	0.7997	5008	,	,		19316	0.8323		0.666	False		,,,				2504	0.7393				p.N2584S		Atlas-SNP	.											.	GPR98	605	.	0			c.A7751G						PASS	.	G	SER/ASN	3558,332		1630,298,17	267.0	261.0	263.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7751	5.9	1.0	5	dbSNP_92	263	5356,2944		1703,1950,497	yes	missense	GPR98	NM_032119.3	46	3333,2248,514	GG,GA,AA		35.4699,8.5347,26.8745	benign	2584/6307	89990324	8914,3276	1945	4150	6095	SO:0001583	missense	84059	exon33			TCTACAATATTAG	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.7751A>G	5.37:g.89990324A>G	ENSP00000384582:p.Asn2584Ser	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	158	156	0.987342	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	1736|1736	0.7948717948717948|0.7948717948717948	471|471	0.9573170731707317|0.9573170731707317	283|283	0.7817679558011049|0.7817679558011049	468|468	0.8181818181818182|0.8181818181818182	514|514	0.6781002638522428|0.6781002638522428	G|G	7.754|7.754	0.703903|0.703903	0.15172|0.15172	0.914653|0.914653	0.645301|0.645301	ENSG00000164199|ENSG00000164199	ENST00000509621|ENST00000405460;ENST00000296619	.|T	.|0.21361	.|2.01	5.88|5.88	5.88|5.88	0.94601|0.94601	.|Na-Ca exchanger/integrin-beta4 (1);	.|0.072501	.|0.85682	.|N	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00119|0.00119	-2.075|-2.075	0.09310|0.09310	P|P	1.0|1.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.41875|0.41875	-0.9484|-0.9484	4|9	.|0.02654	.|T	.|1	.|.	15.2859|15.2859	0.73828|0.73828	0.067:0.0:0.933:0.0|0.067:0.0:0.933:0.0	rs1878878;rs3813833;rs17622157;rs52809440;rs57484012;rs1878878|rs1878878;rs3813833;rs17622157;rs52809440;rs57484012;rs1878878	.|2584;2584	.|E7ETI5;Q8WXG9	.|.;GPR98_HUMAN	V|S	150|2584	.|ENSP00000384582:N2584S	.|ENSP00000296619:N2584S	I|N	+|+	1|2	0|0	GPR98|GPR98	90026080|90026080	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.801000|0.801000	0.45260|0.45260	6.532000|6.532000	0.73825|0.73825	1.505000|1.505000	0.48720|0.48720	-0.119000|-0.119000	0.15052|0.15052	ATA|AAT	A|0.209;G|0.791	0.791	strong		0.438	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
KIAA1549	57670	hgsc.bcm.edu	37	7	138602417	138602417	+	Missense_Mutation	SNP	G	G	A	rs2774960	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:138602417G>A	ENST00000422774.1	-	2	2003	c.1955C>T	c.(1954-1956)cCg>cTg	p.P652L	KIAA1549_ENST00000440172.1_Missense_Mutation_p.P652L|KIAA1549_ENST00000242365.4_Missense_Mutation_p.P602L			Q9HCM3	K1549_HUMAN	KIAA1549	652	Ser-rich.		P -> L (in dbSNP:rs2774960). {ECO:0000269|PubMed:10997877}.			integral component of membrane (GO:0016021)		p.P652L(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CAAGTCACTCGGCATCAGAGA	0.498			O	BRAF	pilocytic astrocytoma								G|||	1962	0.391773	0.7247	0.2478	5008	,	,		20592	0.2014		0.3439	False		,,,				2504	0.2894				p.P652L	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	KIAA1549_ENST00000422774,NS,carcinoma,+1,3	KIAA1549	314	3	1	Substitution - Missense(1)	stomach(1)	c.C1955T						PASS	.	G	LEU/PRO,LEU/PRO	2503,1449		780,943,253	34.0	37.0	36.0		1955,1955	3.3	0.0	7	dbSNP_100	36	2624,5702		435,1754,1974	yes	missense,missense	KIAA1549	NM_001164665.1,NM_020910.2	98,98	1215,2697,2227	AA,AG,GG		31.5157,36.665,41.7576	possibly-damaging,possibly-damaging	652/1951,652/1935	138602417	5127,7151	1976	4163	6139	SO:0001583	missense	57670	exon2			TCACTCGGCATCA		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1955C>T	7.37:g.138602417G>A	ENSP00000416040:p.Pro652Leu	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	815	0.3731684981684982	348	0.7073170731707317	91	0.2513812154696133	124	0.21678321678321677	252	0.3324538258575198	G	11.46	1.645564	0.29246	0.63335	0.315157	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.22336	1.96;1.96;1.96	4.25	3.34	0.38264	.	1.094530	0.07241	N	0.864311	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P;P	0.46327	0.804;0.876	B;B	0.31495	0.062;0.131	T	0.27536	-1.0071	9	0.25106	T	0.35	.	6.9775	0.24683	0.0:0.1788:0.6051:0.2161	rs2774960;rs3735011;rs10362163;rs58911850;rs2774960	652;652	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	L	652;602;652	ENSP00000406661:P652L;ENSP00000242365:P602L;ENSP00000416040:P652L	ENSP00000242365:P602L	P	-	2	0	KIAA1549	138252957	0.022000	0.18835	0.001000	0.08648	0.045000	0.14185	1.919000	0.40015	0.975000	0.38392	0.591000	0.81541	CCG	G|0.595;A|0.405	0.405	strong		0.498	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75982428	75982428	+	Silent	SNP	C	C	T	rs7182906	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.						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	161	3	0.0186335		WXS	Illumina HiSeq	Phase_I	100	97	0.97	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	
LILRB1	10859	hgsc.bcm.edu	37	19	55143452	55143452	+	Missense_Mutation	SNP	T	T	C	rs1061680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55143452T>C	ENST00000396331.1	+	6	782	c.425T>C	c.(424-426)aTc>aCc	p.I142T	AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000324602.7_Missense_Mutation_p.I142T|LILRB1_ENST00000396317.1_Missense_Mutation_p.I142T|LILRB1_ENST00000427581.2_Missense_Mutation_p.I178T|LILRB1_ENST00000448689.1_Missense_Mutation_p.I142T|LILRB1_ENST00000396332.4_Missense_Mutation_p.I142T|LILRB1_ENST00000396315.1_Missense_Mutation_p.I142T|LILRB1_ENST00000434867.2_Missense_Mutation_p.I142T|LILRB1_ENST00000418536.2_Missense_Mutation_p.I142T|LILRB1_ENST00000396327.3_Missense_Mutation_p.I142T|LILRB1_ENST00000396321.2_Missense_Mutation_p.I142T	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	142	Ig-like C2-type 2.		I -> T (in dbSNP:rs1061680). {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)		GGGAATGTAATCCTCCAGTGT	0.552										HNSCC(37;0.09)			N|||	2190	0.4373	0.6059	0.4553	5008	,	,		18519	0.5942		0.2465	False		,,,				2504	0.2311				p.I142T		Atlas-SNP	.											LILRB1,NS,carcinoma,-1,1	LILRB1	140	1	0			c.T425C						scavenged	.	C	THR/ILE,THR/ILE,THR/ILE,THR/ILE	2467,1939	549.6+/-377.8	694,1079,430	104.0	101.0	102.0		425,425,425,425	-0.6	0.0	19	dbSNP_86	102	2380,6220	700.8+/-405.2	323,1734,2243	yes	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	89,89,89,89	1017,2813,2673	CC,CT,TT		27.6744,44.0082,37.2674	benign,benign,benign,benign	142/653,142/652,142/652,142/651	55143452	4847,8159	2203	4300	6503	SO:0001583	missense	10859	exon5			ATGTAATCCTCCA	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.425T>C	19.37:g.55143452T>C	ENSP00000379622:p.Ile142Thr	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	998	0.45695970695970695	313	0.6361788617886179	153	0.42265193370165743	339	0.5926573426573427	193	0.2546174142480211	C	0.004	-2.258264	0.00265	0.559918	0.276744	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.02050	4.48;4.48;4.48;4.48;4.48;4.48;4.48;4.48;4.48;4.48;4.48	1.9	-0.625	0.11548	Immunoglobulin-like fold (1);	0.000000	0.56097	N	0.000039	T	0.00012	0.0000	N	0.00082	-2.215	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	0.0;0.0;0.0;0.0;0.001	T	0.13124	-1.0521	9	0.02654	T	1	.	5.3779	0.16176	0.0:0.4992:0.0:0.5008	rs1061680;rs3202770;rs17845472;rs17858351;rs58070294;rs1061680	142;142;142;142;142	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	T	142;142;142;142;142;142;142;142;178;142;142	ENSP00000379614:I142T;ENSP00000391514:I142T;ENSP00000409968:I142T;ENSP00000379622:I142T;ENSP00000379618:I142T;ENSP00000315997:I142T;ENSP00000405243:I142T;ENSP00000379623:I142T;ENSP00000395004:I178T;ENSP00000379610:I142T;ENSP00000379608:I142T	ENSP00000315997:I142T	I	+	2	0	LILRB1	59835264	0.330000	0.24705	0.001000	0.08648	0.002000	0.02628	0.437000	0.21543	-0.405000	0.07599	-1.160000	0.01791	ATC	T|0.567;C|0.433	0.433	strong		0.552	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
PTPN3	5774	hgsc.bcm.edu	37	9	112166845	112166845	+	Silent	SNP	G	G	A	rs34302609	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:112166845G>A	ENST00000374541.2	-	19	1940	c.1836C>T	c.(1834-1836)aaC>aaT	p.N612N	PTPN3_ENST00000446349.1_Silent_p.N436N|PTPN3_ENST00000394827.3_Silent_p.N80N|PTPN3_ENST00000262539.3_Silent_p.N458N|PTPN3_ENST00000412145.1_Silent_p.N481N	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	612					negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						ggaaaagctggttcagttcat	0.517													G|||	49	0.00978435	0.0023	0.0144	5008	,	,		21400	0.0		0.0328	False		,,,				2504	0.0031				p.N612N		Atlas-SNP	.											.	PTPN3	106	.	0			c.C1836T						PASS	.	G	,,,,,	24,4382	30.8+/-60.4	0,24,2179	114.0	102.0	106.0		1701,1443,1308,975,840,1836	2.2	0.9	9	dbSNP_126	106	260,8340	101.2+/-162.5	4,252,4044	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN3	NM_001145368.1,NM_001145369.1,NM_001145370.1,NM_001145371.1,NM_001145372.1,NM_002829.3	,,,,,	4,276,6223	AA,AG,GG		3.0233,0.5447,2.1836	,,,,,	567/869,481/783,436/738,325/627,280/582,612/914	112166845	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	5774	exon19			AAGCTGGTTCAGT		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.1836C>T	9.37:g.112166845G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_002829	A0AUW9|E7EN99|E9PGU7	Silent	SNP	ENST00000374541.2	37	CCDS6776.1																																																																																			G|0.978;A|0.022	0.022	strong		0.517	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
CENPE	1062	hgsc.bcm.edu	37	4	104117191	104117191	+	Silent	SNP	A	A	G	rs2290943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:104117191A>G	ENST00000265148.3	-	4	332	c.243T>C	c.(241-243)acT>acC	p.T81T	CENPE_ENST00000380026.3_Silent_p.T81T	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	81	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)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.T81T(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		AGGCAAATATAGTACCTGCAA	0.378													A|||	600	0.119808	0.0552	0.1153	5008	,	,		19569	0.1429		0.2207	False		,,,				2504	0.0828				p.T81T		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	1	1	Substitution - coding silent(1)	stomach(1)	c.T243C						PASS	.	A		252,4154	146.5+/-181.1	8,236,1959	95.0	88.0	91.0		243	-8.4	0.9	4	dbSNP_100	91	1775,6825	319.7+/-314.3	196,1383,2721	no	coding-synonymous	CENPE	NM_001813.2		204,1619,4680	GG,GA,AA		20.6395,5.7195,15.5851		81/2702	104117191	2027,10979	2203	4300	6503	SO:0001819	synonymous_variant	1062	exon4			AAATATAGTACCT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.243T>C	4.37:g.104117191A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																			A|0.848;G|0.152	0.152	strong		0.378	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ZNF839	55778	hgsc.bcm.edu	37	14	102807671	102807671	+	Missense_Mutation	SNP	C	C	T	rs9464	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102807671C>T	ENST00000558850.1	+	8	1941	c.1591C>T	c.(1591-1593)Cca>Tca	p.P531S	ZNF839_ENST00000420933.2_3'UTR|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000262236.5_Missense_Mutation_p.P533S|ZNF839_ENST00000559185.1_Missense_Mutation_p.P531S|ZNF839_ENST00000442396.2_Missense_Mutation_p.P647S	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	531			P -> S (in dbSNP:rs9464).				metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TTTTTCCCCTCCAGTAAATGT	0.537													C|||	368	0.0734824	0.1906	0.0403	5008	,	,		18164	0.001		0.0616	False		,,,				2504	0.0256				p.P647S		Atlas-SNP	.											.	ZNF839	41	.	0			c.C1939T						PASS	.	C	SER/PRO	667,3377		54,559,1409	133.0	132.0	132.0		1939	1.5	0.0	14	dbSNP_52	132	465,7903		15,435,3734	yes	missense	ZNF839	NM_018335.3	74	69,994,5143	TT,TC,CC		5.5569,16.4936,9.1202	benign	647/928	102807671	1132,11280	2022	4184	6206	SO:0001583	missense	55778	exon8			TCCCCTCCAGTAA	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1591C>T	14.37:g.102807671C>T	ENSP00000453363:p.Pro531Ser	Somatic	312	0	0		WXS	Illumina HiSeq	Phase_I	347	130	0.37464	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Missense_Mutation	SNP	ENST00000558850.1	37	CCDS58336.1	141	0.06456043956043957	83	0.16869918699186992	17	0.04696132596685083	0	0.0	41	0.05408970976253298	C	8.132	0.783314	0.16189	0.164936	0.055569	ENSG00000022976	ENST00000442396;ENST00000262236;ENST00000398436;ENST00000420933	T;T	0.17370	2.28;2.33	4.56	1.54	0.23209	.	1.160120	0.06378	N	0.714782	T	0.00039	0.0001	N	0.19112	0.55	0.09310	N	1	B;B;B	0.33103	0.397;0.187;0.187	B;B;B	0.28991	0.097;0.058;0.058	T	0.38243	-0.9670	10	0.15499	T	0.54	.	13.5885	0.61946	0.0:0.5279:0.4721:0.0	rs9464;rs3209420;rs52826173;rs59898673;rs9464	647;533;531	A8K0R7-5;A8K0R7-2;A8K0R7	.;.;ZN839_HUMAN	S	647;533;199;65	ENSP00000399863:P647S;ENSP00000262236:P533S	ENSP00000262236:P533S	P	+	1	0	ZNF839	101877424	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.167000	0.16602	0.074000	0.16767	0.514000	0.50259	CCA	T|0.080;G|0.001	0.080	strong		0.537	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376951	168376951	+	lincRNA	SNP	T	T	C	rs34562778|rs71305246	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168376951T>C	ENST00000538528.1	-	0	668																											GTGGGGGTCATTACCCCTGCA	0.637													N|||	1522	0.303914	0.1762	0.3098	5008	,	,		18415	0.4762		0.2565	False		,,,				2504	0.3436				p.M128V		Atlas-SNP	.											.	.	.	.	0			c.A382G						PASS	.						21.0	19.0	19.0					6																	168376951		692	1591	2283			0	exon1			GGGTCATTACCCC																													6.37:g.168376951T>C		Somatic	425	0	0		WXS	Illumina HiSeq	Phase_I	524	83	0.158397	NM_001129895		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																				CTC|0.500;TTA|0.500	.	alt		0.637	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
IDUA	3425	hgsc.bcm.edu	37	4	994452	994452	+	Silent	SNP	C	C	T	rs3755954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:994452C>T	ENST00000247933.4	+	3	440	c.352C>T	c.(352-354)Ctg>Ttg	p.L118L	IDUA_ENST00000514224.1_5'UTR|IDUA_ENST00000453894.1_Silent_p.L71L	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	118					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)			GGACGGGTACCTGGACCTTCT	0.672													C|||	812	0.162141	0.1626	0.2046	5008	,	,		16145	0.1478		0.2505	False		,,,				2504	0.0552				p.L118L		Atlas-SNP	.											.	IDUA	33	.	0			c.C352T						PASS	.	C		859,3543	333.3+/-302.9	105,649,1447	71.0	63.0	66.0		352	-0.7	0.6	4	dbSNP_107	66	2075,6525	358.1+/-331.0	250,1575,2475	yes	coding-synonymous	IDUA	NM_000203.3		355,2224,3922	TT,TC,CC		24.1279,19.5139,22.5658		118/654	994452	2934,10068	2201	4300	6501	SO:0001819	synonymous_variant	3425	exon3			GGGTACCTGGACC	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.352C>T	4.37:g.994452C>T		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	221	96	0.434389	NM_000203	B3KWK6	Silent	SNP	ENST00000247933.4	37	CCDS3343.1																																																																																			C|0.784;T|0.216	0.216	strong		0.672	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
FARP2	9855	hgsc.bcm.edu	37	2	242396209	242396209	+	Missense_Mutation	SNP	C	C	A	rs145630778		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242396209C>A	ENST00000264042.3	+	14	1629	c.1459C>A	c.(1459-1461)Ccc>Acc	p.P487T	FARP2_ENST00000545004.1_Missense_Mutation_p.P487T|FARP2_ENST00000373287.4_Missense_Mutation_p.P487T	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	487	Pro-rich.				actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		CCGGAAGAGCCCCCTGAGTCT	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		17269	0.0		0.001	False		,,,				2504	0.0				p.P487T		Atlas-SNP	.											.	FARP2	92	.	0			c.C1459A						PASS	.	C	THR/PRO	0,4406		0,0,2203	85.0	85.0	85.0		1459	3.0	0.2	2	dbSNP_134	85	1,8599	2.2+/-6.3	0,1,4299	yes	missense	FARP2	NM_014808.2	38	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	487/1055	242396209	1,13005	2203	4300	6503	SO:0001583	missense	9855	exon14			AAGAGCCCCCTGA	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1459C>A	2.37:g.242396209C>A	ENSP00000264042:p.Pro487Thr	Somatic	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	258	120	0.465116	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.91	1.485420	0.26686	0.0	1.16E-4	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	T;T;D	0.81499	-0.98;-1.49;-1.5	5.18	3.03	0.35002	.	0.717669	0.13260	N	0.401364	T	0.67552	0.2905	L	0.32530	0.975	0.26033	N	0.981711	P;B;B	0.34724	0.465;0.328;0.22	B;B;B	0.34242	0.178;0.124;0.058	T	0.53322	-0.8455	10	0.12103	T	0.63	.	9.2186	0.37362	0.0:0.7326:0.0:0.2674	.	487;487;487	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	T	487	ENSP00000264042:P487T;ENSP00000443876:P487T;ENSP00000362384:P487T	ENSP00000264042:P487T	P	+	1	0	FARP2	242044882	1.000000	0.71417	0.234000	0.24042	0.857000	0.48899	3.646000	0.54396	1.195000	0.43115	-0.192000	0.12808	CCC	C|1.000;A|0.000	0.000	strong		0.617	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
CD109	135228	hgsc.bcm.edu	37	6	74497009	74497009	+	Missense_Mutation	SNP	A	A	G	rs2351528	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:74497009A>G	ENST00000287097.5	+	21	2502	c.2390A>G	c.(2389-2391)aAt>aGt	p.N797S	CD109_ENST00000437994.2_Missense_Mutation_p.N797S|CD109_ENST00000422508.2_Missense_Mutation_p.N720S			Q6YHK3	CD109_HUMAN	CD109 molecule	797			N -> S (in dbSNP:rs2351528). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, 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						ATGACTTCAAATGAAATAAAT	0.378													G|||	1865	0.372404	0.4675	0.4049	5008	,	,		19371	0.4087		0.339	False		,,,				2504	0.2178				p.N797S		Atlas-SNP	.											CD109,caecum,carcinoma,0,1	CD109	170	1	0			c.A2390G						scavenged	.	G	SER/ASN,SER/ASN,SER/ASN	2051,2355	608.2+/-391.1	495,1061,647	65.0	68.0	67.0		2390,2159,2390	1.6	0.1	6	dbSNP_100	67	3057,5543	660.2+/-401.7	552,1953,1795	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	46,46,46	1047,3014,2442	GG,GA,AA		35.5465,46.5502,39.2742	benign,benign,benign	797/1429,720/1369,797/1446	74497009	5108,7898	2203	4300	6503	SO:0001583	missense	135228	exon21			CTTCAAATGAAAT	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.2390A>G	6.37:g.74497009A>G	ENSP00000287097:p.Asn797Ser	Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	879	0.4024725274725275	250	0.508130081300813	143	0.39502762430939226	239	0.4178321678321678	247	0.3258575197889182	G	0.021	-1.425324	0.01126	0.465502	0.355465	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.22945	1.93;2.15;1.93	5.46	1.63	0.23807	.	1.129070	0.06361	N	0.711652	T	0.10380	0.0254	L	0.53671	1.685	0.58432	P	5.000000000032756E-6	B;B;B	0.24618	0.008;0.107;0.004	B;B;B	0.16289	0.014;0.015;0.009	T	0.29119	-1.0022	9	0.30078	T	0.28	.	10.7397	0.46145	0.8168:0.0:0.1832:0.0	rs2351528;rs4632862;rs52791004;rs60212756;rs2351528	720;797;797	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	S	797;720;797	ENSP00000388062:N797S;ENSP00000404475:N720S;ENSP00000287097:N797S	ENSP00000287097:N797S	N	+	2	0	CD109	74553730	1.000000	0.71417	0.079000	0.20413	0.012000	0.07955	1.818000	0.39012	-0.068000	0.12953	-1.874000	0.00550	AAT	A|0.597;G|0.403	0.403	strong		0.378	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
MYBPC2	4606	hgsc.bcm.edu	37	19	50944294	50944294	+	Missense_Mutation	SNP	C	C	T	rs374005339		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50944294C>T	ENST00000357701.5	+	8	781	c.730C>T	c.(730-732)Cgg>Tgg	p.R244W		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	244					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)		CATGCTGAAGCGGCTGAAAAA	0.602																																					p.R244W		Atlas-SNP	.											.	MYBPC2	103	.	0			c.C730T						PASS	.		TRP/ARG	1,4181		0,1,2090	32.0	34.0	34.0		730	2.2	1.0	19		34	1,8491		0,1,4245	no	missense	MYBPC2	NM_004533.3	101	0,2,6335	TT,TC,CC		0.0118,0.0239,0.0158	probably-damaging	244/1142	50944294	2,12672	2091	4246	6337	SO:0001583	missense	4606	exon8			CTGAAGCGGCTGA		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.730C>T	19.37:g.50944294C>T	ENSP00000350332:p.Arg244Trp	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	203	12	0.0591133	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	.	.	.	.	.	.	.	.	.	.	.	15.42	2.829530	0.50845	2.39E-4	1.18E-4	ENSG00000086967	ENST00000357701	T	0.59638	0.25	3.33	2.23	0.28157	.	0.000000	0.33477	U	0.004875	T	0.69975	0.3171	M	0.66297	2.02	0.35743	D	0.818838	D	0.89917	1.0	D	0.97110	1.0	T	0.76391	-0.2976	10	0.66056	D	0.02	.	9.7381	0.40401	0.368:0.632:0.0:0.0	.	244	Q14324	MYPC2_HUMAN	W	244	ENSP00000350332:R244W	ENSP00000350332:R244W	R	+	1	2	MYBPC2	55636106	1.000000	0.71417	0.999000	0.59377	0.797000	0.45037	1.612000	0.36889	0.910000	0.36722	0.298000	0.19748	CGG	.	.	weak		0.602	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
KCNH3	23416	hgsc.bcm.edu	37	12	49950251	49950251	+	Missense_Mutation	SNP	C	C	G	rs113209368	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:49950251C>G	ENST00000257981.6	+	13	2827	c.2567C>G	c.(2566-2568)cCt>cGt	p.P856R	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	856					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						AGCCCCTCCCCTGGACCAGGT	0.602													C|||	162	0.0323482	0.0038	0.0519	5008	,	,		18702	0.0		0.0547	False		,,,				2504	0.0675				p.P856R		Atlas-SNP	.											.	KCNH3	88	.	0			c.C2567G						PASS	.	C	ARG/PRO	70,4336	62.3+/-99.4	0,70,2133	53.0	48.0	50.0		2567	5.2	1.0	12	dbSNP_132	50	634,7966	159.1+/-212.4	27,580,3693	yes	missense	KCNH3	NM_012284.1	103	27,650,5826	GG,GC,CC		7.3721,1.5887,5.4129	benign	856/1084	49950251	704,12302	2203	4300	6503	SO:0001583	missense	23416	exon13			CCTCCCCTGGACC	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2567C>G	12.37:g.49950251C>G	ENSP00000257981:p.Pro856Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	37	CCDS8786.1	76	0.0347985347985348	3	0.006097560975609756	24	0.06629834254143646	0	0.0	49	0.06464379947229551	C	17.52	3.411384	0.62399	0.015887	0.073721	ENSG00000135519	ENST00000257981	D	0.98777	-5.13	6.04	5.16	0.70880	.	0.000000	0.43919	D	0.000506	T	0.70518	0.3233	N	0.08118	0	0.35735	D	0.818209	D	0.61080	0.989	P	0.47573	0.55	D	0.84904	0.0844	10	0.17369	T	0.5	.	11.04	0.47825	0.0:0.9157:0.0:0.0843	.	856	Q9ULD8	KCNH3_HUMAN	R	856	ENSP00000257981:P856R	ENSP00000257981:P856R	P	+	2	0	KCNH3	48236518	0.893000	0.30496	0.983000	0.44433	0.949000	0.60115	3.227000	0.51262	1.571000	0.49722	0.563000	0.77884	CCT	C|0.951;G|0.049	0.049	strong		0.602	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
MORC3	23515	hgsc.bcm.edu	37	21	37692589	37692589	+	Silent	SNP	A	A	T	rs2236433	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:37692589A>T	ENST00000400485.1	+	1	103	c.27A>T	c.(25-27)atA>atT	p.I9I	AP000692.10_ENST00000608391.1_RNA|MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	9					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						CCCGCGGGATACGCCTCAGCG	0.736													A|||	1134	0.226438	0.0129	0.33	5008	,	,		9235	0.4871		0.1372	False		,,,				2504	0.2648				p.I9I		Atlas-SNP	.											.	MORC3	78	.	0			c.A27T						PASS	.	A		136,3520		5,126,1697	7.0	9.0	8.0		27	2.6	1.0	21	dbSNP_98	8	1112,6928		80,952,2988	no	coding-synonymous	MORC3	NM_015358.2		85,1078,4685	TT,TA,AA		13.8308,3.7199,10.6703		9/940	37692589	1248,10448	1828	4020	5848	SO:0001819	synonymous_variant	23515	exon1			CGGGATACGCCTC	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"""zinc finger, CW-type with coiled-coil domain 3"", ""zinc finger, CW type with coiled-coil domain 3"""	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.27A>T	21.37:g.37692589A>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_015358	A8KA92|Q9UEZ2	Silent	SNP	ENST00000400485.1	37	CCDS42924.1																																																																																			A|0.762;T|0.238	0.238	strong		0.736	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
NLRP13	126204	hgsc.bcm.edu	37	19	56423074	56423074	+	Silent	SNP	C	C	G	rs977070	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	2	0.0188679		WXS	Illumina HiSeq	Phase_I	82	82	1	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	
ASB10	136371	hgsc.bcm.edu	37	7	150873331	150873331	+	Silent	SNP	C	C	T	rs104886486	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:150873331C>T	ENST00000420175.2	-	5	1296	c.1272G>A	c.(1270-1272)tcG>tcA	p.S424S	GBX1_ENST00000475831.1_5'Flank|ASB10_ENST00000422024.1_Silent_p.S469S|ASB10_ENST00000377867.3_Silent_p.S409S|ASB10_ENST00000434669.1_Silent_p.S431S|ASB10_ENST00000275838.1_Silent_p.S386S			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	424	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AATGCTGCAGCGACCTGGGCT	0.667													C|||	13	0.00259585	0.0008	0.0058	5008	,	,		14914	0.0		0.008	False		,,,				2504	0.0				p.S424S		Atlas-SNP	.											.	ASB10	99	.	0			c.G1272A						PASS	.	C	,,	15,4377		0,15,2181	22.0	23.0	23.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1272,1158,1227	-5.7	0.2	7	dbSNP_132	23	119,8445		0,119,4163	no	coding-synonymous,coding-synonymous,coding-synonymous	ASB10	NM_001142459.1,NM_001142460.1,NM_080871.3	,,	0,134,6344	TT,TC,CC		1.3895,0.3415,1.0343	,,	424/468,386/430,409/453	150873331	134,12822	2196	4282	6478	SO:0001819	synonymous_variant	136371	exon5			CTGCAGCGACCTG	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"""Ankyrin repeat domain containing"""	17185	protein-coding gene	gene with protein product		615054	"""ankyrin repeat and SOCS box-containing 10"", ""glaucoma 1, open angle, F (adult-onset)"""	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.1272G>A	7.37:g.150873331C>T		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	141	98	0.695035	NM_001142459	A0AVH0|Q6ZUL6	Silent	SNP	ENST00000420175.2	37	CCDS47750.2																																																																																			C|0.992;T|0.008	0.008	strong		0.667	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871	
GLI2	2736	hgsc.bcm.edu	37	2	121742307	121742307	+	Silent	SNP	C	C	T	rs13008360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:121742307C>T	ENST00000452319.1	+	12	2004	c.1944C>T	c.(1942-1944)acC>acT	p.T648T	GLI2_ENST00000361492.4_Silent_p.T648T|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Silent_p.T320T					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)				CCATCAAGACCGAGAGCTCCG	0.701													C|||	40	0.00798722	0.0015	0.0101	5008	,	,		16587	0.0		0.0308	False		,,,				2504	0.0				p.T648T		Atlas-SNP	.											GLI2,NS,carcinoma,0,1	GLI2	187	1	0			c.C1944T						scavenged	.	C		26,4366		0,26,2170	21.0	22.0	22.0		1944	-5.5	1.0	2	dbSNP_121	22	229,8367		4,221,4073	no	coding-synonymous	GLI2	NM_005270.4		4,247,6243	TT,TC,CC		2.664,0.592,1.9634		648/1587	121742307	255,12733	2196	4298	6494	SO:0001819	synonymous_variant	2736	exon11			CAAGACCGAGAGC		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.1944C>T	2.37:g.121742307C>T		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			C|0.984;T|0.016	0.016	strong		0.701	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
EXD3	54932	hgsc.bcm.edu	37	9	140201433	140201433	+	Missense_Mutation	SNP	G	G	A	rs118011827	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:140201433G>A	ENST00000340951.4	-	22	2795	c.2600C>T	c.(2599-2601)cCa>cTa	p.P867L	EXD3_ENST00000342129.4_Missense_Mutation_p.P505L	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						GCTGGGGGCTGGGCTCGGCTC	0.652													G|||	39	0.00778754	0.0	0.0014	5008	,	,		13463	0.0		0.008	False		,,,				2504	0.0307				p.P867L		Atlas-SNP	.											.	EXD3	86	.	0			c.C2600T						PASS	.	G	LEU/PRO	4,3848		0,4,1922	18.0	22.0	21.0		2600	-6.2	0.0	9	dbSNP_132	21	42,8162		0,42,4060	yes	missense	EXD3	NM_017820.3	98	0,46,5982	AA,AG,GG		0.5119,0.1038,0.3816	benign	867/877	140201433	46,12010	1926	4102	6028	SO:0001583	missense	54932	exon22			GGGGCTGGGCTCG		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.2600C>T	9.37:g.140201433G>A	ENSP00000340474:p.Pro867Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	47	30	0.638298	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	10.02	1.235692	0.22626	0.001038	0.005119	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.66460	-0.21;0.63	3.79	-6.17	0.02091	.	.	.	.	.	T	0.32704	0.0838	N	0.22421	0.69	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.09377	0.004;0.002	T	0.12319	-1.0552	9	0.30078	T	0.28	.	2.0959	0.03667	0.122:0.226:0.3855:0.2666	.	505;867	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	L	505;867	ENSP00000343705:P505L;ENSP00000340474:P867L	ENSP00000340474:P867L	P	-	2	0	EXD3	139321254	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.324000	0.01116	-1.915000	0.01077	-1.086000	0.02197	CCA	G|0.996;A|0.004	0.004	strong		0.652	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
TMEM119	338773	hgsc.bcm.edu	37	12	108985945	108985945	+	Missense_Mutation	SNP	A	A	G	rs7975237	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	210	106	0.504762	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	
C1orf110	339512	hgsc.bcm.edu	37	1	162825457	162825457	+	Missense_Mutation	SNP	C	C	A	rs77227460	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:162825457C>A	ENST00000367910.1	-	3	399	c.279G>T	c.(277-279)agG>agT	p.R93S	C1orf110_ENST00000367912.2_Missense_Mutation_p.R92S|C1orf110_ENST00000524691.1_5'UTR|C1orf110_ENST00000367911.2_Missense_Mutation_p.R88S	NM_178550.4	NP_848645.3	Q86UF4	CA110_HUMAN	chromosome 1 open reading frame 110	93										endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	12						TGTGCTTCTGCCTTCCCTGTG	0.423													C|||	421	0.0840655	0.062	0.1167	5008	,	,		19440	0.001		0.1948	False		,,,				2504	0.0624				p.R93S		Atlas-SNP	.											.	C1orf110	22	.	0			c.G279T						PASS	.	C	SER/ARG	284,3568		11,262,1653	136.0	128.0	131.0		279	-8.7	0.0	1	dbSNP_131	131	1625,6637		164,1297,2670	yes	missense	C1orf110	NM_178550.4	110	175,1559,4323	AA,AC,CC		19.6684,7.3728,15.7586	benign	93/303	162825457	1909,10205	1926	4131	6057	SO:0001583	missense	339512	exon3			CTTCTGCCTTCCC	BC040018	CCDS44269.1	1q23.3	2012-06-26			ENSG00000185860	ENSG00000185860			28736	protein-coding gene	gene with protein product						12477932	Standard	NM_178550		Approved	MGC48998	uc001gck.2	Q86UF4	OTTHUMG00000034421	ENST00000367910.1:c.279G>T	1.37:g.162825457C>A	ENSP00000356886:p.Arg93Ser	Somatic	309	1	0.00323625		WXS	Illumina HiSeq	Phase_I	428	148	0.345794	NM_178550	Q5JSG1|Q6ZW57	Missense_Mutation	SNP	ENST00000367910.1	37	CCDS44269.1	232	0.10622710622710622	33	0.06707317073170732	51	0.1408839779005525	0	0.0	148	0.19525065963060687	C	8.612	0.889379	0.17540	0.073728	0.196684	ENSG00000185860	ENST00000367912;ENST00000367911;ENST00000367910	.	.	.	4.33	-8.67	0.00863	.	1.055600	0.07432	N	0.895798	T	0.07234	0.0183	N	0.22421	0.69	0.20873	N	0.99984	B;B	0.11235	0.004;0.004	B;B	0.16289	0.015;0.015	T	0.16719	-1.0393	8	0.36615	T	0.2	-0.0422	4.4614	0.11668	0.0971:0.4166:0.0975:0.3887	.	92;93	Q86UF4-2;Q86UF4	.;CA110_HUMAN	S	92;88;93	.	ENSP00000356886:R93S	R	-	3	2	C1orf110	161092081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.208000	0.01229	-2.256000	0.00695	-1.099000	0.02127	AGG	C|0.875;A|0.125	0.125	strong		0.423	C1orf110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083211.2	NM_178550	
OR2C1	4993	hgsc.bcm.edu	37	16	3406626	3406626	+	Missense_Mutation	SNP	G	G	A	rs11648783	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3406626G>A	ENST00000304936.2	+	1	738	c.686G>A	c.(685-687)cGc>cAc	p.R229H		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	229			R -> H (in dbSNP:rs11648783). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9847080}.		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						CTGAAAATCCGCTCTGCAGAG	0.547													G|||	1265	0.252596	0.3389	0.2421	5008	,	,		21776	0.1429		0.2614	False		,,,				2504	0.2474				p.R229H		Atlas-SNP	.											.	OR2C1	38	.	0			c.G686A						PASS	.		HIS/ARG	1522,2872	481.7+/-359.2	249,1024,924	123.0	103.0	110.0		686	-5.3	0.3	16	dbSNP_120	110	2366,6234	395.9+/-345.2	330,1706,2264	no	missense	OR2C1	NM_012368.2	29	579,2730,3188	AA,AG,GG		27.5116,34.6381,29.9215	benign	229/313	3406626	3888,9106	2197	4300	6497	SO:0001583	missense	4993	exon1			AAATCCGCTCTGC	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.686G>A	16.37:g.3406626G>A	ENSP00000307726:p.Arg229His	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_012368	A0AVA4|Q6IF34|Q6IF55	Missense_Mutation	SNP	ENST00000304936.2	37	CCDS10502.1	563	0.25778388278388276	184	0.37398373983739835	92	0.2541436464088398	81	0.14160839160839161	206	0.2717678100263852	g	4.555	0.103149	0.08731	0.346381	0.275116	ENSG00000168158	ENST00000304936	T	0.39229	1.09	5.0	-5.29	0.02747	GPCR, rhodopsin-like superfamily (1);	0.596862	0.14073	N	0.343234	T	0.00012	0.0000	N	0.13003	0.285	0.80722	P	0.0	B	0.14012	0.009	B	0.10450	0.005	T	0.41538	-0.9503	9	0.62326	D	0.03	.	2.6261	0.04930	0.3111:0.2577:0.3384:0.0928	rs11648783;rs56545253;rs59091664;rs11648783	229	O95371	OR2C1_HUMAN	H	229	ENSP00000307726:R229H	ENSP00000307726:R229H	R	+	2	0	OR2C1	3346627	0.000000	0.05858	0.334000	0.25495	0.003000	0.03518	-0.888000	0.04148	-0.962000	0.03604	-2.321000	0.00252	CGC	G|0.723;A|0.277	0.277	strong		0.547	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3		
HOXB8	3218	hgsc.bcm.edu	37	17	46690777	46690777	+	Silent	SNP	A	A	G	rs45441492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46690777A>G	ENST00000239144.4	-	2	753	c.519T>C	c.(517-519)cgT>cgC	p.R173R	HOXB8_ENST00000576562.1_Silent_p.R172R|HOXB7_ENST00000567101.2_Intron|HOXB7_ENST00000239165.7_5'Flank	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	173					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|dorsal spinal cord development (GO:0021516)|embryonic skeletal system morphogenesis (GO:0048704)|grooming behavior (GO:0007625)|negative regulation of myeloid cell differentiation (GO:0045638)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(8)|urinary_tract(2)	11						TTCGCCGCTTACGAGTCAGAT	0.557													G|||	304	0.0607029	0.1536	0.0519	5008	,	,		8833	0.001		0.0278	False		,,,				2504	0.0368				p.R173R		Atlas-SNP	.											.	HOXB8	26	.	0			c.T519C						PASS	.	G		658,3748	764.6+/-413.3	52,554,1597	106.0	101.0	102.0		519	3.1	1.0	17	dbSNP_127	102	459,8141	798.8+/-407.4	16,427,3857	no	coding-synonymous	HOXB8	NM_024016.3		68,981,5454	GG,GA,AA		5.3372,14.9342,8.5883		173/244	46690777	1117,11889	2203	4300	6503	SO:0001819	synonymous_variant	3218	exon2			CCGCTTACGAGTC		CCDS11533.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120068	ENSG00000120068		"""Homeoboxes / ANTP class : HOXL subclass"""	5119	protein-coding gene	gene with protein product		142963	"""homeo box B8"""	HOX2, HOX2D		1973146, 1358459	Standard	XM_005257286		Approved		uc002inw.3	P17481	OTTHUMG00000159904	ENST00000239144.4:c.519T>C	17.37:g.46690777A>G		Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	182	180	0.989011	NM_024016	Q9H1I2	Silent	SNP	ENST00000239144.4	37	CCDS11533.1																																																																																			A|0.924;G|0.076	0.076	strong		0.557	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3		
PCDH9	5101	hgsc.bcm.edu	37	13	67800419	67800419	+	Silent	SNP	C	C	G	rs41283952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:67800419C>G	ENST00000377865.2	-	1	2288	c.2154G>C	c.(2152-2154)gtG>gtC	p.V718V	PCDH9_ENST00000328454.5_Silent_p.V718V|PCDH9_ENST00000377861.3_Silent_p.V718V|PCDH9_ENST00000456367.1_Silent_p.V718V|PCDH9_ENST00000544246.1_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	196	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	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	
TMEM245	23731	hgsc.bcm.edu	37	9	111881927	111881927	+	Silent	SNP	T	T	C	rs6825	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:111881927T>C	ENST00000374586.3	-	1	298	c.267A>G	c.(265-267)ctA>ctG	p.L89L		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	89						integral component of membrane (GO:0016021)											AAGTGCCGCATAGCACGGCCC	0.701													C|||	1632	0.325879	0.2035	0.4179	5008	,	,		10967	0.2937		0.4652	False		,,,				2504	0.316				p.L89L		Atlas-SNP	.											C9orf5,NS,carcinoma,0,1	.	.	1	0			c.A267G						PASS	.	C		911,3171		141,629,1271	12.0	21.0	18.0		267	2.7	1.0	9	dbSNP_52	18	3699,4635		871,1957,1339	no	coding-synonymous	C9orf5	NM_032012.3		1012,2586,2610	CC,CT,TT		44.3844,22.3175,37.1295		89/880	111881927	4610,7806	2041	4167	6208	SO:0001819	synonymous_variant	23731	exon1			GCCGCATAGCACG	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.267A>G	9.37:g.111881927T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Silent	SNP	ENST00000374586.3	37	CCDS43858.1																																																																																			T|0.679;C|0.321	0.321	strong		0.701	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012	
MTIF2	4528	hgsc.bcm.edu	37	2	55490788	55490788	+	Silent	SNP	T	T	C	rs1134722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:55490788T>C	ENST00000263629.4	-	4	522	c.207A>G	c.(205-207)ctA>ctG	p.L69L	MTIF2_ENST00000446660.1_5'UTR|MTIF2_ENST00000394600.3_Silent_p.L69L|MTIF2_ENST00000403721.1_Silent_p.L69L	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	69					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.L69L(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	24						TTTTTGTTACTAGAAGCCTAT	0.493													T|||	300	0.0599042	0.0711	0.0331	5008	,	,		16067	0.0645		0.0517	False		,,,				2504	0.0675				p.L69L		Atlas-SNP	.											MTIF2,NS,carcinoma,0,1	MTIF2	64	1	1	Substitution - coding silent(1)	stomach(1)	c.A207G						PASS	.	T	,	302,4104	165.4+/-196.9	13,276,1914	66.0	64.0	65.0		207,207	-3.4	0.2	2	dbSNP_86	65	493,8107	141.9+/-198.1	20,453,3827	no	coding-synonymous,coding-synonymous	MTIF2	NM_001005369.1,NM_002453.2	,	33,729,5741	CC,CT,TT		5.7326,6.8543,6.1126	,	69/728,69/728	55490788	795,12211	2203	4300	6503	SO:0001819	synonymous_variant	4528	exon4			TGTTACTAGAAGC	L34600	CCDS1853.1	2p16.1	2008-02-05			ENSG00000085760	ENSG00000085760			7441	protein-coding gene	gene with protein product		603766				9925935, 7829522	Standard	XM_005264335		Approved	IF-2mt	uc002ryo.3	P46199	OTTHUMG00000129338	ENST00000263629.4:c.207A>G	2.37:g.55490788T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_002453	D6W5D0	Silent	SNP	ENST00000263629.4	37	CCDS1853.1																																																																																			T|0.941;C|0.059	0.059	strong		0.493	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453	
SLC10A6	345274	hgsc.bcm.edu	37	4	87769929	87769929	+	Missense_Mutation	SNP	T	T	C	rs13106574	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:87769929T>C	ENST00000273905.6	-	1	487	c.340A>G	c.(340-342)Att>Gtt	p.I114V	SLC10A6_ENST00000505535.1_5'UTR	NM_197965.2	NP_932069.1	Q3KNW5	SOAT_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 6	114			I -> V (in dbSNP:rs13106574). {ECO:0000269|PubMed:15489334}.		sodium-dependent organic anion transport (GO:0043251)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)|sodium-dependent organic anion transmembrane transporter activity (GO:0043250)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)	9		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.00099)		AAGGTGAAAATGTTAGAGATG	0.488													T|||	495	0.0988419	0.118	0.1268	5008	,	,		17437	0.001		0.1769	False		,,,				2504	0.0736				p.I114V		Atlas-SNP	.											.	SLC10A6	40	.	0			c.A340G						PASS	.	T	VAL/ILE	518,3888	237.4+/-249.2	30,458,1715	78.0	84.0	82.0		340	2.6	1.0	4	dbSNP_121	82	1726,6874	315.7+/-312.4	178,1370,2752	yes	missense	SLC10A6	NM_197965.2	29	208,1828,4467	CC,CT,TT		20.0698,11.7567,17.2536	benign	114/378	87769929	2244,10762	2203	4300	6503	SO:0001583	missense	345274	exon1			TGAAAATGTTAGA	AJ583502	CCDS3614.1	4q22.1	2013-07-18	2013-07-18		ENSG00000145283	ENSG00000145283		"""Solute carriers"""	30603	protein-coding gene	gene with protein product		613366				15020217, 17491011	Standard	NM_197965		Approved	SOAT	uc003hqd.2	Q3KNW5	OTTHUMG00000130596	ENST00000273905.6:c.340A>G	4.37:g.87769929T>C	ENSP00000273905:p.Ile114Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	144	56	0.388889	NM_197965	Q70EX7	Missense_Mutation	SNP	ENST00000273905.6	37	CCDS3614.1	224	0.10256410256410256	54	0.10975609756097561	46	0.1270718232044199	0	0.0	124	0.16358839050131926	T	10.69	1.422271	0.25639	0.117567	0.200698	ENSG00000145283	ENST00000273905	T	0.08984	3.03	5.59	2.64	0.31445	.	0.077016	0.52532	N	0.000071	T	0.00012	0.0000	N	0.13272	0.32	0.41065	P	0.014599000000000029	B	0.25169	0.119	B	0.31812	0.136	T	0.47394	-0.9121	9	0.15066	T	0.55	-17.4279	5.4631	0.16627	0.0:0.1238:0.1603:0.7158	rs13106574;rs52789983;rs59733764;rs13106574	114	Q3KNW5	SOAT_HUMAN	V	114	ENSP00000273905:I114V	ENSP00000273905:I114V	I	-	1	0	SLC10A6	87988953	1.000000	0.71417	0.956000	0.39512	0.893000	0.52053	1.263000	0.33004	0.751000	0.32900	0.533000	0.62120	ATT	T|0.854;C|0.146	0.146	strong		0.488	SLC10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253043.2	NM_197965	
DHX37	57647	hgsc.bcm.edu	37	12	125434716	125434716	+	Silent	SNP	G	G	A	rs4078216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:125434716G>A	ENST00000308736.2	-	24	3293	c.3195C>T	c.(3193-3195)gcC>gcT	p.A1065A	DHX37_ENST00000544745.1_Silent_p.A852A	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	1065							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)		GCAGGAACCGGGCAAAGTGCT	0.647													G|||	1296	0.258786	0.0537	0.268	5008	,	,		18264	0.5605		0.2197	False		,,,				2504	0.2587				p.A1065A		Atlas-SNP	.											DHX37,NS,carcinoma,0,1	DHX37	114	1	0			c.C3195T						PASS	.	G		346,4060	180.8+/-209.0	14,318,1871	61.0	59.0	59.0		3195	0.0	0.7	12	dbSNP_108	59	2001,6599	347.5+/-326.6	232,1537,2531	no	coding-synonymous	DHX37	NM_032656.3		246,1855,4402	AA,AG,GG		23.2674,7.8529,18.0455		1065/1158	125434716	2347,10659	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon24			GAACCGGGCAAAG	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.3195C>T	12.37:g.125434716G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																			G|0.776;N|0.000	.	strong		0.647	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
PARD3	56288	hgsc.bcm.edu	37	10	34630575	34630575	+	Silent	SNP	T	T	A	rs141191270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:34630575T>A	ENST00000374789.3	-	16	2722	c.2397A>T	c.(2395-2397)gcA>gcT	p.A799A	PARD3_ENST00000374790.3_Silent_p.A739A|PARD3_ENST00000374776.1_Silent_p.A783A|PARD3_ENST00000374788.3_Silent_p.A796A|PARD3_ENST00000374794.3_Silent_p.A739A|PARD3_ENST00000350537.4_Silent_p.A783A|PARD3_ENST00000346874.4_Silent_p.A799A|PARD3_ENST00000545260.1_Silent_p.A739A|PARD3_ENST00000545693.1_Silent_p.A783A|PARD3_ENST00000544292.1_Silent_p.A513A|PARD3_ENST00000340077.5_Silent_p.A796A|PARD3_ENST00000374773.1_Silent_p.A796A	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	799	Interacts with PRKCI and PRKCZ. {ECO:0000250}.				apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				AATCACTGATTGCAGCCTTGG	0.478																																					p.A799A		Atlas-SNP	.											.	PARD3	131	.	0			c.A2397T						PASS	.	T	,,,,,,,,,,	3,4403	6.2+/-15.9	0,3,2200	128.0	117.0	120.0		2388,2349,2397,2349,2349,2217,2217,2388,2388,2349,2397	-11.3	0.0	10	dbSNP_134	120	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PARD3	NM_001184785.1,NM_001184786.1,NM_001184787.1,NM_001184788.1,NM_001184789.1,NM_001184790.1,NM_001184791.1,NM_001184792.1,NM_001184793.1,NM_001184794.1,NM_019619.3	,,,,,,,,,,	0,5,6498	AA,AT,TT		0.0233,0.0681,0.0384	,,,,,,,,,,	796/1354,783/1341,799/1320,783/1311,783/1274,739/1267,739/1245,796/1032,796/1001,783/989,799/1357	34630575	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	56288	exon16			ACTGATTGCAGCC	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"""atypical PKC isotype-specific interacting protein"", ""par-3 family cell polarity regulator alpha"", ""protein phosphatase 1, regulatory subunit 118"""	606745	"""par-3 (partitioning defective 3, C.elegans) homolog"", ""par-3 partitioning defective 3 homolog (C. elegans)"""			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.2397A>T	10.37:g.34630575T>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	88	69	0.784091	NM_001184787	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Silent	SNP	ENST00000374789.3	37	CCDS7178.1																																																																																			T|0.999;A|0.001	0.001	strong		0.478	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	
PEAR1	375033	hgsc.bcm.edu	37	1	156879580	156879580	+	Silent	SNP	C	C	T	rs3737224	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156879580C>T	ENST00000338302.3	+	13	1674	c.1449C>T	c.(1447-1449)ccC>ccT	p.P483P	PEAR1_ENST00000292357.7_Silent_p.P483P			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	483					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)					CCTGCCCACCCGGAACCTGGG	0.622													C|||	885	0.176717	0.1589	0.1037	5008	,	,		17946	0.3145		0.1024	False		,,,				2504	0.1871				p.P483P		Atlas-SNP	.											.	PEAR1	118	.	0			c.C1449T						PASS	.	C		687,3719	286.9+/-279.0	57,573,1573	51.0	49.0	50.0		1449	-2.0	0.9	1	dbSNP_107	50	891,7709	199.2+/-243.3	50,791,3459	no	coding-synonymous	PEAR1	NM_001080471.1		107,1364,5032	TT,TC,CC		10.3605,15.5924,12.1329		483/1038	156879580	1578,11428	2203	4300	6503	SO:0001819	synonymous_variant	375033	exon12			CCCACCCGGAACC	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.1449C>T	1.37:g.156879580C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	188	72	0.382979	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			C|0.847;T|0.153	0.153	strong		0.622	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
SWSAP1	126074	hgsc.bcm.edu	37	19	11486354	11486354	+	Missense_Mutation	SNP	C	C	A	rs146815699	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11486354C>A	ENST00000312423.2	+	2	411	c.352C>A	c.(352-354)Ctt>Att	p.L118I	CTD-2342J14.6_ENST00000590399.1_RNA	NM_175871.3	NP_787067.2	Q6NVH7	SWAP1_HUMAN	SWIM-type zinc finger 7 associated protein 1	118					ATP catabolic process (GO:0006200)|double-strand break repair via homologous recombination (GO:0000724)|protein stabilization (GO:0050821)	nucleus (GO:0005634)|Shu complex (GO:0097196)	ATPase activity (GO:0016887)|single-stranded DNA binding (GO:0003697)										CATTGCCTTACTTCTAGACAC	0.652													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17164	0.0		0.002	False		,,,				2504	0.0				p.L118I		Atlas-SNP	.											.	.	.	.	0			c.C352A						PASS	.	C	ILE/LEU	5,4401	9.9+/-24.2	0,5,2198	73.0	72.0	72.0		352	5.3	1.0	19	dbSNP_134	72	39,8561	26.8+/-75.7	0,39,4261	yes	missense	C19orf39	NM_175871.3	5	0,44,6459	AA,AC,CC		0.4535,0.1135,0.3383	possibly-damaging	118/230	11486354	44,12962	2203	4300	6503	SO:0001583	missense	126074	exon2			GCCTTACTTCTAG	AK092438	CCDS12259.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000173928	ENSG00000173928			26638	protein-coding gene	gene with protein product	"""zinc finger, SWIM-type containing 7 associated protein 1"", ""SWS1-associated protein 1"""	614536	"""chromosome 19 open reading frame 39"""	C19orf39		21965664	Standard	NM_175871		Approved	FLJ35119, ZSWIM7AP1, SWS1AP1	uc002mrg.1	Q6NVH7		ENST00000312423.2:c.352C>A	19.37:g.11486354C>A	ENSP00000310008:p.Leu118Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_175871	Q8NAM1	Missense_Mutation	SNP	ENST00000312423.2	37	CCDS12259.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	24.3	4.520751	0.85495	0.001135	0.004535	ENSG00000173928	ENST00000312423	T	0.41400	1.0	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000007	T	0.63307	0.2500	M	0.65975	2.015	0.45216	D	0.998223	D	0.76494	0.999	D	0.87578	0.998	T	0.65038	-0.6265	10	0.59425	D	0.04	-11.7403	15.9252	0.79611	0.0:1.0:0.0:0.0	.	118	Q6NVH7	CS039_HUMAN	I	118	ENSP00000310008:L118I	ENSP00000310008:L118I	L	+	1	0	C19orf39	11347354	1.000000	0.71417	0.998000	0.56505	0.762000	0.43233	4.466000	0.60148	2.489000	0.83994	0.655000	0.94253	CTT	C|0.997;A|0.003	0.003	strong		0.652	SWSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458789.1	NM_175871	
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12252955	12252955	+	Missense_Mutation	SNP	T	T	G	rs1061622	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:12252955T>G	ENST00000376259.3	+	6	676	c.587T>G	c.(586-588)aTg>aGg	p.M196R	TNFRSF1B_ENST00000492361.1_3'UTR|MIR4632_ENST00000584158.1_RNA	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	196			M -> R (frequent polymorphism; seems to be associated with hyperandrogenism, polycystic ovary syndrome (PCOS) and systemic lupus erythematosus; dbSNP:rs1061622). {ECO:0000269|PubMed:11197692, ECO:0000269|PubMed:11762942, ECO:0000269|PubMed:12161545, ECO:0000269|PubMed:2166946, ECO:0000269|PubMed:2172983, ECO:0000269|Ref.6, ECO:0000269|Ref.7}.		aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)	p.M196R(1)		central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)	AATGCAAGCATGGATGCAGTC	0.637													T|||	975	0.194688	0.1868	0.1268	5008	,	,		15660	0.1498		0.2177	False		,,,				2504	0.2761				p.M196R		Atlas-SNP	.											TNFRSF1B,NS,carcinoma,0,1	TNFRSF1B	28	1	1	Substitution - Missense(1)	stomach(1)	c.T587G	GRCh37	CM022071	TNFRSF1B	M	rs1061622	scavenged	.	T	ARG/MET	929,3477	349.8+/-310.5	94,741,1368	134.0	100.0	112.0		587	-4.1	0.0	1	dbSNP_86	112	2069,6531	355.3+/-329.8	275,1519,2506	yes	missense	TNFRSF1B	NM_001066.2	91	369,2260,3874	GG,GT,TT		24.0581,21.0849,23.0509	benign	196/462	12252955	2998,10008	2203	4300	6503	SO:0001583	missense	7133	exon6			CAAGCATGGATGC	M32315	CCDS145.1	1p36.22	2008-02-05			ENSG00000028137	ENSG00000028137		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11917	protein-coding gene	gene with protein product		191191		TNFR2		2158863, 8702885	Standard	NM_001066		Approved	TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b	uc001att.3	P20333	OTTHUMG00000001829	ENST00000376259.3:c.587T>G	1.37:g.12252955T>G	ENSP00000365435:p.Met196Arg	Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	44	12	0.272727	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	37	CCDS145.1	430	0.19688644688644688	104	0.21138211382113822	56	0.15469613259668508	95	0.1660839160839161	175	0.23087071240105542	T	10.29	1.310596	0.23821	0.210849	0.240581	ENSG00000028137	ENST00000376259;ENST00000400863	T	0.60548	0.18	4.15	-4.13	0.03904	TNFR/CD27/30/40/95 cysteine-rich region (1);	1.471100	0.03493	N	0.216872	T	0.00012	0.0000	N	0.13198	0.31	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.07947	-1.0746	9	0.38643	T	0.18	-9.0951	7.0833	0.25244	0.0:0.5369:0.1669:0.2962	rs1061622;rs1681698;rs2228492;rs13306722;rs17037789;rs17883437;rs52797629;rs60195947;rs1061622	196	P20333	TNR1B_HUMAN	R	196	ENSP00000365435:M196R	ENSP00000365435:M196R	M	+	2	0	TNFRSF1B	12175542	0.000000	0.05858	0.000000	0.03702	0.905000	0.53344	-1.738000	0.01842	-0.694000	0.05113	0.482000	0.46254	ATG	T|0.792;G|0.208	0.208	strong		0.637	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011718	46011718	+	Silent	SNP	T	T	C	rs587693578	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:46011718T>C	ENST00000400368.1	-	1	668	c.648A>G	c.(646-648)ccA>ccG	p.P216P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	216	29 X 5 AA repeats of C-C-X(3).					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						TGCAGCAAGTTGGCTGGCAGC	0.667													.|||	174	0.0347444	0.1248	0.0115	5008	,	,		21644	0.001		0.0	False		,,,				2504	0.0				p.P216P		Atlas-SNP	.											KRTAP10-6,caecum,carcinoma,-2,1	KRTAP10-6	57	1	0			c.A648G						scavenged	.						94.0	122.0	112.0					21																	46011718		2195	4300	6495	SO:0001819	synonymous_variant	386674	exon1			GCAAGTTGGCTGG	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.648A>G	21.37:g.46011718T>C		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	345	29	0.084058	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.667	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
C5orf42	65250	hgsc.bcm.edu	37	5	37153871	37153871	+	Missense_Mutation	SNP	G	G	T	rs77014998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:37153871G>T	ENST00000508244.1	-	40	8275	c.8182C>A	c.(8182-8184)Cct>Act	p.P2728T	C5orf42_ENST00000425232.2_Missense_Mutation_p.P2728T|C5orf42_ENST00000274258.7_Missense_Mutation_p.P1626T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2728						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AGCATTTCAGGCTTGGGGAAA	0.358													G|||	13	0.00259585	0.0	0.0058	5008	,	,		19975	0.0		0.0089	False		,,,				2504	0.0				p.P2728T		Atlas-SNP	.											.	C5orf42	422	.	0			c.C8182A						PASS	.	G	THR/PRO	20,4386	27.2+/-55.0	0,20,2183	93.0	83.0	86.0		8182	2.3	0.0	5	dbSNP_131	86	99,8501	54.4+/-115.2	1,97,4202	yes	missense	C5orf42	NM_023073.3	38	1,117,6385	TT,TG,GG		1.1512,0.4539,0.915	benign	2728/3198	37153871	119,12887	2203	4300	6503	SO:0001583	missense	65250	exon41			TTTCAGGCTTGGG		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.8182C>A	5.37:g.37153871G>T	ENSP00000421690:p.Pro2728Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	3.383	-0.126029	0.06795	0.004539	0.011512	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.17854	2.25;2.25;2.35;2.34	5.41	2.29	0.28610	.	1.705140	0.03544	N	0.224372	T	0.07052	0.0179	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.29274	-1.0017	10	0.16420	T	0.52	.	4.6926	0.12788	0.1913:0.0:0.5443:0.2644	.	2728;1626	E9PH94;Q9H799	.;CE042_HUMAN	T	2728;2728;1626;1794;1662	ENSP00000421690:P2728T;ENSP00000389014:P2728T;ENSP00000274258:P1626T;ENSP00000424223:P1794T	ENSP00000274258:P1626T	P	-	1	0	C5orf42	37189628	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	0.288000	0.18939	0.645000	0.30675	0.591000	0.81541	CCT	G|0.992;T|0.008	0.008	strong		0.358	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
VPS13B	157680	hgsc.bcm.edu	37	8	100874154	100874154	+	Missense_Mutation	SNP	G	G	A	rs149318176	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:100874154G>A	ENST00000358544.2	+	58	11381	c.11270G>A	c.(11269-11271)cGg>cAg	p.R3757Q	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.R3732Q	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3757					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)			GGCCTGTCCCGGCTGGGCATC	0.677													G|||	5	0.000998403	0.0	0.0014	5008	,	,		14908	0.0		0.001	False		,,,				2504	0.0031				p.R3757Q	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G11270A						PASS	.	G	GLN/ARG,GLN/ARG	0,4392		0,0,2196	16.0	18.0	18.0		11270,11195	5.8	1.0	8	dbSNP_134	18	23,8565		0,23,4271	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	43,43	0,23,6467	AA,AG,GG		0.2678,0.0,0.1772	probably-damaging,probably-damaging	3757/4023,3732/3998	100874154	23,12957	2196	4294	6490	SO:0001583	missense	157680	exon58			TGTCCCGGCTGGG	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.11270G>A	8.37:g.100874154G>A	ENSP00000351346:p.Arg3757Gln	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	83	28	0.337349	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463122	0.96257	0.0	0.002678	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.69306	-0.39;-0.39	5.78	5.78	0.91487	Autophagy-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77260	0.4104	L	0.40543	1.245	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.87578	0.948;0.998	T	0.74873	-0.3516	10	0.41790	T	0.15	.	20.0204	0.97499	0.0:0.0:1.0:0.0	.	3732;3757	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	Q	3732;3757	ENSP00000349685:R3732Q;ENSP00000351346:R3757Q	ENSP00000349685:R3732Q	R	+	2	0	VPS13B	100943330	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.628000	0.83189	2.729000	0.93468	0.650000	0.86243	CGG	G|0.998;A|0.002	0.002	strong		0.677	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656607	46656607	+	Silent	SNP	G	G	A	rs8143066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46656607G>A	ENST00000253255.5	-	1	2612	c.2613C>T	c.(2611-2613)atC>atT	p.I871I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	871	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AGAGCTGGTTGATACCCCACT	0.413													A|||	1229	0.245407	0.6785	0.134	5008	,	,		20155	0.001		0.16	False		,,,				2504	0.0787				p.I871I		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C2613T						PASS	.	A		2654,1752	520.9+/-370.4	793,1068,342	70.0	70.0	70.0		2613	-1.7	0.0	22	dbSNP_116	70	1260,7340	760.1+/-407.6	88,1084,3128	no	coding-synonymous	PKDREJ	NM_006071.1		881,2152,3470	AA,AG,GG		14.6512,39.764,30.0938		871/2254	46656607	3914,9092	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			CTGGTTGATACCC	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2613C>T	22.37:g.46656607G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.722;A|0.278	0.278	strong		0.413	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
KIF4B	285643	hgsc.bcm.edu	37	5	154395458	154395458	+	Missense_Mutation	SNP	G	G	A	rs17116710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	256	0	0		WXS	Illumina HiSeq	Phase_I	241	108	0.448133	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		
ALG6	29929	hgsc.bcm.edu	37	1	63902524	63902524	+	Missense_Mutation	SNP	C	C	G	rs41285372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:63902524C>G	ENST00000371108.4	+	15	1662	c.1357C>G	c.(1357-1359)Ctg>Gtg	p.L453V	ALG6_ENST00000263440.4_Missense_Mutation_p.L455V|ALG6_ENST00000494765.1_3'UTR	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	453					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|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)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						TATGGTGCTTCTGACGTTGAT	0.383													C|||	21	0.00419329	0.0008	0.0043	5008	,	,		18422	0.0		0.0159	False		,,,				2504	0.001				p.L453V		Atlas-SNP	.											.	ALG6	33	.	0			c.C1357G						PASS	.	C	VAL/LEU	24,4382	30.8+/-60.4	1,22,2180	227.0	214.0	219.0		1357	3.2	1.0	1	dbSNP_127	219	152,8448	72.9+/-135.5	1,150,4149	yes	missense	ALG6	NM_013339.3	32	2,172,6329	GG,GC,CC		1.7674,0.5447,1.3532	possibly-damaging	453/508	63902524	176,12830	2203	4300	6503	SO:0001583	missense	29929	exon15			GTGCTTCTGACGT	AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	2.4.1.267		23157	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	604566	"""asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""			10359825, 11875054	Standard	NM_013339		Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.1357C>G	1.37:g.63902524C>G	ENSP00000360149:p.Leu453Val	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	180	135	0.75	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	37	CCDS30735.1	13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	16.45	3.125406	0.56721	0.005447	0.017674	ENSG00000088035	ENST00000371108;ENST00000263440;ENST00000423077	D;D	0.83755	-1.76;-1.76	5.06	3.19	0.36642	.	0.079049	0.53938	D	0.000045	D	0.86100	0.5852	M	0.73962	2.25	0.58432	D	0.999999	D;D	0.89917	1.0;0.977	D;D	0.87578	0.998;0.919	D	0.85509	0.1196	10	0.45353	T	0.12	-16.66	11.1039	0.48190	0.0:0.8472:0.0:0.1528	rs41285372	200;455	B4DHV8;A2A2G4	.;.	V	453;455;200	ENSP00000360149:L453V;ENSP00000263440:L455V	ENSP00000263440:L455V	L	+	1	2	ALG6	63675112	0.985000	0.35326	0.997000	0.53966	0.749000	0.42624	2.010000	0.40913	0.647000	0.30713	0.484000	0.47621	CTG	C|0.987;G|0.013	0.013	strong		0.383	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339	
IFNA1	3439	hgsc.bcm.edu	37	9	21440916	21440916	+	Missense_Mutation	SNP	C	C	T	rs2230050	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:21440916C>T	ENST00000276927.1	+	1	477	c.410C>T	c.(409-411)gCg>gTg	p.A137V		NM_024013.2	NP_076918.1	P01562	IFNA1_HUMAN	interferon, alpha 1	137			A -> V (in alpha-1B; dbSNP:rs2230050). {ECO:0000269|Ref.9}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|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)|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)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)	7				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		CTGATGAATGCGGACTCCATC	0.498													c|||	118	0.0235623	0.0764	0.013	5008	,	,		18884	0.001		0.005	False		,,,				2504	0.002				p.A137V		Atlas-SNP	.											IFNA1,NS,carcinoma,-1,1	IFNA1	21	1	0			c.C410T						scavenged	.	C	VAL/ALA	264,3734		11,242,1746	17.0	21.0	19.0		410	0.5	0.0	9	dbSNP_134	19	25,8205		0,25,4090	no	missense	IFNA1	NM_024013.2	64	11,267,5836	TT,TC,CC		0.3038,6.6033,2.3634	benign	137/190	21440916	289,11939	1999	4115	6114	SO:0001583	missense	3439	exon1			TGAATGCGGACTC		CCDS6508.1	9p22	2010-12-10			ENSG00000197919	ENSG00000197919		"""Interferons"""	5417	protein-coding gene	gene with protein product	"""IFN-alpha 1b"", ""interferon alpha 1b"""	147660				1385305	Standard	NM_024013		Approved	IFNA@, IFL, IFN, IFN-ALPHA, IFNA13, IFN-alphaD	uc003zpd.2	P01562	OTTHUMG00000019673	ENST00000276927.1:c.410C>T	9.37:g.21440916C>T	ENSP00000276927:p.Ala137Val	Somatic	714	0	0		WXS	Illumina HiSeq	Phase_I	634	176	0.277603	NM_024013	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Missense_Mutation	SNP	ENST00000276927.1	37	CCDS6508.1	.	.	.	.	.	.	.	.	.	.	C	7.309	0.614657	0.14129	0.066033	0.003038	ENSG00000197919	ENST00000276927	T	0.05580	3.42	3.12	0.511	0.16989	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.388379	0.22170	N	0.063657	T	0.00271	0.0008	N	0.11927	0.2	0.09310	N	1	B	0.09022	0.002	B	0.13407	0.009	T	0.43702	-0.9375	10	0.39692	T	0.17	.	3.5529	0.07853	0.5394:0.2403:0.0:0.2203	.	137	P01562	IFNA1_HUMAN	V	137	ENSP00000276927:A137V	ENSP00000276927:A137V	A	+	2	0	IFNA1	21430916	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.127000	0.15790	-0.015000	0.14150	-0.607000	0.04081	GCG	C|0.946;T|0.054	0.054	strong		0.498	IFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051902.1	NM_024013	
TELO2	9894	hgsc.bcm.edu	37	16	1555505	1555505	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1555505C>T	ENST00000262319.6	+	16	2216	c.1937C>T	c.(1936-1938)cCa>cTa	p.P646L	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	646					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)				CCGTGCCTGCCAGAGGCAGCC	0.667																																					p.P646L		Atlas-SNP	.											.	TELO2	44	.	0			c.C1937T						PASS	.						33.0	37.0	36.0					16																	1555505		2198	4297	6495	SO:0001583	missense	9894	exon16			GCCTGCCAGAGGC	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.1937C>T	16.37:g.1555505C>T	ENSP00000262319:p.Pro646Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	C	9.403	1.078424	0.20227	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.14893	2.47	3.64	1.62	0.23740	.	0.309815	0.24107	N	0.041482	T	0.12305	0.0299	L	0.50333	1.59	0.21147	N	0.999776	B	0.26635	0.155	B	0.20384	0.029	T	0.27706	-1.0066	10	0.22706	T	0.39	-0.0024	5.4471	0.16541	0.1965:0.693:0.0:0.1106	.	646	Q9Y4R8	TELO2_HUMAN	L	169;646	ENSP00000262319:P646L	ENSP00000262319:P646L	P	+	2	0	TELO2	1495506	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.334000	0.19787	0.069000	0.16605	-1.436000	0.01078	CCA	.	.	none		0.667	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73207372	73207372	+	Missense_Mutation	SNP	T	T	A	rs1478453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:73207372T>A	ENST00000426542.2	+	34	4940	c.4920T>A	c.(4918-4920)caT>caA	p.H1640Q	ARHGEF28_ENST00000513042.2_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.H1327Q|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.H1596Q|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.H560Q|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.H1640Q|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.H1640Q			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1640	Interaction with microtubules. {ECO:0000250}.		H -> Q (in dbSNP:rs1478453). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)										TTCCTTTCCATGAAAGCAGCA	0.433													C|||	1514	0.302316	0.3775	0.2205	5008	,	,		21416	0.2242		0.4165	False		,,,				2504	0.2219				p.H1640Q		Atlas-SNP	.											.	.	.	.	0			c.T4920A						PASS	.	C	GLN/HIS,GLN/HIS	1490,2658		283,924,867	34.0	34.0	34.0		4920,4920	-1.8	0.2	5	dbSNP_88	34	3351,5079		686,1979,1550	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	24,24	969,2903,2417	AA,AT,TT		39.7509,35.9209,38.4878	benign,benign	1640/1732,1640/1706	73207372	4841,7737	2074	4215	6289	SO:0001583	missense	64283	exon35			TTTCCATGAAAGC		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.4920T>A	5.37:g.73207372T>A	ENSP00000412175:p.His1640Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	693	0.3173076923076923	168	0.34146341463414637	94	0.2596685082872928	119	0.20804195804195805	312	0.41160949868073876	C	0.326	-0.959181	0.02267	0.359209	0.397509	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.28069	3.28;3.29;3.27;3.05;3.29;3.27;3.1;1.63	5.29	-1.84	0.07809	.	1.137660	0.07014	N	0.825584	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B;B	0.12013	0.001;0.001;0.003;0.005;0.003	B;B;B;B;B	0.08055	0.001;0.001;0.001;0.003;0.003	T	0.44544	-0.9321	9	0.08599	T	0.76	.	0.8513	0.01173	0.1562:0.3484:0.2187:0.2768	rs1478453;rs17553541;rs52807010;rs57886667;rs1478453	1327;1640;1640;560;1640	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	Q	1640;1640;1640;1596;1640;1640;1327;560	ENSP00000296794:H1640Q;ENSP00000441913:H1640Q;ENSP00000441436:H1640Q;ENSP00000287898:H1596Q;ENSP00000411459:H1640Q;ENSP00000412175:H1640Q;ENSP00000296799:H1327Q;ENSP00000421081:H560Q	ENSP00000287898:H1596Q	H	+	3	2	RP11-428C6.1	73243128	0.000000	0.05858	0.192000	0.23308	0.155000	0.21991	-0.559000	0.05971	-1.238000	0.02535	-1.929000	0.00512	CAT	T|0.663;A|0.337	0.337	strong		0.433	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
RPS6KB2	6199	hgsc.bcm.edu	37	11	67200812	67200812	+	Splice_Site	SNP	C	C	T	rs55987642	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:67200812C>T	ENST00000312629.5	+	10	845	c.800C>T	c.(799-801)cCg>cTg	p.P267L	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	267	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> L (in dbSNP:rs55987642). {ECO:0000269|PubMed:17344846}.		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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			CTCCTCCAGCCGCCCTTCACC	0.657													C|||	122	0.024361	0.0023	0.0245	5008	,	,		16838	0.0427		0.0437	False		,,,				2504	0.0153				p.P267L		Atlas-SNP	.											.	RPS6KB2	92	.	0			c.C800T						PASS	.	C	LEU/PRO	46,3876		1,44,1916	85.0	95.0	92.0		800	4.4	0.7	11	dbSNP_129	92	443,7805		11,421,3692	yes	missense-near-splice	RPS6KB2	NM_003952.2	98	12,465,5608	TT,TC,CC		5.371,1.1729,4.0181	benign	267/483	67200812	489,11681	1961	4124	6085	SO:0001630	splice_region_variant	6199	exon10			TCCAGCCGCCCTT	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.799-1C>T	11.37:g.67200812C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	37	CCDS41677.1	65	0.02976190476190476	1	0.0020325203252032522	10	0.027624309392265192	21	0.03671328671328671	33	0.04353562005277045	C	10.88	1.475162	0.26511	0.011729	0.05371	ENSG00000175634	ENST00000312629	T	0.25749	1.78	4.44	4.44	0.53790	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.140047	0.47852	D	0.000214	T	0.08492	0.0211	L	0.45470	1.425	0.80722	D	1	B;D	0.89917	0.231;1.0	B;D	0.91635	0.175;0.999	T	0.04053	-1.0981	10	0.02654	T	1	.	16.8602	0.86016	0.0:1.0:0.0:0.0	rs55987642;rs61891597	267;267	Q9BRS0;Q9UBS0	.;KS6B2_HUMAN	L	267	ENSP00000308413:P267L	ENSP00000308413:P267L	P	+	2	0	RPS6KB2	66957388	1.000000	0.71417	0.695000	0.30226	0.002000	0.02628	7.081000	0.76844	2.293000	0.77203	0.561000	0.74099	CCG	C|0.963;T|0.037	0.037	strong		0.657	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	Missense_Mutation
MMP8	4317	hgsc.bcm.edu	37	11	102595579	102595579	+	Missense_Mutation	SNP	G	G	C	rs17099450	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102595579G>C	ENST00000236826.3	-	1	106	c.8C>G	c.(7-9)tCc>tGc	p.S3C		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	3			S -> C (in dbSNP:rs17099450). {ECO:0000269|Ref.2}.		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)	CGTCTTCAGGGAGAACATGAT	0.468													G|||	199	0.0397364	0.0514	0.0389	5008	,	,		18266	0.0089		0.0417	False		,,,				2504	0.0542				p.S3C		Atlas-SNP	.											.	MMP8	68	.	0			c.C8G						PASS	.	G	CYS/SER	213,4193	130.2+/-166.9	7,199,1997	147.0	154.0	152.0		8	-10.2	0.0	11	dbSNP_123	152	441,8157	133.9+/-191.4	13,415,3871	yes	missense	MMP8	NM_002424.2	112	20,614,5868	CC,CG,GG		5.1291,4.8343,5.0292	benign	3/468	102595579	654,12350	2203	4299	6502	SO:0001583	missense	4317	exon1			TTCAGGGAGAACA	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.8C>G	11.37:g.102595579G>C	ENSP00000236826:p.Ser3Cys	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	335	80	0.238806	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	73	0.033424908424908424	23	0.046747967479674794	16	0.04419889502762431	3	0.005244755244755245	31	0.040897097625329816	G	11.83	1.756524	0.31137	0.048343	0.051291	ENSG00000118113	ENST00000236826	T	0.13901	2.55	5.26	-10.2	0.00374	.	5.605950	0.00166	N	0.000000	T	0.00815	0.0027	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24368	-1.0162	10	0.52906	T	0.07	.	0.229	0.00177	0.2519:0.1874:0.2546:0.3061	rs17099450;rs52812571;rs17099450	3	P22894	MMP8_HUMAN	C	3	ENSP00000236826:S3C	ENSP00000236826:S3C	S	-	2	0	MMP8	102100789	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.482000	0.02320	-1.792000	0.01259	-1.067000	0.02272	TCC	G|0.946;C|0.054	0.054	strong		0.468	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
ADAM7	8756	hgsc.bcm.edu	37	8	24359068	24359068	+	Silent	SNP	G	G	A	rs13277171	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:24359068G>A	ENST00000175238.6	+	20	2270	c.2187G>A	c.(2185-2187)ctG>ctA	p.L729L	RP11-561E1.1_ENST00000519364.1_RNA|ADAM7_ENST00000520720.1_Silent_p.L501L|ADAM7_ENST00000380789.1_Silent_p.L729L|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA	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	124	0	0		WXS	Illumina HiSeq	Phase_I	119	74	0.621849	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	
VWDE	221806	hgsc.bcm.edu	37	7	12428803	12428803	+	Missense_Mutation	SNP	G	G	A	rs848016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:12428803G>A	ENST00000275358.3	-	3	613	c.425C>T	c.(424-426)tCt>tTt	p.S142F		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	142						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TAAGTATACAGAAAAGTTCCC	0.418													A|||	3441	0.687101	0.9319	0.6758	5008	,	,		18556	0.6171		0.5537	False		,,,				2504	0.5736				p.S142F		Atlas-SNP	.											.	VWDE	123	.	0			c.C425T						PASS	.	A	PHE/SER	1212,172		528,156,8	102.0	103.0	103.0		425	3.5	0.4	7	dbSNP_86	103	1718,1464		464,790,337	yes	missense	VWDE	NM_001135924.1	155	992,946,345	AA,AG,GG		46.0088,12.4277,35.83	benign	142/1591	12428803	2930,1636	692	1591	2283	SO:0001583	missense	221806	exon3			TATACAGAAAAGT		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.425C>T	7.37:g.12428803G>A	ENSP00000275358:p.Ser142Phe	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	1481	0.6781135531135531	457	0.9288617886178862	245	0.6767955801104972	353	0.6171328671328671	426	0.5620052770448549	A	0.005	-2.132119	0.00338	0.875723	0.539912	ENSG00000146530	ENST00000275358;ENST00000541006	T	0.64085	-0.08	4.68	3.5	0.40072	.	0.501867	0.22766	N	0.055898	T	0.00012	0.0000	N	0.00079	-2.23	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38908	-0.9639	9	0.02654	T	1	.	6.8821	0.24179	0.7927:0.0:0.0737:0.1336	rs848016;rs971938;rs1638226;rs17540002;rs52819655;rs57187888;rs848016	142	Q8N2E2	VWDE_HUMAN	F	142	ENSP00000275358:S142F	ENSP00000275358:S142F	S	-	2	0	VWDE	12395328	0.940000	0.31905	0.358000	0.25811	0.300000	0.27592	1.711000	0.37930	0.369000	0.24510	-0.360000	0.07572	TCT	G|0.324;A|0.676	0.676	strong		0.418	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
GUSB	2990	hgsc.bcm.edu	37	7	65429359	65429359	+	Silent	SNP	G	G	A	rs1061361	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:65429359G>A	ENST00000304895.4	-	11	1870	c.1740C>T	c.(1738-1740)taC>taT	p.Y580Y	GUSB_ENST00000345660.6_Silent_p.Y529Y|GUSB_ENST00000421103.1_Silent_p.Y434Y	NM_000181.3	NP_000172.2	P08236	BGLR_HUMAN	glucuronidase, beta	580					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-glucuronidase activity (GO:0004566)			breast(1)|cervix(2)|kidney(2)|large_intestine(4)|lung(10)|skin(1)	20						CTCCAACCACGTATTTTCTGC	0.453													G|||	712	0.142173	0.0825	0.2147	5008	,	,		20195	0.1468		0.1064	False		,,,				2504	0.2035				p.Y580Y		Atlas-SNP	.											.	GUSB	52	.	0			c.C1740T						PASS	.	G		309,4097	168.0+/-198.9	10,289,1904	101.0	83.0	89.0		1740	-1.4	0.9	7	dbSNP_86	89	966,7630	207.6+/-249.3	59,848,3391	no	coding-synonymous	GUSB	NM_000181.3		69,1137,5295	AA,AG,GG		11.2378,7.0132,9.8062		580/652	65429359	1275,11727	2203	4298	6501	SO:0001819	synonymous_variant	2990	exon11			AACCACGTATTTT	M15182	CCDS5530.1, CCDS64665.1	7q11.21	2012-10-02			ENSG00000169919	ENSG00000169919	3.2.1.31		4696	protein-coding gene	gene with protein product		611499				3468507	Standard	NM_000181		Approved		uc003tun.3	P08236	OTTHUMG00000023735	ENST00000304895.4:c.1740C>T	7.37:g.65429359G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	155	93	0.6	NM_000181	B4E1F6|E9PCV0|Q549U0|Q96CL9	Silent	SNP	ENST00000304895.4	37	CCDS5530.1																																																																																			G|1.000;|0.000	.	weak		0.453	GUSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251637.3	NM_000181	
PAXIP1	22976	hgsc.bcm.edu	37	7	154760666	154760666	+	Silent	SNP	C	C	T	rs61752011	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:154760666C>T	ENST00000404141.1	-	7	1399	c.1245G>A	c.(1243-1245)ccG>ccA	p.P415P	PAXIP1_ENST00000397192.1_Silent_p.P415P|PAXIP1_ENST00000473219.1_5'UTR			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	82	0	0		WXS	Illumina HiSeq	Phase_I	63	14	0.222222	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	
ASPG	374569	hgsc.bcm.edu	37	14	104559852	104559852	+	Silent	SNP	T	T	C	rs941953	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104559852T>C	ENST00000551177.1	+	3	308	c.216T>C	c.(214-216)atT>atC	p.I72I	ASPG_ENST00000455920.2_Silent_p.I72I|ASPG_ENST00000546892.2_Silent_p.I72I	NM_001080464.2	NP_001073933.2	Q86U10	LPP60_HUMAN	asparaginase	72	Asparaginase.|Asparaginase/glutaminase. {ECO:0000255|PROSITE-ProRule:PRU01068}.				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						ACCAGAGGATTCTCTACACCG	0.622													C|||	2067	0.41274	0.6823	0.3314	5008	,	,		13262	0.3869		0.1809	False		,,,				2504	0.3712				p.I72I		Atlas-SNP	.											.	ASPG	34	.	0			c.T216C						PASS	.	C		2280,1854		606,1068,393	69.0	81.0	77.0		216	1.6	0.8	14	dbSNP_86	77	1413,6957		119,1175,2891	no	coding-synonymous	ASPG	NM_001080464.2		725,2243,3284	CC,CT,TT		16.8817,44.8476,29.5345		72/574	104559852	3693,8811	2067	4185	6252	SO:0001819	synonymous_variant	374569	exon3			GAGGATTCTCTAC		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.216T>C	14.37:g.104559852T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	153	89	0.581699	NM_001080464	B9EGQ2|Q8IV80	Silent	SNP	ENST00000551177.1	37	CCDS45170.2	788	0.3608058608058608	317	0.6443089430894309	126	0.34806629834254144	218	0.3811188811188811	127	0.16754617414248021	C	2.774	-0.255089	0.05829	0.551524	0.168817	ENSG00000166183	ENST00000551170	.	.	.	3.57	1.64	0.23874	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19575	P	0.9999653784	.	.	.	.	.	.	T	0.39820	-0.9595	3	.	.	.	-22.8141	3.8673	0.09021	0.1665:0.4251:0.0:0.4083	rs941953;rs1744283;rs59940089;rs941953	.	.	.	P	9	.	.	S	+	1	0	ASPG	103629605	0.001000	0.12720	0.761000	0.31378	0.086000	0.17979	-0.340000	0.07821	0.172000	0.19760	-1.140000	0.01884	TCT	T|0.625;C|0.375	0.375	strong		0.622	ASPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407005.1	NM_001080464	
SCN3A	6328	hgsc.bcm.edu	37	2	166003479	166003479	+	Silent	SNP	G	G	A	rs16850131	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	230	0	0		WXS	Illumina HiSeq	Phase_I	244	114	0.467213	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	
EPG5	57724	hgsc.bcm.edu	37	18	43496539	43496539	+	Missense_Mutation	SNP	G	G	A	rs78339727	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:43496539G>A	ENST00000282041.5	-	18	3282	c.3248C>T	c.(3247-3249)tCg>tTg	p.S1083L	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1083					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						GAGGAGATGCGATAAAAACCT	0.488													G|||	75	0.014976	0.0045	0.0072	5008	,	,		19660	0.002		0.0268	False		,,,				2504	0.0358				p.S1083L		Atlas-SNP	.											.	EPG5	199	.	0			c.C3248T						PASS	.	G	LEU/SER	27,4031		0,27,2002	53.0	55.0	55.0		3248	5.8	1.0	18	dbSNP_131	55	231,8135		2,227,3954	yes	missense	EPG5	NM_020964.2	145	2,254,5956	AA,AG,GG		2.7612,0.6654,2.0766	probably-damaging	1083/2580	43496539	258,12166	2029	4183	6212	SO:0001583	missense	57724	exon18			AGATGCGATAAAA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.3248C>T	18.37:g.43496539G>A	ENSP00000282041:p.Ser1083Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	27	0.012362637362637362	3	0.006097560975609756	2	0.0055248618784530384	1	0.0017482517482517483	21	0.027704485488126648	G	18.92	3.726301	0.69074	0.006654	0.027612	ENSG00000152223	ENST00000282041	T	0.12361	2.69	5.78	5.78	0.91487	.	1.225840	0.05281	N	0.519454	T	0.13415	0.0325	L	0.59436	1.845	0.46458	D	0.99905	D;D	0.69078	0.997;0.997	P;P	0.55222	0.771;0.704	T	0.00329	-1.1813	10	0.62326	D	0.03	-6.3143	15.4766	0.75485	0.0:0.138:0.862:0.0	.	1083;1083	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	L	1083	ENSP00000282041:S1083L	ENSP00000282041:S1083L	S	-	2	0	EPG5	41750537	1.000000	0.71417	0.964000	0.40570	0.470000	0.32858	3.769000	0.55303	2.737000	0.93849	0.563000	0.77884	TCG	G|0.979;A|0.021	0.021	strong		0.488	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
EFTUD1	79631	hgsc.bcm.edu	37	15	82456227	82456227	+	Missense_Mutation	SNP	T	T	C	rs1128431	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	168	0	0		WXS	Illumina HiSeq	Phase_I	90	16	0.177778	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	
AK1	203	hgsc.bcm.edu	37	9	130634103	130634103	+	Splice_Site	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:130634103C>T	ENST00000373176.1	-	5	475	c.323G>A	c.(322-324)cGg>cAg	p.R108Q	MIR4672_ENST00000583126.1_RNA|AK1_ENST00000373156.1_Splice_Site_p.R108Q|RP11-203J24.9_ENST00000476274.2_RNA|AK1_ENST00000223836.10_Splice_Site_p.R124Q	NM_000476.2	NP_000467.1			adenylate kinase 1									p.R108P(1)		endometrium(1)|prostate(1)	2						GTGCCTTACCCGTCGCTCAAA	0.602																																					p.R108Q		Atlas-SNP	.											AK1,NS,carcinoma,0,1	AK1	13	1	1	Substitution - Missense(1)	endometrium(1)	c.G323A						scavenged	.						141.0	119.0	126.0					9																	130634103		2203	4300	6503	SO:0001630	splice_region_variant	203	exon5			CTTACCCGTCGCT	J04809	CCDS6881.1	9q34.1	2008-02-05			ENSG00000106992	ENSG00000106992	2.7.4.3	"""Adenylate kinases"""	361	protein-coding gene	gene with protein product		103000					Standard	NM_000476		Approved		uc004bsm.4	P00568	OTTHUMG00000020722	ENST00000373176.1:c.324+1G>A	9.37:g.130634103C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	64	2	0.03125	NM_000476		Missense_Mutation	SNP	ENST00000373176.1	37	CCDS6881.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.07|14.07	2.424940|2.424940	0.43020|0.43020	.|.	.|.	ENSG00000106992|ENSG00000106992	ENST00000413016|ENST00000373176;ENST00000373156;ENST00000223836	.|T;T;T	.|0.63580	.|-0.05;-0.05;-0.05	4.89|4.89	3.0|3.0	0.34707|0.34707	.|.	.|0.108733	.|0.64402	.|D	.|0.000008	T|T	0.31513|0.31513	0.0799|0.0799	N|N	0.02721|0.02721	-0.515|-0.515	0.40516|0.40516	D|D	0.980787|0.980787	.|B	.|0.10296	.|0.003	.|B	.|0.09377	.|0.004	T|T	0.07462|0.07462	-1.0771|-1.0771	5|10	.|0.23891	.|T	.|0.37	-7.6885|-7.6885	6.7894|6.7894	0.23692|0.23692	0.0:0.6559:0.0:0.3441|0.0:0.6559:0.0:0.3441	.|.	.|108	.|P00568	.|KAD1_HUMAN	R|Q	49|108;108;124	.|ENSP00000362271:R108Q;ENSP00000362249:R108Q;ENSP00000223836:R124Q	.|ENSP00000223836:R124Q	G|R	-|-	1|2	0|0	AK1|AK1	129673924|129673924	1.000000|1.000000	0.71417|0.71417	0.957000|0.957000	0.39632|0.39632	0.913000|0.913000	0.54294|0.54294	1.517000|1.517000	0.35867|0.35867	1.176000|1.176000	0.42840|0.42840	0.555000|0.555000	0.69702|0.69702	GGA|CGG	.	.	none		0.602	AK1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054307.1		Missense_Mutation
MUC17	140453	hgsc.bcm.edu	37	7	100681172	100681172	+	Missense_Mutation	SNP	A	A	G	rs28555173	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681172A>G	ENST00000306151.4	+	3	6539	c.6475A>G	c.(6475-6477)Aga>Gga	p.R2159G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2159	59 X approximate tandem repeats.|Ser-rich.		R -> G (in dbSNP:rs61382267).		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)					TTATAGTGACAGAAGAACTCC	0.468													G|||	1192	0.238019	0.351	0.1023	5008	,	,		26575	0.251		0.1213	False		,,,				2504	0.2883				p.R2159G		Atlas-SNP	.											.	MUC17	804	.	0			c.A6475G						PASS	.	G	GLY/ARG	1346,3060	692.8+/-405.6	209,928,1066	223.0	221.0	222.0		6475	-1.6	0.0	7	dbSNP_125	222	998,7602	773.4+/-407.7	56,886,3358	yes	missense	MUC17	NM_001040105.1	125	265,1814,4424	GG,GA,AA		11.6047,30.5493,18.0225	benign	2159/4494	100681172	2344,10662	2203	4300	6503	SO:0001583	missense	140453	exon3			AGTGACAGAAGAA	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.6475A>G	7.37:g.100681172A>G	ENSP00000302716:p.Arg2159Gly	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	222	219	0.986486	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	427	0.1955128205128205	158	0.32113821138211385	42	0.11602209944751381	138	0.24125874125874125	89	0.11741424802110818	G	0.045	-1.267844	0.01433	0.305493	0.116047	ENSG00000169876	ENST00000306151	T	0.02863	4.13	0.791	-1.58	0.08479	.	.	.	.	.	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.21821	0.061	B	0.11329	0.006	T	0.33394	-0.9870	8	0.09843	T	0.71	.	3.0068	0.06031	0.457:0.0:0.3444:0.1986	rs61382267	2159	Q685J3	MUC17_HUMAN	G	2159	ENSP00000302716:R2159G	ENSP00000302716:R2159G	R	+	1	2	MUC17	100467892	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.438000	0.06905	-2.952000	0.00293	-3.178000	0.00056	AGA	A|0.823;G|0.177	0.177	strong		0.468	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TBC1D10C	374403	hgsc.bcm.edu	37	11	67172911	67172911	+	Silent	SNP	C	C	T	rs61734600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:67172911C>T	ENST00000542590.1	+	3	308	c.294C>T	c.(292-294)cgC>cgT	p.R98R	TBC1D10C_ENST00000312390.5_Silent_p.R98R|TBC1D10C_ENST00000526387.1_Silent_p.R98R			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	98	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CTGCCCTGCGCGCCCGATGCT	0.652													C|||	303	0.0605032	0.0794	0.0461	5008	,	,		18421	0.1141		0.0348	False		,,,				2504	0.0164				p.R98R		Atlas-SNP	.											.	TBC1D10C	42	.	0			c.C294T						PASS	.	C		323,4077	166.9+/-198.0	16,291,1893	47.0	44.0	45.0		294	-3.7	0.9	11	dbSNP_129	45	284,8306	106.2+/-167.1	7,270,4018	no	coding-synonymous	TBC1D10C	NM_198517.2		23,561,5911	TT,TC,CC		3.3062,7.3409,4.6728		98/447	67172911	607,12383	2200	4295	6495	SO:0001819	synonymous_variant	374403	exon4			CCTGCGCGCCCGA	BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.294C>T	11.37:g.67172911C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_001256508	G3V1D6	Silent	SNP	ENST00000542590.1	37	CCDS8162.1																																																																																			C|0.948;T|0.052	0.052	strong		0.652	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395492.2	NM_198517	
ARSD	414	hgsc.bcm.edu	37	X	2836047	2836047	+	Missense_Mutation	SNP	C	C	T	rs67359049		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	95	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	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		
CYP2A7	1549	hgsc.bcm.edu	37	19	41383134	41383134	+	Silent	SNP	A	A	G	rs147847954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	227	0	0		WXS	Illumina HiSeq	Phase_I	168	66	0.392857	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	
RRM2	6241	hgsc.bcm.edu	37	2	10262859	10262859	+	5'UTR	SNP	G	G	A	rs72542787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:10262859G>A	ENST00000304567.5	+	0	3				RRM2_ENST00000360566.2_Silent_p.G38G|RP11-254F7.4_ENST00000607140.1_lincRNA	NM_001034.3	NP_001025.1	P31350	RIR2_HUMAN	ribonucleotide reductase M2						deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein heterotetramerization (GO:0051290)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|skin(1)	19	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.188)|OV - Ovarian serous cystadenocarcinoma(76;0.221)	Cladribine(DB00242)|Gallium nitrate(DB05260)	GGAGTGAGGGGTCGCCCGTGC	0.682													G|||	204	0.0407348	0.0265	0.0418	5008	,	,		12237	0.001		0.0875	False		,,,				2504	0.0521				p.G38G		Atlas-SNP	.											.	RRM2	63	.	0			c.G114A						PASS	.	G		49,1335		1,47,644	27.0	48.0	42.0		114	-4.5	0.0	2	dbSNP_130	42	325,2855		15,295,1280	no	coding-synonymous	RRM2	NM_001165931.1		16,342,1924	AA,AG,GG		10.2201,3.5405,8.1946		38/450	10262859	374,4190	692	1590	2282	SO:0001623	5_prime_UTR_variant	6241	exon1			TGAGGGGTCGCCC		CCDS1669.1, CCDS54334.1	2p25-p24	2012-10-02	2009-07-10		ENSG00000171848	ENSG00000171848	1.17.4.1		10452	protein-coding gene	gene with protein product		180390	"""ribonucleotide reductase M2 polypeptide"""				Standard	NM_001034		Approved		uc021vdr.1	P31350	OTTHUMG00000090449	ENST00000304567.5:c.-67G>A	2.37:g.10262859G>A		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	170	96	0.564706	NM_001165931	B2R9B5|J3KP43|Q5WRU7	Silent	SNP	ENST00000304567.5	37	CCDS1669.1																																																																																			G|0.956;A|0.044	0.044	strong		0.682	RRM2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364902.2		
CNR2	1269	hgsc.bcm.edu	37	1	24201448	24201448	+	Silent	SNP	C	C	T	rs3003336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:24201448C>T	ENST00000374472.4	-	2	821	c.660G>A	c.(658-660)gtG>gtA	p.V220V	CNR2_ENST00000536471.1_Silent_p.V220V	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	220					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)	p.V220V(1)		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)	ACAAGCTGGCCACATGCTGAT	0.572													T|||	3272	0.653355	0.7943	0.6383	5008	,	,		23489	0.502		0.5875	False		,,,				2504	0.6973				p.V220V		Atlas-SNP	.											CNR2,NS,carcinoma,0,1	CNR2	78	1	1	Substitution - coding silent(1)	stomach(1)	c.G660A						PASS	.	T		3313,1093	393.7+/-329.0	1263,787,153	64.0	59.0	61.0		660	2.2	1.0	1	dbSNP_101	61	4940,3660	523.3+/-380.3	1408,2124,768	no	coding-synonymous	CNR2	NM_001841.2		2671,2911,921	TT,TC,CC		42.5581,24.8071,36.5447		220/361	24201448	8253,4753	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			GCTGGCCACATGC	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.660G>A	1.37:g.24201448C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			C|0.364;T|0.636	0.636	strong		0.572	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
USH2A	7399	hgsc.bcm.edu	37	1	215848587	215848587	+	Silent	SNP	T	T	C	rs2797234	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:215848587T>C	ENST00000307340.3	-	63	13052	c.12666A>G	c.(12664-12666)acA>acG	p.T4222T	USH2A_ENST00000366943.2_Silent_p.T4222T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4222	Fibronectin type-III 27. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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.T4222T(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)		TATACATAAATGTATTCCTTT	0.413										HNSCC(13;0.011)			T|||	1518	0.303115	0.1793	0.4539	5008	,	,		20174	0.3155		0.3738	False		,,,				2504	0.2781				p.T4222T		Atlas-SNP	.											USH2A,NS,carcinoma,0,2	USH2A	1168	2	1	Substitution - coding silent(1)	stomach(1)	c.A12666G						PASS	.	T		983,3423	369.8+/-319.3	127,729,1347	114.0	112.0	113.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	12666	-0.2	0.0	1	dbSNP_100	113	3357,5243	498.4+/-374.7	670,2017,1613	no	coding-synonymous	USH2A	NM_206933.2		797,2746,2960	CC,CT,TT		39.0349,22.3105,33.3692		4222/5203	215848587	4340,8666	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon63			CATAAATGTATTC	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.12666A>G	1.37:g.215848587T>C		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	245	97	0.395918	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			T|0.680;C|0.320	0.320	strong		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
GCN1L1	10985	hgsc.bcm.edu	37	12	120589064	120589064	+	Silent	SNP	G	G	C	rs2286045	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:120589064G>C	ENST00000300648.6	-	34	4206	c.4194C>G	c.(4192-4194)gcC>gcG	p.A1398A		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1398					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCAGGCCATAGGCGGCCCCTT	0.587													C|||	1915	0.382388	0.6573	0.17	5008	,	,		17533	0.5427		0.1561	False		,,,				2504	0.229				p.A1398A		Atlas-SNP	.											GCN1L1,colon,carcinoma,0,1	GCN1L1	207	1	0			c.C4194G						PASS	.	C		2419,1901		682,1055,423	48.0	54.0	52.0		4194	-10.6	0.0	12	dbSNP_100	52	1304,7214		126,1052,3081	no	coding-synonymous	GCN1L1	NM_006836.1		808,2107,3504	CC,CG,GG		15.3088,44.0046,28.9998		1398/2672	120589064	3723,9115	2160	4259	6419	SO:0001819	synonymous_variant	10985	exon34			GCCATAGGCGGCC	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.4194C>G	12.37:g.120589064G>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	135	50	0.37037	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			G|0.685;C|0.315	0.315	strong		0.587	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
SSPO	23145	hgsc.bcm.edu	37	7	149473614	149473614	+	RNA	SNP	A	A	G	rs117048984	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149473614A>G	ENST00000378016.2	+	0	230							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)			TGTCCTATCTACAAGTGAGTA	0.647													A|||	81	0.0161741	0.0023	0.0375	5008	,	,		12978	0.0		0.0408	False		,,,				2504	0.0112				p.Y77C		Atlas-SNP	.											.	.	.	.	0			c.A230G						PASS	.	A	CYS/TYR	24,3720		1,22,1849	8.0	9.0	8.0		230	3.8	1.0	7	dbSNP_132	8	323,7807		2,319,3744	yes	missense	SSPO	NM_198455.2	194	3,341,5593	GG,GA,AA		3.9729,0.641,2.9224	probably-damaging	77/5148	149473614	347,11527	1872	4065	5937			23145	exon2			CTATCTACAAGTG	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.149473614A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	37	30	0.810811	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				A|0.980;G|0.020	0.020	strong		0.647	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
FBN3	84467	hgsc.bcm.edu	37	19	8212263	8212263	+	Silent	SNP	G	G	A	rs11878432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:8212263G>A	ENST00000600128.1	-	2	516	c.102C>T	c.(100-102)gaC>gaT	p.D34D	FBN3_ENST00000270509.2_Silent_p.D34D|FBN3_ENST00000601739.1_Silent_p.D34D			Q75N90	FBN3_HUMAN	fibrillin 3	34						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						CCAAGGCCCCGTCCCAGCGGC	0.692													G|||	1058	0.211262	0.1135	0.2075	5008	,	,		14258	0.2163		0.3499	False		,,,				2504	0.1984				p.D34D		Atlas-SNP	.											.	FBN3	300	.	0			c.C102T						PASS	.	G		724,3650		69,586,1532	11.0	13.0	12.0		102	-9.6	0.0	19	dbSNP_120	12	2897,5663		520,1857,1903	no	coding-synonymous	FBN3	NM_032447.3		589,2443,3435	AA,AG,GG		33.8435,16.5524,27.996		34/2810	8212263	3621,9313	2187	4280	6467	SO:0001819	synonymous_variant	84467	exon1			GGCCCCGTCCCAG		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.102C>T	19.37:g.8212263G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.760;A|0.240	0.240	strong		0.692	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
ZNF99	7652	hgsc.bcm.edu	37	19	22942061	22942061	+	Missense_Mutation	SNP	A	A	C	rs61753878	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22942061A>C	ENST00000596209.1	-	4	740	c.650T>G	c.(649-651)aTt>aGt	p.I217S	ZNF99_ENST00000397104.3_Intron	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	217					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(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				CTTATGTTTAATAAGGGTTGA	0.303													A|||	449	0.0896565	0.0681	0.0879	5008	,	,		17504	0.0933		0.0934	False		,,,				2504	0.1125				p.I217S		Atlas-SNP	.											.	ZNF99	273	.	0			c.T650G						PASS	.																																			SO:0001583	missense	7652	exon4			TGTTTAATAAGGG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.650T>G	19.37:g.22942061A>C	ENSP00000472969:p.Ile217Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	17	12	0.705882	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1																																																																																			A|0.910;C|0.090	0.090	strong		0.303	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
DNAJB8	165721	hgsc.bcm.edu	37	3	128182074	128182074	+	Silent	SNP	G	G	A	rs2981026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:128182074G>A	ENST00000469083.1	-	2	2572	c.15C>T	c.(13-15)taC>taT	p.Y5Y	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Silent_p.Y5Y			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	5	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				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)		CCAGCACTTCGTAGTAGTTAG	0.632													G|||	1540	0.307508	0.1316	0.3573	5008	,	,		16196	0.4891		0.2753	False		,,,				2504	0.3558				p.Y5Y		Atlas-SNP	.											.	DNAJB8	34	.	0			c.C15T						PASS	.	G		658,3748	268.6+/-268.5	48,562,1593	55.0	57.0	56.0		15	0.9	1.0	3	dbSNP_101	56	2275,6325	374.6+/-337.4	318,1639,2343	no	coding-synonymous	DNAJB8	NM_153330.2		366,2201,3936	AA,AG,GG		26.4535,14.9342,22.5511		5/233	128182074	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	165721	exon3			CACTTCGTAGTAG		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.15C>T	3.37:g.128182074G>A		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	203	94	0.463054	NM_153330	B3KWV7	Silent	SNP	ENST00000469083.1	37	CCDS3048.1																																																																																			G|0.724;A|0.276	0.276	strong		0.632	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
ATP5SL	55101	hgsc.bcm.edu	37	19	41944237	41944237	+	Missense_Mutation	SNP	T	T	C	rs2231940	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41944237T>C	ENST00000221943.9	-	2	106	c.101A>G	c.(100-102)aAt>aGt	p.N34S	ATP5SL_ENST00000301183.11_Missense_Mutation_p.N40S|ATP5SL_ENST00000595425.1_Missense_Mutation_p.N34S|ATP5SL_ENST00000417807.3_Missense_Mutation_p.N40S|ATP5SL_ENST00000590641.2_Missense_Mutation_p.N40S|ATP5SL_ENST00000438807.3_Missense_Mutation_p.N34S|ATP5SL_ENST00000592922.2_Missense_Mutation_p.N34S|ATP5SL_ENST00000597457.1_Missense_Mutation_p.N34S|ATP5SL_ENST00000589970.1_Missense_Mutation_p.N34S	NM_018035.2	NP_060505.2	Q9NW81	AT5SL_HUMAN	ATP5S-like	34			N -> S (in dbSNP:rs2231940). {ECO:0000269|PubMed:14702039}.			mitochondrion (GO:0005739)		p.N34S(1)		breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	11						CTTCTTCTGATTGCCCTCTGG	0.572													T|||	1930	0.385383	0.1604	0.5144	5008	,	,		19085	0.5635		0.4066	False		,,,				2504	0.3926				p.N40S		Atlas-SNP	.											ATP5SL,NS,carcinoma,0,1	ATP5SL	20	1	1	Substitution - Missense(1)	stomach(1)	c.A119G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	949,3457	360.9+/-315.4	107,735,1361	131.0	117.0	122.0		119,119,101,101,101,101	-6.2	0.0	19	dbSNP_98	122	3409,5191	503.6+/-375.9	697,2015,1588	yes	missense,missense,missense,missense,missense,missense	ATP5SL	NM_001167867.1,NM_001167868.1,NM_001167869.1,NM_001167870.1,NM_001167871.1,NM_018035.2	46,46,46,46,46,46	804,2750,2949	CC,CT,TT		39.6395,21.5388,33.5076	benign,benign,benign,benign,benign,benign	40/264,40/192,34/186,34/159,34/231,34/258	41944237	4358,8648	2203	4300	6503	SO:0001583	missense	55101	exon2			TTCTGATTGCCCT	AK001103	CCDS33032.1, CCDS54269.1, CCDS54270.1, CCDS54271.1, CCDS59389.1, CCDS59390.1	19q13.2	2007-12-13				ENSG00000105341			25496	protein-coding gene	gene with protein product						12477932	Standard	NM_001167867		Approved	FLJ10241	uc002oqv.3	Q9NW81		ENST00000221943.9:c.101A>G	19.37:g.41944237T>C	ENSP00000221943:p.Asn34Ser	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	164	78	0.47561	NM_001167867	B4DDC0|B4DMZ4|B4DP55|B4DXE8|F5H4W7|K7EMF6|Q96D43	Missense_Mutation	SNP	ENST00000221943.9	37	CCDS33032.1	865	0.39606227106227104	84	0.17073170731707318	157	0.43370165745856354	307	0.5367132867132867	317	0.4182058047493404	T	0.758	-0.770415	0.02974	0.215388	0.396395	ENSG00000105341	ENST00000221943;ENST00000438807;ENST00000417807;ENST00000301183;ENST00000507129	T;T;T;T	0.24538	3.12;1.86;3.08;1.85	3.37	-6.19	0.02078	.	1.568770	0.04028	N	0.300879	T	0.00012	0.0000	N	0.05230	-0.09	0.80722	P	0.0	B;B;B;B;B;B;B	0.16603	0.018;0.015;0.015;0.015;0.01;0.001;0.005	B;B;B;B;B;B;B	0.16722	0.016;0.01;0.01;0.01;0.007;0.007;0.011	T	0.39702	-0.9601	9	0.07482	T	0.82	-25.6535	8.2286	0.31584	0.1416:0.5785:0.0:0.28	rs2231940;rs3182916;rs17318700;rs52816424;rs61271390;rs2231940	40;40;34;34;34;34;40	B4DFT4;B4DDC0;Q9NW81-2;B4DMZ4;E9PDC6;Q9NW81;F5H4W7	.;.;.;.;.;AT5SL_HUMAN;.	S	34;34;40;40;110	ENSP00000221943:N34S;ENSP00000397413:N34S;ENSP00000403910:N40S;ENSP00000301183:N40S	ENSP00000221943:N34S	N	-	2	0	ATP5SL	46636077	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-6.233000	0.00074	-1.890000	0.01111	-1.151000	0.01829	AAT	T|0.640;C|0.360	0.360	strong		0.572	ATP5SL-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460602.1	NM_018035	
SCARB1	949	hgsc.bcm.edu	37	12	125302137	125302137	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:125302137G>A	ENST00000415380.2	-	2	368	c.243C>T	c.(241-243)ggC>ggT	p.G81G	SCARB1_ENST00000261693.6_Silent_p.G81G|SCARB1_ENST00000376788.1_Intron|SCARB1_ENST00000546215.1_Silent_p.G81G|SCARB1_ENST00000339570.5_Silent_p.G81G|SCARB1_ENST00000535005.1_5'UTR|SCARB1_ENST00000544327.1_Silent_p.G27G|SCARB1_ENST00000540495.1_Silent_p.G44G|SCARB1_ENST00000541205.1_Silent_p.G40G			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1	81					adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	GCGGCTTCTCGCCCTTCAGGA	0.622																																					p.G81G		Atlas-SNP	.											SCARB1,colon,carcinoma,0,1	SCARB1	40	1	0			c.C243T						scavenged	.						62.0	64.0	63.0					12																	125302137		2203	4300	6503	SO:0001819	synonymous_variant	949	exon2			CTTCTCGCCCTTC	Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"""	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.243C>T	12.37:g.125302137G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	3	0.0263158	NM_005505	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Silent	SNP	ENST00000415380.2	37																																																																																				.	.	none		0.622	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505	
FLG	2312	hgsc.bcm.edu	37	1	152277055	152277055	+	Missense_Mutation	SNP	C	C	G	rs2065955	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152277055C>G	ENST00000368799.1	-	3	10342	c.10307G>C	c.(10306-10308)gGa>gCa	p.G3436A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3436	Ser-rich.		G -> A (in dbSNP:rs2065955).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCCGGGTGTCCACGAATGGT	0.597									Ichthyosis				C|||	2575	0.514177	0.7882	0.4481	5008	,	,		18425	0.6349		0.1481	False		,,,				2504	0.4427				p.G3436A		Atlas-SNP	.											.	FLG	900	.	0			c.G10307C						PASS	.	C	ALA/GLY	3017,1389	686.4+/-404.7	1050,917,236	295.0	296.0	295.0		10307	-1.1	0.0	1	dbSNP_94	295	1294,7306	254.0+/-279.5	122,1050,3128	no	missense	FLG	NM_002016.1	60	1172,1967,3364	GG,GC,CC		15.0465,31.5252,33.1462	possibly-damaging	3436/4062	152277055	4311,8695	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGGTGTCCACGAA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10307G>C	1.37:g.152277055C>G	ENSP00000357789:p.Gly3436Ala	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	388	131	0.337629	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	949	0.43452380952380953	355	0.7215447154471545	137	0.3784530386740331	342	0.5979020979020979	115	0.1517150395778364	C	3.831	-0.035729	0.07497	0.684748	0.150465	ENSG00000143631	ENST00000368799	T	0.07114	3.22	3.31	-1.14	0.09741	.	.	.	.	.	T	0.04634	0.0126	L	0.57536	1.79	0.80722	P	0.0	P	0.46327	0.876	P	0.54312	0.748	T	0.23261	-1.0193	8	0.18710	T	0.47	-3.9699	3.0433	0.06145	0.1908:0.4576:0.0:0.3516	rs56734521	3436	P20930	FILA_HUMAN	A	3436	ENSP00000357789:G3436A	ENSP00000357789:G3436A	G	-	2	0	FLG	150543679	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.597000	0.05713	-0.563000	0.06078	-0.396000	0.06452	GGA	C|0.615;G|0.385	0.385	strong		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC4	4585	hgsc.bcm.edu	37	3	195506982	195506982	+	Silent	SNP	G	G	C	rs562381906	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195506982G>C	ENST00000463781.3	-	2	11928	c.11469C>G	c.(11467-11469)acC>acG	p.T3823T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T3823T	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)		CAGGAAGAGGGGTGGTGTCAC	0.592													.|||	152	0.0303514	0.112	0.0029	5008	,	,		9549	0.0		0.002	False		,,,				2504	0.0				p.T3823T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C11469G						scavenged	.						5.0	5.0	5.0					3																	195506982		422	1223	1645	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.11469C>G	3.37:g.195506982G>C		Somatic	173	9	0.0520231		WXS	Illumina HiSeq	Phase_I	155	13	0.083871	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																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC39A8	64116	hgsc.bcm.edu	37	4	103228734	103228734	+	Silent	SNP	C	C	T	rs35411892	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:103228734C>T	ENST00000394833.2	-	3	887	c.411G>A	c.(409-411)acG>acA	p.T137T	SLC39A8_ENST00000424970.2_Silent_p.T137T|SLC39A8_ENST00000356736.4_Silent_p.T137T|SLC39A8_ENST00000510255.1_5'UTR	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	137					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)			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)		GATTAATAATCGTCACTGACA	0.393													C|||	821	0.163938	0.1604	0.1844	5008	,	,		18210	0.1171		0.1551	False		,,,				2504	0.2117				p.T137T		Atlas-SNP	.											.	SLC39A8	24	.	0			c.G411A						PASS	.	C	,,,	688,3718	280.8+/-275.6	49,590,1564	97.0	106.0	103.0		411,411,210,411	-11.1	0.0	4	dbSNP_126	103	1514,7086	284.2+/-296.5	122,1270,2908	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A8	NM_001135146.1,NM_001135147.1,NM_001135148.1,NM_022154.5	,,,	171,1860,4472	TT,TC,CC		17.6047,15.6151,16.9306	,,,	137/461,137/445,70/394,137/461	103228734	2202,10804	2203	4300	6503	SO:0001819	synonymous_variant	64116	exon3			AATAATCGTCACT		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.411G>A	4.37:g.103228734C>T		Somatic	344	1	0.00290698		WXS	Illumina HiSeq	Phase_I	351	169	0.481481	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Silent	SNP	ENST00000394833.2	37	CCDS3656.1																																																																																			C|0.841;T|0.159	0.159	strong		0.393	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
PNPLA1	285848	hgsc.bcm.edu	37	6	36270130	36270130	+	Missense_Mutation	SNP	C	C	A	rs12199580	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:36270130C>A	ENST00000394571.2	+	6	1268	c.1268C>A	c.(1267-1269)cCc>cAc	p.P423H	PNPLA1_ENST00000388715.3_Missense_Mutation_p.P328H|PNPLA1_ENST00000312917.5_Missense_Mutation_p.P337H	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	423	Pro-rich.		P -> H (in dbSNP:rs12199580). {ECO:0000269|PubMed:14702039, 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						CCCACTTCACCCAGGCCATCC	0.607											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1414	0.282348	0.1679	0.5231	5008	,	,		20276	0.1756		0.4036	False		,,,				2504	0.2515				p.P423H		Atlas-SNP	.											PNPLA1,back,malignant_melanoma,-1,1	PNPLA1	92	1	0			c.C1268A						scavenged	.	C	HIS/PRO,HIS/PRO,HIS/PRO	913,3493	351.3+/-311.2	103,707,1393	131.0	118.0	122.0		1010,1268,983	1.7	0.0	6	dbSNP_120	122	3723,4877	530.7+/-381.8	819,2085,1396	yes	missense,missense,missense	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	77,77,77	922,2792,2789	AA,AC,CC		43.2907,20.7217,35.6451	benign,benign,benign	337/447,423/533,328/438	36270130	4636,8370	2203	4300	6503	SO:0001583	missense	285848	exon6			CTTCACCCAGGCC		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.1268C>A	6.37:g.36270130C>A	ENSP00000378072:p.Pro423His	Somatic	106	1	0.00943396	861	WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	736	0.336996336996337	81	0.16463414634146342	193	0.5331491712707183	138	0.24125874125874125	324	0.42744063324538256	C	10.48	1.363188	0.24684	0.207217	0.432907	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.35605	1.32;1.31;1.3;1.3	4.64	1.74	0.24563	.	0.692649	0.12534	N	0.460552	T	0.08447	0.0210	N	0.19112	0.55	0.80722	P	0.0	B;B	0.20261	0.005;0.043	B;B	0.21546	0.005;0.035	T	0.22208	-1.0223	9	0.42905	T	0.14	-1.6793	5.3121	0.15835	0.3599:0.5418:0.0:0.0983	rs12199580;rs58373772;rs12199580	423;337	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	H	328;337;424;423	ENSP00000373367:P328H;ENSP00000321116:P337H;ENSP00000391868:P424H;ENSP00000378072:P423H	ENSP00000321116:P337H	P	+	2	0	PNPLA1	36378108	0.004000	0.15560	0.002000	0.10522	0.121000	0.20230	0.074000	0.14662	0.112000	0.17975	0.650000	0.86243	CCC	C|0.661;A|0.339	0.339	strong		0.607	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
KCNG2	26251	hgsc.bcm.edu	37	18	77659553	77659553	+	Silent	SNP	C	C	T	rs75339189	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:77659553C>T	ENST00000316249.3	+	2	1138	c.1138C>T	c.(1138-1140)Ctg>Ttg	p.L380L	KCNG2_ENST00000590307.1_3'UTR	NM_012283.1	NP_036415.1	Q9UJ96	KCNG2_HUMAN	potassium voltage-gated channel, subfamily G, member 2	380					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(2)|endometrium(4)|lung(7)|skin(1)|upper_aerodigestive_tract(4)	18		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;6.92e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0244)		CCCGCGCAGCCTGCCCGGGCA	0.677													C|||	212	0.0423323	0.0083	0.0706	5008	,	,		10473	0.0169		0.1093	False		,,,				2504	0.0256				p.L380L		Atlas-SNP	.											.	KCNG2	48	.	0			c.C1138T						PASS	.	C		104,4300	78.8+/-117.2	2,100,2100	50.0	46.0	47.0		1138	1.0	1.0	18	dbSNP_131	47	926,7670	203.0+/-246.1	47,832,3419	no	coding-synonymous	KCNG2	NM_012283.1		49,932,5519	TT,TC,CC		10.7725,2.3615,7.9231		380/467	77659553	1030,11970	2202	4298	6500	SO:0001819	synonymous_variant	26251	exon2			CGCAGCCTGCCCG	AJ011021	CCDS12019.1	18q23	2011-07-05			ENSG00000178342	ENSG00000178342		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6249	protein-coding gene	gene with protein product		605696				10551266, 16382104	Standard	NM_012283		Approved	Kv6.2, KCNF2	uc010xfl.2	Q9UJ96	OTTHUMG00000044541	ENST00000316249.3:c.1138C>T	18.37:g.77659553C>T		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	279	124	0.444444	NM_012283		Silent	SNP	ENST00000316249.3	37	CCDS12019.1																																																																																			C|0.926;T|0.074	0.074	strong		0.677	KCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103906.1	NM_012283	
EGFR	1956	hgsc.bcm.edu	37	7	55268916	55268916	+	Silent	SNP	C	C	T	rs2293347|rs587778251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:55268916C>T	ENST00000275493.2	+	25	3159	c.2982C>T	c.(2980-2982)gaC>gaT	p.D994D	EGFR_ENST00000454757.2_Silent_p.D941D|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Silent_p.D949D	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	994					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)			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)	GTCCTACAGACTCCAACTTCT	0.512		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			t|||	710	0.141773	0.0129	0.1542	5008	,	,		18651	0.247		0.1113	False		,,,				2504	0.2301				p.D994D		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	20426	.	0			c.C2982T						PASS	.	T		121,4285	90.6+/-129.3	1,119,2083	151.0	139.0	143.0		2982	3.8	1.0	7	dbSNP_100	143	795,7805	185.7+/-233.4	42,711,3547	no	coding-synonymous	EGFR	NM_005228.3		43,830,5630	TT,TC,CC		9.2442,2.7463,7.0429		994/1211	55268916	916,12090	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon25	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	TACAGACTCCAAC		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.2982C>T	7.37:g.55268916C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	252	85	0.337302	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.894;T|0.106	0.106	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
OR11H6	122748	hgsc.bcm.edu	37	14	20691962	20691962	+	Missense_Mutation	SNP	C	C	G	rs9323693	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20691962C>G	ENST00000315519.2	+	1	172	c.94C>G	c.(94-96)Ctc>Gtc	p.L32V		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	32			L -> V (in dbSNP:rs9323693).			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)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		TGAGTTTGTCCTCCTGGGTTT	0.428													c|||	498	0.0994409	0.121	0.049	5008	,	,		20383	0.0903		0.0815	False		,,,				2504	0.1339				p.L32V		Atlas-SNP	.											.	OR11H6	60	.	0			c.C94G						PASS	.	C	VAL/LEU	429,3977	209.8+/-230.5	18,393,1792	133.0	130.0	131.0		94	4.6	1.0	14	dbSNP_119	131	633,7967	164.2+/-216.6	34,565,3701	yes	missense	OR11H6	NM_001004480.1	32	52,958,5493	GG,GC,CC		7.3605,9.7367,8.1655	benign	32/331	20691962	1062,11944	2203	4300	6503	SO:0001583	missense	122748	exon1			TTTGTCCTCCTGG		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.94C>G	14.37:g.20691962C>G	ENSP00000319071:p.Leu32Val	Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	376	136	0.361702	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	204	0.09340659340659341	72	0.14634146341463414	17	0.04696132596685083	53	0.09265734265734266	62	0.08179419525065963	C	13.14	2.149408	0.37923	0.097367	0.073605	ENSG00000176219	ENST00000315519	T	0.00563	6.58	4.57	4.57	0.56435	.	0.000000	0.44483	D	0.000445	T	0.00012	0.0000	H	0.95611	3.695	0.35325	P	0.21487999999999996	P	0.45672	0.864	B	0.42214	0.38	T	0.18555	-1.0333	9	0.87932	D	0	.	15.2129	0.73241	0.0:1.0:0.0:0.0	rs9323693;rs17211271;rs52805624;rs9323693	32	Q8NGC7	O11H6_HUMAN	V	32	ENSP00000319071:L32V	ENSP00000319071:L32V	L	+	1	0	OR11H6	19761802	0.297000	0.24408	1.000000	0.80357	0.759000	0.43091	0.917000	0.28665	2.521000	0.84997	0.442000	0.29010	CTC	C|0.918;G|0.082	0.082	strong		0.428	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
SSPO	23145	hgsc.bcm.edu	37	7	149528262	149528262	+	RNA	SNP	C	C	T	rs10261977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149528262C>T	ENST00000378016.2	+	0	15181							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)			CACGGAGCTTCGAAACTTCAC	0.612													C|||	934	0.186502	0.1936	0.1945	5008	,	,		13639	0.1736		0.1511	False		,,,				2504	0.2209				p.R5060X		Atlas-SNP	.											.	.	.	.	0			c.C15178T						PASS	.	C	stop/ARG	746,3058		77,592,1233	42.0	46.0	45.0		15197	3.3	0.9	7	dbSNP_119	45	1356,6878		107,1142,2868	yes	stop-gained	SSPO	NM_198455.2		184,1734,4101	TT,TC,CC		16.4683,19.6109,17.4614		5060/5148	149528262	2102,9936	1902	4117	6019			23145	exon108			GAGCTTCGAAACT	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.149528262C>T		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	172	41	0.238372	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.823;T|0.177	0.177	strong		0.612	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
GLRA4	441509	hgsc.bcm.edu	37	X	102978806	102978806	+	Silent	SNP	G	G	C	rs5945807	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:102978806G>C	ENST00000372617.4	-	5	975	c.555C>G	c.(553-555)acC>acG	p.T185T	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	185						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)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GCATCGTGCAGGTCTGGATGT	0.493													G|||	602	0.15947	0.0287	0.1412	3775	,	,		15940	0.0079		0.2594	False		,,,				2504	0.2014				p.T185T		Atlas-SNP	.											.	GLRA4	86	.	0			c.C555G						PASS	.	G	,	255,3201		12,191,40,1240,530	114.0	104.0	107.0		555,555	-2.6	1.0	X	dbSNP_114	107	2449,4069		338,1067,706,952,1098	no	coding-synonymous,coding-synonymous	GLRA4	NM_001024452.2,NM_001172285.1	,	350,1258,746,2192,1628	CC,CG,C,GG,G		37.5729,7.3785,27.1105	,	185/418,185/343	102978806	2704,7270	2013	4161	6174	SO:0001819	synonymous_variant	441509	exon5			CGTGCAGGTCTGG	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"""Ligand-gated ion channels / Glycine receptors"""	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.555C>G	X.37:g.102978806G>C		Somatic	650	1	0.00153846		WXS	Illumina HiSeq	Phase_I	306	299	0.977124	NM_001024452		Silent	SNP	ENST00000372617.4	37	CCDS43980.2																																																																																			0|0.009;C|0.169	0.169	strong		0.493	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
ABCG5	64240	hgsc.bcm.edu	37	2	44040401	44040401	+	Missense_Mutation	SNP	G	G	C	rs6720173	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	155	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	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	
SSUH2	51066	hgsc.bcm.edu	37	3	8675447	8675447	+	Missense_Mutation	SNP	C	C	T	rs112366230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:8675447C>T	ENST00000317371.4	-	11	1403	c.178G>A	c.(178-180)Gcc>Acc	p.A60T	SSUH2_ENST00000341795.3_Missense_Mutation_p.A60T|SSUH2_ENST00000415132.1_Missense_Mutation_p.A60T|SSUH2_ENST00000544814.1_Missense_Mutation_p.A82T			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	60						cytoplasm (GO:0005737)											CTGAGGAGGGCTTCCCGGGCC	0.657													C|||	67	0.0133786	0.0424	0.0086	5008	,	,		13880	0.0		0.003	False		,,,				2504	0.002				p.A82T		Atlas-SNP	.											.	.	.	.	0			c.G244A						PASS	.	C	THR/ALA	156,4248		3,150,2049	27.0	30.0	29.0		178	5.1	1.0	3	dbSNP_132	29	73,8519		1,71,4224	yes	missense	C3orf32	NM_015931.1	58	4,221,6273	TT,TC,CC		0.8496,3.5422,1.7621	probably-damaging	60/354	8675447	229,12767	2202	4296	6498	SO:0001583	missense	51066	exon4			GGAGGGCTTCCCG	AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.178G>A	3.37:g.8675447C>T	ENSP00000324551:p.Ala60Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	182	96	0.527473	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	C	21.1	4.092595	0.76756	0.035422	0.008496	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814;ENST00000427408	T;T;T;T;T	0.54675	0.61;0.61;0.59;0.61;0.56	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.43897	0.1268	M	0.83953	2.67	0.46061	D	0.998843	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.68416	-0.5414	10	0.72032	D	0.01	-39.6842	14.128	0.65235	0.0:1.0:0.0:0.0	.	82;60	F5H2S5;Q9Y2M2	.;CC032_HUMAN	T	60;60;60;82;82	ENSP00000339150:A60T;ENSP00000324551:A60T;ENSP00000410757:A60T;ENSP00000439378:A82T;ENSP00000401289:A82T	ENSP00000324551:A60T	A	-	1	0	C3orf32	8650447	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	4.952000	0.63618	2.407000	0.81776	0.484000	0.47621	GCC	C|0.986;T|0.014	0.014	strong		0.657	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931	
CCDC180	100499483	hgsc.bcm.edu	37	9	100122291	100122291	+	Missense_Mutation	SNP	T	T	C	rs3747495	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100122291T>C	ENST00000357054.1	+	37	4371	c.3436T>C	c.(3436-3438)Ttc>Ctc	p.F1146L	CCDC180_ENST00000395220.1_3'UTR|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Missense_Mutation_p.F1175L|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	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	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	
KLHL1	57626	hgsc.bcm.edu	37	13	70681598	70681598	+	Silent	SNP	T	T	C	rs3751427	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:70681598T>C	ENST00000377844.4	-	1	993	c.234A>G	c.(232-234)tcA>tcG	p.S78S	ATXN8OS_ENST00000424524.1_RNA|KLHL1_ENST00000545028.1_5'UTR|ATXN8OS_ENST00000414504.2_RNA	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	78	Ser-rich.				actin cytoskeleton organization (GO:0030036)|adult walking behavior (GO:0007628)|cerebellar Purkinje cell layer development (GO:0021680)|dendrite development (GO:0016358)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	actin binding (GO:0003779)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(56)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84		Breast(118;0.000162)		COAD - Colon adenocarcinoma(199;0.000193)|GBM - Glioblastoma multiforme(99;0.000211)		gggaggacgatgaagaggaag	0.592													c|||	848	0.169329	0.2489	0.0865	5008	,	,		17084	0.2897		0.0577	False		,,,				2504	0.1115				p.S78S		Atlas-SNP	.											.	KLHL1	164	.	0			c.A234G						PASS	.	G		934,3472	737.4+/-410.9	99,736,1368	80.0	85.0	83.0		234	-8.5	0.0	13	dbSNP_107	83	482,8118	797.8+/-407.4	15,452,3833	no	coding-synonymous	KLHL1	NM_020866.2		114,1188,5201	CC,CT,TT		5.6047,21.1984,10.8873		78/749	70681598	1416,11590	2203	4300	6503	SO:0001819	synonymous_variant	57626	exon1			GGACGATGAAGAG	AB040923	CCDS9445.1, CCDS73582.1	13q21	2013-01-30	2013-01-30		ENSG00000150361	ENSG00000150361		"""Kelch-like"", ""BTB/POZ domain containing"""	6352	protein-coding gene	gene with protein product	"""Kelch-like protein 1"", ""Mayven-related protein 2"""	605332	"""kelch (Drosophila)-like 1"", ""kelch-like 1 (Drosophila)"""			10888605	Standard	NM_020866		Approved	KIAA1490, MRP2, FLJ30047	uc001vip.3	Q9NR64	OTTHUMG00000017056	ENST00000377844.4:c.234A>G	13.37:g.70681598T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Silent	SNP	ENST00000377844.4	37	CCDS9445.1																																																																																			T|0.866;C|0.134	0.134	strong		0.592	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866	
SUPT16H	11198	hgsc.bcm.edu	37	14	21831419	21831419	+	Silent	SNP	C	C	T	rs61746713	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21831419C>T	ENST00000216297.2	-	12	1706	c.1368G>A	c.(1366-1368)cgG>cgA	p.R456R		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	456					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|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)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		GTAATGCTGCCCGAGAACCTC	0.373													C|||	227	0.0453275	0.0076	0.0389	5008	,	,		18562	0.0		0.1203	False		,,,				2504	0.0706				p.R456R		Atlas-SNP	.											SUPT16H,NS,carcinoma,-1,1	SUPT16H	84	1	0			c.G1368A						PASS	.	C		122,4284	88.2+/-126.9	4,114,2085	80.0	82.0	81.0		1368	-0.9	1.0	14	dbSNP_129	81	1025,7573	218.1+/-256.6	57,911,3331	no	coding-synonymous	SUPT16H	NM_007192.3		61,1025,5416	TT,TC,CC		11.9214,2.769,8.8204		456/1048	21831419	1147,11857	2203	4299	6502	SO:0001819	synonymous_variant	11198	exon12			TGCTGCCCGAGAA	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 140 kDa subunit"""	605012	"""suppressor of Ty (S.cerevisiae) 16 homolog"""			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.1368G>A	14.37:g.21831419C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	58	0.617021	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Silent	SNP	ENST00000216297.2	37	CCDS9569.1																																																																																			C|0.925;T|0.075	0.075	strong		0.373	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		
NKAIN4	128414	hgsc.bcm.edu	37	20	61878950	61878950	+	Missense_Mutation	SNP	A	A	C	rs872808	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	304	1	0.00328947		WXS	Illumina HiSeq	Phase_I	288	122	0.423611	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	
CROCC	9696	hgsc.bcm.edu	37	1	17273396	17273396	+	Silent	SNP	A	A	G	rs7537468	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:17273396A>G	ENST00000375541.5	+	17	2493	c.2424A>G	c.(2422-2424)ctA>ctG	p.L808L	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)		AGGGCTCCCTACGAGTGGCGG	0.692																																					p.L808L		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.A2424G						scavenged	.	A		216,4104		1,214,1945	14.0	13.0	13.0		2424	1.4	0.8	1	dbSNP_116	13	1332,7146		2,1328,2909	no	coding-synonymous	CROCC	NM_014675.3		3,1542,4854	GG,GA,AA		15.7113,5.0,12.0956		808/2018	17273396	1548,11250	2160	4239	6399	SO:0001819	synonymous_variant	9696	exon17			CTCCCTACGAGTG	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.2424A>G	1.37:g.17273396A>G		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	67	14	0.208955	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			A|0.845;G|0.155	0.155	strong		0.692	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
LPL	4023	hgsc.bcm.edu	37	8	19810826	19810826	+	Silent	SNP	G	G	A	rs248	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:19810826G>A	ENST00000311322.8	+	4	905	c.435G>A	c.(433-435)gaG>gaA	p.E145E		NM_000237.2	NP_000228.1	P06858	LIPL_HUMAN	lipoprotein lipase	145					chylomicron remodeling (GO:0034371)|fatty acid biosynthetic process (GO:0006633)|lipoprotein metabolic process (GO:0042157)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of sequestering of triglyceride (GO:0010890)|response to cold (GO:0009409)|response to drug (GO:0042493)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle remodeling (GO:0034372)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phospholipase activity (GO:0004620)|receptor binding (GO:0005102)|triglyceride binding (GO:0017129)|triglyceride lipase activity (GO:0004806)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	36				Colorectal(111;0.0577)|COAD - Colon adenocarcinoma(73;0.216)	AST-120(DB05269)|Tyloxapol(DB06439)	CAAAGGAGGAGTTTAACTACC	0.373													G|||	194	0.038738	0.0522	0.0403	5008	,	,		17263	0.001		0.0666	False		,,,				2504	0.0297				p.E145E		Atlas-SNP	.											.	LPL	78	.	0			c.G435A						PASS	.	G		245,4161	143.5+/-178.5	3,239,1961	91.0	90.0	90.0		435	1.5	1.0	8	dbSNP_36	90	606,7994	158.9+/-212.3	19,568,3713	no	coding-synonymous	LPL	NM_000237.2		22,807,5674	AA,AG,GG		7.0465,5.5606,6.5431		145/476	19810826	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	4023	exon4			GGAGGAGTTTAAC		CCDS6012.1	8p22	2012-10-02			ENSG00000175445	ENSG00000175445	3.1.1.34		6677	protein-coding gene	gene with protein product		609708		LIPD			Standard	NM_000237		Approved		uc003wzk.4	P06858	OTTHUMG00000036645	ENST00000311322.8:c.435G>A	8.37:g.19810826G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	109	30	0.275229	NM_000237	B2R5T9|Q16282|Q16283|Q96FC4	Silent	SNP	ENST00000311322.8	37	CCDS6012.1																																																																																			G|0.944;A|0.056	0.056	strong		0.373	LPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089113.3		
DCAF5	8816	hgsc.bcm.edu	37	14	69521345	69521345	+	Silent	SNP	G	G	A	rs61741172	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:69521345G>A	ENST00000341516.5	-	9	2205	c.2058C>T	c.(2056-2058)acC>acT	p.T686T	DCAF5_ENST00000553293.1_5'Flank|DCAF5_ENST00000556847.1_Silent_p.T604T|DCAF5_ENST00000554215.1_Silent_p.T604T|DCAF5_ENST00000557386.1_Silent_p.T685T	NM_001284206.1|NM_001284207.1|NM_003861.2	NP_001271135.1|NP_001271136.1|NP_003852.1	Q96JK2	DCAF5_HUMAN	DDB1 and CUL4 associated factor 5	686					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|mitochondrion (GO:0005739)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|upper_aerodigestive_tract(2)	29						CTGCCTCCCCGGTCACCAAGG	0.473													G|||	643	0.128395	0.0182	0.1715	5008	,	,		17008	0.001		0.3787	False		,,,				2504	0.1207				p.T686T		Atlas-SNP	.											.	DCAF5	67	.	0			c.C2058T						PASS	.	G		296,4110	151.4+/-185.3	16,264,1923	98.0	107.0	104.0		2058	-5.5	0.0	14	dbSNP_129	104	3045,5555	456.4+/-364.1	565,1915,1820	no	coding-synonymous	DCAF5	NM_003861.2		581,2179,3743	AA,AG,GG		35.407,6.7181,25.6881		686/943	69521345	3341,9665	2203	4300	6503	SO:0001819	synonymous_variant	8816	exon9			CTCCCCGGTCACC	AB058727	CCDS32106.1, CCDS61480.1, CCDS61481.1, CCDS73646.1	14q23-q24.1	2013-01-09	2009-07-17	2009-07-17				"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20224	protein-coding gene	gene with protein product		603812	"""WD repeat domain 22"""	WDR22		9740667, 9521877	Standard	NM_003861		Approved	BCRP2, D14S1461E, BCRG2, KIAA1824	uc001xkp.3	Q96JK2		ENST00000341516.5:c.2058C>T	14.37:g.69521345G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_003861	B2RN31|G3V4J7|O60559|Q8N3V3|Q8N3V5	Silent	SNP	ENST00000341516.5	37	CCDS32106.1																																																																																			G|0.761;A|0.239	0.239	strong		0.473	DCAF5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414806.2	NM_003861	
POMT1	10585	hgsc.bcm.edu	37	9	134385435	134385435	+	Nonsense_Mutation	SNP	C	C	T	rs386738991|rs3887873	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:134385435C>T	ENST00000372228.3	+	8	930	c.751C>T	c.(751-753)Cag>Tag	p.Q251*	POMT1_ENST00000404875.2_Intron|POMT1_ENST00000354713.4_Intron|POMT1_ENST00000423007.1_Intron|POMT1_ENST00000341012.7_Intron|POMT1_ENST00000541219.1_Intron|POMT1_ENST00000402686.3_Intron|POMT1_ENST00000419118.2_Intron	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	251			Q -> R (in dbSNP:rs2296949). {ECO:0000269|PubMed:10366449, ECO:0000269|PubMed:14702039}.|Q -> W (requires 2 nucleotide substitutions; dbSNP:rs3887873).		carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		GGGGCAGATGCAGATGTCACA	0.572													C|||	394	0.0786741	0.1248	0.0793	5008	,	,		19038	0.001		0.1461	False		,,,				2504	0.0266				p.Q251X		Atlas-SNP	.											.	POMT1	59	.	0			c.C751T						PASS	.	C	,,,,stop/GLN	395,4011		22,351,1830	72.0	61.0	65.0		,,,,751	-1.1	0.0	9	dbSNP_108	65	871,7729		65,741,3494	yes	intron,intron,intron,intron,stop-gained	POMT1	NM_001077365.1,NM_001077366.1,NM_001136113.1,NM_001136114.1,NM_007171.3	,,,,	87,1092,5324	TT,TC,CC		10.1279,8.965,9.734	,,,,	,,,,251/748	134385435	1266,11740	2203	4300	6503	SO:0001587	stop_gained	10585	exon8			CAGATGCAGATGT	AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	9202	protein-coding gene	gene with protein product	"""dolichyl-phosphate-mannose-protein mannosyltransferase"""	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.751C>T	9.37:g.134385435C>T	ENSP00000361302:p.Gln251*	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Nonsense_Mutation	SNP	ENST00000372228.3	37	CCDS6943.1	147	0.0673076923076923	34	0.06910569105691057	29	0.08011049723756906	1	0.0017482517482517483	83	0.10949868073878628	C	12.05	1.821679	0.32237	0.08965	0.101279	ENSG00000130714	ENST00000441334;ENST00000372228;ENST00000448212	.	.	.	2.2	-1.1	0.09872	.	4.494090	0.00649	U	0.000543	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-18.2385	2.8102	0.05440	0.3724:0.2516:0.376:0.0	rs3887873;rs52806687;rs57618284;rs3887873	.	.	.	X	134;251;197	.	.	Q	+	1	0	POMT1	133375256	0.274000	0.24191	0.001000	0.08648	0.049000	0.14656	-0.097000	0.11042	-0.288000	0.09051	-0.234000	0.12200	CAG	C|0.904;T|0.096	0.096	strong		0.572	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171	
TPO	7173	hgsc.bcm.edu	37	2	1497803	1497803	+	Silent	SNP	C	C	T	rs1126797	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000329066.4_Silent_p.D666D|TPO_ENST00000382198.1_Silent_p.D493D|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000382201.3_Silent_p.D609D|TPO_ENST00000349624.3_Silent_p.D493D|TPO_ENST00000346956.3_Silent_p.D666D	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	83	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	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	
SV2B	9899	hgsc.bcm.edu	37	15	91825027	91825027	+	Silent	SNP	C	C	T	rs1117388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:91825027C>T	ENST00000394232.1	+	10	1913	c.1443C>T	c.(1441-1443)gaC>gaT	p.D481D	SV2B_ENST00000330276.4_Silent_p.D481D|SV2B_ENST00000545111.2_Silent_p.D330D	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	481					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)			ATTTTGAAGACGTAACATCAA	0.363													T|||	1668	0.333067	0.7617	0.1758	5008	,	,		23051	0.1419		0.2117	False		,,,				2504	0.1871				p.D481D		Atlas-SNP	.											.	SV2B	98	.	0			c.C1443T						PASS	.	T	,	2942,1454	469.8+/-355.6	1014,914,270	112.0	105.0	107.0		990,1443	0.7	1.0	15	dbSNP_86	107	1690,6906	737.8+/-407.0	174,1342,2782	no	coding-synonymous,coding-synonymous	SV2B	NM_001167580.1,NM_014848.4	,	1188,2256,3052	TT,TC,CC		19.6603,33.0755,35.6527	,	330/533,481/684	91825027	4632,8360	2198	4298	6496	SO:0001819	synonymous_variant	9899	exon11			TGAAGACGTAACA	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.1443C>T	15.37:g.91825027C>T		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	56	43	0.767857	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																			C|0.652;T|0.348	0.348	strong		0.363	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
OR10G3	26533	hgsc.bcm.edu	37	14	22038450	22038450	+	Silent	SNP	G	G	A	rs11626669	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:22038450G>A	ENST00000303532.1	-	1	425	c.426C>T	c.(424-426)agC>agT	p.S142S		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	142						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(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		CAAGCAAGGCGCTCAGCTTAG	0.597													A|||	2364	0.472045	0.4402	0.6643	5008	,	,		20195	0.498		0.4125	False		,,,				2504	0.4131				p.S142S		Atlas-SNP	.											.	OR10G3	40	.	0			c.C426T						PASS	.	A		1949,2457	622.0+/-393.9	435,1079,689	60.0	59.0	59.0		426	-4.1	0.0	14	dbSNP_120	59	3769,4831	615.0+/-396.3	817,2135,1348	no	coding-synonymous	OR10G3	NM_001005465.1		1252,3214,2037	AA,AG,GG		43.8256,44.2351,43.9643		142/314	22038450	5718,7288	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			CAAGGCGCTCAGC		CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"""GPCR / Class A : Olfactory receptors"""	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.426C>T	14.37:g.22038450G>A		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	146	143	0.979452	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			G|0.547;A|0.453	0.453	strong		0.597	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
OR12D2	26529	hgsc.bcm.edu	37	6	29364815	29364815	+	Missense_Mutation	SNP	C	C	G	rs2073154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29364815C>G	ENST00000383555.2	+	1	400	c.339C>G	c.(337-339)ttC>ttG	p.F113L	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	113			F -> L (in dbSNP:rs2073154).			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(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CCATGTTGTTCGCCGTGATGG	0.493													G|||	1598	0.319089	0.1921	0.3458	5008	,	,		21376	0.3641		0.4533	False		,,,				2504	0.2873				p.F113L		Atlas-SNP	.											.	OR12D2	42	.	0			c.C339G						PASS	.	G	LEU/PHE	670,2350		75,520,915	85.0	86.0	86.0		339	1.0	0.0	6	dbSNP_96	86	2409,3007		534,1341,833	yes	missense	OR12D2	NM_013936.3	22	609,1861,1748	GG,GC,CC		44.4793,22.1854,36.4983	benign	113/308	29364815	3079,5357	1510	2708	4218	SO:0001583	missense	26529	exon1			GTTGTTCGCCGTG		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.339C>G	6.37:g.29364815C>G	ENSP00000373047:p.Phe113Leu	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	247	246	0.995951	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	787	0.36034798534798534	101	0.20528455284552846	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	G	0	-2.845655	0.00067	0.221854	0.444793	ENSG00000168787	ENST00000383555	T	0.72394	-0.65	3.94	1.01	0.19927	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	N	0.000302	T	0.04048	0.0113	N	0.00014	-2.9	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29761	-1.0001	9	0.02654	T	1	.	3.1878	0.06607	0.1594:0.3698:0.3452:0.1256	rs2073154;rs52828851;rs59971655;rs2073154	113	P58182	O12D2_HUMAN	L	113	ENSP00000373047:F113L	ENSP00000373047:F113L	F	+	3	2	OR12D2	29472794	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.355000	0.07671	-0.258000	0.09446	-0.980000	0.02579	TTC	C|0.628;G|0.372	0.372	strong		0.493	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
SUPT3H	8464	hgsc.bcm.edu	37	6	44982593	44982593	+	Silent	SNP	G	G	A	rs12528232	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:44982593G>A	ENST00000371459.1	-	5	474	c.309C>T	c.(307-309)atC>atT	p.I103I	SUPT3H_ENST00000371461.2_Silent_p.I114I|SUPT3H_ENST00000371460.1_Silent_p.I114I|SUPT3H_ENST00000306867.5_Silent_p.I103I	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	192	0	0		WXS	Illumina HiSeq	Phase_I	147	62	0.421769	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	
GPR98	84059	hgsc.bcm.edu	37	5	90020923	90020923	+	Silent	SNP	T	T	G	rs16869042	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	143	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	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	
TRAF7	84231	hgsc.bcm.edu	37	16	2222286	2222286	+	Silent	SNP	C	C	T	rs11547311	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2222286C>T	ENST00000326181.6	+	8	702	c.570C>T	c.(568-570)caC>caT	p.H190H		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	190					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						ACTGCCGGCACGGCTGCCGGG	0.647													C|||	152	0.0303514	0.0038	0.0663	5008	,	,		13645	0.0		0.0795	False		,,,				2504	0.0215				p.H190H		Atlas-SNP	.											.	TRAF7	158	.	0			c.C570T						PASS	.	C		68,4324	57.4+/-93.9	1,66,2129	36.0	38.0	37.0		570	-0.6	1.0	16	dbSNP_120	37	659,7939	164.9+/-217.2	21,617,3661	no	coding-synonymous	TRAF7	NM_032271.2		22,683,5790	TT,TC,CC		7.6646,1.5483,5.5966		190/671	2222286	727,12263	2196	4299	6495	SO:0001819	synonymous_variant	84231	exon8			CCGGCACGGCTGC	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"""RING-type (C3HC4) zinc fingers"", ""WD repeat domain containing"""	20456	protein-coding gene	gene with protein product		606692	"""ring finger and WD repeat domain 1"", ""TNF receptor-associated factor 7"""	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.570C>T	16.37:g.2222286C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_032271	Q9H073	Silent	SNP	ENST00000326181.6	37	CCDS10461.1																																																																																			C|0.945;T|0.055	0.055	strong		0.647	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271	
OR1F1	4992	hgsc.bcm.edu	37	16	3254418	3254418	+	Missense_Mutation	SNP	C	C	G	rs61731432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3254418C>G	ENST00000304646.2	+	1	172	c.172C>G	c.(172-174)Ccc>Gcc	p.P58A	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	58					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						CCTGCACACCCCCATGTACTT	0.532													C|||	62	0.0123802	0.0	0.0072	5008	,	,		21743	0.001		0.0467	False		,,,				2504	0.0092				p.P58A		Atlas-SNP	.											.	OR1F1	36	.	0			c.C172G						PASS	.	C	ALA/PRO	56,4338	55.5+/-91.7	0,56,2141	223.0	185.0	198.0		172	5.3	1.0	16	dbSNP_129	198	426,8174	131.5+/-189.3	13,400,3887	yes	missense	OR1F1	NM_012360.1	27	13,456,6028	GG,GC,CC		4.9535,1.2745,3.7094	benign	58/313	3254418	482,12512	2197	4300	6497	SO:0001583	missense	4992	exon1			CACACCCCCATGT	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.172C>G	16.37:g.3254418C>G	ENSP00000305424:p.Pro58Ala	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	227	97	0.427313	NM_012360	O15246|Q6IFL5	Missense_Mutation	SNP	ENST00000304646.2	37	CCDS10496.1	37	0.01694139194139194	0	0.0	1	0.0027624309392265192	0	0.0	36	0.047493403693931395	C	13.66	2.302814	0.40795	0.012745	0.049535	ENSG00000168124	ENST00000304646	T	0.02015	4.5	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000032	T	0.01523	0.0049	H	0.95745	3.715	0.47659	D	0.999484	B	0.24651	0.108	B	0.32342	0.144	T	0.00950	-1.1503	10	0.87932	D	0	.	16.3456	0.83132	0.0:1.0:0.0:0.0	rs61731432	58	O43749	OR1F1_HUMAN	A	58	ENSP00000305424:P58A	ENSP00000305424:P58A	P	+	1	0	OR1F1	3194419	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	4.559000	0.60796	2.451000	0.82905	0.385000	0.25706	CCC	C|0.968;G|0.032	0.032	strong		0.532	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1		
CAMSAP1	157922	hgsc.bcm.edu	37	9	138742077	138742077	+	Silent	SNP	C	C	G	rs35981196	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:138742077C>G	ENST00000389532.4	-	7	1015	c.951G>C	c.(949-951)ccG>ccC	p.P317P	CAMSAP1_ENST00000409386.3_Silent_p.P328P|CAMSAP1_ENST00000312405.6_Silent_p.P39P	NM_015447.3	NP_056262.3	Q5T5Y3	CAMP1_HUMAN	calmodulin regulated spectrin-associated protein 1	317	CH.				cytoskeleton organization (GO:0007010)|neuron projection development (GO:0031175)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|spectrin binding (GO:0030507)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(11)|lung(16)|ovary(3)|pancreas(1)|skin(1)	47				OV - Ovarian serous cystadenocarcinoma(145;1.4e-06)|Epithelial(140;1.11e-05)		CCATAACATTCGGCTAAAAGA	0.378													C|||	609	0.121605	0.2057	0.0879	5008	,	,		18956	0.0		0.1322	False		,,,				2504	0.1462				p.P317P		Atlas-SNP	.											.	CAMSAP1	142	.	0			c.G951C						PASS	.	C		884,3522	337.3+/-304.8	105,674,1424	44.0	42.0	43.0		951	-10.7	0.0	9	dbSNP_126	43	1523,7077	283.9+/-296.4	134,1255,2911	no	coding-synonymous	CAMSAP1	NM_015447.3		239,1929,4335	GG,GC,CC		17.7093,20.0635,18.5068		317/1603	138742077	2407,10599	2203	4300	6503	SO:0001819	synonymous_variant	157922	exon7			AACATTCGGCTAA	AJ519841	CCDS35176.2	9q34.3	2008-02-05			ENSG00000130559	ENSG00000130559			19946	protein-coding gene	gene with protein product		613774				12477932	Standard	NM_015447		Approved	FLJ31228, DKFZp434F195	uc004cgr.4	Q5T5Y3	OTTHUMG00000020918	ENST00000389532.4:c.951G>C	9.37:g.138742077C>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_015447	A1L4L2|B2REB2|B2REB3|Q70W33|Q8NCY0|Q96E80|Q96FM3|Q9UFJ5	Silent	SNP	ENST00000389532.4	37	CCDS35176.2																																																																																			C|0.836;G|0.164	0.164	strong		0.378	CAMSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055024.2	XM_351857	
SARS	6301	hgsc.bcm.edu	37	1	109779073	109779073	+	Missense_Mutation	SNP	G	G	A	rs140717526	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109779073G>A	ENST00000234677.2	+	9	1235	c.1160G>A	c.(1159-1161)gGa>gAa	p.G387E	SARS_ENST00000369923.4_Missense_Mutation_p.G387E|SARS_ENST00000468588.1_3'UTR	NM_006513.3	NP_006504.2	P49591	SYSC_HUMAN	seryl-tRNA synthetase	387					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|RNA binding (GO:0003723)|serine-tRNA ligase activity (GO:0004828)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	17		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0301)|Lung(183;0.0677)|COAD - Colon adenocarcinoma(174;0.116)|Epithelial(280;0.233)	L-Serine(DB00133)	CCGGGCTCAGGAGCCTTCCGT	0.507													G|||	14	0.00279553	0.0008	0.0101	5008	,	,		16569	0.0		0.005	False		,,,				2504	0.001				p.G387E		Atlas-SNP	.											.	SARS	43	.	0			c.G1160A						PASS	.	G	GLU/GLY	14,4392	21.2+/-45.6	0,14,2189	84.0	90.0	88.0		1160	6.1	0.8	1	dbSNP_134	88	152,8448	73.8+/-136.5	4,144,4152	yes	missense	SARS	NM_006513.3	98	4,158,6341	AA,AG,GG		1.7674,0.3177,1.2763	benign	387/515	109779073	166,12840	2203	4300	6503	SO:0001583	missense	6301	exon9			GCTCAGGAGCCTT	BC009390	CCDS795.1	1p13.3	2011-07-01			ENSG00000031698	ENSG00000031698	6.1.1.11	"""Aminoacyl tRNA synthetases / Class II"""	10537	protein-coding gene	gene with protein product	"""serine tRNA ligase 1, cytoplasmic"""	607529				9431993	Standard	NM_006513		Approved	SERS	uc001dwu.2	P49591	OTTHUMG00000011726	ENST00000234677.2:c.1160G>A	1.37:g.109779073G>A	ENSP00000234677:p.Gly387Glu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	86	59	0.686047	NM_006513	B2R6Y9|Q5T5C8|Q9NSE3	Missense_Mutation	SNP	ENST00000234677.2	37	CCDS795.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	g	14.77	2.635160	0.47049	0.003177	0.017674	ENSG00000031698	ENST00000234677;ENST00000369923	T;T	0.78924	-1.22;-1.22	6.08	6.08	0.98989	Aminoacyl-tRNA synthetase, class II (1);	0.262046	0.44902	D	0.000404	T	0.61048	0.2316	L	0.43701	1.375	0.58432	D	0.999999	B;B;B	0.27380	0.177;0.051;0.177	B;B;B	0.23275	0.036;0.045;0.045	T	0.61028	-0.7145	10	0.44086	T	0.13	-10.2916	14.8883	0.70587	0.0:0.1428:0.8572:0.0	.	387;387;387	Q53HA4;Q5T5C7;P49591	.;.;SYSC_HUMAN	E	387	ENSP00000234677:G387E;ENSP00000358939:G387E	ENSP00000234677:G387E	G	+	2	0	SARS	109580596	1.000000	0.71417	0.824000	0.32777	0.993000	0.82548	3.498000	0.53302	2.894000	0.99253	0.655000	0.94253	GGA	G|0.989;A|0.011	0.011	strong		0.507	SARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032394.2	NM_006513	
HEATR2	54919	hgsc.bcm.edu	37	7	796430	796430	+	Silent	SNP	C	C	T	rs73036225	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:796430C>T	ENST00000297440.6	+	6	1289	c.1269C>T	c.(1267-1269)tcC>tcT	p.S423S	HEATR2_ENST00000313147.5_Silent_p.S423S	NM_017802.3	NP_060272.3	Q86Y56	HEAT2_HUMAN	HEAT repeat containing 2	423						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)		GTACCAGATCCGCAGAGCTCG	0.597													c|||	473	0.0944489	0.0129	0.1066	5008	,	,		18605	0.0		0.2127	False		,,,				2504	0.1718				p.S423S		Atlas-SNP	.											.	HEATR2	62	.	0			c.C1269T						PASS	.			224,4182	134.1+/-170.4	5,214,1984	87.0	88.0	87.0		1269	-11.0	0.0	7	dbSNP_130	87	1948,6652	339.0+/-323.0	232,1484,2584	no	coding-synonymous	HEATR2	NM_017802.3		237,1698,4568	TT,TC,CC		22.6512,5.084,16.7		423/856	796430	2172,10834	2203	4300	6503	SO:0001819	synonymous_variant	54919	exon6			CAGATCCGCAGAG	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.1269C>T	7.37:g.796430C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	125	67	0.536	NM_017802	Q69YL1|Q96FI9|Q9NX75	Silent	SNP	ENST00000297440.6	37	CCDS34580.1	206	0.09432234432234432	7	0.014227642276422764	33	0.09116022099447514	0	0.0	166	0.21899736147757257	C	4.574	0.106613	0.08780	0.05084	0.226512	ENSG00000164818	ENST00000440747	.	.	.	5.49	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999992945	.	.	.	.	.	.	T	0.07635	-1.0762	3	.	.	.	-15.5902	10.2483	0.43354	0.1267:0.621:0.065:0.1874	.	.	.	.	C	225	.	.	R	+	1	0	HEATR2	762956	0.003000	0.15002	0.000000	0.03702	0.005000	0.04900	-1.344000	0.02639	-3.807000	0.00104	-2.136000	0.00340	CGC	C|0.850;T|0.150	0.150	strong		0.597	HEATR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322542.1	NM_017802	
FAT4	79633	hgsc.bcm.edu	37	4	126372742	126372742	+	Missense_Mutation	SNP	G	G	A	rs1567047	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:126372742G>A	ENST00000394329.3	+	9	10584	c.10571G>A	c.(10570-10572)gGc>gAc	p.G3524D	FAT4_ENST00000335110.5_Missense_Mutation_p.G1822D	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3524	Cadherin 34. {ECO:0000255|PROSITE- ProRule:PRU00043}.		G -> D (in dbSNP:rs1567047).		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						AAACGGCCAGGCACTTTGGTG	0.478													G|||	1155	0.230631	0.0242	0.2522	5008	,	,		18233	0.3909		0.2952	False		,,,				2504	0.2628				p.G3524D		Atlas-SNP	.											.	FAT4	1752	.	0			c.G10571A						PASS	.	G	ASP/GLY	292,4114	157.8+/-190.6	10,272,1921	121.0	118.0	119.0		10571	5.8	0.9	4	dbSNP_88	119	2578,6022	417.3+/-352.4	400,1778,2122	yes	missense	FAT4	NM_024582.4	94	410,2050,4043	AA,AG,GG		29.9767,6.6273,22.0667	probably-damaging	3524/4982	126372742	2870,10136	2203	4300	6503	SO:0001583	missense	79633	exon9			GGCCAGGCACTTT	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.10571G>A	4.37:g.126372742G>A	ENSP00000377862:p.Gly3524Asp	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	117	112	0.957265	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	565	0.2586996336996337	15	0.03048780487804878	107	0.2955801104972376	225	0.39335664335664333	218	0.287598944591029	G	23.6	4.435957	0.83885	0.066273	0.299767	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.54071	0.59;0.59	5.77	5.77	0.91146	Cadherin (3);Cadherin-like (1);	0.000000	0.33670	U	0.004671	T	0.00012	0.0000	M	0.77616	2.38	0.09310	P	0.9999999999954321	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.05801	-1.0863	9	0.66056	D	0.02	.	19.9983	0.97395	0.0:0.0:1.0:0.0	rs1567047;rs52797800;rs60153785;rs1567047	1822;3524;3524	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	D	3524;1822	ENSP00000377862:G3524D;ENSP00000335169:G1822D	ENSP00000335169:G1822D	G	+	2	0	FAT4	126592192	1.000000	0.71417	0.935000	0.37517	0.783000	0.44284	9.666000	0.98612	2.724000	0.93272	0.561000	0.74099	GGC	G|0.769;A|0.231	0.231	strong		0.478	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
CABIN1	23523	hgsc.bcm.edu	37	22	24567795	24567795	+	Missense_Mutation	SNP	C	C	T	rs145513360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:24567795C>T	ENST00000398319.2	+	34	6257	c.5872C>T	c.(5872-5874)Cgg>Tgg	p.R1958W	CABIN1_ENST00000485008.1_3'UTR|CABIN1_ENST00000405822.2_Missense_Mutation_p.R1879W|CABIN1_ENST00000337989.7_Missense_Mutation_p.R383W|CABIN1_ENST00000263119.5_Missense_Mutation_p.R1958W	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1958					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)			breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						CTCTGTCCAGCGGCCCAGTGA	0.607													C|||	3	0.000599042	0.0	0.0	5008	,	,		19053	0.0		0.003	False		,,,				2504	0.0				p.R1958W		Atlas-SNP	.											.	CABIN1	153	.	0			c.C5872T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	123.0	115.0	118.0		5872,5722,5872	2.7	0.9	22	dbSNP_134	118	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	CABIN1	NM_001199281.1,NM_001201429.1,NM_012295.3	101,101,101	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging,probably-damaging	1958/2221,1908/2171,1958/2221	24567795	4,13002	2203	4300	6503	SO:0001583	missense	23523	exon34			GTCCAGCGGCCCA	AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.5872C>T	22.37:g.24567795C>T	ENSP00000381364:p.Arg1958Trp	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	160	94	0.5875	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.75	3.465698	0.63513	0.0	4.65E-4	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319;ENST00000337989;ENST00000403176	T;T;T;T	0.19806	2.12;2.12;2.12;2.12	4.9	2.7	0.31948	.	0.150708	0.43110	D	0.000609	T	0.30008	0.0751	N	0.24115	0.695	0.39027	D	0.959857	D;D	0.89917	0.999;1.0	P;D	0.79784	0.9;0.993	T	0.12192	-1.0557	10	0.72032	D	0.01	.	12.406	0.55441	0.3019:0.698:0.0:0.0	.	1879;1958	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	W	1958;1879;1958;383;382	ENSP00000263119:R1958W;ENSP00000384694:R1879W;ENSP00000381364:R1958W;ENSP00000336991:R383W	ENSP00000263119:R1958W	R	+	1	2	CABIN1	22897795	0.011000	0.17503	0.915000	0.36163	0.505000	0.33919	0.127000	0.15790	0.689000	0.31550	0.650000	0.86243	CGG	C|0.999;T|0.001	0.001	strong		0.607	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
B2M	567	hgsc.bcm.edu	37	15	45003746	45003746	+	Start_Codon_SNP	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:45003746T>G	ENST00000558401.1	+	1	72	c.2T>G	c.(1-3)aTg>aGg	p.M1R	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000544417.1_Start_Codon_SNP_p.M1R|B2M_ENST00000559916.1_Start_Codon_SNP_p.M1R	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.M1R(3)|p.M1K(2)|p.M1T(2)|p.?(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CGGGCCGAGATGTCTCGCTCC	0.612																																					p.M1R		Atlas-SNP	.											B2M,caecum,carcinoma,-1,17	B2M	99	17	8	Substitution - Missense(7)|Unknown(1)	haematopoietic_and_lymphoid_tissue(7)|lung(1)	c.T2G						PASS	.						126.0	92.0	104.0					15																	45003746		2198	4298	6496	SO:0001582	initiator_codon_variant	567	exon1			CCGAGATGTCTCG	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.2T>G	15.37:g.45003746T>G	ENSP00000452780:p.Met1Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	17.67	3.446958	0.63178	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01304	5.03	5.35	4.22	0.49857	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.80722	D	1	D;D;D	0.63880	0.989;0.993;0.981	P;P;P	0.59288	0.847;0.855;0.708	T	0.21415	-1.0246	8	0.87932	D	0	.	8.1513	0.31143	0.0:0.0894:0.0:0.9106	.	1;1;1	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	R	1	ENSP00000437604:M1R	ENSP00000340858:M1R	M	+	2	0	B2M	42791038	0.961000	0.32948	0.428000	0.26697	0.026000	0.11368	1.415000	0.34748	1.147000	0.42369	0.533000	0.62120	ATG	.	.	none		0.612	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	Missense_Mutation
OR1A2	26189	hgsc.bcm.edu	37	17	3100827	3100827	+	Silent	SNP	T	T	C	rs2241093	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	89	0	0		WXS	Illumina HiSeq	Phase_I	87	85	0.977012	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	
IMPACT	55364	hgsc.bcm.edu	37	18	22020467	22020467	+	Missense_Mutation	SNP	T	T	A	rs582234	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:22020467T>A	ENST00000284202.4	+	6	516	c.375T>A	c.(373-375)gaT>gaA	p.D125E	RP11-178F10.1_ENST00000579049.1_RNA	NM_018439.3	NP_060909	Q9P2X3	IMPCT_HUMAN	impact RWD domain protein	125			D -> E (in dbSNP:rs582234).		negative regulation of protein phosphorylation (GO:0001933)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00018)|all_epithelial(16;1.5e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)					TAGGCCCAGATGTAAAGAAGA	0.363													T|||	427	0.0852636	0.0356	0.1556	5008	,	,		19660	0.0188		0.1322	False		,,,				2504	0.1227				p.D125E		Atlas-SNP	.											.	IMPACT	37	.	0			c.T375A						PASS	.	T	GLU/ASP	285,4121	158.9+/-191.5	10,265,1928	126.0	117.0	120.0		375	-9.9	0.0	18	dbSNP_83	120	1317,7283	259.7+/-282.8	114,1089,3097	yes	missense	IMPACT	NM_018439.3	45	124,1354,5025	AA,AT,TT		15.314,6.4685,12.3174	benign	125/321	22020467	1602,11404	2203	4300	6503	SO:0001583	missense	55364	exon6			CCCAGATGTAAAG	AB026264	CCDS11886.1	18q11.2-q12.1	2012-12-07	2012-12-07		ENSG00000154059	ENSG00000154059			20387	protein-coding gene	gene with protein product	"""RWD domain containing 5"""	615319	"""Impact homolog (mouse)"""			11116084	Standard	NM_018439		Approved	RWDD5	uc002kvh.4	Q9P2X3	OTTHUMG00000131943	ENST00000284202.4:c.375T>A	18.37:g.22020467T>A	ENSP00000284202:p.Asp125Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_018439	A8MXG0|Q49AM0|Q9H2X4	Missense_Mutation	SNP	ENST00000284202.4	37	CCDS11886.1	187	0.08562271062271062	21	0.042682926829268296	59	0.16298342541436464	6	0.01048951048951049	101	0.13324538258575197	T	7.378	0.628265	0.14257	0.064685	0.15314	ENSG00000154059	ENST00000284202	T	0.27557	1.66	4.97	-9.94	0.00449	.	0.453643	0.24303	N	0.039716	T	0.00039	0.0001	L	0.46614	1.455	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.44436	-0.9328	9	0.02654	T	1	.	2.223	0.03977	0.3214:0.3618:0.1897:0.1271	rs582234;rs1303257;rs11557328;rs17797897;rs582234	125	Q9P2X3	IMPCT_HUMAN	E	125	ENSP00000284202:D125E	ENSP00000284202:D125E	D	+	3	2	IMPACT	20274465	0.000000	0.05858	0.000000	0.03702	0.497000	0.33675	-2.367000	0.01078	-2.168000	0.00778	-0.433000	0.05886	GAT	T|0.899;A|0.101	0.101	strong		0.363	IMPACT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254901.1	NM_018439	
CASR	846	hgsc.bcm.edu	37	3	122003757	122003757	+	Missense_Mutation	SNP	G	G	T	rs1801725	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122003757G>T	ENST00000490131.1	+	7	3328	c.2956G>T	c.(2956-2958)Gcc>Tcc	p.A986S	AC068754.1_ENST00000408547.1_RNA|CASR_ENST00000498619.1_Missense_Mutation_p.A996S|CASR_ENST00000296154.5_Missense_Mutation_p.A986S	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	986			A -> S (associated with high serum level of calcium; is also a potential predisposing factor in disorders of bone and mineral metabolism; dbSNP:rs1801725). {ECO:0000269|PubMed:10023897, ECO:0000269|PubMed:11161843, ECO:0000269|PubMed:14985373, ECO:0000269|PubMed:15531522, ECO:0000269|PubMed:16598859, ECO:0000269|PubMed:17698911, ECO:0000269|PubMed:18756473, ECO:0000269|Ref.5}.		anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	TCAGAAGAACGCCATGGCCCA	0.582													G|||	472	0.0942492	0.0098	0.1066	5008	,	,		20250	0.0367		0.1451	False		,,,				2504	0.2065				p.A996S		Atlas-SNP	.											.	CASR	190	.	0			c.G2986T	GRCh37	CM012741	CASR	M	rs1801725	PASS	.	G	SER/ALA,SER/ALA	179,4227	115.0+/-153.0	1,177,2025	69.0	65.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2956,2986	4.9	0.6	3	dbSNP_89	67	1272,7328	254.3+/-279.6	109,1054,3137	yes	missense,missense	CASR	NM_000388.3,NM_001178065.1	99,99	110,1231,5162	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.7907,4.0626,11.1564	benign,benign	986/1079,996/1089	122003757	1451,11555	2203	4300	6503	SO:0001583	missense	846	exon7			AAGAACGCCATGG	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"""GPCR / Class C : Calcium-sensing receptors"""	1514	protein-coding gene	gene with protein product	"""severe neonatal hyperparathyroidism"""	601199	"""hypocalciuric hypercalcemia 1"""	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.2956G>T	3.37:g.122003757G>T	ENSP00000418685:p.Ala986Ser	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	259	113	0.436293	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	37	CCDS3010.1	166	0.076007326007326	2	0.0040650406504065045	49	0.13535911602209943	10	0.017482517482517484	105	0.13852242744063326	G	10.51	1.370984	0.24771	0.040626	0.147907	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.91237	-2.81;-2.8;-2.81	5.79	4.92	0.64577	.	0.112422	0.64402	D	0.000010	T	0.01627	0.0052	N	0.11201	0.11	0.22989	P	0.99846151	B;B	0.27951	0.195;0.195	B;B	0.22753	0.041;0.041	T	0.52388	-0.8582	9	0.39692	T	0.17	.	13.8067	0.63236	0.0731:0.0:0.9269:0.0	rs1801725;rs17251741;rs17838787;rs60137063;rs1801725	996;986	E7ENE0;P41180	.;CASR_HUMAN	S	986;996;986	ENSP00000418685:A986S;ENSP00000420194:A996S;ENSP00000296154:A986S	ENSP00000296154:A986S	A	+	1	0	CASR	123486447	0.999000	0.42202	0.567000	0.28434	0.776000	0.43924	3.138000	0.50570	1.465000	0.48006	0.561000	0.74099	GCC	G|0.904;T|0.096	0.096	strong		0.582	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388	
PPP1R42	286187	hgsc.bcm.edu	37	8	67926717	67926717	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:67926717T>C	ENST00000324682.5	-	3	384	c.240A>G	c.(238-240)caA>caG	p.Q80Q	PPP1R42_ENST00000517834.1_Intron|PPP1R42_ENST00000522909.1_Silent_p.Q80Q	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	80					regulation of phosphatase activity (GO:0010921)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|manchette (GO:0002177)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)	actin binding (GO:0003779)|dynein binding (GO:0045502)|tubulin binding (GO:0015631)										TACAATTGTTTTGTAGGTACA	0.274																																					p.Q80Q		Atlas-SNP	.											.	PPP1R42	2	.	0			c.A240G						PASS	.						97.0	109.0	105.0					8																	67926717		2203	4294	6497	SO:0001819	synonymous_variant	286187	exon3			ATTGTTTTGTAGG	BC055413	CCDS34902.1	8q13.1-q13.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000178125	ENSG00000178125		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	33732	protein-coding gene	gene with protein product	"""testis leucine-rich repeat"""		"""leucine rich repeat containing 67"""	LRRC67			Standard	NM_001013626		Approved	dtr, TLLR	uc003xxc.3	Q7Z4L9	OTTHUMG00000164745	ENST00000324682.5:c.240A>G	8.37:g.67926717T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	73	60	0.821918	NM_001013626		Silent	SNP	ENST00000324682.5	37	CCDS34902.1																																																																																			.	.	none		0.274	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626	
HIST2H2AB	317772	hgsc.bcm.edu	37	1	149859287	149859287	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:149859287G>A	ENST00000331128.3	-	1	179	c.180C>T	c.(178-180)acC>acT	p.T60T	BOLA1_ENST00000369153.2_5'Flank|HIST2H2BE_ENST00000369155.2_5'Flank	NM_175065.2	NP_778235.1	Q8IUE6	H2A2B_HUMAN	histone cluster 2, H2ab	60						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	15	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GAATTTCCGCGGTCAGGTACT	0.662																																					p.T60T		Atlas-SNP	.											HIST2H2AB,NS,carcinoma,-1,1	HIST2H2AB	49	1	0			c.C180T						scavenged	.						50.0	53.0	52.0					1																	149859287		2203	4300	6503	SO:0001819	synonymous_variant	317772	exon1			TTCCGCGGTCAGG	AY131972	CCDS938.1	1q21.2	2011-01-27	2006-10-11		ENSG00000184270	ENSG00000184270		"""Histones / Replication-dependent"""	20508	protein-coding gene	gene with protein product		615014	"""histone 2, H2ab"""			12408966	Standard	NM_175065		Approved		uc001ete.3	Q8IUE6	OTTHUMG00000012085	ENST00000331128.3:c.180C>T	1.37:g.149859287G>A		Somatic	257	2	0.0077821		WXS	Illumina HiSeq	Phase_I	293	3	0.0102389	NM_175065		Silent	SNP	ENST00000331128.3	37	CCDS938.1																																																																																			.	.	none		0.662	HIST2H2AB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033440.1	NM_175065	
PLXNC1	10154	hgsc.bcm.edu	37	12	94631496	94631496	+	Silent	SNP	C	C	T	rs2230755	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:94631496C>T	ENST00000258526.4	+	10	2286	c.2037C>T	c.(2035-2037)aaC>aaT	p.N679N		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	679					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						GGAAAAGCAACGTGATAGTAA	0.398													C|||	306	0.0611022	0.1566	0.0591	5008	,	,		21079	0.0119		0.0298	False		,,,				2504	0.0164				p.N679N		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C2037T						PASS	.	C		589,3817	259.5+/-263.1	47,495,1661	94.0	80.0	85.0		2037	-3.6	0.9	12	dbSNP_98	85	296,8304	108.8+/-169.4	5,286,4009	no	coding-synonymous	PLXNC1	NM_005761.2		52,781,5670	TT,TC,CC		3.4419,13.3681,6.8046		679/1569	94631496	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon10			AAGCAACGTGATA	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.2037C>T	12.37:g.94631496C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	54	12	0.222222	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			C|0.929;T|0.071	0.071	strong		0.398	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
AKAP9	10142	hgsc.bcm.edu	37	7	91641928	91641928	+	Silent	SNP	A	A	G	rs13245393	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91641928A>G	ENST00000359028.2	+	10	3765	c.3540A>G	c.(3538-3540)gaA>gaG	p.E1180E	AKAP9_ENST00000356239.3_Silent_p.E1168E|AKAP9_ENST00000358100.2_Silent_p.E1180E			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1180					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)			ACCAGTTAGAACTACAGACTA	0.328			T	BRAF	papillary thyroid								G|||	1872	0.373802	0.5076	0.3573	5008	,	,		18366	0.1617		0.3867	False		,,,				2504	0.41				p.E1168E		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.A3504G						PASS	.	G	,	2279,2127	576.6+/-384.3	583,1113,507	75.0	77.0	76.0		3504,3504	-0.3	1.0	7	dbSNP_121	76	3467,5133	632.0+/-398.6	678,2111,1511	no	coding-synonymous,coding-synonymous	AKAP9	NM_005751.4,NM_147185.2	,	1261,3224,2018	GG,GA,AA		40.314,48.2751,44.1796	,	1168/3908,1168/3900	91641928	5746,7260	2203	4300	6503	SO:0001819	synonymous_variant	10142	exon9			GTTAGAACTACAG	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.3540A>G	7.37:g.91641928A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				A|0.589;G|0.411	0.411	strong		0.328	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
CDK18	5129	hgsc.bcm.edu	37	1	205492679	205492679	+	Missense_Mutation	SNP	G	G	A	rs4623769	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:205492679G>A	ENST00000360066.2	+	3	500	c.199G>A	c.(199-201)Ggg>Agg	p.G67R	CDK18_ENST00000509056.1_Intron|CDK18_ENST00000506784.1_Missense_Mutation_p.G67R|CDK18_ENST00000429964.2_Missense_Mutation_p.G67R	NM_002596.3|NM_212502.2|NM_212503.2	NP_002587.2|NP_997667.1|NP_997668.1	Q07002	CDK18_HUMAN	cyclin-dependent kinase 18	65							ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(2)|endometrium(2)|large_intestine(2)|lung(10)|stomach(2)|urinary_tract(1)	19						AACAGACAGCGGGGAGGAGCC	0.677													G|||	503	0.100439	0.171	0.1441	5008	,	,		16267	0.0407		0.0507	False		,,,				2504	0.0869				p.G67R	Pancreas(180;489 2072 28461 40831 44265)	Atlas-SNP	.											.	CDK18	75	.	0			c.G199A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	599,3797		38,523,1637	12.0	14.0	14.0		199,199,199	3.8	0.5	1	dbSNP_111	14	424,8164		12,400,3882	yes	missense,missense,missense	CDK18	NM_002596.3,NM_212502.2,NM_212503.2	125,125,125	50,923,5519	AA,AG,GG		4.9371,13.626,7.8789	benign,benign,benign	67/475,67/475,67/505	205492679	1023,11961	2198	4294	6492	SO:0001583	missense	5129	exon3			GACAGCGGGGAGG	X66362	CCDS1454.1, CCDS44300.1	1q31-q32	2011-11-08	2009-12-16	2009-12-16	ENSG00000117266	ENSG00000117266		"""Cyclin-dependent kinases"""	8751	protein-coding gene	gene with protein product		169190	"""PCTAIRE protein kinase 3"""	PCTK3		1437147, 19884882	Standard	NM_002596		Approved	PCTAIRE3	uc010pri.2	Q07002	OTTHUMG00000037203	ENST00000360066.2:c.199G>A	1.37:g.205492679G>A	ENSP00000353176:p.Gly67Arg	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	326	115	0.352761	NM_212503	Q5VXQ2|Q6V3A2|Q6V3A3|Q96F90	Missense_Mutation	SNP	ENST00000360066.2	37	CCDS44300.1	193	0.08836996336996338	78	0.15853658536585366	43	0.11878453038674033	31	0.05419580419580419	41	0.05408970976253298	G	11.51	1.660892	0.29515	0.13626	0.049371	ENSG00000117266	ENST00000429964;ENST00000506784;ENST00000360066;ENST00000443813;ENST00000419301	T;T;T;T;T	0.70869	-0.4;-0.52;-0.4;1.46;1.33	5.67	3.76	0.43208	.	0.577198	0.17972	N	0.155802	T	0.00440	0.0014	L	0.60455	1.87	0.58432	P	1.0000000000287557E-6	B;B	0.20780	0.048;0.027	B;B	0.15870	0.014;0.008	T	0.14531	-1.0469	9	0.23302	T	0.38	-23.597	9.8988	0.41335	0.1696:0.0:0.8304:0.0	rs4623769;rs58502063;rs4623769	67;67	Q07002-3;Q07002-2	.;.	R	67;67;67;46;67	ENSP00000399082:G67R;ENSP00000423665:G67R;ENSP00000353176:G67R;ENSP00000397831:G46R;ENSP00000391324:G67R	ENSP00000353176:G67R	G	+	1	0	CDK18	203759302	0.950000	0.32346	0.507000	0.27676	0.569000	0.35902	2.371000	0.44248	0.718000	0.32166	0.591000	0.81541	GGG	G|0.915;A|0.085	0.085	strong		0.677	CDK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090407.2	NM_002596	
CILP2	148113	hgsc.bcm.edu	37	19	19654517	19654517	+	Missense_Mutation	SNP	G	G	A	rs146711114	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19654517G>A	ENST00000291495.5	+	8	1248	c.1163G>A	c.(1162-1164)cGg>cAg	p.R388Q	CILP2_ENST00000586018.1_Missense_Mutation_p.R394Q	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	388						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						TGCGACCCCCGGCCCCGAGAG	0.657													G|||	5	0.000998403	0.0	0.0	5008	,	,		15785	0.0		0.001	False		,,,				2504	0.0041				p.R388Q		Atlas-SNP	.											.	CILP2	84	.	0			c.G1163A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	114.0	138.0	130.0		1163	-6.0	0.0	19	dbSNP_134	130	23,8577	15.3+/-51.7	0,23,4277	yes	missense	CILP2	NM_153221.2	43	0,23,6480	AA,AG,GG		0.2674,0.0,0.1768	benign	388/1157	19654517	23,12983	2203	4300	6503	SO:0001583	missense	148113	exon8			ACCCCCGGCCCCG	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1163G>A	19.37:g.19654517G>A	ENSP00000291495:p.Arg388Gln	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	154	68	0.441558	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.673	0.492689	0.12702	0.0	0.002674	ENSG00000160161	ENST00000291495	T	0.53640	0.61	4.22	-5.97	0.02227	.	0.509864	0.19308	N	0.117476	T	0.23572	0.0570	N	0.17082	0.46	0.09310	N	1	B;B	0.11235	0.004;0.004	B;B	0.04013	0.001;0.001	T	0.26395	-1.0104	10	0.11794	T	0.64	-1.2252	13.3923	0.60830	0.3674:0.0:0.6326:0.0	.	388;388	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	Q	388	ENSP00000291495:R388Q	ENSP00000291495:R388Q	R	+	2	0	CILP2	19515517	0.000000	0.05858	0.037000	0.18230	0.449000	0.32228	-1.455000	0.02379	-1.148000	0.02847	-0.465000	0.05216	CGG	G|0.998;A|0.002	0.002	strong		0.657	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20740252	20740252	+	Nonsense_Mutation	SNP	C	C	A	rs199807662		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:20740252C>A	ENST00000427390.2	-	8	1588	c.1498G>T	c.(1498-1500)Gag>Tag	p.E500*		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	500	Gln-rich.|Glu-rich.									NS(3)|endometrium(4)|kidney(1)|skin(3)	11						tcctcctgctcgtgcatcttc	0.562																																					p.E500X		Atlas-SNP	.											.	GOLGA6L6	37	.	0			c.G1498T						PASS	.						12.0	13.0	12.0					15																	20740252		563	1370	1933	SO:0001587	stop_gained	727832	exon8			CCTGCTCGTGCAT	AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1498G>T	15.37:g.20740252C>A	ENSP00000398615:p.Glu500*	Somatic	304	2	0.00657895		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_001145004	D3YTC0	Nonsense_Mutation	SNP	ENST00000427390.2	37	CCDS45184.1	.	.	.	.	.	.	.	.	.	.	C	16.03	3.008530	0.54361	.	.	ENSG00000215405	ENST00000427390	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999956437	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	.	.	.	.	.	.	.	.	X	500	.	ENSP00000398615:E500X	E	-	1	0	GOLGA6L6	19000266	0.546000	0.26457	0.022000	0.16811	0.022000	0.10575	0.233000	0.17911	0.149000	0.19098	0.152000	0.16155	GAG	.	.	weak		0.562	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414660.3	NM_001145004	
FAM162B	221303	hgsc.bcm.edu	37	6	117086378	117086378	+	Missense_Mutation	SNP	C	C	A	rs654128	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:117086378C>A	ENST00000368557.4	-	2	359	c.213G>T	c.(211-213)caG>caT	p.Q71H		NM_001085480.2	NP_001078949.1	Q5T6X4	F162B_HUMAN	family with sequence similarity 162, member B	71			Q -> H (in dbSNP:rs654128).			integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)	6						TCTTGTCGAACTGCGAAGGCC	0.617													C|||	429	0.0856629	0.0787	0.1182	5008	,	,		15996	0.0655		0.1491	False		,,,				2504	0.0276				p.Q71H		Atlas-SNP	.											.	FAM162B	19	.	0			c.G213T						PASS	.	C	HIS/GLN	407,3927		21,365,1781	54.0	61.0	59.0	http://www.ncbi.nlm.nih.gov/pubmed?term	213	-7.3	0.3	6	dbSNP_83	59	1354,7202		116,1122,3040	yes	missense	FAM162B	NM_001085480.2	24	137,1487,4821	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	15.8252,9.3909,13.6618	possibly-damaging	71/163	117086378	1761,11129	2167	4278	6445	SO:0001583	missense	221303	exon2			GTCGAACTGCGAA	BC038997	CCDS43497.1	6q22.31	2014-01-28	2008-06-05	2008-06-05	ENSG00000183807	ENSG00000183807			21549	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 189"""	C6orf189			Standard	NM_001085480		Approved	bA86F4.2	uc003pxi.2	Q5T6X4	OTTHUMG00000015446	ENST00000368557.4:c.213G>T	6.37:g.117086378C>A	ENSP00000357545:p.Gln71His	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	25	8	0.32	NM_001085480	Q8IXW8	Missense_Mutation	SNP	ENST00000368557.4	37	CCDS43497.1	215	0.09844322344322344	37	0.07520325203252033	46	0.1270718232044199	26	0.045454545454545456	106	0.13984168865435356	C	10.99	1.505972	0.26949	0.093909	0.158252	ENSG00000183807	ENST00000368557	T	0.31769	1.48	3.65	-7.29	0.01451	.	0.412070	0.26397	N	0.024604	T	0.15955	0.0384	L	0.41236	1.265	0.52501	P	4.700000000001925E-5	D	0.55385	0.971	P	0.54372	0.75	T	0.14671	-1.0464	9	0.46703	T	0.11	-4.7106	11.3138	0.49379	0.0:0.6433:0.1333:0.2234	rs654128;rs3737130;rs17264045;rs60583751;rs654128	71	Q5T6X4	F162B_HUMAN	H	71	ENSP00000357545:Q71H	ENSP00000357545:Q71H	Q	-	3	2	FAM162B	117193071	0.004000	0.15560	0.346000	0.25655	0.172000	0.22775	-2.282000	0.01156	-1.544000	0.01721	-1.069000	0.02264	CAG	C|0.895;A|0.105	0.105	strong		0.617	FAM162B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041965.1	XM_927381	
CCAR1	55749	hgsc.bcm.edu	37	10	70513684	70513684	+	Silent	SNP	A	A	G	rs5030887	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70513684A>G	ENST00000265872.6	+	11	1313	c.1194A>G	c.(1192-1194)caA>caG	p.Q398Q	SNORD98_ENST00000408255.1_RNA|CCAR1_ENST00000543719.1_Silent_p.Q383Q|CCAR1_ENST00000535016.1_Silent_p.Q383Q	NM_001282959.1|NM_001282960.1|NM_018237.2	NP_001269888.1|NP_001269889.1|NP_060707.2	Q8IX12	CCAR1_HUMAN	cell division cycle and apoptosis regulator 1	398					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(7)|skin(3)	56						TTGATGCTCAATTTACATGGG	0.368													G|||	504	0.100639	0.2912	0.0447	5008	,	,		17921	0.0317		0.003	False		,,,				2504	0.0542				p.Q398Q		Atlas-SNP	.											.	CCAR1	118	.	0			c.A1194G						PASS	.	G		1141,3265	714.8+/-408.4	159,823,1221	194.0	196.0	196.0		1194	5.1	1.0	10	dbSNP_113	196	62,8538	816.5+/-406.9	0,62,4238	no	coding-synonymous	CCAR1	NM_018237.2		159,885,5459	GG,GA,AA		0.7209,25.8965,9.2496		398/1151	70513684	1203,11803	2203	4300	6503	SO:0001819	synonymous_variant	55749	exon11			TGCTCAATTTACA	AY249140	CCDS7282.1, CCDS60547.1	10q22.1	2004-02-19			ENSG00000060339	ENSG00000060339			24236	protein-coding gene	gene with protein product		612569				12816952	Standard	NM_018237		Approved	FLJ10590, CARP-1, CARP1	uc001joo.3	Q8IX12	OTTHUMG00000018361	ENST00000265872.6:c.1194A>G	10.37:g.70513684A>G		Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	183	123	0.672131	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Silent	SNP	ENST00000265872.6	37	CCDS7282.1																																																																																			A|0.900;G|0.100	0.100	strong		0.368	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237	
LDHA	3939	hgsc.bcm.edu	37	11	18422487	18422487	+	Silent	SNP	C	C	A	rs61736803	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18422487C>A	ENST00000422447.3	+	4	621	c.348C>A	c.(346-348)atC>atA	p.I116I	LDHA_ENST00000227157.4_Silent_p.I116I|LDHA_ENST00000396222.2_Silent_p.I116I|LDHA_ENST00000379412.5_Silent_p.I116I|LDHA_ENST00000540430.1_Silent_p.I145I|LDHA_ENST00000542179.1_Silent_p.I116I|LDHA_ENST00000430553.2_Intron	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	116					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|cellular response to extracellular stimulus (GO:0031668)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	L-lactate dehydrogenase activity (GO:0004459)			central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(4)	12						ACGTGAACATCTTTAAATTCA	0.413													C|||	488	0.0974441	0.0469	0.1527	5008	,	,		11417	0.0645		0.1521	False		,,,				2504	0.1043				p.I145I		Atlas-SNP	.											.	LDHA	118	.	0			c.C435A						PASS	.	C	,,,,	333,4065	174.8+/-204.3	17,299,1883	94.0	78.0	84.0		,435,348,348,348	5.0	1.0	11	dbSNP_129	84	1464,7122	279.1+/-293.8	109,1246,2938	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LDHA	NM_001135239.1,NM_001165414.1,NM_001165415.1,NM_001165416.1,NM_005566.3	,,,,	126,1545,4821	AA,AC,CC		17.051,7.5716,13.8401	,,,,	,145/362,116/275,116/242,116/333	18422487	1797,11187	2199	4293	6492	SO:0001819	synonymous_variant	3939	exon4			GAACATCTTTAAA	X02152	CCDS7839.1, CCDS44549.1, CCDS53609.1, CCDS53610.1, CCDS53611.1	11p15.1	2012-10-02			ENSG00000134333	ENSG00000134333	1.1.1.27		6535	protein-coding gene	gene with protein product		150000				3000353	Standard	NM_005566		Approved		uc010rdd.2	P00338	OTTHUMG00000167721	ENST00000422447.3:c.348C>A	11.37:g.18422487C>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_001165414	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Silent	SNP	ENST00000422447.3	37	CCDS7839.1																																																																																			C|0.911;A|0.089	0.089	strong		0.413	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566	
CFAP221	200373	hgsc.bcm.edu	37	2	120383248	120383248	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:120383248A>G	ENST00000413369.3	+	15	1587	c.1500A>G	c.(1498-1500)aaA>aaG	p.K500K	PCDP1_ENST00000602047.1_Silent_p.K214K|PCDP1_ENST00000597189.1_3'UTR	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					GCCAAGCAAAACAATCGATAG	0.428																																					p.K500K		Atlas-SNP	.											.	.	.	.	0			c.A1500G						PASS	.						130.0	111.0	117.0					2																	120383248		2203	4300	6503	SO:0001819	synonymous_variant	0	exon15			AGCAAAACAATCG																												ENST00000413369.3:c.1500A>G	2.37:g.120383248A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	113	36	0.318584	NM_001271049		Silent	SNP	ENST00000413369.3	37	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	A	2.807	-0.247935	0.05867	.	.	ENSG00000163075	ENST00000443972;ENST00000413057	.	.	.	4.45	0.852	0.18995	.	.	.	.	.	T	0.30885	0.0779	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25082	-1.0142	4	.	.	.	-6.3731	6.1027	0.20057	0.6942:0.0:0.3058:0.0	.	.	.	.	S	59;48	.	.	N	+	2	0	AC069154.2	120099718	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	0.160000	0.16462	0.142000	0.18901	0.533000	0.62120	AAC	.	.	none		0.428	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1		
TSPAN32	10077	hgsc.bcm.edu	37	11	2325427	2325427	+	Missense_Mutation	SNP	T	T	C	rs61744929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2325427T>C	ENST00000182290.4	+	3	409	c.272T>C	c.(271-273)aTg>aCg	p.M91T	TSPAN32_ENST00000381121.3_Missense_Mutation_p.M91T|TSPAN32_ENST00000451520.2_Missense_Mutation_p.M80T|C11orf21_ENST00000470369.1_5'Flank|TSPAN32_ENST00000483227.1_3'UTR|C11orf21_ENST00000381153.3_5'Flank	NM_139022.2	NP_620591.3	Q96QS1	TSN32_HUMAN	tetraspanin 32	91					cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|defense response to protozoan (GO:0042832)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|platelet aggregation (GO:0070527)|regulation of defense response to virus (GO:0050688)	cell surface (GO:0009986)|integrin alphaIIb-beta3 complex (GO:0070442)|intracellular (GO:0005622)				breast(1)|central_nervous_system(1)|lung(4)|ovary(1)|skin(1)	8		all_epithelial(84;4.89e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		CAGGGCCTCATGGCAGGGGTG	0.632													T|||	19	0.00379393	0.0015	0.0043	5008	,	,		16077	0.0		0.0099	False		,,,				2504	0.0041				p.M91T		Atlas-SNP	.											.	TSPAN32	19	.	0			c.T272C						PASS	.	T	THR/MET	8,4390		0,8,2191	37.0	34.0	35.0		272	4.1	1.0	11	dbSNP_129	35	119,8465		0,119,4173	yes	missense	TSPAN32	NM_139022.2	81	0,127,6364	CC,CT,TT		1.3863,0.1819,0.9783	benign	91/321	2325427	127,12855	2199	4292	6491	SO:0001583	missense	10077	exon3			GCCTCATGGCAGG	AF176070	CCDS7733.1	11p15	2013-02-14	2005-08-16	2005-08-16	ENSG00000064201	ENSG00000064201		"""Tetraspanins"""	13410	protein-coding gene	gene with protein product		603853	"""pan-hematopoietic expression"""	TSSC6, PHEMX		10072438, 10950922	Standard	NM_139022		Approved		uc001lvy.1	Q96QS1	OTTHUMG00000009762	ENST00000182290.4:c.272T>C	11.37:g.2325427T>C	ENSP00000182290:p.Met91Thr	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_139022	Q96KX4|Q9HC50|Q9HC51|Q9Y5U1	Missense_Mutation	SNP	ENST00000182290.4	37	CCDS7733.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	10.19	1.282156	0.23392	0.001819	0.013863	ENSG00000064201	ENST00000182290;ENST00000381121;ENST00000451520;ENST00000444307;ENST00000381117	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.24	4.12	4.12	0.48240	.	0.146307	0.30649	N	0.009173	T	0.78572	0.4304	L	0.51422	1.61	0.31276	N	0.691117	D;D;P;D;P;D	0.63880	0.993;0.978;0.936;0.991;0.948;0.978	P;P;P;P;P;P	0.60609	0.877;0.649;0.556;0.736;0.684;0.733	T	0.80294	-0.1443	10	0.42905	T	0.14	-24.6332	9.7847	0.40668	0.0:0.0:0.0:1.0	rs61744929	78;91;61;91;91;80	B4DQ90;Q96QS1-5;G3XAG6;Q96QS1-3;Q96QS1;F8WCN6	.;.;.;.;TSN32_HUMAN;.	T	91;91;80;61;61	ENSP00000182290:M91T;ENSP00000370513:M91T;ENSP00000405205:M80T;ENSP00000370509:M61T	ENSP00000182290:M91T	M	+	2	0	TSPAN32	2282003	0.988000	0.35896	1.000000	0.80357	0.169000	0.22640	0.386000	0.20702	1.636000	0.50526	0.443000	0.29094	ATG	T|0.992;C|0.008	0.008	strong		0.632	TSPAN32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026912.2	NM_139024	
DUSP27	92235	hgsc.bcm.edu	37	1	167096931	167096931	+	Missense_Mutation	SNP	A	A	C	rs267746	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:167096931A>C	ENST00000361200.2	+	6	2729	c.2563A>C	c.(2563-2565)Aaa>Caa	p.K855Q	DUSP27_ENST00000443333.1_Missense_Mutation_p.K855Q|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.K855Q			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	855			K -> Q (in dbSNP:rs267746). {ECO:0000269|PubMed:15489334}.		protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GTCTGAGTACAAAATGGAAAA	0.498													A|||	1016	0.202875	0.4138	0.1398	5008	,	,		22916	0.127		0.16	False		,,,				2504	0.0849				p.K855Q		Atlas-SNP	.											.	DUSP27	235	.	0			c.A2563C						PASS	.	A	GLN/LYS	1654,2752	503.5+/-365.6	319,1016,868	70.0	62.0	64.0		2563	3.0	1.0	1	dbSNP_79	64	1479,7121	281.4+/-295.0	128,1223,2949	yes	missense	DUSP27	NM_001080426.1	53	447,2239,3817	CC,CA,AA		17.1977,37.5397,24.0889	benign	855/1159	167096931	3133,9873	2203	4300	6503	SO:0001583	missense	92235	exon5			GAGTACAAAATGG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2563A>C	1.37:g.167096931A>C	ENSP00000354483:p.Lys855Gln	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	434	0.1987179487179487	200	0.4065040650406504	53	0.1464088397790055	73	0.12762237762237763	108	0.1424802110817942	A	1.366	-0.587281	0.03799	0.375397	0.171977	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03242	4.0;4.0;4.0	5.47	2.98	0.34508	.	0.225631	0.36482	N	0.002580	T	0.01156	0.0038	L	0.39898	1.24	0.35006	P	0.24358400000000002	B	0.19706	0.038	B	0.13407	0.009	T	0.40289	-0.9571	9	0.09843	T	0.71	-21.8314	12.2843	0.54783	0.4647:0.5353:0.0:0.0	rs267746;rs59992554;rs267746	855	Q5VZP5	DUS27_HUMAN	Q	855	ENSP00000354483:K855Q;ENSP00000271385:K855Q;ENSP00000404874:K855Q	ENSP00000271385:K855Q	K	+	1	0	DUSP27	165363555	0.999000	0.42202	0.985000	0.45067	0.162000	0.22319	2.360000	0.44151	0.873000	0.35799	-0.485000	0.04761	AAA	A|0.780;C|0.220	0.220	strong		0.498	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
MUC17	140453	hgsc.bcm.edu	37	7	100684573	100684573	+	Silent	SNP	G	G	A	rs144023476	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100684573G>A	ENST00000306151.4	+	3	9940	c.9876G>A	c.(9874-9876)acG>acA	p.T3292T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3292	59 X approximate tandem repeats.|Ser-rich.				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)					GCACCACAACGGTGGCCAGTT	0.512													G|||	172	0.034345	0.0688	0.0072	5008	,	,		27204	0.0298		0.0149	False		,,,				2504	0.0317				p.T3292T		Atlas-SNP	.											MUC17,NS,haematopoietic_neoplasm,0,1	MUC17	804	1	0			c.G9876A						scavenged	.	G		35,4371	28.1+/-56.4	2,31,2170	331.0	330.0	330.0		9876	-2.6	0.0	7	dbSNP_134	330	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	MUC17	NM_001040105.1		2,36,6465	AA,AG,GG		0.0581,0.7944,0.3076		3292/4494	100684573	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACAACGGTGGCC	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.9876G>A	7.37:g.100684573G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	207	22	0.10628	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.984;A|0.016	0.016	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SCFD2	152579	hgsc.bcm.edu	37	4	53751932	53751932	+	Silent	SNP	C	C	T	rs2306600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:53751932C>T	ENST00000401642.3	-	8	2077	c.1944G>A	c.(1942-1944)tcG>tcA	p.S648S	SCFD2_ENST00000388940.4_Silent_p.S603S	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	648					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)					breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CTGGCTTCAACGATGCCACAA	0.547													C|||	719	0.14357	0.1339	0.1455	5008	,	,		20399	0.2341		0.0964	False		,,,				2504	0.1104				p.S648S		Atlas-SNP	.											SCFD2,colon,carcinoma,0,3	SCFD2	78	3	0			c.G1944A						PASS	.	C		633,3773	273.7+/-271.5	48,537,1618	115.0	106.0	109.0		1944	-5.9	0.0	4	dbSNP_100	109	856,7744	195.9+/-241.0	37,782,3481	no	coding-synonymous	SCFD2	NM_152540.3		85,1319,5099	TT,TC,CC		9.9535,14.3668,11.4486		648/685	53751932	1489,11517	2203	4300	6503	SO:0001819	synonymous_variant	152579	exon8			CTTCAACGATGCC	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1944G>A	4.37:g.53751932C>T		Somatic	425	0	0		WXS	Illumina HiSeq	Phase_I	357	161	0.45098	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Silent	SNP	ENST00000401642.3	37	CCDS33984.1																																																																																			C|0.864;T|0.136	0.136	strong		0.547	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
PRR14	78994	hgsc.bcm.edu	37	16	30666367	30666367	+	Missense_Mutation	SNP	C	C	T	rs3747481	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:30666367C>T	ENST00000542965.2	+	7	1532	c.1076C>T	c.(1075-1077)cCg>cTg	p.P359L	PRR14_ENST00000571654.1_Intron|PRR14_ENST00000300835.4_Missense_Mutation_p.P359L			Q9BWN1	PRR14_HUMAN	proline rich 14	359	Pro-rich.		P -> L (in dbSNP:rs3747481). {ECO:0000269|PubMed:15489334}.							breast(3)|endometrium(5)|kidney(1)|large_intestine(3)|lung(5)|skin(1)	18			Colorectal(24;0.103)			CGACCACGGCCGCGGCGGCAC	0.706													C|||	1827	0.364816	0.438	0.2017	5008	,	,		12033	0.1062		0.2773	False		,,,				2504	0.7382				p.P359L		Atlas-SNP	.											.	PRR14	45	.	0			c.C1076T						PASS	.	C	LEU/PRO	1781,2607		360,1061,773	25.0	31.0	29.0		1076	4.4	1.0	16	dbSNP_107	29	2266,6326		306,1654,2336	yes	missense	PRR14	NM_024031.2	98	666,2715,3109	TT,TC,CC		26.3734,40.588,31.1787	probably-damaging	359/586	30666367	4047,8933	2194	4296	6490	SO:0001583	missense	78994	exon8			CACGGCCGCGGCG	AK074783	CCDS10687.1	16p11.2	2008-02-05			ENSG00000156858	ENSG00000156858			28458	protein-coding gene	gene with protein product						12477932	Standard	NM_024031		Approved	MGC3121	uc002dyy.3	Q9BWN1	OTTHUMG00000132414	ENST00000542965.2:c.1076C>T	16.37:g.30666367C>T	ENSP00000441641:p.Pro359Leu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_024031	Q8WTX2	Missense_Mutation	SNP	ENST00000542965.2	37	CCDS10687.1	547	0.25045787545787546	211	0.42886178861788615	76	0.20994475138121546	49	0.08566433566433566	211	0.2783641160949868	C	17.54	3.414049	0.62511	0.40588	0.263734	ENSG00000156858	ENST00000287463;ENST00000300835;ENST00000542965	T;T	0.62639	0.01;0.01	5.37	4.42	0.53409	.	0.646742	0.15365	N	0.266168	T	0.00012	0.0000	M	0.69823	2.125	0.25924	P	0.9830724	B	0.26041	0.14	B	0.23419	0.046	T	0.32719	-0.9896	9	0.49607	T	0.09	-5.2848	7.1976	0.25862	0.1676:0.7454:0.0:0.087	rs3747481;rs17845665;rs17858601;rs60779979;rs3747481	359	Q9BWN1	PRR14_HUMAN	L	332;359;359	ENSP00000300835:P359L;ENSP00000441641:P359L	ENSP00000287463:P332L	P	+	2	0	PRR14	30573868	0.756000	0.28383	0.953000	0.39169	0.994000	0.84299	1.134000	0.31442	1.257000	0.44085	0.563000	0.77884	CCG	C|0.701;T|0.299	0.299	strong		0.706	PRR14-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434433.1	NM_024031	
ZNF175	7728	hgsc.bcm.edu	37	19	52085095	52085095	+	Silent	SNP	G	G	A	rs35431178	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52085095G>A	ENST00000262259.2	+	4	613	c.255G>A	c.(253-255)ccG>ccA	p.P85P	ZNF175_ENST00000436511.2_Silent_p.P85P	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	85	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)		AAAAGGAGCCGCGTGTGGAGG	0.458													g|||	231	0.0461262	0.0303	0.072	5008	,	,		18263	0.002		0.1083	False		,,,				2504	0.0307				p.P85P		Atlas-SNP	.											.	ZNF175	65	.	0			c.G255A						PASS	.	A		172,4234	113.8+/-151.8	3,166,2034	85.0	78.0	80.0		255	-1.2	0.0	19	dbSNP_126	80	992,7608	213.6+/-253.5	62,868,3370	yes	coding-synonymous	ZNF175	NM_007147.2		65,1034,5404	AA,AG,GG		11.5349,3.9038,8.9497		85/712	52085095	1164,11842	2203	4300	6503	SO:0001819	synonymous_variant	7728	exon4			GGAGCCGCGTGTG	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.255G>A	19.37:g.52085095G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	35	0.393258	NM_007147	A8K9H2	Silent	SNP	ENST00000262259.2	37	CCDS12837.1																																																																																			G|0.916;A|0.084	0.084	strong		0.458	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
DERL3	91319	hgsc.bcm.edu	37	22	24179922	24179922	+	Missense_Mutation	SNP	G	G	C	rs3177243	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:24179922G>C	ENST00000318109.7	-	5	463	c.447C>G	c.(445-447)ttC>ttG	p.F149L	DERL3_ENST00000406855.3_Missense_Mutation_p.F149L|DERL3_ENST00000464023.1_5'Flank|DERL3_ENST00000476077.1_Missense_Mutation_p.F149L|DERL3_ENST00000404056.1_Intron			Q96Q80	DERL3_HUMAN	derlin 3	149			F -> L (in dbSNP:rs3177243). {ECO:0000269|Ref.2}.		endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of endoplasmic reticulum membrane (GO:0030176)		p.F149L(1)		ovary(1)|prostate(1)|skin(1)	3						ACGGTGCCTGGAAAGTGAGCA	0.642													G|||	638	0.127396	0.2648	0.1427	5008	,	,		19663	0.0159		0.1431	False		,,,				2504	0.0297				p.F149L		Atlas-SNP	.											DERL3,NS,carcinoma,0,1	DERL3	14	1	1	Substitution - Missense(1)	prostate(1)	c.C447G						scavenged	.	G	LEU/PHE,LEU/PHE,LEU/PHE	1124,3282	391.2+/-328.0	149,826,1228	53.0	54.0	54.0		447,447,447	5.3	1.0	22	dbSNP_105	54	1367,7233	262.5+/-284.5	103,1161,3036	yes	missense,missense,missense	DERL3	NM_001002862.2,NM_001135751.1,NM_198440.3	22,22,22	252,1987,4264	CC,CG,GG		15.8953,25.5107,19.1527	benign,benign,benign	149/236,149/240,149/206	24179922	2491,10515	2203	4300	6503	SO:0001583	missense	91319	exon5			TGCCTGGAAAGTG	AB049213	CCDS33615.1, CCDS42986.1, CCDS46672.1	22q11.23	2012-02-01	2012-02-01	2004-11-02	ENSG00000099958	ENSG00000099958			14236	protein-coding gene	gene with protein product		610305	"""chromosome 22 open reading frame 14"", ""Der1-like domain family, member 3"""	C22orf14		15215855	Standard	NM_198440		Approved	FLJ43842, MGC71803, derlin-3, IZP6	uc002zyk.4	Q96Q80	OTTHUMG00000150743	ENST00000318109.7:c.447C>G	22.37:g.24179922G>C	ENSP00000315303:p.Phe149Leu	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_001135751	F2Z3B6|Q6ICJ6|Q6PEX0|Q6ZUB5	Missense_Mutation	SNP	ENST00000318109.7	37	CCDS33615.1	320	0.14652014652014653	139	0.28252032520325204	54	0.14917127071823205	10	0.017482517482517484	117	0.15435356200527706	G	21.5	4.152228	0.78001	0.255107	0.158953	ENSG00000099958	ENST00000406855;ENST00000318109;ENST00000476077	T;T;T	0.30182	1.54;1.54;1.54	5.27	5.27	0.74061	.	0.109923	0.64402	D	0.000007	T	0.00012	0.0000	M	0.75150	2.29	0.09310	P	0.99999999891888	B;B	0.31581	0.058;0.329	B;B	0.37304	0.105;0.246	T	0.10543	-1.0625	9	0.56958	D	0.05	.	18.3218	0.90241	0.0:0.0:1.0:0.0	rs3177243;rs60204233	149;149	Q96Q80-2;Q96Q80	.;DERL3_HUMAN	L	149	ENSP00000384744:F149L;ENSP00000315303:F149L;ENSP00000419399:F149L	ENSP00000315303:F149L	F	-	3	2	DERL3	22509922	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	3.908000	0.56355	2.655000	0.90218	0.558000	0.71614	TTC	G|0.825;C|0.175	0.175	strong		0.642	DERL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319905.1	NM_198440	
CRELD2	79174	hgsc.bcm.edu	37	22	50313438	50313438	+	Silent	SNP	T	T	C	rs9616388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50313438T>C	ENST00000328268.4	+	3	347	c.273T>C	c.(271-273)aaT>aaC	p.N91N	CRELD2_ENST00000407217.3_Silent_p.N91N|ALG12_ENST00000330817.6_5'Flank|CRELD2_ENST00000403427.3_Silent_p.N91N|CRELD2_ENST00000404488.3_Silent_p.N91N	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	91						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)	p.N91N(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		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;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		TCGAATGCAATCAGATGCTAG	0.562													C|||	1251	0.2498	0.3994	0.1354	5008	,	,		18561	0.1052		0.1978	False		,,,				2504	0.3313				p.N91N		Atlas-SNP	.											CRELD2_ENST00000404488,NS,carcinoma,0,3	CRELD2	57	3	1	Substitution - coding silent(1)	stomach(1)	c.T273C						PASS	.	C	,	1526,2876	658.8+/-400.5	263,1000,938	40.0	41.0	41.0		273,273	3.2	0.7	22	dbSNP_119	41	1682,6918	730.4+/-406.8	176,1330,2794	no	coding-synonymous,coding-synonymous	CRELD2	NM_001135101.1,NM_024324.3	,	439,2330,3732	CC,CT,TT		19.5581,34.6661,24.6731	,	91/403,91/354	50313438	3208,9794	2201	4300	6501	SO:0001819	synonymous_variant	79174	exon3			ATGCAATCAGATG	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.273T>C	22.37:g.50313438T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	141	87	0.617021	NM_024324	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Silent	SNP	ENST00000328268.4	37	CCDS14082.1																																																																																			T|0.754;C|0.246	0.246	strong		0.562	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377092	168377092	+	lincRNA	SNP	G	G	T	rs199609073|rs75642682	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168377092G>T	ENST00000538528.1	-	0	527																											CCTGCAGTGTGGGGGGAGGAG	0.622																																					p.H81N		Atlas-SNP	.											.	.	.	.	0			c.C241A						PASS	.						4.0	6.0	5.0					6																	168377092		630	1507	2137			0	exon1			CAGTGTGGGGGGA																													6.37:g.168377092G>T		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	354	23	0.0649718	NM_001129895		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																				.	.	weak		0.622	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
MUC17	140453	hgsc.bcm.edu	37	7	100682156	100682156	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682156A>G	ENST00000306151.4	+	3	7523	c.7459A>G	c.(7459-7461)Atg>Gtg	p.M2487V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2487	59 X approximate tandem repeats.|Ser-rich.				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)					CAGCACACCTATGACCACTTC	0.493																																					p.M2487V		Atlas-SNP	.											MUC17,bladder,carcinoma,-2,2	MUC17	804	2	0			c.A7459G						scavenged	.						285.0	288.0	287.0					7																	100682156		2203	4300	6503	SO:0001583	missense	140453	exon3			ACACCTATGACCA	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.7459A>G	7.37:g.100682156A>G	ENSP00000302716:p.Met2487Val	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	268	13	0.0485075	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.296	-0.976703	0.02215	.	.	ENSG00000169876	ENST00000306151	T	0.02032	4.49	1.06	-2.02	0.07388	.	.	.	.	.	T	0.00906	0.0030	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46261	-0.9204	9	0.15952	T	0.53	.	4.2578	0.10726	0.345:0.2168:0.4382:0.0	.	2487	Q685J3	MUC17_HUMAN	V	2487	ENSP00000302716:M2487V	ENSP00000302716:M2487V	M	+	1	0	MUC17	100468876	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-3.180000	0.00569	-1.550000	0.01708	-1.389000	0.01157	ATG	.	.	none		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CPZ	8532	hgsc.bcm.edu	37	4	8603117	8603117	+	Missense_Mutation	SNP	A	A	T	rs35993494	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:8603117A>T	ENST00000360986.4	+	3	563	c.389A>T	c.(388-390)cAg>cTg	p.Q130L	CPZ_ENST00000382480.2_5'UTR|CPZ_ENST00000429646.2_5'Flank|CPZ_ENST00000315782.6_Missense_Mutation_p.Q119L|CPZ_ENST00000506287.1_3'UTR	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	130	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		Q -> L (in dbSNP:rs35993494).		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						GAGGTCTGCCAGCCCGCCTTC	0.682													A|||	506	0.101038	0.0408	0.0749	5008	,	,		16996	0.0446		0.162	False		,,,				2504	0.1963				p.Q130L		Atlas-SNP	.											.	CPZ	95	.	0			c.A389T						PASS	.	A	LEU/GLN,,LEU/GLN	321,4077		9,303,1887	24.0	28.0	27.0		389,,356	0.8	1.0	4	dbSNP_126	27	1571,7021		157,1257,2882	yes	missense,utr-5,missense	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	113,,113	166,1560,4769	TT,TA,AA		18.2845,7.2988,14.5651	benign,,benign	130/653,,119/642	8603117	1892,11098	2199	4296	6495	SO:0001583	missense	8532	exon3			TCTGCCAGCCCGC	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.389A>T	4.37:g.8603117A>T	ENSP00000354255:p.Gln130Leu	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	11	5	0.454545	NM_001014447	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	196	0.08974358974358974	20	0.04065040650406504	29	0.08011049723756906	22	0.038461538461538464	125	0.16490765171503957	A	5.045	0.193960	0.09599	0.072988	0.182845	ENSG00000109625	ENST00000360986;ENST00000315782	T;T	0.75821	-0.97;-0.97	3.41	0.837	0.18896	Frizzled domain (5);	0.788238	0.11423	N	0.565573	T	0.00109	0.0003	N	0.05441	-0.05	0.24497	P	0.99427309	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.05194	-1.0900	9	0.02654	T	1	-21.0897	4.2433	0.10660	0.3522:0.0:0.1083:0.5395	rs35993494;rs61734028	119;130	Q66K79-2;Q66K79	.;CBPZ_HUMAN	L	130;119	ENSP00000354255:Q130L;ENSP00000315074:Q119L	ENSP00000315074:Q119L	Q	+	2	0	CPZ	8654017	0.176000	0.23096	0.977000	0.42913	0.179000	0.23085	0.639000	0.24690	-0.007000	0.14345	0.459000	0.35465	CAG	A|0.884;T|0.116	0.116	strong		0.682	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
ASAP3	55616	hgsc.bcm.edu	37	1	23763449	23763449	+	Silent	SNP	G	G	A	rs115515935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:23763449G>A	ENST00000336689.3	-	15	1475	c.1431C>T	c.(1429-1431)cgC>cgT	p.R477R	ASAP3_ENST00000495646.1_5'Flank|ASAP3_ENST00000437606.2_Silent_p.R468R	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	132	0	0		WXS	Illumina HiSeq	Phase_I	90	71	0.788889	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	
ZNF697	90874	hgsc.bcm.edu	37	1	120166528	120166528	+	Silent	SNP	A	A	G	rs374393078		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:120166528A>G	ENST00000421812.2	-	3	557	c.438T>C	c.(436-438)caT>caC	p.H146H		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	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)			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)		CCAGGGAGAGATGTCGCCTCC	0.706																																					p.H146H		Atlas-SNP	.											.	ZNF697	26	.	0			c.T438C						PASS	.	A		1,3997		0,1,1998	15.0	19.0	18.0		438	-2.7	0.9	1		18	0,8274		0,0,4137	no	coding-synonymous	ZNF697	NM_001080470.1		0,1,6135	GG,GA,AA		0.0,0.025,0.0081		146/546	120166528	1,12271	1999	4137	6136	SO:0001819	synonymous_variant	90874	exon3			GGAGAGATGTCGC	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.438T>C	1.37:g.120166528A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	162	40	0.246914	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	37	CCDS44202.1																																																																																			.	.	none		0.706	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	
TFG	10342	hgsc.bcm.edu	37	3	100455433	100455433	+	Silent	SNP	T	T	G	rs12562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:100455433T>G	ENST00000240851.4	+	6	934	c.594T>G	c.(592-594)gcT>gcG	p.A198A	TFG_ENST00000476228.1_Silent_p.A198A|TFG_ENST00000490574.1_Silent_p.A198A|TFG_ENST00000418917.2_Silent_p.A198A	NM_001195478.1|NM_001195479.1|NM_006070.5	NP_001182407.1|NP_001182408.1|NP_006061.2	Q92734	TFG_HUMAN	TRK-fused gene	198					cell death (GO:0008219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	signal transducer activity (GO:0004871)		TFG/NR4A3(2)|TFG/NTRK1_ENST00000392302(5)|TFG/ALK(9)	large_intestine(4)|lung(2)|prostate(1)|stomach(1)	8						CACCCAGTGCTCCTGCAGAAG	0.507			T	"""NTRK1, ALK"""	"""papillary thyroid, ALCL, NSCLC"""								T|||	2	0.000399361	0.0	0.0	5008	,	,		17057	0.0		0.002	False		,,,				2504	0.0				p.A198A		Atlas-SNP	.		Dom	yes		3	3q11-q12	10342	TRK-fused gene		"""E, L"""	.	TFG	42	.	0			c.T594G						PASS	.	T	,,,	9,4397	15.5+/-35.6	0,9,2194	69.0	63.0	65.0		594,594,594,594	2.6	1.0	3	dbSNP_52	65	69,8531	41.7+/-99.0	0,69,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TFG	NM_001007565.2,NM_001195478.1,NM_001195479.1,NM_006070.5	,,,	0,78,6425	GG,GT,TT		0.8023,0.2043,0.5997	,,,	198/401,198/401,198/397,198/401	100455433	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	10342	exon6			CAGTGCTCCTGCA	BC009241	CCDS2939.1, CCDS56266.1	3q12.2	2013-03-13	2001-12-04		ENSG00000114354	ENSG00000114354			11758	protein-coding gene	gene with protein product		602498				9169129, 23479643	Standard	NM_001007565		Approved	TF6, FLJ36137, SPG57	uc003dui.3	Q92734	OTTHUMG00000159085	ENST00000240851.4:c.594T>G	3.37:g.100455433T>G		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	256	132	0.515625	NM_006070	D3DN49|G5E9V1|Q15656|Q969I2	Silent	SNP	ENST00000240851.4	37	CCDS2939.1																																																																																			T|0.993;G|0.007	0.007	strong		0.507	TFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353242.1	NM_006070	
CPO	130749	hgsc.bcm.edu	37	2	207833983	207833983	+	Silent	SNP	A	A	G	rs7582305	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:207833983A>G	ENST00000272852.3	+	9	994	c.948A>G	c.(946-948)acA>acG	p.T316T		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	316						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		ACAGTGGAACATATGGGTTTG	0.512													A|||	1443	0.288139	0.3714	0.2003	5008	,	,		19868	0.2589		0.3032	False		,,,				2504	0.2526				p.T316T		Atlas-SNP	.											CPO,NS,carcinoma,+2,1	CPO	42	1	0			c.A948G						PASS	.	A		1560,2846	489.4+/-361.5	292,976,935	143.0	127.0	132.0		948	-10.3	0.0	2	dbSNP_116	132	2629,5971	424.1+/-354.6	404,1821,2075	no	coding-synonymous	CPO	NM_173077.2		696,2797,3010	GG,GA,AA		30.5698,35.4063,32.2082		316/375	207833983	4189,8817	2203	4300	6503	SO:0001819	synonymous_variant	130749	exon9			TGGAACATATGGG		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.948A>G	2.37:g.207833983A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	116	71	0.612069	NM_173077	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																			A|0.685;G|0.315	0.315	strong		0.512	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
FMO4	2329	hgsc.bcm.edu	37	1	171303810	171303810	+	Missense_Mutation	SNP	C	C	T	rs144578261	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171303810C>T	ENST00000367749.3	+	8	1418	c.1088C>T	c.(1087-1089)gCg>gTg	p.A363V		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	363					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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33	all_cancers(6;3.9e-08)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					CTAGAGAGAGCGACATTAGCC	0.403													C|||	2	0.000399361	0.0	0.0	5008	,	,		19559	0.0		0.0	False		,,,				2504	0.002				p.A363V	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											FMO4,NS,NS,-1,1	FMO4	64	1	0			c.C1088T						scavenged	.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	87.0	88.0	88.0		1088	5.6	0.1	1	dbSNP_134	88	3,8597	3.0+/-9.4	0,3,4297	yes	missense	FMO4	NM_002022.1	64	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	benign	363/559	171303810	4,13002	2203	4300	6503	SO:0001583	missense	2329	exon8			AGAGAGCGACATT	BC002780	CCDS1295.1	1q24.3	2011-08-04			ENSG00000076258	ENSG00000076258	1.14.13.8		3772	protein-coding gene	gene with protein product		136131		FMO2		8311461	Standard	NM_002022		Approved		uc001gho.3	P31512	OTTHUMG00000035506	ENST00000367749.3:c.1088C>T	1.37:g.171303810C>T	ENSP00000356723:p.Ala363Val	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	156	63	0.403846	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.966086	0.53507	2.27E-4	3.49E-4	ENSG00000076258	ENST00000367749	T	0.58060	0.36	5.63	5.63	0.86233	.	0.633406	0.17137	N	0.185613	T	0.43919	0.1269	M	0.66939	2.045	0.38079	D	0.936608	P	0.38048	0.616	B	0.33568	0.166	T	0.56780	-0.7922	10	0.87932	D	0	-2.4899	19.2618	0.93971	0.0:1.0:0.0:0.0	.	363	P31512	FMO4_HUMAN	V	363	ENSP00000356723:A363V	ENSP00000356723:A363V	A	+	2	0	FMO4	169570434	0.106000	0.21978	0.117000	0.21633	0.428000	0.31595	3.801000	0.55545	2.632000	0.89209	0.650000	0.86243	GCG	C|1.000;T|0.000	0.000	weak		0.403	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347398	140347398	+	Silent	SNP	C	C	T	rs12153295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140347398C>T	ENST00000289269.5	+	1	1579	c.1047C>T	c.(1045-1047)tgC>tgT	p.C349C	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000289272.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	349	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(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)			CAGGTCACTGCAAGGTGCTGG	0.572													C|||	381	0.0760783	0.0514	0.1254	5008	,	,		19977	0.0188		0.1451	False		,,,				2504	0.0624				p.C349C	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C1047T						PASS	.	C	,,,,,,,,,,,,,,,,,,	338,4068	177.6+/-206.5	8,322,1873	64.0	56.0	58.0		,1047,,,,,,,,,,,,,,,,,1047	4.7	1.0	5	dbSNP_120	58	1350,7250	264.3+/-285.5	98,1154,3048	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	,,,,,,,,,,,,,,,,,,	106,1476,4921	TT,TC,CC		15.6977,7.6714,12.9786	,,,,,,,,,,,,,,,,,,	,349/1008,,,,,,,,,,,,,,,,,349/885	140347398	1688,11318	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			TCACTGCAAGGTG	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.1047C>T	5.37:g.140347398C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			C|0.881;T|0.119	0.119	strong		0.572	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
PSG11	5680	hgsc.bcm.edu	37	19	43528921	43528921	+	Missense_Mutation	SNP	C	C	G	rs558961472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43528921C>G	ENST00000401740.1	-	2	455	c.352G>C	c.(352-354)Gga>Cga	p.G118R	PSG11_ENST00000320078.7_Missense_Mutation_p.G118R|PSG11_ENST00000403486.1_Intron|PSG11_ENST00000306322.7_Intron			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	118	Ig-like V-type.				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)				GTGTAGGATCCTGCGTCCTCC	0.458													.|||	2	0.000399361	0.0	0.0	5008	,	,		20669	0.0		0.0	False		,,,				2504	0.002				p.G118R		Atlas-SNP	.											PSG11,NS,carcinoma,+2,1	PSG11	57	1	0			c.G352C						scavenged	.						154.0	147.0	150.0					19																	43528921		2199	4294	6493	SO:0001583	missense	5680	exon2			AGGATCCTGCGTC	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.352G>C	19.37:g.43528921C>G	ENSP00000384995:p.Gly118Arg	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	359	27	0.0752089	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	c	10.99	1.507740	0.27036	.	.	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.11821	2.74;2.74	0.929	0.929	0.19449	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.32912	0.0845	M	0.79805	2.47	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.05354	-1.0890	9	0.59425	D	0.04	.	5.2086	0.15304	0.0:1.0:0.0:0.0	.	118	Q9UQ72	PSG11_HUMAN	R	118	ENSP00000319140:G118R;ENSP00000384995:G118R	ENSP00000319140:G118R	G	-	1	0	PSG11	48220761	0.007000	0.16637	0.011000	0.14972	0.029000	0.11900	0.559000	0.23485	0.795000	0.33922	0.184000	0.17185	GGA	.	.	none		0.458	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693003	187693003	+	Missense_Mutation	SNP	A	A	T	rs10195632	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187693003A>T	ENST00000295131.2	-	9	1649	c.1610T>A	c.(1609-1611)tTt>tAt	p.F537Y		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	537				F -> Y (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ACTAGTGTGAAATTTTCCACT	0.398													T|||	872	0.174121	0.4213	0.1066	5008	,	,		15598	0.0208		0.1103	False		,,,				2504	0.1115				p.F537Y		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.T1610A						PASS	.	T	TYR/PHE	1755,2651	643.9+/-397.9	345,1065,793	87.0	82.0	84.0		1610	-0.8	0.0	2	dbSNP_119	84	980,7620	773.6+/-407.7	44,892,3364	yes	missense	ZSWIM2	NM_182521.2	22	389,1957,4157	TT,TA,AA		11.3953,39.832,21.0288	benign	537/634	187693003	2735,10271	2203	4300	6503	SO:0001583	missense	151112	exon9			GTGTGAAATTTTC	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1610T>A	2.37:g.187693003A>T	ENSP00000295131:p.Phe537Tyr	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	223	123	0.55157	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	T	0.003	-2.476034	0.00165	0.39832	0.113953	ENSG00000163012	ENST00000295131	T	0.21031	2.03	4.48	-0.832	0.10785	.	1.451510	0.04341	N	0.354113	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41574	-0.9501	9	0.02654	T	1	2.3903	0.1252	0.00068	0.306:0.1875:0.1577:0.3489	rs10195632;rs17856917;rs52835959;rs10195632	537	Q8NEG5	ZSWM2_HUMAN	Y	537	ENSP00000295131:F537Y	ENSP00000295131:F537Y	F	-	2	0	ZSWIM2	187401248	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.020000	0.03618	-0.653000	0.05401	-0.496000	0.04628	TTT	A|0.813;T|0.187	0.187	strong		0.398	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
MICA	100507436	hgsc.bcm.edu	37	6	31379931	31379931	+	Missense_Mutation	SNP	G	G	A	rs1063635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31379931G>A	ENST00000449934.2	+	4	875	c.821G>A	c.(820-822)cGa>cAa	p.R274Q	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)				AGGATTTGCCGAGGAGAGGAG	0.602													a|||	2921	0.583267	0.7519	0.6196	5008	,	,		19002	0.4226		0.5089	False		,,,				2504	0.5716				p.R274Q		Atlas-SNP	.											.	MICA	21	.	0			c.G821A						PASS	.						20.0	19.0	19.0					6																	31379931		692	1591	2283	SO:0001583	missense	100507436	exon4			TTTGCCGAGGAGA	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.821G>A	6.37:g.31379931G>A	ENSP00000413079:p.Arg274Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	126	69	0.547619	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	N	0.751	-0.772915	0.02951	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.02763	4.17;4.17	2.72	-0.104	0.13605	.	0.817674	0.09786	N	0.756012	T	0.00496	0.0016	.	.	.	0.80722	P	0.0	B;B	0.18610	0.029;0.009	B;B	0.14023	0.01;0.003	T	0.46911	-0.9157	8	0.21540	T	0.41	.	1.3364	0.02145	0.2905:0.4047:0.1327:0.1721	rs1063635;rs16899611;rs17794659;rs17845523;rs17858413;rs17884605;rs1063635	136;274	Q5SS58;Q96QC4	.;.	Q	136;274;231;274;165	ENSP00000413079:R274Q;ENSP00000402410:R165Q	ENSP00000365394:R274Q	R	+	2	0	MICA	31487910	0.000000	0.05858	0.012000	0.15200	0.088000	0.18126	-0.399000	0.07250	-0.066000	0.12998	-0.621000	0.04028	CGA	G|0.488;A|0.512	0.512	strong		0.602	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
EI24	9538	hgsc.bcm.edu	37	11	125452313	125452313	+	Missense_Mutation	SNP	A	A	G	rs4627097	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125452313A>G	ENST00000343678.4	+	10	985	c.743A>G	c.(742-744)cAt>cGt	p.H248R	EI24_ENST00000278903.6_Silent_p.A285A|STT3A-AS1_ENST00000532714.1_RNA|EI24_ENST00000530985.1_3'UTR|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	60	0	0		WXS	Illumina HiSeq	Phase_I	81	52	0.641975	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	
PKDREJ	10343	hgsc.bcm.edu	37	22	46657261	46657261	+	Silent	SNP	A	A	G	rs6007747	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46657261A>G	ENST00000253255.5	-	1	1958	c.1959T>C	c.(1957-1959)gaT>gaC	p.D653D		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	653	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CTCCTAGAGAATCATAGACCT	0.463													G|||	1229	0.245407	0.6785	0.134	5008	,	,		15446	0.001		0.16	False		,,,				2504	0.0787				p.D653D		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T1959C						PASS	.	G		2648,1758		791,1066,346	67.0	74.0	72.0		1959	0.8	0.4	22	dbSNP_114	72	1257,7343		90,1077,3133	no	coding-synonymous	PKDREJ	NM_006071.1		881,2143,3479	GG,GA,AA		14.6163,39.9001,30.0246		653/2254	46657261	3905,9101	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			TAGAGAATCATAG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1959T>C	22.37:g.46657261A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.721;G|0.279	0.279	strong		0.463	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
RAB23	51715	hgsc.bcm.edu	37	6	57055354	57055354	+	Missense_Mutation	SNP	C	C	T	rs1040461	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:57055354C>T	ENST00000317483.3	-	7	1238	c.619G>A	c.(619-621)Ggt>Agt	p.G207S	RAB23_ENST00000468148.1_Missense_Mutation_p.G207S	NM_016277.3	NP_057361.3	Q9ULC3	RAB23_HUMAN	RAB23, member RAS oncogene family	207			G -> S (in dbSNP:rs1040461). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		autophagic vacuole assembly (GO:0000045)|cellular defense response (GO:0006968)|cilium assembly (GO:0042384)|craniofacial suture morphogenesis (GO:0097094)|embryonic digit morphogenesis (GO:0042733)|GTP catabolic process (GO:0006184)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription factor import into nucleus (GO:0042992)|protein transport (GO:0015031)|regulation of smoothened signaling pathway (GO:0008589)|small GTPase mediated signal transduction (GO:0007264)|spinal cord dorsal/ventral patterning (GO:0021513)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	8	Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TTGAGGGTACCTGAATTCTGA	0.428													T|||	578	0.115415	0.1989	0.0937	5008	,	,		18583	0.0883		0.0944	False		,,,				2504	0.0675				p.G207S		Atlas-SNP	.											.	RAB23	22	.	0			c.G619A						PASS	.	T	SER/GLY,SER/GLY	806,3600	749.5+/-412.0	55,696,1452	187.0	173.0	178.0		619,619	5.8	1.0	6	dbSNP_86	178	690,7910	788.2+/-407.6	30,630,3640	yes	missense,missense	RAB23	NM_016277.3,NM_183227.1	56,56	85,1326,5092	TT,TC,CC		8.0233,18.2932,11.5024	benign,benign	207/238,207/238	57055354	1496,11510	2203	4300	6503	SO:0001583	missense	51715	exon7			GGGTACCTGAATT	AB034244	CCDS4962.1	6p12.1	2008-05-15			ENSG00000112210	ENSG00000112210		"""RAB, member RAS oncogene"""	14263	protein-coding gene	gene with protein product		606144					Standard	NM_016277		Approved		uc003pdt.3	Q9ULC3	OTTHUMG00000014918	ENST00000317483.3:c.619G>A	6.37:g.57055354C>T	ENSP00000320413:p.Gly207Ser	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	164	76	0.463415	NM_016277	B2R9I5|Q68DJ6|Q8NI06|Q9P023	Missense_Mutation	SNP	ENST00000317483.3	37	CCDS4962.1	232	0.10622710622710622	88	0.17886178861788618	32	0.08839779005524862	39	0.06818181818181818	73	0.09630606860158311	T	8.357	0.832163	0.16820	0.182932	0.080233	ENSG00000112210	ENST00000317483;ENST00000468148	T;T	0.63744	-0.06;-0.06	5.79	5.79	0.91817	.	0.086937	0.85682	N	0.000000	T	0.11965	0.0291	N	0.01576	-0.805	0.50171	P	1.4199999999997548E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.08743	-1.0707	9	0.02654	T	1	-2.1513	11.9425	0.52909	0.0:0.0678:0.0:0.9322	rs1040461;rs52810972;rs57342085;rs1040461	207	Q9ULC3	RAB23_HUMAN	S	207	ENSP00000320413:G207S;ENSP00000417610:G207S	ENSP00000320413:G207S	G	-	1	0	RAB23	57163313	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.015000	0.57152	1.029000	0.39812	-0.521000	0.04368	GGT	C|0.892;T|0.108	0.108	strong		0.428	RAB23-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041042.1		
ZDHHC4	55146	hgsc.bcm.edu	37	7	6621277	6621277	+	Missense_Mutation	SNP	G	G	A	rs11559146	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:6621277G>A	ENST00000396706.2	+	4	600	c.157G>A	c.(157-159)Gtg>Atg	p.V53M	AC079742.4_ENST00000434951.1_RNA|ZDHHC4_ENST00000396709.1_Missense_Mutation_p.V53M|ZDHHC4_ENST00000405731.3_Missense_Mutation_p.V53M|ZDHHC4_ENST00000396707.2_Missense_Mutation_p.V53M|ZDHHC4_ENST00000396713.2_Missense_Mutation_p.V53M|ZDHHC4_ENST00000335965.6_Missense_Mutation_p.V53M			Q9NPG8	ZDHC4_HUMAN	zinc finger, DHHC-type containing 4	53			V -> M (in dbSNP:rs11559146). {ECO:0000269|Ref.6}.			Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.1)		TCAGAGAGCCGTGCATGGATT	0.353													G|||	1633	0.326078	0.4418	0.3732	5008	,	,		20902	0.2351		0.2813	False		,,,				2504	0.2761				p.V53M		Atlas-SNP	.											.	ZDHHC4	36	.	0			c.G157A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL	1711,2695	515.0+/-368.8	328,1055,820	149.0	143.0	145.0		157,157,157,157	-8.1	0.0	7	dbSNP_120	145	2355,6245	394.1+/-344.6	327,1701,2272	yes	missense,missense,missense,missense	ZDHHC4	NM_001134387.1,NM_001134388.1,NM_001134389.1,NM_018106.3	21,21,21,21	655,2756,3092	AA,AG,GG		27.3837,38.8334,31.2625	benign,benign,benign,benign	53/345,53/345,53/345,53/345	6621277	4066,8940	2203	4300	6503	SO:0001583	missense	55146	exon4			AGAGCCGTGCATG	AF201931	CCDS5352.1	7p22.1	2011-01-11			ENSG00000136247	ENSG00000136247		"""Zinc fingers, DHHC-type"""	18471	protein-coding gene	gene with protein product							Standard	NM_018106		Approved	FLJ10479, ZNF374	uc003sqj.3	Q9NPG8	OTTHUMG00000023579	ENST00000396706.2:c.157G>A	7.37:g.6621277G>A	ENSP00000379934:p.Val53Met	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	333	136	0.408408	NM_018106	A4D2N9|Q53EV7|Q6FIB5|Q9H0R9	Missense_Mutation	SNP	ENST00000396706.2	37	CCDS5352.1	678	0.31043956043956045	216	0.43902439024390244	131	0.36187845303867405	112	0.1958041958041958	219	0.28891820580474936	g	6.178	0.400937	0.11696	0.388334	0.273837	ENSG00000136247	ENST00000405731;ENST00000396713;ENST00000396707;ENST00000335965;ENST00000396709;ENST00000483589;ENST00000396706	T;T;T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27;1.41;1.27	4.61	-8.12	0.01078	.	1.440670	0.03927	N	0.284580	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B;B	0.12013	0.003;0.005	B;B	0.08055	0.002;0.003	T	0.34502	-0.9826	9	0.30078	T	0.28	-34.9452	14.5694	0.68202	0.1382:0.1161:0.7457:0.0	rs11559146;rs28642371;rs59223464	53;53	Q9NPG8;C9J5I9	ZDHC4_HUMAN;.	M	53	ENSP00000385027:V53M;ENSP00000379941:V53M;ENSP00000379935:V53M;ENSP00000337475:V53M;ENSP00000379937:V53M;ENSP00000418496:V53M;ENSP00000379934:V53M	ENSP00000337475:V53M	V	+	1	0	ZDHHC4	6587802	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.776000	0.04674	-1.758000	0.01315	-1.155000	0.01812	GTG	G|0.691;A|0.309	0.309	strong		0.353	ZDHHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207477.3	NM_018106	
CCDC102B	79839	hgsc.bcm.edu	37	18	66678326	66678326	+	Silent	SNP	T	T	C	rs3763951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:66678326T>C	ENST00000360242.5	+	7	1536	c.1419T>C	c.(1417-1419)aaT>aaC	p.N473N	CCDC102B_ENST00000319445.6_Silent_p.N473N|CCDC102B_ENST00000584156.1_Silent_p.N473N	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	473										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)				AGGGACTCAATCAAAAAGAAG	0.363													C|||	419	0.0836661	0.0431	0.085	5008	,	,		17731	0.2341		0.0249	False		,,,				2504	0.0429				p.N473N		Atlas-SNP	.											.	CCDC102B	92	.	0			c.T1419C						PASS	.	C	,	156,4250	810.2+/-416.0	2,152,2049	95.0	92.0	93.0		1419,1419	3.3	0.0	18	dbSNP_107	93	257,8343	807.1+/-407.2	3,251,4046	no	coding-synonymous,coding-synonymous	CCDC102B	NM_001093729.1,NM_024781.2	,	5,403,6095	CC,CT,TT		2.9884,3.5406,3.1755	,	473/514,473/514	66678326	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	79839	exon9			ACTCAATCAAAAA	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.1419T>C	18.37:g.66678326T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Silent	SNP	ENST00000360242.5	37	CCDS11996.2																																																																																			T|0.949;C|0.051	0.051	strong		0.363	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
ACSM5	54988	hgsc.bcm.edu	37	16	20435262	20435262	+	Silent	SNP	T	T	G	rs12103211	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:20435262T>G	ENST00000331849.4	+	6	939	c.792T>G	c.(790-792)tcT>tcG	p.S264S		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	264					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						TGACCGAATCTGACATCTTCT	0.473													G|||	765	0.152756	0.3646	0.0634	5008	,	,		20759	0.0615		0.0487	False		,,,				2504	0.1309				p.S264S		Atlas-SNP	.											.	ACSM5	101	.	0			c.T792G						PASS	.	G		1453,2953	681.4+/-404.0	239,975,989	196.0	183.0	187.0		792	-5.5	0.2	16	dbSNP_120	187	498,8102	796.9+/-407.5	14,470,3816	no	coding-synonymous	ACSM5	NM_017888.2		253,1445,4805	GG,GT,TT		5.7907,32.9778,15.0008		264/580	20435262	1951,11055	2203	4300	6503	SO:0001819	synonymous_variant	54988	exon6			CGAATCTGACATC		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.792T>G	16.37:g.20435262T>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	152	75	0.493421	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Silent	SNP	ENST00000331849.4	37	CCDS10585.1																																																																																			T|0.853;G|0.147	0.147	strong		0.473	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
MUT	4594	hgsc.bcm.edu	37	6	49425446	49425446	+	Silent	SNP	T	T	C	rs138085432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:49425446T>C	ENST00000274813.3	-	3	838	c.711A>G	c.(709-711)ccA>ccG	p.P237P		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	237					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)	TTTTCATGGATGGTTCTGGAG	0.313													T|||	53	0.0105831	0.0023	0.0101	5008	,	,		17146	0.0		0.0129	False		,,,				2504	0.0307				p.P237P		Atlas-SNP	.											.	MUT	70	.	0			c.A711G						PASS	.	T		23,4379	28.1+/-56.4	0,23,2178	57.0	51.0	53.0		711	0.7	1.0	6	dbSNP_134	53	115,8475	58.3+/-119.8	1,113,4181	no	coding-synonymous	MUT	NM_000255.3		1,136,6359	CC,CT,TT		1.3388,0.5225,1.0622		237/751	49425446	138,12854	2201	4295	6496	SO:0001819	synonymous_variant	4594	exon3			CATGGATGGTTCT		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.711A>G	6.37:g.49425446T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Silent	SNP	ENST00000274813.3	37	CCDS4924.1																																																																																			T|0.991;C|0.009	0.009	strong		0.313	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
ZNF555	148254	hgsc.bcm.edu	37	19	2852744	2852744	+	Silent	SNP	C	C	T	rs35627030	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2852744C>T	ENST00000334241.4	+	4	819	c.681C>T	c.(679-681)acC>acT	p.T227T	AC006130.3_ENST00000589365.1_RNA|ZNF555_ENST00000591539.1_Silent_p.T226T	NM_001172775.1|NM_152791.4	NP_001166246.1|NP_690004.4	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	227					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)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)|urinary_tract(4)	23				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)		CTGAGAAAACCTACGAATGTA	0.423													C|||	358	0.0714856	0.0628	0.0706	5008	,	,		23853	0.0		0.1471	False		,,,				2504	0.0798				p.T227T		Atlas-SNP	.											.	ZNF555	61	.	0			c.C681T						PASS	.	C	,	340,4066	178.7+/-207.4	14,312,1877	102.0	90.0	94.0		678,681	-0.2	0.0	19	dbSNP_126	94	1177,7423	239.9+/-270.8	77,1023,3200	no	coding-synonymous,coding-synonymous	ZNF555	NM_001172775.1,NM_152791.4	,	91,1335,5077	TT,TC,CC		13.686,7.7167,11.6638	,	226/628,227/629	2852744	1517,11489	2203	4300	6503	SO:0001819	synonymous_variant	148254	exon4			GAAAACCTACGAA	AL832140	CCDS12096.1, CCDS59329.1	19p13.3	2013-09-20			ENSG00000186300	ENSG00000186300		"""Zinc fingers, C2H2-type"", ""-"""	28382	protein-coding gene	gene with protein product						12477932	Standard	NM_152791		Approved	MGC26707	uc002lwo.3	Q8NEP9	OTTHUMG00000180500	ENST00000334241.4:c.681C>T	19.37:g.2852744C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_152791	A8KA89|K7EQM2|Q8NA46|Q96MP1	Silent	SNP	ENST00000334241.4	37	CCDS12096.1																																																																																			C|0.893;T|0.107	0.107	strong		0.423	ZNF555-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451637.3	NM_152791	
SSH1	54434	hgsc.bcm.edu	37	12	109198832	109198832	+	Splice_Site	SNP	G	G	A	rs140151008	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:109198832G>A	ENST00000326495.5	-	10	1047	c.954C>T	c.(952-954)ctC>ctT	p.L318L	SSH1_ENST00000360239.3_Splice_Site_p.S22L|SSH1_ENST00000326470.5_Splice_Site_p.L329L|SSH1_ENST00000551165.1_Splice_Site_p.L318L	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	318	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						TGCCTCTTACGAGATAAAGAT	0.433													G|||	17	0.00339457	0.0	0.0	5008	,	,		19464	0.0		0.004	False		,,,				2504	0.0133				p.L329L		Atlas-SNP	.											.	SSH1	144	.	0			c.C987T						PASS	.	G	,,	6,4400	12.9+/-30.5	0,6,2197	125.0	118.0	120.0		954,987,954	-1.8	1.0	12	dbSNP_134	120	63,8537	38.8+/-94.9	0,63,4237	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SSH1	NM_001161330.1,NM_001161331.1,NM_018984.3	,,	0,69,6434	AA,AG,GG		0.7326,0.1362,0.5305	,,	318/693,329/704,318/1050	109198832	69,12937	2203	4300	6503	SO:0001630	splice_region_variant	54434	exon9			TCTTACGAGATAA	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.954+1C>T	12.37:g.109198832G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Silent	SNP	ENST00000326495.5	37	CCDS9121.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.44	3.625527	0.66901	0.001362	0.007326	ENSG00000084112	ENST00000360239	D	0.86164	-2.08	5.13	-1.82	0.07857	.	.	.	.	.	T	0.67268	0.2875	.	.	.	0.27735	N	0.944678	B	0.19935	0.04	B	0.06405	0.002	T	0.55798	-0.8084	7	.	.	.	-29.1082	7.2487	0.26138	0.3231:0.4661:0.2108:0.0	.	22	Q8WYL5-4	.	L	22	ENSP00000353374:S22L	.	S	-	2	0	SSH1	107722961	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	1.002000	0.29796	-0.089000	0.12484	0.655000	0.94253	TCG	G|0.996;A|0.004	0.004	strong		0.433	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	Silent
OR51S1	119692	hgsc.bcm.edu	37	11	4870284	4870284	+	Missense_Mutation	SNP	G	G	C	rs35918613	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4870284G>C	ENST00000322101.2	-	1	230	c.155C>G	c.(154-156)aCc>aGc	p.T52S	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	52						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)		CCAGAGGATGGTGCCATTTCC	0.562													G|||	249	0.0497204	0.0136	0.0937	5008	,	,		20000	0.0		0.1481	False		,,,				2504	0.0174				p.T52S		Atlas-SNP	.											.	OR51S1	83	.	0			c.C155G						PASS	.	G	SER/THR	165,4237	109.9+/-148.2	3,159,2039	110.0	89.0	96.0		155	3.2	0.0	11	dbSNP_126	96	1167,7429	239.4+/-270.5	98,971,3229	yes	missense	OR51S1	NM_001004758.1	58	101,1130,5268	CC,CG,GG		13.5761,3.7483,10.2477	possibly-damaging	52/324	4870284	1332,11666	2201	4298	6499	SO:0001583	missense	119692	exon1			AGGATGGTGCCAT	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.155C>G	11.37:g.4870284G>C	ENSP00000322754:p.Thr52Ser	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	287	143	0.498258	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	166	0.076007326007326	8	0.016260162601626018	47	0.1298342541436464	0	0.0	111	0.14643799472295516	G	5.974	0.363637	0.11296	0.037483	0.135761	ENSG00000176922	ENST00000322101	T	0.72167	-0.63	5.12	3.21	0.36854	GPCR, rhodopsin-like superfamily (1);	0.148610	0.31233	N	0.008005	T	0.00552	0.0018	L	0.47190	1.495	0.80722	P	0.0	P	0.35793	0.521	B	0.38378	0.272	T	0.21518	-1.0243	9	0.38643	T	0.18	-10.8146	8.4532	0.32884	0.2454:0.0:0.7546:0.0	rs35918613;rs61744402	52	Q8NGJ8	O51S1_HUMAN	S	52	ENSP00000322754:T52S	ENSP00000322754:T52S	T	-	2	0	OR51S1	4826860	0.000000	0.05858	0.006000	0.13384	0.038000	0.13279	0.091000	0.15046	1.390000	0.46547	0.563000	0.77884	ACC	G|0.898;C|0.102	0.102	strong		0.562	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
TRMU	55687	hgsc.bcm.edu	37	22	46731689	46731689	+	Missense_Mutation	SNP	G	G	T	rs11090865	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46731689G>T	ENST00000290846.4	+	1	368	c.28G>T	c.(28-30)Gcc>Tcc	p.A10S	TRMU_ENST00000381019.3_Missense_Mutation_p.A10S|TRMU_ENST00000424260.2_5'Flank	NM_018006.4	NP_060476.2	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	10			A -> S (decreased activity; dbSNP:rs11090865). {ECO:0000269|PubMed:16826519, ECO:0000269|PubMed:19732863}.		tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|sulfurtransferase activity (GO:0016783)|tRNA binding (GO:0000049)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)	10		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)		CGTCGTGTGCGCCCTGTCCGG	0.751													G|||	529	0.105631	0.2436	0.0692	5008	,	,		10046	0.001		0.1223	False		,,,				2504	0.0358				p.A10S		Atlas-SNP	.											.	TRMU	23	.	0			c.G28T	GRCh37	CM063224	TRMU	M	rs11090865	PASS	.	G	SER/ALA	847,3317		81,685,1316	7.0	9.0	8.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	28	4.5	1.0	22	dbSNP_120	8	805,7339		37,731,3304	yes	missense	TRMU	NM_018006.4	99	118,1416,4620	TT,TG,GG		9.8846,20.341,13.4222	probably-damaging	10/422	46731689	1652,10656	2082	4072	6154	SO:0001583	missense	55687	exon1			GTGTGCGCCCTGT	AY062123	CCDS14075.1, CCDS63510.1	22q13	2005-08-11	2005-08-11	2005-08-11	ENSG00000100416	ENSG00000100416	2.1.1.61		25481	protein-coding gene	gene with protein product		610230	"""tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase """	TRMT		14746906	Standard	XM_005261678		Approved	FLJ10140, MTO2	uc003bhp.3	O75648	OTTHUMG00000150424	ENST00000290846.4:c.28G>T	22.37:g.46731689G>T	ENSP00000290846:p.Ala10Ser	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_018006	A8K3U7|Q05C99|Q5W9C8|Q66K31|Q6ICC3|Q9NWC1	Missense_Mutation	SNP	ENST00000290846.4	37	CCDS14075.1	237	0.10851648351648352	111	0.22560975609756098	32	0.08839779005524862	0	0.0	94	0.12401055408970976	G	34	5.364808	0.95877	0.20341	0.098846	ENSG00000100416	ENST00000290846;ENST00000381019	T;T	0.68479	-0.33;-0.33	4.49	4.49	0.54785	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.00178	0.0005	H	0.94345	3.525	0.09310	P	1.0	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.80764	0.981;0.968;0.994	T	0.02437	-1.1159	9	0.87932	D	0	-6.6109	16.1042	0.81209	0.0:0.0:1.0:0.0	rs11090865;rs11090865	10;10;10	B4DHM1;O75648-2;O75648	.;.;MTU1_HUMAN	S	10	ENSP00000290846:A10S;ENSP00000370407:A10S	ENSP00000290846:A10S	A	+	1	0	TRMU	45110353	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	7.674000	0.83992	2.308000	0.77769	0.467000	0.42956	GCC	G|0.890;T|0.110	0.110	strong		0.751	TRMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318042.2	NM_018006	
GNA14	9630	hgsc.bcm.edu	37	9	80040566	80040566	+	Silent	SNP	C	C	T	rs1801259	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	126	121	0.960317	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		
KALRN	8997	hgsc.bcm.edu	37	3	124351424	124351424	+	Silent	SNP	T	T	C	rs1660038	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:124351424T>C	ENST00000291478.5	+	2	406	c.243T>C	c.(241-243)ctT>ctC	p.L81L	KALRN_ENST00000428018.2_Silent_p.L81L|KALRN_ENST00000393496.1_Silent_p.L151L|KALRN_ENST00000360013.3_Silent_p.L1778L	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1778	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						TGCGTCGGCTTAACAGCGGGA	0.557													C|||	3544	0.707668	0.8048	0.6873	5008	,	,		19108	0.9216		0.5984	False		,,,				2504	0.4826				p.L1778L		Atlas-SNP	.											.	KALRN	556	.	0			c.T5334C						PASS	.	C	,	3337,1069	387.9+/-326.7	1267,803,133	70.0	74.0	73.0		5334,243	1.9	1.0	3	dbSNP_89	73	4925,3675	527.3+/-381.1	1423,2079,798	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_007064.3	,	2690,2882,931	CC,CT,TT		42.7326,24.2624,36.4755	,	1778/2987,81/1290	124351424	8262,4744	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon35			TCGGCTTAACAGC	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	ENST00000291478.5:c.243T>C	3.37:g.124351424T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	1579	0.722985347985348	384	0.7804878048780488	231	0.638121546961326	518	0.9055944055944056	446	0.5883905013192612	C	9.679	1.148701	0.21288	0.757376	0.572674	ENSG00000160145	ENST00000354186	T	0.70516	-0.49	5.04	1.88	0.25563	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999986052	.	.	.	.	.	.	T	0.18398	-1.0338	6	0.87932	D	0	.	6.2538	0.20861	0.0:0.3055:0.4074:0.2871	rs1660038;rs56621483;rs59741739;rs1660038	.	.	.	S	1747	ENSP00000346122:L1747S	ENSP00000346122:L1747S	L	+	2	0	KALRN	125834114	0.998000	0.40836	0.996000	0.52242	0.929000	0.56500	0.388000	0.20735	-0.045000	0.13468	-0.302000	0.09304	TTA	T|0.326;C|0.674	0.674	strong		0.557	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	
KLHL33	123103	hgsc.bcm.edu	37	14	20897064	20897064	+	Missense_Mutation	SNP	C	C	T	rs7145318	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20897064C>T	ENST00000344581.4	-	4	1768	c.1546G>A	c.(1546-1548)Gct>Act	p.A516T		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	516			A -> T (in dbSNP:rs7145318).									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)		TGCTGCACAGCGGGCAGTGTC	0.587													T|||	3232	0.645367	0.7542	0.4957	5008	,	,		19958	0.5972		0.6203	False		,,,				2504	0.68				p.A516T		Atlas-SNP	.											.	KLHL33	37	.	0			c.G1546A						PASS	.	T	THR/ALA	989,395		351,287,54	74.0	71.0	72.0		1546	-1.8	0.0	14	dbSNP_116	72	1835,1347		519,797,275	yes	missense	KLHL33	NM_001109997.2	58	870,1084,329	TT,TC,CC		42.3319,28.5405,38.1516	benign	516/534	20897064	2824,1742	692	1591	2283	SO:0001583	missense	123103	exon4			GCACAGCGGGCAG		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.1546G>A	14.37:g.20897064C>T	ENSP00000341549:p.Ala516Thr	Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	306	181	0.591503	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	37	CCDS53882.1	1363	0.6240842490842491	369	0.75	200	0.5524861878453039	333	0.5821678321678322	461	0.6081794195250659	T	0.067	-1.210039	0.01555	0.714595	0.576681	ENSG00000185271	ENST00000344581	T	0.72394	-0.65	4.98	-1.81	0.07882	.	0.469168	0.19354	N	0.116322	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.39722	-0.9600	9	0.02654	T	1	.	7.0501	0.25069	0.0:0.4489:0.1929:0.3582	rs7145318;rs17211411;rs52824240;rs57617834;rs7145318	516	A6NCF5	KLH33_HUMAN	T	516	ENSP00000341549:A516T	ENSP00000341549:A516T	A	-	1	0	KLHL33	19966904	.	.	0.001000	0.08648	0.763000	0.43281	.	.	-0.418000	0.07450	-0.254000	0.11334	GCT	C|0.365;N|0.001	.	strong		0.587	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
IFRD1	3475	hgsc.bcm.edu	37	7	112112279	112112279	+	Silent	SNP	G	G	A	rs2074796	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:112112279G>A	ENST00000403825.3	+	10	1308	c.1047G>A	c.(1045-1047)cgG>cgA	p.R349R	IFRD1_ENST00000005558.4_Silent_p.R349R|IFRD1_ENST00000535603.1_Silent_p.R299R	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	349					adult somatic muscle development (GO:0007527)|multicellular organismal development (GO:0007275)|myoblast fate determination (GO:0007518)	nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|urinary_tract(1)	15						GTTAGGAACGGGATTTTCCAA	0.378													G|||	1233	0.246206	0.3623	0.1614	5008	,	,		20407	0.1915		0.2525	False		,,,				2504	0.1994				p.R349R		Atlas-SNP	.											IFRD1,NS,carcinoma,+1,2	IFRD1	46	2	0			c.G1047A						scavenged	.	G	,,,	1516,2890	482.1+/-359.3	257,1002,944	118.0	117.0	117.0		1047,897,897,1047	1.7	1.0	7	dbSNP_96	117	2108,6492	362.6+/-332.8	265,1578,2457	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFRD1	NM_001007245.2,NM_001197079.1,NM_001197080.1,NM_001550.3	,,,	522,2580,3401	AA,AG,GG		24.5116,34.4076,27.8641	,,,	349/452,299/402,299/402,349/452	112112279	3624,9382	2203	4300	6503	SO:0001819	synonymous_variant	3475	exon11			GGAACGGGATTTT	Y10313	CCDS34736.1, CCDS56504.1	7q31.1	2005-10-17			ENSG00000006652	ENSG00000006652			5456	protein-coding gene	gene with protein product		603502				9722946	Standard	NM_001550		Approved	PC4, TIS7	uc003vgh.3	O00458	OTTHUMG00000155124	ENST00000403825.3:c.1047G>A	7.37:g.112112279G>A		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	159	88	0.553459	NM_001007245	B7Z5G1|O75234|Q5U013|Q9BVE4	Silent	SNP	ENST00000403825.3	37	CCDS34736.1																																																																																			G|0.736;A|0.264	0.264	strong		0.378	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	
ATXN3	4287	hgsc.bcm.edu	37	14	92537388	92537388	+	Silent	SNP	T	T	C	rs12896589|rs141993435		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:92537388T>C	ENST00000532032.1	-	10	891	c.882A>G	c.(880-882)caA>caG	p.Q294Q	ATXN3_ENST00000503767.1_Silent_p.Q279Q|ATXN3_ENST00000545170.1_Silent_p.Q303Q|ATXN3_ENST00000429774.2_Silent_p.Q287Q|ATXN3_ENST00000393287.5_Silent_p.Q294Q|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000340660.6_Silent_p.Q239Q|ATXN3_ENST00000502250.1_Silent_p.Q115Q			P54252	ATX3_HUMAN	ataxin 3	294	Poly-Gln.				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)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		gttgctgcttttgctgctgTC	0.408																																					p.K133E	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											.	ATXN3	46	.	0			c.A397G						PASS	.						32.0	35.0	34.0					14																	92537388		2200	4298	6498	SO:0001819	synonymous_variant	4287	exon6			CTGCTTTTGCTGC	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.882A>G	14.37:g.92537388T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_001164778	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37																																																																																				T|0.928;C|0.072	0.072	strong		0.408	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
CABS1	85438	hgsc.bcm.edu	37	4	71201943	71201943	+	Silent	SNP	A	A	G	rs13039	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:71201943A>G	ENST00000273936.5	+	1	1261	c.1187A>G	c.(1186-1188)tAa>tGa	p.*396*		NM_033122.3	NP_149113.3	Q96KC9	CABS1_HUMAN	calcium-binding protein, spermatid-specific 1	0					spermatogenesis (GO:0007283)	mitochondrial inner membrane (GO:0005743)|motile cilium (GO:0031514)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(4)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TTCATGATTTAAAAGCAACAA	0.373													G|||	991	0.197883	0.2247	0.1902	5008	,	,		20279	0.1726		0.1948	False		,,,				2504	0.1963				p.X396X		Atlas-SNP	.											.	CABS1	75	.	0			c.A1187G						PASS	.	G		851,3551		74,703,1424	37.0	38.0	38.0		1187	1.9	1.0	4	dbSNP_52	38	1350,7246		99,1152,3047	no	coding-synonymous	CABS1	NM_033122.3		173,1855,4471	GG,GA,AA		15.705,19.3321,16.9334		396/396	71201943	2201,10797	2201	4298	6499	SO:0001819	synonymous_variant	85438	exon1			TGATTTAAAAGCA	AF380838	CCDS3539.1	4q13.3	2013-10-11	2011-01-25	2011-01-25	ENSG00000145309	ENSG00000145309			30710	protein-coding gene	gene with protein product	"""casein-like phosphoprotein"""		"""chromosome 4 open reading frame 35"""	C4orf35		19208547, 19271754	Standard	NM_033122		Approved	NYD-SP26, FLJ32897, CLPH	uc003hff.3	Q96KC9	OTTHUMG00000129405	ENST00000273936.5:c.1187A>G	4.37:g.71201943A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_033122	B2RCB5|Q86UE0|Q96M17	Silent	SNP	ENST00000273936.5	37	CCDS3539.1																																																																																			A|0.812;G|0.188	0.188	strong		0.373	CABS1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251561.3	NM_033122	
GPR1	2825	hgsc.bcm.edu	37	2	207041441	207041441	+	Silent	SNP	G	G	A	rs3732082	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:207041441G>A	ENST00000407325.2	-	3	893	c.531C>T	c.(529-531)gaC>gaT	p.D177D	GPR1_ENST00000437420.1_Silent_p.D177D	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	177					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		ACTCCACAGTGTCCCGGAAGT	0.433													G|||	1729	0.345248	0.4531	0.3112	5008	,	,		20700	0.2569		0.3738	False		,,,				2504	0.2853				p.D177D		Atlas-SNP	.											.	GPR1	38	.	0			c.C531T						PASS	.	G	,	1959,2447	546.9+/-377.1	446,1067,690	77.0	79.0	78.0		531,531	-1.2	0.6	2	dbSNP_107	78	2983,5617	460.2+/-365.1	530,1923,1847	no	coding-synonymous,coding-synonymous	GPR1	NM_001098199.1,NM_005279.3	,	976,2990,2537	AA,AG,GG		34.686,44.4621,37.9978	,	177/356,177/356	207041441	4942,8064	2203	4300	6503	SO:0001819	synonymous_variant	2825	exon3			CACAGTGTCCCGG		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.531C>T	2.37:g.207041441G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	54	43	0.796296	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Silent	SNP	ENST00000407325.2	37	CCDS2368.1																																																																																			G|0.626;A|0.374	0.374	strong		0.433	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
SLC7A2	6542	hgsc.bcm.edu	37	8	17396415	17396415	+	Intron	SNP	G	G	A	rs13259978	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17396415G>A	ENST00000494857.1	+	3	196				SLC7A2_ENST00000004531.10_Missense_Mutation_p.D28N|SLC7A2_ENST00000398090.3_Missense_Mutation_p.D28N|SLC7A2_ENST00000522656.1_Intron|SLC7A2_ENST00000470360.1_Missense_Mutation_p.D28N	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|||	53	0.0105831	0.0015	0.0101	5008	,	,		17605	0.0		0.0358	False		,,,				2504	0.0082				p.D28N		Atlas-SNP	.											.	SLC7A2	157	.	0			c.G82A						PASS	.						99.0	89.0	92.0					8																	17396415		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>A	8.37:g.17396415G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	121	76	0.628099	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	37	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	G	9.073	0.997403	0.19043	.	.	ENSG00000003989	ENST00000470360;ENST00000004531;ENST00000398090	D;D;D	0.88975	-2.45;-2.3;-2.45	3.54	-1.78	0.07957	.	.	.	.	.	T	0.73768	0.3629	.	.	.	0.80722	P	0.0	B;B	0.15141	0.012;0.012	B;B	0.12156	0.007;0.007	T	0.58211	-0.7676	7	0.21540	T	0.41	.	0.5525	0.00665	0.1741:0.3011:0.1787:0.3461	.	28;28	P52569-3;P52569-2	.;.	N	28	ENSP00000419873:D28N;ENSP00000004531:D28N;ENSP00000381164:D28N	ENSP00000004531:D28N	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	0.011	strong		0.413	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046	
CCR4	1233	hgsc.bcm.edu	37	3	32995928	32995928	+	Silent	SNP	C	C	T	rs2228428	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:32995928C>T	ENST00000330953.5	+	2	1182	c.1014C>T	c.(1012-1014)taC>taT	p.Y338Y		NM_005508.4	NP_005499.1	P51679	CCR4_HUMAN	chemokine (C-C motif) receptor 4	338					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuron migration (GO:0001764)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of positive chemotaxis (GO:0050927)|response to antibiotic (GO:0046677)|response to bacterium (GO:0009617)|response to radiation (GO:0009314)|tolerance induction (GO:0002507)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			NS(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)|stomach(1)	16						TCCAAATTTACTCTGCTGACA	0.463													C|||	735	0.146765	0.0356	0.2349	5008	,	,		19281	0.0208		0.3141	False		,,,				2504	0.1922				p.Y338Y		Atlas-SNP	.											.	CCR4	36	.	0			c.C1014T						PASS	.	C		348,4054	164.0+/-195.7	14,320,1867	52.0	52.0	52.0		1014	2.1	0.0	3	dbSNP_98	52	2713,5887	421.9+/-353.9	446,1821,2033	no	coding-synonymous	CCR4	NM_005508.4		460,2141,3900	TT,TC,CC		31.5465,7.9055,23.5425		338/361	32995928	3061,9941	2201	4300	6501	SO:0001819	synonymous_variant	1233	exon2			AATTTACTCTGCT	X85740	CCDS2656.1	3p24-p21.3	2012-08-08			ENSG00000183813	ENSG00000183813		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1605	protein-coding gene	gene with protein product		604836				7642634, 8884276	Standard	NM_005508		Approved	CC-CKR-4, CMKBR4, CKR4, k5-5, ChemR13, CD194	uc003cfg.1	P51679	OTTHUMG00000130752	ENST00000330953.5:c.1014C>T	3.37:g.32995928C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	192	96	0.5	NM_005508	Q9ULY6|Q9ULY7	Silent	SNP	ENST00000330953.5	37	CCDS2656.1																																																																																			C|0.799;T|0.201	0.201	strong		0.463	CCR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253252.2		
SUSD1	64420	hgsc.bcm.edu	37	9	114820741	114820741	+	Silent	SNP	G	G	A	rs2296213	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:114820741G>A	ENST00000374270.3	-	14	2248	c.2076C>T	c.(2074-2076)tgC>tgT	p.C692C	SUSD1_ENST00000374263.3_Silent_p.C692C|SUSD1_ENST00000374264.2_Silent_p.C692C	NM_022486.3	NP_071931.2	Q6UWL2	SUSD1_HUMAN	sushi domain containing 1	692						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						GTAATATAATGCAGTAATCAC	0.368													G|||	263	0.052516	0.0809	0.0216	5008	,	,		22437	0.0724		0.006	False		,,,				2504	0.0634				p.C692C		Atlas-SNP	.											.	SUSD1	51	.	0			c.C2076T						PASS	.	G		309,4097	167.3+/-198.3	6,297,1900	89.0	83.0	85.0		2076	2.7	1.0	9	dbSNP_100	85	87,8513	49.8+/-109.6	0,87,4213	no	coding-synonymous	SUSD1	NM_022486.3		6,384,6113	AA,AG,GG		1.0116,7.0132,3.0447		692/748	114820741	396,12610	2203	4300	6503	SO:0001819	synonymous_variant	64420	exon14			TATAATGCAGTAA	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.2076C>T	9.37:g.114820741G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_022486	A1A4C5|A8KA03|Q5T8V6|Q5T8V7|Q6P9G7|Q8WU83|Q96DM9|Q9H6V2|Q9NTA7	Silent	SNP	ENST00000374270.3	37	CCDS6783.1	82	0.037545787545787544	30	0.06097560975609756	10	0.027624309392265192	38	0.06643356643356643	4	0.005277044854881266	G	9.467	1.094501	0.20471	0.070132	0.010116	ENSG00000106868	ENST00000355396	.	.	.	5.73	2.66	0.31614	.	.	.	.	.	T	0.09862	0.0242	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02917	-1.1094	4	.	.	.	-1.4249	9.7174	0.40283	0.3205:0.0:0.6795:0.0	rs2296213;rs17845639;rs17858571;rs56505675;rs2296213	.	.	.	Y	676	.	.	H	-	1	0	SUSD1	113860562	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	1.735000	0.38176	0.266000	0.21894	0.655000	0.94253	CAT	G|0.966;A|0.034	0.034	strong		0.368	SUSD1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053668.3	NM_022486	
KCNQ3	3786	hgsc.bcm.edu	37	8	133184914	133184914	+	Silent	SNP	G	G	C	rs17575754	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:133184914G>C	ENST00000388996.4	-	7	1491	c.1071C>G	c.(1069-1071)ctC>ctG	p.L357L	KCNQ3_ENST00000519445.1_Silent_p.L357L|KCNQ3_ENST00000521134.1_Silent_p.L237L	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	357					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	CCTGCACCTTGAGGGCCAGCC	0.602													G|||	121	0.0241613	0.003	0.0303	5008	,	,		19240	0.0		0.0835	False		,,,				2504	0.0123				p.L357L		Atlas-SNP	.											.	KCNQ3	164	.	0			c.C1071G						PASS	.	G	,	65,4341	62.3+/-99.4	0,65,2138	145.0	114.0	125.0		711,1071	0.6	1.0	8	dbSNP_123	125	607,7993	158.9+/-212.3	28,551,3721	no	coding-synonymous,coding-synonymous	KCNQ3	NM_001204824.1,NM_004519.3	,	28,616,5859	CC,CG,GG		7.0581,1.4753,5.1668	,	237/753,357/873	133184914	672,12334	2203	4300	6503	SO:0001819	synonymous_variant	3786	exon7			CACCTTGAGGGCC	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1071C>G	8.37:g.133184914G>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																			G|0.954;C|0.046	0.046	strong		0.602	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
CPAMD8	27151	hgsc.bcm.edu	37	19	17088319	17088319	+	Missense_Mutation	SNP	G	G	T	rs3745335	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17088319G>T	ENST00000443236.1	-	15	1789	c.1758C>A	c.(1756-1758)gaC>gaA	p.D586E	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	539						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						TCACACACACGTCGACCTCAG	0.597													g|||	1748	0.349042	0.503	0.3012	5008	,	,		17953	0.2837		0.2863	False		,,,				2504	0.3067				p.D586E		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C1758A						PASS	.	G	GLU/ASP	1694,2282		352,990,646	31.0	38.0	36.0		1758	-4.9	0.0	19	dbSNP_107	36	2249,6059		294,1661,2199	yes	missense	CPAMD8	NM_015692.2	45	646,2651,2845	TT,TG,GG		27.0703,42.6056,32.0987	benign	586/1933	17088319	3943,8341	1988	4154	6142	SO:0001583	missense	27151	exon15			ACACACGTCGACC	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.1758C>A	19.37:g.17088319G>T	ENSP00000402505:p.Asp586Glu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	749|749	0.34294871794871795|0.34294871794871795	244|244	0.4959349593495935|0.4959349593495935	114|114	0.3149171270718232|0.3149171270718232	167|167	0.291958041958042|0.291958041958042	224|224	0.2955145118733509|0.2955145118733509	g|g	1.841|1.841	-0.467320|-0.467320	0.04476|0.04476	0.426056|0.426056	0.270703|0.270703	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|T	.|0.63744	.|-0.06	2.45|2.45	-4.91|-4.91	0.03085|0.03085	Alpha-2-macroglobulin, N-terminal 2 (1);|.	1.225170|.	0.06333|.	U|.	0.706515|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.16307|0.16307	0.4|0.4	0.27253|0.27253	P|P	0.9588331|0.9588331	B|.	0.09022|.	0.002|.	B|.	0.18871|.	0.023|.	T|T	0.38650|0.38650	-0.9651|-0.9651	8|5	0.05620|.	T|.	0.96|.	.|.	1.0551|1.0551	0.01588|0.01588	0.1807:0.1571:0.437:0.2253|0.1807:0.1571:0.437:0.2253	rs3745335;rs57288934;rs3745335|rs3745335;rs57288934;rs3745335	539|.	Q8IZJ3|.	CPMD8_HUMAN|.	E|K	586|597	.|ENSP00000402505:T597K	ENSP00000291440:D586E|.	D|T	-|-	3|2	2|0	CPAMD8|CPAMD8	16949319|16949319	0.133000|0.133000	0.22466|0.22466	0.028000|0.028000	0.17463|0.17463	0.151000|0.151000	0.21798|0.21798	-0.780000|-0.780000	0.04654|0.04654	-2.316000|-2.316000	0.00645|0.00645	-1.631000|-1.631000	0.00782|0.00782	GAC|ACG	.	.	weak		0.597	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
ZNF197	10168	hgsc.bcm.edu	37	3	44683454	44683454	+	Missense_Mutation	SNP	G	G	C	rs148794995	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:44683454G>C	ENST00000396058.1	+	5	999	c.832G>C	c.(832-834)Gac>Cac	p.D278H	RP11-944L7.4_ENST00000457331.1_RNA|ZNF197_ENST00000383745.2_Intron|ZNF197_ENST00000383744.4_Intron|ZNF197_ENST00000344387.4_Missense_Mutation_p.D278H			O14709	ZN197_HUMAN	zinc finger protein 197	278	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(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(1)|skin(1)	25				KIRC - Kidney renal clear cell carcinoma(197;0.0478)|Kidney(197;0.0598)		TCAAAGAGCAGACTCTCATAA	0.428													G|||	5	0.000998403	0.0015	0.0	5008	,	,		20240	0.0		0.003	False		,,,				2504	0.0				p.D278H		Atlas-SNP	.											.	ZNF197	81	.	0			c.G832C						PASS	.	G	,HIS/ASP	5,4401	9.9+/-24.2	0,5,2198	52.0	46.0	48.0		,832	3.5	0.9	3	dbSNP_134	48	29,8571	19.8+/-62.0	0,29,4271	yes	intron,missense	ZNF197	NM_001024855.1,NM_006991.3	,81	0,34,6469	CC,CG,GG		0.3372,0.1135,0.2614	,probably-damaging	,278/1030	44683454	34,12972	2203	4300	6503	SO:0001583	missense	10168	exon6			AGAGCAGACTCTC	AF011573	CCDS2717.1, CCDS33743.1	3p21	2013-01-09	2003-10-07		ENSG00000186448	ENSG00000186448		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12988	protein-coding gene	gene with protein product			"""zinc finger protein 166"""	ZNF166		9380504, 8353497	Standard	XM_005264783		Approved	P18, D3S1363E, ZKSCAN9, ZSCAN41	uc003cnm.3	O14709	OTTHUMG00000133089	ENST00000396058.1:c.832G>C	3.37:g.44683454G>C	ENSP00000379370:p.Asp278His	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_006991	B2RAH8|Q86VG0	Missense_Mutation	SNP	ENST00000396058.1	37	CCDS2717.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.88	2.964376	0.53507	0.001135	0.003372	ENSG00000186448	ENST00000536299;ENST00000344387;ENST00000396058	T;T	0.06449	3.3;3.3	4.4	3.53	0.40419	Krueppel-associated box (1);	0.223039	0.22644	N	0.057419	T	0.05686	0.0149	N	0.14661	0.345	0.24906	N	0.992075	D	0.64830	0.994	P	0.52710	0.707	T	0.33904	-0.9850	10	0.15066	T	0.55	.	6.8742	0.24137	0.2053:0.0:0.7947:0.0	.	278	O14709	ZN197_HUMAN	H	278	ENSP00000345809:D278H;ENSP00000379370:D278H	ENSP00000345809:D278H	D	+	1	0	ZNF197	44658458	0.343000	0.24818	0.927000	0.36925	0.993000	0.82548	3.487000	0.53222	1.209000	0.43321	0.557000	0.71058	GAC	G|0.998;C|0.002	0.002	strong		0.428	ZNF197-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256747.4	NM_006991	
FAM196A	642938	hgsc.bcm.edu	37	10	128974621	128974621	+	Silent	SNP	C	C	T	rs2489386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:128974621C>T	ENST00000522781.1	-	4	594	c.39G>A	c.(37-39)acG>acA	p.T13T	FAM196A_ENST00000424811.2_Silent_p.T13T|DOCK1_ENST00000280333.6_Intron	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	13										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CACTCTCCGACGTTGTGAGTA	0.537													c|||	2647	0.528554	0.2436	0.5634	5008	,	,		17793	0.7401		0.5875	False		,,,				2504	0.6104				p.T13T		Atlas-SNP	.											.	FAM196A	55	.	0			c.G39A						PASS	.	T	,	1262,3144		189,884,1130	91.0	95.0	94.0		39,	-7.7	0.0	10	dbSNP_100	94	5012,3586		1476,2060,763	no	coding-synonymous,intron	DOCK1,FAM196A	NM_001039762.2,NM_001380.3	,	1665,2944,1893	TT,TC,CC		41.7074,28.6428,48.2467	,	13/480,	128974621	6274,6730	2203	4299	6502	SO:0001819	synonymous_variant	642938	exon4			CTCCGACGTTGTG		CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 141"""	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.39G>A	10.37:g.128974621C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	58	0.95082	NM_001039762	B2RNT4|B7ZME7	Silent	SNP	ENST00000522781.1	37	CCDS31312.1																																																																																			C|0.469;T|0.531	0.531	strong		0.537	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762	
PLEC	5339	hgsc.bcm.edu	37	8	145008560	145008560	+	Silent	SNP	A	A	G	rs11783799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145008560A>G	ENST00000322810.4	-	11	1675	c.1506T>C	c.(1504-1506)gaT>gaC	p.D502D	PLEC_ENST00000398774.2_Silent_p.D333D|PLEC_ENST00000527096.1_Silent_p.D388D|PLEC_ENST00000357649.2_Silent_p.D369D|PLEC_ENST00000345136.3_Silent_p.D365D|PLEC_ENST00000356346.3_Silent_p.D351D|PLEC_ENST00000436759.2_Silent_p.D392D|PLEC_ENST00000354958.2_Silent_p.D343D|PLEC_ENST00000354589.3_Silent_p.D365D	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	180	0	0		WXS	Illumina HiSeq	Phase_I	250	138	0.552	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	
KIF2C	11004	hgsc.bcm.edu	37	1	45218895	45218895	+	Silent	SNP	A	A	T	rs3795713	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:45218895A>T	ENST00000372224.4	+	6	644	c.531A>T	c.(529-531)cgA>cgT	p.R177R	KIF2C_ENST00000372222.3_Silent_p.R64R|KIF2C_ENST00000372217.1_Silent_p.R123R|KIF2C_ENST00000493027.1_Intron|KIF2C_ENST00000372218.4_Intron	NM_006845.3	NP_006836.2	Q99661	KIF2C_HUMAN	kinesin family member 2C	177	Globular. {ECO:0000255}.				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)					ATTCCATCCGAGGCAGCTCTT	0.532													a|||	1435	0.286542	0.4818	0.2781	5008	,	,		22360	0.2857		0.1392	False		,,,				2504	0.181				p.R177R		Atlas-SNP	.											KIF2C,NS,carcinoma,+2,1	KIF2C	68	1	0			c.A531T						scavenged	.	A		1963,2443	554.2+/-379.0	456,1051,696	171.0	148.0	156.0		531	1.6	0.9	1	dbSNP_107	156	1457,7143	277.9+/-293.1	130,1197,2973	no	coding-synonymous	KIF2C	NM_006845.3		586,2248,3669	TT,TA,AA		16.9419,44.5529,26.2956		177/726	45218895	3420,9586	2203	4300	6503	SO:0001819	synonymous_variant	11004	exon6			CATCCGAGGCAGC	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.531A>T	1.37:g.45218895A>T		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	90	22	0.244444	NM_006845	B3ITR9|Q5JR88|Q6ICU1|Q96C18|Q96HB8|Q9BWV8	Silent	SNP	ENST00000372224.4	37	CCDS512.1																																																																																			A|0.741;T|0.259	0.259	strong		0.532	KIF2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023180.1	NM_006845	
BEST1	7439	hgsc.bcm.edu	37	11	61730183	61730183	+	Silent	SNP	C	C	T	rs1800008	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:61730183C>T	ENST00000378043.4	+	10	2200	c.1557C>T	c.(1555-1557)agC>agT	p.S519S	BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000449131.2_Silent_p.S459S|BEST1_ENST00000378042.3_Silent_p.S432S|BEST1_ENST00000301774.9_Silent_p.S147S|FTH1_ENST00000529191.1_Intron|FTH1_ENST00000529631.1_Intron	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	83	0	0		WXS	Illumina HiSeq	Phase_I	71	22	0.309859	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	
ARID4B	51742	hgsc.bcm.edu	37	1	235383188	235383188	+	Silent	SNP	A	A	G	rs4659654	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:235383188A>G	ENST00000264183.3	-	16	2000	c.1503T>C	c.(1501-1503)gaT>gaC	p.D501D	ARID4B_ENST00000349213.3_Silent_p.D501D|ARID4B_ENST00000366603.2_Silent_p.D501D	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	501	Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			CATCTTTGTCATCCAGATTTT	0.328													G|||	2261	0.451478	0.4433	0.5115	5008	,	,		15454	0.251		0.4791	False		,,,				2504	0.5982				p.D501D		Atlas-SNP	.											ARID4B_ENST00000264183,NS,carcinoma,0,1	ARID4B	142	1	0			c.T1503C						scavenged	.	G	,,	2101,2305	601.5+/-389.7	494,1113,596	209.0	191.0	197.0		1503,1503,1503	-1.5	0.0	1	dbSNP_111	197	3988,4610	599.8+/-394.1	924,2140,1235	no	coding-synonymous,coding-synonymous,coding-synonymous	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	,,	1418,3253,1831	GG,GA,AA		46.3829,47.685,46.8241	,,	501/1313,501/1313,501/1227	235383188	6089,6915	2203	4299	6502	SO:0001819	synonymous_variant	51742	exon16			TTTGTCATCCAGA	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1503T>C	1.37:g.235383188A>G		Somatic	301	3	0.00996678		WXS	Illumina HiSeq	Phase_I	374	241	0.644385	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	37	CCDS31061.1																																																																																			A|0.549;G|0.451	0.451	strong		0.328	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
COL5A1	1289	hgsc.bcm.edu	37	9	137686951	137686951	+	Silent	SNP	G	G	A	rs41310207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:137686951G>A	ENST00000371817.3	+	33	3138	c.2724G>A	c.(2722-2724)ccG>ccA	p.P908P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	908	Triple-helical region.		P -> L (found in a renal cell carcinoma case; somatic mutation). {ECO:0000269|PubMed:21248752}.		axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AGCCAGGACCGCGGGGGCAGC	0.622													G|||	63	0.0125799	0.0015	0.0187	5008	,	,		15385	0.001		0.0408	False		,,,				2504	0.0061				p.P908P		Atlas-SNP	.											COL5A1,NS,carcinoma,+1,1	COL5A1	323	1	0			c.G2724A						PASS	.	G		23,4383	29.9+/-59.1	0,23,2180	51.0	59.0	56.0		2724	-8.9	1.0	9	dbSNP_127	56	325,8275	114.4+/-174.4	9,307,3984	no	coding-synonymous	COL5A1	NM_000093.3		9,330,6164	AA,AG,GG		3.7791,0.522,2.6757		908/1839	137686951	348,12658	2203	4300	6503	SO:0001819	synonymous_variant	1289	exon33			AGGACCGCGGGGG	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.2724G>A	9.37:g.137686951G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			G|0.975;A|0.025	0.025	strong		0.622	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
MRAP2	112609	hgsc.bcm.edu	37	6	84799185	84799185	+	Silent	SNP	C	C	T	rs2875382	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:84799185C>T	ENST00000257776.4	+	4	738	c.603C>T	c.(601-603)caC>caT	p.H201H		NM_138409.2	NP_612418.2	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	201					energy homeostasis (GO:0097009)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|identical protein binding (GO:0042802)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)	p.H201H(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(4)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	19						AGACCTCACACAAAGACCTGG	0.413													T|||	1749	0.349241	0.711	0.2666	5008	,	,		20311	0.1736		0.2306	False		,,,				2504	0.2219				p.H201H		Atlas-SNP	.											MRAP2,NS,carcinoma,0,1	MRAP2	40	1	1	Substitution - coding silent(1)	stomach(1)	c.C603T						scavenged	.	T		2840,1566	489.9+/-361.6	915,1010,278	94.0	100.0	98.0		603	-0.5	0.0	6	dbSNP_101	98	1802,6798	732.8+/-406.9	196,1410,2694	no	coding-synonymous	MRAP2	NM_138409.2		1111,2420,2972	TT,TC,CC		20.9535,35.5424,35.6912		201/206	84799185	4642,8364	2203	4300	6503	SO:0001819	synonymous_variant	112609	exon4			CTCACACAAAGAC	AK090775	CCDS5001.1	6q14.3	2009-10-06	2008-07-16	2008-07-16	ENSG00000135324	ENSG00000135324			21232	protein-coding gene	gene with protein product		615410	"""chromosome 6 open reading frame 117"""	C6orf117			Standard	NM_138409		Approved	bA51G5.2	uc003pkg.4	Q96G30	OTTHUMG00000015121	ENST00000257776.4:c.603C>T	6.37:g.84799185C>T		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_138409	A8K9M1|Q8IXM9|Q8N2D1	Silent	SNP	ENST00000257776.4	37	CCDS5001.1																																																																																			C|0.654;T|0.346	0.346	strong		0.413	MRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041367.1	NM_138409	
USP25	29761	hgsc.bcm.edu	37	21	17181168	17181168	+	Nonsense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:17181168T>G	ENST00000285679.6	+	8	1190	c.821T>G	c.(820-822)tTa>tGa	p.L274*	USP25_ENST00000400183.2_Nonsense_Mutation_p.L274*|USP25_ENST00000547201.1_3'UTR|USP25_ENST00000351097.5_Intron|USP25_ENST00000285681.2_Nonsense_Mutation_p.L274*	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	274	USP.				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)		TTAGATTGGTTAGAAGATGCC	0.333																																					p.L274X		Atlas-SNP	.											.	USP25	156	.	0			c.T821G						PASS	.						76.0	73.0	74.0					21																	17181168		2203	4300	6503	SO:0001587	stop_gained	29761	exon8			ATTGGTTAGAAGA	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.821T>G	21.37:g.17181168T>G	ENSP00000285679:p.Leu274*	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	80	15	0.1875	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Nonsense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	T	39	7.408059	0.98265	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183	.	.	.	4.83	4.83	0.62350	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7222	0.69314	0.0:0.0:0.0:1.0	.	.	.	.	X	274	.	ENSP00000285679:L274X	L	+	2	0	USP25	16103039	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	1.928000	0.55862	0.482000	0.46254	TTA	.	.	none		0.333	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
CWC27	10283	hgsc.bcm.edu	37	5	64097145	64097145	+	Missense_Mutation	SNP	C	C	G	rs7735338	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:64097145C>G	ENST00000381070.3	+	9	983	c.766C>G	c.(766-768)Cca>Gca	p.P256A	CWC27_ENST00000508024.1_Missense_Mutation_p.P256A	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	256			P -> A (in dbSNP:rs7735338). {ECO:0000269|PubMed:9610721}.		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						AGGTGATGCACCAGATTTAGT	0.219													G|||	2068	0.412939	0.5023	0.2161	5008	,	,		14340	0.5069		0.341	False		,,,				2504	0.409				p.P256A		Atlas-SNP	.											.	CWC27	47	.	0			c.C766G						PASS	.	G	ALA/PRO	1832,2476		420,992,742	22.0	24.0	23.0		766	0.3	0.0	5	dbSNP_116	23	2614,5830		451,1712,2059	yes	missense	CWC27	NM_005869.2	27	871,2704,2801	GG,GC,CC		30.9569,42.5255,34.8651	benign	256/473	64097145	4446,8306	2154	4222	6376	SO:0001583	missense	10283	exon9			GATGCACCAGATT	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.766C>G	5.37:g.64097145C>G	ENSP00000370460:p.Pro256Ala	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	130	62	0.476923	NM_005869	O60529|O60530|Q96EM3	Missense_Mutation	SNP	ENST00000381070.3	37	CCDS3982.2	888	0.4065934065934066	252	0.5121951219512195	90	0.24861878453038674	280	0.48951048951048953	266	0.35092348284960423	G	0.003	-2.554159	0.00138	0.425255	0.309569	ENSG00000153015	ENST00000381070;ENST00000508024;ENST00000538793	T;T	0.38401	1.14;1.14	4.77	0.351	0.16042	.	1.357770	0.04661	N	0.408922	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	0.04013	0.0;0.0;0.0;0.001	T	0.44892	-0.9298	9	0.09084	T	0.74	.	0.394	0.00415	0.2246:0.159:0.2921:0.3243	rs7735338;rs52792258;rs7735338	256;256;256;256	Q6UX04-2;Q6UX04;F5H636;D6REK3	.;CWC27_HUMAN;.;.	A	256	ENSP00000370460:P256A;ENSP00000426802:P256A	ENSP00000370460:P256A	P	+	1	0	CWC27	64132901	0.995000	0.38212	0.032000	0.17829	0.000000	0.00434	0.229000	0.17833	-0.290000	0.09025	-1.721000	0.00707	CCA	C|0.646;G|0.354	0.354	strong		0.219	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
MYLK4	340156	hgsc.bcm.edu	37	6	2749381	2749381	+	Missense_Mutation	SNP	C	C	T	rs2296356	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:2749381C>T	ENST00000274643.7	-	2	490	c.148G>A	c.(148-150)Gga>Aga	p.G50R	MYLK4_ENST00000268446.5_Missense_Mutation_p.G50R	NM_001012418.3	NP_001012418.2	Q86YV6	MYLK4_HUMAN	myosin light chain kinase family, member 4	50			G -> R (in dbSNP:rs2296356). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.			extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|skin(1)	23	Ovarian(93;0.0412)	all_hematologic(90;0.0897)				TCATTATGTCCAGATCTTGAA	0.383													C|||	786	0.156949	0.0325	0.2651	5008	,	,		19893	0.3194		0.1153	False		,,,				2504	0.1237				p.G50R		Atlas-SNP	.											.	MYLK4	74	.	0			c.G148A						PASS	.	C	ARG/GLY	270,4136	153.3+/-186.9	9,252,1942	129.0	134.0	132.0		148	4.8	0.2	6	dbSNP_100	132	1176,7424	239.7+/-270.7	78,1020,3202	yes	missense	MYLK4	NM_001012418.3	125	87,1272,5144	TT,TC,CC		13.6744,6.128,11.1179	possibly-damaging	50/389	2749381	1446,11560	2203	4300	6503	SO:0001583	missense	340156	exon2			TATGTCCAGATCT		CCDS34330.1	6p25.2	2008-01-23			ENSG00000145949	ENSG00000145949			27972	protein-coding gene	gene with protein product	"""caMLCK like"""						Standard	NM_001012418		Approved	SgK085	uc003mty.4	Q86YV6	OTTHUMG00000014121	ENST00000274643.7:c.148G>A	6.37:g.2749381C>T	ENSP00000274643:p.Gly50Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_001012418	A2RUC0|Q5TAW2	Missense_Mutation	SNP	ENST00000274643.7	37	CCDS34330.1	371	0.16987179487179488	20	0.04065040650406504	79	0.21823204419889503	184	0.32167832167832167	88	0.11609498680738786	C	10.14	1.269128	0.23221	0.06128	0.136744	ENSG00000145949	ENST00000268446;ENST00000274643	T;T	0.66638	0.11;-0.22	5.65	4.79	0.61399	.	.	.	.	.	T	0.29882	0.0747	N	0.08118	0	0.38215	P	0.05940500000000004	B	0.16396	0.017	B	0.12837	0.008	T	0.09122	-1.0689	8	0.38643	T	0.18	.	13.8942	0.63761	0.0:0.8476:0.1524:0.0	rs2296356;rs52819487;rs2296356	50	Q86YV6	MYLK4_HUMAN	R	50	ENSP00000268446:G50R;ENSP00000274643:G50R	ENSP00000268446:G50R	G	-	1	0	MYLK4	2694380	0.094000	0.21725	0.169000	0.22859	0.186000	0.23388	2.859000	0.48364	1.398000	0.46701	-0.127000	0.14921	GGA	C|0.865;T|0.135	0.135	strong		0.383	MYLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039632.2	NM_001012418	
PSPH	5723	hgsc.bcm.edu	37	7	56088811	56088811	+	Missense_Mutation	SNP	T	T	C	rs78599516	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:56088811T>C	ENST00000395471.3	-	4	900	c.95A>G	c.(94-96)gAt>gGt	p.D32G	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Missense_Mutation_p.D32G			P78330	SERB_HUMAN	phosphoserine phosphatase	32			D -> N (in PSPHD; dbSNP:rs28933976). {ECO:0000269|PubMed:14673469}.		cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GGCTAGCTCATCGATTCCTTC	0.448																																					p.D32G		Atlas-SNP	.											.	PSPH	23	.	0			c.A95G						PASS	.	T	GLY/ASP	1124,3282		0,1124,1079	142.0	108.0	120.0		95	4.4	1.0	7	dbSNP_132	120	256,8344		0,256,4044	yes	missense	PSPH	NM_004577.3	94	0,1380,5123	CC,CT,TT		2.9767,25.5107,10.6105	possibly-damaging	32/226	56088811	1380,11626	2203	4300	6503	SO:0001583	missense	5723	exon4			AGCTCATCGATTC	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.95A>G	7.37:g.56088811T>C	ENSP00000378854:p.Asp32Gly	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	401	116	0.289277	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	708	0.3241758241758242	240	0.4878048780487805	97	0.26795580110497236	227	0.3968531468531469	144	0.18997361477572558	T	14.84	2.655594	0.47467	0.255107	0.029767	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626;ENST00000419984;ENST00000421312	D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-1.91;-1.91	5.6	4.44	0.53790	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);Phosphoserine phosphatase, domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.96269	3.795	0.80722	D	1	P;P	0.49185	0.92;0.846	D;D	0.65773	0.938;0.938	T	0.00000	-1.3334	10	0.87932	D	0	-27.8562	13.1471	0.59467	0.0:0.069:0.0:0.931	.	32;32	Q53EY1;P78330	.;SERB_HUMAN	G	32	ENSP00000275605:D32G;ENSP00000378854:D32G;ENSP00000398653:D32G;ENSP00000399660:D32G;ENSP00000390952:D32G	ENSP00000275605:D32G	D	-	2	0	PSPH	56056305	1.000000	0.71417	0.988000	0.46212	0.010000	0.07245	6.109000	0.71528	0.409000	0.25649	-1.431000	0.01090	GAT	T|0.746;C|0.254	0.254	strong		0.448	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
EYS	346007	hgsc.bcm.edu	37	6	66204945	66204945	+	Missense_Mutation	SNP	G	G	A	rs12193967	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:66204945G>A	ENST00000370621.3	-	4	885	c.359C>T	c.(358-360)aCg>aTg	p.T120M	EYS_ENST00000370618.3_Missense_Mutation_p.T120M|EYS_ENST00000342421.5_Missense_Mutation_p.T120M|EYS_ENST00000503581.1_Missense_Mutation_p.T120M|EYS_ENST00000370616.2_Missense_Mutation_p.T120M|EYS_ENST00000393380.2_Missense_Mutation_p.T120M			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	120			T -> M (in dbSNP:rs12193967). {ECO:0000269|PubMed:15489334, 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						CTGATCTTCCGTTGTGGTATT	0.363													G|||	853	0.170327	0.0091	0.2378	5008	,	,		21685	0.2411		0.2396	False		,,,				2504	0.1963				p.T120M		Atlas-SNP	.											.	EYS	527	.	0			c.C359T						PASS	.	G	MET/THR,MET/THR,MET/THR	198,4208	122.1+/-159.5	1,196,2006	75.0	70.0	72.0		359,359,359	-1.7	0.0	6	dbSNP_120	72	1891,6709	334.9+/-321.2	219,1453,2628	yes	missense,missense,missense	EYS	NM_198283.1,NM_001142801.1,NM_001142800.1	81,81,81	220,1649,4634	AA,AG,GG		21.9884,4.4939,16.0618	benign,benign,benign	120/595,120/620,120/3145	66204945	2089,10917	2203	4300	6503	SO:0001583	missense	346007	exon4			TCTTCCGTTGTGG		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.359C>T	6.37:g.66204945G>A	ENSP00000359655:p.Thr120Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	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		402	0.18406593406593408	10	0.02032520325203252	71	0.19613259668508287	143	0.25	178	0.23482849604221637	G	12.18	1.859263	0.32884	0.044939	0.219884	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	D;D;D;D;D;D	0.90261	-1.66;-1.65;-1.65;-2.64;-2.6;-2.6	4.92	-1.74	0.08056	.	.	.	.	.	T	0.66752	0.2821	N	0.24115	0.695	0.80722	P	0.0	B;B;B	0.22080	0.063;0.064;0.038	B;B;B	0.19666	0.026;0.008;0.006	T	0.46582	-0.9181	8	0.59425	D	0.04	.	3.9978	0.09566	0.4037:0.0:0.3099:0.2865	rs12193967;rs52829139;rs58893692;rs12193967	120;120;120	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	M	120	ENSP00000424243:T120M;ENSP00000359655:T120M;ENSP00000359650:T120M;ENSP00000377042:T120M;ENSP00000341818:T120M;ENSP00000359652:T120M	ENSP00000341818:T120M	T	-	2	0	EYS	66261666	0.001000	0.12720	0.006000	0.13384	0.581000	0.36288	0.007000	0.13174	-0.672000	0.05266	-0.186000	0.12905	ACG	A|0.168;G|0.832	0.168	strong		0.363	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
TAMM41	132001	hgsc.bcm.edu	37	3	11887993	11887993	+	Missense_Mutation	SNP	G	G	A	rs144232229	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:11887993G>A	ENST00000444133.2	-	1	260	c.118C>T	c.(118-120)Ccg>Tcg	p.P40S	TAMM41_ENST00000273037.5_Missense_Mutation_p.P40S|TAMM41_ENST00000455809.1_Missense_Mutation_p.P40S			Q96BW9	TAM41_HUMAN	TAM41, mitochondrial translocator assembly and maintenance protein, homolog (S. cerevisiae)	40					cardiolipin biosynthetic process (GO:0032049)|CDP-diacylglycerol biosynthetic process (GO:0016024)	extrinsic component of mitochondrial inner membrane (GO:0031314)	phosphatidate cytidylyltransferase activity (GO:0004605)										TCTGAACTCGGCCCTGCCTGG	0.627													G|||	48	0.00958466	0.0008	0.0115	5008	,	,		17354	0.001		0.0239	False		,,,				2504	0.0143				p.P40S		Atlas-SNP	.											.	.	.	.	0			c.C118T						PASS	.						64.0	63.0	64.0					3																	11887993		2203	4300	6503	SO:0001583	missense	132001	exon1			AACTCGGCCCTGC		CCDS2607.1, CCDS68345.1	3p25.2	2013-10-18	2011-08-09	2011-08-09	ENSG00000144559	ENSG00000144559			25187	protein-coding gene	gene with protein product		614948	"""chromosome 3 open reading frame 31"""	C3orf31		19237595	Standard	XM_005264873		Approved	MGC16471, DKFZp434E0519	uc003bwh.3	Q96BW9	OTTHUMG00000129741	ENST00000444133.2:c.118C>T	3.37:g.11887993G>A	ENSP00000388598:p.Pro40Ser	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	148	65	0.439189	NM_138807	B4DIY7|C9J2U4	Missense_Mutation	SNP	ENST00000444133.2	37		23	0.010531135531135532	0	0.0	4	0.011049723756906077	1	0.0017482517482517483	18	0.023746701846965697	G	10.06	1.245903	0.22796	.	.	ENSG00000144559	ENST00000455809;ENST00000273037;ENST00000444133	T;T;T	0.27104	1.69;1.69;1.69	4.71	4.71	0.59529	.	0.256821	0.39274	N	0.001418	T	0.07188	0.0182	N	0.16266	0.395	0.31193	N	0.700731	B;B;B	0.28584	0.216;0.016;0.207	B;B;B	0.29353	0.042;0.013;0.101	T	0.06445	-1.0826	10	0.08837	T	0.75	-16.0459	13.039	0.58889	0.0:0.0:1.0:0.0	.	40;40;40	B4DIY7;C9J2U4;Q96BW9	.;.;TAM41_HUMAN	S	40	ENSP00000398596:P40S;ENSP00000273037:P40S;ENSP00000388598:P40S	ENSP00000273037:P40S	P	-	1	0	TAMM41	11862993	1.000000	0.71417	0.998000	0.56505	0.528000	0.34623	1.028000	0.30128	2.445000	0.82738	0.467000	0.42956	CCG	G|0.984;A|0.016	0.016	strong		0.627	TAMM41-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000339258.2	NM_138807	
CIB1	10519	hgsc.bcm.edu	37	15	90771704	90771704	+	IGR	SNP	G	G	A	rs3751656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:90771704G>A	ENST00000328649.6	-	0	1247				SEMA4B_ENST00000379122.3_Intron|SEMA4B_ENST00000411539.2_Silent_p.P781P|SEMA4B_ENST00000332496.6_Silent_p.P781P	NM_006384.3	NP_006375.2	Q99828	CIB1_HUMAN	calcium and integrin binding 1 (calmyrin)						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to growth factor stimulus (GO:0071363)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to tumor necrosis factor (GO:0071356)|cytoplasmic microtubule organization (GO:0031122)|double-strand break repair (GO:0006302)|endomitotic cell cycle (GO:0007113)|extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|platelet formation (GO:0030220)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of male germ cell proliferation (GO:2000256)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell division (GO:0051302)|regulation of cell proliferation (GO:0042127)|response to ischemia (GO:0002931)|spermatid development (GO:0007286)|thrombopoietin-mediated signaling pathway (GO:0038163)	cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|protein anchor (GO:0043495)|Ras GTPase binding (GO:0017016)			lung(1)|prostate(1)	2	Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303)		BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			CTAGCACCCCGCTCGATCACC	0.652													A|||	1128	0.22524	0.379	0.1729	5008	,	,		15349	0.1062		0.2406	False		,,,				2504	0.1616				p.P781P		Atlas-SNP	.											.	SEMA4B	51	.	0			c.G2343A						PASS	.	A	,	1333,2557		238,857,850	21.0	24.0	23.0		2343,2343	-9.5	0.0	15	dbSNP_107	23	1777,6455		182,1413,2521	no	coding-synonymous,coding-synonymous	SEMA4B	NM_020210.3,NM_198925.2	,	420,2270,3371	AA,AG,GG		21.5865,34.2674,25.6558	,	781/838,781/838	90771704	3110,9012	1945	4116	6061	SO:0001628	intergenic_variant	10509	exon15			CACCCCGCTCGAT	U82226	CCDS10360.1, CCDS73781.1	15q25.3-q26	2013-01-10			ENSG00000185043	ENSG00000185043		"""EF-hand domain containing"""	16920	protein-coding gene	gene with protein product		602293				9030514, 10826701	Standard	NM_006384		Approved	SIP2-28, CALMYRIN, CIB, KIP	uc031qtq.1	Q99828	OTTHUMG00000149808		15.37:g.90771704G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	30	29	0.966667	NM_020210	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Silent	SNP	ENST00000328649.6	37	CCDS10360.1																																																																																			G|0.746;A|0.254	0.254	strong		0.652	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1		
DUSP22	56940	hgsc.bcm.edu	37	6	350829	350829	+	Silent	SNP	G	G	A	rs1129085	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:350829G>A	ENST00000344450.5	+	8	959	c.516G>A	c.(514-516)ccG>ccA	p.P172P	DUSP22_ENST00000419235.2_3'UTR|DUSP22_ENST00000604971.1_3'UTR	NM_020185.3	NP_064570.1	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	172					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		CAGCCGCTCCGGGAATTCTGA	0.403																																					p.P172P		Atlas-SNP	.											.	DUSP22	55	.	0			c.G516A						PASS	.	A		1964,2442		21,1922,260	126.0	121.0	123.0		516	-9.6	0.0	6	dbSNP_86	123	2683,5917		27,2629,1644	no	coding-synonymous	DUSP22	NM_020185.3		48,4551,1904	AA,AG,GG		31.1977,44.5756,35.7297		172/185	350829	4647,8359	2203	4300	6503	SO:0001819	synonymous_variant	56940	exon8			CGCTCCGGGAATT	AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	16077	protein-coding gene	gene with protein product						9205128, 11717427	Standard	NM_001286555		Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000344450.5:c.516G>A	6.37:g.350829G>A		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	314	73	0.232484	NM_020185	B4DK56|Q59GW2|Q5VWR2|Q96AR1	Silent	SNP	ENST00000344450.5	37	CCDS4468.1																																																																																			G|0.581;A|0.419	0.419	strong		0.403	DUSP22-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039621.1	NM_020185	
ATXN3	4287	hgsc.bcm.edu	37	14	92549586	92549586	+	Silent	SNP	G	G	A	rs16999141	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:92549586G>A	ENST00000532032.1	-	7	501	c.492C>T	c.(490-492)gtC>gtT	p.V164V	ATXN3_ENST00000503767.1_Silent_p.V149V|ATXN3_ENST00000545170.1_Silent_p.V164V|ATXN3_ENST00000393287.5_Silent_p.V164V|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000429774.2_Silent_p.V149V|ATXN3_ENST00000340660.6_Silent_p.V109V|ATXN3_ENST00000502250.1_5'UTR			P54252	ATX3_HUMAN	ataxin 3	164	Josephin. {ECO:0000255|PROSITE- ProRule:PRU00331}.				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.V164V(1)		endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		CACCCTTAACGACAAATATAG	0.368													A|||	2838	0.566693	0.736	0.3905	5008	,	,		16657	0.5565		0.4513	False		,,,				2504	0.592				p.V164V	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											ATXN3,NS,carcinoma,0,1	ATXN3	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C492T						PASS	.	A	,,,,,,,,,,,	2945,1461	470.4+/-355.7	991,963,249	79.0	76.0	77.0		447,339,,,,,129,,282,,492,327	3.1	1.0	14	dbSNP_123	77	4099,4501	590.9+/-392.8	998,2103,1199	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,coding-synonymous,utr-5,coding-synonymous,intron,coding-synonymous,coding-synonymous	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	,,,,,,,,,,,	1989,3066,1448	AA,AG,GG		47.6628,33.1593,45.8404	,,,,,,,,,,,	149/347,113/311,,,,,43/241,,94/292,,164/362,109/307	92549586	7044,5962	2203	4300	6503	SO:0001819	synonymous_variant	4287	exon7			CTTAACGACAAAT	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.492C>T	14.37:g.92549586G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Silent	SNP	ENST00000532032.1	37																																																																																				G|0.463;A|0.537	0.537	strong		0.368	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
LIPG	9388	hgsc.bcm.edu	37	18	47093864	47093864	+	Missense_Mutation	SNP	C	C	T	rs2000813	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	107	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	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	
ZKSCAN5	23660	hgsc.bcm.edu	37	7	99128904	99128904	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99128904A>G	ENST00000394170.2	+	7	1803	c.1552A>G	c.(1552-1554)Atg>Gtg	p.M518V	ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.M518V|ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.M518V	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	518					regulation of transcription, DNA-templated (GO:0006355)|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(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GGGAATTCCCATGAAAGAGAT	0.413																																					p.M518V		Atlas-SNP	.											ZKSCAN5,colon,carcinoma,-1,1	ZKSCAN5	63	1	0			c.A1552G						scavenged	.						101.0	104.0	103.0					7																	99128904		2203	4300	6503	SO:0001583	missense	23660	exon7			ATTCCCATGAAAG	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12867	protein-coding gene	gene with protein product		611272	"""zinc finger protein homologous to Zfp95 in mouse"", ""zinc finger protein 95 homolog (mouse)"""	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.1552A>G	7.37:g.99128904A>G	ENSP00000377725:p.Met518Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	249	4	0.0160643	NM_145102	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	.	.	.	.	.	.	.	.	.	.	A	0.018	-1.467276	0.01053	.	.	ENSG00000196652	ENST00000537357;ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.06933	3.24;3.24;3.24	5.06	2.65	0.31530	.	0.280453	0.32081	N	0.006616	T	0.04003	0.0112	N	0.08118	0	0.24609	N	0.993733	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35151	-0.9800	10	0.66056	D	0.02	.	5.454	0.16580	0.7356:0.1747:0.0898:0.0	.	518;518	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	V	518	ENSP00000322872:M518V;ENSP00000392104:M518V;ENSP00000377725:M518V	ENSP00000322872:M518V	M	+	1	0	ZKSCAN5	98966840	0.138000	0.22547	0.828000	0.32881	0.794000	0.44872	0.809000	0.27168	0.480000	0.27534	0.383000	0.25322	ATG	.	.	none		0.413	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569	
KRT77	374454	hgsc.bcm.edu	37	12	53090181	53090181	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53090181G>A	ENST00000341809.3	-	3	820	c.792C>T	c.(790-792)agC>agT	p.S264S	KRT77_ENST00000537195.1_Silent_p.S31S|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	264	Coil 1B.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.S264S(1)		NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						AGTCATTCTCGCTGCCAGTCC	0.567																																					p.S264S		Atlas-SNP	.											KRT77,NS,carcinoma,0,1	KRT77	58	1	1	Substitution - coding silent(1)	lung(1)	c.C792T						scavenged	.						176.0	125.0	142.0					12																	53090181		2203	4300	6503	SO:0001819	synonymous_variant	374454	exon3			ATTCTCGCTGCCA	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.792C>T	12.37:g.53090181G>A		Somatic	51	1	0.0196078		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	37	CCDS8837.1																																																																																			.	.	none		0.567	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078	
UMODL1	89766	hgsc.bcm.edu	37	21	43557559	43557559	+	Silent	SNP	T	T	A	rs3819141	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43557559T>A	ENST00000408910.2	+	22	3786	c.3786T>A	c.(3784-3786)ccT>ccA	p.P1262P	UMODL1_ENST00000408989.2_Silent_p.P1390P|UMODL1_ENST00000400427.1_Silent_p.P1318P|UMODL1_ENST00000400424.2_Silent_p.P1190P|UMODL1_ENST00000400423.2_3'UTR	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1262					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						GTGAGCCTCCTCATGCAGAAG	0.612													A|||	1680	0.335463	0.1785	0.3703	5008	,	,		16653	0.4097		0.3718	False		,,,				2504	0.409				p.P1390P	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.T4170A						PASS	.	A	,,,	875,3285		99,677,1304	145.0	155.0	152.0		3786,3954,3570,4170	-4.8	0.0	21	dbSNP_107	152	3189,5253		592,2005,1624	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	691,2682,2928	AA,AT,TT		37.7754,21.0337,32.2488	,,,	1262/1319,1318/1375,1190/1247,1390/1447	43557559	4064,8538	2080	4221	6301	SO:0001819	synonymous_variant	89766	exon21			GCCTCCTCATGCA		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.3786T>A	21.37:g.43557559T>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	235	62	0.26383	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			T|0.652;A|0.348	0.348	strong		0.612	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
ARHGEF39	84904	hgsc.bcm.edu	37	9	35662251	35662251	+	Missense_Mutation	SNP	T	T	C	rs2297879	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:35662251T>C	ENST00000378387.3	-	8	1034	c.917A>G	c.(916-918)cAt>cGt	p.H306R	ARHGEF39_ENST00000343259.3_Silent_p.S186S|ARHGEF39_ENST00000378395.2_Missense_Mutation_p.H270R|ARHGEF39_ENST00000490970.1_5'UTR	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	306	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		H -> R (in dbSNP:rs2297879).		positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)										TAGCTTCTCATGAGGGAAGGA	0.527													T|||	1531	0.305711	0.0628	0.3545	5008	,	,		20777	0.503		0.325	False		,,,				2504	0.3763				p.H306R		Atlas-SNP	.											.	.	.	.	0			c.A917G						PASS	.	T	ARG/HIS	531,3875	240.9+/-251.5	36,459,1708	112.0	98.0	103.0		917	2.4	0.2	9	dbSNP_100	103	2729,5871	436.5+/-358.3	426,1877,1997	yes	missense	C9orf100	NM_032818.2	29	462,2336,3705	CC,CT,TT		31.7326,12.0517,25.0654	benign	306/336	35662251	3260,9746	2203	4300	6503	SO:0001583	missense	84904	exon8			TTCTCATGAGGGA	AK001187	CCDS6584.2	9p13.3	2012-08-08	2012-08-08	2012-08-08	ENSG00000137135	ENSG00000137135			25909	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 100"""	C9orf100		22327280	Standard	XR_242516		Approved	FLJ14642	uc003zxm.1	Q8N4T4	OTTHUMG00000019869	ENST00000378387.3:c.917A>G	9.37:g.35662251T>C	ENSP00000367638:p.His306Arg	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	131	59	0.450382	NM_032818	Q49AG0|Q6TPQ2|Q96ST6	Missense_Mutation	SNP	ENST00000378387.3	37	CCDS6584.2	724	0.3315018315018315	49	0.09959349593495935	136	0.3756906077348066	285	0.4982517482517482	254	0.33509234828496043	T	5.983	0.365374	0.11352	0.120517	0.317326	ENSG00000137135	ENST00000378387;ENST00000378395	T;T	0.41065	1.01;1.01	5.97	2.39	0.29439	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.34399	P	0.304968	B	0.02656	0.0	B	0.01281	0.0	T	0.47971	-0.9075	8	0.13853	T	0.58	-7.3161	7.5244	0.27647	0.0:0.2434:0.0:0.7566	rs2297879;rs58265228;rs2297879	306	Q8N4T4	CI100_HUMAN	R	306;270	ENSP00000367638:H306R;ENSP00000367648:H270R	ENSP00000367638:H306R	H	-	2	0	C9orf100	35652251	0.163000	0.22920	0.163000	0.22734	0.974000	0.67602	0.418000	0.21230	0.169000	0.19679	-0.250000	0.11733	CAT	T|0.720;C|0.280	0.280	strong		0.527	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052330.1	NM_032818	
SLC25A13	10165	hgsc.bcm.edu	37	7	95800820	95800820	+	Silent	SNP	T	T	C	rs2301629	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:95800820T>C	ENST00000265631.5	-	12	1330	c.1194A>G	c.(1192-1194)ttA>ttG	p.L398L	SLC25A13_ENST00000416240.2_Silent_p.L399L|SLC25A13_ENST00000542654.1_Silent_p.L290L			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	398					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	CAACTCCCAATAACTGTGGCA	0.353													T|||	2049	0.409145	0.2481	0.3357	5008	,	,		19178	0.6071		0.3469	False		,,,				2504	0.5389				p.L399L		Atlas-SNP	.											SLC25A13,caecum,carcinoma,0,1	SLC25A13	131	1	0			c.A1197G						PASS	.	T	,	1175,3231	412.4+/-336.1	170,835,1198	82.0	79.0	80.0		1197,1194	-0.1	1.0	7	dbSNP_100	80	2989,5611	463.7+/-366.0	520,1949,1831	no	coding-synonymous,coding-synonymous	SLC25A13	NM_001160210.1,NM_014251.2	,	690,2784,3029	CC,CT,TT		34.7558,26.6682,32.016	,	399/677,398/676	95800820	4164,8842	2203	4300	6503	SO:0001819	synonymous_variant	10165	exon12			TCCCAATAACTGT	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"""Solute carriers"", ""EF-hand domain containing"""	10983	protein-coding gene	gene with protein product	"""mitochondrial aspartate glutamate carrier 2"""	603859	"""solute carrier family 25, member 13 (citrin)"""	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.1194A>G	7.37:g.95800820T>C		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	244	168	0.688525	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Silent	SNP	ENST00000265631.5	37	CCDS5645.1																																																																																			T|0.645;C|0.355	0.355	strong		0.353	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251	
PTPRJ	5795	hgsc.bcm.edu	37	11	48145166	48145166	+	Splice_Site	SNP	G	G	A	rs2270993	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	75	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	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
ACVR2B	93	hgsc.bcm.edu	37	3	38524664	38524664	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38524664C>T	ENST00000352511.4	+	11	1852	c.1380C>T	c.(1378-1380)tgC>tgT	p.C460C		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	460	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		TCGAGGAGTGCTGGGACCATG	0.587																																					p.C460C		Atlas-SNP	.											ACVR2B_ENST00000352511,NS,carcinoma,0,2	ACVR2B	88	2	0			c.C1380T						scavenged	.						206.0	184.0	192.0					3																	38524664		2203	4300	6503	SO:0001819	synonymous_variant	93	exon11			GGAGTGCTGGGAC	X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.1380C>T	3.37:g.38524664C>T		Somatic	233	2	0.00858369		WXS	Illumina HiSeq	Phase_I	188	2	0.0106383	NM_001106	Q4VAV0	Silent	SNP	ENST00000352511.4	37	CCDS2679.1																																																																																			.	.	none		0.587	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106	
TBC1D2	55357	hgsc.bcm.edu	37	9	100971024	100971024	+	Silent	SNP	G	G	A	rs148143158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100971024G>A	ENST00000375064.1	-	9	2114	c.2076C>T	c.(2074-2076)ccC>ccT	p.P692P	TBC1D2_ENST00000375063.1_Silent_p.P232P|TBC1D2_ENST00000342112.5_Silent_p.P474P|TBC1D2_ENST00000493589.2_5'UTR|TBC1D2_ENST00000375066.5_Silent_p.P692P	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	692	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GGAGCTTGTCGGGGAAGCTGG	0.642													G|||	16	0.00319489	0.0	0.0043	5008	,	,		18428	0.0		0.004	False		,,,				2504	0.0092				p.P692P		Atlas-SNP	.											TBC1D2_ENST00000375063,NS,carcinoma,0,2	TBC1D2	70	2	0			c.C2076T						PASS	.	G		9,4397	14.3+/-33.2	0,9,2194	90.0	89.0	90.0		2076	-2.2	1.0	9	dbSNP_134	90	37,8563	24.6+/-71.5	0,37,4263	yes	coding-synonymous	TBC1D2	NM_018421.3		0,46,6457	AA,AG,GG		0.4302,0.2043,0.3537		692/918	100971024	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	55357	exon9			CTTGTCGGGGAAG	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.2076C>T	9.37:g.100971024G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	245	121	0.493878	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Silent	SNP	ENST00000375064.1	37																																																																																				G|0.996;A|0.004	0.004	strong		0.642	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
KRT5	3852	hgsc.bcm.edu	37	12	52908872	52908872	+	Missense_Mutation	SNP	C	C	T	rs11549949	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	76	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	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		
STAB2	55576	hgsc.bcm.edu	37	12	104086631	104086631	+	Silent	SNP	C	C	T	rs703651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:104086631C>T	ENST00000388887.2	+	31	3543	c.3339C>T	c.(3337-3339)aaC>aaT	p.N1113N		NM_017564.9	NP_060034.9			stabilin 2									p.N1113N(1)		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						ATGGGGACAACGCAGCCACAA	0.448													C|||	2343	0.467851	0.4463	0.4092	5008	,	,		18770	0.5585		0.4632	False		,,,				2504	0.4499				p.N1113N		Atlas-SNP	.											STAB2,rectum,carcinoma,0,2	STAB2	370	2	1	Substitution - coding silent(1)	stomach(1)	c.C3339T						PASS	.	C		1941,2465	550.9+/-378.2	420,1101,682	164.0	139.0	147.0		3339	-9.7	0.0	12	dbSNP_86	147	3825,4775	536.4+/-383.0	839,2147,1314	no	coding-synonymous	STAB2	NM_017564.9		1259,3248,1996	TT,TC,CC		44.4767,44.0536,44.3334		1113/2552	104086631	5766,7240	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon31			GGACAACGCAGCC	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.3339C>T	12.37:g.104086631C>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	205	110	0.536585	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.546;T|0.453	0.453	strong		0.448	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
CCDC107	203260	hgsc.bcm.edu	37	9	35660990	35660990	+	Missense_Mutation	SNP	A	A	G	rs1339374	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:35660990A>G	ENST00000426546.2	+	5	724	c.658A>G	c.(658-660)Att>Gtt	p.I220V	ARHGEF39_ENST00000343259.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000378409.3_Missense_Mutation_p.I193V|CCDC107_ENST00000327351.2_3'UTR|ARHGEF39_ENST00000378387.3_3'UTR|ARHGEF39_ENST00000490970.1_5'Flank|CCDC107_ENST00000378406.1_3'UTR|RMRP_ENST00000602361.1_lincRNA|CCDC107_ENST00000421582.2_3'UTR|CCDC107_ENST00000378407.3_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	220			I -> V (in dbSNP:rs1339374). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.4}.			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)			CGAGGAGGAGATTGGTGACAG	0.552													G|||	4073	0.813299	0.5968	0.8703	5008	,	,		20167	0.9782		0.8181	False		,,,				2504	0.8906				p.I220V		Atlas-SNP	.											.	CCDC107	12	.	0			c.A658G						PASS	.	G	VAL/ILE,,,,VAL/ILE	2784,1622	495.0+/-363.1	903,978,322	89.0	88.0	88.0		577,,,,658	1.2	0.4	9	dbSNP_88	88	6870,1730	313.7+/-311.4	2729,1412,159	yes	missense,utr-3,utr-3,utr-3,missense	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	29,,,,29	3632,2390,481	GG,GA,AA		20.1163,36.8134,25.7727	benign,,,,benign	193/257,,,,220/284	35660990	9654,3352	2203	4300	6503	SO:0001583	missense	203260	exon5			GAGGAGATTGGTG	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.658A>G	9.37:g.35660990A>G	ENSP00000414964:p.Ile220Val	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Missense_Mutation	SNP	ENST00000426546.2	37	CCDS6583.1	1809	0.8282967032967034	317	0.6443089430894309	308	0.850828729281768	566	0.9895104895104895	618	0.8153034300791556	G	0.008	-1.863490	0.00552	0.631866	0.798837	ENSG00000159884	ENST00000426546;ENST00000378409	T;T	0.30448	1.95;1.53	5.08	1.22	0.21188	.	0.730594	0.12230	N	0.487558	T	0.00012	0.0000	N	0.08118	0	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40232	-0.9574	9	0.02654	T	1	1.2077	7.7533	0.28909	0.4372:0.0:0.5628:0.0	rs1339374;rs17856574;rs52795236;rs59175010;rs1339374	193;220	F8W8S5;Q8WV48	.;CC107_HUMAN	V	220;193	ENSP00000414964:I220V;ENSP00000367665:I193V	ENSP00000367665:I193V	I	+	1	0	CCDC107	35650990	0.069000	0.21087	0.364000	0.25888	0.018000	0.09664	-0.106000	0.10890	-0.128000	0.11641	-1.201000	0.01664	ATT	A|0.226;G|0.774	0.774	strong		0.552	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
NKAPL	222698	hgsc.bcm.edu	37	6	28227436	28227436	+	Missense_Mutation	SNP	A	A	G	rs12000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:28227436A>G	ENST00000343684.3	+	1	339	c.287A>G	c.(286-288)tAc>tGc	p.Y96C	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	96			Y -> C (in dbSNP:rs12000). {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						GGATATCGCTACCATCGTCAC	0.572													A|||	2217	0.442692	0.6959	0.353	5008	,	,		19456	0.4444		0.2167	False		,,,				2504	0.3947				p.Y96C		Atlas-SNP	.											.	NKAPL	72	.	0			c.A287G						PASS	.	A	CYS/TYR	2555,1851	634.6+/-396.2	755,1045,403	61.0	61.0	61.0		287	1.9	0.0	6	dbSNP_52	61	1757,6843	317.8+/-313.4	171,1415,2714	yes	missense	NKAPL	NM_001007531.1	194	926,2460,3117	GG,GA,AA		20.4302,42.0109,33.1539	benign	96/403	28227436	4312,8694	2203	4300	6503	SO:0001583	missense	222698	exon1			ATCGCTACCATCG	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.287A>G	6.37:g.28227436A>G	ENSP00000345716:p.Tyr96Cys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	883	0.4043040293040293	350	0.7113821138211383	135	0.3729281767955801	248	0.43356643356643354	150	0.19788918205804748	A	10.43	1.347619	0.24426	0.579891	0.204302	ENSG00000189134	ENST00000343684	T	0.14516	2.5	4.31	1.87	0.25490	.	0.882652	0.09597	N	0.780706	T	0.02494	0.0076	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.43734	-0.9373	9	0.39692	T	0.17	-1.0519	3.6366	0.08151	0.7037:0.0:0.1045:0.1918	rs12000;rs1133598;rs1679733;rs3195472;rs3734565;rs52814218;rs56901220;rs12000	96	Q5M9Q1	NKAPL_HUMAN	C	96	ENSP00000345716:Y96C	ENSP00000345716:Y96C	Y	+	2	0	NKAPL	28335415	0.000000	0.05858	0.004000	0.12327	0.022000	0.10575	-0.091000	0.11146	0.302000	0.22762	0.533000	0.62120	TAC	A|0.613;G|0.387	0.387	strong		0.572	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
TENM4	26011	hgsc.bcm.edu	37	11	78369573	78369573	+	Missense_Mutation	SNP	C	C	T	rs75922333	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:78369573C>T	ENST00000278550.7	-	34	8302	c.7840G>A	c.(7840-7842)Gtg>Atg	p.V2614M		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2614					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)										TGGGTATCCACCCCATCAATG	0.557													C|||	17	0.00339457	0.0023	0.0014	5008	,	,		20854	0.0		0.0129	False		,,,				2504	0.0				p.V2614M		Atlas-SNP	.											.	.	.	.	0			c.G7840A						PASS	.	C	MET/VAL	16,4072		0,16,2028	44.0	47.0	46.0		7840	1.8	0.7	11	dbSNP_131	46	155,8247		2,151,4048	yes	missense	ODZ4	NM_001098816.2	21	2,167,6076	TT,TC,CC		1.8448,0.3914,1.3691	benign	2614/2770	78369573	171,12319	2044	4201	6245	SO:0001583	missense	26011	exon34			TATCCACCCCATC	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.7840G>A	11.37:g.78369573C>T	ENSP00000278550:p.Val2614Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	14	0.00641025641025641	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	C	9.623	1.134402	0.21123	0.003914	0.018448	ENSG00000149256	ENST00000278550	D	0.89485	-2.52	5.65	1.78	0.24846	.	0.375145	0.29273	N	0.012631	T	0.59595	0.2205	N	0.08118	0	0.27241	N	0.959155	B	0.13145	0.007	B	0.09377	0.004	T	0.54022	-0.8355	9	.	.	.	.	9.0578	0.36416	0.0:0.5855:0.0:0.4145	.	2614	Q6N022	TEN4_HUMAN	M	2614	ENSP00000278550:V2614M	.	V	-	1	0	ODZ4	78047221	0.005000	0.15991	0.705000	0.30386	0.942000	0.58702	-0.244000	0.08903	0.185000	0.20105	-0.137000	0.14449	GTG	C|0.990;T|0.010	0.010	strong		0.557	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
SF3A2	8175	hgsc.bcm.edu	37	19	2248185	2248185	+	Silent	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2248185A>T	ENST00000221494.5	+	9	1453	c.1035A>T	c.(1033-1035)ccA>ccT	p.P345P	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	345	Pro-rich.				gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		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)		GGGTTCACCCACCAGCCCCCG	0.741																																					p.P345P		Atlas-SNP	.											SF3A2,colon,carcinoma,0,1	SF3A2	22	1	0			c.A1035T						scavenged	.						2.0	3.0	3.0					19																	2248185		1454	3177	4631	SO:0001819	synonymous_variant	8175	exon9			TCACCCACCAGCC	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"""splicing factor 3a, subunit 2, 66kD"""			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1035A>T	19.37:g.2248185A>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	15	10	0.666667	NM_007165	B2RBU1|D6W605|O75245	Silent	SNP	ENST00000221494.5	37	CCDS12084.1																																																																																			.	.	none		0.741	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3		
PDE9A	5152	hgsc.bcm.edu	37	21	44189166	44189166	+	Silent	SNP	T	T	C	rs1045382	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:44189166T>C	ENST00000291539.6	+	17	1551	c.1491T>C	c.(1489-1491)ccT>ccC	p.P497P	PDE9A_ENST00000539837.1_Silent_p.P369P|PDE9A_ENST00000398225.3_Silent_p.P456P|PDE9A_ENST00000398227.3_Silent_p.P337P|PDE9A_ENST00000398229.3_Silent_p.P363P|PDE9A_ENST00000328862.6_Silent_p.P471P|PDE9A_ENST00000398224.3_Silent_p.P370P|PDE9A_ENST00000398236.3_Silent_p.P411P|PDE9A_ENST00000335440.6_Silent_p.P395P|PDE9A_ENST00000349112.3_Silent_p.P369P|PDE9A_ENST00000335512.4_Silent_p.P437P|PDE9A_ENST00000380328.2_Silent_p.P444P|PDE9A_ENST00000398234.3_Silent_p.P396P|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000398232.3_Silent_p.P430P	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	497	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	AAGGCCTTCCTGTGGCACCGT	0.512													C|||	2569	0.512979	0.6853	0.4352	5008	,	,		24371	0.4236		0.3718	False		,,,				2504	0.5726				p.P497P		Atlas-SNP	.											.	PDE9A	69	.	0			c.T1491C						PASS	.	C	,,,,,,,,,,,,,,,,,,,	2761,1645	502.9+/-365.4	856,1049,298	171.0	147.0	155.0		1311,1110,1107,1332,1188,870,870,1233,1011,840,1089,1185,870,840,1290,1368,1413,870,870,1491	-9.5	0.1	21	dbSNP_86	155	3112,5488	658.8+/-401.6	587,1938,1775	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	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	,,,,,,,,,,,,,,,,,,,	1443,2987,2073	CC,CT,TT		36.186,37.3355,45.1561	,,,,,,,,,,,,,,,,,,,	437/534,370/467,369/466,444/541,396/493,290/387,290/387,411/508,337/434,280/377,363/460,395/492,290/387,280/377,430/527,456/553,471/568,290/387,290/387,497/594	44189166	5873,7133	2203	4300	6503	SO:0001819	synonymous_variant	5152	exon17			CCTTCCTGTGGCA	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1491T>C	21.37:g.44189166T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	267	76	0.284644	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Silent	SNP	ENST00000291539.6	37	CCDS13690.1																																																																																			T|0.555;C|0.445	0.445	strong		0.512	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
TAGLN3	29114	hgsc.bcm.edu	37	3	111719786	111719786	+	Silent	SNP	A	A	T	rs2292583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:111719786A>T	ENST00000393917.2	+	3	900	c.348A>T	c.(346-348)ctA>ctT	p.L116L	TAGLN3_ENST00000478951.1_Silent_p.L116L|TAGLN3_ENST00000486460.1_Silent_p.L32L|TAGLN3_ENST00000273368.4_Silent_p.L116L|TAGLN3_ENST00000455401.2_Silent_p.L116L	NM_013259.2	NP_037391.2	Q9UI15	TAGL3_HUMAN	transgelin 3	116	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				central nervous system development (GO:0007417)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				endometrium(2)|lung(5)|urinary_tract(1)	8						CGGTGGATCTATGGGAAGGTA	0.488													A|||	662	0.132188	0.0129	0.1643	5008	,	,		20800	0.3026		0.0716	False		,,,				2504	0.1575				p.L116L		Atlas-SNP	.											.	TAGLN3	44	.	0			c.A348T						PASS	.	A	,,	135,4271	97.6+/-136.3	2,131,2070	113.0	116.0	115.0		348,348,348	-11.7	0.0	3	dbSNP_100	115	676,7924	169.4+/-220.8	27,622,3651	no	coding-synonymous,coding-synonymous,coding-synonymous	TAGLN3	NM_001008272.1,NM_001008273.1,NM_013259.2	,,	29,753,5721	TT,TA,AA		7.8605,3.064,6.2356	,,	116/200,116/200,116/200	111719786	811,12195	2203	4300	6503	SO:0001819	synonymous_variant	29114	exon3			GGATCTATGGGAA	AF303058	CCDS33816.1	3q13.2	2008-02-05			ENSG00000144834	ENSG00000144834			29868	protein-coding gene	gene with protein product		607953				8015377, 11238712	Standard	NM_013259		Approved	NP25, NP22	uc003dyo.3	Q9UI15	OTTHUMG00000159281	ENST00000393917.2:c.348A>T	3.37:g.111719786A>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001008272	D3DN64|Q96A74	Silent	SNP	ENST00000393917.2	37	CCDS33816.1																																																																																			A|0.919;T|0.081	0.081	strong		0.488	TAGLN3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354331.1	NM_013259	
AIM1	202	hgsc.bcm.edu	37	6	106999822	106999822	+	Missense_Mutation	SNP	G	G	A	rs2297970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:106999822G>A	ENST00000369066.3	+	12	4671	c.4184G>A	c.(4183-4185)tGt>tAt	p.C1395Y	AIM1_ENST00000487681.1_3'UTR|AIM1_ENST00000535438.1_Missense_Mutation_p.C214Y	NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.C1395Y(1)		breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GGCAAAAATTGTAAGATCTCT	0.353													G|||	997	0.199081	0.121	0.1988	5008	,	,		15007	0.0565		0.2873	False		,,,				2504	0.3609				p.C1395Y		Atlas-SNP	.											AIM1,NS,carcinoma,0,1	AIM1	161	1	1	Substitution - Missense(1)	stomach(1)	c.G4184A						PASS	.	G	TYR/CYS	658,3748	276.0+/-272.9	44,570,1589	93.0	102.0	99.0		4184	5.0	1.0	6	dbSNP_100	99	2629,5969	421.7+/-353.8	418,1793,2088	yes	missense	AIM1	NM_001624.2	194	462,2363,3677	AA,AG,GG		30.5769,14.9342,25.2768	benign	1395/1724	106999822	3287,9717	2203	4299	6502	SO:0001583	missense	202	exon12			AAAATTGTAAGAT	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.4184G>A	6.37:g.106999822G>A	ENSP00000358062:p.Cys1395Tyr	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	128	46	0.359375	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	395	0.18086080586080586	65	0.13211382113821138	76	0.20994475138121546	29	0.050699300699300696	225	0.29683377308707126	G	10.73	1.432797	0.25813	0.149342	0.305769	ENSG00000112297	ENST00000369066;ENST00000457437;ENST00000535438	T;T;T	0.75589	-0.95;-0.95;-0.95	5.9	5.03	0.67393	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.376576	0.37483	N	0.002062	T	0.49167	0.1541	N	0.17723	0.515	0.30327	P	0.7869889999999999	B;B	0.30793	0.137;0.295	B;B	0.41374	0.115;0.355	T	0.52320	-0.8591	9	0.34782	T	0.22	.	8.4927	0.33110	0.0702:0.0:0.6658:0.264	rs2297970;rs17562712;rs2297970	214;1395	B4DU04;Q9Y4K1	.;AIM1_HUMAN	Y	1395;214;214	ENSP00000358062:C1395Y;ENSP00000391419:C214Y;ENSP00000439183:C214Y	ENSP00000358062:C1395Y	C	+	2	0	AIM1	107106515	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.941000	0.29005	1.489000	0.48450	0.563000	0.77884	TGT	G|0.768;A|0.232	0.232	strong		0.353	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
NFXL1	152518	hgsc.bcm.edu	37	4	47901476	47901476	+	Missense_Mutation	SNP	G	G	A	rs12651301	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:47901476G>A	ENST00000507489.1	-	6	913	c.737C>T	c.(736-738)cCg>cTg	p.P246L	NFXL1_ENST00000381538.3_Missense_Mutation_p.P246L|NFXL1_ENST00000329043.3_Missense_Mutation_p.P246L	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	246			P -> L (in dbSNP:rs12651301).			integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						CACAAGCCACGGATCTAAAGG	0.403													G|||	1947	0.388778	0.329	0.3415	5008	,	,		17069	0.6002		0.327	False		,,,				2504	0.3487				p.P246L		Atlas-SNP	.											.	NFXL1	79	.	0			c.C737T						PASS	.	G	LEU/PRO	1465,2941	472.4+/-356.4	258,949,996	107.0	100.0	103.0		737	5.6	0.8	4	dbSNP_120	103	2666,5934	429.1+/-356.1	428,1810,2062	yes	missense	NFXL1	NM_152995.4	98	686,2759,3058	AA,AG,GG		31.0,33.2501,31.7623	probably-damaging	246/912	47901476	4131,8875	2203	4300	6503	SO:0001583	missense	152518	exon6			AGCCACGGATCTA	AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"""ovarian zinc finger protein"""						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.737C>T	4.37:g.47901476G>A	ENSP00000422037:p.Pro246Leu	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	173	93	0.537572	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Missense_Mutation	SNP	ENST00000507489.1	37	CCDS3478.2	913	0.41804029304029305	163	0.3313008130081301	126	0.34806629834254144	360	0.6293706293706294	264	0.3482849604221636	G	17.25	3.343126	0.61073	0.332501	0.31	ENSG00000170448	ENST00000381538;ENST00000507489;ENST00000329043	T;T;T	0.44881	0.91;0.91;0.91	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.74258	2.255	0.09310	P	0.9999999999929254	D	0.89917	1.0	D	0.97110	1.0	T	0.48387	-0.9040	9	0.27082	T	0.32	-8.0752	19.5578	0.95358	0.0:0.0:1.0:0.0	rs12651301;rs17463743;rs52793103;rs12651301	246	Q6ZNB6	NFXL1_HUMAN	L	246	ENSP00000370949:P246L;ENSP00000422037:P246L;ENSP00000333113:P246L	ENSP00000333113:P246L	P	-	2	0	NFXL1	47596233	1.000000	0.71417	0.786000	0.31890	0.282000	0.26991	9.434000	0.97515	2.625000	0.88918	0.655000	0.94253	CCG	G|0.647;A|0.353	0.353	strong		0.403	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995	
TET2	54790	hgsc.bcm.edu	37	4	106196819	106196819	+	Missense_Mutation	SNP	G	G	T	rs142312318	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:106196819G>T	ENST00000540549.1	+	11	6012	c.5152G>T	c.(5152-5154)Gta>Tta	p.V1718L	TET2_ENST00000513237.1_Missense_Mutation_p.V1739L|TET2_ENST00000380013.4_Missense_Mutation_p.V1718L|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1718			V -> L (in refractory anemia with ringed sideroblasts; somatic mutation in an acute myeloid leukemia sample; dbSNP:rs142312318). {ECO:0000269|PubMed:19372255, ECO:0000269|PubMed:19420352}.		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.V1718L(6)		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)		TGTACATCATGTAGGGAAATT	0.418			"""Mis N, F"""		MDS								G|||	3	0.000599042	0.0	0.0014	5008	,	,		23074	0.0		0.001	False		,,,				2504	0.001				p.V1718L		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,lymphoid_neoplasm,0,8	TET2	1762	8	6	Substitution - Missense(6)	haematopoietic_and_lymphoid_tissue(6)	c.G5152T						PASS	.	G	LEU/VAL	1,1383		0,1,691	114.0	95.0	101.0		5152	-2.3	0.0	4	dbSNP_134	101	21,3161		0,21,1570	yes	missense	TET2	NM_001127208.2	32	0,22,2261	TT,TG,GG		0.66,0.0723,0.4818	possibly-damaging	1718/2003	106196819	22,4544	692	1591	2283	SO:0001583	missense	54790	exon11			CATCATGTAGGGA	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.5152G>T	4.37:g.106196819G>T	ENSP00000442788:p.Val1718Leu	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	200	95	0.475	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	0.311	-0.968065	0.02232	7.23E-4	0.0066	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.02158	4.42;4.42;4.42	5.16	-2.29	0.06805	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.00998	0.0033	N	0.21583	0.68	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.17433	0.018;0.012	T	0.49011	-0.8983	9	0.08837	T	0.75	-0.48	5.6612	0.17670	0.3513:0.2405:0.4082:0.0	.	1739;1718	E7EQS8;Q6N021	.;TET2_HUMAN	L	1718;1739;1718	ENSP00000442788:V1718L;ENSP00000425443:V1739L;ENSP00000369351:V1718L	ENSP00000369351:V1718L	V	+	1	0	TET2	106416268	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.054000	0.11826	-0.328000	0.08539	-0.373000	0.07131	GTA	G|0.999;T|0.001	0.001	strong		0.418	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
SDCBP2	27111	hgsc.bcm.edu	37	20	1293149	1293149	+	Silent	SNP	C	C	T	rs55648421	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1293149C>T	ENST00000360779.3	-	7	737	c.564G>A	c.(562-564)ccG>ccA	p.P188P	SDCBP2_ENST00000467129.1_5'Flank|SDCBP2_ENST00000381812.1_Silent_p.P188P|SDCBP2_ENST00000381808.3_Silent_p.P103P|SDCBP2_ENST00000339987.3_Silent_p.P188P	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	188					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						TCCGCTGGAACGGCCTGGCAG	0.622													C|||	34	0.00678914	0.0008	0.0	5008	,	,		20948	0.0099		0.0169	False		,,,				2504	0.0061				p.P188P		Atlas-SNP	.											SDCBP2_ENST00000381812,NS,carcinoma,-1,3	SDCBP2	78	3	0			c.G564A						PASS	.	C	,,	1,4405	2.1+/-5.4	0,1,2202	83.0	69.0	74.0		564,309,564	-9.4	0.4	20	dbSNP_129	74	79,8521	46.3+/-105.2	1,77,4222	no	coding-synonymous,coding-synonymous,coding-synonymous	SDCBP2	NM_001199784.1,NM_015685.5,NM_080489.4	,,	1,78,6424	TT,TC,CC		0.9186,0.0227,0.6151	,,	188/293,103/208,188/293	1293149	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	27111	exon7			CTGGAACGGCCTG	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.564G>A	20.37:g.1293149C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Silent	SNP	ENST00000360779.3	37	CCDS42848.1																																																																																			C|0.993;T|0.007	0.007	strong		0.622	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489	
ERO1LB	56605	hgsc.bcm.edu	37	1	236381825	236381825	+	Missense_Mutation	SNP	G	G	C	rs1055851	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:236381825G>C	ENST00000354619.5	-	16	1596	c.1395C>G	c.(1393-1395)caC>caG	p.H465Q	GPR137B_ENST00000477559.1_Intron	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	465			H -> Q (in dbSNP:rs1055851). {ECO:0000269|PubMed:10818100}.		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)	ATTACCTACTGTGTTGTAATA	0.323													G|||	2851	0.569289	0.4803	0.5821	5008	,	,		15123	0.8839		0.4006	False		,,,				2504	0.5297				p.H465Q		Atlas-SNP	.											.	ERO1LB	48	.	0			c.C1395G						PASS	.	G	GLN/HIS	2147,2251	560.0+/-380.4	511,1125,563	57.0	63.0	61.0		1395	4.6	1.0	1	dbSNP_86	61	3443,5119	496.6+/-374.3	679,2085,1517	yes	missense	ERO1LB	NM_019891.3	24	1190,3210,2080	CC,CG,GG		40.2126,48.8176,43.1327	benign	465/468	236381825	5590,7370	2199	4281	6480	SO:0001583	missense	56605	exon16			CCTACTGTGTTGT	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.1395C>G	1.37:g.236381825G>C	ENSP00000346635:p.His465Gln	Somatic	281	1	0.00355872		WXS	Illumina HiSeq	Phase_I	303	183	0.60396	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	1234	0.565018315018315	229	0.4654471544715447	209	0.5773480662983426	509	0.8898601398601399	287	0.3786279683377309	G	9.953	1.220760	0.22457	0.488176	0.402126	ENSG00000086619	ENST00000354619	T	0.29397	1.57	5.54	4.62	0.57501	.	0.301526	0.36932	N	0.002322	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999999994	B	0.06786	0.001	B	0.04013	0.001	T	0.37731	-0.9693	9	0.21014	T	0.42	-19.4628	10.5749	0.45221	0.0766:0.169:0.7544:0.0	rs1055851;rs1749597;rs3196339;rs10317930;rs12735870;rs52808904;rs1055851	465	Q86YB8	ERO1B_HUMAN	Q	465	ENSP00000346635:H465Q	ENSP00000346635:H465Q	H	-	3	2	ERO1LB	234448448	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.371000	0.20450	2.600000	0.87896	0.650000	0.86243	CAC	G|0.530;C|0.470	0.470	strong		0.323	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891	
YAF2	10138	hgsc.bcm.edu	37	12	42554505	42554505	+	Silent	SNP	A	A	G	rs1059360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:42554505A>G	ENST00000534854.2	-	4	496	c.429T>C	c.(427-429)gcT>gcC	p.A143A	YAF2_ENST00000380788.3_Silent_p.A134A|YAF2_ENST00000327791.4_Silent_p.A119A|YAF2_ENST00000442791.3_Silent_p.A167A|YAF2_ENST00000380790.4_Silent_p.A101A	NM_005748.4	NP_005739.2	Q8IY57	YAF2_HUMAN	YY1 associated factor 2	143					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)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(1)	8	all_cancers(12;0.000425)	Lung NSC(34;0.0402)|all_lung(34;0.057)		GBM - Glioblastoma multiforme(48;0.0514)		GATCTGCAGAAGCAGCACTAG	0.458													A|||	1832	0.365815	0.2451	0.2896	5008	,	,		17235	0.4573		0.3946	False		,,,				2504	0.4591				p.A167A		Atlas-SNP	.											.	YAF2	16	.	0			c.T501C						PASS	.	A	,,	1187,3219	415.2+/-337.1	147,893,1163	91.0	79.0	83.0		303,501,429	0.6	1.0	12	dbSNP_86	83	3258,5342	487.8+/-372.2	593,2072,1635	no	coding-synonymous,coding-synonymous,coding-synonymous	YAF2	NM_001190977.1,NM_001190979.1,NM_005748.4	,,	740,2965,2798	GG,GA,AA		37.8837,26.9405,34.1765	,,	101/139,167/205,143/181	42554505	4445,8561	2203	4300	6503	SO:0001819	synonymous_variant	10138	exon5			TGCAGAAGCAGCA	U72209	CCDS31775.1, CCDS53778.1, CCDS53779.1, CCDS53780.1	12q12	2014-09-04			ENSG00000015153	ENSG00000015153			17363	protein-coding gene	gene with protein product		607534				9016636	Standard	NM_001190977		Approved		uc001rmw.3	Q8IY57	OTTHUMG00000169380	ENST00000534854.2:c.429T>C	12.37:g.42554505A>G		Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	137	135	0.985401	NM_001190979	A8K5P0|B4DFU3|G3V465|Q99710	Silent	SNP	ENST00000534854.2	37	CCDS31775.1																																																																																			A|0.654;G|0.346	0.346	strong		0.458	YAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403781.1		
BRCA1	672	hgsc.bcm.edu	37	17	41246481	41246481	+	Missense_Mutation	SNP	T	T	C	rs80357796|rs1799950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:41246481T>C	ENST00000357654.3	-	10	1185	c.1067A>G	c.(1066-1068)cAg>cGg	p.Q356R	BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.Q356R|BRCA1_ENST00000309486.4_Missense_Mutation_p.Q60R|BRCA1_ENST00000493795.1_Missense_Mutation_p.Q309R|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.Q356R|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.Q356R	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	145	0	0		WXS	Illumina HiSeq	Phase_I	157	81	0.515924	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1268579	1268579	+	Missense_Mutation	SNP	T	T	G	rs190148881	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1268579T>G	ENST00000529681.1	+	31	10527	c.10469T>G	c.(10468-10470)gTg>gGg	p.V3490G	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.V3493G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3490	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.|V -> G (in Ref. 4; CAA96577). {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)		p.V3469G(1)		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)		CCTTCCACGGTGACTTCCCAC	0.667																																					p.V3490G		Atlas-SNP	.											MUC5B,NS,carcinoma,0,5	MUC5B	473	5	1	Substitution - Missense(1)	skin(1)	c.T10469G						scavenged	.						101.0	122.0	115.0					11																	1268579		2134	4215	6349	SO:0001583	missense	727897	exon31			CCACGGTGACTTC	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.10469T>G	11.37:g.1268579T>G	ENSP00000436812:p.Val3490Gly	Somatic	516	2	0.00387597		WXS	Illumina HiSeq	Phase_I	393	33	0.0839695	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	29	0.013278388278388278	10	0.02032520325203252	7	0.019337016574585635	2	0.0034965034965034965	10	0.013192612137203167	t	2.632	-0.286071	0.05605	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21932	1.98;2.17	1.44	-1.72	0.08107	.	.	.	.	.	T	0.10165	0.0249	L	0.43152	1.355	0.09310	N	1	P;P	0.44090	0.826;0.563	P;B	0.48571	0.582;0.032	T	0.14504	-1.0470	9	0.87932	D	0	.	2.5883	0.04836	0.0:0.381:0.2946:0.3243	.	4018;3493	A7Y9J9;E9PBJ0	.;.	G	3490;3493;3462;3395	ENSP00000436812:V3490G;ENSP00000415793:V3493G	ENSP00000343037:V3462G	V	+	2	0	MUC5B	1225155	0.000000	0.05858	0.001000	0.08648	0.089000	0.18198	-2.439000	0.01016	-0.179000	0.10654	0.246000	0.17985	GTG	T|0.984;G|0.016	0.016	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ITPA	3704	hgsc.bcm.edu	37	20	3204084	3204084	+	Silent	SNP	G	G	A	rs9101	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000483354.1_3'UTR|ITPA_ENST00000455664.2_Silent_p.E170E	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						PASS	.	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	65	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	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		
ATM	472	hgsc.bcm.edu	37	11	108106435	108106435	+	Missense_Mutation	SNP	A	A	G	rs148590073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108106435A>G	ENST00000452508.2	+	6	559	c.370A>G	c.(370-372)Atc>Gtc	p.I124V	ATM_ENST00000278616.4_Missense_Mutation_p.I124V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	124					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)			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)	CTTAAATTATATCATGGATAC	0.308			"""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)			A|||	7	0.00139776	0.0053	0.0	5008	,	,		18157	0.0		0.0	False		,,,				2504	0.0				p.I124V		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	ATM	1657	.	0			c.A370G	GRCh37	CD000908	ATM	D	rs148590073	PASS	.	A	VAL/ILE	35,4367	40.0+/-72.8	0,35,2166	113.0	116.0	115.0		370	0.4	1.0	11	dbSNP_134	115	0,8596		0,0,4298	yes	missense	ATM	NM_000051.3	29	0,35,6464	GG,GA,AA		0.0,0.7951,0.2693	benign	124/3057	108106435	35,12963	2201	4298	6499	SO:0001583	missense	472	exon5	Familial Cancer Database	AT, Louis-Bar syndrome	AATTATATCATGG	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.370A>G	11.37:g.108106435A>G	ENSP00000388058:p.Ile124Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	212	64	0.301887	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	5.116	0.207058	0.09704	0.007951	0.0	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.70045	-0.45;-0.45;-0.45	5.62	0.39	0.16275	Telomere-length maintenance and DNA damage repair (1);	0.272984	0.36101	N	0.002796	T	0.18130	0.0435	N	0.00801	-1.175	0.22581	N	0.998968	B	0.06786	0.001	B	0.08055	0.003	T	0.31724	-0.9933	10	0.06494	T	0.89	.	5.4836	0.16737	0.294:0.0:0.5308:0.1751	.	124	Q13315	ATM_HUMAN	V	124	ENSP00000435747:I124V;ENSP00000278616:I124V;ENSP00000388058:I124V	ENSP00000278616:I124V	I	+	1	0	ATM	107611645	0.996000	0.38824	0.976000	0.42696	0.990000	0.78478	0.866000	0.27954	0.174000	0.19809	0.477000	0.44152	ATC	A|0.997;G|0.003	0.003	strong		0.308	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
AIM1L	55057	hgsc.bcm.edu	37	1	26673076	26673076	+	5'Flank	SNP	G	G	A	rs11247924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:26673076G>A	ENST00000308182.5	-	0	0				RN7SL490P_ENST00000579210.1_RNA|AIM1L_ENST00000527815.1_5'Flank			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like								carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-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;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		GTGGGGGGCCGCTGCCGCCAT	0.622													G|||	899	0.179513	0.1505	0.1931	5008	,	,		15200	0.1458		0.1918	False		,,,				2504	0.2311				p.R25W		Atlas-SNP	.											.	AIM1L	98	.	0			c.C73T						PASS	.	G	TRP/ARG	524,3272		33,458,1407	13.0	15.0	14.0		73	3.0	1.0	1	dbSNP_120	14	1591,6607		162,1267,2670	yes	missense	AIM1L	NM_001039775.3	101	195,1725,4077	AA,AG,GG		19.4072,13.804,17.6338	benign	25/1662	26673076	2115,9879	1898	4099	5997	SO:0001631	upstream_gene_variant	55057	exon2			GGGGCCGCTGCCG			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490		1.37:g.26673076G>A	Exception_encountered	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	14	0.254545	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	37		377	0.17261904761904762	71	0.1443089430894309	73	0.20165745856353592	101	0.17657342657342656	132	0.1741424802110818	G	18.91	3.724308	0.68959	0.13804	0.194072	ENSG00000176092	ENST00000538018;ENST00000475866	T	0.22134	1.97	5.04	3.01	0.34805	.	.	.	.	.	T	0.00039	0.0001	L	0.29908	0.895	0.41275	P	0.013122999999999996	D	0.89917	1.0	D	0.80764	0.994	T	0.10823	-1.0613	8	0.59425	D	0.04	.	9.8058	0.40792	0.0:0.0:0.6286:0.3714	rs11247924;rs60455159	25	E7ET48	.	W	25	ENSP00000428746:R25W	ENSP00000428746:R25W	R	-	1	2	AIM1L	26545663	0.127000	0.22367	1.000000	0.80357	0.970000	0.65996	0.700000	0.25601	1.096000	0.41439	0.655000	0.94253	CGG	G|0.828;A|0.172	0.172	strong		0.622	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2	
SPARCL1	8404	hgsc.bcm.edu	37	4	88416188	88416188	+	Missense_Mutation	SNP	G	G	T	rs13051	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:88416188G>T	ENST00000282470.6	-	3	616	c.146C>A	c.(145-147)gCt>gAt	p.A49D	SPARCL1_ENST00000418378.1_Missense_Mutation_p.A49D|SPARCL1_ENST00000503414.1_De_novo_Start_OutOfFrame	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	49			A -> D (in dbSNP:rs13051). {ECO:0000269|PubMed:7600298}.		signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.A49D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		ATTTTCTTCAGCTTCAGCCCT	0.353													T|||	2881	0.57528	0.882	0.5029	5008	,	,		16934	0.4375		0.3787	False		,,,				2504	0.5562				p.A49D		Atlas-SNP	.											SPARCL1,NS,carcinoma,0,1	SPARCL1	59	1	1	Substitution - Missense(1)	stomach(1)	c.C146A						scavenged	.	T	ASP/ALA,ASP/ALA	3556,850	333.3+/-302.9	1435,686,82	155.0	164.0	161.0		146,146	3.0	0.9	4	dbSNP_52	161	3196,5404	653.0+/-401.0	601,1994,1705	yes	missense,missense	SPARCL1	NM_001128310.1,NM_004684.4	126,126	2036,2680,1787	TT,TG,GG		37.1628,19.2919,48.0855	benign,benign	49/665,49/665	88416188	6752,6254	2203	4300	6503	SO:0001583	missense	8404	exon3			TCTTCAGCTTCAG	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.146C>A	4.37:g.88416188G>T	ENSP00000282470:p.Ala49Asp	Somatic	329	2	0.00607903		WXS	Illumina HiSeq	Phase_I	265	259	0.977359	NM_004684	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	37	CCDS3622.1	1128	0.5164835164835165	433	0.8800813008130082	189	0.5220994475138122	231	0.40384615384615385	275	0.3627968337730871	T	0.010	-1.742076	0.00675	0.807081	0.371628	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000509407;ENST00000434434;ENST00000535835;ENST00000512317;ENST00000543631;ENST00000458304	T;T;T;T;T;T;T;T	0.49720	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.77	4.1	3.02	0.34903	.	0.436671	0.23219	N	0.050581	T	0.00012	0.0000	N	0.01168	-0.975	0.53005	P	3.399999999997849E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.31888	-0.9927	9	0.09338	T	0.73	-1.8696	8.876	0.35345	0.0:0.0:0.514:0.486	rs13051;rs1049542;rs3189720;rs7698628;rs17855569;rs60110307;rs13051	49	Q14515	SPRL1_HUMAN	D	49	ENSP00000282470:A49D;ENSP00000414856:A49D;ENSP00000423483:A49D;ENSP00000416971:A49D;ENSP00000438188:A49D;ENSP00000423448:A49D;ENSP00000444832:A49D;ENSP00000406251:A49D	ENSP00000282470:A49D	A	-	2	0	SPARCL1	88635212	0.942000	0.31987	0.909000	0.35828	0.011000	0.07611	0.896000	0.28377	0.458000	0.26988	-0.256000	0.11100	GCT	G|0.474;T|0.526	0.526	strong		0.353	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
PAPOLB	56903	hgsc.bcm.edu	37	7	4901385	4901385	+	Missense_Mutation	SNP	A	A	C	rs3750009	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:4901385A>C	ENST00000404991.1	-	1	240	c.54T>G	c.(52-54)aaT>aaG	p.N18K	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	18					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		CGCCGTAGCGATTCGGCGGCG	0.672													C|||	2479	0.495008	0.708	0.3689	5008	,	,		13116	0.4117		0.341	False		,,,				2504	0.5409				p.N19K		Atlas-SNP	.											.	PAPOLB	93	.	0			c.T57G						PASS	.	C	,LYS/ASN	2462,1420		806,850,285	10.0	11.0	11.0		,57	3.2	0.2	7	dbSNP_107	11	3180,5066		607,1966,1550	yes	intron,missense	RADIL,PAPOLB	NM_018059.4,NM_020144.4	,94	1413,2816,1835	CC,CA,AA		38.5642,36.5791,46.5204	,benign	,19/638	4901385	5642,6486	1941	4123	6064	SO:0001583	missense	56903	exon1			GTAGCGATTCGGC	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.54T>G	7.37:g.4901385A>C	ENSP00000384700:p.Asn18Lys	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	47	15	0.319149	NM_020144	Q75LH1|Q8NE14	Missense_Mutation	SNP	ENST00000404991.1	37		948	0.4340659340659341	356	0.7235772357723578	128	0.35359116022099446	208	0.36363636363636365	256	0.33773087071240104	C	0.005	-2.186441	0.00305	0.634209	0.385642	ENSG00000218823	ENST00000404991	.	.	.	4.13	3.25	0.37280	.	.	.	.	.	T	0.00012	0.0000	N	0.00025	-2.685	0.47621	P	5.300000000000304E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42015	-0.9476	7	0.02654	T	1	.	3.8434	0.08925	0.1922:0.6117:0.0:0.1961	rs3750009;rs9655434;rs57255641;rs3750009	19	A4D1Z6	.	K	18	.	ENSP00000384700:N18K	N	-	3	2	PAPOLB	4867911	1.000000	0.71417	0.189000	0.23252	0.003000	0.03518	0.699000	0.25586	0.718000	0.32166	-0.121000	0.15023	AAT	A|0.534;C|0.466	0.466	strong		0.672	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144	
SAMD15	161394	hgsc.bcm.edu	37	14	77844592	77844592	+	Silent	SNP	T	T	A	rs10133824	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77844592T>A	ENST00000216471.4	+	1	1117	c.831T>A	c.(829-831)ggT>ggA	p.G277G	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	277										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AGGAGGCAGGTCTAGAGCCTC	0.502													T|||	760	0.151757	0.0968	0.2666	5008	,	,		18706	0.0159		0.2038	False		,,,				2504	0.2311				p.G277G		Atlas-SNP	.											.	SAMD15	60	.	0			c.T831A						PASS	.	T		558,3848	242.1+/-252.3	32,494,1677	67.0	71.0	70.0		831	-0.7	0.0	14	dbSNP_119	70	1685,6915	300.8+/-305.1	182,1321,2797	no	coding-synonymous	SAMD15	NM_001010860.1		214,1815,4474	AA,AT,TT		19.593,12.6645,17.2459		277/675	77844592	2243,10763	2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			GGCAGGTCTAGAG	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.831T>A	14.37:g.77844592T>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																			T|0.848;A|0.152	0.152	strong		0.502	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
MUC17	140453	hgsc.bcm.edu	37	7	100677405	100677405	+	Missense_Mutation	SNP	G	G	A	rs141963257	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677405G>A	ENST00000306151.4	+	3	2772	c.2708G>A	c.(2707-2709)cGt>cAt	p.R903H		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	903	59 X approximate tandem repeats.|Ser-rich.				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)					ACTGAAGCCCGTTCGTCTCCT	0.527													g|||	903	0.180312	0.2413	0.0836	5008	,	,		32677	0.1944		0.0964	False		,,,				2504	0.2382				p.R903H		Atlas-SNP	.											.	MUC17	804	.	0			c.G2708A						PASS	.						318.0	302.0	307.0					7																	100677405		2203	4300	6503	SO:0001583	missense	140453	exon3			AAGCCCGTTCGTC	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.2708G>A	7.37:g.100677405G>A	ENSP00000302716:p.Arg903His	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	330	73	0.221212	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	0.072	-1.199648	0.01581	.	.	ENSG00000169876	ENST00000306151	T	0.02890	4.12	0.579	-1.16	0.09678	.	.	.	.	.	T	0.01592	0.0051	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45041	-0.9288	9	0.40728	T	0.16	.	4.33	0.11059	0.2123:0.3746:0.4131:0.0	.	903	Q685J3	MUC17_HUMAN	H	903	ENSP00000302716:R903H	ENSP00000302716:R903H	R	+	2	0	MUC17	100464125	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.209000	0.01228	-3.371000	0.00177	-3.222000	0.00052	CGT	.	.	weak		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
BTBD16	118663	hgsc.bcm.edu	37	10	124036328	124036328	+	Missense_Mutation	SNP	G	G	A	rs11200524	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124036328G>A	ENST00000260723.4	+	3	292	c.41G>A	c.(40-42)cGg>cAg	p.R14Q	BTBD16_ENST00000368994.2_Missense_Mutation_p.R15Q	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	14								p.R14Q(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)				CTGGAACGCCGGGTCACTGGC	0.473													G|||	431	0.0860623	0.0015	0.2017	5008	,	,		19105	0.2173		0.0298	False		,,,				2504	0.0409				p.R14Q		Atlas-SNP	.											BTBD16,NS,carcinoma,0,1	BTBD16	44	1	1	Substitution - Missense(1)	stomach(1)	c.G41A						scavenged	.	G	GLN/ARG	39,4367	43.8+/-77.6	1,37,2165	94.0	94.0	94.0		41	2.1	0.1	10	dbSNP_120	94	223,8377	91.6+/-153.7	5,213,4082	yes	missense	BTBD16	NM_144587.2	43	6,250,6247	AA,AG,GG		2.593,0.8852,2.0145	benign	14/507	124036328	262,12744	2203	4300	6503	SO:0001583	missense	118663	exon3			AACGCCGGGTCAC	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.41G>A	10.37:g.124036328G>A	ENSP00000260723:p.Arg14Gln	Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	210	0.09615384615384616	2	0.0040650406504065045	61	0.1685082872928177	124	0.21678321678321677	23	0.030343007915567283	G	7.086	0.571149	0.13623	0.008852	0.02593	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.18960	2.18;2.18	4.9	2.07	0.26955	.	0.253869	0.27302	N	0.019989	T	0.00012	0.0000	M	0.72479	2.2	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.11690	-1.0577	9	0.42905	T	0.14	-20.4823	6.708	0.23262	0.2888:0.0:0.7112:0.0	rs11200524	15;14	Q32M84-2;Q32M84	.;BTBDG_HUMAN	Q	14;15	ENSP00000260723:R14Q;ENSP00000357990:R15Q	ENSP00000260723:R14Q	R	+	2	0	BTBD16	124026318	0.000000	0.05858	0.065000	0.19835	0.004000	0.04260	-0.711000	0.05019	0.371000	0.24564	-0.141000	0.14075	CGG	G|0.959;A|0.041	0.041	strong		0.473	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
FLG	2312	hgsc.bcm.edu	37	1	152280691	152280691	+	Missense_Mutation	SNP	A	A	T	rs117945779	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280691A>T	ENST00000368799.1	-	3	6706	c.6671T>A	c.(6670-6672)cTg>cAg	p.L2224Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2224	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGCCCACCAGTGAGTGTCT	0.542									Ichthyosis				-|||	959	0.191494	0.1936	0.1873	5008	,	,		22319	0.3026		0.0706	False		,,,				2504	0.2014				p.L2224Q		Atlas-SNP	.											FLG,NS,malignant_melanoma,+1,1	FLG	900	1	0			c.T6671A						PASS	.						260.0	255.0	257.0					1																	152280691		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCCACCAGTGAGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6671T>A	1.37:g.152280691A>T	ENSP00000357789:p.Leu2224Gln	Somatic	367	0	0		WXS	Illumina HiSeq	Phase_I	640	36	0.05625	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	t	2.028	-0.423196	0.04734	.	.	ENSG00000143631	ENST00000368799	T	0.02656	4.21	0.883	-0.332	0.12675	.	.	.	.	.	T	0.00144	0.0004	N	0.00034	-2.56	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	9	0.08381	T	0.77	.	1.4068	0.02283	0.3248:0.2503:0.0:0.4249	.	2224	P20930	FILA_HUMAN	Q	2224	ENSP00000357789:L2224Q	ENSP00000357789:L2224Q	L	-	2	0	FLG	150547315	0.313000	0.24554	0.000000	0.03702	0.001000	0.01503	-0.556000	0.05992	-0.732000	0.04856	-0.721000	0.03606	CTG	.	.	weak		0.542	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MYOM2	9172	hgsc.bcm.edu	37	8	2054066	2054066	+	Silent	SNP	A	A	G	rs17684416	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:2054066A>G	ENST00000262113.4	+	22	2910	c.2769A>G	c.(2767-2769)caA>caG	p.Q923Q	MYOM2_ENST00000523438.1_Silent_p.Q348Q	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	923	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)		TCGATGAACAAGGCAACATCT	0.483													A|||	871	0.173922	0.0855	0.2046	5008	,	,		17443	0.2857		0.1799	False		,,,				2504	0.1503				p.Q923Q		Atlas-SNP	.											.	MYOM2	251	.	0			c.A2769G						PASS	.	A		415,3991	203.8+/-226.2	21,373,1809	149.0	134.0	139.0		2769	-10.1	0.0	8	dbSNP_123	139	1368,7232	266.0+/-286.5	127,1114,3059	no	coding-synonymous	MYOM2	NM_003970.2		148,1487,4868	GG,GA,AA		15.907,9.419,13.7091		923/1466	2054066	1783,11223	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon22			TGAACAAGGCAAC		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.2769A>G	8.37:g.2054066A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	242	87	0.359504	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			A|0.843;G|0.157	0.157	strong		0.483	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
NEIL2	252969	hgsc.bcm.edu	37	8	11640784	11640784	+	Silent	SNP	A	A	G	rs8191642	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:11640784A>G	ENST00000284503.6	+	4	1163	c.564A>G	c.(562-564)ccA>ccG	p.P188P	NEIL2_ENST00000455213.2_Silent_p.P188P|NEIL2_ENST00000528323.1_Silent_p.P72P|NEIL2_ENST00000436750.3_Silent_p.P188P|NEIL2_ENST00000403422.3_Silent_p.P127P	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	188					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		GCTCTTCCCCAGTGGTCACAC	0.512								Base excision repair (BER), DNA glycosylases					A|||	1075	0.214657	0.4175	0.1816	5008	,	,		23263	0.0109		0.2376	False		,,,				2504	0.1503				p.P188P		Atlas-SNP	.											.	NEIL2	14	.	0			c.A564G						PASS	.	A	,,,	1609,2797	498.9+/-364.3	284,1041,878	219.0	196.0	204.0		564,381,216,564	-7.4	0.0	8	dbSNP_117	204	1943,6657	343.0+/-324.7	224,1495,2581	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	,,,	508,2536,3459	GG,GA,AA		22.593,36.5184,27.3105	,,,	188/333,127/272,72/217,188/333	11640784	3552,9454	2203	4300	6503	SO:0001819	synonymous_variant	252969	exon4			TTCCCCAGTGGTC	AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"""nei like 2 (E. coli)"""			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.564A>G	8.37:g.11640784A>G		Somatic	413	1	0.00242131		WXS	Illumina HiSeq	Phase_I	484	154	0.318182	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Silent	SNP	ENST00000284503.6	37	CCDS5984.1																																																																																			A|0.751;G|0.249	0.249	strong		0.512	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324237	39324237	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39324237C>G	ENST00000391356.2	-	1	187	c.188G>C	c.(187-189)aGc>aCc	p.S63T		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	63	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			cctgcagcagctgggtttgca	0.627																																					p.S63T		Atlas-SNP	.											KRTAP4-3,NS,carcinoma,-1,1	KRTAP4-3	40	1	0			c.G188C						scavenged	.						3.0	5.0	4.0					17																	39324237		1480	3536	5016	SO:0001583	missense	85290	exon1			CAGCAGCTGGGTT	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.188G>C	17.37:g.39324237C>G	ENSP00000375151:p.Ser63Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	2	0.0229885	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	0.578	-0.838330	0.02692	.	.	ENSG00000196156	ENST00000391356	T	0.01335	5.0	4.13	-2.75	0.05914	.	.	.	.	.	T	0.01061	0.0035	N	0.20881	0.62	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.47573	-0.9107	9	0.14252	T	0.57	.	8.0489	0.30566	0.3482:0.2735:0.3783:0.0	.	63	Q9BYR4	KRA43_HUMAN	T	63	ENSP00000375151:S63T	ENSP00000375151:S63T	S	-	2	0	KRTAP4-3	36577763	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.870000	0.00346	-0.385000	0.07833	-2.956000	0.00083	AGC	.	.	none		0.627	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
ATP8B2	57198	hgsc.bcm.edu	37	1	154316434	154316434	+	Silent	SNP	C	C	T	rs2274988	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154316434C>T	ENST00000368489.3	+	18	1923	c.1923C>T	c.(1921-1923)taC>taT	p.Y641Y		NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	627					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)			AAGAGTACTACGAGGAGTGGG	0.602													C|||	983	0.196286	0.2549	0.1657	5008	,	,		18937	0.125		0.2525	False		,,,				2504	0.1544				p.Y641Y		Atlas-SNP	.											ATP8B2,colon,carcinoma,0,1	ATP8B2	158	1	0			c.C1923T						PASS	.	C		987,3419	363.6+/-316.6	118,751,1334	46.0	47.0	47.0		1923	-2.8	0.0	1	dbSNP_100	47	2129,6471	358.9+/-331.3	282,1565,2453	no	coding-synonymous	ATP8B2	NM_020452.3		400,2316,3787	TT,TC,CC		24.7558,22.4013,23.9582		641/1224	154316434	3116,9890	2203	4300	6503	SO:0001819	synonymous_variant	57198	exon18			GTACTACGAGGAG	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.1923C>T	1.37:g.154316434C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368489.3	37	CCDS1066.1																																																																																			C|0.774;T|0.226	0.226	strong		0.602	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452	
CSF2RB	1439	hgsc.bcm.edu	37	22	37329999	37329999	+	Silent	SNP	C	C	T	rs1801117	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:37329999C>T	ENST00000403662.3	+	10	1500	c.1278C>T	c.(1276-1278)agC>agT	p.S426S	CSF2RB_ENST00000406230.1_Silent_p.S432S|CSF2RB_ENST00000536485.1_Silent_p.S373S|CSF2RB_ENST00000262825.5_Silent_p.S432S			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	426	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)	GGATCTGGAGCGAGTGGAGTG	0.652													C|||	941	0.187899	0.2648	0.1268	5008	,	,		17303	0.0734		0.2187	False		,,,				2504	0.2137				p.S426S		Atlas-SNP	.											.	CSF2RB	104	.	0			c.C1278T						PASS	.	C		1042,3364	379.7+/-323.4	133,776,1294	61.0	59.0	59.0		1278	0.2	1.0	22	dbSNP_89	59	1958,6642	343.7+/-325.0	234,1490,2576	no	coding-synonymous	CSF2RB	NM_000395.2		367,2266,3870	TT,TC,CC		22.7674,23.6496,23.0663		426/898	37329999	3000,10006	2203	4300	6503	SO:0001819	synonymous_variant	1439	exon10			CTGGAGCGAGTGG	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.1278C>T	22.37:g.37329999C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_000395	Q5JZI1|Q6ICE0	Silent	SNP	ENST00000403662.3	37	CCDS13936.1																																																																																			C|0.793;T|0.207	0.207	strong		0.652	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
ZNF805	390980	hgsc.bcm.edu	37	19	57764770	57764770	+	Missense_Mutation	SNP	G	G	A	rs10421632	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	141	0	0		WXS	Illumina HiSeq	Phase_I	130	130	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	
UTP20	27340	hgsc.bcm.edu	37	12	101776996	101776996	+	Missense_Mutation	SNP	G	G	C	rs1061436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:101776996G>C	ENST00000261637.4	+	59	8008	c.7834G>C	c.(7834-7836)Gag>Cag	p.E2612Q		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2612			E -> Q (in dbSNP:rs1061436).		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						GGTGAAGGAAGAGCTCGGCAG	0.532													G|||	435	0.086861	0.0182	0.1153	5008	,	,		14588	0.0278		0.165	False		,,,				2504	0.1401				p.E2612Q		Atlas-SNP	.											.	UTP20	222	.	0			c.G7834C						PASS	.	G	GLN/GLU	169,4237	111.2+/-149.4	4,161,2038	62.0	70.0	67.0		7834	2.4	0.0	12	dbSNP_86	67	1432,7168	275.4+/-291.8	119,1194,2987	yes	missense	UTP20	NM_014503.2	29	123,1355,5025	CC,CG,GG		16.6512,3.8357,12.3097	benign	2612/2786	101776996	1601,11405	2203	4300	6503	SO:0001583	missense	27340	exon59			AAGGAAGAGCTCG	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.7834G>C	12.37:g.101776996G>C	ENSP00000261637:p.Glu2612Gln	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	203	0.09294871794871795	11	0.022357723577235773	46	0.1270718232044199	16	0.027972027972027972	130	0.17150395778364116	G	12.10	1.836371	0.32421	0.038357	0.166512	ENSG00000120800	ENST00000261637	T	0.04970	3.52	5.46	2.43	0.29744	.	0.501020	0.18522	N	0.138727	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.35656	0.514	B	0.25291	0.059	T	0.43734	-0.9373	9	0.15499	T	0.54	-4.2624	10.1662	0.42882	0.0699:0.2572:0.6729:0.0	rs1061436;rs3202548;rs3816569;rs17415284;rs1061436	2612	O75691	UTP20_HUMAN	Q	2612	ENSP00000261637:E2612Q	ENSP00000261637:E2612Q	E	+	1	0	UTP20	100301127	0.416000	0.25424	0.002000	0.10522	0.001000	0.01503	2.618000	0.46393	0.657000	0.30906	0.643000	0.83706	GAG	G|0.878;C|0.122	0.122	strong		0.532	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
OR2G3	81469	hgsc.bcm.edu	37	1	247769752	247769752	+	Missense_Mutation	SNP	A	A	G	rs61730407	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247769752A>G	ENST00000320002.2	+	1	897	c.865A>G	c.(865-867)Atc>Gtc	p.I289V	RNU6-691P_ENST00000516585.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_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	149	0	0		WXS	Illumina HiSeq	Phase_I	163	159	0.97546	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		
SIK3	23387	hgsc.bcm.edu	37	11	116719841	116719841	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:116719841C>T	ENST00000292055.4	-	21	3531	c.3496G>A	c.(3496-3498)Gct>Act	p.A1166T	SIK3_ENST00000375288.1_Missense_Mutation_p.A501T|SIK3_ENST00000434315.2_Missense_Mutation_p.A1005T|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000542607.1_Missense_Mutation_p.A1106T|SIK3_ENST00000446921.2_Missense_Mutation_p.A1164T|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000375300.1_Missense_Mutation_p.A1224T	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	1166					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						CATACATAAGCATCGTCGCTG	0.602																																					p.A1166T		Atlas-SNP	.											.	SIK3	112	.	0			c.G3496A						PASS	.						170.0	122.0	139.0					11																	116719841		2201	4292	6493	SO:0001583	missense	23387	exon21			CATAAGCATCGTC	AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.3496G>A	11.37:g.116719841C>T	ENSP00000292055:p.Ala1166Thr	Somatic	326	1	0.00306748		WXS	Illumina HiSeq	Phase_I	461	306	0.663774	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.5|28.5	4.921494|4.921494	0.92249|0.92249	.|.	.|.	ENSG00000160584|ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315|ENST00000445177;ENST00000454905;ENST00000446921	T;T;T;D;T|.	0.81821|.	-1.44;-1.42;0.59;-1.54;-1.17|.	5.26|5.26	4.35|4.35	0.52113|0.52113	.|.	0.000000|.	0.41194|.	U|.	0.000938|.	T|T	0.56108|0.56108	0.1963|0.1963	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999998|0.999998	D;D;D;B|.	0.89917|.	1.0;1.0;1.0;0.117|.	D;D;D;B|.	0.87578|.	0.998;0.998;0.998;0.138|.	T|T	0.52087|0.52087	-0.8622|-0.8622	10|5	0.87932|.	D|.	0|.	.|.	13.8208|13.8208	0.63320|0.63320	0.0:0.9254:0.0:0.0746|0.0:0.9254:0.0:0.0746	.|.	1106;1005;1166;501|.	A1A5A8;A1A5A9;Q9Y2K2;Q9Y2K2-2|.	.;.;SIK3_HUMAN;.|.	T|Y	1224;1166;501;1106;1005|1265;5;1128	ENSP00000364449:A1224T;ENSP00000292055:A1166T;ENSP00000364437:A501T;ENSP00000438108:A1106T;ENSP00000415873:A1005T|.	ENSP00000292055:A1166T|.	A|C	-|-	1|2	0|0	SIK3|SIK3	116225051|116225051	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.993000|0.993000	0.82548|0.82548	7.456000|7.456000	0.80751|0.80751	1.223000|1.223000	0.43536|0.43536	0.557000|0.557000	0.71058|0.71058	GCT|TGC	.	.	none		0.602	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164	
FLRT2	23768	hgsc.bcm.edu	37	14	86088573	86088573	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:86088573C>T	ENST00000330753.4	+	2	1482	c.715C>T	c.(715-717)Cgt>Tgt	p.R239C	FLRT2_ENST00000554746.1_Missense_Mutation_p.R239C	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	239					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|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)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TTCAATTGTACGTAATTCGCT	0.512																																					p.R239C		Atlas-SNP	.											FLRT2,NS,carcinoma,0,1	FLRT2	168	1	0			c.C715T						scavenged	.						86.0	85.0	85.0					14																	86088573		2203	4300	6503	SO:0001583	missense	23768	exon2			ATTGTACGTAATT	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.715C>T	14.37:g.86088573C>T	ENSP00000332879:p.Arg239Cys	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	199	2	0.0100503	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	C	15.16	2.752457	0.49362	.	.	ENSG00000185070	ENST00000330753;ENST00000554746	T;T	0.57907	0.37;0.37	5.78	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.64832	0.2634	L	0.47716	1.5	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65018	-0.6270	10	0.42905	T	0.14	-16.9625	14.4373	0.67290	0.2907:0.7093:0.0:0.0	.	239	O43155	FLRT2_HUMAN	C	239	ENSP00000332879:R239C;ENSP00000451050:R239C	ENSP00000332879:R239C	R	+	1	0	FLRT2	85158326	0.994000	0.37717	0.692000	0.30179	0.564000	0.35744	3.215000	0.51169	1.359000	0.45940	0.650000	0.86243	CGT	.	.	none		0.512	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
GPR161	23432	hgsc.bcm.edu	37	1	168059866	168059866	+	Silent	SNP	A	A	G	rs275149	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:168059866A>G	ENST00000367838.1	-	6	1453	c.1140T>C	c.(1138-1140)ggT>ggC	p.G380G	GPR161_ENST00000539777.1_Silent_p.G302G|GPR161_ENST00000271357.5_Silent_p.G380G|GPR161_ENST00000537209.1_Silent_p.G400G|GPR161_ENST00000367835.1_Silent_p.G380G|GPR161_ENST00000367836.1_Silent_p.G248G|GPR161_ENST00000361697.2_Silent_p.G380G|GPR161_ENST00000546300.1_Silent_p.G266G	NM_001267611.1|NM_153832.2	NP_001254540.1|NP_722561.1	Q8N6U8	GP161_HUMAN	G protein-coupled receptor 161	380					G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	all_hematologic(923;0.215)					GGGGCTGTCCACCTGCCATGA	0.597													G|||	1605	0.320487	0.5257	0.4063	5008	,	,		18253	0.1518		0.2634	False		,,,				2504	0.2147				p.G400G		Atlas-SNP	.											GPR161,colon,carcinoma,0,2	GPR161	56	2	0			c.T1200C						scavenged	.	G		2723,1683		837,1049,317	40.0	40.0	40.0		1140	-9.6	0.0	1	dbSNP_79	40	2891,5709		499,1893,1908	no	coding-synonymous	GPR161	NM_153832.1		1336,2942,2225	GG,GA,AA		33.6163,38.1979,43.1647		380/530	168059866	5614,7392	2203	4300	6503	SO:0001819	synonymous_variant	23432	exon5			CTGTCCACCTGCC	AF091890	CCDS1268.1, CCDS58042.1, CCDS58043.1, CCDS58044.1, CCDS58045.1, CCDS72978.1	1q23.3	2012-08-21			ENSG00000143147	ENSG00000143147		"""GPCR / Class A : Orphans"""	23694	protein-coding gene	gene with protein product		612250				11959142	Standard	NM_153832		Approved	RE2	uc009wvo.4	Q8N6U8	OTTHUMG00000034651	ENST00000367838.1:c.1140T>C	1.37:g.168059866A>G		Somatic	133	2	0.0150376		WXS	Illumina HiSeq	Phase_I	133	48	0.360902	NM_001267609	B3KV34|B7Z5D7|B7Z5E8|B7Z5Z6|F5GXD6|F5H6J7|O75963|Q5TGK0|Q5TGK1|Q5TGK2	Silent	SNP	ENST00000367838.1	37	CCDS1268.1																																																																																			A|0.580;G|0.420	0.420	strong		0.597	GPR161-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083829.1	NM_007369	
PFKP	5214	hgsc.bcm.edu	37	10	3172145	3172145	+	Silent	SNP	C	C	T	rs1052337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	93	2	0.0215054		WXS	Illumina HiSeq	Phase_I	55	47	0.854545	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	
DNTTIP2	30836	hgsc.bcm.edu	37	1	94343023	94343023	+	Silent	SNP	A	A	G	rs2391322	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:94343023A>G	ENST00000436063.2	-	2	525	c.468T>C	c.(466-468)ccT>ccC	p.P156P	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	156					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TTTTTTCTGTAGGAAGCACAA	0.393													G|||	2188	0.436901	0.3782	0.3718	5008	,	,		20363	0.5585		0.3499	False		,,,				2504	0.5266				p.P156P		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.T468C						PASS	.	G		1395,2271		250,895,688	112.0	104.0	106.0		468	-0.4	0.0	1	dbSNP_100	106	2925,5263		505,1915,1674	no	coding-synonymous	DNTTIP2	NM_014597.4		755,2810,2362	GG,GA,AA		35.723,38.0524,36.4434		156/757	94343023	4320,7534	1833	4094	5927	SO:0001819	synonymous_variant	30836	exon2			TTCTGTAGGAAGC	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.468T>C	1.37:g.94343023A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Silent	SNP	ENST00000436063.2	37	CCDS44174.1																																																																																			A|0.587;G|0.413	0.413	strong		0.393	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
JMY	133746	hgsc.bcm.edu	37	5	78610361	78610361	+	Silent	SNP	C	C	T	rs61751239	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:78610361C>T	ENST00000396137.4	+	9	2808	c.2346C>T	c.(2344-2346)ccC>ccT	p.P782P	JMY_ENST00000412001.1_Intron	NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	782	Pro-rich.				'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.P428P(1)|p.P782P(1)		endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		AACTGCCTCCCACTATATCTC	0.473													C|||	47	0.00938498	0.0008	0.0202	5008	,	,		15320	0.0		0.0298	False		,,,				2504	0.002				p.P782P		Atlas-SNP	.											.	JMY	82	.	2	Substitution - coding silent(2)	lung(2)	c.C2346T						PASS	.	C		17,4049		0,17,2016	201.0	204.0	203.0		2346	3.2	0.5	5	dbSNP_129	203	239,8145		3,233,3956	no	coding-synonymous	JMY	NM_152405.4		3,250,5972	TT,TC,CC		2.8507,0.4181,2.0562		782/989	78610361	256,12194	2033	4192	6225	SO:0001819	synonymous_variant	133746	exon9			GCCTCCCACTATA	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.2346C>T	5.37:g.78610361C>T		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	235	110	0.468085	NM_152405	A1L4P5|B5MDS2|B5MDT0	Silent	SNP	ENST00000396137.4	37	CCDS4047.3																																																																																			C|0.983;T|0.017	0.017	strong		0.473	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	
EIF5B	9669	hgsc.bcm.edu	37	2	99978048	99978048	+	Silent	SNP	G	G	A	rs12233086	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	241	0	0		WXS	Illumina HiSeq	Phase_I	265	133	0.501887	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	
SIRPA	140885	hgsc.bcm.edu	37	20	1896060	1896060	+	Missense_Mutation	SNP	T	T	C	rs114499682|rs386811663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1896060T>C	ENST00000358771.4	+	2	547	c.395T>C	c.(394-396)gTg>gCg	p.V132A	SIRPA_ENST00000356025.3_Missense_Mutation_p.V132A|SIRPA_ENST00000400068.3_Missense_Mutation_p.V132A	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	132	Ig-like V-type.		V -> T (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CCCGATGACGTGGAGTTTAAG	0.527													T|||	2050	0.409345	0.2761	0.4222	5008	,	,		15517	0.625		0.3171	False		,,,				2504	0.453				p.V132A	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,caecum,carcinoma,+1,2	SIRPA	83	2	0			c.T395C						scavenged	.						110.0	94.0	99.0					20																	1896060		2199	4290	6489	SO:0001583	missense	140885	exon3			ATGACGTGGAGTT	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.395T>C	20.37:g.1896060T>C	ENSP00000351621:p.Val132Ala	Somatic	434	1	0.00230415		WXS	Illumina HiSeq	Phase_I	224	26	0.116071	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.858225	0.32791	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.63913	-0.07;-0.07;-0.07	5.11	-4.1	0.03940	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	2.497550	0.01234	N	0.008420	T	0.55257	0.1909	L	0.47190	1.495	0.09310	N	1	B;B;B	0.18741	0.028;0.011;0.03	B;B;B	0.33295	0.113;0.125;0.161	T	0.39165	-0.9627	10	0.33141	T	0.24	.	4.5618	0.12163	0.5656:0.1906:0.0:0.2438	.	112;132;132	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	A	132	ENSP00000382941:V132A;ENSP00000348307:V132A;ENSP00000351621:V132A	ENSP00000348307:V132A	V	+	2	0	SIRPA	1844060	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-1.908000	0.01587	-0.575000	0.05982	-0.530000	0.04314	GTG	T|0.684;C|0.317	0.317	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
INSL3	3640	hgsc.bcm.edu	37	19	17932138	17932138	+	Missense_Mutation	SNP	T	T	C	rs6523	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17932138T>C	ENST00000317306.7	-	1	194	c.178A>G	c.(178-180)Acc>Gcc	p.T60A	INSL3_ENST00000379695.5_Missense_Mutation_p.T60A	NM_005543.3	NP_005534.2	P51460	INSL3_HUMAN	insulin-like 3 (Leydig cell)	60			T -> A (common polymorphism; dbSNP:rs6523). {ECO:0000269|PubMed:10729310, ECO:0000269|PubMed:10759163, ECO:0000269|PubMed:11095425, ECO:0000269|PubMed:11182749, ECO:0000269|PubMed:11380919, ECO:0000269|PubMed:11383919, ECO:0000269|PubMed:11746019, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8020942, ECO:0000269|PubMed:8034302}.		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|perinuclear region of cytoplasm (GO:0048471)	insulin receptor binding (GO:0005158)|protease binding (GO:0002020)|receptor binding (GO:0005102)			breast(1)|lung(1)	2						TCGCCTCCGGTCGCAGGCCTC	0.701													C|||	3436	0.686102	0.8631	0.6124	5008	,	,		13644	0.6151		0.6481	False		,,,				2504	0.6115				p.T60A		Atlas-SNP	.											INSL3,NS,carcinoma,0,1	INSL3	8	1	0			c.A178G						PASS	.	C	ALA/THR	3090,632		1308,474,79	3.0	4.0	4.0		178	1.2	0.0	19	dbSNP_52	4	5029,2275		1741,1547,364	no	missense	INSL3	NM_005543.2	58	3049,2021,443	CC,CT,TT		31.1473,16.9801,26.365	benign	60/132	17932138	8119,2907	1861	3652	5513	SO:0001583	missense	3640	exon1			CTCCGGTCGCAGG		CCDS12365.1, CCDS58655.1	19p13.2-p12	2013-02-26	2003-05-13			ENSG00000248099		"""Endogenous ligands"""	6086	protein-coding gene	gene with protein product	"""prepro-INSL3"""	146738	"""relaxin-like factor"""	RLNL		8020942	Standard	NM_001265587		Approved	RLF, MGC119818, MGC119819	uc010ebf.2	P51460		ENST00000317306.7:c.178A>G	19.37:g.17932138T>C	ENSP00000321724:p.Thr60Ala	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	18	6	0.333333	NM_005543	B4DZ72|G3XAG0|Q3KPI5|Q3KPI6|Q6YNB5|Q9UEA2|Q9UPH6	Missense_Mutation	SNP	ENST00000317306.7	37	CCDS12365.1	1503	0.6881868131868132	409	0.8313008130081301	237	0.6546961325966851	364	0.6363636363636364	493	0.6503957783641161	C	0.049	-1.256708	0.01457	0.830199	0.688527	ENSG00000248099	ENST00000317306;ENST00000379695	D;D	0.87809	-2.3;-1.8	3.48	1.21	0.21127	Insulin-like (4);	.	.	.	.	T	0.00012	0.0000	N	0.00263	-1.745	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.38457	-0.9660	8	0.02654	T	1	.	6.0014	0.19523	0.0:0.6253:0.0:0.3747	rs6523;rs2286662;rs11540330;rs17403483;rs2286662	60;60	G3XAG0;P51460	.;INSL3_HUMAN	A	60	ENSP00000321724:T60A;ENSP00000369017:T60A	ENSP00000321724:T60A	T	-	1	0	INSL3	17793138	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.870000	0.04228	0.199000	0.20427	-0.338000	0.08134	ACC	T|0.225;G|0.175	.	strong		0.701	INSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466836.1	NM_005543	
SERPINI2	5276	hgsc.bcm.edu	37	3	167189607	167189607	+	Missense_Mutation	SNP	A	A	C	rs17246389	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000461846.1_Missense_Mutation_p.L6V|SERPINI2_ENST00000471111.1_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	67	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	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	
SENP3	26168	hgsc.bcm.edu	37	17	7468277	7468277	+	Splice_Site	SNP	C	C	T	rs35596387	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7468277C>T	ENST00000429205.2	+	4	1006	c.957C>T	c.(955-957)agC>agT	p.S319S	SENP3_ENST00000321337.7_Splice_Site_p.S319S|SENP3_ENST00000578868.1_3'UTR|SENP3-EIF4A1_ENST00000579777.1_RNA			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	319						cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				TTCCACCAGGCATCTTGGACG	0.532													C|||	125	0.0249601	0.0	0.0086	5008	,	,		19654	0.0		0.0388	False		,,,				2504	0.0818				p.S319S		Atlas-SNP	.											.	SENP3	18	.	0			c.C957T						PASS	.	C		21,3889		0,21,1934	53.0	56.0	55.0		957	4.5	1.0	17	dbSNP_126	55	266,8028		7,252,3888	yes	coding-synonymous-near-splice	SENP3	NM_015670.5		7,273,5822	TT,TC,CC		3.2071,0.5371,2.3517		319/575	7468277	287,11917	1955	4147	6102	SO:0001630	splice_region_variant	26168	exon4			ACCAGGCATCTTG	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.956-1C>T	17.37:g.7468277C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	37																																																																																				C|0.976;T|0.024	0.024	strong		0.532	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	Silent
NETO1	81832	hgsc.bcm.edu	37	18	70526301	70526301	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:70526301T>C	ENST00000327305.6	-	4	886	c.229A>G	c.(229-231)Aga>Gga	p.R77G	NETO1_ENST00000299430.2_Missense_Mutation_p.R76G|NETO1_ENST00000397929.1_Missense_Mutation_p.R76G|NETO1_ENST00000580049.1_5'UTR|NETO1_ENST00000583169.1_Missense_Mutation_p.R77G	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	77	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		ATGCACTGTCTTGGAGCGGCT	0.368																																					p.R77G		Atlas-SNP	.											.	NETO1	178	.	0			c.A229G						PASS	.						57.0	57.0	57.0					18																	70526301		2203	4300	6503	SO:0001583	missense	81832	exon4			ACTGTCTTGGAGC	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.229A>G	18.37:g.70526301T>C	ENSP00000313088:p.Arg77Gly	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	150	51	0.34	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	T	9.808	1.182281	0.21787	.	.	ENSG00000166342	ENST00000327305;ENST00000299430;ENST00000397929	T;T;T	0.23754	1.89;1.89;2.15	5.35	5.35	0.76521	CUB (5);	0.000000	0.64402	D	0.000003	T	0.23532	0.0569	N	0.01482	-0.84	0.80722	D	1	D;D;P	0.76494	0.999;0.989;0.592	D;D;B	0.80764	0.994;0.985;0.241	T	0.50233	-0.8852	10	0.25751	T	0.34	-24.7403	15.6405	0.76997	0.0:0.0:0.0:1.0	.	76;76;77	Q8TDF5-1;Q8TDF5-2;Q8TDF5	.;.;NETO1_HUMAN	G	77;76;76	ENSP00000313088:R77G;ENSP00000299430:R76G;ENSP00000381024:R76G	ENSP00000299430:R76G	R	-	1	2	NETO1	68677281	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.054000	0.57434	2.159000	0.67721	0.533000	0.62120	AGA	.	.	none		0.368	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999	
PCDHB6	56130	hgsc.bcm.edu	37	5	140531374	140531374	+	Silent	SNP	T	T	C	rs17844437	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140531374T>C	ENST00000231136.1	+	1	1536	c.1536T>C	c.(1534-1536)ttT>ttC	p.F512F	PCDHB6_ENST00000543635.1_Silent_p.F376F	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	512	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)	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)			GCCACCTGTTTGCCCTCAGGT	0.682													C|||	250	0.0499201	0.0038	0.121	5008	,	,		16596	0.0169		0.1044	False		,,,				2504	0.0399				p.F512F		Atlas-SNP	.											.	PCDHB6	161	.	0			c.T1536C						PASS	.	C		102,4304	810.0+/-416.0	2,98,2103	81.0	84.0	83.0		1536	0.2	0.4	5	dbSNP_123	83	923,7677	772.0+/-407.7	49,825,3426	no	coding-synonymous	PCDHB6	NM_018939.2		51,923,5529	CC,CT,TT		10.7326,2.315,7.881		512/795	140531374	1025,11981	2203	4300	6503	SO:0001819	synonymous_variant	56130	exon1			CCTGTTTGCCCTC	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.1536T>C	5.37:g.140531374T>C		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	187	94	0.502674	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																			T|0.924;C|0.076	0.076	strong		0.682	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
HLX	3142	hgsc.bcm.edu	37	1	221054571	221054571	+	Missense_Mutation	SNP	G	G	A	rs373398191		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:221054571G>A	ENST00000366903.6	+	2	2129	c.628G>A	c.(628-630)Ggg>Agg	p.G210R	HLX_ENST00000549319.1_5'Flank|HLA-AS1_ENST00000552026.1_RNA	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	210					cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		GCGGCCCGCCGGGGTGCACCT	0.577																																					p.G210R		Atlas-SNP	.											HLX,NS,carcinoma,-1,1	HLX	67	1	0			c.G628A						scavenged	.	G	ARG/GLY	0,4406		0,0,2203	108.0	118.0	115.0		628	5.8	0.1	1		115	1,8599	1.2+/-3.3	0,1,4299	no	missense	HLX	NM_021958.3	125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	210/489	221054571	1,13005	2203	4300	6503	SO:0001583	missense	3142	exon2			CCCGCCGGGGTGC	BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"""Homeoboxes / ANTP class : NKL subclass"""	4978	protein-coding gene	gene with protein product		142995	"""H2.0 (Drosophila)-like homeo box 1"", ""H2.0-like homeobox 1 (Drosophila)"", ""H2.0-like homeobox 1"""	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.628G>A	1.37:g.221054571G>A	ENSP00000355870:p.Gly210Arg	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	272	4	0.0147059	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.227763	0.79576	0.0	1.16E-4	ENSG00000136630	ENST00000366903	D	0.90444	-2.67	5.82	5.82	0.92795	.	0.092932	0.44688	D	0.000421	D	0.87237	0.6127	L	0.29908	0.895	0.80722	D	1	D	0.57257	0.979	P	0.44518	0.452	D	0.85465	0.1169	10	0.26408	T	0.33	-23.1752	19.6956	0.96023	0.0:0.0:1.0:0.0	.	210	Q14774	HLX_HUMAN	R	210	ENSP00000355870:G210R	ENSP00000355870:G210R	G	+	1	0	HLX	219121194	1.000000	0.71417	0.085000	0.20634	0.344000	0.29017	9.137000	0.94496	2.756000	0.94617	0.561000	0.74099	GGG	.	.	none		0.577	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
TRAK1	22906	hgsc.bcm.edu	37	3	42251263	42251263	+	Silent	SNP	C	C	T	rs2290134	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:42251263C>T	ENST00000327628.5	+	14	2149	c.1749C>T	c.(1747-1749)tcC>tcT	p.S583S	TRAK1_ENST00000341421.3_Silent_p.S525S|TRAK1_ENST00000396175.1_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	52	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	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	
ZNF99	7652	hgsc.bcm.edu	37	19	22940827	22940827	+	Silent	SNP	T	T	C	rs142615427	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22940827T>C	ENST00000596209.1	-	4	1974	c.1884A>G	c.(1882-1884)aaA>aaG	p.K628K	ZNF99_ENST00000397104.3_Silent_p.K537K	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	628					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(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGCTAAAAGCTTTGCCACATT	0.383													T|||	447	0.0892572	0.0681	0.0879	5008	,	,		20061	0.0933		0.0924	False		,,,				2504	0.1115				p.K628K		Atlas-SNP	.											.	ZNF99	273	.	0			c.A1884G						PASS	.	T		247,3709		8,231,1739	36.0	38.0	37.0		1611	0.0	0.1	19	dbSNP_134	37	697,7647		32,633,3507	no	coding-synonymous	ZNF99	NM_001080409.2		40,864,5246	CC,CT,TT		8.3533,6.2437,7.6748		537/912	22940827	944,11356	1978	4172	6150	SO:0001819	synonymous_variant	7652	exon4			AAAAGCTTTGCCA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1884A>G	19.37:g.22940827T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_001080409	M0R335	Silent	SNP	ENST00000596209.1	37	CCDS59369.1																																																																																			T|0.921;C|0.079	0.079	strong		0.383	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
GANC	2595	hgsc.bcm.edu	37	15	42643538	42643538	+	Missense_Mutation	SNP	A	A	G	rs7180279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42643538A>G	ENST00000318010.8	+	23	2783	c.2543A>G	c.(2542-2544)cAg>cGg	p.Q848R	RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000356316.3_5'UTR	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	848			Q -> R (in dbSNP:rs7180279). {ECO:0000269|PubMed:12370436}.		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)	TTTGCTGACCAGAGGGGTCAT	0.483													A|||	744	0.148562	0.2035	0.2925	5008	,	,		17919	0.0972		0.0477	False		,,,				2504	0.1288				p.Q848R		Atlas-SNP	.											.	GANC	57	.	0			c.A2543G						PASS	.	A	ARG/GLN	781,3625	315.8+/-294.3	67,647,1489	133.0	120.0	124.0		2543	2.8	0.8	15	dbSNP_116	124	486,8112	141.9+/-198.1	12,462,3825	yes	missense	GANC	NM_198141.2	43	79,1109,5314	GG,GA,AA		5.6525,17.7258,9.7432	benign	848/915	42643538	1267,11737	2203	4299	6502	SO:0001583	missense	2595	exon23			CTGACCAGAGGGG	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.2543A>G	15.37:g.42643538A>G	ENSP00000326227:p.Gln848Arg	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	97	19	0.195876	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	250	0.11446886446886446	102	0.2073170731707317	83	0.2292817679558011	37	0.06468531468531469	28	0.036939313984168866	A	11.83	1.755487	0.31046	0.177258	0.056525	ENSG00000214013	ENST00000318010	D	0.86297	-2.1	5.38	2.85	0.33270	.	0.928257	0.09209	N	0.833473	T	0.00073	0.0002	N	0.03608	-0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.06643	-1.0815	9	0.28530	T	0.3	-1.9263	5.2189	0.15358	0.7246:0.1809:0.0945:0.0	rs7180279;rs52792254;rs60285266;rs7180279	848	Q8TET4	GANC_HUMAN	R	848	ENSP00000326227:Q848R	ENSP00000447925:Q80R	Q	+	2	0	GANC	40430830	0.000000	0.05858	0.765000	0.31456	0.678000	0.39670	0.861000	0.27885	2.051000	0.60960	0.528000	0.53228	CAG	A|0.898;G|0.102	0.102	strong		0.483	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
SPATA3	130560	hgsc.bcm.edu	37	2	231861071	231861071	+	Silent	SNP	T	T	C	rs61738380	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231861071T>C	ENST00000452881.1	+	1	231	c.123T>C	c.(121-123)agT>agC	p.S41S	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_Silent_p.S41S|SPATA3_ENST00000424440.1_Silent_p.S41S|SPATA3_ENST00000455816.1_Silent_p.S41S			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	41			Missing.							endometrium(2)|lung(1)	3						AGCAGCCTAGTCCTGAATCCA	0.597																																					p.S41S		Atlas-SNP	.											SPATA3,colon,carcinoma,0,2	SPATA3	52	2	0			c.T123C						scavenged	.						135.0	148.0	144.0					2																	231861071		692	1591	2283	SO:0001819	synonymous_variant	130560	exon1			GCCTAGTCCTGAA	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.123T>C	2.37:g.231861071T>C		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_139073	Q86WX5|Q8N9Y6	Silent	SNP	ENST00000452881.1	37	CCDS2481.1																																																																																			T|0.222;C|0.778	0.778	strong		0.597	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
MRGPRF	116535	hgsc.bcm.edu	37	11	68773403	68773403	+	Silent	SNP	G	G	A	rs11544722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68773403G>A	ENST00000309099.6	-	3	757	c.375C>T	c.(373-375)tgC>tgT	p.C125C	MRGPRF_ENST00000441623.1_Silent_p.C125C|RP11-554A11.5_ENST00000562506.1_RNA	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	125						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TAAGGAACATGCAGAGCCCCA	0.687													G|||	1164	0.232428	0.2065	0.1354	5008	,	,		14674	0.2272		0.2694	False		,,,				2504	0.3037				p.C125C		Atlas-SNP	.											.	MRGPRF	22	.	0			c.C375T						PASS	.	G	,	885,3459		100,685,1387	21.0	21.0	21.0		375,375	2.7	0.8	11	dbSNP_120	21	2185,6331		295,1595,2368	no	coding-synonymous,coding-synonymous	MRGPRF	NM_001098515.1,NM_145015.4	,	395,2280,3755	AA,AG,GG		25.6576,20.3729,23.8725	,	125/344,125/344	68773403	3070,9790	2172	4258	6430	SO:0001819	synonymous_variant	116535	exon3			GAACATGCAGAGC	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"""GPCR / Class A : Orphans"""	24828	protein-coding gene	gene with protein product		607233	"""G protein-coupled receptor 168"", ""G protein-coupled receptor 140"""	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.375C>T	11.37:g.68773403G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_001098515	B3KV43|Q8NBK8	Silent	SNP	ENST00000309099.6	37	CCDS8188.1																																																																																			G|0.763;A|0.237	0.237	strong		0.687	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015	
CCDC37	348807	hgsc.bcm.edu	37	3	126137558	126137558	+	Silent	SNP	C	C	T	rs4679242|rs386665601	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126137558C>T	ENST00000352312.1	+	7	690	c.591C>T	c.(589-591)gcC>gcT	p.A197A	CCDC37_ENST00000505024.1_Silent_p.A198A|CCDC37_ENST00000393425.1_Silent_p.A198A	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	197										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)		AGAAGGACGCCGCCTTGTTCG	0.652													C|||	1248	0.249201	0.3623	0.2666	5008	,	,		14683	0.1339		0.1869	False		,,,				2504	0.2669				p.A197A		Atlas-SNP	.											.	CCDC37	69	.	0			c.C591T						PASS	.	C		1565,2827		278,1009,909	47.0	51.0	50.0		591	-5.7	0.0	3	dbSNP_111	50	1826,6770		204,1418,2676	no	coding-synonymous	CCDC37	NM_182628.2		482,2427,3585	TT,TC,CC		21.2424,35.633,26.1087		197/612	126137558	3391,9597	2196	4298	6494	SO:0001819	synonymous_variant	348807	exon7			GGACGCCGCCTTG	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.591C>T	3.37:g.126137558C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			C|0.760;T|0.240	0.240	strong		0.652	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
HOXA1	3198	hgsc.bcm.edu	37	7	27135096	27135096	+	Missense_Mutation	SNP	G	G	T	rs45571645	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:27135096G>T	ENST00000343060.4	-	1	497	c.436C>A	c.(436-438)Cac>Aac	p.H146N	HOXA1_ENST00000355633.5_Intron|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000495032.1_RNA|HOTAIRM1_ENST00000425358.2_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	146	Poly-His.				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						TAACCCTGGTGGTGGTGGTGA	0.557													G|||	27	0.00539137	0.0	0.0058	5008	,	,		15833	0.0		0.0179	False		,,,				2504	0.0051				p.H146N		Atlas-SNP	.											.	HOXA1	64	.	0			c.C436A						PASS	.	G	ASN/HIS,	18,4388	27.2+/-55.0	0,18,2185	65.0	67.0	67.0		436,	5.0	1.0	7	dbSNP_127	67	166,8434	78.4+/-141.0	0,166,4134	yes	missense,intron	HOXA1	NM_005522.4,NM_153620.2	68,	0,184,6319	TT,TG,GG		1.9302,0.4085,1.4147	possibly-damaging,	146/336,	27135096	184,12822	2203	4300	6503	SO:0001583	missense	3198	exon1			CCTGGTGGTGGTG		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.436C>A	7.37:g.27135096G>T	ENSP00000343246:p.His146Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	122	48	0.393443	NM_005522	A4D184|B2R8U7|O43363	Missense_Mutation	SNP	ENST00000343060.4	37	CCDS5401.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	G	14.49	2.552098	0.45487	0.004085	0.019302	ENSG00000105991	ENST00000343060	T	0.28454	1.61	5.01	5.01	0.66863	.	0.069967	0.64402	D	0.000017	T	0.17152	0.0412	M	0.62723	1.935	0.80722	D	1	B	0.34061	0.436	B	0.30179	0.112	T	0.03121	-1.1070	10	0.29301	T	0.29	.	15.8497	0.78921	0.0:0.0:1.0:0.0	rs45571645;rs61733418	146	P49639	HXA1_HUMAN	N	146	ENSP00000343246:H146N	ENSP00000343246:H146N	H	-	1	0	HOXA1	27101621	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.375000	0.52410	2.612000	0.88384	0.561000	0.74099	CAC	G|0.988;T|0.012	0.012	strong		0.557	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1		
NLRP13	126204	hgsc.bcm.edu	37	19	56424443	56424443	+	Missense_Mutation	SNP	T	T	C	rs303997	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	134	2	0.0149254		WXS	Illumina HiSeq	Phase_I	140	140	1	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	
CLSTN3	9746	hgsc.bcm.edu	37	12	7281317	7281317	+	5'Flank	SNP	C	C	T	rs10963	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7281317C>T	ENST00000266546.6	+	0	0				RP11-273B20.1_ENST00000544657.1_RNA|RP11-273B20.1_ENST00000538062.1_RNA|RBP5_ENST00000266560.3_Missense_Mutation_p.D19N|RBP5_ENST00000542370.1_Missense_Mutation_p.D19N	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3						homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						TGCAGGTAGTCCTCCATGTTC	0.552													C|||	1014	0.202476	0.2095	0.1686	5008	,	,		-128	0.3938		0.1103	False		,,,				2504	0.1145				p.D19N		Atlas-SNP	.											.	RBP5	20	.	0			c.G55A						PASS	.	C	ASN/ASP	969,3437	337.6+/-304.9	109,751,1343	142.0	114.0	123.0		55	1.3	1.0	12	dbSNP_52	123	864,7736	182.2+/-230.7	47,770,3483	yes	missense	RBP5	NM_031491.2	23	156,1521,4826	TT,TC,CC		10.0465,21.9927,14.0935	benign	19/136	7281317	1833,11173	2203	4300	6503	SO:0001631	upstream_gene_variant	83758	exon1			GGTAGTCCTCCAT	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167		12.37:g.7281317C>T	Exception_encountered	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	207	101	0.487923	NM_031491	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	451	0.2065018315018315	89	0.18089430894308944	52	0.143646408839779	224	0.3916083916083916	86	0.11345646437994723	C	10.81	1.456633	0.26161	0.219927	0.100465	ENSG00000139194	ENST00000266560;ENST00000542370	T;T	0.23552	1.9;1.9	3.25	1.29	0.21616	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.562793	0.18253	N	0.146895	T	0.00012	0.0000	L	0.41236	1.265	0.46376	P	9.829999999999561E-4	B	0.09022	0.002	B	0.14023	0.01	T	0.45352	-0.9267	9	0.33141	T	0.24	.	5.8178	0.18506	0.0:0.4674:0.3927:0.1398	rs10963;rs1139108;rs1801503;rs3203160;rs11540815;rs17342618;rs17350246;rs56609724;rs59039984;rs10963	19	P82980	RET5_HUMAN	N	19	ENSP00000266560:D19N;ENSP00000438083:D19N	ENSP00000266560:D19N	D	-	1	0	RBP5	7172584	0.151000	0.22747	0.954000	0.39281	0.939000	0.58152	0.199000	0.17237	0.340000	0.23745	0.491000	0.48974	GAC	C|0.823;T|0.177	0.177	strong		0.552	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
SEPT1	1731	hgsc.bcm.edu	37	16	30393147	30393147	+	Missense_Mutation	SNP	C	C	A	rs34518080	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:30393147C>A	ENST00000571393.1	-	5	425	c.239G>T	c.(238-240)gGt>gTt	p.G80V	SEPT1_ENST00000605106.1_Missense_Mutation_p.G85V|SEPT1_ENST00000321367.3_Missense_Mutation_p.G127V|SEPT1_ENST00000570039.1_5'Flank			Q8WYJ6	SEPT1_HUMAN	septin 1	80	Septin-type G.		G -> V (in dbSNP:rs34518080).		cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			CACTTTCACACCCCCTTCCTC	0.607													C|||	69	0.013778	0.0008	0.0159	5008	,	,		17801	0.002		0.0437	False		,,,				2504	0.0112				p.G127V		Atlas-SNP	.											.	SEPT1	34	.	0			c.G380T						PASS	.	C	,,VAL/GLY	27,4367	34.3+/-65.2	0,27,2170	149.0	132.0	138.0		,,239	5.1	0.8	16	dbSNP_126	138	338,8262	115.5+/-175.4	7,324,3969	yes	intron,intron,missense	SEPT1,ZNF48	NM_001214906.1,NM_001214907.1,NM_052838.4	,,109	7,351,6139	AA,AC,CC		3.9302,0.6145,2.809	,,probably-damaging	,,80/368	30393147	365,12629	2197	4300	6497	SO:0001583	missense	1731	exon5			TTCACACCCCCTT	AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"""Septins"""	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984	ENST00000571393.1:c.239G>T	16.37:g.30393147C>A	ENSP00000460441:p.Gly80Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	128	125	0.976562	NM_052838	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Missense_Mutation	SNP	ENST00000571393.1	37		39	0.017857142857142856	2	0.0040650406504065045	9	0.024861878453038673	1	0.0017482517482517483	27	0.03562005277044855	C	12.63	1.995467	0.35226	0.006145	0.039302	ENSG00000180096	ENST00000321367	.	.	.	5.06	5.06	0.68205	.	0.112623	0.39475	N	0.001348	T	0.59972	0.2233	M	0.85462	2.755	0.80722	D	1	D;P	0.89917	1.0;0.649	D;B	0.78314	0.991;0.355	T	0.78876	-0.2031	9	0.87932	D	0	.	17.5745	0.87944	0.0:1.0:0.0:0.0	rs34518080;rs34518080	127;80	B4E0I4;Q8WYJ6	.;SEPT1_HUMAN	V	80	.	ENSP00000324511:G80V	G	-	2	0	SEPT1	30300648	1.000000	0.71417	0.835000	0.33067	0.002000	0.02628	7.773000	0.85462	2.508000	0.84585	0.655000	0.94253	GGT	C|0.975;A|0.025	0.025	strong		0.607	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838	
APBA2	321	hgsc.bcm.edu	37	15	29368269	29368269	+	Silent	SNP	G	G	A	rs149285403	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:29368269G>A	ENST00000558402.1	+	7	1643	c.1044G>A	c.(1042-1044)gtG>gtA	p.V348V	APBA2_ENST00000561069.1_Silent_p.V348V|APBA2_ENST00000558259.1_Silent_p.V348V|APBA2_ENST00000411764.1_Silent_p.V348V|APBA2_ENST00000558330.1_Silent_p.V348V			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	348					in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CAAAGAAGGTGGCATCATTTC	0.378																																					p.V348V		Atlas-SNP	.											.	APBA2	132	.	0			c.G1044A						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	185.0	185.0	185.0		1044,1044	3.9	1.0	15	dbSNP_134	185	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	0,20,6483	AA,AG,GG		0.2093,0.0454,0.1538	,	348/738,348/750	29368269	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	321	exon5			GAAGGTGGCATCA	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1044G>A	15.37:g.29368269G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	95	76	0.8	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	37	CCDS10022.1																																																																																			G|0.999;A|0.001	0.001	strong		0.378	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
SYNPO	11346	hgsc.bcm.edu	37	5	149998128	149998128	+	Missense_Mutation	SNP	G	G	A	rs6579797	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149998128G>A	ENST00000394243.1	+	2	573	c.199G>A	c.(199-201)Gac>Aac	p.D67N	SYNPO_ENST00000522122.1_Missense_Mutation_p.D67N	NM_001166208.1	NP_001159680.1	Q8N3V7	SYNPO_HUMAN	synaptopodin	67					positive regulation of actin filament bundle assembly (GO:0032233)|regulation of stress fiber assembly (GO:0051492)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic membrane (GO:0045211)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin binding (GO:0003779)			NS(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(4)|prostate(1)|urinary_tract(2)	18		Medulloblastoma(196;0.134)|all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GAGTGGGGACGACTCTGCCTG	0.667													A|||	861	0.171925	0.2648	0.0461	5008	,	,		18209	0.2738		0.0149	False		,,,				2504	0.1922				p.D67N		Atlas-SNP	.											SYNPO_ENST00000394243,colon,carcinoma,0,1	SYNPO	147	1	0			c.G199A						PASS	.	A	ASN/ASP,ASN/ASP	325,1059		33,259,400	50.0	64.0	60.0		199,199	3.6	0.1	5	dbSNP_116	60	41,3141		0,41,1550	yes	missense,missense	SYNPO	NM_001166208.1,NM_001166209.1	23,23	33,300,1950	AA,AG,GG		1.2885,23.4827,8.0158	,	67/930,67/930	149998128	366,4200	692	1591	2283	SO:0001583	missense	11346	exon2			GGGGACGACTCTG	AF499137	CCDS4308.1, CCDS54937.1, CCDS54938.1	5q33.1	2008-02-05			ENSG00000171992	ENSG00000171992			30672	protein-coding gene	gene with protein product		608155				9314539, 10470851	Standard	NM_007286		Approved	KIAA1029	uc003lsn.3	Q8N3V7	OTTHUMG00000130078	ENST00000394243.1:c.199G>A	5.37:g.149998128G>A	ENSP00000377789:p.Asp67Asn	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	228	120	0.526316	NM_001166209	A5PKZ8|D3DQG8|O15271|Q9UPX1	Missense_Mutation	SNP	ENST00000394243.1	37	CCDS54937.1	312	0.14285714285714285	130	0.26422764227642276	14	0.03867403314917127	157	0.2744755244755245	11	0.014511873350923483	A	0.175	-1.067557	0.01934	0.234827	0.012885	ENSG00000171992	ENST00000394243;ENST00000522122	T;T	0.22134	1.97;1.97	3.56	3.56	0.40772	.	1.605810	0.04156	N	0.322269	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39840	-0.9594	9	0.02654	T	1	-0.7622	5.5763	0.17225	0.8694:0.0:0.1306:0.0	rs6579797;rs6579797	67	Q8N3V7	SYNPO_HUMAN	N	67	ENSP00000377789:D67N;ENSP00000428378:D67N	ENSP00000377789:D67N	D	+	1	0	SYNPO	149978321	0.124000	0.22315	0.069000	0.20011	0.651000	0.38670	1.109000	0.31135	0.442000	0.26555	-0.521000	0.04368	GAC	G|0.850;A|0.150	0.150	strong		0.667	SYNPO-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252371.1	NM_007286	
ZNF493	284443	hgsc.bcm.edu	37	19	21607296	21607296	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21607296G>A	ENST00000355504.4	+	2	1717	c.1451G>A	c.(1450-1452)cGa>cAa	p.R484Q	ZNF493_ENST00000392288.2_Missense_Mutation_p.R612Q|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	484					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(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						GCTTTTAACCGATCTTCAATC	0.368																																					p.R612Q		Atlas-SNP	.											ZNF493_ENST00000392288,NS,carcinoma,0,4	ZNF493	178	4	0			c.G1835A						scavenged	.						33.0	35.0	35.0					19																	21607296		2201	4298	6499	SO:0001583	missense	284443	exon4			TTAACCGATCTTC	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1451G>A	19.37:g.21607296G>A	ENSP00000347691:p.Arg484Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	4	0.056338	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	0.005	-2.171271	0.00315	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.07567	3.18;3.18	0.859	-1.72	0.08107	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03136	0.0092	L	0.27944	0.81	0.09310	N	1	B;B	0.31077	0.307;0.199	B;B	0.17979	0.02;0.002	T	0.42292	-0.9460	9	0.02654	T	1	.	1.7831	0.03036	0.3925:0.0:0.3315:0.276	.	484;612	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	Q	612;484	ENSP00000376110:R612Q;ENSP00000347691:R484Q	ENSP00000347691:R484Q	R	+	2	0	ZNF493	21399136	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.205000	0.00141	-1.052000	0.03222	-1.038000	0.02383	CGA	.	.	none		0.368	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
PLK2	10769	hgsc.bcm.edu	37	5	57753149	57753149	+	Silent	SNP	A	A	G	rs17767072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:57753149A>G	ENST00000274289.3	-	7	1167	c.867T>C	c.(865-867)taT>taC	p.Y289Y	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	289	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		TTATGCACCTATAAGTTTCTT	0.423													A|||	590	0.117812	0.1967	0.2017	5008	,	,		18271	0.0		0.1282	False		,,,				2504	0.0624				p.Y289Y		Atlas-SNP	.											.	PLK2	71	.	0			c.T867C						PASS	.	A		789,3617	315.8+/-294.3	89,611,1503	64.0	65.0	65.0		867	0.6	1.0	5	dbSNP_123	65	957,7643	209.0+/-250.3	56,845,3399	no	coding-synonymous	PLK2	NM_006622.2		145,1456,4902	GG,GA,AA		11.1279,17.9074,13.4246		289/686	57753149	1746,11260	2203	4300	6503	SO:0001819	synonymous_variant	10769	exon7			GCACCTATAAGTT		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"""serum-inducible kinase"""	607023	"""polo-like kinase 2 (Drosophila)"""				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.867T>C	5.37:g.57753149A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	37	CCDS3974.1																																																																																			A|0.871;G|0.129	0.129	strong		0.423	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622	
SACM1L	22908	hgsc.bcm.edu	37	3	45754685	45754685	+	Silent	SNP	A	A	G	rs2271619	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:45754685A>G	ENST00000389061.5	+	6	744	c.540A>G	c.(538-540)ccA>ccG	p.P180P	SACM1L_ENST00000418611.1_Silent_p.P77P|SACM1L_ENST00000541314.1_Silent_p.P119P	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	180	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		CTGCACAGCCAGAGGTAATGT	0.363													A|||	688	0.13738	0.2095	0.1138	5008	,	,		18601	0.12		0.1203	False		,,,				2504	0.092				p.P180P		Atlas-SNP	.											.	SACM1L	38	.	0			c.A540G						PASS	.	A		883,3523	342.0+/-307.0	87,709,1407	73.0	74.0	74.0		540	4.4	1.0	3	dbSNP_100	74	1103,7497	228.7+/-263.7	62,979,3259	no	coding-synonymous	SACM1L	NM_014016.3		149,1688,4666	GG,GA,AA		12.8256,20.0409,15.2699		180/588	45754685	1986,11020	2203	4300	6503	SO:0001819	synonymous_variant	22908	exon6			ACAGCCAGAGGTA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.540A>G	3.37:g.45754685A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_014016	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Silent	SNP	ENST00000389061.5	37	CCDS33745.1																																																																																			A|0.856;G|0.144	0.144	strong		0.363	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016	
GLOD4	51031	hgsc.bcm.edu	37	17	663472	663472	+	Missense_Mutation	SNP	C	C	A	rs77166377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:663472C>A	ENST00000301328.5	-	10	906	c.883G>T	c.(883-885)Gca>Tca	p.A295S	GLOD4_ENST00000536578.1_Missense_Mutation_p.A271S|GLOD4_ENST00000575800.1_5'Flank|GLOD4_ENST00000301329.6_Missense_Mutation_p.A280S			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4	295				A -> S (in Ref. 1; AAG17987). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TTATCTGCTGCCATTGCCTGT	0.408													C|||	40	0.00798722	0.0	0.0144	5008	,	,		16550	0.0		0.0278	False		,,,				2504	0.002				p.A280S		Atlas-SNP	.											.	GLOD4	12	.	0			c.G838T						PASS	.	C	SER/ALA	24,4382	31.7+/-61.6	0,24,2179	169.0	141.0	151.0		838	5.1	1.0	17	dbSNP_131	151	294,8306	108.4+/-169.1	5,284,4011	yes	missense	GLOD4	NM_016080.3	99	5,308,6190	AA,AC,CC		3.4186,0.5447,2.445	benign	280/299	663472	318,12688	2203	4300	6503	SO:0001583	missense	51031	exon9			CTGCTGCCATTGC	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.883G>T	17.37:g.663472C>A	ENSP00000301328:p.Ala295Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_016080	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	37		35	0.016025641025641024	0	0.0	5	0.013812154696132596	0	0.0	30	0.0395778364116095	C	17.67	3.445852	0.63178	0.005447	0.034186	ENSG00000167699	ENST00000301329;ENST00000397393;ENST00000301328;ENST00000536578	T;T;T	0.45668	0.9;0.9;0.89	6.02	5.05	0.67936	.	0.147602	0.64402	N	0.000011	T	0.15003	0.0362	M	0.69463	2.115	0.44702	D	0.997696	B;B;B	0.24426	0.026;0.103;0.038	B;B;B	0.24394	0.022;0.053;0.029	T	0.09207	-1.0685	10	0.38643	T	0.18	-8.9032	15.7871	0.78315	0.1371:0.8629:0.0:0.0	.	271;295;280	B7Z403;Q9HC38;Q9HC38-2	.;GLOD4_HUMAN;.	S	280;483;295;271	ENSP00000301329:A280S;ENSP00000301328:A295S;ENSP00000444315:A271S	ENSP00000301328:A295S	A	-	1	0	GLOD4	610222	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	4.689000	0.61723	1.545000	0.49373	0.655000	0.94253	GCA	C|0.975;A|0.025	0.025	strong		0.408	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
FLG2	388698	hgsc.bcm.edu	37	1	152328282	152328282	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152328282T>C	ENST00000388718.5	-	3	2052	c.1980A>G	c.(1978-1980)tcA>tcG	p.S660S	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	660	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACCTGAGCCTGATCCATATT	0.488																																					p.S660S		Atlas-SNP	.											FLG2,NS,carcinoma,0,4	FLG2	431	4	0			c.A1980G						scavenged	.						236.0	247.0	244.0					1																	152328282		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			TGAGCCTGATCCA	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1980A>G	1.37:g.152328282T>C		Somatic	303	6	0.019802		WXS	Illumina HiSeq	Phase_I	375	8	0.0213333	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			.	.	none		0.488	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
CNIH4	29097	hgsc.bcm.edu	37	1	224553602	224553602	+	Missense_Mutation	SNP	G	G	A	rs74546314	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:224553602G>A	ENST00000465271.1	+	3	235	c.160G>A	c.(160-162)Ggc>Agc	p.G54S	CNIH4_ENST00000468318.1_3'UTR|CNIH4_ENST00000366856.3_Missense_Mutation_p.G54S|CNIH4_ENST00000366858.3_Missense_Mutation_p.G54S|CNIH4_ENST00000366857.5_Missense_Mutation_p.G54S	NM_014184.3	NP_054903.1	Q9P003	CNIH4_HUMAN	cornichon family AMPA receptor auxiliary protein 4	54					intracellular signal transduction (GO:0035556)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(3)|lung(2)|ovary(2)	7				GBM - Glioblastoma multiforme(131;0.00341)		AGAATTGATTGGCCATACCAT	0.388													G|||	6	0.00119808	0.0	0.0	5008	,	,		20879	0.0		0.006	False		,,,				2504	0.0				p.G54S		Atlas-SNP	.											.	CNIH4	17	.	0			c.G160A						PASS	.	G	SER/GLY	1,4405	2.1+/-5.4	0,1,2202	465.0	346.0	386.0		160	5.2	1.0	1	dbSNP_131	386	39,8561	26.3+/-74.7	0,39,4261	yes	missense	CNIH4	NM_014184.2	56	0,40,6463	AA,AG,GG		0.4535,0.0227,0.3076	possibly-damaging	54/140	224553602	40,12966	2203	4300	6503	SO:0001583	missense	29097	exon3			TTGATTGGCCATA		CCDS1543.1, CCDS60429.1, CCDS60430.1	1q42.12	2013-08-28	2013-08-28		ENSG00000143771	ENSG00000143771			25013	protein-coding gene	gene with protein product			"""cornichon homolog 4 (Drosophila)"""			11042152	Standard	NM_014184		Approved	HSPC163	uc001hom.2	Q9P003	OTTHUMG00000037635	ENST00000465271.1:c.160G>A	1.37:g.224553602G>A	ENSP00000420443:p.Gly54Ser	Somatic	425	0	0		WXS	Illumina HiSeq	Phase_I	546	184	0.336996	NM_014184	A8K1Q8|B2R553|Q9H0X8	Missense_Mutation	SNP	ENST00000465271.1	37	CCDS1543.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	21.9	4.211635	0.79240	2.27E-4	0.004535	ENSG00000143771	ENST00000465271;ENST00000366858;ENST00000366857;ENST00000366856	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.24	5.24	0.73138	.	0.099013	0.64402	D	0.000002	T	0.31327	0.0793	L	0.33137	0.985	0.80722	D	1	P	0.49090	0.919	P	0.45753	0.492	T	0.04053	-1.0981	10	0.20519	T	0.43	-21.4206	19.1891	0.93656	0.0:0.0:1.0:0.0	.	54	Q9P003	CNIH4_HUMAN	S	54	ENSP00000420443:G54S;ENSP00000355823:G54S;ENSP00000355822:G54S;ENSP00000355821:G54S	ENSP00000355821:G54S	G	+	1	0	CNIH4	222620225	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.205000	0.95048	2.607000	0.88179	0.462000	0.41574	GGC	G|0.997;A|0.003	0.003	strong		0.388	CNIH4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091754.1	NM_014184	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702688	27702688	+	Silent	SNP	C	C	T	rs7087552	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:27702688C>T	ENST00000438700.3	-	1	609	c.492G>A	c.(490-492)gaG>gaA	p.E164E		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	164					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						CTAGGTCTTCCTCTTCGTCCT	0.652													C|||	993	0.198283	0.3805	0.2839	5008	,	,		14646	0.0129		0.2137	False		,,,				2504	0.0665				p.E164E		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G492A						PASS	.	C		1586,2820	485.3+/-360.3	282,1022,899	90.0	100.0	96.0		492	-5.0	0.0	10	dbSNP_116	96	1936,6664	332.3+/-320.0	234,1468,2598	no	coding-synonymous	PTCHD3	NM_001034842.3		516,2490,3497	TT,TC,CC		22.5116,35.9964,27.0798		164/768	27702688	3522,9484	2203	4300	6503	SO:0001819	synonymous_variant	374308	exon1			GTCTTCCTCTTCG	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.492G>A	10.37:g.27702688C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	78	15	0.192308	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			C|0.764;T|0.236	0.236	strong		0.652	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
CD300A	11314	hgsc.bcm.edu	37	17	72469966	72469966	+	Missense_Mutation	SNP	G	G	A	rs2272111	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:72469966G>A	ENST00000360141.3	+	2	620	c.332G>A	c.(331-333)cGa>cAa	p.R111Q	CD300A_ENST00000361933.3_Intron|CD300A_ENST00000310828.5_Intron|CD300A_ENST00000577511.1_5'UTR|CD300A_ENST00000392625.3_Intron	NM_001256841.1|NM_007261.3	NP_001243770.1|NP_009192.2	Q9UGN4	CLM8_HUMAN	CD300a molecule	111	Ig-like V-type.		R -> Q (in dbSNP:rs2272111). {ECO:0000269|PubMed:12483297, ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|immune system process (GO:0002376)|negative regulation of activation of JAK2 kinase activity (GO:1902569)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of eosinophil activation (GO:1902567)|negative regulation of eosinophil migration (GO:2000417)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell activation involved in immune response (GO:0033007)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of neutrophil activation (GO:1902564)|negative regulation of NK T cell activation (GO:0051134)|negative regulation of phagocytosis, engulfment (GO:0060101)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|regulation of T cell receptor signaling pathway (GO:0050856)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)|signaling receptor activity (GO:0038023)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(4)|urinary_tract(1)	16						CCATGGCTCCGAGACTTTCAT	0.567													G|||	1731	0.345647	0.705	0.2161	5008	,	,		17525	0.1964		0.1978	False		,,,				2504	0.2577				p.R111Q		Atlas-SNP	.											.	CD300A	40	.	0			c.G332A						PASS	.	G	GLN/ARG	2763,1643	659.8+/-400.6	875,1013,315	125.0	131.0	129.0		332	-2.2	0.0	17	dbSNP_100	129	1761,6839	319.5+/-314.2	187,1387,2726	no	missense	CD300A	NM_007261.2	43	1062,2400,3041	AA,AG,GG		20.4767,37.2901,34.7839	benign	111/300	72469966	4524,8482	2203	4300	6503	SO:0001583	missense	11314	exon2			GGCTCCGAGACTT	BC032352	CCDS32720.1, CCDS58590.1	17q25.2	2013-01-11	2006-03-28		ENSG00000167851	ENSG00000167851		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19319	protein-coding gene	gene with protein product		606790	"""CD300a antigen"""			9701027, 10746781	Standard	NM_007261		Approved	Irp60, CMRF35H, CMRF-35-H9, IRC1, IRC2, IGSF12	uc002jkv.4	Q9UGN4	OTTHUMG00000067612	ENST00000360141.3:c.332G>A	17.37:g.72469966G>A	ENSP00000353259:p.Arg111Gln	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	243	104	0.427984	NM_007261	A8MW96|O95100|Q9HD97|Q9P0F3|Q9UBK4|Q9UMS9|Q9UMT0	Missense_Mutation	SNP	ENST00000360141.3	37	CCDS32720.1	652	0.29853479853479853	334	0.6788617886178862	71	0.19613259668508287	107	0.18706293706293706	140	0.18469656992084432	G	0.945	-0.708406	0.03230	0.627099	0.204767	ENSG00000167851	ENST00000360141	T	0.02863	4.13	1.13	-2.22	0.06952	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.16368	0.405	0.58432	P	1.999999999946489E-6	B	0.15473	0.013	B	0.16289	0.015	T	0.11717	-1.0576	8	0.12103	T	0.63	.	4.3704	0.11244	0.4976:0.0:0.5024:0.0	rs2272111;rs11869780;rs59752364;rs2272111	111	Q9UGN4	CLM8_HUMAN	Q	111	ENSP00000353259:R111Q	ENSP00000353259:R111Q	R	+	2	0	CD300A	69981561	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.049000	0.00629	-0.558000	0.06118	-1.277000	0.01392	CGA	.	.	weak		0.567	CD300A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145091.1	NM_007261	
POLN	353497	hgsc.bcm.edu	37	4	2160894	2160894	+	Silent	SNP	C	C	T	rs10488836	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:2160894C>T	ENST00000511885.2	-	14	1952	c.1599G>A	c.(1597-1599)ttG>ttA	p.L533L	POLN_ENST00000382865.1_Silent_p.L533L|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	533					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)			GCCTGTATTCCAAAATTATCT	0.358								DNA polymerases (catalytic subunits)					C|||	1009	0.201478	0.2579	0.1686	5008	,	,		20719	0.3363		0.0706	False		,,,				2504	0.1442				p.L533L		Atlas-SNP	.											.	POLN	82	.	0			c.G1599A						PASS	.	C		1012,3394	376.1+/-321.9	116,780,1307	100.0	99.0	100.0		1599	3.6	1.0	4	dbSNP_119	100	521,8079	146.5+/-202.0	16,489,3795	no	coding-synonymous	POLN	NM_181808.2		132,1269,5102	TT,TC,CC		6.0581,22.9687,11.7869		533/901	2160894	1533,11473	2203	4300	6503	SO:0001819	synonymous_variant	353497	exon12			GTATTCCAAAATT	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.1599G>A	4.37:g.2160894C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Silent	SNP	ENST00000511885.2	37	CCDS3360.1	430	0.19688644688644688	124	0.25203252032520324	62	0.1712707182320442	191	0.3339160839160839	53	0.06992084432717678	C	9.161	1.018610	0.19355	0.229687	0.060581	ENSG00000130997	ENST00000511098	.	.	.	4.45	3.6	0.41247	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999996907	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.9353	7.6446	0.28312	0.0:0.887:0.0:0.113	rs10488836;rs58340560;rs10488836	.	.	.	X	166	.	.	W	-	2	0	POLN	2130692	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.431000	0.44775	2.460000	0.83146	0.650000	0.86243	TGG	C|0.840;T|0.160	0.160	strong		0.358	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
FAM160A1	729830	hgsc.bcm.edu	37	4	152577473	152577473	+	Nonsense_Mutation	SNP	C	C	T	rs367582779		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:152577473C>T	ENST00000505231.1	+	10	2800	c.2641C>T	c.(2641-2643)Cag>Tag	p.Q881*	FAM160A1_ENST00000435205.1_Nonsense_Mutation_p.Q881*			Q05DH4	F16A1_HUMAN	family with sequence similarity 160, member A1	881										endometrium(2)|kidney(1)	3						GATCATTACTCAGCTAGCCAG	0.507																																					p.Q881X		Atlas-SNP	.											.	FAM160A1	60	.	0			c.C2641T						PASS	.	C	stop/GLN	0,1384		0,0,692	87.0	76.0	79.0		2641	5.4	0.9	4		79	1,3181		0,1,1590	no	stop-gained	FAM160A1	NM_001109977.1		0,1,2282	TT,TC,CC		0.0314,0.0,0.0219		881/1041	152577473	1,4565	692	1591	2283	SO:0001587	stop_gained	729830	exon12			ATTACTCAGCTAG		CCDS47146.1	4q31.3	2012-11-30			ENSG00000164142	ENSG00000164142			34237	protein-coding gene	gene with protein product							Standard	NM_001109977		Approved	FLJ43373	uc003imj.2	Q05DH4	OTTHUMG00000161675	ENST00000505231.1:c.2641C>T	4.37:g.152577473C>T	ENSP00000421580:p.Gln881*	Somatic	278	1	0.00359712		WXS	Illumina HiSeq	Phase_I	181	122	0.674033	NM_001109977	Q6ZUS2	Nonsense_Mutation	SNP	ENST00000505231.1	37	CCDS47146.1	.	.	.	.	.	.	.	.	.	.	C	43	10.373391	0.99393	0.0	3.14E-4	ENSG00000164142	ENST00000435205;ENST00000505231	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	.	19.281	0.94052	0.0:1.0:0.0:0.0	.	.	.	.	X	881	.	ENSP00000413196:Q881X	Q	+	1	0	FAM160A1	152796923	1.000000	0.71417	0.851000	0.33527	0.980000	0.70556	7.730000	0.84881	2.568000	0.86640	0.561000	0.74099	CAG	.	.	weak		0.507	FAM160A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365691.1	NM_001109977	
DFNB31	25861	hgsc.bcm.edu	37	9	117169033	117169033	+	Missense_Mutation	SNP	A	A	G	rs942519	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:117169033A>G	ENST00000362057.3	-	9	2006	c.1838T>C	c.(1837-1839)aTg>aCg	p.M613T	DFNB31_ENST00000265134.6_Missense_Mutation_p.M230T|DFNB31_ENST00000374059.3_Missense_Mutation_p.M262T	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	613	Pro-rich.		M -> T (in dbSNP:rs942519). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCAGGAAGGCATGGAGGAAGG	0.672													G|||	2412	0.481629	0.3585	0.5159	5008	,	,		18367	0.503		0.5149	False		,,,				2504	0.5675				p.M613T		Atlas-SNP	.											.	DFNB31	100	.	0			c.T1838C						PASS	.	G	THR/MET,THR/MET,THR/MET	1703,2703	635.7+/-396.4	337,1029,837	55.0	48.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	689,1838,1838	0.1	0.0	9	dbSNP_86	50	4695,3903	531.4+/-382.0	1252,2191,856	yes	missense,missense,missense	DFNB31	NM_001083885.2,NM_001173425.1,NM_015404.3	81,81,81	1589,3220,1693	GG,GA,AA		45.3943,38.6518,49.2002	benign,benign,benign	230/525,613/907,613/908	117169033	6398,6606	2203	4299	6502	SO:0001583	missense	25861	exon9			GAAGGCATGGAGG	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.1838T>C	9.37:g.117169033A>G	ENSP00000354623:p.Met613Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_001173425	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	37	CCDS6806.1	1062	0.48626373626373626	180	0.36585365853658536	194	0.5359116022099447	301	0.5262237762237763	387	0.5105540897097626	G	0.006	-2.069501	0.00382	0.386518	0.546057	ENSG00000095397	ENST00000265134;ENST00000374059;ENST00000362057	T;T;T	0.06294	4.22;4.2;3.32	4.57	0.0558	0.14316	.	0.410282	0.22939	N	0.053805	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33752	-0.9856	9	0.14656	T	0.56	-1.0976	0.056	0.00013	0.2798:0.192:0.248:0.2803	rs942519;rs60418846;rs942519	613;613;262	B9EGE6;Q9P202;Q9P202-4	.;WHRN_HUMAN;.	T	230;262;613	ENSP00000265134:M230T;ENSP00000363172:M262T;ENSP00000354623:M613T	ENSP00000265134:M230T	M	-	2	0	DFNB31	116208854	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	1.225000	0.32551	-0.207000	0.10187	-1.383000	0.01170	ATG	A|0.511;G|0.489	0.489	strong		0.672	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
SPAG17	200162	hgsc.bcm.edu	37	1	118537074	118537074	+	Silent	SNP	A	A	G	rs12031260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:118537074A>G	ENST00000336338.5	-	35	5198	c.5133T>C	c.(5131-5133)ccT>ccC	p.P1711P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1711						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)		GGAGATTAGGAGGGACAATTG	0.418													A|||	643	0.128395	0.034	0.0418	5008	,	,		19044	0.3204		0.0616	False		,,,				2504	0.1881				p.P1711P		Atlas-SNP	.											.	SPAG17	263	.	0			c.T5133C						PASS	.	A		182,4224	115.0+/-153.0	4,174,2025	189.0	165.0	173.0		5133	2.0	1.0	1	dbSNP_120	173	491,8107	143.0+/-199.1	16,459,3824	no	coding-synonymous	SPAG17	NM_206996.2		20,633,5849	GG,GA,AA		5.7106,4.1307,5.1753		1711/2224	118537074	673,12331	2203	4299	6502	SO:0001819	synonymous_variant	200162	exon35			ATTAGGAGGGACA		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.5133T>C	1.37:g.118537074A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	60	42	0.7	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			A|0.919;G|0.081	0.081	strong		0.418	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
KDM5A	5927	hgsc.bcm.edu	37	12	406292	406292	+	Silent	SNP	G	G	A	rs2229351	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:406292G>A	ENST00000399788.2	-	25	4511	c.4149C>T	c.(4147-4149)tcC>tcT	p.S1383S	KDM5A_ENST00000382815.4_Silent_p.S1383S	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	1383					chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						CCACCTCCTCGGATTTGATGG	0.418			T	NUP98	AML								G|||	1766	0.352636	0.3306	0.3199	5008	,	,		18093	0.5109		0.2326	False		,,,				2504	0.3661				p.S1383S		Atlas-SNP	.		Dom	yes		12	12p11	5927	"""lysine (K)-specific demethylase 5A, JARID1A"""		L	KDM5A_ENST00000399788,trunk,malignant_melanoma,-1,2	KDM5A	307	2	0			c.C4149T						PASS	.	G		1187,2579		201,785,897	65.0	64.0	64.0		4149	-3.8	1.0	12	dbSNP_98	64	2087,6129		276,1535,2297	no	coding-synonymous	KDM5A	NM_001042603.1		477,2320,3194	AA,AG,GG		25.4017,31.5189,27.3243		1383/1691	406292	3274,8708	1883	4108	5991	SO:0001819	synonymous_variant	5927	exon25			CTCCTCGGATTTG		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.4149C>T	12.37:g.406292G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Silent	SNP	ENST00000399788.2	37	CCDS41736.1																																																																																			T|0.139;G|0.444;C|0.211;A|0.206	0.206	strong		0.418	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056	
COL6A3	1293	hgsc.bcm.edu	37	2	238280553	238280553	+	Silent	SNP	G	G	A	rs35114079	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238280553G>A	ENST00000295550.4	-	9	4559	c.4107C>T	c.(4105-4107)atC>atT	p.I1369I	COL6A3_ENST00000392004.3_Silent_p.I1163I|COL6A3_ENST00000392003.2_Silent_p.I962I|COL6A3_ENST00000472056.1_Silent_p.I762I|COL6A3_ENST00000353578.4_Silent_p.I1163I|COL6A3_ENST00000347401.3_Silent_p.I1168I|COL6A3_ENST00000346358.4_Silent_p.I1169I|COL6A3_ENST00000409809.1_Silent_p.I1163I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1369	Nonhelical region.|VWFA 7. {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)		CGTTCCTGGCGATCGTGAAAG	0.612													G|||	14	0.00279553	0.0015	0.0014	5008	,	,		16527	0.0		0.006	False		,,,				2504	0.0051				p.I1369I		Atlas-SNP	.											.	COL6A3	608	.	0			c.C4107T						PASS	.	G	,,,,	7,4399	12.9+/-30.5	0,7,2196	60.0	56.0	57.0		4107,2886,3489,2286,3489	-9.3	0.0	2	dbSNP_126	57	71,8529	42.2+/-99.7	0,71,4229	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	0,78,6425	AA,AG,GG		0.8256,0.1589,0.5997	,,,,	1369/3178,962/1037,1163/1238,762/2571,1163/2972	238280553	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon9			CCTGGCGATCGTG	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.4107C>T	2.37:g.238280553G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	77	28	0.363636	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
VSIG10L	147645	hgsc.bcm.edu	37	19	51837171	51837171	+	Silent	SNP	A	A	G	rs7255306	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51837171A>G	ENST00000335624.4	-	9	2447	c.2448T>C	c.(2446-2448)ccT>ccC	p.P816P		NM_001163922.1	NP_001157394.1	Q86VR7	VS10L_HUMAN	V-set and immunoglobulin domain containing 10 like	816						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)	4						CCAAGGTAGAAGGATGCTTCT	0.522													G|||	2184	0.436102	0.8449	0.2493	5008	,	,		18798	0.249		0.2992	False		,,,				2504	0.3497				p.P816P		Atlas-SNP	.											.	VSIG10L	40	.	0			c.T2448C						PASS	.	G		1078,306		415,248,29	54.0	59.0	57.0		2448	-7.8	0.0	19	dbSNP_116	57	936,2246		142,652,797	no	coding-synonymous	VSIG10L	NM_001163922.1		557,900,826	GG,GA,AA		29.4155,22.1098,44.1086		816/868	51837171	2014,2552	692	1591	2283	SO:0001819	synonymous_variant	147645	exon9			GGTAGAAGGATGC		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.2448T>C	19.37:g.51837171A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001163922		Silent	SNP	ENST00000335624.4	37	CCDS54300.1																																																																																			A|0.563;G|0.437	0.437	strong		0.522	VSIG10L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464535.1	NM_001163922	
CCDC154	645811	hgsc.bcm.edu	37	16	1493909	1493909	+	Missense_Mutation	SNP	C	C	T	rs34470360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1493909C>T	ENST00000389176.3	-	2	278	c.112G>A	c.(112-114)Gag>Aag	p.E38K	LA16c-390E6.5_ENST00000566287.1_RNA|CCDC154_ENST00000409671.1_5'UTR	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	38						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						CTCAAGGGCTCGGGGCTGGCC	0.672													C|||	189	0.0377396	0.0219	0.0778	5008	,	,		14648	0.0		0.0815	False		,,,				2504	0.0245				p.E38K		Atlas-SNP	.											CCDC154,lymph_node,lymphoid_neoplasm,0,1	CCDC154	27	1	0			c.G112A						PASS	.	C	LYS/GLU	45,1339		0,45,647	32.0	41.0	38.0		112	1.8	0.0	16	dbSNP_126	38	287,2893		11,265,1314	yes	missense	CCDC154	NM_001143980.1	56	11,310,1961	TT,TC,CC		9.0252,3.2514,7.2743	benign	38/668	1493909	332,4232	692	1590	2282	SO:0001583	missense	645811	exon2			AGGGCTCGGGGCT			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.112G>A	16.37:g.1493909C>T	ENSP00000373828:p.Glu38Lys	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	91	58	0.637363	NM_001143980	G9JV18	Missense_Mutation	SNP	ENST00000389176.3	37		112	0.05128205128205128	13	0.026422764227642278	31	0.0856353591160221	0	0.0	68	0.08970976253298153	C	16.13	3.035901	0.54896	0.032514	0.090252	ENSG00000197599	ENST00000389176	.	.	.	3.92	1.81	0.25067	.	0.519476	0.14412	N	0.321234	T	0.00637	0.0021	L	0.29908	0.895	0.80722	P	0.0	P	0.36874	0.572	B	0.22152	0.038	T	0.08269	-1.0730	8	0.45353	T	0.12	-13.11	5.2955	0.15751	0.0:0.6759:0.2065:0.1176	rs34470360;rs34470360	38	A6NI56	CC154_HUMAN	K	38	.	ENSP00000373828:E38K	E	-	1	0	CCDC154	1433910	0.000000	0.05858	0.004000	0.12327	0.025000	0.11179	-0.709000	0.05030	0.272000	0.22027	0.549000	0.68633	GAG	C|0.950;T|0.050	0.050	strong		0.672	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
PTPRK	5796	hgsc.bcm.edu	37	6	128388799	128388799	+	Silent	SNP	G	G	T	rs35030557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:128388799G>T	ENST00000368215.3	-	12	2021	c.2022C>A	c.(2020-2022)ctC>ctA	p.L674L	PTPRK_ENST00000368213.5_Silent_p.L674L|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368210.3_Silent_p.L674L|PTPRK_ENST00000368226.4_Silent_p.L674L|RP11-103C16.2_ENST00000417390.1_RNA|PTPRK_ENST00000368207.3_Silent_p.L674L|PTPRK_ENST00000368227.3_Silent_p.L674L|PTPRK_ENST00000532331.1_Silent_p.L674L			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	674	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.			AEL -> CRT (in Ref. 2; AAC37599). {ECO:0000305}.	cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)		PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		TTCCCGGGGGGAGTTCTGCAG	0.552													G|||	1228	0.245208	0.0408	0.4092	5008	,	,		15066	0.2411		0.4334	False		,,,				2504	0.2157				p.L674L		Atlas-SNP	.											.	PTPRK	330	.	0			c.C2022A						PASS	.	G	,	422,3984	206.8+/-228.3	22,378,1803	114.0	111.0	112.0		2022,2022	-11.9	0.0	6	dbSNP_126	112	3675,4925	527.0+/-381.1	772,2131,1397	no	coding-synonymous,coding-synonymous	PTPRK	NM_001135648.1,NM_002844.3	,	794,2509,3200	TT,TG,GG		42.7326,9.5778,31.5008	,	674/1447,674/1441	128388799	4097,8909	2203	4300	6503	SO:0001819	synonymous_variant	5796	exon12			CGGGGGGAGTTCT	L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2022C>A	6.37:g.128388799G>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	95	89	0.936842	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Silent	SNP	ENST00000368215.3	37																																																																																				T|0.314;G|0.686;C|0.000	0.314	strong		0.552	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
CDC14A	8556	hgsc.bcm.edu	37	1	100949860	100949860	+	Silent	SNP	G	G	A	rs2270694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:100949860G>A	ENST00000336454.3	+	11	1345	c.990G>A	c.(988-990)tcG>tcA	p.S330S	CDC14A_ENST00000544534.1_Silent_p.S330S|CDC14A_ENST00000542213.1_Silent_p.S272S|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000370124.3_Silent_p.S330S|CDC14A_ENST00000361544.6_Silent_p.S330S|RP5-837M10.4_ENST00000432210.1_RNA	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	330	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		AACAAGCATCGTTGTGGGTCC	0.328													G|||	442	0.0882588	0.059	0.0965	5008	,	,		17962	0.0625		0.1441	False		,,,				2504	0.091				p.S330S		Atlas-SNP	.											.	CDC14A	65	.	0			c.G990A						PASS	.	G	,,	257,4145	131.4+/-167.9	6,245,1950	39.0	36.0	37.0		990,990,990	-6.6	0.1	1	dbSNP_100	37	1144,7452	220.1+/-257.9	79,986,3233	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	85,1231,5183	AA,AG,GG		13.3085,5.8383,10.7786	,,	330/595,330/624,330/384	100949860	1401,11597	2201	4298	6499	SO:0001819	synonymous_variant	8556	exon11			AGCATCGTTGTGG	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.990G>A	1.37:g.100949860G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	35	10	0.285714	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			G|0.905;A|0.095	0.095	strong		0.328	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
SEC31B	25956	hgsc.bcm.edu	37	10	102269206	102269206	+	Missense_Mutation	SNP	A	A	G	rs3763695	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102269206A>G	ENST00000370345.3	-	4	363	c.266T>C	c.(265-267)gTt>gCt	p.V89A	SEC31B_ENST00000535773.1_Intron|SEC31B_ENST00000370329.5_Missense_Mutation_p.V89A|SEC31B_ENST00000451524.1_Missense_Mutation_p.V89A|NDUFB8_ENST00000557395.1_Intron|NDUFB8_ENST00000531258.1_Intron	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	89			V -> A (in dbSNP:rs3763695). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CCCGCCGCCAACAATAACCCC	0.522											OREG0020441	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	928	0.185304	0.1997	0.1844	5008	,	,		16965	0.1319		0.1909	False		,,,				2504	0.2157				p.V89A		Atlas-SNP	.											.	SEC31B	84	.	0			c.T266C						PASS	.	G	ALA/VAL	856,3550	742.3+/-411.4	86,684,1433	47.0	51.0	50.0		266	5.4	1.0	10	dbSNP_107	50	1889,6711	727.5+/-406.6	216,1457,2627	yes	missense	SEC31B	NM_015490.3	64	302,2141,4060	GG,GA,AA		21.9651,19.4281,21.1056	benign	89/1180	102269206	2745,10261	2203	4300	6503	SO:0001583	missense	25956	exon4			CCGCCAACAATAA	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.266T>C	10.37:g.102269206A>G	ENSP00000359370:p.Val89Ala	Somatic	71	0	0	1365	WXS	Illumina HiSeq	Phase_I	55	41	0.745455	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	395	0.18086080586080586	71	0.1443089430894309	71	0.19613259668508287	94	0.16433566433566432	159	0.20976253298153033	G	9.995	1.231922	0.22626	0.194281	0.219651	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000370329	T;T;T	0.24908	1.83;1.83;1.83	5.36	5.36	0.76844	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.216027	0.45126	N	0.000397	T	0.00012	0.0000	N	0.00507	-1.42	0.09310	P	1.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.29882	-0.9997	9	0.07325	T	0.83	-5.3373	7.5007	0.27516	0.2557:0.0:0.7443:0.0	rs3763695;rs59707262;rs3763695	89;89;89;89	B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;SC31B_HUMAN	A	89	ENSP00000359370:V89A;ENSP00000391178:V89A;ENSP00000359354:V89A	ENSP00000359354:V89A	V	-	2	0	SEC31B	102259196	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	5.183000	0.65065	1.419000	0.47118	-0.213000	0.12676	GTT	A|0.809;G|0.191	0.191	strong		0.522	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
RPTOR	57521	hgsc.bcm.edu	37	17	78921117	78921117	+	Silent	SNP	C	C	T	rs4969231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78921117C>T	ENST00000306801.3	+	27	3593	c.3231C>T	c.(3229-3231)aaC>aaT	p.N1077N	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Silent_p.N919N	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	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	129	126	0.976744	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	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19725280	19725280	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:19725280C>T	ENST00000284885.3	-	10	1144	c.1111G>A	c.(1111-1113)Gga>Aga	p.G371R		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	371	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.G371R(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						AAGGTGCTTCCCTGAATCCTT	0.343																																					p.G371R		Atlas-SNP	.											TMPRSS15,extremity,malignant_melanoma,0,1	TMPRSS15	189	1	1	Substitution - Missense(1)	skin(1)	c.G1111A						scavenged	.						113.0	122.0	119.0					21																	19725280		2203	4300	6503	SO:0001583	missense	5651	exon10			TGCTTCCCTGAAT		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1111G>A	21.37:g.19725280C>T	ENSP00000284885:p.Gly371Arg	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	297	3	0.010101	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.755703	0.49362	.	.	ENSG00000154646	ENST00000284885	T	0.02345	4.33	5.2	4.3	0.51218	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.371433	0.23524	N	0.047252	T	0.18676	0.0448	M	0.90019	3.08	0.42726	D	0.993695	D	0.89917	1.0	D	0.76575	0.988	T	0.02313	-1.1178	9	.	.	.	.	13.5122	0.61519	0.0:0.9232:0.0:0.0768	.	371	P98073	ENTK_HUMAN	R	371	ENSP00000284885:G371R	.	G	-	1	0	TMPRSS15	18647151	0.960000	0.32886	0.262000	0.24481	0.311000	0.27955	3.456000	0.53000	1.283000	0.44513	0.655000	0.94253	GGA	.	.	none		0.343	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
TIAM2	26230	hgsc.bcm.edu	37	6	155451352	155451352	+	Missense_Mutation	SNP	G	G	A	rs931312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:155451352G>A	ENST00000461783.3	+	6	2268	c.995G>A	c.(994-996)cGt>cAt	p.R332H	TIAM2_ENST00000318981.5_Missense_Mutation_p.R332H|TIAM2_ENST00000360366.4_Missense_Mutation_p.R332H|TIAM2_ENST00000456144.1_Missense_Mutation_p.R332H|TIAM2_ENST00000529824.2_Missense_Mutation_p.R332H|TIAM2_ENST00000367174.2_5'UTR			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	332			R -> H (in dbSNP:rs931312).		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)		CTGAGCAACCGTGTCTCTTTT	0.577													G|||	1178	0.235224	0.0711	0.2464	5008	,	,		19702	0.3026		0.175	False		,,,				2504	0.4417				p.R332H		Atlas-SNP	.											.	TIAM2	161	.	0			c.G995A						PASS	.	G	HIS/ARG	496,3910	230.1+/-244.4	30,436,1737	83.0	79.0	81.0		995	5.0	0.4	6	dbSNP_86	81	1567,7033	293.5+/-301.4	137,1293,2870	yes	missense	TIAM2	NM_012454.3	29	167,1729,4607	AA,AG,GG		18.2209,11.2574,15.8619	probably-damaging	332/1702	155451352	2063,10943	2203	4300	6503	SO:0001583	missense	26230	exon3			GCAACCGTGTCTC		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.995G>A	6.37:g.155451352G>A	ENSP00000437188:p.Arg332His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	440	0.20146520146520147	41	0.08333333333333333	86	0.23756906077348067	194	0.33916083916083917	119	0.15699208443271767	G	15.18	2.757389	0.49468	0.112574	0.182209	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.08282	3.22;3.11;3.2;3.22;3.24;3.2	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.19604	0.0471	M	0.72118	2.19	0.09310	P	1.0	D	0.89917	1.0	D	0.78314	0.991	T	0.00800	-1.1561	9	0.40728	T	0.16	.	16.8516	0.85995	0.0:0.0:1.0:0.0	rs931312;rs56418104;rs57922078;rs931312	332	Q8IVF5	TIAM2_HUMAN	H	332;578;332;332;332;332;332	ENSP00000437188:R332H;ENSP00000434901:R332H;ENSP00000407746:R332H;ENSP00000327315:R332H;ENSP00000353528:R332H;ENSP00000433348:R332H	ENSP00000327315:R332H	R	+	2	0	TIAM2	155493044	1.000000	0.71417	0.427000	0.26684	0.008000	0.06430	7.136000	0.77285	2.489000	0.83994	0.655000	0.94253	CGT	G|0.815;A|0.185	0.185	strong		0.577	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
FAM98A	25940	hgsc.bcm.edu	37	2	33820635	33820635	+	Silent	SNP	C	C	T	rs72785999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:33820635C>T	ENST00000238823.8	-	2	263	c.123G>A	c.(121-123)gaG>gaA	p.E41E	FAM98A_ENST00000441530.2_5'UTR|FAM98A_ENST00000498340.1_5'UTR|FAM98A_ENST00000403368.1_Silent_p.E41E			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	41							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(1)	24	all_hematologic(175;0.115)					GTTTGGTAAACTCGGGGGAAC	0.448													C|||	15	0.00299521	0.0	0.0029	5008	,	,		15482	0.0		0.0099	False		,,,				2504	0.0031				p.E41E		Atlas-SNP	.											.	FAM98A	42	.	0			c.G123A						PASS	.	C		11,4395	17.9+/-39.9	1,9,2193	105.0	107.0	106.0		123	4.1	1.0	2	dbSNP_130	106	74,8526	42.2+/-99.7	0,74,4226	no	coding-synonymous	FAM98A	NM_015475.3		1,83,6419	TT,TC,CC		0.8605,0.2497,0.6535		41/519	33820635	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	25940	exon2			GGTAAACTCGGGG		CCDS33179.1	2p22.3	2006-11-29		2005-11-20	ENSG00000119812	ENSG00000119812			24520	protein-coding gene	gene with protein product						12477932	Standard	NM_015475		Approved	DKFZP564F0522	uc002rpa.1	Q8NCA5	OTTHUMG00000152152	ENST00000238823.8:c.123G>A	2.37:g.33820635C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	171	94	0.549708	NM_015475	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	37	CCDS33179.1																																																																																			C|0.995;T|0.005	0.005	strong		0.448	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475	
LASP1	3927	hgsc.bcm.edu	37	17	37070658	37070658	+	Silent	SNP	A	A	G	rs525989	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:37070658A>G	ENST00000318008.6	+	5	769	c.438A>G	c.(436-438)tcA>tcG	p.S146S	LASP1_ENST00000433206.2_Silent_p.S90S|LASP1_ENST00000435347.3_Silent_p.S146S	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	146					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						GTCGGGATTCACAGGACGGCA	0.627			T	MLL	AML								G|||	3389	0.676717	0.9175	0.5519	5008	,	,		14614	0.5933		0.6471	False		,,,				2504	0.5562				p.S146S		Atlas-SNP	.		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	LASP1,colon,carcinoma,0,3	LASP1	24	3	0			c.A438G						PASS	.	G		3809,595	250.9+/-257.8	1657,495,50	27.0	33.0	31.0		438	0.4	0.6	17	dbSNP_83	31	5638,2962	443.3+/-360.3	1872,1894,534	no	coding-synonymous	LASP1	NM_006148.2		3529,2389,584	GG,GA,AA		34.4419,13.5104,27.3531		146/262	37070658	9447,3557	2202	4300	6502	SO:0001819	synonymous_variant	3927	exon5			GGATTCACAGGAC		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.438A>G	17.37:g.37070658A>G		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	201	197	0.980099	NM_006148	B4DGQ0|Q96ED2|Q96IG0	Silent	SNP	ENST00000318008.6	37	CCDS11331.1																																																																																			A|0.285;G|0.715	0.715	strong		0.627	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148	
HDHD1	8226	hgsc.bcm.edu	37	X	6995417	6995417	+	Silent	SNP	C	C	T	rs2379207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:6995417C>T	ENST00000381077.5	-	3	430	c.354G>A	c.(352-354)gcG>gcA	p.A118A	HDHD1_ENST00000412827.2_Silent_p.A75A|HDHD1_ENST00000540122.1_Silent_p.A118A|HDHD1_ENST00000424830.2_Silent_p.A141A	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	118					nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)			breast(2)|large_intestine(1)|lung(3)	6						TATCGAACGACGCGGACCCCG	0.587													C|||	961	0.25457	0.0537	0.3372	3775	,	,		11649	0.2153		0.1779	False		,,,				2504	0.2658				p.A141A		Atlas-SNP	.											.	HDHD1	21	.	0			c.G423A						PASS	.	C	,,,	354,3193		16,254,68,1218,503	44.0	46.0	46.0		423,354,225,354	-1.5	0.0	X	dbSNP_100	46	1568,4975		152,846,418,1370,1389	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDHD1	NM_001135565.1,NM_001178135.1,NM_001178136.1,NM_012080.4	,,,	168,1100,486,2588,1892	TT,TC,T,CC,C		23.9645,9.9803,19.0486	,,,	141/252,118/209,75/186,118/229	6995417	1922,8168	2059	4175	6234	SO:0001819	synonymous_variant	8226	exon4			GAACGACGCGGAC	M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"""family with sequence similarity 16, member A, X-linked"", ""haloacid dehalogenase-like hydrolase domain containing 1A"""	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.354G>A	X.37:g.6995417C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	96	93	0.96875	NM_001135565	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Silent	SNP	ENST00000381077.5	37	CCDS48075.1																																																																																			C|0.748;0|0.031	.	strong		0.587	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080	
MTHFSD	64779	hgsc.bcm.edu	37	16	86565882	86565882	+	Missense_Mutation	SNP	G	G	C	rs3751802	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:86565882G>C	ENST00000360900.6	-	8	912	c.887C>G	c.(886-888)tCc>tGc	p.S296C	MTHFSD_ENST00000322911.6_Missense_Mutation_p.S295C|MTHFSD_ENST00000543303.2_Missense_Mutation_p.S295C|MTHFSD_ENST00000546093.1_Missense_Mutation_p.S133C|MTHFSD_ENST00000381214.5_Missense_Mutation_p.S296C	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	296			S -> C (in dbSNP:rs3751802).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						CCCTGGTGGGGAGCCAGGGGC	0.667													G|||	1332	0.265974	0.3434	0.3617	5008	,	,		14758	0.3393		0.1292	False		,,,				2504	0.1585				p.S296C		Atlas-SNP	.											.	MTHFSD	52	.	0			c.C887G						PASS	.	G	CYS/SER,CYS/SER,CYS/SER,CYS/SER,CYS/SER	931,2819		143,645,1087	13.0	17.0	15.0		887,887,884,827,884	2.1	0.0	16	dbSNP_107	15	960,7224		65,830,3197	yes	missense,missense,missense,missense,missense	MTHFSD	NM_001159377.1,NM_001159378.1,NM_001159379.1,NM_001159380.1,NM_022764.2	112,112,112,112,112	208,1475,4284	CC,CG,GG		11.7302,24.8267,15.8455	benign,benign,benign,benign,benign	296/384,296/384,295/383,276/364,295/383	86565882	1891,10043	1875	4092	5967	SO:0001583	missense	64779	exon8			GGTGGGGAGCCAG	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.887C>G	16.37:g.86565882G>C	ENSP00000354152:p.Ser296Cys	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	134	19	0.141791	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	37	CCDS54047.1	560	0.2564102564102564	182	0.3699186991869919	100	0.27624309392265195	188	0.32867132867132864	90	0.11873350923482849	G	10.62	1.402316	0.25291	0.248267	0.117302	ENSG00000103248	ENST00000543303;ENST00000381214;ENST00000360900;ENST00000322911;ENST00000546093	T;T;T;T	0.19250	2.42;2.42;2.42;2.16	5.28	2.07	0.26955	.	2.349280	0.01872	U	0.037275	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.09022	0.002;0.002;0.001;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.001	T	0.44267	-0.9339	9	0.52906	T	0.07	.	8.4011	0.32586	0.089:0.3996:0.5114:0.0	rs3751802;rs3751802	296;295;296;295	E9PAM1;B7ZLC0;Q2M296;Q2M296-2	.;.;MTHSD_HUMAN;.	C	294;296;296;295;133	ENSP00000370612:S296C;ENSP00000354152:S296C;ENSP00000326777:S295C;ENSP00000438761:S133C	ENSP00000326777:S295C	S	-	2	0	MTHFSD	85123383	0.127000	0.22367	0.005000	0.12908	0.224000	0.24922	2.975000	0.49281	0.181000	0.19994	0.609000	0.83330	TCC	G|0.733;C|0.267	0.267	strong		0.667	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764	
PRF1	5551	hgsc.bcm.edu	37	10	72360197	72360197	+	Silent	SNP	T	T	C	rs116554195	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72360197T>C	ENST00000441259.1	-	2	622	c.462A>G	c.(460-462)gcA>gcG	p.A154A	PRF1_ENST00000373209.2_Silent_p.A154A	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	154	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CAAAGTTGGCTGCCTGTGAGT	0.612			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				T|||	76	0.0151757	0.0378	0.0086	5008	,	,		17805	0.0		0.0109	False		,,,				2504	0.0092				p.A154A		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.A462G						PASS	.	T	,	135,4271	95.7+/-134.4	1,133,2069	81.0	71.0	74.0		462,462	-8.4	0.0	10	dbSNP_132	74	71,8529	41.7+/-99.0	0,71,4229	no	coding-synonymous,coding-synonymous	PRF1	NM_001083116.1,NM_005041.4	,	1,204,6298	CC,CT,TT		0.8256,3.064,1.5839	,	154/556,154/556	72360197	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GTTGGCTGCCTGT	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.462A>G	10.37:g.72360197T>C		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	126	92	0.730159	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			T|0.987;C|0.013	0.013	strong		0.612	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
NWD1	284434	hgsc.bcm.edu	37	19	16872940	16872940	+	Silent	SNP	G	G	A	rs773852	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:16872940G>A	ENST00000552788.1	+	6	2124	c.2124G>A	c.(2122-2124)ttG>ttA	p.L708L	NWD1_ENST00000339803.6_Silent_p.L573L|NWD1_ENST00000379808.3_Silent_p.L708L|NWD1_ENST00000549814.1_Silent_p.L708L|NWD1_ENST00000524140.2_Silent_p.L708L|NWD1_ENST00000523826.1_Silent_p.L502L			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	708							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CACTGAACTTGGACCGAAAGG	0.577													G|||	2002	0.39976	0.6172	0.2709	5008	,	,		17692	0.1895		0.3917	False		,,,				2504	0.4223				p.L708L		Atlas-SNP	.											.	NWD1	303	.	0			c.G2124A						PASS	.	G		2500,1906	627.0+/-394.8	705,1090,408	71.0	54.0	60.0		2124	2.2	1.0	19	dbSNP_86	60	3430,5170	501.9+/-375.6	681,2068,1551	no	coding-synonymous	NWD1	NM_001007525.3		1386,3158,1959	AA,AG,GG		39.8837,43.2592,45.5943		708/1433	16872940	5930,7076	2203	4300	6503	SO:0001819	synonymous_variant	284434	exon8			GAACTTGGACCGA	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2124G>A	19.37:g.16872940G>A		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																				G|0.570;A|0.430	0.430	strong		0.577	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
MUC2	4583	hgsc.bcm.edu	37	11	1093481	1093481	+	Missense_Mutation	SNP	C	C	T	rs547164370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1093481C>T	ENST00000441003.2	+	30	5327	c.5300C>T	c.(5299-5301)aCg>aTg	p.T1767M	MUC2_ENST00000359061.5_Splice_Site_p.T1734M|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.T55M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					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)	accccaaccacggtactcatc	0.612													c|||	7	0.00139776	0.0	0.0014	5008	,	,		26176	0.005		0.001	False		,,,				2504	0.0				p.T1767M		Atlas-SNP	.											.	MUC2	614	.	0			c.C5300T						PASS	.																																			SO:0001583	missense	4583	exon30			CAACCACGGTACT	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.5300C>T	11.37:g.1093481C>T	ENSP00000415183:p.Thr1767Met	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	20	0.289855	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.092	-0.186712	0.06340	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.12879	2.64;3.12;2.78	1.77	-3.54	0.04653	.	0.173549	0.20316	U	0.094725	T	0.06325	0.0163	.	.	.	0.09310	N	1	B	0.33073	0.396	B	0.24848	0.056	T	0.14952	-1.0454	9	0.66056	D	0.02	.	1.3227	0.02119	0.1446:0.3605:0.1442:0.3508	.	1767	E7EUV1	.	M	1767;1734;55	ENSP00000415183:T1767M;ENSP00000351956:T1734M;ENSP00000331373:T55M	ENSP00000331373:T55M	T	+	2	0	MUC2	1083481	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.581000	0.23819	-1.920000	0.01069	-1.152000	0.01820	ACG	.	.	none		0.612	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FAM131C	348487	hgsc.bcm.edu	37	1	16385184	16385184	+	Silent	SNP	G	G	A	rs75273615	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16385184G>A	ENST00000375662.4	-	7	774	c.591C>T	c.(589-591)agC>agT	p.S197S	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	197								p.S197S(1)		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)		CGCTGGGAAGGCTGTCCTGAA	0.642																																					p.S197S		Atlas-SNP	.											FAM131C,NS,haematopoietic_neoplasm,0,1	FAM131C	21	1	1	Substitution - coding silent(1)	lung(1)	c.C591T						scavenged	.						20.0	20.0	20.0					1																	16385184		2002	4131	6133	SO:0001819	synonymous_variant	348487	exon7			GGGAAGGCTGTCC		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.591C>T	1.37:g.16385184G>A		Somatic	906	3	0.00331126		WXS	Illumina HiSeq	Phase_I	393	145	0.368957	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.740;A|0.260	0.260	strong		0.642	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
TRIP6	7205	hgsc.bcm.edu	37	7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	rs2437100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100465824G>A	ENST00000200457.4	+	3	692	c.332G>A	c.(331-333)cGg>cAg	p.R111Q		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	111			R -> Q (in dbSNP:rs2437100). {ECO:0000269|PubMed:15489334}.		focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					AATGGGGGTCGGGGTCATGCG	0.672													G|||	32	0.00638978	0.0008	0.0058	5008	,	,		14361	0.0		0.0268	False		,,,				2504	0.0				p.R111Q		Atlas-SNP	.											.	TRIP6	45	.	0			c.G332A						PASS	.	G	GLN/ARG	21,4385	29.0+/-57.7	0,21,2182	41.0	41.0	41.0		332	4.5	0.8	7	dbSNP_100	41	176,8424	80.6+/-143.3	1,174,4125	yes	missense	TRIP6	NM_003302.2	43	1,195,6307	AA,AG,GG		2.0465,0.4766,1.5147	probably-damaging	111/477	100465824	197,12809	2203	4300	6503	SO:0001583	missense	7205	exon3			GGGGTCGGGGTCA	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.332G>A	7.37:g.100465824G>A	ENSP00000200457:p.Arg111Gln	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	105	73	0.695238	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	26	0.011904761904761904	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	23	0.030343007915567283	G	18.42	3.619897	0.66787	0.004766	0.020465	ENSG00000087077	ENST00000200457	T	0.59502	0.26	4.53	4.53	0.55603	.	0.374538	0.26931	N	0.021774	T	0.33089	0.0851	L	0.47716	1.5	0.28405	N	0.918477	D	0.69078	0.997	P	0.53518	0.728	T	0.40646	-0.9552	10	0.11794	T	0.64	.	12.7393	0.57241	0.0:0.0:1.0:0.0	rs2437100	111	Q15654	TRIP6_HUMAN	Q	111	ENSP00000200457:R111Q	ENSP00000200457:R111Q	R	+	2	0	TRIP6	100303760	0.997000	0.39634	0.757000	0.31301	0.054000	0.15201	3.870000	0.56070	2.074000	0.62210	0.455000	0.32223	CGG	G|0.985;A|0.015	0.015	strong		0.672	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
RGPD3	653489	hgsc.bcm.edu	37	2	107040985	107040985	+	Silent	SNP	T	T	C	rs140856347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:107040985T>C	ENST00000409886.3	-	20	3525	c.3438A>G	c.(3436-3438)cgA>cgG	p.R1146R	RGPD3_ENST00000304514.7_Silent_p.R1146R	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1146	RanBD1 1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				protein targeting to Golgi (GO:0000042)			p.R1146R(2)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTGCTGCCAATCGCTCTAGTT	0.463													.|||	1440	0.28754	0.1868	0.2378	5008	,	,		15088	0.627		0.16	False		,,,				2504	0.2403				p.R1146R		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,2	RGPD3	316	2	2	Substitution - coding silent(2)	kidney(2)	c.A3438G						scavenged	.						17.0	13.0	14.0					2																	107040985		682	1556	2238	SO:0001819	synonymous_variant	653489	exon20			TGCCAATCGCTCT		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.3438A>G	2.37:g.107040985T>C		Somatic	33	1	0.030303		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_001144013	B8ZZM4	Silent	SNP	ENST00000409886.3	37	CCDS46379.1																																																																																			.	.	weak		0.463	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
FCRL4	83417	hgsc.bcm.edu	37	1	157559122	157559122	+	Missense_Mutation	SNP	C	C	T	rs11582663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:157559122C>T	ENST00000271532.1	-	3	314	c.179G>A	c.(178-180)cGg>cAg	p.R60Q	FCRL4_ENST00000448509.2_5'Flank	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	60	Ig-like C2-type 1.		R -> Q (in dbSNP:rs11582663).		immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				CCAGTAGTGCCGATGATACCA	0.517													C|||	234	0.0467252	0.0045	0.0692	5008	,	,		19974	0.001		0.1581	False		,,,				2504	0.0204				p.R60Q		Atlas-SNP	.											.	FCRL4	95	.	0			c.G179A						PASS	.	C	GLN/ARG	136,4270	98.0+/-136.7	5,126,2072	109.0	93.0	99.0		179	-3.9	0.0	1	dbSNP_120	99	1305,7295	257.9+/-281.7	88,1129,3083	yes	missense	FCRL4	NM_031282.2	43	93,1255,5155	TT,TC,CC		15.1744,3.0867,11.0795	benign	60/516	157559122	1441,11565	2203	4300	6503	SO:0001583	missense	83417	exon3			TAGTGCCGATGAT	AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.179G>A	1.37:g.157559122C>T	ENSP00000271532:p.Arg60Gln	Somatic	437	0	0		WXS	Illumina HiSeq	Phase_I	594	594	1	NM_031282	Q96PJ3|Q96RE0	Missense_Mutation	SNP	ENST00000271532.1	37	CCDS1166.1	157	0.07188644688644688	4	0.008130081300813009	29	0.08011049723756906	0	0.0	124	0.16358839050131926	C	0.693	-0.793811	0.02862	0.030867	0.151744	ENSG00000163518	ENST00000271532	T	0.54279	0.58	1.95	-3.9	0.04181	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.13286	0.0322	L	0.36672	1.1	0.80722	P	0.0	B	0.24043	0.096	B	0.23419	0.046	T	0.18241	-1.0343	8	0.38643	T	0.18	.	0.1358	0.00078	0.342:0.2316:0.1692:0.2572	rs11582663;rs52802570;rs59243416;rs11582663	60	Q96PJ5	FCRL4_HUMAN	Q	60	ENSP00000271532:R60Q	ENSP00000271532:R60Q	R	-	2	0	FCRL4	155825746	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.398000	0.02066	-1.082000	0.02213	CGG	C|0.911;T|0.089	0.089	strong		0.517	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282	
COX10	1352	hgsc.bcm.edu	37	17	14005439	14005439	+	Silent	SNP	G	G	A	rs2159132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:14005439G>A	ENST00000261643.3	+	4	581	c.504G>A	c.(502-504)ctG>ctA	p.L168L	COX10_ENST00000537334.1_5'UTR|COX10_ENST00000536205.1_Intron	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	168					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TCGCAGCTCTGGTTGTAAGTA	0.493													A|||	2463	0.491813	0.5053	0.4813	5008	,	,		15872	0.3462		0.5855	False		,,,				2504	0.5348				p.L168L		Atlas-SNP	.											.	COX10	36	.	0			c.G504A						PASS	.	A		2250,2156	583.9+/-385.9	553,1144,506	158.0	133.0	142.0		504	-10.5	0.0	17	dbSNP_96	142	4975,3625	523.5+/-380.3	1422,2131,747	yes	coding-synonymous	COX10	NM_001303.3		1975,3275,1253	AA,AG,GG		42.1512,48.9333,44.4487		168/444	14005439	7225,5781	2203	4300	6503	SO:0001819	synonymous_variant	1352	exon4			AGCTCTGGTTGTA	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"""Mitochondrial respiratory chain complex assembly factors"""	2260	protein-coding gene	gene with protein product	"""heme A: farnesyltransferase"", ""protoheme IX farnesyltransferase, mitochondrial"", ""heme O synthase"""	602125	"""COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)"", ""COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"""			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.504G>A	17.37:g.14005439G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	39	0.336207	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	37	CCDS11166.1																																																																																			G|0.468;A|0.532	0.532	strong		0.493	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
KCNU1	157855	hgsc.bcm.edu	37	8	36663795	36663795	+	Silent	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:36663795A>T	ENST00000399881.3	+	5	514	c.477A>T	c.(475-477)gcA>gcT	p.A159A		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	159					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AGTTTATGGCAGCTGATGACA	0.343																																					p.A159A		Atlas-SNP	.											KCNU1_ENST00000399881,NS,carcinoma,+2,2	KCNU1	359	2	0			c.A477T						scavenged	.						80.0	77.0	78.0					8																	36663795		1851	4103	5954	SO:0001819	synonymous_variant	157855	exon5			TATGGCAGCTGAT	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.477A>T	8.37:g.36663795A>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	181	2	0.0110497	NM_001031836		Silent	SNP	ENST00000399881.3	37	CCDS55220.1																																																																																			.	.	none		0.343	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
GNB5	10681	hgsc.bcm.edu	37	15	52446260	52446260	+	Silent	SNP	C	C	T	rs35581121	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52446260C>T	ENST00000261837.7	-	4	317	c.252G>A	c.(250-252)gcG>gcA	p.A84A	GNB5_ENST00000396335.4_Silent_p.A42A|GNB5_ENST00000560116.1_Silent_p.A42A|GNB5_ENST00000358784.7_Silent_p.A42A	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	84					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		CCACCCGCTCCGCCACCTGGT	0.562													C|||	84	0.0167732	0.0008	0.0389	5008	,	,		18869	0.001		0.0378	False		,,,				2504	0.0174				p.A84A		Atlas-SNP	.											.	GNB5	28	.	0			c.G252A						PASS	.	C	,	36,4354	40.0+/-72.8	1,34,2160	79.0	67.0	71.0		126,252	-11.1	0.0	15	dbSNP_126	71	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,343,6140	TT,TC,CC		3.6921,0.82,2.7204	,	42/354,84/396	52446260	353,12623	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			CCGCTCCGCCACC	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"""WD repeat domain containing"""	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.252G>A	15.37:g.52446260C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	26	6	0.230769	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;T|0.027	0.027	strong		0.562	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
C1orf106	55765	hgsc.bcm.edu	37	1	200880869	200880869	+	Missense_Mutation	SNP	A	A	C	rs45547233	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	180	0	0		WXS	Illumina HiSeq	Phase_I	158	47	0.297468	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	
GTPBP10	85865	hgsc.bcm.edu	37	7	90001496	90001496	+	Missense_Mutation	SNP	G	G	C	rs35001814	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:90001496G>C	ENST00000222511.6	+	5	558	c.492G>C	c.(490-492)ttG>ttC	p.L164F	GTPBP10_ENST00000257659.8_Missense_Mutation_p.L85F	NM_033107.3	NP_149098.2	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 (putative)	164	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.		L -> F (in dbSNP:rs35001814).		ribosome biogenesis (GO:0042254)	chromosome (GO:0005694)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)	10						AATCCTCTTTGCTAAGTTGTG	0.308													G|||	253	0.0505192	0.0068	0.0965	5008	,	,		16095	0.002		0.1302	False		,,,				2504	0.045				p.L164F		Atlas-SNP	.											.	GTPBP10	31	.	0			c.G492C						PASS	.	G	PHE/LEU,PHE/LEU	130,4276	92.0+/-130.7	3,124,2076	72.0	67.0	69.0		255,492	1.6	1.0	7	dbSNP_126	69	1291,7307	249.9+/-277.0	96,1099,3104	yes	missense,missense	GTPBP10	NM_001042717.2,NM_033107.3	22,22	99,1223,5180	CC,CG,GG		15.0151,2.9505,10.9274	probably-damaging,probably-damaging	85/309,164/388	90001496	1421,11583	2203	4299	6502	SO:0001583	missense	85865	exon5			CTCTTTGCTAAGT		CCDS5617.1, CCDS43614.1	7q21.13	2006-08-15			ENSG00000105793	ENSG00000105793			25106	protein-coding gene	gene with protein product		610920				12477932	Standard	NM_001042717		Approved	DKFZP686A10121, FLJ38242	uc003ukm.2	A4D1E9	OTTHUMG00000023655	ENST00000222511.6:c.492G>C	7.37:g.90001496G>C	ENSP00000222511:p.Leu164Phe	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	58	0.54717	NM_033107	B4DFY6|Q3B7A6|Q5H9V2|Q8IXG8|Q8N982|Q8WU16|Q9BSP1|Q9Y6T6	Missense_Mutation	SNP	ENST00000222511.6	37	CCDS5617.1	136	0.06227106227106227	5	0.01016260162601626	39	0.10773480662983426	0	0.0	92	0.12137203166226913	G	13.87	2.366126	0.41902	0.029505	0.150151	ENSG00000105793	ENST00000426366;ENST00000450619;ENST00000257659;ENST00000222511	T;T;T;T	0.37915	1.34;1.34;1.17;1.17	5.91	1.58	0.23477	GTP1/OBG (1);GTP-binding domain, HSR1-related (1);	0.000000	0.85682	D	0.000000	T	0.00356	0.0011	L	0.49640	1.575	0.09310	P	0.99999601463	D;D;D;D	0.89917	1.0;1.0;1.0;0.993	D;D;D;D	0.91635	0.999;0.995;0.996;0.914	T	0.04708	-1.0932	8	.	.	.	-0.0399	11.8102	0.52179	0.3465:0.0:0.6535:0.0	rs35001814	85;164;155;181	A4D1E9-2;A4D1E9;C9J8R7;C9JNI1	.;GTPBA_HUMAN;.;.	F	155;181;85;164	ENSP00000405697:L155F;ENSP00000389510:L181F;ENSP00000257659:L85F;ENSP00000222511:L164F	.	L	+	3	2	GTPBP10	89839432	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.259000	0.32956	0.399000	0.25367	-0.136000	0.14681	TTG	G|0.908;C|0.092	0.092	strong		0.308	GTPBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059976.3	NM_033107	
GRIN3B	116444	hgsc.bcm.edu	37	19	1003158	1003158	+	Silent	SNP	C	C	T	rs35163060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1003158C>T	ENST00000234389.3	+	2	475	c.456C>T	c.(454-456)gcC>gcT	p.A152A	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	152					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)	TGCACTGGGCCAGCCCCCTGG	0.692													c|||	695	0.138778	0.32	0.0504	5008	,	,		13453	0.121		0.0606	False		,,,				2504	0.0552				p.A152A		Atlas-SNP	.											.	GRIN3B	46	.	0			c.C456T						PASS	.	C		1064,3154		120,824,1165	8.0	9.0	8.0		456	2.3	1.0	19	dbSNP_126	8	555,7779		30,495,3642	no	coding-synonymous	GRIN3B	NM_138690.1		150,1319,4807	TT,TC,CC		6.6595,25.2252,12.8983		152/1044	1003158	1619,10933	2109	4167	6276	SO:0001819	synonymous_variant	116444	exon2			CTGGGCCAGCCCC		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.456C>T	19.37:g.1003158C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			C|0.875;T|0.125	0.125	strong		0.692	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
IFNA1	3439	hgsc.bcm.edu	37	9	21440535	21440535	+	Missense_Mutation	SNP	T	T	C	rs1758567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:21440535T>C	ENST00000276927.1	+	1	96	c.29T>C	c.(28-30)gTc>gCc	p.V10A		NM_024013.2	NP_076918.1	P01562	IFNA1_HUMAN	interferon, alpha 1	10			V -> A (in dbSNP:rs1758567). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.8, ECO:0000269|Ref.9}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|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)|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)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)	7				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		TTACTGATGGTCCTGGTGGTG	0.537																																					p.V10A		Atlas-SNP	.											.	IFNA1	21	.	0			c.T29C						PASS	.						123.0	112.0	116.0					9																	21440535		2203	4300	6503	SO:0001583	missense	3439	exon1			TGATGGTCCTGGT		CCDS6508.1	9p22	2010-12-10			ENSG00000197919	ENSG00000197919		"""Interferons"""	5417	protein-coding gene	gene with protein product	"""IFN-alpha 1b"", ""interferon alpha 1b"""	147660				1385305	Standard	NM_024013		Approved	IFNA@, IFL, IFN, IFN-ALPHA, IFNA13, IFN-alphaD	uc003zpd.2	P01562	OTTHUMG00000019673	ENST00000276927.1:c.29T>C	9.37:g.21440535T>C	ENSP00000276927:p.Val10Ala	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	213	80	0.375587	NM_024013	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Missense_Mutation	SNP	ENST00000276927.1	37	CCDS6508.1	112	0.05128205128205128	50	0.1016260162601626	11	0.03038674033149171	2	0.0034965034965034965	49	0.06464379947229551	C	1.442	-0.567396	0.03910	.	.	ENSG00000197919	ENST00000276927	T	0.02837	4.14	3.27	1.27	0.21489	.	0.733687	0.12514	N	0.462263	T	0.00039	0.0001	N	0.00128	-2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41592	-0.9500	9	0.02654	T	1	.	3.6277	0.08119	0.1942:0.5767:0.0:0.2291	rs1758567;rs2773832;rs56880282;rs1758567	10	P01562	IFNA1_HUMAN	A	10	ENSP00000276927:V10A	ENSP00000276927:V10A	V	+	2	0	IFNA1	21430535	0.000000	0.05858	0.210000	0.23637	0.526000	0.34562	-0.714000	0.05002	-0.080000	0.12685	-0.260000	0.10688	GTC	T|0.954;C|0.046	0.046	strong		0.537	IFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051902.1	NM_024013	
CCDC40	55036	hgsc.bcm.edu	37	17	78023722	78023722	+	Silent	SNP	C	C	T	rs2289531	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78023722C>T	ENST00000397545.4	+	6	900	c.873C>T	c.(871-873)ttC>ttT	p.F291F	CCDC40_ENST00000269318.5_Silent_p.F291F|CCDC40_ENST00000374877.3_Silent_p.F291F|CCDC40_ENST00000374876.4_Silent_p.F291F	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	291					axonemal dynein complex assembly (GO:0070286)|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 (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)		p.F291F(1)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TGGTAAGATTCCAGGCTGCCC	0.562													C|||	562	0.11222	0.121	0.062	5008	,	,		18960	0.1617		0.0924	False		,,,				2504	0.1053				p.F291F		Atlas-SNP	.											CCDC40,NS,carcinoma,0,1	CCDC40	198	1	1	Substitution - coding silent(1)	stomach(1)	c.C873T						PASS	.	C		417,3537		20,377,1580	81.0	89.0	87.0		873	4.1	1.0	17	dbSNP_100	87	775,7537		34,707,3415	no	coding-synonymous	CCDC40	NM_017950.3		54,1084,4995	TT,TC,CC		9.3239,10.5463,9.7179		291/1143	78023722	1192,11074	1977	4156	6133	SO:0001819	synonymous_variant	55036	exon6			AAGATTCCAGGCT	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.873C>T	17.37:g.78023722C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			C|0.893;T|0.107	0.107	strong		0.562	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
ZNF480	147657	hgsc.bcm.edu	37	19	52825235	52825235	+	Silent	SNP	A	A	G	rs8102373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52825235A>G	ENST00000595962.1	+	5	798	c.732A>G	c.(730-732)tcA>tcG	p.S244S	ZNF480_ENST00000335090.6_Silent_p.S167S|ZNF480_ENST00000334564.7_Silent_p.S201S|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000490272.1_3'UTR	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	244					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		GTCGCAATTCACACCTTGCAG	0.368													A|||	2636	0.526358	0.5371	0.5101	5008	,	,		20260	0.3998		0.6123	False		,,,				2504	0.5654				p.S244S		Atlas-SNP	.											ZNF480_ENST00000468240,NS,carcinoma,+1,2	ZNF480	123	2	0			c.A732G						PASS	.	A		2320,2086	586.1+/-386.4	622,1076,505	41.0	41.0	41.0		732	-2.0	0.0	19	dbSNP_116	41	5037,3563	616.4+/-396.5	1472,2093,735	no	coding-synonymous	ZNF480	NM_144684.2		2094,3169,1240	GG,GA,AA		41.4302,47.3445,43.4338		244/536	52825235	7357,5649	2203	4300	6503	SO:0001819	synonymous_variant	147657	exon5			CAATTCACACCTT	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"""Zinc fingers, C2H2-type"", ""-"""	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.732A>G	19.37:g.52825235A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	118	44	0.372881	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Silent	SNP	ENST00000595962.1	37	CCDS12850.2																																																																																			A|0.449;G|0.551	0.551	strong		0.368	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684	
IGSF10	285313	hgsc.bcm.edu	37	3	151171439	151171439	+	Missense_Mutation	SNP	A	A	C	rs7619322	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151171439A>C	ENST00000282466.3	-	3	447	c.448T>G	c.(448-450)Tat>Gat	p.Y150D		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	150			Y -> D (in dbSNP:rs7619322).		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)			TTGAGCCCATAAAAAACCTCT	0.423													A|||	3645	0.727835	0.6891	0.7075	5008	,	,		16508	0.745		0.7435	False		,,,				2504	0.7607				p.Y150D		Atlas-SNP	.											.	IGSF10	279	.	0			c.T448G						PASS	.	A	ASP/TYR	3031,1375	682.8+/-404.2	1038,955,210	75.0	82.0	79.0		448	-2.5	0.0	3	dbSNP_116	79	6262,2338	702.1+/-405.3	2290,1682,328	yes	missense	IGSF10	NM_178822.4	160	3328,2637,538	CC,CA,AA		27.186,31.2074,28.5484	possibly-damaging	150/2624	151171439	9293,3713	2203	4300	6503	SO:0001583	missense	285313	exon3			GCCCATAAAAAAC	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.448T>G	3.37:g.151171439A>C	ENSP00000282466:p.Tyr150Asp	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	1613	0.7385531135531136	357	0.725609756097561	254	0.7016574585635359	431	0.7534965034965035	571	0.7532981530343008	A	15.79	2.936281	0.52972	0.687926	0.72814	ENSG00000152580	ENST00000282466	T	0.51574	0.7	5.53	-2.47	0.06442	.	0.700710	0.12290	N	0.482074	T	0.00012	0.0000	N	0.02916	-0.46	0.30101	P	0.807391	P	0.50710	0.938	P	0.55087	0.768	T	0.47058	-0.9146	9	0.30854	T	0.27	.	0.6669	0.00852	0.4402:0.1168:0.2:0.243	rs7619322;rs52823444;rs60638999;rs7619322	150	Q6WRI0	IGS10_HUMAN	D	150	ENSP00000282466:Y150D	ENSP00000282466:Y150D	Y	-	1	0	IGSF10	152654129	1.000000	0.71417	0.026000	0.17262	0.939000	0.58152	2.414000	0.44627	-0.442000	0.07190	0.528000	0.53228	TAT	A|0.276;C|0.724	0.724	strong		0.423	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
ST14	6768	hgsc.bcm.edu	37	11	130058047	130058047	+	Silent	SNP	A	A	G	rs62642510	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:130058047A>G	ENST00000278742.5	+	2	538	c.120A>G	c.(118-120)ccA>ccG	p.P40P		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	40					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)	AGTTCCTGCCAGTCAACAACG	0.632													G|||	512	0.102236	0.3245	0.0562	5008	,	,		17883	0.0		0.0378	False		,,,				2504	0.0061				p.P40P		Atlas-SNP	.											.	ST14	82	.	0			c.A120G						PASS	.	G		1201,3201	707.7+/-407.5	179,843,1179	68.0	62.0	64.0		120	-9.9	0.0	11	dbSNP_129	64	371,8223	802.5+/-407.3	6,359,3932	no	coding-synonymous	ST14	NM_021978.3		185,1202,5111	GG,GA,AA		4.317,27.2831,12.096		40/856	130058047	1572,11424	2201	4297	6498	SO:0001819	synonymous_variant	6768	exon2			CCTGCCAGTCAAC	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.120A>G	11.37:g.130058047A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	178	128	0.719101	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	CCDS8487.1																																																																																			A|0.885;G|0.115	0.115	strong		0.632	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
RORA	6095	hgsc.bcm.edu	37	15	60803741	60803741	+	Silent	SNP	C	C	T	rs61740274	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:60803741C>T	ENST00000335670.6	-	5	604	c.504G>A	c.(502-504)caG>caA	p.Q168Q	RP11-219B17.1_ENST00000559824.1_RNA|RP11-219B17.1_ENST00000501579.2_RNA|RORA_ENST00000261523.5_Silent_p.Q201Q|RP11-219B17.1_ENST00000558235.1_RNA|RORA_ENST00000309157.4_Silent_p.Q193Q|RORA_ENST00000449337.2_Silent_p.Q113Q|RP11-219B17.1_ENST00000558140.1_RNA|RORA_ENST00000560004.1_5'UTR|RP11-219B17.1_ENST00000559902.1_RNA	NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	168	Hinge.|Poly-Gln.				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						GGTCGCGCTGCTGCTGCTGCA	0.542													C|||	219	0.04373	0.0363	0.0634	5008	,	,		18969	0.0		0.0865	False		,,,				2504	0.0409				p.Q201Q		Atlas-SNP	.											.	RORA	114	.	0			c.G603A						PASS	.	C	,,,	225,4181	133.7+/-170.0	4,217,1982	97.0	77.0	84.0		579,603,504,339	5.0	1.0	15	dbSNP_129	84	888,7712	199.0+/-243.2	56,776,3468	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RORA	NM_002943.3,NM_134260.2,NM_134261.2,NM_134262.2	,,,	60,993,5450	TT,TC,CC		10.3256,5.1067,8.5576	,,,	193/549,201/557,168/524,113/469	60803741	1113,11893	2203	4300	6503	SO:0001819	synonymous_variant	6095	exon6			GCGCTGCTGCTGC	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.504G>A	15.37:g.60803741C>T		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	146	27	0.184932	NM_134260	P35397|P35399|P45445|Q495X4|Q96H83	Silent	SNP	ENST00000335670.6	37	CCDS10177.1																																																																																			C|0.924;T|0.076	0.076	strong		0.542	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2		
OR2L3	391192	hgsc.bcm.edu	37	1	248224746	248224746	+	Missense_Mutation	SNP	G	G	T	rs6697812	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248224746G>T	ENST00000359959.3	+	1	763	c.763G>T	c.(763-765)Gtc>Ttc	p.V255F	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, 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)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	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;0.0278)			TGCACCTTTTGTCTACACTTA	0.493													g|||	137	0.0273562	0.0068	0.0432	5008	,	,		20709	0.0		0.0905	False		,,,				2504	0.0072				p.V255F		Atlas-SNP	.											.	OR2L3	97	.	0			c.G763T						PASS	.	G	PHE/VAL,	60,4346	58.1+/-94.6	0,60,2143	125.0	118.0	120.0		763,	-4.0	0.0	1	dbSNP_116	120	756,7838	177.5+/-227.1	32,692,3573	no	missense,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	50,	32,752,5716	TT,TG,GG		8.7968,1.3618,6.2769	benign,	255/313,	248224746	816,12184	2203	4297	6500	SO:0001583	missense	391192	exon1			CCTTTTGTCTACA	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.763G>T	1.37:g.248224746G>T	ENSP00000353044:p.Val255Phe	Somatic	290	1	0.00344828		WXS	Illumina HiSeq	Phase_I	365	203	0.556164	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	73	0.033424908424908424	5	0.01016260162601626	16	0.04419889502762431	0	0.0	52	0.06860158311345646	G	0.008	-1.882849	0.00532	0.013618	0.087968	ENSG00000198128	ENST00000359959	T	0.36878	1.23	2.01	-4.03	0.04021	GPCR, rhodopsin-like superfamily (1);	1.925040	0.04254	N	0.339066	T	0.00384	0.0012	N	0.01267	-0.92	0.09310	N	1	B	0.02656	0.0	B	0.12156	0.007	T	0.06588	-1.0818	10	0.24483	T	0.36	.	1.0083	0.01492	0.2749:0.1294:0.3575:0.2383	rs6697812	255	Q8NG85	OR2L3_HUMAN	F	255	ENSP00000353044:V255F	ENSP00000353044:V255F	V	+	1	0	OR2L3	246291369	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.951000	0.00048	-2.222000	0.00727	-3.156000	0.00058	GTC	.	.	weak		0.493	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580772	140580772	+	Silent	SNP	T	T	C	rs57636116	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140580772T>C	ENST00000354757.3	+	1	1425	c.1425T>C	c.(1423-1425)gcT>gcC	p.A475A	PCDHB11_ENST00000536699.1_Silent_p.A110A	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	475	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)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTGTCAGCGCTACAGACAGAG	0.622													t|||	548	0.109425	0.1029	0.1744	5008	,	,		17056	0.0407		0.1581	False		,,,				2504	0.093				p.A475A		Atlas-SNP	.											.	PCDHB11	162	.	0			c.T1425C						PASS	.	T		490,3916	777.8+/-414.3	28,434,1741	130.0	124.0	126.0		1425	0.4	0.0	5	dbSNP_129	126	1426,7170	745.9+/-407.3	129,1168,3001	no	coding-synonymous	PCDHB11	NM_018931.2		157,1602,4742	CC,CT,TT		16.5891,11.1212,14.7362		475/798	140580772	1916,11086	2203	4298	6501	SO:0001819	synonymous_variant	56125	exon1			CAGCGCTACAGAC	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1425T>C	5.37:g.140580772T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_018931	B4DSF7|Q2M223	Silent	SNP	ENST00000354757.3	37	CCDS4253.1																																																																																			T|0.869;C|0.131	0.131	strong		0.622	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
GBP7	388646	hgsc.bcm.edu	37	1	89613280	89613280	+	Silent	SNP	G	G	A	rs115454072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89613280G>A	ENST00000294671.2	-	8	1473	c.1335C>T	c.(1333-1335)gaC>gaT	p.D445D		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	445						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)		CTAGTGTATAGTCCTGTTCAA	0.443													G|||	115	0.0229633	0.0166	0.0159	5008	,	,		18197	0.0119		0.0278	False		,,,				2504	0.0429				p.D445D		Atlas-SNP	.											.	GBP7	57	.	0			c.C1335T						PASS	.	G		71,4335	64.1+/-101.4	0,71,2132	171.0	171.0	171.0		1335	-0.8	0.0	1	dbSNP_132	171	215,8385	90.6+/-152.8	1,213,4086	no	coding-synonymous	GBP7	NM_207398.2		1,284,6218	AA,AG,GG		2.5,1.6114,2.199		445/639	89613280	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	388646	exon8			TGTATAGTCCTGT	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.1335C>T	1.37:g.89613280G>A		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			G|0.976;A|0.024	0.024	strong		0.443	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
C14orf80	283643	hgsc.bcm.edu	37	14	105965155	105965155	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105965155A>G	ENST00000392523.4	+	9	1481	c.1360A>G	c.(1360-1362)Acg>Gcg	p.T454A	C14orf80_ENST00000334656.7_Missense_Mutation_p.T311A|C14orf80_ENST00000392522.3_Missense_Mutation_p.T385A|C14orf80_ENST00000329886.7_Missense_Mutation_p.T313A|C14orf80_ENST00000450383.1_Missense_Mutation_p.T207A|C14orf80_ENST00000354560.6_Missense_Mutation_p.T352A|C14orf80_ENST00000392527.1_Missense_Mutation_p.T311A			Q86SX3	CN080_HUMAN	chromosome 14 open reading frame 80	454										central_nervous_system(1)	1		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.239)		GGTGATCAGGACGCTGAGGAG	0.701																																					p.T385A		Atlas-SNP	.											C14orf80_ENST00000392522,NS,carcinoma,-2,2	C14orf80	19	2	0			c.A1153G						scavenged	.						36.0	36.0	36.0					14																	105965155		2187	4294	6481	SO:0001583	missense	283643	exon8			ATCAGGACGCTGA		CCDS45180.1, CCDS45181.1, CCDS45182.1, CCDS55955.1	14q32.33	2012-09-25			ENSG00000185347	ENSG00000185347			20127	protein-coding gene	gene with protein product							Standard	NM_001134875		Approved		uc001yrn.3	Q86SX3	OTTHUMG00000170426	ENST00000392523.4:c.1360A>G	14.37:g.105965155A>G	ENSP00000376308:p.Thr454Ala	Somatic	500	4	0.008		WXS	Illumina HiSeq	Phase_I	566	9	0.0159011	NM_001134875	B5MDG3|E9PAQ4|Q86TT3|Q86TT4|Q86TT5|Q96B41|Q9H7H4	Missense_Mutation	SNP	ENST00000392523.4	37		.	.	.	.	.	.	.	.	.	.	.	0.012	-1.677822	0.00751	.	.	ENSG00000185347	ENST00000329886;ENST00000392527;ENST00000334656;ENST00000392522;ENST00000392523;ENST00000354560;ENST00000548920;ENST00000450383	.	.	.	3.39	-2.87	0.05700	.	2.250380	0.02325	N	0.073370	T	0.15869	0.0382	N	0.12746	0.255	0.09310	N	1	B;B;B;B;B;B	0.12630	0.001;0.0;0.001;0.006;0.001;0.002	B;B;B;B;B;B	0.13407	0.003;0.001;0.002;0.009;0.002;0.002	T	0.08411	-1.0723	9	0.09843	T	0.71	-0.0281	0.8271	0.01123	0.3974:0.162:0.2779:0.1627	.	333;352;385;454;311;313	C9JZD4;Q86SX3-2;E9PAQ4;Q86SX3;B5MDG3;Q86SX3-3	.;.;.;CN080_HUMAN;.;.	A	313;311;311;385;454;352;314;207	.	ENSP00000333010:T313A	T	+	1	0	C14orf80	105036200	0.002000	0.14202	0.000000	0.03702	0.077000	0.17291	0.152000	0.16302	-0.251000	0.09542	0.260000	0.18958	ACG	.	.	none		0.701	C14orf80-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409090.1	NM_001134875	
PKD1	5310	hgsc.bcm.edu	37	16	2140454	2140454	+	Silent	SNP	T	T	C	rs3087632	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2140454T>C	ENST00000262304.4	-	45	12484	c.12276A>G	c.(12274-12276)gcA>gcG	p.A4092A	PKD1_ENST00000423118.1_Silent_p.A4091A|MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4092					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						ACAGCCGCAGTGCCCAGAGCC	0.697													c|||	1384	0.276358	0.7186	0.2104	5008	,	,		16523	0.0		0.1988	False		,,,				2504	0.09				p.A4092A		Atlas-SNP	.											.	PKD1	184	.	0			c.A12276G						PASS	.		,	2623,1743		806,1011,366	19.0	25.0	23.0		12273,12276	-8.0	0.3	16	dbSNP_102	23	1600,6984		151,1298,2843	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	957,2309,3209	CC,CT,TT		18.6393,39.9221,32.61	,	4091/4303,4092/4304	2140454	4223,8727	2183	4292	6475	SO:0001819	synonymous_variant	5310	exon45			CCGCAGTGCCCAG	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.12276A>G	16.37:g.2140454T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_001009944	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			T|0.696;C|0.304	0.304	strong		0.697	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
SCFD1	23256	hgsc.bcm.edu	37	14	31099738	31099738	+	Missense_Mutation	SNP	A	A	G	rs229150	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:31099738A>G	ENST00000458591.2	+	3	415	c.188A>G	c.(187-189)aAg>aGg	p.K63R	SCFD1_ENST00000541123.1_5'UTR|SCFD1_ENST00000396629.2_Intron|SCFD1_ENST00000544052.2_5'UTR|SCFD1_ENST00000421551.3_Intron	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	63			K -> R (in dbSNP:rs229150). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle docking involved in exocytosis (GO:0006904)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi transport complex (GO:0017119)|Golgi-associated vesicle (GO:0005798)|plasma membrane (GO:0005886)	syntaxin binding (GO:0019905)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)	13	Hepatocellular(127;0.0877)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)	GBM - Glioblastoma multiforme(265;0.0181)		CTATCTGTGAAGGAGCTAAGA	0.323													A|||	2893	0.577676	0.7935	0.5029	5008	,	,		17065	0.7103		0.3608	False		,,,				2504	0.4254				p.K63R		Atlas-SNP	.											SCFD1,NS,carcinoma,0,1	SCFD1	43	1	0			c.A188G						PASS	.	A	ARG/LYS,	3123,1283	699.6+/-406.5	1127,869,207	152.0	159.0	157.0		188,	5.6	1.0	14	dbSNP_79	157	2940,5658	457.1+/-364.2	506,1928,1865	yes	missense,utr-5	SCFD1	NM_016106.2,NM_182835.1	26,	1633,2797,2072	GG,GA,AA		34.194,29.1194,46.6241	benign,	63/643,	31099738	6063,6941	2203	4299	6502	SO:0001583	missense	23256	exon3			CTGTGAAGGAGCT	AF110646	CCDS9639.1, CCDS45092.1, CCDS58308.1	14q12	2006-04-04	2004-01-15	2004-01-16	ENSG00000092108	ENSG00000092108			20726	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 163"""	C14orf163			Standard	NM_016106		Approved	RA410, KIAA0917, STXBP1L2, SLY1	uc001wqm.2	Q8WVM8	OTTHUMG00000029420	ENST00000458591.2:c.188A>G	14.37:g.31099738A>G	ENSP00000390783:p.Lys63Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	150	57	0.38	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	37	CCDS9639.1	1221	0.5590659340659341	388	0.7886178861788617	169	0.46685082872928174	405	0.708041958041958	259	0.341688654353562	A	15.51	2.853519	0.51270	0.708806	0.34194	ENSG00000092108	ENST00000458591;ENST00000557076	T;T	0.29917	1.55;1.55	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.49126	1.545	0.09310	P	1.0	B	0.17667	0.023	B	0.32928	0.155	T	0.25676	-1.0125	9	0.42905	T	0.14	-17.8222	15.7861	0.78304	1.0:0.0:0.0:0.0	rs229150;rs230378;rs17362188;rs17851559;rs52794734;rs60052190;rs229150	63	Q8WVM8	SCFD1_HUMAN	R	63;38	ENSP00000390783:K63R;ENSP00000450755:K38R	ENSP00000309417:K71R	K	+	2	0	SCFD1	30169489	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.719000	0.91436	2.129000	0.65627	0.528000	0.53228	AAG	G|0.519;N|0.000	0.519	strong		0.323	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835	
CDC27	996	hgsc.bcm.edu	37	17	45234713	45234713	+	Silent	SNP	T	T	C	rs139751753		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45234713T>C	ENST00000066544.3	-	6	606	c.513A>G	c.(511-513)acA>acG	p.T171T	CDC27_ENST00000531206.1_Silent_p.T171T|CDC27_ENST00000527547.1_Silent_p.T171T|CDC27_ENST00000446365.2_Silent_p.T110T|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	171					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.T171T(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						TCTGTAAAGATGTGAATTTAA	0.373																																					p.T171T		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	2	3	Substitution - coding silent(3)	prostate(3)	c.A513G						scavenged	.						77.0	77.0	77.0					17																	45234713		2203	4300	6503	SO:0001819	synonymous_variant	996	exon6			TAAAGATGTGAAT	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.513A>G	17.37:g.45234713T>C		Somatic	282	3	0.0106383		WXS	Illumina HiSeq	Phase_I	347	40	0.115274	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			.	.	weak		0.373	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
SEC23A	10484	hgsc.bcm.edu	37	14	39517925	39517925	+	Silent	SNP	T	T	C	rs11556216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:39517925T>C	ENST00000307712.6	-	15	2185	c.1668A>G	c.(1666-1668)aaA>aaG	p.K556K	SEC23A_ENST00000536508.1_Silent_p.K430K|SEC23A_ENST00000537403.1_Silent_p.K354K|SEC23A_ENST00000545328.2_Silent_p.K527K	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	25	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	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		
CENPE	1062	hgsc.bcm.edu	37	4	104082349	104082349	+	Silent	SNP	C	C	T	rs2251634	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:104082349C>T	ENST00000265148.3	-	20	2114	c.2025G>A	c.(2023-2025)caG>caA	p.Q675Q	CENPE_ENST00000380026.3_Silent_p.Q650Q	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	675					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TTGCCTCCAACTGGCTTTGAT	0.328													T|||	2254	0.45008	0.674	0.353	5008	,	,		15920	0.3006		0.4076	False		,,,				2504	0.4141				p.Q675Q		Atlas-SNP	.											.	CENPE	253	.	0			c.G2025A						PASS	.	T		2584,1820	528.4+/-372.4	753,1078,371	137.0	130.0	132.0		2025	-1.7	0.8	4	dbSNP_100	132	3376,5220	637.2+/-399.2	685,2006,1607	no	coding-synonymous	CENPE	NM_001813.2		1438,3084,1978	TT,TC,CC		39.2741,41.3261,45.8462		675/2702	104082349	5960,7040	2202	4298	6500	SO:0001819	synonymous_variant	1062	exon20			CTCCAACTGGCTT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.2025G>A	4.37:g.104082349C>T		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	181	93	0.513812	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																			T|0.446;G|0.001	0.446	strong		0.328	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FARP2	9855	hgsc.bcm.edu	37	2	242371101	242371101	+	Missense_Mutation	SNP	C	C	T	rs757978	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242371101C>T	ENST00000264042.3	+	9	949	c.779C>T	c.(778-780)aCc>aTc	p.T260I	FARP2_ENST00000545004.1_Missense_Mutation_p.T260I|FARP2_ENST00000373287.4_Missense_Mutation_p.T260I	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	260	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		T -> I (in dbSNP:rs757978).		actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		CAGGGCACCACCAAAATCAAC	0.383													C|||	403	0.0804712	0.1082	0.0807	5008	,	,		11204	0.0238		0.0974	False		,,,				2504	0.0838				p.T260I		Atlas-SNP	.											.	FARP2	92	.	0			c.C779T						PASS	.	C	ILE/THR	426,3980	206.2+/-227.9	22,382,1799	118.0	106.0	110.0	http://www.ncbi.nlm.nih.gov/pubmed?term	779	4.8	1.0	2	dbSNP_86	110	961,7639	210.5+/-251.4	47,867,3386	yes	missense	FARP2	NM_014808.2	89	69,1249,5185	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	11.1744,9.6686,10.6643	probably-damaging	260/1055	242371101	1387,11619	2203	4300	6503	SO:0001583	missense	9855	exon9			GCACCACCAAAAT	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.779C>T	2.37:g.242371101C>T	ENSP00000264042:p.Thr260Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	171	0.0782967032967033	51	0.10365853658536585	22	0.06077348066298342	19	0.033216783216783216	79	0.10422163588390501	c	21.0	4.075661	0.76415	0.096686	0.111744	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	D;D;D	0.87179	-2.22;-2.22;-2.22	4.79	4.79	0.61399	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.126402	0.53938	D	0.000056	T	0.23688	0.0573	L	0.49640	1.575	0.09310	P	0.999999999237139	D;D;D	0.89917	1.0;0.988;1.0	D;D;D	0.97110	0.999;0.944;1.0	T	0.65092	-0.6252	9	0.30078	T	0.28	.	18.2564	0.90021	0.0:1.0:0.0:0.0	rs757978;rs17452163;rs59395776;rs757978	260;260;260	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	I	260	ENSP00000264042:T260I;ENSP00000443876:T260I;ENSP00000362384:T260I	ENSP00000264042:T260I	T	+	2	0	FARP2	242019774	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.828000	0.69307	2.382000	0.81193	0.539000	0.68188	ACC	C|0.901;T|0.099	0.099	strong		0.383	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
MRPL43	84545	hgsc.bcm.edu	37	10	102746503	102746503	+	Intron	SNP	C	C	T	rs2863095	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102746503C>T	ENST00000318325.2	-	3	519				MRPL43_ENST00000477279.1_3'UTR|MRPL43_ENST00000370234.4_Intron|MRPL43_ENST00000370241.3_Intron|MRPL43_ENST00000318364.8_Silent_p.V156V|RP11-108L7.4_ENST00000447344.1_RNA|MRPL43_ENST00000299179.5_Intron|C10orf2_ENST00000370228.1_5'Flank|MRPL43_ENST00000493646.1_5'UTR|MRPL43_ENST00000370236.1_Silent_p.V156V|MRPL43_ENST00000342071.1_Intron|MRPL43_ENST00000370242.4_Intron|C10orf2_ENST00000311916.2_5'Flank	NM_176792.2	NP_789762.1	Q8N983	RM43_HUMAN	mitochondrial ribosomal protein L43						translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|skin(2)|upper_aerodigestive_tract(1)	4		Colorectal(252;0.234)		Epithelial(162;6.21e-09)|all cancers(201;3.14e-07)		ACTGTGCTTGCACCTGGGCTG	0.617													C|||	1766	0.352636	0.3941	0.2882	5008	,	,		17301	0.5268		0.1829	False		,,,				2504	0.3374				p.V156V		Atlas-SNP	.											.	MRPL43	16	.	0			c.G468A						PASS	.	C	,,,	1555,2851	484.6+/-360.1	276,1003,924	83.0	78.0	80.0		468,,,	1.5	0.0	10	dbSNP_101	80	1787,6813	321.3+/-315.0	192,1403,2705	no	coding-synonymous,intron,intron,intron	MRPL43	NM_032112.2,NM_176792.2,NM_176793.1,NM_176794.1	,,,	468,2406,3629	TT,TC,CC		20.7791,35.2928,25.6958	,,,	156/160,,,	102746503	3342,9664	2203	4300	6503	SO:0001627	intron_variant	84545	exon3			TGCTTGCACCTGG	AB049656	CCDS7502.1, CCDS7503.1, CCDS7504.1, CCDS7505.1	10q24.31	2012-09-13			ENSG00000055950	ENSG00000055950		"""Mitochondrial ribosomal proteins / large subunits"""	14517	protein-coding gene	gene with protein product		611848					Standard	NM_176792		Approved	bMRP36a	uc001ksa.1	Q8N983	OTTHUMG00000018920	ENST00000318325.2:c.465+2G>A	10.37:g.102746503C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	10	0.196078	NM_032112	B1AL06|B1AL07|B1AL09|B1AL10|C9J5Q3|D3DR71|Q5JW06|Q7Z719|Q7Z7H6|Q86XN1|Q9BYC7	Silent	SNP	ENST00000318325.2	37	CCDS7502.1																																																																																			C|0.704;T|0.296	0.296	strong		0.617	MRPL43-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049902.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29910622	29910622	+	Silent	SNP	C	C	T	rs199501996	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29910622C>T	ENST00000396634.1	+	4	503	c.162C>T	c.(160-162)gaC>gaT	p.D54D	HLA-A_ENST00000376806.5_Silent_p.D54D|HLA-A_ENST00000376802.2_Silent_p.D54D|HLA-A_ENST00000376809.5_Silent_p.D54D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	54	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)	p.D54D(2)		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						ACGTGGACGACACGCAGTTCG	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)																											p.D54D		Atlas-SNP	.											HLA-A,NS,carcinoma,0,4	HLA-A	89	4	2	Substitution - coding silent(2)	prostate(2)	c.C162T						PASS	.						47.0	40.0	42.0					6																	29910622		2202	4299	6501	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGACGACACGCAG	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.162C>T	6.37:g.29910622C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	140	20	0.142857	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.998;T|0.002	0.002	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ACSL1	2180	hgsc.bcm.edu	37	4	185724503	185724503	+	Missense_Mutation	SNP	C	C	T	rs114493597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:185724503C>T	ENST00000515030.1	-	2	491	c.166G>A	c.(166-168)Gac>Aac	p.D56N	ACSL1_ENST00000504342.1_Missense_Mutation_p.D56N|ACSL1_ENST00000513317.1_Missense_Mutation_p.D56N|ACSL1_ENST00000507295.1_Missense_Mutation_p.D56N|ACSL1_ENST00000454703.2_Intron|ACSL1_ENST00000437665.3_5'UTR|ACSL1_ENST00000281455.2_Missense_Mutation_p.D56N|ACSL1_ENST00000504900.1_Missense_Mutation_p.D56N			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	56				CD -> WH (in Ref. 2; AAB00959). {ECO:0000305}.	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)	ATGGAGAGGTCGCATGGCGGC	0.592													C|||	3	0.000599042	0.0	0.0	5008	,	,		18362	0.0		0.003	False		,,,				2504	0.0				p.D56N		Atlas-SNP	.											.	ACSL1	77	.	0			c.G166A						PASS	.	C	ASN/ASP	3,4403	6.2+/-15.9	0,3,2200	64.0	58.0	60.0		166	5.0	1.0	4	dbSNP_133	60	33,8567	22.2+/-67.0	0,33,4267	yes	missense	ACSL1	NM_001995.2	23	0,36,6467	TT,TC,CC		0.3837,0.0681,0.2768	possibly-damaging	56/699	185724503	36,12970	2203	4300	6503	SO:0001583	missense	2180	exon2			AGAGGTCGCATGG	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.166G>A	4.37:g.185724503C>T	ENSP00000422607:p.Asp56Asn	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	93	64	0.688172	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Missense_Mutation	SNP	ENST00000515030.1	37	CCDS3839.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	19.38	3.815734	0.70912	6.81E-4	0.003837	ENSG00000151726	ENST00000515030;ENST00000281455;ENST00000507295;ENST00000504342;ENST00000513317;ENST00000504900	T;T;T;T;T;T	0.23950	2.07;2.07;1.88;2.07;2.0;2.2	5.04	5.04	0.67666	.	0.045032	0.85682	D	0.000000	T	0.49253	0.1546	M	0.69463	2.115	0.80722	D	1	B;B;D;B	0.89917	0.312;0.02;1.0;0.037	B;B;D;B	0.71870	0.052;0.035;0.975;0.035	T	0.33033	-0.9884	10	0.31617	T	0.26	-33.9469	18.5929	0.91220	0.0:1.0:0.0:0.0	.	56;56;56;56	E7EPM6;B7Z452;D6RER0;P33121	.;.;.;ACSL1_HUMAN	N	56	ENSP00000422607:D56N;ENSP00000281455:D56N;ENSP00000426244:D56N;ENSP00000425006:D56N;ENSP00000426150:D56N;ENSP00000424935:D56N	ENSP00000281455:D56N	D	-	1	0	ACSL1	185961497	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.213000	0.77950	2.614000	0.88457	0.655000	0.94253	GAC	C|0.998;T|0.002	0.002	strong		0.592	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	
UMOD	7369	hgsc.bcm.edu	37	16	20359831	20359831	+	Silent	SNP	C	C	T	rs13335818	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:20359831C>T	ENST00000570689.1	-	3	938	c.792G>A	c.(790-792)gtG>gtA	p.V264V	UMOD_ENST00000396134.2_Silent_p.V297V|UMOD_ENST00000396138.4_Silent_p.V313V|UMOD_ENST00000424589.1_Silent_p.V297V|UMOD_ENST00000396142.2_Silent_p.V264V|UMOD_ENST00000302509.4_Silent_p.V264V			P07911	UROM_HUMAN	uromodulin	264					cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)			endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						CACAGGCCTTCACCTGGACGG	0.667													c|||	603	0.120407	0.093	0.1671	5008	,	,		18285	0.0139		0.1998	False		,,,				2504	0.1524				p.V264V		Atlas-SNP	.											.	UMOD	128	.	0			c.G792A						PASS	.		,	441,3961		23,395,1783	17.0	19.0	18.0		792,792	2.7	1.0	16	dbSNP_121	18	1575,7015		153,1269,2873	no	coding-synonymous,coding-synonymous	UMOD	NM_001008389.1,NM_003361.2	,	176,1664,4656	TT,TC,CC		18.3353,10.0182,15.5172	,	264/641,264/641	20359831	2016,10976	2201	4295	6496	SO:0001819	synonymous_variant	7369	exon3			GGCCTTCACCTGG	M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"""Tamm-Horsfall glycoprotein"", ""uromucoid"""	191845	"""uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"""			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.792G>A	16.37:g.20359831C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	37	23	0.621622	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Silent	SNP	ENST00000570689.1	37	CCDS10583.1																																																																																			C|0.866;T|0.134	0.134	strong		0.667	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1		
C2CD2	25966	hgsc.bcm.edu	37	21	43327793	43327793	+	Silent	SNP	C	C	T	rs3746904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43327793C>T	ENST00000380486.3	-	9	1360	c.1119G>A	c.(1117-1119)tcG>tcA	p.S373S	C2CD2_ENST00000329623.7_Silent_p.S218S	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	373						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						AGCCCAGCACCGAGCTGCCGC	0.642													C|||	1832	0.365815	0.3169	0.4683	5008	,	,		15888	0.3859		0.3509	False		,,,				2504	0.3538				p.S373S		Atlas-SNP	.											C2CD2,NS,carcinoma,0,1	C2CD2	47	1	0			c.G1119A						PASS	.	C	,	1580,2826		320,940,943	22.0	25.0	24.0		1119,654	-7.6	0.0	21	dbSNP_107	24	3014,5586		524,1966,1810	no	coding-synonymous,coding-synonymous	C2CD2	NM_015500.1,NM_199050.2	,	844,2906,2753	TT,TC,CC		35.0465,35.8602,35.3222	,	373/697,218/542	43327793	4594,8412	2203	4300	6503	SO:0001819	synonymous_variant	25966	exon9			CAGCACCGAGCTG	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1119G>A	21.37:g.43327793C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Silent	SNP	ENST00000380486.3	37	CCDS42933.1																																																																																			C|0.655;T|0.345	0.345	strong		0.642	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
DTX2	113878	hgsc.bcm.edu	37	7	76111835	76111835	+	Silent	SNP	G	G	A	rs4236506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76111835G>A	ENST00000324432.5	+	5	789	c.279G>A	c.(277-279)cgG>cgA	p.R93R	DTX2_ENST00000430490.2_Silent_p.R93R|DTX2_ENST00000413936.2_Silent_p.R93R|DTX2_ENST00000307569.8_Silent_p.R93R|DTX2_ENST00000446820.2_Silent_p.R93R|DTX2_ENST00000446600.1_Silent_p.R2R|DTX2_ENST00000472426.1_3'UTR	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	262	0	0		WXS	Illumina HiSeq	Phase_I	282	169	0.599291	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		
C18orf8	29919	hgsc.bcm.edu	37	18	21109997	21109997	+	Silent	SNP	C	C	T	rs34136453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:21109997C>T	ENST00000269221.3	+	17	1610	c.1500C>T	c.(1498-1500)taC>taT	p.Y500Y	C18orf8_ENST00000591367.1_3'UTR|C18orf8_ENST00000590868.1_Silent_p.Y452Y	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	500	Mic1.					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)					CTCAGCATTACCTACATGAAC	0.438													C|||	27	0.00539137	0.0023	0.0014	5008	,	,		22282	0.001		0.0109	False		,,,				2504	0.0112				p.Y500Y		Atlas-SNP	.											.	C18orf8	58	.	0			c.C1500T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	299.0	297.0	298.0		1500	3.5	0.6	18	dbSNP_126	298	67,8533	41.7+/-99.0	0,67,4233	no	coding-synonymous	C18orf8	NM_013326.3		0,77,6426	TT,TC,CC		0.7791,0.227,0.592		500/658	21109997	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	29919	exon17			GCATTACCTACAT	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.1500C>T	18.37:g.21109997C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	203	109	0.536946	NM_013326	Q9BU17|Q9Y5M0	Silent	SNP	ENST00000269221.3	37	CCDS32803.1																																																																																			C|0.993;T|0.007	0.007	strong		0.438	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326	
LURAP1L	286343	hgsc.bcm.edu	37	9	12775880	12775880	+	Missense_Mutation	SNP	T	T	G	rs201963967		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:12775880T>G	ENST00000319264.3	+	1	861	c.166T>G	c.(166-168)Tgc>Ggc	p.C56G	LURAP1L_ENST00000489107.1_3'UTR|RP11-3L8.3_ENST00000417638.1_RNA	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	59	Gly-rich.							p.C56G(1)									cggcggcggctgcagtagcag	0.687																																					p.C56G		Atlas-SNP	.											C9orf150,caecum,carcinoma,0,3	.	.	3	1	Substitution - Missense(1)	ovary(1)	c.T166G						scavenged	.						4.0	4.0	4.0					9																	12775880		1740	3236	4976	SO:0001583	missense	286343	exon1			GGCGGCTGCAGTA	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.166T>G	9.37:g.12775880T>G	ENSP00000321026:p.Cys56Gly	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	14	3	0.214286	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Missense_Mutation	SNP	ENST00000319264.3	37	CCDS6473.1	.	.	.	.	.	.	.	.	.	.	T	6.415	0.444604	0.12164	.	.	ENSG00000153714	ENST00000319264	T	0.42900	0.96	4.66	0.578	0.17391	.	1.586600	0.03312	N	0.190713	T	0.18087	0.0434	.	.	.	0.51482	P	7.500000000004725E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.20009	-1.0288	8	0.08837	T	0.75	.	1.2788	0.02036	0.1736:0.1011:0.2715:0.4538	.	59	Q8IV03	CI150_HUMAN	G	56	ENSP00000321026:C56G	ENSP00000321026:C56G	C	+	1	0	C9orf150	12765880	0.074000	0.21230	0.846000	0.33378	0.825000	0.46686	-0.127000	0.10547	0.663000	0.31027	0.454000	0.30748	TGC	.	.	weak		0.687	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
HEG1	57493	hgsc.bcm.edu	37	3	124746049	124746049	+	Splice_Site	SNP	A	A	G	rs2981546	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:124746049A>G	ENST00000311127.4	-	3	980	c.913T>C	c.(913-915)Tct>Cct	p.S305P		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	305			S -> P (in dbSNP:rs2981546).		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						TGGCACTCACATGAGGAAAGG	0.463													A|||	2448	0.488818	0.3744	0.4755	5008	,	,		21467	0.4782		0.5457	False		,,,				2504	0.6053				p.S305P		Atlas-SNP	.											.	HEG1	109	.	0			c.T913C						PASS	.	A	PRO/SER	1429,2527		246,937,795	40.0	42.0	41.0		913	-9.6	0.0	3	dbSNP_101	41	4192,4114		1040,2112,1001	yes	missense-near-splice	HEG1	NM_020733.1	74	1286,3049,1796	GG,GA,AA		49.5305,36.1223,45.8408	possibly-damaging	305/1382	124746049	5621,6641	1978	4153	6131	SO:0001630	splice_region_variant	57493	exon3			ACTCACATGAGGA	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.913+1T>C	3.37:g.124746049A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	1037	0.4748168498168498	176	0.35772357723577236	169	0.46685082872928174	278	0.486013986013986	414	0.5461741424802111	A	10.69	1.421656	0.25639	0.361223	0.504695	ENSG00000173706	ENST00000311127	T	0.46819	0.86	4.78	-9.56	0.00566	.	.	.	.	.	T	0.00012	0.0000	N	0.21448	0.665	0.58432	P	1.0000000000287557E-6	B;B	0.14805	0.011;0.002	B;B	0.12156	0.007;0.003	T	0.36480	-0.9746	7	.	.	.	.	4.5132	0.11921	0.1547:0.446:0.2977:0.1016	rs2981546;rs17238378;rs52812106;rs61451362;rs2981546	305;305	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	P	305	ENSP00000311502:S305P	.	S	-	1	0	HEG1	126228739	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-1.905000	0.01591	-1.952000	0.01027	0.528000	0.53228	TCT	A|0.534;G|0.466	0.466	strong		0.463	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	Missense_Mutation
ADAMTSL2	9719	hgsc.bcm.edu	37	9	136412296	136412296	+	Silent	SNP	C	C	T	rs2073877	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136412296C>T	ENST00000354484.4	+	9	1457	c.900C>T	c.(898-900)atC>atT	p.I300I	ADAMTSL2_ENST00000393061.3_Silent_p.I409I|ADAMTSL2_ENST00000393060.1_Silent_p.I300I	NM_001145320.1	NP_001138792.1	Q86TH1	ATL2_HUMAN	ADAMTS-like 2	300					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(145;9.31e-08)|Epithelial(140;6.62e-07)|all cancers(34;7.74e-06)		TCGAGTACATCGTGGCACAGG	0.607													C|||	480	0.0958466	0.0129	0.0951	5008	,	,		17249	0.1419		0.1521	False		,,,				2504	0.1033				p.I300I		Atlas-SNP	.											.	ADAMTSL2	40	.	0			c.C900T						PASS	.	C	,	170,4236	113.3+/-151.4	4,162,2037	150.0	143.0	145.0		900,900	-6.0	0.9	9	dbSNP_96	145	1105,7495	229.7+/-264.3	79,947,3274	no	coding-synonymous,coding-synonymous	ADAMTSL2	NM_001145320.1,NM_014694.3	,	83,1109,5311	TT,TC,CC		12.8488,3.8584,9.8032	,	300/952,300/952	136412296	1275,11731	2203	4300	6503	SO:0001819	synonymous_variant	9719	exon9			GTACATCGTGGCA	AB011177	CCDS6976.1	9q34.3	2005-01-12			ENSG00000197859	ENSG00000197859			14631	protein-coding gene	gene with protein product		612277				9628581, 14667842	Standard	NM_014694		Approved	KIAA0605	uc004cei.3	Q86TH1	OTTHUMG00000131706	ENST00000354484.4:c.900C>T	9.37:g.136412296C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_014694	B1B0D5|O60345	Silent	SNP	ENST00000354484.4	37	CCDS6976.1																																																																																			C|0.895;T|0.105	0.105	strong		0.607	ADAMTSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254619.1	NM_014694	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435901	7435901	+	Missense_Mutation	SNP	C	C	T	rs56269914	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:7435901C>T	ENST00000319098.4	-	1	799	c.706G>A	c.(706-708)Gac>Aac	p.D236N	SORCS2_ENST00000507866.2_Intron|SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000329016.9_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	236	Saposin B-type 2. {ECO:0000255|PROSITE- ProRule:PRU00415}.				sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						AGTGCTTGGTCAGCAGGGACA	0.592													C|||	29	0.00579073	0.0	0.0058	5008	,	,		18774	0.0		0.0249	False		,,,				2504	0.0				p.D236N		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G706A						PASS	.	C	ASN/ASP,	23,3917		0,23,1947	44.0	46.0	45.0		706,	1.7	0.0	4	dbSNP_129	45	222,8060		2,218,3921	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	23,	2,241,5868	TT,TC,CC		2.6805,0.5838,2.0046	benign,	236/522,	7435901	245,11977	1970	4141	6111	SO:0001583	missense	768239	exon1			CTTGGTCAGCAGG	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.706G>A	4.37:g.7435901C>T	ENSP00000317445:p.Asp236Asn	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	25	0.011446886446886446	0	0.0	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	10.77	1.444126	0.25987	0.005838	0.026805	ENSG00000178597	ENST00000319098	T	0.67345	-0.26	3.64	1.72	0.24424	Saposin-like (2);Saposin B (2);	.	.	.	.	T	0.19005	0.0456	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.09377	0.004	T	0.17379	-1.0371	9	0.66056	D	0.02	.	4.2889	0.10869	0.0:0.6206:0.2383:0.141	rs56269914;rs61752581	236	Q6NUJ1	SAPL1_HUMAN	N	236	ENSP00000317445:D236N	ENSP00000317445:D236N	D	-	1	0	PSAPL1	7486802	0.001000	0.12720	0.002000	0.10522	0.006000	0.05464	0.773000	0.26661	0.271000	0.22005	0.561000	0.74099	GAC	C|0.986;T|0.014	0.014	strong		0.592	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
KIAA0754	643314	hgsc.bcm.edu	37	1	39879340	39879340	+	Missense_Mutation	SNP	G	G	C	rs141110458	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879340G>C	ENST00000530275.1	+	1	3190	c.2995G>C	c.(2995-2997)Gct>Cct	p.A999P	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	999	Ala-rich.									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)			CTCCCCAGCTGCTGCAGTGCC	0.711													G|||	13	0.00259585	0.0	0.0029	5008	,	,		10576	0.001		0.006	False		,,,				2504	0.0041				p.A1135P		Atlas-SNP	.											.	KIAA0754	93	.	0			c.G3403C						PASS	.	G	,PRO/ALA,	5,3513		0,5,1754	6.0	9.0	8.0		,3403,	0.2	0.0	1	dbSNP_134	8	77,7935		0,77,3929	no	intron,missense,intron	MACF1,KIAA0754	NM_012090.4,NM_015038.1,NM_033044.3	,27,	0,82,5683	CC,CG,GG		0.9611,0.1421,0.7112	,probably-damaging,	,1135/1428,	39879340	82,11448	1759	4006	5765	SO:0001583	missense	643314	exon1			CCAGCTGCTGCAG			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.2995G>C	1.37:g.39879340G>C	ENSP00000431179:p.Ala999Pro	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	61	37	0.606557	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		22	0.010073260073260074	7	0.014227642276422764	5	0.013812154696132596	7	0.012237762237762238	3	0.00395778364116095	G	13.78	2.338002	0.41398	0.001421	0.009611	ENSG00000255103	ENST00000530275	T	0.24151	1.87	4.56	0.241	0.15494	.	.	.	.	.	T	0.13243	0.0321	N	0.14661	0.345	0.09310	N	1	D	0.56968	0.978	P	0.54706	0.759	T	0.10337	-1.0634	9	0.25751	T	0.34	.	2.6328	0.04949	0.0953:0.1583:0.4215:0.3249	.	999	O94854	K0754_HUMAN	P	999	ENSP00000431179:A999P	ENSP00000431179:A999P	A	+	1	0	RP4-562N20.1	39651927	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.456000	0.06754	0.200000	0.20447	0.498000	0.49722	GCT	G|0.990;C|0.010	0.010	strong		0.711	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
FCGR3A	2214	hgsc.bcm.edu	37	1	161596072	161596072	+	Intron	SNP	T	T	C	rs71632959		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161596072T>C	ENST00000540048.1	-	2	94				FCGR3B_ENST00000294800.3_Missense_Mutation_p.D147G|FCGR3B_ENST00000531221.1_Missense_Mutation_p.D183G|FCGR3B_ENST00000367964.2_Missense_Mutation_p.D147G|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000403078.3_Intron			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						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)	ATACTTCCTGTCTTTGCCATT	0.458																																					p.D183G		Atlas-SNP	.											FCGR3B,colon,carcinoma,-1,2	FCGR3B	35	2	0			c.A548G						scavenged	.						149.0	146.0	147.0					1																	161596072		2192	4299	6491	SO:0001627	intron_variant	2215	exon4			TTCCTGTCTTTGC	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	ENST00000540048.1:c.61+4085A>G	1.37:g.161596072T>C		Somatic	235	2	0.00851064		WXS	Illumina HiSeq	Phase_I	662	29	0.0438066	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	37		.	.	.	.	.	.	.	.	.	.	-	0.009	-1.847230	0.00568	.	.	ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221	T;T;T	0.12465	2.68;2.68;2.68	2.35	0.00415	0.14057	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.555110	0.00166	N	0.000000	T	0.00666	0.0022	N	0.00182	-1.905	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41395	-0.9511	10	0.09338	T	0.73	.	4.6205	0.12447	0.0:0.4114:0.4391:0.1494	.	147	O75015	FCG3B_HUMAN	G	147;147;183	ENSP00000356941:D147G;ENSP00000294800:D147G;ENSP00000433642:D183G	ENSP00000294800:D147G	D	-	2	0	FCGR3B	159862696	0.000000	0.05858	0.043000	0.18650	0.061000	0.15899	-0.679000	0.05203	-0.519000	0.06444	-1.160000	0.01791	GAC	T|0.500;C|0.500	0.500	weak		0.458	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
NUF2	83540	hgsc.bcm.edu	37	1	163297322	163297322	+	Silent	SNP	A	A	C	rs16852612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:163297322A>C	ENST00000271452.3	+	3	447	c.168A>C	c.(166-168)gtA>gtC	p.V56V	NUF2_ENST00000367900.3_Silent_p.V56V|NUF2_ENST00000524800.1_Silent_p.V56V|NUF2_ENST00000490881.1_3'UTR	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	56	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					TACAAATAGTATATGGAATTC	0.353													A|||	391	0.0780751	0.0408	0.1441	5008	,	,		17943	0.0238		0.1769	False		,,,				2504	0.0358				p.V56V		Atlas-SNP	.											.	NUF2	138	.	0			c.A168C						PASS	.	A	,	238,4168	139.2+/-174.8	7,224,1972	173.0	174.0	174.0		168,168	-8.7	0.1	1	dbSNP_123	174	1443,7157	276.9+/-292.6	125,1193,2982	no	coding-synonymous,coding-synonymous	NUF2	NM_031423.3,NM_145697.2	,	132,1417,4954	CC,CA,AA		16.7791,5.4017,12.9248	,	56/465,56/465	163297322	1681,11325	2203	4300	6503	SO:0001819	synonymous_variant	83540	exon3			AATAGTATATGGA	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"""cancer/testis antigen 106"""	611772	"""cell division cycle associated 1"", ""NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.168A>C	1.37:g.163297322A>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	240	181	0.754167	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Silent	SNP	ENST00000271452.3	37	CCDS1245.1																																																																																			A|0.888;C|0.112	0.112	strong		0.353	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	
P2RX7	5027	hgsc.bcm.edu	37	12	121605355	121605355	+	Missense_Mutation	SNP	G	G	A	rs7958311	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:121605355G>A	ENST00000546057.1	+	8	952	c.809G>A	c.(808-810)cGt>cAt	p.R270H	P2RX7_ENST00000541446.1_Intron|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000377162.2_Intron|P2RX7_ENST00000328963.5_Missense_Mutation_p.R100H|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	187	0	0		WXS	Illumina HiSeq	Phase_I	202	100	0.49505	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	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71277083	71277083	+	Silent	SNP	C	C	T	rs146926834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	231	123	0.532468	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		
CELSR2	1952	hgsc.bcm.edu	37	1	109793034	109793034	+	Silent	SNP	C	C	T	rs142746289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109793034C>T	ENST00000271332.3	+	1	394	c.333C>T	c.(331-333)ccC>ccT	p.P111P		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	111					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)		AAGGCTGCCCCTGGAGCTGTC	0.627													C|||	13	0.00259585	0.0	0.0115	5008	,	,		15400	0.0		0.004	False		,,,				2504	0.001				p.P111P	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C333T						PASS	.	C		12,4394		0,12,2191	67.0	71.0	70.0		333	-1.7	1.0	1	dbSNP_134	70	142,8458		5,132,4163	no	coding-synonymous	CELSR2	NM_001408.2		5,144,6354	TT,TC,CC		1.6512,0.2724,1.1841		111/2924	109793034	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	1952	exon1			CTGCCCCTGGAGC	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.333C>T	1.37:g.109793034C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	32	24	0.75	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			C|0.989;T|0.011	0.011	strong		0.627	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
NDC80	10403	hgsc.bcm.edu	37	18	2595443	2595443	+	Missense_Mutation	SNP	G	G	T	rs12456560	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:2595443G>T	ENST00000261597.4	+	11	1226	c.1044G>T	c.(1042-1044)gaG>gaT	p.E348D		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	348	Interaction with NEK2 and ZWINT.|Interaction with SMC1A.|Interaction with the N-terminus of CDCA1.		E -> D (in dbSNP:rs12456560).		attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						TAAAACAGGAGAACACTCGAC	0.323													G|||	464	0.0926518	0.0242	0.1758	5008	,	,		14466	0.0923		0.1491	False		,,,				2504	0.0685				p.E348D		Atlas-SNP	.											.	NDC80	62	.	0			c.G1044T						PASS	.	G	ASP/GLU	189,4217	120.8+/-158.4	4,181,2018	57.0	57.0	57.0		1044	2.8	1.0	18	dbSNP_120	57	1113,7487	228.6+/-263.6	76,961,3263	yes	missense	NDC80	NM_006101.2	45	80,1142,5281	TT,TG,GG		12.9419,4.2896,10.0108	possibly-damaging	348/643	2595443	1302,11704	2203	4300	6503	SO:0001583	missense	10403	exon11			ACAGGAGAACACT	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1044G>T	18.37:g.2595443G>T	ENSP00000261597:p.Glu348Asp	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	185	75	0.405405	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	254	0.1163003663003663	13	0.026422764227642278	56	0.15469613259668508	70	0.12237762237762238	115	0.1517150395778364	G	16.76	3.212324	0.58452	0.042896	0.129419	ENSG00000080986	ENST00000261597;ENST00000543946	T	0.64260	-0.09	5.6	2.8	0.32819	.	0.000000	0.85682	D	0.000000	T	0.00967	0.0032	M	0.66939	2.045	0.21105	P	0.999781786	D	0.76494	0.999	D	0.70016	0.967	T	0.38286	-0.9668	9	0.48119	T	0.1	-14.4068	10.391	0.44168	0.2169:0.0:0.7831:0.0	rs12456560;rs17536325;rs52834012;rs60715245;rs12456560	348	O14777	NDC80_HUMAN	D	348	ENSP00000261597:E348D	ENSP00000261597:E348D	E	+	3	2	NDC80	2585443	1.000000	0.71417	0.996000	0.52242	0.988000	0.76386	4.342000	0.59341	0.704000	0.31869	0.650000	0.86243	GAG	G|0.900;N|0.000	.	strong		0.323	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
PER2	8864	hgsc.bcm.edu	37	2	239162318	239162318	+	Silent	SNP	G	G	A	rs10195959	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:239162318G>A	ENST00000254657.3	-	19	2625	c.2346C>T	c.(2344-2346)tcC>tcT	p.S782S	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	782					circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		AATCTATTCCGGAAGTATTTC	0.433													G|||	243	0.0485224	0.1513	0.0216	5008	,	,		16914	0.0		0.0209	False		,,,				2504	0.0072				p.S782S		Atlas-SNP	.											PER2,NS,carcinoma,0,1	PER2	85	1	0			c.C2346T						PASS	.	G		443,3719		13,417,1651	10.0	12.0	11.0		2346	0.2	0.3	2	dbSNP_119	11	136,8322		0,136,4093	no	coding-synonymous	PER2	NM_022817.2		13,553,5744	AA,AG,GG		1.6079,10.6439,4.588		782/1256	239162318	579,12041	2081	4229	6310	SO:0001819	synonymous_variant	8864	exon19			TATTCCGGAAGTA	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"""period (Drosophila) homolog 2"", ""period homolog 2 (Drosophila)"""			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2346C>T	2.37:g.239162318G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	37	CCDS2528.1																																																																																			G|0.950;A|0.050	0.050	strong		0.433	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	
LTF	4057	hgsc.bcm.edu	37	3	46496910	46496910	+	Silent	SNP	G	G	A	rs145526650	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46496910G>A	ENST00000231751.4	-	5	817	c.522C>T	c.(520-522)gcC>gcT	p.A174A	LTF_ENST00000417439.1_Silent_p.A174A|LTF_ENST00000426532.2_Silent_p.A130A	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	174	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)	p.A174A(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		GAACACAGCTGGCTGAGAAGA	0.567													G|||	5	0.000998403	0.0008	0.0	5008	,	,		21912	0.0		0.004	False		,,,				2504	0.0				p.A174A		Atlas-SNP	.											LTF,NS,carcinoma,0,1	LTF	98	1	1	Substitution - coding silent(1)	kidney(1)	c.C522T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	99.0	80.0	86.0		390,522	0.6	0.3	3	dbSNP_134	86	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	0,39,6464	AA,AG,GG		0.3953,0.1135,0.2999	,	130/667,174/711	46496910	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	4057	exon5			ACAGCTGGCTGAG		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.522C>T	3.37:g.46496910G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	161	80	0.496894	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	G	10.21	1.287664	0.23478	0.001135	0.003953	ENSG00000012223	ENST00000443743	.	.	.	4.89	0.614	0.17603	.	.	.	.	.	T	0.64057	0.2564	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64972	-0.6281	5	0.72032	D	0.01	0.0819	10.0059	0.41957	0.0:0.428:0.4338:0.1382	.	.	.	.	L	107	.	ENSP00000393737:P107L	P	-	2	0	LTF	46471914	0.807000	0.29009	0.279000	0.24732	0.998000	0.95712	1.015000	0.29963	0.190000	0.20209	0.655000	0.94253	CCA	G|0.998;A|0.002	0.002	strong		0.567	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
WWC2	80014	hgsc.bcm.edu	37	4	184192231	184192231	+	Splice_Site	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:184192231A>G	ENST00000403733.3	+	16	2599		c.e16-1		WWC2_ENST00000513834.1_Splice_Site|WWC2_ENST00000448232.2_Splice_Site|WWC2_ENST00000504005.1_Splice_Site	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2						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)		TCACTTACATAGGCTGGAACT	0.318																																					.		Atlas-SNP	.											WWC2,NS,carcinoma,0,1	WWC2	78	1	0			c.2401-2A>G						scavenged	.						30.0	29.0	29.0					4																	184192231		2203	4296	6499	SO:0001630	splice_region_variant	80014	exon16			TTACATAGGCTGG	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.2401-1A>G	4.37:g.184192231A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	68	3	0.0441176	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Splice_Site	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	A	18.71	3.681262	0.68042	.	.	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4782	0.75501	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WWC2	184429225	1.000000	0.71417	0.938000	0.37757	0.976000	0.68499	7.743000	0.85020	2.237000	0.73441	0.460000	0.39030	.	.	.	none		0.318	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	Intron
TTC16	158248	hgsc.bcm.edu	37	9	130489558	130489558	+	Silent	SNP	A	A	G	rs472144	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:130489558A>G	ENST00000373289.3	+	12	1658	c.1578A>G	c.(1576-1578)aaA>aaG	p.K526K	PTRH1_ENST00000419060.1_5'Flank|PTRH1_ENST00000429848.1_5'Flank|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	526										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GGATGCTTAAACGGCACGAGT	0.607													G|||	3098	0.61861	0.7844	0.6037	5008	,	,		21776	0.3661		0.6173	False		,,,				2504	0.6667				p.K526K		Atlas-SNP	.											TTC16,NS,carcinoma,0,1	TTC16	55	1	0			c.A1578G						PASS	.	G		3259,1147	393.3+/-328.8	1211,837,155	33.0	31.0	32.0		1578	1.3	0.0	9	dbSNP_83	32	5006,3592	506.6+/-376.6	1456,2094,749	no	coding-synonymous	TTC16	NM_144965.1		2667,2931,904	GG,GA,AA		41.7772,26.0327,36.4426		526/874	130489558	8265,4739	2203	4299	6502	SO:0001819	synonymous_variant	158248	exon12			GCTTAAACGGCAC	AK057342	CCDS6875.1	9q34.13	2013-01-10			ENSG00000167094	ENSG00000167094		"""Tetratricopeptide (TTC) repeat domain containing"""	26536	protein-coding gene	gene with protein product						12477932	Standard	NM_144965		Approved	FLJ32780	uc004brq.1	Q8NEE8	OTTHUMG00000020711	ENST00000373289.3:c.1578A>G	9.37:g.130489558A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Silent	SNP	ENST00000373289.3	37	CCDS6875.1																																																																																			A|0.377;G|0.623	0.623	strong		0.607	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
SPTA1	6708	hgsc.bcm.edu	37	1	158624528	158624528	+	Missense_Mutation	SNP	G	G	T	rs35948326	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158624528G>T	ENST00000368147.4	-	21	3089	c.2909C>A	c.(2908-2910)gCt>gAt	p.A970D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	970			A -> D (in dbSNP:rs35948326).		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)					CACTGGTGCAGCCTGTTGTTG	0.517													G|||	71	0.0141773	0.0	0.0389	5008	,	,		16229	0.0		0.0408	False		,,,				2504	0.0031				p.A970D		Atlas-SNP	.											SPTA1,NS,carcinoma,-1,1	SPTA1	720	1	0			c.C2909A	GRCh37	CM930690	SPTA1	M	rs35948326	PASS	.	G	ASP/ALA	28,3874		0,28,1923	60.0	59.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2909	5.2	1.0	1	dbSNP_126	59	413,7891		9,395,3748	yes	missense	SPTA1	NM_003126.2	126	9,423,5671	TT,TG,GG		4.9735,0.7176,3.613	benign	970/2420	158624528	441,11765	1951	4152	6103	SO:0001583	missense	6708	exon21			GGTGCAGCCTGTT	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.2909C>A	1.37:g.158624528G>T	ENSP00000357129:p.Ala970Asp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	38	0.0173992673992674	0	0.0	14	0.03867403314917127	0	0.0	24	0.0316622691292876	G	10.91	1.483079	0.26598	0.007176	0.049735	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.56275	0.63;0.47	5.22	5.22	0.72569	Src homology-3 domain (1);	0.271352	0.19680	N	0.108540	T	0.13884	0.0336	N	0.12746	0.255	0.39397	A	0.96652	B	0.06786	0.001	B	0.10450	0.005	T	0.10941	-1.0608	9	0.12430	T	0.62	.	7.7628	0.28961	0.1671:0.0:0.8329:0.0	rs35948326;rs61820504	970	P02549	SPTA1_HUMAN	D	970	ENSP00000357130:A970D;ENSP00000357129:A970D	ENSP00000357129:A970D	A	-	2	0	SPTA1	156891152	1.000000	0.71417	0.980000	0.43619	0.587000	0.36485	5.364000	0.66110	2.732000	0.93576	0.591000	0.81541	GCT	G|0.972;T|0.028	0.028	strong		0.517	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
CERKL	375298	hgsc.bcm.edu	37	2	182468803	182468803	+	Missense_Mutation	SNP	T	T	G	rs61750041	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:182468803T>G	ENST00000339098.5	-	2	241	c.242A>C	c.(241-243)gAt>gCt	p.D81A	CERKL_ENST00000479558.1_5'UTR|CERKL_ENST00000374970.2_Missense_Mutation_p.D81A|CERKL_ENST00000410087.3_Missense_Mutation_p.D81A|CERKL_ENST00000374969.2_Missense_Mutation_p.D81A|CERKL_ENST00000409440.3_Missense_Mutation_p.D81A			Q49MI3	CERKL_HUMAN	ceramide kinase-like	81					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)			ATACTTAGAATCACCTGAAAA	0.358													T|||	781	0.15595	0.1044	0.1945	5008	,	,		17869	0.2808		0.165	False		,,,				2504	0.0603				p.D81A		Atlas-SNP	.											.	CERKL	138	.	0			c.A242C						PASS	.	T	ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP,ALA/ASP	492,3912		31,430,1741	34.0	34.0	34.0		242,242,242,242,242	3.0	0.4	2	dbSNP_129	34	1097,7491		81,935,3278	yes	missense,missense,missense,missense,missense	CERKL	NM_001030311.2,NM_001030312.2,NM_001030313.2,NM_001160277.1,NM_201548.4	126,126,126,126,126	112,1365,5019	GG,GT,TT		12.7736,11.1717,12.2306	benign,benign,benign,benign,benign	81/559,81/420,81/464,81/515,81/533	182468803	1589,11403	2202	4294	6496	SO:0001583	missense	375298	exon2			TTAGAATCACCTG	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.242A>C	2.37:g.182468803T>G	ENSP00000341159:p.Asp81Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_001160277	B2RPL2|B4DEY1|Q49MH9|Q49MI0|Q49MI1|Q49MI2|Q5DVJ2|Q5DVJ4|Q5DVJ5|Q6UZF6|Q6ZP59	Missense_Mutation	SNP	ENST00000339098.5	37	CCDS42789.1	424	0.19413919413919414	61	0.12398373983739837	74	0.20441988950276244	157	0.2744755244755245	132	0.1741424802110818	T	14.01	2.406816	0.42715	0.111717	0.127736	ENSG00000188452	ENST00000410087;ENST00000409440;ENST00000374969;ENST00000339098;ENST00000374970	T;T;T;T;T	0.30714	2.26;2.51;1.52;2.53;1.52	5.4	2.99	0.34606	.	0.896212	0.09452	N	0.800322	T	0.00012	0.0000	N	0.24115	0.695	0.46437	P	9.569999999999856E-4	P;P;P;P;P	0.46512	0.879;0.617;0.655;0.775;0.717	B;B;B;B;B	0.38264	0.227;0.121;0.269;0.225;0.15	T	0.14587	-1.0467	9	0.06891	T	0.86	.	4.8592	0.13575	0.2878:0.079:0.0:0.6332	.	81;81;81;81;81	B4DEY1;Q49MI3-4;Q49MI3-3;Q49MI3-2;Q49MI3	.;.;.;.;CERKL_HUMAN	A	81	ENSP00000386725:D81A;ENSP00000387080:D81A;ENSP00000364108:D81A;ENSP00000341159:D81A;ENSP00000364109:D81A	ENSP00000341159:D81A	D	-	2	0	CERKL	182177048	0.997000	0.39634	0.375000	0.26029	0.935000	0.57460	1.753000	0.38359	0.350000	0.24002	0.528000	0.53228	GAT	T|0.866;G|0.134	0.134	strong		0.358	CERKL-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334811.1		
TCEB3B	51224	hgsc.bcm.edu	37	18	44560337	44560337	+	Silent	SNP	G	G	T	rs3744864	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:44560337G>T	ENST00000332567.4	-	1	1651	c.1299C>A	c.(1297-1299)gtC>gtA	p.V433V	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	433					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						GGCTTTCCTGGACAGGAGGCA	0.567													G|||	26	0.00519169	0.0	0.0159	5008	,	,		17739	0.001		0.0139	False		,,,				2504	0.0				p.V433V		Atlas-SNP	.											TCEB3B,NS,carcinoma,-1,1	TCEB3B	141	1	0			c.C1299A						PASS	.	G	,	11,4393	16.8+/-37.8	0,11,2191	81.0	78.0	79.0		1299,	1.0	0.0	18	dbSNP_107	79	97,8503	53.6+/-114.3	0,97,4203	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,108,6394	TT,TG,GG		1.1279,0.2498,0.8305	,	433/754,	44560337	108,12896	2202	4300	6502	SO:0001819	synonymous_variant	51224	exon1			TTCCTGGACAGGA	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.1299C>A	18.37:g.44560337G>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.992;T|0.008	0.008	strong		0.567	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
CCDC110	256309	hgsc.bcm.edu	37	4	186381115	186381115	+	Missense_Mutation	SNP	G	G	T	rs7699687	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:186381115G>T	ENST00000307588.3	-	6	701	c.626C>A	c.(625-627)cCa>cAa	p.P209Q	CCDC110_ENST00000510617.1_Missense_Mutation_p.P209Q|CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000393540.3_Missense_Mutation_p.P172Q	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	209			P -> Q (in dbSNP:rs7699687).			nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		CATCACATTTGGAGGTGCAGT	0.318													T|||	1931	0.385583	0.2837	0.3631	5008	,	,		20802	0.2827		0.5378	False		,,,				2504	0.4888				p.P209Q		Atlas-SNP	.											.	CCDC110	78	.	0			c.C626A						PASS	.	T	GLN/PRO,GLN/PRO	1456,2944	638.7+/-397.0	242,972,986	49.0	49.0	49.0		515,626	1.8	0.0	4	dbSNP_116	49	4848,3752	521.1+/-379.8	1370,2108,822	yes	missense,missense	CCDC110	NM_001145411.1,NM_152775.3	76,76	1612,3080,1808	TT,TG,GG		43.6279,33.0909,48.4923	benign,benign	172/797,209/834	186381115	6304,6696	2200	4300	6500	SO:0001583	missense	256309	exon6			ACATTTGGAGGTG	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.626C>A	4.37:g.186381115G>T	ENSP00000306776:p.Pro209Gln	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	80	15	0.1875	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	37	CCDS3843.1	857	0.3923992673992674	151	0.30691056910569103	147	0.40607734806629836	159	0.27797202797202797	400	0.5277044854881267	T	0	-2.589066	0.00128	0.330909	0.563721	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617;ENST00000506876	T;T;T;T	0.33654	3.7;3.62;3.62;1.4	5.8	1.82	0.25136	.	0.491396	0.18891	N	0.128315	T	0.00012	0.0000	N	0.00128	-2.045	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	0.47249	-0.9132	9	0.02654	T	1	-1.5854	8.3569	0.32335	0.1266:0.0:0.3965:0.4769	rs7699687;rs17303666;rs60542216;rs7699687	209;172;209	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	Q	172;209;209;229	ENSP00000377172:P172Q;ENSP00000306776:P209Q;ENSP00000427246:P209Q;ENSP00000425276:P229Q	ENSP00000306776:P209Q	P	-	2	0	CCDC110	186618109	0.168000	0.22989	0.003000	0.11579	0.439000	0.31926	1.049000	0.30392	-0.137000	0.11455	-0.264000	0.10439	CCA	G|0.564;T|0.436	0.436	strong		0.318	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
COL6A3	1293	hgsc.bcm.edu	37	2	238249108	238249108	+	Silent	SNP	T	T	C	rs61729844	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238249108T>C	ENST00000295550.4	-	38	8903	c.8451A>G	c.(8449-8451)ccA>ccG	p.P2817P	COL6A3_ENST00000472056.1_Silent_p.P2210P|COL6A3_ENST00000353578.4_Silent_p.P2611P|COL6A3_ENST00000347401.3_Silent_p.P2616P|COL6A3_ENST00000346358.4_Silent_p.P2617P|COL6A3_ENST00000409809.1_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	49	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	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	
PKD1L1	168507	hgsc.bcm.edu	37	7	47917087	47917087	+	Splice_Site	SNP	C	C	T	rs72601626	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:47917087C>T	ENST00000289672.2	-	22	3713	c.3663G>A	c.(3661-3663)ccG>ccA	p.P1221P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1221	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				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						GTCCACGTACCGGTTTTCCAG	0.582													C|||	239	0.0477236	0.0227	0.0331	5008	,	,		16430	0.0595		0.0746	False		,,,				2504	0.0521				p.P1221P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G3663A						PASS	.	C		101,4305	81.9+/-120.4	0,101,2102	148.0	138.0	141.0		3663	4.4	0.9	7	dbSNP_130	141	602,7998	159.4+/-212.7	23,556,3721	yes	coding-synonymous-near-splice	PKD1L1	NM_138295.3		23,657,5823	TT,TC,CC		7.0,2.2923,5.4052		1221/2850	47917087	703,12303	2203	4300	6503	SO:0001630	splice_region_variant	168507	exon22			ACGTACCGGTTTT	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.3663+1G>A	7.37:g.47917087C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			C|0.942;T|0.058	0.058	strong		0.582	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	Silent
DKKL1	27120	hgsc.bcm.edu	37	19	49867913	49867913	+	Missense_Mutation	SNP	G	G	A	rs919364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49867913G>A	ENST00000221498.2	+	2	490	c.85G>A	c.(85-87)Gct>Act	p.A29T	DKKL1_ENST00000594268.1_Intron|TEAD2_ENST00000593945.1_5'Flank|TEAD2_ENST00000601519.1_5'Flank|TEAD2_ENST00000539846.1_5'Flank|TEAD2_ENST00000311227.2_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	230	0	0		WXS	Illumina HiSeq	Phase_I	220	108	0.490909	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	
KLRG1	10219	hgsc.bcm.edu	37	12	9161648	9161648	+	Silent	SNP	T	T	C	rs3026251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	231	0	0		WXS	Illumina HiSeq	Phase_I	200	74	0.37	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	
NLRP9	338321	hgsc.bcm.edu	37	19	56249672	56249672	+	Silent	SNP	A	A	G	rs56211941	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	143	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	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	
HFE	3077	hgsc.bcm.edu	37	6	26091185	26091185	+	Missense_Mutation	SNP	A	A	T	rs1800730	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26091185A>T	ENST00000357618.5	+	2	315	c.193A>T	c.(193-195)Agt>Tgt	p.S65C	HFE_ENST00000317896.7_Missense_Mutation_p.S65C|HFE_ENST00000336625.8_Missense_Mutation_p.S65C|HFE_ENST00000353147.5_Intron|HFE_ENST00000397022.3_Missense_Mutation_p.S42C|HFE_ENST00000309234.6_Missense_Mutation_p.S65C|HFE_ENST00000461397.1_Missense_Mutation_p.S65C|HFE_ENST00000470149.1_Missense_Mutation_p.S65C|HFE_ENST00000488199.1_Intron|HFE_ENST00000352392.4_Intron|HFE_ENST00000349999.4_Intron	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	65	Alpha-1.		S -> C (in HFE1; mild form; dbSNP:rs1800730). {ECO:0000269|PubMed:10194428, ECO:0000269|PubMed:10575540, ECO:0000269|PubMed:12542741, ECO:0000269|PubMed:14633868, ECO:0000269|Ref.25}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGATCATGAGAGTCGCCGTGT	0.517									Hemochromatosis				A|||	20	0.00399361	0.0	0.0043	5008	,	,		20230	0.0		0.0159	False		,,,				2504	0.001				p.S65C		Atlas-SNP	.											.	HFE	37	.	0			c.A193T	GRCh37	CM990718	HFE	M	rs1800730	PASS	.	A	CYS/SER,CYS/SER,CYS/SER,CYS/SER,,,CYS/SER,,	14,4392	20.2+/-43.8	0,14,2189	135.0	124.0	128.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	193,193,193,193,,,124,,	4.1	1.0	6	dbSNP_89	128	130,8470	66.0+/-128.3	2,126,4172	yes	missense,missense,missense,missense,intron,intron,missense,intron,intron	HFE	NM_000410.3,NM_139003.2,NM_139004.2,NM_139006.2,NM_139007.2,NM_139008.2,NM_139009.2,NM_139010.2,NM_139011.2	112,112,112,112,,,112,,	2,140,6361	TT,TA,AA		1.5116,0.3177,1.1072	probably-damaging,probably-damaging,probably-damaging,probably-damaging,,,probably-damaging,,	65/349,65/243,65/257,65/335,,,42/326,,	26091185	144,12862	2203	4300	6503	SO:0001583	missense	3077	exon2	Familial Cancer Database		CATGAGAGTCGCC		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"""Immunoglobulin superfamily / C1-set domain containing"""	4886	protein-coding gene	gene with protein product	"""high Fe"""	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.193A>T	6.37:g.26091185A>T	ENSP00000417404:p.Ser65Cys	Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	237	105	0.443038	NM_139006	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	16	0.007326007326007326	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	A	19.87	3.907261	0.72868	0.003177	0.015116	ENSG00000010704	ENST00000397022;ENST00000317896;ENST00000535098;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000309234	D;T;D;D;T;D;D	0.90620	-2.7;5.72;-2.7;-2.7;5.72;-2.7;-2.7	5.3	4.13	0.48395	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.569228	0.17597	N	0.168562	D	0.93523	0.7933	M	0.86864	2.845	0.37344	A	0.910532	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.993;0.999	D;D;D;D;P;D	0.91635	0.95;0.999;0.999;0.917;0.765;0.95	D	0.93126	0.6529	9	0.87932	D	0	.	7.6454	0.28316	0.9059:0.0:0.0941:0.0	rs1800730;rs28934888	65;65;65;65;42;65	Q6B0J5;Q30201-7;Q30201-10;Q30201-3;Q30201-5;Q30201	.;.;.;.;.;HFE_HUMAN	C	42;65;65;65;65;65;65;65	ENSP00000380217:S42C;ENSP00000313776:S65C;ENSP00000417404:S65C;ENSP00000419725:S65C;ENSP00000337819:S65C;ENSP00000420802:S65C;ENSP00000311698:S65C	ENSP00000311698:S65C	S	+	1	0	HFE	26199164	0.996000	0.38824	0.998000	0.56505	0.939000	0.58152	1.962000	0.40442	1.028000	0.39785	0.533000	0.62120	AGT	A|0.990;T|0.010	0.010	strong		0.517	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1		
SVEP1	79987	hgsc.bcm.edu	37	9	113221247	113221247	+	Missense_Mutation	SNP	T	T	C	rs7038903	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:113221247T>C	ENST00000401783.2	-	19	3805	c.3469A>G	c.(3469-3471)Atc>Gtc	p.I1157V	SVEP1_ENST00000302728.8_Missense_Mutation_p.I1157V|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.I1134V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1157			I -> V (in dbSNP:rs7038903).		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						CATTCTGTGATGGATCTGGAA	0.428													T|||	879	0.175519	0.3003	0.183	5008	,	,		19641	0.0913		0.1421	False		,,,				2504	0.1227				p.I1157V		Atlas-SNP	.											.	SVEP1	326	.	0			c.A3469G						PASS	.	T	VAL/ILE	940,2834		109,722,1056	95.0	93.0	94.0		3469	5.6	1.0	9	dbSNP_116	94	1244,6990		104,1036,2977	yes	missense	SVEP1	NM_153366.3	29	213,1758,4033	CC,CT,TT		15.1081,24.9073,18.1879	possibly-damaging	1157/3572	113221247	2184,9824	1887	4117	6004	SO:0001583	missense	79987	exon19			CTGTGATGGATCT	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.3469A>G	9.37:g.113221247T>C	ENSP00000384917:p.Ile1157Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	157	65	0.414013	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	380	0.17399267399267399	150	0.3048780487804878	62	0.1712707182320442	55	0.09615384615384616	113	0.14907651715039577	T	16.69	3.193795	0.58017	0.249073	0.151081	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.15017	2.46;2.46;2.46	5.6	5.6	0.85130	Tyrosine-protein kinase ephrin type A/B receptor-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.20986	0.625	0.27289	P	0.9578915	D;D	0.69078	0.958;0.997	D;D	0.80764	0.97;0.994	T	0.49790	-0.8902	9	0.30078	T	0.28	.	15.7828	0.78275	0.0:0.0:0.0:1.0	rs7038903;rs61264667;rs7038903	1157;1157	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	V	1157;1134;1157	ENSP00000384917:I1157V;ENSP00000363593:I1134V;ENSP00000304118:I1157V	ENSP00000304118:I1157V	I	-	1	0	SVEP1	112261068	1.000000	0.71417	1.000000	0.80357	0.492000	0.33523	7.647000	0.83462	2.125000	0.65367	0.482000	0.46254	ATC	T|0.828;C|0.172	0.172	strong		0.428	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OR9G4	283189	hgsc.bcm.edu	37	11	56511160	56511160	+	Missense_Mutation	SNP	A	A	G	rs11228763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56511160A>G	ENST00000302957.3	-	1	127	c.128T>C	c.(127-129)tTt>tCt	p.F43S		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	43			F -> S (in dbSNP:rs11228763).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F43S(1)		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						AAACACTCCAAATAGAATCGG	0.438													A|||	504	0.100639	0.084	0.0994	5008	,	,		18457	0.119		0.1004	False		,,,				2504	0.1053				p.F43S		Atlas-SNP	.											OR9G4,NS,carcinoma,0,1	OR9G4	73	1	1	Substitution - Missense(1)	stomach(1)	c.T128C						PASS	.	A	SER/PHE	403,3999	199.4+/-223.0	16,371,1814	76.0	70.0	72.0		128	4.0	0.9	11	dbSNP_120	72	729,7863	177.5+/-227.1	34,661,3601	yes	missense	OR9G4	NM_001005284.1	155	50,1032,5415	GG,GA,AA		8.4846,9.1549,8.7117	probably-damaging	43/328	56511160	1132,11862	2201	4296	6497	SO:0001583	missense	283189	exon1			ACTCCAAATAGAA	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.128T>C	11.37:g.56511160A>G	ENSP00000307515:p.Phe43Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_001005284	Q6IF62|Q96RA9	Missense_Mutation	SNP	ENST00000302957.3	37	CCDS31537.1	234	0.10714285714285714	47	0.09552845528455285	34	0.09392265193370165	69	0.12062937062937062	84	0.11081794195250659	A	11.63	1.696822	0.30142	0.091549	0.084846	ENSG00000172457	ENST00000302957	T	0.04551	3.6	5.16	4.03	0.46877	.	0.000000	0.40385	N	0.001114	T	0.00271	0.0008	M	0.81497	2.545	0.48395	P	3.5799999999996945E-4	D	0.76494	0.999	D	0.80764	0.994	T	0.02070	-1.1219	9	0.87932	D	0	-25.4032	10.0006	0.41927	0.9198:0.0:0.0802:0.0	rs11228763;rs11228763	43	Q8NGQ1	OR9G4_HUMAN	S	43	ENSP00000307515:F43S	ENSP00000307515:F43S	F	-	2	0	OR9G4	56267736	0.010000	0.17322	0.852000	0.33557	0.080000	0.17528	1.752000	0.38349	0.980000	0.38523	0.448000	0.29417	TTT	A|0.905;G|0.095	0.095	strong		0.438	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284	
C1orf127	148345	hgsc.bcm.edu	37	1	11015165	11015165	+	Missense_Mutation	SNP	A	A	G	rs75130475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11015165A>G	ENST00000377008.4	-	8	802	c.356T>C	c.(355-357)aTt>aCt	p.I119T	C1orf127_ENST00000377004.4_Missense_Mutation_p.I286T			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	119										NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		GGTTTCCTCAATGTAGGAACC	0.522													A|||	1143	0.228235	0.0991	0.2752	5008	,	,		20517	0.2341		0.164	False		,,,				2504	0.4294				p.I286T		Atlas-SNP	.											.	C1orf127	134	.	0			c.T857C						PASS	.	A	THR/ILE	441,3965	212.8+/-232.6	18,405,1780	130.0	121.0	124.0		857	-6.0	0.0	1	dbSNP_131	124	1305,7295	258.7+/-282.2	109,1087,3104	yes	missense	C1orf127	NM_001170754.1	89	127,1492,4884	GG,GA,AA		15.1744,10.0091,13.4246	possibly-damaging	286/824	11015165	1746,11260	2203	4300	6503	SO:0001583	missense	148345	exon9			TCCTCAATGTAGG	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.356T>C	1.37:g.11015165A>G	ENSP00000366207:p.Ile119Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	55	43	0.781818	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		415	0.190018315018315	47	0.09552845528455285	95	0.26243093922651933	141	0.2465034965034965	132	0.1741424802110818	A	10.67	1.416568	0.25552	0.100091	0.151744	ENSG00000175262	ENST00000377004;ENST00000377008	T;T	0.23754	1.89;1.89	4.94	-6.01	0.02199	.	2.410650	0.01815	N	0.033671	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.33103	0.278;0.278;0.397	B;B;B	0.28139	0.086;0.086;0.086	T	0.28170	-1.0052	9	0.13470	T	0.59	2.0094	1.0442	0.01566	0.2004:0.2288:0.3268:0.2439	.	137;137;119	B7ZLG7;Q8N9H9-2;Q8N9H9	.;.;CA127_HUMAN	T	286;119	ENSP00000366203:I286T;ENSP00000366207:I119T	ENSP00000366203:I286T	I	-	2	0	C1orf127	10937752	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-1.247000	0.02893	-0.647000	0.05444	-0.361000	0.07541	ATT	A|0.843;G|0.157	0.157	strong		0.522	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
RAET1E	135250	hgsc.bcm.edu	37	6	150211100	150211100	+	Silent	SNP	T	T	C	rs3798763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:150211100T>C	ENST00000357183.4	-	2	399	c.267A>G	c.(265-267)gaA>gaG	p.E89E	RAET1E-AS1_ENST00000605899.1_RNA|RAET1E_ENST00000529948.1_Silent_p.E89E|RAET1E_ENST00000532335.1_Silent_p.E89E|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000367363.3_Silent_p.E53E	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	89	MHC class I alpha-1 like.				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)		TTTGGGTCAATTCTCCCCAAG	0.498													t|||	1122	0.224042	0.0386	0.3689	5008	,	,		20232	0.3333		0.2604	False		,,,				2504	0.2219				p.E89E		Atlas-SNP	.											.	RAET1E	20	.	0			c.A267G						PASS	.	T		302,4104	163.6+/-195.4	16,270,1917	116.0	107.0	110.0		267	-4.1	0.0	6	dbSNP_107	110	2245,6355	380.1+/-339.5	283,1679,2338	yes	coding-synonymous	RAET1E	NM_139165.2		299,1949,4255	CC,CT,TT		26.1047,6.8543,19.5833		89/264	150211100	2547,10459	2203	4300	6503	SO:0001819	synonymous_variant	135250	exon2			GGTCAATTCTCCC	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.267A>G	6.37:g.150211100T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	189	99	0.52381	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Silent	SNP	ENST00000357183.4	37	CCDS5221.1																																																																																			T|0.790;C|0.210	0.210	strong		0.498	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
OR52E6	390078	hgsc.bcm.edu	37	11	5862731	5862731	+	Missense_Mutation	SNP	A	A	G	rs10838719	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5862731A>G	ENST00000329322.5	-	1	396	c.397T>C	c.(397-399)Tgg>Cgg	p.W133R	OR52E6_ENST00000379946.2_Missense_Mutation_p.W137R|TRIM5_ENST00000380027.1_Intron	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	133			W -> R (in dbSNP:rs10838719).			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(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGGTGTACCAAAGAGGTTTG	0.473													A|||	1940	0.38738	0.2352	0.389	5008	,	,		21277	0.4593		0.5258	False		,,,				2504	0.3753				p.W133R		Atlas-SNP	.											OR52E6,NS,carcinoma,+2,2	OR52E6	70	2	0			c.T397C						scavenged	.	A	ARG/TRP	1206,3196	418.7+/-338.4	169,868,1164	207.0	187.0	194.0		397	-6.9	0.0	11	dbSNP_120	194	4339,4253	579.2+/-390.9	1071,2197,1028	no	missense	OR52E6	NM_001005167.1	101	1240,3065,2192	GG,GA,AA		49.4995,27.3966,42.6735	benign	133/314	5862731	5545,7449	2201	4296	6497	SO:0001583	missense	390078	exon1			TGTACCAAAGAGG	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.397T>C	11.37:g.5862731A>G	ENSP00000328878:p.Trp133Arg	Somatic	243	2	0.00823045		WXS	Illumina HiSeq	Phase_I	214	91	0.425234	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	864	0.3956043956043956	94	0.1910569105691057	141	0.38950276243093923	250	0.4370629370629371	379	0.5	a	0.012	-1.656056	0.00779	0.273966	0.505005	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.32272	1.46;1.46	3.45	-6.91	0.01649	GPCR, rhodopsin-like superfamily (1);	1.171350	0.06439	N	0.725641	T	0.00012	0.0000	N	0.00000	-4.27	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.53034	-0.8495	9	0.02654	T	1	.	5.0066	0.14291	0.3246:0.0:0.2032:0.4721	rs10838719	133	Q96RD3	O52E6_HUMAN	R	133;137	ENSP00000328878:W133R;ENSP00000369279:W137R	ENSP00000328878:W133R	W	-	1	0	OR52E6	5819307	0.000000	0.05858	0.000000	0.03702	0.882000	0.50991	-0.533000	0.06157	-1.517000	0.01780	-0.319000	0.08680	TGG	A|0.622;G|0.378	0.378	strong		0.473	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69040500	69040500	+	Silent	SNP	G	G	A	rs2280310	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:69040500G>A	ENST00000295381.3	+	6	1172	c.753G>A	c.(751-753)caG>caA	p.Q251Q	ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000467265.1_Silent_p.Q212Q|ARHGAP25_ENST00000497079.1_Silent_p.Q245Q|ARHGAP25_ENST00000409220.1_Silent_p.Q245Q|ARHGAP25_ENST00000409030.3_Silent_p.Q244Q|ARHGAP25_ENST00000409202.3_Silent_p.Q252Q|ARHGAP25_ENST00000544262.1_Silent_p.Q226Q	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	251	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)	p.Q245Q(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CCTGGAGCCAGTACGAAGGGT	0.512													G|||	1491	0.297724	0.2927	0.3213	5008	,	,		19180	0.4425		0.1839	False		,,,				2504	0.2556				p.Q252Q		Atlas-SNP	.											ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	1	Substitution - coding silent(1)	stomach(1)	c.G756A						PASS	.	G	,,,	1189,3217	416.7+/-337.7	153,883,1167	108.0	94.0	99.0		756,735,636,732	3.6	1.0	2	dbSNP_100	99	1653,6947	305.0+/-307.2	171,1311,2818	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	,,,	324,2194,3985	AA,AG,GG		19.2209,26.9859,21.8515	,,,	252/647,245/640,212/607,244/639	69040500	2842,10164	2203	4300	6503	SO:0001819	synonymous_variant	9938	exon6			GAGCCAGTACGAA	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.753G>A	2.37:g.69040500G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Silent	SNP	ENST00000295381.3	37		616	0.28205128205128205	140	0.2845528455284553	112	0.30939226519337015	225	0.39335664335664333	139	0.18337730870712401	G	9.214	1.031745	0.19590	0.269859	0.192209	ENSG00000163219	ENST00000497259	.	.	.	5.73	3.62	0.41486	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38351	-0.9665	3	.	.	.	.	12.3657	0.55226	0.1637:0.0:0.8363:0.0	rs2280310;rs58055279;rs2280310	.	.	.	N	111	.	.	S	+	2	0	ARHGAP25	68894004	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	0.624000	0.24462	1.432000	0.47375	0.655000	0.94253	AGT	G|0.744;A|0.256	0.256	strong		0.512	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
C1orf127	148345	hgsc.bcm.edu	37	1	11008695	11008695	+	Silent	SNP	T	T	C	rs17036032	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11008695T>C	ENST00000377008.4	-	11	1442	c.996A>G	c.(994-996)ccA>ccG	p.P332P	C1orf127_ENST00000377004.4_Silent_p.P499P			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	332	Pro-rich.									NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TTGGCAAGACTGGACGTGGCC	0.667													T|||	1061	0.211861	0.0522	0.2565	5008	,	,		16937	0.2321		0.1421	False		,,,				2504	0.4468				p.P499P		Atlas-SNP	.											.	C1orf127	134	.	0			c.A1497G						PASS	.	T		272,4134	151.4+/-185.3	5,262,1936	51.0	51.0	51.0		1497	-5.4	0.0	1	dbSNP_123	51	1164,7436	235.8+/-268.3	88,988,3224	no	coding-synonymous	C1orf127	NM_001170754.1		93,1250,5160	CC,CT,TT		13.5349,6.1734,11.0411		499/824	11008695	1436,11570	2203	4300	6503	SO:0001819	synonymous_variant	148345	exon12			CAAGACTGGACGT	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.996A>G	1.37:g.11008695T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	46	32	0.695652	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		377	0.17261904761904762	33	0.06707317073170732	88	0.2430939226519337	142	0.24825174825174826	114	0.1503957783641161	T	6.065	0.380333	0.11466	0.061734	0.135349	ENSG00000175262	ENST00000418570;ENST00000520253	.	.	.	4.51	-5.45	0.02616	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.49687	P	1.8899999999999473E-4	.	.	.	.	.	.	T	0.41034	-0.9531	3	.	.	.	-0.7605	0.2364	0.00186	0.2766:0.1805:0.2818:0.2611	rs17036032;rs17036032	.	.	.	R	334;451	.	.	Q	-	2	0	C1orf127	10931282	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.740000	0.01839	-0.824000	0.04295	0.402000	0.26972	CAG	T|0.858;C|0.142	0.142	strong		0.667	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
VTCN1	79679	hgsc.bcm.edu	37	1	117753455	117753455	+	Missense_Mutation	SNP	A	A	G	rs34957002	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:117753455A>G	ENST00000369458.3	-	1	101	c.23T>C	c.(22-24)cTc>cCc	p.L8P	VTCN1_ENST00000328189.3_Missense_Mutation_p.L8P|VTCN1_ENST00000463461.1_5'UTR	NM_024626.3	NP_078902.2			V-set domain containing T cell activation inhibitor 1											large_intestine(7)|lung(4)|upper_aerodigestive_tract(1)	12	Lung SC(450;0.225)	all_cancers(81;6.05e-06)|all_epithelial(167;5.59e-07)|all_lung(203;2.85e-06)|Lung NSC(69;2e-05)		Lung(183;0.0664)|LUSC - Lung squamous cell carcinoma(189;0.214)|Colorectal(144;0.23)		CCTCCAGAAGAGGATCTGCCC	0.557													A|||	35	0.00698882	0.0008	0.0159	5008	,	,		20543	0.0		0.0189	False		,,,				2504	0.0041				p.L8P		Atlas-SNP	.											.	VTCN1	26	.	0			c.T23C						PASS	.	A	PRO/LEU	24,4382	29.9+/-59.1	0,24,2179	93.0	94.0	93.0		23	3.8	1.0	1	dbSNP_126	93	204,8396	88.4+/-150.7	1,202,4097	yes	missense	VTCN1	NM_024626.2	98	1,226,6276	GG,GA,AA		2.3721,0.5447,1.753	benign	8/283	117753455	228,12778	2203	4300	6503	SO:0001583	missense	79679	exon1			CAGAAGAGGATCT	BX648021	CCDS894.1, CCDS58019.1, CCDS58020.1	1p12	2013-01-29			ENSG00000134258	ENSG00000134258		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28873	protein-coding gene	gene with protein product	"""B7 family member, H4"", ""B7 superfamily member 1"""	608162				12818165, 12818166	Standard	NM_024626		Approved	B7-H4, FLJ22418, B7S1, B7X, B7H4	uc001ehb.3	Q7Z7D3	OTTHUMG00000012118	ENST00000369458.3:c.23T>C	1.37:g.117753455A>G	ENSP00000358470:p.Leu8Pro	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	49	36	0.734694	NM_001253850		Missense_Mutation	SNP	ENST00000369458.3	37	CCDS894.1	23	0.010531135531135532	0	0.0	8	0.022099447513812154	0	0.0	15	0.01978891820580475	A	13.96	2.393669	0.42410	0.005447	0.023721	ENSG00000134258	ENST00000369458;ENST00000328189	T;T	0.28069	3.18;1.63	3.81	3.81	0.43845	.	4.750870	0.02239	N	0.065550	T	0.09158	0.0226	N	0.08118	0	0.80722	D	1	B;B	0.31790	0.101;0.34	B;B	0.29077	0.019;0.098	T	0.04281	-1.0963	10	0.87932	D	0	.	9.1289	0.36833	1.0:0.0:0.0:0.0	rs34957002	8;8	Q7Z7D3-2;Q7Z7D3	.;VTCN1_HUMAN	P	8	ENSP00000358470:L8P;ENSP00000328168:L8P	ENSP00000328168:L8P	L	-	2	0	VTCN1	117554978	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.949000	0.56668	1.721000	0.51461	0.455000	0.32223	CTC	A|0.983;G|0.017	0.017	strong		0.557	VTCN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000033500.2	NM_024626	
ETV3L	440695	hgsc.bcm.edu	37	1	157069134	157069134	+	Missense_Mutation	SNP	G	G	A	rs61730132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:157069134G>A	ENST00000454449.2	-	2	379	c.95C>T	c.(94-96)tCg>tTg	p.S32L		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	32					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				GCCTGGGGACGACTCGGCTTT	0.642													G|||	26	0.00519169	0.0008	0.0029	5008	,	,		17095	0.0		0.0109	False		,,,				2504	0.0123				p.S32L		Atlas-SNP	.											.	ETV3L	73	.	0			c.C95T						PASS	.	G	LEU/SER	5,4401	9.9+/-24.2	0,5,2198	51.0	51.0	51.0		95	4.0	1.0	1	dbSNP_129	51	74,8526	43.6+/-101.6	0,74,4226	yes	missense	ETV3L	NM_001004341.2	145	0,79,6424	AA,AG,GG		0.8605,0.1135,0.6074	probably-damaging	32/362	157069134	79,12927	2203	4300	6503	SO:0001583	missense	440695	exon2			GGGGACGACTCGG	AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"""ets variant gene 3-like"""				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.95C>T	1.37:g.157069134G>A	ENSP00000430271:p.Ser32Leu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	231	94	0.406926	NM_001004341		Missense_Mutation	SNP	ENST00000454449.2	37	CCDS30893.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	24.7	4.556591	0.86231	0.001135	0.008605	ENSG00000253831	ENST00000454449	T	0.12255	2.7	4.96	4.03	0.46877	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.32802	N	0.005635	T	0.16685	0.0401	L	0.34521	1.04	0.40492	D	0.980559	D	0.89917	1.0	D	0.78314	0.991	T	0.02625	-1.1132	10	0.87932	D	0	.	14.2718	0.66155	0.0:0.1505:0.8495:0.0	rs61730132	32	Q6ZN32	ETV3L_HUMAN	L	32	ENSP00000430271:S32L	ENSP00000430271:S32L	S	-	2	0	ETV3L	155335758	1.000000	0.71417	0.954000	0.39281	0.918000	0.54935	5.422000	0.66453	1.271000	0.44313	0.655000	0.94253	TCG	G|0.994;A|0.006	0.006	strong		0.642	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341	
LIPF	8513	hgsc.bcm.edu	37	10	90429652	90429652	+	Missense_Mutation	SNP	A	A	G	rs814628	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:90429652A>G	ENST00000238983.4	+	5	527	c.481A>G	c.(481-483)Act>Gct	p.T161A	LIPF_ENST00000608620.1_Missense_Mutation_p.T128A|LIPF_ENST00000355843.2_Missense_Mutation_p.T138A|LIPF_ENST00000394375.3_Missense_Mutation_p.T171A	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	161			T -> A (in dbSNP:rs814628). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)			NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	TGTAAAGAAAACTGGACAGAA	0.403													A|||	841	0.167931	0.0098	0.2046	5008	,	,		22220	0.3056		0.174	False		,,,				2504	0.2076				p.T171A		Atlas-SNP	.											.	LIPF	62	.	0			c.A511G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR	199,4207	124.5+/-161.8	2,195,2006	217.0	202.0	207.0		382,511,412,481	5.2	1.0	10	dbSNP_86	207	1510,7090	286.1+/-297.5	158,1194,2948	yes	missense,missense,missense,missense	LIPF	NM_001198828.1,NM_001198829.1,NM_001198830.1,NM_004190.3	58,58,58,58	160,1389,4954	GG,GA,AA		17.5581,4.5166,13.1401	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	128/366,171/409,138/376,161/399	90429652	1709,11297	2203	4300	6503	SO:0001583	missense	8513	exon6			AAGAAAACTGGAC	X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.481A>G	10.37:g.90429652A>G	ENSP00000238983:p.Thr161Ala	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	93	72	0.774194	NM_001198829	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Missense_Mutation	SNP	ENST00000238983.4	37	CCDS7389.1	371	0.16987179487179488	4	0.008130081300813009	59	0.16298342541436464	175	0.30594405594405594	133	0.17546174142480211	A	18.63	3.665012	0.67700	0.045166	0.175581	ENSG00000182333	ENST00000394375;ENST00000238983;ENST00000355843	T;T;T	0.61980	0.06;0.06;0.06	5.24	5.24	0.73138	Alpha/beta hydrolase fold-1 (1);	0.000000	0.56097	D	0.000024	T	0.00012	0.0000	H	0.96333	3.805	0.18873	P	0.9999861833	D;D;D;D	0.65815	0.994;0.993;0.994;0.995	P;P;D;D	0.67900	0.896;0.881;0.954;0.927	T	0.00883	-1.1528	9	0.87932	D	0	-32.3374	14.2637	0.66102	1.0:0.0:0.0:0.0	rs814628;rs1214455;rs17287058;rs52818200;rs57331422;rs814628	128;171;138;161	Q5VXI8;F5H1P4;Q658L8;P07098	.;.;.;LIPG_HUMAN	A	171;161;128	ENSP00000377900:T171A;ENSP00000238983:T161A;ENSP00000348101:T128A	ENSP00000238983:T161A	T	+	1	0	LIPF	90419632	1.000000	0.71417	1.000000	0.80357	0.502000	0.33828	8.620000	0.90943	2.194000	0.70268	0.528000	0.53228	ACT	A|0.851;G|0.149	0.149	strong		0.403	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1		
MUC17	140453	hgsc.bcm.edu	37	7	100678932	100678932	+	Missense_Mutation	SNP	A	A	G	rs114941002		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678932A>G	ENST00000306151.4	+	3	4299	c.4235A>G	c.(4234-4236)gAg>gGg	p.E1412G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1412	59 X approximate tandem repeats.|Ser-rich.				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)					GTCAGTTCTGAGGCTAGCACC	0.502																																					p.E1412G		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.A4235G						scavenged	.						272.0	277.0	275.0					7																	100678932		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTCTGAGGCTAG	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.4235A>G	7.37:g.100678932A>G	ENSP00000302716:p.Glu1412Gly	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	218	31	0.142202	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	1.916	-0.449416	0.04572	.	.	ENSG00000169876	ENST00000306151	T	0.02737	4.18	0.838	-0.578	0.11724	.	.	.	.	.	T	0.01592	0.0051	N	0.17082	0.46	0.09310	N	1	B	0.27765	0.188	B	0.19946	0.027	T	0.48502	-0.9030	9	0.23891	T	0.37	.	3.0434	0.06146	0.6909:0.0:0.3091:0.0	.	1412	Q685J3	MUC17_HUMAN	G	1412	ENSP00000302716:E1412G	ENSP00000302716:E1412G	E	+	2	0	MUC17	100465652	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.362000	0.07602	-0.153000	0.11137	0.113000	0.15668	GAG	.	.	weak		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MOCOS	55034	hgsc.bcm.edu	37	18	33848581	33848581	+	Missense_Mutation	SNP	T	T	C	rs1057251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:33848581T>C	ENST00000261326.5	+	15	2621	c.2600T>C	c.(2599-2601)gTg>gCg	p.V867A		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						GTGCTCCCTGTGTTGAAAGAG	0.403													T|||	363	0.072484	0.0378	0.1758	5008	,	,		17797	0.0704		0.0775	False		,,,				2504	0.0429				p.V867A		Atlas-SNP	.											.	MOCOS	84	.	0			c.T2600C						PASS	.	T	ALA/VAL	201,4205	127.0+/-164.0	5,191,2007	238.0	205.0	216.0		2600	5.7	0.9	18	dbSNP_86	216	1000,7600	215.6+/-254.9	50,900,3350	yes	missense	MOCOS	NM_017947.2	64	55,1091,5357	CC,CT,TT		11.6279,4.562,9.2342	benign	867/889	33848581	1201,11805	2203	4300	6503	SO:0001583	missense	55034	exon15			TCCCTGTGTTGAA	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.2600T>C	18.37:g.33848581T>C	ENSP00000261326:p.Val867Ala	Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	225	102	0.453333	NM_017947		Missense_Mutation	SNP	ENST00000261326.5	37	CCDS11919.1	174	0.07967032967032966	17	0.034552845528455285	61	0.1685082872928177	40	0.06993006993006994	56	0.07387862796833773	T	15.18	2.755988	0.49362	0.04562	0.116279	ENSG00000075643	ENST00000261326	T	0.15603	2.41	5.74	5.74	0.90152	Molybdenum cofactor sulfurase, C-terminal (1);	0.436137	0.23116	N	0.051751	T	0.00039	0.0001	M	0.71581	2.175	0.39071	P	0.03928100000000001	P	0.44429	0.835	B	0.32342	0.144	T	0.18023	-1.0350	9	0.62326	D	0.03	-8.0317	12.7596	0.57356	0.0:0.0:0.0:1.0	rs1057251;rs3197888;rs52803362;rs57783980;rs1057251	867	Q96EN8	MOCOS_HUMAN	A	867	ENSP00000261326:V867A	ENSP00000261326:V867A	V	+	2	0	MOCOS	32102579	1.000000	0.71417	0.904000	0.35570	0.642000	0.38348	4.257000	0.58816	2.323000	0.78572	0.529000	0.55759	GTG	T|0.921;C|0.079	0.079	strong		0.403	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		
IL20RA	53832	hgsc.bcm.edu	37	6	137323213	137323213	+	Missense_Mutation	SNP	G	G	A	rs1342642	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:137323213G>A	ENST00000316649.5	-	7	1379	c.1144C>T	c.(1144-1146)Ctc>Ttc	p.L382F	IL20RA_ENST00000541547.1_Missense_Mutation_p.L333F|RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000367748.1_Missense_Mutation_p.L271F|IL20RA_ENST00000468393.1_5'Flank	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	382			L -> F (in dbSNP:rs1342642). {ECO:0000269|Ref.1}.		cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		TGCTGGGTGAGAGAAGTACCT	0.463													G|||	1000	0.199681	0.2383	0.183	5008	,	,		19502	0.0714		0.2594	False		,,,				2504	0.2301				p.L382F		Atlas-SNP	.											.	IL20RA	54	.	0			c.C1144T						PASS	.	G	PHE/LEU	977,3429	366.4+/-317.8	118,741,1344	79.0	74.0	76.0		1144	0.2	0.0	6	dbSNP_88	76	2322,6278	387.8+/-342.3	319,1684,2297	yes	missense	IL20RA	NM_014432.2	22	437,2425,3641	AA,AG,GG		27.0,22.1743,25.3652	possibly-damaging	382/554	137323213	3299,9707	2203	4300	6503	SO:0001583	missense	53832	exon7			GGGTGAGAGAAGT	AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"""Interleukins and interleukin receptors"""	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.1144C>T	6.37:g.137323213G>A	ENSP00000314976:p.Leu382Phe	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	158	72	0.455696	NM_014432	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Missense_Mutation	SNP	ENST00000316649.5	37	CCDS5181.1	450	0.20604395604395603	137	0.2784552845528455	69	0.19060773480662985	47	0.08216783216783216	197	0.2598944591029024	G	15.12	2.740564	0.49045	0.221743	0.27	ENSG00000016402	ENST00000316649;ENST00000367748;ENST00000541547	T;T;T	0.62232	0.3;1.76;0.04	5.76	0.246	0.15516	.	6.474150	0.00914	N	0.002515	T	0.48150	0.1484	L	0.56769	1.78	0.80722	P	0.0	P;P	0.49961	0.899;0.93	P;B	0.48840	0.592;0.38	T	0.18745	-1.0327	9	0.46703	T	0.11	-0.0228	6.7229	0.23340	0.0755:0.4712:0.3326:0.1207	rs1342642;rs17310128;rs52809262;rs61018497;rs1342642	271;382	Q9UHF4-2;Q9UHF4	.;I20RA_HUMAN	F	382;271;333	ENSP00000314976:L382F;ENSP00000356722:L271F;ENSP00000437843:L333F	ENSP00000314976:L382F	L	-	1	0	IL20RA	137364906	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.732000	0.26072	0.013000	0.14918	0.655000	0.94253	CTC	G|0.794;N|0.001	.	strong		0.463	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432	
ALAD	210	hgsc.bcm.edu	37	9	116153891	116153891	+	Missense_Mutation	SNP	C	C	G	rs1800435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116153891C>G	ENST00000409155.3	-	4	373	c.177G>C	c.(175-177)aaG>aaC	p.K59N	ALAD_ENST00000482001.1_5'UTR|ALAD_ENST00000277315.5_Missense_Mutation_p.K42N	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	59			K -> N (in allele ALAD*2; 10% of population; fully active octamer; dbSNP:rs1800435). {ECO:0000269|PubMed:1716854, ECO:0000269|Ref.5}.		cellular response to interleukin-4 (GO:0071353)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protein homooligomerization (GO:0051260)|protoporphyrinogen IX biosynthetic process (GO:0006782)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|identical protein binding (GO:0042802)|lead ion binding (GO:0032791)|porphobilinogen synthase activity (GO:0004655)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|stomach(1)	9					Aminolevulinic acid(DB00855)	CTTCCAGCCGCTTCACACCAT	0.577													G|||	318	0.0634984	0.0023	0.0533	5008	,	,		19212	0.0397		0.0825	False		,,,				2504	0.1585				p.K59N		Atlas-SNP	.											.	ALAD	36	.	0			c.G177C	GRCh37	CM057644	ALAD	M	rs1800435	PASS	.	G	ASN/LYS	66,4340	819.9+/-416.4	0,66,2137	72.0	67.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	177	3.6	1.0	9	dbSNP_89	69	717,7883	786.5+/-407.6	33,651,3616	yes	missense	ALAD	NM_000031.5	94	33,717,5753	GG,GC,CC		8.3372,1.498,6.0203	benign	59/331	116153891	783,12223	2203	4300	6503	SO:0001583	missense	210	exon4			CAGCCGCTTCACA	M13928	CCDS6794.2	9q32	2010-04-29	2010-04-29		ENSG00000148218	ENSG00000148218	4.2.1.24		395	protein-coding gene	gene with protein product	"""porphobilinogen synthase"""	125270	"""aminolevulinate, delta-, dehydratase"""			6839527, 6378062	Standard	NM_000031		Approved	ALADH, PBGS	uc011lxf.2	P13716	OTTHUMG00000020522	ENST00000409155.3:c.177G>C	9.37:g.116153891C>G	ENSP00000386284:p.Lys59Asn	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	143	60	0.41958	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Missense_Mutation	SNP	ENST00000409155.3	37	CCDS6794.2	102	0.046703296703296704	1	0.0020325203252032522	20	0.055248618784530384	27	0.0472027972027972	54	0.0712401055408971	G	2.241	-0.373809	0.05034	0.01498	0.083372	ENSG00000148218	ENST00000409155;ENST00000277315;ENST00000448137	D;D;D	0.86562	-2.14;-2.14;-2.14	5.65	3.56	0.40772	Aldolase-type TIM barrel (1);	0.040549	0.85682	N	0.000000	T	0.05593	0.0147	N	0.00300	-1.685	0.19575	N	0.999965	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38286	-0.9668	10	0.07325	T	0.83	-9.5195	6.9633	0.24610	0.0774:0.129:0.6608:0.1328	rs1800435;rs11556129;rs17766140	59;42;88	P13716;B7Z3I9;P13716-2	HEM2_HUMAN;.;.	N	59;42;68	ENSP00000386284:K59N;ENSP00000277315:K42N;ENSP00000392748:K68N	ENSP00000277315:K42N	K	-	3	2	ALAD	115193712	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	1.925000	0.40074	1.399000	0.46721	-0.120000	0.15030	AAG	C|0.938;G|0.062	0.062	strong		0.577	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945	
MICAL3	57553	hgsc.bcm.edu	37	22	18300879	18300879	+	Silent	SNP	G	G	A	rs11704809	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	118	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	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		
OTOP1	133060	hgsc.bcm.edu	37	4	4228418	4228418	+	Silent	SNP	G	G	A	rs199644487		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:4228418G>A	ENST00000296358.4	-	1	198	c.174C>T	c.(172-174)gcC>gcT	p.A58A		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	58					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TCAGCATCTCGGCCAGTTTCT	0.736																																					p.A58A		Atlas-SNP	.											OTOP1,NS,haematopoietic_neoplasm,0,1	OTOP1	118	1	0			c.C174T						scavenged	.						8.0	8.0	8.0					4																	4228418		2131	4172	6303	SO:0001819	synonymous_variant	133060	exon1			CATCTCGGCCAGT	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.174C>T	4.37:g.4228418G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	25	8	0.32	NM_177998	A1L476	Silent	SNP	ENST00000296358.4	37	CCDS3372.1																																																																																			G|0.994;A|0.006	0.006	weak		0.736	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
NES	10763	hgsc.bcm.edu	37	1	156639636	156639636	+	Silent	SNP	G	G	A	rs11549292	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156639636G>A	ENST00000368223.3	-	4	4476	c.4344C>T	c.(4342-4344)gcC>gcT	p.A1448A		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1448	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)	p.A1448A(1)		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)					AGCTACTCAGGGCCTGGAGGC	0.637													G|||	1122	0.224042	0.0204	0.2882	5008	,	,		15261	0.2946		0.3032	False		,,,				2504	0.2996				p.A1448A		Atlas-SNP	.											NES,NS,carcinoma,0,1	NES	196	1	1	Substitution - coding silent(1)	prostate(1)	c.C4344T						PASS	.	G		300,4102		13,274,1914	31.0	34.0	33.0		4344	-0.5	0.0	1	dbSNP_120	33	2450,6148		356,1738,2205	no	coding-synonymous	NES	NM_006617.1		369,2012,4119	AA,AG,GG		28.495,6.8151,21.1538		1448/1622	156639636	2750,10250	2201	4299	6500	SO:0001819	synonymous_variant	10763	exon4			ACTCAGGGCCTGG	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.4344C>T	1.37:g.156639636G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	128	47	0.367188	NM_006617	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	37	CCDS1151.1																																																																																			G|0.773;A|0.227	0.227	strong		0.637	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
CENPW	387103	hgsc.bcm.edu	37	6	126661502	126661502	+	Missense_Mutation	SNP	G	G	T	rs41285260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:126661502G>T	ENST00000368328.4	+	1	183	c.83G>T	c.(82-84)cGa>cTa	p.R28L	CENPW_ENST00000368326.1_Missense_Mutation_p.R28L|CENPW_ENST00000368325.1_Missense_Mutation_p.R28L			Q5EE01	CENPW_HUMAN	centromere protein W	28					CENP-A containing nucleosome assembly (GO:0034080)|chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|kinetochore assembly (GO:0051382)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|kinetochore (GO:0000776)|nucleus (GO:0005634)	DNA binding (GO:0003677)			kidney(2)|large_intestine(1)|lung(3)	6						GTCTTCAAGCGAAAGAAGCCT	0.527													G|||	258	0.0515176	0.025	0.0735	5008	,	,		17642	0.0		0.1093	False		,,,				2504	0.0654				p.R28L		Atlas-SNP	.											.	CENPW	7	.	0			c.G83T						PASS	.	G	LEU/ARG	142,4264	100.3+/-138.9	3,136,2064	84.0	78.0	80.0		83	-2.2	0.0	6	dbSNP_127	80	762,7838	182.2+/-230.7	25,712,3563	yes	missense	CENPW	NM_001012507.2	102	28,848,5627	TT,TG,GG		8.8605,3.2229,6.9506	possibly-damaging	28/89	126661502	904,12102	2203	4300	6503	SO:0001583	missense	387103	exon1			TCAAGCGAAAGAA	BC039556	CCDS34529.1, CCDS69196.1, CCDS75516.1	6q22.32	2013-11-05	2010-04-16	2010-04-16	ENSG00000203760	ENSG00000203760			21488	protein-coding gene	gene with protein product	"""cancer-upregulated gene 2"""	611264	"""chromosome 6 open reading frame 173"""	C6orf173		17610844, 19070575	Standard	NM_001286524		Approved	CUG2	uc003qao.3	Q5EE01	OTTHUMG00000015518	ENST00000368328.4:c.83G>T	6.37:g.126661502G>T	ENSP00000357311:p.Arg28Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001012507	A6NIR0|A6NJC2	Missense_Mutation	SNP	ENST00000368328.4	37	CCDS34529.1	116	0.05311355311355311	12	0.024390243902439025	28	0.07734806629834254	0	0.0	76	0.10026385224274406	G	14.95	2.687974	0.48097	0.032229	0.088605	ENSG00000203760	ENST00000368326;ENST00000368325;ENST00000368328	T	0.22743	1.94	5.32	-2.24	0.06909	Histone-fold (1);	1.159190	0.06545	N	0.743893	T	0.04497	0.0123	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.12837	0.008	T	0.44967	-0.9293	9	0.72032	D	0.01	-7.9028	3.7386	0.08521	0.4097:0.0:0.3194:0.2709	rs41285260	28	Q5EE01	CENPW_HUMAN	L	28	ENSP00000357311:R28L	ENSP00000357308:R28L	R	+	2	0	CENPW	126703195	0.015000	0.18098	0.000000	0.03702	0.917000	0.54804	-0.203000	0.09438	-0.711000	0.04995	-0.309000	0.09137	CGA	G|0.937;T|0.063	0.063	strong		0.527	CENPW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042104.1		
TMEM89	440955	hgsc.bcm.edu	37	3	48659009	48659009	+	Missense_Mutation	SNP	G	G	T	rs9834639	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48659009G>T	ENST00000330862.3	-	1	279	c.181C>A	c.(181-183)Cct>Act	p.P61T		NM_001008269.1	NP_001008270.1	A2RUT3	TMM89_HUMAN	transmembrane protein 89	61			P -> T (in dbSNP:rs9834639).			integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|lung(1)|stomach(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		CTTGCTCCAGGGCCCAGCCAG	0.652													G|||	549	0.109625	0.2685	0.0937	5008	,	,		14325	0.0228		0.0825	False		,,,				2504	0.0235				p.P61T		Atlas-SNP	.											.	TMEM89	10	.	0			c.C181A						PASS	.	G	THR/PRO	1030,3376	355.6+/-313.1	110,810,1283	54.0	47.0	49.0		181	2.8	0.9	3	dbSNP_119	49	653,7947	157.7+/-211.4	32,589,3679	yes	missense	TMEM89	NM_001008269.1	38	142,1399,4962	TT,TG,GG		7.593,23.3772,12.9402	possibly-damaging	61/160	48659009	1683,11323	2203	4300	6503	SO:0001583	missense	440955	exon1			CTCCAGGGCCCAG	AX657016	CCDS33751.1	3p21.31	2005-11-02			ENSG00000183396	ENSG00000183396			32372	protein-coding gene	gene with protein product							Standard	NM_001008269		Approved		uc011bbo.2	A2RUT3	OTTHUMG00000156647	ENST00000330862.3:c.181C>A	3.37:g.48659009G>T	ENSP00000329557:p.Pro61Thr	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	182	98	0.538462	NM_001008269		Missense_Mutation	SNP	ENST00000330862.3	37	CCDS33751.1	236	0.10805860805860806	123	0.25	31	0.0856353591160221	19	0.033216783216783216	63	0.08311345646437995	G	12.61	1.990025	0.35131	0.233772	0.07593	ENSG00000183396	ENST00000330862	T	0.41400	1.0	4.7	2.84	0.33178	.	0.841083	0.09976	N	0.731570	T	0.00012	0.0000	N	0.22421	0.69	0.43517	P	0.004214999999999969	B	0.21452	0.056	B	0.20384	0.029	T	0.17899	-1.0354	9	0.59425	D	0.04	-4.1779	7.6057	0.28101	0.0:0.1817:0.6301:0.1883	rs9834639;rs58298641;rs9834639	61	A2RUT3	TMM89_HUMAN	T	61	ENSP00000329557:P61T	ENSP00000329557:P61T	P	-	1	0	TMEM89	48634013	0.989000	0.36119	0.922000	0.36590	0.007000	0.05969	1.725000	0.38074	0.547000	0.28938	0.462000	0.41574	CCT	G|0.878;T|0.122	0.122	strong		0.652	TMEM89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345046.1	NM_001008269	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388379	1388379	+	Missense_Mutation	SNP	G	G	A	rs56109734	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	210	4	0.0190476		WXS	Illumina HiSeq	Phase_I	190	45	0.236842	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	
LRBA	987	hgsc.bcm.edu	37	4	151207127	151207127	+	Missense_Mutation	SNP	C	C	T	rs3749574	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:151207127C>T	ENST00000357115.3	-	55	8353	c.8110G>A	c.(8110-8112)Gcg>Acg	p.A2704T	LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000535741.1_Missense_Mutation_p.A2693T|LRBA_ENST00000510413.1_Missense_Mutation_p.A2692T	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	277	0	0		WXS	Illumina HiSeq	Phase_I	168	118	0.702381	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		
PML	5371	hgsc.bcm.edu	37	15	74336656	74336656	+	Silent	SNP	C	C	T	rs61751122	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:74336656C>T	ENST00000268058.3	+	9	2052	c.1956C>T	c.(1954-1956)gcC>gcT	p.A652A	PML_ENST00000565898.1_Silent_p.A604A	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	652					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						ACTCCAAGGCCGTGTCCCTGG	0.617			T	"""RARA, PAX5"""	"""APL, ALL"""								C|||	172	0.034345	0.0893	0.0173	5008	,	,		17889	0.001		0.0159	False		,,,				2504	0.0256				p.A652A		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.C1956T						PASS	.	C		319,4077	170.1+/-200.6	6,307,1885	70.0	67.0	68.0		1956	-10.4	0.1	15	dbSNP_129	68	168,8426	78.4+/-141.0	2,164,4131	no	coding-synonymous	PML	NM_033238.2		8,471,6016	TT,TC,CC		1.9549,7.2566,3.749		652/883	74336656	487,12503	2198	4297	6495	SO:0001819	synonymous_variant	5371	exon9			CAAGGCCGTGTCC	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.1956C>T	15.37:g.74336656C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	40	32	0.8	NM_033238	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Silent	SNP	ENST00000268058.3	37	CCDS10255.1																																																																																			C|0.967;T|0.033	0.033	strong		0.617	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
C3orf58	205428	hgsc.bcm.edu	37	3	143691672	143691672	+	Silent	SNP	C	C	T	rs151261436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:143691672C>T	ENST00000315691.3	+	1	1033	c.498C>T	c.(496-498)gaC>gaT	p.D166D	C3orf58_ENST00000441925.2_5'Flank|C3orf58_ENST00000495414.1_5'Flank|C3orf58_ENST00000493396.1_3'UTR	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	166					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCTGGTCGGACCTGGTGCACT	0.706													C|||	40	0.00798722	0.0	0.0173	5008	,	,		15173	0.0		0.0268	False		,,,				2504	0.001				p.D166D		Atlas-SNP	.											.	C3orf58	36	.	0			c.C498T						PASS	.	C		11,4247		0,11,2118	7.0	7.0	7.0		498	2.7	1.0	3	dbSNP_134	7	84,8290		0,84,4103	no	coding-synonymous	C3orf58	NM_173552.3		0,95,6221	TT,TC,CC		1.0031,0.2583,0.7521		166/431	143691672	95,12537	2129	4187	6316	SO:0001819	synonymous_variant	205428	exon1			GTCGGACCTGGTG	AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"""deleted in autism 1"", ""hypoxia and Akt induced stem cell factor"""	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.498C>T	3.37:g.143691672C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_173552	B2RCF2|B7Z1W3	Silent	SNP	ENST00000315691.3	37	CCDS3130.1																																																																																			C|0.989;T|0.011	0.011	strong		0.706	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552	
TPPP	11076	hgsc.bcm.edu	37	5	678087	678087	+	Missense_Mutation	SNP	C	C	T	rs570878136	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:678087C>T	ENST00000360578.5	-	2	210	c.89G>A	c.(88-90)aGg>aAg	p.R30K	CTD-2589H19.6_ENST00000607068.1_RNA	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	30	Mediates interaction with LIMK1.				microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.R30K(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		CAGCGACAGCCTCTTGGCTGC	0.677													C|||	15	0.00299521	0.0061	0.0	5008	,	,		16462	0.0069		0.0	False		,,,				2504	0.0				p.R30K		Atlas-SNP	.											TPPP,NS,carcinoma,0,1	TPPP	24	1	1	Substitution - Missense(1)	prostate(1)	c.G89A						scavenged	.						14.0	17.0	16.0					5																	678087		2199	4295	6494	SO:0001583	missense	11076	exon2			GACAGCCTCTTGG	AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368			24164	protein-coding gene	gene with protein product	"""brain specific protein p25 alpha"""	608773				10083737, 12093283, 15590652, 17105200	Standard	NM_007030		Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.89G>A	5.37:g.678087C>T	ENSP00000353785:p.Arg30Lys	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	303	14	0.0462046	NM_007030		Missense_Mutation	SNP	ENST00000360578.5	37	CCDS3856.1	.	.	.	.	.	.	.	.	.	.	c	14.67	2.605282	0.46423	.	.	ENSG00000171368	ENST00000360578	T	0.45276	0.9	5.23	5.23	0.72850	.	0.149935	0.44902	D	0.000407	T	0.29588	0.0738	L	0.29908	0.895	0.44635	D	0.997618	B	0.15141	0.012	B	0.13407	0.009	T	0.11867	-1.0570	10	0.05436	T	0.98	-54.1656	16.5545	0.84482	0.0:1.0:0.0:0.0	.	30	O94811	TPPP_HUMAN	K	30	ENSP00000353785:R30K	ENSP00000353785:R30K	R	-	2	0	TPPP	731087	1.000000	0.71417	0.998000	0.56505	0.405000	0.30901	4.081000	0.57627	2.437000	0.82529	0.491000	0.48974	AGG	.	.	none		0.677	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253645.3	NM_007030	
FGFBP2	83888	hgsc.bcm.edu	37	4	15964574	15964574	+	Missense_Mutation	SNP	C	C	T	rs62617788	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:15964574C>T	ENST00000259989.6	-	1	285	c.179G>A	c.(178-180)cGt>cAt	p.R60H	FGFBP2_ENST00000509331.1_Intron	NM_031950.3	NP_114156.1	Q9BYJ0	FGFP2_HUMAN	fibroblast growth factor binding protein 2	60						extracellular region (GO:0005576)				central_nervous_system(1)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	9						GCAGTCGACACGAAGCCAGAC	0.577													C|||	53	0.0105831	0.0008	0.0159	5008	,	,		20019	0.0		0.0338	False		,,,				2504	0.0072				p.R60H		Atlas-SNP	.											.	FGFBP2	22	.	0			c.G179A						PASS	.	C	HIS/ARG	25,4381	24.3+/-50.5	0,25,2178	63.0	55.0	58.0		179	0.0	0.0	4	dbSNP_129	58	288,8312	87.9+/-150.2	3,282,4015	yes	missense	FGFBP2	NM_031950.3	29	3,307,6193	TT,TC,CC		3.3488,0.5674,2.4066	benign	60/224	15964574	313,12693	2203	4300	6503	SO:0001583	missense	83888	exon1			TCGACACGAAGCC	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.179G>A	4.37:g.15964574C>T	ENSP00000259989:p.Arg60His	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_031950		Missense_Mutation	SNP	ENST00000259989.6	37	CCDS3419.1	32	0.014652014652014652	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	24	0.0316622691292876	C	9.649	1.140959	0.21205	0.005674	0.033488	ENSG00000137441	ENST00000259989	T	0.15372	2.43	2.98	0.029	0.14161	.	0.156992	0.36628	N	0.002500	T	0.03136	0.0092	L	0.34521	1.04	0.09310	N	1	B	0.13594	0.008	B	0.15052	0.012	T	0.19516	-1.0303	10	0.54805	T	0.06	-4.4055	3.8097	0.08792	0.1881:0.5955:0.0:0.2164	rs62617788	60	Q9BYJ0	FGFP2_HUMAN	H	60	ENSP00000259989:R60H	ENSP00000259989:R60H	R	-	2	0	FGFBP2	15573672	0.650000	0.27331	0.000000	0.03702	0.000000	0.00434	2.247000	0.43151	-0.589000	0.05874	-0.851000	0.03033	CGT	C|0.978;T|0.022	0.022	strong		0.577	FGFBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250324.1	NM_031950	
CRISPLD1	83690	hgsc.bcm.edu	37	8	75927053	75927053	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:75927053C>T	ENST00000262207.4	+	6	1101	c.633C>T	c.(631-633)aaC>aaT	p.N211N	CRISPLD1_ENST00000523524.1_Silent_p.N23N|CRISPLD1_ENST00000517786.1_Silent_p.N25N	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	211					face morphogenesis (GO:0060325)	extracellular vesicular exosome (GO:0070062)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(7)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(64;0.0799)		Epithelial(68;0.155)|BRCA - Breast invasive adenocarcinoma(89;0.161)			AAAGGGGAAACTGGTGGGGCC	0.408																																					p.N211N		Atlas-SNP	.											CRISPLD1,colon,carcinoma,+2,1	CRISPLD1	94	1	0			c.C633T						scavenged	.						44.0	42.0	42.0					8																	75927053		2202	4299	6501	SO:0001819	synonymous_variant	83690	exon6			GGGAAACTGGTGG	AL834301	CCDS6219.1, CCDS69497.1, CCDS75754.1	8q21.13	2005-09-23	2005-02-16	2005-02-16	ENSG00000121005	ENSG00000121005			18206	protein-coding gene	gene with protein product			"""LCCL domain containing cysteine-rich secretory protein 1"""	LCRISP1			Standard	NM_031461		Approved	Cocoacrisp, DKFZp762F133	uc003yan.3	Q9H336	OTTHUMG00000164529	ENST00000262207.4:c.633C>T	8.37:g.75927053C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	111	4	0.036036	NM_031461	B2RA60|B7Z929	Silent	SNP	ENST00000262207.4	37	CCDS6219.1																																																																																			.	.	none		0.408	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461	
CPA1	1357	hgsc.bcm.edu	37	7	130023539	130023539	+	Silent	SNP	C	C	T	rs12706927	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:130023539C>T	ENST00000011292.3	+	6	750	c.600C>T	c.(598-600)taC>taT	p.Y200Y	CPA1_ENST00000484324.1_Silent_p.Y112Y	NM_001868.2	NP_001859.1	P15085	CBPA1_HUMAN	carboxypeptidase A1 (pancreatic)	200					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)					CTCAAGACTACGGGCAGGATG	0.587													C|||	384	0.0766773	0.0953	0.0562	5008	,	,		18446	0.006		0.1133	False		,,,				2504	0.1012				p.Y200Y		Atlas-SNP	.											.	CPA1	73	.	0			c.C600T						PASS	.	C		437,3969	212.2+/-232.1	19,399,1785	151.0	129.0	137.0		600	0.6	1.0	7	dbSNP_121	137	1026,7574	219.2+/-257.4	64,898,3338	no	coding-synonymous	CPA1	NM_001868.2		83,1297,5123	TT,TC,CC		11.9302,9.9183,11.2487		200/420	130023539	1463,11543	2203	4300	6503	SO:0001819	synonymous_variant	1357	exon6			AGACTACGGGCAG		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.600C>T	7.37:g.130023539C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	104	26	0.25	NM_001868	A4D1M1|Q53XU0|Q9BS67|Q9UCF2	Silent	SNP	ENST00000011292.3	37	CCDS5820.1																																																																																			C|0.903;T|0.097	0.097	strong		0.587	CPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349736.2	NM_001868	
CGNL1	84952	hgsc.bcm.edu	37	15	57839587	57839587	+	Missense_Mutation	SNP	A	A	G	rs16977594	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:57839587A>G	ENST00000281282.5	+	19	3886	c.3808A>G	c.(3808-3810)Atg>Gtg	p.M1270V		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	1270	Poly-Asp.|Tail.		M -> V (in dbSNP:rs16977594).			myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)	p.M1270V(1)		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)		GCTGGATGACATGGATGACGA	0.557													A|||	531	0.10603	0.2753	0.0274	5008	,	,		19217	0.0308		0.0159	False		,,,				2504	0.1033				p.M1270V		Atlas-SNP	.											CGNL1,NS,carcinoma,0,1	CGNL1	125	1	1	Substitution - Missense(1)	stomach(1)	c.A3808G						PASS	.	A	VAL/MET	950,3434	360.1+/-315.1	108,734,1350	157.0	163.0	161.0		3808	-5.2	0.5	15	dbSNP_123	161	138,8446	69.0+/-131.5	3,132,4157	yes	missense	CGNL1	NM_032866.3	21	111,866,5507	GG,GA,AA		1.6076,21.6697,8.3899	benign	1270/1303	57839587	1088,11880	2192	4292	6484	SO:0001583	missense	84952	exon19			GATGACATGGATG	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.3808A>G	15.37:g.57839587A>G	ENSP00000281282:p.Met1270Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	65	15	0.230769	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	169	0.07738095238095238	133	0.2703252032520325	11	0.03038674033149171	15	0.026223776223776224	10	0.013192612137203167	A	4.077	0.012131	0.07912	0.216697	0.016076	ENSG00000128849	ENST00000281282	T	0.75154	-0.91	4.79	-5.17	0.02849	.	0.693382	0.13085	N	0.415016	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	0.12066	-1.0562	9	0.40728	T	0.16	-4.3624	3.2421	0.06784	0.1762:0.1697:0.4551:0.199	rs16977594;rs52812772;rs56614646;rs61651064;rs16977594	1270	Q0VF96	CGNL1_HUMAN	V	1270	ENSP00000281282:M1270V	ENSP00000281282:M1270V	M	+	1	0	CGNL1	55626879	0.000000	0.05858	0.539000	0.28077	0.406000	0.30931	-0.660000	0.05317	-0.788000	0.04504	0.379000	0.24179	ATG	A|0.914;G|0.086	0.086	strong		0.557	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
CHRNA2	1135	hgsc.bcm.edu	37	8	27324822	27324822	+	Missense_Mutation	SNP	T	T	C	rs891398	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:27324822T>C	ENST00000520933.2	-	4	526	c.373A>G	c.(373-375)Act>Gct	p.T125A	CHRNA2_ENST00000407991.1_Missense_Mutation_p.T125A|CHRNA2_ENST00000240132.2_Missense_Mutation_p.T110A			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	125			T -> A (in dbSNP:rs891398). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8906617, ECO:0000269|Ref.2}.		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)	CCAAAATCAGTGGGGTTCCAG	0.542													C|||	3056	0.610224	0.8298	0.5562	5008	,	,		19073	0.6498		0.5119	False		,,,				2504	0.4121				p.T125A		Atlas-SNP	.											.	CHRNA2	48	.	0			c.A373G						PASS	.	C	ALA/THR	3356,1050	383.5+/-324.9	1276,804,123	110.0	108.0	109.0		373	3.5	0.1	8	dbSNP_86	109	4189,4411	586.2+/-392.0	1038,2113,1149	yes	missense	CHRNA2	NM_000742.3	58	2314,2917,1272	CC,CT,TT		48.7093,23.8311,41.9883	benign	125/530	27324822	7545,5461	2203	4300	6503	SO:0001583	missense	1135	exon5			AATCAGTGGGGTT	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.373A>G	8.37:g.27324822T>C	ENSP00000429616:p.Thr125Ala	Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	247	244	0.987854	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	1376	0.63003663003663	406	0.8252032520325203	206	0.569060773480663	392	0.6853146853146853	372	0.49076517150395776	C	0.014	-1.604403	0.00849	0.761689	0.487093	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132	T;T;T	0.78364	-1.17;-1.17;-1.17	5.52	3.46	0.39613	Neurotransmitter-gated ion-channel ligand-binding (3);	0.291760	0.38058	N	0.001824	T	0.00012	0.0000	N	0.00873	-1.125	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40327	-0.9569	9	0.08381	T	0.77	.	5.715	0.17954	0.1611:0.655:0.0:0.184	rs891398;rs2229958;rs3735756;rs17378583;rs57810583;rs891398	125	Q15822	ACHA2_HUMAN	A	125;125;110	ENSP00000385026:T125A;ENSP00000429616:T125A;ENSP00000240132:T110A	ENSP00000240132:T110A	T	-	1	0	CHRNA2	27380739	0.019000	0.18553	0.076000	0.20297	0.013000	0.08279	0.603000	0.24149	1.342000	0.45619	-0.119000	0.15052	ACT	T|0.402;C|0.598	0.598	strong		0.542	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693104	187693104	+	Silent	SNP	C	C	T	rs10172225	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187693104C>T	ENST00000295131.2	-	9	1548	c.1509G>A	c.(1507-1509)gtG>gtA	p.V503V		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	503					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TCCCAAATGACACAGTGGGTA	0.333													T|||	872	0.174121	0.4213	0.1066	5008	,	,		18832	0.0208		0.1103	False		,,,				2504	0.1115				p.V503V		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.G1509A						PASS	.	T		1766,2640	643.0+/-397.8	353,1060,790	64.0	64.0	64.0		1509	1.2	0.0	2	dbSNP_119	64	979,7621	773.0+/-407.7	44,891,3365	no	coding-synonymous	ZSWIM2	NM_182521.2		397,1951,4155	TT,TC,CC		11.3837,40.0817,21.1056		503/634	187693104	2745,10261	2203	4300	6503	SO:0001819	synonymous_variant	151112	exon9			AAATGACACAGTG	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1509G>A	2.37:g.187693104C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Silent	SNP	ENST00000295131.2	37	CCDS33348.1																																																																																			C|0.805;T|0.195	0.195	strong		0.333	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
SEMG1	6406	hgsc.bcm.edu	37	20	43836173	43836173	+	Missense_Mutation	SNP	T	T	A	rs2301366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:43836173T>A	ENST00000372781.3	+	2	292	c.235T>A	c.(235-237)Tcc>Acc	p.S79T	SEMG1_ENST00000244069.6_Missense_Mutation_p.S79T	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	79	Repeat-rich region. {ECO:0000250}.		S -> T (less common genetic variant; dbSNP:rs2301366). {ECO:0000269|PubMed:14562960, 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)	p.S79T(1)		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)				TCATGACCAGTCCCGAAAAAG	0.388													A|||	1407	0.28095	0.5446	0.3256	5008	,	,		20945	0.0913		0.1988	False		,,,				2504	0.1728				p.S79T		Atlas-SNP	.											SEMG1,NS,carcinoma,-2,3	SEMG1	71	3	1	Substitution - Missense(1)	stomach(1)	c.T235A						PASS	.	A	THR/SER	2084,2322	603.9+/-390.2	510,1064,629	147.0	134.0	139.0		235	-0.0	0.0	20	dbSNP_100	139	1827,6773	731.5+/-406.8	187,1453,2660	yes	missense	SEMG1	NM_003007.3	58	697,2517,3289	AA,AT,TT		21.2442,47.2991,30.0707		79/463	43836173	3911,9095	2203	4300	6503	SO:0001583	missense	6406	exon2			GACCAGTCCCGAA		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.235T>A	20.37:g.43836173T>A	ENSP00000361867:p.Ser79Thr	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	248	117	0.471774	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	563	0.25778388278388276	251	0.5101626016260162	102	0.281767955801105	61	0.10664335664335664	149	0.19656992084432717	A	0.005	-2.180094	0.00308	0.472991	0.212442	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.03553	3.89;3.89	1.3	-0.029	0.13920	.	.	.	.	.	T	0.00012	0.0000	N	0.00036	-2.535	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.38045	-0.9679	8	0.02654	T	1	.	2.1602	0.03823	0.4149:0.2948:0.0:0.2903	rs2301366;rs2301366	79;79;79	P04279-2;P04279;E7EPD3	.;SEMG1_HUMAN;.	T	79	ENSP00000244069:S79T;ENSP00000361867:S79T	ENSP00000244069:S79T	S	+	1	0	SEMG1	43269587	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.394000	0.07296	-0.543000	0.06240	-0.375000	0.07067	TCC	T|0.724;A|0.276	0.276	strong		0.388	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
ARID4A	5926	hgsc.bcm.edu	37	14	58831995	58831995	+	Missense_Mutation	SNP	A	A	G	rs377087834		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:58831995A>G	ENST00000355431.3	+	20	3561	c.3188A>G	c.(3187-3189)cAa>cGa	p.Q1063R	ARID4A_ENST00000395168.3_Missense_Mutation_p.Q1063R|ARID4A_ENST00000348476.3_Missense_Mutation_p.Q1063R|ARID4A_ENST00000431317.2_Missense_Mutation_p.Q1063R	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	1063					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						ATAATTGTACAAGAGAGAGAG	0.383																																					p.Q1063R		Atlas-SNP	.											.	ARID4A	222	.	0			c.A3188G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN	1,4395		0,1,2197	59.0	61.0	60.0		3188,3188,3188	4.2	0.6	14		60	2,8576		0,2,4287	no	missense,missense,missense	ARID4A	NM_002892.3,NM_023000.2,NM_023001.2	43,43,43	0,3,6484	GG,GA,AA		0.0233,0.0227,0.0231	benign,benign,benign	1063/1258,1063/1204,1063/1189	58831995	3,12971	2198	4289	6487	SO:0001583	missense	5926	exon20			TTGTACAAGAGAG	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.3188A>G	14.37:g.58831995A>G	ENSP00000347602:p.Gln1063Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	6.768	0.510652	0.12883	2.27E-4	2.33E-4	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.17370	2.43;2.43;2.46;2.43;2.28	5.46	4.25	0.50352	.	0.533378	0.21403	N	0.075117	T	0.12817	0.0311	L	0.44542	1.39	0.30980	N	0.722581	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.003;0.002;0.004	T	0.08973	-1.0696	10	0.17832	T	0.49	-11.3967	7.5328	0.27693	0.6734:0.2537:0.0729:0.0	.	1063;1063;1063	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	R	1063;1063;1063;1063;741	ENSP00000347602:Q1063R;ENSP00000344556:Q1063R;ENSP00000378597:Q1063R;ENSP00000397368:Q1063R;ENSP00000416053:Q741R	ENSP00000344556:Q1063R	Q	+	2	0	ARID4A	57901748	1.000000	0.71417	0.605000	0.28930	0.958000	0.62258	3.193000	0.50997	2.082000	0.62665	0.455000	0.32223	CAA	.	.	weak		0.383	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
IL17RB	55540	hgsc.bcm.edu	37	3	53892830	53892830	+	Missense_Mutation	SNP	T	T	C	rs2232346	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:53892830T>C	ENST00000288167.3	+	9	841	c.832T>C	c.(832-834)Ttc>Ctc	p.F278L	RP11-884K10.7_ENST00000607783.1_RNA	NM_018725.3	NP_061195.2	Q9NRM6	I17RB_HUMAN	interleukin 17 receptor B	278			F -> L (in dbSNP:rs2232346). {ECO:0000269|Ref.5}.		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)		AGGCGTCCCTTTCCCTCTGGA	0.493													T|||	35	0.00698882	0.0023	0.0086	5008	,	,		21148	0.0		0.0249	False		,,,				2504	0.001				p.F278L		Atlas-SNP	.											.	IL17RB	27	.	0			c.T832C						PASS	.	T	LEU/PHE	22,4384	29.9+/-59.1	0,22,2181	83.0	75.0	77.0		832	-8.2	0.0	3	dbSNP_98	77	236,8364	95.4+/-157.2	4,228,4068	yes	missense	IL17RB	NM_018725.3	22	4,250,6249	CC,CT,TT		2.7442,0.4993,1.9837	benign	278/503	53892830	258,12748	2203	4300	6503	SO:0001583	missense	55540	exon9			GTCCCTTTCCCTC	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.832T>C	3.37:g.53892830T>C	ENSP00000288167:p.Phe278Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	18	0.290323	NM_018725	Q9BPZ0|Q9NRL4|Q9NRM5	Missense_Mutation	SNP	ENST00000288167.3	37	CCDS2874.1	27	0.012362637362637362	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	22	0.029023746701846966	T	6.318	0.426778	0.11987	0.004993	0.027442	ENSG00000056736	ENST00000288167;ENST00000494338	T;T	0.13307	3.32;2.6	4.94	-8.22	0.01037	.	2.450880	0.01295	N	0.010152	T	0.01730	0.0055	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31420	-0.9944	10	0.10636	T	0.68	2.6701	1.4097	0.02288	0.4558:0.2473:0.1139:0.1829	rs2232346;rs17580134;rs52815784;rs2232346	278	Q9NRM6	I17RB_HUMAN	L	278;262	ENSP00000288167:F278L;ENSP00000418638:F262L	ENSP00000288167:F278L	F	+	1	0	IL17RB	53867870	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.597000	0.05713	-1.314000	0.02300	-0.256000	0.11100	TTC	T|0.982;C|0.018	0.018	strong		0.493	IL17RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350563.1	NM_172234	
GJA9	81025	hgsc.bcm.edu	37	1	39340504	39340504	+	Silent	SNP	T	T	G	rs41270783	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39340504T>G	ENST00000360786.3	-	1	1519	c.1267A>C	c.(1267-1269)Aga>Cga	p.R423R	RP5-864K19.4_ENST00000456813.1_RNA|MYCBP_ENST00000397572.2_5'Flank|GJA9_ENST00000357771.3_Silent_p.R423R|RP5-864K19.4_ENST00000433671.2_RNA|GJA9_ENST00000454994.2_Silent_p.R423R|RP5-864K19.4_ENST00000443161.1_RNA|MYCBP_ENST00000489803.1_5'UTR			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	423					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)			CATGTAGCTCTAAGCCACCGC	0.507													T|||	347	0.0692891	0.1059	0.0389	5008	,	,		18745	0.001		0.0726	False		,,,				2504	0.1084				p.R423R		Atlas-SNP	.											.	GJA9	55	.	0			c.A1267C						PASS	.	T		364,4042	186.4+/-213.3	15,334,1854	93.0	92.0	92.0		1267	0.6	0.0	1	dbSNP_127	92	523,8077	147.3+/-202.7	22,479,3799	no	coding-synonymous	GJA9	NM_030772.4		37,813,5653	GG,GT,TT		6.0814,8.2615,6.8199		423/516	39340504	887,12119	2203	4300	6503	SO:0001819	synonymous_variant	81025	exon2			TAGCTCTAAGCCA	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.1267A>C	1.37:g.39340504T>G		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	170	35	0.205882	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000360786.3	37	CCDS432.1																																																																																			T|0.935;G|0.065	0.065	strong		0.507	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
PAG1	55824	hgsc.bcm.edu	37	8	81897200	81897200	+	Silent	SNP	C	C	T	rs7006101	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:81897200C>T	ENST00000220597.4	-	7	1397	c.687G>A	c.(685-687)tcG>tcA	p.S229S		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	229					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TTCTGTCCACCGAGGCATATT	0.488													C|||	704	0.140575	0.2852	0.0865	5008	,	,		20851	0.001		0.1083	False		,,,				2504	0.1605				p.S229S		Atlas-SNP	.											.	PAG1	39	.	0			c.G687A						PASS	.	C		1092,3314	394.2+/-329.2	141,810,1252	121.0	119.0	120.0		687	-11.1	0.0	8	dbSNP_116	120	849,7751	193.2+/-239.0	40,769,3491	no	coding-synonymous	PAG1	NM_018440.3		181,1579,4743	TT,TC,CC		9.8721,24.7844,14.9239		229/433	81897200	1941,11065	2203	4300	6503	SO:0001819	synonymous_variant	55824	exon7			GTCCACCGAGGCA	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"""Csk-binding protein"", ""transmembrane adaptor protein PAG"""	605767	"""phosphoprotein associated with glycosphingolipid microdomains 1"""			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.687G>A	8.37:g.81897200C>T		Somatic	381	1	0.00262467		WXS	Illumina HiSeq	Phase_I	529	177	0.334594	NM_018440	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Silent	SNP	ENST00000220597.4	37	CCDS6227.1																																																																																			C|0.853;T|0.147	0.147	strong		0.488	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440	
MUC17	140453	hgsc.bcm.edu	37	7	100678622	100678622	+	Missense_Mutation	SNP	G	G	A	rs77299546	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678622G>A	ENST00000306151.4	+	3	3989	c.3925G>A	c.(3925-3927)Gtg>Atg	p.V1309M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1309	59 X approximate tandem repeats.|Ser-rich.				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)					TAAAGGTCCTGTGGTCACTTC	0.448																																					p.V1309M		Atlas-SNP	.											.	MUC17	804	.	0			c.G3925A						PASS	.						236.0	226.0	229.0					7																	100678622		2203	4300	6503	SO:0001583	missense	140453	exon3			GGTCCTGTGGTCA	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.3925G>A	7.37:g.100678622G>A	ENSP00000302716:p.Val1309Met	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	264	90	0.340909	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.174	-1.068527	0.01934	.	.	ENSG00000169876	ENST00000306151	T	0.02763	4.17	0.471	-0.621	0.11564	.	.	.	.	.	T	0.04272	0.0118	L	0.29908	0.895	0.09310	N	1	D	0.54964	0.969	P	0.55667	0.781	T	0.44143	-0.9347	8	0.33940	T	0.23	.	.	.	.	.	1309	Q685J3	MUC17_HUMAN	M	1309	ENSP00000302716:V1309M	ENSP00000302716:V1309M	V	+	1	0	MUC17	100465342	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.596000	0.05720	-0.241000	0.09681	-1.379000	0.01178	GTG	G|0.936;A|0.064	0.064	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TNFSF9	8744	hgsc.bcm.edu	37	19	6534728	6534728	+	Missense_Mutation	SNP	G	G	C	rs61750000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6534728G>C	ENST00000245817.3	+	3	454	c.416G>C	c.(415-417)gGa>gCa	p.G139A		NM_003811.3	NP_003802.1	P41273	TNFL9_HUMAN	tumor necrosis factor (ligand) superfamily, member 9	139					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	5						GCCAAGGCTGGAGTCTACTAT	0.637													g|||	5	0.000998403	0.0	0.0	5008	,	,		10547	0.0		0.005	False		,,,				2504	0.0				p.G139A		Atlas-SNP	.											.	TNFSF9	17	.	0			c.G416C						PASS	.		ALA/GLY	4,4374		0,4,2185	59.0	60.0	60.0		416	4.1	0.0	19	dbSNP_129	60	42,8548		0,42,4253	yes	missense	TNFSF9	NM_003811.3	60	0,46,6438	CC,CG,GG		0.4889,0.0914,0.3547	probably-damaging	139/255	6534728	46,12922	2189	4295	6484	SO:0001583	missense	8744	exon3			AGGCTGGAGTCTA	U03398	CCDS12169.1	19p13.3	2008-07-22				ENSG00000125657		"""Tumor necrosis factor (ligand) superfamily"""	11939	protein-coding gene	gene with protein product	"""receptor 4-1BB ligand"", ""homolog of mouse 4-1BB-L"""	606182				8405064, 8088337	Standard	NM_003811		Approved	4-1BB-L	uc002mfh.2	P41273		ENST00000245817.3:c.416G>C	19.37:g.6534728G>C	ENSP00000245817:p.Gly139Ala	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_003811	Q2M3S2	Missense_Mutation	SNP	ENST00000245817.3	37	CCDS12169.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	g	17.69	3.450738	0.63290	9.14E-4	0.004889	ENSG00000125657	ENST00000245817	D	0.99928	-8.08	4.13	4.13	0.48395	Tumour necrosis factor (3);Tumour necrosis factor-like (2);Tumour necrosis factor, conserved site (1);	0.000000	0.47093	U	0.000253	D	0.99887	0.9946	M	0.71581	2.175	0.24658	N	0.993484	D	0.89917	1.0	D	0.91635	0.999	D	0.98667	1.0686	10	0.87932	D	0	-29.5602	12.2711	0.54706	0.0:0.0:1.0:0.0	rs61750000	139	P41273	TNFL9_HUMAN	A	139	ENSP00000245817:G139A	ENSP00000245817:G139A	G	+	2	0	TNFSF9	6485728	0.980000	0.34600	0.025000	0.17156	0.008000	0.06430	4.189000	0.58358	2.026000	0.59711	0.466000	0.42574	GGA	G|0.997;C|0.003	0.003	strong		0.637	TNFSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457856.1	NM_003811	
ZC3H11A	9877	hgsc.bcm.edu	37	1	203821334	203821334	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:203821334C>T	ENST00000545588.1	+	17	6067	c.2240C>T	c.(2239-2241)tCa>tTa	p.S747L	ZC3H11A_ENST00000332127.4_Missense_Mutation_p.S747L|ZC3H11A_ENST00000367212.3_Missense_Mutation_p.S747L|ZC3H11A_ENST00000367214.1_Missense_Mutation_p.S747L|ZC3H11A_ENST00000367210.1_Missense_Mutation_p.S747L	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	747					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			GGCCCTTCCTCATCCCAAATG	0.483																																					p.S747L		Atlas-SNP	.											ZC3H11A,NS,carcinoma,0,1	ZC3H11A	71	1	0			c.C2240T						scavenged	.						26.0	30.0	29.0					1																	203821334		2188	4287	6475	SO:0001583	missense	9877	exon20			CTTCCTCATCCCA		CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"""Zinc fingers, CCCH-type domain containing"""	29093	protein-coding gene	gene with protein product		613513	"""zinc finger CCCH-type domain containing 11A"""	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.2240C>T	1.37:g.203821334C>T	ENSP00000438527:p.Ser747Leu	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	362	3	0.00828729	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Missense_Mutation	SNP	ENST00000545588.1	37	CCDS30978.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.749482	0.49257	.	.	ENSG00000058673	ENST00000367214;ENST00000537080;ENST00000367212;ENST00000332127;ENST00000545588;ENST00000367210	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	5.56	5.56	0.83823	.	0.304354	0.30446	N	0.009605	T	0.66694	0.2815	M	0.72118	2.19	0.45852	D	0.998711	D	0.89917	1.0	D	0.76575	0.988	T	0.60409	-0.7269	10	0.15952	T	0.53	-28.67	18.3078	0.90188	0.0:1.0:0.0:0.0	.	747	O75152	ZC11A_HUMAN	L	747;693;747;747;747;747	ENSP00000356183:S747L;ENSP00000356181:S747L;ENSP00000333253:S747L;ENSP00000438527:S747L;ENSP00000356179:S747L	ENSP00000333253:S747L	S	+	2	0	ZC3H11A	202087957	1.000000	0.71417	1.000000	0.80357	0.251000	0.25915	5.671000	0.68095	2.619000	0.88677	0.557000	0.71058	TCA	.	.	none		0.483	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827	
KRT75	9119	hgsc.bcm.edu	37	12	52818377	52818377	+	Missense_Mutation	SNP	C	C	T	rs61730614	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52818377C>T	ENST00000252245.5	-	9	1800	c.1580G>A	c.(1579-1581)cGg>cAg	p.R527Q	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	527	Tail.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R527Q(1)		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)		CCCTAAGCCCCGGTTGCTGGT	0.622													C|||	816	0.162939	0.09	0.2493	5008	,	,		18615	0.1558		0.164	False		,,,				2504	0.2065				p.R527Q		Atlas-SNP	.											KRT75,rectum,NS,0,2	KRT75	75	2	1	Substitution - Missense(1)	large_intestine(1)	c.G1580A						scavenged	.	C	GLN/ARG	495,3911	230.4+/-244.6	28,439,1736	159.0	158.0	158.0		1580	4.8	1.0	12	dbSNP_129	158	1401,7199	270.1+/-288.8	115,1171,3014	yes	missense	KRT75	NM_004693.2	43	143,1610,4750	TT,TC,CC		16.2907,11.2347,14.5779	probably-damaging	527/552	52818377	1896,11110	2203	4300	6503	SO:0001583	missense	9119	exon9			AAGCCCCGGTTGC	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.1580G>A	12.37:g.52818377C>T	ENSP00000252245:p.Arg527Gln	Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	182	84	0.461538	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	346	0.15842490842490842	41	0.08333333333333333	78	0.2154696132596685	95	0.1660839160839161	132	0.1741424802110818	C	15.92	2.976106	0.53720	0.112347	0.162907	ENSG00000170454	ENST00000252245	D	0.87809	-2.3	4.83	4.83	0.62350	.	0.000000	0.40064	N	0.001187	T	0.00328	0.0010	L	0.43152	1.355	0.30791	P	0.7408779999999999	D	0.89917	1.0	D	0.74023	0.982	T	0.18935	-1.0321	9	0.16420	T	0.52	.	13.2889	0.60260	0.0:1.0:0.0:0.0	.	527	O95678	K2C75_HUMAN	Q	527	ENSP00000252245:R527Q	ENSP00000252245:R527Q	R	-	2	0	KRT75	51104644	0.574000	0.26684	0.995000	0.50966	0.493000	0.33554	1.022000	0.30052	2.503000	0.84419	0.561000	0.74099	CGG	C|0.848;T|0.152	0.152	strong		0.622	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
TMEM170B	100113407	hgsc.bcm.edu	37	6	11538534	11538534	+	Silent	SNP	C	C	T	rs821443	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	19	19	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	
BMP5	653	hgsc.bcm.edu	37	6	55739553	55739553	+	Silent	SNP	A	A	G	rs3734444	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:55739553A>G	ENST00000370830.3	-	1	809	c.111T>C	c.(109-111)agT>agC	p.S37S	BMP5_ENST00000446683.2_Silent_p.S37S	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	37					cartilage development (GO:0051216)|growth (GO:0040007)|male genitalia development (GO:0030539)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of steroid biosynthetic process (GO:0010894)|ossification (GO:0001503)|pattern specification process (GO:0007389)|positive regulation of dendrite development (GO:1900006)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)|type B pancreatic cell development (GO:0003323)	extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	45	Lung NSC(77;0.0462)		LUSC - Lung squamous cell carcinoma(124;0.181)			TATAAATAAAACTGGAGTGAA	0.433													A|||	2179	0.435104	0.6256	0.5259	5008	,	,		16999	0.1875		0.4592	False		,,,				2504	0.3436				p.S37S		Atlas-SNP	.											.	BMP5	94	.	0			c.T111C						PASS	.	A		2659,1747	646.8+/-398.4	799,1061,343	173.0	173.0	173.0		111	4.6	1.0	6	dbSNP_107	173	3721,4879	529.0+/-381.5	793,2135,1372	no	coding-synonymous	BMP5	NM_021073.2		1592,3196,1715	GG,GA,AA		43.2674,39.6505,49.0543		37/455	55739553	6380,6626	2203	4300	6503	SO:0001819	synonymous_variant	653	exon1			AATAAAACTGGAG		CCDS4958.1	6p12.1	2014-01-30			ENSG00000112175	ENSG00000112175		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1072	protein-coding gene	gene with protein product		112265				1427904, 11580864	Standard	NM_021073		Approved		uc003pcq.3	P22003	OTTHUMG00000014903	ENST00000370830.3:c.111T>C	6.37:g.55739553A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Silent	SNP	ENST00000370830.3	37	CCDS4958.1																																																																																			A|0.533;G|0.467	0.467	strong		0.433	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1		
TOLLIP	54472	hgsc.bcm.edu	37	11	1309956	1309956	+	Silent	SNP	C	C	T	rs3750920	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1309956C>T	ENST00000317204.6	-	4	540	c.417G>A	c.(415-417)ccG>ccA	p.P139P	TOLLIP_ENST00000263646.7_Silent_p.P111P|TOLLIP_ENST00000528719.1_5'UTR|TOLLIP_ENST00000527886.1_Silent_p.P70P|TOLLIP_ENST00000527938.1_Intron|TOLLIP_ENST00000525159.1_Silent_p.P78P|TOLLIP_ENST00000542915.1_Silent_p.P89P	NM_019009.3	NP_061882.2	Q9H0E2	TOLIP_HUMAN	toll interacting protein	139					autophagy (GO:0006914)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte activation (GO:0045321)|phosphorylation (GO:0016310)|positive regulation of protein sumoylation (GO:0033235)|protein localization to endosome (GO:0036010)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|interleukin-1 receptor complex (GO:0045323)|interleukin-18 receptor complex (GO:0045092)|nuclear body (GO:0016604)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|signal transducer activity (GO:0004871)|Toll-like receptor binding (GO:0035325)			large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	6		all_cancers(49;7.62e-05)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.00152)|Lung(200;0.09)|LUSC - Lung squamous cell carcinoma(625;0.107)		TCAGGGACTCCGGGATGGTGA	0.637													c|||	1803	0.360024	0.2761	0.3415	5008	,	,		17466	0.3165		0.4573	False		,,,				2504	0.4315				p.P139P		Atlas-SNP	.											TOLLIP,NS,carcinoma,0,1	TOLLIP	25	1	0			c.G417A						scavenged	.			1317,3087	440.2+/-345.9	205,907,1090	157.0	96.0	117.0		417	-4.6	0.7	11	dbSNP_107	117	3776,4820	535.5+/-382.8	847,2082,1369	no	coding-synonymous	TOLLIP	NM_019009.3		1052,2989,2459	TT,TC,CC		43.9274,29.9046,39.1769		139/275	1309956	5093,7907	2202	4298	6500	SO:0001819	synonymous_variant	54472	exon4			GGACTCCGGGATG	AJ242972	CCDS7723.1	11p	2008-02-05			ENSG00000078902	ENSG00000078902			16476	protein-coding gene	gene with protein product		606277				9426216, 10854325	Standard	NM_019009		Approved	IL-1RAcPIP	uc001lte.3	Q9H0E2	OTTHUMG00000133333	ENST00000317204.6:c.417G>A	11.37:g.1309956C>T		Somatic	152	2	0.0131579		WXS	Illumina HiSeq	Phase_I	154	82	0.532468	NM_019009	B3KXC6|Q9H9E6|Q9UJ69	Silent	SNP	ENST00000317204.6	37	CCDS7723.1																																																																																			C|0.625;T|0.375	0.375	strong		0.637	TOLLIP-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000257162.2	NM_019009	
KRT84	3890	hgsc.bcm.edu	37	12	52777578	52777578	+	Missense_Mutation	SNP	C	C	T	rs386763043|rs1613931	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52777578C>T	ENST00000257951.3	-	2	617	c.551G>A	c.(550-552)cGg>cAg	p.R184Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	184	Coil 1A.|Rod.		R -> Q (in dbSNP:rs1613931).		hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)	p.R184L(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CTCTAGGAACCGAACCTAAAT	0.493													C|||	1664	0.332268	0.6172	0.3199	5008	,	,		22846	0.1954		0.2068	False		,,,				2504	0.226				p.R184Q		Atlas-SNP	.											KRT84,colon,carcinoma,0,1	KRT84	61	1	1	Substitution - Missense(1)	large_intestine(1)	c.G551A						PASS	.	C	GLN/ARG	2138,2268		715,708,780	57.0	58.0	57.0		551	5.3	1.0	12	dbSNP_89	57	1299,7301		180,939,3181	yes	missense	KRT84	NM_033045.3	43	895,1647,3961	TT,TC,CC		15.1047,48.5247,26.4263	probably-damaging	184/601	52777578	3437,9569	2203	4300	6503	SO:0001583	missense	3890	exon2			AGGAACCGAACCT	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.551G>A	12.37:g.52777578C>T	ENSP00000257951:p.Arg184Gln	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	113	44	0.389381	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	664	0.304029304029304	288	0.5853658536585366	100	0.27624309392265195	117	0.20454545454545456	159	0.20976253298153033	C	36	5.730439	0.96856	0.485247	0.151047	ENSG00000161849	ENST00000257951	D	0.92099	-2.97	5.32	5.32	0.75619	Filament (1);	0.000000	0.45867	D	0.000325	T	0.00012	0.0000	M	0.87180	2.865	0.21355	P	0.999713097	D	0.89917	1.0	D	0.91635	0.999	T	0.21415	-1.0246	9	0.72032	D	0.01	.	19.5787	0.95455	0.0:1.0:0.0:0.0	rs1613931;rs61083896	184	Q9NSB2	KRT84_HUMAN	Q	184	ENSP00000257951:R184Q	ENSP00000257951:R184Q	R	-	2	0	KRT84	51063845	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	5.903000	0.69877	2.941000	0.99782	0.655000	0.94253	CGG	C|0.686;T|0.314	0.314	strong		0.493	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
KRT32	3882	hgsc.bcm.edu	37	17	39623363	39623363	+	Missense_Mutation	SNP	T	T	C	rs3744786	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39623363T>C	ENST00000225899.3	-	1	318	c.215A>G	c.(214-216)cAg>cGg	p.Q72R	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	72	Head.		Q -> R (in dbSNP:rs3744786).		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)				ACTGGCTGCCTGGCAGGAACT	0.602													C|||	1630	0.325479	0.1672	0.3963	5008	,	,		18029	0.3413		0.3032	False		,,,				2504	0.4959				p.Q72R		Atlas-SNP	.											.	KRT32	57	.	0			c.A215G						PASS	.	C	ARG/GLN	852,3554	728.1+/-409.9	77,698,1428	42.0	45.0	44.0		215	-2.1	0.0	17	dbSNP_107	44	2815,5785	656.2+/-401.3	466,1883,1951	yes	missense	KRT32	NM_002278.3	43	543,2581,3379	CC,CT,TT		32.7326,19.3373,28.1947	benign	72/449	39623363	3667,9339	2203	4300	6503	SO:0001583	missense	3882	exon1			GCTGCCTGGCAGG	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.215A>G	17.37:g.39623363T>C	ENSP00000225899:p.Gln72Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	634	0.2902930402930403	85	0.17276422764227642	155	0.4281767955801105	175	0.30594405594405594	219	0.28891820580474936	C	0.807	-0.753225	0.03041	0.193373	0.327326	ENSG00000108759	ENST00000225899	T	0.81163	-1.46	4.87	-2.1	0.07210	.	0.966650	0.08412	N	0.949751	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	0.21245	-1.0251	9	0.23891	T	0.37	.	10.2254	0.43222	0.0:0.4491:0.0:0.5509	rs3744786;rs57183809;rs3744786	72	Q14532	K1H2_HUMAN	R	72	ENSP00000225899:Q72R	ENSP00000225899:Q72R	Q	-	2	0	KRT32	36876889	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.471000	0.06631	-0.904000	0.03876	-1.977000	0.00459	CAG	C|0.286;N|0.000	0.286	strong		0.602	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
PBK	55872	hgsc.bcm.edu	37	8	27667969	27667969	+	Silent	SNP	C	C	G	rs2294092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:27667969C>G	ENST00000301905.4	-	8	1285	c.822G>C	c.(820-822)gcG>gcC	p.A274A	ESCO2_ENST00000397418.2_Intron|PBK_ENST00000522944.1_Silent_p.A285A	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	274	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		TAGTTCCCAACGCTGCATAGT	0.348													G|||	2100	0.419329	0.4289	0.4179	5008	,	,		21634	0.3829		0.4592	False		,,,				2504	0.4039				p.A274A		Atlas-SNP	.											.	PBK	29	.	0			c.G822C						PASS	.	G		1863,2543	632.3+/-395.8	398,1067,738	119.0	108.0	112.0		822	-1.2	1.0	8	dbSNP_100	112	3804,4796	612.0+/-395.9	843,2118,1339	no	coding-synonymous	PBK	NM_018492.2		1241,3185,2077	GG,GC,CC		44.2326,42.2833,43.5722		274/323	27667969	5667,7339	2203	4300	6503	SO:0001819	synonymous_variant	55872	exon8			TCCCAACGCTGCA	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.822G>C	8.37:g.27667969C>G		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	202	129	0.638614	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Silent	SNP	ENST00000301905.4	37	CCDS6063.1																																																																																			C|0.567;G|0.433	0.433	strong		0.348	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12888397	12888397	+	Missense_Mutation	SNP	C	C	T	rs202156326	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:12888397C>T	ENST00000535591.1	-	2	322	c.127G>A	c.(127-129)Gat>Aat	p.D43N		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	43					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)			p.D43N(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						TCAAGCCCATCGAGCACAGCT	0.627													.|||	63	0.0125799	0.0454	0.0043	5008	,	,		16628	0.0		0.0	False		,,,				2504	0.0				p.D43N		Atlas-SNP	.											PRAMEF11,NS,other,0,1	PRAMEF11	72	1	1	Substitution - Missense(1)	pancreas(1)	c.G127A						scavenged	.																																			SO:0001583	missense	440560	exon2			GCCCATCGAGCAC	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.127G>A	1.37:g.12888397C>T	ENSP00000439551:p.Asp43Asn	Somatic	505	102	0.20198		WXS	Illumina HiSeq	Phase_I	351	79	0.225071	NM_001146344		Missense_Mutation	SNP	ENST00000535591.1	37	CCDS53268.1	.	.	.	.	.	.	.	.	.	.	.	13.12	2.143414	0.37825	.	.	ENSG00000204513	ENST00000535591;ENST00000331684;ENST00000437584	T;T	0.05996	3.36;3.36	1.45	1.45	0.22620	.	0.744226	0.12606	N	0.454302	T	0.10766	0.0263	M	0.77712	2.385	0.09310	N	1	D	0.53745	0.962	P	0.44921	0.464	T	0.18366	-1.0339	10	0.87932	D	0	.	6.4008	0.21638	0.0:1.0:0.0:0.0	.	43	O60813	PRA11_HUMAN	N	43;84;43	ENSP00000439551:D43N;ENSP00000391839:D43N	ENSP00000328783:D84N	D	-	1	0	PRAMEF11	12810984	0.004000	0.15560	0.007000	0.13788	0.013000	0.08279	0.287000	0.18920	1.122000	0.41944	0.380000	0.24917	GAT	C|0.250;T|0.750	0.750	weak		0.627	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
PDE4A	5141	hgsc.bcm.edu	37	19	10577843	10577843	+	Missense_Mutation	SNP	C	C	A	rs1051738	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:10577843C>A	ENST00000352831.6	+	15	2317	c.2207C>A	c.(2206-2208)gCg>gAg	p.A736E	PDE4A_ENST00000380702.2_Missense_Mutation_p.A714E|PDE4A_ENST00000592685.1_Missense_Mutation_p.A714E|PDE4A_ENST00000440014.2_Missense_Mutation_p.A675E|PDE4A_ENST00000344979.3_Missense_Mutation_p.A497E|PDE4A_ENST00000293683.5_Missense_Mutation_p.A710E	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	736			A -> E (in dbSNP:rs1051738). {ECO:0000269|PubMed:2160582, ECO:0000269|PubMed:7772058}.		cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)	p.A497E(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	GCATTGACTGCGCAGGGATTG	0.562													c|||	943	0.188299	0.3033	0.1369	5008	,	,		20073	0.1389		0.1521	False		,,,				2504	0.1575				p.A736E		Atlas-SNP	.											PDE4A,NS,carcinoma,0,1	PDE4A	236	1	1	Substitution - Missense(1)	stomach(1)	c.C2207A						PASS	.		GLU/ALA,GLU/ALA,GLU/ALA,GLU/ALA	1259,3147	430.6+/-342.6	174,911,1118	79.0	68.0	72.0		2207,2129,2024,1490	-4.4	0.0	19	dbSNP_86	72	1536,7064	288.5+/-298.8	136,1264,2900	yes	missense,missense,missense,missense	PDE4A	NM_001111307.1,NM_001111308.1,NM_001111309.1,NM_006202.2	107,107,107,107	310,2175,4018	AA,AC,CC		17.8605,28.5747,21.4901	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	736/887,710/861,675/826,497/648	10577843	2795,10211	2203	4300	6503	SO:0001583	missense	5141	exon15			TGACTGCGCAGGG		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"""Phosphodiesterases"""	8780	protein-coding gene	gene with protein product	"""phosphodiesterase E2 dunce homolog (Drosophila)"""	600126	"""phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"""	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.2207C>A	19.37:g.10577843C>A	ENSP00000270474:p.Ala736Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	115	113	0.982609	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	37	CCDS45961.1	388	0.17765567765567766	141	0.2865853658536585	60	0.16574585635359115	64	0.11188811188811189	123	0.16226912928759896	c	12.92	2.081865	0.36758	0.285747	0.178605	ENSG00000065989	ENST00000380702;ENST00000352831;ENST00000293683;ENST00000440014;ENST00000344979	T;T;T;T;T	0.68181	-0.29;-0.29;-0.31;-0.29;-0.02	4.22	-4.39	0.03611	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P;P;B	0.45044	0.524;0.712;0.849;0.22	B;B;B;B	0.43990	0.209;0.209;0.438;0.13	T	0.04153	-1.0973	8	0.20046	T	0.44	.	1.5445	0.02562	0.1194:0.281:0.2644:0.3353	rs1051738;rs3192118;rs12985325;rs17000756;rs17000757;rs52837164;rs56425781;rs60390680;rs1051738	497;675;710;736	P27815-4;P27815-6;P27815-2;P27815	.;.;.;PDE4A_HUMAN	E	714;736;710;675;497	ENSP00000370078:A714E;ENSP00000270474:A736E;ENSP00000293683:A710E;ENSP00000394754:A675E;ENSP00000341007:A497E	ENSP00000293683:A710E	A	+	2	0	PDE4A	10438843	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.502000	0.02279	-0.449000	0.07117	-0.330000	0.08379	GCG	A|0.205;C|0.795	0.205	strong		0.562	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		
FAM149A	25854	hgsc.bcm.edu	37	4	187078745	187078745	+	Missense_Mutation	SNP	A	A	G	rs113168248	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187078745A>G	ENST00000356371.5	+	8	1474	c.1474A>G	c.(1474-1476)Aaa>Gaa	p.K492E	FAM149A_ENST00000389354.5_Missense_Mutation_p.K201E|FAM149A_ENST00000514153.1_Missense_Mutation_p.K201E|FAM149A_ENST00000502970.1_Missense_Mutation_p.K201E|FAM149A_ENST00000503432.1_Missense_Mutation_p.K201E|FAM149A_ENST00000227065.4_Missense_Mutation_p.K201E|FAM149A_ENST00000514829.1_3'UTR			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	492										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		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;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		AGAAACATTGAAAGTGGCTGG	0.468													A|||	11	0.00219649	0.0008	0.0043	5008	,	,		20772	0.0		0.007	False		,,,				2504	0.0				p.K201E		Atlas-SNP	.											.	FAM149A	52	.	0			c.A601G						PASS	.	A	GLU/LYS,GLU/LYS	6,4400	11.4+/-27.6	0,6,2197	70.0	80.0	77.0		601,601	3.5	0.1	4	dbSNP_132	77	62,8538	37.8+/-93.5	0,62,4238	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	56,56	0,68,6435	GG,GA,AA		0.7209,0.1362,0.5228	benign,benign	201/483,201/483	187078745	68,12938	2203	4300	6503	SO:0001583	missense	25854	exon7			ACATTGAAAGTGG	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.1474A>G	4.37:g.187078745A>G	ENSP00000348732:p.Lys492Glu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	5	0.131579	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	A	8.161	0.789539	0.16258	0.001362	0.007209	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	T;T;T;T;T;T	0.13420	2.68;2.59;2.68;2.68;2.68;2.68	5.97	3.47	0.39725	.	0.209202	0.42821	D	0.000654	T	0.08403	0.0209	L	0.53729	1.69	0.09310	N	1	P;B;P	0.42692	0.525;0.217;0.787	B;B;B	0.40199	0.182;0.089;0.322	T	0.13602	-1.0503	10	0.22706	T	0.39	-18.2705	6.3912	0.21587	0.7847:0.0:0.0763:0.139	.	492;492;201	A5PLN7-3;A5PLN7;B4DHZ9	.;F149A_HUMAN;.	E	201;492;201;201;201;201	ENSP00000426835:K201E;ENSP00000348732:K492E;ENSP00000227065:K201E;ENSP00000427155:K201E;ENSP00000424380:K201E;ENSP00000374005:K201E	ENSP00000227065:K201E	K	+	1	0	FAM149A	187315739	0.986000	0.35501	0.050000	0.19076	0.009000	0.06853	3.318000	0.51975	1.056000	0.40484	0.524000	0.50904	AAA	A|0.995;G|0.005	0.005	strong		0.468	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
PAK7	57144	hgsc.bcm.edu	37	20	9523244	9523244	+	Missense_Mutation	SNP	C	C	T	rs150828790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:9523244C>T	ENST00000378429.3	-	10	2539	c.1993G>A	c.(1993-1995)Gac>Aac	p.D665N	PAK7_ENST00000378423.1_Missense_Mutation_p.D665N|PAK7_ENST00000353224.5_Missense_Mutation_p.D665N	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	665	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			TTGTGTAGGTCCTTCACTCTT	0.478													C|||	3	0.000599042	0.0008	0.0	5008	,	,		20256	0.0		0.002	False		,,,				2504	0.0				p.D665N		Atlas-SNP	.											.	PAK7	194	.	0			c.G1993A						PASS	.	C	ASN/ASP,ASN/ASP	0,4406		0,0,2203	156.0	158.0	157.0		1993,1993	5.5	1.0	20	dbSNP_134	157	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	PAK7	NM_020341.3,NM_177990.2	23,23	0,18,6485	TT,TC,CC		0.2093,0.0,0.1384	benign,benign	665/720,665/720	9523244	18,12988	2203	4300	6503	SO:0001583	missense	57144	exon9			GTAGGTCCTTCAC	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.1993G>A	20.37:g.9523244C>T	ENSP00000367686:p.Asp665Asn	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	189	96	0.507937	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	13.57	2.276632	0.40294	0.0	0.002093	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423	T;T;T	0.13538	2.58;2.58;2.58	5.48	5.48	0.80851	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.042605	0.85682	D	0.000000	T	0.12263	0.0298	N	0.25992	0.78	0.58432	D	0.999996	B	0.09022	0.002	B	0.10450	0.005	T	0.15492	-1.0435	9	.	.	.	.	19.3557	0.94412	0.0:1.0:0.0:0.0	.	665	Q9P286	PAK7_HUMAN	N	665	ENSP00000367686:D665N;ENSP00000322957:D665N;ENSP00000367679:D665N	.	D	-	1	0	PAK7	9471244	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.034000	0.57289	2.597000	0.87782	0.655000	0.94253	GAC	C|0.999;T|0.001	0.001	strong		0.478	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
ATP13A5	344905	hgsc.bcm.edu	37	3	193080414	193080414	+	Missense_Mutation	SNP	C	C	G	rs6797429	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:193080414C>G	ENST00000342358.4	-	4	514	c.397G>C	c.(397-399)Gaa>Caa	p.E133Q		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	133			E -> Q (in dbSNP:rs6797429).			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		TTCTGCACTTCCATGCACCGC	0.483													G|||	2573	0.513778	0.646	0.5259	5008	,	,		21621	0.3859		0.5288	False		,,,				2504	0.4427				p.E133Q		Atlas-SNP	.											.	ATP13A5	171	.	0			c.G397C						PASS	.	G	GLN/GLU	2716,1690	513.1+/-368.2	845,1026,332	142.0	137.0	138.0		397	5.6	0.8	3	dbSNP_116	138	4451,4149	566.6+/-388.7	1179,2093,1028	yes	missense	ATP13A5	NM_198505.2	29	2024,3119,1360	GG,GC,CC		48.2442,38.3568,44.8947	benign	133/1219	193080414	7167,5839	2203	4300	6503	SO:0001583	missense	344905	exon4			GCACTTCCATGCA	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.397G>C	3.37:g.193080414C>G	ENSP00000341942:p.Glu133Gln	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	1159	0.5306776556776557	317	0.6443089430894309	202	0.5580110497237569	233	0.40734265734265734	407	0.5369393139841688	G	0.411	-0.913282	0.02415	0.616432	0.517558	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.26223	1.75;1.75	5.6	5.6	0.85130	.	0.268854	0.32548	N	0.005941	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31392	-0.9945	9	0.09590	T	0.72	-2.1229	13.3521	0.60607	0.0:0.3026:0.6974:0.0	rs6797429;rs59343082;rs6797429	133	Q4VNC0	AT135_HUMAN	Q	133;155	ENSP00000341942:E133Q;ENSP00000389416:E155Q	ENSP00000341942:E133Q	E	-	1	0	ATP13A5	194563108	1.000000	0.71417	0.815000	0.32552	0.069000	0.16628	2.617000	0.46385	1.534000	0.49203	-0.120000	0.15030	GAA	C|0.453;G|0.547	0.547	strong		0.483	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
KLHL34	257240	hgsc.bcm.edu	37	X	21675125	21675125	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:21675125G>A	ENST00000379499.2	-	1	1323	c.782C>T	c.(781-783)aCg>aTg	p.T261M		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	261						extracellular space (GO:0005615)				cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						GCGGGAGGGCGTCGTGTGGTA	0.706													G|||	1	0.000264901	0.0	0.0	3775	,	,		9852	0.0		0.0	False		,,,				2504	0.001				p.T261M		Atlas-SNP	.											.	KLHL34	76	.	0			c.C782T						PASS	.						16.0	18.0	17.0					X																	21675125		2197	4282	6479	SO:0001583	missense	257240	exon1			GAGGGCGTCGTGT	AK092279	CCDS14199.1	Xp22.12	2013-02-22	2013-02-22		ENSG00000185915	ENSG00000185915		"""Kelch-like"", ""BTB/POZ domain containing"""	26634	protein-coding gene	gene with protein product			"""kelch-like 34 (Drosophila)"""				Standard	NM_153270		Approved	FLJ34960, RP11-450P7.3	uc004czz.1	Q8N239	OTTHUMG00000021234	ENST00000379499.2:c.782C>T	X.37:g.21675125G>A	ENSP00000368813:p.Thr261Met	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	87	83	0.954023	NM_153270		Missense_Mutation	SNP	ENST00000379499.2	37	CCDS14199.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.747283	0.00086	.	.	ENSG00000185915	ENST00000379499	T	0.72394	-0.65	4.76	3.89	0.44902	.	0.552287	0.18919	N	0.127528	T	0.38480	0.1042	N	0.01168	-0.975	0.09310	N	1	B	0.20887	0.049	B	0.12837	0.008	T	0.24693	-1.0153	10	0.27082	T	0.32	.	8.1602	0.31194	0.0844:0.0:0.7565:0.1591	.	261	Q8N239	KLH34_HUMAN	M	261	ENSP00000368813:T261M	ENSP00000368813:T261M	T	-	2	0	KLHL34	21585046	0.003000	0.15002	0.038000	0.18304	0.365000	0.29674	1.693000	0.37742	0.990000	0.38787	0.422000	0.28245	ACG	.	.	none		0.706	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1	NM_153270	
HS3ST2	9956	hgsc.bcm.edu	37	16	22826339	22826339	+	Silent	SNP	A	A	G	rs208951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:22826339A>G	ENST00000261374.3	+	1	842	c.408A>G	c.(406-408)gtA>gtG	p.V136V		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	136					carbohydrate metabolic process (GO:0005975)|circadian rhythm (GO:0007623)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 2 activity (GO:0033871)|sulfotransferase activity (GO:0008146)			breast(2)|kidney(1)|large_intestine(5)|liver(2)|lung(5)|ovary(1)|pancreas(2)|skin(1)	19				GBM - Glioblastoma multiforme(48;0.0299)		TTATCCGAGTACACCCGGACG	0.642													G|||	2053	0.409944	0.5393	0.4741	5008	,	,		13709	0.3571		0.3688	False		,,,				2504	0.2863				p.V136V		Atlas-SNP	.											.	HS3ST2	59	.	0			c.A408G						PASS	.	G		2219,2135		595,1029,553	18.0	22.0	20.0		408	3.1	1.0	16	dbSNP_79	20	3139,5409		615,1909,1750	no	coding-synonymous	HS3ST2	NM_006043.1		1210,2938,2303	GG,GA,AA		36.722,49.0354,41.5284		136/368	22826339	5358,7544	2177	4274	6451	SO:0001819	synonymous_variant	9956	exon1			CCGAGTACACCCG	AF105374	CCDS10606.1	16p12	2008-02-05			ENSG00000122254	ENSG00000122254	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5195	protein-coding gene	gene with protein product		604056				9988767	Standard	NM_006043		Approved	3OST2	uc002dli.3	Q9Y278	OTTHUMG00000094785	ENST00000261374.3:c.408A>G	16.37:g.22826339A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	134	56	0.41791	NM_006043	Q52LZ1	Silent	SNP	ENST00000261374.3	37	CCDS10606.1																																																																																			A|0.600;G|0.400	0.400	strong		0.642	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043	
GANC	2595	hgsc.bcm.edu	37	15	42643529	42643529	+	Missense_Mutation	SNP	T	T	C	rs7181742	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42643529T>C	ENST00000318010.8	+	23	2774	c.2534T>C	c.(2533-2535)tTt>tCt	p.F845S	RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000356316.3_5'UTR	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	845			F -> S (in dbSNP:rs7181742). {ECO:0000269|PubMed:12370436}.		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)	TATTCCAGTTTTGCTGACCAG	0.488													C|||	1895	0.378395	0.7405	0.3847	5008	,	,		17663	0.1577		0.1332	False		,,,				2504	0.364				p.F845S		Atlas-SNP	.											.	GANC	57	.	0			c.T2534C						PASS	.	C	SER/PHE	2763,1643	503.7+/-365.6	905,953,345	118.0	107.0	111.0		2534	3.5	1.0	15	dbSNP_116	111	1195,7403	763.2+/-407.6	97,1001,3201	yes	missense	GANC	NM_198141.2	155	1002,1954,3546	CC,CT,TT		13.8986,37.2901,30.4368	benign	845/915	42643529	3958,9046	2203	4299	6502	SO:0001583	missense	2595	exon23			CCAGTTTTGCTGA	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.2534T>C	15.37:g.42643529T>C	ENSP00000326227:p.Phe845Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	94	20	0.212766	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	616	0.28205128205128205	334	0.6788617886178862	119	0.3287292817679558	73	0.12762237762237763	90	0.11873350923482849	C	10.48	1.362931	0.24684	0.627099	0.138986	ENSG00000214013	ENST00000318010	D	0.85773	-2.03	5.38	3.48	0.39840	.	0.456476	0.26045	N	0.026670	T	0.00012	0.0000	N	0.00377	-1.585	0.09310	P	0.9999999897697	B	0.02656	0.0	B	0.01281	0.0	T	0.45629	-0.9248	9	0.02654	T	1	-7.2067	4.1575	0.10268	0.0915:0.1781:0.5876:0.1428	rs7181742;rs52820484;rs58917918;rs7181742	845	Q8TET4	GANC_HUMAN	S	845	ENSP00000326227:F845S	ENSP00000447925:F77S	F	+	2	0	GANC	40430821	1.000000	0.71417	1.000000	0.80357	0.562000	0.35680	2.048000	0.41278	0.677000	0.31305	-0.128000	0.14901	TTT	T|0.702;C|0.298	0.298	strong		0.488	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
MYO9A	4649	hgsc.bcm.edu	37	15	72180440	72180440	+	Silent	SNP	C	C	T	rs148060237	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:72180440C>T	ENST00000356056.5	-	27	5632	c.5160G>A	c.(5158-5160)tcG>tcA	p.S1720S	MYO9A_ENST00000564571.1_Silent_p.S1720S|MYO9A_ENST00000444904.1_Silent_p.S1701S|MYO9A_ENST00000563542.1_5'Flank|MYO9A_ENST00000424560.1_Silent_p.S1791S	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1720	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CATCAACTGACGAAAATCGCT	0.333													C|||	38	0.00758786	0.0008	0.0072	5008	,	,		17410	0.0		0.0288	False		,,,				2504	0.0031				p.S1720S		Atlas-SNP	.											.	MYO9A	203	.	0			c.G5160A						PASS	.	C		17,4379	24.3+/-50.5	0,17,2181	119.0	110.0	113.0		5160	0.3	1.0	15	dbSNP_134	113	186,8408	84.0+/-146.5	1,184,4112	no	coding-synonymous	MYO9A	NM_006901.2		1,201,6293	TT,TC,CC		2.1643,0.3867,1.5627		1720/2549	72180440	203,12787	2198	4297	6495	SO:0001819	synonymous_variant	4649	exon27			AACTGACGAAAAT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.5160G>A	15.37:g.72180440C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	57	16	0.280702	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	37	CCDS10239.1																																																																																			C|0.983;T|0.017	0.017	strong		0.333	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
CSMD1	64478	hgsc.bcm.edu	37	8	3165949	3165949	+	Silent	SNP	G	G	C	rs141170475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:3165949G>C	ENST00000520002.1	-	25	4266	c.3711C>G	c.(3709-3711)acC>acG	p.T1237T	CSMD1_ENST00000400186.3_Silent_p.T1237T|CSMD1_ENST00000602557.1_Silent_p.T1237T|CSMD1_ENST00000537824.1_Silent_p.T1236T|CSMD1_ENST00000542608.1_Silent_p.T1236T|CSMD1_ENST00000602723.1_Silent_p.T1237T|CSMD1_ENST00000539096.1_Silent_p.T1236T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1237	Sushi 7. {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)		CTACAGTGTCGGTAAAGTGGC	0.512													G|||	9	0.00179712	0.0008	0.0029	5008	,	,		19169	0.0		0.006	False		,,,				2504	0.0				p.T1236T		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C3708G						PASS	.	G		3,4029		0,3,2013	117.0	109.0	111.0		3708	-10.8	0.0	8	dbSNP_134	111	60,8296		0,60,4118	no	coding-synonymous	CSMD1	NM_033225.5		0,63,6131	CC,CG,GG		0.718,0.0744,0.5086		1236/3565	3165949	63,12325	2016	4178	6194	SO:0001819	synonymous_variant	64478	exon24			AGTGTCGGTAAAG			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.3711C>G	8.37:g.3165949G>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	288	104	0.361111	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		6	0.0027472527472527475	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	0.021	-1.429808	0.01117	7.44E-4	0.00718	ENSG00000183117	ENST00000335551	.	.	.	5.4	-10.8	0.00216	.	.	.	.	.	T	0.30792	0.0776	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54873	-0.8228	4	.	.	.	.	3.0972	0.06313	0.1074:0.4238:0.1731:0.2956	.	.	.	.	G	717	.	.	R	-	1	2	CSMD1	3153356	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	-2.190000	0.01247	-4.494000	0.00046	-2.717000	0.00132	CGA	A|0.000;C|0.004;G|0.996	0.004	strong		0.512	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
KCNK16	83795	hgsc.bcm.edu	37	6	39284148	39284148	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:39284148C>T	ENST00000373229.5	-	5	745	c.732G>A	c.(730-732)ctG>ctA	p.L244L	KCNK17_ENST00000373231.4_5'Flank|KCNK16_ENST00000437525.2_Silent_p.L244L|KCNK16_ENST00000373227.4_Intron|KCNK16_ENST00000507712.1_Intron|KCNK16_ENST00000425054.2_Intron|KCNK17_ENST00000453413.2_5'Flank	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	244					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						CCAGCCACGCCAGGCCCAGGA	0.627																																					p.L244L		Atlas-SNP	.											.	KCNK16	59	.	0			c.G732A						PASS	.						32.0	34.0	33.0					6																	39284148		2203	4300	6503	SO:0001819	synonymous_variant	83795	exon5			CCACGCCAGGCCC	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.732G>A	6.37:g.39284148C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Silent	SNP	ENST00000373229.5	37	CCDS4843.1																																																																																			.	.	none		0.627	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115	
MYBPC1	4604	hgsc.bcm.edu	37	12	102069077	102069077	+	Silent	SNP	A	A	G	rs764291	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:102069077A>G	ENST00000550270.1	+	25	2796	c.2796A>G	c.(2794-2796)ccA>ccG	p.P932P	MYBPC1_ENST00000392934.3_Silent_p.P901P|MYBPC1_ENST00000549145.1_Silent_p.P945P|MYBPC1_ENST00000541119.1_Silent_p.P902P|MYBPC1_ENST00000452455.2_Silent_p.P932P|MYBPC1_ENST00000547509.1_Silent_p.P900P|MYBPC1_ENST00000545503.2_Silent_p.P914P|MYBPC1_ENST00000550501.1_Intron|MYBPC1_ENST00000361685.2_Silent_p.P939P|MYBPC1_ENST00000551300.1_Silent_p.P815P|MYBPC1_ENST00000441232.1_Silent_p.P932P|MYBPC1_ENST00000361466.2_Silent_p.P939P|MYBPC1_ENST00000553190.1_Silent_p.P914P|MYBPC1_ENST00000547405.1_Silent_p.P888P|MYBPC1_ENST00000536007.1_Silent_p.P895P|MYBPC1_ENST00000360610.2_Silent_p.P932P			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	932					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						TAGACCGTCCAGGTCCACCCC	0.448													A|||	719	0.14357	0.0416	0.1297	5008	,	,		23895	0.1091		0.2525	False		,,,				2504	0.2147				p.P939P		Atlas-SNP	.											.	MYBPC1	235	.	0			c.A2817G						PASS	.	A	,,,	363,4043	185.3+/-212.5	15,333,1855	95.0	79.0	84.0		2817,2817,2796,2742	-11.5	0.9	12	dbSNP_86	84	2428,6172	401.6+/-347.2	330,1768,2202	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYBPC1	NM_002465.2,NM_206819.1,NM_206820.1,NM_206821.1	,,,	345,2101,4057	GG,GA,AA		28.2326,8.2388,21.4593	,,,	939/1172,939/1149,932/1142,914/1124	102069077	2791,10215	2203	4300	6503	SO:0001819	synonymous_variant	4604	exon26			CCGTCCAGGTCCA		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.2796A>G	12.37:g.102069077A>G		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	197	89	0.451777	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Silent	SNP	ENST00000550270.1	37	CCDS9085.1																																																																																			A|0.807;G|0.193	0.193	strong		0.448	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
DISC1	27185	hgsc.bcm.edu	37	1	232144598	232144598	+	Missense_Mutation	SNP	A	A	T	rs821616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:232144598A>T	ENST00000439617.2	+	11	2163	c.2110A>T	c.(2110-2112)Agc>Tgc	p.S704C	DISC1_ENST00000535983.1_Missense_Mutation_p.R683S|DISC1_ENST00000366637.3_Missense_Mutation_p.S36C|DISC1_ENST00000427560.1_3'UTR|DISC1_ENST00000537876.1_3'UTR	NM_001164537.1|NM_001164540.1|NM_018662.2	NP_001158009.1|NP_001158012.1|NP_061132.2	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	704	Interaction with ATF4 and ATF5.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.		S -> C (in dbSNP:rs821616). {ECO:0000269|PubMed:10814723, ECO:0000269|PubMed:15939883}.		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)				GCTTATCCAGAGCCTACAGCT	0.522													A|||	1253	0.2502	0.3782	0.1369	5008	,	,		17579	0.1052		0.2873	False		,,,				2504	0.2689				p.S736C		Atlas-SNP	.											.	DISC1	207	.	0			c.A2206T	GRCh37	CM051907	DISC1	M	rs821616	PASS	.	A	CYS/SER,CYS/SER,CYS/SER,CYS/SER,SER/ARG,,CYS/SER	1286,2646		215,856,895	72.0	73.0	73.0		2110,2206,2110,1744,2049,,2110	2.4	0.2	1	dbSNP_86	73	2374,5932		316,1742,2095	yes	missense,missense,missense,missense,missense,utr-3,missense	DISC1	NM_001012957.1,NM_001164537.1,NM_001164538.1,NM_001164540.1,NM_001164541.1,NM_001164547.1,NM_018662.2	112,112,112,112,110,,112	531,2598,2990	TT,TA,AA		28.5817,32.706,29.9068	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging	704/833,736/887,704/804,582/733,683/696,,704/855	232144598	3660,8578	1966	4153	6119	SO:0001583	missense	27185	exon12			ATCCAGAGCCTAC	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	ENST00000439617.2:c.2110A>T	1.37:g.232144598A>T	ENSP00000403888:p.Ser704Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	134	49	0.365672	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000439617.2	37		543|543	0.24862637362637363|0.24862637362637363	192|192	0.3902439024390244|0.3902439024390244	64|64	0.17679558011049723|0.17679558011049723	63|63	0.11013986013986014|0.11013986013986014	224|224	0.2955145118733509|0.2955145118733509	A|A	15.93|15.93	2.976831|2.976831	0.53720|0.53720	0.32706|0.32706	0.285817|0.285817	ENSG00000162946|ENSG00000162946	ENST00000535983;ENST00000422590|ENST00000439617;ENST00000366637;ENST00000366638;ENST00000532576;ENST00000427560	T|T	0.11169|0.10860	2.8|2.83	4.72|4.72	2.37|2.37	0.29283|0.29283	.|.	.|0.192478	.|0.44688	.|D	.|0.000431	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.43439|0.43439	P|P	0.0043840000000000545|0.0043840000000000545	D|D;D;D;D;P;P;D	0.71674|0.76494	0.998|0.997;0.985;0.999;0.999;0.924;0.924;0.969	D|P;P;D;D;P;P;P	0.66979|0.63192	0.948|0.799;0.694;0.912;0.912;0.621;0.621;0.621	T|T	0.43393|0.43393	-0.9394|-0.9394	6|8	.|0.54805	.|T	.|0.06	-7.3327|-7.3327	4.8096|4.8096	0.13337|0.13337	0.687:0.0:0.313:0.0|0.687:0.0:0.313:0.0	rs821616;rs52820800;rs821616|rs821616;rs52820800;rs821616	683|736;582;736;704;582;704;704	C4P0A3|C4P096;C4P094;E2QRA4;C4P098;F5H1F1;Q9NRI5-2;Q9NRI5	.|.;.;.;.;.;.;DISC1_HUMAN	S|C	683;106|704;704;736;582;36	ENSP00000443996:R683S|ENSP00000403888:S704C	.|ENSP00000355597:S704C	R|S	+|+	3|1	2|0	DISC1|DISC1	230211221|230211221	1.000000|1.000000	0.71417|0.71417	0.206000|0.206000	0.23566|0.23566	0.628000|0.628000	0.37860|0.37860	2.731000|2.731000	0.47343|0.47343	0.839000|0.839000	0.34971|0.34971	0.528000|0.528000	0.53228|0.53228	AGA|AGC	A|0.747;T|0.253	0.253	strong		0.522	DISC1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000092351.2	NM_018662	
UBP1	7342	hgsc.bcm.edu	37	3	33434831	33434831	+	Silent	SNP	G	G	A	rs2293250	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:33434831G>A	ENST00000283629.3	-	14	2035	c.1506C>T	c.(1504-1506)acC>acT	p.T502T	UBP1_ENST00000283628.5_Silent_p.T502T|UBP1_ENST00000447368.2_Silent_p.T466T|UBP1_ENST00000486388.1_5'UTR	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	502					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						TGTGAATACCGGTGGGACCCT	0.368													A|||	2705	0.540136	0.5552	0.6326	5008	,	,		16560	0.6141		0.4732	False		,,,				2504	0.4468				p.T502T		Atlas-SNP	.											.	UBP1	42	.	0			c.C1506T						PASS	.	A	,,	2543,1863	540.7+/-375.6	712,1119,372	79.0	79.0	79.0		1398,1506,1506	-2.0	1.0	3	dbSNP_100	79	3856,4744	609.5+/-395.5	848,2160,1292	no	coding-synonymous,coding-synonymous,coding-synonymous	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	,,	1560,3279,1664	AA,AG,GG		44.8372,42.2833,49.2004	,,	466/505,502/541,502/541	33434831	6399,6607	2203	4300	6503	SO:0001819	synonymous_variant	7342	exon14			AATACCGGTGGGA	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.1506C>T	3.37:g.33434831G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	112	48	0.428571	NM_014517	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Silent	SNP	ENST00000283629.3	37	CCDS2659.1																																																																																			G|0.490;N|0.001	.	strong		0.368	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517	
FAM179A	165186	hgsc.bcm.edu	37	2	29246044	29246044	+	Missense_Mutation	SNP	T	T	C	rs6721861	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:29246044T>C	ENST00000379558.4	+	12	1955	c.1604T>C	c.(1603-1605)gTg>gCg	p.V535A	FAM179A_ENST00000403861.2_Missense_Mutation_p.V480A|FAM179A_ENST00000465300.1_3'UTR	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	535			V -> A (in dbSNP:rs6721861).							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						GTGTGCTTGGTGGTGACTGGG	0.632													C|||	2376	0.474441	0.6218	0.3991	5008	,	,		18661	0.7044		0.3191	False		,,,				2504	0.2515				p.V535A		Atlas-SNP	.											FAM179A,NS,carcinoma,0,1	FAM179A	106	1	0			c.T1604C						scavenged	.	C	ALA/VAL	2279,1877		635,1009,434	26.0	32.0	30.0		1604	4.6	0.6	2	dbSNP_116	30	2777,5625		504,1769,1928	yes	missense	FAM179A	NM_199280.2	64	1139,2778,2362	CC,CT,TT		33.0517,45.1636,40.2612	benign	535/1020	29246044	5056,7502	2078	4201	6279	SO:0001583	missense	165186	exon12			GCTTGGTGGTGAC	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.1604T>C	2.37:g.29246044T>C	ENSP00000368876:p.Val535Ala	Somatic	238	2	0.00840336		WXS	Illumina HiSeq	Phase_I	206	87	0.42233	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	1135	0.5196886446886447	336	0.6829268292682927	153	0.42265193370165743	413	0.722027972027972	233	0.3073878627968338	C	4.363	0.066975	0.08388	0.548364	0.330517	ENSG00000189350	ENST00000379558;ENST00000403861;ENST00000440012	T;T;T	0.14022	2.54;2.54;2.54	5.5	4.61	0.57282	Armadillo-like helical (1);Armadillo-type fold (1);CLASP N-terminal domain (1);	0.095117	0.45867	N	0.000327	T	0.00012	0.0000	N	0.00325	-1.645	0.53688	P	2.199999999996649E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38802	-0.9644	9	0.02654	T	1	.	10.4738	0.44652	0.1336:0.7963:0.0:0.07	rs6721861;rs6721861	480;535	F8W8E4;Q6ZUX3	.;F179A_HUMAN	A	535;480;30	ENSP00000368876:V535A;ENSP00000384699:V480A;ENSP00000396739:V30A	ENSP00000368876:V535A	V	+	2	0	FAM179A	29099548	0.997000	0.39634	0.553000	0.28255	0.740000	0.42216	3.939000	0.56591	0.680000	0.31366	-0.128000	0.14901	GTG	T|0.456;C|0.544	0.544	strong		0.632	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
E2F4	1874	hgsc.bcm.edu	37	16	67233266	67233266	+	IGR	SNP	A	A	C	rs12923138	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:67233266A>C	ENST00000379378.3	+	0	2096				MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000393997.2_Missense_Mutation_p.K66Q|ELMO3_ENST00000360833.1_Missense_Mutation_p.K66Q|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)		GATTGCCATCAAGATGCGTGA	0.682													C|||	2989	0.596845	0.9614	0.4308	5008	,	,		9802	0.4117		0.4612	False		,,,				2504	0.5521				p.K66Q		Atlas-SNP	.											.	ELMO3	41	.	0			c.A196C						PASS	.	C	GLN/LYS	3688,520		1635,418,51	32.0	40.0	37.0		196	4.2	1.0	16	dbSNP_121	37	3712,4724		832,2048,1338	yes	missense	ELMO3	NM_024712.3	53	2467,2466,1389	CC,CA,AA		44.0019,12.3574,41.4742	benign	66/774	67233266	7400,5244	2104	4218	6322	SO:0001628	intergenic_variant	79767	exon1			GCCATCAAGATGC	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.67233266A>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	43	7	0.162791	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	1205	0.5517399267399268	469	0.9532520325203252	173	0.47790055248618785	220	0.38461538461538464	343	0.4525065963060686	C	8.190	0.795820	0.16327	0.876426	0.440019	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.13901	2.55;2.55	5.19	4.18	0.49190	.	0.078682	0.52532	N	0.000076	T	0.00012	0.0000	N	0.00392	-1.555	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33904	-0.9850	9	0.21014	T	0.42	-13.512	7.9999	0.30291	0.1828:0.6409:0.1763:0.0	rs12923138;rs60324424;rs12923138	66;66	F8W9E7;Q96BJ8-3	.;.	Q	66	ENSP00000354077:K66Q;ENSP00000377566:K66Q	ENSP00000354077:K66Q	K	+	1	0	ELMO3	65790767	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	2.004000	0.40854	1.197000	0.43143	-0.215000	0.12644	AAG	A|0.448;C|0.552	0.552	strong		0.682	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
ERMARD	55780	hgsc.bcm.edu	37	6	170169688	170169688	+	Missense_Mutation	SNP	A	A	G	rs61738268	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170169688A>G	ENST00000366773.3	+	12	1145	c.1112A>G	c.(1111-1113)cAt>cGt	p.H371R	ERMARD_ENST00000392095.4_Missense_Mutation_p.H245R|ERMARD_ENST00000366772.2_Missense_Mutation_p.H371R|ERMARD_ENST00000418781.3_Missense_Mutation_p.H371R|RP1-266L20.9_ENST00000586101.1_RNA|ERMARD_ENST00000588451.1_Missense_Mutation_p.H235R	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	371					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											ATAAGAGATCATTTAAGCCAC	0.388													A|||	37	0.00738818	0.0	0.013	5008	,	,		16813	0.0		0.0119	False		,,,				2504	0.0164				p.H371R		Atlas-SNP	.											.	C6orf70	63	.	0			c.A1112G						PASS	.	A	ARG/HIS	5,4401		0,5,2198	58.0	54.0	56.0		1112	-4.5	0.0	6	dbSNP_129	56	108,8492		2,104,4194	yes	missense	C6orf70	NM_018341.1	29	2,109,6392	GG,GA,AA		1.2558,0.1135,0.8688	benign	371/679	170169688	113,12893	2203	4300	6503	SO:0001583	missense	55780	exon12			GAGATCATTTAAG	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1112A>G	6.37:g.170169688A>G	ENSP00000355735:p.His371Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	20	0.009157509157509158	0	0.0	8	0.022099447513812154	0	0.0	12	0.0158311345646438	.	0.029	-1.347487	0.01266	0.001135	0.012558	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.35605	1.3;1.36	5.34	-4.53	0.03462	.	0.650998	0.14673	N	0.305256	T	0.06690	0.0171	N	0.12502	0.225	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.09377	0.004;0.003;0.001	T	0.34254	-0.9836	10	0.20519	T	0.43	.	15.5024	0.75709	0.816:0.0:0.184:0.0	rs61738268	371;371;371	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	R	371;371;371;245;19	ENSP00000355735:H371R;ENSP00000375945:H245R	ENSP00000355733:H19R	H	+	2	0	C6orf70	169911613	0.000000	0.05858	0.000000	0.03702	0.473000	0.32948	-1.487000	0.02310	-0.732000	0.04856	-0.426000	0.05927	CAT	A|0.991;G|0.009	0.009	strong		0.388	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
CSRP2BP	57325	hgsc.bcm.edu	37	20	18168099	18168099	+	Missense_Mutation	SNP	G	G	A	rs376874386		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:18168099G>A	ENST00000435364.3	+	10	2686	c.2345G>A	c.(2344-2346)cGc>cAc	p.R782H	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.R781H|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.R654H	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	782	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						AGGCTCCGGCGCTGATGCGAA	0.413																																					p.R782H		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.G2345A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	73.0	73.0	73.0		2345	5.9	1.0	20		73	1,8599	1.2+/-3.3	0,1,4299	no	missense	CSRP2BP	NM_020536.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	782/783	18168099	1,13005	2203	4300	6503	SO:0001583	missense	57325	exon10			TCCGGCGCTGATG	AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"""cysteine rich protein 2 binding protein"", ""ATAC component 2 homolog (Drosophila)"""					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.2345G>A	20.37:g.18168099G>A	ENSP00000392318:p.Arg782His	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	G	36	5.598337	0.96614	0.0	1.16E-4	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.28666	1.6;1.61;1.6;1.63	5.87	5.87	0.94306	GCN5-related N-acetyltransferase (GNAT) domain (1);	0.000000	0.85682	D	0.000000	T	0.58779	0.2146	M	0.72576	2.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.58945	-0.7546	10	0.87932	D	0	.	20.2147	0.98293	0.0:0.0:1.0:0.0	.	654;782	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	H	782;781;782;654	ENSP00000278816:R782H;ENSP00000366909:R781H;ENSP00000392318:R782H;ENSP00000425909:R654H	ENSP00000278816:R782H	R	+	2	0	CSRP2BP	18116099	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.750000	0.98875	2.785000	0.95823	0.591000	0.81541	CGC	.	.	weak		0.413	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536	
OR51S1	119692	hgsc.bcm.edu	37	11	4870139	4870139	+	Silent	SNP	G	G	A	rs11602455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4870139G>A	ENST00000322101.2	-	1	375	c.300C>T	c.(298-300)gtC>gtT	p.V100V	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_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	126	0	0		WXS	Illumina HiSeq	Phase_I	124	120	0.967742	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	
HS1BP3	64342	hgsc.bcm.edu	37	2	20818764	20818764	+	Missense_Mutation	SNP	C	C	T	rs3732149	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:20818764C>T	ENST00000304031.3	-	7	1187	c.1162G>A	c.(1162-1164)Gcc>Acc	p.A388T		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	388			A -> T (in dbSNP:rs3732149). {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)					AGGCTGGGGGCGGCCTGGGCT	0.637													C|||	743	0.148363	0.1248	0.1398	5008	,	,		16574	0.0913		0.2048	False		,,,				2504	0.1871				p.A388T		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G1162A						PASS	.	C	THR/ALA	611,3795	265.3+/-266.6	43,525,1635	76.0	84.0	81.0		1162	-1.7	0.0	2	dbSNP_107	81	1793,6807	321.5+/-315.1	190,1413,2697	yes	missense	HS1BP3	NM_022460.3	58	233,1938,4332	TT,TC,CC		20.8488,13.8675,18.4838	benign	388/393	20818764	2404,10602	2203	4300	6503	SO:0001583	missense	64342	exon7			TGGGGGCGGCCTG		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.1162G>A	2.37:g.20818764C>T	ENSP00000305193:p.Ala388Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	179	70	0.391061	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Missense_Mutation	SNP	ENST00000304031.3	37	CCDS1700.1	310	0.14194139194139194	66	0.13414634146341464	59	0.16298342541436464	44	0.07692307692307693	141	0.18601583113456466	C	0.009	-1.802600	0.00611	0.138675	0.208488	ENSG00000118960	ENST00000304031	T	0.20200	2.09	5.84	-1.71	0.08133	.	0.813759	0.10956	N	0.615542	T	0.00012	0.0000	L	0.54323	1.7	0.28058	P	0.9330867	B	0.13594	0.008	B	0.08055	0.003	T	0.41770	-0.9490	9	0.14656	T	0.56	-2.4403	5.7246	0.18006	0.1467:0.3933:0.0:0.46	rs3732149;rs17662808;rs17855692;rs3732149	388	Q53T59	H1BP3_HUMAN	T	388	ENSP00000305193:A388T	ENSP00000305193:A388T	A	-	1	0	HS1BP3	20682245	0.000000	0.05858	0.015000	0.15790	0.064000	0.16182	-1.464000	0.02359	-0.708000	0.05015	-1.202000	0.01658	GCC	C|0.834;T|0.166	0.166	strong		0.637	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
VCAM1	7412	hgsc.bcm.edu	37	1	101203698	101203698	+	Silent	SNP	C	C	T	rs3176878	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:101203698C>T	ENST00000294728.2	+	9	2180	c.2079C>T	c.(2077-2079)gaC>gaT	p.D693D	VCAM1_ENST00000370119.4_Silent_p.D631D|VCAM1_ENST00000370115.1_Silent_p.D494D|VCAM1_ENST00000347652.2_Silent_p.D601D	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	225	0	0		WXS	Illumina HiSeq	Phase_I	112	78	0.696429	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	
TRIM22	10346	hgsc.bcm.edu	37	11	5730294	5730294	+	Silent	SNP	C	C	T	rs61735276	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5730294C>T	ENST00000379965.3	+	8	1190	c.913C>T	c.(913-915)Ctg>Ttg	p.L305L	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	305	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)			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)		GGACGTGATGCTGAATCCAGG	0.398													C|||	166	0.033147	0.0257	0.0418	5008	,	,		20353	0.0		0.0437	False		,,,				2504	0.0603				p.L305L	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.C913T						PASS	.	C	,	94,3848		0,94,1877	107.0	99.0	101.0		901,913	0.1	0.0	11	dbSNP_129	101	312,8022		7,298,3862	no	coding-synonymous,coding-synonymous	TRIM22	NM_001199573.1,NM_006074.4	,	7,392,5739	TT,TC,CC		3.7437,2.3846,3.3073	,	301/495,305/499	5730294	406,11870	1971	4167	6138	SO:0001819	synonymous_variant	10346	exon8			GTGATGCTGAATC	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.913C>T	11.37:g.5730294C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_006074	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			C|0.969;T|0.031	0.031	strong		0.398	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
DDX31	64794	hgsc.bcm.edu	37	9	135521303	135521303	+	Silent	SNP	C	C	T	rs306537	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:135521303C>T	ENST00000372159.3	-	13	1825	c.1674G>A	c.(1672-1674)ctG>ctA	p.L558L	DDX31_ENST00000372153.1_Silent_p.L558L|DDX31_ENST00000438527.3_Silent_p.L429L|DDX31_ENST00000310532.2_Silent_p.L558L	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	558	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		TGCCGCCATGCAGCCGTAGGA	0.612													C|||	455	0.0908546	0.1324	0.121	5008	,	,		18566	0.1171		0.0417	False		,,,				2504	0.0368				p.L558L		Atlas-SNP	.											.	DDX31	76	.	0			c.G1674A						PASS	.	C	,	477,3929	222.6+/-239.4	28,421,1754	32.0	31.0	31.0		1674,1674	3.7	1.0	9	dbSNP_79	31	366,8234	121.7+/-180.7	3,360,3937	no	coding-synonymous,coding-synonymous	DDX31	NM_022779.7,NM_138620.1	,	31,781,5691	TT,TC,CC		4.2558,10.8261,6.4816	,	558/852,558/586	135521303	843,12163	2203	4300	6503	SO:0001819	synonymous_variant	64794	exon13			GCCATGCAGCCGT	AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"""DEAD-boxes"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16715	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 25"""		"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"""				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.1674G>A	9.37:g.135521303C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Silent	SNP	ENST00000372159.3	37	CCDS6951.1																																																																																			C|0.927;T|0.073	0.073	strong		0.612	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620	
UTP15	84135	hgsc.bcm.edu	37	5	72868447	72868447	+	Silent	SNP	T	T	C	rs16870610	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:72868447T>C	ENST00000296792.4	+	7	1062	c.807T>C	c.(805-807)gaT>gaC	p.D269D	UTP15_ENST00000508491.1_Silent_p.D250D|UTP15_ENST00000543251.1_Silent_p.D79D	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	269					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)		GCTCACTGGATAGGTTGGCat	0.348													T|||	331	0.0660942	0.0499	0.0173	5008	,	,		17274	0.12		0.0497	False		,,,				2504	0.0838				p.D269D		Atlas-SNP	.											.	UTP15	30	.	0			c.T807C						PASS	.	T		197,4209	122.5+/-159.9	5,187,2011	122.0	122.0	122.0		807	-1.0	1.0	5	dbSNP_123	122	377,8223	124.1+/-182.9	7,363,3930	no	coding-synonymous	UTP15	NM_032175.2		12,550,5941	CC,CT,TT		4.3837,4.4712,4.4133		269/519	72868447	574,12432	2203	4300	6503	SO:0001819	synonymous_variant	84135	exon7			ACTGGATAGGTTG	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.807T>C	5.37:g.72868447T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Silent	SNP	ENST00000296792.4	37	CCDS34186.1	139	0.06364468864468864	25	0.0508130081300813	8	0.022099447513812154	66	0.11538461538461539	40	0.052770448548812667	T	13.30	2.194860	0.38806	0.044712	0.043837	ENSG00000164338	ENST00000509005	.	.	.	5.79	-0.955	0.10356	.	.	.	.	.	T	0.01320	0.0043	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03587	-1.1022	4	.	.	.	.	11.0541	0.47907	0.0:0.689:0.0:0.311	rs16870610;rs16870610	.	.	.	T	296	.	.	I	+	2	0	UTP15	72904203	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	1.109000	0.31135	-0.119000	0.11830	0.533000	0.62120	ATA	T|0.945;C|0.055	0.055	strong		0.348	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175	
ZNF709	163051	hgsc.bcm.edu	37	19	12575152	12575152	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:12575152C>T	ENST00000397732.3	-	4	1755	c.1584G>A	c.(1582-1584)ggG>ggA	p.G528G	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Silent_p.G528G	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	528					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.G528G(2)		large_intestine(3)|upper_aerodigestive_tract(3)	6						AGGGTTTCTCCCCAGTGTGAG	0.423																																					p.G528G	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											ZNF709_ENST00000397732,NS,carcinoma,0,4	ZNF709	80	4	2	Substitution - coding silent(2)	lung(1)|endometrium(1)	c.G1584A						scavenged	.																																			SO:0001819	synonymous_variant	163051	exon4			TTTCTCCCCAGTG	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.1584G>A	19.37:g.12575152C>T		Somatic	128	3	0.0234375		WXS	Illumina HiSeq	Phase_I	92	3	0.0326087	NM_152601	A8K4E6	Silent	SNP	ENST00000397732.3	37	CCDS42504.1																																																																																			.	.	none		0.423	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601	
MATN2	4147	hgsc.bcm.edu	37	8	99006736	99006736	+	Silent	SNP	C	C	T	rs11559202	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:99006736C>T	ENST00000520016.1	+	6	1234	c.1110C>T	c.(1108-1110)caC>caT	p.H370H	MATN2_ENST00000521689.1_Silent_p.H370H|MATN2_ENST00000254898.5_Silent_p.H370H|MATN2_ENST00000524308.1_Intron|MATN2_ENST00000522025.2_Silent_p.H86H			O00339	MATN2_HUMAN	matrilin 2	370	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					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)			CATCTAATCACGGATGTCAGC	0.428													C|||	609	0.121605	0.1505	0.1052	5008	,	,		18994	0.0774		0.1471	False		,,,				2504	0.1135				p.H370H		Atlas-SNP	.											.	MATN2	165	.	0			c.C1110T						PASS	.	C	,	518,3370		29,460,1455	194.0	189.0	190.0		1110,1110	-11.5	0.0	8	dbSNP_120	190	1435,6851		126,1183,2834	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	155,1643,4289	TT,TC,CC		17.3184,13.323,16.0424	,	370/957,370/938	99006736	1953,10221	1944	4143	6087	SO:0001819	synonymous_variant	4147	exon7			TAATCACGGATGT	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.1110C>T	8.37:g.99006736C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	156	62	0.397436	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	263	0.12042124542124542	74	0.15040650406504066	42	0.11602209944751381	37	0.06468531468531469	110	0.14511873350923482	C	2.388	-0.340579	0.05243	0.13323	0.173184	ENSG00000132561	ENST00000518154;ENST00000521041	.	.	.	5.73	-11.5	0.00074	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.20926	P	0.999823375	.	.	.	.	.	.	T	0.19160	-1.0314	3	.	.	.	-19.9164	13.3653	0.60680	0.0779:0.5461:0.0:0.376	rs11559202;rs17850659;rs11559202	.	.	.	W	153;125	.	.	R	+	1	2	MATN2	99075912	0.001000	0.12720	0.006000	0.13384	0.489000	0.33432	-2.225000	0.01212	-3.033000	0.00265	-1.740000	0.00687	CGG	C|0.872;T|0.128	0.128	strong		0.428	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
ISOC2	79763	hgsc.bcm.edu	37	19	55967848	55967848	+	Silent	SNP	C	C	T	rs11555784	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55967848C>T	ENST00000425675.2	-	2	66	c.6G>A	c.(4-6)gcG>gcA	p.A2A	ISOC2_ENST00000438389.2_Silent_p.A2A|ISOC2_ENST00000085068.3_Silent_p.A2A			Q96AB3	ISOC2_HUMAN	isochorismatase domain containing 2	2					protein destabilization (GO:0031648)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			endometrium(1)|lung(4)|ovary(1)|stomach(1)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0535)		GCCTGGCAGCCGCCATTTTCT	0.642													.|||	227	0.0453275	0.1316	0.0331	5008	,	,		15010	0.0		0.0268	False		,,,				2504	0.0031				p.A2A		Atlas-SNP	.											.	ISOC2	16	.	0			c.G6A						PASS	.	C	,,	528,3878	229.1+/-243.8	32,464,1707	44.0	44.0	44.0		6,6,6	-2.1	0.1	19	dbSNP_126	44	295,8303	103.6+/-164.7	7,281,4011	no	coding-synonymous,coding-synonymous,coding-synonymous	ISOC2	NM_001136201.1,NM_001136202.1,NM_024710.2	,,	39,745,5718	TT,TC,CC		3.431,11.9837,6.3288	,,	2/206,2/136,2/222	55967848	823,12181	2203	4299	6502	SO:0001819	synonymous_variant	79763	exon2			GGCAGCCGCCATT	AK027122	CCDS12925.1, CCDS46194.1, CCDS46195.1	19q13.42	2011-07-14			ENSG00000063241	ENSG00000063241			26278	protein-coding gene	gene with protein product		612928				17658461	Standard	NM_024710		Approved	FLJ23469	uc002qla.3	Q96AB3		ENST00000425675.2:c.6G>A	19.37:g.55967848C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_001136202	Q6ZN91|Q9H5G0	Silent	SNP	ENST00000425675.2	37	CCDS46195.1																																																																																			C|0.939;T|0.061	0.061	strong		0.642	ISOC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453179.1	NM_024710	
CECR1	51816	hgsc.bcm.edu	37	22	17669306	17669306	+	Missense_Mutation	SNP	T	T	C	rs2231495	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:17669306T>C	ENST00000399839.1	-	7	1274	c.1004A>G	c.(1003-1005)cAt>cGt	p.H335R	CECR1_ENST00000399837.2_Missense_Mutation_p.H335R|CECR1_ENST00000330232.4_Missense_Mutation_p.H94R|CECR1_ENST00000449907.2_Missense_Mutation_p.H293R|CECR1_ENST00000262607.3_Missense_Mutation_p.H335R|CECR1_ENST00000480276.1_5'Flank	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	93	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	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		
OR51S1	119692	hgsc.bcm.edu	37	11	4869906	4869906	+	Missense_Mutation	SNP	A	A	C	rs7117260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4869906A>C	ENST00000322101.2	-	1	608	c.533T>G	c.(532-534)cTc>cGc	p.L178R	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	178			L -> R (in dbSNP:rs7117260).			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)		GACCTGTGGGAGGCAGTAGGG	0.527													c|||	2513	0.501797	0.6233	0.4135	5008	,	,		19677	0.0942		0.6054	False		,,,				2504	0.7137				p.L178R		Atlas-SNP	.											.	OR51S1	83	.	0			c.T533G						PASS	.	T	ARG/LEU	2633,1769	524.3+/-371.3	812,1009,380	105.0	108.0	107.0		533	-8.9	0.0	11	dbSNP_116	107	5384,3212	485.0+/-371.5	1678,2028,592	yes	missense	OR51S1	NM_001004758.1	102	2490,3037,972	CC,CA,AA		37.3662,40.1863,38.3213	benign	178/324	4869906	8017,4981	2201	4298	6499	SO:0001583	missense	119692	exon1			TGTGGGAGGCAGT	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.533T>G	11.37:g.4869906A>C	ENSP00000322754:p.Leu178Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	965	0.44184981684981683	300	0.6097560975609756	175	0.48342541436464087	48	0.08391608391608392	442	0.58311345646438	c	0.007	-1.965406	0.00461	0.598137	0.626338	ENSG00000176922	ENST00000322101	T	0.36878	1.23	5.25	-8.88	0.00789	GPCR, rhodopsin-like superfamily (1);	1.124130	0.06837	N	0.794977	T	0.00012	0.0000	N	0.00204	-1.855	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40553	-0.9557	9	0.02654	T	1	-5.0E-4	11.6806	0.51455	0.1617:0.5479:0.0:0.2904	rs7117260;rs52824745;rs58968377;rs7117260	178	Q8NGJ8	O51S1_HUMAN	R	178	ENSP00000322754:L178R	ENSP00000322754:L178R	L	-	2	0	OR51S1	4826482	0.000000	0.05858	0.000000	0.03702	0.413000	0.31143	-5.132000	0.00148	-2.327000	0.00636	-2.069000	0.00389	CTC	A|0.479;C|0.521	0.521	strong		0.527	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
PPP4R1	9989	hgsc.bcm.edu	37	18	9570320	9570320	+	Missense_Mutation	SNP	T	T	C	rs329003	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:9570320T>C	ENST00000400556.3	-	11	1481	c.1408A>G	c.(1408-1410)Ata>Gta	p.I470V	PPP4R1_ENST00000400555.3_Missense_Mutation_p.I453V	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	470			I -> V (in dbSNP:rs329003).		dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						TCAAGCTCTATGTCTAGATCT	0.493													T|||	204	0.0407348	0.0091	0.0793	5008	,	,		16476	0.0		0.1153	False		,,,				2504	0.0215				p.I470V	Melanoma(188;1232 2082 5061 11948 35994)	Atlas-SNP	.											.	PPP4R1	63	.	0			c.A1408G						PASS	.	T	VAL/ILE,VAL/ILE	82,3576		0,82,1747	77.0	71.0	73.0		1408,1357	-4.3	0.0	18	dbSNP_79	73	868,7300		54,760,3270	yes	missense,missense	PPP4R1	NM_001042388.1,NM_005134.2	29,29	54,842,5017	CC,CT,TT		10.6268,2.2417,8.0331	benign,benign	470/951,453/934	9570320	950,10876	1829	4084	5913	SO:0001583	missense	9989	exon11			GCTCTATGTCTAG	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.1408A>G	18.37:g.9570320T>C	ENSP00000383402:p.Ile470Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	150	60	0.4	NM_001042388	Q99774|Q9UNQ7	Missense_Mutation	SNP	ENST00000400556.3	37	CCDS42412.1	112	0.05128205128205128	1	0.0020325203252032522	30	0.08287292817679558	0	0.0	81	0.10686015831134564	T	4.242	0.043900	0.08196	0.022417	0.106268	ENSG00000154845	ENST00000400556;ENST00000400555;ENST00000285124	T;T	0.13657	2.57;2.57	5.27	-4.34	0.03666	Armadillo-type fold (1);	1.091820	0.07025	N	0.827457	T	0.00073	0.0002	N	0.02011	-0.69	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.43048	-0.9415	8	.	.	.	-0.1993	1.7761	0.03022	0.1213:0.2652:0.1782:0.4353	rs329003;rs52816270;rs60829427;rs329003	453;470;453	A8K923;Q8TF05;Q8TF05-2	.;PP4R1_HUMAN;.	V	470;453;381	ENSP00000383402:I470V;ENSP00000383401:I453V	.	I	-	1	0	PPP4R1	9560320	0.000000	0.05858	0.020000	0.16555	0.948000	0.59901	-0.285000	0.08410	-0.407000	0.07576	0.482000	0.46254	ATA	T|0.940;C|0.060	0.060	strong		0.493	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
CXorf65	158830	hgsc.bcm.edu	37	X	70324157	70324157	+	Silent	SNP	C	C	T	rs1130009	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	111	104	0.936937	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	
APBB2	323	hgsc.bcm.edu	37	4	40818179	40818179	+	Missense_Mutation	SNP	T	T	C	rs112788816	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:40818179T>C	ENST00000295974.8	-	18	2836	c.2207A>G	c.(2206-2208)aAt>aGt	p.N736S	RP11-632F7.3_ENST00000513127.1_RNA|APBB2_ENST00000504305.1_Missense_Mutation_p.N188S|APBB2_ENST00000506352.1_Missense_Mutation_p.N715S|APBB2_ENST00000513140.1_Missense_Mutation_p.N714S|APBB2_ENST00000502841.1_Missense_Mutation_p.N188S|APBB2_ENST00000543538.1_Missense_Mutation_p.N188S|APBB2_ENST00000508593.1_Missense_Mutation_p.N737S	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	736	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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						TCGTTTTACATTGGTTGTGAC	0.488													T|||	26	0.00519169	0.0023	0.0058	5008	,	,		19924	0.001		0.0149	False		,,,				2504	0.0031				p.N737S	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.A2210G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	25,3899		0,25,1937	213.0	210.0	211.0		2207,563,563,563,563,2210,2141	5.5	1.0	4	dbSNP_132	211	166,8138		2,162,3988	yes	missense,missense,missense,missense,missense,missense,missense	APBB2	NM_001166050.1,NM_001166051.1,NM_001166052.1,NM_001166053.1,NM_001166054.1,NM_004307.1,NM_173075.4	46,46,46,46,46,46,46	2,187,5925	CC,CT,TT		1.999,0.6371,1.562	benign,benign,benign,benign,benign,benign,benign	736/759,188/211,188/211,188/211,188/211,737/760,714/737	40818179	191,12037	1962	4152	6114	SO:0001583	missense	323	exon18			TTTACATTGGTTG	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.2207A>G	4.37:g.40818179T>C	ENSP00000295974:p.Asn736Ser	Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	237	107	0.451477	NM_004307	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	37	CCDS54761.1	16	0.007326007326007326	2	0.0040650406504065045	3	0.008287292817679558	1	0.0017482517482517483	10	0.013192612137203167	T	6.513	0.462936	0.12402	0.006371	0.01999	ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000543538;ENST00000513140;ENST00000508593;ENST00000502841;ENST00000506352;ENST00000504305	T;T;T;T;T;T;T	0.37584	2.9;1.19;2.84;2.9;1.19;2.84;1.19	5.53	5.53	0.82687	.	0.042264	0.85682	D	0.000000	T	0.05318	0.0141	N	0.00823	-1.155	0.47153	D	0.999335	B;B;B	0.12013	0.003;0.005;0.005	B;B;B	0.12156	0.003;0.007;0.003	T	0.20009	-1.0288	10	0.10377	T	0.69	-21.7649	10.0801	0.42384	0.0:0.0748:0.0:0.9252	.	737;714;736	E9PG87;Q92870-2;Q92870	.;.;APBB2_HUMAN	S	736;735;188;714;737;188;715;188	ENSP00000295974:N736S;ENSP00000439357:N188S;ENSP00000426018:N714S;ENSP00000427211:N737S;ENSP00000425802:N188S;ENSP00000421539:N715S;ENSP00000423765:N188S	ENSP00000295974:N736S	N	-	2	0	APBB2	40512936	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.952000	0.70282	2.105000	0.64084	0.528000	0.53228	AAT	T|0.991;C|0.009	0.009	strong		0.488	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
RHPN2	85415	hgsc.bcm.edu	37	19	33493200	33493200	+	Missense_Mutation	SNP	G	G	A	rs200623446	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:33493200G>A	ENST00000254260.3	-	9	1093	c.1058C>T	c.(1057-1059)gCg>gTg	p.A353V	RHPN2_ENST00000400226.4_Missense_Mutation_p.A202V	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	353	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)					GGCCAGGGCCGCGTAGTGGTG	0.637																																					p.A353V		Atlas-SNP	.											RHPN2,caecum,carcinoma,-1,17	RHPN2	107	17	0			c.C1058T						scavenged	.						50.0	48.0	49.0					19																	33493200		2203	4300	6503	SO:0001583	missense	85415	exon9			AGGGCCGCGTAGT	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.1058C>T	19.37:g.33493200G>A	ENSP00000254260:p.Ala353Val	Somatic	167	3	0.0179641		WXS	Illumina HiSeq	Phase_I	182	22	0.120879	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	G	10.17	1.276172	0.23307	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.18810	2.19;2.19	4.61	-4.16	0.03869	BRO1 domain (3);	1.055030	0.07227	N	0.861852	T	0.14830	0.0358	L	0.39898	1.24	0.09310	N	1	B	0.18013	0.025	B	0.15484	0.013	T	0.36114	-0.9761	10	0.30078	T	0.28	0.2931	7.8623	0.29517	0.0:0.2524:0.4684:0.2792	.	353	Q8IUC4	RHPN2_HUMAN	V	353;83;202	ENSP00000254260:A353V;ENSP00000402244:A202V	ENSP00000254260:A353V	A	-	2	0	RHPN2	38185040	0.000000	0.05858	0.001000	0.08648	0.375000	0.29983	0.178000	0.16820	-0.540000	0.06265	0.455000	0.32223	GCG	G|0.935;A|0.065	0.065	strong		0.637	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
CLCNKA	1187	hgsc.bcm.edu	37	1	16351275	16351275	+	Missense_Mutation	SNP	A	A	G	rs10927887	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16351275A>G	ENST00000331433.4	+	4	266	c.247A>G	c.(247-249)Agg>Ggg	p.R83G	CLCNKA_ENST00000420078.1_Missense_Mutation_p.R83G|CLCNKA_ENST00000375692.1_Missense_Mutation_p.R83G|CLCNKA_ENST00000464764.1_Intron|CLCNKA_ENST00000439316.2_Intron			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	83			R -> G (in dbSNP:rs10927887). {ECO:0000269|Ref.3}.		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)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		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)	Niflumic Acid(DB04552)	GTGGCTGTACAGGGAGATTGG	0.617													G|||	3220	0.642971	0.7201	0.4467	5008	,	,		9165	0.7688		0.5636	False		,,,				2504	0.6299				p.R83G		Atlas-SNP	.											.	CLCNKA	56	.	0			c.A247G						PASS	.	G	GLY/ARG,GLY/ARG	3067,1339	445.9+/-347.8	1060,947,196	101.0	77.0	85.0		247,247	0.9	1.0	1	dbSNP_120	85	4748,3852	542.8+/-384.3	1336,2076,888	no	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	125,125	2396,3023,1084	GG,GA,AA		44.7907,30.3904,39.9123	benign,benign	83/687,83/688	16351275	7815,5191	2203	4300	6503	SO:0001583	missense	1187	exon4			CTGTACAGGGAGA		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.247A>G	1.37:g.16351275A>G	ENSP00000332771:p.Arg83Gly	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	114	89	0.780702	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	1365	0.625	348	0.7073170731707317	172	0.47513812154696133	428	0.7482517482517482	417	0.5501319261213721	G	4.371	0.068461	0.08436	0.696096	0.552093	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000331433	D;D;D	0.92495	-3.05;-3.05;-3.05	4.0	0.872	0.19113	Chloride channel, core (2);	0.865352	0.10003	N	0.728172	T	0.00012	0.0000	L	0.45352	1.415	0.41837	P	0.009898999999999991	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46414	-0.9193	9	0.28530	T	0.3	.	7.3212	0.26528	0.3182:0.3866:0.2951:0.0	rs10927887	83;83	Q5T5Q4;P51800	.;CLCKA_HUMAN	G	83	ENSP00000364844:R83G;ENSP00000410353:R83G;ENSP00000332771:R83G	ENSP00000332771:R83G	R	+	1	2	CLCNKA	16223862	0.847000	0.29606	0.991000	0.47740	0.505000	0.33919	0.593000	0.23999	-0.153000	0.11137	-1.325000	0.01285	AGG	A|0.397;G|0.603	0.603	strong		0.617	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
LIG4	3981	hgsc.bcm.edu	37	13	108863591	108863591	+	Missense_Mutation	SNP	G	G	A	rs1805388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:108863591G>A	ENST00000356922.4	-	2	298	c.26C>T	c.(25-27)aCt>aTt	p.T9I	LIG4_ENST00000405925.1_Missense_Mutation_p.T9I|LIG4_ENST00000442234.1_Missense_Mutation_p.T9I	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	9			T -> I (associated with resistance to multiple myeloma; dbSNP:rs1805388). {ECO:0000269|PubMed:12471202}.		cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					AGATGCAACAGTTTGTGAAGT	0.353								Non-homologous end-joining					G|||	730	0.145767	0.0893	0.2161	5008	,	,		17385	0.2103		0.163	False		,,,				2504	0.0879				p.T9I		Atlas-SNP	.											.	LIG4	91	.	0			c.C26T	GRCh37	CM023643	LIG4	M	rs1805388	PASS	.	G	ILE/THR,ILE/THR,ILE/THR	450,3928		19,412,1758	30.0	30.0	30.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	26,26,26	4.1	0.7	13	dbSNP_92	30	1310,7160		112,1086,3037	yes	missense,missense,missense	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	89,89,89	131,1498,4795	AA,AG,GG		15.4664,10.2787,13.6986	possibly-damaging,possibly-damaging,possibly-damaging	9/912,9/912,9/912	108863591	1760,11088	2189	4235	6424	SO:0001583	missense	3981	exon3			GCAACAGTTTGTG	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.26C>T	13.37:g.108863591G>A	ENSP00000349393:p.Thr9Ile	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	335	0.1533882783882784	37	0.07520325203252033	66	0.18232044198895028	108	0.1888111888111888	124	0.16358839050131926	G	14.90	2.672135	0.47781	0.102787	0.154664	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.19669	2.13;2.13;2.13	5.82	4.09	0.47781	DNA ligase, ATP-dependent, N-terminal (2);	0.487586	0.24061	N	0.041916	T	0.00012	0.0000	N	0.08118	0	0.30067	P	0.810381	P	0.35780	0.52	B	0.32342	0.144	T	0.33343	-0.9872	9	0.49607	T	0.09	.	10.8846	0.46960	0.1496:0.0:0.8504:0.0	rs1805388;rs17379563;rs52823564;rs61630348;rs1805388	9	P49917	DNLI4_HUMAN	I	9	ENSP00000385955:T9I;ENSP00000402030:T9I;ENSP00000349393:T9I	ENSP00000349393:T9I	T	-	2	0	LIG4	107661592	1.000000	0.71417	0.730000	0.30809	0.908000	0.53690	4.882000	0.63121	0.814000	0.34374	0.643000	0.83706	ACT	G|0.856;N|0.000	.	strong		0.353	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
ABCB1	5243	hgsc.bcm.edu	37	7	87178735	87178735	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:87178735G>A	ENST00000265724.3	-	15	2071	c.1654C>T	c.(1654-1656)Ctc>Ttc	p.L552F	ABCB1_ENST00000543898.1_Missense_Mutation_p.L488F	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	552	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	TCCAGCAGGAGGATCTTGGGG	0.562																																					p.L552F		Atlas-SNP	.											ABCB1,NS,carcinoma,+2,1	ABCB1	263	1	0			c.C1654T						scavenged	.						125.0	104.0	111.0					7																	87178735		2203	4300	6503	SO:0001583	missense	5243	exon15			GCAGGAGGATCTT	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.1654C>T	7.37:g.87178735G>A	ENSP00000265724:p.Leu552Phe	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	253	3	0.0118577	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	G	32	5.106184	0.94292	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.84146	-1.81;-1.81	5.8	5.8	0.92144	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.93115	0.7808	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.996;1.0	D	0.93263	0.6645	10	0.87932	D	0	-15.3275	20.051	0.97627	0.0:0.0:1.0:0.0	.	488;552	B5AK60;P08183	.;MDR1_HUMAN	F	333;552;488	ENSP00000265724:L552F;ENSP00000444095:L488F	ENSP00000265724:L552F	L	-	1	0	ABCB1	87016671	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.774000	0.75012	2.740000	0.93945	0.650000	0.86243	CTC	.	.	none		0.562	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
ZNF618	114991	hgsc.bcm.edu	37	9	116812084	116812084	+	Silent	SNP	C	C	T	rs7856141	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116812084C>T	ENST00000374126.5	+	15	2601	c.2502C>T	c.(2500-2502)aaC>aaT	p.N834N	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Silent_p.N741N			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	834					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						AGCTCATCAACGAGGTGAAGG	0.637													C|||	339	0.0676917	0.1271	0.0605	5008	,	,		19158	0.0		0.0895	False		,,,				2504	0.0399				p.N741N		Atlas-SNP	.											.	ZNF618	184	.	0			c.C2223T						PASS	.	C		488,3642		20,448,1597	61.0	68.0	65.0		2223	-11.3	0.1	9	dbSNP_116	65	707,7651		34,639,3506	no	coding-synonymous	ZNF618	NM_133374.2		54,1087,5103	TT,TC,CC		8.459,11.816,9.5692		741/862	116812084	1195,11293	2065	4179	6244	SO:0001819	synonymous_variant	114991	exon14			CATCAACGAGGTG	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.2502C>T	9.37:g.116812084C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				C|0.923;T|0.077	0.077	strong		0.637	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
TRIM71	131405	hgsc.bcm.edu	37	3	32933036	32933036	+	Silent	SNP	G	G	A	rs13096271	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:32933036G>A	ENST00000383763.5	+	4	2403	c.2340G>A	c.(2338-2340)tcG>tcA	p.S780S		NM_001039111.1	NP_001034200.1	Q2Q1W2	LIN41_HUMAN	tripartite motif containing 71, E3 ubiquitin protein ligase	780					fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|miRNA metabolic process (GO:0010586)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|positive regulation of gene silencing by miRNA (GO:2000637)|protein autoubiquitination (GO:0051865)|regulation of gene silencing by miRNA (GO:0060964)|regulation of neural precursor cell proliferation (GO:2000177)|stem cell proliferation (GO:0072089)	cytoplasmic mRNA processing body (GO:0000932)	ligase activity (GO:0016874)|miRNA binding (GO:0035198)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACTGCCAGTCGGCACGCTTTC	0.612													G|||	719	0.14357	0.1044	0.0836	5008	,	,		18483	0.2907		0.0855	False		,,,				2504	0.1472				p.S780S		Atlas-SNP	.											TRIM71,NS,meningioma,+1,1	TRIM71	73	1	0			c.G2340A						PASS	.	G		352,3574		27,298,1638	39.0	41.0	41.0		2340	-11.9	0.0	3	dbSNP_121	41	815,7499		39,737,3381	no	coding-synonymous	TRIM71	NM_001039111.1		66,1035,5019	AA,AG,GG		9.8027,8.9659,9.5343		780/869	32933036	1167,11073	1963	4157	6120	SO:0001819	synonymous_variant	131405	exon4			CCAGTCGGCACGC		CCDS43060.1	3p22.3	2014-02-17	2012-02-29		ENSG00000206557	ENSG00000206557		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	32669	protein-coding gene	gene with protein product			"""tripartite motif-containing 71"", ""tripartite motif containing 71"""				Standard	NM_001039111		Approved	LIN41, LIN-41	uc003cff.3	Q2Q1W2	OTTHUMG00000155778	ENST00000383763.5:c.2340G>A	3.37:g.32933036G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_001039111		Silent	SNP	ENST00000383763.5	37	CCDS43060.1																																																																																			G|0.873;A|0.127	0.127	strong		0.612	TRIM71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341565.3	NM_001039111	
MLX	6945	hgsc.bcm.edu	37	17	40722162	40722162	+	Silent	SNP	G	G	A	rs1474040	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	180	68	0.377778	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	
CCDC57	284001	hgsc.bcm.edu	37	17	80159665	80159665	+	Silent	SNP	G	G	A	rs11653797	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80159665G>A	ENST00000389641.4	-	2	192	c.156C>T	c.(154-156)tgC>tgT	p.C52C	CCDC57_ENST00000392347.1_Silent_p.C52C|CCDC57_ENST00000392343.3_Silent_p.C52C			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	52										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			CCTCCTGCAGGCACCGCAGTT	0.672													G|||	556	0.111022	0.0552	0.1268	5008	,	,		17085	0.0565		0.1998	False		,,,				2504	0.1401				p.C52C		Atlas-SNP	.											.	CCDC57	102	.	0			c.C156T						PASS	.	G		406,3868		19,368,1750	50.0	57.0	55.0		156	-0.8	0.5	17	dbSNP_120	55	1893,6617		204,1485,2566	no	coding-synonymous	CCDC57	NM_198082.2		223,1853,4316	AA,AG,GG		22.2444,9.4993,17.9834		52/916	80159665	2299,10485	2137	4255	6392	SO:0001819	synonymous_variant	284001	exon2			CTGCAGGCACCGC	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.156C>T	17.37:g.80159665G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	226	117	0.517699	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37																																																																																				G|0.859;A|0.141	0.141	strong		0.672	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
RASGRF1	5923	hgsc.bcm.edu	37	15	79298523	79298523	+	Silent	SNP	G	G	A	rs894780	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:79298523G>A	ENST00000419573.3	-	15	2393	c.2119C>T	c.(2119-2121)Ctg>Ttg	p.L707L	RASGRF1_ENST00000558480.2_Intron|RASGRF1_ENST00000394745.3_5'Flank|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	707	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GGGCACCTCAGCCACCTGGCA	0.607													G|||	332	0.0662939	0.0061	0.0605	5008	,	,		21301	0.0972		0.1163	False		,,,				2504	0.0685				p.L707L		Atlas-SNP	.											.	RASGRF1	168	.	0			c.C2119T						PASS	.	G	,	96,4296	75.2+/-113.4	2,92,2102	110.0	96.0	100.0		,2119	1.3	0.1	15	dbSNP_86	100	885,7701	198.6+/-242.9	71,743,3479	no	intron,coding-synonymous	RASGRF1	NM_001145648.1,NM_002891.4	,	73,835,5581	AA,AG,GG		10.3075,2.1858,7.5589	,	,707/1274	79298523	981,11997	2196	4293	6489	SO:0001819	synonymous_variant	5923	exon15			ACCTCAGCCACCT	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.2119C>T	15.37:g.79298523G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	68	52	0.764706	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																			G|0.921;T|0.000	.	strong		0.607	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
LILRA4	23547	hgsc.bcm.edu	37	19	54848145	54848145	+	Missense_Mutation	SNP	G	G	A	rs75547479	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848145G>A	ENST00000291759.4	-	6	1278	c.1222C>T	c.(1222-1224)Cac>Tac	p.H408Y	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	408	Ig-like C2-type 4.				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)		TCACTGGGGTGAGACAGCAGG	0.592													G|||	74	0.0147764	0.0333	0.0014	5008	,	,		17303	0.0		0.001	False		,,,				2504	0.0286				p.H408Y		Atlas-SNP	.											.	LILRA4	91	.	0			c.C1222T						PASS	.						112.0	91.0	98.0					19																	54848145		2203	4300	6503	SO:0001583	missense	23547	exon6			TGGGGTGAGACAG	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.1222C>T	19.37:g.54848145G>A	ENSP00000291759:p.His408Tyr	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	182	19	0.104396	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	6.455	0.452105	0.12283	.	.	ENSG00000239961	ENST00000291759	T	0.00724	5.78	2.4	0.177	0.15054	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.662820	0.00932	N	0.002721	T	0.01523	0.0049	M	0.81341	2.54	0.09310	N	1	B	0.14438	0.01	B	0.09377	0.004	T	0.56056	-0.8042	10	0.20519	T	0.43	.	4.4089	0.11423	0.3496:0.0:0.6504:0.0	.	408	P59901	LIRA4_HUMAN	Y	408	ENSP00000291759:H408Y	ENSP00000291759:H408Y	H	-	1	0	LILRA4	59539957	0.000000	0.05858	0.008000	0.14137	0.035000	0.12851	-1.057000	0.03486	0.109000	0.17891	0.455000	0.32223	CAC	A|0.005;G|0.995	0.005	strong		0.592	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
ERAP1	51752	hgsc.bcm.edu	37	5	96129543	96129543	+	Missense_Mutation	SNP	C	C	T	rs27895	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:96129543C>T	ENST00000443439.2	-	6	1103	c.1037G>A	c.(1036-1038)gGc>gAc	p.G346D	ERAP1_ENST00000296754.3_Missense_Mutation_p.G346D	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	346			G -> D (in dbSNP:rs27895). {ECO:0000269|Ref.3}.		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)		CATTGTGATGCCAAGCTTACT	0.398													C|||	519	0.103634	0.2375	0.0476	5008	,	,		17744	0.001		0.0636	False		,,,				2504	0.1094				p.G346D		Atlas-SNP	.											.	ERAP1	59	.	0			c.G1037A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	820,3586	325.6+/-299.2	77,666,1460	63.0	57.0	59.0		1037,1037,1037	3.1	1.0	5	dbSNP_76	59	593,8007	157.3+/-211.0	12,569,3719	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	94,94,94	89,1235,5179	TT,TC,CC		6.8953,18.611,10.8642	benign,benign,benign	346/942,346/942,346/949	96129543	1413,11593	2203	4300	6503	SO:0001583	missense	51752	exon6			GTGATGCCAAGCT	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.1037G>A	5.37:g.96129543C>T	ENSP00000406304:p.Gly346Asp	Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	246	119	0.48374	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	177	0.08104395604395605	106	0.21544715447154472	21	0.058011049723756904	0	0.0	50	0.06596306068601583	C	11.92	1.781519	0.31502	0.18611	0.068953	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.02472	4.28;4.28	5.82	3.1	0.35709	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.425013	0.28940	N	0.013641	T	0.00012	0.0000	N	0.21448	0.665	0.25970	P	0.9825164	B;B;B	0.17038	0.0;0.02;0.016	B;B;B	0.23716	0.001;0.048;0.028	T	0.49744	-0.8907	9	0.33940	T	0.23	.	9.2579	0.37595	0.0:0.7475:0.1202:0.1323	rs27895;rs639135;rs59167594;rs27895	346;346;346	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	D	346	ENSP00000296754:G346D;ENSP00000406304:G346D	ENSP00000296754:G346D	G	-	2	0	ERAP1	96155299	0.005000	0.15991	0.998000	0.56505	0.810000	0.45777	0.726000	0.25984	0.391000	0.25143	-0.885000	0.02943	GGC	C|0.903;T|0.097	0.097	strong		0.398	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
COL27A1	85301	hgsc.bcm.edu	37	9	116931666	116931666	+	Missense_Mutation	SNP	A	A	T	rs2567705	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116931666A>T	ENST00000356083.3	+	3	2222	c.1831A>T	c.(1831-1833)Atc>Ttc	p.I611F		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	611	Pro-rich.		I -> F (in dbSNP:rs2567705). {ECO:0000269|PubMed:15489334}.		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						TGGCTATTCGATCTTCCACCT	0.647													T|||	1457	0.290935	0.3654	0.2795	5008	,	,		16947	0.1151		0.4215	False		,,,				2504	0.2454				p.I611F		Atlas-SNP	.											.	COL27A1	200	.	0			c.A1831T						PASS	.	T	PHE/ILE	1664,2742	652.9+/-399.5	313,1038,852	59.0	66.0	64.0		1831	4.7	0.7	9	dbSNP_100	64	3368,5232	639.6+/-399.5	666,2036,1598	yes	missense	COL27A1	NM_032888.2	21	979,3074,2450	TT,TA,AA		39.1628,37.7667,38.6898	benign	611/1861	116931666	5032,7974	2203	4300	6503	SO:0001583	missense	85301	exon3			TATTCGATCTTCC	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.1831A>T	9.37:g.116931666A>T	ENSP00000348385:p.Ile611Phe	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	64	24	0.375	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	657	0.3008241758241758	180	0.36585365853658536	114	0.3149171270718232	58	0.10139860139860139	305	0.4023746701846966	T	11.39	1.623941	0.28889	0.377667	0.391628	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.96136	-3.92;-2.73	4.66	4.66	0.58398	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.48087	P	4.1400000000002546E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27262	-1.0079	8	0.02654	T	1	.	7.5893	0.28012	0.1893:0.0:0.0:0.8107	rs2567705;rs17801180;rs59019220;rs2567705	611;558	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	F	611;611;558;558	ENSP00000348385:I611F;ENSP00000391328:I558F	ENSP00000348385:I611F	I	+	1	0	COL27A1	115971487	0.777000	0.28628	0.708000	0.30435	0.682000	0.39822	0.927000	0.28818	0.823000	0.34589	-0.364000	0.07487	ATC	A|0.648;T|0.352	0.352	strong		0.647	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1817367	1817367	+	Silent	SNP	G	G	A	rs7003969	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:1817367G>A	ENST00000398564.1	+	7	705	c.705G>A	c.(703-705)gaG>gaA	p.E235E	ARHGEF10_ENST00000520359.1_Silent_p.E211E|ARHGEF10_ENST00000262112.6_Silent_p.E235E|ARHGEF10_ENST00000349830.3_Silent_p.E210E|ARHGEF10_ENST00000518288.1_Silent_p.E235E|ARHGEF10_ENST00000398560.1_Silent_p.E235E			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	278	0	0		WXS	Illumina HiSeq	Phase_I	279	85	0.304659	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			
NUP210	23225	hgsc.bcm.edu	37	3	13399786	13399786	+	Missense_Mutation	SNP	G	G	A	rs6795271	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	179	0	0		WXS	Illumina HiSeq	Phase_I	178	81	0.455056	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	
ZNF431	170959	hgsc.bcm.edu	37	19	21326358	21326358	+	Missense_Mutation	SNP	A	A	G	rs17445374	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21326358A>G	ENST00000311048.7	+	2	152	c.8A>G	c.(7-9)gAc>gGc	p.D3G	ZNF431_ENST00000600692.1_Missense_Mutation_p.D3G|ZNF431_ENST00000594425.1_Missense_Mutation_p.D3G|ZNF431_ENST00000599296.1_Missense_Mutation_p.D3G	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	3			D -> G (in dbSNP:rs17445374).		cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						CCATAGGACGACTTGAAATAT	0.423													.|||	681	0.135982	0.2814	0.1196	5008	,	,		16594	0.002		0.165	False		,,,				2504	0.0593				p.D3G		Atlas-SNP	.											.	ZNF431	71	.	0			c.A8G						PASS	.	A	GLY/ASP	1097,3309		132,833,1238	92.0	85.0	87.0		8	-0.9	0.0	19	dbSNP_123	87	1066,7534		64,938,3298	yes	missense	ZNF431	NM_133473.2	94	196,1771,4536	GG,GA,AA		12.3953,24.8979,16.6308	benign	3/577	21326358	2163,10843	2203	4300	6503	SO:0001583	missense	170959	exon2			AGGACGACTTGAA	AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"""Zinc fingers, C2H2-type"", ""-"""	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.8A>G	19.37:g.21326358A>G	ENSP00000308578:p.Asp3Gly	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_133473	A8KAK7|Q8IWC4	Missense_Mutation	SNP	ENST00000311048.7	37	CCDS32979.1	311	0.1423992673992674	131	0.266260162601626	46	0.1270718232044199	0	0.0	134	0.17678100263852242	.	3.920	-0.018374	0.07681	0.248979	0.123953	ENSG00000196705	ENST00000311048	T	0.07800	3.16	0.461	-0.922	0.10468	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.29378	0.243	B	0.24541	0.054	T	0.48768	-0.9006	7	0.25751	T	0.34	.	.	.	.	rs17445374;rs57055495;rs17445374	3	Q8TF32	ZN431_HUMAN	G	3	ENSP00000308578:D3G	ENSP00000308578:D3G	D	+	2	0	ZNF431	21118198	0.001000	0.12720	0.000000	0.03702	0.012000	0.07955	0.501000	0.22578	-0.604000	0.05760	0.248000	0.18094	GAC	A|0.836;G|0.164	0.164	strong		0.423	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098	
HSPA12A	259217	hgsc.bcm.edu	37	10	118435989	118435989	+	Silent	SNP	C	C	A	rs11197793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:118435989C>A	ENST00000369209.3	-	11	1415	c.1311G>T	c.(1309-1311)tcG>tcT	p.S437S		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	437						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		GCATCCCCTGCGAGGACCACT	0.532													C|||	28	0.00559105	0.0008	0.0101	5008	,	,		22502	0.0		0.0199	False		,,,				2504	0.0				p.S437S		Atlas-SNP	.											.	HSPA12A	81	.	0			c.G1311T						PASS	.	C		10,4234		0,10,2112	106.0	109.0	108.0		1311	-11.3	0.3	10	dbSNP_120	108	115,8393		0,115,4139	no	coding-synonymous	HSPA12A	NM_025015.2		0,125,6251	AA,AC,CC		1.3517,0.2356,0.9802		437/676	118435989	125,12627	2122	4254	6376	SO:0001819	synonymous_variant	259217	exon11			CCCCTGCGAGGAC	AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"""Heat shock proteins / HSP70"""	19022	protein-coding gene	gene with protein product		610701	"""heat shock 70kD protein 12A"""			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.1311G>T	10.37:g.118435989C>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_025015		Silent	SNP	ENST00000369209.3	37	CCDS41569.1																																																																																			C|0.991;A|0.009	0.009	strong		0.532	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015	
GPR151	134391	hgsc.bcm.edu	37	5	145894882	145894882	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145894882G>A	ENST00000311104.2	-	1	871	c.795C>T	c.(793-795)ccC>ccT	p.P265P		NM_194251.2	NP_919227.2	Q8TDV0	GP151_HUMAN	G protein-coupled receptor 151	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(2)	14			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTACCCATTCGGGGAGCCACA	0.507																																					p.P265P	Pancreas(78;420 1386 18535 37114 49710)	Atlas-SNP	.											.	GPR151	35	.	0			c.C795T						PASS	.						54.0	56.0	56.0					5																	145894882		2203	4300	6503	SO:0001819	synonymous_variant	134391	exon1			CCATTCGGGGAGC	AY255557	CCDS34266.1	5q32	2012-08-21						"""GPCR / Class A : Orphans"""	23624	protein-coding gene	gene with protein product	"""galanin receptor 4"""					12679517	Standard	NM_194251		Approved	PGR7, GALR4	uc003lod.1	Q8TDV0		ENST00000311104.2:c.795C>T	5.37:g.145894882G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	113	32	0.283186	NM_194251	Q86SN8|Q8NGV2	Silent	SNP	ENST00000311104.2	37	CCDS34266.1																																																																																			.	.	none		0.507	GPR151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373457.1	NM_194251	
TUBA3D	113457	hgsc.bcm.edu	37	2	132238286	132238286	+	Silent	SNP	C	C	T	rs111626841	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:132238286C>T	ENST00000321253.6	+	4	1127	c.1020C>T	c.(1018-1020)acC>acT	p.T340T		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	340					'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)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		CCAAGCGCACCATCCAGTTTG	0.562													.|||	839	0.167532	0.4592	0.1037	5008	,	,		15998	0.004		0.0924	False		,,,				2504	0.0644				p.T340T	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											.	TUBA3D	60	.	0			c.C1020T						PASS	.	T		1721,2685	627.4+/-394.9	382,957,864	78.0	81.0	80.0		1020	1.5	1.0	2	dbSNP_132	80	712,7888	779.9+/-407.7	41,630,3629	no	coding-synonymous	TUBA3D	NM_080386.2		423,1587,4493	TT,TC,CC		8.2791,39.0604,18.7068		340/451	132238286	2433,10573	2203	4300	6503	SO:0001819	synonymous_variant	113457	exon4			GCGCACCATCCAG	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.1020C>T	2.37:g.132238286C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	138	50	0.362319	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000321253.6	37	CCDS33290.1																																																																																			C|0.831;T|0.169	0.169	strong		0.562	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
AP5B1	91056	hgsc.bcm.edu	37	11	65547333	65547333	+	Missense_Mutation	SNP	G	G	A	rs12146493	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65547333G>A	ENST00000532090.2	-	2	841	c.631C>T	c.(631-633)Ctc>Ttc	p.L211F		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	211	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						TTATCCGTGAGCAGTCCCCCC	0.672													G|||	1521	0.303714	0.4576	0.2363	5008	,	,		16088	0.3413		0.3231	False		,,,				2504	0.0849				p.L211F		Atlas-SNP	.											AP5B1_ENST00000532090,NS,carcinoma,0,2	AP5B1	40	2	0			c.C631T						scavenged	.	G	PHE/LEU	1619,2289		351,917,686	30.0	36.0	34.0		460	4.6	1.0	11	dbSNP_120	34	2644,5616		421,1802,1907	yes	missense	DKFZp761E198	NM_138368.3	22	772,2719,2593	AA,AG,GG		32.0097,41.4278,35.0345	probably-damaging	154/822	65547333	4263,7905	1954	4130	6084	SO:0001583	missense	91056	exon2			CCGTGAGCAGTCC	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.631C>T	11.37:g.65547333G>A	ENSP00000454303:p.Leu211Phe	Somatic	356	2	0.00561798		WXS	Illumina HiSeq	Phase_I	365	166	0.454795	NM_138368	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Missense_Mutation	SNP	ENST00000532090.2	37	CCDS58146.1																																																																																			G|0.644;A|0.356	0.356	strong		0.672	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368	
ECT2L	345930	hgsc.bcm.edu	37	6	139206937	139206937	+	Silent	SNP	A	A	G	rs17067993	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:139206937A>G	ENST00000423192.1	+	17	2390	c.2229A>G	c.(2227-2229)caA>caG	p.Q743Q	ECT2L_ENST00000367682.2_Silent_p.Q743Q|ECT2L_ENST00000541398.1_Intron			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	743	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						CAATTGACCAAATCAAAAAAT	0.413			"""N, Splice, Mis"""		ETP ALL								A|||	640	0.127796	0.2474	0.0346	5008	,	,		19865	0.2183		0.0209	False		,,,				2504	0.0491				p.Q743Q		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A2229G						PASS	.	A	,	710,3218		66,578,1320	59.0	60.0	59.0		2229,2229	0.5	0.7	6	dbSNP_123	59	161,8151		0,161,3995	no	coding-synonymous,coding-synonymous	ECT2L	NM_001077706.2,NM_001195037.2	,	66,739,5315	GG,GA,AA		1.937,18.0754,7.116	,	743/905,743/905	139206937	871,11369	1964	4156	6120	SO:0001819	synonymous_variant	345930	exon17			TGACCAAATCAAA		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.2229A>G	6.37:g.139206937A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Silent	SNP	ENST00000423192.1	37	CCDS43508.1																																																																																			A|0.902;G|0.098	0.098	strong		0.413	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60021761	60021761	+	Missense_Mutation	SNP	C	C	T	rs35211496	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	25	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	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		
ADAD2	161931	hgsc.bcm.edu	37	16	84229892	84229892	+	Missense_Mutation	SNP	C	C	T	rs141742506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:84229892C>T	ENST00000315906.5	+	8	1494	c.1442C>T	c.(1441-1443)aCc>aTc	p.T481I	ADAD2_ENST00000268624.3_Missense_Mutation_p.T563I|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	481	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						ACCCCTGACACCTGCCGTGGC	0.687													C|||	15	0.00299521	0.0008	0.0029	5008	,	,		16705	0.0		0.0119	False		,,,				2504	0.0				p.T563I		Atlas-SNP	.											.	ADAD2	46	.	0			c.C1688T						PASS	.	C	ILE/THR,ILE/THR	12,4382		0,12,2185	36.0	45.0	42.0		1442,1688	-1.2	0.4	16	dbSNP_134	42	122,8462		1,120,4171	yes	missense,missense	ADAD2	NM_001145400.1,NM_139174.3	89,89	1,132,6356	TT,TC,CC		1.4212,0.2731,1.0325	possibly-damaging,possibly-damaging	481/584,563/666	84229892	134,12844	2197	4292	6489	SO:0001583	missense	161931	exon9			CTGACACCTGCCG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1442C>T	16.37:g.84229892C>T	ENSP00000325153:p.Thr481Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	104	11	0.105769	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	37	CCDS45536.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	4.708	0.131702	0.08981	0.002731	0.014212	ENSG00000140955	ENST00000315906;ENST00000268624	D;D	0.93659	-3.26;-3.26	4.63	-1.16	0.09678	Adenosine deaminase/editase (2);	0.429950	0.20572	N	0.089706	D	0.88633	0.6489	M	0.79258	2.445	0.25992	N	0.982239	P;P	0.52692	0.837;0.955	P;P	0.47528	0.448;0.549	T	0.82444	-0.0454	10	0.44086	T	0.13	-29.923	2.7582	0.05299	0.3015:0.3169:0.294:0.0877	.	481;563	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	I	481;563	ENSP00000325153:T481I;ENSP00000268624:T563I	ENSP00000268624:T563I	T	+	2	0	ADAD2	82787393	0.000000	0.05858	0.434000	0.26772	0.036000	0.12997	-0.303000	0.08210	0.026000	0.15269	-1.792000	0.00626	ACC	C|0.991;T|0.009	0.009	strong		0.687	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388693	1388693	+	Missense_Mutation	SNP	C	C	G	rs78906219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1388693C>G	ENST00000324803.4	+	1	3354	c.394C>G	c.(394-396)Cat>Gat	p.H132D		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	132					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.H132D(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|||	864	0.172524	0.112	0.2421	5008	,	,		13504	0.0546		0.2783	False		,,,				2504	0.2178				p.H132D		Atlas-SNP	.											CRIPAK,caecum,carcinoma,0,2	CRIPAK	185	2	1	Substitution - Missense(1)	skin(1)	c.C394G						scavenged	.						68.0	69.0	68.0					4																	1388693		2197	4291	6488	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.394C>G	4.37:g.1388693C>G	ENSP00000323978:p.His132Asp	Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	45	35	0.777778	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.898|0.898	-0.723180|-0.723180	0.03158|0.03158	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000324803|ENST00000382944	T|.	0.18657|.	2.2|.	0.666|0.666	-0.474|-0.474	0.12108|0.12108	.|.	.|.	.|.	.|.	.|.	T|T	0.12178|0.12178	0.0296|0.0296	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.33929|0.33929	-0.9849|-0.9849	8|5	0.28530|0.05833	T|T	0.3|0.94	.|.	2.4426|2.4426	0.04498|0.04498	0.0:0.4251:0.3263:0.2486|0.0:0.4251:0.3263:0.2486	.|.	132|.	Q8N1N5|.	CRPAK_HUMAN|.	D|R	132|115	ENSP00000323978:H132D|.	ENSP00000323978:H132D|ENSP00000372402:P115R	H|P	+|+	1|2	0|0	CRIPAK|CRIPAK	1378693|1378693	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-1.786000|-1.786000	0.01766|0.01766	-0.170000|-0.170000	0.10816|0.10816	-1.737000|-1.737000	0.00689|0.00689	CAT|CCA	G|1.000;|0.000	1.000	weak		0.697	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
C10orf71	118461	hgsc.bcm.edu	37	10	50532812	50532812	+	Missense_Mutation	SNP	A	A	G	rs11101093	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	232	0	0		WXS	Illumina HiSeq	Phase_I	164	35	0.213415	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	
C1orf127	148345	hgsc.bcm.edu	37	1	11014118	11014118	+	Missense_Mutation	SNP	C	C	T	rs45537241	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11014118C>T	ENST00000377008.4	-	9	1002	c.556G>A	c.(556-558)Gcc>Acc	p.A186T	C1orf127_ENST00000377004.4_Missense_Mutation_p.A353T			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	186										NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		AGGACCGGGGCAGCCATCTCG	0.567													C|||	1099	0.219449	0.0666	0.2752	5008	,	,		19057	0.2331		0.164	False		,,,				2504	0.4294				p.A353T		Atlas-SNP	.											.	C1orf127	134	.	0			c.G1057A						PASS	.	C	THR/ALA	334,4072	176.2+/-205.4	10,314,1879	127.0	127.0	127.0		1057	-9.4	0.0	1	dbSNP_127	127	1301,7299	258.1+/-281.9	109,1083,3108	yes	missense	C1orf127	NM_001170754.1	58	119,1397,4987	TT,TC,CC		15.1279,7.5806,12.5711	possibly-damaging	353/824	11014118	1635,11371	2203	4300	6503	SO:0001583	missense	148345	exon10			CCGGGGCAGCCAT	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.556G>A	1.37:g.11014118C>T	ENSP00000366207:p.Ala186Thr	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	150	105	0.7	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		404	0.184981684981685	37	0.07520325203252033	95	0.26243093922651933	140	0.24475524475524477	132	0.1741424802110818	C	10.67	1.414656	0.25465	0.075806	0.151279	ENSG00000175262	ENST00000377004;ENST00000377008	T;T	0.23950	1.88;1.88	5.07	-9.42	0.00610	.	1.465320	0.04235	N	0.335928	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.14012	0.009;0.009;0.009	B;B;B	0.14023	0.007;0.007;0.01	T	0.26360	-1.0105	9	0.20519	T	0.43	-0.8287	0.8276	0.01124	0.2794:0.1313:0.1779:0.4113	rs45537241	204;204;186	B7ZLG7;Q8N9H9-2;Q8N9H9	.;.;CA127_HUMAN	T	353;186	ENSP00000366203:A353T;ENSP00000366207:A186T	ENSP00000366203:A353T	A	-	1	0	C1orf127	10936705	0.000000	0.05858	0.000000	0.03702	0.391000	0.30476	-1.475000	0.02335	-2.102000	0.00845	-0.345000	0.07892	GCC	C|0.852;T|0.148	0.148	strong		0.567	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
SCML4	256380	hgsc.bcm.edu	37	6	108029109	108029109	+	Silent	SNP	T	T	C	rs3734754	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:108029109T>C	ENST00000369020.3	-	7	1325	c.1080A>G	c.(1078-1080)ccA>ccG	p.P360P	SCML4_ENST00000369022.2_Silent_p.P302P|SCML4_ENST00000369025.2_Silent_p.P118P	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	360					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)		CCAGAGCCTGTGGGTCGGCGT	0.632													C|||	1125	0.224641	0.1778	0.1354	5008	,	,		18716	0.369		0.1978	False		,,,				2504	0.2301				p.P360P		Atlas-SNP	.											SCML4_ENST00000369020,colon,carcinoma,0,1	SCML4	65	1	0			c.A1080G						scavenged	.	C		272,1112		23,226,443	48.0	57.0	54.0		1080	-8.3	0.3	6	dbSNP_107	54	573,2609		54,465,1072	no	coding-synonymous	SCML4	NM_198081.3		77,691,1515	CC,CT,TT		18.0075,19.6532,18.5064		360/415	108029109	845,3721	692	1591	2283	SO:0001819	synonymous_variant	256380	exon7			AGCCTGTGGGTCG		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.1080A>G	6.37:g.108029109T>C		Somatic	171	3	0.0175439		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Silent	SNP	ENST00000369020.3	37	CCDS5060.2																																																																																			T|0.784;C|0.216	0.216	strong		0.632	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
PLEC	5339	hgsc.bcm.edu	37	8	145001588	145001588	+	Missense_Mutation	SNP	C	C	T	rs11136334	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145001588C>T	ENST00000322810.4	-	27	4326	c.4157G>A	c.(4156-4158)cGg>cAg	p.R1386Q	PLEC_ENST00000398774.2_Missense_Mutation_p.R1217Q|PLEC_ENST00000527096.1_Missense_Mutation_p.R1272Q|PLEC_ENST00000357649.2_Missense_Mutation_p.R1253Q|PLEC_ENST00000345136.3_Missense_Mutation_p.R1249Q|PLEC_ENST00000356346.3_Missense_Mutation_p.R1235Q|PLEC_ENST00000436759.2_Missense_Mutation_p.R1276Q|PLEC_ENST00000354958.2_Missense_Mutation_p.R1227Q|PLEC_ENST00000354589.3_Missense_Mutation_p.R1249Q	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1386	Globular 1.		R -> Q (in dbSNP:rs11136334).		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						CTGCTCCTGCCGCAGCTGCTC	0.736													C|||	1156	0.230831	0.028	0.2954	5008	,	,		13418	0.1429		0.4274	False		,,,				2504	0.3476				p.R1386Q		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	0			c.G4157A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	388,3674		38,312,1681	12.0	16.0	15.0		3746,3758,3746,3650,4157,3680,3704,3827	-0.7	1.0	8	dbSNP_120	15	3413,4885		747,1919,1483	no	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	43,43,43,43,43,43,43,43	785,2231,3164	TT,TC,CC		41.1304,9.5519,30.7524	benign,benign,benign,benign,benign,benign,benign,benign	1249/4548,1253/4552,1249/4548,1217/4516,1386/4685,1227/4526,1235/4534,1276/4575	145001588	3801,8559	2031	4149	6180	SO:0001583	missense	5339	exon27			TCCTGCCGCAGCT	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.4157G>A	8.37:g.145001588C>T	ENSP00000323856:p.Arg1386Gln	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	536	0.2454212454212454	15	0.03048780487804878	108	0.2983425414364641	94	0.16433566433566432	319	0.420844327176781	C	12.61	1.989397	0.35131	0.095519	0.411304	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38;1.38	5.1	-0.662	0.11413	.	1.260670	0.05768	N	0.606168	T	0.00012	0.0000	N	0.02011	-0.69	0.41093	P	0.014382000000000006	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	0.44605	-0.9317	9	0.19590	T	0.45	.	4.6892	0.12772	0.2556:0.2308:0.0:0.5136	rs11136334	1276;1235;1227;1386;1217;1249;1253;1249	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	Q	1249;1253;1249;1217;1386;1227;1235;1276;1272	ENSP00000344848:R1249Q;ENSP00000350277:R1253Q;ENSP00000346602:R1249Q;ENSP00000381756:R1217Q;ENSP00000323856:R1386Q;ENSP00000347044:R1227Q;ENSP00000348702:R1235Q;ENSP00000388180:R1276Q;ENSP00000434583:R1272Q	ENSP00000323856:R1386Q	R	-	2	0	PLEC	145073576	0.001000	0.12720	0.979000	0.43373	0.833000	0.47200	0.002000	0.13061	-0.040000	0.13580	-0.369000	0.07265	CGG	C|0.706;T|0.294	0.294	strong		0.736	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
FLG	2312	hgsc.bcm.edu	37	1	152286002	152286002	+	Missense_Mutation	SNP	T	T	C	rs386635459|rs2011331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152286002T>C	ENST00000368799.1	-	3	1395	c.1360A>G	c.(1360-1362)Aca>Gca	p.T454A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	454	Ser-rich.		T -> A (in dbSNP:rs2011331).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGGCCACGTGTGGACTCTTGG	0.587									Ichthyosis				-|||	2324	0.464058	0.5204	0.4539	5008	,	,		18904	0.6587		0.173	False		,,,				2504	0.4939				p.T454A		Atlas-SNP	.											.	FLG	900	.	0			c.A1360G						PASS	.	C	ALA/THR	2058,2348		473,1112,618	201.0	196.0	198.0		1360	-6.9	0.0	1	dbSNP_92	198	1461,7139		126,1209,2965	no	missense	FLG	NM_002016.1	58	599,2321,3583	CC,CT,TT		16.9884,46.709,27.0567	benign	454/4062	152286002	3519,9487	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CACGTGTGGACTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1360A>G	1.37:g.152286002T>C	ENSP00000357789:p.Thr454Ala	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	466	170	0.364807	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	869	0.39789377289377287	240	0.4878048780487805	136	0.3756906077348066	360	0.6293706293706294	133	0.17546174142480211	-	3.629	-0.075933	0.07184	0.46709	0.169884	ENSG00000143631	ENST00000368799	T	0.02197	4.4	3.43	-6.86	0.01676	.	.	.	.	.	T	0.00210	0.0006	N	0.05230	-0.09	0.80722	P	0.0	B	0.19935	0.04	B	0.11329	0.006	T	0.48559	-0.9025	8	0.05620	T	0.96	.	0.0862	0.00036	0.2681:0.2448:0.199:0.2881	rs60352258	454	P20930	FILA_HUMAN	A	454	ENSP00000357789:T454A	ENSP00000357789:T454A	T	-	1	0	FLG	150552626	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.855000	0.00729	-3.086000	0.00249	-1.512000	0.00943	ACA	T|0.667;C|0.333	0.333	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
OR13C5	138799	hgsc.bcm.edu	37	9	107361642	107361642	+	Missense_Mutation	SNP	G	G	A	rs1851722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:107361642G>A	ENST00000374779.2	-	1	146	c.53C>T	c.(52-54)tCt>tTt	p.S18F		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	18			S -> F (in dbSNP:rs1851722).			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						TGGGTGACCAGAAAGTCCCTT	0.388													G|||	1205	0.240615	0.0998	0.366	5008	,	,		20151	0.38		0.2445	False		,,,				2504	0.1943				p.S18F		Atlas-SNP	.											.	OR13C5	60	.	0			c.C53T						PASS	.						49.0	52.0	51.0					9																	107361642		2201	4294	6495	SO:0001583	missense	138799	exon1			TGACCAGAAAGTC		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.53C>T	9.37:g.107361642G>A	ENSP00000363911:p.Ser18Phe	Somatic	501	1	0.00199601		WXS	Illumina HiSeq	Phase_I	417	154	0.369305	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	599	0.2742673992673993	53	0.10772357723577236	127	0.35082872928176795	218	0.3811188811188811	201	0.26517150395778366	G	15.10	2.732376	0.48939	.	.	ENSG00000255800	ENST00000374779	T	0.00441	7.41	3.84	2.91	0.33838	.	0.000000	0.36932	U	0.002336	T	0.00012	0.0000	M	0.76170	2.325	0.80722	P	0.0	D	0.60575	0.988	P	0.54924	0.764	T	0.49143	-0.8970	9	0.87932	D	0	.	10.221	0.43196	0.0:0.0:0.8:0.2	rs1851722;rs35304986;rs57432004;rs1851722	18	Q8NGS8	O13C5_HUMAN	F	18	ENSP00000363911:S18F	ENSP00000363911:S18F	S	-	2	0	OR13C5	106401463	0.025000	0.19082	0.002000	0.10522	0.240000	0.25518	2.042000	0.41222	0.777000	0.33496	0.531000	0.56144	TCT	G|1.000;|0.000	.	weak		0.388	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
FBXL4	26235	hgsc.bcm.edu	37	6	99374400	99374400	+	Silent	SNP	G	G	A	rs1011676	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:99374400G>A	ENST00000369244.2	-	4	893	c.465C>T	c.(463-465)ctC>ctT	p.L155L	FBXL4_ENST00000229971.1_Silent_p.L155L	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	155					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		CAGAACAAGCGAGAATTCTAA	0.393													G|||	162	0.0323482	0.0023	0.0389	5008	,	,		19465	0.0		0.0636	False		,,,				2504	0.0695				p.L155L		Atlas-SNP	.											.	FBXL4	54	.	0			c.C465T						PASS	.	G		81,4325	69.8+/-107.6	1,79,2123	93.0	89.0	90.0		465	-0.9	1.0	6	dbSNP_86	90	700,7900	172.3+/-223.0	43,614,3643	no	coding-synonymous	FBXL4	NM_012160.3		44,693,5766	AA,AG,GG		8.1395,1.8384,6.0049		155/622	99374400	781,12225	2203	4300	6503	SO:0001819	synonymous_variant	26235	exon3			ACAAGCGAGAATT	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"""F-boxes / Leucine-rich repeats"""	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.465C>T	6.37:g.99374400G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	137	54	0.394161	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Silent	SNP	ENST00000369244.2	37	CCDS5041.1																																																																																			G|0.955;A|0.045	0.045	strong		0.393	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2		
UMOD	7369	hgsc.bcm.edu	37	16	20359633	20359633	+	Silent	SNP	C	C	T	rs28544423	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:20359633C>T	ENST00000570689.1	-	4	1031	c.885G>A	c.(883-885)ggG>ggA	p.G295G	UMOD_ENST00000396134.2_Silent_p.G328G|UMOD_ENST00000396138.4_Silent_p.G344G|UMOD_ENST00000424589.1_Silent_p.G328G|UMOD_ENST00000396142.2_Silent_p.G295G|UMOD_ENST00000302509.4_Silent_p.G295G			P07911	UROM_HUMAN	uromodulin	295					cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)			endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						CCTCACACGTCCCCTCCACGG	0.567													c|||	580	0.115815	0.0673	0.1599	5008	,	,		20928	0.0129		0.1998	False		,,,				2504	0.1697				p.G295G		Atlas-SNP	.											.	UMOD	128	.	0			c.G885A						PASS	.		,	337,4069	175.5+/-204.9	17,303,1883	196.0	177.0	183.0		885,885	-4.2	0.5	16	dbSNP_125	183	1626,6974	301.8+/-305.6	154,1318,2828	no	coding-synonymous,coding-synonymous	UMOD	NM_001008389.1,NM_003361.2	,	171,1621,4711	TT,TC,CC		18.907,7.6487,15.093	,	295/641,295/641	20359633	1963,11043	2203	4300	6503	SO:0001819	synonymous_variant	7369	exon4			ACACGTCCCCTCC	M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"""Tamm-Horsfall glycoprotein"", ""uromucoid"""	191845	"""uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"""			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.885G>A	16.37:g.20359633C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	70	28	0.4	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Silent	SNP	ENST00000570689.1	37	CCDS10583.1																																																																																			C|0.858;T|0.142	0.142	strong		0.567	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1		
NLRP10	338322	hgsc.bcm.edu	37	11	7981521	7981521	+	Silent	SNP	C	C	T	rs11608118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	113	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	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	
KANK3	256949	hgsc.bcm.edu	37	19	8389405	8389405	+	Silent	SNP	G	G	A	rs12981073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:8389405G>A	ENST00000593649.1	-	10	2375	c.2310C>T	c.(2308-2310)gcC>gcT	p.A770A	KANK3_ENST00000330915.3_Silent_p.A770A			Q6NY19	KANK3_HUMAN	KN motif and ankyrin repeat domains 3	770										breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	9						CAGCCTCCAGGGCGATGGCCA	0.632													G|||	769	0.153554	0.295	0.1383	5008	,	,		18814	0.0655		0.1223	False		,,,				2504	0.0961				p.A770A		Atlas-SNP	.											.	KANK3	35	.	0			c.C2310T						PASS	.	G		1101,3305	379.2+/-323.2	134,833,1236	26.0	26.0	26.0		2310	1.2	1.0	19	dbSNP_121	26	1053,7547	214.2+/-253.9	70,913,3317	no	coding-synonymous	KANK3	NM_198471.2		204,1746,4553	AA,AG,GG		12.2442,24.9887,16.5616		770/822	8389405	2154,10852	2203	4300	6503	SO:0001819	synonymous_variant	256949	exon10			CTCCAGGGCGATG	AK128815	CCDS12199.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000186994		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	24796	protein-coding gene	gene with protein product		614611	"""ankyrin repeat domain 47"""	ANKRD47		17996375, 19554261	Standard	NM_198471		Approved	FLJ46061	uc010dwa.3	Q6NY19		ENST00000593649.1:c.2310C>T	19.37:g.8389405G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	155	68	0.43871	NM_198471	Q6NZI1|Q6ZQR3|Q8IUV2	Silent	SNP	ENST00000593649.1	37																																																																																				G|0.840;A|0.159	0.159	strong		0.632	KANK3-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000461379.1	NM_198471	
DIS3L2	129563	hgsc.bcm.edu	37	2	233201328	233201328	+	Silent	SNP	A	A	G	rs3811578	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:233201328A>G	ENST00000409307.1	+	20	2646	c.2646A>G	c.(2644-2646)tcA>tcG	p.S882S	DIS3L2_ENST00000325385.7_Silent_p.S882S|DIS3L2_ENST00000273009.6_Intron					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CCGAGGACTCAAGCACCAGCT	0.662													A|||	1012	0.202077	0.1732	0.2579	5008	,	,		9237	0.4484		0.0865	False		,,,				2504	0.0665				p.S882S		Atlas-SNP	.											.	DIS3L2	77	.	0			c.A2646G						PASS	.	A		549,3537		37,475,1531	15.0	21.0	19.0		2646	2.9	0.7	2	dbSNP_107	19	690,7680		28,634,3523	no	coding-synonymous	DIS3L2	NM_152383.4		65,1109,5054	GG,GA,AA		8.2437,13.4361,9.947		882/886	233201328	1239,11217	2043	4185	6228	SO:0001819	synonymous_variant	129563	exon21			GGACTCAAGCACC	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.2646A>G	2.37:g.233201328A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_152383		Silent	SNP	ENST00000409307.1	37	CCDS42834.1	473	0.21657509157509158	65	0.13211382113821138	69	0.19060773480662985	279	0.48776223776223776	60	0.079155672823219	A	8.285	0.816528	0.16607	0.134361	0.082437	ENSG00000144535	ENST00000418143	.	.	.	4.06	2.89	0.33648	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22656	P	0.99888447	.	.	.	.	.	.	T	0.50013	-0.8877	3	.	.	.	.	5.6377	0.17546	0.875:0.0:0.125:0.0	rs3811578;rs3811578	.	.	.	E	163	.	.	K	+	1	0	DIS3L2	232909572	0.000000	0.05858	0.693000	0.30195	0.069000	0.16628	-0.295000	0.08298	1.622000	0.50330	0.529000	0.55759	AAG	A|0.797;G|0.203	0.203	strong		0.662	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	
CFAP57	149465	hgsc.bcm.edu	37	1	43638457	43638457	+	Silent	SNP	T	T	A	rs1782387	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43638457T>A	ENST00000372492.4	+	2	357	c.33T>A	c.(31-33)gtT>gtA	p.V11V	WDR65_ENST00000528956.1_Silent_p.V11V|EBNA1BP2_ENST00000236051.2_5'Flank|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	183	0	0		WXS	Illumina HiSeq	Phase_I	65	16	0.246154	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		
FNBP4	23360	hgsc.bcm.edu	37	11	47745589	47745589	+	Missense_Mutation	SNP	T	T	C	rs34242224	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47745589T>C	ENST00000263773.5	-	14	2467	c.2455A>G	c.(2455-2457)Ata>Gta	p.I819V	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	819						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						CCTGTAGCTATAGCTGACTGG	0.388													T|||	153	0.0305511	0.0053	0.0504	5008	,	,		18832	0.0		0.0875	False		,,,				2504	0.0235				p.I819V		Atlas-SNP	.											.	FNBP4	99	.	0			c.A2455G						PASS	.	T	VAL/ILE	58,3696		1,56,1820	107.0	106.0	106.0		2455	-6.8	0.7	11	dbSNP_126	106	721,7531		28,665,3433	yes	missense	FNBP4	NM_015308.2	29	29,721,5253	CC,CT,TT		8.7373,1.545,6.4884	benign	819/1018	47745589	779,11227	1877	4126	6003	SO:0001583	missense	23360	exon14			TAGCTATAGCTGA	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.2455A>G	11.37:g.47745589T>C	ENSP00000263773:p.Ile819Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	37	CCDS41644.1	97	0.044413919413919416	6	0.012195121951219513	24	0.06629834254143646	0	0.0	67	0.08839050131926121	T	6.862	0.528323	0.13127	0.01545	0.087373	ENSG00000109920	ENST00000263773	T	0.41758	0.99	5.07	-6.82	0.01698	.	1.374210	0.03891	N	0.278631	T	0.00580	0.0019	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05971	-1.0853	9	0.27785	T	0.31	-0.4376	0.5329	0.00631	0.2012:0.2622:0.2042:0.3325	rs34242224	819	Q8N3X1	FNBP4_HUMAN	V	819	ENSP00000263773:I819V	ENSP00000263773:I819V	I	-	1	0	FNBP4	47702165	0.000000	0.05858	0.694000	0.30210	0.903000	0.53119	-2.117000	0.01326	-0.837000	0.04223	0.459000	0.35465	ATA	T|0.943;C|0.057	0.057	strong		0.388	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		
PIEZO2	63895	hgsc.bcm.edu	37	18	10681711	10681711	+	Missense_Mutation	SNP	C	C	T	rs3748428	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:10681711C>T	ENST00000503781.3	-	47	7386	c.7387G>A	c.(7387-7389)Gtt>Att	p.V2463I	PIEZO2_ENST00000581680.1_5'Flank|PIEZO2_ENST00000285141.4_Missense_Mutation_p.V255I|PIEZO2_ENST00000538948.1_Missense_Mutation_p.V420I|PIEZO2_ENST00000302079.6_Missense_Mutation_p.V2400I|PIEZO2_ENST00000580640.1_Missense_Mutation_p.V2488I	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	137	0	0		WXS	Illumina HiSeq	Phase_I	114	66	0.578947	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	
GPR97	222487	hgsc.bcm.edu	37	16	57707249	57707249	+	Silent	SNP	C	C	T	rs73552781	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57707249C>T	ENST00000333493.4	+	2	236	c.75C>T	c.(73-75)acC>acT	p.T25T	GPR97_ENST00000450388.3_5'UTR|GPR97_ENST00000327655.6_5'UTR	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	25					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAAAGCCCACCGAAGGGCCAA	0.547													C|||	176	0.0351438	0.087	0.0187	5008	,	,		21297	0.001		0.0378	False		,,,				2504	0.0092				p.T25T		Atlas-SNP	.											.	GPR97	74	.	0			c.C75T						PASS	.	C		375,4021	190.5+/-216.4	14,347,1837	82.0	74.0	77.0		75	-6.8	0.0	16	dbSNP_130	77	318,8282	113.1+/-173.2	10,298,3992	no	coding-synonymous	GPR97	NM_170776.4		24,645,5829	TT,TC,CC		3.6977,8.5305,5.3324		25/550	57707249	693,12303	2198	4300	6498	SO:0001819	synonymous_variant	222487	exon2			GCCCACCGAAGGG	AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.75C>T	16.37:g.57707249C>T		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	193	170	0.880829	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Silent	SNP	ENST00000333493.4	37	CCDS10786.1																																																																																			C|0.957;T|0.043	0.043	strong		0.547	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
PODN	127435	hgsc.bcm.edu	37	1	53535499	53535499	+	Missense_Mutation	SNP	C	C	T	rs17107831	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:53535499C>T	ENST00000312553.5	+	2	123	c.116C>T	c.(115-117)gCa>gTa	p.A39V	PODN_ENST00000395871.2_Missense_Mutation_p.A39V|RP11-334A14.5_ENST00000447867.1_RNA|PODN_ENST00000371500.3_Missense_Mutation_p.A20V	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						CGCCCAGGCGCATCTGACTCG	0.687													C|||	324	0.0646965	0.0862	0.0533	5008	,	,		15647	0.0417		0.0457	False		,,,				2504	0.0869				p.A39V		Atlas-SNP	.											.	PODN	86	.	0			c.C116T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	295,4013		14,267,1873	9.0	11.0	10.0		59,59,116,116	-2.8	0.0	1	dbSNP_123	10	425,8051		12,401,3825	yes	missense,missense,missense,missense	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	64,64,64,64	26,668,5698	TT,TC,CC		5.0142,6.8477,5.632	benign,benign,benign,benign	20/643,20/643,39/520,39/662	53535499	720,12064	2154	4238	6392	SO:0001583	missense	127435	exon2			CAGGCGCATCTGA	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.116C>T	1.37:g.53535499C>T	ENSP00000308315:p.Ala39Val	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	73	19	0.260274	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Missense_Mutation	SNP	ENST00000312553.5	37	CCDS573.1	124	0.056776556776556776	42	0.08536585365853659	25	0.06906077348066299	20	0.03496503496503497	37	0.048812664907651716	C	10.10	1.257525	0.22965	0.068477	0.050142	ENSG00000174348	ENST00000371500;ENST00000395871;ENST00000312553	T;T;T	0.61627	0.86;0.09;0.88	2.97	-2.79	0.05841	.	2.383590	0.01887	N	0.038265	T	0.02119	0.0066	.	.	.	0.09310	N	1	B;B;B	0.14012	0.009;0.009;0.009	B;B;B	0.20767	0.031;0.019;0.031	T	0.10989	-1.0606	9	0.49607	T	0.09	.	4.4141	0.11447	0.5121:0.1939:0.294:0.0	rs17107831;rs17107831	39;20;39	Q7Z5L7-4;Q7Z5L7-2;Q7Z5L7-3	.;.;.	V	20;39;39	ENSP00000360555:A20V;ENSP00000379212:A39V;ENSP00000308315:A39V	ENSP00000308315:A39V	A	+	2	0	PODN	53308087	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.018000	0.03626	-0.522000	0.06417	-0.479000	0.04858	GCA	C|0.933;T|0.067	0.067	strong		0.687	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703	
PLCL2	23228	hgsc.bcm.edu	37	3	17053613	17053613	+	Silent	SNP	C	C	T	rs61751588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:17053613C>T	ENST00000418129.2	+	2	2862	c.2397C>T	c.(2395-2397)ccC>ccT	p.P799P	PLCL2_ENST00000432376.1_Silent_p.P799P|PLCL2_ENST00000396755.2_Silent_p.P799P	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	925	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				B cell proliferation involved in immune response (GO:0002322)|B-1a B cell differentiation (GO:0002337)|gamma-aminobutyric acid signaling pathway (GO:0007214)|intracellular signal transduction (GO:0035556)|lipid metabolic process (GO:0006629)|negative regulation of B cell receptor signaling pathway (GO:0050859)|positive regulation of receptor binding (GO:1900122)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|GABA receptor binding (GO:0050811)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	43						ATGCCCAGCCCCCTATACGGG	0.438													C|||	34	0.00678914	0.0008	0.0043	5008	,	,		17519	0.0		0.0258	False		,,,				2504	0.0041				p.P799P		Atlas-SNP	.											.	PLCL2	145	.	0			c.C2397T						PASS	.	C	,	19,4387	24.3+/-50.5	1,17,2185	60.0	65.0	64.0		2779,2397	-0.4	1.0	3	dbSNP_129	64	175,8423	75.1+/-137.7	3,169,4127	yes	coding-synonymous,coding-synonymous	PLCL2	NM_001144382.1,NM_015184.5	,	4,186,6312	TT,TC,CC		2.0354,0.4312,1.4918	,	925/1128,799/1002	17053613	194,12810	2203	4299	6502	SO:0001819	synonymous_variant	23228	exon2			CCAGCCCCCTATA	AB029015	CCDS33713.1, CCDS74911.1	3p25.3-p25.1	2008-03-18	2002-02-18	2002-02-22	ENSG00000154822	ENSG00000154822			9064	protein-coding gene	gene with protein product		614276	"""phospholipase C, epsilon 2"""	PLCE2		10470851	Standard	NM_015184		Approved	KIAA1092	uc011awd.2	Q9UPR0	OTTHUMG00000155467	ENST00000418129.2:c.2397C>T	3.37:g.17053613C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Silent	SNP	ENST00000418129.2	37	CCDS33713.1	23	0.010531135531135532	0	0.0	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	9.281	1.048206	0.19827	0.004312	0.020354	ENSG00000154822	ENST00000419842	T	0.20069	2.1	5.53	-0.419	0.12340	.	0.164246	0.53938	D	0.000054	T	0.04407	0.0121	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12142	-1.0559	7	0.10636	T	0.68	.	9.1754	0.37109	0.4233:0.203:0.3736:0.0	rs61751588	.	.	.	L	543	ENSP00000404433:P543L	ENSP00000404433:P543L	P	+	2	0	PLCL2	17028617	0.893000	0.30496	0.989000	0.46669	0.984000	0.73092	-0.009000	0.12765	0.255000	0.21593	0.491000	0.48974	CCC	C|0.987;T|0.013	0.013	strong		0.438	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3		
EPHA3	2042	hgsc.bcm.edu	37	3	89498428	89498428	+	Silent	SNP	G	G	A	rs1398197	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:89498428G>A	ENST00000336596.2	+	14	2625	c.2400G>A	c.(2398-2400)aaG>aaA	p.K800K	EPHA3_ENST00000494014.1_Silent_p.K800K	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	800	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		CCTACCGCAAGTTCACGTCAG	0.443										TSP Lung(6;0.00050)			G|||	564	0.11262	0.2625	0.0879	5008	,	,		16928	0.0516		0.0457	False		,,,				2504	0.0593				p.K800K		Atlas-SNP	.											.	EPHA3	501	.	0			c.G2400A						PASS	.	G		999,3407	373.2+/-320.7	121,757,1325	231.0	216.0	221.0		2400	-2.4	1.0	3	dbSNP_88	221	502,8098	143.9+/-199.8	14,474,3812	no	coding-synonymous	EPHA3	NM_005233.5		135,1231,5137	AA,AG,GG		5.8372,22.6736,11.5408		800/984	89498428	1501,11505	2203	4300	6503	SO:0001819	synonymous_variant	2042	exon14			CCGCAAGTTCACG	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.2400G>A	3.37:g.89498428G>A		Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	332	151	0.454819	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																			G|0.889;A|0.111	0.111	strong		0.443	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
KCNA10	3744	hgsc.bcm.edu	37	1	111060669	111060669	+	Silent	SNP	T	T	C	rs1281175	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:111060669T>C	ENST00000369771.2	-	1	1128	c.741A>G	c.(739-741)ctA>ctG	p.L247L		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	247					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)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	TGACCACCTTTAGCTCCCTAT	0.557													C|||	3126	0.624201	0.5144	0.7839	5008	,	,		19924	0.5853		0.7336	False		,,,				2504	0.5869				p.L247L		Atlas-SNP	.											.	KCNA10	92	.	0			c.A741G						PASS	.	C		2451,1955	553.3+/-378.7	676,1099,428	164.0	132.0	143.0		741	3.7	1.0	1	dbSNP_87	143	6283,2317	389.5+/-342.9	2289,1705,306	no	coding-synonymous	KCNA10	NM_005549.2		2965,2804,734	CC,CT,TT		26.9419,44.3713,32.8464		247/512	111060669	8734,4272	2203	4300	6503	SO:0001819	synonymous_variant	3744	exon1			CACCTTTAGCTCC	U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.741A>G	1.37:g.111060669T>C		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_005549		Silent	SNP	ENST00000369771.2	37	CCDS826.1																																																																																			T|0.326;C|0.674	0.674	strong		0.557	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549	
ABCF2	10061	hgsc.bcm.edu	37	7	150912786	150912786	+	Silent	SNP	T	T	C	rs7786151	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:150912786T>C	ENST00000287844.2	-	13	1543	c.1434A>G	c.(1432-1434)tcA>tcG	p.S478S	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Silent_p.S478S	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	478	ABC transporter 2. {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)		ACTCCAAAGGTGAGAGATCTA	0.468													C|||	436	0.0870607	0.1573	0.1196	5008	,	,		21058	0.0159		0.0775	False		,,,				2504	0.0521				p.S478S		Atlas-SNP	.											.	ABCF2	54	.	0			c.A1434G						PASS	.	C	,	640,3766	766.9+/-413.5	46,548,1609	154.0	135.0	141.0		1434,1434	-10.0	0.3	7	dbSNP_116	141	835,7765	781.0+/-407.6	47,741,3512	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	93,1289,5121	CC,CT,TT		9.7093,14.5256,11.3409	,	478/635,478/624	150912786	1475,11531	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon13			CAAAGGTGAGAGA	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.1434A>G	7.37:g.150912786T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	112	17	0.151786	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			T|0.901;C|0.099	0.099	strong		0.468	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
SPTBN4	57731	hgsc.bcm.edu	37	19	41008049	41008049	+	Silent	SNP	A	A	G	rs814526	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41008049A>G	ENST00000352632.3	+	9	998	c.912A>G	c.(910-912)gtA>gtG	p.V304V	SPTBN4_ENST00000344104.3_Silent_p.V304V|SPTBN4_ENST00000595535.1_Silent_p.V304V|SPTBN4_ENST00000338932.3_Silent_p.V304V|SPTBN4_ENST00000598249.1_Silent_p.V304V			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	304					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)			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)			TGGACCAGGTATTGGAGGTGG	0.602													G|||	1891	0.377596	0.6596	0.2507	5008	,	,		17749	0.1766		0.3598	False		,,,				2504	0.3119				p.V304V		Atlas-SNP	.											.	SPTBN4	213	.	0			c.A912G						PASS	.	G		2696,1710	514.4+/-368.6	815,1066,322	67.0	64.0	65.0		912	0.9	0.9	19	dbSNP_86	65	3140,5460	655.9+/-401.3	554,2032,1714	no	coding-synonymous	SPTBN4	NM_020971.2		1369,3098,2036	GG,GA,AA		36.5116,38.8107,44.8716		304/2565	41008049	5836,7170	2203	4300	6503	SO:0001819	synonymous_variant	57731	exon9			CCAGGTATTGGAG	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.912A>G	19.37:g.41008049A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	36	0.590164	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																			A|0.581;G|0.419	0.419	strong		0.602	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
FN1	2335	hgsc.bcm.edu	37	2	216248820	216248820	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:216248820G>T	ENST00000359671.1	-	29	4809	c.4544C>A	c.(4543-4545)aCc>aAc	p.T1515N	FN1_ENST00000356005.4_Missense_Mutation_p.T1515N|FN1_ENST00000354785.4_Missense_Mutation_p.T1606N|FN1_ENST00000323926.6_Missense_Mutation_p.T1606N|FN1_ENST00000432072.2_Missense_Mutation_p.T1606N|FN1_ENST00000336916.4_Missense_Mutation_p.T1515N|FN1_ENST00000357009.2_Missense_Mutation_p.T1515N|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000346544.3_Missense_Mutation_p.T1515N|FN1_ENST00000421182.1_Missense_Mutation_p.T1515N|FN1_ENST00000345488.5_Missense_Mutation_p.T1515N|FN1_ENST00000357867.4_Missense_Mutation_p.T1515N|FN1_ENST00000446046.1_Missense_Mutation_p.T1515N|FN1_ENST00000443816.1_Missense_Mutation_p.T1515N			P02751	FINC_HUMAN	fibronectin 1	1515	Cell-attachment.|Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		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)	CACAGTGATGGTATAATCAAC	0.498																																					p.T1606N		Atlas-SNP	.											.	FN1	521	.	0			c.C4817A						PASS	.						131.0	120.0	123.0					2																	216248820		2203	4300	6503	SO:0001583	missense	2335	exon30			GTGATGGTATAAT		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.4544C>A	2.37:g.216248820G>T	ENSP00000352696:p.Thr1515Asn	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	71	19	0.267606	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	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	G	20.8	4.046748	0.75846	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37	5.83	4.94	0.65067	.	0.000000	0.64402	D	0.000001	T	0.63331	0.2502	L	0.39898	1.24	0.27525	N	0.951287	D;D;D;D;D;P;D;D;D;D	0.76494	0.999;0.999;0.999;0.997;0.999;0.922;0.999;0.999;0.999;0.995	D;D;D;D;D;P;D;D;D;D	0.83275	0.977;0.995;0.996;0.969;0.987;0.905;0.987;0.977;0.977;0.969	T	0.56426	-0.7981	10	0.46703	T	0.11	.	14.3418	0.66633	0.0705:0.0:0.9295:0.0	.	1606;1606;1515;1515;1515;1515;1516;1515;1515;1606	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	N	1515;1606;1515;1515;1606;1516;1515;1515;1515;1515;1515;1515;1606;1515;322	ENSP00000394423:T1515N;ENSP00000323534:T1606N;ENSP00000338200:T1515N;ENSP00000350534:T1515N;ENSP00000346839:T1606N;ENSP00000352696:T1515N;ENSP00000265312:T1515N;ENSP00000273049:T1515N;ENSP00000349509:T1515N;ENSP00000410422:T1515N;ENSP00000415018:T1515N;ENSP00000399538:T1606N;ENSP00000348285:T1515N;ENSP00000416139:T322N	ENSP00000265313:T1516N	T	-	2	0	FN1	215957065	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.391000	0.73208	2.756000	0.94617	0.655000	0.94253	ACC	.	.	none		0.498	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
HHLA1	10086	hgsc.bcm.edu	37	8	133092138	133092138	+	Missense_Mutation	SNP	G	G	A	rs2403730	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:133092138G>A	ENST00000414222.1	-	10	751	c.752C>T	c.(751-753)cCc>cTc	p.P251L	HHLA1_ENST00000434736.2_Missense_Mutation_p.P287L|OC90_ENST00000262283.5_Intron	NM_001145095.1	NP_001138567.1	C9JL84	HHLA1_HUMAN	HERV-H LTR-associating 1	251						extracellular region (GO:0005576)		p.P251L(1)		endometrium(6)|kidney(1)|lung(2)|skin(1)|stomach(2)	12						CCAGTGTCCGGGGCTTGTACT	0.552													G|||	1284	0.25639	0.1672	0.389	5008	,	,		18254	0.1984		0.3032	False		,,,				2504	0.2945				p.P251L		Atlas-SNP	.											HHLA1,NS,carcinoma,0,1	HHLA1	35	1	1	Substitution - Missense(1)	stomach(1)	c.C752T						scavenged	.	G	LEU/PRO	285,1099		31,223,438	108.0	83.0	90.0		752	-0.7	0.0	8	dbSNP_100	90	1033,2149		152,729,710	yes	missense	HHLA1	NM_001145095.1	98	183,952,1148	AA,AG,GG		32.4639,20.5925,28.8655	benign	251/532	133092138	1318,3248	692	1591	2283	SO:0001583	missense	10086	exon10			TGTCCGGGGCTTG	AF110315		8q24	2011-03-01			ENSG00000132297	ENSG00000132297			4904	protein-coding gene	gene with protein product		604109		PLA2L		10329003	Standard	NM_001145095		Approved		uc011liy.1	C9JL84	OTTHUMG00000140390	ENST00000414222.1:c.752C>T	8.37:g.133092138G>A	ENSP00000388322:p.Pro251Leu	Somatic	471	3	0.00636943		WXS	Illumina HiSeq	Phase_I	580	351	0.605172	NM_001145095		Missense_Mutation	SNP	ENST00000414222.1	37		551	0.2522893772893773	69	0.1402439024390244	135	0.3729281767955801	125	0.21853146853146854	222	0.2928759894459103	G	10.85	1.468091	0.26335	0.205925	0.324639	ENSG00000132297	ENST00000414222;ENST00000434736	.	.	.	4.82	-0.714	0.11219	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.10450	0.001;0.005	T	0.45026	-0.9289	7	0.26408	T	0.33	.	0.6554	0.00834	0.3373:0.1655:0.3274:0.1697	rs2403730;rs3739279;rs17571473;rs52807392;rs56513099;rs59545753;rs2403730	251;108	C9JL84;C9JL84-2	HHLA1_HUMAN;.	L	251;287	.	ENSP00000388322:P251L	P	-	2	0	HHLA1	133161320	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.195000	0.09546	-0.034000	0.13713	-0.142000	0.14014	CCC	G|0.754;A|0.246	0.246	strong		0.552	HHLA1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XR_017860	
KIF13A	63971	hgsc.bcm.edu	37	6	17794494	17794494	+	Silent	SNP	G	G	A	rs3734234	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:17794494G>A	ENST00000259711.6	-	25	3313	c.3208C>T	c.(3208-3210)Ctg>Ttg	p.L1070L	KIF13A_ENST00000378816.5_Silent_p.L1070L|KIF13A_ENST00000378814.5_Silent_p.L1070L|KIF13A_ENST00000378826.2_Silent_p.L1070L|KIF13A_ENST00000378843.2_Silent_p.L1070L	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1070					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)			TAACTGTCCAGCCCTCTTTGG	0.473													G|||	1878	0.375	0.146	0.4207	5008	,	,		17815	0.5823		0.4314	False		,,,				2504	0.3804				p.L1070L		Atlas-SNP	.											.	KIF13A	276	.	0			c.C3208T						PASS	.	G	,,,	683,3075		67,549,1263	107.0	99.0	101.0		3208,3208,3208,3208	3.6	1.0	6	dbSNP_107	101	3639,4613		806,2027,1293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	873,2576,2556	AA,AG,GG		44.0984,18.1746,35.9867	,,,	1070/1771,1070/1758,1070/1750,1070/1806	17794494	4322,7688	1879	4126	6005	SO:0001819	synonymous_variant	63971	exon25			TGTCCAGCCCTCT	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.3208C>T	6.37:g.17794494G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			G|0.609;A|0.391	0.391	strong		0.473	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
XIRP2	129446	hgsc.bcm.edu	37	2	168115710	168115710	+	Missense_Mutation	SNP	T	T	G	rs3749006	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168115710T>G	ENST00000409728.1	+	11	2842	c.2753T>G	c.(2752-2754)gTt>gGt	p.V918G	XIRP2_ENST00000409605.1_Missense_Mutation_p.V663G|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.V885G|XIRP2_ENST00000409043.1_Missense_Mutation_p.V885G|XIRP2_ENST00000420519.1_Missense_Mutation_p.V918G|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409195.1_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					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)		p.V918G(1)		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						CCTTGGCATGTTGAAACAACA	0.378													G|||	993	0.198283	0.3154	0.1297	5008	,	,		19526	0.1974		0.1143	False		,,,				2504	0.1759				p.V918G		Atlas-SNP	.											XIRP2_ENST00000409728,NS,carcinoma,0,1	XIRP2	914	1	1	Substitution - Missense(1)	stomach(1)	c.T2753G						PASS	.	G	GLY/VAL,GLY/VAL,,GLY/VAL,	1061,2691		155,751,970	94.0	86.0	88.0		2654,2753,,1988,	0.6	0.0	2	dbSNP_107	88	800,7418		42,716,3351	yes	missense,missense,utr-3,missense,utr-3	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	109,109,,109,	197,1467,4321	GG,GT,TT		9.7347,28.2783,15.5472	,,,,	885/939,918/972,,663/717,	168115710	1861,10109	1876	4109	5985	SO:0001583	missense	129446	exon11			GGCATGTTGAAAC	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	ENST00000409728.1:c.2753T>G	2.37:g.168115710T>G	ENSP00000386619:p.Val918Gly	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	92	33	0.358696	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	424	0.19413919413919414	175	0.3556910569105691	44	0.12154696132596685	115	0.20104895104895104	90	0.11873350923482849	G	1.293	-0.607143	0.03717	0.282783	0.097347	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.74526	-0.81;-0.85;-0.81;-0.85;-0.78	5.78	0.61	0.17580	.	.	.	.	.	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	0.13791	-1.0496	7	0.02654	T	1	.	6.9138	0.24349	0.4555:0.0:0.4348:0.1097	rs3749006;rs52810449;rs58687090;rs3749006	885;918	A4UGR9-4;A4UGR9-6	.;.	G	885;918;885;918;663	ENSP00000386454:V885G;ENSP00000386619:V918G;ENSP00000386724:V885G;ENSP00000415541:V918G;ENSP00000386981:V663G	ENSP00000386454:V885G	V	+	2	0	XIRP2	167823956	0.001000	0.12720	0.001000	0.08648	0.253000	0.25986	-0.469000	0.06648	-0.148000	0.11234	-0.225000	0.12378	GTT	T|0.808;G|0.192	0.192	strong		0.378	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
CCDC108	255101	hgsc.bcm.edu	37	2	219900068	219900068	+	Intron	SNP	C	C	T	rs17852959	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219900068C>T	ENST00000341552.5	-	5	626				CCDC108_ENST00000410037.1_Intron|CCDC108_ENST00000295729.2_Missense_Mutation_p.V161M|CCDC108_ENST00000324264.6_Missense_Mutation_p.V161M|CCDC108_ENST00000453220.1_Intron|CCDC108_ENST00000441968.1_Intron|CCDC108_ENST00000409865.3_Intron	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108							integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.V161M(1)		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)		TCATACTGCACGTATTTTAAA	0.363													C|||	457	0.091254	0.0439	0.0893	5008	,	,		21263	0.1597		0.0885	False		,,,				2504	0.089				p.V161M		Atlas-SNP	.											CCDC108_ENST00000295729,NS,carcinoma,0,1	CCDC108	208	1	1	Substitution - Missense(1)	stomach(1)	c.G481A						scavenged	.	C	MET/VAL,	202,4150		7,188,1981	28.0	30.0	29.0		481,	2.7	0.0	2	dbSNP_123	29	764,7720		25,714,3503	yes	missense,intron	CCDC108	NM_152389.2,NM_194302.2	21,	32,902,5484	TT,TC,CC		9.0052,4.6415,7.5257	,	161/165,	219900068	966,11870	2176	4242	6418	SO:0001627	intron_variant	255101	exon4			ACTGCACGTATTT	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.542+133G>A	2.37:g.219900068C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	59	7	0.118644	NM_152389	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	210	0.09615384615384616	24	0.04878048780487805	29	0.08011049723756906	90	0.15734265734265734	67	0.08839050131926121	C	1.176	-0.639592	0.03557	0.046415	0.090052	ENSG00000181378	ENST00000295729;ENST00000324264	T;T	0.53640	0.61;0.61	2.72	2.72	0.32119	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	D	0.89917	1.0	D	0.67900	0.954	T	0.01993	-1.1233	8	0.17369	T	0.5	.	9.1072	0.36705	0.0:1.0:0.0:0.0	rs17852959;rs59675281	161	E9PCR1	.	M	161	ENSP00000295729:V161M;ENSP00000313807:V161M	ENSP00000295729:V161M	V	-	1	0	CCDC108	219608312	0.000000	0.05858	0.021000	0.16686	0.024000	0.10985	-0.214000	0.09292	1.828000	0.53243	0.561000	0.74099	GTG	C|0.904;T|0.096	0.096	strong		0.363	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
NLRP2	55655	hgsc.bcm.edu	37	19	55494320	55494320	+	Silent	SNP	G	G	A	rs147207921	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55494320G>A	ENST00000543010.1	+	6	1397	c.1254G>A	c.(1252-1254)ccG>ccA	p.P418P	NLRP2_ENST00000391721.4_Silent_p.P394P|NLRP2_ENST00000339757.7_Silent_p.P396P|NLRP2_ENST00000427260.2_Silent_p.P395P|NLRP2_ENST00000263437.6_Silent_p.P415P|NLRP2_ENST00000537859.1_Silent_p.P396P|NLRP2_ENST00000538819.1_Silent_p.P394P|NLRP2_ENST00000448584.2_Silent_p.P418P	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	418	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)		GGGAGGACCCGGTCCCCACCT	0.706													G|||	54	0.0107827	0.0076	0.0187	5008	,	,		14301	0.001		0.0278	False		,,,				2504	0.002				p.P418P		Atlas-SNP	.											.	NLRP2	161	.	0			c.G1254A						PASS	.	G	,,,	35,4343		0,35,2154	16.0	16.0	16.0		1254,1188,1185,1254	-3.9	0.0	19	dbSNP_134	16	234,8306		0,234,4036	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	0,269,6190	AA,AG,GG		2.74,0.7995,2.0824	,,,	418/1063,396/1041,395/1040,418/1063	55494320	269,12649	2189	4270	6459	SO:0001819	synonymous_variant	55655	exon6			GGACCCGGTCCCC	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.1254G>A	19.37:g.55494320G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	141	73	0.51773	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			G|0.987;A|0.013	0.013	weak		0.706	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
TYW1	55253	hgsc.bcm.edu	37	7	66660242	66660242	+	Missense_Mutation	SNP	A	A	G	rs2949097		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:66660242A>G	ENST00000359626.5	+	15	2059	c.1895A>G	c.(1894-1896)cAc>cGc	p.H632R		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	632			H -> R (in dbSNP:rs2949097). {ECO:0000269|PubMed:14702039}.		tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)	p.H632R(1)		breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				CAGTTTGTCCACGAGTTGGTG	0.473																																					p.H632R		Atlas-SNP	.											TYW1,NS,carcinoma,0,1	TYW1	71	1	1	Substitution - Missense(1)	stomach(1)	c.A1895G						scavenged	.						143.0	147.0	146.0					7																	66660242		2201	4298	6499	SO:0001583	missense	55253	exon15			TTGTCCACGAGTT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1895A>G	7.37:g.66660242A>G	ENSP00000352645:p.His632Arg	Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	194	57	0.293814	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Missense_Mutation	SNP	ENST00000359626.5	37	CCDS5538.1	423	0.1936813186813187	166	0.33739837398373984	76	0.20994475138121546	42	0.07342657342657342	139	0.18337730870712401	G	0.041	-1.284326	0.01398	.	.	ENSG00000198874	ENST00000359626	T	0.39592	1.07	3.7	-1.73	0.08081	tRNA wybutosine-synthesis (1);	0.536026	0.18649	N	0.135065	T	0.00012	0.0000	N	0.00332	-1.63	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46176	-0.9210	9	0.22706	T	0.39	.	10.5776	0.45235	0.6569:0.0:0.3431:0.0	rs2949097;rs3210780	632	Q9NV66	TYW1_HUMAN	R	632	ENSP00000352645:H632R	ENSP00000352645:H632R	H	+	2	0	TYW1	66297677	0.000000	0.05858	0.006000	0.13384	0.030000	0.12068	0.026000	0.13599	-0.771000	0.04608	-1.185000	0.01705	CAC	A|0.500;G|0.500	0.500	weak		0.473	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
CTDNEP1	23399	hgsc.bcm.edu	37	17	7154582	7154582	+	Missense_Mutation	SNP	T	T	C	rs3744399	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7154582T>C	ENST00000573600.1	-	2	455	c.34A>G	c.(34-36)Acg>Gcg	p.T12A	CTDNEP1_ENST00000318988.6_Missense_Mutation_p.T12A|CTDNEP1_ENST00000574322.1_Missense_Mutation_p.T12A|ELP5_ENST00000574993.1_5'Flank|ELP5_ENST00000396628.2_5'Flank|ELP5_ENST00000356683.2_5'Flank|ELP5_ENST00000354429.2_5'Flank|ELP5_ENST00000396627.2_5'Flank|ELP5_ENST00000573657.1_5'Flank|ELP5_ENST00000574255.1_5'Flank|CTDNEP1_ENST00000572043.1_Intron|RP1-4G17.5_ENST00000577138.1_Intron			O95476	CNEP1_HUMAN	CTD nuclear envelope phosphatase 1	12			T -> A (in dbSNP:rs3744399). {ECO:0000269|PubMed:16533400, ECO:0000269|Ref.1}.		gamete generation (GO:0007276)|mesoderm development (GO:0007498)|nuclear envelope organization (GO:0006998)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of triglyceride biosynthetic process (GO:0010867)|protein dephosphorylation (GO:0006470)|protein localization to nucleus (GO:0034504)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|Nem1-Spo7 phosphatase complex (GO:0071595)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(9)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	15						GCCACGAACGTGCGCAGCCCC	0.726													T|||	548	0.109425	0.0053	0.1643	5008	,	,		9597	0.0883		0.1362	False		,,,				2504	0.2055				p.T12A		Atlas-SNP	.											CTDNEP1,NS,carcinoma,0,2	CTDNEP1	26	2	0			c.A34G						scavenged	.	T	ALA/THR,ALA/THR	135,4269		6,123,2073	20.0	23.0	22.0		34,34	4.9	1.0	17	dbSNP_107	22	1274,7322		103,1068,3127	no	missense,missense	CTDNEP1	NM_001143775.1,NM_015343.4	58,58	109,1191,5200	CC,CT,TT		14.8208,3.0654,10.8385	benign,benign	12/245,12/245	7154582	1409,11591	2202	4298	6500	SO:0001583	missense	23399	exon1			CGAACGTGCGCAG	AJ011916	CCDS11093.1	17p13	2012-11-27	2010-10-27	2010-10-27	ENSG00000175826	ENSG00000175826		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	19085	protein-coding gene	gene with protein product	"""C-terminal domain nuclear envelope phosphatase 1"""	610684	"""dullard homolog (Xenopus laevis)"""	DULLARD		12083771, 17141153	Standard	NM_015343		Approved	HSA011916, NET56	uc002gfd.2	O95476	OTTHUMG00000102180	ENST00000573600.1:c.34A>G	17.37:g.7154582T>C	ENSP00000461749:p.Thr12Ala	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_001143775	D3DTN7|Q96GQ9	Missense_Mutation	SNP	ENST00000573600.1	37	CCDS11093.1	227	0.10393772893772894	5	0.01016260162601626	68	0.1878453038674033	54	0.0944055944055944	100	0.13192612137203166	T	6.967	0.548401	0.13312	0.030654	0.148208	ENSG00000175826	ENST00000318988	T	0.12984	2.63	4.88	4.88	0.63580	.	0.129530	0.50627	N	0.000103	T	0.00012	0.0000	N	0.15975	0.35	0.09310	P	0.9999999999999994	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	9	0.02654	T	1	1.2704	7.1651	0.25685	0.0:0.0969:0.0:0.9031	rs3744399	12	O95476	CNEP1_HUMAN	A	12	ENSP00000321732:T12A	ENSP00000321732:T12A	T	-	1	0	CTDNEP1	7095306	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.353000	0.44089	2.062000	0.61559	0.528000	0.53228	ACG	T|0.898;C|0.102	0.102	strong		0.726	CTDNEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440215.1	NM_015343	
OBSCN	84033	hgsc.bcm.edu	37	1	228492044	228492044	+	Intron	SNP	G	G	A	rs1150910	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:228492044G>A	ENST00000422127.1	+	44	11703				OBSCN_ENST00000366707.4_Silent_p.E1371E|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000359599.6_3'UTR|OBSCN_ENST00000570156.2_Silent_p.E4681E|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)				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	91	0	0		WXS	Illumina HiSeq	Phase_I	113	40	0.353982	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	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389161	1389161	+	Missense_Mutation	SNP	A	A	G	rs71614973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1389161A>G	ENST00000324803.4	+	1	3822	c.862A>G	c.(862-864)Agt>Ggt	p.S288G		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	288					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)			GCCGATGTGGAGTGCCCGCCT	0.687													A|||	1051	0.209864	0.1362	0.2983	5008	,	,		13955	0.0536		0.3748	False		,,,				2504	0.2382				p.S288G		Atlas-SNP	.											.	CRIPAK	185	.	0			c.A862G						PASS	.						127.0	128.0	128.0					4																	1389161		2202	4298	6500	SO:0001583	missense	285464	exon1			ATGTGGAGTGCCC	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.862A>G	4.37:g.1389161A>G	ENSP00000323978:p.Ser288Gly	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	33	30	0.909091	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	A	1.586	-0.530434	0.04112	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.21734	1.99	0.815	-1.63	0.08345	.	.	.	.	.	T	0.06917	0.0176	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.39761	-0.9598	8	0.07175	T	0.84	.	2.8991	0.05700	0.2283:0.0:0.4427:0.329	.	288	Q8N1N5	CRPAK_HUMAN	G	288;230	ENSP00000323978:S288G	ENSP00000323978:S288G	S	+	1	0	CRIPAK	1379161	0.046000	0.20272	0.000000	0.03702	0.001000	0.01503	-1.350000	0.02624	-1.564000	0.01678	-0.530000	0.04314	AGT	G|1.000;|0.000	1.000	weak		0.687	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
U2AF2	11338	hgsc.bcm.edu	37	19	56181019	56181019	+	Silent	SNP	C	C	T	rs147666260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.12_ENST00000585940.1_RNA|U2AF2_ENST00000590551.1_Silent_p.P250P|CTD-2537I9.13_ENST00000592252.1_RNA			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	151	0	0		WXS	Illumina HiSeq	Phase_I	162	81	0.5	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	
MYO1H	283446	hgsc.bcm.edu	37	12	109848567	109848567	+	Silent	SNP	T	T	C	rs7315991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:109848567T>C	ENST00000431443.2	+	12	1386	c.1386T>C	c.(1384-1386)tcT>tcC	p.S462S	MYO1H_ENST00000310903.5_Silent_p.S452S	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	462	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						GAATCATATCTATTCTGGTGA	0.378													C|||	2732	0.545527	0.7458	0.5922	5008	,	,		17613	0.4544		0.4722	False		,,,				2504	0.411				p.S452S		Atlas-SNP	.											MYO1H,NS,carcinoma,+1,1	MYO1H	98	1	0			c.T1356C						PASS	.	C		2559,1105		892,775,165	77.0	69.0	72.0		1356	2.9	1.0	12	dbSNP_116	72	3943,4229		951,2041,1094	no	coding-synonymous	MYO1H	NM_001101421.3		1843,2816,1259	CC,CT,TT		48.2501,30.1583,45.0659		452/1023	109848567	6502,5334	1832	4086	5918	SO:0001819	synonymous_variant	283446	exon12			CATATCTATTCTG		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.1386T>C	12.37:g.109848567T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				T|0.459;C|0.541	0.541	strong		0.378	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
TYR	7299	hgsc.bcm.edu	37	11	88911696	88911696	+	Missense_Mutation	SNP	C	C	A	rs1042602	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:88911696C>A	ENST00000263321.5	+	1	1077	c.575C>A	c.(574-576)tCt>tAt	p.S192Y	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	192			S -> Y (associated with SHEP3; light/dark skin; dbSNP:rs1042602). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:11153699, ECO:0000269|PubMed:11214319, ECO:0000269|PubMed:15146472, ECO:0000269|PubMed:17952075, ECO:0000269|PubMed:17999355, ECO:0000269|PubMed:2342539}.		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CTTGGGGGATCTGAAATCTGG	0.423													C|||	618	0.123403	0.0121	0.2378	5008	,	,		21077	0.001		0.3718	False		,,,				2504	0.0634				p.S192Y		Atlas-SNP	.											TYR,NS,carcinoma,0,1	TYR	130	1	0			c.C575A	GRCh37	CM076581	TYR	M	rs1042602	PASS	.	C	TYR/SER	333,4069	174.4+/-204.0	13,307,1881	193.0	181.0	185.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	575	6.1	0.0	11	dbSNP_86	185	3239,5359	486.7+/-371.9	592,2055,1652	yes	missense	TYR	NM_000372.4	144	605,2362,3533	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	37.6716,7.5647,27.4769	probably-damaging	192/530	88911696	3572,9428	2201	4299	6500	SO:0001583	missense	7299	exon1			GGGGATCTGAAAT	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.575C>A	11.37:g.88911696C>A	ENSP00000263321:p.Ser192Tyr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	182	124	0.681319	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	399	0.18269230769230768	7	0.014227642276422764	112	0.30939226519337015	1	0.0017482517482517483	279	0.36807387862796836	C	17.00	3.275960	0.59649	0.075647	0.376716	ENSG00000077498	ENST00000263321	D	0.98732	-5.1	6.07	6.07	0.98685	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.065875	0.64402	D	0.000008	T	0.00039	0.0001	M	0.70275	2.135	0.47737	P	4.92000000000048E-4	D	0.69078	0.997	D	0.71656	0.974	T	0.00000	-1.7843	8	.	.	.	.	15.3849	0.74691	0.1393:0.8607:0.0:0.0	rs61569485	192	P14679	TYRO_HUMAN	Y	192	ENSP00000263321:S192Y	.	S	+	2	0	TYR	88551344	0.660000	0.27420	0.028000	0.17463	0.775000	0.43874	4.436000	0.59948	2.885000	0.99019	0.655000	0.94253	TCT	C|0.751;A|0.249	0.249	strong		0.423	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
ZNF98	148198	hgsc.bcm.edu	37	19	22586192	22586192	+	Silent	SNP	A	A	G	rs1368476	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22586192A>G	ENST00000357774.5	-	2	274	c.153T>C	c.(151-153)ttT>ttC	p.F51F	ZNF98_ENST00000601553.1_Silent_p.F51F	NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	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)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				CCTCACCCACAAAGACCAGGT	0.368													N|||	1945	0.388379	0.3858	0.4769	5008	,	,		14594	0.3988		0.4612	False		,,,				2504	0.2434				p.F51F		Atlas-SNP	.											.	ZNF98	230	.	0			c.T153C						PASS	.						73.0	76.0	75.0					19																	22586192		2171	4270	6441	SO:0001819	synonymous_variant	148198	exon2			ACCCACAAAGACC		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.153T>C	19.37:g.22586192A>G		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	138	56	0.405797	NM_001098626		Silent	SNP	ENST00000357774.5	37	CCDS46031.1																																																																																			G|1.000;|0.000	1.000	weak		0.368	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
CHN2	1124	hgsc.bcm.edu	37	7	29519929	29519929	+	Missense_Mutation	SNP	A	A	G	rs3750103	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:29519929A>G	ENST00000222792.6	+	7	1141	c.611A>G	c.(610-612)cAc>cGc	p.H204R	CHN2_ENST00000546235.1_Missense_Mutation_p.H189R|CHN2_ENST00000424025.2_Intron|CHN2_ENST00000439711.2_Missense_Mutation_p.H68R|CHN2_ENST00000421775.2_Missense_Mutation_p.H68R|CHN2_ENST00000539389.1_Missense_Mutation_p.H60R|CHN2_ENST00000435288.2_Intron|CHN2_ENST00000495789.2_Missense_Mutation_p.H217R|CHN2_ENST00000539406.1_Missense_Mutation_p.H279R|CHN2_ENST00000409041.4_Missense_Mutation_p.H68R	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	204			H -> R (in dbSNP:rs3750103). {ECO:0000269|PubMed:14702039}.		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						GCCCTCACACACAACGACAAC	0.502													A|||	637	0.127196	0.1445	0.1225	5008	,	,		18677	0.2192		0.0517	False		,,,				2504	0.09				p.H204R	Ovarian(1;44 48 13232 18918 31480)	Atlas-SNP	.											.	CHN2	98	.	0			c.A611G						PASS	.	A	ARG/HIS,ARG/HIS	642,3764	277.2+/-273.6	45,552,1606	230.0	173.0	192.0		203,611	4.4	1.0	7	dbSNP_107	192	424,8176	131.0+/-188.9	16,392,3892	yes	missense,missense	CHN2	NM_001039936.1,NM_004067.2	29,29	61,944,5498	GG,GA,AA		4.9302,14.571,8.1962	benign,benign	68/333,204/469	29519929	1066,11940	2203	4300	6503	SO:0001583	missense	1124	exon7			TCACACACAACGA	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.611A>G	7.37:g.29519929A>G	ENSP00000222792:p.His204Arg	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	375	136	0.362667	NM_004067	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Missense_Mutation	SNP	ENST00000222792.6	37	CCDS5420.1	242	0.1108058608058608	59	0.11991869918699187	40	0.11049723756906077	105	0.18356643356643357	38	0.05013192612137203	A	12.70	2.015624	0.35511	0.14571	0.049302	ENSG00000106069	ENST00000539406;ENST00000222792;ENST00000495789;ENST00000539389;ENST00000546235;ENST00000409041;ENST00000439711;ENST00000421775	D;D;D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.55	4.38	0.52667	.	0.249845	0.47852	D	0.000217	T	0.00300	0.0009	N	0.19112	0.55	0.26411	P	0.9762527	B;B;B;B;B;B;B;B;B;B;B;B	0.30439	0.0;0.013;0.279;0.001;0.019;0.0;0.009;0.0;0.0;0.001;0.0;0.001	B;B;B;B;B;B;B;B;B;B;B;B	0.25140	0.001;0.006;0.058;0.0;0.017;0.0;0.021;0.0;0.002;0.004;0.003;0.004	T	0.10894	-1.0610	9	0.19147	T	0.46	.	12.2032	0.54337	0.8248:0.1752:0.0:0.0	rs3750103;rs52805840;rs57756092;rs3750103	189;217;279;68;68;68;68;68;60;204;68;204	B7Z1W9;B7Z1V0;F5H003;B3VCF5;B3VCF4;B3VCF7;B3VCF3;B3VCF6;B3VCG1;A4D1A2;E9PGE0;P52757	.;.;.;.;.;.;.;.;.;.;.;CHIO_HUMAN	R	279;204;217;60;189;68;68;68	ENSP00000444063:H279R;ENSP00000222792:H204R;ENSP00000438587:H217R;ENSP00000440526:H60R;ENSP00000442812:H189R;ENSP00000386849:H68R;ENSP00000387425:H68R;ENSP00000394284:H68R	ENSP00000222792:H204R	H	+	2	0	CHN2	29486454	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	6.889000	0.75627	0.980000	0.38523	0.533000	0.62120	CAC	A|0.901;G|0.099	0.099	strong		0.502	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067	
CLEC4M	10332	hgsc.bcm.edu	37	19	7831628	7831628	+	Missense_Mutation	SNP	G	G	A	rs2277998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:7831628G>A	ENST00000327325.5	+	5	989	c.871G>A	c.(871-873)Gac>Aac	p.D291N	CLEC4M_ENST00000596363.1_Missense_Mutation_p.D263N|CLEC4M_ENST00000394122.2_Missense_Mutation_p.D279N|CLEC4M_ENST00000359059.5_Missense_Mutation_p.D224N|CLEC4M_ENST00000597522.1_Missense_Mutation_p.D199N|CLEC4M_ENST00000334806.5_Missense_Mutation_p.D240N|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	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	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	175	95	0.542857	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	
VMO1	284013	hgsc.bcm.edu	37	17	4689313	4689313	+	Missense_Mutation	SNP	G	G	C	rs2279961	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4689313G>C	ENST00000328739.5	-	2	309	c.230C>G	c.(229-231)aCt>aGt	p.T77S	VMO1_ENST00000354194.4_Intron|GLTPD2_ENST00000331264.7_5'Flank|VMO1_ENST00000416307.2_Missense_Mutation_p.T77S|VMO1_ENST00000441199.2_Missense_Mutation_p.T77S	NM_182566.2	NP_872372.1	Q7Z5L0	VMO1_HUMAN	vitelline membrane outer layer 1 homolog (chicken)	77			T -> S (in dbSNP:rs2279961).			extracellular vesicular exosome (GO:0070062)				kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|pancreas(1)	11						ATTCAGTGCAGTGTCGTCGCC	0.622													G|||	474	0.0946486	0.115	0.1052	5008	,	,		18607	0.0992		0.0994	False		,,,				2504	0.0501				p.T77S		Atlas-SNP	.											.	VMO1	19	.	0			c.C230G						PASS	.	G	SER/THR,SER/THR,,SER/THR	551,3855	249.3+/-256.8	32,487,1684	755.0	684.0	708.0		230,230,,230	4.4	0.9	17	dbSNP_100	708	914,7686	203.0+/-246.1	59,796,3445	yes	missense,missense,intron,missense	VMO1	NM_001144939.1,NM_001144940.1,NM_001144941.1,NM_182566.2	58,58,,58	91,1283,5129	CC,CG,GG		10.6279,12.5057,11.264	probably-damaging,probably-damaging,,probably-damaging	77/115,77/103,,77/203	4689313	1465,11541	2203	4300	6503	SO:0001583	missense	284013	exon2			AGTGCAGTGTCGT	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.230C>G	17.37:g.4689313G>C	ENSP00000328397:p.Thr77Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_182566	C9JQ15|E9PAU9|E9PGP4|Q3SXP1|Q8IUY1	Missense_Mutation	SNP	ENST00000328739.5	37	CCDS11055.1	241	0.11034798534798534	63	0.12804878048780488	36	0.09944751381215469	64	0.11188811188811189	78	0.10290237467018469	G	16.26	3.073061	0.55646	0.125057	0.106279	ENSG00000182853	ENST00000328739;ENST00000416307;ENST00000441199	T;T;T	0.52295	0.67;0.67;0.67	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.01523	0.0049	M	0.82132	2.575	0.09310	P	1.0	D;D;D	0.89917	1.0;1.0;0.98	D;D;P	0.97110	1.0;0.999;0.767	T	0.44952	-0.9294	9	0.66056	D	0.02	-14.9036	12.404	0.55428	0.0:0.0:1.0:0.0	rs2279961;rs4080467;rs17765171;rs2279961	77;77;77	C9JQ15;E9PAU9;Q7Z5L0	.;.;VMO1_HUMAN	S	77	ENSP00000328397:T77S;ENSP00000390450:T77S;ENSP00000408166:T77S	ENSP00000328397:T77S	T	-	2	0	VMO1	4636053	1.000000	0.71417	0.920000	0.36463	0.019000	0.09904	7.187000	0.77730	2.286000	0.76751	0.563000	0.77884	ACT	G|0.901;C|0.099	0.099	strong		0.622	VMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439587.1	NM_182566	
VEGFC	7424	hgsc.bcm.edu	37	4	177713326	177713326	+	Missense_Mutation	SNP	T	T	A	rs55728985	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:177713326T>A	ENST00000280193.2	-	1	555	c.140A>T	c.(139-141)gAg>gTg	p.E47V		NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	47					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|induction of positive chemotaxis (GO:0050930)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of lymphangiogenesis (GO:1901492)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein secretion (GO:0050714)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to drug (GO:0042493)|signal transduction (GO:0007165)|substrate-dependent cell migration (GO:0006929)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)			biliary_tract(1)|cervix(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(2)|skin(2)	41		Breast(14;0.000223)|Renal(120;0.00988)|Prostate(90;0.00996)|Melanoma(52;0.0101)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;1.59e-18)|Epithelial(43;3.68e-16)|OV - Ovarian serous cystadenocarcinoma(60;8.52e-09)|GBM - Glioblastoma multiforme(59;0.000546)|STAD - Stomach adenocarcinoma(60;0.00308)|Colorectal(24;0.025)|COAD - Colon adenocarcinoma(29;0.0359)|LUSC - Lung squamous cell carcinoma(193;0.0397)		TACCGTGGCCTCGCCCGCGTC	0.716													T|||	7	0.00139776	0.0	0.0043	5008	,	,		9648	0.0		0.004	False		,,,				2504	0.0				p.E47V		Atlas-SNP	.											VEGFC,NS,carcinoma,-1,1	VEGFC	94	1	0			c.A140T						PASS	.	T	VAL/GLU	1,3751		0,1,1875	18.0	22.0	21.0		140	3.1	1.0	4	dbSNP_129	21	43,8131		0,43,4044	yes	missense	VEGFC	NM_005429.2	121	0,44,5919	AA,AT,TT		0.5261,0.0267,0.3689	benign	47/421	177713326	44,11882	1876	4087	5963	SO:0001583	missense	7424	exon1			GTGGCCTCGCCCG	BC035212	CCDS43285.1	4q34.3	2013-02-18				ENSG00000150630			12682	protein-coding gene	gene with protein product	"""vascular endothelial growth factor-related protein"""	601528				8617204	Standard	NM_005429		Approved	VRP	uc003ius.1	P49767		ENST00000280193.2:c.140A>T	4.37:g.177713326T>A	ENSP00000280193:p.Glu47Val	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	15	4	0.266667	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	37	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.330343	0.60743	2.67E-4	0.005261	ENSG00000150630	ENST00000280193	.	.	.	4.3	3.13	0.36017	.	0.089559	0.43110	D	0.000613	T	0.44829	0.1312	L	0.57536	1.79	0.38259	D	0.941825	D	0.59357	0.985	P	0.50270	0.636	T	0.57590	-0.7785	9	0.72032	D	0.01	-12.749	6.7656	0.23564	0.0:0.1111:0.0:0.8889	rs55728985;rs62617087	47	P49767	VEGFC_HUMAN	V	47	.	ENSP00000280193:E47V	E	-	2	0	VEGFC	177950320	0.986000	0.35501	0.998000	0.56505	0.332000	0.28634	1.525000	0.35953	1.577000	0.49804	0.254000	0.18369	GAG	T|0.996;A|0.004	0.004	strong		0.716	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429	
SLC22A14	9389	hgsc.bcm.edu	37	3	38355225	38355225	+	Missense_Mutation	SNP	G	G	A	rs73064822	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	59	0	0		WXS	Illumina HiSeq	Phase_I	35	11	0.314286	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	
TTLL6	284076	hgsc.bcm.edu	37	17	46894377	46894377	+	Missense_Mutation	SNP	A	A	C	rs3959442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46894377A>C	ENST00000393382.3	-	1	199	c.58T>G	c.(58-60)Tgg>Ggg	p.W20G	TTLL6_ENST00000470462.2_5'UTR	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CTGCTAGTCCAGCTTGCAACC	0.667													A|||	1360	0.271565	0.3434	0.4063	5008	,	,		12670	0.1875		0.2664	False		,,,				2504	0.1708				p.W20G		Atlas-SNP	.											.	TTLL6	113	.	0			c.T58G						PASS	.	A	GLY/TRP	456,928		79,298,315	40.0	51.0	48.0		58	-0.6	0.0	17	dbSNP_108	48	862,2320		120,622,849	yes	missense	TTLL6	NM_001130918.1	184	199,920,1164	CC,CA,AA		27.0899,32.948,28.8655		20/892	46894377	1318,3248	692	1591	2283	SO:0001583	missense	284076	exon1			TAGTCCAGCTTGC	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.58T>G	17.37:g.46894377A>C	ENSP00000377043:p.Trp20Gly	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_001130918		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	606	0.2774725274725275	163	0.3313008130081301	145	0.4005524861878453	95	0.1660839160839161	203	0.2678100263852243	A	0.930	-0.713124	0.03206	0.32948	0.270899	ENSG00000170703	ENST00000440941;ENST00000418322	.	.	.	4.19	-0.634	0.11516	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.47509	-0.9112	5	0.29301	T	0.29	.	5.1484	0.14996	0.5233:0.3665:0.0:0.1101	rs3959442	.	.	.	G	20;22	.	ENSP00000403514:W22G	W	-	1	0	TTLL6	44249376	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.112000	0.10791	-0.138000	0.11434	-0.294000	0.09567	TGG	T|0.000;G|0.000;C|0.278;A|0.721	0.278	strong		0.667	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
PLEC	5339	hgsc.bcm.edu	37	8	144997656	144997656	+	Silent	SNP	C	C	T	rs7016416	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144997656C>T	ENST00000322810.4	-	31	7021	c.6852G>A	c.(6850-6852)gcG>gcA	p.A2284A	PLEC_ENST00000398774.2_Silent_p.A2115A|PLEC_ENST00000527096.1_Silent_p.A2170A|PLEC_ENST00000357649.2_Silent_p.A2151A|PLEC_ENST00000345136.3_Silent_p.A2147A|PLEC_ENST00000356346.3_Silent_p.A2133A|PLEC_ENST00000436759.2_Silent_p.A2174A|PLEC_ENST00000354958.2_Silent_p.A2125A|PLEC_ENST00000354589.3_Silent_p.A2147A	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						PASS	.	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	38	0	0		WXS	Illumina HiSeq	Phase_I	22	18	0.818182	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	
CFAP57	149465	hgsc.bcm.edu	37	1	43638436	43638436	+	Silent	SNP	G	G	T	rs6695238	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43638436G>T	ENST00000372492.4	+	2	336	c.12G>T	c.(10-12)gtG>gtT	p.V4V	WDR65_ENST00000528956.1_Silent_p.V4V|EBNA1BP2_ENST00000236051.2_5'Flank|EBNA1BP2_ENST00000472982.1_5'Flank|EBNA1BP2_ENST00000431635.2_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		4										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)				TGTCAGCCGTGGTAGCTCAGA	0.547													G|||	341	0.0680911	0.1899	0.0576	5008	,	,		10442	0.001		0.0368	False		,,,				2504	0.0123				p.V4V		Atlas-SNP	.											.	WDR65	76	.	0			c.G12T						PASS	.	G	,,	714,3692	295.6+/-283.7	65,584,1554	116.0	104.0	108.0		12,12,12	2.1	1.0	1	dbSNP_116	108	354,8246	119.5+/-178.9	6,342,3952	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	71,926,5506	TT,TG,GG		4.1163,16.2052,8.2116	,,	4/699,4/699,4/699	43638436	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon2			AGCCGTGGTAGCT																												ENST00000372492.4:c.12G>T	1.37:g.43638436G>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	69	53	0.768116	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.920;T|0.080	0.080	strong		0.547	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
ZNF277	11179	hgsc.bcm.edu	37	7	111981007	111981007	+	Missense_Mutation	SNP	G	G	A	rs11539696	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:111981007G>A	ENST00000361822.3	+	11	1219	c.1090G>A	c.(1090-1092)Gtg>Atg	p.V364M	AC004112.4_ENST00000431064.1_RNA|AC004112.4_ENST00000411413.1_RNA	NM_021994.2	NP_068834.2	Q9NRM2	ZN277_HUMAN	zinc finger protein 277	364			V -> M (in dbSNP:rs11539696).		cellular response to hydrogen peroxide (GO:0070301)|regulation of cellular senescence (GO:2000772)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			breast(4)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	15						TGGCTGCCATGTGAAGTTCAA	0.408													G|||	228	0.0455272	0.0416	0.0331	5008	,	,		14280	0.0248		0.0726	False		,,,				2504	0.0532				p.V364M		Atlas-SNP	.											.	ZNF277	46	.	0			c.G1090A						PASS	.	G	MET/VAL	188,4218	118.8+/-156.5	6,176,2021	107.0	107.0	107.0		1090	-0.1	0.0	7	dbSNP_120	107	576,8024	153.7+/-208.1	26,524,3750	yes	missense	ZNF277	NM_021994.2	21	32,700,5771	AA,AG,GG		6.6977,4.2669,5.8742	possibly-damaging	364/451	111981007	764,12242	2203	4300	6503	SO:0001583	missense	11179	exon11			TGCCATGTGAAGT	AF209198	CCDS5755.2	7q31.1	2012-10-05	2007-10-23	2007-10-23	ENSG00000198839	ENSG00000198839			13070	protein-coding gene	gene with protein product		605465	"""zinc finger protein (C2H2 type) 277"", ""zinc finger protein 277 pseudogene"""	ZNF277P		10860669, 16213364, 16395595	Standard	NM_021994		Approved	NRIF4	uc003vge.2	Q9NRM2	OTTHUMG00000150209	ENST00000361822.3:c.1090G>A	7.37:g.111981007G>A	ENSP00000354501:p.Val364Met	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	238	138	0.579832	NM_021994	Q75MZ2|Q75MZ3|Q8WY14	Missense_Mutation	SNP	ENST00000361822.3	37	CCDS5755.2	104	0.047619047619047616	19	0.03861788617886179	8	0.022099447513812154	17	0.02972027972027972	60	0.079155672823219	G	11.73	1.725045	0.30593	0.042669	0.066977	ENSG00000198839	ENST00000361822	T	0.44083	0.93	6.03	-0.106	0.13596	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	1.181470	0.05958	N	0.640143	T	0.01092	0.0036	N	0.08118	0	0.80722	P	0.0	B	0.31026	0.304	B	0.31016	0.123	T	0.13202	-1.0518	9	0.46703	T	0.11	1.0764	4.44	0.11570	0.2114:0.0989:0.5774:0.1122	rs11539696;rs17492506;rs52818523;rs11539696	364	Q9NRM2	ZN277_HUMAN	M	364	ENSP00000354501:V364M	ENSP00000354501:V364M	V	+	1	0	ZNF277	111768243	0.825000	0.29262	0.000000	0.03702	0.915000	0.54546	0.676000	0.25247	0.057000	0.16193	-0.378000	0.06908	GTG	G|0.943;A|0.057	0.057	strong		0.408	ZNF277-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316843.2	NM_021994	
FARP2	9855	hgsc.bcm.edu	37	2	242373714	242373714	+	Missense_Mutation	SNP	C	C	T	rs372818608		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242373714C>T	ENST00000264042.3	+	10	1179	c.1009C>T	c.(1009-1011)Cgg>Tgg	p.R337W	FARP2_ENST00000545004.1_Missense_Mutation_p.R337W|FARP2_ENST00000373287.4_Missense_Mutation_p.R337W	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	337					actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		CTTCTTCAGCCGGGGCTCCTC	0.463																																					p.R337W		Atlas-SNP	.											.	FARP2	92	.	0			c.C1009T						PASS	.	C	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	78.0	81.0	80.0		1009	4.1	1.0	2		80	0,8600		0,0,4300	no	missense	FARP2	NM_014808.2	101	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	337/1055	242373714	2,13004	2203	4300	6503	SO:0001583	missense	9855	exon10			TTCAGCCGGGGCT	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1009C>T	2.37:g.242373714C>T	ENSP00000264042:p.Arg337Trp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	90	4	0.0444444	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696420	0.68386	4.54E-4	0.0	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000413432	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	5.04	4.13	0.48395	FERM adjacent (FA) (1);	0.062830	0.64402	D	0.000012	D	0.93851	0.8033	M	0.88105	2.93	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.94179	0.7430	10	0.66056	D	0.02	.	12.8745	0.57982	0.3929:0.6071:0.0:0.0	.	337;337;337	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	W	337;337;337;24	ENSP00000264042:R337W;ENSP00000443876:R337W;ENSP00000362384:R337W;ENSP00000412772:R24W	ENSP00000264042:R337W	R	+	1	2	FARP2	242022387	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.660000	0.37397	1.023000	0.39654	0.557000	0.71058	CGG	.	.	weak		0.463	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
TUBB8	347688	hgsc.bcm.edu	37	10	93994	93994	+	Missense_Mutation	SNP	A	A	G	rs61839058	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:93994A>G	ENST00000309812.4	-	4	400	c.338T>C	c.(337-339)aTg>aCg	p.M113T	TUBB8_ENST00000332708.5_3'UTR|TUBB8_ENST00000447903.2_Missense_Mutation_p.M41T|TUBB8_ENST00000413237.3_5'UTR	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	113					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)			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)		CACTGACTCCATCAGCTCCGC	0.612																																					p.M113T	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.T338C						PASS	.						64.0	56.0	59.0					10																	93994		2203	4300	6503	SO:0001583	missense	347688	exon4			GACTCCATCAGCT	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.338T>C	10.37:g.93994A>G	ENSP00000311042:p.Met113Thr	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	223	42	0.188341	NM_177987	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	A	5.128	0.209250	0.09757	.	.	ENSG00000173876	ENST00000447903;ENST00000272035;ENST00000440680;ENST00000328974	T	0.67523	-0.27	.	.	.	Tubulin/FtsZ, GTPase domain (4);	0.210109	0.29218	U	0.012784	T	0.49304	0.1549	.	.	.	0.26286	N	0.978194	B;B	0.32302	0.0;0.363	B;B	0.29440	0.0;0.102	T	0.45056	-0.9287	8	0.87932	D	0	.	4.5487	0.12098	0.9994:0.0:6.0E-4:0.0	rs61839058	76;113	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	T	41;79;76;113	ENSP00000403895:M41T	ENSP00000272035:M79T	M	-	2	0	RP11-631M21.2	83994	1.000000	0.71417	0.302000	0.25058	0.306000	0.27790	6.213000	0.72194	0.103000	0.17682	0.102000	0.15555	ATG	A|1.000;|0.000	.	weak		0.612	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103027234	103027234	+	Missense_Mutation	SNP	A	A	G	rs17301750	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:103027234A>G	ENST00000375735.2	+	26	4006	c.3862A>G	c.(3862-3864)Act>Gct	p.T1288A	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.T1288A	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1288	Stem. {ECO:0000250}.		T -> A (in dbSNP:rs17301750).		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)		CCAAAGTCGAACTATGAAGCT	0.358													A|||	382	0.076278	0.0023	0.0922	5008	,	,		15673	0.0923		0.1233	False		,,,				2504	0.1002				p.T1288A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A3862G						PASS	.	A	ALA/THR,ALA/THR	97,3585		2,93,1746	96.0	95.0	95.0		3862,3862	4.1	1.0	11	dbSNP_123	95	944,7242		58,828,3207	yes	missense,missense	DYNC2H1	NM_001080463.1,NM_001377.2	58,58	60,921,4953	GG,GA,AA		11.5319,2.6344,8.7715	benign,benign	1288/4315,1288/4308	103027234	1041,10827	1841	4093	5934	SO:0001583	missense	79659	exon26			AGTCGAACTATGA	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.3862A>G	11.37:g.103027234A>G	ENSP00000364887:p.Thr1288Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	153	117	0.764706	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	190	0.08699633699633699	3	0.006097560975609756	33	0.09116022099447514	50	0.08741258741258741	104	0.13720316622691292	A	6.130	0.392124	0.11581	0.026344	0.115319	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.60424	0.19;0.19	5.27	4.1	0.47936	Dynein heavy chain, domain-2 (1);	0.981166	0.08306	N	0.966220	T	0.00524	0.0017	L	0.54323	1.7	0.38246	P	0.05853600000000003	B;B	0.11235	0.004;0.004	B;B	0.16722	0.016;0.014	T	0.18681	-1.0329	9	0.08599	T	0.76	.	11.2807	0.49192	0.8632:0.0:0.0:0.1368	rs17301750;rs52791460;rs17301750	1288;1288	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	A	1288	ENSP00000364887:T1288A;ENSP00000381167:T1288A	ENSP00000364887:T1288A	T	+	1	0	DYNC2H1	102532444	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	4.416000	0.59815	0.796000	0.33947	0.460000	0.39030	ACT	A|0.912;G|0.088	0.088	strong		0.358	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
ZNF732	654254	hgsc.bcm.edu	37	4	289877	289877	+	Missense_Mutation	SNP	G	G	T	rs62619793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:289877G>T	ENST00000419098.1	-	2	81	c.71C>A	c.(70-72)gCc>gAc	p.A24D		NM_001137608.1	NP_001131080.1	B4DXR9	ZN732_HUMAN	zinc finger protein 732	24	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(1)|lung(2)	3						ATTCTGCTGGGCAGGGTCCAG	0.423													.|||	191	0.038139	0.0968	0.0317	5008	,	,		17640	0.0		0.0298	False		,,,				2504	0.0112				p.A23D		Atlas-SNP	.											.	ZNF732	117	.	0			c.C68A						PASS	.						33.0	32.0	32.0					4																	289877		692	1590	2282	SO:0001583	missense	654254	exon1			TGCTGGGCAGGGT	AK302099	CCDS46990.1	4p16.3	2014-02-12	2009-07-22		ENSG00000186777	ENSG00000186777		"""Zinc fingers, C2H2-type"", ""-"""	37138	protein-coding gene	gene with protein product							Standard	NM_001137608		Approved	FLJ59067	uc011buu.1	B4DXR9	OTTHUMG00000159883	ENST00000419098.1:c.71C>A	4.37:g.289877G>T	ENSP00000415774:p.Ala24Asp	Somatic	326	1	0.00306748		WXS	Illumina HiSeq	Phase_I	291	138	0.474227	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	37	CCDS46990.1	90	0.04120879120879121	57	0.11585365853658537	11	0.03038674033149171	0	0.0	22	0.029023746701846966	G	6.253	0.414829	0.11870	.	.	ENSG00000186777	ENST00000419098	T	0.02525	4.26	1.22	1.22	0.21188	Krueppel-associated box (4);	.	.	.	.	T	0.00109	0.0003	M	0.88310	2.945	0.80722	P	0.0	B	0.20368	0.044	B	0.28991	0.097	T	0.03566	-1.1024	8	0.72032	D	0.01	.	5.3307	0.15930	0.0:0.0:1.0:0.0	rs62619793	24	B4DXR9	ZN732_HUMAN	D	24	ENSP00000415774:A24D	ENSP00000415774:A24D	A	-	2	0	ZNF732	279877	0.000000	0.05858	0.082000	0.20525	0.084000	0.17831	-1.252000	0.02880	0.300000	0.22699	0.305000	0.20034	GCC	G|0.958;T|0.042	0.042	strong		0.423	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608	
KIAA1217	56243	hgsc.bcm.edu	37	10	24813454	24813454	+	Missense_Mutation	SNP	G	G	A	rs10828663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:24813454G>A	ENST00000376454.3	+	13	2689	c.2659G>A	c.(2659-2661)Gcg>Acg	p.A887T	KIAA1217_ENST00000376462.1_Missense_Mutation_p.A807T|KIAA1217_ENST00000376452.3_Missense_Mutation_p.A852T|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000307544.6_Missense_Mutation_p.A570T|KIAA1217_ENST00000396445.1_Missense_Mutation_p.A570T|KIAA1217_ENST00000458595.1_Missense_Mutation_p.A852T|KIAA1217_ENST00000396446.1_Missense_Mutation_p.A570T|KIAA1217_ENST00000376451.2_Missense_Mutation_p.A570T	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	887			A -> T (in dbSNP:rs10828663). {ECO:0000269|PubMed:15489334}.		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						GGTTCGCCACGCGCAGAGCTC	0.672													G|||	939	0.1875	0.2133	0.2147	5008	,	,		18777	0.1081		0.2893	False		,,,				2504	0.1104				p.A887T		Atlas-SNP	.											KIAA1217,colon,carcinoma,0,2	KIAA1217	235	2	0			c.G2659A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	1043,3363	382.1+/-324.3	133,777,1293	68.0	56.0	60.0		2419,2554,2659	4.6	0.2	10	dbSNP_120	60	2478,6122	407.7+/-349.2	342,1794,2164	yes	missense,missense,missense	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	58,58,58	475,2571,3457	AA,AG,GG		28.814,23.6723,27.0721	possibly-damaging,possibly-damaging,possibly-damaging	807/1265,852/1310,887/1944	24813454	3521,9485	2203	4300	6503	SO:0001583	missense	56243	exon13			CGCCACGCGCAGA	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.2659G>A	10.37:g.24813454G>A	ENSP00000365637:p.Ala887Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	46	33	0.717391	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	470	0.21520146520146521	111	0.22560975609756098	84	0.23204419889502761	61	0.10664335664335664	214	0.28232189973614774	G	12.63	1.996660	0.35226	0.236723	0.28814	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000438429;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451;ENST00000396446	T;T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.51	4.61	0.57282	.	0.267267	0.35739	N	0.003003	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.34103	0.086;0.106;0.086;0.103;0.437;0.166;0.143;0.035	B;B;B;B;B;B;B;B	0.21360	0.012;0.011;0.011;0.025;0.034;0.024;0.022;0.016	T	0.25433	-1.0132	9	0.13853	T	0.58	.	14.3498	0.66694	0.0717:0.0:0.9283:0.0	rs10828663;rs17588312;rs60956410;rs10828663	852;852;570;570;570;570;887;887	Q5T5P2-7;A6NLF3;Q5T5P2-4;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2;Q5T5P2-2	.;.;.;.;.;.;SKT_HUMAN;.	T	807;852;852;570;887;852;702;570;570;570;570;570	ENSP00000365645:A807T;ENSP00000365639:A852T;ENSP00000392625:A852T;ENSP00000365637:A887T;ENSP00000365635:A852T;ENSP00000404798:A702T;ENSP00000302343:A570T;ENSP00000379722:A570T;ENSP00000365634:A570T;ENSP00000379723:A570T	ENSP00000302343:A570T	A	+	1	0	KIAA1217	24853460	0.984000	0.35163	0.212000	0.23672	0.004000	0.04260	4.371000	0.59523	1.336000	0.45506	-0.258000	0.10820	GCG	G|0.760;A|0.240	0.240	strong		0.672	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
EXPH5	23086	hgsc.bcm.edu	37	11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	rs10890850	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108383560T>A	ENST00000265843.4	-	6	2784	c.2674A>T	c.(2674-2676)Aat>Tat	p.N892Y	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000443411.1_Missense_Mutation_p.N704Y|EXPH5_ENST00000525344.1_Missense_Mutation_p.N885Y|EXPH5_ENST00000428840.1_Missense_Mutation_p.N816Y	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	892			N -> Y (in dbSNP:rs10890850).		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)		AGGGAAGAATTCTTTGATGGT	0.438													T|||	270	0.0539137	0.1316	0.0115	5008	,	,		19382	0.0119		0.002	False		,,,				2504	0.0757				p.N892Y		Atlas-SNP	.											.	EXPH5	193	.	0			c.A2674T						PASS	.	T	TYR/ASN	493,3909	229.8+/-244.2	29,435,1737	182.0	167.0	172.0		2674	-2.0	0.0	11	dbSNP_120	172	9,8587	7.1+/-27.0	0,9,4289	yes	missense	EXPH5	NM_015065.2	143	29,444,6026	AA,AT,TT		0.1047,11.1995,3.8621	benign	892/1990	108383560	502,12496	2201	4298	6499	SO:0001583	missense	23086	exon6			AAGAATTCTTTGA		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.2674A>T	11.37:g.108383560T>A	ENSP00000265843:p.Asn892Tyr	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	211	60	0.28436	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	59	0.027014652014652016	46	0.09349593495934959	5	0.013812154696132596	7	0.012237762237762238	1	0.0013192612137203166	T	14.92	2.680490	0.47886	0.111995	0.001047	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04603	4.17;4.1;3.95;4.17;4.02;3.59	5.74	-1.97	0.07503	.	0.712890	0.13437	N	0.387972	T	0.00109	0.0003	L	0.44542	1.39	0.09310	N	1	P	0.49090	0.919	B	0.43445	0.42	T	0.40813	-0.9543	10	0.72032	D	0.01	-0.8859	6.5046	0.22188	0.0:0.4682:0.1578:0.3739	rs10890850;rs10890850	892	Q8NEV8	EXPH5_HUMAN	Y	892;816;704;885;816;704	ENSP00000265843:N892Y;ENSP00000391966:N816Y;ENSP00000411390:N704Y;ENSP00000432546:N885Y;ENSP00000432683:N816Y;ENSP00000446434:N704Y	ENSP00000265843:N892Y	N	-	1	0	EXPH5	107888770	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	-0.173000	0.09854	-0.270000	0.09285	0.460000	0.39030	AAT	T|0.967;A|0.033	0.033	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
ST8SIA2	8128	hgsc.bcm.edu	37	15	92987938	92987938	+	Silent	SNP	C	C	G	rs2305561	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:92987938C>G	ENST00000268164.3	+	5	858	c.621C>G	c.(619-621)ccC>ccG	p.P207P	ST8SIA2_ENST00000539113.1_Silent_p.P186P	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	207					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|ganglioside biosynthetic process (GO:0001574)|N-glycan processing (GO:0006491)|nervous system development (GO:0007399)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	early endosome (GO:0005769)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|recycling endosome (GO:0055037)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			CCATGAACCCCTCGGTCATCC	0.592													C|||	1121	0.223842	0.5968	0.1297	5008	,	,		18692	0.0258		0.1054	False		,,,				2504	0.1125				p.P207P		Atlas-SNP	.											.	ST8SIA2	41	.	0			c.C621G						PASS	.	C		2271,2125	597.1+/-388.8	587,1097,514	69.0	70.0	70.0		621	-0.2	1.0	15	dbSNP_100	70	1159,7437	236.8+/-268.9	83,993,3222	no	coding-synonymous	ST8SIA2	NM_006011.3		670,2090,3736	GG,GC,CC		13.483,48.3394,26.4009		207/376	92987938	3430,9562	2198	4298	6496	SO:0001819	synonymous_variant	8128	exon5			GAACCCCTCGGTC	U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557		"""Sialyltransferases"""	10870	protein-coding gene	gene with protein product		602546	"""sialyltransferase 8 (alpha-2, 8-sialytransferase) B"""	SIAT8B		7559389	Standard	NM_006011		Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.621C>G	15.37:g.92987938C>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	97	17	0.175258	NM_006011	Q4VAZ0|Q92470|Q92746	Silent	SNP	ENST00000268164.3	37	CCDS10372.1																																																																																			C|0.758;G|0.242	0.242	strong		0.592	ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313526.1	NM_006011	
ZNF440	126070	hgsc.bcm.edu	37	19	11943713	11943713	+	Silent	SNP	G	G	A	rs56167415	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11943713G>A	ENST00000304060.5	+	4	1886	c.1722G>A	c.(1720-1722)agG>agA	p.R574R		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	574					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						TGCATGTAAGGAATGTGGGAA	0.453													g|||	338	0.067492	0.0083	0.1023	5008	,	,		22084	0.0		0.2048	False		,,,				2504	0.0511				p.R574R		Atlas-SNP	.											.	ZNF440	56	.	0			c.G1722A						PASS	.	G		174,4206	102.1+/-140.7	2,170,2018	66.0	65.0	65.0		1722	-1.6	0.0	19	dbSNP_129	65	1845,6735	313.5+/-311.4	184,1477,2629	no	coding-synonymous	ZNF440	NM_152357.2		186,1647,4647	AA,AG,GG		21.5035,3.9726,15.5787		574/596	11943713	2019,10941	2190	4290	6480	SO:0001819	synonymous_variant	126070	exon4			TGTAAGGAATGTG	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.1722G>A	19.37:g.11943713G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	58	20	0.344828	NM_152357	Q8N1R9	Silent	SNP	ENST00000304060.5	37	CCDS42503.1																																																																																			G|0.863;A|0.137	0.137	strong		0.453	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357	
PTCH1	5727	hgsc.bcm.edu	37	9	98221978	98221978	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:98221978G>T	ENST00000331920.6	-	17	3090	c.2791C>A	c.(2791-2793)Ccc>Acc	p.P931T	PTCH1_ENST00000437951.1_Missense_Mutation_p.P865T|PTCH1_ENST00000429896.2_Missense_Mutation_p.P780T|PTCH1_ENST00000421141.1_Missense_Mutation_p.P780T|PTCH1_ENST00000418258.1_Missense_Mutation_p.P780T|PTCH1_ENST00000430669.2_Missense_Mutation_p.P865T|PTCH1_ENST00000375274.2_Missense_Mutation_p.P930T	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	931					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.P931fs*27(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				TACGCGACGGGGTCGTTGCTG	0.542																																					p.P931T		Atlas-SNP	.											PTCH1_ENST00000430669,NS,lymphoid_neoplasm,+2,4	PTCH1	1850	4	1	Complex - frameshift(1)	skin(1)	c.C2791A						scavenged	.						121.0	102.0	108.0					9																	98221978		2203	4300	6503	SO:0001583	missense	5727	exon17			CGACGGGGTCGTT	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2791C>A	9.37:g.98221978G>T	ENSP00000332353:p.Pro931Thr	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	173	2	0.0115607	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.952473	0.34471	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.90504	-2.68;-2.67;-2.66;-2.66;-2.67;-2.66;-2.68	5.14	4.24	0.50183	.	0.106616	0.64402	D	0.000003	D	0.88540	0.6464	L	0.60455	1.87	0.80722	D	1	B;P;B	0.40230	0.328;0.708;0.213	B;B;B	0.38264	0.155;0.269;0.262	D	0.88191	0.2877	10	0.46703	T	0.11	-18.8885	15.1079	0.72334	0.0:0.0:0.8573:0.1427	.	865;930;931	Q13635-3;Q13635-2;Q13635	.;.;PTC1_HUMAN	T	931;865;780;780;367;865;780;930	ENSP00000332353:P931T;ENSP00000389744:P865T;ENSP00000399981:P780T;ENSP00000396135:P780T;ENSP00000410287:P865T;ENSP00000414823:P780T;ENSP00000364423:P930T	ENSP00000332353:P931T	P	-	1	0	PTCH1	97261799	1.000000	0.71417	0.804000	0.32291	0.166000	0.22503	9.263000	0.95617	1.371000	0.46172	0.563000	0.77884	CCC	.	.	none		0.542	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
SVEP1	79987	hgsc.bcm.edu	37	9	113312231	113312231	+	Missense_Mutation	SNP	G	G	C	rs61751937	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:113312231G>C	ENST00000401783.2	-	2	1021	c.685C>G	c.(685-687)Cga>Gga	p.R229G	SVEP1_ENST00000302728.8_Missense_Mutation_p.R229G|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.R206G|SVEP1_ENST00000374461.1_Missense_Mutation_p.R206G	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	229	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						TTCAGCTCTCGAATGTTCCCT	0.493													G|||	66	0.0131789	0.0015	0.0144	5008	,	,		22248	0.0		0.0338	False		,,,				2504	0.0204				p.R229G		Atlas-SNP	.											.	SVEP1	326	.	0			c.C685G						PASS	.	G	GLY/ARG	19,3863		0,19,1922	116.0	109.0	111.0		685	4.6	1.0	9	dbSNP_129	111	222,8076		4,214,3931	yes	missense	SVEP1	NM_153366.3	125	4,233,5853	CC,CG,GG		2.6753,0.4894,1.9787	probably-damaging	229/3572	113312231	241,11939	1941	4149	6090	SO:0001583	missense	79987	exon2			GCTCTCGAATGTT	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.685C>G	9.37:g.113312231G>C	ENSP00000384917:p.Arg229Gly	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	38	0.0173992673992674	0	0.0	7	0.019337016574585635	0	0.0	31	0.040897097625329816	G	19.22	3.785977	0.70337	0.004894	0.026753	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	5.5	4.59	0.56863	von Willebrand factor, type A (3);	0.066403	0.56097	D	0.000023	T	0.66790	0.2825	L	0.39085	1.19	0.35851	D	0.826799	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.85130	0.997;0.959;0.95	D	0.84708	0.0732	10	0.72032	D	0.01	.	15.7144	0.77655	0.0:0.0:0.8548:0.1452	rs61751937	229;229;229	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	G	229;206;229;206	ENSP00000384917:R229G;ENSP00000363593:R206G;ENSP00000304118:R229G;ENSP00000363585:R206G	ENSP00000304118:R229G	R	-	1	2	SVEP1	112352052	1.000000	0.71417	0.993000	0.49108	0.957000	0.61999	7.152000	0.77419	1.411000	0.46957	0.563000	0.77884	CGA	G|0.954;C|0.046	0.046	strong		0.493	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
RGS3	5998	hgsc.bcm.edu	37	9	116346118	116346118	+	Missense_Mutation	SNP	G	G	A	rs41305473	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116346118G>A	ENST00000374140.2	+	21	2635	c.2426G>A	c.(2425-2427)cGg>cAg	p.R809Q	RGS3_ENST00000342620.5_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000350696.5_Missense_Mutation_p.R809Q|RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000462143.1_Missense_Mutation_p.R130Q|RGS3_ENST00000343817.5_Missense_Mutation_p.R528Q|RGS3_ENST00000374134.3_Missense_Mutation_p.R130Q	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	809	Pro-rich.		R -> Q (in dbSNP:rs41305473).		inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						TCCCCCACCCGGGACCTTCCA	0.617													g|||	428	0.0854633	0.18	0.0692	5008	,	,		17267	0.0		0.1034	False		,,,				2504	0.0389				p.R809Q		Atlas-SNP	.											.	RGS3	251	.	0			c.G2426A						PASS	.	G	GLN/ARG,GLN/ARG,,GLN/ARG	803,3603	322.9+/-297.8	85,633,1485	128.0	142.0	137.0		389,1583,,2426	2.6	1.0	9	dbSNP_127	137	900,7700	200.7+/-244.4	40,820,3440	yes	missense,missense,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4	43,43,,43	125,1453,4925	AA,AG,GG		10.4651,18.2251,13.094	benign,benign,,benign	130/520,528/918,,809/1199	116346118	1703,11303	2203	4300	6503	SO:0001583	missense	5998	exon21			CCACCCGGGACCT	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.2426G>A	9.37:g.116346118G>A	ENSP00000363255:p.Arg809Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	102	41	0.401961	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	190	0.08699633699633699	82	0.16666666666666666	28	0.07734806629834254	0	0.0	80	0.10554089709762533	g	4.500	0.092706	0.08632	0.182251	0.104651	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000343817;ENST00000462143;ENST00000374134	T;T;T;T;T	0.55760	1.0;1.0;0.5;0.51;0.51	4.97	2.57	0.30868	.	0.286735	0.28914	N	0.013727	T	0.00039	0.0001	N	0.01874	-0.695	0.09310	P	0.999999999897227	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	0.14896	-1.0456	9	0.05525	T	0.97	.	2.2403	0.04018	0.5987:0.1609:0.0857:0.1548	rs41305473;rs61754069	148;705;130;528;699;809	B4DWF9;P49796-6;Q6ZV17;P49796-4;B3KWG8;P49796	.;.;.;.;.;RGS3_HUMAN	Q	809;809;528;130;130	ENSP00000363255:R809Q;ENSP00000259406:R809Q;ENSP00000340284:R528Q;ENSP00000420356:R130Q;ENSP00000363249:R130Q	ENSP00000340284:R528Q	R	+	2	0	RGS3	115385939	0.847000	0.29606	0.953000	0.39169	0.214000	0.24535	0.807000	0.27140	0.424000	0.26061	-0.285000	0.09966	CGG	G|0.884;A|0.116	0.116	strong		0.617	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
ARSD	414	hgsc.bcm.edu	37	X	2836041	2836041	+	Missense_Mutation	SNP	A	A	T	rs67272620		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	98	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	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		
OBSCN	84033	hgsc.bcm.edu	37	1	228526665	228526665	+	Silent	SNP	T	T	C	rs505629	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:228526665T>C	ENST00000422127.1	+	69	17240	c.17196T>C	c.(17194-17196)gcT>gcC	p.A5732A	OBSCN_ENST00000366707.4_Silent_p.A3366A|OBSCN_ENST00000570156.2_Silent_p.A6689A|OBSCN_ENST00000366709.4_Silent_p.A2851A|OBSCN_ENST00000284548.11_Silent_p.A5732A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5732	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)				TGCCCATAGCTGTGGCCGGCC	0.642													C|||	2476	0.494409	0.5522	0.4294	5008	,	,		19542	0.5665		0.5209	False		,,,				2504	0.3609				p.A6689A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T20067C						PASS	.	C	,	2109,1709		638,833,438	12.0	16.0	14.0		17196,17196	-10.4	0.0	1	dbSNP_83	14	4313,3431		1295,1723,854	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1933,2556,1292	CC,CT,TT		44.3053,44.7617,44.456	,	5732/7969,5732/6621	228526665	6422,5140	1909	3872	5781	SO:0001819	synonymous_variant	84033	exon80			CATAGCTGTGGCC	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.17196T>C	1.37:g.228526665T>C		Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	340	127	0.373529	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	1131	0.5178571428571429	265	0.5386178861788617	152	0.4198895027624309	324	0.5664335664335665	390	0.5145118733509235	C	7.567	0.665825	0.14710	0.552383	0.556947	ENSG00000154358	ENST00000441106	.	.	.	5.19	-10.4	0.00318	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.32467	P	0.543358	.	.	.	.	.	.	T	0.07966	-1.0745	3	.	.	.	.	7.4233	0.27083	0.1602:0.5481:0.1388:0.1528	rs505629;rs1684872;rs36173159	.	.	.	R	348	.	.	C	+	1	0	OBSCN	226593288	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-3.780000	0.00368	-3.977000	0.00085	-2.292000	0.00266	TGT	T|0.479;C|0.521	0.521	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
GUCY2F	2986	hgsc.bcm.edu	37	X	108708552	108708552	+	Missense_Mutation	SNP	A	A	G	rs12008095	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	108	108	1	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	
NBEAL2	23218	hgsc.bcm.edu	37	3	47043622	47043622	+	Silent	SNP	G	G	A	rs2305635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:47043622G>A	ENST00000450053.3	+	31	5174	c.4995G>A	c.(4993-4995)gtG>gtA	p.V1665V	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Silent_p.V1481V	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1665					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CCTGGCTGGTGCCACTGGTGC	0.647													G|||	1603	0.320088	0.2163	0.317	5008	,	,		16773	0.3373		0.3926	False		,,,				2504	0.3701				p.V1665V		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G4995A						PASS	.	G		906,3076		135,636,1220	7.0	8.0	8.0		4995	1.7	1.0	3	dbSNP_100	8	3067,4923		683,1701,1611	no	coding-synonymous	NBEAL2	NM_015175.1		818,2337,2831	AA,AG,GG		38.3855,22.7524,33.1858		1665/2755	47043622	3973,7999	1991	3995	5986	SO:0001819	synonymous_variant	23218	exon31			GCTGGTGCCACTG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4995G>A	3.37:g.47043622G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	82	51	0.621951	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	689|689	0.31547619047619047|0.31547619047619047	101|101	0.20528455284552846|0.20528455284552846	105|105	0.2900552486187845|0.2900552486187845	186|186	0.32517482517482516|0.32517482517482516	297|297	0.391820580474934|0.391820580474934	G|G	6.501|6.501	0.460666|0.460666	0.12342|0.12342	0.227524|0.227524	0.383855|0.383855	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	4.49|4.49	1.71|1.71	0.24356|0.24356	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43972|0.43972	-0.9358|-0.9358	3|3	.|.	.|.	.|.	.|.	4.6581|4.6581	0.12628|0.12628	0.2533:0.0:0.5966:0.1501|0.2533:0.0:0.5966:0.1501	rs2305635;rs17223759;rs2305635|rs2305635;rs17223759;rs2305635	.|.	.|.	.|.	T|Y	34|953	.|.	.|.	A|C	+|+	1|2	0|0	NBEAL2|NBEAL2	47018626|47018626	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.750000|0.750000	0.42670|0.42670	0.763000|0.763000	0.26517|0.26517	0.168000|0.168000	0.19655|0.19655	-0.263000|-0.263000	0.10527|0.10527	GCC|TGC	G|0.685;A|0.315	0.315	strong		0.647	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
ZNF813	126017	hgsc.bcm.edu	37	19	53994083	53994083	+	Silent	SNP	T	T	C	rs150664026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53994083T>C	ENST00000396403.4	+	4	725	c.597T>C	c.(595-597)tcT>tcC	p.S199S	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	199					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)		TCCGGAATTCTTCGTTACTCA	0.368													.|||	12	0.00239617	0.0083	0.0014	5008	,	,		20858	0.0		0.0	False		,,,				2504	0.0				p.S199S		Atlas-SNP	.											ZNF813_ENST00000396403,NS,carcinoma,+1,1	ZNF813	81	1	0			c.T597C						scavenged	.	T		31,4353		0,31,2161	79.0	87.0	84.0		597	0.5	0.0	19	dbSNP_134	84	2,8584		0,2,4291	no	coding-synonymous	ZNF813	NM_001004301.3		0,33,6452	CC,CT,TT		0.0233,0.7071,0.2544		199/618	53994083	33,12937	2192	4293	6485	SO:0001819	synonymous_variant	126017	exon4			GAATTCTTCGTTA	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.597T>C	19.37:g.53994083T>C		Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	260	5	0.0192308	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			T|0.999;C|0.001	0.001	strong		0.368	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
FAM210B	116151	hgsc.bcm.edu	37	20	54941140	54941140	+	Missense_Mutation	SNP	C	C	T	rs6099115	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:54941140C>T	ENST00000371384.3	+	3	467	c.376C>T	c.(376-378)Cct>Tct	p.P126S		NM_080821.2	NP_543011.2	Q96KR6	F210B_HUMAN	family with sequence similarity 210, member B	126	DUF1279.		P -> S (in dbSNP:rs6099115).			integral component of membrane (GO:0016021)											TGTGGACATGCCTGCAATCCT	0.418													T|||	1149	0.229433	0.5499	0.1484	5008	,	,		18844	0.001		0.1938	False		,,,				2504	0.1258				p.P126S		Atlas-SNP	.											.	.	.	.	0			c.C376T						PASS	.	T	SER/PRO	2171,2235	592.3+/-387.8	531,1109,563	65.0	62.0	63.0		376	3.3	1.0	20	dbSNP_114	63	1472,7128	749.9+/-407.4	127,1218,2955	yes	missense	C20orf108	NM_080821.2	74	658,2327,3518	TT,TC,CC		17.1163,49.2737,28.0101	benign	126/193	54941140	3643,9363	2203	4300	6503	SO:0001583	missense	116151	exon3			GACATGCCTGCAA	AL121914	CCDS13450.1	20q13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000124098	ENSG00000124098			16102	protein-coding gene	gene with protein product	"""hypothetical protein LOC116151"""		"""chromosome 20 open reading frame 108"""	C20orf108		11780052	Standard	NM_080821		Approved	dJ1167H4.1, DKFZP434A1114	uc002xxc.3	Q96KR6	OTTHUMG00000032793	ENST00000371384.3:c.376C>T	20.37:g.54941140C>T	ENSP00000360437:p.Pro126Ser	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	119	45	0.378151	NM_080821	B2RBQ9|E1P5Y7|Q8WVN2|Q9BYL6|Q9H418	Missense_Mutation	SNP	ENST00000371384.3	37	CCDS13450.1	463	0.211996336996337	266	0.540650406504065	59	0.16298342541436464	0	0.0	138	0.1820580474934037	T	1.259	-0.616284	0.03663	0.492737	0.171163	ENSG00000124098	ENST00000371384	T	0.27890	1.64	5.56	3.28	0.37604	Domain of unknown function DUF1279 (1);	0.225853	0.46758	N	0.000274	T	0.00012	0.0000	N	0.05230	-0.09	0.58432	P	4.000000000004E-6	B	0.09022	0.002	B	0.20577	0.03	T	0.46219	-0.9207	9	0.07813	T	0.8	-2.3755	4.0206	0.09664	0.4248:0.1575:0.0:0.4177	rs6099115;rs52826804;rs58841026;rs6099115	126	Q96KR6	CT108_HUMAN	S	126	ENSP00000360437:P126S	ENSP00000360437:P126S	P	+	1	0	C20orf108	54374547	0.995000	0.38212	0.996000	0.52242	0.752000	0.42762	0.723000	0.25939	0.373000	0.24621	-1.239000	0.01543	CCT	C|0.729;T|0.271	0.271	strong		0.418	FAM210B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079800.2	NM_080821	
PLEKHA6	22874	hgsc.bcm.edu	37	1	204199614	204199614	+	Missense_Mutation	SNP	C	C	T	rs10900562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:204199614C>T	ENST00000272203.3	-	18	2826	c.2510G>A	c.(2509-2511)aGg>aAg	p.R837K	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.R857K	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	837			R -> K (in dbSNP:rs10900562). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			CCGCTTCTCCCTCATGGAGCC	0.652													T|||	2557	0.510583	0.6914	0.5375	5008	,	,		13874	0.4802		0.4334	False		,,,				2504	0.3579				p.R837K		Atlas-SNP	.											PLEKHA6,colon,carcinoma,0,1	PLEKHA6	115	1	0			c.G2510A						PASS	.	T	LYS/ARG	2895,1507		980,935,286	22.0	21.0	22.0		2510	2.9	1.0	1	dbSNP_120	22	3909,4671		909,2091,1290	yes	missense	PLEKHA6	NM_014935.2	26	1889,3026,1576	TT,TC,CC		45.5594,34.2344,47.589	benign	837/1049	204199614	6804,6178	2201	4290	6491	SO:0001583	missense	22874	exon18			TTCTCCCTCATGG	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2510G>A	1.37:g.204199614C>T	ENSP00000272203:p.Arg837Lys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	223	221	0.991031	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	1131	0.5178571428571429	332	0.6747967479674797	193	0.5331491712707183	277	0.48426573426573427	329	0.4340369393139842	T	9.062	0.994763	0.19043	0.657656	0.455594	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.22743	1.94;2.4	5.24	2.91	0.33838	.	0.157126	0.56097	N	0.000034	T	0.00012	0.0000	N	0.10972	0.075	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.30707	-0.9969	9	0.15499	T	0.54	-21.9669	9.0092	0.36131	0.0:0.216:0.0:0.7839	rs10900562;rs58953574;rs10900562	837	Q9Y2H5	PKHA6_HUMAN	K	837;857	ENSP00000272203:R837K;ENSP00000402046:R857K	ENSP00000272203:R837K	R	-	2	0	PLEKHA6	202466237	1.000000	0.71417	0.999000	0.59377	0.790000	0.44656	3.200000	0.51051	0.026000	0.15269	-1.390000	0.01156	AGG	C|0.466;T|0.534	0.534	strong		0.652	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
OR5J2	282775	hgsc.bcm.edu	37	11	55944474	55944474	+	Silent	SNP	G	G	A	rs4489763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	498	1	0.00200803		WXS	Illumina HiSeq	Phase_I	443	181	0.408578	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	
FRMD4A	55691	hgsc.bcm.edu	37	10	13735947	13735947	+	Silent	SNP	A	A	G	rs2296596	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:13735947A>G	ENST00000357447.2	-	15	1436	c.1068T>C	c.(1066-1068)ggT>ggC	p.G356G	FRMD4A_ENST00000492155.1_5'UTR|FRMD4A_ENST00000358621.4_Silent_p.G341G|FRMD4A_ENST00000378503.1_Silent_p.G356G|FRMD4A_ENST00000342409.2_Silent_p.G372G	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	356					establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)				breast(4)|endometrium(9)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	41						TCCCCTTGCTACCCATGTTGG	0.622													G|||	652	0.130192	0.1989	0.0735	5008	,	,		19362	0.1081		0.1103	False		,,,				2504	0.1207				p.G356G		Atlas-SNP	.											.	FRMD4A	108	.	0			c.T1068C						PASS	.	G		796,3610	751.1+/-412.2	59,678,1466	111.0	91.0	98.0		1068	-0.4	1.0	10	dbSNP_100	98	907,7693	778.0+/-407.7	34,839,3427	no	coding-synonymous	FRMD4A	NM_018027.3		93,1517,4893	GG,GA,AA		10.5465,18.0663,13.094		356/1040	13735947	1703,11303	2203	4300	6503	SO:0001819	synonymous_variant	55691	exon15			CTTGCTACCCATG	AB037715	CCDS7101.1	10p14	2004-07-15	2004-07-15	2004-07-15	ENSG00000151474	ENSG00000151474			25491	protein-coding gene	gene with protein product			"""FERM domain containing 4"""	FRMD4		10718198	Standard	NM_018027		Approved	FLJ10210, KIAA1294, bA295P9.4	uc001ims.3	Q9P2Q2	OTTHUMG00000017708	ENST00000357447.2:c.1068T>C	10.37:g.13735947A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	68	20	0.294118	NM_018027	A7E2Y3|Q5T377	Silent	SNP	ENST00000357447.2	37	CCDS7101.1																																																																																			A|0.869;G|0.131	0.131	strong		0.622	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027	
PSMF1	9491	hgsc.bcm.edu	37	20	1115919	1115919	+	Missense_Mutation	SNP	A	A	G	rs2235587	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1115919A>G	ENST00000335877.6	+	4	697	c.521A>G	c.(520-522)cAc>cGc	p.H174R	PSMF1_ENST00000246015.4_Missense_Mutation_p.H174R|PSMF1_ENST00000438768.2_Intron|PSMF1_ENST00000333082.3_Missense_Mutation_p.H174R|PSMF1_ENST00000484891.1_3'UTR|PSMF1_ENST00000381898.4_Missense_Mutation_p.H86R	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	174	Pro-rich.		H -> R (in dbSNP:rs2235587).		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 endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|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)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						ATTCCTCCACACCACCCACAC	0.602													A|||	1010	0.201677	0.0121	0.2089	5008	,	,		16562	0.4841		0.1471	False		,,,				2504	0.2178				p.H174R		Atlas-SNP	.											.	PSMF1	27	.	0			c.A521G						PASS	.	A	ARG/HIS,ARG/HIS	149,4257	103.4+/-141.9	1,147,2055	62.0	57.0	59.0		521,521	2.9	0.8	20	dbSNP_98	59	1292,7308	257.5+/-281.5	92,1108,3100	yes	missense,missense	PSMF1	NM_006814.3,NM_178578.2	29,29	93,1255,5155	GG,GA,AA		15.0233,3.3818,11.0795	benign,benign	174/272,174/272	1115919	1441,11565	2203	4300	6503	SO:0001583	missense	9491	exon4			CTCCACACCACCC	D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"""Proteasome (prosome, macropain) subunits"""	9571	protein-coding gene	gene with protein product	"""proteasome inhibitor hP131 subunit"""					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.521A>G	20.37:g.1115919A>G	ENSP00000338039:p.His174Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Missense_Mutation	SNP	ENST00000335877.6	37	CCDS13010.1	477	0.2184065934065934	6	0.012195121951219513	72	0.19889502762430938	281	0.49125874125874125	118	0.15567282321899736	A	0.042	-1.282104	0.01398	0.033818	0.150233	ENSG00000125818	ENST00000333082;ENST00000381898;ENST00000381899;ENST00000454500;ENST00000246015;ENST00000335877	T;T;T;T;T	0.37584	1.73;1.19;1.8;1.73;1.73	5.22	2.91	0.33838	.	0.428883	0.22081	N	0.064884	T	0.00012	0.0000	N	0.00082	-2.215	0.39337	P	0.03448300000000004	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.44559	-0.9320	9	0.07813	T	0.8	-1.4721	5.6549	0.17637	0.5751:0.3398:0.0851:0.0	rs2235587;rs52829784;rs59036473;rs2235587	86;86;174;174	F5H4Z3;B4DUJ0;Q5QPM7;Q92530	.;.;.;PSMF1_HUMAN	R	174;86;174;86;174;174	ENSP00000327704:H174R;ENSP00000371323:H86R;ENSP00000371324:H174R;ENSP00000246015:H174R;ENSP00000338039:H174R	ENSP00000246015:H174R	H	+	2	0	PSMF1	1063919	0.759000	0.28416	0.835000	0.33067	0.505000	0.33919	2.007000	0.40883	0.414000	0.25790	-0.321000	0.08615	CAC	A|0.849;G|0.151	0.151	strong		0.602	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578	
ANKRD20A1	84210	hgsc.bcm.edu	37	9	67938633	67938633	+	Missense_Mutation	SNP	G	G	T	rs200989194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:67938633G>T	ENST00000377477.2	+	6	880	c.768G>T	c.(766-768)aaG>aaT	p.K256N	RNU6-368P_ENST00000391117.1_RNA	NM_032250.3	NP_115626.2	Q5TYW2	A20A1_HUMAN	ankyrin repeat domain 20 family, member A1	256						plasma membrane (GO:0005886)		p.K256N(2)		kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	11						AACATAAAAAGAAGATACTTA	0.249																																					p.K256N		Atlas-SNP	.											ANKRD20A1,bladder,carcinoma,0,3	ANKRD20A1	16	3	2	Substitution - Missense(2)	urinary_tract(1)|kidney(1)	c.G768T						scavenged	.						9.0	11.0	10.0					9																	67938633		1501	3099	4600	SO:0001583	missense	84210	exon6			TAAAAAGAAGATA	AL136793	CCDS6620.1	9p12	2014-04-16	2005-08-23	2005-08-23	ENSG00000196774	ENSG00000260691		"""Ankyrin repeat domain containing"""	23665	protein-coding gene	gene with protein product			"""ankyrin repeat domain 20A"""	ANKRD20A			Standard	NM_032250		Approved	DKFZp434A171		Q5TYW2	OTTHUMG00000188594	ENST00000377477.2:c.768G>T	9.37:g.67938633G>T	ENSP00000366697:p.Lys256Asn	Somatic	617	3	0.00486224		WXS	Illumina HiSeq	Phase_I	257	7	0.0272374	NM_032250	Q9H0H6	Missense_Mutation	SNP	ENST00000377477.2	37	CCDS6620.1	.	.	.	.	.	.	.	.	.	.	.	8.301	0.819993	0.16678	.	.	ENSG00000196774	ENST00000377477	T	0.37752	1.18	1.4	-1.97	0.07503	Ankyrin repeat-containing domain (2);	.	.	.	.	T	0.13372	0.0324	N	0.05230	-0.09	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.19745	-1.0296	9	0.29301	T	0.29	.	1.5748	0.02622	0.4716:0.0:0.2145:0.3139	.	256	Q5TYW2	A20A1_HUMAN	N	256	ENSP00000366697:K256N	ENSP00000366697:K256N	K	+	3	2	ANKRD20A1	67528453	0.778000	0.28640	0.019000	0.16419	0.050000	0.14768	0.163000	0.16520	-0.458000	0.07023	-1.594000	0.00841	AAG	G|0.990;T|0.010	0.010	strong		0.249	ANKRD20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083800.1		
ZNF705A	440077	hgsc.bcm.edu	37	12	8329652	8329652	+	Missense_Mutation	SNP	A	A	G	rs10743251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:8329652A>G	ENST00000359286.4	+	5	465	c.376A>G	c.(376-378)Act>Gct	p.T126A		NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	126			T -> A (in dbSNP:rs10743251).		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.T126A(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		AGAAGATTGCACTCACAGTTC	0.403																																					p.T126A		Atlas-SNP	.											ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	1	Substitution - Missense(1)	stomach(1)	c.A376G						scavenged	.						99.0	99.0	99.0					12																	8329652		2202	4291	6493	SO:0001583	missense	440077	exon5			GATTGCACTCACA	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.376A>G	12.37:g.8329652A>G	ENSP00000352233:p.Thr126Ala	Somatic	392	4	0.0102041		WXS	Illumina HiSeq	Phase_I	298	105	0.352349	NM_001004328		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	1046	0.47893772893772896	208	0.42276422764227645	167	0.4613259668508287	276	0.4825174825174825	395	0.521108179419525	.	7.485	0.649440	0.14516	.	.	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.07216	3.21;3.21	1.35	1.35	0.21983	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.20807	0.61	0.80722	P	0.0	B	0.28850	0.225	B	0.17979	0.02	T	0.39121	-0.9629	8	0.28530	T	0.3	.	4.2628	0.10749	0.6373:0.3627:0.0:0.0	rs10743251;rs57777260	126	Q6ZN79	Z705A_HUMAN	A	126	ENSP00000379816:T126A;ENSP00000352233:T126A	ENSP00000352233:T126A	T	+	1	0	ZNF705A	8220919	0.067000	0.21026	0.047000	0.18901	0.094000	0.18550	2.005000	0.40864	0.891000	0.36235	0.329000	0.21502	ACT	A|0.527;G|0.473	0.473	strong		0.403	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
CCDC110	256309	hgsc.bcm.edu	37	4	186380515	186380515	+	Missense_Mutation	SNP	G	G	A	rs11132306	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:186380515G>A	ENST00000307588.3	-	6	1301	c.1226C>T	c.(1225-1227)tCt>tTt	p.S409F	CCDC110_ENST00000510617.1_Missense_Mutation_p.S409F|CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Missense_Mutation_p.S372F	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	409			S -> F (in dbSNP:rs11132306).			nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		CTCATTTTCAGATATTATTGA	0.343													A|||	1925	0.384385	0.2784	0.3631	5008	,	,		17341	0.2837		0.5378	False		,,,				2504	0.4888				p.S409F		Atlas-SNP	.											.	CCDC110	78	.	0			c.C1226T						PASS	.	A	PHE/SER,PHE/SER	1456,2950	679.6+/-403.7	229,998,976	120.0	119.0	119.0		1115,1226	0.5	0.1	4	dbSNP_120	119	4851,3745	532.4+/-382.2	1369,2113,816	yes	missense,missense	CCDC110	NM_001145411.1,NM_152775.3	155,155	1598,3111,1792	AA,AG,GG		43.5668,33.0458,48.5079	benign,benign	372/797,409/834	186380515	6307,6695	2203	4298	6501	SO:0001583	missense	256309	exon6			TTTTCAGATATTA	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.1226C>T	4.37:g.186380515G>A	ENSP00000306776:p.Ser409Phe	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	70	7	0.1	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	37	CCDS3843.1	855	0.3914835164835165	148	0.3008130081300813	147	0.40607734806629836	160	0.27972027972027974	400	0.5277044854881267	A	0.001	-3.126688	0.00031	0.330458	0.564332	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.06449	3.3;3.3;3.31	5.81	0.54	0.17163	.	1.009930	0.07947	N	0.980197	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	0.37150	-0.9718	9	0.08837	T	0.75	0.2386	3.5186	0.07734	0.4227:0.0:0.2103:0.367	rs11132306;rs52793635;rs61201878;rs11132306	409;372;409	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	F	372;409;409	ENSP00000377172:S372F;ENSP00000306776:S409F;ENSP00000427246:S409F	ENSP00000306776:S409F	S	-	2	0	CCDC110	186617509	0.000000	0.05858	0.070000	0.20053	0.085000	0.17905	-0.922000	0.04004	-0.122000	0.11766	-0.254000	0.11334	TCT	G|0.562;A|0.438	0.438	strong		0.343	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
PCDHA3	56145	hgsc.bcm.edu	37	5	140181734	140181734	+	Missense_Mutation	SNP	A	A	G	rs3733708	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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|PCDHA2_ENST00000520672.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_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	116	0	0		WXS	Illumina HiSeq	Phase_I	103	66	0.640777	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	
MYO5B	4645	hgsc.bcm.edu	37	18	47363963	47363963	+	Missense_Mutation	SNP	T	T	C	rs112417235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:47363963T>C	ENST00000285039.7	-	37	5361	c.5062A>G	c.(5062-5064)Atg>Gtg	p.M1688V	SCARNA17_ENST00000589499.1_RNA|MYO5B_ENST00000324581.6_Missense_Mutation_p.M803V|RP11-886H22.1_ENST00000590532.2_Missense_Mutation_p.M11V|MYO5B_ENST00000592688.1_Missense_Mutation_p.M258V	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1688	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.		M -> V. {ECO:0000269|PubMed:21206382}.		endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		GCGTTGATCATGTAGAAGAGC	0.517													T|||	82	0.0163738	0.0015	0.0288	5008	,	,		23453	0.0		0.0358	False		,,,				2504	0.0245				p.M1688V		Atlas-SNP	.											.	MYO5B	178	.	0			c.A5062G						PASS	.	T	VAL/MET	24,4024		0,24,2000	65.0	62.0	63.0		5062	2.4	1.0	18	dbSNP_132	63	256,8102		2,252,3925	no	missense	MYO5B	NM_001080467.2	21	2,276,5925	CC,CT,TT		3.0629,0.5929,2.257	benign	1688/1849	47363963	280,12126	2024	4179	6203	SO:0001583	missense	4645	exon37			TGATCATGTAGAA	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.5062A>G	18.37:g.47363963T>C	ENSP00000285039:p.Met1688Val	Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	334	109	0.326347	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	34	0.015567765567765568	0	0.0	11	0.03038674033149171	0	0.0	23	0.030343007915567283	T	11.24	1.579427	0.28180	0.005929	0.030629	ENSG00000167306	ENST00000285039;ENST00000324581	D;T	0.85629	-2.01;2.61	4.77	2.37	0.29283	Dilute (1);Dil domain (1);	0.264499	0.42172	N	0.000759	T	0.48484	0.1502	N	0.05230	-0.09	0.29582	N	0.849093	B;P	0.45283	0.001;0.855	B;P	0.44647	0.004;0.456	T	0.63292	-0.6670	10	0.54805	T	0.06	.	8.8779	0.35356	0.0:0.156:0.0:0.844	.	1688;803	Q9ULV0;Q9H6Y6	MYO5B_HUMAN;.	V	1688;803	ENSP00000285039:M1688V;ENSP00000315531:M803V	ENSP00000285039:M1688V	M	-	1	0	MYO5B	45617961	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.620000	0.36976	0.412000	0.25729	-0.353000	0.07706	ATG	T|0.979;C|0.021	0.021	strong		0.517	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
NBPF10	100132406	hgsc.bcm.edu	37	1	145323666	145323666	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:145323666A>G	ENST00000342960.5	+	27	3538	c.3503A>G	c.(3502-3504)gAc>gGc	p.D1168G	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	755						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.D1168G(2)		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)		ATTAAAAAGGACGAAGAAGAG	0.468																																					p.D1168G		Atlas-SNP	.											NBPF10,NS,carcinoma,-1,6	NBPF10	221	6	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.A3503G						scavenged	.																																			SO:0001583	missense	100132406	exon27			AAAAGGACGAAGA	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.3503A>G	1.37:g.145323666A>G	ENSP00000345684:p.Asp1168Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	176	4	0.0227273	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	8.978	0.974738	0.18736	.	.	ENSG00000163386	ENST00000342960	T	0.03524	3.9	.	.	.	.	.	.	.	.	T	0.02380	0.0073	L	0.60455	1.87	0.09310	N	1	.	.	.	.	.	.	T	0.42965	-0.9420	5	0.45353	T	0.12	.	.	.	.	.	.	.	.	G	1168	ENSP00000345684:D1168G	ENSP00000345684:D1168G	D	+	2	0	NBPF10	144035023	0.002000	0.14202	0.003000	0.11579	0.095000	0.18619	-0.338000	0.07842	0.386000	0.24997	0.128000	0.15822	GAC	.	.	none		0.468	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
OSER1	51526	hgsc.bcm.edu	37	20	42825929	42825929	+	Silent	SNP	C	C	T	rs8268	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:42825929C>T	ENST00000372970.2	-	6	822	c.642G>A	c.(640-642)gtG>gtA	p.V214V	OSER1_ENST00000255174.2_Silent_p.V214V			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	214					cellular response to hydrogen peroxide (GO:0070301)												AAAAGGAATACACTTCCATAT	0.498													C|||	1496	0.298722	0.41	0.1124	5008	,	,		23065	0.4147		0.1471	False		,,,				2504	0.317				p.V214V		Atlas-SNP	.											.	C20orf111	28	.	0			c.G642A						PASS	.	C		1506,2900	480.4+/-358.8	237,1032,934	144.0	123.0	130.0		642	-3.3	0.9	20	dbSNP_52	130	1152,7448	237.6+/-269.4	73,1006,3221	no	coding-synonymous	C20orf111	NM_016470.7		310,2038,4155	TT,TC,CC		13.3953,34.1807,20.4367		214/293	42825929	2658,10348	2203	4300	6503	SO:0001819	synonymous_variant	51526	exon4			GGAATACACTTCC	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.642G>A	20.37:g.42825929C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	152	150	0.986842	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Silent	SNP	ENST00000372970.2	37	CCDS13327.1																																																																																			C|0.766;T|0.234	0.234	strong		0.498	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	
FAM183A	440585	hgsc.bcm.edu	37	1	43618596	43618596	+	Silent	SNP	G	G	A	rs12074551	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	158	0	0		WXS	Illumina HiSeq	Phase_I	144	24	0.166667	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	
ALDH5A1	7915	hgsc.bcm.edu	37	6	24503590	24503590	+	Missense_Mutation	SNP	C	C	T	rs2760118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:24503590C>T	ENST00000357578.3	+	3	683	c.538C>T	c.(538-540)Cac>Tac	p.H180Y	ALDH5A1_ENST00000491546.1_Missense_Mutation_p.H152Y|ALDH5A1_ENST00000546278.1_Missense_Mutation_p.H92Y|ALDH5A1_ENST00000348925.2_Missense_Mutation_p.H180Y	NM_001080.3	NP_001071.1	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5 family, member A1	180			H -> Y (83% of activity; dbSNP:rs2760118). {ECO:0000269|PubMed:14635103, ECO:0000269|PubMed:14702039}.		acetate metabolic process (GO:0006083)|central nervous system development (GO:0007417)|galactosylceramide metabolic process (GO:0006681)|gamma-aminobutyric acid catabolic process (GO:0009450)|glucose metabolic process (GO:0006006)|glucosylceramide metabolic process (GO:0006678)|glutamate metabolic process (GO:0006536)|glutamine metabolic process (GO:0006541)|glutathione metabolic process (GO:0006749)|glycerophospholipid metabolic process (GO:0006650)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|protein homotetramerization (GO:0051289)|respiratory electron transport chain (GO:0022904)|short-chain fatty acid metabolic process (GO:0046459)|succinate metabolic process (GO:0006105)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	protein homodimerization activity (GO:0042803)|succinate-semialdehyde dehydrogenase (NAD+) activity (GO:0004777)|succinate-semialdehyde dehydrogenase [NAD(P)+] activity (GO:0009013)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|skin(2)|urinary_tract(1)	20					Chlormerodrin(DB00534)|Succinic acid(DB00139)|Valproic Acid(DB00313)	AGACATTATCCACACCCCGGC	0.567													T|||	1576	0.314696	0.466	0.219	5008	,	,		19092	0.1667		0.3231	False		,,,				2504	0.3221				p.H180Y		Atlas-SNP	.											.	ALDH5A1	42	.	0			c.C538T	GRCh37	CM083577	ALDH5A1	M	rs2760118	PASS	.	T	TYR/HIS,TYR/HIS	1937,2469	622.5+/-394.0	430,1077,696	49.0	49.0	49.0		538,538	-0.0	0.0	6	dbSNP_100	49	2891,5709	671.4+/-402.8	470,1951,1879	yes	missense,missense	ALDH5A1	NM_001080.3,NM_170740.1	83,83	900,3028,2575	TT,TC,CC		33.6163,43.9628,37.1213	benign,benign	180/536,180/549	24503590	4828,8178	2203	4300	6503	SO:0001583	missense	7915	exon3			ATTATCCACACCC	L34820	CCDS4555.1, CCDS4556.1	6p22	2013-06-03	2008-07-31		ENSG00000112294	ENSG00000112294	1.2.1.24	"""Aldehyde dehydrogenases"""	408	protein-coding gene	gene with protein product	"""succinate-semialdehyde dehydrogenase"""	610045				7814412, 9059628	Standard	NM_001080		Approved	SSADH, SSDH	uc003nef.3	P51649	OTTHUMG00000014356	ENST00000357578.3:c.538C>T	6.37:g.24503590C>T	ENSP00000350191:p.His180Tyr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	29	28	0.965517	NM_001080	B2RD26|G5E949|Q546H9|Q8N3W6	Missense_Mutation	SNP	ENST00000357578.3	37	CCDS4555.1	670	0.3067765567765568	224	0.45528455284552843	91	0.2513812154696133	105	0.18356643356643357	250	0.32981530343007914	T	5.650	0.304590	0.10678	0.439628	0.336163	ENSG00000112294	ENST00000357578;ENST00000546278;ENST00000491546;ENST00000348925	T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98	5.22	-0.0441	0.13856	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.816074	0.11105	N	0.599274	T	0.31513	0.0799	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04737	-1.0930	9	0.51188	T	0.08	0.2889	1.8122	0.03092	0.1336:0.3194:0.3093:0.2376	rs2760118;rs3765309;rs52829319;rs60953148;rs2760118	180;180	P51649;G5E949	SSDH_HUMAN;.	Y	180;92;152;180	ENSP00000350191:H180Y;ENSP00000438193:H92Y;ENSP00000417687:H152Y;ENSP00000314649:H180Y	ENSP00000314649:H180Y	H	+	1	0	ALDH5A1	24611569	0.029000	0.19370	0.013000	0.15412	0.241000	0.25554	0.812000	0.27211	-0.423000	0.07394	-0.269000	0.10298	CAC	C|0.656;T|0.344	0.344	strong		0.567	ALDH5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040007.2		
KALRN	8997	hgsc.bcm.edu	37	3	123946895	123946895	+	Silent	SNP	G	G	A	rs2293641|rs36107295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:123946895G>A	ENST00000240874.3	+	2	283	c.126G>A	c.(124-126)aaG>aaA	p.K42K	KALRN_ENST00000460856.1_Silent_p.K42K|KALRN_ENST00000360013.3_Silent_p.K42K	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	42	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						TAAAGGAAAAGGTGGCCTTCG	0.453													A|||	700	0.139776	0.2194	0.1182	5008	,	,		20205	0.1637		0.0457	False		,,,				2504	0.1196				p.K42K		Atlas-SNP	.											.	KALRN	556	.	0			c.G126A						PASS	.	A	,	845,3561	745.6+/-411.7	86,673,1444	262.0	251.0	255.0		126,126	5.1	1.0	3	dbSNP_100	255	371,8229	802.7+/-407.3	8,355,3937	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	94,1028,5381	AA,AG,GG		4.314,19.1784,9.3495	,	42/2987,42/1664	123946895	1216,11790	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon2			GGAAAAGGTGGCC	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.126G>A	3.37:g.123946895G>A		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	250	118	0.472	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	302	0.1382783882783883	126	0.25609756097560976	45	0.12430939226519337	93	0.16258741258741258	38	0.05013192612137203	A	9.441	1.088054	0.20390	0.191784	0.04314	ENSG00000160145	ENST00000448253;ENST00000354186	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06607	-1.0817	3	.	.	.	.	11.0603	0.47944	0.9273:0.0:0.0727:0.0	rs2293641;rs2293641	.	.	.	K	70;20	.	.	R	+	2	0	KALRN	125429585	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.718000	0.47236	0.969000	0.38237	-0.269000	0.10298	AGG	G|0.891;A|0.109	0.109	strong		0.453	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
INTS10	55174	hgsc.bcm.edu	37	8	19677915	19677915	+	Silent	SNP	G	G	A	rs7822495	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:19677915G>A	ENST00000397977.3	+	4	725	c.327G>A	c.(325-327)cgG>cgA	p.R109R	INTS10_ENST00000521758.1_Intron	NM_018142.2	NP_060612.2	Q9NVR2	INT10_HUMAN	integrator complex subunit 10	109					snRNA processing (GO:0016180)	integrator complex (GO:0032039)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	20				Colorectal(111;0.057)|COAD - Colon adenocarcinoma(73;0.215)		TTCCTGGTCGGGTCCAGTGTG	0.423													G|||	1221	0.24381	0.2784	0.2781	5008	,	,		19987	0.2927		0.169	False		,,,				2504	0.1994				p.R109R		Atlas-SNP	.											.	INTS10	46	.	0			c.G327A						PASS	.	G		978,2756		129,720,1018	135.0	128.0	130.0		327	-5.2	0.7	8	dbSNP_116	130	1465,6735		144,1177,2779	no	coding-synonymous	INTS10	NM_018142.2		273,1897,3797	AA,AG,GG		17.8659,26.1918,20.4709		109/711	19677915	2443,9491	1867	4100	5967	SO:0001819	synonymous_variant	55174	exon4			TGGTCGGGTCCAG	AK001431	CCDS6011.2	8p21.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000104613	ENSG00000104613			25548	protein-coding gene	gene with protein product		611353	"""chromosome 8 open reading frame 35"""	C8orf35		16239144	Standard	XM_005273558		Approved	FLJ10569, INT10	uc003wzj.3	Q9NVR2	OTTHUMG00000131065	ENST00000397977.3:c.327G>A	8.37:g.19677915G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	198	122	0.616162	NM_018142	Q6IA93|Q7L538|Q7L8C8|Q9H3W8	Silent	SNP	ENST00000397977.3	37	CCDS6011.2																																																																																			G|0.763;A|0.237	0.237	strong		0.423	INTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253724.2	NM_018142	
PARP9	83666	hgsc.bcm.edu	37	3	122259640	122259640	+	Missense_Mutation	SNP	T	T	C	rs28365795	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122259640T>C	ENST00000360356.2	-	8	1776	c.1549A>G	c.(1549-1551)Atc>Gtc	p.I517V	PARP9_ENST00000471785.1_Missense_Mutation_p.I482V|PARP9_ENST00000492382.1_Missense_Mutation_p.I62V|PARP9_ENST00000477522.2_Missense_Mutation_p.I482V|PARP9_ENST00000462315.1_Missense_Mutation_p.I482V	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	517			I -> V (in dbSNP:rs28365795). {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)		ATCAGATTGATGGCAGGAGAT	0.448													T|||	640	0.127796	0.0938	0.111	5008	,	,		18669	0.1101		0.1541	False		,,,				2504	0.1769				p.I517V		Atlas-SNP	.											.	PARP9	72	.	0			c.A1549G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	515,3891	235.2+/-247.8	29,457,1717	126.0	126.0	126.0		1549,1444,1444,1444,1444,1549	2.7	0.1	3	dbSNP_125	126	1351,7249	264.2+/-285.4	120,1111,3069	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	29,29,29,29,29,29	149,1568,4786	CC,CT,TT		15.7093,11.6886,14.3472	benign,benign,benign,benign,benign,benign	517/855,482/820,482/820,482/820,482/711,517/855	122259640	1866,11140	2203	4300	6503	SO:0001583	missense	83666	exon8			GATTGATGGCAGG	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.1549A>G	3.37:g.122259640T>C	ENSP00000353512:p.Ile517Val	Somatic	278	1	0.00359712		WXS	Illumina HiSeq	Phase_I	222	95	0.427928	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Missense_Mutation	SNP	ENST00000360356.2	37	CCDS3014.1	254	0.1163003663003663	51	0.10365853658536585	49	0.13535911602209943	51	0.08916083916083917	103	0.1358839050131926	T	5.844	0.339849	0.11069	0.116886	0.157093	ENSG00000138496	ENST00000360356;ENST00000492382;ENST00000477522;ENST00000471785;ENST00000452457;ENST00000462315	T;T;T;T;T	0.17054	3.33;2.79;3.18;3.18;2.3	5.07	2.68	0.31781	.	0.119302	0.38164	N	0.001786	T	0.00073	0.0002	M	0.65975	2.015	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.27264	0.156;0.007;0.173;0.059	B;B;B;B	0.24848	0.043;0.008;0.056;0.043	T	0.11203	-1.0597	9	0.49607	T	0.09	.	4.3067	0.10951	0.1743:0.0929:0.0:0.7328	rs28365795;rs28365795	482;517;62;482	E9PFM7;Q8IXQ6;G5E9U8;Q8IXQ6-2	.;PARP9_HUMAN;.;.	V	517;62;482;482;440;482	ENSP00000353512:I517V;ENSP00000417664:I62V;ENSP00000419506:I482V;ENSP00000419001:I482V;ENSP00000418894:I482V	ENSP00000353512:I517V	I	-	1	0	PARP9	123742330	0.598000	0.26882	0.051000	0.19133	0.335000	0.28730	0.977000	0.29475	0.403000	0.25479	0.528000	0.53228	ATC	T|0.867;C|0.133	0.133	strong		0.448	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458	
MIA3	375056	hgsc.bcm.edu	37	1	222802376	222802376	+	Missense_Mutation	SNP	A	A	G	rs2936052	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:222802376A>G	ENST00000344922.5	+	4	1839	c.1814A>G	c.(1813-1815)aAa>aGa	p.K605R	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000470521.1_3'UTR|MIA3_ENST00000344441.6_Missense_Mutation_p.K605R	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	104	0	0		WXS	Illumina HiSeq	Phase_I	122	76	0.622951	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	
RP1L1	94137	hgsc.bcm.edu	37	8	10465748	10465748	+	Missense_Mutation	SNP	T	T	C	rs11783478	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:10465748T>C	ENST00000382483.3	-	4	6083	c.5860A>G	c.(5860-5862)Acc>Gcc	p.T1954A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2034	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				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)		TCTGGCTGGGTCTGCCCTTCT	0.592													C|||	3252	0.649361	0.4728	0.6657	5008	,	,		17892	0.9772		0.5089	False		,,,				2504	0.683				p.T1954A		Atlas-SNP	.											RP1L1,NS,carcinoma,0,1	RP1L1	453	1	0			c.A5860G						PASS	.	C	ALA/THR	2073,2053		537,999,527	120.0	143.0	135.0		5860	-2.3	0.0	8	dbSNP_120	135	4468,3940		1204,2060,940	yes	missense	RP1L1	NM_178857.5	58	1741,3059,1467	CC,CT,TT		46.8601,49.7576,47.8139	benign	1954/2401	10465748	6541,5993	2063	4204	6267	SO:0001583	missense	94137	exon4			GCTGGGTCTGCCC	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.5860A>G	8.37:g.10465748T>C	ENSP00000371923:p.Thr1954Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	1397	0.6396520146520146	216	0.43902439024390244	234	0.6464088397790055	558	0.9755244755244755	389	0.5131926121372031	C	0.111	-1.139015	0.01742	0.502424	0.531399	ENSG00000183638	ENST00000382483	T	0.04234	3.67	1.24	-2.32	0.06745	.	.	.	.	.	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	0.32981	-0.9886	8	0.02654	T	1	.	3.7577	0.08592	0.0:0.3311:0.1964:0.4725	rs11783478;rs52832454;rs11783478	1954	A6NKC6	.	A	1954	ENSP00000371923:T1954A	ENSP00000371923:T1954A	T	-	1	0	RP1L1	10503158	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.487000	0.00977	-1.392000	0.02082	-0.684000	0.03749	ACC	T|0.395;C|0.605	0.605	strong		0.592	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
PCNT	5116	hgsc.bcm.edu	37	21	47821588	47821588	+	Missense_Mutation	SNP	A	A	G	rs6518291	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:47821588A>G	ENST00000359568.5	+	26	5022	c.4915A>G	c.(4915-4917)Ata>Gta	p.I1639V	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1639			I -> V (in dbSNP:rs6518291).		brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					GGGTCCAGAAATACAGTTAGA	0.607													G|||	1676	0.334665	0.5862	0.2752	5008	,	,		13466	0.1935		0.2167	False		,,,				2504	0.3037				p.I1639V		Atlas-SNP	.											.	PCNT	283	.	0			c.A4915G						PASS	.	G	VAL/ILE	2361,2045	566.8+/-382.0	625,1111,467	84.0	81.0	82.0		4915	1.8	0.0	21	dbSNP_116	82	1718,6882	737.3+/-407.0	156,1406,2738	yes	missense	PCNT	NM_006031.5	29	781,2517,3205	GG,GA,AA		19.9767,46.414,31.3624	benign	1639/3337	47821588	4079,8927	2203	4300	6503	SO:0001583	missense	5116	exon26			CCAGAAATACAGT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.4915A>G	21.37:g.47821588A>G	ENSP00000352572:p.Ile1639Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	132	83	0.628788	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	655	0.2999084249084249	285	0.5792682926829268	87	0.24033149171270718	112	0.1958041958041958	171	0.22559366754617413	G	0.492	-0.875115	0.02550	0.53586	0.199767	ENSG00000160299	ENST00000359568	T	0.53857	0.6	5.64	1.8	0.24995	.	2.616870	0.02237	N	0.065411	T	0.00012	0.0000	N	0.00879	-1.12	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44329	-0.9335	9	0.28530	T	0.3	.	6.0333	0.19692	0.294:0.1264:0.5796:0.0	rs6518291;rs60162159;rs6518291	1521;1639	O95613-2;O95613	.;PCNT_HUMAN	V	1639	ENSP00000352572:I1639V	ENSP00000352572:I1639V	I	+	1	0	PCNT	46646016	0.015000	0.18098	0.000000	0.03702	0.002000	0.02628	1.769000	0.38522	-0.135000	0.11495	-0.119000	0.15052	ATA	A|0.679;G|0.321	0.321	strong		0.607	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
KANSL1	284058	hgsc.bcm.edu	37	17	44109474	44109474	+	Missense_Mutation	SNP	G	G	A	rs7220988	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:44109474G>A	ENST00000262419.6	-	14	3499	c.3029C>T	c.(3028-3030)cCg>cTg	p.P1010L	KANSL1_ENST00000432791.1_Missense_Mutation_p.P1010L|KANSL1_ENST00000574590.1_Missense_Mutation_p.P1010L|KANSL1_ENST00000393476.3_Missense_Mutation_p.P304L|KANSL1_ENST00000572904.1_Missense_Mutation_p.P1010L|KANSL1_ENST00000575318.1_Missense_Mutation_p.P946L	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1010	Sufficient for interaction with KAT8.		P -> L (in dbSNP:rs7220988). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TAAGTGTCGCGGAGTGTCCCG	0.597													G|||	1567	0.312899	0.2186	0.2651	5008	,	,		13953	0.1062		0.3579	False		,,,				2504	0.6411				p.P1010L		Atlas-SNP	.											.	.	.	.	0			c.C3029T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	1093,3313	393.5+/-328.9	121,851,1231	62.0	60.0	60.0		3026,3029,3029	4.6	1.0	17	dbSNP_116	60	3412,5188	502.6+/-375.7	702,2008,1590	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	98,98,98	823,2859,2821	AA,AG,GG		39.6744,24.8071,34.6379	benign,benign,benign	1009/1105,1010/1106,1010/1106	44109474	4505,8501	2203	4300	6503	SO:0001583	missense	284058	exon14			TGTCGCGGAGTGT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3029C>T	17.37:g.44109474G>A	ENSP00000262419:p.Pro1010Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	537	0.24587912087912087	110	0.22357723577235772	105	0.2900552486187845	54	0.0944055944055944	268	0.35356200527704484	G	14.23	2.474360	0.43942	0.248071	0.396744	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.39997	1.05;1.05;1.05	5.72	4.63	0.57726	.	0.394200	0.25402	N	0.030934	T	0.00012	0.0000	N	0.02539	-0.55	0.33231	P	0.444067	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	0.42849	-0.9427	9	0.07990	T	0.79	-1.2731	6.9006	0.24281	0.807:0.0:0.193:0.0	rs7220988;rs17298984;rs52815397;rs60940197;rs7220988	278;341;1010;1010	B3KT49;Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;.;K1267_HUMAN	L	1010;1010;304	ENSP00000262419:P1010L;ENSP00000387393:P1010L;ENSP00000377117:P304L	ENSP00000262419:P1010L	P	-	2	0	KIAA1267	41465321	0.949000	0.32298	0.984000	0.44739	0.979000	0.70002	3.997000	0.57016	0.995000	0.38917	0.561000	0.74099	CCG	G|0.694;A|0.306	0.306	strong		0.597	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
COPB1	1315	hgsc.bcm.edu	37	11	14515829	14515829	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:14515829T>C	ENST00000249923.3	-	3	548	c.248A>G	c.(247-249)gAa>gGa	p.E83G	PSMA1_ENST00000555531.1_3'UTR|COPB1_ENST00000439561.2_Missense_Mutation_p.E83G|PSMA1_ENST00000419365.2_3'UTR	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	83					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						AGGAACAATTTCCCAAAATAC	0.363																																					p.E83G		Atlas-SNP	.											.	COPB1	81	.	0			c.A248G						PASS	.						84.0	88.0	87.0					11																	14515829		2200	4294	6494	SO:0001583	missense	1315	exon3			ACAATTTCCCAAA	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"""coatomer protein complex, subunit beta"""	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.248A>G	11.37:g.14515829T>C	ENSP00000249923:p.Glu83Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.997254	0.93167	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234;ENST00000529866;ENST00000534771	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.31	5.31	0.75309	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80137	-0.1508	10	0.87932	D	0	-14.0469	15.2851	0.73822	0.0:0.0:0.0:1.0	.	83	P53618	COPB_HUMAN	G	83	ENSP00000249923:E83G;ENSP00000397873:E83G;ENSP00000436383:E83G;ENSP00000431530:E83G;ENSP00000436401:E83G	ENSP00000249923:E83G	E	-	2	0	COPB1	14472405	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.004000	0.58718	0.533000	0.62120	GAA	.	.	none		0.363	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451	
KIAA1731	85459	hgsc.bcm.edu	37	11	93430474	93430474	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:93430474C>G	ENST00000325212.6	+	15	2558	c.2396C>G	c.(2395-2397)cCt>cGt	p.P799R	KIAA1731_ENST00000411936.1_Missense_Mutation_p.P799R|KIAA1731_ENST00000531700.1_Intron|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	799						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AGTTCTCTGCCTGTTAAAGTT	0.368																																					p.P799R		Atlas-SNP	.											.	KIAA1731	173	.	0			c.C2396G						PASS	.						92.0	72.0	78.0					11																	93430474		692	1591	2283	SO:0001583	missense	85459	exon15			CTCTGCCTGTTAA	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.2396C>G	11.37:g.93430474C>G	ENSP00000316681:p.Pro799Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	229	79	0.344978	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	37	CCDS44708.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.270850	0.23221	.	.	ENSG00000166004	ENST00000325212;ENST00000411936	T;T	0.36520	1.25;1.25	4.06	4.06	0.47325	.	0.167616	0.28889	N	0.013807	T	0.45816	0.1361	L	0.39898	1.24	0.80722	D	1	D	0.61697	0.99	P	0.59487	0.858	T	0.39057	-0.9632	10	0.52906	T	0.07	-2.8388	14.1939	0.65656	0.0:1.0:0.0:0.0	.	799	Q9C0D2	K1731_HUMAN	R	799	ENSP00000316681:P799R;ENSP00000406505:P799R	ENSP00000316681:P799R	P	+	2	0	KIAA1731	93070122	0.138000	0.22547	0.099000	0.21106	0.016000	0.09150	1.386000	0.34419	2.547000	0.85894	0.650000	0.86243	CCT	.	.	none		0.368	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
CH25H	9023	hgsc.bcm.edu	37	10	90966996	90966996	+	Silent	SNP	C	C	G	rs10887932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:90966996C>G	ENST00000371852.2	-	1	75	c.54G>C	c.(52-54)ctG>ctC	p.L18L		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	18					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		GCTGCAGGAACAGCTGCCCGG	0.622													C|||	1404	0.280351	0.0083	0.2637	5008	,	,		19159	0.7371		0.1392	False		,,,				2504	0.3344				p.L18L		Atlas-SNP	.											.	CH25H	19	.	0			c.G54C						PASS	.	C		121,4283		6,109,2087	18.0	22.0	20.0		54	-2.1	0.2	10	dbSNP_120	20	1020,7578		63,894,3342	no	coding-synonymous	CH25H	NM_003956.3		69,1003,5429	GG,GC,CC		11.8632,2.7475,8.7756		18/273	90966996	1141,11861	2202	4299	6501	SO:0001819	synonymous_variant	9023	exon1			CAGGAACAGCTGC	AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"""Fatty acid hydroxylase domain containing"""	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.54G>C	10.37:g.90966996C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	80	21	0.2625	NM_003956	B2RBY3	Silent	SNP	ENST00000371852.2	37	CCDS7400.1																																																																																			C|0.834;G|0.166	0.166	strong		0.622	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956	
ZNF281	23528	hgsc.bcm.edu	37	1	200378495	200378495	+	Silent	SNP	C	C	T	rs374232799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:200378495C>T	ENST00000294740.3	-	2	463	c.339G>A	c.(337-339)tcG>tcA	p.S113S	ZNF281_ENST00000367352.3_Silent_p.S77S|ZNF281_ENST00000367353.1_Silent_p.S113S	NM_001281293.1|NM_001281294.1|NM_012482.4	NP_001268222.1|NP_001268223.1|NP_036614.1	Q9Y2X9	ZN281_HUMAN	zinc finger protein 281	113					embryonic body morphogenesis (GO:0010172)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|stem cell differentiation (GO:0048863)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|endometrium(3)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	27						AGGTCCTCTGCGAGGGGAAGG	0.662																																					p.S113S		Atlas-SNP	.											.	ZNF281	74	.	0			c.G339A						PASS	.	C		0,4176		0,0,2088	7.0	6.0	6.0		339	3.2	1.0	1		6	2,8178		0,2,4088	no	coding-synonymous	ZNF281	NM_012482.3		0,2,6176	TT,TC,CC		0.0244,0.0,0.0162		113/896	200378495	2,12354	2088	4090	6178	SO:0001819	synonymous_variant	23528	exon2			CCTCTGCGAGGGG	AF125158	CCDS1402.1, CCDS60384.1	1q32.1	2012-08-08			ENSG00000162702	ENSG00000162702		"""Zinc fingers, C2H2-type"""	13075	protein-coding gene	gene with protein product						10448078	Standard	NM_012482		Approved	ZBP-99	uc001gve.3	Q9Y2X9	OTTHUMG00000035724	ENST00000294740.3:c.339G>A	1.37:g.200378495C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	38	26	0.684211	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Silent	SNP	ENST00000294740.3	37	CCDS1402.1																																																																																			.	.	none		0.662	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482	
CNNM1	26507	hgsc.bcm.edu	37	10	101122084	101122084	+	Silent	SNP	C	C	T	rs117724968	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:101122084C>T	ENST00000356713.4	+	4	2248	c.1959C>T	c.(1957-1959)aaC>aaT	p.N653N	CNNM1_ENST00000446890.1_Silent_p.N582N|CNNM1_ENST00000370534.4_Silent_p.N288N|CNNM1_ENST00000370528.3_Silent_p.N582N	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	653					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		ATGAGAAGAACAAGAAGGCCC	0.522													c|||	12	0.00239617	0.0	0.0101	5008	,	,		7521	0.0		0.002	False		,,,				2504	0.0031				p.N653N		Atlas-SNP	.											.	CNNM1	101	.	0			c.C1959T						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	74.0	69.0	71.0		1959	4.4	1.0	10	dbSNP_132	71	37,8563	24.6+/-71.5	0,37,4263	no	coding-synonymous	CNNM1	NM_020348.2		0,41,6462	TT,TC,CC		0.4302,0.0908,0.3152		653/952	101122084	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	26507	exon4			GAAGAACAAGAAG	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.1959C>T	10.37:g.101122084C>T		Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	132	93	0.704545	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	37	CCDS7478.2																																																																																			C|0.997;T|0.003	0.003	strong		0.522	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
SLC22A18AS	5003	hgsc.bcm.edu	37	11	2920666	2920666	+	Missense_Mutation	SNP	C	C	T	rs365605	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2920666C>T	ENST00000533594.1	-	3	762	c.266G>A	c.(265-267)gGt>gAt	p.G89D	SLC22A18_ENST00000312221.5_5'Flank|SLC22A18AS_ENST00000455942.2_Intron|SLC22A18_ENST00000347936.2_5'Flank|SLC22A18_ENST00000380574.1_5'Flank|SLC22A18_ENST00000449793.2_5'Flank	NM_007105.2	NP_009036.2	Q8N1D0	BWR1B_HUMAN	solute carrier family 22 (organic cation transporter), member 18 antisense	89			G -> D (in dbSNP:rs365605). {ECO:0000269|PubMed:9520460, ECO:0000269|PubMed:9570947}.							NS(1)|endometrium(2)	3						tgagaagccacctctcccaaa	0.542													T|||	3070	0.613019	0.7322	0.6599	5008	,	,		21315	0.3958		0.663	False		,,,				2504	0.591				p.G89D		Atlas-SNP	.											.	SLC22A18AS	7	.	0			c.G266A						PASS	.	T	ASP/GLY	1003,381		371,261,60	105.0	91.0	95.0		266	0.5	0.0	11	dbSNP_80	95	2098,1084		694,710,187	yes	missense	SLC22A18AS	NM_007105.2	94	1065,971,247	TT,TC,CC		34.0666,27.5289,32.085	benign	89/254	2920666	3101,1465	692	1591	2283	SO:0001583	missense	5003	exon3			AAGCCACCTCTCC	AF035407	CCDS7739.1	11p15.5	2011-02-10	2005-08-23	2005-08-23	ENSG00000254827	ENSG00000254827			10965	protein-coding gene	gene with protein product		603240	"""solute carrier family 22 (organic cation transporter), member 1-like antisense"""	BWSCR1B, ORCTL2S, SLC22A1LS		9570947, 9520460, 15175115	Standard	NM_007105		Approved	BWR1B, p27-BWR1B	uc001lwv.4	Q8N1D0	OTTHUMG00000010038	ENST00000533594.1:c.266G>A	11.37:g.2920666C>T	ENSP00000433282:p.Gly89Asp	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	129	125	0.968992	NM_007105	E9PLK8|O43563	Missense_Mutation	SNP	ENST00000533594.1	37	CCDS7739.1	1327	0.6076007326007326	351	0.7134146341463414	236	0.6519337016574586	232	0.40559440559440557	508	0.6701846965699209	T	1.784	-0.481197	0.04383	0.724711	0.659334	ENSG00000254827	ENST00000533594	T	0.45668	0.89	1.82	0.512	0.16994	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.29119	-1.0022	7	0.87932	D	0	.	4.8799	0.13674	0.0:0.5735:0.0:0.4265	rs365605;rs56832497;rs365605	89	E9PLK8	.	D	89	ENSP00000433282:G89D	ENSP00000433282:G89D	G	-	2	0	SLC22A18AS	2877242	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.377000	0.07456	-0.224000	0.09928	-1.140000	0.01884	GGT	C|0.393;T|0.607	0.607	strong		0.542	SLC22A18AS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027771.3	NM_007105	
UTP18	51096	hgsc.bcm.edu	37	17	49350802	49350802	+	Silent	SNP	A	A	C	rs2318789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:49350802A>C	ENST00000225298.7	+	5	759	c.702A>C	c.(700-702)ggA>ggC	p.G234G		NM_016001.2	NP_057085.2	Q9Y5J1	UTP18_HUMAN	UTP18 small subunit (SSU) processome component homolog (yeast)	234					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			TTCCAAGAGGAATCTTGAAGG	0.398													A|||	2134	0.426118	0.1248	0.4424	5008	,	,		13944	0.6071		0.4791	False		,,,				2504	0.5808				p.G234G		Atlas-SNP	.											.	UTP18	28	.	0			c.A702C						PASS	.	A		655,3107		56,543,1282	131.0	123.0	125.0		702	0.6	1.0	17	dbSNP_100	125	3821,4393		903,2015,1189	no	coding-synonymous	UTP18	NM_016001.2		959,2558,2471	CC,CA,AA		46.5181,17.411,37.3747		234/557	49350802	4476,7500	1881	4107	5988	SO:0001819	synonymous_variant	51096	exon5			AAGAGGAATCTTG	AF151806	CCDS42362.1	17q21.33	2013-05-21	2011-12-09	2006-05-16	ENSG00000011260	ENSG00000011260		"""WD repeat domain containing"""	24274	protein-coding gene	gene with protein product		612816	"""WD repeat domain 50"""	WDR50		10810093, 8619474, 15590835	Standard	NM_016001		Approved	CGI-48	uc002its.3	Q9Y5J1	OTTHUMG00000162370	ENST00000225298.7:c.702A>C	17.37:g.49350802A>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_016001	Q9H4N6	Silent	SNP	ENST00000225298.7	37	CCDS42362.1																																																																																			A|0.569;C|0.431	0.431	strong		0.398	UTP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368654.1	NM_016001	
CSN1S1	1446	hgsc.bcm.edu	37	4	70807771	70807771	+	Missense_Mutation	SNP	C	C	T	rs10030475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:70807771C>T	ENST00000246891.4	+	13	399	c.350C>T	c.(349-351)gCc>gTc	p.A117V	CSN1S1_ENST00000507763.1_Missense_Mutation_p.A108V|CSN1S1_ENST00000444405.3_Missense_Mutation_p.A108V|CSN1S1_ENST00000505782.1_Missense_Mutation_p.A101V|CSN1S1_ENST00000507772.1_Missense_Mutation_p.A109V	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	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	291	290	0.996564	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		
GHRL	51738	hgsc.bcm.edu	37	3	10328453	10328453	+	Missense_Mutation	SNP	T	T	A	rs4684677	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:10328453T>A	ENST00000335542.8	-	5	1139	c.269A>T	c.(268-270)cAg>cTg	p.Q90L	GHRLOS_ENST00000439539.3_RNA|GHRL_ENST00000476283.1_5'UTR|GHRL_ENST00000422159.1_Intron|LINC00852_ENST00000475197.1_RNA|GHRL_ENST00000429122.1_Missense_Mutation_p.Q90L|GHRLOS_ENST00000603771.1_RNA|GHRL_ENST00000437422.2_Missense_Mutation_p.Q78L|GHRL_ENST00000430179.1_Missense_Mutation_p.Q89L|GHRL_ENST00000439975.2_Missense_Mutation_p.Q39L|GHRL_ENST00000446937.2_Intron|LINC00852_ENST00000538717.1_RNA|GHRL_ENST00000449554.2_Missense_Mutation_p.Q89L|GHRLOS_ENST00000605105.1_RNA|GHRL_ENST00000457360.1_Missense_Mutation_p.Q90L|GHRL_ENST00000449238.2_Missense_Mutation_p.Q77L|GHRL_ENST00000450603.1_Missense_Mutation_p.Q90L|GHRLOS_ENST00000605014.1_RNA|GHRL_ENST00000287656.7_Missense_Mutation_p.Q89L			Q9UBU3	GHRL_HUMAN	ghrelin/obestatin prepropeptide	90			Q -> L (in dbSNP:rs4684677).		actin polymerization or depolymerization (GO:0008154)|activation of MAPK activity (GO:0000187)|adult feeding behavior (GO:0008343)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|cortisol secretion (GO:0043400)|decidualization (GO:0046697)|dendrite development (GO:0016358)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|glucose metabolic process (GO:0006006)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of circadian sleep/wake cycle, REM sleep (GO:0042322)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin secretion (GO:0046676)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of locomotion (GO:0040013)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of synapse assembly (GO:0051965)|regulation of cell proliferation (GO:0042127)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to estrogen (GO:0043627)|response to hormone (GO:0009725)	axon (GO:0030424)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|ghrelin receptor binding (GO:0031768)|growth hormone-releasing hormone activity (GO:0016608)|protein tyrosine kinase activator activity (GO:0030296)			breast(2)|large_intestine(1)|lung(1)|ovary(1)	5						CTGCTGGTACTGAACCCCTGA	0.582											OREG0015386	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	307	0.0613019	0.0053	0.2392	5008	,	,		19509	0.006		0.0746	False		,,,				2504	0.0542				p.Q90L		Atlas-SNP	.											.	GHRL	8	.	0			c.A269T	GRCh37	CM024761	GHRL	M	rs4684677	PASS	.	T	LEU/GLN,LEU/GLN,LEU/GLN,LEU/GLN,LEU/GLN	63,4343	60.5+/-97.4	0,63,2140	72.0	59.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	266,233,230,116,269	4.8	1.0	3	dbSNP_111	63	507,8093	143.6+/-199.6	14,479,3807	yes	missense,missense,missense,missense,missense	GHRL	NM_001134941.1,NM_001134944.1,NM_001134945.1,NM_001134946.1,NM_016362.3	113,113,113,113,113	14,542,5947	AA,AT,TT		5.8953,1.4299,4.3826	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	89/117,78/106,77/105,39/67,90/118	10328453	570,12436	2203	4300	6503	SO:0001583	missense	51738	exon4			TGGTACTGAACCC	AF296558	CCDS33700.1, CCDS46747.1, CCDS46748.1, CCDS46749.1, CCDS46750.1	3p26-p25	2013-02-26	2008-07-02		ENSG00000157017	ENSG00000157017		"""Endogenous ligands"""	18129	protein-coding gene	gene with protein product	"""prepro-appetite regulatory hormone"""	605353	"""ghrelin, growth hormone secretagogue receptor ligand"""			10930375, 10604470, 16284174	Standard	NR_024133		Approved	MTLRP, ghrelin, obestatin	uc010hdj.2	Q9UBU3	OTTHUMG00000155360	ENST00000335542.8:c.269A>T	3.37:g.10328453T>A	ENSP00000335074:p.Gln90Leu	Somatic	146	0	0	663	WXS	Illumina HiSeq	Phase_I	109	54	0.495413	NM_016362	A8CF34|A8CF38|A8CF42|A8DN29|A8DN30|Q86YP8|Q8TAT9|Q9H3R3	Missense_Mutation	SNP	ENST00000335542.8	37	CCDS33700.1	143	0.06547619047619048	4	0.008130081300813009	73	0.20165745856353592	5	0.008741258741258742	61	0.08047493403693931	T	18.90	3.720946	0.68959	0.014299	0.058953	ENSG00000157017	ENST00000335542;ENST00000430179;ENST00000450603;ENST00000449554;ENST00000449238;ENST00000437422;ENST00000287656;ENST00000457360;ENST00000439975;ENST00000429122	T;T;T;T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36;0.36	4.76	4.76	0.60689	Motilin/ghrelin-associated peptide (1);	0.115879	0.39210	N	0.001439	T	0.00144	0.0004	M	0.67953	2.075	0.30139	P	0.80414	D;D;D;D;D	0.76494	0.989;0.996;0.997;0.996;0.999	D;D;D;D;D	0.80764	0.985;0.99;0.994;0.99;0.994	T	0.09930	-1.0652	9	0.51188	T	0.08	-19.1235	10.5811	0.45257	0.0:0.0:0.0:1.0	rs4684677;rs17847133;rs52799511;rs4684677	77;78;90;89;39	Q9UBU3-4;Q9UBU3-3;Q9UBU3;Q9UBU3-2;Q9UBU3-5	.;.;GHRL_HUMAN;.;.	L	90;89;90;89;77;78;89;90;39;90	ENSP00000335074:Q90L;ENSP00000399922:Q89L;ENSP00000389192:Q90L;ENSP00000415521:Q89L;ENSP00000388145:Q77L;ENSP00000416768:Q78L;ENSP00000287656:Q89L;ENSP00000391406:Q90L;ENSP00000403725:Q39L;ENSP00000414819:Q90L	ENSP00000287656:Q89L	Q	-	2	0	GHRL	10303453	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.169000	0.58223	1.992000	0.58205	0.533000	0.62120	CAG	T|0.950;A|0.050	0.050	strong		0.582	GHRL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000339625.1	NM_016362	
MUC17	140453	hgsc.bcm.edu	37	7	100679390	100679390	+	Missense_Mutation	SNP	A	A	G	rs150982179		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100679390A>G	ENST00000306151.4	+	3	4757	c.4693A>G	c.(4693-4695)Acc>Gcc	p.T1565A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1565	59 X approximate tandem repeats.|Ser-rich.				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)					CAGCATGCAAACCTCAACTTA	0.488																																					p.T1565A		Atlas-SNP	.											MUC17,NS,carcinoma,-2,1	MUC17	804	1	0			c.A4693G						scavenged	.						265.0	248.0	254.0					7																	100679390		2203	4300	6503	SO:0001583	missense	140453	exon3			ATGCAAACCTCAA	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.4693A>G	7.37:g.100679390A>G	ENSP00000302716:p.Thr1565Ala	Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	330	34	0.10303	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	1.177	-0.639202	0.03557	.	.	ENSG00000169876	ENST00000306151	T	0.01887	4.58	0.364	0.364	0.16124	.	.	.	.	.	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B	0.16802	0.019	B	0.06405	0.002	T	0.47586	-0.9106	8	0.06236	T	0.91	.	.	.	.	.	1565	Q685J3	MUC17_HUMAN	A	1565	ENSP00000302716:T1565A	ENSP00000302716:T1565A	T	+	1	0	MUC17	100466110	0.012000	0.17670	0.001000	0.08648	0.002000	0.02628	1.128000	0.31369	0.391000	0.25143	0.102000	0.15555	ACC	.	.	weak		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PIEZO1	9780	hgsc.bcm.edu	37	16	88779132	88779132	+	IGR	SNP	C	C	T	rs2290895	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88779132C>T	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Missense_Mutation_p.H186Y|CTU2_ENST00000378384.3_Missense_Mutation_p.H99Y|CTU2_ENST00000312060.5_Missense_Mutation_p.H186Y|CTU2_ENST00000567949.1_Missense_Mutation_p.H257Y	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						CCAGCAGCAGCATGTGCTGGG	0.701													C|||	594	0.11861	0.2262	0.0778	5008	,	,		10102	0.0605		0.1143	False		,,,				2504	0.0665				p.H186Y		Atlas-SNP	.											.	CTU2	66	.	0			c.C556T						PASS	.	C	TYR/HIS,TYR/HIS	945,3435		94,757,1339	18.0	23.0	21.0		556,556	3.5	0.9	16	dbSNP_100	21	1044,7540		60,924,3308	yes	missense,missense	CTU2	NM_001012759.1,NM_001012762.1	83,83	154,1681,4647	TT,TC,CC		12.1622,21.5753,15.3425	benign,benign	186/516,186/486	88779132	1989,10975	2190	4292	6482	SO:0001628	intergenic_variant	348180	exon7			CAGCAGCATGTGC	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.88779132C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	219	29	0.13242	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	271	0.12408424908424909	115	0.23373983739837398	39	0.10773480662983426	30	0.05244755244755245	87	0.11477572559366754	C	14.65	2.599754	0.46318	0.215753	0.121622	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.18016	2.24;2.5;2.51	4.46	3.49	0.39957	.	0.600559	0.16874	N	0.195994	T	0.00012	0.0000	L	0.51422	1.61	0.45452	P	0.0015800000000000258	P;P;P	0.45902	0.868;0.868;0.867	B;B;B	0.40825	0.341;0.32;0.171	T	0.36529	-0.9744	9	0.11794	T	0.64	.	12.8476	0.57839	0.1649:0.8351:0.0:0.0	rs2290895;rs57345845	99;186;186	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	Y	99;186;186	ENSP00000367635:H99Y;ENSP00000308617:H186Y;ENSP00000388320:H186Y	ENSP00000308617:H186Y	H	+	1	0	CTU2	87306633	0.000000	0.05858	0.924000	0.36721	0.685000	0.39939	-0.113000	0.10774	0.967000	0.38186	0.650000	0.86243	CAT	C|0.860;T|0.140	0.140	strong		0.701	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
KCNK16	83795	hgsc.bcm.edu	37	6	39290200	39290200	+	Silent	SNP	C	C	T	rs3734619	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:39290200C>T	ENST00000373229.5	-	1	130	c.117G>A	c.(115-117)gcG>gcA	p.A39A	KCNK16_ENST00000437525.2_Silent_p.A39A|KCNK16_ENST00000373227.4_Silent_p.A39A|KCNK16_ENST00000507712.1_5'UTR|KCNK16_ENST00000425054.2_Silent_p.A39A	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	39					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)	13						ACTGAGCCTCCGCCTGCCTCT	0.617													C|||	1934	0.386182	0.5386	0.4049	5008	,	,		19138	0.3681		0.3628	False		,,,				2504	0.2096				p.A39A		Atlas-SNP	.											KCNK16_ENST00000425054,NS,carcinoma,-1,2	KCNK16	59	2	0			c.G117A						PASS	.	C	,,,	2177,2229	578.1+/-384.6	552,1073,578	46.0	40.0	42.0		117,117,117,117	-11.8	0.1	6	dbSNP_107	42	3304,5296	486.2+/-371.8	638,2028,1634	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNK16	NM_001135105.1,NM_001135106.1,NM_001135107.1,NM_032115.3	,,,	1190,3101,2212	TT,TC,CC		38.4186,49.4099,42.1421	,,,	39/323,39/295,39/263,39/310	39290200	5481,7525	2203	4300	6503	SO:0001819	synonymous_variant	83795	exon1			AGCCTCCGCCTGC	AF358909	CCDS4843.1, CCDS47420.1, CCDS47421.1, CCDS47422.1	6p21.2-p21.1	2012-03-07			ENSG00000095981	ENSG00000095981		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14464	protein-coding gene	gene with protein product		607369				11263999, 16382106	Standard	NM_032115		Approved	K2p16.1, TALK-1, TALK1	uc003ooq.3	Q96T55	OTTHUMG00000014645	ENST00000373229.5:c.117G>A	6.37:g.39290200C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Silent	SNP	ENST00000373229.5	37	CCDS4843.1																																																																																			C|0.591;T|0.409	0.409	strong		0.617	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115	
OR51F1	256892	hgsc.bcm.edu	37	11	4790410	4790410	+	Silent	SNP	A	A	G	rs1030724	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790410A>G	ENST00000380383.1	-	1	758	c.759T>C	c.(757-759)caT>caC	p.H253H	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Silent_p.H246H|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, 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)			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)		CTGCTCCCACATGGGAGACAC	0.493													G|||	1079	0.215455	0.4561	0.2017	5008	,	,		21390	0.0		0.2704	False		,,,				2504	0.0654				p.H246H		Atlas-SNP	.											OR51F1,right_upper_lobe,carcinoma,-2,1	OR51F1	60	1	0			c.T738C						PASS	.	G		1965,2437	619.1+/-393.3	445,1075,681	101.0	91.0	95.0		738	2.3	1.0	11	dbSNP_86	95	2178,6418	712.3+/-405.9	291,1596,2411	no	coding-synonymous	OR51F1	NM_001004752.1		736,2671,3092	GG,GA,AA		25.3374,44.6388,31.8741		246/313	4790410	4143,8855	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			TCCCACATGGGAG	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.759T>C	11.37:g.4790410A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	188	98	0.521277	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.707;G|0.293	0.293	strong		0.493	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
C17orf62	79415	hgsc.bcm.edu	37	17	80404555	80404555	+	Missense_Mutation	SNP	G	G	A	rs72857481	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80404555G>A	ENST00000437807.2	-	5	462	c.145C>T	c.(145-147)Ctc>Ttc	p.L49F	C17orf62_ENST00000583617.1_Missense_Mutation_p.L49F|C17orf62_ENST00000306645.5_Missense_Mutation_p.L49F|C17orf62_ENST00000577436.1_Missense_Mutation_p.L35F|C17orf62_ENST00000578913.1_Missense_Mutation_p.L49F|C17orf62_ENST00000585080.1_Missense_Mutation_p.L49F|C17orf62_ENST00000578919.1_Missense_Mutation_p.L49F|C17orf62_ENST00000336995.7_Intron|C17orf62_ENST00000577732.1_Missense_Mutation_p.L49F|C17orf62_ENST00000583359.1_5'UTR|C17orf62_ENST00000585064.1_Missense_Mutation_p.L49F|C17orf62_ENST00000434650.2_Missense_Mutation_p.L35F|C17orf62_ENST00000342572.8_Intron	NM_001193653.1|NM_001193657.1	NP_001180582.1|NP_001180586.1	Q9BQA9	CQ062_HUMAN	chromosome 17 open reading frame 62	49						integral component of membrane (GO:0016021)				breast(2)|large_intestine(2)|skin(2)|urinary_tract(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ACGTAGAAGAGCTTCCAGCCC	0.647													G|||	34	0.00678914	0.0	0.0072	5008	,	,		17150	0.0		0.0229	False		,,,				2504	0.0061				p.L49F		Atlas-SNP	.											.	C17orf62	23	.	0			c.C145T						PASS	.	G	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	15,4391	22.3+/-47.3	0,15,2188	96.0	93.0	94.0		145,145,103,145,145,145,145	2.6	1.0	17	dbSNP_130	94	165,8435	77.5+/-140.1	1,163,4136	yes	missense,missense,missense,missense,missense,missense,missense	C17orf62	NM_001033046.3,NM_001100407.2,NM_001100408.2,NM_001193653.1,NM_001193654.1,NM_001193655.1,NM_001193657.1	22,22,22,22,22,22,22	1,178,6324	AA,AG,GG		1.9186,0.3404,1.384	benign,benign,benign,benign,benign,benign,benign	49/188,49/188,35/174,49/188,49/188,49/188,49/188	80404555	180,12826	2203	4300	6503	SO:0001583	missense	79415	exon5			AGAAGAGCTTCCA	AK074950	CCDS32776.1, CCDS45817.1	17q25.3	2014-06-09			ENSG00000178927	ENSG00000178927			28672	protein-coding gene	gene with protein product							Standard	NM_001100407		Approved	MGC4368, FLJ90469	uc021ufr.1	Q9BQA9		ENST00000437807.2:c.145C>T	17.37:g.80404555G>A	ENSP00000388909:p.Leu49Phe	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_001193657	E1B6X3|Q96NR1	Missense_Mutation	SNP	ENST00000437807.2	37	CCDS32776.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	0	0.0	18	0.023746701846965697	G	11.50	1.658734	0.29515	0.003404	0.019186	ENSG00000178927	ENST00000437807;ENST00000306645;ENST00000434650	.	.	.	4.96	2.58	0.30949	.	.	.	.	.	T	0.35098	0.0920	L	0.41824	1.3	0.80722	D	1	B;B	0.12013	0.002;0.005	B;B	0.14023	0.006;0.01	T	0.46679	-0.9174	8	0.52906	T	0.07	.	11.0231	0.47730	0.1877:0.0:0.8123:0.0	.	35;49	E1B6X3;Q9BQA9	.;CQ062_HUMAN	F	49;49;35	.	ENSP00000307765:L49F	L	-	1	0	C17orf62	77997844	1.000000	0.71417	1.000000	0.80357	0.608000	0.37181	3.151000	0.50670	1.086000	0.41228	0.561000	0.74099	CTC	G|0.989;A|0.011	0.011	strong		0.647	C17orf62-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443260.1	NM_001033046	
TAAR5	9038	hgsc.bcm.edu	37	6	132910634	132910634	+	Silent	SNP	C	C	T	rs3813354	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:132910634C>T	ENST00000258034.2	-	1	243	c.192G>A	c.(190-192)gcG>gcA	p.A64A		NM_003967.2	NP_003958.2	O14804	TAAR5_HUMAN	trace amine associated receptor 5	64					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|trimethylamine receptor activity (GO:1990081)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	32	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		GCGTGTGAAGCGCTTTGAAGT	0.557													C|||	1198	0.239217	0.1929	0.1859	5008	,	,		19545	0.3204		0.1044	False		,,,				2504	0.3947				p.A64A		Atlas-SNP	.											TAAR5,NS,carcinoma,-1,1	TAAR5	53	1	0			c.G192A						scavenged	.	C		714,3692	296.4+/-284.2	63,588,1552	192.0	190.0	191.0		192	-6.8	0.0	6	dbSNP_107	191	811,7789	187.7+/-234.9	39,733,3528	no	coding-synonymous	TAAR5	NM_003967.2		102,1321,5080	TT,TC,CC		9.4302,16.2052,11.7254		64/338	132910634	1525,11481	2203	4300	6503	SO:0001819	synonymous_variant	9038	exon1			GTGAAGCGCTTTG	AF021818	CCDS5156.1	6q23.2	2012-08-08			ENSG00000135569	ENSG00000135569		"""GPCR / Class A : Trace amine associated receptors"""	30236	protein-coding gene	gene with protein product		607405				9464258, 15718104	Standard	NM_003967		Approved	PNR	uc003qdk.2	O14804	OTTHUMG00000015581	ENST00000258034.2:c.192G>A	6.37:g.132910634C>T		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	98	57	0.581633	NM_003967	D8KZS1|Q2M1V1|Q4VBL1|Q5VUQ3|Q6NTA8	Silent	SNP	ENST00000258034.2	37	CCDS5156.1																																																																																			C|0.845;T|0.155	0.155	strong		0.557	TAAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042257.1	NM_003967	
RIMS4	140730	hgsc.bcm.edu	37	20	43386414	43386414	+	Splice_Site	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:43386414T>A	ENST00000372851.3	-	4	416		c.e4-2		RIMS4_ENST00000541604.2_Splice_Site	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)				central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				CCACATCCCCTGGAAGAGGCA	0.562																																					.		Atlas-SNP	.											.	RIMS4	47	.	0			c.353-2A>T						PASS	.						83.0	69.0	74.0					20																	43386414		2203	4300	6503	SO:0001630	splice_region_variant	140730	exon5			ATCCCCTGGAAGA		CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"""chromosome 20 open reading frame 190"""	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546	ENST00000372851.3:c.350-2A>T	20.37:g.43386414T>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	80	26	0.325	NM_001205317	A4FU94|E1P613|Q3MI44|Q5JWT7	Splice_Site	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.680306	0.68042	.	.	ENSG00000101098	ENST00000372851;ENST00000541604	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3453	0.83126	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RIMS4	42819828	1.000000	0.71417	0.999000	0.59377	0.492000	0.33523	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	.	.	.	none		0.562	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970	Intron
TRDN	10345	hgsc.bcm.edu	37	6	123869607	123869607	+	Missense_Mutation	SNP	G	G	C	rs9490809	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:123869607G>C	ENST00000398178.3	-	3	404	c.383C>G	c.(382-384)aCt>aGt	p.T128S	TRDN_ENST00000334268.4_Missense_Mutation_p.T128S|TRDN_ENST00000546248.1_Missense_Mutation_p.T128S|TRDN_ENST00000542443.1_Missense_Mutation_p.T128S	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	128			T -> S (in dbSNP:rs9490809). {ECO:0000269|PubMed:15489334}.		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)		ACCTTTATCAGTATCTTCGTC	0.368													G|||	1968	0.392971	0.5363	0.3372	5008	,	,		16140	0.0813		0.5298	False		,,,				2504	0.4192				p.T128S		Atlas-SNP	.											TRDN,NS,carcinoma,-1,1	TRDN	88	1	0			c.C383G						PASS	.	G	SER/THR	2066,1694		570,926,384	60.0	57.0	58.0		383	2.0	0.2	6	dbSNP_119	58	4418,3802		1206,2006,898	yes	missense	TRDN	NM_006073.2	58	1776,2932,1282	CC,CG,GG		46.253,45.0532,45.8765	benign	128/730	123869607	6484,5496	1880	4110	5990	SO:0001583	missense	10345	exon3			TTATCAGTATCTT	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.383C>G	6.37:g.123869607G>C	ENSP00000381240:p.Thr128Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001256022	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	834	0.38186813186813184	256	0.5203252032520326	137	0.3784530386740331	46	0.08041958041958042	395	0.521108179419525	G	0.108	-1.141849	0.01728	0.549468	0.53747	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268;ENST00000542014;ENST00000543022;ENST00000546248;ENST00000333613;ENST00000542443;ENST00000265491	T;T;T;T	0.63580	0.58;0.58;0.58;-0.05	5.05	1.97	0.26223	Aspartyl beta-hydroxylase/Triadin domain (1);	1.405680	0.04389	N	0.362083	T	0.36220	0.0959	L	0.56769	1.78	0.80722	P	0.0	B;P;B;B;B	0.46220	0.066;0.874;0.058;0.058;0.058	B;B;B;B;B	0.44163	0.036;0.443;0.026;0.026;0.038	T	0.08700	-1.0709	9	0.12430	T	0.62	1.6996	4.2229	0.10567	0.3838:0.2427:0.3736:0.0	rs9490809;rs11537943;rs17747145;rs52833290;rs9490809	128;128;128;128;128	F5H6E3;F5H2W7;Q5SWK9;Q8IVK2;Q13061	.;.;.;.;TRDN_HUMAN	S	128;128;128;128;128;128;33;128;33	ENSP00000381240:T128S;ENSP00000333984:T128S;ENSP00000439281:T128S;ENSP00000437684:T128S	ENSP00000265491:T33S	T	-	2	0	TRDN	123911306	0.644000	0.27277	0.170000	0.22879	0.038000	0.13279	-0.006000	0.12833	0.376000	0.24707	0.643000	0.83706	ACT	G|0.614;C|0.386	0.386	strong		0.368	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
DGCR6	8214	hgsc.bcm.edu	37	22	18893995	18893995	+	Silent	SNP	C	C	G	rs409155	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:18893995C>G	ENST00000331444.6	+	1	260	c.108C>G	c.(106-108)ccC>ccG	p.P36P	DGCR6_ENST00000608842.1_Silent_p.P36P|DGCR6_ENST00000413981.1_Intron	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6	36					cell adhesion (GO:0007155)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|upper_aerodigestive_tract(1)	3						AGGAGTTGCCCAGGTAcgcgg	0.721													C|||	222	0.0443291	0.0325	0.0173	5008	,	,		11099	0.0367		0.0358	False		,,,				2504	0.0961				p.P36P		Atlas-SNP	.											.	DGCR6	12	.	0			c.C108G						PASS	.	C		132,4238		4,124,2057	13.0	15.0	14.0		108	2.9	1.0	22	dbSNP_80	14	296,8258		7,282,3988	no	coding-synonymous	DGCR6	NM_005675.4		11,406,6045	GG,GC,CC		3.4604,3.0206,3.3117		36/221	18893995	428,12496	2185	4277	6462	SO:0001819	synonymous_variant	8214	exon1			GTTGCCCAGGTAC	X96484	CCDS13753.1	22q11.21	2008-06-12			ENSG00000183628	ENSG00000183628			2846	protein-coding gene	gene with protein product		601279				8733130	Standard	NM_005675		Approved		uc002zoh.4	Q14129	OTTHUMG00000150162	ENST00000331444.6:c.108C>G	22.37:g.18893995C>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	14	0.291667	NM_005675	B2RCH5|D3DX15|G5E9J8|Q9BY28	Silent	SNP	ENST00000331444.6	37	CCDS13753.1																																																																																			C|0.969;G|0.031	0.031	strong		0.721	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316631.2	NM_005675	
LARP4B	23185	hgsc.bcm.edu	37	10	909711	909711	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:909711A>G	ENST00000316157.3	-	4	442	c.402T>C	c.(400-402)taT>taC	p.Y134Y		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	134					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(2)|skin(2)|urinary_tract(2)	38						GCAGAGAGTCATATTCTGAGG	0.473																																					p.Y134Y		Atlas-SNP	.											.	LARP4B	110	.	0			c.T402C						PASS	.						99.0	100.0	100.0					10																	909711		2203	4300	6503	SO:0001819	synonymous_variant	23185	exon5			AGAGTCATATTCT	D86971	CCDS31131.1	10p15.3	2011-08-24	2009-06-09	2009-06-09	ENSG00000107929	ENSG00000107929		"""La ribonucleoprotein domain containing"""	28987	protein-coding gene	gene with protein product			"""KIAA0217"", ""La ribonucleoprotein domain family, member 5"""	KIAA0217, LARP5		9039502, 20573744	Standard	NM_015155		Approved		uc031ptb.1	Q92615	OTTHUMG00000017534	ENST00000316157.3:c.402T>C	10.37:g.909711A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	70	10	0.142857	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Silent	SNP	ENST00000316157.3	37	CCDS31131.1																																																																																			.	.	none		0.473	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155	
USH1C	10083	hgsc.bcm.edu	37	11	17531146	17531146	+	Intron	SNP	G	G	A	rs17776775	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:17531146G>A	ENST00000318024.4	-	16	1393				USH1C_ENST00000527020.1_Intron|USH1C_ENST00000529563.1_Intron|USH1C_ENST00000527720.1_Intron|USH1C_ENST00000005226.7_Silent_p.A590A	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						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						GAGAGGATGAGGCGCTCACAT	0.672													G|||	345	0.0688898	0.0076	0.0389	5008	,	,		7889	0.0397		0.0527	False		,,,				2504	0.2198				p.A590A		Atlas-SNP	.											.	USH1C	157	.	0			c.C1770T						PASS	.	G	,	77,4311		2,73,2119	11.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,1770	4.6	0.6	11	dbSNP_123	13	396,8166		10,376,3895	no	intron,coding-synonymous	USH1C	NM_005709.3,NM_153676.3	,	12,449,6014	AA,AG,GG		4.6251,1.7548,3.6525	,	,590/900	17531146	473,12477	2194	4281	6475	SO:0001627	intron_variant	10083	exon18			GGATGAGGCGCTC	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.1285-7619C>T	11.37:g.17531146G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	43	27	0.627907	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			A|0.048;G|0.952	0.048	strong		0.672	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
DOCK8	81704	hgsc.bcm.edu	37	9	304670	304670	+	Missense_Mutation	SNP	C	C	T	rs146490788	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:304670C>T	ENST00000453981.1	+	5	606	c.494C>T	c.(493-495)tCg>tTg	p.S165L	DOCK8_ENST00000432829.2_Missense_Mutation_p.S97L|DOCK8_ENST00000469391.1_Missense_Mutation_p.S97L			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	165					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)		ACGTTTGAGTCGGAAACCTTG	0.463																																					p.S165L		Atlas-SNP	.											.	DOCK8	401	.	0			c.C494T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	3,4403	6.2+/-15.9	0,3,2200	127.0	134.0	132.0		290,290,494	6.0	1.0	9	dbSNP_134	132	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	145,145,145	0,10,6493	TT,TC,CC		0.0814,0.0681,0.0769	benign,benign,benign	97/2000,97/2032,165/2100	304670	10,12996	2203	4300	6503	SO:0001583	missense	81704	exon5			TTGAGTCGGAAAC	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.494C>T	9.37:g.304670C>T	ENSP00000408464:p.Ser165Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676168	0.67928	6.81E-4	8.14E-4	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000487230;ENST00000469391	T;T;T;T	0.32272	2.59;2.59;1.46;2.59	6.02	6.02	0.97574	.	0.139758	0.49916	D	0.000133	T	0.41971	0.1182	N	0.19112	0.55	0.58432	D	0.999999	B;D;B	0.89917	0.158;1.0;0.031	B;D;B	0.83275	0.029;0.996;0.006	T	0.11203	-1.0597	10	0.25751	T	0.34	.	18.7213	0.91694	0.0:1.0:0.0:0.0	.	97;165;165	E9PH09;A2A349;Q8NF50	.;.;DOCK8_HUMAN	L	165;165;97;97;97	ENSP00000408464:S165L;ENSP00000394888:S97L;ENSP00000418318:S97L;ENSP00000419438:S97L	ENSP00000287364:S165L	S	+	2	0	DOCK8	294670	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	5.226000	0.65299	2.865000	0.98341	0.655000	0.94253	TCG	C|0.999;T|0.001	0.001	strong		0.463	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999922	46999922	+	Missense_Mutation	SNP	G	G	T	rs4926046	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.						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	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	98	26	0.265306	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	
ZNF285	26974	hgsc.bcm.edu	37	19	44891009	44891009	+	Silent	SNP	C	C	T	rs139913772	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44891009C>T	ENST00000330997.4	-	4	1462	c.1398G>A	c.(1396-1398)gcG>gcA	p.A466A	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Silent_p.A466A|ZNF285_ENST00000591679.1_Silent_p.A473A	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	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)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						CAGAGCTATACGCAAAATCCT	0.423																																					p.A466A		Atlas-SNP	.											ZNF285,NS,carcinoma,0,2	ZNF285	86	2	0			c.G1398A						PASS	.	T		0,4406		0,0,2203	84.0	85.0	85.0		1398	-6.9	0.0	19	dbSNP_134	85	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	ZNF285	NM_152354.3		0,8,6495	TT,TC,CC		0.093,0.0,0.0615		466/591	44891009	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			GCTATACGCAAAA	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.1398G>A	19.37:g.44891009C>T		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	200	84	0.42	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	37	CCDS12638.1																																																																																			C|0.999;T|0.001	0.001	strong		0.423	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
MKI67	4288	hgsc.bcm.edu	37	10	129905896	129905896	+	Missense_Mutation	SNP	T	T	A	rs3740423	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129905896T>A	ENST00000368654.3	-	13	4583	c.4208A>T	c.(4207-4209)gAg>gTg	p.E1403V	MKI67_ENST00000368653.3_Missense_Mutation_p.E1043V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1403	16 X 122 AA approximate repeats.		E -> V (in dbSNP:rs3740423).		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)	p.E1403V(1)		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)				GGCTGAGAGCTCCTTCTGTAC	0.498													T|||	701	0.139976	0.0098	0.281	5008	,	,		20464	0.1181		0.1958	False		,,,				2504	0.181				p.E1403V		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	stomach(1)	c.A4208T						PASS	.	T	VAL/GLU,VAL/GLU	136,4270	96.2+/-134.9	2,132,2069	295.0	272.0	280.0		3128,4208	2.7	0.0	10	dbSNP_107	280	1574,7026	294.2+/-301.7	146,1282,2872	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	121,121	148,1414,4941	AA,AT,TT		18.3023,3.0867,13.1478	possibly-damaging,possibly-damaging	1043/2897,1403/3257	129905896	1710,11296	2203	4300	6503	SO:0001583	missense	4288	exon13			GAGAGCTCCTTCT	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.4208A>T	10.37:g.129905896T>A	ENSP00000357643:p.Glu1403Val	Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	252	122	0.484127	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	342	0.1565934065934066	6	0.012195121951219513	104	0.287292817679558	83	0.1451048951048951	149	0.19656992084432717	T	13.96	2.391928	0.42410	0.030867	0.183023	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.05580	3.42;3.42	3.81	2.66	0.31614	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	D;D;D	0.89917	0.997;1.0;0.999	P;D;D	0.80764	0.855;0.994;0.971	T	0.42396	-0.9454	8	0.41790	T	0.15	.	4.0897	0.09963	0.0:0.113:0.2103:0.6767	rs3740423;rs16912224;rs17731403;rs52833862;rs3740423	1402;1043;1403	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	1403;1043;1402	ENSP00000357643:E1403V;ENSP00000357642:E1043V	ENSP00000357642:E1043V	E	-	2	0	MKI67	129795886	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-1.195000	0.03043	0.650000	0.30769	0.459000	0.35465	GAG	T|0.852;A|0.148	0.148	strong		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
AP3B2	8120	hgsc.bcm.edu	37	15	83378366	83378366	+	Silent	SNP	G	G	A	rs200226421	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:83378366G>A	ENST00000261722.3	-	1	300	c.93C>T	c.(91-93)atC>atT	p.I31I	AP3B2_ENST00000535359.1_Silent_p.I31I|AP3B2_ENST00000561455.1_5'Flank|AP3B2_ENST00000542200.1_Silent_p.I31I|AP3B2_ENST00000535348.1_Silent_p.I31I|AC105339.1_ENST00000440479.1_lincRNA	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	31					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|intracellular protein transport (GO:0006886)|post-Golgi vesicle-mediated transport (GO:0006892)	AP-3 adaptor complex (GO:0030123)|COPI-coated vesicle (GO:0030137)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(4)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(2)	41			BRCA - Breast invasive adenocarcinoma(143;0.229)			CGGAGGAGAAGATGCCGCCGC	0.761													G|||	25	0.00499201	0.0008	0.0029	5008	,	,		8047	0.0		0.0199	False		,,,				2504	0.002				p.I31I		Atlas-SNP	.											.	AP3B2	103	.	0			c.C93T						PASS	.	G		0,2962		0,0,1481	2.0	3.0	3.0		93	1.7	1.0	15		3	42,6932		0,42,3445	no	coding-synonymous	AP3B2	NM_004644.3		0,42,4926	AA,AG,GG		0.6022,0.0,0.4227		31/1083	83378366	42,9894	1481	3487	4968	SO:0001819	synonymous_variant	8120	exon1			GGAGAAGATGCCG	U37673	CCDS45331.1, CCDS61736.1, CCDS61737.1	15q	2008-07-07			ENSG00000103723	ENSG00000103723			567	protein-coding gene	gene with protein product		602166				7671305, 1851215	Standard	NM_004644		Approved	NAPTB	uc010uoh.2	Q13367	OTTHUMG00000168009	ENST00000261722.3:c.93C>T	15.37:g.83378366G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	37	CCDS45331.1																																																																																			.	.	weak		0.761	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1		
PRSS41	360226	hgsc.bcm.edu	37	16	2849372	2849372	+	RNA	SNP	C	C	A	rs201777593		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2849372C>A	ENST00000399677.1	+	0	382				SNORA3_ENST00000408792.1_RNA			Q7RTY9	PRS41_HUMAN	protease, serine, 41							anchored component of membrane (GO:0031225)|intracellular organelle (GO:0043229)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)										CTACAGCAGTCGTTACAAAGT	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		17254	0.0		0.001	False		,,,				2504	0.0				p.R128S		Atlas-SNP	.											.	.	.	.	0			c.C382A						PASS	.						176.0	134.0	147.0					16																	2849372		692	1591	2283			360226	exon3			AGCAGTCGTTACA			16p13.3	2014-04-01			ENSG00000215148	ENSG00000215148		"""Serine peptidases / Serine peptidases"""	30715	other	unknown	"""testis serine protease 1"""					12838346	Standard	NM_001135086		Approved	TESSP1	uc010uwi.2	Q7RTY9	OTTHUMG00000128932		16.37:g.2849372C>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001135086		Missense_Mutation	SNP	ENST00000399677.1	37																																																																																				.	.	weak		0.552	PRSS41-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000436450.1	NM_183379	
MUC17	140453	hgsc.bcm.edu	37	7	100682097	100682097	+	Missense_Mutation	SNP	C	C	T	rs138703892		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682097C>T	ENST00000306151.4	+	3	7464	c.7400C>T	c.(7399-7401)cCg>cTg	p.P2467L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2467	59 X approximate tandem repeats.|Ser-rich.				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)	p.P2467L(1)		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)					AGCACCACGCCGGTGGTCAGT	0.527													N|||	1	0.000199681	0.0	0.0	5008	,	,		27678	0.001		0.0	False		,,,				2504	0.0				p.P2467L		Atlas-SNP	.											MUC17,colon,carcinoma,0,1	MUC17	804	1	1	Substitution - Missense(1)	large_intestine(1)	c.C7400T						scavenged	.						325.0	322.0	323.0					7																	100682097		2203	4300	6503	SO:0001583	missense	140453	exon3			CCACGCCGGTGGT	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.7400C>T	7.37:g.100682097C>T	ENSP00000302716:p.Pro2467Leu	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	246	8	0.0325203	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	N	2.249	-0.372040	0.05034	.	.	ENSG00000169876	ENST00000306151	T	0.03242	4.0	1.43	-2.86	0.05717	.	.	.	.	.	T	0.01905	0.0060	N	0.12746	0.255	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.45571	-0.9252	9	0.29301	T	0.29	.	3.6112	0.08061	0.233:0.5958:0.0:0.1711	.	2467	Q685J3	MUC17_HUMAN	L	2467	ENSP00000302716:P2467L	ENSP00000302716:P2467L	P	+	2	0	MUC17	100468817	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.286000	0.00022	-1.279000	0.02405	-1.368000	0.01194	CCG	C|1.000;T|0.000	0.000	strong		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
BFSP1	631	hgsc.bcm.edu	37	20	17477592	17477592	+	Missense_Mutation	SNP	C	C	T	rs6080719	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:17477592C>T	ENST00000377873.3	-	7	1072	c.1033G>A	c.(1033-1035)Ggt>Agt	p.G345S	BFSP1_ENST00000377868.2_Missense_Mutation_p.G220S|BFSP1_ENST00000536626.1_Missense_Mutation_p.G206S|BFSP1_ENST00000544874.1_Missense_Mutation_p.G206S	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	61	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	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	
OR52J3	119679	hgsc.bcm.edu	37	11	5068297	5068297	+	Missense_Mutation	SNP	G	G	A	rs58664826	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5068297G>A	ENST00000380370.1	+	1	542	c.542G>A	c.(541-543)tGt>tAt	p.C181Y		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	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)|endometrium(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		CATTCCTACTGTGAGCACATG	0.423													G|||	504	0.100639	0.0242	0.2767	5008	,	,		23123	0.0863		0.1372	False		,,,				2504	0.0562				p.C181Y		Atlas-SNP	.											.	OR52J3	77	.	0			c.G542A						PASS	.	G	TYR/CYS	164,4238	109.5+/-147.8	2,160,2039	198.0	169.0	179.0		542	4.2	1.0	11	dbSNP_129	179	1059,7537	224.4+/-260.8	66,927,3305	yes	missense	OR52J3	NM_001001916.2	194	68,1087,5344	AA,AG,GG		12.3197,3.7256,9.4091	probably-damaging	181/312	5068297	1223,11775	2201	4298	6499	SO:0001583	missense	119679	exon1			CCTACTGTGAGCA	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.542G>A	11.37:g.5068297G>A	ENSP00000369728:p.Cys181Tyr	Somatic	461	1	0.0021692		WXS	Illumina HiSeq	Phase_I	379	173	0.456464	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	250	0.11446886446886446	11	0.022357723577235773	78	0.2154696132596685	62	0.10839160839160839	99	0.13060686015831136	G	19.90	3.912644	0.72983	0.037256	0.123197	ENSG00000205495	ENST00000380370	T	0.61980	0.06	4.19	4.19	0.49359	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000088	T	0.00210	0.0006	M	0.94101	3.495	0.21290	P	0.999736777	D	0.89917	1.0	D	0.97110	1.0	T	0.09618	-1.0666	9	0.87932	D	0	.	15.2669	0.73669	0.0:0.0:1.0:0.0	rs58664826;rs61729561	181	Q8NH60	O52J3_HUMAN	Y	181	ENSP00000369728:C181Y	ENSP00000369728:C181Y	C	+	2	0	OR52J3	5024873	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.316000	0.79007	2.143000	0.66587	0.655000	0.94253	TGT	G|0.894;A|0.106	0.106	strong		0.423	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
C11orf30	56946	hgsc.bcm.edu	37	11	76257215	76257215	+	Silent	SNP	T	T	C	rs3753051	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:76257215T>C	ENST00000529032.1	+	19	3648	c.3648T>C	c.(3646-3648)acT>acC	p.T1216T	C11orf30_ENST00000525919.1_Silent_p.T1217T|C11orf30_ENST00000343878.3_Intron|C11orf30_ENST00000334736.3_Silent_p.T1216T|C11orf30_ENST00000524767.1_Silent_p.T1231T|C11orf30_ENST00000533248.1_Silent_p.T1125T|C11orf30_ENST00000525038.1_Silent_p.T1217T|C11orf30_ENST00000524490.1_Silent_p.T1118T			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						scavenged	.	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	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	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	
HNF1A	6927	hgsc.bcm.edu	37	12	121432117	121432117	+	Silent	SNP	G	G	C	rs56348580	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:121432117G>C	ENST00000257555.6	+	4	1090	c.864G>C	c.(862-864)ggG>ggC	p.G288G	HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000400024.2_Silent_p.G288G|HNF1A_ENST00000543427.1_Silent_p.G171G|HNF1A_ENST00000402929.1_Silent_p.G288G|HNF1A_ENST00000544413.1_Silent_p.G288G|HNF1A_ENST00000541395.1_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	60	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	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	
NBAS	51594	hgsc.bcm.edu	37	2	15378808	15378808	+	Silent	SNP	C	C	G	rs34080125	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:15378808C>G	ENST00000281513.5	-	45	5752	c.5727G>C	c.(5725-5727)ctG>ctC	p.L1909L	NBAS_ENST00000441750.1_Silent_p.L1789L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1909					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						CTTCCACAGACAGCTTAAAAA	0.353													C|||	304	0.0607029	0.0439	0.0447	5008	,	,		16253	0.1032		0.0139	False		,,,				2504	0.0992				p.L1909L		Atlas-SNP	.											.	NBAS	246	.	0			c.G5727C						PASS	.	C		208,4198	116.7+/-154.6	10,188,2005	55.0	56.0	56.0		5727	-8.7	0.0	2	dbSNP_126	56	106,8494	56.8+/-118.0	2,102,4196	no	coding-synonymous	NBAS	NM_015909.2		12,290,6201	GG,GC,CC		1.2326,4.7208,2.4143		1909/2372	15378808	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	51594	exon45			CACAGACAGCTTA	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.5727G>C	2.37:g.15378808C>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1	120	0.054945054945054944	21	0.042682926829268296	14	0.03867403314917127	76	0.13286713286713286	9	0.011873350923482849	C	0.017	-1.494484	0.01009	0.047208	0.012326	ENSG00000151779	ENST00000442506	.	.	.	5.97	-8.7	0.00851	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.999999999962185	.	.	.	.	.	.	T	0.10086	-1.0645	3	.	.	.	.	5.0613	0.14559	0.0854:0.3429:0.0908:0.4809	rs34080125	.	.	.	S	957	.	.	C	-	2	0	NBAS	15296259	0.000000	0.05858	0.003000	0.11579	0.319000	0.28217	-1.046000	0.03525	-2.477000	0.00525	-0.345000	0.07892	TGT	C|0.967;G|0.033	0.033	strong		0.353	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
PI4KA	5297	hgsc.bcm.edu	37	22	21066789	21066789	+	Silent	SNP	A	A	G	rs5996654	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:21066789A>G	ENST00000572273.1	-	50	5843	c.5613T>C	c.(5611-5613)acT>acC	p.T1871T	PI4KA_ENST00000255882.6_Silent_p.T1929T|PI4KA_ENST00000414196.3_Silent_p.T681T			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1871	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.T1871T(1)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-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)			GGAAGGCCAGAGTGGACTCAT	0.662																																					p.T1929T	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	1	Substitution - coding silent(1)	stomach(1)	c.T5787C						scavenged	.						23.0	25.0	24.0					22																	21066789		2198	4284	6482	SO:0001819	synonymous_variant	5297	exon50			GGCCAGAGTGGAC	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.5613T>C	22.37:g.21066789A>G		Somatic	412	3	0.00728155		WXS	Illumina HiSeq	Phase_I	359	138	0.384401	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				A|0.618;G|0.382	0.382	strong		0.662	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
DCST1	149095	hgsc.bcm.edu	37	1	155019698	155019698	+	Missense_Mutation	SNP	G	G	A	rs200041699	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:155019698G>A	ENST00000295542.1	+	14	1618	c.1522G>A	c.(1522-1524)Ggg>Agg	p.G508R	RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000392480.1_Missense_Mutation_p.G508R|DCST1_ENST00000368419.2_Missense_Mutation_p.G508R|DCST1_ENST00000423025.2_Missense_Mutation_p.G483R	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	508						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	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)			GGTGAAGGTCGGGGGAGACTC	0.542													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18587	0.0		0.0	False		,,,				2504	0.0				p.G508R		Atlas-SNP	.											.	DCST1	69	.	0			c.G1522A						PASS	.	G	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	82.0	81.0	81.0		1447,1522	4.9	0.0	1		81	0,8600		0,0,4300	no	missense,missense	DCST1	NM_001143687.2,NM_152494.3	125,125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	483/682,508/707	155019698	1,13005	2203	4300	6503	SO:0001583	missense	149095	exon14			AAGGTCGGGGGAG	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.1522G>A	1.37:g.155019698G>A	ENSP00000295542:p.Gly508Arg	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	253	144	0.56917	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	37	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.496614	0.44352	2.27E-4	0.0	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.88	4.88	0.63580	Dendritic cell-specific transmembrane protein-like (1);	0.308295	0.33005	N	0.005381	T	0.20455	0.0492	L	0.40543	1.245	0.19300	N	0.999974	D;P	0.57571	0.98;0.932	P;P	0.54060	0.741;0.741	T	0.06899	-1.0801	10	0.13853	T	0.58	-11.7727	13.7183	0.62712	0.0:0.0:1.0:0.0	.	483;508	E9PHV3;Q5T197	.;DCST1_HUMAN	R	508;508;483;508	ENSP00000295542:G508R;ENSP00000376271:G508R;ENSP00000387369:G483R;ENSP00000357404:G508R	ENSP00000295542:G508R	G	+	1	0	DCST1	153286322	1.000000	0.71417	0.023000	0.16930	0.036000	0.12997	4.814000	0.62627	2.688000	0.91661	0.655000	0.94253	GGG	G|0.999;A|0.001	0.001	weak		0.542	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
CA10	56934	hgsc.bcm.edu	37	17	49713300	49713300	+	Silent	SNP	G	G	A	rs11870209	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:49713300G>A	ENST00000285273.4	-	8	1816	c.705C>T	c.(703-705)taC>taT	p.Y235Y	CA10_ENST00000442502.2_Silent_p.Y235Y|CA10_ENST00000451037.2_Silent_p.Y235Y|CA10_ENST00000340813.6_Silent_p.Y241Y|CA10_ENST00000570565.1_Silent_p.Y160Y|CA10_ENST00000571918.1_5'UTR	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	235					brain development (GO:0007420)			p.Y235Y(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	TCGACCCATCGTAAGTGATGA	0.403													G|||	1823	0.364018	0.2481	0.4496	5008	,	,		18533	0.3442		0.4911	False		,,,				2504	0.3497				p.Y235Y		Atlas-SNP	.											CA10,NS,carcinoma,0,2	CA10	84	2	1	Substitution - coding silent(1)	stomach(1)	c.C705T						PASS	.	G	,,	1231,3175	428.7+/-342.0	182,867,1154	116.0	106.0	109.0		705,705,705	-9.6	0.5	17	dbSNP_120	109	4165,4435	568.5+/-389.0	1014,2137,1149	no	coding-synonymous,coding-synonymous,coding-synonymous	CA10	NM_001082533.1,NM_001082534.1,NM_020178.4	,,	1196,3004,2303	AA,AG,GG		48.4302,27.9392,41.4885	,,	235/329,235/329,235/329	49713300	5396,7610	2203	4300	6503	SO:0001819	synonymous_variant	56934	exon8			CCCATCGTAAGTG	AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"""Carbonic anhydrases"""	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.705C>T	17.37:g.49713300G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_001082534	B2R7J0|B4DGL6	Silent	SNP	ENST00000285273.4	37	CCDS32684.1																																																																																			G|0.606;A|0.394	0.394	strong		0.403	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178	
DIDO1	11083	hgsc.bcm.edu	37	20	61528044	61528044	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:61528044G>A	ENST00000266070.4	-	7	2218	c.1893C>T	c.(1891-1893)tcC>tcT	p.S631S	DIDO1_ENST00000395335.2_Silent_p.S631S|DIDO1_ENST00000395343.1_Silent_p.S631S|DIDO1_ENST00000395340.1_Silent_p.S631S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	631					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)					CCAAAGCAGCGGAGCCAGGGA	0.647																																					p.S631S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C1893T						PASS	.						46.0	52.0	50.0					20																	61528044		2203	4300	6503	SO:0001819	synonymous_variant	11083	exon7			AGCAGCGGAGCCA	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.1893C>T	20.37:g.61528044G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_080797	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																																																																																			.	.	none		0.647	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
SLC8A3	6547	hgsc.bcm.edu	37	14	70634801	70634801	+	Silent	SNP	T	T	C	rs17765575	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:70634801T>C	ENST00000381269.2	-	2	1092	c.339A>G	c.(337-339)acA>acG	p.T113T	SLC8A3_ENST00000357887.3_Silent_p.T113T|SLC8A3_ENST00000534137.1_Silent_p.T113T|SLC8A3_ENST00000528359.1_Silent_p.T113T|SLC8A3_ENST00000356921.2_Silent_p.T113T	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	113					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		GTTTCTTAATTGTCACCTCCC	0.488													C|||	367	0.0732827	0.0461	0.0865	5008	,	,		22443	0.0486		0.1581	False		,,,				2504	0.0389				p.T113T		Atlas-SNP	.											.	SLC8A3	234	.	0			c.A339G						PASS	.	C	,,,	270,4136	801.6+/-415.6	9,252,1942	103.0	89.0	94.0		339,339,339,339	-9.9	0.6	14	dbSNP_123	94	1417,7183	752.6+/-407.4	131,1155,3014	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC8A3	NM_033262.3,NM_058240.2,NM_182932.1,NM_183002.1	,,,	140,1407,4956	CC,CT,TT		16.4767,6.128,12.9709	,,,	113/926,113/925,113/922,113/928	70634801	1687,11319	2203	4300	6503	SO:0001819	synonymous_variant	6547	exon2			CTTAATTGTCACC	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"""Solute carriers"""	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.339A>G	14.37:g.70634801T>C		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	354	130	0.367232	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	37	CCDS35498.1																																																																																			T|0.893;C|0.107	0.107	strong		0.488	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
RBM17	84991	hgsc.bcm.edu	37	10	6139078	6139078	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:6139078A>G	ENST00000446108.1	+	2	694	c.50A>G	c.(49-51)gAa>gGa	p.E17G	RBM17_ENST00000379888.4_Missense_Mutation_p.E17G	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	17					alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						TCAAAAACAGAAGGCTGGTCC	0.468																																					p.E17G		Atlas-SNP	.											.	RBM17	45	.	0			c.A50G						PASS	.						106.0	106.0	106.0					10																	6139078		2203	4300	6503	SO:0001583	missense	84991	exon2			AAACAGAAGGCTG	AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	16944	protein-coding gene	gene with protein product	"""splicing factor 45kDa"""	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.50A>G	10.37:g.6139078A>G	ENSP00000388638:p.Glu17Gly	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	118	5	0.0423729	NM_001145547	Q96GY6	Missense_Mutation	SNP	ENST00000446108.1	37	CCDS7077.1	.	.	.	.	.	.	.	.	.	.	A	19.61	3.859257	0.71834	.	.	ENSG00000134453	ENST00000379888;ENST00000432931;ENST00000446108;ENST00000418631	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	4.64	3.5	0.40072	.	0.049423	0.85682	N	0.000000	T	0.41534	0.1163	L	0.51422	1.61	0.80722	D	1	P	0.39216	0.664	B	0.32928	0.155	T	0.25502	-1.0130	10	0.40728	T	0.16	-25.6691	10.0431	0.42171	0.9194:0.0:0.0806:0.0	.	17	Q96I25	SPF45_HUMAN	G	17	ENSP00000369218:E17G;ENSP00000408214:E17G;ENSP00000388638:E17G;ENSP00000402303:E17G	ENSP00000369218:E17G	E	+	2	0	RBM17	6179084	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.815000	0.91973	0.738000	0.32606	0.377000	0.23210	GAA	.	.	none		0.468	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905	
ZNF146	7705	hgsc.bcm.edu	37	19	36727365	36727365	+	Missense_Mutation	SNP	G	G	A	rs2070132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	102	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	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	
ZSCAN25	221785	hgsc.bcm.edu	37	7	99217424	99217424	+	Silent	SNP	G	G	A	rs10282706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99217424G>A	ENST00000394152.2	+	4	522	c.195G>A	c.(193-195)gaG>gaA	p.E65E	ZSCAN25_ENST00000334715.3_Silent_p.E65E|ZSCAN25_ENST00000262941.6_Silent_p.E65E|ZSCAN25_ENST00000466948.1_3'UTR	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	65	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)										AGCTCCAGGAGCTCTGTCGTC	0.612													A|||	1722	0.34385	0.6914	0.1916	5008	,	,		18685	0.2817		0.0596	False		,,,				2504	0.3384				p.E65E		Atlas-SNP	.											.	.	.	.	0			c.G195A						PASS	.	A		2514,1892	542.5+/-376.0	714,1086,403	71.0	79.0	77.0		195	-0.9	1.0	7	dbSNP_119	77	674,7926	788.3+/-407.6	32,610,3658	no	coding-synonymous	ZNF498	NM_145115.2		746,1696,4061	AA,AG,GG		7.8372,42.9414,24.5118		65/545	99217424	3188,9818	2203	4300	6503	SO:0001819	synonymous_variant	221785	exon4			CCAGGAGCTCTGT	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.195G>A	7.37:g.99217424G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	122	43	0.352459	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Silent	SNP	ENST00000394152.2	37	CCDS5671.2																																																																																			G|0.735;A|0.265	0.265	strong		0.612	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
DOCK2	1794	hgsc.bcm.edu	37	5	169127097	169127097	+	Silent	SNP	C	C	A	rs2112703	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	164	0	0		WXS	Illumina HiSeq	Phase_I	151	86	0.569536	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	
MUC6	4588	hgsc.bcm.edu	37	11	1017575	1017575	+	Silent	SNP	C	C	T	rs76222533		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1017575C>T	ENST00000421673.2	-	31	5276	c.5226G>A	c.(5224-5226)acG>acA	p.T1742T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1742	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)		AGGTTTTGGCCGTGCTAAATG	0.537													-|||	1	0.000199681	0.0	0.0014	5008	,	,		39036	0.0		0.0	False		,,,				2504	0.0				p.T1742T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	0			c.G5226A						scavenged	.						697.0	677.0	684.0					11																	1017575		2190	4282	6472	SO:0001819	synonymous_variant	4588	exon31			TTTGGCCGTGCTA	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.5226G>A	11.37:g.1017575C>T		Somatic	906	88	0.0971302		WXS	Illumina HiSeq	Phase_I	678	57	0.0840708	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			C|0.500;T|0.500	0.500	strong		0.537	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ZNF33B	7582	hgsc.bcm.edu	37	10	43089370	43089370	+	Missense_Mutation	SNP	T	T	A	rs71505625	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:43089370T>A	ENST00000359467.3	-	5	1142	c.1028A>T	c.(1027-1029)cAt>cTt	p.H343L	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	343					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						TCGAGTGAGATGTGACTTCTC	0.413													t|||	7	0.00139776	0.0	0.0014	5008	,	,		22122	0.0		0.004	False		,,,				2504	0.002				p.H343L	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A1028T						PASS	.	T	LEU/HIS	2,4404	4.2+/-10.8	0,2,2201	121.0	119.0	120.0		1028	2.3	1.0	10	dbSNP_130	120	20,8580	14.6+/-50.1	0,20,4280	no	missense	ZNF33B	NM_006955.1	99	0,22,6481	AA,AT,TT		0.2326,0.0454,0.1692	probably-damaging	343/779	43089370	22,12984	2203	4300	6503	SO:0001583	missense	7582	exon5			GTGAGATGTGACT	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.1028A>T	10.37:g.43089370T>A	ENSP00000352444:p.His343Leu	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	132	23	0.174242	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	4.540	0.100297	0.08731	4.54E-4	0.002326	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.18338	2.22	2.28	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.207772	0.24160	N	0.040988	T	0.09774	0.0240	N	0.20483	0.58	0.09310	N	0.999998	B	0.10296	0.003	B	0.08055	0.003	T	0.24119	-1.0169	10	0.32370	T	0.25	.	8.5071	0.33195	0.0:0.0:0.0:1.0	.	343	Q06732	ZN33B_HUMAN	L	343;309	ENSP00000352444:H343L	ENSP00000352444:H343L	H	-	2	0	ZNF33B	42409376	0.000000	0.05858	0.998000	0.56505	0.966000	0.64601	0.224000	0.17738	1.324000	0.45282	0.341000	0.21757	CAT	T|0.998;A|0.002	0.002	strong		0.413	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
HTRA1	5654	hgsc.bcm.edu	37	10	124249118	124249118	+	Silent	SNP	C	C	T	rs17624021	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124249118C>T	ENST00000368984.3	+	3	881	c.753C>T	c.(751-753)atC>atT	p.I251I		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	251	Serine protease.				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)				AAGCAGACATCGCACTCATCA	0.527													C|||	116	0.0231629	0.0219	0.0173	5008	,	,		18824	0.001		0.0398	False		,,,				2504	0.0348				p.I251I		Atlas-SNP	.											.	HTRA1	40	.	0			c.C753T						PASS	.	C		126,4280	92.5+/-131.2	2,122,2079	118.0	90.0	100.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	753	-3.4	0.3	10	dbSNP_123	100	431,8169	132.5+/-190.1	12,407,3881	no	coding-synonymous	HTRA1	NM_002775.4		14,529,5960	TT,TC,CC		5.0116,2.8597,4.2826		251/481	124249118	557,12449	2203	4300	6503	SO:0001819	synonymous_variant	5654	exon3			AGACATCGCACTC	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.753C>T	10.37:g.124249118C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_002775	D3DRE4|Q9UNS5	Silent	SNP	ENST00000368984.3	37	CCDS7630.1																																																																																			C|0.966;T|0.034	0.034	strong		0.527	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775	
ALPK1	80216	hgsc.bcm.edu	37	4	113345147	113345147	+	Missense_Mutation	SNP	A	A	G	rs6533616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:113345147A>G	ENST00000458497.1	+	6	802	c.523A>G	c.(523-525)Aat>Gat	p.N175D	ALPK1_ENST00000177648.9_Missense_Mutation_p.N175D|ALPK1_ENST00000504176.2_Missense_Mutation_p.N97D	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	100	0	0		WXS	Illumina HiSeq	Phase_I	52	12	0.230769	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	
HKDC1	80201	hgsc.bcm.edu	37	10	71010375	71010375	+	Silent	SNP	C	C	T	rs5030948	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:71010375C>T	ENST00000354624.5	+	12	1936	c.1803C>T	c.(1801-1803)ttC>ttT	p.F601F	HKDC1_ENST00000395086.2_Silent_p.F601F	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	601	Glucose-binding. {ECO:0000255}.|Hexokinase type-1 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						GCTTCACATTCTCATTTCCCT	0.557													C|||	689	0.13758	0.0136	0.1945	5008	,	,		19179	0.0794		0.2674	False		,,,				2504	0.1912				p.F601F		Atlas-SNP	.											HKDC1,NS,carcinoma,+1,1	HKDC1	98	1	0			c.C1803T						scavenged	.	C		226,4180	136.5+/-172.5	7,212,1984	109.0	110.0	109.0		1803	4.1	1.0	10	dbSNP_113	109	2080,6520	360.0+/-331.8	237,1606,2457	no	coding-synonymous	HKDC1	NM_025130.3		244,1818,4441	TT,TC,CC		24.186,5.1294,17.7303		601/918	71010375	2306,10700	2203	4300	6503	SO:0001819	synonymous_variant	80201	exon12			CACATTCTCATTT		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.1803C>T	10.37:g.71010375C>T		Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	37	24	0.648649	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Silent	SNP	ENST00000354624.5	37	CCDS7288.1																																																																																			C|0.835;T|0.165	0.165	strong		0.557	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
CRACR2A	84766	hgsc.bcm.edu	37	12	3788188	3788188	+	Silent	SNP	C	C	T	rs3803135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:3788188C>T	ENST00000252322.1	-	6	885	c.417G>A	c.(415-417)aaG>aaA	p.K139K	EFCAB4B_ENST00000440314.2_Silent_p.K139K|EFCAB4B_ENST00000444507.1_Silent_p.K139K	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		139					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			ACAGATACACCTTCTCTTCAT	0.557													C|||	776	0.154952	0.1324	0.2262	5008	,	,		20581	0.128		0.1113	False		,,,				2504	0.2076				p.K139K		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.G417A						PASS	.	C	,	590,3816	259.5+/-263.1	48,494,1661	188.0	152.0	164.0		417,417	2.7	1.0	12	dbSNP_107	164	966,7634	210.7+/-251.5	53,860,3387	no	coding-synonymous,coding-synonymous	EFCAB4B	NM_001144958.1,NM_032680.3	,	101,1354,5048	TT,TC,CC		11.2326,13.3908,11.9637	,	139/732,139/396	3788188	1556,11450	2203	4300	6503	SO:0001819	synonymous_variant	84766	exon6			ATACACCTTCTCT																												ENST00000252322.1:c.417G>A	12.37:g.3788188C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	162	77	0.475309	NM_001144958	B4E1X0|B9EK63	Silent	SNP	ENST00000252322.1	37	CCDS8522.1																																																																																			C|0.862;T|0.138	0.138	strong		0.557	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
MUC17	140453	hgsc.bcm.edu	37	7	100678481	100678481	+	Missense_Mutation	SNP	A	A	T	rs73168389	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678481A>T	ENST00000306151.4	+	3	3848	c.3784A>T	c.(3784-3786)Acc>Tcc	p.T1262S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1262	59 X approximate tandem repeats.|Ser-rich.				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)					CTCTCCTACAACCGCTGAAGG	0.527																																					p.T1262S		Atlas-SNP	.											.	MUC17	804	.	0			c.A3784T						PASS	.	T	SER/THR	586,3820		0,586,1617	284.0	275.0	278.0		3784	-0.9	0.0	7	dbSNP_130	278	392,8208		0,392,3908	no	missense	MUC17	NM_001040105.1	58	0,978,5525	TT,TA,AA		4.5581,13.3,7.5196	probably-damaging	1262/4494	100678481	978,12028	2203	4300	6503	SO:0001583	missense	140453	exon3			CCTACAACCGCTG	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.3784A>T	7.37:g.100678481A>T	ENSP00000302716:p.Thr1262Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	300	89	0.296667	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.067	-1.210490	0.01555	0.133	0.045581	ENSG00000169876	ENST00000306151	T	0.02323	4.34	0.438	-0.877	0.10621	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.09310	N	1	D	0.55385	0.971	B	0.42188	0.379	T	0.20538	-1.0272	8	0.06494	T	0.89	.	.	.	.	.	1262	Q685J3	MUC17_HUMAN	S	1262	ENSP00000302716:T1262S	ENSP00000302716:T1262S	T	+	1	0	MUC17	100465201	0.001000	0.12720	0.002000	0.10522	0.004000	0.04260	-1.637000	0.02015	-1.145000	0.02858	-1.640000	0.00773	ACC	A|0.973;T|0.027	0.027	strong		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
RNF213	57674	hgsc.bcm.edu	37	17	78263486	78263486	+	Missense_Mutation	SNP	T	T	C	rs17853989	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78263486T>C	ENST00000582970.1	+	6	1105	c.962T>C	c.(961-963)aTg>aCg	p.M321T	RNF213_ENST00000319921.4_Missense_Mutation_p.M321T|RNF213_ENST00000456466.1_Missense_Mutation_p.M321T|RNF213_ENST00000508628.2_Missense_Mutation_p.M370T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	321				M -> T (in Ref. 4; AAH36891/AAH40341). {ECO:0000305}.	ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.M321T(1)|p.M370T(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AAGGACGAGATGGCTGCTGCT	0.473													t|||	1101	0.219848	0.4531	0.1268	5008	,	,		16968	0.0665		0.165	False		,,,				2504	0.1851				p.M321T		Atlas-SNP	.											RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	2	Substitution - Missense(2)	stomach(2)	c.T962C						PASS	.	T	THR/MET,THR/MET	1746,2660	517.3+/-369.4	354,1038,811	60.0	66.0	64.0		1109,962	-8.7	0.0	17	dbSNP_123	64	1624,6976	299.3+/-304.4	153,1318,2829	yes	missense,missense	RNF213	NM_020914.4,NM_020954.2	81,81	507,2356,3640	CC,CT,TT		18.8837,39.6278,25.9111	benign,benign	370/5257,321/1064	78263486	3370,9636	2203	4300	6503	SO:0001583	missense	57674	exon6			ACGAGATGGCTGC	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.962T>C	17.37:g.78263486T>C	ENSP00000464087:p.Met321Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	433	0.19826007326007325	213	0.4329268292682927	45	0.12430939226519337	37	0.06468531468531469	138	0.1820580474934037	t	4.375	0.069242	0.08436	0.396278	0.188837	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.39229	1.09;1.09	4.4	-8.69	0.00855	.	615.921000	0.00166	N	0.000012	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	0.14117	-1.0484	9	0.06891	T	0.86	-2.4186	4.0565	0.09819	0.3513:0.2506:0.0:0.3981	rs17853989;rs17857133	321;321	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	T	321;370;321;321	ENSP00000392123:M321T;ENSP00000324392:M321T	ENSP00000324392:M321T	M	+	2	0	RNF213	75878081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.421000	0.02455	-2.102000	0.00845	-2.512000	0.00187	ATG	T|0.759;C|0.241	0.241	strong		0.473	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
COL10A1	1300	hgsc.bcm.edu	37	6	116446576	116446576	+	Missense_Mutation	SNP	A	A	G	rs1064583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:116446576A>G	ENST00000327673.4	-	1	487	c.80T>C	c.(79-81)aTg>aCg	p.M27T	COL10A1_ENST00000243222.4_Missense_Mutation_p.M27T|NT5DC1_ENST00000319550.4_Intron			Q03692	COAA1_HUMAN	collagen, type X, alpha 1	27	Nonhelical region (NC2).		M -> T (in dbSNP:rs1064583). {ECO:0000269|PubMed:15880705, ECO:0000269|PubMed:1764025}.		cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	cell cortex (GO:0005938)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|lung(6)|skin(3)|upper_aerodigestive_tract(1)	13		all_cancers(87;0.0176)|all_epithelial(87;0.0263)|Colorectal(196;0.234)		all cancers(137;0.0157)|OV - Ovarian serous cystadenocarcinoma(136;0.0325)|GBM - Glioblastoma multiforme(226;0.0446)|Epithelial(106;0.0711)		GCCTGTGGGCATTTGGTATCG	0.398													G|||	2231	0.445487	0.736	0.3329	5008	,	,		16919	0.2579		0.3956	False		,,,				2504	0.3773				p.M27T		Atlas-SNP	.											.	COL10A1	51	.	0			c.T80C						PASS	.	G	,THR/MET	3084,1322	444.5+/-347.4	1096,892,215	261.0	243.0	249.0		,80	6.1	0.9	6	dbSNP_86	249	3384,5216	641.0+/-399.6	645,2094,1561	yes	intron,missense	COL10A1,NT5DC1	NM_152729.2,NM_000493.3	,81	1741,2986,1776	GG,GA,AA		39.3488,30.0045,49.7309	,benign	,27/681	116446576	6468,6538	2203	4300	6503	SO:0001583	missense	1300	exon2			GTGGGCATTTGGT		CCDS5105.1	6q21-q22	2013-01-16	2008-07-29		ENSG00000123500	ENSG00000123500		"""Collagens"""	2185	protein-coding gene	gene with protein product	"""Schmid metaphyseal chondrodysplasia"""	120110				2037056	Standard	XM_006715332		Approved		uc003pwm.3	Q03692	OTTHUMG00000015426	ENST00000327673.4:c.80T>C	6.37:g.116446576A>G	ENSP00000327368:p.Met27Thr	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	244	243	0.995902	NM_000493	A1L4P2	Missense_Mutation	SNP	ENST00000327673.4	37	CCDS5105.1	924	0.4230769230769231	346	0.7032520325203252	135	0.3729281767955801	144	0.2517482517482518	299	0.3944591029023747	G	0.013	-1.633148	0.00806	0.699955	0.393488	ENSG00000123500	ENST00000243222;ENST00000327673;ENST00000452729;ENST00000418500	D;D;D;T	0.89552	-2.53;-2.53;-2.51;-0.36	6.06	6.06	0.98353	.	0.435749	0.22816	N	0.055291	T	0.45276	0.1334	N	0.00268	-1.735	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38650	-0.9651	9	0.26408	T	0.33	.	8.6061	0.33773	0.076:0.0:0.7387:0.1853	rs1064583;rs52830706;rs59696986;rs1064583	27	Q03692	COAA1_HUMAN	T	27	ENSP00000243222:M27T;ENSP00000327368:M27T;ENSP00000411285:M27T;ENSP00000392712:M27T	ENSP00000243222:M27T	M	-	2	0	COL10A1	116553269	0.995000	0.38212	0.876000	0.34364	0.004000	0.04260	2.657000	0.46724	1.593000	0.50029	-0.119000	0.15052	ATG	A|0.536;G|0.464	0.464	strong		0.398	COL10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041926.1		
FLG	2312	hgsc.bcm.edu	37	1	152281007	152281007	+	Missense_Mutation	SNP	A	A	G	rs7512553	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152281007A>G	ENST00000368799.1	-	3	6390	c.6355T>C	c.(6355-6357)Tat>Cat	p.Y2119H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2119	Ser-rich.		Y -> H (in dbSNP:rs7512553).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCTGATCATAATGGGATCCT	0.572									Ichthyosis				-|||	1641	0.327676	0.3843	0.3357	5008	,	,		29956	0.4355		0.1282	False		,,,				2504	0.3395				p.Y2119H		Atlas-SNP	.											FLG,brain,glioma,+2,1	FLG	900	1	0			c.T6355C						scavenged	.	G	HIS/TYR	1451,2955		0,1451,752	349.0	263.0	292.0		6355	1.3	0.0	1	dbSNP_116	292	1089,7511		0,1089,3211	yes	missense	FLG	NM_002016.1	83	0,2540,3963	GG,GA,AA		12.6628,32.9324,19.5294	benign	2119/4062	152281007	2540,10466	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATCATAATGGGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6355T>C	1.37:g.152281007A>G	ENSP00000357789:p.Tyr2119His	Somatic	383	2	0.00522193		WXS	Illumina HiSeq	Phase_I	750	204	0.272	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	4.212	0.038141	0.08148	0.329324	0.126628	ENSG00000143631	ENST00000368799	T	0.02345	4.33	3.26	1.28	0.21552	.	.	.	.	.	T	0.00178	0.0005	N	0.00049	-2.42	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30707	-0.9969	9	0.14656	T	0.56	.	3.5172	0.07728	0.2299:0.0:0.5769:0.1931	.	2119	P20930	FILA_HUMAN	H	2119	ENSP00000357789:Y2119H	ENSP00000357789:Y2119H	Y	-	1	0	FLG	150547631	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.121000	0.15667	-0.057000	0.13199	-3.035000	0.00072	TAT	A|0.030;G|0.970	0.970	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CCL23	6368	hgsc.bcm.edu	37	17	34340284	34340284	+	Missense_Mutation	SNP	C	C	T	rs1003645	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	125	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	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	
QRSL1	55278	hgsc.bcm.edu	37	6	107113715	107113715	+	Silent	SNP	G	G	A	rs2015205	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	180	177	0.983333	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	
FCHO2	115548	hgsc.bcm.edu	37	5	72348272	72348272	+	Missense_Mutation	SNP	A	A	G	rs185435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:72348272A>G	ENST00000430046.2	+	13	1227	c.1111A>G	c.(1111-1113)Atg>Gtg	p.M371V	FCHO2_ENST00000341845.6_Missense_Mutation_p.M371V|FCHO2_ENST00000512348.1_Missense_Mutation_p.M338V	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2	371			M -> V (in dbSNP:rs185435).		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)		ACATCACACAATGGCTTCTTT	0.353													a|||	1303	0.260184	0.4637	0.1686	5008	,	,		16879	0.1696		0.1332	False		,,,				2504	0.274				p.M371V		Atlas-SNP	.											.	FCHO2	96	.	0			c.A1111G						PASS	.	G	VAL/MET,VAL/MET	1515,2181		319,877,652	83.0	79.0	81.0		1012,1111	-1.4	1.0	5	dbSNP_79	81	1208,6984		96,1016,2984	yes	missense,missense	FCHO2	NM_001146032.1,NM_138782.2	21,21	415,1893,3636	GG,GA,AA		14.7461,40.9903,22.9055	benign,benign	338/778,371/811	72348272	2723,9165	1848	4096	5944	SO:0001583	missense	115548	exon13			CACACAATGGCTT	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.1111A>G	5.37:g.72348272A>G	ENSP00000393776:p.Met371Val	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	214	213	0.995327	NM_138782	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	ENST00000430046.2	37	CCDS47230.1	475	0.2174908424908425	214	0.4349593495934959	78	0.2154696132596685	91	0.1590909090909091	92	0.12137203166226913	a	7.694	0.691582	0.15039	0.409903	0.147461	ENSG00000157107	ENST00000430046;ENST00000341845;ENST00000512348	T;T;T	0.16597	2.33;2.33;2.33	5.47	-1.4	0.08968	.	0.579933	0.19150	N	0.121462	T	0.00012	0.0000	L	0.34521	1.04	0.44652	P	0.0023680000000000367	B;B	0.16396	0.002;0.017	B;B	0.12156	0.004;0.007	T	0.48115	-0.9063	9	0.33141	T	0.24	-1.5884	6.281	0.21007	0.6173:0.1201:0.2627:0.0	rs185435;rs517724;rs60622989;rs185435	338;371	E9PG79;Q0JRZ9	.;FCHO2_HUMAN	V	371;371;338	ENSP00000393776:M371V;ENSP00000344034:M371V;ENSP00000427296:M338V	ENSP00000344034:M371V	M	+	1	0	FCHO2	72384028	0.117000	0.22190	0.970000	0.41538	0.885000	0.51271	0.401000	0.20948	-0.486000	0.06744	-0.266000	0.10368	ATG	A|0.768;G|0.232	0.232	strong		0.353	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368795.3	XM_291142	
MROH7	374977	hgsc.bcm.edu	37	1	55166842	55166842	+	Silent	SNP	C	C	T	rs1065173	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:55166842C>T	ENST00000421030.2	+	19	3417	c.3132C>T	c.(3130-3132)ccC>ccT	p.P1044P	MROH7-TTC4_ENST00000414150.2_Silent_p.P1044P|MROH7_ENST00000454855.2_Silent_p.P562P|MROH7_ENST00000409996.1_Silent_p.P612P	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	1044						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.P1044P(2)|p.P1041P(1)									CCCTCCTGCCCTCCATGGTGA	0.587													C|||	1252	0.25	0.264	0.2248	5008	,	,		20949	0.1141		0.3191	False		,,,				2504	0.318				p.P1044P		Atlas-SNP	.											HEATR8_ENST00000421030,NS,carcinoma,0,2	.	.	2	3	Substitution - coding silent(3)	prostate(3)	c.C3132T						PASS	.	C		1058,3036		132,794,1121	66.0	70.0	69.0		3132	-1.7	1.0	1	dbSNP_86	69	2549,5863		376,1797,2033	no	coding-synonymous	HEATR8	NM_001039464.2		508,2591,3154	TT,TC,CC		30.3019,25.8427,28.8422		1044/1324	55166842	3607,8899	2047	4206	6253	SO:0001819	synonymous_variant	374977	exon19			CCTGCCCTCCATG	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.3132C>T	1.37:g.55166842C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	91	26	0.285714	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	37	CCDS41342.2																																																																																			C|0.744;T|0.256	0.256	strong		0.587	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
AP1B1	162	hgsc.bcm.edu	37	22	29755888	29755888	+	Silent	SNP	T	T	C	rs2072051	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:29755888T>C	ENST00000405198.1	-	3	235	c.204A>G	c.(202-204)ctA>ctG	p.L68L	AP1B1_ENST00000356015.2_Silent_p.L68L|AP1B1_ENST00000402502.1_Silent_p.L68L|AP1B1_ENST00000432560.2_Silent_p.L68L|AP1B1_ENST00000357586.2_Silent_p.L68L|AP1B1_ENST00000317368.7_Silent_p.L68L|AP1B1_ENST00000415447.1_Silent_p.L68L			Q10567	AP1B1_HUMAN	adaptor-related protein complex 1, beta 1 subunit	68					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|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)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						AGAGGTATACTAGCTTCTTCA	0.527											OREG0026449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3350	0.66893	0.8782	0.4481	5008	,	,		21958	0.7252		0.5726	False		,,,				2504	0.5838				p.L68L		Atlas-SNP	.											.	AP1B1	72	.	0			c.A204G						PASS	.	C	,,	3653,753	308.8+/-290.8	1512,629,62	137.0	116.0	123.0		204,204,204	2.8	1.0	22	dbSNP_96	123	4702,3898	545.4+/-384.8	1306,2090,904	no	coding-synonymous,coding-synonymous,coding-synonymous	AP1B1	NM_001127.3,NM_001166019.1,NM_145730.2	,,	2818,2719,966	CC,CT,TT		45.3256,17.0903,35.7604	,,	68/950,68/920,68/940	29755888	8355,4651	2203	4300	6503	SO:0001819	synonymous_variant	162	exon4			GTATACTAGCTTC	L13939	CCDS13855.1, CCDS13856.1, CCDS13856.2, CCDS54515.1	22q12.2	2010-06-18			ENSG00000100280	ENSG00000100280			554	protein-coding gene	gene with protein product		600157		ADTB1, CLAPB2		7987321, 8812422	Standard	NM_145730		Approved	BAM22, AP105A	uc003afj.3	Q10567	OTTHUMG00000151109	ENST00000405198.1:c.204A>G	22.37:g.29755888T>C		Somatic	158	0	0	812	WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_001127	C9JRD1|F8WDL0|P78436|Q20WL3|Q86X54	Silent	SNP	ENST00000405198.1	37	CCDS13855.1																																																																																			T|0.337;C|0.663	0.663	strong		0.527	AP1B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321374.1	NM_001127	
CPS1	1373	hgsc.bcm.edu	37	2	211456639	211456639	+	Silent	SNP	C	C	T	rs386654705|rs2229589	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:211456639C>T	ENST00000233072.5	+	10	1228	c.1032C>T	c.(1030-1032)acC>acT	p.T344T	CPS1_ENST00000430249.2_Silent_p.T350T|CPS1_ENST00000451903.2_5'Flank	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	344	Glutamine amidotransferase type-1.		T -> A (in dbSNP:rs1047883). {ECO:0000269|PubMed:12853138, ECO:0000269|PubMed:9711878, ECO:0000269|Ref.11}.|T -> S (in dbSNP:rs1047883).		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)	TGGACAACACCCTCCCTGCTG	0.433													C|||	2961	0.591254	0.6679	0.4914	5008	,	,		16517	0.5585		0.5646	False		,,,				2504	0.6196				p.T350T		Atlas-SNP	.											.	CPS1	485	.	0			c.C1050T						PASS	.	C	,	2891,1515	671.6+/-402.5	962,967,274	83.0	77.0	79.0		1050,1032	3.0	1.0	2	dbSNP_98	79	4881,3719	617.7+/-396.7	1361,2159,780	no	coding-synonymous,coding-synonymous	CPS1	NM_001122633.2,NM_001875.4	,	2323,3126,1054	TT,TC,CC		43.2442,34.3849,40.243	,	350/1507,344/1501	211456639	7772,5234	2203	4300	6503	SO:0001819	synonymous_variant	1373	exon11			CAACACCCTCCCT	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.1032C>T	2.37:g.211456639C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	70	21	0.3	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	37	CCDS2393.1																																																																																			C|0.408;T|0.592	0.592	strong		0.433	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
ANKRD61	100310846	hgsc.bcm.edu	37	7	6071060	6071060	+	Silent	SNP	G	G	A	rs4724769	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	162	0	0		WXS	Illumina HiSeq	Phase_I	200	132	0.66	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		
USH2A	7399	hgsc.bcm.edu	37	1	215901492	215901492	+	Silent	SNP	C	C	T	rs2820718	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:215901492C>T	ENST00000307340.3	-	61	12332	c.11946G>A	c.(11944-11946)ctG>ctA	p.L3982L	USH2A_ENST00000366943.2_Silent_p.L3982L	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3982	Fibronectin type-III 25. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		TCCAATTCAACAGAACTGAAT	0.493										HNSCC(13;0.011)			C|||	595	0.11881	0.1687	0.0965	5008	,	,		17267	0.003		0.1879	False		,,,				2504	0.1155				p.L3982L		Atlas-SNP	.											.	USH2A	1168	.	0			c.G11946A						PASS	.	C		755,3651	308.6+/-290.6	75,605,1523	112.0	108.0	110.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11946	3.6	0.5	1	dbSNP_100	110	1587,7013	296.9+/-303.1	138,1311,2851	no	coding-synonymous	USH2A	NM_206933.2		213,1916,4374	TT,TC,CC		18.4535,17.1357,18.0071		3982/5203	215901492	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon61			ATTCAACAGAACT	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.11946G>A	1.37:g.215901492C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	269	182	0.67658	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			C|0.836;T|0.164	0.164	strong		0.493	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
STXBP2	6813	hgsc.bcm.edu	37	19	7712050	7712050	+	Silent	SNP	C	C	T	rs146425381	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:7712050C>T	ENST00000221283.5	+	17	1486	c.1455C>T	c.(1453-1455)gaC>gaT	p.D485D	STXBP2_ENST00000441779.2_Silent_p.D496D|STXBP2_ENST00000602355.1_Silent_p.D20D|STXBP2_ENST00000414284.2_Silent_p.D482D	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	485					leukocyte mediated cytotoxicity (GO:0001909)|neutrophil degranulation (GO:0043312)|protein transport (GO:0015031)|regulation of mast cell degranulation (GO:0043304)|vesicle docking involved in exocytosis (GO:0006904)	azurophil granule (GO:0042582)|cytolytic granule (GO:0044194)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin-3 binding (GO:0030348)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	23						GCCGCCAGGACGCCGTGGAGG	0.721													C|||	3	0.000599042	0.0	0.0014	5008	,	,		13459	0.0		0.002	False		,,,				2504	0.0				p.D496D		Atlas-SNP	.											.	STXBP2	63	.	0			c.C1488T						PASS	.	C	,	0,4384		0,0,2192	22.0	28.0	26.0		1446,1455	-3.5	0.5	19	dbSNP_134	26	14,8528		0,14,4257	no	coding-synonymous,coding-synonymous	STXBP2	NM_001127396.1,NM_006949.2	,	0,14,6449	TT,TC,CC		0.1639,0.0,0.1083	,	482/591,485/594	7712050	14,12912	2192	4271	6463	SO:0001819	synonymous_variant	6813	exon17			CCAGGACGCCGTG	U63533	CCDS12181.1, CCDS45948.1, CCDS62522.1	19p13.3-p13.2	2014-09-17				ENSG00000076944			11445	protein-coding gene	gene with protein product		601717				8921365	Standard	NM_001127396		Approved	UNC18B, Hunc18b	uc010xjr.3	Q15833		ENST00000221283.5:c.1455C>T	19.37:g.7712050C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	50	15	0.3	NM_001272034	B4E175|E7EQD5|Q9BU65	Silent	SNP	ENST00000221283.5	37	CCDS12181.1																																																																																			C|0.999;T|0.001	0.001	strong		0.721	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949	
LRIG3	121227	hgsc.bcm.edu	37	12	59313248	59313248	+	Intron	SNP	G	G	A	rs12426969	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:59313248G>A	ENST00000320743.3	-	1	523				RP11-150C16.1_ENST00000547590.1_RNA|LRIG3_ENST00000379141.4_Silent_p.L6L	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3						otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			GAGAACAACAGAAGTACGTCC	0.478			T	ROS1	NSCLC								A|||	404	0.0806709	0.0424	0.1686	5008	,	,		18317	0.0446		0.0994	False		,,,				2504	0.0879				p.L6L		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	.	LRIG3	120	.	0			c.C16T						PASS	.						68.0	56.0	60.0					12																	59313248		692	1591	2283	SO:0001627	intron_variant	121227	exon1			ACAACAGAAGTAC	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.236+532C>T	12.37:g.59313248G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_001136051	Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																			G|0.903;A|0.097	0.097	strong		0.478	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377	
SLITRK3	22865	hgsc.bcm.edu	37	3	164906800	164906800	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:164906800G>T	ENST00000475390.1	-	2	2262	c.1819C>A	c.(1819-1821)Ctg>Atg	p.L607M	SLITRK3_ENST00000241274.3_Missense_Mutation_p.L607M			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	607	LRRCT 2.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						AGAACTTCCAGCTCAATAGTG	0.542										HNSCC(40;0.11)																											p.L607M		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C1819A						PASS	.						61.0	57.0	58.0					3																	164906800		2203	4300	6503	SO:0001583	missense	22865	exon2			CTTCCAGCTCAAT	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.1819C>A	3.37:g.164906800G>T	ENSP00000420091:p.Leu607Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	87	15	0.172414	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	6.538	0.467489	0.12402	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.54675	0.56;0.56	5.76	4.8	0.61643	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.30185	N	0.010219	T	0.32133	0.0819	N	0.10809	0.05	0.33093	D	0.538255	B	0.12013	0.005	B	0.11329	0.006	T	0.36890	-0.9729	10	0.45353	T	0.12	-9.1664	9.2667	0.37645	0.0785:0.0:0.7817:0.1398	.	607	O94933	SLIK3_HUMAN	M	607	ENSP00000420091:L607M;ENSP00000241274:L607M	ENSP00000241274:L607M	L	-	1	2	SLITRK3	166389494	0.021000	0.18746	0.997000	0.53966	0.879000	0.50718	0.452000	0.21795	1.403000	0.46800	0.655000	0.94253	CTG	.	.	none		0.542	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
MUC4	4585	hgsc.bcm.edu	37	3	195515305	195515305	+	Missense_Mutation	SNP	G	G	A	rs13077555		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195515305G>A	ENST00000463781.3	-	2	3605	c.3146C>T	c.(3145-3147)gCa>gTa	p.A1049V	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1049V	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)			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)		ACCTGTGGATGCTGAGGAAAA	0.562																																					p.A1049V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,2	MUC4	1505	2	0			c.C3146T						scavenged	.						12.0	10.0	11.0					3																	195515305		680	1573	2253	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.3146C>T	3.37:g.195515305G>A	ENSP00000417498:p.Ala1049Val	Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	172	10	0.0581395	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	.	.	.	.	.	.	.	.	.	.	-	5.046	0.194076	0.09599	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.49;1.48	0.577	-1.15	0.09709	.	.	.	.	.	T	0.14570	0.0352	N	0.19112	0.55	0.09310	N	1	B	0.17667	0.023	B	0.11329	0.006	T	0.22452	-1.0216	8	.	.	.	.	2.1781	0.03867	0.4294:0.0:0.329:0.2415	.	1049	E7ESK3	.	V	1049	ENSP00000417498:A1049V;ENSP00000420243:A1049V	.	A	-	2	0	MUC4	196999700	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.259000	0.18405	-2.557000	0.00476	-2.092000	0.00371	GCA	G|0.750;T|0.250	.	alt		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RSPH6A	81492	hgsc.bcm.edu	37	19	46318312	46318312	+	Silent	SNP	C	C	T	rs45598433	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46318312C>T	ENST00000221538.3	-	1	265	c.123G>A	c.(121-123)gaG>gaA	p.E41E	SYMPK_ENST00000598155.1_5'Flank|RSPH6A_ENST00000597055.1_Silent_p.E41E	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	41						intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						GCTGCCTCTCCTCGGGGTCCG	0.677													C|||	22	0.00439297	0.0008	0.0058	5008	,	,		14993	0.0		0.0129	False		,,,				2504	0.0041				p.E41E		Atlas-SNP	.											.	RSPH6A	70	.	0			c.G123A						PASS	.	C		14,4392	20.2+/-43.8	0,14,2189	40.0	41.0	40.0		123	1.7	0.0	19	dbSNP_127	40	188,8412	80.4+/-143.0	1,186,4113	no	coding-synonymous	RSPH6A	NM_030785.3		1,200,6302	TT,TC,CC		2.186,0.3177,1.5531		41/718	46318312	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	81492	exon1			CCTCTCCTCGGGG	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"""radial spokehead-like 1"""	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.123G>A	19.37:g.46318312C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_030785	Q53FE2|Q6PEZ9	Silent	SNP	ENST00000221538.3	37	CCDS12675.1																																																																																			C|0.987;T|0.013	0.013	strong		0.677	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1		
KLHL17	339451	hgsc.bcm.edu	37	1	899824	899824	+	Silent	SNP	C	C	T	rs201807567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:899824C>T	ENST00000338591.3	+	11	1721	c.1614C>T	c.(1612-1614)aaC>aaT	p.N538N	PLEKHN1_ENST00000379410.3_5'Flank|PLEKHN1_ENST00000379407.3_5'Flank|PLEKHN1_ENST00000379409.2_5'Flank	NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	538	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CAGGGGGCAACGACGGCACCA	0.667													C|||	11	0.00219649	0.0	0.0014	5008	,	,		10445	0.001		0.006	False		,,,				2504	0.0031				p.N538N		Atlas-SNP	.											.	KLHL17	31	.	0			c.C1614T						PASS	.	C		1,4119		0,1,2059	15.0	16.0	16.0		1614	-2.8	1.0	1		16	27,8173		0,27,4073	no	coding-synonymous	KLHL17	NM_198317.2		0,28,6132	TT,TC,CC		0.3293,0.0243,0.2273		538/643	899824	28,12292	2060	4100	6160	SO:0001819	synonymous_variant	339451	exon11			GGGCAACGACGGC	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"""Kelch-like"", ""BTB/POZ domain containing"""	24023	protein-coding gene	gene with protein product	"""actinfilin"""		"""kelch-like 17 (Drosophila)"""			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1614C>T	1.37:g.899824C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	48	38	0.791667	NM_198317	Q5SV94	Silent	SNP	ENST00000338591.3	37	CCDS30550.1																																																																																			C|0.996;T|0.004	0.004	strong		0.667	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317	
RGPD3	653489	hgsc.bcm.edu	37	2	107040572	107040572	+	Missense_Mutation	SNP	T	T	C	rs3870235		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:107040572T>C	ENST00000409886.3	-	20	3938	c.3851A>G	c.(3850-3852)cAc>cGc	p.H1284R	RGPD3_ENST00000304514.7_Missense_Mutation_p.H1284R	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1284					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						CTCATCAAAGTGGAAAAGATT	0.403																																					p.H1284R		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,4	RGPD3	316	4	0			c.A3851G						scavenged	.						183.0	135.0	149.0					2																	107040572		659	1516	2175	SO:0001583	missense	653489	exon20			TCAAAGTGGAAAA		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.3851A>G	2.37:g.107040572T>C	ENSP00000386588:p.His1284Arg	Somatic	1233	2	0.00162206		WXS	Illumina HiSeq	Phase_I	162	151	0.932099	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.926314	0.00054	.	.	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.34859	1.34;1.34	2.35	2.35	0.29111	.	.	.	.	.	T	0.10723	0.0262	N	0.00926	-1.1	0.45261	P	0.0017359999999999598	B	0.02656	0.0	B	0.01281	0.0	T	0.30937	-0.9961	8	0.10636	T	0.68	-3.2817	7.1563	0.25639	0.0:0.8506:0.0:0.1494	.	1284	A6NKT7	RGPD3_HUMAN	R	1284	ENSP00000386588:H1284R;ENSP00000303659:H1284R	ENSP00000303659:H1284R	H	-	2	0	RGPD3	106407004	1.000000	0.71417	0.999000	0.59377	0.042000	0.13812	4.693000	0.61753	0.328000	0.23435	-1.128000	0.01989	CAC	.	.	weak		0.403	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
ME3	10873	hgsc.bcm.edu	37	11	86153911	86153911	+	Silent	SNP	G	G	A	rs7548	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:86153911G>A	ENST00000393324.3	-	13	1858	c.1605C>T	c.(1603-1605)taC>taT	p.Y535Y	RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000359636.2_Silent_p.Y535Y|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						scavenged	.	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	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	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		
TK1	7083	hgsc.bcm.edu	37	17	76178748	76178748	+	Silent	SNP	T	T	C	rs1143697	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76178748T>C	ENST00000301634.7	-	4	463	c.225A>G	c.(223-225)gcA>gcG	p.A75A	TK1_ENST00000590862.1_Silent_p.A75A|TK1_ENST00000590430.1_Intron|TK1_ENST00000588734.1_Silent_p.A75A|TK1_ENST00000405273.1_Silent_p.A75A	NM_003258.4	NP_003249.3	P04183	KITH_HUMAN	thymidine kinase 1, soluble	75					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|digestive tract development (GO:0048565)|DNA replication (GO:0006260)|fetal process involved in parturition (GO:0060138)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to copper ion (GO:0046688)|response to cortisol (GO:0051414)|response to nutrient levels (GO:0031667)|response to toxic substance (GO:0009636)|skeletal muscle cell proliferation (GO:0014856)|small molecule metabolic process (GO:0044281)|thymidine metabolic process (GO:0046104)	cytosol (GO:0005829)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|nucleoside kinase activity (GO:0019206)|thymidine kinase activity (GO:0004797)|zinc ion binding (GO:0008270)	p.A75A(1)		endometrium(1)|large_intestine(1)|urinary_tract(2)	4			BRCA - Breast invasive adenocarcinoma(99;0.00269)|OV - Ovarian serous cystadenocarcinoma(97;0.0804)|Lung(188;0.23)		Trifluridine(DB00432)|Zidovudine(DB00495)	AGGCGGGCAGTGCCTCCATGG	0.632													C|||	3416	0.682109	0.8707	0.6686	5008	,	,		14475	0.622		0.4523	False		,,,				2504	0.7352				p.A75A		Atlas-SNP	.											TK1_ENST00000301634,NS,carcinoma,0,1	TK1	23	1	1	Substitution - coding silent(1)	stomach(1)	c.A225G						PASS	.	C		3616,782		1501,614,84	44.0	30.0	35.0		225	-11.0	0.1	17	dbSNP_86	35	3810,4784		851,2108,1338	no	coding-synonymous	TK1	NM_003258.4		2352,2722,1422	CC,CT,TT		44.3333,17.7808,42.8417		75/235	76178748	7426,5566	2199	4297	6496	SO:0001819	synonymous_variant	7083	exon4			GGGCAGTGCCTCC		CCDS11754.1	17q23.2-q25.3	2012-10-02			ENSG00000167900	ENSG00000167900	2.7.1.21		11830	protein-coding gene	gene with protein product		188300					Standard	NM_003258		Approved		uc002juw.2	P04183	OTTHUMG00000150674	ENST00000301634.7:c.225A>G	17.37:g.76178748T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_003258	B2RC58|Q969V0|Q9UMG9	Silent	SNP	ENST00000301634.7	37	CCDS11754.1																																																																																			T|0.400;G|0.007	.	strong		0.632	TK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319577.1	NM_003258	
EP300	2033	hgsc.bcm.edu	37	22	41546158	41546158	+	Missense_Mutation	SNP	C	C	A	rs148884710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:41546158C>A	ENST00000263253.7	+	14	3992	c.2773C>A	c.(2773-2775)Cct>Act	p.P925T		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	925					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)	p.P925T(1)		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						AGCGTCTGTTCCTACCCCAAC	0.522			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				C|||	8	0.00159744	0.0	0.0014	5008	,	,		20472	0.0		0.007	False		,,,				2504	0.0				p.P925T		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	EP300,NS,lymphoid_neoplasm,0,1	EP300	367	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2773A						PASS	.	C	THR/PRO	10,4394	16.8+/-37.8	0,10,2192	64.0	48.0	53.0		2773	3.8	0.9	22	dbSNP_134	53	55,8545	35.3+/-89.8	3,49,4248	yes	missense	EP300	NM_001429.3	38	3,59,6440	AA,AC,CC		0.6395,0.2271,0.4998	benign	925/2415	41546158	65,12939	2202	4300	6502	SO:0001583	missense	2033	exon14	Familial Cancer Database	Broad Thumb-Hallux syndrome	TCTGTTCCTACCC	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.2773C>A	22.37:g.41546158C>A	ENSP00000263253:p.Pro925Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	13.29	2.193769	0.38707	0.002271	0.006395	ENSG00000100393	ENST00000263253	D	0.83992	-1.79	5.92	3.85	0.44370	.	0.135740	0.33401	N	0.004949	T	0.68183	0.2973	L	0.47716	1.5	0.35741	D	0.818666	B	0.13594	0.008	B	0.16722	0.016	T	0.67608	-0.5627	10	0.22706	T	0.39	-8.5427	8.0505	0.30575	0.0:0.7318:0.1307:0.1375	.	925	Q09472	EP300_HUMAN	T	925	ENSP00000263253:P925T	ENSP00000263253:P925T	P	+	1	0	EP300	39876104	0.960000	0.32886	0.934000	0.37439	0.957000	0.61999	1.349000	0.33998	0.859000	0.35456	-0.373000	0.07131	CCT	C|0.995;A|0.005	0.005	strong		0.522	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
PCDHA13	56136	hgsc.bcm.edu	37	5	140262492	140262492	+	Silent	SNP	A	A	T	rs11744560	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140262492A>T	ENST00000289272.2	+	1	639	c.639A>T	c.(637-639)acA>acT	p.T213T	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA13_ENST00000409494.1_Silent_p.T213T|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	213	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(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TATTACTGACAGCCAGTGATG	0.453													.|||	405	0.0808706	0.0809	0.1239	5008	,	,		21202	0.0179		0.1421	False		,,,				2504	0.0521				p.T213T	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.A639T						PASS	.	A	,,,,,,,,,,,,,,,,	394,4012	197.1+/-221.3	12,370,1821	59.0	61.0	60.0		,,,,639,,,,,,,,,,,,639	0.2	0.8	5	dbSNP_120	60	1320,7280	260.1+/-283.0	91,1138,3071	no	intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	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_031865.1	,,,,,,,,,,,,,,,,	103,1508,4892	TT,TA,AA		15.3488,8.9424,13.1785	,,,,,,,,,,,,,,,,	,,,,213/951,,,,,,,,,,,,213/808	140262492	1714,11292	2203	4300	6503	SO:0001819	synonymous_variant	56136	exon1			ACTGACAGCCAGT	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"""Cadherins / Protocadherins : Clustered"""	8667	other	complex locus constituent	"""KIAA0345-like 1"", ""ortholog of mouse CNR5"""	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.639A>T	5.37:g.140262492A>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_031865	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																			A|0.877;T|0.123	0.123	strong		0.453	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	
MEP1B	4225	hgsc.bcm.edu	37	18	29788107	29788107	+	Silent	SNP	G	G	A	rs4799640	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:29788107G>A	ENST00000269202.6	+	9	839	c.792G>A	c.(790-792)tcG>tcA	p.S264S	MEP1B_ENST00000581447.1_Silent_p.S264S	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	264	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TTATGGACTCGTGCAGTTTTG	0.408													G|||	1154	0.230431	0.2814	0.1902	5008	,	,		19138	0.126		0.2207	False		,,,				2504	0.3078				p.S264S		Atlas-SNP	.											.	MEP1B	54	.	0			c.G792A						PASS	.	G		1006,2760		141,724,1018	220.0	213.0	215.0		792	-10.8	0.3	18	dbSNP_111	215	2010,6240		255,1500,2370	no	coding-synonymous	MEP1B	NM_005925.2		396,2224,3388	AA,AG,GG		24.3636,26.7127,25.0999		264/702	29788107	3016,9000	1883	4125	6008	SO:0001819	synonymous_variant	4225	exon9			GGACTCGTGCAGT	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.792G>A	18.37:g.29788107G>A		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	222	89	0.400901	NM_005925	B7ZM35|B9EGL6|Q670J1	Silent	SNP	ENST00000269202.6	37	CCDS45846.1																																																																																			G|0.778;A|0.222	0.222	strong		0.408	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
SLAIN1	122060	hgsc.bcm.edu	37	13	78320801	78320801	+	Missense_Mutation	SNP	C	C	G	rs144139933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:78320801C>G	ENST00000466548.1	+	5	1029	c.1003C>G	c.(1003-1005)Cct>Gct	p.P335A	SLAIN1_ENST00000488699.1_Missense_Mutation_p.P193A|SLAIN1_ENST00000465831.1_3'UTR|SLAIN1_ENST00000358679.3_Missense_Mutation_p.P72A|SLAIN1_ENST00000314070.5_Intron|SLAIN1_ENST00000267219.8_Missense_Mutation_p.P116A|SLAIN1_ENST00000418532.1_Missense_Mutation_p.P116A|SLAIN1_ENST00000351546.3_Missense_Mutation_p.P72A	NM_001242868.1	NP_001229797.1	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1	335										breast(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0853)		TTTGCCACCACCTCAGCCTCG	0.468													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19409	0.0		0.005	False		,,,				2504	0.0				p.P357A		Atlas-SNP	.											.	SLAIN1	43	.	0			c.C1069G						PASS	.	C	ALA/PRO,ALA/PRO,,,ALA/PRO,ALA/PRO	2,4404	4.2+/-10.8	0,2,2201	158.0	150.0	153.0		577,1069,,,211,214	5.9	1.0	13	dbSNP_134	153	21,8579	16.6+/-54.9	0,21,4279	yes	missense,missense,intron,intron,missense,missense	SLAIN1	NM_001040153.3,NM_001242868.1,NM_001242869.1,NM_001242870.1,NM_001242871.1,NM_144595.3	27,27,,,27,27	0,23,6480	GG,GC,CC		0.2442,0.0454,0.1768	probably-damaging,probably-damaging,,,probably-damaging,probably-damaging	193/427,357/591,,,71/305,72/306	78320801	23,12983	2203	4300	6503	SO:0001583	missense	122060	exon4			CCACCACCTCAGC	AK054608	CCDS9460.1, CCDS31995.1, CCDS31995.2, CCDS55901.1, CCDS73588.1, CCDS73589.1	13q22.3	2006-09-12	2006-09-12	2006-09-12	ENSG00000139737	ENSG00000139737			26387	protein-coding gene	gene with protein product		610491	"""chromosome 13 open reading frame 32"""	C13orf32		16546155	Standard	NM_001040153		Approved	FLJ30046	uc001vkk.3	Q8ND83	OTTHUMG00000017110	ENST00000466548.1:c.1003C>G	13.37:g.78320801C>G	ENSP00000419730:p.Pro335Ala	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	181	95	0.524862	NM_001242868	A8K0Z9|B7Z209|Q5T6P4|Q5T6P7|Q8ND10|Q96NV0	Missense_Mutation	SNP	ENST00000466548.1	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	20.3	3.960845	0.74016	4.54E-4	0.002442	ENSG00000139737	ENST00000466548;ENST00000389459;ENST00000418532;ENST00000442759;ENST00000446759;ENST00000488699;ENST00000267219;ENST00000351546;ENST00000441784;ENST00000462234;ENST00000496045;ENST00000474663;ENST00000358679	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.73489	0.3593	M	0.69823	2.125	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.71414	0.973;0.973;0.96	T	0.74697	-0.3578	8	.	.	.	-15.4977	20.3325	0.98724	0.0:1.0:0.0:0.0	.	71;193;335	B7Z326;B7Z209;Q8ND83	.;.;SLAI1_HUMAN	A	335;335;116;116;166;193;116;72;72;72;72;72;72	.	.	P	+	1	0	SLAIN1	77218802	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.733000	0.68571	2.805000	0.96524	0.655000	0.94253	CCT	C|0.999;G|0.001	0.001	strong		0.468	SLAIN1-009	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000355018.1	NM_144595	
ATRNL1	26033	hgsc.bcm.edu	37	10	117486763	117486763	+	Silent	SNP	G	G	T	rs2254619	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	41	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	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	
PYCRL	65263	hgsc.bcm.edu	37	8	144689146	144689146	+	Missense_Mutation	SNP	C	C	T	rs2242089	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144689146C>T	ENST00000220966.6	-	3	378	c.349G>A	c.(349-351)Gtg>Atg	p.V117M	PYCRL_ENST00000377579.3_De_novo_Start_InFrame|PYCRL_ENST00000495276.1_5'UTR	NM_023078.3	NP_075566.2	Q53H96	P5CR3_HUMAN	pyrroline-5-carboxylate reductase-like	105					L-proline biosynthetic process (GO:0055129)		pyrroline-5-carboxylate reductase activity (GO:0004735)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	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;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		L-Proline(DB00172)	CTCAGAGACACCCCAGCAGCC	0.627													C|||	1231	0.245807	0.1808	0.2233	5008	,	,		19504	0.371		0.2008	False		,,,				2504	0.2669				p.V117M		Atlas-SNP	.											PYCRL,NS,carcinoma,0,1	PYCRL	14	1	0			c.G349A	GRCh37	CM067455	PYCRL	M	rs2242089	PASS	.	C	MET/VAL	821,3585	323.7+/-298.2	76,669,1458	76.0	72.0	73.0		349	2.0	0.3	8	dbSNP_98	73	1565,7035	293.2+/-301.3	156,1253,2891	yes	missense	PYCRL	NM_023078.3	21	232,1922,4349	TT,TC,CC		18.1977,18.6337,18.3454	probably-damaging	117/287	144689146	2386,10620	2203	4300	6503	SO:0001583	missense	65263	exon3			GAGACACCCCAGC	AF086378	CCDS6407.2	8q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000104524	ENSG00000104524			25846	protein-coding gene	gene with protein product							Standard	NM_023078		Approved	FLJ13852	uc003yyy.3	Q53H96	OTTHUMG00000157010	ENST00000220966.6:c.349G>A	8.37:g.144689146C>T	ENSP00000220966:p.Val117Met	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	253	72	0.284585	NM_023078	B3KMB5|B4DVT6|H0Y6C3|Q8N3N9|Q96HX4|Q9H896	Missense_Mutation	SNP	ENST00000220966.6	37	CCDS6407.2	526	0.24084249084249085	89	0.18089430894308944	62	0.1712707182320442	222	0.3881118881118881	153	0.20184696569920843	C	15.51	2.855574	0.51376	0.186337	0.181977	ENSG00000104524	ENST00000220966;ENST00000433751	T;T	0.65732	-0.17;-0.17	4.82	2.0	0.26442	NAD(P)-binding domain (1);	0.273444	0.36200	N	0.002732	T	0.00012	0.0000	M	0.88906	2.99	0.09310	P	0.9999999999965832	D;D	0.67145	0.996;0.995	P;P	0.61201	0.83;0.885	T	0.12967	-1.0527	9	0.72032	D	0.01	-23.9758	7.7118	0.28682	0.0:0.7091:0.0:0.2909	rs2242089;rs11549788;rs60863986;rs2242089	117;105	D3DWK4;Q53H96	.;P5CR3_HUMAN	M	117;112	ENSP00000220966:V117M;ENSP00000404493:V112M	ENSP00000220966:V117M	V	-	1	0	PYCRL	144760289	0.313000	0.24554	0.347000	0.25668	0.682000	0.39822	0.873000	0.28052	0.101000	0.17610	0.448000	0.29417	GTG	C|0.785;T|0.215	0.215	strong		0.627	PYCRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347081.2	NM_023078	
REXO4	57109	hgsc.bcm.edu	37	9	136277482	136277482	+	Missense_Mutation	SNP	T	T	C	rs2285487	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136277482T>C	ENST00000371942.3	-	4	1046	c.847A>G	c.(847-849)Act>Gct	p.T283A	REXO4_ENST00000371935.2_Intron|REXO4_ENST00000478037.1_5'UTR	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	138	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	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		
MDN1	23195	hgsc.bcm.edu	37	6	90368380	90368380	+	Silent	SNP	G	G	A	rs34732313	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	261	0	0		WXS	Illumina HiSeq	Phase_I	213	96	0.450704	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		
PLB1	151056	hgsc.bcm.edu	37	2	28761981	28761981	+	Missense_Mutation	SNP	G	G	C	rs6753929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:28761981G>C	ENST00000327757.5	+	11	678	c.634G>C	c.(634-636)Gta>Cta	p.V212L	PLB1_ENST00000422425.2_Missense_Mutation_p.V223L	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	212	4 X 308-326 AA approximate repeats.		V -> L (in dbSNP:rs6753929).		glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					CAGAGCATTTGTAAACCTGGT	0.557													G|||	999	0.199481	0.0923	0.304	5008	,	,		19379	0.2232		0.2425	False		,,,				2504	0.2014				p.V223L		Atlas-SNP	.											.	PLB1	255	.	0			c.G667C						PASS	.	G	LEU/VAL,LEU/VAL	591,3815	259.2+/-262.9	47,497,1659	129.0	105.0	113.0		667,634	5.7	1.0	2	dbSNP_116	113	2244,6356	380.3+/-339.6	280,1684,2336	yes	missense,missense	PLB1	NM_001170585.1,NM_153021.4	32,32	327,2181,3995	CC,CG,GG		26.093,13.4135,21.7976	probably-damaging,probably-damaging	223/1448,212/1459	28761981	2835,10171	2203	4300	6503	SO:0001583	missense	151056	exon11			GCATTTGTAAACC		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.634G>C	2.37:g.28761981G>C	ENSP00000330442:p.Val212Leu	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	205	106	0.517073	NM_001170585	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	CCDS33168.1	463|463	0.211996336996337|0.211996336996337	52|52	0.10569105691056911|0.10569105691056911	113|113	0.31215469613259667|0.31215469613259667	114|114	0.1993006993006993|0.1993006993006993	184|184	0.24274406332453827|0.24274406332453827	G|G	19.90|19.90	3.912156|3.912156	0.72983|0.72983	0.134135|0.134135	0.26093|0.26093	ENSG00000163803|ENSG00000163803	ENST00000404858|ENST00000416713;ENST00000327757;ENST00000422425	.|T;T;T	.|0.41400	.|1.0;2.21;2.01	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.075093	.|0.52532	.|D	.|0.000077	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.90145|0.90145	3.09|3.09	0.09310|0.09310	P|P	1.0|1.0	.|D;D	.|0.89917	.|1.0;0.995	.|D;D	.|0.87578	.|0.998;0.957	T|T	0.02313|0.02313	-1.1178|-1.1178	4|9	.|0.56958	.|D	.|0.05	-23.1992|-23.1992	15.3191|15.3191	0.74105|0.74105	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs6753929;rs52831699;rs59816904;rs6753929|rs6753929;rs52831699;rs59816904;rs6753929	.|223;212	.|Q6P1J6-3;Q6P1J6	.|.;PLB1_HUMAN	F|L	221|167;212;223	.|ENSP00000407076:V167L;ENSP00000330442:V212L;ENSP00000416440:V223L	.|ENSP00000330442:V212L	L|V	+|+	3|1	2|0	PLB1|PLB1	28615485|28615485	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.596000|0.596000	0.36781|0.36781	3.117000|3.117000	0.50407|0.50407	2.688000|2.688000	0.91661|0.91661	0.591000|0.591000	0.81541|0.81541	TTG|GTA	A|0.000;C|0.213;G|0.787	0.213	strong		0.557	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
MUC16	94025	hgsc.bcm.edu	37	19	9066580	9066580	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9066580T>C	ENST00000397910.4	-	3	21069	c.20866A>G	c.(20866-20868)Acc>Gcc	p.T6956A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6958	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						GAAATGCTGGTCTCTCTCAGT	0.448																																					p.T6956A		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+2,3	MUC16	4315	3	0			c.A20866G						scavenged	.						152.0	147.0	149.0					19																	9066580		1939	4148	6087	SO:0001583	missense	94025	exon3			TGCTGGTCTCTCT	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.20866A>G	19.37:g.9066580T>C	ENSP00000381008:p.Thr6956Ala	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	197	4	0.0203046	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	3.869	-0.028217	0.07589	.	.	ENSG00000181143	ENST00000397910	T	0.02301	4.35	2.77	-2.73	0.05950	.	.	.	.	.	T	0.02571	0.0078	L	0.46157	1.445	.	.	.	B	0.23540	0.087	B	0.31614	0.133	T	0.42999	-0.9418	8	0.87932	D	0	.	3.3322	0.07088	0.5457:0.1287:0.0:0.3256	.	6956	B5ME49	.	A	6956	ENSP00000381008:T6956A	ENSP00000381008:T6956A	T	-	1	0	MUC16	8927580	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.024000	0.03603	-0.773000	0.04596	-0.876000	0.02978	ACC	.	.	none		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
AMPH	273	hgsc.bcm.edu	37	7	38431415	38431415	+	Silent	SNP	C	C	T	rs55969455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:38431415C>T	ENST00000356264.2	-	19	2027	c.1812G>A	c.(1810-1812)ggG>ggA	p.G604G	AMPH_ENST00000325590.5_Silent_p.G562G|AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000428293.2_Silent_p.G562G	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	604					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GGTCAGCAGCCCCCATGGCTG	0.567													C|||	28	0.00559105	0.0	0.0072	5008	,	,		15344	0.0		0.0219	False		,,,				2504	0.001				p.G604G		Atlas-SNP	.											.	AMPH	157	.	0			c.G1812A						PASS	.	C	,	20,4386	26.2+/-53.5	0,20,2183	52.0	51.0	51.0		1812,1686	-6.7	0.0	7	dbSNP_129	51	170,8430	76.9+/-139.5	0,170,4130	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	0,190,6313	TT,TC,CC		1.9767,0.4539,1.4609	,	604/696,562/654	38431415	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	273	exon19			AGCAGCCCCCATG		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1812G>A	7.37:g.38431415C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	156	101	0.647436	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	37	CCDS5456.1	22	0.010073260073260074	0	0.0	4	0.011049723756906077	0	0.0	18	0.023746701846965697	C	2.923	-0.222811	0.06061	0.004539	0.019767	ENSG00000078053	ENST00000441628	T	0.31769	1.48	3.51	-6.71	0.01760	.	0.915112	0.09049	N	0.856102	T	0.04452	0.0122	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.29731	-1.0002	7	0.11182	T	0.66	-2.7575	3.3029	0.06989	0.3659:0.2867:0.0:0.3473	rs55969455	.	.	.	S	487	ENSP00000415085:G487S	ENSP00000415085:G487S	G	-	1	0	AMPH	38397940	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.401000	0.07232	-1.160000	0.02804	-2.069000	0.00389	GGC	C|0.987;T|0.013	0.013	strong		0.567	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
CFAP57	149465	hgsc.bcm.edu	37	1	43664218	43664218	+	Silent	SNP	C	C	T	rs603123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	151	0	0		WXS	Illumina HiSeq	Phase_I	85	83	0.976471	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		
PGM2L1	283209	hgsc.bcm.edu	37	11	74109166	74109166	+	Missense_Mutation	SNP	A	A	G	rs12049823	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:74109166A>G	ENST00000298198.4	-	1	352	c.41T>C	c.(40-42)cTc>cCc	p.L14P	MIR548AL_ENST00000578416.1_RNA|RP11-702H23.4_ENST00000533008.1_RNA|RP11-702H23.4_ENST00000531906.1_RNA	NM_173582.3	NP_775853.2	Q6PCE3	PGM2L_HUMAN	phosphoglucomutase 2-like 1	14			L -> P (in dbSNP:rs12049823). {ECO:0000269|PubMed:15489334}.		glucose metabolic process (GO:0006006)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	glucose-1,6-bisphosphate synthase activity (GO:0047933)|intramolecular transferase activity, phosphotransferases (GO:0016868)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(11;3.32e-06)					GGGGGCGTGGAGCAGGTTGGA	0.672													A|||	941	0.187899	0.112	0.1311	5008	,	,		13499	0.2669		0.161	False		,,,				2504	0.2771				p.L14P		Atlas-SNP	.											PGM2L1,NS,carcinoma,0,1	PGM2L1	59	1	0			c.T41C						PASS	.	A	PRO/LEU	514,3886	234.6+/-247.4	28,458,1714	124.0	113.0	117.0		41	3.7	1.0	11	dbSNP_120	117	1284,7302	253.9+/-279.4	102,1080,3111	yes	missense	PGM2L1	NM_173582.3	98	130,1538,4825	GG,GA,AA		14.9546,11.6818,13.8457	benign	14/623	74109166	1798,11188	2200	4293	6493	SO:0001583	missense	283209	exon1			GCGTGGAGCAGGT	AB019210	CCDS8231.1	11q13.3	2008-12-01			ENSG00000165434	ENSG00000165434			20898	protein-coding gene	gene with protein product	"""glucose-1,6-bisphosphate synthase"""	611610				17804405	Standard	NM_173582		Approved	FLJ32029, BM32A	uc001ovb.1	Q6PCE3	OTTHUMG00000168132	ENST00000298198.4:c.41T>C	11.37:g.74109166A>G	ENSP00000298198:p.Leu14Pro	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_173582	Q96MQ7|Q9UIK3	Missense_Mutation	SNP	ENST00000298198.4	37	CCDS8231.1	395	0.18086080586080586	57	0.11585365853658537	46	0.1270718232044199	163	0.28496503496503495	129	0.17018469656992086	A	13.57	2.275855	0.40294	0.116818	0.149546	ENSG00000165434	ENST00000298198	T	0.18174	2.23	4.87	3.72	0.42706	.	0.431607	0.21265	N	0.077402	T	0.00012	0.0000	L	0.52573	1.65	0.19575	P	0.9999695974	B	0.02656	0.0	B	0.01281	0.0	T	0.28138	-1.0053	9	0.62326	D	0.03	-5.4947	5.7867	0.18336	0.8788:0.0:0.1212:0.0	rs12049823;rs17854987;rs61002785;rs12049823	14	Q6PCE3	PGM2L_HUMAN	P	14	ENSP00000298198:L14P	ENSP00000298198:L14P	L	-	2	0	PGM2L1	73786814	1.000000	0.71417	1.000000	0.80357	0.729000	0.41735	1.992000	0.40737	2.037000	0.60232	0.379000	0.24179	CTC	A|0.843;G|0.157	0.157	strong		0.672	PGM2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398324.1	NM_173582	
MTUS1	57509	hgsc.bcm.edu	37	8	17612518	17612518	+	Missense_Mutation	SNP	A	A	G	rs61733696	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17612518A>G	ENST00000262102.6	-	2	1023	c.799T>C	c.(799-801)Tct>Cct	p.S267P	MTUS1_ENST00000381862.3_Missense_Mutation_p.S267P|MTUS1_ENST00000381869.3_Missense_Mutation_p.S267P|MTUS1_ENST00000519263.1_Missense_Mutation_p.S267P	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	267					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)		TTTCCTGAAGAACATGCACAC	0.428													A|||	159	0.0317492	0.0	0.0144	5008	,	,		21815	0.0714		0.0288	False		,,,				2504	0.0491				p.S267P		Atlas-SNP	.											.	MTUS1	144	.	0			c.T799C						PASS	.	A	PRO/SER,PRO/SER	28,3874		0,28,1923	213.0	195.0	201.0		799,799	4.3	0.9	8	dbSNP_129	201	290,8006		4,282,3862	yes	missense,missense	MTUS1	NM_001001924.2,NM_001001925.2	74,74	4,310,5785	GG,GA,AA		3.4957,0.7176,2.607	probably-damaging,probably-damaging	267/1271,267/1217	17612518	318,11880	1951	4148	6099	SO:0001583	missense	57509	exon2			CTGAAGAACATGC	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.799T>C	8.37:g.17612518A>G	ENSP00000262102:p.Ser267Pro	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	89	61	0.685393	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	60	0.027472527472527472	0	0.0	10	0.027624309392265192	26	0.045454545454545456	24	0.0316622691292876	A	12.91	2.078409	0.36662	0.007176	0.034957	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.30182	2.45;2.5;2.45;1.54	4.29	4.29	0.51040	.	0.100277	0.43260	D	0.000582	T	0.09379	0.0231	L	0.32530	0.975	0.33123	D	0.541998	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.996;0.996	T	0.35895	-0.9770	10	0.87932	D	0	-13.4164	10.1107	0.42561	1.0:0.0:0.0:0.0	rs61733696	267;267;267	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	P	267	ENSP00000371293:S267P;ENSP00000262102:S267P;ENSP00000430167:S267P;ENSP00000371286:S267P	ENSP00000262102:S267P	S	-	1	0	MTUS1	17656798	0.024000	0.19004	0.900000	0.35374	0.186000	0.23388	0.880000	0.28159	2.163000	0.67991	0.482000	0.46254	TCT	A|0.971;G|0.029	0.029	strong		0.428	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
MST1R	4486	hgsc.bcm.edu	37	3	49928866	49928866	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49928866C>T	ENST00000296474.3	-	16	3527	c.3500G>A	c.(3499-3501)gGt>gAt	p.G1167D	MST1R_ENST00000344206.4_Missense_Mutation_p.G1118D	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	1167	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GAGCAGGTCACCGTGGCACAT	0.607																																					p.G1167D		Atlas-SNP	.											MST1R_ENST00000296474,NS,neuroblastoma,-1,2	MST1R	205	2	0			c.G3500A						scavenged	.						83.0	74.0	77.0					3																	49928866		2203	4300	6503	SO:0001583	missense	4486	exon16			AGGTCACCGTGGC	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.3500G>A	3.37:g.49928866C>T	ENSP00000296474:p.Gly1167Asp	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	204	4	0.0196078	NM_002447	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	37	CCDS2807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	29.1|29.1	4.980229|4.980229	0.92982|0.92982	.|.	.|.	ENSG00000164078|ENSG00000164078	ENST00000296474;ENST00000344206|ENST00000434765;ENST00000440292	D;D|.	0.89939|.	-2.59;-2.59|.	4.88|4.88	4.88|4.88	0.63580|0.63580	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);|.	0.193910|.	0.53938|.	D|.	0.000041|.	D|D	0.88310|0.88310	0.6402|0.6402	H|H	0.96970|0.96970	3.915|3.915	0.80722|0.80722	D|D	1|1	D|.	0.60575|.	0.988|.	P|.	0.55824|.	0.785|.	D|D	0.92237|0.92237	0.5797|0.5797	10|5	0.87932|.	D|.	0|.	-4.2361|-4.2361	18.407|18.407	0.90539|0.90539	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1167|.	Q04912|.	RON_HUMAN|.	D|M	1167;1118|145;188	ENSP00000296474:G1167D;ENSP00000341325:G1118D|.	ENSP00000296474:G1167D|.	G|V	-|-	2|1	0|0	MST1R|MST1R	49903870|49903870	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.979000|0.979000	0.70002|0.70002	7.540000|7.540000	0.82074|0.82074	2.587000|2.587000	0.87381|0.87381	0.632000|0.632000	0.83419|0.83419	GGT|GTG	.	.	none		0.607	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
OR10X1	128367	hgsc.bcm.edu	37	1	158549420	158549420	+	Silent	SNP	C	C	T	rs863361	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158549420C>T	ENST00000368150.1	-	1	269	c.270G>A	c.(268-270)acG>acA	p.T90T		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	90						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)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					CGATGGTCAGCGTATAGCAGG	0.493													T|||	2596	0.518371	0.6324	0.4164	5008	,	,		21121	0.5853		0.4732	False		,,,				2504	0.4141				p.T90T		Atlas-SNP	.											OR10X1,face,carcinoma,-2,1	OR10X1	96	1	0			c.G270A						scavenged	.	T		2726,1680	510.9+/-367.7	824,1078,301	106.0	100.0	102.0		270	-7.3	0.0	1	dbSNP_86	102	3829,4771	612.1+/-395.9	876,2077,1347	no	coding-synonymous	OR10X1	NM_001004477.1		1700,3155,1648	TT,TC,CC		44.5233,38.1298,49.6002		90/327	158549420	6555,6451	2203	4300	6503	SO:0001819	synonymous_variant	128367	exon1			GGTCAGCGTATAG	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.270G>A	1.37:g.158549420C>T		Somatic	154	2	0.012987		WXS	Illumina HiSeq	Phase_I	257	154	0.599222	NM_001004477	Q6IFR8	Silent	SNP	ENST00000368150.1	37	CCDS30900.1																																																																																			C|0.471;T|0.529	0.529	strong		0.493	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
CD300A	11314	hgsc.bcm.edu	37	17	72469958	72469958	+	Silent	SNP	A	A	G	rs1127737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:72469958A>G	ENST00000360141.3	+	2	612	c.324A>G	c.(322-324)ccA>ccG	p.P108P	CD300A_ENST00000361933.3_Intron|CD300A_ENST00000310828.5_Intron|CD300A_ENST00000577511.1_5'UTR|CD300A_ENST00000392625.3_Intron	NM_001256841.1|NM_007261.3	NP_001243770.1|NP_009192.2	Q9UGN4	CLM8_HUMAN	CD300a molecule	108	Ig-like V-type.				cell adhesion (GO:0007155)|immune system process (GO:0002376)|negative regulation of activation of JAK2 kinase activity (GO:1902569)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of eosinophil activation (GO:1902567)|negative regulation of eosinophil migration (GO:2000417)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell activation involved in immune response (GO:0033007)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of neutrophil activation (GO:1902564)|negative regulation of NK T cell activation (GO:0051134)|negative regulation of phagocytosis, engulfment (GO:0060101)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|regulation of T cell receptor signaling pathway (GO:0050856)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)|signaling receptor activity (GO:0038023)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(4)|urinary_tract(1)	16						TGGATACACCATGGCTCCGAG	0.567													a|||	3441	0.687101	0.9614	0.6657	5008	,	,		17609	0.7212		0.4483	False		,,,				2504	0.5419				p.P108P		Atlas-SNP	.											.	CD300A	40	.	0			c.A324G						PASS	.	G		3914,492	781.4+/-414.5	1743,428,32	122.0	132.0	128.0		324	-6.8	0.0	17	dbSNP_86	128	3721,4879	530.4+/-381.8	802,2117,1381	no	coding-synonymous	CD300A	NM_007261.2		2545,2545,1413	GG,GA,AA		43.2674,11.1666,41.2963		108/300	72469958	7635,5371	2203	4300	6503	SO:0001819	synonymous_variant	11314	exon2			TACACCATGGCTC	BC032352	CCDS32720.1, CCDS58590.1	17q25.2	2013-01-11	2006-03-28		ENSG00000167851	ENSG00000167851		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19319	protein-coding gene	gene with protein product		606790	"""CD300a antigen"""			9701027, 10746781	Standard	NM_007261		Approved	Irp60, CMRF35H, CMRF-35-H9, IRC1, IRC2, IGSF12	uc002jkv.4	Q9UGN4	OTTHUMG00000067612	ENST00000360141.3:c.324A>G	17.37:g.72469958A>G		Somatic	279	1	0.00358423		WXS	Illumina HiSeq	Phase_I	263	107	0.406844	NM_007261	A8MW96|O95100|Q9HD97|Q9P0F3|Q9UBK4|Q9UMS9|Q9UMT0	Silent	SNP	ENST00000360141.3	37	CCDS32720.1																																																																																			A|0.418;G|0.582	0.582	strong		0.567	CD300A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145091.1	NM_007261	
FAT4	79633	hgsc.bcm.edu	37	4	126241565	126241565	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:126241565C>T	ENST00000394329.3	+	1	4012	c.3999C>T	c.(3997-3999)ctC>ctT	p.L1333L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1333	Cadherin 13. {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.L1333L(4)		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						TTGGTGAACTCGTGTCCTCTG	0.358																																					p.L1333L		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	2	4	Substitution - coding silent(4)	lung(4)	c.C3999T						PASS	.						139.0	131.0	133.0					4																	126241565		1890	4108	5998	SO:0001819	synonymous_variant	79633	exon1			TGAACTCGTGTCC	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.3999C>T	4.37:g.126241565C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			.	.	none		0.358	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
PLAUR	5329	hgsc.bcm.edu	37	19	44153100	44153100	+	Missense_Mutation	SNP	A	A	G	rs4760	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44153100A>G	ENST00000340093.3	-	7	1179	c.950T>C	c.(949-951)cTc>cCc	p.L317P	PLAUR_ENST00000339082.3_Intron|PLAUR_ENST00000601723.1_Missense_Mutation_p.L268P|PLAUR_ENST00000221264.4_Missense_Mutation_p.L272P	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	317			L -> P (in dbSNP:rs4760). {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)			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)	GGTGATGGTGAGGCTGAGATG	0.602													A|||	343	0.0684904	0.0038	0.0821	5008	,	,		19100	0.0		0.1491	False		,,,				2504	0.1339				p.L317P		Atlas-SNP	.											.	PLAUR	71	.	0			c.T950C						PASS	.	A	,PRO/LEU,PRO/LEU	132,4274	95.7+/-134.4	3,126,2074	96.0	84.0	88.0		,815,950	2.9	0.1	19	dbSNP_52	88	1327,7273	259.1+/-282.5	91,1145,3064	yes	intron,missense,missense	PLAUR	NM_001005376.2,NM_001005377.2,NM_002659.3	,98,98	94,1271,5138	GG,GA,AA		15.4302,2.9959,11.2179	,probably-damaging,probably-damaging	,272/291,317/336	44153100	1459,11547	2203	4300	6503	SO:0001583	missense	5329	exon7			ATGGTGAGGCTGA		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.950T>C	19.37:g.44153100A>G	ENSP00000339328:p.Leu317Pro	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	148	68	0.459459	NM_002659	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	Missense_Mutation	SNP	ENST00000340093.3	37	CCDS12628.1	146	0.06684981684981685	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	119	0.15699208443271767	A	14.78	2.637424	0.47049	0.029959	0.154302	ENSG00000011422	ENST00000340093;ENST00000221264	T;T	0.13538	2.62;2.58	3.94	2.93	0.34026	.	0.809357	0.10433	N	0.675276	T	0.00109	0.0003	L	0.55481	1.735	0.37595	P	0.07964499999999997	D;D	0.64830	0.99;0.994	D;P	0.63192	0.912;0.84	T	0.10800	-1.0614	9	0.54805	T	0.06	-5.0102	5.7743	0.18271	0.8805:0.0:0.1195:0.0	rs4760;rs3199954;rs4760	272;317	Q03405-3;Q03405	.;UPAR_HUMAN	P	317;272	ENSP00000339328:L317P;ENSP00000221264:L272P	ENSP00000221264:L272P	L	-	2	0	PLAUR	48844940	0.632000	0.27172	0.117000	0.21633	0.262000	0.26303	2.117000	0.41939	0.881000	0.35993	0.260000	0.18958	CTC	A|0.908;G|0.092	0.092	strong		0.602	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463571.1	NM_002659	
SH3TC1	54436	hgsc.bcm.edu	37	4	8229140	8229140	+	Missense_Mutation	SNP	G	G	T	rs141562329	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:8229140G>T	ENST00000245105.3	+	12	1786	c.1719G>T	c.(1717-1719)agG>agT	p.R573S	SH3TC1_ENST00000514274.1_3'UTR|SH3TC1_ENST00000539824.1_Missense_Mutation_p.R497S	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	573										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCAGCAGGAGGCTCAAGCTGT	0.692													G|||	13	0.00259585	0.0	0.0	5008	,	,		15676	0.001		0.003	False		,,,				2504	0.0092				p.R573S	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.G1719T						PASS	.	G	SER/ARG	0,4340		0,0,2170	35.0	40.0	38.0		1719	2.4	0.8	4	dbSNP_134	38	18,8450		0,18,4216	yes	missense	SH3TC1	NM_018986.3	110	0,18,6386	TT,TG,GG		0.2126,0.0,0.1405	possibly-damaging	573/1337	8229140	18,12790	2170	4234	6404	SO:0001583	missense	54436	exon12			CAGGAGGCTCAAG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.1719G>T	4.37:g.8229140G>T	ENSP00000245105:p.Arg573Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.49	2.849206	0.51270	0.0	0.002126	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.79845	-1.31;-1.31	4.51	2.42	0.29668	Tetratricopeptide-like helical (1);	0.373920	0.30003	N	0.010654	T	0.79639	0.4480	L	0.49126	1.545	0.09310	N	1	P	0.48911	0.917	P	0.50314	0.637	T	0.71394	-0.4606	10	0.66056	D	0.02	-17.1056	10.2336	0.43268	0.2842:0.0:0.7158:0.0	.	573	Q8TE82	S3TC1_HUMAN	S	311;573;497;402	ENSP00000245105:R573S;ENSP00000441045:R497S	ENSP00000245105:R573S	R	+	3	2	SH3TC1	8280040	0.976000	0.34144	0.808000	0.32385	0.871000	0.50021	0.768000	0.26590	0.892000	0.36259	-0.254000	0.11334	AGG	G|0.999;T|0.001	0.001	strong		0.692	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
HLA-A	3105	hgsc.bcm.edu	37	6	29912348	29912348	+	Missense_Mutation	SNP	A	A	G	rs1137078	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29912348A>G	ENST00000396634.1	+	7	1308	c.967A>G	c.(967-969)Act>Gct	p.T323A	HLA-A_ENST00000376806.5_Missense_Mutation_p.T323A|HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.T323A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	323					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						AGCTGTGATCACTGGAGCTGT	0.592									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|||	1292	0.257987	0.3994	0.2305	5008	,	,		19059	0.1984		0.1769	False		,,,				2504	0.2311				p.T323A		Atlas-SNP	.											.	HLA-A	89	.	0			c.A967G						PASS	.						111.0	106.0	108.0					6																	29912348		1511	2709	4220	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTGATCACTGGAG	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.967A>G	6.37:g.29912348A>G	ENSP00000379873:p.Thr323Ala	Somatic	334	1	0.00299401		WXS	Illumina HiSeq	Phase_I	241	108	0.448133	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	527	0.2413003663003663	198	0.4024390243902439	87	0.24033149171270718	121	0.21153846153846154	121	0.15963060686015831	.	3.109	-0.183024	0.06340	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00648	6.02;5.99;6.02	3.09	-6.18	0.02085	.	0.889866	0.09141	U	0.842941	T	0.00241	0.0007	L	0.43701	1.375	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	0.06405	0.0;0.001;0.002;0.001;0.002	T	0.39231	-0.9624	9	0.87932	D	0	.	5.3051	0.15799	0.3194:0.2957:0.3849:0.0	rs1137078;rs2231112;rs3179280;rs9260189;rs17424431;rs17845173;rs17857981;rs41558515	202;323;323;323;323	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	A	323	ENSP00000379873:T323A;ENSP00000366002:T323A;ENSP00000366005:T323A	ENSP00000366002:T323A	T	+	1	0	HLA-A	30020327	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.200000	0.03029	-1.981000	0.00989	-1.713000	0.00713	ACT	A|0.761;G|0.239	0.239	strong		0.592	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
COPE	11316	hgsc.bcm.edu	37	19	19023853	19023853	+	Silent	SNP	T	T	C	rs3177137	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19023853T>C	ENST00000262812.4	-	2	177	c.129A>G	c.(127-129)ctA>ctG	p.L43L	COPE_ENST00000351079.4_Silent_p.L43L|COPE_ENST00000600932.1_Silent_p.L43L|AC002985.3_ENST00000596918.1_3'UTR|COPE_ENST00000598969.1_5'UTR|COPE_ENST00000349893.4_Silent_p.L43L	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	43					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CTGGGCTTGATAGCTGTGGGA	0.617													C|||	1753	0.35004	0.3222	0.5836	5008	,	,		18947	0.1925		0.4871	False		,,,				2504	0.2434				p.L43L		Atlas-SNP	.											COPE,NS,adenoma,0,1	COPE	26	1	0			c.A129G						PASS	.	C	,,	1594,2812	663.6+/-401.2	303,988,912	127.0	91.0	103.0		129,129,129	-9.8	0.0	19	dbSNP_105	103	4168,4432	585.7+/-391.9	997,2174,1129	no	coding-synonymous,coding-synonymous,coding-synonymous	COPE	NM_007263.3,NM_199442.1,NM_199444.1	,,	1300,3162,2041	CC,CT,TT		48.4651,36.1779,44.3026	,,	43/309,43/258,43/257	19023853	5762,7244	2203	4300	6503	SO:0001819	synonymous_variant	11316	exon2			GCTTGATAGCTGT	AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.129A>G	19.37:g.19023853T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Silent	SNP	ENST00000262812.4	37	CCDS12387.1																																																																																			T|0.586;C|0.414	0.414	strong		0.617	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263	
NDUFA2	4695	hgsc.bcm.edu	37	5	140026868	140026868	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140026868C>T	ENST00000252102.4	-	2	382	c.181G>A	c.(181-183)Gtg>Atg	p.V61M	IK_ENST00000417647.2_5'Flank|NDUFA2_ENST00000512088.1_Missense_Mutation_p.V61M|NDUFA2_ENST00000510680.1_5'UTR|MIR3655_ENST00000581765.1_RNA	NM_001185012.1|NM_002488.4	NP_001171941.1|NP_002479.1	O43678	NDUA2_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa	61					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)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(3)|large_intestine(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGGGCTGCACATCGGAGCAT	0.627																																					p.V61M		Atlas-SNP	.											NDUFA2,colon,carcinoma,+2,1	NDUFA2	13	1	0			c.G181A						scavenged	.						82.0	73.0	76.0					5																	140026868		2203	4300	6503	SO:0001583	missense	4695	exon2			GCTGCACATCGGA	AF047185	CCDS4234.1, CCDS54911.1	5q31.2	2011-07-04	2002-08-29		ENSG00000131495	ENSG00000131495		"""Mitochondrial respiratory chain complex / Complex I"""	7685	protein-coding gene	gene with protein product	"""complex I B8 subunit"""	602137	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 (8kD, B8)"""			9425316, 9763676	Standard	NM_002488		Approved	B8	uc003lgp.3	O43678	OTTHUMG00000129505	ENST00000252102.4:c.181G>A	5.37:g.140026868C>T	ENSP00000252102:p.Val61Met	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	150	3	0.02	NM_001185012	D6RJD6|Q6IAY8	Missense_Mutation	SNP	ENST00000252102.4	37	CCDS4234.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.997269	0.93167	.	.	ENSG00000131495	ENST00000252102;ENST00000512088	.	.	.	6.04	4.22	0.49857	Ribosomal protein/NADH dehydrogenase domain (2);Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75838	0.3904	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.72625	0.978	T	0.76887	-0.2793	8	0.48119	T	0.1	-6.8192	11.2839	0.49210	0.127:0.8067:0.0:0.0663	.	61	O43678	NDUA2_HUMAN	M	61	.	ENSP00000252102:V61M	V	-	1	0	NDUFA2	140007052	0.998000	0.40836	0.929000	0.37066	0.977000	0.68977	3.436000	0.52856	1.577000	0.49804	0.563000	0.77884	GTG	.	.	none		0.627	NDUFA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251679.2	NM_002488	
ASCC3	10973	hgsc.bcm.edu	37	6	101094554	101094554	+	Silent	SNP	A	A	G	rs239239	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:101094554A>G	ENST00000369162.2	-	22	3914	c.3570T>C	c.(3568-3570)ccT>ccC	p.P1190P		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1190	SEC63 1.				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)			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)		TCCTTGTGATAGGCTGAATGG	0.403													G|||	2861	0.571286	0.6006	0.6153	5008	,	,		17369	0.7302		0.5408	False		,,,				2504	0.3681				p.P1190P		Atlas-SNP	.											.	ASCC3	205	.	0			c.T3570C						PASS	.	G		2602,1804	530.4+/-372.9	766,1070,367	130.0	112.0	118.0		3570	2.6	1.0	6	dbSNP_79	118	4540,4060	558.4+/-387.2	1210,2120,970	no	coding-synonymous	ASCC3	NM_006828.2		1976,3190,1337	GG,GA,AA		47.2093,40.9442,45.0869		1190/2203	101094554	7142,5864	2203	4300	6503	SO:0001819	synonymous_variant	10973	exon22			TGTGATAGGCTGA	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.3570T>C	6.37:g.101094554A>G		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	199	72	0.361809	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	37	CCDS5046.1																																																																																			A|0.438;G|0.562	0.562	strong		0.403	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
PARP15	165631	hgsc.bcm.edu	37	3	122296638	122296638	+	Missense_Mutation	SNP	G	G	A	rs1875272	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122296638G>A	ENST00000464300.2	+	1	190	c.124G>A	c.(124-126)Gtg>Atg	p.V42M	PARP15_ENST00000483793.1_Missense_Mutation_p.V42M	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	42				V -> M (in Ref. 4; AAY64451). {ECO:0000305}.	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)		GGCGGGGAGCGTGCTGCCGGC	0.697													G|||	1182	0.236022	0.2564	0.33	5008	,	,		14132	0.247		0.2197	False		,,,				2504	0.1472				p.V42M		Atlas-SNP	.											PARP15_ENST00000464300,NS,carcinoma,0,1	PARP15	115	1	0			c.G124A						scavenged	.						27.0	30.0	29.0					3																	122296638		692	1591	2283	SO:0001583	missense	165631	exon1			GGGAGCGTGCTGC	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.124G>A	3.37:g.122296638G>A	ENSP00000417214:p.Val42Met	Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	554	0.25366300366300365	125	0.2540650406504065	105	0.2900552486187845	155	0.270979020979021	169	0.22295514511873352	G	10.71	1.427298	0.25726	.	.	ENSG00000173200	ENST00000464300;ENST00000483793	T;T	0.15139	2.62;2.45	2.55	0.535	0.17133	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.999999999950489E-6	P	0.39551	0.678	B	0.20577	0.03	T	0.47799	-0.9089	7	0.52906	T	0.07	.	4.5242	0.11973	0.1537:0.229:0.6174:0.0	rs1875272;rs1875272	42	C9J7L3	.	M	42	ENSP00000417214:V42M;ENSP00000417785:V42M	ENSP00000417214:V42M	V	+	1	0	PARP15	123779328	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.711000	0.05019	0.116000	0.18110	0.561000	0.74099	GTG	G|0.744;A|0.256	0.256	strong		0.697	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
CRACR2A	84766	hgsc.bcm.edu	37	12	3806147	3806147	+	Missense_Mutation	SNP	T	T	C	rs200051200|rs9788233	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:3806147T>C	ENST00000252322.1	-	4	487	c.19A>G	c.(19-21)Agg>Ggg	p.R7G	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.R7G|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.R7G	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		7			R -> G (in dbSNP:rs9788233).		activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			GAGACTACCCTCCCGTCAGGG	0.572													T|||	816	0.162939	0.1165	0.2277	5008	,	,		18703	0.1835		0.1143	False		,,,				2504	0.2086				p.R7G		Atlas-SNP	.											EFCAB4B_ENST00000444507,NS,carcinoma,+2,8	EFCAB4B	100	8	0			c.A19G						scavenged	.	T	GLY/ARG,GLY/ARG	488,3918		41,406,1756	20.0	19.0	19.0		19,19	1.9	0.0	12	dbSNP_119	19	798,7802		51,696,3553	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	125,125	92,1102,5309	CC,CT,TT		9.2791,11.0758,9.8877	benign,benign	7/732,7/396	3806147	1286,11720	2203	4300	6503	SO:0001583	missense	84766	exon4			CTACCCTCCCGTC																												ENST00000252322.1:c.19A>G	12.37:g.3806147T>C	ENSP00000252322:p.Arg7Gly	Somatic	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	322	0.14743589743589744	58	0.11788617886178862	78	0.2154696132596685	112	0.1958041958041958	74	0.09762532981530343	T	12.61	1.989014	0.35131	0.110758	0.092791	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.62788	-0.0;2.36;2.39	5.56	1.85	0.25348	.	0.486738	0.19351	N	0.116388	T	0.00039	0.0001	M	0.64997	1.995	0.80722	P	0.0	B;B;B	0.19331	0.035;0.034;0.035	B;B;B	0.22601	0.018;0.04;0.018	T	0.06285	-1.0835	9	0.56958	D	0.05	-0.6578	4.089	0.09960	0.0:0.1814:0.1785:0.6401	rs9788233;rs9788233	7;7;7	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	G	7	ENSP00000409382:R7G;ENSP00000412496:R7G;ENSP00000252322:R7G	ENSP00000252322:R7G	R	-	1	2	EFCAB4B	3676408	0.003000	0.15002	0.000000	0.03702	0.012000	0.07955	1.314000	0.33597	0.363000	0.24346	0.519000	0.50382	AGG	T|0.870;C|0.130	0.130	strong		0.572	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
GRIN3B	116444	hgsc.bcm.edu	37	19	1005531	1005531	+	Silent	SNP	G	G	C	rs12973948	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1005531G>C	ENST00000234389.3	+	3	2050	c.2031G>C	c.(2029-2031)ctG>ctC	p.L677L	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	677					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)	TCGAGGAGCTGTCGGGGATCC	0.697													g|||	1175	0.234625	0.1293	0.2291	5008	,	,		11122	0.1706		0.3738	False		,,,				2504	0.3037				p.L677L		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G2031C						PASS	.	G		733,3665		74,585,1540	22.0	22.0	22.0		2031	3.3	1.0	19	dbSNP_121	22	3190,5408		595,2000,1704	no	coding-synonymous	GRIN3B	NM_138690.1		669,2585,3244	CC,CG,GG		37.1017,16.6667,30.1862		677/1044	1005531	3923,9073	2199	4299	6498	SO:0001819	synonymous_variant	116444	exon3			GGAGCTGTCGGGG		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.2031G>C	19.37:g.1005531G>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			C|0.264;G|0.736;T|0.000	0.264	strong		0.697	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
MUC17	140453	hgsc.bcm.edu	37	7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	rs147173571		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678032T>C	ENST00000306151.4	+	3	3399	c.3335T>C	c.(3334-3336)cTg>cCg	p.L1112P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1112	59 X approximate tandem repeats.|Ser-rich.				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)					AGCACCAGGCTGGTGGTCAGT	0.512																																					p.L1112P		Atlas-SNP	.											.	MUC17	804	.	0			c.T3335C						PASS	.						494.0	394.0	428.0					7																	100678032		2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGGCTGGTGGT	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.3335T>C	7.37:g.100678032T>C	ENSP00000302716:p.Leu1112Pro	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	753	89	0.118194	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.149	-1.093913	0.01858	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.693	-0.391	0.12446	.	.	.	.	.	T	0.01320	0.0043	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48055	-0.9068	8	0.25751	T	0.34	.	.	.	.	.	1112	Q685J3	MUC17_HUMAN	P	1112	ENSP00000302716:L1112P	ENSP00000302716:L1112P	L	+	2	0	MUC17	100464752	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-6.070000	0.00082	-0.165000	0.10908	-1.364000	0.01208	CTG	.	.	weak		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MUC17	140453	hgsc.bcm.edu	37	7	100678442	100678442	+	Missense_Mutation	SNP	C	C	G	rs4729653	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678442C>G	ENST00000306151.4	+	3	3809	c.3745C>G	c.(3745-3747)Cct>Gct	p.P1249A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1249	59 X approximate tandem repeats.|Ser-rich.		P -> A (in dbSNP:rs4729653).		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)					CACCAGCACACCTGTGACCAC	0.493																																					p.P1249A		Atlas-SNP	.											.	MUC17	804	.	0			c.C3745G						PASS	.	G	ALA/PRO	422,3984	166.9+/-198.0	0,422,1781	293.0	286.0	288.0		3745	-1.5	0.0	7	dbSNP_111	288	264,8336	76.9+/-139.5	0,264,4036	no	missense	MUC17	NM_001040105.1	27	0,686,5817	GG,GC,CC		3.0698,9.5778,5.2745	benign	1249/4494	100678442	686,12320	2203	4300	6503	SO:0001583	missense	140453	exon3			AGCACACCTGTGA	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.3745C>G	7.37:g.100678442C>G	ENSP00000302716:p.Pro1249Ala	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	258	67	0.25969	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	374	0.17124542124542125	131	0.266260162601626	38	0.10497237569060773	131	0.229020979020979	74	0.09762532981530343	C	0.005	-2.127578	0.00342	0.095778	0.030698	ENSG00000169876	ENST00000306151	T	0.03124	4.04	0.74	-1.48	0.08745	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.46317	-0.9200	9	0.06757	T	0.87	.	1.083	0.01647	0.2005:0.2015:0.4007:0.1974	rs4729653;rs4729653	1249	Q685J3	MUC17_HUMAN	A	1249	ENSP00000302716:P1249A	ENSP00000302716:P1249A	P	+	1	0	MUC17	100465162	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-6.093000	0.00081	-3.113000	0.00241	-1.285000	0.01374	CCT	C|0.918;G|0.082	0.082	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
UGT2B4	7363	hgsc.bcm.edu	37	4	70346565	70346565	+	Missense_Mutation	SNP	A	A	T	rs13119049|rs67904882	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:70346565A>T	ENST00000305107.6	-	6	1420	c.1374T>A	c.(1372-1374)gaT>gaA	p.D458E	AC108078.1_ENST00000583573.1_RNA|UGT2B4_ENST00000381096.3_Missense_Mutation_p.D322E|UGT2B4_ENST00000512583.1_3'UTR|UGT2B4_ENST00000506580.1_5'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	458			D -> E (in dbSNP:rs13119049). {ECO:0000269|PubMed:10376768, ECO:0000269|Ref.7}.		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)	AGACTGCTCGATCAAGGGGCT	0.428													a|||	654	0.130591	0.1362	0.2205	5008	,	,		17820	0.0		0.2266	False		,,,				2504	0.0951				p.D458E		Atlas-SNP	.											.	UGT2B4	105	.	0			c.T1374A						PASS	.	A	GLU/ASP	628,3778		44,540,1619	112.0	113.0	112.0		1374	-3.8	0.0	4	dbSNP_121	112	2045,6555		261,1523,2516	no	missense	UGT2B4	NM_021139.2	45	305,2063,4135	TT,TA,AA		23.7791,14.2533,20.5521	possibly-damaging	458/529	70346565	2673,10333	2203	4300	6503	SO:0001583	missense	7363	exon6			TGCTCGATCAAGG	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.1374T>A	4.37:g.70346565A>T	ENSP00000305221:p.Asp458Glu	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Missense_Mutation	SNP	ENST00000305107.6	37	CCDS43234.1	257	0.11767399267399267	52	0.10569105691056911	71	0.19613259668508287	0	0.0	134	0.17678100263852242	A	13.26	2.184106	0.38609	0.142533	0.237791	ENSG00000156096	ENST00000305107;ENST00000381096	T;T	0.72282	-0.64;-0.64	2.11	-3.83	0.04269	.	0.000000	0.64402	U	0.000002	T	0.00039	0.0001	L	0.45352	1.415	0.58432	P	5.999999999950489E-6	B;B	0.33413	0.411;0.388	P;P	0.50162	0.633;0.513	T	0.50101	-0.8867	9	0.87932	D	0	.	11.9884	0.53161	0.1949:0.0:0.8051:0.0	rs13119049;rs52797972	322;458	A6NCP7;P06133	.;UD2B4_HUMAN	E	458;322	ENSP00000305221:D458E;ENSP00000370486:D322E	ENSP00000305221:D458E	D	-	3	2	UGT2B4	70381154	0.392000	0.25229	0.004000	0.12327	0.636000	0.38137	0.578000	0.23773	-1.145000	0.02858	0.254000	0.18369	GAT	A|0.853;T|0.147	0.147	strong		0.428	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
SSPO	23145	hgsc.bcm.edu	37	7	149518961	149518961	+	RNA	SNP	T	T	C	rs1008335	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149518961T>C	ENST00000378016.2	+	0	12765							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)			TGCCTGAGGCTTGGACGCTGT	0.667													C|||	2318	0.462859	0.7481	0.3833	5008	,	,		17849	0.4256		0.3091	False		,,,				2504	0.3303				p.A4255A		Atlas-SNP	.											.	.	.	.	0			c.T12765C						PASS	.	C		2831,1417		970,891,263	15.0	18.0	17.0		12779	2.1	0.8	7	dbSNP_86	17	2794,5670		476,1842,1914	yes	coding-notMod3	SSPO	NM_198455.2		1446,2733,2177	CC,CT,TT		33.0104,33.3569,44.2495			149518961	5625,7087	2124	4232	6356			23145	exon90			TGAGGCTTGGACG	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.149518961T>C		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	174	40	0.229885	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				T|0.554;C|0.446	0.446	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
LGR4	55366	hgsc.bcm.edu	37	11	27406844	27406844	+	Silent	SNP	G	G	A	rs6484295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:27406844G>A	ENST00000379214.4	-	5	1016	c.573C>T	c.(571-573)agC>agT	p.S191S	LGR4_ENST00000480977.2_Silent_p.S143S|LGR4_ENST00000389858.4_Silent_p.S167S	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	191					bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						AGTCAGGGATGCTTGAGATCT	0.473													G|||	1825	0.364417	0.3654	0.2219	5008	,	,		17834	0.4494		0.3082	False		,,,				2504	0.4346				p.S191S		Atlas-SNP	.											.	LGR4	87	.	0			c.C573T						PASS	.	G		1465,2939	473.3+/-356.6	256,953,993	124.0	130.0	128.0		573	5.8	1.0	11	dbSNP_116	128	2643,5955	426.7+/-355.4	407,1829,2063	no	coding-synonymous	LGR4	NM_018490.2		663,2782,3056	AA,AG,GG		30.7397,33.2652,31.5951		191/952	27406844	4108,8894	2202	4299	6501	SO:0001819	synonymous_variant	55366	exon5			AGGGATGCTTGAG	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.573C>T	11.37:g.27406844G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Silent	SNP	ENST00000379214.4	37	CCDS31449.1																																																																																			G|0.665;A|0.335	0.335	strong		0.473	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	
LAMC1	3915	hgsc.bcm.edu	37	1	183091040	183091040	+	Missense_Mutation	SNP	G	G	A	rs147401305	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:183091040G>A	ENST00000258341.4	+	12	2430	c.2173G>A	c.(2173-2175)Gcc>Acc	p.A725T		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	725	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|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-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.A725S(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						TGTGCTTTGCGCCTGCAATGG	0.478																																					p.A725T		Atlas-SNP	.											LAMC1,NS,carcinoma,0,1	LAMC1	176	1	1	Substitution - Missense(1)	lung(1)	c.G2173A						scavenged	.	G	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	132.0	117.0	122.0		2173	1.5	0.5	1	dbSNP_134	122	4,8596	3.7+/-12.6	0,4,4296	yes	missense	LAMC1	NM_002293.3	58	0,7,6496	AA,AG,GG		0.0465,0.0681,0.0538	benign	725/1610	183091040	7,12999	2203	4300	6503	SO:0001583	missense	3915	exon12			CTTTGCGCCTGCA	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.2173G>A	1.37:g.183091040G>A	ENSP00000258341:p.Ala725Thr	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	146	88	0.60274	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	1.387	-0.581931	0.03827	6.81E-4	4.65E-4	ENSG00000135862	ENST00000258341	T	0.61627	0.09	5.17	1.54	0.23209	EGF-like, laminin (3);	0.249221	0.46442	N	0.000296	T	0.17959	0.0431	N	0.00621	-1.32	0.19945	N	0.999948	B	0.02656	0.0	B	0.04013	0.001	T	0.29027	-1.0025	10	0.07990	T	0.79	.	5.4496	0.16556	0.6007:0.0:0.2809:0.1184	.	725	P11047	LAMC1_HUMAN	T	725	ENSP00000258341:A725T	ENSP00000258341:A725T	A	+	1	0	LAMC1	181357663	0.001000	0.12720	0.533000	0.28001	0.645000	0.38454	0.530000	0.23036	0.013000	0.14918	-0.946000	0.02672	GCC	G|0.999;A|0.001	0.001	strong		0.478	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
FAM200B	285550	hgsc.bcm.edu	37	4	15689928	15689928	+	Missense_Mutation	SNP	G	G	A	rs4235380	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:15689928G>A	ENST00000422728.2	+	2	2166	c.1328G>A	c.(1327-1329)aGt>aAt	p.S443N	FAM200B_ENST00000504137.1_Intron	NM_001145191.1	NP_001138663.1	P0CF97	F200B_HUMAN	family with sequence similarity 200, member B	443							nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						aatgaactgagtttaaaacta	0.303													G|||	1574	0.314297	0.2201	0.3602	5008	,	,		18299	0.4683		0.2763	False		,,,				2504	0.2894				p.S443N		Atlas-SNP	.											.	FAM200B	56	.	0			c.G1328A						PASS	.	G	ASN/SER	319,1065		34,251,407	52.0	41.0	44.0		1328	2.5	1.0	4	dbSNP_111	44	961,2215		150,661,777	yes	missense	FAM200B	NM_001145191.1	46	184,912,1184	AA,AG,GG		30.2582,23.0491,28.0702	benign	443/658	15689928	1280,3280	692	1588	2280	SO:0001583	missense	285550	exon2			AACTGAGTTTAAA	BC048993	CCDS47028.1	4p15.32	2014-04-02			ENSG00000237765	ENSG00000237765			27740	protein-coding gene	gene with protein product	"""chromosome 4 open reading frame 53"""						Standard	NM_001145191		Approved	C4orf53	uc003gof.4	P0CF97	OTTHUMG00000160279	ENST00000422728.2:c.1328G>A	4.37:g.15689928G>A	ENSP00000393017:p.Ser443Asn	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	184	97	0.527174	NM_001145191		Missense_Mutation	SNP	ENST00000422728.2	37	CCDS47028.1	712	0.326007326007326	116	0.23577235772357724	126	0.34806629834254144	260	0.45454545454545453	210	0.2770448548812665	G	0.141	-1.101788	0.01828	0.230491	0.302582	ENSG00000237765	ENST00000422728	T	0.80214	-1.35	2.48	2.48	0.30137	Ribonuclease H-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.49798	P	1.7699999999998273E-4	B	0.09022	0.002	B	0.08055	0.003	T	0.35773	-0.9775	7	.	.	.	.	8.5475	0.33430	0.0:0.0:1.0:0.0	rs4235380;rs16898467;rs52818507;rs57685138;rs4235380	443	P0CF97	F200B_HUMAN	N	443	ENSP00000393017:S443N	.	S	+	2	0	FAM200B	15299026	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	2.988000	0.49386	1.712000	0.51347	0.484000	0.47621	AGT	G|0.679;A|0.321	0.321	strong		0.303	FAM200B-005	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360100.1	NM_001145191	
MUC2	4583	hgsc.bcm.edu	37	11	1092973	1092973	+	Missense_Mutation	SNP	C	C	T	rs55847666		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1092973C>T	ENST00000441003.2	+	30	4819	c.4792C>T	c.(4792-4794)Ccc>Tcc	p.P1598S	MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	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						scavenged	.						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	70	0	0		WXS	Illumina HiSeq	Phase_I	64	5	0.078125	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	
CTAGE5	4253	hgsc.bcm.edu	37	14	39764176	39764176	+	Missense_Mutation	SNP	G	G	C	rs17855896	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:39764176G>C	ENST00000280083.3	+	8	929	c.615G>C	c.(613-615)aaG>aaC	p.K205N	RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.K740N|CTAGE5_ENST00000556148.1_Missense_Mutation_p.K130N|CTAGE5_ENST00000341502.5_Missense_Mutation_p.K205N|CTAGE5_ENST00000396165.4_Missense_Mutation_p.K176N|CTAGE5_ENST00000396158.2_Missense_Mutation_p.K210N|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.K176N|CTAGE5_ENST00000341749.3_Missense_Mutation_p.K193N|CTAGE5_ENST00000553352.1_Missense_Mutation_p.K176N|CTAGE5_ENST00000557038.1_Missense_Mutation_p.K125N|CTAGE5_ENST00000348007.3_Missense_Mutation_p.K205N			O15320	CTGE5_HUMAN	CTAGE family, member 5	205			K -> N (in dbSNP:rs17855896). {ECO:0000269|PubMed:15489334}.		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)		AACGACTGAAGATAGCAATAA	0.328													G|||	96	0.0191693	0.0008	0.0288	5008	,	,		21174	0.001		0.0636	False		,,,				2504	0.0102				p.K210N		Atlas-SNP	.											.	CTAGE5	75	.	0			c.G630C						PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	55,4351	54.9+/-90.9	1,53,2149	90.0	93.0	92.0		615,579,615,528	4.7	1.0	14	dbSNP_123	92	538,8062	149.1+/-204.2	11,516,3773	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	94,94,94,94	12,569,5922	CC,CG,GG		6.2558,1.2483,4.5594	benign,benign,benign,benign	205/805,193/793,205/762,176/776	39764176	593,12413	2203	4300	6503	SO:0001583	missense	4253	exon8			ACTGAAGATAGCA	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.615G>C	14.37:g.39764176G>C	ENSP00000280083:p.Lys205Asn	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	335	198	0.591045	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	60	0.027472527472527472	1	0.0020325203252032522	11	0.03038674033149171	1	0.0017482517482517483	47	0.06200527704485488	G	13.74	2.326136	0.41197	0.012483	0.062558	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.78481	2.28;-1.18;2.28;-1.18;-1.18;-0.59;-1.18;-0.59;-1.18;-1.18	5.69	4.69	0.59074	.	0.246033	0.21178	N	0.078874	T	0.28797	0.0714	M	0.72118	2.19	0.26845	N	0.968287	B;B;B;B;B;B	0.26935	0.164;0.042;0.044;0.023;0.025;0.023	B;B;B;B;B;B	0.30401	0.115;0.073;0.049;0.073;0.049;0.073	T	0.51108	-0.8747	9	.	.	.	.	9.1812	0.37143	0.132:0.0:0.868:0.0	rs17855896	167;210;205;205;176;193	F8W9E1;O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;.;CTGE5_HUMAN;.;.	N	740;193;125;167;176;205;210;205;130;205;176	ENSP00000452252:K740N;ENSP00000343897:K193N;ENSP00000450869:K125N;ENSP00000379468:K176N;ENSP00000339286:K205N;ENSP00000379462:K210N;ENSP00000280083:K205N;ENSP00000452562:K130N;ENSP00000343912:K205N;ENSP00000450449:K176N	.	K	+	3	2	CTAGE5;RP11-407N17.3	38833927	0.998000	0.40836	0.997000	0.53966	0.778000	0.44026	1.302000	0.33459	2.676000	0.91093	0.557000	0.71058	AAG	G|0.960;C|0.040	0.040	strong		0.328	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
VPS13C	54832	hgsc.bcm.edu	37	15	62212781	62212781	+	Silent	SNP	T	T	C	rs17238189	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:62212781T>C	ENST00000261517.5	-	56	7201	c.7128A>G	c.(7126-7128)caA>caG	p.Q2376Q	VPS13C_ENST00000249837.3_Silent_p.Q2333Q|VPS13C_ENST00000395898.3_Silent_p.Q2333Q|VPS13C_ENST00000395896.4_Silent_p.Q2376Q	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						GAATTGCCATTTGTGGCTCAG	0.303													T|||	603	0.120407	0.093	0.2046	5008	,	,		16094	0.2054		0.0249	False		,,,				2504	0.1084				p.Q2376Q		Atlas-SNP	.											.	VPS13C	506	.	0			c.A7128G						PASS	.	T	,,,	431,3975	199.8+/-223.2	25,381,1797	63.0	67.0	65.0		7128,6999,6999,7128	2.2	1.0	15	dbSNP_123	65	189,8397	81.2+/-143.8	3,183,4107	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	,,,	28,564,5904	CC,CT,TT		2.2013,9.7821,4.7722	,,,	2376/3629,2333/3711,2333/3586,2376/3754	62212781	620,12372	2203	4293	6496	SO:0001819	synonymous_variant	54832	exon56			TGCCATTTGTGGC	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.7128A>G	15.37:g.62212781T>C		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	167	33	0.197605	NM_020821		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																			T|0.930;C|0.070	0.070	strong		0.303	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
DHRS4	10901	hgsc.bcm.edu	37	14	24424367	24424367	+	Silent	SNP	G	G	A	rs12147221	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24424367G>A	ENST00000313250.5	+	2	455	c.252G>A	c.(250-252)acG>acA	p.T84T	DHRS4_ENST00000397075.3_Silent_p.T84T|DHRS4_ENST00000558581.1_Silent_p.T84T|DHRS4_ENST00000421831.1_Silent_p.T66T|DHRS4_ENST00000397073.2_Silent_p.T66T|DHRS4_ENST00000308178.8_Silent_p.T66T|DHRS4_ENST00000559632.1_Silent_p.T84T|DHRS4_ENST00000543741.2_Silent_p.T84T|DHRS4_ENST00000558263.1_Silent_p.T84T|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000382761.3_Silent_p.T66T|DHRS4_ENST00000397074.3_Silent_p.T84T	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	84					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	TGAGCGTGACGGGCACCGTGT	0.682													.|||	1006	0.200879	0.5998	0.1095	5008	,	,		15536	0.0099		0.0785	False		,,,				2504	0.0491				p.T84T		Atlas-SNP	.											.	DHRS4	22	.	0			c.G252A						PASS	.	G		2291,2115		588,1115,500	37.0	41.0	39.0		252	-6.6	0.3	14	dbSNP_120	39	612,7988		6,600,3694	no	coding-synonymous	DHRS4	NM_021004.2		594,1715,4194	AA,AG,GG		7.1163,48.0027,22.3205		84/279	24424367	2903,10103	2203	4300	6503	SO:0001819	synonymous_variant	10901	exon2			CGTGACGGGCACC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.252G>A	14.37:g.24424367G>A		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	398	270	0.678392	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Silent	SNP	ENST00000313250.5	37	CCDS9605.1																																																																																			G|0.796;A|0.204	0.204	strong		0.682	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
MUC17	140453	hgsc.bcm.edu	37	7	100678610	100678610	+	Missense_Mutation	SNP	A	A	T	rs78010183	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678610A>T	ENST00000306151.4	+	3	3977	c.3913A>T	c.(3913-3915)Act>Tct	p.T1305S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1305	59 X approximate tandem repeats.|Ser-rich.				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)					TCCTGTTGACACTAAAGGTCC	0.458																																					p.T1305S		Atlas-SNP	.											.	MUC17	804	.	0			c.A3913T						PASS	.						240.0	230.0	233.0					7																	100678610		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTGACACTAAAG	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.3913A>T	7.37:g.100678610A>T	ENSP00000302716:p.Thr1305Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	242	85	0.35124	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	0.022	-1.413760	0.01145	.	.	ENSG00000169876	ENST00000306151	T	0.02323	4.34	0.471	-0.942	0.10398	.	.	.	.	.	T	0.01870	0.0059	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.49670	-0.8915	8	0.18710	T	0.47	.	.	.	.	.	1305	Q685J3	MUC17_HUMAN	S	1305	ENSP00000302716:T1305S	ENSP00000302716:T1305S	T	+	1	0	MUC17	100465330	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.508000	0.06344	-3.256000	0.00203	-4.074000	0.00012	ACT	A|0.943;T|0.057	0.057	strong		0.458	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
C9orf40	55071	hgsc.bcm.edu	37	9	77563087	77563087	+	Silent	SNP	C	C	T	rs2769058	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:77563087C>T	ENST00000376854.5	-	2	736	c.462G>A	c.(460-462)caG>caA	p.Q154Q		NM_017998.2	NP_060468.2	Q8IXQ3	CI040_HUMAN	chromosome 9 open reading frame 40	154								p.Q154Q(1)		lung(2)|stomach(1)	3						TCCTCCAGTACTGGAAGGTAT	0.383													C|||	1619	0.323283	0.2398	0.3458	5008	,	,		16486	0.3988		0.3429	False		,,,				2504	0.3221				p.Q154Q		Atlas-SNP	.											C9orf40,NS,carcinoma,0,1	C9orf40	5	1	1	Substitution - coding silent(1)	stomach(1)	c.G462A						PASS	.	C		1158,3248	410.4+/-335.4	156,846,1201	106.0	99.0	102.0		462	6.0	1.0	9	dbSNP_100	102	2773,5827	439.5+/-359.2	444,1885,1971	no	coding-synonymous	C9orf40	NM_017998.2		600,2731,3172	TT,TC,CC		32.2442,26.2823,30.2245		154/195	77563087	3931,9075	2203	4300	6503	SO:0001819	synonymous_variant	55071	exon2			CCAGTACTGGAAG	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.462G>A	9.37:g.77563087C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_017998	Q9NWD3	Silent	SNP	ENST00000376854.5	37	CCDS6648.1																																																																																			C|0.688;T|0.312	0.312	strong		0.383	C9orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052702.1	NM_017998	
SUCLG2	8801	hgsc.bcm.edu	37	3	67579535	67579535	+	Missense_Mutation	SNP	T	T	C	rs74675534	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:67579535T>C	ENST00000307227.5	-	3	329	c.302A>G	c.(301-303)aAa>aGa	p.K101R	SUCLG2_ENST00000493112.1_Missense_Mutation_p.K101R|SUCLG2_ENST00000492795.1_Missense_Mutation_p.K101R	NM_003848.3	NP_003839.2	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming, beta subunit	101	ATP-grasp.				cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|succinyl-CoA metabolic process (GO:0006104)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|succinate-CoA ligase complex (GDP-forming) (GO:0045244)	ATP binding (GO:0005524)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|succinate-CoA ligase (GDP-forming) activity (GO:0004776)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	10		Renal(2;0.00294)|Lung NSC(201;0.012)|Hepatocellular(537;0.121)		BRCA - Breast invasive adenocarcinoma(55;3.53e-05)|Epithelial(33;0.000153)	Succinic acid(DB00139)	AACACCTCCTTTCAAACCACT	0.383													T|||	9	0.00179712	0.0008	0.0	5008	,	,		17705	0.0		0.007	False		,,,				2504	0.001				p.K101R		Atlas-SNP	.											.	SUCLG2	95	.	0			c.A302G						PASS	.	T	ARG/LYS,ARG/LYS	6,3664		0,6,1829	156.0	147.0	150.0		302,302	5.0	1.0	3	dbSNP_131	150	86,8080		1,84,3998	yes	missense,missense	SUCLG2	NM_001177599.1,NM_003848.3	26,26	1,90,5827	CC,CT,TT		1.0531,0.1635,0.7773	benign,benign	101/441,101/433	67579535	92,11744	1835	4083	5918	SO:0001583	missense	8801	exon3			CCTCCTTTCAAAC	AF058954	CCDS43104.1, CCDS54605.1	3p14.3	2004-05-17			ENSG00000172340	ENSG00000172340	6.2.1.4		11450	protein-coding gene	gene with protein product		603922				9765291	Standard	NM_001177599		Approved		uc003dna.4	Q96I99	OTTHUMG00000158740	ENST00000307227.5:c.302A>G	3.37:g.67579535T>C	ENSP00000307432:p.Lys101Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_001177599	C9JVT2|O95195|Q6NUH7|Q86VX8|Q8WUQ1	Missense_Mutation	SNP	ENST00000307227.5	37	CCDS43104.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	17.48	3.401307	0.62288	0.001635	0.010531	ENSG00000172340	ENST00000493112;ENST00000307227;ENST00000541608;ENST00000492795	T;T;T	0.70399	-0.48;-0.48;-0.48	5.01	5.01	0.66863	ATP-grasp fold, subdomain 1 (1);ATP-grasp fold, succinyl-CoA synthetase-type (1);	0.143233	0.64402	D	0.000006	T	0.73666	0.3616	M	0.88775	2.98	0.80722	D	1	B	0.25955	0.138	B	0.36766	0.232	T	0.79006	-0.1979	10	0.66056	D	0.02	.	14.7526	0.69536	0.0:0.0:0.0:1.0	.	101	Q96I99	SUCB2_HUMAN	R	101;101;53;101	ENSP00000419325:K101R;ENSP00000307432:K101R;ENSP00000417589:K101R	ENSP00000307432:K101R	K	-	2	0	SUCLG2	67662225	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.957000	0.87870	1.884000	0.54569	0.377000	0.23210	AAA	T|0.993;C|0.007	0.007	strong		0.383	SUCLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351993.1	NM_003848	
HLA-B	3106	hgsc.bcm.edu	37	6	31324547	31324547	+	Missense_Mutation	SNP	G	G	C	rs1065386|rs281864604	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31324547G>C	ENST00000412585.2	-	2	289	c.261C>G	c.(259-261)aaC>aaG	p.N87K		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	87	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)	p.N87K(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						AGATCTGTGTGTTCCGGTCCC	0.662									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	2278	0.454872	0.3676	0.4179	5008	,	,		6866	0.5853		0.3936	False		,,,				2504	0.5276				p.N87K		Atlas-SNP	.											HLA-B,NS,lymphoid_neoplasm,-2,2	HLA-B	54	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C261G						scavenged	.	C	LYS/ASN	834,3406		230,374,1516	66.0	64.0	65.0		261	-1.2	0.0	6	dbSNP_86	65	1737,6553		553,631,2961	no	missense	HLA-B	NM_005514.6	94	783,1005,4477	CC,CG,GG		20.953,19.6698,20.5188		87/363	31324547	2571,9959	2120	4145	6265	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CTGTGTGTTCCGG	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.261C>G	6.37:g.31324547G>C	ENSP00000399168:p.Asn87Lys	Somatic	145	2	0.0137931		WXS	Illumina HiSeq	Phase_I	161	57	0.354037	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	760	0.34798534798534797	120	0.24390243902439024	97	0.26795580110497236	301	0.5262237762237763	242	0.31926121372031663	N	7.741	0.701384	0.15172	0.196698	0.20953	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00705	5.81;5.81	3.2	-1.24	0.09435	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.715036	0.10428	U	0.675817	T	0.01421	0.0046	M	0.87758	2.905	0.80722	P	0.0	B;B;D	0.54207	0.147;0.334;0.965	B;B;D	0.63192	0.119;0.185;0.912	T	0.17745	-1.0359	9	0.66056	D	0.02	.	7.0496	0.25065	0.0:0.4051:0.4134:0.1816	rs1131200;rs2308411;rs3177919;rs3190898	87;87;62	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	K	87;98	ENSP00000399168:N87K;ENSP00000405931:N98K	ENSP00000399168:N87K	N	-	3	2	HLA-B	31432526	0.013000	0.17824	0.000000	0.03702	0.000000	0.00434	-1.228000	0.02948	-0.885000	0.03971	-1.610000	0.00802	AAC	G|0.668;C|0.332	0.332	strong		0.662	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
CCDC110	256309	hgsc.bcm.edu	37	4	186380295	186380295	+	Silent	SNP	A	A	G	rs36007437	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:186380295A>G	ENST00000307588.3	-	6	1521	c.1446T>C	c.(1444-1446)aaT>aaC	p.N482N	CCDC110_ENST00000510617.1_Silent_p.N482N|CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Silent_p.N445N	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	482						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		CTTCAACCAGATTCTTAAGTT	0.279													A|||	1477	0.294928	0.1536	0.3213	5008	,	,		17558	0.2808		0.4374	False		,,,				2504	0.3354				p.N482N		Atlas-SNP	.											.	CCDC110	78	.	0			c.T1446C						PASS	.	A	,	924,3482		103,718,1382	41.0	42.0	42.0		1335,1446	-1.8	0.0	4	dbSNP_126	42	4240,4320		1091,2058,1131	no	coding-synonymous,coding-synonymous	CCDC110	NM_001145411.1,NM_152775.3	,	1194,2776,2513	GG,GA,AA		49.5327,20.9714,39.8272	,	445/797,482/834	186380295	5164,7802	2203	4280	6483	SO:0001819	synonymous_variant	256309	exon6			AACCAGATTCTTA	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.1446T>C	4.37:g.186380295A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	73	15	0.205479	NM_152775	Q86YI9|Q8N7W0	Silent	SNP	ENST00000307588.3	37	CCDS3843.1																																																																																			A|0.623;G|0.377	0.377	strong		0.279	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
UNC45B	146862	hgsc.bcm.edu	37	17	33513337	33513337	+	Missense_Mutation	SNP	T	T	A	rs11654824	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33513337T>A	ENST00000268876.5	+	20	2652	c.2555T>A	c.(2554-2556)aTc>aAc	p.I852N	UNC45B_ENST00000394570.2_Missense_Mutation_p.I850N|UNC45B_ENST00000591048.1_Missense_Mutation_p.I771N|UNC45B_ENST00000433649.1_Missense_Mutation_p.I850N|UNC45B_ENST00000378449.1_Missense_Mutation_p.I771N|RP11-799D4.2_ENST00000590144.1_RNA	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	852			I -> N (in dbSNP:rs11654824).		cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TGGTTGGAGATCCTCCAGCGG	0.567													T|||	169	0.033746	0.0053	0.0317	5008	,	,		19749	0.0		0.0905	False		,,,				2504	0.0501				p.I852N		Atlas-SNP	.											.	UNC45B	133	.	0			c.T2555A						PASS	.	T	ASN/ILE,ASN/ILE	65,4341	61.1+/-98.1	2,61,2140	82.0	82.0	82.0		2549,2555	6.0	1.0	17	dbSNP_120	82	627,7973	163.0+/-215.7	13,601,3686	yes	missense,missense	UNC45B	NM_001033576.1,NM_173167.2	149,149	15,662,5826	AA,AT,TT		7.2907,1.4753,5.3206	possibly-damaging,possibly-damaging	850/930,852/932	33513337	692,12314	2203	4300	6503	SO:0001583	missense	146862	exon20			TGGAGATCCTCCA	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.2555T>A	17.37:g.33513337T>A	ENSP00000268876:p.Ile852Asn	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	102	0.046703296703296704	5	0.01016260162601626	16	0.04419889502762431	0	0.0	81	0.10686015831134564	T	17.96	3.516186	0.64634	0.014753	0.072907	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.51574	0.7;1.45;0.7	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.03564	0.0102	M	0.75615	2.305	0.09310	P	0.999999791172	D;D;P	0.89917	0.999;1.0;0.93	D;D;P	0.91635	0.997;0.999;0.496	T	0.39961	-0.9588	9	0.87932	D	0	-26.2242	15.7258	0.77756	0.0:0.0:0.0:1.0	rs11654824;rs52819819;rs11654824	771;850;852	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	N	852;852;850;771	ENSP00000268876:I852N;ENSP00000412840:I850N;ENSP00000367710:I771N	ENSP00000268876:I852N	I	+	2	0	UNC45B	30537450	1.000000	0.71417	0.958000	0.39756	0.992000	0.81027	7.886000	0.87288	2.311000	0.77944	0.533000	0.62120	ATC	T|0.948;A|0.052	0.052	strong		0.567	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
RBM19	9904	hgsc.bcm.edu	37	12	114282496	114282496	+	Missense_Mutation	SNP	C	C	T	rs2075387	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	55	0	0		WXS	Illumina HiSeq	Phase_I	49	33	0.673469	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	
PLIN4	729359	hgsc.bcm.edu	37	19	4513549	4513549	+	Silent	SNP	G	G	A	rs146566557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4513549G>A	ENST00000301286.3	-	3	380	c.381C>T	c.(379-381)agC>agT	p.S127S		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	127	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						CTGTGACCCCGCTGGACACCA	0.667													G|||	4	0.000798722	0.0008	0.0	5008	,	,		17859	0.001		0.002	False		,,,				2504	0.0				p.S127S		Atlas-SNP	.											.	PLIN4	191	.	0			c.C381T						PASS	.	G		2,3976		0,2,1987	26.0	30.0	29.0		381	-10.7	0.0	19	dbSNP_134	29	37,8263		0,37,4113	no	coding-synonymous	PLIN4	NM_001080400.1		0,39,6100	AA,AG,GG		0.4458,0.0503,0.3176		127/1358	4513549	39,12239	1989	4150	6139	SO:0001819	synonymous_variant	729359	exon3			GACCCCGCTGGAC	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.381C>T	19.37:g.4513549G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			G|0.998;A|0.002	0.002	strong		0.667	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
METTL25	84190	hgsc.bcm.edu	37	12	82792792	82792792	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:82792792T>G	ENST00000248306.3	+	4	819	c.750T>G	c.(748-750)aaT>aaG	p.N250K	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	250							methyltransferase activity (GO:0008168)										AAGTGCAAAATAAAGTTAAAA	0.343																																					p.N250K		Atlas-SNP	.											.	.	.	.	0			c.T750G						PASS	.						60.0	57.0	58.0					12																	82792792		2203	4299	6502	SO:0001583	missense	84190	exon4			GCAAAATAAAGTT	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.750T>G	12.37:g.82792792T>G	ENSP00000248306:p.Asn250Lys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	T	0.058	-1.231429	0.01505	.	.	ENSG00000127720	ENST00000248306	T	0.29142	1.58	5.39	-0.792	0.10925	.	1.047890	0.07359	N	0.883727	T	0.07548	0.0190	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30119	-0.9989	10	0.05525	T	0.97	-2.823	1.9271	0.03319	0.1244:0.1816:0.1292:0.5648	.	250	Q8N6Q8	CL026_HUMAN	K	250	ENSP00000248306:N250K	ENSP00000248306:N250K	N	+	3	2	C12orf26	81316923	0.162000	0.22906	0.000000	0.03702	0.023000	0.10783	0.214000	0.17541	-0.265000	0.09352	-0.418000	0.06021	AAT	.	.	none		0.343	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
DACT2	168002	hgsc.bcm.edu	37	6	168711107	168711107	+	Silent	SNP	G	G	A	rs111574499	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168711107G>A	ENST00000366795.3	-	3	487	c.399C>T	c.(397-399)gaC>gaT	p.D133D	DACT2_ENST00000610183.1_Intron|DACT2_ENST00000607983.1_Intron|DACT2_ENST00000366796.3_Silent_p.D133D	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	133					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)		AGGATCCACCGTCGCTCATCT	0.627													g|||	165	0.0329473	0.0129	0.0403	5008	,	,		18848	0.004		0.0666	False		,,,				2504	0.0501				p.D133D		Atlas-SNP	.											DACT2_ENST00000366795,NS,carcinoma,0,1	DACT2	46	1	0			c.C399T						scavenged	.			24,1360		0,24,668	63.0	75.0	71.0		399	-9.2	0.0	6	dbSNP_132	71	201,2981		6,189,1396	no	coding-synonymous	DACT2	NM_214462.3		6,213,2064	AA,AG,GG		6.3168,1.7341,4.9277		133/775	168711107	225,4341	692	1591	2283	SO:0001819	synonymous_variant	168002	exon3			TCCACCGTCGCTC	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.399C>T	6.37:g.168711107G>A		Somatic	233	4	0.0171674		WXS	Illumina HiSeq	Phase_I	265	136	0.513208	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Silent	SNP	ENST00000366795.3	37	CCDS47519.1																																																																																			G|0.968;A|0.032	0.032	strong		0.627	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
TEDDM1	127670	hgsc.bcm.edu	37	1	182369078	182369078	+	Silent	SNP	G	G	A	rs6698722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:182369078G>A	ENST00000367565.1	-	1	673	c.543C>T	c.(541-543)ccC>ccT	p.P181P		NM_172000.3	NP_741997.3	Q5T9Z0	TEDM1_HUMAN	transmembrane epididymal protein 1	181						integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(2)	7						AGCCAGAGACGGGTCTGTATA	0.507													A|||	4275	0.853634	0.9569	0.8156	5008	,	,		21560	0.8373		0.8171	False		,,,				2504	0.7955				p.P181P		Atlas-SNP	.											.	TEDDM1	32	.	0			c.C543T						PASS	.	A		4082,324	173.7+/-203.5	1896,290,17	76.0	75.0	75.0		543	-8.7	0.0	1	dbSNP_116	75	6819,1781	322.6+/-315.6	2694,1431,175	no	coding-synonymous	TEDDM1	NM_172000.3		4590,1721,192	AA,AG,GG		20.7093,7.3536,16.1848		181/274	182369078	10901,2105	2203	4300	6503	SO:0001819	synonymous_variant	127670	exon1			AGAGACGGGTCTG	AJ515384	CCDS30953.1	1q25.3	2009-09-17		2005-08-09	ENSG00000203730	ENSG00000203730			30233	protein-coding gene	gene with protein product	"""putative membrane protein HE9"", ""transmembrane protein 45C"", ""epididymal protein 9"""						Standard	NM_172000		Approved	HE9, Epdd1, TMEM45C, EDDM9	uc001gpe.3	Q5T9Z0	OTTHUMG00000037398	ENST00000367565.1:c.543C>T	1.37:g.182369078G>A		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	357	227	0.635854	NM_172000	Q8IVJ0	Silent	SNP	ENST00000367565.1	37	CCDS30953.1																																																																																			G|0.154;A|0.846	0.846	strong		0.507	TEDDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091029.1	NM_172000	
KIAA1024	23251	hgsc.bcm.edu	37	15	79748603	79748603	+	Silent	SNP	C	C	T	rs7183867	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:79748603C>T	ENST00000305428.3	+	2	189	c.114C>T	c.(112-114)ttC>ttT	p.F38F		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	38						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						GTGCCCGGTTCGACCTGTCGC	0.473													C|||	941	0.187899	0.5287	0.0634	5008	,	,		16769	0.0823		0.0636	False		,,,				2504	0.0521				p.F38F		Atlas-SNP	.											.	KIAA1024	146	.	0			c.C114T						PASS	.	C		1963,2429	555.4+/-379.2	442,1079,675	116.0	110.0	112.0		114	-8.4	0.0	15	dbSNP_116	112	537,8049	148.8+/-204.0	15,507,3771	no	coding-synonymous	KIAA1024	NM_015206.2		457,1586,4446	TT,TC,CC		6.2544,44.6949,19.2634		38/917	79748603	2500,10478	2196	4293	6489	SO:0001819	synonymous_variant	23251	exon2			CCGGTTCGACCTG	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.114C>T	15.37:g.79748603C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	97	22	0.226804	NM_015206	A7MD43	Silent	SNP	ENST00000305428.3	37	CCDS32306.1																																																																																			C|0.813;T|0.187	0.187	strong		0.473	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
MUC17	140453	hgsc.bcm.edu	37	7	100680120	100680120	+	Missense_Mutation	SNP	C	C	A	rs147991653	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680120C>A	ENST00000306151.4	+	3	5487	c.5423C>A	c.(5422-5424)aCt>aAt	p.T1808N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1808	59 X approximate tandem repeats.|Ser-rich.				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)	p.T1808N(1)		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)					GAAGGAATGACTCCATTAACA	0.512													-|||	4	0.000798722	0.0008	0.0	5008	,	,		25905	0.003		0.0	False		,,,				2504	0.0				p.T1808N		Atlas-SNP	.											MUC17,extremity,malignant_melanoma,0,2	MUC17	804	2	1	Substitution - Missense(1)	skin(1)	c.C5423A						scavenged	.						246.0	249.0	248.0					7																	100680120		2203	4300	6503	SO:0001583	missense	140453	exon3			GAATGACTCCATT	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.5423C>A	7.37:g.100680120C>A	ENSP00000302716:p.Thr1808Asn	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	338	49	0.14497	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	76	0.0347985347985348	28	0.056910569105691054	21	0.058011049723756904	12	0.02097902097902098	15	0.01978891820580475	c	0.142	-1.100945	0.01843	.	.	ENSG00000169876	ENST00000306151	T	0.02177	4.41	0.471	-0.615	0.11587	.	.	.	.	.	T	0.00210	0.0006	N	0.19112	0.55	0.09310	N	1	D	0.58620	0.983	B	0.40677	0.337	T	0.51988	-0.8635	8	0.32370	T	0.25	.	.	.	.	.	1808	Q685J3	MUC17_HUMAN	N	1808	ENSP00000302716:T1808N	ENSP00000302716:T1808N	T	+	2	0	MUC17	100466840	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	0.305000	0.19254	-0.243000	0.09653	-1.404000	0.01136	ACT	C|0.975;A|0.025	0.025	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
NBEAL2	23218	hgsc.bcm.edu	37	3	47036756	47036756	+	Missense_Mutation	SNP	C	C	G	rs11720139	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:47036756C>G	ENST00000450053.3	+	13	1710	c.1531C>G	c.(1531-1533)Cgc>Ggc	p.R511G	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.R511G	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	511			R -> G (in dbSNP:rs11720139).		blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CCTGGAGGCCCGCTGCCAAGA	0.657													C|||	1586	0.316693	0.2027	0.3141	5008	,	,		19464	0.3383		0.3936	False		,,,				2504	0.3712				p.R511G		Atlas-SNP	.											NBEAL2_ENST00000450053,NS,carcinoma,0,4	NBEAL2	267	4	0			c.C1531G						PASS	.	C	GLY/ARG	789,3121		86,617,1252	8.0	10.0	9.0		1531	4.5	0.9	3	dbSNP_120	9	2983,5223		583,1817,1703	yes	missense	NBEAL2	NM_015175.1	125	669,2434,2955	GG,GC,CC		36.3515,20.179,31.1324	possibly-damaging	511/2755	47036756	3772,8344	1955	4103	6058	SO:0001583	missense	23218	exon13			GAGGCCCGCTGCC	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.1531C>G	3.37:g.47036756C>G	ENSP00000415034:p.Arg511Gly	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	680	0.31135531135531136	91	0.18495934959349594	105	0.2900552486187845	186	0.32517482517482516	298	0.39313984168865435	C	5.007	0.187024	0.09547	0.20179	0.363515	ENSG00000160796	ENST00000292309;ENST00000450053;ENST00000296147	T;T	0.33438	1.41;1.41	4.54	4.54	0.55810	Armadillo-like helical (1);Armadillo-type fold (1);	0.311770	0.31685	N	0.007232	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	1.0	B;B	0.31383	0.321;0.094	B;B	0.26094	0.066;0.041	T	0.47636	-0.9102	9	0.27082	T	0.32	.	11.5906	0.50943	0.1783:0.8216:0.0:0.0	rs11720139;rs58658507;rs11720139	477;511	Q6ZNJ1-4;Q6ZNJ1	.;NBEL2_HUMAN	G	511;511;477	ENSP00000292309:R511G;ENSP00000415034:R511G	ENSP00000292309:R511G	R	+	1	0	NBEAL2	47011760	0.414000	0.25408	0.870000	0.34147	0.094000	0.18550	1.491000	0.35583	2.506000	0.84524	0.655000	0.94253	CGC	C|0.687;G|0.313	0.313	strong		0.657	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43826204	43826204	+	Missense_Mutation	SNP	C	C	T	rs7297737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:43826204C>T	ENST00000389420.3	-	21	2998	c.2999G>A	c.(2998-3000)cGt>cAt	p.R1000H	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.R154H|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.R1000H	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1000	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.		R -> H (in dbSNP:rs7297737).		extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GTCAGCAAGACGATGGCCAAA	0.433													C|||	183	0.0365415	0.0015	0.0086	5008	,	,		16709	0.0694		0.0348	False		,,,				2504	0.0716				p.R1000H		Atlas-SNP	.											ADAMTS20_ENST00000389420,colon,carcinoma,-1,1	ADAMTS20	635	1	0			c.G2999A						scavenged	.	C	HIS/ARG	26,4380	31.7+/-61.6	0,26,2177	128.0	125.0	126.0		2999	-1.3	0.1	12	dbSNP_116	126	243,8357	97.7+/-159.3	6,231,4063	yes	missense	ADAMTS20	NM_025003.3	29	6,257,6240	TT,TC,CC		2.8256,0.5901,2.0683	benign	1000/1911	43826204	269,12737	2203	4300	6503	SO:0001583	missense	80070	exon21			GCAAGACGATGGC	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2999G>A	12.37:g.43826204C>T	ENSP00000374071:p.Arg1000His	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	167	70	0.419162	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	78	0.03571428571428571	0	0.0	5	0.013812154696132596	44	0.07692307692307693	29	0.03825857519788918	C	5.530	0.282795	0.10458	0.005901	0.028256	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	4.89	-1.3	0.09259	.	0.364200	0.23662	N	0.045818	T	0.02610	0.0079	L	0.42529	1.33	0.27320	N	0.957055	B;B	0.30634	0.015;0.288	B;B	0.29176	0.009;0.099	T	0.03717	-1.1010	10	0.42905	T	0.14	.	11.5449	0.50688	0.0:0.5165:0.0:0.4835	rs7297737;rs52825347;rs59491718;rs7297737	1000;154	P59510;E9PBD5	ATS20_HUMAN;.	H	1000;166;154;1000;1000	ENSP00000374071:R1000H;ENSP00000447427:R166H;ENSP00000378911:R154H;ENSP00000448341:R1000H	ENSP00000374068:R1000H	R	-	2	0	ADAMTS20	42112471	0.859000	0.29813	0.064000	0.19789	0.839000	0.47603	1.193000	0.32162	-0.387000	0.07809	-0.794000	0.03295	CGT	C|0.968;T|0.032	0.032	strong		0.433	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
REXO1	57455	hgsc.bcm.edu	37	19	1819125	1819125	+	Missense_Mutation	SNP	T	T	C	rs2396359	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1819125T>C	ENST00000170168.4	-	8	2750	c.2656A>G	c.(2656-2658)Agt>Ggt	p.S886G	MIR1909_ENST00000411312.1_RNA|CTB-31O20.4_ENST00000593201.1_RNA	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	886			S -> G (in dbSNP:rs2396359). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		CTGCGGCCACTGGTTTCTGGA	0.672													.|||	1907	0.380791	0.5802	0.4207	5008	,	,		12655	0.3819		0.2097	False		,,,				2504	0.2577				p.S886G		Atlas-SNP	.											REXO1,NS,carcinoma,0,1	REXO1	55	1	0			c.A2656G						PASS	.	T	GLY/SER	2323,2079		630,1063,508	25.0	29.0	28.0		2656	1.9	0.4	19	dbSNP_100	28	1844,6748		200,1444,2652	yes	missense	REXO1	NM_020695.3	56	830,2507,3160	CC,CT,TT		21.4618,47.2285,32.0686	benign	886/1222	1819125	4167,8827	2201	4296	6497	SO:0001583	missense	57455	exon8			GGCCACTGGTTTC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.2656A>G	19.37:g.1819125T>C	ENSP00000170168:p.Ser886Gly	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	168	78	0.464286	NM_020695	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	800	0.3663003663003663	287	0.5833333333333334	135	0.3729281767955801	224	0.3916083916083916	154	0.20316622691292877	T	9.016	0.983646	0.18889	0.527715	0.214618	ENSG00000079313	ENST00000170168;ENST00000543452	T	0.13778	2.56	3.98	1.86	0.25419	.	0.272384	0.33075	U	0.005318	T	0.00012	0.0000	N	0.17082	0.46	0.37150	P	0.09788699999999995	B;B	0.22276	0.005;0.067	B;B	0.16722	0.004;0.016	T	0.35001	-0.9806	9	0.36615	T	0.2	-8.8227	6.6073	0.22731	0.0:0.1987:0.0:0.8013	rs2396359;rs11537979;rs17853032;rs2396359	195;886	B4DWY3;Q8N1G1	.;REXO1_HUMAN	G	886;158	ENSP00000170168:S886G	ENSP00000170168:S886G	S	-	1	0	REXO1	1770125	0.620000	0.27068	0.435000	0.26784	0.448000	0.32197	0.966000	0.29331	0.214000	0.20742	0.459000	0.35465	AGT	T|0.668;C|0.332	0.332	strong		0.672	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
DSG1	1828	hgsc.bcm.edu	37	18	28934408	28934408	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:28934408C>T	ENST00000257192.4	+	15	2461	c.2249C>T	c.(2248-2250)aCc>aTc	p.T750I	RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG1_ENST00000462981.2_Missense_Mutation_p.T109I	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	750					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)			TTCTTGGATACCCTGGGACCT	0.463																																					p.T750I		Atlas-SNP	.											DSG1,NS,carcinoma,-1,1	DSG1	176	1	0			c.C2249T						scavenged	.						124.0	124.0	124.0					18																	28934408		2203	4300	6503	SO:0001583	missense	1828	exon15			TGGATACCCTGGG	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.2249C>T	18.37:g.28934408C>T	ENSP00000257192:p.Thr750Ile	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	217	3	0.0138249	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.307282	0.40795	.	.	ENSG00000134760	ENST00000257192	T	0.77229	-1.08	6.04	5.14	0.70334	Cadherin, cytoplasmic domain (1);	0.081639	0.52532	D	0.000067	D	0.84120	0.5402	L	0.52011	1.625	0.34932	D	0.749495	D	0.76494	0.999	D	0.73380	0.98	D	0.87750	0.2591	10	0.62326	D	0.03	.	14.369	0.66826	0.2661:0.7339:0.0:0.0	.	750	Q02413	DSG1_HUMAN	I	750	ENSP00000257192:T750I	ENSP00000257192:T750I	T	+	2	0	DSG1	27188406	0.975000	0.34042	0.966000	0.40874	0.834000	0.47266	2.481000	0.45215	2.873000	0.98535	0.563000	0.77884	ACC	.	.	none		0.463	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
DNAH9	1770	hgsc.bcm.edu	37	17	11651057	11651057	+	Missense_Mutation	SNP	A	A	G	rs3744581	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	scavenged	.	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	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	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	
UMODL1	89766	hgsc.bcm.edu	37	21	43504228	43504228	+	Silent	SNP	T	T	C	rs7278485	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43504228T>C	ENST00000408910.2	+	3	354	c.354T>C	c.(352-354)ccT>ccC	p.P118P	UMODL1_ENST00000408989.2_Silent_p.P118P|UMODL1_ENST00000400427.1_Silent_p.P46P|UMODL1_ENST00000400424.2_Silent_p.P46P	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	118	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				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						CGTCAAGACCTGGGGCCTGCC	0.572													C|||	3342	0.667332	0.7935	0.5821	5008	,	,		19053	0.5496		0.6223	False		,,,				2504	0.7249				p.P118P	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											UMODL1_ENST00000408989,NS,carcinoma,+1,4	UMODL1	186	4	0			c.T354C						PASS	.	C	,,,	2972,888		1143,686,101	123.0	137.0	133.0		354,138,138,354	-7.7	0.0	21	dbSNP_116	133	5159,3081		1600,1959,561	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	2743,2645,662	CC,CT,TT		37.3908,23.0052,32.8017	,,,	118/1319,46/1375,46/1247,118/1447	43504228	8131,3969	1930	4120	6050	SO:0001819	synonymous_variant	89766	exon3			AAGACCTGGGGCC		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.354T>C	21.37:g.43504228T>C		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	173	170	0.982659	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			T|0.347;C|0.653	0.653	strong		0.572	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
THBS1	7057	hgsc.bcm.edu	37	15	39880818	39880818	+	Silent	SNP	C	C	T	rs41338344	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:39880818C>T	ENST00000260356.5	+	10	1728	c.1563C>T	c.(1561-1563)aaC>aaT	p.N521N		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	521	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)		TCTGCAACAACCCCACACCCC	0.537													C|||	64	0.0127796	0.003	0.0274	5008	,	,		20155	0.0		0.0318	False		,,,				2504	0.0092				p.N521N		Atlas-SNP	.											.	THBS1	106	.	0			c.C1563T						PASS	.	C		34,4366	39.2+/-71.8	0,34,2166	94.0	89.0	91.0		1563	4.8	1.0	15	dbSNP_127	91	301,8293	109.6+/-170.1	4,293,4000	no	coding-synonymous	THBS1	NM_003246.2		4,327,6166	TT,TC,CC		3.5024,0.7727,2.5781		521/1171	39880818	335,12659	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon10			CAACAACCCCACA		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.1563C>T	15.37:g.39880818C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	54	15	0.277778	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.975;T|0.025	0.025	strong		0.537	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
GLIS2	84662	hgsc.bcm.edu	37	16	4382351	4382351	+	Silent	SNP	C	C	A	rs34543395	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4382351C>A	ENST00000262366.3	+	3	891	c.70C>A	c.(70-72)Cgg>Agg	p.R24R	PAM16_ENST00000577031.1_Intron|GLIS2_ENST00000433375.1_Silent_p.R24R			Q9BZE0	GLIS2_HUMAN	GLIS family zinc finger 2	24					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|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)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|cervix(4)|endometrium(1)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	11						AAGAGAGAAGCGGGAGAGGAC	0.682													C|||	8	0.00159744	0.0	0.0014	5008	,	,		17887	0.0		0.007	False		,,,				2504	0.0				p.R24R		Atlas-SNP	.											.	GLIS2	29	.	0			c.C70A						PASS	.	C		12,4380	17.9+/-39.9	0,12,2184	38.0	40.0	39.0		70	2.0	1.0	16	dbSNP_126	39	133,8465	67.0+/-129.4	3,127,4169	no	coding-synonymous	GLIS2	NM_032575.2		3,139,6353	AA,AC,CC		1.5469,0.2732,1.1162		24/525	4382351	145,12845	2196	4299	6495	SO:0001819	synonymous_variant	84662	exon1			GAGAAGCGGGAGA	AF325914	CCDS10511.1	16p13.3	2013-01-08			ENSG00000126603	ENSG00000126603		"""Zinc fingers, C2H2-type"""	29450	protein-coding gene	gene with protein product	"""nephrocystin-7"""	608539				11741991, 14500813, 17618285	Standard	NM_032575		Approved	NPHP7	uc002cwc.1	Q9BZE0	OTTHUMG00000129467	ENST00000262366.3:c.70C>A	16.37:g.4382351C>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_032575	B3KX84	Silent	SNP	ENST00000262366.3	37	CCDS10511.1																																																																																			C|0.993;A|0.007	0.007	strong		0.682	GLIS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251630.1	NM_032575	
ZSWIM1	90204	hgsc.bcm.edu	37	20	44511627	44511627	+	Silent	SNP	C	C	T	rs11086984	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44511627C>T	ENST00000372523.1	+	2	491	c.396C>T	c.(394-396)ttC>ttT	p.F132F	ZSWIM1_ENST00000372520.1_Silent_p.F132F	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	132						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				TCCAAGTATTCAAGAAGTTTA	0.542													C|||	210	0.0419329	0.0227	0.0735	5008	,	,		21210	0.001		0.1064	False		,,,				2504	0.0215				p.F132F		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.C396T						PASS	.	C		181,4225	116.7+/-154.6	5,171,2027	112.0	103.0	106.0		396	4.4	1.0	20	dbSNP_120	106	896,7704	200.3+/-244.1	49,798,3453	no	coding-synonymous	ZSWIM1	NM_080603.4		54,969,5480	TT,TC,CC		10.4186,4.108,8.2808		132/486	44511627	1077,11929	2203	4300	6503	SO:0001819	synonymous_variant	90204	exon2			AGTATTCAAGAAG	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"""Zinc fingers, SWIM-type"""	16155	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 162"""	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.396C>T	20.37:g.44511627C>T		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	248	124	0.5	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Silent	SNP	ENST00000372523.1	37	CCDS13382.2																																																																																			C|0.930;T|0.070	0.070	strong		0.542	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603	
PDZRN4	29951	hgsc.bcm.edu	37	12	41967677	41967677	+	Silent	SNP	G	G	A	rs3747556	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	128	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	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	
KIF18B	146909	hgsc.bcm.edu	37	17	43004436	43004436	+	Missense_Mutation	SNP	G	G	A	rs61739617	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:43004436G>A	ENST00000593135.1	-	14	2384	c.2287C>T	c.(2287-2289)Ccc>Tcc	p.P763S	KIF18B_ENST00000438933.2_Missense_Mutation_p.P775S|KIF18B_ENST00000590129.1_Missense_Mutation_p.P784S|KIF18B_ENST00000587309.1_Missense_Mutation_p.P775S|KIF18B_ENST00000339151.4_Missense_Mutation_p.P766S	NM_001265577.1	NP_001252506.1	Q86Y91	KI18B_HUMAN	kinesin family member 18B	775					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|regulation of cell division (GO:0051302)	astral microtubule (GO:0000235)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule plus-end (GO:0035371)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)	21		Prostate(33;0.155)				GTGAACAGGGGCACAGGTGCC	0.637													G|||	119	0.023762	0.0045	0.0274	5008	,	,		18938	0.0		0.0716	False		,,,				2504	0.0225				p.P775S		Atlas-SNP	.											.	KIF18B	63	.	0			c.C2323T						PASS	.	G	SER/PRO	87,3959		1,85,1937	29.0	32.0	31.0		2296	0.3	0.0	17	dbSNP_129	31	594,7746		23,548,3599	yes	missense	KIF18B	NM_001080443.1	74	24,633,5536	AA,AG,GG		7.1223,2.1503,5.4981	benign	766/856	43004436	681,11705	2023	4170	6193	SO:0001583	missense	146909	exon14			ACAGGGGCACAGG		CCDS45709.1, CCDS58555.1, CCDS45709.2	17q21.31	2014-09-04			ENSG00000186185			"""Kinesins"""	27102	protein-coding gene	gene with protein product		614570				16084724	Standard	NM_001264573		Approved		uc010wjh.3	Q86Y91	OTTHUMG00000179867	ENST00000593135.1:c.2287C>T	17.37:g.43004436G>A	ENSP00000465992:p.Pro763Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_001264573	A6NJI2|B7ZM49|B9EGM8|D5L6I1	Missense_Mutation	SNP	ENST00000593135.1	37	CCDS45709.2	68	0.031135531135531136	4	0.008130081300813009	12	0.03314917127071823	0	0.0	52	0.06860158311345646	G	6.660	0.490236	0.12702	0.021503	0.071223	ENSG00000186185	ENST00000438933;ENST00000339151;ENST00000376982	T;T	0.74632	-0.84;-0.86	4.77	0.265	0.15612	.	.	.	.	.	T	0.15262	0.0368	L	0.56769	1.78	0.09310	N	1	B;B;B	0.34103	0.31;0.437;0.437	B;B;B	0.40444	0.176;0.329;0.329	T	0.39035	-0.9633	9	0.39692	T	0.17	.	3.0678	0.06220	0.3388:0.0:0.4714:0.1898	.	775;772;784	Q86Y91;Q86Y91-3;Q86Y91-2	KI18B_HUMAN;.;.	S	775;766;775	ENSP00000412798:P775S;ENSP00000341466:P766S	ENSP00000341466:P766S	P	-	1	0	KIF18B	40359962	0.012000	0.17670	0.008000	0.14137	0.002000	0.02628	0.279000	0.18771	-0.044000	0.13491	-0.136000	0.14681	CCC	G|0.965;A|0.035	0.035	strong		0.637	KIF18B-001	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000448724.1	NM_001080443	
HIST1H1T	3010	hgsc.bcm.edu	37	6	26108168	26108168	+	Missense_Mutation	SNP	G	G	A	rs2051542	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26108168G>A	ENST00000338379.4	-	1	196	c.154C>T	c.(154-156)Ctt>Ttt	p.L52F		NM_005323.3	NP_005314.2	P22492	H1T_HUMAN	histone cluster 1, H1t	52	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.		L -> F (in dbSNP:rs2051542).		binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|nucleosome assembly (GO:0006334)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(1)|lung(3)|ovary(2)|prostate(1)	9						GACACTGAAAGGGCCTCGGTG	0.527													G|||	1087	0.217053	0.0734	0.2133	5008	,	,		19174	0.5506		0.0865	False		,,,				2504	0.2045				p.L52F		Atlas-SNP	.											.	HIST1H1T	40	.	0			c.C154T						PASS	.	G	PHE/LEU	396,4010		21,354,1828	121.0	102.0	108.0		154	0.1	0.0	6	dbSNP_94	108	539,8061		14,511,3775	yes	missense	HIST1H1T	NM_005323.3	22	35,865,5603	AA,AG,GG		6.2674,8.9877,7.189	probably-damaging	52/208	26108168	935,12071	2203	4300	6503	SO:0001583	missense	3010	exon1			CTGAAAGGGCCTC	M60094	CCDS34349.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000187475	ENSG00000187475		"""Histones / Replication-dependent"""	4720	protein-coding gene	gene with protein product		142712	"""H1 histone family, member T (testis-specific)"", ""histone 1, H1t"""	H1FT		8175896, 12408966	Standard	NM_005323		Approved	H1t	uc003ngj.3	P22492	OTTHUMG00000014430	ENST00000338379.4:c.154C>T	6.37:g.26108168G>A	ENSP00000341214:p.Leu52Phe	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	177	80	0.451977	NM_005323	Q6ISI1|Q8IUE8	Missense_Mutation	SNP	ENST00000338379.4	37	CCDS34349.1	531	0.24313186813186813	45	0.09146341463414634	55	0.15193370165745856	355	0.6206293706293706	76	0.10026385224274406	.	16.65	3.183196	0.57800	0.089877	0.062674	ENSG00000187475	ENST00000338379	T	0.31247	1.5	5.35	0.107	0.14544	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.384631	0.25030	N	0.033689	T	0.35098	0.0920	M	0.70595	2.14	0.58432	P	5.999999999950489E-6	D	0.69078	0.997	D	0.70227	0.968	T	0.32241	-0.9914	9	0.87932	D	0	-8.8048	8.9725	0.35915	0.1617:0.5443:0.294:0.0	rs2051542;rs3799376;rs59662229;rs2051542	52	P22492	H1T_HUMAN	F	52	ENSP00000341214:L52F	ENSP00000341214:L52F	L	-	1	0	HIST1H1T	26216147	0.040000	0.19996	0.001000	0.08648	0.001000	0.01503	0.451000	0.21779	0.088000	0.17205	-0.176000	0.13171	CTT	G|0.838;A|0.162	0.162	strong		0.527	HIST1H1T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040093.2	NM_005323	
TBC1D32	221322	hgsc.bcm.edu	37	6	121401996	121401996	+	Missense_Mutation	SNP	T	T	G	rs56300302	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:121401996T>G	ENST00000398212.2	-	32	3744	c.3695A>C	c.(3694-3696)gAa>gCa	p.E1232A	TBC1D32_ENST00000398197.2_5'UTR|TBC1D32_ENST00000275159.6_Missense_Mutation_p.E1273A	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						PASS	.	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	164	0	0		WXS	Illumina HiSeq	Phase_I	194	113	0.582474	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	
PNLIPRP3	119548	hgsc.bcm.edu	37	10	118231317	118231317	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:118231317C>T	ENST00000369230.3	+	10	1244	c.1098C>T	c.(1096-1098)agC>agT	p.S366S		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	366	PLAT.				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)		TCAGTGGAAGCGAAGTCACTC	0.453																																					p.S366S		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.C1098T						PASS	.						203.0	209.0	207.0					10																	118231317		2203	4300	6503	SO:0001819	synonymous_variant	119548	exon10			TGGAAGCGAAGTC	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.1098C>T	10.37:g.118231317C>T		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	200	86	0.43	NM_001011709		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																			.	.	none		0.453	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404	
HNRNPU	3192	hgsc.bcm.edu	37	1	245027349	245027349	+	Silent	SNP	C	C	T	rs6675421	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:245027349C>T	ENST00000283179.9	-	1	424	c.261G>A	c.(259-261)gaG>gaA	p.E87E	HNRNPU_ENST00000444376.2_Silent_p.E87E|RP11-11N7.4_ENST00000610145.1_lincRNA			Q00839	HNRPU_HUMAN	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	87	Asp/Glu-rich (acidic).|Poly-Glu.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasmic ribonucleoprotein granule (GO:0036464)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20	all_cancers(71;6.97e-06)|all_epithelial(71;0.000104)|all_neural(11;0.0269)|Breast(184;0.0545)|Glioma(6;0.0724)|Ovarian(71;0.0761)|all_lung(81;0.0989)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.00868)			cttcctcttcctcctcctctt	0.711													C|||	1428	0.285144	0.4017	0.3919	5008	,	,		13947	0.1706		0.2644	False		,,,				2504	0.1912				p.E87E	NSCLC(33;911 1010 3329 23631 49995)	Atlas-SNP	.											.	HNRNPU	64	.	0			c.G261A						PASS	.		,	1397,2783		245,907,938	7.0	9.0	8.0		261,261	2.8	1.0	1	dbSNP_116	8	1866,6558		215,1436,2561	no	coding-synonymous,coding-synonymous	HNRNPU	NM_004501.3,NM_031844.2	,	460,2343,3499	TT,TC,CC		22.151,33.4211,25.8886	,	87/807,87/826	245027349	3263,9341	2090	4212	6302	SO:0001819	synonymous_variant	3192	exon1			CTCTTCCTCCTCC	X65488	CCDS31081.1, CCDS41479.1	1q44	2011-10-24		2007-08-16	ENSG00000153187	ENSG00000153187			5048	protein-coding gene	gene with protein product		602869		HNRPU		7509195, 8068679	Standard	NM_031844		Approved	SAF-A, hnRNPU	uc001iaz.1	Q00839	OTTHUMG00000040396	ENST00000283179.9:c.261G>A	1.37:g.245027349C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_004501	O75507|Q8N174|Q96HY9|Q9BQ09	Silent	SNP	ENST00000283179.9	37	CCDS41479.1																																																																																			C|0.723;T|0.277	0.277	strong		0.711	HNRNPU-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097163.3	NM_031844	
USPL1	10208	hgsc.bcm.edu	37	13	31233063	31233063	+	Missense_Mutation	SNP	G	G	A	rs3742302	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:31233063G>A	ENST00000255304.4	+	9	3191	c.2849G>A	c.(2848-2850)aGt>aAt	p.S950N		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	950			S -> N (in dbSNP:rs3742302). {ECO:0000269|PubMed:15489334}.		Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		GATATTGCCAGTGAGTCTGCA	0.413													A|||	2377	0.474641	0.8177	0.3876	5008	,	,		20540	0.1786		0.4006	False		,,,				2504	0.454				p.S950N	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.G2849A						PASS	.	A	ASN/SER	3374,1032	380.2+/-323.6	1295,784,124	151.0	152.0	152.0		2849	3.3	0.0	13	dbSNP_107	152	3532,5068	631.7+/-398.5	722,2088,1490	yes	missense	USPL1	NM_005800.4	46	2017,2872,1614	AA,AG,GG		41.0698,23.4226,46.9014	benign	950/1093	31233063	6906,6100	2203	4300	6503	SO:0001583	missense	10208	exon9			TTGCCAGTGAGTC	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 22"""	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.2849G>A	13.37:g.31233063G>A	ENSP00000255304:p.Ser950Asn	Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	954	0.4368131868131868	407	0.8272357723577236	153	0.42265193370165743	100	0.17482517482517482	294	0.38786279683377306	A	0	-2.731200	0.00089	0.765774	0.410698	ENSG00000132952	ENST00000255304	T	0.13307	2.6	5.75	3.31	0.37934	.	0.929244	0.09333	N	0.816635	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	0.28681	-1.0036	9	0.14252	T	0.57	-7.2328	12.7153	0.57111	0.7979:0.0:0.2021:0.0	rs3742302;rs17682754;rs17846218;rs17859235;rs52806569;rs60783730;rs3742302	950	Q5W0Q7	USPL1_HUMAN	N	950	ENSP00000255304:S950N	ENSP00000255304:S950N	S	+	2	0	USPL1	30131063	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.530000	0.02221	-0.104000	0.12154	-2.276000	0.00273	AGT	G|0.506;N|0.000	.	strong		0.413	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800	
TMEM259	91304	hgsc.bcm.edu	37	19	1012120	1012120	+	Silent	SNP	G	G	A	rs7145	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1012120G>A	ENST00000356663.3	-	5	907	c.786C>T	c.(784-786)taC>taT	p.Y262Y	TMEM259_ENST00000333175.5_Silent_p.Y262Y	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	262						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GGATGTCATCGTAGCCCAGGA	0.692													g|||	698	0.139377	0.143	0.1124	5008	,	,		14783	0.0972		0.1561	False		,,,				2504	0.18				p.Y262Y		Atlas-SNP	.											C19orf6,NS,carcinoma,0,1	.	.	1	0			c.C786T						PASS	.	G	,	499,3899	217.4+/-235.8	29,441,1729	34.0	28.0	30.0		786,786	-6.6	0.8	19	dbSNP_52	30	1238,7358	228.9+/-263.8	91,1056,3151	no	coding-synonymous,coding-synonymous	C19orf6	NM_001033026.1,NM_033420.3	,	120,1497,4880	AA,AG,GG		14.402,11.3461,13.3677	,	262/621,262/409	1012120	1737,11257	2199	4298	6497	SO:0001819	synonymous_variant	91304	exon5			GTCATCGTAGCCC	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.786C>T	19.37:g.1012120G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_033420	O60392|Q8NF79|Q96H30	Silent	SNP	ENST00000356663.3	37	CCDS32862.1																																																																																			G|0.868;A|0.132	0.132	strong		0.692	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420	
OR5H2	79310	hgsc.bcm.edu	37	3	98002587	98002587	+	Missense_Mutation	SNP	A	A	G	rs16839611	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:98002587A>G	ENST00000355273.2	+	1	856	c.856A>G	c.(856-858)Ata>Gta	p.I286V	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	286			I -> V (in dbSNP:rs16839611).			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(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						TTATACAATCATAATTCCTTT	0.328													A|||	2547	0.508586	0.6626	0.4524	5008	,	,		17384	0.75		0.2296	False		,,,				2504	0.3783				p.I286V		Atlas-SNP	.											.	OR5H2	63	.	0			c.A856G						PASS	.	A	VAL/ILE	2689,1717	644.4+/-398.0	815,1059,329	53.0	51.0	51.0		856	-1.4	0.0	3	dbSNP_123	51	2102,6498	358.0+/-331.0	273,1556,2471	yes	missense	OR5H2	NM_001005482.1	29	1088,2615,2800	GG,GA,AA		24.4419,38.9696,36.8368	possibly-damaging	286/315	98002587	4791,8215	2203	4300	6503	SO:0001583	missense	79310	exon1			ACAATCATAATTC		CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"""GPCR / Class A : Olfactory receptors"""	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.856A>G	3.37:g.98002587A>G	ENSP00000347418:p.Ile286Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	1099	0.5032051282051282	316	0.6422764227642277	152	0.4198895027624309	451	0.7884615384615384	180	0.23746701846965698	A	0	-2.745156	0.00087	0.610304	0.244419	ENSG00000197938	ENST00000355273	T	0.00018	9.07	3.03	-1.37	0.09056	GPCR, rhodopsin-like superfamily (1);	0.337021	0.21263	N	0.077457	T	0.00012	0.0000	N	0.02403	-0.565	0.80722	P	0.0	P	0.46706	0.883	P	0.50570	0.644	T	0.48502	-0.9030	9	0.02654	T	1	.	4.6526	0.12603	0.4826:0.3037:0.2137:0.0	rs16839611;rs52809881;rs61556920;rs16839611	286	Q8NGV7	OR5H2_HUMAN	V	286	ENSP00000347418:I286V	ENSP00000347418:I286V	I	+	1	0	OR5H2	99485277	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	-0.054000	0.11826	-0.778000	0.04566	-1.509000	0.00949	ATA	A|0.567;G|0.433	0.433	strong		0.328	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2		
DFNB31	25861	hgsc.bcm.edu	37	9	117186712	117186712	+	Missense_Mutation	SNP	C	C	T	rs4978584	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:117186712C>T	ENST00000362057.3	-	6	1486	c.1318G>A	c.(1318-1320)Gcc>Acc	p.A440T	DFNB31_ENST00000265134.6_Missense_Mutation_p.A57T|DFNB31_ENST00000374059.3_Missense_Mutation_p.A89T	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	440			A -> T (in dbSNP:rs4978584).		inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCCATGGTGGCGTGTTCCTGC	0.647													c|||	1143	0.228235	0.0552	0.366	5008	,	,		16701	0.3383		0.2117	False		,,,				2504	0.2679				p.A440T		Atlas-SNP	.											DFNB31,colon,carcinoma,0,1	DFNB31	100	1	0			c.G1318A						scavenged	.	T	THR/ALA,THR/ALA,THR/ALA	366,4040	187.4+/-214.1	11,344,1848	88.0	67.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	169,1318,1318	3.7	0.9	9	dbSNP_111	74	1975,6625	346.7+/-326.3	206,1563,2531	yes	missense,missense,missense	DFNB31	NM_001083885.2,NM_001173425.1,NM_015404.3	58,58,58	217,1907,4379	TT,TC,CC		22.9651,8.3069,17.9994	benign,benign,benign	57/525,440/907,440/908	117186712	2341,10665	2203	4300	6503	SO:0001583	missense	25861	exon6			TGGTGGCGTGTTC	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.1318G>A	9.37:g.117186712C>T	ENSP00000354623:p.Ala440Thr	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	170	70	0.411765	NM_001173425	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	37	CCDS6806.1	519	0.23763736263736263	31	0.06300813008130081	124	0.3425414364640884	204	0.35664335664335667	160	0.21108179419525067	c	14.77	2.634648	0.47049	0.083069	0.229651	ENSG00000095397	ENST00000265134;ENST00000374059;ENST00000362057	T;T;T	0.08807	3.96;3.94;3.05	5.49	3.67	0.42095	.	0.333730	0.33591	N	0.004742	T	0.00012	0.0000	L	0.54908	1.71	0.09310	P	0.9999999999998859	B;B;B	0.13145	0.007;0.007;0.006	B;B;B	0.14023	0.002;0.002;0.01	T	0.46373	-0.9196	9	0.29301	T	0.29	-26.1527	9.6473	0.39875	0.0:0.7871:0.0:0.2129	rs4978584;rs52803964;rs61211333;rs4978584	440;440;89	B9EGE6;Q9P202;Q9P202-4	.;WHRN_HUMAN;.	T	57;89;440	ENSP00000265134:A57T;ENSP00000363172:A89T;ENSP00000354623:A440T	ENSP00000265134:A57T	A	-	1	0	DFNB31	116226533	0.990000	0.36364	0.919000	0.36401	0.787000	0.44495	2.536000	0.45693	0.818000	0.34468	-0.215000	0.12644	GCC	C|0.802;T|0.198	0.198	strong		0.647	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
LY6H	4062	hgsc.bcm.edu	37	8	144240257	144240257	+	Silent	SNP	C	C	G	rs9694368	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144240257C>G	ENST00000430474.2	-	3	315	c.150G>C	c.(148-150)acG>acC	p.T50T	LY6H_ENST00000342752.4_Silent_p.T71T|LY6H_ENST00000414417.2_Silent_p.T71T	NM_002347.4	NP_002338.3	O94772	LY6H_HUMAN	lymphocyte antigen 6 complex, locus H	50	UPAR/Ly6.				nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.T50T(1)		endometrium(1)|lung(1)|stomach(2)	4	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)					TGGCACACACCGTGTCGGACG	0.602													C|||	1610	0.321486	0.3101	0.2968	5008	,	,		16990	0.2768		0.3917	False		,,,				2504	0.3282				p.T71T		Atlas-SNP	.											LY6H,NS,carcinoma,0,1	LY6H	12	1	1	Substitution - coding silent(1)	stomach(1)	c.G213C						scavenged	.	C	,,	1375,3031	453.2+/-350.3	209,957,1037	154.0	124.0	134.0		213,213,150	-6.5	0.8	8	dbSNP_119	134	3680,4920	527.3+/-381.1	774,2132,1394	no	coding-synonymous,coding-synonymous,coding-synonymous	LY6H	NM_001130478.1,NM_001135655.1,NM_002347.4	,,	983,3089,2431	GG,GC,CC		42.7907,31.2074,38.8667	,,	71/162,71/162,50/141	144240257	5055,7951	2203	4300	6503	SO:0001819	synonymous_variant	4062	exon3			ACACACCGTGTCG	AB012293	CCDS6396.1, CCDS47926.1	8q24.3	2008-08-01			ENSG00000176956	ENSG00000176956			6728	protein-coding gene	gene with protein product		603625				9799603	Standard	NM_001130478		Approved	NMLY6	uc011lkb.2	O94772	OTTHUMG00000154890	ENST00000430474.2:c.150G>C	8.37:g.144240257C>G		Somatic	190	2	0.0105263		WXS	Illumina HiSeq	Phase_I	214	123	0.574766	NM_001135655	B2RAD2|J3KQI0|Q6IAX0	Silent	SNP	ENST00000430474.2	37	CCDS6396.1																																																																																			C|0.620;G|0.380	0.380	strong		0.602	LY6H-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337535.1		
SCNN1G	6340	hgsc.bcm.edu	37	16	23200761	23200761	+	Silent	SNP	T	T	C	rs5734	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:23200761T>C	ENST00000300061.2	+	3	530	c.387T>C	c.(385-387)taT>taC	p.Y129Y		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	129					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)|sodium channel activity (GO:0005272)|WW domain binding (GO:0050699)			NS(2)|autonomic_ganglia(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	34				GBM - Glioblastoma multiforme(48;0.0366)	Amiloride(DB00594)|Triamterene(DB00384)	AGTCCCTGTATGGCTTTCCAG	0.587													C|||	1197	0.239018	0.1324	0.3934	5008	,	,		16730	0.1677		0.335	False		,,,				2504	0.2485				p.Y129Y		Atlas-SNP	.											.	SCNN1G	82	.	0			c.T387C						PASS	.	C		742,3652	753.6+/-412.4	58,626,1513	78.0	86.0	83.0		387	-5.3	0.0	16	dbSNP_52	83	2759,5841	677.3+/-403.4	459,1841,2000	no	coding-synonymous	SCNN1G	NM_001039.3		517,2467,3513	CC,CT,TT		32.0814,16.8867,26.9432		129/650	23200761	3501,9493	2197	4300	6497	SO:0001819	synonymous_variant	6340	exon3			CCTGTATGGCTTT	U48937	CCDS10608.1	16p12	2012-02-28	2012-02-28		ENSG00000166828	ENSG00000166828		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10602	protein-coding gene	gene with protein product		600761	"""sodium channel, nonvoltage-gated 1, gamma"", ""sodium channel, non-voltage-gated 1, gamma"""			7490094	Standard	NM_001039		Approved	ENaCgamma, SCNEG	uc002dlm.1	P51170	OTTHUMG00000131609	ENST00000300061.2:c.387T>C	16.37:g.23200761T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Silent	SNP	ENST00000300061.2	37	CCDS10608.1																																																																																			T|0.744;C|0.256	0.256	strong		0.587	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039	
CMYA5	202333	hgsc.bcm.edu	37	5	79041057	79041057	+	Missense_Mutation	SNP	A	A	G	rs12514461	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79041057A>G	ENST00000446378.2	+	4	10778	c.10747A>G	c.(10747-10749)Aaa>Gaa	p.K3583E		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3583	B-box coiled-coil; BBC.		K -> E (in dbSNP:rs12514461). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)		AAACTGTAGTAAAAATGAGAA	0.353													A|||	499	0.0996406	0.0393	0.1744	5008	,	,		18473	0.0833		0.1252	False		,,,				2504	0.1186				p.K3583E		Atlas-SNP	.											.	CMYA5	643	.	0			c.A10747G						PASS	.	A	GLU/LYS	176,3482		8,160,1661	30.0	30.0	30.0		10747	5.4	1.0	5	dbSNP_120	30	903,7257		57,789,3234	yes	missense	CMYA5	NM_153610.3	56	65,949,4895	GG,GA,AA		11.0662,4.8114,9.1301	benign	3583/4070	79041057	1079,10739	1829	4080	5909	SO:0001583	missense	202333	exon4			TGTAGTAAAAATG	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.10747A>G	5.37:g.79041057A>G	ENSP00000394770:p.Lys3583Glu	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	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	222	0.10164835164835165	20	0.04065040650406504	58	0.16022099447513813	45	0.07867132867132867	99	0.13060686015831136	A	14.25	2.478239	0.44044	0.048114	0.110662	ENSG00000164309	ENST00000446378	T	0.26518	1.73	5.43	5.43	0.79202	.	0.000000	0.53938	D	0.000044	T	0.00144	0.0004	L	0.61036	1.89	0.28591	P	0.9096466	D	0.57899	0.981	P	0.53490	0.727	T	0.13202	-1.0518	9	0.59425	D	0.04	.	8.2949	0.31980	0.8513:0.0:0.1487:0.0	rs12514461;rs52825873;rs58659811;rs12514461	3583	Q8N3K9	CMYA5_HUMAN	E	3583	ENSP00000394770:K3583E	ENSP00000394770:K3583E	K	+	1	0	CMYA5	79076813	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.280000	0.58959	2.179000	0.69175	0.533000	0.62120	AAA	A|0.904;G|0.096	0.096	strong		0.353	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21976289	21976289	+	5'UTR	SNP	C	C	T	rs141127873	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:21976289C>T	ENST00000374765.4	-	0	53				RAP1GAP_ENST00000542643.2_5'UTR|RAP1GAP_ENST00000290101.4_Splice_Site_p.G15G|RAP1GAP_ENST00000374757.3_5'UTR	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein						GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		ACTTGTCCACCCTGAAACACA	0.592													C|||	17	0.00339457	0.0008	0.0072	5008	,	,		16650	0.0		0.008	False		,,,				2504	0.0031				p.G15G		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.G45A						PASS	.	C	,,	7,2927		0,7,1460	67.0	65.0	65.0		,45,	2.4	1.0	1	dbSNP_134	65	75,6603		0,75,3264	yes	utr-5,coding-synonymous-near-splice,utr-5	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	0,82,4724	TT,TC,CC		1.1231,0.2386,0.8531	,,	,15/728,	21976289	82,9530	1467	3339	4806	SO:0001623	5_prime_UTR_variant	5909	exon2			GTCCACCCTGAAA	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.-148G>A	1.37:g.21976289C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	163	42	0.257669	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			C|0.996;T|0.004	0.004	strong		0.592	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
ADAD2	161931	hgsc.bcm.edu	37	16	84227713	84227713	+	Intron	SNP	C	C	T	rs78344060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:84227713C>T	ENST00000315906.5	+	2	470				ADAD2_ENST00000268624.3_Missense_Mutation_p.R174C|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2						RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						AACAGGGTGgcgtgggctctg	0.542													C|||	192	0.0383387	0.025	0.0029	5008	,	,		16875	0.0843		0.0159	False		,,,				2504	0.0573				p.R174C		Atlas-SNP	.											ADAD2,caecum,carcinoma,0,1	ADAD2	46	1	0			c.C520T						PASS	.	C	,CYS/ARG	115,4285	87.8+/-126.4	0,115,2085	79.0	71.0	74.0		,520	-0.5	0.0	16	dbSNP_131	74	181,8419	82.3+/-144.9	4,173,4123	yes	intron,missense	ADAD2	NM_001145400.1,NM_139174.3	,180	4,288,6208	TT,TC,CC		2.1047,2.6136,2.2769	,	,174/666	84227713	296,12704	2200	4300	6500	SO:0001627	intron_variant	161931	exon2			GGGTGGCGTGGGC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.419-335C>T	16.37:g.84227713C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	137	30	0.218978	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	37	CCDS45536.1	58	0.026556776556776556	12	0.024390243902439025	2	0.0055248618784530384	33	0.057692307692307696	11	0.014511873350923483	C	7.789	0.711261	0.15239	0.026136	0.021047	ENSG00000140955	ENST00000268624	T	0.21031	2.03	2.79	-0.462	0.12168	.	13.425500	0.00166	N	0.000000	T	0.01029	0.0034	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21075	-1.0256	10	0.42905	T	0.14	.	2.4646	0.04549	0.2464:0.4688:0.0:0.2848	.	174	Q8NCV1-2	.	C	174	ENSP00000268624:R174C	ENSP00000268624:R174C	R	+	1	0	ADAD2	82785214	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.063000	0.03465	-0.070000	0.12908	-0.254000	0.11334	CGT	C|0.975;T|0.025	0.025	strong		0.542	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
FLG	2312	hgsc.bcm.edu	37	1	152284549	152284549	+	Missense_Mutation	SNP	G	G	C	rs141646551	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152284549G>C	ENST00000368799.1	-	3	2848	c.2813C>G	c.(2812-2814)aCa>aGa	p.T938R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	938	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.T938R(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCGCCTGCTTGTCCTGGACCC	0.572									Ichthyosis				-|||	170	0.0339457	0.0	0.0403	5008	,	,		21979	0.0754		0.007	False		,,,				2504	0.0603				p.T938R		Atlas-SNP	.											FLG,rectum,NS,0,1	FLG	900	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2813G						scavenged	.						325.0	297.0	306.0					1																	152284549		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGCTTGTCCTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2813C>G	1.37:g.152284549G>C	ENSP00000357789:p.Thr938Arg	Somatic	412	3	0.00728155		WXS	Illumina HiSeq	Phase_I	546	31	0.0567766	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	5.712	0.315925	0.10789	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.04083	3.71	3.85	0.458	0.16670	.	.	.	.	.	T	0.01124	0.0037	L	0.38531	1.155	0.09310	N	1	B	0.14805	0.011	B	0.23018	0.043	T	0.48163	-0.9059	9	0.30854	T	0.27	.	2.2232	0.03978	0.119:0.1996:0.4931:0.1882	.	938	P20930	FILA_HUMAN	R	938;145	ENSP00000357789:T938R	ENSP00000357789:T938R	T	-	2	0	FLG	150551173	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.641000	0.02007	0.119000	0.18210	0.473000	0.43528	ACA	G|0.989;C|0.011	0.011	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PZP	5858	hgsc.bcm.edu	37	12	9305473	9305473	+	Silent	SNP	T	T	C	rs10771357	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:9305473T>C	ENST00000261336.2	-	31	4096	c.4068A>G	c.(4066-4068)caA>caG	p.Q1356Q	PZP_ENST00000381997.2_Silent_p.Q1142Q	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1356					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						CATCGCAAGTTTGGGGCACAG	0.438													T|||	3281	0.655152	0.5318	0.5937	5008	,	,		-128	0.8899		0.6322	False		,,,				2504	0.6472				p.Q1356Q	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.A4068G						PASS	.	T		2445,1961	620.5+/-393.6	678,1089,436	139.0	127.0	131.0		4068	-1.4	0.9	12	dbSNP_120	131	5379,3221	651.5+/-400.8	1674,2031,595	yes	coding-synonymous	PZP	NM_002864.2		2352,3120,1031	CC,CT,TT		37.4535,44.5075,39.8431		1356/1483	9305473	7824,5182	2203	4300	6503	SO:0001819	synonymous_variant	5858	exon31			GCAAGTTTGGGGC	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.4068A>G	12.37:g.9305473T>C		Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	163	162	0.993865	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																			T|0.362;C|0.638	0.638	strong		0.438	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
ALK	238	hgsc.bcm.edu	37	2	30143499	30143499	+	Silent	SNP	G	G	C	rs4358080	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:30143499G>C	ENST00000389048.3	-	1	933	c.27C>G	c.(25-27)ctC>ctG	p.L9L	ALK_ENST00000431873.1_Silent_p.L9L	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	9					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)	GCAGCGGCAGGAGCCACAGGA	0.736			"""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				C|||	4476	0.89377	0.8003	0.938	5008	,	,		12200	0.998		0.8837	False		,,,				2504	0.8916				p.L9L		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C27G						PASS	.	C		2838,380		1249,340,20	3.0	5.0	4.0		27	2.1	1.0	2	dbSNP_111	4	6073,509		2805,463,23	no	coding-synonymous	ALK	NM_004304.4		4054,803,43	CC,CG,GG		7.7332,11.8086,9.0714		9/1621	30143499	8911,889	1609	3291	4900	SO:0001819	synonymous_variant	238	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CGGCAGGAGCCAC	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.27C>G	2.37:g.30143499G>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.120;C|0.880	0.880	strong		0.736	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
PFKM	5213	hgsc.bcm.edu	37	12	48539482	48539482	+	Silent	SNP	T	T	G	rs8716	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000547587.1_Silent_p.A778A|PFKM_ENST00000395233.2_Silent_p.A747A|PFKM_ENST00000340802.6_Silent_p.A849A|PFKM_ENST00000551804.1_Silent_p.A747A	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	108	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	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	
PHYHIP	9796	hgsc.bcm.edu	37	8	22084503	22084503	+	Silent	SNP	C	C	T	rs11547656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:22084503C>T	ENST00000321613.3	-	4	657	c.201G>A	c.(199-201)ccG>ccA	p.P67P	PHYHIP_ENST00000454243.2_Silent_p.P67P	NM_001099335.1	NP_001092805.1	Q92561	PHYIP_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein	67	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.									endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	10				Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0629)		TCATGGGCAGCGGCACTGCCT	0.622													C|||	1615	0.322484	0.2398	0.3401	5008	,	,		20345	0.2044		0.4304	False		,,,				2504	0.4325				p.P67P		Atlas-SNP	.											.	PHYHIP	24	.	0			c.G201A						PASS	.	C	,	1098,3244		154,790,1227	51.0	60.0	57.0		201,201	-11.4	0.4	8	dbSNP_120	57	3514,5002		728,2058,1472	no	coding-synonymous,coding-synonymous	PHYHIP	NM_001099335.1,NM_014759.3	,	882,2848,2699	TT,TC,CC		41.2635,25.2879,35.8687	,	67/331,67/331	22084503	4612,8246	2171	4258	6429	SO:0001819	synonymous_variant	9796	exon3			GGGCAGCGGCACT	D87463	CCDS43723.1	8p21.2	2010-02-17	2006-01-09		ENSG00000168490	ENSG00000168490			16865	protein-coding gene	gene with protein product		608511	"""phytanoyl-CoA hydroxylase interacting protein"", ""DYRK1A interacting protein 3"""	DYRK1AP3		9039502, 10686344	Standard	NM_014759		Approved	KIAA0273, PAHX-AP	uc003xbj.4	Q92561	OTTHUMG00000163776	ENST00000321613.3:c.201G>A	8.37:g.22084503C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	81	50	0.617284	NM_014759	D3DSR1|Q8N4I9	Silent	SNP	ENST00000321613.3	37	CCDS43723.1																																																																																			T|0.357;G|0.000;C|0.642	0.357	strong		0.622	PHYHIP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375388.1	NM_014759	
MUC4	4585	hgsc.bcm.edu	37	3	195511790	195511790	+	Missense_Mutation	SNP	G	G	A	rs71291863		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195511790G>A	ENST00000463781.3	-	2	7120	c.6661C>T	c.(6661-6663)Cac>Tac	p.H2221Y	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H2221Y	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)		GGGATGGCGTGACCTGTGGAT	0.597																																					p.H2221Y		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,1	MUC4	1505	1	0			c.C6661T						scavenged	.						34.0	32.0	33.0					3																	195511790		679	1585	2264	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.6661C>T	3.37:g.195511790G>A	ENSP00000417498:p.His2221Tyr	Somatic	452	1	0.00221239		WXS	Illumina HiSeq	Phase_I	358	4	0.0111732	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	0.111	-1.137820	0.01742	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.56;1.56	.	.	.	.	.	.	.	.	T	0.12178	0.0296	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.22487	-1.0215	6	.	.	.	.	.	.	.	.	2221	E7ESK3	.	Y	2221	ENSP00000417498:H2221Y;ENSP00000420243:H2221Y	.	H	-	1	0	MUC4	196996185	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	-0.178000	0.09782	-2.619000	0.00441	-2.366000	0.00237	CAC	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MARCH7	64844	hgsc.bcm.edu	37	2	160604452	160604452	+	Silent	SNP	C	C	T	rs11555185	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160604452C>T	ENST00000259050.4	+	5	773	c.651C>T	c.(649-651)gaC>gaT	p.D217D	MARCH7_ENST00000409175.1_Silent_p.D217D|MARCH7_ENST00000539065.1_Silent_p.D161D|MARCH7_ENST00000473749.1_3'UTR|MARCH7_ENST00000409591.1_Silent_p.D179D	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	217	Ser-rich.				protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.D217D(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						GTTCTAGGGACTCCAGAAATT	0.378													C|||	1104	0.220447	0.0287	0.4928	5008	,	,		17238	0.2698		0.33	False		,,,				2504	0.1227				p.D217D		Atlas-SNP	.											MARCH7,colon,carcinoma,0,2	MARCH7	48	2	1	Substitution - coding silent(1)	stomach(1)	c.C651T						scavenged	.	C		305,4101	165.1+/-196.6	10,285,1908	84.0	85.0	85.0		651	2.8	0.9	2	dbSNP_120	85	2715,5885	431.8+/-356.9	425,1865,2010	no	coding-synonymous	MARCH7	NM_022826.2		435,2150,3918	TT,TC,CC		31.5698,6.9224,23.2201		217/705	160604452	3020,9986	2203	4300	6503	SO:0001819	synonymous_variant	64844	exon5			TAGGGACTCCAGA	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.651C>T	2.37:g.160604452C>T		Somatic	342	2	0.00584795		WXS	Illumina HiSeq	Phase_I	305	162	0.531148	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Silent	SNP	ENST00000259050.4	37	CCDS2210.1																																																																																			C|0.761;T|0.239	0.239	strong		0.378	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
CTAGE4	100128553	hgsc.bcm.edu	37	7	143882673	143882673	+	Missense_Mutation	SNP	C	C	T	rs201010806	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:143882673C>T	ENST00000486333.1	+	1	2115	c.2077C>T	c.(2077-2079)Ctt>Ttt	p.L693F		NM_198495.2	NP_940897.2	Q8IX94	CTGE4_HUMAN	CTAGE family, member 4	693	Pro-rich.					integral component of membrane (GO:0016021)				endometrium(1)|ovary(2)	3						TGGCCCTGGCCTTATTCCTCC	0.488																																					p.L693F		Atlas-SNP	.											CTAGE4,NS,carcinoma,0,1	CTAGE4	10	1	0			c.C2077T						scavenged	.						3.0	4.0	4.0					7																	143882673		116	650	766	SO:0001583	missense	100128553	exon1			CCTGGCCTTATTC	AF338232	CCDS55176.1	7q35	2009-10-15			ENSG00000225932	ENSG00000225932			24772	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 4"""	608910				12839582, 11149944	Standard	NM_198495		Approved	FLJ43692, cTAGE-4	uc010lpc.3	Q8IX94	OTTHUMG00000157997	ENST00000486333.1:c.2077C>T	7.37:g.143882673C>T	ENSP00000419539:p.Leu693Phe	Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	215	72	0.334884	NM_198495	A8K871|O95046	Missense_Mutation	SNP	ENST00000486333.1	37	CCDS55176.1	.	.	.	.	.	.	.	.	.	.	.	0.639	-0.814097	0.02798	.	.	ENSG00000225932	ENST00000486333	T	0.05447	3.44	.	.	.	.	.	.	.	.	T	0.00666	0.0022	N	0.00016	-2.855	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36625	-0.9740	7	0.02654	T	1	.	.	.	.	.	693	Q8IX94	CTGE4_HUMAN	F	693	ENSP00000419539:L693F	ENSP00000419539:L693F	L	+	1	0	CTAGE4	143513606	0.830000	0.29337	0.003000	0.11579	0.003000	0.03518	0.348000	0.20031	-1.497000	0.01826	-1.514000	0.00941	CTT	.	.	weak		0.488	CTAGE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349970.1	NM_198495	
IL12B	3593	hgsc.bcm.edu	37	5	158750329	158750329	+	Missense_Mutation	SNP	C	C	T	rs3213096	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:158750329C>T	ENST00000231228.2	-	3	552	c.97G>A	c.(97-99)Gta>Ata	p.V33I		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	33	Ig-like C2-type.		V -> I (in dbSNP:rs3213096). {ECO:0000269|Ref.5}.		cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interferon-gamma production (GO:0032729)|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 lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|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)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)			cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	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)			TCCAATTCTACGACATAAACT	0.502													C|||	19	0.00379393	0.0	0.0043	5008	,	,		20539	0.0		0.0099	False		,,,				2504	0.0061				p.V33I		Atlas-SNP	.											.	IL12B	30	.	0			c.G97A						PASS	.	C	ILE/VAL	7,4399	12.9+/-30.5	0,7,2196	61.0	56.0	58.0		97	5.2	0.9	5	dbSNP_106	58	49,8551	31.2+/-83.2	0,49,4251	yes	missense	IL12B	NM_002187.2	29	0,56,6447	TT,TC,CC		0.5698,0.1589,0.4306	benign	33/329	158750329	56,12950	2203	4300	6503	SO:0001583	missense	3593	exon3			ATTCTACGACATA	M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5970	protein-coding gene	gene with protein product	"""natural killer cell stimulatory factor-2"", ""cytotoxic lymphocyte maturation factor 2, p40"", ""interleukin 12, p40"", ""natural killer cell stimulatory factor, 40 kD subunit"", ""interleukin-12 beta chain"", ""IL12, subunit p40"""	161561	"""interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"""	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.97G>A	5.37:g.158750329C>T	ENSP00000231228:p.Val33Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_002187		Missense_Mutation	SNP	ENST00000231228.2	37	CCDS4346.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	9.248	1.040122	0.19669	0.001589	0.005698	ENSG00000113302	ENST00000231228	T	0.22743	1.94	6.02	5.16	0.70880	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054974	0.64402	D	0.000001	T	0.20210	0.0486	M	0.79475	2.455	0.45791	D	0.998676	B	0.09022	0.002	B	0.12156	0.007	T	0.03473	-1.1033	10	0.46703	T	0.11	-3.6912	11.4605	0.50208	0.0:0.9177:0.0:0.0823	rs3213096;rs17056679;rs17875310;rs52806839;rs56592501;rs3213096	33	P29460	IL12B_HUMAN	I	33	ENSP00000231228:V33I	ENSP00000231228:V33I	V	-	1	0	IL12B	158682907	0.822000	0.29219	0.877000	0.34402	0.087000	0.18053	1.240000	0.32731	1.568000	0.49683	-0.137000	0.14449	GTA	C|0.994;T|0.006	0.006	strong		0.502	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187	
SPATA20	64847	hgsc.bcm.edu	37	17	48625928	48625928	+	Missense_Mutation	SNP	C	C	G	rs8076632	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48625928C>G	ENST00000356488.4	+	3	345	c.262C>G	c.(262-264)Cag>Gag	p.Q88E	SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Missense_Mutation_p.Q104E|SPATA20_ENST00000393244.3_Missense_Mutation_p.Q44E	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	88			Q -> E (in dbSNP:rs8076632). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CCCCTGGGGACAGGAAGCCTT	0.637													C|||	1690	0.33746	0.6831	0.2767	5008	,	,		18074	0.0625		0.3499	False		,,,				2504	0.184				p.Q104E		Atlas-SNP	.											SPATA20,NS,carcinoma,0,1	SPATA20	59	1	0			c.C310G						PASS	.	C	GLU/GLN	2797,1607	646.3+/-398.3	904,989,309	72.0	81.0	78.0		310	4.6	1.0	17	dbSNP_116	78	3108,5492	464.2+/-366.2	561,1986,1753	yes	missense	SPATA20	NM_022827.2	29	1465,2975,2062	GG,GC,CC		36.1395,36.4896,45.4091	benign	104/803	48625928	5905,7099	2202	4300	6502	SO:0001583	missense	64847	exon4			TGGGGACAGGAAG		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.262C>G	17.37:g.48625928C>G	ENSP00000348878:p.Gln88Glu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	746	0.3415750915750916	324	0.6585365853658537	113	0.31215469613259667	48	0.08391608391608392	261	0.34432717678100266	C	10.44	1.351888	0.24512	0.635104	0.361395	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.35973	1.28;1.28;1.28	4.59	4.59	0.56863	Thioredoxin-like fold (2);Domain of unknown function DUF255 (1);	0.057503	0.64402	D	0.000001	T	0.00012	0.0000	N	0.00507	-1.42	0.20403	P	0.9999042779	B;B;B	0.14012	0.009;0.009;0.003	B;B;B	0.12156	0.007;0.007;0.007	T	0.39375	-0.9617	9	0.02654	T	1	-19.6545	15.7482	0.77962	0.0:1.0:0.0:0.0	rs8076632;rs11559097;rs17855972;rs57357545;rs8076632	88;88;104	B4DZC5;Q8TB22;Q8TB22-2	.;SPT20_HUMAN;.	E	104;88;44	ENSP00000006658:Q104E;ENSP00000348878:Q88E;ENSP00000376935:Q44E	ENSP00000006658:Q104E	Q	+	1	0	SPATA20	45980927	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.181000	0.65054	2.368000	0.80403	0.561000	0.74099	CAG	C|0.583;G|0.417	0.417	strong		0.637	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
ZNF16	7564	hgsc.bcm.edu	37	8	146157265	146157265	+	Missense_Mutation	SNP	C	C	T	rs80044147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:146157265C>T	ENST00000276816.4	-	4	1094	c.908G>A	c.(907-909)aGc>aAc	p.S303N	ZNF16_ENST00000394909.2_Missense_Mutation_p.S303N	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	303	Required for nuclear localization.				cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|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(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		CGAGTTCTGGCTGAAGGCTTT	0.478													C|||	5	0.000998403	0.0008	0.0	5008	,	,		20412	0.0		0.004	False		,,,				2504	0.0				p.S303N		Atlas-SNP	.											.	ZNF16	80	.	0			c.G908A						PASS	.	C	ASN/SER,ASN/SER	9,4397	15.5+/-35.6	0,9,2194	72.0	72.0	72.0		908,908	3.1	1.0	8	dbSNP_132	72	31,8569	22.2+/-67.0	0,31,4269	yes	missense,missense	ZNF16	NM_001029976.2,NM_006958.2	46,46	0,40,6463	TT,TC,CC		0.3605,0.2043,0.3076	benign,benign	303/683,303/683	146157265	40,12966	2203	4300	6503	SO:0001583	missense	7564	exon3			TTCTGGCTGAAGG	X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"""Zinc fingers, C2H2-type"""	12947	protein-coding gene	gene with protein product		601262	"""zinc finger protein 16 (KOX 9)"""				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.908G>A	8.37:g.146157265C>T	ENSP00000276816:p.Ser303Asn	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	159	48	0.301887	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Missense_Mutation	SNP	ENST00000276816.4	37	CCDS6437.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	8.817	0.936690	0.18206	0.002043	0.003605	ENSG00000170631	ENST00000276816;ENST00000394909	T;T	0.19394	2.15;2.15	4.02	3.11	0.35812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11110	0.0271	N	0.17594	0.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12268	-1.0554	9	0.42905	T	0.14	.	3.0488	0.06162	0.1772:0.5474:0.1724:0.103	.	303	P17020	ZNF16_HUMAN	N	303	ENSP00000276816:S303N;ENSP00000378369:S303N	ENSP00000276816:S303N	S	-	2	0	ZNF16	146128069	0.000000	0.05858	1.000000	0.80357	0.988000	0.76386	-1.354000	0.02614	2.056000	0.61249	0.563000	0.77884	AGC	C|0.998;T|0.002	0.002	strong		0.478	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958	
FBXL7	23194	hgsc.bcm.edu	37	5	15936591	15936591	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:15936591C>T	ENST00000504595.1	+	4	1253	c.772C>T	c.(772-774)Cgg>Tgg	p.R258W	FBXL7_ENST00000510662.1_Missense_Mutation_p.R211W|FBXL7_ENST00000329673.7_Missense_Mutation_p.R246W|MIR887_ENST00000401258.1_RNA	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	258					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.R258W(2)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						CAGCTTGACCCGGGAGGCCTC	0.582																																					p.R258W		Atlas-SNP	.											FBXL7,colon,carcinoma,0,3	FBXL7	138	3	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C772T						scavenged	.						51.0	51.0	51.0					5																	15936591		2101	4220	6321	SO:0001583	missense	23194	exon4			TTGACCCGGGAGG	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"""F-boxes / Leucine-rich repeats"""	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.772C>T	5.37:g.15936591C>T	ENSP00000423630:p.Arg258Trp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	87	2	0.0229885	NM_012304	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	37	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.386340	0.61956	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.53857	0.6;0.6;0.6	5.31	5.31	0.75309	.	0.053169	0.85682	D	0.000000	T	0.65217	0.2670	L	0.61036	1.89	0.80722	D	1	D	0.71674	0.998	P	0.54174	0.744	T	0.69146	-0.5222	10	0.72032	D	0.01	.	18.9742	0.92728	0.0:1.0:0.0:0.0	.	258	Q9UJT9	FBXL7_HUMAN	W	258;211;246	ENSP00000423630:R258W;ENSP00000425184:R211W;ENSP00000329632:R246W	ENSP00000329632:R246W	R	+	1	2	FBXL7	15989591	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.940000	0.70187	2.495000	0.84180	0.655000	0.94253	CGG	.	.	none		0.582	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559679	140559679	+	Silent	SNP	C	C	G	rs17844507	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140559679C>G	ENST00000239444.2	+	1	2309	c.2064C>G	c.(2062-2064)acC>acG	p.T688T	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	688					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)			ACTCTCTCACCGTCTACCTGG	0.677													C|||	542	0.108227	0.1021	0.1744	5008	,	,		16544	0.0407		0.1531	False		,,,				2504	0.093				p.T688T		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C2064G						PASS	.	C		495,3909		29,437,1736	82.0	80.0	81.0		2064	-1.2	0.0	5	dbSNP_123	81	1406,7190		121,1164,3013	no	coding-synonymous	PCDHB8	NM_019120.3		150,1601,4749	GG,GC,CC		16.3564,11.2398,14.6231		688/802	140559679	1901,11099	2202	4298	6500	SO:0001819	synonymous_variant	56128	exon1			TCTCACCGTCTAC	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.2064C>G	5.37:g.140559679C>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	55	34	0.618182	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			C|0.863;G|0.137	0.137	strong		0.677	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
SLC5A8	160728	hgsc.bcm.edu	37	12	101587518	101587518	+	Missense_Mutation	SNP	C	C	T	rs1709189	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	213	0	0		WXS	Illumina HiSeq	Phase_I	165	73	0.442424	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	
PYGB	5834	hgsc.bcm.edu	37	20	25259006	25259006	+	Missense_Mutation	SNP	G	G	T	rs2228976	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:25259006G>T	ENST00000216962.4	+	8	1017	c.907G>T	c.(907-909)Gcc>Tcc	p.A303S		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	303			A -> S (in dbSNP:rs2228976).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)	p.A303S(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						CGTGGTGGCCGCCACGCTCCA	0.607													g|||	813	0.16234	0.053	0.1297	5008	,	,		17613	0.3512		0.1849	False		,,,				2504	0.1155				p.A303S		Atlas-SNP	.											PYGB,NS,carcinoma,0,2	PYGB	84	2	1	Substitution - Missense(1)	stomach(1)	c.G907T						PASS	.	G	SER/ALA	352,4054	181.2+/-209.3	10,332,1861	80.0	73.0	75.0		907	3.6	1.0	20	dbSNP_98	75	1597,7003	296.5+/-302.9	154,1289,2857	yes	missense	PYGB	NM_002862.3	99	164,1621,4718	TT,TG,GG		18.5698,7.9891,14.9854	probably-damaging	303/844	25259006	1949,11057	2203	4300	6503	SO:0001583	missense	5834	exon8			GTGGCCGCCACGC		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.907G>T	20.37:g.25259006G>T	ENSP00000216962:p.Ala303Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	CCDS13171.1	427	0.1955128205128205	29	0.05894308943089431	58	0.16022099447513813	198	0.34615384615384615	142	0.18733509234828497	G	29.8	5.036398	0.93630	0.079891	0.185698	ENSG00000100994	ENST00000216962	D	0.96459	-4.02	3.61	3.61	0.41365	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.89095	3.005	0.09310	P	0.9999999999226815	D	0.55385	0.971	D	0.66084	0.941	T	0.00000	-1.8628	9	0.54805	T	0.06	-33.8764	15.4242	0.75038	0.0:0.0:1.0:0.0	rs2228976;rs3818199;rs2228976	303	P11216	PYGB_HUMAN	S	303	ENSP00000216962:A303S	ENSP00000216962:A303S	A	+	1	0	PYGB	25207006	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.378000	0.97191	2.027000	0.59764	0.462000	0.41574	GCC	G|0.833;T|0.167	0.167	strong		0.607	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
UGT3A2	167127	hgsc.bcm.edu	37	5	36039683	36039683	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:36039683G>A	ENST00000282507.3	-	5	1072	c.971C>T	c.(970-972)cCc>cTc	p.P324L	UGT3A2_ENST00000513300.1_Missense_Mutation_p.P290L|UGT3A2_ENST00000504954.1_5'Flank|UGT3A2_ENST00000545528.1_Missense_Mutation_p.P22L	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	324					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CACCCCTTGGGGTAGGTGAGC	0.502																																					p.P324L		Atlas-SNP	.											UGT3A2,rectum,carcinoma,-1,1	UGT3A2	117	1	0			c.C971T						scavenged	.						143.0	131.0	135.0					5																	36039683		2203	4300	6503	SO:0001583	missense	167127	exon5			CCTTGGGGTAGGT		CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"""UDP glucuronosyltransferases"""	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.971C>T	5.37:g.36039683G>A	ENSP00000282507:p.Pro324Leu	Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	132	2	0.0151515	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.113366	0.77210	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.68765	-0.35;-0.35;-0.35	3.18	3.18	0.36537	.	0.074676	0.53938	D	0.000051	D	0.83727	0.5317	H	0.96111	3.77	0.21782	N	0.999546	P;P	0.50066	0.738;0.931	P;P	0.55455	0.776;0.737	T	0.78740	-0.2086	10	0.87932	D	0	.	14.2717	0.66155	0.0:0.0:1.0:0.0	.	290;324	E9PFK7;Q3SY77	.;UD3A2_HUMAN	L	324;290;22	ENSP00000282507:P324L;ENSP00000427404:P290L;ENSP00000445367:P22L	ENSP00000282507:P324L	P	-	2	0	UGT3A2	36075440	0.996000	0.38824	0.009000	0.14445	0.320000	0.28249	5.518000	0.67068	2.077000	0.62373	0.591000	0.81541	CCC	.	.	none		0.502	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914	
CENPO	79172	hgsc.bcm.edu	37	2	25022598	25022598	+	Missense_Mutation	SNP	A	A	G	rs1550116	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:25022598A>G	ENST00000380834.2	+	3	526	c.101A>G	c.(100-102)cAg>cGg	p.Q34R	CENPO_ENST00000473706.1_Missense_Mutation_p.Q28R|CENPO_ENST00000260662.1_Missense_Mutation_p.Q34R			Q9BU64	CENPO_HUMAN	centromere protein O	34			Q -> R (in dbSNP:rs1550116). {ECO:0000269|PubMed:14702039}.		CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					TCCCGTAAACAGTCTGAAGAG	0.498													A|||	663	0.132388	0.1097	0.1138	5008	,	,		19092	0.2063		0.1461	False		,,,				2504	0.0859				p.Q34R		Atlas-SNP	.											.	CENPO	18	.	0			c.A101G						PASS	.	A	ARG/GLN,ARG/GLN	486,3920	226.5+/-242.0	21,444,1738	89.0	99.0	96.0		83,101	-3.6	0.0	2	dbSNP_88	96	1275,7325	252.5+/-278.5	85,1105,3110	yes	missense,missense	CENPO	NM_001199803.1,NM_024322.2	43,43	106,1549,4848	GG,GA,AA		14.8256,11.0304,13.5399	benign,benign	28/295,34/301	25022598	1761,11245	2203	4300	6503	SO:0001583	missense	79172	exon3			GTAAACAGTCTGA	AK027859	CCDS1714.1, CCDS56113.1	2p23.3	2013-11-05			ENSG00000138092	ENSG00000138092			28152	protein-coding gene	gene with protein product		611504				16622420, 16622419	Standard	NM_024322		Approved	MGC11266, CENP-O	uc002rfp.2	Q9BU64	OTTHUMG00000125525	ENST00000380834.2:c.101A>G	2.37:g.25022598A>G	ENSP00000370214:p.Gln34Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_024322	B2RDC0|D6W536|Q53T55|Q96JV3	Missense_Mutation	SNP	ENST00000380834.2	37	CCDS1714.1	332	0.152014652014652	47	0.09552845528455285	54	0.14917127071823205	123	0.21503496503496503	108	0.1424802110817942	A	2.705	-0.270191	0.05716	0.110304	0.148256	ENSG00000138092	ENST00000380834;ENST00000473706;ENST00000260662	T;T;T	0.44482	0.92;0.95;0.92	4.75	-3.63	0.04529	.	0.848021	0.10091	N	0.717152	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	0.26503	-1.0101	9	0.44086	T	0.13	-23.6971	6.5348	0.22346	0.4062:0.1499:0.4439:0.0	rs1550116;rs52799040;rs61143613;rs1550116	28;34	Q9BU64-2;Q9BU64	.;CENPO_HUMAN	R	34;28;34	ENSP00000370214:Q34R;ENSP00000417787:Q28R;ENSP00000260662:Q34R	ENSP00000260662:Q34R	Q	+	2	0	CENPO	24876102	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	0.288000	0.18939	-0.951000	0.03654	-0.792000	0.03331	CAG	A|0.859;G|0.141	0.141	strong		0.498	CENPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246856.2	NM_024322	
TTLL4	9654	hgsc.bcm.edu	37	2	219602499	219602499	+	Missense_Mutation	SNP	G	G	C	rs3731877	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000258398.4_Missense_Mutation_p.E34Q|TTLL4_ENST00000457313.1_Intron	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	167	0	0		WXS	Illumina HiSeq	Phase_I	113	32	0.283186	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	
SPSB1	80176	hgsc.bcm.edu	37	1	9416346	9416346	+	Silent	SNP	C	C	T	rs3795309	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:9416346C>T	ENST00000328089.6	+	2	737	c.396C>T	c.(394-396)ctC>ctT	p.L132L	SPSB1_ENST00000377399.2_Silent_p.L132L|SPSB1_ENST00000357898.3_Silent_p.L132L	NM_025106.3	NP_079382.2	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box containing 1	132	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(2)|lung(5)|prostate(2)	13	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)		ACACAACCCTCGTGGGGAATA	0.637													C|||	987	0.197085	0.0651	0.1758	5008	,	,		16950	0.2798		0.3161	False		,,,				2504	0.183				p.L132L		Atlas-SNP	.											.	SPSB1	22	.	0			c.C396T						PASS	.	C		426,3980	202.8+/-225.5	28,370,1805	44.0	44.0	44.0		396	-5.8	0.9	1	dbSNP_107	44	2571,6029	411.1+/-350.4	378,1815,2107	no	coding-synonymous	SPSB1	NM_025106.3		406,2185,3912	TT,TC,CC		29.8953,9.6686,23.0432		132/274	9416346	2997,10009	2203	4300	6503	SO:0001819	synonymous_variant	80176	exon2			AACCCTCGTGGGG		CCDS102.1	1p36.22	2008-02-05			ENSG00000171621	ENSG00000171621			30628	protein-coding gene	gene with protein product		611657				15713673, 12076535	Standard	NM_025106		Approved	SSB-1	uc010oae.2	Q96BD6	OTTHUMG00000001279	ENST00000328089.6:c.396C>T	1.37:g.9416346C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	39	28	0.717949	NM_025106	A2A275|Q59FA1|Q5TIH9|Q9BRY9|Q9H6C5	Silent	SNP	ENST00000328089.6	37	CCDS102.1																																																																																			C|0.763;T|0.237	0.237	strong		0.637	SPSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003727.2	NM_025106	
LSS	4047	hgsc.bcm.edu	37	21	47614443	47614443	+	Silent	SNP	A	A	G	rs2254522	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:47614443A>G	ENST00000397728.3	-	20	2028	c.1950T>C	c.(1948-1950)caT>caC	p.H650H	AP001468.1_ENST00000594486.1_5'Flank|LSS_ENST00000522411.1_Silent_p.H639H|LSS_ENST00000356396.4_Silent_p.H650H|LSS_ENST00000457828.2_Silent_p.H570H	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	650					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)					AGCATGTGTTATGGATCTGGG	0.622													G|||	1695	0.338458	0.3253	0.2637	5008	,	,		20984	0.5655		0.1958	False		,,,				2504	0.3221				p.H650H	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.T1950C						PASS	.	G	,,,	1379,3027	687.5+/-404.9	223,933,1047	98.0	78.0	85.0		1950,1917,1710,1950	1.2	1.0	21	dbSNP_100	85	1740,6860	735.0+/-406.9	167,1406,2727	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	,,,	390,2339,3774	GG,GA,AA		20.2326,31.2982,23.9812	,,,	650/733,639/722,570/653,650/733	47614443	3119,9887	2203	4300	6503	SO:0001819	synonymous_variant	4047	exon20			TGTGTTATGGATC	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.1950T>C	21.37:g.47614443A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	141	76	0.539007	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	ENST00000397728.3	37	CCDS13733.1	703	0.3218864468864469	126	0.25609756097560976	76	0.20994475138121546	347	0.6066433566433567	154	0.20316622691292877	G	5.699	0.313580	0.10789	0.312982	0.202326	ENSG00000160285	ENST00000419093	.	.	.	5.07	1.21	0.21127	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999816	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0859	0.36581	0.3764:0.0:0.6236:0.0	rs2254522;rs2254522	.	.	.	Q	18	.	.	X	-	1	0	LSS	46438871	1.000000	0.71417	0.967000	0.41034	0.432000	0.31715	2.487000	0.45268	-0.190000	0.10465	-0.726000	0.03593	TAA	A|0.712;C|0.002	.	strong		0.622	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
AIM1L	55057	hgsc.bcm.edu	37	1	26673108	26673108	+	5'Flank	SNP	C	C	T	rs11247925	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:26673108C>T	ENST00000308182.5	-	0	0				RN7SL490P_ENST00000579210.1_RNA|AIM1L_ENST00000527815.1_5'Flank			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like								carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|pancreas(1)|skin(2)	12		all_cancers(24;4.67e-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;1.51e-27)|Colorectal(126;1.61e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000792)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|STAD - Stomach adenocarcinoma(196;0.00154)|GBM - Glioblastoma multiforme(114;0.00858)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.165)|LUSC - Lung squamous cell carcinoma(448;0.239)		ACTTACCACTCGGGCCTTGGC	0.637													C|||	898	0.179313	0.1505	0.1931	5008	,	,		16282	0.1438		0.1918	False		,,,				2504	0.2321				p.R14Q		Atlas-SNP	.											.	AIM1L	98	.	0			c.G41A						PASS	.	C	GLN/ARG	533,3273		35,463,1405	9.0	10.0	10.0		41	2.4	1.0	1	dbSNP_120	10	1557,6629		156,1245,2692	yes	missense	AIM1L	NM_001039775.3	43	191,1708,4097	TT,TC,CC		19.0203,14.0042,17.4283	benign	14/1662	26673108	2090,9902	1903	4093	5996	SO:0001631	upstream_gene_variant	55057	exon2			ACCACTCGGGCCT			1p35	2010-07-14			ENSG00000176092	ENSG00000176092			17295	protein-coding gene	gene with protein product	"""beta-gamma crystallin domain containing 2"""						Standard	NM_001039775		Approved	CRYBG2, FLJ38020	uc001bmd.4	Q8N1P7	OTTHUMG00000003490		1.37:g.26673108C>T	Exception_encountered	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	63	18	0.285714	NM_001039775	B2RNG3|Q5T137|Q5T150	Missense_Mutation	SNP	ENST00000308182.5	37		375	0.1717032967032967	71	0.1443089430894309	73	0.20165745856353592	99	0.17307692307692307	132	0.1741424802110818	C	13.55	2.270057	0.40194	0.140042	0.190203	ENSG00000176092	ENST00000538018;ENST00000449629;ENST00000475866	T	0.18657	2.2	5.29	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.46028	P	0.0011759999999999549	P	0.40230	0.708	B	0.28232	0.087	T	0.25572	-1.0128	8	0.02654	T	1	.	5.4485	0.16550	0.0:0.6438:0.1767:0.1795	rs11247925;rs61517510;rs11247925	14	E7ET48	.	Q	14	ENSP00000428746:R14Q	ENSP00000363323:R14Q	R	-	2	0	AIM1L	26545695	0.405000	0.25336	0.996000	0.52242	0.572000	0.35998	0.092000	0.15066	0.242000	0.21303	0.655000	0.94253	CGA	C|0.834;T|0.166	0.166	strong		0.637	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2	
CAST	831	hgsc.bcm.edu	37	5	96031569	96031569	+	5'UTR	SNP	A	A	G	rs9667	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:96031569A>G	ENST00000341926.3	+	0	81				AC020900.2_ENST00000580431.1_RNA|CAST_ENST00000508608.1_Silent_p.Q41Q|CAST_ENST00000338252.3_5'UTR|CAST_ENST00000325674.7_Silent_p.Q56Q|CAST_ENST00000395813.1_Silent_p.Q56Q|CAST_ENST00000508830.1_Silent_p.Q56Q|CAST_ENST00000395812.2_Silent_p.Q56Q|CAST_ENST00000510756.1_Silent_p.Q56Q|CAST_ENST00000359176.4_Silent_p.Q56Q			P20810	ICAL_HUMAN	calpastatin						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)		GCAGCAGTCAATCCTCCAGAA	0.428													A|||	1014	0.202476	0.1225	0.2305	5008	,	,		16879	0.253		0.1889	False		,,,				2504	0.2526				p.Q56Q		Atlas-SNP	.											.	CAST	58	.	0			c.A168G						PASS	.	A	,	500,3220		38,424,1398	42.0	40.0	41.0		168,	-8.6	0.0	5	dbSNP_52	41	1564,6620		154,1256,2682	no	coding-synonymous,utr-5	CAST	NM_001042440.2,NM_001190442.1	,	192,1680,4080	GG,GA,AA		19.1105,13.4409,17.3387	,	56/751,	96031569	2064,9840	1860	4092	5952	SO:0001623	5_prime_UTR_variant	831	exon3			CAGTCAATCCTCC	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.-82A>G	5.37:g.96031569A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	184	90	0.48913	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Silent	SNP	ENST00000341926.3	37		408	0.18681318681318682	50	0.1016260162601626	73	0.20165745856353592	143	0.25	142	0.18733509234828497	A	1.723	-0.496032	0.04291	0.134409	0.191105	ENSG00000153113	ENST00000512620	.	.	.	5.18	-8.58	0.00897	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.37307	P	0.091028	.	.	.	.	.	.	T	0.16600	-1.0397	3	.	.	.	-0.5219	8.4796	0.33034	0.6194:0.2114:0.1693:0.0	rs9667;rs27894;rs1135385;rs3198018;rs9667	.	.	.	S	39	.	.	N	+	2	0	CAST	96057325	0.000000	0.05858	0.002000	0.10522	0.226000	0.24999	-1.032000	0.03574	-1.388000	0.02092	0.459000	0.35465	AAT	A|0.818;G|0.182	0.182	strong		0.428	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	
SH3BGR	6450	hgsc.bcm.edu	37	21	40871810	40871810	+	Missense_Mutation	SNP	T	T	C	rs9974333	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:40871810T>C	ENST00000333634.4	+	4	641	c.563T>C	c.(562-564)gTg>gCg	p.V188A	SH3BGR_ENST00000380634.1_Missense_Mutation_p.V77A|SH3BGR_ENST00000380637.3_Missense_Mutation_p.V77A|SH3BGR_ENST00000380631.1_Missense_Mutation_p.V77A|SH3BGR_ENST00000458295.1_Intron	NM_007341.2	NP_031367	P55822	SH3BG_HUMAN	SH3 domain binding glutamate-rich protein	188	Glu-rich (acidic).		V -> A (in dbSNP:rs9974333). {ECO:0000269|PubMed:15489334}.		positive regulation of signal transduction (GO:0009967)|protein complex assembly (GO:0006461)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(2)	8		all_cancers(19;1.16e-23)|all_epithelial(19;1.22e-20)|Prostate(19;2.55e-06)|Breast(209;0.0133)		STAD - Stomach adenocarcinoma(101;0.00151)		AGTGAAGATGTGGGCAACCTC	0.468													C|||	2759	0.550919	0.4334	0.6124	5008	,	,		20218	0.6905		0.5288	False		,,,				2504	0.545				p.V188A		Atlas-SNP	.											SH3BGR,NS,carcinoma,-1,2	SH3BGR	29	2	0			c.T563C						scavenged	.	C	ALA/VAL,ALA/VAL	1983,2423		447,1089,667	124.0	114.0	117.0		230,563	-1.8	0.0	21	dbSNP_119	117	4599,4001		1239,2121,940	yes	missense,missense	SH3BGR	NM_001001713.1,NM_007341.2	64,64	1686,3210,1607	CC,CT,TT		46.5233,45.0068,49.3926	benign,benign	77/129,188/240	40871810	6582,6424	2203	4300	6503	SO:0001583	missense	6450	exon4			AAGATGTGGGCAA		CCDS13666.1, CCDS33560.1	21q22.3	2014-02-19	2014-02-19		ENSG00000185437	ENSG00000185437			10822	protein-coding gene	gene with protein product	"""21-glutamic acid-rich protein"""	602230	"""SH3 domain binding glutamic acid-rich protein"""			9050928	Standard	NM_007341		Approved	21-GARP	uc002yya.3	P55822	OTTHUMG00000074113	ENST00000333634.4:c.563T>C	21.37:g.40871810T>C	ENSP00000332513:p.Val188Ala	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	107	74	0.691589	NM_007341	A6ND59|D3DSI2|Q9BRB8	Missense_Mutation	SNP	ENST00000333634.4	37	CCDS13666.1	1189	0.5444139194139194	194	0.3943089430894309	210	0.580110497237569	390	0.6818181818181818	395	0.521108179419525	.	2.530	-0.308722	0.05458	0.450068	0.534767	ENSG00000185437	ENST00000380637;ENST00000380634;ENST00000440288;ENST00000380631;ENST00000333634;ENST00000423596;ENST00000447939	T;T;T;T;T;T;T	0.56275	1.03;1.03;1.06;1.03;1.98;0.8;0.47	4.96	-1.76	0.08006	.	1.400190	0.03918	N	0.282949	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	0.43940	-0.9360	9	0.02654	T	1	.	0.4012	0.00426	0.2399:0.2441:0.2734:0.2426	rs9974333;rs11575940;rs52803258;rs61401446;rs9974333	188	P55822	SH3BG_HUMAN	A	77;77;77;77;188;30;21	ENSP00000370011:V77A;ENSP00000370008:V77A;ENSP00000401572:V77A;ENSP00000370005:V77A;ENSP00000332513:V188A;ENSP00000413981:V30A;ENSP00000403115:V21A	ENSP00000332513:V188A	V	+	2	0	SH3BGR	39793680	0.000000	0.05858	0.006000	0.13384	0.035000	0.12851	-1.098000	0.03346	-0.467000	0.06932	-0.231000	0.12243	GTG	T|0.476;C|0.524	0.524	strong		0.468	SH3BGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157377.6	NM_007341	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100636586	100636586	+	Silent	SNP	G	G	A	rs4965583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:100636586G>A	ENST00000268070.4	-	15	2217	c.2112C>T	c.(2110-2112)ggC>ggT	p.G704G		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	704	Spacer.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		GGCTGAAGTCGCCCTTCACCA	0.577													g|||	1321	0.263778	0.2504	0.2925	5008	,	,		17908	0.5		0.1262	False		,,,				2504	0.1595				p.G704G		Atlas-SNP	.											.	ADAMTS17	127	.	0			c.C2112T						PASS	.	G		1028,3378	376.8+/-322.2	113,802,1288	110.0	118.0	115.0		2112	-9.5	0.9	15	dbSNP_111	115	1127,7473	231.2+/-265.3	82,963,3255	no	coding-synonymous	ADAMTS17	NM_139057.2		195,1765,4543	AA,AG,GG		13.1047,23.3318,16.5693		704/1096	100636586	2155,10851	2203	4300	6503	SO:0001819	synonymous_variant	170691	exon15			GAAGTCGCCCTTC	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.2112C>T	15.37:g.100636586G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	37	CCDS10383.1																																																																																			G|0.801;A|0.199	0.199	strong		0.577	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
LAMA2	3908	hgsc.bcm.edu	37	6	129813053	129813053	+	Missense_Mutation	SNP	A	A	G	rs2244008	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:129813053A>G	ENST00000421865.2	+	57	7955	c.7906A>G	c.(7906-7908)Aca>Gca	p.T2636A	LAMA2_ENST00000498257.1_3'UTR	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2636	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		T -> A (in dbSNP:rs2244008).		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)	p.T2636A(1)		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)		CAGCATCTTTACAGTTCAAGT	0.373													A|||	559	0.111621	0.121	0.0749	5008	,	,		19091	0.1319		0.0686	False		,,,				2504	0.1483				p.T2636A		Atlas-SNP	.											LAMA2,NS,carcinoma,0,1	LAMA2	481	1	1	Substitution - Missense(1)	stomach(1)	c.A7906G						scavenged	.	A	ALA/THR,ALA/THR	509,3897	230.7+/-244.8	36,437,1730	39.0	41.0	40.0		7894,7906	5.5	1.0	6	dbSNP_100	40	542,8058	149.1+/-204.2	18,506,3776	yes	missense,missense	LAMA2	NM_001079823.1,NM_000426.3	58,58	54,943,5506	GG,GA,AA		6.3023,11.5524,8.0809	benign,benign	2632/3119,2636/3123	129813053	1051,11955	2203	4300	6503	SO:0001583	missense	3908	exon57			ATCTTTACAGTTC	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.7906A>G	6.37:g.129813053A>G	ENSP00000400365:p.Thr2636Ala	Somatic	60	2	0.0333333		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	220	0.10073260073260074	52	0.10569105691056911	26	0.0718232044198895	88	0.15384615384615385	54	0.0712401055408971	A	13.41	2.230055	0.39399	0.115524	0.063023	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.77358	-1.09	5.46	5.46	0.80206	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.239075	0.49916	D	0.000140	T	0.62986	0.2473	M	0.70842	2.15	0.29946	P	0.8206370000000001	B;B	0.15930	0.015;0.015	B;B	0.14023	0.01;0.01	T	0.62374	-0.6868	8	.	.	.	.	10.9615	0.47387	0.9268:0.0:0.0732:0.0	rs2244008;rs59479676;rs2244008	2637;2636	A6NF00;P24043	.;LAMA2_HUMAN	A	2636;2635;2636;654	ENSP00000400365:T2636A	.	T	+	1	0	LAMA2	129854746	1.000000	0.71417	0.959000	0.39883	0.653000	0.38743	4.011000	0.57124	2.196000	0.70406	0.482000	0.46254	ACA	A|0.905;C|0.001	.	strong		0.373	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
PDLIM7	9260	hgsc.bcm.edu	37	5	176916516	176916516	+	Silent	SNP	C	C	T	rs335462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:176916516C>T	ENST00000355841.2	-	9	813	c.747G>A	c.(745-747)ccG>ccA	p.P249P	PDLIM7_ENST00000359895.2_Silent_p.P215P|PDLIM7_ENST00000356618.4_Missense_Mutation_p.G229S|PDLIM7_ENST00000393551.1_Missense_Mutation_p.G229S	NM_005451.3	NP_005442.2	Q9NR12	PDLI7_HUMAN	PDZ and LIM domain 7 (enigma)	249					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of osteoblast differentiation (GO:0045669)|receptor-mediated endocytosis (GO:0006898)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ruffle (GO:0001726)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	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)			TGGGCGTGGCCGGCTGGCTGT	0.701													C|||	2191	0.4375	0.3918	0.3761	5008	,	,		15052	0.3889		0.5278	False		,,,				2504	0.5				p.P249P		Atlas-SNP	.											PDLIM7,NS,carcinoma,0,1	PDLIM7	32	1	0			c.G747A						scavenged	.	C	,	1675,2719		314,1047,836	20.0	25.0	23.0		747,645	-10.5	0.7	5	dbSNP_79	23	4502,4088		1196,2110,989	no	coding-synonymous,coding-synonymous	PDLIM7	NM_005451.3,NM_203352.1	,	1510,3157,1825	TT,TC,CC		47.5902,38.1202,47.5739	,	249/458,215/424	176916516	6177,6807	2197	4295	6492	SO:0001819	synonymous_variant	9260	exon9			CGTGGCCGGCTGG	BC001093	CCDS4422.1, CCDS4423.1, CCDS4424.1	5q35.3	2008-02-05			ENSG00000196923	ENSG00000196923			22958	protein-coding gene	gene with protein product		605903				11874232	Standard	NM_005451		Approved	ENIGMA	uc003mhc.1	Q9NR12	OTTHUMG00000130853	ENST00000355841.2:c.747G>A	5.37:g.176916516C>T		Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	54	37	0.685185	NM_005451	Q14250|Q5XG82|Q6NVZ5|Q96C91|Q9BXB8|Q9BXB9	Silent	SNP	ENST00000355841.2	37	CCDS4422.1	964	0.4413919413919414	197	0.40040650406504064	151	0.4171270718232044	200	0.34965034965034963	416	0.5488126649076517	C	18.15	3.560441	0.65538	0.381202	0.524098	ENSG00000196923	ENST00000356618;ENST00000393551	T;T	0.14893	2.47;2.47	5.23	-10.5	0.00291	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.45150	P	0.0018319999999999448	B	0.10296	0.003	B	0.14023	0.01	T	0.43605	-0.9381	7	0.26408	T	0.33	.	3.1136	0.06367	0.0856:0.2287:0.2775:0.4081	rs335462;rs337408;rs1625748;rs3175031;rs335462	229	Q9NR12-4	.	S	229	ENSP00000349030:G229S;ENSP00000377182:G229S	ENSP00000349030:G229S	G	-	1	0	PDLIM7	176849122	0.000000	0.05858	0.695000	0.30226	0.984000	0.73092	-5.689000	0.00104	-1.901000	0.01096	-0.378000	0.06908	GGC	C|0.555;T|0.445	0.445	strong		0.701	PDLIM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253423.1	NM_005451	
FUK	197258	hgsc.bcm.edu	37	16	70503095	70503095	+	Missense_Mutation	SNP	A	A	G	rs113497209	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:70503095A>G	ENST00000288078.6	+	10	1056	c.824A>G	c.(823-825)aAc>aGc	p.N275S	FUK_ENST00000378912.2_Missense_Mutation_p.N307S|FUK_ENST00000571514.1_Intron	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	275						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				ATGGCTGAGAACGTGACCAGG	0.597													A|||	23	0.00459265	0.0015	0.0058	5008	,	,		20513	0.0		0.0169	False		,,,				2504	0.0				p.N275S		Atlas-SNP	.											.	FUK	72	.	0			c.A824G						PASS	.	A	SER/ASN	17,3987		0,17,1985	125.0	128.0	127.0		824	4.6	0.9	16	dbSNP_132	127	138,8182		1,136,4023	yes	missense	FUK	NM_145059.2	46	1,153,6008	GG,GA,AA		1.6587,0.4246,1.2577	benign	275/1085	70503095	155,12169	2002	4160	6162	SO:0001583	missense	197258	exon10			CTGAGAACGTGAC		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"""L-fucose kinase"""	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.824A>G	16.37:g.70503095A>G	ENSP00000288078:p.Asn275Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	95	21	0.221053	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	15	0.006868131868131868	0	0.0	3	0.008287292817679558	0	0.0	12	0.0158311345646438	A	13.85	2.359884	0.41801	0.004246	0.016587	ENSG00000157353	ENST00000288078;ENST00000378912	T;T	0.27256	1.68;1.68	5.66	4.58	0.56647	L-fucokinase (1);	0.410519	0.28290	N	0.015885	T	0.10121	0.0248	L	0.47716	1.5	0.49213	D	0.999761	B;P	0.39576	0.169;0.679	B;B	0.41946	0.051;0.371	T	0.04752	-1.0929	10	0.10377	T	0.69	-8.5588	5.1681	0.15096	0.8085:0.0:0.1915:0.0	.	307;275	Q8N0W3-2;Q8N0W3	.;FUK_HUMAN	S	275;307	ENSP00000288078:N275S;ENSP00000368192:N307S	ENSP00000288078:N275S	N	+	2	0	FUK	69060596	0.977000	0.34250	0.930000	0.37139	0.743000	0.42351	4.008000	0.57103	2.175000	0.68902	0.528000	0.53228	AAC	A|0.989;G|0.011	0.011	strong		0.597	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
SVEP1	79987	hgsc.bcm.edu	37	9	113208250	113208250	+	Missense_Mutation	SNP	T	T	G	rs7863519	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:113208250T>G	ENST00000401783.2	-	26	4666	c.4330A>C	c.(4330-4332)Atg>Ctg	p.M1444L	SVEP1_ENST00000302728.8_Missense_Mutation_p.M1444L|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Missense_Mutation_p.M1421L	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1444	Pentaxin.		M -> L (in dbSNP:rs7863519).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.M1444L(2)		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						GATGGGAGCATGCCATCTAGC	0.438													C|||	1701	0.339657	0.4569	0.2205	5008	,	,		20843	0.4504		0.1918	False		,,,				2504	0.3037				p.M1444L		Atlas-SNP	.											SVEP1,NS,carcinoma,0,2	SVEP1	326	2	2	Substitution - Missense(2)	prostate(2)	c.A4330C						PASS	.	C	LEU/MET	1478,2424		275,928,748	119.0	114.0	116.0		4330	3.6	0.0	9	dbSNP_116	116	1600,6712		164,1272,2720	yes	missense	SVEP1	NM_153366.3	15	439,2200,3468	GG,GT,TT		19.2493,37.878,25.2006	benign	1444/3572	113208250	3078,9136	1951	4156	6107	SO:0001583	missense	79987	exon26			GGAGCATGCCATC	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.4330A>C	9.37:g.113208250T>G	ENSP00000384917:p.Met1444Leu	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	194	108	0.556701	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	699	0.32005494505494503	228	0.4634146341463415	80	0.22099447513812154	241	0.42132867132867136	150	0.19788918205804748	C	0.025	-1.378392	0.01204	0.37878	0.192493	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.71817	3.35;3.35;-0.6	5.5	3.62	0.41486	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.301359	0.35466	N	0.003189	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.08055	0.0;0.003	T	0.41197	-0.9522	9	0.10377	T	0.69	.	8.2245	0.31560	0.0:0.6915:0.1135:0.195	rs7863519;rs52830057;rs60340468;rs7863519	1444;1444	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	L	1444;1421;1444	ENSP00000384917:M1444L;ENSP00000363593:M1421L;ENSP00000304118:M1444L	ENSP00000304118:M1444L	M	-	1	0	SVEP1	112248071	0.004000	0.15560	0.023000	0.16930	0.138000	0.21146	0.095000	0.15127	0.361000	0.24292	-0.119000	0.15052	ATG	T|0.684;G|0.316	0.316	strong		0.438	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HLA-C	3107	hgsc.bcm.edu	37	6	31238155	31238155	+	Missense_Mutation	SNP	G	G	A	rs1050328	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31238155G>A	ENST00000376228.5	-	4	741	c.727C>T	c.(727-729)Cgg>Tgg	p.R243W	HLA-C_ENST00000383329.3_Missense_Mutation_p.R243W	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	243	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						TCCCCATCCCGCTGCCAGGTC	0.632													G|||	1934	0.386182	0.3714	0.428	5008	,	,		14977	0.5675		0.327	False		,,,				2504	0.2505				p.R243W		Atlas-SNP	.											HLA-C,colon,carcinoma,+1,1	HLA-C	92	1	0			c.C727T						scavenged	.	G	TRP/ARG	1452,2948		276,900,1024	38.0	37.0	37.0		727	0.7	1.0	6	dbSNP_86	37	2279,6297		360,1559,2369	no	missense	HLA-C	NM_002117.5	101	636,2459,3393	AA,AG,GG		26.5742,33.0,28.7531	probably-damaging	243/367	31238155	3731,9245	2200	4288	6488	SO:0001583	missense	3107	exon4			CATCCCGCTGCCA	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.727C>T	6.37:g.31238155G>A	ENSP00000365402:p.Arg243Trp	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	263	117	0.444867	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	832	0.38095238095238093	157	0.31910569105691056	140	0.3867403314917127	306	0.534965034965035	229	0.3021108179419525	.	3.864	-0.029320	0.07589	0.33	0.265742	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.03181	4.02;4.02	2.67	0.7	0.18099	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.232985	0.21532	U	0.073034	T	0.01835	0.0058	M	0.83953	2.67	0.46609	P	8.749999999999591E-4	B;B;B;B	0.10296	0.003;0.0;0.001;0.0	B;B;B;B	0.06405	0.002;0.0;0.0;0.0	T	0.24977	-1.0145	9	0.48119	T	0.1	.	2.7344	0.05236	0.1696:0.0:0.5518:0.2786	rs1050328;rs2308614;rs3177868;rs3190622;rs12721973;rs17840005	243;243;243;243	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	W	243;243;243;280	ENSP00000365402:R243W;ENSP00000372819:R243W	ENSP00000365402:R243W	R	-	1	2	HLA-C	31346134	0.000000	0.05858	0.987000	0.45799	0.454000	0.32378	-0.406000	0.07187	0.168000	0.19655	0.298000	0.19748	CGG	G|0.695;A|0.305	0.305	strong		0.632	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229890	87229890	+	Missense_Mutation	SNP	G	G	A	rs72688509	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:87229890G>A	ENST00000297524.3	-	3	1091	c.988C>T	c.(988-990)Ctt>Ttt	p.L330F	SLC7A13_ENST00000419776.2_Missense_Mutation_p.L321F|SLC7A13_ENST00000520624.1_5'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	330						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						TGACTATTAAGTGTATTAAAT	0.348													G|||	34	0.00678914	0.0008	0.0086	5008	,	,		15711	0.0		0.0209	False		,,,				2504	0.0061				p.L330F		Atlas-SNP	.											.	SLC7A13	97	.	0			c.C988T						PASS	.	G	PHE/LEU	34,4372	37.6+/-69.7	0,34,2169	85.0	96.0	92.0		988	4.4	0.0	8	dbSNP_130	92	249,8351	98.1+/-159.7	2,245,4053	yes	missense	SLC7A13	NM_138817.2	22	2,279,6222	AA,AG,GG		2.8953,0.7717,2.1759	probably-damaging	330/471	87229890	283,12723	2203	4300	6503	SO:0001583	missense	157724	exon3			TATTAAGTGTATT	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.988C>T	8.37:g.87229890G>A	ENSP00000297524:p.Leu330Phe	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	21	0.009615384615384616	0	0.0	4	0.011049723756906077	0	0.0	17	0.022427440633245383	G	17.01	3.279848	0.59758	0.007717	0.028953	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.90261	-2.64;-2.64	5.27	4.4	0.53042	Amino acid permease domain (1);	0.000000	0.53938	D	0.000058	D	0.86577	0.5966	M	0.66506	2.035	0.26823	N	0.96874	D;D	0.89917	0.959;1.0	P;D	0.85130	0.748;0.997	T	0.82967	-0.0194	10	0.62326	D	0.03	.	12.0277	0.53380	0.0845:0.0:0.9155:0.0	.	321;330	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	F	330;321	ENSP00000297524:L330F;ENSP00000410982:L321F	ENSP00000297524:L330F	L	-	1	0	SLC7A13	87299006	0.401000	0.25303	0.023000	0.16930	0.087000	0.18053	0.692000	0.25482	1.343000	0.45638	0.650000	0.86243	CTT	G|0.979;A|0.021	0.021	strong		0.348	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	
CFAP69	79846	hgsc.bcm.edu	37	7	89906609	89906609	+	Silent	SNP	C	C	T	rs3761805	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:89906609C>T	ENST00000389297.4	+	11	1367	c.1116C>T	c.(1114-1116)aaC>aaT	p.N372N	C7orf63_ENST00000316089.8_Silent_p.N372N|C7orf63_ENST00000497910.1_Silent_p.N354N	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		372										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						TACTATTCAACGTAATTGTGA	0.284													T|||	2022	0.403754	0.4206	0.3905	5008	,	,		16063	0.6855		0.2286	False		,,,				2504	0.2802				p.N372N		Atlas-SNP	.											C7orf63_ENST00000389297,colon,carcinoma,+2,2	C7orf63	158	2	0			c.C1116T						scavenged	.	T	,	1262,2320		226,810,755	39.0	41.0	40.0		1116,1062	1.1	1.0	7	dbSNP_107	40	1491,6557		133,1225,2666	no	coding-synonymous,coding-synonymous	C7orf63	NM_001039706.2,NM_001160138.1	,	359,2035,3421	TT,TC,CC		18.5263,35.2317,23.6715	,	372/942,354/924	89906609	2753,8877	1791	4024	5815	SO:0001819	synonymous_variant	79846	exon11			ATTCAACGTAATT																												ENST00000389297.4:c.1116C>T	7.37:g.89906609C>T		Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	187	56	0.299465	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Silent	SNP	ENST00000389297.4	37	CCDS43613.2																																																																																			C|0.602;T|0.398	0.398	strong		0.284	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197304	39197304	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39197304T>C	ENST00000306271.4	-	1	409	c.346A>G	c.(346-348)Atc>Gtc	p.I116V		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	116						keratin filament (GO:0045095)		p.I116V(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CACCACCTGATACGGGTGCTC	0.662																																					p.I116V		Atlas-SNP	.											KRTAP1-1,NS,malignant_melanoma,0,1	KRTAP1-1	23	1	1	Substitution - Missense(1)	NS(1)	c.A346G						PASS	.						22.0	27.0	25.0					17																	39197304		2019	4148	6167	SO:0001583	missense	81851	exon1			ACCTGATACGGGT	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.346A>G	17.37:g.39197304T>C	ENSP00000305975:p.Ile116Val	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	135	13	0.0962963	NM_030967	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	T	8.173	0.792133	0.16258	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.29655	1.56	4.28	-1.23	0.09465	.	.	.	.	.	T	0.12135	0.0295	N	0.03253	-0.375	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34079	-0.9843	9	0.20046	T	0.44	.	9.4726	0.38851	0.0:0.573:0.0:0.427	.	116	Q07627	KRA11_HUMAN	V	116;106	ENSP00000305975:I116V	ENSP00000305975:I116V	I	-	1	0	KRTAP1-1	36450830	0.132000	0.22450	0.024000	0.17045	0.516000	0.34256	0.017000	0.13399	-0.199000	0.10317	0.529000	0.55759	ATC	.	.	none		0.662	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
DCAF8L1	139425	hgsc.bcm.edu	37	X	27999146	27999146	+	Silent	SNP	C	C	T	rs41311803	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	253	0	0		WXS	Illumina HiSeq	Phase_I	117	114	0.974359	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	
ZNF345	25850	hgsc.bcm.edu	37	19	37369032	37369032	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:37369032G>C	ENST00000529555.1	+	2	2088	c.1300G>C	c.(1300-1302)Gct>Cct	p.A434P	ZNF345_ENST00000589046.1_Missense_Mutation_p.A434P|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.A434P			Q14585	ZN345_HUMAN	zinc finger protein 345	434					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	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(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GTGTGGGAAGGCTTTTTATAG	0.423																																					p.A434P		Atlas-SNP	.											.	ZNF345	68	.	0			c.G1300C						PASS	.						79.0	81.0	80.0					19																	37369032		2203	4300	6503	SO:0001583	missense	25850	exon4			GGGAAGGCTTTTT	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.1300G>C	19.37:g.37369032G>C	ENSP00000431202:p.Ala434Pro	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	56	0.554455	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340040	0.24339	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.14391	2.51;2.51	3.0	-0.576	0.11731	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13586	0.0329	M	0.64260	1.97	0.09310	N	1	B	0.26041	0.14	B	0.29663	0.105	T	0.35549	-0.9784	9	0.72032	D	0.01	.	3.2328	0.06754	0.3529:0.0:0.4485:0.1985	.	434	Q14585	ZN345_HUMAN	P	434;434;198	ENSP00000431216:A434P;ENSP00000431202:A434P	ENSP00000442320:A198P	A	+	1	0	ZNF345	42060872	0.000000	0.05858	0.250000	0.24296	0.522000	0.34438	-1.705000	0.01896	-0.091000	0.12440	0.655000	0.94253	GCT	.	.	none		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
TPSD1	23430	hgsc.bcm.edu	37	16	1306680	1306680	+	Silent	SNP	C	C	T	rs1969653	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1306680C>T	ENST00000211076.3	+	2	394	c.246C>T	c.(244-246)tgC>tgT	p.C82C	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Silent_p.C75C	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	82	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				CGGCGCACTGCGTGGAACCGT	0.706													-|||	857	0.171126	0.289	0.2522	5008	,	,		17255	0.122		0.0994	False		,,,				2504	0.0787				p.C82C		Atlas-SNP	.											.	TPSD1	47	.	0			c.C246T						PASS	.	C		1176,3222		169,838,1192	39.0	48.0	45.0		246	-3.0	0.0	16	dbSNP_92	45	797,7799		30,737,3531	no	coding-synonymous	TPSD1	NM_012217.2		199,1575,4723	TT,TC,CC		9.2718,26.7394,15.1839		82/243	1306680	1973,11021	2199	4298	6497	SO:0001819	synonymous_variant	23430	exon2			GCACTGCGTGGAA	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.246C>T	16.37:g.1306680C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	157	81	0.515924	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Silent	SNP	ENST00000211076.3	37	CCDS10432.1																																																																																			C|0.850;T|0.150	0.150	strong		0.706	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
DNHD1	144132	hgsc.bcm.edu	37	11	6585670	6585670	+	Silent	SNP	C	C	T	rs16915423	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6585670C>T	ENST00000527990.2	+	30	10392	c.10392C>T	c.(10390-10392)gaC>gaT	p.D3464D	DNHD1_ENST00000254579.6_Silent_p.D3464D			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3464					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)		AGCTACTGGACGAGTGGTTAG	0.552													C|||	600	0.119808	0.295	0.0922	5008	,	,		21225	0.0149		0.0169	False		,,,				2504	0.1166				p.D3464D		Atlas-SNP	.											.	DNHD1	198	.	0			c.C10392T						PASS	.	C		356,1028		43,270,379	115.0	110.0	112.0		10392	-1.9	0.9	11	dbSNP_123	112	81,3101		0,81,1510	no	coding-synonymous	DNHD1	NM_144666.2		43,351,1889	TT,TC,CC		2.5456,25.7225,9.5707		3464/4754	6585670	437,4129	692	1591	2283	SO:0001819	synonymous_variant	144132	exon32			ACTGGACGAGTGG	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.10392C>T	11.37:g.6585670C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	237	116	0.489451	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			C|0.905;T|0.095	0.095	strong		0.552	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
IQCE	23288	hgsc.bcm.edu	37	7	2644519	2644519	+	Missense_Mutation	SNP	C	C	T	rs2293404	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:2644519C>T	ENST00000402050.2	+	19	1821	c.1637C>T	c.(1636-1638)gCt>gTt	p.A546V	IQCE_ENST00000438376.2_Missense_Mutation_p.A530V|IQCE_ENST00000325979.7_Missense_Mutation_p.A481V|IQCE_ENST00000404984.1_Missense_Mutation_p.A495V	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	546	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.		A -> V (in dbSNP:rs2293404).			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)		TGACAGGCGGCTGTGGTGCTT	0.642													C|||	2062	0.411741	0.3956	0.4625	5008	,	,		18690	0.495		0.326	False		,,,				2504	0.3998				p.A546V		Atlas-SNP	.											IQCE,NS,carcinoma,0,1	IQCE	66	1	0			c.C1637T						PASS	.	C	VAL/ALA,VAL/ALA	1489,2673		282,925,874	43.0	49.0	47.0		1589,1637	4.9	0.0	7	dbSNP_100	47	2309,6123		307,1695,2214	yes	missense,missense	IQCE	NM_001100390.1,NM_152558.3	64,64	589,2620,3088	TT,TC,CC		27.3838,35.7761,30.1572	benign,benign	530/680,546/696	2644519	3798,8796	2081	4216	6297	SO:0001583	missense	23288	exon19			AGGCGGCTGTGGT	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.1637C>T	7.37:g.2644519C>T	ENSP00000385597:p.Ala546Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	83	27	0.325301	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	878	0.40201465201465203	187	0.3800813008130081	144	0.39779005524861877	298	0.5209790209790209	249	0.32849604221635886	C	7.940	0.742568	0.15642	0.357761	0.273838	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979;ENST00000423196	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	4.9	4.9	0.64082	.	0.472269	0.21142	N	0.079466	T	0.00012	0.0000	L	0.46741	1.465	0.58432	P	1.0000000000287557E-6	B;B;P;P	0.38745	0.187;0.187;0.645;0.592	B;B;B;B	0.40444	0.19;0.176;0.329;0.221	T	0.51585	-0.8687	9	0.39692	T	0.17	-6.2302	13.6658	0.62393	0.0:1.0:0.0:0.0	rs2293404;rs52800467;rs61534484;rs2293404	481;530;546;530	B4DXN1;B4DDX4;Q6IPM2;Q6IPM2-4	.;.;IQCE_HUMAN;.	V	546;495;530;481;126	ENSP00000385597:A546V;ENSP00000385945:A495V;ENSP00000396178:A530V;ENSP00000313772:A481V;ENSP00000405982:A126V	ENSP00000313772:A481V	A	+	2	0	IQCE	2611045	0.889000	0.30405	0.031000	0.17742	0.630000	0.37929	2.567000	0.45956	2.286000	0.76751	0.650000	0.86243	GCT	C|0.622;T|0.378	0.378	strong		0.642	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
PTCH2	8643	hgsc.bcm.edu	37	1	45294295	45294295	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:45294295C>T	ENST00000372192.3	-	12	1603	c.1473G>A	c.(1471-1473)atG>atA	p.M491I	PTCH2_ENST00000447098.2_Missense_Mutation_p.M491I	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	491	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)					GACACTCGCCCATGCGCTCCT	0.632									Basal Cell Nevus syndrome																												p.M491I		Atlas-SNP	.											.	PTCH2	96	.	0			c.G1473A						PASS	.						71.0	55.0	60.0					1																	45294295		2202	4300	6502	SO:0001583	missense	8643	exon12	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	CTCGCCCATGCGC	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.1473G>A	1.37:g.45294295C>T	ENSP00000361266:p.Met491Ile	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	67	4	0.0597015	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	37	CCDS516.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.275107	0.40194	.	.	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.94184	-3.37;-3.37	4.47	-3.0	0.05480	Sterol-sensing domain (1);	0.196196	0.35320	N	0.003287	T	0.79776	0.4504	N	0.05467	-0.045	0.29800	N	0.832513	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.003	T	0.68228	-0.5464	10	0.18276	T	0.48	-34.0928	7.4614	0.27298	0.1257:0.1735:0.0:0.7008	.	491;491	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	I	491	ENSP00000389703:M491I;ENSP00000361266:M491I	ENSP00000361266:M491I	M	-	3	0	PTCH2	45066882	0.000000	0.05858	0.640000	0.29408	0.929000	0.56500	-3.137000	0.00588	-0.491000	0.06697	0.462000	0.41574	ATG	.	.	none		0.632	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
ADAM21	8747	hgsc.bcm.edu	37	14	70924507	70924507	+	Silent	SNP	A	A	C	rs3751524	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:70924507A>C	ENST00000603540.1	+	2	549	c.291A>C	c.(289-291)gcA>gcC	p.A97A	ADAM21_ENST00000267499.3_Silent_p.A97A|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	97					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.A97A(1)		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)		ATGACCGTGCACTCCTGGAGG	0.512																																					p.A97A		Atlas-SNP	.											ADAM21,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - coding silent(1)	stomach(1)	c.A291C						scavenged	.						95.0	103.0	101.0					14																	70924507		2203	4300	6503	SO:0001819	synonymous_variant	8747	exon2			CCGTGCACTCCTG	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.291A>C	14.37:g.70924507A>C		Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	242	73	0.301653	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			A|0.780;C|0.220	0.220	strong		0.512	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
UBR4	23352	hgsc.bcm.edu	37	1	19433449	19433449	+	Silent	SNP	A	A	G	rs6426677	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19433449A>G	ENST00000375254.3	-	82	12144	c.12117T>C	c.(12115-12117)gtT>gtC	p.V4039V	UBR4_ENST00000375217.2_Silent_p.V4032V|UBR4_ENST00000375224.1_5'Flank|UBR4_ENST00000375226.2_Silent_p.V4015V|UBR4_ENST00000375267.2_Silent_p.V4039V	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4039					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)			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)		TGAGGGCCTCAACGGGGACAT	0.602													G|||	3602	0.719249	0.8366	0.7334	5008	,	,		18352	0.8105		0.6083	False		,,,				2504	0.5706				p.V4039V		Atlas-SNP	.											.	UBR4	415	.	0			c.T12117C						PASS	.	G		3555,851	335.2+/-303.8	1434,687,82	43.0	42.0	42.0		12117	-11.3	0.0	1	dbSNP_116	42	5182,3418	503.2+/-375.9	1576,2030,694	no	coding-synonymous	UBR4	NM_020765.2		3010,2717,776	GG,GA,AA		39.7442,19.3146,32.8233		4039/5184	19433449	8737,4269	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon82			GGCCTCAACGGGG	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.12117T>C	1.37:g.19433449A>G		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	157	120	0.764331	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			A|0.311;G|0.689	0.689	strong		0.602	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
BCOR	54880	hgsc.bcm.edu	37	X	39932808	39932808	+	Silent	SNP	G	G	A	rs144606152	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:39932808G>A	ENST00000378444.4	-	4	2019	c.1791C>T	c.(1789-1791)caC>caT	p.H597H	BCOR_ENST00000397354.3_Silent_p.H597H|BCOR_ENST00000378455.4_Silent_p.H597H|BCOR_ENST00000342274.4_Silent_p.H597H	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	597					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GCTGGCCCACGTGCTGAATAA	0.607			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic						G|||	63	0.0166887	0.0015	0.0159	3775	,	,		12801	0.0		0.0437	False		,,,				2504	0.0061				p.H597H		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C1791T						PASS	.	G	,,,	22,3811		0,19,3,1612,568	68.0	65.0	66.0		1791,1791,1791,1791	-1.4	0.9	X	dbSNP_134	66	372,6356		5,260,102,2163,1770	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	,,,	5,279,105,3775,2338	AA,AG,A,GG,G		5.5291,0.574,3.7307	,,,	597/1722,597/1704,597/1756,597/1722	39932808	394,10167	2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			GCCCACGTGCTGA	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.1791C>T	X.37:g.39932808G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	38	36	0.947368	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			G|0.963;A|0.037	0.037	strong		0.607	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
SELL	6402	hgsc.bcm.edu	37	1	169676486	169676486	+	Missense_Mutation	SNP	A	A	G	rs1131498	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:169676486A>G	ENST00000236147.4	-	4	776	c.616T>C	c.(616-618)Ttt>Ctt	p.F206L	SELL_ENST00000463108.1_5'UTR|C1orf112_ENST00000498289.1_Intron	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	193	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)					GACTTACCAAACTGACACTGG	0.433													A|||	666	0.132987	0.1278	0.1801	5008	,	,		17777	0.005		0.2376	False		,,,				2504	0.1309				p.F206L		Atlas-SNP	.											.	SELL	43	.	0			c.T616C	GRCh37	CM004878	SELL	M	rs1131498	PASS	.	A	LEU/PHE	541,3247		36,469,1389	75.0	72.0	73.0	http://www.ncbi.nlm.nih.gov/pubmed?term	616	3.2	1.0	1	dbSNP_86	73	2204,6036		262,1680,2178	yes	missense	SELL	NM_000655.4	22	298,2149,3567	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	26.7476,14.2819,22.8217	benign	206/386	169676486	2745,9283	1894	4120	6014	SO:0001583	missense	6402	exon4			TACCAAACTGACA	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.616T>C	1.37:g.169676486A>G	ENSP00000236147:p.Phe206Leu	Somatic	240	2	0.00833333		WXS	Illumina HiSeq	Phase_I	316	310	0.981013	NM_000655	B2R6Q8|P15023|Q9UJ43	Missense_Mutation	SNP	ENST00000236147.4	37	CCDS53427.1	301	0.13782051282051283	47	0.09552845528455285	67	0.1850828729281768	3	0.005244755244755245	184	0.24274406332453827	A	14.06	2.422432	0.43020	0.142819	0.267476	ENSG00000188404	ENST00000236147	D	0.91180	-2.8	5.61	3.16	0.36331	Complement control module (1);	0.397771	0.21578	N	0.072293	T	0.77267	0.4105	M	0.65975	2.015	0.43377	P	0.0045239999999999725	B;B	0.22800	0.075;0.075	B;B	0.13407	0.009;0.009	T	0.64647	-0.6358	9	0.19590	T	0.45	.	5.6888	0.17817	0.6843:0.0:0.0767:0.2389	rs1131498;rs2229567;rs3177980;rs3191470;rs17417179;rs17526012;rs59082452;rs3177980	206;193	Q8WW79;P14151	.;LYAM1_HUMAN	L	206	ENSP00000236147:F206L	ENSP00000236147:F206L	F	-	1	0	SELL	167943110	0.002000	0.14202	0.997000	0.53966	0.990000	0.78478	0.396000	0.20867	1.064000	0.40671	0.533000	0.62120	TTT	A|0.861;G|0.139	0.139	strong		0.433	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655	
TTC28	23331	hgsc.bcm.edu	37	22	28559120	28559120	+	Silent	SNP	G	G	C	rs17486417	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:28559120G>C	ENST00000397906.2	-	6	1542	c.1401C>G	c.(1399-1401)ctC>ctG	p.L467L		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	467					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						CCCGGTCCTTGAGATCCTCAG	0.552													G|||	678	0.135383	0.0794	0.0821	5008	,	,		18257	0.1736		0.1342	False		,,,				2504	0.2106				p.L467L		Atlas-SNP	.											.	TTC28	84	.	0			c.C1401G						PASS	.	G		116,1268		5,106,581	47.0	38.0	41.0		1401	2.6	1.0	22	dbSNP_123	41	450,2732		25,400,1166	no	coding-synonymous	TTC28	NM_001145418.1		30,506,1747	CC,CG,GG		14.142,8.3815,12.396		467/2482	28559120	566,4000	692	1591	2283	SO:0001819	synonymous_variant	23331	exon6			GTCCTTGAGATCC	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.1401C>G	22.37:g.28559120G>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			G|0.870;C|0.128	0.128	strong		0.552	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
PKD1	5310	hgsc.bcm.edu	37	16	2140554	2140554	+	Missense_Mutation	SNP	G	G	A	rs3209986	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2140554G>A	ENST00000262304.4	-	45	12384	c.12176C>T	c.(12175-12177)gCc>gTc	p.A4059V	PKD1_ENST00000423118.1_Missense_Mutation_p.A4058V|MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4059			A -> V (in dbSNP:rs3209986). {ECO:0000269|PubMed:11773467, ECO:0000269|PubMed:11967008, ECO:0000269|PubMed:15772804, ECO:0000269|PubMed:18837007}.		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						CAGGGCCTGGGCCACGCTCCA	0.657													g|||	183	0.0365415	0.0015	0.0403	5008	,	,		16353	0.0		0.0895	False		,,,				2504	0.0644				p.A4059V		Atlas-SNP	.											.	PKD1	184	.	0			c.C12176T						PASS	.		VAL/ALA,VAL/ALA	63,4301		0,63,2119	29.0	29.0	29.0		12173,12176	1.2	0.0	16	dbSNP_105	29	690,7888		24,642,3623	yes	missense,missense	PKD1	NM_000296.3,NM_001009944.2	64,64	24,705,5742	AA,AG,GG		8.0438,1.4436,5.8183	possibly-damaging,possibly-damaging	4058/4303,4059/4304	2140554	753,12189	2182	4289	6471	SO:0001583	missense	5310	exon45			GCCTGGGCCACGC	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.12176C>T	16.37:g.2140554G>A	ENSP00000262304:p.Ala4059Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_001009944	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	89	0.04075091575091575	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	68	0.08970976253298153	g	11.48	1.651367	0.29336	0.014436	0.080438	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.68624	-0.34;-0.34	4.51	1.25	0.21368	Polycystin cation channel, PKD1/PKD2 (1);	0.761139	0.12152	N	0.494771	T	0.03695	0.0105	L	0.57536	1.79	0.09310	N	1	B;B	0.15930	0.006;0.015	B;B	0.16289	0.006;0.015	T	0.03840	-1.0999	10	0.20046	T	0.44	.	4.5328	0.12013	0.1004:0.2633:0.5216:0.1147	rs3209986	4058;4059	P98161-3;P98161	.;PKD1_HUMAN	V	4059;4058;3393	ENSP00000262304:A4059V;ENSP00000399501:A4058V	ENSP00000262304:A4059V	A	-	2	0	PKD1	2080555	0.001000	0.12720	0.007000	0.13788	0.204000	0.24138	0.472000	0.22116	0.882000	0.36016	0.306000	0.20318	GCC	G|0.950;A|0.050	0.050	strong		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
SLC5A8	160728	hgsc.bcm.edu	37	12	101560328	101560328	+	Missense_Mutation	SNP	C	C	A	rs164365	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	125	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	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	
ARAP2	116984	hgsc.bcm.edu	37	4	36230634	36230634	+	Missense_Mutation	SNP	G	G	A	rs141442791	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:36230634G>A	ENST00000303965.4	-	2	964	c.475C>T	c.(475-477)Cca>Tca	p.P159S		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	159					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TTCAGGTGTGGTTCCTCTGCA	0.393													G|||	7	0.00139776	0.0	0.0014	5008	,	,		20594	0.0		0.006	False		,,,				2504	0.0				p.P159S		Atlas-SNP	.											.	ARAP2	210	.	0			c.C475T						PASS	.	G	SER/PRO	3,4403	4.2+/-10.8	0,3,2200	69.0	65.0	67.0		475	-0.6	0.0	4	dbSNP_134	67	16,8584	11.9+/-42.8	0,16,4284	yes	missense	ARAP2	NM_015230.3	74	0,19,6484	AA,AG,GG		0.186,0.0681,0.1461	benign	159/1705	36230634	19,12987	2203	4300	6503	SO:0001583	missense	116984	exon2			GGTGTGGTTCCTC	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16924	protein-coding gene	gene with protein product		606645	"""centaurin, delta 1"""	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.475C>T	4.37:g.36230634G>A	ENSP00000302895:p.Pro159Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	5.262	0.233857	0.09969	6.81E-4	0.00186	ENSG00000047365	ENST00000303965	T	0.62639	0.01	5.5	-0.558	0.11796	.	0.647728	0.14546	N	0.312977	T	0.34395	0.0896	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.0;0.001	T	0.12889	-1.0530	10	0.16420	T	0.52	.	3.6174	0.08082	0.3113:0.0:0.427:0.2617	.	89;159	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	S	159	ENSP00000302895:P159S	ENSP00000302895:P159S	P	-	1	0	ARAP2	35907029	0.888000	0.30383	0.021000	0.16686	0.262000	0.26303	1.029000	0.30140	0.010000	0.14839	0.650000	0.86243	CCA	G|0.998;A|0.002	0.002	strong		0.393	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230	
PNP	4860	hgsc.bcm.edu	37	14	20940606	20940606	+	Missense_Mutation	SNP	G	G	A	rs1049564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20940606G>A	ENST00000361505.5	+	2	297	c.151G>A	c.(151-153)Ggt>Agt	p.G51S	RP11-203M5.8_ENST00000554678.1_lincRNA	NM_000270.3	NP_000261.2	P01298	PAHO_HUMAN	purine nucleoside phosphorylase	0					digestion (GO:0007586)|protein secretion (GO:0009306)	extracellular region (GO:0005576)	hormone activity (GO:0005179)|receptor binding (GO:0005102)	p.G51S(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|stomach(2)	10						CTTTGACTACGGTGAAATCCC	0.473													A|||	1025	0.204673	0.2474	0.2104	5008	,	,		20475	0.2063		0.1998	False		,,,				2504	0.1462				p.G51S		Atlas-SNP	.											PNP,NS,carcinoma,0,1	PNP	21	1	1	Substitution - Missense(1)	stomach(1)	c.G151A	GRCh37	CM073244	PNP	M	rs1049564	PASS	.	A	SER/GLY	1083,3323	720.9+/-409.1	121,841,1241	83.0	74.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	151	5.5	1.0	14	dbSNP_86	77	1522,7078	747.4+/-407.3	143,1236,2921	yes	missense	PNP	NM_000270.3	56	264,2077,4162	AA,AG,GG		17.6977,24.5801,20.0292	benign	51/290	20940606	2605,10401	2203	4300	6503	SO:0001583	missense	4860	exon2			GACTACGGTGAAA		CCDS9552.1	14q11.2	2014-09-17	2009-12-02	2009-12-02	ENSG00000198805	ENSG00000198805	2.4.2.1		7892	protein-coding gene	gene with protein product		164050	"""nucleoside phosphorylase"""	NP		6087295	Standard	NM_000270		Approved	PUNP	uc001vxo.4	P00491	OTTHUMG00000029546	ENST00000361505.5:c.151G>A	14.37:g.20940606G>A	ENSP00000354532:p.Gly51Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	179	62	0.346369	NM_000270		Missense_Mutation	SNP	ENST00000361505.5	37	CCDS9552.1	484|484	0.2216117216117216|0.2216117216117216	139|139	0.28252032520325204|0.28252032520325204	84|84	0.23204419889502761|0.23204419889502761	120|120	0.2097902097902098|0.2097902097902098	141|141	0.18601583113456466|0.18601583113456466	A|A	2.844|2.844	-0.239923|-0.239923	0.05944|0.05944	0.245801|0.245801	0.176977|0.176977	ENSG00000198805|ENSG00000198805	ENST00000554469|ENST00000553418;ENST00000361505;ENST00000553591	.|T;D;D	.|0.94232	.|-0.88;-3.38;-3.38	5.54|5.54	5.54|5.54	0.83059|0.83059	.|Nucleoside phosphorylase domain (1);	0.389474|0.389474	0.33290|0.33290	N|N	0.005067|0.005067	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00683|0.00683	-1.26|-1.26	0.58432|0.58432	P|P	8.000000000008E-6|8.000000000008E-6	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.001;0.0;0.0	T|T	0.34428|0.34428	-0.9829|-0.9829	5|9	.|0.02654	.|T	.|1	-9.946|-9.946	6.5054|6.5054	0.22192|0.22192	0.7854:0.0:0.0759:0.1387|0.7854:0.0:0.0759:0.1387	rs1049564;rs1760937;rs2070219;rs17012367;rs17879175;rs17884346;rs58995400;rs1049564|rs1049564;rs1760937;rs2070219;rs17012367;rs17879175;rs17884346;rs58995400;rs1049564	.|51;51;51	.|Q8N7G1;G3V2H3;P00491	.|.;.;PNPH_HUMAN	R|S	51|51;51;90	.|ENSP00000450663:G51S;ENSP00000354532:G51S;ENSP00000452421:G90S	.|ENSP00000354532:G51S	G|G	+|+	1|1	0|0	PNP|PNP	20010446|20010446	0.331000|0.331000	0.24713|0.24713	0.998000|0.998000	0.56505|0.56505	0.741000|0.741000	0.42261|0.42261	1.210000|1.210000	0.32370|0.32370	1.120000|1.120000	0.41904|0.41904	-0.254000|-0.254000	0.11334|0.11334	GGG|GGT	G|0.786;A|0.214	0.214	strong		0.473	PNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073646.2	NM_000270.2	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144921924	144921924	+	Silent	SNP	G	G	A	rs71664015	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:144921924G>A	ENST00000369354.3	-	9	1294	c.1105C>T	c.(1105-1107)Ctg>Ttg	p.L369L	PDE4DIP_ENST00000313382.9_Silent_p.L435L|PDE4DIP_ENST00000369356.4_Silent_p.L369L|PDE4DIP_ENST00000529945.1_Silent_p.L532L|PDE4DIP_ENST00000313431.9_Silent_p.L532L|PDE4DIP_ENST00000369351.3_Silent_p.L369L|PDE4DIP_ENST00000369359.4_Silent_p.L506L|PDE4DIP_ENST00000479408.2_Silent_p.L156L|PDE4DIP_ENST00000530740.1_Silent_p.L506L|PDE4DIP_ENST00000369349.3_Silent_p.L369L			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	369					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)		GCATCAGCCAGTTGGCGCTCT	0.463			T	PDGFRB	MPD																																p.L532L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C1594T						PASS	.	G	,,,,	203,4203		0,203,2000	375.0	388.0	384.0		1594,1105,1303,1105,1105	5.8	1.0	1	dbSNP_130	384	1431,7161		0,1431,2865	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	,,,,	0,1634,4865	AA,AG,GG		16.655,4.6074,12.5712	,,,,	532/1133,369/970,435/2241,369/2363,369/2347	144921924	1634,11364	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon5			CAGCCAGTTGGCG	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.1105C>T	1.37:g.144921924G>A		Somatic	382	1	0.0026178		WXS	Illumina HiSeq	Phase_I	412	119	0.288835	NM_001002811	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																																																																																			A|0.001;C|0.795	0.001	strong		0.463	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
VRK1	7443	hgsc.bcm.edu	37	14	97321689	97321689	+	Silent	SNP	C	C	T	rs2230532	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	108	0	0		WXS	Illumina HiSeq	Phase_I	114	66	0.578947	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	
STIM1	6786	hgsc.bcm.edu	37	11	4103524	4103524	+	Silent	SNP	A	A	G	rs2304891	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	170	0	0		WXS	Illumina HiSeq	Phase_I	148	144	0.972973	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	
CEP63	80254	hgsc.bcm.edu	37	3	134225969	134225969	+	Silent	SNP	T	T	C	rs9827878	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:134225969T>C	ENST00000337090.3	+	3	236	c.63T>C	c.(61-63)tgT>tgC	p.C21C	CEP63_ENST00000332047.5_Silent_p.C21C|CEP63_ENST00000354446.3_Silent_p.C21C|CEP63_ENST00000606977.1_Silent_p.C21C|CEP63_ENST00000513612.2_Silent_p.C21C|CEP63_ENST00000504013.1_3'UTR|CEP63_ENST00000383229.3_Silent_p.C21C			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	21					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						TGACATCTTGTGAAGCAGAAC	0.348													T|||	861	0.171925	0.1415	0.1153	5008	,	,		14824	0.2183		0.17	False		,,,				2504	0.2076				p.C21C		Atlas-SNP	.											.	CEP63	56	.	0			c.T63C						PASS	.	T	,,,	551,3855	246.8+/-255.3	34,483,1686	97.0	98.0	98.0		63,63,63,63	4.5	1.0	3	dbSNP_119	98	1342,7258	262.3+/-284.3	108,1126,3066	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CEP63	NM_001042383.1,NM_001042384.1,NM_001042400.1,NM_025180.3	,,,	142,1609,4752	CC,CT,TT		15.6047,12.5057,14.5548	,,,	21/496,21/476,21/542,21/704	134225969	1893,11113	2203	4300	6503	SO:0001819	synonymous_variant	80254	exon3			ATCTTGTGAAGCA	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.63T>C	3.37:g.134225969T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	140	72	0.514286	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Silent	SNP	ENST00000337090.3	37	CCDS3086.1																																																																																			T|0.841;C|0.159	0.159	strong		0.348	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
ABCA2	20	hgsc.bcm.edu	37	9	139905141	139905141	+	Silent	SNP	G	G	A	rs112887513	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139905141G>A	ENST00000371605.3	-	39	6249	c.6102C>T	c.(6100-6102)gcC>gcT	p.A2034A	ABCA2_ENST00000341511.6_Silent_p.A2035A|ABCA2_ENST00000265662.5_Silent_p.A2035A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	2034					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)		GCCGCTCACTGGCCACGTCCA	0.637													g|||	329	0.0656949	0.0234	0.0447	5008	,	,		5333	0.0437		0.0586	False		,,,				2504	0.1677				p.A2065A		Atlas-SNP	.											.	ABCA2	113	.	0			c.C6195T						PASS	.	C	,	105,4197		4,97,2050	99.0	111.0	107.0		6105,6195	0.7	0.3	9	dbSNP_132	107	572,7938		15,542,3698	yes	coding-synonymous,coding-synonymous	ABCA2	NM_001606.4,NM_212533.2	,	19,639,5748	AA,AG,GG		6.7215,2.4407,5.2841	,	2035/2437,2065/2467	139905141	677,12135	2151	4255	6406	SO:0001819	synonymous_variant	20	exon40			CTCACTGGCCACG	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.6102C>T	9.37:g.139905141G>A		Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	378	194	0.513228	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				A|0.055;C|0.000;G|0.945	0.055	strong		0.637	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606	
RP1	6101	hgsc.bcm.edu	37	8	55541738	55541738	+	Missense_Mutation	SNP	A	A	C	rs147009600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:55541738A>C	ENST00000220676.1	+	4	5444	c.5296A>C	c.(5296-5298)Aat>Cat	p.N1766H		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1766					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)			CATGTGTGGCAATGCAGACAC	0.438													A|||	2	0.000399361	0.0	0.0	5008	,	,		23417	0.0		0.0	False		,,,				2504	0.002				p.N1766H	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A5296C						PASS	.	A	HIS/ASN	0,4406		0,0,2203	95.0	92.0	93.0		5296	3.5	0.9	8	dbSNP_134	93	6,8594	5.0+/-18.6	0,6,4294	yes	missense	RP1	NM_006269.1	68	0,6,6497	CC,CA,AA		0.0698,0.0,0.0461	benign	1766/2157	55541738	6,13000	2203	4300	6503	SO:0001583	missense	6101	exon4			TGTGGCAATGCAG	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.5296A>C	8.37:g.55541738A>C	ENSP00000220676:p.Asn1766His	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	100	15	0.15	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	8.388	0.839077	0.16891	0.0	6.98E-4	ENSG00000104237	ENST00000220676	T	0.47177	0.85	5.93	3.47	0.39725	.	0.241833	0.28977	N	0.013529	T	0.35941	0.0949	L	0.33485	1.01	0.26317	N	0.977733	B	0.18461	0.028	B	0.15870	0.014	T	0.16041	-1.0416	10	0.30078	T	0.28	.	12.782	0.57483	0.6029:0.397:0.0:0.0	.	1766	P56715	RP1_HUMAN	H	1766	ENSP00000220676:N1766H	ENSP00000220676:N1766H	N	+	1	0	RP1	55704291	0.998000	0.40836	0.854000	0.33618	0.698000	0.40448	3.291000	0.51764	0.454000	0.26884	0.533000	0.62120	AAT	A|0.999;C|0.001	0.001	strong		0.438	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
PPHLN1	51535	hgsc.bcm.edu	37	12	42839923	42839923	+	Missense_Mutation	SNP	G	G	A	rs201876048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:42839923G>A	ENST00000395568.2	+	12	1265	c.1181G>A	c.(1180-1182)cGt>cAt	p.R394H	PPHLN1_ENST00000317560.9_Intron|PPHLN1_ENST00000432191.2_Missense_Mutation_p.R370H|PPHLN1_ENST00000256678.8_Missense_Mutation_p.R299H	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	394					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)		aaacgggttcgtcggacgaca	0.622													G|||	3	0.000599042	0.0	0.0014	5008	,	,		11704	0.0		0.002	False		,,,				2504	0.0				p.R394H		Atlas-SNP	.											.	PPHLN1	101	.	0			c.G1181A						PASS	.	G	HIS/ARG,HIS/ARG	1,4325		0,1,2162	7.0	8.0	8.0		1109,1181	0.2	0.1	12		8	18,8426		0,18,4204	yes	missense,missense	PPHLN1	NM_001143787.1,NM_016488.6	29,29	0,19,6366	AA,AG,GG		0.2132,0.0231,0.1488	probably-damaging,probably-damaging	370/435,394/459	42839923	19,12751	2163	4222	6385	SO:0001583	missense	51535	exon12			GGGTTCGTCGGAC	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.1181G>A	12.37:g.42839923G>A	ENSP00000378935:p.Arg394His	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_016488	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	37	CCDS31777.1	.	.	.	.	.	.	.	.	.	.	G	5.312	0.242935	0.10077	2.31E-4	0.002132	ENSG00000134283	ENST00000395568;ENST00000256678;ENST00000432191	.	.	.	0.158	0.158	0.14942	.	0.000000	0.85682	U	0.000000	T	0.12263	0.0298	N	0.02011	-0.69	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.20706	-1.0267	8	0.87932	D	0	.	.	.	.	.	299;345;370;394	F8W6A0;B7Z695;Q8NEY8-3;Q8NEY8	.;.;.;PPHLN_HUMAN	H	394;299;370	.	ENSP00000256678:R299H	R	+	2	0	PPHLN1	41126190	0.328000	0.24687	0.148000	0.22405	0.150000	0.21749	0.251000	0.18257	0.202000	0.20498	0.205000	0.17691	CGT	.	.	weak		0.622	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515	
HELZ2	85441	hgsc.bcm.edu	37	20	62191558	62191558	+	Silent	SNP	G	G	A	rs3810479	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	56	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	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	
CEACAM20	125931	hgsc.bcm.edu	37	19	45021210	45021210	+	RNA	SNP	G	G	A	rs10414398	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45021210G>A	ENST00000454753.1	-	0	1384							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)				GGTCAGGCTGGAGTTGAGCTC	0.567													G|||	938	0.1873	0.3033	0.2608	5008	,	,		19063	0.1369		0.0746	False		,,,				2504	0.1462				p.S369F		Atlas-SNP	.											.	CEACAM20	31	.	0			c.C1106T						PASS	.	G	PHE/SER,,,PHE/SER	966,3270		117,732,1269	75.0	73.0	74.0		1106,,,1106	2.4	0.0	19	dbSNP_119	74	699,7777		29,641,3568	yes	missense,intron,intron,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	155,,,155	146,1373,4837	AA,AG,GG		8.2468,22.8045,13.0979	probably-damaging,,,probably-damaging	369/597,,,369/585	45021210	1665,11047	2118	4238	6356			125931	exon6			AGGCTGGAGTTGA	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.45021210G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				G|0.836;A|0.164	0.164	strong		0.567	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377135	168377135	+	lincRNA	SNP	T	T	C	rs372663828		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168377135T>C	ENST00000538528.1	-	0	484																											CTGCAGTGTGTTGGGAGGAGG	0.622																																					p.Q66Q		Atlas-SNP	.											.	.	.	.	0			c.A198G						PASS	.						5.0	7.0	6.0					6																	168377135		670	1551	2221			0	exon1			AGTGTGTTGGGAG																													6.37:g.168377135T>C		Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	418	24	0.0574163	NM_001129895		Silent	SNP	ENST00000538528.1	37																																																																																				.	.	weak		0.622	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
AGXT2	64902	hgsc.bcm.edu	37	5	35037115	35037115	+	Missense_Mutation	SNP	C	C	T	rs37369	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:35037115C>T	ENST00000231420.6	-	4	618	c.418G>A	c.(418-420)Gtc>Atc	p.V140I	AC010368.1_ENST00000390793.2_RNA	NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	140			V -> I (in dbSNP:rs37369). {ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	TGGAAGAAGACGGTGCTTGTA	0.522													C|||	1971	0.39357	0.6309	0.3242	5008	,	,		20047	0.5744		0.0865	False		,,,				2504	0.2515				p.V140I		Atlas-SNP	.											.	AGXT2	89	.	0			c.G418A						PASS	.	C	ILE/VAL	2374,2032	611.2+/-391.7	641,1092,470	112.0	108.0	109.0	http://www.ncbi.nlm.nih.gov/pubmed?term	418	0.6	0.0	5	dbSNP_76	109	734,7866	177.8+/-227.3	29,676,3595	yes	missense	AGXT2	NM_031900.3	29	670,1768,4065	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	8.5349,46.1189,23.8967	benign	140/515	35037115	3108,9898	2203	4300	6503	SO:0001583	missense	64902	exon4			AGAAGACGGTGCT	AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"""beta-alanine-pyruvate aminotransferase"", ""beta-ALAAT II"""	612471	"""alanine-glyoxylate aminotransferase 2"""			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.418G>A	5.37:g.35037115C>T	ENSP00000231420:p.Val140Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_031900	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Missense_Mutation	SNP	ENST00000231420.6	37	CCDS3908.1	799	0.3658424908424908	302	0.6138211382113821	86	0.23756906077348067	346	0.6048951048951049	65	0.08575197889182058	C	0.008	-1.929815	0.00488	0.538811	0.085349	ENSG00000113492	ENST00000231420	T	0.19105	2.17	5.7	0.622	0.17648	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.351663	0.31495	N	0.007546	T	0.00012	0.0000	N	0.00996	-1.065	0.50039	P	1.5100000000001224E-4	B;B	0.10296	0.002;0.003	B;B	0.11329	0.006;0.003	T	0.35400	-0.9790	9	0.08179	T	0.78	-5.5	6.7804	0.23642	0.0:0.2668:0.4002:0.333	rs37369;rs1141800;rs3205606;rs52830900;rs57886686;rs37369	140;140	E9PDL7;Q9BYV1	.;AGT2_HUMAN	I	140	ENSP00000231420:V140I	ENSP00000231420:V140I	V	-	1	0	AGXT2	35072872	0.043000	0.20138	0.032000	0.17829	0.046000	0.14306	0.282000	0.18829	-0.208000	0.10171	-0.143000	0.13931	GTC	C|0.692;T|0.308	0.308	strong		0.522	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900	
KIAA0195	9772	hgsc.bcm.edu	37	17	73493874	73493874	+	Silent	SNP	G	G	C	rs12949173	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73493874G>C	ENST00000314256.7	+	27	3814	c.3420G>C	c.(3418-3420)ctG>ctC	p.L1140L	KIAA0195_ENST00000579208.1_Silent_p.L791L|KIAA0195_ENST00000375248.5_Silent_p.L1150L|AC100787.1_ENST00000579379.1_RNA	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	94	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	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	
PLXNB1	5364	hgsc.bcm.edu	37	3	48461313	48461313	+	Silent	SNP	C	C	G	rs2362450	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48461313C>G	ENST00000358536.4	-	11	2651	c.2382G>C	c.(2380-2382)ccG>ccC	p.P794P	PLXNB1_ENST00000358459.4_Intron|PLXNB1_ENST00000456774.1_Intron|PLXNB1_ENST00000448774.2_Intron|PLXNB1_ENST00000296440.6_Silent_p.P794P	NM_002673.4	NP_002664.2	O43157	PLXB1_HUMAN	plexin B1	794	Pro-rich.				axon guidance (GO:0007411)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast proliferation (GO:0033689)|neuron projection morphogenesis (GO:0048812)|ossification involved in bone maturation (GO:0043931)|positive regulation of axonogenesis (GO:0050772)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	GTPase activating protein binding (GO:0032794)|receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CTACCTCTGACGGTGACAGCG	0.657													G|||	2165	0.432308	0.6399	0.3357	5008	,	,		14003	0.3135		0.4652	False		,,,				2504	0.3088				p.P794P		Atlas-SNP	.											PLXNB1,colon,carcinoma,-2,1	PLXNB1	150	1	0			c.G2382C						PASS	.	G	,	2736,1668		872,992,338	13.0	16.0	15.0		2382,2382	3.7	0.8	3	dbSNP_100	15	4083,4505		994,2095,1205	no	coding-synonymous,coding-synonymous	PLXNB1	NM_001130082.1,NM_002673.4	,	1866,3087,1543	GG,GC,CC		47.5431,37.8747,47.5139	,	794/2136,794/2136	48461313	6819,6173	2202	4294	6496	SO:0001819	synonymous_variant	5364	exon11			CTCTGACGGTGAC	X87904	CCDS2765.1	3p21.31	2008-07-18			ENSG00000164050	ENSG00000164050		"""Plexins"""	9103	protein-coding gene	gene with protein product		601053		PLXN5		8570614, 11035813	Standard	XM_005265234		Approved	SEP, KIAA0407	uc003csw.2	O43157	OTTHUMG00000133527	ENST00000358536.4:c.2382G>C	3.37:g.48461313C>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	227	104	0.45815	NM_001130082	A6H8Y2|Q6NY20|Q9UIV7|Q9UJ92|Q9UJ93	Silent	SNP	ENST00000358536.4	37	CCDS2765.1																																																																																			C|0.517;G|0.483	0.483	strong		0.657	PLXNB1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344454.1	NM_002673	
AOC3	8639	hgsc.bcm.edu	37	17	41003914	41003914	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:41003914A>G	ENST00000308423.2	+	1	714	c.554A>G	c.(553-555)aAc>aGc	p.N185S	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	185					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)	ATGATCTTCAACAGAGAGCTG	0.602																																					p.N185S	NSCLC(3;192 220 10664 11501 16477)	Atlas-SNP	.											AOC3,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	AOC3	88	1	0			c.A554G						scavenged	.						31.0	30.0	30.0					17																	41003914		2203	4297	6500	SO:0001583	missense	8639	exon1			TCTTCAACAGAGA	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.554A>G	17.37:g.41003914A>G	ENSP00000312326:p.Asn185Ser	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	195	3	0.0153846	NM_003734	B2RCI5|K7ESB3|L0L8N9|Q45F94	Missense_Mutation	SNP	ENST00000308423.2	37	CCDS11444.1	.	.	.	.	.	.	.	.	.	.	A	1.663	-0.510892	0.04231	.	.	ENSG00000131471	ENST00000308423	T	0.16597	2.33	4.25	4.25	0.50352	Copper amine oxidase, N3-terminal (1);Copper amine oxidase, N2/N3-terminal (1);Copper amine oxidase, N-terminal (1);	1.338580	0.04529	N	0.386019	T	0.14399	0.0348	L	0.40543	1.245	0.24276	N	0.995226	B	0.02656	0.0	B	0.12837	0.008	T	0.41034	-0.9531	10	0.09338	T	0.73	.	5.699	0.17871	0.7393:0.1722:0.0885:0.0	.	185	Q16853	AOC3_HUMAN	S	185	ENSP00000312326:N185S	ENSP00000312326:N185S	N	+	2	0	AOC3	38257440	0.000000	0.05858	0.090000	0.20809	0.898000	0.52572	0.877000	0.28106	1.912000	0.55364	0.402000	0.26972	AAC	.	.	none		0.602	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734	
GDPD5	81544	hgsc.bcm.edu	37	11	75150971	75150971	+	Silent	SNP	G	G	A	rs115438239	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:75150971G>A	ENST00000336898.3	-	15	2346	c.1509C>T	c.(1507-1509)gcC>gcT	p.A503A	GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000529721.1_Silent_p.A503A|GDPD5_ENST00000526177.1_Silent_p.A365A|GDPD5_ENST00000533805.1_Silent_p.A258A|GDPD5_ENST00000533784.1_Silent_p.A384A|GDPD5_ENST00000376282.3_Silent_p.A384A	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	503					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						AGACCAGGTCGGCAGTGACCC	0.612													G|||	10	0.00199681	0.0008	0.0	5008	,	,		19335	0.003		0.006	False		,,,				2504	0.0				p.A503A		Atlas-SNP	.											.	GDPD5	49	.	0			c.C1509T						PASS	.	G		2,4398	4.2+/-10.8	0,2,2198	124.0	101.0	109.0		1509	-7.7	0.7	11	dbSNP_132	109	27,8559	19.2+/-60.6	0,27,4266	no	coding-synonymous	GDPD5	NM_030792.6		0,29,6464	AA,AG,GG		0.3145,0.0455,0.2233		503/606	75150971	29,12957	2200	4293	6493	SO:0001819	synonymous_variant	81544	exon15			CAGGTCGGCAGTG	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.1509C>T	11.37:g.75150971G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Silent	SNP	ENST00000336898.3	37	CCDS8238.1																																																																																			G|0.997;A|0.003	0.003	strong		0.612	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792	
VPS13A	23230	hgsc.bcm.edu	37	9	79897117	79897117	+	Silent	SNP	G	G	A	rs11145366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:79897117G>A	ENST00000360280.3	+	29	3305	c.3045G>A	c.(3043-3045)ccG>ccA	p.P1015P	VPS13A_ENST00000376636.3_Silent_p.P1015P|VPS13A_ENST00000376634.4_Silent_p.P1015P|VPS13A_ENST00000357409.5_Silent_p.P1015P|VPS13A_ENST00000423463.2_3'UTR	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	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	155	153	0.987097	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	
LVRN	206338	hgsc.bcm.edu	37	5	115351066	115351066	+	Silent	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:115351066T>A	ENST00000357872.4	+	17	2692	c.2568T>A	c.(2566-2568)atT>atA	p.I856I	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		856						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AAGAAAAGATTCAACTTGCTT	0.343																																					p.I856I		Atlas-SNP	.											FLJ90650,caecum,carcinoma,0,1	.	.	1	0			c.T2568A						scavenged	.						91.0	87.0	88.0					5																	115351066		2202	4300	6502	SO:0001819	synonymous_variant	0	exon17			AAAGATTCAACTT																												ENST00000357872.4:c.2568T>A	5.37:g.115351066T>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	35	3	0.0857143	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			.	.	none		0.343	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
HHLA2	11148	hgsc.bcm.edu	37	3	108081247	108081247	+	Silent	SNP	G	G	A	rs16854512	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000467562.1_Silent_p.A290A|HHLA2_ENST00000489514.2_Silent_p.A354A|HHLA2_ENST00000491820.1_Silent_p.A354A	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	116	0	0		WXS	Illumina HiSeq	Phase_I	94	35	0.37234	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	
ALDH9A1	223	hgsc.bcm.edu	37	1	165664562	165664562	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:165664562G>A	ENST00000354775.4	-	2	558	c.254C>T	c.(253-255)gCt>gTt	p.A85V	ALDH9A1_ENST00000538148.1_5'UTR|ALDH9A1_ENST00000461664.1_5'UTR	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	61					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TATTTTAAAAGCAGCCTTTGC	0.398																																					p.A85V	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.C254T						PASS	.						99.0	98.0	98.0					1																	165664562		2203	4300	6503	SO:0001583	missense	223	exon2			TTAAAAGCAGCCT	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.254C>T	1.37:g.165664562G>A	ENSP00000346827:p.Ala85Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	23	0.232323	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Missense_Mutation	SNP	ENST00000354775.4	37	CCDS1250.2	.	.	.	.	.	.	.	.	.	.	G	22.0	4.232550	0.79688	.	.	ENSG00000143149	ENST00000354775	D	0.94330	-3.4	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.96318	0.8799	M	0.81179	2.53	0.52099	D	0.999942	D;D	0.76494	0.999;0.999	D;D	0.72625	0.978;0.978	D	0.96736	0.9543	9	0.87932	D	0	.	16.7765	0.85552	0.0:0.0:1.0:0.0	.	75;85	B4DX14;B9EKV4	.;.	V	85	ENSP00000346827:A85V	ENSP00000346827:A85V	A	-	2	0	ALDH9A1	163931186	1.000000	0.71417	1.000000	0.80357	0.478000	0.33099	7.115000	0.77110	2.545000	0.85829	0.655000	0.94253	GCT	.	.	none		0.398	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
SBDS	51119	hgsc.bcm.edu	37	7	66459316	66459316	+	Silent	SNP	G	G	A	rs113993989	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:66459316G>A	ENST00000246868.2	-	2	324	c.141C>T	c.(139-141)ctC>ctT	p.L47L	TYW1_ENST00000359626.5_5'Flank	NM_016038.2	NP_057122.2	Q9Y3A5	SBDS_HUMAN	Shwachman-Bodian-Diamond syndrome	47					bone marrow development (GO:0048539)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|inner cell mass cell proliferation (GO:0001833)|leukocyte chemotaxis (GO:0030595)|mature ribosome assembly (GO:0042256)|mitotic spindle stabilization (GO:0043148)|ribosomal large subunit biogenesis (GO:0042273)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			cervix(1)|endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7						GAACTTCATCGAGGTCTTTTT	0.408			Gene Conversion			"""AML, MDS"""			Shwachman-Diamond syndrome				G|||	69	0.013778	0.0136	0.0043	5008	,	,		19688	0.0337		0.006	False		,,,				2504	0.0082				p.L47L		Atlas-SNP	.	yes	Rec		Schwachman-Diamond syndrome	7	7q11	51119	Shwachman-Bodian-Diamond syndrome protein		L	.	SBDS	20	.	0			c.C141T						PASS	.	G		45,4361	46.0+/-80.4	0,45,2158	107.0	98.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	141	-5.8	0.9	7	dbSNP_132	101	33,8567	21.0+/-64.5	0,33,4267	no	coding-synonymous	SBDS	NM_016038.2		0,78,6425	AA,AG,GG		0.3837,1.0213,0.5997		47/251	66459316	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	51119	exon2	Familial Cancer Database	Shwachman syndrome, Shwachman-Bodian syndrome, Congenital Lipomatosis of the Pancreas	TTCATCGAGGTCT	AF151855	CCDS5537.1	7q11.22	2014-09-17			ENSG00000126524	ENSG00000126524			19440	protein-coding gene	gene with protein product		607444				12496757	Standard	NM_016038		Approved	CGI-97, FLJ10917, SDS, SWDS	uc003tvm.1	Q9Y3A5	OTTHUMG00000023165	ENST00000246868.2:c.141C>T	7.37:g.66459316G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	88	33	0.375	NM_016038	A8K0P4|Q96FX0|Q9NV53	Silent	SNP	ENST00000246868.2	37	CCDS5537.1																																																																																			G|0.989;A|0.011	0.011	strong		0.408	SBDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251746.2	NM_016038	
CDC27	996	hgsc.bcm.edu	37	17	45234727	45234727	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45234727T>A	ENST00000066544.3	-	6	592	c.499A>T	c.(499-501)Aca>Tca	p.T167S	CDC27_ENST00000531206.1_Missense_Mutation_p.T167S|CDC27_ENST00000527547.1_Missense_Mutation_p.T167S|CDC27_ENST00000446365.2_Missense_Mutation_p.T106S|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	167					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						AATTTAAATGTTTGGTCAGGA	0.368																																					p.T167S		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,+2,10	CDC27	337	10	0			c.A499T						scavenged	.						73.0	73.0	73.0					17																	45234727		2203	4300	6503	SO:0001583	missense	996	exon6			TAAATGTTTGGTC	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.499A>T	17.37:g.45234727T>A	ENSP00000066544:p.Thr167Ser	Somatic	250	3	0.012		WXS	Illumina HiSeq	Phase_I	323	13	0.0402477	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.623232	0.46840	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.67171	-0.25;-0.25;0.04;-0.25;0.89	5.39	5.39	0.77823	.	0.119985	0.64402	D	0.000020	T	0.47192	0.1432	N	0.08118	0	0.39122	D	0.961682	P;P;P;B	0.38677	0.475;0.528;0.642;0.211	B;B;B;B	0.36092	0.049;0.217;0.204;0.067	T	0.59762	-0.7393	10	0.72032	D	0.01	-19.1215	13.3763	0.60741	0.0:0.0:0.0:1.0	.	106;167;167;167	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	167;167;106;167;167	ENSP00000066544:T167S;ENSP00000434614:T167S;ENSP00000392802:T106S;ENSP00000437339:T167S;ENSP00000432105:T167S	ENSP00000066544:T167S	T	-	1	0	CDC27	42589726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.374000	0.66167	2.053000	0.61076	0.528000	0.53228	ACA	.	.	none		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489749	32489749	+	Silent	SNP	G	G	C	rs1064594		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489749G>C	ENST00000374975.3	-	2	365	c.303C>G	c.(301-303)cgC>cgG	p.R101R		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						CCACCGCGGCGCGCCTGTCTT	0.662																																					p.R101R		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.C303G						PASS	.	C		2544,1408		1175,194,607	33.0	29.0	30.0		303	-1.5	0.0	6	dbSNP_86	30	5096,2670		2414,268,1201	no	coding-synonymous	HLA-DRB5	NM_002125.3		3589,462,1808	CC,CG,GG		34.3806,35.6275,34.8012		101/267	32489749	7640,4078	1976	3883	5859	SO:0001819	synonymous_variant	3127	exon2			CGCGGCGCGCCTG		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.303C>G	6.37:g.32489749G>C		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	26	25	0.961538	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			G|0.339;C|0.661	0.661	strong		0.662	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
OR4A16	81327	hgsc.bcm.edu	37	11	55111238	55111238	+	Missense_Mutation	SNP	C	C	A	rs11229158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	337	1	0.00296736		WXS	Illumina HiSeq	Phase_I	304	162	0.532895	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	
ZNF804B	219578	hgsc.bcm.edu	37	7	88965021	88965021	+	Missense_Mutation	SNP	G	G	A	rs10487075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:88965021G>A	ENST00000333190.4	+	4	3334	c.2725G>A	c.(2725-2727)Gaa>Aaa	p.E909K		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	909			E -> K (in dbSNP:rs10487075).				metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TGGCCCTTCAGAAACCACAGA	0.458										HNSCC(36;0.09)			G|||	269	0.0537141	0.003	0.0576	5008	,	,		17988	0.0843		0.0994	False		,,,				2504	0.0409				p.E909K		Atlas-SNP	.											.	ZNF804B	322	.	0			c.G2725A						PASS	.	G	LYS/GLU	105,4301	80.9+/-119.3	1,103,2099	85.0	90.0	88.0		2725	2.0	0.1	7	dbSNP_119	88	917,7683	203.2+/-246.3	43,831,3426	yes	missense	ZNF804B	NM_181646.2	56	44,934,5525	AA,AG,GG		10.6628,2.3831,7.8579	benign	909/1350	88965021	1022,11984	2203	4300	6503	SO:0001583	missense	219578	exon4			CCTTCAGAAACCA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2725G>A	7.37:g.88965021G>A	ENSP00000329638:p.Glu909Lys	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	172	107	0.622093	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	148	0.06776556776556776	1	0.0020325203252032522	29	0.08011049723756906	39	0.06818181818181818	79	0.10422163588390501	G	12.56	1.975107	0.34848	0.023831	0.106628	ENSG00000182348	ENST00000333190	T	0.04970	3.52	5.1	2.02	0.26589	.	1.409490	0.03949	N	0.288266	T	0.00144	0.0004	L	0.32530	0.975	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.37033	-0.9723	10	0.66056	D	0.02	-2.7179	6.8002	0.23746	0.2428:0.1476:0.6096:0.0	rs10487075;rs17679226;rs56460583;rs60463003;rs10487075	909	A4D1E1	Z804B_HUMAN	K	909	ENSP00000329638:E909K	ENSP00000329638:E909K	E	+	1	0	ZNF804B	88802957	0.003000	0.15002	0.089000	0.20774	0.044000	0.14063	0.532000	0.23067	0.710000	0.31997	0.655000	0.94253	GAA	G|0.916;A|0.084	0.084	strong		0.458	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
ZNF341	84905	hgsc.bcm.edu	37	20	32371640	32371640	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:32371640T>C	ENST00000375200.1	+	12	2187	c.1822T>C	c.(1822-1824)Tat>Cat	p.Y608H	ZNF341_ENST00000342427.2_Missense_Mutation_p.Y601H	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	608					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(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						GCGGGAGCATTATCTCAAACT	0.612																																					p.Y601H		Atlas-SNP	.											ZNF341,NS,carcinoma,-1,1	ZNF341	73	1	0			c.T1801C						scavenged	.						84.0	72.0	76.0					20																	32371640		2203	4300	6503	SO:0001583	missense	84905	exon12			GAGCATTATCTCA	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.1822T>C	20.37:g.32371640T>C	ENSP00000364346:p.Tyr608His	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	117	2	0.017094	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Missense_Mutation	SNP	ENST00000375200.1	37		.	.	.	.	.	.	.	.	.	.	T	14.18	2.458716	0.43634	.	.	ENSG00000131061	ENST00000342427;ENST00000375200	T;T	0.03889	3.77;3.77	4.45	4.45	0.53987	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.391329	0.26457	N	0.024268	T	0.05731	0.0150	N	0.02129	-0.67	0.49483	D	0.999798	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.998	T	0.62760	-0.6786	10	0.15066	T	0.55	-9.591	14.2085	0.65750	0.0:0.0:0.0:1.0	.	549;608;601	Q504V9;Q9BYN7;Q9BYN7-2	.;ZN341_HUMAN;.	H	601;608	ENSP00000344308:Y601H;ENSP00000364346:Y608H	ENSP00000344308:Y601H	Y	+	1	0	ZNF341	31835301	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.366000	0.79548	2.018000	0.59344	0.381000	0.24937	TAT	.	.	none		0.612	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
DIAPH3	81624	hgsc.bcm.edu	37	13	60240961	60240961	+	Silent	SNP	C	C	T	rs9538494	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:60240961C>T	ENST00000400324.4	-	28	3559	c.3339G>A	c.(3337-3339)ttG>ttA	p.L1113L	DIAPH3_ENST00000400319.1_Silent_p.L1043L|DIAPH3_ENST00000400330.1_Silent_p.L1113L|DIAPH3_ENST00000377908.2_Silent_p.L1102L|DIAPH3_ENST00000400320.1_Silent_p.L1067L	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	1113					actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		ACCCTTCTGTCAACTGCACTT	0.368													C|||	736	0.146965	0.0242	0.2147	5008	,	,		17183	0.1071		0.2594	False		,,,				2504	0.1902				p.L1113L		Atlas-SNP	.											.	DIAPH3	139	.	0			c.G3339A						PASS	.	C		241,3523		9,223,1650	110.0	101.0	104.0		3339	4.1	1.0	13	dbSNP_119	104	2196,6046		292,1612,2217	no	coding-synonymous	DIAPH3	NM_001042517.1		301,1835,3867	TT,TC,CC		26.644,6.4028,20.2982		1113/1194	60240961	2437,9569	1882	4121	6003	SO:0001819	synonymous_variant	81624	exon28			TTCTGTCAACTGC	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"""diaphanous (Drosophila, homolog) 3"", ""auditory neuropathy, autosomal dominant 1"", ""diaphanous homolog 3 (Drosophila)"""	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.3339G>A	13.37:g.60240961C>T		Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	286	283	0.98951	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	37	CCDS41898.1																																																																																			C|0.820;T|0.180	0.180	strong		0.368	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
ECM1	1893	hgsc.bcm.edu	37	1	150484987	150484987	+	Missense_Mutation	SNP	G	G	A	rs13294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:150484987G>A	ENST00000369047.4	+	8	1368	c.1243G>A	c.(1243-1245)Ggt>Agt	p.G415S	ECM1_ENST00000346569.6_Missense_Mutation_p.G290S|ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000369049.4_Missense_Mutation_p.G442S	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	415			G -> S (in dbSNP:rs13294). {ECO:0000269|PubMed:12603844, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9367673}.		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)			CATTGACATCGGTCGAGTCAC	0.572													A|||	1335	0.266573	0.1747	0.2709	5008	,	,		19087	0.2371		0.3827	False		,,,				2504	0.2986				p.G442S	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.G1324A						PASS	.	A	SER/GLY,SER/GLY,SER/GLY	917,3489	739.0+/-411.0	107,703,1393	122.0	106.0	111.0		1324,1243,868	4.2	1.0	1	dbSNP_52	111	3534,5066	631.3+/-398.5	750,2034,1516	yes	missense,missense,missense	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	56,56,56	857,2737,2909	AA,AG,GG		41.093,20.8125,34.2227	benign,benign,benign	442/568,415/541,290/416	150484987	4451,8555	2203	4300	6503	SO:0001583	missense	1893	exon8			GACATCGGTCGAG	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.1243G>A	1.37:g.150484987G>A	ENSP00000358043:p.Gly415Ser	Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	214	118	0.551402	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Missense_Mutation	SNP	ENST00000369047.4	37	CCDS953.1	621	0.28434065934065933	84	0.17073170731707318	116	0.32044198895027626	136	0.23776223776223776	285	0.3759894459102902	A	0.158	-1.083944	0.01888	0.208125	0.41093	ENSG00000143369	ENST00000369049;ENST00000369047;ENST00000346569	T;T;T	0.72505	-0.66;-0.66;-0.66	4.17	4.17	0.49024	.	0.128269	0.49305	N	0.000143	T	0.11024	0.0269	N	0.00146	-1.995	0.37322	P	0.09041100000000002	B;B;B	0.10296	0.003;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.10989	-1.0606	9	0.19590	T	0.45	-9.9071	6.5783	0.22579	0.8895:0.0:0.1105:0.0	rs13294;rs1050877;rs3170610;rs17357598;rs17650780;rs17856688;rs56766781;rs13294	442;290;415	Q16610-4;Q16610-2;Q16610	.;.;ECM1_HUMAN	S	442;415;290	ENSP00000358045:G442S;ENSP00000358043:G415S;ENSP00000271630:G290S	ENSP00000271630:G290S	G	+	1	0	ECM1	148751611	1.000000	0.71417	1.000000	0.80357	0.294000	0.27393	0.899000	0.28417	0.736000	0.32559	-0.521000	0.04368	GGT	A|0.317;C|0.005	0.317	strong		0.572	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
AGGF1	55109	hgsc.bcm.edu	37	5	76332530	76332530	+	Silent	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	163	0	0		WXS	Illumina HiSeq	Phase_I	158	8	0.0506329	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	
Unknown	0	hgsc.bcm.edu	37	11	5989415	5989415	+	IGR	SNP	C	C	T	rs7114672	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5989415C>T								OR56A3 (19824 upstream) : OR52L1 (17706 downstream)																							ATGATGAACACCTGAAGGAAG	0.517													.|||	2363	0.471845	0.733	0.3444	5008	,	,		22147	0.3194		0.3897	False		,,,				2504	0.4509				p.V104M		Atlas-SNP	.											.	.	.	.	0			c.G310A						PASS	.	T	MET/VAL	995,389		361,273,58	72.0	66.0	68.0		310	3.4	1.0	11	dbSNP_116	68	1476,1706		476,524,591	yes	missense	OR56A5	NM_001146033.1	21	837,797,649	TT,TC,CC		46.3859,28.1069,45.8826	benign	104/314	5989415	2471,2095	692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			TGAACACCTGAAG																													11.37:g.5989415C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_001146033		Missense_Mutation	SNP		37																																																																																				A|0.039;C|0.419;T|0.541	0.541	strong	0	0.517								
HLA-C	3107	hgsc.bcm.edu	37	6	31239108	31239108	+	Missense_Mutation	SNP	T	T	A	rs1131118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	45	15	0.333333	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	
TCERG1L	256536	hgsc.bcm.edu	37	10	132961454	132961454	+	Missense_Mutation	SNP	C	C	T	rs118074196	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:132961454C>T	ENST00000368642.4	-	6	1050	c.965G>A	c.(964-966)gGg>gAg	p.G322E		NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	322										cervix(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	31		all_cancers(35;1.22e-10)|all_epithelial(44;2.65e-09)|Lung NSC(174;0.00188)|all_lung(145;0.00307)|Melanoma(40;0.0179)|all_neural(114;0.0424)|Breast(234;0.0743)|Colorectal(57;0.09)		all cancers(32;0.000899)|OV - Ovarian serous cystadenocarcinoma(35;0.0021)|Epithelial(32;0.00276)		CTCTCCTCCCCCCAGCATCGG	0.547													C|||	50	0.00998403	0.0008	0.0159	5008	,	,		17069	0.0		0.0368	False		,,,				2504	0.001				p.G322E		Atlas-SNP	.											.	TCERG1L	91	.	0			c.G965A						PASS	.	C	GLU/GLY	14,4378		0,14,2182	33.0	31.0	32.0		965	1.6	0.0	10	dbSNP_132	32	221,8361		4,213,4074	yes	missense	TCERG1L	NM_174937.3	98	4,227,6256	TT,TC,CC		2.5752,0.3188,1.8113	benign	322/587	132961454	235,12739	2196	4291	6487	SO:0001583	missense	256536	exon6			CCTCCCCCCAGCA	AK096269	CCDS7662.2	10q26.3	2006-04-12			ENSG00000176769	ENSG00000176769			23533	protein-coding gene	gene with protein product							Standard	NM_174937		Approved	FLJ38950	uc001lkp.3	Q5VWI1	OTTHUMG00000019276	ENST00000368642.4:c.965G>A	10.37:g.132961454C>T	ENSP00000357631:p.Gly322Glu	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_174937	Q5VWI2|Q86XM8	Missense_Mutation	SNP	ENST00000368642.4	37	CCDS7662.2	33	0.01510989010989011	0	0.0	6	0.016574585635359115	0	0.0	27	0.03562005277044855	C	0	-2.791991	0.00077	0.003188	0.025752	ENSG00000176769	ENST00000368642	T	0.22336	1.96	3.95	1.64	0.23874	.	0.950279	0.08679	N	0.909722	T	0.01353	0.0044	N	0.03608	-0.345	0.09310	N	1	B	0.25904	0.137	B	0.20767	0.031	T	0.31806	-0.9930	10	0.02654	T	1	-0.2517	4.043	0.09760	0.5535:0.2653:0.0:0.1812	.	322	Q5VWI1	TCRGL_HUMAN	E	322	ENSP00000357631:G322E	ENSP00000357631:G322E	G	-	2	0	TCERG1L	132851444	0.000000	0.05858	0.013000	0.15412	0.039000	0.13416	0.526000	0.22971	0.160000	0.19432	0.655000	0.94253	GGG	C|0.983;T|0.017	0.017	strong		0.547	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937	
ARSD	414	hgsc.bcm.edu	37	X	2833628	2833628	+	Silent	SNP	A	A	C	rs373216270		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	187	0	0		WXS	Illumina HiSeq	Phase_I	95	25	0.263158	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		
HLA-B	3106	hgsc.bcm.edu	37	6	31324911	31324911	+	Missense_Mutation	SNP	C	C	G	rs1050462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31324911C>G	ENST00000412585.2	-	1	53	c.25G>C	c.(25-27)Gtc>Ctc	p.V9L		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	9			V -> L (in dbSNP:rs1050462).		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						AGCAGGAGGACGGTTCGGGGC	0.692									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	1155	0.230631	0.1233	0.245	5008	,	,		8959	0.25		0.3062	False		,,,				2504	0.2679				p.V9L		Atlas-SNP	.											HLA-B,cerebellum,glioma,0,1	HLA-B	54	1	0			c.G25C						scavenged	.	C	LEU/VAL	238,3960		11,216,1872	13.0	12.0	12.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	25	2.5	0.1	6	dbSNP_86	12	981,7141		59,863,3139	yes	missense	HLA-B	NM_005514.6	32	70,1079,5011	GG,GC,CC		12.0783,5.6694,9.8945		9/363	31324911	1219,11101	2099	4061	6160	SO:0001583	missense	3106	exon1	Familial Cancer Database	;Lichen Sclerosis, Familial	GGAGGACGGTTCG	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.25G>C	6.37:g.31324911C>G	ENSP00000399168:p.Val9Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	121	8	0.0661157	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	494	0.2261904761904762	61	0.12398373983739837	84	0.23204419889502761	135	0.23601398601398602	214	0.28232189973614774	N	8.101	0.776701	0.16120	0.056694	0.120783	ENSG00000234745	ENST00000412585	T	0.00597	6.31	3.34	2.47	0.30058	.	0.330918	0.16642	N	0.205609	T	0.00109	0.0003	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.12400	-1.0549	8	0.02654	T	1	.	8.6444	0.33996	0.0:0.237:0.763:0.0	rs1050462;rs2308334;rs3177903;rs3190781;rs9266204;rs17416898;rs17840061	9	P01889	1B07_HUMAN	L	9	ENSP00000399168:V9L	ENSP00000399168:V9L	V	-	1	0	HLA-B	31432890	0.007000	0.16637	0.054000	0.19295	0.040000	0.13550	0.447000	0.21710	0.756000	0.33013	-0.435000	0.05868	GTC	C|0.792;G|0.208	0.208	strong		0.692	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
TRPM6	140803	hgsc.bcm.edu	37	9	77436641	77436641	+	Silent	SNP	G	G	A	rs7018994	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:77436641G>A	ENST00000360774.1	-	8	1191	c.954C>T	c.(952-954)ggC>ggT	p.G318G	TRPM6_ENST00000376864.4_Silent_p.G318G|TRPM6_ENST00000483186.1_5'UTR|TRPM6_ENST00000361255.3_Silent_p.G313G|TRPM6_ENST00000376872.3_Silent_p.G318G|TRPM6_ENST00000449912.2_Silent_p.G313G|TRPM6_ENST00000451710.3_Silent_p.G318G|TRPM6_ENST00000376871.3_Silent_p.G318G	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	318					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						CCCTACCTGTGCCCTCACACA	0.572													G|||	1797	0.358826	0.0673	0.4438	5008	,	,		17635	0.5536		0.3787	False		,,,				2504	0.4714				p.G318G		Atlas-SNP	.											.	TRPM6	377	.	0			c.C954T						PASS	.	G	,,	512,3894	234.6+/-247.4	26,460,1717	143.0	105.0	118.0		939,939,954	4.6	1.0	9	dbSNP_116	118	3043,5557	467.6+/-367.1	549,1945,1806	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	575,2405,3523	AA,AG,GG		35.3837,11.6205,27.3335	,,	313/2018,313/2018,318/2023	77436641	3555,9451	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon8			ACCTGTGCCCTCA	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.954C>T	9.37:g.77436641G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			G|0.701;A|0.299	0.299	strong		0.572	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
FBXO25	26260	hgsc.bcm.edu	37	8	381344	381344	+	Missense_Mutation	SNP	C	C	G	rs28438773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	134	0	0		WXS	Illumina HiSeq	Phase_I	140	56	0.4	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	
MKX	283078	hgsc.bcm.edu	37	10	27964470	27964470	+	Silent	SNP	G	G	A	rs2253230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:27964470G>A	ENST00000375790.5	-	6	1284	c.852C>T	c.(850-852)aaC>aaT	p.N284N	MKX_ENST00000419761.1_Silent_p.N284N			Q8IYA7	MKX_HUMAN	mohawk homeobox	284					collagen fibril organization (GO:0030199)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|positive regulation of collagen biosynthetic process (GO:0032967)|tendon cell differentiation (GO:0035990)|tendon sheath development (GO:0002932)	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)|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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16						TATTGGATCCGTTTTCCAGAG	0.378													G|||	1428	0.285144	0.295	0.353	5008	,	,		19342	0.121		0.338	False		,,,				2504	0.3384				p.N284N		Atlas-SNP	.											.	MKX	43	.	0			c.C852T						PASS	.	G	,	1379,3027	457.5+/-351.6	235,909,1059	79.0	67.0	71.0		852,852	-2.1	1.0	10	dbSNP_100	71	2853,5747	447.7+/-361.6	469,1915,1916	no	coding-synonymous,coding-synonymous	MKX	NM_001242702.1,NM_173576.2	,	704,2824,2975	AA,AG,GG		33.1744,31.2982,32.5388	,	284/353,284/353	27964470	4232,8774	2203	4300	6503	SO:0001819	synonymous_variant	283078	exon6			GGATCCGTTTTCC	BC036207	CCDS7156.1	10p12.1	2011-06-20	2006-03-31	2006-03-31	ENSG00000150051	ENSG00000150051		"""Homeoboxes / TALE class"""	23729	protein-coding gene	gene with protein product		601332	"""chromosome 10 open reading frame 48"", ""iroquois homeobox protein-like 1"""	C10orf48, IRXL1		16408284	Standard	NM_173576		Approved	MGC39616	uc001itx.4	Q8IYA7	OTTHUMG00000017862	ENST00000375790.5:c.852C>T	10.37:g.27964470G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_001242702	B3KWM5	Silent	SNP	ENST00000375790.5	37	CCDS7156.1																																																																																			G|0.693;A|0.307	0.307	strong		0.378	MKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047332.3	NM_173576	
TRIM51	84767	hgsc.bcm.edu	37	11	55655597	55655597	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55655597A>G	ENST00000449290.2	+	4	689	c.597A>G	c.(595-597)gaA>gaG	p.E199E	TRIM51_ENST00000244891.3_Silent_p.E56E	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	199						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										ATCACTTGGAAAGGCTGCGAA	0.433																																					p.E199E		Atlas-SNP	.											SPRYD5_ENST00000327733,NS,carcinoma,+2,2	.	.	2	0			c.A597G						scavenged	.						61.0	58.0	59.0					11																	55655597		2201	4296	6497	SO:0001819	synonymous_variant	84767	exon4			CTTGGAAAGGCTG	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.597A>G	11.37:g.55655597A>G		Somatic	850	52	0.0611765		WXS	Illumina HiSeq	Phase_I	814	59	0.0724816	NM_032681	A6NMG2	Silent	SNP	ENST00000449290.2	37																																																																																				.	.	none		0.433	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
RAD9A	5883	hgsc.bcm.edu	37	11	67160961	67160961	+	Intron	SNP	A	A	G	rs2066496|rs386754479	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:67160961A>G	ENST00000307980.2	+	4	327				RNU6-1238P_ENST00000517215.1_RNA	NM_001243224.1|NM_004584.2	NP_001230153.1|NP_004575.1	Q99638	RAD9A_HUMAN	RAD9 homolog A (S. pombe)						cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|enzyme binding (GO:0019899)|exodeoxyribonuclease III activity (GO:0008853)|histone deacetylase binding (GO:0042826)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			lung(7)|upper_aerodigestive_tract(1)	8			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			GTCTTATCCCATGCAGTCTTT	0.562								Other conserved DNA damage response genes					a|||	869	0.173522	0.3328	0.1081	5008	,	,		18773	0.2292		0.0775	False		,,,				2504	0.046				p.M1V		Atlas-SNP	.											.	RAD9A	15	.	0			c.A1G						PASS	.	G		1244,3156	426.2+/-341.1	170,904,1126	79.0	72.0	74.0			-7.3	0.0	11	dbSNP_98	74	597,7993	158.8+/-212.2	14,569,3712	no	intron	RAD9A	NM_004584.2		184,1473,4838	GG,GA,AA		6.9499,28.2727,14.1724			67160961	1841,11149	2200	4295	6495	SO:0001627	intron_variant	5883	exon1			TATCCCATGCAGT	U53174	CCDS8159.1	11q13.1-q13.2	2008-02-05	2003-07-21	2003-07-23	ENSG00000172613	ENSG00000172613			9827	protein-coding gene	gene with protein product		603761	"""RAD9 (S. pombe) homolog"""	RAD9		8943031	Standard	NM_004584		Approved		uc001okr.3	Q99638	OTTHUMG00000167670	ENST00000307980.2:c.235-6A>G	11.37:g.67160961A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_001243224	B2RCZ8|Q6FI29|Q96C41	Missense_Mutation	SNP	ENST00000307980.2	37	CCDS8159.1																																																																																			A|0.819;G|0.181	0.181	strong		0.562	RAD9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395481.2	NM_004584	
CTCFL	140690	hgsc.bcm.edu	37	20	56099114	56099114	+	Missense_Mutation	SNP	C	C	G	rs6070128	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:56099114C>G	ENST00000608263.1	-	1	809	c.148G>C	c.(148-150)Gag>Cag	p.E50Q	CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000429804.3_Missense_Mutation_p.E50Q|CTCFL_ENST00000609232.1_Missense_Mutation_p.E50Q|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000243914.3_Missense_Mutation_p.E50Q|CTCFL_ENST00000422869.2_Missense_Mutation_p.E50Q|CTCFL_ENST00000608158.1_Missense_Mutation_p.E50Q|CTCFL_ENST00000433949.3_Intron|CTCFL_ENST00000608440.1_Missense_Mutation_p.E50Q|CTCFL_ENST00000432255.2_Missense_Mutation_p.E50Q|CTCFL_ENST00000608425.1_Missense_Mutation_p.E50Q|CTCFL_ENST00000423479.3_Missense_Mutation_p.E50Q|CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000481655.2_Missense_Mutation_p.E50Q|CTCFL_ENST00000371196.2_Missense_Mutation_p.E50Q	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	50			E -> Q (in dbSNP:rs6070128).		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)			GAGGTACGCTCGGCCTCCAAC	0.582													C|||	1428	0.285144	0.0862	0.2882	5008	,	,		19373	0.3651		0.4165	False		,,,				2504	0.3344				p.E50Q		Atlas-SNP	.											CTCFL,caecum,carcinoma,0,1	CTCFL	97	1	0			c.G148C						PASS	.	C	GLN/GLU	565,3841	254.0+/-259.7	33,499,1671	154.0	169.0	164.0		148	-4.7	0.0	20	dbSNP_114	164	3513,5087	512.5+/-378.0	711,2091,1498	yes	missense	CTCFL	NM_080618.2	29	744,2590,3169	GG,GC,CC		40.8488,12.8234,31.3548	benign	50/664	56099114	4078,8928	2203	4300	6503	SO:0001583	missense	140690	exon1			TACGCTCGGCCTC		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.148G>C	20.37:g.56099114C>G	ENSP00000476783:p.Glu50Gln	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	155	85	0.548387	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	688	0.315018315018315	45	0.09146341463414634	116	0.32044198895027626	219	0.38286713286713286	308	0.40633245382585753	C	6.687	0.495343	0.12762	0.128234	0.408488	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000422109;ENST00000426658;ENST00000432255;ENST00000422869	T;T;T;T;T;T;T;T;T	0.12147	2.71;2.75;2.75;2.93;2.81;3.1;2.79;3.39;2.79	4.0	-4.73	0.03259	.	1.342910	0.05297	N	0.522327	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.15141	0.0;0.0;0.005;0.012;0.005;0.011;0.0;0.0	B;B;B;B;B;B;B;B	0.12156	0.003;0.003;0.007;0.006;0.005;0.007;0.002;0.001	T	0.48514	-0.9029	9	0.22706	T	0.39	-1.0843	9.003	0.36094	0.0:0.2572:0.5775:0.1653	rs6070128;rs6070128	50;50;50;50;50;50;50;50	A6XGM3;A6XGM0;A6XGM9;A6XGM8;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;.;.;.;CTCFL_HUMAN	Q	50	ENSP00000415579:E50Q;ENSP00000243914:E50Q;ENSP00000360239:E50Q;ENSP00000415329:E50Q;ENSP00000392034:E50Q;ENSP00000413713:E50Q;ENSP00000403369:E50Q;ENSP00000409344:E50Q;ENSP00000399061:E50Q	ENSP00000243914:E50Q	E	-	1	0	CTCFL	55532520	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.230000	0.09083	-1.292000	0.02366	-0.150000	0.13652	GAG	C|0.675;G|0.325	0.325	strong		0.582	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
EGF	1950	hgsc.bcm.edu	37	4	110883121	110883121	+	Missense_Mutation	SNP	G	G	A	rs11568943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:110883121G>A	ENST00000265171.5	+	8	1737	c.1292G>A	c.(1291-1293)aGa>aAa	p.R431K	EGF_ENST00000509793.1_Missense_Mutation_p.R389K|EGF_ENST00000503392.1_Missense_Mutation_p.R431K	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	431	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> K (in dbSNP:rs11568943). {ECO:0000269|Ref.2}.		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)	GTGCTTGAGAGAGATGGGAAA	0.398													G|||	828	0.165335	0.2995	0.1167	5008	,	,		20785	0.1944		0.0577	False		,,,				2504	0.0992				p.R431K		Atlas-SNP	.											.	EGF	113	.	0			c.G1292A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	1035,3371	381.1+/-324.0	132,771,1300	268.0	273.0	271.0		1292,1166,1292	-2.8	0.0	4	dbSNP_120	271	575,8025	155.5+/-209.5	20,535,3745	yes	missense,missense,missense	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	26,26,26	152,1306,5045	AA,AG,GG		6.686,23.4907,12.3789	benign,benign,benign	431/1167,389/1166,431/1208	110883121	1610,11396	2203	4300	6503	SO:0001583	missense	1950	exon8			TTGAGAGAGATGG	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.1292G>A	4.37:g.110883121G>A	ENSP00000265171:p.Arg431Lys	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	190	73	0.384211	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Missense_Mutation	SNP	ENST00000265171.5	37	CCDS3689.1	356	0.163003663003663	149	0.30284552845528456	38	0.10497237569060773	120	0.2097902097902098	49	0.06464379947229551	G	2.294	-0.361788	0.05103	0.234907	0.06686	ENSG00000138798	ENST00000509793;ENST00000265171;ENST00000503392	D;D;D	0.87179	-2.22;-2.22;-2.22	5.22	-2.84	0.05751	Epidermal growth factor-like (1);	1.231300	0.05217	N	0.507915	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.09377	0.001;0.004;0.001	T	0.06303	-1.0834	9	0.06099	T	0.92	.	4.3771	0.11275	0.2893:0.2917:0.3452:0.0738	rs11568943;rs17041083;rs52832100;rs11568943	431;389;431	E7EVD2;P01133-2;P01133	.;.;EGF_HUMAN	K	389;431;431	ENSP00000424316:R389K;ENSP00000265171:R431K;ENSP00000421384:R431K	ENSP00000265171:R431K	R	+	2	0	EGF	111102570	0.000000	0.05858	0.031000	0.17742	0.707000	0.40811	-1.978000	0.01494	-0.283000	0.09115	-0.867000	0.03001	AGA	G|0.845;A|0.155	0.155	strong		0.398	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		
ZNF99	7652	hgsc.bcm.edu	37	19	22942335	22942335	+	Missense_Mutation	SNP	G	G	A	rs61740110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22942335G>A	ENST00000596209.1	-	4	466	c.376C>T	c.(376-378)Cac>Tac	p.H126Y	ZNF99_ENST00000397104.3_Missense_Mutation_p.H147Y	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	126					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.H147Y(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GCTTCTTCGTGCATCTTACCC	0.303													G|||	425	0.0848642	0.0545	0.085	5008	,	,		16121	0.0933		0.0905	False		,,,				2504	0.1115				p.H126Y		Atlas-SNP	.											ZNF99,right_upper_lobe,carcinoma,+2,2	ZNF99	273	2	1	Substitution - Missense(1)	stomach(1)	c.C376T						PASS	.	G	TYR/HIS	194,3542		6,182,1680	109.0	104.0	105.0		439	-1.8	0.0	19	dbSNP_129	105	748,7460		39,670,3395	yes	missense	ZNF99	NM_001080409.2	83	45,852,5075	AA,AG,GG		9.1131,5.1927,7.8868	benign	147/912	22942335	942,11002	1868	4104	5972	SO:0001583	missense	7652	exon4			CTTCGTGCATCTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.376C>T	19.37:g.22942335G>A	ENSP00000472969:p.His126Tyr	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	184	0.08424908424908426	30	0.06097560975609756	37	0.10220994475138122	52	0.09090909090909091	65	0.08575197889182058	N	0.004	-2.248013	0.00271	0.051927	0.091131	ENSG00000213973	ENST00000397104	T	0.06218	3.33	0.88	-1.76	0.08006	.	.	.	.	.	T	0.00144	0.0004	L	0.50993	1.605	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.47799	-0.9089	8	0.08837	T	0.75	.	5.1406	0.14957	0.2404:0.0:0.7596:0.0	rs61740110	147	A8MXY4	ZNF99_HUMAN	Y	147	ENSP00000380293:H147Y	ENSP00000380293:H147Y	H	-	1	0	ZNF99	22734175	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.366000	0.20365	-0.982000	0.03515	-1.014000	0.02459	CAC	G|0.915;A|0.085	0.085	strong		0.303	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
PLXNA1	5361	hgsc.bcm.edu	37	3	126735453	126735453	+	Silent	SNP	C	C	T	rs9858521	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	162	0	0		WXS	Illumina HiSeq	Phase_I	166	86	0.518072	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	
OR51F1	256892	hgsc.bcm.edu	37	11	4790758	4790758	+	Silent	SNP	G	G	A	rs11033796	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790758G>A	ENST00000380383.1	-	1	410	c.411C>T	c.(409-411)gaC>gaT	p.D137D	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Silent_p.D130D|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	137						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)		ACCTCAGAGGGTCACAGATGG	0.418													A|||	1167	0.233027	0.5174	0.2104	5008	,	,		21796	0.0		0.2714	False		,,,				2504	0.0654				p.D130D		Atlas-SNP	.											.	OR51F1	60	.	0			c.C390T						PASS	.	A		2151,2251	595.0+/-388.3	532,1087,582	79.0	80.0	79.0		390	-0.9	0.5	11	dbSNP_120	79	2183,6413	712.0+/-405.9	292,1599,2407	no	coding-synonymous	OR51F1	NM_001004752.1		824,2686,2989	AA,AG,GG		25.3955,48.8642,33.3436		130/313	4790758	4334,8664	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			CAGAGGGTCACAG	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.411C>T	11.37:g.4790758G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	145	72	0.496552	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				G|0.690;A|0.310	0.310	strong		0.418	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
LYPD5	284348	hgsc.bcm.edu	37	19	44306482	44306482	+	Silent	SNP	C	C	T	rs11879355	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44306482C>T	ENST00000377950.3	-	1	131	c.51G>A	c.(49-51)gcG>gcA	p.A17A	LYPD5_ENST00000414615.2_Intron|LYPD5_ENST00000594013.1_5'Flank	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	75	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	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	
UNC5C	8633	hgsc.bcm.edu	37	4	96091414	96091414	+	Missense_Mutation	SNP	C	C	T	rs34585936	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:96091414C>T	ENST00000453304.1	-	15	2869	c.2521G>A	c.(2521-2523)Gct>Act	p.A841T		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	841			A -> T (in dbSNP:rs34585936).		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)		ATGCTGAAAGCACTGGGCCCC	0.582													C|||	92	0.0183706	0.0023	0.0231	5008	,	,		18103	0.0347		0.0209	False		,,,				2504	0.0174				p.A841T		Atlas-SNP	.											.	UNC5C	141	.	0			c.G2521A						PASS	.	C	THR/ALA	32,4374	37.6+/-69.7	0,32,2171	178.0	169.0	172.0		2521	5.5	0.7	4	dbSNP_126	172	173,8427	80.6+/-143.3	1,171,4128	yes	missense	UNC5C	NM_003728.3	58	1,203,6299	TT,TC,CC		2.0116,0.7263,1.5762	probably-damaging	841/932	96091414	205,12801	2203	4300	6503	SO:0001583	missense	8633	exon15			TGAAAGCACTGGG	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.2521G>A	4.37:g.96091414C>T	ENSP00000406022:p.Ala841Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	90	35	0.388889	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	38	0.0173992673992674	2	0.0040650406504065045	4	0.011049723756906077	18	0.03146853146853147	14	0.018469656992084433	C	33	5.275814	0.95459	0.007263	0.020116	ENSG00000182168	ENST00000453304;ENST00000331502	T	0.23348	1.91	5.51	5.51	0.81932	Death (1);DEATH-like (2);	0.052554	0.85682	D	0.000000	T	0.32133	0.0819	M	0.83483	2.645	0.80722	D	1	D	0.67145	0.996	D	0.71870	0.975	T	0.50816	-0.8783	10	0.72032	D	0.01	.	19.6101	0.95602	0.0:1.0:0.0:0.0	rs34585936	841	O95185	UNC5C_HUMAN	T	841;800	ENSP00000406022:A841T	ENSP00000328673:A800T	A	-	1	0	UNC5C	96310437	1.000000	0.71417	0.712000	0.30502	0.752000	0.42762	7.651000	0.83577	2.868000	0.98415	0.557000	0.71058	GCT	C|0.983;T|0.017	0.017	strong		0.582	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
PLEC	5339	hgsc.bcm.edu	37	8	144992900	144992900	+	Silent	SNP	G	G	A	rs17062686	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144992900G>A	ENST00000322810.4	-	32	11669	c.11500C>T	c.(11500-11502)Ctg>Ttg	p.L3834L	PLEC_ENST00000398774.2_Silent_p.L3665L|PLEC_ENST00000527096.1_Silent_p.L3720L|PLEC_ENST00000357649.2_Silent_p.L3701L|PLEC_ENST00000345136.3_Silent_p.L3697L|PLEC_ENST00000356346.3_Silent_p.L3683L|PLEC_ENST00000436759.2_Silent_p.L3724L|PLEC_ENST00000354958.2_Silent_p.L3675L|PLEC_ENST00000354589.3_Silent_p.L3697L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3834	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						GAACCGGGCAGGTAGACACCA	0.667													G|||	85	0.0169728	0.0023	0.0115	5008	,	,		16451	0.0		0.0517	False		,,,				2504	0.0225				p.L3834L		Atlas-SNP	.											.	PLEC	1144	.	0			c.C11500T						PASS	.	G	,,,,,,,	32,3900		1,30,1935	20.0	26.0	24.0		11170,11047,11023,11500,10993,11089,11101,11089	-0.8	0.0	8	dbSNP_123	24	408,7866		8,392,3737	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	,,,,,,,	9,422,5672	AA,AG,GG		4.9311,0.8138,3.6048	,,,,,,,	3724/4575,3683/4534,3675/4526,3834/4685,3665/4516,3697/4548,3701/4552,3697/4548	144992900	440,11766	1966	4137	6103	SO:0001819	synonymous_variant	5339	exon32			CGGGCAGGTAGAC	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.11500C>T	8.37:g.144992900G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	52	0.382353	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.970;A|0.030	0.030	strong		0.667	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
PTPRO	5800	hgsc.bcm.edu	37	12	15661564	15661564	+	Missense_Mutation	SNP	G	G	A	rs71459181	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:15661564G>A	ENST00000281171.4	+	7	1657	c.1327G>A	c.(1327-1329)Gtt>Att	p.V443I	PTPRO_ENST00000348962.2_Missense_Mutation_p.V443I|PTPRO_ENST00000543886.1_Missense_Mutation_p.V443I	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	443	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				GAGTGTCCACGTTTTAAGCTC	0.502													G|||	18	0.00359425	0.0008	0.0072	5008	,	,		18994	0.0		0.0089	False		,,,				2504	0.0031				p.V443I		Atlas-SNP	.											.	PTPRO	148	.	0			c.G1327A						PASS	.	G	ILE/VAL,ILE/VAL	14,4392	22.3+/-47.3	0,14,2189	100.0	93.0	95.0		1327,1327	4.6	0.2	12	dbSNP_130	95	121,8479	62.8+/-124.8	2,117,4181	yes	missense,missense	PTPRO	NM_002848.3,NM_030667.2	29,29	2,131,6370	AA,AG,GG		1.407,0.3177,1.038	benign,benign	443/1189,443/1217	15661564	135,12871	2203	4300	6503	SO:0001583	missense	5800	exon7			GTCCACGTTTTAA	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9678	protein-coding gene	gene with protein product	"""osteoclastic transmembrane protein-tyrosine phosphatase"""	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.1327G>A	12.37:g.15661564G>A	ENSP00000281171:p.Val443Ile	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	198	109	0.550505	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	37	CCDS8675.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	14.57	2.576090	0.45902	0.003177	0.01407	ENSG00000151490	ENST00000281171;ENST00000543886;ENST00000348962	T;T;T	0.57752	0.38;0.38;0.38	5.44	4.55	0.56014	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46442	D	0.000284	T	0.20941	0.0504	N	0.12182	0.205	0.80722	D	1	P;P;B	0.40398	0.669;0.716;0.233	B;B;B	0.28385	0.053;0.089;0.04	T	0.07751	-1.0756	10	0.28530	T	0.3	.	12.3796	0.55299	0.0767:0.0:0.9233:0.0	.	443;443;443	Q16827-2;Q16827;Q8IYG3	.;PTPRO_HUMAN;.	I	443	ENSP00000281171:V443I;ENSP00000444173:V443I;ENSP00000343434:V443I	ENSP00000281171:V443I	V	+	1	0	PTPRO	15552831	0.869000	0.29996	0.175000	0.22980	0.976000	0.68499	1.352000	0.34033	1.537000	0.49254	0.655000	0.94253	GTT	G|0.991;A|0.009	0.009	strong		0.502	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		
ACTR1B	10120	hgsc.bcm.edu	37	2	98275354	98275354	+	Missense_Mutation	SNP	G	G	A	rs11692435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:98275354G>A	ENST00000289228.5	-	5	644	c.428C>T	c.(427-429)gCt>gTt	p.A143V		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	143			A -> V (in dbSNP:rs11692435).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						ACTGAGCACAGCCTGCATGGA	0.607													G|||	119	0.023762	0.0023	0.0375	5008	,	,		19640	0.0		0.0835	False		,,,				2504	0.0061				p.A143V		Atlas-SNP	.											ACTR1B,NS,adenoma,0,1	ACTR1B	34	1	0			c.C428T						PASS	.	G	VAL/ALA	70,4336		1,68,2134	103.0	109.0	107.0		428	4.8	1.0	2	dbSNP_120	107	716,7884		31,654,3615	yes	missense	ACTR1B	NM_005735.3	64	32,722,5749	AA,AG,GG		8.3256,1.5887,6.0434	probably-damaging	143/377	98275354	786,12220	2203	4300	6503	SO:0001583	missense	10120	exon5			AGCACAGCCTGCA	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"""ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"""	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.428C>T	2.37:g.98275354G>A	ENSP00000289228:p.Ala143Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	67	41	0.61194	NM_005735	D3DVH2|Q53SK5|Q9BRB7	Missense_Mutation	SNP	ENST00000289228.5	37	CCDS2033.1	89	0.04075091575091575	0	0.0	19	0.052486187845303865	0	0.0	70	0.09234828496042216	.	29.3	4.990255	0.93106	0.015887	0.083256	ENSG00000115073	ENST00000289228	D	0.97811	-4.55	4.79	4.79	0.61399	.	0.000000	0.85682	D	0.000000	D	0.88108	0.6348	H	0.98664	4.295	0.09310	P	0.99999999810745	D	0.89917	1.0	D	0.91635	0.999	T	0.74509	-0.3642	9	0.87932	D	0	.	15.6865	0.77415	0.0:0.0:1.0:0.0	rs11692435;rs52812960;rs58086465;rs11692435	143	P42025	ACTY_HUMAN	V	143	ENSP00000289228:A143V	ENSP00000289228:A143V	A	-	2	0	ACTR1B	97641786	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	9.697000	0.98697	2.369000	0.80426	0.655000	0.94253	GCT	G|0.950;A|0.050	0.050	strong		0.607	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43828141	43828141	+	Missense_Mutation	SNP	T	T	A	rs7302446	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:43828141T>A	ENST00000389420.3	-	19	2626	c.2627A>T	c.(2626-2628)aAg>aTg	p.K876M	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.K30M|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.K876M	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	876	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		K -> M (in dbSNP:rs7302446).		extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ATGATCACTCTTATGTATGCA	0.338													T|||	183	0.0365415	0.0015	0.0086	5008	,	,		19783	0.0694		0.0348	False		,,,				2504	0.0716				p.K876M		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A2627T						PASS	.	T	MET/LYS	26,4380	29.9+/-59.1	0,26,2177	81.0	67.0	72.0		2627	3.7	1.0	12	dbSNP_116	72	239,8355	90.4+/-152.6	5,229,4063	yes	missense	ADAMTS20	NM_025003.3	95	5,255,6240	AA,AT,TT		2.781,0.5901,2.0385	probably-damaging	876/1911	43828141	265,12735	2203	4297	6500	SO:0001583	missense	80070	exon19			TCACTCTTATGTA	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2627A>T	12.37:g.43828141T>A	ENSP00000374071:p.Lys876Met	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	153	61	0.398693	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	78	0.03571428571428571	0	0.0	5	0.013812154696132596	44	0.07692307692307693	29	0.03825857519788918	T	14.92	2.679115	0.47886	0.005901	0.02781	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	4.91	3.72	0.42706	.	0.121955	0.35708	N	0.003035	T	0.10208	0.0250	M	0.77616	2.38	0.36197	D	0.850469	D;D	0.65815	0.988;0.995	P;P	0.58928	0.848;0.844	T	0.55749	-0.8092	10	0.66056	D	0.02	.	4.4211	0.11481	0.1495:0.1519:0.0:0.6986	rs7302446;rs52813354;rs7302446	876;30	P59510;E9PBD5	ATS20_HUMAN;.	M	876;42;30;876;876	ENSP00000374071:K876M;ENSP00000447427:K42M;ENSP00000378911:K30M;ENSP00000448341:K876M	ENSP00000374068:K876M	K	-	2	0	ADAMTS20	42114408	0.997000	0.39634	0.994000	0.49952	0.925000	0.55904	0.528000	0.23002	0.913000	0.36797	0.533000	0.62120	AAG	T|0.974;A|0.026	0.026	strong		0.338	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
TUBA1C	84790	hgsc.bcm.edu	37	12	49663751	49663751	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:49663751C>T	ENST00000301072.6	+	3	642	c.367C>T	c.(367-369)Cgc>Tgc	p.R123C	TUBA1C_ENST00000541364.1_Missense_Mutation_p.R193C|TUBA1C_ENST00000549183.1_Missense_Mutation_p.R123C|RP11-161H23.5_ENST00000550468.2_RNA	NM_032704.3	NP_116093.1	Q9BQE3	TBA1C_HUMAN	tubulin, alpha 1c	123					'de novo' posttranslational protein folding (GO:0051084)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasmic microtubule (GO:0005881)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)	13						GGACCGAATTCGCAAGCTGGT	0.428																																					p.R123C		Atlas-SNP	.											TUBA1C,NS,carcinoma,0,1	TUBA1C	32	1	0			c.C367T						scavenged	.						155.0	149.0	151.0					12																	49663751		2203	4300	6503	SO:0001583	missense	84790	exon3			CGAATTCGCAAGC	BC004949	CCDS8782.1	12q13.12	2007-03-16	2007-02-12	2007-02-12		ENSG00000167553		"""Tubulins"""	20768	protein-coding gene	gene with protein product			"""tubulin, alpha 6"""	TUBA6		7821789	Standard	NM_032704		Approved	MGC14580, MGC10851, bcm948	uc001rtt.1	Q9BQE3		ENST00000301072.6:c.367C>T	12.37:g.49663751C>T	ENSP00000301072:p.Arg123Cys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	218	3	0.0137615	NM_032704		Missense_Mutation	SNP	ENST00000301072.6	37	CCDS8782.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141023	0.56936	.	.	ENSG00000167553	ENST00000541364;ENST00000301072;ENST00000549183;ENST00000321665	T;T;T	0.73789	-0.78;-0.78;-0.78	3.99	3.99	0.46301	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.90000	0.6878	H	0.98218	4.175	0.58432	D	0.999995	D;D	0.89917	1.0;0.995	D;P	0.71414	0.973;0.763	D	0.92198	0.5765	10	0.72032	D	0.01	.	11.6145	0.51080	0.1786:0.8214:0.0:0.0	.	193;123	F5H5D3;Q9BQE3	.;TBA1C_HUMAN	C	193;123;123;123	ENSP00000443475:R193C;ENSP00000301072:R123C;ENSP00000448211:R123C	ENSP00000301072:R123C	R	+	1	0	TUBA1C	47950018	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.686000	0.54685	2.504000	0.84457	0.455000	0.32223	CGC	.	.	none		0.428	TUBA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404424.1	NM_032704	
CRLF1	9244	hgsc.bcm.edu	37	19	18705145	18705145	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:18705145T>C	ENST00000392386.3	-	7	1317	c.1124A>G	c.(1123-1125)aAg>aGg	p.K375R	CRLF1_ENST00000594325.1_5'UTR	NM_004750.4	NP_004741.1	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	375					negative regulation of motor neuron apoptotic process (GO:2000672)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|ureteric bud development (GO:0001657)	CRLF-CLCF1 complex (GO:0097058)|extracellular space (GO:0005615)	cytokine binding (GO:0019955)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	9						CGCGTGCTTCTTGAGCCAGCC	0.701																																					p.K375R		Atlas-SNP	.											CRLF1,bladder,carcinoma,+1,1	CRLF1	32	1	0			c.A1124G						scavenged	.						31.0	29.0	29.0					19																	18705145		2203	4300	6503	SO:0001583	missense	9244	exon7			TGCTTCTTGAGCC	AF059293	CCDS32962.1	19p12	2013-02-11				ENSG00000006016		"""Fibronectin type III domain containing"""	2364	protein-coding gene	gene with protein product	"""cold-induced sweating syndrome"""	604237				9686600	Standard	NM_004750		Approved	CLF-1, CLF, CISS, CISS1	uc010ebt.2	O75462		ENST00000392386.3:c.1124A>G	19.37:g.18705145T>C	ENSP00000376188:p.Lys375Arg	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	106	4	0.0377358	NM_004750	Q9UHH5	Missense_Mutation	SNP	ENST00000392386.3	37	CCDS32962.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.777681	0.31502	.	.	ENSG00000006016	ENST00000392386	D	0.82081	-1.57	3.91	3.91	0.45181	.	0.231995	0.34484	N	0.003922	T	0.66819	0.2828	N	0.12569	0.235	0.31270	N	0.691855	B	0.12630	0.006	B	0.08055	0.003	T	0.63747	-0.6567	10	0.27082	T	0.32	-27.308	10.7407	0.46152	0.0:0.0:0.0:1.0	.	375	O75462	CRLF1_HUMAN	R	375	ENSP00000376188:K375R	ENSP00000376188:K375R	K	-	2	0	CRLF1	18566145	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.994000	0.63901	1.641000	0.50575	0.402000	0.26972	AAG	.	.	none		0.701	CRLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465129.1		
KIAA0754	643314	hgsc.bcm.edu	37	1	39879435	39879435	+	Silent	SNP	C	C	A	rs112569629		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879435C>A	ENST00000530275.1	+	1	3285	c.3090C>A	c.(3088-3090)ccC>ccA	p.P1030P	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1030	Ala-rich.									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)			TGCCCACCCCCGAGGAATCTG	0.672																																					p.P1166P		Atlas-SNP	.											.	KIAA0754	93	.	0			c.C3498A						PASS	.						21.0	24.0	23.0					1																	39879435		1962	4129	6091	SO:0001819	synonymous_variant	643314	exon1			CACCCCCGAGGAA			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.3090C>A	1.37:g.39879435C>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	74	44	0.594595	NM_015038	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	37																																																																																				C|0.995;A|0.005	0.005	weak		0.672	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
ENG	2022	hgsc.bcm.edu	37	9	130605385	130605385	+	Silent	SNP	C	C	T	rs45605432|rs11545664	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:130605385C>T	ENST00000373203.4	-	2	607	c.207G>A	c.(205-207)ctG>ctA	p.L69L	RNA5SP296_ENST00000410523.1_RNA|ENG_ENST00000344849.3_Silent_p.L69L	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	51	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	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		
OR51B2	79345	hgsc.bcm.edu	37	11	5344592	5344592	+	Missense_Mutation	SNP	A	A	C	rs11036814	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	136	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	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	
PBK	55872	hgsc.bcm.edu	37	8	27685663	27685663	+	Silent	SNP	C	C	T	rs55973425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:27685663C>T	ENST00000301905.4	-	3	574	c.111G>A	c.(109-111)aaG>aaA	p.K37K	PBK_ENST00000522944.1_Silent_p.K37K	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	37	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		CAAAGCCAAGCTTCTGCATAA	0.299													C|||	5	0.000998403	0.0008	0.0	5008	,	,		16110	0.0		0.004	False		,,,				2504	0.0				p.K37K		Atlas-SNP	.											.	PBK	29	.	0			c.G111A						PASS	.	C		7,4399	11.4+/-27.6	0,7,2196	64.0	70.0	68.0		111	4.9	1.0	8	dbSNP_129	68	27,8573	18.5+/-59.3	0,27,4273	no	coding-synonymous	PBK	NM_018492.2		0,34,6469	TT,TC,CC		0.314,0.1589,0.2614		37/323	27685663	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	55872	exon3			GCCAAGCTTCTGC	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.111G>A	8.37:g.27685663C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Silent	SNP	ENST00000301905.4	37	CCDS6063.1																																																																																			C|0.998;T|0.002	0.002	strong		0.299	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
ATP9A	10079	hgsc.bcm.edu	37	20	50346491	50346491	+	Missense_Mutation	SNP	C	C	A	rs142435125	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:50346491C>A	ENST00000338821.5	-	2	359	c.95G>T	c.(94-96)gGt>gTt	p.G32V	ATP9A_ENST00000402822.1_Missense_Mutation_p.G32V|ATP9A_ENST00000477492.1_5'UTR|ATP9A_ENST00000311637.5_Missense_Mutation_p.G17V	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	32					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						CTCCCCTCCACCGCAGCATCT	0.597													C|||	30	0.00599042	0.0	0.0014	5008	,	,		17873	0.0		0.003	False		,,,				2504	0.0266				p.G32V		Atlas-SNP	.											.	ATP9A	135	.	0			c.G95T						PASS	.	C	VAL/GLY	3,4403	6.2+/-15.9	0,3,2200	90.0	85.0	87.0		95	5.3	1.0	20	dbSNP_134	87	36,8564	24.6+/-71.5	0,36,4264	yes	missense	ATP9A	NM_006045.1	109	0,39,6464	AA,AC,CC		0.4186,0.0681,0.2999	benign	32/1048	50346491	39,12967	2203	4300	6503	SO:0001583	missense	10079	exon2			CCTCCACCGCAGC	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.95G>T	20.37:g.50346491C>A	ENSP00000342481:p.Gly32Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.40	3.615508	0.66672	6.81E-4	0.004186	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;T;T	0.54071	0.59;0.59;0.59	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.52108	0.1714	L	0.43152	1.355	0.58432	D	0.999996	B;P	0.36789	0.073;0.57	B;B	0.39805	0.31;0.147	T	0.53995	-0.8359	10	0.51188	T	0.08	-14.3884	19.2362	0.93861	0.0:1.0:0.0:0.0	.	32;32	O75110-2;O75110	.;ATP9A_HUMAN	V	17;32;32	ENSP00000309086:G17V;ENSP00000342481:G32V;ENSP00000385875:G32V	ENSP00000309086:G17V	G	-	2	0	ATP9A	49779898	1.000000	0.71417	0.997000	0.53966	0.922000	0.55478	7.257000	0.78362	2.608000	0.88229	0.563000	0.77884	GGT	C|0.997;A|0.003	0.003	strong		0.597	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
CD101	9398	hgsc.bcm.edu	37	1	117560058	117560058	+	Missense_Mutation	SNP	C	C	G	rs17235773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:117560058C>G	ENST00000256652.4	+	5	1633	c.1575C>G	c.(1573-1575)agC>agG	p.S525R	CD101_ENST00000369470.1_Missense_Mutation_p.S525R	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	525	Ig-like C2-type 4.		S -> R (in dbSNP:rs17235773).		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						GAGATCTGAGCTGGACTCAGA	0.473													C|||	169	0.033746	0.0522	0.0461	5008	,	,		22414	0.0		0.0596	False		,,,				2504	0.0082				p.S525R		Atlas-SNP	.											.	CD101	95	.	0			c.C1575G						PASS	.	C	ARG/SER	304,4102	164.0+/-195.7	8,288,1907	71.0	74.0	73.0		1575	2.6	0.4	1	dbSNP_123	73	558,8042	151.8+/-206.5	22,514,3764	yes	missense	CD101	NM_004258.3	110	30,802,5671	GG,GC,CC		6.4884,6.8997,6.6277	probably-damaging	525/1022	117560058	862,12144	2203	4300	6503	SO:0001583	missense	9398	exon5			TCTGAGCTGGACT	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.1575C>G	1.37:g.117560058C>G	ENSP00000256652:p.Ser525Arg	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	88	18	0.204545	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	93	0.042582417582417584	31	0.06300813008130081	15	0.04143646408839779	0	0.0	47	0.06200527704485488	C	15.24	2.776063	0.49786	0.068997	0.064884	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.22336	1.96;1.96	4.52	2.59	0.31030	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.767080	0.12461	N	0.466920	T	0.14874	0.0359	M	0.62723	1.935	0.29048	N	0.884698	P	0.50710	0.938	P	0.50314	0.637	T	0.07731	-1.0757	10	0.72032	D	0.01	0.0806	5.94	0.19187	0.0:0.6883:0.2048:0.107	rs17235773	525	Q93033	IGSF2_HUMAN	R	525	ENSP00000256652:S525R;ENSP00000358482:S525R	ENSP00000256652:S525R	S	+	3	2	CD101	117361581	0.066000	0.20996	0.440000	0.26846	0.797000	0.45037	0.049000	0.14099	0.611000	0.30052	0.655000	0.94253	AGC	C|0.944;G|0.056	0.056	strong		0.473	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
HCN1	348980	hgsc.bcm.edu	37	5	45262443	45262443	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:45262443C>T	ENST00000303230.4	-	8	2310	c.2253G>A	c.(2251-2253)ccG>ccA	p.P751P		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	751	Gln-rich.				apical protein localization (GO:0045176)|cellular response to cAMP (GO:0071320)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|retinal cone cell development (GO:0046549)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|intracellular cAMP activated cation channel activity (GO:0005222)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(3)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(21)|liver(1)|lung(98)|ovary(1)|prostate(7)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(5)	156						GCTGCGGGGACGgctgctgtg	0.637																																					p.P751P		Atlas-SNP	.											HCN1,right_upper_lobe,carcinoma,0,1	HCN1	298	1	0			c.G2253A						scavenged	.						47.0	48.0	48.0					5																	45262443		2203	4300	6503	SO:0001819	synonymous_variant	348980	exon8			CGGGGACGGCTGC	AF064876	CCDS3952.1	5p12	2011-07-05			ENSG00000164588	ENSG00000164588		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	4845	protein-coding gene	gene with protein product		602780		BCNG1		9405696, 9630217, 16382102	Standard	NM_021072		Approved	BCNG-1, HAC-2	uc003jok.3	O60741	OTTHUMG00000131155	ENST00000303230.4:c.2253G>A	5.37:g.45262443C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	110	3	0.0272727	NM_021072		Silent	SNP	ENST00000303230.4	37	CCDS3952.1																																																																																			.	.	none		0.637	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072	
ZNF772	400720	hgsc.bcm.edu	37	19	57984918	57984918	+	Silent	SNP	A	A	G	rs2074058	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57984918A>G	ENST00000343280.4	-	5	1454	c.1194T>C	c.(1192-1194)agT>agC	p.S398S	ZNF772_ENST00000425074.3_3'UTR|ZNF772_ENST00000601768.1_Intron|AC004076.9_ENST00000596831.1_Intron|ZNF772_ENST00000427512.2_Silent_p.S286S|ZNF772_ENST00000356584.3_Silent_p.S357S|ZNF772_ENST00000600175.1_Intron|AC004076.9_ENST00000415705.3_Intron	NM_001024596.2	NP_001019767.1	Q68DY9	ZN772_HUMAN	zinc finger protein 772	398					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)		CAGTATGAACACTCCAATGTT	0.413													A|||	2073	0.413938	0.3154	0.4524	5008	,	,		22319	0.5893		0.2783	False		,,,				2504	0.4785				p.S398S	Melanoma(5;289 436 14293 15924 30817)	Atlas-SNP	.											.	ZNF772	42	.	0			c.T1194C						PASS	.	A	,	1364,3042	454.2+/-350.6	198,968,1037	132.0	121.0	125.0		1194,1071	-1.1	1.0	19	dbSNP_96	125	2446,6154	402.6+/-347.5	329,1788,2183	no	coding-synonymous,coding-synonymous	ZNF772	NM_001024596.2,NM_001144068.1	,	527,2756,3220	GG,GA,AA		28.4419,30.9578,29.2942	,	398/490,357/449	57984918	3810,9196	2203	4300	6503	SO:0001819	synonymous_variant	400720	exon5			ATGAACACTCCAA	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.1194T>C	19.37:g.57984918A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	106	62	0.584906	NM_001024596	A6NJK9|B4DH56|B4DYS0	Silent	SNP	ENST00000343280.4	37	CCDS33133.1																																																																																			A|0.659;G|0.341	0.341	strong		0.413	ZNF772-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397447.1	NM_001024596	
ATP6V0A1	535	hgsc.bcm.edu	37	17	40632729	40632729	+	Silent	SNP	C	C	T	rs41283429	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:40632729C>T	ENST00000343619.4	+	8	801	c.678C>T	c.(676-678)ggC>ggT	p.G226G	ATP6V0A1_ENST00000393829.2_Silent_p.G226G|ATP6V0A1_ENST00000585525.1_Silent_p.G183G|ATP6V0A1_ENST00000546249.1_Silent_p.G226G|ATP6V0A1_ENST00000537728.1_Silent_p.G183G|ATP6V0A1_ENST00000544137.1_Intron|ATP6V0A1_ENST00000264649.6_Silent_p.G233G	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	226					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|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)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|urinary_tract(3)	26		all_cancers(22;1.18e-05)|Breast(137;0.000105)|all_epithelial(22;0.000254)		BRCA - Breast invasive adenocarcinoma(366;0.137)		TCTTCCAAGGCGATCAGCTGA	0.443													C|||	88	0.0175719	0.0076	0.0259	5008	,	,		16990	0.0		0.0368	False		,,,				2504	0.0235				p.G233G		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.C699T						PASS	.	C	,,	52,4354	52.3+/-87.9	0,52,2151	95.0	93.0	94.0		699,678,678	-6.6	1.0	17	dbSNP_127	94	348,8252	118.1+/-177.6	8,332,3960	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A1	NM_001130020.1,NM_001130021.1,NM_005177.3	,,	8,384,6111	TT,TC,CC		4.0465,1.1802,3.0755	,,	233/839,226/838,226/832	40632729	400,12606	2203	4300	6503	SO:0001819	synonymous_variant	535	exon8			CCAAGGCGATCAG	U73006	CCDS11426.1, CCDS45683.1, CCDS45684.1	17q21	2010-04-21	2006-01-20	2002-05-10	ENSG00000033627	ENSG00000033627		"""ATPases / V-type"""	865	protein-coding gene	gene with protein product		192130	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1A (110/116kD)"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 1"", ""ATPase, H+ transporting, lysosomal V0 subunit A1"""	VPP1, ATP6N1, ATP6N1A		7774924	Standard	NM_001130020		Approved	a1, Vph1, Stv1	uc002hzs.3	Q93050		ENST00000343619.4:c.678C>T	17.37:g.40632729C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	72	38	0.527778	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Silent	SNP	ENST00000343619.4	37	CCDS45684.1																																																																																			C|0.969;T|0.031	0.031	strong		0.443	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020	
CD207	50489	hgsc.bcm.edu	37	2	71062648	71062648	+	Missense_Mutation	SNP	G	G	A	rs10489990	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:71062648G>A	ENST00000410009.3	-	2	209	c.164C>T	c.(163-165)gCc>gTc	p.A55V		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	55			A -> V (in dbSNP:rs10489990).		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)	p.A55V(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						CAGGACGGAGGCGACCAGGAC	0.602													G|||	1424	0.284345	0.1346	0.3963	5008	,	,		19468	0.3075		0.3608	False		,,,				2504	0.3047				p.A55V		Atlas-SNP	.											CD207,NS,carcinoma,0,1	CD207	47	1	1	Substitution - Missense(1)	stomach(1)	c.C164T						PASS	.	G	VAL/ALA	640,3582		45,550,1516	68.0	77.0	74.0		164	4.0	0.0	2	dbSNP_119	74	2952,5510		522,1908,1801	yes	missense	CD207	NM_015717.3	64	567,2458,3317	AA,AG,GG		34.8854,15.1587,28.3191	possibly-damaging	55/329	71062648	3592,9092	2111	4231	6342	SO:0001583	missense	50489	exon2			ACGGAGGCGACCA	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.164C>T	2.37:g.71062648G>A	ENSP00000386378:p.Ala55Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	136	55	0.404412	NM_015717		Missense_Mutation	SNP	ENST00000410009.3	37		645	0.29532967032967034	66	0.13414634146341464	137	0.3784530386740331	181	0.31643356643356646	261	0.34432717678100266	G	16.18	3.049152	0.55110	0.151587	0.348854	ENSG00000116031	ENST00000410009	T	0.04156	3.69	4.87	4.0	0.46444	.	0.407067	0.21670	N	0.070893	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.30068	0.267	B	0.30401	0.115	T	0.42464	-0.9450	9	0.11182	T	0.66	.	9.7514	0.40478	0.0984:0.0:0.9016:0.0	rs10489990;rs52834864;rs59407760;rs10489990	55	Q9UJ71	CLC4K_HUMAN	V	55	ENSP00000386378:A55V	ENSP00000386378:A55V	A	-	2	0	CD207	70916156	0.695000	0.27747	0.024000	0.17045	0.048000	0.14542	2.131000	0.42074	1.365000	0.46057	-0.136000	0.14681	GCC	G|0.716;A|0.284	0.284	strong		0.602	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998886	72998886	+	Silent	SNP	T	T	C	rs3809997	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	50	0	0		WXS	Illumina HiSeq	Phase_I	42	16	0.380952	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	
TNRC6A	27327	hgsc.bcm.edu	37	16	24834233	24834233	+	Silent	SNP	C	C	T	rs2303085	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:24834233C>T	ENST00000395799.3	+	24	5541	c.5412C>T	c.(5410-5412)caC>caT	p.H1804H	TNRC6A_ENST00000432286.2_Silent_p.H282H|TNRC6A_ENST00000315183.7_Silent_p.H1755H	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1804	RRM.|Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|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)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.H1804H(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GCATGCAGCACGGCCCGCTGA	0.557													c|||	1106	0.220847	0.1626	0.2637	5008	,	,		22656	0.4038		0.166	False		,,,				2504	0.137				p.H1804H		Atlas-SNP	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	1	Substitution - coding silent(1)	stomach(1)	c.C5412T						PASS	.	C		692,3702	289.5+/-280.5	45,602,1550	124.0	101.0	109.0		5412	1.9	1.0	16	dbSNP_100	109	1175,7425	239.4+/-270.5	78,1019,3203	no	coding-synonymous	TNRC6A	NM_014494.2		123,1621,4753	TT,TC,CC		13.6628,15.7487,14.3682		1804/1963	24834233	1867,11127	2197	4300	6497	SO:0001819	synonymous_variant	27327	exon24			GCAGCACGGCCCG	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5412C>T	16.37:g.24834233C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	152	69	0.453947	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2	506	0.2316849816849817	63	0.12804878048780488	80	0.22099447513812154	230	0.4020979020979021	133	0.17546174142480211	c	9.384	1.073739	0.20147	0.157487	0.136628	ENSG00000090905	ENST00000450465	.	.	.	5.27	1.87	0.25490	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44787	-0.9305	3	.	.	.	-6.083	7.3864	0.26884	0.0:0.4108:0.0:0.5892	rs2303085;rs57489138;rs2303085	.	.	.	W	695	.	.	R	+	1	2	TNRC6A	24741734	0.979000	0.34478	1.000000	0.80357	0.993000	0.82548	0.189000	0.17037	0.338000	0.23692	-0.310000	0.09108	CGG	C|0.816;T|0.184	0.184	strong		0.557	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
FAR2	55711	hgsc.bcm.edu	37	12	29423460	29423460	+	Silent	SNP	G	G	A	rs2216854	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:29423460G>A	ENST00000536681.3	+	2	324	c.78G>A	c.(76-78)ctG>ctA	p.L26L	FAR2_ENST00000182377.4_Silent_p.L26L|FAR2_ENST00000547116.1_Intron	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	26					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)	p.L26L(1)		central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						GCAAAGTGCTGATGGAGAAGC	0.522													G|||	2143	0.427915	0.6399	0.2781	5008	,	,		19075	0.4058		0.3459	False		,,,				2504	0.3548				p.L26L		Atlas-SNP	.											FAR2,NS,carcinoma,0,1	FAR2	60	1	1	Substitution - coding silent(1)	stomach(1)	c.G78A						PASS	.	G		2631,1775	643.9+/-397.9	785,1061,357	79.0	77.0	78.0		78	2.2	1.0	12	dbSNP_96	78	3261,5339	489.3+/-372.6	641,1979,1680	no	coding-synonymous	FAR2	NM_018099.3		1426,3040,2037	AA,AG,GG		37.9186,40.286,45.3022		26/516	29423460	5892,7114	2203	4300	6503	SO:0001819	synonymous_variant	55711	exon2			AGTGCTGATGGAG	AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	25531	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 10E, member 2"""		"""male sterility domain containing 1"""	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.78G>A	12.37:g.29423460G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	164	69	0.420732	NM_018099	F8VV73|Q9H0D5|Q9NVW8	Silent	SNP	ENST00000536681.3	37	CCDS8717.1																																																																																			G|0.554;A|0.446	0.446	strong		0.522	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099	
ZFHX4	79776	hgsc.bcm.edu	37	8	77765398	77765398	+	Missense_Mutation	SNP	A	A	G	rs16919452	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:77765398A>G	ENST00000521891.2	+	10	6689	c.6241A>G	c.(6241-6243)Att>Gtt	p.I2081V	ZFHX4_ENST00000518282.1_Missense_Mutation_p.I2055V|ZFHX4_ENST00000050961.6_Missense_Mutation_p.I2036V|ZFHX4_ENST00000455469.2_Missense_Mutation_p.I2036V	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2036					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(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CTTTCCTTCCATTATGATGCA	0.607										HNSCC(33;0.089)			A|||	413	0.0824681	0.0091	0.1945	5008	,	,		10324	0.1825		0.0328	False		,,,				2504	0.0501				p.I2081V		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A6241G						PASS	.	A	VAL/ILE	38,3882		0,38,1922	17.0	18.0	17.0		6241	2.5	0.8	8	dbSNP_123	17	249,7885		1,247,3819	yes	missense	ZFHX4	NM_024721.4	29	1,285,5741	GG,GA,AA		3.0612,0.9694,2.381	benign	2081/3617	77765398	287,11767	1960	4067	6027	SO:0001583	missense	79776	exon10			CCTTCCATTATGA		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6241A>G	8.37:g.77765398A>G	ENSP00000430497:p.Ile2081Val	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	240	152	0.633333	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	185	0.08470695970695971	5	0.01016260162601626	60	0.16574585635359115	95	0.1660839160839161	25	0.032981530343007916	A	15.02	2.708696	0.48517	0.009694	0.030612	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.46819	0.86;0.91;0.88;0.87	3.76	2.55	0.30701	.	0.152178	0.29853	U	0.011031	T	0.00073	0.0002	N	0.19112	0.55	0.28432	P	0.9172272	B;B;B	0.15473	0.008;0.013;0.013	B;B;B	0.14023	0.003;0.01;0.006	T	0.14035	-1.0487	9	0.15499	T	0.54	.	9.1445	0.36923	0.8362:0.0:0.0:0.1638	rs16919452;rs16919452	2036;2036;2081	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	V	2081;2065;2036;2036;2055	ENSP00000430497:I2081V;ENSP00000399605:I2036V;ENSP00000050961:I2036V;ENSP00000430848:I2055V	ENSP00000050961:I2036V	I	+	1	0	ZFHX4	77927953	1.000000	0.71417	0.818000	0.32626	0.930000	0.56654	1.529000	0.35996	0.594000	0.29761	0.374000	0.22700	ATT	A|0.927;G|0.073	0.073	strong		0.607	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
COX5B	1329	hgsc.bcm.edu	37	2	98264478	98264478	+	Silent	SNP	C	C	T	rs142899936		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:98264478C>T	ENST00000258424.2	+	4	344	c.297C>T	c.(295-297)agC>agT	p.S99S	COX5B_ENST00000464949.1_3'UTR	NM_001862.2	NP_001853.2	P10606	COX5B_HUMAN	cytochrome c oxidase subunit Vb	99					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)|metal ion binding (GO:0046872)			endometrium(1)|lung(1)|urinary_tract(1)	3						ACAATACCAGCGTCGTCTGGT	0.522																																					p.S99S		Atlas-SNP	.											.	COX5B	9	.	0			c.C297T						PASS	.	C		1,4405		0,1,2202	65.0	61.0	62.0		297	-3.5	0.1	2	dbSNP_134	62	1,8599		0,1,4299	no	coding-synonymous	COX5B	NM_001862.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		99/130	98264478	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1329	exon4			TACCAGCGTCGTC	BC006229	CCDS2032.1	2q11.2	2011-07-04			ENSG00000135940	ENSG00000135940	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2269	protein-coding gene	gene with protein product		123866					Standard	NM_001862		Approved		uc002sya.3	P10606	OTTHUMG00000130548	ENST00000258424.2:c.297C>T	2.37:g.98264478C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	151	58	0.384106	NM_001862	Q53YB7|Q96J18|Q99610	Silent	SNP	ENST00000258424.2	37	CCDS2032.1																																																																																			C|1.000;T|0.000	0.000	weak		0.522	COX5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252972.2	NM_001862	
TYW1	55253	hgsc.bcm.edu	37	7	66660247	66660247	+	Silent	SNP	T	T	C	rs55673383		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:66660247T>C	ENST00000359626.5	+	15	2064	c.1900T>C	c.(1900-1902)Ttg>Ctg	p.L634L		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	634					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)	p.L634L(1)		breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				TGTCCACGAGTTGGTGGATCT	0.478																																					p.L634L		Atlas-SNP	.											TYW1,NS,carcinoma,0,1	TYW1	71	1	1	Substitution - coding silent(1)	stomach(1)	c.T1900C						scavenged	.						147.0	152.0	150.0					7																	66660247		2203	4299	6502	SO:0001819	synonymous_variant	55253	exon15			CACGAGTTGGTGG	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1900T>C	7.37:g.66660247T>C		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	185	56	0.302703	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																			T|0.500;C|0.500	0.500	weak		0.478	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
COL6A3	1293	hgsc.bcm.edu	37	2	238247734	238247734	+	Missense_Mutation	SNP	C	C	G	rs36104025	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000353578.4_Missense_Mutation_p.D2625H|COL6A3_ENST00000347401.3_Missense_Mutation_p.D2630H|COL6A3_ENST00000346358.4_Missense_Mutation_p.D2631H|COL6A3_ENST00000409809.1_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	53	22	0.415094	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	
ZNF276	92822	hgsc.bcm.edu	37	16	89799950	89799950	+	Silent	SNP	C	C	T	rs17177891	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:89799950C>T	ENST00000443381.2	+	8	1438	c.1341C>T	c.(1339-1341)ggC>ggT	p.G447G	ZNF276_ENST00000568064.1_Silent_p.G355G|ZNF276_ENST00000289816.5_Silent_p.G372G|ZNF276_ENST00000446326.2_Silent_p.G233G	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	447					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)	14		Lung NSC(15;2.19e-05)|all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.0278)		TGTACCGAGGCGCTGACGGCA	0.627													C|||	364	0.0726837	0.0068	0.0187	5008	,	,		17139	0.2579		0.0656	False		,,,				2504	0.0164				p.G447G		Atlas-SNP	.											ZNF276_ENST00000443381,colon,carcinoma,0,2	ZNF276	70	2	0			c.C1341T						scavenged	.	C	,	91,4303	73.1+/-111.1	0,91,2106	89.0	81.0	84.0		1341,1116	-6.2	0.2	16	dbSNP_123	84	696,7904	169.9+/-221.1	27,642,3631	no	coding-synonymous,coding-synonymous	ZNF276	NM_001113525.1,NM_152287.3	,	27,733,5737	TT,TC,CC		8.093,2.071,6.0566	,	447/615,372/540	89799950	787,12207	2197	4300	6497	SO:0001819	synonymous_variant	92822	exon8			CCGAGGCGCTGAC	AK026482	CCDS10986.1, CCDS45554.1	16q24.3	2014-02-17	2006-02-10	2006-02-10	ENSG00000158805	ENSG00000158805		"""Zinc fingers, C2H2-type"""	23330	protein-coding gene	gene with protein product	"""centromere protein Z"", ""zinc finger, AD-type"""	608460	"""zinc finger protein 276 homolog (mouse)"""	ZFP276		10936049, 20813266	Standard	NM_152287		Approved	MGC45417, ZNF477, CENPZ, CENP-Z, ZADT	uc002fos.4	Q8N554	OTTHUMG00000138050	ENST00000443381.2:c.1341C>T	16.37:g.89799950C>T		Somatic	282	2	0.0070922		WXS	Illumina HiSeq	Phase_I	200	33	0.165	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Silent	SNP	ENST00000443381.2	37	CCDS45554.1																																																																																			C|0.932;T|0.068	0.068	strong		0.627	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287	
LARS	51520	hgsc.bcm.edu	37	5	145543972	145543972	+	Silent	SNP	G	G	A	rs3763373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145543972G>A	ENST00000394434.2	-	6	661	c.495C>T	c.(493-495)ggC>ggT	p.G165G	LARS_ENST00000274562.9_Silent_p.G138G|LARS_ENST00000510191.1_Silent_p.G111G|LARS_ENST00000511505.1_5'UTR|LARS_ENST00000545646.1_Silent_p.G119G	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						PASS	.	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	296	2	0.00675676		WXS	Illumina HiSeq	Phase_I	219	217	0.990868	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	
CBX5	23468	hgsc.bcm.edu	37	12	54639963	54639963	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:54639963G>A	ENST00000439541.2	-	4	486	c.361C>T	c.(361-363)Ctg>Ttg	p.L121L	CBX5_ENST00000209875.4_Silent_p.L121L|CBX5_ENST00000550411.1_Silent_p.L121L	NM_001127321.1	NP_001120793.1	P45973	CBX5_HUMAN	chromobox homolog 5	121	Chromo 2; shadow subtype. {ECO:0000255|PROSITE-ProRule:PRU00053}.|Interaction with ASXL1.				blood coagulation (GO:0007596)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	chromocenter (GO:0010369)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear heterochromatin (GO:0005720)|nuclear pericentric heterochromatin (GO:0031618)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|protein binding, bridging (GO:0030674)|repressing transcription factor binding (GO:0070491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						TCTGGTTCCAGTCCTCTCTCA	0.403																																					p.L121L	Colon(153;588 2459 18334 48613)	Atlas-SNP	.											.	CBX5	24	.	0			c.C361T						PASS	.						196.0	176.0	183.0					12																	54639963		2203	4300	6503	SO:0001819	synonymous_variant	23468	exon4			GTTCCAGTCCTCT	U26311	CCDS8875.1	12q13.13	2010-07-06	2010-06-24		ENSG00000094916	ENSG00000094916			1555	protein-coding gene	gene with protein product	"""HP1 alpha homolog (Drosophila)"""	604478	"""chromobox homolog 5 (Drosophila HP1 alpha)"", ""chromobox homolog 5 (HP1 alpha homolog, Drosophila)"""			8663349	Standard	NM_012117		Approved	HP1Hs-alpha, HP1, HP1-ALPHA	uc001sfj.4	P45973		ENST00000439541.2:c.361C>T	12.37:g.54639963G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_012117	B2R8T9	Silent	SNP	ENST00000439541.2	37	CCDS8875.1																																																																																			.	.	none		0.403	CBX5-004	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405468.1	NM_012117	
TFAP2D	83741	hgsc.bcm.edu	37	6	50683009	50683009	+	Missense_Mutation	SNP	T	T	C	rs78648104	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:50683009T>C	ENST00000008391.3	+	2	448	c.220T>C	c.(220-222)Ttc>Ctc	p.F74L		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					CCACCAGTCCTTCCATTACGA	0.577													T|||	398	0.0794728	0.0045	0.0274	5008	,	,		16330	0.1815		0.1173	False		,,,				2504	0.0736				p.F74L		Atlas-SNP	.											.	TFAP2D	144	.	0			c.T220C						PASS	.	T	LEU/PHE	82,4324	71.4+/-109.4	0,82,2121	236.0	191.0	206.0		220	5.1	1.0	6	dbSNP_131	206	752,7848	180.8+/-229.6	28,696,3576	yes	missense	TFAP2D	NM_172238.3	22	28,778,5697	CC,CT,TT		8.7442,1.8611,6.4124	benign	74/453	50683009	834,12172	2203	4300	6503	SO:0001583	missense	83741	exon2			CAGTCCTTCCATT	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"""	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.220T>C	6.37:g.50683009T>C	ENSP00000008391:p.Phe74Leu	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	212	111	0.523585	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	203	0.09294871794871795	0	0.0	7	0.019337016574585635	108	0.1888111888111888	88	0.11609498680738786	T	11.80	1.745353	0.30955	0.018611	0.087442	ENSG00000008197	ENST00000008391	D	0.96940	-4.18	5.07	5.07	0.68467	.	0.307122	0.36854	N	0.002363	D	0.92708	0.7682	N	0.08118	0	0.09310	P	0.99999999396351	P	0.43392	0.805	P	0.57776	0.827	D	0.93611	0.6939	9	0.33141	T	0.24	-19.6224	15.1241	0.72469	0.0:0.0:0.0:1.0	.	74	Q7Z6R9	AP2D_HUMAN	L	74	ENSP00000008391:F74L	ENSP00000008391:F74L	F	+	1	0	TFAP2D	50790968	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.816000	0.86201	2.022000	0.59522	0.533000	0.62120	TTC	T|0.925;C|0.075	0.075	strong		0.577	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504794	227504794	+	Silent	SNP	T	T	C	rs11804613	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:227504794T>C	ENST00000366769.3	-	1	1381	c.90A>G	c.(88-90)acA>acG	p.T30T	CDC42BPA_ENST00000366767.3_Silent_p.T30T|CDC42BPA_ENST00000535525.1_Silent_p.T30T|CDC42BPA_ENST00000366764.2_Silent_p.T30T|CDC42BPA_ENST00000334218.5_Silent_p.T30T|CDC42BPA_ENST00000366766.2_Silent_p.T30T|CDC42BPA_ENST00000366765.3_Silent_p.T30T	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TATCCAGTAATGTCTCCACAC	0.438													N|||	1358	0.271166	0.3411	0.2954	5008	,	,		16521	0.3363		0.1521	False		,,,				2504	0.2147				p.T30T		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.A90G						PASS	.	C	,	1318,3088	696.9+/-406.1	191,936,1076	135.0	121.0	126.0		90,90	-9.6	0.0	1	dbSNP_120	126	1229,7371	762.3+/-407.6	80,1069,3151	no	coding-synonymous,coding-synonymous	CDC42BPA	NM_003607.3,NM_014826.4	,	271,2005,4227	CC,CT,TT		14.2907,29.9138,19.5833	,	30/1720,30/1639	227504794	2547,10459	2203	4300	6503	SO:0001819	synonymous_variant	8476	exon1			CAGTAATGTCTCC	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.90A>G	1.37:g.227504794T>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	324	202	0.623457	NM_003607		Silent	SNP	ENST00000366769.3	37	CCDS1558.1																																																																																			T|0.768;C|0.232	0.232	strong		0.438	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
ZNF679	168417	hgsc.bcm.edu	37	7	63727212	63727212	+	Missense_Mutation	SNP	A	A	T	rs571908143		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:63727212A>T	ENST00000421025.1	+	5	1470	c.1201A>T	c.(1201-1203)Atg>Ttg	p.M401L	ZNF679_ENST00000255746.4_Missense_Mutation_p.M401L	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	401					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)|lung(11)|skin(1)|stomach(1)	18						TCATAAGAGTATGCATACTGG	0.333																																					p.M401L		Atlas-SNP	.											.	ZNF679	80	.	0			c.A1201T						PASS	.						25.0	25.0	25.0					7																	63727212		692	1591	2283	SO:0001583	missense	168417	exon5			AAGAGTATGCATA	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"""Zinc fingers, C2H2-type"", ""-"""	28650	protein-coding gene	gene with protein product	"""hypothetical protein MGC42415"""					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.1201A>T	7.37:g.63727212A>T	ENSP00000416809:p.Met401Leu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	33	0.767442	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.598500	0.28445	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.00949	5.51;5.51	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00440	0.0014	N	0.00801	-1.175	0.20196	N	0.999922	B	0.06786	0.001	B	0.09377	0.004	T	0.46952	-0.9154	9	0.72032	D	0.01	.	5.4486	0.16550	1.0:0.0:0.0:0.0	.	401	Q8IYX0	ZN679_HUMAN	L	401	ENSP00000416809:M401L;ENSP00000255746:M401L	ENSP00000255746:M401L	M	+	1	0	ZNF679	63364647	0.000000	0.05858	0.487000	0.27428	0.488000	0.33401	0.021000	0.13489	0.165000	0.19558	0.163000	0.16589	ATG	.	.	none		0.333	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363	
ATP8B3	148229	hgsc.bcm.edu	37	19	1811547	1811547	+	Silent	SNP	A	A	G	rs12609187	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1811547A>G	ENST00000310127.6	-	2	427	c.189T>C	c.(187-189)ccT>ccC	p.P63P	ATP8B3_ENST00000539485.1_Silent_p.P63P|ATP8B3_ENST00000525591.1_Silent_p.P10P|ATP8B3_ENST00000526092.2_Silent_p.P10P	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	63					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)		GCCTCCTCTCAGGTGCCCCTC	0.642													g|||	4155	0.829673	0.9047	0.853	5008	,	,		15619	0.7758		0.826	False		,,,				2504	0.771				p.P63P		Atlas-SNP	.											.	ATP8B3	108	.	0			c.T189C						PASS	.	G	,	3657,421		1638,381,20	48.0	57.0	54.0		30,189	1.4	0.0	19	dbSNP_120	54	7008,1336		2931,1146,95	no	coding-synonymous,coding-synonymous	ATP8B3	NM_001178002.1,NM_138813.2	,	4569,1527,115	GG,GA,AA		16.0115,10.3237,14.1443	,	10/1264,63/1301	1811547	10665,1757	2039	4172	6211	SO:0001819	synonymous_variant	148229	exon2			CCTCTCAGGTGCC	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.189T>C	19.37:g.1811547A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	59	57	0.966102	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Silent	SNP	ENST00000310127.6	37	CCDS45901.1	1839	0.842032967032967	460	0.9349593495934959	311	0.8591160220994475	448	0.7832167832167832	620	0.8179419525065963	g	6.120	0.390398	0.11581	0.896763	0.839885	ENSG00000130270	ENST00000533993	.	.	.	2.42	1.37	0.22104	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	T	0.14868	-1.0457	3	.	.	.	.	4.6624	0.12648	0.3214:0.0:0.6786:0.0	rs12609187;rs12971336;rs56730608;rs12609187	.	.	.	P	26	.	.	L	-	2	0	ATP8B3	1762547	0.061000	0.20836	0.000000	0.03702	0.001000	0.01503	1.533000	0.36040	0.142000	0.18901	-0.215000	0.12644	CTG	A|0.151;G|0.849	0.849	strong		0.642	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
H1FNT	341567	hgsc.bcm.edu	37	12	48723324	48723324	+	Missense_Mutation	SNP	C	C	G	rs2732441	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	79	0	0		WXS	Illumina HiSeq	Phase_I	80	77	0.9625	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	
HGFAC	3083	hgsc.bcm.edu	37	4	3451109	3451109	+	Missense_Mutation	SNP	G	G	A	rs2498323	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:3451109G>A	ENST00000382774.3	+	14	2046	c.1931G>A	c.(1930-1932)cGg>cAg	p.R644Q	HGFAC_ENST00000511533.1_Missense_Mutation_p.R651Q	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	644	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> Q (in dbSNP:rs2498323).		proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		ATCAACGACCGGATACGGCCT	0.617													G|||	338	0.067492	0.0915	0.0893	5008	,	,		16261	0.0476		0.0815	False		,,,				2504	0.0256				p.R644Q		Atlas-SNP	.											HGFAC,NS,carcinoma,0,1	HGFAC	69	1	0			c.G1931A						PASS	.	G	GLN/ARG	441,3965	210.5+/-231.0	25,391,1787	51.0	54.0	53.0		1931	1.0	0.5	4	dbSNP_100	53	860,7738	194.4+/-239.8	45,770,3484	yes	missense	HGFAC	NM_001528.2	43	70,1161,5271	AA,AG,GG		10.0023,10.0091,10.0046	probably-damaging	644/656	3451109	1301,11703	2203	4299	6502	SO:0001583	missense	3083	exon14			ACGACCGGATACG	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.1931G>A	4.37:g.3451109G>A	ENSP00000372224:p.Arg644Gln	Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	282	135	0.478723	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	152	0.0695970695970696	44	0.08943089430894309	36	0.09944751381215469	13	0.022727272727272728	59	0.07783641160949868	G	10.44	1.351224	0.24512	0.100091	0.100023	ENSG00000109758	ENST00000382774;ENST00000511533	D;D	0.92595	-3.07;-3.07	4.05	1.02	0.19986	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.582688	0.16495	N	0.211938	T	0.05181	0.0138	N	0.01679	-0.765	0.80722	P	0.0	P;P	0.50528	0.936;0.931	B;B	0.35510	0.204;0.176	T	0.61098	-0.7131	9	0.11485	T	0.65	.	5.0764	0.14634	0.3074:0.161:0.5316:0.0	rs2498323;rs17192693;rs61402798;rs2498323	651;644	D6RAR4;Q04756	.;HGFA_HUMAN	Q	644;651	ENSP00000372224:R644Q;ENSP00000421801:R651Q	ENSP00000372224:R644Q	R	+	2	0	HGFAC	3420907	0.093000	0.21703	0.502000	0.27614	0.139000	0.21198	0.641000	0.24720	0.349000	0.23975	0.561000	0.74099	CGG	G|0.909;A|0.091	0.091	strong		0.617	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
GSAP	54103	hgsc.bcm.edu	37	7	76984961	76984961	+	Missense_Mutation	SNP	T	T	C	rs375426636		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76984961T>C	ENST00000257626.7	-	15	1109	c.1031A>G	c.(1030-1032)tAt>tGt	p.Y344C		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	344					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										AGCCACATAATAGTCTATAGA	0.393																																					p.Y344C		Atlas-SNP	.											.	PION	74	.	0			c.A1031G						PASS	.						95.0	98.0	97.0					7																	76984961		2203	4300	6503	SO:0001583	missense	54103	exon15			ACATAATAGTCTA		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.1031A>G	7.37:g.76984961T>C	ENSP00000257626:p.Tyr344Cys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	163	106	0.650307	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	37	CCDS34672.2	.	.	.	.	.	.	.	.	.	.	T	11.76	1.734928	0.30774	.	.	ENSG00000186088	ENST00000257626	T	0.19669	2.13	5.87	1.96	0.26148	.	0.000000	0.64402	U	0.000007	T	0.18964	0.0455	M	0.69823	2.125	0.80722	D	1	B;B	0.29508	0.246;0.119	B;B	0.28139	0.086;0.048	T	0.03739	-1.1008	9	.	.	.	.	4.7934	0.13259	0.1393:0.1571:0.0:0.7037	.	344;344	A4D1B5-3;A4D1B5	.;GSAP_HUMAN	C	344	ENSP00000257626:Y344C	.	Y	-	2	0	PION	76822897	0.986000	0.35501	0.774000	0.31636	0.613000	0.37349	0.377000	0.20552	1.056000	0.40484	0.533000	0.62120	TAT	.	.	weak		0.393	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
COL6A6	131873	hgsc.bcm.edu	37	3	130282383	130282383	+	Missense_Mutation	SNP	C	C	A	rs114511272	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:130282383C>A	ENST00000358511.6	+	2	567	c.536C>A	c.(535-537)aCg>aAg	p.T179K	COL6A6_ENST00000453409.2_Missense_Mutation_p.T179K	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	179	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 matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.T179M(1)		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						GCCATGGCCACGTCTCAGTTT	0.468													C|||	43	0.00858626	0.0008	0.0072	5008	,	,		19242	0.006		0.0189	False		,,,				2504	0.0123				p.T179K		Atlas-SNP	.											COL6A6_ENST00000358511,colon,carcinoma,-1,3	COL6A6	497	3	1	Substitution - Missense(1)	breast(1)	c.C536A						PASS	.	C	LYS/THR	13,3867		0,13,1927	72.0	72.0	72.0		536	5.3	0.9	3	dbSNP_132	72	129,8135		1,127,4004	yes	missense	COL6A6	NM_001102608.1	78	1,140,5931	AA,AC,CC		1.561,0.3351,1.1693	probably-damaging	179/2264	130282383	142,12002	1940	4132	6072	SO:0001583	missense	131873	exon2			TGGCCACGTCTCA	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.536C>A	3.37:g.130282383C>A	ENSP00000351310:p.Thr179Lys	Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	207	91	0.439614	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	2	0.0034965034965034965	14	0.018469656992084433	C	23.3	4.401156	0.83120	0.003351	0.01561	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.78246	-1.16;-1.16	5.3	5.3	0.74995	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000008	T	0.79516	0.4459	M	0.71206	2.165	0.42732	D	0.993717	D	0.89917	1.0	D	0.97110	1.0	T	0.82671	-0.0342	10	0.39692	T	0.17	.	18.0868	0.89460	0.0:1.0:0.0:0.0	.	179	A6NMZ7	CO6A6_HUMAN	K	179	ENSP00000351310:T179K;ENSP00000399236:T179K	ENSP00000351310:T179K	T	+	2	0	COL6A6	131765073	0.889000	0.30405	0.859000	0.33776	0.964000	0.63967	1.641000	0.37197	2.652000	0.90054	0.561000	0.74099	ACG	C|0.992;A|0.008	0.008	strong		0.468	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
SH3RF1	57630	hgsc.bcm.edu	37	4	170037572	170037572	+	Missense_Mutation	SNP	G	G	A	rs3811813	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	88	17	0.193182	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	
RNF213	57674	hgsc.bcm.edu	37	17	78261730	78261730	+	Silent	SNP	G	G	A	rs17853714	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78261730G>A	ENST00000582970.1	+	4	521	c.378G>A	c.(376-378)ccG>ccA	p.P126P	RNF213_ENST00000319921.4_Silent_p.P126P|RNF213_ENST00000456466.1_Silent_p.P126P|RNF213_ENST00000508628.2_Silent_p.P175P	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	126					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TTTCAAACCCGTGGCCTCAGG	0.632													G|||	584	0.116613	0.0862	0.0893	5008	,	,		13894	0.0655		0.162	False		,,,				2504	0.183				p.P126P		Atlas-SNP	.											.	RNF213	766	.	0			c.G378A						PASS	.	G	,	451,3923		26,399,1762	30.0	28.0	28.0		525,378	-7.2	0.0	17	dbSNP_123	28	1547,7007		142,1263,2872	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	168,1662,4634	AA,AG,GG		18.0851,10.3109,15.4548	,	175/5257,126/1064	78261730	1998,10930	2187	4277	6464	SO:0001819	synonymous_variant	57674	exon4			AAACCCGTGGCCT	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.378G>A	17.37:g.78261730G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	130	62	0.476923	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			G|0.861;A|0.139	0.139	strong		0.632	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
OGFOD3	79701	hgsc.bcm.edu	37	17	80373377	80373377	+	Missense_Mutation	SNP	G	G	T	rs8072110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80373377G>T	ENST00000313056.5	-	2	352	c.201C>A	c.(199-201)gaC>gaA	p.D67E	Y_RNA_ENST00000364369.1_RNA|OGFOD3_ENST00000329197.5_Missense_Mutation_p.D67E|HEXDC_ENST00000337014.6_5'Flank	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	67			D -> E (in dbSNP:rs8072110).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|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)										CGACCCCGTCGTCGGCCCCCA	0.682													G|||	272	0.0543131	0.0325	0.062	5008	,	,		14915	0.0268		0.0795	False		,,,				2504	0.0808				p.D67E		Atlas-SNP	.											C17orf101_ENST00000313056,NS,carcinoma,-2,2	.	.	2	0			c.C201A						PASS	.	G	GLU/ASP,GLU/ASP	185,4221	116.7+/-154.6	0,185,2018	60.0	63.0	62.0		201,201	-10.0	0.0	17	dbSNP_116	62	613,7985	160.0+/-213.2	19,575,3705	yes	missense,missense	C17orf101	NM_024648.2,NM_175902.4	45,45	19,760,5723	TT,TG,GG		7.1296,4.1988,6.1366	benign,benign	67/320,67/332	80373377	798,12206	2203	4299	6502	SO:0001583	missense	79701	exon2			CCCGTCGTCGGCC	BC023602	CCDS11811.1, CCDS11812.1	17q25.3	2012-10-23	2012-10-23	2012-10-23	ENSG00000181396	ENSG00000181396			26174	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 101"""	C17orf101		12477932	Standard	NM_175902		Approved	FLJ22222	uc002keu.2	Q6PK18		ENST00000313056.5:c.201C>A	17.37:g.80373377G>T	ENSP00000320116:p.Asp67Glu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Missense_Mutation	SNP	ENST00000313056.5	37	CCDS11811.1	112	0.05128205128205128	20	0.04065040650406504	24	0.06629834254143646	10	0.017482517482517484	58	0.07651715039577836	G	6.803	0.517190	0.13005	0.041988	0.071296	ENSG00000181396	ENST00000313056;ENST00000329197	T;T	0.31247	1.96;1.5	5.0	-10.0	0.00425	.	0.192020	0.42172	N	0.000760	T	0.00608	0.0020	L	0.42245	1.32	0.09310	N	1	B;P	0.46784	0.015;0.884	B;B	0.38428	0.005;0.273	T	0.18366	-1.0339	10	0.12103	T	0.63	-15.7127	4.5638	0.12173	0.1501:0.2714:0.4884:0.0901	rs8072110;rs52808192;rs59805729;rs8072110	67;67	Q6PK18;Q6PK18-2	CQ101_HUMAN;.	E	67	ENSP00000320116:D67E;ENSP00000330075:D67E	ENSP00000320116:D67E	D	-	3	2	C17orf101	77966666	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-3.001000	0.00652	-2.999000	0.00276	-2.569000	0.00171	GAC	G|0.944;T|0.056	0.056	strong		0.682	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
PSMB8	5696	hgsc.bcm.edu	37	6	32811629	32811629	+	Missense_Mutation	SNP	G	G	T	rs2071543	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32811629G>T	ENST00000374882.3	-	1	195	c.145C>A	c.(145-147)Cag>Aag	p.Q49K	PSMB8_ENST00000395339.3_Missense_Mutation_p.Q49K|PSMB9_ENST00000395330.1_5'Flank|TAPSAR1_ENST00000453426.1_lincRNA|PSMB8_ENST00000374881.2_Intron	NM_148919.3	NP_683720.2	P28062	PSB8_HUMAN	proteasome (prosome, macropain) subunit, beta type, 8	49			Q -> K (in dbSNP:rs2071543). {ECO:0000269|Ref.7}.		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)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|fat cell differentiation (GO:0045444)|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)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	11					Carfilzomib(DB08889)	GCCCCGACCTGCATTCCCCGG	0.667													G|||	761	0.151957	0.0961	0.1888	5008	,	,		15795	0.1677		0.1471	False		,,,				2504	0.1902				p.Q49K	NSCLC(48;53 1172 10859 13624 22883)	Atlas-SNP	.											.	PSMB8	42	.	0			c.C145A	GRCh37	CM014742	PSMB8	M	rs2071543	PASS	.	G	,LYS/GLN	349,2669		26,297,1186	75.0	96.0	88.0		,145	5.6	1.0	6	dbSNP_96	88	723,4693		47,629,2032	yes	intron,missense	PSMB8	NM_004159.4,NM_148919.3	,53	73,926,3218	TT,TG,GG		13.3493,11.5639,12.7105	,benign	,49/277	32811629	1072,7362	1509	2708	4217	SO:0001583	missense	5696	exon1			CGACCTGCATTCC		CCDS4756.1, CCDS4757.1	6p21.3	2013-03-27	2013-03-27		ENSG00000204264	ENSG00000204264		"""Proteasome (prosome, macropain) subunits"""	9545	protein-coding gene	gene with protein product		177046	"""proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)"", ""large multifunctional peptidase 7"""	LMP7		1529427, 10329130	Standard	XM_005275000		Approved	RING10, D6S216E, PSMB5i, beta5i	uc003oce.3	P28062	OTTHUMG00000031285	ENST00000374882.3:c.145C>A	6.37:g.32811629G>T	ENSP00000364016:p.Gln49Lys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_148919	B0UZC0|Q29824|Q5JNW6|Q5QNR8|Q96J48	Missense_Mutation	SNP	ENST00000374882.3	37	CCDS4757.1	311	0.1423992673992674	37	0.07520325203252033	60	0.16574585635359115	98	0.17132867132867133	116	0.15303430079155672	G	17.49	3.403017	0.62288	0.115639	0.133493	ENSG00000204264	ENST00000395339;ENST00000374882	T;T	0.38077	1.16;1.88	5.64	5.64	0.86602	.	0.173730	0.50627	D	0.000108	T	0.26304	0.0642	M	0.69823	2.125	0.09310	P	1.0	B;B	0.28880	0.226;0.0	B;B	0.28638	0.092;0.001	T	0.08106	-1.0738	9	0.31617	T	0.26	-27.3219	15.5538	0.76173	0.0:0.0:1.0:0.0	rs2071543;rs11540145;rs52809374;rs57969734;rs2071543	49;49	B7Z6U7;P28062	.;PSB8_HUMAN	K	49	ENSP00000378748:Q49K;ENSP00000364016:Q49K	ENSP00000364016:Q49K	Q	-	1	0	PSMB8	32919607	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	4.246000	0.58740	2.817000	0.96982	0.643000	0.83706	CAG	G|0.865;T|0.135	0.135	strong		0.667	PSMB8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076617.3	NM_148919	
DST	667	hgsc.bcm.edu	37	6	56485023	56485023	+	Missense_Mutation	SNP	T	T	C	rs35497571	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56485023T>C	ENST00000370765.6	-	23	3916	c.3809A>G	c.(3808-3810)aAa>aGa	p.K1270R	DST_ENST00000370769.4_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0					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)			TAATTTATTTTTTTGTTGCTC	0.338													T|||	40	0.00798722	0.0015	0.0086	5008	,	,		20428	0.0		0.0239	False		,,,				2504	0.0082				p.K1270R		Atlas-SNP	.											.	DST	1427	.	0			c.A3809G						PASS	.	T	ARG/LYS,	26,4380	29.0+/-57.7	0,26,2177	54.0	58.0	57.0		3809,	3.3	0.1	6	dbSNP_126	57	239,8361	91.4+/-153.5	5,229,4066	yes	missense,intron	DST	NM_001723.5,NM_015548.4	26,	5,255,6243	CC,CT,TT		2.7791,0.5901,2.0375	,	1270/2650,	56485023	265,12741	2203	4300	6503	SO:0001583	missense	667	exon23			TTATTTTTTTGTT	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	ENST00000370765.6:c.3809A>G	6.37:g.56485023T>C	ENSP00000359801:p.Lys1270Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	28	0.01282051282051282	3	0.006097560975609756	5	0.013812154696132596	0	0.0	20	0.026385224274406333	T	12.17	1.857887	0.32791	0.005901	0.027791	ENSG00000151914	ENST00000370765	T	0.30981	1.51	4.46	3.29	0.37713	.	.	.	.	.	T	0.11239	0.0274	.	.	.	0.09310	N	0.999997	B	0.06786	0.001	B	0.10450	0.005	T	0.07233	-1.0783	7	0.56958	D	0.05	.	9.8723	0.41182	0.0:0.081:0.0:0.919	rs35497571	1270	Q03001-3	.	R	1270	ENSP00000359801:K1270R	ENSP00000359801:K1270R	K	-	2	0	DST	56592982	0.977000	0.34250	0.112000	0.21494	0.613000	0.37349	2.680000	0.46918	0.754000	0.32968	0.455000	0.32223	AAA	T|0.983;C|0.017	0.017	strong		0.338	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
THOC5	8563	hgsc.bcm.edu	37	22	29908072	29908072	+	Missense_Mutation	SNP	C	C	T	rs1049534	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:29908072C>T	ENST00000490103.1	-	18	1857	c.1735G>A	c.(1735-1737)Gtt>Att	p.V579I	CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397873.2_Missense_Mutation_p.V579I|THOC5_ENST00000397871.1_Missense_Mutation_p.V579I|THOC5_ENST00000397872.1_Missense_Mutation_p.V579I	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	579			V -> I (in dbSNP:rs1049534). {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						AGCTGGAAAACAGGTGGGATG	0.542													T|||	1112	0.222045	0.0983	0.1988	5008	,	,		21300	0.4167		0.2425	False		,,,				2504	0.184				p.V579I		Atlas-SNP	.											.	THOC5	58	.	0			c.G1735A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	559,3847	774.1+/-414.0	35,489,1679	128.0	99.0	109.0		1735,1735,1735,1735	1.1	0.1	22	dbSNP_86	109	1957,6643	725.1+/-406.5	224,1509,2567	yes	missense,missense,missense,missense	THOC5	NM_001002877.1,NM_001002878.1,NM_001002879.1,NM_003678.4	29,29,29,29	259,1998,4246	TT,TC,CC		22.7558,12.6872,19.3449	benign,benign,benign,benign	579/684,579/684,579/684,579/684	29908072	2516,10490	2203	4300	6503	SO:0001583	missense	8563	exon19			GGAAAACAGGTGG	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.1735G>A	22.37:g.29908072C>T	ENSP00000420306:p.Val579Ile	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	249	247	0.991968	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	589	0.2696886446886447	58	0.11788617886178862	66	0.18232044198895028	273	0.4772727272727273	192	0.2532981530343008	T	0.010	-1.780653	0.00634	0.126872	0.227558	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.20598	2.06;2.06;2.06;2.06	6.06	1.09	0.20402	.	0.352841	0.34338	N	0.004059	T	0.00012	0.0000	N	0.01188	-0.97	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.48007	-0.9072	9	0.18710	T	0.47	-21.0443	13.851	0.63496	0.0:0.467:0.0:0.533	rs1049534;rs17844989;rs17857748;rs52805826;rs58951214;rs1049534	579	Q13769	THOC5_HUMAN	I	579	ENSP00000420306:V579I;ENSP00000380970:V579I;ENSP00000380969:V579I;ENSP00000380971:V579I	ENSP00000380969:V579I	V	-	1	0	THOC5	28238072	0.001000	0.12720	0.139000	0.22197	0.186000	0.23388	-0.307000	0.08167	-0.692000	0.05128	-2.276000	0.00273	GTT	C|0.771;T|0.229	0.229	strong		0.542	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
NDUFS1	4719	hgsc.bcm.edu	37	2	207008763	207008763	+	Silent	SNP	C	C	A	rs1127566	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:207008763C>A	ENST00000233190.6	-	10	1232	c.966G>T	c.(964-966)gcG>gcT	p.A322A	NDUFS1_ENST00000432169.1_Silent_p.A211A|NDUFS1_ENST00000423725.1_Silent_p.A265A|NDUFS1_ENST00000455934.2_Silent_p.A336A|NDUFS1_ENST00000440274.1_Silent_p.A286A|NDUFS1_ENST00000457011.1_Silent_p.A206A|NDUFS1_ENST00000449699.1_Silent_p.A322A	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	322					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.A322A(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CGCGAGAGAGCGCATCCTCCC	0.388													C|||	2315	0.46226	0.6475	0.5778	5008	,	,		18330	0.2609		0.4831	False		,,,				2504	0.316				p.A336A		Atlas-SNP	.											NDUFS1,NS,carcinoma,0,1	NDUFS1	82	1	1	Substitution - coding silent(1)	prostate(1)	c.G1008T						PASS	.	C	,,,,	2800,1606	664.4+/-401.4	896,1008,299	104.0	100.0	102.0		858,633,795,1008,966	-1.0	1.0	2	dbSNP_86	102	3828,4772	538.9+/-383.5	857,2114,1329	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDUFS1	NM_001199981.1,NM_001199982.1,NM_001199983.1,NM_001199984.1,NM_005006.6	,,,,	1753,3122,1628	AA,AC,CC		44.5116,36.4503,49.0389	,,,,	286/692,211/617,265/671,336/742,322/728	207008763	6628,6378	2203	4300	6503	SO:0001819	synonymous_variant	4719	exon10			AGAGAGCGCATCC		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.966G>T	2.37:g.207008763C>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	46	36	0.782609	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Silent	SNP	ENST00000233190.6	37	CCDS2366.1																																																																																			C|0.495;A|0.505	0.505	strong		0.388	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006	
NUP133	55746	hgsc.bcm.edu	37	1	229631734	229631734	+	Missense_Mutation	SNP	T	T	C	rs11805194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:229631734T>C	ENST00000261396.3	-	7	971	c.880A>G	c.(880-882)Atc>Gtc	p.I294V	NUP133_ENST00000537506.1_Missense_Mutation_p.I278V	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	294			I -> V (in dbSNP:rs11805194).		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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.I294V(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CATTTACTGATGTTTGAACTC	0.368													T|||	1062	0.212061	0.2617	0.3012	5008	,	,		18607	0.1577		0.2068	False		,,,				2504	0.1431				p.I294V		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - Missense(1)	stomach(1)	c.A880G						scavenged	.	T	VAL/ILE	1097,3309	392.1+/-328.4	134,829,1240	104.0	100.0	101.0		880	1.7	1.0	1	dbSNP_120	101	1818,6782	324.6+/-316.5	191,1436,2673	yes	missense	NUP133	NM_018230.2	29	325,2265,3913	CC,CT,TT		21.1395,24.8979,22.4127	benign	294/1157	229631734	2915,10091	2203	4300	6503	SO:0001583	missense	55746	exon7			TACTGATGTTTGA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.880A>G	1.37:g.229631734T>C	ENSP00000261396:p.Ile294Val	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	207	71	0.342995	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	451	0.2065018315018315	122	0.24796747967479674	93	0.2569060773480663	80	0.13986013986013987	156	0.20580474934036938	T	12.64	1.999786	0.35320	0.248979	0.211395	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.60424	0.19;0.19;0.19	5.57	1.67	0.24075	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.164275	0.52532	D	0.000067	T	0.00012	0.0000	L	0.41236	1.265	0.31397	P	0.677155	B	0.06786	0.001	B	0.06405	0.002	T	0.11155	-1.0599	9	0.30854	T	0.27	-22.3481	3.4333	0.07436	0.0942:0.1504:0.1651:0.5903	rs11805194;rs17756650;rs52814082;rs61334161;rs11805194	294	Q8WUM0	NU133_HUMAN	V	294;294;294;278	ENSP00000261396:I294V;ENSP00000355640:I294V;ENSP00000443496:I278V	ENSP00000261396:I294V	I	-	1	0	NUP133	227698357	0.960000	0.32886	0.982000	0.44146	0.917000	0.54804	0.306000	0.19279	0.408000	0.25621	0.528000	0.53228	ATC	C|0.213;N|0.000	0.213	strong		0.368	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
CCDC169	728591	hgsc.bcm.edu	37	13	36871782	36871782	+	Silent	SNP	G	G	T	rs201215750	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:36871782G>T	ENST00000239859.7	-	1	106	c.75C>A	c.(73-75)gtC>gtA	p.V25V	CCDC169_ENST00000491049.2_5'UTR|CCDC169_ENST00000239860.6_5'UTR|CCDC169-SOHLH2_ENST00000511166.1_5'UTR|CCDC169_ENST00000477250.1_5'UTR|CCDC169_ENST00000379862.2_5'UTR|SOHLH2_ENST00000554962.1_5'UTR|CCDC169_ENST00000379864.2_5'UTR|CCDC169_ENST00000503173.1_Silent_p.V25V|CCDC169_ENST00000510088.1_5'UTR			A6NNP5	CC169_HUMAN	coiled-coil domain containing 169	25										breast(1)|endometrium(1)	2						ACTTCTTGCGGACTTCTTCCA	0.617																																					p.V25V		Atlas-SNP	.											.	CCDC169	20	.	0			c.C75A						PASS	.	G	,,,,,,,	0,1384		0,0,692	52.0	53.0	52.0		75,,,,,,75,	2.3	1.0	13		52	15,3167		1,13,1577	no	coding-synonymous,utr-5,utr-5,utr-5,utr-5,utr-5,coding-synonymous,utr-5	CCDC169,CCDC169-SOHLH2	NM_001144981.2,NM_001144982.2,NM_001144983.2,NM_001144984.2,NM_001144985.2,NM_001144986.2,NM_001198908.1,NM_001198910.1	,,,,,,,	1,13,2269	TT,TG,GG		0.4714,0.0,0.3285	,,,,,,,	25/215,,,,,,25/242,	36871782	15,4551	692	1591	2283	SO:0001819	synonymous_variant	728591	exon1			CTTGCGGACTTCT		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.75C>A	13.37:g.36871782G>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_001144981	A6NC13|A6NCT2|B7ZW45|B7ZW49|B9EJF2|Q9H1T4|Q9H1T5	Silent	SNP	ENST00000239859.7	37	CCDS45028.1																																																																																			G|0.993;T|0.007	0.007	strong		0.617	CCDC169-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368255.1	NM_001144981	
HYKK	123688	hgsc.bcm.edu	37	15	78825562	78825562	+	Silent	SNP	C	C	T	rs12906951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:78825562C>T	ENST00000569878.1	+	4	672	c.672C>T	c.(670-672)caC>caT	p.H224H	HYKK_ENST00000388988.4_Silent_p.H224H|HYKK_ENST00000408962.2_Intron|HYKK_ENST00000563233.1_Intron			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						scavenged	.	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	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	63	42	0.666667	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	
AFF3	3899	hgsc.bcm.edu	37	2	100218080	100218080	+	Silent	SNP	G	G	A	rs4851214	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:100218080G>A	ENST00000409236.2	-	12	1300	c.1188C>T	c.(1186-1188)gcC>gcT	p.A396A	AFF3_ENST00000409579.1_Silent_p.A421A|AFF3_ENST00000317233.4_Silent_p.A396A|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	11	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	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	
LY75	4065	hgsc.bcm.edu	37	2	160676427	160676427	+	Missense_Mutation	SNP	C	C	A	rs386652068|rs12692566	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160676427C>A	ENST00000263636.4	-	29	3990	c.3963G>T	c.(3961-3963)aaG>aaT	p.K1321N	LY75_ENST00000554112.1_Missense_Mutation_p.K1321N|LY75_ENST00000553424.1_Missense_Mutation_p.K1321N|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.K1321N|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.K1321N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1321	C-type lectin 8. {ECO:0000255|PROSITE- ProRule:PRU00040}.		K -> N (in dbSNP:rs12692566). {ECO:0000269|PubMed:12824192, ECO:0000269|PubMed:9553150}.		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)		ACATAAGAGACTTATCTAGAG	0.323													A|||	4234	0.845447	0.9017	0.879	5008	,	,		16930	0.9058		0.8042	False		,,,				2504	0.726				p.K1321N		Atlas-SNP	.											.	LY75	151	.	0			c.G3963T						PASS	.	A	ASN/LYS,ASN/LYS,ASN/LYS	3915,485	216.8+/-235.3	1740,435,25	49.0	52.0	51.0		3963,3963,3963	4.5	1.0	2	dbSNP_121	51	7118,1482	278.7+/-293.6	2953,1212,135	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	94,94,94	4693,1647,160	AA,AC,CC		17.2326,11.0227,15.1308	benign,benign,benign	1321/1874,1321/1818,1321/1723	160676427	11033,1967	2200	4300	6500	SO:0001583	missense	4065	exon29			AAGAGACTTATCT	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.3963G>T	2.37:g.160676427C>A	ENSP00000263636:p.Lys1321Asn	Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	1875	0.8585164835164835	451	0.9166666666666666	316	0.8729281767955801	512	0.8951048951048951	596	0.7862796833773087	A	1.043	-0.678141	0.03378	0.889773	0.827674	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2	5.65	4.5	0.54988	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.00012	0.0000	N	0.00996	-1.065	0.51767	P	6.60000000000105E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.0	T	0.30149	-0.9988	8	0.02654	T	1	-7.854	3.4073	0.07345	0.5441:0.2602:0.0703:0.1254	rs12692566;rs17827187;rs52796730;rs56698280;rs12692566	1321;1321;1321	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	N	1321	ENSP00000451511:K1321N;ENSP00000451446:K1321N;ENSP00000263636:K1321N;ENSP00000423463:K1321N;ENSP00000421035:K1321N	ENSP00000423463:K1321N	K	-	3	2	LY75;LY75-CD302	160384673	0.998000	0.40836	1.000000	0.80357	0.980000	0.70556	0.420000	0.21263	0.427000	0.26145	-0.335000	0.08231	AAG	C|0.148;A|0.852	0.852	strong		0.323	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
GMNC	647309	hgsc.bcm.edu	37	3	190578566	190578566	+	Missense_Mutation	SNP	A	A	G	rs13075089	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:190578566A>G	ENST00000442080.1	-	2	84	c.85T>C	c.(85-87)Tct>Cct	p.S29P	GMNC_ENST00000479491.1_Intron	NM_001146686.2	NP_001140158.1	A6NCL1	GEMC1_HUMAN	geminin coiled-coil domain containing	29					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication initiation (GO:0006270)	nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(3)|skin(1)	5						TCAACACTAGATTCTGACGTT	0.498													A|||	2225	0.444289	0.4327	0.3833	5008	,	,		18611	0.4484		0.4095	False		,,,				2504	0.5348				p.S29P		Atlas-SNP	.											.	GMNC	12	.	0			c.T85C						PASS	.	A	PRO/SER	532,852		109,314,269	104.0	93.0	97.0		85	2.9	1.0	3	dbSNP_121	97	1269,1913		238,793,560	yes	missense	GMNC	NM_001146686.2	74	347,1107,829	GG,GA,AA		39.8806,38.4393,39.4437	benign	29/335	190578566	1801,2765	692	1591	2283	SO:0001583	missense	647309	exon2			CACTAGATTCTGA	BC031680	CCDS54697.1	3q28	2011-08-19	2011-08-19		ENSG00000205835	ENSG00000205835			40049	protein-coding gene	gene with protein product		614448				20383140, 20855966	Standard	NM_001146686		Approved	GEMC1	uc011bsl.1	A6NCL1	OTTHUMG00000156195	ENST00000442080.1:c.85T>C	3.37:g.190578566A>G	ENSP00000406164:p.Ser29Pro	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	NM_001146686		Missense_Mutation	SNP	ENST00000442080.1	37	CCDS54697.1	893	0.4088827838827839	205	0.4166666666666667	141	0.38950276243093923	232	0.40559440559440557	315	0.4155672823218997	A	10.59	1.391691	0.25118	0.384393	0.398806	ENSG00000205835	ENST00000442080	.	.	.	5.41	2.91	0.33838	.	0.349592	0.27640	N	0.018470	T	0.00012	0.0000	M	0.62723	1.935	0.31069	P	0.7132769999999999	P	0.48503	0.911	P	0.55577	0.779	T	0.38478	-0.9659	8	0.44086	T	0.13	-1.1021	8.9669	0.35883	0.7036:0.0:0.0:0.2964	rs13075089;rs58186737	29	A6NCL1	GEMC1_HUMAN	P	29	.	ENSP00000406164:S29P	S	-	1	0	RP11-332P22.1	192061260	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.748000	0.26305	0.312000	0.23038	0.533000	0.62120	TCT	A|0.589;G|0.411	0.411	strong		0.498	GMNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343364.1	NM_001146686	
COL6A3	1293	hgsc.bcm.edu	37	2	238244781	238244781	+	Missense_Mutation	SNP	T	T	C	rs11690358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238244781T>C	ENST00000295550.4	-	40	9414	c.8962A>G	c.(8962-8964)Atg>Gtg	p.M2988V	COL6A3_ENST00000472056.1_Missense_Mutation_p.M2381V|COL6A3_ENST00000353578.4_Missense_Mutation_p.M2782V|COL6A3_ENST00000347401.3_Missense_Mutation_p.M2787V|COL6A3_ENST00000346358.4_Missense_Mutation_p.M2788V|COL6A3_ENST00000409809.1_Missense_Mutation_p.M2782V	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	74	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	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	
HTT	3064	hgsc.bcm.edu	37	4	3148653	3148653	+	Missense_Mutation	SNP	T	T	G	rs1143646	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:3148653T>G	ENST00000355072.5	+	25	3418	c.3273T>G	c.(3271-3273)atT>atG	p.I1091M		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1091			I -> M (in dbSNP:rs1143646).		anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		ATGCTTTGATTTTGGCCGGAA	0.502													T|||	112	0.0223642	0.0023	0.0231	5008	,	,		19236	0.0		0.0487	False		,,,				2504	0.045				p.I1091M		Atlas-SNP	.											.	HTT	221	.	0			c.T3273G						PASS	.	T	MET/ILE	35,3891		0,35,1928	351.0	350.0	351.0		3273	-4.2	0.0	4	dbSNP_86	351	403,7927		11,381,3773	yes	missense	HTT	NM_002111.6	10	11,416,5701	GG,GT,TT		4.8379,0.8915,3.5738	benign	1091/3143	3148653	438,11818	1963	4165	6128	SO:0001583	missense	3064	exon25			TTTGATTTTGGCC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.3273T>G	4.37:g.3148653T>G	ENSP00000347184:p.Ile1091Met	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	213	99	0.464789	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	50	0.022893772893772892	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	41	0.05408970976253298	T	13.78	2.338654	0.41398	0.008915	0.048379	ENSG00000197386	ENST00000355072	T	0.64803	-0.12	4.68	-4.18	0.03846	Armadillo-type fold (1);	0.398024	0.28057	N	0.016777	T	0.08223	0.0205	L	0.40543	1.245	0.25629	N	0.986323	P	0.35208	0.49	B	0.32624	0.149	T	0.07947	-1.0746	10	0.33940	T	0.23	.	2.2434	0.04025	0.2123:0.3798:0.1117:0.2962	rs1143646;rs3025846;rs17362442;rs17781557;rs17781557	1091	P42858	HD_HUMAN	M	1091	ENSP00000347184:I1091M	ENSP00000347184:I1091M	I	+	3	3	HTT	3118451	0.381000	0.25140	0.023000	0.16930	0.993000	0.82548	-0.425000	0.07017	-0.600000	0.05790	0.460000	0.39030	ATT	T|0.968;G|0.032	0.032	strong		0.502	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
KIF7	374654	hgsc.bcm.edu	37	15	90188392	90188392	+	Silent	SNP	A	A	T	rs72750755	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:90188392A>T	ENST00000394412.3	-	10	2119	c.2043T>A	c.(2041-2043)gtT>gtA	p.V681V		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	681	Sufficient for interaction with NPHP1.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			TGCTCCCACCAACTGCTGCAA	0.667													a|||	90	0.0179712	0.0	0.0187	5008	,	,		16240	0.0		0.0338	False		,,,				2504	0.044				p.V681V		Atlas-SNP	.											.	KIF7	130	.	0			c.T2043A						PASS	.			33,4367	37.6+/-69.7	0,33,2167	27.0	31.0	30.0		2043	-3.7	0.0	15	dbSNP_130	30	364,8234	116.5+/-176.2	5,354,3940	no	coding-synonymous	KIF7	NM_198525.2		5,387,6107	TT,TA,AA		4.2335,0.75,3.0543		681/1344	90188392	397,12601	2200	4299	6499	SO:0001819	synonymous_variant	374654	exon10			CCCACCAACTGCT	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"""Kinesins"""	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.2043T>A	15.37:g.90188392A>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	26	17	0.653846	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Silent	SNP	ENST00000394412.3	37	CCDS32325.2																																																																																			A|0.976;T|0.024	0.024	strong		0.667	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
RBM5	10181	hgsc.bcm.edu	37	3	50144951	50144951	+	Silent	SNP	T	T	C	rs1061474	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	234	109	0.465812	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	
IGSF10	285313	hgsc.bcm.edu	37	3	151165678	151165678	+	Silent	SNP	T	T	C	rs9871952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151165678T>C	ENST00000282466.3	-	4	2090	c.2091A>G	c.(2089-2091)caA>caG	p.Q697Q		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	697					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)			ATGTACGGAGTTGTGCACCTG	0.498													C|||	3938	0.786342	0.8185	0.7695	5008	,	,		20283	0.7649		0.7724	False		,,,				2504	0.7914				p.Q697Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.A2091G						PASS	.	C		3583,823	330.4+/-301.5	1464,655,84	75.0	70.0	72.0		2091	-10.5	0.0	3	dbSNP_119	72	6533,2067	357.9+/-330.9	2494,1545,261	no	coding-synonymous	IGSF10	NM_178822.4		3958,2200,345	CC,CT,TT		24.0349,18.6791,22.2205		697/2624	151165678	10116,2890	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon4			ACGGAGTTGTGCA	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.2091A>G	3.37:g.151165678T>C		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	217	217	1	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			T|0.213;C|0.787	0.787	strong		0.498	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
AP3D1	8943	hgsc.bcm.edu	37	19	2138654	2138654	+	Silent	SNP	T	T	G	rs25672	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2138654T>G	ENST00000345016.5	-	2	387	c.156A>C	c.(154-156)atA>atC	p.I52I	AP3D1_ENST00000356926.4_Silent_p.I52I|AP3D1_ENST00000350812.6_Silent_p.I52I|AP3D1_ENST00000355272.6_Silent_p.I52I	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	52					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)		CCTTCACCGCTATGTTGTCCT	0.522													G|||	1184	0.236422	0.1127	0.2911	5008	,	,		21431	0.1994		0.4453	False		,,,				2504	0.1881				p.I52I		Atlas-SNP	.											.	AP3D1	81	.	0			c.A156C						PASS	.	G	,	708,3638		83,542,1548	150.0	152.0	151.0		156,156	-3.4	0.6	19	dbSNP_72	151	3636,4882		782,2072,1405	no	coding-synonymous,coding-synonymous	AP3D1	NM_001077523.1,NM_003938.5	,	865,2614,2953	GG,GT,TT		42.6861,16.2908,33.7687	,	52/1113,52/1154	2138654	4344,8520	2173	4259	6432	SO:0001819	synonymous_variant	8943	exon2			CACCGCTATGTTG	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.156A>C	19.37:g.2138654T>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	70	43	0.614286	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																			T|0.695;G|0.304;N|0.000;A|0.000	0.304	strong		0.522	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
GOT2	2806	hgsc.bcm.edu	37	16	58750604	58750604	+	Silent	SNP	G	G	A	rs1058192	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:58750604G>A	ENST00000245206.5	-	7	944	c.816C>T	c.(814-816)tgC>tgT	p.C272C	GOT2_ENST00000434819.2_Silent_p.C229C|GOT2_ENST00000564400.1_Intron	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	272					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)	p.C272C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	ATTGGCAGAGGCAAACATTAA	0.502													A|||	3607	0.720248	0.8896	0.7738	5008	,	,		20689	0.6478		0.67	False		,,,				2504	0.5798				p.C272C		Atlas-SNP	.											GOT2,NS,carcinoma,0,1	GOT2	42	1	1	Substitution - coding silent(1)	prostate(1)	c.C816T						PASS	.	A		3702,694	289.8+/-280.6	1553,596,49	73.0	60.0	65.0		816	0.8	1.0	16	dbSNP_86	65	5574,3026	466.3+/-366.7	1803,1968,529	no	coding-synonymous	GOT2	NM_002080.2		3356,2564,578	AA,AG,GG		35.186,15.7871,28.6242		272/431	58750604	9276,3720	2198	4300	6498	SO:0001819	synonymous_variant	2806	exon7			GCAGAGGCAAACA		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.816C>T	16.37:g.58750604G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	80	9	0.1125	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	37	CCDS10801.1																																																																																			G|0.286;A|0.714	0.714	strong		0.502	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
FLNB	2317	hgsc.bcm.edu	37	3	58109162	58109162	+	Missense_Mutation	SNP	G	G	A	rs1131356	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:58109162G>A	ENST00000295956.4	+	21	3634	c.3469G>A	c.(3469-3471)Gac>Aac	p.D1157N	FLNB_ENST00000490882.1_Missense_Mutation_p.D1157N|FLNB_ENST00000419752.2_Missense_Mutation_p.D988N|FLNB_ENST00000493452.1_Missense_Mutation_p.D988N|FLNB_ENST00000429972.2_Missense_Mutation_p.D1157N|FLNB_ENST00000348383.5_Missense_Mutation_p.D1157N|FLNB_ENST00000357272.4_Missense_Mutation_p.D1157N|FLNB_ENST00000358537.3_Missense_Mutation_p.D1157N	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1157	Interaction with FBLP1.		D -> N (in dbSNP:rs1131356). {ECO:0000269|PubMed:11153914, ECO:0000269|PubMed:18487259, ECO:0000269|PubMed:9651345}.		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)		CCTTAGCGTCGACTGCTCGGA	0.582													G|||	2735	0.546126	0.4758	0.4726	5008	,	,		16378	0.9187		0.2803	False		,,,				2504	0.5828				p.D1157N		Atlas-SNP	.											.	FLNB	430	.	0			c.G3469A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	1813,2593	529.0+/-372.6	370,1073,760	64.0	72.0	69.0		3469,3469,3469,3469	5.1	0.9	3	dbSNP_86	69	2097,6503	360.6+/-332.0	263,1571,2466	yes	missense,missense,missense,missense	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	23,23,23,23	633,2644,3226	AA,AG,GG		24.3837,41.1484,30.063	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1157/2634,1157/2592,1157/2579,1157/2603	58109162	3910,9096	2203	4300	6503	SO:0001583	missense	2317	exon21			AGCGTCGACTGCT	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.3469G>A	3.37:g.58109162G>A	ENSP00000295956:p.Asp1157Asn	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	77	74	0.961039	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	1105	0.5059523809523809	232	0.4715447154471545	145	0.4005524861878453	521	0.9108391608391608	207	0.27308707124010556	G	18.92	3.725331	0.68959	0.411484	0.243837	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.95	5.08	0.68730	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.69248	2.105	0.09310	P	0.9999999382633	D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.987;1.0;1.0	D;D;D;P;D;D	0.91635	0.985;0.918;0.998;0.863;0.999;0.999	T	0.39251	-0.9623	9	0.54805	T	0.06	.	15.2231	0.73330	0.0672:0.0:0.9328:0.0	rs1131356;rs17058842;rs56425027;rs58310728;rs1131356	1157;1157;988;988;1157;1157	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	N	1157;1157;1157;1157;1157;1157;988;988	ENSP00000295956:D1157N;ENSP00000420213:D1157N;ENSP00000351339:D1157N;ENSP00000415599:D1157N;ENSP00000232447:D1157N;ENSP00000349819:D1157N;ENSP00000418510:D988N;ENSP00000414532:D988N	ENSP00000295956:D1157N	D	+	1	0	FLNB	58084202	1.000000	0.71417	0.888000	0.34837	0.016000	0.09150	9.869000	0.99810	1.537000	0.49254	0.563000	0.77884	GAC	G|0.596;A|0.404	0.404	strong		0.582	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
RAC2	5880	hgsc.bcm.edu	37	22	37622815	37622815	+	Silent	SNP	A	A	G	rs1064498	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:37622815A>G	ENST00000249071.6	-	6	598	c.477T>C	c.(475-477)gcT>gcC	p.A159A	RAC2_ENST00000406508.1_Silent_p.A115A|RAC2_ENST00000405484.1_Silent_p.A152A	NM_002872.3	NP_002863.1	P15153	RAC2_HUMAN	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)	159					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|cell projection assembly (GO:0030031)|G-protein coupled receptor signaling pathway (GO:0007186)|lymphocyte aggregation (GO:0071593)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neutrophil chemotaxis (GO:0090023)|regulation of cell-substrate adhesion (GO:0010810)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of neutrophil migration (GO:1902622)|regulation of respiratory burst (GO:0060263)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)	12					Dextromethorphan(DB00514)	TCTGGGTGAGAGCTGAGCACT	0.632													g|||	1239	0.247404	0.4508	0.1023	5008	,	,		15446	0.3105		0.1501	False		,,,				2504	0.1104				p.A159A		Atlas-SNP	.											.	RAC2	22	.	0			c.T477C						PASS	.			1718,2688	650.4+/-399.0	342,1034,827	57.0	65.0	62.0		477	-0.1	0.9	22	dbSNP_86	62	1212,7386	761.9+/-407.6	81,1050,3168	no	coding-synonymous	RAC2	NM_002872.3		423,2084,3995	GG,GA,AA		14.0963,38.9923,22.5315		159/193	37622815	2930,10074	2203	4299	6502	SO:0001819	synonymous_variant	5880	exon6			GGTGAGAGCTGAG	M64595	CCDS13945.1	22q13.1	2014-09-17			ENSG00000128340	ENSG00000128340		"""Endogenous ligands"""	9802	protein-coding gene	gene with protein product		602049				2674130	Standard	NM_002872		Approved	EN-7	uc003arc.3	P15153	OTTHUMG00000150540	ENST00000249071.6:c.477T>C	22.37:g.37622815A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_002872	Q9UDJ4	Silent	SNP	ENST00000249071.6	37	CCDS13945.1																																																																																			T|0.000;G|0.229;A|0.771	0.229	strong		0.632	RAC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318812.1		
RTP4	64108	hgsc.bcm.edu	37	3	187089031	187089031	+	Missense_Mutation	SNP	C	C	A	rs1003995|rs3926263	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	43	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	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	
VARS	7407	hgsc.bcm.edu	37	6	31748675	31748675	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31748675C>T	ENST00000375663.3	-	23	3130	c.2690G>A	c.(2689-2691)aGc>aAc	p.S897N	Y_RNA_ENST00000364685.1_RNA|VARS_ENST00000482996.1_5'UTR	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	897					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)	CTCCACCTCGCTGGGATCCAG	0.652																																					p.S897N		Atlas-SNP	.											VARS,NS,carcinoma,+1,1	VARS	76	1	0			c.G2690A						scavenged	.						85.0	75.0	78.0					6																	31748675		2203	4300	6503	SO:0001583	missense	7407	exon23			ACCTCGCTGGGAT	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.2690G>A	6.37:g.31748675C>T	ENSP00000364815:p.Ser897Asn	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	121	2	0.0165289	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	37	CCDS34412.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.464959	0.43839	.	.	ENSG00000204394	ENST00000375663	T	0.04317	3.65	5.01	5.01	0.66863	Aminoacyl-tRNA synthetase, class Ia (1);	0.314348	0.35903	N	0.002918	T	0.01695	0.0054	N	0.16567	0.415	0.80722	D	1	B	0.11235	0.004	B	0.19666	0.026	T	0.46884	-0.9159	10	0.49607	T	0.09	-16.9105	11.5255	0.50578	0.0:0.8195:0.1805:0.0	.	897	P26640	SYVC_HUMAN	N	897	ENSP00000364815:S897N	ENSP00000364815:S897N	S	-	2	0	VARS	31856654	0.996000	0.38824	0.984000	0.44739	0.983000	0.72400	3.399000	0.52586	2.606000	0.88127	0.655000	0.94253	AGC	.	.	none		0.652	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295	
DHX38	9785	hgsc.bcm.edu	37	16	72137561	72137561	+	Silent	SNP	G	G	A	rs2240243	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:72137561G>A	ENST00000268482.3	+	13	2207	c.1698G>A	c.(1696-1698)acG>acA	p.T566T	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	566	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CTCAGCTGACGCAGTACCTGC	0.552													A|||	2368	0.472843	0.7814	0.3112	5008	,	,		19860	0.3105		0.3519	False		,,,				2504	0.4622				p.T566T	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.G1698A						PASS	.	A		3037,1359	451.2+/-349.6	1063,911,224	123.0	98.0	107.0		1698	-2.3	1.0	16	dbSNP_98	107	3170,5430	655.0+/-401.2	571,2028,1701	no	coding-synonymous	DHX38	NM_014003.3		1634,2939,1925	AA,AG,GG		36.8605,30.9145,47.7608		566/1228	72137561	6207,6789	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon13			GCTGACGCAGTAC	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"""DEAH-boxes"""	17211	protein-coding gene	gene with protein product		605584	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"""	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.1698G>A	16.37:g.72137561G>A		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			G|0.533;A|0.467	0.467	strong		0.552	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
SPEG	10290	hgsc.bcm.edu	37	2	220353532	220353532	+	Missense_Mutation	SNP	C	C	A	rs13026308	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220353532C>A	ENST00000312358.7	+	34	8191	c.8059C>A	c.(8059-8061)Ccc>Acc	p.P2687T	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2687	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		P -> T (in dbSNP:rs13026308). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:15185077, 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)		TCCAGAGGTACCCCAGACCTA	0.612													C|||	423	0.0844649	0.0144	0.1398	5008	,	,		15942	0.0456		0.1511	False		,,,				2504	0.1115				p.P2687T		Atlas-SNP	.											.	SPEG	272	.	0			c.C8059A						PASS	.	C	THR/PRO	105,3903		2,101,1901	25.0	28.0	27.0		8059	4.4	1.0	2	dbSNP_121	27	1078,7246		61,956,3145	yes	missense	SPEG	NM_005876.4	38	63,1057,5046	AA,AC,CC		12.9505,2.6198,9.5929	probably-damaging	2687/3268	220353532	1183,11149	2004	4162	6166	SO:0001583	missense	10290	exon34			GAGGTACCCCAGA	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.8059C>A	2.37:g.220353532C>A	ENSP00000311684:p.Pro2687Thr	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	172	127	0.738372	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	197	0.0902014652014652	13	0.026422764227642278	42	0.11602209944751381	24	0.04195804195804196	118	0.15567282321899736	C	13.22	2.173152	0.38413	0.026198	0.129505	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.48836	0.8	4.38	4.38	0.52667	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.37012	N	0.002295	T	0.00300	0.0009	L	0.35414	1.06	0.09310	P	1.0	D	0.69078	0.997	P	0.60789	0.879	T	0.02220	-1.1193	9	0.35671	T	0.21	.	14.4358	0.67279	0.0:0.8523:0.1477:0.0	rs13026308;rs59720840;rs13026308	2687	Q15772	SPEG_HUMAN	T	2687	ENSP00000311684:P2687T	ENSP00000265327:P2687T	P	+	1	0	SPEG	220061776	0.993000	0.37304	0.999000	0.59377	0.987000	0.75469	3.087000	0.50167	2.272000	0.75746	0.563000	0.77884	CCC	C|0.913;A|0.087	0.087	strong		0.612	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
KIAA1429	25962	hgsc.bcm.edu	37	8	95541459	95541459	+	Missense_Mutation	SNP	A	A	C	rs76706433	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:95541459A>C	ENST00000297591.5	-	7	794	c.719T>G	c.(718-720)gTa>gGa	p.V240G	KIAA1429_ENST00000421249.2_Missense_Mutation_p.V240G|KIAA1429_ENST00000437199.1_Missense_Mutation_p.V240G	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	240	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)			ttcctcttctacttctccttc	0.438													A|||	46	0.0091853	0.0	0.0144	5008	,	,		18908	0.0		0.0348	False		,,,				2504	0.001				p.V240G		Atlas-SNP	.											.	KIAA1429	176	.	0			c.T719G						PASS	.	A	GLY/VAL,GLY/VAL	12,4394	20.2+/-43.8	0,12,2191	301.0	233.0	256.0		719,719	5.2	1.0	8	dbSNP_131	256	125,8475	64.6+/-126.8	1,123,4176	yes	missense,missense	KIAA1429	NM_015496.4,NM_183009.2	109,109	1,135,6367	CC,CA,AA		1.4535,0.2724,1.0534	benign,benign	240/1813,240/1148	95541459	137,12869	2203	4300	6503	SO:0001583	missense	25962	exon7			TCTTCTACTTCTC	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.719T>G	8.37:g.95541459A>C	ENSP00000297591:p.Val240Gly	Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	269	167	0.620818	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Missense_Mutation	SNP	ENST00000297591.5	37	CCDS34923.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	A	13.18	2.159820	0.38119	0.002724	0.014535	ENSG00000164944	ENST00000297591;ENST00000437199;ENST00000421249	T;T;T	0.51325	0.71;0.72;0.71	5.23	5.23	0.72850	.	0.252999	0.29956	N	0.010778	T	0.18635	0.0447	N	0.19112	0.55	0.54753	D	0.999981	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.06607	-1.0817	10	0.54805	T	0.06	-13.0312	11.147	0.48436	0.8458:0.1542:0.0:0.0	.	240;240	Q69YN4-4;Q69YN4	.;VIR_HUMAN	G	240	ENSP00000297591:V240G;ENSP00000395600:V240G;ENSP00000398390:V240G	ENSP00000297591:V240G	V	-	2	0	KIAA1429	95610635	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.497000	0.53295	2.098000	0.63641	0.482000	0.46254	GTA	A|0.989;C|0.011	0.011	strong		0.438	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
C1orf159	54991	hgsc.bcm.edu	37	1	1021346	1021346	+	Silent	SNP	A	A	G	rs10907177	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1021346A>G	ENST00000379339.1	-	9	675	c.465T>C	c.(463-465)atT>atC	p.I155I	C1orf159_ENST00000421241.2_Silent_p.I119I|C1orf159_ENST00000437760.1_Silent_p.I119I|C1orf159_ENST00000482816.1_5'UTR|C1orf159_ENST00000379319.1_Silent_p.I119I|C1orf159_ENST00000379320.1_Silent_p.I119I|C1orf159_ENST00000294576.5_Silent_p.I119I|C1orf159_ENST00000448924.1_Silent_p.I155I			Q96HA4	CA159_HUMAN	chromosome 1 open reading frame 159	155						integral component of membrane (GO:0016021)						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;2.96e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.77e-22)|Colorectal(212;6.51e-05)|COAD - Colon adenocarcinoma(227;0.000214)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|Kidney(185;0.00254)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)		GGCCGGAGCTAATGAAGAACG	0.622													G|||	896	0.178914	0.239	0.1311	5008	,	,		16405	0.122		0.1809	False		,,,				2504	0.1881				p.I119I		Atlas-SNP	.											.	C1orf159	9	.	0			c.T357C						PASS	.	G		1072,3334	717.9+/-408.8	131,810,1262	68.0	66.0	67.0		357	2.8	0.9	1	dbSNP_120	67	1362,7238	753.5+/-407.4	103,1156,3041	no	coding-synonymous	C1orf159	NM_017891.4		234,1966,4303	GG,GA,AA		15.8372,24.3305,18.7144		119/199	1021346	2434,10572	2203	4300	6503	SO:0001819	synonymous_variant	54991	exon7			GGAGCTAATGAAG	AK128434	CCDS7.2	1p36.33	2008-02-05			ENSG00000131591	ENSG00000131591			26062	protein-coding gene	gene with protein product						12975309	Standard	NM_017891		Approved	FLJ20584	uc001acu.2	Q96HA4	OTTHUMG00000000745	ENST00000379339.1:c.465T>C	1.37:g.1021346A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	47	31	0.659574	NM_017891	B3KQ46|Q5T2W6|Q6UX67|Q6ZR77|Q9NWV0	Silent	SNP	ENST00000379339.1	37																																																																																				A|0.814;G|0.186	0.186	strong		0.622	C1orf159-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000001851.2	NM_017891	
TOMM40	10452	hgsc.bcm.edu	37	19	45397229	45397229	+	Silent	SNP	G	G	A	rs1160983	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45397229G>A	ENST00000426677.2	+	5	729	c.549G>A	c.(547-549)tcG>tcA	p.S183S	TOMM40_ENST00000405636.2_Silent_p.S183S|TOMM40_ENST00000252487.5_Silent_p.S183S|TOMM40_ENST00000592434.1_Silent_p.S183S	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	183					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)		CCCAGCAGTCGAAGTTTGTGA	0.652													G|||	269	0.0537141	0.0893	0.0216	5008	,	,		16952	0.0913		0.0298	False		,,,				2504	0.0143				p.S183S		Atlas-SNP	.											.	TOMM40	13	.	0			c.G549A						PASS	.	G	,,	393,4013	185.7+/-212.7	20,353,1830	50.0	49.0	50.0		549,549,549	-9.5	1.0	19	dbSNP_87	50	286,8314	103.8+/-164.8	5,276,4019	no	coding-synonymous,coding-synonymous,coding-synonymous	TOMM40	NM_001128916.1,NM_001128917.1,NM_006114.2	,,	25,629,5849	AA,AG,GG		3.3256,8.9197,5.2207	,,	183/362,183/362,183/362	45397229	679,12327	2203	4300	6503	SO:0001819	synonymous_variant	10452	exon5			GCAGTCGAAGTTT	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.549G>A	19.37:g.45397229G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_001128917	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Silent	SNP	ENST00000426677.2	37	CCDS12646.1																																																																																			G|0.950;A|0.050	0.050	strong		0.652	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1		
MEGF11	84465	hgsc.bcm.edu	37	15	66214785	66214785	+	Silent	SNP	G	G	A	rs11637551	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:66214785G>A	ENST00000409699.2	-	15	2020	c.1848C>T	c.(1846-1848)caC>caT	p.H616H	MEGF11_ENST00000422354.1_Silent_p.H616H|MEGF11_ENST00000288745.3_Silent_p.H541H|MEGF11_ENST00000395614.1_De_novo_Start_OutOfFrame|MEGF11_ENST00000360698.4_Silent_p.H616H|MEGF11_ENST00000395625.2_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	139	0	0		WXS	Illumina HiSeq	Phase_I	68	50	0.735294	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	
GCN1L1	10985	hgsc.bcm.edu	37	12	120602208	120602208	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:120602208A>G	ENST00000300648.6	-	18	1792	c.1780T>C	c.(1780-1782)Tct>Cct	p.S594P		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	594					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCCCAAGAGAGGACAGCAGC	0.622																																					p.S594P		Atlas-SNP	.											.	GCN1L1	207	.	0			c.T1780C						PASS	.						75.0	80.0	78.0					12																	120602208		1969	4161	6130	SO:0001583	missense	10985	exon18			CAAGAGAGGACAG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.1780T>C	12.37:g.120602208A>G	ENSP00000300648:p.Ser594Pro	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	A	16.79	3.220268	0.58560	.	.	ENSG00000089154	ENST00000300648	T	0.05199	3.48	5.83	4.67	0.58626	Armadillo-like helical (1);Domain of unknown function DUF3554 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.17619	0.0423	M	0.74881	2.28	0.80722	D	1	D	0.54047	0.964	P	0.54590	0.756	T	0.01570	-1.1322	10	0.30854	T	0.27	.	13.3498	0.60595	0.8686:0.1314:0.0:0.0	.	594	Q92616	GCN1L_HUMAN	P	594	ENSP00000300648:S594P	ENSP00000300648:S594P	S	-	1	0	GCN1L1	119086591	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.545000	0.67237	1.022000	0.39626	0.533000	0.62120	TCT	.	.	none		0.622	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
OR4A16	81327	hgsc.bcm.edu	37	11	55111584	55111584	+	Missense_Mutation	SNP	A	A	T	rs10896659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55111584A>T	ENST00000314721.2	+	1	958	c.908A>T	c.(907-909)aAg>aTg	p.K303M		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	303			K -> M (in dbSNP:rs10896659).			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						TGGTGTGAAAAGTTAAGTATA	0.323													.|||	2066	0.41254	0.1853	0.5504	5008	,	,		18442	0.5387		0.494	False		,,,				2504	0.408				p.K303M		Atlas-SNP	.											.	OR4A16	120	.	0			c.A908T						PASS	.	A	MET/LYS	1017,3385	362.1+/-316.0	130,757,1314	36.0	36.0	36.0		908	1.8	0.0	11	dbSNP_120	36	4172,4418	547.8+/-385.2	1032,2108,1155	yes	missense	OR4A16	NM_001005274.1	95	1162,2865,2469	TT,TA,AA		48.5681,23.1031,39.94	benign	303/329	55111584	5189,7803	2201	4295	6496	SO:0001583	missense	81327	exon1			GTGAAAAGTTAAG	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.908A>T	11.37:g.55111584A>T	ENSP00000325128:p.Lys303Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	965	0.44184981684981683	68	0.13821138211382114	207	0.5718232044198895	307	0.5367132867132867	383	0.5052770448548812	a	10.04	1.242232	0.22796	0.231031	0.485681	ENSG00000181961	ENST00000314721	T	0.39592	1.07	3.02	1.79	0.24919	.	.	.	.	.	T	0.00012	0.0000	L	0.52905	1.665	0.80722	P	0.0	B	0.23249	0.082	B	0.22601	0.04	T	0.41288	-0.9517	8	0.49607	T	0.09	.	6.2828	0.21017	0.7663:0.0:0.0:0.2337	rs10896659;rs52838177;rs58877730;rs10896659	303	Q8NH70	O4A16_HUMAN	M	303	ENSP00000325128:K303M	ENSP00000325128:K303M	K	+	2	0	OR4A16	54868160	0.017000	0.18338	0.018000	0.16275	0.016000	0.09150	1.722000	0.38042	0.320000	0.23234	0.346000	0.21813	AAG	A|0.589;T|0.411	0.411	strong		0.323	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274	
MS4A6E	245802	hgsc.bcm.edu	37	11	60102507	60102507	+	Missense_Mutation	SNP	G	G	T	rs2304933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:60102507G>T	ENST00000300182.4	+	1	204	c.139G>T	c.(139-141)Gtt>Ttt	p.V47F		NM_139249.2	NP_640342.1	Q96DS6	M4A6E_HUMAN	membrane-spanning 4-domains, subfamily A, member 6E	47			V -> F (in dbSNP:rs2304933). {ECO:0000269|PubMed:11486273}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|lung(9)|stomach(1)	13						AAAAGTCAAAGTTATTGGGGT	0.473													G|||	1291	0.257788	0.2262	0.4222	5008	,	,		19383	0.255		0.3111	False		,,,				2504	0.1319				p.V47F		Atlas-SNP	.											.	MS4A6E	22	.	0			c.G139T						PASS	.	G	PHE/VAL	1137,3269	405.8+/-333.6	146,845,1212	95.0	87.0	90.0		139	2.2	0.2	11	dbSNP_100	90	2890,5710	451.5+/-362.7	507,1876,1917	yes	missense	MS4A6E	NM_139249.2	50	653,2721,3129	TT,TG,GG		33.6047,25.8057,30.9626	possibly-damaging	47/148	60102507	4027,8979	2203	4300	6503	SO:0001583	missense	245802	exon1			GTCAAAGTTATTG	AF354931	CCDS7984.1	11q12	2008-03-25				ENSG00000166926			14285	protein-coding gene	gene with protein product		608402				11486273	Standard	NM_139249		Approved		uc001npd.3	Q96DS6		ENST00000300182.4:c.139G>T	11.37:g.60102507G>T	ENSP00000300182:p.Val47Phe	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	182	100	0.549451	NM_139249	Q3MIL2|Q8NE56|Q96PG4|Q96PG5	Missense_Mutation	SNP	ENST00000300182.4	37	CCDS7984.1	649	0.29716117216117216	127	0.258130081300813	126	0.34806629834254144	149	0.26048951048951047	247	0.3258575197889182	G	9.946	1.218706	0.22373	0.258057	0.336047	ENSG00000166926	ENST00000300182	T	0.15017	2.46	2.23	2.23	0.28157	.	0.707310	0.13082	N	0.415235	T	0.00012	0.0000	L	0.44542	1.39	0.48696	P	3.0600000000002847E-4	D	0.67145	0.996	P	0.58970	0.849	T	0.46359	-0.9197	9	0.52906	T	0.07	.	7.8596	0.29501	0.0:0.0:1.0:0.0	rs2304933;rs17154793;rs52836443;rs59632781;rs2304933	47	Q96DS6	M4A6E_HUMAN	F	47	ENSP00000300182:V47F	ENSP00000300182:V47F	V	+	1	0	MS4A6E	59859083	0.021000	0.18746	0.234000	0.24042	0.295000	0.27426	0.209000	0.17435	1.226000	0.43582	0.305000	0.20034	GTT	G|0.705;T|0.295	0.295	strong		0.473	MS4A6E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394296.1		
C19orf48	84798	hgsc.bcm.edu	37	19	51301395	51301395	+	Missense_Mutation	SNP	C	C	T	rs4801853	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51301395C>T	ENST00000598463.1	-	5	1409	c.311G>A	c.(310-312)gGg>gAg	p.G104E	C19orf48_ENST00000596655.1_Missense_Mutation_p.G104E|SNORD88B_ENST00000408454.1_RNA|C19orf48_ENST00000345523.4_Missense_Mutation_p.G104E|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000391812.1_Missense_Mutation_p.G104E|C19orf48_ENST00000595794.1_5'Flank			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48	104			G -> E (in dbSNP:rs4801853).							endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		CTGCTTCACCCCTGGAGCACC	0.617													c|||	1652	0.329872	0.1309	0.2161	5008	,	,		21442	0.6538		0.3012	False		,,,				2504	0.3753				p.G104E		Atlas-SNP	.											.	C19orf48	11	.	0			c.G311A						PASS	.	T	GLU/GLY,GLU/GLY	680,3726	290.4+/-280.9	45,590,1568	87.0	89.0	88.0		311,311	-2.2	0.0	19	dbSNP_111	88	2413,6187	397.0+/-345.6	350,1713,2237	yes	missense,missense	C19orf48	NM_199249.1,NM_199250.1	98,98	395,2303,3805	TT,TC,CC		28.0581,15.4335,23.7813	probably-damaging,probably-damaging	104/118,104/118	51301395	3093,9913	2203	4300	6503	SO:0001583	missense	84798	exon5			TTCACCCCTGGAG	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"""multidrug resistance-related protein"""					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		ENST00000598463.1:c.311G>A	19.37:g.51301395C>T	ENSP00000471463:p.Gly104Glu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_199249		Missense_Mutation	SNP	ENST00000598463.1	37	CCDS12803.1	769	0.35210622710622713	71	0.1443089430894309	80	0.22099447513812154	383	0.6695804195804196	235	0.3100263852242744	c	3.466	-0.108946	0.06924	0.154335	0.280581	ENSG00000167747	ENST00000391812;ENST00000345523	T;T	0.35048	1.33;1.33	1.67	-2.21	0.06973	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.55172	0.97	B	0.41332	0.354	T	0.41645	-0.9497	8	0.87932	D	0	.	2.7674	0.05324	0.0:0.4002:0.2503:0.3495	rs4801853;rs17657787;rs58154692;rs4801853	104	Q6RUI8	CS048_HUMAN	E	104	ENSP00000375688:G104E;ENSP00000301419:G104E	ENSP00000301419:G104E	G	-	2	0	C19orf48	55993207	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.508000	0.06344	-0.483000	0.06772	-0.215000	0.12644	GGG	C|0.714;N|0.001	.	strong		0.617	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712	
NBAS	51594	hgsc.bcm.edu	37	2	15372562	15372562	+	Missense_Mutation	SNP	C	C	T	rs6710817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:15372562C>T	ENST00000281513.5	-	47	6245	c.6220G>A	c.(6220-6222)Gcc>Acc	p.A2074T	NBAS_ENST00000441750.1_Missense_Mutation_p.A1954T	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2074			A -> T (in dbSNP:rs6710817). {ECO:0000269|PubMed:15489334}.		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.A2074T(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						TCCACACTGGCGTGGACTGCT	0.478													C|||	535	0.106829	0.1392	0.1037	5008	,	,		21651	0.1012		0.0636	False		,,,				2504	0.1155				p.A2074T		Atlas-SNP	.											NBAS,NS,carcinoma,0,1	NBAS	246	1	1	Substitution - Missense(1)	stomach(1)	c.G6220A						scavenged	.	C	THR/ALA	581,3825	256.4+/-261.2	47,487,1669	116.0	86.0	96.0		6220	3.9	0.6	2	dbSNP_116	96	595,8005	157.5+/-211.1	25,545,3730	yes	missense	NBAS	NM_015909.2	58	72,1032,5399	TT,TC,CC		6.9186,13.1866,9.042	benign	2074/2372	15372562	1176,11830	2203	4300	6503	SO:0001583	missense	51594	exon47			CACTGGCGTGGAC	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.6220G>A	2.37:g.15372562C>T	ENSP00000281513:p.Ala2074Thr	Somatic	77	2	0.025974		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	227	0.10393772893772894	64	0.13008130081300814	40	0.11049723756906077	75	0.13111888111888112	48	0.0633245382585752	C	6.976	0.550110	0.13374	0.131866	0.069186	ENSG00000151779	ENST00000441750;ENST00000281513;ENST00000417461	T;T;T	0.44881	1.47;1.47;0.91	5.67	3.86	0.44501	.	0.467569	0.26224	N	0.025606	T	0.00178	0.0005	N	0.12182	0.205	0.43637	P	0.003967000000000054	P;B	0.44139	0.827;0.011	B;B	0.31390	0.129;0.004	T	0.09400	-1.0676	9	0.87932	D	0	.	6.2337	0.20750	0.1479:0.7061:0.0:0.146	rs6710817;rs17854714;rs52836783;rs59262520;rs6710817	1954;2074	A2RRP1-2;A2RRP1	.;NBAS_HUMAN	T	1954;2074;166	ENSP00000413201:A1954T;ENSP00000281513:A2074T;ENSP00000392421:A166T	ENSP00000281513:A2074T	A	-	1	0	NBAS	15290013	0.160000	0.22878	0.631000	0.29282	0.309000	0.27889	0.316000	0.19469	0.732000	0.32470	0.655000	0.94253	GCC	C|0.899;T|0.101	0.101	strong		0.478	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
KRT72	140807	hgsc.bcm.edu	37	12	52981627	52981627	+	Missense_Mutation	SNP	A	A	T	rs7310138	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52981627A>T	ENST00000537672.2	-	7	1108	c.1098T>A	c.(1096-1098)gaT>gaA	p.D366E	KRT72_ENST00000293745.2_Missense_Mutation_p.D366E|KRT72_ENST00000398066.3_Missense_Mutation_p.D178E|KRT72_ENST00000354310.4_Missense_Mutation_p.D324E	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	366	Coil 2.|Rod.		D -> E (in dbSNP:rs7310138). {ECO:0000269|PubMed:15489334}.			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)		CCGTCTCCAGATCGGCACACT	0.607													A|||	713	0.142372	0.1127	0.1455	5008	,	,		20020	0.1349		0.2465	False		,,,				2504	0.0808				p.D366E		Atlas-SNP	.											.	KRT72	70	.	0			c.T1098A						PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP	602,3804	259.2+/-262.9	48,506,1649	30.0	29.0	29.0		1098,972,1098	1.0	1.0	12	dbSNP_116	29	1976,6624	340.3+/-323.5	233,1510,2557	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	45,45,45	281,2016,4206	TT,TA,AA		22.9767,13.6632,19.8216	benign,benign,benign	366/512,324/470,366/512	52981627	2578,10428	2203	4300	6503	SO:0001583	missense	140807	exon7			CTCCAGATCGGCA	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.1098T>A	12.37:g.52981627A>T	ENSP00000441160:p.Asp366Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	364	0.16666666666666666	55	0.11178861788617886	58	0.16022099447513813	71	0.12412587412587413	180	0.23746701846965698	A	9.862	1.196455	0.22037	0.136632	0.229767	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36	4.87	0.958	0.19619	Filament (1);	0.104637	0.41500	D	0.000872	T	0.00039	0.0001	N	0.01874	-0.695	0.58432	P	1.999999999946489E-6	B;B	0.13594	0.002;0.008	B;B	0.25759	0.001;0.063	T	0.19451	-1.0305	9	0.62326	D	0.03	.	9.4894	0.38951	0.369:0.0:0.631:0.0	rs7310138;rs17674666;rs7310138	324;366	B4DEI8;Q14CN4	.;K2C72_HUMAN	E	366;366;324;178	ENSP00000441160:D366E;ENSP00000293745:D366E;ENSP00000346269:D324E;ENSP00000446151:D178E	ENSP00000293745:D366E	D	-	3	2	KRT72	51267894	0.000000	0.05858	0.971000	0.41717	0.046000	0.14306	-0.414000	0.07114	0.055000	0.16094	-0.268000	0.10319	GAT	A|0.813;T|0.187	0.187	strong		0.607	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
DHRS4L2	317749	hgsc.bcm.edu	37	14	24470138	24470138	+	Nonsense_Mutation	SNP	C	C	T	rs1811890	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24470138C>T	ENST00000335125.6	+	4	601	c.475C>T	c.(475-477)Cga>Tga	p.R159*	DHRS4L2_ENST00000545240.1_Intron|DHRS4L2_ENST00000382755.4_Nonsense_Mutation_p.R157*|DHRS4L2_ENST00000543805.1_Intron|DHRS4L2_ENST00000397071.1_Intron|DHRS4L2_ENST00000537912.1_Intron|DHRS4L2_ENST00000534993.1_Intron|DHRS4L2_ENST00000558753.1_Intron	NM_198083.3	NP_932349.2	Q6PKH6	DR4L2_HUMAN	dehydrogenase/reductase (SDR family) member 4 like 2	157						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	10				GBM - Glioblastoma multiforme(265;0.00962)		AATGGAGAAACGAGGGTACAG	0.547													c|||	645	0.128794	0.0416	0.1138	5008	,	,		21065	0.2232		0.0795	False		,,,				2504	0.2106				p.R159X		Atlas-SNP	.											DHRS4L2,NS,carcinoma,-1,1	DHRS4L2	29	1	0			c.C475T						PASS	.	C	stop/ARG,stop/ARG,,stop/ARG	172,4222		6,160,2031	70.0	76.0	74.0		289,172,,475	2.8	1.0	14	dbSNP_92	74	606,7988		11,584,3702	no	stop-gained,stop-gained,intron,stop-gained	DHRS4L2	NM_001193635.1,NM_001193636.1,NM_001193637.1,NM_198083.3	,,,	17,744,5733	TT,TC,CC		7.0514,3.9144,5.9901	,,,	97/171,58/132,,159/233	24470138	778,12210	2197	4297	6494	SO:0001587	stop_gained	317749	exon4			GAGAAACGAGGGT		CCDS9606.2, CCDS73621.1	14q11.2	2011-09-14			ENSG00000187630	ENSG00000187630	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	19731	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 3"""	615196					Standard	NM_001193635		Approved	SDR25C3	uc001wlf.3	Q6PKH6	OTTHUMG00000028778	ENST00000335125.6:c.475C>T	14.37:g.24470138C>T	ENSP00000334801:p.Arg159*	Somatic	639	1	0.00156495		WXS	Illumina HiSeq	Phase_I	1347	637	0.472903	NM_198083	Q3YLD4	Nonsense_Mutation	SNP	ENST00000335125.6	37	CCDS9606.2	257	0.11767399267399267	29	0.05894308943089431	40	0.11049723756906077	134	0.23426573426573427	54	0.0712401055408971	-	33	5.247139	0.95305	0.039144	0.070514	ENSG00000187630	ENST00000348916;ENST00000335125;ENST00000382755	.	.	.	3.76	2.84	0.33178	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.09310	P	0.999999999590057	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1511	0.42794	0.2015:0.7985:0.0:0.0	rs1811890;rs58573619;rs1811890	.	.	.	X	97;159;157	.	ENSP00000334801:R159X	R	+	1	2	DHRS4L2	23539978	1.000000	0.71417	0.999000	0.59377	0.668000	0.39293	2.341000	0.43983	0.536000	0.28733	0.194000	0.17425	CGA	.	.	weak		0.547	DHRS4L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000071858.4		
ZNF668	79759	hgsc.bcm.edu	37	16	31072912	31072912	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:31072912G>A	ENST00000538906.1	-	3	2121	c.1337C>T	c.(1336-1338)cCg>cTg	p.P446L	ZNF668_ENST00000539836.3_Missense_Mutation_p.P469L|ZNF668_ENST00000394983.2_Missense_Mutation_p.P446L|ZNF668_ENST00000300849.4_Missense_Mutation_p.P446L|ZNF668_ENST00000426488.2_Missense_Mutation_p.P469L|ZNF668_ENST00000417110.2_Missense_Mutation_p.G34R|ZNF668_ENST00000535577.1_Missense_Mutation_p.P446L	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	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)|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						CCCTGCTGCCGGGGCGGCTGA	0.711																																					p.P469L	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C1406T						PASS	.						32.0	40.0	37.0					16																	31072912		2194	4298	6492	SO:0001583	missense	79759	exon4			GCTGCCGGGGCGG		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.1337C>T	16.37:g.31072912G>A	ENSP00000440149:p.Pro446Leu	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	37	CCDS10701.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.02|11.02	1.515722|1.515722	0.27123|0.27123	.|.	.|.	ENSG00000232748|ENSG00000167394	ENST00000417110|ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	.|T;T;T;T;T	.|0.08546	.|3.08;3.09;3.09;3.09;3.09	4.84|4.84	4.84|4.84	0.62591|0.62591	.|.	.|0.000000	.|0.40302	.|N	.|0.001138	T|T	0.07548|0.07548	0.0190|0.0190	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|P	.|0.50708	.|0.648	T|T	0.51702|0.51702	-0.8672|-0.8672	6|10	0.87932|0.21540	D|T	0|0.41	-20.0419|-20.0419	14.9766|14.9766	0.71277|0.71277	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|446	.|Q96K58	.|ZN668_HUMAN	R|L	34|469;446;446;446;446	.|ENSP00000442573:P469L;ENSP00000441349:P446L;ENSP00000440149:P446L;ENSP00000378434:P446L;ENSP00000300849:P446L	ENSP00000391989:G34R|ENSP00000300849:P446L	G|P	+|-	1|2	0|0	AC135050.1|ZNF668	30980413|30980413	0.837000|0.837000	0.29446|0.29446	0.637000|0.637000	0.29366|0.29366	0.430000|0.430000	0.31655|0.31655	1.657000|1.657000	0.37366|0.37366	2.531000|2.531000	0.85337|0.85337	0.462000|0.462000	0.41574|0.41574	GGG|CCG	.	.	none		0.711	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
CEP350	9857	hgsc.bcm.edu	37	1	180080290	180080290	+	Silent	SNP	T	T	A	rs12126496	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:180080290T>A	ENST00000367607.3	+	38	9766	c.9348T>A	c.(9346-9348)ctT>ctA	p.L3116L	CEP350_ENST00000490141.1_3'UTR	NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	3116					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						GAATGCTACTTGTGTGACATC	0.463													T|||	211	0.0421326	0.0045	0.0476	5008	,	,		22888	0.0139		0.0984	False		,,,				2504	0.0603				p.L3116L		Atlas-SNP	.											.	CEP350	418	.	0			c.T9348A						PASS	.	T		104,4302	80.9+/-119.3	1,102,2100	92.0	77.0	83.0		9348	3.5	1.0	1	dbSNP_120	83	945,7655	207.7+/-249.4	70,805,3425	no	coding-synonymous	CEP350	NM_014810.4		71,907,5525	AA,AT,TT		10.9884,2.3604,8.0655		3116/3118	180080290	1049,11957	2203	4300	6503	SO:0001819	synonymous_variant	9857	exon38			GCTACTTGTGTGA	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.9348T>A	1.37:g.180080290T>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	191	111	0.581152	NM_014810	O75068|Q8TDK3|Q8WY20	Silent	SNP	ENST00000367607.3	37	CCDS1336.1	107	0.04899267399267399	4	0.008130081300813009	19	0.052486187845303865	2	0.0034965034965034965	82	0.10817941952506596	T	6.854	0.526772	0.13066	0.023604	0.109884	ENSG00000135837	ENST00000429851	.	.	.	5.9	3.47	0.39725	.	.	.	.	.	T	0.01695	0.0054	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00759	-1.1578	4	.	.	.	.	6.3592	0.21419	0.14:0.0739:0.0:0.7861	rs12126496;rs12126496	.	.	.	S	1291	.	.	C	+	1	0	CEP350	178346913	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.274000	0.33132	1.066000	0.40716	0.528000	0.53228	TGT	T|0.938;A|0.062	0.062	strong		0.463	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
CHD4	1108	hgsc.bcm.edu	37	12	6709059	6709059	+	Silent	SNP	G	G	A	rs11539542	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6709059G>A	ENST00000357008.2	-	10	1525	c.1362C>T	c.(1360-1362)gtC>gtT	p.V454V	CHD4_ENST00000544484.1_Silent_p.V451V|CHD4_ENST00000309577.6_Silent_p.V454V|CHD4_ENST00000544040.1_Silent_p.V447V	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	454					ATP-dependent chromatin remodeling (GO:0043044)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|RNA polymerase II repressing transcription factor binding (GO:0001103)|zinc ion binding (GO:0008270)			central_nervous_system(2)	2						CATCCTTGCAGACCCGACAGA	0.542													g|||	491	0.0980431	0.1278	0.0634	5008	,	,		18827	0.004		0.1322	False		,,,				2504	0.1442				p.V454V	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.C1362T						PASS	.			574,3832	255.8+/-260.9	39,496,1668	211.0	201.0	204.0		1362	1.3	1.0	12	dbSNP_120	204	1396,7204	271.9+/-289.8	122,1152,3026	no	coding-synonymous	CHD4	NM_001273.2		161,1648,4694	AA,AG,GG		16.2326,13.0277,15.1469		454/1913	6709059	1970,11036	2203	4300	6503	SO:0001819	synonymous_variant	1108	exon10			CTTGCAGACCCGA	X86691	CCDS8552.1	12p13	2013-01-28				ENSG00000111642		"""Zinc fingers, PHD-type"""	1919	protein-coding gene	gene with protein product		603277				7575689, 8843877	Standard	XM_006718958		Approved	Mi-2b, Mi2-BETA	uc001qpo.3	Q14839		ENST00000357008.2:c.1362C>T	12.37:g.6709059G>A		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	198	91	0.459596	NM_001273	Q8IXZ5	Silent	SNP	ENST00000357008.2	37	CCDS8552.1																																																																																			G|0.872;A|0.128	0.128	strong		0.542	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273	
EPHB1	2047	hgsc.bcm.edu	37	3	134911655	134911655	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:134911655C>T	ENST00000398015.3	+	11	2490	c.2120C>T	c.(2119-2121)tCt>tTt	p.S707F	EPHB1_ENST00000493838.1_Missense_Mutation_p.S268F	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	707	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> T (in an ovarian undifferentiated carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GCATTGGATTCTTTCCTCAGG	0.507																																					p.S707F		Atlas-SNP	.											EPHB1_ENST00000398015,colon,carcinoma,-1,7	EPHB1	519	7	0			c.C2120T						scavenged	.						102.0	98.0	99.0					3																	134911655		2183	4297	6480	SO:0001583	missense	2047	exon11			TGGATTCTTTCCT	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.2120C>T	3.37:g.134911655C>T	ENSP00000381097:p.Ser707Phe	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	296	3	0.0101351	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.702354	0.88924	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.63744	-0.06;-0.06	5.44	5.44	0.79542	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.77103	0.4081	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78645	-0.2123	10	0.87932	D	0	.	19.2763	0.94032	0.0:1.0:0.0:0.0	.	707	P54762	EPHB1_HUMAN	F	707;268	ENSP00000381097:S707F;ENSP00000419574:S268F	ENSP00000381097:S707F	S	+	2	0	EPHB1	136394345	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.772000	0.85439	2.567000	0.86603	0.561000	0.74099	TCT	.	.	none		0.507	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
TPTE	7179	hgsc.bcm.edu	37	21	10942756	10942756	+	Nonsense_Mutation	SNP	G	G	A	rs1810540	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:10942756G>A	ENST00000361285.4	-	13	1014	c.685C>T	c.(685-687)Cga>Tga	p.R229*	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Nonsense_Mutation_p.R191*|TPTE_ENST00000298232.7_Nonsense_Mutation_p.R211*	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	411	3	0.00729927		WXS	Illumina HiSeq	Phase_I	640	224	0.35	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		
PDF	64146	hgsc.bcm.edu	37	16	69364030	69364030	+	Silent	SNP	G	G	A	rs3852691	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:69364030G>A	ENST00000288022.1	-	1	468	c.444C>T	c.(442-444)ttC>ttT	p.F148F	COG8_ENST00000306875.4_Intron|COG8_ENST00000564419.1_5'Flank|RP11-343C2.12_ENST00000562949.1_Intron	NM_022341.1	NP_071736.1	Q9HBH1	DEFM_HUMAN	peptide deformylase (mitochondrial)	148					N-terminal protein amino acid modification (GO:0031365)|peptidyl-methionine modification (GO:0018206)|positive regulation of cell proliferation (GO:0008284)|translation (GO:0006412)	mitochondrion (GO:0005739)	iron ion binding (GO:0005506)|peptide deformylase activity (GO:0042586)	p.F148F(1)		NS(1)|prostate(1)	2						CGCGCAGGGGGAAGGGCTCCA	0.731													-|||	383	0.0764776	0.1331	0.0692	5008	,	,		11967	0.0258		0.0547	False		,,,				2504	0.0798				p.F148F		Atlas-SNP	.											PDF,NS,carcinoma,0,1	PDF	4	1	1	Substitution - coding silent(1)	prostate(1)	c.C444T						PASS	.		,	488,3644		35,418,1613	10.0	10.0	10.0		444,	-0.1	1.0	16	dbSNP_108	10	439,7599		14,411,3594	no	coding-synonymous,intron	PDF,COG8	NM_022341.1,NM_032382.4	,	49,829,5207	AA,AG,GG		5.4616,11.8103,7.6171	,	148/244,	69364030	927,11243	2066	4019	6085	SO:0001819	synonymous_variant	64146	exon1			CAGGGGGAAGGGC	AF239156	CCDS10875.1	16q22.1	2008-02-05				ENSG00000258429	3.5.1.88		30012	protein-coding gene	gene with protein product						11060042, 15489958	Standard	NM_022341		Approved		uc002ewx.1	Q9HBH1		ENST00000288022.1:c.444C>T	16.37:g.69364030G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	61	10	0.163934	NM_022341	Q8WUN6	Silent	SNP	ENST00000288022.1	37	CCDS10875.1																																																																																			G|0.930;A|0.070	0.070	strong		0.731	PDF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413022.1	NM_022341	
KCNE1	3753	hgsc.bcm.edu	37	21	35821821	35821821	+	Missense_Mutation	SNP	T	T	C	rs1805127	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:35821821T>C	ENST00000337385.3	-	3	487	c.112A>G	c.(112-114)Agt>Ggt	p.S38G	KCNE1_ENST00000432085.1_Missense_Mutation_p.S38G|KCNE1_ENST00000399289.3_Missense_Mutation_p.S38G|KCNE1_ENST00000399286.2_Missense_Mutation_p.S38G|KCNE1_ENST00000399284.1_Missense_Mutation_p.S38G|KCNE1_ENST00000416357.2_Missense_Mutation_p.S38G	NM_001270402.1|NM_001270403.1	NP_001257331.1|NP_001257332.1	P15382	KCNE1_HUMAN	potassium voltage-gated channel, Isk-related family, member 1	38			S -> G (in dbSNP:rs1805127). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16823764, ECO:0000269|PubMed:7828904}.		cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular response to cAMP (GO:0071320)|membrane repolarization (GO:0086009)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|protein N-linked glycosylation (GO:0006487)|protein O-linked glycosylation (GO:0006493)|regulation of delayed rectifier potassium channel activity (GO:1902259)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	potassium channel regulator activity (GO:0015459)|telethonin binding (GO:0031433)|voltage-gated potassium channel activity (GO:0005249)			large_intestine(4)|lung(1)|ovary(2)	7					Indapamide(DB00808)	TTGCCGTCACTGCTGCGGGGG	0.607													C|||	3375	0.673922	0.7247	0.6138	5008	,	,		18741	0.7083		0.6243	False		,,,				2504	0.6636				p.S38G		Atlas-SNP	.											.	KCNE1	23	.	0			c.A112G	GRCh37	CM062783	KCNE1	M	rs1805127	PASS	.	C	GLY/SER,GLY/SER,GLY/SER,GLY/SER	3132,1274	432.2+/-343.2	1101,930,172	78.0	65.0	69.0		112,112,112,112	0.2	0.0	21	dbSNP_89	69	5477,3123	476.5+/-369.4	1740,1997,563	yes	missense,missense,missense,missense	KCNE1	NM_000219.3,NM_001127668.1,NM_001127669.1,NM_001127670.1	56,56,56,56	2841,2927,735	CC,CT,TT		36.314,28.9151,33.8075	benign,benign,benign,benign	38/130,38/130,38/130,38/130	35821821	8609,4397	2203	4300	6503	SO:0001583	missense	3753	exon3			CGTCACTGCTGCG	L28168	CCDS13636.1	21q22.1-q22.2	2014-09-17			ENSG00000180509	ENSG00000180509		"""Potassium channels"""	6240	protein-coding gene	gene with protein product		176261				8432548	Standard	NM_001127670		Approved	minK, ISK, JLNS2, LQT5	uc010gmp.4	P15382	OTTHUMG00000086236	ENST00000337385.3:c.112A>G	21.37:g.35821821T>C	ENSP00000337255:p.Ser38Gly	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	145	50	0.344828	NM_001127669	A5H1P2|Q8N709|Q91Z94	Missense_Mutation	SNP	ENST00000337385.3	37	CCDS13636.1	1459	0.668040293040293	370	0.7520325203252033	228	0.6298342541436464	394	0.6888111888111889	467	0.6160949868073878	C	10.57	1.386290	0.25031	0.710849	0.63686	ENSG00000180509	ENST00000399289;ENST00000337385;ENST00000432085;ENST00000399286;ENST00000416357;ENST00000399284	D;D;D;D;D;D	0.92699	-3.09;-3.09;-3.09;-3.09;-3.09;-3.09	5.16	0.18	0.15068	.	1.125680	0.06713	N	0.773538	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40251	-0.9573	9	0.22109	T	0.4	-0.9157	5.8765	0.18832	0.0:0.3705:0.144:0.4854	rs1805127;rs8179018;rs60471919;rs1805127	38	P15382	KCNE1_HUMAN	G	38	ENSP00000382228:S38G;ENSP00000337255:S38G;ENSP00000412498:S38G;ENSP00000382226:S38G;ENSP00000416258:S38G;ENSP00000382225:S38G	ENSP00000337255:S38G	S	-	1	0	KCNE1	34743691	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.889000	0.04144	-0.024000	0.13941	-0.880000	0.02959	AGT	.	.	weak		0.607	KCNE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194155.1		
C1orf127	148345	hgsc.bcm.edu	37	1	11017141	11017141	+	Intron	SNP	G	G	A	rs75810903	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11017141G>A	ENST00000377008.4	-	7	724				C1orf127_ENST00000377004.4_Silent_p.L239L			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127											NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		ATAGTGGCAGGAGCTCAGCAG	0.602													G|||	16	0.00319489	0.0008	0.0014	5008	,	,		15143	0.002		0.0099	False		,,,				2504	0.002				p.L239L		Atlas-SNP	.											.	C1orf127	134	.	0			c.C717T						PASS	.	G		3,1381		0,3,689	33.0	41.0	38.0		717	-4.9	0.0	1	dbSNP_132	38	36,3146		0,36,1555	yes	coding-synonymous	C1orf127	NM_001170754.1		0,39,2244	AA,AG,GG		1.1314,0.2168,0.8541		239/824	11017141	39,4527	692	1591	2283	SO:0001627	intron_variant	148345	exon8			TGGCAGGAGCTCA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.277+500C>T	1.37:g.11017141G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		8	0.003663003663003663	0	0.0	0	0.0	1	0.0017482517482517483	7	0.009234828496042216	G	3.484	-0.105372	0.06967	0.002168	0.011314	ENSG00000175262	ENST00000520253	.	.	.	5.39	-4.9	0.03094	.	.	.	.	.	T	0.19208	0.0461	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.32025	-0.9922	4	.	.	.	.	6.7834	0.23659	0.1109:0.62:0.1446:0.1245	.	.	.	.	F	217	.	.	S	-	2	0	C1orf127	10939728	0.067000	0.21026	0.024000	0.17045	0.510000	0.34073	-0.085000	0.11250	-0.691000	0.05135	0.561000	0.74099	TCC	G|0.996;A|0.004	0.004	strong		0.602	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
MOV10L1	54456	hgsc.bcm.edu	37	22	50530501	50530501	+	Missense_Mutation	SNP	A	A	T	rs9617066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50530501A>T	ENST00000262794.5	+	2	252	c.169A>T	c.(169-171)Atg>Ttg	p.M57L	MOV10L1_ENST00000545383.1_Missense_Mutation_p.M57L|MOV10L1_ENST00000395843.1_De_novo_Start_InFrame|MOV10L1_ENST00000475190.1_3'UTR|MOV10L1_ENST00000540615.1_Missense_Mutation_p.M37L|MOV10L1_ENST00000395858.3_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	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	228	118	0.517544	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	
LAMA2	3908	hgsc.bcm.edu	37	6	129571330	129571330	+	Missense_Mutation	SNP	G	G	A	rs3816665	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:129571330G>A	ENST00000421865.2	+	13	1905	c.1856G>A	c.(1855-1857)cGt>cAt	p.R619H		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	619	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.		R -> H (in dbSNP:rs3816665). {ECO:0000269|Ref.8}.		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)		GATACAGAACGTGTTCTCCAG	0.393													A|||	1357	0.270966	0.5961	0.134	5008	,	,		18775	0.0843		0.1551	False		,,,				2504	0.2403				p.R619H		Atlas-SNP	.											.	LAMA2	481	.	0			c.G1856A						PASS	.	A	HIS/ARG,HIS/ARG	2304,2102	574.2+/-383.7	631,1042,530	167.0	146.0	153.0		1856,1856	-5.1	0.0	6	dbSNP_107	153	1204,7396	763.4+/-407.6	90,1024,3186	yes	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	29,29	721,2066,3716	AA,AG,GG		14.0,47.7077,26.9722	benign,benign	619/3123,619/3119	129571330	3508,9498	2203	4300	6503	SO:0001583	missense	3908	exon13			CAGAACGTGTTCT	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.1856G>A	6.37:g.129571330G>A	ENSP00000400365:p.Arg619His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	99	57	0.575758	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	485	0.22206959706959706	272	0.5528455284552846	47	0.1298342541436464	46	0.08041958041958042	120	0.158311345646438	A	1.385	-0.582320	0.03827	0.522923	0.14	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.36340	1.26	5.69	-5.14	0.02875	Laminin B type IV (2);Laminin B, subgroup (1);	1.488520	0.03600	N	0.233286	T	0.14917	0.0360	L	0.46157	1.445	0.80722	P	0.0	B;B	0.11235	0.004;0.0	B;B	0.08055	0.003;0.002	T	0.15065	-1.0450	9	0.30854	T	0.27	.	16.1314	0.81445	0.1712:0.0906:0.7382:0.0	rs3816665;rs52811738;rs58534796;rs3816665	619;619	A6NF00;P24043	.;LAMA2_HUMAN	H	619	ENSP00000400365:R619H	ENSP00000346769:R619H	R	+	2	0	LAMA2	129613023	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-1.575000	0.02131	-1.322000	0.02278	-2.044000	0.00415	CGT	G|0.744;A|0.256	0.256	strong		0.393	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
KRTAP13-3	337960	hgsc.bcm.edu	37	21	31797919	31797919	+	Silent	SNP	G	G	A	rs73356706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31797919G>A	ENST00000390690.2	-	1	367	c.312C>T	c.(310-312)tcC>tcT	p.S104S		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	104						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AGCAGCTATTGGATCCAAAAC	0.532													-|||	210	0.0419329	0.1505	0.0144	5008	,	,		18568	0.0		0.001	False		,,,				2504	0.0				p.S104S		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.C312T						PASS	.	G		432,3908		23,386,1761	51.0	57.0	55.0		312	3.4	0.3	21	dbSNP_130	55	9,8569		0,9,4280	no	coding-synonymous	KRTAP13-3	NM_181622.1		23,395,6041	AA,AG,GG		0.1049,9.9539,3.4138		104/173	31797919	441,12477	2170	4289	6459	SO:0001819	synonymous_variant	337960	exon1			GCTATTGGATCCA	AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"""Keratin associated proteins"""	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.312C>T	21.37:g.31797919G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	171	61	0.356725	NM_181622	Q3LI78	Silent	SNP	ENST00000390690.2	37	CCDS13591.1																																																																																			G|0.975;A|0.025	0.025	strong		0.532	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2		
TIAM1	7074	hgsc.bcm.edu	37	21	32638550	32638550	+	Missense_Mutation	SNP	C	C	T	rs2070418|rs386817934	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:32638550C>T	ENST00000286827.3	-	5	1210	c.739G>A	c.(739-741)Ggg>Agg	p.G247R	TIAM1_ENST00000541036.1_Missense_Mutation_p.G247R|TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	247			G -> R (in dbSNP:rs2070418).|G -> V (in dbSNP:rs2070417).	G -> M (in Ref. 1; AAA98443). {ECO:0000305}.	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						CCCGGCCCCCCGTTTGCTGTC	0.537													C|||	1069	0.213458	0.0159	0.2594	5008	,	,		16363	0.4107		0.1133	False		,,,				2504	0.3476				p.G247R		Atlas-SNP	.											.	TIAM1	522	.	0			c.G739A						PASS	.	C	ARG/GLY	148,4258	88.2+/-126.9	6,136,2061	69.0	73.0	71.0		739	4.5	1.0	21	dbSNP_96	71	730,7870	141.4+/-197.7	39,652,3609	yes	missense	TIAM1	NM_003253.2	125	45,788,5670	TT,TC,CC		8.4884,3.3591,6.7507	probably-damaging	247/1592	32638550	878,12128	2203	4300	6503	SO:0001583	missense	7074	exon5			GCCCCCCGTTTGC		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.739G>A	21.37:g.32638550C>T	ENSP00000286827:p.Gly247Arg	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	122	49	0.401639	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	351	0.16071428571428573	7	0.014227642276422764	80	0.22099447513812154	196	0.34265734265734266	68	0.08970976253298153	C	13.23	2.176241	0.38413	0.033591	0.084884	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.39229	1.11;1.09	5.4	4.49	0.54785	.	0.367039	0.30869	N	0.008718	T	0.00012	0.0000	L	0.36672	1.1	0.25471	P	0.9878204	P;P;P	0.46656	0.882;0.813;0.813	B;B;B	0.34824	0.19;0.093;0.093	T	0.42050	-0.9474	9	0.44086	T	0.13	.	17.6719	0.88221	0.0:0.8674:0.1326:0.0	rs2070418;rs56928974;rs2070418	247;247;247	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	R	247;88;247	ENSP00000286827:G247R;ENSP00000441570:G247R	ENSP00000286827:G247R	G	-	1	0	TIAM1	31560421	0.911000	0.30947	0.998000	0.56505	0.993000	0.82548	2.031000	0.41117	2.803000	0.96430	0.585000	0.79938	GGG	C|0.874;A|0.001	.	strong		0.537	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
ITGA2	3673	hgsc.bcm.edu	37	5	52351413	52351413	+	Silent	SNP	G	G	A	rs1062535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:52351413G>A	ENST00000296585.5	+	8	968	c.825G>A	c.(823-825)acG>acA	p.T275T		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	275	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|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)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				GAAGTGCTACGAAAGTAATGG	0.368																																					p.T275T		Atlas-SNP	.											.	ITGA2	211	.	0			c.G825A	GRCh37	CM993454	ITGA2	M	rs1062535	PASS	.	A		1442,2964	467.6+/-354.9	240,962,1001	165.0	157.0	160.0		825	0.4	0.9	5	dbSNP_86	160	3426,5174	504.5+/-376.2	655,2116,1529	no	coding-synonymous	ITGA2	NM_002203.3		895,3078,2530	AA,AG,GG		39.8372,32.7281,37.4289		275/1182	52351413	4868,8138	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon8			TGCTACGAAAGTA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.825G>A	5.37:g.52351413G>A		Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			G|0.627;A|0.373	0.373	strong		0.368	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
CPB2	1361	hgsc.bcm.edu	37	13	46648094	46648094	+	Missense_Mutation	SNP	C	C	T	rs3742264	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:46648094C>T	ENST00000181383.4	-	6	521	c.505G>A	c.(505-507)Gca>Aca	p.A169T	CPB2_ENST00000439329.3_Missense_Mutation_p.A169T|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606243.1_RNA|CPB2-AS1_ENST00000606351.1_RNA|CPB2-AS1_ENST00000606991.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	169			A -> T (in dbSNP:rs3742264). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1939207}.		blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		TTTTTGGCTGCTTGTTCTTTT	0.378													T|||	1539	0.307308	0.4251	0.304	5008	,	,		17258	0.256		0.336	False		,,,				2504	0.1738				p.A169T		Atlas-SNP	.											.	CPB2	60	.	0			c.G505A	GRCh37	CM063919	CPB2	M	rs3742264	PASS	.	T	THR/ALA,THR/ALA	1714,2692	650.9+/-399.1	329,1056,818	110.0	97.0	102.0		505,505	2.7	0.0	13	dbSNP_107	102	2782,5818	677.6+/-403.4	441,1900,1959	yes	missense,missense	CPB2	NM_001872.3,NM_016413.3	58,58	770,2956,2777	TT,TC,CC		32.3488,38.9015,34.5687	benign,benign	169/424,169/361	46648094	4496,8510	2203	4300	6503	SO:0001583	missense	1361	exon6			TGGCTGCTTGTTC	M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"""thrombin-activatable fibrinolysis inhibitor"", ""carboxypeptidase U"", ""plasma carboxypeptidase B"", ""carboxypeptidase R"""	603101	"""carboxypeptidase B2 (plasma, carboxypeptidase U)"""			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.505G>A	13.37:g.46648094C>T	ENSP00000181383:p.Ala169Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_001872	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Missense_Mutation	SNP	ENST00000181383.4	37	CCDS9401.1	744	0.34065934065934067	205	0.4166666666666667	114	0.3149171270718232	158	0.2762237762237762	267	0.35224274406332456	T	4.510	0.094684	0.08681	0.389015	0.323488	ENSG00000080618	ENST00000181383;ENST00000439329	T;T	0.29397	1.57;2.83	5.17	2.66	0.31614	Peptidase M14, carboxypeptidase A (2);	0.842873	0.10925	N	0.619022	T	0.00012	0.0000	N	0.04686	-0.185	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48714	-0.9011	9	0.11485	T	0.65	.	4.6888	0.12771	0.1407:0.1611:0.0:0.6983	rs3742264;rs52803778;rs57767929;rs3742264	169;169	Q96IY4-2;Q96IY4	.;CBPB2_HUMAN	T	169	ENSP00000181383:A169T;ENSP00000400714:A169T	ENSP00000181383:A169T	A	-	1	0	CPB2	45546095	0.000000	0.05858	0.046000	0.18839	0.841000	0.47740	0.765000	0.26546	0.049000	0.15920	-0.360000	0.07572	GCA	C|0.653;T|0.347	0.347	strong		0.378	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872	
SLAMF1	6504	hgsc.bcm.edu	37	1	160616703	160616703	+	Missense_Mutation	SNP	G	G	T	rs2295612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:160616703G>T	ENST00000302035.6	-	1	382	c.33C>A	c.(31-33)ttC>ttA	p.F11L	SLAMF1_ENST00000538290.1_Missense_Mutation_p.F11L|SLAMF1_ENST00000235739.5_Missense_Mutation_p.F11L|SLAMF1_ENST00000355199.3_Missense_Mutation_p.F11L	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	11			F -> L (in dbSNP:rs2295612).		lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.F11F(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			GAAACAGCACGAAGGTCAAGG	0.567													G|||	493	0.0984425	0.0061	0.2075	5008	,	,		19271	0.0347		0.2167	False		,,,				2504	0.09				p.F11L		Atlas-SNP	.											SLAMF1,colon,carcinoma,0,1	SLAMF1	74	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C33A						PASS	.	G	LEU/PHE	158,4248	105.6+/-144.1	3,152,2048	68.0	62.0	64.0		33	0.8	0.0	1	dbSNP_100	64	1748,6852	308.2+/-308.8	190,1368,2742	yes	missense	SLAMF1	NM_003037.2	22	193,1520,4790	TT,TG,GG		20.3256,3.586,14.6548	benign	11/336	160616703	1906,11100	2203	4300	6503	SO:0001583	missense	6504	exon1			CAGCACGAAGGTC	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10903	protein-coding gene	gene with protein product		603492	"""signaling lymphocytic activation molecule"""	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.33C>A	1.37:g.160616703G>T	ENSP00000306190:p.Phe11Leu	Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	285	169	0.592982	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	267	0.12225274725274725	6	0.012195121951219513	77	0.212707182320442	18	0.03146853146853147	166	0.21899736147757257	G	0.031	-1.336977	0.01287	0.03586	0.203256	ENSG00000117090	ENST00000302035;ENST00000235739;ENST00000392208;ENST00000538290;ENST00000355199	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	3.84	0.793	0.18632	Signaling lymphocytic activation molecule, N-terminal (2);	1.960650	0.02772	N	0.119850	T	0.07548	0.0190	N	0.20685	0.6	0.80722	P	0.0	B;B	0.12630	0.006;0.002	B;B	0.14023	0.01;0.006	T	0.07539	-1.0767	9	0.05833	T	0.94	-13.3109	5.3222	0.15887	0.2009:0.0:0.632:0.1672	rs2295612;rs58261892;rs2295612	11;11	B4E2E4;Q13291	.;SLAF1_HUMAN	L	11	ENSP00000306190:F11L;ENSP00000235739:F11L;ENSP00000438406:F11L;ENSP00000347333:F11L	ENSP00000235739:F11L	F	-	3	2	SLAMF1	158883327	0.062000	0.20869	0.006000	0.13384	0.001000	0.01503	-0.151000	0.10175	-0.038000	0.13624	-1.119000	0.02030	TTC	G|0.877;T|0.123	0.123	strong		0.567	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1		
ADAMTS13	11093	hgsc.bcm.edu	37	9	136324239	136324239	+	Silent	SNP	C	C	A	rs1055432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136324239C>A	ENST00000371929.3	+	29	4665	c.4221C>A	c.(4219-4221)acC>acA	p.T1407T	CACFD1_ENST00000540581.1_5'Flank|CACFD1_ENST00000542192.1_5'Flank|ADAMTS13_ENST00000356589.2_Silent_p.T1320T|CACFD1_ENST00000291722.7_5'Flank|ADAMTS13_ENST00000371910.1_Silent_p.T203T|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000371916.1_3'UTR|CACFD1_ENST00000316948.4_5'Flank|ADAMTS13_ENST00000355699.2_Silent_p.T1351T	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	1407	CUB 2.				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)		AGTACTGGACCCTCCAATCAT	0.592													C|||	1155	0.230631	0.025	0.3271	5008	,	,		17137	0.1925		0.334	False		,,,				2504	0.3732				p.T1407T		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C4221A						PASS	.	C	,,	333,4065	171.9+/-202.1	22,289,1888	40.0	37.0	38.0		4221,3960,4053	3.0	0.7	9	dbSNP_86	38	2881,5717	444.4+/-360.7	466,1949,1884	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	488,2238,3772	AA,AC,CC		33.5078,7.5716,24.7307	,,	1407/1428,1320/1341,1351/1372	136324239	3214,9782	2199	4299	6498	SO:0001819	synonymous_variant	11093	exon29			CTGGACCCTCCAA	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.4221C>A	9.37:g.136324239C>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	139	73	0.52518	NM_139025	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			C|0.769;A|0.231	0.231	strong		0.592	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
TTC5	91875	hgsc.bcm.edu	37	14	20770036	20770036	+	Missense_Mutation	SNP	T	T	C	rs3742945	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20770036T>C	ENST00000258821.3	-	2	196	c.140A>G	c.(139-141)cAg>cGg	p.Q47R		NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	47			Q -> R (in dbSNP:rs3742945). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		DNA repair (GO:0006281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_cancers(95;0.00092)		Epithelial(56;1.1e-06)|all cancers(55;8.07e-06)	GBM - Glioblastoma multiforme(265;0.0106)		CATCTCCTTCTGCACATCCTG	0.458													C|||	3734	0.745607	0.7579	0.8559	5008	,	,		22041	0.7956		0.7406	False		,,,				2504	0.6043				p.Q47R		Atlas-SNP	.											TTC5,NS,adenoma,0,1	TTC5	34	1	0			c.A140G						scavenged	.	C	ARG/GLN	3294,1112	398.1+/-330.7	1231,832,140	237.0	181.0	200.0		140	0.4	0.9	14	dbSNP_107	200	6294,2306	387.1+/-342.1	2309,1676,315	yes	missense	TTC5	NM_138376.2	43	3540,2508,455	CC,CT,TT		26.814,25.2383,26.2802	benign	47/441	20770036	9588,3418	2203	4300	6503	SO:0001583	missense	91875	exon2			TCCTTCTGCACAT	BC008647	CCDS9546.1	14q11.2	2013-01-11			ENSG00000136319	ENSG00000136319		"""Tetratricopeptide (TTC) repeat domain containing"""	19274	protein-coding gene	gene with protein product						11511361	Standard	NM_138376		Approved	Strap	uc001vwt.3	Q8N0Z6	OTTHUMG00000029506	ENST00000258821.3:c.140A>G	14.37:g.20770036T>C	ENSP00000258821:p.Gln47Arg	Somatic	292	2	0.00684932		WXS	Illumina HiSeq	Phase_I	364	136	0.373626	NM_138376	A8MQ18|Q96HF9	Missense_Mutation	SNP	ENST00000258821.3	37	CCDS9546.1	1696	0.7765567765567766	370	0.7520325203252033	302	0.8342541436464088	459	0.8024475524475524	565	0.7453825857519789	C	0.248	-1.008434	0.02112	0.747617	0.73186	ENSG00000136319	ENST00000258821	T	0.28666	1.6	4.31	0.384	0.16244	Tetratricopeptide-like helical (1);	0.511690	0.21623	N	0.071602	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	0.27262	-1.0079	9	0.08179	T	0.78	.	8.8128	0.34978	0.0:0.4622:0.0:0.5378	rs3742945;rs17845175;rs17856898;rs17857985;rs17859578;rs52798233;rs60485527;rs3742945	47	Q8N0Z6	TTC5_HUMAN	R	47	ENSP00000258821:Q47R	ENSP00000258821:Q47R	Q	-	2	0	TTC5	19839876	0.000000	0.05858	0.892000	0.35008	0.788000	0.44548	-0.336000	0.07863	-0.367000	0.08052	-0.996000	0.02517	CAG	T|0.243;C|0.757	0.757	strong		0.458	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376	
TTN	7273	hgsc.bcm.edu	37	2	179440029	179440029	+	Silent	SNP	G	G	A	rs12464787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179440029G>A	ENST00000591111.1	-	276	66131	c.65907C>T	c.(65905-65907)agC>agT	p.S21969S	TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Silent_p.S23610S|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Silent_p.S21042S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000460472.2_Silent_p.S14545S|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Silent_p.S14670S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN_ENST00000342175.6_Silent_p.S14737S			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	152	0	0		WXS	Illumina HiSeq	Phase_I	147	80	0.544218	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	
SIVA1	10572	hgsc.bcm.edu	37	14	105222037	105222037	+	Silent	SNP	C	C	T	rs1132975	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105222037C>T	ENST00000329967.6	+	2	291	c.189C>T	c.(187-189)gcC>gcT	p.A63A	SIVA1_ENST00000347067.5_Intron	NM_006427.3	NP_006418.2	O15304	SIVA_HUMAN	SIVA1, apoptosis-inducing factor	63					activation-induced cell death of T cells (GO:0006924)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	CD27 receptor binding (GO:0005175)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|prostate(1)	3		all_cancers(154;0.14)|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;0.173)		AAGGCTGTGCCGTCGTTCACC	0.622													C|||	2170	0.433307	0.2398	0.5014	5008	,	,		18850	0.624		0.34	False		,,,				2504	0.546				p.A63A		Atlas-SNP	.											.	SIVA1	12	.	0			c.C189T						PASS	.	C	,	1189,3217	416.5+/-337.6	169,851,1183	79.0	76.0	77.0		189,	0.0	0.0	14	dbSNP_86	77	2917,5683	455.5+/-363.8	501,1915,1884	no	coding-synonymous,intron	SIVA1	NM_006427.3,NM_021709.2	,	670,2766,3067	TT,TC,CC		33.9186,26.9859,31.57	,	63/176,	105222037	4106,8900	2203	4300	6503	SO:0001819	synonymous_variant	10572	exon2			CTGTGCCGTCGTT	U82938	CCDS9992.1, CCDS9993.1	14q32.33	2007-03-19							17712	protein-coding gene	gene with protein product		605567				9177220	Standard	NM_006427		Approved	SIVA, Siva-1, Siva-2, CD27BP	uc001yph.3	O15304		ENST00000329967.6:c.189C>T	14.37:g.105222037C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_006427	Q96P98|Q9UPD6	Silent	SNP	ENST00000329967.6	37	CCDS9992.1	905	0.4143772893772894	140	0.2845528455284553	168	0.46408839779005523	345	0.6031468531468531	252	0.3324538258575198	C	8.528	0.870369	0.17322	0.269859	0.339186	ENSG00000184990	ENST00000556195	.	.	.	5.03	0.00199	0.14048	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47341	P	6.099999999999994E-4	.	.	.	.	.	.	T	0.46498	-0.9187	3	.	.	.	-12.2268	8.0122	0.30359	0.0:0.5495:0.0:0.4505	rs1132975;rs3194340;rs3803306;rs59682710;rs1132975	.	.	.	L	81	.	.	P	+	2	0	SIVA1	104293082	0.000000	0.05858	0.002000	0.10522	0.873000	0.50193	-0.220000	0.09215	-0.046000	0.13446	-0.251000	0.11542	CCG	C|0.646;T|0.354	0.354	strong		0.622	SIVA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410541.1	NM_006427	
ZNF195	7748	hgsc.bcm.edu	37	11	3380678	3380678	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:3380678C>T	ENST00000399602.4	-	6	1686	c.1560G>A	c.(1558-1560)aaG>aaA	p.K520K	ZNF195_ENST00000354599.6_Silent_p.K448K|ZNF195_ENST00000429541.2_Silent_p.K452K|ZNF195_ENST00000343338.7_Silent_p.K452K|ZNF195_ENST00000526601.1_Silent_p.K501K|ZNF195_ENST00000005082.9_Silent_p.K497K|ZNF195_ENST00000528796.1_Intron	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	520					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(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		ATTTGTAGGGCTTCTCTCCAG	0.403																																					p.K520K		Atlas-SNP	.											ZNF195,NS,carcinoma,0,4	ZNF195	77	4	0			c.G1560A						scavenged	.						168.0	171.0	170.0					11																	3380678		2064	4218	6282	SO:0001819	synonymous_variant	7748	exon6			GTAGGGCTTCTCT		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"""Zinc fingers, C2H2-type"", ""-"""	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.1560G>A	11.37:g.3380678C>T		Somatic	94	3	0.0319149		WXS	Illumina HiSeq	Phase_I	94	3	0.0319149	NM_001130520	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Silent	SNP	ENST00000399602.4	37	CCDS44522.1																																																																																			.	.	none		0.403	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2		
SLC13A4	26266	hgsc.bcm.edu	37	7	135376041	135376041	+	Missense_Mutation	SNP	G	G	A	rs36004833	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:135376041G>A	ENST00000354042.4	-	13	2040	c.1351C>T	c.(1351-1353)Ccc>Tcc	p.P451S	C7orf73_ENST00000422968.1_Intron	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	451			P -> S (in dbSNP:rs36004833).		sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						GTGATGATGGGCTCGGTCCCC	0.517													G|||	62	0.0123802	0.0023	0.0187	5008	,	,		15980	0.0		0.0437	False		,,,				2504	0.002				p.P451S		Atlas-SNP	.											.	SLC13A4	56	.	0			c.C1351T						PASS	.	G	SER/PRO	32,4374	36.8+/-68.6	0,32,2171	110.0	102.0	105.0		1351	3.8	1.0	7	dbSNP_126	105	319,8281	113.7+/-173.7	10,299,3991	yes	missense	SLC13A4	NM_012450.2	74	10,331,6162	AA,AG,GG		3.7093,0.7263,2.6988	benign	451/627	135376041	351,12655	2203	4300	6503	SO:0001583	missense	26266	exon13			TGATGGGCTCGGT	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1351C>T	7.37:g.135376041G>A	ENSP00000297282:p.Pro451Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	86	27	0.313953	NM_012450	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	37	CCDS5840.1	38	0.0173992673992674	0	0.0	9	0.024861878453038673	0	0.0	29	0.03825857519788918	G	15.31	2.795824	0.50208	0.007263	0.037093	ENSG00000164707	ENST00000354042	T	0.69685	-0.42	5.64	3.84	0.44239	.	0.154187	0.64402	N	0.000014	T	0.22859	0.0552	L	0.37800	1.135	0.51482	D	0.999929	B;B	0.29378	0.243;0.1	B;B	0.28849	0.067;0.095	T	0.28235	-1.0050	10	0.44086	T	0.13	-19.6445	10.3058	0.43680	0.1606:0.0:0.8394:0.0	rs36004833	320;451	Q59HF0;Q9UKG4	.;S13A4_HUMAN	S	451	ENSP00000297282:P451S	ENSP00000297282:P451S	P	-	1	0	SLC13A4	135026581	1.000000	0.71417	0.990000	0.47175	0.592000	0.36648	4.874000	0.63064	0.738000	0.32606	0.650000	0.86243	CCC	G|0.976;A|0.024	0.024	strong		0.517	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450	
HIVEP3	59269	hgsc.bcm.edu	37	1	42046613	42046613	+	Silent	SNP	G	G	T	rs12132697	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:42046613G>T	ENST00000372583.1	-	4	4741	c.3856C>A	c.(3856-3858)Cgg>Agg	p.R1286R	HIVEP3_ENST00000247584.5_Silent_p.R1286R|HIVEP3_ENST00000372584.1_Silent_p.R1286R|HIVEP3_ENST00000460604.1_5'Flank|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	103	0	0		WXS	Illumina HiSeq	Phase_I	86	63	0.732558	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	
RTEL1	51750	hgsc.bcm.edu	37	20	62322290	62322290	+	Missense_Mutation	SNP	G	G	A	rs190887884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62322290G>A	ENST00000360203.5	+	27	2871	c.2546G>A	c.(2545-2547)gGc>gAc	p.G849D	RTEL1_ENST00000318100.4_Missense_Mutation_p.G849D|RTEL1_ENST00000508582.2_Missense_Mutation_p.G873D|RTEL1_ENST00000370018.3_Missense_Mutation_p.G849D|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.G849D|RTEL1_ENST00000370003.1_Missense_Mutation_p.G94D					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)			GGGAGCCCTGGCGAGGAGCAG	0.687													G|||	23	0.00459265	0.0023	0.0058	5008	,	,		15022	0.0		0.0099	False		,,,				2504	0.0061				p.G873D		Atlas-SNP	.											.	RTEL1	114	.	0			c.G2618A						PASS	.	G	ASP/GLY,ASP/GLY	9,4167		0,9,2079	14.0	15.0	14.0		2546,2618	-0.1	0.0	20		14	113,8185		0,113,4036	yes	missense,missense	RTEL1	NM_016434.3,NM_032957.4	94,94	0,122,6115	AA,AG,GG		1.3618,0.2155,0.978	benign,benign	849/1220,873/1244	62322290	122,12352	2088	4149	6237	SO:0001583	missense	51750	exon27			GCCCTGGCGAGGA	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.2546G>A	20.37:g.62322290G>A	ENSP00000353332:p.Gly849Asp	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	11.51	1.659474	0.29515	0.002155	0.013618	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000370003	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	4.77	-0.131	0.13494	.	0.888187	0.09800	N	0.754121	T	0.04679	0.0127	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.34290	0.052;0.447;0.003;0.008	B;B;B;B	0.35413	0.075;0.202;0.017;0.046	T	0.38972	-0.9636	10	0.23302	T	0.38	-13.4816	2.5812	0.04818	0.4374:0.0:0.343:0.2196	.	873;94;849;849	Q9NZ71-7;Q9NZ71-5;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	D	849;849;873;849;94	ENSP00000359035:G849D;ENSP00000322287:G849D;ENSP00000424307:G873D;ENSP00000353332:G849D;ENSP00000359020:G94D	ENSP00000353332:G849D	G	+	2	0	AL353715.1	61792734	0.001000	0.12720	0.005000	0.12908	0.006000	0.05464	0.096000	0.15147	0.093000	0.17368	-0.217000	0.12591	GGC	G|0.994;A|0.006	0.006	strong		0.687	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957	
AKNAD1	254268	hgsc.bcm.edu	37	1	109377070	109377070	+	Splice_Site	SNP	C	C	A	rs12060255	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109377070C>A	ENST00000370001.3	-	9	2013	c.1745G>T	c.(1744-1746)gGg>gTg	p.G582V	AKNAD1_ENST00000369994.1_Splice_Site_p.G552V|AKNAD1_ENST00000369995.3_Splice_Site_p.G582V|AKNAD1_ENST00000357393.4_Splice_Site_p.G289V	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	582			G -> V (in dbSNP:rs12060255).			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						GGACATTACCCCAGAGTTAGA	0.443													C|||	666	0.132987	0.2095	0.0951	5008	,	,		18089	0.12		0.1133	False		,,,				2504	0.09				p.G582V		Atlas-SNP	.											.	AKNAD1	83	.	0			c.G1745T						PASS	.	C	VAL/GLY	821,3585	301.8+/-287.1	84,653,1466	63.0	56.0	59.0		1745	-0.0	0.0	1	dbSNP_120	59	972,7628	196.2+/-241.2	54,864,3382	yes	missense-near-splice	AKNAD1	NM_152763.3	109	138,1517,4848	AA,AC,CC		11.3023,18.6337,13.7859	possibly-damaging	582/837	109377070	1793,11213	2203	4300	6503	SO:0001630	splice_region_variant	254268	exon9			ATTACCCCAGAGT	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.1746+1G>T	1.37:g.109377070C>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	36	27	0.75	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	300	0.13736263736263737	114	0.23170731707317074	37	0.10220994475138122	66	0.11538461538461539	83	0.10949868073878628	C	8.353	0.831248	0.16820	0.186337	0.113023	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.15834	3.17;2.39;3.08;3.15	3.31	-0.038	0.13881	.	.	.	.	.	T	0.02727	0.0082	L	0.29908	0.895	0.58432	P	1.0000000000287557E-6	B;P	0.37864	0.396;0.61	B;B	0.30029	0.1;0.11	T	0.40079	-0.9582	8	0.42905	T	0.14	5.4051	2.5826	0.04822	0.2287:0.5013:0.0:0.2699	rs12060255	289;582	B4DET8;Q5T1N1	.;AKND1_HUMAN	V	582;289;552;582	ENSP00000359018:G582V;ENSP00000349968:G289V;ENSP00000359011:G552V;ENSP00000359012:G582V	ENSP00000349968:G289V	G	-	2	0	AKNAD1	109178593	0.007000	0.16637	0.001000	0.08648	0.052000	0.14988	0.598000	0.24074	0.207000	0.20607	0.462000	0.41574	GGG	C|0.870;A|0.130	0.130	strong		0.443	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	Missense_Mutation
PRB1	5542	hgsc.bcm.edu	37	12	11506288	11506288	+	Missense_Mutation	SNP	T	T	C	rs140825288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:11506288T>C	ENST00000500254.2	-	4	387	c.350A>G	c.(349-351)aAa>aGa	p.K117R	PRB1_ENST00000545626.1_Intron|PRB1_ENST00000546254.1_Missense_Mutation_p.K117R	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1	0	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-[PAQ]-Q-[GE]-[GD]- [NKS]-[KSQRN]-[PRQS]-[QS] [GPS]-[PQAR]- [PSR].		Missing (in allele M).|Missing (in clone CP-4).|Missing (in clone CP-5).			extracellular region (GO:0005576)		p.K117R(2)		NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			ACCTTGAGGTTTGTTGCCTCC	0.612													t|||	39	0.00778754	0.0106	0.0086	5008	,	,		16399	0.0079		0.0099	False		,,,				2504	0.001				p.K117R		Atlas-SNP	.											PRB1,NS,carcinoma,0,2	PRB1	33	2	2	Substitution - Missense(2)	prostate(1)|central_nervous_system(1)	c.A350G						scavenged	.						92.0	112.0	105.0					12																	11506288		2098	4245	6343	SO:0001583	missense	5542	exon4			TGAGGTTTGTTGC		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.350A>G	12.37:g.11506288T>C	ENSP00000420826:p.Lys117Arg	Somatic	173	4	0.0231214		WXS	Illumina HiSeq	Phase_I	452	15	0.0331858	NM_199353	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Missense_Mutation	SNP	ENST00000500254.2	37	CCDS8642.1	.	.	.	.	.	.	.	.	.	.	.	0.021	-1.431560	0.01108	.	.	ENSG00000251655	ENST00000500254;ENST00000546254	T;T	0.04119	3.7;3.7	1.29	-1.39	0.08997	.	.	.	.	.	T	0.03871	0.0109	L	0.39147	1.195	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.08055	0.002;0.003	T	0.44544	-0.9321	8	.	.	.	.	5.2744	0.15641	0.0:0.2701:0.0:0.7299	.	257;117	Q86YA1;G3V1M9	.;.	R	117	ENSP00000420826:K117R;ENSP00000442127:K117R	.	K	-	2	0	PRB1	11397555	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.188000	0.17018	-0.320000	0.08640	0.113000	0.15668	AAA	.	.	weak		0.612	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039	
SLC25A48	153328	hgsc.bcm.edu	37	5	135178142	135178142	+	Silent	SNP	A	A	G	rs6596270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:135178142A>G	ENST00000420621.1	+	2	256	c.84A>G	c.(82-84)acA>acG	p.T28T	SLC25A48_ENST00000412661.2_Silent_p.T28T|SLC25A48_ENST00000433282.2_5'UTR|SLC25A48_ENST00000425402.1_Silent_p.T28T|SLC25A48_ENST00000274513.5_Silent_p.T28T			Q6ZT89	S2548_HUMAN	solute carrier family 25, member 48	28					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						CTCTGGACACAGTCAAGGTAC	0.507													G|||	691	0.137979	0.208	0.1225	5008	,	,		17766	0.0099		0.2117	False		,,,				2504	0.1104				p.T28T		Atlas-SNP	.											.	SLC25A48	37	.	0			c.A84G						PASS	.	G		740,3508		73,594,1457	132.0	143.0	140.0		84	-1.4	1.0	5	dbSNP_116	140	1786,6722		184,1418,2652	no	coding-synonymous	SLC25A48	NM_145282.4		257,2012,4109	GG,GA,AA		20.992,17.42,19.8024		28/158	135178142	2526,10230	2124	4254	6378	SO:0001819	synonymous_variant	153328	exon2			GGACACAGTCAAG		CCDS43366.2	5q31.1	2013-05-22			ENSG00000145832	ENSG00000145832		"""Solute carriers"""	30451	protein-coding gene	gene with protein product	"""HCC-down-regulated mitochondrial carrier protein"""					15322095, 19303656	Standard	NM_145282		Approved	FLJ44862, HDMCP	uc003lba.3	Q6ZT89	OTTHUMG00000157007	ENST00000420621.1:c.84A>G	5.37:g.135178142A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_145282	Q8TAV9	Silent	SNP	ENST00000420621.1	37																																																																																				A|0.820;G|0.180	0.180	strong		0.507	SLC25A48-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_145282	
OR7A17	26333	hgsc.bcm.edu	37	19	14992031	14992031	+	Missense_Mutation	SNP	A	A	G	rs10405129	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14992031A>G	ENST00000327462.2	-	1	233	c.137T>C	c.(136-138)aTc>aCc	p.I46T		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	46			I -> T (in dbSNP:rs10405129).			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)					TGTGGCCAGGATGATGAGCAG	0.512													.|||	1668	0.333067	0.118	0.3098	5008	,	,		14451	0.6121		0.3161	False		,,,				2504	0.3701				p.I46T		Atlas-SNP	.											.	OR7A17	37	.	0			c.T137C						PASS	.	A	THR/ILE	761,3645	303.8+/-288.1	58,645,1500	63.0	54.0	57.0		137	2.7	1.0	19	dbSNP_119	57	2550,6040	408.0+/-349.4	379,1792,2124	yes	missense	OR7A17	NM_030901.1	89	437,2437,3624	GG,GA,AA		29.6857,17.2719,25.4771	possibly-damaging	46/310	14992031	3311,9685	2203	4295	6498	SO:0001583	missense	26333	exon1			GCCAGGATGATGA	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.137T>C	19.37:g.14992031A>G	ENSP00000328144:p.Ile46Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	72	27	0.375	NM_030901	Q6IFQ6|Q96R98	Missense_Mutation	SNP	ENST00000327462.2	37	CCDS12319.1	697	0.3191391941391941	44	0.08943089430894309	92	0.2541436464088398	328	0.5734265734265734	233	0.3073878627968338	a	15.41	2.826814	0.50739	0.172719	0.296857	ENSG00000185385	ENST00000327462	T	0.00640	6.03	2.66	2.66	0.31614	GPCR, rhodopsin-like superfamily (1);	0.196463	0.24599	U	0.037150	T	0.00012	0.0000	M	0.92367	3.3	0.43947	P	0.003390000000000004	P	0.38551	0.636	P	0.47102	0.537	T	0.12837	-1.0532	9	0.87932	D	0	.	5.9636	0.19313	0.7299:0.2701:0.0:0.0	rs10405129;rs35310775;rs10405129	46	O14581	OR7AH_HUMAN	T	46	ENSP00000328144:I46T	ENSP00000328144:I46T	I	-	2	0	OR7A17	14853031	0.159000	0.22864	1.000000	0.80357	0.881000	0.50899	4.413000	0.59795	1.499000	0.48617	0.324000	0.21423	ATC	A|0.747;G|0.253	0.253	strong		0.512	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
PNPLA2	57104	hgsc.bcm.edu	37	11	823809	823809	+	Silent	SNP	C	C	G	rs1135628	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:823809C>G	ENST00000336615.4	+	7	1075	c.873C>G	c.(871-873)ccC>ccG	p.P291P	AP006621.8_ENST00000532946.1_RNA|AP006621.8_ENST00000528982.1_RNA	NM_020376.3	NP_065109.1	Q96AD5	PLPL2_HUMAN	patatin-like phospholipase domain containing 2	291					acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of sequestering of triglyceride (GO:0010891)|phospholipid metabolic process (GO:0006644)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|lung(4)|prostate(1)|urinary_tract(1)	9		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.63e-25)|Epithelial(43;1.28e-24)|OV - Ovarian serous cystadenocarcinoma(40;7.09e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGCAGCTGCCCGGAGAAGATC	0.692													C|||	1338	0.267173	0.0809	0.1888	5008	,	,		11210	0.4127		0.2644	False		,,,				2504	0.4274				p.P291P		Atlas-SNP	.											.	PNPLA2	26	.	0			c.C873G						PASS	.	C		405,3963		28,349,1807	14.0	14.0	14.0		873	-4.6	0.0	11	dbSNP_86	14	2070,6504		260,1550,2477	no	coding-synonymous	PNPLA2	NM_020376.3		288,1899,4284	GG,GC,CC		24.1428,9.272,19.1238		291/505	823809	2475,10467	2184	4287	6471	SO:0001819	synonymous_variant	57104	exon7			GCTGCCCGGAGAA	AJ278475	CCDS7718.1	11p15.5	2014-03-14			ENSG00000177666	ENSG00000177666	3.1.1.3	"""Patatin-like phospholipase domain containing"""	30802	protein-coding gene	gene with protein product		609059				8619474, 16799181, 19029121	Standard	NM_020376		Approved	desnutrin, TTS-2.2, ATGL, FP17548, iPLA2zeta	uc001lrt.3	Q96AD5	OTTHUMG00000133309	ENST00000336615.4:c.873C>G	11.37:g.823809C>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_020376	O60643|Q5EFF5|Q6XYE5|Q96ET6|Q9NQ61|Q9NQ62	Silent	SNP	ENST00000336615.4	37	CCDS7718.1																																																																																			C|0.796;G|0.204	0.204	strong		0.692	PNPLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257106.1	NM_020376	
CRADD	8738	hgsc.bcm.edu	37	12	94243853	94243853	+	Silent	SNP	C	C	T	rs56944668	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	160	0	0		WXS	Illumina HiSeq	Phase_I	85	61	0.717647	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	
SMURF1	57154	hgsc.bcm.edu	37	7	98645367	98645367	+	Silent	SNP	C	C	T	rs559762342		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:98645367C>T	ENST00000361125.1	-	11	1489	c.1170G>A	c.(1168-1170)tcG>tcA	p.S390S	SMURF1_ENST00000361368.2_Silent_p.S364S|AC004893.11_ENST00000468960.2_RNA|AC004893.11_ENST00000482799.2_RNA	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	390					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			GCTGCTGAAGCGACAGTTCGT	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		18698	0.0		0.0	False		,,,				2504	0.001				p.S390S		Atlas-SNP	.											SMURF1,NS,carcinoma,0,1	SMURF1	58	1	0			c.G1170A						scavenged	.						128.0	123.0	125.0					7																	98645367		2203	4300	6503	SO:0001819	synonymous_variant	57154	exon11			CTGAAGCGACAGT	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.1170G>A	7.37:g.98645367C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	163	3	0.0184049	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Silent	SNP	ENST00000361125.1	37	CCDS34690.1																																																																																			.	.	none		0.542	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
GIPC1	10755	hgsc.bcm.edu	37	19	14590279	14590279	+	Missense_Mutation	SNP	G	G	C	rs45458894	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14590279G>C	ENST00000393033.4	-	7	982	c.713C>G	c.(712-714)aCt>aGt	p.T238S	GIPC1_ENST00000393028.1_Missense_Mutation_p.T141S|GIPC1_ENST00000393029.3_Missense_Mutation_p.T141S|GIPC1_ENST00000586027.1_Missense_Mutation_p.T238S|GIPC1_ENST00000591349.1_Missense_Mutation_p.T141S|GIPC1_ENST00000345425.2_Missense_Mutation_p.T238S	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	238					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						CCCTCGGCCAGTGCCCAGTTG	0.672													G|||	370	0.0738818	0.1067	0.1138	5008	,	,		12295	0.005		0.0805	False		,,,				2504	0.0654				p.T238S	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											.	GIPC1	21	.	0			c.C713G						PASS	.	G	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	429,3921		21,387,1767	10.0	11.0	11.0		713,422,713,422,713,422	4.3	1.0	19	dbSNP_127	11	542,7996		12,518,3739	no	missense,missense,missense,missense,missense,missense	GIPC1	NM_005716.2,NM_202467.1,NM_202468.1,NM_202469.1,NM_202470.1,NM_202494.1	58,58,58,58,58,58	33,905,5506	CC,CG,GG		6.3481,9.8621,7.5341	benign,benign,benign,benign,benign,benign	238/334,141/237,238/334,141/237,238/334,141/237	14590279	971,11917	2175	4269	6444	SO:0001583	missense	10755	exon6			CGGCCAGTGCCCA	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.713C>G	19.37:g.14590279G>C	ENSP00000376753:p.Thr238Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Missense_Mutation	SNP	ENST00000393033.4	37	CCDS12310.1	172	0.07875457875457875	54	0.10975609756097561	52	0.143646408839779	0	0.0	66	0.0870712401055409	G	8.377	0.836601	0.16891	0.098621	0.063481	ENSG00000123159	ENST00000393033;ENST00000345425;ENST00000393029;ENST00000393028;ENST00000351277	T;T;D;D	0.84944	-1.37;-1.37;-1.92;-1.92	4.3	4.3	0.51218	.	0.058205	0.64402	D	0.000002	T	0.01156	0.0038	N	0.13352	0.335	0.09310	P	0.99999010649	B	0.11235	0.004	B	0.12156	0.007	T	0.40308	-0.9570	9	0.02654	T	1	-8.2812	14.2592	0.66073	0.0:0.0:1.0:0.0	rs45458894;rs61731621	238	O14908	GIPC1_HUMAN	S	238;238;141;141;238	ENSP00000376753:T238S;ENSP00000340698:T238S;ENSP00000376749:T141S;ENSP00000376748:T141S	ENSP00000340698:T238S	T	-	2	0	GIPC1	14451279	0.998000	0.40836	1.000000	0.80357	0.871000	0.50021	2.615000	0.46368	1.961000	0.56991	0.561000	0.74099	ACT	G|0.904;C|0.096	0.096	strong		0.672	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		
NAV2	89797	hgsc.bcm.edu	37	11	20089944	20089944	+	Splice_Site	SNP	T	T	C	rs1442710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:20089944T>C	ENST00000396087.3	+	24	5250	c.5151T>C	c.(5149-5151)aaT>aaC	p.N1717N	NAV2_ENST00000360655.4_Splice_Site_p.N1597N|NAV2_ENST00000396085.1_Splice_Site_p.N1661N|NAV2_ENST00000527559.2_Splice_Site_p.N1646N|NAV2_ENST00000349880.4_Splice_Site_p.N1661N|NAV2_ENST00000540292.1_Splice_Site_p.N1648N|NAV2_ENST00000311043.8_Splice_Site_p.N725N|NAV2_ENST00000533917.1_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	89	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	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
TMEM259	91304	hgsc.bcm.edu	37	19	1010406	1010406	+	Silent	SNP	G	G	A	rs62131162	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	16	0	0		WXS	Illumina HiSeq	Phase_I	14	11	0.785714	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	
LARS	51520	hgsc.bcm.edu	37	5	145523105	145523105	+	Silent	SNP	G	G	A	rs11540217	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145523105G>A	ENST00000394434.2	-	19	1913	c.1747C>T	c.(1747-1749)Ctg>Ttg	p.L583L	LARS_ENST00000274562.9_Silent_p.L556L|LARS_ENST00000510191.1_Silent_p.L529L|LARS_ENST00000545646.1_Silent_p.L537L	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	56	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	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	
SSPO	23145	hgsc.bcm.edu	37	7	149519184	149519184	+	RNA	SNP	C	C	T	rs1008336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149519184C>T	ENST00000378016.2	+	0	12988							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)			CCTGGCCTCTCGCTCTGGGTC	0.726													C|||	893	0.178315	0.1581	0.196	5008	,	,		13745	0.1736		0.1561	False		,,,				2504	0.2209				p.R4330C		Atlas-SNP	.											.	.	.	.	0			c.C12988T						PASS	.	C		567,3237		42,483,1377	25.0	27.0	26.0		13002	3.6	1.0	7	dbSNP_86	26	1371,6847		107,1157,2845	no	coding-notMod3	SSPO	NM_198455.2		149,1640,4222	TT,TC,CC		16.6829,14.9054,16.1204			149519184	1938,10084	1902	4109	6011			23145	exon90			GCCTCTCGCTCTG	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.149519184C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	15	4	0.266667	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.831;T|0.169	0.169	strong		0.726	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
PLXNB2	23654	hgsc.bcm.edu	37	22	50722167	50722167	+	Missense_Mutation	SNP	T	T	C	rs28470336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50722167T>C	ENST00000449103.1	-	15	2574	c.2434A>G	c.(2434-2436)Acg>Gcg	p.T812A	PLXNB2_ENST00000359337.4_Missense_Mutation_p.T812A|PLXNB2_ENST00000496720.1_5'UTR			O15031	PLXB2_HUMAN	plexin B2	812	IPT/TIG 1.				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)		AGGGGGCCCGTCTCAGGCTGG	0.657													T|||	94	0.01877	0.0053	0.0288	5008	,	,		9866	0.0		0.0457	False		,,,				2504	0.0215				p.T812A		Atlas-SNP	.											.	PLXNB2	172	.	0			c.A2434G						PASS	.	T	ALA/THR	21,3845		0,21,1912	26.0	30.0	29.0		2434	4.2	1.0	22	dbSNP_125	29	465,7793		12,441,3676	yes	missense	PLXNB2	NM_012401.3	58	12,462,5588	CC,CT,TT		5.6309,0.5432,4.0086	possibly-damaging	812/1839	50722167	486,11638	1933	4129	6062	SO:0001583	missense	23654	exon15			GGCCCGTCTCAGG		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.2434A>G	22.37:g.50722167T>C	ENSP00000409171:p.Thr812Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	43	0.632353	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	53	0.024267399267399268	3	0.006097560975609756	9	0.024861878453038673	4	0.006993006993006993	37	0.048812664907651716	T	11.16	1.555922	0.27827	0.005432	0.056309	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.77877	-1.13;-1.13	4.22	4.22	0.49857	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.115149	0.38605	N	0.001639	T	0.20007	0.0481	L	0.41492	1.28	0.09310	N	1	B	0.17852	0.024	B	0.23150	0.044	T	0.37337	-0.9710	10	0.44086	T	0.13	.	7.017	0.24892	0.2026:0.0:0.0:0.7974	rs28470336	812	O15031	PLXB2_HUMAN	A	812	ENSP00000409171:T812A;ENSP00000352288:T812A	ENSP00000352288:T812A	T	-	1	0	PLXNB2	49064294	0.000000	0.05858	0.978000	0.43139	0.451000	0.32288	0.424000	0.21330	1.780000	0.52325	0.397000	0.26171	ACG	T|0.968;C|0.032	0.032	strong		0.657	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
WDR33	55339	hgsc.bcm.edu	37	2	128464116	128464116	+	Silent	SNP	G	G	A	rs34550770	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:128464116G>A	ENST00000322313.4	-	22	3950	c.3792C>T	c.(3790-3792)ggC>ggT	p.G1264G		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	1264					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		CAGGTCCTGGGCCCCCTCGGC	0.493													G|||	191	0.038139	0.0053	0.0519	5008	,	,		18704	0.0		0.1143	False		,,,				2504	0.0337				p.G1264G		Atlas-SNP	.											.	WDR33	136	.	0			c.C3792T						PASS	.	G		89,4317	75.2+/-113.4	0,89,2114	47.0	51.0	50.0		3792	4.2	1.0	2	dbSNP_126	50	802,7798	186.7+/-234.1	45,712,3543	no	coding-synonymous	WDR33	NM_018383.4		45,801,5657	AA,AG,GG		9.3256,2.02,6.8507		1264/1337	128464116	891,12115	2203	4300	6503	SO:0001819	synonymous_variant	55339	exon22			TCCTGGGCCCCCT		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.3792C>T	2.37:g.128464116G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_018383	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	37	CCDS2150.1																																																																																			G|0.935;A|0.065	0.065	strong		0.493	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
RTP4	64108	hgsc.bcm.edu	37	3	187088812	187088812	+	Missense_Mutation	SNP	C	C	T	rs3821812	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	167	76	0.45509	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	
FAM205A	259308	hgsc.bcm.edu	37	9	34726182	34726182	+	Missense_Mutation	SNP	A	A	G	rs521630	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34726182A>G	ENST00000378788.3	-	4	1094	c.1055T>C	c.(1054-1056)tTt>tCt	p.F352S		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	352				F -> S (in Ref. 1; BAC86357). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						AATGGTCTCAAATCTATGAAG	0.478													A|||	2384	0.476038	0.3873	0.4035	5008	,	,		12504	0.5188		0.4612	False		,,,				2504	0.6186				p.F352S		Atlas-SNP	.											.	FAM205A	45	.	0			c.T1055C						PASS	.						46.0	40.0	42.0					9																	34726182		645	1214	1859	SO:0001583	missense	259308	exon4			GTCTCAAATCTAT		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.1055T>C	9.37:g.34726182A>G	ENSP00000417711:p.Phe352Ser	Somatic	554	1	0.00180505		WXS	Illumina HiSeq	Phase_I	265	262	0.988679	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	702	0.32142857142857145	129	0.2621951219512195	116	0.32044198895027626	174	0.3041958041958042	283	0.3733509234828496	A	7.626	0.677781	0.14841	.	.	ENSG00000205108	ENST00000378788	T	0.22336	1.96	3.94	-0.148	0.13424	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.34241	0.444	B	0.29077	0.098	T	0.48186	-0.9057	8	0.32370	T	0.25	.	3.7282	0.08482	0.5927:0.1901:0.2171:0.0	rs521630	352	Q6ZU69	F205A_HUMAN	S	352	ENSP00000417711:F352S	ENSP00000417711:F352S	F	-	2	0	RP11-195F19.10	34716182	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.606000	0.05654	-0.118000	0.11851	0.454000	0.30748	TTT	.	.	weak		0.478	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
ABCA1	19	hgsc.bcm.edu	37	9	107620867	107620867	+	Missense_Mutation	SNP	C	C	T	rs2230806	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:107620867C>T	ENST00000374736.3	-	7	1050	c.656G>A	c.(655-657)aGg>aAg	p.R219K	ABCA1_ENST00000423487.2_Missense_Mutation_p.R219K	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	219			R -> K (common polymorphism; associated with a decreased severity of CAD; dbSNP:rs2230806). {ECO:0000269|PubMed:10938021, ECO:0000269|PubMed:11238261, ECO:0000269|PubMed:11257261, ECO:0000269|PubMed:11476965, ECO:0000269|PubMed:12624133, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:15520867}.		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)	p.R219K(1)		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)	CAGTTTCTCCCTTGGTAGGCC	0.468													C|||	2202	0.439696	0.7103	0.3487	5008	,	,		19674	0.4147		0.2425	False		,,,				2504	0.3671				p.R219K		Atlas-SNP	.											ABCA1,NS,carcinoma,0,1	ABCA1	244	1	1	Substitution - Missense(1)	stomach(1)	c.G656A	GRCh37	CM030397	ABCA1	M	rs2230806	PASS	.	C	LYS/ARG	2672,1734	648.2+/-398.7	820,1032,351	154.0	151.0	152.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	656	0.1	0.2	9	dbSNP_98	152	2420,6180	400.1+/-346.7	322,1776,2202	yes	missense	ABCA1	NM_005502.3	26	1142,2808,2553	TT,TC,CC		28.1395,39.3554,39.1512	benign	219/2262	107620867	5092,7914	2203	4300	6503	SO:0001583	missense	19	exon7			TTCTCCCTTGGTA	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.656G>A	9.37:g.107620867C>T	ENSP00000363868:p.Arg219Lys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	169	65	0.384615	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	916	0.4194139194139194	356	0.7235772357723578	127	0.35082872928176795	250	0.4370629370629371	183	0.24142480211081793	C	7.792	0.711767	0.15306	0.606446	0.281395	ENSG00000165029	ENST00000374736;ENST00000423487	D;D	0.94931	-2.23;-3.56	6.17	0.0573	0.14322	.	0.632115	0.18950	N	0.126712	T	0.00012	0.0000	N	0.04880	-0.145	0.28835	P	0.896936	B	0.02656	0.0	B	0.01281	0.0	T	0.46119	-0.9214	9	0.16896	T	0.51	.	8.2419	0.31665	0.0:0.3764:0.0:0.6236	rs2230806;rs2234884;rs2853572;rs52801000;rs61696010;rs2230806	219	O95477	ABCA1_HUMAN	K	219	ENSP00000363868:R219K;ENSP00000416623:R219K	ENSP00000363868:R219K	R	-	2	0	ABCA1	106660688	0.825000	0.29262	0.227000	0.23927	0.534000	0.34807	0.318000	0.19504	0.083000	0.17047	0.655000	0.94253	AGG	C|0.587;T|0.413	0.413	strong		0.468	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
KCNH6	81033	hgsc.bcm.edu	37	17	61607708	61607708	+	Silent	SNP	T	T	C	rs7221517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:61607708T>C	ENST00000583023.1	+	4	491	c.480T>C	c.(478-480)caT>caC	p.H160H	KCNH6_ENST00000456941.2_Silent_p.H160H|KCNH6_ENST00000581784.1_Silent_p.H160H|KCNH6_ENST00000314672.5_Silent_p.H160H|KCNH6_ENST00000580652.1_Silent_p.H160H	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	160					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)	AGGGCTCTCATGGCAGGCCAG	0.642													C|||	1439	0.28734	0.27	0.3141	5008	,	,		17600	0.2252		0.3797	False		,,,				2504	0.2607				p.H160H		Atlas-SNP	.											.	KCNH6	122	.	0			c.T480C						PASS	.	C	,	1337,3069	690.5+/-405.3	181,975,1047	84.0	73.0	77.0		480,480	-9.4	0.0	17	dbSNP_116	77	3044,5556	659.9+/-401.7	586,1872,1842	no	coding-synonymous,coding-synonymous	KCNH6	NM_030779.2,NM_173092.1	,	767,2847,2889	CC,CT,TT		35.3953,30.345,33.6845	,	160/995,160/906	61607708	4381,8625	2203	4300	6503	SO:0001819	synonymous_variant	81033	exon4			CTCTCATGGCAGG	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.480T>C	17.37:g.61607708T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_030779	Q9BRD7	Silent	SNP	ENST00000583023.1	37	CCDS11638.1																																																																																			T|0.671;C|0.329	0.329	strong		0.642	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
CCDC185	164127	hgsc.bcm.edu	37	1	223567803	223567803	+	Missense_Mutation	SNP	G	G	A	rs10907376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:223567803G>A	ENST00000366875.3	+	1	1089	c.986G>A	c.(985-987)gGc>gAc	p.G329D		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		329			G -> D (in dbSNP:rs10907376). {ECO:0000269|PubMed:15489334}.							breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		GAGCAGCGCGGCCTGCGGCGG	0.697													G|||	881	0.175919	0.1831	0.1916	5008	,	,		14025	0.1101		0.2734	False		,,,				2504	0.1227				p.G329D		Atlas-SNP	.											C1orf65,NS,carcinoma,0,4	C1orf65	71	4	0			c.G986A						PASS	.	G	ASP/GLY	834,3424		100,634,1395	11.0	10.0	11.0		986	-0.7	0.0	1	dbSNP_120	11	2191,6245		296,1599,2323	no	missense	C1orf65	NM_152610.2	94	396,2233,3718	AA,AG,GG		25.972,19.5867,23.8302	probably-damaging	329/624	223567803	3025,9669	2129	4218	6347	SO:0001583	missense	164127	exon1			AGCGCGGCCTGCG																												ENST00000366875.3:c.986G>A	1.37:g.223567803G>A	ENSP00000355840:p.Gly329Asp	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	147	58	0.394558	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	448	0.20512820512820512	88	0.17886178861788618	86	0.23756906077348067	72	0.1258741258741259	202	0.26649076517150394	G	5.552	0.286677	0.10513	0.195867	0.25972	ENSG00000178395	ENST00000366875	T	0.23147	1.92	4.71	-0.728	0.11162	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.29432	0.244	B	0.24848	0.056	T	0.42292	-0.9460	8	0.17369	T	0.5	.	1.5099	0.02494	0.1275:0.3469:0.209:0.3166	rs10907376;rs17481328;rs17852895;rs17858889;rs58442298;rs10907376	329	Q8N715	CA065_HUMAN	D	329	ENSP00000355840:G329D	ENSP00000355840:G329D	G	+	2	0	C1orf65	221634426	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-0.021000	0.12504	-0.055000	0.13244	0.650000	0.86243	GGC	G|0.814;A|0.186	0.186	strong		0.697	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
XRCC4	7518	hgsc.bcm.edu	37	5	82648943	82648943	+	Splice_Site	SNP	G	G	A	rs1805377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:82648943G>A	ENST00000511817.1	+	8	973		c.e8-1		XRCC4_ENST00000396027.4_Intron|XRCC4_ENST00000282268.3_Intron|XRCC4_ENST00000338635.6_Splice_Site			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4						cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		TTTCTTTTCAGTTCTAGGCCT	0.343								Non-homologous end-joining					A|||	1879	0.3752	0.4758	0.3329	5008	,	,		16220	0.7044		0.1402	False		,,,				2504	0.1718				.		Atlas-SNP	.											.	XRCC4	37	.	0			c.894-1G>A	GRCh37	CS075240	XRCC4	S	rs1805377	PASS	.	A	,,	1933,2469	591.6+/-387.6	422,1089,690	76.0	86.0	82.0		,,	-0.1	0.7	5	dbSNP_92	82	1052,7548	764.1+/-407.6	64,924,3312	yes	intron,splice-3,intron	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	,,	486,2013,4002	AA,AG,GG		12.2326,43.9119,22.958	,,	,,	82648943	2985,10017	2201	4300	6501	SO:0001630	splice_region_variant	7518	exon8			TTTTCAGTTCTAG	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.894-1G>A	5.37:g.82648943G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	164	73	0.445122	NM_022406	A8K3X4|Q9BS72|Q9UP94	Splice_Site	SNP	ENST00000511817.1	37	CCDS4059.1	858	0.39285714285714285	239	0.48577235772357724	115	0.31767955801104975	394	0.6888111888111889	110	0.14511873350923482	A	0.718	-0.784496	0.02907	0.439119	0.122326	ENSG00000152422	ENST00000338635;ENST00000511817;ENST00000514538	.	.	.	5.51	-0.0652	0.13769	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3151	0.07030	0.3839:0.0:0.2655:0.3506	rs1805377;rs3777014;rs61086000;rs1805377	.	.	.	.	-1	.	.	.	+	.	.	XRCC4	82684699	0.003000	0.15002	0.723000	0.30687	0.002000	0.02628	-0.958000	0.03857	-0.153000	0.11137	-2.023000	0.00429	.	G|0.679;A|0.321	0.321	strong		0.343	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	Intron
SYT14	255928	hgsc.bcm.edu	37	1	210334081	210334081	+	Silent	SNP	T	T	C	rs17188183	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:210334081T>C	ENST00000472886.1	+	8	1376	c.1362T>C	c.(1360-1362)taT>taC	p.Y454Y	SYT14_ENST00000399639.2_3'UTR|SYT14_ENST00000422431.1_Silent_p.Y518Y|SYT14_ENST00000534859.1_Silent_p.Y480Y|SYT14_ENST00000537238.1_Silent_p.Y416Y|SYT14_ENST00000367019.1_Silent_p.Y473Y|SYT14_ENST00000367015.1_Silent_p.Y416Y|SYT14_ENST00000271745.7_3'UTR			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	454	C2 2. {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)		TAGATACATATGTTAAGTTAA	0.318													T|||	377	0.0752796	0.0121	0.0677	5008	,	,		17664	0.0486		0.1402	False		,,,				2504	0.1268				p.Y518Y		Atlas-SNP	.											.	SYT14	89	.	0			c.T1554C						PASS	.	T	,,,	117,4289	86.3+/-125.0	3,111,2089	76.0	76.0	76.0		1554,1419,1497,1362	4.7	1.0	1	dbSNP_123	76	1169,7431	237.2+/-269.1	83,1003,3214	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYT14	NM_001146261.1,NM_001146262.1,NM_001146264.1,NM_153262.2	,,,	86,1114,5303	CC,CT,TT		13.593,2.6555,9.8877	,,,	518/620,473/575,499/601,454/556	210334081	1286,11720	2203	4300	6503	SO:0001819	synonymous_variant	255928	exon10			TACATATGTTAAG	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.1362T>C	1.37:g.210334081T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	53	0.401515	NM_001146261	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Silent	SNP	ENST00000472886.1	37	CCDS31014.1																																																																																			T|0.914;C|0.086	0.086	strong		0.318	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912002	45912002	+	Missense_Mutation	SNP	A	A	C	rs735482	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45912002A>C	ENST00000309424.3	+	3	1264	c.776A>C	c.(775-777)aAa>aCa	p.K259T	CD3EAP_ENST00000589804.1_Missense_Mutation_p.K261T|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000423698.2_3'UTR|ERCC1_ENST00000588738.1_5'Flank	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	259			K -> T (in dbSNP:rs735482).		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)		CCCAAAGGGAAAGAAACCTTC	0.547													C|||	1436	0.286741	0.3109	0.2233	5008	,	,		15739	0.4613		0.1322	False		,,,				2504	0.2781				p.K259T		Atlas-SNP	.											.	CD3EAP	27	.	0			c.A776C						PASS	.	C	,,THR/LYS	1193,3213	689.1+/-405.1	169,855,1179	67.0	70.0	69.0		,,776	-1.8	0.0	19	dbSNP_86	69	1160,7440	741.9+/-407.2	81,998,3221	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,78	250,1853,4400	CC,CA,AA		13.4884,27.0767,18.0917	,,benign	,,259/511	45912002	2353,10653	2203	4300	6503	SO:0001583	missense	10849	exon3			AAGGGAAAGAAAC	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.776A>C	19.37:g.45912002A>C	ENSP00000310966:p.Lys259Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	570	0.260989010989011	131	0.266260162601626	72	0.19889502762430938	259	0.4527972027972028	108	0.1424802110817942	C	8.088	0.773935	0.16051	0.270767	0.134884	ENSG00000117877	ENST00000309424	T	0.11495	2.77	5.06	-1.76	0.08006	.	0.717583	0.12315	N	0.479769	T	0.00012	0.0000	N	0.00621	-1.32	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42749	-0.9433	9	0.14656	T	0.56	0.2029	1.8433	0.03154	0.1195:0.3621:0.259:0.2595	rs735482;rs61340218;rs735482	261;259	O15446-2;O15446	.;RPA34_HUMAN	T	259	ENSP00000310966:K259T	ENSP00000310966:K259T	K	+	2	0	CD3EAP	50603842	0.006000	0.16342	0.007000	0.13788	0.245000	0.25701	0.192000	0.17096	-0.095000	0.12351	-0.217000	0.12591	AAA	A|0.771;C|0.229	0.229	strong		0.547	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
OR4D2	124538	hgsc.bcm.edu	37	17	56247454	56247454	+	Silent	SNP	A	A	G	rs9912728	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:56247454A>G	ENST00000545221.1	+	1	438	c.438A>G	c.(436-438)gtA>gtG	p.V146V		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	146						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						GGCTGGTGGTAGCCACCTGGG	0.572													G|||	460	0.091853	0.1483	0.0375	5008	,	,		18401	0.002		0.1153	False		,,,				2504	0.1227				p.V146V		Atlas-SNP	.											.	OR4D2	48	.	0			c.A438G						PASS	.	G		605,3801	769.3+/-413.7	45,515,1643	95.0	93.0	94.0		438	4.7	0.7	17	dbSNP_119	94	967,7633	774.7+/-407.7	53,861,3386	no	coding-synonymous	OR4D2	NM_001004707.3		98,1376,5029	GG,GA,AA		11.2442,13.7313,12.0867		146/308	56247454	1572,11434	2203	4300	6503	SO:0001819	synonymous_variant	124538	exon1			GGTGGTAGCCACC		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.438A>G	17.37:g.56247454A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_001004707	Q6IFN8|Q96R75	Silent	SNP	ENST00000545221.1	37	CCDS32688.1																																																																																			A|0.890;G|0.110	0.110	strong		0.572	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1		
OR6P1	128366	hgsc.bcm.edu	37	1	158533140	158533140	+	Silent	SNP	A	A	G	rs12080815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158533140A>G	ENST00000334632.1	-	1	254	c.255T>C	c.(253-255)ttT>ttC	p.F85F		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	85						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(4)|lung(1)	6						CCTGGGTAAGAAAGGCTGCCA	0.483													A|||	2524	0.503994	0.5794	0.4135	5008	,	,		21013	0.5863		0.4732	False		,,,				2504	0.4131				p.F85F		Atlas-SNP	.											OR6P1,NS,carcinoma,0,1	OR6P1	47	1	0			c.T255C						PASS	.	A		785,599		208,369,115	63.0	54.0	57.0		255	1.4	0.9	1	dbSNP_120	57	1454,1728		346,762,483	no	coding-synonymous	OR6P1	NM_001160325.1		554,1131,598	GG,GA,AA		45.6945,43.2803,49.0364		85/318	158533140	2239,2327	692	1591	2283	SO:0001819	synonymous_variant	128366	exon1			GGTAAGAAAGGCT	BK004193	CCDS53391.1	1q23.1	2012-08-09			ENSG00000186440	ENSG00000186440		"""GPCR / Class A : Olfactory receptors"""	15036	protein-coding gene	gene with protein product							Standard	NM_001160325		Approved		uc010pim.2	Q8NGX9	OTTHUMG00000019633	ENST00000334632.1:c.255T>C	1.37:g.158533140A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	60	0.618557	NM_001160325	Q6IFR9	Silent	SNP	ENST00000334632.1	37	CCDS53391.1																																																																																			A|0.465;G|0.535	0.535	strong		0.483	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
FAM179B	23116	hgsc.bcm.edu	37	14	45481271	45481271	+	Silent	SNP	C	C	T	rs144530053	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:45481271C>T	ENST00000361577.3	+	7	3445	c.3231C>T	c.(3229-3231)ccC>ccT	p.P1077P	FAM179B_ENST00000382233.2_3'UTR|FAM179B_ENST00000361462.2_Silent_p.P1077P|KLHL28_ENST00000553817.1_Intron	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1077	Ser-rich.									endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						AACAAAGCCCCAGTGCAGGTA	0.308													C|||	17	0.00339457	0.0008	0.0086	5008	,	,		15361	0.0		0.0099	False		,,,				2504	0.0				p.P1077P		Atlas-SNP	.											.	FAM179B	115	.	0			c.C3231T						PASS	.	C		10,4388	15.5+/-35.6	0,10,2189	39.0	41.0	41.0		3231	5.0	0.0	14	dbSNP_134	41	163,8435	75.4+/-138.0	1,161,4137	no	coding-synonymous	FAM179B	NM_015091.2		1,171,6326	TT,TC,CC		1.8958,0.2274,1.3312		1077/1721	45481271	173,12823	2199	4299	6498	SO:0001819	synonymous_variant	23116	exon7			AAGCCCCAGTGCA	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.3231C>T	14.37:g.45481271C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	170	107	0.629412	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	37	CCDS9681.1																																																																																			C|0.990;T|0.010	0.010	strong		0.308	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	
OR2G3	81469	hgsc.bcm.edu	37	1	247769062	247769062	+	Missense_Mutation	SNP	A	A	G	rs61748963	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247769062A>G	ENST00000320002.2	+	1	207	c.175A>G	c.(175-177)Atg>Gtg	p.M59V	RNU6-691P_ENST00000516585.1_RNA|RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	59						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)			TCATACCCCAATGTACTTTTT	0.423													A|||	288	0.057508	0.0053	0.0994	5008	,	,		21406	0.005		0.1083	False		,,,				2504	0.1002				p.M59V		Atlas-SNP	.											OR2G3,NS,carcinoma,-2,2	OR2G3	108	2	0			c.A175G						PASS	.	A	VAL/MET	109,4297	83.9+/-122.4	1,107,2095	268.0	260.0	263.0		175	3.8	0.8	1	dbSNP_129	263	1048,7552	223.0+/-259.9	74,900,3326	yes	missense	OR2G3	NM_001001914.1	21	75,1007,5421	GG,GA,AA		12.186,2.4739,8.8959	probably-damaging	59/310	247769062	1157,11849	2203	4300	6503	SO:0001583	missense	81469	exon1			ACCCCAATGTACT	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.175A>G	1.37:g.247769062A>G	ENSP00000326301:p.Met59Val	Somatic	459	1	0.00217865		WXS	Illumina HiSeq	Phase_I	560	346	0.617857	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Missense_Mutation	SNP	ENST00000320002.2	37	CCDS31093.1	134	0.06135531135531135	3	0.006097560975609756	46	0.1270718232044199	2	0.0034965034965034965	83	0.10949868073878628	A	9.626	1.135224	0.21123	0.024739	0.12186	ENSG00000177476	ENST00000320002	T	0.09350	2.99	3.79	3.79	0.43588	GPCR, rhodopsin-like superfamily (1);	0.149295	0.29572	U	0.011778	T	0.00271	0.0008	H	0.95917	3.74	0.38059	P	0.06399999999999995	B	0.24963	0.115	B	0.29077	0.098	T	0.06734	-1.0810	9	0.87932	D	0	.	10.8362	0.46688	1.0:0.0:0.0:0.0	rs61748963	59	Q8NGZ4	OR2G3_HUMAN	V	59	ENSP00000326301:M59V	ENSP00000326301:M59V	M	+	1	0	OR2G3	245835685	1.000000	0.71417	0.785000	0.31869	0.054000	0.15201	7.298000	0.78815	1.719000	0.51432	0.398000	0.26397	ATG	A|0.914;G|0.086	0.086	strong		0.423	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1		
MRGPRX4	117196	hgsc.bcm.edu	37	11	18195448	18195448	+	Silent	SNP	C	C	T	rs4630269	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18195448C>T	ENST00000314254.3	+	1	1065	c.645C>T	c.(643-645)taC>taT	p.Y215Y	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CCAGGCTGTACGTGACCATCC	0.552													C|||	1653	0.330072	0.2542	0.3415	5008	,	,		20894	0.4415		0.3032	False		,,,				2504	0.3374				p.Y215Y		Atlas-SNP	.											MRGPRX4,NS,adenoma,0,1	MRGPRX4	68	1	0			c.C645T						scavenged	.	C		1077,3321	389.8+/-327.4	131,815,1253	112.0	102.0	105.0		645	-4.1	0.0	11	dbSNP_111	105	2447,6139	404.8+/-348.3	336,1775,2182	no	coding-synonymous	MRGPRX4	NM_054032.3		467,2590,3435	TT,TC,CC		28.4999,24.4884,27.1411		215/323	18195448	3524,9460	2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			GCTGTACGTGACC	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.645C>T	11.37:g.18195448C>T		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	37	CCDS7831.1																																																																																			C|0.710;T|0.290	0.290	strong		0.552	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
DOCK11	139818	hgsc.bcm.edu	37	X	117722176	117722176	+	Silent	SNP	G	G	A	rs41312765	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:117722176G>A	ENST00000276202.7	+	17	1935	c.1872G>A	c.(1870-1872)gaG>gaA	p.E624E	DOCK11_ENST00000276204.6_Silent_p.E624E	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	624					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						AGGTTGAAGAGTTTGTTCCAG	0.328													G|||	283	0.0749669	0.0053	0.0548	3775	,	,		13491	0.005		0.1163	False		,,,				2504	0.1186				p.E624E		Atlas-SNP	.											.	DOCK11	185	.	0			c.G1872A						PASS	.	G		86,3745		1,68,16,1561,555	92.0	87.0	89.0		1872	4.0	1.0	X	dbSNP_127	89	876,5851		36,546,258,1846,1613	no	coding-synonymous	DOCK11	NM_144658.3		37,614,274,3407,2168	AA,AG,A,GG,G		13.0221,2.2448,9.1116		624/2074	117722176	962,9596	2201	4299	6500	SO:0001819	synonymous_variant	139818	exon17			TGAAGAGTTTGTT	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.1872G>A	X.37:g.117722176G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			G|0.917;A|0.083	0.083	strong		0.328	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
KIAA0754	643314	hgsc.bcm.edu	37	1	39879410	39879410	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879410C>T	ENST00000530275.1	+	1	3260	c.3065C>T	c.(3064-3066)tCc>tTc	p.S1022F	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1022	Ala-rich.									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)			GAATCCGCCTCCGCAGCTGTT	0.687																																					p.S1158F		Atlas-SNP	.											KIAA0754_ENST00000530275,NS,carcinoma,-1,2	KIAA0754	93	2	0			c.C3473T						scavenged	.						18.0	22.0	21.0					1																	39879410		1946	4130	6076	SO:0001583	missense	643314	exon1			CCGCCTCCGCAGC			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.3065C>T	1.37:g.39879410C>T	ENSP00000431179:p.Ser1022Phe	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	58	9	0.155172	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	N	12.12	1.842527	0.32606	.	.	ENSG00000255103	ENST00000530275	T	0.24350	1.86	4.0	2.07	0.26955	.	.	.	.	.	T	0.15522	0.0374	N	0.08118	0	0.09310	N	1	P	0.42203	0.773	P	0.44422	0.449	T	0.11299	-1.0593	9	0.72032	D	0.01	.	6.6382	0.22895	0.1876:0.5829:0.2295:0.0	.	1022	O94854	K0754_HUMAN	F	1022	ENSP00000431179:S1022F	ENSP00000431179:S1022F	S	+	2	0	RP4-562N20.1	39651997	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.547000	0.02186	0.468000	0.27243	0.391000	0.25812	TCC	.	.	none		0.687	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
SSPO	23145	hgsc.bcm.edu	37	7	149516881	149516881	+	RNA	SNP	G	G	T	rs1005603	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149516881G>T	ENST00000378016.2	+	0	12083							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)			TCCCTGAGAAGCCGCAGCTGC	0.672													G|||	1041	0.207867	0.2708	0.2003	5008	,	,		14695	0.1746		0.1551	False		,,,				2504	0.2168				p.S4028I		Atlas-SNP	.											.	.	.	.	0			c.G12083T						PASS	.	G		752,2948		88,576,1186	11.0	16.0	14.0		12097	3.1	1.0	7	dbSNP_86	14	1258,6762		91,1076,2843	yes	coding-notMod3	SSPO	NM_198455.2		179,1652,4029	TT,TG,GG		15.6858,20.3243,17.1502			149516881	2010,9710	1850	4010	5860			23145	exon85			TGAGAAGCCGCAG	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.149516881G>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	58	17	0.293103	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.799;T|0.201	0.201	strong		0.672	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
TAP2	6891	hgsc.bcm.edu	37	6	32798548	32798548	+	Silent	SNP	G	G	A	rs1042116	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32798548G>A	ENST00000452392.2	-	8	1481	c.1308C>T	c.(1306-1308)aaC>aaT	p.N436N	TAP2_ENST00000374897.2_Silent_p.N436N|TAP2_ENST00000374899.4_Silent_p.N436N|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)	CAGCTCCCACGTTGCTGAGCA	0.522													G|||	214	0.0427316	0.0068	0.0634	5008	,	,		18305	0.0188		0.1183	False		,,,				2504	0.0235				p.N436N		Atlas-SNP	.											.	TAP2	98	.	0			c.C1308T						PASS	.	G	,	90,2932		0,90,1421	54.0	44.0	48.0		1308,1308	-2.4	1.0	6	dbSNP_86	48	586,4832		28,530,2151	no	coding-synonymous,coding-synonymous	TAP2	NM_000544.3,NM_018833.2	,	28,620,3572	AA,AG,GG		10.8158,2.9782,8.0095	,	436/704,436/654	32798548	676,7764	1511	2709	4220	SO:0001819	synonymous_variant	6891	exon8			TCCCACGTTGCTG	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.1308C>T	6.37:g.32798548G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000452392.2	37																																																																																				.	.	weak		0.522	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
SLC6A11	6538	hgsc.bcm.edu	37	3	10885920	10885920	+	Silent	SNP	T	T	C	rs2304725	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:10885920T>C	ENST00000254488.2	+	5	711	c.645T>C	c.(643-645)tcT>tcC	p.S215S		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	215					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|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 binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	TGGCCATCTCTGACGGGATCG	0.597													t|||	1874	0.374201	0.3011	0.2161	5008	,	,		19545	0.4276		0.325	False		,,,				2504	0.5808				p.S215S		Atlas-SNP	.											SLC6A11,NS,adenoma,0,1	SLC6A11	87	1	0			c.T645C						scavenged	.	T		1369,3037	453.8+/-350.4	214,941,1048	100.0	86.0	91.0		645	-11.5	0.0	3	dbSNP_100	91	2893,5707	454.0+/-363.4	495,1903,1902	yes	coding-synonymous	SLC6A11	NM_014229.1		709,2844,2950	CC,CT,TT		33.6395,31.0713,32.7695		215/633	10885920	4262,8744	2203	4300	6503	SO:0001819	synonymous_variant	6538	exon5			CATCTCTGACGGG	S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"""Solute carriers"""	11044	protein-coding gene	gene with protein product	"""GABA transporter 3"""	607952	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 11"""			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.645T>C	3.37:g.10885920T>C		Somatic	177	2	0.0112994		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	NM_014229	B2R6U6|Q8IYC9	Silent	SNP	ENST00000254488.2	37	CCDS2602.1																																																																																			T|0.655;C|0.345	0.345	strong		0.597	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140774076	140774076	+	Missense_Mutation	SNP	G	G	T	rs367855808		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140774076G>T	ENST00000398604.2	+	1	1696	c.1696G>T	c.(1696-1698)Gcc>Tcc	p.A566S	PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	566					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)			CCTGTACCCCGCCCTCCCCAC	0.667																																					p.A566S		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G1696T						PASS	.	A	,SER/ALA,,,,,,,,,,,SER/ALA	0,4406		0,0,2203	91.0	106.0	101.0		,1696,,,,,,,,,,,1696	-10.1	0.0	5		101	1,8595		0,1,4297	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	0,1,6500	TT,TG,GG		0.0116,0.0,0.0077	,,,,,,,,,,,,	,566/821,,,,,,,,,,,566/933	140774076	1,13001	2203	4298	6501	SO:0001583	missense	9708	exon1			TACCCCGCCCTCC	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.1696G>T	5.37:g.140774076G>T	ENSP00000381605:p.Ala566Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	182	83	0.456044	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.677464	0.00751	0.0	1.16E-4	ENSG00000253767	ENST00000398604	T	0.46063	0.88	5.06	-10.1	0.00402	Cadherin-like (1);	1.441770	0.05974	N	0.642917	T	0.13329	0.0323	N	0.02379	-0.575	0.09310	N	1	B;B	0.21071	0.051;0.004	B;B	0.19391	0.025;0.006	T	0.11767	-1.0574	10	0.07813	T	0.8	.	9.2393	0.37486	0.6616:0.0594:0.0798:0.1992	.	566;566	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	S	566	ENSP00000381605:A566S	ENSP00000381605:A566S	A	+	1	0	PCDHGA8	140754260	0.000000	0.05858	0.000000	0.03702	0.625000	0.37756	-8.772000	0.00017	-3.686000	0.00121	-1.652000	0.00757	GCC	.	.	weak		0.667	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
TG	7038	hgsc.bcm.edu	37	8	133899008	133899008	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:133899008C>A	ENST00000220616.4	+	9	1431	c.1391C>A	c.(1390-1392)cCa>cAa	p.P464Q	TG_ENST00000377869.1_Missense_Mutation_p.P464Q	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	464					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)		ACCACCAACCCAAAGAGACTC	0.463																																					p.P464Q		Atlas-SNP	.											.	TG	416	.	0			c.C1391A						PASS	.						57.0	63.0	61.0					8																	133899008		2203	4300	6503	SO:0001583	missense	7038	exon9			CCAACCCAAAGAG	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.1391C>A	8.37:g.133899008C>A	ENSP00000220616:p.Pro464Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	170	72	0.423529	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.164144	0.78339	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	D;T	0.81499	-1.5;-1.43	5.8	5.8	0.92144	.	0.190696	0.37348	N	0.002135	D	0.88894	0.6561	M	0.72894	2.215	0.40203	D	0.977531	D	0.76494	0.999	D	0.66602	0.945	D	0.88843	0.3314	10	0.52906	T	0.07	.	19.0314	0.92959	0.0:1.0:0.0:0.0	.	464	P01266	THYG_HUMAN	Q	464	ENSP00000367100:P464Q;ENSP00000220616:P464Q	ENSP00000220616:P464Q	P	+	2	0	TG	133968190	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.334000	0.65923	2.740000	0.93945	0.650000	0.86243	CCA	.	.	none		0.463	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
PCGF3	10336	hgsc.bcm.edu	37	4	755129	755129	+	Silent	SNP	C	C	T	rs2242234	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:755129C>T	ENST00000362003.5	+	9	920	c.525C>T	c.(523-525)cgC>cgT	p.R175R	PCGF3_ENST00000470161.2_Silent_p.R175R|RP11-440L14.1_ENST00000503571.1_RNA|PCGF3_ENST00000521023.2_Silent_p.R141R|PCGF3_ENST00000505655.2_Silent_p.R175R	NM_006315.4	NP_006306.2	Q3KNV8	PCGF3_HUMAN	polycomb group ring finger 3	175					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(1)	7						AGTGGATCCGCTGCTCAGCCC	0.542													C|||	283	0.0565096	0.0121	0.049	5008	,	,		17446	0.125		0.0577	False		,,,				2504	0.0501				p.R175R		Atlas-SNP	.											.	PCGF3	23	.	0			c.C525T						PASS	.	C		61,3893		1,59,1917	62.0	68.0	66.0		525	3.2	1.0	4	dbSNP_98	66	510,7788		13,484,3652	no	coding-synonymous	PCGF3	NM_006315.4		14,543,5569	TT,TC,CC		6.1461,1.5427,4.6605		175/243	755129	571,11681	1977	4149	6126	SO:0001819	synonymous_variant	10336	exon9			GATCCGCTGCTCA	AK093869	CCDS3339.2	4p16.3	2013-01-09	2005-01-17	2005-01-19	ENSG00000185619	ENSG00000185619		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	10066	protein-coding gene	gene with protein product			"""ring finger protein 3"""	RNF3			Standard	XM_005272250		Approved	FLJ36550, DONG1, RNF3A, MGC40413	uc003gbe.3	Q3KNV8	OTTHUMG00000119000	ENST00000362003.5:c.525C>T	4.37:g.755129C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	162	72	0.444444	NM_006315	D3DVN1|O15262	Silent	SNP	ENST00000362003.5	37	CCDS3339.2																																																																																			C|0.930;T|0.070	0.070	strong		0.542	PCGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239197.2	NM_006315	
KCNK10	54207	hgsc.bcm.edu	37	14	88652389	88652389	+	Silent	SNP	C	C	T	rs3742692	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:88652389C>T	ENST00000340700.5	-	7	1558	c.1107G>A	c.(1105-1107)gcG>gcA	p.A369A	KCNK10_ENST00000319231.5_Silent_p.A374A|KCNK10_ENST00000312350.5_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	101	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	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	
MYBPC3	4607	hgsc.bcm.edu	37	11	47365164	47365164	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47365164T>C	ENST00000545968.1	-	13	1156	c.1102A>G	c.(1102-1104)Aag>Gag	p.K368E	MYBPC3_ENST00000256993.4_Missense_Mutation_p.K368E|MYBPC3_ENST00000399249.2_Missense_Mutation_p.K368E	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	368	Ig-like C2-type 2.				cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		GGCTCCAGCTTCTTCTGAAAG	0.647																																					p.K368E		Atlas-SNP	.											.	MYBPC3	102	.	0			c.A1102G						PASS	.						52.0	50.0	51.0					11																	47365164		1941	4129	6070	SO:0001583	missense	4607	exon13			CCAGCTTCTTCTG	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.1102A>G	11.37:g.47365164T>C	ENSP00000442795:p.Lys368Glu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	4	0.0412371	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	t	25.9	4.686390	0.88639	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.67865	-0.29;-0.29;-0.29	4.99	4.99	0.66335	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79587	0.4471	M	0.77616	2.38	0.46396	D	0.999024	D	0.69078	0.997	D	0.68621	0.959	T	0.80899	-0.1176	9	0.51188	T	0.08	.	11.5285	0.50595	0.0:0.0:0.1496:0.8504	.	368	Q14896	MYPC3_HUMAN	E	368	ENSP00000442795:K368E;ENSP00000382193:K368E;ENSP00000256993:K368E	ENSP00000256993:K368E	K	-	1	0	MYBPC3	47321740	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.639000	0.54339	2.103000	0.63969	0.456000	0.33151	AAG	.	.	none		0.647	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
MTX3	345778	hgsc.bcm.edu	37	5	79282798	79282798	+	Missense_Mutation	SNP	G	G	C	rs9293796	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79282798G>C	ENST00000512528.1	-	7	734	c.714C>G	c.(712-714)agC>agG	p.S238R	MTX3_ENST00000509852.1_Missense_Mutation_p.S238R|MTX3_ENST00000512560.1_Missense_Mutation_p.S177R			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	91	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	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	
UCN3	114131	hgsc.bcm.edu	37	10	5415954	5415954	+	Missense_Mutation	SNP	A	A	G	rs10904481	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:5415954A>G	ENST00000380433.3	+	2	499	c.271A>G	c.(271-273)Aga>Gga	p.R91G		NM_053049.2	NP_444277.2	Q969E3	UCN3_HUMAN	urocortin 3	91			R -> G (in dbSNP:rs10904481). {ECO:0000269|PubMed:11329063, ECO:0000269|PubMed:11416224, ECO:0000269|PubMed:15489334}.		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|digestion (GO:0007586)|positive regulation of insulin secretion (GO:0032024)|positive regulation of membrane potential (GO:0045838)|response to corticosterone (GO:0051412)|response to glucose (GO:0009749)|response to immobilization stress (GO:0035902)|response to starvation (GO:0042594)	axon terminus (GO:0043679)|extracellular space (GO:0005615)|varicosity (GO:0043196)				endometrium(1)|large_intestine(1)	2						GGGTGGAGCCAGAGGCACCCG	0.622													.|||	2233	0.445887	0.3268	0.5476	5008	,	,		10804	0.5546		0.3121	False		,,,				2504	0.5603				p.R91G		Atlas-SNP	.											.	UCN3	13	.	0			c.A271G						PASS	.	G	GLY/ARG	1489,2913		260,969,972	54.0	55.0	54.0		271	2.5	0.0	10	dbSNP_120	54	2544,6056		381,1782,2137	yes	missense	UCN3	NM_053049.2	125	641,2751,3109	GG,GA,AA		29.5814,33.8255,31.0183	benign	91/162	5415954	4033,8969	2201	4300	6501	SO:0001583	missense	114131	exon2			GGAGCCAGAGGCA	AF361943	CCDS7065.1	10p15.1	2013-02-28	2012-10-17		ENSG00000178473	ENSG00000178473		"""Endogenous ligands"""	17781	protein-coding gene	gene with protein product	"""stresscopin"", ""prepro-urocortin 3"""	605901				11416224	Standard	NM_053049		Approved	UCNIII, SPC	uc001ihx.1	Q969E3	OTTHUMG00000017594	ENST00000380433.3:c.271A>G	10.37:g.5415954A>G	ENSP00000369798:p.Arg91Gly	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	37	35	0.945946	NM_053049	Q496H2|Q5SR91	Missense_Mutation	SNP	ENST00000380433.3	37	CCDS7065.1	876	0.4010989010989011	163	0.3313008130081301	178	0.49171270718232046	303	0.5297202797202797	232	0.30606860158311344	G	0.005	-2.183623	0.00305	0.338255	0.295814	ENSG00000178473	ENST00000380433	T	0.28069	1.63	5.48	2.52	0.30459	.	0.373259	0.19525	N	0.112193	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	0.47686	-0.9098	9	0.02654	T	1	9.0E-4	6.6036	0.22714	0.2114:0.0:0.6631:0.1256	rs10904481;rs10904481	91	Q969E3	UCN3_HUMAN	G	91	ENSP00000369798:R91G	ENSP00000369798:R91G	R	+	1	2	UCN3	5405954	.	.	0.000000	0.03702	0.002000	0.02628	.	.	0.009000	0.14813	-0.320000	0.08662	AGA	A|0.639;G|0.361	0.361	strong		0.622	UCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046547.1	NM_053049	
VN1R1	57191	hgsc.bcm.edu	37	19	57967049	57967049	+	Missense_Mutation	SNP	G	G	T	rs61744949	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57967049G>T	ENST00000321039.3	-	1	805	c.806C>A	c.(805-807)gCc>gAc	p.A269D	AC004076.9_ENST00000596831.1_Missense_Mutation_p.P107T|AC004076.9_ENST00000415705.3_5'UTR	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	269			A -> D (in allele VN1R1*3; dbSNP:rs61744949). {ECO:0000269|PubMed:10973240, ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		TGTGGCTCTGGCTTCCTGGGA	0.488													G|||	2070	0.413339	0.3109	0.451	5008	,	,		18776	0.5913		0.2783	False		,,,				2504	0.4806				p.A269D		Atlas-SNP	.											.	VN1R1	48	.	0			c.C806A						PASS	.	G	ASP/ALA	1342,3064	450.2+/-349.3	188,966,1049	126.0	88.0	101.0		806	-0.9	0.0	19	dbSNP_129	101	2454,6146	404.0+/-348.0	330,1794,2176	yes	missense	VN1R1	NM_020633.3	126	518,2760,3225	TT,TG,GG		28.5349,30.4585,29.1865	possibly-damaging	269/354	57967049	3796,9210	2203	4300	6503	SO:0001583	missense	57191	exon1			GCTCTGGCTTCCT	AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	13548	protein-coding gene	gene with protein product		605234	"""vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1"""	VNR19I1		10973240	Standard	NM_020633		Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.806C>A	19.37:g.57967049G>T	ENSP00000322339:p.Ala269Asp	Somatic	415	0	0		WXS	Illumina HiSeq	Phase_I	321	142	0.442368	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	37	CCDS12951.1	877	0.4015567765567766	149	0.30284552845528456	135	0.3729281767955801	368	0.6433566433566433	225	0.29683377308707126	G	10.04	1.242857	0.22796	0.304585	0.285349	ENSG00000178201	ENST00000321039	T	0.09255	3.0	4.17	-0.913	0.10500	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.25060	0.705	0.80722	P	0.0	B	0.25609	0.13	B	0.31016	0.123	T	0.24621	-1.0155	8	0.56958	D	0.05	.	4.0826	0.09932	0.3162:0.3379:0.3459:0.0	rs61744949	269	Q9GZP7	VN1R1_HUMAN	D	269	ENSP00000322339:A269D	ENSP00000322339:A269D	A	-	2	0	VN1R1	62658861	0.996000	0.38824	0.000000	0.03702	0.015000	0.08874	0.517000	0.22832	-0.140000	0.11394	0.650000	0.86243	GCC	G|0.675;T|0.325	0.325	strong		0.488	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633	
ZBTB1	22890	hgsc.bcm.edu	37	14	64988924	64988924	+	Silent	SNP	T	T	C	rs10133411	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:64988924T>C	ENST00000554015.1	+	4	1133	c.702T>C	c.(700-702)caT>caC	p.H234H	ZBTB1_ENST00000358738.3_Silent_p.H234H|RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Silent_p.H234H			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	234					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		TAGATGAGCATGTGCTAACCT	0.368													T|||	812	0.162141	0.0401	0.1254	5008	,	,		21323	0.2083		0.2326	False		,,,				2504	0.2331				p.H234H		Atlas-SNP	.											ZBTB1_ENST00000394712,adrenal_gland,adrenal_cortical_adenoma,0,2	ZBTB1	93	2	0			c.T702C						PASS	.	T	,	347,4059	179.7+/-208.2	16,315,1872	70.0	70.0	70.0		702,702	-1.9	1.0	14	dbSNP_119	70	1883,6717	335.4+/-321.4	212,1459,2629	yes	coding-synonymous,coding-synonymous	ZBTB1	NM_001123329.1,NM_014950.2	,	228,1774,4501	CC,CT,TT		21.8953,7.8756,17.1459	,	234/714,234/645	64988924	2230,10776	2203	4300	6503	SO:0001819	synonymous_variant	22890	exon2			TGAGCATGTGCTA	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.702T>C	14.37:g.64988924T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	126	77	0.611111	NM_014950	A8K6S8|Q86SW8	Silent	SNP	ENST00000554015.1	37	CCDS45126.1																																																																																			T|0.831;C|0.169	0.169	strong		0.368	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1		
GANAB	23193	hgsc.bcm.edu	37	11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	rs76572368	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:62397114T>C	ENST00000356638.3	-	15	1796	c.1780A>G	c.(1780-1782)Atg>Gtg	p.M594V	GANAB_ENST00000346178.4_Missense_Mutation_p.M616V|GANAB_ENST00000534779.1_Missense_Mutation_p.M502V|GANAB_ENST00000540933.1_Missense_Mutation_p.M497V	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	594					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 lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|glucosidase II complex (GO:0017177)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|glucan 1,3-alpha-glucosidase activity (GO:0033919)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|skin(2)|urinary_tract(3)	35					Miglitol(DB00491)	GGGCGTTCCATGCCCCCAGAG	0.597													T|||	89	0.0177716	0.0008	0.0389	5008	,	,		20960	0.001		0.0547	False		,,,				2504	0.0051				p.M616V	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.A1846G						PASS	.	T	VAL/MET,VAL/MET	28,4376	31.7+/-61.6	0,28,2174	37.0	37.0	37.0		1780,1846	-4.7	0.1	11	dbSNP_131	37	362,8236	115.7+/-175.5	10,342,3947	yes	missense,missense	GANAB	NM_198334.1,NM_198335.2	21,21	10,370,6121	CC,CT,TT		4.2103,0.6358,2.9995	benign,benign	594/945,616/967	62397114	390,12612	2202	4299	6501	SO:0001583	missense	23193	exon16			GTTCCATGCCCCC	AF144074	CCDS8026.1, CCDS41656.1, CCDS60817.1, CCDS60818.1	11q12.3	2012-10-02			ENSG00000089597	ENSG00000089597	3.2.1.20		4138	protein-coding gene	gene with protein product		104160				10764838, 6342981	Standard	NM_198335		Approved	GluII, G2AN, KIAA0088	uc001nua.4	Q14697	OTTHUMG00000167696	ENST00000356638.3:c.1780A>G	11.37:g.62397114T>C	ENSP00000349053:p.Met594Val	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	228	92	0.403509	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	37	CCDS8026.1	53	0.024267399267399268	0	0.0	14	0.03867403314917127	0	0.0	39	0.051451187335092345	T	7.943	0.743196	0.15642	0.006358	0.042103	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933	D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78	5.31	-4.7	0.03288	Glycoside hydrolase, superfamily (1);	0.908173	0.09646	N	0.774318	T	0.25419	0.0618	N	0.00368	-1.59	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	0.53961	-0.8364	10	0.29301	T	0.29	0.5168	8.9385	0.35715	0.0:0.4806:0.1198:0.3996	.	480;502;594;616	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	V	616;594;502;497	ENSP00000340466:M616V;ENSP00000349053:M594V;ENSP00000435306:M502V;ENSP00000442962:M497V	ENSP00000340466:M616V	M	-	1	0	GANAB	62153690	0.000000	0.05858	0.133000	0.22050	0.980000	0.70556	-1.352000	0.02619	-0.731000	0.04862	0.533000	0.62120	ATG	T|0.974;C|0.026	0.026	strong		0.597	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334	
UGGT2	55757	hgsc.bcm.edu	37	13	96638651	96638651	+	Missense_Mutation	SNP	C	C	T	rs12863903	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:96638651C>T	ENST00000376747.3	-	9	1037	c.967G>A	c.(967-969)Gct>Act	p.A323T	UGGT2_ENST00000467305.1_5'UTR|UGGT2_ENST00000376714.3_3'UTR|UGGT2_ENST00000397618.3_Missense_Mutation_p.A323T	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	58	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	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	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702725	27702725	+	Missense_Mutation	SNP	A	A	G	rs6482626	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:27702725A>G	ENST00000438700.3	-	1	572	c.455T>C	c.(454-456)cTg>cCg	p.L152P		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						GCCGGTGCCCAGCGCGGCTGT	0.672													A|||	994	0.198482	0.3805	0.2853	5008	,	,		12858	0.0129		0.2137	False		,,,				2504	0.0665				p.L152P		Atlas-SNP	.											.	PTCHD3	140	.	0			c.T455C						PASS	.	A	PRO/LEU	1561,2845	463.0+/-353.4	279,1003,921	62.0	71.0	68.0		455	3.6	0.0	10	dbSNP_116	68	1921,6679	319.3+/-314.1	234,1453,2613	yes	missense	PTCHD3	NM_001034842.3	98	513,2456,3534	GG,GA,AA		22.3372,35.429,26.7723	probably-damaging	152/768	27702725	3482,9524	2203	4300	6503	SO:0001583	missense	374308	exon1			GTGCCCAGCGCGG	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.455T>C	10.37:g.27702725A>G	ENSP00000417658:p.Leu152Pro	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	65	13	0.2	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	437	0.2000915750915751	176	0.35772357723577236	90	0.24861878453038674	10	0.017482517482517484	161	0.21240105540897097	A	16.00	2.997444	0.54147	0.35429	0.223372	ENSG00000182077	ENST00000438700	D	0.91351	-2.83	3.62	3.62	0.41486	.	0.165305	0.41938	N	0.000787	T	0.00012	0.0000	M	0.68952	2.095	0.20403	P	0.9999007308	D	0.76494	0.999	D	0.70935	0.971	T	0.00000	-1.3717	9	0.87932	D	0	-16.4668	10.9518	0.47334	1.0:0.0:0.0:0.0	rs6482626;rs17388746;rs57918946;rs6482626	152	Q3KNS1	PTHD3_HUMAN	P	152	ENSP00000417658:L152P	ENSP00000417658:L152P	L	-	2	0	PTCHD3	27742731	0.990000	0.36364	0.011000	0.14972	0.015000	0.08874	4.227000	0.58612	1.528000	0.49103	0.454000	0.30748	CTG	A|0.769;G|0.231	0.231	strong		0.672	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
GPATCH1	55094	hgsc.bcm.edu	37	19	33602757	33602757	+	Silent	SNP	C	C	T	rs10420258	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:33602757C>T	ENST00000170564.2	+	12	2027	c.1713C>T	c.(1711-1713)caC>caT	p.H571H		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	571					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)					GGTTCACTCACGCCAAGGAGG	0.552													C|||	1019	0.203474	0.1082	0.1254	5008	,	,		17067	0.3333		0.1382	False		,,,				2504	0.3211				p.H571H	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C1713T						PASS	.	C		481,3925	226.2+/-241.8	23,435,1745	116.0	97.0	103.0		1713	-4.7	0.4	19	dbSNP_119	103	1334,7266	262.1+/-284.2	97,1140,3063	no	coding-synonymous	GPATCH1	NM_018025.2		120,1575,4808	TT,TC,CC		15.5116,10.9169,13.9551		571/932	33602757	1815,11191	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon12			CACTCACGCCAAG	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.1713C>T	19.37:g.33602757C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	147	56	0.380952	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.829;T|0.171	0.171	strong		0.552	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
PCDHB6	56130	hgsc.bcm.edu	37	5	140532165	140532165	+	Missense_Mutation	SNP	G	G	A	rs17844444	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140532165G>A	ENST00000231136.1	+	1	2327	c.2327G>A	c.(2326-2328)gGc>gAc	p.G776D	PCDHB6_ENST00000543635.1_Missense_Mutation_p.G640D	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	776			G -> D (in dbSNP:rs17844444). {ECO:0000269|PubMed:14702039}.		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)			CCTCCTCAGGGCACTGAGAGA	0.463													G|||	522	0.104233	0.0877	0.1744	5008	,	,		16904	0.0407		0.1521	False		,,,				2504	0.093				p.G776D		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G2327A						PASS	.	G	ASP/GLY	454,3950	216.4+/-235.1	27,400,1775	106.0	116.0	112.0		2327	-6.8	0.0	5	dbSNP_123	112	1415,7185	273.0+/-290.4	122,1171,3007	yes	missense	PCDHB6	NM_018939.2	94	149,1571,4782	AA,AG,GG		16.4535,10.3088,14.3725	benign	776/795	140532165	1869,11135	2202	4300	6502	SO:0001583	missense	56130	exon1			CTCAGGGCACTGA	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.2327G>A	5.37:g.140532165G>A	ENSP00000231136:p.Gly776Asp	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	231	114	0.493506	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	247	0.1130952380952381	50	0.1016260162601626	55	0.15193370165745856	26	0.045454545454545456	116	0.15303430079155672	G	4.294	0.053859	0.08291	0.103088	0.164535	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.13778	2.56;2.56	4.51	-6.84	0.01687	.	.	.	.	.	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41270	-0.9518	8	0.08837	T	0.75	.	5.1621	0.15066	0.6481:0.113:0.1258:0.1132	rs17844444	776	Q9Y5E3	PCDB6_HUMAN	D	640;776	ENSP00000438466:G640D;ENSP00000231136:G776D	ENSP00000231136:G776D	G	+	2	0	PCDHB6	140512349	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-2.107000	0.01337	-1.373000	0.02134	0.556000	0.70494	GGC	G|0.864;A|0.136	0.136	strong		0.463	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
LPAR1	1902	hgsc.bcm.edu	37	9	113637854	113637854	+	Silent	SNP	G	G	A	rs3739709	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:113637854G>A	ENST00000374431.3	-	5	1325	c.942C>T	c.(940-942)cgC>cgT	p.R314R	LPAR1_ENST00000358883.4_Silent_p.R314R|LPAR1_ENST00000541779.1_Silent_p.R315R|LPAR1_ENST00000374430.2_Silent_p.R314R|LPAR1_ENST00000538760.1_Silent_p.R315R	NM_057159.2	NP_476500.1	Q92633	LPAR1_HUMAN	lysophosphatidic acid receptor 1	314					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|bleb assembly (GO:0032060)|cellular response to oxygen levels (GO:0071453)|G-protein coupled receptor signaling pathway (GO:0007186)|myelination (GO:0042552)|negative regulation of neuron projection development (GO:0010977)|positive regulation of apoptotic process (GO:0043065)|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 dendritic spine development (GO:0060999)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle cell chemotaxis (GO:0071673)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(6)|skin(1)	21						TTTCTTTGTCGCGGTAGGAGT	0.562													G|||	670	0.133786	0.0113	0.1643	5008	,	,		17668	0.1905		0.1988	False		,,,				2504	0.1524				p.R314R	NSCLC(115;661 2323 9836 34256)	Atlas-SNP	.											LPAR1,NS,carcinoma,-1,2	LPAR1	48	2	0			c.C942T						PASS	.	G	,	198,4208	124.1+/-161.4	5,188,2010	169.0	166.0	167.0		942,942	-9.9	0.6	9	dbSNP_107	167	1657,6943	306.2+/-307.8	153,1351,2796	no	coding-synonymous,coding-synonymous	LPAR1	NM_001401.3,NM_057159.2	,	158,1539,4806	AA,AG,GG		19.2674,4.4939,14.2626	,	314/365,314/365	113637854	1855,11151	2203	4300	6503	SO:0001819	synonymous_variant	1902	exon4			TTTGTCGCGGTAG	U80811	CCDS6777.1	9q	2012-08-08	2008-04-11	2008-04-11	ENSG00000198121	ENSG00000198121		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	3166	protein-coding gene	gene with protein product		602282	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2"""	EDG2		8922387, 9070858	Standard	NM_001401		Approved	edg-2, rec.1.3, vzg-1, Gpcr26, Mrec1.3, LPA1, GPR26	uc004bfc.3	Q92633	OTTHUMG00000020486	ENST00000374431.3:c.942C>T	9.37:g.113637854G>A		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	235	122	0.519149	NM_001401	B4DK36|O00656|O00722|P78351	Silent	SNP	ENST00000374431.3	37	CCDS6777.1																																																																																			G|0.863;A|0.137	0.137	strong		0.562	LPAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053631.1	NM_057159	
FAM134A	79137	hgsc.bcm.edu	37	2	220046840	220046840	+	Missense_Mutation	SNP	G	G	A	rs3210652	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220046840G>A	ENST00000430297.2	+	9	1257	c.1121G>A	c.(1120-1122)cGt>cAt	p.R374H		NM_024293.4	NP_077269.3	Q8NC44	F134A_HUMAN	family with sequence similarity 134, member A	374			R -> H (in dbSNP:rs3210652).			integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	19		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTACTAGGCCGTCCTCAAGCT	0.607													G|||	477	0.0952476	0.0144	0.121	5008	,	,		17377	0.1706		0.1382	False		,,,				2504	0.0644				p.R374H		Atlas-SNP	.											.	FAM134A	34	.	0			c.G1121A						PASS	.	G	HIS/ARG	142,4264	99.4+/-138.0	4,134,2065	108.0	116.0	113.0		1121	2.8	0.1	2	dbSNP_105	113	1136,7464	235.0+/-267.7	76,984,3240	yes	missense	FAM134A	NM_024293.4	29	80,1118,5305	AA,AG,GG		13.2093,3.2229,9.8262	benign	374/544	220046840	1278,11728	2203	4300	6503	SO:0001583	missense	79137	exon9			TAGGCCGTCCTCA	AK074983	CCDS2434.1	2q36.1	2008-02-05	2007-05-01	2007-05-01	ENSG00000144567	ENSG00000144567			28450	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 17"""	C2orf17			Standard	NM_024293		Approved	MGC3035	uc002vjw.4	Q8NC44	OTTHUMG00000154577	ENST00000430297.2:c.1121G>A	2.37:g.220046840G>A	ENSP00000395249:p.Arg374His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	69	20	0.289855	NM_024293	Q6P1P5|Q9H0K7	Missense_Mutation	SNP	ENST00000430297.2	37	CCDS2434.1	252	0.11538461538461539	9	0.018292682926829267	42	0.11602209944751381	96	0.16783216783216784	105	0.13852242744063326	G	0.016	-1.529021	0.00951	0.032229	0.132093	ENSG00000144567	ENST00000458520;ENST00000430297;ENST00000443518	T;T	0.46451	0.87;1.56	4.79	2.82	0.32997	.	0.845757	0.10489	N	0.668677	T	0.00039	0.0001	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	0.22977	-1.0201	9	0.16420	T	0.52	1.384	9.1598	0.37016	0.2336:0.6345:0.1318:0.0	rs3210652;rs3731899;rs3210652	167;374	E7EUL4;Q8NC44	.;F134A_HUMAN	H	167;374;167	ENSP00000403898:R167H;ENSP00000395249:R374H	ENSP00000395249:R374H	R	+	2	0	FAM134A	219755084	0.011000	0.17503	0.053000	0.19242	0.013000	0.08279	1.578000	0.36525	1.232000	0.43678	-0.165000	0.13383	CGT	G|0.902;A|0.098	0.098	strong		0.607	FAM134A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336147.2	NM_024293	
SIK1	150094	hgsc.bcm.edu	37	21	44846016	44846016	+	Missense_Mutation	SNP	C	C	T	rs3746951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:44846016C>T	ENST00000270162.6	-	2	175	c.43G>A	c.(43-45)Ggt>Agt	p.G15S		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	15			G -> S (in dbSNP:rs3746951). {ECO:0000269|PubMed:17344846}.		cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	TGGCCCTGACCCTGGCCCGCG	0.692													C|||	834	0.166534	0.0129	0.2925	5008	,	,		11980	0.2153		0.2684	False		,,,				2504	0.1299				p.G15S		Atlas-SNP	.											.	SIK1	65	.	0			c.G43A						PASS	.	C	SER/GLY	212,4172		8,196,1988	15.0	17.0	16.0		43	2.4	0.5	21	dbSNP_107	16	2211,6371		269,1673,2349	yes	missense	SIK1	NM_173354.3	56	277,1869,4337	TT,TC,CC		25.7632,4.8358,18.6873	benign	15/784	44846016	2423,10543	2192	4291	6483	SO:0001583	missense	150094	exon2			CCTGACCCTGGCC	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.43G>A	21.37:g.44846016C>T	ENSP00000270162:p.Gly15Ser	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	19	0.296875	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	435	0.19917582417582416	11	0.022357723577235773	95	0.26243093922651933	122	0.21328671328671328	207	0.27308707124010556	C	9.340	1.062697	0.19987	0.048358	0.257632	ENSG00000142178	ENST00000270162	T	0.70869	-0.52	3.5	2.39	0.29439	Protein kinase-like domain (1);	0.506824	0.20703	N	0.087231	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.06607	-1.0817	9	0.09084	T	0.74	.	5.0217	0.14365	0.0:0.6186:0.0:0.3814	rs3746951;rs3746951	15	P57059	SIK1_HUMAN	S	15	ENSP00000270162:G15S	ENSP00000270162:G15S	G	-	1	0	SIK1	43670444	0.800000	0.28916	0.467000	0.27180	0.405000	0.30901	1.484000	0.35508	1.506000	0.48736	0.405000	0.27470	GGT	C|0.827;T|0.173	0.173	strong		0.692	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
TSSK2	23617	hgsc.bcm.edu	37	22	19119545	19119545	+	Silent	SNP	C	C	T	rs45604134	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	93	0	0		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	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		
PKHD1	5314	hgsc.bcm.edu	37	6	51917968	51917968	+	Silent	SNP	T	T	G	rs4715271	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:51917968T>G	ENST00000371117.3	-	21	2321	c.2046A>C	c.(2044-2046)ccA>ccC	p.P682P	PKHD1_ENST00000340994.4_Silent_p.P682P	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	682					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)					GAACCAGCACTGGGGAGTTTG	0.527													T|||	294	0.0587061	0.0242	0.0749	5008	,	,		19890	0.0407		0.1113	False		,,,				2504	0.0583				p.P682P		Atlas-SNP	.											PKHD1_ENST00000340994,NS,malignant_melanoma,-1,4	PKHD1	927	4	0			c.A2046C						PASS	.	T	,	168,4238	110.8+/-149.0	5,158,2040	71.0	73.0	72.0		2046,2046	-11.3	0.0	6	dbSNP_111	72	952,7648	207.9+/-249.5	60,832,3408	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	65,990,5448	GG,GT,TT		11.0698,3.813,8.6114	,	682/4075,682/3397	51917968	1120,11886	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon21			CAGCACTGGGGAG	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.2046A>C	6.37:g.51917968T>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	101	38	0.376238	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			T|0.921;G|0.079	0.079	strong		0.527	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
RPSA	3921	hgsc.bcm.edu	37	3	39453160	39453160	+	Silent	SNP	G	G	A	rs2269350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:39453160G>A	ENST00000301821.6	+	5	628	c.519G>A	c.(517-519)ttG>ttA	p.L173L	RPSA_ENST00000478027.1_3'UTR|RPSA_ENST00000443003.1_Silent_p.L178L|SNORA62_ENST00000365493.1_RNA	NM_001012321.1|NM_002295.4	NP_001012321.1|NP_002286.2			ribosomal protein SA											endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)		CAGTGGGTTTGATGTGGTGGA	0.512													G|||	1256	0.250799	0.152	0.3084	5008	,	,		20924	0.2778		0.3082	False		,,,				2504	0.2566				p.L173L		Atlas-SNP	.											.	RPSA	15	.	0			c.G519A						PASS	.	G	,	733,3673	303.8+/-288.1	51,631,1521	150.0	150.0	150.0		519,519	2.8	1.0	3	dbSNP_100	150	2788,5812	439.2+/-359.1	457,1874,1969	no	coding-synonymous,coding-synonymous	RPSA	NM_001012321.1,NM_002295.4	,	508,2505,3490	AA,AG,GG		32.4186,16.6364,27.0721	,	173/296,173/296	39453160	3521,9485	2203	4300	6503	SO:0001819	synonymous_variant	3921	exon4			GGGTTTGATGTGG	S37431	CCDS2686.1	3p21.3	2014-09-17	2002-08-29	2005-02-11	ENSG00000168028	ENSG00000168028			6502	protein-coding gene	gene with protein product		150370	"""laminin receptor 1 (67kD, ribosomal protein SA)"""	LAMR1		1534510, 8760291	Standard	NM_001012321		Approved	LRP, 37LRP, p40, SA	uc003cjp.3	P08865	OTTHUMG00000131296	ENST00000301821.6:c.519G>A	3.37:g.39453160G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001012321		Silent	SNP	ENST00000301821.6	37	CCDS2686.1																																																																																			G|0.745;A|0.255	0.255	strong		0.512	RPSA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254064.3	NM_002295	
STYK1	55359	hgsc.bcm.edu	37	12	10783729	10783729	+	Silent	SNP	A	A	G	rs2290717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:10783729A>G	ENST00000075503.3	-	5	886	c.366T>C	c.(364-366)agT>agC	p.S122S		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						CACAGCTACCACTGCAAATCT	0.507										HNSCC(73;0.22)			A|||	1268	0.253195	0.1097	0.2378	5008	,	,		15618	0.2063		0.3787	False		,,,				2504	0.3773				p.S122S		Atlas-SNP	.											.	STYK1	55	.	0			c.T366C						PASS	.	A		701,3705	294.7+/-283.3	52,597,1554	77.0	74.0	75.0		366	-1.7	0.0	12	dbSNP_100	75	3696,4904	527.5+/-381.2	799,2098,1403	no	coding-synonymous	STYK1	NM_018423.2		851,2695,2957	GG,GA,AA		42.9767,15.9101,33.8075		122/423	10783729	4397,8609	2203	4300	6503	SO:0001819	synonymous_variant	55359	exon5			GCTACCACTGCAA	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.366T>C	12.37:g.10783729A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	115	111	0.965217	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Silent	SNP	ENST00000075503.3	37	CCDS8629.1																																																																																			A|0.701;G|0.299	0.299	strong		0.507	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423	
PGM1	5236	hgsc.bcm.edu	37	1	64114301	64114301	+	Missense_Mutation	SNP	T	T	C	rs11208257	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:64114301T>C	ENST00000371084.3	+	8	1471	c.1258T>C	c.(1258-1260)Tat>Cat	p.Y420H	PGM1_ENST00000540265.1_Missense_Mutation_p.Y223H|PGM1_ENST00000371083.4_Missense_Mutation_p.Y438H	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	78	0	0		WXS	Illumina HiSeq	Phase_I	44	6	0.136364	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	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887936	9887936	+	Missense_Mutation	SNP	G	G	C	rs17805544	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:9887936G>C	ENST00000306084.6	+	2	1659	c.1460G>C	c.(1459-1461)aGa>aCa	p.R487T	TXNDC2_ENST00000357775.5_Missense_Mutation_p.R420T|TXNDC2_ENST00000536353.2_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	487	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.		R -> T (in dbSNP:rs17805544). {ECO:0000269|PubMed:14702039}.		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						AGGACCATCAGACCATTCTTC	0.592													G|||	195	0.0389377	0.003	0.0519	5008	,	,		17872	0.0		0.1402	False		,,,				2504	0.0143				p.R487T		Atlas-SNP	.											.	TXNDC2	168	.	0			c.G1460C						PASS	.	G	THR/ARG,THR/ARG	118,4288	89.2+/-127.9	2,114,2087	113.0	86.0	95.0		1460,1259	-2.0	0.0	18	dbSNP_123	95	1189,7411	242.6+/-272.5	71,1047,3182	yes	missense,missense	TXNDC2	NM_001098529.1,NM_032243.5	71,71	73,1161,5269	CC,CG,GG		13.8256,2.6782,10.0492	possibly-damaging,possibly-damaging	487/554,420/487	9887936	1307,11699	2203	4300	6503	SO:0001583	missense	84203	exon2			CCATCAGACCATT	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.1460G>C	18.37:g.9887936G>C	ENSP00000304908:p.Arg487Thr	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	294	141	0.479592	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	136	0.06227106227106227	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	117	0.15435356200527706	G	7.347	0.622026	0.14193	0.026782	0.138256	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.03212	4.01;4.01	4.05	-1.97	0.07503	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.327137	0.31897	N	0.006882	T	0.00012	0.0000	N	0.02765	-0.5	0.80722	P	0.0	P	0.52692	0.955	P	0.48488	0.579	T	0.50980	-0.8763	8	.	.	.	-8.6918	9.7446	0.40440	0.5675:0.0:0.4325:0.0	rs17805544;rs52812014;rs17805544	487	Q86VQ3	TXND2_HUMAN	T	285;420;487;472	ENSP00000350419:R420T;ENSP00000304908:R487T	.	R	+	2	0	TXNDC2	9877936	0.864000	0.29904	0.001000	0.08648	0.001000	0.01503	-0.041000	0.12084	-0.707000	0.05022	-1.847000	0.00572	AGA	G|0.916;C|0.084	0.084	strong		0.592	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
RELN	5649	hgsc.bcm.edu	37	7	103141351	103141351	+	Silent	SNP	G	G	A	rs2229862	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:103141351G>A	ENST00000428762.1	-	53	8667	c.8508C>T	c.(8506-8508)ttC>ttT	p.F2836F	CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Silent_p.F2836F|RELN_ENST00000343529.5_Silent_p.F2836F	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2836					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)		ACTTCTGATAGAACCTAAACC	0.438													G|||	108	0.0215655	0.0008	0.0288	5008	,	,		18759	0.0		0.0736	False		,,,				2504	0.0133				p.F2836F	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C8508T						PASS	.	G	,	54,4352	52.3+/-87.9	0,54,2149	146.0	144.0	145.0		8508,8508	4.3	1.0	7	dbSNP_131	145	467,8133	138.3+/-195.1	13,441,3846	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	13,495,5995	AA,AG,GG		5.4302,1.2256,4.0058	,	2836/3461,2836/3459	103141351	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon53			CTGATAGAACCTA		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.8508C>T	7.37:g.103141351G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	185	182	0.983784	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			T|0.003;G|0.860;C|0.102;A|0.035	0.035	strong		0.438	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
ADI1	55256	hgsc.bcm.edu	37	2	3504687	3504687	+	Silent	SNP	A	A	G	rs9950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:3504687A>G	ENST00000327435.6	-	3	566	c.318T>C	c.(316-318)gaT>gaC	p.D106D	ADI1_ENST00000382093.5_Silent_p.D100D	NM_018269.3	NP_060739.2			acireductone dioxygenase 1									p.D106D(1)		breast(2)|large_intestine(2)|lung(4)|ovary(1)|stomach(1)	10	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0729)|Epithelial(75;0.173)|all cancers(51;0.228)		TGTCCCTCACATCGAAGTACC	0.537													A|||	2672	0.533546	0.8918	0.451	5008	,	,		19687	0.4484		0.3887	False		,,,				2504	0.3446				p.D106D		Atlas-SNP	.											ADI1,NS,carcinoma,0,1	ADI1	12	1	1	Substitution - coding silent(1)	stomach(1)	c.T318C						scavenged	.	A		3535,871	743.8+/-411.5	1431,673,99	221.0	165.0	184.0		318	-7.0	0.2	2	dbSNP_52	184	3057,5543	469.8+/-367.7	558,1941,1801	no	coding-synonymous	ADI1	NM_018269.3		1989,2614,1900	GG,GA,AA		35.5465,19.7685,49.3157		106/180	3504687	6592,6414	2203	4300	6503	SO:0001819	synonymous_variant	55256	exon3			CCTCACATCGAAG		CCDS1653.1	2p25.2	2013-05-29			ENSG00000182551	ENSG00000182551	1.13.11.54		30576	protein-coding gene	gene with protein product	"""membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1"""	613400				14718544, 15938715	Standard	NM_018269		Approved	SIPL, MTCBP-1, ARD, APL1, FLJ10913, HMFT1638, mtnD	uc002qxp.4	Q9BV57	OTTHUMG00000112441	ENST00000327435.6:c.318T>C	2.37:g.3504687A>G		Somatic	194	2	0.0103093		WXS	Illumina HiSeq	Phase_I	164	76	0.463415	NM_018269		Silent	SNP	ENST00000327435.6	37	CCDS1653.1																																																																																			A|0.473;G|0.527	0.527	strong		0.537	ADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000231914.6	NM_018269	
PPL	5493	hgsc.bcm.edu	37	16	4935985	4935985	+	Missense_Mutation	SNP	C	C	G	rs35869286	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4935985C>G	ENST00000345988.2	-	22	2760	c.2671G>C	c.(2671-2673)Gag>Cag	p.E891Q	PPL_ENST00000590782.2_Missense_Mutation_p.E889Q	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	891			E -> Q (in dbSNP:rs35869286).		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.E891K(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						TTCCACGCCTCCTCCACTCCA	0.557													C|||	164	0.0327476	0.0303	0.0245	5008	,	,		19112	0.006		0.0706	False		,,,				2504	0.0307				p.E891Q		Atlas-SNP	.											PPL,NS,carcinoma,0,1	PPL	168	1	1	Substitution - Missense(1)	lung(1)	c.G2671C						PASS	.	C	GLN/GLU	191,4203	116.7+/-154.6	5,181,2011	71.0	74.0	73.0		2671	3.8	0.1	16	dbSNP_126	73	638,7960	153.4+/-207.8	27,584,3688	yes	missense	PPL	NM_002705.4	29	32,765,5699	GG,GC,CC		7.4203,4.3468,6.3808	benign	891/1757	4935985	829,12163	2197	4299	6496	SO:0001583	missense	5493	exon22			ACGCCTCCTCCAC	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.2671G>C	16.37:g.4935985C>G	ENSP00000340510:p.Glu891Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	78	0.03571428571428571	10	0.02032520325203252	7	0.019337016574585635	3	0.005244755244755245	58	0.07651715039577836	C	7.631	0.678938	0.14841	0.043468	0.074203	ENSG00000118898	ENST00000345988	T	0.58652	0.32	4.71	3.75	0.43078	.	0.060179	0.64402	N	0.000004	T	0.07593	0.0191	M	0.74881	2.28	0.40865	D	0.983862	B	0.16396	0.017	B	0.17433	0.018	T	0.37979	-0.9682	10	0.62326	D	0.03	.	17.7271	0.88368	0.0:0.8745:0.1255:0.0	rs35869286	891	O60437	PEPL_HUMAN	Q	891	ENSP00000340510:E891Q	ENSP00000340510:E891Q	E	-	1	0	PPL	4875986	1.000000	0.71417	0.050000	0.19076	0.032000	0.12392	6.068000	0.71201	0.430000	0.26230	-2.039000	0.00418	GAG	C|0.942;G|0.058	0.058	strong		0.557	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
CLEC19A	728276	hgsc.bcm.edu	37	16	19310092	19310092	+	Silent	SNP	T	T	C	rs1548450	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:19310092T>C	ENST00000465414.1	+	2	259	c.186T>C	c.(184-186)gcT>gcC	p.A62A	CLEC19A_ENST00000493231.1_Silent_p.A62A			Q6UXS0	CL19A_HUMAN	C-type lectin domain family 19, member A	62	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)										AGACCTGGGCTGAGGCCGACC	0.582													T|||	2340	0.467252	0.6815	0.3415	5008	,	,		15617	0.5099		0.2962	False		,,,				2504	0.3988				p.A62A		Atlas-SNP	.											CLEC19A_ENST00000465414,NS,carcinoma,0,2	CLEC19A	4	2	0			c.T186C						PASS	.																																			SO:0001819	synonymous_variant	728276	exon2			CTGGGCTGAGGCC			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.186T>C	16.37:g.19310092T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	140	54	0.385714	NM_001256720	Q0VF32	Silent	SNP	ENST00000465414.1	37																																																																																				T|0.566;C|0.434	0.434	strong		0.582	CLEC19A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254277.2	NM_00125672	
SEMA4A	64218	hgsc.bcm.edu	37	1	156146218	156146218	+	Silent	SNP	C	C	T	rs12401573	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156146218C>T	ENST00000368285.3	+	15	1983	c.1716C>T	c.(1714-1716)ccC>ccT	p.P572P	SEMA4A_ENST00000368286.2_Silent_p.P440P|SEMA4A_ENST00000368284.1_Silent_p.P440P|SEMA4A_ENST00000355014.2_Silent_p.P572P|SEMA4A_ENST00000368282.1_Silent_p.P572P	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	572					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|regulation of cell shape (GO:0008360)|regulation of endothelial cell migration (GO:0010594)|semaphorin-plexin signaling pathway (GO:0071526)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|ovary(2)|skin(2)	5	Hepatocellular(266;0.158)					TGGCTGTCCCCAACTCCATCC	0.522													c|||	2158	0.430911	0.3949	0.5231	5008	,	,		17757	0.2321		0.6044	False		,,,				2504	0.4407				p.P572P		Atlas-SNP	.											.	SEMA4A	75	.	0			c.C1716T						PASS	.	T	,,,	1860,2546	538.7+/-375.1	401,1058,744	51.0	51.0	51.0		1716,1716,1320,1716	1.9	1.0	1	dbSNP_120	51	5056,3544	629.7+/-398.3	1488,2080,732	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEMA4A	NM_001193300.1,NM_001193301.1,NM_001193302.1,NM_022367.3	,,,	1889,3138,1476	TT,TC,CC		41.2093,42.2152,46.8245	,,,	572/762,572/762,440/630,572/762	156146218	6916,6090	2203	4300	6503	SO:0001819	synonymous_variant	64218	exon15			TGTCCCCAACTCC	AK022416	CCDS1132.1, CCDS53378.1	1q22	2014-01-28			ENSG00000196189	ENSG00000196189		"""Semaphorins"""	10729	protein-coding gene	gene with protein product		607292		SEMAB		7748561	Standard	NM_022367		Approved	SemB, FLJ12287, CORD10	uc009wrq.3	Q9H3S1	OTTHUMG00000014042	ENST00000368285.3:c.1716C>T	1.37:g.156146218C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_001193300	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Silent	SNP	ENST00000368285.3	37	CCDS1132.1																																																																																			C|0.508;T|0.492	0.492	strong		0.522	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039484.2	NM_022367	
TNS1	7145	hgsc.bcm.edu	37	2	218683257	218683257	+	Silent	SNP	A	A	G	rs2571442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:218683257A>G	ENST00000171887.4	-	24	3938	c.3486T>C	c.(3484-3486)gcT>gcC	p.A1162A	TNS1_ENST00000419504.1_Silent_p.A1149A|TNS1_ENST00000430930.1_Silent_p.A1141A	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1162					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)		ACTGAGCTCGAGCCTGGCTTT	0.612													G|||	2016	0.402556	0.4977	0.4294	5008	,	,		18855	0.246		0.4066	False		,,,				2504	0.4121				p.A1162A		Atlas-SNP	.											.	TNS1	251	.	0			c.T3486C						PASS	.	G		2023,2383	612.3+/-391.9	468,1087,648	55.0	59.0	57.0		3486	0.2	0.9	2	dbSNP_100	57	3561,5039	627.6+/-398.0	749,2063,1488	no	coding-synonymous	TNS1	NM_022648.4		1217,3150,2136	GG,GA,AA		41.407,45.9147,42.934		1162/1736	218683257	5584,7422	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon24			AGCTCGAGCCTGG	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.3486T>C	2.37:g.218683257A>G		Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	113	110	0.973451	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			T|0.000;G|0.418;A|0.582	0.418	strong		0.612	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
MLC1	23209	hgsc.bcm.edu	37	22	50502526	50502526	+	Silent	SNP	A	A	G	rs11568187	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50502526A>G	ENST00000311597.5	-	11	1602	c.996T>C	c.(994-996)agT>agC	p.S332S	MLC1_ENST00000538737.1_Silent_p.S298S|MLC1_ENST00000395876.2_Silent_p.S332S|MLC1_ENST00000535444.1_Silent_p.S253S|MLC1_ENST00000431262.2_Silent_p.S302S|MLC1_ENST00000450140.2_Silent_p.S280S|MLC1_ENST00000483836.1_5'UTR	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	190	0	0		WXS	Illumina HiSeq	Phase_I	154	39	0.253247	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	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21176135	21176135	+	Missense_Mutation	SNP	T	T	C	rs1546308	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:21176135T>C	ENST00000421593.2	+	5	500	c.500T>C	c.(499-501)gTa>gCa	p.V167A	LST3_ENST00000540229.1_Intron|LST3_ENST00000381541.3_Missense_Mutation_p.V214A|SLCO1B3_ENST00000553473.1_Intron|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.V214A	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	167				V -> A (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						ACTGTGAATGTAATGGGAATG	0.338													C|||	4806	0.959665	0.9599	0.9078	5008	,	,		16740	0.998		0.9443	False		,,,				2504	0.9724				p.V167A		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.T500C						PASS	.	C	ALA/VAL	4134,150		1995,144,3	193.0	193.0	193.0		500	2.5	0.0	12	dbSNP_88	193	8047,515		3781,485,15	yes	missense	SLCO1B7	NM_001009562.4	64	5776,629,18	CC,CT,TT		6.0149,3.5014,5.1767		167/641	21176135	12181,665	2142	4281	6423	SO:0001583	missense	338821	exon5			TGAATGTAATGGG	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.500T>C	12.37:g.21176135T>C	ENSP00000394168:p.Val167Ala	Somatic	506	1	0.00197628		WXS	Illumina HiSeq	Phase_I	427	425	0.995316	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	2098	0.9606227106227107	477	0.9695121951219512	332	0.9171270718232044	570	0.9965034965034965	719	0.9485488126649076	.	2.451	-0.326432	0.05350	0.964986	0.939851	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.80566	-1.39;-1.39;-1.26	2.54	2.54	0.30619	.	0.348037	0.32120	N	0.006543	T	0.00012	0.0000	N	0.00332	-1.63	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.37526	-0.9702	9	0.22706	T	0.39	.	7.439	0.27172	0.0:0.7659:0.0:0.2341	rs1546308;rs52795424;rs1546308	167;214	G3V0H7;F5H094	.;.	A	214;214;167	ENSP00000370952:V214A;ENSP00000452013:V214A;ENSP00000394168:V167A	ENSP00000370952:V214A	V	+	2	0	SLCO1B7;RP11-545J16.1	21067402	0.033000	0.19621	0.002000	0.10522	0.129000	0.20672	2.365000	0.44196	0.392000	0.25172	-1.063000	0.02288	GTA	T|0.041;C|0.959	0.959	strong		0.338	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	
NRG2	9542	hgsc.bcm.edu	37	5	139422232	139422232	+	Silent	SNP	G	G	A	rs144634106	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:139422232G>A	ENST00000361474.1	-	1	647	c.423C>T	c.(421-423)gcC>gcT	p.A141A	NRG2_ENST00000289422.7_Silent_p.A141A|NRG2_ENST00000358522.3_Silent_p.A141A|NRG2_ENST00000394770.1_Silent_p.A141A|NRG2_ENST00000545385.1_Silent_p.A141A|NRG2_ENST00000541337.1_Silent_p.A141A|NRG2_ENST00000289409.4_Silent_p.A141A	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	141					embryo development (GO:0009790)|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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGAGCCGCCGGCTGGGACCA	0.697													G|||	134	0.0267572	0.0272	0.0403	5008	,	,		7889	0.0		0.0616	False		,,,				2504	0.0082				p.A141A		Atlas-SNP	.											.	NRG2	69	.	0			c.C423T						PASS	.	G	,,,,	145,4055		4,137,1959	6.0	8.0	7.0		423,423,423,423,423	-0.9	1.0	5	dbSNP_134	7	503,7855		16,471,3692	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NRG2	NM_001184935.1,NM_004883.2,NM_013981.3,NM_013982.2,NM_013983.2	,,,,	20,608,5651	AA,AG,GG		6.0182,3.4524,5.1601	,,,,	141/785,141/851,141/845,141/859,141/853	139422232	648,11910	2100	4179	6279	SO:0001819	synonymous_variant	9542	exon1			GCCGCCGGCTGGG		CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.423C>T	5.37:g.139422232G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_013982		Silent	SNP	ENST00000361474.1	37	CCDS4217.1																																																																																			G|0.965;A|0.035	0.035	strong		0.697	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982	
SYTL5	94122	hgsc.bcm.edu	37	X	37935844	37935844	+	Silent	SNP	G	G	A	rs12558731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:37935844G>A	ENST00000357972.5	+	6	1125	c.579G>A	c.(577-579)tcG>tcA	p.S193S	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000456733.2_Silent_p.S193S|SYTL5_ENST00000297875.2_Silent_p.S193S			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	193					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						AGTTCAGATCGGCAACCAGAG	0.338													A|||	12	0.00317881	0.0015	0.013	3775	,	,		12229	0.0		0.001	False		,,,				2504	0.0				p.S193S		Atlas-SNP	.											.	SYTL5	72	.	0			c.G579A						PASS	.	A	,,	5,3828		0,4,1,1627,570	68.0	52.0	57.0		579,579,579	5.2	1.0	X	dbSNP_120	57	75,6653		0,55,20,2373,1852	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL5	NM_001163334.1,NM_001163335.1,NM_138780.2	,,	0,59,21,4000,2422	AA,AG,A,GG,G		1.1147,0.1304,0.7575	,,	193/753,193/731,193/731	37935844	80,10481	2202	4300	6502	SO:0001819	synonymous_variant	94122	exon5			CAGATCGGCAACC		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.579G>A	X.37:g.37935844G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	41	40	0.97561	NM_001163334	A2RRF2	Silent	SNP	ENST00000357972.5	37	CCDS14244.1																																																																																			G|0.993;A|0.007	0.007	strong		0.338	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780	
MEF2A	4205	hgsc.bcm.edu	37	15	100252892	100252892	+	Silent	SNP	A	A	G	rs34851361	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:100252892A>G	ENST00000557785.1	+	11	1759	c.1410A>G	c.(1408-1410)ccA>ccG	p.P470P	MEF2A_ENST00000449277.2_Silent_p.P402P|MEF2A_ENST00000557942.1_Silent_p.P478P|MEF2A_ENST00000558812.1_Silent_p.P410P|MEF2A_ENST00000453228.2_Silent_p.P470P|MEF2A_ENST00000338042.6_Silent_p.P479P|MEF2A_ENST00000354410.5_Silent_p.P472P	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	480					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)			TCCATTCTCCAATTGTGCTTG	0.562													A|||	151	0.0301518	0.0129	0.0418	5008	,	,		14123	0.0		0.0795	False		,,,				2504	0.0256				p.P472P		Atlas-SNP	.											.	MEF2A	138	.	0			c.A1416G						PASS	.	A	,,,,	85,4001		0,85,1958	38.0	40.0	39.0		1410,1230,1206,1410,1416	-11.9	0.0	15	dbSNP_126	39	705,7679		32,641,3519	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	,,,,	32,726,5477	GG,GA,AA		8.4089,2.0803,6.3352	,,,,	470/498,410/438,402/430,470/498,472/500	100252892	790,11680	2043	4192	6235	SO:0001819	synonymous_variant	4205	exon11			TTCTCCAATTGTG		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.1410A>G	15.37:g.100252892A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	104	22	0.211538	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																			A|0.949;G|0.051	0.051	strong		0.562	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
FASN	2194	hgsc.bcm.edu	37	17	80045086	80045086	+	Silent	SNP	G	G	C	rs4485435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80045086G>C	ENST00000306749.2	-	21	3485	c.3267C>G	c.(3265-3267)gcC>gcG	p.A1089A		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1089					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)	GGACGCCTCCGGCCACTGTGA	0.672													.|||	1117	0.223043	0.3222	0.4092	5008	,	,		11177	0.1121		0.2217	False		,,,				2504	0.0726				p.A1089A	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C3267G						PASS	.						18.0	19.0	19.0					17																	80045086		2185	4286	6471	SO:0001819	synonymous_variant	2194	exon21			GCCTCCGGCCACT	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.3267C>G	17.37:g.80045086G>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			G|0.762;C|0.238	0.238	strong		0.672	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
STIL	6491	hgsc.bcm.edu	37	1	47746678	47746678	+	Silent	SNP	G	G	C	rs10789505	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:47746678G>C	ENST00000360380.3	-	13	1815	c.1452C>G	c.(1450-1452)tcC>tcG	p.S484S	STIL_ENST00000371877.3_Silent_p.S484S|STIL_ENST00000396221.2_Silent_p.S484S|STIL_ENST00000337817.5_Silent_p.S484S|STIL_ENST00000243182.6_Silent_p.S484S	NM_001282936.1	NP_001269865.1	Q15468	STIL_HUMAN	SCL/TAL1 interrupting locus	484					cell proliferation (GO:0008283)|determination of left/right symmetry (GO:0007368)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural tube closure (GO:0001843)|neural tube development (GO:0021915)|notochord development (GO:0030903)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	36		Acute lymphoblastic leukemia(5;0.00116)|all_hematologic(5;0.00444)				TTCCTCTCAAGGAAGGCTCTC	0.438													G|||	1162	0.232029	0.3911	0.0677	5008	,	,		17252	0.3095		0.0905	False		,,,				2504	0.1994				p.S484S		Atlas-SNP	.											.	STIL	91	.	0			c.C1452G						PASS	.	G	,	1488,2918	477.4+/-357.9	243,1002,958	124.0	118.0	120.0		1452,1452	-3.3	0.0	1	dbSNP_120	120	658,7942	167.5+/-219.3	21,616,3663	no	coding-synonymous,coding-synonymous	STIL	NM_001048166.1,NM_003035.2	,	264,1618,4621	CC,CG,GG		7.6512,33.7721,16.5001	,	484/1289,484/1288	47746678	2146,10860	2203	4300	6503	SO:0001819	synonymous_variant	6491	exon12			TCTCAAGGAAGGC	M74558	CCDS548.1, CCDS41329.1, CCDS72785.1, CCDS72786.1	1p32	2010-02-09	2005-11-29	2005-11-29	ENSG00000123473	ENSG00000123473			10879	protein-coding gene	gene with protein product		181590	"""TAL1 (SCL) interrupting locus"""	SIL		2209547	Standard	NM_003035		Approved	MCPH7	uc001crd.1	Q15468	OTTHUMG00000007851	ENST00000360380.3:c.1452C>G	1.37:g.47746678G>C		Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	157	113	0.719745	NM_003035	Q5T0C5|Q68CN9	Silent	SNP	ENST00000360380.3	37	CCDS548.1	474	0.21703296703296704	203	0.41260162601626016	29	0.08011049723756906	178	0.3111888111888112	64	0.08443271767810026	G	2.296	-0.361387	0.05103	0.337721	0.076512	ENSG00000123473	ENST00000436811	.	.	.	5.14	-3.31	0.04988	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.47058	-0.9146	3	.	.	.	-3.396	1.0397	0.01556	0.3133:0.0919:0.2388:0.3561	rs10789505;rs10789505	.	.	.	V	18	.	.	L	-	1	0	STIL	47519265	0.001000	0.12720	0.001000	0.08648	0.594000	0.36715	0.169000	0.16641	-0.453000	0.07076	0.655000	0.94253	CTT	G|0.817;C|0.183	0.183	strong		0.438	STIL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021649.2	NM_003035	
GLI3	2737	hgsc.bcm.edu	37	7	42004600	42004600	+	Silent	SNP	G	G	A	rs34089404	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:42004600G>A	ENST00000395925.3	-	15	4155	c.4071C>T	c.(4069-4071)taC>taT	p.Y1357Y	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1357					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|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)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						CTGGCCCTTGGTAGATGTTGA	0.642									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				A|||	277	0.0553115	0.0666	0.0403	5008	,	,		18248	0.0069		0.0736	False		,,,				2504	0.0818				p.Y1357Y		Atlas-SNP	.											.	GLI3	312	.	0			c.C4071T						PASS	.	A		241,4165	792.7+/-415.2	9,223,1971	35.0	34.0	34.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4071	-1.0	0.4	7	dbSNP_126	34	765,7833	776.2+/-407.7	40,685,3574	no	coding-synonymous	GLI3	NM_000168.5		49,908,5545	AA,AG,GG		8.8974,5.4698,7.7361		1357/1581	42004600	1006,11998	2203	4299	6502	SO:0001819	synonymous_variant	2737	exon15	Familial Cancer Database	;	CCCTTGGTAGATG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.4071C>T	7.37:g.42004600G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	144	44	0.305556	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																			G|0.927;A|0.073	0.073	strong		0.642	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
OR5D18	219438	hgsc.bcm.edu	37	11	55587914	55587914	+	Missense_Mutation	SNP	A	A	G	rs55832853	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55587914A>G	ENST00000333976.4	+	1	829	c.809A>G	c.(808-810)cAc>cGc	p.H270R		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	270			H -> R (in dbSNP:rs55832853).			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(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				AACTCCAGGCACACAGTCAAA	0.498													N|||	1167	0.233027	0.0204	0.3228	5008	,	,		18084	0.3889		0.2903	False		,,,				2504	0.2372				p.H270R		Atlas-SNP	.											OR5D18,NS,carcinoma,-1,1	OR5D18	121	1	0			c.A809G						scavenged	.	A	ARG/HIS	288,4112		11,266,1923	89.0	86.0	87.0		809	2.4	1.0	11	dbSNP_129	87	2368,6224		350,1668,2278	no	missense	OR5D18	NM_001001952.1	29	361,1934,4201	GG,GA,AA		27.5605,6.5455,20.4433	benign	270/314	55587914	2656,10336	2200	4296	6496	SO:0001583	missense	219438	exon1			CCAGGCACACAGT	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.809A>G	11.37:g.55587914A>G	ENSP00000335025:p.His270Arg	Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	576	0.26373626373626374	15	0.03048780487804878	126	0.34806629834254144	212	0.3706293706293706	223	0.2941952506596306	.	0.046	-1.267286	0.01433	0.065455	0.275605	ENSG00000186119	ENST00000333976	T	0.00044	8.83	5.03	2.44	0.29823	GPCR, rhodopsin-like superfamily (1);	0.181667	0.26939	N	0.021727	T	0.00012	0.0000	N	0.13098	0.295	0.80722	P	0.0	B	0.11235	0.004	B	0.18263	0.021	T	0.25676	-1.0125	9	0.62326	D	0.03	-11.8734	5.983	0.19417	0.5245:0.1337:0.0:0.3418	rs55832853;rs61896324	270	Q8NGL1	OR5DI_HUMAN	R	270	ENSP00000335025:H270R	ENSP00000335025:H270R	H	+	2	0	OR5D18	55344490	0.000000	0.05858	0.973000	0.42090	0.199000	0.23934	0.454000	0.21827	0.236000	0.21180	-0.508000	0.04489	CAC	A|0.774;G|0.226	0.226	strong		0.498	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952	
FCGBP	8857	hgsc.bcm.edu	37	19	40363926	40363926	+	Missense_Mutation	SNP	C	C	G	rs3746013	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40363926C>G	ENST00000221347.6	-	31	14723	c.14716G>C	c.(14716-14718)Gat>Cat	p.D4906H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4906	VWFD 12. {ECO:0000255|PROSITE- ProRule:PRU00580}.		D -> H (in dbSNP:rs3746013). {ECO:0000269|PubMed:9182547}.			extracellular vesicular exosome (GO:0070062)		p.D4906H(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)			CGTTGGAGATCTCCAGCTGCA	0.597													C|||	1444	0.288339	0.23	0.1614	5008	,	,		21074	0.5387		0.1998	False		,,,				2504	0.2904				p.D4906H		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	stomach(1)	c.G14716C						PASS	.	C	HIS/ASP	1012,3394	376.8+/-322.2	113,786,1304	95.0	77.0	83.0		14716	-1.0	0.0	19	dbSNP_107	83	1829,6771	327.7+/-318.0	189,1451,2660	yes	missense	FCGBP	NM_003890.2	81	302,2237,3964	GG,GC,CC		21.2674,22.9687,21.8438	probably-damaging	4906/5406	40363926	2841,10165	2203	4300	6503	SO:0001583	missense	8857	exon31			GGAGATCTCCAGC	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.14716G>C	19.37:g.40363926C>G	ENSP00000221347:p.Asp4906His	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	180	89	0.494444	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	648	0.2967032967032967	109	0.22154471544715448	63	0.17403314917127072	321	0.5611888111888111	155	0.20448548812664907	C	9.033	0.987678	0.18966	0.229687	0.212674	ENSG00000090920	ENST00000221347	T	0.59502	0.26	5.34	-1.04	0.10068	von Willebrand factor, type D domain (3);	0.249576	0.34046	U	0.004304	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	D	0.69078	0.997	D	0.74674	0.984	T	0.45571	-0.9252	9	0.14656	T	0.56	.	6.206	0.20604	0.0:0.5518:0.2287:0.2194	rs3746013;rs61020961;rs3746013	4906	Q9Y6R7	FCGBP_HUMAN	H	4906	ENSP00000221347:D4906H	ENSP00000221347:D4906H	D	-	1	0	FCGBP	45055766	0.000000	0.05858	0.005000	0.12908	0.014000	0.08584	0.392000	0.20801	-0.030000	0.13804	0.313000	0.20887	GAT	C|0.746;G|0.254	0.254	strong		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SLC1A4	6509	hgsc.bcm.edu	37	2	65245365	65245365	+	Missense_Mutation	SNP	G	G	A	rs759458	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	120	0	0		WXS	Illumina HiSeq	Phase_I	108	41	0.37963	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	
IGSF10	285313	hgsc.bcm.edu	37	3	151166058	151166058	+	Missense_Mutation	SNP	G	G	A	rs17204557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	382	0	0		WXS	Illumina HiSeq	Phase_I	330	155	0.469697	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	
BCL9L	283149	hgsc.bcm.edu	37	11	118769604	118769604	+	Silent	SNP	C	C	T	rs61751532	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118769604C>T	ENST00000334801.3	-	8	4984	c.4020G>A	c.(4018-4020)caG>caA	p.Q1340Q	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1340	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TGGGGAAGTACTGGAGGGTGC	0.617													c|||	123	0.0245607	0.0015	0.0375	5008	,	,		17998	0.001		0.0875	False		,,,				2504	0.0061				p.Q1340Q		Atlas-SNP	.											.	BCL9L	254	.	0			c.G4020A						PASS	.			82,4318	69.8+/-107.6	0,82,2118	68.0	70.0	69.0		4020	0.8	1.0	11	dbSNP_129	69	722,7868	173.3+/-223.8	40,642,3613	no	coding-synonymous	BCL9L	NM_182557.2		40,724,5731	TT,TC,CC		8.4051,1.8636,6.1894		1340/1500	118769604	804,12186	2200	4295	6495	SO:0001819	synonymous_variant	283149	exon8			GAAGTACTGGAGG	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.4020G>A	11.37:g.118769604C>T		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	327	221	0.675841	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			C|0.941;T|0.059	0.059	strong		0.617	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
NUFIP2	57532	hgsc.bcm.edu	37	17	27613677	27613677	+	Silent	SNP	G	G	A	rs12452857	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:27613677G>A	ENST00000225388.4	-	2	1393	c.1335C>T	c.(1333-1335)ccC>ccT	p.P445P	NUFIP2_ENST00000579665.1_Intron	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	445						cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			CAGAAGAGATGGGTGTTAGAG	0.433													G|||	772	0.154153	0.0371	0.2839	5008	,	,		20061	0.0119		0.2773	False		,,,				2504	0.2403				p.P445P		Atlas-SNP	.											.	NUFIP2	60	.	0			c.C1335T						PASS	.	G		333,4073	174.4+/-204.0	7,319,1877	81.0	81.0	81.0		1335	4.1	1.0	17	dbSNP_120	81	2433,6167	401.1+/-347.0	365,1703,2232	no	coding-synonymous	NUFIP2	NM_020772.2		372,2022,4109	AA,AG,GG		28.2907,7.5579,21.2671		445/696	27613677	2766,10240	2203	4300	6503	SO:0001819	synonymous_variant	57532	exon2			AGAGATGGGTGTT	AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.1335C>T	17.37:g.27613677G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	142	77	0.542253	NM_020772	A1L3A6|Q9P2M5	Silent	SNP	ENST00000225388.4	37	CCDS32600.1																																																																																			G|0.815;A|0.185	0.185	strong		0.433	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772	
TOMM5	401505	hgsc.bcm.edu	37	9	37592452	37592452	+	Silent	SNP	G	G	A	rs7021977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:37592452G>A	ENST00000321301.6	-	1	187	c.78C>T	c.(76-78)tcC>tcT	p.S26S	RP11-613M10.8_ENST00000537239.2_Silent_p.S5S|TOMM5_ENST00000377773.5_Silent_p.S26S|TOMM5_ENST00000401811.3_Silent_p.S26S|RP11-613M10.9_ENST00000540557.1_Intron|TOMM5_ENST00000544379.1_Silent_p.S26S	NM_001001790.2	NP_001001790.1	Q8N4H5	TOM5_HUMAN	translocase of outer mitochondrial membrane 5 homolog (yeast)	26					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial outer membrane translocase complex (GO:0005742)|mitochondrion (GO:0005739)											TCCGTATGGAGGAGATCACAT	0.612													G|||	714	0.142572	0.3124	0.1268	5008	,	,		17367	0.001		0.1581	False		,,,				2504	0.0542				p.S26S		Atlas-SNP	.											.	TOMM5	3	.	0			c.C78T						PASS	.	G	,,	1220,2892		180,860,1016	61.0	68.0	66.0		78,78,78	-0.7	1.0	9	dbSNP_116	66	1266,7130		100,1066,3032	no	coding-synonymous,coding-synonymous,coding-synonymous	TOMM5	NM_001001790.2,NM_001134484.1,NM_001134485.1	,,	280,1926,4048	AA,AG,GG		15.0786,29.6693,19.8753	,,	26/52,26/93,26/86	37592452	2486,10022	2056	4198	6254	SO:0001819	synonymous_variant	401505	exon1			TATGGAGGAGATC	BC029423	CCDS43803.1, CCDS47967.1, CCDS47968.1	9p13.2	2008-08-21	2008-08-21	2008-08-21	ENSG00000175768	ENSG00000175768			31369	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 105"""	C9orf105		18331822	Standard	NM_001001790		Approved	bA613M10.3	uc011lql.2	Q8N4H5	OTTHUMG00000019923	ENST00000321301.6:c.78C>T	9.37:g.37592452G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_001134485	B2DG07|F6S928|Q5JRT7	Silent	SNP	ENST00000321301.6	37	CCDS43803.1																																																																																			G|0.834;A|0.166	0.166	strong		0.612	TOMM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052468.2		
PHC2	1912	hgsc.bcm.edu	37	1	33790496	33790496	+	Silent	SNP	G	G	A	rs11554674	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:33790496G>A	ENST00000257118.5	-	14	2600	c.2547C>T	c.(2545-2547)taC>taT	p.Y849Y	PHC2_ENST00000431992.1_Silent_p.Y820Y|PHC2_ENST00000373422.3_Silent_p.Y455Y|PHC2_ENST00000419414.2_Silent_p.Y850Y|PHC2_ENST00000373418.3_Silent_p.Y314Y|RP11-415J8.3_ENST00000457957.2_RNA|PHC2_ENST00000485928.1_5'UTR|RP11-415J8.3_ENST00000587696.1_RNA|RP11-415J8.3_ENST00000588828.1_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	99	0	0		WXS	Illumina HiSeq	Phase_I	71	25	0.352113	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	
SNX13	23161	hgsc.bcm.edu	37	7	17854532	17854532	+	Silent	SNP	G	G	T	rs2723501	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:17854532G>T	ENST00000409389.1	-	20	2194	c.2022C>A	c.(2020-2022)ccC>ccA	p.P674P	SNX13_ENST00000496855.1_5'UTR|SNX13_ENST00000428135.3_Silent_p.P663P			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	674	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)					GAGCTAAAGCGGGGGATGCCT	0.383													T|||	3494	0.697684	0.8661	0.5807	5008	,	,		12907	0.7192		0.5239	False		,,,				2504	0.7096				p.P663P		Atlas-SNP	.											.	SNX13	113	.	0			c.C1989A						PASS	.	T		2905,807		1147,611,98	82.0	73.0	76.0		1989	-4.5	1.0	7	dbSNP_100	76	4355,3819		1168,2019,900	no	coding-synonymous	SNX13	NM_015132.4		2315,2630,998	TT,TG,GG		46.7213,21.7403,38.9197		663/958	17854532	7260,4626	1856	4087	5943	SO:0001819	synonymous_variant	23161	exon20			TAAAGCGGGGGAT	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.2022C>A	7.37:g.17854532G>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Silent	SNP	ENST00000409389.1	37																																																																																				G|0.331;T|0.669	0.669	strong		0.383	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156909695	156909695	+	Silent	SNP	G	G	A	rs2275199	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156909695G>A	ENST00000361409.2	-	36	4363	c.3621C>T	c.(3619-3621)aaC>aaT	p.N1207N	ARHGEF11_ENST00000315174.8_Silent_p.N623N|ARHGEF11_ENST00000368194.3_Silent_p.N1247N|ARHGEF11_ENST00000487682.1_5'UTR	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1207					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)					GATGTCGCAGGTTCTCCACTG	0.597													G|||	955	0.190695	0.1634	0.1628	5008	,	,		20161	0.2867		0.174	False		,,,				2504	0.1656				p.N1247N		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.C3741T						PASS	.	G	,	739,3667	301.0+/-286.6	72,595,1536	49.0	52.0	51.0		3621,3741	1.2	1.0	1	dbSNP_100	51	1450,7150	273.7+/-290.8	129,1192,2979	no	coding-synonymous,coding-synonymous	ARHGEF11	NM_014784.2,NM_198236.1	,	201,1787,4515	AA,AG,GG		16.8605,16.7726,16.8307	,	1207/1523,1247/1563	156909695	2189,10817	2203	4300	6503	SO:0001819	synonymous_variant	9826	exon37			TCGCAGGTTCTCC	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.3621C>T	1.37:g.156909695G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	17	16	0.941176	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	37	CCDS1162.1																																																																																			G|0.817;A|0.183	0.183	strong		0.597	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
TXNDC16	57544	hgsc.bcm.edu	37	14	52981664	52981664	+	Missense_Mutation	SNP	G	G	C	rs117463339	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:52981664G>C	ENST00000281741.4	-	8	910	c.539C>G	c.(538-540)gCt>gGt	p.A180G	TXNDC16_ENST00000554399.1_Intron	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	180				A -> G (in Ref. 1; BAA92582). {ECO:0000305}.	cell redox homeostasis (GO:0045454)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(3)|skin(1)	21	Breast(41;0.0716)					ATACACAAAAGCGGCTTCCAT	0.363													G|||	73	0.0145767	0.0061	0.0101	5008	,	,		18339	0.004		0.0258	False		,,,				2504	0.0286				p.A180G		Atlas-SNP	.											.	TXNDC16	59	.	0			c.C539G						PASS	.	G	GLY/ALA,GLY/ALA	36,4370	40.8+/-73.8	0,36,2167	130.0	133.0	132.0		524,539	5.7	1.0	14	dbSNP_132	132	264,8334	102.1+/-163.3	2,260,4037	yes	missense,missense	TXNDC16	NM_001160047.1,NM_020784.2	60,60	2,296,6204	CC,CG,GG		3.0705,0.8171,2.307	probably-damaging,probably-damaging	175/821,180/826	52981664	300,12704	2203	4299	6502	SO:0001583	missense	57544	exon8			ACAAAAGCGGCTT	AB037765	CCDS32083.1	14q22.1	2007-08-16	2007-08-16	2007-08-16		ENSG00000087301			19965	protein-coding gene	gene with protein product			"""KIAA1344"""	KIAA1344			Standard	NM_020784		Approved		uc001wzs.3	Q9P2K2		ENST00000281741.4:c.539C>G	14.37:g.52981664G>C	ENSP00000281741:p.Ala180Gly	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	100	37	0.37	NM_020784	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Missense_Mutation	SNP	ENST00000281741.4	37	CCDS32083.1	33	0.01510989010989011	3	0.006097560975609756	7	0.019337016574585635	0	0.0	23	0.030343007915567283	G	25.2	4.612167	0.87258	0.008171	0.030705	ENSG00000087301	ENST00000281741	T	0.36157	1.27	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.36717	0.0977	M	0.72894	2.215	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.54510	-0.8283	10	0.87932	D	0	-44.0895	17.2216	0.86959	0.0:0.0:1.0:0.0	.	175;180	B7ZME4;Q9P2K2	.;TXD16_HUMAN	G	180	ENSP00000281741:A180G	ENSP00000281741:A180G	A	-	2	0	TXNDC16	52051414	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.007000	0.63984	2.681000	0.91329	0.563000	0.77884	GCT	G|0.979;C|0.021	0.021	strong		0.363	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699	
DISC1	27185	hgsc.bcm.edu	37	1	231902975	231902975	+	Missense_Mutation	SNP	C	C	T	rs28930675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:231902975C>T	ENST00000602281.1	+	5	1411	c.1358C>T	c.(1357-1359)aCg>aTg	p.T453M	DISC1_ENST00000366633.3_Missense_Mutation_p.T453M|DISC1_ENST00000535983.1_Missense_Mutation_p.T453M|DISC1_ENST00000439617.2_Missense_Mutation_p.T453M|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000366636.4_Missense_Mutation_p.T453M|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000602873.1_Missense_Mutation_p.T103M|DISC1_ENST00000537876.1_Missense_Mutation_p.T453M|DISC1_ENST00000539444.1_Missense_Mutation_p.T453M	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	453	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)				GTGTCCATCACGAGACGAGAC	0.507													C|||	7	0.00139776	0.0008	0.0	5008	,	,		18597	0.0		0.001	False		,,,				2504	0.0051				p.T485M		Atlas-SNP	.											.	DISC1	207	.	0			c.C1454T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	111.0	98.0	102.0		1358,1358,1454,1358,1358,,1358,1358,1358,1358,1358,1358,1358,1358,308,1358	3.7	0.2	1	dbSNP_125	102	25,8575	18.5+/-59.3	0,25,4275	yes	missense,missense,missense,missense,missense,intron,missense,missense,missense,missense,missense,missense,missense,missense,missense,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_001164549.1,NM_001164556.1,NM_018662.2	81,81,81,81,81,,81,81,81,81,81,81,81,81,81,81	0,26,6477	TT,TC,CC		0.2907,0.0227,0.1999	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	453/833,453/679,485/887,453/804,453/756,,453/696,453/682,453/663,453/580,453/560,453/560,453/552,453/548,103/202,453/855	231902975	26,12980	2203	4300	6503	SO:0001583	missense	27185	exon6			CCATCACGAGACG	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.1358C>T	1.37:g.231902975C>T	ENSP00000473425:p.Thr453Met	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	124	32	0.258065	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	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	12.61	1.989191	0.35131	2.27E-4	0.002907	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944	T;T;T;T;T;T;T;T	0.13901	2.92;2.73;2.72;2.57;2.9;2.57;2.57;2.55	3.74	3.74	0.42951	.	0.423266	0.24527	N	0.037752	T	0.23572	0.0570	M	0.62723	1.935	0.20638	N	0.999871	D;D;D;D;D;D;D;P;D;D;P;D;D;D;D;D;D;P	0.64830	0.992;0.992;0.988;0.983;0.989;0.966;0.979;0.941;0.994;0.988;0.941;0.994;0.988;0.979;0.988;0.979;0.988;0.941	P;P;P;P;P;B;B;B;P;P;B;P;P;B;P;B;P;B	0.54346	0.731;0.749;0.504;0.516;0.512;0.367;0.434;0.407;0.663;0.663;0.236;0.663;0.59;0.434;0.59;0.434;0.663;0.236	T	0.03413	-1.1039	10	0.59425	D	0.04	-3.9113	9.0698	0.36486	0.0:0.8923:0.0:0.1077	rs28930675	485;485;453;453;453;453;453;103;453;453;453;453;453;453;453;453;453;453	C4P096;E2QRA4;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0C1;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P0B1;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	M	453;453;453;485;453;453;453;453;453;453	ENSP00000403888:T453M;ENSP00000355596:T453M;ENSP00000443996:T453M;ENSP00000440909:T453M;ENSP00000355593:T453M;ENSP00000440953:T453M;ENSP00000295051:T453M;ENSP00000441193:T453M	ENSP00000295051:T453M	T	+	2	0	DISC1	229969598	0.470000	0.25854	0.174000	0.22961	0.391000	0.30476	1.717000	0.37991	2.063000	0.61619	0.655000	0.94253	ACG	C|0.998;T|0.002	0.002	strong		0.507	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
KDR	3791	hgsc.bcm.edu	37	4	55973911	55973911	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:55973911C>T	ENST00000263923.4	-	10	1700	c.1405G>A	c.(1405-1407)Gag>Aag	p.E469K		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	469	Ig-like C2-type 5.				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)			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)	CACCTGGGCTCGTTGGCGCAC	0.512			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)																											p.E469K		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	0			c.G1405A						scavenged	.						165.0	141.0	149.0					4																	55973911		2203	4300	6503	SO:0001583	missense	3791	exon10			TGGGCTCGTTGGC	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.1405G>A	4.37:g.55973911C>T	ENSP00000263923:p.Glu469Lys	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	161	2	0.0124224	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	C	8.608	0.888541	0.17540	.	.	ENSG00000128052	ENST00000263923	T	0.75477	-0.94	5.29	-2.4	0.06583	Immunoglobulin subtype (1);Immunoglobulin-like (1);	2.299140	0.01142	N	0.006236	T	0.38321	0.1036	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.49476	-0.8936	10	0.05959	T	0.93	.	1.3869	0.02242	0.1184:0.2106:0.2613:0.4097	.	469;469	P35968-2;P35968	.;VGFR2_HUMAN	K	469	ENSP00000263923:E469K	ENSP00000263923:E469K	E	-	1	0	KDR	55668668	0.002000	0.14202	0.000000	0.03702	0.436000	0.31835	0.095000	0.15127	-0.556000	0.06134	-0.657000	0.03884	GAG	.	.	none		0.512	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
AVPR1B	553	hgsc.bcm.edu	37	1	206225260	206225260	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:206225260C>G	ENST00000367126.4	+	1	1285	c.820C>G	c.(820-822)Cgg>Ggg	p.R274G	RP11-38J22.3_ENST00000425896.1_RNA	NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	274					activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)|skin(2)	20			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)	CACCATCTCACGGGCCAAGAT	0.597																																					p.R274G		Atlas-SNP	.											.	AVPR1B	47	.	0			c.C820G						PASS	.						71.0	68.0	69.0					1																	206225260		2203	4300	6503	SO:0001583	missense	553	exon1			ATCTCACGGGCCA	D31833	CCDS73015.1	1q32	2014-05-06			ENSG00000198049	ENSG00000198049		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	896	protein-coding gene	gene with protein product		600264		AVPR3		7929452, 8586456	Standard	NM_000707		Approved		uc001hds.2	P47901	OTTHUMG00000184377	ENST00000367126.4:c.820C>G	1.37:g.206225260C>G	ENSP00000356094:p.Arg274Gly	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	190	39	0.205263	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	37	CCDS30994.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.537242	0.45176	.	.	ENSG00000198049	ENST00000367126	T	0.40756	1.02	5.34	-0.645	0.11475	GPCR, rhodopsin-like superfamily (1);	0.081659	0.48767	D	0.000165	T	0.65974	0.2743	M	0.85777	2.775	0.25895	N	0.983424	D	0.89917	1.0	D	0.83275	0.996	T	0.67189	-0.5733	10	0.72032	D	0.01	-31.1727	16.7694	0.85533	0.7528:0.2472:0.0:0.0	.	274	P47901	V1BR_HUMAN	G	274	ENSP00000356094:R274G	ENSP00000356094:R274G	R	+	1	2	AVPR1B	204391883	0.001000	0.12720	0.110000	0.21437	0.836000	0.47400	0.017000	0.13399	-0.086000	0.12550	0.462000	0.41574	CGG	.	.	none		0.597	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707	
PRTG	283659	hgsc.bcm.edu	37	15	55970041	55970041	+	Silent	SNP	A	A	G	rs11854213	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:55970041A>G	ENST00000389286.4	-	8	1382	c.1335T>C	c.(1333-1335)aaT>aaC	p.N445N	RP11-420M1.2_ENST00000561155.1_RNA	NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		CTTTGTCTGAATTATAAAGTG	0.408													A|||	1210	0.241613	0.298	0.1225	5008	,	,		15648	0.4038		0.0964	False		,,,				2504	0.2321				p.N445N		Atlas-SNP	.											.	PRTG	110	.	0			c.T1335C						PASS	.	A		1026,2692		150,726,983	123.0	116.0	118.0		1335	-0.2	1.0	15	dbSNP_120	118	786,7406		45,696,3355	no	coding-synonymous	PRTG	NM_173814.4		195,1422,4338	GG,GA,AA		9.5947,27.5955,15.2141		445/1151	55970041	1812,10098	1859	4096	5955	SO:0001819	synonymous_variant	283659	exon8			GTCTGAATTATAA	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.1335T>C	15.37:g.55970041A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	94	27	0.287234	NM_173814		Silent	SNP	ENST00000389286.4	37	CCDS42040.1																																																																																			A|0.787;G|0.213	0.213	strong		0.408	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
PRTG	283659	hgsc.bcm.edu	37	15	55972797	55972797	+	Missense_Mutation	SNP	T	T	C	rs16976466	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:55972797T>C	ENST00000389286.4	-	5	753	c.706A>G	c.(706-708)Aca>Gca	p.T236A	RP11-420M1.2_ENST00000561155.1_RNA	NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		GCTATAATTGTTGGTGTGTGG	0.353													T|||	1111	0.221845	0.2988	0.1009	5008	,	,		13043	0.3214		0.0974	False		,,,				2504	0.229				p.T236A		Atlas-SNP	.											.	PRTG	110	.	0			c.A706G						PASS	.	T	ALA/THR	1024,2680		152,720,980	172.0	161.0	165.0		706	0.2	0.9	15	dbSNP_123	165	806,7394		42,722,3336	yes	missense	PRTG	NM_173814.4	58	194,1442,4316	CC,CT,TT		9.8293,27.6458,15.373	benign	236/1151	55972797	1830,10074	1852	4100	5952	SO:0001583	missense	283659	exon5			TAATTGTTGGTGT	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.706A>G	15.37:g.55972797T>C	ENSP00000373937:p.Thr236Ala	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	141	29	0.205674	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	423	0.1936813186813187	135	0.27439024390243905	44	0.12154696132596685	170	0.2972027972027972	74	0.09762532981530343	T	10.54	1.379977	0.24944	0.276458	0.098293	ENSG00000166450	ENST00000389286	T	0.66460	-0.21	5.42	0.203	0.15195	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.382139	0.28647	N	0.014605	T	0.00012	0.0000	L	0.33753	1.03	0.54753	P	1.8999999999991246E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.17715	-1.0360	9	0.12430	T	0.62	-3.5581	6.225	0.20703	0.147:0.4944:0.0:0.3586	rs16976466;rs52831048;rs56497285;rs16976466	236	Q2VWP7	PRTG_HUMAN	A	236	ENSP00000373937:T236A	ENSP00000373937:T236A	T	-	1	0	PRTG	53760089	0.014000	0.17966	0.943000	0.38184	0.750000	0.42670	0.139000	0.16036	0.014000	0.14944	0.377000	0.23210	ACA	C|0.201;N|0.000	0.201	strong		0.353	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
MUC17	140453	hgsc.bcm.edu	37	7	100681920	100681920	+	Missense_Mutation	SNP	C	C	T	rs200222893|rs140211048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681920C>T	ENST00000306151.4	+	3	7287	c.7223C>T	c.(7222-7224)cCg>cTg	p.P2408L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2408	59 X approximate tandem repeats.|Ser-rich.				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)					AGCACCATGCCGGTGGTCAGT	0.512																																					p.P2408L		Atlas-SNP	.											MUC17,NS,carcinoma,-1,1	MUC17	804	1	0			c.C7223T						PASS	.	C	LEU/PRO	1,4405		0,1,2202	381.0	361.0	368.0		7223	-1.5	0.0	7	dbSNP_134	368	1,8599		0,1,4299	no	missense	MUC17	NM_001040105.1	98	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	2408/4494	100681920	2,13004	2203	4300	6503	SO:0001583	missense	140453	exon3			CCATGCCGGTGGT	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.7223C>T	7.37:g.100681920C>T	ENSP00000302716:p.Pro2408Leu	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	314	16	0.0509554	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	2.505	-0.314307	0.05422	2.27E-4	1.16E-4	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.762	-1.52	0.08637	.	.	.	.	.	T	0.06005	0.0156	L	0.34521	1.04	0.09310	N	1	D	0.76494	0.999	D	0.63283	0.913	T	0.24764	-1.0151	9	0.23302	T	0.38	.	3.7422	0.08534	0.0:0.6508:0.0:0.3492	.	2408	Q685J3	MUC17_HUMAN	L	2408	ENSP00000302716:P2408L	ENSP00000302716:P2408L	P	+	2	0	MUC17	100468640	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.422000	0.02453	-1.381000	0.02112	-1.368000	0.01194	CCG	C|1.000;T|0.000	0.000	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
GLG1	2734	hgsc.bcm.edu	37	16	74490556	74490556	+	Silent	SNP	G	G	A	rs9945	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74490556G>A	ENST00000422840.2	-	25	3362	c.3363C>T	c.(3361-3363)taC>taT	p.Y1121Y	GLG1_ENST00000205061.5_Silent_p.Y1121Y|RNU6-237P_ENST00000515985.1_RNA|GLG1_ENST00000447066.2_Silent_p.Y1110Y	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	1121					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						CCTTTGCTGCGTAACTCCACA	0.443													G|||	707	0.141174	0.261	0.1124	5008	,	,		19372	0.0089		0.1779	False		,,,				2504	0.0982				p.Y1121Y		Atlas-SNP	.											.	GLG1	106	.	0			c.C3363T						PASS	.	G	,,	1142,3254	406.0+/-333.7	147,848,1203	132.0	128.0	130.0		3330,3363,3363	-1.8	1.0	16	dbSNP_52	130	1580,7020	295.5+/-302.4	145,1290,2865	no	coding-synonymous,coding-synonymous,coding-synonymous	GLG1	NM_001145666.1,NM_001145667.1,NM_012201.5	,,	292,2138,4068	AA,AG,GG		18.3721,25.9782,20.9449	,,	1110/1193,1121/1180,1121/1204	74490556	2722,10274	2198	4300	6498	SO:0001819	synonymous_variant	2734	exon25			TGCTGCGTAACTC		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.3363C>T	16.37:g.74490556G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	96	79	0.822917	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Silent	SNP	ENST00000422840.2	37	CCDS45527.1																																																																																			T|0.028;G|0.674;C|0.146;A|0.153	0.153	strong		0.443	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	
JAK1	3716	hgsc.bcm.edu	37	1	65310489	65310489	+	Silent	SNP	T	T	C	rs2230588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:65310489T>C	ENST00000342505.4	-	16	2447	c.2199A>G	c.(2197-2199)ccA>ccG	p.P733P	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	733	Protein kinase 1. {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)	GCTTGATGAATGGGCCACACT	0.562			Mis		ALL								C|||	1866	0.372604	0.6604	0.3199	5008	,	,		18529	0.2996		0.2525	False		,,,				2504	0.2198				p.P733P		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A2199G						PASS	.	C		2469,1773		752,965,404	93.0	110.0	104.0		2199	-10.0	0.0	1	dbSNP_98	104	1963,6487		242,1479,2504	no	coding-synonymous	JAK1	NM_002227.2		994,2444,2908	CC,CT,TT		23.2308,41.7963,34.9196		733/1155	65310489	4432,8260	2121	4225	6346	SO:0001819	synonymous_variant	3716	exon16			GATGAATGGGCCA	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.2199A>G	1.37:g.65310489T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	107	79	0.738318	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			T|0.670;C|0.330	0.330	strong		0.562	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
C20orf85	128602	hgsc.bcm.edu	37	20	56735761	56735761	+	Silent	SNP	C	C	T	rs61749694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:56735761C>T	ENST00000371168.3	+	4	358	c.297C>T	c.(295-297)atC>atT	p.I99I		NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	chromosome 20 open reading frame 85	99			I -> V (in dbSNP:rs17440813).							kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	13	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)		BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)			AGGGCTTCATCGGCTGGAGAT	0.577													C|||	9	0.00179712	0.0	0.0029	5008	,	,		19067	0.0		0.007	False		,,,				2504	0.0				p.I99I		Atlas-SNP	.											.	C20orf85	35	.	0			c.C297T						PASS	.	C		6,4400	9.9+/-24.2	0,6,2197	46.0	40.0	42.0		297	1.3	1.0	20	dbSNP_129	42	43,8557	27.9+/-77.7	0,43,4257	no	coding-synonymous	C20orf85	NM_178456.2		0,49,6454	TT,TC,CC		0.5,0.1362,0.3767		99/138	56735761	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	128602	exon4			CTTCATCGGCTGG	AL354776	CCDS13465.1	20q13.32	2012-10-29			ENSG00000124237	ENSG00000124237			16216	protein-coding gene	gene with protein product	"""Low in Lung Cancer 1"""						Standard	NM_178456		Approved	bA196N14.1, LLC1	uc002xyv.3	Q9H1P6	OTTHUMG00000032836	ENST00000371168.3:c.297C>T	20.37:g.56735761C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_178456		Silent	SNP	ENST00000371168.3	37	CCDS13465.1																																																																																			C|0.997;T|0.003	0.003	strong		0.577	C20orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079866.2	NM_178456	
FBN3	84467	hgsc.bcm.edu	37	19	8154990	8154990	+	Silent	SNP	C	C	T	rs35002391	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:8154990C>T	ENST00000600128.1	-	49	6591	c.6177G>A	c.(6175-6177)gaG>gaA	p.E2059E	FBN3_ENST00000270509.2_Silent_p.E2059E|FBN3_ENST00000601739.1_Silent_p.E2059E			Q75N90	FBN3_HUMAN	fibrillin 3	2059	TB 8.					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						CACCGCTGCCCTCCTGGGGAC	0.632													C|||	1228	0.245208	0.3691	0.219	5008	,	,		18512	0.0724		0.337	False		,,,				2504	0.18				p.E2059E		Atlas-SNP	.											.	FBN3	300	.	0			c.G6177A						PASS	.	C		1599,2807	488.0+/-361.1	299,1001,903	39.0	41.0	40.0		6177	0.3	1.0	19	dbSNP_126	40	3155,5445	472.1+/-368.3	586,1983,1731	no	coding-synonymous	FBN3	NM_032447.3		885,2984,2634	TT,TC,CC		36.686,36.2914,36.5524		2059/2810	8154990	4754,8252	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon48			GCTGCCCTCCTGG		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.6177G>A	19.37:g.8154990C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1	574	0.26282051282051283	181	0.3678861788617886	89	0.24585635359116023	48	0.08391608391608392	256	0.33773087071240104	C	0.118	-1.128823	0.01756	0.362914	0.36686	ENSG00000142449	ENST00000341066	.	.	.	3.83	0.32	0.15878	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999917993	.	.	.	.	.	.	T	0.39461	-0.9613	4	0.22706	T	0.39	.	11.4047	0.49892	0.0:0.6267:0.0:0.3733	rs35002391	.	.	.	K	179	.	ENSP00000341317:R179K	R	-	2	0	FBN3	8060990	0.033000	0.19621	0.998000	0.56505	0.071000	0.16799	-0.251000	0.08818	-0.046000	0.13446	-1.598000	0.00824	AGG	C|0.668;T|0.332	0.332	strong		0.632	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
RNF39	80352	hgsc.bcm.edu	37	6	30041009	30041009	+	Missense_Mutation	SNP	A	A	G	rs2074479	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:30041009A>G	ENST00000244360.6	-	3	704	c.607T>C	c.(607-609)Tcc>Ccc	p.S203P	RNF39_ENST00000376751.3_Missense_Mutation_p.S203P	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	203			S -> P (in dbSNP:rs2074479). {ECO:0000269|PubMed:14574404}.			cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										GATGACTTGGATGTTGGGACT	0.468													g|||	958	0.191294	0.2988	0.1744	5008	,	,		20885	0.1905		0.0954	False		,,,				2504	0.1575				p.S203P	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											RNF39_ENST00000244360,NS,carcinoma,+1,1	RNF39	27	1	0			c.T607C						PASS	.		PRO/SER,PRO/SER	772,2250		93,586,832	131.0	128.0	129.0		607,607	4.0	0.7	6	dbSNP_96	129	650,4768		48,554,2107	yes	missense,missense	RNF39	NM_025236.3,NM_170769.2	74,74	141,1140,2939	GG,GA,AA		11.997,25.546,16.8483	benign,benign	203/421,203/355	30041009	1422,7018	1511	2709	4220	SO:0001583	missense	80352	exon3			ACTTGGATGTTGG	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"""RING-type (C3HC4) zinc fingers"""	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.607T>C	6.37:g.30041009A>G	ENSP00000244360:p.Ser203Pro	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	37	CCDS4673.1	404	0.184981684981685	146	0.2967479674796748	72	0.19889502762430938	115	0.20104895104895104	71	0.09366754617414248	g	0.008	-1.893380	0.00522	0.25546	0.11997	ENSG00000204618	ENST00000376751;ENST00000244360	T;T	0.70399	0.04;-0.48	3.99	3.99	0.46301	.	0.546488	0.13684	N	0.370007	T	0.19167	0.0460	N	0.01874	-0.695	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07139	-1.0788	9	0.13470	T	0.59	-19.0329	7.844	0.29414	0.1163:0.0:0.8837:0.0	rs2074479;rs52821835;rs60743069;rs2074479	203;203	Q9H2S5;Q9H2S5-2	RNF39_HUMAN;.	P	203	ENSP00000365942:S203P;ENSP00000244360:S203P	ENSP00000244360:S203P	S	-	1	0	RNF39	30148988	0.782000	0.28689	0.659000	0.29680	0.025000	0.11179	0.836000	0.27545	1.050000	0.40346	-0.372000	0.07161	TCC	A|0.808;G|0.192	0.192	strong		0.468	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769	
ARSD	414	hgsc.bcm.edu	37	X	2833643	2833643	+	Missense_Mutation	SNP	C	C	A	rs115332247		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	194	0	0		WXS	Illumina HiSeq	Phase_I	95	28	0.294737	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		
ITGA2B	3674	hgsc.bcm.edu	37	17	42453065	42453065	+	Missense_Mutation	SNP	A	A	C	rs5911	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:42453065A>C	ENST00000262407.5	-	26	2652	c.2621T>G	c.(2620-2622)aTc>aGc	p.I874S	ITGA2B_ENST00000353281.4_Missense_Mutation_p.I874S	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	874			I -> S (alloantigen HPA-3B; dbSNP:rs5911). {ECO:0000269|PubMed:10391209}.		axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	GGGGCTGGGGATGGGCAGCCC	0.682													G|||	2005	0.400359	0.4334	0.3646	5008	,	,		14408	0.4563		0.3887	False		,,,				2504	0.3354				p.I874S		Atlas-SNP	.											ITGA2B,NS,carcinoma,0,1	ITGA2B	88	1	0			c.T2621G	GRCh37	CM994214	ITGA2B	M	rs5911	PASS	.	G	SER/ILE	1714,2676		332,1050,813	20.0	20.0	20.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2621	3.4	0.7	17	dbSNP_52	20	3211,5373		621,1969,1702	yes	missense	ITGA2B	NM_000419.3	142	953,3019,2515	CC,CA,AA		37.4068,39.0433,37.9605	benign	874/1040	42453065	4925,8049	2195	4292	6487	SO:0001583	missense	3674	exon26			CTGGGGATGGGCA		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.2621T>G	17.37:g.42453065A>C	ENSP00000262407:p.Ile874Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	37	CCDS32665.1	883	0.4043040293040293	213	0.4329268292682927	129	0.356353591160221	238	0.4160839160839161	303	0.3997361477572559	G	11.70	1.717176	0.30413	0.390433	0.374068	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.38401	1.14;1.14	3.42	3.42	0.39159	Integrin alpha-2 (1);	0.248312	0.21041	U	0.081164	T	0.00012	0.0000	N	0.02011	-0.69	0.21740	P	0.99956448	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.46527	-0.9185	9	0.11182	T	0.66	.	6.9702	0.24644	0.1262:0.0:0.8738:0.0	rs5911;rs57227599;rs5911	472;874	Q59FA8;P08514	.;ITA2B_HUMAN	S	874	ENSP00000262407:I874S;ENSP00000340536:I874S	ENSP00000262407:I874S	I	-	2	0	ITGA2B	39808591	0.005000	0.15991	0.721000	0.30653	0.185000	0.23345	1.255000	0.32909	1.033000	0.39918	-0.320000	0.08662	ATC	A|0.621;C|0.379	0.379	strong		0.682	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
UGT1A6	54578	hgsc.bcm.edu	37	2	234652347	234652347	+	Intron	SNP	C	C	G	rs13009407	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:234652347C>G	ENST00000305139.6	+	2	1000				UGT1A10_ENST00000373445.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A6_ENST00000373424.1_Intron|DNAJB3_ENST00000449667.1_RNA|UGT1A1_ENST00000609637.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A1_ENST00000608381.1_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)	CGCCCTCCGCCCCCGCCTCGC	0.642													C|||	731	0.145966	0.0121	0.1628	5008	,	,		15622	0.0407		0.2356	False		,,,				2504	0.3313				p.G72G		Atlas-SNP	.											.	.	.	.	0			c.G216C						PASS	.	C	,,,,,,,,,	223,3791		17,189,1801	92.0	104.0	100.0		216,,,,,,,,,	-7.1	0.0	2	dbSNP_121	100	2166,6190		285,1596,2297	no	coding-synonymous,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	,,,,,,,,,	302,1785,4098	GG,GC,CC		25.9215,5.5556,19.3129	,,,,,,,,,	72/146,,,,,,,,,	234652347	2389,9981	2007	4178	6185	SO:0001627	intron_variant	414061	exon1			CTCCGCCCCCGCC	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.862-23333C>G	2.37:g.234652347C>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_001001394	A6NKK6|B8K289|Q96TE7	Silent	SNP	ENST00000305139.6	37	CCDS2507.1																																																																																			C|0.867;G|0.133	0.133	strong		0.642	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862	
DNMT1	1786	hgsc.bcm.edu	37	19	10265593	10265593	+	Silent	SNP	G	G	T	rs2228613	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:10265593G>T	ENST00000340748.4	-	19	1819	c.1584C>A	c.(1582-1584)atC>atA	p.I528I	DNMT1_ENST00000540357.1_Silent_p.I528I|DNMT1_ENST00000359526.4_Silent_p.I544I			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	528	DNA replication foci-targeting sequence. {ECO:0000250}.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CGATCTTGTTGATCAGGTCCT	0.498													G|||	199	0.0397364	0.0212	0.0403	5008	,	,		21065	0.001		0.0865	False		,,,				2504	0.0562				p.I544I		Atlas-SNP	.											.	DNMT1	148	.	0			c.C1632A						PASS	.	G	,	168,4238	112.1+/-150.2	2,164,2037	133.0	112.0	119.0		1632,1584	3.4	1.0	19	dbSNP_98	119	802,7798	187.9+/-235.0	37,728,3535	no	coding-synonymous,coding-synonymous	DNMT1	NM_001130823.1,NM_001379.2	,	39,892,5572	TT,TG,GG		9.3256,3.813,7.4581	,	544/1633,528/1617	10265593	970,12036	2203	4300	6503	SO:0001819	synonymous_variant	1786	exon20			CTTGTTGATCAGG	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.1584C>A	19.37:g.10265593G>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	116	59	0.508621	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent	SNP	ENST00000340748.4	37	CCDS12228.1																																																																																			T|0.063;G|0.937;C|0.000	0.063	strong		0.498	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
MMP8	4317	hgsc.bcm.edu	37	11	102584104	102584104	+	Missense_Mutation	SNP	T	T	G	rs35866072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102584104T>G	ENST00000236826.3	-	10	1477	c.1379A>C	c.(1378-1380)aAa>aCa	p.K460T		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	460			K -> T (in dbSNP:rs35866072). {ECO:0000269|Ref.2}.		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)	GTTAAGCCATTTATTGCCTCT	0.378													T|||	442	0.0882588	0.2224	0.0591	5008	,	,		20837	0.0089		0.0437	False		,,,				2504	0.0552				p.K460T		Atlas-SNP	.											.	MMP8	68	.	0			c.A1379C						PASS	.	T	THR/LYS	879,3527	341.2+/-306.6	90,699,1414	194.0	170.0	178.0		1379	-8.0	0.0	11	dbSNP_126	178	461,8137	137.6+/-194.5	14,433,3852	yes	missense	MMP8	NM_002424.2	78	104,1132,5266	GG,GT,TT		5.3617,19.9501,10.3045	benign	460/468	102584104	1340,11664	2203	4299	6502	SO:0001583	missense	4317	exon10			AGCCATTTATTGC	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.1379A>C	11.37:g.102584104T>G	ENSP00000236826:p.Lys460Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	207	68	0.328502	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	176	0.08058608058608059	122	0.24796747967479674	20	0.055248618784530384	3	0.005244755244755245	31	0.040897097625329816	T	6.566	0.472756	0.12461	0.199501	0.053617	ENSG00000118113	ENST00000236826	T	0.13657	2.57	5.59	-8.0	0.01126	Hemopexin/matrixin (2);	.	.	.	.	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B;B	0.11235	0.004;0.002	B;B	0.14023	0.01;0.01	T	0.46857	-0.9161	8	0.37606	T	0.19	.	3.8104	0.08795	0.147:0.5539:0.0895:0.2096	rs35866072;rs59529121;rs61751463	460;460	A8K9E4;P22894	.;MMP8_HUMAN	T	460	ENSP00000236826:K460T	ENSP00000236826:K460T	K	-	2	0	MMP8	102089314	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	-0.226000	0.09139	-1.793000	0.01258	-0.371000	0.07208	AAA	T|0.907;G|0.093	0.093	strong		0.378	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
SORT1	6272	hgsc.bcm.edu	37	1	109897103	109897103	+	Silent	SNP	A	A	G	rs11142	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109897103A>G	ENST00000256637.6	-	5	652	c.594T>C	c.(592-594)ttT>ttC	p.F198F	SORT1_ENST00000538502.1_Silent_p.F62F|SORT1_ENST00000482236.1_5'Flank	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	198					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)		CTGATGATCTAAAGATTCTTC	0.403													.|||	3888	0.776358	0.6884	0.853	5008	,	,		19794	0.9563		0.7147	False		,,,				2504	0.7188				p.F198F		Atlas-SNP	.											SORT1,colon,carcinoma,0,1	SORT1	48	1	0			c.T594C						PASS	.	G	,	2945,1461	471.1+/-356.0	989,967,247	152.0	143.0	146.0		186,594	4.2	1.0	1	dbSNP_52	146	6259,2341	392.2+/-343.9	2280,1699,321	no	coding-synonymous,coding-synonymous	SORT1	NM_001205228.1,NM_002959.5	,	3269,2666,568	GG,GA,AA		27.2209,33.1593,29.2327	,	62/695,198/832	109897103	9204,3802	2203	4300	6503	SO:0001819	synonymous_variant	6272	exon5			TGATCTAAAGATT	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.594T>C	1.37:g.109897103A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	78	76	0.974359	NM_002959	B4DWI3|C0JYZ0|Q8IZ49	Silent	SNP	ENST00000256637.6	37	CCDS798.1																																																																																			A|0.257;G|0.743	0.743	strong		0.403	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959	
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105897003	105897003	+	Silent	SNP	G	G	A	rs2241799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	219	0	0		WXS	Illumina HiSeq	Phase_I	223	90	0.403587	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	
GYS1	2997	hgsc.bcm.edu	37	19	49485548	49485548	+	Silent	SNP	G	G	A	rs5464	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49485548G>A	ENST00000323798.3	-	7	1222	c.1026C>T	c.(1024-1026)ttC>ttT	p.F342F	GYS1_ENST00000541188.1_Silent_p.F262F|GYS1_ENST00000263276.6_Silent_p.F278F|GYS1_ENST00000540532.1_Missense_Mutation_p.S223F|GYS1_ENST00000544287.1_5'UTR	NM_002103.4	NP_002094.2	P13807	GYS1_HUMAN	glycogen synthase 1 (muscle)	342					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|heart development (GO:0007507)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|inclusion body (GO:0016234)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		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;0.000164)|all cancers(93;0.000226)|GBM - Glioblastoma multiforme(486;0.00561)|Epithelial(262;0.0286)		ATGCCTCCAGGAAGACGTCAG	0.517													G|||	1275	0.254593	0.2943	0.2608	5008	,	,		17958	0.2183		0.2922	False		,,,				2504	0.1953				p.F342F		Atlas-SNP	.											.	GYS1	59	.	0			c.C1026T						PASS	.	G	,	1243,3163	431.0+/-342.8	197,849,1157	110.0	101.0	104.0		834,1026	4.2	1.0	19	dbSNP_52	104	2535,6065	415.4+/-351.8	365,1805,2130	no	coding-synonymous,coding-synonymous	GYS1	NM_001161587.1,NM_002103.4	,	562,2654,3287	AA,AG,GG		29.4767,28.2115,29.0481	,	278/674,342/738	49485548	3778,9228	2203	4300	6503	SO:0001819	synonymous_variant	2997	exon7			CTCCAGGAAGACG		CCDS12747.1, CCDS54292.1	19q13.3	2013-02-22			ENSG00000104812	ENSG00000104812	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4706	protein-coding gene	gene with protein product		138570		GYS			Standard	NM_002103		Approved	GSY	uc002plp.3	P13807	OTTHUMG00000150723	ENST00000323798.3:c.1026C>T	19.37:g.49485548G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	125	66	0.528	NM_002103	Q9BTT9	Silent	SNP	ENST00000323798.3	37	CCDS12747.1	589	0.2696886446886447	156	0.3170731707317073	100	0.27624309392265195	134	0.23426573426573427	199	0.262532981530343	G	12.39	1.922336	0.33908	0.282115	0.294767	ENSG00000104812	ENST00000540532	T	0.26373	1.74	5.21	4.16	0.48862	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.39974	P	0.025175999999999976	.	.	.	.	.	.	T	0.43669	-0.9377	4	.	.	.	-31.0172	8.5832	0.33642	0.1731:0.0:0.8269:0.0	rs5464;rs2228476;rs8192706;rs13306416;rs16981011;rs16981013;rs17206756;rs5464	.	.	.	F	223	ENSP00000445197:S223F	.	S	-	2	0	GYS1	54177360	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.703000	0.37846	2.613000	0.88420	0.650000	0.86243	TCC	G|0.713;A|0.287	0.287	strong		0.517	GYS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319791.1	NM_002103	
TNFAIP8	25816	hgsc.bcm.edu	37	5	118728953	118728953	+	Silent	SNP	G	G	C	rs3203922	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:118728953G>C	ENST00000503646.1	+	3	1162	c.474G>C	c.(472-474)gtG>gtC	p.V158V	TNFAIP8_ENST00000504642.1_Silent_p.V160V|TNFAIP8_ENST00000504771.2_Silent_p.V158V|TNFAIP8_ENST00000415806.2_3'UTR|TNFAIP8_ENST00000513374.1_Silent_p.V170V|TNFAIP8_ENST00000274456.6_Silent_p.V148V			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	214	0	0		WXS	Illumina HiSeq	Phase_I	174	76	0.436782	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	
C1orf35	79169	hgsc.bcm.edu	37	1	228290223	228290223	+	Silent	SNP	G	G	C	rs377443672	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:228290223G>C	ENST00000272139.4	-	4	564	c.330C>G	c.(328-330)ccC>ccG	p.P110P	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	110							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				CCTTCTCCTCGGGGTCGCCTC	0.721													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		9295	0.0		0.003	False		,,,				2504	0.0				p.P110P		Atlas-SNP	.											.	C1orf35	17	.	0			c.C330G						PASS	.	G		0,4340		0,0,2170	10.0	13.0	12.0		330	-8.1	0.6	1		12	9,8471		0,9,4231	no	coding-synonymous	C1orf35	NM_024319.2		0,9,6401	CC,CG,GG		0.1061,0.0,0.0702		110/264	228290223	9,12811	2170	4240	6410	SO:0001819	synonymous_variant	79169	exon4			CTCCTCGGGGTCG	AY137773	CCDS1566.1	1q42.13	2012-06-25			ENSG00000143793	ENSG00000143793			19032	protein-coding gene	gene with protein product	"""multiple myeloma tumor-associated protein 2"""					12545221	Standard	NM_024319		Approved	MGC4174, MMTAG2	uc001hrx.3	Q9BU76	OTTHUMG00000037793	ENST00000272139.4:c.330C>G	1.37:g.228290223G>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	175	66	0.377143	NM_024319	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Silent	SNP	ENST00000272139.4	37	CCDS1566.1																																																																																			.	.	none		0.721	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319	
OLFML1	283298	hgsc.bcm.edu	37	11	7509566	7509566	+	Missense_Mutation	SNP	A	A	T	rs12805648	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:7509566A>T	ENST00000329293.3	+	2	732	c.338A>T	c.(337-339)gAa>gTa	p.E113V	CTD-2516F10.2_ENST00000530201.1_RNA|OLFML1_ENST00000530135.1_Missense_Mutation_p.E113V|OLFML1_ENST00000528758.1_Intron	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	113			E -> V (in dbSNP:rs12805648). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16554811}.			extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GAGTGCATCGAATCAGAGGAC	0.463													A|||	833	0.166334	0.1271	0.2219	5008	,	,		18704	0.1558		0.1889	False		,,,				2504	0.1677				p.E113V		Atlas-SNP	.											OLFML1,NS,carcinoma,+1,3	OLFML1	54	3	0			c.A338T						PASS	.	A	VAL/GLU	579,3823	257.7+/-262.0	40,499,1662	98.0	86.0	90.0		338	5.7	0.3	11	dbSNP_121	90	1455,7137	279.3+/-293.9	127,1201,2968	yes	missense	OLFML1	NM_198474.3	121	167,1700,4630	TT,TA,AA		16.9344,13.1531,15.6534	possibly-damaging	113/403	7509566	2034,10960	2201	4296	6497	SO:0001583	missense	283298	exon2			GCATCGAATCAGA	AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.338A>T	11.37:g.7509566A>T	ENSP00000332511:p.Glu113Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	37	CCDS7779.1	412	0.18864468864468864	91	0.18495934959349594	74	0.20441988950276244	95	0.1660839160839161	152	0.20052770448548812	A	14.68	2.606394	0.46527	0.131531	0.169344	ENSG00000183801	ENST00000530135;ENST00000329293	D;D	0.89552	-2.53;-2.53	5.68	5.68	0.88126	.	0.282271	0.38164	N	0.001796	T	0.00524	0.0017	M	0.66939	2.045	0.09310	P	0.9999999999982478	B	0.21753	0.06	B	0.20384	0.029	T	0.46582	-0.9181	9	0.66056	D	0.02	.	12.3098	0.54922	1.0:0.0:0.0:0.0	rs12805648;rs12805648	113	Q6UWY5	OLFL1_HUMAN	V	113	ENSP00000433455:E113V;ENSP00000332511:E113V	ENSP00000332511:E113V	E	+	2	0	OLFML1	7466142	1.000000	0.71417	0.281000	0.24762	0.705000	0.40729	5.476000	0.66793	2.167000	0.68274	0.482000	0.46254	GAA	A|0.833;T|0.167	0.167	strong		0.463	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474	
ZNF556	80032	hgsc.bcm.edu	37	19	2877426	2877426	+	Missense_Mutation	SNP	C	C	T	rs34849844	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2877426C>T	ENST00000307635.2	+	4	557	c.470C>T	c.(469-471)aCc>aTc	p.T157I	ZNF556_ENST00000586426.1_Missense_Mutation_p.T156I	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	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)			endometrium(2)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(3)|skin(7)	31				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)		AAACTCTTCACCCATTCCTCA	0.423													C|||	33	0.00658946	0.0015	0.0101	5008	,	,		20726	0.001		0.0159	False		,,,				2504	0.0072				p.T157I		Atlas-SNP	.											.	ZNF556	73	.	0			c.C470T						PASS	.	C	ILE/THR	15,4391	22.3+/-47.3	0,15,2188	136.0	123.0	127.0		470	-0.3	0.0	19	dbSNP_126	127	157,8443	74.8+/-137.4	3,151,4146	yes	missense	ZNF556	NM_024967.1	89	3,166,6334	TT,TC,CC		1.8256,0.3404,1.3225	benign	157/457	2877426	172,12834	2203	4300	6503	SO:0001583	missense	80032	exon4			TCTTCACCCATTC	BC009374	CCDS12097.1, CCDS74254.1	19p13.3	2013-09-20			ENSG00000172000	ENSG00000172000		"""Zinc fingers, C2H2-type"", ""-"""	25669	protein-coding gene	gene with protein product						12477932	Standard	XM_005259647		Approved	FLJ11637	uc002lwp.1	Q9HAH1	OTTHUMG00000180501	ENST00000307635.2:c.470C>T	19.37:g.2877426C>T	ENSP00000302603:p.Thr157Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	37	CCDS12097.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	C	8.841	0.942299	0.18281	0.003404	0.018256	ENSG00000172000	ENST00000307635	T	0.28666	1.6	2.27	-0.272	0.12919	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09291	0.0229	L	0.35487	1.065	0.09310	N	1	B	0.30068	0.267	B	0.24541	0.054	T	0.14924	-1.0455	9	0.44086	T	0.13	.	5.1815	0.15161	0.1587:0.4899:0.3514:0.0	rs34849844;rs62126859	157	Q9HAH1	ZN556_HUMAN	I	157	ENSP00000302603:T157I	ENSP00000302603:T157I	T	+	2	0	ZNF556	2828426	0.000000	0.05858	0.004000	0.12327	0.205000	0.24178	-3.911000	0.00336	0.139000	0.18822	0.407000	0.27541	ACC	C|0.987;T|0.013	0.013	strong		0.423	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967	
LLGL2	3993	hgsc.bcm.edu	37	17	73568055	73568055	+	Silent	SNP	C	C	T	rs1661714	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	89	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	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	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230408	23230408	+	Missense_Mutation	SNP	A	A	C	rs552295669		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:23230408A>C	ENST00000526893.1	+	1	449	c.175A>C	c.(175-177)Agc>Cgc	p.S59R	IGLL5_ENST00000532223.2_Missense_Mutation_p.S59R|IGLL5_ENST00000531372.1_Missense_Mutation_p.S59R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	59						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AGTTGGAAGCAGCCGATCCAG	0.657																																					p.S59R		Atlas-SNP	.											.	IGLL5	26	.	0			c.A175C						PASS	.																																			SO:0001583	missense	100423062	exon1			GGAAGCAGCCGAT	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.175A>C	22.37:g.23230408A>C	ENSP00000431254:p.Ser59Arg	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	145	38	0.262069	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.848880	0.32699	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00593	6.34;6.35	3.92	-0.722	0.11184	.	.	.	.	.	T	0.00496	0.0016	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.15870	0.014	T	0.45175	-0.9279	9	0.72032	D	0.01	.	3.8729	0.09044	0.4764:0.1955:0.3281:0.0	.	59	B9A064	IGLL5_HUMAN	R	59	ENSP00000436353:S59R;ENSP00000431254:S59R	ENSP00000431254:S59R	S	+	1	0	IGLL5	21560408	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.203000	0.17315	-0.212000	0.10109	0.523000	0.50628	AGC	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
MUC4	4585	hgsc.bcm.edu	37	3	195508982	195508982	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195508982C>T	ENST00000463781.3	-	2	9928	c.9469G>A	c.(9469-9471)Gac>Aac	p.D3157N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3157N	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.D3157N(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)		GAGGAAGTGTCGGTGACAGGA	0.592																																					p.D3157N		Atlas-SNP	.											MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	NS(2)	c.G9469A						scavenged	.						5.0	4.0	4.0					3																	195508982		544	1292	1836	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	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.9469G>A	3.37:g.195508982C>T	ENSP00000417498:p.Asp3157Asn	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	239	15	0.0627615	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	7.037	0.561794	0.13498	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.51;1.42	.	.	.	.	.	.	.	.	T	0.12220	0.0297	N	0.19112	0.55	0.09310	N	1	D	0.52996	0.957	B	0.29077	0.098	T	0.19484	-1.0304	7	.	.	.	.	6.8901	0.24224	0.0:0.9999:0.0:1.0E-4	.	3029	E7ESK3	.	N	3157	ENSP00000417498:D3157N;ENSP00000420243:D3157N	.	D	-	1	0	MUC4	196993761	0.000000	0.05858	0.028000	0.17463	0.028000	0.11728	-0.476000	0.06591	0.073000	0.16731	0.074000	0.15403	GAC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209815	84209815	+	Missense_Mutation	SNP	C	C	G	rs2288021	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	1	0.00699301		WXS	Illumina HiSeq	Phase_I	122	94	0.770492	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	
CHRNA1	1134	hgsc.bcm.edu	37	2	175614716	175614716	+	Silent	SNP	G	G	A	rs2229957	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:175614716G>A	ENST00000261007.5	-	8	1101	c.1035C>T	c.(1033-1035)caC>caT	p.H345H	CHRNA1_ENST00000348749.5_Silent_p.H320H|CHRNA1_ENST00000409219.1_Silent_p.H320H|AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000409542.1_Silent_p.H238H	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	345					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|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)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	TGGGTGAGCGGTGGTGTGTGT	0.562													G|||	614	0.122604	0.1808	0.0519	5008	,	,		18200	0.0565		0.0706	False		,,,				2504	0.2157				p.H345H		Atlas-SNP	.											.	CHRNA1	92	.	0			c.C1035T						PASS	.	G	,	697,3709	291.3+/-281.4	56,585,1562	189.0	145.0	160.0		960,1035	5.4	1.0	2	dbSNP_98	160	569,8031	154.3+/-208.6	15,539,3746	no	coding-synonymous,coding-synonymous	CHRNA1	NM_000079.3,NM_001039523.2	,	71,1124,5308	AA,AG,GG		6.6163,15.8193,9.734	,	320/458,345/483	175614716	1266,11740	2203	4300	6503	SO:0001819	synonymous_variant	1134	exon8			TGAGCGGTGGTGT	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.1035C>T	2.37:g.175614716G>A		Somatic	280	1	0.00357143		WXS	Illumina HiSeq	Phase_I	228	110	0.482456	NM_001039523	B4DRV6|D3DPE8	Silent	SNP	ENST00000261007.5	37	CCDS33331.1																																																																																			T|0.025;G|0.730;C|0.169;A|0.077	0.077	strong		0.562	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1		
GBP4	115361	hgsc.bcm.edu	37	1	89655994	89655994	+	Silent	SNP	C	C	T	rs1410871	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89655994C>T	ENST00000355754.6	-	7	1021	c.924G>A	c.(922-924)ggG>ggA	p.G308G		NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	308	GTPase domain (Globular). {ECO:0000250}.					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)		CCACCAGAGTCCCCAGCCCTG	0.413													C|||	537	0.107228	0.3207	0.0403	5008	,	,		18431	0.0119		0.0298	False		,,,				2504	0.044				p.G308G		Atlas-SNP	.											.	GBP4	89	.	0			c.G924A						PASS	.	C		1199,3207	383.7+/-325.0	172,855,1176	56.0	58.0	57.0		924	-4.2	0.0	1	dbSNP_88	57	229,8371	89.4+/-151.6	1,227,4072	no	coding-synonymous	GBP4	NM_052941.4		173,1082,5248	TT,TC,CC		2.6628,27.2129,10.9795		308/641	89655994	1428,11578	2203	4300	6503	SO:0001819	synonymous_variant	115361	exon7			CAGAGTCCCCAGC	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.924G>A	1.37:g.89655994C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	86	84	0.976744	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Silent	SNP	ENST00000355754.6	37	CCDS721.1																																																																																			C|0.898;T|0.102	0.102	strong		0.413	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941	
CHIA	27159	hgsc.bcm.edu	37	1	111854889	111854889	+	Missense_Mutation	SNP	A	A	G	rs41282492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:111854889A>G	ENST00000369740.1	+	4	236	c.133A>G	c.(133-135)Aac>Gac	p.N45D	CHIA_ENST00000483391.1_Intron|CHIA_ENST00000430615.1_Intron|CHIA_ENST00000353665.6_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.N45D|CHIA_ENST00000451398.2_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	45			N -> D (increased chitinase activity; when associated with N-47 and M-61; dbSNP:rs41282492). {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)		CATGCCTGACAACATCGACCC	0.572													G|||	544	0.108626	0.2126	0.0836	5008	,	,		17991	0.0		0.1093	False		,,,				2504	0.0971				p.N45D		Atlas-SNP	.											CHIA_ENST00000369740,NS,carcinoma,-1,1	CHIA	115	1	0			c.A133G						PASS	.	G	,ASP/ASN	775,3397		67,641,1378	96.0	97.0	97.0		,133	-2.9	0.0	1	dbSNP_127	97	976,7454		49,878,3288	yes	intron,missense	CHIA	NM_021797.2,NM_201653.2	,23	116,1519,4666	GG,GA,AA		11.5777,18.5762,13.8946	,benign	,45/477	111854889	1751,10851	2086	4215	6301	SO:0001583	missense	27159	exon4			CCTGACAACATCG	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.133A>G	1.37:g.111854889A>G	ENSP00000358755:p.Asn45Asp	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	109	11	0.100917	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	229	0.10485347985347986	105	0.21341463414634146	36	0.09944751381215469	0	0.0	88	0.11609498680738786	G	0.032	-1.328299	0.01309	0.185762	0.115777	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.04654	3.58;3.58	5.08	-2.92	0.05615	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.460557	0.17861	N	0.159511	T	0.00637	0.0021	N	0.10760	0.04	0.24700	P	0.99326224	B	0.02656	0.0	B	0.14023	0.01	T	0.44345	-0.9334	9	0.02654	T	1	-5.6473	13.4826	0.61345	0.6795:0.0:0.3205:0.0	rs41282492;rs61752465	45	Q9BZP6	CHIA_HUMAN	D	45	ENSP00000358755:N45D;ENSP00000341828:N45D	ENSP00000341828:N45D	N	+	1	0	CHIA	111656412	0.001000	0.12720	0.006000	0.13384	0.382000	0.30200	0.070000	0.14573	-0.854000	0.04131	-0.766000	0.03442	AAC	A|0.881;G|0.119	0.119	strong		0.572	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
ABR	29	hgsc.bcm.edu	37	17	970419	970419	+	Silent	SNP	G	G	A	rs199545490		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:970419G>A	ENST00000302538.5	-	10	1226	c.1080C>T	c.(1078-1080)ccC>ccT	p.P360P	ABR_ENST00000291107.2_Silent_p.P323P|ABR_ENST00000574437.1_Silent_p.P314P|ABR_ENST00000536794.2_Silent_p.P142P|ABR_ENST00000544583.2_Silent_p.P314P	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	360	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CAGACTCCTCGGGGGATGGAA	0.582																																					p.P360P	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											ABR,colon,carcinoma,0,1	ABR	119	1	0			c.C1080T						scavenged	.						35.0	33.0	34.0					17																	970419		2203	4300	6503	SO:0001819	synonymous_variant	29	exon10			CTCCTCGGGGGAT	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	81	protein-coding gene	gene with protein product		600365	"""active BCR-related gene"""			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.1080C>T	17.37:g.970419G>A		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Silent	SNP	ENST00000302538.5	37	CCDS10999.1																																																																																			G|0.999;A|0.001	0.001	weak		0.582	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4		
LRRC37A3	374819	hgsc.bcm.edu	37	17	62892031	62892031	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:62892031C>T	ENST00000584306.1	-	3	1875	c.1345G>A	c.(1345-1347)Gta>Ata	p.V449I	RP11-927P21.1_ENST00000584959.1_RNA|RP11-927P21.1_ENST00000577938.1_RNA|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.V449I|LRRC37A3_ENST00000577487.1_5'Flank|LRRC37A3_ENST00000339474.5_Intron|RP11-927P21.1_ENST00000584131.1_RNA|LRRC37A3_ENST00000400877.3_Intron	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	449						integral component of membrane (GO:0016021)		p.V449I(4)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GGAGGTTCTACATCATTACCT	0.542																																					p.V449I		Atlas-SNP	.											LRRC37A3,NS,carcinoma,0,4	LRRC37A3	75	4	4	Substitution - Missense(4)	kidney(4)	c.G1345A						scavenged	.						1.0	1.0	1.0					17																	62892031		69	307	376	SO:0001583	missense	374819	exon3			GTTCTACATCATT	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.1345G>A	17.37:g.62892031C>T	ENSP00000464535:p.Val449Ile	Somatic	470	3	0.00638298		WXS	Illumina HiSeq	Phase_I	367	51	0.138965	NM_199340	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	13.61	2.287768	0.40494	.	.	ENSG00000176809	ENST00000319651	T	0.66460	-0.21	2.12	-2.37	0.06643	.	.	.	.	.	T	0.47060	0.1425	L	0.42245	1.32	0.80722	P	0.0	B	0.29716	0.255	B	0.22152	0.038	T	0.37686	-0.9695	8	0.42905	T	0.14	.	0.6971	0.00901	0.2393:0.3528:0.2366:0.1713	.	449	O60309	L37A3_HUMAN	I	449	ENSP00000325713:V449I	ENSP00000325713:V449I	V	-	1	0	LRRC37A3	60322493	0.000000	0.05858	0.000000	0.03702	0.159000	0.22180	-1.266000	0.02842	-0.164000	0.10927	0.162000	0.16502	GTA	T|1.000;|0.000	1.000	weak		0.542	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
ZNF319	57567	hgsc.bcm.edu	37	16	58035429	58035429	+	5'Flank	SNP	C	C	A	rs3743559	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:58035429C>A	ENST00000299237.2	-	0	0				USB1_ENST00000565662.1_3'UTR|USB1_ENST00000423271.3_Silent_p.S14S|USB1_ENST00000561743.1_Intron|USB1_ENST00000563149.1_Silent_p.S14S|USB1_ENST00000539737.2_Silent_p.S14S|USB1_ENST00000219281.3_Silent_p.S14S	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319						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(2)|lung(4)|ovary(1)|urinary_tract(1)	8						GCAGCGGCTCCGAGGATGAGT	0.692											OREG0023837	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	307	0.0613019	0.0061	0.0548	5008	,	,		11852	0.0823		0.0845	False		,,,				2504	0.0951				p.S14S		Atlas-SNP	.											.	.	.	.	0			c.C42A						PASS	.	C	,,	72,4290		0,72,2109	14.0	17.0	16.0		42,42,42	-9.8	0.5	16	dbSNP_107	16	699,7891		30,639,3626	no	coding-synonymous,coding-synonymous,coding-synonymous	C16orf57	NM_001195302.1,NM_001204911.1,NM_024598.3	,,	30,711,5735	AA,AC,CC		8.1374,1.6506,5.9527	,,	14/248,14/187,14/266	58035429	771,12181	2181	4295	6476	SO:0001631	upstream_gene_variant	79650	exon1			CGGCTCCGAGGAT	AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"""Zinc fingers, C2H2-type"""	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9			16.37:g.58035429C>A	Exception_encountered	Somatic	179	0	0	1027	WXS	Illumina HiSeq	Phase_I	184	166	0.902174	NM_024598	Q52LH8	Silent	SNP	ENST00000299237.2	37	CCDS32462.1																																																																																			C|0.939;A|0.061	0.061	strong		0.692	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1		
PKP1	5317	hgsc.bcm.edu	37	1	201285712	201285712	+	Silent	SNP	C	C	T	rs7514146	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201285712C>T	ENST00000352845.3	+	4	733	c.733C>T	c.(733-735)Ctg>Ttg	p.L245L	PKP1_ENST00000367324.3_Silent_p.L245L|PKP1_ENST00000263946.3_Silent_p.L245L|PKP1_ENST00000475988.1_3'UTR			Q13835	PKP1_HUMAN	plakophilin 1	245					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						GTGCAGTGGGCTGACCATCCC	0.572													C|||	756	0.150958	0.3064	0.0821	5008	,	,		19582	0.0099		0.0994	False		,,,				2504	0.1881				p.L245L		Atlas-SNP	.											.	PKP1	127	.	0			c.C733T						PASS	.	C	,	1172,3234	408.2+/-334.5	174,824,1205	74.0	57.0	63.0		733,733	3.9	1.0	1	dbSNP_116	63	808,7792	186.2+/-233.7	33,742,3525	no	coding-synonymous,coding-synonymous	PKP1	NM_000299.3,NM_001005337.2	,	207,1566,4730	TT,TC,CC		9.3953,26.6001,15.2237	,	245/748,245/727	201285712	1980,11026	2203	4300	6503	SO:0001819	synonymous_variant	5317	exon4			AGTGGGCTGACCA	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.733C>T	1.37:g.201285712C>T		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	329	110	0.334347	NM_001005337	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	37	CCDS30966.1																																																																																			C|0.863;T|0.137	0.137	strong		0.572	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
TMEM132C	92293	hgsc.bcm.edu	37	12	129190480	129190480	+	Silent	SNP	G	G	A	rs7316019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:129190480G>A	ENST00000435159.2	+	9	2967	c.2967G>A	c.(2965-2967)ccG>ccA	p.P989P	TMEM132C_ENST00000315208.8_Silent_p.P605P|TMEM132C_ENST00000537538.1_Silent_p.P374P	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	989						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						ATGCGCCGCCGCCCCAGGACG	0.642													G|||	733	0.146366	0.3933	0.0663	5008	,	,		14516	0.0228		0.0765	False		,,,				2504	0.0685				p.P989P		Atlas-SNP	.											.	TMEM132C	142	.	0			c.G2967A						PASS	.	G		475,909		86,303,303	22.0	31.0	28.0		2967	-9.5	0.0	12	dbSNP_116	28	239,2943		6,227,1358	no	coding-synonymous	TMEM132C	NM_001136103.2		92,530,1661	AA,AG,GG		7.511,34.3208,15.6373		989/1109	129190480	714,3852	692	1591	2283	SO:0001819	synonymous_variant	92293	exon9			GCCGCCGCCCCAG	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.2967G>A	12.37:g.129190480G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_001136103	Q69YX8	Silent	SNP	ENST00000435159.2	37																																																																																				G|0.870;A|0.130	0.130	strong		0.642	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
KIAA0754	643314	hgsc.bcm.edu	37	1	39879405	39879405	+	Silent	SNP	C	C	T	rs548996855|rs199726261		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879405C>T	ENST00000530275.1	+	1	3255	c.3060C>T	c.(3058-3060)tcC>tcT	p.S1020S	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1020	Ala-rich.									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)			CAGAGGAATCCGCCTCCGCAG	0.682																																					p.S1156S		Atlas-SNP	.											.	KIAA0754	93	.	0			c.C3468T						PASS	.						18.0	21.0	20.0					1																	39879405		1939	4131	6070	SO:0001819	synonymous_variant	643314	exon1			GGAATCCGCCTCC			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.3060C>T	1.37:g.39879405C>T		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	55	20	0.363636	NM_015038	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	37																																																																																				.	.	none		0.682	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
TDRD5	163589	hgsc.bcm.edu	37	1	179600001	179600001	+	Missense_Mutation	SNP	A	A	G	rs6704505	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:179600001A>G	ENST00000367614.1	+	7	1431	c.1072A>G	c.(1072-1074)Aaa>Gaa	p.K358E	TDRD5_ENST00000444136.1_Missense_Mutation_p.K358E|TDRD5_ENST00000294848.8_Missense_Mutation_p.K358E	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	358	HTH OST-type 3. {ECO:0000255|PROSITE- ProRule:PRU00975}.		K -> E (in dbSNP:rs6704505).		DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)				NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						TGAGTTCAGGAAAGGACACCA	0.393													G|||	397	0.0792732	0.0908	0.0447	5008	,	,		16652	0.1081		0.0855	False		,,,				2504	0.0521				p.K358E		Atlas-SNP	.											.	TDRD5	149	.	0			c.A1072G						PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS,,GLU/LYS	416,3990	787.3+/-414.9	18,380,1805	142.0	132.0	136.0		1072,1072,1072,,1072	5.4	1.0	1	dbSNP_116	136	816,7784	781.8+/-407.6	54,708,3538	yes	missense,missense,missense,utr-5,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_001199092.1,NM_173533.3	56,56,56,,56	72,1088,5343	GG,GA,AA		9.4884,9.4417,9.4726	benign,benign,benign,,benign	358/1036,358/1036,358/982,,358/982	179600001	1232,11774	2203	4300	6503	SO:0001583	missense	163589	exon7			TTCAGGAAAGGAC	AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.1072A>G	1.37:g.179600001A>G	ENSP00000356586:p.Lys358Glu	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	359	132	0.367688	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	165	0.07554945054945054	39	0.07926829268292683	20	0.055248618784530384	49	0.08566433566433566	57	0.07519788918205805	G	5.912	0.352299	0.11182	0.094417	0.094884	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.39997	1.05;1.05;1.05	5.4	5.4	0.78164	.	0.634403	0.15010	N	0.285631	T	0.00412	0.0013	N	0.00197	-1.87	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10613	-1.0622	9	0.02654	T	1	-12.8039	12.5316	0.56117	0.0815:0.0:0.9185:0.0	rs6704505;rs17369799;rs52834975;rs57881501;rs6704505	358;358	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	E	358	ENSP00000356586:K358E;ENSP00000294848:K358E;ENSP00000406052:K358E	ENSP00000294848:K358E	K	+	1	0	TDRD5	177866624	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	3.889000	0.56212	1.423000	0.47198	-0.128000	0.14901	AAA	A|0.911;G|0.089	0.089	strong		0.393	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
MGAT4A	11320	hgsc.bcm.edu	37	2	99271976	99271976	+	Missense_Mutation	SNP	T	T	C	rs61748145	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:99271976T>C	ENST00000264968.3	-	7	1069	c.706A>G	c.(706-708)Aca>Gca	p.T236A	MGAT4A_ENST00000461884.1_5'Flank|MGAT4A_ENST00000414521.2_Missense_Mutation_p.T108A|MGAT4A_ENST00000393487.1_Missense_Mutation_p.T236A|MGAT4A_ENST00000409391.1_Missense_Mutation_p.T236A			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	236					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|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-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						TTTTGCTTTGTTCTCCATCTG	0.279													T|||	17	0.00339457	0.0008	0.0043	5008	,	,		20215	0.0		0.0099	False		,,,				2504	0.0031				p.T236A		Atlas-SNP	.											.	MGAT4A	51	.	0			c.A706G						PASS	.	T	ALA/THR,ALA/THR	12,4394	21.2+/-45.6	0,12,2191	94.0	88.0	90.0		322,706	5.1	1.0	2	dbSNP_129	90	92,8506	51.9+/-112.3	0,92,4207	yes	missense,missense	MGAT4A	NM_001160154.1,NM_012214.2	58,58	0,104,6398	CC,CT,TT		1.07,0.2724,0.7998	possibly-damaging,possibly-damaging	108/424,236/536	99271976	104,12900	2203	4299	6502	SO:0001583	missense	11320	exon8			GCTTTGTTCTCCA	AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7047	protein-coding gene	gene with protein product		604623	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"""			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.706A>G	2.37:g.99271976T>C	ENSP00000264968:p.Thr236Ala	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	37	CCDS2036.1	8	0.003663003663003663	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	4	0.005277044854881266	T	24.9	4.578058	0.86645	0.002724	0.0107	ENSG00000071073	ENST00000393487;ENST00000414521;ENST00000264968;ENST00000409391	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.12	5.12	0.69794	.	0.093140	0.85682	D	0.000000	T	0.63046	0.2478	M	0.90082	3.085	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.83275	0.996;0.992	T	0.73883	-0.3842	10	0.52906	T	0.07	-3.5017	14.3832	0.66926	0.0:0.0:0.0:1.0	rs61748145	108;236	E9PEN2;Q9UM21	.;MGT4A_HUMAN	A	236;108;236;236	ENSP00000377127:T236A;ENSP00000404889:T108A;ENSP00000264968:T236A;ENSP00000386841:T236A	ENSP00000264968:T236A	T	-	1	0	MGAT4A	98638408	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.938000	0.87678	2.044000	0.60594	0.533000	0.62120	ACA	T|0.993;C|0.007	0.007	strong		0.279	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214	
PIK3R1	5295	hgsc.bcm.edu	37	5	67522722	67522722	+	Silent	SNP	C	C	T	rs706713	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:67522722C>T	ENST00000521381.1	+	2	835	c.219C>T	c.(217-219)taC>taT	p.Y73Y	PIK3R1_ENST00000521657.1_Silent_p.Y73Y|PIK3R1_ENST00000396611.1_Silent_p.Y73Y|PIK3R1_ENST00000274335.5_Silent_p.Y73Y	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	73	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|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)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CGGGAACTTACGTAGAATATA	0.498			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)			T|||	2100	0.419329	0.4425	0.3602	5008	,	,		16257	0.6746		0.2455	False		,,,				2504	0.3456				p.Y73Y		Atlas-SNP	.		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	.	PIK3R1	869	.	1	Whole gene deletion(1)	large_intestine(1)	c.C219T						PASS	.	T		1803,2603	606.6+/-390.8	360,1083,760	45.0	56.0	53.0		219	-9.6	0.2	5	dbSNP_86	53	2012,6588	713.3+/-405.9	256,1500,2544	no	coding-synonymous	PIK3R1	NM_181523.2		616,2583,3304	TT,TC,CC		23.3953,40.9215,29.3326		73/725	67522722	3815,9191	2203	4300	6503	SO:0001819	synonymous_variant	5295	exon2			AACTTACGTAGAA	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.219C>T	5.37:g.67522722C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	174	78	0.448276	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Silent	SNP	ENST00000521381.1	37	CCDS3993.1																																																																																			C|0.633;T|0.367	0.367	strong		0.498	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	
HOXA7	3204	hgsc.bcm.edu	37	7	27196116	27196116	+	Missense_Mutation	SNP	C	C	T	rs78410337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:27196116C>T	ENST00000242159.3	-	1	182	c.49G>A	c.(49-51)Ggg>Agg	p.G17R	HOXA7_ENST00000523796.2_5'Flank|RP1-170O19.21_ENST00000602610.1_lincRNA|HOXA-AS3_ENST00000518947.2_RNA	NM_006896.3	NP_008827.2	P31268	HXA7_HUMAN	homeobox A7	17					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						AGAGAAGCCCCCGCCGTATAT	0.532													C|||	13	0.00259585	0.0	0.0029	5008	,	,		12045	0.0		0.0109	False		,,,				2504	0.0				p.G17R		Atlas-SNP	.											.	HOXA7	34	.	0			c.G49A						PASS	.	C	ARG/GLY	18,4380		0,18,2181	64.0	81.0	75.0		49	5.2	1.0	7	dbSNP_131	75	98,8490		0,98,4196	yes	missense	HOXA7	NM_006896.3	125	0,116,6377	TT,TC,CC		1.1411,0.4093,0.8933	probably-damaging	17/231	27196116	116,12870	2199	4294	6493	SO:0001583	missense	3204	exon1			AAGCCCCCGCCGT		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.49G>A	7.37:g.27196116C>T	ENSP00000242159:p.Gly17Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	164	47	0.286585	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	37	CCDS5408.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	32	5.110578	0.94292	0.004093	0.011411	ENSG00000122592	ENST00000242159;ENST00000519842	T;D	0.82081	1.53;-1.57	5.21	5.21	0.72293	.	0.121540	0.52532	D	0.000067	T	0.79834	0.4514	M	0.84948	2.725	0.80722	D	1	P	0.40144	0.704	B	0.31390	0.129	D	0.86042	0.1520	10	0.87932	D	0	.	18.7386	0.91765	0.0:1.0:0.0:0.0	.	17	P31268	HXA7_HUMAN	R	17	ENSP00000242159:G17R;ENSP00000428563:G17R	ENSP00000242159:G17R	G	-	1	0	HOXA7	27162641	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.510000	0.81708	2.599000	0.87857	0.561000	0.74099	GGG	C|0.993;T|0.007	0.007	strong		0.532	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1		
ZNF862	643641	hgsc.bcm.edu	37	7	149559465	149559465	+	Silent	SNP	C	C	T	rs2074701	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149559465C>T	ENST00000223210.4	+	7	3461	c.3216C>T	c.(3214-3216)ggC>ggT	p.G1072G	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	1072					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						CTGTGAACGGCGTGGCCGTCA	0.612													C|||	2193	0.437899	0.4743	0.487	5008	,	,		21205	0.3264		0.5686	False		,,,				2504	0.3344				p.G1072G		Atlas-SNP	.											ZNF862,NS,carcinoma,0,1	ZNF862	97	1	0			c.C3216T						PASS	.	C		2229,2119		580,1069,525	47.0	58.0	54.0		3216	-10.4	0.1	7	dbSNP_96	54	5033,3517		1511,2011,753	no	coding-synonymous	ZNF862	NM_001099220.1		2091,3080,1278	TT,TC,CC		41.1345,48.7351,43.6967		1072/1170	149559465	7262,5636	2174	4275	6449	SO:0001819	synonymous_variant	643641	exon7			GAACGGCGTGGCC	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.3216C>T	7.37:g.149559465C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																			C|0.500;T|0.500	0.500	strong		0.612	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
ZSWIM4	65249	hgsc.bcm.edu	37	19	13934296	13934296	+	Missense_Mutation	SNP	A	A	G	rs76549352	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13934296A>G	ENST00000254323.2	+	10	2035	c.1846A>G	c.(1846-1848)Atg>Gtg	p.M616V	ZSWIM4_ENST00000440752.2_Missense_Mutation_p.M450V	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	616							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			GGCTTCCACCATGTTGACGGC	0.592													A|||	35	0.00698882	0.0008	0.0101	5008	,	,		20199	0.0		0.0199	False		,,,				2504	0.0072				p.M616V		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.A1846G						PASS	.	A	VAL/MET	26,4380		0,26,2177	41.0	32.0	35.0		1846	3.4	1.0	19	dbSNP_131	35	228,8372		3,222,4075	yes	missense	ZSWIM4	NM_023072.2	21	3,248,6252	GG,GA,AA		2.6512,0.5901,1.9529	possibly-damaging	616/990	13934296	254,12752	2203	4300	6503	SO:0001583	missense	65249	exon10			TCCACCATGTTGA	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"""Zinc fingers, SWIM-type"""	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.1846A>G	19.37:g.13934296A>G	ENSP00000254323:p.Met616Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	22	0.010073260073260074	0	0.0	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	16.68	3.191716	0.58017	0.005901	0.026512	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.50001	0.77;0.76	4.48	3.44	0.39384	.	0.000000	0.64402	D	0.000007	T	0.36413	0.0966	M	0.70595	2.14	0.37386	D	0.912244	P;D	0.63046	0.75;0.992	B;P	0.61275	0.396;0.886	T	0.59456	-0.7451	10	0.72032	D	0.01	-29.3762	9.2182	0.37360	0.8166:0.1834:0.0:0.0	.	450;616	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	V	616;450	ENSP00000254323:M616V;ENSP00000405278:M450V	ENSP00000254323:M616V	M	+	1	0	ZSWIM4	13795296	1.000000	0.71417	0.996000	0.52242	0.823000	0.46562	6.801000	0.75170	0.717000	0.32145	0.482000	0.46254	ATG	A|0.987;G|0.013	0.013	strong		0.592	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
DAAM2	23500	hgsc.bcm.edu	37	6	39855288	39855288	+	Silent	SNP	C	C	A	rs35383047	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:39855288C>A	ENST00000398904.2	+	16	2162	c.1980C>A	c.(1978-1980)atC>atA	p.I660I	RP11-61I13.3_ENST00000420293.1_RNA|DAAM2_ENST00000274867.4_Silent_p.I660I|RP11-61I13.3_ENST00000607215.1_RNA|RP11-61I13.3_ENST00000606829.1_RNA|RP11-61I13.3_ENST00000430595.1_RNA|RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000538976.1_Silent_p.I660I			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	660	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					CTGAAGACATCTACCTGGCTT	0.537													C|||	793	0.158347	0.2753	0.1009	5008	,	,		18699	0.1806		0.0626	False		,,,				2504	0.1166				p.I660I		Atlas-SNP	.											.	DAAM2	101	.	0			c.C1980A						PASS	.	C	,	853,3023		90,673,1175	64.0	69.0	67.0		1980,1980	4.5	1.0	6	dbSNP_126	67	406,7864		12,382,3741	no	coding-synonymous,coding-synonymous	DAAM2	NM_001201427.1,NM_015345.3	,	102,1055,4916	AA,AC,CC		4.9093,22.0072,10.3656	,	660/1069,660/1068	39855288	1259,10887	1938	4135	6073	SO:0001819	synonymous_variant	23500	exon16			AGACATCTACCTG	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1980C>A	6.37:g.39855288C>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Silent	SNP	ENST00000398904.2	37	CCDS56426.1																																																																																			C|0.882;A|0.118	0.118	strong		0.537	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
FAM193B	54540	hgsc.bcm.edu	37	5	176963389	176963389	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:176963389G>A	ENST00000514747.1	-	4	1094	c.1046C>T	c.(1045-1047)cCg>cTg	p.P349L	FAM193B_ENST00000508298.1_Intron|FAM193B_ENST00000329540.5_5'UTR|FAM193B_ENST00000443375.2_Missense_Mutation_p.P236L	NM_001190946.1	NP_001177875.1	Q96PV7	F193B_HUMAN	family with sequence similarity 193, member B	349	Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(3)	4						CTGAGAGCTCGGGGGTGGGAG	0.582																																					p.P349L		Atlas-SNP	.											FLJ10404,NS,carcinoma,0,3	FAM193B	28	3	0			c.C1046T						scavenged	.						15.0	16.0	16.0					5																	176963389		1997	4141	6138	SO:0001583	missense	54540	exon4			GAGCTCGGGGGTG		CCDS54954.1	5q35	2010-02-17			ENSG00000146067	ENSG00000146067			25524	protein-coding gene	gene with protein product		615813				11572484	Standard	NR_024019		Approved	KIAA1931, FLJ10404	uc003mhu.3	Q96PV7	OTTHUMG00000163396	ENST00000514747.1:c.1046C>T	5.37:g.176963389G>A	ENSP00000422131:p.Pro349Leu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	83	2	0.0240964	NM_001190946	E9PET5|Q9NW00	Missense_Mutation	SNP	ENST00000514747.1	37	CCDS54954.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.859218	0.32884	.	.	ENSG00000146067	ENST00000514747;ENST00000443375	T;T	0.72282	-0.64;-0.64	5.63	4.76	0.60689	.	0.412228	0.20038	U	0.100577	T	0.63129	0.2485	L	0.43152	1.355	0.46167	D	0.998902	B;B	0.21309	0.054;0.054	B;B	0.17098	0.017;0.007	T	0.59364	-0.7468	10	0.41790	T	0.15	-4.0854	12.8445	0.57821	0.0752:0.0:0.9248:0.0	.	349;236	E9PET5;E9PEZ8	.;.	L	349;236	ENSP00000422131:P349L;ENSP00000410098:P236L	ENSP00000410098:P236L	P	-	2	0	FAM193B	176895995	0.883000	0.30277	0.109000	0.21407	0.974000	0.67602	4.457000	0.60088	1.378000	0.46305	0.563000	0.77884	CCG	.	.	none		0.582	FAM193B-003	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373121.1	NM_019057	
MUC5B	727897	hgsc.bcm.edu	37	11	1263523	1263523	+	Missense_Mutation	SNP	G	G	A	rs1541314	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1263523G>A	ENST00000529681.1	+	31	5471	c.5413G>A	c.(5413-5415)Ggc>Agc	p.G1805S	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.G1808S	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1805	7 X Cys-rich subdomain repeats.|Thr-rich.		G -> S (in dbSNP:rs1541314). {ECO:0000269|PubMed:9013550}.		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)		AGGGGTTGCAGGCGGGGACAT	0.582													g|||	328	0.0654952	0.0234	0.1095	5008	,	,		18135	0.0496		0.0815	False		,,,				2504	0.091				p.G1805S		Atlas-SNP	.											.	MUC5B	473	.	0			c.G5413A						PASS	.		SER/GLY	68,3940		0,68,1936	58.0	68.0	65.0		5413	1.1	0.0	11	dbSNP_88	65	596,7732		22,552,3590	yes	missense	MUC5B	NM_002458.2	56	22,620,5526	AA,AG,GG		7.1566,1.6966,5.3826	possibly-damaging	1805/5763	1263523	664,11672	2004	4164	6168	SO:0001583	missense	727897	exon31			GTTGCAGGCGGGG	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.5413G>A	11.37:g.1263523G>A	ENSP00000436812:p.Gly1805Ser	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	218	109	0.5	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	156	0.07142857142857142	12	0.024390243902439025	38	0.10497237569060773	43	0.07517482517482517	63	0.08311345646437995	g	13.68	2.308444	0.40895	0.016966	0.071566	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17370	2.28;2.28	4.32	1.15	0.20763	.	.	.	.	.	T	0.00637	0.0021	M	0.62154	1.92	0.80722	P	0.0	P;P	0.47034	0.817;0.889	B;P	0.50896	0.426;0.653	T	0.07385	-1.0775	8	0.87932	D	0	.	7.167	0.25695	0.1554:0.3933:0.4513:0.0	rs1541314;rs52836874;rs57142305;rs1541314	2498;1808	A7Y9J9;E9PBJ0	.;.	S	1805;1808;1806;1875	ENSP00000436812:G1805S;ENSP00000415793:G1808S	ENSP00000343037:G1806S	G	+	1	0	MUC5B	1220099	0.003000	0.15002	0.000000	0.03702	0.452000	0.32318	0.480000	0.22244	-0.043000	0.13513	0.306000	0.20318	GGC	G|0.928;A|0.072	0.072	strong		0.582	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
RNF151	146310	hgsc.bcm.edu	37	16	2017772	2017772	+	Missense_Mutation	SNP	G	G	A	rs62617081	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2017772G>A	ENST00000569714.1	+	3	204	c.196G>A	c.(196-198)Gtt>Att	p.V66I	SNHG9_ENST00000459373.1_lincRNA|RNF151_ENST00000569210.2_Intron|RPS2_ENST00000526522.1_5'Flank|RNF151_ENST00000321392.3_Missense_Mutation_p.V65I|RPS2_ENST00000343262.4_5'Flank|RPS2_ENST00000529806.1_5'Flank	NM_174903.4	NP_777563.2	Q2KHN1	RN151_HUMAN	ring finger protein 151	66					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2						AAGGAAAAAGGTTGTCCACAT	0.522													A|||	194	0.038738	0.0991	0.0187	5008	,	,		19997	0.0		0.0149	False		,,,				2504	0.0358				p.V66I		Atlas-SNP	.											.	RNF151	12	.	0			c.G196A						PASS	.	A	ILE/VAL	333,3523		15,303,1610	71.0	68.0	69.0		196	0.8	0.6	16	dbSNP_129	69	195,8085		2,191,3947	yes	missense	RNF151	NM_174903.4	29	17,494,5557	AA,AG,GG		2.3551,8.6359,4.3507	benign	66/246	2017772	528,11608	1928	4140	6068	SO:0001583	missense	146310	exon3			AAAAAGGTTGTCC	BC029501	CCDS58405.1	16p13.3	2013-01-09			ENSG00000179580	ENSG00000179580		"""RING-type (C3HC4) zinc fingers"""	23235	protein-coding gene	gene with protein product						12477932	Standard	NM_174903		Approved		uc002cnt.1	Q2KHN1	OTTHUMG00000176852	ENST00000569714.1:c.196G>A	16.37:g.2017772G>A	ENSP00000456566:p.Val66Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_174903	Q8NHS5	Missense_Mutation	SNP	ENST00000569714.1	37	CCDS58405.1	72	0.03296703296703297	56	0.11382113821138211	5	0.013812154696132596	0	0.0	11	0.014511873350923483	a	0.032	-1.328926	0.01298	0.086359	0.023551	ENSG00000179580	ENST00000321392	D	0.85411	-1.98	4.73	0.833	0.18875	Zinc finger, RING/FYVE/PHD-type (1);	0.346485	0.29451	N	0.012111	T	0.01454	0.0047	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11227	-1.0596	9	0.18710	T	0.47	-4.4465	0.1777	0.00120	0.3801:0.1532:0.1881:0.2787	rs62617081	66	Q2KHN1	RN151_HUMAN	I	65	ENSP00000325794:V65I	ENSP00000325794:V65I	V	+	1	0	RNF151	1957773	0.997000	0.39634	0.614000	0.29051	0.116000	0.19942	0.979000	0.29500	-0.093000	0.12396	-0.361000	0.07541	GTT	G|0.972;A|0.028	0.028	strong		0.522	RNF151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434030.1	NM_174903	
ZNF596	169270	hgsc.bcm.edu	37	8	196274	196274	+	Missense_Mutation	SNP	T	T	G	rs2072174	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:196274T>G	ENST00000398612.1	+	6	1810	c.1427T>G	c.(1426-1428)gTa>gGa	p.V476G	ZNF596_ENST00000320552.2_Missense_Mutation_p.V406G|ZNF596_ENST00000308811.4_Missense_Mutation_p.V476G	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	476			V -> G (in dbSNP:rs2072174).		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)|large_intestine(6)|lung(5)	14		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)		AAACCATATGTATGTCCTCTA	0.343													T|||	848	0.169329	0.0862	0.1844	5008	,	,		21716	0.3294		0.0855	False		,,,				2504	0.1922				p.V476G		Atlas-SNP	.											.	ZNF596	34	.	0			c.T1427G						PASS	.	T	GLY/VAL,GLY/VAL,GLY/VAL	424,3982		21,382,1800	65.0	70.0	68.0		1427,1427,1427	-4.3	0.0	8	dbSNP_96	68	768,7832		37,694,3569	yes	missense,missense,missense	ZNF596	NM_001042415.1,NM_001042416.1,NM_173539.2	109,109,109	58,1076,5369	GG,GT,TT		8.9302,9.6232,9.165	benign,benign,benign	476/505,476/505,476/505	196274	1192,11814	2203	4300	6503	SO:0001583	missense	169270	exon6			CATATGTATGTCC	BC026190	CCDS5951.2	8p23.3	2013-01-08			ENSG00000172748	ENSG00000172748		"""Zinc fingers, C2H2-type"", ""-"""	27268	protein-coding gene	gene with protein product						12477932	Standard	NM_001287256		Approved		uc003wot.3	Q8TC21	OTTHUMG00000086931	ENST00000398612.1:c.1427T>G	8.37:g.196274T>G	ENSP00000381613:p.Val476Gly	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	39	0.367925	NM_173539	B2R8P4|O95015|Q8N9X0	Missense_Mutation	SNP	ENST00000398612.1	37	CCDS5951.2	395	0.18086080586080586	47	0.09552845528455285	70	0.19337016574585636	213	0.3723776223776224	65	0.08575197889182058	.	1.112	-0.657800	0.03454	0.096232	0.089302	ENSG00000172748	ENST00000308811;ENST00000320552;ENST00000398612	T;T;T	0.18810	2.19;2.19;2.19	2.54	-4.35	0.03656	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.25426	0.745	0.80722	P	0.0	B	0.22414	0.069	B	0.24541	0.054	T	0.48375	-0.9041	8	0.56958	D	0.05	.	0.6924	0.00893	0.2214:0.2891:0.1225:0.367	rs2072174;rs52816203;rs2072174	476	Q8TC21	ZN596_HUMAN	G	476;406;476	ENSP00000310033:V476G;ENSP00000318719:V406G;ENSP00000381613:V476G	ENSP00000310033:V476G	V	+	2	0	ZNF596	186274	0.000000	0.05858	0.041000	0.18516	0.060000	0.15804	-1.577000	0.02127	-0.910000	0.03847	-0.313000	0.08912	GTA	G|0.132;N|0.001	0.132	strong		0.343	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539	
WDR48	57599	hgsc.bcm.edu	37	3	39111140	39111140	+	Silent	SNP	C	C	A	rs2293312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:39111140C>A	ENST00000302313.5	+	7	605	c.577C>A	c.(577-579)Cgg>Agg	p.R193R	WDR48_ENST00000544962.1_Intron|WDR48_ENST00000396258.3_Silent_p.R111R|WDR48_ENST00000418020.1_5'UTR	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	115	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	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	
RANBP2	5903	hgsc.bcm.edu	37	2	109381438	109381438	+	Silent	SNP	A	A	G	rs61748149	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:109381438A>G	ENST00000283195.6	+	20	4569	c.4443A>G	c.(4441-4443)ggA>ggG	p.G1481G		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1481					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)		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						CAAAGGAAGGACAGTGGGATT	0.398													A|||	345	0.0688898	0.0477	0.062	5008	,	,		21024	0.0317		0.0527	False		,,,				2504	0.1575				p.G1481G		Atlas-SNP	.											.	RANBP2	488	.	0			c.A4443G						PASS	.	A		204,4202	126.6+/-163.6	4,196,2003	67.0	65.0	66.0		4443	-2.2	1.0	2	dbSNP_129	66	513,8085	144.8+/-200.6	18,477,3804	no	coding-synonymous	RANBP2	NM_006267.4		22,673,5807	GG,GA,AA		5.9665,4.63,5.5137		1481/3225	109381438	717,12287	2203	4299	6502	SO:0001819	synonymous_variant	5903	exon20			GGAAGGACAGTGG	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.4443A>G	2.37:g.109381438A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	180	88	0.488889	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																			A|0.942;G|0.058	0.058	strong		0.398	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
PKD1	5310	hgsc.bcm.edu	37	16	2140680	2140680	+	Missense_Mutation	SNP	T	T	C	rs10960	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2140680T>C	ENST00000262304.4	-	44	12341	c.12133A>G	c.(12133-12135)Atc>Gtc	p.I4045V	PKD1_ENST00000423118.1_Missense_Mutation_p.I4044V|MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4045			I -> V (in dbSNP:rs10960). {ECO:0000269|PubMed:10647901, ECO:0000269|PubMed:11058904, ECO:0000269|PubMed:11773467, ECO:0000269|PubMed:11967008, ECO:0000269|PubMed:12070253, ECO:0000269|PubMed:15772804, ECO:0000269|PubMed:18837007, ECO:0000269|PubMed:9521593}.		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						CCTACCAGGATGGCCAGCTGG	0.652													c|||	1262	0.251997	0.6346	0.2046	5008	,	,		15937	0.0		0.1968	False		,,,				2504	0.0849				p.I4045V		Atlas-SNP	.											.	PKD1	184	.	0			c.A12133G						PASS	.		VAL/ILE,VAL/ILE	2428,1940	521.7+/-370.6	675,1078,431	31.0	35.0	33.0		12130,12133	-1.5	0.1	16	dbSNP_52	33	1605,6993	722.4+/-406.4	145,1315,2839	yes	missense,missense	PKD1	NM_000296.3,NM_001009944.2	29,29	820,2393,3270	CC,CT,TT		18.6671,44.4139,31.1044	benign,benign	4044/4303,4045/4304	2140680	4033,8933	2184	4299	6483	SO:0001583	missense	5310	exon44			CCAGGATGGCCAG	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.12133A>G	16.37:g.2140680T>C	ENSP00000262304:p.Ile4045Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001009944	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	522	0.23901098901098902	295	0.5995934959349594	81	0.22375690607734808	0	0.0	146	0.19261213720316622	c	0.012	-1.659587	0.00772	0.555861	0.186671	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.69040	-0.37;-0.37	3.49	-1.55	0.08558	Polycystin cation channel, PKD1/PKD2 (1);	0.414816	0.23431	N	0.048256	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	0.09377	0.003;0.004	T	0.43940	-0.9360	9	0.17369	T	0.5	.	0.9634	0.01400	0.2747:0.2029:0.1051:0.4173	rs10960;rs3209985;rs11544588;rs17134793	4044;4045	P98161-3;P98161	.;PKD1_HUMAN	V	4045;4044;3379	ENSP00000262304:I4045V;ENSP00000399501:I4044V	ENSP00000262304:I4045V	I	-	1	0	PKD1	2080681	0.001000	0.12720	0.083000	0.20561	0.108000	0.19459	-0.085000	0.11250	-0.387000	0.07809	-0.674000	0.03794	ATC	T|0.709;C|0.291	0.291	strong		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
ATP11A	23250	hgsc.bcm.edu	37	13	113527967	113527967	+	Silent	SNP	G	G	A	rs1320525	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:113527967G>A	ENST00000487903.1	+	27	3226	c.3138G>A	c.(3136-3138)tcG>tcA	p.S1046S	ATP11A_ENST00000283558.8_Silent_p.S1046S|ATP11A_ENST00000375645.3_Silent_p.S1046S|ATP11A_ENST00000375630.2_Silent_p.S1046S			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1046					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)				TTGTCTTTTCGCTTCTCTGGG	0.393											OREG0003854	type=REGULATORY REGION|Gene=ATP11A|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	1877	0.3748	0.298	0.3761	5008	,	,		21339	0.4742		0.3658	False		,,,				2504	0.3845				p.S1046S		Atlas-SNP	.											.	ATP11A	225	.	0			c.G3138A						PASS	.	G	,	1360,3046	451.2+/-349.6	220,920,1063	205.0	169.0	181.0		3138,3138	2.5	1.0	13	dbSNP_88	181	3364,5236	499.4+/-375.0	674,2016,1610	no	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	894,2936,2673	AA,AG,GG		39.1163,30.867,36.3217	,	1046/1135,1046/1192	113527967	4724,8282	2203	4300	6503	SO:0001819	synonymous_variant	23250	exon27			CTTTTCGCTTCTC	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.3138G>A	13.37:g.113527967G>A		Somatic	218	0	0	1451	WXS	Illumina HiSeq	Phase_I	224	103	0.459821	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1																																																																																			G|0.623;A|0.377	0.377	strong		0.393	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
TTLL4	9654	hgsc.bcm.edu	37	2	219610433	219610433	+	Silent	SNP	A	A	G	rs586194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219610433A>G	ENST00000392102.1	+	7	2146	c.1806A>G	c.(1804-1806)gaA>gaG	p.E602E	TTLL4_ENST00000442769.1_Silent_p.E602E|TTLL4_ENST00000258398.4_Silent_p.E602E|TTLL4_ENST00000457313.1_Silent_p.E437E	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	602					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)		TTCCCTGGGAACAGAGGAAGT	0.507													G|||	2450	0.489217	0.9168	0.438	5008	,	,		20186	0.1409		0.4672	False		,,,				2504	0.3292				p.E602E	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.A1806G						PASS	.	G		3726,680	287.2+/-279.2	1577,572,54	50.0	49.0	49.0		1806	-0.1	1.0	2	dbSNP_83	49	4092,4508	588.7+/-392.4	992,2108,1200	no	coding-synonymous	TTLL4	NM_014640.4		2569,2680,1254	GG,GA,AA		47.5814,15.4335,39.8893		602/1200	219610433	7818,5188	2203	4300	6503	SO:0001819	synonymous_variant	9654	exon7			CTGGGAACAGAGG		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.1806A>G	2.37:g.219610433A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	83	18	0.216867	NM_014640	A8K6V5|Q8WW29	Silent	SNP	ENST00000392102.1	37	CCDS2422.1																																																																																			A|0.446;G|0.554	0.554	strong		0.507	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
IP6K2	51447	hgsc.bcm.edu	37	3	48732480	48732480	+	Intron	SNP	T	T	C	rs17080319	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48732480T>C	ENST00000328631.5	-	2	426				IP6K2_ENST00000413298.1_Intron|IP6K2_ENST00000432678.2_Intron|IP6K2_ENST00000450045.1_Intron|IP6K2_ENST00000436134.1_Intron|IP6K2_ENST00000449610.1_Missense_Mutation_p.D82G|IP6K2_ENST00000431721.2_Missense_Mutation_p.D137G|IP6K2_ENST00000443964.1_Missense_Mutation_p.D141G|IP6K2_ENST00000446860.1_Missense_Mutation_p.D140G|IP6K2_ENST00000453202.1_Missense_Mutation_p.D82G|IP6K2_ENST00000340879.4_Intron|IP6K2_ENST00000417896.1_Missense_Mutation_p.D82G	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	100	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	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	
ARSG	22901	hgsc.bcm.edu	37	17	66366659	66366659	+	Missense_Mutation	SNP	C	C	G	rs144503106	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:66366659C>G	ENST00000448504.2	+	8	1772	c.976C>G	c.(976-978)Cgt>Ggt	p.R326G	ARSG_ENST00000452479.2_Missense_Mutation_p.R162G|ARSG_ENST00000582154.1_3'UTR	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	326					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)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.R326C(1)		NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTGGCAAACTCGTCAAGGTAA	0.552													C|||	19	0.00379393	0.0008	0.0058	5008	,	,		18113	0.001		0.0129	False		,,,				2504	0.0				p.R326G		Atlas-SNP	.											ARSG,rectum,carcinoma,0,1	ARSG	55	1	1	Substitution - Missense(1)	large_intestine(1)	c.C976G						PASS	.	C	GLY/ARG	12,4394	20.2+/-43.8	0,12,2191	99.0	82.0	87.0		976	4.0	0.0	17	dbSNP_134	87	186,8414	82.6+/-145.2	1,184,4115	yes	missense	ARSG	NM_014960.3	125	1,196,6306	GG,GC,CC		2.1628,0.2724,1.5224	benign	326/526	66366659	198,12808	2203	4300	6503	SO:0001583	missense	22901	exon8			CAAACTCGTCAAG	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.976C>G	17.37:g.66366659C>G	ENSP00000407193:p.Arg326Gly	Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	253	130	0.513834	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	37	CCDS11676.1	15	0.006868131868131868	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	11	0.014511873350923483	C	4.144	0.025005	0.08054	0.002724	0.021628	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.0	3.97	0.46021	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.826360	0.11156	N	0.593620	T	0.11623	0.0283	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13098	-1.0522	9	0.11794	T	0.64	.	7.5126	0.27583	0.1953:0.6383:0.1664:0.0	.	326	Q96EG1	ARSG_HUMAN	G	326;225	.	ENSP00000407193:R225G	R	+	1	0	ARSG	63878254	0.000000	0.05858	0.018000	0.16275	0.037000	0.13140	0.480000	0.22244	2.596000	0.87737	0.561000	0.74099	CGT	C|0.988;G|0.012	0.012	strong		0.552	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
PARK2	5071	hgsc.bcm.edu	37	6	162864492	162864492	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:162864492G>C	ENST00000366898.1	-	2	123	c.21C>G	c.(19-21)ttC>ttG	p.F7L	PARK2_ENST00000366892.1_Missense_Mutation_p.F7L|PARK2_ENST00000366897.1_Missense_Mutation_p.F7L|PARK2_ENST00000366896.1_Missense_Mutation_p.F7L|PARK2_ENST00000338468.3_5'UTR|PARK2_ENST00000366894.1_5'UTR	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	7	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		GGCTGGAGTTGAACCTGACAA	0.498																																					p.F7L		Atlas-SNP	.											.	PARK2	96	.	0			c.C21G						PASS	.						108.0	93.0	98.0					6																	162864492		2203	4300	6503	SO:0001583	missense	5071	exon2			GGAGTTGAACCTG		CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"""Parkinson disease"""	8607	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase"""	602544	"""Parkinson disease (autosomal recessive, juvenile) 2, parkin"", ""parkinson protein 2, E3 ubiquitin protein ligase (parkin)"""			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.21C>G	6.37:g.162864492G>C	ENSP00000355865:p.Phe7Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	129	35	0.271318	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.621739	0.66787	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366892;ENST00000542682	D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.84	5.63	5.63	0.86233	Ubiquitin supergroup (1);Ubiquitin (1);	0.058575	0.64402	D	0.000002	D	0.96367	0.8815	M	0.61703	1.905	0.33112	D	0.540611	D;P;D;D	0.76494	0.999;0.88;0.997;0.995	D;D;D;D	0.80764	0.994;0.946;0.958;0.958	D	0.95572	0.8639	10	0.44086	T	0.13	.	14.8348	0.70175	0.0:0.0:0.8561:0.1438	.	7;7;7;7	O60260-5;Q5VVX3;Q5VVX4;O60260	.;.;.;PRKN2_HUMAN	L	7;7;7;7;6	ENSP00000355865:F7L;ENSP00000355863:F7L;ENSP00000355862:F7L;ENSP00000355858:F7L	ENSP00000355858:F7L	F	-	3	2	PARK2	162784482	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.700000	0.54786	2.805000	0.96524	0.655000	0.94253	TTC	.	.	none		0.498	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1		
TCF3	6929	hgsc.bcm.edu	37	19	1615393	1615393	+	Silent	SNP	C	C	T	rs143212973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1615393C>T	ENST00000262965.5	-	18	2057	c.1713G>A	c.(1711-1713)gaG>gaA	p.E571E	TCF3_ENST00000395423.3_Silent_p.E575E|TCF3_ENST00000344749.5_Intron|TCF3_ENST00000588136.1_Intron|TCF3_ENST00000453954.2_Intron|RNU6-1223P_ENST00000517124.1_RNA	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0					anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	16		Acute lymphoblastic leukemia(61;5.94e-12)|all_hematologic(61;1.27e-07)		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)		TGCGCCCCAGCTCCTTAAAGG	0.637			T	"""PBX1, HLF, TFPT"""	pre B-ALL								C|||	6	0.00119808	0.0	0.0	5008	,	,		14615	0.0		0.006	False		,,,				2504	0.0				p.E571E		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.G1713A						PASS	.	C	,	12,4394	20.2+/-43.8	0,12,2191	98.0	97.0	97.0		,1713	3.4	1.0	19	dbSNP_134	97	52,8548	33.8+/-87.4	2,48,4250	no	intron,coding-synonymous	TCF3	NM_001136139.2,NM_003200.3	,	2,60,6441	TT,TC,CC		0.6047,0.2724,0.4921	,	,571/655	1615393	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	6929	exon18			CCCCAGCTCCTTA	M65214	CCDS12074.1, CCDS45899.1	19p13.3	2014-02-13	2013-02-26		ENSG00000071564	ENSG00000071564		"""Basic helix-loop-helix proteins"""	11633	protein-coding gene	gene with protein product	"""transcription factor E2-alpha"", ""immunoglobulin transcription factor 1"", ""kappa-E2-binding factor"", ""E2A immunoglobulin enhancer-binding factor E12/E47"", ""VDR interacting repressor"""	147141				2308859, 1967983	Standard	NM_003200		Approved	E2A, ITF1, MGC129647, MGC129648, bHLHb21, VDIR, E47	uc002ltt.4	P15923	OTTHUMG00000180031	ENST00000262965.5:c.1713G>A	19.37:g.1615393C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_003200	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000262965.5	37	CCDS12074.1																																																																																			C|0.997;T|0.003	0.003	strong		0.637	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200	
CALU	813	hgsc.bcm.edu	37	7	128388648	128388648	+	Missense_Mutation	SNP	G	G	A	rs2290228	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:128388648G>A	ENST00000249364.4	+	2	113	c.11G>A	c.(10-12)cGa>cAa	p.R4Q	CALU_ENST00000535011.2_Missense_Mutation_p.R4Q|CALU_ENST00000479257.1_Missense_Mutation_p.R12Q|CALU_ENST00000535623.1_Missense_Mutation_p.R12Q|CALU_ENST00000542996.2_Missense_Mutation_p.R12Q|CALU_ENST00000538546.1_Intron|CALU_ENST00000449187.2_Missense_Mutation_p.R4Q	NM_001219.4	NP_001210.1	O43852	CALU_HUMAN	calumenin	4			R -> Q (in dbSNP:rs2290228). {ECO:0000269|Ref.4}.		blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)			kidney(2)|large_intestine(3)|lung(5)	10						ATGGACCTGCGACAGTTTCTT	0.418													G|||	855	0.170727	0.0961	0.1859	5008	,	,		19745	0.1974		0.159	False		,,,				2504	0.2454				p.R12Q		Atlas-SNP	.											.	CALU	42	.	0			c.G35A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG	485,3921	225.9+/-241.6	29,427,1747	84.0	81.0	82.0		11,35,35,11,,11	5.9	1.0	7	dbSNP_100	82	1415,7185	273.1+/-290.5	115,1185,3000	yes	missense,missense,missense,missense,intron,missense	CALU	NM_001130674.2,NM_001199671.1,NM_001199672.1,NM_001199673.1,NM_001199674.1,NM_001219.4	43,43,43,43,,43	144,1612,4747	AA,AG,GG		16.4535,11.0077,14.6086	benign,benign,benign,benign,,benign	4/316,12/324,12/324,4/225,,4/316	128388648	1900,11106	2203	4300	6503	SO:0001583	missense	813	exon3			ACCTGCGACAGTT	AF013759	CCDS5805.1, CCDS47703.1, CCDS56506.1, CCDS56507.1, CCDS56508.1	7q32	2013-01-10			ENSG00000128595	ENSG00000128595		"""EF-hand domain containing"""	1458	protein-coding gene	gene with protein product		603420				9598325	Standard	NM_001219		Approved		uc003vnq.3	O43852	OTTHUMG00000158274	ENST00000249364.4:c.11G>A	7.37:g.128388648G>A	ENSP00000249364:p.Arg4Gln	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	100	17	0.17	NM_001199671	B3KPG9|D6QS48|D6QS49|D6QS50|D6QS51|D6QS52|D6QS53|D6QS54|D6QS55|D6QS56|D6QS57|D6QS58|D6QS59|F5H1Q9|F5H879|O60456|Q6FHB9|Q96RL3|Q9NR43	Missense_Mutation	SNP	ENST00000249364.4	37	CCDS5805.1	345	0.15796703296703296	46	0.09349593495934959	60	0.16574585635359115	116	0.20279720279720279	123	0.16226912928759896	G	17.69	3.452475	0.63290	0.110077	0.164535	ENSG00000128595	ENST00000542996;ENST00000535623;ENST00000538394;ENST00000537667;ENST00000535011;ENST00000537014;ENST00000249364;ENST00000449187;ENST00000342367;ENST00000479257	T;T;T;T;T;T	0.61510	2.71;0.1;2.5;2.74;2.74;2.71	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	M	0.68593	2.085	0.09310	P	1.0	B;B	0.20368	0.044;0.003	B;B	0.09377	0.004;0.001	T	0.06899	-1.0801	9	0.18710	T	0.47	-2.4555	17.8434	0.88721	0.0:0.0:1.0:0.0	rs2290228;rs10399443;rs11545532;rs61408000;rs2290228	12;4	D6QS48;O43852	.;CALU_HUMAN	Q	12;12;4;4;4;4;4;4;4;12	ENSP00000438248:R12Q;ENSP00000439139:R12Q;ENSP00000442110:R4Q;ENSP00000249364:R4Q;ENSP00000408838:R4Q;ENSP00000420381:R12Q	ENSP00000249364:R4Q	R	+	2	0	CALU	128175884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.343000	0.52167	2.814000	0.96858	0.591000	0.81541	CGA	G|0.841;A|0.159	0.159	strong		0.418	CALU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350533.1	NM_001219	
ANXA7	310	hgsc.bcm.edu	37	10	75139952	75139952	+	Missense_Mutation	SNP	C	C	T	rs10159690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:75139952C>T	ENST00000372921.5	-	10	982	c.926G>A	c.(925-927)cGt>cAt	p.R309H	ANXA7_ENST00000535178.1_Missense_Mutation_p.R179H|RP11-537A6.9_ENST00000427492.1_RNA	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	331					autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					GTTCTCATCACGATTTCCCTG	0.388																																					p.R331H		Atlas-SNP	.											ANXA7,colon,carcinoma,-1,1	ANXA7	50	1	0			c.G992A						scavenged	.						159.0	156.0	157.0					10																	75139952		2203	4300	6503	SO:0001583	missense	310	exon11			TCATCACGATTTC	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"""Annexins"""	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.926G>A	10.37:g.75139952C>T	ENSP00000362012:p.Arg309His	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	62	3	0.0483871	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	37	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416323	0.83449	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178	T;T;T	0.17370	2.28;2.28;2.28	6.17	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.55226	0.1907	H	0.98178	4.165	0.51767	D	0.999933	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.998;0.996;0.998;0.997	T	0.68469	-0.5400	10	0.87932	D	0	.	10.012	0.41992	0.1369:0.7898:0.0:0.0733	rs10159690;rs10159690	309;309;236;309;331	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	H	309;331;179	ENSP00000362012:R309H;ENSP00000362010:R331H;ENSP00000442864:R179H	ENSP00000362010:R331H	R	-	2	0	ANXA7	74809958	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	4.762000	0.62250	1.575000	0.49775	0.655000	0.94253	CGT	C|0.994;T|0.006	0.006	strong		0.388	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156	
USPL1	10208	hgsc.bcm.edu	37	13	31231806	31231806	+	Missense_Mutation	SNP	T	T	C	rs7984952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:31231806T>C	ENST00000255304.4	+	9	1934	c.1592T>C	c.(1591-1593)tTa>tCa	p.L531S		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	531			L -> S (in dbSNP:rs7984952). {ECO:0000269|PubMed:15489334}.		Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|protein desumoylation (GO:0016926)	Cajal body (GO:0015030)|extracellular space (GO:0005615)	SUMO binding (GO:0032183)|SUMO-specific isopeptidase activity (GO:0070140)			breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(15)|pancreas(3)|skin(3)	34		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0306)|Epithelial(112;0.131)|OV - Ovarian serous cystadenocarcinoma(117;0.134)		CCAGTATCTTTAACATCGTGT	0.433													C|||	2397	0.478634	0.823	0.389	5008	,	,		20093	0.1796		0.4016	False		,,,				2504	0.4642				p.L531S	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.T1592C						PASS	.	C	SER/LEU	3409,997	371.7+/-320.1	1322,765,116	128.0	123.0	125.0		1592	3.5	0.0	13	dbSNP_116	125	3537,5063	631.3+/-398.5	724,2089,1487	yes	missense	USPL1	NM_005800.4	145	2046,2854,1603	CC,CT,TT		41.1279,22.6282,46.5939	benign	531/1093	31231806	6946,6060	2203	4300	6503	SO:0001583	missense	10208	exon9			TATCTTTAACATC	X59131	CCDS9336.1	13q12-q14	2012-11-14	2005-11-24	2005-11-24	ENSG00000132952	ENSG00000132952			20294	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 22"""	C13orf22		22878415	Standard	NM_005800		Approved	bA121O19.1, D13S106E	uc001utc.2	Q5W0Q7	OTTHUMG00000016675	ENST00000255304.4:c.1592T>C	13.37:g.31231806T>C	ENSP00000255304:p.Leu531Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	956	0.43772893772893773	408	0.8292682926829268	154	0.425414364640884	100	0.17482517482517482	294	0.38786279683377306	C	10.88	1.475572	0.26511	0.773718	0.411279	ENSG00000132952	ENST00000255304	T	0.07908	3.15	5.54	3.46	0.39613	.	1.048920	0.07340	N	0.880541	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	0.15235	-1.0444	9	0.10636	T	0.68	-0.3858	8.089	0.30790	0.1311:0.7144:0.0:0.1545	rs7984952;rs17609480;rs17857154;rs61445569;rs7984952	531	Q5W0Q7	USPL1_HUMAN	S	531	ENSP00000255304:L531S	ENSP00000255304:L531S	L	+	2	0	USPL1	30129806	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.369000	0.20416	0.715000	0.32103	-0.119000	0.15052	TTA	T|0.507;C|0.493	0.493	strong		0.433	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800	
DLC1	10395	hgsc.bcm.edu	37	8	12958025	12958025	+	Silent	SNP	C	C	A	rs3739298	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:12958025C>A	ENST00000276297.4	-	9	2230	c.1821G>T	c.(1819-1821)gcG>gcT	p.A607A	DLC1_ENST00000520226.1_Silent_p.A96A|DLC1_ENST00000512044.2_Silent_p.A204A|DLC1_ENST00000358919.2_Silent_p.A170A	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	607					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						CGCTGGGGGGCGCGTGGCTGG	0.677													C|||	1753	0.35004	0.1059	0.4957	5008	,	,		16123	0.6161		0.3241	False		,,,				2504	0.3292				p.A607A		Atlas-SNP	.											.	DLC1	411	.	0			c.G1821T						PASS	.	C	,,	722,3672		59,604,1534	36.0	43.0	41.0		288,510,1821	-0.5	0.0	8	dbSNP_107	41	2817,5767		473,1871,1948	no	coding-synonymous,coding-synonymous,coding-synonymous	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	,,	532,2475,3482	AA,AC,CC		32.8169,16.4315,27.2692	,,	96/1018,170/1092,607/1529	12958025	3539,9439	2197	4292	6489	SO:0001819	synonymous_variant	10395	exon9			GGGGGGCGCGTGG	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.1821G>T	8.37:g.12958025C>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	27	0.6	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																			C|0.703;A|0.297	0.297	strong		0.677	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
ADRA2B	151	hgsc.bcm.edu	37	2	96781257	96781257	+	Missense_Mutation	SNP	C	C	G	rs9333568	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:96781257C>G	ENST00000409345.3	-	1	727	c.632G>C	c.(631-633)gGg>gCg	p.G211A		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	211			G -> A (in dbSNP:rs9333568). {ECO:0000269|Ref.6}.		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)	CCCAGGCCCCCCCTTGGCCCT	0.617													C|||	83	0.0165735	0.0015	0.0173	5008	,	,		18913	0.0		0.0527	False		,,,				2504	0.0164				p.G211A		Atlas-SNP	.											ADRA2B_ENST00000409345,brain,glioma,-1,2	ADRA2B	115	2	0			c.G632C						PASS	.	C	ALA/GLY	51,4029		0,51,1989	31.0	35.0	34.0		632	1.1	0.0	2	dbSNP_119	34	463,7887		14,435,3726	yes	missense	ADRA2B	NM_000682.5	60	14,486,5715	GG,GC,CC		5.5449,1.25,4.1352	benign	211/448	96781257	514,11916	2040	4175	6215	SO:0001583	missense	151	exon1			GGCCCCCCCTTGG	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.632G>C	2.37:g.96781257C>G	ENSP00000387281:p.Gly211Ala	Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	252	136	0.539683	NM_000682	Q4TUH9|Q53RF2|Q9BZK0	Missense_Mutation	SNP	ENST00000409345.3	37	CCDS56129.1	46	0.021062271062271064	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	36	0.047493403693931395	C	1.675	-0.507932	0.04231	0.0125	0.055449	ENSG00000222040	ENST00000409345	T	0.71698	-0.59	4.97	1.06	0.20224	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.10723	0.0262	L	0.31752	0.955	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.07654	-1.0761	9	0.31617	T	0.26	.	4.2171	0.10540	0.0:0.5505:0.1693:0.2802	rs9333568	211	P18089	ADA2B_HUMAN	A	211	ENSP00000387281:G211A	ENSP00000387281:G211A	G	-	2	0	ADRA2B	96144984	0.000000	0.05858	0.002000	0.10522	0.335000	0.28730	-0.954000	0.03873	0.717000	0.32145	-1.453000	0.01033	GGG	C|0.952;G|0.048	0.048	strong		0.617	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1		
DNAH17	8632	hgsc.bcm.edu	37	17	76503624	76503624	+	Silent	SNP	C	C	T	rs626439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76503624C>T	ENST00000585328.1	-	28	4615	c.4491G>A	c.(4489-4491)gaG>gaA	p.E1497E	DNAH17_ENST00000389840.5_Silent_p.E1496E	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1496	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(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)			TGAAGATGCTCTCCAGGTGGC	0.597													C|||	1621	0.323682	0.1906	0.4164	5008	,	,		19385	0.4583		0.2406	False		,,,				2504	0.3845				p.E1500E		Atlas-SNP	.											.	DNAH17	347	.	0			c.G4500A						PASS	.	C		776,3486		77,622,1432	46.0	53.0	51.0		4500	4.0	1.0	17	dbSNP_83	51	1990,6540		240,1510,2515	no	coding-synonymous	DNAH17	NM_173628.3		317,2132,3947	TT,TC,CC		23.3294,18.2074,21.6229		1500/4463	76503624	2766,10026	2131	4265	6396	SO:0001819	synonymous_variant	8632	exon28			GATGCTCTCCAGG	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.4491G>A	17.37:g.76503624C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				C|0.716;T|0.284	0.284	strong		0.597	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
PBLD	64081	hgsc.bcm.edu	37	10	70066553	70066553	+	Missense_Mutation	SNP	G	G	A	rs12359690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70066553G>A	ENST00000358769.2	-	2	251	c.49C>T	c.(49-51)Cgt>Tgt	p.R17C	PBLD_ENST00000495025.2_Missense_Mutation_p.R17C|PBLD_ENST00000309049.4_Missense_Mutation_p.R17C|PBLD_ENST00000432941.1_Missense_Mutation_p.R17C	NM_022129.3	NP_071412.2	P30039	PBLD_HUMAN	phenazine biosynthesis-like protein domain containing	17			R -> C (in dbSNP:rs12359690). {ECO:0000269|PubMed:15806103}.		biosynthetic process (GO:0009058)|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 SMAD protein import into nucleus (GO:0060392)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	isomerase activity (GO:0016853)			endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21						GGATTCCCACGAAATGCTCTT	0.383													G|||	117	0.0233626	0.0461	0.0245	5008	,	,		18502	0.0		0.0318	False		,,,				2504	0.0072				p.R17C		Atlas-SNP	.											.	PBLD	53	.	0			c.C49T						PASS	.	G	CYS/ARG,CYS/ARG	186,4220	119.6+/-157.3	6,174,2023	89.0	82.0	85.0		49,49	0.5	0.9	10	dbSNP_120	85	399,8201	127.2+/-185.5	8,383,3909	yes	missense,missense	PBLD	NM_001033083.1,NM_022129.3	180,180	14,557,5932	AA,AG,GG		4.6395,4.2215,4.4979	benign,benign	17/281,17/289	70066553	585,12421	2203	4300	6503	SO:0001583	missense	64081	exon2			TCCCACGAAATGC	AK027673	CCDS7277.2, CCDS44413.1	10q21.3	2006-11-27			ENSG00000108187	ENSG00000108187			23301	protein-coding gene	gene with protein product	MAWD binding protein	612189				11355021	Standard	XM_005270028		Approved	MAWBP, MAWDBP, FLJ14767	uc001jns.1	P30039	OTTHUMG00000073949	ENST00000358769.2:c.49C>T	10.37:g.70066553G>A	ENSP00000351619:p.Arg17Cys	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_022129	A8MZJ3|C9JIM0|Q9HCC2	Missense_Mutation	SNP	ENST00000358769.2	37	CCDS7277.2	53	0.024267399267399268	25	0.0508130081300813	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	11.72	1.723233	0.30503	0.042215	0.046395	ENSG00000108187	ENST00000358769;ENST00000309049;ENST00000432941;ENST00000277795	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.51	0.525	0.17072	.	0.445102	0.24249	N	0.040187	T	0.04363	0.0120	L	0.55017	1.72	0.21416	N	0.999695	B;B;B	0.16802	0.002;0.019;0.008	B;B;B	0.16289	0.001;0.015;0.007	T	0.11641	-1.0579	10	0.56958	D	0.05	0.3367	8.8276	0.35065	0.4705:0.0:0.5295:0.0	rs12359690;rs52804292;rs12359690	17;17;17	F8W7D0;C9JIM0;P30039	.;.;PBLD_HUMAN	C	17	ENSP00000351619:R17C;ENSP00000308466:R17C;ENSP00000395534:R17C;ENSP00000277795:R17C	ENSP00000277795:R17C	R	-	1	0	PBLD	69736559	0.038000	0.19896	0.910000	0.35882	0.979000	0.70002	-0.107000	0.10873	-0.157000	0.11059	-1.002000	0.02502	CGT	G|0.961;A|0.039	0.039	strong		0.383	PBLD-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048314.1	NM_022129	
NKAIN4	128414	hgsc.bcm.edu	37	20	61880169	61880169	+	Missense_Mutation	SNP	T	T	G	rs1129659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	51	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	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	
SH3GLB2	56904	hgsc.bcm.edu	37	9	131772399	131772399	+	Splice_Site	SNP	G	G	A	rs11537525		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:131772399G>A	ENST00000372564.3	-	8	883	c.738C>T	c.(736-738)caC>caT	p.H246H	SH3GLB2_ENST00000417224.1_Splice_Site_p.H246H|SH3GLB2_ENST00000416629.1_Splice_Site_p.H225H|SH3GLB2_ENST00000372559.1_Splice_Site_p.H246H|SH3GLB2_ENST00000372554.4_Splice_Site_p.H250H	NM_020145.2	NP_064530.1	Q9NR46	SHLB2_HUMAN	SH3-domain GRB2-like endophilin B2	246	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.					cytoplasm (GO:0005737)				NS(1)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)	12						TGGGACTCACGTGAGTGCTAC	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		18560	0.0		0.001	False		,,,				2504	0.0				p.H246H		Atlas-SNP	.											SH3GLB2,NS,haematopoietic_neoplasm,0,1	SH3GLB2	32	1	0			c.C738T						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	95.0	89.0	91.0		738	-1.9	0.8	9	dbSNP_120	91	14,8586	10.5+/-38.8	0,14,4286	yes	coding-synonymous-near-splice	SH3GLB2	NM_020145.2		0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153		246/396	131772399	15,12991	2203	4300	6503	SO:0001630	splice_region_variant	56904	exon8			ACTCACGTGAGTG	AF257319	CCDS6916.1, CCDS69680.1	9q34	2008-02-05	2001-12-04		ENSG00000148341	ENSG00000148341			10834	protein-coding gene	gene with protein product		609288	"""SH3-domain, GRB2-like, endophilin B2"""			11161816	Standard	NM_020145		Approved	KIAA1848	uc004bwv.3	Q9NR46	OTTHUMG00000020769	ENST00000372564.3:c.738+1C>T	9.37:g.131772399G>A		Somatic	289	2	0.00692042		WXS	Illumina HiSeq	Phase_I	300	145	0.483333	NM_020145	A6NC47|A8MPS4|Q8WY61|Q96JH9	Silent	SNP	ENST00000372564.3	37	CCDS6916.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	SH3GLB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054535.2		Silent
MUC17	140453	hgsc.bcm.edu	37	7	100677988	100677988	+	Missense_Mutation	SNP	T	T	A	rs11769696	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677988T>A	ENST00000306151.4	+	3	3355	c.3291T>A	c.(3289-3291)agT>agA	p.S1097R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1097	59 X approximate tandem repeats.|Ser-rich.				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)					CAACTTATAGTGAAGGAAGCA	0.517																																					p.S1097R		Atlas-SNP	.											.	MUC17	804	.	0			c.T3291A						PASS	.	T	ARG/SER	790,3616		0,790,1413	479.0	384.0	416.0		3291	-1.1	0.0	7	dbSNP_120	416	931,7669		0,931,3369	no	missense	MUC17	NM_001040105.1	110	0,1721,4782	AA,AT,TT		10.8256,17.9301,13.2324	benign	1097/4494	100677988	1721,11285	2203	4300	6503	SO:0001583	missense	140453	exon3			TTATAGTGAAGGA	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.3291T>A	7.37:g.100677988T>A	ENSP00000302716:p.Ser1097Arg	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	929	263	0.2831	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	T	0.381	-0.928558	0.02359	0.179301	0.108256	ENSG00000169876	ENST00000306151	T	0.02606	4.23	0.542	-1.08	0.09936	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	N	1	B	0.27594	0.182	B	0.13407	0.009	T	0.47262	-0.9131	8	0.33141	T	0.24	.	.	.	.	rs11769696	1097	Q685J3	MUC17_HUMAN	R	1097	ENSP00000302716:S1097R	ENSP00000302716:S1097R	S	+	3	2	MUC17	100464708	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	-0.298000	0.08265	-1.276000	0.02414	0.165000	0.16767	AGT	T|0.991;A|0.009	0.009	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ZEB2	9839	hgsc.bcm.edu	37	2	145156851	145156851	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:145156851G>A	ENST00000558170.2	-	8	3087	c.1903C>T	c.(1903-1905)Ctc>Ttc	p.L635F	ZEB2_ENST00000539609.3_Missense_Mutation_p.L611F|ZEB2_ENST00000303660.4_Missense_Mutation_p.L635F|ZEB2_ENST00000409487.3_Missense_Mutation_p.L635F	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	635					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)	p.L635I(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		GATGACAAGAGGAGGGCTTTA	0.428																																					p.L635F	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											ZEB2,NS,carcinoma,0,1	ZEB2	218	1	1	Substitution - Missense(1)	endometrium(1)	c.C1903T						scavenged	.						66.0	67.0	67.0					2																	145156851		2203	4300	6503	SO:0001583	missense	9839	exon8			ACAAGAGGAGGGC	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	14881	protein-coding gene	gene with protein product	"""SMAD interacting protein 1"""	605802	"""zinc finger homeobox 1b"""	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.1903C>T	2.37:g.145156851G>A	ENSP00000454157:p.Leu635Phe	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	162	3	0.0185185	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Missense_Mutation	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.049787	0.36181	.	.	ENSG00000169554	ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902	T;T;T;T	0.13778	2.58;2.56;2.56;2.71	5.75	5.75	0.90469	.	0.120820	0.56097	D	0.000025	T	0.21468	0.0517	L	0.38175	1.15	0.54753	D	0.999989	P;D;P;D	0.62365	0.865;0.965;0.845;0.991	B;P;B;P	0.55455	0.295;0.656;0.298;0.776	T	0.00150	-1.1986	10	0.46703	T	0.11	-6.942	13.6118	0.62083	0.0799:0.0:0.9201:0.0	.	611;500;634;635	F5H814;Q53TD9;A0JP08;O60315	.;.;.;ZEB2_HUMAN	F	611;635;635;635	ENSP00000443792:L611F;ENSP00000302501:L635F;ENSP00000386854:L635F;ENSP00000395496:L635F	ENSP00000302501:L635F	L	-	1	0	ZEB2	144873321	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.818000	0.48041	2.705000	0.92388	0.655000	0.94253	CTC	.	.	none		0.428	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795	
SYNE2	23224	hgsc.bcm.edu	37	14	64496763	64496763	+	Silent	SNP	T	T	C	rs11850509	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:64496763T>C	ENST00000344113.4	+	44	7077	c.6865T>C	c.(6865-6867)Ttg>Ctg	p.L2289L	SYNE2_ENST00000358025.3_Silent_p.L2289L|SYNE2_ENST00000554584.1_Silent_p.L2289L|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2289					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGAGGAAAAATTGCAGAAACT	0.378													T|||	441	0.0880591	0.1891	0.0893	5008	,	,		19034	0.0575		0.0298	False		,,,				2504	0.0419				p.L2289L		Atlas-SNP	.											.	SYNE2	577	.	0			c.T6865C						PASS	.	T	,	516,3146		36,444,1351	71.0	67.0	68.0		6865,6865	-9.7	0.9	14	dbSNP_120	68	356,7812		14,328,3742	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	50,772,5093	CC,CT,TT		4.3585,14.0907,7.3711	,	2289/6886,2289/6908	64496763	872,10958	1831	4084	5915	SO:0001819	synonymous_variant	23224	exon44			GAAAAATTGCAGA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.6865T>C	14.37:g.64496763T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			T|0.938;C|0.062	0.062	strong		0.378	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
UBR4	23352	hgsc.bcm.edu	37	1	19415304	19415304	+	Silent	SNP	C	C	T	rs1043899	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19415304C>T	ENST00000375254.3	-	98	14406	c.14379G>A	c.(14377-14379)aaG>aaA	p.K4793K	UBR4_ENST00000375217.2_Silent_p.K4786K|UBR4_ENST00000543981.1_Silent_p.K457K|UBR4_ENST00000429347.2_Silent_p.K316K|UBR4_ENST00000375224.1_Silent_p.K500K|UBR4_ENST00000375226.2_Silent_p.K4769K|UBR4_ENST00000375267.2_Silent_p.K4793K	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	4793					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)			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)		TGGCCATGCGCTTCTTCTCTG	0.582													C|||	2964	0.591853	0.5091	0.6787	5008	,	,		20830	0.7589		0.5775	False		,,,				2504	0.4847				p.K4793K		Atlas-SNP	.											.	UBR4	415	.	0			c.G14379A						PASS	.	C		2322,2084	604.4+/-390.3	622,1078,503	89.0	84.0	86.0		14379	4.5	1.0	1	dbSNP_86	86	4865,3735	618.1+/-396.7	1393,2079,828	no	coding-synonymous	UBR4	NM_020765.2		2015,3157,1331	TT,TC,CC		43.4302,47.2991,44.7409		4793/5184	19415304	7187,5819	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon98			CATGCGCTTCTTC	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.14379G>A	1.37:g.19415304C>T		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	146	106	0.726027	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			C|0.426;T|0.574	0.574	strong		0.582	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
SPARCL1	8404	hgsc.bcm.edu	37	4	88415636	88415636	+	Missense_Mutation	SNP	G	G	C	rs1049544	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:88415636G>C	ENST00000282470.6	-	4	786	c.316C>G	c.(316-318)Cac>Gac	p.H106D	SPARCL1_ENST00000418378.1_Missense_Mutation_p.H106D|SPARCL1_ENST00000503414.1_5'UTR	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	106			H -> D (in dbSNP:rs1049544). {ECO:0000269|PubMed:7600298}.		signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.H106D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		ACACTTAAGTGACCATCACTG	0.428													C|||	2883	0.575679	0.8828	0.5043	5008	,	,		19259	0.4375		0.3787	False		,,,				2504	0.5562				p.H106D		Atlas-SNP	.											SPARCL1,NS,carcinoma,0,1	SPARCL1	59	1	1	Substitution - Missense(1)	stomach(1)	c.C316G						PASS	.	C	ASP/HIS,ASP/HIS	3557,849	333.3+/-302.9	1435,687,81	146.0	137.0	140.0		316,316	4.2	0.0	4	dbSNP_86	140	3197,5403	652.8+/-401.0	601,1995,1704	yes	missense,missense	SPARCL1	NM_001128310.1,NM_004684.4	81,81	2036,2682,1785	CC,CG,GG		37.1744,19.2692,48.0701	benign,benign	106/665,106/665	88415636	6754,6252	2203	4300	6503	SO:0001583	missense	8404	exon4			TTAAGTGACCATC	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.316C>G	4.37:g.88415636G>C	ENSP00000282470:p.His106Asp	Somatic	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	275	273	0.992727	NM_004684	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	37	CCDS3622.1	1128	0.5164835164835165	433	0.8800813008130082	189	0.5220994475138122	231	0.40384615384615385	275	0.3627968337730871	C	0.004	-2.345033	0.00222	0.807308	0.371744	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000509407;ENST00000434434;ENST00000535835;ENST00000512317	T;T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05;1.05	5.1	4.25	0.50352	.	0.302477	0.31760	N	0.007107	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	0.39333	-0.9619	9	0.02654	T	1	-9.5256	7.9807	0.30181	0.0:0.7512:0.1608:0.088	rs1049544;rs3189722;rs3763393;rs17846057;rs17859050;rs52829980;rs59760974;rs1049544	106	Q14515	SPRL1_HUMAN	D	106	ENSP00000282470:H106D;ENSP00000414856:H106D;ENSP00000423483:H106D;ENSP00000416971:H106D;ENSP00000438188:H106D;ENSP00000423448:H106D	ENSP00000282470:H106D	H	-	1	0	SPARCL1	88634660	0.001000	0.12720	0.015000	0.15790	0.002000	0.02628	0.940000	0.28992	0.820000	0.34516	-0.120000	0.15030	CAC	G|0.488;C|0.512	0.512	strong		0.428	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
PEAK1	79834	hgsc.bcm.edu	37	15	77407114	77407114	+	Missense_Mutation	SNP	C	C	G	rs1867780	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	54	0	0		WXS	Illumina HiSeq	Phase_I	27	4	0.148148	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		
TMEM82	388595	hgsc.bcm.edu	37	1	16069644	16069644	+	Silent	SNP	C	C	T	rs11584945	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	96	0	0		WXS	Illumina HiSeq	Phase_I	76	16	0.210526	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	
FRY	10129	hgsc.bcm.edu	37	13	32811607	32811607	+	Missense_Mutation	SNP	G	G	A	rs2806639	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	58	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	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	
SKAP1	8631	hgsc.bcm.edu	37	17	46474118	46474118	+	Silent	SNP	G	G	T	rs11079820	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46474118G>T	ENST00000336915.6	-	2	145	c.76C>A	c.(76-78)Cgg>Agg	p.R26R	SKAP1_ENST00000584924.1_Silent_p.R26R	NM_001075099.1|NM_003726.3	NP_001068567.1|NP_003717.3	Q86WV1	SKAP1_HUMAN	src kinase associated phosphoprotein 1	26					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						TTCTCATTCCGCAAACCTTCT	0.403													G|||	454	0.090655	0.1899	0.1556	5008	,	,		16367	0.003		0.0596	False		,,,				2504	0.0327				p.R26R		Atlas-SNP	.											.	SKAP1	41	.	0			c.C76A						PASS	.	G	,	737,3669	305.2+/-288.9	56,625,1522	151.0	158.0	156.0		76,76	2.4	1.0	17	dbSNP_120	156	524,8076	146.5+/-202.0	12,500,3788	no	coding-synonymous,coding-synonymous	SKAP1	NM_001075099.1,NM_003726.3	,	68,1125,5310	TT,TG,GG		6.093,16.7272,9.6955	,	26/359,26/360	46474118	1261,11745	2203	4300	6503	SO:0001819	synonymous_variant	8631	exon2			CATTCCGCAAACC	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.76C>A	17.37:g.46474118G>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_003726	D3DTV1|O15268	Silent	SNP	ENST00000336915.6	37	CCDS32674.1																																																																																			G|0.903;T|0.097	0.097	strong		0.403	SKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443432.1	NM_003726	
ACE	1636	hgsc.bcm.edu	37	17	61573777	61573777	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:61573777C>A	ENST00000290866.4	+	23	3427	c.3403C>A	c.(3403-3405)Cag>Aag	p.Q1135K	ACE_ENST00000428043.1_Missense_Mutation_p.Q1135K|ACE_ENST00000413513.3_Intron|ACE_ENST00000290863.6_Missense_Mutation_p.Q561K|ACE_ENST00000490216.2_Missense_Mutation_p.Q561K|ACE_ENST00000577647.1_Missense_Mutation_p.Q561K|ACE_ENST00000421982.2_Intron	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1135	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)	CTTCATCATCCAGTTCCAGTT	0.657																																					p.Q1135K		Atlas-SNP	.											.	ACE	187	.	0			c.C3403A						PASS	.						104.0	99.0	100.0					17																	61573777		2203	4300	6503	SO:0001583	missense	1636	exon23			ATCATCCAGTTCC	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.3403C>A	17.37:g.61573777C>A	ENSP00000290866:p.Gln1135Lys	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	248	124	0.5	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.258736	0.39896	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863	T;T;T	0.37584	1.19;1.19;1.19	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.73110	0.3545	H	0.95950	3.745	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.922;0.995	T	0.83186	-0.0086	10	0.87932	D	0	-44.5904	18.2622	0.90039	0.0:1.0:0.0:0.0	.	561;1135	P12821-3;P12821	.;ACE_HUMAN	K	1135;1135;561	ENSP00000290866:Q1135K;ENSP00000397593:Q1135K;ENSP00000290863:Q561K	ENSP00000290863:Q561K	Q	+	1	0	ACE	58927509	1.000000	0.71417	1.000000	0.80357	0.328000	0.28507	7.726000	0.84824	2.393000	0.81446	0.484000	0.47621	CAG	.	.	none		0.657	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
SLC6A15	55117	hgsc.bcm.edu	37	12	85257230	85257230	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:85257230C>A	ENST00000266682.5	-	11	2347	c.1806G>T	c.(1804-1806)tgG>tgT	p.W602C	SLC6A15_ENST00000309283.7_Missense_Mutation_p.W310C|SLC6A15_ENST00000552192.1_Missense_Mutation_p.W495C	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	602					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						TATCTTCAATCCATGCGTTAT	0.303																																					p.W602C		Atlas-SNP	.											.	SLC6A15	159	.	0			c.G1806T						PASS	.						85.0	91.0	89.0					12																	85257230		2203	4296	6499	SO:0001583	missense	55117	exon11			TTCAATCCATGCG	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.1806G>T	12.37:g.85257230C>A	ENSP00000266682:p.Trp602Cys	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	241	76	0.315353	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283503	0.80803	.	.	ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000552192;ENST00000548267	T;T;T	0.75704	-0.96;-0.96;-0.96	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.90417	0.7000	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.92239	0.5799	10	0.87932	D	0	.	19.8516	0.96743	0.0:1.0:0.0:0.0	.	310;602	F8WJN6;Q9H2J7	.;S6A15_HUMAN	C	310;602;495;80	ENSP00000311645:W310C;ENSP00000266682:W602C;ENSP00000450145:W495C	ENSP00000266682:W602C	W	-	3	0	SLC6A15	83781361	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.395000	0.79876	2.685000	0.91497	0.585000	0.79938	TGG	.	.	none		0.303	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
IP6K2	51447	hgsc.bcm.edu	37	3	48725707	48725707	+	Silent	SNP	C	C	T	rs1048940	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	230	0	0		WXS	Illumina HiSeq	Phase_I	201	95	0.472637	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	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103158278	103158278	+	Missense_Mutation	SNP	C	C	T	rs10895391	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:103158278C>T	ENST00000375735.2	+	75	11183	c.11039C>T	c.(11038-11040)gCg>gTg	p.A3680V	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.A3687V	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3680			A -> V (in dbSNP:rs10895391). {ECO:0000269|PubMed:12056414}.		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)		GTAGTACAGGCGCTAAGACCG	0.328													C|||	1434	0.286342	0.1725	0.2464	5008	,	,		17114	0.3016		0.338	False		,,,				2504	0.3998				p.A3687V		Atlas-SNP	.											DYNC2H1_ENST00000398093,colon,carcinoma,-1,1	DYNC2H1	246	1	0			c.C11060T						PASS	.	C	VAL/ALA,VAL/ALA	742,2904		81,580,1162	89.0	83.0	85.0		11060,11039	5.8	1.0	11	dbSNP_120	85	2869,5279		511,1847,1716	yes	missense,missense	DYNC2H1	NM_001080463.1,NM_001377.2	64,64	592,2427,2878	TT,TC,CC		35.2111,20.3511,30.6173	benign,benign	3687/4315,3680/4308	103158278	3611,8183	1823	4074	5897	SO:0001583	missense	79659	exon76			TACAGGCGCTAAG	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.11039C>T	11.37:g.103158278C>T	ENSP00000364887:p.Ala3680Val	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	352	214	0.607955	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	608	0.2783882783882784	90	0.18292682926829268	102	0.281767955801105	157	0.2744755244755245	259	0.341688654353562	C	21.8	4.207195	0.79127	0.203511	0.352111	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.09911	2.93;2.93	5.79	5.79	0.91817	Dynein heavy chain (1);	0.054526	0.64402	D	0.000001	T	0.00012	0.0000	M	0.63428	1.95	0.09310	P	0.9999999859533	P;P	0.46656	0.596;0.882	B;B	0.38655	0.201;0.278	T	0.53143	-0.8480	9	0.45353	T	0.12	.	19.6264	0.95679	0.0:1.0:0.0:0.0	rs10895391;rs52827900;rs58780461;rs10895391	3680;3687	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	V	3680;3687	ENSP00000364887:A3680V;ENSP00000381167:A3687V	ENSP00000364887:A3680V	A	+	2	0	DYNC2H1	102663488	1.000000	0.71417	0.999000	0.59377	0.951000	0.60555	6.123000	0.71614	2.746000	0.94184	0.655000	0.94253	GCG	C|0.709;T|0.291	0.291	strong		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
ANK3	288	hgsc.bcm.edu	37	10	61832626	61832626	+	Silent	SNP	G	G	A	rs41274674	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:61832626G>A	ENST00000280772.2	-	37	8204	c.8013C>T	c.(8011-8013)agC>agT	p.S2671S	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2671					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TCTCTGGGCTGCTGGGCAGAC	0.557													G|||	138	0.0275559	0.0537	0.0245	5008	,	,		18965	0.0		0.0378	False		,,,				2504	0.0123				p.S2671S		Atlas-SNP	.											.	ANK3	703	.	0			c.C8013T						PASS	.	G	,,,	277,4129	157.0+/-190.0	6,265,1932	89.0	80.0	83.0		,,,8013	5.8	1.0	10	dbSNP_127	83	350,8250	118.5+/-177.9	10,330,3960	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	16,595,5892	AA,AG,GG		4.0698,6.2869,4.8209	,,,	,,,2671/4378	61832626	627,12379	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			TGGGCTGCTGGGC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8013C>T	10.37:g.61832626G>A		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	153	120	0.784314	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			G|0.957;A|0.043	0.043	strong		0.557	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
GRIN3B	116444	hgsc.bcm.edu	37	19	1004844	1004844	+	Silent	SNP	T	T	C	rs4806909	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1004844T>C	ENST00000234389.3	+	3	1363	c.1344T>C	c.(1342-1344)ccT>ccC	p.P448P	GRIN3B_ENST00000588335.1_3'UTR|AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	448					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)	GCCTGGACCCTGGCACCAACG	0.652													N|||	1605	0.320487	0.4213	0.2421	5008	,	,		15607	0.1667		0.3847	False		,,,				2504	0.3323				p.P448P		Atlas-SNP	.											GRIN3B,rectum,carcinoma,0,1	GRIN3B	46	1	0			c.T1344C						PASS	.	C		1841,2565	616.7+/-392.8	383,1075,745	51.0	50.0	50.0		1344	-9.2	0.0	19	dbSNP_111	50	3312,5280	623.5+/-397.5	640,2032,1624	no	coding-synonymous	GRIN3B	NM_138690.1		1023,3107,2369	CC,CT,TT		38.5475,41.7839,39.6446		448/1044	1004844	5153,7845	2203	4296	6499	SO:0001819	synonymous_variant	116444	exon3			GGACCCTGGCACC		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.1344T>C	19.37:g.1004844T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	47	10	0.212766	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			T|0.639;C|0.361	0.361	strong		0.652	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
ACOT4	122970	hgsc.bcm.edu	37	14	74060476	74060476	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:74060476C>A	ENST00000326303.4	+	2	782	c.528C>A	c.(526-528)agC>agA	p.S176R		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	176					acyl-CoA metabolic process (GO:0006637)|dicarboxylic acid catabolic process (GO:0043649)|dicarboxylic acid metabolic process (GO:0043648)|long-chain fatty acid metabolic process (GO:0001676)|saturated monocarboxylic acid metabolic process (GO:0032788)|short-chain fatty acid metabolic process (GO:0046459)|succinyl-CoA metabolic process (GO:0006104)|unsaturated monocarboxylic acid metabolic process (GO:0032789)|very long-chain fatty acid metabolic process (GO:0000038)	peroxisome (GO:0005777)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|succinyl-CoA hydrolase activity (GO:0004778)			endometrium(1)|large_intestine(3)|lung(4)	8				BRCA - Breast invasive adenocarcinoma(234;0.00331)		ATCGAGCCAGCCTCCTTGCTG	0.463																																					p.S176R		Atlas-SNP	.											.	ACOT4	25	.	0			c.C528A						PASS	.						102.0	96.0	98.0					14																	74060476		2203	4300	6503	SO:0001583	missense	122970	exon2			AGCCAGCCTCCTT	BC031799	CCDS9817.1	14q24.1	2011-02-16			ENSG00000177465	ENSG00000177465		"""Acyl CoA thioesterases"""	19748	protein-coding gene	gene with protein product		614314				16103133, 16940157	Standard	NM_152331		Approved	FLJ31235, PTE-Ib, PTE2B	uc001xoo.3	Q8N9L9	OTTHUMG00000169485	ENST00000326303.4:c.528C>A	14.37:g.74060476C>A	ENSP00000323071:p.Ser176Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	181	85	0.469613	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677650	0.68042	.	.	ENSG00000177465	ENST00000326303	T	0.39592	1.07	5.25	2.34	0.29019	.	0.451951	0.27437	N	0.019371	T	0.64427	0.2597	M	0.91561	3.22	0.37397	D	0.912664	D	0.76494	0.999	D	0.66979	0.948	T	0.68573	-0.5373	10	0.87932	D	0	-1.9598	6.2571	0.20879	0.0:0.6343:0.1404:0.2253	.	176	Q8N9L9	ACOT4_HUMAN	R	176	ENSP00000323071:S176R	ENSP00000323071:S176R	S	+	3	2	ACOT4	73130229	0.523000	0.26274	1.000000	0.80357	0.995000	0.86356	-0.120000	0.10660	0.554000	0.29061	0.561000	0.74099	AGC	.	.	none		0.463	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331	
MYH1	4619	hgsc.bcm.edu	37	17	10409241	10409241	+	Missense_Mutation	SNP	T	T	C	rs73974725	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:10409241T>C	ENST00000226207.5	-	19	2156	c.2062A>G	c.(2062-2064)Atg>Gtg	p.M688V	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	688	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						TCATGCTCCATGGCACCTAAA	0.478													T|||	74	0.0147764	0.0129	0.0086	5008	,	,		16370	0.0		0.0348	False		,,,				2504	0.0164				p.M688V		Atlas-SNP	.											.	MYH1	403	.	0			c.A2062G						PASS	.	T	VAL/MET	88,4318	73.1+/-111.1	2,84,2117	126.0	107.0	113.0		2062	5.5	1.0	17	dbSNP_130	113	286,8314	107.2+/-168.0	3,280,4017	yes	missense	MYH1	NM_005963.3	21	5,364,6134	CC,CT,TT		3.3256,1.9973,2.8756	probably-damaging	688/1940	10409241	374,12632	2203	4300	6503	SO:0001583	missense	4619	exon19			GCTCCATGGCACC		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2062A>G	17.37:g.10409241T>C	ENSP00000226207:p.Met688Val	Somatic	410	1	0.00243902		WXS	Illumina HiSeq	Phase_I	389	204	0.524422	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	31	0.014194139194139194	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	26	0.03430079155672823	T	15.92	2.976426	0.53720	0.019973	0.033256	ENSG00000109061	ENST00000226207	T	0.71222	-0.55	5.47	5.47	0.80525	Myosin head, motor domain (2);	0.000000	0.52532	U	0.000072	T	0.42743	0.1216	L	0.46670	1.46	0.58432	D	0.999993	B	0.09022	0.002	B	0.22880	0.042	T	0.55289	-0.8164	10	0.39692	T	0.17	.	15.8518	0.78937	0.0:0.0:0.0:1.0	.	688	P12882	MYH1_HUMAN	V	688	ENSP00000226207:M688V	ENSP00000226207:M688V	M	-	1	0	MYH1	10349966	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.825000	0.86693	2.216000	0.71823	0.528000	0.53228	ATG	T|0.975;C|0.025	0.025	strong		0.478	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
ARHGEF7	8874	hgsc.bcm.edu	37	13	111870037	111870037	+	Silent	SNP	T	T	C	rs2296354	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:111870037T>C	ENST00000375741.2	+	6	793	c.543T>C	c.(541-543)gaT>gaC	p.D181D	ARHGEF7_ENST00000375723.1_Silent_p.D3D|ARHGEF7_ENST00000375736.4_Silent_p.D3D|ARHGEF7_ENST00000370623.3_Silent_p.D88D|ARHGEF7_ENST00000544132.1_5'UTR|ARHGEF7_ENST00000317133.5_Silent_p.D160D|ARHGEF7_ENST00000375737.5_Silent_p.D78D|ARHGEF7_ENST00000218789.5_Silent_p.D3D|ARHGEF7_ENST00000426073.2_Silent_p.D3D|ARHGEF7_ENST00000375739.2_Silent_p.D131D	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	181					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			ACATGACCGATAATAGCAACA	0.388													T|||	1246	0.248802	0.025	0.1225	5008	,	,		18731	0.6825		0.174	False		,,,				2504	0.271				p.D181D		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.T543C						PASS	.	T	,,,,	223,4183	134.5+/-170.7	3,217,1983	115.0	109.0	111.0		543,393,9,9,480	-3.1	0.4	13	dbSNP_100	111	1437,7163	276.7+/-292.4	115,1207,2978	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF7	NM_001113511.1,NM_001113512.1,NM_001113513.1,NM_003899.3,NM_145735.2	,,,,	118,1424,4961	CC,CT,TT		16.7093,5.0613,12.7633	,,,,	181/804,131/754,3/647,3/647,160/783	111870037	1660,11346	2203	4300	6503	SO:0001819	synonymous_variant	8874	exon6			GACCGATAATAGC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.543T>C	13.37:g.111870037T>C		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	239	114	0.476987	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	37	CCDS45068.1																																																																																			T|0.807;C|0.193	0.193	strong		0.388	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	
TUBB8	347688	hgsc.bcm.edu	37	10	94026	94026	+	Silent	SNP	G	G	A	rs10904032	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:94026G>A	ENST00000309812.4	-	4	368	c.306C>T	c.(304-306)gcC>gcT	p.A102A	TUBB8_ENST00000332708.5_Missense_Mutation_p.P66L|TUBB8_ENST00000447903.2_Silent_p.A30A|TUBB8_ENST00000413237.3_5'UTR	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	102					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)			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)		AGTGTCCCTTGGCCCAGTTGT	0.572																																					p.A102A	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.C306T						PASS	.	G		693,3713		18,657,1528	68.0	56.0	60.0		306		0.4	10	dbSNP_120	60	3519,5081		504,2511,1285	no	coding-synonymous	TUBB8	NM_177987.2		522,3168,2813	AA,AG,GG		40.9186,15.7286,32.3851		102/445	94026	4212,8794	2203	4300	6503	SO:0001819	synonymous_variant	347688	exon4			TCCCTTGGCCCAG	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.306C>T	10.37:g.94026G>A		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	236	35	0.148305	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1	587	0.26877289377289376	72	0.14634146341463414	129	0.356353591160221	89	0.1555944055944056	297	0.391820580474934	G	10.07	1.248892	0.22880	0.157286	0.409186	ENSG00000173876	ENST00000309812;ENST00000332708	.	.	.	.	.	.	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40997	-0.9533	3	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	rs10904032;rs59810031	.	.	.	L	110;66	.	ENSP00000311042:P110L	P	-	2	0	RP11-631M21.2	84026	0.240000	0.23847	0.361000	0.25849	0.365000	0.29674	-3.811000	0.00360	0.119000	0.18210	0.121000	0.15741	CCA	G|0.731;A|0.269	0.269	strong		0.572	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
CRYZ	1429	hgsc.bcm.edu	37	1	75172001	75172001	+	Silent	SNP	T	T	A	rs7527057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:75172001T>A	ENST00000340866.5	-	9	1056	c.969A>T	c.(967-969)ggA>ggT	p.G323G	CRYZ_ENST00000370872.3_Silent_p.G186G|CRYZ_ENST00000417775.1_Silent_p.G323G|CRYZ_ENST00000370871.3_Silent_p.G289G|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	298	2	0.00671141		WXS	Illumina HiSeq	Phase_I	174	172	0.988506	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		
PFKP	5214	hgsc.bcm.edu	37	10	3150973	3150973	+	Silent	SNP	C	C	T	rs1132173	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:3150973C>T	ENST00000381125.4	+	9	1027	c.951C>T	c.(949-951)ttC>ttT	p.F317F	PFKP_ENST00000381075.2_Silent_p.F309F	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	317	N-terminal catalytic PFK domain 1.				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)		CTTCGGCATTCGACAGGATCT	0.582													C|||	1855	0.370407	0.2791	0.4006	5008	,	,		18762	0.5099		0.332	False		,,,				2504	0.3681				p.F317F		Atlas-SNP	.											.	PFKP	182	.	0			c.C951T						PASS	.	C	,	1129,3277	404.0+/-332.9	145,839,1219	140.0	127.0	131.0		927,951	-7.6	0.5	10	dbSNP_86	131	2815,5785	444.8+/-360.8	435,1945,1920	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	580,2784,3139	TT,TC,CC		32.7326,25.6241,30.3245	,	309/777,317/785	3150973	3944,9062	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon9			GGCATTCGACAGG	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.951C>T	10.37:g.3150973C>T		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	165	37	0.224242	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																			C|0.668;N|0.000	.	strong		0.582	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
PI3	5266	hgsc.bcm.edu	37	20	43803613	43803613	+	Missense_Mutation	SNP	C	C	T	rs17333103	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	161	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	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	
KIF5C	3800	hgsc.bcm.edu	37	2	149806388	149806388	+	Silent	SNP	C	C	T	rs60169973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:149806388C>T	ENST00000435030.1	+	9	1118	c.750C>T	c.(748-750)gaC>gaT	p.D250D	KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Silent_p.D18D|KIF5C_ENST00000414838.2_Silent_p.D155D			O60282	KIF5C_HUMAN	kinesin family member 5C	250	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CTGTTCTTGACGAAGCTAAAA	0.443													C|||	654	0.130591	0.3086	0.0965	5008	,	,		18947	0.0159		0.0924	False		,,,				2504	0.0716				p.D250D		Atlas-SNP	.											.	KIF5C	166	.	0			c.C750T						PASS	.	C		997,2855		141,715,1070	105.0	102.0	103.0		461	-7.3	0.3	2	dbSNP_129	103	701,7595		36,629,3483	no	coding-synonymous	KIF5C	NM_004522.1		177,1344,4553	TT,TC,CC		8.4499,25.8827,13.9776		250/958	149806388	1698,10450	1926	4148	6074	SO:0001819	synonymous_variant	3800	exon9			TCTTGACGAAGCT	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.750C>T	2.37:g.149806388C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	155	67	0.432258	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				C|0.884;T|0.116	0.116	strong		0.443	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
EXOC4	60412	hgsc.bcm.edu	37	7	133689801	133689801	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:133689801A>G	ENST00000253861.4	+	16	2514	c.2485A>G	c.(2485-2487)Agc>Ggc	p.S829G	EXOC4_ENST00000541309.1_Missense_Mutation_p.S117G|EXOC4_ENST00000539845.1_Missense_Mutation_p.S728G|EXOC4_ENST00000545148.1_Missense_Mutation_p.S439G	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	829					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				AGAGGCCATGAGCGCCAGCCT	0.493																																					p.S829G		Atlas-SNP	.											EXOC4_ENST00000545148,NS,carcinoma,0,2	EXOC4	118	2	0			c.A2485G						PASS	.						131.0	125.0	127.0					7																	133689801		2203	4300	6503	SO:0001583	missense	60412	exon16			GCCATGAGCGCCA	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2485A>G	7.37:g.133689801A>G	ENSP00000253861:p.Ser829Gly	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	61	9	0.147541	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.714902	0.48622	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.44	4.28	0.50868	.	0.052853	0.85682	D	0.000000	T	0.53867	0.1823	L	0.46819	1.47	0.45239	D	0.998246	B;B;B	0.17038	0.001;0.02;0.001	B;B;B	0.25759	0.003;0.063;0.001	T	0.50363	-0.8837	9	0.48119	T	0.1	.	8.4959	0.33127	0.8499:0.0:0.1501:0.0	.	361;439;829	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	G	829;448;728;439;117	.	ENSP00000253861:S829G	S	+	1	0	EXOC4	133340341	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	4.678000	0.61641	0.903000	0.36546	0.402000	0.26972	AGC	.	.	none		0.493	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
FNDC1	84624	hgsc.bcm.edu	37	6	159667972	159667972	+	Missense_Mutation	SNP	C	C	T	rs61746218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159667972C>T	ENST00000297267.9	+	15	4861	c.4661C>T	c.(4660-4662)aCg>aTg	p.T1554M	FNDC1_ENST00000340366.6_Missense_Mutation_p.T1491M	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1554					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)		GCAGTACCTACGGAAGAGGCC	0.428													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		18897	0.0		0.004	False		,,,				2504	0.0082				p.T1554M		Atlas-SNP	.											.	FNDC1	250	.	0			c.C4661T						PASS	.	C	MET/THR	6,3840		0,6,1917	133.0	128.0	129.0		4661	5.5	0.8	6	dbSNP_129	129	65,8205		0,65,4070	yes	missense	FNDC1	NM_032532.2	81	0,71,5987	TT,TC,CC		0.786,0.156,0.586	probably-damaging	1554/1895	159667972	71,12045	1923	4135	6058	SO:0001583	missense	84624	exon15			TACCTACGGAAGA	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.4661C>T	6.37:g.159667972C>T	ENSP00000297267:p.Thr1554Met	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	8	0.003663003663003663	0	0.0	5	0.013812154696132596	0	0.0	3	0.00395778364116095	C	14.60	2.584588	0.46110	0.00156	0.00786	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.09817	2.94;3.75	5.54	5.54	0.83059	.	0.207947	0.41001	D	0.000969	T	0.10294	0.0252	M	0.64997	1.995	0.33849	D	0.632415	D	0.56746	0.977	P	0.45794	0.493	T	0.04796	-1.0926	9	.	.	.	-21.4287	17.2366	0.87000	0.0:1.0:0.0:0.0	rs61746218	1554	Q4ZHG4	FNDC1_HUMAN	M	1554;1491	ENSP00000297267:T1554M;ENSP00000342460:T1491M	.	T	+	2	0	FNDC1	159587962	0.988000	0.35896	0.765000	0.31456	0.577000	0.36160	2.989000	0.49393	2.588000	0.87417	0.591000	0.81541	ACG	C|0.995;T|0.005	0.005	strong		0.428	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
SYTL1	84958	hgsc.bcm.edu	37	1	27679797	27679797	+	Missense_Mutation	SNP	A	A	G	rs3813795	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:27679797A>G	ENST00000543823.1	+	13	1829	c.1367A>G	c.(1366-1368)cAg>cGg	p.Q456R	SYTL1_ENST00000490170.1_3'UTR|SYTL1_ENST00000318074.5_Missense_Mutation_p.Q444R			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	456	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.			Q -> R (in Ref. 1; AAK67636 and 4; AAH09224). {ECO:0000305}.	exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)			NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		GATGACAGCCAGGCCAGCCGC	0.622													G|||	2415	0.482228	0.3495	0.4294	5008	,	,		17413	0.25		0.6819	False		,,,				2504	0.7331				p.Q456R		Atlas-SNP	.											.	SYTL1	57	.	0			c.A1367G						PASS	.	G	ARG/GLN,ARG/GLN	1815,2591		364,1087,752	40.0	34.0	36.0		1367,1331	2.7	1.0	1	dbSNP_107	36	5980,2620		2098,1784,418	yes	missense,missense	SYTL1	NM_001193308.1,NM_032872.2	43,43	2462,2871,1170	GG,GA,AA		30.4651,41.1938,40.0661	benign,benign	456/563,444/551	27679797	7795,5211	2203	4300	6503	SO:0001583	missense	84958	exon14			ACAGCCAGGCCAG	AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.1367A>G	1.37:g.27679797A>G	ENSP00000440704:p.Gln456Arg	Somatic	204	2	0.00980392		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_001193308	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Missense_Mutation	SNP	ENST00000543823.1	37	CCDS53286.1	1009	0.461996336996337	180	0.36585365853658536	162	0.44751381215469616	150	0.26223776223776224	517	0.6820580474934037	G	4.608	0.112983	0.08831	0.411938	0.695349	ENSG00000142765	ENST00000318074;ENST00000543823	T;T	0.06608	3.28;3.28	5.57	2.68	0.31781	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.275589	0.35970	N	0.002873	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.29971	-0.9994	9	0.02654	T	1	-27.6108	4.7453	0.13035	0.3872:0.1479:0.4649:0.0	rs3813795;rs11553996;rs17348927;rs60548466;rs3813795	456;444	Q8IYJ3;Q8IYJ3-2	SYTL1_HUMAN;.	R	444;456	ENSP00000316464:Q444R;ENSP00000440704:Q456R	ENSP00000316464:Q444R	Q	+	2	0	SYTL1	27552384	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	0.946000	0.29069	0.327000	0.23409	-0.215000	0.12644	CAG	A|0.473;G|0.527	0.527	strong		0.622	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872	
USB1	79650	hgsc.bcm.edu	37	16	58054099	58054099	+	Missense_Mutation	SNP	C	C	G	rs16959641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:58054099C>G	ENST00000539737.2	+	6	773	c.694C>G	c.(694-696)Caa>Gaa	p.Q232E	USB1_ENST00000561743.1_Missense_Mutation_p.Q199E|USB1_ENST00000219281.3_Missense_Mutation_p.Q250E	NM_001195302.1	NP_001182231.1			U6 snRNA biogenesis 1																		GCACACTGAGCAAGTCCGCTG	0.562													C|||	301	0.0601038	0.0008	0.0533	5008	,	,		22174	0.0833		0.0855	False		,,,				2504	0.0951				p.Q250E		Atlas-SNP	.											.	.	.	.	0			c.C748G						PASS	.	C	GLU/GLN,GLU/GLN	58,4338	56.2+/-92.4	0,58,2140	151.0	116.0	128.0		694,748	5.6	0.9	16	dbSNP_123	128	719,7881	175.8+/-225.7	36,647,3617	yes	missense,missense	C16orf57	NM_001195302.1,NM_024598.3	29,29	36,705,5757	GG,GC,CC		8.3605,1.3194,5.9788	benign,benign	232/248,250/266	58054099	777,12219	2198	4300	6498	SO:0001583	missense	79650	exon7			ACTGAGCAAGTCC	AK023216	CCDS10791.1, CCDS55997.1, CCDS55998.1	16q13	2014-09-17	2012-08-21	2012-08-21	ENSG00000103005	ENSG00000103005			25792	protein-coding gene	gene with protein product	"""HVSL motif containing 1"", ""poikiloderma with neutropenia"", ""U six biogenesis 1"", ""mutated in poikiloderma with neutropenia protein 1"""	613276	"""chromosome 16 open reading frame 57"""	C16orf57		20004881, 20503306, 22899009	Standard	NM_024598		Approved	FLJ13154, HVSL1, Mpn1	uc002emz.3	Q9BQ65	OTTHUMG00000133456	ENST00000539737.2:c.694C>G	16.37:g.58054099C>G	ENSP00000446143:p.Gln232Glu	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	248	201	0.810484	NM_024598		Missense_Mutation	SNP	ENST00000539737.2	37	CCDS55998.1	129	0.059065934065934064	1	0.0020325203252032522	18	0.049723756906077346	51	0.08916083916083917	59	0.07783641160949868	C	7.987	0.752377	0.15778	0.013194	0.083605	ENSG00000103005	ENST00000219281;ENST00000543731;ENST00000539737	T;T	0.51325	0.71;0.71	5.59	5.59	0.84812	.	0.104707	0.64402	D	0.000004	T	0.01061	0.0035	N	0.12831	0.26	0.09310	P	1.0	B;B	0.21225	0.053;0.051	B;B	0.21917	0.036;0.037	T	0.03945	-1.0990	9	0.02654	T	1	-20.0903	16.7251	0.85419	0.0:1.0:0.0:0.0	rs16959641;rs16959641	232;250	B4DZW5;Q9BQ65	.;CP057_HUMAN	E	250;198;232	ENSP00000219281:Q250E;ENSP00000446143:Q232E	ENSP00000219281:Q250E	Q	+	1	0	C16orf57	56611600	0.989000	0.36119	0.887000	0.34795	0.718000	0.41266	2.124000	0.42006	2.807000	0.96579	0.549000	0.68633	CAA	C|0.938;G|0.062	0.062	strong		0.562	USB1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000429947.1	NM_024598	
ALCAM	214	hgsc.bcm.edu	37	3	105260524	105260524	+	Silent	SNP	T	T	C	rs35271455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:105260524T>C	ENST00000306107.5	+	8	1406	c.906T>C	c.(904-906)gaT>gaC	p.D302D	ALCAM_ENST00000389927.4_Intron|ALCAM_ENST00000481337.1_3'UTR|ALCAM_ENST00000472644.2_Silent_p.D302D|ALCAM_ENST00000486979.2_Silent_p.D251D	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	302	Ig-like C2-type 1.				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						CACTGACGGATGTGAGGCGCA	0.418													T|||	35	0.00698882	0.0	0.0	5008	,	,		19669	0.0		0.0179	False		,,,				2504	0.0174				p.D302D		Atlas-SNP	.											.	ALCAM	71	.	0			c.T906C						PASS	.	T		17,4389	23.3+/-48.9	0,17,2186	170.0	136.0	148.0		906	2.5	1.0	3	dbSNP_126	148	100,8500	55.2+/-116.2	0,100,4200	no	coding-synonymous	ALCAM	NM_001627.3		0,117,6386	CC,CT,TT		1.1628,0.3858,0.8996		302/584	105260524	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	214	exon8			GACGGATGTGAGG	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.906T>C	3.37:g.105260524T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Silent	SNP	ENST00000306107.5	37	CCDS33810.1																																																																																			T|0.991;C|0.009	0.009	strong		0.418	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
PEAR1	375033	hgsc.bcm.edu	37	1	156883215	156883215	+	Missense_Mutation	SNP	C	C	A	rs822442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156883215C>A	ENST00000338302.3	+	21	2769	c.2544C>A	c.(2542-2544)aaC>aaA	p.N848K	PEAR1_ENST00000292357.7_Missense_Mutation_p.N848K			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	848	Pro-rich.		N -> K (in dbSNP:rs822442).		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)					GCCTGCAGAACCCTGAGCGGC	0.647													C|||	950	0.189696	0.2481	0.1023	5008	,	,		16630	0.2897		0.1034	False		,,,				2504	0.1585				p.N848K		Atlas-SNP	.											.	PEAR1	118	.	0			c.C2544A						PASS	.	C	LYS/ASN	1001,3405	334.4+/-303.4	112,777,1314	41.0	43.0	42.0		2544	2.6	0.0	1	dbSNP_86	42	992,7608	197.1+/-241.8	60,872,3368	yes	missense	PEAR1	NM_001080471.1	94	172,1649,4682	AA,AC,CC		11.5349,22.719,15.3237	benign	848/1038	156883215	1993,11013	2203	4300	6503	SO:0001583	missense	375033	exon20			GCAGAACCCTGAG	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.2544C>A	1.37:g.156883215C>A	ENSP00000344465:p.Asn848Lys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	160	60	0.375	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	416	0.19047619047619047	106	0.21544715447154472	42	0.11602209944751381	193	0.3374125874125874	75	0.09894459102902374	C	0.022	-1.409761	0.01155	0.22719	0.115349	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.89050	-2.46;-2.46	5.66	2.64	0.31445	.	1.164240	0.06539	N	0.742807	T	0.71247	0.3317	L	0.36672	1.1	0.80722	P	0.0	B	0.21520	0.057	B	0.14023	0.01	T	0.44003	-0.9356	9	0.20519	T	0.43	.	10.6155	0.45447	0.2184:0.6563:0.1253:0.0	rs822442	848	Q5VY43	PEAR1_HUMAN	K	848	ENSP00000344465:N848K;ENSP00000292357:N848K	ENSP00000292357:N848K	N	+	3	2	PEAR1	155149839	0.001000	0.12720	0.003000	0.11579	0.069000	0.16628	1.345000	0.33953	0.269000	0.21961	0.563000	0.77884	AAC	C|0.841;A|0.159	0.159	strong		0.647	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
LARS	51520	hgsc.bcm.edu	37	5	145508636	145508636	+	Missense_Mutation	SNP	T	T	C	rs61732383|rs35977062	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145508636T>C	ENST00000394434.2	-	26	2840	c.2674A>G	c.(2674-2676)Aat>Gat	p.N892D	LARS_ENST00000274562.9_Missense_Mutation_p.N865D|LARS_ENST00000510191.1_Missense_Mutation_p.N838D|LARS_ENST00000545646.1_Missense_Mutation_p.N846D	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	124	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	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	
SAMD15	161394	hgsc.bcm.edu	37	14	77843971	77843971	+	Silent	SNP	C	C	T	rs45540040	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77843971C>T	ENST00000216471.4	+	1	496	c.210C>T	c.(208-210)gaC>gaT	p.D70D	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	70										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGGAGCCAGACAGTGCTAAGA	0.547													c|||	709	0.141573	0.059	0.2651	5008	,	,		18232	0.0159		0.2038	False		,,,				2504	0.2311				p.D70D		Atlas-SNP	.											.	SAMD15	60	.	0			c.C210T						PASS	.	G		409,3997	201.8+/-224.7	16,377,1810	97.0	93.0	94.0		210	-2.1	0.0	14	dbSNP_127	94	1685,6915	307.2+/-308.3	182,1321,2797	no	coding-synonymous	SAMD15	NM_001010860.1		198,1698,4607	TT,TC,CC		19.593,9.2828,16.1003		70/675	77843971	2094,10912	2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			GCCAGACAGTGCT	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.210C>T	14.37:g.77843971C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	93	58	0.623656	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																			C|0.848;T|0.152	0.152	strong		0.547	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
GPLD1	2822	hgsc.bcm.edu	37	6	24489652	24489652	+	Missense_Mutation	SNP	C	C	T	rs1126617	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:24489652C>T	ENST00000230036.1	-	1	198	c.88G>A	c.(88-90)Gta>Ata	p.V30I	GPLD1_ENST00000474784.1_5'UTR	NM_001503.3	NP_001494.2	P80108	PHLD_HUMAN	glycosylphosphatidylinositol specific phospholipase D1	30			V -> I (in dbSNP:rs1126617). {ECO:0000269|PubMed:11072085, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		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						CCTATTTCTACGTGTGTTGAA	0.463													C|||	1345	0.26857	0.3139	0.2089	5008	,	,		23090	0.1667		0.332	False		,,,				2504	0.2894				p.V30I		Atlas-SNP	.											.	GPLD1	91	.	0			c.G88A						PASS	.	C	ILE/VAL,ILE/VAL	1367,3039	453.2+/-350.3	210,947,1046	131.0	107.0	115.0		88,88	-6.8	0.1	6	dbSNP_86	115	2890,5710	452.1+/-362.9	465,1960,1875	yes	missense,missense	GPLD1	NM_001503.2,NM_177483.1	29,29	675,2907,2921	TT,TC,CC		33.6047,31.0259,32.731	benign,benign	30/841,30/177	24489652	4257,8749	2203	4300	6503	SO:0001583	missense	2822	exon1			TTTCTACGTGTGT	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.88G>A	6.37:g.24489652C>T	ENSP00000230036:p.Val30Ile	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	111	108	0.972973	NM_001503	Q15127|Q15128|Q2M2F2|Q5T3Y0|Q7Z6T8|Q8TCV0|Q8WW82|Q96ID6|Q9H167|Q9H4M1|Q9UJC9	Missense_Mutation	SNP	ENST00000230036.1	37	CCDS4553.1	606	0.2774725274725275	147	0.29878048780487804	93	0.2569060773480663	108	0.1888111888111888	258	0.3403693931398417	C	0.006	-2.052583	0.00394	0.310259	0.336047	ENSG00000112293	ENST00000230036;ENST00000378243	T	0.38722	1.12	4.89	-6.76	0.01732	.	0.560584	0.17082	N	0.187745	T	0.03651	0.0104	N	0.01751	-0.74	0.80722	P	0.0	B;B	0.13594	0.004;0.008	B;B	0.14023	0.002;0.01	T	0.24440	-1.0160	9	0.02654	T	1	-2.006	14.647	0.68767	0.0:0.3288:0.0:0.6712	rs1126617;rs1804164;rs2235500;rs3181755;rs17374253;rs17404904;rs59497448;rs1126617	30;30	P80108-2;P80108	.;PHLD_HUMAN	I	30	ENSP00000230036:V30I	ENSP00000230036:V30I	V	-	1	0	GPLD1	24597631	0.004000	0.15560	0.147000	0.22382	0.007000	0.05969	-0.977000	0.03782	-1.433000	0.01977	-0.991000	0.02546	GTA	C|0.700;T|0.299	0.299	strong		0.463	GPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043315.1	NM_001503	
RAD21L1	642636	hgsc.bcm.edu	37	20	1221038	1221038	+	Silent	SNP	T	T	C	rs16992733	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1221038T>C	ENST00000409241.1	+	8	909	c.816T>C	c.(814-816)acT>acC	p.T272T	RAD21L1_ENST00000402452.1_Silent_p.T272T|RAD21L1_ENST00000381882.2_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	110	58	0.527273	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		
RFX4	5992	hgsc.bcm.edu	37	12	107113769	107113769	+	Silent	SNP	G	G	A	rs17038732	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:107113769G>A	ENST00000392842.1	+	12	1584	c.1170G>A	c.(1168-1170)gaG>gaA	p.E390E	RFX4_ENST00000357881.4_Silent_p.E399E|RP11-144F15.1_ENST00000551505.1_Intron|RFX4_ENST00000229387.5_Silent_p.E296E|RP11-482D24.3_ENST00000552415.1_RNA	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	390	Necessary for dimerization.				cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						TCTTGGAGGAGCAGTCTCCCA	0.502													G|||	353	0.0704872	0.1944	0.0519	5008	,	,		17906	0.0099		0.0199	False		,,,				2504	0.0307				p.E399E		Atlas-SNP	.											.	RFX4	218	.	0			c.G1197A						PASS	.	G	,,	706,3700	294.4+/-283.1	60,586,1557	210.0	187.0	195.0		1197,888,1170	-0.2	1.0	12	dbSNP_123	195	158,8442	75.1+/-137.7	0,158,4142	no	coding-synonymous,coding-synonymous,coding-synonymous	RFX4	NM_001206691.1,NM_032491.5,NM_213594.2	,,	60,744,5699	AA,AG,GG		1.8372,16.0236,6.6431	,,	399/745,296/642,390/736	107113769	864,12142	2203	4300	6503	SO:0001819	synonymous_variant	5992	exon12			GGAGGAGCAGTCT	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1170G>A	12.37:g.107113769G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	202	102	0.504951	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																			G|0.928;A|0.072	0.072	strong		0.502	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
PCSK7	9159	hgsc.bcm.edu	37	11	117096652	117096652	+	Silent	SNP	G	G	A	rs2277287	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117096652G>A	ENST00000320934.3	-	6	1485	c.855C>T	c.(853-855)agC>agT	p.S285S	PCSK7_ENST00000540028.1_5'Flank	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	285	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CTCACCTGCAGCTGTAGATGT	0.552			T	IGH@	MLCLS						OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1249	0.249401	0.3381	0.2666	5008	,	,		17158	0.1508		0.1928	False		,,,				2504	0.2771				p.S285S		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C855T						PASS	.	G		1333,3069	445.7+/-347.8	189,955,1057	127.0	90.0	102.0		855	2.7	1.0	11	dbSNP_100	102	1788,6804	323.2+/-315.9	181,1426,2689	no	coding-synonymous	PCSK7	NM_004716.2		370,2381,3746	AA,AG,GG		20.8101,30.2817,24.0188		285/786	117096652	3121,9873	2201	4296	6497	SO:0001819	synonymous_variant	9159	exon6			CCTGCAGCTGTAG	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.855C>T	11.37:g.117096652G>A		Somatic	117	0	0	1478	WXS	Illumina HiSeq	Phase_I	155	43	0.277419	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			G|0.759;A|0.241	0.241	strong		0.552	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140768442	140768442	+	Missense_Mutation	SNP	G	G	T	rs201053346		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140768442G>T	ENST00000519479.1	+	1	991	c.991G>T	c.(991-993)Gtg>Ttg	p.V331L	PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	331	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAATGCACAGTGGAGGTAGA	0.413																																					p.V331L		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.G991T						PASS	.	G	LEU/VAL,,,,,,,,,,,LEU/VAL	0,3830		0,0,1915	86.0	80.0	82.0		991,,,,,,,,,,,991	4.2	0.1	5		82	3,8283		0,3,4140	yes	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGB3,PCDHGB2,PCDHGB1,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_018922.2,NM_018923.2,NM_018924.2,NM_032098.1	32,,,,,,,,,,,32	0,3,6055	TT,TG,GG		0.0362,0.0,0.0248	,,,,,,,,,,,	331/924,,,,,,,,,,,331/804	140768442	3,12113	1915	4143	6058	SO:0001583	missense	8641	exon1			TGCACAGTGGAGG	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.991G>T	5.37:g.140768442G>T	ENSP00000428288:p.Val331Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	13.67	2.306759	0.40795	0.0	3.62E-4	ENSG00000253953	ENST00000519479	T	0.01787	4.64	5.09	4.2	0.49525	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.06781	0.0173	M	0.74389	2.26	0.25118	N	0.990664	P;D	0.55385	0.918;0.971	P;P	0.53102	0.596;0.718	T	0.09552	-1.0669	9	0.49607	T	0.09	.	14.1498	0.65375	0.0773:0.0:0.9227:0.0	.	331;331	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	L	331	ENSP00000428288:V331L	ENSP00000428288:V331L	V	+	1	0	PCDHGB4	140748626	0.998000	0.40836	0.109000	0.21407	0.063000	0.16089	2.244000	0.43124	2.525000	0.85131	0.655000	0.94253	GTG	.	.	weak		0.413	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
CRACR2A	84766	hgsc.bcm.edu	37	12	3788222	3788222	+	Missense_Mutation	SNP	G	G	A	rs242017	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:3788222G>A	ENST00000252322.1	-	6	851	c.383C>T	c.(382-384)gCa>gTa	p.A128V	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.A128V|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.A128V	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		128			A -> V (in dbSNP:rs242017). {ECO:0000269|PubMed:15489334}.		activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			CTGTTCACCTGCATCTTCCTG	0.557													G|||	1135	0.226637	0.1785	0.3372	5008	,	,		20510	0.1319		0.2644	False		,,,				2504	0.272				p.A128V		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.C383T						PASS	.	G	VAL/ALA,VAL/ALA	856,3550	336.3+/-304.3	100,656,1447	154.0	127.0	136.0		383,383	0.9	0.0	12	dbSNP_79	136	2439,6161	402.8+/-347.6	320,1799,2181	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	64,64	420,2455,3628	AA,AG,GG		28.3605,19.4281,25.3345	benign,benign	128/732,128/396	3788222	3295,9711	2203	4300	6503	SO:0001583	missense	84766	exon6			TCACCTGCATCTT																												ENST00000252322.1:c.383C>T	12.37:g.3788222G>A	ENSP00000252322:p.Ala128Val	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	502	0.22985347985347984	93	0.18902439024390244	123	0.3397790055248619	81	0.14160839160839161	205	0.2704485488126649	G	9.608	1.130430	0.21041	0.194281	0.283605	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.62941	-0.01;2.43;2.46	4.18	0.878	0.19150	EF-hand-like domain (1);	0.821237	0.11051	N	0.605064	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	P;P;B	0.35656	0.514;0.493;0.361	B;B;B	0.33620	0.036;0.167;0.081	T	0.19910	-1.0291	9	0.16420	T	0.52	-0.6969	6.8838	0.24189	0.0:0.1663:0.4941:0.3396	rs242017;rs3803134;rs17697944;rs52823302;rs59003580;rs242017	128;128;128	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	V	128	ENSP00000409382:A128V;ENSP00000412496:A128V;ENSP00000252322:A128V	ENSP00000252322:A128V	A	-	2	0	EFCAB4B	3658483	0.000000	0.05858	0.002000	0.10522	0.682000	0.39822	0.131000	0.15870	0.291000	0.22468	0.561000	0.74099	GCA	G|0.756;N|0.000	.	strong		0.557	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
OXNAD1	92106	hgsc.bcm.edu	37	3	16336381	16336381	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:16336381A>G	ENST00000285083.5	+	6	774	c.309A>G	c.(307-309)ccA>ccG	p.P103P	OXNAD1_ENST00000435829.2_Silent_p.P121P|OXNAD1_ENST00000605932.1_Silent_p.P103P|OXNAD1_ENST00000606098.1_Silent_p.P103P|OXNAD1_ENST00000544043.1_Silent_p.P121P	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	103	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.					mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						TCTTTATTCCAGGAGTCTCTG	0.363																																					p.P103P		Atlas-SNP	.											.	OXNAD1	31	.	0			c.A309G						PASS	.						140.0	143.0	142.0					3																	16336381		2203	4300	6503	SO:0001819	synonymous_variant	92106	exon6			TATTCCAGGAGTC	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.309A>G	3.37:g.16336381A>G		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	214	94	0.439252	NM_138381	Q2HYC7|Q59FA4	Silent	SNP	ENST00000285083.5	37	CCDS2630.1																																																																																			.	.	none		0.363	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
PARD3B	117583	hgsc.bcm.edu	37	2	205829991	205829991	+	Silent	SNP	C	C	T	rs236843	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000349953.3_Silent_p.A113A|PARD3B_ENST00000358768.2_Silent_p.A113A|PARD3B_ENST00000351153.1_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	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	102	78	0.764706	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	
ELAVL1	1994	hgsc.bcm.edu	37	19	8028544	8028544	+	Silent	SNP	A	A	G	rs14394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:8028544A>G	ENST00000407627.2	-	6	933	c.804T>C	c.(802-804)ggT>ggC	p.G268G	ELAVL1_ENST00000351593.5_Silent_p.G295G|ELAVL1_ENST00000593807.1_3'UTR|ELAVL1_ENST00000596459.1_Silent_p.G268G	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	268	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TGGTGACGGCACCAAACGGCC	0.547													G|||	763	0.152356	0.1634	0.1585	5008	,	,		18524	0.0456		0.3101	False		,,,				2504	0.0808				p.G268G		Atlas-SNP	.											.	ELAVL1	44	.	0			c.T804C						PASS	.	G		871,3535	743.3+/-411.4	87,697,1419	135.0	115.0	121.0		804	-5.1	0.3	19	dbSNP_52	121	2454,6146	697.0+/-404.9	337,1780,2183	no	coding-synonymous	ELAVL1	NM_001419.2		424,2477,3602	GG,GA,AA		28.5349,19.7685,25.5651		268/327	8028544	3325,9681	2203	4300	6503	SO:0001819	synonymous_variant	1994	exon6			GACGGCACCAAAC	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"""RNA binding motif (RRM) containing"""	3312	protein-coding gene	gene with protein product	"""embryonic lethal, abnormal vision, drosophila, homolog-like 1"", ""Hu antigen R"""	603466	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"""	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.804T>C	19.37:g.8028544A>G		Somatic	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	255	120	0.470588	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Silent	SNP	ENST00000407627.2	37	CCDS12193.1																																																																																			A|0.776;G|0.224	0.224	strong		0.547	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419	
SMYD4	114826	hgsc.bcm.edu	37	17	1731268	1731268	+	Silent	SNP	T	T	C	rs8067660	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:1731268T>C	ENST00000305513.7	-	2	188	c.21A>G	c.(19-21)gaA>gaG	p.E7E	AC130689.1_ENST00000582190.1_RNA|RPA1_ENST00000254719.5_5'Flank	NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	7							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						ATGATTTCCATTCATCCACAG	0.398													C|||	2951	0.589257	0.6815	0.4971	5008	,	,		20661	0.4583		0.7634	False		,,,				2504	0.4857				p.E7E		Atlas-SNP	.											.	SMYD4	50	.	0			c.A21G						PASS	.	C		3151,1255	429.9+/-342.4	1129,893,181	105.0	95.0	98.0		21	-2.1	1.0	17	dbSNP_116	98	6780,1820	326.4+/-317.4	2669,1442,189	no	coding-synonymous	SMYD4	NM_052928.2		3798,2335,370	CC,CT,TT		21.1628,28.4839,23.6429		7/805	1731268	9931,3075	2203	4300	6503	SO:0001819	synonymous_variant	114826	exon2			TTTCCATTCATCC	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.21A>G	17.37:g.1731268T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Silent	SNP	ENST00000305513.7	37	CCDS11013.1																																																																																			T|0.294;C|0.706	0.706	strong		0.398	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
SZT2	23334	hgsc.bcm.edu	37	1	43870071	43870071	+	Silent	SNP	C	C	A	rs41312024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43870071C>A	ENST00000562955.1	+	4	348	c.348C>A	c.(346-348)atC>atA	p.I116I	SZT2_ENST00000372450.4_Silent_p.I114I|SZT2_ENST00000310739.4_Silent_p.I116I	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	116					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						CAGGGGAGATCTTGTTTGATG	0.562													C|||	18	0.00359425	0.0	0.0058	5008	,	,		18752	0.0		0.0139	False		,,,				2504	0.0				p.I116I		Atlas-SNP	.											.	SZT2	383	.	0			c.C348A						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	95.0	91.0	93.0		348	1.4	1.0	1	dbSNP_127	93	147,8453	71.0+/-133.6	0,147,4153	no	coding-synonymous	SZT2	NM_015284.3		0,162,6341	AA,AC,CC		1.7093,0.3404,1.2456		116/3376	43870071	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	23334	exon4			GGAGATCTTGTTT	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.348C>A	1.37:g.43870071C>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	83	68	0.819277	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																			C|0.990;A|0.010	0.010	strong		0.562	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
LRP2	4036	hgsc.bcm.edu	37	2	170088351	170088351	+	Splice_Site	SNP	G	G	A	rs2302694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:170088351G>A	ENST00000263816.3	-	31	5385	c.5100C>T	c.(5098-5100)tcC>tcT	p.S1700S		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1700	EGF-like 7. {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)"""	ATGGATTCACGGCTGCATGAG	0.488													G|||	920	0.183706	0.4228	0.1931	5008	,	,		19030	0.0526		0.1093	False		,,,				2504	0.0654				p.S1700S		Atlas-SNP	.											.	LRP2	751	.	0			c.C5100T						PASS	.	G		1684,2722	509.1+/-367.1	321,1042,840	49.0	54.0	52.0		5100	-1.4	0.0	2	dbSNP_100	52	969,7631	209.8+/-250.9	68,833,3399	yes	coding-synonymous-near-splice	LRP2	NM_004525.2		389,1875,4239	AA,AG,GG		11.2674,38.2206,20.3983		1700/4656	170088351	2653,10353	2203	4300	6503	SO:0001630	splice_region_variant	4036	exon31			ATTCACGGCTGCA		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.5099-1C>T	2.37:g.170088351G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	212	96	0.45283	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.806;A|0.194	0.194	strong		0.488	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	Silent
NAB1	4664	hgsc.bcm.edu	37	2	191550256	191550256	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:191550256T>C	ENST00000337386.5	+	8	1611	c.1150T>C	c.(1150-1152)Tat>Cat	p.Y384H	AC006460.2_ENST00000411949.1_RNA|AC006460.2_ENST00000428032.1_RNA|NAB1_ENST00000357215.5_Missense_Mutation_p.Y355H|NAB1_ENST00000409641.1_Missense_Mutation_p.Y383H|NAB1_ENST00000545490.1_Missense_Mutation_p.Y124H|NAB1_ENST00000409581.1_Missense_Mutation_p.Y384H|AC006460.2_ENST00000421437.1_RNA	NM_005966.3	NP_005957.2	Q13506	NAB1_HUMAN	NGFI-A binding protein 1 (EGR1 binding protein 1)	384					endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of epidermis development (GO:0045682)|regulation of transcription, DNA-templated (GO:0006355)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				kidney(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0405)|all cancers(119;0.109)			CCAAGCTGGCTATGAGAGACT	0.468																																					p.Y384H		Atlas-SNP	.											NAB1,NS,carcinoma,-1,2	NAB1	31	2	0			c.T1150C						scavenged	.						69.0	63.0	65.0					2																	191550256		2203	4300	6503	SO:0001583	missense	4664	exon8			GCTGGCTATGAGA		CCDS2307.1	2q32.3-q33	2008-05-23			ENSG00000138386	ENSG00000138386			7626	protein-coding gene	gene with protein product	"""EGR1 binding protein 1"""	600800				7624335, 8668170, 9418898	Standard	XM_005246579		Approved		uc002usb.3	Q13506	OTTHUMG00000132689	ENST00000337386.5:c.1150T>C	2.37:g.191550256T>C	ENSP00000336894:p.Tyr384His	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	203	3	0.0147783	NM_005966	O75383|O75384|Q6GTU1|Q9UEV1	Missense_Mutation	SNP	ENST00000337386.5	37	CCDS2307.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.57|14.57	2.573503|2.573503	0.45902|0.45902	.|.	.|.	ENSG00000138386|ENSG00000138386	ENST00000434473|ENST00000409581;ENST00000337386;ENST00000357215;ENST00000409641;ENST00000545490	.|.	.|.	.|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|Nab1, C-terminal (1);	.|0.420625	.|0.26642	.|N	.|0.023246	T|T	0.45337|0.45337	0.1337|0.1337	N|N	0.19112|0.19112	0.55|0.55	0.32708|0.32708	N|N	0.511939|0.511939	.|P;P;P	.|0.43231	.|0.763;0.801;0.801	.|P;P;P	.|0.51742	.|0.447;0.678;0.678	T|T	0.53872|0.53872	-0.8377|-0.8377	5|9	.|0.28530	.|T	.|0.3	-0.9421|-0.9421	14.5475|14.5475	0.68041|0.68041	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|355;383;384	.|F8W8J7;B8ZZS2;Q13506	.|.;.;NAB1_HUMAN	P|H	136|384;384;355;383;124	.|.	.|ENSP00000336894:Y384H	L|Y	+|+	2|1	0|0	NAB1|NAB1	191258501|191258501	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.809000|0.809000	0.45718|0.45718	2.801000|2.801000	0.47908|0.47908	2.216000|2.216000	0.71823|0.71823	0.533000|0.533000	0.62120|0.62120	CTA|TAT	.	.	none		0.468	NAB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255986.1	NM_005966	
PKDREJ	10343	hgsc.bcm.edu	37	22	46657798	46657798	+	Silent	SNP	A	A	G	rs6007748	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46657798A>G	ENST00000253255.5	-	1	1421	c.1422T>C	c.(1420-1422)gaT>gaC	p.D474D		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	474	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		AAGAAAATCTATCAGAGACAA	0.393													A|||	1198	0.239217	0.6558	0.1326	5008	,	,		18300	0.001		0.16	False		,,,				2504	0.0787				p.D474D		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T1422C						PASS	.	A		2538,1868	631.6+/-395.7	719,1100,384	98.0	103.0	101.0		1422	-7.0	0.0	22	dbSNP_114	101	1255,7345	250.8+/-277.5	87,1081,3132	no	coding-synonymous	PKDREJ	NM_006071.1		806,2181,3516	GG,GA,AA		14.593,42.3967,29.1635		474/2254	46657798	3793,9213	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			AAATCTATCAGAG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.1422T>C	22.37:g.46657798A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.737;G|0.263	0.263	strong		0.393	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
CYB5RL	606495	hgsc.bcm.edu	37	1	54661150	54661150	+	Missense_Mutation	SNP	C	C	T	rs946448	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:54661150C>T	ENST00000534324.1	-	1	139	c.140G>A	c.(139-141)aGg>aAg	p.R47K	CYB5RL_ENST00000401046.3_5'UTR|MRPL37_ENST00000487096.1_Intron|RP11-446E24.4_ENST00000311841.7_Missense_Mutation_p.R47K|CYB5RL_ENST00000537208.1_Missense_Mutation_p.R47K|CYB5RL_ENST00000542737.1_Missense_Mutation_p.R47K|CYB5RL_ENST00000419823.2_Missense_Mutation_p.R47K|CYB5RL_ENST00000287899.8_Missense_Mutation_p.R47K|CYB5RL_ENST00000497820.1_Missense_Mutation_p.R47K			Q6IPT4	NB5R5_HUMAN	cytochrome b5 reductase-like	47	Oxidoreductase-like.		R -> K (in dbSNP:rs946448). {ECO:0000269|PubMed:15489334}.				cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|urinary_tract(1)	8						TGCCTCCCACCTTGCCAGATC	0.607													C|||	1584	0.316294	0.2118	0.3213	5008	,	,		14903	0.255		0.3519	False		,,,				2504	0.4806				p.R47K		Atlas-SNP	.											.	CYB5RL	17	.	0			c.G140A						PASS	.	C	LYS/ARG	875,3219		95,685,1267	46.0	48.0	47.0		140	4.2	1.0	1	dbSNP_86	47	2866,5494		514,1838,1828	yes	missense	CYB5RL	NM_001031672.2	26	609,2523,3095	TT,TC,CC		34.2823,21.3727,30.0385	benign	47/316	54661150	3741,8713	2047	4180	6227	SO:0001583	missense	606495	exon3			TCCCACCTTGCCA		CCDS44151.1	1p32.3	2011-04-08			ENSG00000215883	ENSG00000215883			32220	protein-coding gene	gene with protein product						12477932	Standard	NM_001031672		Approved	LOC606495	uc009vzo.3	Q6IPT4	OTTHUMG00000008082	ENST00000534324.1:c.140G>A	1.37:g.54661150C>T	ENSP00000434343:p.Arg47Lys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_001031672	B7ZBS4|Q8NF25	Missense_Mutation	SNP	ENST00000534324.1	37	CCDS44151.1	669	0.30631868131868134	110	0.22357723577235772	144	0.39779005524861877	143	0.25	272	0.35883905013192613	C	20.2	3.956210	0.73902	0.213727	0.342823	ENSG00000215883	ENST00000419823;ENST00000534324;ENST00000287899;ENST00000542737;ENST00000537208;ENST00000497820	T;T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03;1.03	5.17	4.24	0.50183	Oxidoreductase-like, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.26092	0.79	0.42558	P	0.006867999999999985	B	0.26775	0.159	B	0.24848	0.056	T	0.41088	-0.9528	8	0.29301	T	0.29	.	8.214	0.31501	0.0:0.8334:0.0:0.1666	rs946448;rs3737834;rs17390104;rs60484336;rs946448	47	Q6IPT4	NB5R5_HUMAN	K	47	ENSP00000409075:R47K;ENSP00000434343:R47K;ENSP00000287899:R47K;ENSP00000438151:R47K;ENSP00000443797:R47K;ENSP00000431157:R47K	ENSP00000287899:R47K	R	-	2	0	CYB5RL	54433738	0.172000	0.23043	1.000000	0.80357	0.997000	0.91878	0.880000	0.28159	2.689000	0.91719	0.561000	0.74099	AGG	C|0.708;T|0.292	0.292	strong		0.607	CYB5RL-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388318.1	NM_001031672	
ZSCAN5A	79149	hgsc.bcm.edu	37	19	56736102	56736102	+	Missense_Mutation	SNP	A	A	T	rs201600248		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56736102A>T	ENST00000587340.1	-	4	1009	c.314T>A	c.(313-315)aTg>aAg	p.M105K	ZSCAN5A_ENST00000592355.1_Missense_Mutation_p.M105K|ZSCAN5A_ENST00000254165.3_Intron|ZSCAN5A_ENST00000391713.1_Missense_Mutation_p.M105K|ZSCAN5A_ENST00000587492.1_Intron			Q9BUG6	ZSA5A_HUMAN	zinc finger and SCAN domain containing 5A	105	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)	p.M105K(2)		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						ACCGTTCATCATGACTAAGAC	0.552																																					p.M105K		Atlas-SNP	.											ZSCAN5A,trunk,malignant_melanoma,0,2	ZSCAN5A	118	2	2	Substitution - Missense(2)	skin(2)	c.T314A						scavenged	.						19.0	19.0	19.0					19																	56736102		2141	4214	6355	SO:0001583	missense	79149	exon2			TTCATCATGACTA	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.314T>A	19.37:g.56736102A>T	ENSP00000467631:p.Met105Lys	Somatic	900	1	0.00111111		WXS	Illumina HiSeq	Phase_I	690	9	0.0130435	NM_024303	B4DX98|Q49A73|Q53F04|Q8N7B3	Missense_Mutation	SNP	ENST00000587340.1	37	CCDS12941.1	.	.	.	.	.	.	.	.	.	.	A	0.004	-2.262023	0.00262	.	.	ENSG00000131848	ENST00000391713	T	0.03745	3.82	2.27	-1.24	0.09435	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.00637	0.0021	N	0.00086	-2.195	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.44817	-0.9303	9	0.02654	T	1	.	2.254	0.04051	0.2591:0.3296:0.0:0.4112	.	105	Q9BUG6	ZSA5A_HUMAN	K	105	ENSP00000375593:M105K	ENSP00000375593:M105K	M	-	2	0	ZSCAN5A	61427914	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.751000	0.00792	-0.413000	0.07507	-0.669000	0.03829	ATG	.	.	weak		0.552	ZSCAN5A-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458110.1	NM_024303	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350481	65350481	+	Missense_Mutation	SNP	C	C	T	rs3805466	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:65350481C>T	ENST00000284037.5	+	21	3724	c.3335C>T	c.(3334-3336)tCa>tTa	p.S1112L	ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000511297.1_Missense_Mutation_p.S1108L|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.S1112L|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.S1112L	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1112			S -> L (in dbSNP:rs3805466).		basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		GAGTTCCACTCAGCGGGAAGA	0.488													C|||	418	0.0834665	0.0121	0.2219	5008	,	,		18342	0.1339		0.0417	False		,,,				2504	0.0726				p.S1112L		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.C3335T						PASS	.	C	LEU/SER,LEU/SER	101,4305	79.9+/-118.3	0,101,2102	60.0	58.0	59.0		3335,3335	5.8	1.0	5	dbSNP_107	59	410,8190	128.3+/-186.6	9,392,3899	yes	missense,missense	ERBB2IP	NM_001006600.1,NM_018695.2	145,145	9,493,6001	TT,TC,CC		4.7674,2.2923,3.929	benign,benign	1112/1303,1112/1372	65350481	511,12495	2203	4300	6503	SO:0001583	missense	55914	exon21			TCCACTCAGCGGG		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.3335C>T	5.37:g.65350481C>T	ENSP00000284037:p.Ser1112Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	208	0.09523809523809523	9	0.018292682926829267	67	0.1850828729281768	96	0.16783216783216784	36	0.047493403693931395	C	18.19	3.569735	0.65765	0.022923	0.047674	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T	0.39592	1.3;1.3;1.3;1.49;1.07;1.37;1.3;1.33;1.07	5.76	5.76	0.90799	.	0.259894	0.39985	N	0.001207	T	0.00109	0.0003	L	0.47190	1.495	0.20307	P	0.9999122916	P;P;B;P;P;P;P	0.48764	0.835;0.594;0.444;0.773;0.651;0.835;0.915	B;B;B;P;B;B;P	0.53185	0.311;0.164;0.206;0.529;0.084;0.407;0.72	T	0.00017	-1.2377	9	0.72032	D	0.01	.	19.943	0.97172	0.0:1.0:0.0:0.0	rs3805466;rs61274806;rs3805466	1112;1112;1112;1108;1112;1112;1112	Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;LAP2_HUMAN;.;.	L	1112;1112;1112;1112;1112;1112;1108;1112;1112	ENSP00000284037:S1112L;ENSP00000370330:S1112L;ENSP00000370326:S1112L;ENSP00000370323:S1112L;ENSP00000370322:S1112L;ENSP00000370325:S1112L;ENSP00000422766:S1108L;ENSP00000426632:S1112L;ENSP00000422015:S1112L	ENSP00000284037:S1112L	S	+	2	0	ERBB2IP	65386237	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.210000	0.77924	2.722000	0.93159	0.650000	0.86243	TCA	C|0.936;T|0.064	0.064	strong		0.488	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
PLEC	5339	hgsc.bcm.edu	37	8	144991925	144991925	+	Missense_Mutation	SNP	G	G	A	rs189061273	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144991925G>A	ENST00000322810.4	-	32	12644	c.12475C>T	c.(12475-12477)Ctc>Ttc	p.L4159F	PLEC_ENST00000398774.2_Missense_Mutation_p.L3990F|PLEC_ENST00000527096.1_Missense_Mutation_p.L4045F|PLEC_ENST00000357649.2_Missense_Mutation_p.L4026F|PLEC_ENST00000345136.3_Missense_Mutation_p.L4022F|PLEC_ENST00000356346.3_Missense_Mutation_p.L4008F|PLEC_ENST00000436759.2_Missense_Mutation_p.L4049F|PLEC_ENST00000354958.2_Missense_Mutation_p.L4000F|PLEC_ENST00000354589.3_Missense_Mutation_p.L4022F	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4159	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						AGGGAGATGAGCTTCCCAGAG	0.637													G|||	14	0.00279553	0.0	0.0	5008	,	,		18649	0.0139		0.0	False		,,,				2504	0.0				p.L4159F		Atlas-SNP	.											PLEC_ENST00000436759,bladder,carcinoma,+2,3	PLEC	1144	3	0			c.C12475T						PASS	.						49.0	57.0	54.0					8																	144991925		2110	4197	6307	SO:0001583	missense	5339	exon32			AGATGAGCTTCCC	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.12475C>T	8.37:g.144991925G>A	ENSP00000323856:p.Leu4159Phe	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	63	0.617647	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	10	0.004578754578754579	0	0.0	0	0.0	10	0.017482517482517484	0	0.0	G	8.561	0.877675	0.17395	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4	4.98	4.98	0.66077	.	0.420113	0.19781	U	0.106211	T	0.37758	0.1015	N	0.14661	0.345	0.34450	D	0.700616	P;P;P;P;P;P;P;P	0.49090	0.919;0.919;0.919;0.868;0.919;0.919;0.919;0.919	P;P;P;B;P;P;P;P	0.45506	0.483;0.483;0.483;0.289;0.483;0.483;0.483;0.483	T	0.63637	-0.6592	10	0.54805	T	0.06	.	13.0686	0.59048	0.0:0.0:0.8393:0.1607	.	4049;4008;4000;4159;3990;4022;4026;4022	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	F	4022;4026;4022;3990;4159;4000;4008;4049;4045	ENSP00000344848:L4022F;ENSP00000350277:L4026F;ENSP00000346602:L4022F;ENSP00000381756:L3990F;ENSP00000323856:L4159F;ENSP00000347044:L4000F;ENSP00000348702:L4008F;ENSP00000388180:L4049F;ENSP00000434583:L4045F	ENSP00000323856:L4159F	L	-	1	0	PLEC	145063913	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.222000	0.32515	2.597000	0.87782	0.549000	0.68633	CTC	G|0.995;A|0.005	0.005	strong		0.637	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
E4F1	1877	hgsc.bcm.edu	37	16	2285357	2285357	+	Silent	SNP	C	C	T	rs26840	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2285357C>T	ENST00000301727.4	+	14	2187	c.2139C>T	c.(2137-2139)atC>atT	p.I713I	E4F1_ENST00000565090.1_Silent_p.I536I|DNASE1L2_ENST00000320700.5_5'Flank|DNASE1L2_ENST00000382437.4_5'Flank|RP11-304L19.12_ENST00000564055.1_lincRNA|DNASE1L2_ENST00000564065.1_5'Flank|DNASE1L2_ENST00000567494.1_5'Flank|E4F1_ENST00000564139.1_3'UTR	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	77	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	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	
FBXO7	25793	hgsc.bcm.edu	37	22	32880006	32880006	+	Silent	SNP	A	A	G	rs41311141	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:32880006A>G	ENST00000266087.7	+	3	867	c.540A>G	c.(538-540)ccA>ccG	p.P180P	FBXO7_ENST00000397426.1_Silent_p.P66P|FBXO7_ENST00000382058.3_Silent_p.P101P	NM_012179.3	NP_036311.3	Q9Y3I1	FBX7_HUMAN	F-box protein 7	180	Important for dimerization and interaction with PSMF1.				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						GGCAAGTGCCACATTCATTAG	0.448													A|||	65	0.0129792	0.0023	0.0173	5008	,	,		18985	0.0		0.0437	False		,,,				2504	0.0061				p.P180P		Atlas-SNP	.											.	FBXO7	131	.	0			c.A540G						PASS	.	A	,	35,4371	40.8+/-73.8	0,35,2168	268.0	221.0	237.0		303,540	-7.0	1.0	22	dbSNP_127	237	402,8198	127.3+/-185.7	13,376,3911	no	coding-synonymous,coding-synonymous	FBXO7	NM_001033024.1,NM_012179.3	,	13,411,6079	GG,GA,AA		4.6744,0.7944,3.36	,	101/444,180/523	32880006	437,12569	2203	4300	6503	SO:0001819	synonymous_variant	25793	exon3			AGTGCCACATTCA	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.540A>G	22.37:g.32880006A>G		Somatic	375	1	0.00266667		WXS	Illumina HiSeq	Phase_I	324	140	0.432099	NM_012179	B4DNB3|B4DWX5|Q5TGC4|Q5TI86|Q96HM6|Q9UF21|Q9UKT2	Silent	SNP	ENST00000266087.7	37	CCDS13907.1																																																																																			A|0.969;G|0.030;T|0.000	0.030	strong		0.448	FBXO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129001.1		
RPL7A	6130	hgsc.bcm.edu	37	9	136216882	136216882	+	Silent	SNP	G	G	A	rs7700	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136216882G>A	ENST00000323345.6	+	4	420	c.390G>A	c.(388-390)acG>acA	p.T130T	MED22_ENST00000471524.1_5'Flank|SNORD24_ENST00000383884.1_RNA|RPL7A_ENST00000315731.4_Silent_p.T15T|MED22_ENST00000343730.5_5'Flank|MED22_ENST00000476080.1_5'Flank|RPL7A_ENST00000463740.1_3'UTR|SNORD36C_ENST00000516733.1_RNA|SURF1_ENST00000495952.1_5'Flank|MED22_ENST00000344469.5_5'Flank|SNORD36B_ENST00000363961.1_RNA|MED22_ENST00000491289.1_5'Flank|SNORD36A_ENST00000362874.1_RNA|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	101	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	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	
ZNF805	390980	hgsc.bcm.edu	37	19	57760057	57760057	+	Missense_Mutation	SNP	G	G	A	rs3746231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	124	124	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	
ZNF394	84124	hgsc.bcm.edu	37	7	99091599	99091599	+	Silent	SNP	C	C	T	rs78336331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99091599C>T	ENST00000337673.6	-	3	1442	c.1239G>A	c.(1237-1239)ccG>ccA	p.P413P	ZNF789_ENST00000494186.1_Intron|ZNF789_ENST00000493485.1_Intron|ZNF394_ENST00000394177.3_5'Flank|ZNF394_ENST00000426306.2_3'UTR	NM_032164.2	NP_115540.2	Q53GI3	ZN394_HUMAN	zinc finger protein 394	413					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(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(5)|stomach(1)|urinary_tract(1)	16	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					GACAGGTGTACGGCTTCTCGC	0.493													C|||	96	0.0191693	0.0008	0.0303	5008	,	,		19826	0.0327		0.008	False		,,,				2504	0.0337				p.P413P	Ovarian(24;589 697 9939 12704 40742)	Atlas-SNP	.											ZNF394,NS,carcinoma,-1,1	ZNF394	48	1	0			c.G1239A						PASS	.	C		21,4385	28.1+/-56.4	0,21,2182	100.0	101.0	101.0		1239	-7.1	0.0	7	dbSNP_132	101	135,8465	68.7+/-131.2	2,131,4167	no	coding-synonymous	ZNF394	NM_032164.2		2,152,6349	TT,TC,CC		1.5698,0.4766,1.1994		413/562	99091599	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	84124	exon3			GGTGTACGGCTTC	BC025241	CCDS5666.1	7q22.1	2014-01-28			ENSG00000160908	ENSG00000160908		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	18832	protein-coding gene	gene with protein product							Standard	NM_032164		Approved	ZKSCAN14, FLJ12298, ZSCAN46	uc003uqs.3	Q53GI3	OTTHUMG00000154660	ENST00000337673.6:c.1239G>A	7.37:g.99091599C>T		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	293	105	0.358362	NM_032164	A4D281|Q05DA6|Q6P5X9|Q8TB27|Q9HA37|Q9UD51	Silent	SNP	ENST00000337673.6	37	CCDS5666.1																																																																																			C|0.986;T|0.014	0.014	strong		0.493	ZNF394-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336498.1	NM_032164	
FLG	2312	hgsc.bcm.edu	37	1	152280559	152280559	+	Missense_Mutation	SNP	T	T	C	rs150122015		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280559T>C	ENST00000368799.1	-	3	6838	c.6803A>G	c.(6802-6804)cAt>cGt	p.H2268R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2268	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGCAGATCCATGATGGTTTCT	0.577									Ichthyosis																												p.H2268R		Atlas-SNP	.											.	FLG	900	.	0			c.A6803G						PASS	.						193.0	195.0	194.0					1																	152280559		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATCCATGATGGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6803A>G	1.37:g.152280559T>C	ENSP00000357789:p.His2268Arg	Somatic	374	0	0		WXS	Illumina HiSeq	Phase_I	516	65	0.125969	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	T	4.647	0.120247	0.08881	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.03951	3.75	3.41	-3.72	0.04411	.	.	.	.	.	T	0.00906	0.0030	N	0.25426	0.745	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46652	-0.9176	9	0.35671	T	0.21	.	4.5351	0.12024	0.0:0.3477:0.2913:0.361	.	2268	P20930	FILA_HUMAN	R	2268;178	ENSP00000357789:H2268R	ENSP00000271820:H178R	H	-	2	0	FLG	150547183	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.010000	0.12743	-0.886000	0.03966	-0.665000	0.03846	CAT	.	.	weak		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
NUDT12	83594	hgsc.bcm.edu	37	5	102894977	102894977	+	Silent	SNP	T	T	C	rs7734923	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:102894977T>C	ENST00000230792.2	-	3	495	c.399A>G	c.(397-399)agA>agG	p.R133R	NUDT12_ENST00000507423.1_Silent_p.R115R	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	133					NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		CAGAATTATTTCTCTTTTCAC	0.388													T|||	499	0.0996406	0.1407	0.1499	5008	,	,		17247	0.0129		0.1561	False		,,,				2504	0.0399				p.R133R		Atlas-SNP	.											.	NUDT12	27	.	0			c.A399G						PASS	.	T		556,3848	248.1+/-256.1	29,498,1675	54.0	59.0	58.0		399	3.7	1.0	5	dbSNP_116	58	1445,7153	273.3+/-290.6	111,1223,2965	no	coding-synonymous	NUDT12	NM_031438.2		140,1721,4640	CC,CT,TT		16.8062,12.6249,15.3899		133/463	102894977	2001,11001	2202	4299	6501	SO:0001819	synonymous_variant	83594	exon3			ATTATTTCTCTTT	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"""Nudix motif containing"", ""Ankyrin repeat domain containing"""	18826	protein-coding gene	gene with protein product	"""nucleoside diphosphate linked moiety X-type motif 12"""	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.399A>G	5.37:g.102894977T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_031438	B3KUW2|Q8TAL7	Silent	SNP	ENST00000230792.2	37	CCDS4096.1																																																																																			T|0.863;C|0.137	0.137	strong		0.388	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438	
R3HCC1	203069	hgsc.bcm.edu	37	8	23148930	23148930	+	Silent	SNP	A	A	G	rs200790441|rs2272762	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:23148930A>G	ENST00000411463.1	+	6	1029	c.1029A>G	c.(1027-1029)acA>acG	p.T343T	R3HCC1_ENST00000522012.1_3'UTR|R3HCC1_ENST00000518454.1_Silent_p.T116T|R3HCC1_ENST00000265806.6_Silent_p.T116T			Q9Y3T6	R3HC1_HUMAN	R3H domain and coiled-coil containing 1	343							nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			central_nervous_system(1)|skin(2)	3						ATTTGGACACATCCTCCTTCG	0.532													G|||	2791	0.557308	0.4312	0.4597	5008	,	,		21514	0.7996		0.5427	False		,,,				2504	0.5624				p.T116T		Atlas-SNP	.											R3HCC1,colon,carcinoma,0,1	R3HCC1	11	1	0			c.A348G						scavenged	.	G		630,754		147,336,209	131.0	119.0	123.0		348	-7.5	0.3	8	dbSNP_100	123	1849,1333		528,793,270	no	coding-synonymous	R3HCC1	NM_001136108.1		675,1129,479	GG,GA,AA		41.8919,45.5202,45.7074		116/254	23148930	2479,2087	692	1591	2283	SO:0001819	synonymous_variant	203069	exon5			GGACACATCCTCC		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.1029A>G	8.37:g.23148930A>G		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001136108	B7ZLI1	Silent	SNP	ENST00000411463.1	37																																																																																				A|0.395;G|0.605	0.605	strong		0.532	R3HCC1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001136108	
PDLIM5	10611	hgsc.bcm.edu	37	4	95496882	95496882	+	Missense_Mutation	SNP	C	C	T	rs2452600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:95496882C>T	ENST00000317968.4	+	5	543	c.407C>T	c.(406-408)tCt>tTt	p.S136F	PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000542407.1_Missense_Mutation_p.S14F|PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000538141.1_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	255	0	0		WXS	Illumina HiSeq	Phase_I	230	107	0.465217	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		
TSHZ1	10194	hgsc.bcm.edu	37	18	72999359	72999359	+	Missense_Mutation	SNP	T	T	C	rs55679337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	123	0	0		WXS	Illumina HiSeq	Phase_I	104	40	0.384615	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	
MPZL3	196264	hgsc.bcm.edu	37	11	118110977	118110977	+	Silent	SNP	T	T	C	rs2853006	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118110977T>C	ENST00000278949.4	-	2	244	c.189A>G	c.(187-189)aaA>aaG	p.K63K	MPZL3_ENST00000527472.1_Silent_p.K51K|MPZL3_ENST00000525386.1_Intron			Q6UWV2	MPZL3_HUMAN	myelin protein zero-like 3	63	Ig-like V-type.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|hair cycle (GO:0042633)	integral component of membrane (GO:0016021)		p.K63K(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.046)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		CTATAGTAAGTTTGTCAGTGA	0.428													C|||	3967	0.792133	0.9236	0.7666	5008	,	,		19793	0.6806		0.7117	False		,,,				2504	0.8303				p.K63K		Atlas-SNP	.											MPZL3,NS,carcinoma,0,1	MPZL3	22	1	1	Substitution - coding silent(1)	stomach(1)	c.A189G						scavenged	.	C		3934,466	219.1+/-236.9	1766,402,32	258.0	201.0	220.0		189	-2.5	1.0	11	dbSNP_100	220	6266,2326	390.0+/-343.1	2296,1674,326	no	coding-synonymous	MPZL3	NM_198275.1		4062,2076,358	CC,CT,TT		27.0717,10.5909,21.4901		63/236	118110977	10200,2792	2200	4296	6496	SO:0001819	synonymous_variant	196264	exon2			AGTAAGTTTGTCA	AK095399	CCDS8392.1, CCDS66241.1	11q23.3	2013-01-11			ENSG00000160588	ENSG00000160588		"""Immunoglobulin superfamily / V-set domain containing"""	27279	protein-coding gene	gene with protein product		611707				17273165	Standard	NM_198275		Approved		uc001psm.3	Q6UWV2	OTTHUMG00000166966	ENST00000278949.4:c.189A>G	11.37:g.118110977T>C		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	375	101	0.269333	NM_198275	A8K025|B4DLD5|B4E2I8	Silent	SNP	ENST00000278949.4	37	CCDS8392.1																																																																																			T|0.217;C|0.783	0.783	strong		0.428	MPZL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392109.1	NM_198275	
TMEM44	93109	hgsc.bcm.edu	37	3	194353875	194353875	+	Missense_Mutation	SNP	G	G	T	rs1675955	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:194353875G>T	ENST00000392432.2	-	1	275	c.70C>A	c.(70-72)Cac>Aac	p.H24N	TMEM44_ENST00000273580.7_Missense_Mutation_p.H24N|TMEM44_ENST00000347147.4_Missense_Mutation_p.H24N|TMEM44_ENST00000381975.3_Missense_Mutation_p.H24N|TMEM44_ENST00000473092.1_Missense_Mutation_p.H24N|AC046143.3_ENST00000447139.1_RNA|TMEM44_ENST00000330115.3_Intron	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	24			H -> N (in dbSNP:rs1675955). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)		CAGACGCGGTGGCGGGCGAAG	0.771													G|||	1821	0.363618	0.3722	0.3127	5008	,	,		8730	0.2619		0.4771	False		,,,				2504	0.3763				p.H24N		Atlas-SNP	.											.	TMEM44	42	.	0			c.C70A						PASS	.	G	ASN/HIS,ASN/HIS,ASN/HIS,ASN/HIS	1585,2533		359,867,833	16.0	17.0	17.0		70,70,70,70	2.8	1.0	3	dbSNP_89	17	3754,4378		957,1840,1269	yes	missense,missense,missense,missense	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	68,68,68,68	1316,2707,2102	TT,TG,GG		46.1633,38.4896,43.5837	benign,benign,benign,benign	24/429,24/476,24/397,24/439	194353875	5339,6911	2059	4066	6125	SO:0001583	missense	93109	exon1			CGCGGTGGCGGGC	AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.70C>A	3.37:g.194353875G>T	ENSP00000376227:p.His24Asn	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_138399	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	774	0.3543956043956044	175	0.3556910569105691	105	0.2900552486187845	134	0.23426573426573427	360	0.47493403693931396	G	17.20	3.328680	0.60743	0.384896	0.461633	ENSG00000145014	ENST00000392432;ENST00000273580;ENST00000347147;ENST00000381975;ENST00000473092	T;T;T;T;T	0.29397	1.98;1.59;1.59;1.57;1.59	3.74	2.81	0.32909	.	0.381317	0.19732	N	0.107322	T	0.00012	0.0000	L	0.51422	1.61	0.45284	P	0.0017200000000000548	B;P;B;B;B	0.41848	0.187;0.763;0.341;0.187;0.187	B;B;B;B;B	0.42282	0.073;0.382;0.08;0.107;0.051	T	0.48293	-0.9048	9	0.17832	T	0.49	-7.5477	8.235	0.31620	0.0:0.2725:0.7275:0.0	rs1675955;rs59796673;rs1675955	24;24;24;24;24	E9PGA9;Q2T9K0;Q2T9K0-4;Q2T9K0-2;Q2T9K0-6	.;TMM44_HUMAN;.;.;.	N	24	ENSP00000376227:H24N;ENSP00000273580:H24N;ENSP00000333355:H24N;ENSP00000371402:H24N;ENSP00000418674:H24N	ENSP00000273580:H24N	H	-	1	0	TMEM44	195835164	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.517000	0.45529	1.918000	0.55548	0.467000	0.42956	CAC	G|0.652;T|0.348	0.348	strong		0.771	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399	
NMUR2	56923	hgsc.bcm.edu	37	5	151775064	151775064	+	Missense_Mutation	SNP	C	C	G	rs4958535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:151775064C>G	ENST00000255262.3	-	3	1058	c.893G>C	c.(892-894)aGt>aCt	p.S298T	NMUR2_ENST00000518933.1_5'UTR	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	298			S -> T (in dbSNP:rs4958535).		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)	p.S298I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CAGGGATTCACTCCACTCCTC	0.463													G|||	615	0.122804	0.0121	0.2954	5008	,	,		19189	0.0258		0.2038	False		,,,				2504	0.1667				p.S298T		Atlas-SNP	.											NMUR2,NS,carcinoma,0,1	NMUR2	111	1	1	Substitution - Missense(1)	lung(1)	c.G893C						scavenged	.	G	THR/SER	234,4172	805.3+/-415.8	7,220,1976	170.0	146.0	154.0		893	3.0	0.6	5	dbSNP_111	154	1556,7044	745.2+/-407.3	149,1258,2893	yes	missense	NMUR2	NM_020167.4	58	156,1478,4869	GG,GC,CC		18.093,5.3109,13.7629	benign	298/416	151775064	1790,11216	2203	4300	6503	SO:0001583	missense	56923	exon3			GATTCACTCCACT	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.893G>C	5.37:g.151775064C>G	ENSP00000255262:p.Ser298Thr	Somatic	275	2	0.00727273		WXS	Illumina HiSeq	Phase_I	235	116	0.493617	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	286	0.13095238095238096	6	0.012195121951219513	98	0.27071823204419887	21	0.03671328671328671	161	0.21240105540897097	G	4.243	0.044036	0.08196	0.053109	0.18093	ENSG00000132911	ENST00000255262	T	0.70399	-0.48	5.8	2.97	0.34412	GPCR, rhodopsin-like superfamily (1);	0.066370	0.64402	N	0.000008	T	0.00012	0.0000	N	0.00864	-1.135	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.15838	-1.0423	9	0.02654	T	1	-6.2	5.7952	0.18383	0.0664:0.1169:0.5467:0.27	rs4958535;rs17448483;rs52795325;rs4958535	298	Q9GZQ4	NMUR2_HUMAN	T	298	ENSP00000255262:S298T	ENSP00000255262:S298T	S	-	2	0	NMUR2	151755257	1.000000	0.71417	0.589000	0.28718	0.921000	0.55340	3.998000	0.57024	0.060000	0.16281	-0.120000	0.15030	AGT	C|0.866;G|0.134	0.134	strong		0.463	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167	
CFAP53	220136	hgsc.bcm.edu	37	18	47788544	47788544	+	Silent	SNP	T	T	G	rs112087763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:47788544T>G	ENST00000398545.4	-	2	232	c.115A>C	c.(115-117)Aga>Cga	p.R39R		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)		CGTCGGATTCTTTCTAGATGG	0.438													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19087	0.0		0.004	False		,,,				2504	0.001				p.R39R		Atlas-SNP	.											.	CCDC11	59	.	0			c.A115C						PASS	.	T		1,3831		0,1,1915	113.0	108.0	109.0		115	4.0	0.2	18	dbSNP_132	109	24,8220		0,24,4098	no	coding-synonymous	CCDC11	NM_145020.3		0,25,6013	GG,GT,TT		0.2911,0.0261,0.207		39/515	47788544	25,12051	1916	4122	6038	SO:0001819	synonymous_variant	220136	exon2			GGATTCTTTCTAG																												ENST00000398545.4:c.115A>C	18.37:g.47788544T>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_145020		Silent	SNP	ENST00000398545.4	37	CCDS11940.2																																																																																			T|0.997;G|0.003	0.003	strong		0.438	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
VWA5A	4013	hgsc.bcm.edu	37	11	124006993	124006993	+	Missense_Mutation	SNP	G	G	A	rs2276053	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:124006993G>A	ENST00000456829.2	+	13	1768	c.1517G>A	c.(1516-1518)aGg>aAg	p.R506K	VWA5A_ENST00000360334.4_Intron|VWA5A_ENST00000392748.1_Missense_Mutation_p.R506K	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	506			R -> K (in dbSNP:rs2276053). {ECO:0000269|PubMed:9417908}.							autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						CTGACCGGGAGGATGCCAGTG	0.478													G|||	598	0.119409	0.1861	0.0764	5008	,	,		20037	0.0575		0.1014	False		,,,				2504	0.1421				p.R506K		Atlas-SNP	.											.	VWA5A	102	.	0			c.G1517A						PASS	.	G	LYS/ARG,LYS/ARG	747,3655	306.6+/-289.6	58,631,1512	79.0	76.0	77.0		1517,1517	-10.7	0.0	11	dbSNP_100	77	921,7677	204.1+/-246.9	47,827,3425	yes	missense,missense	VWA5A	NM_001130142.1,NM_014622.4	26,26	105,1458,4937	AA,AG,GG		10.7118,16.9696,12.8308	benign,benign	506/787,506/787	124006993	1668,11332	2201	4299	6500	SO:0001583	missense	4013	exon12			CCGGGAGGATGCC	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1517G>A	11.37:g.124006993G>A	ENSP00000407726:p.Arg506Lys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	195	47	0.241026	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	233	0.10668498168498168	91	0.18495934959349594	35	0.09668508287292818	27	0.0472027972027972	80	0.10554089709762533	G	0.186	-1.057595	0.01965	0.169696	0.107118	ENSG00000110002	ENST00000456829;ENST00000392748	T;T	0.03607	3.87;3.87	5.35	-10.7	0.00240	.	3.151380	0.01991	N	0.045531	T	0.00012	0.0000	N	0.00152	-1.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38436	-0.9661	9	0.05833	T	0.94	6.056	2.6497	0.04995	0.4098:0.1332:0.0708:0.3862	rs2276053;rs61387352;rs2276053	506	O00534	VMA5A_HUMAN	K	506	ENSP00000407726:R506K;ENSP00000376504:R506K	ENSP00000376504:R506K	R	+	2	0	VWA5A	123512203	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.735000	0.00802	-3.343000	0.00183	-1.099000	0.02127	AGG	G|0.883;A|0.117	0.117	strong		0.478	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	
CYP17A1	1586	hgsc.bcm.edu	37	10	104596924	104596924	+	Silent	SNP	C	C	A	rs6163	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	144	0	0		WXS	Illumina HiSeq	Phase_I	82	53	0.646341	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	
INADL	10207	hgsc.bcm.edu	37	1	62516683	62516683	+	Missense_Mutation	SNP	G	G	C	rs2498982	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:62516683G>C	ENST00000371158.2	+	31	4192	c.4078G>C	c.(4078-4080)Gtc>Ctc	p.V1360L	INADL_ENST00000543708.1_Missense_Mutation_p.V144L|INADL_ENST00000316485.6_Missense_Mutation_p.V1360L|INADL_ENST00000545929.1_Missense_Mutation_p.V33L	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1360			V -> L (in dbSNP:rs2498982). {ECO:0000269|PubMed:11374908, ECO:0000269|PubMed:9280290}.		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)		p.V1360L(1)		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						AGATGGCAGCGTCGAAGTTGG	0.398													C|||	2859	0.570887	0.767	0.5591	5008	,	,		21408	0.2778		0.5467	False		,,,				2504	0.6411				p.V1360L		Atlas-SNP	.											INADL,NS,carcinoma,0,1	INADL	179	1	1	Substitution - Missense(1)	stomach(1)	c.G4078C						PASS	.	C	LEU/VAL	3120,1286	436.6+/-344.7	1097,926,180	143.0	138.0	139.0		4078	-0.7	0.0	1	dbSNP_100	139	4775,3825	540.0+/-383.7	1347,2081,872	yes	missense	INADL	NM_176877.2	32	2444,3007,1052	CC,CG,GG		44.4767,29.1875,39.2972	benign	1360/1802	62516683	7895,5111	2203	4300	6503	SO:0001583	missense	10207	exon31			GGCAGCGTCGAAG	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.4078G>C	1.37:g.62516683G>C	ENSP00000360200:p.Val1360Leu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	65	63	0.969231	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	1146	0.5247252747252747	358	0.7276422764227642	211	0.5828729281767956	157	0.2744755244755245	420	0.554089709762533	C	0.012	-1.656752	0.00779	0.708125	0.555233	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000307297;ENST00000543708;ENST00000545929	T;T;T;T;T	0.28454	2.8;2.65;3.32;2.33;1.61	4.99	-0.716	0.11212	.	0.998751	0.08103	N	0.997479	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.001;0.0;0.002;0.0;0.0;0.001	T	0.40515	-0.9559	9	0.02654	T	1	.	6.6747	0.23087	0.1239:0.244:0.5507:0.0814	rs2498982;rs59954436;rs2498982	33;144;819;1360;1360;1360	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	L	1360;1360;1360;1360;144;144;33	ENSP00000360200:V1360L;ENSP00000326199:V1360L;ENSP00000307496:V144L;ENSP00000445790:V144L;ENSP00000440094:V33L	ENSP00000307496:V144L	V	+	1	0	INADL	62289271	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-0.401000	0.07232	-0.124000	0.11724	-1.838000	0.00587	GTC	G|0.424;C|0.576	0.576	strong		0.398	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
TPTE	7179	hgsc.bcm.edu	37	21	10943003	10943003	+	Missense_Mutation	SNP	C	C	T	rs1810856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:10943003C>T	ENST00000361285.4	-	12	913	c.584G>A	c.(583-585)cGa>cAa	p.R195Q	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.R157Q|TPTE_ENST00000298232.7_Missense_Mutation_p.R177Q	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						scavenged	.						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	281	2	0.00711744		WXS	Illumina HiSeq	Phase_I	525	146	0.278095	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		
MSS51	118490	hgsc.bcm.edu	37	10	75184444	75184444	+	Missense_Mutation	SNP	A	A	G	rs11591720	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:75184444A>G	ENST00000372912.1	-	6	1252	c.1250T>C	c.(1249-1251)cTc>cCc	p.L417P	MSS51_ENST00000299432.2_Missense_Mutation_p.L417P			Q4VC12	MSS51_HUMAN	MSS51 mitochondrial translational activator	417			L -> P (in dbSNP:rs11591720).		social behavior (GO:0035176)		metal ion binding (GO:0046872)										TTCAGGTTTGAGGGACATGAA	0.458													A|||	23	0.00459265	0.0008	0.0115	5008	,	,		18599	0.0		0.0129	False		,,,				2504	0.001				p.L417P		Atlas-SNP	.											ZMYND17,bladder,carcinoma,+1,1	.	.	1	0			c.T1250C						PASS	.	A	PRO/LEU	13,4393	20.2+/-43.8	0,13,2190	138.0	127.0	131.0		1250	4.5	1.0	10	dbSNP_120	131	156,8444	72.9+/-135.5	2,152,4146	yes	missense	ZMYND17	NM_001024593.1	98	2,165,6336	GG,GA,AA		1.814,0.2951,1.2994	probably-damaging	417/461	75184444	169,12837	2203	4300	6503	SO:0001583	missense	118490	exon7			GGTTTGAGGGACA	AK096884	CCDS31221.1	10q22.3	2013-01-10	2013-01-10	2012-02-24	ENSG00000166343	ENSG00000166343		"""Zinc fingers, MYND-type"""	21000	protein-coding gene	gene with protein product		614773	"""zinc finger, MYND-type containing 17"", ""MSS51 mitochondrial translational activator homolog (S. cerevisiae)"""	ZMYND17		19710419	Standard	NM_001024593		Approved	FLJ39565	uc001jud.3	Q4VC12	OTTHUMG00000018464	ENST00000372912.1:c.1250T>C	10.37:g.75184444A>G	ENSP00000362003:p.Leu417Pro	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	129	34	0.263566	NM_001024593	A6NGH6|Q2VP95|Q5F2H5|Q7Z3M9|Q8N8G0	Missense_Mutation	SNP	ENST00000372912.1	37	CCDS31221.1	18	0.008241758241758242	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	11	0.014511873350923483	A	19.63	3.863421	0.71949	0.002951	0.01814	ENSG00000166343	ENST00000299432;ENST00000372912	T;T	0.51817	0.69;0.69	5.62	4.46	0.54185	.	0.222144	0.40222	N	0.001159	T	0.46639	0.1403	M	0.63843	1.955	0.80722	D	1	D;D	0.76494	0.999;0.992	D;P	0.68483	0.958;0.831	T	0.58306	-0.7659	10	0.66056	D	0.02	-6.2465	11.1753	0.48595	0.846:0.154:0.0:0.0	rs11591720;rs52830361;rs11591720	196;417	Q4VC12-2;Q4VC12	.;ZMY17_HUMAN	P	417	ENSP00000299432:L417P;ENSP00000362003:L417P	ENSP00000299432:L417P	L	-	2	0	ZMYND17	74854450	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	2.685000	0.46959	0.924000	0.37069	0.455000	0.32223	CTC	A|0.989;G|0.011	0.011	strong		0.458	MSS51-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048652.3	NM_178451	
KLHL7	55975	hgsc.bcm.edu	37	7	23212627	23212627	+	Silent	SNP	A	A	G	rs118185564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:23212627A>G	ENST00000339077.5	+	10	1683	c.1440A>G	c.(1438-1440)aaA>aaG	p.K480K	KLHL7_ENST00000322231.7_Silent_p.K458K|KLHL7_ENST00000545443.1_Silent_p.K458K|KLHL7_ENST00000409689.1_Silent_p.K432K|KLHL7_ENST00000539124.1_Silent_p.K404K|AC005082.1_ENST00000366347.4_Intron|KLHL7_ENST00000542558.1_Silent_p.K255K	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	480					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TATTTGTAAAAGACAAGATAT	0.368													A|||	17	0.00339457	0.0008	0.0	5008	,	,		17141	0.0		0.0139	False		,,,				2504	0.002				p.K480K		Atlas-SNP	.											.	KLHL7	102	.	0			c.A1440G						PASS	.	A	,	8,4398	14.3+/-33.2	0,8,2195	283.0	269.0	273.0		1440,1296	2.2	1.0	7	dbSNP_132	273	53,8547	33.8+/-87.4	0,53,4247	no	coding-synonymous,coding-synonymous	KLHL7	NM_001031710.2,NM_018846.4	,	0,61,6442	GG,GA,AA		0.6163,0.1816,0.469	,	480/587,432/539	23212627	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	55975	exon10			TGTAAAAGACAAG		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"""Kelch-like"", ""BTB/POZ domain containing"""	15646	protein-coding gene	gene with protein product	"""retinitis pigmentosa 42"""	611119	"""kelch-like 7 (Drosophila)"""			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.1440A>G	7.37:g.23212627A>G		Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	437	278	0.636156	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Silent	SNP	ENST00000339077.5	37	CCDS34609.1																																																																																			A|0.994;G|0.006	0.006	strong		0.368	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846	
TBC1D15	64786	hgsc.bcm.edu	37	12	72307616	72307616	+	Silent	SNP	A	A	G	rs3759171	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:72307616A>G	ENST00000550746.1	+	13	1426	c.1362A>G	c.(1360-1362)caA>caG	p.Q454Q	TBC1D15_ENST00000548679.1_3'UTR|TBC1D15_ENST00000485960.2_Silent_p.Q437Q|TBC1D15_ENST00000319106.8_Silent_p.Q445Q|TBC1D15_ENST00000393309.3_Silent_p.Q208Q	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	454	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						GATATGTTCAAGGAATGAGTG	0.358													G|||	3334	0.665735	0.9349	0.5634	5008	,	,		16358	0.8819		0.2674	False		,,,				2504	0.5613				p.Q454Q		Atlas-SNP	.											.	TBC1D15	99	.	0			c.A1362G						PASS	.	G	,,	3753,653	262.5+/-264.9	1611,531,61	111.0	117.0	115.0		1311,1335,1362	1.8	1.0	12	dbSNP_107	115	2365,6235	680.3+/-403.6	345,1675,2280	yes	coding-synonymous,coding-synonymous,coding-synonymous	TBC1D15	NM_001146213.1,NM_001146214.1,NM_022771.4	,,	1956,2206,2341	GG,GA,AA		27.5,14.8207,47.0398	,,	437/675,445/683,454/692	72307616	6118,6888	2203	4300	6503	SO:0001819	synonymous_variant	64786	exon13			TGTTCAAGGAATG	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1362A>G	12.37:g.72307616A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	69	22	0.318841	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Silent	SNP	ENST00000550746.1	37	CCDS31858.1																																																																																			A|0.446;G|0.554	0.554	strong		0.358	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	
KRTAP21-2	337978	hgsc.bcm.edu	37	21	32119495	32119495	+	Missense_Mutation	SNP	C	C	G	rs12053674	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:32119495C>G	ENST00000333892.2	-	1	56	c.26G>C	c.(25-27)tGc>tCc	p.C9S		NM_181617.1	NP_853648.1	Q3LI59	KR212_HUMAN	keratin associated protein 21-2	9				C -> S (in Ref. 1; BAE46374). {ECO:0000305}.		intermediate filament (GO:0005882)	structural constituent of cutaneous appendage (GO:0030281)			lung(4)|skin(2)|upper_aerodigestive_tract(1)	7						gccccCACAGCAGTTTCTGTA	0.493													G|||	1043	0.208267	0.385	0.0519	5008	,	,		20384	0.3571		0.0686	False		,,,				2504	0.0706				p.C9S		Atlas-SNP	.											.	KRTAP21-2	16	.	0			c.G26C						PASS	.	G	SER/CYS	1449,2957	682.0+/-404.1	230,989,984	152.0	153.0	153.0		26	-0.7	0.0	21	dbSNP_120	153	410,8190	801.0+/-407.4	12,386,3902	yes	missense	KRTAP21-2	NM_181617.1	112	242,1375,4886	GG,GC,CC		4.7674,32.887,14.2934	benign	9/84	32119495	1859,11147	2203	4300	6503	SO:0001583	missense	337978	exon1			CCACAGCAGTTTC	AP001709	CCDS13605.1	21q22.1	2006-03-13			ENSG00000187026	ENSG00000187026		"""Keratin associated proteins"""	18946	protein-coding gene	gene with protein product						12359730	Standard	NM_181617		Approved	KAP21.2	uc011adh.2	Q3LI59	OTTHUMG00000057769	ENST00000333892.2:c.26G>C	21.37:g.32119495C>G	ENSP00000334287:p.Cys9Ser	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	272	88	0.323529	NM_181617		Missense_Mutation	SNP	ENST00000333892.2	37	CCDS13605.1	443	0.20283882783882784	160	0.3252032520325203	17	0.04696132596685083	210	0.36713286713286714	56	0.07387862796833773	G	1.078	-0.667704	0.03428	0.32887	0.047674	ENSG00000187026	ENST00000333892	T	0.08634	3.07	4.81	-0.735	0.11137	.	0.422367	0.17443	N	0.174059	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43491	-0.9388	8	0.02654	T	1	-0.3615	3.4867	0.07622	0.0867:0.3986:0.2439:0.2709	rs12053674;rs52790703;rs12053674	9	Q3LI59	KR212_HUMAN	S	9	ENSP00000334287:C9S	ENSP00000334287:C9S	C	-	2	0	KRTAP21-2	31041366	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.538000	0.06120	-0.040000	0.13580	-0.371000	0.07208	TGC	C|0.840;G|0.160	0.160	strong		0.493	KRTAP21-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128221.2		
RAET1E	135250	hgsc.bcm.edu	37	6	150210723	150210723	+	Missense_Mutation	SNP	C	C	T	rs6925151	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:150210723C>T	ENST00000357183.4	-	3	515	c.383G>A	c.(382-384)cGt>cAt	p.R128H	RAET1E-AS1_ENST00000605899.1_RNA|RAET1E_ENST00000529948.1_Missense_Mutation_p.R128H|RAET1E_ENST00000532335.1_Missense_Mutation_p.R128H|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000367363.3_Missense_Mutation_p.R92H	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	128	MHC class I alpha-2 like.		R -> H (in dbSNP:rs6925151). {ECO:0000269|PubMed:11827464}.		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)		TTCTGCTTCACGTTGACAAAA	0.473													N|||	1603	0.320088	0.3873	0.3919	5008	,	,		21977	0.3343		0.2634	False		,,,				2504	0.2219				p.R128H		Atlas-SNP	.											.	RAET1E	20	.	0			c.G383A						PASS	.	C	HIS/ARG	1630,2776	501.8+/-365.1	307,1016,880	116.0	91.0	100.0		383	-7.3	0.0	6	dbSNP_116	100	2259,6341	381.7+/-340.1	287,1685,2328	yes	missense	RAET1E	NM_139165.2	29	594,2701,3208	TT,TC,CC		26.2674,36.995,29.9016	probably-damaging	128/264	150210723	3889,9117	2203	4300	6503	SO:0001583	missense	135250	exon3			GCTTCACGTTGAC	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.383G>A	6.37:g.150210723C>T	ENSP00000349709:p.Arg128His	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	260	106	0.407692	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	37	CCDS5221.1	704	0.32234432234432236	180	0.36585365853658536	140	0.3867403314917127	184	0.32167832167832167	200	0.2638522427440633	C	6.278	0.419453	0.11928	0.36995	0.262674	ENSG00000164520	ENST00000532335;ENST00000357183;ENST00000367363;ENST00000529948	T;T;T;T	0.14266	2.52;2.52;5.82;2.52	3.68	-7.35	0.01422	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.760140	0.03138	N	0.166124	T	0.02119	0.0066	L	0.45137	1.4	0.80722	P	0.0	P;P;B	0.36712	0.566;0.511;0.268	B;B;B	0.28991	0.097;0.059;0.034	T	0.04178	-1.0971	9	0.34782	T	0.22	0.0031	3.9402	0.09323	0.1823:0.1457:0.0907:0.5813	rs6925151;rs52833814;rs57214334;rs6925151	128;92;128	Q8TD07;Q8TD07-2;Q8TD07-3	N2DL4_HUMAN;.;.	H	128;128;92;128	ENSP00000437067:R128H;ENSP00000349709:R128H;ENSP00000356332:R92H;ENSP00000432366:R128H	ENSP00000349709:R128H	R	-	2	0	RAET1E	150252416	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.205000	0.01232	-3.716000	0.00116	-1.421000	0.01109	CGT	C|0.693;T|0.307	0.307	strong		0.473	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
FSIP2	401024	hgsc.bcm.edu	37	2	186671912	186671912	+	Missense_Mutation	SNP	G	G	A	rs1862066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:186671912G>A	ENST00000424728.1	+	17	17879	c.17879G>A	c.(17878-17880)cGt>cAt	p.R5960H	FSIP2_ENST00000343098.5_Missense_Mutation_p.R6049H			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5960				R -> H (in Ref. 3; AK126051/BAC86406). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						ATTTTCCAACGTCAGGTTAAC	0.353													A|||	2707	0.540535	0.5582	0.4928	5008	,	,		18277	0.4702		0.5099	False		,,,				2504	0.6544				p.R6049H		Atlas-SNP	.											FSIP2_ENST00000343098,caecum,carcinoma,+1,2	FSIP2	251	2	0			c.G18146A						PASS	.	A	HIS/ARG	2085,1589		587,911,339	137.0	131.0	133.0		18146	3.7	0.6	2	dbSNP_92	133	4350,3806		1155,2040,883	yes	missense	FSIP2	NM_173651.2	29	1742,2951,1222	AA,AG,GG		46.665,43.2499,45.6044	benign	6049/6997	186671912	6435,5395	1837	4078	5915	SO:0001583	missense	401024	exon17			TCCAACGTCAGGT	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.17879G>A	2.37:g.186671912G>A	ENSP00000401306:p.Arg5960His	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	200	91	0.455	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		1108	0.5073260073260073	275	0.5589430894308943	185	0.511049723756906	268	0.46853146853146854	380	0.5013192612137203	A	0.015	-1.549129	0.00926	0.567501	0.53335	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.38560	1.13;1.14	4.8	3.65	0.41850	.	0.119549	0.38058	N	0.001825	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.47736	-0.9094	7	0.02654	T	1	.	6.2369	0.20768	0.8006:0.0:0.1994:0.0	rs1862066;rs17826552;rs58334158;rs1862066	.	.	.	H	6049;5960	ENSP00000344403:R6049H;ENSP00000401306:R5960H	ENSP00000344403:R6049H	R	+	2	0	FSIP2	186380157	0.775000	0.28604	0.573000	0.28510	0.499000	0.33736	1.351000	0.34022	0.343000	0.23821	-0.490000	0.04691	CGT	G|0.479;A|0.521	0.521	strong		0.353	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
FANCA	2175	hgsc.bcm.edu	37	16	89809319	89809319	+	Silent	SNP	T	T	C	rs1800358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:89809319T>C	ENST00000389301.3	-	37	3684	c.3654A>G	c.(3652-3654)ccA>ccG	p.P1218P	FANCA_ENST00000568369.1_Silent_p.P1218P	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1218					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GGTTGGGTGCTGGGGAGGCAG	0.542			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	789	0.157548	0.2216	0.0389	5008	,	,		18197	0.2629		0.0765	False		,,,				2504	0.1299				p.P1218P		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.A3654G						PASS	.	C		924,3472	736.3+/-410.8	87,750,1361	71.0	71.0	71.0		3654	-9.7	0.0	16	dbSNP_89	71	791,7809	783.2+/-407.6	36,719,3545	no	coding-synonymous	FANCA	NM_000135.2		123,1469,4906	CC,CT,TT		9.1977,21.0191,13.1964		1218/1456	89809319	1715,11281	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon37	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGGTGCTGGGGAG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3654A>G	16.37:g.89809319T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	14	0.142857	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			T|0.874;C|0.126	0.126	strong		0.542	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ZBBX	79740	hgsc.bcm.edu	37	3	167023573	167023573	+	Missense_Mutation	SNP	C	C	T	rs140166106	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:167023573C>T	ENST00000392766.2	-	17	1923	c.1583G>A	c.(1582-1584)aGc>aAc	p.S528N	ZBBX_ENST00000392767.2_Missense_Mutation_p.S528N|ZBBX_ENST00000392764.1_Missense_Mutation_p.S499N|ZBBX_ENST00000307529.5_Missense_Mutation_p.S528N|ZBBX_ENST00000455345.2_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	343	0	0		WXS	Illumina HiSeq	Phase_I	310	125	0.403226	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	
SF3A3	10946	hgsc.bcm.edu	37	1	38449910	38449910	+	Silent	SNP	T	T	C	rs11210870	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:38449910T>C	ENST00000373019.4	-	6	1354	c.399A>G	c.(397-399)gaA>gaG	p.E133E	SF3A3_ENST00000489537.1_5'UTR|SF3A3_ENST00000448721.2_Silent_p.E80E	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	133					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CATATCCCTCTTCATCTGTGA	0.453													T|||	1467	0.292931	0.2511	0.3703	5008	,	,		20157	0.2421		0.2753	False		,,,				2504	0.365				p.E133E		Atlas-SNP	.											.	SF3A3	37	.	0			c.A399G						PASS	.	T		1139,3267	402.6+/-332.4	140,859,1204	115.0	88.0	97.0		399	4.3	1.0	1	dbSNP_120	97	2495,6105	405.2+/-348.4	341,1813,2146	no	coding-synonymous	SF3A3	NM_006802.2		481,2672,3350	CC,CT,TT		29.0116,25.8511,27.941		133/502	38449910	3634,9372	2203	4300	6503	SO:0001819	synonymous_variant	10946	exon6			TCCCTCTTCATCT	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"""splicing factor 3a, subunit 3, 60kD"""			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.399A>G	1.37:g.38449910T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	60	53	0.883333	NM_006802	D3DPT5|Q15460|Q5VT87	Silent	SNP	ENST00000373019.4	37	CCDS428.1																																																																																			T|0.718;C|0.282	0.282	strong		0.453	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802	
XIRP2	129446	hgsc.bcm.edu	37	2	168106085	168106085	+	Missense_Mutation	SNP	G	G	A	rs16853328	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168106085G>A	ENST00000409195.1	+	9	8272	c.8183G>A	c.(8182-8184)aGc>aAc	p.S2728N	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.S2506N|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.S2728N	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2553			G -> D (in dbSNP:rs3749002).		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						ACAGACCACAGCTATGAAAGT	0.353													G|||	865	0.172724	0.2882	0.1196	5008	,	,		20459	0.12		0.1123	False		,,,				2504	0.1708				p.S2728N		Atlas-SNP	.											.	XIRP2	914	.	0			c.G8183A						PASS	.	G	,,,ASN/SER,ASN/SER	959,2729		131,697,1016	83.0	80.0	81.0		,,,8183,7517	0.5	0.0	2	dbSNP_123	81	796,7374		42,712,3331	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,46,46	173,1409,4347	AA,AG,GG		9.743,26.0033,14.8001	,,,benign,benign	,,,2728/3550,2506/3328	168106085	1755,10103	1844	4085	5929	SO:0001583	missense	129446	exon9			ACCACAGCTATGA	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.8183G>A	2.37:g.168106085G>A	ENSP00000386840:p.Ser2728Asn	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	143	61	0.426573	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	353	0.16163003663003664	151	0.30691056910569103	42	0.11602209944751381	72	0.1258741258741259	88	0.11609498680738786	G	4.989	0.183668	0.09495	0.260033	0.09743	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02812	4.16;4.16;4.15	6.07	0.503	0.16940	.	1.274170	0.04825	N	0.437620	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.09377	0.002;0.004;0.004	T	0.48186	-0.9057	9	0.16420	T	0.52	0.7895	1.5737	0.02620	0.3016:0.1424:0.4114:0.1447	rs16853328;rs52831947;rs59277562;rs16853328	2553;2553;2506	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	N	2728;2728;2506;142	ENSP00000386840:S2728N;ENSP00000295237:S2728N;ENSP00000387255:S2506N	ENSP00000295237:S2728N	S	+	2	0	XIRP2	167814331	0.000000	0.05858	0.000000	0.03702	0.139000	0.21198	0.218000	0.17622	0.145000	0.18977	-0.182000	0.12963	AGC	G|0.837;A|0.163	0.163	strong		0.353	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
MDN1	23195	hgsc.bcm.edu	37	6	90408589	90408589	+	Silent	SNP	A	A	G	rs3736984	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	66	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	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		
CSMD1	64478	hgsc.bcm.edu	37	8	3224561	3224561	+	Silent	SNP	T	T	C	rs4875703	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:3224561T>C	ENST00000520002.1	-	21	3666	c.3111A>G	c.(3109-3111)acA>acG	p.T1037T	CSMD1_ENST00000400186.3_Silent_p.T1037T|CSMD1_ENST00000602557.1_Silent_p.T1037T|CSMD1_ENST00000537824.1_Silent_p.T1036T|CSMD1_ENST00000542608.1_Silent_p.T1036T|CSMD1_ENST00000602723.1_Silent_p.T1037T|CSMD1_ENST00000539096.1_Silent_p.T1036T			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1037	CUB 6. {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)		TACCTGAAAATGTGATATTGA	0.438													C|||	1428	0.285144	0.326	0.3775	5008	,	,		19000	0.3284		0.2505	False		,,,				2504	0.1554				p.T1036T		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A3108G						PASS	.	C		1128,2830		161,806,1012	54.0	59.0	58.0		3108	-10.2	0.0	8	dbSNP_111	58	1976,6340		226,1524,2408	no	coding-synonymous	CSMD1	NM_033225.5		387,2330,3420	CC,CT,TT		23.7614,28.4992,25.2892		1036/3565	3224561	3104,9170	1979	4158	6137	SO:0001819	synonymous_variant	64478	exon20			TGAAAATGTGATA			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.3111A>G	8.37:g.3224561T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	171	99	0.578947	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		685	0.31364468864468864	170	0.34552845528455284	118	0.3259668508287293	211	0.3688811188811189	186	0.24538258575197888	C	0.133	-1.111616	0.01813	0.284992	0.237614	ENSG00000183117	ENST00000335551	.	.	.	5.09	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999945	.	.	.	.	.	.	T	0.35549	-0.9784	3	.	.	.	.	11.8873	0.52610	0.0:0.2765:0.4646:0.259	rs4875703;rs57705395;rs4875703	.	.	.	V	517	.	.	I	-	1	0	CSMD1	3211968	0.002000	0.14202	0.025000	0.17156	0.066000	0.16364	-1.405000	0.02492	-5.492000	0.00013	-2.764000	0.00121	ATT	T|0.701;C|0.299	0.299	strong		0.438	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
USP20	10868	hgsc.bcm.edu	37	9	132636920	132636920	+	Silent	SNP	C	C	T	rs35899714	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:132636920C>T	ENST00000315480.4	+	18	1964	c.1806C>T	c.(1804-1806)caC>caT	p.H602H	USP20_ENST00000358355.1_Silent_p.H602H|USP20_ENST00000372429.3_Silent_p.H602H			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	602	USP.				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)				TCAACAGCCACGTCTCCTTCC	0.587													C|||	231	0.0461262	0.0159	0.0576	5008	,	,		21525	0.003		0.0785	False		,,,				2504	0.09				p.H602H		Atlas-SNP	.											.	USP20	186	.	0			c.C1806T						PASS	.	C	,,	94,4154		0,94,2030	73.0	81.0	79.0		1806,1806,1806	0.3	1.0	9	dbSNP_126	79	794,7660		42,710,3475	no	coding-synonymous,coding-synonymous,coding-synonymous	USP20	NM_001008563.3,NM_001110303.2,NM_006676.6	,,	42,804,5505	TT,TC,CC		9.392,2.2128,6.991	,,	602/915,602/915,602/915	132636920	888,11814	2124	4227	6351	SO:0001819	synonymous_variant	10868	exon18			CAGCCACGTCTCC	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.1806C>T	9.37:g.132636920C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	194	94	0.484536	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Silent	SNP	ENST00000315480.4	37	CCDS43892.1																																																																																			C|0.937;T|0.063	0.063	strong		0.587	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		
GPR133	283383	hgsc.bcm.edu	37	12	131620650	131620650	+	Missense_Mutation	SNP	C	C	T	rs61746588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:131620650C>T	ENST00000261654.5	+	22	2895	c.2336C>T	c.(2335-2337)gCt>gTt	p.A779V	GPR133_ENST00000540207.1_3'UTR|GPR133_ENST00000376682.4_Missense_Mutation_p.A465V|GPR133_ENST00000535015.1_Missense_Mutation_p.A811V|GPR133_ENST00000543617.1_Missense_Mutation_p.A298V	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	779					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)		GGCGTGCTTGCTGTCAACGGT	0.622													C|||	11	0.00219649	0.0	0.0086	5008	,	,		20891	0.0		0.003	False		,,,				2504	0.002				p.A779V		Atlas-SNP	.											.	GPR133	136	.	0			c.C2336T						PASS	.	C	VAL/ALA	7,4399	12.9+/-30.5	0,7,2196	288.0	182.0	218.0		2336	3.7	0.0	12	dbSNP_129	218	49,8551	31.7+/-84.0	0,49,4251	yes	missense	GPR133	NM_198827.3	64	0,56,6447	TT,TC,CC		0.5698,0.1589,0.4306	probably-damaging	779/875	131620650	56,12950	2203	4300	6503	SO:0001583	missense	283383	exon22			TGCTTGCTGTCAA	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.2336C>T	12.37:g.131620650C>T	ENSP00000261654:p.Ala779Val	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	197	82	0.416244	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	6	0.0027472527472527475	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	12.69	2.013191	0.35511	0.001589	0.005698	ENSG00000111452	ENST00000261654;ENST00000535015;ENST00000376682;ENST00000543617	T;T;T;T	0.42900	1.32;1.31;0.96;0.96	4.6	3.71	0.42584	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.36991	0.0987	M	0.63428	1.95	0.58432	D	0.999998	P;P;B	0.42123	0.586;0.771;0.333	P;B;B	0.48089	0.566;0.444;0.348	T	0.18713	-1.0328	10	0.17369	T	0.5	.	10.3596	0.43984	0.0:0.902:0.0:0.098	rs61746588	811;132;779	B7ZLF7;Q9NSM3;Q6QNK2	.;.;GP133_HUMAN	V	779;811;465;298	ENSP00000261654:A779V;ENSP00000444425:A811V;ENSP00000365872:A465V;ENSP00000438021:A298V	ENSP00000261654:A779V	A	+	2	0	GPR133	130186603	1.000000	0.71417	0.036000	0.18154	0.315000	0.28087	4.744000	0.62118	0.913000	0.36797	0.491000	0.48974	GCT	C|0.997;T|0.003	0.003	strong		0.622	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
NECAB2	54550	hgsc.bcm.edu	37	16	84012104	84012104	+	Silent	SNP	T	T	C	rs925331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:84012104T>C	ENST00000305202.4	+	3	299	c.282T>C	c.(280-282)ctT>ctC	p.L94L	NECAB2_ENST00000565691.1_Missense_Mutation_p.L20S	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	94	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.|EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						ATGGCGTCCTTAATGAGAAAG	0.512													C|||	1641	0.327676	0.7988	0.2262	5008	,	,		21000	0.1181		0.1163	False		,,,				2504	0.1963				p.L94L		Atlas-SNP	.											.	NECAB2	36	.	0			c.T282C						PASS	.	C		3051,1349	448.5+/-348.7	1060,931,209	156.0	139.0	145.0		282	0.5	0.5	16	dbSNP_86	145	911,7689	778.0+/-407.7	63,785,3452	yes	coding-synonymous	NECAB2	NM_019065.2		1123,1716,3661	CC,CT,TT		10.593,30.6591,30.4769		94/387	84012104	3962,9038	2200	4300	6500	SO:0001819	synonymous_variant	54550	exon3			CGTCCTTAATGAG	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	23746	protein-coding gene	gene with protein product			"""EF-hand calcium binding protein 2"""	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.282T>C	16.37:g.84012104T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	99	80	0.808081	NM_019065	A2RRG3|O75547|Q6ZSK0	Silent	SNP	ENST00000305202.4	37	CCDS10940.1																																																																																			T|0.692;C|0.308	0.308	strong		0.512	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065	
P2RY12	64805	hgsc.bcm.edu	37	3	151056616	151056616	+	Silent	SNP	G	G	A	rs6785930	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151056616G>A	ENST00000302632.3	-	3	317	c.18C>T	c.(16-18)aaC>aaT	p.N6N	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000491549.1_Intron|MED12L_ENST00000474524.1_Intron	NM_022788.4|NM_176876.2	NP_073625.1|NP_795345.1	Q9H244	P2Y12_HUMAN	purinergic receptor P2Y, G-protein coupled, 12	6					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell projection organization (GO:0030030)|G-protein coupled purinergic nucleotide receptor signaling pathway (GO:0035589)|G-protein coupled receptor signaling pathway (GO:0007186)|hemostasis (GO:0007599)|negative regulation of cell differentiation (GO:0045596)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of GTPase activity (GO:0043547)|positive regulation of ion transport (GO:0043270)|potassium ion transmembrane transport (GO:0071805)|protein kinase B signaling (GO:0043491)|regulation of calcium ion transport (GO:0051924)	basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	ADP receptor activity (GO:0001621)|G-protein coupled adenosine receptor activity (GO:0001609)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)	17			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)		Clopidogrel(DB00758)|Epoprostenol(DB01240)|Prasugrel(DB06209)|Ticagrelor(DB08816)|Ticlopidine(DB00208)|Treprostinil(DB00374)	CAGAGGTGAGGTTGTCGACGG	0.458													G|||	1211	0.241813	0.1672	0.2781	5008	,	,		17210	0.2113		0.3151	False		,,,				2504	0.273				p.N6N		Atlas-SNP	.											P2RY12,NS,malignant_melanoma,-1,1	P2RY12	36	1	0			c.C18T						PASS	.	G	,,	836,3570	333.1+/-302.8	80,676,1447	72.0	68.0	69.0		18,,18	4.1	0.9	3	dbSNP_116	69	2721,5879	433.3+/-357.4	427,1867,2006	no	coding-synonymous,intron,coding-synonymous	P2RY12,MED12L	NM_022788.3,NM_053002.4,NM_176876.1	,,	507,2543,3453	AA,AG,GG		31.6395,18.9741,27.3489	,,	6/343,,6/343	151056616	3557,9449	2203	4300	6503	SO:0001819	synonymous_variant	64805	exon3			GGTGAGGTTGTCG	AJ320495	CCDS3159.1	3q24-q25	2014-09-17			ENSG00000169313	ENSG00000169313		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	18124	protein-coding gene	gene with protein product		600515				11502873, 11104774	Standard	NM_022788		Approved	P2Y12, SP1999, HORK3	uc003eyw.1	Q9H244	OTTHUMG00000159863	ENST00000302632.3:c.18C>T	3.37:g.151056616G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	109	51	0.46789	NM_022788	D3DNJ5|Q546J7	Silent	SNP	ENST00000302632.3	37	CCDS3159.1																																																																																			G|0.736;A|0.264	0.264	strong		0.458	P2RY12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357796.1		
TAS2R46	259292	hgsc.bcm.edu	37	12	11214360	11214360	+	Silent	SNP	C	C	T	rs73260771	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	245	0	0		WXS	Illumina HiSeq	Phase_I	255	116	0.454902	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	
ZNF676	163223	hgsc.bcm.edu	37	19	22364230	22364230	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22364230C>A	ENST00000397121.2	-	3	606	c.289G>T	c.(289-291)Ggt>Tgt	p.G97C		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	97					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TTATTATAACCTTCTTTGTGC	0.313																																					p.G97C		Atlas-SNP	.											ZNF676,NS,carcinoma,+1,2	ZNF676	146	2	0			c.G289T						PASS	.						131.0	121.0	124.0					19																	22364230		1971	4181	6152	SO:0001583	missense	163223	exon3			TATAACCTTCTTT	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.289G>T	19.37:g.22364230C>A	ENSP00000380310:p.Gly97Cys	Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	282	100	0.35461	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	0.866	-0.733679	0.03111	.	.	ENSG00000196109	ENST00000397121	T	0.07688	3.17	0.398	-0.797	0.10909	.	.	.	.	.	T	0.09247	0.0228	M	0.70842	2.15	0.09310	N	1	B	0.16396	0.017	B	0.16289	0.015	T	0.33650	-0.9860	9	0.37606	T	0.19	.	4.101	0.10014	0.6355:0.3645:0.0:0.0	.	97	Q8N7Q3	ZN676_HUMAN	C	97	ENSP00000380310:G97C	ENSP00000380310:G97C	G	-	1	0	ZNF676	22156070	0.000000	0.05858	0.011000	0.14972	0.153000	0.21895	-0.155000	0.10115	-0.683000	0.05190	0.186000	0.17326	GGT	.	.	none		0.313	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
CTTN	2017	hgsc.bcm.edu	37	11	70253475	70253475	+	Silent	SNP	C	C	T	rs2298397	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	67	22	0.328358	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	
KRR1	11103	hgsc.bcm.edu	37	12	75900588	75900588	+	Silent	SNP	A	A	G	rs2070162	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:75900588A>G	ENST00000229214.4	-	3	390	c.367T>C	c.(367-369)Tta>Cta	p.L123L	KRR1_ENST00000438169.2_Silent_p.L123L	NM_007043.6	NP_008974.5	Q13601	KRR1_HUMAN	KRR1, small subunit (SSU) processome component, homolog (yeast)	123					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(1)	11						CTCCTTGCTAACAGTTTTATC	0.388													A|||	1163	0.232228	0.1936	0.3588	5008	,	,		17068	0.121		0.2336	False		,,,				2504	0.3078				p.L123L		Atlas-SNP	.											.	KRR1	37	.	0			c.T367C						PASS	.	A		898,3508	345.4+/-308.5	99,700,1404	125.0	120.0	122.0		367	5.5	1.0	12	dbSNP_96	122	2145,6455	367.7+/-334.8	271,1603,2426	no	coding-synonymous	KRR1	NM_007043.6		370,2303,3830	GG,GA,AA		24.9419,20.3813,23.3969		123/382	75900588	3043,9963	2203	4300	6503	SO:0001819	synonymous_variant	11103	exon3			TTGCTAACAGTTT	U55766	CCDS9012.1	12q	2011-03-15	2006-05-18	2006-05-18	ENSG00000111615	ENSG00000111615			5176	protein-coding gene	gene with protein product		612817	"""HIV-1 rev binding protein 2"", ""HIV-1 Rev binding protein 2"""	HRB2		7505766, 11027267, 11359931, 8675026	Standard	NM_007043		Approved	RIP-1	uc001sxt.3	Q13601	OTTHUMG00000169759	ENST00000229214.4:c.367T>C	12.37:g.75900588A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_007043	A0FIK6|A0JLP0|B2R989|E7EUQ0|Q8NEA8|Q8TC37|Q96AT5	Silent	SNP	ENST00000229214.4	37	CCDS9012.1																																																																																			A|0.777;G|0.223	0.223	strong		0.388	KRR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405727.1	NM_007043	
T	6862	hgsc.bcm.edu	37	6	166571935	166571935	+	Silent	SNP	C	C	T	rs35819705	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:166571935C>T	ENST00000296946.2	-	9	1644	c.1176G>A	c.(1174-1176)gcG>gcA	p.A392A	T_ENST00000366871.3_Silent_p.A334A	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	392					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)		AGGAAGAGGGCGCCGAGACCG	0.711									Chordoma, Familial Clustering of				C|||	1194	0.238419	0.0499	0.3213	5008	,	,		15354	0.3095		0.2783	False		,,,				2504	0.32				p.A392A		Atlas-SNP	.											.	T	77	.	0			c.G1176A						PASS	.	C		362,4042	183.3+/-210.9	15,332,1855	52.0	61.0	58.0		1176	-6.6	0.0	6	dbSNP_126	58	2610,5986	418.2+/-352.7	403,1804,2091	no	coding-synonymous	T	NM_003181.2		418,2136,3946	TT,TC,CC		30.363,8.2198,22.8615		392/436	166571935	2972,10028	2202	4298	6500	SO:0001819	synonymous_variant	6862	exon9	Familial Cancer Database		AGAGGGCGCCGAG	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.1176G>A	6.37:g.166571935C>T		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	136	132	0.970588	NM_003181	E7ERD6|Q4KMP4	Silent	SNP	ENST00000296946.2	37	CCDS5290.1																																																																																			C|0.771;T|0.229	0.229	strong		0.711	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
ACKR4	51554	hgsc.bcm.edu	37	3	132319604	132319604	+	Silent	SNP	A	A	C	rs139873131	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:132319604A>C	ENST00000249887.2	+	2	459	c.363A>C	c.(361-363)ctA>ctC	p.L121L	ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000355458.3_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4	121					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										TGTACACACTAAACTTTGTCT	0.423													A|||	32	0.00638978	0.0	0.0072	5008	,	,		26372	0.0		0.0229	False		,,,				2504	0.0041				p.L121L		Atlas-SNP	.											.	CCRL1	30	.	0			c.A363C						PASS	.	A	,,	11,4395	16.8+/-37.8	0,11,2192	98.0	98.0	98.0		363,,363	-2.9	0.3	3	dbSNP_134	98	131,8469	57.9+/-119.4	0,131,4169	no	coding-synonymous,intron,coding-synonymous	CCRL1,ACAD11	NM_016557.2,NM_032169.4,NM_178445.1	,,	0,142,6361	CC,CA,AA		1.5233,0.2497,1.0918	,,	121/351,,121/351	132319604	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	51554	exon1			CACACTAAACTTT	AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"""GPCR / Class A : Chemokine receptors : Atypical"""	1611	protein-coding gene	gene with protein product		606065	"""chemokine (C-C motif) receptor-like 1"""	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.363A>C	3.37:g.132319604A>C		Somatic	542	1	0.00184502		WXS	Illumina HiSeq	Phase_I	608	172	0.282895	NM_178445	B2R9U7	Silent	SNP	ENST00000249887.2	37	CCDS3075.1																																																																																			A|0.990;C|0.010	0.010	strong		0.423	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557	
ZBTB17	7709	hgsc.bcm.edu	37	1	16271260	16271260	+	Silent	SNP	G	G	A	rs9661939	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16271260G>A	ENST00000375743.4	-	8	1234	c.1002C>T	c.(1000-1002)ttC>ttT	p.F334F	ZBTB17_ENST00000479282.1_5'Flank|ZBTB17_ENST00000375733.2_Silent_p.F334F|ZBTB17_ENST00000448462.2_Silent_p.F271F|ZBTB17_ENST00000537142.1_Silent_p.F252F	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17	334				F -> S (in Ref. 2; BAG63326). {ECO:0000305}.	activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|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;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		CCCGGCACGAGAAGGGCTTCT	0.667													G|||	1043	0.208267	0.0779	0.3098	5008	,	,		16462	0.0169		0.3052	False		,,,				2504	0.41				p.F334F		Atlas-SNP	.											.	ZBTB17	45	.	0			c.C1002T						PASS	.	G	,	478,3928	216.4+/-235.1	27,424,1752	42.0	43.0	43.0		756,1002	5.5	1.0	1	dbSNP_119	43	2602,5998	412.5+/-350.8	413,1776,2111	no	coding-synonymous,coding-synonymous	ZBTB17	NM_001242884.1,NM_003443.2	,	440,2200,3863	AA,AG,GG		30.2558,10.8488,23.6814	,	252/722,334/804	16271260	3080,9926	2203	4300	6503	SO:0001819	synonymous_variant	7709	exon8			GCACGAGAAGGGC	U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12936	protein-coding gene	gene with protein product		604084	"""zinc finger protein 151 (pHZ-67)"", ""zinc finger protein 60"""	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.1002C>T	1.37:g.16271260G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	72	16	0.222222	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Silent	SNP	ENST00000375743.4	37	CCDS165.1																																																																																			G|0.802;A|0.198	0.198	strong		0.667	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443	
SPAG17	200162	hgsc.bcm.edu	37	1	118693217	118693217	+	Silent	SNP	T	T	C	rs1935992	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	269	2	0.00743494		WXS	Illumina HiSeq	Phase_I	148	34	0.22973	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	
EIF2A	83939	hgsc.bcm.edu	37	3	150280445	150280445	+	Missense_Mutation	SNP	C	C	G	rs1132979	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:150280445C>G	ENST00000460851.1	+	4	399	c.290C>G	c.(289-291)aCt>aGt	p.T97S	SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000487799.1_Missense_Mutation_p.T72S|EIF2A_ENST00000406576.3_Missense_Mutation_p.T97S|EIF2A_ENST00000273435.5_Missense_Mutation_p.T92S			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	97			T -> S (in dbSNP:rs1132979). {ECO:0000269|PubMed:12133843, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3, ECO:0000269|Ref.4, ECO:0000269|Ref.6}.		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)	p.T72S(1)		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)			CAGCCTTACACTAGTAAGTAT	0.403													C|||	1774	0.354233	0.1611	0.3631	5008	,	,		16648	0.4861		0.3588	False		,,,				2504	0.4683				p.T97S		Atlas-SNP	.											EIF2A_ENST00000487799,NS,carcinoma,0,1	EIF2A	59	1	1	Substitution - Missense(1)	stomach(1)	c.C290G						PASS	.	C	SER/THR	631,3103		45,541,1281	67.0	61.0	63.0		290	5.9	1.0	3	dbSNP_86	63	2865,5335		508,1849,1743	yes	missense	EIF2A	NM_032025.3	58	553,2390,3024	GG,GC,CC		34.939,16.8988,29.2945	benign	97/586	150280445	3496,8438	1867	4100	5967	SO:0001583	missense	83939	exon4			CTTACACTAGTAA	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.290C>G	3.37:g.150280445C>G	ENSP00000417229:p.Thr97Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Missense_Mutation	SNP	ENST00000460851.1	37	CCDS46935.1	797	0.3649267399267399	90	0.18292682926829268	141	0.38950276243093923	287	0.5017482517482518	279	0.36807387862796836	C	13.40	2.226881	0.39399	0.168988	0.34939	ENSG00000144895	ENST00000487799;ENST00000460851;ENST00000406576;ENST00000482093;ENST00000273435	T;T;T;T;T	0.54071	0.9;0.9;0.59;0.9;0.9	5.86	5.86	0.93980	WD40/YVTN repeat-like-containing domain (1);	0.266752	0.40222	N	0.001157	T	0.00012	0.0000	N	0.05012	-0.13	0.09310	P	1.0	B;B;B	0.13145	0.007;0.001;0.004	B;B;B	0.12156	0.007;0.002;0.003	T	0.43228	-0.9404	9	0.10902	T	0.67	-6.8954	20.1894	0.98226	0.0:1.0:0.0:0.0	rs1132979;rs2049228;rs3194341;rs11537792;rs16862740;rs17418293;rs52804311;rs1132979	97;72;97	B4DF96;B4DQ14;Q9BY44	.;.;EIF2A_HUMAN	S	72;97;97;97;92	ENSP00000420537:T72S;ENSP00000417229:T97S;ENSP00000385292:T97S;ENSP00000418698:T97S;ENSP00000273435:T92S	ENSP00000273435:T92S	T	+	2	0	EIF2A	151763135	0.999000	0.42202	1.000000	0.80357	0.933000	0.57130	2.755000	0.47540	2.781000	0.95711	0.591000	0.81541	ACT	C|0.635;G|0.365	0.365	strong		0.403	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025	
ZNF208	7757	hgsc.bcm.edu	37	19	22154954	22154954	+	Missense_Mutation	SNP	C	C	T	rs2214301	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22154954C>T	ENST00000397126.4	-	4	3030	c.2882G>A	c.(2881-2883)aGt>aAt	p.S961N	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	961					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)				CTTATGATAACTAAGGGTTGA	0.338													N|||	2870	0.573083	0.6233	0.6326	5008	,	,		20861	0.6935		0.5716	False		,,,				2504	0.3405				p.S961N		Atlas-SNP	.											.	ZNF208	817	.	0			c.G2882A						PASS	.	G	ASN/SER	2644,1464		859,926,269	33.0	36.0	35.0		2882	-6.0	0.0	19	dbSNP_96	35	4807,3623		1360,2087,768	no	missense	ZNF208	NM_007153.3	46	2219,3013,1037	TT,TC,CC		42.9775,35.6378,40.5727		961/1281	22154954	7451,5087	2054	4215	6269	SO:0001583	missense	7757	exon4			TGATAACTAAGGG	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.2882G>A	19.37:g.22154954C>T	ENSP00000380315:p.Ser961Asn	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	1395	0.6387362637362637	330	0.6707317073170732	212	0.585635359116022	408	0.7132867132867133	445	0.5870712401055409	c	4.003	-0.002218	0.07819	0.643622	0.570225	ENSG00000160321	ENST00000397126	T	0.15718	2.4	3.0	-6.0	0.02206	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.34428	-0.9829	5	0.14252	T	0.57	.	2.2281	0.03990	0.2513:0.2554:0.3681:0.1252	rs52821215;rs58796195;rs62110923	.	.	.	N	961	ENSP00000380315:S961N	ENSP00000380315:S961N	S	-	2	0	ZNF208	21946794	0.000000	0.05858	0.000000	0.03702	0.321000	0.28281	-0.748000	0.04818	-2.641000	0.00429	0.109000	0.15622	AGT	C|0.353;T|0.647	0.647	strong		0.338	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
NUP54	53371	hgsc.bcm.edu	37	4	77038912	77038912	+	Missense_Mutation	SNP	A	A	T	rs144785979	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:77038912A>T	ENST00000264883.3	-	11	1440	c.1300T>A	c.(1300-1302)Ttg>Atg	p.L434M	NUP54_ENST00000458189.2_Missense_Mutation_p.L254M|NUP54_ENST00000514987.1_Missense_Mutation_p.L386M|NUP54_ENST00000342467.6_Missense_Mutation_p.L218M	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	434	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						TGAGACATCAATTCATTTAGT	0.373													A|||	2	0.000399361	0.0	0.0	5008	,	,		20100	0.0		0.002	False		,,,				2504	0.0				p.L434M		Atlas-SNP	.											.	NUP54	48	.	0			c.T1300A						PASS	.	A	MET/LEU	1,4405	2.1+/-5.4	0,1,2202	116.0	109.0	111.0		1300	-1.2	1.0	4	dbSNP_134	111	4,8594	3.7+/-12.6	0,4,4295	yes	missense	NUP54	NM_017426.2	15	0,5,6497	TT,TA,AA		0.0465,0.0227,0.0384	possibly-damaging	434/508	77038912	5,12999	2203	4299	6502	SO:0001583	missense	53371	exon11			ACATCAATTCATT	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.1300T>A	4.37:g.77038912A>T	ENSP00000264883:p.Leu434Met	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	256	115	0.449219	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	CCDS3576.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	13.35	2.209809	0.39003	2.27E-4	4.65E-4	ENSG00000138750	ENST00000264883;ENST00000342467;ENST00000514987;ENST00000458189	.	.	.	5.88	-1.16	0.09678	.	0.000000	0.64402	D	0.000001	T	0.64757	0.2627	M	0.75615	2.305	0.47905	D	0.999546	P;P;D	0.52996	0.926;0.918;0.957	P;B;P	0.56612	0.802;0.436;0.802	T	0.64419	-0.6412	9	0.49607	T	0.09	-7.8541	9.651	0.39897	0.1989:0.1983:0.6027:0.0	.	386;218;434	B4DT35;Q7Z3B4-2;Q7Z3B4	.;.;NUP54_HUMAN	M	434;218;386;254	.	ENSP00000264883:L434M	L	-	1	2	NUP54	77257936	0.991000	0.36638	0.980000	0.43619	0.416000	0.31233	0.731000	0.26058	-0.151000	0.11176	-2.917000	0.00090	TTG	A|0.999;T|0.001	0.001	strong		0.373	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
MUC5B	727897	hgsc.bcm.edu	37	11	1248960	1248960	+	Silent	SNP	G	G	A	rs2075855	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1248960G>A	ENST00000529681.1	+	7	781	c.723G>A	c.(721-723)acG>acA	p.T241T	MUC5B_ENST00000447027.1_Silent_p.T241T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	241	VWFD 1. {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)		ATGGGCCCACGGAGCAGTGCC	0.701													g|||	304	0.0607029	0.0219	0.1037	5008	,	,		14179	0.0456		0.0765	False		,,,				2504	0.0818				p.T241T		Atlas-SNP	.											MUC5B,colon,carcinoma,+1,2	MUC5B	473	2	0			c.G723A						scavenged	.	G		76,3702		0,76,1813	17.0	19.0	18.0		723	-7.0	0.8	11	dbSNP_96	18	483,7555		10,463,3546	no	coding-synonymous	MUC5B	NM_002458.2		10,539,5359	AA,AG,GG		6.009,2.0116,4.7309		241/5763	1248960	559,11257	1889	4019	5908	SO:0001819	synonymous_variant	727897	exon7			GCCCACGGAGCAG	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.723G>A	11.37:g.1248960G>A		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.929;A|0.071	0.071	strong		0.701	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SAAL1	113174	hgsc.bcm.edu	37	11	18127464	18127464	+	Missense_Mutation	SNP	C	C	T	rs77233279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18127464C>T	ENST00000524803.1	-	1	174	c.125G>A	c.(124-126)gGa>gAa	p.G42E	SAAL1_ENST00000533851.1_5'UTR|SAAL1_ENST00000529318.1_Missense_Mutation_p.G42E|SAAL1_ENST00000300013.4_Missense_Mutation_p.G42E			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	42										breast(2)|large_intestine(5)|lung(8)	15						CTGGATGAGTCCGCTGAGGAC	0.682											OREG0020819	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	50	0.00998403	0.0015	0.0086	5008	,	,		14972	0.001		0.0408	False		,,,				2504	0.0				p.G42E		Atlas-SNP	.											SAAL1,NS,carcinoma,0,1	SAAL1	34	1	0			c.G125A						PASS	.	C	GLU/GLY	27,4371		0,27,2172	61.0	43.0	49.0		125	4.5	1.0	11	dbSNP_131	49	248,8334		3,242,4046	yes	missense	SAAL1	NM_138421.2	98	3,269,6218	TT,TC,CC		2.8898,0.6139,2.1186	benign	42/475	18127464	275,12705	2199	4291	6490	SO:0001583	missense	113174	exon1			ATGAGTCCGCTGA	AK123457	CCDS31439.1	11p15.1	2005-10-28			ENSG00000166788	ENSG00000166788			25158	protein-coding gene	gene with protein product							Standard	NM_138421		Approved	FLJ41463	uc001mnq.3	Q96ER3	OTTHUMG00000166428	ENST00000524803.1:c.125G>A	11.37:g.18127464C>T	ENSP00000432487:p.Gly42Glu	Somatic	42	0	0	723	WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_138421	A6NH05	Missense_Mutation	SNP	ENST00000524803.1	37	CCDS31439.1	33|33	0.01510989010989011|0.01510989010989011	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	30|30	0.0395778364116095|0.0395778364116095	C|C	9.842|9.842	1.191290|1.191290	0.21954|0.21954	0.006139|0.006139	0.028898|0.028898	ENSG00000166788|ENSG00000166788	ENST00000532452|ENST00000524803;ENST00000300013;ENST00000529318;ENST00000530180	.|T;T;T;T	.|0.33865	.|1.39;1.39;1.39;1.39	5.46|5.46	4.48|4.48	0.54585|0.54585	.|.	.|0.168649	.|0.52532	.|D	.|0.000068	T|T	0.04048|0.04048	0.0113|0.0113	N|N	0.14661|0.14661	0.345|0.345	0.30455|0.30455	N|N	0.774862|0.774862	.|B;B;B	.|0.26845	.|0.161;0.161;0.161	.|B;B;B	.|0.24394	.|0.053;0.033;0.033	T|T	0.06881|0.06881	-1.0802|-1.0802	5|10	.|0.14656	.|T	.|0.56	-5.7028|-5.7028	7.9343|7.9343	0.29920|0.29920	0.1614:0.7563:0.0:0.0823|0.1614:0.7563:0.0:0.0823	.|.	.|42;42;42	.|E9PRZ1;G1UCX3;Q96ER3	.|.;.;SAAL1_HUMAN	N|E	35|42	.|ENSP00000432487:G42E;ENSP00000300013:G42E;ENSP00000432216:G42E;ENSP00000431489:G42E	.|ENSP00000300013:G42E	D|G	-|-	1|2	0|0	SAAL1|SAAL1	18084040|18084040	0.556000|0.556000	0.26538|0.26538	1.000000|1.000000	0.80357|0.80357	0.909000|0.909000	0.53808|0.53808	0.892000|0.892000	0.28322|0.28322	2.720000|2.720000	0.93068|0.93068	0.655000|0.655000	0.94253|0.94253	GAC|GGA	C|0.981;T|0.019	0.019	strong		0.682	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421	
PCED1A	64773	hgsc.bcm.edu	37	20	2816821	2816821	+	Silent	SNP	C	C	T	rs2274669	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:2816821C>T	ENST00000360652.2	-	7	1483	c.981G>A	c.(979-981)ccG>ccA	p.P327P	PCED1A_ENST00000356872.3_Silent_p.P276P	NM_022760.4	NP_073597.2	Q9H1Q7	PED1A_HUMAN	PC-esterase domain containing 1A	327																	gctgaggaagcgggtagggaa	0.607													C|||	1085	0.216653	0.0151	0.1499	5008	,	,		15550	0.3899		0.2306	False		,,,				2504	0.3436				p.P327P		Atlas-SNP	.											FAM113A,colon,carcinoma,0,1	.	.	1	0			c.G981A						scavenged	.	C		230,4176	135.3+/-171.4	10,210,1983	73.0	81.0	78.0		981	-7.0	0.2	20	dbSNP_100	78	1846,6754	329.0+/-318.6	208,1430,2662	no	coding-synonymous	FAM113A	NM_022760.3		218,1640,4645	TT,TC,CC		21.4651,5.2202,15.9619		327/455	2816821	2076,10930	2203	4300	6503	SO:0001819	synonymous_variant	64773	exon7			AGGAAGCGGGTAG	AK026029	CCDS13035.1, CCDS59442.1	20p13	2012-06-11	2012-06-11	2012-06-11	ENSG00000132635	ENSG00000132635			16212	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 81"", ""family with sequence similarity 113, member A"""	C20orf81, FAM113A		20056006	Standard	NM_022760		Approved	bA12M19.1, FLJ22376	uc002wgz.2	Q9H1Q7	OTTHUMG00000031716	ENST00000360652.2:c.981G>A	20.37:g.2816821C>T		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	238	3	0.012605	NM_022760	Q5JUA5|Q5JUA6|Q6PK19|Q86WF5|Q96CG7|Q9H1Q6|Q9H6D1	Silent	SNP	ENST00000360652.2	37	CCDS13035.1																																																																																			C|0.833;G|0.000;T|0.167	0.167	strong		0.607	PCED1A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077676.2	NM_022760	
FLG	2312	hgsc.bcm.edu	37	1	152280864	152280864	+	Silent	SNP	A	A	G	rs2184954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280864A>G	ENST00000368799.1	-	3	6533	c.6498T>C	c.(6496-6498)tcT>tcC	p.S2166S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2166	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCTGTGATGAGACCCTGAGT	0.557									Ichthyosis				-|||	2322	0.463658	0.5204	0.4524	5008	,	,		24600	0.6577		0.172	False		,,,				2504	0.4949				p.S2166S		Atlas-SNP	.											.	FLG	900	.	0			c.T6498C						PASS	.	G		2056,2350	607.5+/-391.0	471,1114,618	381.0	336.0	351.0		6498	-4.8	0.0	1	dbSNP_96	351	1453,7145	750.6+/-407.4	125,1203,2971	no	coding-synonymous	FLG	NM_002016.1		596,2317,3589	GG,GA,AA		16.8993,46.6636,26.984		2166/4062	152280864	3509,9495	2203	4299	6502	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGATGAGACCCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6498T>C	1.37:g.152280864A>G		Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	495	240	0.484848	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			.	.	weak		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC5B	727897	hgsc.bcm.edu	37	11	1263776	1263776	+	Missense_Mutation	SNP	C	C	T	rs2943510	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1263776C>T	ENST00000529681.1	+	31	5724	c.5666C>T	c.(5665-5667)cCa>cTa	p.P1889L	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.P1892L	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1889	7 X Cys-rich subdomain repeats.|Thr-rich.		P -> L (in dbSNP:rs2943510). {ECO:0000269|PubMed:9013550}.		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)		CCCAGTACCCCAGCCACCAGC	0.592													C|||	595	0.11881	0.0998	0.2147	5008	,	,		18334	0.0526		0.1312	False		,,,				2504	0.1319				p.P1889L		Atlas-SNP	.											.	MUC5B	473	.	0			c.C5666T						PASS	.	C	LEU/PRO	421,3957	185.3+/-212.5	16,389,1784	78.0	99.0	92.0		5666	2.7	0.0	11	dbSNP_101	92	1067,7491	217.4+/-256.1	67,933,3279	yes	missense	MUC5B	NM_002458.2	98	83,1322,5063	TT,TC,CC		12.4679,9.6163,11.5028	probably-damaging	1889/5763	1263776	1488,11448	2189	4279	6468	SO:0001583	missense	727897	exon31			GTACCCCAGCCAC	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.5666C>T	11.37:g.1263776C>T	ENSP00000436812:p.Pro1889Leu	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	239	136	0.569038	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	265	0.12133699633699634	45	0.09146341463414634	71	0.19613259668508287	43	0.07517482517482517	106	0.13984168865435356	C	10.98	1.504368	0.26949	0.096163	0.124679	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.19394	2.15;2.34	2.72	2.72	0.32119	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.29627	0.144;0.252	B;B	0.18561	0.022;0.022	T	0.23726	-1.0180	8	0.87932	D	0	.	9.1961	0.37228	0.0:0.8804:0.0:0.1196	rs2943510;rs58124603;rs2943510	2582;1892	A7Y9J9;E9PBJ0	.;.	L	1889;1892;1890;1959	ENSP00000436812:P1889L;ENSP00000415793:P1892L	ENSP00000343037:P1890L	P	+	2	0	MUC5B	1220352	0.000000	0.05858	0.001000	0.08648	0.142000	0.21351	0.339000	0.19875	1.534000	0.49203	0.089000	0.15464	CCA	C|0.873;T|0.127	0.127	strong		0.592	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PLCH1	23007	hgsc.bcm.edu	37	3	155301264	155301264	+	Silent	SNP	T	T	C	rs9289957	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:155301264T>C	ENST00000340059.7	-	5	731	c.732A>G	c.(730-732)caA>caG	p.Q244Q	PLCH1_ENST00000460012.1_Silent_p.Q226Q|PLCH1_ENST00000334686.6_Silent_p.Q226Q|PLCH1_ENST00000494598.1_Silent_p.Q244Q|PLCH1_ENST00000414191.1_Silent_p.Q226Q|PLCH1_ENST00000447496.2_Silent_p.Q244Q	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	244					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			ATGATACCTTTTGCTCCACCT	0.338													T|||	108	0.0215655	0.0008	0.0346	5008	,	,		15835	0.0		0.0726	False		,,,				2504	0.0102				p.Q244Q		Atlas-SNP	.											.	PLCH1	406	.	0			c.A732G						PASS	.	T	,,	54,4352	52.3+/-87.9	0,54,2149	99.0	104.0	103.0		732,732,678	2.8	1.0	3	dbSNP_119	103	576,8024	152.7+/-207.2	18,540,3742	no	coding-synonymous,coding-synonymous,coding-synonymous	PLCH1	NM_001130960.1,NM_001130961.1,NM_014996.2	,,	18,594,5891	CC,CT,TT		6.6977,1.2256,4.8439	,,	244/1694,244/1003,226/1656	155301264	630,12376	2203	4300	6503	SO:0001819	synonymous_variant	23007	exon5			TACCTTTTGCTCC	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.732A>G	3.37:g.155301264T>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Silent	SNP	ENST00000340059.7	37	CCDS46939.1																																																																																			T|0.957;C|0.043	0.043	strong		0.338	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
ANO7	50636	hgsc.bcm.edu	37	2	242151585	242151585	+	Silent	SNP	C	C	T	rs7593101	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242151585C>T	ENST00000274979.8	+	16	1903	c.1800C>T	c.(1798-1800)taC>taT	p.Y600Y	ANO7_ENST00000402430.3_Silent_p.Y599Y	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	600					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						TCAACTTCTACTCCTCACCCG	0.567													C|||	795	0.158746	0.2716	0.2032	5008	,	,		21437	0.0		0.2416	False		,,,				2504	0.0532				p.Y600Y		Atlas-SNP	.											.	ANO7	136	.	0			c.C1800T						PASS	.	C		1105,3301	394.4+/-329.3	129,847,1227	188.0	147.0	161.0		1800	2.0	0.9	2	dbSNP_116	161	1988,6612	347.2+/-326.5	226,1536,2538	no	coding-synonymous	ANO7	NM_001001891.3		355,2383,3765	TT,TC,CC		23.1163,25.0794,23.7813		600/934	242151585	3093,9913	2203	4300	6503	SO:0001819	synonymous_variant	50636	exon16			CTTCTACTCCTCA	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.1800C>T	2.37:g.242151585C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	131	67	0.51145	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			C|0.787;T|0.213	0.213	strong		0.567	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
NUBP1	4682	hgsc.bcm.edu	37	16	10846511	10846511	+	Silent	SNP	G	G	A	rs2233535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:10846511G>A	ENST00000283027.5	+	4	322	c.303G>A	c.(301-303)aaG>aaA	p.K101K	NUBP1_ENST00000571790.1_3'UTR|NUBP1_ENST00000433392.2_Silent_p.K101K	NM_002484.2	NP_002475.2			nucleotide binding protein 1											large_intestine(2)|lung(3)|ovary(1)|skin(4)	10						CGATTCCCAAGATAATGGGAT	0.438													G|||	6	0.00119808	0.0	0.0	5008	,	,		20464	0.0		0.006	False		,,,				2504	0.0				p.K101K		Atlas-SNP	.											.	NUBP1	31	.	0			c.G303A						PASS	.	G		4,4390	6.2+/-15.9	0,4,2193	212.0	197.0	202.0		303	0.8	1.0	16	dbSNP_98	202	43,8557	29.0+/-79.6	0,43,4257	no	coding-synonymous	NUBP1	NM_002484.2		0,47,6450	AA,AG,GG		0.5,0.091,0.3617		101/321	10846511	47,12947	2197	4300	6497	SO:0001819	synonymous_variant	4682	exon4			TCCCAAGATAATG	U01833	CCDS10543.1, CCDS61839.1	16p13.13	2014-01-13	2011-05-19		ENSG00000103274	ENSG00000103274			8041	protein-coding gene	gene with protein product		600280	"""nucleotide binding protein 1 (E.coli MinD like)"", ""nucleotide binding protein 1 (MinD homolog, E. coli)"""	NBP1		7926816	Standard	NM_002484		Approved	NBP35	uc002daa.1	P53384	OTTHUMG00000129751	ENST00000283027.5:c.303G>A	16.37:g.10846511G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	161	72	0.447205	NM_002484		Silent	SNP	ENST00000283027.5	37	CCDS10543.1																																																																																			G|0.997;A|0.003	0.003	strong		0.438	NUBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251964.2	NM_002484	
NEU4	129807	hgsc.bcm.edu	37	2	242757820	242757820	+	Missense_Mutation	SNP	G	G	A	rs11545301	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242757820G>A	ENST00000391969.2	+	5	1612	c.901G>A	c.(901-903)Ggg>Agg	p.G301R	NEU4_ENST00000407683.1_Missense_Mutation_p.G301R|NEU4_ENST00000404257.1_Missense_Mutation_p.G313R|NEU4_ENST00000405370.1_Missense_Mutation_p.G301R|NEU4_ENST00000325935.6_Missense_Mutation_p.G314R	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	301	Pro-rich.		G -> R (in dbSNP:rs11545301). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14962670, ECO:0000269|PubMed:15498874}.		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)		AGTGGGCCCCGGGAGTCCCCT	0.701													G|||	1213	0.242212	0.2988	0.2176	5008	,	,		13537	0.1002		0.2783	False		,,,				2504	0.2924				p.G314R		Atlas-SNP	.											.	NEU4	39	.	0			c.G940A						PASS	.		ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	1158,3026		168,822,1102	9.0	12.0	11.0		940,901,901,901,937	-3.2	0.0	2	dbSNP_120	11	2335,5971		357,1621,2175	yes	missense,missense,missense,missense,missense	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	125,125,125,125,125	525,2443,3277	AA,AG,GG		28.1122,27.6769,27.9664	benign,benign,benign,benign,benign	314/498,301/485,301/485,301/485,313/497	242757820	3493,8997	2092	4153	6245	SO:0001583	missense	129807	exon4			GGCCCCGGGAGTC	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.901G>A	2.37:g.242757820G>A	ENSP00000375830:p.Gly301Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_001167599	A8K056|J3KNJ5|Q96D64	Missense_Mutation	SNP	ENST00000391969.2	37	CCDS54442.1	531	0.24313186813186813	153	0.31097560975609756	92	0.2541436464088398	62	0.10839160839160839	224	0.2955145118733509	G	1.760	-0.486996	0.04352	0.276769	0.281122	ENSG00000204099	ENST00000407683;ENST00000405370;ENST00000472793;ENST00000404257;ENST00000391969;ENST00000325935	T;T;T;T;T	0.75367	-0.92;-0.92;-0.93;-0.92;-0.93	3.37	-3.25	0.05079	Neuraminidase (1);	1.630680	0.03917	N	0.282864	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.03566	-1.1024	9	0.09084	T	0.74	-3.816	5.0178	0.14345	0.4482:0.0:0.4064:0.1453	rs11545301	313;313;301	A8K211;Q8WWR8-2;Q8WWR8	.;.;NEUR4_HUMAN	R	301;301;311;313;301;314	ENSP00000385402:G301R;ENSP00000384804:G301R;ENSP00000385149:G313R;ENSP00000375830:G301R;ENSP00000320318:G314R	ENSP00000320318:G314R	G	+	1	0	NEU4	242406493	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.972000	0.03802	-0.372000	0.07992	-0.529000	0.04317	GGG	G|0.725;A|0.275	0.275	strong		0.701	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
RP1L1	94137	hgsc.bcm.edu	37	8	10465942	10465942	+	Missense_Mutation	SNP	T	T	A	rs28446662	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:10465942T>A	ENST00000382483.3	-	4	5889	c.5666A>T	c.(5665-5667)gAt>gTt	p.D1889V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1969					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)		GGTCTCTACATCTTCTGACTC	0.602													t|||	1189	0.23742	0.1679	0.3386	5008	,	,		16217	0.3929		0.2147	False		,,,				2504	0.1227				p.D1889V		Atlas-SNP	.											.	RP1L1	453	.	0			c.A5666T						PASS	.	T	VAL/ASP	726,3178		68,590,1294	158.0	174.0	169.0		5666	-2.8	0.0	8	dbSNP_125	169	1669,6635		168,1333,2651	no	missense	RP1L1	NM_178857.5	152	236,1923,3945	AA,AT,TT		20.0987,18.5963,19.6183	benign	1889/2401	10465942	2395,9813	1952	4152	6104	SO:0001583	missense	94137	exon4			TCTACATCTTCTG	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.5666A>T	8.37:g.10465942T>A	ENSP00000371923:p.Asp1889Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	129	77	0.596899	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	566	0.2591575091575092	62	0.12601626016260162	102	0.281767955801105	238	0.4160839160839161	164	0.21635883905013192	t	3.686	-0.064495	0.07273	0.185963	0.200987	ENSG00000183638	ENST00000382483	T	0.07688	3.17	1.4	-2.8	0.05823	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.46105	-0.9215	8	0.30078	T	0.28	.	4.5421	0.12064	0.0:0.1945:0.191:0.6145	rs28446662	1889	A6NKC6	.	V	1889	ENSP00000371923:D1889V	ENSP00000371923:D1889V	D	-	2	0	RP1L1	10503352	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.203000	0.03019	-0.837000	0.04223	-0.375000	0.07067	GAT	T|0.764;A|0.236	0.236	strong		0.602	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
DDX58	23586	hgsc.bcm.edu	37	9	32480251	32480251	+	Missense_Mutation	SNP	A	A	T	rs17217280	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:32480251A>T	ENST00000379883.2	-	12	1897	c.1740T>A	c.(1738-1740)gaT>gaA	p.D580E	DDX58_ENST00000379882.1_Missense_Mutation_p.D535E|DDX58_ENST00000545044.1_Missense_Mutation_p.D377E|DDX58_ENST00000542096.1_Missense_Mutation_p.D509E|DDX58_ENST00000379868.1_Missense_Mutation_p.D377E	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	580	Interaction with ZC3HAV1.		D -> E (in dbSNP:rs17217280). {ECO:0000269|PubMed:11890704, ECO:0000269|Ref.1}.		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)		GCTCAATCTCATCGAATCCTG	0.428													A|||	284	0.0567093	0.0068	0.1009	5008	,	,		19368	0.0129		0.1362	False		,,,				2504	0.0562				p.D580E		Atlas-SNP	.											.	DDX58	82	.	0			c.T1740A						PASS	.	A	GLU/ASP	142,4264	99.8+/-138.5	2,138,2063	154.0	135.0	141.0		1740	4.7	1.0	9	dbSNP_123	141	1268,7332	251.8+/-278.1	93,1082,3125	yes	missense	DDX58	NM_014314.3	45	95,1220,5188	TT,TA,AA		14.7442,3.2229,10.8412	possibly-damaging	580/926	32480251	1410,11596	2203	4300	6503	SO:0001583	missense	23586	exon12			AATCTCATCGAAT	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.1740T>A	9.37:g.32480251A>T	ENSP00000369213:p.Asp580Glu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	160	82	0.5125	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	169	0.07738095238095238	6	0.012195121951219513	47	0.1298342541436464	11	0.019230769230769232	105	0.13852242744063326	A	21.6	4.172154	0.78452	0.032229	0.147442	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096;ENST00000545044	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	4.67	4.67	0.58626	.	0.144833	0.46758	D	0.000261	T	0.00440	0.0014	M	0.79011	2.435	0.24770	P	0.99287946	D;P;B;P	0.55800	0.973;0.886;0.037;0.818	P;P;B;B	0.55011	0.766;0.489;0.037;0.215	T	0.12502	-1.0545	9	0.21014	T	0.42	-18.2098	13.7947	0.63164	1.0:0.0:0.0:0.0	rs17217280;rs17217280	377;535;509;580	F5H5W6;O95786-2;B3KWW1;O95786	.;.;.;DDX58_HUMAN	E	535;580;377;509;377	ENSP00000369212:D535E;ENSP00000369213:D580E;ENSP00000369197:D377E;ENSP00000442160:D509E;ENSP00000443055:D377E	ENSP00000369197:D377E	D	-	3	2	DDX58	32470251	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	1.645000	0.37238	2.051000	0.60960	0.533000	0.62120	GAT	A|0.906;T|0.094	0.094	strong		0.428	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
ADCY3	109	hgsc.bcm.edu	37	2	25064157	25064157	+	Silent	SNP	G	G	C	rs2241758	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:25064157G>C	ENST00000260600.5	-	5	2018	c.1167C>G	c.(1165-1167)ctC>ctG	p.L389L	ADCY3_ENST00000405392.1_5'UTR	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	389					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)|sensory perception of smell (GO:0007608)|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)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					CCAGCCCCATGAGGATGGAGC	0.637													G|||	354	0.0706869	0.003	0.2118	5008	,	,		17354	0.1012		0.0855	False		,,,				2504	0.0153				p.L389L		Atlas-SNP	.											.	ADCY3	114	.	0			c.C1167G						PASS	.	G		86,4304		2,82,2111	34.0	36.0	35.0		1167	2.7	1.0	2	dbSNP_98	35	622,7966		15,592,3687	no	coding-synonymous	ADCY3	NM_004036.3		17,674,5798	CC,CG,GG		7.2427,1.959,5.4554		389/1145	25064157	708,12270	2195	4294	6489	SO:0001819	synonymous_variant	109	exon5			CCCCATGAGGATG	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.1167C>G	2.37:g.25064157G>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																			G|0.925;C|0.075	0.075	strong		0.637	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
TRPM6	140803	hgsc.bcm.edu	37	9	77376647	77376647	+	Missense_Mutation	SNP	T	T	C	rs2274924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:77376647T>C	ENST00000360774.1	-	27	4987	c.4750A>G	c.(4750-4752)Aag>Gag	p.K1584E	TRPM6_ENST00000376864.4_Missense_Mutation_p.K1584E|TRPM6_ENST00000361255.3_Missense_Mutation_p.K1579E|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Missense_Mutation_p.K1579E|TRPM6_ENST00000451710.3_Missense_Mutation_p.K1584E|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	1584			K -> E (in dbSNP:rs2274924). {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)	p.K1584E(1)		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						TTCTTTTTCTTTGACAGTCTC	0.428													T|||	1477	0.294928	0.4463	0.147	5008	,	,		18536	0.3155		0.1571	False		,,,				2504	0.316				p.K1584E		Atlas-SNP	.											TRPM6,caecum,carcinoma,+2,2	TRPM6	377	2	1	Substitution - Missense(1)	stomach(1)	c.A4750G						PASS	.	T	GLU/LYS,GLU/LYS,GLU/LYS	1727,2679	519.0+/-369.9	333,1061,809	204.0	177.0	186.0		4735,4735,4750	4.6	0.6	9	dbSNP_100	186	1335,7265	261.9+/-284.1	91,1153,3056	yes	missense,missense,missense	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	56,56,56	424,2214,3865	CC,CT,TT		15.5233,39.1966,23.543	benign,benign,benign	1579/2018,1579/2018,1584/2023	77376647	3062,9944	2203	4300	6503	SO:0001583	missense	140803	exon27			TTTTCTTTGACAG	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.4750A>G	9.37:g.77376647T>C	ENSP00000354006:p.Lys1584Glu	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	261	127	0.48659	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	544	0.2490842490842491	190	0.3861788617886179	46	0.1270718232044199	182	0.3181818181818182	126	0.1662269129287599	T	16.64	3.179714	0.57800	0.391966	0.155233	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864	T;T;T;T;T	0.56444	0.55;0.55;0.56;0.55;0.46	5.77	4.64	0.57946	.	0.437410	0.27039	N	0.021226	T	0.00012	0.0000	L	0.59436	1.845	0.34496	P	0.294519	P;P;P	0.42692	0.682;0.675;0.787	B;B;P	0.46758	0.326;0.426;0.526	T	0.36187	-0.9758	9	0.62326	D	0.03	.	10.7405	0.46149	0.0:0.0749:0.0:0.9251	rs2274924;rs61238454;rs2274924	1584;1579;1579	Q9BX84;Q9BX84-3;Q9BX84-2	TRPM6_HUMAN;.;.	E	1584;1584;1579;1579;1584	ENSP00000354006:K1584E;ENSP00000407341:K1584E;ENSP00000396672:K1579E;ENSP00000354962:K1579E;ENSP00000366060:K1584E	ENSP00000354006:K1584E	K	-	1	0	TRPM6	76566467	0.888000	0.30383	0.558000	0.28319	0.405000	0.30901	1.602000	0.36783	1.131000	0.42111	0.528000	0.53228	AAG	T|0.756;C|0.244	0.244	strong		0.428	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
OR2T8	343172	hgsc.bcm.edu	37	1	248084473	248084473	+	Silent	SNP	C	C	A	rs143274587	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248084473C>A	ENST00000319968.4	+	1	154	c.154C>A	c.(154-156)Cgg>Agg	p.R52R		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	52						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(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	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)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CTGGGACCACCGGCTCCACAC	0.532													C|||	694	0.138578	0.2247	0.2378	5008	,	,		14789	0.002		0.1571	False		,,,				2504	0.0736				p.R52R		Atlas-SNP	.											OR2T8,NS,carcinoma,-1,1	OR2T8	67	1	0			c.C154A						PASS	.						61.0	60.0	60.0					1																	248084473		2201	4297	6498	SO:0001819	synonymous_variant	343172	exon1			GACCACCGGCTCC		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.154C>A	1.37:g.248084473C>A		Somatic	703	0	0		WXS	Illumina HiSeq	Phase_I	433	175	0.404157	NM_001005522		Silent	SNP	ENST00000319968.4	37	CCDS31100.1																																																																																			C|0.887;A|0.113	0.113	strong		0.532	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
TRIOBP	11078	hgsc.bcm.edu	37	22	38122122	38122122	+	Missense_Mutation	SNP	T	T	C	rs5756795	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:38122122T>C	ENST00000406386.3	+	7	3814	c.3559T>C	c.(3559-3561)Ttc>Ctc	p.F1187L		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1187			F -> L (in dbSNP:rs5756795).		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)					GCCATCCCTCTTCTTCCAGGA	0.632													T|||	1686	0.336661	0.1543	0.2867	5008	,	,		14041	0.5863		0.3877	False		,,,				2504	0.3088				p.F1187L		Atlas-SNP	.											.	TRIOBP	262	.	0			c.T3559C						PASS	.	T	LEU/PHE	708,3228		74,560,1334	66.0	75.0	72.0		3559	2.9	1.0	22	dbSNP_114	72	3573,4719		767,2039,1340	yes	missense	TRIOBP	NM_001039141.2	22	841,2599,2674	CC,CT,TT		43.0897,17.9878,35.0098	probably-damaging	1187/2366	38122122	4281,7947	1968	4146	6114	SO:0001583	missense	11078	exon7			TCCCTCTTCTTCC	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.3559T>C	22.37:g.38122122T>C	ENSP00000384312:p.Phe1187Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	816	0.37362637362637363	84	0.17073170731707318	113	0.31215469613259667	331	0.5786713286713286	288	0.37994722955145116	T	13.53	2.265441	0.40095	0.179878	0.430897	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.17691	2.26	5.38	2.89	0.33648	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.999999820884	B	0.12630	0.006	B	0.11329	0.006	T	0.37596	-0.9699	8	0.46703	T	0.11	.	4.6783	0.12722	0.0:0.1944:0.1676:0.638	rs5756795	1187	Q9H2D6	TARA_HUMAN	L	1187	ENSP00000384312:F1187L	ENSP00000384312:F1187L	F	+	1	0	TRIOBP	36452068	0.854000	0.29725	0.996000	0.52242	0.993000	0.82548	1.321000	0.33678	0.893000	0.36288	0.369000	0.22263	TTC	T|0.609;C|0.391	0.391	strong		0.632	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
AHNAK2	113146	hgsc.bcm.edu	37	14	105413220	105413220	+	Silent	SNP	A	A	C	rs151173659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105413220A>C	ENST00000333244.5	-	7	8687	c.8568T>G	c.(8566-8568)ctT>ctG	p.L2856L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2856						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)			CAGTGGTCTTAAGATCCCCTT	0.637													.|||	57	0.0113818	0.0386	0.0029	5008	,	,		17917	0.0		0.0	False		,,,				2504	0.0041				p.L2856L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T8568G						PASS	.	G		157,3765		7,143,1811	126.0	144.0	138.0		8568	-0.0	0.0	14	dbSNP_134	138	6,8298		0,6,4146	no	coding-synonymous	AHNAK2	NM_138420.2		7,149,5957	CC,CA,AA		0.0723,4.0031,1.3332		2856/5796	105413220	163,12063	1961	4152	6113	SO:0001819	synonymous_variant	113146	exon7			GGTCTTAAGATCC	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.8568T>G	14.37:g.105413220A>C		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	249	167	0.670683	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.994;C|0.006	0.006	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NOD2	64127	hgsc.bcm.edu	37	16	50733859	50733859	+	Silent	SNP	C	C	G	rs2067085	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	17	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	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	
CGN	57530	hgsc.bcm.edu	37	1	151491656	151491656	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:151491656C>T	ENST00000271636.7	+	2	794	c.661C>T	c.(661-663)Cgg>Tgg	p.R221W		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	215	Head.|Interacts with ZO-2.				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)			CCGCCTCCCACGGGACACCTT	0.622																																					p.R221W		Atlas-SNP	.											CGN,NS,carcinoma,0,1	CGN	106	1	0			c.C661T						scavenged	.						83.0	91.0	89.0					1																	151491656		2203	4299	6502	SO:0001583	missense	57530	exon2			CTCCCACGGGACA	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.661C>T	1.37:g.151491656C>T	ENSP00000271636:p.Arg221Trp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	.	.	.	.	.	.	.	.	.	.	C	18.93	3.727612	0.69074	.	.	ENSG00000143375	ENST00000427934;ENST00000271636	T;T	0.65178	0.8;-0.14	5.18	0.958	0.19619	.	0.492439	0.21593	N	0.072063	T	0.47021	0.1423	L	0.57536	1.79	0.09310	N	1	D	0.69078	0.997	P	0.47470	0.548	T	0.50583	-0.8811	9	.	.	.	-19.8131	14.725	0.69339	0.6113:0.3887:0.0:0.0	.	215	Q9P2M7	CING_HUMAN	W	221	ENSP00000410836:R221W;ENSP00000271636:R221W	.	R	+	1	2	CGN	149758280	0.128000	0.22383	0.039000	0.18376	0.313000	0.28021	0.190000	0.17057	0.091000	0.17302	0.561000	0.74099	CGG	.	.	none		0.622	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
FRMD6	122786	hgsc.bcm.edu	37	14	52186966	52186966	+	Silent	SNP	G	G	A	rs2277495	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:52186966G>A	ENST00000344768.5	+	11	1414	c.1218G>A	c.(1216-1218)acG>acA	p.T406T	FRMD6_ENST00000395718.2_Silent_p.T398T|FRMD6_ENST00000553556.1_Silent_p.T48T|FRMD6_ENST00000554167.1_Silent_p.T329T|FRMD6_ENST00000356218.4_Silent_p.T398T			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	406					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					CCCGGGACACGGGGCCAGAAG	0.617													G|||	1149	0.229433	0.1021	0.2795	5008	,	,		17792	0.2649		0.3211	False		,,,				2504	0.2352				p.T406T		Atlas-SNP	.											.	FRMD6	100	.	0			c.G1218A						PASS	.	G	,	550,3856	248.1+/-256.1	45,460,1698	64.0	61.0	62.0		1194,1194	-12.0	0.0	14	dbSNP_100	62	2673,5927	428.0+/-355.8	395,1883,2022	no	coding-synonymous,coding-synonymous	FRMD6	NM_001042481.1,NM_152330.3	,	440,2343,3720	AA,AG,GG		31.0814,12.483,24.7809	,	398/615,398/615	52186966	3223,9783	2203	4300	6503	SO:0001819	synonymous_variant	122786	exon11			GGACACGGGGCCA	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"""expanded homolog"""	614555	"""chromosome 14 open reading frame 31"""	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.1218G>A	14.37:g.52186966G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	112	74	0.660714	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	37	CCDS58318.1																																																																																			G|0.751;C|0.000;A|0.249	0.249	strong		0.617	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330	
MUC4	4585	hgsc.bcm.edu	37	3	195508903	195508903	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195508903G>A	ENST00000463781.3	-	2	10007	c.9548C>T	c.(9547-9549)aCg>aTg	p.T3183M	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3183M	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.T3183I(1)|p.T3183M(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)		AGGAAGAGGCGTGGTGTCACC	0.592																																					p.T3183M		Atlas-SNP	.											MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	NS(2)	c.C9548T						scavenged	.						3.0	2.0	2.0					3																	195508903		442	957	1399	SO:0001583	missense	4585	exon2			AGAGGCGTGGTGT	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.9548C>T	3.37:g.195508903G>A	ENSP00000417498:p.Thr3183Met	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	245	14	0.0571429	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	1.721	-0.496684	0.04291	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.38887	1.11;1.23	.	.	.	.	.	.	.	.	T	0.34395	0.0896	N	0.19112	0.55	0.09310	N	1	D	0.69078	0.997	P	0.55615	0.78	T	0.16247	-1.0409	7	.	.	.	.	4.5608	0.12160	0.0:0.4156:0.5844:0.0	.	3055	E7ESK3	.	M	3183	ENSP00000417498:T3183M;ENSP00000420243:T3183M	.	T	-	2	0	MUC4	196993682	0.001000	0.12720	0.010000	0.14722	0.010000	0.07245	0.267000	0.18552	0.073000	0.16731	0.074000	0.15403	ACG	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC17A4	10050	hgsc.bcm.edu	37	6	25773809	25773809	+	Silent	SNP	A	A	G	rs2275906	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:25773809A>G	ENST00000377905.4	+	8	1013	c.894A>G	c.(892-894)ttA>ttG	p.L298L	SLC17A4_ENST00000439485.2_Intron|SLC17A4_ENST00000397076.2_Silent_p.L68L	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	298					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						GGGCCATTTTAGTCTCTTATT	0.453													A|||	485	0.096845	0.0295	0.111	5008	,	,		19912	0.0546		0.1421	False		,,,				2504	0.1748				p.L298L		Atlas-SNP	.											.	SLC17A4	79	.	0			c.A894G						PASS	.	A		181,4225	117.1+/-155.0	6,169,2028	171.0	151.0	158.0		894	-2.7	0.0	6	dbSNP_100	158	1251,7349	249.6+/-276.8	85,1081,3134	no	coding-synonymous	SLC17A4	NM_005495.2		91,1250,5162	GG,GA,AA		14.5465,4.108,11.0103		298/498	25773809	1432,11574	2203	4300	6503	SO:0001819	synonymous_variant	10050	exon8			CATTTTAGTCTCT	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.894A>G	6.37:g.25773809A>G		Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	301	136	0.451827	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Silent	SNP	ENST00000377905.4	37	CCDS4564.1																																																																																			A|0.903;G|0.097	0.097	strong		0.453	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1		
HIST1H4H	8365	hgsc.bcm.edu	37	6	26285503	26285503	+	Silent	SNP	C	C	T	rs41266829	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26285503C>T	ENST00000377727.1	-	1	234	c.225G>A	c.(223-225)gaG>gaA	p.E75E	HIST1H4H_ENST00000289352.1_Silent_p.E75E	NM_003543.3	NP_003534.1	P62805	H4_HUMAN	histone cluster 1, H4h	75					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						GTTTGGCGTGCTCTGTGTAAG	0.547										HNSCC(76;0.23)			C|||	497	0.0992412	0.0953	0.1153	5008	,	,		20440	0.0506		0.16	False		,,,				2504	0.0808				p.E75E		Atlas-SNP	.											HIST1H4H,colon,carcinoma,0,1	HIST1H4H	16	1	0			c.G225A						PASS	.	C		468,3938		30,408,1765	180.0	145.0	157.0		225	3.5	1.0	6	dbSNP_127	157	1297,7303		81,1135,3084	no	coding-synonymous	HIST1H4H	NM_003543.3		111,1543,4849	TT,TC,CC		15.0814,10.6219,13.5707		75/104	26285503	1765,11241	2203	4300	6503	SO:0001819	synonymous_variant	8365	exon1			GGCGTGCTCTGTG	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.225G>A	6.37:g.26285503C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	156	78	0.5	NM_003543	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377727.1	37	CCDS4604.1																																																																																			C|0.869;T|0.131	0.131	strong		0.547	HIST1H4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040119.1	NM_003543	
SLC7A13	157724	hgsc.bcm.edu	37	8	87229739	87229739	+	Missense_Mutation	SNP	C	C	T	rs4419794	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:87229739C>T	ENST00000297524.3	-	3	1242	c.1139G>A	c.(1138-1140)aGg>aAg	p.R380K	SLC7A13_ENST00000419776.2_Missense_Mutation_p.R371K|SLC7A13_ENST00000520624.1_5'Flank	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	157	0	0		WXS	Illumina HiSeq	Phase_I	143	87	0.608392	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	
BSN	8927	hgsc.bcm.edu	37	3	49701983	49701983	+	Silent	SNP	G	G	A	rs9858542	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49701983G>A	ENST00000296452.4	+	9	11850	c.11736G>A	c.(11734-11736)acG>acA	p.T3912T		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3912					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GCAAACTGACGGAAGGTATGC	0.637													G|||	978	0.195288	0.2171	0.17	5008	,	,		17930	0.0516		0.3241	False		,,,				2504	0.1994				p.T3912T		Atlas-SNP	.											BSN,NS,carcinoma,+1,1	BSN	272	1	0			c.G11736A						PASS	.	G		1044,3362	379.7+/-323.4	120,804,1279	48.0	54.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11736	-10.1	0.6	3	dbSNP_119	52	2577,6023	416.5+/-352.1	402,1773,2125	yes	coding-synonymous	BSN	NM_003458.3		522,2577,3404	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	29.9651,23.695,27.841		3912/3927	49701983	3621,9385	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon9			ACTGACGGAAGGT	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.11736G>A	3.37:g.49701983G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	34	22	0.647059	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			G|0.749;A|0.251	0.251	strong		0.637	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
KCTD18	130535	hgsc.bcm.edu	37	2	201355106	201355106	+	Missense_Mutation	SNP	G	G	A	rs13018579	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:201355106G>A	ENST00000359878.3	-	7	1508	c.998C>T	c.(997-999)gCc>gTc	p.A333V	KCTD18_ENST00000468413.1_5'Flank|KCTD18_ENST00000409157.1_Missense_Mutation_p.A333V	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	333			A -> V (in dbSNP:rs13018579). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GCCCACCAGGGCCGTGGCTCT	0.642													G|||	497	0.0992412	0.0393	0.1427	5008	,	,		16517	0.002		0.2336	False		,,,				2504	0.1115				p.A333V		Atlas-SNP	.											.	KCTD18	44	.	0			c.C998T						PASS	.	G	VAL/ALA	299,4107	160.3+/-192.7	8,283,1912	44.0	48.0	47.0		998	2.4	0.0	2	dbSNP_121	47	1952,6648	341.4+/-324.0	238,1476,2586	yes	missense	KCTD18	NM_152387.2	64	246,1759,4498	AA,AG,GG		22.6977,6.7862,17.3074	benign	333/427	201355106	2251,10755	2203	4300	6503	SO:0001583	missense	130535	exon7			ACCAGGGCCGTGG	AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 18"""				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.998C>T	2.37:g.201355106G>A	ENSP00000352941:p.Ala333Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	67	21	0.313433	NM_152387	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	37	CCDS2330.1	266	0.12179487179487179	27	0.054878048780487805	65	0.17955801104972377	1	0.0017482517482517483	173	0.22823218997361477	G	11.88	1.770629	0.31320	0.067862	0.226977	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.35236	1.32;1.32	4.22	2.38	0.29361	.	1.417830	0.04433	N	0.369665	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.17038	0.02	B	0.17433	0.018	T	0.20505	-1.0273	9	0.05959	T	0.93	0.2009	6.6967	0.23203	0.0926:0.0:0.7314:0.176	rs13018579;rs17532385;rs57796327;rs13018579	333	Q6PI47	KCD18_HUMAN	V	333	ENSP00000352941:A333V;ENSP00000386751:A333V	ENSP00000352941:A333V	A	-	2	0	KCTD18	201063351	0.072000	0.21174	0.000000	0.03702	0.004000	0.04260	2.880000	0.48530	0.404000	0.25506	0.655000	0.94253	GCC	G|0.849;A|0.151	0.151	strong		0.642	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387	
RETNLB	84666	hgsc.bcm.edu	37	3	108475974	108475974	+	Missense_Mutation	SNP	G	G	A	rs11708527	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:108475974G>A	ENST00000295755.6	-	1	257	c.59C>T	c.(58-60)cCg>cTg	p.P20L	RETNLB_ENST00000482939.1_5'Flank	NM_032579.2	NP_115968.1	Q9BQ08	RETNB_HUMAN	resistin like beta	20			P -> L (in dbSNP:rs11708527).		cell proliferation (GO:0008283)	extracellular region (GO:0005576)				endometrium(1)|kidney(3)|lung(10)|prostate(1)|skin(1)	16						AGTACTCCCCGGGTTGATCAG	0.532													G|||	1005	0.200679	0.1165	0.232	5008	,	,		19248	0.0377		0.2783	False		,,,				2504	0.3804				p.P20L		Atlas-SNP	.											RETNLB,NS,carcinoma,+1,1	RETNLB	38	1	0			c.C59T						scavenged	.	G	LEU/PRO	644,3762	276.6+/-273.2	45,554,1604	68.0	62.0	64.0		59	2.5	0.0	3	dbSNP_120	64	2467,6133	405.7+/-348.6	360,1747,2193	yes	missense	RETNLB	NM_032579.2	98	405,2301,3797	AA,AG,GG		28.686,14.6164,23.9197	possibly-damaging	20/112	108475974	3111,9895	2203	4300	6503	SO:0001583	missense	84666	exon1			CTCCCCGGGTTGA	AF290873	CCDS2953.1	3q13.1	2008-02-05			ENSG00000163515	ENSG00000163515			20388	protein-coding gene	gene with protein product		605645				10921885, 12574343	Standard	NM_032579		Approved	HXCP2, FIZZ2, RELMb	uc003dxh.2	Q9BQ08	OTTHUMG00000159393	ENST00000295755.6:c.59C>T	3.37:g.108475974G>A	ENSP00000295755:p.Pro20Leu	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_032579	Q14D27	Missense_Mutation	SNP	ENST00000295755.6	37	CCDS2953.1	352	0.16117216117216118	43	0.08739837398373984	76	0.20994475138121546	23	0.04020979020979021	210	0.2770448548812665	G	12.09	1.833577	0.32421	0.146164	0.28686	ENSG00000163515	ENST00000295755	T	0.41758	0.99	4.38	2.52	0.30459	.	0.512899	0.16570	N	0.208678	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	P	0.41848	0.763	B	0.28638	0.092	T	0.30822	-0.9965	9	0.48119	T	0.1	-0.3382	5.1548	0.15029	0.1077:0.0:0.6897:0.2027	rs11708527;rs52797386;rs57988437;rs11708527	20	Q9BQ08	RETNB_HUMAN	L	20	ENSP00000295755:P20L	ENSP00000295755:P20L	P	-	2	0	RETNLB	109958664	0.000000	0.05858	0.001000	0.08648	0.097000	0.18754	0.091000	0.15046	0.450000	0.26774	0.655000	0.94253	CCG	G|0.795;A|0.205	0.205	strong		0.532	RETNLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355093.1		
SDPR	8436	hgsc.bcm.edu	37	2	192711385	192711385	+	Silent	SNP	G	G	A	rs35883486	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:192711385G>A	ENST00000304141.4	-	1	596	c.267C>T	c.(265-267)tcC>tcT	p.S89S	AC098617.1_ENST00000424116.2_RNA	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)			TGCCCTTCACGGAGCCCTCCA	0.582													G|||	97	0.019369	0.0091	0.0144	5008	,	,		20010	0.003		0.0278	False		,,,				2504	0.045				p.S89S		Atlas-SNP	.											SDPR,caecum,carcinoma,0,1	SDPR	67	1	0			c.C267T						PASS	.	G		52,4354	52.3+/-87.9	0,52,2151	110.0	93.0	99.0		267	-3.9	0.9	2	dbSNP_126	99	254,8346	99.3+/-160.8	4,246,4050	no	coding-synonymous	SDPR	NM_004657.5		4,298,6201	AA,AG,GG		2.9535,1.1802,2.3528		89/426	192711385	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	8436	exon1			CTTCACGGAGCCC	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.267C>T	2.37:g.192711385G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	204	105	0.514706	NM_004657		Silent	SNP	ENST00000304141.4	37	CCDS2313.1																																																																																			G|0.977;A|0.023	0.023	strong		0.582	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657	
PGR	5241	hgsc.bcm.edu	37	11	100933412	100933412	+	Missense_Mutation	SNP	C	C	A	rs1042838	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:100933412C>A	ENST00000325455.5	-	4	3431	c.1978G>T	c.(1978-1980)Gtg>Ttg	p.V660L	PGR_ENST00000263463.5_Intron|PGR_ENST00000534013.1_Missense_Mutation_p.V66L	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	660			V -> L (in dbSNP:rs1042838). {ECO:0000269|PubMed:12644308, ECO:0000269|PubMed:3551956, ECO:0000269|Ref.3}.		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)	GGAACGCCCACTGGCTGTGGG	0.418													C|||	358	0.0714856	0.0061	0.1369	5008	,	,		15303	0.0099		0.1789	False		,,,				2504	0.0665				p.V660L	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.G1978T	GRCh37	CM043326	PGR	M	rs1042838	PASS	.	C	LEU/VAL,LEU/VAL	132,4274	95.3+/-134.0	1,130,2072	124.0	108.0	113.0		1978,1486	4.5	1.0	11	dbSNP_86	113	1414,7186	272.8+/-290.3	107,1200,2993	yes	missense,missense	PGR	NM_000926.4,NM_001202474.1	32,32	108,1330,5065	AA,AC,CC		16.4419,2.9959,11.8868	benign,benign	660/934,496/770	100933412	1546,11460	2203	4300	6503	SO:0001583	missense	5241	exon4			CGCCCACTGGCTG	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.1978G>T	11.37:g.100933412C>A	ENSP00000325120:p.Val660Leu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	170	68	0.4	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	207	0.09478021978021978	6	0.012195121951219513	54	0.14917127071823205	4	0.006993006993006993	143	0.18865435356200527	C	11.58	1.681111	0.29872	0.029959	0.164419	ENSG00000082175	ENST00000325455;ENST00000534013	D;D	0.86366	-1.67;-2.11	5.41	4.49	0.54785	Nuclear hormone receptor, ligand-binding (1);	0.704963	0.13868	N	0.357217	T	0.00384	0.0012	L	0.43757	1.38	0.09310	P	0.99999999182884	B	0.12630	0.006	B	0.09377	0.004	T	0.23940	-1.0174	9	0.27082	T	0.32	.	5.3111	0.15831	0.1488:0.6304:0.1439:0.077	rs1042838;rs11571223;rs17656622;rs52792239;rs56653495;rs1042838	660	P06401	PRGR_HUMAN	L	660;66	ENSP00000325120:V660L;ENSP00000436561:V66L	ENSP00000325120:V660L	V	-	1	0	PGR	100438622	0.159000	0.22864	0.998000	0.56505	0.714000	0.41099	0.674000	0.25218	2.512000	0.84698	0.591000	0.81541	GTG	C|0.893;A|0.107	0.107	strong		0.418	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
SRBD1	55133	hgsc.bcm.edu	37	2	45645512	45645512	+	Silent	SNP	C	C	T	rs2276655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:45645512C>T	ENST00000263736.4	-	18	2387	c.2325G>A	c.(2323-2325)acG>acA	p.T775T	SRBD1_ENST00000535761.1_Silent_p.T294T|SRBD1_ENST00000490133.1_5'UTR	NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	775					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			ACCTGCAAAACGTTCGGATAT	0.403													T|||	971	0.19389	0.3215	0.2421	5008	,	,		19287	0.1359		0.0944	False		,,,				2504	0.1493				p.T775T		Atlas-SNP	.											.	SRBD1	107	.	0			c.G2325A						PASS	.	T		1301,3105	697.5+/-406.2	207,887,1109	277.0	177.0	211.0		2325	0.6	1.0	2	dbSNP_100	211	751,7849	785.5+/-407.6	34,683,3583	no	coding-synonymous	SRBD1	NM_018079.4		241,1570,4692	TT,TC,CC		8.7326,29.5279,15.7773		775/996	45645512	2052,10954	2203	4300	6503	SO:0001819	synonymous_variant	55133	exon18			GCAAAACGTTCGG	AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.2325G>A	2.37:g.45645512C>T		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	210	208	0.990476	NM_018079	Q53T56|Q96TA4|Q9NW11	Silent	SNP	ENST00000263736.4	37	CCDS1823.1																																																																																			C|0.840;T|0.160	0.160	strong		0.403	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3	NM_018079	
SOWAHC	65124	hgsc.bcm.edu	37	2	110373197	110373197	+	Silent	SNP	G	G	A	rs1560884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:110373197G>A	ENST00000356454.3	+	1	1287	c.1131G>A	c.(1129-1131)aaG>aaA	p.K377K	SEPT10_ENST00000397712.2_5'Flank|SEPT10_ENST00000415095.1_5'Flank|SEPT10_ENST00000397714.2_5'Flank|SEPT10_ENST00000356688.4_5'Flank|SEPT10_ENST00000545389.1_5'Flank|SEPT10_ENST00000334001.6_5'Flank|SEPT10_ENST00000437928.1_5'Flank	NM_023016.3	NP_075392.2	Q53LP3	SWAHC_HUMAN	sosondowah ankyrin repeat domain family member C	377																	GTGGGAAAAAGGCCTCCCAGT	0.657													G|||	1623	0.324081	0.2526	0.4697	5008	,	,		16294	0.3929		0.2575	False		,,,				2504	0.3149				p.K377K		Atlas-SNP	.											.	.	.	.	0			c.G1131A						PASS	.	G		1206,3200	388.6+/-327.0	156,894,1153	48.0	55.0	53.0		1131	1.6	0.1	2	dbSNP_88	53	2121,6479	341.3+/-324.0	258,1605,2437	no	coding-synonymous	ANKRD57	NM_023016.3		414,2499,3590	AA,AG,GG		24.6628,27.3718,25.5805		377/526	110373197	3327,9679	2203	4300	6503	SO:0001819	synonymous_variant	65124	exon1			GAAAAAGGCCTCC	AK023346	CCDS33270.1	2q13	2013-01-10	2012-01-12	2012-01-12	ENSG00000198142	ENSG00000198142		"""Ankyrin repeat domain containing"""	26149	protein-coding gene	gene with protein product			"""ankyrin repeat domain 57"""	C2orf26, ANKRD57		22234889	Standard	NM_023016		Approved	FLJ21870	uc002tfb.3	Q53LP3	OTTHUMG00000153219	ENST00000356454.3:c.1131G>A	2.37:g.110373197G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_023016	Q8NE15|Q9H6U1	Silent	SNP	ENST00000356454.3	37	CCDS33270.1																																																																																			G|0.728;A|0.272	0.272	strong		0.657	SOWAHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330168.1	NM_023016	
IGFN1	91156	hgsc.bcm.edu	37	1	201166383	201166383	+	De_novo_Start_OutOfFrame	SNP	G	G	A	rs4915221	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201166383G>A	ENST00000295591.8	+	0	435				IGFN1_ENST00000451870.2_Missense_Mutation_p.R102H|IGFN1_ENST00000335211.4_Missense_Mutation_p.R102H			Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1							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						GATCTGTACCGCTGCACAGCA	0.547													g|||	3669	0.732628	0.8101	0.5735	5008	,	,		22538	0.8562		0.5547	False		,,,				2504	0.7965				p.R102H		Atlas-SNP	.											.	IGFN1	220	.	0			c.G305A						PASS	.	A	HIS/ARG	1065,319		406,253,33	146.0	135.0	138.0		305	3.2	1.0	1	dbSNP_111	138	1812,1370		519,774,298	yes	missense	IGFN1	NM_001164586.1	29	925,1027,331	AA,AG,GG		43.0547,23.0491,36.9908		102/3709	201166383	2877,1689	692	1591	2283			91156	exon5			TGTACCGCTGCAC	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	ENST00000295591.8:c.-8216G>A	1.37:g.201166383G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	38	0.365385	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000295591.8	37		1519	0.6955128205128205	387	0.7865853658536586	212	0.585635359116022	493	0.8618881118881119	427	0.5633245382585752	g	13.61	2.290057	0.40494	0.769509	0.569453	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.44083	0.93;0.93	5.04	3.18	0.36537	.	.	.	.	.	T	0.00012	0.0000	M	0.68952	2.095	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.10941	-1.0608	6	0.32370	T	0.25	.	7.9743	0.30145	0.1909:0.0:0.8091:0.0	rs4915221;rs17461911;rs52829174;rs56471819;rs60470802;rs4915221	.	.	.	H	102	ENSP00000334714:R102H;ENSP00000398386:R102H	ENSP00000334714:R102H	R	+	2	0	IGFN1	199433006	1.000000	0.71417	1.000000	0.80357	0.033000	0.12548	0.498000	0.22530	0.545000	0.28902	-1.004000	0.02495	CGC	G|0.289;A|0.710	0.710	strong		0.547	IGFN1-201	KNOWN	basic	protein_coding	protein_coding		NM_178275	
OR51E1	143503	hgsc.bcm.edu	37	11	4674575	4674575	+	Missense_Mutation	SNP	G	G	A	rs3817098	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	158	153	0.968354	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	
FAM26F	441168	hgsc.bcm.edu	37	6	116784797	116784797	+	Missense_Mutation	SNP	G	G	A	rs11544160	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:116784797G>A	ENST00000368605.1	+	3	972	c.877G>A	c.(877-879)Gaa>Aaa	p.E293K	RP1-93H18.6_ENST00000476099.1_RNA|FAM26F_ENST00000368606.3_Missense_Mutation_p.E121K	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	293			E -> K (in dbSNP:rs11544160).		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)		CAGGTCTACTGAAGGAGATAC	0.378													G|||	188	0.0375399	0.0023	0.0476	5008	,	,		17648	0.0099		0.0716	False		,,,				2504	0.0716				p.S293T		Atlas-SNP	.											.	FAM26F	12	.	0			c.T877A						PASS	.	G	LYS/GLU	67,4339	61.1+/-98.1	0,67,2136	169.0	180.0	176.0		877	1.8	0.0	6	dbSNP_120	176	683,7917	170.9+/-221.9	27,629,3644	yes	missense	FAM26F	NM_001010919.1	56	27,696,5780	AA,AG,GG		7.9419,1.5207,5.7666	probably-damaging	293/316	116784797	750,12256	2203	4300	6503	SO:0001583	missense	441168	exon3			TCTACTGAAGGAG	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.877G>A	6.37:g.116784797G>A	ENSP00000357594:p.Glu293Lys	Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	210	104	0.495238	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	84	0.038461538461538464	0	0.0	19	0.052486187845303865	6	0.01048951048951049	59	0.07783641160949868	G	12.21	1.868797	0.32977	0.015207	0.079419	ENSG00000188820	ENST00000368606;ENST00000368605;ENST00000368604	T;T;T	0.34667	1.37;2.42;1.35	4.89	1.77	0.24775	.	1.107720	0.07034	N	0.828925	T	0.21550	0.0519	M	0.77313	2.365	0.09310	N	1	B	0.32653	0.379	B	0.28553	0.091	T	0.38308	-0.9667	10	0.59425	D	0.04	-0.5113	9.7317	0.40366	0.2707:0.0:0.7293:0.0	rs11544160;rs60777515;rs11544160	293	Q5R3K3	FA26F_HUMAN	K	121;293;136	ENSP00000357595:E121K;ENSP00000357594:E293K;ENSP00000357593:E136K	ENSP00000357593:E136K	E	+	1	0	FAM26F	116891490	0.001000	0.12720	0.003000	0.11579	0.002000	0.02628	0.322000	0.19576	0.591000	0.29711	0.655000	0.94253	GAA	G|0.951;A|0.049	0.049	strong		0.378	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919	
ZNF22	7570	hgsc.bcm.edu	37	10	45499009	45499009	+	Missense_Mutation	SNP	A	A	G	rs3740093	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:45499009A>G	ENST00000298299.3	+	2	786	c.193A>G	c.(193-195)Agt>Ggt	p.S65G	CEP164P1_ENST00000456938.2_RNA|C10orf25_ENST00000298298.1_5'Flank	NM_006963.4	NP_008894.2	P17026	ZNF22_HUMAN	zinc finger protein 22	65			S -> G (in dbSNP:rs3740093).		odontogenesis (GO:0042476)|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(2)|endometrium(1)|kidney(2)|lung(2)	8		Prostate(175;0.0352)|all_neural(218;0.202)				AAAGAGTTTCAGTCAGAGTTC	0.383													A|||	172	0.034345	0.003	0.0101	5008	,	,		19023	0.0903		0.0427	False		,,,				2504	0.0276				p.S65G		Atlas-SNP	.											.	ZNF22	28	.	0			c.A193G						PASS	.	A	GLY/SER	38,4368	42.3+/-75.8	0,38,2165	57.0	58.0	57.0		193	4.0	1.0	10	dbSNP_107	57	416,8184	131.3+/-189.1	6,404,3890	yes	missense	ZNF22	NM_006963.4	56	6,442,6055	GG,GA,AA		4.8372,0.8625,3.4907	possibly-damaging	65/225	45499009	454,12552	2203	4300	6503	SO:0001583	missense	7570	exon2			AGTTTCAGTCAGA	BC041139	CCDS7211.1	10q11	2013-01-08	2012-07-12		ENSG00000165512	ENSG00000165512		"""Zinc fingers, C2H2-type"""	13012	protein-coding gene	gene with protein product		194529					Standard	NM_006963		Approved	KOX15, HKR-T1, ZNF422, Zfp422	uc001jbw.3	P17026	OTTHUMG00000018064	ENST00000298299.3:c.193A>G	10.37:g.45499009A>G	ENSP00000298299:p.Ser65Gly	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	27	6	0.222222	NM_006963	Q5T741|Q96FM4	Missense_Mutation	SNP	ENST00000298299.3	37	CCDS7211.1	105	0.04807692307692308	2	0.0040650406504065045	6	0.016574585635359115	63	0.11013986013986014	34	0.044854881266490766	A	12.94	2.089623	0.36855	0.008625	0.048372	ENSG00000165512	ENST00000298299	T	0.56275	0.47	5.12	3.98	0.46160	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.108383	0.41712	D	0.000823	T	0.01061	0.0035	L	0.49455	1.56	0.34819	P	0.26148800000000005	B	0.02656	0.0	B	0.04013	0.001	T	0.15235	-1.0444	9	0.59425	D	0.04	-25.481	9.1349	0.36868	0.9134:0.0:0.0866:0.0	rs3740093;rs52824035;rs3740093	65	P17026	ZNF22_HUMAN	G	65	ENSP00000298299:S65G	ENSP00000298299:S65G	S	+	1	0	ZNF22	44819015	0.000000	0.05858	1.000000	0.80357	0.893000	0.52053	0.771000	0.26633	0.951000	0.37770	-0.290000	0.09829	AGT	A|0.958;G|0.042	0.042	strong		0.383	ZNF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047761.1	NM_006963	
FHL3	2275	hgsc.bcm.edu	37	1	38463504	38463504	+	Silent	SNP	C	C	T	rs7366048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:38463504C>T	ENST00000373016.3	-	5	708	c.540G>A	c.(538-540)ccG>ccA	p.P180P	FHL3_ENST00000485803.1_5'UTR	NM_001243878.1|NM_004468.4	NP_001230807.1|NP_004459.2	Q13643	FHL3_HUMAN	four and a half LIM domains 3	180	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|muscle organ development (GO:0007517)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|stress fiber (GO:0001725)|Z disc (GO:0030018)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				CTCGATGCCACGGCTGATCAC	0.587													C|||	2883	0.575679	0.6861	0.5202	5008	,	,		20028	0.6756		0.4205	False		,,,				2504	0.5225				p.P180P		Atlas-SNP	.											.	FHL3	9	.	0			c.G540A						PASS	.	C		2872,1534	672.8+/-402.7	950,972,281	77.0	75.0	76.0		540	1.9	1.0	1	dbSNP_116	76	3598,5002	520.1+/-379.6	732,2134,1434	no	coding-synonymous	FHL3	NM_004468.4		1682,3106,1715	TT,TC,CC		41.8372,34.8162,49.7463		180/281	38463504	6470,6536	2203	4300	6503	SO:0001819	synonymous_variant	2275	exon5			ATGCCACGGCTGA	BC011697	CCDS30678.1	1p34.3	2008-02-05			ENSG00000183386	ENSG00000183386			3704	protein-coding gene	gene with protein product		602790				8753811, 10226657	Standard	NM_004468		Approved	SLIM2	uc001cck.3	Q13643	OTTHUMG00000004434	ENST00000373016.3:c.540G>A	1.37:g.38463504C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	88	70	0.795455	NM_004468	D3DPT6|Q6I9T0|Q9BVA2	Silent	SNP	ENST00000373016.3	37	CCDS30678.1																																																																																			C|0.477;T|0.523	0.523	strong		0.587	FHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012958.1	NM_004468	
CLEC1B	51266	hgsc.bcm.edu	37	12	10150974	10150974	+	Missense_Mutation	SNP	A	A	G	rs2273986	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:10150974A>G	ENST00000298527.6	-	2	249	c.70T>C	c.(70-72)Tct>Cct	p.S24P	CLEC1B_ENST00000348658.4_Intron|CLEC1B_ENST00000428126.2_Intron	NM_016509.3	NP_057593.3	Q9P126	CLC1B_HUMAN	C-type lectin domain family 1, member B	24			S -> P (in dbSNP:rs2273986). {ECO:0000269|PubMed:12975309}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|platelet formation (GO:0030220)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(12)|stomach(1)|urinary_tract(1)	19						GAGGATGCAGAGCCAACTGTA	0.567													G|||	2014	0.402157	0.469	0.4265	5008	,	,		17791	0.3363		0.492	False		,,,				2504	0.2699				p.S24P		Atlas-SNP	.											.	CLEC1B	39	.	0			c.T70C						PASS	.	G	,PRO/SER	1768,2436		373,1022,707	86.0	93.0	91.0		,70	1.3	0.0	12	dbSNP_100	91	3717,4713		846,2025,1344	yes	intron,missense	CLEC1B	NM_001099431.1,NM_016509.3	,74	1219,3047,2051	GG,GA,AA		44.0925,42.0552,43.4146	,benign	,24/230	10150974	5485,7149	2102	4215	6317	SO:0001583	missense	51266	exon2			ATGCAGAGCCAAC	AF124841	CCDS41751.1, CCDS41752.1	12p13.31	2006-04-12				ENSG00000165682		"""C-type lectin domain containing"""	24356	protein-coding gene	gene with protein product		606783				10671229, 11745369	Standard	NM_016509		Approved	CLEC2	uc001qwu.3	Q9P126		ENST00000298527.6:c.70T>C	12.37:g.10150974A>G	ENSP00000298527:p.Ser24Pro	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	174	77	0.442529	NM_016509	Q6UWX7|Q8NHR6	Missense_Mutation	SNP	ENST00000298527.6	37	CCDS41752.1	901	0.4125457875457875	215	0.4369918699186992	150	0.4143646408839779	174	0.3041958041958042	362	0.47757255936675463	G	0.017	-1.503403	0.00992	0.420552	0.440925	ENSG00000165682	ENST00000298527	T	0.01414	4.92	4.37	1.28	0.21552	.	0.126684	0.36101	N	0.002786	T	0.00012	0.0000	N	0.00389	-1.56	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.25012	-1.0144	9	0.02654	T	1	.	4.0145	0.09637	0.3312:0.1746:0.4942:0.0	rs2273986;rs60448232	24	Q9P126	CLC1B_HUMAN	P	24	ENSP00000298527:S24P	ENSP00000298527:S24P	S	-	1	0	CLEC1B	10042241	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.653000	0.05360	-0.334000	0.08463	-0.684000	0.03749	TCT	A|0.594;G|0.406	0.406	strong		0.567	CLEC1B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399922.1	NM_016509	
CDH20	28316	hgsc.bcm.edu	37	18	59166541	59166541	+	Silent	SNP	C	C	T	rs12964819	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:59166541C>T	ENST00000262717.4	+	3	767	c.369C>T	c.(367-369)gaC>gaT	p.D123D	CDH20_ENST00000538374.1_Silent_p.D123D|CDH20_ENST00000536675.2_Silent_p.D123D			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	123	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(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				AGAGGCTCGACCGAGAGGAAA	0.542													T|||	3116	0.622204	0.6157	0.5576	5008	,	,		18062	0.5417		0.6531	False		,,,				2504	0.728				p.D123D		Atlas-SNP	.											CDH20,NS,carcinoma,+2,1	CDH20	117	1	0			c.C369T						PASS	.	T		2838,1568	489.7+/-361.6	912,1014,277	61.0	50.0	54.0		369	-1.8	0.6	18	dbSNP_121	54	5733,2867	449.1+/-362.0	1916,1901,483	no	coding-synonymous	CDH20	NM_031891.2		2828,2915,760	TT,TC,CC		33.3372,35.5878,34.0996		123/802	59166541	8571,4435	2203	4300	6503	SO:0001819	synonymous_variant	28316	exon2			GCTCGACCGAGAG	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.369C>T	18.37:g.59166541C>T		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	127	125	0.984252	NM_031891	Q495S3	Silent	SNP	ENST00000262717.4	37	CCDS11977.1																																																																																			C|0.363;T|0.637	0.637	strong		0.542	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
Unknown	0	hgsc.bcm.edu	37	11	89819431	89819431	+	IGR	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:89819431C>T								TRIM49C (12873 upstream) : SNORD56 (32127 downstream)																							AGGCCCCTTACTGCTTACAAT	0.428																																					p.T105I		Atlas-SNP	.											.	.	.	.	0			c.C314T						PASS	.						97.0	72.0	80.0					11																	89819431		682	1559	2241	SO:0001628	intergenic_variant	642623	exon1			CCCTTACTGCTTA																													11.37:g.89819431C>T		Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	411	270	0.656934	NM_001143975		Missense_Mutation	SNP		37																																																																																				.	.	none	0	0.428								
PCMT1	5110	hgsc.bcm.edu	37	6	150114745	150114745	+	Missense_Mutation	SNP	G	G	A	rs4816	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:150114745G>A	ENST00000367380.5	+	5	565	c.358G>A	c.(358-360)Gta>Ata	p.V120I	RP11-350J20.5_ENST00000455607.2_RNA|PCMT1_ENST00000544496.1_Missense_Mutation_p.V85I|PCMT1_ENST00000367378.1_Missense_Mutation_p.V178I|PCMT1_ENST00000464889.1_Missense_Mutation_p.V178I|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	185	0	0		WXS	Illumina HiSeq	Phase_I	174	96	0.551724	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			
HELQ	113510	hgsc.bcm.edu	37	4	84370091	84370091	+	Silent	SNP	A	A	G	rs13141136	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:84370091A>G	ENST00000295488.3	-	3	1198	c.1036T>C	c.(1036-1038)Ttg>Ctg	p.L346L	HELQ_ENST00000510985.1_Silent_p.L346L	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	346	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						ACAGAATTCAATGTTAAACAA	0.318								Other identified genes with known or suspected DNA repair function					A|||	2076	0.414537	0.1059	0.5245	5008	,	,		16998	0.6766		0.3787	False		,,,				2504	0.5204				p.L346L		Atlas-SNP	.											.	HELQ	95	.	0			c.T1036C						PASS	.	A		687,3715	266.2+/-267.1	54,579,1568	37.0	37.0	37.0		1036	-6.4	0.3	4	dbSNP_121	37	3504,5090	492.3+/-373.3	712,2080,1505	no	coding-synonymous	HELQ	NM_133636.2		766,2659,3073	GG,GA,AA		40.7726,15.6065,32.2484		346/1102	84370091	4191,8805	2201	4297	6498	SO:0001819	synonymous_variant	113510	exon3			AATTCAATGTTAA	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1036T>C	4.37:g.84370091A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			A|0.654;G|0.346	0.346	strong		0.318	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
TSHZ1	10194	hgsc.bcm.edu	37	18	72997677	72997677	+	Silent	SNP	C	C	T	rs3826609	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	67	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	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	
RASAL1	8437	hgsc.bcm.edu	37	12	113541999	113541999	+	Silent	SNP	C	C	T	rs148186900	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113541999C>T	ENST00000261729.5	-	18	2247	c.1932G>A	c.(1930-1932)acG>acA	p.T644T	RASAL1_ENST00000446861.3_Silent_p.T616T|RASAL1_ENST00000546530.1_Silent_p.T646T|RASAL1_ENST00000548055.1_Silent_p.T645T|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	644	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						GCAGCGCCCCCGTGCCGTCCT	0.697													C|||	15	0.00299521	0.0	0.0144	5008	,	,		14490	0.0		0.001	False		,,,				2504	0.0041				p.T646T		Atlas-SNP	.											RASAL1,NS,carcinoma,-1,1	RASAL1	89	1	0			c.G1938A						scavenged	.	C	,,	8,4392		0,8,2192	29.0	26.0	27.0		1938,1848,1932	-5.9	0.1	12	dbSNP_134	27	42,8554		0,42,4256	no	coding-synonymous,coding-synonymous,coding-synonymous	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	,,	0,50,6448	TT,TC,CC		0.4886,0.1818,0.3847	,,	646/807,616/777,644/805	113541999	50,12946	2200	4298	6498	SO:0001819	synonymous_variant	8437	exon18			CGCCCCCGTGCCG	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.1932G>A	12.37:g.113541999C>T		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	308	4	0.012987	NM_001193520	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Silent	SNP	ENST00000261729.5	37	CCDS9165.1																																																																																			C|0.997;T|0.003	0.003	strong		0.697	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
LATS2	26524	hgsc.bcm.edu	37	13	21562832	21562832	+	Missense_Mutation	SNP	C	C	T	rs2770928	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:21562832C>T	ENST00000382592.4	-	4	1492	c.1087G>A	c.(1087-1089)Ggc>Agc	p.G363S	LATS2_ENST00000542899.1_Missense_Mutation_p.G363S|LATS2_ENST00000472754.1_5'Flank	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		GAGGTGCTGCCCAATTCATAC	0.716													T|||	4258	0.85024	0.6876	0.9135	5008	,	,		9653	0.997		0.8767	False		,,,				2504	0.8466				p.G363S		Atlas-SNP	.											LATS2_ENST00000382592,NS,carcinoma,0,1	LATS2	176	1	0			c.G1087A						PASS	.	T	SER/GLY	3174,1152		1175,824,164	25.0	27.0	26.0		1087	-1.1	0.0	13	dbSNP_100	26	7379,969		3255,869,50	yes	missense	LATS2	NM_014572.2	56	4430,1693,214	TT,TC,CC		11.6076,26.6297,16.735	benign	363/1089	21562832	10553,2121	2163	4174	6337	SO:0001583	missense	26524	exon4			TGCTGCCCAATTC	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.1087G>A	13.37:g.21562832C>T	ENSP00000372035:p.Gly363Ser	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	1898	0.8690476190476191	334	0.6788617886178862	330	0.9116022099447514	572	1.0	662	0.8733509234828496	T	4.469	0.087000	0.08583	0.733703	0.883924	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.57436	0.4;0.4	4.94	-1.07	0.09968	.	1.091720	0.06907	N	0.806929	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.47315	-0.9127	9	0.02654	T	1	.	11.4202	0.49976	0.0:0.4735:0.0:0.5265	rs2770928;rs60641998	363	Q9NRM7	LATS2_HUMAN	S	363	ENSP00000372035:G363S;ENSP00000441817:G363S	ENSP00000372035:G363S	G	-	1	0	LATS2	20460832	0.893000	0.30496	0.000000	0.03702	0.051000	0.14879	0.768000	0.26590	-0.622000	0.05626	-1.487000	0.00979	GGC	T|0.842;G|0.000;C|0.158;A|0.000	0.842	strong		0.716	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
NAP1L3	4675	hgsc.bcm.edu	37	X	92927728	92927728	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:92927728T>C	ENST00000373079.3	-	1	839	c.576A>G	c.(574-576)gaA>gaG	p.E192E	FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000322139.4_5'Flank|NAP1L3_ENST00000475430.2_Silent_p.E185E|FAM133A_ENST00000332647.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	192	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						GGTTTTCTTCTTCCTCACCCT	0.438																																					p.E192E		Atlas-SNP	.											.	NAP1L3	81	.	0			c.A576G						PASS	.						80.0	79.0	79.0					X																	92927728		2203	4300	6503	SO:0001819	synonymous_variant	4675	exon1			TTCTTCTTCCTCA		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.576A>G	X.37:g.92927728T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	78	5	0.0641026	NM_004538	B2RCM0|O60788	Silent	SNP	ENST00000373079.3	37	CCDS14465.1																																																																																			.	.	none		0.438	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538	
KLHL13	90293	hgsc.bcm.edu	37	X	117053499	117053499	+	Silent	SNP	C	C	T	rs6645994	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:117053499C>T	ENST00000262820.3	-	4	1464	c.555G>A	c.(553-555)gtG>gtA	p.V185V	KLHL13_ENST00000371878.1_Silent_p.V134V|KLHL13_ENST00000371882.1_Silent_p.V134V|KLHL13_ENST00000540167.1_Silent_p.V169V|KLHL13_ENST00000545703.1_Silent_p.V143V|KLHL13_ENST00000539496.1_Silent_p.V188V|KLHL13_ENST00000541812.1_Silent_p.V169V|KLHL13_ENST00000469946.1_Silent_p.V134V|KLHL13_ENST00000371876.1_Silent_p.V134V	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	185					cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						ATATGAGAAACACTTTACAGA	0.403													T|||	956	0.253245	0.6142	0.0793	3775	,	,		12883	0.0		0.0537	False		,,,				2504	0.0358				p.V188V		Atlas-SNP	.											.	KLHL13	87	.	0			c.G564A						PASS	.	T	,,,,,	2628,1207		767,687,407,178,164	72.0	84.0	80.0		564,537,507,507,429,555	-7.5	0.6	X	dbSNP_116	80	513,6215		22,320,149,2086,1723	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLHL13	NM_001168299.1,NM_001168300.1,NM_001168301.1,NM_001168302.1,NM_001168303.1,NM_033495.3	,,,,,	789,1007,556,2264,1887	TT,TC,T,CC,C		7.6249,31.4733,29.7359	,,,,,	188/659,179/650,169/640,169/640,143/614,185/656	117053499	3141,7422	2203	4300	6503	SO:0001819	synonymous_variant	90293	exon5			GAGAAACACTTTA	AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"""Kelch-like"", ""BTB/POZ domain containing"""	22931	protein-coding gene	gene with protein product		300655	"""BTB and kelch domain containing 2, KIAA1309"", ""kelch-like 13 (Drosophila)"""	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.555G>A	X.37:g.117053499C>T		Somatic	393	0	0		WXS	Illumina HiSeq	Phase_I	132	129	0.977273	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Silent	SNP	ENST00000262820.3	37	CCDS14571.1																																																																																			C|0.688;0|0.003	.	strong		0.403	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495	
CPSF4	10898	hgsc.bcm.edu	37	7	99050039	99050039	+	Silent	SNP	G	G	A	rs17854665	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99050039G>A	ENST00000292476.5	+	6	556	c.546G>A	c.(544-546)ccG>ccA	p.P182P	CPSF4_ENST00000441580.1_Silent_p.P129P|CPSF4_ENST00000451876.1_Silent_p.P150P|ATP5J2_ENST00000466753.1_Intron|ATP5J2-PTCD1_ENST00000413834.1_Intron|ATP5J2-PTCD1_ENST00000437572.1_Intron|PTCD1_ENST00000555673.1_Intron|CPSF4_ENST00000436336.2_Silent_p.P182P|CPSF4_ENST00000471455.1_3'UTR			O95639	CPSF4_HUMAN	cleavage and polyadenylation specific factor 4, 30kDa	182					modification by virus of host mRNA processing (GO:0046778)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|mRNA processing (GO:0006397)|viral life cycle (GO:0019058)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(5)	14	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CCCCACTGCCGCAGCAGACAC	0.607													G|||	461	0.0920527	0.2352	0.0648	5008	,	,		19334	0.0317		0.0308	False		,,,				2504	0.0429				p.P182P		Atlas-SNP	.											.	CPSF4	24	.	0			c.G546A						PASS	.	G	,,	846,3560	332.5+/-302.5	79,688,1436	117.0	121.0	119.0		546,,546	-11.4	0.3	7	dbSNP_123	119	351,8249	118.6+/-178.1	9,333,3958	no	coding-synonymous,intron,coding-synonymous	CPSF4,ATP5J2-PTCD1	NM_001081559.1,NM_001198879.1,NM_006693.2	,,	88,1021,5394	AA,AG,GG		4.0814,19.2011,9.2034	,,	182/245,,182/270	99050039	1197,11809	2203	4300	6503	SO:0001819	synonymous_variant	10898	exon6			ACTGCCGCAGCAG		CCDS5664.1, CCDS47652.1	7q22	2007-10-18	2002-08-29		ENSG00000160917	ENSG00000160917			2327	protein-coding gene	gene with protein product		603052	"""cleavage and polyadenylation specific factor 4, 30kD subunit"""			9651582, 9224719	Standard	NM_006693		Approved	NAR, CPSF30	uc003uqj.3	O95639	OTTHUMG00000154599	ENST00000292476.5:c.546G>A	7.37:g.99050039G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_001081559	D6W5S8|Q6FGE6|Q86TF8|Q9BTW6	Silent	SNP	ENST00000292476.5	37	CCDS5664.1	178|178	0.0815018315018315|0.0815018315018315	107|107	0.21747967479674796|0.21747967479674796	30|30	0.08287292817679558|0.08287292817679558	17|17	0.02972027972027972|0.02972027972027972	24|24	0.0316622691292876|0.0316622691292876	G|G	16.75|16.75	3.209745|3.209745	0.58343|0.58343	0.192011|0.192011	0.040814|0.040814	ENSG00000160917|ENSG00000160917	ENST00000440514|ENST00000452047	.|T	.|0.33438	.|1.41	5.71|5.71	-11.4|-11.4	0.00090|0.00090	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999989511|0.9999999999989511	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.10314|0.10314	-1.0635|-1.0635	3|4	.|.	.|.	.|.	-11.2942|-11.2942	5.2709|5.2709	0.15624|0.15624	0.6014:0.1406:0.145:0.113|0.6014:0.1406:0.145:0.113	rs17854665;rs60730079;rs17854665|rs17854665;rs60730079;rs17854665	.|.	.|.	.|.	T|H	64|118	.|ENSP00000392584:R118H	.|.	A|R	+|+	1|2	0|0	CPSF4|CPSF4	98887975|98887975	0.107000|0.107000	0.21998|0.21998	0.299000|0.299000	0.25016|0.25016	0.966000|0.966000	0.64601|0.64601	-0.743000|-0.743000	0.04845|0.04845	-2.112000|-2.112000	0.00835|0.00835	-1.202000|-1.202000	0.01658|0.01658	GCA|CGC	G|0.909;A|0.091	0.091	strong		0.607	CPSF4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336254.1		
GRIN3A	116443	hgsc.bcm.edu	37	9	104385711	104385711	+	Missense_Mutation	SNP	C	C	T	rs10989563|rs35768024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:104385711C>T	ENST00000361820.3	-	5	3103	c.2503G>A	c.(2503-2505)Gat>Aat	p.D835N		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	835			D -> N (in dbSNP:rs10989563). {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)	TTCTCTGGATCATTCCTATAT	0.438													C|||	659	0.131589	0.0703	0.1671	5008	,	,		19009	0.0466		0.2386	False		,,,				2504	0.1667				p.D835N		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G2503A						PASS	.	C	ASN/ASP	396,4010		22,352,1829	116.0	105.0	109.0		2503	5.7	1.0	9	dbSNP_120	109	1649,6951		257,1135,2908	yes	missense	GRIN3A	NM_133445.2	23	279,1487,4737	TT,TC,CC		19.1744,8.9877,15.7235	probably-damaging	835/1116	104385711	2045,10961	2203	4300	6503	SO:0001583	missense	116443	exon5			CTGGATCATTCCT		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.2503G>A	9.37:g.104385711C>T	ENSP00000355155:p.Asp835Asn	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	168	84	0.5	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	251	0.11492673992673992	24	0.04878048780487805	63	0.17403314917127072	22	0.038461538461538464	142	0.18733509234828497	C	28.4	4.921160	0.92249	0.089877	0.191744	ENSG00000198785	ENST00000361820	T	0.27104	1.69	5.72	5.72	0.89469	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.113021	0.64402	D	0.000020	T	0.00109	0.0003	L	0.57536	1.79	0.09310	P	0.9999999709858	D	0.76494	0.999	D	0.72338	0.977	T	0.00081	-1.2106	9	0.25751	T	0.34	.	19.8937	0.96942	0.0:1.0:0.0:0.0	rs10989563;rs10989563	835	Q8TCU5	NMD3A_HUMAN	N	835	ENSP00000355155:D835N	ENSP00000355155:D835N	D	-	1	0	GRIN3A	103425532	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.716000	0.92895	0.650000	0.86243	GAT	CA|0.500;TG|0.500	.	alt		0.438	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
UPK1A	11045	hgsc.bcm.edu	37	19	36157740	36157740	+	Missense_Mutation	SNP	C	C	T	rs61741212	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36157740C>T	ENST00000222275.2	+	1	26	c.26C>T	c.(25-27)gCc>gTc	p.A9V	UPK1A_ENST00000379013.2_Missense_Mutation_p.A9V|RN7SL765P_ENST00000580260.1_RNA|UPK1A-AS1_ENST00000443196.1_RNA	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	9					epithelial cell differentiation (GO:0030855)|protein oligomerization (GO:0051259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	monosaccharide binding (GO:0048029)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(2)|stomach(2)	9	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)			GCAGCGGAGGCCGAGAAGGGA	0.612													C|||	764	0.152556	0.2753	0.0562	5008	,	,		17149	0.0278		0.1123	False		,,,				2504	0.2249				p.A9V		Atlas-SNP	.											.	UPK1A	23	.	0			c.C26T						PASS	.	C	VAL/ALA	1011,3395	375.1+/-321.5	123,765,1315	147.0	136.0	139.0		26	-3.1	0.0	19	dbSNP_129	139	949,7651	209.6+/-250.7	53,843,3404	yes	missense	UPK1A	NM_007000.2	64	176,1608,4719	TT,TC,CC		11.0349,22.946,15.07	benign	9/259	36157740	1960,11046	2203	4300	6503	SO:0001583	missense	11045	exon1			CGGAGGCCGAGAA	AF085807	CCDS12470.1, CCDS62640.1	19q13.1	2013-02-14			ENSG00000105668	ENSG00000105668		"""Tetraspanins"""	12577	protein-coding gene	gene with protein product		611557				9846985, 10404304	Standard	NM_007000		Approved	TSPAN21	uc002oaw.3	O00322	OTTHUMG00000048115	ENST00000222275.2:c.26C>T	19.37:g.36157740C>T	ENSP00000222275:p.Ala9Val	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	235	107	0.455319	NM_007000	Q3KNU5|Q3KNU6	Missense_Mutation	SNP	ENST00000222275.2	37	CCDS12470.1	259	0.11858974358974358	130	0.26422764227642276	27	0.07458563535911603	14	0.024475524475524476	88	0.11609498680738786	C	13.21	2.167807	0.38315	0.22946	0.110349	ENSG00000105668	ENST00000222275;ENST00000379013	T;T	0.06849	3.43;3.25	4.23	-3.14	0.05250	.	1.673270	0.03514	N	0.219987	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.0	T	0.46965	-0.9153	9	0.30854	T	0.27	.	1.2775	0.02033	0.1348:0.2769:0.1798:0.4085	rs61741212	9;9	O00322-2;O00322	.;UPK1A_HUMAN	V	9	ENSP00000222275:A9V;ENSP00000368298:A9V	ENSP00000222275:A9V	A	+	2	0	UPK1A	40849580	0.000000	0.05858	0.002000	0.10522	0.060000	0.15804	-1.225000	0.02956	-0.417000	0.07461	0.655000	0.94253	GCC	C|0.856;T|0.144	0.144	strong		0.612	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3		
CEACAM20	125931	hgsc.bcm.edu	37	19	45029208	45029208	+	RNA	SNP	G	G	A	rs10408247	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45029208G>A	ENST00000454753.1	-	0	400							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)				ACTTTGGGTGGCATCAAGTGG	0.567													G|||	1455	0.290535	0.6445	0.2911	5008	,	,		18869	0.1815		0.0765	False		,,,				2504	0.1442				p.A41V		Atlas-SNP	.											.	CEACAM20	31	.	0			c.C122T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	2132,2024		560,1012,506	115.0	123.0	120.0		122,122,122,122	0.0	0.0	19	dbSNP_119	120	731,7695		31,669,3513	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	64,64,64,64	591,1681,4019	AA,AG,GG		8.6755,48.7007,22.7547	benign,benign,benign,benign	41/597,41/492,41/504,41/585	45029208	2863,9719	2078	4213	6291			125931	exon2			TGGGTGGCATCAA	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.45029208G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	238	105	0.441176	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				G|0.725;A|0.275	0.275	strong		0.567	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
NLRP5	126206	hgsc.bcm.edu	37	19	56549532	56549532	+	Silent	SNP	A	A	G	rs306447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56549532A>G	ENST00000390649.3	+	10	2757	c.2757A>G	c.(2755-2757)agA>agG	p.R919R		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	919					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.R919R(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)		ATGCCTTGAGAGTCTCCCAGT	0.522													G|||	1518	0.303115	0.4834	0.1758	5008	,	,		21896	0.3016		0.2406	False		,,,				2504	0.2157				p.R919R		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - coding silent(1)	stomach(1)	c.A2757G						PASS	.	G		1782,2452		384,1014,719	133.0	134.0	134.0		2757	-2.2	0.0	19	dbSNP_79	134	1872,6602		218,1436,2583	no	coding-synonymous	NLRP5	NM_153447.4		602,2450,3302	GG,GA,AA		22.0911,42.0879,28.7535		919/1201	56549532	3654,9054	2117	4237	6354	SO:0001819	synonymous_variant	126206	exon10			CTTGAGAGTCTCC	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.2757A>G	19.37:g.56549532A>G		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	207	97	0.468599	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			A|0.693;G|0.307	0.307	strong		0.522	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
BOD1L1	259282	hgsc.bcm.edu	37	4	13602793	13602793	+	Missense_Mutation	SNP	C	C	G	rs199927242		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:13602793C>G	ENST00000040738.5	-	10	5866	c.5731G>C	c.(5731-5733)Gtg>Ctg	p.V1911L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1911						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGCTCTACCACAGTACCAATC	0.443													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23179	0.0		0.0	False		,,,				2504	0.0				p.V1911L		Atlas-SNP	.											.	.	.	.	0			c.G5731C						PASS	.	C	LEU/VAL	1,4405	2.1+/-5.4	0,1,2202	119.0	118.0	118.0		5731	2.8	0.0	4		118	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BOD1L	NM_148894.2	32	0,2,6501	GG,GC,CC		0.0116,0.0227,0.0154	benign	1911/3052	13602793	2,13004	2203	4300	6503	SO:0001583	missense	259282	exon10			CTACCACAGTACC	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.5731G>C	4.37:g.13602793C>G	ENSP00000040738:p.Val1911Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	147	68	0.462585	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	5.583	0.292461	0.10567	2.27E-4	1.16E-4	ENSG00000038219	ENST00000040738	T	0.08807	3.05	4.79	2.8	0.32819	.	0.896444	0.09441	N	0.801789	T	0.06050	0.0157	N	0.19112	0.55	0.09310	N	1	B	0.22003	0.063	B	0.19148	0.024	T	0.40232	-0.9574	10	0.33940	T	0.23	0.4353	7.6976	0.28604	0.0:0.7633:0.0:0.2367	.	1911	Q8NFC6	BOD1L_HUMAN	L	1911	ENSP00000040738:V1911L	ENSP00000040738:V1911L	V	-	1	0	BOD1L	13211891	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	0.762000	0.26503	0.812000	0.34326	0.561000	0.74099	GTG	.	.	weak		0.443	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
DES	1674	hgsc.bcm.edu	37	2	220286142	220286142	+	Silent	SNP	G	G	A	rs1058284	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	89	64	0.719101	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	
OR10G3	26533	hgsc.bcm.edu	37	14	22038525	22038525	+	Silent	SNP	G	G	T	rs11626693	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:22038525G>T	ENST00000303532.1	-	1	350	c.351C>A	c.(349-351)acC>acA	p.T117T		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	117						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(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		AGGCCATTAGGGTGTAGAGGA	0.527													G|||	1822	0.363818	0.5371	0.2277	5008	,	,		21719	0.2966		0.3072	False		,,,				2504	0.3538				p.T117T		Atlas-SNP	.											.	OR10G3	40	.	0			c.C351A						PASS	.	G		2158,2248	583.6+/-385.9	549,1060,594	58.0	56.0	56.0		351	-3.3	0.1	14	dbSNP_120	56	2429,6171	401.1+/-347.0	347,1735,2218	no	coding-synonymous	OR10G3	NM_001005465.1		896,2795,2812	TT,TG,GG		28.2442,48.9787,35.2683		117/314	22038525	4587,8419	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			CATTAGGGTGTAG		CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"""GPCR / Class A : Olfactory receptors"""	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.351C>A	14.37:g.22038525G>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	178	68	0.382022	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			G|0.656;T|0.344	0.344	strong		0.527	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
C19orf44	84167	hgsc.bcm.edu	37	19	16612011	16612011	+	Silent	SNP	T	T	C	rs728117	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:16612011T>C	ENST00000221671.3	+	2	564	c.408T>C	c.(406-408)tcT>tcC	p.S136S	C19orf44_ENST00000594035.1_Silent_p.S136S|CTD-3222D19.2_ENST00000409035.1_Intron	NM_032207.2	NP_115583.1	Q9H6X5	CS044_HUMAN	chromosome 19 open reading frame 44	136										endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(2)	16						GAATCCTCTCTGGGGGTGCAC	0.512													C|||	1835	0.366414	0.643	0.3415	5008	,	,		17337	0.1736		0.3221	False		,,,				2504	0.2546				p.S136S		Atlas-SNP	.											.	C19orf44	47	.	0			c.T408C						PASS	.	C		2698,1708	509.6+/-367.3	843,1012,348	55.0	61.0	59.0		408	-2.9	0.0	19	dbSNP_86	59	2642,5958	684.2+/-403.9	411,1820,2069	no	coding-synonymous	C19orf44	NM_032207.2		1254,2832,2417	CC,CT,TT		30.7209,38.7653,41.058		136/658	16612011	5340,7666	2203	4300	6503	SO:0001819	synonymous_variant	84167	exon2			CCTCTCTGGGGGT	AK025395	CCDS12345.1, CCDS74306.1	19p13.11	2011-11-24			ENSG00000105072	ENSG00000105072			26141	protein-coding gene	gene with protein product						12477932	Standard	NM_032207		Approved	FLJ21742	uc002neh.1	Q9H6X5		ENST00000221671.3:c.408T>C	19.37:g.16612011T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_032207	Q8N6Y7	Silent	SNP	ENST00000221671.3	37	CCDS12345.1																																																																																			T|0.663;C|0.337	0.337	strong		0.512	C19orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461218.1	NM_032207	
CLCN7	1186	hgsc.bcm.edu	37	16	1504437	1504437	+	Silent	SNP	C	C	T	rs12935737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1504437C>T	ENST00000382745.4	-	13	1733	c.1128G>A	c.(1126-1128)ccG>ccA	p.P376P	CLCN7_ENST00000262318.8_Silent_p.P352P|LA16c-390E6.4_ENST00000563610.1_RNA|CLCN7_ENST00000448525.1_Silent_p.P352P	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	376					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				CGATGAAGACCGGGATCTCGT	0.597													C|||	187	0.0373403	0.0197	0.0706	5008	,	,		19133	0.0		0.0875	False		,,,				2504	0.0245				p.P376P		Atlas-SNP	.											CLCN7,NS,carcinoma,0,1	CLCN7	53	1	0			c.G1128A						PASS	.	C	,	149,4249	102.5+/-141.1	0,149,2050	121.0	94.0	103.0		1056,1128	-4.9	0.9	16	dbSNP_121	103	889,7711	198.5+/-242.8	42,805,3453	no	coding-synonymous,coding-synonymous	CLCN7	NM_001114331.1,NM_001287.4	,	42,954,5503	TT,TC,CC		10.3372,3.3879,7.9858	,	352/782,376/806	1504437	1038,11960	2199	4300	6499	SO:0001819	synonymous_variant	1186	exon13			GAAGACCGGGATC	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.1128G>A	16.37:g.1504437C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			C|0.926;T|0.074	0.074	strong		0.597	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
SCN5A	6331	hgsc.bcm.edu	37	3	38645420	38645420	+	Missense_Mutation	SNP	T	T	C	rs1805124	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38645420T>C	ENST00000333535.4	-	12	1822	c.1673A>G	c.(1672-1674)cAc>cGc	p.H558R	SCN5A_ENST00000425664.1_Missense_Mutation_p.H558R|SCN5A_ENST00000423572.2_Missense_Mutation_p.H558R|SCN5A_ENST00000450102.2_Missense_Mutation_p.H558R|SCN5A_ENST00000449557.2_Missense_Mutation_p.H558R|SCN5A_ENST00000455624.2_Missense_Mutation_p.H558R|SCN5A_ENST00000451551.2_Missense_Mutation_p.H558R|SCN5A_ENST00000413689.1_Missense_Mutation_p.H558R|SCN5A_ENST00000414099.2_Missense_Mutation_p.H558R|SCN5A_ENST00000443581.1_Missense_Mutation_p.H558R			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	558			H -> R (channels properties are similar to wild-type; the double mutant Arg-558/ Ile-512 channel shows that Arg-558 eliminates the negative shift induced by Ile-512 but only partially restores the kinetic abnormalities; can modulate the gating defects caused by Ala-2006 and other mutations; dbSNP:rs1805124). {ECO:0000269|PubMed:11997281, ECO:0000269|PubMed:12051963, ECO:0000269|PubMed:12454206, ECO:0000269|PubMed:12569159, ECO:0000269|PubMed:14500339, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18368697, ECO:0000269|PubMed:18378609}.		AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CAGTGATGTGTGGTGGCTCTC	0.627													C|||	1154	0.230431	0.3094	0.2277	5008	,	,		17254	0.1012		0.2167	False		,,,				2504	0.273				p.H558R		Atlas-SNP	.											SCN5A_ENST00000413689,colon,carcinoma,0,3	SCN5A	634	3	0			c.A1673G	GRCh37	CM031355	SCN5A	M	rs1805124	scavenged	.	C	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	1151,3037		156,839,1099	48.0	54.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1673,1673,1673,1673,1673,1673	2.4	1.0	3	dbSNP_89	52	1957,6475		248,1461,2507	yes	missense,missense,missense,missense,missense,missense	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	29,29,29,29,29,29	404,2300,3606	CC,CT,TT		23.2092,27.4833,24.6276	benign,benign,benign,benign,benign,benign	558/2016,558/2017,558/1999,558/1984,558/1963,558/2017	38645420	3108,9512	2094	4216	6310	SO:0001583	missense	6331	exon12			GATGTGTGGTGGC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1673A>G	3.37:g.38645420T>C	ENSP00000328968:p.His558Arg	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	196	71	0.362245	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	450	0.20604395604395603	147	0.29878048780487804	75	0.20718232044198895	63	0.11013986013986014	165	0.21767810026385223	C	0.349	-0.945829	0.02304	0.274833	0.232092	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.94613	-3.39;-3.41;-3.41;-3.46;-3.41;-3.39;-3.42;-3.47;-3.46;-3.46	4.27	2.44	0.29823	Domain of unknown function DUF3451 (1);	0.329193	0.30602	N	0.009278	T	0.00012	0.0000	N	0.00114	-2.085	0.44771	P	0.0022280000000000078	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	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.45702	-0.9243	9	0.02654	T	1	.	15.5745	0.76365	0.0:0.9158:0.0:0.0842	rs1805124;rs58801095;rs1805124	558;558;558;558;558;558;558	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	R	558	ENSP00000398962:H558R;ENSP00000398266:H558R;ENSP00000410257:H558R;ENSP00000388797:H558R;ENSP00000397915:H558R;ENSP00000416634:H558R;ENSP00000328968:H558R;ENSP00000399524:H558R;ENSP00000403355:H558R;ENSP00000413996:H558R	ENSP00000328968:H558R	H	-	2	0	SCN5A	38620424	0.998000	0.40836	0.992000	0.48379	0.570000	0.35934	1.656000	0.37355	0.109000	0.17891	-2.400000	0.00224	CAC	T|0.790;C|0.210	0.210	strong		0.627	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
SEMA4G	57715	hgsc.bcm.edu	37	10	102743494	102743494	+	Missense_Mutation	SNP	G	G	A	rs41291464	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102743494G>A	ENST00000370250.4	+	14	2496	c.2123G>A	c.(2122-2124)cGc>cAc	p.R708H	MRPL43_ENST00000370241.3_Intron|RP11-108L7.4_ENST00000447344.1_RNA|SEMA4G_ENST00000210633.3_Missense_Mutation_p.R713H|MRPL43_ENST00000299179.5_Intron|MRPL43_ENST00000493646.1_5'Flank|MRPL43_ENST00000342071.1_Intron|MRPL43_ENST00000370242.4_Intron|SEMA4G_ENST00000517724.1_Intron|MRPL43_ENST00000318325.2_Intron	NM_017893.3	NP_060363.2	Q9NTN9	SEM4G_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G	708					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Colorectal(252;0.234)		Epithelial(162;3.71e-09)|all cancers(201;2.1e-07)		AGACGAGGGCGCCGACGGAAA	0.632													g|||	37	0.00738818	0.0	0.0101	5008	,	,		12493	0.0		0.0249	False		,,,				2504	0.0051				p.R713H		Atlas-SNP	.											.	SEMA4G	55	.	0			c.G2138A						PASS	.		,HIS/ARG,,,	35,4371	40.0+/-72.8	0,35,2168	40.0	37.0	38.0		,2138,,,	1.1	0.0	10	dbSNP_127	38	296,8304	106.8+/-167.6	8,280,4012	yes	intron,missense,intron,intron,intron	SEMA4G,MRPL43	NM_001203244.1,NM_017893.3,NM_176792.2,NM_176793.1,NM_176794.1	,29,,,	8,315,6180	AA,AG,GG		3.4419,0.7944,2.545	,benign,,,	,713/844,,,	102743494	331,12675	2203	4300	6503	SO:0001583	missense	57715	exon14			GAGGGCGCCGACG	AB046839	CCDS7501.1, CCDS55724.1	10q24.31	2013-01-11			ENSG00000095539	ENSG00000095539		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10735	protein-coding gene	gene with protein product							Standard	NM_017893		Approved	FLJ20590, KIAA1619	uc001krw.2	Q9NTN9	OTTHUMG00000018922	ENST00000370250.4:c.2123G>A	10.37:g.102743494G>A	ENSP00000359270:p.Arg708His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	60	17	0.283333	NM_017893	A1A5C6|A6NJY8|Q58EY1|Q9HCF3	Missense_Mutation	SNP	ENST00000370250.4	37		19	0.0086996336996337	1	0.0020325203252032522	0	0.0	0	0.0	18	0.023746701846965697	g	9.445	1.088965	0.20390	0.007944	0.034419	ENSG00000095539	ENST00000370250;ENST00000210633	T;T	0.20069	2.1;2.16	5.34	1.08	0.20341	.	0.213352	0.23095	N	0.051989	T	0.03564	0.0102	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.20505	-1.0273	10	0.66056	D	0.02	.	9.0697	0.36484	0.2909:0.0:0.7091:0.0	rs41291464	713	Q9NTN9-2	.	H	708;713	ENSP00000359270:R708H;ENSP00000210633:R713H	ENSP00000210633:R713H	R	+	2	0	SEMA4G	102733484	0.000000	0.05858	0.005000	0.12908	0.989000	0.77384	0.033000	0.13754	-0.066000	0.12998	0.550000	0.68814	CGC	G|0.981;A|0.019	0.019	strong		0.632	SEMA4G-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049920.2		
HLA-C	3107	hgsc.bcm.edu	37	6	31237858	31237858	+	Silent	SNP	T	T	C	rs281860578|rs34794906	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31237858T>C	ENST00000376228.5	-	5	914	c.900A>G	c.(898-900)ccA>ccG	p.P300P	HLA-C_ENST00000383329.3_Silent_p.P300P	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	300	Connecting peptide.				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						GCTGGGAAGATGGCTCTGGGA	0.592													t|||	2055	0.410343	0.4463	0.4438	5008	,	,		15975	0.5665		0.337	False		,,,				2504	0.2526				p.P300P		Atlas-SNP	.											.	HLA-C	92	.	0			c.A900G						PASS	.	C		1466,2932		353,760,1086	42.0	43.0	43.0		900	-5.3	0.0	6	dbSNP_126	43	2113,6485		349,1415,2535	no	coding-synonymous	HLA-C	NM_002117.5		702,2175,3621	CC,CT,TT		24.5755,33.3333,27.5392		300/367	31237858	3579,9417	2199	4299	6498	SO:0001819	synonymous_variant	3107	exon5			GGAAGATGGCTCT	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.900A>G	6.37:g.31237858T>C		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	243	70	0.288066	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1																																																																																			T|0.659;C|0.341	0.341	strong		0.592	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
ATAD3C	219293	hgsc.bcm.edu	37	1	1390875	1390875	+	Silent	SNP	C	C	T	rs1781147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1390875C>T	ENST00000378785.2	+	5	1409	c.414C>T	c.(412-414)gaC>gaT	p.D138D		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	138							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	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)		GACCCCAGGACGTGCTGGAGG	0.677													c|||	2129	0.42512	0.528	0.4323	5008	,	,		12946	0.499		0.1879	False		,,,				2504	0.4489				p.D138D		Atlas-SNP	.											ATAD3C,NS,carcinoma,+2,1	ATAD3C	23	1	0			c.C414T						scavenged	.	C		656,728		164,328,200	61.0	62.0	62.0		414	-1.4	0.2	1	dbSNP_89	62	617,2565		72,473,1046	no	coding-synonymous	ATAD3C	NM_001039211.2		236,801,1246	TT,TC,CC		19.3903,47.3988,27.88		138/412	1390875	1273,3293	692	1591	2283	SO:0001819	synonymous_variant	219293	exon5			CCAGGACGTGCTG	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.414C>T	1.37:g.1390875C>T		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	81	14	0.17284	NM_001039211	Q8N1Z5	Silent	SNP	ENST00000378785.2	37	CCDS44039.1																																																																																			C|0.608;T|0.392	0.392	strong		0.677	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
CNR2	1269	hgsc.bcm.edu	37	1	24201919	24201919	+	Silent	SNP	T	T	C	rs35761398|rs2502992	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:24201919T>C	ENST00000374472.4	-	2	350	c.189A>G	c.(187-189)caA>caG	p.Q63Q	CNR2_ENST00000536471.1_Silent_p.Q63Q	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	63			Q -> R (high incidence in Japanese depressed subjects; dbSNP:rs2501432). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18286196}.		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)	p.Q63Q(1)		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)	TCCGGCGGAGTTGGTGGGAGG	0.552													C|||	3275	0.653954	0.7958	0.6383	5008	,	,		19878	0.503		0.5875	False		,,,				2504	0.6973				p.Q63Q		Atlas-SNP	.											CNR2,NS,carcinoma,-1,2	CNR2	78	2	1	Substitution - coding silent(1)	stomach(1)	c.A189G						PASS	.	C		3214,1192		1261,692,250	60.0	70.0	67.0		189	3.0	1.0	1	dbSNP_100	67	4758,3842		1403,1952,945	no	coding-synonymous	CNR2	NM_001841.2		2664,2644,1195	CC,CT,TT		44.6744,27.054,38.7052		63/361	24201919	7972,5034	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			GCGGAGTTGGTGG	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.189A>G	1.37:g.24201919T>C		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			CC|1.000;|0.000	.	alt		0.552	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
PCDHA8	56140	hgsc.bcm.edu	37	5	140222641	140222641	+	Missense_Mutation	SNP	A	A	G	rs6580012	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140222641A>G	ENST00000531613.1	+	1	1735	c.1735A>G	c.(1735-1737)Aag>Gag	p.K579E	PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.K579E|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	579			K -> E (in dbSNP:rs6580012).		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)|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)			CGCAGCGAGCAAGCTGGTGCC	0.677													.|||	2882	0.575479	0.7345	0.562	5008	,	,		14758	0.5268		0.4911	False		,,,				2504	0.5072				p.K579E		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,0,4	PCDHA8	366	4	0			c.A1735G						scavenged	.	G	,,,,,,,GLU/LYS,,,GLU/LYS	3133,1257		1169,795,231	52.0	57.0	55.0		,,,,,,,1735,,,1735	0.4	0.0	5	dbSNP_116	55	4023,4497		1149,1725,1386	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	,,,,,,,56,,,56	2318,2520,1617	GG,GA,AA		47.2183,28.6333,44.5701	,,,,,,,,,,	,,,,,,,579/951,,,579/815	140222641	7156,5754	2195	4260	6455	SO:0001583	missense	56140	exon1			GCGAGCAAGCTGG	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.1735A>G	5.37:g.140222641A>G	ENSP00000434655:p.Lys579Glu	Somatic	46	2	0.0434783		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	1207	0.5526556776556777	350	0.7113821138211383	184	0.5082872928176796	302	0.527972027972028	371	0.4894459102902375	G	1.084	-0.665977	0.03428	0.713667	0.472183	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.19806	2.12;2.12	3.49	0.381	0.16228	Cadherin-like (1);	0.000000	0.36932	N	0.002335	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	0.34750	-0.9816	9	0.02654	T	1	.	6.1288	0.20194	0.2432:0.4246:0.3322:0.0	rs6580012;rs17844319	579;579	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	E	579	ENSP00000434655:K579E;ENSP00000367363:K579E	ENSP00000367363:K579E	K	+	1	0	PCDHA8	140202825	0.192000	0.23301	0.000000	0.03702	0.029000	0.11900	1.550000	0.36223	-0.581000	0.05937	-0.665000	0.03846	AAG	A|0.480;G|0.520	0.520	strong		0.677	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
GNPAT	8443	hgsc.bcm.edu	37	1	231408091	231408091	+	Missense_Mutation	SNP	A	A	G	rs11558492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	289	288	0.99654	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		
FAT4	79633	hgsc.bcm.edu	37	4	126238924	126238924	+	Missense_Mutation	SNP	A	A	T	rs6847454	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:126238924A>T	ENST00000394329.3	+	1	1371	c.1358A>T	c.(1357-1359)cAg>cTg	p.Q453L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	453	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> L (in dbSNP:rs6847454).		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						GCAGCAGTCCAGGCGCGCTCT	0.557											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2135	0.426318	0.615	0.4092	5008	,	,		18623	0.2371		0.4205	False		,,,				2504	0.3845				p.Q453L		Atlas-SNP	.											.	FAT4	1752	.	0			c.A1358T						PASS	.	A	LEU/GLN	2215,1847		622,971,438	43.0	46.0	45.0		1358	-2.6	0.1	4	dbSNP_116	45	3559,4781		753,2053,1364	yes	missense	FAT4	NM_024582.4	113	1375,3024,1802	TT,TA,AA		42.6739,45.4702,46.557	benign	453/4982	126238924	5774,6628	2031	4170	6201	SO:0001583	missense	79633	exon1			CAGTCCAGGCGCG	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.1358A>T	4.37:g.126238924A>T	ENSP00000377862:p.Gln453Leu	Somatic	176	0	0	1548	WXS	Illumina HiSeq	Phase_I	97	20	0.206186	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	914	0.4184981684981685	309	0.6280487804878049	150	0.4143646408839779	134	0.23426573426573427	321	0.4234828496042216	A	1.356	-0.590036	0.03799	0.545298	0.426739	ENSG00000196159	ENST00000394329	T	0.53640	0.61	3.81	-2.64	0.06114	Cadherin (4);Cadherin-like (1);	1.015660	0.07944	U	0.979875	T	0.00012	0.0000	N	0.08118	0	0.38401	P	0.05432099999999995	B	0.09022	0.002	B	0.13407	0.009	T	0.45101	-0.9284	9	0.28530	T	0.3	.	7.174	0.25734	0.3191:0.1978:0.4831:0.0	rs6847454;rs52793335;rs58376448;rs6847454	453	Q6V0I7	FAT4_HUMAN	L	453	ENSP00000377862:Q453L	ENSP00000377862:Q453L	Q	+	2	0	FAT4	126458374	0.049000	0.20398	0.080000	0.20451	0.545000	0.35147	0.150000	0.16263	-0.504000	0.06577	0.459000	0.35465	CAG	A|0.518;T|0.482	0.482	strong		0.557	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
TJP2	9414	hgsc.bcm.edu	37	9	71841018	71841018	+	Silent	SNP	A	A	G	rs17062695	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:71841018A>G	ENST00000377245.4	+	7	1345	c.1137A>G	c.(1135-1137)ctA>ctG	p.L379L	TJP2_ENST00000535702.1_Silent_p.L383L|TJP2_ENST00000539225.1_Silent_p.L410L|TJP2_ENST00000348208.4_Silent_p.L379L|TJP2_ENST00000265384.7_Silent_p.L379L|TJP2_ENST00000453658.2_Silent_p.L356L	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	379	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						AACTACAGCTAGTGGTGTTGA	0.408													A|||	558	0.111422	0.1596	0.1066	5008	,	,		18995	0.1151		0.0616	False		,,,				2504	0.0971				p.L410L		Atlas-SNP	.											.	TJP2	120	.	0			c.A1230G						PASS	.	A	,,,,,	623,3783	272.8+/-271.0	39,545,1619	73.0	71.0	72.0		1068,1149,1230,1137,1137,1137	-12.1	0.2	9	dbSNP_123	72	522,8078	147.4+/-202.8	13,496,3791	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,,,,	52,1041,5410	GG,GA,AA		6.0698,14.1398,8.8036	,,,,,	356/1021,383/1158,410/1222,379/994,379/1191,379/1044	71841018	1145,11861	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon7			ACAGCTAGTGGTG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1137A>G	9.37:g.71841018A>G		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	265	126	0.475472	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			A|0.907;G|0.093	0.093	strong		0.408	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
AKR7A2	8574	hgsc.bcm.edu	37	1	19635011	19635011	+	Missense_Mutation	SNP	C	C	T	rs1043657	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	123	94	0.764228	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	
IMMT	10989	hgsc.bcm.edu	37	2	86385728	86385728	+	Silent	SNP	C	C	T	rs1131071	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:86385728C>T	ENST00000410111.3	-	10	1536	c.1149G>A	c.(1147-1149)ggG>ggA	p.G383G	IMMT_ENST00000449247.2_Silent_p.G372G|IMMT_ENST00000254636.5_Silent_p.G284G|IMMT_ENST00000409051.2_Silent_p.G336G|IMMT_ENST00000442664.2_Silent_p.G382G|IMMT_ENST00000490238.1_5'UTR|Y_RNA_ENST00000363371.1_RNA	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	383					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						TTCCTTTCCACCCAGGAAGGA	0.408													C|||	955	0.190695	0.0166	0.134	5008	,	,		19362	0.4831		0.1153	False		,,,				2504	0.2423				p.G383G		Atlas-SNP	.											.	IMMT	65	.	0			c.G1149A						PASS	.	C	,,	150,3620		1,148,1736	78.0	71.0	73.0		1146,1116,1149	-3.3	1.0	2	dbSNP_86	73	865,7359		46,773,3293	no	coding-synonymous,coding-synonymous,coding-synonymous	IMMT	NM_001100169.1,NM_001100170.1,NM_006839.2	,,	47,921,5029	TT,TC,CC		10.518,3.9788,8.4626	,,	382/758,372/748,383/759	86385728	1015,10979	1885	4112	5997	SO:0001819	synonymous_variant	10989	exon10			TTTCCACCCAGGA	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.1149G>A	2.37:g.86385728C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	113	63	0.557522	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	422	0.19322344322344323	5	0.01016260162601626	60	0.16574585635359115	268	0.46853146853146854	89	0.11741424802110818	C	9.632	1.136682	0.21123	0.039788	0.10518	ENSG00000132305	ENST00000419070	.	.	.	5.95	-3.3	0.05003	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47971	-0.9075	3	.	.	.	-20.4341	3.2081	0.06672	0.1606:0.1607:0.4468:0.2319	rs2288123;rs59197674;rs2288123	.	.	.	M	238	.	.	V	-	1	0	IMMT	86239239	0.989000	0.36119	0.964000	0.40570	0.991000	0.79684	0.164000	0.16542	-0.411000	0.07530	-0.355000	0.07637	GTG	T|0.180;G|0.013	0.180	strong		0.408	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
NBPF14	25832	hgsc.bcm.edu	37	1	148004783	148004783	+	Missense_Mutation	SNP	C	C	A	rs147480284	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:148004783C>A	ENST00000369219.1	-	22	2547	c.2531G>T	c.(2530-2532)aGc>aTc	p.S844I				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	844	NBPF 10. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.S844I(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)					CATCAGCATGCTGTTGAGCCT	0.453													-|||	73	0.0145767	0.0008	0.0187	5008	,	,		15184	0.001		0.0537	False		,,,				2504	0.0041				p.S844I		Atlas-SNP	.											NBPF14,NS,adenoma,0,2	NBPF14	107	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2531T						scavenged	.	C	ILE/SER	84,3292		31,22,1635	72.0	122.0	108.0		2531	0.5	0.0	1	dbSNP_134	108	565,7627		134,297,3665	no	missense	NBPF14	NM_015383.1	142	165,319,5300	AA,AC,CC		6.897,2.4882,5.6103	possibly-damaging	844/922	148004783	649,10919	1688	4096	5784	SO:0001583	missense	25832	exon22			AGCATGCTGTTGA	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.2531G>T	1.37:g.148004783C>A	ENSP00000358221:p.Ser844Ile	Somatic	529	2	0.00378072		WXS	Illumina HiSeq	Phase_I	412	393	0.953883	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		61|61	0.027930402930402932|0.027930402930402932	1|1	0.0020325203252032522|0.0020325203252032522	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	54|54	0.0712401055408971|0.0712401055408971	c|c	9.996|9.996	1.232277|1.232277	0.22626|0.22626	0.024882|0.024882	0.06897|0.06897	ENSG00000122497|ENSG00000122497	ENST00000310701|ENST00000369219;ENST00000369368	.|T	.|0.06608	.|3.28	0.464|0.464	0.464|0.464	0.16706|0.16706	.|DUF1220 (2);	.|.	.|.	.|.	.|.	T|T	0.02571|0.02571	0.0078|0.0078	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B;P;P	.|0.51653	.|0.228;0.947;0.858	.|B;P;P	.|0.54026	.|0.215;0.699;0.74	T|T	0.48068|0.48068	-0.9067|-0.9067	4|8	.|0.21014	.|T	.|0.42	.|.	.|.	.|.	.|.	.|.	.|192;825;844	.|F8WEX8;B4DH59;Q5TI25	.|.;.;NBPFE_HUMAN	S|I	850|844;192	.|ENSP00000358221:S844I	.|ENSP00000358221:S844I	A|S	-|-	1|2	0|0	NBPF14|NBPF14	146471407|146471407	0.009000|0.009000	0.17119|0.17119	0.004000|0.004000	0.12327|0.12327	0.011000|0.011000	0.07611|0.07611	0.685000|0.685000	0.25378|0.25378	0.550000|0.550000	0.28991|0.28991	0.388000|0.388000	0.25769|0.25769	GCA|AGC	C|0.960;A|0.040	0.040	strong		0.453	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383	
BCAN	63827	hgsc.bcm.edu	37	1	156627996	156627996	+	Silent	SNP	T	T	C	rs2298135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156627996T>C	ENST00000329117.5	+	12	2706	c.2370T>C	c.(2368-2370)caT>caC	p.H790H	RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	790	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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 disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGGTGTGGCATGATCAGGGAC	0.592											OREG0013880	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	735	0.146765	0.0219	0.1441	5008	,	,		18252	0.2937		0.0408	False		,,,				2504	0.2751				p.H790H		Atlas-SNP	.											.	BCAN	174	.	0			c.T2370C						PASS	.	T		113,4293	86.3+/-125.0	1,111,2091	131.0	101.0	111.0		2370	-2.2	1.0	1	dbSNP_100	111	322,8278	112.9+/-173.0	5,312,3983	no	coding-synonymous	BCAN	NM_021948.4		6,423,6074	CC,CT,TT		3.7442,2.5647,3.3446		790/912	156627996	435,12571	2203	4300	6503	SO:0001819	synonymous_variant	63827	exon12			GTGGCATGATCAG	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.2370T>C	1.37:g.156627996T>C		Somatic	258	0	0	1779	WXS	Illumina HiSeq	Phase_I	317	103	0.324921	NM_021948	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	37	CCDS1149.1																																																																																			T|0.928;C|0.072	0.072	strong		0.592	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
VNN2	8875	hgsc.bcm.edu	37	6	133073844	133073844	+	Silent	SNP	C	C	T	rs33980664	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:133073844C>T	ENST00000326499.6	-	4	706	c.582G>A	c.(580-582)ccG>ccA	p.P194P	RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000526192.1_5'Flank|VNN2_ENST00000525289.1_Intron|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	84	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	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		
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	98	0	0		WXS	Illumina HiSeq	Phase_I	159	103	0.647799	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		
LCP1	3936	hgsc.bcm.edu	37	13	46705031	46705031	+	Missense_Mutation	SNP	C	C	T	rs534221736		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:46705031C>T	ENST00000398576.2	-	18	2057	c.1669G>A	c.(1669-1671)Gat>Aat	p.D557N	LCP1_ENST00000435666.2_Missense_Mutation_p.D126N|LCP1_ENST00000323076.2_Missense_Mutation_p.D557N			P13796	PLSL_HUMAN	lymphocyte cytosolic protein 1 (L-plastin)	557	Actin-binding 2.|CH 4. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)		TGGATGGCATCGATGAGGTCC	0.423			T	BCL6	NHL								C|||	1	0.000199681	0.0008	0.0	5008	,	,		19094	0.0		0.0	False		,,,				2504	0.0				p.D557N		Atlas-SNP	.		Dom	yes		13	13q14.1-q14.3	3936	lymphocyte cytosolic protein 1 (L-plastin)		L	LCP1,colon,carcinoma,0,1	LCP1	69	1	0			c.G1669A						scavenged	.						198.0	183.0	188.0					13																	46705031		2203	4300	6503	SO:0001583	missense	3936	exon15			TGGCATCGATGAG	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.1669G>A	13.37:g.46705031C>T	ENSP00000381581:p.Asp557Asn	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	231	3	0.012987	NM_002298	B2R613|B4DUA0|Q5TBN4	Missense_Mutation	SNP	ENST00000398576.2	37	CCDS9403.1	.	.	.	.	.	.	.	.	.	.	C	34	5.365069	0.95877	.	.	ENSG00000136167	ENST00000323076;ENST00000398576;ENST00000435666	D;D;D	0.94330	-3.4;-3.4;-3.4	5.36	5.36	0.76844	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.94745	0.8304	L	0.44542	1.39	0.80722	D	1	B;D	0.61697	0.425;0.99	B;D	0.66847	0.242;0.947	D	0.92906	0.6343	10	0.25751	T	0.34	-25.6654	18.4418	0.90669	0.0:1.0:0.0:0.0	.	126;557	B4DUA0;P13796	.;PLSL_HUMAN	N	557;557;126	ENSP00000315757:D557N;ENSP00000381581:D557N;ENSP00000405134:D126N	ENSP00000315757:D557N	D	-	1	0	LCP1	45603032	1.000000	0.71417	0.960000	0.40013	0.925000	0.55904	7.763000	0.85283	2.673000	0.90976	0.609000	0.83330	GAT	.	.	none		0.423	LCP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044800.3	NM_002298	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798259	55798259	+	Missense_Mutation	SNP	G	G	T	rs12224086	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	316	0	0		WXS	Illumina HiSeq	Phase_I	287	127	0.442509	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	
NQO2	4835	hgsc.bcm.edu	37	6	3010390	3010390	+	Missense_Mutation	SNP	C	C	T	rs1143684	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:3010390C>T	ENST00000338130.2	+	6	851	c.139C>T	c.(139-141)Ctt>Ttt	p.L47F	NQO2_ENST00000380430.1_Missense_Mutation_p.L47F|NQO2_ENST00000606474.1_3'UTR|NQO2_ENST00000380455.4_Missense_Mutation_p.L47F|NQO2_ENST00000380454.4_Missense_Mutation_p.L47F|NQO2_ENST00000380441.1_Missense_Mutation_p.L47F			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	47			L -> F (in dbSNP:rs1143684). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1691923, ECO:0000269|PubMed:8182056, ECO:0000269|Ref.3, ECO:0000269|Ref.4, ECO:0000269|Ref.7}.		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)	TGCCATGAACCTTGAGCCGAG	0.423													T|||	3994	0.797524	0.9849	0.768	5008	,	,		17970	0.6558		0.7893	False		,,,				2504	0.7198				p.L47F		Atlas-SNP	.											.	NQO2	21	.	0			c.C139T						PASS	.	T	PHE/LEU	4234,172	113.3+/-151.4	2036,162,5	84.0	76.0	79.0		139	5.6	1.0	6	dbSNP_86	79	6728,1872	334.1+/-320.8	2624,1480,196	yes	missense	NQO2	NM_000904.3	22	4660,1642,201	TT,TC,CC		21.7674,3.9038,15.7158	benign	47/232	3010390	10962,2044	2203	4300	6503	SO:0001583	missense	4835	exon3			ATGAACCTTGAGC	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.139C>T	6.37:g.3010390C>T	ENSP00000337773:p.Leu47Phe	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_000904	B2R492|Q5TD04	Missense_Mutation	SNP	ENST00000338130.2	37	CCDS4481.1	1751	0.8017399267399268	480	0.975609756097561	280	0.7734806629834254	386	0.6748251748251748	605	0.7981530343007915	T	1.141	-0.649564	0.03506	0.960962	0.782326	ENSG00000124588	ENST00000426637;ENST00000380472;ENST00000538898;ENST00000397717;ENST00000338130;ENST00000380441;ENST00000380455;ENST00000380454;ENST00000380430	T;T;T;T;T;T;T;T	0.06142	3.34;3.34;3.34;3.34;3.34;3.34;3.34;3.34	5.63	5.63	0.86233	Flavodoxin-like fold (1);	0.000000	0.85682	N	0.000000	T	0.00241	0.0007	N	0.00004	-3.395	0.48395	P	3.530000000000477E-4	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.39251	-0.9623	9	0.02654	T	1	-12.5742	9.6892	0.40118	0.0:0.0785:0.0:0.9215	rs1143684;rs2756081;rs17856164;rs60515731;rs1143684	47;94	P16083;Q59EN2	NQO2_HUMAN;.	F	47;47;94;47;47;47;47;47;47	ENSP00000406951:L47F;ENSP00000369839:L47F;ENSP00000380829:L47F;ENSP00000337773:L47F;ENSP00000369806:L47F;ENSP00000369822:L47F;ENSP00000369821:L47F;ENSP00000369795:L47F	ENSP00000337773:L47F	L	+	1	0	NQO2	2955389	1.000000	0.71417	0.988000	0.46212	0.159000	0.22180	5.048000	0.64238	0.967000	0.38186	-0.360000	0.07572	CTT	C|0.183;T|0.817	0.817	strong		0.423	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		
PAPOLB	56903	hgsc.bcm.edu	37	7	4900341	4900341	+	Silent	SNP	G	G	A	rs17135247	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:4900341G>A	ENST00000404991.1	-	1	1284	c.1098C>T	c.(1096-1098)agC>agT	p.S366S	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	366					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)			kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		TTTGAAAGAAGCTTGGAGCTT	0.418													G|||	1179	0.235423	0.0325	0.2622	5008	,	,		20833	0.3105		0.2515	False		,,,				2504	0.3967				p.S367S		Atlas-SNP	.											PAPOLB_ENST00000404991,NS,carcinoma,-1,2	PAPOLB	93	2	0			c.C1101T						PASS	.	G	,	281,4119	146.5+/-181.1	9,263,1928	128.0	130.0	129.0		,1101	4.5	1.0	7	dbSNP_123	129	2363,6237	387.8+/-342.3	330,1703,2267	no	intron,coding-synonymous	RADIL,PAPOLB	NM_018059.4,NM_020144.4	,	339,1966,4195	AA,AG,GG		27.4767,6.3864,20.3385	,	,367/638	4900341	2644,10356	2200	4300	6500	SO:0001819	synonymous_variant	56903	exon1			AAAGAAGCTTGGA	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1098C>T	7.37:g.4900341G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	342	108	0.315789	NM_020144	Q75LH1|Q8NE14	Silent	SNP	ENST00000404991.1	37																																																																																				G|0.777;A|0.223	0.223	strong		0.418	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144	
ASB11	140456	hgsc.bcm.edu	37	X	15332558	15332558	+	Intron	SNP	A	A	G	rs5935944	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:15332558A>G	ENST00000480796.1	-	1	232				ASB11_ENST00000537676.1_Silent_p.R17R|ASB11_ENST00000344384.4_Silent_p.R17R|ASB11_ENST00000380470.3_Intron			Q8WXH4	ASB11_HUMAN	ankyrin repeat and SOCS box containing 11, E3 ubiquitin protein ligase						intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(1)	16	Hepatocellular(33;0.183)					ACCTTCTGATACGTTCTGAAA	0.363													A|||	1356	0.359205	0.1059	0.2161	3775	,	,		13644	0.3185		0.2952	False		,,,				2504	0.4581				p.R17R		Atlas-SNP	.											.	ASB11	79	.	0			c.T51C						PASS	.	A	,,	751,3084		61,504,125,1067,446	141.0	125.0	131.0		51,,	5.8	0.1	X	dbSNP_114	131	2634,4094		381,1177,695,870,1177	no	coding-synonymous,intron,intron	ASB11	NM_001012428.2,NM_001201583.1,NM_080873.2	,,	442,1681,820,1937,1623	GG,GA,G,AA,A		39.1498,19.5828,32.0458	,,	17/303,,	15332558	3385,7178	2203	4300	6503	SO:0001627	intron_variant	140456	exon1			TCTGATACGTTCT	AF425642	CCDS14164.1, CCDS35209.1, CCDS56596.1	Xp22.31	2014-02-10	2014-02-10		ENSG00000165192	ENSG00000165192		"""Ankyrin repeat domain containing"""	17186	protein-coding gene	gene with protein product		300626	"""ankyrin repeat and SOCS box-containing 11"", ""ankyrin repeat and SOCS box containing 11"""			24337577	Standard	NM_080873		Approved	DKFZp779E2460	uc004cwp.2	Q8WXH4	OTTHUMG00000021173	ENST00000480796.1:c.181+988T>C	X.37:g.15332558A>G		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001012428	E9PEN1|Q3SYC4|Q7Z667	Silent	SNP	ENST00000480796.1	37	CCDS14164.1																																																																																			A|0.680;0|0.003	.	strong		0.363	ASB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055852.2		
RANBP2	5903	hgsc.bcm.edu	37	2	109374952	109374952	+	Silent	SNP	A	A	G	rs826549	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:109374952A>G	ENST00000283195.6	+	18	2676	c.2550A>G	c.(2548-2550)tcA>tcG	p.S850S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	850					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.S850S(1)	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						GACCAGACTCAGTGCCTGATG	0.423																																					p.S850S		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,1	RANBP2	488	1	1	Substitution - coding silent(1)	stomach(1)	c.A2550G						scavenged	.	G		2554,1850		991,572,639	117.0	171.0	153.0		2550	-2.5	0.6	2	dbSNP_86	153	1455,7145		235,985,3080	no	coding-synonymous	RANBP2	NM_006267.4		1226,1557,3719	GG,GA,AA		16.9186,42.0073,30.829		850/3225	109374952	4009,8995	2202	4300	6502	SO:0001819	synonymous_variant	5903	exon18			AGACTCAGTGCCT	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.2550A>G	2.37:g.109374952A>G		Somatic	338	2	0.00591716		WXS	Illumina HiSeq	Phase_I	227	94	0.414097	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																			A|0.745;G|0.255	0.255	strong		0.423	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
SP140	11262	hgsc.bcm.edu	37	2	231110582	231110582	+	Silent	SNP	C	C	T	rs28445040	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231110582C>T	ENST00000392045.3	+	7	783	c.669C>T	c.(667-669)tcC>tcT	p.S223S	SP140_ENST00000486687.2_Intron|SP140_ENST00000417495.3_Silent_p.S220S|SP140_ENST00000350136.5_Silent_p.S203S|SP140_ENST00000420434.3_Silent_p.S223S|SP140_ENST00000343805.6_Intron	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	223					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		CTGCAGTGTCCTGTAAACTTG	0.403													C|||	546	0.109026	0.1142	0.1124	5008	,	,		22407	0.001		0.168	False		,,,				2504	0.1503				p.S223S		Atlas-SNP	.											.	SP140	121	.	0			c.C669T						PASS	.	C		419,3421		19,381,1520	119.0	107.0	110.0		669	-0.1	0.0	2	dbSNP_125	110	1521,6763		123,1275,2744	no	coding-synonymous	SP140	NM_007237.4		142,1656,4264	TT,TC,CC		18.3607,10.9115,16.0013		223/868	231110582	1940,10184	1920	4142	6062	SO:0001819	synonymous_variant	11262	exon7			AGTGTCCTGTAAA	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"""Zinc fingers, PHD-type"""	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.669C>T	2.37:g.231110582C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	188	64	0.340426	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Silent	SNP	ENST00000392045.3	37	CCDS42831.1																																																																																			C|0.854;T|0.146	0.146	strong		0.403	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237	
NKX2-3	159296	hgsc.bcm.edu	37	10	101293035	101293035	+	Silent	SNP	C	C	A	rs41290504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	114	0	0		WXS	Illumina HiSeq	Phase_I	88	20	0.227273	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		
LRRFIP1	9208	hgsc.bcm.edu	37	2	238668802	238668802	+	Silent	SNP	A	A	G	rs3213868	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238668802A>G	ENST00000392000.4	+	10	960	c.843A>G	c.(841-843)acA>acG	p.T281T	LRRFIP1_ENST00000308482.9_Silent_p.T471T|LRRFIP1_ENST00000289175.6_Silent_p.T225T|LRRFIP1_ENST00000244815.5_Silent_p.T257T	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	281					innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		CCAAGATGACAAAAGAAGAGT	0.448													G|||	1813	0.362021	0.3487	0.3012	5008	,	,		20595	0.505		0.2515	False		,,,				2504	0.3896				p.T471T		Atlas-SNP	.											LRRFIP1_ENST00000392000,colon,carcinoma,+1,3	LRRFIP1	171	3	0			c.A1413G						PASS	.	G	,,,,	1561,2845	669.1+/-402.1	299,963,941	105.0	100.0	102.0		1413,675,843,675,771	-10.8	0.0	2	dbSNP_106	102	2000,6600	722.2+/-406.4	218,1564,2518	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,,,	517,2527,3459	GG,GA,AA		23.2558,35.429,27.3797	,,,,	471/641,225/395,281/809,225/753,257/785	238668802	3561,9445	2203	4300	6503	SO:0001819	synonymous_variant	9208	exon19			GATGACAAAAGAA	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"""GC-binding factor 2"""	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.843A>G	2.37:g.238668802A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Silent	SNP	ENST00000392000.4	37	CCDS46552.1																																																																																			A|0.676;G|0.324	0.324	strong		0.448	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
ANKRD35	148741	hgsc.bcm.edu	37	1	145562087	145562087	+	Missense_Mutation	SNP	G	G	A	rs41315701	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:145562087G>A	ENST00000355594.4	+	10	1862	c.1775G>A	c.(1774-1776)cGa>cAa	p.R592Q		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	592			R -> Q (in dbSNP:rs41315701).							NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CCTGGGGCTCGAGGAGAGCCT	0.582													G|||	619	0.123602	0.0129	0.111	5008	,	,		17919	0.1319		0.2117	False		,,,				2504	0.183				p.R592Q	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G1775A						PASS	.	G	GLN/ARG	231,4175		11,209,1983	37.0	49.0	45.0		1775	0.9	0.0	1	dbSNP_127	45	1959,6639		230,1499,2570	yes	missense	ANKRD35	NM_144698.3	43	241,1708,4553	AA,AG,GG		22.7844,5.2429,16.841	benign	592/1002	145562087	2190,10814	2203	4299	6502	SO:0001583	missense	148741	exon10			GGGCTCGAGGAGA	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1775G>A	1.37:g.145562087G>A	ENSP00000347802:p.Arg592Gln	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	119	32	0.268908	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	316	0.1446886446886447	8	0.016260162601626018	44	0.12154696132596685	95	0.1660839160839161	169	0.22295514511873352	G	3.749	-0.052032	0.07362	0.052429	0.227844	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.44482	0.92	4.87	0.923	0.19413	.	0.734278	0.11613	N	0.546527	T	0.09024	0.0223	L	0.27053	0.805	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.29488	-1.0010	9	0.20046	T	0.44	-1.5743	4.2906	0.10876	0.2782:0.1674:0.5544:0.0	rs41315701	592	Q8N283	ANR35_HUMAN	Q	501;592	ENSP00000347802:R592Q	ENSP00000347802:R592Q	R	+	2	0	ANKRD35	144273444	0.002000	0.14202	0.000000	0.03702	0.073000	0.16967	1.200000	0.32247	0.014000	0.14944	0.655000	0.94253	CGA	G|0.837;A|0.163	0.163	strong		0.582	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
MACROD2	140733	hgsc.bcm.edu	37	20	14066276	14066276	+	Missense_Mutation	SNP	C	C	T	rs2990505	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:14066276C>T	ENST00000310348.4	+	3	173	c.173C>T	c.(172-174)aCt>aTt	p.T58I	MACROD2_ENST00000217246.4_Missense_Mutation_p.T58I			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	58			T -> I (in dbSNP:rs2990505). {ECO:0000269|PubMed:14702039}.		brain development (GO:0007420)|cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.T58I(1)		breast(2)|kidney(4)|large_intestine(5)|lung(8)|skin(1)	20		all_neural(2;0.0381)|Acute lymphoblastic leukemia(2;0.175)				GAAGAAAATACTCAGGAAACA	0.313													C|||	1291	0.257788	0.3056	0.2983	5008	,	,		12783	0.1895		0.2346	False		,,,				2504	0.2587				p.T58I		Atlas-SNP	.											C20orf133,NS,carcinoma,0,1	MACROD2	34	1	1	Substitution - Missense(1)	stomach(1)	c.C173T						PASS	.	C	ILE/THR	1061,2531		162,737,897	59.0	54.0	55.0		173	4.8	1.0	20	dbSNP_101	55	1704,6412		192,1320,2546	yes	missense	MACROD2	NM_080676.5	89	354,2057,3443	TT,TC,CC		20.9956,29.5379,23.6163	benign	58/426	14066276	2765,8943	1796	4058	5854	SO:0001583	missense	140733	exon3			AAAATACTCAGGA	BC101218	CCDS13120.2, CCDS33443.1	20p12.1	2011-04-28	2007-07-24	2007-07-24	ENSG00000172264	ENSG00000172264			16126	protein-coding gene	gene with protein product		611567	"""chromosome 20 open reading frame 133"""	C20orf133			Standard	NM_080676		Approved	dJ631M13.5	uc002wot.3	A1Z1Q3	OTTHUMG00000031919	ENST00000310348.4:c.173C>T	20.37:g.14066276C>T	ENSP00000309809:p.Thr58Ile	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	159	81	0.509434	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	542	0.24816849816849818	158	0.32113821138211385	98	0.27071823204419887	114	0.1993006993006993	172	0.22691292875989447	C	12.51	1.960781	0.34565	0.295379	0.209956	ENSG00000172264	ENST00000217246;ENST00000310348	T;T	0.39997	1.05;1.05	5.76	4.81	0.61882	.	1.553840	0.03488	N	0.216141	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	0.9999999999999948	B;B	0.26975	0.099;0.165	B;B	0.30105	0.015;0.111	T	0.06826	-1.0805	9	0.48119	T	0.1	0.6917	12.9468	0.58376	0.0:0.9198:0.0:0.0802	rs2990505;rs52812396;rs59845301;rs2990505	58;58	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	I	58	ENSP00000217246:T58I;ENSP00000309809:T58I	ENSP00000217246:T58I	T	+	2	0	MACROD2	14014276	0.996000	0.38824	0.985000	0.45067	0.976000	0.68499	2.427000	0.44740	2.724000	0.93272	0.585000	0.79938	ACT	C|0.749;T|0.251	0.251	strong		0.313	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676	
COL5A3	50509	hgsc.bcm.edu	37	19	10114740	10114740	+	Missense_Mutation	SNP	T	T	A	rs62104337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:10114740T>A	ENST00000264828.3	-	5	761	c.676A>T	c.(676-678)Aac>Tac	p.N226Y		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	226	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)			GGTGCCAGGTTGTCACAGTCG	0.592													T|||	570	0.113818	0.0703	0.1383	5008	,	,		18679	0.0169		0.1849	False		,,,				2504	0.182				p.N226Y		Atlas-SNP	.											.	COL5A3	243	.	0			c.A676T						PASS	.	T	TYR/ASN	475,3931	223.6+/-240.1	36,403,1764	97.0	80.0	86.0		676	-9.8	0.0	19	dbSNP_129	86	1715,6885	312.5+/-310.9	166,1383,2751	yes	missense	COL5A3	NM_015719.3	143	202,1786,4515	AA,AT,TT		19.9419,10.7808,16.8384	benign	226/1746	10114740	2190,10816	2203	4300	6503	SO:0001583	missense	50509	exon5			CCAGGTTGTCACA	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.676A>T	19.37:g.10114740T>A	ENSP00000264828:p.Asn226Tyr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	208	107	0.514423	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	227	0.10393772893772894	28	0.056910569105691054	55	0.15193370165745856	7	0.012237762237762238	137	0.18073878627968337	T	11.09	1.537247	0.27475	0.107808	0.199419	ENSG00000080573	ENST00000264828	D	0.89552	-2.53	4.87	-9.75	0.00506	.	1.096820	0.06921	N	0.809338	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	B	0.14805	0.011	B	0.11329	0.006	T	0.30446	-0.9978	9	0.59425	D	0.04	.	5.4774	0.16704	0.0979:0.1549:0.5336:0.2137	rs62104337	226	P25940	CO5A3_HUMAN	Y	226	ENSP00000264828:N226Y	ENSP00000264828:N226Y	N	-	1	0	COL5A3	9975740	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.497000	0.02289	-1.889000	0.01112	-0.684000	0.03749	AAC	T|0.838;A|0.162	0.162	strong		0.592	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
USH2A	7399	hgsc.bcm.edu	37	1	216258213	216258213	+	Missense_Mutation	SNP	A	A	G	rs56222536	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:216258213A>G	ENST00000307340.3	-	25	5380	c.4994T>C	c.(4993-4995)aTc>aCc	p.I1665T	RP11-22M7.2_ENST00000446411.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.I1665T|RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA	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	86	0	0		WXS	Illumina HiSeq	Phase_I	132	85	0.643939	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	
STK36	27148	hgsc.bcm.edu	37	2	219562675	219562675	+	Missense_Mutation	SNP	G	G	A	rs1863704	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219562675G>A	ENST00000295709.3	+	25	3287	c.3008G>A	c.(3007-3009)gGt>gAt	p.G1003D	STK36_ENST00000392105.3_Missense_Mutation_p.G982D|STK36_ENST00000392106.2_Missense_Mutation_p.G982D|STK36_ENST00000440309.1_Missense_Mutation_p.G1003D	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	260	0	0		WXS	Illumina HiSeq	Phase_I	125	36	0.288	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		
PCDHA13	56136	hgsc.bcm.edu	37	5	140262582	140262582	+	Nonsense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140262582C>G	ENST00000289272.2	+	1	729	c.729C>G	c.(727-729)taC>taG	p.Y243*	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA13_ENST00000409494.1_Nonsense_Mutation_p.Y243*|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	243	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(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGAATTTTACCAATCCGTTT	0.453																																					p.Y243X	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.C729G						PASS	.						72.0	71.0	71.0					5																	140262582		2203	4300	6503	SO:0001587	stop_gained	56136	exon1			ATTTTACCAATCC	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"""Cadherins / Protocadherins : Clustered"""	8667	other	complex locus constituent	"""KIAA0345-like 1"", ""ortholog of mouse CNR5"""	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.729C>G	5.37:g.140262582C>G	ENSP00000289272:p.Tyr243*	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	141	49	0.347518	NM_031865	O75277	Nonsense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998714	0.54147	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	.	.	.	5.58	-0.292	0.12839	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	1.8341	0.03136	0.1235:0.1792:0.3522:0.345	.	.	.	.	X	243	.	ENSP00000289272:Y243X	Y	+	3	2	PCDHA13	140242766	0.000000	0.05858	0.101000	0.21167	0.535000	0.34838	-1.244000	0.02902	-0.053000	0.13289	0.561000	0.74099	TAC	.	.	none		0.453	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	
USH2A	7399	hgsc.bcm.edu	37	1	216219781	216219781	+	Missense_Mutation	SNP	A	A	G	rs6657250	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:216219781A>G	ENST00000307340.3	-	32	6703	c.6317T>C	c.(6316-6318)aTa>aCa	p.I2106T	USH2A_ENST00000366943.2_Missense_Mutation_p.I2106T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2106	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T (in dbSNP:rs6657250). {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)	p.I2106T(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)		ACCTGTGACTATGTAGTTCTC	0.398										HNSCC(13;0.011)			G|||	2983	0.595647	0.7965	0.4669	5008	,	,		15317	0.4544		0.6551	False		,,,				2504	0.5				p.I2106T		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	1	1	Substitution - Missense(1)	stomach(1)	c.T6317C						PASS	.	G	THR/ILE	3352,1054	385.8+/-325.9	1266,820,117	103.0	87.0	93.0		6317	5.4	1.0	1	dbSNP_116	93	5758,2842	448.5+/-361.8	1946,1866,488	yes	missense	USH2A	NM_206933.2	89	3212,2686,605	GG,GA,AA		33.0465,23.9219,29.9554	benign	2106/5203	216219781	9110,3896	2203	4300	6503	SO:0001583	missense	7399	exon32			GTGACTATGTAGT	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.6317T>C	1.37:g.216219781A>G	ENSP00000305941:p.Ile2106Thr	Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	1344	0.6153846153846154	399	0.8109756097560976	192	0.5303867403314917	259	0.4527972027972028	494	0.6517150395778364	G	0.007	-1.964884	0.00461	0.760781	0.669535	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.49432	0.78;0.78	5.42	5.42	0.78866	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.473539	0.17776	N	0.162428	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37820	-0.9689	9	0.14656	T	0.56	.	5.3694	0.16131	0.1724:0.0:0.6652:0.1624	rs6657250;rs52823385;rs59743196;rs6657250	2106	O75445	USH2A_HUMAN	T	2106	ENSP00000305941:I2106T;ENSP00000355910:I2106T	ENSP00000305941:I2106T	I	-	2	0	USH2A	214286404	0.866000	0.29940	0.992000	0.48379	0.091000	0.18340	0.988000	0.29616	1.442000	0.47568	-0.128000	0.14901	ATA	A|0.338;G|0.661	0.661	strong		0.398	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
SUPT6H	6830	hgsc.bcm.edu	37	17	27016529	27016529	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:27016529C>T	ENST00000314616.6	+	25	3575	c.3292C>T	c.(3292-3294)Cga>Tga	p.R1098*	SUPT6H_ENST00000347486.4_Nonsense_Mutation_p.R1098*	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1098	Interaction with KDM6A. {ECO:0000250}.				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)					AAACCCAGAGCGACTGAAAGA	0.557																																					p.R1098X		Atlas-SNP	.											SUPT6H,NS,carcinoma,0,1	SUPT6H	165	1	0			c.C3292T						scavenged	.						69.0	67.0	68.0					17																	27016529		2203	4300	6503	SO:0001587	stop_gained	6830	exon25			CCAGAGCGACTGA	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.3292C>T	17.37:g.27016529C>T	ENSP00000319104:p.Arg1098*	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	132	2	0.0151515	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Nonsense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	C	41	8.621950	0.98888	.	.	ENSG00000109111	ENST00000314616	.	.	.	5.39	2.03	0.26663	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.5718	13.8916	0.63742	0.5285:0.4715:0.0:0.0	.	.	.	.	X	1098	.	ENSP00000319104:R1098X	R	+	1	2	SUPT6H	24040656	1.000000	0.71417	0.993000	0.49108	0.903000	0.53119	1.513000	0.35823	0.582000	0.29556	-0.182000	0.12963	CGA	.	.	none		0.557	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
SLC35B1	10237	hgsc.bcm.edu	37	17	47783663	47783663	+	Missense_Mutation	SNP	C	C	T	rs1135034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:47783663C>T	ENST00000240333.6	-	3	363	c.242G>A	c.(241-243)cGt>cAt	p.R81H	RP11-613C6.2_ENST00000512720.1_RNA|SLC35B1_ENST00000415270.2_Missense_Mutation_p.R118H			P78383	S35B1_HUMAN	solute carrier family 35, member B1	81			R -> H (in dbSNP:rs1135034). {ECO:0000269|PubMed:15489334}.		transport (GO:0006810)|UDP-galactose transmembrane transport (GO:0072334)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	UDP-galactose transmembrane transporter activity (GO:0005459)			endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(1)	7						GCTCCGGGTACGATCCACCCT	0.413													.|||	260	0.0519169	0.1006	0.036	5008	,	,		12590	0.0		0.0865	False		,,,				2504	0.0153				p.R81H		Atlas-SNP	.											.	SLC35B1	21	.	0			c.G242A						PASS	.	C	HIS/ARG	378,4028	190.9+/-216.7	15,348,1840	45.0	41.0	43.0		242	4.8	1.0	17	dbSNP_86	43	733,7867	176.9+/-226.6	27,679,3594	yes	missense	SLC35B1	NM_005827.1	29	42,1027,5434	TT,TC,CC		8.5233,8.5792,8.5422	benign	81/323	47783663	1111,11895	2203	4300	6503	SO:0001583	missense	10237	exon3			CGGGTACGATCCA	D16978	CCDS11552.1, CCDS11552.2	17q21.32	2013-05-22			ENSG00000121073	ENSG00000121073		"""Solute carriers"""	20798	protein-coding gene	gene with protein product		610790				9010752	Standard	NM_005827		Approved	UGTREL1	uc002iph.1	P78383	OTTHUMG00000161638	ENST00000240333.6:c.242G>A	17.37:g.47783663C>T	ENSP00000240333:p.Arg81His	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_005827	B4DEC4|J3KQV4|Q96EW7	Missense_Mutation	SNP	ENST00000240333.6	37	CCDS11552.1	114|114	0.0521978021978022|0.0521978021978022	35|35	0.07113821138211382|0.07113821138211382	18|18	0.049723756906077346|0.049723756906077346	0|0	0.0|0.0	61|61	0.08047493403693931|0.08047493403693931	C|C	14.60|14.60	2.582492|2.582492	0.46006|0.46006	0.085792|0.085792	0.085233|0.085233	ENSG00000121073|ENSG00000121073	ENST00000240333;ENST00000415270;ENST00000503334;ENST00000508520;ENST00000435059;ENST00000514907;ENST00000515850;ENST00000511763;ENST00000511657|ENST00000376622	T;T;T;T;T;T;T;T|.	0.70516|.	1.54;1.54;-0.49;1.54;1.54;1.54;-0.49;-0.49|.	4.77|4.77	4.77|4.77	0.60923|0.60923	.|.	0.159646|.	0.56097|.	D|.	0.000024|.	T|T	0.02267|0.02267	0.0070|0.0070	N|N	0.11651|0.11651	0.15|0.15	0.19300|0.19300	P|P	0.9999774126|0.9999774126	B;B;B|.	0.15719|.	0.003;0.008;0.014|.	B;B;B|.	0.15484|.	0.013;0.005;0.013|.	T|T	0.32745|0.32745	-0.9895|-0.9895	9|5	0.44086|0.45353	T|T	0.13|0.12	-6.1857|-6.1857	17.5988|17.5988	0.88020|0.88020	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs1135034;rs3197489;rs11552687;rs11552688;rs17422721;rs17850814;rs1135034|rs1135034;rs3197489;rs11552687;rs11552688;rs17422721;rs17850814;rs1135034	81;14;81|.	B4DJG9;D3DTX1;P78383|.	.;.;S35B1_HUMAN|.	H|I	81;118;14;84;81;50;115;38;14|102	ENSP00000240333:R81H;ENSP00000409548:R118H;ENSP00000423323:R14H;ENSP00000424367:R84H;ENSP00000426961:R50H;ENSP00000427689:R115H;ENSP00000422104:R38H;ENSP00000426402:R14H|.	ENSP00000240333:R81H|ENSP00000365809:V102I	R|V	-|-	2|1	0|0	SLC35B1|SLC35B1	45138662|45138662	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.511000|4.511000	0.60462|0.60462	2.465000|2.465000	0.83290|0.83290	0.655000|0.655000	0.94253|0.94253	CGT|GTA	C|0.928;T|0.072	0.072	strong		0.413	SLC35B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365564.2	NM_005827	
ALX4	60529	hgsc.bcm.edu	37	11	44286566	44286566	+	Silent	SNP	G	G	A	rs3802805	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	122	118	0.967213	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		
KPNA5	3841	hgsc.bcm.edu	37	6	117045491	117045491	+	Silent	SNP	T	T	C	rs2243368	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:117045491T>C	ENST00000368564.1	+	10	1100	c.952T>C	c.(952-954)Tta>Cta	p.L318L	KPNA5_ENST00000356348.1_Silent_p.L318L			O15131	IMA6_HUMAN	karyopherin alpha 5 (importin alpha 6)	315	NLS binding site (minor). {ECO:0000250}.				cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(6)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0298)|all cancers(137;0.0461)|OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.212)		ATCACCTGCATTAAGGGCAGT	0.274													T|||	103	0.0205671	0.0038	0.0259	5008	,	,		18165	0.0		0.0755	False		,,,				2504	0.0041				p.L318L		Atlas-SNP	.											.	KPNA5	57	.	0			c.T952C						PASS	.	T		69,4337	61.1+/-98.1	1,67,2135	90.0	89.0	89.0		952	1.5	1.0	6	dbSNP_98	89	614,7976	159.2+/-212.6	20,574,3701	no	coding-synonymous	KPNA5	NM_002269.2		21,641,5836	CC,CT,TT		7.1478,1.566,5.2555		318/540	117045491	683,12313	2203	4295	6498	SO:0001819	synonymous_variant	3841	exon10			CCTGCATTAAGGG	AF005361	CCDS5111.1	6q22.2	2013-02-14			ENSG00000196911	ENSG00000196911		"""Importins"", ""Armadillo repeat containing"""	6398	protein-coding gene	gene with protein product		604545				9395085	Standard	NM_002269		Approved	SRP6, IPOA6	uc003pxh.3	O15131	OTTHUMG00000015448	ENST00000368564.1:c.952T>C	6.37:g.117045491T>C		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	228	92	0.403509	NM_002269	B2RAI5|Q86X23	Silent	SNP	ENST00000368564.1	37	CCDS5111.1																																																																																			T|0.959;C|0.041	0.041	strong		0.274	KPNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041967.1	NM_002269	
TJP1	7082	hgsc.bcm.edu	37	15	30008889	30008889	+	Silent	SNP	G	G	A	rs2229518	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:30008889G>A	ENST00000346128.6	-	23	4602	c.4128C>T	c.(4126-4128)gcC>gcT	p.A1376A	TJP1_ENST00000545208.2_Silent_p.A1296A|TJP1_ENST00000356107.6_Silent_p.A1376A|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	134	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	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	
SCN7A	6332	hgsc.bcm.edu	37	2	167313451	167313451	+	Missense_Mutation	SNP	T	T	C	rs11888208	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:167313451T>C	ENST00000409855.1	-	10	1345	c.1219A>G	c.(1219-1221)Ata>Gta	p.I407V		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	407			I -> V (in dbSNP:rs11888208).		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	TTCTTAGATATTTCACCAACT	0.333													T|||	593	0.118411	0.177	0.0692	5008	,	,		5681	0.0208		0.1362	False		,,,				2504	0.1564				p.I407V		Atlas-SNP	.											.	SCN7A	410	.	0			c.A1219G						PASS	.	T	VAL/ILE	552,3072		45,462,1305	70.0	62.0	64.0		1219	3.0	0.0	2	dbSNP_120	64	1238,6908		100,1038,2935	yes	missense	SCN7A	NM_002976.3	29	145,1500,4240	CC,CT,TT		15.1976,15.2318,15.2082	benign	407/1683	167313451	1790,9980	1812	4073	5885	SO:0001583	missense	6332	exon10			TAGATATTTCACC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1219A>G	2.37:g.167313451T>C	ENSP00000386796:p.Ile407Val	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	185	76	0.410811	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	217	0.09935897435897435	74	0.15040650406504066	29	0.08011049723756906	12	0.02097902097902098	102	0.1345646437994723	T	12.48	1.952025	0.34471	0.152318	0.151976	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992	D;D	0.96554	-4.03;-4.05	5.35	3.01	0.34805	.	1.133800	0.06559	N	0.746436	T	0.06325	0.0163	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.66035	-0.6023	9	0.72032	D	0.01	.	4.7931	0.13259	0.0:0.4109:0.0:0.5891	rs11888208;rs52816781;rs60443139;rs11888208	407	Q01118	SCN7A_HUMAN	V	407	ENSP00000386796:I407V;ENSP00000413699:I407V	ENSP00000259060:I407V	I	-	1	0	SCN7A	167021697	0.429000	0.25530	0.003000	0.11579	0.002000	0.02628	2.172000	0.42463	0.868000	0.35678	0.454000	0.30748	ATA	T|0.896;C|0.104	0.104	strong		0.333	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
NSUN2	54888	hgsc.bcm.edu	37	5	6604787	6604787	+	Silent	SNP	C	C	T	rs13181449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:6604787C>T	ENST00000264670.6	-	16	2060	c.1749G>A	c.(1747-1749)acG>acA	p.T583T	NSUN2_ENST00000506139.1_Silent_p.T548T|NSUN2_ENST00000539938.1_Silent_p.T347T	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	583					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CTTTGATCCCCGTGTTAATAA	0.453													C|||	1112	0.222045	0.0371	0.1427	5008	,	,		19971	0.4623		0.1899	False		,,,				2504	0.3139				p.T583T		Atlas-SNP	.											.	NSUN2	82	.	0			c.G1749A						PASS	.	C	,	255,4151	145.0+/-179.8	8,239,1956	81.0	83.0	83.0		1644,1749	-10.7	0.0	5	dbSNP_121	83	1753,6847	316.6+/-312.8	186,1381,2733	yes	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	194,1620,4689	TT,TC,CC		20.3837,5.7876,15.439	,	548/733,583/768	6604787	2008,10998	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon16			GATCCCCGTGTTA	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.1749G>A	5.37:g.6604787C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			C|0.819;T|0.181	0.181	strong		0.453	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77353973	77353973	+	Missense_Mutation	SNP	G	G	T	rs9930984	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:77353973G>T	ENST00000282849.5	-	16	2723	c.2305C>A	c.(2305-2307)Ctc>Atc	p.L769I		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	769	Spacer.		L -> I (in dbSNP:rs9930984). {ECO:0000269|PubMed:15489334}.		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GCTGGAATGAGGACCACCGGA	0.488													T|||	3180	0.634984	0.7731	0.6268	5008	,	,		16886	0.8681		0.3648	False		,,,				2504	0.4918				p.L769I		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.C2305A						PASS	.	T	ILE/LEU	3290,1106	395.1+/-329.5	1247,796,155	47.0	53.0	51.0		2305	2.1	0.0	16	dbSNP_119	51	3395,5205	638.9+/-399.4	683,2029,1588	yes	missense	ADAMTS18	NM_199355.2	5	1930,2825,1743	TT,TG,GG		39.4767,25.1592,48.5611	benign	769/1222	77353973	6685,6311	2198	4300	6498	SO:0001583	missense	170692	exon16			GAATGAGGACCAC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2305C>A	16.37:g.77353973G>T	ENSP00000282849:p.Leu769Ile	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	11	0.177419	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	1348	0.6172161172161172	368	0.7479674796747967	207	0.5718232044198895	493	0.8618881118881119	280	0.36939313984168864	T	0.356	-0.942285	0.02322	0.748408	0.394767	ENSG00000140873	ENST00000282849	T	0.51574	0.7	5.54	2.08	0.27032	ADAM-TS Spacer 1 (1);	1.032820	0.07672	N	0.935568	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.10450	0.005;0.001	T	0.33497	-0.9866	9	0.46703	T	0.11	.	5.8572	0.18727	0.0:0.2071:0.1293:0.6636	rs9930984;rs17855795;rs52810859;rs59142387;rs9930984	769;769	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	I	769	ENSP00000282849:L769I	ENSP00000282849:L769I	L	-	1	0	ADAMTS18	75911474	0.998000	0.40836	0.004000	0.12327	0.076000	0.17211	2.540000	0.45727	-0.130000	0.11599	-1.221000	0.01599	CTC	G|0.434;T|0.566	0.566	strong		0.488	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
MICALCL	84953	hgsc.bcm.edu	37	11	12315915	12315915	+	Missense_Mutation	SNP	A	A	G	rs1493954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:12315915A>G	ENST00000256186.2	+	3	1228	c.937A>G	c.(937-939)Agc>Ggc	p.S313G		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	313			S -> G (in dbSNP:rs1493954). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		TCGCTCATTCAGCCTTCGGAA	0.572													A|||	2659	0.53095	0.618	0.4755	5008	,	,		17570	0.6786		0.3429	False		,,,				2504	0.4939				p.S313G		Atlas-SNP	.											.	MICALCL	59	.	0			c.A937G						PASS	.	A	GLY/SER	2129,1777		601,927,425	87.0	97.0	94.0		937	5.4	0.1	11	dbSNP_88	94	2779,5495		490,1799,1848	yes	missense	MICALCL	NM_032867.2	56	1091,2726,2273	GG,GA,AA		33.5871,45.4941,40.2956	benign	313/696	12315915	4908,7272	1953	4137	6090	SO:0001583	missense	84953	exon3			TCATTCAGCCTTC	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.937A>G	11.37:g.12315915A>G	ENSP00000256186:p.Ser313Gly	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_032867	Q7RTP7|Q96JU6	Missense_Mutation	SNP	ENST00000256186.2	37	CCDS41620.1	1080	0.4945054945054945	284	0.5772357723577236	154	0.425414364640884	381	0.666083916083916	261	0.34432717678100266	A	9.494	1.101419	0.20632	0.545059	0.335871	ENSG00000133808	ENST00000256186	T	0.37915	1.17	5.41	5.41	0.78517	.	0.217809	0.32640	N	0.005834	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B	0.22851	0.076	B	0.20384	0.029	T	0.35500	-0.9786	9	0.22109	T	0.4	.	11.8195	0.52230	1.0:0.0:0.0:0.0	rs1493954;rs56583837;rs57257051;rs1493954	313	Q6ZW33	MICLK_HUMAN	G	313	ENSP00000256186:S313G	ENSP00000256186:S313G	S	+	1	0	MICALCL	12272491	0.750000	0.28316	0.132000	0.22025	0.076000	0.17211	3.504000	0.53347	2.049000	0.60858	0.455000	0.32223	AGC	A|0.511;C|0.004	.	strong		0.572	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
MDM1	56890	hgsc.bcm.edu	37	12	68709892	68709892	+	Missense_Mutation	SNP	C	C	T	rs17224810	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:68709892C>T	ENST00000303145.7	-	8	1233	c.1147G>A	c.(1147-1149)Gtt>Att	p.V383I	MDM1_ENST00000540418.1_Missense_Mutation_p.V103I|MDM1_ENST00000411698.2_Missense_Mutation_p.V348I	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	383			V -> I (in dbSNP:rs17224810).		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)		TTGCTACTAACGGTTCCTTCT	0.408													C|||	687	0.137181	0.059	0.3098	5008	,	,		19331	0.1131		0.1859	False		,,,				2504	0.0951				p.V383I		Atlas-SNP	.											MDM1,caecum,carcinoma,+1,1	MDM1	74	1	0			c.G1147A						scavenged	.	C	ILE/VAL,ILE/VAL	396,4010	197.1+/-221.3	19,358,1826	86.0	80.0	82.0		1042,1147	-6.2	0.0	12	dbSNP_123	82	1678,6922	307.6+/-308.5	189,1300,2811	yes	missense,missense	MDM1	NM_001205028.1,NM_017440.4	29,29	208,1658,4637	TT,TC,CC		19.5116,8.9877,15.9465	benign,benign	348/680,383/715	68709892	2074,10932	2203	4300	6503	SO:0001583	missense	56890	exon8			TACTAACGGTTCC	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.1147G>A	12.37:g.68709892C>T	ENSP00000302537:p.Val383Ile	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	179	77	0.430168	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	320	0.14652014652014653	26	0.052845528455284556	94	0.2596685082872928	66	0.11538461538461539	134	0.17678100263852242	C	0.004	-2.246298	0.00271	0.089877	0.195116	ENSG00000111554	ENST00000540418;ENST00000303145;ENST00000411698	T;T;T	0.19105	2.17;2.17;2.17	5.77	-6.15	0.02105	.	0.637167	0.15333	N	0.267906	T	0.00012	0.0000	N	0.04203	-0.255	0.34656	P	0.27787300000000004	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.41413	-0.9510	8	.	.	.	-2.47	15.5588	0.76223	0.0:0.5298:0.0:0.4702	rs17224810;rs52820856;rs56563436;rs56944808;rs17224810	348;383	E7EPQ3;Q8TC05	.;MDM1_HUMAN	I	103;383;348	ENSP00000443815:V103I;ENSP00000302537:V383I;ENSP00000391006:V348I	.	V	-	1	0	MDM1	66996159	0.310000	0.24527	0.043000	0.18650	0.010000	0.07245	-0.243000	0.08915	-1.379000	0.02118	-2.048000	0.00412	GTT	C|0.857;T|0.143	0.143	strong		0.408	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128	
GC	2638	hgsc.bcm.edu	37	4	72618323	72618323	+	Missense_Mutation	SNP	G	G	T	rs4588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:72618323G>T	ENST00000273951.8	-	11	1650	c.1307C>A	c.(1306-1308)aCg>aAg	p.T436K	GC_ENST00000503472.1_5'UTR|GC_ENST00000504199.1_Missense_Mutation_p.T455K|GC_ENST00000513476.1_Missense_Mutation_p.T436K	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	173	0	0		WXS	Illumina HiSeq	Phase_I	160	74	0.4625	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		
ST20	400410	hgsc.bcm.edu	37	15	80191280	80191280	+	Missense_Mutation	SNP	T	T	A	rs184575290	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:80191280T>A	ENST00000478497.1	-	3	912	c.233A>T	c.(232-234)tAc>tTc	p.Y78F	ST20_ENST00000485386.1_Missense_Mutation_p.Y78F|MTHFS_ENST00000258874.3_5'Flank|ST20_ENST00000562759.1_Missense_Mutation_p.Y78F|ST20-MTHFS_ENST00000479961.1_Intron|MTHFS_ENST00000559722.1_5'Flank|ST20-MTHFS_ENST00000494999.1_Intron	NM_001100879.1	NP_001094349.1	Q9HBF5	ST20_HUMAN	suppressor of tumorigenicity 20	78					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)			kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						TATTTAAAAGTAGAAGTATGT	0.333													T|||	3	0.000599042	0.0	0.0	5008	,	,		18184	0.0		0.003	False		,,,				2504	0.0				p.Y78F		Atlas-SNP	.											ST20,NS,carcinoma,+1,1	ST20	9	1	0			c.A233T						PASS	.	T	PHE/TYR,PHE/TYR,PHE/TYR,	3,4391	6.2+/-15.9	0,3,2194	74.0	78.0	77.0		233,233,233,	-1.1	0.0	15		77	29,8561	17.9+/-57.8	0,29,4266	yes	missense,missense,missense,intron	ST20,ST20-MTHFS	NM_001100879.1,NM_001100880.2,NM_001199757.1,NM_001199760.1	22,22,22,	0,32,6460	AA,AT,TT		0.3376,0.0683,0.2465	possibly-damaging,possibly-damaging,possibly-damaging,	78/80,78/80,78/80,	80191280	32,12952	2197	4295	6492	SO:0001583	missense	400410	exon3			TAAAAGTAGAAGT	AF249277	CCDS42067.1	15q25.1	2007-07-16				ENSG00000180953			33520	protein-coding gene	gene with protein product							Standard	NM_001100879		Approved	HCCS-1		Q9HBF5		ENST00000478497.1:c.233A>T	15.37:g.80191280T>A	ENSP00000453502:p.Tyr78Phe	Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	129	87	0.674419	NM_001199757		Missense_Mutation	SNP	ENST00000478497.1	37	CCDS42067.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	12.63	1.994958	0.35226	6.83E-4	0.003376	ENSG00000180953	ENST00000322484;ENST00000417278	.	.	.	1.78	-1.14	0.09741	.	.	.	.	.	T	0.16854	0.0405	.	.	.	0.09310	N	1	P	0.46020	0.871	B	0.31812	0.136	T	0.13150	-1.0520	7	0.87932	D	0	.	5.9491	0.19235	0.0:0.0:0.5632:0.4368	.	78	Q9HBF5	ST20_HUMAN	F	78	.	ENSP00000319125:Y78F	Y	-	2	0	ST20	77978335	0.002000	0.14202	0.000000	0.03702	0.446000	0.32137	-0.513000	0.06305	-0.277000	0.09193	0.172000	0.16884	TAC	T|0.998;A|0.002	0.002	strong		0.333	ST20-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416728.2		
NUP62	23636	hgsc.bcm.edu	37	19	50412217	50412217	+	Missense_Mutation	SNP	C	C	G	rs1062798	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50412217C>G	ENST00000596217.1	-	2	2735	c.848G>C	c.(847-849)aGc>aCc	p.S283T	NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000597723.1_Intron|NUP62_ENST00000413454.1_Missense_Mutation_p.S283T|NUP62_ENST00000352066.3_Missense_Mutation_p.S283T|NUP62_ENST00000597029.1_Missense_Mutation_p.S283T|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000422090.2_Missense_Mutation_p.S283T			P37198	NUP62_HUMAN	nucleoporin 62kDa	283	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.		S -> T (in dbSNP:rs1062798). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:1915414}.		carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|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 programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		gctgctgctgctggtggtggt	0.627													C|||	1584	0.316294	0.2383	0.379	5008	,	,		15105	0.3938		0.3827	False		,,,				2504	0.229				p.S283T		Atlas-SNP	.											NUP62,NS,carcinoma,0,2	NUP62	50	2	0			c.G848C						scavenged	.	C	THR/SER,THR/SER,THR/SER,THR/SER,THR/SER,	997,3405		118,761,1322	31.0	29.0	30.0		848,848,848,848,848,	0.8	0.0	19	dbSNP_86	30	3113,5481		577,1959,1761	yes	missense,missense,missense,missense,missense,intron	NUP62,IL4I1	NM_001193357.1,NM_012346.4,NM_016553.4,NM_153718.3,NM_153719.3,NM_172374.1	58,58,58,58,58,	695,2720,3083	GG,GC,CC		36.2229,22.6488,31.6251	benign,benign,benign,benign,benign,	283/523,283/523,283/523,283/523,283/523,	50412217	4110,8886	2201	4297	6498	SO:0001583	missense	23636	exon3			CTGCTGCTGGTGG	X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"""nuclear pore glycoprotein p62"""	605815	"""nucleoporin 62kD"""			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.848G>C	19.37:g.50412217C>G	ENSP00000471191:p.Ser283Thr	Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	73	71	0.972603	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Missense_Mutation	SNP	ENST00000596217.1	37	CCDS12788.1	763	0.34935897435897434	103	0.20934959349593496	134	0.3701657458563536	230	0.4020979020979021	296	0.39050131926121373	C	0.016	-1.533751	0.00951	0.226488	0.362229	ENSG00000213024	ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.36157	1.27;1.27;1.27	4.24	0.801	0.18679	Nucleoporin, NSP1-like, C-terminal (1);	1.330530	0.05670	N	0.588508	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	0.45366	-0.9266	8	.	.	.	-2.1099	13.4683	0.61268	0.0:0.2452:0.7548:0.0	rs1062798;rs3203778;rs3745497;rs4009638;rs5828420;rs17844993;rs17857752;rs52814004	283	P37198	NUP62_HUMAN	T	283	ENSP00000305503:S283T;ENSP00000407331:S283T;ENSP00000387991:S283T	.	S	-	2	0	NUP62	55104029	0.050000	0.20438	0.000000	0.03702	0.004000	0.04260	1.221000	0.32503	0.190000	0.20209	-1.162000	0.01777	AGC	C|0.677;G|0.323	0.323	strong		0.627	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21940555	21940555	+	Missense_Mutation	SNP	C	C	T	rs2275363	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:21940555C>T	ENST00000374765.4	-	8	519	c.319G>A	c.(319-321)Gct>Act	p.A107T	RAP1GAP_ENST00000542643.2_Missense_Mutation_p.A107T|RAP1GAP_ENST00000290101.4_Missense_Mutation_p.A171T|RAP1GAP_ENST00000374761.2_Missense_Mutation_p.A138T|RAP1GAP_ENST00000374757.3_5'UTR|RAP1GAP_ENST00000374763.2_Missense_Mutation_p.A107T	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	107			A -> T (in dbSNP:rs2275363). {ECO:0000269|PubMed:1904317}.		GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		CCGAGGGCAGCGTCCAGTGAG	0.597													T|||	1968	0.392971	0.3646	0.2781	5008	,	,		18116	0.4196		0.4443	False		,,,				2504	0.4325				p.A171T		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.G511A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA	1614,2792	659.9+/-400.6	288,1038,877	79.0	68.0	72.0		319,511,319	-1.5	1.0	1	dbSNP_100	72	3919,4681	600.8+/-394.3	893,2133,1274	yes	missense,missense,missense	RAP1GAP	NM_002885.2,NM_001145658.1,NM_001145657.1	58,58,58	1181,3171,2151	TT,TC,CC		45.5698,36.6319,42.5419	benign,benign,benign	107/664,171/728,107/682	21940555	5533,7473	2203	4300	6503	SO:0001583	missense	5909	exon8			GGGCAGCGTCCAG	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.319G>A	1.37:g.21940555C>T	ENSP00000363897:p.Ala107Thr	Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	74	71	0.959459	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Missense_Mutation	SNP	ENST00000374765.4	37	CCDS218.1	879	0.4024725274725275	173	0.3516260162601626	107	0.2955801104972376	259	0.4527972027972028	340	0.44854881266490765	T	10.96	1.498257	0.26861	0.366319	0.455698	ENSG00000076864	ENST00000290101;ENST00000374761;ENST00000542643;ENST00000374765;ENST00000374763;ENST00000374758;ENST00000359708;ENST00000374757	D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27;-3.27	4.82	-1.45	0.08828	.	0.647253	0.15734	N	0.247262	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.06405	0.001;0.001;0.002;0.001	T	0.22591	-1.0212	9	0.15952	T	0.53	-27.1196	10.5468	0.45064	0.0:0.5514:0.0:0.4486	rs2275363;rs58221509;rs2275363	107;107;138;107	P47736-2;P47736;P47736-3;Q7Z5S8	.;RPGP1_HUMAN;.;.	T	171;138;107;107;138;107;171;249	ENSP00000290101:A171T;ENSP00000363893:A138T;ENSP00000441661:A107T;ENSP00000363897:A107T;ENSP00000352739:A171T	ENSP00000290101:A171T	A	-	1	0	RAP1GAP	21813142	0.000000	0.05858	0.951000	0.38953	0.989000	0.77384	-1.035000	0.03564	-0.517000	0.06461	-0.361000	0.07541	GCT	C|0.587;T|0.413	0.413	strong		0.597	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
MFI2	4241	hgsc.bcm.edu	37	3	196743130	196743130	+	Silent	SNP	T	T	C	rs6779362	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:196743130T>C	ENST00000296350.5	-	8	1124	c.1011A>G	c.(1009-1011)acA>acG	p.T337T		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	337	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)	p.T337T(1)		breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-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;0.00536)		CATAGGTCTGTGTGGCGATGG	0.592													C|||	1598	0.319089	0.4743	0.2046	5008	,	,		20505	0.2976		0.2455	False		,,,				2504	0.2883				p.T337T		Atlas-SNP	.											MFI2,NS,carcinoma,0,1	MFI2	88	1	1	Substitution - coding silent(1)	prostate(1)	c.A1011G						scavenged	.	C		1920,2486	626.5+/-394.7	422,1076,705	99.0	90.0	93.0		1011	-9.7	0.4	3	dbSNP_116	93	2006,6594	721.7+/-406.4	243,1520,2537	no	coding-synonymous	MFI2	NM_005929.5		665,2596,3242	CC,CT,TT		23.3256,43.5769,30.1861		337/739	196743130	3926,9080	2203	4300	6503	SO:0001819	synonymous_variant	4241	exon8			GGTCTGTGTGGCG		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.1011A>G	3.37:g.196743130T>C		Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	111	47	0.423423	NM_005929	Q9BQE2	Silent	SNP	ENST00000296350.5	37	CCDS3325.1																																																																																			T|0.686;C|0.314	0.314	strong		0.592	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
KCNJ12	3768	hgsc.bcm.edu	37	17	21318741	21318741	+	Silent	SNP	C	C	T	rs75113504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:21318741C>T	ENST00000583088.1	+	3	982	c.87C>T	c.(85-87)aaC>aaT	p.N29N	KCNJ12_ENST00000331718.5_Silent_p.N29N	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	29					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)	CGGGCGCCAACGGCTTCGGCA	0.652										Prostate(3;0.18)																											p.N29N		Atlas-SNP	.											KCNJ12,NS,neuroblastoma,0,2	.	.	2	0			c.C87T						PASS	.	C		846,3560		0,846,1357	81.0	69.0	73.0		87	-6.0	0.9	17	dbSNP_131	73	1238,7362		0,1238,3062	no	coding-synonymous	KCNJ12	NM_021012.4		0,2084,4419	TT,TC,CC		14.3953,19.2011,16.0234		29/434	21318741	2084,10922	2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			CGCCAACGGCTTC	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.87C>T	17.37:g.21318741C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	117	12	0.102564	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			C|0.883;T|0.117	0.117	strong		0.652	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789317	117789317	+	Silent	SNP	T	T	C	rs201746372|rs58754377|rs201369736		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789317T>C	ENST00000430170.2	-	2	345	c.258A>G	c.(256-258)ccA>ccG	p.P86P	TMPRSS13_ENST00000445164.2_Silent_p.P86P|TMPRSS13_ENST00000526090.1_Silent_p.P86P|TMPRSS13_ENST00000528626.1_Silent_p.P86P|TMPRSS13_ENST00000524993.1_Silent_p.P86P	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	86	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		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)		ATGCCCGGGCTGGAGATGCCT	0.652																																					p.P86P		Atlas-SNP	.											TMPRSS13,caecum,carcinoma,0,1	TMPRSS13	75	1	1	Deletion - In frame(1)	urinary_tract(1)	c.A258G						PASS	.						34.0	41.0	38.0					11																	117789317		1955	4135	6090	SO:0001819	synonymous_variant	84000	exon2			CCGGGCTGGAGAT	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	ENST00000430170.2:c.258A>G	11.37:g.117789317T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	268	13	0.0485075	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	37	CCDS58185.1																																																																																			.	.	weak		0.652	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
PRF1	5551	hgsc.bcm.edu	37	10	72360224	72360224	+	Silent	SNP	C	C	T	rs115281140	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72360224C>T	ENST00000441259.1	-	2	595	c.435G>A	c.(433-435)gtG>gtA	p.V145V	PRF1_ENST00000373209.2_Silent_p.V145V	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	145	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CGGCCACAGACACATGCACAT	0.612			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				C|||	64	0.0127796	0.0287	0.0086	5008	,	,		16983	0.0		0.0109	False		,,,				2504	0.0092				p.V145V		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,NS,carcinoma,-2,1	PRF1	64	1	0			c.G435A						scavenged	.	C	,	88,4318	73.6+/-111.7	1,86,2116	88.0	76.0	80.0		435,435	2.8	0.0	10	dbSNP_132	80	71,8529	41.7+/-99.0	0,71,4229	no	coding-synonymous,coding-synonymous	PRF1	NM_001083116.1,NM_005041.4	,	1,157,6345	TT,TC,CC		0.8256,1.9973,1.2225	,	145/556,145/556	72360224	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CACAGACACATGC	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.435G>A	10.37:g.72360224C>T		Somatic	226	2	0.00884956		WXS	Illumina HiSeq	Phase_I	119	87	0.731092	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			C|0.990;T|0.010	0.010	strong		0.612	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
IL1RAP	3556	hgsc.bcm.edu	37	3	190363594	190363594	+	Silent	SNP	G	G	A	rs34879831	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:190363594G>A	ENST00000412504.2	+	10	1560	c.1308G>A	c.(1306-1308)aaG>aaA	p.K436K	IL1RAP_ENST00000072516.3_Silent_p.K436K|IL1RAP_ENST00000439062.1_Silent_p.K436K|IL1RAP_ENST00000443369.2_Silent_p.K436K|IL1RAP_ENST00000447382.1_Silent_p.K436K|IL1RAP_ENST00000317757.3_Silent_p.K436K			Q9NPH3	IL1AP_HUMAN	interleukin 1 receptor accessory protein	436	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-2 biosynthetic process (GO:0042094)|protein complex assembly (GO:0006461)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20	all_cancers(143;3.61e-10)|Ovarian(172;0.0733)|Breast(254;0.21)		Lung(62;1.95e-06)|LUSC - Lung squamous cell carcinoma(58;2.05e-06)	GBM - Glioblastoma multiforme(93;0.00851)		TTGGATACAAGCTGTGCATCT	0.408													G|||	817	0.163139	0.3109	0.111	5008	,	,		19560	0.0179		0.1541	False		,,,				2504	0.1595				p.K436K		Atlas-SNP	.											.	IL1RAP	96	.	0			c.G1308A						PASS	.	G	,,,	1217,3189	423.0+/-339.9	158,901,1144	99.0	94.0	96.0		1308,1308,1308,1308	4.8	1.0	3	dbSNP_126	96	1390,7210	269.7+/-288.6	115,1160,3025	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL1RAP	NM_001167928.1,NM_001167929.1,NM_001167931.1,NM_002182.3	,,,	273,2061,4169	AA,AG,GG		16.1628,27.6214,20.0446	,,,	436/571,436/571,436/688,436/571	190363594	2607,10399	2203	4300	6503	SO:0001819	synonymous_variant	3556	exon10			ATACAAGCTGTGC	AB006537	CCDS3298.1, CCDS46982.1, CCDS54696.1	3q28	2013-01-11			ENSG00000196083	ENSG00000196083		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5995	protein-coding gene	gene with protein product		602626				9479509, 9065432	Standard	NM_002182		Approved	IL-1RAcP, IL1R3, C3orf13	uc003fsq.3	Q9NPH3	OTTHUMG00000156211	ENST00000412504.2:c.1308G>A	3.37:g.190363594G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_001167929	B1NLD0|D3DNW0|O14915|Q86WJ7	Silent	SNP	ENST00000412504.2	37	CCDS3298.1																																																																																			G|0.811;A|0.189	0.189	strong		0.408	IL1RAP-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343497.1		
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346468	140346468	+	Silent	SNP	T	T	A	rs155364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140346468T>A	ENST00000289269.5	+	1	649	c.117T>A	c.(115-117)ccT>ccA	p.P39P	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000289272.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	39					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)			tACCTGGCCCTGCGGCCTCCC	0.706													A|||	2918	0.582668	0.7352	0.5994	5008	,	,		15939	0.6111		0.5209	False		,,,				2504	0.3988				p.P39P	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											PCDHAC2,NS,carcinoma,0,1	PCDHAC2	142	1	0			c.T117A						PASS	.	A	,,,,,,,,,,,,,,,,,,	3069,1221		1139,791,215	9.0	8.0	8.0		,117,,,,,,,,,,,,,,,,,117	-1.1	1.0	5	dbSNP_79	8	4360,4002		1212,1936,1033	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	,,,,,,,,,,,,,,,,,,	2351,2727,1248	AA,AT,TT		47.8594,28.4615,41.282	,,,,,,,,,,,,,,,,,,	,39/1008,,,,,,,,,,,,,,,,,39/885	140346468	7429,5223	2145	4181	6326	SO:0001819	synonymous_variant	56134	exon1			TGGCCCTGCGGCC	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.117T>A	5.37:g.140346468T>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			T|0.409;A|0.591	0.591	strong		0.706	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
CRACR2A	84766	hgsc.bcm.edu	37	12	3782647	3782647	+	Missense_Mutation	SNP	A	A	T	rs36030417	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:3782647A>T	ENST00000252322.1	-	7	1104	c.636T>A	c.(634-636)caT>caA	p.H212Q	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.H212Q|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.H212Q	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		212			H -> Q (in dbSNP:rs36030417).		activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TCTTCTCCTCATGGGCTTCTT	0.488													A|||	855	0.170727	0.115	0.2363	5008	,	,		20099	0.127		0.1471	False		,,,				2504	0.2689				p.H212Q		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.T636A						PASS	.	A	GLN/HIS,GLN/HIS	550,3856	247.5+/-255.7	36,478,1689	151.0	143.0	145.0		636,636	-8.5	0.2	12	dbSNP_126	145	1227,7373	246.9+/-275.2	90,1047,3163	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	24,24	126,1525,4852	TT,TA,AA		14.2674,12.483,13.6629	possibly-damaging,possibly-damaging	212/732,212/396	3782647	1777,11229	2203	4300	6503	SO:0001583	missense	84766	exon7			CTCCTCATGGGCT																												ENST00000252322.1:c.636T>A	12.37:g.3782647A>T	ENSP00000252322:p.His212Gln	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	126	47	0.373016	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	332	0.152014652014652	56	0.11382113821138211	86	0.23756906077348067	83	0.1451048951048951	107	0.14116094986807387	A	11.01	1.511825	0.27036	0.12483	0.142674	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.20738	2.05;2.7;2.68	4.55	-8.51	0.00923	.	0.241821	0.41001	D	0.000976	T	0.00012	0.0000	L	0.61218	1.895	0.43203	P	0.004942000000000002	B;P;D	0.56035	0.366;0.949;0.974	B;P;P	0.49140	0.085;0.578;0.601	T	0.04140	-1.0974	9	0.13470	T	0.59	-14.6484	9.6521	0.39904	0.3381:0.0924:0.5695:0.0	rs36030417;rs61907257	212;212;212	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	Q	212	ENSP00000409382:H212Q;ENSP00000412496:H212Q;ENSP00000252322:H212Q	ENSP00000252322:H212Q	H	-	3	2	EFCAB4B	3652908	0.000000	0.05858	0.217000	0.23759	0.545000	0.35147	-3.808000	0.00361	-2.641000	0.00429	-1.844000	0.00574	CAT	A|0.861;T|0.139	0.139	strong		0.488	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
OR1K1	392392	hgsc.bcm.edu	37	9	125562527	125562527	+	Silent	SNP	T	T	C	rs10985782	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:125562527T>C	ENST00000277309.2	+	1	158	c.126T>C	c.(124-126)ggT>ggC	p.G42G		NM_080859.1	NP_543135.1	Q8NGR3	OR1K1_HUMAN	olfactory receptor, family 1, subfamily K, member 1	42						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G42G(1)		endometrium(1)|large_intestine(8)|lung(2)|ovary(1)|skin(4)|stomach(1)	17						GCCTCCTGGGTAATGGACTCA	0.547													t|||	608	0.121406	0.1687	0.1282	5008	,	,		20797	0.0486		0.1282	False		,,,				2504	0.1207				p.G42G		Atlas-SNP	.											OR1K1,NS,carcinoma,0,1	OR1K1	34	1	1	Substitution - coding silent(1)	stomach(1)	c.T126C						PASS	.	C		585,3821	257.4+/-261.8	39,507,1657	118.0	93.0	102.0		126	-8.8	0.0	9	dbSNP_120	102	1094,7506	229.1+/-263.9	64,966,3270	no	coding-synonymous	OR1K1	NM_080859.1		103,1473,4927	CC,CT,TT		12.7209,13.2773,12.9094		42/317	125562527	1679,11327	2203	4300	6503	SO:0001819	synonymous_variant	392392	exon1			CCTGGGTAATGGA	AL359512	CCDS35132.1	9q33	2013-09-20			ENSG00000165204	ENSG00000165204		"""GPCR / Class A : Olfactory receptors"""	8212	protein-coding gene	gene with protein product							Standard	NM_080859		Approved	hg99, MNAB	uc011lze.2	Q8NGR3	OTTHUMG00000020625	ENST00000277309.2:c.126T>C	9.37:g.125562527T>C		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	249	129	0.518072	NM_080859	B9EH41|Q4VXB7|Q96R23	Silent	SNP	ENST00000277309.2	37	CCDS35132.1																																																																																			T|0.876;C|0.124	0.124	strong		0.547	OR1K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053958.1		
MMEL1	79258	hgsc.bcm.edu	37	1	2526746	2526746	+	Missense_Mutation	SNP	A	A	G	rs3748816	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:2526746A>G	ENST00000378412.3	-	16	1714	c.1553T>C	c.(1552-1554)aTg>aCg	p.M518T	MMEL1_ENST00000502556.1_Missense_Mutation_p.M361T|MMEL1_ENST00000288709.6_Missense_Mutation_p.M509T			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	518			M -> T (in dbSNP:rs3748816). {ECO:0000269|PubMed:15489334}.			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)		GCGCCTGTTCATCTCCTCCAG	0.647													G|||	2711	0.541334	0.7284	0.487	5008	,	,		15245	0.5407		0.332	False		,,,				2504	0.5429				p.M518T		Atlas-SNP	.											.	MMEL1	64	.	0			c.T1553C						PASS	.	G	THR/MET	3002,1404	459.8+/-352.4	1022,958,223	70.0	66.0	67.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1553	-5.5	0.0	1	dbSNP_107	67	2892,5708	671.0+/-402.8	487,1918,1895	yes	missense	MMEL1	NM_033467.3	81	1509,2876,2118	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	33.6279,31.8656,45.3175	benign	518/780	2526746	5894,7112	2203	4300	6503	SO:0001583	missense	79258	exon16			CTGTTCATCTCCT	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.1553T>C	1.37:g.2526746A>G	ENSP00000367668:p.Met518Thr	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	146	39	0.267123	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	37	CCDS30569.2	1043	0.4775641025641026	347	0.7052845528455285	165	0.4558011049723757	278	0.486013986013986	253	0.3337730870712401	G	0	-2.755514	0.00085	0.681344	0.336279	ENSG00000142606	ENST00000378411;ENST00000288709;ENST00000378412;ENST00000502556	D;D;D	0.81579	-1.51;-1.51;-1.51	4.89	-5.48	0.02592	.	1.727810	0.02496	N	0.089927	T	0.00012	0.0000	N	0.00446	-1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	9	0.08381	T	0.77	-0.0773	2.1612	0.03825	0.1136:0.2449:0.3589:0.2826	rs3748816;rs61663127;rs3748816	518	Q495T6	MMEL1_HUMAN	T	361;509;518;361	ENSP00000288709:M509T;ENSP00000367668:M518T;ENSP00000422492:M361T	ENSP00000288709:M509T	M	-	2	0	MMEL1	2516606	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.199000	0.00561	-1.671000	0.01466	-2.367000	0.00236	ATG	A|0.529;G|0.471	0.471	strong		0.647	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12248942	12248942	+	Silent	SNP	A	A	G	rs945439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:12248942A>G	ENST00000376259.3	+	2	257	c.168A>G	c.(166-168)aaA>aaG	p.K56K	TNFRSF1B_ENST00000492361.1_Intron|MIR4632_ENST00000584158.1_RNA|TNFRSF1B_ENST00000536782.1_Silent_p.K56K	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	56					aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)	GCTGCAGCAAATGCTCGCCGG	0.632													G|||	998	0.199281	0.2012	0.134	5008	,	,		18420	0.1548		0.2147	False		,,,				2504	0.273				p.K56K		Atlas-SNP	.											.	TNFRSF1B	28	.	0			c.A168G						PASS	.	G		976,3430	729.2+/-410.0	109,758,1336	38.0	41.0	40.0		168	2.5	0.0	1	dbSNP_86	40	2082,6518	714.2+/-406.0	274,1534,2492	no	coding-synonymous	TNFRSF1B	NM_001066.2		383,2292,3828	GG,GA,AA		24.2093,22.1516,23.5122		56/462	12248942	3058,9948	2203	4300	6503	SO:0001819	synonymous_variant	7133	exon2			CAGCAAATGCTCG	M32315	CCDS145.1	1p36.22	2008-02-05			ENSG00000028137	ENSG00000028137		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11917	protein-coding gene	gene with protein product		191191		TNFR2		2158863, 8702885	Standard	NM_001066		Approved	TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b	uc001att.3	P20333	OTTHUMG00000001829	ENST00000376259.3:c.168A>G	1.37:g.12248942A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Silent	SNP	ENST00000376259.3	37	CCDS145.1																																																																																			A|0.787;G|0.213	0.213	strong		0.632	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066	
FAM198A	729085	hgsc.bcm.edu	37	3	43095101	43095101	+	Missense_Mutation	SNP	A	A	G	rs536119	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	148	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	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	
SCN7A	6332	hgsc.bcm.edu	37	2	167262353	167262353	+	Missense_Mutation	SNP	C	C	G	rs3791251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:167262353C>G	ENST00000409855.1	-	25	4912	c.4786G>C	c.(4786-4788)Gtt>Ctt	p.V1596L		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1596			V -> L (in dbSNP:rs3791251).		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	ATTTCTGAAACAACTTTCTCC	0.418													G|||	378	0.0754792	0.031	0.0288	5008	,	,		18649	0.1121		0.0775	False		,,,				2504	0.1288				p.V1596L		Atlas-SNP	.											.	SCN7A	410	.	0			c.G4786C						PASS	.	G	LEU/VAL	167,3595		3,161,1717	168.0	165.0	166.0		4786	1.6	0.5	2	dbSNP_107	166	803,7421		39,725,3348	yes	missense	SCN7A	NM_002976.3	32	42,886,5065	GG,GC,CC		9.7641,4.4391,8.0928	benign	1596/1683	167262353	970,11016	1881	4112	5993	SO:0001583	missense	6332	exon25			CTGAAACAACTTT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4786G>C	2.37:g.167262353C>G	ENSP00000386796:p.Val1596Leu	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	154	0.07051282051282051	9	0.018292682926829267	10	0.027624309392265192	79	0.1381118881118881	56	0.07387862796833773	G	2.352	-0.348732	0.05208	0.044391	0.097641	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.96427	-4.01	4.51	1.57	0.23409	.	0.443058	0.19214	N	0.119842	T	0.03095	0.0091	N	0.00583	-1.355	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.57797	-0.7749	9	0.30078	T	0.28	.	9.0712	0.36493	0.0:0.1307:0.4321:0.4372	rs3791251;rs52802159;rs3791251	1596	Q01118	SCN7A_HUMAN	L	1596	ENSP00000386796:V1596L	ENSP00000259060:V1596L	V	-	1	0	SCN7A	166970599	0.000000	0.05858	0.516000	0.27786	0.134000	0.20937	-0.387000	0.07361	-0.020000	0.14032	-0.824000	0.03097	GTT	C|0.920;G|0.080	0.080	strong		0.418	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
SNED1	25992	hgsc.bcm.edu	37	2	241979550	241979550	+	Silent	SNP	T	T	C	rs7571117	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241979550T>C	ENST00000310397.8	+	7	1104	c.1104T>C	c.(1102-1104)aaT>aaC	p.N368N	SNED1_ENST00000342631.6_Silent_p.N368N|SNED1_ENST00000401884.1_Silent_p.N368N|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000405547.3_Silent_p.N368N	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	368	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Follistatin-like 1.				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)		AGGTGGAGAATGGCTCTGCGG	0.612													C|||	2241	0.447484	0.6059	0.3473	5008	,	,		19799	0.3214		0.4602	False		,,,				2504	0.4213				p.N368N		Atlas-SNP	.											.	SNED1	76	.	0			c.T1104C						PASS	.	C		2626,1640		827,972,334	32.0	39.0	37.0		1104	-4.8	0.0	2	dbSNP_116	37	4146,4356		1043,2060,1148	no	coding-synonymous	SNED1	NM_001080437.1		1870,3032,1482	CC,CT,TT		48.765,38.4435,46.9612		368/1414	241979550	6772,5996	2133	4251	6384	SO:0001819	synonymous_variant	25992	exon7			GGAGAATGGCTCT	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.1104T>C	2.37:g.241979550T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	46	0.365079	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1	954|954	0.4368131868131868|0.4368131868131868	291|291	0.5914634146341463|0.5914634146341463	130|130	0.35911602209944754|0.35911602209944754	189|189	0.3304195804195804|0.3304195804195804	344|344	0.45382585751978893|0.45382585751978893	C|C	0.088|0.088	-1.172244|-1.172244	0.01646|0.01646	0.615565|0.615565	0.48765|0.48765	ENSG00000162804|ENSG00000162804	ENST00000431690|ENST00000401644	.|.	.|.	.|.	4.73|4.73	-4.77|-4.77	0.03219|0.03219	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43686|0.43686	-0.9376|-0.9376	3|3	.|.	.|.	.|.	.|.	2.7388|2.7388	0.05247|0.05247	0.1001:0.2577:0.1972:0.445|0.1001:0.2577:0.1972:0.445	rs7571117;rs61028234;rs7571117|rs7571117;rs61028234;rs7571117	.|.	.|.	.|.	T|R	26|65	.|.	.|.	M|W	+|+	2|1	0|0	SNED1|SNED1	241628223|241628223	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-1.799000|-1.799000	0.01746|0.01746	-1.361000|-1.361000	0.02169|0.02169	-0.972000|-0.972000	0.02603|0.02603	ATG|TGG	T|0.554;C|0.446	0.446	strong		0.612	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
TRAF3	7187	hgsc.bcm.edu	37	14	103336727	103336727	+	Silent	SNP	G	G	A	rs142350527	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:103336727G>A	ENST00000560371.1	+	2	406	c.189G>A	c.(187-189)ccG>ccA	p.P63P	TRAF3_ENST00000351691.5_Silent_p.P63P|TRAF3_ENST00000539721.1_Silent_p.P63P|TRAF3_ENST00000347662.4_Silent_p.P63P|TRAF3_ENST00000392745.2_Silent_p.P63P	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	63					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|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)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		TGTGCAGCCCGAAGCAGACCG	0.617													G|||	23	0.00459265	0.0	0.0159	5008	,	,		16014	0.0		0.0119	False		,,,				2504	0.0				p.P63P		Atlas-SNP	.											.	TRAF3	60	.	0			c.G189A						PASS	.	G	,,,	8,4398	14.3+/-33.2	0,8,2195	76.0	65.0	68.0		189,189,189,189	-10.9	0.4	14	dbSNP_134	68	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRAF3	NM_001199427.1,NM_003300.3,NM_145725.2,NM_145726.2	,,,	0,36,6467	AA,AG,GG		0.3256,0.1816,0.2768	,,,	63/486,63/569,63/569,63/544	103336727	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	7187	exon3			CAGCCCGAAGCAG	U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.189G>A	14.37:g.103336727G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_145726	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Silent	SNP	ENST00000560371.1	37	CCDS9975.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138740037	138740037	+	Missense_Mutation	SNP	G	G	C	rs2297236	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:138740037G>C	ENST00000242351.5	-	10	2417	c.2101C>G	c.(2101-2103)Cag>Gag	p.Q701E	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.Q823E	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	701			Q -> E (in dbSNP:rs2297236). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.Q701E(1)		cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						TTTGCTGGCTGATGGCTACAA	0.443													G|||	2830	0.565096	0.4629	0.5879	5008	,	,		17578	0.6776		0.5586	False		,,,				2504	0.5777				p.Q701E		Atlas-SNP	.											ZC3HAV1,NS,carcinoma,0,2	ZC3HAV1	75	2	1	Substitution - Missense(1)	prostate(1)	c.C2101G						PASS	.	G	GLU/GLN	2024,2382	562.9+/-381.1	494,1036,673	74.0	73.0	74.0		2101	1.8	0.0	7	dbSNP_100	74	4874,3726	617.9+/-396.7	1388,2098,814	yes	missense	ZC3HAV1	NM_020119.3	29	1882,3134,1487	CC,CG,GG		43.3256,45.9374,46.9629	possibly-damaging	701/903	138740037	6898,6108	2203	4300	6503	SO:0001583	missense	56829	exon10			CTGGCTGATGGCT	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2101C>G	7.37:g.138740037G>C	ENSP00000242351:p.Gln701Glu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	26	7	0.269231	NM_020119	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	1263	0.5782967032967034	236	0.4796747967479675	203	0.5607734806629834	396	0.6923076923076923	428	0.5646437994722955	G	9.696	1.153136	0.21371	0.459374	0.566744	ENSG00000105939	ENST00000242351;ENST00000464606	T;T	0.06933	3.3;3.24	3.68	1.78	0.24846	.	0.662632	0.13300	N	0.398338	T	0.00012	0.0000	M	0.70595	2.14	0.58432	P	1.0000000000287557E-6	B	0.21452	0.056	B	0.19148	0.024	T	0.26815	-1.0092	9	0.12103	T	0.63	.	6.474	0.22024	0.0:0.2016:0.5901:0.2083	rs2297236;rs17682077;rs52835032;rs57637678;rs2297236	701	Q7Z2W4	ZCCHV_HUMAN	E	701;823	ENSP00000242351:Q701E;ENSP00000418385:Q823E	ENSP00000242351:Q701E	Q	-	1	0	ZC3HAV1	138390577	0.003000	0.15002	0.030000	0.17652	0.039000	0.13416	0.699000	0.25586	0.508000	0.28173	0.591000	0.81541	CAG	G|0.451;C|0.549	0.549	strong		0.443	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
CCDC67	159989	hgsc.bcm.edu	37	11	93129483	93129483	+	Missense_Mutation	SNP	G	G	C	rs386756254|rs12288277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	141	0	0		WXS	Illumina HiSeq	Phase_I	253	60	0.237154	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	
EPHB3	2049	hgsc.bcm.edu	37	3	184290348	184290348	+	Silent	SNP	G	G	A	rs9862375	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:184290348G>A	ENST00000330394.2	+	3	692	c.240G>A	c.(238-240)gtG>gtA	p.V80V	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	80	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			CATACCAGGTGTGTAATGTGC	0.547													G|||	288	0.057508	0.0877	0.072	5008	,	,		19487	0.0		0.1074	False		,,,				2504	0.0143				p.V80V		Atlas-SNP	.											.	EPHB3	114	.	0			c.G240A						PASS	.	G		379,4027	189.9+/-215.9	20,339,1844	65.0	60.0	62.0		240	5.5	1.0	3	dbSNP_119	62	837,7763	191.8+/-238.0	49,739,3512	no	coding-synonymous	EPHB3	NM_004443.3		69,1078,5356	AA,AG,GG		9.7326,8.6019,9.3495		80/999	184290348	1216,11790	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon3			CCAGGTGTGTAAT	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.240G>A	3.37:g.184290348G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	171	85	0.497076	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			G|0.918;A|0.082	0.082	strong		0.547	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
LAMA5	3911	hgsc.bcm.edu	37	20	60897104	60897104	+	Missense_Mutation	SNP	C	C	T	rs141208202	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	47	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	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	
OPN1LW	5956	hgsc.bcm.edu	37	X	153421912	153421912	+	Silent	SNP	T	T	C	rs1065439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:153421912T>C	ENST00000369951.4	+	5	948	c.888T>C	c.(886-888)ggT>ggC	p.G296G		NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	296					phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|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)			endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	15	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CCAACCCTGGTTACGCCTTCC	0.537													C|||	566	0.149934	0.3245	0.0548	3775	,	,		14896	0.0159		0.0606	False		,,,				2504	0.0225				p.G296G		Atlas-SNP	.											.	OPN1LW	87	.	0			c.T888C						PASS	.	C		1383,2445		200,780,203,652,361	392.0	348.0	363.0		888	4.6	1.0	X	dbSNP_86	363	609,6091		23,378,185,2027,1659	no	coding-synonymous	OPN1LW	NM_020061.4		223,1158,388,2679,2020	CC,CT,C,TT,T		9.0896,36.1285,18.921		296/365	153421912	1992,8536	2196	4272	6468	SO:0001819	synonymous_variant	5956	exon5			CCCTGGTTACGCC	Z68193	CCDS14742.1	Xq28	2013-01-08	2008-04-16		ENSG00000102076	ENSG00000102076		"""GPCR / Class A : Opsin receptors"""	9936	protein-coding gene	gene with protein product	"""cone dystrophy 5 (X-linked)"""	300822	"""color blindness, protan"", ""red cone photoreceptor pigment"""	CBBM, RCP, CBP			Standard	NM_020061		Approved	COD5	uc004fjz.4	P04000	OTTHUMG00000034295	ENST00000369951.4:c.888T>C	X.37:g.153421912T>C		Somatic	695	2	0.0028777		WXS	Illumina HiSeq	Phase_I	352	345	0.980114	NM_020061		Silent	SNP	ENST00000369951.4	37	CCDS14742.1																																																																																			0|0.004;C|0.185	0.185	strong		0.537	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
SNF8	11267	hgsc.bcm.edu	37	17	47007963	47007963	+	Silent	SNP	C	C	T	rs2270576	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:47007963C>T	ENST00000502492.1	-	8	1033	c.651G>A	c.(649-651)ctG>ctA	p.L217L	AC091133.1_ENST00000435491.1_RNA|SNF8_ENST00000290330.3_Silent_p.L216L|SNF8_ENST00000514089.1_5'UTR			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	35	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	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	
OR8D2	283160	hgsc.bcm.edu	37	11	124189729	124189729	+	Missense_Mutation	SNP	C	C	T	rs2512219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:124189729C>T	ENST00000357438.2	-	1	455	c.365G>A	c.(364-366)cGt>cAt	p.R122H		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	122			R -> H (in dbSNP:rs2512219).			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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		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;0.0525)		AGCAACATAACGGTCATATTC	0.413													C|||	1390	0.277556	0.4531	0.2003	5008	,	,		21904	0.1895		0.1292	False		,,,				2504	0.3384				p.R122H		Atlas-SNP	.											.	OR8D2	65	.	0			c.G365A						PASS	.	C	HIS/ARG	1863,2539	632.0+/-395.8	384,1095,722	93.0	88.0	90.0		365	1.6	0.3	11	dbSNP_100	90	1275,7323	759.9+/-407.6	112,1051,3136	yes	missense	OR8D2	NM_001002918.1	29	496,2146,3858	TT,TC,CC		14.829,42.3217,24.1385	benign	122/312	124189729	3138,9862	2201	4299	6500	SO:0001583	missense	283160	exon1			ACATAACGGTCAT	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"""GPCR / Class A : Olfactory receptors"""	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.365G>A	11.37:g.124189729C>T	ENSP00000350022:p.Arg122His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	113	39	0.345133	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	37	CCDS31707.1	520	0.23809523809523808	224	0.45528455284552843	71	0.19613259668508287	124	0.21678321678321677	101	0.13324538258575197	t	8.823	0.938032	0.18206	0.423217	0.14829	ENSG00000197263	ENST00000357438	T	0.77489	-1.1	3.59	1.61	0.23674	GPCR, rhodopsin-like superfamily (1);	0.277746	0.25817	N	0.028104	T	0.00012	0.0000	M	0.81179	2.53	0.31244	P	0.6948639999999999	B	0.06786	0.001	B	0.04013	0.001	T	0.27905	-1.0060	9	0.87932	D	0	.	9.5229	0.39147	0.0:0.8075:0.0:0.1925	rs2512219;rs52814690;rs56609149;rs61070044;rs2512219	122	Q9GZM6	OR8D2_HUMAN	H	122	ENSP00000350022:R122H	ENSP00000350022:R122H	R	-	2	0	OR8D2	123694939	0.978000	0.34361	0.318000	0.25279	0.021000	0.10359	5.273000	0.65564	0.473000	0.27368	-0.271000	0.10264	CGT	C|0.749;T|0.250	0.250	strong		0.413	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918	
HCAR3	8843	hgsc.bcm.edu	37	12	123200937	123200937	+	Silent	SNP	T	T	G	rs1696352	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:123200937T>G	ENST00000528880.2	-	1	502	c.348A>C	c.(346-348)atA>atC	p.I116I	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	116					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)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9					Niacin(DB00627)	CCGTGAGGAATATGATGCTGC	0.557													N|||	2322	0.463658	0.5008	0.4409	5008	,	,		18413	0.495		0.5726	False		,,,				2504	0.2853				p.I116I		Atlas-SNP	.											.	HCAR3	49	.	0			c.A348C						PASS	.	G		2232,2174	585.5+/-386.3	583,1066,554	72.0	72.0	72.0		348	1.3	1.0	12	dbSNP_89	72	4931,3669	526.8+/-381.0	1416,2099,785	no	coding-synonymous	HCAR3	NM_006018.2		1999,3165,1339	GG,GT,TT		42.6628,49.3418,44.9254		116/388	123200937	7163,5843	2203	4300	6503	SO:0001819	synonymous_variant	8843	exon1			GAGGAATATGATG	D10923	CCDS53842.1	12q24.31	2012-08-08	2011-05-30	2011-05-30		ENSG00000255398		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	16824	protein-coding gene	gene with protein product		606039	"""G protein-coupled receptor 109B"""	GPR109B		7505609, 9205127, 18983141, 21454438	Standard	NM_006018		Approved	HCA3, HM74	uc001ucy.4	P49019		ENST00000528880.2:c.348A>C	12.37:g.123200937T>G		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_006018	A8K4G5|B2R830|E9PI97|Q8NGE4	Silent	SNP	ENST00000528880.2	37	CCDS53842.1																																																																																			T|0.468;G|0.532	0.532	strong		0.557	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387549.2	NM_006018	
SLC17A5	26503	hgsc.bcm.edu	37	6	74354175	74354175	+	Silent	SNP	C	C	T	rs472294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:74354175C>T	ENST00000355773.5	-	2	514	c.246G>A	c.(244-246)gcG>gcA	p.A82A	SLC17A5_ENST00000481996.1_5'UTR|SLC17A5_ENST00000393019.3_Silent_p.A82A	NM_012434.4	NP_036566.1	Q9NRA2	S17A5_HUMAN	solute carrier family 17 (acidic sugar transporter), member 5	82					amino acid transport (GO:0006865)|anion transport (GO:0006820)|ion transport (GO:0006811)|proton transport (GO:0015992)|sialic acid transport (GO:0015739)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	sialic acid transmembrane transporter activity (GO:0015136)|sugar:proton symporter activity (GO:0005351)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GCTCTGGACACGCCTTGGAAG	0.343													C|||	667	0.133187	0.1641	0.1571	5008	,	,		15464	0.1845		0.0726	False		,,,				2504	0.0838				p.A82A		Atlas-SNP	.											.	SLC17A5	42	.	0			c.G246A						PASS	.	C		695,3711	291.5+/-281.6	62,571,1570	74.0	72.0	73.0		246	1.6	0.8	6	dbSNP_83	73	631,7969	162.6+/-215.3	25,581,3694	no	coding-synonymous	SLC17A5	NM_012434.4		87,1152,5264	TT,TC,CC		7.3372,15.7739,10.1953		82/496	74354175	1326,11680	2203	4300	6503	SO:0001819	synonymous_variant	26503	exon2			TGGACACGCCTTG	AJ387747	CCDS4981.1	6q13	2013-07-18	2013-07-18		ENSG00000119899	ENSG00000119899		"""Solute carriers"""	10933	protein-coding gene	gene with protein product		604322	"""sialic acid storage disease"", ""solute carrier family 17 (anion/sugar transporter), member 5"""	SIASD		10581036, 8198127	Standard	NM_012434		Approved	AST, SD, ISSD, NSD, SIALIN, SLD	uc003phn.4	Q9NRA2	OTTHUMG00000015039	ENST00000355773.5:c.246G>A	6.37:g.74354175C>T		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_012434	Q5SZ76|Q8NBR5|Q9UGH0	Silent	SNP	ENST00000355773.5	37	CCDS4981.1																																																																																			C|0.888;T|0.112	0.112	strong		0.343	SLC17A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041228.1		
DNAH17	8632	hgsc.bcm.edu	37	17	76433899	76433899	+	Missense_Mutation	SNP	G	G	A	rs386799532|rs61742072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76433899G>A	ENST00000585328.1	-	74	11966	c.11842C>T	c.(11842-11844)Cac>Tac	p.H3948Y	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Missense_Mutation_p.H3947Y	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3947	AAA 6. {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(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)			GTGCTGTAGTGCTCCAGCTTC	0.617													G|||	530	0.105831	0.0257	0.1095	5008	,	,		17133	0.1012		0.1889	False		,,,				2504	0.1309				p.H3953Y		Atlas-SNP	.											DNAH17,NS,carcinoma,+1,1	DNAH17	347	1	0			c.C11857T						PASS	.	G	TYR/HIS	203,4201		5,193,2004	48.0	49.0	49.0		11857	3.0	1.0	17	dbSNP_129	49	1438,7158		136,1166,2996	yes	missense	DNAH17	NM_173628.3	83	141,1359,5000	AA,AG,GG		16.7287,4.6094,12.6231	benign	3953/4463	76433899	1641,11359	2202	4298	6500	SO:0001583	missense	8632	exon74			TGTAGTGCTCCAG	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.11842C>T	17.37:g.76433899G>A	ENSP00000465516:p.His3948Tyr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	108	63	0.583333	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		278	0.12728937728937728	30	0.06097560975609756	46	0.1270718232044199	59	0.10314685314685315	143	0.18865435356200527	G	12.35	1.912274	0.33721	0.046094	0.167287	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.08282	3.11	5.07	2.96	0.34315	.	0.000000	0.53938	D	0.000049	T	0.00012	0.0000	L	0.43554	1.36	0.51767	P	6.60000000000105E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.37337	-0.9710	9	0.33940	T	0.23	.	14.0729	0.64870	0.0:0.0:0.6129:0.387	.	3948	E7EUM8	.	Y	3948;3947	ENSP00000374490:H3947Y	ENSP00000300671:H3948Y	H	-	1	0	DNAH17	73945494	0.997000	0.39634	0.997000	0.53966	0.720000	0.41350	2.564000	0.45931	1.112000	0.41740	0.561000	0.74099	CAC	G|0.865;A|0.135	0.135	strong		0.617	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
MDH1B	130752	hgsc.bcm.edu	37	2	207619779	207619779	+	Silent	SNP	A	A	G	rs59358632	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:207619779A>G	ENST00000374412.3	-	5	1139	c.864T>C	c.(862-864)ggT>ggC	p.G288G	MDH1B_ENST00000454776.2_Silent_p.G288G|MDH1B_ENST00000392214.2_Intron|MDH1B_ENST00000449792.1_Silent_p.G190G	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	288					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)		CTTTCGCTTCACCTTCCACCC	0.428													A|||	573	0.114417	0.2595	0.0548	5008	,	,		19768	0.0526		0.0586	False		,,,				2504	0.0818				p.G288G	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.T864C						PASS	.	A		1059,3347	386.5+/-326.1	130,799,1274	92.0	85.0	87.0		864	-5.9	0.0	2	dbSNP_129	87	649,7951	165.8+/-217.9	31,587,3682	no	coding-synonymous	MDH1B	NM_001039845.1		161,1386,4956	GG,GA,AA		7.5465,24.0354,13.1324		288/519	207619779	1708,11298	2203	4300	6503	SO:0001819	synonymous_variant	130752	exon5			CGCTTCACCTTCC		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.864T>C	2.37:g.207619779A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	124	28	0.225806	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Silent	SNP	ENST00000374412.3	37	CCDS33365.1																																																																																			A|0.884;G|0.116	0.116	strong		0.428	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	
PTCD1	26024	hgsc.bcm.edu	37	7	99017737	99017737	+	Silent	SNP	G	G	A	rs114658645	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99017737G>A	ENST00000292478.4	-	8	2206	c.1956C>T	c.(1954-1956)gaC>gaT	p.D652D	ATP5J2-PTCD1_ENST00000413834.1_Silent_p.D701D|PTCD1_ENST00000555673.1_Silent_p.D701D	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	652					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)	p.D652D(1)		endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CTCGGAAGCCGTCAATCTTCT	0.547													G|||	166	0.033147	0.0098	0.0432	5008	,	,		18400	0.0486		0.0308	False		,,,				2504	0.044				p.D701D		Atlas-SNP	.											PTCD1,caecum,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C2103T						PASS	.	G	,	54,4352	53.6+/-89.4	1,52,2150	109.0	117.0	114.0		2103,1956	-1.3	1.0	7	dbSNP_132	114	338,8262	116.6+/-176.3	10,318,3972	no	coding-synonymous,coding-synonymous	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	,	11,370,6122	AA,AG,GG		3.9302,1.2256,3.014	,	701/750,652/701	99017737	392,12614	2203	4300	6503	SO:0001819	synonymous_variant	100526740	exon9			GAAGCCGTCAATC	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.1956C>T	7.37:g.99017737G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	173	64	0.369942	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Silent	SNP	ENST00000292478.4	37	CCDS34691.1																																																																																			G|0.968;A|0.032	0.032	strong		0.547	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
DNA2	1763	hgsc.bcm.edu	37	10	70178965	70178965	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70178965T>C	ENST00000358410.3	-	19	2843	c.2793A>G	c.(2791-2793)ggA>ggG	p.G931G	DNA2_ENST00000399179.2_Silent_p.G693G|DNA2_ENST00000399180.2_Silent_p.G1017G	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	931	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						AGGGACTGCATCCAGCCTAAA	0.323																																					p.G931G		Atlas-SNP	.											.	DNA2	76	.	0			c.A2793G						PASS	.						54.0	46.0	49.0					10																	70178965		1838	4091	5929	SO:0001819	synonymous_variant	1763	exon19			ACTGCATCCAGCC	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.2793A>G	10.37:g.70178965T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37		.	.	.	.	.	.	.	.	.	.	T	8.699	0.909289	0.17833	.	.	ENSG00000138346	ENST00000440722	.	.	.	5.39	-0.794	0.10918	.	.	.	.	.	T	0.50990	0.1648	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40997	-0.9533	4	.	.	.	.	5.9261	0.19112	0.3798:0.0:0.2894:0.3308	.	.	.	.	V	253	.	.	M	-	1	0	DNA2	69848971	1.000000	0.71417	0.989000	0.46669	0.871000	0.50021	0.478000	0.22212	0.009000	0.14813	0.482000	0.46254	ATG	.	.	none		0.323	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
ITGA7	3679	hgsc.bcm.edu	37	12	56092682	56092682	+	Silent	SNP	C	C	T	rs3847675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:56092682C>T	ENST00000555728.1	-	7	970	c.942G>A	c.(940-942)ggG>ggA	p.G314G	ITGA7_ENST00000394229.2_Silent_p.G270G|ITGA7_ENST00000394230.2_Silent_p.G274G|ITGA7_ENST00000347027.6_Silent_p.G270G|ITGA7_ENST00000257880.7_Silent_p.G314G|ITGA7_ENST00000553804.1_Silent_p.G274G|ITGA7_ENST00000452168.2_Silent_p.G177G|ITGA7_ENST00000257879.6_Silent_p.G270G			Q13683	ITA7_HUMAN	integrin, alpha 7	314					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CCAGACCTTTCCCCGAGTCAA	0.617													C|||	175	0.0349441	0.0023	0.0648	5008	,	,		15771	0.0		0.0994	False		,,,				2504	0.0276				p.G274G		Atlas-SNP	.											ITGA7_ENST00000553804,rectum,carcinoma,0,2	ITGA7	194	2	0			c.G822A						PASS	.	C	,,	63,4343		0,63,2140	19.0	20.0	20.0		822,531,810	4.5	1.0	12	dbSNP_108	20	710,7890		38,634,3628	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGA7	NM_001144996.1,NM_001144997.1,NM_002206.2	,,	38,697,5768	TT,TC,CC		8.2558,1.4299,5.9434	,,	274/1142,177/1045,270/1138	56092682	773,12233	2203	4300	6503	SO:0001819	synonymous_variant	3679	exon6			ACCTTTCCCCGAG		CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.942G>A	12.37:g.56092682C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Silent	SNP	ENST00000555728.1	37																																																																																				C|0.941;T|0.059	0.059	strong		0.617	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
PRPF4B	8899	hgsc.bcm.edu	37	6	4044109	4044109	+	Silent	SNP	G	G	A	rs12195092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:4044109G>A	ENST00000337659.6	+	6	1813	c.1713G>A	c.(1711-1713)caG>caA	p.Q571Q	PRPF4B_ENST00000538861.1_Silent_p.Q557Q	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	571					mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GCAGCCCCCAGAGCAGTACGA	0.398													G|||	30	0.00599042	0.0015	0.0058	5008	,	,		18977	0.0		0.0219	False		,,,				2504	0.002				p.Q571Q		Atlas-SNP	.											.	PRPF4B	140	.	0			c.G1713A						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	90.0	85.0	87.0		1713	4.5	1.0	6	dbSNP_120	87	218,8382	91.4+/-153.5	1,216,4083	no	coding-synonymous	PRPF4B	NM_003913.4		1,231,6271	AA,AG,GG		2.5349,0.3404,1.7915		571/1008	4044109	233,12773	2203	4300	6503	SO:0001819	synonymous_variant	8899	exon6			CCCCCAGAGCAGT	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"""PRP4 pre-mRNA processing factor 4 homolog B (yeast)"""			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.1713G>A	6.37:g.4044109G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Silent	SNP	ENST00000337659.6	37	CCDS4488.1																																																																																			G|0.982;A|0.018	0.018	strong		0.398	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2		
LLGL2	3993	hgsc.bcm.edu	37	17	73567846	73567846	+	Missense_Mutation	SNP	C	C	T	rs1661715	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73567846C>T	ENST00000392550.3	+	18	2392	c.2275C>T	c.(2275-2277)Cct>Tct	p.P759S	LLGL2_ENST00000577200.1_Missense_Mutation_p.P759S|LLGL2_ENST00000167462.5_Missense_Mutation_p.P759S	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	759			P -> S (in dbSNP:rs1661715). {ECO:0000269|PubMed:15489334}.		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)			AATGGATGAGCCTGTGCGGGC	0.697													C|||	1552	0.309904	0.5915	0.2435	5008	,	,		17459	0.1508		0.2823	False		,,,				2504	0.1687				p.P759S		Atlas-SNP	.											LLGL2_ENST00000167462,rectum,carcinoma,0,6	LLGL2	155	6	0			c.C2275T						PASS	.	C	SER/PRO,SER/PRO	2440,1962		693,1054,454	29.0	31.0	30.0		2275,2275	4.4	0.8	17	dbSNP_89	30	2542,6054		397,1748,2153	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	74,74	1090,2802,2607	TT,TC,CC		29.5719,44.5706,38.329	benign,benign	759/1021,759/1016	73567846	4982,8016	2201	4298	6499	SO:0001583	missense	3993	exon18			GATGAGCCTGTGC	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.2275C>T	17.37:g.73567846C>T	ENSP00000376333:p.Pro759Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	711	0.32554945054945056	322	0.6544715447154471	87	0.24033149171270718	81	0.14160839160839161	221	0.29155672823219	C	12.78	2.039977	0.35989	0.554294	0.295719	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.08008	3.14;3.26	5.4	4.41	0.53225	.	0.209202	0.51477	D	0.000100	T	0.00012	0.0000	L	0.57536	1.79	0.27633	P	0.947969	B;P;B;B	0.36789	0.434;0.57;0.01;0.003	B;B;B;B	0.39904	0.166;0.313;0.015;0.004	T	0.06516	-1.0822	9	0.33141	T	0.24	-0.6264	10.9596	0.47376	0.1462:0.713:0.1408:0.0	rs1661715;rs17855941;rs60583153;rs1661715	748;748;759;759	B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;L2GL2_HUMAN	S	759;759;748	ENSP00000167462:P759S;ENSP00000376333:P759S	ENSP00000167462:P759S	P	+	1	0	LLGL2	71079441	0.854000	0.29725	0.840000	0.33206	0.932000	0.56968	2.448000	0.44926	1.245000	0.43885	0.549000	0.68633	CCT	C|0.622;T|0.378	0.378	strong		0.697	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
SDK1	221935	hgsc.bcm.edu	37	7	4050731	4050731	+	Silent	SNP	C	C	T	rs61752593	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:4050731C>T	ENST00000404826.2	+	15	2404	c.2265C>T	c.(2263-2265)agC>agT	p.S755S	SDK1_ENST00000389531.3_Silent_p.S755S	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	755	Fibronectin type-III 1. {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)		GCCAGTACAGCGCCGAGACAA	0.607													C|||	465	0.0928514	0.0469	0.1081	5008	,	,		17111	0.0595		0.1312	False		,,,				2504	0.1391				p.S755S		Atlas-SNP	.											.	SDK1	361	.	0			c.C2265T						PASS	.	C		295,4111	160.3+/-192.7	4,287,1912	35.0	31.0	33.0		2265	1.1	0.6	7	dbSNP_129	33	1388,7212	266.1+/-286.5	119,1150,3031	no	coding-synonymous	SDK1	NM_152744.3		123,1437,4943	TT,TC,CC		16.1395,6.6954,12.9402		755/2214	4050731	1683,11323	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon15			GTACAGCGCCGAG	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.2265C>T	7.37:g.4050731C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			C|0.882;T|0.118	0.118	strong		0.607	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
KLK6	5653	hgsc.bcm.edu	37	19	51465096	51465096	+	Silent	SNP	C	C	G	rs1701950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51465096C>G	ENST00000376851.3	-	5	925	c.486G>C	c.(484-486)ctG>ctC	p.L162L	KLK6_ENST00000456750.2_Silent_p.L55L|KLK6_ENST00000376853.4_Intron|CTB-147C22.8_ENST00000601506.1_RNA|KLK6_ENST00000594641.1_Silent_p.L162L|KLK6_ENST00000391808.1_Silent_p.L55L|KLK6_ENST00000310157.2_Silent_p.L162L	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	162	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				amyloid precursor protein metabolic process (GO:0042982)|central nervous system development (GO:0007417)|collagen catabolic process (GO:0030574)|hormone metabolic process (GO:0042445)|myelination (GO:0042552)|neuron death (GO:0070997)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|protein autoprocessing (GO:0016540)|regulation of cell differentiation (GO:0045595)|regulation of neuron projection development (GO:0010975)|response to wounding (GO:0009611)|tissue regeneration (GO:0042246)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|skin(4)	13		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00372)|GBM - Glioblastoma multiforme(134;0.00871)		CACGGGACACCAGGTGGATGT	0.577													C|||	408	0.0814696	0.1853	0.049	5008	,	,		19122	0.0		0.1024	False		,,,				2504	0.0266				p.L162L		Atlas-SNP	.											.	KLK6	35	.	0			c.G486C						PASS	.		,,	739,3667		59,621,1523	156.0	120.0	132.0		486,165,486	2.0	1.0	19	dbSNP_89	132	883,7717		45,793,3462	no	coding-synonymous,coding-synonymous,coding-synonymous	KLK6	NM_001012964.1,NM_001012965.1,NM_002774.3	,,	104,1414,4985	GG,GC,CC		10.2674,16.7726,12.4712	,,	162/245,55/138,162/245	51465096	1622,11384	2203	4300	6503	SO:0001819	synonymous_variant	5653	exon5			GGACACCAGGTGG	U62801	CCDS12811.1, CCDS42599.1	19q13.3	2011-09-07	2006-10-27			ENSG00000167755		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6367	protein-coding gene	gene with protein product		602652	"""protease, serine, 18"", ""kallikrein 6 (neurosin, zyme)"""	PRSS9, PRSS18		9003450, 16800724, 16800723	Standard	NM_002774		Approved	Bssp, Klk7, neurosin	uc002pui.3	Q92876		ENST00000376851.3:c.486G>C	19.37:g.51465096C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	114	60	0.526316	NM_001012964	A6NJA1|A8MW09|Q6H301	Silent	SNP	ENST00000376851.3	37	CCDS12811.1																																																																																			C|0.883;G|0.117	0.117	strong		0.577	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774	
CLCN7	1186	hgsc.bcm.edu	37	16	1500501	1500501	+	Silent	SNP	C	C	T	rs117461525	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1500501C>T	ENST00000382745.4	-	17	2219	c.1614G>A	c.(1612-1614)gcG>gcA	p.A538A	CLCN7_ENST00000262318.8_Silent_p.A514A|LA16c-390E6.4_ENST00000563610.1_RNA|CLCN7_ENST00000448525.1_Silent_p.A514A	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	538					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				CACTCACCGCCGCCCCCGTGA	0.697													C|||	187	0.0373403	0.0189	0.0749	5008	,	,		11861	0.0		0.0875	False		,,,				2504	0.0225				p.A538A		Atlas-SNP	.											.	CLCN7	53	.	0			c.G1614A						PASS	.	C	,	145,4175		2,141,2017	15.0	18.0	17.0		1542,1614	-9.0	0.9	16	dbSNP_132	17	851,7713		35,781,3466	no	coding-synonymous,coding-synonymous	CLCN7	NM_001114331.1,NM_001287.4	,	37,922,5483	TT,TC,CC		9.9369,3.3565,7.7305	,	514/782,538/806	1500501	996,11888	2160	4282	6442	SO:0001819	synonymous_variant	1186	exon17			CACCGCCGCCCCC	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.1614G>A	16.37:g.1500501C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			C|0.940;T|0.060	0.060	strong		0.697	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77359919	77359919	+	Missense_Mutation	SNP	A	A	T	rs11640912	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:77359919A>T	ENST00000282849.5	-	13	2294	c.1876T>A	c.(1876-1878)Tta>Ata	p.L626I		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	626	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.		L -> I (in dbSNP:rs11640912). {ECO:0000269|PubMed:11867212, ECO:0000269|PubMed:15489334}.		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GGACAGAATAAGCCACCATAC	0.368													T|||	2201	0.439497	0.146	0.5562	5008	,	,		19296	0.8681		0.3618	False		,,,				2504	0.3916				p.L626I		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.T1876A						PASS	.	T	ILE/LEU	905,3491	739.6+/-411.1	96,713,1389	70.0	64.0	66.0		1876	4.8	1.0	16	dbSNP_120	66	3239,5361	649.3+/-400.6	615,2009,1676	yes	missense	ADAMTS18	NM_199355.2	5	711,2722,3065	TT,TA,AA		37.6628,20.5869,31.8867	benign	626/1222	77359919	4144,8852	2198	4300	6498	SO:0001583	missense	170692	exon13			AGAATAAGCCACC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.1876T>A	16.37:g.77359919A>T	ENSP00000282849:p.Leu626Ile	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	132	22	0.166667	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	1037	0.4748168498168498	72	0.14634146341463414	195	0.5386740331491713	494	0.8636363636363636	276	0.3641160949868074	T	16.49	3.137533	0.56936	0.205869	0.376628	ENSG00000140873	ENST00000282849	T	0.03553	3.89	5.98	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.33624	1.015	0.80722	P	0.0	B;B	0.15930	0.015;0.007	B;B	0.11329	0.006;0.005	T	0.12218	-1.0556	9	0.87932	D	0	.	8.6403	0.33972	0.1282:0.0:0.1344:0.7373	rs11640912;rs17855796;rs52810617;rs11640912	626;626	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	I	626	ENSP00000282849:L626I	ENSP00000282849:L626I	L	-	1	2	ADAMTS18	75917420	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	4.234000	0.58658	1.087000	0.41251	-0.265000	0.10407	TTA	A|0.625;T|0.375	0.375	strong		0.368	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
R3HCC1L	27291	hgsc.bcm.edu	37	10	99969507	99969507	+	Missense_Mutation	SNP	C	C	T	rs35122894	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:99969507C>T	ENST00000298999.3	+	5	1939	c.1636C>T	c.(1636-1638)Cct>Tct	p.P546S	R3HCC1L_ENST00000370584.3_Missense_Mutation_p.P546S|R3HCC1L_ENST00000370586.2_Intron|R3HCC1L_ENST00000314594.5_5'UTR	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	546			P -> S (in dbSNP:rs35122894).				nucleotide binding (GO:0000166)										TGTATCTTTTCCTGATAGGGA	0.428													C|||	48	0.00958466	0.0015	0.013	5008	,	,		19570	0.0		0.0258	False		,,,				2504	0.0112				p.P546S		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.C1636T						PASS	.	C	SER/PRO	23,4383	29.9+/-59.1	0,23,2180	138.0	133.0	134.0		1636	-0.9	0.4	10	dbSNP_126	134	271,8329	102.9+/-164.1	5,261,4034	yes	missense	C10orf28	NM_014472.4	74	5,284,6214	TT,TC,CC		3.1512,0.522,2.2605	benign	546/779	99969507	294,12712	2203	4300	6503	SO:0001583	missense	27291	exon4			TCTTTTCCTGATA	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.1636C>T	10.37:g.99969507C>T	ENSP00000298999:p.Pro546Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	60	20	0.333333	NM_001256620	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	26	0.011904761904761904	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	18	0.023746701846965697	C	0.006	-2.029569	0.00410	0.00522	0.031512	ENSG00000166024	ENST00000370584;ENST00000298999	T;T	0.06142	3.34;3.34	4.85	-0.872	0.10638	.	0.467092	0.20282	N	0.095430	T	0.01558	0.0050	L	0.46741	1.465	0.19575	N	0.999967	B;B	0.26975	0.1;0.165	B;B	0.30855	0.032;0.121	T	0.36720	-0.9736	9	.	.	.	-3.1923	4.044	0.09764	0.0:0.3398:0.343:0.3172	rs35122894	546;546	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	S	546	ENSP00000359616:P546S;ENSP00000298999:P546S	.	P	+	1	0	C10orf28	99959497	0.975000	0.34042	0.373000	0.26003	0.026000	0.11368	0.183000	0.16919	0.153000	0.19213	0.491000	0.48974	CCT	C|0.980;T|0.020	0.020	strong		0.428	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
TAT	6898	hgsc.bcm.edu	37	16	71602660	71602660	+	Missense_Mutation	SNP	G	G	A	rs142634310	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:71602660G>A	ENST00000355962.4	-	11	1311	c.1178C>T	c.(1177-1179)aCg>aTg	p.T393M	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	393					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	TAACCGCTCCGTGAACTCCAC	0.517																																					p.T393M	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.C1178T						PASS	.	G	MET/THR	0,4396		0,0,2198	82.0	69.0	73.0		1178	4.9	1.0	16	dbSNP_134	73	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TAT	NM_000353.2	81	0,3,6495	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	393/455	71602660	3,12993	2198	4300	6498	SO:0001583	missense	6898	exon11			CGCTCCGTGAACT		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.1178C>T	16.37:g.71602660G>A	ENSP00000348234:p.Thr393Met	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	156	32	0.205128	NM_000353	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	37	CCDS10903.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.353229	0.82132	0.0	3.49E-4	ENSG00000198650	ENST00000355962	D	0.90676	-2.71	5.93	4.93	0.64822	Tyrosine aminotransferase (1);Aminotransferase, class I/classII (1);Tyrosine/nicotianamine aminotransferase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.94089	0.8105	L	0.55103	1.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93537	0.6874	10	0.49607	T	0.09	-17.5761	18.7826	0.91941	0.0:0.1252:0.8748:0.0	.	393	P17735	ATTY_HUMAN	M	393	ENSP00000348234:T393M	ENSP00000348234:T393M	T	-	2	0	TAT	70160161	1.000000	0.71417	0.970000	0.41538	0.977000	0.68977	7.610000	0.82949	2.826000	0.97356	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.517	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1		
TRPV2	51393	hgsc.bcm.edu	37	17	16336992	16336992	+	Silent	SNP	C	C	G	rs14039	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:16336992C>G	ENST00000338560.7	+	13	2493	c.2094C>G	c.(2092-2094)ccC>ccG	p.P698P	TRPV2_ENST00000577397.1_Silent_p.P268P	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	698					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.P698P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		ATGGCAGCCCCGATGAGCGCT	0.627													C|||	1443	0.288139	0.3124	0.3401	5008	,	,		20447	0.2232		0.3579	False		,,,				2504	0.2137				p.P698P		Atlas-SNP	.											TRPV2,NS,carcinoma,0,1	TRPV2	74	1	1	Substitution - coding silent(1)	stomach(1)	c.C2094G						scavenged	.	C		1464,2942	469.4+/-355.4	260,944,999	111.0	97.0	102.0		2094	-5.2	0.1	17	dbSNP_52	102	3244,5356	485.9+/-371.7	609,2026,1665	no	coding-synonymous	TRPV2	NM_016113.4		869,2970,2664	GG,GC,CC		37.7209,33.2274,36.1987		698/765	16336992	4708,8298	2203	4300	6503	SO:0001819	synonymous_variant	51393	exon13			CAGCCCCGATGAG	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.2094C>G	17.37:g.16336992C>G		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	136	58	0.426471	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1																																																																																			T|0.000;G|0.355;C|0.645	0.355	strong		0.627	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
SP110	3431	hgsc.bcm.edu	37	2	231077676	231077676	+	Missense_Mutation	SNP	G	G	A	rs11556887|rs397693036	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231077676G>A	ENST00000358662.4	-	4	461	c.383C>T	c.(382-384)gCa>gTa	p.A128V	SP110_ENST00000258381.6_Missense_Mutation_p.A128V|SP110_ENST00000540870.1_Missense_Mutation_p.A134V|SP110_ENST00000258382.5_Missense_Mutation_p.A128V|SP110_ENST00000392048.3_Missense_Mutation_p.A128V|SP110_ENST00000338556.3_5'UTR|SP110_ENST00000486146.2_5'Flank	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	128			A -> V (in dbSNP:rs11556887). {ECO:0000269|PubMed:16816019}.		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)	p.A128V(1)		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)		GCTTCCTTCTGCTAGGCCAGT	0.567													G|||	484	0.0966454	0.0166	0.049	5008	,	,		16828	0.0764		0.0875	False		,,,				2504	0.2689				p.A134V		Atlas-SNP	.											SP110,NS,carcinoma,0,1	SP110	105	1	1	Substitution - Missense(1)	stomach(1)	c.C401T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	123,4283	92.0+/-130.7	2,119,2082	93.0	92.0	93.0		401,383,383,383	-1.1	0.0	2	dbSNP_120	93	805,7795	187.9+/-235.0	36,733,3531	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	64,64,64,64	38,852,5613	AA,AG,GG		9.3605,2.7916,7.1352	probably-damaging,probably-damaging,probably-damaging,probably-damaging	134/556,128/690,128/550,128/714	231077676	928,12078	2203	4300	6503	SO:0001583	missense	3431	exon5			CCTTCTGCTAGGC	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.383C>T	2.37:g.231077676G>A	ENSP00000351488:p.Ala128Val	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	269	141	0.524164	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	146	0.06684981684981685	7	0.014227642276422764	24	0.06629834254143646	47	0.08216783216783216	68	0.08970976253298153	G	16.05	3.013296	0.54468	0.027916	0.093605	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000409815;ENST00000455674	T;T;T;T;T;T;T	0.08984	3.03;3.03;3.03;3.03;3.03;3.03;3.03	4.11	-1.09	0.09904	.	0.193316	0.25704	N	0.028844	T	0.00496	0.0016	L	0.58101	1.795	0.09310	N	0.999999	P;P;D;D	0.76494	0.762;0.762;0.998;0.999	B;B;P;D	0.68765	0.282;0.282;0.896;0.96	T	0.12993	-1.0526	10	0.30078	T	0.28	.	1.4596	0.02393	0.1903:0.3143:0.3343:0.1611	rs11556887;rs56849823;rs11556887	128;134;128;128	G5E9C0;F5H1M1;Q9HB58;Q9HB58-6	.;.;SP110_HUMAN;.	V	128;128;128;128;134;128;82	ENSP00000258381:A128V;ENSP00000351488:A128V;ENSP00000375902:A128V;ENSP00000258382:A128V;ENSP00000439558:A134V;ENSP00000387172:A128V;ENSP00000393992:A82V	ENSP00000258381:A128V	A	-	2	0	SP110	230785920	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	0.122000	0.15687	-0.221000	0.09973	0.650000	0.86243	GCA	G|0.925;A|0.075	0.075	strong		0.567	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
ACE	1636	hgsc.bcm.edu	37	17	61574642	61574642	+	Missense_Mutation	SNP	G	G	A	rs200754517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:61574642G>A	ENST00000290866.4	+	25	3860	c.3836G>A	c.(3835-3837)cGg>cAg	p.R1279Q	ACE_ENST00000428043.1_Intron|ACE_ENST00000413513.3_Missense_Mutation_p.R664Q|ACE_ENST00000290863.6_Missense_Mutation_p.R705Q|ACE_ENST00000490216.2_Intron|ACE_ENST00000577647.1_Intron|ACE_ENST00000421982.2_Missense_Mutation_p.R484Q	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1279			R -> Q (in dbSNP:rs4980). {ECO:0000269|PubMed:10391210}.		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)	CTCAGCCAGCGGCTCTTCAGC	0.711													g|||	18	0.00359425	0.0045	0.0086	5008	,	,		10868	0.0		0.004	False		,,,				2504	0.002				p.R1279Q		Atlas-SNP	.											.	ACE	187	.	0			c.G3836A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	12,4210		0,12,2099	6.0	7.0	7.0		3836,1991,2114	1.4	1.0	17	dbSNP_134	7	45,8275		0,45,4115	no	missense,missense,missense	ACE	NM_000789.3,NM_001178057.1,NM_152830.2	43,43,43	0,57,6214	AA,AG,GG		0.5409,0.2842,0.4545	probably-damaging,probably-damaging,probably-damaging	1279/1307,664/692,705/733	61574642	57,12485	2111	4160	6271	SO:0001583	missense	1636	exon25			GCCAGCGGCTCTT	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.3836G>A	17.37:g.61574642G>A	ENSP00000290866:p.Arg1279Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	g	15.64	2.894563	0.52121	0.002842	0.005409	ENSG00000159640	ENST00000290866;ENST00000290863;ENST00000413513;ENST00000421982	T;T;T;T	0.36157	1.27;1.46;1.3;1.4	5.0	1.38	0.22167	.	0.443891	0.20440	N	0.092294	T	0.24470	0.0593	M	0.74881	2.28	0.19775	N	0.999959	B;B;B;B	0.24963	0.037;0.056;0.115;0.016	B;B;B;B	0.19148	0.007;0.008;0.024;0.002	T	0.30592	-0.9973	10	0.66056	D	0.02	-41.0389	3.9711	0.09454	0.3618:0.0:0.4692:0.169	rs4980;rs4980	484;664;705;1279	F6X3S4;B4DXI3;P12821-3;P12821	.;.;.;ACE_HUMAN	Q	1279;705;664;484	ENSP00000290866:R1279Q;ENSP00000290863:R705Q;ENSP00000392247:R664Q;ENSP00000387760:R484Q	ENSP00000290863:R705Q	R	+	2	0	ACE	58928374	0.856000	0.29760	0.991000	0.47740	0.992000	0.81027	1.973000	0.40550	0.505000	0.28104	0.457000	0.33378	CGG	.	.	weak		0.711	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
PCDHA10	56139	hgsc.bcm.edu	37	5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	rs142356019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA6_ENST00000527624.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.V509M|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	509	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)	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)			CTACGTGTCGGTGCACGCGGA	0.697													.|||	119	0.023762	0.0121	0.0346	5008	,	,		14546	0.0		0.0716	False		,,,				2504	0.0072				p.V509M		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1525A						PASS	.	G	,MET/VAL,,,,,,,,,,,MET/VAL,MET/VAL	120,4272		4,112,2080	66.0	73.0	71.0		,1525,,,,,,,,,,,1525,1525	3.6	1.0	5	dbSNP_134	71	477,8069		47,383,3843	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	,21,,,,,,,,,,,21,21	51,495,5923	AA,AG,GG		5.5816,2.7322,4.6143	,,,,,,,,,,,,,	,509/949,,,,,,,,,,,509/845,509/686	140237158	597,12341	2196	4273	6469	SO:0001583	missense	56139	exon1			GTGTCGGTGCACG	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.1525G>A	5.37:g.140237158G>A	ENSP00000304234:p.Val509Met	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	87	0.03983516483516483	9	0.018292682926829267	19	0.052486187845303865	0	0.0	59	0.07783641160949868	G	14.28	2.487603	0.44249	0.027322	0.055816	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.67698	-0.28;-0.28	3.63	3.63	0.41609	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17323	0.0416	M	0.64404	1.975	0.43489	P	0.004271000000000025	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	T	0.65446	-0.6166	8	0.59425	D	0.04	.	9.6727	0.40021	0.0974:0.0:0.9026:0.0	.	509;509;509	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	M	509	ENSP00000421030:V509M;ENSP00000304234:V509M	ENSP00000304234:V509M	V	+	1	0	PCDHA10	140217342	.	.	0.998000	0.56505	0.648000	0.38561	.	.	2.007000	0.58848	0.561000	0.74099	GTG	G|0.957;A|0.043	0.043	strong		0.697	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
GAD2	2572	hgsc.bcm.edu	37	10	26575277	26575277	+	Silent	SNP	T	T	C	rs531559223		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:26575277T>C	ENST00000376261.3	+	13	1743	c.1240T>C	c.(1240-1242)Ttg>Ctg	p.L414L	GAD2_ENST00000259271.3_Silent_p.L414L	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	414					glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CTTGTAGGGATTGATGCAGAA	0.363													T|||	1	0.000199681	0.0	0.0	5008	,	,		18191	0.0		0.0	False		,,,				2504	0.001				p.L414L		Atlas-SNP	.											.	GAD2	116	.	0			c.T1240C						PASS	.						102.0	91.0	95.0					10																	26575277		2203	4300	6503	SO:0001819	synonymous_variant	2572	exon13			TAGGGATTGATGC	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"""glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"""			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.1240T>C	10.37:g.26575277T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	56	15	0.267857	NM_000818	Q9UD87	Silent	SNP	ENST00000376261.3	37	CCDS7149.1																																																																																			.	.	none		0.363	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818	
ACAN	176	hgsc.bcm.edu	37	15	89398553	89398553	+	Missense_Mutation	SNP	C	C	A	rs35430524	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:89398553C>A	ENST00000561243.1	+	11	2737	c.2737C>A	c.(2737-2739)Cct>Act	p.P913T	ACAN_ENST00000439576.2_Missense_Mutation_p.P913T|ACAN_ENST00000559004.1_Missense_Mutation_p.P913T|ACAN_ENST00000352105.7_Missense_Mutation_p.P913T			P16112	PGCA_HUMAN	aggrecan	912	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)	p.P913T(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)			CTCAGGCCTGCCTGTGGAAAG	0.587													C|||	487	0.0972444	0.0129	0.147	5008	,	,		19326	0.1944		0.0795	False		,,,				2504	0.0941				p.P913T		Atlas-SNP	.											ACAN,NS,carcinoma,0,1	ACAN	220	1	1	Substitution - Missense(1)	stomach(1)	c.C2737A						PASS	.	C	THR/PRO,THR/PRO	111,3835		3,105,1865	42.0	47.0	45.0		2737,2737	5.3	1.0	15	dbSNP_126	45	783,7521		26,731,3395	yes	missense,missense	ACAN	NM_013227.3,NM_001135.3	38,38	29,836,5260	AA,AC,CC		9.4292,2.813,7.298	benign,benign	913/2531,913/2432	89398553	894,11356	1973	4152	6125	SO:0001583	missense	176	exon12			GGCCTGCCTGTGG	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.2737C>A	15.37:g.89398553C>A	ENSP00000453342:p.Pro913Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	79	54	0.683544	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	224	0.10256410256410256	7	0.014227642276422764	39	0.10773480662983426	115	0.20104895104895104	63	0.08311345646437995	C	14.56	2.570930	0.45798	0.02813	0.094292	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.05447	3.75;3.44	5.33	5.33	0.75918	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.34597	P	0.283867	B;B	0.24963	0.115;0.115	B;B	0.27796	0.083;0.047	T	0.44757	-0.9307	7	0.39692	T	0.17	-10.1741	11.6358	0.51202	0.0:0.9154:0.0:0.0846	rs35430524	913;913	E7ENV9;E7EX88	.;.	T	913	ENSP00000387356:P913T;ENSP00000341615:P913T	ENSP00000268134:P913T	P	+	1	0	ACAN	87199557	0.973000	0.33851	0.999000	0.59377	0.963000	0.63663	2.252000	0.43196	2.476000	0.83614	0.655000	0.94253	CCT	C|0.901;A|0.099	0.099	strong		0.587	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
ZNF480	147657	hgsc.bcm.edu	37	19	52825032	52825032	+	Missense_Mutation	SNP	C	C	T	rs13343641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52825032C>T	ENST00000595962.1	+	5	595	c.529C>T	c.(529-531)Ccc>Tcc	p.P177S	ZNF480_ENST00000335090.6_Missense_Mutation_p.P100S|ZNF480_ENST00000334564.7_Missense_Mutation_p.P134S|CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000490272.1_3'UTR	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	177			P -> S (in dbSNP:rs13343641).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		TGTCAAAACCCCCATTTTTAA	0.343													C|||	841	0.167931	0.1203	0.1513	5008	,	,		19266	0.2292		0.2177	False		,,,				2504	0.1299				p.P177S		Atlas-SNP	.											.	ZNF480	123	.	0			c.C529T						PASS	.	C	SER/PRO	610,3796	265.0+/-266.4	47,516,1640	84.0	82.0	83.0		529	-2.5	0.0	19	dbSNP_121	83	1736,6864	313.7+/-311.4	167,1402,2731	yes	missense	ZNF480	NM_144684.2	74	214,1918,4371	TT,TC,CC		20.186,13.8448,18.0378	benign	177/536	52825032	2346,10660	2203	4300	6503	SO:0001583	missense	147657	exon5			AAAACCCCCATTT	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"""Zinc fingers, C2H2-type"", ""-"""	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.529C>T	19.37:g.52825032C>T	ENSP00000471754:p.Pro177Ser	Somatic	349	0	0		WXS	Illumina HiSeq	Phase_I	311	128	0.411576	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Missense_Mutation	SNP	ENST00000595962.1	37	CCDS12850.2	401	0.18360805860805862	57	0.11585365853658537	60	0.16574585635359115	124	0.21678321678321677	160	0.21108179419525067	C	8.368	0.834575	0.16820	0.138448	0.20186	ENSG00000198464	ENST00000468240;ENST00000334564;ENST00000335090	T;T;T	0.06142	3.48;3.43;3.34	2.02	-2.54	0.06307	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.29716	0.026;0.255	B;B	0.26614	0.005;0.071	T	0.47774	-0.9091	8	0.72032	D	0.01	.	0.1334	0.00076	0.3098:0.2659:0.1932:0.2311	rs13343641;rs52836994;rs58264265;rs13343641	134;177	F8WEZ9;Q8WV37	.;ZN480_HUMAN	S	177;134;100	ENSP00000417424:P177S;ENSP00000334164:P134S;ENSP00000335670:P100S	ENSP00000334164:P134S	P	+	1	0	ZNF480	57516844	0.000000	0.05858	0.006000	0.13384	0.571000	0.35966	-0.315000	0.08081	-0.333000	0.08476	0.313000	0.20887	CCC	C|0.820;T|0.180	0.180	strong		0.343	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684	
SLAMF1	6504	hgsc.bcm.edu	37	1	160580549	160580549	+	Missense_Mutation	SNP	G	G	T	rs3796504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:160580549G>T	ENST00000302035.6	-	7	1346	c.997C>A	c.(997-999)Cca>Aca	p.P333T	SLAMF1_ENST00000538290.1_3'UTR|SLAMF1_ENST00000235739.5_Missense_Mutation_p.P303T	NM_003037.2	NP_003028.1	Q13291	SLAF1_HUMAN	signaling lymphocytic activation molecule family member 1	333			P -> T (in dbSNP:rs3796504).		lymphocyte activation (GO:0046649)|positive regulation of cell proliferation (GO:0008284)|regulation of catalytic activity (GO:0050790)|regulation of vesicle fusion (GO:0031338)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|phagocytic vesicle (GO:0045335)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(52;4.94e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.0175)			CAGCTCTCTGGAAGTGTCACA	0.458													G|||	198	0.0395367	0.0015	0.0648	5008	,	,		23451	0.005		0.0835	False		,,,				2504	0.0634				p.P333T		Atlas-SNP	.											.	SLAMF1	74	.	0			c.C997A						PASS	.	G	THR/PRO	77,4329	67.6+/-105.2	2,73,2128	189.0	179.0	182.0		997	4.1	1.0	1	dbSNP_107	182	764,7836	181.8+/-230.4	35,694,3571	yes	missense	SLAMF1	NM_003037.2	38	37,767,5699	TT,TG,GG		8.8837,1.7476,6.4662	probably-damaging	333/336	160580549	841,12165	2203	4300	6503	SO:0001583	missense	6504	exon7			TCTCTGGAAGTGT	U33017	CCDS1207.1	1q23.3	2013-01-11	2003-10-29	2003-10-31	ENSG00000117090	ENSG00000117090		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10903	protein-coding gene	gene with protein product		603492	"""signaling lymphocytic activation molecule"""	SLAM		7617038	Standard	XM_005245456		Approved	CD150	uc001fwl.4	Q13291	OTTHUMG00000024006	ENST00000302035.6:c.997C>A	1.37:g.160580549G>T	ENSP00000306190:p.Pro333Thr	Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	416	233	0.560096	NM_003037	Q5W172|Q9HBE8	Missense_Mutation	SNP	ENST00000302035.6	37	CCDS1207.1	91	0.041666666666666664	1	0.0020325203252032522	28	0.07734806629834254	3	0.005244755244755245	59	0.07783641160949868	G	19.02	3.746407	0.69418	0.017476	0.088837	ENSG00000117090	ENST00000302035;ENST00000235739	T;T	0.25912	2.38;1.77	4.08	4.08	0.47627	.	0.637739	0.13461	N	0.386171	T	0.29620	0.0739	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.03202	-1.1061	10	0.72032	D	0.01	-13.9014	12.092	0.53733	0.0:0.0:1.0:0.0	rs3796504;rs17394334;rs61468578;rs3796504	333	Q13291	SLAF1_HUMAN	T	333;303	ENSP00000306190:P333T;ENSP00000235739:P303T	ENSP00000235739:P303T	P	-	1	0	SLAMF1	158847173	0.998000	0.40836	0.996000	0.52242	0.981000	0.71138	3.668000	0.54554	2.539000	0.85634	0.655000	0.94253	CCA	G|0.945;T|0.055	0.055	strong		0.458	SLAMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060454.1		
CCDC110	256309	hgsc.bcm.edu	37	4	186380243	186380243	+	Missense_Mutation	SNP	A	A	C	rs59319722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:186380243A>C	ENST00000307588.3	-	6	1573	c.1498T>G	c.(1498-1500)Tac>Gac	p.Y500D	CCDC110_ENST00000510617.1_Missense_Mutation_p.Y500D|CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Missense_Mutation_p.Y463D	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	500			Y -> D (in dbSNP:rs59319722).			nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TCTTTGCTGTATTCTTCTGTT	0.274													C|||	1927	0.384784	0.2784	0.3631	5008	,	,		16317	0.2857		0.5378	False		,,,				2504	0.4888				p.Y500D		Atlas-SNP	.											.	CCDC110	78	.	0			c.T1498G						PASS	.	C	ASP/TYR,ASP/TYR	1438,2954		230,978,988	27.0	28.0	28.0		1387,1498	4.2	0.1	4	dbSNP_129	28	4818,3740		1364,2090,825	yes	missense,missense	CCDC110	NM_001145411.1,NM_152775.3	160,160	1594,3068,1813	CC,CA,AA		43.7018,32.7413,48.3089	benign,benign	463/797,500/834	186380243	6256,6694	2196	4279	6475	SO:0001583	missense	256309	exon6			TGCTGTATTCTTC	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.1498T>G	4.37:g.186380243A>C	ENSP00000306776:p.Tyr500Asp	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	41	8	0.195122	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	37	CCDS3843.1	856	0.39194139194139194	148	0.3008130081300813	147	0.40607734806629836	161	0.28146853146853146	400	0.5277044854881267	C	0	-2.653368	0.00109	0.327413	0.562982	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.04406	3.63;3.65;3.65	5.96	4.25	0.50352	.	0.427611	0.22036	N	0.065525	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.39057	-0.9632	9	0.02654	T	1	-2.8884	7.4078	0.27001	0.1356:0.7252:0.0:0.1391	rs59319722;rs62345630	500;463;500	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	D	463;500;500	ENSP00000377172:Y463D;ENSP00000306776:Y500D;ENSP00000427246:Y500D	ENSP00000306776:Y500D	Y	-	1	0	CCDC110	186617237	0.987000	0.35691	0.075000	0.20258	0.106000	0.19336	2.024000	0.41049	0.446000	0.26666	-0.121000	0.15023	TAC	A|0.548;C|0.452	0.452	strong		0.274	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
MAP1B	4131	hgsc.bcm.edu	37	5	71495041	71495041	+	Silent	SNP	T	T	C	rs3805452	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:71495041T>C	ENST00000296755.7	+	5	6157	c.5859T>C	c.(5857-5859)ggT>ggC	p.G1953G		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1953					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		CTGAAGAGGGTGGGTACTCAT	0.473													T|||	1513	0.302117	0.1112	0.2723	5008	,	,		18257	0.5526		0.2555	False		,,,				2504	0.3712				p.G1953G	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T5859C						PASS	.	T		576,3830	240.9+/-251.5	37,502,1664	60.0	64.0	63.0		5859	-5.5	0.0	5	dbSNP_107	63	2175,6425	341.2+/-323.9	285,1605,2410	no	coding-synonymous	MAP1B	NM_005909.3		322,2107,4074	CC,CT,TT		25.2907,13.0731,21.1518		1953/2469	71495041	2751,10255	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			AGAGGGTGGGTAC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.5859T>C	5.37:g.71495041T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	51	49	0.960784	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			T|0.749;C|0.251	0.251	strong		0.473	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
ZNF300	91975	hgsc.bcm.edu	37	5	150275835	150275835	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:150275835C>A	ENST00000274599.5	-	6	1386	c.966G>T	c.(964-966)gaG>gaT	p.E322D	ZNF300_ENST00000418587.2_Missense_Mutation_p.E286D|ZNF300_ENST00000427179.1_3'UTR|ZNF300_ENST00000446148.2_Missense_Mutation_p.E338D|ZNF300_ENST00000394226.2_Missense_Mutation_p.E322D	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)	27		Medulloblastoma(196;0.109)|all_hematologic(541;0.131)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CATAAGGTTTCTCCCCAGTAT	0.398																																					p.E338D		Atlas-SNP	.											.	ZNF300	69	.	0			c.G1014T						PASS	.						84.0	89.0	87.0					5																	150275835		2202	4299	6501	SO:0001583	missense	91975	exon7			AGGTTTCTCCCCA	AF395541	CCDS4311.2, CCDS54939.1, CCDS54940.1	5q33.1	2013-01-08			ENSG00000145908	ENSG00000145908		"""Zinc fingers, C2H2-type"", ""-"""	13091	protein-coding gene	gene with protein product		612429				14746915	Standard	NM_052860		Approved		uc021yfx.1	Q96RE9	OTTHUMG00000130076	ENST00000274599.5:c.966G>T	5.37:g.150275835C>A	ENSP00000274599:p.Glu322Asp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	102	26	0.254902	NM_001172831	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Missense_Mutation	SNP	ENST00000274599.5	37	CCDS4311.2	.	.	.	.	.	.	.	.	.	.	C	17.05	3.289152	0.59976	.	.	ENSG00000145908	ENST00000446148;ENST00000274599;ENST00000418587;ENST00000394226	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	3.59	2.71	0.32032	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29817	0.0745	L	0.41961	1.31	0.26287	N	0.97818	P	0.47484	0.896	P	0.50136	0.632	T	0.08432	-1.0722	9	0.72032	D	0.01	.	8.7303	0.34494	0.0:0.8839:0.0:0.1161	.	322	Q96RE9	ZN300_HUMAN	D	338;322;286;322	ENSP00000397178:E338D;ENSP00000274599:E322D;ENSP00000392593:E286D;ENSP00000377773:E322D	ENSP00000274599:E322D	E	-	3	2	ZNF300	150256028	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.994000	0.40757	0.846000	0.35142	0.563000	0.77884	GAG	.	.	none		0.398	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_052860	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144875979	144875979	+	Silent	SNP	G	G	C	rs71664005	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:144875979G>C	ENST00000369354.3	-	29	4890	c.4701C>G	c.(4699-4701)ctC>ctG	p.L1567L	RP4-791M13.5_ENST00000531288.1_RNA|PDE4DIP_ENST00000313382.9_Silent_p.L1523L|PDE4DIP_ENST00000369356.4_Silent_p.L1567L|PDE4DIP_ENST00000369359.4_Silent_p.L1703L|PDE4DIP_ENST00000530740.1_Silent_p.L1703L|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1567	NBPF. {ECO:0000255|PROSITE- ProRule:PRU00647}.				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)		TGAATTACCTGAGGGCCAGTG	0.468			T	PDGFRB	MPD																																p.L1567L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C4701G						PASS	.	G	,,	210,4196		0,210,1993	224.0	225.0	225.0		4569,4701,4701	4.2	1.0	1	dbSNP_130	225	1462,7130		0,1462,2834	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,1672,4827	CC,CG,GG		17.0158,4.7662,12.8635	,,	1523/2241,1567/2363,1567/2347	144875979	1672,11326	2203	4296	6499	SO:0001819	synonymous_variant	9659	exon29			TTACCTGAGGGCC	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.4701C>G	1.37:g.144875979G>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	172	64	0.372093	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																																																																																			G|0.216;C|0.784	0.784	strong		0.468	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
PDE2A	5138	hgsc.bcm.edu	37	11	72288599	72288599	+	Silent	SNP	G	G	A	rs1980091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:72288599G>A	ENST00000334456.5	-	31	2900	c.2655C>T	c.(2653-2655)taC>taT	p.Y885Y	PDE2A_ENST00000376450.3_Silent_p.Y629Y|PDE2A_ENST00000544570.1_Silent_p.Y878Y|PDE2A_ENST00000444035.2_Silent_p.Y876Y|PDE2A_ENST00000540345.1_Silent_p.Y876Y|PDE2A_ENST00000418754.2_Silent_p.Y770Y	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	885	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)	CCACGCGCTCGTACAGCTCTG	0.612													G|||	1435	0.286542	0.2526	0.245	5008	,	,		19145	0.2758		0.3082	False		,,,				2504	0.3507				p.Y885Y		Atlas-SNP	.											PDE2A,NS,adenoma,0,1	PDE2A	156	1	0			c.C2655T						scavenged	.	G	,,	1182,3218	415.7+/-337.3	146,890,1164	93.0	73.0	80.0		2634,2628,2655	-5.0	1.0	11	dbSNP_92	80	2616,5970	421.9+/-353.9	399,1818,2076	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE2A	NM_001143839.3,NM_001146209.2,NM_002599.4	,,	545,2708,3240	AA,AG,GG		30.4682,26.8636,29.2469	,,	878/935,876/933,885/942	72288599	3798,9188	2200	4293	6493	SO:0001819	synonymous_variant	5138	exon31			GCGCTCGTACAGC	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.2655C>T	11.37:g.72288599G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_002599	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Silent	SNP	ENST00000334456.5	37	CCDS8216.1																																																																																			G|0.707;A|0.293	0.293	strong		0.612	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518333	161518333	+	Missense_Mutation	SNP	A	A	C	rs10127939	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161518333A>C	ENST00000436743.1	-	4	351	c.197T>G	c.(196-198)cTc>cGc	p.L66R	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000443193.1_Missense_Mutation_p.L101R|FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000367969.3_Missense_Mutation_p.L102R|FCGR3A_ENST00000540048.1_Missense_Mutation_p.L66R	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)	66	Ig-like C2-type 1.		L -> H (in IMD20; dbSNP:rs10127939). {ECO:0000269|PubMed:23006327, ECO:0000269|PubMed:8608639, ECO:0000269|PubMed:8609432, ECO:0000269|PubMed:8874200}.|L -> R (in dbSNP:rs10127939). {ECO:0000269|PubMed:8609432}.		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)	GCTTGAGATGAGGCTCTCATT	0.557													A|||	195	0.0389377	0.0651	0.0187	5008	,	,		32243	0.0		0.0517	False		,,,				2504	0.045				p.L102R		Atlas-SNP	.											.	FCGR3A	38	.	0			c.T305G	GRCh37	CM962396|CM963029	FCGR3A	M	rs10127939	PASS	.						303.0	293.0	296.0					1																	161518333		2203	4300	6503	SO:0001583	missense	2214	exon3			GAGATGAGGCTCT	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.197T>G	1.37:g.161518333A>C	ENSP00000416607:p.Leu66Arg	Somatic	596	1	0.00167785		WXS	Illumina HiSeq	Phase_I	903	365	0.404208	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	79|79	0.036172161172161175|0.036172161172161175	26|26	0.052845528455284556|0.052845528455284556	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	44|44	0.05804749340369393|0.05804749340369393	A|A	9.586|9.586	1.124988|1.124988	0.20959|0.20959	.|.	.|.	ENSG00000203747|ENSG00000203747	ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336|ENST00000426740	T;T;T;T;T;T|.	0.13196|.	2.61;2.61;2.61;2.61;2.61;2.61|.	4.43|4.43	0.726|0.726	0.18248|0.18248	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.842078|.	0.09930|.	N|.	0.737349|.	T|T	0.14313|0.14313	0.0346|0.0346	L|L	0.39633|0.39633	1.23|1.23	0.09310|0.09310	N|N	1|1	B;P;B|.	0.45569|.	0.097;0.861;0.043|.	B;B;B|.	0.37692|.	0.096;0.256;0.103|.	T|T	0.29579|0.29579	-1.0007|-1.0007	10|5	0.49607|.	T|.	0.09|.	.|.	3.8902|3.8902	0.09116|0.09116	0.6184:0.1841:0.1975:0.0|0.6184:0.1841:0.1975:0.0	rs10127939|rs10127939	66;101;66|.	P08637;E9PG94;Q9UPY7|.	FCG3A_HUMAN;.;.|.	R|A	102;101;66;66;66;65|83	ENSP00000356946:L102R;ENSP00000392047:L101R;ENSP00000416607:L66R;ENSP00000356944:L66R;ENSP00000444971:L66R;ENSP00000396567:L65R|.	ENSP00000356944:L66R|.	L|S	-|-	2|1	0|0	FCGR3A|FCGR3A	159784957|159784957	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.008000|0.008000	0.06430|0.06430	-0.414000|-0.414000	0.07114|0.07114	0.016000|0.016000	0.14998|0.14998	-0.353000|-0.353000	0.07706|0.07706	CTC|TCA	T|0.013;C|0.046;A|0.941	0.046	strong		0.557	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119945484	119945484	+	Missense_Mutation	SNP	A	A	G	rs144062067	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:119945484A>G	ENST00000297350.4	-	2	464	c.86T>C	c.(85-87)cTt>cCt	p.L29P		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	29					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)	p.L29R(2)		breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			GTCATAATGAAGGTACTTTGG	0.443																																					p.L29P		Atlas-SNP	.											TNFRSF11B,NS,carcinoma,0,1	TNFRSF11B	87	1	2	Substitution - Missense(2)	prostate(2)	c.T86C						scavenged	.	A	PRO/LEU	3,4403	6.2+/-15.9	0,3,2200	227.0	216.0	220.0		86	6.2	1.0	8	dbSNP_134	220	0,8600		0,0,4300	no	missense	TNFRSF11B	NM_002546.3	98	0,3,6500	GG,GA,AA		0.0,0.0681,0.0231	probably-damaging	29/402	119945484	3,13003	2203	4300	6503	SO:0001583	missense	4982	exon2			TAATGAAGGTACT	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"""Tumor necrosis factor receptor superfamily"""	11909	protein-coding gene	gene with protein product		602643	"""osteoprotegerin"""	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.86T>C	8.37:g.119945484A>G	ENSP00000297350:p.Leu29Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	114	3	0.0263158	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	37	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	A	4.646	0.120168	0.08881	6.81E-4	0.0	ENSG00000164761	ENST00000297350	T	0.72282	-0.64	6.17	6.17	0.99709	TNFR/CD27/30/40/95 cysteine-rich region (1);	0.326569	0.32416	N	0.006136	T	0.58750	0.2144	L	0.37750	1.13	0.80722	D	1	B	0.16166	0.016	B	0.12156	0.007	T	0.54275	-0.8318	9	.	.	.	-22.2212	10.4761	0.44665	0.9279:0.0:0.0721:0.0	.	29	O00300	TR11B_HUMAN	P	29	ENSP00000297350:L29P	.	L	-	2	0	TNFRSF11B	120014665	1.000000	0.71417	0.995000	0.50966	0.268000	0.26511	1.175000	0.31944	2.371000	0.80710	0.533000	0.62120	CTT	A|1.000;G|0.000	0.000	strong		0.443	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
EXOC6B	23233	hgsc.bcm.edu	37	2	72958333	72958333	+	Silent	SNP	T	T	C	rs61736520	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:72958333T>C	ENST00000272427.6	-	4	499	c.369A>G	c.(367-369)caA>caG	p.Q123Q	EXOC6B_ENST00000410104.1_Silent_p.Q123Q	NM_015189.1	NP_056004.1	Q9Y2D4	EXC6B_HUMAN	exocyst complex component 6B	123					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)				breast(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	10						TATTTCTCTGTTGTAGTCGAC	0.383													T|||	1002	0.20008	0.5968	0.0994	5008	,	,		18213	0.001		0.1213	False		,,,				2504	0.0215				p.Q123Q		Atlas-SNP	.											.	EXOC6B	93	.	0			c.A369G						PASS	.	T		1734,1952		422,890,531	60.0	59.0	60.0		369	2.2	1.0	2	dbSNP_129	60	940,7274		48,844,3215	no	coding-synonymous	EXOC6B	NM_015189.1		470,1734,3746	CC,CT,TT		11.4439,47.0429,22.4706		123/812	72958333	2674,9226	1843	4107	5950	SO:0001819	synonymous_variant	23233	exon4			TCTCTGTTGTAGT	AB023136	CCDS46333.1	2p13.2	2013-01-22	2006-11-07	2006-11-07	ENSG00000144036	ENSG00000144036			17085	protein-coding gene	gene with protein product		607880	"""SEC15-like 2 (S. cerevisiae)"", ""SEC15 homolog B (S. cerevisiae)"""	SEC15L2, SEC15B		10231032, 11406615	Standard	NM_015189		Approved	KIAA0919	uc010fep.3	Q9Y2D4	OTTHUMG00000152723	ENST00000272427.6:c.369A>G	2.37:g.72958333T>C		Somatic	397	0	0		WXS	Illumina HiSeq	Phase_I	387	184	0.475452	NM_015189	B8ZZY3	Silent	SNP	ENST00000272427.6	37	CCDS46333.1																																																																																			T|0.816;C|0.184	0.184	strong		0.383	EXOC6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327558.1	XM_039570	
NDST3	9348	hgsc.bcm.edu	37	4	119161795	119161795	+	Silent	SNP	G	G	A	rs617430	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	192	0	0		WXS	Illumina HiSeq	Phase_I	87	24	0.275862	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	
MYH11	4629	hgsc.bcm.edu	37	16	15841773	15841773	+	Silent	SNP	G	G	A	rs12931799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:15841773G>A	ENST00000300036.5	-	18	2317	c.2208C>T	c.(2206-2208)atC>atT	p.I736I	MYH11_ENST00000576790.2_Silent_p.I736I|MYH11_ENST00000452625.2_Silent_p.I743I|MYH11_ENST00000396324.3_Silent_p.I743I	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	736	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						AGCCTTTGGGGATGGCATTCG	0.607			T	CBFB	AML								G|||	484	0.0966454	0.1596	0.0548	5008	,	,		19990	0.1101		0.0368	False		,,,				2504	0.089				p.I743I		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.C2229T						PASS	.	G	,,,	636,3758	272.5+/-270.8	41,554,1602	86.0	80.0	82.0		2229,2229,2208,2208	-3.2	1.0	16	dbSNP_121	82	309,8291	109.6+/-170.1	3,303,3994	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	44,857,5596	AA,AG,GG		3.593,14.4743,7.2726	,,,	743/1946,743/1980,736/1973,736/1939	15841773	945,12049	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon19			TTTGGGGATGGCA	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.2208C>T	16.37:g.15841773G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			G|0.917;A|0.083	0.083	strong		0.607	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
OSGIN1	29948	hgsc.bcm.edu	37	16	83999033	83999033	+	Silent	SNP	A	A	G	rs173776	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:83999033A>G	ENST00000343939.2	+	7	1487	c.1104A>G	c.(1102-1104)tcA>tcG	p.S368S	OSGIN1_ENST00000361711.3_Silent_p.S285S|OSGIN1_ENST00000393306.1_Silent_p.S285S			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	368					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						CCCCGGCCTCAGACCCTGTCC	0.711													G|||	1647	0.328874	0.7421	0.1715	5008	,	,		13678	0.1052		0.1978	False		,,,				2504	0.2474				p.S285S		Atlas-SNP	.											.	OSGIN1	33	.	0			c.A855G						PASS	.	G	,,	2804,1566		932,940,313	21.0	26.0	24.0		1104,855,855	-6.6	0.4	16	dbSNP_79	24	1482,7028		147,1188,2920	no	coding-synonymous,coding-synonymous,coding-synonymous	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	,,	1079,2128,3233	GG,GA,AA		17.4148,35.8352,33.2764	,,	368/561,285/478,285/478	83999033	4286,8594	2185	4255	6440	SO:0001819	synonymous_variant	29948	exon6			GGCCTCAGACCCT	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.1104A>G	16.37:g.83999033A>G		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	21	19	0.904762	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	37																																																																																				A|0.701;G|0.299	0.299	strong		0.711	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
GRAMD1C	54762	hgsc.bcm.edu	37	3	113594377	113594377	+	Silent	SNP	A	A	G	rs13079383	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113594377A>G	ENST00000358160.4	+	4	798	c.306A>G	c.(304-306)ctA>ctG	p.L102L	GRAMD1C_ENST00000479212.1_3'UTR|GRAMD1C_ENST00000452134.2_5'UTR	NM_017577.4	NP_060047.3	Q8IYS0	GRM1C_HUMAN	GRAM domain containing 1C	102	GRAM.					integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(2)|skin(3)	26						AGGGACGACTATACCTTTCAG	0.328													A|||	1213	0.242212	0.0651	0.3314	5008	,	,		17431	0.2738		0.3638	False		,,,				2504	0.2607				p.L102L		Atlas-SNP	.											.	GRAMD1C	71	.	0			c.A306G						PASS	.	A		470,3936	223.9+/-240.3	23,424,1756	158.0	154.0	155.0		306	-11.6	0.6	3	dbSNP_121	155	3211,5389	485.0+/-371.5	607,1997,1696	no	coding-synonymous	GRAMD1C	NM_017577.4		630,2421,3452	GG,GA,AA		37.3372,10.6673,28.3023		102/663	113594377	3681,9325	2203	4300	6503	SO:0001819	synonymous_variant	54762	exon4			ACGACTATACCTT		CCDS33826.1, CCDS54625.1	3q13.31	2005-11-02			ENSG00000178075	ENSG00000178075			25252	protein-coding gene	gene with protein product						12975309	Standard	NM_017577		Approved	DKFZp434C0328	uc003eaq.4	Q8IYS0	OTTHUMG00000159340	ENST00000358160.4:c.306A>G	3.37:g.113594377A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_017577	A8K9Y1|A8KA99|Q6AW94|Q6UWN1|Q8N6S0|Q9UF46	Silent	SNP	ENST00000358160.4	37	CCDS33826.1																																																																																			A|0.724;G|0.276	0.276	strong		0.328	GRAMD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354733.1	NM_017577	
CAPN1	823	hgsc.bcm.edu	37	11	64950970	64950970	+	Silent	SNP	C	C	T	rs17583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:64950970C>T	ENST00000527323.1	+	3	603	c.363C>T	c.(361-363)atC>atT	p.I121I	CAPN1_ENST00000527469.1_3'UTR|CAPN1_ENST00000279247.6_Silent_p.I121I|CAPN1_ENST00000524773.1_Silent_p.I121I|CAPN1_ENST00000533129.1_Silent_p.I121I|CAPN1_ENST00000533820.1_Silent_p.I121I|AP003068.23_ENST00000526623.1_5'Flank			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit	121	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				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)		TGGCGGCCATCGCCTCCCTCA	0.637													C|||	1225	0.244609	0.053	0.4035	5008	,	,		17061	0.2966		0.3012	False		,,,				2504	0.2791				p.I121I		Atlas-SNP	.											CAPN1,colon,carcinoma,0,1	CAPN1	44	1	0			c.C363T						scavenged	.	C	,,	387,3821		14,359,1731	43.0	49.0	47.0		363,363,363	-3.1	0.9	11	dbSNP_63	47	2406,6032		320,1766,2133	no	coding-synonymous,coding-synonymous,coding-synonymous	CAPN1	NM_001198868.1,NM_001198869.1,NM_005186.3	,,	334,2125,3864	TT,TC,CC		28.5139,9.1968,22.086	,,	121/715,121/715,121/715	64950970	2793,9853	2104	4219	6323	SO:0001819	synonymous_variant	823	exon4			GGCCATCGCCTCC	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	ENST00000527323.1:c.363C>T	11.37:g.64950970C>T		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	171	86	0.502924	NM_001198869	Q2TTR0|Q6DHV4	Silent	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			C|0.734;T|0.266	0.266	strong		0.637	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
H2AFV	94239	hgsc.bcm.edu	37	7	44874131	44874131	+	Missense_Mutation	SNP	A	A	G	rs114398265		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:44874131A>G	ENST00000308153.4	-	5	447	c.356T>C	c.(355-357)aTt>aCt	p.I119T	H2AFV_ENST00000222690.6_Intron|H2AFV_ENST00000437072.1_Intron|H2AFV_ENST00000521529.1_3'UTR|H2AFV_ENST00000381124.5_3'UTR|H2AFV_ENST00000349299.3_Missense_Mutation_p.I81T|H2AFV_ENST00000350771.3_Missense_Mutation_p.I93T	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	119						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.I119T(1)		endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						CTTCTTTCCAATCAGAGATTT	0.368																																					p.I119T		Atlas-SNP	.											H2AFV,NS,carcinoma,0,1	H2AFV	14	1	1	Substitution - Missense(1)	prostate(1)	c.T356C						scavenged	.						88.0	76.0	80.0					7																	44874131		2203	4300	6503	SO:0001583	missense	94239	exon5			TTTCCAATCAGAG	AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968		"""Histones / Replication-independent"""	20664	protein-coding gene	gene with protein product				H2AV			Standard	NM_012412		Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000308153.4:c.356T>C	7.37:g.44874131A>G	ENSP00000308405:p.Ile119Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	187	5	0.026738	NM_012412	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Missense_Mutation	SNP	ENST00000308153.4	37	CCDS5496.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.801702	0.50315	.	.	ENSG00000105968	ENST00000349299;ENST00000308153;ENST00000350771	T;D;T	0.83163	0.93;-1.69;0.89	5.61	5.61	0.85477	Histone-fold (1);Histone H2A (2);	.	.	.	.	D	0.82444	0.5038	M	0.69523	2.12	0.80722	D	1	B;B;B	0.17852	0.001;0.024;0.0	B;B;B	0.18871	0.005;0.023;0.001	T	0.80027	-0.1554	9	0.62326	D	0.03	-10.9595	14.0456	0.64704	1.0:0.0:0.0:0.0	.	93;81;119	A6NKY0;A6NFA8;Q71UI9	.;.;H2AV_HUMAN	T	81;119;93	ENSP00000342714:I81T;ENSP00000308405:I119T;ENSP00000340708:I93T	ENSP00000308405:I119T	I	-	2	0	H2AFV	44840656	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.631000	0.90991	2.261000	0.74972	0.533000	0.62120	ATT	A|0.999;G|0.001	0.001	weak		0.368	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412	
MCM8	84515	hgsc.bcm.edu	37	20	5933108	5933108	+	Missense_Mutation	SNP	C	C	A	rs236110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:5933108C>A	ENST00000378896.3	+	3	564	c.187C>A	c.(187-189)Cag>Aag	p.Q63K	TRMT6_ENST00000473131.1_5'Flank|MCM8_ENST00000378886.2_Missense_Mutation_p.Q63K|TRMT6_ENST00000453074.2_5'Flank|TRMT6_ENST00000203001.2_5'Flank|MCM8_ENST00000378883.1_Missense_Mutation_p.Q63K|MCM8_ENST00000265187.4_Missense_Mutation_p.Q63K	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	63			Q -> K (in dbSNP:rs236110).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						AAAGACCCCACAGTCAATGCA	0.348													C|||	1309	0.261382	0.503	0.1643	5008	,	,		18160	0.1726		0.1143	False		,,,				2504	0.2464				p.Q63K		Atlas-SNP	.											.	MCM8	125	.	0			c.C187A						PASS	.	C	LYS/GLN,LYS/GLN	1955,2451	552.1+/-378.4	420,1115,668	107.0	124.0	118.0		187,187	0.2	0.4	20	dbSNP_79	118	1014,7586	215.7+/-255.0	54,906,3340	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	53,53	474,2021,4008	AA,AC,CC		11.7907,44.3713,22.8279	benign,benign	63/841,63/825	5933108	2969,10037	2203	4300	6503	SO:0001583	missense	84515	exon3			ACCCCACAGTCAA	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.187C>A	20.37:g.5933108C>A	ENSP00000368174:p.Gln63Lys	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	223	110	0.493274	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	503	0.2303113553113553	259	0.5264227642276422	51	0.1408839779005525	98	0.17132867132867133	95	0.12532981530343007	C	7.402	0.633016	0.14322	0.443713	0.117907	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000399350;ENST00000378886;ENST00000265187	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	0.235	0.235	0.15431	.	0.363100	0.25997	N	0.026972	T	0.00012	0.0000	N	0.22421	0.69	0.42593	P	0.00674600000000003	B;B;B;B	0.25486	0.038;0.127;0.012;0.01	B;B;B;B	0.23275	0.012;0.045;0.002;0.001	T	0.44360	-0.9333	8	0.06494	T	0.89	.	.	.	.	rs236110;rs52832932;rs59009216;rs236110	63;63;63;63	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	K	63	ENSP00000368174:Q63K;ENSP00000368161:Q63K;ENSP00000368164:Q63K;ENSP00000265187:Q63K	ENSP00000265187:Q63K	Q	+	1	0	MCM8	5881108	0.505000	0.26131	0.430000	0.26722	0.422000	0.31414	0.356000	0.20181	0.308000	0.22923	0.313000	0.20887	CAG	C|0.763;A|0.237	0.237	strong		0.348	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856817	144856817	+	Splice_Site	SNP	T	T	C	rs3844239		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:144856817T>C	ENST00000369354.3	-	40	6857	c.6668A>G	c.(6667-6669)gAg>gGg	p.E2223G	PDE4DIP_ENST00000313382.9_Splice_Site_p.E2117G|PDE4DIP_ENST00000369356.4_Splice_Site_p.E2223G|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Splice_Site_p.E2359G|PDE4DIP_ENST00000530740.1_Splice_Site_p.E2308G|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2223					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)	p.E2223G(2)		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)		TGTGATTACCTCTGTGCCTTG	0.478			T	PDGFRB	MPD																																p.E2223G		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,caecum,carcinoma,0,4	PDE4DIP	817	4	2	Substitution - Missense(2)	prostate(2)	c.A6668G						scavenged	.						52.0	38.0	43.0					1																	144856817		2202	4294	6496	SO:0001630	splice_region_variant	9659	exon40			ATTACCTCTGTGC	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.6669+1A>G	1.37:g.144856817T>C		Somatic	109	2	0.0183486		WXS	Illumina HiSeq	Phase_I	135	8	0.0592593	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	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	14.30|14.30	2.495079|2.495079	0.44352|0.44352	.|.	.|.	ENSG00000178104|ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359|ENST00000530130	T;T;T;T;T|.	0.01871|.	4.59;4.69;4.67;4.69;4.69|.	4.52|4.52	3.39|3.39	0.38822|0.38822	.|.	.|.	.|.	.|.	.|.	T|T	0.52885|0.52885	0.1762|0.1762	M|M	0.73598|0.73598	2.24|2.24	0.80722|0.80722	D|D	1|1	B;B|.	0.17852|.	0.0;0.024|.	B;B|.	0.20184|.	0.0;0.028|.	T|T	0.54193|0.54193	-0.8330|-0.8330	9|5	0.59425|.	D|.	0.04|.	.|.	8.6174|8.6174	0.33840|0.33840	0.0:0.0946:0.0:0.9054|0.0:0.0946:0.0:0.9054	rs3844239|rs3844239	2117;2223|.	Q5VU43-3;Q5VU43|.	.;MYOME_HUMAN|.	G|G	2117;2223;2223;2308;2359|300	ENSP00000327209:E2117G;ENSP00000358360:E2223G;ENSP00000358363:E2223G;ENSP00000435654:E2308G;ENSP00000358366:E2359G|.	ENSP00000327209:E2117G|.	E|R	-|-	2|1	0|2	PDE4DIP|PDE4DIP	143568174|143568174	1.000000|1.000000	0.71417|0.71417	0.886000|0.886000	0.34754|0.34754	0.224000|0.224000	0.24922|0.24922	3.513000|3.513000	0.53414|0.53414	0.702000|0.702000	0.31825|0.31825	-0.566000|-0.566000	0.04163|0.04163	GAG|AGG	.	.	weak		0.478	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	Missense_Mutation
OR4X2	119764	hgsc.bcm.edu	37	11	48266736	48266736	+	Nonsense_Mutation	SNP	C	C	G	rs7120775	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	242	2	0.00826446		WXS	Illumina HiSeq	Phase_I	190	94	0.494737	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	
ANKRD36	375248	hgsc.bcm.edu	37	2	97909661	97909661	+	Silent	SNP	A	A	C	rs199689273		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	947	5	0.00527983		WXS	Illumina HiSeq	Phase_I	1099	90	0.0818926	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		
TTC39A	22996	hgsc.bcm.edu	37	1	51767352	51767352	+	Silent	SNP	G	G	A	rs41287290	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:51767352G>A	ENST00000447632.2	-	12	1101	c.1053C>T	c.(1051-1053)ttC>ttT	p.F351F	TTC39A_ENST00000262676.5_3'UTR|TTC39A_ENST00000262675.7_Silent_p.F288F|TTC39A_ENST00000413473.2_Silent_p.F319F|TTC39A_ENST00000371750.5_Silent_p.F316F|TTC39A_ENST00000371747.3_Silent_p.F350F|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	121	0	0		WXS	Illumina HiSeq	Phase_I	88	29	0.329545	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		
KRT5	3852	hgsc.bcm.edu	37	12	52912909	52912909	+	Missense_Mutation	SNP	G	G	T	rs641615	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52912909G>T	ENST00000252242.4	-	2	981	c.591C>A	c.(589-591)gaC>gaA	p.D197E		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	197	Coil 1A.|Rod.		D -> E (in dbSNP:rs641615). {ECO:0000269|PubMed:2447486, ECO:0000269|PubMed:2476664}.		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)		TCCACTTGGTGTCCAGAACCT	0.532													G|||	1077	0.215056	0.1089	0.2233	5008	,	,		19702	0.3393		0.2823	False		,,,				2504	0.1554				p.D197E		Atlas-SNP	.											.	KRT5	88	.	0			c.C591A						PASS	.						58.0	51.0	54.0					12																	52912909		2202	4296	6498	SO:0001583	missense	3852	exon2			CTTGGTGTCCAGA		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.591C>A	12.37:g.52912909G>T	ENSP00000252242:p.Asp197Glu	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	126	34	0.269841	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	37	CCDS8830.1	555	0.2541208791208791	58	0.11788617886178862	91	0.2513812154696133	199	0.3479020979020979	207	0.27308707124010556	G	5.448	0.267812	0.10349	.	.	ENSG00000186081	ENST00000252242;ENST00000456000;ENST00000549420	T;T	0.72282	-0.64;-0.64	5.31	2.41	0.29592	Filament (1);	0.000000	0.64402	D	0.000015	T	0.00012	0.0000	N	0.00001	-3.76	0.38288	P	0.05736600000000003	B	0.18741	0.03	B	0.15052	0.012	T	0.46105	-0.9215	9	0.02654	T	1	.	7.4373	0.27162	0.0684:0.3532:0.4752:0.1032	rs641615;rs1042272;rs3176960;rs3181708;rs17400360;rs59010565	197	P13647	K2C5_HUMAN	E	197;162;87	ENSP00000252242:D197E;ENSP00000447209:D87E	ENSP00000252242:D197E	D	-	3	2	KRT5	51199176	0.997000	0.39634	1.000000	0.80357	0.999000	0.98932	0.484000	0.22308	0.792000	0.33850	0.655000	0.94253	GAC	G|0.790;T|0.210	0.210	strong		0.532	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
GTSE1	51512	hgsc.bcm.edu	37	22	46704243	46704243	+	Silent	SNP	C	C	T	rs6008598	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46704243C>T	ENST00000454366.1	+	4	377	c.165C>T	c.(163-165)ttC>ttT	p.F55F		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	36					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		AAGTCTTCTTCGGACCCTTTG	0.388													C|||	750	0.14976	0.3858	0.0951	5008	,	,		17943	0.002		0.1302	False		,,,				2504	0.0419				p.F55F	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.C165T						PASS	.	C		1512,2894	479.0+/-358.4	277,958,968	92.0	100.0	97.0		165	0.7	0.9	22	dbSNP_114	97	957,7643	208.9+/-250.2	53,851,3396	no	coding-synonymous	GTSE1	NM_016426.6		330,1809,4364	TT,TC,CC		11.1279,34.3168,18.9835		55/740	46704243	2469,10537	2203	4300	6503	SO:0001819	synonymous_variant	51512	exon4			CTTCTTCGGACCC	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.165C>T	22.37:g.46704243C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	37	CCDS14074.2																																																																																			C|0.821;T|0.179	0.179	strong		0.388	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
PLIN3	10226	hgsc.bcm.edu	37	19	4852137	4852137	+	Silent	SNP	C	C	T	rs1055919	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4852137C>T	ENST00000221957.4	-	5	701	c.525G>A	c.(523-525)tcG>tcA	p.S175S	PLIN3_ENST00000592528.1_Silent_p.S163S|PLIN3_ENST00000585479.1_Silent_p.S175S	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	175					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	AGCCCATGACCGATTGGACGC	0.662											OREG0025175	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2411	0.48143	0.4297	0.5231	5008	,	,		15629	0.4821		0.4682	False		,,,				2504	0.5348				p.S175S		Atlas-SNP	.											PLIN3,colon,carcinoma,0,1	PLIN3	36	1	0			c.G525A						scavenged	.	C	,,	1855,2551	535.3+/-374.2	402,1051,750	75.0	55.0	62.0		525,489,525	-10.3	0.0	19	dbSNP_86	62	3698,4902	527.2+/-381.1	768,2162,1370	no	coding-synonymous,coding-synonymous,coding-synonymous	PLIN3	NM_001164189.1,NM_001164194.1,NM_005817.4	,,	1170,3213,2120	TT,TC,CC		43.0,42.1017,42.6957	,,	175/434,163/423,175/435	4852137	5553,7453	2203	4300	6503	SO:0001819	synonymous_variant	10226	exon5			CATGACCGATTGG	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.525G>A	19.37:g.4852137C>T		Somatic	157	1	0.00636943	622	WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_001164189	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Silent	SNP	ENST00000221957.4	37	CCDS12137.1																																																																																			C|0.557;T|0.443	0.443	strong		0.662	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817	
HOXD10	3236	hgsc.bcm.edu	37	2	176982173	176982173	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:176982173C>T	ENST00000249501.4	+	1	867	c.612C>T	c.(610-612)ccC>ccT	p.P204P	HOXD10_ENST00000490088.2_Intron	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	204					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|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)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		TGAACGAGCCCGTGAGCGGCC	0.647																																					p.P204P		Atlas-SNP	.											HOXD10,NS,carcinoma,0,1	HOXD10	65	1	0			c.C612T						scavenged	.						24.0	30.0	28.0					2																	176982173		2195	4286	6481	SO:0001819	synonymous_variant	3236	exon1			CGAGCCCGTGAGC		CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"""Homeoboxes / ANTP class : HOXL subclass"""	5133	protein-coding gene	gene with protein product		142984	"""homeo box D10"""	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.612C>T	2.37:g.176982173C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	96	3	0.03125	NM_002148	Q6NT10	Silent	SNP	ENST00000249501.4	37	CCDS2266.1																																																																																			.	.	none		0.647	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2		
HERC2	8924	hgsc.bcm.edu	37	15	28459393	28459393	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:28459393C>T	ENST00000261609.7	-	41	6492	c.6384G>A	c.(6382-6384)gtG>gtA	p.V2128V		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)		CCTGCGGGCGCACCCTGCGCC	0.672																																					p.V2128V		Atlas-SNP	.											.	HERC2	501	.	0			c.G6384A						PASS	.						24.0	25.0	25.0					15																	28459393		2195	4293	6488	SO:0001819	synonymous_variant	8924	exon41			CGGGCGCACCCTG	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.6384G>A	15.37:g.28459393C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	53	45	0.849057	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			.	.	none		0.672	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
SH2D4B	387694	hgsc.bcm.edu	37	10	82363340	82363340	+	Silent	SNP	C	C	A	rs7069048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:82363340C>A	ENST00000470604.2	+	5	646	c.646C>A	c.(646-648)Cgg>Agg	p.R216R	SH2D4B_ENST00000339284.2_Silent_p.R217R|SH2D4B_ENST00000313455.4_Silent_p.R168R			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						PASS	.	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	123	0	0		WXS	Illumina HiSeq	Phase_I	76	15	0.197368	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	
TNFRSF19	55504	hgsc.bcm.edu	37	13	24243204	24243204	+	Missense_Mutation	SNP	G	G	A	rs3751362	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:24243204G>A	ENST00000382258.4	+	9	1417	c.1213G>A	c.(1213-1215)Gtc>Atc	p.V405I	TNFRSF19_ENST00000403372.2_Missense_Mutation_p.V273I|TNFRSF19_ENST00000248484.4_Missense_Mutation_p.V405I|TNFRSF19_ENST00000382263.3_Missense_Mutation_p.V405I	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	405			V -> I (in dbSNP:rs3751362). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)	p.V405I(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		GAGTGGTGCTGTCATCCACCC	0.488													G|||	803	0.160343	0.1899	0.2032	5008	,	,		15005	0.2262		0.0646	False		,,,				2504	0.1207				p.V405I		Atlas-SNP	.											TNFRSF19,NS,carcinoma,0,1	TNFRSF19	52	1	1	Substitution - Missense(1)	stomach(1)	c.G1213A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	776,3630	313.0+/-292.9	57,662,1484	53.0	49.0	50.0		1213,817,1213,1213	-8.4	0.0	13	dbSNP_107	50	767,7833	182.6+/-231.0	32,703,3565	yes	missense,missense,missense,missense	TNFRSF19	NM_001204458.1,NM_001204459.1,NM_018647.3,NM_148957.3	29,29,29,29	89,1365,5049	AA,AG,GG		8.9186,17.6123,11.8638	benign,benign,benign,benign	405/418,273/286,405/424,405/418	24243204	1543,11463	2203	4300	6503	SO:0001583	missense	55504	exon9			GGTGCTGTCATCC	AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"""Tumor necrosis factor receptor superfamily"""	11915	protein-coding gene	gene with protein product	"""toxicity and JNK inducer"""	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.1213G>A	13.37:g.24243204G>A	ENSP00000371693:p.Val405Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_018647	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	37	CCDS9302.1	319	0.14606227106227107	82	0.16666666666666666	61	0.1685082872928177	136	0.23776223776223776	40	0.052770448548812667	G	8.461	0.855398	0.17106	0.176123	0.089186	ENSG00000127863	ENST00000248484;ENST00000403372;ENST00000382258;ENST00000382263	T;T;T;T	0.77489	-1.1;1.48;-1.1;-1.1	5.71	-8.41	0.00961	.	2.679170	0.01088	N	0.005136	T	0.00039	0.0001	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.05468	-1.0883	9	0.18276	T	0.48	2.0E-4	13.5002	0.61449	0.1673:0.109:0.7238:0.0	rs3751362;rs3751362	273;405;405	B4E2I6;Q9NS68;Q9NS68-2	.;TNR19_HUMAN;.	I	405;273;405;405	ENSP00000248484:V405I;ENSP00000385408:V273I;ENSP00000371693:V405I;ENSP00000371698:V405I	ENSP00000248484:V405I	V	+	1	0	TNFRSF19	23141204	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.574000	0.05868	-1.806000	0.01237	-0.136000	0.14681	GTC	G|0.874;A|0.126	0.126	strong		0.488	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647	
PRB2	653247	hgsc.bcm.edu	37	12	11546309	11546309	+	Missense_Mutation	SNP	C	C	G	rs201308939		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:11546309C>G	ENST00000389362.4	-	3	738	c.703G>C	c.(703-705)Gcc>Ccc	p.A235P	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	235	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)		p.A214P(1)|p.A235P(1)		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)			GGAGATCGGGCACTTTGGGAC	0.612																																					p.A235P		Atlas-SNP	.											PRB2_ENST00000389362,trunk,malignant_melanoma,0,2	PRB2	168	2	2	Substitution - Missense(2)	skin(2)	c.G703C						scavenged	.						249.0	265.0	259.0					12																	11546309		2203	4297	6500	SO:0001583	missense	653247	exon3			ATCGGGCACTTTG	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.703G>C	12.37:g.11546309C>G	ENSP00000374013:p.Ala235Pro	Somatic	623	6	0.00963082		WXS	Illumina HiSeq	Phase_I	591	10	0.0169205	NM_006248	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	37	CCDS41757.2	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.112856	0.00353	.	.	ENSG00000121335	ENST00000389362	T	0.03860	3.78	1.17	-2.34	0.06704	.	.	.	.	.	T	0.01092	0.0036	N	0.00621	-1.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46762	-0.9168	9	0.09084	T	0.74	.	1.6626	0.02795	0.2887:0.3081:0.0:0.4032	.	235	P02812	PRB2_HUMAN	P	235	ENSP00000374013:A235P	ENSP00000374013:A235P	A	-	1	0	PRB2	11437576	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.155000	0.00580	-0.311000	0.08754	-2.162000	0.00326	GCC	.	.	weak		0.612	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
NPY2R	4887	hgsc.bcm.edu	37	4	156135676	156135676	+	Silent	SNP	C	C	T	rs1047214	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:156135676C>T	ENST00000329476.3	+	2	1074	c.585C>T	c.(583-585)atC>atT	p.I195I	NPY2R_ENST00000506608.1_Silent_p.I195I	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	195					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	TTGAGATCATCCCGGACTTTG	0.512													T|||	3507	0.70028	0.9395	0.5014	5008	,	,		21126	0.8115		0.5447	False		,,,				2504	0.5634				p.I195I		Atlas-SNP	.											.	NPY2R	87	.	0			c.C585T	GRCh37	CM057405	NPY2R	M	rs1047214	PASS	.	T		3841,565	248.4+/-256.2	1684,473,46	101.0	102.0	102.0		585	-6.2	0.2	4	dbSNP_86	102	4559,4041	556.1+/-386.8	1206,2147,947	no	coding-synonymous	NPY2R	NM_000910.2		2890,2620,993	TT,TC,CC		46.9884,12.8234,35.4144		195/382	156135676	8400,4606	2203	4300	6503	SO:0001819	synonymous_variant	4887	exon2			GATCATCCCGGAC	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"""GPCR / Class A : Neuropeptide receptors : Y"""	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.585C>T	4.37:g.156135676C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	99	76	0.767677	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Silent	SNP	ENST00000329476.3	37	CCDS3791.1																																																																																			C|0.329;N|0.000	.	strong		0.512	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910	
PPID	5481	hgsc.bcm.edu	37	4	159631991	159631991	+	Missense_Mutation	SNP	G	G	T	rs9410	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:159631991G>T	ENST00000307720.3	-	8	1011	c.904C>A	c.(904-906)Cta>Ata	p.L302I		NM_005038.2	NP_005029.1	Q08752	PPID_HUMAN	peptidylprolyl isomerase D	302	Interaction with HSP90AB1. {ECO:0000250}.		L -> I (in dbSNP:rs9410). {ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|cellular response to UV-A (GO:0071492)|chaperone-mediated protein folding (GO:0061077)|lipid particle organization (GO:0034389)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein secretion (GO:0050714)|positive regulation of viral genome replication (GO:0045070)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|protein transport (GO:0015031)|viral release from host cell (GO:0019076)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|estrogen receptor binding (GO:0030331)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|transcription factor binding (GO:0008134)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.0159)		GATGGGTCTAGTTCAAGAGCC	0.343													t|||	1319	0.263379	0.3729	0.1412	5008	,	,		19147	0.125		0.2883	False		,,,				2504	0.319				p.L302I		Atlas-SNP	.											.	PPID	22	.	0			c.C904A						PASS	.	C	ILE/LEU	1660,2744	655.0+/-399.8	318,1024,860	120.0	129.0	126.0		904	1.5	1.0	4	dbSNP_52	126	2585,6015	688.6+/-404.3	378,1829,2093	yes	missense	PPID	NM_005038.2	5	696,2853,2953	TT,TG,GG		30.0581,37.693,32.6438	benign	302/371	159631991	4245,8759	2202	4300	6502	SO:0001583	missense	5481	exon8			GGTCTAGTTCAAG		CCDS3801.1	4q31.3	2013-01-10	2008-10-24		ENSG00000171497	ENSG00000171497		"""Tetratricopeptide (TTC) repeat domain containing"""	9257	protein-coding gene	gene with protein product	"""cyclophilin 40"""	601753	"""peptidylprolyl isomerase D (cyclophilin D)"""			8509368	Standard	NM_005038		Approved	CYP-40	uc003iqc.3	Q08752	OTTHUMG00000161927	ENST00000307720.3:c.904C>A	4.37:g.159631991G>T	ENSP00000303754:p.Leu302Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	67	48	0.716418	NM_005038	B2R9V2	Missense_Mutation	SNP	ENST00000307720.3	37	CCDS3801.1	539	0.2467948717948718	189	0.38414634146341464	53	0.1464088397790055	82	0.14335664335664336	215	0.2836411609498681	t	8.045	0.764641	0.15914	0.37693	0.300581	ENSG00000171497	ENST00000307720	T	0.65916	-0.18	5.44	1.47	0.22746	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.361838	0.19645	N	0.109351	T	0.00012	0.0000	L	0.28740	0.885	0.43930	P	0.0034119999999999706	B	0.02656	0.0	B	0.08055	0.003	T	0.39722	-0.9600	9	0.19147	T	0.46	-0.692	9.2507	0.37554	0.0:0.0612:0.3483:0.5905	rs9410;rs1134310;rs3196517;rs7689418;rs17295391;rs17353893;rs17843955;rs52790371;rs58555274;rs7689418	302	Q08752	PPID_HUMAN	I	302	ENSP00000303754:L302I	ENSP00000303754:L302I	L	-	1	2	PPID	159851441	1.000000	0.71417	0.994000	0.49952	0.914000	0.54420	1.265000	0.33027	-0.053000	0.13289	-1.061000	0.02294	CTA	G|0.586;T|0.237	0.237	strong		0.343	PPID-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366436.1	NM_005038	
SLC6A15	55117	hgsc.bcm.edu	37	12	85277561	85277561	+	Intron	SNP	T	T	A	rs17183577	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:85277561T>A	ENST00000266682.5	-	5	1298				SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000450363.3_Missense_Mutation_p.D278V|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						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	188	0	0		WXS	Illumina HiSeq	Phase_I	175	175	1	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	
TRPV4	59341	hgsc.bcm.edu	37	12	110240838	110240838	+	Silent	SNP	T	T	G	rs3825394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:110240838T>G	ENST00000418703.2	-	3	764	c.670A>C	c.(670-672)Agg>Cgg	p.R224R	TRPV4_ENST00000536838.1_Silent_p.R190R|TRPV4_ENST00000346520.2_Silent_p.R224R|TRPV4_ENST00000541794.1_Silent_p.R224R|TRPV4_ENST00000544971.1_Silent_p.R224R|TRPV4_ENST00000392719.2_Silent_p.R224R|TRPV4_ENST00000261740.2_Silent_p.R224R|TRPV4_ENST00000537083.1_Silent_p.R224R	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	224					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						ATGAACTCCCTCATGTTGCCG	0.637													G|||	3778	0.754393	0.7284	0.7017	5008	,	,		20128	0.9683		0.5288	False		,,,				2504	0.8384				p.R224R		Atlas-SNP	.											.	TRPV4	88	.	0			c.A670C						PASS	.	G	,,,,	3018,1388	457.6+/-351.7	1054,910,239	108.0	88.0	95.0		670,568,670,670,670	4.5	1.0	12	dbSNP_107	95	4536,4064	558.9+/-387.3	1187,2162,951	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	,,,,	2241,3072,1190	GG,GT,TT		47.2558,31.5025,41.9191	,,,,	224/825,190/838,224/765,224/872,224/812	110240838	7554,5452	2203	4300	6503	SO:0001819	synonymous_variant	59341	exon3			ACTCCCTCATGTT	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18083	protein-coding gene	gene with protein product	"""osmosensitive transient receptor potential channel 4"""	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.670A>C	12.37:g.110240838T>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	121	40	0.330579	NM_001177433	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																			T|0.359;G|0.641	0.641	strong		0.637	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
SPNS2	124976	hgsc.bcm.edu	37	17	4434031	4434031	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4434031G>A	ENST00000329078.3	+	4	888	c.678G>A	c.(676-678)acG>acA	p.T226T		NM_001124758.1	NP_001118230.1	Q8IVW8	SPNS2_HUMAN	spinster homolog 2 (Drosophila)	226					B cell homeostasis (GO:0001782)|bone development (GO:0060348)|lymph node development (GO:0048535)|lymphocyte migration (GO:0072676)|regulation of eye pigmentation (GO:0048073)|regulation of humoral immune response (GO:0002920)|sphingolipid metabolic process (GO:0006665)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell homeostasis (GO:0043029)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	sphingolipid transporter activity (GO:0046624)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6						CCAAGAACACGCGTACGCTCA	0.627																																					p.T226T		Atlas-SNP	.											SPNS2,colon,carcinoma,+1,1	SPNS2	24	1	0			c.G678A						PASS	.						69.0	61.0	63.0					17																	4434031		1568	3582	5150	SO:0001819	synonymous_variant	124976	exon4			GAACACGCGTACG	BC041772	CCDS42237.1	17p13.2	2008-12-15				ENSG00000183018			26992	protein-coding gene	gene with protein product		612584				12815463	Standard	NM_001124758		Approved		uc002fxx.2	Q8IVW8		ENST00000329078.3:c.678G>A	17.37:g.4434031G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	205	103	0.502439	NM_001124758	B9A1T3	Silent	SNP	ENST00000329078.3	37	CCDS42237.1																																																																																			.	.	none		0.627	SPNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438802.1		
SARDH	1757	hgsc.bcm.edu	37	9	136536679	136536679	+	Silent	SNP	G	G	A	rs129932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	250	1	0.004		WXS	Illumina HiSeq	Phase_I	225	104	0.462222	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		
OR10R2	343406	hgsc.bcm.edu	37	1	158450382	158450382	+	Missense_Mutation	SNP	C	C	T	rs1418843	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158450382C>T	ENST00000368152.1	+	1	715	c.715C>T	c.(715-717)Ctc>Ttc	p.L239F	RP11-144L1.4_ENST00000419738.1_RNA|RP11-144L1.4_ENST00000426251.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	239			L -> F (in dbSNP:rs1418843).			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)					TGTTTCTTATCTCTGCATTCT	0.428													C|||	2177	0.434704	0.3828	0.3833	5008	,	,		21090	0.5685		0.4573	False		,,,				2504	0.3804				p.L239F		Atlas-SNP	.											.	OR10R2	81	.	0			c.C715T						PASS	.	C	PHE/LEU	1721,2685	515.5+/-368.9	330,1061,812	144.0	125.0	132.0		715	-1.4	0.7	1	dbSNP_88	132	3725,4875	530.6+/-381.8	844,2037,1419	yes	missense	OR10R2	NM_001004472.1	22	1174,3098,2231	TT,TC,CC		43.314,39.0604,41.873	benign	239/336	158450382	5446,7560	2203	4300	6503	SO:0001583	missense	343406	exon1			TCTTATCTCTGCA	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.715C>T	1.37:g.158450382C>T	ENSP00000357134:p.Leu239Phe	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	212	131	0.617925	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	37	CCDS30898.1	1035	0.4739010989010989	190	0.3861788617886179	140	0.3867403314917127	349	0.6101398601398601	356	0.46965699208443273	c	10.58	1.389376	0.25118	0.390604	0.43314	ENSG00000198965	ENST00000368152	T	0.00152	8.66	4.2	-1.39	0.08997	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	N	0.16307	0.4	0.80722	P	0.0	B	0.31705	0.336	B	0.35073	0.195	T	0.01266	-1.1401	8	0.21540	T	0.41	.	1.3235	0.02121	0.2586:0.3163:0.2627:0.1624	rs1418843;rs17629511;rs60545544;rs1418843	239	Q8NGX6	O10R2_HUMAN	F	239	ENSP00000357134:L239F	ENSP00000357134:L239F	L	+	1	0	OR10R2	156717006	0.000000	0.05858	0.713000	0.30519	0.816000	0.46133	-6.666000	0.00057	-0.551000	0.06175	-0.152000	0.13540	CTC	C|0.554;N|0.000	.	strong		0.428	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472	
CCDC108	255101	hgsc.bcm.edu	37	2	219890814	219890814	+	Missense_Mutation	SNP	C	C	T	rs114017706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219890814C>T	ENST00000341552.5	-	14	2362	c.2279G>A	c.(2278-2280)cGg>cAg	p.R760Q	CCDC108_ENST00000453220.1_Missense_Mutation_p.R760Q|CCDC108_ENST00000441968.1_Missense_Mutation_p.R760Q	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	760						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)		GCCTCGTGCCCGCACCGTCAG	0.597													C|||	75	0.014976	0.0499	0.0086	5008	,	,		20085	0.0		0.002	False		,,,				2504	0.001				p.R760Q		Atlas-SNP	.											CCDC108,right_upper_lobe,carcinoma,+1,1	CCDC108	208	1	0			c.G2279A						PASS	.	C	GLN/ARG	149,4257	103.8+/-142.4	1,147,2055	80.0	71.0	74.0		2279	-1.5	0.0	2	dbSNP_132	74	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CCDC108	NM_194302.2	43	1,152,6350	TT,TC,CC		0.0581,3.3818,1.1841	possibly-damaging	760/1926	219890814	154,12852	2203	4300	6503	SO:0001583	missense	255101	exon14			CGTGCCCGCACCG	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.2279G>A	2.37:g.219890814C>T	ENSP00000340776:p.Arg760Gln	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	164	47	0.286585	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	21	0.009615384615384616	16	0.032520325203252036	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	12.23	1.874254	0.33069	0.033818	5.81E-4	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.06068	3.35;3.35;3.35	4.87	-1.46	0.08800	.	0.698236	0.11855	N	0.522902	T	0.01454	0.0047	L	0.55103	1.725	0.09310	N	1	P	0.39404	0.672	B	0.28139	0.086	T	0.34428	-0.9829	10	0.35671	T	0.21	-7.944	6.1253	0.20176	0.0:0.4501:0.1226:0.4273	.	760	Q6ZU64	CC108_HUMAN	Q	760	ENSP00000340776:R760Q;ENSP00000413377:R760Q;ENSP00000409117:R760Q	ENSP00000340776:R760Q	R	-	2	0	CCDC108	219599058	0.000000	0.05858	0.003000	0.11579	0.588000	0.36517	-0.972000	0.03802	-0.213000	0.10094	0.561000	0.74099	CGG	C|0.989;T|0.011	0.011	strong		0.597	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
DHRS4	10901	hgsc.bcm.edu	37	14	24424420	24424420	+	Splice_Site	SNP	C	C	T	rs537144117	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24424420C>T	ENST00000313250.5	+	2	508	c.305C>T	c.(304-306)aCg>aTg	p.T102M	DHRS4_ENST00000397075.3_Splice_Site_p.T102M|DHRS4_ENST00000558581.1_Splice_Site_p.T102M|DHRS4_ENST00000421831.1_Splice_Site_p.T84M|DHRS4_ENST00000397073.2_Splice_Site_p.T84M|DHRS4_ENST00000308178.8_Splice_Site_p.T84M|DHRS4_ENST00000559632.1_Splice_Site_p.T102M|DHRS4_ENST00000543741.2_Splice_Site_p.T102M|DHRS4_ENST00000558263.1_Splice_Site_p.T102M|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000382761.3_Splice_Site_p.T84M|DHRS4_ENST00000397074.3_Splice_Site_p.T102M	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	102				T -> M (in Ref. 1; AAD02292). {ECO:0000305}.	alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)	p.T102M(4)		central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CTGGTGGCCACGGTGAGCTGC	0.652													.|||	14	0.00279553	0.0008	0.0	5008	,	,		13962	0.003		0.004	False		,,,				2504	0.0061				p.T102M		Atlas-SNP	.											DHRS4,NS,carcinoma,0,5	DHRS4	22	5	4	Substitution - Missense(4)	central_nervous_system(2)|lung(1)|kidney(1)	c.C305T						scavenged	.																																			SO:0001630	splice_region_variant	10901	exon2			TGGCCACGGTGAG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.306+1C>T	14.37:g.24424420C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	278	57	0.205036	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	.	8.197	0.797295	0.16327	.	.	ENSG00000157326	ENST00000313250;ENST00000421831;ENST00000397073;ENST00000308178;ENST00000382761;ENST00000397075;ENST00000397074;ENST00000543741	T;T;D;D;D;D;D;D	0.88201	0.93;0.93;-2.35;-2.35;-2.35;-2.35;-2.35;-2.35	3.78	0.837	0.18896	NAD(P)-binding domain (1);	0.264094	0.42294	N	0.000732	D	0.83839	0.5341	M	0.77712	2.385	0.36055	D	0.841007	P;B;B;B;B;B	0.45011	0.848;0.001;0.002;0.065;0.05;0.035	B;B;B;B;B;B	0.34180	0.177;0.002;0.001;0.016;0.064;0.044	T	0.80294	-0.1443	10	0.37606	T	0.19	.	7.6245	0.28204	0.0:0.6987:0.0:0.3013	.	102;102;102;102;102;102	Q9BTZ2-5;F5GWZ1;Q9BTZ2-2;Q9BTZ2-7;Q9BTZ2-4;Q9BTZ2	.;.;.;.;.;DHRS4_HUMAN	M	102;84;84;84;84;102;102;102	ENSP00000326219:T102M;ENSP00000404147:T84M;ENSP00000380263:T84M;ENSP00000311993:T84M;ENSP00000372209:T84M;ENSP00000380265:T102M;ENSP00000380264:T102M;ENSP00000440508:T102M	ENSP00000311993:T84M	T	+	2	0	DHRS4	23494260	0.410000	0.25376	0.968000	0.41197	0.539000	0.34962	-0.130000	0.10498	-0.015000	0.14150	0.479000	0.44913	ACG	.	.	none		0.652	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		Missense_Mutation
OR6F1	343169	hgsc.bcm.edu	37	1	247875415	247875415	+	Missense_Mutation	SNP	A	A	G	rs2282316	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247875415A>G	ENST00000302084.2	-	1	690	c.643T>C	c.(643-645)Ttt>Ctt	p.F215L	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	215			F -> L (in dbSNP:rs2282316).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F215L(1)		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)			TAGGAGACAAAGGTGATGAGG	0.552													G|||	1763	0.352037	0.6929	0.2017	5008	,	,		22569	0.2401		0.2058	False		,,,				2504	0.2638				p.F215L		Atlas-SNP	.											OR6F1,NS,carcinoma,0,1	OR6F1	88	1	1	Substitution - Missense(1)	stomach(1)	c.T643C						PASS	.	G	LEU/PHE	2663,1743	519.4+/-370.0	775,1113,315	132.0	116.0	122.0		643	-1.8	0.0	1	dbSNP_100	122	1976,6624	722.5+/-406.4	219,1538,2543	yes	missense	OR6F1	NM_001005286.1	22	994,2651,2858	GG,GA,AA		22.9767,39.5597,35.6682	benign	215/309	247875415	4639,8367	2203	4300	6503	SO:0001583	missense	343169	exon1			AGACAAAGGTGAT	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.643T>C	1.37:g.247875415A>G	ENSP00000305640:p.Phe215Leu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	132	86	0.651515	NM_001005286	B2RNV6|Q6IF02|Q96R39	Missense_Mutation	SNP	ENST00000302084.2	37	CCDS31095.1	708	0.3241758241758242	342	0.6951219512195121	88	0.2430939226519337	130	0.22727272727272727	148	0.19525065963060687	G	0.007	-1.995955	0.00435	0.604403	0.229767	ENSG00000169214	ENST00000302084	T	0.00017	9.09	3.72	-1.83	0.07833	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34268	N	0.004102	T	0.00012	0.0000	N	0.00329	-1.635	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50541	-0.8816	9	0.15066	T	0.55	-10.0518	2.2613	0.04068	0.3244:0.121:0.4315:0.1232	rs2282316;rs56501180;rs60719956;rs2282316	215	Q8NGZ6	OR6F1_HUMAN	L	215	ENSP00000305640:F215L	ENSP00000305640:F215L	F	-	1	0	OR6F1	245942038	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.023000	0.03607	-0.547000	0.06207	-1.054000	0.02325	TTT	A|0.635;G|0.365	0.365	strong		0.552	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286	
SETX	23064	hgsc.bcm.edu	37	9	135203838	135203838	+	Silent	SNP	G	G	A	rs3739921	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:135203838G>A	ENST00000224140.5	-	10	3329	c.3147C>T	c.(3145-3147)caC>caT	p.H1049H	SETX_ENST00000393220.1_Silent_p.H1049H|SETX_ENST00000372169.2_Silent_p.H1049H	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1049					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CTGTTGAAACGTGCTGCTCTG	0.378													G|||	572	0.114217	0.0401	0.0937	5008	,	,		19543	0.2083		0.0616	False		,,,				2504	0.1861				p.H1049H		Atlas-SNP	.											.	SETX	234	.	0			c.C3147T						PASS	.	G		182,4224	118.8+/-156.5	2,178,2023	140.0	139.0	139.0		3147	-3.4	0.0	9	dbSNP_107	139	690,7910	171.3+/-222.3	24,642,3634	no	coding-synonymous	SETX	NM_015046.5		26,820,5657	AA,AG,GG		8.0233,4.1307,6.7046		1049/2678	135203838	872,12134	2203	4300	6503	SO:0001819	synonymous_variant	23064	exon10			TGAAACGTGCTGC	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.3147C>T	9.37:g.135203838G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Silent	SNP	ENST00000224140.5	37	CCDS6947.1																																																																																			G|0.910;A|0.090	0.090	strong		0.378	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
ATP10D	57205	hgsc.bcm.edu	37	4	47560163	47560163	+	Silent	SNP	C	C	A	rs11729411	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:47560163C>A	ENST00000273859.3	+	12	2576	c.2307C>A	c.(2305-2307)atC>atA	p.I769I	AC092597.3_ENST00000508081.1_RNA	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	769					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)	p.I769I(1)		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						TCCTACACATCCTGCCCTTTG	0.483													C|||	1125	0.224641	0.1785	0.2925	5008	,	,		20635	0.2986		0.2127	False		,,,				2504	0.1748				p.I769I		Atlas-SNP	.											ATP10D,NS,carcinoma,0,1	ATP10D	168	1	1	Substitution - coding silent(1)	stomach(1)	c.C2307A						PASS	.	C		849,3557	334.9+/-303.7	87,675,1441	141.0	120.0	127.0		2307	3.2	1.0	4	dbSNP_120	127	1925,6675	340.3+/-323.5	217,1491,2592	no	coding-synonymous	ATP10D	NM_020453.3		304,2166,4033	AA,AC,CC		22.3837,19.2692,21.3286		769/1427	47560163	2774,10232	2203	4300	6503	SO:0001819	synonymous_variant	57205	exon12			ACACATCCTGCCC	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.2307C>A	4.37:g.47560163C>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	215	211	0.981395	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Silent	SNP	ENST00000273859.3	37	CCDS3476.1																																																																																			C|0.779;A|0.221	0.221	strong		0.483	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
DMBT1	1755	hgsc.bcm.edu	37	10	124351974	124351974	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124351974T>G	ENST00000338354.3	+	20	2469	c.2363T>G	c.(2362-2364)tTt>tGt	p.F788C	DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000368955.3_Missense_Mutation_p.F778C|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368909.3_Missense_Mutation_p.F788C|DMBT1_ENST00000344338.3_Missense_Mutation_p.F778C			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	788	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				AATGCCCGGTTTGGCCAGGGC	0.617																																					p.F788C	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.T2363G						PASS	.						172.0	135.0	147.0					10																	124351974		1994	4114	6108	SO:0001583	missense	1755	exon20			CCCGGTTTGGCCA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2363T>G	10.37:g.124351974T>G	ENSP00000342210:p.Phe788Cys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	78	26	0.333333	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	T	8.174	0.792281	0.16258	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	3.86	3.86	0.44501	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	D	0.84547	0.5496	H	0.97962	4.115	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.998;0.999	D	0.86955	0.2088	9	0.87932	D	0	.	8.6056	0.33771	0.1713:0.0:0.0:0.8286	.	549;788;778;788	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	C	788;788;788;788;788;788;778;788;778	ENSP00000342210:F788C;ENSP00000343175:F778C;ENSP00000357905:F788C;ENSP00000357951:F778C	ENSP00000342210:F788C	F	+	2	0	DMBT1	124341964	1.000000	0.71417	0.015000	0.15790	0.070000	0.16714	3.795000	0.55499	1.525000	0.49052	0.456000	0.33151	TTT	.	.	none		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
APOBEC2	10930	hgsc.bcm.edu	37	6	41029109	41029109	+	Silent	SNP	T	T	C	rs2073014	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:41029109T>C	ENST00000244669.2	+	2	218	c.174T>C	c.(172-174)aaT>aaC	p.N58N		NM_006789.3	NP_006780.1	Q9Y235	ABEC2_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2	58					cytidine deamination (GO:0009972)|DNA demethylation (GO:0080111)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)		cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|prostate(2)|skin(1)	10	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGTTCCGGAATGTGGAGTACA	0.502													T|||	923	0.184305	0.0333	0.2305	5008	,	,		16964	0.2669		0.168	False		,,,				2504	0.2873				p.N58N	Ovarian(118;1320 2185 8096 29684)	Atlas-SNP	.											.	APOBEC2	30	.	0			c.T174C						PASS	.	T		312,4094	167.3+/-198.3	13,286,1904	78.0	77.0	77.0		174	-2.4	1.0	6	dbSNP_96	77	1748,6852	316.8+/-312.9	181,1386,2733	no	coding-synonymous	APOBEC2	NM_006789.3		194,1672,4637	CC,CT,TT		20.3256,7.0813,15.8388		58/225	41029109	2060,10946	2203	4300	6503	SO:0001819	synonymous_variant	10930	exon2			CCGGAATGTGGAG	AF161698	CCDS4848.1	6p21	2008-02-05			ENSG00000124701	ENSG00000124701		"""Apolipoprotein B mRNA editing enzymes"""	605	protein-coding gene	gene with protein product		604797				10403781	Standard	NM_006789		Approved	ARCD1, ARP1	uc003opl.3	Q9Y235	OTTHUMG00000014670	ENST00000244669.2:c.174T>C	6.37:g.41029109T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_006789	B2R899|Q53F28|Q5TGU5|Q5TGU6	Silent	SNP	ENST00000244669.2	37	CCDS4848.1																																																																																			T|0.840;C|0.160	0.160	strong		0.502	APOBEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040498.1	NM_006789	
BEND7	222389	hgsc.bcm.edu	37	10	13534851	13534851	+	Silent	SNP	A	A	G	rs2251555	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:13534851A>G	ENST00000396900.2	-	5	596	c.597T>C	c.(595-597)ccT>ccC	p.P199P	BEND7_ENST00000341083.3_Silent_p.P147P|BEND7_ENST00000396898.2_Silent_p.P212P|BEND7_ENST00000378605.3_Silent_p.P160P			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	199						extracellular vesicular exosome (GO:0070062)		p.P147P(1)|p.P160P(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						GGGAAATTGGAGGTTGTTGTC	0.413													G|||	2407	0.480631	0.4887	0.5533	5008	,	,		19988	0.3403		0.5378	False		,,,				2504	0.5041				p.P160P		Atlas-SNP	.											BEND7_ENST00000378605,colon,carcinoma,0,4	BEND7	85	4	2	Substitution - coding silent(2)	stomach(2)	c.T480C						PASS	.	G	,	2261,2143	543.9+/-376.4	580,1101,521	71.0	73.0	73.0		480,441	4.5	1.0	10	dbSNP_100	73	4934,3666	513.7+/-378.2	1412,2110,778	no	coding-synonymous,coding-synonymous	BEND7	NM_001100912.1,NM_152751.2	,	1992,3211,1299	GG,GA,AA		42.6279,48.6603,44.6709	,	160/375,147/469	13534851	7195,5809	2202	4300	6502	SO:0001819	synonymous_variant	222389	exon4			AATTGGAGGTTGT	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.597T>C	10.37:g.13534851A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001100912	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				A|0.476;G|0.524	0.524	strong		0.413	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
THSD7A	221981	hgsc.bcm.edu	37	7	11521428	11521428	+	Silent	SNP	A	A	G	rs61996277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	273	0	0		WXS	Illumina HiSeq	Phase_I	336	121	0.360119	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	
ZNF667	63934	hgsc.bcm.edu	37	19	56954103	56954103	+	Silent	SNP	C	C	A	rs7253217	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56954103C>A	ENST00000504904.3	-	7	980	c.261G>T	c.(259-261)ggG>ggT	p.G87G	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Silent_p.G215G|ZNF667_ENST00000292069.6_Silent_p.G87G			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	87					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)		CACATTTAGACCCCGAGTCTG	0.348													C|||	810	0.161741	0.1483	0.1873	5008	,	,		17863	0.0754		0.2406	False		,,,				2504	0.1697				p.G87G		Atlas-SNP	.											.	ZNF667	95	.	0			c.G261T						PASS	.	C		629,3655		54,521,1567	44.0	48.0	46.0		261	1.0	0.5	19	dbSNP_116	46	1560,6690		146,1268,2711	no	coding-synonymous	ZNF667	NM_022103.3		200,1789,4278	AA,AC,CC		18.9091,14.6825,17.4645		87/611	56954103	2189,10345	2142	4125	6267	SO:0001819	synonymous_variant	63934	exon5			TTTAGACCCCGAG		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.261G>T	19.37:g.56954103C>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	32	20	0.625	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			C|0.825;A|0.175	0.175	strong		0.348	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
PKM	5315	hgsc.bcm.edu	37	15	72501072	72501072	+	Silent	SNP	C	C	T	rs11558376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:72501072C>T	ENST00000335181.5	-	6	829	c.726G>A	c.(724-726)gcG>gcA	p.A242A	PKM_ENST00000449901.2_Silent_p.A227A|PKM_ENST00000389093.3_Silent_p.A242A|PKM_ENST00000568883.1_Silent_p.A77A|PKM_ENST00000565184.1_Silent_p.A242A|PKM_ENST00000565154.1_Silent_p.A242A|PKM_ENST00000319622.6_Silent_p.A242A|PKM_ENST00000568459.1_Silent_p.A242A	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	242					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	GGATGAATGACGCAAACACCA	0.493													C|||	4	0.000798722	0.0	0.0	5008	,	,		21170	0.0		0.004	False		,,,				2504	0.0				p.A316A		Atlas-SNP	.											PKM2,NS,neuroblastoma,-1,2	PKM	25	2	0			c.G948A						PASS	.	C	,,,,,,	1,4397	2.1+/-5.4	0,1,2198	203.0	180.0	188.0		948,504,681,741,726,726,726	-10.5	0.5	15	dbSNP_120	188	15,8579	11.2+/-40.8	0,15,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PKM2	NM_001206796.1,NM_001206797.1,NM_001206798.1,NM_001206799.1,NM_002654.4,NM_182470.2,NM_182471.2	,,,,,,	0,16,6480	TT,TC,CC		0.1745,0.0227,0.1232	,,,,,,	316/606,168/458,227/517,247/537,242/532,242/532,242/532	72501072	16,12976	2199	4297	6496	SO:0001819	synonymous_variant	5315	exon7			GAATGACGCAAAC	M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.726G>A	15.37:g.72501072C>T		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	85	64	0.752941	NM_001206796	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Silent	SNP	ENST00000335181.5	37	CCDS32284.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1		
MYSM1	114803	hgsc.bcm.edu	37	1	59127086	59127086	+	Silent	SNP	G	G	A	rs7523134	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:59127086G>A	ENST00000472487.1	-	18	2301	c.2262C>T	c.(2260-2262)ctC>ctT	p.L754L	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	754					chromatin remodeling (GO:0006338)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(7;9.36e-06)					ACCTATGGGAGAGCCTGTATT	0.353													G|||	1241	0.247804	0.1339	0.2421	5008	,	,		17586	0.3095		0.2843	False		,,,				2504	0.3047				p.L754L		Atlas-SNP	.											.	MYSM1	50	.	0			c.C2262T						PASS	.	G		636,3036		55,526,1255	179.0	164.0	168.0		2262	-10.3	0.1	1	dbSNP_116	168	2406,5750		365,1676,2037	no	coding-synonymous	MYSM1	NM_001085487.2		420,2202,3292	AA,AG,GG		29.4998,17.3203,25.7186		754/829	59127086	3042,8786	1836	4078	5914	SO:0001819	synonymous_variant	114803	exon18			ATGGGAGAGCCTG	AB067502	CCDS41343.1	1p32.1	2009-02-11	2009-02-11		ENSG00000162601	ENSG00000162601			29401	protein-coding gene	gene with protein product		612176				11572484, 17428495, 17707232	Standard	NM_001085487		Approved	KIAA1915	uc009wab.2	Q5VVJ2	OTTHUMG00000009533	ENST00000472487.1:c.2262C>T	1.37:g.59127086G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																			G|0.742;A|0.258	0.258	strong		0.353	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481	
KIAA1324	57535	hgsc.bcm.edu	37	1	109714593	109714593	+	Silent	SNP	C	C	T	rs112023388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109714593C>T	ENST00000369939.3	+	4	756	c.573C>T	c.(571-573)ttC>ttT	p.F191F	KIAA1324_ENST00000529753.1_Silent_p.F191F	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	191					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)		CCGTTAACTTCGAATACTACT	0.537																																					p.F191F		Atlas-SNP	.											.	KIAA1324	77	.	0			c.C573T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	156.0	133.0	141.0		573	-3.8	1.0	1	dbSNP_132	141	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	KIAA1324	NM_020775.3		0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308		191/1014	109714593	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	57535	exon4			TAACTTCGAATAC	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.573C>T	1.37:g.109714593C>T		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	160	122	0.7625	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																			C|0.999;T|0.001	0.001	strong		0.537	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
LANCL2	55915	hgsc.bcm.edu	37	7	55433880	55433880	+	Silent	SNP	G	G	C	rs2272262	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:55433880G>C	ENST00000254770.2	+	1	740	c.162G>C	c.(160-162)gcG>gcC	p.A54A		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	54					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)			GTCCCCCGGCGACCACGGATG	0.726													C|||	1451	0.289736	0.4357	0.1988	5008	,	,		12860	0.1558		0.331	False		,,,				2504	0.2526				p.A54A		Atlas-SNP	.											.	LANCL2	54	.	0			c.G162C						PASS	.	C		1722,2634		395,932,851	8.0	11.0	10.0		162	1.4	0.0	7	dbSNP_100	10	2782,5752		515,1752,2000	no	coding-synonymous	LANCL2	NM_018697.3		910,2684,2851	CC,CG,GG		32.599,39.5317,34.9418		54/451	55433880	4504,8386	2178	4267	6445	SO:0001819	synonymous_variant	55915	exon1			CCCGGCGACCACG	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.162G>C	7.37:g.55433880G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	69	22	0.318841	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Silent	SNP	ENST00000254770.2	37	CCDS5517.1																																																																																			G|0.685;C|0.315	0.315	strong		0.726	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697	
GFPT2	9945	hgsc.bcm.edu	37	5	179734200	179734200	+	Silent	SNP	A	A	G	rs73343449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.			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	149	3	0.0201342		WXS	Illumina HiSeq	Phase_I	153	67	0.437909	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	
VIPR2	7434	hgsc.bcm.edu	37	7	158827326	158827326	+	Silent	SNP	G	G	A	rs2071624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:158827326G>A	ENST00000262178.2	-	9	1010	c.825C>T	c.(823-825)aaC>aaT	p.N275N	VIPR2_ENST00000402066.1_Silent_p.N416N|VIPR2_ENST00000377633.3_Silent_p.N259N	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	275					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CACTGTGGTCGTTTGTATCCC	0.483													G|||	1739	0.347244	0.2383	0.2723	5008	,	,		20595	0.5962		0.2525	False		,,,				2504	0.3885				p.N275N	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.C825T						PASS	.	G		916,3490	348.7+/-310.1	95,726,1382	119.0	107.0	111.0		825	-3.8	0.9	7	dbSNP_96	111	1565,7035	293.8+/-301.5	131,1303,2866	no	coding-synonymous	VIPR2	NM_003382.4		226,2029,4248	AA,AG,GG		18.1977,20.7898,19.0758		275/439	158827326	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	7434	exon9			GTGGTCGTTTGTA	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12695	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 2"""	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.825C>T	7.37:g.158827326G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	112	32	0.285714	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1																																																																																			G|0.742;N|0.000	.	strong		0.483	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
LRRN1	57633	hgsc.bcm.edu	37	3	3886847	3886847	+	Silent	SNP	G	G	C	rs3749349	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:3886847G>C	ENST00000319331.3	+	2	1283	c.522G>C	c.(520-522)ctG>ctC	p.L174L	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	174						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)		GGCTCCACCTGAACTCCAACA	0.403													G|||	1070	0.213658	0.295	0.147	5008	,	,		18549	0.2679		0.1044	False		,,,				2504	0.2076				p.L174L		Atlas-SNP	.											.	LRRN1	82	.	0			c.G522C						PASS	.	G		1040,3366	371.0+/-319.8	118,804,1281	98.0	105.0	102.0		522	-4.1	1.0	3	dbSNP_107	102	1063,7537	223.1+/-260.0	63,937,3300	no	coding-synonymous	LRRN1	NM_020873.5		181,1741,4581	CC,CG,GG		12.3605,23.6042,16.1695		174/717	3886847	2103,10903	2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			CCACCTGAACTCC	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.522G>C	3.37:g.3886847G>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			G|0.820;C|0.180	0.180	strong		0.403	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
FBXO32	114907	hgsc.bcm.edu	37	8	124525483	124525483	+	Silent	SNP	C	C	T	rs3739287	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	204	123	0.602941	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		
FANCA	2175	hgsc.bcm.edu	37	16	89815152	89815152	+	Missense_Mutation	SNP	G	G	A	rs17233497	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:89815152G>A	ENST00000389301.3	-	33	3293	c.3263C>T	c.(3262-3264)tCt>tTt	p.S1088F	FANCA_ENST00000568369.1_Missense_Mutation_p.S1088F	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1088			S -> F (in FA; dbSNP:rs17233497). {ECO:0000269|PubMed:10094191, ECO:0000269|PubMed:18987736}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GCAGAGGACAGACGAAGGCAG	0.587			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	117	0.0233626	0.0038	0.0187	5008	,	,		21735	0.0218		0.0646	False		,,,				2504	0.0123				p.S1088F		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,lymph_node,lymphoid_neoplasm,0,1	FANCA	99	1	0			c.C3263T	GRCh37	CM992318	FANCA	M	rs17233497	PASS	.	G	PHE/SER	73,4323	62.9+/-100.1	0,73,2125	80.0	59.0	66.0		3263	3.7	0.0	16	dbSNP_123	66	697,7903	172.7+/-223.4	27,643,3630	yes	missense	FANCA	NM_000135.2	155	27,716,5755	AA,AG,GG		8.1047,1.6606,5.9249	possibly-damaging	1088/1456	89815152	770,12226	2198	4300	6498	SO:0001583	missense	2175	exon33	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGGACAGACGAAG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3263C>T	16.37:g.89815152G>A	ENSP00000373952:p.Ser1088Phe	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	56	9	0.160714	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	73	0.033424908424908424	3	0.006097560975609756	9	0.024861878453038673	11	0.019230769230769232	50	0.06596306068601583	G	14.27	2.484066	0.44147	0.016606	0.081047	ENSG00000187741	ENST00000389301;ENST00000305699	D	0.85955	-2.05	4.63	3.68	0.42216	.	0.363675	0.24115	N	0.041417	T	0.32556	0.0833	M	0.72118	2.19	0.21020	N	0.999803	P;P;P	0.50272	0.906;0.933;0.933	P;B;B	0.49665	0.618;0.401;0.401	T	0.58589	-0.7610	10	0.66056	D	0.02	-6.0479	8.8363	0.35115	0.1022:0.0:0.8978:0.0	rs17233497;rs17233497	65;1088;1088	B7Z6Y4;B4DRI7;O15360	.;.;FANCA_HUMAN	F	1088;65	ENSP00000373952:S1088F	ENSP00000306281:S65F	S	-	2	0	FANCA	88342653	0.024000	0.19004	0.003000	0.11579	0.202000	0.24057	2.054000	0.41335	1.329000	0.45376	0.462000	0.41574	TCT	G|0.954;A|0.046	0.046	strong		0.587	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
SLC35F1	222553	hgsc.bcm.edu	37	6	118588185	118588185	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:118588185G>A	ENST00000360388.4	+	4	706	c.505G>A	c.(505-507)Gtg>Atg	p.V169M		NM_001029858.3	NP_001025029.2	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	169					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(226;0.217)		GATCCCAGTCGTGATTTTGCT	0.498																																					p.V169M		Atlas-SNP	.											SLC35F1,bladder,carcinoma,-2,2	SLC35F1	65	2	0			c.G505A						scavenged	.						387.0	354.0	365.0					6																	118588185		2203	4300	6503	SO:0001583	missense	222553	exon4			CCAGTCGTGATTT	BC028615	CCDS34524.1	6q22.31	2013-05-22			ENSG00000196376	ENSG00000196376		"""Solute carriers"""	21483	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 169"""	C6orf169			Standard	NM_001029858		Approved	dJ230I3.1	uc003pxx.4	Q5T1Q4	OTTHUMG00000015460	ENST00000360388.4:c.505G>A	6.37:g.118588185G>A	ENSP00000353557:p.Val169Met	Somatic	366	2	0.00546448		WXS	Illumina HiSeq	Phase_I	379	117	0.308707	NM_001029858	E1P564|Q1RMG1|Q4G0U9|Q4G167|Q6N007	Missense_Mutation	SNP	ENST00000360388.4	37	CCDS34524.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974196	0.74246	.	.	ENSG00000196376	ENST00000360388	T	0.71341	-0.56	4.99	4.99	0.66335	.	0.143231	0.46442	D	0.000299	T	0.80788	0.4690	M	0.84433	2.695	0.58432	D	0.999996	D	0.53312	0.959	P	0.55713	0.782	D	0.83597	0.0126	10	0.72032	D	0.01	-26.7614	18.8278	0.92125	0.0:0.0:1.0:0.0	.	169	Q5T1Q4	S35F1_HUMAN	M	169	ENSP00000353557:V169M	ENSP00000353557:V169M	V	+	1	0	SLC35F1	118694878	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	3.849000	0.55910	2.756000	0.94617	0.561000	0.74099	GTG	.	.	none		0.498	SLC35F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041991.2	XM_167044	
KIF21B	23046	hgsc.bcm.edu	37	1	200959302	200959302	+	Silent	SNP	G	G	A	rs2297911	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:200959302G>A	ENST00000422435.2	-	20	3310	c.2994C>T	c.(2992-2994)gaC>gaT	p.D998D	KIF21B_ENST00000461742.2_Silent_p.D998D|KIF21B_ENST00000360529.5_Silent_p.D998D|KIF21B_ENST00000332129.2_Silent_p.D998D	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	998					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)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						TGGCCTGGCAGTCGGTGATGC	0.647													G|||	1321	0.263778	0.4531	0.2032	5008	,	,		20704	0.2976		0.1541	False		,,,				2504	0.1288				p.D998D		Atlas-SNP	.											.	KIF21B	208	.	0			c.C2994T						PASS	.	G		1864,2542	537.6+/-374.8	389,1086,728	86.0	82.0	84.0		2994	3.0	1.0	1	dbSNP_100	84	1535,7065	288.8+/-298.9	131,1273,2896	yes	coding-synonymous	KIF21B	NM_017596.2		520,2359,3624	AA,AG,GG		17.8488,42.3059,26.1341		998/1625	200959302	3399,9607	2203	4300	6503	SO:0001819	synonymous_variant	23046	exon20			CTGGCAGTCGGTG	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.2994C>T	1.37:g.200959302G>A		Somatic	712	1	0.00140449		WXS	Illumina HiSeq	Phase_I	770	196	0.254545	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Silent	SNP	ENST00000422435.2	37	CCDS58056.1																																																																																			G|0.752;A|0.248	0.248	strong		0.647	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
MAP9	79884	hgsc.bcm.edu	37	4	156274377	156274377	+	Missense_Mutation	SNP	T	T	C	rs1058992	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:156274377T>C	ENST00000311277.4	-	11	1759	c.1496A>G	c.(1495-1497)aAg>aGg	p.K499R	AC097467.2_ENST00000598252.1_RNA|AC097467.2_ENST00000417474.1_RNA|AC097467.2_ENST00000597939.1_RNA|AC097467.2_ENST00000610249.1_RNA|AC097467.2_ENST00000595229.1_RNA|AC097467.2_ENST00000609486.1_RNA|AC097467.2_ENST00000599555.2_RNA|AC097467.2_ENST00000608762.1_RNA|AC097467.2_ENST00000593387.2_RNA|AC097467.2_ENST00000608544.1_RNA|AC097467.2_ENST00000608092.1_RNA|AC097467.2_ENST00000601977.1_RNA|AC097467.2_ENST00000608463.1_RNA|AC097467.2_ENST00000608406.1_RNA|MAP9_ENST00000515654.1_Missense_Mutation_p.K475R|AC097467.2_ENST00000609716.1_RNA|AC097467.2_ENST00000609254.1_RNA	NM_001039580.1	NP_001034669.1	Q49MG5	MAP9_HUMAN	microtubule-associated protein 9	499			K -> R (in dbSNP:rs1058992).		cytokinesis (GO:0000910)|regulation of mitosis (GO:0007088)|spindle assembly involved in mitosis (GO:0090307)	astral microtubule (GO:0000235)|mitotic spindle midzone (GO:1990023)		p.K499R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.143)		TTCAGTTTTCTTCTTGTTTTT	0.333													T|||	2048	0.408946	0.6104	0.3228	5008	,	,		14025	0.5863		0.2247	False		,,,				2504	0.2045				p.K499R		Atlas-SNP	.											MAP9,NS,carcinoma,0,1	MAP9	79	1	1	Substitution - Missense(1)	prostate(1)	c.A1496G						PASS	.	T	ARG/LYS	2319,2085	603.3+/-390.1	631,1057,514	108.0	104.0	106.0		1496	4.1	1.0	4	dbSNP_86	106	1857,6739	332.3+/-320.0	193,1471,2634	yes	missense	MAP9	NM_001039580.1	26	824,2528,3148	CC,CT,TT		21.6031,47.3433,32.1231	probably-damaging	499/648	156274377	4176,8824	2202	4298	6500	SO:0001583	missense	79884	exon11			GTTTTCTTCTTGT	AK024812	CCDS35493.1	4q32.1	2008-02-05			ENSG00000164114	ENSG00000164114			26118	protein-coding gene	gene with protein product	"""aster-associated protein"""	610070				16049101	Standard	XM_006714306		Approved	ASAP, FLJ21159	uc003ios.3	Q49MG5	OTTHUMG00000133628	ENST00000311277.4:c.1496A>G	4.37:g.156274377T>C	ENSP00000310593:p.Lys499Arg	Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	117	82	0.700855	NM_001039580	Q4W5I7|Q68DU1|Q9H781|Q9H7B6	Missense_Mutation	SNP	ENST00000311277.4	37	CCDS35493.1	921	0.4217032967032967	307	0.6239837398373984	104	0.287292817679558	329	0.5751748251748252	181	0.23878627968337732	T	10.92	1.487296	0.26686	0.526567	0.216031	ENSG00000164114	ENST00000311277;ENST00000515654	T;T	0.09445	2.98;2.98	5.23	4.05	0.47172	.	0.402707	0.28700	N	0.014428	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	0.9999999999743422	B;B;B	0.32203	0.169;0.36;0.169	B;B;B	0.32022	0.091;0.139;0.091	T	0.19321	-1.0309	9	0.19147	T	0.46	-13.891	8.6845	0.34229	0.0:0.0879:0.0:0.9121	rs17357030	474;499;499	B4DVG9;B9EJB6;Q49MG5	.;.;MAP9_HUMAN	R	499;475	ENSP00000310593:K499R;ENSP00000427402:K475R	ENSP00000310593:K499R	K	-	2	0	MAP9	156493827	0.914000	0.31030	1.000000	0.80357	0.991000	0.79684	0.012000	0.13287	0.930000	0.37217	0.533000	0.62120	AAG	T|0.652;C|0.348	0.348	strong		0.333	MAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257771.3	NM_001039580	
SRRM5	100170229	hgsc.bcm.edu	37	19	44117582	44117582	+	Missense_Mutation	SNP	T	T	C	rs10410000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44117582T>C	ENST00000607544.1	+	3	1631	c.1309T>C	c.(1309-1311)Tgc>Cgc	p.C437R	ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000526798.1_Missense_Mutation_p.C452R|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						scavenged	.						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	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	82	35	0.426829	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	
ZNF615	284370	hgsc.bcm.edu	37	19	52505463	52505463	+	Silent	SNP	C	C	T	rs151263298	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52505463C>T	ENST00000602063.1	-	4	436	c.87G>A	c.(85-87)caG>caA	p.Q29Q	ZNF615_ENST00000598071.1_Silent_p.Q29Q|ZNF615_ENST00000391795.3_Silent_p.Q34Q|ZNF615_ENST00000376716.5_Silent_p.Q29Q|ZNF615_ENST00000595114.1_5'Flank|ZNF615_ENST00000597747.1_Silent_p.Q29Q|ZNF615_ENST00000594083.1_Silent_p.Q29Q			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	29	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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		ACAGGTCCTTCTGAGCAGGGC	0.547													C|||	97	0.019369	0.003	0.013	5008	,	,		16855	0.0		0.0497	False		,,,				2504	0.0348				p.Q29Q		Atlas-SNP	.											.	ZNF615	111	.	0			c.G87A						PASS	.	C	,	43,4363	45.3+/-79.5	0,43,2160	182.0	167.0	173.0		87,87	1.0	0.5	19	dbSNP_134	173	441,8159	133.8+/-191.2	8,425,3867	no	coding-synonymous,coding-synonymous	ZNF615	NM_001199324.1,NM_198480.3	,	8,468,6027	TT,TC,CC		5.1279,0.9759,3.7214	,	29/743,29/732	52505463	484,12522	2203	4300	6503	SO:0001819	synonymous_variant	284370	exon4			GTCCTTCTGAGCA	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.87G>A	19.37:g.52505463C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	190	104	0.547368	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Silent	SNP	ENST00000602063.1	37	CCDS12846.1																																																																																			C|0.966;T|0.034	0.034	strong		0.547	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480	
PKD1	5310	hgsc.bcm.edu	37	16	2161793	2161793	+	Silent	SNP	G	G	A	rs74331768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2161793G>A	ENST00000262304.4	-	15	3583	c.3375C>T	c.(3373-3375)tcC>tcT	p.S1125S	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Silent_p.S1125S	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1125	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						CGGAGGGCAGGGAGGCGCGCA	0.677													g|||	569	0.113618	0.2897	0.111	5008	,	,		15925	0.0		0.0944	False		,,,				2504	0.0143				p.S1125S		Atlas-SNP	.											.	PKD1	184	.	0			c.C3375T						PASS	.	G	,	1046,3330		140,766,1282	20.0	21.0	21.0		3375,3375	-6.9	0.0	16	dbSNP_131	21	826,7752		53,720,3516	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	193,1486,4798	AA,AG,GG		9.6293,23.9031,14.4511	,	1125/4303,1125/4304	2161793	1872,11082	2188	4289	6477	SO:0001819	synonymous_variant	5310	exon15			GGGCAGGGAGGCG	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.3375C>T	16.37:g.2161793G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			G|0.856;A|0.144	0.144	strong		0.677	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
PLCH1	23007	hgsc.bcm.edu	37	3	155200563	155200563	+	Silent	SNP	G	G	T	rs1816522	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:155200563G>T	ENST00000340059.7	-	23	3275	c.3276C>A	c.(3274-3276)ccC>ccA	p.P1092P	PLCH1_ENST00000460012.1_Silent_p.P1054P|PLCH1_ENST00000334686.6_Silent_p.P1054P|PLCH1_ENST00000494598.1_Intron|PLCH1_ENST00000414191.1_Silent_p.P1054P|PLCH1_ENST00000447496.2_3'UTR	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	1092					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CTACAGGATCGGGAGCCAAAT	0.493													G|||	142	0.0283546	0.0053	0.036	5008	,	,		20531	0.0		0.0954	False		,,,				2504	0.0143				p.P1092P		Atlas-SNP	.											PLCH1_ENST00000340059,NS,adenoma,0,2	PLCH1	406	2	0			c.C3276A						PASS	.	G	,,	78,4328	68.7+/-106.4	1,76,2126	178.0	178.0	178.0		3276,,3162	-3.8	0.0	3	dbSNP_92	178	696,7904	172.5+/-223.2	26,644,3630	no	coding-synonymous,utr-3,coding-synonymous	PLCH1	NM_001130960.1,NM_001130961.1,NM_014996.2	,,	27,720,5756	TT,TG,GG		8.093,1.7703,5.9511	,,	1092/1694,,1054/1656	155200563	774,12232	2203	4300	6503	SO:0001819	synonymous_variant	23007	exon23			AGGATCGGGAGCC	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.3276C>A	3.37:g.155200563G>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Silent	SNP	ENST00000340059.7	37	CCDS46939.1																																																																																			A|0.000;G|0.948;T|0.052	0.052	strong		0.493	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
CCDC57	284001	hgsc.bcm.edu	37	17	80059690	80059690	+	Silent	SNP	G	G	A	rs61735692	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80059690G>A	ENST00000389641.4	-	18	2655	c.2619C>T	c.(2617-2619)ggC>ggT	p.G873G	CCDC57_ENST00000392347.1_Silent_p.G873G			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	873										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			GGGTGGCAATGCCTGCCTGCA	0.602													G|||	69	0.013778	0.0038	0.0288	5008	,	,		17944	0.0		0.0398	False		,,,				2504	0.0041				p.G872G		Atlas-SNP	.											.	CCDC57	102	.	0			c.C2616T						PASS	.	G		46,4056		0,46,2005	64.0	71.0	69.0		2616	0.4	0.0	17	dbSNP_129	69	420,7976		15,390,3793	no	coding-synonymous	CCDC57	NM_198082.2		15,436,5798	AA,AG,GG		5.0024,1.1214,3.7286		872/916	80059690	466,12032	2051	4198	6249	SO:0001819	synonymous_variant	284001	exon17			GGCAATGCCTGCC	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.2619C>T	17.37:g.80059690G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37		46	0.021062271062271064	5	0.01016260162601626	7	0.019337016574585635	0	0.0	34	0.044854881266490766	G	3.247	-0.154002	0.06585	0.011214	0.050024	ENSG00000176155	ENST00000392345	.	.	.	2.53	0.444	0.16592	.	.	.	.	.	T	0.03871	0.0109	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.15896	-1.0421	4	.	.	.	.	4.2507	0.10693	0.4561:0.0:0.5439:0.0	.	.	.	.	V	185	.	.	A	-	2	0	CCDC57	77652979	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.849000	0.27723	0.392000	0.25172	-0.224000	0.12420	GCA	G|0.975;A|0.025	0.025	strong		0.602	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
PARP2	10038	hgsc.bcm.edu	37	14	20824181	20824181	+	Silent	SNP	T	T	C	rs3093930	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20824181T>C	ENST00000250416.5	+	11	1158	c.1131T>C	c.(1129-1131)taT>taC	p.Y377Y	PARP2_ENST00000527915.1_Silent_p.Y377Y|PARP2_ENST00000429687.3_Silent_p.Y364Y	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	377	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				base-excision repair (GO:0006284)|DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway (GO:0097191)|protein ADP-ribosylation (GO:0006471)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			central_nervous_system(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)	15	all_cancers(95;0.00092)	all_lung(585;0.235)	Epithelial(56;5.34e-07)|all cancers(55;3.7e-06)	GBM - Glioblastoma multiforme(265;0.00888)|READ - Rectum adenocarcinoma(17;0.0649)		ATGAAAGTTATGAGTTCAAAG	0.418								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					T|||	2557	0.510583	0.2867	0.6225	5008	,	,		20925	0.6002		0.675	False		,,,				2504	0.4724				p.Y377Y		Atlas-SNP	.											.	PARP2	92	.	0			c.T1131C						PASS	.	T	,	1332,2462		232,868,797	150.0	137.0	141.0		1092,1131	2.3	0.4	14	dbSNP_103	141	5527,2693		1864,1799,447	no	coding-synonymous,coding-synonymous	PARP2	NM_001042618.1,NM_005484.3	,	2096,2667,1244	CC,CT,TT		32.7616,35.1081,42.9083	,	364/571,377/584	20824181	6859,5155	1897	4110	6007	SO:0001819	synonymous_variant	10038	exon11			AAGTTATGAGTTC	AF085734	CCDS41910.1, CCDS45077.1	14q11.2-q12	2010-02-16	2008-07-28	2004-08-26	ENSG00000129484	ENSG00000129484		"""Poly (ADP-ribose) polymerases"""	272	protein-coding gene	gene with protein product		607725	"""ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2"", ""poly (ADP-ribose) polymerase family, member 2"""	ADPRTL2		10329013, 18353725	Standard	NM_005484		Approved		uc001vxc.3	Q9UGN5	OTTHUMG00000166106	ENST00000250416.5:c.1131T>C	14.37:g.20824181T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	195	193	0.989744	NM_005484	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Silent	SNP	ENST00000250416.5	37	CCDS41910.1	1261	0.5773809523809523	145	0.29471544715447157	232	0.6408839779005525	370	0.6468531468531469	514	0.6781002638522428	T	3.016	-0.202879	0.06219	0.351081	0.672384	ENSG00000129484	ENST00000539930	.	.	.	6.03	2.32	0.28847	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999773513	.	.	.	.	.	.	.	.	.	.	.	.	.	0.2828	5.6326	0.17518	0.0:0.1499:0.1438:0.7062	rs3093930;rs17308338;rs57586296;rs3093930	.	.	.	R	54	.	.	X	+	1	0	PARP2	19894021	0.080000	0.21391	0.422000	0.26621	0.835000	0.47333	-0.093000	0.11111	0.150000	0.19136	0.533000	0.62120	TGA	T|0.445;C|0.555	0.555	strong		0.418	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2		
ZBTB16	7704	hgsc.bcm.edu	37	11	113934473	113934473	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:113934473C>T	ENST00000335953.4	+	2	831	c.451C>T	c.(451-453)Cgg>Tgg	p.R151W	ZBTB16_ENST00000392996.2_Missense_Mutation_p.R151W	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	151					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		CCGCAAGGCTCGGTACCTCAA	0.607																																					p.R151W		Atlas-SNP	.											ZBTB16_ENST00000335953,NS,carcinoma,-1,1	ZBTB16	101	1	0			c.C451T						scavenged	.						60.0	58.0	59.0					11																	113934473		2201	4296	6497	SO:0001583	missense	7704	exon2			AAGGCTCGGTACC	Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12930	protein-coding gene	gene with protein product	"""promyelocytic leukaemia zinc finger"""	176797	"""zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"""	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.451C>T	11.37:g.113934473C>T	ENSP00000338157:p.Arg151Trp	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	92	3	0.0326087	NM_006006	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.505876	0.64410	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.11821	2.74;2.74	5.67	2.46	0.29980	.	0.270914	0.34853	N	0.003626	T	0.19565	0.0470	L	0.27053	0.805	0.43598	D	0.995957	D;D	0.76494	0.999;0.999	P;P	0.59424	0.857;0.849	T	0.01516	-1.1335	10	0.40728	T	0.16	-15.6439	14.3317	0.66561	0.5505:0.4495:0.0:0.0	.	151;156	Q05516;Q59H43	ZBT16_HUMAN;.	W	151	ENSP00000338157:R151W;ENSP00000376721:R151W	ENSP00000309507:R151W	R	+	1	2	ZBTB16	113439683	0.892000	0.30473	0.998000	0.56505	0.968000	0.65278	1.785000	0.38684	0.774000	0.33427	0.655000	0.94253	CGG	.	.	none		0.607	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006	
GRIN1	2902	hgsc.bcm.edu	37	9	140051238	140051238	+	Silent	SNP	A	A	G	rs6293	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:140051238A>G	ENST00000371561.3	+	5	1886	c.789A>G	c.(787-789)ccA>ccG	p.P263P	GRIN1_ENST00000471122.1_3'UTR|GRIN1_ENST00000315048.3_Silent_p.P263P|GRIN1_ENST00000371555.4_Silent_p.P284P|GRIN1_ENST00000350902.5_Silent_p.P263P|GRIN1_ENST00000371553.3_Silent_p.P284P|GRIN1_ENST00000371559.4_Silent_p.P263P|GRIN1_ENST00000371546.4_Silent_p.P284P|GRIN1_ENST00000371550.4_Silent_p.P263P|GRIN1_ENST00000371560.3_Silent_p.P284P	NM_007327.3	NP_015566.1	Q05586	NMDZ1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 1	263					adult locomotory behavior (GO:0008344)|calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular calcium ion homeostasis (GO:0006874)|cellular response to manganese ion (GO:0071287)|cerebral cortex development (GO:0021987)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|male mating behavior (GO:0060179)|negative regulation of neuron apoptotic process (GO:0043524)|olfactory learning (GO:0008355)|pons maturation (GO:0021586)|positive regulation of apoptotic process (GO:0043065)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prepulse inhibition (GO:0060134)|propylene metabolic process (GO:0018964)|protein tetramerization (GO:0051262)|regulation of axonogenesis (GO:0050770)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange (GO:0043576)|regulation of synapse assembly (GO:0051963)|respiratory gaseous exchange (GO:0007585)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to ethanol (GO:0045471)|response to fungicide (GO:0060992)|response to morphine (GO:0043278)|rhythmic process (GO:0048511)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|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 density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic cleft (GO:0043083)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate binding (GO:0016595)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|voltage-gated cation channel activity (GO:0022843)			NS(1)|breast(1)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;6.87e-05)|Epithelial(140;0.00095)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GCTACGCCCCAGACGGTGAGT	0.687													G|||	705	0.140775	0.0287	0.2032	5008	,	,		12489	0.002		0.337	False		,,,				2504	0.1892				p.P284P	NSCLC(113;717 1653 2089 20474 37618)	Atlas-SNP	.											GRIN1,NS,carcinoma,0,2	GRIN1	51	2	0			c.A852G						PASS	.	G	,,,,	285,4099		15,255,1922	20.0	21.0	21.0		789,852,852,789,789	-5.6	0.9	9	dbSNP_52	21	2706,5866		442,1822,2022	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRIN1	NM_000832.6,NM_001185090.1,NM_001185091.1,NM_007327.3,NM_021569.3	,,,,	457,2077,3944	GG,GA,AA		31.5679,6.5009,23.0858	,,,,	263/886,284/944,284/907,263/939,263/902	140051238	2991,9965	2192	4286	6478	SO:0001819	synonymous_variant	2902	exon6			CGCCCCAGACGGT		CCDS7031.1, CCDS7032.1, CCDS43910.1, CCDS55354.1, CCDS55355.1	9q34.3	2013-01-11			ENSG00000176884	ENSG00000176884		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4584	protein-coding gene	gene with protein product		138249	"""N-methyl-D-aspartate receptor subunit NR1"""	NMDAR1		1350383	Standard	NM_000832		Approved	GluN1	uc004cln.3	Q05586	OTTHUMG00000020976	ENST00000371561.3:c.789A>G	9.37:g.140051238A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_001185091	A6NLK7|A6NLR1|C9K0X1|P35437|Q12867|Q12868|Q5VSF3|Q5VSF4|Q5VSF5|Q5VSF6|Q5VSF7|Q5VSF8|Q9UPF8|Q9UPF9	Silent	SNP	ENST00000371561.3	37	CCDS7031.1																																																																																			A|0.831;G|0.169	0.169	strong		0.687	GRIN1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055267.3	NM_007327	
NUTM2A	728118	hgsc.bcm.edu	37	10	88988232	88988232	+	Missense_Mutation	SNP	G	G	A	rs200425300	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:88988232G>A	ENST00000381707.2	+	2	978	c.595G>A	c.(595-597)Ggg>Agg	p.G199R	NUTM2A_ENST00000381689.4_Missense_Mutation_p.G199R|NUTM2A-AS1_ENST00000451940.2_RNA	NM_001099338.1	NP_001092808.1	Q8IVF1	NTM2A_HUMAN	NUT family member 2A	199																	GAGTGGGGCCGGGGCTTCCAA	0.657													.|||	2	0.000399361	0.0	0.0	5008	,	,		22613	0.0		0.0	False		,,,				2504	0.002				p.G199R		Atlas-SNP	.											FAM22D,NS,carcinoma,-1,2	FAM22A	20	2	0			c.G595A						scavenged	.						27.0	31.0	30.0					10																	88988232		1156	2974	4130	SO:0001583	missense	728118	exon2			GGGGCCGGGGCTT		CCDS44452.1	10q23.2	2013-03-15	2013-03-14	2013-03-14	ENSG00000184923	ENSG00000184923			23438	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member A"""	FAM22A			Standard	NM_001099338		Approved		uc001kek.3	Q8IVF1	OTTHUMG00000018670	ENST00000381707.2:c.595G>A	10.37:g.88988232G>A	ENSP00000371126:p.Gly199Arg	Somatic	457	2	0.00437637		WXS	Illumina HiSeq	Phase_I	360	3	0.00833333	NM_001099338	A6NMX5|C9JDI1|Q5VZW1	Missense_Mutation	SNP	ENST00000381707.2	37	CCDS44452.1	.	.	.	.	.	.	.	.	.	.	g	9.139	1.013331	0.19277	.	.	ENSG00000184923	ENST00000381689;ENST00000381707;ENST00000416901	T;T	0.27402	1.67;1.67	1.29	1.29	0.21616	Nuclear Testis  protein, N-terminal (1);	.	.	.	.	T	0.25306	0.0615	M	0.72118	2.19	0.09310	N	1	P	0.40083	0.702	B	0.28638	0.092	T	0.27020	-1.0086	9	0.72032	D	0.01	.	6.1361	0.20233	0.0:0.0:1.0:0.0	.	199	Q8IVF1	FA22A_HUMAN	R	199;199;126	ENSP00000371107:G199R;ENSP00000371126:G199R	ENSP00000371107:G199R	G	+	1	0	FAM22A	88978212	0.085000	0.21516	0.005000	0.12908	0.003000	0.03518	0.617000	0.24359	1.081000	0.41110	0.374000	0.22700	GGG	G|0.996;A|0.004	0.004	strong		0.657	NUTM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049198.2	NM_001099338	
B4GALNT3	283358	hgsc.bcm.edu	37	12	658993	658993	+	Silent	SNP	C	C	T	rs73592377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:658993C>T	ENST00000266383.5	+	10	925	c.912C>T	c.(910-912)caC>caT	p.H304H		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	304					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)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			CAGCCAGCCACGTGGACTCCT	0.632													C|||	410	0.081869	0.1694	0.0663	5008	,	,		17948	0.001		0.0457	False		,,,				2504	0.0951				p.H304H		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.C912T						PASS	.	C		720,3686	296.7+/-284.4	53,614,1536	58.0	58.0	58.0		912	-1.1	0.2	12	dbSNP_130	58	346,8254	117.0+/-176.6	5,336,3959	yes	coding-synonymous	B4GALNT3	NM_173593.3		58,950,5495	TT,TC,CC		4.0233,16.3414,8.1962		304/999	658993	1066,11940	2203	4300	6503	SO:0001819	synonymous_variant	283358	exon10			CAGCCACGTGGAC	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.912C>T	12.37:g.658993C>T		Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	251	138	0.549801	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	37	CCDS8504.1																																																																																			C|0.925;T|0.075	0.075	strong		0.632	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
PHACTR2	9749	hgsc.bcm.edu	37	6	144074943	144074943	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:144074943C>T	ENST00000427704.2	+	4	445	c.315C>T	c.(313-315)atC>atT	p.I105I	PHACTR2_ENST00000367584.4_Silent_p.I173I|PHACTR2_ENST00000440869.2_Silent_p.I116I|PHACTR2_ENST00000397980.3_Silent_p.I116I|PHACTR2_ENST00000305766.6_Silent_p.I105I|PHACTR2_ENST00000367582.3_Silent_p.I116I	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	105							protein phosphatase inhibitor activity (GO:0004864)	p.I105I(1)|p.I116I(1)		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)		TGATACCCATCGGAGAGGAAT	0.408																																					p.I116I	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											PHACTR2_ENST00000440869,rectum,carcinoma,0,2	PHACTR2	99	2	2	Substitution - coding silent(2)	large_intestine(2)	c.C348T						scavenged	.						88.0	80.0	82.0					6																	144074943		1814	4082	5896	SO:0001819	synonymous_variant	9749	exon4			ACCCATCGGAGAG	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.315C>T	6.37:g.144074943C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	119	2	0.0168067	NM_001100165	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Silent	SNP	ENST00000427704.2	37	CCDS47492.1																																																																																			.	.	none		0.408	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721	
UQCRB	7381	hgsc.bcm.edu	37	8	97243720	97243720	+	Intron	SNP	G	G	A	rs2292835	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:97243720G>A	ENST00000287022.5	-	3	362				UQCRB_ENST00000523920.1_Silent_p.H94H|UQCRB_ENST00000517523.1_Intron|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	5	0	0		WXS	Illumina HiSeq	Phase_I	7	7	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	
OR8J3	81168	hgsc.bcm.edu	37	11	55905078	55905078	+	Missense_Mutation	SNP	C	C	T	rs61742348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	168	87	0.517857	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29911218	29911218	+	Missense_Mutation	SNP	G	G	A	rs1059526	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29911218G>A	ENST00000396634.1	+	5	858	c.517G>A	c.(517-519)Gcg>Acg	p.A173T	HLA-A_ENST00000376806.5_Missense_Mutation_p.A173T|HLA-A_ENST00000376802.2_Missense_Mutation_p.A173T|HLA-A_ENST00000376809.5_Missense_Mutation_p.A173T			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	173	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						CAAGTGGGAGGCGGCCCATGA	0.647									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|||	358	0.0714856	0.0991	0.0259	5008	,	,		12496	0.0913		0.0477	False		,,,				2504	0.0706				p.A173T		Atlas-SNP	.											.	HLA-A	89	.	0			c.G517A						PASS	.	G	THR/ALA	255,2763		14,227,1268	35.0	27.0	30.0		517	2.9	0.4	6	dbSNP_131	30	304,5106		8,288,2409	no	missense	HLA-A	NM_002116.7	58	22,515,3677	AA,AG,GG		5.6192,8.4493,6.6327	possibly-damaging	173/366	29911218	559,7869	1509	2705	4214	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TGGGAGGCGGCCC	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.517G>A	6.37:g.29911218G>A	ENSP00000379873:p.Ala173Thr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	162	73	0.450617	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	134	0.06135531135531135	53	0.10772357723577236	12	0.03314917127071823	37	0.06468531468531469	32	0.04221635883905013	.	4.586	0.108839	0.08780	0.084493	0.056192	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00010	9.41;9.41;9.41;9.41	3.78	2.86	0.33363	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	0.419310	0.16487	U	0.212300	T	0.00178	0.0005	M	0.87180	2.865	0.09310	N	0.999999	P;B;B;B;D;B;B	0.71674	0.944;0.0;0.004;0.002;0.998;0.0;0.0	D;B;B;B;D;B;B	0.81914	0.918;0.008;0.021;0.008;0.995;0.008;0.008	T	0.04870	-1.0921	10	0.48119	T	0.1	.	10.8567	0.46802	0.0:0.1941:0.8059:0.0	rs1059526;rs3173413;rs41555014	52;173;173;173;173;173;173	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	T	173	ENSP00000379873:A173T;ENSP00000366002:A173T;ENSP00000366005:A173T;ENSP00000365998:A173T	ENSP00000365998:A173T	A	+	1	0	HLA-A	30019197	0.000000	0.05858	0.418000	0.26571	0.074000	0.17049	-0.407000	0.07178	0.858000	0.35431	0.485000	0.47835	GCG	A|0.067;G|0.933	0.067	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
XRCC3	7517	hgsc.bcm.edu	37	14	104174950	104174950	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104174950G>T	ENST00000553264.1	-	3	898	c.102C>A	c.(100-102)gaC>gaA	p.D34E	XRCC3_ENST00000554913.1_Missense_Mutation_p.D34E|XRCC3_ENST00000445556.1_Missense_Mutation_p.D34E|XRCC3_ENST00000555055.1_Missense_Mutation_p.D34E|XRCC3_ENST00000554974.1_Intron|AL049840.1_ENST00000429169.1_5'Flank|XRCC3_ENST00000352127.7_Missense_Mutation_p.D34E			O43542	XRCC3_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 3	34					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|response to organic substance (GO:0010033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Rad51C-XRCC3 complex (GO:0033065)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)	4		Melanoma(154;0.155)|all_epithelial(191;0.19)		Epithelial(152;0.239)		GTCTCTTCAAGTCTGGTCCAG	0.498								Direct reversal of damage;Homologous recombination																													p.D34E		Atlas-SNP	.											.	XRCC3	16	.	0			c.C102A						PASS	.						119.0	104.0	109.0					14																	104174950		2203	4300	6503	SO:0001583	missense	7517	exon5			CTTCAAGTCTGGT	AF035586	CCDS9984.1	14q32.3	2006-05-04				ENSG00000126215			12830	protein-coding gene	gene with protein product	"""RAD51-like"""	600675				7603995	Standard	NM_001100118		Approved		uc001ynz.4	O43542		ENST00000553264.1:c.102C>A	14.37:g.104174950G>T	ENSP00000451974:p.Asp34Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	144	46	0.319444	NM_005432	O43568|Q9BU18	Missense_Mutation	SNP	ENST00000553264.1	37	CCDS9984.1	.	.	.	.	.	.	.	.	.	.	G	7.232	0.599455	0.13939	.	.	ENSG00000126215	ENST00000554913;ENST00000352127;ENST00000553264;ENST00000555055;ENST00000445556;ENST00000553361;ENST00000556980;ENST00000555964;ENST00000556682;ENST00000553332;ENST00000554170	T;T;T;T;T;T;T;T	0.60299	1.06;1.06;1.06;1.06;1.06;0.2;0.68;0.59	5.44	-0.127	0.13510	.	0.095213	0.64402	D	0.000001	T	0.35038	0.0918	L	0.45228	1.405	0.23754	N	0.996937	P	0.39535	0.677	B	0.31686	0.134	T	0.36335	-0.9752	10	0.10377	T	0.69	-0.0139	6.7499	0.23482	0.4232:0.0:0.4621:0.1147	.	34	O43542	XRCC3_HUMAN	E	34	ENSP00000451362:D34E;ENSP00000343392:D34E;ENSP00000451974:D34E;ENSP00000452598:D34E;ENSP00000412990:D34E;ENSP00000451118:D34E;ENSP00000451252:D34E;ENSP00000451173:D34E	ENSP00000343392:D34E	D	-	3	2	XRCC3	103244703	0.756000	0.28383	0.283000	0.24790	0.039000	0.13416	0.177000	0.16801	0.039000	0.15632	-0.918000	0.02743	GAC	.	.	none		0.498	XRCC3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414631.1	NM_005432	
B4GALT7	11285	hgsc.bcm.edu	37	5	177035964	177035964	+	Silent	SNP	T	T	C	rs729459	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:177035964T>C	ENST00000029410.5	+	5	888	c.777T>C	c.(775-777)caT>caC	p.H259H	RP11-1277A3.1_ENST00000499900.2_RNA	NM_007255.2	NP_009186.1	Q9UBV7	B4GT7_HUMAN	xylosylprotein beta 1,4-galactosyltransferase, polypeptide 7	259	UDP-alpha-D-galactose binding.				carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|chondroitin sulfate metabolic process (GO:0030204)|extracellular fibril organization (GO:0043206)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of fibroblast proliferation (GO:0048147)|protein N-linked glycosylation (GO:0006487)|proteoglycan metabolic process (GO:0006029)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|manganese ion binding (GO:0030145)|xylosylprotein 4-beta-galactosyltransferase activity (GO:0046525)			endometrium(2)|large_intestine(1)|lung(1)|pancreas(1)|skin(1)|urinary_tract(1)	7	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)			GCCACCTGCATGACCCAGCCT	0.602													t|||	3030	0.605032	0.5893	0.6153	5008	,	,		19107	0.7937		0.5417	False		,,,				2504	0.4898				p.H259H		Atlas-SNP	.											.	B4GALT7	21	.	0			c.T777C						PASS	.	C		2712,1694	651.5+/-399.2	830,1052,321	69.0	66.0	67.0		777	-5.6	0.9	5	dbSNP_86	67	4764,3836	610.1+/-395.6	1323,2118,859	no	coding-synonymous	B4GALT7	NM_007255.2		2153,3170,1180	CC,CT,TT		44.6047,38.4476,42.5188		259/328	177035964	7476,5530	2203	4300	6503	SO:0001819	synonymous_variant	11285	exon5			CCTGCATGACCCA	AB028600	CCDS4429.1	5q35.1-q35.3	2013-02-19	2012-07-18		ENSG00000027847	ENSG00000027847		"""Beta 4-glycosyltransferases"""	930	protein-coding gene	gene with protein product	"""galactosyltransferase I"""	604327				10438455, 10473568	Standard	NM_007255		Approved	XGALT-1, beta4Gal-T7	uc003mhy.3	Q9UBV7	OTTHUMG00000130851	ENST00000029410.5:c.777T>C	5.37:g.177035964T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_007255	B3KN39|Q9UHN2	Silent	SNP	ENST00000029410.5	37	CCDS4429.1																																																																																			T|0.401;C|0.599	0.599	strong		0.602	B4GALT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253421.1	NM_007255	
SPAG17	200162	hgsc.bcm.edu	37	1	118657952	118657952	+	Missense_Mutation	SNP	C	C	T	rs12133381	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:118657952C>T	ENST00000336338.5	-	4	493	c.428G>A	c.(427-429)cGa>cAa	p.R143Q		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	143	Lys-rich.		R -> Q (in dbSNP:rs12133381).			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)		ATTTTCCCGTCGCTGTTGGTC	0.423													C|||	531	0.10603	0.0038	0.0346	5008	,	,		15848	0.2728		0.0586	False		,,,				2504	0.1718				p.R143Q		Atlas-SNP	.											.	SPAG17	263	.	0			c.G428A						PASS	.	C	GLN/ARG	67,4337	61.1+/-98.1	0,67,2135	127.0	130.0	129.0		428	5.0	1.0	1	dbSNP_120	129	469,8131	139.7+/-196.3	15,439,3846	yes	missense	SPAG17	NM_206996.2	43	15,506,5981	TT,TC,CC		5.4535,1.5213,4.1218	probably-damaging	143/2224	118657952	536,12468	2202	4300	6502	SO:0001583	missense	200162	exon4			TCCCGTCGCTGTT		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.428G>A	1.37:g.118657952C>T	ENSP00000337804:p.Arg143Gln	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	112	85	0.758929	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	195	0.08928571428571429	3	0.006097560975609756	14	0.03867403314917127	134	0.23426573426573427	44	0.05804749340369393	C	12.20	1.867742	0.32977	0.015213	0.054535	ENSG00000155761	ENST00000336338	T	0.68331	-0.32	5.92	5.02	0.67125	.	0.164379	0.52532	D	0.000079	T	0.51449	0.1675	M	0.78049	2.395	0.43088	P	0.005241000000000051	P	0.39624	0.681	B	0.29440	0.102	T	0.65553	-0.6140	9	0.87932	D	0	.	14.1699	0.65503	0.0:0.9286:0.0:0.0714	rs12133381;rs52830739;rs12133381	143	Q6Q759	SPG17_HUMAN	Q	143	ENSP00000337804:R143Q	ENSP00000337804:R143Q	R	-	2	0	SPAG17	118459475	1.000000	0.71417	0.975000	0.42487	0.087000	0.18053	2.496000	0.45346	1.522000	0.49001	-0.136000	0.14681	CGA	C|0.932;T|0.068	0.068	strong		0.423	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
KIF13A	63971	hgsc.bcm.edu	37	6	17764530	17764530	+	Silent	SNP	C	C	T	rs9371018	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:17764530C>T	ENST00000259711.6	-	39	5334	c.5229G>A	c.(5227-5229)gaG>gaA	p.E1743E	KIF13A_ENST00000378816.5_Silent_p.E1708E|KIF13A_ENST00000378814.5_Silent_p.E1695E|KIF13A_ENST00000378826.2_Silent_p.E1708E|KIF13A_ENST00000378843.2_Silent_p.E1695E	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	169	0	0		WXS	Illumina HiSeq	Phase_I	165	67	0.406061	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		
PATL1	219988	hgsc.bcm.edu	37	11	59410479	59410479	+	Silent	SNP	A	A	T	rs77793148	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:59410479A>T	ENST00000300146.9	-	16	2007	c.1923T>A	c.(1921-1923)tcT>tcA	p.S641S		NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)	641	Involved in nuclear spleckles localization.|Region C.				cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|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)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						AGAGAAGGAGAGAGAAGGGAC	0.473													A|||	33	0.00658946	0.0008	0.0029	5008	,	,		20188	0.0		0.0239	False		,,,				2504	0.0061				p.S641S		Atlas-SNP	.											.	PATL1	92	.	0			c.T1923A						PASS	.	A		17,3945		0,17,1964	118.0	112.0	114.0		1923	-0.6	1.0	11	dbSNP_132	114	187,8113		2,183,3965	no	coding-synonymous	PATL1	NM_152716.2		2,200,5929	TT,TA,AA		2.253,0.4291,1.6637		641/771	59410479	204,12058	1981	4150	6131	SO:0001819	synonymous_variant	219988	exon16			AAGGAGAGAGAAG	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1923T>A	11.37:g.59410479A>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Silent	SNP	ENST00000300146.9	37	CCDS44613.1																																																																																			A|0.995;G|0.000;T|0.005	0.005	strong		0.473	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716	
HIST1H1A	3024	hgsc.bcm.edu	37	6	26017397	26017397	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26017397C>G	ENST00000244573.3	-	1	643	c.564G>C	c.(562-564)aaG>aaC	p.K188N		NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	188					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						GTTTTACAGCCTTAGCTTTAG	0.453																																					p.K188N		Atlas-SNP	.											.	HIST1H1A	25	.	0			c.G564C						PASS	.						151.0	159.0	156.0					6																	26017397		2203	4300	6503	SO:0001583	missense	3024	exon1			TACAGCCTTAGCT	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.564G>C	6.37:g.26017397C>G	ENSP00000244573:p.Lys188Asn	Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	251	125	0.498008	NM_005325	Q3MJ34	Missense_Mutation	SNP	ENST00000244573.3	37	CCDS4569.1	.	.	.	.	.	.	.	.	.	.	N	10.43	1.346702	0.24426	.	.	ENSG00000124610	ENST00000244573	T	0.20463	2.07	4.31	4.31	0.51392	.	0.070517	0.56097	D	0.000038	T	0.09949	0.0244	L	0.45352	1.415	0.51482	D	0.99992	P	0.37636	0.603	B	0.28385	0.089	T	0.08269	-1.0730	10	0.56958	D	0.05	-13.3791	16.683	0.85297	0.0:1.0:0.0:0.0	.	188	Q02539	H11_HUMAN	N	188	ENSP00000244573:K188N	ENSP00000244573:K188N	K	-	3	2	HIST1H1A	26125376	0.881000	0.30235	0.884000	0.34674	0.057000	0.15508	0.342000	0.19926	2.320000	0.78422	0.609000	0.83330	AAG	.	.	none		0.453	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1	NM_005325	
AIPL1	23746	hgsc.bcm.edu	37	17	6331817	6331817	+	Missense_Mutation	SNP	C	C	T	rs62619924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:6331817C>T	ENST00000381129.3	-	3	366	c.286G>A	c.(286-288)Gtc>Atc	p.V96I	AIPL1_ENST00000571740.1_Missense_Mutation_p.V96I|AIPL1_ENST00000574506.1_Missense_Mutation_p.V84I|AIPL1_ENST00000250087.5_Intron|AIPL1_ENST00000576307.1_Missense_Mutation_p.V36I|AIPL1_ENST00000570466.1_Missense_Mutation_p.V74I|AIPL1_ENST00000575265.1_Missense_Mutation_p.V96I|AIPL1_ENST00000576776.1_Missense_Mutation_p.V96I	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	96	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)		ATGGGGTAGACCCCCGTGTGC	0.632													C|||	22	0.00439297	0.0023	0.0	5008	,	,		18850	0.0		0.0189	False		,,,				2504	0.0				p.V96I		Atlas-SNP	.											.	AIPL1	34	.	0			c.G286A	GRCh37	CM003227	AIPL1	M	rs62619924	PASS	.	C	,ILE/VAL,ILE/VAL	30,4376	36.0+/-67.5	0,30,2173	69.0	57.0	61.0		,106,286	3.8	1.0	17	dbSNP_129	61	187,8413	81.8+/-144.4	1,185,4114	yes	intron,missense,missense	AIPL1	NM_001033054.1,NM_001033055.1,NM_014336.3	,29,29	1,215,6287	TT,TC,CC		2.1744,0.6809,1.6685	,benign,benign	,36/325,96/385	6331817	217,12789	2203	4300	6503	SO:0001583	missense	23746	exon3			GGTAGACCCCCGT	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.286G>A	17.37:g.6331817C>T	ENSP00000370521:p.Val96Ile	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Missense_Mutation	SNP	ENST00000381129.3	37	CCDS11075.1	18	0.008241758241758242	1	0.0020325203252032522	0	0.0	0	0.0	17	0.022427440633245383	C	11.59	1.685305	0.29872	0.006809	0.021744	ENSG00000129221	ENST00000381129;ENST00000381128;ENST00000444243	D	0.88201	-2.35	4.77	3.78	0.43462	.	0.397731	0.27526	N	0.018964	T	0.68229	0.2978	L	0.33485	1.01	0.32392	N	0.553123	B;B;B;B;B	0.25441	0.046;0.029;0.011;0.126;0.016	B;B;B;B;B	0.22386	0.038;0.009;0.022;0.039;0.034	T	0.74325	-0.3702	10	0.35671	T	0.21	-40.7753	6.5941	0.22664	0.1814:0.7207:0.0:0.0979	rs62619924	96;74;96;36;96	Q659W3;Q659W4;F1T0C4;Q9NZN9-2;Q9NZN9	.;.;.;.;AIPL1_HUMAN	I	96;36;96	ENSP00000370521:V96I	ENSP00000370520:V36I	V	-	1	0	AIPL1	6272541	0.050000	0.20438	0.995000	0.50966	0.825000	0.46686	0.274000	0.18680	2.353000	0.79882	0.462000	0.41574	GTC	C|0.985;T|0.015	0.015	strong		0.632	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336	
CDK12	51755	hgsc.bcm.edu	37	17	37627387	37627387	+	Silent	SNP	A	A	G	rs56158954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:37627387A>G	ENST00000447079.4	+	2	1335	c.1302A>G	c.(1300-1302)tcA>tcG	p.S434S	CDK12_ENST00000430627.2_Silent_p.S434S	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	434					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						AGAACAGTTCAGTAGAGGCTA	0.428			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)			A|||	28	0.00559105	0.0	0.0115	5008	,	,		17944	0.0		0.0179	False		,,,				2504	0.002				p.S434S		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	CDK12,NS,carcinoma,0,1	CDK12	161	1	0			c.A1302G						PASS	.	A	,	21,4385	28.1+/-56.4	0,21,2182	68.0	69.0	69.0		1302,1302	2.7	1.0	17	dbSNP_129	69	170,8430	77.8+/-140.4	1,168,4131	no	coding-synonymous,coding-synonymous	CDK12	NM_015083.1,NM_016507.2	,	1,189,6313	GG,GA,AA		1.9767,0.4766,1.4686	,	434/1482,434/1491	37627387	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	51755	exon2			CAGTTCAGTAGAG	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.1302A>G	17.37:g.37627387A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																			A|0.987;G|0.013	0.013	strong		0.428	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
RNF213	57674	hgsc.bcm.edu	37	17	78263514	78263514	+	Silent	SNP	G	G	A	rs17853713	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78263514G>A	ENST00000582970.1	+	6	1133	c.990G>A	c.(988-990)aaG>aaA	p.K330K	RNF213_ENST00000319921.4_Silent_p.K330K|RNF213_ENST00000456466.1_Silent_p.K330K|RNF213_ENST00000508628.2_Silent_p.K379K	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	330					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K379K(1)|p.K330K(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AAGTCGGTAAGAATGAACAAG	0.517													A|||	1103	0.220248	0.4508	0.1254	5008	,	,		16476	0.0665		0.165	False		,,,				2504	0.1912				p.K330K		Atlas-SNP	.											RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	2	Substitution - coding silent(2)	stomach(2)	c.G990A						PASS	.	A	,	1740,2666	647.5+/-398.6	351,1038,814	67.0	71.0	70.0		1137,990	-1.2	0.0	17	dbSNP_123	70	1622,6978	742.2+/-407.2	152,1318,2830	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	503,2356,3644	AA,AG,GG		18.8605,39.4916,25.8496	,	379/5257,330/1064	78263514	3362,9644	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon6			CGGTAAGAATGAA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.990G>A	17.37:g.78263514G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			G|0.760;A|0.240	0.240	strong		0.517	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
SAMD15	161394	hgsc.bcm.edu	37	14	77844265	77844265	+	Missense_Mutation	SNP	G	G	A	rs45527334	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77844265G>A	ENST00000216471.4	+	1	790	c.504G>A	c.(502-504)atG>atA	p.M168I	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	168			M -> I (in dbSNP:rs45527334).							breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CGGAAACCATGTCTGAGGTTT	0.488													G|||	709	0.141573	0.059	0.2651	5008	,	,		18678	0.0159		0.2038	False		,,,				2504	0.2311				p.M168I		Atlas-SNP	.											.	SAMD15	60	.	0			c.G504A						PASS	.	G	ILE/MET	404,4002	194.0+/-219.0	16,372,1815	86.0	94.0	92.0		504	-1.5	0.0	14	dbSNP_127	92	1681,6919	298.1+/-303.7	182,1317,2801	yes	missense	SAMD15	NM_001010860.1	10	198,1689,4616	AA,AG,GG		19.5465,9.1693,16.0311	possibly-damaging	168/675	77844265	2085,10921	2203	4300	6503	SO:0001583	missense	161394	exon1			AACCATGTCTGAG	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.504G>A	14.37:g.77844265G>A	ENSP00000216471:p.Met168Ile	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_001010860	Q2M3P3	Missense_Mutation	SNP	ENST00000216471.4	37	CCDS32126.1	289	0.13232600732600733	31	0.06300813008130081	104	0.287292817679558	8	0.013986013986013986	146	0.19261213720316622	G	11.61	1.688514	0.29962	0.091693	0.195465	ENSG00000100583	ENST00000216471	T	0.18657	2.2	4.45	-1.46	0.08800	.	.	.	.	.	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	0.44667	-0.9313	8	0.42905	T	0.14	5.3758	4.6975	0.12811	0.5573:0.1817:0.261:0.0	rs45527334;rs57688204;rs61729328	168	Q9P1V8	SAM15_HUMAN	I	168	ENSP00000216471:M168I	ENSP00000216471:M168I	M	+	3	0	SAMD15	76914018	0.000000	0.05858	0.000000	0.03702	0.359000	0.29487	-0.322000	0.08007	0.034000	0.15491	0.484000	0.47621	ATG	G|0.848;A|0.152	0.152	strong		0.488	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
LSG1	55341	hgsc.bcm.edu	37	3	194387300	194387300	+	Splice_Site	SNP	C	C	T	rs1675943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:194387300C>T	ENST00000265245.5	-	3	542	c.228G>A	c.(226-228)gaG>gaA	p.E76E	AC046143.1_ENST00000408791.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	76					GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		TATTAAGTTTCTCTGTTCAAA	0.358													C|||	2129	0.42512	0.2587	0.4481	5008	,	,		17143	0.4405		0.5348	False		,,,				2504	0.5051				p.E76E		Atlas-SNP	.											.	LSG1	38	.	0			c.G228A						PASS	.	C		1332,3074	415.2+/-337.1	212,908,1083	54.0	55.0	54.0		228	3.5	1.0	3	dbSNP_89	54	4540,4060	571.5+/-389.6	1223,2094,983	yes	coding-synonymous-near-splice	LSG1	NM_018385.2		1435,3002,2066	TT,TC,CC		47.2093,30.2315,45.1484		76/659	194387300	5872,7134	2203	4300	6503	SO:0001630	splice_region_variant	55341	exon3			AAGTTTCTCTGTT		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"""large subunit GTPase 1 homolog (S. cerevisiae)"""			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.227-1G>A	3.37:g.194387300C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	37	CCDS33922.1																																																																																			C|0.573;T|0.427	0.427	strong		0.358	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	Silent
DNHD1	144132	hgsc.bcm.edu	37	11	6580495	6580495	+	Silent	SNP	G	G	A	rs72901756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6580495G>A	ENST00000527990.2	+	26	9501	c.9501G>A	c.(9499-9501)caG>caA	p.Q3167Q	DNHD1_ENST00000254579.6_Silent_p.Q3167Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3167					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)		TGGAACAGCAGCTGAAAGACT	0.483													G|||	364	0.0726837	0.0204	0.1037	5008	,	,		21689	0.0159		0.0736	False		,,,				2504	0.1789				p.Q3167Q		Atlas-SNP	.											.	DNHD1	198	.	0			c.G9501A						PASS	.	G		45,1339		1,43,648	106.0	90.0	95.0		9501	2.5	0.9	11	dbSNP_130	95	339,2843		20,299,1272	no	coding-synonymous	DNHD1	NM_144666.2		21,342,1920	AA,AG,GG		10.6537,3.2514,8.41		3167/4754	6580495	384,4182	692	1591	2283	SO:0001819	synonymous_variant	144132	exon28			ACAGCAGCTGAAA	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.9501G>A	11.37:g.6580495G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	130	64	0.492308	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.957;A|0.043	0.043	strong		0.483	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
TOP3B	8940	hgsc.bcm.edu	37	22	22318671	22318671	+	Silent	SNP	G	G	A	rs9610729	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:22318671G>A	ENST00000398793.2	-	10	1394	c.960C>T	c.(958-960)caC>caT	p.H320H	TOP3B_ENST00000413067.2_Silent_p.H49H|TOP3B_ENST00000357179.5_Silent_p.H320H	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	320					chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		TCTGCATGGCGTGCTGCGGCC	0.637													G|||	420	0.0838658	0.087	0.1037	5008	,	,		19731	0.0655		0.1183	False		,,,				2504	0.0491				p.H320H		Atlas-SNP	.											.	TOP3B	107	.	0			c.C960T						PASS	.	G		332,4074	175.1+/-204.6	14,304,1885	124.0	96.0	105.0		960	-0.2	1.0	22	dbSNP_119	105	1057,7543	223.3+/-260.1	74,909,3317	no	coding-synonymous	TOP3B	NM_003935.3		88,1213,5202	AA,AG,GG		12.2907,7.5352,10.6797		320/863	22318671	1389,11617	2203	4300	6503	SO:0001819	synonymous_variant	8940	exon10			CATGGCGTGCTGC	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.960C>T	22.37:g.22318671G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_003935	A0M8Q3|Q9BUP5	Silent	SNP	ENST00000398793.2	37	CCDS13797.1	209	0.09569597069597069	46	0.09349593495934959	34	0.09392265193370165	34	0.05944055944055944	95	0.12532981530343007	G	9.153	1.016764	0.19355	0.075352	0.122907	ENSG00000100038	ENST00000457270	.	.	.	5.05	-0.173	0.13322	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17745	-1.0359	3	.	.	.	.	9.575	0.39452	0.6689:0.0:0.3311:0.0	rs9610729;rs17849582;rs9610729	.	.	.	M	115	.	.	T	-	2	0	TOP3B	20648671	0.648000	0.27313	0.998000	0.56505	0.905000	0.53344	-0.179000	0.09768	-0.107000	0.12088	-0.367000	0.07326	ACG	G|0.896;A|0.104	0.104	strong		0.637	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
CD101	9398	hgsc.bcm.edu	37	1	117568217	117568217	+	Missense_Mutation	SNP	G	G	A	rs17229382	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:117568217G>A	ENST00000256652.4	+	8	2573	c.2515G>A	c.(2515-2517)Gta>Ata	p.V839I	CD101_ENST00000369470.1_Missense_Mutation_p.V839I|RP11-27K13.3_ENST00000445523.1_RNA|RP11-27K13.3_ENST00000421254.1_RNA	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	839	Ig-like C2-type 7.				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						CCTGGAGAGTGTAGGCAGCTC	0.478													G|||	39	0.00778754	0.0015	0.0346	5008	,	,		17548	0.001		0.0119	False		,,,				2504	0.0				p.V839I		Atlas-SNP	.											.	CD101	95	.	0			c.G2515A						PASS	.	G	ILE/VAL	18,4388	26.2+/-53.5	0,18,2185	82.0	81.0	81.0		2515	-9.1	0.0	1	dbSNP_123	81	157,8443	75.1+/-137.7	3,151,4146	yes	missense	CD101	NM_004258.3	29	3,169,6331	AA,AG,GG		1.8256,0.4085,1.3455	benign	839/1022	117568217	175,12831	2203	4300	6503	SO:0001583	missense	9398	exon8			GAGAGTGTAGGCA	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.2515G>A	1.37:g.117568217G>A	ENSP00000256652:p.Val839Ile	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	32	25	0.78125	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	30	0.013736263736263736	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	12	0.0158311345646438	G	2.813	-0.246589	0.05867	0.004085	0.018256	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.21543	2.0;2.0	5.17	-9.11	0.00711	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.471490	0.04169	N	0.324475	T	0.03915	0.0110	N	0.22421	0.69	0.09310	N	1	B	0.20164	0.042	B	0.22152	0.038	T	0.23762	-1.0179	10	0.33141	T	0.24	1.885	9.9611	0.41697	0.0:0.4097:0.432:0.1584	rs17229382;rs17229382	839	Q93033	IGSF2_HUMAN	I	839	ENSP00000256652:V839I;ENSP00000358482:V839I	ENSP00000256652:V839I	V	+	1	0	CD101	117369740	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.812000	0.01726	-1.695000	0.01423	-0.867000	0.03001	GTA	G|0.987;A|0.013	0.013	strong		0.478	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189591	11189591	+	Missense_Mutation	SNP	C	C	T	rs62488717		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:11189591C>T	ENST00000382435.4	+	1	1195	c.976C>T	c.(976-978)Cgg>Tgg	p.R326W		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	326						integral component of membrane (GO:0016021)											CATTACAGCCCGGAACCTCAG	0.532																																					p.R326W		Atlas-SNP	.											AMAC1L2,NS,carcinoma,-1,1	.	.	1	0			c.C976T						scavenged	.						69.0	69.0	69.0					8																	11189591		2203	4300	6503	SO:0001583	missense	83650	exon1			ACAGCCCGGAACC	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.976C>T	8.37:g.11189591C>T	ENSP00000371872:p.Arg326Trp	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	201	39	0.19403	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	c	5.532	0.283160	0.10458	.	.	ENSG00000177710	ENST00000382435	T	0.70516	-0.49	.	.	.	.	0.165937	0.28236	N	0.016094	T	0.43389	0.1245	N	0.08118	0	0.24617	N	0.993699	B	0.02656	0.0	B	0.01281	0.0	T	0.23726	-1.0180	8	0.39692	T	0.17	0.2542	.	.	.	rs62488717	326	Q96KT7	S35G5_HUMAN	W	326	ENSP00000371872:R326W	ENSP00000371872:R326W	R	+	1	2	SLC35G5	11227001	0.026000	0.19158	0.289000	0.24876	0.290000	0.27261	1.262000	0.32992	0.064000	0.16427	0.064000	0.15345	CGG	.	.	weak		0.532	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
CHAD	1101	hgsc.bcm.edu	37	17	48545596	48545596	+	Silent	SNP	G	G	A	rs34864120	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48545596G>A	ENST00000508540.1	-	1	731	c.579C>T	c.(577-579)gaC>gaT	p.D193D	ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000300441.4_Intron|CHAD_ENST00000258969.4_Silent_p.D193D|ACSF2_ENST00000427954.2_Intron|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000502667.1_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	193					bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGTTCTCCACGTCGTCCAGGG	0.647													G|||	945	0.188698	0.0946	0.2536	5008	,	,		19319	0.1419		0.2992	False		,,,				2504	0.2045				p.D193D		Atlas-SNP	.											.	CHAD	36	.	0			c.C579T						PASS	.	G	,	606,3800	264.7+/-266.2	39,528,1636	80.0	87.0	85.0		579,	-8.9	0.4	17	dbSNP_126	85	2611,5989	423.0+/-354.2	397,1817,2086	no	coding-synonymous,intron	CHAD,ACSF2	NM_001267.2,NM_025149.4	,	436,2345,3722	AA,AG,GG		30.3605,13.754,24.7347	,	193/360,	48545596	3217,9789	2203	4300	6503	SO:0001819	synonymous_variant	1101	exon1			CTCCACGTCGTCC	U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1909	protein-coding gene	gene with protein product	"""chondroadherin proteoglycan"""	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.579C>T	17.37:g.48545596G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	158	79	0.5	NM_001267	A8K812|Q6GTU0|Q96RJ5	Silent	SNP	ENST00000508540.1	37	CCDS11568.1																																																																																			G|0.767;A|0.233	0.233	strong		0.647	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267	
ZNF705A	440077	hgsc.bcm.edu	37	12	8329833	8329833	+	Missense_Mutation	SNP	G	G	A	rs11043758	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:8329833G>A	ENST00000359286.4	+	5	646	c.557G>A	c.(556-558)cGc>cAc	p.R186H	FAM66C_ENST00000454799.2_RNA|FAM66C_ENST00000456135.2_RNA|FAM66C_ENST00000544214.1_RNA	NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	186			R -> H (in dbSNP:rs11043758).		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.R186H(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		AATTGCTTTCGCCTTAGACGG	0.393																																					p.R186H		Atlas-SNP	.											ZNF705A,NS,carcinoma,0,1	ZNF705A	32	1	1	Substitution - Missense(1)	stomach(1)	c.G557A						scavenged	.						85.0	86.0	86.0					12																	8329833		2198	4290	6488	SO:0001583	missense	440077	exon5			GCTTTCGCCTTAG	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.557G>A	12.37:g.8329833G>A	ENSP00000352233:p.Arg186His	Somatic	316	2	0.00632911		WXS	Illumina HiSeq	Phase_I	232	100	0.431034	NM_001004328		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	992	0.4542124542124542	174	0.35365853658536583	165	0.4558011049723757	275	0.4807692307692308	378	0.49868073878627966	.	0.017	-1.494887	0.01009	.	.	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.03920	3.76;3.76	1.35	-2.7	0.06004	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.01624	-0.795	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34976	-0.9807	7	.	.	.	.	2.8848	0.05658	0.3359:0.0:0.3342:0.3299	rs11043758	186	Q6ZN79	Z705A_HUMAN	H	186	ENSP00000379816:R186H;ENSP00000352233:R186H	.	R	+	2	0	ZNF705A	8221100	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.401000	0.01048	-2.388000	0.00588	-0.724000	0.03597	CGC	G|0.506;A|0.494	0.494	strong		0.393	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
CRYBB3	1417	hgsc.bcm.edu	37	22	25603052	25603052	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:25603052A>G	ENST00000215855.2	+	6	589	c.509A>G	c.(508-510)cAg>cGg	p.Q170R	CRYBB3_ENST00000404334.1_3'UTR	NM_004076.3	NP_004067.1	P26998	CRBB3_HUMAN	crystallin, beta B3	170	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(2)|lung(2)|prostate(1)	5						CGTGGGCGCCAGTACGTGTTT	0.647																																					p.V170G		Atlas-SNP	.											.	CRYBB3	13	.	0			c.T509G						PASS	.						57.0	52.0	54.0					22																	25603052		2201	4300	6501	SO:0001583	missense	1417	exon6			GGCGCCAGTACGT		CCDS13830.1	22q11.23	2008-06-10			ENSG00000100053	ENSG00000100053			2400	protein-coding gene	gene with protein product		123630		CRYB3		8999933	Standard	NM_004076		Approved		uc003abo.2	P26998	OTTHUMG00000150869	ENST00000215855.2:c.509A>G	22.37:g.25603052A>G	ENSP00000215855:p.Gln170Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	127	51	0.401575	NM_004076	Q3B7S9|Q3T1B7|Q6ISK6|Q92965|Q9UH09	Missense_Mutation	SNP	ENST00000215855.2	37	CCDS13830.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816949	0.90790	.	.	ENSG00000100053	ENST00000215855	T	0.80123	-1.34	4.87	4.87	0.63330	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.92001	0.7466	H	0.94222	3.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93900	0.7187	10	0.87932	D	0	.	13.2896	0.60264	1.0:0.0:0.0:0.0	.	170	P26998	CRBB3_HUMAN	R	170	ENSP00000215855:Q170R	ENSP00000215855:Q170R	Q	+	2	0	CRYBB3	23933052	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.664000	0.91139	1.804000	0.52760	0.459000	0.35465	CAG	.	.	none		0.647	CRYBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320352.1	NM_004076	
CCDC129	223075	hgsc.bcm.edu	37	7	31682829	31682829	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:31682829G>C	ENST00000407970.3	+	11	1883	c.1845G>C	c.(1843-1845)gaG>gaC	p.E615D	CCDC129_ENST00000409210.1_Missense_Mutation_p.E523D|CCDC129_ENST00000451887.2_Missense_Mutation_p.E641D|CCDC129_ENST00000319386.3_Missense_Mutation_p.E467D	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	615										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TTGACTCTGAGGCCCCACGAG	0.498																																					p.E641D		Atlas-SNP	.											.	CCDC129	127	.	0			c.G1923C						PASS	.						119.0	112.0	114.0					7																	31682829		2203	4300	6503	SO:0001583	missense	223075	exon11			CTCTGAGGCCCCA	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.1845G>C	7.37:g.31682829G>C	ENSP00000384416:p.Glu615Asp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	91	26	0.285714	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	12.14	1.847181	0.32606	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.19394	2.15;2.42;2.41;2.16	6.02	1.06	0.20224	.	0.998383	0.08108	N	0.996656	T	0.18509	0.0444	L	0.55103	1.725	0.09310	N	1	B;B;B;B	0.24186	0.025;0.099;0.099;0.099	B;B;B;B	0.26202	0.022;0.067;0.067;0.067	T	0.38373	-0.9664	10	0.22706	T	0.39	-6.6287	3.9948	0.09553	0.2297:0.0:0.4889:0.2814	.	641;625;615;467	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	D	467;615;641;625;523	ENSP00000313062:E467D;ENSP00000384416:E615D;ENSP00000395835:E641D;ENSP00000387214:E523D	ENSP00000313062:E467D	E	+	3	2	CCDC129	31649354	0.017000	0.18338	0.000000	0.03702	0.307000	0.27823	0.200000	0.17257	-0.075000	0.12798	0.655000	0.94253	GAG	.	.	none		0.498	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
HS6ST1	9394	hgsc.bcm.edu	37	2	129025800	129025800	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:129025800T>C	ENST00000259241.6	-	2	1185	c.1172A>G	c.(1171-1173)gAt>gGt	p.D391G		NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	391					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)		CTCGTCGGCATCCTCCCGCGG	0.692																																					p.D391G		Atlas-SNP	.											.	HS6ST1	31	.	0			c.A1172G						PASS	.						21.0	23.0	22.0					2																	129025800		2013	4161	6174	SO:0001583	missense	9394	exon2			TCGGCATCCTCCC	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.1172A>G	2.37:g.129025800T>C	ENSP00000259241:p.Asp391Gly	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	96	5	0.0520833	NM_004807	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Missense_Mutation	SNP	ENST00000259241.6	37	CCDS42748.1	.	.	.	.	.	.	.	.	.	.	T	6.511	0.462424	0.12342	.	.	ENSG00000136720	ENST00000259241	D	0.82893	-1.66	4.19	2.98	0.34508	.	0.419922	0.27622	N	0.018544	T	0.70710	0.3255	L	0.29908	0.895	0.32984	D	0.524007	B	0.02656	0.0	B	0.01281	0.0	T	0.65726	-0.6098	9	.	.	.	-2.5669	9.8137	0.40840	0.0:0.0842:0.0:0.9158	.	391	O60243	H6ST1_HUMAN	G	391	ENSP00000259241:D391G	.	D	-	2	0	HS6ST1	128742270	0.994000	0.37717	0.051000	0.19133	0.159000	0.22180	2.428000	0.44749	0.558000	0.29135	0.260000	0.18958	GAT	.	.	none		0.692	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331572.1	NM_004807	
HLA-A	3105	hgsc.bcm.edu	37	6	29912087	29912087	+	Missense_Mutation	SNP	G	G	T	rs1059632	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29912087G>T	ENST00000396634.1	+	6	1149	c.808G>T	c.(808-810)Gct>Tct	p.A270S	HLA-A_ENST00000376806.5_Missense_Mutation_p.A270S|HLA-A_ENST00000376802.2_Missense_Mutation_p.A270S|HLA-A_ENST00000376809.5_Missense_Mutation_p.A270S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	270	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						GAAGTGGGCGGCTGTGGTGGT	0.627									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.A270S		Atlas-SNP	.											.	HLA-A	89	.	0			c.G808T						PASS	.						31.0	31.0	31.0					6																	29912087		1510	2705	4215	SO:0001583	missense	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TGGGCGGCTGTGG	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.808G>T	6.37:g.29912087G>T	ENSP00000379873:p.Ala270Ser	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	198	50	0.252525	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.494	0.862723	0.17178	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809;ENST00000376802	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	3.69	2.8	0.32819	Immunoglobulin-like (4);Immunoglobulin C1-set (8);Immunoglobulin-like fold (4);	0.636476	0.12630	U	0.452285	T	0.17280	0.0415	L	0.55481	1.735	0.58432	P	1.999999999946489E-6	P;B;D;B;D;B;B	0.62365	0.823;0.0;0.991;0.0;0.991;0.0;0.0	D;B;D;B;D;B;B	0.91635	0.973;0.038;0.999;0.038;0.999;0.038;0.038	T	0.03157	-1.1066	9	0.49607	T	0.09	.	8.6885	0.34251	0.0:0.0:0.7739:0.2261	rs2231093;rs17840079	149;270;270;270;270;270;270	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	S	270;270;58;270;270	ENSP00000379873:A270S;ENSP00000366002:A270S;ENSP00000366005:A270S;ENSP00000365998:A270S	ENSP00000365998:A270S	A	+	1	0	HLA-A	30020066	0.000000	0.05858	0.652000	0.29579	0.832000	0.47134	0.401000	0.20948	0.870000	0.35726	0.485000	0.47835	GCT	G|0.860;T|0.140	0.140	strong		0.627	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SSPO	23145	hgsc.bcm.edu	37	7	149521544	149521544	+	RNA	SNP	C	C	T	rs12673475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149521544C>T	ENST00000378016.2	+	0	13623							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)			TGCCGCCCAGCGCCCTGGCCC	0.687													C|||	826	0.164936	0.1097	0.1931	5008	,	,		15920	0.1736		0.1551	False		,,,				2504	0.2209				p.S4541S		Atlas-SNP	.											.	.	.	.	0			c.C13623T						PASS	.	C		466,3646		29,408,1619	19.0	24.0	22.0		13637	-2.5	0.0	7	dbSNP_120	22	1419,6941		113,1193,2874	no	coding-notMod3	SSPO	NM_198455.2		142,1601,4493	TT,TC,CC		16.9737,11.3327,15.1139			149521544	1885,10587	2056	4180	6236			23145	exon95			GCCCAGCGCCCTG	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.149521544C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	20	4	0.2	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.845;T|0.155	0.155	strong		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
NPAT	4863	hgsc.bcm.edu	37	11	108044204	108044204	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108044204C>G	ENST00000278612.8	-	13	1612	c.1507G>C	c.(1507-1509)Gat>Cat	p.D503H	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	503					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)		TCAGGCTGATCAGGCTGTAAC	0.368																																					p.D503H		Atlas-SNP	.											.	NPAT	124	.	0			c.G1507C						PASS	.						127.0	122.0	123.0					11																	108044204		1867	4096	5963	SO:0001583	missense	4863	exon13			GCTGATCAGGCTG	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.1507G>C	11.37:g.108044204C>G	ENSP00000278612:p.Asp503His	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	386	99	0.256477	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	C	4.278	0.050716	0.08243	.	.	ENSG00000149308	ENST00000278612	T	0.28069	1.63	6.08	4.21	0.49690	.	0.380295	0.29493	N	0.011997	T	0.44265	0.1285	M	0.62723	1.935	0.29803	N	0.832279	D;P	0.56287	0.975;0.956	P;P	0.56960	0.81;0.551	T	0.46289	-0.9202	10	0.62326	D	0.03	-4.1581	9.7917	0.40710	0.1397:0.7908:0.0:0.0695	.	503;503	B9EG70;Q14207	.;NPAT_HUMAN	H	503	ENSP00000278612:D503H	ENSP00000278612:D503H	D	-	1	0	NPAT	107549414	0.946000	0.32159	0.671000	0.29857	0.037000	0.13140	0.380000	0.20602	0.897000	0.36392	-0.181000	0.13052	GAT	.	.	none		0.368	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519	
SPTBN5	51332	hgsc.bcm.edu	37	15	42145049	42145049	+	Silent	SNP	C	C	T	rs55978013	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42145049C>T	ENST00000320955.6	-	60	10547	c.10320G>A	c.(10318-10320)gaG>gaA	p.E3440E	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3440					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)		GCAGGAGTCCCTCCCAGCAGG	0.692													C|||	329	0.0656949	0.0061	0.1153	5008	,	,		14946	0.0159		0.0964	False		,,,				2504	0.1309				p.E3405E		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G10215A						PASS	.	C		86,3790		1,84,1853	18.0	23.0	21.0		10215	0.0	0.1	15	dbSNP_129	21	814,7460		41,732,3364	no	coding-synonymous	SPTBN5	NM_016642.2		42,816,5217	TT,TC,CC		9.838,2.2188,7.4074		3405/3640	42145049	900,11250	1938	4137	6075	SO:0001819	synonymous_variant	51332	exon60			GAGTCCCTCCCAG	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.10320G>A	15.37:g.42145049C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	89	26	0.292135	NM_016642		Silent	SNP	ENST00000320955.6	37																																																																																				C|0.936;T|0.064	0.064	strong		0.692	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
GGT6	124975	hgsc.bcm.edu	37	17	4463796	4463796	+	Silent	SNP	G	G	A	rs7216474	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4463796G>A	ENST00000574154.1	-	1	317	c.21C>T	c.(19-21)ccC>ccT	p.P7P	GGT6_ENST00000381550.3_Silent_p.P7P|GGT6_ENST00000301395.3_Silent_p.P7P|GGT6_ENST00000573591.1_5'Flank			Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6	7					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						GATAGACCACGGGCTCTTCTG	0.657													G|||	740	0.147764	0.0658	0.111	5008	,	,		16135	0.0942		0.2286	False		,,,				2504	0.2566				p.P7P		Atlas-SNP	.											.	GGT6	22	.	0			c.C21T						PASS	.	G	,	371,4035	187.8+/-214.3	15,341,1847	69.0	61.0	64.0		21,21	-7.4	0.0	17	dbSNP_116	64	1957,6643	344.0+/-325.1	214,1529,2557	no	coding-synonymous,coding-synonymous	GGT6	NM_001122890.1,NM_153338.2	,	229,1870,4404	AA,AG,GG		22.7558,8.4203,17.8994	,	7/494,7/462	4463796	2328,10678	2203	4300	6503	SO:0001819	synonymous_variant	124975	exon1			GACCACGGGCTCT	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.21C>T	17.37:g.4463796G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_001122890	B4DUH4|Q8NCM0	Silent	SNP	ENST00000574154.1	37	CCDS45582.1																																																																																			G|0.838;A|0.162	0.162	strong		0.657	GGT6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439122.1	NM_153338	
EPHB1	2047	hgsc.bcm.edu	37	3	134898789	134898789	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:134898789T>C	ENST00000398015.3	+	10	2217	c.1847T>C	c.(1846-1848)gTa>gCa	p.V616A	EPHB1_ENST00000493838.1_Missense_Mutation_p.V177A	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	616					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)	p.V616A(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						GAGATTGATGTATCTTTTGTG	0.488																																					p.V616A		Atlas-SNP	.											EPHB1_ENST00000398015,rectum,carcinoma,0,2	EPHB1	519	2	2	Substitution - Missense(2)	large_intestine(2)	c.T1847C						scavenged	.						155.0	149.0	151.0					3																	134898789		1956	4168	6124	SO:0001583	missense	2047	exon10			TTGATGTATCTTT	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.1847T>C	3.37:g.134898789T>C	ENSP00000381097:p.Val616Ala	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	261	3	0.0114943	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	T	6.218	0.408331	0.11754	.	.	ENSG00000154928	ENST00000398015;ENST00000493838	T;T	0.08370	3.1;3.1	5.83	5.83	0.93111	Protein kinase-like domain (1);	0.140958	0.46145	D	0.000316	T	0.04952	0.0133	N	0.15975	0.35	0.80722	D	1	B	0.32188	0.359	B	0.28553	0.091	T	0.16867	-1.0388	10	0.02654	T	1	.	16.1997	0.82060	0.0:0.0:0.0:1.0	.	616	P54762	EPHB1_HUMAN	A	616;177	ENSP00000381097:V616A;ENSP00000419574:V177A	ENSP00000381097:V616A	V	+	2	0	EPHB1	136381479	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.240000	0.73641	0.528000	0.53228	GTA	.	.	none		0.488	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
SLC1A1	6505	hgsc.bcm.edu	37	9	4576680	4576680	+	Silent	SNP	T	T	C	rs301430	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:4576680T>C	ENST00000262352.3	+	10	1346	c.1110T>C	c.(1108-1110)acT>acC	p.T370T		NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	370					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	TGGATGGGACTGCGCTCTATG	0.517													C|||	2295	0.458267	0.5129	0.3833	5008	,	,		20896	0.5883		0.328	False		,,,				2504	0.4376				p.T370T		Atlas-SNP	.											.	SLC1A1	43	.	0			c.T1110C						PASS	.	C		2188,2218	589.6+/-387.2	534,1120,549	230.0	207.0	215.0		1110	-11.1	0.0	9	dbSNP_79	215	2418,6182	699.4+/-405.1	358,1702,2240	yes	coding-synonymous	SLC1A1	NM_004170.5		892,2822,2789	CC,CT,TT		28.1163,49.6596,35.4144		370/525	4576680	4606,8400	2203	4300	6503	SO:0001819	synonymous_variant	6505	exon10			TGGGACTGCGCTC		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"""Solute carriers"""	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.1110T>C	9.37:g.4576680T>C		Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	247	117	0.473684	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Silent	SNP	ENST00000262352.3	37	CCDS6452.1	982	0.44963369963369965	241	0.4898373983739837	142	0.39226519337016574	349	0.6101398601398601	250	0.32981530343007914	C	1.345	-0.593042	0.03771	0.496596	0.281163	ENSG00000106688	ENST00000422398	.	.	.	5.54	-11.1	0.00147	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999986	.	.	.	.	.	.	T	0.29305	-1.0016	3	.	.	.	.	1.9715	0.03407	0.1473:0.2551:0.3025:0.2951	rs301430;rs301978;rs2146420;rs57708047;rs301430	.	.	.	R	133	.	.	C	+	1	0	SLC1A1	4566680	0.000000	0.05858	0.007000	0.13788	0.243000	0.25628	-6.163000	0.00078	-3.284000	0.00196	-3.707000	0.00023	TGC	T|0.604;C|0.396	0.396	strong		0.517	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1		
ABCA13	154664	hgsc.bcm.edu	37	7	48313510	48313510	+	Missense_Mutation	SNP	A	A	G	rs17547830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:48313510A>G	ENST00000435803.1	+	17	4271	c.4247A>G	c.(4246-4248)cAt>cGt	p.H1416R		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1416				H -> R (in Ref. 1; AAP13576). {ECO:0000305}.	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						TCACAAGGTCATCTTCAAAAT	0.303													A|||	938	0.1873	0.1566	0.2032	5008	,	,		17417	0.0129		0.3917	False		,,,				2504	0.1871				p.H1416R		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A4247G						PASS	.	A	ARG/HIS	671,2947		69,533,1207	39.0	36.0	37.0		4247	-7.5	0.0	7	dbSNP_123	37	2865,5253		499,1867,1693	yes	missense	ABCA13	NM_152701.3	29	568,2400,2900	GG,GA,AA		35.2919,18.5462,30.1295	benign	1416/5059	48313510	3536,8200	1809	4059	5868	SO:0001583	missense	154664	exon17			AAGGTCATCTTCA	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.4247A>G	7.37:g.48313510A>G	ENSP00000411096:p.His1416Arg	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	477	0.2184065934065934	85	0.17276422764227642	80	0.22099447513812154	5	0.008741258741258742	307	0.4050131926121372	A	3.082	-0.188874	0.06299	0.185462	0.352919	ENSG00000179869	ENST00000435803	D	0.85088	-1.94	5.04	-7.5	0.01351	.	0.720289	0.12327	N	0.478767	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.19192	-1.0313	8	.	.	.	.	2.3723	0.04333	0.2845:0.3312:0.2764:0.1079	rs17547830;rs52821200;rs58931054;rs17547830	1416	Q86UQ4	ABCAD_HUMAN	R	1416	ENSP00000411096:H1416R	.	H	+	2	0	ABCA13	48284056	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.100000	0.10990	-1.571000	0.01663	-0.464000	0.05259	CAT	A|0.781;G|0.219	0.219	strong		0.303	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
ZNF283	284349	hgsc.bcm.edu	37	19	44351836	44351836	+	Silent	SNP	G	G	A	rs957569	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44351836G>A	ENST00000324461.7	+	7	1380	c.1083G>A	c.(1081-1083)caG>caA	p.Q361Q	ZNF283_ENST00000588797.1_Silent_p.Q222Q	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	361					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)				GTGGCTATCAGCTTACTCAGC	0.388													A|||	3417	0.682308	0.8533	0.536	5008	,	,		21154	0.374		0.7684	False		,,,				2504	0.7843				p.Q361Q		Atlas-SNP	.											.	ZNF283	83	.	0			c.G1083A						PASS	.	A		3652,694	263.8+/-265.7	1537,578,58	79.0	93.0	88.0		1083	1.8	1.0	19	dbSNP_86	88	6547,2021	342.6+/-324.5	2517,1513,254	no	coding-synonymous	ZNF283	NM_181845.1		4054,2091,312	AA,AG,GG		23.5878,15.9687,21.0237		361/680	44351836	10199,2715	2173	4284	6457	SO:0001819	synonymous_variant	284349	exon7			CTATCAGCTTACT	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.1083G>A	19.37:g.44351836G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Silent	SNP	ENST00000324461.7	37	CCDS46097.1																																																																																			G|0.328;A|0.672	0.672	strong		0.388	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
FSIP2	401024	hgsc.bcm.edu	37	2	186671357	186671357	+	Missense_Mutation	SNP	G	G	A	rs17826534	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:186671357G>A	ENST00000424728.1	+	17	17324	c.17324G>A	c.(17323-17325)cGa>cAa	p.R5775Q	FSIP2_ENST00000343098.5_Missense_Mutation_p.R5864Q			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5775				R -> Q (in Ref. 3; AK126051). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						CAAAACCAACGAGAAAGTAAA	0.343													G|||	2701	0.539337	0.5582	0.4928	5008	,	,		18055	0.4702		0.5099	False		,,,				2504	0.6483				p.R5864Q		Atlas-SNP	.											FSIP2_ENST00000343098,caecum,carcinoma,+1,2	FSIP2	251	2	0			c.G17591A						PASS	.	G	GLN/ARG	2031,1573		567,897,338	73.0	70.0	71.0		17591	3.1	0.0	2	dbSNP_123	71	4338,3802		1152,2034,884	yes	missense	FSIP2	NM_173651.2	43	1719,2931,1222	AA,AG,GG		46.7076,43.6459,45.7681	possibly-damaging	5864/6997	186671357	6369,5375	1802	4070	5872	SO:0001583	missense	401024	exon17			ACCAACGAGAAAG	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.17324G>A	2.37:g.186671357G>A	ENSP00000401306:p.Arg5775Gln	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	176	68	0.386364	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		1108	0.5073260073260073	275	0.5589430894308943	185	0.511049723756906	268	0.46853146853146854	380	0.5013192612137203	G	0.224	-1.026172	0.02045	0.563541	0.532924	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.43294	0.95;0.96	4.85	3.07	0.35406	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.43956	-0.9359	6	0.23302	T	0.38	.	6.5117	0.22226	0.0:0.7165:0.1857:0.0979	rs17826534;rs52791591;rs58063906;rs17826534	.	.	.	Q	5864;5775	ENSP00000344403:R5864Q;ENSP00000401306:R5775Q	ENSP00000344403:R5864Q	R	+	2	0	FSIP2	186379602	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.408000	0.21065	0.651000	0.30788	-0.203000	0.12734	CGA	G|0.487;A|0.513	0.513	strong		0.343	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
ADCK1	57143	hgsc.bcm.edu	37	14	78399654	78399654	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:78399654C>T	ENST00000238561.5	+	11	1591	c.1492C>T	c.(1492-1494)Ctc>Ttc	p.L498F	ADCK1_ENST00000556560.1_3'UTR|ADCK1_ENST00000341211.5_Missense_Mutation_p.L430F	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	505						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)		CCTCCATGAGCTCATCCTGCG	0.517																																					p.L498F		Atlas-SNP	.											.	ADCK1	81	.	0			c.C1492T						PASS	.						130.0	122.0	124.0					14																	78399654		2203	4300	6503	SO:0001583	missense	57143	exon11			CATGAGCTCATCC	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.1492C>T	14.37:g.78399654C>T	ENSP00000238561:p.Leu498Phe	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	268	122	0.455224	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Missense_Mutation	SNP	ENST00000238561.5	37	CCDS9869.1	.	.	.	.	.	.	.	.	.	.	C	8.266	0.812185	0.16537	.	.	ENSG00000063761	ENST00000238561;ENST00000341211	T;T	0.68479	-0.33;1.07	5.58	4.66	0.58398	.	0.194806	0.45126	N	0.000398	T	0.58104	0.2099	L	0.50333	1.59	0.80722	D	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.12837	0.003;0.008;0.007	T	0.52555	-0.8560	10	0.23302	T	0.38	-20.9933	10.9445	0.47294	0.0:0.9076:0.0:0.0924	.	505;430;498	Q86TW2;Q9UIE6;Q86TW2-2	ADCK1_HUMAN;.;.	F	498;430	ENSP00000238561:L498F;ENSP00000339663:L430F	ENSP00000238561:L498F	L	+	1	0	ADCK1	77469407	1.000000	0.71417	0.458000	0.27068	0.072000	0.16883	2.926000	0.48892	1.298000	0.44778	0.655000	0.94253	CTC	.	.	none		0.517	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
FAM78B	149297	hgsc.bcm.edu	37	1	166039898	166039898	+	Silent	SNP	C	C	G	rs41269662	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:166039898C>G	ENST00000338353.3	-	3	955	c.366G>C	c.(364-366)gtG>gtC	p.V122V	FAM78B_ENST00000354422.3_Silent_p.V122V			Q5VT40	FA78B_HUMAN	family with sequence similarity 78, member B	122										central_nervous_system(1)|endometrium(5)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)					CAACCAGGGTCACAGTTTCTG	0.542													C|||	1120	0.223642	0.211	0.3156	5008	,	,		19058	0.256		0.1501	False		,,,				2504	0.2178				p.V122V		Atlas-SNP	.											.	FAM78B	51	.	0			c.G366C						PASS	.	C		895,3511	347.2+/-309.4	91,713,1399	139.0	128.0	132.0		366	4.6	1.0	1	dbSNP_127	132	1132,7468	233.9+/-267.0	76,980,3244	no	coding-synonymous	FAM78B	NM_001017961.3		167,1693,4643	GG,GC,CC		13.1628,20.3132,15.5851		122/262	166039898	2027,10979	2203	4300	6503	SO:0001819	synonymous_variant	149297	exon2			CAGGGTCACAGTT	AL626787	CCDS30931.1	1q24.1	2008-02-05			ENSG00000188859	ENSG00000188859			13495	protein-coding gene	gene with protein product							Standard	NM_001017961		Approved		uc021pee.1	Q5VT40	OTTHUMG00000034705	ENST00000338353.3:c.366G>C	1.37:g.166039898C>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	103	32	0.31068	NM_001017961	B7Z693	Silent	SNP	ENST00000338353.3	37	CCDS30931.1																																																																																			C|0.820;G|0.180	0.180	strong		0.542	FAM78B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343108.1	NM_001017961	
MMAB	326625	hgsc.bcm.edu	37	12	109994870	109994870	+	Missense_Mutation	SNP	A	A	T	rs9593	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:109994870A>T	ENST00000545712.2	-	9	1109	c.716T>A	c.(715-717)aTg>aAg	p.M239K	MMAB_ENST00000266839.5_Missense_Mutation_p.M148K|MMAB_ENST00000540016.1_Missense_Mutation_p.M187K	NM_052845.3	NP_443077.1	Q96EY8	MMAB_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblB type	239			M -> K (common polymorphism; dbSNP:rs9593). {ECO:0000269|PubMed:12471062, ECO:0000269|PubMed:12514191, ECO:0000269|PubMed:15489334}.		cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|cob(I)yrinic acid a,c-diamide adenosyltransferase activity (GO:0008817)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTCATTTTTCATGTATATTTT	0.512													T|||	2571	0.513379	0.7542	0.4914	5008	,	,		20645	0.3125		0.5447	False		,,,				2504	0.3783				p.M239K		Atlas-SNP	.											MMAB,rectum,carcinoma,+1,1	MMAB	16	1	0			c.T716A						PASS	.	T	LYS/MET	3176,1230	426.6+/-341.2	1136,904,163	124.0	109.0	114.0		716	1.4	1.0	12	dbSNP_52	114	4579,4021	556.3+/-386.8	1228,2123,949	yes	missense	MMAB	NM_052845.3	95	2364,3027,1112	TT,TA,AA		46.7558,27.9165,40.3737	benign	239/251	109994870	7755,5251	2203	4300	6503	SO:0001583	missense	326625	exon9			TTTTTCATGTATA	AF550404	CCDS9131.1	12q24	2014-07-18	2005-07-11		ENSG00000139428	ENSG00000139428			19331	protein-coding gene	gene with protein product	"""ATP:cob(I)alamin adenosyltransferase"", ""cilia and flagella associated protein 23"""	607568	"""methylmalonic aciduria (cobalamin deficiency) type B"""			12471062, 12514191	Standard	NM_052845		Approved	cblB, CFAP23	uc001tou.3	Q96EY8	OTTHUMG00000169255	ENST00000545712.2:c.716T>A	12.37:g.109994870A>T	ENSP00000445920:p.Met239Lys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_052845	C5HU05|Q9BSH0	Missense_Mutation	SNP	ENST00000545712.2	37	CCDS9131.1	1122	0.5137362637362637	350	0.7113821138211383	184	0.5082872928176796	167	0.291958041958042	421	0.5554089709762533	T	0.014	-1.584380	0.00872	0.720835	0.532442	ENSG00000139428	ENST00000545712;ENST00000266839	D;D	0.89343	-2.5;-2.31	5.43	1.38	0.22167	Adenosylcobalamin biosynthesis, ATP:cob(I)alamin adenosyltransferase-like (2);	0.390145	0.26616	N	0.023396	T	0.00012	0.0000	N	0.00029	-2.62	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47018	-0.9149	9	0.02654	T	1	-9.3558	0.606	0.00753	0.2411:0.2393:0.1239:0.3958	rs9593;rs3168651;rs61082361;rs9593	239	Q96EY8	MMAB_HUMAN	K	239;148	ENSP00000445920:M239K;ENSP00000266839:M148K	ENSP00000266839:M148K	M	-	2	0	MMAB	108479253	0.931000	0.31567	0.989000	0.46669	0.229000	0.25112	-0.119000	0.10676	0.059000	0.16252	-0.364000	0.07487	ATG	A|0.431;T|0.569	0.569	strong		0.512	MMAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403128.2		
MMP27	64066	hgsc.bcm.edu	37	11	102563739	102563739	+	Silent	SNP	C	C	T	rs1276289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102563739C>T	ENST00000260229.4	-	9	1318	c.1227G>A	c.(1225-1227)ggG>ggA	p.G409G		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	409					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	TCTGCGGGAACCCTTTGTCCA	0.438													C|||	2254	0.45008	0.2186	0.5072	5008	,	,		19176	0.629		0.4453	False		,,,				2504	0.5429				p.G409G		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	0			c.G1227A						PASS	.	C		1205,3201	419.8+/-338.8	150,905,1148	193.0	181.0	185.0		1227	-5.4	0.3	11	dbSNP_87	185	3891,4707	544.7+/-384.6	858,2175,1266	no	coding-synonymous	MMP27	NM_022122.2		1008,3080,2414	TT,TC,CC		45.2547,27.3491,39.1879		409/514	102563739	5096,7908	2203	4299	6502	SO:0001819	synonymous_variant	64066	exon9			CGGGAACCCTTTG	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1227G>A	11.37:g.102563739C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	163	57	0.349693	NM_022122	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																			C|0.594;T|0.406	0.406	strong		0.438	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
DMWD	1762	hgsc.bcm.edu	37	19	46289009	46289009	+	Missense_Mutation	SNP	G	G	A	rs146577305	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46289009G>A	ENST00000270223.6	-	3	1790	c.1745C>T	c.(1744-1746)gCg>gTg	p.A582V	AC011530.4_ENST00000593999.1_Missense_Mutation_p.R75C|DMWD_ENST00000377735.3_Missense_Mutation_p.A582V|DMWD_ENST00000601370.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	582										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		CGGGCACAGCGCAGTGCCCAG	0.697													G|||	26	0.00519169	0.0	0.0058	5008	,	,		14380	0.0		0.0159	False		,,,				2504	0.0061				p.A582V		Atlas-SNP	.											.	DMWD	46	.	0			c.C1745T						PASS	.	G	VAL/ALA	21,4375		0,21,2177	20.0	24.0	23.0		1745	4.3	0.1	19	dbSNP_134	23	226,8364		2,222,4071	yes	missense	DMWD	NM_004943.1	64	2,243,6248	AA,AG,GG		2.631,0.4777,1.902	possibly-damaging	582/675	46289009	247,12739	2198	4295	6493	SO:0001583	missense	1762	exon3			CACAGCGCAGTGC	L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"""WD repeat domain containing"""	2936	protein-coding gene	gene with protein product		609857	"""dystrophia myotonica-containing WD repeat motif"""			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1745C>T	19.37:g.46289009G>A	ENSP00000270223:p.Ala582Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_004943		Missense_Mutation	SNP	ENST00000270223.6	37	CCDS33054.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	17.93	3.509977	0.64522	0.004777	0.02631	ENSG00000185800	ENST00000377735;ENST00000270223	D;D	0.81996	-1.56;-1.56	4.29	4.29	0.51040	.	0.067052	0.64402	D	0.000014	T	0.67674	0.2918	L	0.29908	0.895	0.38820	D	0.955606	P;D;D	0.58620	0.832;0.983;0.972	B;P;P	0.60012	0.371;0.867;0.74	T	0.81247	-0.1019	10	0.66056	D	0.02	-23.9487	14.6065	0.68483	0.0:0.0:1.0:0.0	.	267;582;582	Q8WUW6;G5E9A7;Q09019	.;.;DMWD_HUMAN	V	582	ENSP00000366964:A582V;ENSP00000270223:A582V	ENSP00000270223:A582V	A	-	2	0	DMWD	50980849	0.996000	0.38824	0.083000	0.20561	0.256000	0.26092	7.191000	0.77763	2.402000	0.81655	0.462000	0.41574	GCG	G|0.986;A|0.014	0.014	strong		0.697	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943	
HLA-A	3105	hgsc.bcm.edu	37	6	29910604	29910604	+	Silent	SNP	C	C	A	rs12721675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29910604C>A	ENST00000396634.1	+	4	485	c.144C>A	c.(142-144)gcC>gcA	p.A48A	HLA-A_ENST00000376806.5_Silent_p.A48A|HLA-A_ENST00000376802.2_Silent_p.A48A|HLA-A_ENST00000376809.5_Silent_p.A48A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	48	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						GCTTCATCGCCGTGGGCTACG	0.701									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|||	1915	0.382388	0.4425	0.4597	5008	,	,		15112	0.3899		0.3807	False		,,,				2504	0.2403				p.A48A		Atlas-SNP	.											HLA-A,NS,carcinoma,0,4	HLA-A	89	4	0			c.C144A						scavenged	.						33.0	29.0	30.0					6																	29910604		2201	4298	6499	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CATCGCCGTGGGC	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.144C>A	6.37:g.29910604C>A		Somatic	118	2	0.0169492		WXS	Illumina HiSeq	Phase_I	112	14	0.125	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			A|0.361;C|0.639	0.361	strong		0.701	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
GTSE1	51512	hgsc.bcm.edu	37	22	46719100	46719100	+	Missense_Mutation	SNP	C	C	G	rs6008684	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46719100C>G	ENST00000454366.1	+	8	1658	c.1446C>G	c.(1444-1446)gaC>gaG	p.D482E		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	463					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		ACTCCCCGGACAGCTCAACAC	0.557													C|||	573	0.114417	0.2791	0.0692	5008	,	,		20772	0.001		0.1223	False		,,,				2504	0.0327				p.D482E	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.C1446G						PASS	.	C	GLU/ASP	1138,3268	405.8+/-333.6	152,834,1217	158.0	146.0	150.0		1446	-4.4	0.0	22	dbSNP_114	150	953,7647	208.4+/-249.9	55,843,3402	yes	missense	GTSE1	NM_016426.6	45	207,1677,4619	GG,GC,CC		11.0814,25.8284,16.0772	possibly-damaging	482/740	46719100	2091,10915	2203	4300	6503	SO:0001583	missense	51512	exon8			CCCGGACAGCTCA	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1446C>G	22.37:g.46719100C>G	ENSP00000415430:p.Asp482Glu	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Missense_Mutation	SNP	ENST00000454366.1	37	CCDS14074.2	263	0.12042124542124542	135	0.27439024390243905	32	0.08839779005524862	0	0.0	96	0.1266490765171504	C	4.984	0.182775	0.09495	0.258284	0.110814	ENSG00000075218	ENST00000454366;ENST00000361934	T	0.06142	3.34	3.31	-4.36	0.03645	.	1.514080	0.03735	N	0.254078	T	0.00012	0.0000	M	0.66939	2.045	0.80722	P	0.0	B;B	0.25609	0.007;0.13	B;B	0.22880	0.028;0.042	T	0.42832	-0.9428	9	0.49607	T	0.09	0.0	3.1854	0.06599	0.2794:0.2923:0.0:0.4283	rs6008684;rs6008684	463;442	Q9NYZ3;B4DZT6	GTSE1_HUMAN;.	E	482;442	ENSP00000415430:D482E	ENSP00000354634:D442E	D	+	3	2	GTSE1	45097764	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.322000	0.08007	-0.816000	0.04340	0.313000	0.20887	GAC	C|0.856;G|0.144	0.144	strong		0.557	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
CYP2F1	1572	hgsc.bcm.edu	37	19	41628014	41628014	+	Missense_Mutation	SNP	G	G	C	rs75405062		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41628014G>C	ENST00000331105.2	+	6	870	c.798G>C	c.(796-798)caG>caC	p.Q266H		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	266			Q -> H (in allele CYP2F1*3). {ECO:0000269|PubMed:11827709}.		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						ACTTCATCCAGTGCTTCCTCA	0.572																																					p.Q266H		Atlas-SNP	.											CYP2F1,NS,carcinoma,+2,1	CYP2F1	60	1	0			c.G798C						scavenged	.	C	HIS/GLN	162,3888		1,160,1864	50.0	48.0	48.0		798	-4.7	0.4	19	dbSNP_132	48	113,8171		0,113,4029	no	missense	CYP2F1	NM_000774.3	24	1,273,5893	CC,CG,GG		1.3641,4.0,2.2296	benign	266/492	41628014	275,12059	2025	4142	6167	SO:0001583	missense	1572	exon6			CATCCAGTGCTTC	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.798G>C	19.37:g.41628014G>C	ENSP00000333534:p.Gln266His	Somatic	74	8	0.108108		WXS	Illumina HiSeq	Phase_I	67	12	0.179104	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	449	0.20558608058608058	107	0.21747967479674796	82	0.2265193370165746	109	0.19055944055944055	151	0.19920844327176782	N	5.932	0.355925	0.11239	0.04	0.013641	ENSG00000197446	ENST00000331105	T	0.12569	2.67	3.27	-4.65	0.03339	.	0.052380	0.64402	U	0.000001	T	0.00012	0.0000	N	0.02247	-0.625	0.51767	P	6.20000000000065E-5	D;B;B	0.64830	0.994;0.227;0.021	P;B;B	0.59595	0.86;0.017;0.007	T	0.42310	-0.9459	9	0.87932	D	0	.	8.662	0.34099	0.0:0.6997:0.1315:0.1688	.	52;266;266	B4DL83;Q32MN5;P24903	.;.;CP2F1_HUMAN	H	266	ENSP00000333534:Q266H	ENSP00000333534:Q266H	Q	+	3	2	CYP2F1	46319854	0.006000	0.16342	0.412000	0.26496	0.011000	0.07611	0.096000	0.15147	-1.780000	0.01279	-2.252000	0.00282	CAG	G|0.250;C|0.750	0.750	weak		0.572	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
KIAA0556	23247	hgsc.bcm.edu	37	16	27761040	27761040	+	Missense_Mutation	SNP	C	C	T	rs61734902	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:27761040C>T	ENST00000261588.4	+	16	2778	c.2759C>T	c.(2758-2760)cCg>cTg	p.P920L		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	920						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						ACGGAGCTCCCGGGGGACATC	0.652													C|||	210	0.0419329	0.0076	0.0331	5008	,	,		17965	0.0536		0.0825	False		,,,				2504	0.0409				p.P920L		Atlas-SNP	.											.	KIAA0556	348	.	0			c.C2759T						PASS	.	C	LEU/PRO	80,4314	68.1+/-105.8	0,80,2117	46.0	45.0	45.0		2759	2.4	0.2	16	dbSNP_129	45	622,7978	157.6+/-211.2	29,564,3707	yes	missense	KIAA0556	NM_015202.2	98	29,644,5824	TT,TC,CC		7.2326,1.8207,5.4025	benign	920/1619	27761040	702,12292	2197	4300	6497	SO:0001583	missense	23247	exon16			AGCTCCCGGGGGA	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.2759C>T	16.37:g.27761040C>T	ENSP00000261588:p.Pro920Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	92	0.04212454212454213	5	0.01016260162601626	10	0.027624309392265192	22	0.038461538461538464	55	0.07255936675461741	C	10.12	1.263013	0.23051	0.018207	0.072326	ENSG00000047578	ENST00000261588	T	0.09255	3.0	4.7	2.41	0.29592	.	0.286026	0.32901	N	0.005518	T	0.00384	0.0012	N	0.08118	0	0.39096	D	0.961187	P	0.36874	0.572	B	0.26864	0.074	T	0.52764	-0.8532	10	0.62326	D	0.03	-18.5382	11.5487	0.50708	0.7134:0.2866:0.0:0.0	rs61734902	920	O60303	K0556_HUMAN	L	920	ENSP00000261588:P920L	ENSP00000261588:P920L	P	+	2	0	KIAA0556	27668541	1.000000	0.71417	0.213000	0.23690	0.005000	0.04900	5.475000	0.66787	0.252000	0.21531	-1.014000	0.02459	CCG	C|0.951;T|0.049	0.049	strong		0.652	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
AHNAK	79026	hgsc.bcm.edu	37	11	62284888	62284888	+	Silent	SNP	G	G	A	rs11555628	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:62284888G>A	ENST00000378024.4	-	5	17275	c.17001C>T	c.(16999-17001)acC>acT	p.T5667T	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_5'Flank	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5667					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)			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)				GGCCAGAGAAGGTAAATTTGG	0.537													G|||	103	0.0205671	0.0015	0.0476	5008	,	,		18673	0.001		0.0606	False		,,,				2504	0.0061				p.T5667T		Atlas-SNP	.											.	AHNAK	532	.	0			c.C17001T						PASS	.	G	,	36,4368	40.0+/-72.8	0,36,2166	54.0	54.0	54.0		17001,	2.0	1.0	11	dbSNP_120	54	430,8168	131.0+/-188.9	13,404,3882	no	coding-synonymous,intron	AHNAK	NM_001620.1,NM_024060.2	,	13,440,6048	AA,AG,GG		5.0012,0.8174,3.5841	,	5667/5891,	62284888	466,12536	2202	4299	6501	SO:0001819	synonymous_variant	79026	exon5			AGAGAAGGTAAAT	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.17001C>T	11.37:g.62284888G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	144	67	0.465278	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																			G|0.966;C|0.000;A|0.034	0.034	strong		0.537	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
GRM8	2918	hgsc.bcm.edu	37	7	126542667	126542667	+	Missense_Mutation	SNP	A	A	T	rs78124913	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:126542667A>T	ENST00000339582.2	-	6	1893	c.1085T>A	c.(1084-1086)tTc>tAc	p.F362Y	GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000358373.3_Missense_Mutation_p.F362Y|GRM8_ENST00000444921.2_Missense_Mutation_p.F362Y|GRM8_ENST00000405249.1_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	177	0	0		WXS	Illumina HiSeq	Phase_I	130	31	0.238462	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		
UGT2A1	10941	hgsc.bcm.edu	37	4	70512773	70512773	+	Missense_Mutation	SNP	A	A	G	rs41292307	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:70512773A>G	ENST00000503640.1	-	1	645	c.590T>C	c.(589-591)tTa>tCa	p.L197S	UGT2A1_ENST00000512704.1_Missense_Mutation_p.L197S|UGT2A1_ENST00000514019.1_Missense_Mutation_p.L197S|UGT2A1_ENST00000286604.4_Missense_Mutation_p.L197S	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	197					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)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						GAGTTCTGATAAAACAGCAGG	0.423													A|||	351	0.0700879	0.0038	0.0807	5008	,	,		18794	0.001		0.161	False		,,,				2504	0.1299				p.L197S		Atlas-SNP	.											.	UGT2A1	131	.	0			c.T590C						PASS	.	A	SER/LEU	167,4239	109.9+/-148.2	4,159,2040	92.0	80.0	84.0		590	5.8	0.4	4	dbSNP_127	84	1581,7017	294.8+/-302.1	136,1309,2854	yes	missense	UGT2A1	NM_006798.2	145	140,1468,4894	GG,GA,AA		18.388,3.7903,13.442	possibly-damaging	197/528	70512773	1748,11256	2203	4299	6502	SO:0001583	missense	10941	exon2			TCTGATAAAACAG	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.590T>C	4.37:g.70512773A>G	ENSP00000424478:p.Leu197Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_001252274	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	149	0.06822344322344322	3	0.006097560975609756	31	0.0856353591160221	0	0.0	115	0.1517150395778364	A	14.39	2.519890	0.44866	0.037903	0.18388	ENSG00000173610	ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T	0.64803	-0.12;0.02;-0.12;-0.12	5.78	5.78	0.91487	.	0.378699	0.25762	N	0.028474	T	0.00384	0.0012	L	0.49350	1.555	.	.	.	D;P;D;D	0.89917	1.0;0.92;1.0;0.999	D;B;D;D	0.79784	0.993;0.388;0.993;0.986	T	0.08146	-1.0736	9	0.54805	T	0.06	.	14.0552	0.64764	1.0:0.0:0.0:0.0	rs41292307	197;197;197;197	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1	.;.;.;UD2A1_HUMAN	S	197	ENSP00000424478:L197S;ENSP00000421432:L197S;ENSP00000425497:L197S;ENSP00000286604:L197S	ENSP00000286604:L197S	L	-	2	0	UGT2A1	70547362	0.949000	0.32298	0.364000	0.25888	0.503000	0.33858	4.429000	0.59901	2.215000	0.71742	0.482000	0.46254	TTA	A|0.882;G|0.118	0.118	strong		0.423	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
ABCC5	10057	hgsc.bcm.edu	37	3	183660585	183660585	+	Silent	SNP	G	G	A	rs3749442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:183660585G>A	ENST00000334444.6	-	25	3864	c.3624C>T	c.(3622-3624)ctC>ctT	p.L1208L	ABCC5_ENST00000265586.6_Silent_p.L1165L	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1208	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)			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)	TCTTTAGGACGAGAGGGAGGT	0.507													G|||	1247	0.249002	0.1944	0.2709	5008	,	,		20136	0.4365		0.1769	False		,,,				2504	0.1881				p.L1208L		Atlas-SNP	.											.	ABCC5	142	.	0			c.C3624T						PASS	.	G		631,3227		49,533,1347	96.0	93.0	94.0		3624	3.4	1.0	3	dbSNP_107	94	1436,6808		136,1164,2822	no	coding-synonymous	ABCC5	NM_005688.2		185,1697,4169	AA,AG,GG		17.4187,16.3556,17.0798		1208/1438	183660585	2067,10035	1929	4122	6051	SO:0001819	synonymous_variant	10057	exon25			TAGGACGAGAGGG	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.3624C>T	3.37:g.183660585G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	119	48	0.403361	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			G|0.765;A|0.235	0.235	strong		0.507	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
SEMA7A	8482	hgsc.bcm.edu	37	15	74703929	74703929	+	Silent	SNP	T	T	C	rs741761	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:74703929T>C	ENST00000261918.4	-	12	2093	c.1545A>G	c.(1543-1545)caA>caG	p.Q515Q	SEMA7A_ENST00000543145.2_Silent_p.Q501Q|SEMA7A_ENST00000542748.1_Silent_p.Q350Q	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	515					axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						TGCAGCGGCCTTGGTCCCAGC	0.662													C|||	2479	0.495008	0.7073	0.2421	5008	,	,		17720	0.5496		0.2654	False		,,,				2504	0.5675				p.Q515Q		Atlas-SNP	.											.	SEMA7A	58	.	0			c.A1545G						PASS	.	C	,,	2850,1544	482.1+/-359.3	923,1004,270	50.0	56.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1503,1050,1545	1.1	1.0	15	dbSNP_86	54	2247,6345	706.2+/-405.5	318,1611,2367	no	coding-synonymous,coding-synonymous,coding-synonymous	SEMA7A	NM_001146029.1,NM_001146030.1,NM_003612.3	,,	1241,2615,2637	CC,CT,TT		26.1522,35.1388,39.25	,,	501/653,350/502,515/667	74703929	5097,7889	2197	4296	6493	SO:0001819	synonymous_variant	8482	exon12			GCGGCCTTGGTCC	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"""Semaphorins"", ""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10741	protein-coding gene	gene with protein product	"""John Milton Hagen blood group"", ""H-Sema K1"""	607961	"""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A"", ""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"""	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1545A>G	15.37:g.74703929T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	55	46	0.836364	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Silent	SNP	ENST00000261918.4	37	CCDS10262.1																																																																																			T|0.582;C|0.418	0.418	strong		0.662	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612	
TYR	7299	hgsc.bcm.edu	37	11	88911218	88911218	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:88911218A>G	ENST00000263321.5	+	1	599	c.97A>G	c.(97-99)Aag>Gag	p.K33E	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	33					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CCTGATGGAGAAGGAATGCTG	0.547																																					p.K33E		Atlas-SNP	.											TYR,NS,carcinoma,-2,2	TYR	130	2	0			c.A97G						scavenged	.						77.0	75.0	76.0					11																	88911218		2201	4299	6500	SO:0001583	missense	7299	exon1			ATGGAGAAGGAAT	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.97A>G	11.37:g.88911218A>G	ENSP00000263321:p.Lys33Glu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	198	2	0.010101	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.415648	0.83449	.	.	ENSG00000077498	ENST00000263321	D	0.99259	-5.64	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.99530	0.9832	M	0.91920	3.255	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.98310	1.0523	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	33	P14679	TYRO_HUMAN	E	33	ENSP00000263321:K33E	.	K	+	1	0	TYR	88550866	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	8.750000	0.91623	2.326000	0.78906	0.533000	0.62120	AAG	.	.	none		0.547	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
NPAS3	64067	hgsc.bcm.edu	37	14	34247747	34247747	+	Silent	SNP	C	C	T	rs147070037	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:34247747C>T	ENST00000356141.4	+	9	1122	c.1122C>T	c.(1120-1122)gaC>gaT	p.D374D	NPAS3_ENST00000357798.5_Silent_p.D361D|NPAS3_ENST00000551492.1_Silent_p.D379D|NPAS3_ENST00000346562.2_Silent_p.D342D|NPAS3_ENST00000548645.1_Silent_p.D344D			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	374	PAC.|PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		ATGCTGAAGACGTGGAGGGCA	0.493													C|||	3	0.000599042	0.0	0.0	5008	,	,		19225	0.0		0.003	False		,,,				2504	0.0				p.D374D		Atlas-SNP	.											.	NPAS3	266	.	0			c.C1122T						PASS	.	C	,,,	1,4405	2.1+/-5.4	0,1,2202	117.0	102.0	107.0		1122,1032,1026,1083	-6.6	0.2	14	dbSNP_134	107	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPAS3	NM_001164749.1,NM_001165893.1,NM_022123.2,NM_173159.2	,,,	0,21,6482	TT,TC,CC		0.2326,0.0227,0.1615	,,,	374/934,344/904,342/902,361/921	34247747	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	64067	exon9			TGAAGACGTGGAG	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"""Basic helix-loop-helix proteins"""	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.1122C>T	14.37:g.34247747C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	166	108	0.650602	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Silent	SNP	ENST00000356141.4	37	CCDS53891.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	8.823	0.937989	0.18206	2.27E-4	0.002326	ENSG00000151322	ENST00000552874	.	.	.	6.03	-6.63	0.01807	.	.	.	.	.	T	0.67552	0.2905	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70385	-0.4886	4	.	.	.	.	19.2046	0.93724	0.0:0.2337:0.0:0.7663	.	.	.	.	M	121	.	.	T	+	2	0	NPAS3	33317498	0.002000	0.14202	0.183000	0.23137	0.952000	0.60782	-1.517000	0.02248	-1.491000	0.01840	-0.226000	0.12346	ACG	C|0.999;T|0.001	0.001	strong		0.493	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1		
CTDSP1	58190	hgsc.bcm.edu	37	2	219267781	219267781	+	Silent	SNP	C	C	T	rs2227255	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219267781C>T	ENST00000273062.2	+	5	738	c.402C>T	c.(400-402)caC>caT	p.H134H	CTDSP1_ENST00000443891.1_Silent_p.H133H|MIR26B_ENST00000362251.2_RNA|CTDSP1_ENST00000488627.1_3'UTR	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	134	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				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)		AGCGTCCTCACGTGGATGAGT	0.672													C|||	2331	0.465455	0.0318	0.5764	5008	,	,		13304	0.6915		0.6163	False		,,,				2504	0.5849				p.H134H		Atlas-SNP	.											CTDSP1,colon,carcinoma,0,1	CTDSP1	19	1	0			c.C402T						scavenged	.	C	,,,	597,3809	262.8+/-265.1	39,519,1645	69.0	64.0	66.0		399,,402,399	-2.7	0.6	2	dbSNP_96	66	5248,3352	642.6+/-399.8	1604,2040,656	no	coding-synonymous,utr-5,coding-synonymous,coding-synonymous	CTDSP1	NM_001206878.1,NM_001206879.1,NM_021198.2,NM_182642.2	,,,	1643,2559,2301	TT,TC,CC		38.9767,13.5497,44.9408	,,,	133/261,,134/262,133/261	219267781	5845,7161	2203	4300	6503	SO:0001819	synonymous_variant	58190	exon5			TCCTCACGTGGAT	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.402C>T	2.37:g.219267781C>T		Somatic	267	2	0.00749064		WXS	Illumina HiSeq	Phase_I	169	166	0.982249	NM_021198	C9IYG0|Q7Z5Q3|Q7Z5Q4	Silent	SNP	ENST00000273062.2	37	CCDS2416.1	1121	0.5132783882783882	26	0.052845528455284556	212	0.585635359116022	401	0.701048951048951	482	0.6358839050131926	C	6.359	0.434375	0.12045	0.135497	0.610233	ENSG00000144579	ENST00000452977;ENST00000428361	.	.	.	4.91	-2.71	0.05986	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999968	.	.	.	.	.	.	T	0.34403	-0.9830	3	.	.	.	-16.9965	12.043	0.53464	0.0:0.4326:0.0:0.5674	rs2227255;rs58989933;rs2227255	.	.	.	M	127;135	.	.	T	+	2	0	CTDSP1	218976025	0.000000	0.05858	0.627000	0.29227	0.863000	0.49368	-2.503000	0.00965	-0.677000	0.05231	-1.174000	0.01732	ACG	C|0.533;T|0.467	0.467	strong		0.672	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	NM_182642, NM_021198	
HMMR	3161	hgsc.bcm.edu	37	5	162901156	162901156	+	Missense_Mutation	SNP	G	G	A	rs2303078	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:162901156G>A	ENST00000358715.3	+	10	1031	c.995G>A	c.(994-996)cGt>cAt	p.R332H	HMMR_ENST00000393915.4_Missense_Mutation_p.R333H|HMMR_ENST00000432118.2_Missense_Mutation_p.R246H|HMMR_ENST00000353866.3_Missense_Mutation_p.R317H			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	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	314	156	0.496815	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	
EMC1	23065	hgsc.bcm.edu	37	1	19566881	19566881	+	Silent	SNP	C	C	T	rs12084825	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19566881C>T	ENST00000477853.1	-	7	738	c.696G>A	c.(694-696)gaG>gaA	p.E232E	RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375208.3_Silent_p.E210E|EMC1_ENST00000375199.3_Silent_p.E232E	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	214	0	0		WXS	Illumina HiSeq	Phase_I	116	91	0.784483	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	
LMO7	4008	hgsc.bcm.edu	37	13	76335109	76335109	+	Silent	SNP	A	A	G	rs17706535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:76335109A>G	ENST00000341547.4	+	5	1668	c.408A>G	c.(406-408)ggA>ggG	p.G136G	LMO7_ENST00000465261.2_5'UTR|LMO7_ENST00000377534.3_Silent_p.G136G|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000526202.1_Silent_p.G45G|LMO7_ENST00000357063.3_Silent_p.G136G|LMO7_ENST00000321797.8_5'UTR	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	136	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)		AACAGATTGGATTGAAAGAAG	0.358													A|||	341	0.0680911	0.0053	0.0922	5008	,	,		16064	0.003		0.1292	False		,,,				2504	0.1401				p.G136G		Atlas-SNP	.											.	LMO7	334	.	0			c.A408G						PASS	.	A	,	99,4307	76.8+/-115.0	4,91,2108	77.0	76.0	76.0		408,	4.4	1.0	13	dbSNP_123	76	982,7618	212.5+/-252.8	56,870,3374	no	coding-synonymous,utr-5	LMO7	NM_005358.5,NM_015842.2	,	60,961,5482	GG,GA,AA		11.4186,2.2469,8.3115	,	136/1350,	76335109	1081,11925	2203	4300	6503	SO:0001819	synonymous_variant	4008	exon5			GATTGGATTGAAA	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	ENST00000341547.4:c.408A>G	13.37:g.76335109A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Silent	SNP	ENST00000341547.4	37	CCDS9454.1																																																																																			A|0.921;G|0.079	0.079	strong		0.358	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358	
UGGT2	55757	hgsc.bcm.edu	37	13	96555149	96555149	+	Missense_Mutation	SNP	C	C	T	rs33949518	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	111	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	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	
CCDC8	83987	hgsc.bcm.edu	37	19	46915091	46915091	+	Missense_Mutation	SNP	T	T	C	rs74516985	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46915091T>C	ENST00000307522.3	-	1	1750	c.977A>G	c.(976-978)gAc>gGc	p.D326G		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	326					microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)		TGCCCCCTGGTCAGCTGGGGC	0.622													T|||	55	0.0109824	0.0	0.0043	5008	,	,		17258	0.0		0.0447	False		,,,				2504	0.0072				p.D326G		Atlas-SNP	.											CCDC8,NS,haematopoietic_neoplasm,0,1	CCDC8	56	1	0			c.A977G						PASS	.	T	GLY/ASP	28,4378	34.3+/-65.2	0,28,2175	89.0	95.0	93.0		977	-1.2	0.0	19	dbSNP_131	93	259,8341	97.9+/-159.5	3,253,4044	yes	missense	CCDC8	NM_032040.3	94	3,281,6219	CC,CT,TT		3.0116,0.6355,2.2067	benign	326/539	46915091	287,12719	2203	4300	6503	SO:0001583	missense	83987	exon1			CCCTGGTCAGCTG	BC025243	CCDS12685.1	19q13.33	2012-04-17			ENSG00000169515	ENSG00000169515		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25367	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 20"""	614145				11230166	Standard	NM_032040		Approved	DKFZp564K0322, 3M3, PPP1R20	uc002pep.3	Q9H0W5	OTTHUMG00000162348	ENST00000307522.3:c.977A>G	19.37:g.46915091T>C	ENSP00000303158:p.Asp326Gly	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	185	103	0.556757	NM_032040	Q8TB26	Missense_Mutation	SNP	ENST00000307522.3	37	CCDS12685.1	36|36	0.016483516483516484|0.016483516483516484	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	36|36	0.047493403693931395|0.047493403693931395	T|T	11.57|11.57	1.676642|1.676642	0.29783|0.29783	0.006355|0.006355	0.030116|0.030116	ENSG00000169515|ENSG00000169515	ENST00000307522|ENST00000540252	T|.	0.12039|.	2.72|.	4.21|4.21	-1.2|-1.2	0.09554|0.09554	.|.	0.805863|.	0.10411|.	N|.	0.677845|.	T|T	0.02304|0.02304	0.0071|0.0071	N|N	0.25647|0.25647	0.755|0.755	0.09310|0.09310	N|N	1|1	B|.	0.09022|.	0.002|.	B|.	0.09377|.	0.004|.	T|T	0.20174|0.20174	-1.0283|-1.0283	10|6	0.41790|0.02654	T|T	0.15|1	1.4359|1.4359	4.006|4.006	0.09602|0.09602	0.1575:0.3231:0.0:0.5194|0.1575:0.3231:0.0:0.5194	.|.	326|.	Q9H0W5|.	CCDC8_HUMAN|.	G|A	326|173	ENSP00000303158:D326G|.	ENSP00000303158:D326G|ENSP00000441180:T173A	D|T	-|-	2|1	0|0	CCDC8|CCDC8	51606931|51606931	0.000000|0.000000	0.05858|0.05858	0.010000|0.010000	0.14722|0.14722	0.070000|0.070000	0.16714|0.16714	-0.876000|-0.876000	0.04201|0.04201	-0.051000|-0.051000	0.13334|0.13334	0.402000|0.402000	0.26972|0.26972	GAC|ACC	T|0.980;C|0.020	0.020	strong		0.622	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040	
MYO7B	4648	hgsc.bcm.edu	37	2	128367241	128367241	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:128367241G>A	ENST00000409816.2	+	22	3007	c.2975G>A	c.(2974-2976)cGg>cAg	p.R992Q	MYO7B_ENST00000428314.1_Missense_Mutation_p.R992Q|MYO7B_ENST00000389524.4_Missense_Mutation_p.R992Q			Q6PIF6	MYO7B_HUMAN	myosin VIIB	992	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					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)		CACATCCGGCGGCCCCTCCGA	0.587																																					p.R992Q		Atlas-SNP	.											MYO7B_ENST00000428314,NS,carcinoma,+1,2	MYO7B	359	2	0			c.G2975A						scavenged	.						90.0	101.0	97.0					2																	128367241		2009	4162	6171	SO:0001583	missense	4648	exon23			TCCGGCGGCCCCT		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.2975G>A	2.37:g.128367241G>A	ENSP00000386461:p.Arg992Gln	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	234	5	0.0213675	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	G	11.71	1.720104	0.30503	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.87966	-2.32;-2.32;-2.32	5.28	1.43	0.22495	MyTH4 domain (2);	0.587434	0.16502	N	0.211620	T	0.79323	0.4426	L	0.38649	1.16	0.09310	N	1	B	0.17268	0.021	B	0.09377	0.004	T	0.65903	-0.6055	10	0.45353	T	0.12	.	9.2107	0.37318	0.4505:0.0:0.5495:0.0	.	992	Q6PIF6	MYO7B_HUMAN	Q	992	ENSP00000374175:R992Q;ENSP00000415090:R992Q;ENSP00000386461:R992Q	ENSP00000374175:R992Q	R	+	2	0	MYO7B	128083711	0.000000	0.05858	0.104000	0.21259	0.677000	0.39632	-0.204000	0.09425	-0.013000	0.14199	-0.258000	0.10820	CGG	.	.	none		0.587	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
CRHR2	1395	hgsc.bcm.edu	37	7	30695202	30695202	+	Silent	SNP	C	C	T	rs2240403	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:30695202C>T	ENST00000471646.1	-	10	1464	c.1047G>A	c.(1045-1047)tcG>tcA	p.S349S	CRHR2_ENST00000506074.2_Silent_p.S349S|CRHR2_ENST00000341843.4_Silent_p.S335S|CRHR2_ENST00000348438.4_Silent_p.S376S	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	349					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CCACCTGGAACGACTGCAGGA	0.597													C|||	685	0.136781	0.1089	0.0951	5008	,	,		20091	0.1806		0.0706	False		,,,				2504	0.227				p.S376S		Atlas-SNP	.											.	CRHR2	104	.	0			c.G1128A						PASS	.	C	,,,,	463,3943	217.1+/-235.6	22,419,1762	78.0	76.0	77.0		1128,1005,1044,1047,1047	-10.2	0.4	7	dbSNP_98	77	767,7833	180.5+/-229.4	35,697,3568	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRHR2	NM_001202475.1,NM_001202481.1,NM_001202482.1,NM_001202483.1,NM_001883.4	,,,,	57,1116,5330	TT,TC,CC		8.9186,10.5084,9.4572	,,,,	376/439,335/398,348/411,349/388,349/412	30695202	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	1395	exon11			CTGGAACGACTGC		CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.1047G>A	7.37:g.30695202C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	33	0.33	NM_001202475	B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Silent	SNP	ENST00000471646.1	37	CCDS5429.1																																																																																			C|0.902;T|0.098	0.098	strong		0.597	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3		
MED12L	116931	hgsc.bcm.edu	37	3	151112568	151112568	+	Silent	SNP	G	G	A	rs3732768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151112568G>A	ENST00000474524.1	+	37	5666	c.5628G>A	c.(5626-5628)tcG>tcA	p.S1876S	MED12L_ENST00000273432.4_Silent_p.S1736S	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1876						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAATCACATCGCAGCAGCAGT	0.547													G|||	1497	0.298922	0.3707	0.2233	5008	,	,		16917	0.2778		0.2028	False		,,,				2504	0.3763				p.S1876S		Atlas-SNP	.											MED12L,NS,carcinoma,+1,2	MED12L	271	2	0			c.G5628A						PASS	.	G		1547,2859	487.8+/-361.0	282,983,938	90.0	90.0	90.0		5628	-11.8	0.0	3	dbSNP_107	90	1835,6765	327.5+/-317.9	210,1415,2675	no	coding-synonymous	MED12L	NM_053002.4		492,2398,3613	AA,AG,GG		21.3372,35.1112,26.0034		1876/2146	151112568	3382,9624	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon37			CACATCGCAGCAG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5628G>A	3.37:g.151112568G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			G|0.724;A|0.276	0.276	strong		0.547	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242102	81242102	+	RNA	SNP	G	G	A	rs6420424	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	59	0	0		WXS	Illumina HiSeq	Phase_I	65	8	0.123077	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		
DBNDD1	79007	hgsc.bcm.edu	37	16	90075226	90075226	+	Silent	SNP	C	C	T	rs4362387	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:90075226C>T	ENST00000002501.6	-	3	416	c.285G>A	c.(283-285)tcG>tcA	p.S95S	DBNDD1_ENST00000304733.3_Silent_p.S115S|DBNDD1_ENST00000568838.1_Silent_p.S215S|DBNDD1_ENST00000392973.3_Silent_p.S101S	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1	95						cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		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;0.0275)		TCTCGTCGTCCGAGTCAGCAA	0.642													C|||	285	0.0569089	0.0053	0.0706	5008	,	,		20383	0.1587		0.0457	False		,,,				2504	0.0235				p.S115S		Atlas-SNP	.											.	DBNDD1	9	.	0			c.G345A						PASS	.	C	,	47,4035		0,47,1994	40.0	44.0	43.0		285,345	-10.5	0.0	16	dbSNP_111	43	495,7867		14,467,3700	no	coding-synonymous,coding-synonymous	DBNDD1	NM_001042610.1,NM_024043.2	,	14,514,5694	TT,TC,CC		5.9196,1.1514,4.3555	,	95/159,115/179	90075226	542,11902	2041	4181	6222	SO:0001819	synonymous_variant	79007	exon3			GTCGTCCGAGTCA	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.285G>A	16.37:g.90075226C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	61	15	0.245902	NM_024043	B4DQS3|Q69YT2|Q9BW25	Silent	SNP	ENST00000002501.6	37	CCDS42223.1																																																																																			C|0.947;T|0.053	0.053	strong		0.642	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043	
GPR108	56927	hgsc.bcm.edu	37	19	6733582	6733582	+	Splice_Site	SNP	G	G	A	rs201134279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6733582G>A	ENST00000264080.7	-	8	748	c.722C>T	c.(721-723)aCg>aTg	p.T241M	GPR108_ENST00000598626.1_5'Flank|GPR108_ENST00000430424.4_De_novo_Start_InFrame	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	241						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						TCCGCTCACCGTGATGTCGAA	0.632													G|||	21	0.00419329	0.0	0.0	5008	,	,		16071	0.0		0.005	False		,,,				2504	0.0164				p.T241M		Atlas-SNP	.											.	GPR108	35	.	0			c.C722T						PASS	.	G	MET/THR	11,4095		0,11,2042	81.0	79.0	80.0		722	3.9	1.0	19		80	45,8347		0,45,4151	yes	missense-near-splice	GPR108	NM_001080452.1	81	0,56,6193	AA,AG,GG		0.5362,0.2679,0.4481	probably-damaging	241/544	6733582	56,12442	2053	4196	6249	SO:0001630	splice_region_variant	56927	exon8			CTCACCGTGATGT		CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"""GPCR / Unclassified : 7TM orphan receptors"""	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.723+1C>T	19.37:g.6733582G>A		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001080452	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	37	CCDS42479.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	32	5.147240	0.94603	0.002679	0.005362	ENSG00000125734	ENST00000264080	T	0.26373	1.74	3.92	3.92	0.45320	.	0.198041	0.28600	U	0.014764	T	0.38665	0.1049	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.34700	-0.9818	10	0.48119	T	0.1	-26.584	11.595	0.50968	0.0:0.0:1.0:0.0	.	241	Q9NPR9	GP108_HUMAN	M	241	ENSP00000264080:T241M	ENSP00000264080:T241M	T	-	2	0	GPR108	6684582	0.981000	0.34729	0.999000	0.59377	0.813000	0.45954	1.961000	0.40432	2.172000	0.68678	0.555000	0.69702	ACG	G|0.995;A|0.005	0.005	strong		0.632	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2		Missense_Mutation
NFKBIB	4793	hgsc.bcm.edu	37	19	39399416	39399416	+	Missense_Mutation	SNP	C	C	T	rs17886215		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:39399416C>T	ENST00000313582.5	+	6	1049	c.1015C>T	c.(1015-1017)Cgg>Tgg	p.R339W	NFKBIB_ENST00000392079.3_3'UTR	NM_002503.4	NP_002494.2	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta	339			R -> W (in dbSNP:rs17886215). {ECO:0000269|Ref.3}.		innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|signal transduction (GO:0007165)|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)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	8	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CAGCCAAACCCGGCTGCCTCC	0.547																																					p.R339W	Pancreas(165;1492 2005 6979 7739 34483)	Atlas-SNP	.											.	NFKBIB	23	.	0			c.C1015T						PASS	.	C	,TRP/ARG	0,4406		0,0,2203	81.0	89.0	87.0		,1015	0.3	0.0	19	dbSNP_124	87	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,missense	NFKBIB	NM_001001716.1,NM_002503.4	,101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,possibly-damaging	,339/357	39399416	3,13003	2203	4300	6503	SO:0001583	missense	4793	exon6			CAAACCCGGCTGC	L40407	CCDS12524.1, CCDS74362.1	19q13.1	2013-01-10				ENSG00000104825		"""Ankyrin repeat domain containing"""	7798	protein-coding gene	gene with protein product		604495				9763672	Standard	NM_002503		Approved	IKBB, TRIP9	uc002ojw.3	Q15653		ENST00000313582.5:c.1015C>T	19.37:g.39399416C>T	ENSP00000312988:p.Arg339Trp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_002503	A8K3F4|Q96BJ7	Missense_Mutation	SNP	ENST00000313582.5	37	CCDS12524.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.739866	0.30865	0.0	3.49E-4	ENSG00000104825	ENST00000313582	T	0.54675	0.56	5.08	0.314	0.15847	.	1.956000	0.02482	N	0.088598	T	0.36690	0.0976	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.28650	-1.0037	10	0.56958	D	0.05	1.3469	2.9887	0.05977	0.1946:0.4876:0.0:0.3178	rs17886215;rs17886215	339	Q15653	IKBB_HUMAN	W	339	ENSP00000312988:R339W	ENSP00000312988:R339W	R	+	1	2	NFKBIB	44091256	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.182000	0.09726	0.293000	0.22520	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.547	NFKBIB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438155.1	NM_002503	
ZGRF1	55345	hgsc.bcm.edu	37	4	113524723	113524723	+	Missense_Mutation	SNP	G	G	A	rs17669218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	210	0	0		WXS	Illumina HiSeq	Phase_I	90	19	0.211111	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		
ACRV1	56	hgsc.bcm.edu	37	11	125547897	125547897	+	Silent	SNP	T	T	C	rs556986916|rs555402913	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125547897T>C	ENST00000533904.1	-	2	690	c.348A>G	c.(346-348)ggA>ggG	p.G116G	ACRV1_ENST00000530048.1_Silent_p.G61G|ACRV1_ENST00000425431.1_Intron|ACRV1_ENST00000527795.1_Silent_p.G46G|ACRV1_ENST00000315608.3_Silent_p.G116G|ACRV1_ENST00000445562.1_Intron|ACRV1_ENST00000348856.3_Silent_p.G61G|ACRV1_ENST00000345274.1_Silent_p.G46G|ACRV1_ENST00000353070.1_Intron|ACRV1_ENST00000453509.1_Silent_p.G46G			P26436	ASPX_HUMAN	acrosomal vesicle protein 1	116	4 X 4 AA repeats of S-G-E-H.|9 X 5 AA repeats of [SV]-G-E-Q-[PSA].				multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				kidney(1)|large_intestine(3)|lung(2)	6	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0179)|Lung NSC(97;0.0185)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0713)		AAGGCTGTTCTCCTGAAGGCT	0.527																																					p.G116G		Atlas-SNP	.											ACRV1,caecum,carcinoma,-1,1	ACRV1	21	1	0			c.A348G						scavenged	.						154.0	136.0	142.0					11																	125547897		2201	4299	6500	SO:0001819	synonymous_variant	56	exon2			CTGTTCTCCTGAA	AK223335	CCDS8460.1, CCDS8461.1, CCDS44759.1, CCDS44761.1	11q24.2	2012-05-16			ENSG00000134940	ENSG00000134940			127	protein-coding gene	gene with protein product	"""sperm protein 10"""	102525				1693291, 8288254	Standard	NM_001612		Approved	SPACA2, SP-10, D11S4365	uc001qcs.3	P26436	OTTHUMG00000165854	ENST00000533904.1:c.348A>G	11.37:g.125547897T>C		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	376	4	0.0106383	NM_001612	Q53FF4	Silent	SNP	ENST00000533904.1	37	CCDS8460.1																																																																																			.	.	none		0.527	ACRV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386722.1	NM_001612	
TNS1	7145	hgsc.bcm.edu	37	2	218682771	218682771	+	Silent	SNP	A	A	G	rs3796026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:218682771A>G	ENST00000171887.4	-	24	4424	c.3972T>C	c.(3970-3972)ggT>ggC	p.G1324G	TNS1_ENST00000419504.1_Silent_p.G1311G|TNS1_ENST00000430930.1_Silent_p.G1303G	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1324					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)		TAGAATAGCCACCATAGGCCA	0.657													A|||	1667	0.332867	0.2443	0.4121	5008	,	,		16095	0.246		0.4056	False		,,,				2504	0.411				p.G1324G		Atlas-SNP	.											.	TNS1	251	.	0			c.T3972C						PASS	.	A		1033,3371		148,737,1317	21.0	22.0	22.0		3972	-6.1	1.0	2	dbSNP_107	22	3418,5176		734,1950,1613	no	coding-synonymous	TNS1	NM_022648.4		882,2687,2930	GG,GA,AA		39.7719,23.4559,34.2437		1324/1736	218682771	4451,8547	2202	4297	6499	SO:0001819	synonymous_variant	7145	exon24			ATAGCCACCATAG	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.3972T>C	2.37:g.218682771A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			A|0.689;G|0.311	0.311	strong		0.657	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
GHRHR	2692	hgsc.bcm.edu	37	7	31011677	31011677	+	Silent	SNP	C	C	T	rs740336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:31011677C>T	ENST00000326139.2	+	6	610	c.564C>T	c.(562-564)caC>caT	p.H188H	GHRHR_ENST00000409316.1_Missense_Mutation_p.T6I|GHRHR_ENST00000461424.1_3'UTR|GHRHR_ENST00000409904.3_Silent_p.H124H	NM_000823.3	NP_000814.2	Q02643	GHRHR_HUMAN	growth hormone releasing hormone receptor	188					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP-mediated signaling (GO:0019933)|cell maturation (GO:0048469)|cellular response to insulin stimulus (GO:0032869)|determination of adult lifespan (GO:0008340)|growth hormone secretion (GO:0030252)|hormone metabolic process (GO:0042445)|lactation (GO:0007595)|multicellular organismal reproductive process (GO:0048609)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of multicellular organism growth (GO:0040018)|regulation of intracellular steroid hormone receptor signaling pathway (GO:0033143)|regulation of protein metabolic process (GO:0051246)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|somatotropin secreting cell development (GO:0060133)|water homeostasis (GO:0030104)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nuclear matrix (GO:0016363)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	G-protein coupled receptor activity (GO:0004930)|growth factor binding (GO:0019838)|growth hormone-releasing hormone receptor activity (GO:0016520)|peptide hormone binding (GO:0017046)			biliary_tract(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(18)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35					Sermorelin(DB00010)|Tesamorelin(DB08869)	CCCTTTTCCACAGCGACGACA	0.587													C|||	299	0.0597045	0.1301	0.0231	5008	,	,		18976	0.005		0.0239	False		,,,				2504	0.0838				p.H188H		Atlas-SNP	.											.	GHRHR	55	.	0			c.C564T						PASS	.	C		487,3919	229.8+/-244.2	26,435,1742	109.0	80.0	90.0		564	-6.8	0.0	7	dbSNP_86	90	191,8409	85.0+/-147.5	1,189,4110	no	coding-synonymous	GHRHR	NM_000823.3		27,624,5852	TT,TC,CC		2.2209,11.0531,5.213		188/424	31011677	678,12328	2203	4300	6503	SO:0001819	synonymous_variant	2692	exon6			TTTCCACAGCGAC		CCDS5432.1	7p14	2012-08-10			ENSG00000106128	ENSG00000106128		"""GPCR / Class B : Glucagon receptors"""	4266	protein-coding gene	gene with protein product		139191				7680413, 7514564	Standard	NM_000823		Approved		uc003tbx.3	Q02643	OTTHUMG00000152801	ENST00000326139.2:c.564C>T	7.37:g.31011677C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	170	52	0.305882	NM_000823	Q99863	Silent	SNP	ENST00000326139.2	37	CCDS5432.1	96	0.04395604395604396	65	0.13211382113821138	11	0.03038674033149171	1	0.0017482517482517483	19	0.025065963060686015	C	9.268	1.044992	0.19748	0.110531	0.022209	ENSG00000106128	ENST00000409316	.	.	.	4.57	-6.82	0.01698	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.50632	P	1.2000000000000899E-4	B	0.28933	0.228	B	0.20955	0.032	T	0.18650	-1.0330	6	0.87932	D	0	.	1.8357	0.03139	0.2142:0.1391:0.3996:0.2471	rs740336;rs9718454;rs56649853;rs740336	6	Q9HB43	.	I	6	.	ENSP00000386602:T6I	T	+	2	0	GHRHR	30978202	0.000000	0.05858	0.000000	0.03702	0.148000	0.21650	-3.064000	0.00622	-1.131000	0.02910	0.561000	0.74099	ACA	C|0.943;T|0.057	0.057	strong		0.587	GHRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327967.2		
HLA-C	3107	hgsc.bcm.edu	37	6	31238068	31238068	+	Missense_Mutation	SNP	C	C	T	rs1050276	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31238068C>T	ENST00000376228.5	-	4	828	c.814G>A	c.(814-816)Gtg>Atg	p.V272M	HLA-C_ENST00000383329.3_Missense_Mutation_p.V272M	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	272	Alpha-3.|Ig-like C1-type.		V -> M (in dbSNP:rs1050276).		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						GAAGGCACCACCACAGCTGCC	0.622													C|||	347	0.0692891	0.0076	0.0994	5008	,	,		16190	0.1905		0.0368	False		,,,				2504	0.0399				p.V272M		Atlas-SNP	.											.	HLA-C	92	.	0			c.G814A						PASS	.	C	MET/VAL	33,4373		0,33,2170	47.0	41.0	43.0		814	1.7	1.0	6	dbSNP_86	43	269,8331		4,261,4035	no	missense	HLA-C	NM_002117.5	21	4,294,6205	TT,TC,CC		3.1279,0.749,2.322	benign	272/367	31238068	302,12704	2203	4300	6503	SO:0001583	missense	3107	exon4			GCACCACCACAGC	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.814G>A	6.37:g.31238068C>T	ENSP00000365402:p.Val272Met	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	222	75	0.337838	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	148|148	0.06776556776556776|0.06776556776556776	3|3	0.006097560975609756|0.006097560975609756	28|28	0.07734806629834254|0.07734806629834254	93|93	0.16258741258741258|0.16258741258741258	24|24	0.0316622691292876|0.0316622691292876	.|.	1.486|1.486	-0.555821|-0.555821	0.03967|0.03967	0.00749|0.00749	0.031279|0.031279	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.02837|.	4.14;4.14|.	2.67|2.67	1.71|1.71	0.24356|0.24356	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);|.	1.048890|.	0.07676|.	U|.	0.936276|.	T|.	0.45716|.	0.1356|.	M|M	0.77820|0.77820	2.39|2.39	0.43457|0.43457	P|P	0.0043480000000000185|0.0043480000000000185	B;B;B;B|.	0.23490|.	0.086;0.004;0.004;0.008|.	B;B;B;B|.	0.25405|.	0.06;0.008;0.026;0.031|.	T|.	0.41840|.	-0.9486|.	9|.	0.66056|.	D|.	0.02|.	.|.	7.132|7.132	0.25507|0.25507	0.0:0.718:0.282:0.0|0.0:0.718:0.282:0.0	rs1050276;rs2308619;rs3177863;rs17840046|rs1050276;rs2308619;rs3177863;rs17840046	272;272;272;272|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	M|X	272;272;272;309|235	ENSP00000365402:V272M;ENSP00000372819:V272M|.	ENSP00000365402:V272M|.	V|W	-|-	1|3	0|0	HLA-C|HLA-C	31346047|31346047	0.701000|0.701000	0.27806|0.27806	0.983000|0.983000	0.44433|0.44433	0.246000|0.246000	0.25737|0.25737	1.404000|1.404000	0.34623|0.34623	0.631000|0.631000	0.30412|0.30412	0.298000|0.298000	0.19748|0.19748	GTG|TGG	C|0.963;T|0.037	0.037	strong		0.622	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
GPATCH1	55094	hgsc.bcm.edu	37	19	33579128	33579128	+	Silent	SNP	T	T	C	rs7259333	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:33579128T>C	ENST00000170564.2	+	2	476	c.162T>C	c.(160-162)agT>agC	p.S54S		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	54					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)					GGGCCTTTAGTGGAGGTTTCT	0.363													C|||	2674	0.533946	0.8018	0.2867	5008	,	,		13444	0.5099		0.2416	False		,,,				2504	0.6728				p.S54S	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.T162C						PASS	.	C		3204,1202	416.7+/-337.7	1159,886,158	96.0	101.0	99.0		162	-4.0	0.7	19	dbSNP_116	99	2313,6287	705.1+/-405.5	284,1745,2271	no	coding-synonymous	GPATCH1	NM_018025.2		1443,2631,2429	CC,CT,TT		26.8953,27.281,42.4189		54/932	33579128	5517,7489	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon2			CTTTAGTGGAGGT	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.162T>C	19.37:g.33579128T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	150	69	0.46	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			T|0.549;C|0.451	0.451	strong		0.363	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
CNOT11	55571	hgsc.bcm.edu	37	2	101879023	101879023	+	Silent	SNP	G	G	A	rs1007752	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:101879023G>A	ENST00000289382.3	+	3	865	c.702G>A	c.(700-702)acG>acA	p.T234T		NM_017546.4	NP_060016.3	Q9UKZ1	CNO11_HUMAN	CCR4-NOT transcription complex, subunit 11	234					cell proliferation (GO:0008283)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|nucleus (GO:0005634)											AATTGCCAACGCAAAGCAAAG	0.443													G|||	72	0.014377	0.0015	0.0317	5008	,	,		16489	0.0		0.0408	False		,,,				2504	0.0072				p.T234T		Atlas-SNP	.											.	.	.	.	0			c.G702A						PASS	.	G		31,4375	39.2+/-71.8	0,31,2172	89.0	88.0	88.0		702	-11.6	0.4	2	dbSNP_86	88	403,8197	127.8+/-186.1	11,381,3908	no	coding-synonymous	C2orf29	NM_017546.4		11,412,6080	AA,AG,GG		4.686,0.7036,3.3369		234/511	101879023	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	55571	exon3			GCCAACGCAAAGC	AF103798	CCDS2050.1	2q12.1	2013-01-24	2013-01-24	2013-01-24	ENSG00000158435	ENSG00000158435			25217	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 29"""	C2orf29		10497265, 23232451, 23303381	Standard	NM_017546		Approved	C40	uc002taw.4	Q9UKZ1	OTTHUMG00000130686	ENST00000289382.3:c.702G>A	2.37:g.101879023G>A		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	238	128	0.537815	NM_017546	Q6P2M9|Q8N681	Silent	SNP	ENST00000289382.3	37	CCDS2050.1																																																																																			G|0.972;A|0.028	0.028	strong		0.443	CNOT11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253181.1	NM_017546	
CEACAM6	4680	hgsc.bcm.edu	37	19	42260569	42260569	+	Silent	SNP	G	G	A	rs1805223	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:42260569G>A	ENST00000199764.6	+	2	344	c.126G>A	c.(124-126)ccG>ccA	p.P42P	AC011513.4_ENST00000601409.1_RNA|CEA_ENST00000598976.1_Intron	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	42	Ig-like V-type.				cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.P42P(1)		breast(1)|kidney(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		AATCCACGCCGTTCAATGTCG	0.527													g|||	1280	0.255591	0.1399	0.2911	5008	,	,		18831	0.2738		0.2873	False		,,,				2504	0.3354				p.P42P		Atlas-SNP	.											CEACAM6,NS,carcinoma,0,1	CEACAM6	52	1	1	Substitution - coding silent(1)	stomach(1)	c.G126A						PASS	.	G		745,3661	305.5+/-289.0	63,619,1521	170.0	156.0	161.0		126	-5.1	0.0	19	dbSNP_92	161	2502,6098	410.2+/-350.1	384,1734,2182	no	coding-synonymous	CEACAM6	NM_002483.4		447,2353,3703	AA,AG,GG		29.093,16.9088,24.9654		42/345	42260569	3247,9759	2203	4300	6503	SO:0001819	synonymous_variant	4680	exon2			CACGCCGTTCAAT	M29541	CCDS12585.1	19q13.1-q13.2	2013-01-29			ENSG00000086548	ENSG00000086548		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1818	protein-coding gene	gene with protein product		163980		NCA			Standard	NM_002483		Approved	CD66c	uc002orm.2	P40199	OTTHUMG00000151064	ENST00000199764.6:c.126G>A	19.37:g.42260569G>A		Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	239	129	0.539749	NM_002483	Q13774|Q14920|Q53XP7	Silent	SNP	ENST00000199764.6	37	CCDS12585.1																																																																																			.	.	weak		0.527	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1		
CEP112	201134	hgsc.bcm.edu	37	17	64023624	64023624	+	Missense_Mutation	SNP	T	T	C	rs17704679	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:64023624T>C	ENST00000392769.2	-	16	1869	c.1651A>G	c.(1651-1653)Aaa>Gaa	p.K551E	CEP112_ENST00000541355.1_Missense_Mutation_p.K186E|CEP112_ENST00000535342.2_Missense_Mutation_p.K551E|CEP112_ENST00000537949.1_Missense_Mutation_p.K509E	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	551			K -> E (in dbSNP:rs17704679). {ECO:0000269|PubMed:14702039}.		receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						ATTACCTTTTTTTCATAGATG	0.239													T|||	1908	0.38099	0.5991	0.317	5008	,	,		16784	0.0913		0.5249	False		,,,				2504	0.2822				p.K551E		Atlas-SNP	.											.	CEP112	192	.	0			c.A1651G						PASS	.	T	GLU/LYS,GLU/LYS	2540,1732		783,974,379	31.0	31.0	31.0		1651,1651	3.3	1.0	17	dbSNP_123	31	4730,3652		1396,1938,857	yes	missense,missense	CEP112	NM_001199165.1,NM_145036.3	56,56	2179,2912,1236	CC,CT,TT		43.5696,40.5431,42.5478	benign,benign	551/956,551/956	64023624	7270,5384	2136	4191	6327	SO:0001583	missense	201134	exon16			CCTTTTTTTCATA	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.1651A>G	17.37:g.64023624T>C	ENSP00000376522:p.Lys551Glu	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	228	127	0.557018	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Missense_Mutation	SNP	ENST00000392769.2	37	CCDS32710.1	875	0.40064102564102566	288	0.5853658536585366	123	0.3397790055248619	66	0.11538461538461539	398	0.525065963060686	T	17.86	3.491676	0.64074	0.594569	0.564304	ENSG00000154240	ENST00000535342;ENST00000392769;ENST00000541355;ENST00000537949	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	5.51	3.27	0.37495	.	0.286088	0.37530	N	0.002050	T	0.00012	0.0000	L	0.39397	1.21	0.35545	P	0.19661399999999996	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.39078	-0.9631	9	0.14252	T	0.57	-4.5094	9.033	0.36271	0.0:0.1516:0.0:0.8484	rs17704679;rs17704679	509;551	F5GYE8;Q8N8E3	.;CE112_HUMAN	E	551;551;186;509	ENSP00000442784:K551E;ENSP00000376522:K551E;ENSP00000443711:K186E;ENSP00000440775:K509E	ENSP00000376522:K551E	K	-	1	0	CEP112	61454086	0.998000	0.40836	0.982000	0.44146	0.996000	0.88848	3.243000	0.51392	0.877000	0.35895	0.528000	0.53228	AAA	C|0.474;N|0.000	0.474	strong		0.239	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
ITPR2	3709	hgsc.bcm.edu	37	12	26810777	26810777	+	Silent	SNP	T	T	C	rs2291264	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:26810777T>C	ENST00000381340.3	-	18	2471	c.2055A>G	c.(2053-2055)tcA>tcG	p.S685S		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	685					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)	CAATGTCATCTGAAAGGATGG	0.408													C|||	1990	0.397364	0.1921	0.4524	5008	,	,		19311	0.6518		0.3628	False		,,,				2504	0.409				p.S685S		Atlas-SNP	.											.	ITPR2	270	.	0			c.A2055G						PASS	.	C		830,2970		97,636,1167	114.0	106.0	108.0		2055	-4.6	0.1	12	dbSNP_100	108	2898,5330		505,1888,1721	no	coding-synonymous	ITPR2	NM_002223.2		602,2524,2888	CC,CT,TT		35.2212,21.8421,30.9943		685/2702	26810777	3728,8300	1900	4114	6014	SO:0001819	synonymous_variant	3709	exon18			GTCATCTGAAAGG	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.2055A>G	12.37:g.26810777T>C		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	230	103	0.447826	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.606;C|0.394	0.394	strong		0.408	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
DYNC2H1	79659	hgsc.bcm.edu	37	11	102991197	102991197	+	Missense_Mutation	SNP	C	C	T	rs17301182	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102991197C>T	ENST00000375735.2	+	7	1165	c.1021C>T	c.(1021-1023)Cat>Tat	p.H341Y	DYNC2H1_ENST00000334267.7_Missense_Mutation_p.H341Y|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.H341Y	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	341	Stem. {ECO:0000250}.		H -> Y (in dbSNP:rs17301182).		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)		TAGAACAATTCATGAGAAGTT	0.318													C|||	359	0.0716853	0.0053	0.0908	5008	,	,		14191	0.0933		0.1252	False		,,,				2504	0.0706				p.H341Y		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.C1021T						PASS	.	C	TYR/HIS,TYR/HIS	124,3480		2,120,1680	100.0	100.0	100.0		1021,1021	4.0	1.0	11	dbSNP_123	100	937,7189		59,819,3185	yes	missense,missense	DYNC2H1	NM_001080463.1,NM_001377.2	83,83	61,939,4865	TT,TC,CC		11.5309,3.4406,9.0452	benign,benign	341/4315,341/4308	102991197	1061,10669	1802	4063	5865	SO:0001583	missense	79659	exon7			ACAATTCATGAGA	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.1021C>T	11.37:g.102991197C>T	ENSP00000364887:p.His341Tyr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	137	102	0.744526	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	192	0.08791208791208792	5	0.01016260162601626	33	0.09116022099447514	49	0.08566433566433566	105	0.13852242744063326	C	10.31	1.313794	0.23908	0.034406	0.115309	ENSG00000187240	ENST00000375735;ENST00000334267;ENST00000398093	T;T;T	0.59502	0.26;0.26;0.26	4.89	3.95	0.45737	Dynein heavy chain, domain-1 (1);	0.698644	0.12319	U	0.479443	T	0.00666	0.0022	L	0.49350	1.555	0.23473	P	0.99760364	P;B;B	0.41848	0.763;0.085;0.087	B;B;B	0.43783	0.431;0.173;0.17	T	0.17410	-1.0370	9	0.48119	T	0.1	.	14.57	0.68205	0.1474:0.8526:0.0:0.0	rs17301182;rs17301182	341;341;341	Q8NCM8-3;Q8NCM8;Q8NCM8-2	.;DYHC2_HUMAN;.	Y	341	ENSP00000364887:H341Y;ENSP00000334021:H341Y;ENSP00000381167:H341Y	ENSP00000334021:H341Y	H	+	1	0	DYNC2H1	102496407	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.609000	0.46317	1.142000	0.42291	0.585000	0.79938	CAT	C|0.912;N|0.001	.	strong		0.318	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
RPS15	6209	hgsc.bcm.edu	37	19	1440068	1440068	+	Missense_Mutation	SNP	G	G	C	rs201657403		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1440068G>C	ENST00000586686.2	+	3	179	c.140G>C	c.(139-141)cGg>cCg	p.R47P	RPS15_ENST00000589656.2_Missense_Mutation_p.R47P|AC027307.3_ENST00000594262.1_5'Flank|RPS15_ENST00000591032.1_Missense_Mutation_p.R14P|RPS15_ENST00000591804.2_Missense_Mutation_p.R14P|RPS15_ENST00000586096.2_Missense_Mutation_p.R47P|RPS15_ENST00000585665.1_Missense_Mutation_p.R14P|RPS15_ENST00000233609.4_Missense_Mutation_p.R20P|RPS15_ENST00000593052.1_Missense_Mutation_p.R54P			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	49	1	0.0204082		WXS	Illumina HiSeq	Phase_I	39	7	0.179487	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	
OXER1	165140	hgsc.bcm.edu	37	2	42990336	42990336	+	Silent	SNP	T	T	G	rs1992286	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:42990336T>G	ENST00000378661.2	-	1	1065	c.984A>C	c.(982-984)cgA>cgC	p.R328R		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	328					G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						GGTCCAGGGATCGGCAGGCGG	0.592													.|||	3907	0.780152	0.9569	0.7536	5008	,	,		16668	0.8165		0.5408	False		,,,				2504	0.7689				p.R328R		Atlas-SNP	.											OXER1,NS,carcinoma,0,1	OXER1	33	1	0			c.A984C						scavenged	.	G		3884,522	231.4+/-245.2	1712,460,31	41.0	44.0	43.0		984	-2.6	0.0	2	dbSNP_92	43	4706,3894	534.2+/-382.6	1271,2164,865	no	coding-synonymous	OXER1	NM_148962.4		2983,2624,896	GG,GT,TT		45.2791,11.8475,33.9536		328/424	42990336	8590,4416	2203	4300	6503	SO:0001819	synonymous_variant	165140	exon1			CAGGGATCGGCAG	AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"""GPCR / Class A : Leukotriene receptors"""	24884	protein-coding gene	gene with protein product	"""5-oxo-ETE acid G-protein-coupled receptor 1"""					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.984A>C	2.37:g.42990336T>G		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	162	77	0.475309	NM_148962	Q86WP7|Q8NGW4	Silent	SNP	ENST00000378661.2	37	CCDS1810.1																																																																																			G|0.690;N|0.002	0.690	strong		0.592	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962	
SIRPA	140885	hgsc.bcm.edu	37	20	1896059	1896059	+	Missense_Mutation	SNP	G	G	A	rs386811663|rs115287948	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1896059G>A	ENST00000358771.4	+	2	546	c.394G>A	c.(394-396)Gtg>Atg	p.V132M	SIRPA_ENST00000356025.3_Missense_Mutation_p.V132M|SIRPA_ENST00000400068.3_Missense_Mutation_p.V132M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	132	Ig-like V-type.		V -> T (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CCCCGATGACGTGGAGTTTAA	0.527													G|||	2050	0.409345	0.2761	0.4222	5008	,	,		15841	0.625		0.3171	False		,,,				2504	0.453				p.V132M	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,caecum,carcinoma,0,2	SIRPA	83	2	0			c.G394A						scavenged	.						108.0	93.0	98.0					20																	1896059		2198	4290	6488	SO:0001583	missense	140885	exon3			GATGACGTGGAGT	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.394G>A	20.37:g.1896059G>A	ENSP00000351621:p.Val132Met	Somatic	435	4	0.0091954		WXS	Illumina HiSeq	Phase_I	228	25	0.109649	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	G	9.326	1.059262	0.19987	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.64991	-0.13;-0.13;-0.13	5.11	-2.28	0.06826	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	2.497550	0.01234	N	0.008420	T	0.49558	0.1564	L	0.28192	0.835	0.80722	P	0.0	B;B;B	0.27765	0.084;0.005;0.188	B;B;B	0.27887	0.057;0.01;0.084	T	0.39702	-0.9601	9	0.33141	T	0.24	.	9.8059	0.40792	0.7439:0.0:0.2561:0.0	.	112;132;132	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	M	132	ENSP00000382941:V132M;ENSP00000348307:V132M;ENSP00000351621:V132M	ENSP00000348307:V132M	V	+	1	0	SIRPA	1844059	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.421000	0.07053	-0.198000	0.10333	-1.101000	0.02118	GTG	G|0.679;A|0.321	0.321	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
OR4B1	119765	hgsc.bcm.edu	37	11	48238880	48238880	+	Silent	SNP	C	C	T	rs10838833	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	312	0	0		WXS	Illumina HiSeq	Phase_I	272	140	0.514706	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	
RDH13	112724	hgsc.bcm.edu	37	19	55559715	55559715	+	Silent	SNP	G	G	A	rs2305543	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55559715G>A	ENST00000415061.3	-	5	783	c.640C>T	c.(640-642)Ctg>Ttg	p.L214L	CTC-550B14.7_ENST00000593060.1_RNA|RDH13_ENST00000396247.3_Silent_p.L143L|CTC-550B14.6_ENST00000585492.1_RNA	NM_001145971.1	NP_001139443.1	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 (all-trans/9-cis)	214					eye photoreceptor cell development (GO:0042462)|response to high light intensity (GO:0009644)|retina layer formation (GO:0010842)	mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	CGCCGGCTCAGCTCCTTGGTG	0.582													.|||	1574	0.314297	0.2799	0.2219	5008	,	,		19412	0.4593		0.2485	False		,,,				2504	0.3446				p.L214L		Atlas-SNP	.											.	RDH13	43	.	0			c.C640T						PASS	.	G	,	1016,2940		127,762,1089	49.0	51.0	50.0		640,427	3.2	1.0	19	dbSNP_100	50	2065,6275		234,1597,2339	no	coding-synonymous,coding-synonymous	RDH13	NM_001145971.1,NM_138412.3	,	361,2359,3428	AA,AG,GG		24.7602,25.6825,25.0569	,	214/332,143/261	55559715	3081,9215	1978	4170	6148	SO:0001819	synonymous_variant	112724	exon5			GGCTCAGCTCCTT		CCDS42627.1, CCDS54320.1	19q13.42	2011-09-14	2006-05-09			ENSG00000160439	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19978	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 3"""		"""retinol dehydrogenase 13 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_138412		Approved	SDR7C3	uc002qio.3	Q8NBN7		ENST00000415061.3:c.640C>T	19.37:g.55559715G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_001145971	Q6UX79|Q96G88	Silent	SNP	ENST00000415061.3	37	CCDS54320.1																																																																																			G|0.701;A|0.299	0.299	strong		0.582	RDH13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451470.1	NM_138412	
AKAP6	9472	hgsc.bcm.edu	37	14	33014876	33014876	+	Silent	SNP	C	C	T	rs375820695		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:33014876C>T	ENST00000280979.4	+	4	1187	c.1017C>T	c.(1015-1017)ccC>ccT	p.P339P	AKAP6_ENST00000557354.1_Silent_p.P339P|AKAP6_ENST00000557272.1_Silent_p.P339P	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	339					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)		CTGCTCAACCCTCCTCTGAGA	0.498																																					p.P339P	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.C1017T						PASS	.	C		0,4406		0,0,2203	71.0	62.0	65.0		1017	0.4	0.0	14		65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AKAP6	NM_004274.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		339/2320	33014876	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9472	exon4			TCAACCCTCCTCT	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.1017C>T	14.37:g.33014876C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	123	51	0.414634	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	37	CCDS9644.1																																																																																			.	.	weak		0.498	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
MYOM2	9172	hgsc.bcm.edu	37	8	2046700	2046700	+	Missense_Mutation	SNP	C	C	T	rs2294066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	80	0	0		WXS	Illumina HiSeq	Phase_I	89	25	0.280899	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	
NUDT6	11162	hgsc.bcm.edu	37	4	123814308	123814308	+	Missense_Mutation	SNP	C	C	T	rs1048201	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:123814308C>T	ENST00000304430.5	-	5	659	c.626G>A	c.(625-627)cGg>cAg	p.R209Q	NUDT6_ENST00000339154.2_Missense_Mutation_p.R40Q|FGF2_ENST00000264498.3_3'UTR|NUDT6_ENST00000608639.1_5'Flank|NUDT6_ENST00000502270.1_Missense_Mutation_p.R40Q|FGF2_ENST00000608478.1_3'UTR	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	209	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.		R -> Q (in dbSNP:rs1048201).			mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)	p.R40Q(2)|p.R209Q(1)		endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						GTGCTGTTGCCGAATACTCAG	0.403													C|||	1146	0.228834	0.0416	0.1499	5008	,	,		18285	0.4554		0.1779	False		,,,				2504	0.3569				p.R209Q		Atlas-SNP	.											NUDT6_ENST00000304430,NS,carcinoma,0,3	NUDT6	50	3	3	Substitution - Missense(3)	prostate(2)|stomach(1)	c.G626A	GRCh37	CM065349	NUDT6	M	rs1048201	PASS	.	C	,GLN/ARG,GLN/ARG	289,4117	158.9+/-191.5	10,269,1924	87.0	91.0	90.0		,626,119	5.4	1.0	4	dbSNP_86	90	1501,7099	284.4+/-296.6	136,1229,2935	yes	utr-3,missense,missense	FGF2,NUDT6	NM_002006.4,NM_007083.3,NM_198041.1	,43,43	146,1498,4859	TT,TC,CC		17.4535,6.5592,13.7629	,probably-damaging,probably-damaging	,209/317,40/148	123814308	1790,11216	2203	4300	6503	SO:0001583	missense	11162	exon5			TGTTGCCGAATAC	AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"""Nudix motif containing"""	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.626G>A	4.37:g.123814308C>T	ENSP00000306070:p.Arg209Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	58	13	0.224138	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	472	0.21611721611721613	18	0.036585365853658534	56	0.15469613259668508	262	0.458041958041958	136	0.17941952506596306	C	33	5.258099	0.95368	0.065592	0.174535	ENSG00000170917	ENST00000304430;ENST00000339154;ENST00000502270	T;T;T	0.07688	3.17;3.17;3.17	5.41	5.41	0.78517	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.89840	3.065	0.09310	P	0.99999999579817	D	0.89917	1.0	D	0.91635	0.999	T	0.41233	-0.9520	9	0.66056	D	0.02	-11.2049	19.2326	0.93846	0.0:1.0:0.0:0.0	rs1048201;rs3172523;rs3804157;rs52813414;rs58707045;rs1048201	209	P53370	NUDT6_HUMAN	Q	209;40;40	ENSP00000306070:R209Q;ENSP00000344011:R40Q;ENSP00000424117:R40Q	ENSP00000306070:R209Q	R	-	2	0	NUDT6	124033758	1.000000	0.71417	0.998000	0.56505	0.948000	0.59901	7.013000	0.76373	2.538000	0.85594	0.650000	0.86243	CGG	C|0.825;T|0.175	0.175	strong		0.403	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083	
CACNA1B	774	hgsc.bcm.edu	37	9	140773613	140773613	+	Splice_Site	SNP	T	T	A	rs201604190		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:140773613T>A	ENST00000371372.1	+	2	535		c.e2+2		CACNA1B_ENST00000371363.1_Splice_Site|CACNA1B_ENST00000277551.2_Splice_Site|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371357.1_Splice_Site|CACNA1B_ENST00000277549.5_Splice_Site|CACNA1B_ENST00000371355.4_Splice_Site	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit						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)	p.?(2)		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)	GAGCGGCTGGTGAGTGCCCGG	0.632																																					.		Atlas-SNP	.											CACNA1B,colon,carcinoma,0,8	CACNA1B	266	8	2	Unknown(2)	lung(1)|breast(1)	c.390+2T>A						scavenged	.						25.0	29.0	28.0					9																	140773613		2104	4235	6339	SO:0001630	splice_region_variant	774	exon2			GGCTGGTGAGTGC	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.390+2T>A	9.37:g.140773613T>A		Somatic	59	2	0.0338983		WXS	Illumina HiSeq	Phase_I	68	10	0.147059	NM_001243812	B1AQK5	Splice_Site	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.975539	0.74360	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357;ENST00000371355	.	.	.	4.73	3.57	0.40892	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6445	0.51253	0.0:0.0:0.1485:0.8515	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1B	139893434	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.830000	0.86741	0.644000	0.30656	0.459000	0.35465	.	.	.	weak		0.632	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	Intron
VEZT	55591	hgsc.bcm.edu	37	12	95694111	95694111	+	Missense_Mutation	SNP	T	T	G	rs17855934	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:95694111T>G	ENST00000436874.1	+	12	2107	c.2002T>G	c.(2002-2004)Tct>Gct	p.S668A	VEZT_ENST00000356859.4_3'UTR|VEZT_ENST00000261219.6_Missense_Mutation_p.S620A	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	668			S -> A (in dbSNP:rs17855934).		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						ATGTGAAAACTCTCTAGAAGG	0.348													T|||	368	0.0734824	0.0885	0.0908	5008	,	,		18124	0.001		0.1074	False		,,,				2504	0.0808				p.S668A		Atlas-SNP	.											.	VEZT	106	.	0			c.T2002G						PASS	.	T	ALA/SER	285,3407		13,259,1574	41.0	38.0	39.0		2002	4.2	0.2	12	dbSNP_123	39	859,7325		47,765,3280	yes	missense	VEZT	NM_017599.3	99	60,1024,4854	GG,GT,TT		10.4961,7.7194,9.6329	benign	668/780	95694111	1144,10732	1846	4092	5938	SO:0001583	missense	55591	exon12			GAAAACTCTCTAG	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.2002T>G	12.37:g.95694111T>G	ENSP00000410083:p.Ser668Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	150	69	0.46	NM_017599	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Missense_Mutation	SNP	ENST00000436874.1	37	CCDS44954.1	155	0.07097069597069597	35	0.07113821138211382	36	0.09944751381215469	1	0.0017482517482517483	83	0.10949868073878628	T	2.500	-0.315303	0.05422	0.077194	0.104961	ENSG00000028203	ENST00000436874;ENST00000261219;ENST00000397792;ENST00000397796	T;T;T	0.14022	2.54;2.54;2.54	6.02	4.15	0.48705	.	0.352986	0.34777	N	0.003681	T	0.00144	0.0004	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.28490	-1.0042	9	0.29301	T	0.29	-41.0968	6.6237	0.22818	0.0:0.664:0.129:0.207	rs17855934;rs17855934	668	Q9HBM0	VEZA_HUMAN	A	668;620;624;668	ENSP00000410083:S668A;ENSP00000261219:S620A;ENSP00000380894:S624A	ENSP00000261219:S620A	S	+	1	0	VEZT	94218242	0.014000	0.17966	0.215000	0.23724	0.380000	0.30137	0.984000	0.29565	0.872000	0.35775	-0.182000	0.12963	TCT	T|0.924;G|0.076	0.076	strong		0.348	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599	
CST5	1473	hgsc.bcm.edu	37	20	23860178	23860178	+	Missense_Mutation	SNP	A	A	G	rs1799841	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:23860178A>G	ENST00000304710.4	-	1	209	c.136T>C	c.(136-138)Tgt>Cgt	p.C46R		NM_001900.4	NP_001891.2	P28325	CYTD_HUMAN	cystatin D	46			C -> R (in 45% of the population; dbSNP:rs1799841). {ECO:0000269|PubMed:8444475}.		negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.C46R(1)		breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|stomach(1)	11						TCCAGGGCACACTGCACACTC	0.577													g|||	2830	0.565096	0.8139	0.5476	5008	,	,		17019	0.494		0.4453	False		,,,				2504	0.4376				p.C46R		Atlas-SNP	.											CST5,NS,carcinoma,0,1	CST5	24	1	1	Substitution - Missense(1)	stomach(1)	c.T136C						scavenged	.	G	ARG/CYS	3301,1105		1250,801,152	182.0	166.0	171.0		136	-0.4	0.0	20	dbSNP_89	171	3740,4860		816,2108,1376	yes	missense	CST5	NM_001900.4	180	2066,2909,1528	GG,GA,AA		43.4884,25.0794,45.8634	benign	46/143	23860178	7041,5965	2203	4300	6503	SO:0001583	missense	1473	exon1			GGGCACACTGCAC		CCDS13162.1	20p11.21	2008-04-15			ENSG00000170367	ENSG00000170367			2477	protein-coding gene	gene with protein product		123858				1939105	Standard	NM_001900		Approved		uc002wtr.1	P28325	OTTHUMG00000032089	ENST00000304710.4:c.136T>C	20.37:g.23860178A>G	ENSP00000307132:p.Cys46Arg	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_001900	Q5JRF5|Q9UCA0	Missense_Mutation	SNP	ENST00000304710.4	37	CCDS13162.1	1186	0.543040293040293	389	0.790650406504065	192	0.5303867403314917	270	0.47202797202797203	335	0.4419525065963061	N	0.003	-2.500876	0.00157	0.749206	0.434884	ENSG00000170367	ENST00000304710	T	0.24723	1.84	1.99	-0.399	0.12415	Proteinase inhibitor I25, cystatin (2);	0.860793	0.10208	N	0.702474	T	0.00012	0.0000	N	0.00054	-2.38	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37526	-0.9702	9	0.06757	T	0.87	.	0.8314	0.01131	0.162:0.2324:0.3697:0.236	rs1799841;rs52827118;rs61231587;rs1799841	46	P28325	CYTD_HUMAN	R	46	ENSP00000307132:C46R	ENSP00000307132:C46R	C	-	1	0	CST5	23808178	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.217000	0.02979	-0.410000	0.07542	-0.380000	0.06706	TGT	A|0.455;G|0.545	0.545	strong		0.577	CST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078355.2	NM_001900	
MYT1	4661	hgsc.bcm.edu	37	20	62850358	62850358	+	Silent	SNP	C	C	T	rs41279348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62850358C>T	ENST00000328439.1	+	12	2305	c.1941C>T	c.(1939-1941)ctC>ctT	p.L647L	MYT1_ENST00000536311.1_Silent_p.L674L|MYT1_ENST00000360149.4_Silent_p.L349L	NM_004535.2	NP_004526.1	Q99640	PMYT1_HUMAN	myelin transcription factor 1	0					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(12)|liver(1)|lung(17)|ovary(5)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55	all_cancers(38;1.82e-11)|all_epithelial(29;3.3e-13)|Lung NSC(23;5.21e-10)|all_lung(23;1.92e-09)					CTGAGAACCTCAGCACGAAGC	0.592													C|||	398	0.0794728	0.0234	0.0821	5008	,	,		19551	0.0685		0.1282	False		,,,				2504	0.1145				p.L647L	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.C1941T						PASS	.	C		197,4209	123.7+/-161.0	5,187,2011	60.0	48.0	52.0		1941	5.3	1.0	20	dbSNP_127	52	1115,7485	229.6+/-264.2	72,971,3257	no	coding-synonymous	MYT1	NM_004535.2		77,1158,5268	TT,TC,CC		12.9651,4.4712,10.0877		647/1122	62850358	1312,11694	2203	4300	6503	SO:0001819	synonymous_variant	4661	exon12			GAACCTCAGCACG	M96980	CCDS13558.1	20q13.33	2014-03-24			ENSG00000196132	ENSG00000196132		"""Zinc fingers, C2HC-type containing"""	7622	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 2"""	600379		PLPB1		1280325, 9268380	Standard	NM_004535		Approved	MTF1, MYTI, ZC2HC4A, NZF2	uc002yii.3	Q01538	OTTHUMG00000149988	ENST00000328439.1:c.1941C>T	20.37:g.62850358C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	130	67	0.515385	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	37	CCDS13558.1																																																																																			C|0.907;T|0.093	0.093	strong		0.592	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535	
MUC5B	727897	hgsc.bcm.edu	37	11	1265987	1265987	+	Missense_Mutation	SNP	C	C	G	rs3021158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1265987C>G	ENST00000529681.1	+	31	7935	c.7877C>G	c.(7876-7878)aCg>aGg	p.T2626R	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T2629R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2626	11 X approximate tandem repeats, Ser/Thr- rich.|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)		p.T2605R(1)		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)		AGCCCAGGGACGGCACGCACG	0.652													c|||	583	0.116414	0.0915	0.2147	5008	,	,		18972	0.0526		0.1302	False		,,,				2504	0.1319				p.T2626R		Atlas-SNP	.											MUC5AC,brain,glioma,0,1	MUC5B	473	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.C7877G						PASS	.	C	ARG/THR	357,3869		17,323,1773	138.0	169.0	159.0		7877	0.1	0.0	11	dbSNP_101	159	1041,7425		66,909,3258	no	missense	MUC5B	NM_002458.2	71	83,1232,5031	GG,GC,CC		12.2962,8.4477,11.0148	probably-damaging	2626/5763	1265987	1398,11294	2113	4233	6346	SO:0001583	missense	727897	exon31			CAGGGACGGCACG	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.7877C>G	11.37:g.1265987C>G	ENSP00000436812:p.Thr2626Arg	Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	262	138	0.526718	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	259	0.11858974358974358	39	0.07926829268292683	71	0.19613259668508287	43	0.07517482517482517	106	0.13984168865435356	c	3.340	-0.134883	0.06711	0.084477	0.122962	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000537836	T;T	0.19938	2.11;2.29	1.19	0.116	0.14647	.	.	.	.	.	T	0.00039	0.0001	M	0.63843	1.955	0.80722	P	0.0	D;D	0.64830	0.994;0.994	P;P	0.60682	0.878;0.878	T	0.08289	-1.0729	8	0.87932	D	0	.	6.8768	0.24151	0.0:0.8162:0.0:0.1838	.	3264;2629	A7Y9J9;E9PBJ0	.;.	R	2626;2629;2598;2641;167	ENSP00000436812:T2626R;ENSP00000415793:T2629R	ENSP00000343037:T2598R	T	+	2	0	MUC5B	1222563	0.307000	0.24500	0.000000	0.03702	0.007000	0.05969	0.522000	0.22909	0.036000	0.15547	0.205000	0.17691	ACG	C|0.873;G|0.127	0.127	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
GGT1	2678	hgsc.bcm.edu	37	22	25023444	25023444	+	Missense_Mutation	SNP	G	G	T	rs201546887	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:25023444G>T	ENST00000400382.1	+	12	1821	c.1066G>T	c.(1066-1068)Gcc>Tcc	p.A356S	GGT1_ENST00000400383.1_Missense_Mutation_p.A356S|GGT1_ENST00000401885.1_Missense_Mutation_p.A12S|GGT1_ENST00000406383.2_Missense_Mutation_p.A356S|GGT1_ENST00000404532.1_Missense_Mutation_p.A12S|GGT1_ENST00000248923.4_Missense_Mutation_p.A356S|GGT1_ENST00000403838.1_Missense_Mutation_p.A12S|GGT1_ENST00000400380.1_Missense_Mutation_p.A356S|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404223.1_Missense_Mutation_p.A12S|GGT1_ENST00000404920.1_Missense_Mutation_p.A12S			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	350	0	0		WXS	Illumina HiSeq	Phase_I	380	45	0.118421	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	
FMNL1	752	hgsc.bcm.edu	37	17	43316360	43316360	+	Silent	SNP	G	G	A	rs12940312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:43316360G>A	ENST00000331495.3	+	11	1344	c.1008G>A	c.(1006-1008)tcG>tcA	p.S336S	FMNL1_ENST00000587489.1_5'Flank|FMNL1_ENST00000592006.1_3'UTR|CTD-2020K17.3_ENST00000587534.1_RNA|CTD-2020K17.3_ENST00000393507.2_RNA|FMNL1_ENST00000328118.3_Silent_p.S336S	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	336	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						TGGTACATTCGGTGGAGAACA	0.537													G|||	565	0.112819	0.0061	0.0879	5008	,	,		23216	0.1339		0.1083	False		,,,				2504	0.2577				p.S336S	GBM(164;1247 1997 8702 11086 51972)	Atlas-SNP	.											.	FMNL1	78	.	0			c.G1008A						PASS	.	G		90,4316	75.7+/-113.9	1,88,2114	219.0	154.0	176.0		1008	-8.5	0.3	17	dbSNP_121	176	917,7683	204.8+/-247.4	50,817,3433	no	coding-synonymous	FMNL1	NM_005892.3		51,905,5547	AA,AG,GG		10.6628,2.0427,7.7426		336/1101	43316360	1007,11999	2203	4300	6503	SO:0001819	synonymous_variant	752	exon11			ACATTCGGTGGAG	AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"""formin-like"""	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.1008G>A	17.37:g.43316360G>A		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	289	142	0.491349	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Silent	SNP	ENST00000331495.3	37	CCDS11497.1																																																																																			G|0.919;A|0.081	0.081	strong		0.537	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892	
COG3	83548	hgsc.bcm.edu	37	13	46104849	46104849	+	Silent	SNP	C	C	T	rs62637564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:46104849C>T	ENST00000349995.5	+	22	2503	c.2391C>T	c.(2389-2391)caC>caT	p.H797H		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	797					ER to Golgi vesicle-mediated transport (GO:0006888)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|stomach(1)	24		Lung NSC(96;0.000145)|Breast(56;0.000596)|Prostate(109;0.00438)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000124)		AGAAGTTCCACGCTCTGTTAA	0.393													T|||	189	0.0377396	0.115	0.0144	5008	,	,		16886	0.0		0.0169	False		,,,				2504	0.0102				p.H797H	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.C2391T						PASS	.	T		363,4043		11,341,1851	114.0	109.0	111.0		2391	-3.4	0.3	13	dbSNP_129	111	174,8426		4,166,4130	no	coding-synonymous	COG3	NM_031431.3		15,507,5981	TT,TC,CC		2.0233,8.2388,4.1289		797/829	46104849	537,12469	2203	4300	6503	SO:0001819	synonymous_variant	83548	exon22			GTTCCACGCTCTG	AF131829	CCDS9398.1	13q14.11	2008-02-05			ENSG00000136152	ENSG00000136152		"""Components of oligomeric golgi complex"""	18619	protein-coding gene	gene with protein product		606975				11980916	Standard	NM_031431		Approved	SEC34	uc001vak.3	Q96JB2	OTTHUMG00000016855	ENST00000349995.5:c.2391C>T	13.37:g.46104849C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Silent	SNP	ENST00000349995.5	37	CCDS9398.1																																																																																			C|0.964;T|0.036	0.036	strong		0.393	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2		
HDAC9	9734	hgsc.bcm.edu	37	7	18687542	18687542	+	Silent	SNP	A	A	T	rs35614472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:18687542A>T	ENST00000432645.2	+	9	1161	c.1161A>T	c.(1159-1161)ccA>ccT	p.P387P	HDAC9_ENST00000401921.1_Silent_p.P346P|HDAC9_ENST00000406451.4_Silent_p.P387P|HDAC9_ENST00000524023.1_Silent_p.P310P|HDAC9_ENST00000428307.2_Silent_p.P343P|HDAC9_ENST00000417496.2_Silent_p.P385P|HDAC9_ENST00000406072.1_Silent_p.P374P|HDAC9_ENST00000441542.2_Silent_p.P390P|HDAC9_ENST00000456174.2_Silent_p.P359P|HDAC9_ENST00000405010.3_Silent_p.P387P	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	387					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)	AGGGAAAGCCACCCAACAGCA	0.502													A|||	19	0.00379393	0.0015	0.0043	5008	,	,		17684	0.0		0.0139	False		,,,				2504	0.0				p.P390P		Atlas-SNP	.											.	HDAC9	560	.	0			c.A1170T						PASS	.	A	,,,,,,,,	7,4069		0,7,2031	39.0	40.0	39.0		1155,1029,1038,930,1077,1161,1161,1161,1170	-5.0	0.7	7	dbSNP_126	39	115,8287		0,115,4086	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDAC9	NM_001204144.1,NM_001204145.1,NM_001204146.1,NM_001204147.1,NM_001204148.1,NM_014707.1,NM_058176.2,NM_178423.1,NM_178425.2	,,,,,,,,	0,122,6117	TT,TA,AA		1.3687,0.1717,0.9777	,,,,,,,,	385/589,343/547,346/550,310/514,359/563,387/591,387/1012,387/1067,390/1070	18687542	122,12356	2038	4201	6239	SO:0001819	synonymous_variant	9734	exon9			AAAGCCACCCAAC	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.1161A>T	7.37:g.18687542A>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			A|0.992;T|0.008	0.008	strong		0.502	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
LPCAT2	54947	hgsc.bcm.edu	37	16	55562466	55562466	+	Missense_Mutation	SNP	G	G	A	rs837550	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:55562466G>A	ENST00000262134.5	+	3	673	c.489G>A	c.(487-489)atG>atA	p.M163I		NM_017839.4	NP_060309.2	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	163			M -> I (in dbSNP:rs837550).		glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	12						TACCTTCTATGGTATCTCGAA	0.383													G|||	2593	0.517772	0.3389	0.621	5008	,	,		15646	0.4296		0.6461	False		,,,				2504	0.6452				p.M163I		Atlas-SNP	.											.	LPCAT2	35	.	0			c.G489A						PASS	.	G	ILE/MET	1683,2713	510.8+/-367.6	297,1089,812	183.0	166.0	172.0		489	-3.8	0.0	16	dbSNP_86	172	5613,2987	665.5+/-402.3	1838,1937,525	yes	missense	LPCAT2	NM_017839.4	10	2135,3026,1337	AA,AG,GG		34.7326,38.2848,43.8596	benign	163/545	55562466	7296,5700	2198	4300	6498	SO:0001583	missense	54947	exon3			TTCTATGGTATCT	AK000488	CCDS10753.1	16q12.2	2013-01-10	2007-12-17	2007-12-17	ENSG00000087253	ENSG00000087253		"""EF-hand domain containing"""	26032	protein-coding gene	gene with protein product		612040	"""acyltransferase like 1"""	AYTL1		16704971	Standard	NM_017839		Approved	FLJ20481	uc002eie.4	Q7L5N7	OTTHUMG00000133238	ENST00000262134.5:c.489G>A	16.37:g.55562466G>A	ENSP00000262134:p.Met163Ile	Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	418	71	0.169856	NM_017839	A3KBM1|Q6MZJ6|Q9NX23	Missense_Mutation	SNP	ENST00000262134.5	37	CCDS10753.1	1137	0.5206043956043956	167	0.3394308943089431	217	0.5994475138121547	249	0.4353146853146853	504	0.6649076517150396	G	0.010	-1.747828	0.00669	0.382848	0.652674	ENSG00000087253	ENST00000262134	D	0.92911	-3.13	5.8	-3.8	0.04307	Phospholipid/glycerol acyltransferase (2);	0.588370	0.21304	N	0.076759	T	0.00012	0.0000	N	0.00894	-1.105	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.29458	-1.0011	9	0.02654	T	1	-8.4188	7.5195	0.27620	0.4753:0.0:0.3727:0.152	rs837550;rs1052664;rs3193118;rs52823221;rs57713681;rs837550	163	Q7L5N7	PCAT2_HUMAN	I	163	ENSP00000262134:M163I	ENSP00000262134:M163I	M	+	3	0	LPCAT2	54119967	0.003000	0.15002	0.006000	0.13384	0.272000	0.26649	-1.098000	0.03346	-0.392000	0.07751	-0.203000	0.12734	ATG	G|0.457;A|0.543	0.543	strong		0.383	LPCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256977.2	NM_017839	
ADAT3	113179	hgsc.bcm.edu	37	19	1912934	1912934	+	Silent	SNP	T	T	C	rs12984675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1912934T>C	ENST00000602400.1	+	2	1068	c.840T>C	c.(838-840)acT>acC	p.T280T	SCAMP4_ENST00000414057.2_Intron|ADAT3_ENST00000329478.2_Silent_p.T296T|SCAMP4_ENST00000316097.8_Intron|SCAMP4_ENST00000409472.1_Intron			Q96EY9	ADAT3_HUMAN	adenosine deaminase, tRNA-specific 3	280					tRNA processing (GO:0008033)		hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|pancreas(1)|skin(2)	7		Ovarian(11;2.11e-07)|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)		ACCTGTGCACTGGCTACGACC	0.726													C|||	1819	0.363219	0.4803	0.4193	5008	,	,		11860	0.4038		0.2048	False		,,,				2504	0.2863				p.T296T		Atlas-SNP	.											.	ADAT3	15	.	0			c.T888C						PASS	.	C	,	1904,2498	591.8+/-387.6	426,1052,723	57.0	52.0	54.0		,840	-6.8	0.5	19	dbSNP_121	54	1294,7292	728.8+/-406.7	102,1090,3101	no	intron,coding-synonymous	SCAMP4,ADAT3	NM_079834.2,NM_138422.1	,	528,2142,3824	CC,CT,TT		15.071,43.2531,24.6227	,	,280/352	1912934	3198,9790	2201	4293	6494	SO:0001819	synonymous_variant	113179	exon2			GTGCACTGGCTAC	BC011824	CCDS12076.1, CCDS12076.2	19p13.3	2011-05-19	2011-05-19		ENSG00000213638	ENSG00000213638			25151	protein-coding gene	gene with protein product	"""tRNA-specific adenosine deaminase 3 homolog (S. cerevisiae)"""	615302	"""adenosine deaminase, tRNA-specific 3, TAD3 homolog (S. cerevisiae)"""			12457566	Standard	NM_138422		Approved	TAD3	uc002luh.4	Q96EY9	OTTHUMG00000154591	ENST00000602400.1:c.840T>C	19.37:g.1912934T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_138422		Silent	SNP	ENST00000602400.1	37																																																																																				T|0.727;C|0.273	0.273	strong		0.726	ADAT3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138422	
ZNF205	7755	hgsc.bcm.edu	37	16	3170188	3170188	+	Silent	SNP	C	C	T	rs12032	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3170188C>T	ENST00000382192.3	+	7	1732	c.1527C>T	c.(1525-1527)tgC>tgT	p.C509C	RP11-473M20.14_ENST00000576490.1_RNA|ZNF205_ENST00000219091.4_Silent_p.C509C|RP11-473M20.14_ENST00000575139.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	509					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|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)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						GCCCGTTGTGCGGCAAGAGCT	0.706													C|||	1924	0.384185	0.2859	0.4496	5008	,	,		14798	0.4365		0.4076	False		,,,				2504	0.3926				p.C509C		Atlas-SNP	.											.	ZNF205	42	.	0			c.C1527T						PASS	.	C	,	1268,3126	424.7+/-340.5	167,934,1096	42.0	40.0	41.0		1527,1527	-2.4	0.9	16	dbSNP_52	41	3344,5252	484.9+/-371.5	672,2000,1626	no	coding-synonymous,coding-synonymous	ZNF205	NM_001042428.1,NM_003456.2	,	839,2934,2722	TT,TC,CC		38.9018,28.8575,35.5042	,	509/555,509/555	3170188	4612,8378	2197	4298	6495	SO:0001819	synonymous_variant	7755	exon7			GTTGTGCGGCAAG	AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"""Zinc fingers, C2H2-type"", ""-"""	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.1527C>T	16.37:g.3170188C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	22	0.611111	NM_003456	A8MZK0|D3DUB4|Q9BU95	Silent	SNP	ENST00000382192.3	37	CCDS10494.2																																																																																			C|0.639;T|0.361	0.361	strong		0.706	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
CCDC149	91050	hgsc.bcm.edu	37	4	24836619	24836619	+	Silent	SNP	C	C	T	rs16876194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:24836619C>T	ENST00000389609.4	-	9	914	c.771G>A	c.(769-771)caG>caA	p.Q257Q	CCDC149_ENST00000428116.2_Intron|CCDC149_ENST00000504487.1_Silent_p.Q257Q|CCDC149_ENST00000502801.1_Intron	NM_173463.4	NP_775734.2	Q6ZUS6	CC149_HUMAN	coiled-coil domain containing 149	202										cervix(1)|endometrium(1)|large_intestine(2)|lung(3)	7		Breast(46;0.173)				TGGATTTACCCTGGCCCTTCG	0.473													C|||	403	0.0804712	0.1611	0.0576	5008	,	,		18114	0.002		0.0835	False		,,,				2504	0.0654				p.Q257Q		Atlas-SNP	.											.	CCDC149	41	.	0			c.G771A						PASS	.	C	,	679,3727	286.3+/-278.7	51,577,1575	130.0	123.0	125.0		771,771	3.6	0.9	4	dbSNP_123	125	698,7902	173.2+/-223.7	20,658,3622	no	coding-synonymous,coding-synonymous	CCDC149	NM_001130726.2,NM_173463.4	,	71,1235,5197	TT,TC,CC		8.1163,15.4108,10.5874	,	257/530,257/530	24836619	1377,11629	2203	4300	6503	SO:0001819	synonymous_variant	91050	exon9			TTTACCCTGGCCC		CCDS33967.1, CCDS47036.1, CCDS33967.2	4p15.2	2008-03-03				ENSG00000181982			25405	protein-coding gene	gene with protein product						17457313	Standard	NM_173463		Approved	DKFZp761B107	uc003grc.3	Q6ZUS6		ENST00000389609.4:c.771G>A	4.37:g.24836619C>T		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_173463	A6NJE7|B4DK90|B4DZG3|G5EA04|Q6NW41|Q8N3K8	Silent	SNP	ENST00000389609.4	37	CCDS33967.2																																																																																			C|0.904;T|0.096	0.096	strong		0.473	CCDC149-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360157.1	NM_173463	
MCTP1	79772	hgsc.bcm.edu	37	5	94278129	94278129	+	Silent	SNP	T	T	C	rs293035	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:94278129T>C	ENST00000515393.1	-	4	983	c.984A>G	c.(982-984)gtA>gtG	p.V328V	MCTP1_ENST00000429576.2_Silent_p.V107V|MCTP1_ENST00000312216.8_Silent_p.V107V|MCTP1_ENST00000505208.1_Silent_p.V107V	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	328	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)		CATAGTCAAATACCTGAGATG	0.358													T|||	1317	0.262979	0.1838	0.1326	5008	,	,		18700	0.495		0.2406	False		,,,				2504	0.2464				p.V328V		Atlas-SNP	.											.	MCTP1	110	.	0			c.A984G						PASS	.	T	,	907,3499	351.8+/-311.4	93,721,1389	93.0	88.0	89.0		321,984	-0.8	1.0	5	dbSNP_79	89	2130,6470	364.6+/-333.6	254,1622,2424	no	coding-synonymous,coding-synonymous	MCTP1	NM_001002796.2,NM_024717.4	,	347,2343,3813	CC,CT,TT		24.7674,20.5856,23.3508	,	107/779,328/1000	94278129	3037,9969	2203	4300	6503	SO:0001819	synonymous_variant	79772	exon4			GTCAAATACCTGA		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.984A>G	5.37:g.94278129T>C		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	37	CCDS34203.1	634	0.2902930402930403	92	0.18699186991869918	57	0.1574585635359116	301	0.5262237762237763	184	0.24274406332453827	T	12.21	1.871036	0.33069	0.205856	0.247674	ENSG00000175471	ENST00000503301	.	.	.	5.63	-0.839	0.10759	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999988	.	.	.	.	.	.	T	0.46652	-0.9176	3	.	.	.	-12.4535	2.5726	0.04798	0.0915:0.2027:0.201:0.5048	rs293035;rs295203;rs61144873;rs293035	.	.	.	V	137	.	.	I	-	1	0	MCTP1	94303885	0.905000	0.30787	0.998000	0.56505	0.967000	0.64934	-0.263000	0.08670	-0.029000	0.13827	0.533000	0.62120	ATT	T|0.746;C|0.254	0.254	strong		0.358	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	
GLIS1	148979	hgsc.bcm.edu	37	1	54060248	54060248	+	Missense_Mutation	SNP	T	T	C	rs4307514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	92	66	0.717391	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	
CMYA5	202333	hgsc.bcm.edu	37	5	79025157	79025157	+	Missense_Mutation	SNP	A	A	G	rs10942901	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79025157A>G	ENST00000446378.2	+	2	600	c.569A>G	c.(568-570)gAt>gGt	p.D190G		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	190			D -> G (in dbSNP:rs10942901). {ECO:0000269|PubMed:17974005}.		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)		GGCATTTATGATAAAGCAAGA	0.393													A|||	835	0.166733	0.1036	0.1902	5008	,	,		17856	0.2202		0.1471	False		,,,				2504	0.2004				p.D190G		Atlas-SNP	.											.	CMYA5	643	.	0			c.A569G						PASS	.	A	GLY/ASP	388,3280		23,342,1469	45.0	44.0	44.0		569	4.9	0.0	5	dbSNP_120	44	1184,7008		98,988,3010	yes	missense	CMYA5	NM_153610.3	94	121,1330,4479	GG,GA,AA		14.4531,10.578,13.2546	probably-damaging	190/4070	79025157	1572,10288	1834	4096	5930	SO:0001583	missense	202333	exon2			TTTATGATAAAGC	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.569A>G	5.37:g.79025157A>G	ENSP00000394770:p.Asp190Gly	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	205	110	0.536585	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	341	0.15613553113553114	48	0.0975609756097561	67	0.1850828729281768	114	0.1993006993006993	112	0.14775725593667546	A	11.26	1.587130	0.28268	0.10578	0.144531	ENSG00000164309	ENST00000446378	T	0.65549	-0.16	6.06	4.88	0.63580	.	0.255650	0.28082	N	0.016672	T	0.00073	0.0002	L	0.32530	0.975	0.80722	P	0.0	P	0.48407	0.91	P	0.45099	0.469	T	0.25222	-1.0138	9	0.87932	D	0	.	3.4618	0.07536	0.6482:0.1413:0.0751:0.1354	rs10942901;rs10942901	190	Q8N3K9	CMYA5_HUMAN	G	190	ENSP00000394770:D190G	ENSP00000394770:D190G	D	+	2	0	CMYA5	79060913	0.975000	0.34042	0.020000	0.16555	0.282000	0.26991	1.489000	0.35562	1.073000	0.40885	0.533000	0.62120	GAT	A|0.832;G|0.162	0.162	strong		0.393	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
CDH4	1002	hgsc.bcm.edu	37	20	60503350	60503350	+	Missense_Mutation	SNP	A	A	G	rs6142884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:60503350A>G	ENST00000360469.5	+	12	1962	c.1874A>G	c.(1873-1875)aAg>aGg	p.K625R	CDH4_ENST00000543233.1_Missense_Mutation_p.K551R	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	625	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		K -> R (in dbSNP:rs6142884). {ECO:0000269|PubMed:2059658, ECO:0000269|PubMed:7982033}.		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)			ATCTGCGAGAAGCCCAACCTG	0.642													A|||	2841	0.567292	0.2504	0.5793	5008	,	,		19647	0.8413		0.5239	False		,,,				2504	0.7495				p.K625R		Atlas-SNP	.											.	CDH4	172	.	0			c.A1874G						PASS	.	A	ARG/LYS	1393,3013	457.3+/-351.6	248,897,1058	114.0	117.0	116.0		1874	-2.0	0.4	20	dbSNP_114	116	4434,4166	583.4+/-391.6	1136,2162,1002	yes	missense	CDH4	NM_001794.2	26	1384,3059,2060	GG,GA,AA		48.4419,31.616,44.8024	benign	625/917	60503350	5827,7179	2203	4300	6503	SO:0001583	missense	1002	exon12			GCGAGAAGCCCAA	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.1874A>G	20.37:g.60503350A>G	ENSP00000353656:p.Lys625Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	1220	0.5586080586080586	126	0.25609756097560976	206	0.569060773480663	488	0.8531468531468531	400	0.5277044854881267	A	0.007	-1.998776	0.00435	0.31616	0.515581	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.60548	0.18;0.18	4.56	-2.0	0.07433	Cadherin (1);Cadherin-like (1);	0.263746	0.34338	N	0.004045	T	0.00012	0.0000	N	0.01152	-0.98	0.46336	P	0.0010069999999999801	B	0.02656	0.0	B	0.04013	0.001	T	0.36915	-0.9728	8	.	.	.	.	12.4864	0.55874	0.423:0.0:0.577:0.0	rs6142884;rs8120066;rs58243163;rs6142884	625	P55283	CADH4_HUMAN	R	625;533;551	ENSP00000353656:K625R;ENSP00000443301:K551R	.	K	+	2	0	CDH4	59936745	0.994000	0.37717	0.432000	0.26747	0.022000	0.10575	0.395000	0.20850	-0.818000	0.04329	-0.464000	0.05259	AAG	A|0.508;G|0.492	0.492	strong		0.642	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
OPN1LW	5956	hgsc.bcm.edu	37	X	153420176	153420176	+	Missense_Mutation	SNP	A	A	G	rs78093925	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:153420176A>G	ENST00000369951.4	+	4	766	c.706A>G	c.(706-708)Atg>Gtg	p.M236V	OPN1LW_ENST00000463296.1_Intron	NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	236					phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|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)			endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	15	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CGCTATCATCATGCTCTGCTA	0.612													G|||	565	0.149669	0.3192	0.0562	3775	,	,		12001	0.0129		0.0616	False		,,,				2504	0.0297				p.M236V		Atlas-SNP	.											.	OPN1LW	87	.	0			c.A706G						PASS	.	G	VAL/MET	1403,2417		217,767,202,647,356	308.0	226.0	254.0		706	-3.0	0.2	X	dbSNP_131	254	634,6044		36,376,186,2014,1640	yes	missense	OPN1LW	NM_020061.4	21	253,1143,388,2661,1996	GG,GA,G,AA,A		9.4939,36.7277,19.4037	benign	236/365	153420176	2037,8461	2189	4252	6441	SO:0001583	missense	5956	exon4			ATCATCATGCTCT	Z68193	CCDS14742.1	Xq28	2013-01-08	2008-04-16		ENSG00000102076	ENSG00000102076		"""GPCR / Class A : Opsin receptors"""	9936	protein-coding gene	gene with protein product	"""cone dystrophy 5 (X-linked)"""	300822	"""color blindness, protan"", ""red cone photoreceptor pigment"""	CBBM, RCP, CBP			Standard	NM_020061		Approved	COD5	uc004fjz.4	P04000	OTTHUMG00000034295	ENST00000369951.4:c.706A>G	X.37:g.153420176A>G	ENSP00000358967:p.Met236Val	Somatic	639	1	0.00156495		WXS	Illumina HiSeq	Phase_I	319	314	0.984326	NM_020061		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	210	0.12658227848101267	88	0.2233502538071066	12	0.03428571428571429	4	0.007017543859649123	33	0.04583333333333333	G	0.007	-1.991273	0.00439	0.367277	0.094939	ENSG00000102076	ENST00000369951;ENST00000442922	T;T	0.70282	-0.47;-0.47	4.27	-2.95	0.05564	GPCR, rhodopsin-like superfamily (1);	0.428458	0.24742	N	0.035968	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.40459	-0.9562	9	0.25106	T	0.35	.	7.105	0.25358	0.3272:0.3964:0.2763:0.0	.	236	P04000	OPSR_HUMAN	V	236;99	ENSP00000358967:M236V;ENSP00000402493:M99V	ENSP00000358967:M236V	M	+	1	0	OPN1LW	153073370	0.000000	0.05858	0.239000	0.24122	0.134000	0.20937	-1.488000	0.02308	-0.716000	0.04962	-0.775000	0.03384	ATG	A|0.814;G|0.186	0.186	strong		0.612	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125826003	125826003	+	Missense_Mutation	SNP	T	T	C	rs4646750	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:125826003T>C	ENST00000393434.2	-	21	2783	c.2434A>G	c.(2434-2436)Atc>Gtc	p.I812V	ALDH1L1_ENST00000273450.3_Missense_Mutation_p.I822V|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.I812V|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.I711V|ALDH1L1_ENST00000393431.2_3'UTR|ALDH1L1-AS1_ENST00000512384.1_RNA	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	812	Aldehyde dehydrogenase.		I -> V (in dbSNP:rs4646750).		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)	AACCGAGAGATGATCATGACA	0.517													T|||	324	0.0646965	0.112	0.0692	5008	,	,		20531	0.0308		0.0646	False		,,,				2504	0.0327				p.I822V		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.A2464G						PASS	.	T	VAL/ILE	510,3896	235.5+/-248.0	23,464,1716	173.0	150.0	157.0		2434	2.8	1.0	3	dbSNP_111	157	652,7948	165.7+/-217.8	25,602,3673	yes	missense	ALDH1L1	NM_012190.2	29	48,1066,5389	CC,CT,TT		7.5814,11.5751,8.9343	benign	812/903	125826003	1162,11844	2203	4300	6503	SO:0001583	missense	10840	exon21			GAGAGATGATCAT	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.2434A>G	3.37:g.125826003T>C	ENSP00000377083:p.Ile812Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	150	0.06868131868131869	55	0.11178861788617886	26	0.0718232044198895	18	0.03146853146853147	51	0.06728232189973615	T	8.039	0.763418	0.15914	0.115751	0.075814	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434	T;T;T;T	0.05319	3.46;3.46;3.46;3.46	3.98	2.83	0.33086	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.143965	0.44902	N	0.000405	T	0.00073	0.0002	N	0.11064	0.09	0.09310	P	0.9999999999999973	B;B;B	0.28026	0.151;0.198;0.039	B;B;B	0.31016	0.123;0.103;0.069	T	0.41574	-0.9501	9	0.40728	T	0.16	.	7.2766	0.26288	0.0:0.109:0.0:0.891	rs4646750;rs56475654;rs59802481;rs4646750	711;347;812	E9PBX3;Q6ZV71;O75891	.;.;AL1L1_HUMAN	V	822;812;711;812	ENSP00000273450:I822V;ENSP00000420293:I812V;ENSP00000395881:I711V;ENSP00000377083:I812V	ENSP00000273450:I822V	I	-	1	0	ALDH1L1	127308693	1.000000	0.71417	1.000000	0.80357	0.595000	0.36748	1.912000	0.39946	0.606000	0.29965	0.260000	0.18958	ATC	T|0.919;C|0.081	0.081	strong		0.517	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552086	178552086	+	Missense_Mutation	SNP	T	T	G	rs376054177		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:178552086T>G	ENST00000251582.7	-	19	2947	c.2846A>C	c.(2845-2847)aAc>aCc	p.N949T		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	949	TSP type-1 3. {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)		GCGGGTGGTGTTGTCGTGTAG	0.697																																					p.N949T		Atlas-SNP	.											ADAMTS2,NS,malignant_melanoma,0,1	ADAMTS2	190	1	0			c.A2846C						scavenged	.						111.0	112.0	112.0					5																	178552086		2203	4300	6503	SO:0001583	missense	9509	exon19			GTGGTGTTGTCGT	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.2846A>C	5.37:g.178552086T>G	ENSP00000251582:p.Asn949Thr	Somatic	215	3	0.0139535		WXS	Illumina HiSeq	Phase_I	174	4	0.0229885	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.344710	0.41498	.	.	ENSG00000087116	ENST00000251582	T	0.54071	0.59	5.31	4.16	0.48862	.	0.196433	0.35291	N	0.003319	T	0.56031	0.1958	L	0.46741	1.465	0.80722	D	1	D	0.52996	0.957	P	0.56434	0.798	T	0.52381	-0.8583	10	0.32370	T	0.25	.	9.8162	0.40853	0.0:0.0807:0.0:0.9193	.	949	O95450	ATS2_HUMAN	T	949	ENSP00000251582:N949T	ENSP00000251582:N949T	N	-	2	0	ADAMTS2	178484692	1.000000	0.71417	1.000000	0.80357	0.137000	0.21094	1.694000	0.37752	2.008000	0.58898	0.533000	0.62120	AAC	.	.	weak		0.697	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
CELSR3	1951	hgsc.bcm.edu	37	3	48699519	48699519	+	Silent	SNP	C	C	T	rs3733086	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48699519C>T	ENST00000164024.4	-	1	829	c.549G>A	c.(547-549)aaG>aaA	p.K183K	CELSR3_ENST00000544264.1_Silent_p.K183K|RP11-148G20.1_ENST00000421275.1_RNA	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	86	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	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	
KHNYN	23351	hgsc.bcm.edu	37	14	24901433	24901433	+	Silent	SNP	C	C	T	rs17795094	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24901433C>T	ENST00000251343.5	+	3	1105	c.966C>T	c.(964-966)caC>caT	p.H322H	KHNYN_ENST00000556842.1_Silent_p.H322H|CBLN3_ENST00000267406.6_5'Flank|KHNYN_ENST00000554268.1_5'Flank|KHNYN_ENST00000553935.1_Silent_p.H322H|CBLN3_ENST00000555436.1_5'Flank			O15037	KHNYN_HUMAN	KH and NYN domain containing	322							RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						TCTGTGTCCACCGTGAGCCTC	0.647											OREG0022627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	392	0.0782748	0.0416	0.0965	5008	,	,		17135	0.0565		0.1014	False		,,,				2504	0.1135				p.H322H		Atlas-SNP	.											.	KHNYN	46	.	0			c.C966T						PASS	.	C		323,4083	170.5+/-200.9	12,299,1892	71.0	74.0	73.0		966	2.3	0.3	14	dbSNP_123	73	1147,7453	234.6+/-267.5	72,1003,3225	yes	coding-synonymous	KHNYN	NM_015299.2		84,1302,5117	TT,TC,CC		13.3372,7.3309,11.3025		322/679	24901433	1470,11536	2203	4300	6503	SO:0001819	synonymous_variant	23351	exon3			TGTCCACCGTGAG	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.966C>T	14.37:g.24901433C>T		Somatic	138	0	0	774	WXS	Illumina HiSeq	Phase_I	161	96	0.596273	NM_015299	Q86TZ6|Q8IUQ2|Q96BA9	Silent	SNP	ENST00000251343.5	37	CCDS32058.1																																																																																			C|0.904;T|0.096	0.096	strong		0.647	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
INS-IGF2	723961	hgsc.bcm.edu	37	11	2169014	2169014	+	Missense_Mutation	SNP	A	A	G	rs10770125	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2169014A>G	ENST00000397270.1	-	4	489	c.431T>C	c.(430-432)cTt>cCt	p.L144P	IGF2-AS_ENST00000445504.2_RNA|IGF2_ENST00000300632.5_5'UTR|IGF2-AS_ENST00000381361.3_RNA|INS-IGF2_ENST00000481781.1_5'UTR|IGF2-AS_ENST00000381363.4_RNA	NM_001042376.2	NP_001035835.1	F8WCM5	INSR2_HUMAN	INS-IGF2 readthrough	144				L -> P (in Ref. 1; ABD93453/ABD93452). {ECO:0000305}.		extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	5		all_epithelial(84;0.00018)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.0832)|Lung(200;0.156)		CTCCCACACAAGCTCGGTGGT	0.607											OREG0003767	type=REGULATORY REGION|Gene=IGF2|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	A|||	1742	0.347843	0.1233	0.5778	5008	,	,		14613	0.3958		0.4563	False		,,,				2504	0.3272				p.L144P		Atlas-SNP	.											.	INS-IGF2	8	.	0			c.T431C						PASS	.	A	,PRO/LEU	560,2794		70,420,1187	13.0	14.0	14.0		,431	1.1	0.0	11	dbSNP_120	14	3133,4145		756,1621,1262	yes	utr-5,missense	IGF2,INS-IGF2	NM_001007139.4,NM_001042376.2	,98	826,2041,2449	GG,GA,AA		43.0475,16.6965,34.7348	,benign	,144/201	2169014	3693,6939	1677	3639	5316	SO:0001583	missense	723961	exon4			CACACAAGCTCGG	DQ104205	CCDS41598.1	11p15.5	2011-03-23			ENSG00000129965	ENSG00000129965			33527	other	readthrough						16531418	Standard	NM_001042376		Approved		uc001lvm.3	F8WCM5	OTTHUMG00000166213	ENST00000397270.1:c.431T>C	11.37:g.2169014A>G	ENSP00000380440:p.Leu144Pro	Somatic	161	0	0	601	WXS	Illumina HiSeq	Phase_I	115	44	0.382609	NM_001042376	Q1WM24	Missense_Mutation	SNP	ENST00000397270.1	37	CCDS41598.1	840	0.38461538461538464	63	0.12804878048780488	199	0.5497237569060773	226	0.3951048951048951	352	0.46437994722955145	A	12.53	1.966046	0.34659	0.166965	0.430475	ENSG00000129965	ENST00000397270	D	0.96830	-4.14	3.45	1.14	0.20703	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.399999999995849E-5	B	0.32101	0.356	B	0.33568	0.166	T	0.09773	-1.0659	7	0.87932	D	0	.	5.0118	0.14317	0.7437:0.0:0.2563:0.0	rs10770125;rs17881514;rs10770125	144	F8WCM5	.	P	144	ENSP00000380440:L144P	ENSP00000348986:L144P	L	-	2	0	INS-IGF2	2125590	0.155000	0.22806	0.003000	0.11579	0.018000	0.09664	0.621000	0.24418	0.228000	0.21019	0.482000	0.46254	CTT	A|0.652;G|0.348	0.348	strong		0.607	INS-IGF2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000388404.1	NM_001042376.2	
YIPF7	285525	hgsc.bcm.edu	37	4	44626641	44626641	+	Silent	SNP	A	A	G	rs60959366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:44626641A>G	ENST00000332990.5	-	5	673	c.657T>C	c.(655-657)ggT>ggC	p.G219G	YIPF7_ENST00000415895.4_Silent_p.G195G	NM_182592.2	NP_872398.2	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	219						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(1)	12						ACATGGCGCAACCAGACAGGA	0.527													G|||	2764	0.551917	0.6884	0.4625	5008	,	,		17468	0.5585		0.4095	False		,,,				2504	0.5706				p.G219G		Atlas-SNP	.											.	YIPF7	33	.	0			c.T657C						PASS	.	G		2569,1627		797,975,326	50.0	56.0	54.0		657	3.4	0.8	4	dbSNP_129	54	3093,5375		558,1977,1699	no	coding-synonymous	YIPF7	NM_182592.2		1355,2952,2025	GG,GA,AA		36.5257,38.775,44.7094		219/281	44626641	5662,7002	2098	4234	6332	SO:0001819	synonymous_variant	285525	exon5			GGCGCAACCAGAC	AK096895	CCDS54766.1	4p13	2008-08-07			ENSG00000177752	ENSG00000177752		"""Yip1 domain family"""	26825	protein-coding gene	gene with protein product							Standard	NM_182592		Approved	FLJ39576, FinGER9	uc021xnx.1	Q8N8F6	OTTHUMG00000160467	ENST00000332990.5:c.657T>C	4.37:g.44626641A>G		Somatic	411	1	0.00243309		WXS	Illumina HiSeq	Phase_I	391	160	0.409207	NM_182592	Q3SY21|Q3SY22	Silent	SNP	ENST00000332990.5	37	CCDS54766.1																																																																																			A|0.499;G|0.501	0.501	strong		0.527	YIPF7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_182592	
COL6A5	256076	hgsc.bcm.edu	37	3	130150310	130150310	+	Missense_Mutation	SNP	A	A	C	rs61744488	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:130150310A>C	ENST00000432398.2	+	33	5744	c.5250A>C	c.(5248-5250)gaA>gaC	p.E1750D	COL6A5_ENST00000265379.6_Missense_Mutation_p.E1750D	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1750	Nonhelical 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						TTTTTCTAGAAAAATGTCCAG	0.383													A|||	165	0.0329473	0.0015	0.0202	5008	,	,		20457	0.0228		0.0398	False		,,,				2504	0.0879				p.E1750D		Atlas-SNP	.											.	COL6A5	205	.	0			c.A5250C						PASS	.	A	ASP/GLU	20,1364		0,20,672	48.0	41.0	43.0		5250	-4.1	0.1	3	dbSNP_129	43	142,3040		3,136,1452	yes	missense-near-splice	COL6A5	NM_153264.5	45	3,156,2124	CC,CA,AA		4.4626,1.4451,3.548	benign	1750/2527	130150310	162,4404	692	1591	2283	SO:0001583	missense	256076	exon33			TCTAGAAAAATGT	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.5250A>C	3.37:g.130150310A>C	ENSP00000390895:p.Glu1750Asp	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		63|63	0.028846153846153848|0.028846153846153848	4|4	0.008130081300813009|0.008130081300813009	7|7	0.019337016574585635|0.019337016574585635	19|19	0.033216783216783216|0.033216783216783216	33|33	0.04353562005277045|0.04353562005277045	A|A	1.385|1.385	-0.582422|-0.582422	0.03827|0.03827	0.014451|0.014451	0.044626|0.044626	ENSG00000172752|ENSG00000172752	ENST00000432398;ENST00000265379|ENST00000512836	D;D|.	0.89050|.	-2.37;-2.46|.	5.74|5.74	-4.14|-4.14	0.03892|0.03892	.|.	.|.	.|.	.|.	.|.	T|T	0.03739|0.03739	0.0106|0.0106	N|N	0.16903|0.16903	0.455|0.455	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.08055|.	0.003|.	T|T	0.23797|0.23797	-1.0178|-1.0178	9|5	0.12430|.	T|.	0.62|.	.|.	3.4186|3.4186	0.07385|0.07385	0.4523:0.321:0.1311:0.0957|0.4523:0.321:0.1311:0.0957	rs61744488|rs61744488	1750|.	A8TX70-2|.	.|.	D|Q	1750|2	ENSP00000390895:E1750D;ENSP00000265379:E1750D|.	ENSP00000265379:E1750D|.	E|K	+|+	3|1	2|0	COL6A5|COL6A5	131633000|131633000	0.243000|0.243000	0.23878|0.23878	0.080000|0.080000	0.20451|0.20451	0.014000|0.014000	0.08584|0.08584	0.258000|0.258000	0.18387|0.18387	-0.430000|-0.430000	0.07318|0.07318	-1.272000|-1.272000	0.01410|0.01410	GAA|AAA	A|0.971;C|0.029	0.029	strong		0.383	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
GUCY1A2	2977	hgsc.bcm.edu	37	11	106558291	106558291	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:106558291C>A	ENST00000526355.2	-	8	2651	c.2183G>T	c.(2182-2184)cGg>cTg	p.R728L	GUCY1A2_ENST00000282249.2_Missense_Mutation_p.R759L|GUCY1A2_ENST00000347596.2_Missense_Mutation_p.R749L	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	728					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)	GCTTGTCTCCCGGAGGAACAT	0.488																																					p.R759L		Atlas-SNP	.											GUCY1A2,colon,carcinoma,0,2	GUCY1A2	180	2	0			c.G2276T						scavenged	.						137.0	135.0	135.0					11																	106558291		2201	4298	6499	SO:0001583	missense	2977	exon9			GTCTCCCGGAGGA	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.2183G>T	11.37:g.106558291C>A	ENSP00000431245:p.Arg728Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	186	3	0.016129	NM_001256424	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	37	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.796385	0.90453	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.89050	-2.01;-2.46;-2.02	5.31	5.31	0.75309	.	0.000000	0.39985	U	0.001210	D	0.91068	0.7189	L	0.27053	0.805	0.58432	D	0.999998	D;D;D	0.71674	0.997;0.998;0.997	D;D;D	0.80764	0.987;0.994;0.987	D	0.92216	0.5780	10	0.72032	D	0.01	.	18.3247	0.90250	0.0:1.0:0.0:0.0	.	749;759;728	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	L	728;759;749	ENSP00000431245:R728L;ENSP00000282249:R759L;ENSP00000344874:R749L	ENSP00000282249:R759L	R	-	2	0	GUCY1A2	106063501	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.385000	0.79763	2.654000	0.90174	0.305000	0.20034	CGG	.	.	none		0.488	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2		
ABCC3	8714	hgsc.bcm.edu	37	17	48768486	48768486	+	Silent	SNP	A	A	G	rs1051640	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48768486A>G	ENST00000285238.8	+	31	4589	c.4509A>G	c.(4507-4509)gaA>gaG	p.E1503E	RP11-294J22.6_ENST00000574246.1_RNA	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1503	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|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)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TAGTAGCTGAATTTGATTCTC	0.483													A|||	521	0.104034	0.09	0.1095	5008	,	,		21371	0.0417		0.1829	False		,,,				2504	0.1022				p.E1503E		Atlas-SNP	.											.	ABCC3	138	.	0			c.A4509G						PASS	.	A		371,4035	189.9+/-215.9	17,337,1849	120.0	106.0	111.0		4509	0.6	1.0	17	dbSNP_86	111	1533,7067	290.7+/-299.9	149,1235,2916	no	coding-synonymous	ABCC3	NM_003786.3		166,1572,4765	GG,GA,AA		17.8256,8.4203,14.6394		1503/1528	48768486	1904,11102	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon31			AGCTGAATTTGAT	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.4509A>G	17.37:g.48768486A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	135	58	0.42963	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			A|0.876;G|0.124	0.124	strong		0.483	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
MMP10	4319	hgsc.bcm.edu	37	11	102650424	102650424	+	Missense_Mutation	SNP	C	C	T	rs486055	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102650424C>T	ENST00000279441.4	-	2	194	c.158G>A	c.(157-159)aGa>aAa	p.R53K		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	53			R -> K (in dbSNP:rs486055). {ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	ACTGTCCTTTCTTCTAAACTG	0.378													C|||	227	0.0453275	0.0045	0.0663	5008	,	,		19174	0.001		0.1382	False		,,,				2504	0.0358				p.R53K		Atlas-SNP	.											.	MMP10	44	.	0			c.G158A						PASS	.	C	LYS/ARG	120,4286	87.8+/-126.4	2,116,2085	85.0	77.0	80.0		158	4.2	1.0	11	dbSNP_83	80	1343,7255	262.4+/-284.4	108,1127,3064	yes	missense	MMP10	NM_002425.2	26	110,1243,5149	TT,TC,CC		15.6199,2.7236,11.2504	benign	53/477	102650424	1463,11541	2203	4299	6502	SO:0001583	missense	4319	exon2			TCCTTTCTTCTAA	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"""matrix metalloproteinase 10 (stromelysin 2)"""	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.158G>A	11.37:g.102650424C>T	ENSP00000279441:p.Arg53Lys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	191	125	0.65445	NM_002425	B2R9X9|Q53HH9	Missense_Mutation	SNP	ENST00000279441.4	37	CCDS8321.1	138	0.06318681318681318	2	0.0040650406504065045	29	0.08011049723756906	0	0.0	107	0.14116094986807387	c	4.269	0.048987	0.08243	0.027236	0.156199	ENSG00000166670	ENST00000279441;ENST00000539681	T;T	0.32753	1.44;1.44	4.25	4.25	0.50352	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.121332	0.37178	N	0.002214	T	0.00039	0.0001	N	0.13168	0.305	0.09310	N	1	B	0.19073	0.033	B	0.22152	0.038	T	0.34004	-0.9846	10	0.02654	T	1	.	8.6471	0.34011	0.0:0.7624:0.153:0.0845	rs486055;rs17359452;rs17860947;rs60436444;rs486055	53	P09238	MMP10_HUMAN	K	53	ENSP00000279441:R53K;ENSP00000441485:R53K	ENSP00000279441:R53K	R	-	2	0	MMP10	102155634	0.000000	0.05858	0.977000	0.42913	0.046000	0.14306	0.542000	0.23222	2.365000	0.80145	0.591000	0.81541	AGA	C|0.916;T|0.084	0.084	strong		0.378	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
ALKBH8	91801	hgsc.bcm.edu	37	11	107375703	107375703	+	Missense_Mutation	SNP	C	C	T	rs139390837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:107375703C>T	ENST00000428149.2	-	12	1827	c.1676G>A	c.(1675-1677)cGc>cAc	p.R559H	ALKBH8_ENST00000389568.3_Missense_Mutation_p.R559H|ALKBH8_ENST00000429370.1_Intron|ALKBH8_ENST00000417449.2_Missense_Mutation_p.R562H	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	559	Methyltransferase domain.				cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|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)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		GTCATTAATGCGGGGGACAGA	0.453													C|||	7	0.00139776	0.0038	0.0014	5008	,	,		20733	0.0		0.001	False		,,,				2504	0.0				p.R559H		Atlas-SNP	.											.	ALKBH8	88	.	0			c.G1676A						PASS	.	C	HIS/ARG	1,1383		0,1,691	118.0	98.0	104.0		1676	2.1	0.0	11	dbSNP_134	104	0,3182		0,0,1591	yes	missense	ALKBH8	NM_138775.2	29	0,1,2282	TT,TC,CC		0.0,0.0723,0.0219	benign	559/665	107375703	1,4565	692	1591	2283	SO:0001583	missense	91801	exon12			TTAATGCGGGGGA	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"""Alkylation repair homologs"", ""RNA binding motif (RRM) containing"""	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.1676G>A	11.37:g.107375703C>T	ENSP00000415885:p.Arg559His	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	133	36	0.270677	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	37	CCDS8337.2	4	0.0018315018315018315	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	4.450	0.083419	0.08533	7.23E-4	0.0	ENSG00000137760	ENST00000428149;ENST00000389568;ENST00000417449	T;T;T	0.45668	0.89;0.89;0.89	5.07	2.13	0.27403	.	0.956250	0.08831	N	0.887349	T	0.20251	0.0487	N	0.08118	0	0.09310	N	1	B;B	0.25351	0.124;0.001	B;B	0.08055	0.003;0.0	T	0.18272	-1.0342	10	0.42905	T	0.14	-2.6235	4.1101	0.10055	0.0872:0.3134:0.4508:0.1486	.	559;562	Q96BT7;Q96BT7-4	ALKB8_HUMAN;.	H	559;559;562	ENSP00000415885:R559H;ENSP00000374219:R559H;ENSP00000397673:R562H	ENSP00000374219:R559H	R	-	2	0	ALKBH8	106880913	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.511000	0.06321	0.241000	0.21283	-0.865000	0.03005	CGC	C|0.998;T|0.002	0.002	strong		0.453	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775	
ICT1	3396	hgsc.bcm.edu	37	17	73016621	73016621	+	Silent	SNP	C	C	T	rs1044228	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	124	0	0		WXS	Illumina HiSeq	Phase_I	111	108	0.972973	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	
TJP3	27134	hgsc.bcm.edu	37	19	3740658	3740658	+	Silent	SNP	T	T	G	rs10416362	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3740658T>G	ENST00000541714.2	+	14	2202	c.1740T>G	c.(1738-1740)ctT>ctG	p.L580L	TJP3_ENST00000539908.2_Silent_p.L544L|TJP3_ENST00000589378.1_Silent_p.L589L|TJP3_ENST00000262968.9_Silent_p.L613L|TJP3_ENST00000587686.1_Silent_p.L599L|TJP3_ENST00000382008.3_Silent_p.L594L	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	580	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCGGGGTCTTCGTCGAGGAG	0.692													T|||	2761	0.551318	0.5121	0.5865	5008	,	,		11836	0.5228		0.5099	False		,,,				2504	0.6513				p.L589L		Atlas-SNP	.											TJP3,NS,carcinoma,0,1	TJP3	79	1	0			c.T1767G						PASS	.	T		2313,2089		631,1051,519	15.0	18.0	17.0		1839	-9.7	0.0	19	dbSNP_119	17	4479,4113		1202,2075,1019	no	coding-synonymous	TJP3	NM_014428.1		1833,3126,1538	GG,GT,TT		47.8701,47.4557,47.7297		613/953	3740658	6792,6202	2201	4296	6497	SO:0001819	synonymous_variant	27134	exon14			GGGTCTTCGTCGA	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.1740T>G	19.37:g.3740658T>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			T|0.478;G|0.522	0.522	strong		0.692	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
SLC25A37	51312	hgsc.bcm.edu	37	8	23423669	23423669	+	Missense_Mutation	SNP	A	A	G	rs2942194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:23423669A>G	ENST00000519973.1	+	2	457	c.259A>G	c.(259-261)Atc>Gtc	p.I87V	SLC25A37_ENST00000517923.1_3'UTR	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	87			I -> V (in dbSNP:rs2942194).		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)		GTACACAAGTATCTACGGAGC	0.522													A|||	867	0.173123	0.0197	0.2421	5008	,	,		17834	0.2163		0.2922	False		,,,				2504	0.1646				p.I87V		Atlas-SNP	.											.	SLC25A37	27	.	0			c.A259G						PASS	.	A	VAL/ILE	224,3528		8,208,1660	50.0	46.0	48.0		259	3.5	0.6	8	dbSNP_101	48	2270,5940		334,1602,2169	yes	missense	SLC25A37	NM_016612.2	29	342,1810,3829	GG,GA,AA		27.6492,5.9701,20.8494	benign	87/339	23423669	2494,9468	1876	4105	5981	SO:0001583	missense	51312	exon2			ACAAGTATCTACG	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.259A>G	8.37:g.23423669A>G	ENSP00000429200:p.Ile87Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	436	0.19963369963369965	9	0.018292682926829267	101	0.27900552486187846	114	0.1993006993006993	212	0.2796833773087071	A	4.840	0.156136	0.09236	0.059701	0.276492	ENSG00000147454	ENST00000519973;ENST00000523930	T;T	0.79352	-1.26;-1.26	5.63	3.49	0.39957	Mitochondrial carrier domain (2);	0.108721	0.64402	N	0.000008	T	0.00012	0.0000	N	0.02865	-0.47	0.30069	P	0.8102119999999999	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.09818	-1.0657	9	0.02654	T	1	-0.971	5.0266	0.14389	0.4417:0.0:0.5583:0.0	rs2942194;rs3736031;rs17778429;rs61300777;rs2942194	87;87	Q9NYZ2;Q9NYZ2-2	MFRN1_HUMAN;.	V	87;68	ENSP00000429200:I87V;ENSP00000428066:I68V	ENSP00000290075:I87V	I	+	1	0	SLC25A37	23479614	1.000000	0.71417	0.591000	0.28745	0.960000	0.62799	4.460000	0.60108	0.457000	0.26962	0.533000	0.62120	ATC	A|0.818;G|0.182	0.182	strong		0.522	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612	
EBF1	1879	hgsc.bcm.edu	37	5	158139318	158139318	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:158139318C>T	ENST00000313708.6	-	14	1675	c.1393G>A	c.(1393-1395)Gta>Ata	p.V465I	EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000380654.4_Missense_Mutation_p.V434I|EBF1_ENST00000517373.1_Intron	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	465	Pro/Ser/Thr-rich.				multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|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)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGTGGTGATACGCTGCTTGAG	0.587			T	HMGA2	lipoma																																p.V465I		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	EBF1,colon,carcinoma,+2,1	EBF1	110	1	0			c.G1393A						scavenged	.						95.0	73.0	81.0					5																	158139318		2203	4300	6503	SO:0001583	missense	1879	exon14			GTGATACGCTGCT	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"""early B-cell factor"""	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1393G>A	5.37:g.158139318C>T	ENSP00000322898:p.Val465Ile	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	171	3	0.0175439	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	37	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.217227	0.79352	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654	T;T	0.47177	0.85;0.85	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.60894	0.2304	L	0.54323	1.7	0.80722	D	1	P;D;P;D	0.60160	0.879;0.987;0.896;0.969	B;P;B;P	0.62014	0.266;0.897;0.277;0.468	T	0.55598	-0.8116	10	0.22706	T	0.39	-5.7472	18.1731	0.89753	0.0:1.0:0.0:0.0	.	465;452;465;434	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	I	465;465;434	ENSP00000322898:V465I;ENSP00000370029:V434I	ENSP00000322898:V465I	V	-	1	0	EBF1	158071896	1.000000	0.71417	0.961000	0.40146	0.863000	0.49368	7.769000	0.85360	2.357000	0.79964	0.650000	0.86243	GTA	.	.	none		0.587	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007	
CPT2	1376	hgsc.bcm.edu	37	1	53668099	53668099	+	Missense_Mutation	SNP	C	C	T	rs74315294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:53668099C>T	ENST00000371486.3	+	3	853	c.338C>T	c.(337-339)tCg>tTg	p.S113L	CPT2_ENST00000468572.1_3'UTR	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	113			S -> L (in CPT2D; muscular form; frequent mutation; dbSNP:rs74315294). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15622536, ECO:0000269|PubMed:8358442, ECO:0000269|PubMed:9758712}.		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	AGCTACATTTCGGGTAGGTAG	0.418													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		20386	0.0		0.001	False		,,,				2504	0.0				p.S113L		Atlas-SNP	.											CPT2,right_upper_lobe,carcinoma,0,1	CPT2	34	1	0			c.C338T	GRCh37	CM930171	CPT2	M	rs74315294	PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	92.0	89.0	90.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	338	5.9	1.0	1	dbSNP_131	90	16,8584	11.9+/-42.8	0,16,4284	yes	missense	CPT2	NM_000098.2	145	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	probably-damaging	113/659	53668099	18,12988	2203	4300	6503	SO:0001583	missense	1376	exon3			ACATTTCGGGTAG	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.338C>T	1.37:g.53668099C>T	ENSP00000360541:p.Ser113Leu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	123	78	0.634146	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	33	5.265643	0.95399	4.54E-4	0.00186	ENSG00000157184	ENST00000371486	D	0.90676	-2.71	5.88	5.88	0.94601	.	0.064942	0.64402	D	0.000004	D	0.96889	0.8984	H	0.94306	3.52	0.80722	A	1	D	0.76494	0.999	D	0.73708	0.981	D	0.97157	0.9835	9	0.66056	D	0.02	-1.9784	19.8509	0.96740	0.0:1.0:0.0:0.0	.	113	P23786	CPT2_HUMAN	L	113	ENSP00000360541:S113L	ENSP00000360541:S113L	S	+	2	0	CPT2	53440687	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	6.952000	0.75989	2.797000	0.96272	0.561000	0.74099	TCG	C|0.999;T|0.001	0.001	strong		0.418	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098	
REXO1	57455	hgsc.bcm.edu	37	19	1827565	1827565	+	Missense_Mutation	SNP	A	A	G	rs10415018	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1827565A>G	ENST00000170168.4	-	2	1317	c.1223T>C	c.(1222-1224)gTg>gCg	p.V408A	REXO1_ENST00000587524.1_5'Flank	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	408			V -> A (in dbSNP:rs10415018).			nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		GGGCTTCTCCACAGGCCGCCC	0.662													.|||	1236	0.246805	0.3669	0.3458	5008	,	,		13078	0.2629		0.1054	False		,,,				2504	0.1431				p.V408A		Atlas-SNP	.											REXO1,NS,carcinoma,0,1	REXO1	55	1	0			c.T1223C						PASS	.	G	ALA/VAL	1444,2932		232,980,976	15.0	17.0	17.0		1223	-0.9	0.0	19	dbSNP_119	17	857,7703		47,763,3470	no	missense	REXO1	NM_020695.3	64	279,1743,4446	GG,GA,AA		10.0117,32.9982,17.7876	benign	408/1222	1827565	2301,10635	2188	4280	6468	SO:0001583	missense	57455	exon2			TTCTCCACAGGCC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.1223T>C	19.37:g.1827565A>G	ENSP00000170168:p.Val408Ala	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	51	10	0.196078	NM_020695	Q9ULT2	Missense_Mutation	SNP	ENST00000170168.4	37	CCDS32866.1	534	0.2445054945054945	196	0.3983739837398374	107	0.2955801104972376	158	0.2762237762237762	73	0.09630606860158311	G	0.006	-2.052309	0.00394	0.329982	0.100117	ENSG00000079313	ENST00000170168	T	0.10860	2.83	3.97	-0.92	0.10475	.	1.467800	0.03856	N	0.273126	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	0.45629	-0.9248	9	0.08599	T	0.76	1.2749	0.6493	0.00824	0.2097:0.2826:0.2637:0.2441	rs10415018;rs10415018	408	Q8N1G1	REXO1_HUMAN	A	408	ENSP00000170168:V408A	ENSP00000170168:V408A	V	-	2	0	REXO1	1778565	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.507000	0.06352	-0.526000	0.06383	-1.272000	0.01410	GTG	A|0.781;G|0.219	0.219	strong		0.662	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
NAGK	55577	hgsc.bcm.edu	37	2	71297695	71297695	+	Silent	SNP	T	T	C	rs2287328	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:71297695T>C	ENST00000244204.6	+	2	155	c.93T>C	c.(91-93)gaT>gaC	p.D31D	NAGK_ENST00000428360.2_3'UTR|NAGK_ENST00000443872.2_Intron|NAGK_ENST00000455662.2_Silent_p.D77D|NAGK_ENST00000443938.2_Silent_p.D31D|NAGK_ENST00000418807.3_Intron|RP11-467P9.1_ENST00000608897.1_lincRNA			Q9UJ70	NAGK_HUMAN	N-acetylglucosamine kinase	31					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)	CAGAAGCAGATGGACTGAGCA	0.507											OREG0014689	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	718	0.143371	0.115	0.1729	5008	,	,		20063	0.1438		0.1431	False		,,,				2504	0.1605				p.D77D		Atlas-SNP	.											.	NAGK	34	.	0			c.T231C						PASS	.	T		624,3782	269.5+/-269.1	45,534,1624	93.0	99.0	97.0		231	-3.1	1.0	2	dbSNP_100	97	1344,7256	264.3+/-285.5	115,1114,3071	yes	coding-synonymous	NAGK	NM_017567.4		160,1648,4695	CC,CT,TT		15.6279,14.1625,15.1315		77/391	71297695	1968,11038	2203	4300	6503	SO:0001819	synonymous_variant	55577	exon2			AGCAGATGGACTG	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.93T>C	2.37:g.71297695T>C		Somatic	131	0	0	1128	WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_017567	B4DLZ5|Q53HD5|Q6IA84|Q9BS29|Q9BVP0|Q9NV37	Silent	SNP	ENST00000244204.6	37		304	0.1391941391941392	61	0.12398373983739837	64	0.17679558011049723	71	0.12412587412587413	108	0.1424802110817942	T	10.39	1.337451	0.24253	0.141625	0.156279	ENSG00000124357	ENST00000443938	.	.	.	4.95	-3.11	0.05299	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.27262	-1.0079	3	.	.	.	-10.7669	6.0596	0.19830	0.3968:0.0:0.3727:0.2306	rs2287328;rs17501162;rs2287328	.	.	.	T	53	.	.	M	+	2	0	NAGK	71151203	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	0.766000	0.26560	-0.245000	0.09625	-0.490000	0.04691	ATG	T|0.851;C|0.149	0.149	strong		0.507	NAGK-032	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471889.1		
B4GALT3	8703	hgsc.bcm.edu	37	1	161141691	161141691	+	Missense_Mutation	SNP	C	C	T	rs111614721	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161141691C>T	ENST00000319769.5	-	8	1319	c.1097G>A	c.(1096-1098)cGt>cAt	p.R366H	B4GALT3_ENST00000470882.1_5'UTR|PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000367998.1_Missense_Mutation_p.R366H	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	366					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)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)	p.R366H(1)		cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	CATCTCTTGACGGAAGGCTTG	0.607													C|||	7	0.00139776	0.0045	0.0014	5008	,	,		17177	0.0		0.0	False		,,,				2504	0.0				p.R366H		Atlas-SNP	.											B4GALT3,NS,carcinoma,0,1	B4GALT3	39	1	1	Substitution - Missense(1)	lung(1)	c.G1097A						scavenged	.	C	HIS/ARG,HIS/ARG,HIS/ARG	25,4381	30.8+/-60.4	0,25,2178	61.0	69.0	66.0		1097,1097,1097	5.3	1.0	1	dbSNP_132	66	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	B4GALT3	NM_001199873.1,NM_001199874.1,NM_003779.3	29,29,29	0,26,6477	TT,TC,CC		0.0116,0.5674,0.1999	probably-damaging,probably-damaging,probably-damaging	366/394,366/394,366/394	161141691	26,12980	2203	4300	6503	SO:0001583	missense	8703	exon8			TCTTGACGGAAGG	BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.1097G>A	1.37:g.161141691C>T	ENSP00000320965:p.Arg366His	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	187	6	0.0320856	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Missense_Mutation	SNP	ENST00000319769.5	37	CCDS1222.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	16.28	3.077763	0.55753	0.005674	1.16E-4	ENSG00000158850	ENST00000319769;ENST00000407555;ENST00000367998;ENST00000367997	T;T	0.54071	0.59;0.59	5.28	5.28	0.74379	.	0.161578	0.42053	D	0.000766	T	0.40067	0.1102	N	0.22421	0.69	0.42130	D	0.991461	D	0.64830	0.994	P	0.49085	0.6	T	0.45205	-0.9277	10	0.87932	D	0	.	17.8577	0.88771	0.0:1.0:0.0:0.0	.	366	O60512	B4GT3_HUMAN	H	366;343;366;366	ENSP00000320965:R366H;ENSP00000356977:R366H	ENSP00000320965:R366H	R	-	2	0	B4GALT3	159408315	0.748000	0.28294	1.000000	0.80357	0.997000	0.91878	0.931000	0.28871	2.746000	0.94184	0.655000	0.94253	CGT	C|0.998;T|0.002	0.002	strong		0.607	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779	
ZNF727	442319	hgsc.bcm.edu	37	7	63538777	63538777	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:63538777G>A	ENST00000550760.3	+	4	1529	c.1350G>A	c.(1348-1350)aaG>aaA	p.K450K	RP11-3N2.13_ENST00000445978.1_RNA	NM_001159522.1	NP_001152994.1	A8MUV8	ZN727_HUMAN	zinc finger protein 727	450					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(2)|skin(1)|stomach(1)|urinary_tract(1)	8						CTGGAGAGAAGCCCTACAAAT	0.408																																					p.K450K		Atlas-SNP	.											ZNF727,NS,carcinoma,0,1	ZNF727	35	1	0			c.G1350A						scavenged	.						47.0	44.0	45.0					7																	63538777		692	1591	2283	SO:0001819	synonymous_variant	442319	exon4			AGAGAAGCCCTAC			7q11.21	2014-09-09	2014-09-09	2014-09-09	ENSG00000214652	ENSG00000214652		"""Zinc fingers, C2H2-type"", ""-"""	22785	pseudogene	pseudogene			"""zinc finger protein 727, pseudogene"""	ZNF727P			Standard	NM_001159522		Approved		uc011kdm.2	A8MUV8	OTTHUMG00000156536	ENST00000550760.3:c.1350G>A	7.37:g.63538777G>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	128	3	0.0234375	NM_001159522		Silent	SNP	ENST00000550760.3	37	CCDS55113.1																																																																																			.	.	none		0.408	ZNF727-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001159522	
FRG1	2483	hgsc.bcm.edu	37	4	190873335	190873335	+	Missense_Mutation	SNP	C	C	T	rs191989708		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:190873335C>T	ENST00000226798.4	+	3	374	c.152C>T	c.(151-153)aCa>aTa	p.T51I	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	51					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.T51I(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)		TGGACAGTAACAAACTTTGGT	0.318																																					p.T51I		Atlas-SNP	.											FRG1,trunk,malignant_melanoma,0,1	FRG1	76	1	1	Substitution - Missense(1)	skin(1)	c.C152T						scavenged	.						75.0	88.0	84.0					4																	190873335		2201	4292	6493	SO:0001583	missense	2483	exon3			CAGTAACAAACTT	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.152C>T	4.37:g.190873335C>T	ENSP00000226798:p.Thr51Ile	Somatic	154	6	0.038961		WXS	Illumina HiSeq	Phase_I	132	14	0.106061	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	10.16	1.274422	0.23307	.	.	ENSG00000109536	ENST00000226798	T	0.31510	1.49	3.47	3.47	0.39725	.	0.513050	0.23249	N	0.050263	T	0.16171	0.0389	N	0.19112	0.55	0.09310	N	1	P	0.34462	0.454	B	0.26969	0.075	T	0.13176	-1.0519	10	0.48119	T	0.1	-12.4703	8.4161	0.32672	0.2332:0.7668:0.0:0.0	.	51	Q14331	FRG1_HUMAN	I	51	ENSP00000226798:T51I	ENSP00000226798:T51I	T	+	2	0	FRG1	191110329	0.290000	0.24343	0.875000	0.34327	0.947000	0.59692	1.089000	0.30890	2.238000	0.73509	0.539000	0.68188	ACA	.	.	weak		0.318	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
CELSR3	1951	hgsc.bcm.edu	37	3	48681053	48681053	+	Silent	SNP	C	C	T	rs9868809	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	87	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	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	
RNASEL	6041	hgsc.bcm.edu	37	1	182554557	182554557	+	Missense_Mutation	SNP	C	C	T	rs486907	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	351	0	0		WXS	Illumina HiSeq	Phase_I	432	260	0.601852	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	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390155	208390155	+	Silent	SNP	C	C	T	rs4844657	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:208390155C>T	ENST00000367033.3	-	2	1870	c.1113G>A	c.(1111-1113)ctG>ctA	p.L371L		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	371	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		AGCAGGACTGCAGGCGCTCCT	0.612													C|||	639	0.127596	0.0461	0.2046	5008	,	,		22102	0.1429		0.2078	False		,,,				2504	0.0849				p.L371L		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G1113A						PASS	.	C		258,4148	146.5+/-181.1	8,242,1953	70.0	67.0	68.0		1113	0.8	1.0	1	dbSNP_111	68	1646,6954	303.7+/-306.6	167,1312,2821	no	coding-synonymous	PLXNA2	NM_025179.3		175,1554,4774	TT,TC,CC		19.1395,5.8557,14.6394		371/1895	208390155	1904,11102	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			GGACTGCAGGCGC	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.1113G>A	1.37:g.208390155C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	136	88	0.647059	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			C|0.856;T|0.144	0.144	strong		0.612	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
ZSWIM4	65249	hgsc.bcm.edu	37	19	13941022	13941022	+	Missense_Mutation	SNP	A	A	C	rs56177954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13941022A>C	ENST00000254323.2	+	13	2317	c.2128A>C	c.(2128-2130)Aat>Cat	p.N710H	ZSWIM4_ENST00000440752.2_Missense_Mutation_p.N544H	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	710							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			AGCCCTGATGAATATCATGCA	0.582													A|||	34	0.00678914	0.0008	0.0101	5008	,	,		19352	0.0		0.0199	False		,,,				2504	0.0061				p.N710H		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.A2128C						PASS	.	A	HIS/ASN	25,4381	33.5+/-64.1	0,25,2178	68.0	68.0	68.0		2128	3.1	1.0	19	dbSNP_129	68	232,8368	95.6+/-157.4	3,226,4071	yes	missense	ZSWIM4	NM_023072.2	68	3,251,6249	CC,CA,AA		2.6977,0.5674,1.976	benign	710/990	13941022	257,12749	2203	4300	6503	SO:0001583	missense	65249	exon13			CTGATGAATATCA	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"""Zinc fingers, SWIM-type"""	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.2128A>C	19.37:g.13941022A>C	ENSP00000254323:p.Asn710His	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	22	0.010073260073260074	0	0.0	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	16.27	3.077036	0.55753	0.005674	0.026977	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.43294	0.95;0.95	4.16	3.1	0.35709	.	0.280852	0.28618	N	0.014703	T	0.12475	0.0303	L	0.36672	1.1	0.26636	N	0.972389	B;B	0.20988	0.007;0.05	B;B	0.21917	0.003;0.037	T	0.13045	-1.0524	10	0.54805	T	0.06	-40.4042	8.7378	0.34539	0.8078:0.1922:0.0:0.0	rs56177954	544;710	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	H	710;544	ENSP00000254323:N710H;ENSP00000405278:N544H	ENSP00000254323:N710H	N	+	1	0	ZSWIM4	13802022	1.000000	0.71417	0.994000	0.49952	0.820000	0.46376	7.110000	0.77069	0.429000	0.26202	0.402000	0.26972	AAT	A|0.984;C|0.016	0.016	strong		0.582	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
RFWD3	55159	hgsc.bcm.edu	37	16	74664698	74664698	+	Silent	SNP	A	A	G	rs78796563	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74664698A>G	ENST00000361070.4	-	10	1832	c.1735T>C	c.(1735-1737)Tta>Cta	p.L579L	RFWD3_ENST00000571750.1_Silent_p.L579L	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	579					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L579L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TGAGCTACTAACTCCTGCACA	0.473													A|||	67	0.0133786	0.0023	0.0259	5008	,	,		18719	0.0		0.0288	False		,,,				2504	0.0174				p.L579L		Atlas-SNP	.											RFWD3,NS,carcinoma,0,1	RFWD3	49	1	1	Substitution - coding silent(1)	lung(1)	c.T1735C						PASS	.	A		28,4368	32.6+/-62.9	1,26,2171	94.0	70.0	78.0		1735	3.5	0.3	16	dbSNP_132	78	267,8333	102.3+/-163.5	4,259,4037	no	coding-synonymous	RFWD3	NM_018124.3		5,285,6208	GG,GA,AA		3.1047,0.6369,2.2699		579/775	74664698	295,12701	2198	4300	6498	SO:0001819	synonymous_variant	55159	exon10			CTACTAACTCCTG	AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.1735T>C	16.37:g.74664698A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	87	16	0.183908	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Silent	SNP	ENST00000361070.4	37	CCDS32486.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
SAGE1	55511	hgsc.bcm.edu	37	X	134990000	134990000	+	Splice_Site	SNP	C	C	T	rs41301507	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:134990000C>T	ENST00000370709.3	+	9	1159	c.1159C>T	c.(1159-1161)Cat>Tat	p.H387Y	SAGE1_ENST00000324447.3_Splice_Site_p.H387Y|SAGE1_ENST00000535938.1_Splice_Site_p.H387Y|SAGE1_ENST00000537770.1_Intron			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	387						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)					CAGGGATCAGCGTAAGTTTGT	0.428													c|||	207	0.0548344	0.0204	0.0346	3775	,	,		18537	0.0397		0.0527	False		,,,				2504	0.0644				p.H387Y		Atlas-SNP	.											.	SAGE1	160	.	0			c.C1159T						PASS	.	C	TYR/HIS	234,3601		6,195,27,1431,544	179.0	151.0	160.0		1159		0.0	X	dbSNP_127	160	487,6239		13,337,124,2077,1748	yes	missense-near-splice	SAGE1	NM_018666.2	83	19,532,151,3508,2292	TT,TC,T,CC,C		7.2406,6.1017,6.827	benign	387/905	134990000	721,9840	2203	4299	6502	SO:0001630	splice_region_variant	55511	exon10			GATCAGCGTAAGT	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.1159+1C>T	X.37:g.134990000C>T		Somatic	424	0	0		WXS	Illumina HiSeq	Phase_I	191	187	0.979058	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	37	CCDS14652.1	84	0.05063291139240506	10	0.020491803278688523	8	0.022857142857142857	14	0.025179856115107913	22	0.030136986301369864	C	0.001	-3.245180	0.00022	0.061017	0.072406	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000370709	T;T;T	0.48201	0.82;0.82;0.82	.	.	.	.	0.137514	0.47455	U	0.000240	T	0.00784	0.0026	N	0.01576	-0.805	0.80722	P	0.0	B	0.15473	0.013	B	0.06405	0.002	T	0.12656	-1.0539	7	0.02654	T	1	.	.	.	.	rs41301507	387	Q9NXZ1	SAGE1_HUMAN	Y	387	ENSP00000323191:H387Y;ENSP00000445959:H387Y;ENSP00000359743:H387Y	ENSP00000323191:H387Y	H	+	1	0	SAGE1	134817666	0.003000	0.15002	0.009000	0.14445	0.037000	0.13140	-1.917000	0.01575	-1.344000	0.02216	-1.330000	0.01273	CAT	C|0.937;T|0.063	0.063	strong		0.428	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	Missense_Mutation
SCRIB	23513	hgsc.bcm.edu	37	8	144885669	144885669	+	Missense_Mutation	SNP	G	G	C	rs138257744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144885669G>C	ENST00000320476.3	-	24	3493	c.3487C>G	c.(3487-3489)Cag>Gag	p.Q1163E	SCRIB_ENST00000356994.2_Missense_Mutation_p.Q1163E|SCRIB_ENST00000377533.3_Missense_Mutation_p.Q1082E	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1163	Interaction with ARHGEF7.|PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			AGCAGGCTCTGCTGGTTCACC	0.692													G|||	17	0.00339457	0.0	0.0	5008	,	,		11201	0.0169		0.0	False		,,,				2504	0.0				p.Q1163E	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C3487G						PASS	.	G	GLU/GLN,GLU/GLN	2,4362		0,2,2180	20.0	20.0	20.0		3487,3487	4.8	1.0	8	dbSNP_134	20	0,8554		0,0,4277	yes	missense,missense	SCRIB	NM_015356.3,NM_182706.3	29,29	0,2,6457	CC,CG,GG		0.0,0.0458,0.0155	possibly-damaging,possibly-damaging	1163/1631,1163/1656	144885669	2,12916	2182	4277	6459	SO:0001583	missense	23513	exon24			GGCTCTGCTGGTT	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.3487C>G	8.37:g.144885669G>C	ENSP00000322938:p.Gln1163Glu	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	0|0	0.0|0.0	7|7	0.012237762237762238|0.012237762237762238	0|0	0.0|0.0	G|G	17.95|17.95	3.514052|3.514052	0.64522|0.64522	4.58E-4|4.58E-4	0.0|0.0	ENSG00000180900|ENSG00000180900	ENST00000526832|ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	.|T;T;T	.|0.27256	.|1.68;1.68;1.68	4.82|4.82	4.82|4.82	0.62117|0.62117	.|PDZ/DHR/GLGF (4);	.|.	.|.	.|.	.|.	T|T	0.16085|0.16085	0.0387|0.0387	N|N	0.10618|0.10618	0.005|0.005	0.24765|0.24765	N|N	0.99291|0.99291	.|P;P	.|0.48089	.|0.855;0.905	.|P;P	.|0.50860	.|0.634;0.652	T|T	0.13629|0.13629	-1.0502|-1.0502	5|9	.|0.30854	.|T	.|0.27	.|.	15.1122|15.1122	0.72368|0.72368	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1163;1163	.|Q14160;Q14160-3	.|SCRIB_HUMAN;.	G|E	158|1163;1163;1082;532	.|ENSP00000349486:Q1163E;ENSP00000322938:Q1163E;ENSP00000366756:Q1082E	.|ENSP00000322938:Q1163E	A|Q	-|-	2|1	0|0	SCRIB|SCRIB	144957657|144957657	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	5.594000|5.594000	0.67557|0.67557	2.222000|2.222000	0.72286|0.72286	0.456000|0.456000	0.33151|0.33151	GCA|CAG	G|0.999;C|0.001	0.001	strong		0.692	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
CCDC180	100499483	hgsc.bcm.edu	37	9	100070351	100070351	+	Silent	SNP	G	G	C	rs12683119	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100070351G>C	ENST00000357054.1	+	16	1490	c.555G>C	c.(553-555)tcG>tcC	p.S185S	CCDC180_ENST00000395220.1_Silent_p.S185S|CCDC180_ENST00000411667.2_Silent_p.S46S|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Silent_p.S46S|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	133	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	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	
RNF145	153830	hgsc.bcm.edu	37	5	158603839	158603839	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:158603839A>G	ENST00000424310.2	-	5	781	c.422T>C	c.(421-423)aTg>aCg	p.M141T	RNF145_ENST00000520638.1_Missense_Mutation_p.M155T|RNF145_ENST00000518802.1_Missense_Mutation_p.M171T|RNF145_ENST00000274542.2_Missense_Mutation_p.M169T|RNF145_ENST00000519865.1_Missense_Mutation_p.M141T|RNF145_ENST00000521606.2_Missense_Mutation_p.M158T	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	141						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.M169T(4)		endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTTGTTTTCATGACACAGGA	0.363																																					p.M171T		Atlas-SNP	.											RNF145,NS,carcinoma,0,4	RNF145	110	4	4	Substitution - Missense(4)	endometrium(3)|lung(1)	c.T512C						scavenged	.						35.0	33.0	34.0					5																	158603839		2201	4298	6499	SO:0001583	missense	153830	exon5			GTTTTCATGACAC	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.422T>C	5.37:g.158603839A>G	ENSP00000409064:p.Met141Thr	Somatic	224	4	0.0178571		WXS	Illumina HiSeq	Phase_I	240	13	0.0541667	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.282699	0.80692	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.77229	-1.08;-1.06;-1.06;-1.07;-1.07;-1.08;-1.07	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.81725	0.4883	L	0.44542	1.39	0.80722	D	1	D;D;D;D;D;D	0.57257	0.979;0.979;0.979;0.979;0.979;0.974	P;P;P;P;P;P	0.57846	0.828;0.828;0.828;0.828;0.76;0.736	D	0.83797	0.0234	10	0.72032	D	0.01	-20.3428	15.6548	0.77124	1.0:0.0:0.0:0.0	.	157;158;155;171;141;169	E7EW26;B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;.;RN145_HUMAN;.	T	169;141;141;157;158;171;141;155	ENSP00000274542:M169T;ENSP00000430397:M141T;ENSP00000409064:M141T;ENSP00000430753:M157T;ENSP00000445115:M158T;ENSP00000430955:M171T;ENSP00000429071:M155T	ENSP00000274542:M169T	M	-	2	0	RNF145	158536417	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.162000	0.67917	0.377000	0.23210	ATG	.	.	none		0.363	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
KIAA1024	23251	hgsc.bcm.edu	37	15	79749447	79749447	+	Missense_Mutation	SNP	G	G	T	rs11634652	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:79749447G>T	ENST00000305428.3	+	2	1033	c.958G>T	c.(958-960)Gtt>Ttt	p.V320F		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	320			V -> F (in dbSNP:rs11634652).			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						GTATTCCCCGGTTCCTGACAA	0.522													G|||	670	0.133786	0.3321	0.049	5008	,	,		18437	0.0823		0.0636	False		,,,				2504	0.0511				p.V320F		Atlas-SNP	.											.	KIAA1024	146	.	0			c.G958T						PASS	.	G	PHE/VAL	1225,3167	425.3+/-340.8	180,865,1151	127.0	135.0	132.0		958	-1.6	0.0	15	dbSNP_120	132	523,8063	146.5+/-202.0	14,495,3784	yes	missense	KIAA1024	NM_015206.2	50	194,1360,4935	TT,TG,GG		6.0913,27.8916,13.4689	benign	320/917	79749447	1748,11230	2196	4293	6489	SO:0001583	missense	23251	exon2			TCCCCGGTTCCTG	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.958G>T	15.37:g.79749447G>T	ENSP00000307461:p.Val320Phe	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	70	21	0.3	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	285	0.1304945054945055	167	0.3394308943089431	23	0.06353591160220995	46	0.08041958041958042	49	0.06464379947229551	G	10.64	1.407212	0.25378	0.278916	0.060913	ENSG00000169330	ENST00000305428	T	0.32515	1.45	5.01	-1.58	0.08479	.	0.611918	0.15992	N	0.234776	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.29085	0.232	B	0.24701	0.055	T	0.46133	-0.9213	8	.	.	.	.	6.2025	0.20583	0.4768:0.1324:0.3908:0.0	rs11634652;rs52819290;rs56800743;rs11634652	320	Q9UPX6	K1024_HUMAN	F	320	ENSP00000307461:V320F	.	V	+	1	0	KIAA1024	77536502	0.000000	0.05858	0.000000	0.03702	0.935000	0.57460	0.248000	0.18198	-0.097000	0.12307	0.591000	0.81541	GTT	G|0.866;T|0.134	0.134	strong		0.522	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
FPR3	2359	hgsc.bcm.edu	37	19	52327479	52327479	+	Missense_Mutation	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52327479A>T	ENST00000339223.4	+	2	657	c.478A>T	c.(478-480)Aat>Tat	p.N160Y	FPR3_ENST00000595991.1_Missense_Mutation_p.N160Y	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	160					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)			NS(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)	35						TACCTTACCAAATTTCATCTT	0.478																																					p.N160Y		Atlas-SNP	.											.	FPR3	66	.	0			c.A478T						PASS	.						134.0	122.0	126.0					19																	52327479		2203	4300	6503	SO:0001583	missense	2359	exon2			TTACCAAATTTCA		CCDS12841.1	19q13.3-q13.4	2012-08-08	2008-04-17	2008-04-17		ENSG00000187474		"""GPCR / Class A : Formyl peptide receptors"""	3828	protein-coding gene	gene with protein product		136539	"""formyl peptide receptor-like 2"""	FPRL2		1612600, 8198572	Standard	NM_002030		Approved	FPRH1, FMLPY, RMLP-R-I	uc002pxt.1	P25089		ENST00000339223.4:c.478A>T	19.37:g.52327479A>T	ENSP00000341821:p.Asn160Tyr	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	243	97	0.399177	NM_002030		Missense_Mutation	SNP	ENST00000339223.4	37	CCDS12841.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.601169	0.00123	.	.	ENSG00000187474	ENST00000339223	T	0.36520	1.25	2.34	-4.67	0.03319	GPCR, rhodopsin-like superfamily (1);	0.726121	0.12818	N	0.436647	T	0.08268	0.0206	N	0.00926	-1.1	0.09310	N	1	B	0.06786	0.001	B	0.16722	0.016	T	0.19712	-1.0297	10	0.02654	T	1	.	6.9341	0.24457	0.6963:0.0:0.1696:0.1341	.	160	P25089	FPR3_HUMAN	Y	160	ENSP00000341821:N160Y	ENSP00000341821:N160Y	N	+	1	0	FPR3	57019291	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.708000	0.05035	-1.822000	0.01211	-1.486000	0.00981	AAT	.	.	none		0.478	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030	
DIS3L2	129563	hgsc.bcm.edu	37	2	232879671	232879671	+	Missense_Mutation	SNP	C	C	T	rs723044	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:232879671C>T	ENST00000409307.1	+	1	34	c.34C>T	c.(34-36)Ccc>Tcc	p.P12S	DIS3L2_ENST00000325385.7_Missense_Mutation_p.P12S|AC105461.1_ENST00000413841.1_RNA|DIS3L2_ENST00000360410.4_Missense_Mutation_p.P12S|DIS3L2_ENST00000409401.3_Missense_Mutation_p.P12S|DIS3L2_ENST00000273009.6_Missense_Mutation_p.P12S					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		GAACCTCCGGCCCCTGGGGAC	0.502													C|||	448	0.0894569	0.2413	0.0605	5008	,	,		17682	0.003		0.0219	False		,,,				2504	0.0634				p.P12S		Atlas-SNP	.											.	DIS3L2	77	.	0			c.C34T						PASS	.	C	SER/PRO	726,2952		61,604,1174	57.0	58.0	58.0		34	0.3	0.6	2	dbSNP_86	58	237,7947		5,227,3860	yes	missense	DIS3L2	NM_152383.4	74	66,831,5034	TT,TC,CC		2.8959,19.739,8.1184	benign	12/886	232879671	963,10899	1839	4092	5931	SO:0001583	missense	129563	exon2			CTCCGGCCCCTGG	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.34C>T	2.37:g.232879671C>T	ENSP00000386799:p.Pro12Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_001257282		Missense_Mutation	SNP	ENST00000409307.1	37	CCDS42834.1	141	0.06456043956043957	100	0.2032520325203252	22	0.06077348066298342	1	0.0017482517482517483	18	0.023746701846965697	C	0.009	-1.821606	0.00589	0.19739	0.028959	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000360410;ENST00000409401;ENST00000441279;ENST00000431466;ENST00000409307	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.51	0.349	0.16032	.	0.406243	0.21185	N	0.078742	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	0.32534	-0.9903	9	0.16896	T	0.51	-6.9606	5.592	0.17307	0.0:0.513:0.264:0.223	rs723044;rs723044	12;12	Q8IYB7;Q8IYB7-4	DI3L2_HUMAN;.	S	12	ENSP00000273009:P12S;ENSP00000315569:P12S;ENSP00000353584:P12S;ENSP00000386594:P12S;ENSP00000390467:P12S;ENSP00000386799:P12S	ENSP00000273009:P12S	P	+	1	0	DIS3L2	232587915	0.785000	0.28726	0.610000	0.28997	0.012000	0.07955	-0.288000	0.08377	-0.239000	0.09710	-0.244000	0.11960	CCC	C|0.930;T|0.070	0.070	strong		0.502	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	
FAM160A2	84067	hgsc.bcm.edu	37	11	6238960	6238960	+	Missense_Mutation	SNP	C	C	A	rs3750943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6238960C>A	ENST00000449352.2	-	9	2119	c.1856G>T	c.(1855-1857)cGg>cTg	p.R619L	FAM160A2_ENST00000524416.1_Missense_Mutation_p.R619L|FAM160A2_ENST00000529360.1_5'Flank|FAM160A2_ENST00000265978.4_Missense_Mutation_p.R633L			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	619			R -> L (in dbSNP:rs3750943).		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						acccccagcccgccccctcct	0.652													A|||	654	0.130591	0.059	0.0778	5008	,	,		8807	0.2431		0.1461	False		,,,				2504	0.1329				p.R633L		Atlas-SNP	.											.	FAM160A2	100	.	0			c.G1898T						PASS	.	A	LEU/ARG,LEU/ARG	318,4002		17,284,1859	9.0	10.0	10.0		1856,1898	4.0	0.9	11	dbSNP_107	10	1364,7104		122,1120,2992	no	missense,missense	FAM160A2	NM_001098794.1,NM_032127.3	102,102	139,1404,4851	AA,AC,CC		16.1077,7.3611,13.153	benign,benign	619/973,633/987	6238960	1682,11106	2160	4234	6394	SO:0001583	missense	84067	exon9			CCAGCCCGCCCCC		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.1856G>T	11.37:g.6238960C>A	ENSP00000416918:p.Arg619Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	37	CCDS44530.1	320	0.14652014652014653	37	0.07520325203252033	36	0.09944751381215469	125	0.21853146853146854	122	0.16094986807387862	A	1.787	-0.480378	0.04383	0.073611	0.161077	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	T;T;T	0.46819	0.86;0.86;0.86	5.16	3.97	0.46021	.	0.645966	0.14866	N	0.293783	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.24764	-1.0151	9	0.09084	T	0.74	-18.0925	5.0671	0.14587	0.6113:0.1554:0.0:0.2333	rs3750943	619;619;633	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	L	619;544;633;619	ENSP00000416918:R619L;ENSP00000265978:R633L;ENSP00000431773:R619L	ENSP00000265978:R633L	R	-	2	0	FAM160A2	6195536	0.534000	0.26362	0.881000	0.34555	0.135000	0.20990	1.447000	0.35101	0.994000	0.38892	-0.363000	0.07495	CGG	C|0.853;A|0.147	0.147	strong		0.652	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
BDP1	55814	hgsc.bcm.edu	37	5	70858194	70858194	+	Silent	SNP	C	C	T	rs277941	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:70858194C>T	ENST00000358731.4	+	38	7853	c.7590C>T	c.(7588-7590)cgC>cgT	p.R2530R	BDP1_ENST00000380675.2_3'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2530					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)		GTAAGAAACGCCTAAAACCTC	0.373													.|||	1621	0.323682	0.1067	0.4928	5008	,	,		15735	0.505		0.335	False		,,,				2504	0.2986				p.R2530R		Atlas-SNP	.											.	BDP1	204	.	0			c.C7590T						PASS	.	C		549,3081		38,473,1304	74.0	69.0	71.0		7590	-0.1	0.4	5	dbSNP_79	71	2805,5341		509,1787,1777	no	coding-synonymous	BDP1	NM_018429.2		547,2260,3081	TT,TC,CC		34.4341,15.124,28.4817		2530/2625	70858194	3354,8422	1815	4073	5888	SO:0001819	synonymous_variant	55814	exon38			GAAACGCCTAAAA	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.7590C>T	5.37:g.70858194C>T		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Silent	SNP	ENST00000358731.4	37	CCDS43328.1																																																																																			C|0.662;T|0.338	0.338	strong		0.373	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
MLC1	23209	hgsc.bcm.edu	37	22	50515273	50515273	+	Silent	SNP	G	G	A	rs267607236|rs6010165	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50515273G>A	ENST00000311597.5	-	7	1200	c.594C>T	c.(592-594)taC>taT	p.Y198Y	MLC1_ENST00000538737.1_Silent_p.Y164Y|MLC1_ENST00000395876.2_Silent_p.Y198Y|MLC1_ENST00000535444.1_Silent_p.Y119Y|MLC1_ENST00000431262.2_Silent_p.Y168Y|MLC1_ENST00000450140.2_Silent_p.Y146Y	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	73	0	0		WXS	Illumina HiSeq	Phase_I	86	53	0.616279	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	
MTUS1	57509	hgsc.bcm.edu	37	8	17612846	17612846	+	Silent	SNP	T	T	C	rs3739408	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17612846T>C	ENST00000262102.6	-	2	695	c.471A>G	c.(469-471)ctA>ctG	p.L157L	MTUS1_ENST00000381862.3_Silent_p.L157L|MTUS1_ENST00000381869.3_Silent_p.L157L|MTUS1_ENST00000519263.1_Silent_p.L157L	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	157					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)		ATGTTTGGTTTAGCTCCAAGG	0.453													T|||	650	0.129792	0.0635	0.232	5008	,	,		10707	0.1478		0.1521	False		,,,				2504	0.1053				p.L157L		Atlas-SNP	.											.	MTUS1	144	.	0			c.A471G						PASS	.	T	,	298,3654		8,282,1686	144.0	132.0	136.0		471,471	2.9	0.8	8	dbSNP_107	136	1243,7055		80,1083,2986	no	coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2	,	88,1365,4672	CC,CT,TT		14.9795,7.5405,12.5796	,	157/1271,157/1217	17612846	1541,10709	1976	4149	6125	SO:0001819	synonymous_variant	57509	exon2			TTGGTTTAGCTCC	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.471A>G	8.37:g.17612846T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	215	89	0.413953	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			T|0.855;C|0.145	0.145	strong		0.453	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
MLKL	197259	hgsc.bcm.edu	37	16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	rs144526386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74709233C>A	ENST00000306247.7	-	4	944	c.605G>T	c.(604-606)gGc>gTc	p.G202V	MLKL_ENST00000308807.7_Intron	NM_001142497.1	NP_001135969.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						ACTGGCTGAGCCAGTCTTCAC	0.493													C|||	51	0.0101837	0.0023	0.0144	5008	,	,		19105	0.0		0.0209	False		,,,				2504	0.0174				p.G202V		Atlas-SNP	.											.	MLKL	51	.	0			c.G605T						PASS	.	C	VAL/GLY,	17,4379	23.3+/-48.9	0,17,2181	113.0	108.0	110.0		605,	-1.0	0.0	16	dbSNP_134	110	162,8438	76.3+/-139.0	2,158,4140	yes	missense,intron	MLKL	NM_001142497.1,NM_152649.2	109,	2,175,6321	AA,AC,CC		1.8837,0.3867,1.3773	,	202/264,	74709233	179,12817	2198	4300	6498	SO:0001583	missense	197259	exon4			GCTGAGCCAGTCT	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000306247.7:c.605G>T	16.37:g.74709233C>A	ENSP00000303118:p.Gly202Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	25	0.204918	NM_001142497		Missense_Mutation	SNP	ENST00000306247.7	37	CCDS45528.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	8.923	0.961462	0.18583	0.003867	0.018837	ENSG00000168404	ENST00000306247	T	0.12147	2.71	4.96	-1.05	0.10036	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.09310	N	1	D	0.67145	0.996	D	0.65573	0.936	T	0.07501	-1.0769	8	0.48119	T	0.1	.	8.2986	0.32001	0.0:0.4852:0.0:0.5148	.	202	Q8NB16-2	.	V	202	ENSP00000303118:G202V	ENSP00000303118:G202V	G	-	2	0	MLKL	73266734	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.620000	0.05565	-0.228000	0.09869	-0.374000	0.07098	GGC	C|0.986;A|0.014	0.014	strong		0.493	MLKL-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436402.1	NM_152649	
GPR1	2825	hgsc.bcm.edu	37	2	207041053	207041053	+	Missense_Mutation	SNP	T	T	C	rs3732083	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:207041053T>C	ENST00000407325.2	-	3	1281	c.919A>G	c.(919-921)Att>Gtt	p.I307V	GPR1_ENST00000437420.1_Missense_Mutation_p.I307V	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	307			I -> V (in dbSNP:rs3732083). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743}.		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TTCTTACTAATTAGGACATAA	0.488													T|||	2316	0.46246	0.6483	0.5735	5008	,	,		20495	0.2579		0.4831	False		,,,				2504	0.3221				p.I307V		Atlas-SNP	.											.	GPR1	38	.	0			c.A919G						PASS	.	T	VAL/ILE,VAL/ILE	2780,1626	662.2+/-401.0	882,1016,305	101.0	100.0	100.0		919,919	5.7	1.0	2	dbSNP_107	100	3870,4730	542.9+/-384.3	881,2108,1311	yes	missense,missense	GPR1	NM_001098199.1,NM_005279.3	29,29	1763,3124,1616	CC,CT,TT		45.0,36.9042,48.8698	benign,benign	307/356,307/356	207041053	6650,6356	2203	4300	6503	SO:0001583	missense	2825	exon3			TACTAATTAGGAC		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.919A>G	2.37:g.207041053T>C	ENSP00000384345:p.Ile307Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	100	86	0.86	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Missense_Mutation	SNP	ENST00000407325.2	37	CCDS2368.1	1029	0.47115384615384615	308	0.6260162601626016	209	0.5773480662983426	144	0.2517482517482518	368	0.48548812664907653	T	10.35	1.325180	0.24080	0.630958	0.45	ENSG00000183671	ENST00000407325;ENST00000437420	T;T	0.36699	1.24;1.24	5.7	5.7	0.88788	.	0.127093	0.53938	D	0.000051	T	0.00012	0.0000	N	0.08118	0	0.25801	P	0.9845058	B	0.23128	0.08	B	0.14578	0.011	T	0.35351	-0.9792	9	0.35671	T	0.21	.	12.4853	0.55868	0.0:0.0:0.1394:0.8606	rs3732083;rs52828782;rs61202419;rs3732083	307	P46091	GPR1_HUMAN	V	307	ENSP00000384345:I307V;ENSP00000397535:I307V	ENSP00000384345:I307V	I	-	1	0	GPR1	206749298	1.000000	0.71417	0.995000	0.50966	0.599000	0.36880	3.455000	0.52993	2.177000	0.69029	0.533000	0.62120	ATT	T|0.502;C|0.498	0.498	strong		0.488	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
FLG	2312	hgsc.bcm.edu	37	1	152280170	152280170	+	Missense_Mutation	SNP	C	C	G	rs71625201	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280170C>G	ENST00000368799.1	-	3	7227	c.7192G>C	c.(7192-7194)Gag>Cag	p.E2398Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2398	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGTGTGGACTCTTGGTGGCTC	0.587									Ichthyosis				C|||	1655	0.330471	0.1135	0.4092	5008	,	,		20923	0.5665		0.169	False		,,,				2504	0.4908				p.E2398Q		Atlas-SNP	.											.	FLG	900	.	0			c.G7192C						PASS	.	C	GLN/GLU	584,3820	250.6+/-257.6	42,500,1660	70.0	74.0	72.0		7192	-3.5	0.0	1	dbSNP_130	72	1418,7138	262.7+/-284.6	121,1176,2981	no	missense	FLG	NM_002016.1	29	163,1676,4641	GG,GC,CC		16.5732,13.2607,15.4475	benign	2398/4062	152280170	2002,10958	2202	4278	6480	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGACTCTTGGTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7192G>C	1.37:g.152280170C>G	ENSP00000357789:p.Glu2398Gln	Somatic	353	0	0		WXS	Illumina HiSeq	Phase_I	452	137	0.303097	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	602	0.27564102564102566	64	0.13008130081300814	116	0.32044198895027626	294	0.513986013986014	128	0.16886543535620052	C	10.08	1.253118	0.22965	0.132607	0.165732	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01787	4.64	3.76	-3.46	0.04767	.	.	.	.	.	T	0.00815	0.0027	M	0.78223	2.4	0.80722	P	0.0	B	0.20052	0.041	B	0.13407	0.009	T	0.39522	-0.9610	8	0.33141	T	0.24	.	4.314	0.10984	0.0:0.2844:0.322:0.3937	.	2398	P20930	FILA_HUMAN	Q	2398;308	ENSP00000357789:E2398Q	ENSP00000271820:E308Q	E	-	1	0	FLG	150546794	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.310000	0.02725	-0.408000	0.07565	-0.494000	0.04653	GAG	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PCDHA3	56145	hgsc.bcm.edu	37	5	140181892	140181892	+	Silent	SNP	T	T	C	rs3733707	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140181892T>C	ENST00000522353.2	+	1	1110	c.1110T>C	c.(1108-1110)gcT>gcC	p.A370A	PCDHA3_ENST00000532566.2_Silent_p.A370A|PCDHA2_ENST00000520672.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	370	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(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)			CAGTCATCGCTCTGATCAGCG	0.478													.|||	3011	0.601238	0.7572	0.6052	5008	,	,		22120	0.5317		0.5388	False		,,,				2504	0.5235				p.A370A		Atlas-SNP	.											PCDHA3_ENST00000522353,rectum,carcinoma,+2,2	PCDHA3	396	2	0			c.T1110C						scavenged	.	C	,,,,	3224,1182		1184,856,163	124.0	120.0	122.0		,,1110,,1110	3.9	1.0	5	dbSNP_107	122	4542,4058		1193,2156,951	no	intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,,,	2377,3012,1114	CC,CT,TT		47.186,26.8271,40.2891	,,,,	,,370/951,,370/825	140181892	7766,5240	2203	4300	6503	SO:0001819	synonymous_variant	56145	exon1			CATCGCTCTGATC	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.1110T>C	5.37:g.140181892T>C		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	159	76	0.477987	NM_031497	O75286	Silent	SNP	ENST00000522353.2	37	CCDS54915.1																																																																																			T|0.403;C|0.597	0.597	strong		0.478	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
MUC17	140453	hgsc.bcm.edu	37	7	100681444	100681444	+	Silent	SNP	A	A	C	rs201002287	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681444A>C	ENST00000306151.4	+	3	6811	c.6747A>C	c.(6745-6747)acA>acC	p.T2249T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2249	59 X approximate tandem repeats.|Ser-rich.				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)					ACACCAGCACACCTGTGACCA	0.483													A|||	16	0.00319489	0.0106	0.0	5008	,	,		26727	0.002		0.0	False		,,,				2504	0.0				p.T2249T		Atlas-SNP	.											MUC17,caecum,carcinoma,0,2	MUC17	804	2	0			c.A6747C						scavenged	.						299.0	300.0	300.0					7																	100681444		2203	4298	6501	SO:0001819	synonymous_variant	140453	exon3			CAGCACACCTGTG	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.6747A>C	7.37:g.100681444A>C		Somatic	157	5	0.0318471		WXS	Illumina HiSeq	Phase_I	230	16	0.0695652	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			A|0.999;C|0.001	0.001	weak		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
OR6K3	391114	hgsc.bcm.edu	37	1	158687896	158687896	+	Missense_Mutation	SNP	C	C	T	rs857705	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	108	0	0		WXS	Illumina HiSeq	Phase_I	185	62	0.335135	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			
PCMTD1	115294	hgsc.bcm.edu	37	8	52733127	52733127	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:52733127G>A	ENST00000360540.5	-	7	1264	c.858C>T	c.(856-858)aaC>aaT	p.N286N	PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Silent_p.N286N|PCMTD1_ENST00000544451.1_Silent_p.N210N	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	286						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)				ATACGTAAGTGTTAATTCTCT	0.398																																					p.N286N		Atlas-SNP	.											.	PCMTD1	73	.	0			c.C858T						PASS	.						189.0	188.0	188.0					8																	52733127		2203	4300	6503	SO:0001819	synonymous_variant	115294	exon6			GTAAGTGTTAATT		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.858C>T	8.37:g.52733127G>A		Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	518	28	0.0540541	NM_052937	Q96FK9	Silent	SNP	ENST00000360540.5	37	CCDS6148.1																																																																																			.	.	none		0.398	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
NBPF10	100132406	hgsc.bcm.edu	37	1	145296373	145296373	+	Missense_Mutation	SNP	G	G	T	rs3969711	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:145296373G>T	ENST00000342960.5	+	3	330	c.295G>T	c.(295-297)Gtt>Ttt	p.V99F	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	99						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.V99F(1)		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)		TAAAGTCCTAGTTCACTCTCA	0.473																																					p.V99F		Atlas-SNP	.											NBPF10,NS,carcinoma,0,3	NBPF10	221	3	1	Substitution - Missense(1)	kidney(1)	c.G295T						scavenged	.																																			SO:0001583	missense	100132406	exon3			GTCCTAGTTCACT	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.295G>T	1.37:g.145296373G>T	ENSP00000345684:p.Val99Phe	Somatic	48	1	0.0208333		WXS	Illumina HiSeq	Phase_I	141	12	0.0851064	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.249076	0.22880	.	.	ENSG00000163386	ENST00000369339;ENST00000448873;ENST00000342960	T	0.03889	3.77	1.15	-0.158	0.13383	.	.	.	.	.	T	0.03220	0.0094	M	0.72479	2.2	0.09310	N	1	.	.	.	.	.	.	T	0.38757	-0.9646	7	0.87932	D	0	.	3.0726	0.06236	0.7069:0.0:0.2931:0.0	rs3969711;rs4996270	.	.	.	F	99;24;99	ENSP00000345684:V99F	ENSP00000345684:V99F	V	+	1	0	NBPF10	144007730	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.057000	0.14279	-0.026000	0.13895	0.121000	0.15741	GTT	G|0.700;T|0.300	0.300	strong		0.473	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
PSME4	23198	hgsc.bcm.edu	37	2	54127041	54127041	+	Silent	SNP	C	C	T	rs805423	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:54127041C>T	ENST00000404125.1	-	29	3454	c.3399G>A	c.(3397-3399)caG>caA	p.Q1133Q	PSME4_ENST00000421748.2_Silent_p.Q277Q	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	1133					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)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|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)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)			breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CATTCTTTTCCTGTTGGCGTT	0.363													T|||	3048	0.608626	0.6422	0.4741	5008	,	,		19545	0.7331		0.494	False		,,,				2504	0.6483				p.Q1133Q		Atlas-SNP	.											.	PSME4	247	.	0			c.G3399A						PASS	.	T		2587,1819	532.3+/-373.4	767,1053,383	218.0	218.0	218.0		3399	3.2	1.0	2	dbSNP_86	218	4160,4440	587.9+/-392.3	993,2174,1133	no	coding-synonymous	PSME4	NM_014614.2		1760,3227,1516	TT,TC,CC		48.3721,41.2846,48.1239		1133/1844	54127041	6747,6259	2203	4300	6503	SO:0001819	synonymous_variant	23198	exon29			CTTTTCCTGTTGG	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.3399G>A	2.37:g.54127041C>T		Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	285	136	0.477193	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			C|0.452;T|0.548	0.548	strong		0.363	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
COL12A1	1303	hgsc.bcm.edu	37	6	75836079	75836079	+	Missense_Mutation	SNP	A	A	G	rs200450866		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:75836079A>G	ENST00000322507.8	-	39	6757	c.6448T>C	c.(6448-6450)Tat>Cat	p.Y2150H	COL12A1_ENST00000483888.2_Missense_Mutation_p.Y2150H|COL12A1_ENST00000345356.6_Missense_Mutation_p.Y986H|COL12A1_ENST00000416123.2_Missense_Mutation_p.Y2150H	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2150	Fibronectin type-III 17. {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						ACTGGCTTATATACTATTTTA	0.428																																					p.Y2150H		Atlas-SNP	.											.	COL12A1	385	.	0			c.T6448C						PASS	.	A	HIS/TYR,HIS/TYR	0,3684		0,0,1842	108.0	103.0	105.0		6448,2956	5.7	1.0	6		105	3,8163		0,3,4080	yes	missense,missense	COL12A1	NM_004370.5,NM_080645.2	83,83	0,3,5922	GG,GA,AA		0.0367,0.0,0.0253	probably-damaging,probably-damaging	2150/3064,986/1900	75836079	3,11847	1842	4083	5925	SO:0001583	missense	1303	exon39			GCTTATATACTAT	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.6448T>C	6.37:g.75836079A>G	ENSP00000325146:p.Tyr2150His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.498898	0.85069	0.0	3.67E-4	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.7	5.7	0.88788	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78786	0.4338	M	0.86805	2.84	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.83385	0.0014	10	0.87932	D	0	.	15.9743	0.80049	1.0:0.0:0.0:0.0	.	986;2150	Q99715-2;Q99715	.;COCA1_HUMAN	H	2150;2150;986;2150;2150	ENSP00000325146:Y2150H;ENSP00000305147:Y986H;ENSP00000412864:Y2150H;ENSP00000421216:Y2150H	ENSP00000325146:Y2150H	Y	-	1	0	COL12A1	75892799	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.905000	0.92613	2.173000	0.68751	0.528000	0.53228	TAT	.	.	weak		0.428	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
FBXW5	54461	hgsc.bcm.edu	37	9	139836694	139836694	+	Silent	SNP	C	C	T	rs34391108	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139836694C>T	ENST00000325285.3	-	6	979	c.900G>A	c.(898-900)gaG>gaA	p.E300E	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	300					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)		GCCGCAAGCCCTCCTTGGCGT	0.711													C|||	176	0.0351438	0.0023	0.0259	5008	,	,		15047	0.004		0.0477	False		,,,				2504	0.1053				p.E300E		Atlas-SNP	.											.	FBXW5	36	.	0			c.G900A						PASS	.	C		38,4292		1,36,2128	11.0	14.0	13.0		900	0.9	0.9	9	dbSNP_126	13	318,8216		4,310,3953	no	coding-synonymous	FBXW5	NM_018998.2		5,346,6081	TT,TC,CC		3.7263,0.8776,2.7674		300/567	139836694	356,12508	2165	4267	6432	SO:0001819	synonymous_variant	54461	exon6			CAAGCCCTCCTTG	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.900G>A	9.37:g.139836694C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	7	6	0.857143	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Silent	SNP	ENST00000325285.3	37	CCDS7014.1																																																																																			C|0.975;T|0.025	0.025	strong		0.711	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
CMTM1	113540	hgsc.bcm.edu	37	16	66600479	66600479	+	Silent	SNP	G	G	A	rs7193473	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:66600479G>A	ENST00000457188.2	+	1	184	c.63G>A	c.(61-63)ccG>ccA	p.P21P	CMTM1_ENST00000529506.1_5'UTR|CMTM1_ENST00000528324.1_Silent_p.P21P|CMTM1_ENST00000535705.1_Silent_p.P21P|CKLF-CMTM1_ENST00000527729.1_Intron|CMTM1_ENST00000328020.6_Silent_p.P21P|CMTM1_ENST00000533666.1_Silent_p.P21P|CMTM1_ENST00000533953.1_Silent_p.P21P|CMTM1_ENST00000336328.6_Silent_p.P21P|CMTM1_ENST00000379500.2_Silent_p.P21P|CMTM1_ENST00000332695.7_Silent_p.P21P|CMTM1_ENST00000531885.1_Silent_p.P21P	NM_181269.2	NP_851786.1	Q8IZ96	CKLF1_HUMAN	CKLF-like MARVEL transmembrane domain containing 1	21	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0702)|Epithelial(162;0.222)		TGAAACAACCGGAGACTGCCG	0.617													A|||	1606	0.320687	0.5643	0.2723	5008	,	,		12627	0.3006		0.1362	False		,,,				2504	0.2362				p.P21P		Atlas-SNP	.											.	CMTM1	34	.	0			c.G63A						PASS	.	A	,,,,,,,,,,	2276,2126	578.7+/-384.7	572,1132,497	76.0	67.0	70.0		,,,63,63,63,63,63,63,63,63	-5.2	0.0	16	dbSNP_116	70	1031,7569	771.9+/-407.7	71,889,3340	no	intron,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CMTM1,CKLF-CMTM1	NM_001202509.1,NM_001204098.1,NM_001204099.1,NM_052999.3,NM_181268.2,NM_181269.2,NM_181270.2,NM_181271.2,NM_181272.2,NM_181283.2,NM_181296.2	,,,,,,,,,,	643,2021,3837	AA,AG,GG		11.9884,48.2962,25.4345	,,,,,,,,,,	,,,21/287,21/232,21/170,21/115,21/123,21/117,21/62,21/29	66600479	3307,9695	2201	4300	6501	SO:0001819	synonymous_variant	113540	exon1			ACAACCGGAGACT	AF278577	CCDS10810.1, CCDS10811.1, CCDS10812.2, CCDS45503.1, CCDS45504.1, CCDS54019.1, CCDS54020.1, CCDS54021.1	16q22.1	2009-10-06	2005-11-08	2005-11-08	ENSG00000089505	ENSG00000089505			19172	protein-coding gene	gene with protein product		607884	"""chemokine-like factor super family 1"", ""chemokine-like factor superfamily 1"""	CKLFSF1		12782130	Standard	NM_181268		Approved	CKLFH1a, CKLFH	uc002epr.4	Q8IZ96	OTTHUMG00000137502	ENST00000457188.2:c.63G>A	16.37:g.66600479G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	131	25	0.19084	NM_181271	Q2PPY5|Q6PEV5|Q8IU76|Q8IU83|Q8IU86|Q8IU93|Q8IZ87|Q8IZ88|Q8IZ89|Q8IZ90|Q8IZ91|Q8IZ92|Q8IZ93|Q8IZ94|Q8IZ95|Q96JC2|Q96JC3	Silent	SNP	ENST00000457188.2	37	CCDS45503.1																																																																																			G|0.721;A|0.279	0.279	strong		0.617	CMTM1-015	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390261.2	NM_052999	
EPHA2	1969	hgsc.bcm.edu	37	1	16475126	16475126	+	Silent	SNP	C	C	T	rs6678618	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	49	0	0		WXS	Illumina HiSeq	Phase_I	42	10	0.238095	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	
SLC1A6	6511	hgsc.bcm.edu	37	19	15083555	15083555	+	Silent	SNP	G	G	A	rs115001292	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:15083555G>A	ENST00000221742.3	-	1	175	c.168C>T	c.(166-168)aaC>aaT	p.N56N	SLC1A6_ENST00000544886.2_Silent_p.N56N|SLC1A6_ENST00000600144.1_Silent_p.N56N|SLC1A6_ENST00000598504.1_Silent_p.N56N|SLC1A6_ENST00000430939.2_Missense_Mutation_p.R61C	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	56					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						GAATGAAGGCGTTTCGGCGCA	0.637													G|||	44	0.00878594	0.0	0.0245	5008	,	,		19459	0.0		0.0239	False		,,,				2504	0.0031				p.N56N		Atlas-SNP	.											.	SLC1A6	111	.	0			c.C168T						PASS	.	G		7,4393		0,7,2193	29.0	29.0	29.0		168	-4.8	0.9	19	dbSNP_132	29	53,8547		1,51,4248	no	coding-synonymous	SLC1A6	NM_005071.1		1,58,6441	AA,AG,GG		0.6163,0.1591,0.4615		56/565	15083555	60,12940	2200	4300	6500	SO:0001819	synonymous_variant	6511	exon4			GAAGGCGTTTCGG		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.168C>T	19.37:g.15083555G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_001272087	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1	26	0.011904761904761904	0	0.0	6	0.016574585635359115	0	0.0	20	0.026385224274406333	G	10.63	1.404119	0.25291	0.001591	0.006163	ENSG00000105143	ENST00000430939	T	0.75260	-0.92	4.46	-4.79	0.03200	.	.	.	.	.	T	0.37865	0.1019	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32771	-0.9894	8	0.87932	D	0	-17.863	10.8289	0.46649	0.7382:0.0:0.2618:0.0	.	61	E7EV13	.	C	61	ENSP00000409386:R61C	ENSP00000409386:R61C	R	-	1	0	SLC1A6	14944555	0.036000	0.19791	0.931000	0.37212	0.642000	0.38348	-0.826000	0.04429	-0.758000	0.04690	0.313000	0.20887	CGC	G|0.993;A|0.007	0.007	strong		0.637	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
BTN2A2	10385	hgsc.bcm.edu	37	6	26388405	26388405	+	Missense_Mutation	SNP	G	G	A	rs62617839	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26388405G>A	ENST00000356709.4	+	4	718	c.607G>A	c.(607-609)Ggc>Agc	p.G203S	BTN2A2_ENST00000469230.1_Missense_Mutation_p.G203S|BTN2A2_ENST00000416795.2_Missense_Mutation_p.G203S|BTN2A2_ENST00000432533.2_Intron|BTN2A2_ENST00000482536.1_Intron|BTN2A2_ENST00000352867.2_Missense_Mutation_p.G87S	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	203	Ig-like C2-type.				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						TGATGCTGACGGCCTCTTCAT	0.567													G|||	225	0.0449281	0.0575	0.062	5008	,	,		20389	0.005		0.0537	False		,,,				2504	0.0481				p.G203S		Atlas-SNP	.											.	BTN2A2	87	.	0			c.G607A						PASS	.	G	SER/GLY,SER/GLY,,,SER/GLY,SER/GLY	272,4134	153.3+/-186.9	9,254,1940	155.0	127.0	136.0		607,607,,,607,259	3.2	0.3	6	dbSNP_129	136	483,8117	142.2+/-198.4	11,461,3828	yes	missense,missense,intron,intron,missense,missense	BTN2A2	NM_001197237.1,NM_001197238.1,NM_001197239.1,NM_001197240.1,NM_006995.4,NM_181531.2	56,56,,,56,56	20,715,5768	AA,AG,GG		5.6163,6.1734,5.805	possibly-damaging,possibly-damaging,,,possibly-damaging,possibly-damaging	203/524,203/337,,,203/524,87/408	26388405	755,12251	2203	4300	6503	SO:0001583	missense	10385	exon4			GCTGACGGCCTCT	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.607G>A	6.37:g.26388405G>A	ENSP00000349143:p.Gly203Ser	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	138	58	0.42029	NM_001197238	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Missense_Mutation	SNP	ENST00000356709.4	37	CCDS4606.1	97	0.044413919413919416	32	0.06504065040650407	26	0.0718232044198895	1	0.0017482517482517483	38	0.05013192612137203	g	18.11	3.550762	0.65311	0.061734	0.056163	ENSG00000124508	ENST00000469230;ENST00000356709;ENST00000352867;ENST00000493275;ENST00000472507;ENST00000416795;ENST00000483410	T;T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23;2.23	4.11	3.24	0.37175	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	0.113353	0.40144	N	0.001170	T	0.20170	0.0485	M	0.64997	1.995	0.33613	P	0.39618200000000003	D;D;D;P	0.76494	0.999;0.979;0.99;0.928	P;P;P;P	0.62740	0.906;0.63;0.615;0.595	T	0.03545	-1.1026	9	0.54805	T	0.06	.	9.6411	0.39839	0.1072:0.0:0.8928:0.0	rs62617839	87;203;87;203	B4E3J1;Q8WVV5-2;A6NM84;Q8WVV5	.;.;.;BT2A2_HUMAN	S	203;203;87;203;87;203;87	ENSP00000417472:G203S;ENSP00000349143:G203S;ENSP00000337117:G87S;ENSP00000418857:G203S;ENSP00000419226:G87S;ENSP00000399308:G203S;ENSP00000418176:G87S	ENSP00000337117:G87S	G	+	1	0	BTN2A2	26496384	0.999000	0.42202	0.302000	0.25058	0.047000	0.14425	3.881000	0.56152	0.731000	0.32448	0.454000	0.30748	GGC	G|0.941;A|0.059	0.059	strong		0.567	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1		
MLLT6	4302	hgsc.bcm.edu	37	17	36868976	36868976	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:36868976G>A	ENST00000325718.7	+	8	844	c.753G>A	c.(751-753)aaG>aaA	p.K251K	MLLT6_ENST00000378137.5_Silent_p.K251K|CTB-58E17.9_ENST00000579499.1_RNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	251					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					TTAAGCAGAAGCACAAGAAGC	0.587			T	MLL	AL																																p.K251K		Atlas-SNP	.		Dom	yes		17	17q21	4302	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"""		L	.	MLLT6	80	.	0			c.G753A						PASS	.						108.0	104.0	105.0					17																	36868976		2203	4300	6503	SO:0001819	synonymous_variant	4302	exon8			GCAGAAGCACAAG		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"""Zinc fingers, PHD-type"""	7138	protein-coding gene	gene with protein product	"""Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6"", ""trithorax homolog"""	600328	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"""			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.753G>A	17.37:g.36868976G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	34	0.276423	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Silent	SNP	ENST00000325718.7	37	CCDS11327.1																																																																																			.	.	none		0.587	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937	
COL4A2	1284	hgsc.bcm.edu	37	13	111160304	111160304	+	Silent	SNP	G	G	A	rs391859	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:111160304G>A	ENST00000360467.5	+	47	4923	c.4617G>A	c.(4615-4617)gcG>gcA	p.A1539A	COL4A2-AS1_ENST00000417970.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1539	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				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)			CCTGCCTGGCGCGGTTCAGCA	0.632													G|||	505	0.100839	0.0711	0.1974	5008	,	,		17295	0.128		0.0915	False		,,,				2504	0.0542				p.A1539A		Atlas-SNP	.											.	COL4A2	178	.	0			c.G4617A						PASS	.	G		309,3977		14,281,1848	66.0	72.0	70.0		4617	-9.9	0.0	13	dbSNP_80	70	807,7701		39,729,3486	no	coding-synonymous	COL4A2	NM_001846.2		53,1010,5334	AA,AG,GG		9.4852,7.2095,8.7228		1539/1713	111160304	1116,11678	2143	4254	6397	SO:0001819	synonymous_variant	1284	exon47			CCTGGCGCGGTTC	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.4617G>A	13.37:g.111160304G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			G|0.890;A|0.110	0.110	strong		0.632	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
EP400	57634	hgsc.bcm.edu	37	12	132561987	132561987	+	Silent	SNP	C	C	T	rs12311898	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:132561987C>T	ENST00000333577.4	+	54	9358	c.9249C>T	c.(9247-9249)gcC>gcT	p.A3083A	EP400_ENST00000389562.2_Silent_p.A3046A|EP400_ENST00000332482.4_Silent_p.A3010A|EP400_ENST00000330386.6_Silent_p.A2966A|RP13-820C6.2_ENST00000542422.1_RNA|EP400_ENST00000389561.2_Silent_p.A3047A			Q96L91	EP400_HUMAN	E1A binding protein p400	3083					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)		CGACGGCGGCCGGGCAGCAGG	0.627													C|||	437	0.0872604	0.1483	0.0389	5008	,	,		17142	0.0923		0.0596	False		,,,				2504	0.0624				p.A3047A		Atlas-SNP	.											.	EP400	370	.	0			c.C9141T						PASS	.	C		508,3874		31,446,1714	41.0	45.0	44.0		9141	-11.2	0.0	12	dbSNP_120	44	381,8191		15,351,3920	no	coding-synonymous	EP400	NM_015409.4		46,797,5634	TT,TC,CC		4.4447,11.5929,6.8627		3047/3124	132561987	889,12065	2191	4286	6477	SO:0001819	synonymous_variant	57634	exon53			GGCGGCCGGGCAG	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.9249C>T	12.37:g.132561987C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	165	74	0.448485	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				C|0.932;T|0.068	0.068	strong		0.627	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	82	0	0		WXS	Illumina HiSeq	Phase_I	130	31	0.238462	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	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194827	18194827	+	Missense_Mutation	SNP	C	C	G	rs2468774	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18194827C>G	ENST00000314254.3	+	1	444	c.24C>G	c.(22-24)ttC>ttG	p.F8L	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	8			F -> L (in dbSNP:rs2468774). {ECO:0000269|PubMed:11850634}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						TCCCAGTCTTCGGTACAAAAC	0.522													G|||	1654	0.330272	0.2549	0.3415	5008	,	,		19349	0.4395		0.3062	False		,,,				2504	0.3364				p.F8L		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.C24G						PASS	.	G	LEU/PHE	1080,3318	721.3+/-409.2	130,820,1249	164.0	155.0	158.0		24	1.5	0.0	11	dbSNP_100	158	2449,6137	695.9+/-404.8	338,1773,2182	no	missense	MRGPRX4	NM_054032.3	22	468,2593,3431	GG,GC,CC		28.5232,24.5566,27.1796	benign	8/323	18194827	3529,9455	2199	4293	6492	SO:0001583	missense	117196	exon1			AGTCTTCGGTACA	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.24C>G	11.37:g.18194827C>G	ENSP00000314042:p.Phe8Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	172	85	0.494186	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	750	0.3434065934065934	114	0.23170731707317074	120	0.3314917127071823	275	0.4807692307692308	241	0.3179419525065963	G	1.256	-0.617153	0.03663	0.245566	0.285232	ENSG00000179817	ENST00000314254	T	0.16324	2.35	2.42	1.49	0.22878	.	1.996180	0.02024	N	0.048015	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	0.45190	-0.9278	9	0.09590	T	0.72	.	3.8504	0.08953	0.152:0.2516:0.5964:0.0	rs2468774;rs16934999;rs52794849;rs2468774	8	Q96LA9	MRGX4_HUMAN	L	8	ENSP00000314042:F8L	ENSP00000314042:F8L	F	+	3	2	MRGPRX4	18151403	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.053000	0.14184	0.135000	0.18707	-1.305000	0.01319	TTC	C|0.699;G|0.301	0.301	strong		0.522	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
PROM1	8842	hgsc.bcm.edu	37	4	16077401	16077401	+	Silent	SNP	G	G	A	rs10033086	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:16077401G>A	ENST00000510224.1	-	2	377	c.129C>T	c.(127-129)acC>acT	p.T43T	PROM1_ENST00000539194.1_Silent_p.T43T|PROM1_ENST00000508167.1_Silent_p.T43T|PROM1_ENST00000543373.1_Silent_p.T43T|PROM1_ENST00000505450.1_Silent_p.T43T|PROM1_ENST00000540805.1_Silent_p.T43T|PROM1_ENST00000447510.2_Silent_p.T43T			O43490	PROM1_HUMAN	prominin 1	43					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						GGGAGTCTTGGGTCTCATAAT	0.483													G|||	420	0.0838658	0.2632	0.0346	5008	,	,		19188	0.0		0.0388	False		,,,				2504	0.0092				p.T43T		Atlas-SNP	.											PROM1,bladder,carcinoma,-2,1	PROM1	91	1	0			c.C129T						PASS	.	G	,,,,,,	875,2989		108,659,1165	71.0	71.0	71.0		129,129,129,129,129,129,129	0.6	0.1	4	dbSNP_119	71	207,8095		1,205,3945	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PROM1	NM_001145847.1,NM_001145848.1,NM_001145849.1,NM_001145850.1,NM_001145851.1,NM_001145852.1,NM_006017.2	,,,,,,	109,864,5110	AA,AG,GG		2.4934,22.6449,8.8936	,,,,,,	43/857,43/857,43/843,43/835,43/834,43/826,43/866	16077401	1082,11084	1932	4151	6083	SO:0001819	synonymous_variant	8842	exon2			GTCTTGGGTCTCA	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.129C>T	4.37:g.16077401G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_001145847	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Silent	SNP	ENST00000510224.1	37	CCDS47029.1																																																																																			G|0.912;A|0.088	0.088	strong		0.483	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	
KCNA7	3743	hgsc.bcm.edu	37	19	49573438	49573438	+	Missense_Mutation	SNP	A	A	G	rs1017219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49573438A>G	ENST00000221444.1	-	2	1608	c.1253T>C	c.(1252-1254)aTg>aCg	p.M418T		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	418			M -> T (in dbSNP:rs1017219). {ECO:0000269|PubMed:11368907, ECO:0000269|PubMed:11896454}.		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)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	ACAAGGCTGCATGTCCACATG	0.592													a|||	1833	0.366014	0.4766	0.3213	5008	,	,		16717	0.3353		0.328	False		,,,				2504	0.319				p.M418T	Colon(74;686 1235 3793 23366 48562)	Atlas-SNP	.											.	KCNA7	30	.	0			c.T1253C						PASS	.	A	THR/MET	2022,2384	563.5+/-381.2	459,1104,640	77.0	72.0	73.0		1253	3.2	1.0	19	dbSNP_86	73	2989,5611	463.8+/-366.1	533,1923,1844	yes	missense	KCNA7	NM_031886.2	81	992,3027,2484	GG,GA,AA		34.7558,45.892,38.5284	benign	418/457	49573438	5011,7995	2203	4300	6503	SO:0001583	missense	3743	exon2			GGCTGCATGTCCA	AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.1253T>C	19.37:g.49573438A>G	ENSP00000221444:p.Met418Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_031886	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	37	CCDS12755.1	801	0.36675824175824173	240	0.4878048780487805	141	0.38950276243093923	179	0.3129370629370629	241	0.3179419525065963	a	1.053	-0.675176	0.03378	0.45892	0.347558	ENSG00000104848	ENST00000221444	D	0.97455	-4.39	4.27	3.23	0.37069	.	0.869427	0.09899	N	0.741250	T	0.00012	0.0000	N	0.00321	-1.65	0.48632	P	3.170000000000117E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.30446	-0.9978	9	0.23891	T	0.37	.	11.6813	0.51458	0.0899:0.0:0.9101:0.0	rs1017219;rs3810187;rs57874828;rs1017219	418	Q96RP8	KCNA7_HUMAN	T	418	ENSP00000221444:M418T	ENSP00000221444:M418T	M	-	2	0	KCNA7	54265250	0.797000	0.28877	0.994000	0.49952	0.913000	0.54294	0.606000	0.24194	1.179000	0.42884	-0.362000	0.07510	ATG	A|0.619;G|0.381	0.381	strong		0.592	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1	NM_031886	
ARPC1B	10095	hgsc.bcm.edu	37	7	98984354	98984354	+	Missense_Mutation	SNP	G	G	C	rs1045012	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:98984354G>C	ENST00000451682.1	+	5	420	c.111G>C	c.(109-111)aaG>aaC	p.K37N	ARPC1A_ENST00000432884.2_3'UTR|ARPC1B_ENST00000252725.5_Missense_Mutation_p.K37N|ARPC1B_ENST00000474880.1_3'UTR			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	37			K -> N (in dbSNP:rs1045012).		Arp2/3 complex-mediated actin nucleation (GO:0034314)|cellular component movement (GO:0006928)	actin cytoskeleton (GO:0015629)|Arp2/3 protein complex (GO:0005885)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(2)|lung(1)	11	all_cancers(62;3.49e-09)|all_epithelial(64;2.57e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			TCTATGAAAAGAGCGGTGCCA	0.577													G|||	391	0.0780751	0.1778	0.0634	5008	,	,		21294	0.0327		0.0338	False		,,,				2504	0.046				p.K37N		Atlas-SNP	.											.	ARPC1B	41	.	0			c.G111C						PASS	.	G	ASN/LYS	688,3718	289.8+/-280.6	46,596,1561	186.0	161.0	169.0		111	5.2	1.0	7	dbSNP_86	169	359,8241	119.9+/-179.2	11,337,3952	yes	missense	ARPC1B	NM_005720.3	94	57,933,5513	CC,CG,GG		4.1744,15.6151,8.0501	benign	37/373	98984354	1047,11959	2203	4300	6503	SO:0001583	missense	10095	exon3			TGAAAAGAGCGGT	AF006084	CCDS5661.1	7q22.1	2013-03-14	2002-08-29		ENSG00000130429	ENSG00000130429		"""Actin related protein 2/3 complex subunits"", ""WD repeat domain containing"""	704	protein-coding gene	gene with protein product	"""ARP2/3 protein complex subunit p41"", ""actin related protein 2/3 complex, subunit 1A (41 kD)"""	604223	"""actin related protein 2/3 complex, subunit 1B (41 kD)"""			9230079, 9359840	Standard	NM_005720		Approved	ARC41, p40-ARC, p41-ARC	uc003upz.3	O15143	OTTHUMG00000154552	ENST00000451682.1:c.111G>C	7.37:g.98984354G>C	ENSP00000389631:p.Lys37Asn	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	156	67	0.429487	NM_005720	Q9BU00	Missense_Mutation	SNP	ENST00000451682.1	37	CCDS5661.1	145	0.06639194139194139	70	0.14227642276422764	30	0.08287292817679558	18	0.03146853146853147	27	0.03562005277044855	G	12.54	1.969222	0.34754	0.156151	0.041744	ENSG00000130429	ENST00000443222;ENST00000414376;ENST00000252725;ENST00000455009;ENST00000418347;ENST00000417330;ENST00000431816;ENST00000427217;ENST00000458033;ENST00000451682	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	5.17	5.17	0.71159	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.049416	0.85682	D	0.000000	T	0.00784	0.0026	M	0.81239	2.535	0.20403	P	0.9999050461	D;D	0.64830	0.994;0.994	D;D	0.64776	0.929;0.929	T	0.33163	-0.9879	9	0.24483	T	0.36	-37.4929	12.4073	0.55447	0.0777:0.0:0.9223:0.0	rs1045012;rs3174603;rs10341021;rs11556756;rs1045012	37;37	A4D275;O15143	.;ARC1B_HUMAN	N	37	ENSP00000413173:K37N;ENSP00000398620:K37N;ENSP00000252725:K37N;ENSP00000410238:K37N;ENSP00000413067:K37N;ENSP00000403324:K37N;ENSP00000398110:K37N;ENSP00000403211:K37N;ENSP00000388802:K37N;ENSP00000389631:K37N	ENSP00000252725:K37N	K	+	3	2	ARPC1B	98822290	1.000000	0.71417	0.996000	0.52242	0.069000	0.16628	1.437000	0.34991	2.577000	0.86979	0.561000	0.74099	AAG	G|0.926;C|0.074	0.074	strong		0.577	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720	
GAK	2580	hgsc.bcm.edu	37	4	843536	843536	+	Silent	SNP	G	G	A	rs55904229	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:843536G>A	ENST00000314167.4	-	28	3971	c.3861C>T	c.(3859-3861)caC>caT	p.H1287H	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Silent_p.H1208H	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1287	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				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)		TCATCTTGGCGTGCTGCTCGT	0.672													G|||	9	0.00179712	0.0008	0.0	5008	,	,		14022	0.0		0.006	False		,,,				2504	0.002				p.H1287H		Atlas-SNP	.											.	GAK	104	.	0			c.C3861T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	51.0	49.0	50.0		3861	-7.5	0.0	4	dbSNP_129	50	55,8545	34.3+/-88.2	0,55,4245	no	coding-synonymous	GAK	NM_005255.2		0,62,6441	AA,AG,GG		0.6395,0.1589,0.4767		1287/1312	843536	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	2580	exon28			CTTGGCGTGCTGC	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.3861C>T	4.37:g.843536G>A		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	268	132	0.492537	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	1.270	-0.613465	0.03690	0.001589	0.006395	ENSG00000178950	ENST00000511980	.	.	.	4.76	-7.48	0.01360	.	.	.	.	.	T	0.45458	0.1343	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59005	-0.7535	4	.	.	.	-0.8575	11.9205	0.52789	0.7915:0.1057:0.1028:0.0	rs55904229	.	.	.	M	443	.	.	T	-	2	0	GAK	833536	0.555000	0.26530	0.003000	0.11579	0.228000	0.25075	-0.100000	0.10990	-1.556000	0.01695	-0.796000	0.03273	ACG	G|0.997;A|0.003	0.003	strong		0.672	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
ITGA10	8515	hgsc.bcm.edu	37	1	145536082	145536082	+	Missense_Mutation	SNP	G	G	A	rs2274616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:145536082G>A	ENST00000369304.3	+	17	2349	c.2174G>A	c.(2173-2175)cGg>cAg	p.R725Q	ITGA10_ENST00000539363.1_Missense_Mutation_p.R582Q|ITGA10_ENST00000538811.1_Missense_Mutation_p.R594Q	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	231	0	0		WXS	Illumina HiSeq	Phase_I	304	191	0.628289	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	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10575824	10575824	+	Silent	SNP	C	C	A	rs1970817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	107	0	0		WXS	Illumina HiSeq	Phase_I	97	97	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	
SDK2	54549	hgsc.bcm.edu	37	17	71344769	71344769	+	Missense_Mutation	SNP	G	G	A	rs199591952		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:71344769G>A	ENST00000392650.3	-	44	6134	c.6134C>T	c.(6133-6135)aCg>aTg	p.T2045M	SDK2_ENST00000410094.1_5'UTR|SDK2_ENST00000388726.3_Missense_Mutation_p.T2026M	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	2045					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						GGGCTTCTCCGTCAGGCTGCT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		16899	0.001		0.0	False		,,,				2504	0.0				p.T2045M		Atlas-SNP	.											.	SDK2	219	.	0			c.C6134T						PASS	.						61.0	54.0	56.0					17																	71344769		2203	4299	6502	SO:0001583	missense	54549	exon44			TTCTCCGTCAGGC	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.6134C>T	17.37:g.71344769G>A	ENSP00000376421:p.Thr2045Met	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	23.3	4.399737	0.83120	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.62941	-0.01;0.03;1.29	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.76905	0.4053	M	0.62723	1.935	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.76575	0.983;0.988	T	0.80042	-0.1548	10	0.87932	D	0	.	16.6634	0.85247	0.0:0.0:1.0:0.0	.	2045;2026	Q58EX2;Q58EX2-3	SDK2_HUMAN;.	M	1669;2045;2026;1202;2045;386	ENSP00000376421:T2045M;ENSP00000373378:T2026M;ENSP00000407098:T1202M	ENSP00000324967:T2045M	T	-	2	0	SDK2	68856364	1.000000	0.71417	0.919000	0.36401	0.935000	0.57460	7.721000	0.84768	2.204000	0.70986	0.563000	0.77884	ACG	A|0.000;G|1.000	0.000	strong		0.637	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
ATAD3B	83858	hgsc.bcm.edu	37	1	1412681	1412681	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1412681C>T	ENST00000308647.7	+	2	349	c.233C>T	c.(232-234)gCg>gTg	p.A78V	ATAD3B_ENST00000378741.3_5'UTR	NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	78						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			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)		CTGAATCTGGCGCAGATGCAG	0.622																																					p.A78V		Atlas-SNP	.											ATAD3B_ENST00000378741,right_upper_lobe,carcinoma,-1,2	ATAD3B	68	2	0			c.C233T						scavenged	.						46.0	44.0	45.0					1																	1412681		2203	4295	6498	SO:0001583	missense	83858	exon2			ATCTGGCGCAGAT	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.233C>T	1.37:g.1412681C>T	ENSP00000311766:p.Ala78Val	Somatic	392	0	0		WXS	Illumina HiSeq	Phase_I	250	3	0.012	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	14.79	2.639858	0.47153	.	.	ENSG00000160072	ENST00000360489;ENST00000308647	T	0.30448	1.53	2.9	2.9	0.33743	ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523 (1);	0.296096	0.36268	N	0.002685	T	0.37404	0.1002	M	0.71206	2.165	0.80722	D	1	P	0.52577	0.954	P	0.49226	0.603	T	0.30592	-0.9973	10	0.14252	T	0.57	.	12.9335	0.58301	0.0:1.0:0.0:0.0	.	78	Q5T9A4	ATD3B_HUMAN	V	78	ENSP00000311766:A78V	ENSP00000311766:A78V	A	+	2	0	ATAD3B	1402544	0.999000	0.42202	0.766000	0.31476	0.127000	0.20565	4.685000	0.61693	1.460000	0.47911	0.306000	0.20318	GCG	.	.	none		0.622	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
KIAA1671	85379	hgsc.bcm.edu	37	22	25586744	25586744	+	Silent	SNP	T	T	G	rs2330986	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:25586744T>G	ENST00000406486.4	+	13	5805	c.5418T>G	c.(5416-5418)gtT>gtG	p.V1806V	KIAA1671_ENST00000401395.1_Silent_p.V313V|KIAA1671_ENST00000358431.3_Silent_p.V1806V			Q9BY89	K1671_HUMAN	KIAA1671	1806										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						AGAACCAAGTTTGACCAGGTA	0.527													T|||	192	0.0383387	0.0023	0.0403	5008	,	,		17474	0.0		0.0736	False		,,,				2504	0.089				p.V1806V		Atlas-SNP	.											.	KIAA1671	28	.	0			c.T5418G						PASS	.	T		25,1359		0,25,667	114.0	96.0	101.0		5418	-0.9	1.0	22	dbSNP_100	101	304,2878		18,268,1305	no	coding-synonymous	KIAA1671	NM_001145206.1		18,293,1972	GG,GT,TT		9.5537,1.8064,7.2054		1806/1807	25586744	329,4237	692	1591	2283	SO:0001819	synonymous_variant	85379	exon10			CCAAGTTTGACCA		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.5418T>G	22.37:g.25586744T>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	33	0.4125	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			T|0.952;G|0.048	0.048	strong		0.527	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
SYT15	83849	hgsc.bcm.edu	37	10	46968665	46968665	+	Silent	SNP	G	G	A	rs200814731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:46968665G>A	ENST00000374321.4	-	3	337	c.271C>T	c.(271-273)Ctg>Ttg	p.L91L	SYT15_ENST00000374325.3_Silent_p.L91L|SYT15_ENST00000503753.1_Silent_p.L91L|SYT15_ENST00000374323.4_Silent_p.L144L|RP11-38L15.3_ENST00000506914.1_RNA	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CCACTGTGCAGGGGCACCCAA	0.632													G|||	469	0.0936502	0.1051	0.0764	5008	,	,		35813	0.0496		0.1282	False		,,,				2504	0.1002				p.L91L	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											SYT15_ENST00000416127,colon,carcinoma,0,15	SYT15	165	15	0			c.C271T						PASS	.	G	,	277,3977		0,277,1850	55.0	65.0	62.0		271,271	2.7	0.2	10	dbSNP_132	62	613,7885		0,613,3636	no	coding-synonymous,coding-synonymous	SYT15	NM_031912.4,NM_181519.2	,	0,890,5486	AA,AG,GG		7.2135,6.5115,6.9793	,	91/422,91/391	46968665	890,11862	2127	4249	6376	SO:0001819	synonymous_variant	83849	exon3			TGTGCAGGGGCAC	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.271C>T	10.37:g.46968665G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	52	12	0.230769	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Silent	SNP	ENST00000374321.4	37	CCDS44376.1																																																																																			G|0.911;A|0.089	0.089	strong		0.632	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
HMP19	51617	hgsc.bcm.edu	37	5	173491300	173491300	+	Silent	SNP	G	G	A	rs17076802|rs34300847	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:173491300G>A	ENST00000303177.3	+	3	457	c.195G>A	c.(193-195)ccG>ccA	p.P65P	NSG2_ENST00000521585.1_Silent_p.P65P|NSG2_ENST00000521959.1_3'UTR	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	86	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	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		
PRPF4	9128	hgsc.bcm.edu	37	9	116045007	116045007	+	Missense_Mutation	SNP	A	A	C	rs148684386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116045007A>C	ENST00000374198.4	+	4	579	c.477A>C	c.(475-477)aaA>aaC	p.K159N	PRPF4_ENST00000374199.4_Missense_Mutation_p.K158N|PRPF4_ENST00000488937.1_3'UTR	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	159					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						AAAAGTCCAAAGAAGAGGTAG	0.348																																					p.K159N		Atlas-SNP	.											.	PRPF4	56	.	0			c.A477C						PASS	.	A	ASN/LYS	1,4405	2.1+/-5.4	0,1,2202	78.0	76.0	77.0		477	3.5	1.0	9	dbSNP_134	77	3,8597	2.2+/-6.3	0,3,4297	yes	missense	PRPF4	NM_004697.3	94	0,4,6499	CC,CA,AA		0.0349,0.0227,0.0308	benign	159/523	116045007	4,13002	2203	4300	6503	SO:0001583	missense	9128	exon4			GTCCAAAGAAGAG	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.477A>C	9.37:g.116045007A>C	ENSP00000363313:p.Lys159Asn	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Missense_Mutation	SNP	ENST00000374198.4	37	CCDS6791.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.901787	0.33535	2.27E-4	3.49E-4	ENSG00000136875	ENST00000374199;ENST00000374198	T;T	0.63417	-0.04;0.01	5.9	3.5	0.40072	.	0.381275	0.33005	N	0.005394	T	0.45054	0.1323	L	0.29908	0.895	0.44012	D	0.996725	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.22521	-1.0214	10	0.35671	T	0.21	.	6.3671	0.21461	0.7403:0.1367:0.123:0.0	.	174;159	Q59EL4;O43172	.;PRP4_HUMAN	N	158;159	ENSP00000363315:K158N;ENSP00000363313:K159N	ENSP00000363313:K159N	K	+	3	2	PRPF4	115084828	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.947000	0.40293	0.462000	0.27095	0.460000	0.39030	AAA	A|0.999;C|0.001	0.001	strong		0.348	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
ESPNL	339768	hgsc.bcm.edu	37	2	239038912	239038912	+	Silent	SNP	T	T	C	rs57813708	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:239038912T>C	ENST00000343063.3	+	9	1820	c.1557T>C	c.(1555-1557)ctT>ctC	p.L519L	ESPNL_ENST00000409506.1_Silent_p.L151L|ESPNL_ENST00000477241.1_3'UTR|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	227	0	0		WXS	Illumina HiSeq	Phase_I	198	86	0.434343	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	
DHX38	9785	hgsc.bcm.edu	37	16	72139184	72139184	+	Silent	SNP	C	C	A	rs2074626	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:72139184C>A	ENST00000268482.3	+	17	2825	c.2316C>A	c.(2314-2316)gcC>gcA	p.A772A	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	772	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.A772A(1)		endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				ACGCGCCTGCCCTGGCTGTGC	0.577													C|||	2385	0.476238	0.7799	0.3156	5008	,	,		18831	0.3085		0.3559	False		,,,				2504	0.4765				p.A772A	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,NS,carcinoma,0,2	DHX38	91	2	1	Substitution - coding silent(1)	prostate(1)	c.C2316A						scavenged	.	C		3042,1354	691.3+/-405.4	1066,910,222	71.0	66.0	68.0		2316	1.2	0.9	16	dbSNP_96	68	3215,5385	484.9+/-371.5	593,2029,1678	no	coding-synonymous	DHX38	NM_014003.3		1659,2939,1900	AA,AC,CC		37.3837,30.8007,48.1456		772/1228	72139184	6257,6739	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon17			GCCTGCCCTGGCT	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"""DEAH-boxes"""	17211	protein-coding gene	gene with protein product		605584	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"""	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.2316C>A	16.37:g.72139184C>A		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			C|0.529;A|0.471	0.471	strong		0.577	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
TTLL3	26140	hgsc.bcm.edu	37	3	9876987	9876987	+	Silent	SNP	G	G	A	rs1057281	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:9876987G>A	ENST00000547186.1	+	13	2349	c.2133G>A	c.(2131-2133)agG>agA	p.R711R	TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000397241.1_3'UTR|ARPC4-TTLL3_ENST00000397256.1_3'UTR|TTLL3_ENST00000430793.1_3'UTR|TTLL3_ENST00000383827.1_3'UTR|TTLL3_ENST00000426895.4_Silent_p.R854R	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	711					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)					CATTCCAGAGGCGCAGGGGCC	0.557													G|||	596	0.11901	0.211	0.1009	5008	,	,		18562	0.0565		0.1183	False		,,,				2504	0.0726				p.R854R		Atlas-SNP	.											.	TTLL3	51	.	0			c.G2562A						PASS	.	G	,	719,3011		59,601,1205	53.0	58.0	56.0		2562,	-3.6	0.0	3	dbSNP_86	56	1277,6927		107,1063,2932	no	coding-synonymous,utr-3	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	,	166,1664,4137	AA,AG,GG		15.5656,19.2761,16.7253	,	854/916,	9876987	1996,9938	1865	4102	5967	SO:0001819	synonymous_variant	26140	exon13			CCAGAGGCGCAGG		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.2133G>A	3.37:g.9876987G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Silent	SNP	ENST00000547186.1	37																																																																																				G|0.873;A|0.127	0.127	strong		0.557	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656805	46656805	+	Silent	SNP	G	G	A	rs6519994	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46656805G>A	ENST00000253255.5	-	1	2414	c.2415C>T	c.(2413-2415)atC>atT	p.I805I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	805	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CAGTACTCACGATTTCTATTT	0.368													G|||	1190	0.23762	0.6505	0.1297	5008	,	,		20491	0.001		0.161	False		,,,				2504	0.0787				p.I805I		Atlas-SNP	.											PKDREJ,caecum,carcinoma,0,1	PKDREJ	195	1	0			c.C2415T						PASS	.	G		2514,1890	617.9+/-393.1	710,1094,398	66.0	72.0	70.0		2415	-10.2	0.0	22	dbSNP_116	70	1254,7346	249.2+/-276.5	88,1078,3134	no	coding-synonymous	PKDREJ	NM_006071.1		798,2172,3532	AA,AG,GG		14.5814,42.9155,28.9757		805/2254	46656805	3768,9236	2202	4300	6502	SO:0001819	synonymous_variant	10343	exon1			ACTCACGATTTCT	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2415C>T	22.37:g.46656805G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	171	69	0.403509	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.732;A|0.268	0.268	strong		0.368	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
BPI	671	hgsc.bcm.edu	37	20	36932676	36932676	+	Silent	SNP	G	G	C	rs1341024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	99	95	0.959596	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	
FAM81B	153643	hgsc.bcm.edu	37	5	94756010	94756010	+	Missense_Mutation	SNP	C	C	T	rs11555275	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:94756010C>T	ENST00000283357.5	+	5	606	c.560C>T	c.(559-561)gCt>gTt	p.A187V		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	187			A -> V (in dbSNP:rs11555275).			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)		CAAATAAGAGCTCGAGATCAG	0.408													C|||	72	0.014377	0.0015	0.036	5008	,	,		21775	0.0		0.0338	False		,,,				2504	0.0112				p.A187V		Atlas-SNP	.											.	FAM81B	51	.	0			c.C560T						PASS	.	C	VAL/ALA	15,3697		0,15,1841	96.0	89.0	91.0		560	-4.3	0.0	5	dbSNP_120	91	234,7970		4,226,3872	yes	missense	FAM81B	NM_152548.2	64	4,241,5713	TT,TC,CC		2.8523,0.4041,2.0896	benign	187/453	94756010	249,11667	1856	4102	5958	SO:0001583	missense	153643	exon5			TAAGAGCTCGAGA		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.560C>T	5.37:g.94756010C>T	ENSP00000283357:p.Ala187Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_152548		Missense_Mutation	SNP	ENST00000283357.5	37	CCDS43341.1	37	0.01694139194139194	0	0.0	14	0.03867403314917127	0	0.0	23	0.030343007915567283	C	11.77	1.737542	0.30774	0.004041	0.028523	ENSG00000153347	ENST00000283357	T	0.19806	2.12	5.92	-4.31	0.03698	.	1.484280	0.03679	N	0.245167	T	0.04092	0.0114	L	0.37507	1.11	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.30475	-0.9977	10	0.32370	T	0.25	1.3968	12.6219	0.56607	0.1212:0.7033:0.0:0.1755	rs11555275	187	Q96LP2	FA81B_HUMAN	V	187	ENSP00000283357:A187V	ENSP00000283357:A187V	A	+	2	0	FAM81B	94781766	0.001000	0.12720	0.014000	0.15608	0.982000	0.71751	-0.878000	0.04192	-0.662000	0.05338	-0.322000	0.08575	GCT	C|0.978;T|0.022	0.022	strong		0.408	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558528	140558528	+	Missense_Mutation	SNP	A	A	G	rs3733694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140558528A>G	ENST00000239444.2	+	1	1158	c.913A>G	c.(913-915)Aag>Gag	p.K305E	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	305	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		K -> E (in dbSNP:rs3733694).		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)			AATTCGACTAAAGAAACAACT	0.393													A|||	644	0.128594	0.177	0.1787	5008	,	,		31989	0.0407		0.1531	False		,,,				2504	0.093				p.K305E		Atlas-SNP	.											.	PCDHB8	199	.	0			c.A913G						PASS	.	A	GLU/LYS	773,3633	308.8+/-290.8	70,633,1500	119.0	176.0	156.0		913	4.2	0.0	5	dbSNP_107	156	1246,7354	238.5+/-269.9	123,1000,3177	yes	missense	PCDHB8	NM_019120.3	56	193,1633,4677	GG,GA,AA		14.4884,17.5443,15.5236	benign	305/802	140558528	2019,10987	2203	4300	6503	SO:0001583	missense	56128	exon1			CGACTAAAGAAAC	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.913A>G	5.37:g.140558528A>G	ENSP00000239444:p.Lys305Glu	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	214	82	0.383178	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	292	0.1336996336996337	92	0.18699186991869918	57	0.1574585635359116	26	0.045454545454545456	117	0.15435356200527706	A	2.278	-0.365459	0.05069	0.175443	0.144884	ENSG00000120322	ENST00000239444	T	0.01725	4.67	4.25	4.25	0.50352	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	M	0.72479	2.2	0.80722	P	0.0	B	0.33904	0.431	B	0.39971	0.315	T	0.42015	-0.9476	8	0.15952	T	0.53	.	9.2083	0.37302	0.8378:0.0:0.0:0.1622	rs3733694;rs17096956;rs17844492;rs3733694	305	Q9UN66	PCDB8_HUMAN	E	305	ENSP00000239444:K305E	ENSP00000239444:K305E	K	+	1	0	PCDHB8	140538712	0.000000	0.05858	0.017000	0.16124	0.014000	0.08584	-0.201000	0.09464	1.558000	0.49541	0.477000	0.44152	AAG	G|0.146;N|0.001	0.146	strong		0.393	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
NBEAL1	65065	hgsc.bcm.edu	37	2	203990789	203990789	+	Silent	SNP	T	T	G	rs72934556	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:203990789T>G	ENST00000449802.1	+	20	3204	c.2871T>G	c.(2869-2871)gtT>gtG	p.V957V		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	957										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CCCATGGAGTTGCAACTCTTG	0.378													T|||	194	0.038738	0.0061	0.0692	5008	,	,		15752	0.001		0.1223	False		,,,				2504	0.0143				p.V957V		Atlas-SNP	.											.	NBEAL1	266	.	0			c.T2871G						PASS	.	T		34,1350		0,34,658	183.0	149.0	160.0		2871	3.2	1.0	2	dbSNP_130	160	373,2809		20,333,1238	no	coding-synonymous	NBEAL1	NM_001114132.1		20,367,1896	GG,GT,TT		11.7222,2.4566,8.9137		957/2695	203990789	407,4159	692	1591	2283	SO:0001819	synonymous_variant	65065	exon20			TGGAGTTGCAACT	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.2871T>G	2.37:g.203990789T>G		Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	216	44	0.203704	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Silent	SNP	ENST00000449802.1	37	CCDS46495.1																																																																																			T|0.923;G|0.077	0.077	strong		0.378	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
NQO1	1728	hgsc.bcm.edu	37	16	69745145	69745145	+	Missense_Mutation	SNP	G	G	A	rs1800566	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:69745145G>A	ENST00000320623.5	-	6	1070	c.559C>T	c.(559-561)Cct>Tct	p.P187S	NQO1_ENST00000439109.2_Missense_Mutation_p.P115S|NQO1_ENST00000379046.2_Missense_Mutation_p.P149S|NQO1_ENST00000379047.3_Missense_Mutation_p.P153S|NQO1_ENST00000561500.1_Missense_Mutation_p.P149S|snoU13_ENST00000459361.1_RNA|CTD-2033A16.1_ENST00000562696.1_RNA|NQO1_ENST00000564043.1_Missense_Mutation_p.P166S	NM_000903.2	NP_000894.1	P15559	NQO1_HUMAN	NAD(P)H dehydrogenase, quinone 1	187			P -> S (lack of activity; dbSNP:rs1800566). {ECO:0000269|PubMed:10447260, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1737339, ECO:0000269|Ref.3}.		aging (GO:0007568)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cellular amino acid metabolic process (GO:0006521)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|synaptic transmission, cholinergic (GO:0007271)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|poly(A) RNA binding (GO:0044822)|superoxide dismutase activity (GO:0004784)	p.P187S(1)		autonomic_ganglia(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	10					Carboplatin(DB00958)|Cisplatin(DB00515)|Dicoumarol(DB00266)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|Menadione(DB00170)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	GTCAGTTGAGGTTCTAAGACT	0.458													G|||	1447	0.288938	0.1755	0.3329	5008	,	,		21129	0.4187		0.2107	False		,,,				2504	0.3579				p.P187S		Atlas-SNP	.											NQO1,NS,carcinoma,0,1	NQO1	21	1	1	Substitution - Missense(1)	stomach(1)	c.C559T	GRCh37	CM950861	NQO1	M	rs1800566	scavenged	.	G	SER/PRO,SER/PRO,SER/PRO	856,3540	334.4+/-303.4	77,702,1419	154.0	160.0	158.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	559,457,445	5.4	1.0	16	dbSNP_89	158	1709,6891	311.2+/-310.2	177,1355,2768	yes	missense,missense,missense	NQO1	NM_000903.2,NM_001025433.1,NM_001025434.1	74,74,74	254,2057,4187	AA,AG,GG		19.8721,19.4722,19.7368	possibly-damaging,possibly-damaging,possibly-damaging	187/275,153/241,149/237	69745145	2565,10431	2198	4300	6498	SO:0001583	missense	1728	exon6			GTTGAGGTTCTAA	M81600	CCDS10883.1, CCDS32471.1, CCDS32472.1, CCDS67067.1	16q12-q22	2012-10-02	2001-11-30	2001-12-07	ENSG00000181019	ENSG00000181019	1.6.5.2		2874	protein-coding gene	gene with protein product		125860	"""diaphorase (NADH/NADPH) (cytochrome b-5 reductase)"""	NMOR1, DIA4		2843525	Standard	NM_001286137		Approved	DHQU, QR1, DTD	uc002exp.3	P15559	OTTHUMG00000137575	ENST00000320623.5:c.559C>T	16.37:g.69745145G>A	ENSP00000319788:p.Pro187Ser	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	119	19	0.159664	NM_000903	B2R5Y9|B4DNM7|B7ZAD1|Q86UK1	Missense_Mutation	SNP	ENST00000320623.5	37	CCDS10883.1	604	0.2765567765567766	88	0.17886178861788618	120	0.3314917127071823	243	0.42482517482517484	153	0.20184696569920843	G	23.7	4.442223	0.83993	0.194722	0.198721	ENSG00000181019	ENST00000320623;ENST00000379047;ENST00000379046;ENST00000439109	T;T;T;T	0.09723	2.95;3.11;3.11;3.11	5.41	5.41	0.78517	Flavodoxin-like fold (1);	0.050537	0.85682	D	0.000000	T	0.00012	0.0000	M	0.68593	2.085	0.09310	P	0.999999999882097	D;P;B	0.89917	1.0;0.77;0.438	D;B;B	0.91635	0.999;0.356;0.167	T	0.48536	-0.9027	9	0.46703	T	0.11	-14.2172	18.3313	0.90270	0.0:0.0:1.0:0.0	rs1800566;rs4134727;rs4149351;rs57135274;rs1800566	115;153;187	B4DLR8;B7ZAD1;P15559	.;.;NQO1_HUMAN	S	187;153;149;115	ENSP00000319788:P187S;ENSP00000368335:P153S;ENSP00000368334:P149S;ENSP00000398330:P115S	ENSP00000319788:P187S	P	-	1	0	NQO1	68302646	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.220000	0.95180	2.696000	0.92011	0.655000	0.94253	CCT	G|0.761;A|0.239	0.239	strong		0.458	NQO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268956.2		
POLR3B	55703	hgsc.bcm.edu	37	12	106838340	106838340	+	Silent	SNP	T	T	C	rs10861607	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	1	0.00819672		WXS	Illumina HiSeq	Phase_I	118	118	1	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	
CDON	50937	hgsc.bcm.edu	37	11	125873796	125873796	+	Splice_Site	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125873796C>T	ENST00000392693.3	-	10	2154		c.e10+1		CDON_ENST00000263577.7_Splice_Site|CDON_ENST00000531738.1_Splice_Site	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated						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)		CCCTCACTCACCTTTGCTGGT	0.458																																					.		Atlas-SNP	.											.	CDON	137	.	0			c.2026+1G>A						PASS	.						83.0	75.0	78.0					11																	125873796		2201	4299	6500	SO:0001630	splice_region_variant	50937	exon11			CACTCACCTTTGC	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.2026+1G>A	11.37:g.125873796C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	97	5	0.0515464	NM_001243597	O14631	Splice_Site	SNP	ENST00000392693.3	37	CCDS58192.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.483812	0.44147	.	.	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDON	125379006	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	7.440000	0.80464	2.894000	0.99253	0.655000	0.94253	.	.	.	none		0.458	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	Intron
FSIP2	401024	hgsc.bcm.edu	37	2	186670780	186670780	+	Missense_Mutation	SNP	T	T	A	rs16827154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:186670780T>A	ENST00000424728.1	+	17	16747	c.16747T>A	c.(16747-16749)Tac>Aac	p.Y5583N	FSIP2_ENST00000343098.5_Missense_Mutation_p.Y5672N			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5583				Y -> N (in Ref. 3; AK126051). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TGATGAGATATACACACATTT	0.284													T|||	2526	0.504393	0.4365	0.4755	5008	,	,		18268	0.4702		0.508	False		,,,				2504	0.6483				p.Y5672N		Atlas-SNP	.											FSIP2_ENST00000343098,colon,carcinoma,0,2	FSIP2	251	2	0			c.T17014A						PASS	.	T	ASN/TYR	1687,1893		402,883,505	63.0	66.0	65.0		17014	-2.0	0.0	2	dbSNP_123	65	4305,3805		1153,1999,903	yes	missense	FSIP2	NM_173651.2	143	1555,2882,1408	AA,AT,TT		46.9174,47.1229,48.7425	benign	5672/6997	186670780	5992,5698	1790	4055	5845	SO:0001583	missense	401024	exon17			GAGATATACACAC	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.16747T>A	2.37:g.186670780T>A	ENSP00000401306:p.Tyr5583Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	61	0.580952	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Missense_Mutation	SNP	ENST00000424728.1	37		1040	0.47619047619047616	217	0.4410569105691057	176	0.4861878453038674	268	0.46853146853146854	379	0.5	T	10.36	1.328093	0.24080	0.471229	0.530826	ENSG00000188738	ENST00000343098;ENST00000424728	T;T	0.52983	0.64;0.64	4.87	-2.02	0.07388	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	.	.	.	.	.	.	T	0.47484	-0.9114	6	0.30854	T	0.27	.	5.5017	0.16833	0.0:0.2792:0.1607:0.56	rs16827154;rs16827154	.	.	.	N	5672;5583	ENSP00000344403:Y5672N;ENSP00000401306:Y5583N	ENSP00000344403:Y5672N	Y	+	1	0	FSIP2	186379025	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.678000	0.01942	-0.281000	0.09141	-0.202000	0.12741	TAC	T|0.513;A|0.487	0.487	strong		0.284	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
LRP3	4037	hgsc.bcm.edu	37	19	33698448	33698448	+	Silent	SNP	G	G	A	rs3745973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	67	0	0		WXS	Illumina HiSeq	Phase_I	56	28	0.5	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		
OR12D2	26529	hgsc.bcm.edu	37	6	29364835	29364835	+	Missense_Mutation	SNP	T	T	G	rs2073153	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29364835T>G	ENST00000383555.2	+	1	420	c.359T>G	c.(358-360)cTc>cGc	p.L120R	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	120			L -> R (in dbSNP:rs2073153).			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(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						GCATTTGACCTCTCTGTGGCT	0.493													G|||	1597	0.31889	0.1921	0.3458	5008	,	,		21217	0.3641		0.4523	False		,,,				2504	0.2873				p.L120R		Atlas-SNP	.											.	OR12D2	42	.	0			c.T359G	GRCh37	CM035845	OR12D2	M	rs2073153	PASS	.	G	ARG/LEU	669,2353		75,519,917	94.0	94.0	94.0		359	3.0	0.9	6	dbSNP_96	94	2409,3009		534,1341,834	yes	missense	OR12D2	NM_013936.3	102	609,1860,1751	GG,GT,TT		44.4629,22.1377,36.4692	benign	120/308	29364835	3078,5362	1511	2709	4220	SO:0001583	missense	26529	exon1			TTGACCTCTCTGT		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.359T>G	6.37:g.29364835T>G	ENSP00000373047:p.Leu120Arg	Somatic	300	2	0.00666667		WXS	Illumina HiSeq	Phase_I	229	226	0.9869	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	787	0.36034798534798534	101	0.20528455284552846	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	G	0.013	-1.637038	0.00806	0.221377	0.444629	ENSG00000168787	ENST00000383555	T	0.04809	3.55	3.94	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.200095	0.35772	N	0.002997	T	0.00144	0.0004	N	0.00000	-4.03	0.45295	P	0.0017089999999999606	B	0.02656	0.0	B	0.01281	0.0	T	0.35076	-0.9803	9	0.02654	T	1	.	9.9552	0.41661	0.0:0.151:0.692:0.1569	rs2073153;rs58214000	120	P58182	O12D2_HUMAN	R	120	ENSP00000373047:L120R	ENSP00000373047:L120R	L	+	2	0	OR12D2	29472814	0.936000	0.31750	0.926000	0.36857	0.003000	0.03518	4.857000	0.62939	0.329000	0.23460	-0.982000	0.02568	CTC	T|0.650;G|0.350	0.350	strong		0.493	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
MUC16	94025	hgsc.bcm.edu	37	19	9048342	9048342	+	Missense_Mutation	SNP	C	C	T	rs10854118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9048342C>T	ENST00000397910.4	-	5	33492	c.33289G>A	c.(33289-33291)Gtg>Atg	p.V11097M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11099	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.V11097M(1)|p.V6730M(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						GGGGTCACCACTCCTGATACC	0.512													C|||	2196	0.438498	0.4062	0.4092	5008	,	,		23561	0.497		0.4245	False		,,,				2504	0.4571				p.V11097M		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - Missense(2)	stomach(2)	c.G33289A						PASS	.		MET/VAL	1540,2296		332,876,710	77.0	69.0	71.0		33289	-0.5	0.0	19	dbSNP_120	71	3319,4959		658,2003,1478	yes	missense	MUC16	NM_024690.2	21	990,2879,2188	TT,TC,CC		40.0942,40.146,40.1106	benign	11097/14508	9048342	4859,7255	1918	4139	6057	SO:0001583	missense	94025	exon5			TCACCACTCCTGA	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.33289G>A	19.37:g.9048342C>T	ENSP00000381008:p.Val11097Met	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	149	85	0.57047	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	938	0.42948717948717946	183	0.3719512195121951	150	0.4143646408839779	283	0.49475524475524474	322	0.42480211081794195	c	4.287	0.052413	0.08291	0.40146	0.400942	ENSG00000181143	ENST00000397910	T	0.02837	4.14	2.96	-0.543	0.11851	.	.	.	.	.	T	0.00012	0.0000	L	0.35414	1.06	.	.	.	B	0.12630	0.006	B	0.13407	0.009	T	0.40270	-0.9572	8	0.87932	D	0	.	2.2098	0.03945	0.2278:0.2815:0.0:0.4908	rs10854118;rs10854118	11097	B5ME49	.	M	11097	ENSP00000381008:V11097M	ENSP00000381008:V11097M	V	-	1	0	MUC16	8909342	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-5.431000	0.00123	-0.200000	0.10300	-0.447000	0.05616	GTG	C|0.570;T|0.430	0.430	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
F5	2153	hgsc.bcm.edu	37	1	169511734	169511734	+	Missense_Mutation	SNP	T	T	C	rs4525	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:169511734T>C	ENST00000367797.3	-	13	2795	c.2594A>G	c.(2593-2595)cAt>cGt	p.H865R	F5_ENST00000367796.3_Missense_Mutation_p.H870R	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	865	B.		H -> R (in dbSNP:rs4525). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:11758222, ECO:0000269|PubMed:2827731, ECO:0000269|PubMed:3110773, 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)	GGGTCCCTTATGCTTAGCATG	0.448													T|||	1316	0.26278	0.1679	0.3948	5008	,	,		21442	0.248		0.2535	False		,,,				2504	0.3221				p.H865R		Atlas-SNP	.											F5,NS,carcinoma,-1,1	F5	301	1	0			c.A2594G						PASS	.	T	ARG/HIS	814,3592	321.5+/-297.2	68,678,1457	193.0	179.0	184.0		2594	-1.1	0.0	1	dbSNP_52	184	2356,6244	393.9+/-344.5	300,1756,2244	yes	missense	F5	NM_000130.4	29	368,2434,3701	CC,CT,TT		27.3953,18.4748,24.3734	benign	865/2225	169511734	3170,9836	2203	4300	6503	SO:0001583	missense	2153	exon13			CCCTTATGCTTAG	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.2594A>G	1.37:g.169511734T>C	ENSP00000356771:p.His865Arg	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	375	369	0.984	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	532	0.24358974358974358	96	0.1951219512195122	130	0.35911602209944754	113	0.19755244755244755	193	0.2546174142480211	T	5.461	0.270076	0.10349	0.184748	0.273953	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.19806	2.12;2.12	5.72	-1.12	0.09808	.	1.326480	0.04974	N	0.464508	T	0.05181	0.0138	L	0.42245	1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37314	-0.9711	9	0.22109	T	0.4	-5.295	5.176	0.15135	0.0:0.2234:0.2754:0.5013	rs4525;rs3186700;rs52799245;rs57691265;rs4525	865	P12259	FA5_HUMAN	R	865;870	ENSP00000356771:H865R;ENSP00000356770:H870R	ENSP00000356770:H870R	H	-	2	0	F5	167778358	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.167000	0.09940	-0.449000	0.07117	-0.351000	0.07748	CAT	T|0.758;C|0.242	0.242	strong		0.448	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
CR2	1380	hgsc.bcm.edu	37	1	207653364	207653364	+	Missense_Mutation	SNP	A	A	G	rs17618	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:207653364A>G	ENST00000367058.3	+	17	3166	c.2977A>G	c.(2977-2979)Att>Gtt	p.I993V	CR2_ENST00000458541.2_Missense_Mutation_p.I966V|CR2_ENST00000367059.3_Missense_Mutation_p.I931V|CR2_ENST00000367057.3_Missense_Mutation_p.I1052V	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	993			I -> V (in dbSNP:rs17258982). {ECO:0000269|PubMed:2832506}.		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						CTTGATTGTCATTACCTTATA	0.398													G|||	246	0.0491214	0.0643	0.0562	5008	,	,		20250	0.002		0.0716	False		,,,				2504	0.0491				p.I1052V		Atlas-SNP	.											.	CR2	164	.	0			c.A3154G						PASS	.	G	VAL/ILE,VAL/ILE	426,3980	784.9+/-414.7	24,378,1801	226.0	207.0	214.0		3154,2977	2.8	0.0	1	dbSNP_123	214	630,7968	790.3+/-407.6	23,584,3692	yes	missense,missense	CR2	NM_001006658.2,NM_001877.4	29,29	47,962,5493	GG,GA,AA		7.3273,9.6686,8.1206	benign,benign	1052/1093,993/1034	207653364	1056,11948	2203	4299	6502	SO:0001583	missense	1380	exon18			ATTGTCATTACCT	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.2977A>G	1.37:g.207653364A>G	ENSP00000356025:p.Ile993Val	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	296	111	0.375	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	94	0.04304029304029304	25	0.0508130081300813	19	0.052486187845303865	0	0.0	50	0.06596306068601583	G	0.015	-1.556300	0.00910	0.096686	0.073273	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.30448	1.6;1.53;1.75;1.58	4.63	2.75	0.32379	.	.	.	.	.	T	0.00241	0.0007	N	0.01576	-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	0.30475	-0.9977	9	0.02654	T	1	.	6.7795	0.23638	0.2898:0.0:0.7102:0.0	rs17618	931;993;1052	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	V	993;1052;931;966	ENSP00000356025:I993V;ENSP00000356024:I1052V;ENSP00000356026:I931V;ENSP00000404222:I966V	ENSP00000356024:I1052V	I	+	1	0	CR2	205719987	0.004000	0.15560	0.004000	0.12327	0.001000	0.01503	0.535000	0.23114	0.298000	0.22638	-0.320000	0.08662	ATT	A|0.932;G|0.068	0.068	strong		0.398	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
ZNF560	147741	hgsc.bcm.edu	37	19	9579809	9579809	+	Missense_Mutation	SNP	C	C	A	rs61737643	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9579809C>A	ENST00000301480.4	-	9	797	c.584G>T	c.(583-585)tGt>tTt	p.C195F		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	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)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						TGTTTTTAAACAAAAATTATC	0.313													C|||	5	0.000998403	0.0	0.0029	5008	,	,		18821	0.0		0.003	False		,,,				2504	0.0				p.C195F		Atlas-SNP	.											.	ZNF560	162	.	0			c.G584T						PASS	.	C	PHE/CYS	6,4398		0,6,2196	29.0	30.0	30.0		584	0.9	0.0	19	dbSNP_129	30	23,8571		0,23,4274	yes	missense	ZNF560	NM_152476.2	205	0,29,6470	AA,AC,CC		0.2676,0.1362,0.2231	possibly-damaging	195/791	9579809	29,12969	2202	4297	6499	SO:0001583	missense	147741	exon9			TTTAAACAAAAAT	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"""Zinc fingers, C2H2-type"", ""-"""	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.584G>T	19.37:g.9579809C>A	ENSP00000301480:p.Cys195Phe	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	194	85	0.438144	NM_152476	Q495S9|Q495T1	Missense_Mutation	SNP	ENST00000301480.4	37	CCDS12214.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	4.197	0.035323	0.08148	0.001362	0.002676	ENSG00000198028	ENST00000301480	T	0.05258	3.47	1.99	0.933	0.19471	.	.	.	.	.	T	0.01940	0.0061	N	0.13098	0.295	0.09310	N	1	B	0.32010	0.351	B	0.19148	0.024	T	0.43637	-0.9379	9	0.38643	T	0.18	.	3.29	0.06945	0.0:0.5484:0.2782:0.1734	.	195	Q96MR9	ZN560_HUMAN	F	195	ENSP00000301480:C195F	ENSP00000301480:C195F	C	-	2	0	ZNF560	9440809	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.516000	0.06282	0.386000	0.24997	0.555000	0.69702	TGT	C|0.997;A|0.003	0.003	strong		0.313	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476	
WDR12	55759	hgsc.bcm.edu	37	2	203765756	203765756	+	Missense_Mutation	SNP	T	T	C	rs35212307	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:203765756T>C	ENST00000261015.4	-	3	972	c.223A>G	c.(223-225)Atc>Gtc	p.I75V	WDR12_ENST00000477723.1_5'UTR	NM_018256.3	NP_060726.3			WD repeat domain 12											endometrium(3)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)	13						ACTGATGAGATGTTCTCCATT	0.373													T|||	230	0.0459265	0.0136	0.0735	5008	,	,		18111	0.0159		0.1302	False		,,,				2504	0.0143				p.I75V		Atlas-SNP	.											.	WDR12	35	.	0			c.A223G						PASS	.	T	VAL/ILE	149,4257	103.0+/-141.5	2,145,2056	124.0	99.0	108.0		223	4.7	1.0	2	dbSNP_126	108	1117,7483	231.2+/-265.3	71,975,3254	yes	missense	WDR12	NM_018256.3	29	73,1120,5310	CC,CT,TT		12.9884,3.3818,9.734	benign	75/424	203765756	1266,11740	2203	4300	6503	SO:0001583	missense	55759	exon3			ATGAGATGTTCTC	AF242546	CCDS2356.1	2q33.1	2013-01-09			ENSG00000138442	ENSG00000138442		"""WD repeat domain containing"""	14098	protein-coding gene	gene with protein product						16043514, 17353269	Standard	NM_018256		Approved	YTM1, FLJ10881	uc002uzl.3	Q9GZL7	OTTHUMG00000132855	ENST00000261015.4:c.223A>G	2.37:g.203765756T>C	ENSP00000261015:p.Ile75Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	93	20	0.215054	NM_018256		Missense_Mutation	SNP	ENST00000261015.4	37	CCDS2356.1	158	0.07234432234432235	7	0.014227642276422764	34	0.09392265193370165	13	0.022727272727272728	104	0.13720316622691292	T	16.16	3.045462	0.55110	0.033818	0.129884	ENSG00000138442	ENST00000261015	T	0.56103	0.48	5.83	4.69	0.59074	WD40 repeat-like-containing domain (1);	0.043242	0.85682	D	0.000000	T	0.00356	0.0011	L	0.45352	1.415	0.09310	P	0.99999477709	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.06588	-1.0818	9	0.30854	T	0.27	-12.1352	11.3154	0.49388	0.0:0.0707:0.0:0.9293	rs35212307;rs35212307	75;75	Q53T99;Q9GZL7	.;WDR12_HUMAN	V	75	ENSP00000261015:I75V	ENSP00000261015:I75V	I	-	1	0	WDR12	203474001	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	6.288000	0.72679	2.224000	0.72417	0.477000	0.44152	ATC	T|0.919;C|0.081	0.081	strong		0.373	WDR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256329.4	NM_018256	
C16orf96	342346	hgsc.bcm.edu	37	16	4625938	4625938	+	Missense_Mutation	SNP	A	A	T	rs2450386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4625938A>T	ENST00000444310.4	+	5	1457	c.1457A>T	c.(1456-1458)gAt>gTt	p.D486V		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96									p.D486V(1)		NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						ACTCGCAAGGATGGGGTCCCC	0.577													A|||	777	0.155152	0.1301	0.0965	5008	,	,		16929	0.13		0.162	False		,,,				2504	0.2495				p.D486V		Atlas-SNP	.											C16orf96,NS,carcinoma,0,1	C16orf96	28	1	1	Substitution - Missense(1)	endometrium(1)	c.A1457T						PASS	.	A	VAL/ASP	208,1176		14,180,498	80.0	75.0	77.0		1457	-3.3	0.0	16	dbSNP_100	77	515,2667		44,427,1120	yes	missense	C16orf96	NM_001145011.1	152	58,607,1618	TT,TA,AA		16.1848,15.0289,15.8344	benign	486/1142	4625938	723,3843	692	1591	2283	SO:0001583	missense	342346	exon5			GCAAGGATGGGGT		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.1457A>T	16.37:g.4625938A>T	ENSP00000415027:p.Asp486Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001145011		Missense_Mutation	SNP	ENST00000444310.4	37	CCDS53986.1	292	0.1336996336996337	74	0.15040650406504066	41	0.1132596685082873	60	0.1048951048951049	117	0.15435356200527706	A	5.567	0.289366	0.10513	0.150289	0.161848	ENSG00000205832	ENST00000444310	.	.	.	1.78	-3.3	0.05003	.	.	.	.	.	T	0.00073	0.0002	L	0.27053	0.805	0.31961	P	0.608405	B	0.23540	0.087	B	0.20184	0.028	T	0.25012	-1.0144	7	0.30854	T	0.27	.	0.5877	0.00722	0.4543:0.2008:0.1473:0.1976	rs2450386;rs52832531;rs2450386	486	A6NNT2	CP096_HUMAN	V	486	.	ENSP00000415027:D486V	D	+	2	0	C16orf96	4565939	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	0.330000	0.19715	-0.880000	0.03997	-0.991000	0.02546	GAT	A|0.865;T|0.135	0.135	strong		0.577	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
UBE2J1	51465	hgsc.bcm.edu	37	6	90047956	90047956	+	Silent	SNP	G	G	A	rs35213866	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	134	0	0		WXS	Illumina HiSeq	Phase_I	137	52	0.379562	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	
KRT28	162605	hgsc.bcm.edu	37	17	38955173	38955173	+	Silent	SNP	G	G	A	rs7222207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38955173G>A	ENST00000306658.7	-	2	594	c.529C>T	c.(529-531)Cta>Tta	p.L177L		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				ACTTACTTTAGCCTGAAATCA	0.318													G|||	661	0.131989	0.0711	0.1801	5008	,	,		15102	0.0377		0.2306	False		,,,				2504	0.1759				p.L177L	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.C529T						PASS	.	G		448,3958	210.5+/-231.0	30,388,1785	106.0	107.0	107.0		529	3.3	1.0	17	dbSNP_116	107	1964,6634	343.5+/-324.9	219,1526,2554	no	coding-synonymous	KRT28	NM_181535.3		249,1914,4339	AA,AG,GG		22.8425,10.168,18.5481		177/465	38955173	2412,10592	2203	4299	6502	SO:0001819	synonymous_variant	162605	exon2			ACTTTAGCCTGAA	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30842	protein-coding gene	gene with protein product			"""keratin 25D"""	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.529C>T	17.37:g.38955173G>A		Somatic	290	1	0.00344828		WXS	Illumina HiSeq	Phase_I	267	123	0.460674	NM_181535		Silent	SNP	ENST00000306658.7	37	CCDS11376.1																																																																																			G|0.838;A|0.162	0.162	strong		0.318	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100482866	100482866	+	Missense_Mutation	SNP	G	G	A	rs17851246	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:100482866G>A	ENST00000279907.7	-	8	1060	c.848C>T	c.(847-849)aCa>aTa	p.T283I	UHRF1BP1L_ENST00000545232.2_5'UTR|UHRF1BP1L_ENST00000356828.3_Missense_Mutation_p.T283I	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	283				T -> I (in Ref. 1; AAH14891). {ECO:0000305}.						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						TGCGACTACTGTAGAGCTCTA	0.348													G|||	170	0.0339457	0.0015	0.0504	5008	,	,		13331	0.004		0.0686	False		,,,				2504	0.0613				p.T283I		Atlas-SNP	.											.	UHRF1BP1L	144	.	0			c.C848T						PASS	.	G	ILE/THR,ILE/THR	48,4358	49.6+/-84.7	2,44,2157	83.0	81.0	81.0		848,848	4.1	0.9	12	dbSNP_123	81	568,8032	154.2+/-208.4	23,522,3755	yes	missense,missense	UHRF1BP1L	NM_001006947.1,NM_015054.1	89,89	25,566,5912	AA,AG,GG		6.6047,1.0894,4.7363	benign,benign	283/523,283/1465	100482866	616,12390	2203	4300	6503	SO:0001583	missense	23074	exon8			ACTACTGTAGAGC		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.848C>T	12.37:g.100482866G>A	ENSP00000279907:p.Thr283Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Missense_Mutation	SNP	ENST00000279907.7	37	CCDS31882.1	66	0.03021978021978022	1	0.0020325203252032522	13	0.03591160220994475	3	0.005244755244755245	49	0.06464379947229551	G	12.07	1.828787	0.32329	0.010894	0.066047	ENSG00000111647	ENST00000279907;ENST00000356828	T;T	0.30981	2.9;1.51	5.02	4.12	0.48240	.	0.392722	0.29280	N	0.012609	T	0.01695	0.0054	N	0.22421	0.69	0.33622	D	0.604904	B;B	0.30973	0.302;0.136	B;B	0.32465	0.146;0.09	T	0.12682	-1.0538	10	0.66056	D	0.02	-0.9194	13.2532	0.60064	0.0773:0.0:0.9227:0.0	rs17851246	283;283	A0JNW5-2;A0JNW5	.;UH1BL_HUMAN	I	283	ENSP00000279907:T283I;ENSP00000349285:T283I	ENSP00000279907:T283I	T	-	2	0	UHRF1BP1L	99006997	0.990000	0.36364	0.902000	0.35471	0.186000	0.23388	3.614000	0.54160	1.114000	0.41781	0.460000	0.39030	ACA	G|0.954;A|0.046	0.046	strong		0.348	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947	
COL27A1	85301	hgsc.bcm.edu	37	9	117050998	117050998	+	Missense_Mutation	SNP	G	G	A	rs10982134	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	150	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	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	
ELL2	22936	hgsc.bcm.edu	37	5	95236459	95236459	+	Missense_Mutation	SNP	C	C	T	rs3815768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:95236459C>T	ENST00000237853.4	-	7	1241	c.892G>A	c.(892-894)Gca>Aca	p.A298T	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	298			A -> T (in dbSNP:rs3815768). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9108030}.		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)		CTGGTGCCTGCAGCATTCTGA	0.393													C|||	1711	0.341653	0.3699	0.2392	5008	,	,		18726	0.4325		0.2803	False		,,,				2504	0.3456				p.A298T		Atlas-SNP	.											.	ELL2	63	.	0			c.G892A						PASS	.	C	THR/ALA	1538,2868	483.0+/-359.6	271,996,936	68.0	68.0	68.0		892	3.7	1.0	5	dbSNP_107	68	2248,6352	380.4+/-339.6	291,1666,2343	yes	missense	ELL2	NM_012081.5	58	562,2662,3279	TT,TC,CC		26.1395,34.9069,29.1096	benign	298/641	95236459	3786,9220	2203	4300	6503	SO:0001583	missense	22936	exon7			TGCCTGCAGCATT	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.892G>A	5.37:g.95236459C>T	ENSP00000237853:p.Ala298Thr	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	151	149	0.986755	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	37	CCDS4080.1	725	0.33195970695970695	174	0.35365853658536583	84	0.23204419889502761	246	0.43006993006993005	221	0.29155672823219	C	9.940	1.217350	0.22373	0.349069	0.261395	ENSG00000118985	ENST00000237853;ENST00000513343	T;T	0.28454	2.06;1.61	5.7	3.65	0.41850	.	0.261711	0.43110	N	0.000615	T	0.00012	0.0000	N	0.00392	-1.555	0.09310	P	0.9999999999999996	B	0.02656	0.0	B	0.08055	0.003	T	0.46470	-0.9189	9	0.02654	T	1	-0.7066	4.8931	0.13737	0.0:0.6493:0.0:0.3507	rs3815768;rs17855530;rs61132053;rs3815768	298	O00472	ELL2_HUMAN	T	298;116	ENSP00000237853:A298T;ENSP00000423915:A116T	ENSP00000237853:A298T	A	-	1	0	ELL2	95262215	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.128000	0.31369	1.374000	0.46228	0.561000	0.74099	GCA	C|0.695;T|0.305	0.305	strong		0.393	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
MGAT5B	146664	hgsc.bcm.edu	37	17	74921072	74921072	+	Silent	SNP	G	G	C	rs3889145	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:74921072G>C	ENST00000569840.2	+	9	1624	c.1050G>C	c.(1048-1050)cgG>cgC	p.R350R	MGAT5B_ENST00000428789.2_Silent_p.R361R|MGAT5B_ENST00000301618.4_Silent_p.R350R	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	350					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						CGCCAGGCCGGGGAAGCTGCC	0.612													G|||	1087	0.217053	0.1884	0.1988	5008	,	,		10952	0.1677		0.2157	False		,,,				2504	0.3211				p.R361R		Atlas-SNP	.											MGAT5B,NS,carcinoma,0,2	MGAT5B	98	2	0			c.G1083C						scavenged	.	G	,,	857,3549	333.9+/-303.2	85,687,1431	83.0	87.0	86.0		1050,1050,1083	2.1	1.0	17	dbSNP_108	86	2021,6579	352.0+/-328.5	231,1559,2510	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	316,2246,3941	CC,CG,GG		23.5,19.4507,22.1282	,,	350/793,350/791,361/802	74921072	2878,10128	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon8			AGGCCGGGGAAGC	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.1050G>C	17.37:g.74921072G>C		Somatic	91	2	0.021978		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			G|0.785;C|0.215	0.215	strong		0.612	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
LAMTOR5	10542	hgsc.bcm.edu	37	1	110950439	110950439	+	5'Flank	SNP	C	C	T	rs6674775	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:110950439C>T	ENST00000602318.1	-	0	0				LAMTOR5-AS1_ENST00000609512.1_RNA|LAMTOR5_ENST00000602858.1_5'Flank|LAMTOR5_ENST00000474861.2_5'Flank|LAMTOR5-AS1_ENST00000598454.1_RNA|LAMTOR5-AS1_ENST00000609709.1_RNA|LAMTOR5-AS1_ENST00000457535.1_RNA|LAMTOR5-AS1_ENST00000608602.1_RNA|LAMTOR5-AS1_ENST00000609244.1_RNA|LAMTOR5-AS1_ENST00000608486.1_RNA|LAMTOR5-AS1_ENST00000587691.1_RNA|LAMTOR5-AS1_ENST00000608499.1_RNA|LAMTOR5_ENST00000483260.1_5'Flank|LAMTOR5-AS1_ENST00000590413.1_RNA|LAMTOR5_ENST00000256644.4_Missense_Mutation_p.S17N|LAMTOR5-AS1_ENST00000608253.1_RNA|LAMTOR5-AS1_ENST00000608067.1_RNA|LAMTOR5-AS1_ENST00000610148.1_RNA|LAMTOR5-AS1_ENST00000590826.1_RNA			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	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	106	78	0.735849	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	
CCM2	83605	hgsc.bcm.edu	37	7	45104131	45104131	+	Missense_Mutation	SNP	G	G	A	rs11552377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:45104131G>A	ENST00000258781.6	+	4	507	c.358G>A	c.(358-360)Gtc>Atc	p.V120I	CCM2_ENST00000541586.1_Missense_Mutation_p.V62I|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000474617.1_Missense_Mutation_p.V114I|CCM2_ENST00000475551.1_Missense_Mutation_p.V114I|CCM2_ENST00000544363.1_Missense_Mutation_p.V120I|CCM2_ENST00000381112.3_Missense_Mutation_p.V141I	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	54	0	0		WXS	Illumina HiSeq	Phase_I	54	16	0.296296	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	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390162	208390162	+	Missense_Mutation	SNP	T	T	C	rs4844658	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:208390162T>C	ENST00000367033.3	-	2	1863	c.1106A>G	c.(1105-1107)gAg>gGg	p.E369G		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	369	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		E -> G (in dbSNP:rs4844658). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9455484}.		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)		CTGCAGGCGCTCCTTGATCTG	0.602													T|||	594	0.11861	0.0121	0.2032	5008	,	,		21845	0.1429		0.2087	False		,,,				2504	0.0849				p.E369G		Atlas-SNP	.											.	PLXNA2	178	.	0			c.A1106G						PASS	.	T	GLY/GLU	148,4258	101.6+/-140.2	3,142,2058	68.0	66.0	66.0		1106	5.8	1.0	1	dbSNP_111	66	1646,6954	303.3+/-306.4	168,1310,2822	yes	missense	PLXNA2	NM_025179.3	98	171,1452,4880	CC,CT,TT		19.1395,3.3591,13.7936	benign	369/1895	208390162	1794,11212	2203	4300	6503	SO:0001583	missense	5362	exon2			AGGCGCTCCTTGA	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.1106A>G	1.37:g.208390162T>C	ENSP00000356000:p.Glu369Gly	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	145	95	0.655172	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	306	0.1401098901098901	11	0.022357723577235773	64	0.17679558011049723	72	0.1258741258741259	159	0.20976253298153033	T	19.24	3.789846	0.70337	0.033591	0.191395	ENSG00000076356	ENST00000367033	T	0.12039	2.72	5.84	5.84	0.93424	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.123712	0.53938	D	0.000054	T	0.00039	0.0001	M	0.83603	2.65	0.19300	P	0.9999736942	D;P	0.57257	0.979;0.66	P;B	0.57846	0.828;0.215	T	0.07888	-1.0749	9	0.87932	D	0	.	11.3143	0.49383	0.1358:0.0:0.0:0.8642	rs4844658;rs17458917;rs4844658	423;369	O75051-2;O75051	.;PLXA2_HUMAN	G	369	ENSP00000356000:E369G	ENSP00000356000:E369G	E	-	2	0	PLXNA2	206456785	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.876000	0.69667	2.232000	0.73038	0.533000	0.62120	GAG	T|0.865;C|0.135	0.135	strong		0.602	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
CYP2W1	54905	hgsc.bcm.edu	37	7	1023013	1023013	+	Silent	SNP	C	C	T	rs2272375	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:1023013C>T	ENST00000308919.7	+	1	179	c.166C>T	c.(166-168)Ctg>Ttg	p.L56L	CYP2W1_ENST00000340150.6_5'UTR	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	56					small molecule metabolic process (GO:0044281)|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 (GO:0016705)			breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GGACCGGTCCCTGATGGAGGT	0.711													C|||	1804	0.360224	0.5098	0.3343	5008	,	,		12799	0.3115		0.2744	False		,,,				2504	0.3149				p.L56L		Atlas-SNP	.											.	CYP2W1	28	.	0			c.C166T						PASS	.	C		1532,2094		347,838,628	11.0	10.0	10.0		166	4.5	0.8	7	dbSNP_100	10	1881,5021		306,1269,1876	no	coding-synonymous	CYP2W1	NM_017781.2		653,2107,2504	TT,TC,CC		27.253,42.2504,32.4183		56/491	1023013	3413,7115	1813	3451	5264	SO:0001819	synonymous_variant	54905	exon1			CGGTCCCTGATGG	AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"""Cytochrome P450s"""	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.166C>T	7.37:g.1023013C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	24	18	0.75	NM_017781		Silent	SNP	ENST00000308919.7	37	CCDS5319.2																																																																																			C|0.645;T|0.355	0.355	strong		0.711	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781	
DEFB129	140881	hgsc.bcm.edu	37	20	210061	210061	+	Silent	SNP	G	G	A	rs13045643	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	65	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	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	
ALDH4A1	8659	hgsc.bcm.edu	37	1	19212007	19212007	+	Missense_Mutation	SNP	G	G	A	rs139640415	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19212007G>A	ENST00000375341.3	-	5	670	c.413C>T	c.(412-414)cCg>cTg	p.P138L	MIR4695_ENST00000577305.1_RNA|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.P78L|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.P138L|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538839.1_Missense_Mutation_p.P138L|ALDH4A1_ENST00000454547.1_5'UTR	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	138					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)		AGCCCTGCGCGGCCCACTCAG	0.672													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		10477	0.0		0.004	False		,,,				2504	0.0				p.P138L		Atlas-SNP	.											ALDH4A1_ENST00000375341,NS,carcinoma,+1,2	ALDH4A1	72	2	0			c.C413T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	12,4392		0,12,2190	27.0	25.0	26.0		233,413,413	3.5	0.7	1	dbSNP_134	26	12,8588		0,12,4288	yes	missense,missense,missense	ALDH4A1	NM_001161504.1,NM_003748.3,NM_170726.2	98,98,98	0,24,6478	AA,AG,GG		0.1395,0.2725,0.1846	possibly-damaging,possibly-damaging,possibly-damaging	78/504,138/564,138/564	19212007	24,12980	2202	4300	6502	SO:0001583	missense	8659	exon5			CTGCGCGGCCCAC	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.413C>T	1.37:g.19212007G>A	ENSP00000364490:p.Pro138Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	44	32	0.727273	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	37	CCDS188.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	14.66	2.601317	0.46423	0.002725	0.001395	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309;ENST00000375335;ENST00000454547;ENST00000375334;ENST00000432718	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.41	3.54	0.40534	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.237912	0.43416	D	0.000562	T	0.42177	0.1191	M	0.83852	2.665	0.80722	D	1	D	0.53151	0.958	P	0.47864	0.559	T	0.40553	-0.9557	10	0.48119	T	0.1	-36.7716	10.2054	0.43109	0.0751:0.1365:0.7884:0.0	.	138	P30038	AL4A1_HUMAN	L	138;138;138;78;122;36;78;122	ENSP00000290597:P138L;ENSP00000364490:P138L;ENSP00000446071:P138L;ENSP00000442988:P78L;ENSP00000393209:P122L	ENSP00000290597:P138L	P	-	2	0	ALDH4A1	19084594	1.000000	0.71417	0.671000	0.29857	0.115000	0.19883	6.100000	0.71473	0.667000	0.31107	-0.264000	0.10439	CCG	G|0.999;A|0.001	0.001	strong		0.672	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1		
FAM167B	84734	hgsc.bcm.edu	37	1	32713199	32713199	+	Silent	SNP	A	A	G	rs200422136|rs2291063	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32713199A>G	ENST00000373582.3	+	1	366	c.177A>G	c.(175-177)caA>caG	p.Q59Q		NM_032648.2	NP_116037.2	Q9BTA0	F167B_HUMAN	family with sequence similarity 167, member B	59										endometrium(1)|large_intestine(1)|lung(1)|ovary(2)	5						GCAGGGCCCAAGCCAAACCTG	0.642													a|||	842	0.168131	0.1263	0.2176	5008	,	,		18191	0.255		0.0328	False		,,,				2504	0.2393				p.Q59Q		Atlas-SNP	.											.	FAM167B	18	.	0			c.A177G						PASS	.	A		427,3463		27,373,1545	40.0	50.0	47.0		177	1.1	0.0	1	dbSNP_100	47	315,7957		8,299,3829	no	coding-synonymous	FAM167B	NM_032648.2		35,672,5374	GG,GA,AA		3.808,10.9769,6.101		59/164	32713199	742,11420	1945	4136	6081	SO:0001819	synonymous_variant	84734	exon1			GGCCCAAGCCAAA	BC004269	CCDS358.2	1p35.1	2010-08-27	2008-06-11	2008-06-11	ENSG00000183615	ENSG00000183615			28133	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 90"""	C1orf90		12477932	Standard	NM_032648		Approved	MGC10820	uc001buw.3	Q9BTA0	OTTHUMG00000007462	ENST00000373582.3:c.177A>G	1.37:g.32713199A>G		Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	117	84	0.717949	NM_032648	Q5TDH6	Silent	SNP	ENST00000373582.3	37	CCDS358.2																																																																																			A|0.870;G|0.130	0.130	strong		0.642	FAM167B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019615.2	NM_032648	
DVL2	1856	hgsc.bcm.edu	37	17	7129840	7129840	+	Silent	SNP	T	T	C	rs35594616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7129840T>C	ENST00000005340.5	-	14	1944	c.1662A>G	c.(1660-1662)caA>caG	p.Q554Q	DVL2_ENST00000574642.1_5'Flank|DVL2_ENST00000575458.1_Silent_p.Q548Q	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	554					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						GGGCAGGGTATTGGTAGGAGA	0.617													T|||	2602	0.519569	0.416	0.4957	5008	,	,		15735	0.4732		0.6233	False		,,,				2504	0.6176				p.Q554Q		Atlas-SNP	.											.	DVL2	49	.	0			c.A1662G						PASS	.	T		1944,2462	545.8+/-376.9	413,1118,672	51.0	55.0	54.0		1662	-2.7	0.9	17	dbSNP_126	54	5380,3220	646.5+/-400.3	1695,1990,615	no	coding-synonymous	DVL2	NM_004422.2		2108,3108,1287	CC,CT,TT		37.4419,44.1217,43.6875		554/737	7129840	7324,5682	2203	4300	6503	SO:0001819	synonymous_variant	1856	exon14			AGGGTATTGGTAG	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.1662A>G	17.37:g.7129840T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	NM_004422	D3DTN3|Q53XM0	Silent	SNP	ENST00000005340.5	37	CCDS11091.1																																																																																			T|0.449;C|0.551	0.551	strong		0.617	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
WWC1	23286	hgsc.bcm.edu	37	5	167858371	167858371	+	Missense_Mutation	SNP	G	G	T	rs386694705|rs3822660	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:167858371G>T	ENST00000265293.4	+	15	2704	c.2202G>T	c.(2200-2202)atG>atT	p.M734I	WWC1_ENST00000522140.1_3'UTR|WWC1_ENST00000521089.1_Missense_Mutation_p.M734I	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	734	C2.		M -> I (polymorphism; associated with Ala-735; affects KIBRA lipid-binding specificity showing stronger interactions with PI(4)P and PI(5)P; dbSNP:rs3822660). {ECO:0000269|PubMed:23778582}.		cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|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)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GGGTATCCATGTCCTATCCAG	0.562													G|||	805	0.160743	0.2859	0.0663	5008	,	,		16462	0.2312		0.0736	False		,,,				2504	0.0757				p.M734I		Atlas-SNP	.											.	WWC1	98	.	0			c.G2202T						PASS	.						77.0	70.0	73.0					5																	167858371		2203	4300	6503	SO:0001583	missense	23286	exon15			ATCCATGTCCTAT	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"""WW, C2 and coiled-coil domain containing"""	29435	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 168"""	610533	"""WW, C2 and coiled-coil domain containing 1"""			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2202G>T	5.37:g.167858371G>T	ENSP00000265293:p.Met734Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Missense_Mutation	SNP	ENST00000265293.4	37	CCDS4366.1	283|283	0.1295787545787546|0.1295787545787546	108|108	0.21951219512195122|0.21951219512195122	26|26	0.0718232044198895|0.0718232044198895	104|104	0.18181818181818182|0.18181818181818182	45|45	0.059366754617414245|0.059366754617414245	G|G	3.153|3.153	-0.173892|-0.173892	0.06421|0.06421	.|.	.|.	ENSG00000113645|ENSG00000113645	ENST00000265293;ENST00000521089;ENST00000524038|ENST00000393895;ENST00000524228	T;T;T|.	0.35236|.	1.32;1.32;1.32|.	5.24|5.24	1.22|1.22	0.21188|0.21188	C2 calcium/lipid-binding domain, CaLB (1);|.	0.372565|.	0.29668|.	N|.	0.011510|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00088|0.00088	-2.19|-2.19	0.41687|0.41687	P|P	0.010678999999999994|0.010678999999999994	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|T	0.40887|0.40887	-0.9539|-0.9539	9|4	0.02654|.	T|.	1|.	.|.	1.9532|1.9532	0.03371|0.03371	0.1628:0.3846:0.2462:0.2064|0.1628:0.3846:0.2462:0.2064	rs3822660;rs52813396;rs58443717;rs3822660|rs3822660;rs52813396;rs58443717;rs3822660	734;640;640;734|.	Q8IX03-2;F5H498;B3KX05;Q8IX03|.	.;.;.;KIBRA_HUMAN|.	I|F	734;734;60|696;511	ENSP00000265293:M734I;ENSP00000427772:M734I;ENSP00000428084:M60I|.	ENSP00000265293:M734I|.	M|V	+|+	3|1	0|0	WWC1|WWC1	167790949|167790949	0.890000|0.890000	0.30428|0.30428	0.998000|0.998000	0.56505|0.56505	0.989000|0.989000	0.77384|0.77384	-0.057000|-0.057000	0.11768|0.11768	0.200000|0.200000	0.20447|0.20447	0.655000|0.655000	0.94253|0.94253	ATG|GTC	G|0.927;T|0.073	0.073	strong		0.562	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
CRACR2A	84766	hgsc.bcm.edu	37	12	3788145	3788145	+	Missense_Mutation	SNP	C	C	T	rs242018	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:3788145C>T	ENST00000252322.1	-	6	928	c.460G>A	c.(460-462)Gaa>Aaa	p.E154K	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.E154K|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.E154K	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		154			E -> K (in dbSNP:rs242018). {ECO:0000269|PubMed:15489334}.		activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TCCTCATCTTCGCCCATGTCG	0.532													C|||	1114	0.222444	0.1747	0.33	5008	,	,		20677	0.1319		0.2565	False		,,,				2504	0.2689				p.E154K		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.G460A						PASS	.	C	LYS/GLU,LYS/GLU	825,3581	327.7+/-300.2	91,643,1469	205.0	165.0	179.0		460,460	1.5	0.0	12	dbSNP_79	179	2370,6230	395.0+/-344.9	303,1764,2233	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	56,56	394,2407,3702	TT,TC,CC		27.5581,18.7245,24.5656	benign,benign	154/732,154/396	3788145	3195,9811	2203	4300	6503	SO:0001583	missense	84766	exon6			CATCTTCGCCCAT																												ENST00000252322.1:c.460G>A	12.37:g.3788145C>T	ENSP00000252322:p.Glu154Lys	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	488	0.22344322344322345	90	0.18292682926829268	119	0.3287292817679558	81	0.14160839160839161	198	0.2612137203166227	C	6.084	0.383782	0.11524	0.187245	0.275581	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.62941	-0.01;2.41;2.39	4.9	1.51	0.23008	.	0.607794	0.17497	N	0.172133	T	0.00012	0.0000	M	0.72894	2.215	0.80722	P	0.0	B;B;B	0.19817	0.039;0.008;0.008	B;B;B	0.08055	0.003;0.003;0.001	T	0.14727	-1.0462	9	0.32370	T	0.25	-0.0552	4.976	0.14140	0.0:0.5477:0.2293:0.223	rs242018;rs3803136;rs17770609;rs52791075;rs56733254;rs242018	154;154;154	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	K	154	ENSP00000409382:E154K;ENSP00000412496:E154K;ENSP00000252322:E154K	ENSP00000252322:E154K	E	-	1	0	EFCAB4B	3658406	0.005000	0.15991	0.000000	0.03702	0.006000	0.05464	1.008000	0.29872	-0.025000	0.13918	0.561000	0.74099	GAA	C|0.763;T|0.237	0.237	strong		0.532	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
DDX54	79039	hgsc.bcm.edu	37	12	113596866	113596866	+	Missense_Mutation	SNP	G	G	A	rs1048889	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113596866G>A	ENST00000306014.5	-	20	2489	c.2462C>T	c.(2461-2463)cCg>cTg	p.P821L	DDX54_ENST00000314045.7_Missense_Mutation_p.P822L|CCDC42B_ENST00000335621.6_3'UTR|DDX54_ENST00000549271.1_5'UTR|Y_RNA_ENST00000363029.1_RNA	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	821			P -> L (in dbSNP:rs1048889).		ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CTTGAGTTCCGGGCGGACTCG	0.662													G|||	124	0.0247604	0.0023	0.0432	5008	,	,		15410	0.0		0.0805	False		,,,				2504	0.0102				p.P822L		Atlas-SNP	.											.	DDX54	73	.	0			c.C2465T						PASS	.	G	LEU/PRO,,LEU/PRO	56,4350		1,54,2148	17.0	19.0	18.0		2465,,2462	5.1	0.9	12	dbSNP_86	18	498,8102		16,466,3818	yes	missense,utr-3,missense	DDX54,CCDC42B	NM_001111322.1,NM_001144872.1,NM_024072.3	98,,98	17,520,5966	AA,AG,GG		5.7907,1.271,4.2596	benign,,benign	822/883,,821/882	113596866	554,12452	2203	4300	6503	SO:0001583	missense	79039	exon20			AGTTCCGGGCGGA	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.2462C>T	12.37:g.113596866G>A	ENSP00000304072:p.Pro821Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_001111322	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	80	0.03663003663003663	3	0.006097560975609756	16	0.04419889502762431	0	0.0	61	0.08047493403693931	G	14.61	2.587399	0.46110	0.01271	0.057907	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.09350	2.99;2.99	5.06	5.06	0.68205	.	0.218861	0.40908	D	0.000994	T	0.00496	0.0016	L	0.29908	0.895	0.20074	P	0.9999367728	B;B	0.17667	0.009;0.023	B;B	0.15870	0.013;0.014	T	0.23797	-1.0178	9	0.33141	T	0.24	.	16.5805	0.84713	0.0:0.0:1.0:0.0	rs1048889;rs1048889	822;821	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	L	822;821	ENSP00000323858:P822L;ENSP00000304072:P821L	ENSP00000304072:P821L	P	-	2	0	DDX54	112081249	1.000000	0.71417	0.886000	0.34754	0.404000	0.30871	8.858000	0.92256	2.509000	0.84616	0.561000	0.74099	CCG	G|0.963;A|0.037	0.037	strong		0.662	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
PIEZO1	9780	hgsc.bcm.edu	37	16	88781040	88781040	+	IGR	SNP	A	A	G	rs8059048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88781040A>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Missense_Mutation_p.Q416R|CTU2_ENST00000378384.3_Missense_Mutation_p.Q329R|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.Q416R|CTU2_ENST00000567949.1_Missense_Mutation_p.Q487R	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						CGTCTCTCCCAGATGCAGTCA	0.697													A|||	1612	0.321885	0.1793	0.3746	5008	,	,		14539	0.6647		0.1958	False		,,,				2504	0.2536				p.Q416R		Atlas-SNP	.											CTU2_ENST00000453996,NS,carcinoma,0,4	CTU2	66	4	0			c.A1247G						PASS	.	A	ARG/GLN,ARG/GLN	890,3492	338.6+/-305.4	104,682,1405	45.0	46.0	45.0		1247,1247	1.9	0.1	16	dbSNP_116	45	1636,6956	299.7+/-304.6	171,1294,2831	yes	missense,missense	CTU2	NM_001012759.1,NM_001012762.1	43,43	275,1976,4236	GG,GA,AA		19.041,20.3104,19.4697	benign,benign	416/516,416/486	88781040	2526,10448	2191	4296	6487	SO:0001628	intergenic_variant	348180	exon12			TCTCCCAGATGCA	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.88781040A>G		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	144	120	0.833333	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	734	0.3360805860805861	84	0.17073170731707318	126	0.34806629834254144	375	0.6555944055944056	149	0.19656992084432717	A	10.10	1.258563	0.23051	0.203104	0.19041	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.52754	0.65;0.65;0.65	4.32	1.86	0.25419	.	0.070349	0.64402	D	0.000019	T	0.00012	0.0000	L	0.52573	1.65	0.58432	P	4.000000000004E-6	B;B;B	0.15473	0.013;0.01;0.012	B;B;B	0.18263	0.013;0.021;0.009	T	0.35475	-0.9787	9	0.39692	T	0.17	.	4.6795	0.12727	0.4951:0.1719:0.0:0.333	rs8059048;rs60525594;rs8059048	329;416;416	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	R	329;416;416	ENSP00000367635:Q329R;ENSP00000308617:Q416R;ENSP00000388320:Q416R	ENSP00000308617:Q416R	Q	+	2	0	CTU2	87308541	0.004000	0.15560	0.077000	0.20336	0.048000	0.14542	-0.277000	0.08502	0.108000	0.17862	0.379000	0.24179	CAG	A|0.751;G|0.249	0.249	strong		0.697	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
LILRB5	10990	hgsc.bcm.edu	37	19	54756246	54756246	+	Missense_Mutation	SNP	A	A	G	rs117421142	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54756246A>G	ENST00000316219.5	-	11	1663	c.1556T>C	c.(1555-1557)aTc>aCc	p.I519T	LILRB5_ENST00000450632.1_Missense_Mutation_p.I511T|LILRB5_ENST00000449561.2_Missense_Mutation_p.I520T|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000345866.6_Missense_Mutation_p.I420T	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	519					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)		TTCCTCCTGGATGTCAGCAAC	0.597													.|||	120	0.0239617	0.0	0.0072	5008	,	,		14772	0.004		0.0149	False		,,,				2504	0.0982				p.I520T		Atlas-SNP	.											.	LILRB5	176	.	0			c.T1559C						PASS	.	G	THR/ILE,THR/ILE,THR/ILE	20,4386	27.2+/-55.0	0,20,2183	93.0	90.0	91.0		1559,1259,1556	-4.2	0.0	19	dbSNP_132	91	214,8386	90.4+/-152.6	4,206,4090	yes	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	89,89,89	4,226,6273	GG,GA,AA		2.4884,0.4539,1.7992	benign,benign,benign	520/592,420/492,519/591	54756246	234,12772	2203	4300	6503	SO:0001583	missense	10990	exon11			TCCTGGATGTCAG	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.1556T>C	19.37:g.54756246A>G	ENSP00000320390:p.Ile519Thr	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	3	0.005244755244755245	13	0.017150395778364115	a	0.006	-2.099395	0.00360	0.004539	0.024884	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00477	7.24;7.14;7.23;7.21	2.08	-4.16	0.03869	.	.	.	.	.	T	0.00073	0.0002	N	0.03154	-0.405	0.09310	N	1	B;B;B;B	0.26672	0.156;0.001;0.002;0.0	B;B;B;B	0.19666	0.026;0.004;0.002;0.002	T	0.29518	-1.0009	9	0.06365	T	0.9	.	5.7303	0.18036	0.2118:0.0:0.6172:0.171	.	511;420;520;519	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	T	519;511;520;420	ENSP00000320390:I519T;ENSP00000414225:I511T;ENSP00000406478:I520T;ENSP00000263430:I420T	ENSP00000320390:I519T	I	-	2	0	LILRB5	59448058	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.214000	0.01223	-2.013000	0.00949	-2.993000	0.00078	ATC	A|0.985;G|0.015	0.015	strong		0.597	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
DNAH14	127602	hgsc.bcm.edu	37	1	225533684	225533684	+	Missense_Mutation	SNP	A	A	G	rs6667999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225533684A>G	ENST00000445597.2	+	48	8011	c.8011A>G	c.(8011-8013)Aaa>Gaa	p.K2671E	DNAH14_ENST00000430092.1_Missense_Mutation_p.K3474E|DNAH14_ENST00000439375.2_Missense_Mutation_p.K3474E			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2671			K -> E (in dbSNP:rs6667999).		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						AGATGATGACAAAATTGTAGA	0.328													G|||	2649	0.528954	0.6399	0.4697	5008	,	,		18280	0.5089		0.4046	False		,,,				2504	0.5695				p.K3474E		Atlas-SNP	.											.	DNAH14	300	.	0			c.A10420G						PASS	.	G	GLU/LYS	842,542		268,306,118	62.0	46.0	51.0		10420	3.4	0.0	1	dbSNP_116	51	1406,1776		323,760,508	yes	missense	DNAH14	NM_001373.1	56	591,1066,626	GG,GA,AA		44.186,39.1618,49.2335	benign	3474/4516	225533684	2248,2318	692	1591	2283	SO:0001583	missense	127602	exon68			GATGACAAAATTG	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.8011A>G	1.37:g.225533684A>G	ENSP00000409472:p.Lys2671Glu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	156	106	0.679487	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	G	0.005	-2.137791	0.00335	0.608382	0.44186	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.54071	0.59;0.59;0.59	5.34	3.37	0.38596	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45862	-0.9232	7	0.02654	T	1	.	7.3982	0.26948	0.1499:0.0:0.7149:0.1352	rs6667999;rs52791604;rs60868380;rs6667999	3474	Q0VDD8-4	.	E	2671;3474;3474	ENSP00000409472:K2671E;ENSP00000414402:K3474E;ENSP00000392061:K3474E	ENSP00000414402:K3474E	K	+	1	0	DNAH14	223600307	0.836000	0.29430	0.026000	0.17262	0.022000	0.10575	1.958000	0.40402	0.621000	0.30232	-0.294000	0.09567	AAA	A|0.507;G|0.493	0.493	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
MUC17	140453	hgsc.bcm.edu	37	7	100684593	100684593	+	Missense_Mutation	SNP	G	G	A	rs35988443	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100684593G>A	ENST00000306151.4	+	3	9960	c.9896G>A	c.(9895-9897)aGc>aAc	p.S3299N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3299	59 X approximate tandem repeats.|Ser-rich.		S -> N (in dbSNP:rs35988443).		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)					TCTGAAACGAGCACCCTTTCA	0.512													G|||	563	0.11242	0.1634	0.0807	5008	,	,		26032	0.0665		0.1173	False		,,,				2504	0.1084				p.S3299N		Atlas-SNP	.											.	MUC17	804	.	0			c.G9896A						PASS	.	G	ASN/SER	640,3766	275.4+/-272.5	43,554,1606	307.0	314.0	312.0		9896	-1.5	0.0	7	dbSNP_126	312	987,7613	213.6+/-253.5	57,873,3370	no	missense	MUC17	NM_001040105.1	46	100,1427,4976	AA,AG,GG		11.4767,14.5256,12.5096	possibly-damaging	3299/4494	100684593	1627,11379	2203	4300	6503	SO:0001583	missense	140453	exon3			AAACGAGCACCCT	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.9896G>A	7.37:g.100684593G>A	ENSP00000302716:p.Ser3299Asn	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	186	182	0.978495	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	213	0.09752747252747253	65	0.13211382113821138	32	0.08839779005524862	29	0.050699300699300696	87	0.11477572559366754	g	0.265	-0.996778	0.02145	0.145256	0.114767	ENSG00000169876	ENST00000306151	T	0.02121	4.44	0.754	-1.51	0.08664	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.13594	0.008	B	0.15870	0.014	T	0.46275	-0.9203	8	0.24483	T	0.36	.	3.8023	0.08763	0.2104:0.2466:0.543:0.0	rs35988443;rs58884530	3299	Q685J3	MUC17_HUMAN	N	3299	ENSP00000302716:S3299N	ENSP00000302716:S3299N	S	+	2	0	MUC17	100471313	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.085000	0.11250	-1.089000	0.03073	0.134000	0.15878	AGC	G|0.888;A|0.112	0.112	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TGM5	9333	hgsc.bcm.edu	37	15	43531411	43531411	+	Missense_Mutation	SNP	G	G	C	rs28756768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:43531411G>C	ENST00000220420.5	-	8	1062	c.1055C>G	c.(1054-1056)gCa>gGa	p.A352G	TGM5_ENST00000349114.4_Missense_Mutation_p.A270G	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	352			A -> G (in dbSNP:rs28756768). {ECO:0000269|PubMed:11390390}.		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)	GCCTCCATATGCAGGGGGCAG	0.587													C|||	1216	0.242812	0.5053	0.1484	5008	,	,		19080	0.2431		0.0895	False		,,,				2504	0.1125				p.A352G		Atlas-SNP	.											.	TGM5	88	.	0			c.C1055G						PASS	.	C	GLY/ALA,GLY/ALA	1927,2477	623.6+/-394.2	429,1069,704	70.0	71.0	71.0		809,1055	3.7	0.7	15	dbSNP_125	71	848,7750	780.3+/-407.7	48,752,3499	yes	missense,missense	TGM5	NM_004245.3,NM_201631.3	60,60	477,1821,4203	CC,CG,GG		9.8628,43.7557,21.3429	benign,benign	270/639,352/721	43531411	2775,10227	2202	4299	6501	SO:0001583	missense	9333	exon8			CCATATGCAGGGG	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.1055C>G	15.37:g.43531411G>C	ENSP00000220420:p.Ala352Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	50	10	0.2	NM_201631	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	545	0.24954212454212454	269	0.5467479674796748	59	0.16298342541436464	146	0.25524475524475526	71	0.09366754617414248	C	2.348	-0.349613	0.05173	0.437557	0.098628	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	D;D	0.88277	-2.36;-2.36	5.59	3.69	0.42338	Transglutaminase-like (2);	0.397736	0.26955	N	0.021646	T	0.00012	0.0000	N	0.00046	-2.44	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44467	-0.9326	9	0.02654	T	1	-7.8516	7.9641	0.30089	0.0:0.7179:0.1317:0.1505	rs28756768;rs52817033;rs61159524	270;352	O43548-2;O43548	.;TGM5_HUMAN	G	352;270;351	ENSP00000220420:A352G;ENSP00000220419:A270G	ENSP00000220420:A352G	A	-	2	0	TGM5	41318703	0.000000	0.05858	0.732000	0.30844	0.747000	0.42532	-0.763000	0.04740	0.748000	0.32831	-0.120000	0.15030	GCA	G|0.789;C|0.211	0.211	strong		0.587	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
NTRK3	4916	hgsc.bcm.edu	37	15	88576185	88576185	+	Silent	SNP	G	G	C	rs2229910	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:88576185G>C	ENST00000360948.2	-	13	1649	c.1488C>G	c.(1486-1488)gcC>gcG	p.A496A	NTRK3_ENST00000558306.1_5'UTR|NTRK3_ENST00000355254.2_Silent_p.A496A|NTRK3_ENST00000357724.2_Silent_p.A488A|NTRK3_ENST00000540489.2_Silent_p.A496A|NTRK3_ENST00000317501.3_Silent_p.A496A|NTRK3_ENST00000394480.2_Silent_p.A496A|NTRK3_ENST00000542733.2_Silent_p.A398A|NTRK3_ENST00000557856.1_Silent_p.A488A|NTRK3_ENST00000558676.1_Silent_p.A488A	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	496					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A496A(1)	ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGTCGGGCCCGGCATCCAGTG	0.602			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)			G|||	1753	0.35004	0.4395	0.3746	5008	,	,		11027	0.2083		0.3171	False		,,,				2504	0.3916				p.A496A		Atlas-SNP	.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	NTRK3_ENST00000360948,NS,carcinoma,-1,4	NTRK3	587	4	1	Substitution - coding silent(1)	stomach(1)	c.C1488G						scavenged	.	G	,,	1782,2620	525.1+/-371.5	378,1026,797	96.0	63.0	74.0		1488,1488,1488	-5.5	0.0	15	dbSNP_129	74	3053,5545	464.4+/-366.2	548,1957,1794	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK3	NM_001007156.2,NM_001012338.2,NM_002530.3	,,	926,2983,2591	CC,CG,GG		35.5083,40.4816,37.1923	,,	496/613,496/840,496/826	88576185	4835,8165	2201	4299	6500	SO:0001819	synonymous_variant	4916	exon14			GGGCCCGGCATCC	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1488C>G	15.37:g.88576185G>C		Somatic	149	2	0.0134228		WXS	Illumina HiSeq	Phase_I	73	14	0.191781	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	37	CCDS32322.1																																																																																			G|0.647;C|0.353	0.353	strong		0.602	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
SOCS5	9655	hgsc.bcm.edu	37	2	46986716	46986716	+	Silent	SNP	C	C	G	rs41489952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:46986716C>G	ENST00000306503.5	+	2	1219	c.1047C>G	c.(1045-1047)acC>acG	p.T349T	SOCS5_ENST00000394861.2_Silent_p.T349T	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	349					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)			ACAGCCATACCCATGTTAGCA	0.478													C|||	139	0.0277556	0.003	0.0403	5008	,	,		21764	0.001		0.0934	False		,,,				2504	0.0123				p.T349T		Atlas-SNP	.											.	SOCS5	62	.	0			c.C1047G						PASS	.	C	,	93,4313	74.1+/-112.3	1,91,2111	72.0	72.0	72.0		1047,1047	1.5	0.1	2	dbSNP_127	72	859,7741	195.4+/-240.6	46,767,3487	no	coding-synonymous,coding-synonymous	SOCS5	NM_014011.4,NM_144949.2	,	47,858,5598	GG,GC,CC		9.9884,2.1108,7.3197	,	349/537,349/537	46986716	952,12054	2203	4300	6503	SO:0001819	synonymous_variant	9655	exon2			CCATACCCATGTT	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.1047C>G	2.37:g.46986716C>G		Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	216	125	0.578704	NM_144949	Q53SD4|Q8IYZ4	Silent	SNP	ENST00000306503.5	37	CCDS1830.1																																																																																			C|0.935;G|0.065	0.065	strong		0.478	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2		
DSPP	1834	hgsc.bcm.edu	37	4	88537475	88537475	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:88537475G>A	ENST00000282478.7	+	4	3694	c.3661G>A	c.(3661-3663)Gac>Aac	p.D1221N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1221N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1221	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)		tgacagcagcgacagcagtga	0.562																																					p.D1221N		Atlas-SNP	.											DSPP,colon,carcinoma,-1,1	DSPP	174	1	0			c.G3661A						scavenged	.						39.0	58.0	51.0					4																	88537475		1603	2881	4484	SO:0001583	missense	1834	exon5			AGCAGCGACAGCA	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.3661G>A	4.37:g.88537475G>A	ENSP00000282478:p.Asp1221Asn	Somatic	416	1	0.00240385		WXS	Illumina HiSeq	Phase_I	453	7	0.0154525	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	0.597	-0.830744	0.02734	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	3.37	1.6	0.23607	.	0.805118	0.10088	N	0.717527	T	0.79417	0.4442	L	0.34521	1.04	0.09310	N	1	B	0.14805	0.011	B	0.12837	0.008	T	0.60010	-0.7346	10	0.08381	T	0.77	-4.9874	6.3302	0.21266	0.2478:0.0:0.7522:0.0	.	1221	Q9NZW4	DSPP_HUMAN	N	1221	ENSP00000382213:D1221N;ENSP00000282478:D1221N	ENSP00000282478:D1221N	D	+	1	0	DSPP	88756499	0.006000	0.16342	0.011000	0.14972	0.004000	0.04260	0.311000	0.19380	0.235000	0.21160	-1.261000	0.01458	GAC	.	.	none		0.562	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
TTLL9	164395	hgsc.bcm.edu	37	20	30527065	30527065	+	Silent	SNP	T	T	C	rs6061043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:30527065T>C	ENST00000375938.4	+	14	1492	c.1239T>C	c.(1237-1239)caT>caC	p.H413H	TTLL9_ENST00000375921.2_3'UTR|TTLL9_ENST00000375934.4_3'UTR|TTLL9_ENST00000375922.4_Intron|TTLL9_ENST00000535842.1_Silent_p.H413H			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	413					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)	ligase activity (GO:0016874)	p.H413H(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CCAACACACATCTCGGTATGT	0.557													C|||	2128	0.42492	0.8086	0.4006	5008	,	,		17804	0.1171		0.4195	False		,,,				2504	0.2464				p.H413H		Atlas-SNP	.											TTLL9,NS,carcinoma,0,1	TTLL9	95	1	1	Substitution - coding silent(1)	prostate(1)	c.T1239C						PASS	.	C		3006,1022		1134,738,142	57.0	65.0	63.0		1239	2.8	0.9	20	dbSNP_114	63	3460,4900		722,2016,1442	no	coding-synonymous	TTLL9	NM_001008409.2		1856,2754,1584	CC,CT,TT		41.3876,25.3724,47.8043		413/440	30527065	6466,5922	2014	4180	6194	SO:0001819	synonymous_variant	164395	exon14			CACACATCTCGGT	AL031658	CCDS42863.1	20q11	2013-02-14	2005-07-28	2005-07-28		ENSG00000131044		"""Tubulin tyrosine ligase-like family"""	16118	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 125"""	C20orf125		15890843	Standard	NM_001008409		Approved	dJ310O13.1	uc010gdx.1	Q3SXZ7		ENST00000375938.4:c.1239T>C	20.37:g.30527065T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Silent	SNP	ENST00000375938.4	37	CCDS42863.1																																																																																			T|0.572;C|0.428	0.428	strong		0.557	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409	
KIAA1549	57670	hgsc.bcm.edu	37	7	138602523	138602523	+	Missense_Mutation	SNP	T	T	C	rs2774962	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:138602523T>C	ENST00000422774.1	-	2	1897	c.1849A>G	c.(1849-1851)Aga>Gga	p.R617G	KIAA1549_ENST00000440172.1_Missense_Mutation_p.R617G|KIAA1549_ENST00000242365.4_Missense_Mutation_p.R567G			Q9HCM3	K1549_HUMAN	KIAA1549	617	Ser-rich.			R -> G (in Ref. 3; BAB13375). {ECO:0000305}.		integral component of membrane (GO:0016021)		p.R617G(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						AAAGCACCTCTGGGTTTATGC	0.498			O	BRAF	pilocytic astrocytoma								C|||	2502	0.499601	0.944	0.2867	5008	,	,		20995	0.2024		0.4175	False		,,,				2504	0.4407				p.R617G	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	KIAA1549_ENST00000422774,colon,carcinoma,0,3	KIAA1549	314	3	1	Substitution - Missense(1)	stomach(1)	c.A1849G						scavenged	.	C	GLY/ARG,GLY/ARG	3201,563		1361,479,42	38.0	43.0	41.0		1849,1849	0.9	0.0	7	dbSNP_100	41	3231,4987		665,1901,1543	yes	missense,missense	KIAA1549	NM_001164665.1,NM_020910.2	125,125	2026,2380,1585	CC,CT,TT		39.3161,14.9575,46.3195	benign,benign	617/1951,617/1935	138602523	6432,5550	1882	4109	5991	SO:0001583	missense	57670	exon2			CACCTCTGGGTTT		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1849A>G	7.37:g.138602523T>C	ENSP00000416040:p.Arg617Gly	Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	46	44	0.956522	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	994	0.4551282051282051	458	0.9308943089430894	107	0.2955801104972376	124	0.21678321678321677	305	0.4023746701846966	C	2.367	-0.345193	0.05208	0.850425	0.393161	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.22945	1.93;1.93;1.93	3.97	0.882	0.19172	.	1.384970	0.04733	N	0.421435	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	0.21999	-1.0229	9	0.21540	T	0.41	.	3.4217	0.07396	0.2007:0.3444:0.0:0.4549	rs2774962;rs3735010;rs10376674;rs17605959;rs52812915;rs56602304;rs58455329;rs2774962	617;617	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	G	617;567;617	ENSP00000406661:R617G;ENSP00000242365:R567G;ENSP00000416040:R617G	ENSP00000242365:R567G	R	-	1	2	KIAA1549	138253063	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.204000	0.09425	0.061000	0.16311	-0.186000	0.12905	AGA	T|0.509;C|0.491	0.491	strong		0.498	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
FXYD3	5349	hgsc.bcm.edu	37	19	35612159	35612159	+	Intron	SNP	C	C	G	rs2290649	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:35612159C>G	ENST00000344013.6	+	5	293				FXYD3_ENST00000605677.1_Intron|FXYD3_ENST00000346446.5_Intron|FXYD3_ENST00000603449.1_Missense_Mutation_p.P36R|FXYD3_ENST00000535103.1_Intron|FXYD3_ENST00000454903.2_Missense_Mutation_p.P36R|FXYD3_ENST00000604255.1_Intron|FXYD3_ENST00000603524.1_Intron|FXYD3_ENST00000604404.1_Intron|FXYD3_ENST00000603181.1_Intron|FXYD3_ENST00000604621.1_Intron|FXYD3_ENST00000406242.3_Intron|FXYD3_ENST00000406988.1_Intron|FXYD3_ENST00000435734.2_Intron|FXYD3_ENST00000605552.1_Missense_Mutation_p.P36R|FXYD3_ENST00000605550.1_Intron|FXYD3_ENST00000604804.1_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	278	1	0.00359712		WXS	Illumina HiSeq	Phase_I	240	121	0.504167	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	
MTTP	4547	hgsc.bcm.edu	37	4	100512412	100512412	+	Silent	SNP	T	T	C	rs982424	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:100512412T>C	ENST00000265517.5	+	5	725	c.522T>C	c.(520-522)tgT>tgC	p.C174C	MTTP_ENST00000457717.1_Silent_p.C174C|MTTP_ENST00000511045.1_Silent_p.C201C			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	174	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				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)	CTGGAAATTGTAAAGTGACCT	0.408													T|||	824	0.164537	0.2534	0.0951	5008	,	,		15709	0.2232		0.0497	False		,,,				2504	0.1513				p.C174C		Atlas-SNP	.											.	MTTP	127	.	0			c.T522C						PASS	.	T		1064,3342	389.1+/-327.2	135,794,1274	103.0	100.0	101.0		522	-0.6	1.0	4	dbSNP_86	101	598,8002	158.2+/-211.7	21,556,3723	no	coding-synonymous	MTTP	NM_000253.2		156,1350,4997	CC,CT,TT		6.9535,24.1489,12.7787		174/895	100512412	1662,11344	2203	4300	6503	SO:0001819	synonymous_variant	4547	exon6			AAATTGTAAAGTG		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.522T>C	4.37:g.100512412T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	128	60	0.46875	NM_000253	A8K428|Q08AM4|Q6P5T3	Silent	SNP	ENST00000265517.5	37	CCDS3651.1																																																																																			T|0.855;C|0.145	0.145	strong		0.408	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
PCM1	5108	hgsc.bcm.edu	37	8	17824674	17824674	+	Missense_Mutation	SNP	C	C	T	rs565676613		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17824674C>T	ENST00000519253.1	+	21	3658	c.3407C>T	c.(3406-3408)gCa>gTa	p.A1136V	PCM1_ENST00000325083.8_Missense_Mutation_p.A1136V|PCM1_ENST00000524226.1_Missense_Mutation_p.A1137V			Q15154	PCM1_HUMAN	pericentriolar material 1	1136					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.A1136V(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TCATCATTTGCACCAGGTAGG	0.353			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.A1136V		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	PCM1,colon,carcinoma,0,1	PCM1	120	1	1	Substitution - Missense(1)	large_intestine(1)	c.C3407T						PASS	.						43.0	42.0	42.0					8																	17824674		1826	4087	5913	SO:0001583	missense	5108	exon21			CATTTGCACCAGG		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3407C>T	8.37:g.17824674C>T	ENSP00000431099:p.Ala1136Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	134	82	0.61194	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	C	15.01	2.707472	0.48412	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.56776	0.44;0.44;0.44	5.7	4.83	0.62350	.	0.317735	0.40302	N	0.001125	T	0.32882	0.0844	N	0.14661	0.345	0.80722	D	1	P;B;P	0.35575	0.51;0.001;0.51	B;B;B	0.31442	0.13;0.004;0.13	T	0.19976	-1.0289	10	0.40728	T	0.16	-3.1369	11.1977	0.48722	0.0:0.8595:0.0:0.1405	.	1136;1137;1136	E7ETA6;E7EV56;Q15154	.;.;PCM1_HUMAN	V	1136;1136;1137	ENSP00000327077:A1136V;ENSP00000431099:A1136V;ENSP00000430521:A1137V	ENSP00000327077:A1136V	A	+	2	0	PCM1	17868954	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.612000	0.46343	1.584000	0.49913	-0.151000	0.13558	GCA	.	.	none		0.353	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
HSD3B1	3283	hgsc.bcm.edu	37	1	120056849	120056849	+	Silent	SNP	C	C	T	rs141977722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:120056849C>T	ENST00000369413.3	+	4	848	c.703C>T	c.(703-705)Ctg>Ttg	p.L235L	HSD3B1_ENST00000235547.6_Silent_p.L237L|HSD3B1_ENST00000528909.1_Silent_p.L235L			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	235					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	GGCCCACATTCTGGCCTTGAG	0.512													C|||	2	0.000399361	0.0	0.0	5008	,	,		18576	0.0		0.002	False		,,,				2504	0.0				p.L235L		Atlas-SNP	.											.	HSD3B1	53	.	0			c.C703T						PASS	.	C		0,4406		0,0,2203	64.0	69.0	68.0		703	1.2	1.0	1	dbSNP_134	68	20,8580	11.2+/-40.8	0,20,4280	no	coding-synonymous	HSD3B1	NM_000862.2		0,20,6483	TT,TC,CC		0.2326,0.0,0.1538		235/374	120056849	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			CACATTCTGGCCT	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.703C>T	1.37:g.120056849C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	175	65	0.371429	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			C|0.998;T|0.002	0.002	strong		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
JARID2	3720	hgsc.bcm.edu	37	6	15468876	15468876	+	Silent	SNP	C	C	G	rs7768621	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:15468876C>G	ENST00000341776.2	+	5	841	c.597C>G	c.(595-597)acC>acG	p.T199T	JARID2_ENST00000541660.1_Silent_p.T161T|JARID2_ENST00000397311.3_Silent_p.T27T	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	199					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				AAACAGCCACCAACAATGCTT	0.502													C|||	261	0.0521166	0.0061	0.0692	5008	,	,		20354	0.0		0.1243	False		,,,				2504	0.0818				p.T199T		Atlas-SNP	.											.	JARID2	135	.	0			c.C597G						PASS	.	C		108,4298	84.4+/-122.9	2,104,2097	150.0	123.0	132.0		597	3.9	1.0	6	dbSNP_116	132	1196,7404	242.9+/-272.7	83,1030,3187	no	coding-synonymous	JARID2	NM_004973.2		85,1134,5284	GG,GC,CC		13.907,2.4512,10.0261		199/1247	15468876	1304,11702	2203	4300	6503	SO:0001819	synonymous_variant	3720	exon5			AGCCACCAACAAT	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.597C>G	6.37:g.15468876C>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	136	64	0.470588	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																			C|0.903;G|0.096;T|0.000	0.096	strong		0.502	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
CDRT1	374286	hgsc.bcm.edu	37	17	15519029	15519029	+	Silent	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:15519029A>C	ENST00000395906.3	-	2	599	c.600T>G	c.(598-600)acT>acG	p.T200T	RP11-385D13.1_ENST00000455584.2_Silent_p.T510T	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	200										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		ATGTGTGCTGAGTTTTGGCTG	0.468																																					p.T200T		Atlas-SNP	.											.	CDRT1	83	.	0			c.T600G						PASS	.						58.0	62.0	61.0					17																	15519029		2202	4297	6499	SO:0001819	synonymous_variant	374286	exon2			GTGCTGAGTTTTG	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.600T>G	17.37:g.15519029A>C		Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	272	32	0.117647	NM_006382	O43848|O95611	Silent	SNP	ENST00000395906.3	37	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	A	3.489	-0.104310	0.06967	.	.	ENSG00000251537	ENST00000455584	.	.	.	3.68	2.66	0.31614	.	.	.	.	.	T	0.27349	0.0671	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.18085	-1.0348	4	.	.	.	.	5.4733	0.16682	0.1721:0.0:0.8279:0.0	.	.	.	.	R	525	.	.	L	-	2	0	RP11-385D13.1	15459754	0.007000	0.16637	0.004000	0.12327	0.024000	0.10985	1.274000	0.33132	1.021000	0.39600	0.454000	0.30748	CTC	.	.	none		0.468	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
CASP9	842	hgsc.bcm.edu	37	1	15850613	15850613	+	Missense_Mutation	SNP	G	G	A	rs1052571	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15850613G>A	ENST00000333868.5	-	1	177	c.83C>T	c.(82-84)gCc>gTc	p.A28V	CASP9_ENST00000469637.1_Intron|DNAJC16_ENST00000375849.1_5'Flank|CASP9_ENST00000375890.4_Intron|DNAJC16_ENST00000375838.1_5'Flank|CASP9_ENST00000348549.5_Missense_Mutation_p.A28V|DNAJC16_ENST00000375847.3_5'Flank|CASP9_ENST00000546424.1_Missense_Mutation_p.A28V	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	28	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		A -> V (in dbSNP:rs1052571). {ECO:0000269|PubMed:16780893, ECO:0000269|PubMed:8663294, ECO:0000269|PubMed:9890966, ECO:0000269|Ref.9}.		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|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)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		GCTCAGCAGGGCGTCCCAGAG	0.711													G|||	2928	0.584665	0.739	0.4986	5008	,	,		5756	0.6538		0.5149	False		,,,				2504	0.4376				p.A28V		Atlas-SNP	.											.	CASP9	40	.	0			c.C83T						PASS	.						8.0	10.0	10.0					1																	15850613		2109	4166	6275	SO:0001583	missense	842	exon1			AGCAGGGCGTCCC	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.83C>T	1.37:g.15850613G>A	ENSP00000330237:p.Ala28Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	30	29	0.966667	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	37	CCDS158.1	1291	0.5911172161172161	350	0.7113821138211383	179	0.494475138121547	358	0.6258741258741258	404	0.5329815303430079	G	15.45	2.836320	0.50951	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000348549;ENST00000440484	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	4.59	1.33	0.21861	DEATH-like (2);Caspase Recruitment (3);	0.919308	0.09391	N	0.808563	T	0.00012	0.0000	M	0.63428	1.95	0.21290	P	0.999735974	P;B;B	0.42908	0.793;0.009;0.029	B;B;B	0.39562	0.303;0.015;0.015	T	0.33394	-0.9870	9	0.22109	T	0.4	.	4.6003	0.12350	0.2169:0.0:0.6031:0.18	rs1052571;rs3192982;rs59045053;rs1052571	28;28;28	P55211-2;P55211;F8VVS7	.;CASP9_HUMAN;.	V	28	ENSP00000449584:A28V;ENSP00000330237:A28V;ENSP00000255256:A28V;ENSP00000411304:A28V	ENSP00000330237:A28V	A	-	2	0	CASP9	15723200	0.277000	0.24220	0.926000	0.36857	0.713000	0.41058	0.257000	0.18369	0.500000	0.27991	0.305000	0.20034	GCC	G|0.387;A|0.613	0.613	strong		0.711	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
CLEC16A	23274	hgsc.bcm.edu	37	16	11272330	11272330	+	Missense_Mutation	SNP	G	G	A	rs72650689	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:11272330G>A	ENST00000409790.1	+	24	3175	c.2945G>A	c.(2944-2946)aGc>aAc	p.S982N	CLEC16A_ENST00000381822.2_Missense_Mutation_p.S69N	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		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						CTGTCCCCCAGCCTCGTCCCT	0.637													G|||	14	0.00279553	0.0008	0.0	5008	,	,		18303	0.0		0.0089	False		,,,				2504	0.0041				p.S982N		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2945A						PASS	.	G	ASN/SER	6,4296		0,6,2145	63.0	77.0	72.0		2945	4.6	1.0	16	dbSNP_130	72	64,8436		0,64,4186	yes	missense	CLEC16A	NM_015226.2	46	0,70,6331	AA,AG,GG		0.7529,0.1395,0.5468	possibly-damaging	982/1054	11272330	70,12732	2151	4250	6401	SO:0001583	missense	23274	exon23			CCCCCAGCCTCGT	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.2945G>A	16.37:g.11272330G>A	ENSP00000387122:p.Ser982Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	26.8	4.771612	0.90108	0.001395	0.007529	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.55930	0.49	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	L	0.27053	0.805	0.38000	D	0.934194	D;D	0.67145	0.996;0.967	D;P	0.75484	0.986;0.878	T	0.65878	-0.6061	10	0.72032	D	0.01	-25.0792	15.032	0.71713	0.0:0.0:1.0:0.0	.	69;982	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	N	982;982;69	ENSP00000387122:S982N	ENSP00000371244:S69N	S	+	2	0	CLEC16A	11179831	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.910000	0.75741	2.304000	0.77564	0.655000	0.94253	AGC	A|0.006;G|0.994	0.006	strong		0.637	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
HEATR6	63897	hgsc.bcm.edu	37	17	58153586	58153586	+	Missense_Mutation	SNP	G	G	C	rs552733926		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:58153586G>C	ENST00000184956.6	-	2	248	c.232C>G	c.(232-234)Ctt>Gtt	p.L78V	HEATR6_ENST00000585976.1_Missense_Mutation_p.L78V|HEATR6_ENST00000585712.1_5'Flank	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	78							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TGGACAAGAAGAGCACTAACG	0.368																																					p.L78V		Atlas-SNP	.											.	HEATR6	98	.	0			c.C232G						PASS	.						62.0	55.0	57.0					17																	58153586		2203	4300	6503	SO:0001583	missense	63897	exon2			CAAGAAGAGCACT	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.232C>G	17.37:g.58153586G>C	ENSP00000184956:p.Leu78Val	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Missense_Mutation	SNP	ENST00000184956.6	37	CCDS11623.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.171512	0.38315	.	.	ENSG00000068097	ENST00000184956	T	0.44083	0.93	5.1	3.9	0.45041	Armadillo-like helical (1);	0.069197	0.56097	D	0.000024	T	0.32852	0.0843	M	0.64997	1.995	0.35789	D	0.822271	B	0.31077	0.307	B	0.24701	0.055	T	0.50423	-0.8830	10	0.62326	D	0.03	-11.8567	3.2759	0.06898	0.166:0.0:0.5802:0.2538	.	78	Q6AI08	HEAT6_HUMAN	V	78	ENSP00000184956:L78V	ENSP00000184956:L78V	L	-	1	0	HEATR6	55508368	0.992000	0.36948	1.000000	0.80357	0.989000	0.77384	0.478000	0.22212	2.557000	0.86248	0.644000	0.83932	CTT	.	.	none		0.368	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070	
HEATR2	54919	hgsc.bcm.edu	37	7	810219	810219	+	Missense_Mutation	SNP	T	T	C	rs4720951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	148	0	0		WXS	Illumina HiSeq	Phase_I	190	81	0.426316	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	
LBP	3929	hgsc.bcm.edu	37	20	36982754	36982754	+	Missense_Mutation	SNP	G	G	A	rs36015492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:36982754G>A	ENST00000217407.2	+	4	600	c.439G>A	c.(439-441)Gag>Aag	p.E147K		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	147			E -> K (in dbSNP:rs36015492).		acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				GTTGGGCAGCGAGTCCTCCGG	0.572													G|||	36	0.0071885	0.0015	0.0101	5008	,	,		17794	0.0		0.0159	False		,,,				2504	0.0112				p.E147K		Atlas-SNP	.											.	LBP	60	.	0			c.G439A						PASS	.	G	LYS/GLU	13,4393	20.2+/-43.8	0,13,2190	86.0	72.0	77.0		439	4.8	0.2	20	dbSNP_126	77	122,8478	63.5+/-125.6	1,120,4179	yes	missense	LBP	NM_004139.2	56	1,133,6369	AA,AG,GG		1.4186,0.2951,1.038	possibly-damaging	147/482	36982754	135,12871	2203	4300	6503	SO:0001583	missense	3929	exon4			GGCAGCGAGTCCT		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.439G>A	20.37:g.36982754G>A	ENSP00000217407:p.Glu147Lys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	89	51	0.573034	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	15	0.006868131868131868	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	8	0.010554089709762533	G	16.78	3.217753	0.58560	0.002951	0.014186	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.04502	3.61	4.77	4.77	0.60923	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.464529	0.21044	N	0.081102	T	0.05686	0.0149	L	0.60455	1.87	0.09310	N	0.999997	P	0.47484	0.896	B	0.42959	0.403	T	0.12066	-1.0562	10	0.72032	D	0.01	-10.5021	13.4963	0.61428	0.0:0.0:1.0:0.0	rs36015492	147	P18428	LBP_HUMAN	K	147	ENSP00000217407:E147K	ENSP00000217407:E147K	E	+	1	0	LBP	36416168	0.974000	0.33945	0.241000	0.24154	0.385000	0.30292	4.595000	0.61048	2.648000	0.89879	0.561000	0.74099	GAG	G|0.988;A|0.012	0.012	strong		0.572	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
GSAP	54103	hgsc.bcm.edu	37	7	76991935	76991935	+	Missense_Mutation	SNP	C	C	T	rs1527263	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76991935C>T	ENST00000257626.7	-	13	992	c.914G>A	c.(913-915)gGa>gAa	p.G305E		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	305			G -> E (in dbSNP:rs1527263).		positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										TGTGATTTGTCCCCAAGAGGC	0.303													T|||	1512	0.301917	0.5454	0.219	5008	,	,		21657	0.0883		0.2326	False		,,,				2504	0.3231				p.G305E		Atlas-SNP	.											PION,colon,carcinoma,+1,4	PION	74	4	0			c.G914A						PASS	.	T	GLU/GLY	2189,2217	589.8+/-387.2	548,1093,562	98.0	100.0	100.0		914	4.5	0.9	7	dbSNP_88	100	2170,6430	712.4+/-405.9	260,1650,2390	yes	missense	PION	NM_017439.3	98	808,2743,2952	TT,TC,CC		25.2326,49.6823,33.5153	benign	305/855	76991935	4359,8647	2203	4300	6503	SO:0001583	missense	54103	exon13			ATTTGTCCCCAAG		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.914G>A	7.37:g.76991935C>T	ENSP00000257626:p.Gly305Glu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	238	71	0.298319	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	37	CCDS34672.2	615	0.2815934065934066	288	0.5853658536585366	92	0.2541436464088398	52	0.09090909090909091	183	0.24142480211081793	T	0.009	-1.815517	0.00600	0.496823	0.252326	ENSG00000186088	ENST00000257626	T	0.15372	2.43	5.72	4.5	0.54988	.	0.533626	0.16507	N	0.211404	T	0.00012	0.0000	N	0.00926	-1.1	0.53688	P	2.5000000000052758E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43540	-0.9385	9	0.02654	T	1	.	5.7871	0.18338	0.1477:0.0807:0.0:0.7717	rs1527263;rs57606158;rs1527263	305;305	A4D1B5-3;A4D1B5	.;GSAP_HUMAN	E	305	ENSP00000257626:G305E	ENSP00000257626:G305E	G	-	2	0	PION	76829871	0.005000	0.15991	0.947000	0.38551	0.060000	0.15804	1.184000	0.32053	0.999000	0.39023	-0.524000	0.04348	GGA	C|0.675;N|0.000	.	strong		0.303	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
TRUB1	142940	hgsc.bcm.edu	37	10	116702425	116702425	+	Missense_Mutation	SNP	A	A	C	rs34393297	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:116702425A>C	ENST00000298746.3	+	2	369	c.308A>C	c.(307-309)gAa>gCa	p.E103A	TRUB1_ENST00000485065.1_3'UTR	NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	103			E -> A (in dbSNP:rs34393297).		pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		CCTTCTCCAGAATGGACCAAG	0.448													A|||	50	0.00998403	0.0	0.0159	5008	,	,		18006	0.0		0.0318	False		,,,				2504	0.0072				p.E103A		Atlas-SNP	.											.	TRUB1	30	.	0			c.A308C						PASS	.	A	ALA/GLU	37,4369	41.6+/-74.8	0,37,2166	72.0	72.0	72.0		308	4.9	1.0	10	dbSNP_126	72	307,8293	110.6+/-171.0	9,289,4002	yes	missense	TRUB1	NM_139169.4	107	9,326,6168	CC,CA,AA		3.5698,0.8398,2.6449	benign	103/350	116702425	344,12662	2203	4300	6503	SO:0001583	missense	142940	exon2			CTCCAGAATGGAC	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"""TruB pseudouridine (psi) synthase homolog 1 (E. coli)"""			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.308A>C	10.37:g.116702425A>C	ENSP00000298746:p.Glu103Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_139169	B2R716|Q53ES2	Missense_Mutation	SNP	ENST00000298746.3	37	CCDS7591.1	31	0.014194139194139194	0	0.0	7	0.019337016574585635	0	0.0	24	0.0316622691292876	A	15.77	2.931257	0.52866	0.008398	0.035698	ENSG00000165832	ENST00000298746	T	0.46451	0.87	6.07	4.88	0.63580	Pseudouridine synthase, catalytic domain (1);	0.264917	0.42172	D	0.000753	T	0.10809	0.0264	L	0.51422	1.61	0.33403	D	0.577563	B	0.13594	0.008	B	0.08055	0.003	T	0.36986	-0.9725	10	0.72032	D	0.01	-23.0482	9.727	0.40337	0.8261:0.1739:0.0:0.0	rs34393297	103	Q8WWH5	TRUB1_HUMAN	A	103	ENSP00000298746:E103A	ENSP00000298746:E103A	E	+	2	0	TRUB1	116692415	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	0.987000	0.29603	2.326000	0.78906	0.533000	0.62120	GAA	A|0.977;C|0.023	0.023	strong		0.448	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169	
EPB41L3	23136	hgsc.bcm.edu	37	18	5478334	5478334	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:5478334A>G	ENST00000341928.2	-	3	627	c.287T>C	c.(286-288)cTc>cCc	p.L96P	RP11-286N3.1_ENST00000577527.1_RNA|EPB41L3_ENST00000342933.3_Missense_Mutation_p.L96P|EPB41L3_ENST00000544123.1_Missense_Mutation_p.L96P|EPB41L3_ENST00000400111.3_Missense_Mutation_p.L96P|EPB41L3_ENST00000540638.2_Missense_Mutation_p.L96P	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	96					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						AGACCGAGAGAGTTTACTGCT	0.408																																					p.L96P		Atlas-SNP	.											EPB41L3,rectum,carcinoma,+1,1	EPB41L3	222	1	0			c.T287C						scavenged	.						183.0	166.0	172.0					18																	5478334		2203	4300	6503	SO:0001583	missense	23136	exon3			CGAGAGAGTTTAC	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.287T>C	18.37:g.5478334A>G	ENSP00000343158:p.Leu96Pro	Somatic	331	0	0		WXS	Illumina HiSeq	Phase_I	301	5	0.0166113	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	A	19.52	3.842686	0.71488	.	.	ENSG00000082397	ENST00000341928;ENST00000544123;ENST00000342933;ENST00000400111;ENST00000542652	D;D;D;D	0.83755	-1.7;-1.71;-1.7;-1.76	5.17	5.17	0.71159	.	0.178441	0.34268	N	0.004116	D	0.90113	0.6911	M	0.74258	2.255	0.80722	D	1	D;D;D;D	0.89917	1.0;0.986;0.999;1.0	D;P;D;D	0.87578	0.998;0.744;0.996;0.982	D	0.89439	0.3722	10	0.35671	T	0.21	.	15.0254	0.71667	1.0:0.0:0.0:0.0	.	96;96;96;96	F5GX05;Q9Y2J2-3;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	P	96;96;96;96;177	ENSP00000343158:L96P;ENSP00000441174:L96P;ENSP00000341138:L96P;ENSP00000382981:L96P	ENSP00000343158:L96P	L	-	2	0	EPB41L3	5468334	1.000000	0.71417	0.970000	0.41538	0.993000	0.82548	7.474000	0.81024	1.934000	0.56057	0.482000	0.46254	CTC	.	.	none		0.408	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
EPHA2	1969	hgsc.bcm.edu	37	1	16475123	16475123	+	Silent	SNP	C	C	T	rs6678616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	48	0	0		WXS	Illumina HiSeq	Phase_I	43	10	0.232558	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	
LINC00283	100874057	hgsc.bcm.edu	37	13	103395769	103395769	+	RNA	SNP	G	G	C	rs117896704	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:103395769G>C	ENST00000430111.1	+	0	430									long intergenic non-protein coding RNA 283																		CTTTCAGTTTGGTTTTTAAAT	0.353													G|||	46	0.0091853	0.0	0.0086	5008	,	,		21584	0.0		0.0338	False		,,,				2504	0.0061				p.T2426T		Atlas-SNP	.											.	.	.	.	0			c.C7278G						PASS	.	G		8,1376		0,8,684	87.0	64.0	71.0		7278	2.8	0.0	13	dbSNP_132	71	108,3072		0,108,1482	no	coding-synonymous	CCDC168	NM_001146197.1		0,116,2166	CC,CG,GG		3.3962,0.578,2.5416		2426/7082	103395769	116,4448	692	1590	2282			643677	exon4			CAGTTTGGTTTTT			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.103395769G>C		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	203	103	0.507389	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				G|0.986;C|0.014	0.014	strong		0.353	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
NUP98	4928	hgsc.bcm.edu	37	11	3723941	3723941	+	Silent	SNP	C	C	T	rs35488940	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:3723941C>T	ENST00000324932.7	-	23	3684	c.3264G>A	c.(3262-3264)ccG>ccA	p.P1088P	NUP98_ENST00000355260.3_Silent_p.P1088P|NUP98_ENST00000359171.4_Silent_p.P1088P	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1105					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)		CTGTTTTCAACGGAACCTCAG	0.512			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML								C|||	116	0.0231629	0.0076	0.036	5008	,	,		18553	0.001		0.0726	False		,,,				2504	0.0072				p.P1088P		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.G3264A						PASS	.	C	,	76,4326	65.8+/-103.3	1,74,2126	94.0	79.0	84.0		3264,3264	-3.0	0.3	11	dbSNP_126	84	671,7925	169.4+/-220.8	23,625,3650	no	coding-synonymous,coding-synonymous	NUP98	NM_016320.4,NM_139132.3	,	24,699,5776	TT,TC,CC		7.806,1.7265,5.747	,	1088/1801,1088/1727	3723941	747,12251	2201	4298	6499	SO:0001819	synonymous_variant	4928	exon23			TTTCAACGGAACC	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.3264G>A	11.37:g.3723941C>T		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	178	87	0.488764	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	37	CCDS7746.1																																																																																			C|0.951;T|0.049	0.049	strong		0.512	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
TSPAN13	27075	hgsc.bcm.edu	37	7	16823095	16823095	+	Silent	SNP	G	G	A	rs11491	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:16823095G>A	ENST00000262067.4	+	6	1027	c.594G>A	c.(592-594)gcG>gcA	p.A198A		NM_014399.3	NP_055214.1	O95857	TSN13_HUMAN	tetraspanin 13	198						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.A198A(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	7	Lung NSC(10;0.0494)|all_lung(11;0.109)			UCEC - Uterine corpus endometrioid carcinoma (126;0.188)		ACCCCCGCGCGAATCCTAGTG	0.388													G|||	2106	0.420527	0.3056	0.5245	5008	,	,		15724	0.2996		0.5497	False		,,,				2504	0.4939				p.A198A		Atlas-SNP	.											TSPAN13,NS,carcinoma,0,1	TSPAN13	13	1	1	Substitution - coding silent(1)	stomach(1)	c.G594A						PASS	.	G		1390,3016	459.2+/-352.2	238,914,1051	141.0	146.0	144.0		594	-1.4	1.0	7	dbSNP_52	144	4772,3828	611.0+/-395.8	1339,2094,867	no	coding-synonymous	TSPAN13	NM_014399.3		1577,3008,1918	AA,AG,GG		44.5116,31.5479,47.3781		198/205	16823095	6162,6844	2203	4300	6503	SO:0001819	synonymous_variant	27075	exon6			CCGCGCGAATCCT	AF100759	CCDS5363.1	7p21.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000106537	ENSG00000106537		"""Tetraspanins"""	21643	protein-coding gene	gene with protein product		613139	"""transmembrane 4 superfamily member 13"""	TM4SF13			Standard	NM_014399		Approved	NET-6	uc003stq.3	O95857	OTTHUMG00000022968	ENST00000262067.4:c.594G>A	7.37:g.16823095G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_014399		Silent	SNP	ENST00000262067.4	37	CCDS5363.1																																																																																			T|0.000;G|0.537;C|0.000;A|0.463	0.463	strong		0.388	TSPAN13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250178.2	NM_014399	
ABCA4	24	hgsc.bcm.edu	37	1	94496602	94496602	+	Silent	SNP	G	G	T	rs1801666	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:94496602G>T	ENST00000370225.3	-	28	4289	c.4203C>A	c.(4201-4203)ccC>ccA	p.P1401P		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1401					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GGGTCAAAGCGGGGTATTCGC	0.527													G|||	59	0.0117812	0.003	0.0159	5008	,	,		20260	0.0		0.0348	False		,,,				2504	0.0092				p.P1401P		Atlas-SNP	.											.	ABCA4	275	.	0			c.C4203A						PASS	.	G		32,4374	36.8+/-68.6	0,32,2171	119.0	101.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4203	-10.0	0.1	1	dbSNP_89	107	301,8299	109.6+/-170.1	4,293,4003	no	coding-synonymous	ABCA4	NM_000350.2		4,325,6174	TT,TG,GG		3.5,0.7263,2.5604		1401/2274	94496602	333,12673	2203	4300	6503	SO:0001819	synonymous_variant	24	exon28			CAAAGCGGGGTAT	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.4203C>A	1.37:g.94496602G>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	85	19	0.223529	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																			T|0.019;G|0.979;A|0.002	0.019	strong		0.527	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
PEAR1	375033	hgsc.bcm.edu	37	1	156878531	156878531	+	Silent	SNP	T	T	C	rs11264580	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156878531T>C	ENST00000338302.3	+	11	1425	c.1200T>C	c.(1198-1200)caT>caC	p.H400H	PEAR1_ENST00000292357.7_Silent_p.H400H			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	400	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)					AGGACACGCATGGGCCAGGGT	0.716													C|||	1118	0.223243	0.2617	0.1585	5008	,	,		14582	0.3135		0.1243	False		,,,				2504	0.226				p.H400H		Atlas-SNP	.											PEAR1,colon,carcinoma,0,1	PEAR1	118	1	0			c.T1200C						PASS	.	C		1033,3307		130,773,1267	16.0	15.0	15.0		1200	1.9	1.0	1	dbSNP_120	15	1014,7508		64,886,3311	no	coding-synonymous	PEAR1	NM_001080471.1		194,1659,4578	CC,CT,TT		11.8986,23.8018,15.9151		400/1038	156878531	2047,10815	2170	4261	6431	SO:0001819	synonymous_variant	375033	exon10			CACGCATGGGCCA	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.1200T>C	1.37:g.156878531T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	81	20	0.246914	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			T|0.780;C|0.220	0.220	strong		0.716	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
PLK2	10769	hgsc.bcm.edu	37	5	57753116	57753116	+	Silent	SNP	C	C	T	rs17710502	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:57753116C>T	ENST00000274289.3	-	7	1200	c.900G>A	c.(898-900)ccG>ccA	p.P300P	PLK2_ENST00000502671.1_5'UTR	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	300	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				G1/S transition of mitotic cell cycle (GO:0000082)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|mitotic cell cycle checkpoint (GO:0007093)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein phosphorylation (GO:0006468)|Rap protein signal transduction (GO:0032486)|Ras protein signal transduction (GO:0007265)|regulation of centriole replication (GO:0046599)|regulation of synaptic plasticity (GO:0048167)	centriole (GO:0005814)|centrosome (GO:0005813)|dendrite (GO:0030425)|intracellular (GO:0005622)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			endometrium(7)|large_intestine(7)|lung(5)|ovary(3)|prostate(2)|skin(2)	26		all_cancers(5;1.76e-12)|all_epithelial(5;2.09e-13)|all_lung(5;6.64e-05)|Lung NSC(5;0.000127)|Prostate(74;0.055)|Breast(144;0.0602)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;7.03e-37)		GCAATGAGGACGGCATTGTAT	0.433													C|||	607	0.121206	0.202	0.2017	5008	,	,		18580	0.001		0.1292	False		,,,				2504	0.0706				p.P300P		Atlas-SNP	.											.	PLK2	71	.	0			c.G900A						PASS	.	C		814,3592	323.2+/-298.0	90,634,1479	86.0	82.0	83.0		900	-4.1	1.0	5	dbSNP_123	83	960,7640	209.4+/-250.6	55,850,3395	no	coding-synonymous	PLK2	NM_006622.2		145,1484,4874	TT,TC,CC		11.1628,18.4748,13.6399		300/686	57753116	1774,11232	2203	4300	6503	SO:0001819	synonymous_variant	10769	exon7			TGAGGACGGCATT		CCDS3974.1, CCDS75250.1	5q12.1-q13.2	2013-01-18	2010-06-24		ENSG00000145632	ENSG00000145632			19699	protein-coding gene	gene with protein product	"""serum-inducible kinase"""	607023	"""polo-like kinase 2 (Drosophila)"""				Standard	NM_006622		Approved	SNK	uc003jrn.3	Q9NYY3	OTTHUMG00000097047	ENST00000274289.3:c.900G>A	5.37:g.57753116C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	37	CCDS3974.1																																																																																			C|0.868;T|0.132	0.132	strong		0.433	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806863	33806863	+	Silent	SNP	G	G	A	rs12451746	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33806863G>A	ENST00000260908.7	-	2	483	c.366C>T	c.(364-366)caC>caT	p.H122H	SLFN12L_ENST00000449046.1_Silent_p.H153H|SLFN12L_ENST00000361112.4_Silent_p.H151H|RP11-686D22.9_ENST00000587076.1_RNA	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	122						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)	p.H153H(1)		breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						TCACAAAAATGTGAAAGTAGT	0.398													G|||	1646	0.328674	0.3964	0.3473	5008	,	,		20602	0.2589		0.4125	False		,,,				2504	0.2096				p.H122H		Atlas-SNP	.											SLFN12L_ENST00000449046,NS,carcinoma,0,1	SLFN12L	140	1	1	Substitution - coding silent(1)	stomach(1)	c.C366T						PASS	.	G		558,826		115,328,249	114.0	101.0	105.0		366	-5.0	0.0	17	dbSNP_120	105	1355,1827		294,767,530	no	coding-synonymous	SLFN12L	NM_001195790.1		409,1095,779	AA,AG,GG		42.5833,40.3179,41.8966		122/589	33806863	1913,2653	692	1591	2283	SO:0001819	synonymous_variant	100506736	exon2			AAAAATGTGAAAG	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.366C>T	17.37:g.33806863G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	174	94	0.54023	NM_001195790	F5H6G3	Silent	SNP	ENST00000260908.7	37	CCDS56026.1																																																																																			G|0.626;A|0.374	0.374	strong		0.398	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
USH2A	7399	hgsc.bcm.edu	37	1	216462662	216462662	+	Missense_Mutation	SNP	T	T	A	rs1805048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	190	0	0		WXS	Illumina HiSeq	Phase_I	225	131	0.582222	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	
FAM21A	387680	hgsc.bcm.edu	37	10	51853633	51853633	+	Missense_Mutation	SNP	C	C	T	rs199520696	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:51853633C>T	ENST00000282633.5	+	13	1181	c.1136C>T	c.(1135-1137)aCg>aTg	p.T379M	FAM21A_ENST00000399339.2_Missense_Mutation_p.T291M|FAM21A_ENST00000351071.6_Missense_Mutation_p.T379M|FAM21A_ENST00000314664.7_Missense_Mutation_p.T379M	NM_001005751.1	NP_001005751.1	Q641Q2	FA21A_HUMAN	family with sequence similarity 21, member A	379					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)				breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	15						GACCTCTTCACGGAAGCCCCC	0.488																																					p.T379M		Atlas-SNP	.											FAM21A,NS,carcinoma,0,4	FAM21A	32	4	0			c.C1136T						scavenged	.						1.0	1.0	1.0					10																	51853633		353	936	1289	SO:0001583	missense	387680	exon13			TCTTCACGGAAGC	BC082258	CCDS41527.1	10q11.23	2014-06-19			ENSG00000099290	ENSG00000099290			23416	protein-coding gene	gene with protein product			"""family with sequence similarity 21, member B"""	FAM21B			Standard	XM_005269805		Approved	bA56A21.1, bA98I6.1, FLJ10824	uc001jjb.3	Q641Q2	OTTHUMG00000018225	ENST00000282633.5:c.1136C>T	10.37:g.51853633C>T	ENSP00000282633:p.Thr379Met	Somatic	645	3	0.00465116		WXS	Illumina HiSeq	Phase_I	762	217	0.284777	NM_001005751	A2A3S2|A2A3U6|Q6DHY0	Missense_Mutation	SNP	ENST00000282633.5	37	CCDS41527.1	.	.	.	.	.	.	.	.	.	.	C	6.414	0.444490	0.12164	.	.	ENSG00000099290	ENST00000351071;ENST00000314664;ENST00000434114;ENST00000282633;ENST00000399339	.	.	.	3.88	-5.37	0.02681	.	0.781535	0.12699	N	0.446536	T	0.14527	0.0351	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B	0.29253	0.05;0.02;0.005;0.02;0.239	B;B;B;B;B	0.16722	0.013;0.013;0.003;0.013;0.016	T	0.05767	-1.0865	9	0.42905	T	0.14	2.3495	2.2948	0.04147	0.3714:0.2592:0.2739:0.0955	.	379;379;291;379;273	E7ESD2;Q641Q2-2;F8W7U3;Q641Q2;Q5T1D7	.;.;.;FA21A_HUMAN;.	M	379;379;273;379;291	.	ENSP00000282633:T379M	T	+	2	0	FAM21A	51523639	0.024000	0.19004	0.096000	0.21009	0.033000	0.12548	-0.884000	0.04166	-1.796000	0.01253	-1.109000	0.02080	ACG	C|0.796;T|0.205	0.205	strong		0.488	FAM21A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276917.2	NM_001005751	
PLD2	5338	hgsc.bcm.edu	37	17	4720469	4720469	+	Missense_Mutation	SNP	C	C	T	rs1052748	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	204	0	0		WXS	Illumina HiSeq	Phase_I	180	73	0.405556	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	
SEMA3C	10512	hgsc.bcm.edu	37	7	80380645	80380645	+	Silent	SNP	G	G	T	rs138526129		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:80380645G>T	ENST00000265361.3	-	16	2212	c.1651C>A	c.(1651-1653)Cga>Aga	p.R551R	SEMA3C_ENST00000544525.1_Silent_p.R569R|SEMA3C_ENST00000419255.2_Silent_p.R551R	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	551					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						TCTTGTCTTCGGCTCCTCCTG	0.388																																					p.R551R		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C1651A						PASS	.	G		0,4406		0,0,2203	155.0	137.0	143.0		1651	4.7	1.0	7	dbSNP_134	143	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SEMA3C	NM_006379.3		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		551/752	80380645	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon16			GTCTTCGGCTCCT	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.1651C>A	7.37:g.80380645G>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	251	151	0.601594	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			G|1.000;T|0.000	0.000	weak		0.388	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
TJP2	9414	hgsc.bcm.edu	37	9	71851969	71851969	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:71851969T>C	ENST00000377245.4	+	14	2304	c.2096T>C	c.(2095-2097)cTg>cCg	p.L699P	TJP2_ENST00000535702.1_Missense_Mutation_p.L703P|TJP2_ENST00000539225.1_Missense_Mutation_p.L730P|TJP2_ENST00000348208.4_Missense_Mutation_p.L699P|TJP2_ENST00000265384.7_Missense_Mutation_p.L699P|TJP2_ENST00000453658.2_Missense_Mutation_p.L676P	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	699	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						AAGAAGAACCTGAGGAAAAGT	0.532																																					p.L730P		Atlas-SNP	.											.	TJP2	120	.	0			c.T2189C						PASS	.						155.0	165.0	162.0					9																	71851969		2203	4300	6503	SO:0001583	missense	9414	exon14			AGAACCTGAGGAA	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.2096T>C	9.37:g.71851969T>C	ENSP00000366453:p.Leu699Pro	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	148	68	0.459459	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152156	0.57259	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.12361	2.72;2.69;2.72;2.71;2.7;2.74	5.77	5.77	0.91146	Src homology-3 domain (1);Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.374098	0.27927	N	0.017282	T	0.36853	0.0982	M	0.82056	2.57	0.58432	D	0.999998	P;P;D;D;D	0.67145	0.853;0.919;0.963;0.996;0.995	P;P;P;D;D	0.68943	0.502;0.888;0.679;0.95;0.961	T	0.19386	-1.0307	10	0.87932	D	0	.	10.6932	0.45884	0.0:0.0712:0.0:0.9288	.	730;703;699;699;699	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	P	676;699;699;699;703;730	ENSP00000392178:L676P;ENSP00000366453:L699P;ENSP00000345893:L699P;ENSP00000265384:L699P;ENSP00000442090:L703P;ENSP00000438262:L730P	ENSP00000265384:L699P	L	+	2	0	TJP2	71041789	0.994000	0.37717	0.014000	0.15608	0.620000	0.37586	6.251000	0.72441	2.330000	0.79161	0.528000	0.53228	CTG	.	.	none		0.532	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
MATN2	4147	hgsc.bcm.edu	37	8	98943598	98943598	+	Missense_Mutation	SNP	C	C	T	rs2290472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:98943598C>T	ENST00000520016.1	+	2	684	c.560C>T	c.(559-561)aCg>aTg	p.T187M	MATN2_ENST00000524308.1_Missense_Mutation_p.T187M|MATN2_ENST00000522025.2_Intron|MATN2_ENST00000254898.5_Missense_Mutation_p.T187M|MATN2_ENST00000521689.1_Missense_Mutation_p.T187M			O00339	MATN2_HUMAN	matrilin 2	187	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.		T -> M (in dbSNP:rs2290472). {ECO:0000269|PubMed:14702039}.			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)			GCACGGGACACGGGCATCCTA	0.587													C|||	455	0.0908546	0.0083	0.134	5008	,	,		20747	0.0804		0.1829	False		,,,				2504	0.0879				p.T187M		Atlas-SNP	.											MATN2_ENST00000520016,NS,carcinoma,-1,2	MATN2	165	2	0			c.C560T						PASS	.	C	MET/THR,MET/THR	159,4197		2,155,2021	37.0	43.0	41.0		560,560	6.0	1.0	8	dbSNP_100	41	1523,7029		134,1255,2887	yes	missense,missense	MATN2	NM_002380.3,NM_030583.2	81,81	136,1410,4908	TT,TC,CC		17.8087,3.6501,13.0307	probably-damaging,probably-damaging	187/957,187/938	98943598	1682,11226	2178	4276	6454	SO:0001583	missense	4147	exon3			GGGACACGGGCAT	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.560C>T	8.37:g.98943598C>T	ENSP00000430487:p.Thr187Met	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	248	0.11355311355311355	8	0.016260162601626018	55	0.15193370165745856	46	0.08041958041958042	139	0.18337730870712401	C	27.2	4.813845	0.90790	0.036501	0.178087	ENSG00000132561	ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000520016	D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7	5.97	5.97	0.96955	von Willebrand factor, type A (3);	0.094375	0.47093	D	0.000246	T	0.00580	0.0019	N	0.02247	-0.625	0.21147	P	0.999777855	D;D;D;D	0.89917	0.998;0.997;1.0;1.0	D;D;D;D	0.74348	0.953;0.947;0.97;0.983	T	0.63821	-0.6550	9	0.62326	D	0.03	-16.9931	20.4388	0.99107	0.0:1.0:0.0:0.0	rs2290472;rs17761988;rs52834592;rs60490128;rs2290472	187;187;187;187	E9PF03;O00339-2;O00339;Q8N2G3	.;.;MATN2_HUMAN;.	M	187	ENSP00000429977:T187M;ENSP00000254898:T187M;ENSP00000430221:T187M;ENSP00000430487:T187M	ENSP00000254898:T187M	T	+	2	0	MATN2	99012774	1.000000	0.71417	0.997000	0.53966	0.952000	0.60782	5.978000	0.70501	2.836000	0.97738	0.655000	0.94253	ACG	C|0.889;T|0.111	0.111	strong		0.587	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
CIDEB	27141	hgsc.bcm.edu	37	14	24775287	24775287	+	Silent	SNP	G	G	A	rs139893717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24775287G>A	ENST00000336557.5	-	7	1695	c.393C>T	c.(391-393)atC>atT	p.I131I	LTB4R2_ENST00000528054.1_5'Flank|CIDEB_ENST00000258807.5_Silent_p.I131I|NOP9_ENST00000267425.3_3'UTR|CIDEB_ENST00000554411.1_Silent_p.I131I			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	53	0	0		WXS	Illumina HiSeq	Phase_I	83	53	0.638554	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		
GABRB1	2560	hgsc.bcm.edu	37	4	47408709	47408709	+	Silent	SNP	A	A	G	rs6289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:47408709A>G	ENST00000295454.3	+	8	1138	c.846A>G	c.(844-846)acA>acG	p.T282T	GABRB1_ENST00000538619.1_Silent_p.T212T	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	282					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|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)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					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)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|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)	GAATCACGACAGTGCTTACAA	0.443													A|||	1051	0.209864	0.3064	0.1873	5008	,	,		19035	0.0179		0.3062	False		,,,				2504	0.1943				p.T282T		Atlas-SNP	.											.	GABRB1	107	.	0			c.A846G						PASS	.	A		1210,3196	421.9+/-339.5	173,864,1166	149.0	138.0	142.0		846	-9.1	0.6	4	dbSNP_52	142	2850,5750	449.4+/-362.1	449,1952,1899	no	coding-synonymous	GABRB1	NM_000812.3		622,2816,3065	GG,GA,AA		33.1395,27.4626,31.2164		282/475	47408709	4060,8946	2203	4300	6503	SO:0001819	synonymous_variant	2560	exon8			CACGACAGTGCTT		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4081	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 1"""	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.846A>G	4.37:g.47408709A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	170	80	0.470588	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Silent	SNP	ENST00000295454.3	37	CCDS3474.1																																																																																			A|0.721;G|0.279	0.279	strong		0.443	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1		
FAM161A	84140	hgsc.bcm.edu	37	2	62067433	62067433	+	Missense_Mutation	SNP	T	T	C	rs17513722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:62067433T>C	ENST00000405894.3	-	3	807	c.706A>G	c.(706-708)Att>Gtt	p.I236V	FAM161A_ENST00000404929.1_Missense_Mutation_p.I236V	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	236			I -> V (in dbSNP:rs17513722).		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						GGTACTGTAATTGTGGGCACC	0.383													T|||	583	0.116414	0.0408	0.1427	5008	,	,		20146	0.0863		0.2227	False		,,,				2504	0.1217				p.I236V		Atlas-SNP	.											FAM161A_ENST00000405894,colon,carcinoma,+2,3	FAM161A	200	3	0			c.A706G						PASS	.	T	VAL/ILE,VAL/ILE	273,3413		10,253,1580	155.0	138.0	143.0		706,706	4.4	0.4	2	dbSNP_123	143	1956,6208		238,1480,2364	yes	missense,missense	FAM161A	NM_001201543.1,NM_032180.2	29,29	248,1733,3944	CC,CT,TT		23.9588,7.4064,18.8101	benign,benign	236/717,236/661	62067433	2229,9621	1843	4082	5925	SO:0001583	missense	84140	exon3			CTGTAATTGTGGG		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.706A>G	2.37:g.62067433T>C	ENSP00000385893:p.Ile236Val	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	227	88	0.387665	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	317	0.14514652014652016	23	0.046747967479674794	64	0.17679558011049723	56	0.0979020979020979	174	0.22955145118733508	T	12.18	1.860464	0.32884	0.074064	0.239588	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.30981	1.51;1.51	5.55	4.38	0.52667	.	0.219735	0.44285	D	0.000470	T	0.00012	0.0000	L	0.58428	1.81	0.34238	P	0.32269899999999996	P;B	0.49447	0.924;0.354	P;B	0.46543	0.52;0.138	T	0.26849	-1.0091	9	0.17369	T	0.5	-28.9171	7.9646	0.30091	0.0:0.0723:0.1388:0.7889	rs17513722;rs52827054;rs17513722	236;236	Q3B820;Q3B820-3	F161A_HUMAN;.	V	236	ENSP00000385158:I236V;ENSP00000385893:I236V	ENSP00000385158:I236V	I	-	1	0	FAM161A	61920937	0.782000	0.28689	0.442000	0.26870	0.375000	0.29983	1.029000	0.30140	0.919000	0.36945	0.533000	0.62120	ATT	T|0.844;C|0.156	0.156	strong		0.383	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
MMAB	326625	hgsc.bcm.edu	37	12	110011230	110011230	+	Missense_Mutation	SNP	C	C	T	rs10774775|rs36013132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:110011230C>T	ENST00000545712.2	-	1	449	c.56G>A	c.(55-57)cGc>cAc	p.R19H	MVK_ENST00000541384.1_5'Flank|MVK_ENST00000539696.1_5'Flank|MVK_ENST00000539575.1_5'Flank|MMAB_ENST00000266839.5_5'UTR|MVK_ENST00000228510.3_5'Flank|MVK_ENST00000535044.1_3'UTR|MVK_ENST00000392727.3_5'Flank|MMAB_ENST00000540016.1_Missense_Mutation_p.R19H	NM_052845.3	NP_443077.1	Q96EY8	MMAB_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblB type	19			R -> H (in dbSNP:rs10774775).|R -> Q (in dbSNP:rs36013132). {ECO:0000269|PubMed:12471062, ECO:0000269|PubMed:12514191, ECO:0000269|PubMed:15489334}.		cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|cob(I)yrinic acid a,c-diamide adenosyltransferase activity (GO:0008817)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAAGCACCCGCGCAGGCCAAG	0.716													C|||	1427	0.284944	0.438	0.2939	5008	,	,		12948	0.1607		0.2853	False		,,,				2504	0.1994				p.R19H		Atlas-SNP	.											.	MMAB	16	.	0			c.G56A						PASS	.	C	HIS/ARG	1710,2678		354,1002,838	15.0	17.0	16.0		56	3.9	0.9	12	dbSNP_120	16	2293,6297		369,1555,2371	no	missense	MMAB	NM_052845.3	29	723,2557,3209	TT,TC,CC		26.6938,38.9699,30.8445	probably-damaging	19/251	110011230	4003,8975	2194	4295	6489	SO:0001583	missense	326625	exon1			CACCCGCGCAGGC	AF550404	CCDS9131.1	12q24	2014-07-18	2005-07-11		ENSG00000139428	ENSG00000139428			19331	protein-coding gene	gene with protein product	"""ATP:cob(I)alamin adenosyltransferase"", ""cilia and flagella associated protein 23"""	607568	"""methylmalonic aciduria (cobalamin deficiency) type B"""			12471062, 12514191	Standard	NM_052845		Approved	cblB, CFAP23	uc001tou.3	Q96EY8	OTTHUMG00000169255	ENST00000545712.2:c.56G>A	12.37:g.110011230C>T	ENSP00000445920:p.Arg19His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	53	32	0.603774	NM_052845	C5HU05|Q9BSH0	Missense_Mutation	SNP	ENST00000545712.2	37	CCDS9131.1	634	0.2902930402930403	223	0.4532520325203252	112	0.30939226519337015	83	0.1451048951048951	216	0.2849604221635884	C	13.88	2.368378	0.42003	0.389699	0.266938	ENSG00000139428	ENST00000545712;ENST00000542390	D	0.83755	-1.76	4.79	3.89	0.44902	.	0.375104	0.24940	N	0.034391	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.999999808155	D	0.61080	0.989	P	0.47744	0.556	T	0.29458	-1.0011	8	.	.	.	-18.7787	11.184	0.48644	0.0:0.8144:0.1856:0.0	rs10774775	19	Q96EY8	MMAB_HUMAN	H	19	ENSP00000445920:R19H	.	R	-	2	0	MMAB	108495613	0.712000	0.27916	0.852000	0.33557	0.108000	0.19459	1.236000	0.32683	1.351000	0.45789	0.591000	0.81541	CGC	C|0.693;T|0.307	0.307	strong		0.716	MMAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403128.2		
ESYT2	57488	hgsc.bcm.edu	37	7	158536267	158536267	+	Missense_Mutation	SNP	T	T	C	rs2305473	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:158536267T>C	ENST00000251527.5	-	16	1893	c.1828A>G	c.(1828-1830)Agt>Ggt	p.S610G	ESYT2_ENST00000435514.2_Missense_Mutation_p.S45G	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	638	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CCCGAGTTACTGAGCTGGAAG	0.597													T|||	1680	0.335463	0.3994	0.1801	5008	,	,		17999	0.5843		0.17	False		,,,				2504	0.273				p.S610G		Atlas-SNP	.											.	ESYT2	70	.	0			c.A1828G						PASS	.		GLY/SER	1507,2899	479.5+/-358.5	265,977,961	123.0	97.0	106.0		1828	3.0	0.3	7	dbSNP_100	106	1469,7131	279.0+/-293.7	125,1219,2956	yes	missense	ESYT2	NM_020728.2	56	390,2196,3917	CC,CT,TT		17.0814,34.2034,22.8817	benign	610/894	158536267	2976,10030	2203	4300	6503	SO:0001583	missense	57488	exon16			AGTTACTGAGCTG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1828A>G	7.37:g.158536267T>C	ENSP00000251527:p.Ser610Gly	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	122	94	0.770492	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	701	0.320970695970696	187	0.3800813008130081	63	0.17403314917127072	323	0.5646853146853147	128	0.16886543535620052	T	13.55	2.270957	0.40194	0.342034	0.170814	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000435514;ENST00000377650;ENST00000429474	T;T;T	0.24538	1.85;1.85;1.85	5.43	3.0	0.34707	C2 calcium/lipid-binding domain, CaLB (1);	0.146748	0.64402	D	0.000004	T	0.00012	0.0000	M	0.65498	2.005	0.34595	P	0.284046	P;B	0.35033	0.481;0.133	B;B	0.33454	0.164;0.065	T	0.43972	-0.9358	9	0.33940	T	0.23	-25.813	6.7082	0.23262	0.136:0.0742:0.0:0.7898	rs2305473;rs59383218;rs2305473	610;638	A0FGR8-2;A0FGR8	.;ESYT2_HUMAN	G	610;659;601;45;45;434	ENSP00000251527:S610G;ENSP00000275418:S601G;ENSP00000411488:S45G	ENSP00000251527:S610G	S	-	1	0	ESYT2	158229028	1.000000	0.71417	0.309000	0.25155	0.752000	0.42762	3.254000	0.51477	0.343000	0.23821	0.455000	0.32223	AGT	T|0.712;C|0.288	0.288	strong		0.597	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
SMYD1	150572	hgsc.bcm.edu	37	2	88387557	88387557	+	Missense_Mutation	SNP	A	A	C	rs1542087	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:88387557A>C	ENST00000419482.2	+	3	576	c.491A>C	c.(490-492)cAg>cCg	p.Q164P	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Missense_Mutation_p.Q164P|SMYD1_ENST00000468008.1_3'UTR	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	164	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		Q -> P (in dbSNP:rs1542087).		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						CAGAGCCAGCAGTTCAGCATG	0.597													A|||	684	0.136581	0.2579	0.072	5008	,	,		19215	0.0268		0.0964	False		,,,				2504	0.1728				p.Q164P		Atlas-SNP	.											.	SMYD1	95	.	0			c.A491C						PASS	.	A	PRO/GLN	1066,3340	384.7+/-325.4	124,818,1261	119.0	79.0	93.0		491	3.9	1.0	2	dbSNP_88	93	902,7698	199.3+/-243.4	52,798,3450	yes	missense	SMYD1	NM_198274.3	76	176,1616,4711	CC,CA,AA		10.4884,24.1943,15.1315	benign	164/491	88387557	1968,11038	2203	4300	6503	SO:0001583	missense	150572	exon3			GCCAGCAGTTCAG	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.491A>C	2.37:g.88387557A>C	ENSP00000393453:p.Gln164Pro	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	298	130	0.436242	NM_198274	A0AV30|A6NE13	Missense_Mutation	SNP	ENST00000419482.2	37	CCDS33240.1	237	0.10851648351648352	127	0.258130081300813	29	0.08011049723756906	8	0.013986013986013986	73	0.09630606860158311	A	10.29	1.308174	0.23821	0.241943	0.104884	ENSG00000115593	ENST00000419482;ENST00000444564	T;T	0.81415	-1.49;-1.49	5.04	3.86	0.44501	SET domain (2);	0.160261	0.56097	N	0.000024	T	0.00012	0.0000	N	0.11154	0.105	0.09310	P	1.0	B	0.06786	0.001	B	0.14578	0.011	T	0.02966	-1.1088	9	0.25106	T	0.35	-16.3953	11.4736	0.50284	0.8491:0.1509:0.0:0.0	rs1542087;rs60571651;rs1542087	164	Q8NB12	SMYD1_HUMAN	P	164	ENSP00000393453:Q164P;ENSP00000407888:Q164P	ENSP00000393453:Q164P	Q	+	2	0	SMYD1	88168672	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.826000	0.55738	0.834000	0.34852	-0.466000	0.05196	CAG	A|0.865;C|0.135	0.135	strong		0.597	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562285	6562285	+	Silent	SNP	C	C	T	rs2041384	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6562285C>T	ENST00000266556.7	+	2	282	c.117C>T	c.(115-117)tgC>tgT	p.C39C	TAPBPL_ENST00000544021.1_Intron|CD27-AS1_ENST00000545339.1_RNA|CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	39					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						TCCTAGACTGCTTCCTGGCGA	0.652													C|||	1142	0.228035	0.1074	0.1628	5008	,	,		17387	0.3224		0.2932	False		,,,				2504	0.273				p.C39C		Atlas-SNP	.											.	TAPBPL	21	.	0			c.C117T						PASS	.	C		534,3868		40,454,1707	40.0	35.0	37.0		117	3.2	1.0	12	dbSNP_94	37	2464,6132		361,1742,2195	no	coding-synonymous	TAPBPL	NM_018009.4		401,2196,3902	TT,TC,CC		28.6645,12.1308,23.0651		39/469	6562285	2998,10000	2201	4298	6499	SO:0001819	synonymous_variant	55080	exon2			AGACTGCTTCCTG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.117C>T	12.37:g.6562285C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_018009	Q9NWB8	Silent	SNP	ENST00000266556.7	37	CCDS8546.1																																																																																			C|0.782;G|0.000;T|0.218	0.218	strong		0.652	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
EFTUD1	79631	hgsc.bcm.edu	37	15	82444663	82444663	+	Missense_Mutation	SNP	T	T	C	rs2292071	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	92	0	0		WXS	Illumina HiSeq	Phase_I	49	12	0.244898	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	
GPR98	84059	hgsc.bcm.edu	37	5	89943571	89943571	+	Missense_Mutation	SNP	G	G	T	rs2366777	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:89943571G>T	ENST00000405460.2	+	17	3375	c.3279G>T	c.(3277-3279)ttG>ttT	p.L1093F		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1093	Calx-beta 8. {ECO:0000255}.		L -> F (in dbSNP:rs2366777). {ECO:0000269|PubMed:11853319, 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)			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)		TAATCCTCTTGAATTCAACAG	0.368													T|||	4058	0.810304	0.9539	0.8069	5008	,	,		18991	0.8323		0.667	False		,,,				2504	0.7434				p.L1093F		Atlas-SNP	.											.	GPR98	605	.	0			c.G3279T						PASS	.	T	PHE/LEU	3338,322		1525,288,17	82.0	82.0	82.0		3279	2.1	1.0	5	dbSNP_100	82	5258,2898		1680,1898,500	yes	missense	GPR98	NM_032119.3	22	3205,2186,517	TT,TG,GG		35.5321,8.7978,27.2512	benign	1093/6307	89943571	8596,3220	1830	4078	5908	SO:0001583	missense	84059	exon17			CCTCTTGAATTCA	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.3279G>T	5.37:g.89943571G>T	ENSP00000384582:p.Leu1093Phe	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	1741|1741	0.7971611721611722|0.7971611721611722	472|472	0.959349593495935|0.959349593495935	286|286	0.7900552486187845|0.7900552486187845	468|468	0.8181818181818182|0.8181818181818182	515|515	0.679419525065963|0.679419525065963	T|T	2.196|2.196	-0.384083|-0.384083	0.04966|0.04966	0.912022|0.912022	0.644679|0.644679	ENSG00000164199|ENSG00000164199	ENST00000504142|ENST00000405460;ENST00000296619;ENST00000399043	.|T	.|0.28069	.|1.63	5.79|5.79	2.13|2.13	0.27403|0.27403	.|Na-Ca exchanger/integrin-beta4 (1);	.|0.200839	.|0.52532	.|N	.|0.000061	.|T	.|0.00012	.|0.0000	N|N	0.01668|0.01668	-0.77|-0.77	0.09310|0.09310	P|P	0.9999999999996775|0.9999999999996775	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	.|T	.|0.37753	.|-0.9692	.|9	.|0.02654	.|T	.|1	.|.	6.532|6.532	0.22332|0.22332	0.0:0.3877:0.2855:0.3268|0.0:0.3877:0.2855:0.3268	rs2366777;rs17620692;rs58535021;rs2366777|rs2366777;rs17620692;rs58535021;rs2366777	.|1093	.|Q8WXG9	.|GPR98_HUMAN	X|F	682|1093	.|ENSP00000384582:L1093F	.|ENSP00000296619:L1093F	E|L	+|+	1|3	0|2	GPR98|GPR98	89979327|89979327	0.988000|0.988000	0.35896|0.35896	0.996000|0.996000	0.52242|0.52242	0.847000|0.847000	0.48162|0.48162	0.204000|0.204000	0.17335|0.17335	-0.087000|-0.087000	0.12528|0.12528	-0.264000|-0.264000	0.10439|0.10439	GAA|TTG	G|0.206;T|0.794	0.794	strong		0.368	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
SMCO4	56935	hgsc.bcm.edu	37	11	93212254	93212254	+	Silent	SNP	C	C	T	rs2658797	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:93212254C>T	ENST00000298966.2	-	3	487	c.102G>A	c.(100-102)gtG>gtA	p.V34V	SMCO4_ENST00000525141.1_Silent_p.V34V|SMCO4_ENST00000527149.1_Silent_p.V34V	NM_020179.2	NP_064564.1	Q9NRQ5	SMCO4_HUMAN	single-pass membrane protein with coiled-coil domains 4	34						integral component of membrane (GO:0016021)											GCGTGGGCAGCACCACTGTAG	0.642													C|||	3502	0.699281	0.6172	0.7219	5008	,	,		14999	0.9435		0.504	False		,,,				2504	0.7434				p.V34V		Atlas-SNP	.											.	.	.	.	0			c.G102A						PASS	.	C		2766,1636	660.5+/-400.7	879,1008,314	104.0	88.0	93.0		102	5.0	1.0	11	dbSNP_100	93	4236,4360	572.7+/-389.8	1057,2122,1119	no	coding-synonymous	C11orf75	NM_020179.2		1936,3130,1433	TT,TC,CC		49.2787,37.1649,46.1302		34/60	93212254	7002,5996	2201	4298	6499	SO:0001819	synonymous_variant	0	exon3			GGGCAGCACCACT	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.102G>A	11.37:g.93212254C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	133	128	0.962406	NM_020179		Silent	SNP	ENST00000298966.2	37	CCDS8292.1																																																																																			C|0.421;T|0.579	0.579	strong		0.642	SMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394630.1	NM_020179	
SAMD11	148398	hgsc.bcm.edu	37	1	879317	879317	+	Silent	SNP	C	C	T	rs7523549	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:879317C>T	ENST00000342066.3	+	14	1913	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	610					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	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;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		GAGTTTTCTACGTGGCCAGCT	0.682													c|||	457	0.091254	0.2156	0.0778	5008	,	,		13897	0.0665		0.0398	False		,,,				2504	0.0112				p.Y610Y		Atlas-SNP	.											SAMD11,colon,carcinoma,0,2	SAMD11	34	2	0			c.C1830T						PASS	.	C		838,3566		65,708,1429	21.0	28.0	26.0		1830	5.4	1.0	1	dbSNP_116	26	232,8352		5,222,4065	no	coding-synonymous	SAMD11	NM_152486.2		70,930,5494	TT,TC,CC		2.7027,19.0282,8.2384		610/682	879317	1070,11918	2202	4292	6494	SO:0001819	synonymous_variant	148398	exon14			TTTCTACGTGGCC	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.1830C>T	1.37:g.879317C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	79	20	0.253165	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Silent	SNP	ENST00000342066.3	37	CCDS2.2	197	0.0902014652014652	102	0.2073170731707317	26	0.0718232044198895	41	0.07167832167832168	28	0.036939313984168866	C	2.042	-0.419809	0.04734	0.190282	0.027027	ENSG00000187634	ENST00000341065;ENST00000455979	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.00349	-1.1798	3	.	.	.	-28.6146	15.4382	0.75162	0.0:0.8608:0.1392:0.0	rs7523549;rs7523549	.	.	.	M	518;470	.	.	T	+	2	0	SAMD11	869180	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	3.429000	0.52800	2.567000	0.86603	0.555000	0.69702	ACG	C|0.908;T|0.092	0.092	strong		0.682	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486	
KL	9365	hgsc.bcm.edu	37	13	33635910	33635910	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:33635910T>C	ENST00000380099.3	+	4	2702	c.2694T>C	c.(2692-2694)gcT>gcC	p.A898A	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	898	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)		TAAACGAAGCTCTCAAAGGTA	0.473																																					p.A898A		Atlas-SNP	.											.	KL	106	.	0			c.T2694C						PASS	.						77.0	81.0	79.0					13																	33635910		2203	4300	6503	SO:0001819	synonymous_variant	9365	exon4			CGAAGCTCTCAAA	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.2694T>C	13.37:g.33635910T>C		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																			.	.	none		0.473	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
FANCA	2175	hgsc.bcm.edu	37	16	89807233	89807233	+	Silent	SNP	C	C	G	rs11649210	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:89807233C>G	ENST00000389301.3	-	38	3837	c.3807G>C	c.(3805-3807)ctG>ctC	p.L1269L	FANCA_ENST00000568369.1_Silent_p.L1269L|ZNF276_ENST00000289816.5_3'UTR	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	1269					DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GATGTGACGACAGCAGGCCCA	0.463			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	691	0.137979	0.1543	0.0346	5008	,	,		17285	0.2629		0.0736	False		,,,				2504	0.1268				p.L1269L		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.G3807C						PASS	.	G	,,	629,3767	764.9+/-413.3	38,553,1607	84.0	77.0	79.0		3807,,	-7.2	0.1	16	dbSNP_120	79	774,7826	781.2+/-407.6	32,710,3558	no	coding-synonymous,utr-3,utr-3	FANCA,ZNF276	NM_000135.2,NM_001113525.1,NM_152287.3	,,	70,1263,5165	GG,GC,CC		9.0,14.3085,10.7956	,,	1269/1456,,	89807233	1403,11593	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon38	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGACGACAGCAGG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.3807G>C	16.37:g.89807233C>G		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	226	24	0.106195	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.892;G|0.108	0.108	strong		0.463	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
NLRP2	55655	hgsc.bcm.edu	37	19	55494638	55494638	+	Silent	SNP	T	T	C	rs61735084	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55494638T>C	ENST00000543010.1	+	6	1715	c.1572T>C	c.(1570-1572)gaT>gaC	p.D524D	NLRP2_ENST00000391721.4_Silent_p.D500D|NLRP2_ENST00000339757.7_Silent_p.D502D|NLRP2_ENST00000427260.2_Silent_p.D501D|NLRP2_ENST00000263437.6_Silent_p.D521D|NLRP2_ENST00000537859.1_Silent_p.D502D|NLRP2_ENST00000538819.1_Silent_p.D500D|NLRP2_ENST00000448584.2_Silent_p.D524D	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	524	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)		AGGAAGAGGATAGGGACGGCC	0.552													C|||	75	0.014976	0.0234	0.0187	5008	,	,		18328	0.001		0.0278	False		,,,				2504	0.002				p.D524D		Atlas-SNP	.											.	NLRP2	161	.	0			c.T1572C						PASS	.						80.0	74.0	76.0					19																	55494638		2203	4300	6503	SO:0001819	synonymous_variant	55655	exon6			AGAGGATAGGGAC	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.1572T>C	19.37:g.55494638T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	76	21	0.276316	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			T|0.987;C|0.013	0.013	strong		0.552	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
SPATA22	84690	hgsc.bcm.edu	37	17	3343519	3343519	+	Silent	SNP	T	T	C	rs17822627	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:3343519T>C	ENST00000573128.1	-	9	1497	c.1014A>G	c.(1012-1014)gaA>gaG	p.E338E	SPATA22_ENST00000575375.1_Silent_p.E338E|SPATA22_ENST00000355380.4_Silent_p.E295E|SPATA22_ENST00000541913.1_Silent_p.E322E|SPATA22_ENST00000572969.1_Silent_p.E338E|SPATA22_ENST00000397168.3_Silent_p.E338E			Q8NHS9	SPT22_HUMAN	spermatogenesis associated 22	338					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						AAGTTTTTTGTTCAGAAACAG	0.368													T|||	1319	0.263379	0.2095	0.3501	5008	,	,		15510	0.4147		0.1809	False		,,,				2504	0.2035				p.E338E		Atlas-SNP	.											.	SPATA22	49	.	0			c.A1014G						PASS	.	T	,,,,,	1048,3358	375.9+/-321.8	128,792,1283	66.0	73.0	70.0		1014,885,1014,1014,,1014	3.5	1.0	17	dbSNP_123	70	1585,7015	294.4+/-301.9	145,1295,2860	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	SPATA22	NM_001170695.1,NM_001170696.1,NM_001170697.1,NM_001170698.1,NM_001170699.1,NM_032598.4	,,,,,	273,2087,4143	CC,CT,TT		18.4302,23.7857,20.2445	,,,,,	338/364,295/321,338/364,338/364,,338/364	3343519	2633,10373	2203	4300	6503	SO:0001819	synonymous_variant	84690	exon9			TTTTTGTTCAGAA	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.1014A>G	17.37:g.3343519T>C		Somatic	418	1	0.00239234		WXS	Illumina HiSeq	Phase_I	345	150	0.434783	NM_032598	B4DXB1|D3DTI9|J3KN63|Q969H3|Q96JT4	Silent	SNP	ENST00000573128.1	37	CCDS11027.1																																																																																			T|0.774;C|0.226	0.226	strong		0.368	SPATA22-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438067.2	NM_032598	
MYH13	8735	hgsc.bcm.edu	37	17	10236465	10236465	+	Silent	SNP	G	G	A	rs2240579	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:10236465G>A	ENST00000418404.3	-	18	2263	c.2100C>T	c.(2098-2100)aaC>aaT	p.N700N	MYH13_ENST00000252172.4_Silent_p.N700N|RP11-401O9.3_ENST00000577743.1_RNA			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	50	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	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	
RHBDF2	79651	hgsc.bcm.edu	37	17	74475975	74475975	+	Missense_Mutation	SNP	C	C	A	rs3809694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:74475975C>A	ENST00000313080.4	-	4	472	c.199G>T	c.(199-201)Gca>Tca	p.A67S	RHBDF2_ENST00000592378.1_Intron|RHBDF2_ENST00000591885.1_Intron|RHBDF2_ENST00000389760.4_Intron	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	67				A -> S (in Ref. 2; BAF84824 and 4; AAH16034). {ECO:0000305}.	negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						GTGGTGTGTGCAGCCCAGGTC	0.547													C|||	2285	0.45627	0.2587	0.5764	5008	,	,		9807	0.6052		0.4652	False		,,,				2504	0.4755				p.A67S		Atlas-SNP	.											RHBDF2,colon,carcinoma,+1,1	RHBDF2	57	1	0			c.G199T						PASS	.	C	,SER/ALA	1298,3108	416.3+/-337.5	180,938,1085	31.0	30.0	30.0		,199	-2.0	0.0	17	dbSNP_130	30	3956,4640	517.9+/-379.1	897,2162,1239	yes	intron,missense	RHBDF2	NM_001005498.3,NM_024599.5	,99	1077,3100,2324	AA,AC,CC		46.0214,29.4598,40.4092	,	,67/857	74475975	5254,7748	2203	4298	6501	SO:0001583	missense	79651	exon4			TGTGTGCAGCCCA	BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"""rhomboid, veinlet-like 6 (Drosophila)"", ""tylosis with oesophageal cancer"""	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.199G>T	17.37:g.74475975C>A	ENSP00000322775:p.Ala67Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	37	CCDS32743.1	1015	0.46474358974358976	125	0.2540650406504065	195	0.5386740331491713	346	0.6048951048951049	349	0.4604221635883905	C	8.467	0.856677	0.17106	0.294598	0.460214	ENSG00000129667	ENST00000313080	T	0.54675	0.56	4.23	-2.03	0.07365	.	2.935030	0.01893	N	0.038673	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.41998	-0.9477	9	0.19590	T	0.45	7.7057	10.8665	0.46858	0.0:0.5646:0.301:0.1344	rs3809694	67	Q6PJF5	RHDF2_HUMAN	S	67	ENSP00000322775:A67S	ENSP00000322775:A67S	A	-	1	0	RHBDF2	71987570	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	-0.503000	0.06383	-0.407000	0.07576	-0.955000	0.02649	GCA	C|0.600;A|0.400	0.400	strong		0.547	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520259	72520259	+	Missense_Mutation	SNP	C	C	T	rs61573157	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72520259C>T	ENST00000373207.1	+	22	3322	c.3322C>T	c.(3322-3324)Cca>Tca	p.P1108S	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.P1111S	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1108	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						agaccctggcccaaccTCACT	0.637													C|||	332	0.0662939	0.0045	0.0548	5008	,	,		15195	0.0893		0.1123	False		,,,				2504	0.0869				p.P1111S		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.C3331T						PASS	.	C	SER/PRO,SER/PRO	108,4298	82.9+/-121.4	1,106,2096	54.0	52.0	53.0		3322,3331	1.6	0.0	10	dbSNP_129	53	906,7694	201.8+/-245.2	45,816,3439	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	74,74	46,922,5535	TT,TC,CC		10.5349,2.4512,7.7964	benign,benign	1108/1224,1111/1227	72520259	1014,11992	2203	4300	6503	SO:0001583	missense	140766	exon22			CCTGGCCCAACCT	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.3322C>T	10.37:g.72520259C>T	ENSP00000362303:p.Pro1108Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	35	27	0.771429	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	171	0.0782967032967033	4	0.008130081300813009	23	0.06353591160220995	57	0.09965034965034965	87	0.11477572559366754	C	0.453	-0.892934	0.02491	0.024512	0.105349	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.60920	0.15;0.18	4.44	1.59	0.23543	.	0.741231	0.11005	N	0.610093	T	0.00754	0.0025	N	0.19112	0.55	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.07462	-1.0771	9	0.31617	T	0.26	.	4.6654	0.12662	0.0:0.4233:0.1543:0.4224	rs61573157;rs61736606	1108;1111	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	S	1111;1108	ENSP00000362304:P1111S;ENSP00000362303:P1108S	ENSP00000362303:P1108S	P	+	1	0	ADAMTS14	72190265	0.000000	0.05858	0.005000	0.12908	0.012000	0.07955	-0.004000	0.12878	0.241000	0.21283	-0.812000	0.03155	CCA	C|0.925;T|0.075	0.075	strong		0.637	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
PDZD2	23037	hgsc.bcm.edu	37	5	32074099	32074099	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:32074099G>T	ENST00000438447.1	+	18	3275	c.2887G>T	c.(2887-2889)Ggc>Tgc	p.G963C	PDZD2_ENST00000282493.3_Missense_Mutation_p.G963C			O15018	PDZD2_HUMAN	PDZ domain containing 2	963					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						GAGGAAGGTAGGCTGCTACGA	0.602																																					p.G963C		Atlas-SNP	.											PDZD2,NS,carcinoma,-2,1	PDZD2	306	1	0			c.G2887T						scavenged	.						64.0	68.0	67.0					5																	32074099		2203	4300	6503	SO:0001583	missense	23037	exon17			AAGGTAGGCTGCT	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.2887G>T	5.37:g.32074099G>T	ENSP00000402033:p.Gly963Cys	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	170	2	0.0117647	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.745850	0.69418	.	.	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06933	3.24;3.24	5.78	3.9	0.45041	.	0.454783	0.19483	N	0.113177	T	0.12390	0.0301	N	0.24115	0.695	0.27800	N	0.942522	D;D	0.71674	0.997;0.998	P;P	0.60173	0.707;0.87	T	0.05257	-1.0896	10	0.45353	T	0.12	.	9.6094	0.39654	0.0802:0.1875:0.7324:0.0	.	789;963	B4E3P2;O15018	.;PDZD2_HUMAN	C	963;765;963	ENSP00000402033:G963C;ENSP00000282493:G963C	ENSP00000282493:G963C	G	+	1	0	PDZD2	32109856	0.996000	0.38824	0.996000	0.52242	0.992000	0.81027	2.320000	0.43797	1.304000	0.44892	0.563000	0.77884	GGC	.	.	none		0.602	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
NDN	4692	hgsc.bcm.edu	37	15	23931507	23931507	+	Silent	SNP	G	G	A	rs2192206	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:23931507G>A	ENST00000331837.4	-	1	943	c.858C>T	c.(856-858)gaC>gaT	p.D286D		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	286	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				axon extension (GO:0048675)|axonal fasciculation (GO:0007413)|central nervous system development (GO:0007417)|genetic imprinting (GO:0071514)|glial cell migration (GO:0008347)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-embryonic development (GO:0009791)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|respiratory system process (GO:0003016)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|skin(1)	39		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00179)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		AGGCCTGGGGGTCTTTCTTAA	0.602									Prader-Willi syndrome				G|||	949	0.189497	0.0083	0.3026	5008	,	,		16558	0.3482		0.2107	False		,,,				2504	0.1687				p.D286D		Atlas-SNP	.											.	NDN	79	.	0			c.C858T						PASS	.	G		198,4204		8,182,2011	28.0	32.0	30.0		858	-1.8	1.0	15	dbSNP_96	30	1867,6727		206,1455,2636	no	coding-synonymous	NDN	NM_002487.2		214,1637,4647	AA,AG,GG		21.7245,4.498,15.8895		286/322	23931507	2065,10931	2201	4297	6498	SO:0001819	synonymous_variant	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	CTGGGGGTCTTTC	U35139	CCDS10014.1	15q11-q12	2012-12-07	2012-12-07		ENSG00000182636	ENSG00000182636			7675	protein-coding gene	gene with protein product	"""Prader-Willi syndrome chromosome region"""	602117	"""necdin (mouse) homolog"", ""necdin homolog (mouse)"""			9302265	Standard	NM_002487		Approved	HsT16328, PWCR	uc001ywk.3	Q99608	OTTHUMG00000129161	ENST00000331837.4:c.858C>T	15.37:g.23931507G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	30	8	0.266667	NM_002487	B2R6Z5	Silent	SNP	ENST00000331837.4	37	CCDS10014.1																																																																																			G|0.810;A|0.190	0.190	strong		0.602	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487	
TYRO3	7301	hgsc.bcm.edu	37	15	41862801	41862801	+	Splice_Site	SNP	G	G	T	rs200684350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:41862801G>T	ENST00000263798.3	+	12	1707		c.e12-1		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)		TTTCCCCACAGTGGACAGCTT	0.527																																					.		Atlas-SNP	.											TYRO3_ENST00000263798,NS,carcinoma,0,2	TYRO3	169	2	0			c.1484-1G>T						scavenged	.						75.0	75.0	75.0					15																	41862801		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon12			CCCACAGTGGACA	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.1484-1G>T	15.37:g.41862801G>T		Somatic	92	3	0.0326087		WXS	Illumina HiSeq	Phase_I	63	6	0.0952381	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.916766	0.73098	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4637	0.90748	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39650093	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	9.263000	0.95617	2.579000	0.87056	0.563000	0.77884	.	G|0.985;T|0.015	0.015	strong		0.527	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron
S1PR4	8698	hgsc.bcm.edu	37	19	3179021	3179021	+	Silent	SNP	G	G	A	rs34728133	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3179021G>A	ENST00000246115.3	+	1	286	c.231G>A	c.(229-231)tcG>tcA	p.S77S	S1PR4_ENST00000591346.1_Intron	NM_003775.3	NP_003766.1	O95977	S1PR4_HUMAN	sphingosine-1-phosphate receptor 4	77					activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|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)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			breast(1)|kidney(2)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	13						ACATGCGGTCGCGACGCTGGG	0.697													G|||	145	0.0289537	0.0008	0.0274	5008	,	,		13552	0.0		0.0984	False		,,,				2504	0.0266				p.S77S	GBM(82;318 1638 33279 49708)	Atlas-SNP	.											.	S1PR4	31	.	0			c.G231A						PASS	.	G		64,4322		2,60,2131	12.0	12.0	12.0		231	-7.5	0.0	19	dbSNP_126	12	718,7860		32,654,3603	no	coding-synonymous	S1PR4	NM_003775.3		34,714,5734	AA,AG,GG		8.3702,1.4592,6.0321		77/385	3179021	782,12182	2193	4289	6482	SO:0001819	synonymous_variant	8698	exon1			GCGGTCGCGACGC	AJ000479	CCDS12105.1	19p13.3	2012-08-08	2008-04-30	2008-04-30		ENSG00000125910		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	3170	protein-coding gene	gene with protein product		603751	"""endothelial differentiation, G-protein-coupled receptor 6"", ""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 6"""	EDG6		9790765	Standard	NM_003775		Approved		uc002lxg.3	O95977		ENST00000246115.3:c.231G>A	19.37:g.3179021G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_003775	D6W612	Silent	SNP	ENST00000246115.3	37	CCDS12105.1																																																																																			G|0.953;A|0.047	0.047	strong		0.697	S1PR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452517.1	NM_003775	
LGR6	59352	hgsc.bcm.edu	37	1	202276494	202276494	+	Silent	SNP	C	C	T	rs896551	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	246	2	0.00813008		WXS	Illumina HiSeq	Phase_I	302	301	0.996689	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	
RMDN1	51115	hgsc.bcm.edu	37	8	87519315	87519315	+	Missense_Mutation	SNP	T	T	G	rs6980476	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:87519315T>G	ENST00000406452.3	-	2	315	c.156A>C	c.(154-156)aaA>aaC	p.K52N	RMDN1_ENST00000523911.1_Missense_Mutation_p.K8N|RMDN1_ENST00000518772.1_5'UTR|RMDN1_ENST00000430676.2_Missense_Mutation_p.K52N|RMDN1_ENST00000519966.1_Missense_Mutation_p.K52N|CPNE3_ENST00000198765.4_Intron	NM_016033.2	NP_057117.2	Q96DB5	RMD1_HUMAN	regulator of microtubule dynamics 1	52			K -> N (in dbSNP:rs6980476). {ECO:0000269|PubMed:10810093, ECO:0000269|PubMed:14702039}.			microtubule (GO:0005874)|mitochondrion (GO:0005739)											AAAGGCCTCTTTTGAAAGTTC	0.393													T|||	768	0.153355	0.1725	0.134	5008	,	,		16358	0.0496		0.2515	False		,,,				2504	0.1472				p.K52N		Atlas-SNP	.											.	.	.	.	0			c.A156C						PASS	.	T	ASN/LYS	900,3506	345.7+/-308.6	74,752,1377	116.0	126.0	123.0		156	3.3	1.0	8	dbSNP_116	123	2324,6276	390.4+/-343.3	315,1694,2291	yes	missense	FAM82B	NM_016033.2	94	389,2446,3668	GG,GT,TT		27.0233,20.4267,24.7886	benign	52/315	87519315	3224,9782	2203	4300	6503	SO:0001583	missense	51115	exon2			GCCTCTTTTGAAA	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.156A>C	8.37:g.87519315T>G	ENSP00000385927:p.Lys52Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	142	47	0.330986	NM_016033	A9UMZ8|B4DNF5|B4DZW6|B5MC61|C9JSC6|E7EVI2|Q9Y398	Missense_Mutation	SNP	ENST00000406452.3	37	CCDS34918.1	375	0.1717032967032967	81	0.16463414634146342	62	0.1712707182320442	33	0.057692307692307696	199	0.262532981530343	T	12.62	1.991542	0.35131	0.204267	0.270233	ENSG00000176623	ENST00000406452;ENST00000523911;ENST00000519966;ENST00000430676;ENST00000521045	T;T;T;T;T	0.55760	1.15;1.31;0.54;0.5;0.83	4.4	3.26	0.37387	.	0.540958	0.20542	N	0.090295	T	0.00012	0.0000	L	0.50919	1.6	0.09310	P	0.9999999999497646	B;B;B	0.17268	0.021;0.021;0.002	B;B;B	0.15052	0.007;0.012;0.003	T	0.15065	-1.0450	8	.	.	.	-11.069	5.8521	0.18699	0.0:0.1214:0.0:0.8786	rs6980476;rs52814394;rs58444409;rs6980476	52;52;52	B4DZW6;E7EVI2;Q96DB5	.;.;RMD1_HUMAN	N	52;8;52;52;8	ENSP00000385927:K52N;ENSP00000429899:K8N;ENSP00000428661:K52N;ENSP00000409661:K52N;ENSP00000428743:K8N	.	K	-	3	2	FAM82B	87588431	1.000000	0.71417	0.955000	0.39395	0.906000	0.53458	2.340000	0.43974	0.747000	0.32809	0.533000	0.62120	AAA	T|0.790;G|0.210	0.210	strong		0.393	RMDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374770.2	NM_016033	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011719	46011719	+	Missense_Mutation	SNP	G	G	A	rs202022037	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:46011719G>A	ENST00000400368.1	-	1	667	c.647C>T	c.(646-648)cCa>cTa	p.P216L	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	216	29 X 5 AA repeats of C-C-X(3).					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						GCAGCAAGTTGGCTGGCAGCT	0.667													.|||	17	0.00339457	0.0106	0.0029	5008	,	,		21667	0.001		0.0	False		,,,				2504	0.0				p.P216L		Atlas-SNP	.											KRTAP10-6,caecum,carcinoma,-1,1	KRTAP10-6	57	1	0			c.C647T						scavenged	.						93.0	121.0	111.0					21																	46011719		2195	4300	6495	SO:0001583	missense	386674	exon1			CAAGTTGGCTGGC	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.647C>T	21.37:g.46011719G>A	ENSP00000383219:p.Pro216Leu	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	344	28	0.0813954	NM_198688		Missense_Mutation	SNP	ENST00000400368.1	37	CCDS42959.1	.	.	.	.	.	.	.	.	.	.	-	10.60	1.394637	0.25205	.	.	ENSG00000188155	ENST00000400368	T	0.02158	4.42	3.12	2.23	0.28157	.	.	.	.	.	T	0.03695	0.0105	M	0.74647	2.275	0.09310	N	1	B	0.13145	0.007	B	0.11329	0.006	T	0.36114	-0.9761	9	0.72032	D	0.01	.	3.9932	0.09546	0.1273:0.0:0.6351:0.2376	.	216	P60371	KR106_HUMAN	L	216	ENSP00000383219:P216L	ENSP00000383219:P216L	P	-	2	0	KRTAP10-6	44836147	0.000000	0.05858	0.005000	0.12908	0.072000	0.16883	0.690000	0.25451	0.665000	0.31066	-0.302000	0.09304	CCA	.	.	weak		0.667	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
ODF3L2	284451	hgsc.bcm.edu	37	19	464310	464310	+	Missense_Mutation	SNP	A	A	G	rs34551779	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:464310A>G	ENST00000315489.4	-	4	639	c.404T>C	c.(403-405)gTg>gCg	p.V135A	ODF3L2_ENST00000382696.3_Missense_Mutation_p.V99A	NM_182577.2	NP_872383.1	Q3SX64	OD3L2_HUMAN	outer dense fiber of sperm tails 3-like 2	135	Pro-rich.		V -> A (in dbSNP:rs34551779). {ECO:0000269|PubMed:15489334}.			cytoplasmic microtubule (GO:0005881)				large_intestine(1)|lung(2)	3						CCGATGGCGCACAGGGGGCAC	0.677													a|||	2188	0.436901	0.2345	0.549	5008	,	,		11673	0.6637		0.4563	False		,,,				2504	0.3773				p.V135A		Atlas-SNP	.											.	ODF3L2	18	.	0			c.T404C						PASS	.	A	ALA/VAL	936,2648		147,642,1003	7.0	8.0	8.0		404	0.6	0.0	19	dbSNP_126	8	2842,4130		646,1550,1290	no	missense	ODF3L2	NM_182577.2	64	793,2192,2293	GG,GA,AA		40.7631,26.1161,35.7901	benign	135/290	464310	3778,6778	1792	3486	5278	SO:0001583	missense	284451	exon4			TGGCGCACAGGGG	AK097378	CCDS12027.1	19p13.3	2010-04-23	2008-07-04	2008-07-04		ENSG00000181781			26841	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 19"""	C19orf19		14702039	Standard	NM_182577		Approved	FLJ40059	uc002lor.3	Q3SX64		ENST00000315489.4:c.404T>C	19.37:g.464310A>G	ENSP00000318029:p.Val135Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_182577	Q3SX65|Q8N1L2	Missense_Mutation	SNP	ENST00000315489.4	37	CCDS12027.1	1033	0.47298534798534797	113	0.22967479674796748	184	0.5082872928176796	394	0.6888111888111889	342	0.45118733509234826	A	0.019	-1.449968	0.01080	0.261161	0.407631	ENSG00000181781	ENST00000315489;ENST00000382696	T;T	0.41400	1.54;1.0	4.06	0.605	0.17553	.	1.201840	0.05840	N	0.619156	T	0.00012	0.0000	N	0.15975	0.35	0.80722	P	0.0	B;B	0.14012	0.009;0.005	B;B	0.15052	0.012;0.012	T	0.42481	-0.9449	9	0.14656	T	0.56	-0.5868	3.6483	0.08194	0.4816:0.1994:0.3191:0.0	rs34551779	99;135	Q3SX64-2;Q3SX64	.;OD3L2_HUMAN	A	135;99	ENSP00000318029:V135A;ENSP00000372143:V99A	ENSP00000318029:V135A	V	-	2	0	ODF3L2	415310	0.577000	0.26708	0.037000	0.18230	0.001000	0.01503	1.422000	0.34826	0.016000	0.14998	-0.518000	0.04402	GTG	A|0.527;G|0.473	0.473	strong		0.677	ODF3L2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451849.2	NM_182577	
ANKS3	124401	hgsc.bcm.edu	37	16	4776685	4776685	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4776685C>T	ENST00000304283.4	-	5	760	c.466G>A	c.(466-468)Gac>Aac	p.D156N	ANKS3_ENST00000446014.2_Missense_Mutation_p.D27N|ANKS3_ENST00000585773.1_Missense_Mutation_p.D83N|ANKS3_ENST00000450067.2_Intron|ANKS3_ENST00000592711.1_Intron	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	156										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						GCTCCACTGTCCAAGAGGAAC	0.567																																					p.D156N		Atlas-SNP	.											.	ANKS3	44	.	0			c.G466A						PASS	.						95.0	78.0	84.0					16																	4776685		2197	4300	6497	SO:0001583	missense	124401	exon5			CACTGTCCAAGAG	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.466G>A	16.37:g.4776685C>T	ENSP00000304586:p.Asp156Asn	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	5	0.0490196	NM_133450	B4DWU4|D3DUE2|Q8TF25	Missense_Mutation	SNP	ENST00000304283.4	37	CCDS10520.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496348	0.85069	.	.	ENSG00000168096	ENST00000304283;ENST00000446014	T;T	0.65732	-0.12;-0.17	5.35	5.35	0.76521	Ankyrin repeat-containing domain (4);	0.136125	0.64402	D	0.000003	T	0.66317	0.2777	L	0.41573	1.285	0.80722	D	1	P	0.47253	0.892	P	0.51055	0.657	T	0.68416	-0.5414	10	0.62326	D	0.03	-17.1943	18.4258	0.90608	0.0:1.0:0.0:0.0	.	156	Q6ZW76	ANKS3_HUMAN	N	156;27	ENSP00000304586:D156N;ENSP00000406796:D27N	ENSP00000304586:D156N	D	-	1	0	ANKS3	4716686	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.445000	0.80570	2.675000	0.91044	0.555000	0.69702	GAC	.	.	none		0.567	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450	
ZNF100	163227	hgsc.bcm.edu	37	19	21910125	21910125	+	Nonsense_Mutation	SNP	G	G	T	rs138292237	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21910125G>T	ENST00000358296.6	-	5	1187	c.989C>A	c.(988-990)tCa>tAa	p.S330*	ZNF100_ENST00000305570.6_Nonsense_Mutation_p.S266*	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	330					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						AGTAAGGTGTGAGGACCGGTT	0.408													N|||	35	0.00698882	0.0	0.0101	5008	,	,		20645	0.005		0.0189	False		,,,				2504	0.0041				p.S330X		Atlas-SNP	.											.	ZNF100	62	.	0			c.C989A						PASS	.	G	stop/SER	12,4384		0,12,2186	65.0	69.0	68.0		989	-0.5	0.9	19	dbSNP_134	68	108,8482		0,108,4187	no	stop-gained	ZNF100	NM_173531.3		0,120,6373	TT,TG,GG		1.2573,0.273,0.9241		330/543	21910125	120,12866	2198	4295	6493	SO:0001587	stop_gained	163227	exon5			AGGTGTGAGGACC	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.989C>A	19.37:g.21910125G>T	ENSP00000351042:p.Ser330*	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_173531	Q7M4M0	Nonsense_Mutation	SNP	ENST00000358296.6	37	CCDS42538.1	22	0.010073260073260074	0	0.0	4	0.011049723756906077	4	0.006993006993006993	14	0.018469656992084433	.	10.78	1.445657	0.25987	0.00273	0.012573	ENSG00000197020	ENST00000358296	.	.	.	0.841	-0.462	0.12168	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.4567	0.11647	0.4667:0.0:0.5333:0.0	.	.	.	.	X	330	.	ENSP00000351042:S330X	S	-	2	0	ZNF100	21701965	0.007000	0.16637	0.876000	0.34364	0.877000	0.50540	1.566000	0.36396	0.182000	0.20032	0.185000	0.17295	TCA	G|0.990;T|0.010	0.010	strong		0.408	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
C6orf223	221416	hgsc.bcm.edu	37	6	43968412	43968412	+	Missense_Mutation	SNP	C	C	T	rs35703624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43968412C>T	ENST00000336600.5	+	1	76	c.56C>T	c.(55-57)aCg>aTg	p.T19M	RP5-1120P11.1_ENST00000607590.1_RNA|C6orf223_ENST00000448947.2_3'UTR|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000442114.2_5'UTR|C6orf223_ENST00000439969.2_Missense_Mutation_p.T19M	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	19										central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			CCTTCAGCAACGGAGTGGGCC	0.612													C|||	22	0.00439297	0.0023	0.0058	5008	,	,		16264	0.0		0.0149	False		,,,				2504	0.0				p.T19M		Atlas-SNP	.											.	C6orf223	14	.	0			c.C56T						PASS	.	C	MET/THR,MET/THR	12,4392	17.9+/-39.9	0,12,2190	42.0	40.0	41.0		56,56	-6.9	0.0	6	dbSNP_126	41	106,8494	55.6+/-116.7	1,104,4195	yes	missense,missense	C6orf223	NM_153246.4,NM_001171992.1	81,81	1,116,6385	TT,TC,CC		1.2326,0.2725,0.9074	benign,benign	19/243,19/106	43968412	118,12886	2202	4300	6502	SO:0001583	missense	221416	exon1			CAGCAACGGAGTG	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.56C>T	6.37:g.43968412C>T	ENSP00000426159:p.Thr19Met	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	155	64	0.412903	NM_153246	E9PB59|Q8N575	Missense_Mutation	SNP	ENST00000336600.5	37	CCDS34459.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	9.922	1.212319	0.22289	0.002725	0.012326	ENSG00000181577	ENST00000336600;ENST00000439969	T	0.38077	1.16	4.21	-6.91	0.01649	.	3.185210	0.01694	N	0.026816	T	0.06234	0.0161	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.31364	-0.9946	10	0.87932	D	0	.	7.3902	0.26905	0.1084:0.3451:0.0:0.5465	rs35703624	19	Q8N319	CF223_HUMAN	M	19	ENSP00000426159:T19M	ENSP00000426159:T19M	T	+	2	0	C6orf223	44076390	0.000000	0.05858	0.001000	0.08648	0.070000	0.16714	-2.120000	0.01323	-1.415000	0.02022	-1.644000	0.00765	ACG	C|0.993;T|0.007	0.007	strong		0.612	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246	
C5orf34	375444	hgsc.bcm.edu	37	5	43505993	43505993	+	Silent	SNP	A	A	G	rs7710628	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:43505993A>G	ENST00000306862.2	-	4	1164	c.789T>C	c.(787-789)aaT>aaC	p.N263N	RP11-159F24.3_ENST00000505645.1_RNA	NM_198566.2	NP_940968	Q96MH7	CE034_HUMAN	chromosome 5 open reading frame 34	263										breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|stomach(2)	21	Lung NSC(6;2.07e-05)					TGCTGATTTTATTATGAAAAT	0.373													A|||	2013	0.401957	0.6271	0.3818	5008	,	,		20847	0.0893		0.503	False		,,,				2504	0.3303				p.N263N		Atlas-SNP	.											.	C5orf34	47	.	0			c.T789C						PASS	.	A		2603,1803	640.0+/-397.2	788,1027,388	97.0	100.0	99.0		789	1.1	0.1	5	dbSNP_116	99	4196,4404	570.1+/-389.3	1017,2162,1121	no	coding-synonymous	C5orf34	NM_198566.2		1805,3189,1509	GG,GA,AA		48.7907,40.9215,47.7241		263/639	43505993	6799,6207	2203	4300	6503	SO:0001819	synonymous_variant	375444	exon4			GATTTTATTATGA	AK056925	CCDS3946.1	5p12	2012-02-23			ENSG00000172244	ENSG00000172244			24738	protein-coding gene	gene with protein product						12477932	Standard	XM_006714473		Approved	FLJ32363	uc003jnz.2	Q96MH7	OTTHUMG00000131151	ENST00000306862.2:c.789T>C	5.37:g.43505993A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	139	73	0.52518	NM_198566		Silent	SNP	ENST00000306862.2	37	CCDS3946.1																																																																																			A|0.526;G|0.474	0.474	strong		0.373	C5orf34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253843.1	NM_198566	
TEKT5	146279	hgsc.bcm.edu	37	16	10769958	10769958	+	Missense_Mutation	SNP	T	T	C	rs2719710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:10769958T>C	ENST00000283025.2	-	5	1015	c.944A>G	c.(943-945)cAg>cGg	p.Q315R		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	315			Q -> R (in dbSNP:rs2719710).			cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						CTCCCGCAGCTGGATGGAGTT	0.562													C|||	3176	0.634185	0.6944	0.6009	5008	,	,		21094	0.8135		0.3588	False		,,,				2504	0.6748				p.Q315R		Atlas-SNP	.											.	TEKT5	66	.	0			c.A944G						PASS	.	C	ARG/GLN	2872,1522	482.4+/-359.4	936,1000,261	127.0	109.0	115.0		944	2.7	1.0	16	dbSNP_100	115	3382,5218	641.8+/-399.7	664,2054,1582	yes	missense	TEKT5	NM_144674.1	43	1600,3054,1843	CC,CT,TT		39.3256,34.6381,48.1299	benign	315/486	10769958	6254,6740	2197	4300	6497	SO:0001583	missense	146279	exon5			CGCAGCTGGATGG		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.944A>G	16.37:g.10769958T>C	ENSP00000283025:p.Gln315Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	1277	0.5847069597069597	330	0.6707317073170732	193	0.5331491712707183	467	0.8164335664335665	287	0.3786279683377309	C	10.05	1.245159	0.22796	0.653619	0.393256	ENSG00000153060	ENST00000283025	T	0.02525	4.26	4.68	2.67	0.31697	.	0.145954	0.33691	N	0.004648	T	0.00012	0.0000	N	0.04373	-0.215	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.04191	-1.0970	9	0.19147	T	0.46	-30.7844	6.4945	0.22133	0.0:0.5605:0.0:0.4395	rs2719710;rs3803673;rs60988360;rs2719710	315	Q96M29	TEKT5_HUMAN	R	315	ENSP00000283025:Q315R	ENSP00000283025:Q315R	Q	-	2	0	TEKT5	10677459	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	1.681000	0.37618	0.521000	0.28445	-0.213000	0.12676	CAG	T|0.469;C|0.531	0.531	strong		0.562	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
LYZL2	119180	hgsc.bcm.edu	37	10	30918549	30918549	+	Missense_Mutation	SNP	G	G	C	rs201069868	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:30918549G>C	ENST00000375318.2	-	1	142	c.86C>G	c.(85-87)gCg>gGg	p.A29G		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	0					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				GGTGCCTGCCGCAGAGGCTGA	0.527																																					p.A29G		Atlas-SNP	.											LYZL2,NS,adenoma,0,2	LYZL2	33	2	0			c.C86G						scavenged	.						79.0	71.0	74.0					10																	30918549		2203	4300	6503	SO:0001583	missense	119180	exon1			CCTGCCGCAGAGG	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.86C>G	10.37:g.30918549G>C	ENSP00000364467:p.Ala29Gly	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	127	28	0.220472	NM_183058	Q6NZ69	Missense_Mutation	SNP	ENST00000375318.2	37	CCDS7167.2	.	.	.	.	.	.	.	.	.	.	g	0.233	-1.019814	0.02078	.	.	ENSG00000151033	ENST00000375318	T	0.68025	-0.3	2.33	-0.854	0.10705	.	2.470750	0.01887	N	0.038284	T	0.45776	0.1359	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16958	-1.0385	9	0.15499	T	0.54	0.1998	4.5545	0.12130	0.0:0.3972:0.4547:0.1482	.	29	Q7Z4W2-2	.	G	29	ENSP00000364467:A29G	ENSP00000364467:A29G	A	-	2	0	LYZL2	30958555	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.110000	0.10824	-0.224000	0.09928	-0.381000	0.06696	GCG	G|0.894;C|0.106	0.106	strong		0.527	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058	
NDUFA13	51079	hgsc.bcm.edu	37	19	19627083	19627083	+	Silent	SNP	G	G	C	rs11552886		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19627083G>C	ENST00000507754.4	+	1	520	c.36G>C	c.(34-36)ccG>ccC	p.P12P	NDUFA13_ENST00000512771.3_Silent_p.P12P|NDUFA13_ENST00000252576.5_Silent_p.P95P|TSSK6_ENST00000360913.3_5'Flank|NDUFA13_ENST00000428459.2_Silent_p.P12P|CTC-260F20.3_ENST00000555938.1_Silent_p.P12P|TSSK6_ENST00000585580.3_5'Flank|YJEFN3_ENST00000608404.1_Silent_p.P12P|CTC-260F20.3_ENST00000586674.1_3'UTR|NDUFA13_ENST00000503283.1_Silent_p.P12P			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	12					apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)	p.P95P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						ACATGCCTCCGCCGGGGGGCT	0.622																																					p.P12P		Atlas-SNP	.											NDUFA13,NS,carcinoma,0,1	NDUFA13	17	1	1	Substitution - coding silent(1)	ovary(1)	c.G36C						scavenged	.						38.0	43.0	41.0					19																	19627083		2203	4300	6503	SO:0001819	synonymous_variant	51079	exon1			GCCTCCGCCGGGG	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"""Mitochondrial respiratory chain complex / Complex I"""	17194	protein-coding gene	gene with protein product	"""complex I B16.6 subunit"""	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211	ENST00000507754.4:c.36G>C	19.37:g.19627083G>C		Somatic	262	2	0.00763359		WXS	Illumina HiSeq	Phase_I	243	112	0.460905	NM_015965	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Silent	SNP	ENST00000507754.4	37	CCDS12404.2																																																																																			.	.	alt		0.622	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965	
AGR2	10551	hgsc.bcm.edu	37	7	16834597	16834597	+	Silent	SNP	A	A	G	rs6842	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	178	0	0		WXS	Illumina HiSeq	Phase_I	231	229	0.991342	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	
APOB	338	hgsc.bcm.edu	37	2	21225281	21225281	+	Missense_Mutation	SNP	C	C	T	rs1042034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:21225281C>T	ENST00000233242.1	-	29	13140	c.13013G>A	c.(13012-13014)aGt>aAt	p.S4338N	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4338			S -> N (in dbSNP:rs1042034). {ECO:0000269|PubMed:1979313, ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:2883086, ECO:0000269|PubMed:2932736, ECO:0000269|PubMed:2994225, ECO:0000269|PubMed:3030729, ECO:0000269|PubMed:3464946, ECO:0000269|PubMed:3652907, ECO:0000269|PubMed:3759943, ECO:0000269|PubMed:3763409, ECO:0000269|Ref.6}.		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)					GATATAATCACTGAAGATTGT	0.279													T|||	3153	0.629593	0.8759	0.7493	5008	,	,		19325	0.2798		0.7823	False		,,,				2504	0.4151				p.S4338N		Atlas-SNP	.											.	APOB	761	.	0			c.G13013A						PASS	.	T	ASN/SER	3708,690	257.0+/-261.6	1562,584,53	28.0	31.0	30.0	http://www.ncbi.nlm.nih.gov/pubmed?term	13013	1.6	0.0	2	dbSNP_86	30	6721,1869	317.6+/-313.3	2655,1411,229	yes	missense	APOB	NM_000384.2	46	4217,1995,282	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	21.7579,15.6889,19.7028	benign	4338/4564	21225281	10429,2559	2199	4295	6494	SO:0001583	missense	338	exon29			TAATCACTGAAGA	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.13013G>A	2.37:g.21225281C>T	ENSP00000233242:p.Ser4338Asn	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	1446	0.6620879120879121	415	0.8434959349593496	283	0.7817679558011049	166	0.2902097902097902	582	0.7678100263852242	T	0.140	-1.103068	0.01828	0.843111	0.782421	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.36520	1.25	5.41	1.61	0.23674	.	1.173870	0.06125	N	0.669497	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36480	-0.9746	9	0.02654	T	1	.	5.789	0.18349	0.0:0.269:0.1281:0.6029	rs1042034;rs3181514;rs17041706;rs17240958;rs52829794;rs60186088;rs1042034	4338	P04114	APOB_HUMAN	N	4338	ENSP00000233242:S4338N	ENSP00000233242:S4338N	S	-	2	0	APOB	21078786	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.640000	0.24705	-0.124000	0.11724	-0.516000	0.04426	AGT	C|0.265;T|0.735	0.735	strong		0.279	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
WDR16	146845	hgsc.bcm.edu	37	17	9515777	9515777	+	Missense_Mutation	SNP	G	G	A	rs6503235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	53	53	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	
KLRC3	3823	hgsc.bcm.edu	37	12	10588530	10588530	+	Missense_Mutation	SNP	C	C	G	rs75545535		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:10588530C>G	ENST00000539033.1	-	1	70	c.56G>C	c.(55-57)cGg>cCg	p.R19P	KLRC2_ENST00000381901.1_Missense_Mutation_p.R19P|KLRC2_ENST00000536833.2_Intron|KLRC2_ENST00000381902.2_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	513	2	0.00389864		WXS	Illumina HiSeq	Phase_I	564	231	0.409574	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		
CCDC110	256309	hgsc.bcm.edu	37	4	186381165	186381165	+	Silent	SNP	G	G	A	rs7699724	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:186381165G>A	ENST00000307588.3	-	6	651	c.576C>T	c.(574-576)gaC>gaT	p.D192D	CCDC110_ENST00000510617.1_Silent_p.D192D|CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000393540.3_Silent_p.D155D	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	192						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TCTTCAAGATGTCAGAATTTT	0.333													G|||	1931	0.385583	0.2837	0.3631	5008	,	,		19213	0.2827		0.5378	False		,,,				2504	0.4888				p.D192D		Atlas-SNP	.											.	CCDC110	78	.	0			c.C576T						PASS	.	G	,	1460,2942	428.7+/-342.0	241,978,982	64.0	64.0	64.0		465,576	-0.6	0.0	4	dbSNP_116	64	4849,3745	598.8+/-394.0	1374,2101,822	no	coding-synonymous,coding-synonymous	CCDC110	NM_001145411.1,NM_152775.3	,	1615,3079,1804	AA,AG,GG		43.5769,33.1667,48.5457	,	155/797,192/834	186381165	6309,6687	2201	4297	6498	SO:0001819	synonymous_variant	256309	exon6			CAAGATGTCAGAA	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.576C>T	4.37:g.186381165G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	109	26	0.238532	NM_152775	Q86YI9|Q8N7W0	Silent	SNP	ENST00000307588.3	37	CCDS3843.1																																																																																			G|0.547;A|0.453	0.453	strong		0.333	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
DERL1	79139	hgsc.bcm.edu	37	8	124031541	124031541	+	Missense_Mutation	SNP	T	T	C	rs2272722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:124031541T>C	ENST00000259512.4	-	7	811	c.511A>G	c.(511-513)Atc>Gtc	p.I171V	DERL1_ENST00000519018.1_Missense_Mutation_p.I71V|DERL1_ENST00000523036.1_Missense_Mutation_p.I71V|RP11-557C18.3_ENST00000521258.1_RNA|DERL1_ENST00000405944.3_Intron|DERL1_ENST00000419562.2_Missense_Mutation_p.I71V	NM_001134671.2|NM_024295.5	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	derlin 1	171			I -> V (in dbSNP:rs2272722).		endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|intracellular transport of viral protein in host cell (GO:0019060)|response to unfolded protein (GO:0006986)|retrograde protein transport, ER to cytosol (GO:0030970)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)	MHC class I protein binding (GO:0042288)|receptor activity (GO:0004872)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	8	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			AGCTCATTGATTACCCTGCAA	0.388													T|||	265	0.0529153	0.0953	0.0677	5008	,	,		21308	0.005		0.0626	False		,,,				2504	0.0245				p.I171V		Atlas-SNP	.											.	DERL1	27	.	0			c.A511G						PASS	.	T	,VAL/ILE	321,4085	169.1+/-199.8	13,295,1895	64.0	62.0	62.0		,511	4.4	0.8	8	dbSNP_100	62	695,7905	171.3+/-222.3	28,639,3633	yes	intron,missense	DERL1	NM_001134671.1,NM_024295.4	,29	41,934,5528	CC,CT,TT		8.0814,7.2855,7.8118	,benign	,171/252	124031541	1016,11990	2203	4300	6503	SO:0001583	missense	79139	exon7			CATTGATTACCCT	BC002457	CCDS6337.1, CCDS47915.1	8q24.13	2012-02-01	2012-02-01		ENSG00000136986	ENSG00000136986			28454	protein-coding gene	gene with protein product		608813	"""Der1-like domain family, member 1"""			12975309, 15215855	Standard	NM_024295		Approved	MGC3067, PRO2577, FLJ13784, DER1, DER-1, derlin-1	uc003ypl.3	Q9BUN8	OTTHUMG00000165080	ENST00000259512.4:c.511A>G	8.37:g.124031541T>C	ENSP00000259512:p.Ile171Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	147	56	0.380952	NM_024295	B3KW41|E9PH19	Missense_Mutation	SNP	ENST00000259512.4	37	CCDS6337.1	136	0.06227106227106227	54	0.10975609756097561	35	0.09668508287292818	3	0.005244755244755245	44	0.05804749340369393	T	4.278	0.050812	0.08243	0.072855	0.080814	ENSG00000136986	ENST00000259512;ENST00000419562;ENST00000519018;ENST00000523036	T;T;T;T	0.27104	1.69;1.69;1.69;1.69	5.61	4.45	0.53987	.	0.234322	0.45867	D	0.000330	T	0.00241	0.0007	N	0.04959	-0.14	0.35251	D	0.778677	B;B	0.18310	0.027;0.0	B;B	0.22880	0.042;0.002	T	0.29882	-0.9997	10	0.12430	T	0.62	.	8.8661	0.35286	0.0:0.1439:0.0:0.8561	rs2272722;rs52815824;rs60455215;rs2272722	71;171	B4E1G1;Q9BUN8	.;DERL1_HUMAN	V	171;71;71;71	ENSP00000259512:I171V;ENSP00000389965:I71V;ENSP00000430086:I71V;ENSP00000429199:I71V	ENSP00000259512:I171V	I	-	1	0	DERL1	124100722	0.997000	0.39634	0.766000	0.31476	0.958000	0.62258	2.937000	0.48979	0.953000	0.37825	-0.274000	0.10170	ATC	T|0.926;C|0.074	0.074	strong		0.388	DERL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381714.2	NM_024295	
FRMPD4	9758	hgsc.bcm.edu	37	X	12720127	12720127	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:12720127C>T	ENST00000380682.1	+	10	1574	c.1068C>T	c.(1066-1068)atC>atT	p.I356I		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	356	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				positive regulation of synapse structural plasticity (GO:0051835)	cytoskeleton (GO:0005856)|dendritic spine (GO:0043197)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.I346I(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TCAAATACATCGAGTAAGTGT	0.468											OREG0019670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I356I		Atlas-SNP	.											.	FRMPD4	214	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1068T						PASS	.						124.0	103.0	110.0					X																	12720127		2203	4300	6503	SO:0001819	synonymous_variant	9758	exon10			ATACATCGAGTAA	AB002314	CCDS35201.1	Xp22.31	2006-02-09	2006-02-09	2006-02-09	ENSG00000169933	ENSG00000169933			29007	protein-coding gene	gene with protein product		300838	"""PDZ domain containing 10"""	PDZK10, PDZD10		9205841	Standard	NM_014728		Approved	KIAA0316	uc004cuz.2	Q14CM0	OTTHUMG00000021138	ENST00000380682.1:c.1068C>T	X.37:g.12720127C>T		Somatic	101	0	0	682	WXS	Illumina HiSeq	Phase_I	39	39	1	NM_014728	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																			.	.	none		0.468	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712	
CLIP4	79745	hgsc.bcm.edu	37	2	29356669	29356669	+	Silent	SNP	A	A	G	rs3100232	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:29356669A>G	ENST00000320081.5	+	5	771	c.516A>G	c.(514-516)acA>acG	p.T172T	CLIP4_ENST00000404424.1_Silent_p.T172T|CLIP4_ENST00000401617.2_Silent_p.T65T|CLIP4_ENST00000401605.1_Silent_p.T172T	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	172										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TTTTGAAAACATCGAAACCAA	0.333													A|||	2079	0.415136	0.6747	0.317	5008	,	,		17714	0.3204		0.4006	False		,,,				2504	0.2464				p.T172T		Atlas-SNP	.											.	CLIP4	69	.	0			c.A516G						PASS	.	A		2675,1731	649.3+/-398.9	829,1017,357	101.0	97.0	98.0		516	-2.0	1.0	2	dbSNP_103	98	3414,5186	503.0+/-375.8	688,2038,1574	no	coding-synonymous	CLIP4	NM_024692.4		1517,3055,1931	GG,GA,AA		39.6977,39.2873,46.8169		172/706	29356669	6089,6917	2203	4300	6503	SO:0001819	synonymous_variant	79745	exon5			GAAAACATCGAAA	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.516A>G	2.37:g.29356669A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	37	CCDS1770.1																																																																																			A|0.551;G|0.449	0.449	strong		0.333	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
CFAP46	54777	hgsc.bcm.edu	37	10	134659573	134659573	+	Silent	SNP	G	G	A	rs34588833	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:134659573G>A	ENST00000368586.5	-	44	6526	c.6426C>T	c.(6424-6426)gcC>gcT	p.A2142A	TTC40_ENST00000263170.5_Silent_p.A303A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TGGACACGGCGGCCAGCCTCT	0.687													G|||	385	0.076877	0.2345	0.062	5008	,	,		15726	0.0		0.0298	False		,,,				2504	0.002				p.A2142A		Atlas-SNP	.											.	TTC40	100	.	0			c.C6426T						PASS	.	G		543,3789		39,465,1662	16.0	19.0	18.0		1362	-8.8	0.0	10	dbSNP_126	18	105,8453		1,103,4175	no	coding-synonymous	C10orf92	NM_001200049.1		40,568,5837	AA,AG,GG		1.2269,12.5346,5.0272		454/1028	134659573	648,12242	2166	4279	6445	SO:0001819	synonymous_variant	54777	exon44			CACGGCGGCCAGC																												ENST00000368586.5:c.6426C>T	10.37:g.134659573G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			G|0.936;A|0.064	0.064	strong		0.687	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
MUC5B	727897	hgsc.bcm.edu	37	11	1264808	1264808	+	Missense_Mutation	SNP	T	T	G	rs2943528	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1264808T>G	ENST00000529681.1	+	31	6756	c.6698T>G	c.(6697-6699)gTg>gGg	p.V2233G	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.V2236G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2233	7 X Cys-rich subdomain repeats.|Thr-rich.			V -> G (in Ref. 4; CAA96577). {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)		CCTTCCACGGTGACTTCCCAC	0.652																																					p.V2233G		Atlas-SNP	.											.	MUC5B	473	.	0			c.T6698G						PASS	.						94.0	126.0	116.0					11																	1264808		2112	4198	6310	SO:0001583	missense	727897	exon31			CCACGGTGACTTC	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.6698T>G	11.37:g.1264808T>G	ENSP00000436812:p.Val2233Gly	Somatic	448	1	0.00223214		WXS	Illumina HiSeq	Phase_I	445	153	0.34382	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	204	0.09340659340659341	34	0.06910569105691057	50	0.13812154696132597	35	0.06118881118881119	85	0.11213720316622691	t	3.185	-0.167068	0.06461	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21932	1.98;2.17	0.593	0.593	0.17478	.	.	.	.	.	T	0.00109	0.0003	L	0.43152	1.355	0.80722	P	0.0	P;P	0.47604	0.898;0.898	B;B	0.28849	0.094;0.095	T	0.23691	-1.0181	8	0.87932	D	0	.	6.7213	0.23332	0.0:0.0:0.0:1.0	rs2943528	2871;2236	A7Y9J9;E9PBJ0	.;.	G	2233;2236;2234;2248	ENSP00000436812:V2233G;ENSP00000415793:V2236G	ENSP00000343037:V2234G	V	+	2	0	MUC5B	1221384	0.000000	0.05858	0.003000	0.11579	0.044000	0.14063	-3.817000	0.00359	0.466000	0.27193	0.254000	0.18369	GTG	T|0.921;G|0.079	0.079	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
IQGAP3	128239	hgsc.bcm.edu	37	1	156499969	156499969	+	Silent	SNP	T	T	C	rs386635735|rs1171566	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156499969T>C	ENST00000361170.2	-	34	4342	c.4332A>G	c.(4330-4332)ctA>ctG	p.L1444L	snoU13_ENST00000458777.1_RNA	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1444					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)					CAAGTCGGCGTAGGTTCCGCA	0.647													C|||	3033	0.605631	0.8449	0.4424	5008	,	,		406	0.6022		0.33	False		,,,				2504	0.6851				p.L1444L		Atlas-SNP	.											IQGAP3,NS,carcinoma,0,1	IQGAP3	146	1	0			c.A4332G						PASS	.	C		3226,1180	404.0+/-332.9	1179,868,156	52.0	46.0	48.0		4332	4.5	1.0	1	dbSNP_87	48	2795,5805	665.5+/-402.3	475,1845,1980	no	coding-synonymous	IQGAP3	NM_178229.4		1654,2713,2136	CC,CT,TT		32.5,26.7817,46.294		1444/1632	156499969	6021,6985	2203	4300	6503	SO:0001819	synonymous_variant	128239	exon34			TCGGCGTAGGTTC	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.4332A>G	1.37:g.156499969T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	176	173	0.982955	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																			T|0.489;C|0.511	0.511	strong		0.647	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
CDHR2	54825	hgsc.bcm.edu	37	5	176011889	176011889	+	Silent	SNP	G	G	A	rs4868660	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	221	0	0		WXS	Illumina HiSeq	Phase_I	237	110	0.464135	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	
ASCC3	10973	hgsc.bcm.edu	37	6	101296389	101296389	+	Missense_Mutation	SNP	G	G	A	rs9390698	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	182	0	0		WXS	Illumina HiSeq	Phase_I	153	63	0.411765	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	
OR5K3	403277	hgsc.bcm.edu	37	3	98109640	98109640	+	Missense_Mutation	SNP	G	G	A	rs13068323	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:98109640G>A	ENST00000383695.1	+	1	131	c.131G>A	c.(130-132)gGt>gAt	p.G44D	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	44			G -> D (in dbSNP:rs13068323).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						GGGAACATTGGTTTGGTGGCA	0.413													G|||	825	0.164736	0.1271	0.1153	5008	,	,		21130	0.2222		0.162	False		,,,				2504	0.1943				p.G44D		Atlas-SNP	.											OR5K3,rectum,carcinoma,-1,1	OR5K3	60	1	0			c.G131A						PASS	.	G	ASP/GLY	594,3812	260.1+/-263.5	41,512,1650	277.0	258.0	264.0		131	5.3	0.9	3	dbSNP_121	264	1263,7337	252.8+/-278.7	96,1071,3133	yes	missense	OR5K3	NM_001005516.1	94	137,1583,4783	AA,AG,GG		14.686,13.4816,14.278	probably-damaging	44/322	98109640	1857,11149	2203	4300	6503	SO:0001583	missense	403277	exon1			ACATTGGTTTGGT		CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"""GPCR / Class A : Olfactory receptors"""	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.131G>A	3.37:g.98109640G>A	ENSP00000373194:p.Gly44Asp	Somatic	476	1	0.00210084		WXS	Illumina HiSeq	Phase_I	422	213	0.504739	NM_001005516		Missense_Mutation	SNP	ENST00000383695.1	37	CCDS33803.1	362	0.16575091575091574	69	0.1402439024390244	50	0.13812154696132597	114	0.1993006993006993	129	0.17018469656992086	G	12.49	1.955038	0.34471	0.134816	0.14686	ENSG00000206536	ENST00000383695	T	0.01981	4.52	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	D	0.000846	T	0.00012	0.0000	M	0.93462	3.42	0.58432	P	8.000000000008E-6	D	0.58268	0.982	D	0.65010	0.931	T	0.01972	-1.1237	9	0.87932	D	0	-25.2713	11.9377	0.52882	0.0:0.0:0.8262:0.1737	rs13068323;rs13068323	44	A6NET4	OR5K3_HUMAN	D	44	ENSP00000373194:G44D	ENSP00000373194:G44D	G	+	2	0	OR5K3	99592330	0.000000	0.05858	0.936000	0.37596	0.090000	0.18270	-0.556000	0.05992	2.633000	0.89246	0.603000	0.83216	GGT	G|0.846;A|0.154	0.154	strong		0.413	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1		
DDX51	317781	hgsc.bcm.edu	37	12	132626668	132626668	+	Missense_Mutation	SNP	T	T	C	rs17418886|rs1133690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	114	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	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	
MROH2B	133558	hgsc.bcm.edu	37	5	41054934	41054934	+	Silent	SNP	A	A	G	rs325874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	109	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	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	
FLG	2312	hgsc.bcm.edu	37	1	152281690	152281690	+	Missense_Mutation	SNP	C	C	T	rs12407748	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152281690C>T	ENST00000368799.1	-	3	5707	c.5672G>A	c.(5671-5673)cGg>cAg	p.R1891Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1891	Ser-rich.		R -> Q (in dbSNP:rs12407748).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCTGTCGGCCCGAGAGGAAGC	0.567									Ichthyosis				C|||	1440	0.28754	0.0113	0.3905	5008	,	,		19138	0.5843		0.1421	False		,,,				2504	0.4315				p.R1891Q		Atlas-SNP	.											.	FLG	900	.	0			c.G5672A						PASS	.	C	GLN/ARG	162,4244	108.6+/-147.0	2,158,2043	272.0	275.0	274.0		5672	-3.6	0.0	1	dbSNP_120	274	1242,7358	249.3+/-276.6	97,1048,3155	no	missense	FLG	NM_002016.1	43	99,1206,5198	TT,TC,CC		14.4419,3.6768,10.795	possibly-damaging	1891/4062	152281690	1404,11602	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCGGCCCGAGAGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5672G>A	1.37:g.152281690C>T	ENSP00000357789:p.Arg1891Gln	Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	467	152	0.325482	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	549	0.25137362637362637	9	0.018292682926829267	114	0.3149171270718232	316	0.5524475524475524	110	0.14511873350923482	C	4.339	0.062313	0.08388	0.036768	0.144419	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.03358	3.96	1.78	-3.57	0.04612	.	.	.	.	.	T	0.00524	0.0017	N	0.13235	0.315	0.80722	P	0.0	P	0.39250	0.665	B	0.33890	0.172	T	0.39272	-0.9622	8	0.08599	T	0.76	.	7.8311	0.29342	0.0:0.7145:0.0:0.2855	rs12407748;rs35359555;rs12407748	1891	P20930	FILA_HUMAN	Q	1891;126	ENSP00000357789:R1891Q	ENSP00000271820:R126Q	R	-	2	0	FLG	150548314	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.006000	0.00315	-1.013000	0.03383	-1.309000	0.01313	CGG	C|0.851;T|0.149	0.149	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TSNAX	7257	hgsc.bcm.edu	37	1	231665038	231665038	+	Silent	SNP	C	C	T	rs138421350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:231665038C>T	ENST00000366639.4	+	2	212	c.54C>T	c.(52-54)ttC>ttT	p.F18F	TSNAX_ENST00000602825.1_3'UTR|RP11-295G20.2_ENST00000450783.1_RNA|RP11-295G20.2_ENST00000416221.1_RNA|RP11-295G20.2_ENST00000440665.1_RNA|TSNAX-DISC1_ENST00000602962.1_Silent_p.F18F|RP11-295G20.2_ENST00000454631.1_RNA|RP11-295G20.2_ENST00000425412.1_RNA	NM_005999.2	NP_005990.1	Q99598	TSNAX_HUMAN	translin-associated factor X	18					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		all_cancers(173;0.0395)|Acute lymphoblastic leukemia(190;3.76e-06)|Prostate(94;0.116)				ATGACAATTTCCCACATAACC	0.398													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18625	0.0		0.0	False		,,,				2504	0.002				p.F18F		Atlas-SNP	.											.	TSNAX	14	.	0			c.C54T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	174.0	158.0	163.0		54	2.5	1.0	1	dbSNP_134	163	8,8592	7.1+/-27.0	0,8,4292	no	coding-synonymous	TSNAX	NM_005999.2		0,10,6493	TT,TC,CC		0.093,0.0454,0.0769		18/291	231665038	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	7257	exon2			CAATTTCCCACAT	X95073	CCDS1596.1	1q42.2	2008-02-05			ENSG00000116918	ENSG00000116918			12380	protein-coding gene	gene with protein product		602964				9013868	Standard	NM_005999		Approved	TRAX	uc001huw.3	Q99598	OTTHUMG00000039486	ENST00000366639.4:c.54C>T	1.37:g.231665038C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	190	67	0.352632	NM_005999	B1APC6	Silent	SNP	ENST00000366639.4	37	CCDS1596.1																																																																																			C|0.999;T|0.001	0.001	strong		0.398	TSNAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095267.2	NM_005999	
ODF4	146852	hgsc.bcm.edu	37	17	8243598	8243598	+	Missense_Mutation	SNP	C	C	T	rs73250854	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8243598C>T	ENST00000328248.2	+	1	417	c.229C>T	c.(229-231)Cgc>Tgc	p.R77C	ODF4_ENST00000584943.1_Intron|RP11-849F2.4_ENST00000585275.1_lincRNA	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	77					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						ACACAGCTTCCGCTGGATGGC	0.567													C|||	492	0.0982428	0.1694	0.098	5008	,	,		18973	0.0139		0.1024	False		,,,				2504	0.0849				p.R77C		Atlas-SNP	.											ODF4,colon,carcinoma,0,1	ODF4	23	1	0			c.C229T						PASS	.	C	CYS/ARG	627,3779	273.1+/-271.2	48,531,1624	71.0	63.0	66.0		229	2.8	0.0	17	dbSNP_130	66	961,7639	210.0+/-251.0	51,859,3390	yes	missense	ODF4	NM_153007.4	180	99,1390,5014	TT,TC,CC		11.1744,14.2306,12.2097	probably-damaging	77/258	8243598	1588,11418	2203	4300	6503	SO:0001583	missense	146852	exon1			AGCTTCCGCTGGA	AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"""cancer/testis antigen 136"""	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.229C>T	17.37:g.8243598C>T	ENSP00000331086:p.Arg77Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	120	65	0.541667	NM_153007	Q8J021	Missense_Mutation	SNP	ENST00000328248.2	37	CCDS11140.1	208	0.09523809523809523	85	0.17276422764227642	35	0.09668508287292818	9	0.015734265734265736	79	0.10422163588390501	C	12.36	1.916018	0.33815	0.142306	0.111744	ENSG00000184650	ENST00000328248	T	0.41758	0.99	4.89	2.84	0.33178	.	0.778936	0.11350	N	0.573108	T	0.00178	0.0005	L	0.42245	1.32	0.58432	P	1.0000000000287557E-6	D	0.69078	0.997	P	0.58130	0.833	T	0.06481	-1.0824	9	0.87932	D	0	-6.3939	5.6501	0.17612	0.1938:0.7066:0.0:0.0996	.	77	Q2M2E3	ODFP4_HUMAN	C	77	ENSP00000331086:R77C	ENSP00000331086:R77C	R	+	1	0	ODF4	8184323	0.013000	0.17824	0.001000	0.08648	0.003000	0.03518	0.702000	0.25631	0.615000	0.30124	0.655000	0.94253	CGC	C|0.881;T|0.119	0.119	strong		0.567	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1		
CUBN	8029	hgsc.bcm.edu	37	10	17113563	17113563	+	Silent	SNP	C	C	T	rs1801225	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	31	0	0		WXS	Illumina HiSeq	Phase_I	22	4	0.181818	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	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656511	46656511	+	Silent	SNP	A	A	G	rs9627324	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46656511A>G	ENST00000253255.5	-	1	2708	c.2709T>C	c.(2707-2709)atT>atC	p.I903I		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	903	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		ACATTGTAGAAATGGGACCAT	0.408													A|||	1229	0.245407	0.6785	0.134	5008	,	,		21872	0.001		0.16	False		,,,				2504	0.0787				p.I903I		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T2709C						PASS	.	A		2655,1751	638.7+/-397.0	794,1067,342	97.0	100.0	99.0		2709	-10.7	0.0	22	dbSNP_119	99	1259,7341	250.5+/-277.4	88,1083,3129	no	coding-synonymous	PKDREJ	NM_006071.1		882,2150,3471	GG,GA,AA		14.6395,39.7413,30.0938		903/2254	46656511	3914,9092	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			TGTAGAAATGGGA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2709T>C	22.37:g.46656511A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.733;G|0.267	0.267	strong		0.408	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
TG	7038	hgsc.bcm.edu	37	8	134108453	134108453	+	Silent	SNP	C	C	T	rs2069568	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:134108453C>T	ENST00000220616.4	+	43	7448	c.7408C>T	c.(7408-7410)Ctg>Ttg	p.L2470L	SLA_ENST00000517648.1_Intron|SLA_ENST00000395352.3_Intron|SLA_ENST00000524345.1_Intron|SLA_ENST00000338087.5_Intron|TG_ENST00000519543.1_Silent_p.L603L|TG_ENST00000542445.1_Silent_p.L840L|TG_ENST00000377869.1_Silent_p.L2413L|SLA_ENST00000518565.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2470					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)		AATGCAGCTCCTGGCCGTGAG	0.493													C|||	1726	0.344649	0.1452	0.3098	5008	,	,		21493	0.4038		0.4791	False		,,,				2504	0.4397				p.L2470L		Atlas-SNP	.											.	TG	416	.	0			c.C7408T						PASS	.	C	,,	905,3501	349.8+/-310.5	92,721,1390	169.0	159.0	163.0		,,7408	4.6	1.0	8	dbSNP_96	163	4022,4578	555.8+/-386.7	940,2142,1218	no	intron,intron,coding-synonymous	SLA,TG	NM_001045556.2,NM_001045557.2,NM_003235.4	,,	1032,2863,2608	TT,TC,CC		46.7674,20.5402,37.8825	,,	,,2470/2769	134108453	4927,8079	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon43			CAGCTCCTGGCCG	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.7408C>T	8.37:g.134108453C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	225	131	0.582222	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	820	0.37545787545787546	93	0.18902439024390244	131	0.36187845303867405	224	0.3916083916083916	372	0.49076517150395776	C	8.661	0.900554	0.17686	0.205402	0.467674	ENSG00000042832	ENST00000519178	.	.	.	5.46	4.58	0.56647	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999972	.	.	.	.	.	.	T	0.52434	-0.8576	3	.	.	.	.	10.5409	0.45033	0.0:0.9081:0.0:0.0919	rs2069568;rs3739265;rs17704072;rs2069568	.	.	.	L	925	.	.	P	+	2	0	TG	134177635	0.995000	0.38212	1.000000	0.80357	0.853000	0.48598	1.553000	0.36255	2.552000	0.86080	0.655000	0.94253	CCT	C|0.629;T|0.371	0.371	strong		0.493	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
RHBG	57127	hgsc.bcm.edu	37	1	156351699	156351699	+	Missense_Mutation	SNP	G	G	A	rs3748569	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156351699G>A	ENST00000368249.1	+	6	981	c.943G>A	c.(943-945)Ggg>Agg	p.G315R	RHBG_ENST00000368246.2_Missense_Mutation_p.G315R|RHBG_ENST00000255013.3_Missense_Mutation_p.G246R|RHBG_ENST00000451864.2_Intron|RHBG_ENST00000537040.1_Missense_Mutation_p.G153R|RHBG_ENST00000400992.2_Missense_Mutation_p.G283R	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	315			G -> R (in dbSNP:rs3748569). {ECO:0000269|PubMed:15489334}.		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)					CTTCTTGGCTGGGACTGTCTC	0.572													G|||	2728	0.544728	0.5719	0.6037	5008	,	,		18935	0.7014		0.4095	False		,,,				2504	0.4438				p.G315R		Atlas-SNP	.											.	RHBG	133	.	0			c.G943A						PASS	.	G	ARG/GLY	2175,1959		576,1023,468	95.0	106.0	103.0		943	4.4	1.0	1	dbSNP_107	103	3575,4831		782,2011,1410	yes	missense	RHBG	NM_020407.3	125	1358,3034,1878	AA,AG,GG		42.5291,47.3875,45.8533	probably-damaging	315/459	156351699	5750,6790	2067	4203	6270	SO:0001583	missense	57127	exon6			TTGGCTGGGACTG	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.943G>A	1.37:g.156351699G>A	ENSP00000357232:p.Gly315Arg	Somatic	321	2	0.00623053		WXS	Illumina HiSeq	Phase_I	412	260	0.631068	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		1209	0.5535714285714286	287	0.5833333333333334	208	0.574585635359116	403	0.7045454545454546	311	0.4102902374670185	G	26.5	4.744673	0.89663	0.526125	0.425291	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000537040;ENST00000400992;ENST00000255013	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	4.44	4.44	0.53790	Ammonium transporter AmtB-like (3);	0.049574	0.85682	D	0.000000	T	0.67325	0.2881	M	0.93763	3.455	0.09310	P	1.0	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.986;0.998;1.0;0.999	T	0.77643	-0.2511	9	0.72032	D	0.01	-1.7511	14.5902	0.68359	0.0:0.0:1.0:0.0	rs3748569;rs17855953;rs52807244;rs58877861;rs3748569	315;153;283;352	Q9H310;F5GWZ4;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.;.	R	315;315;153;283;246	ENSP00000357232:G315R;ENSP00000357229:G315R;ENSP00000441197:G153R;ENSP00000383777:G283R;ENSP00000255013:G246R	ENSP00000255013:G246R	G	+	1	0	RHBG	154618323	1.000000	0.71417	0.957000	0.39632	0.996000	0.88848	7.438000	0.80431	2.286000	0.76751	0.561000	0.74099	GGG	G|0.472;A|0.528	0.528	strong		0.572	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
CLTCL1	8218	hgsc.bcm.edu	37	22	19175133	19175133	+	Silent	SNP	C	C	A	rs187075533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:19175133C>A	ENST00000263200.10	-	29	4614	c.4542G>T	c.(4540-4542)ctG>ctT	p.L1514L	CLTCL1_ENST00000427926.1_Silent_p.L1514L|CLTCL1_ENST00000442042.2_Intron|CLTCL1_ENST00000353891.5_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1514	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TGCCCTTGTACAGATAGGCCG	0.552			T	?	ALCL								C|||	5	0.000998403	0.0038	0.0	5008	,	,		22029	0.0		0.0	False		,,,				2504	0.0				p.L1514L		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.G4542T						PASS	.	C	,	6,4122		0,6,2058	103.0	106.0	105.0		,4542	0.4	0.8	22		105	2,8402		0,2,4200	no	intron,coding-synonymous	CLTCL1	NM_001835.3,NM_007098.3	,	0,8,6258	AA,AC,CC		0.0238,0.1453,0.0638	,	,1514/1641	19175133	8,12524	2064	4202	6266	SO:0001819	synonymous_variant	8218	exon29			CTTGTACAGATAG		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.4542G>T	22.37:g.19175133C>A		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	215	108	0.502326	NM_007098	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																			C|0.999;A|0.001	0.001	strong		0.552	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
ZNF845	91664	hgsc.bcm.edu	37	19	53854397	53854397	+	Missense_Mutation	SNP	G	G	C	rs10415799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	272	0	0		WXS	Illumina HiSeq	Phase_I	231	229	0.991342	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	
ASUN	55726	hgsc.bcm.edu	37	12	27064232	27064232	+	Silent	SNP	C	C	T	rs3210635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:27064232C>T	ENST00000261191.7	-	15	2360	c.1824G>A	c.(1822-1824)gaG>gaA	p.E608E	ASUN_ENST00000539625.1_Silent_p.E507E	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	608					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)											CTTTTCCACGCTCTAAGATTC	0.328													C|||	2901	0.579273	0.5514	0.4366	5008	,	,		15972	0.7609		0.492	False		,,,				2504	0.6207				p.E608E		Atlas-SNP	.											.	.	.	.	0			c.G1824A						PASS	.	C		2267,2139	595.0+/-388.3	581,1105,517	83.0	82.0	82.0		1824	3.1	1.0	12	dbSNP_105	82	4070,4528	557.5+/-387.1	983,2104,1212	no	coding-synonymous	C12orf11	NM_018164.2		1564,3209,1729	TT,TC,CC		47.3366,48.5474,48.7312		608/707	27064232	6337,6667	2203	4299	6502	SO:0001819	synonymous_variant	55726	exon15			TCCACGCTCTAAG	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.1824G>A	12.37:g.27064232C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	135	132	0.977778	NM_018164	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Silent	SNP	ENST00000261191.7	37	CCDS8708.1																																																																																			C|0.475;T|0.525	0.525	strong		0.328	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164	
GCN1L1	10985	hgsc.bcm.edu	37	12	120591143	120591143	+	Silent	SNP	A	A	G	rs12312562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:120591143A>G	ENST00000300648.6	-	33	3948	c.3936T>C	c.(3934-3936)taT>taC	p.Y1312Y	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1312					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCACAGCATCATAGCTGGCAT	0.557													G|||	1712	0.341853	0.5053	0.1441	5008	,	,		21235	0.5546		0.1551	False		,,,				2504	0.2342				p.Y1312Y		Atlas-SNP	.											GCN1L1,colon,carcinoma,0,1	GCN1L1	207	1	0			c.T3936C						PASS	.	G		1762,2454		393,976,739	71.0	78.0	76.0		3936	-12.2	0.0	12	dbSNP_120	76	1258,7180		118,1022,3079	no	coding-synonymous	GCN1L1	NM_006836.1		511,1998,3818	GG,GA,AA		14.9087,41.7932,23.866		1312/2672	120591143	3020,9634	2108	4219	6327	SO:0001819	synonymous_variant	10985	exon33			AGCATCATAGCTG	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3936T>C	12.37:g.120591143A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																			A|0.657;G|0.343	0.343	strong		0.557	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
NINL	22981	hgsc.bcm.edu	37	20	25456698	25456698	+	Missense_Mutation	SNP	C	C	T	rs35666277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:25456698C>T	ENST00000278886.6	-	17	3302	c.3229G>A	c.(3229-3231)Gat>Aat	p.D1077N	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1077			D -> N (in dbSNP:rs35666277).		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						TCTCTCAAATCTACATGTTTC	0.448													C|||	234	0.0467252	0.0552	0.0375	5008	,	,		20678	0.0704		0.0507	False		,,,				2504	0.0133				p.D1077N		Atlas-SNP	.											.	NINL	148	.	0			c.G3229A						PASS	.	C	ASN/ASP	246,4160	143.5+/-178.5	6,234,1963	105.0	92.0	96.0		3229	0.4	0.0	20	dbSNP_126	96	346,8254	118.1+/-177.6	6,334,3960	yes	missense	NINL	NM_025176.4	23	12,568,5923	TT,TC,CC		4.0233,5.5833,4.5517	benign	1077/1383	25456698	592,12414	2203	4300	6503	SO:0001583	missense	22981	exon17			TCAAATCTACATG		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3229G>A	20.37:g.25456698C>T	ENSP00000278886:p.Asp1077Asn	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	190	95	0.5	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	112	0.05128205128205128	25	0.0508130081300813	16	0.04419889502762431	33	0.057692307692307696	38	0.05013192612137203	C	3.038	-0.198210	0.06219	0.055833	0.040233	ENSG00000101004	ENST00000278886	T	0.05717	3.4	4.85	0.428	0.16499	.	1.212680	0.05789	N	0.610003	T	0.00524	0.0017	N	0.19112	0.55	0.09310	N	1	B	0.18741	0.03	B	0.20767	0.031	T	0.43814	-0.9368	10	0.56958	D	0.05	-1.439	4.2465	0.10674	0.1553:0.4901:0.0:0.3546	rs35666277	1077	Q9Y2I6	NINL_HUMAN	N	1077	ENSP00000278886:D1077N	ENSP00000278886:D1077N	D	-	1	0	NINL	25404698	0.080000	0.21391	0.001000	0.08648	0.013000	0.08279	0.133000	0.15912	0.462000	0.27095	0.561000	0.74099	GAT	C|0.953;T|0.047	0.047	strong		0.448	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
TLR8	51311	hgsc.bcm.edu	37	X	12937513	12937513	+	Silent	SNP	C	C	T	rs2159377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:12937513C>T	ENST00000218032.6	+	2	441	c.354C>T	c.(352-354)gaC>gaT	p.D118D	TLR8_ENST00000311912.5_Silent_p.D136D	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	118					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	ATATCACAGACGGGGCATTCC	0.428													C|||	1412	0.37404	0.1316	0.219	3775	,	,		13960	0.5774		0.1322	False		,,,				2504	0.3793				p.D118D		Atlas-SNP	.											.	TLR8	134	.	0			c.C354T						PASS	.	C		534,3301		39,380,76,1213,495	114.0	117.0	116.0		354	-5.5	0.1	X	dbSNP_96	116	1169,5559		70,727,302,1631,1570	no	coding-synonymous	TLR8	NM_138636.4		109,1107,378,2844,2065	TT,TC,T,CC,C		17.3751,13.9244,16.1223		118/1042	12937513	1703,8860	2203	4300	6503	SO:0001819	synonymous_variant	51311	exon2			CACAGACGGGGCA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.354C>T	X.37:g.12937513C>T		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	70	68	0.971429	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																			C|0.738;0|0.006	.	strong		0.428	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
KRTAP6-1	337966	hgsc.bcm.edu	37	21	31986163	31986163	+	Missense_Mutation	SNP	C	C	T	rs138494765		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31986163C>T	ENST00000329122.2	-	1	86	c.61G>A	c.(61-63)Gga>Aga	p.G21R	KRTAP20-1_ENST00000334664.2_5'Flank	NM_181602.1	NP_853633.1	Q3LI64	KRA61_HUMAN	keratin associated protein 6-1	21						cytosol (GO:0005829)|intermediate filament (GO:0005882)				breast(2)|endometrium(1)|lung(7)	10						CCCAGGCCTCCATAGCCACAG	0.592																																					p.G21R		Atlas-SNP	.											.	KRTAP6-1	21	.	0			c.G61A						PASS	.	C	ARG/GLY	0,4406		0,0,2203	181.0	178.0	179.0		61	3.1	1.0	21	dbSNP_134	179	2,8598	2.2+/-6.3	0,2,4298	yes	missense	KRTAP6-1	NM_181602.1	125	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	21/72	31986163	2,13004	2203	4300	6503	SO:0001583	missense	337966	exon1			GGCCTCCATAGCC	AP001708	CCDS13602.1	21q22.1	2006-03-13			ENSG00000184724	ENSG00000184724		"""Keratin associated proteins"""	18931	protein-coding gene	gene with protein product						12359730	Standard	NM_181602		Approved	KAP6.1, C21orf103	uc002yop.3	Q3LI64	OTTHUMG00000057788	ENST00000329122.2:c.61G>A	21.37:g.31986163C>T	ENSP00000332690:p.Gly21Arg	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	383	158	0.412533	NM_181602		Missense_Mutation	SNP	ENST00000329122.2	37	CCDS13602.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.802250	0.31869	0.0	2.33E-4	ENSG00000184724	ENST00000329122	T	0.23552	1.9	4.91	3.08	0.35506	.	0.237368	0.21800	U	0.068932	T	0.20740	0.0499	.	.	.	0.26580	N	0.973391	B	0.28552	0.215	B	0.28991	0.097	T	0.17899	-1.0354	9	0.87932	D	0	.	8.6058	0.33773	0.0:0.7606:0.1541:0.0853	.	21	Q3LI64	KRA61_HUMAN	R	21	ENSP00000332690:G21R	ENSP00000332690:G21R	G	-	1	0	KRTAP6-1	30908034	0.000000	0.05858	0.982000	0.44146	0.940000	0.58332	-1.080000	0.03407	0.786000	0.33708	0.643000	0.83706	GGA	C|1.000;T|0.000	0.000	weak		0.592	KRTAP6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128240.2	NM_181602	
EPS8L1	54869	hgsc.bcm.edu	37	19	55587822	55587822	+	Missense_Mutation	SNP	G	G	A	rs12609976	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55587822G>A	ENST00000201647.6	+	2	66	c.10G>A	c.(10-12)Gcc>Acc	p.A4T	EPS8L1_ENST00000540810.1_5'UTR|EPS8L1_ENST00000586329.1_Intron|EPS8L1_ENST00000592824.1_3'UTR	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	4			A -> T (in dbSNP:rs12609976). {ECO:0000269|PubMed:12620401, ECO:0000269|PubMed:15498874}.		positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CATGAGCACCGCCACAGGGTA	0.672													N|||	489	0.0976438	0.0408	0.1455	5008	,	,		12199	0.1002		0.162	False		,,,				2504	0.0716				p.A4T	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											EPS8L1,NS,carcinoma,0,1	EPS8L1	122	1	0			c.G10A						scavenged	.		THR/ALA	237,4167		12,213,1977	35.0	40.0	39.0		10	2.5	0.6	19	dbSNP_120	39	1436,7162		141,1154,3004	yes	missense	EPS8L1	NM_133180.2	58	153,1367,4981	AA,AG,GG		16.7016,5.3815,12.8673	benign	4/724	55587822	1673,11329	2202	4299	6501	SO:0001583	missense	54869	exon2			AGCACCGCCACAG	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.10G>A	19.37:g.55587822G>A	ENSP00000201647:p.Ala4Thr	Somatic	310	3	0.00967742		WXS	Illumina HiSeq	Phase_I	274	150	0.547445	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	267	0.12225274725274725	17	0.034552845528455285	56	0.15469613259668508	62	0.10839160839160839	132	0.1741424802110818	N	4.224	0.040468	0.08148	0.053815	0.167016	ENSG00000131037	ENST00000201647	T	0.04275	3.66	2.54	2.54	0.30619	.	1.601540	0.05427	N	0.545204	T	0.00012	0.0000	N	0.08118	0	0.35532	P	0.197631	B	0.02656	0.0	B	0.01281	0.0	T	0.40887	-0.9539	9	0.02654	T	1	-1.0811	4.8871	0.13708	0.8496:0.0:0.1504:0.0	rs12609976;rs57914190;rs12609976	4	Q8TE68	ES8L1_HUMAN	T	4	ENSP00000201647:A4T	ENSP00000201647:A4T	A	+	1	0	EPS8L1	60279634	0.000000	0.05858	0.570000	0.28473	0.481000	0.33189	-0.017000	0.12590	0.409000	0.25649	-1.729000	0.00701	GCC	G|0.878;A|0.122	0.122	strong		0.672	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
RELN	5649	hgsc.bcm.edu	37	7	103292201	103292201	+	Missense_Mutation	SNP	G	G	A	rs78008536	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:103292201G>A	ENST00000428762.1	-	15	1958	c.1799C>T	c.(1798-1800)tCc>tTc	p.S600F	RELN_ENST00000343529.5_Missense_Mutation_p.S600F|RELN_ENST00000424685.2_Missense_Mutation_p.S600F	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	600					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)		GAGGGACCAGGAGCGCCCATG	0.473													G|||	30	0.00599042	0.0008	0.013	5008	,	,		15954	0.0		0.0169	False		,,,				2504	0.0031				p.S600F	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C1799T						PASS	.	G	PHE/SER,PHE/SER	12,4394	19.1+/-41.9	0,12,2191	72.0	58.0	63.0		1799,1799	5.8	1.0	7	dbSNP_131	63	130,8470	66.3+/-128.7	1,128,4171	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	155,155	1,140,6362	AA,AG,GG		1.5116,0.2724,1.0918	probably-damaging,probably-damaging	600/3461,600/3459	103292201	142,12864	2203	4300	6503	SO:0001583	missense	5649	exon15			GACCAGGAGCGCC		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.1799C>T	7.37:g.103292201G>A	ENSP00000392423:p.Ser600Phe	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	19	0.0086996336996337	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	13	0.017150395778364115	G	26.8	4.768385	0.90020	0.002724	0.015116	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.34072	1.38;1.38;1.38	5.8	5.8	0.92144	.	0.055760	0.85682	D	0.000000	T	0.30947	0.0781	L	0.47016	1.485	0.51767	D	0.999932	P;P	0.52061	0.95;0.612	P;B	0.54238	0.746;0.424	T	0.20907	-1.0261	10	0.87932	D	0	.	15.5384	0.76021	0.0:0.1373:0.8627:0.0	.	600;600	P78509-2;P78509	.;RELN_HUMAN	F	600	ENSP00000392423:S600F;ENSP00000345694:S600F;ENSP00000388446:S600F	ENSP00000345694:S600F	S	-	2	0	RELN	103079437	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.513000	0.81739	2.758000	0.94735	0.563000	0.77884	TCC	G|0.990;A|0.010	0.010	strong		0.473	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
ZNF471	57573	hgsc.bcm.edu	37	19	57036012	57036012	+	Missense_Mutation	SNP	G	G	T	rs11667052	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57036012G>T	ENST00000308031.5	+	5	709	c.576G>T	c.(574-576)atG>atT	p.M192I	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	192			M -> I (in dbSNP:rs11667052). {ECO:0000269|PubMed:10718198}.		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		AAAATTCTATGGTAATAAAAC	0.299													G|||	920	0.183706	0.2337	0.1398	5008	,	,		18537	0.0526		0.2813	False		,,,				2504	0.182				p.M192I	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.G576T						PASS	.	G	ILE/MET	1006,3392		119,768,1312	26.0	28.0	27.0		576	1.7	0.0	19	dbSNP_120	27	2159,6419		308,1543,2438	yes	missense	ZNF471	NM_020813.2	10	427,2311,3750	TT,TG,GG		25.169,22.874,24.3912	benign	192/627	57036012	3165,9811	2199	4289	6488	SO:0001583	missense	57573	exon5			TTCTATGGTAATA	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.576G>T	19.37:g.57036012G>T	ENSP00000309161:p.Met192Ile	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	428	0.19597069597069597	120	0.24390243902439024	59	0.16298342541436464	34	0.05944055944055944	215	0.2836411609498681	G	1.290	-0.607754	0.03717	0.22874	0.25169	ENSG00000196263	ENST00000308031	T	0.14516	2.5	3.87	1.71	0.24356	.	.	.	.	.	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46205	-0.9208	8	0.23302	T	0.38	.	6.9352	0.24463	0.3009:0.0:0.6991:0.0	rs11667052;rs52814044;rs58037293;rs11667052	192	Q9BX82	ZN471_HUMAN	I	192	ENSP00000309161:M192I	ENSP00000309161:M192I	M	+	3	0	ZNF471	61727824	.	.	0.001000	0.08648	0.789000	0.44602	.	.	0.427000	0.26145	-0.253000	0.11424	ATG	G|0.792;T|0.208	0.208	strong		0.299	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
TUBB6	84617	hgsc.bcm.edu	37	18	12308793	12308793	+	Splice_Site	SNP	G	G	C	rs11267036	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:12308793G>C	ENST00000317702.5	+	2	399	c.165G>C	c.(163-165)tcG>tcC	p.S55S	TUBB6_ENST00000590967.1_Splice_Site_p.S55S|TUBB6_ENST00000591909.1_Splice_Site_p.S55S|TUBB6_ENST00000586653.1_Splice_Site_p.S55S|TUBB6_ENST00000592683.1_Splice_Site_p.S55S|TUBB6_ENST00000591208.1_Splice_Site_p.S55S			Q9BUF5	TBB6_HUMAN	tubulin, beta 6 class V	55					'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)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)	14				READ - Rectum adenocarcinoma(1;0.0649)		ATGAGTCATCGTGTGAGTAGC	0.642													G|||	648	0.129393	0.084	0.1801	5008	,	,		10583	0.1478		0.1322	False		,,,				2504	0.1329				p.S55S		Atlas-SNP	.											.	TUBB6	35	.	0			c.G165C						PASS	.	G		356,4050	181.2+/-209.3	12,332,1859	46.0	47.0	46.0		165	-7.4	0.8	18	dbSNP_120	46	968,7632	207.9+/-249.5	49,870,3381	yes	coding-synonymous-near-splice	TUBB6	NM_032525.1		61,1202,5240	CC,CG,GG		11.2558,8.0799,10.1799		55/447	12308793	1324,11682	2203	4300	6503	SO:0001630	splice_region_variant	84617	exon2			GTCATCGTGTGAG	AK001295	CCDS11858.1	18p11.21	2011-10-10	2011-10-10		ENSG00000176014	ENSG00000176014		"""Tubulins"""	20776	protein-coding gene	gene with protein product	"""tubulin beta MGC4083"", ""class V beta-tubulin"""	615103	"""tubulin, beta 6"""			12477932	Standard	NM_032525		Approved	MGC4083, HsT1601	uc002kqw.3	Q9BUF5	OTTHUMG00000131692	ENST00000317702.5:c.166+1G>C	18.37:g.12308793G>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_032525	B3KM76|Q9HA42	Silent	SNP	ENST00000317702.5	37	CCDS11858.1																																																																																			G|0.887;C|0.113	0.113	strong		0.642	TUBB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254600.2	NM_032525	Silent
MOK	5891	hgsc.bcm.edu	37	14	102698131	102698131	+	Silent	SNP	G	G	A	rs7152550	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102698131G>A	ENST00000361847.2	-	10	1125	c.894C>T	c.(892-894)agC>agT	p.S298S	MOK_ENST00000522874.1_Silent_p.S297S|MOK_ENST00000519058.1_Intron|MOK_ENST00000522867.1_Intron|MOK_ENST00000524370.1_Intron|MOK_ENST00000517966.1_Intron|MOK_ENST00000520266.1_Intron|MOK_ENST00000524214.1_Silent_p.S268S|MOK_ENST00000561150.1_Intron|MOK_ENST00000523231.1_Intron|MOK_ENST00000522534.1_Intron|MOK_ENST00000193029.6_Intron	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	298					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)										CTTTTCTGTGGCTGCCCAGAG	0.567													G|||	279	0.0557109	0.0166	0.049	5008	,	,		17613	0.003		0.0795	False		,,,				2504	0.1431				p.S298S		Atlas-SNP	.											.	.	.	.	0			c.C894T						PASS	.	G		121,4285	89.7+/-128.4	1,119,2083	108.0	110.0	109.0		894	-1.0	0.0	14	dbSNP_116	109	617,7983	161.4+/-214.4	17,583,3700	no	coding-synonymous	MOK	NM_014226.1		18,702,5783	AA,AG,GG		7.1744,2.7463,5.6743		298/420	102698131	738,12268	2203	4300	6503	SO:0001819	synonymous_variant	5891	exon10			TCTGTGGCTGCCC	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.894C>T	14.37:g.102698131G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Silent	SNP	ENST00000361847.2	37	CCDS9971.1	81	0.03708791208791209	10	0.02032520325203252	21	0.058011049723756904	2	0.0034965034965034965	48	0.0633245382585752	G	4.163	0.028658	0.08054	0.027463	0.071744	ENSG00000080823	ENST00000521937	.	.	.	4.73	-1.03	0.10102	.	.	.	.	.	T	0.01661	0.0053	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.17531	-1.0366	4	.	.	.	-17.238	4.5829	0.12267	0.0905:0.4589:0.3077:0.1429	rs7152550;rs7152550	.	.	.	S	10	.	.	P	-	1	0	RAGE	101767884	0.002000	0.14202	0.000000	0.03702	0.025000	0.11179	0.206000	0.17375	-0.088000	0.12506	-0.391000	0.06502	CCA	G|0.951;A|0.049	0.049	strong		0.567	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
KIF26A	26153	hgsc.bcm.edu	37	14	104642422	104642422	+	Silent	SNP	A	A	G	rs3742947	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104642422A>G	ENST00000423312.2	+	12	3297	c.3297A>G	c.(3295-3297)gcA>gcG	p.A1099A	KIF26A_ENST00000315264.7_Silent_p.A960A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1099					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		TGGAGGGGGCAGCCTGGGCCG	0.687													G|||	1559	0.311302	0.1437	0.3617	5008	,	,		14259	0.4067		0.3062	False		,,,				2504	0.409				p.A1099A		Atlas-SNP	.											.	KIF26A	84	.	0			c.A3297G						PASS	.	G		464,2976		33,398,1289	4.0	6.0	6.0		3297	-8.6	0.0	14	dbSNP_107	6	2073,5659		312,1449,2105	no	coding-synonymous	KIF26A	NM_015656.1		345,1847,3394	GG,GA,AA		26.8107,13.4884,22.7086		1099/1883	104642422	2537,8635	1720	3866	5586	SO:0001819	synonymous_variant	26153	exon12			GGGGGCAGCCTGG	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.3297A>G	14.37:g.104642422A>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	21	7	0.333333	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			A|0.697;G|0.303	0.303	strong		0.687	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
C1orf87	127795	hgsc.bcm.edu	37	1	60503762	60503762	+	Silent	SNP	T	T	C	rs17560663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:60503762T>C	ENST00000371201.3	-	6	872	c.765A>G	c.(763-765)ctA>ctG	p.L255L	C1orf87_ENST00000450089.2_Intron	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87	255							calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						AAAACCAGAGTAGCTTTTCAT	0.353													T|||	404	0.0806709	0.0113	0.1282	5008	,	,		17242	0.0218		0.1859	False		,,,				2504	0.093				p.L255L	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.A765G						PASS	.	T		151,4255	102.5+/-141.1	4,143,2056	75.0	69.0	71.0		765	-4.0	0.9	1	dbSNP_123	71	1480,7120	279.8+/-294.2	137,1206,2957	no	coding-synonymous	C1orf87	NM_152377.2		141,1349,5013	CC,CT,TT		17.2093,3.4271,12.5404		255/547	60503762	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	127795	exon6			CCAGAGTAGCTTT	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.765A>G	1.37:g.60503762T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	33	31	0.939394	NM_152377	Q6ZU07|Q8IVS0	Silent	SNP	ENST00000371201.3	37	CCDS614.1																																																																																			T|0.897;C|0.103	0.103	strong		0.353	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	
MUC4	4585	hgsc.bcm.edu	37	3	195507251	195507251	+	Missense_Mutation	SNP	G	G	T	rs201456607|rs74187968		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195507251G>T	ENST00000463781.3	-	2	11659	c.11200C>A	c.(11200-11202)Cct>Act	p.P3734T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3734T	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	308	14	0.0454545		WXS	Illumina HiSeq	Phase_I	419	43	0.102625	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	
CEP350	9857	hgsc.bcm.edu	37	1	180000542	180000542	+	Missense_Mutation	SNP	G	G	T	rs12125245	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:180000542G>T	ENST00000367607.3	+	15	4056	c.3638G>T	c.(3637-3639)gGg>gTg	p.G1213V		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	1213	Ser-rich.		G -> V (in dbSNP:rs12125245).		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						AAGAAATCTGGGACCAGCAGC	0.393													G|||	258	0.0515176	0.0045	0.062	5008	,	,		11324	0.0139		0.1123	False		,,,				2504	0.0838				p.G1213V		Atlas-SNP	.											.	CEP350	418	.	0			c.G3638T						PASS	.	G	VAL/GLY	114,4292	83.9+/-122.4	1,112,2090	49.0	50.0	50.0		3638	5.1	1.0	1	dbSNP_120	50	1038,7562	217.6+/-256.2	81,876,3343	yes	missense	CEP350	NM_014810.4	109	82,988,5433	TT,TG,GG		12.0698,2.5874,8.8575	benign	1213/3118	180000542	1152,11854	2203	4300	6503	SO:0001583	missense	9857	exon15			AATCTGGGACCAG	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.3638G>T	1.37:g.180000542G>T	ENSP00000356579:p.Gly1213Val	Somatic	388	1	0.00257732		WXS	Illumina HiSeq	Phase_I	456	297	0.651316	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	120	0.054945054945054944	4	0.008130081300813009	23	0.06353591160220995	2	0.0034965034965034965	91	0.12005277044854881	G	8.716	0.913218	0.17907	0.025874	0.120698	ENSG00000135837	ENST00000367607	T	0.55930	0.49	6.02	5.05	0.67936	.	0.153716	0.29638	N	0.011596	T	0.00468	0.0015	N	0.11560	0.145	0.22541	P	0.999003279	B;B	0.13145	0.007;0.001	B;B	0.10450	0.005;0.002	T	0.04229	-1.0967	8	.	.	.	.	13.8485	0.63481	0.0:0.0:0.7807:0.2193	rs12125245;rs52816080;rs58708432;rs12125245	1213;1213	E7EU22;Q5VT06	.;CE350_HUMAN	V	1213	ENSP00000356579:G1213V	.	G	+	2	0	CEP350	178267165	0.993000	0.37304	1.000000	0.80357	0.841000	0.47740	2.281000	0.43452	2.850000	0.98022	0.650000	0.86243	GGG	G|0.929;T|0.071	0.071	strong		0.393	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
OR8K5	219453	hgsc.bcm.edu	37	11	55927584	55927584	+	Missense_Mutation	SNP	A	A	T	rs141612231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55927584A>T	ENST00000313447.1	-	1	209	c.210T>A	c.(208-210)gaT>gaA	p.D70E		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	70						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)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				AATTACCAAGATCAACAAAAG	0.403													A|||	5	0.000998403	0.0015	0.0	5008	,	,		21723	0.0		0.003	False		,,,				2504	0.0				p.D70E		Atlas-SNP	.											.	OR8K5	82	.	0			c.T210A						PASS	.	A	GLU/ASP	4,4398	8.1+/-20.4	0,4,2197	109.0	108.0	109.0		210	-1.8	1.0	11	dbSNP_134	109	44,8548	29.6+/-80.5	0,44,4252	yes	missense	OR8K5	NM_001004058.2	45	0,48,6449	TT,TA,AA		0.5121,0.0909,0.3694	probably-damaging	70/308	55927584	48,12946	2201	4296	6497	SO:0001583	missense	219453	exon1			ACCAAGATCAACA	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.210T>A	11.37:g.55927584A>T	ENSP00000323853:p.Asp70Glu	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	193	99	0.512953	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	15.04	2.715189	0.48622	9.09E-4	0.005121	ENSG00000181752	ENST00000313447	T	0.01152	5.26	3.87	-1.8	0.07907	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01976	0.0062	L	0.43701	1.375	0.23260	N	0.998023	D	0.89917	1.0	D	0.83275	0.996	T	0.45381	-0.9265	9	0.87932	D	0	.	4.7748	0.13173	0.4794:0.0:0.3737:0.1469	.	70	Q8NH50	OR8K5_HUMAN	E	70	ENSP00000323853:D70E	ENSP00000323853:D70E	D	-	3	2	OR8K5	55684160	0.000000	0.05858	0.991000	0.47740	0.512000	0.34134	-1.621000	0.02044	-0.081000	0.12662	-0.377000	0.06932	GAT	A|0.998;T|0.002	0.002	strong		0.403	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058	
PRDM2	7799	hgsc.bcm.edu	37	1	14105139	14105139	+	Missense_Mutation	SNP	T	T	A	rs2076324|rs369010172	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:14105139T>A	ENST00000235372.7	+	8	1705	c.849T>A	c.(847-849)gaT>gaA	p.D283E	PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000311066.5_Missense_Mutation_p.D283E|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.D82E|PRDM2_ENST00000343137.4_Missense_Mutation_p.D82E	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	283	Asp/Glu-rich (acidic).		D -> E (in dbSNP:rs2076324).	EDEEEEEDDDDDELEDEG -> VGGGGGVVVVVSWKARGE (in Ref. 6; AAA87023). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		aagaagaagatgatgatgatg	0.483													A|||	1859	0.371206	0.208	0.5375	5008	,	,		20316	0.3988		0.327	False		,,,				2504	0.4908				p.D283E		Atlas-SNP	.											.	PRDM2	147	.	0			c.T849A						PASS	.	A	GLU/ASP,,GLU/ASP,GLU/ASP	1104,3302	717.2+/-408.7	142,820,1241	63.0	64.0	63.0		246,,849,849	-3.6	0.5	1	dbSNP_96	63	3066,5534	652.7+/-401.0	525,2016,1759	yes	missense,intron,missense,missense	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	45,,45,45	667,2836,3000	AA,AT,TT		35.6512,25.0567,32.0621	benign,,benign,benign	82/1482,,283/1719,283/1683	14105139	4170,8836	2203	4300	6503	SO:0001583	missense	7799	exon8			AGAAGATGATGAT	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.849T>A	1.37:g.14105139T>A	ENSP00000235372:p.Asp283Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	57	13	0.22807	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	771	0.35302197802197804	99	0.20121951219512196	186	0.5138121546961326	243	0.42482517482517484	243	0.32058047493403696	A	0.003	-2.513786	0.00151	0.250567	0.356512	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.01446	4.98;4.88;4.91;4.91	2.02	-3.62	0.04543	.	0.430301	0.17431	N	0.174473	T	0.00012	0.0000	N	0.00742	-1.23	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.12013	0.003;0.0;0.003;0.005	B;B;B;B	0.06405	0.001;0.0;0.001;0.002	T	0.11743	-1.0575	9	0.02654	T	1	.	3.3022	0.06987	0.2462:0.0:0.158:0.5958	rs62648362	283;141;283;283	A8MW16;Q5THJ0;Q13029;Q13029-2	.;.;PRDM2_HUMAN;.	E	283;283;283;82;82	ENSP00000235372:D283E;ENSP00000312352:D283E;ENSP00000411103:D82E;ENSP00000341621:D82E	ENSP00000235372:D283E	D	+	3	2	PRDM2	13977726	0.931000	0.31567	0.455000	0.27031	0.122000	0.20287	-0.258000	0.08733	-1.465000	0.01899	-0.376000	0.06991	GAT	T|0.662;A|0.338	0.338	strong		0.483	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52115645	52115645	+	Missense_Mutation	SNP	G	G	C	rs3829655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52115645G>C	ENST00000534261.2	-	10	1894	c.1495C>G	c.(1495-1497)Ccc>Gcc	p.P499A	SIGLEC5_ENST00000570106.2_Missense_Mutation_p.P499A|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.P499A|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.P499A|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.P499A			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	499			P -> A (in dbSNP:rs3829655). {ECO:0000269|PubMed:15489334}.		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)		TGATCTCCGGGGCTGTCTGGC	0.498													G|||	2180	0.435304	0.3275	0.4683	5008	,	,		19086	0.5794		0.4225	False		,,,				2504	0.4223				p.P499A		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.C1495G						PASS	.	G	ALA/PRO	1423,2983	460.7+/-352.7	244,935,1024	72.0	75.0	74.0		1495	-1.3	0.0	19	dbSNP_107	74	3753,4847	527.6+/-381.2	800,2153,1347	yes	missense	SIGLEC5	NM_003830.2	27	1044,3088,2371	CC,CG,GG		43.6395,32.2969,39.797	benign	499/552	52115645	5176,7830	2203	4300	6503	SO:0001583	missense	8778	exon9			CTCCGGGGCTGTC	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.1495C>G	19.37:g.52115645G>C	ENSP00000473238:p.Pro499Ala	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	970	0.4441391941391941	151	0.30691056910569103	166	0.4585635359116022	319	0.5576923076923077	334	0.44063324538258575	G	8.436	0.849683	0.17034	0.322969	0.436395	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.59364	0.27;0.27	3.52	-1.27	0.09347	.	.	.	.	.	T	0.00012	0.0000	M	0.64567	1.98	0.80722	P	0.0	P	0.52463	0.953	B	0.42462	0.388	T	0.40270	-0.9572	8	0.52906	T	0.07	.	1.8675	0.03201	0.1081:0.1749:0.3589:0.3581	rs3829655;rs17852717;rs3829655	499	O15389	SIGL5_HUMAN	A	499	ENSP00000222107:P499A;ENSP00000415200:P499A	ENSP00000222107:P499A	P	-	1	0	SIGLEC5	56807457	0.005000	0.15991	0.005000	0.12908	0.005000	0.04900	0.278000	0.18753	-0.109000	0.12044	-0.152000	0.13540	CCC	G|0.577;C|0.423	0.423	strong		0.498	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561340	32561340	+	Missense_Mutation	SNP	G	G	A	rs78337553		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:32561340G>A	ENST00000345122.3	+	2	1780	c.1465G>A	c.(1465-1467)Gag>Aag	p.E489K	ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.E489K|ARHGAP5_ENST00000432921.1_Missense_Mutation_p.E489K|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.E489K|ARHGAP5_ENST00000396582.2_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	489	FF 4.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.E489K(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AGCCAAAGAAGAGTTTCAAGA	0.343																																					p.E489K	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											ARHGAP5,NS,carcinoma,0,1	ARHGAP5	166	1	1	Substitution - Missense(1)	stomach(1)	c.G1465A						PASS	.						60.0	61.0	61.0					14																	32561340		2203	4298	6501	SO:0001583	missense	394	exon2			AAAGAAGAGTTTC	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1465G>A	14.37:g.32561340G>A	ENSP00000371897:p.Glu489Lys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	160	11	0.06875	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741262	0.69304	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	6.02	6.02	0.97574	FF domain (2);	0.044905	0.85682	D	0.000000	T	0.39009	0.1062	N	0.22421	0.69	0.80722	D	1	P;P	0.42296	0.734;0.775	P;P	0.52066	0.562;0.689	T	0.11060	-1.0603	10	0.62326	D	0.03	.	20.547	0.99278	0.0:0.0:1.0:0.0	.	489;489	Q13017-2;Q13017	.;RHG05_HUMAN	K	489	ENSP00000452222:E489K;ENSP00000441692:E489K;ENSP00000371897:E489K;ENSP00000393307:E489K	ENSP00000371897:E489K	E	+	1	0	ARHGAP5	31631091	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.850000	0.98022	0.650000	0.86243	GAG	G|0.999;A|0.001	0.001	weak		0.343	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
TCN1	6947	hgsc.bcm.edu	37	11	59623433	59623433	+	Silent	SNP	G	G	A	rs1042613	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:59623433G>A	ENST00000257264.3	-	6	950	c.846C>T	c.(844-846)agC>agT	p.S282S	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	282	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)	p.S282S(1)		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)	CGTTTGGATTGCTGAATGCTC	0.433													a|||	1491	0.297724	0.5484	0.1556	5008	,	,		17327	0.1607		0.2266	False		,,,				2504	0.274				p.S282S		Atlas-SNP	.											TCN1,NS,carcinoma,0,1	TCN1	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C846T						PASS	.			2036,2366	610.4+/-391.6	470,1096,635	129.0	130.0	130.0		846	2.2	0.0	11	dbSNP_86	130	1898,6692	727.3+/-406.6	211,1476,2608	no	coding-synonymous	TCN1	NM_001062.3		681,2572,3243	AA,AG,GG		22.0955,46.2517,30.2802		282/434	59623433	3934,9058	2201	4295	6496	SO:0001819	synonymous_variant	6947	exon6			TGGATTGCTGAAT	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.846C>T	11.37:g.59623433G>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	180	86	0.477778	NM_001062	A8KAC5|Q8WV77	Silent	SNP	ENST00000257264.3	37	CCDS7978.1																																																																																			G|0.704;A|0.296	0.296	strong		0.433	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062	
B3GNTL1	146712	hgsc.bcm.edu	37	17	81006629	81006629	+	Silent	SNP	C	C	T	rs7406119	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:81006629C>T	ENST00000320865.3	-	2	106	c.93G>A	c.(91-93)ccG>ccA	p.P31P	B3GNTL1_ENST00000576599.1_De_novo_Start_OutOfFrame|B3GNTL1_ENST00000571954.1_5'UTR	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	31							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)			CGTCCAGCCACGGTTCAGCGT	0.423													C|||	968	0.193291	0.2194	0.1628	5008	,	,		21632	0.2073		0.2177	False		,,,				2504	0.1401				p.P31P		Atlas-SNP	.											.	B3GNTL1	40	.	0			c.G93A						PASS	.	C		881,3525	343.8+/-307.8	90,701,1412	91.0	91.0	91.0		93	-8.3	0.0	17	dbSNP_116	91	2081,6519	359.5+/-331.6	256,1569,2475	no	coding-synonymous	B3GNTL1	NM_001009905.1		346,2270,3887	TT,TC,CC		24.1977,19.9955,22.7741		31/362	81006629	2962,10044	2203	4300	6503	SO:0001819	synonymous_variant	146712	exon2			CAGCCACGGTTCA	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.93G>A	17.37:g.81006629C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	161	88	0.546584	NM_001009905	Q6GV30|Q8WUT3	Silent	SNP	ENST00000320865.3	37	CCDS32778.1																																																																																			C|0.782;T|0.218	0.218	strong		0.423	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
GTSE1	51512	hgsc.bcm.edu	37	22	46712077	46712077	+	Silent	SNP	C	C	T	rs9615947	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46712077C>T	ENST00000454366.1	+	7	1412	c.1200C>T	c.(1198-1200)gtC>gtT	p.V400V		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	381					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		CCAAGCGGGTCGATGTTTCTG	0.657													C|||	203	0.0405351	0.0038	0.0576	5008	,	,		12399	0.003		0.1223	False		,,,				2504	0.0327				p.V400V	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.C1200T						PASS	.	C		82,4324		2,78,2123	32.0	36.0	35.0		1200	-7.1	0.0	22	dbSNP_119	35	900,7696		48,804,3446	no	coding-synonymous	GTSE1	NM_016426.6		50,882,5569	TT,TC,CC		10.47,1.8611,7.5527		400/740	46712077	982,12020	2203	4298	6501	SO:0001819	synonymous_variant	51512	exon7			GCGGGTCGATGTT	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1200C>T	22.37:g.46712077C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	91	34	0.373626	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	37	CCDS14074.2																																																																																			C|0.933;T|0.067	0.067	strong		0.657	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
ZNF460	10794	hgsc.bcm.edu	37	19	57802824	57802824	+	Silent	SNP	G	G	A	rs2041110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57802824G>A	ENST00000360338.3	+	3	1237	c.915G>A	c.(913-915)aaG>aaA	p.K305K	ZNF460_ENST00000537645.1_Silent_p.K264K	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	305					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(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		ACAATGAGAAGAAACCCTTCG	0.463													a|||	933	0.186302	0.0983	0.3084	5008	,	,		23078	0.1657		0.2515	False		,,,				2504	0.1728				p.K305K		Atlas-SNP	.											.	ZNF460	59	.	0			c.G915A						PASS	.	A		534,3872	776.9+/-414.2	29,476,1698	100.0	89.0	93.0		915	-3.0	0.0	19	dbSNP_94	93	2197,6403	711.0+/-405.8	294,1609,2397	no	coding-synonymous	ZNF460	NM_006635.3		323,2085,4095	AA,AG,GG		25.5465,12.1198,20.998		305/563	57802824	2731,10275	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TGAGAAGAAACCC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.915G>A	19.37:g.57802824G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			G|0.806;A|0.194	0.194	strong		0.463	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
PLD2	5338	hgsc.bcm.edu	37	17	4722785	4722785	+	Silent	SNP	G	G	A	rs1052751	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4722785G>A	ENST00000263088.6	+	23	2501	c.2370G>A	c.(2368-2370)ctG>ctA	p.L790L	PLD2_ENST00000572940.1_Silent_p.L790L	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	790					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)	TGGCCGTGCTGATCGAGGACA	0.602													G|||	605	0.120807	0.1293	0.1715	5008	,	,		18999	0.0427		0.1829	False		,,,				2504	0.09				p.L790L		Atlas-SNP	.											.	PLD2	138	.	0			c.G2370A						PASS	.	G		510,3896	234.9+/-247.6	33,444,1726	107.0	79.0	88.0		2370	3.4	1.0	17	dbSNP_86	88	1459,7141	278.7+/-293.6	136,1187,2977	no	coding-synonymous	PLD2	NM_002663.4		169,1631,4703	AA,AG,GG		16.9651,11.5751,15.1392		790/934	4722785	1969,11037	2203	4300	6503	SO:0001819	synonymous_variant	5338	exon23			CGTGCTGATCGAG	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.2370G>A	17.37:g.4722785G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Silent	SNP	ENST00000263088.6	37	CCDS11057.1																																																																																			G|0.863;A|0.137	0.137	strong		0.602	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
PTGDR	5729	hgsc.bcm.edu	37	14	52735108	52735108	+	Silent	SNP	C	C	T	rs34968651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:52735108C>T	ENST00000306051.2	+	1	678	c.576C>T	c.(574-576)ggC>ggT	p.G192G	PTGDR_ENST00000553372.1_Silent_p.G192G	NM_000953.2	NP_000944.1	Q13258	PD2R_HUMAN	prostaglandin D2 receptor (DP)	192					adenosine metabolic process (GO:0046085)|cellular response to prostaglandin D stimulus (GO:0071799)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|male sex determination (GO:0030238)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin D receptor activity (GO:0004956)|prostaglandin J receptor activity (GO:0001785)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	ACGAGGAGGGCTCGCTGTCGG	0.627													C|||	406	0.0810703	0.0068	0.0519	5008	,	,		17584	0.123		0.0905	False		,,,				2504	0.1493				p.G192G		Atlas-SNP	.											.	PTGDR	58	.	0			c.C576T						PASS	.	C		95,4311	77.3+/-115.6	0,95,2108	98.0	85.0	89.0		576	-1.4	0.9	14	dbSNP_126	89	742,7858	179.9+/-228.9	26,690,3584	no	coding-synonymous	PTGDR	NM_000953.2		26,785,5692	TT,TC,CC		8.6279,2.1562,6.4355		192/360	52735108	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	5729	exon1			GGAGGGCTCGCTG	U31332	CCDS9707.1, CCDS61454.1	14q22.1	2012-08-08			ENSG00000168229	ENSG00000168229		"""GPCR / Class A : Prostanoid receptors"""	9591	protein-coding gene	gene with protein product		604687				7642548	Standard	NM_000953		Approved	DP, DP1, PTGDR1	uc001wzq.3	Q13258	OTTHUMG00000140299	ENST00000306051.2:c.576C>T	14.37:g.52735108C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	104	41	0.394231	NM_000953	G3V5L3|Q13250|Q13251|Q1ZZ52	Silent	SNP	ENST00000306051.2	37	CCDS9707.1																																																																																			C|0.932;T|0.068	0.068	strong		0.627	PTGDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276889.1	NM_000953	
ZNF468	90333	hgsc.bcm.edu	37	19	53344919	53344919	+	Missense_Mutation	SNP	T	T	G	rs58239286	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53344919T>G	ENST00000595646.1	-	4	748	c.628A>C	c.(628-630)Atg>Ctg	p.M210L	ZNF468_ENST00000390651.4_Missense_Mutation_p.M157L|ZNF468_ENST00000243639.4_3'UTR|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_Missense_Mutation_p.M157L			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	210					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(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		TTTTCTCTCATGTGTACTTCC	0.323													-|||	1114	0.222444	0.3238	0.1326	5008	,	,		20903	0.0605		0.1491	False		,,,				2504	0.3916				p.M210L		Atlas-SNP	.											.	ZNF468	46	.	0			c.A628C						PASS	.	T	LEU/MET,LEU/MET	1348,3058	442.9+/-346.8	205,938,1060	85.0	86.0	86.0		628,469	0.3	0.0	19	dbSNP_129	86	1599,7001	294.2+/-301.7	152,1295,2853	yes	missense,missense	ZNF468	NM_001008801.1,NM_199132.1	15,15	357,2233,3913	GG,GT,TT		18.593,30.5946,22.6588	benign,benign	210/523,157/470	53344919	2947,10059	2203	4300	6503	SO:0001583	missense	90333	exon4			CTCTCATGTGTAC	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.628A>C	19.37:g.53344919T>G	ENSP00000470381:p.Met210Leu	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	37	CCDS33094.1	368	0.1684981684981685	162	0.32926829268292684	59	0.16298342541436464	32	0.055944055944055944	115	0.1517150395778364	t	6.884	0.532532	0.13127	0.305946	0.18593	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651	T;T	0.13901	2.55;2.55	1.38	0.328	0.15918	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.45877	-0.9231	8	0.66056	D	0.02	.	4.4541	0.11635	0.0:0.2097:0.0:0.7903	rs58239286;rs61744274	210	Q5VIY5	ZN468_HUMAN	L	210;157;157	ENSP00000379690:M157L;ENSP00000445669:M157L	ENSP00000243639:M210L	M	-	1	0	ZNF468	58036731	0.128000	0.22383	0.000000	0.03702	0.153000	0.21895	0.706000	0.25690	0.043000	0.15746	0.147000	0.16070	ATG	T|0.795;G|0.205	0.205	strong		0.323	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
TMEM132D	121256	hgsc.bcm.edu	37	12	129559421	129559421	+	Missense_Mutation	SNP	C	C	T	rs73159540	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:129559421C>T	ENST00000422113.2	-	9	2625	c.2299G>A	c.(2299-2301)Gtc>Atc	p.V767I	TMEM132D_ENST00000389441.4_Missense_Mutation_p.V305I	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	767					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)		TCCACCTTGACCAGGGTGCCT	0.463													C|||	414	0.0826677	0.0045	0.0778	5008	,	,		21102	0.1161		0.1173	False		,,,				2504	0.1217				p.V767I		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G2299A						PASS	.	C	ILE/VAL	88,4318	75.7+/-113.9	1,86,2116	146.0	128.0	134.0		2299	4.2	1.0	12	dbSNP_130	134	927,7673	204.9+/-247.5	54,819,3427	yes	missense	TMEM132D	NM_133448.2	29	55,905,5543	TT,TC,CC		10.7791,1.9973,7.8041	possibly-damaging	767/1100	129559421	1015,11991	2203	4300	6503	SO:0001583	missense	121256	exon9			CCTTGACCAGGGT	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.2299G>A	12.37:g.129559421C>T	ENSP00000408581:p.Val767Ile	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	192	99	0.515625	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	195	0.08928571428571429	4	0.008130081300813009	33	0.09116022099447514	64	0.11188811188811189	94	0.12401055408970976	C	9.353	1.066018	0.20067	0.019973	0.107791	ENSG00000151952	ENST00000389441;ENST00000422113	T;T	0.14022	2.54;2.54	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000004	T	0.00241	0.0007	N	0.17345	0.48	0.18873	P	0.999981947	B;P	0.50528	0.211;0.936	B;P	0.56398	0.066;0.797	T	0.37126	-0.9719	8	.	.	.	-31.7501	16.8845	0.86072	0.0:1.0:0.0:0.0	.	767;305	Q14C87;Q14C87-2	T132D_HUMAN;.	I	305;767	ENSP00000374092:V305I;ENSP00000408581:V767I	.	V	-	1	0	TMEM132D	128125374	1.000000	0.71417	0.953000	0.39169	0.326000	0.28443	2.480000	0.45206	2.033000	0.60031	0.462000	0.41574	GTC	C|0.919;T|0.081	0.081	strong		0.463	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
ADORA3	140	hgsc.bcm.edu	37	1	112043139	112043139	+	Silent	SNP	G	G	A	rs2789537	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:112043139G>A	ENST00000241356.4	-	2	795	c.390C>T	c.(388-390)gcC>gcT	p.A130A	ADORA3_ENST00000369716.4_Intron|ADORA3_ENST00000486342.1_5'UTR|ADORA3_ENST00000369717.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	130					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	AAAGGCCCAGGGCCAGCCATA	0.507													G|||	108	0.0215655	0.0272	0.0144	5008	,	,		20977	0.0109		0.0209	False		,,,				2504	0.0307				p.A130A		Atlas-SNP	.											.	ADORA3	104	.	0			c.C390T						PASS	.	G	,,	100,4306	77.3+/-115.6	1,98,2104	84.0	94.0	90.0		390,,	0.1	1.0	1	dbSNP_100	90	160,8440	76.0+/-138.7	2,156,4142	no	coding-synonymous,intron,intron	ADORA3	NM_000677.3,NM_001081976.1,NM_020683.6	,,	3,254,6246	AA,AG,GG		1.8605,2.2696,1.9991	,,	130/319,,	112043139	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	140	exon2			GCCCAGGGCCAGC	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.390C>T	1.37:g.112043139G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	71	18	0.253521	NM_000677	A2A3P4|Q6UWU0|Q9BYZ1	Silent	SNP	ENST00000241356.4	37	CCDS839.1																																																																																			G|0.981;A|0.019	0.019	strong		0.507	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
MUC7	4589	hgsc.bcm.edu	37	4	71347333	71347333	+	Missense_Mutation	SNP	C	C	T	rs72655156	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:71347333C>T	ENST00000304887.5	+	3	1062	c.872C>T	c.(871-873)aCa>aTa	p.T291I	MUC7_ENST00000456088.1_Missense_Mutation_p.T291I|MUC7_ENST00000413702.1_Missense_Mutation_p.T291I	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	291	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			TCTGCAACTACACCAGCTCCA	0.562													-|||	28	0.00559105	0.0	0.0086	5008	,	,		22130	0.0		0.0199	False		,,,				2504	0.002				p.T291I		Atlas-SNP	.											.	MUC7	91	.	0			c.C872T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	16,4390		0,16,2187	389.0	355.0	367.0		872,872,872	1.5	0.0	4	dbSNP_131	367	195,8405		1,193,4106	yes	missense,missense,missense	MUC7	NM_001145006.1,NM_001145007.1,NM_152291.2	89,89,89	1,209,6293	TT,TC,CC		2.2674,0.3631,1.6223	probably-damaging,probably-damaging,probably-damaging	291/378,291/378,291/378	71347333	211,12795	2203	4300	6503	SO:0001583	missense	4589	exon4			CAACTACACCAGC	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.872C>T	4.37:g.71347333C>T	ENSP00000302021:p.Thr291Ile	Somatic	398	1	0.00251256		WXS	Illumina HiSeq	Phase_I	409	185	0.452323	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	24	0.01098901098901099	0	0.0	6	0.016574585635359115	0	0.0	18	0.023746701846965697	-	9.647	1.140465	0.21205	0.003631	0.022674	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.58210	0.35;0.35;0.35	1.52	1.52	0.23074	.	.	.	.	.	T	0.36276	0.0961	N	0.19112	0.55	0.09310	N	1	D	0.71674	0.998	D	0.74023	0.982	T	0.28713	-1.0035	8	.	.	.	.	8.9663	0.35879	0.0:1.0:0.0:0.0	.	291	Q8TAX7	MUC7_HUMAN	I	291	ENSP00000407422:T291I;ENSP00000400585:T291I;ENSP00000302021:T291I	.	T	+	2	0	MUC7	71381922	0.384000	0.25164	0.002000	0.10522	0.002000	0.02628	3.421000	0.52742	1.122000	0.41944	0.505000	0.49811	ACA	C|0.985;T|0.015	0.015	strong		0.562	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
EPHX1	2052	hgsc.bcm.edu	37	1	226019633	226019633	+	Missense_Mutation	SNP	T	T	C	rs1051740	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:226019633T>C	ENST00000366837.4	+	3	533	c.337T>C	c.(337-339)Tac>Cac	p.Y113H	EPHX1_ENST00000272167.5_Missense_Mutation_p.Y113H|EPHX1_ENST00000467015.1_3'UTR	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	86	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	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	
IL17RD	54756	hgsc.bcm.edu	37	3	57136585	57136585	+	Missense_Mutation	SNP	C	C	T	rs17057718	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:57136585C>T	ENST00000296318.7	-	10	989	c.901G>A	c.(901-903)Gtg>Atg	p.V301M	IL17RD_ENST00000320057.5_Missense_Mutation_p.V157M|IL17RD_ENST00000463523.1_Missense_Mutation_p.V157M|IL17RD_ENST00000427856.2_Missense_Mutation_p.V277M	NM_017563.3	NP_060033.3	Q8NFM7	I17RD_HUMAN	interleukin 17 receptor D	301			V -> M (in dbSNP:rs17057718).		signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)	16				KIRC - Kidney renal clear cell carcinoma(284;0.0173)|Kidney(284;0.0204)		GTGATGGCCACGGCTCTGATG	0.488													C|||	1031	0.205871	0.0408	0.3271	5008	,	,		17270	0.376		0.1471	False		,,,				2504	0.228				p.V301M		Atlas-SNP	.											.	IL17RD	93	.	0			c.G901A						PASS	.	C	MET/VAL	317,4089	168.0+/-198.9	12,293,1898	56.0	58.0	57.0		901	3.6	0.2	3	dbSNP_123	57	1306,7294	257.3+/-281.4	94,1118,3088	yes	missense	IL17RD	NM_017563.3	21	106,1411,4986	TT,TC,CC		15.186,7.1947,12.4789	benign	301/740	57136585	1623,11383	2203	4300	6503	SO:0001583	missense	54756	exon10			TGGCCACGGCTCT	AF494208	CCDS2880.2	3p21.1	2008-02-05			ENSG00000144730	ENSG00000144730		"""Interleukins and interleukin receptors"""	17616	protein-coding gene	gene with protein product		606807				11802164, 12604616	Standard	NM_017563		Approved	SEF, IL17RLM, FLJ35755, IL-17RD	uc003dil.3	Q8NFM7	OTTHUMG00000150171	ENST00000296318.7:c.901G>A	3.37:g.57136585C>T	ENSP00000296318:p.Val301Met	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_017563	Q2NKP7|Q58EZ7|Q6RVF4|Q6UWI5|Q8N113|Q8NFS0|Q9UFA0	Missense_Mutation	SNP	ENST00000296318.7	37	CCDS2880.2	456	0.2087912087912088	23	0.046747967479674794	96	0.26519337016574585	225	0.39335664335664333	112	0.14775725593667546	C	9.731	1.162180	0.21538	0.071947	0.15186	ENSG00000144730	ENST00000296318;ENST00000320057;ENST00000427856;ENST00000463523	T;T;T;T	0.10382	2.88;2.9;2.88;2.9	5.48	3.57	0.40892	.	0.104633	0.64402	D	0.000004	T	0.00012	0.0000	N	0.08118	0	0.27204	P	0.9600953	P;P;P	0.42357	0.669;0.466;0.777	B;B;B	0.31869	0.065;0.052;0.137	T	0.44967	-0.9293	9	0.33940	T	0.23	-19.0964	4.6136	0.12415	0.0:0.6131:0.0:0.3869	rs17057718;rs17057718	157;301;277	B4DXM5;Q8NFM7;Q8NFM7-3	.;I17RD_HUMAN;.	M	301;157;277;157	ENSP00000296318:V301M;ENSP00000322250:V157M;ENSP00000399209:V277M;ENSP00000417516:V157M	ENSP00000296318:V301M	V	-	1	0	IL17RD	57111625	0.894000	0.30519	0.215000	0.23724	0.320000	0.28249	1.488000	0.35551	1.557000	0.49525	-0.136000	0.14681	GTG	C|0.840;T|0.160	0.160	strong		0.488	IL17RD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316680.1	NM_017563	
NOL8	55035	hgsc.bcm.edu	37	9	95076771	95076771	+	Silent	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:95076771A>C	ENST00000535387.1	-	6	2135	c.2136T>G	c.(2134-2136)tcT>tcG	p.S712S	NOL8_ENST00000358855.4_Silent_p.S644S|NOL8_ENST00000542053.1_Silent_p.S644S|NOL8_ENST00000442668.2_Silent_p.S712S|NOL8_ENST00000545558.1_Silent_p.S712S					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CGCTTGAATCAGACCGCTCTT	0.428																																					p.S712S		Atlas-SNP	.											.	NOL8	118	.	0			c.T2136G						PASS	.						57.0	51.0	53.0					9																	95076771		1899	4115	6014	SO:0001819	synonymous_variant	55035	exon7			TGAATCAGACCGC	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2136T>G	9.37:g.95076771A>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	90	24	0.266667	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			.	.	none		0.428	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
SLC25A15	10166	hgsc.bcm.edu	37	13	41379272	41379272	+	Silent	SNP	C	C	T	rs9577152	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:41379272C>T	ENST00000338625.4	+	4	569	c.333C>T	c.(331-333)gcC>gcT	p.A111A	SLC25A15_ENST00000478827.1_3'UTR	NM_014252.3	NP_055067.1	Q9Y619	ORNT1_HUMAN	solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15	111					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|L-ornithine transmembrane transport (GO:1903352)|mitochondrial ornithine transport (GO:0000066)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	L-ornithine transmembrane transporter activity (GO:0000064)	p.A111A(1)		endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|stomach(1)|urinary_tract(1)	14		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.48e-08)|Epithelial(112;7.51e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000191)|GBM - Glioblastoma multiforme(144;0.00231)|BRCA - Breast invasive adenocarcinoma(63;0.0704)	L-Ornithine(DB00129)	AGAATGCAGCCGCCGGTTCCT	0.542													T|||	568	0.113419	0.2443	0.0548	5008	,	,		16921	0.0526		0.0825	False		,,,				2504	0.0726				p.A111A		Atlas-SNP	.											SLC25A15,NS,carcinoma,0,1	SLC25A15	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C333T						PASS	.	T		819,3587	749.2+/-412.0	84,651,1468	91.0	84.0	86.0		333	-8.9	0.0	13	dbSNP_119	86	809,7791	782.3+/-407.6	35,739,3526	yes	coding-synonymous	SLC25A15	NM_014252.3		119,1390,4994	TT,TC,CC		9.407,18.5883,12.5173		111/302	41379272	1628,11378	2203	4300	6503	SO:0001819	synonymous_variant	10166	exon4			TGCAGCCGCCGGT	AF112968	CCDS9373.1	13q14	2013-05-22			ENSG00000102743	ENSG00000102743		"""Solute carriers"""	10985	protein-coding gene	gene with protein product	"""ornithine transporter 1"""	603861		ORNT1, HHH		10369256	Standard	NM_014252		Approved	ORC1, D13S327	uc001uxn.3	Q9Y619	OTTHUMG00000016776	ENST00000338625.4:c.333C>T	13.37:g.41379272C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	52	0.55914	NM_014252	Q5VZD8|Q9HC45	Silent	SNP	ENST00000338625.4	37	CCDS9373.1																																																																																			C|0.883;T|0.117	0.117	strong		0.542	SLC25A15-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276149.2	NM_014252	
LARS	51520	hgsc.bcm.edu	37	5	145539996	145539996	+	Silent	SNP	T	T	G	rs11540214	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145539996T>G	ENST00000394434.2	-	7	814	c.648A>C	c.(646-648)tcA>tcC	p.S216S	LARS_ENST00000274562.9_Silent_p.S189S|LARS_ENST00000510191.1_Silent_p.S162S|LARS_ENST00000511505.1_5'UTR|LARS_ENST00000545646.1_Silent_p.S170S	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	128	0	0		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	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	
EPSTI1	94240	hgsc.bcm.edu	37	13	43462435	43462435	+	IGR	SNP	T	T	C	rs375469696		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:43462435T>C	ENST00000398762.3	-	0	957				EPSTI1_ENST00000313624.7_3'UTR|EPSTI1_ENST00000313640.7_Missense_Mutation_p.E395G			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)		AAATATGAGTTCAGGAATCAG	0.408																																					p.E395G		Atlas-SNP	.											EPSTI1,NS,carcinoma,+1,1	EPSTI1	47	1	0			c.A1184G						scavenged	.						86.0	84.0	85.0					13																	43462435		2203	4300	6503	SO:0001628	intergenic_variant	94240	exon13			ATGAGTTCAGGAA	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.43462435T>C		Somatic	229	3	0.0131004		WXS	Illumina HiSeq	Phase_I	225	4	0.0177778	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	37	CCDS9387.1	.	.	.	.	.	.	.	.	.	.	T	15.26	2.780683	0.49891	.	.	ENSG00000133106	ENST00000313640	.	.	.	5.3	4.13	0.48395	.	1.707420	0.03444	N	0.209625	T	0.46698	0.1406	.	.	.	0.19775	N	0.999953	P	0.40180	0.705	B	0.44044	0.439	T	0.39482	-0.9612	8	0.87932	D	0	-0.0281	9.2901	0.37782	0.0:0.0:0.2024:0.7976	.	395	Q96J88-3	.	G	395	.	ENSP00000318982:E395G	E	-	2	0	EPSTI1	42360435	0.514000	0.26202	0.014000	0.15608	0.548000	0.35241	0.960000	0.29253	0.964000	0.38108	0.533000	0.62120	GAA	.	.	none		0.408	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264	
C4orf36	132989	hgsc.bcm.edu	37	4	87809020	87809020	+	Missense_Mutation	SNP	C	C	G	rs72613147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:87809020C>G	ENST00000473559.1	-	7	910	c.247G>C	c.(247-249)Gtg>Ctg	p.V83L	C4orf36_ENST00000295898.3_Missense_Mutation_p.V83L|C4orf36_ENST00000503001.1_5'Flank			Q96KX1	CD036_HUMAN	chromosome 4 open reading frame 36	83								p.V83L(1)		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)		AGACGCTTCACTTCATACTCC	0.378													C|||	736	0.146965	0.0121	0.1945	5008	,	,		22337	0.1825		0.1759	False		,,,				2504	0.229				p.V83L		Atlas-SNP	.											C4orf36,NS,carcinoma,0,1	C4orf36	10	1	1	Substitution - Missense(1)	prostate(1)	c.G247C						PASS	.	C	LEU/VAL	169,4237	112.1+/-150.2	7,155,2041	84.0	78.0	80.0		247	0.2	1.0	4	dbSNP_130	80	1555,7045	291.7+/-300.5	137,1281,2882	yes	missense	C4orf36	NM_144645.3	32	144,1436,4923	GG,GC,CC		18.0814,3.8357,13.2554	benign	83/118	87809020	1724,11282	2203	4300	6503	SO:0001583	missense	132989	exon4			GCTTCACTTCATA	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.247G>C	4.37:g.87809020C>G	ENSP00000420949:p.Val83Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_144645		Missense_Mutation	SNP	ENST00000473559.1	37	CCDS3615.1	323	0.1478937728937729	11	0.022357723577235773	60	0.16574585635359115	118	0.2062937062937063	134	0.17678100263852242	C	7.612	0.675093	0.14841	0.038357	0.180814	ENSG00000163633	ENST00000295898;ENST00000473559;ENST00000506308	T;T;T	0.31247	1.5;1.5;1.5	5.23	0.167	0.15006	.	0.618498	0.16276	N	0.221587	T	0.00012	0.0000	N	0.03608	-0.345	0.51767	P	6.700000000003925E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.35599	-0.9782	9	0.06099	T	0.92	-8.0956	4.5836	0.12271	0.0:0.2137:0.4169:0.3693	.	83	Q96KX1	CD036_HUMAN	L	83	ENSP00000295898:V83L;ENSP00000420949:V83L;ENSP00000421141:V83L	ENSP00000295898:V83L	V	-	1	0	C4orf36	88028044	0.888000	0.30383	0.994000	0.49952	0.447000	0.32167	0.418000	0.21230	0.137000	0.18759	-0.311000	0.09066	GTG	C|0.864;G|0.136	0.136	strong		0.378	C4orf36-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253045.2	NM_144645	
ANKAR	150709	hgsc.bcm.edu	37	2	190569908	190569908	+	Missense_Mutation	SNP	G	G	A	rs116660656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:190569908G>A	ENST00000520309.1	+	8	1956	c.1868G>A	c.(1867-1869)tGt>tAt	p.C623Y	ANKAR_ENST00000438402.2_Missense_Mutation_p.C623Y|ANKAR_ENST00000313581.4_Missense_Mutation_p.C623Y|ANKAR_ENST00000281412.6_Missense_Mutation_p.C387Y|ANKAR_ENST00000431575.2_Missense_Mutation_p.C552Y	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	623				C -> Y (in Ref. 3; AAH47413). {ECO:0000305}.		integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(16)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(2)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00156)|Epithelial(96;0.0256)|all cancers(119;0.0744)			ATTGCTCTCTGTAGGAAGGAT	0.403													G|||	40	0.00798722	0.0008	0.0058	5008	,	,		17427	0.0		0.0258	False		,,,				2504	0.0092				p.C623Y		Atlas-SNP	.											.	ANKAR	184	.	0			c.G1868A						PASS	.	G	TYR/CYS	15,4391	21.2+/-45.6	0,15,2188	145.0	141.0	142.0		1868	3.0	1.0	2	dbSNP_132	142	236,8364	95.9+/-157.7	3,230,4067	yes	missense	ANKAR	NM_144708.3	194	3,245,6255	AA,AG,GG		2.7442,0.3404,1.9299	benign	623/1435	190569908	251,12755	2203	4300	6503	SO:0001583	missense	150709	exon8			CTCTCTGTAGGAA	AJ549812	CCDS33351.1, CCDS33351.2	2q32.2	2013-02-14			ENSG00000151687	ENSG00000151687		"""Ankyrin repeat domain containing"", ""Armadillo repeat containing"""	26350	protein-coding gene	gene with protein product		609803				15110750	Standard	NM_144708		Approved	FLJ25415	uc002uqw.2	Q7Z5J8	OTTHUMG00000154398	ENST00000520309.1:c.1868G>A	2.37:g.190569908G>A	ENSP00000427882:p.Cys623Tyr	Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	235	110	0.468085	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	37	CCDS33351.2	23	0.010531135531135532	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	20	0.026385224274406333	G	15.26	2.781995	0.49891	0.003404	0.027442	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.84	2.97	0.34412	.	0.580099	0.16803	N	0.198888	T	0.30039	0.0752	L	0.33792	1.035	0.40694	D	0.982421	.	.	.	.	.	.	T	0.23762	-1.0179	8	0.35671	T	0.21	-1.9537	7.6426	0.28303	0.4252:0.0:0.5748:0.0	.	.	.	.	Y	623;623;623;552;387	ENSP00000427882:C623Y;ENSP00000313513:C623Y;ENSP00000397243:C623Y;ENSP00000393043:C552Y;ENSP00000281412:C387Y	ENSP00000281412:C387Y	C	+	2	0	ANKAR	190278153	0.095000	0.21747	0.981000	0.43875	0.973000	0.67179	0.169000	0.16641	0.332000	0.23536	-0.345000	0.07892	TGT	G|0.983;A|0.017	0.017	strong		0.403	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708	
CPAMD8	27151	hgsc.bcm.edu	37	19	17088299	17088299	+	Missense_Mutation	SNP	T	T	C	rs1824152	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17088299T>C	ENST00000443236.1	-	15	1809	c.1778A>G	c.(1777-1779)cAt>cGt	p.H593R	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	546						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						CACGGCCAGATGAAGAGAGGT	0.592													t|||	2839	0.566893	0.9213	0.3963	5008	,	,		17909	0.5625		0.3777	False		,,,				2504	0.408				p.H593R		Atlas-SNP	.											.	CPAMD8	192	.	0			c.A1778G						PASS	.	C	ARG/HIS	3115,813		1259,597,108	39.0	45.0	43.0		1778	-5.2	0.0	19	dbSNP_92	43	2825,5453		475,1875,1789	no	missense	CPAMD8	NM_015692.2	29	1734,2472,1897	CC,CT,TT		34.1266,20.6976,48.6646	benign	593/1933	17088299	5940,6266	1964	4139	6103	SO:0001583	missense	27151	exon15			GCCAGATGAAGAG	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.1778A>G	19.37:g.17088299T>C	ENSP00000402505:p.His593Arg	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	1126|1126	0.5155677655677655|0.5155677655677655	415|415	0.8434959349593496|0.8434959349593496	136|136	0.3756906077348066|0.3756906077348066	306|306	0.534965034965035|0.534965034965035	269|269	0.3548812664907652|0.3548812664907652	t|t	0.001|0.001	-2.964973|-2.964973	0.00049|0.00049	0.793024|0.793024	0.341266|0.341266	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	2.62|2.62	-5.24|-5.24	0.02789|0.02789	Alpha-2-macroglobulin, N-terminal 2 (1);|.	1.028330|.	0.07794|.	N|.	0.955448|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.10664|0.10664	0.02|0.02	0.21604|0.21604	P|P	0.999620117|0.999620117	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.10847|0.10847	-1.0612|-1.0612	8|4	0.15066|.	T|.	0.55|.	.|.	8.2718|8.2718	0.31849|0.31849	0.1001:0.314:0.0:0.5859|0.1001:0.314:0.0:0.5859	rs1824152;rs3745334;rs60607898;rs1824152|rs1824152;rs3745334;rs60607898;rs1824152	546|.	Q8IZJ3|.	CPMD8_HUMAN|.	R|V	593|604	.|.	ENSP00000291440:H593R|.	H|I	-|-	2|1	0|0	CPAMD8|CPAMD8	16949299|16949299	0.003000|0.003000	0.15002|0.15002	0.004000|0.004000	0.12327|0.12327	0.081000|0.081000	0.17604|0.17604	-0.493000|-0.493000	0.06459|0.06459	-3.135000|-3.135000	0.00235|0.00235	-4.516000|-4.516000	0.00005|0.00005	CAT|ATC	.	.	weak		0.592	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
MICAL1	64780	hgsc.bcm.edu	37	6	109767396	109767396	+	Missense_Mutation	SNP	G	G	A	rs199541635		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:109767396G>A	ENST00000358807.3	-	19	2835	c.2524C>T	c.(2524-2526)Cgc>Tgc	p.R842C	MICAL1_ENST00000368952.4_Missense_Mutation_p.R861C|MICAL1_ENST00000358577.3_Missense_Mutation_p.R756C	NM_022765.3	NP_073602.3	Q8TDZ2	MICA1_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 1	842					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of protein phosphorylation (GO:0001933)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|sulfur oxidation (GO:0019417)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)	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)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|liver(1)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0142)|all cancers(137;0.0197)|OV - Ovarian serous cystadenocarcinoma(136;0.0233)|BRCA - Breast invasive adenocarcinoma(108;0.0574)		AGGGCGTGGCGGGCCAAGGCG	0.667																																					p.R842C		Atlas-SNP	.											MICAL1,NS,carcinoma,+1,1	MICAL1	79	1	0			c.C2524T						scavenged	.	G	CYS/ARG,CYS/ARG	0,4402		0,0,2201	26.0	30.0	29.0		2266,2524	5.6	1.0	6		29	2,8592		0,2,4295	yes	missense,missense	MICAL1	NM_001159291.1,NM_022765.3	180,180	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging,probably-damaging	756/982,842/1068	109767396	2,12994	2201	4297	6498	SO:0001583	missense	64780	exon19			CGTGGCGGGCCAA	AB048948	CCDS5076.1, CCDS55047.1	6q21	2013-03-26	2013-03-26	2005-02-16	ENSG00000135596	ENSG00000135596			20619	protein-coding gene	gene with protein product		607129	"""NEDD9 interacting protein with calponin homology and LIM domains"""	NICAL		11827972	Standard	NM_022765		Approved	MICAL, FLJ11937, DKFZp434B1517, FLJ21739	uc003ptk.3	Q8TDZ2	OTTHUMG00000015350	ENST00000358807.3:c.2524C>T	6.37:g.109767396G>A	ENSP00000351664:p.Arg842Cys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	146	3	0.0205479	NM_022765	B7Z3R5|E1P5F0|Q7Z633|Q8IVS9|Q96G47|Q9H6X6|Q9H7I0|Q9HAA1|Q9UFF7	Missense_Mutation	SNP	ENST00000358807.3	37	CCDS5076.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.229240	0.79688	0.0	2.33E-4	ENSG00000135596	ENST00000358807;ENST00000368952;ENST00000358577;ENST00000368957;ENST00000335266	T;T;T	0.52983	0.65;0.65;0.64	5.56	5.56	0.83823	.	0.835193	0.10911	N	0.620566	T	0.41213	0.1149	L	0.40543	1.245	0.48975	D	0.999738	D;D;D	0.71674	0.991;0.998;0.996	B;P;B	0.50049	0.425;0.629;0.425	T	0.35151	-0.9800	10	0.66056	D	0.02	.	15.0246	0.71659	0.0:0.0:1.0:0.0	.	861;756;842	B7Z3R5;Q8TDZ2-2;Q8TDZ2	.;.;MICA1_HUMAN	C	842;861;756;366;98	ENSP00000351664:R842C;ENSP00000357948:R861C;ENSP00000351385:R756C	ENSP00000335372:R98C	R	-	1	0	MICAL1	109874089	0.984000	0.35163	0.983000	0.44433	0.998000	0.95712	2.215000	0.42862	2.608000	0.88229	0.655000	0.94253	CGC	.	.	weak		0.667	MICAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041759.2	NM_022765	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388553	1388553	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	251	3	0.0119522		WXS	Illumina HiSeq	Phase_I	227	14	0.061674	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	
WDR27	253769	hgsc.bcm.edu	37	6	170068086	170068086	+	Missense_Mutation	SNP	C	C	T	rs41265385	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170068086C>T	ENST00000448612.1	-	5	761	c.652G>A	c.(652-654)Ggc>Agc	p.G218S	WDR27_ENST00000333572.6_Missense_Mutation_p.G218S|WDR27_ENST00000423258.1_Intron|WDR27_ENST00000546525.1_5'Flank|WDR27_ENST00000420344.2_Intron	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	188						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		ACCTTAAAGCCTCTGTCCTCA	0.657													C|||	989	0.197484	0.236	0.17	5008	,	,		16456	0.2768		0.0895	False		,,,				2504	0.1943				p.G218S		Atlas-SNP	.											.	WDR27	129	.	0			c.G652A						PASS	.	C	,SER/GLY	929,3345		97,735,1305	37.0	45.0	43.0		,652	4.1	1.0	6	dbSNP_127	43	740,7732		35,670,3531	yes	intron,missense	WDR27	NM_001202550.1,NM_182552.4	,56	132,1405,4836	TT,TC,CC		8.7347,21.7361,13.0943	,benign	,218/896	170068086	1669,11077	2137	4236	6373	SO:0001583	missense	253769	exon5			TAAAGCCTCTGTC	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"""WD repeat domain containing"""	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.652G>A	6.37:g.170068086C>T	ENSP00000416289:p.Gly218Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	37	CCDS47520.2	388	0.17765567765567766	99	0.20121951219512196	58	0.16022099447513813	158	0.2762237762237762	73	0.09630606860158311	C	6.941	0.543423	0.13250	0.217361	0.087347	ENSG00000184465	ENST00000448612;ENST00000333572	T;T	0.57273	0.41;0.41	5.25	4.1	0.47936	.	0.385807	0.25827	N	0.028056	T	0.07007	0.0178	N	0.00746	-1.225	0.09310	P	0.9999999999990632	B;B	0.16396	0.003;0.017	B;B	0.13407	0.008;0.009	T	0.23013	-1.0200	9	0.12430	T	0.62	-17.128	9.4629	0.38796	0.0:0.0875:0.0:0.9125	rs41265385	218;218	F2Z2U5;C9JGV0	.;.	S	218	ENSP00000416289:G218S;ENSP00000330265:G218S	ENSP00000330265:G218S	G	-	1	0	WDR27	169810011	1.000000	0.71417	0.996000	0.52242	0.880000	0.50808	2.800000	0.47900	0.850000	0.35239	-0.302000	0.09304	GGC	C|0.840;T|0.160	0.160	strong		0.657	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
KIAA1279	26128	hgsc.bcm.edu	37	10	70748784	70748784	+	Missense_Mutation	SNP	G	G	A	rs2255607	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70748784G>A	ENST00000361983.4	+	1	298	c.196G>A	c.(196-198)Ggc>Agc	p.G66S		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	66			G -> S (in dbSNP:rs2255607). {ECO:0000269|PubMed:10574462}.		cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						GGCCGAGGACGGCCCGGGTGC	0.701													G|||	1772	0.353834	0.329	0.3156	5008	,	,		14045	0.3562		0.4811	False		,,,				2504	0.2812				p.G66S		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G196A						PASS	.	G	SER/GLY	1507,2899		265,977,961	30.0	37.0	35.0		196	-0.1	0.0	10	dbSNP_100	35	4153,4441		1010,2133,1154	no	missense	KIAA1279	NM_015634.3	56	1275,3110,2115	AA,AG,GG		48.3244,34.2034,43.5385	possibly-damaging	66/622	70748784	5660,7340	2203	4297	6500	SO:0001583	missense	26128	exon1			GAGGACGGCCCGG	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.196G>A	10.37:g.70748784G>A	ENSP00000354848:p.Gly66Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	16	11	0.6875	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Missense_Mutation	SNP	ENST00000361983.4	37	CCDS7284.1	880	0.40293040293040294	168	0.34146341463414637	133	0.3674033149171271	221	0.38636363636363635	358	0.47229551451187335	G	1.857	-0.463542	0.04476	0.342034	0.483244	ENSG00000198954	ENST00000361983	T	0.41400	1.0	5.24	-0.111	0.13576	.	0.508915	0.22554	N	0.058552	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45293	-0.9271	9	0.08837	T	0.75	-22.3659	3.8437	0.08925	0.2493:0.0:0.4709:0.2798	rs2255607;rs57824932	66	Q96EK5	KBP_HUMAN	S	66	ENSP00000354848:G66S	ENSP00000354848:G66S	G	+	1	0	KIAA1279	70418790	0.000000	0.05858	0.002000	0.10522	0.047000	0.14425	0.211000	0.17474	-0.053000	0.13289	-0.158000	0.13435	GGC	G|0.584;A|0.416	0.416	strong		0.701	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634	
YARS	8565	hgsc.bcm.edu	37	1	33245802	33245802	+	Silent	SNP	C	C	G	rs699005	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:33245802C>G	ENST00000373477.4	-	11	2126	c.1218G>C	c.(1216-1218)ctG>ctC	p.L406L	YARS_ENST00000469100.1_5'UTR	NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	406	tRNA-binding. {ECO:0000255|PROSITE- ProRule:PRU00209}.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)|tyrosyl-tRNA aminoacylation (GO:0006437)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|interleukin-8 receptor binding (GO:0005153)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)|tRNA binding (GO:0000049)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	CGAACTGTACCAGGCCGCTCA	0.582													C|||	438	0.0874601	0.0998	0.1787	5008	,	,		21031	0.001		0.1074	False		,,,				2504	0.0746				p.L406L		Atlas-SNP	.											.	YARS	34	.	0			c.G1218C						PASS	.	C		421,3985	205.2+/-227.1	21,379,1803	223.0	182.0	196.0		1218	2.5	1.0	1	dbSNP_86	196	864,7736	195.4+/-240.6	40,784,3476	no	coding-synonymous	YARS	NM_003680.3		61,1163,5279	GG,GC,CC		10.0465,9.5552,9.8801		406/529	33245802	1285,11721	2203	4300	6503	SO:0001819	synonymous_variant	8565	exon11			CTGTACCAGGCCG	U89436	CCDS368.1	1p35.1	2014-09-17			ENSG00000134684	ENSG00000134684	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	12840	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 1, cytoplasmic"""	603623				8552597, 9162081	Standard	NM_003680		Approved	YTS, YRS, tyrRS	uc001bvy.1	P54577	OTTHUMG00000003933	ENST00000373477.4:c.1218G>C	1.37:g.33245802C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	71	14	0.197183	NM_003680	B3KWK4|D3DPQ4|O43276|Q53EN1	Silent	SNP	ENST00000373477.4	37	CCDS368.1																																																																																			C|0.899;G|0.101	0.101	strong		0.582	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011225.1	NM_003680	
NDUFA6	4700	hgsc.bcm.edu	37	22	42486723	42486723	+	Missense_Mutation	SNP	G	G	A	rs1801311	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:42486723G>A	ENST00000498737.2	-	1	236	c.104C>T	c.(103-105)gCt>gTt	p.A35V	NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|RP1-257I20.14_ENST00000602718.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6_ENST00000602404.1_Missense_Mutation_p.A9V|NDUFA6-AS1_ENST00000608974.1_RNA|NDUFA6-AS1_ENST00000595777.1_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	111	0	0		WXS	Illumina HiSeq	Phase_I	104	100	0.961538	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	
STON2	85439	hgsc.bcm.edu	37	14	81743565	81743565	+	Missense_Mutation	SNP	T	T	C	rs36017951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:81743565T>C	ENST00000267540.2	-	4	2290	c.2090A>G	c.(2089-2091)aAt>aGt	p.N697S	STON2_ENST00000555447.1_Missense_Mutation_p.N697S|STON2_ENST00000556280.1_5'Flank	NM_033104.3	NP_149095.2	Q8WXE9	STON2_HUMAN	stonin 2	697	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				hematopoietic progenitor cell differentiation (GO:0002244)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|synaptic vesicle (GO:0008021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(13)|pancreas(2)|prostate(1)|skin(5)	34				BRCA - Breast invasive adenocarcinoma(234;0.0348)		CTCTGCCCCATTGACACTTGT	0.547													T|||	186	0.0371406	0.0318	0.0173	5008	,	,		20569	0.0407		0.0378	False		,,,				2504	0.0542				p.N697S		Atlas-SNP	.											.	STON2	94	.	0			c.A2090G						PASS	.	T	SER/ASN	147,4259	104.3+/-142.8	2,143,2058	114.0	113.0	113.0		2090	3.4	1.0	14	dbSNP_126	113	362,8238	120.8+/-180.0	9,344,3947	yes	missense	STON2	NM_033104.2	46	11,487,6005	CC,CT,TT		4.2093,3.3364,3.9136	benign	697/906	81743565	509,12497	2203	4300	6503	SO:0001583	missense	85439	exon6			GCCCCATTGACAC	AB208948	CCDS9875.1, CCDS58332.1	14q31.1	2007-08-01				ENSG00000140022			30652	protein-coding gene	gene with protein product	"""stoned B homolog 2 (Drosophila)"""	608467				11381094, 11454741	Standard	NM_033104		Approved	STNB2, STN2	uc001xvk.2	Q8WXE9		ENST00000267540.2:c.2090A>G	14.37:g.81743565T>C	ENSP00000267540:p.Asn697Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	196	66	0.336735	NM_001256430	G3V2T7|Q17R24|Q59H11|Q6NT47|Q96RI7|Q96RU6	Missense_Mutation	SNP	ENST00000267540.2	37	CCDS9875.1	71	0.03250915750915751	11	0.022357723577235773	9	0.024861878453038673	24	0.04195804195804196	27	0.03562005277044855	T	4.448	0.082943	0.08533	0.033364	0.042093	ENSG00000140022	ENST00000555447;ENST00000546306;ENST00000267540	T;T	0.19394	2.15;2.15	5.84	3.42	0.39159	Clathrin adaptor, mu subunit, C-terminal (3);	0.398828	0.28140	N	0.016443	T	0.02230	0.0069	N	0.12182	0.205	0.29333	N	0.866527	B;B	0.17038	0.02;0.016	B;B	0.19666	0.026;0.015	T	0.21449	-1.0245	10	0.23891	T	0.37	-10.1981	8.4561	0.32899	0.0:0.2217:0.0:0.7783	rs36017951	697;697	Q8WXE9;G3V2T7	STON2_HUMAN;.	S	697;709;697	ENSP00000450857:N697S;ENSP00000267540:N697S	ENSP00000267540:N697S	N	-	2	0	STON2	80813318	0.976000	0.34144	0.963000	0.40424	0.393000	0.30537	1.389000	0.34453	0.438000	0.26450	0.528000	0.53228	AAT	T|0.961;C|0.039	0.039	strong		0.547	STON2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413317.1	NM_033104	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062052	64062052	+	Missense_Mutation	SNP	G	G	A	rs10878074	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:64062052G>A	ENST00000324472.4	-	1	305	c.122C>T	c.(121-123)gCc>gTc	p.A41V	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	41			A -> V (in dbSNP:rs10878074). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GCCGCCTAGGGCCGACTTTTC	0.657													G|||	1979	0.395168	0.4425	0.2565	5008	,	,		14964	0.5714		0.1978	False		,,,				2504	0.4509				p.A41V		Atlas-SNP	.											.	DPY19L2	97	.	0			c.C122T						PASS	.	G	VAL/ALA	1679,2717		309,1061,828	32.0	41.0	38.0		122	-0.6	0.0	12	dbSNP_120	38	1704,6888		179,1346,2771	yes	missense	DPY19L2	NM_173812.4	64	488,2407,3599	AA,AG,GG		19.8324,38.1938,26.0471	benign	41/759	64062052	3383,9605	2198	4296	6494	SO:0001583	missense	283417	exon1			CCTAGGGCCGACT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.122C>T	12.37:g.64062052G>A	ENSP00000315988:p.Ala41Val	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	146	60	0.410959	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	766	0.3507326007326007	189	0.38414634146341464	99	0.27348066298342544	330	0.5769230769230769	148	0.19525065963060687	G	4.869	0.161472	0.09287	0.381938	0.198324	ENSG00000177990	ENST00000324472;ENST00000542209	T;T	0.39787	1.06;1.82	1.61	-0.623	0.11556	.	0.555051	0.14868	N	0.293715	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	1.0000000000287557E-6	B	0.10296	0.003	B	0.04013	0.001	T	0.44937	-0.9295	8	.	.	.	.	2.4499	0.04516	0.2454:0.3274:0.4272:0.0	rs10878074	41	Q6NUT2	D19L2_HUMAN	V	41	ENSP00000315988:A41V;ENSP00000444932:A41V	.	A	-	2	0	DPY19L2	62348319	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.946000	0.29069	-0.190000	0.10465	0.195000	0.17529	GCC	G|0.718;A|0.282	0.282	strong		0.657	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
TUSC5	286753	hgsc.bcm.edu	37	17	1183612	1183612	+	Missense_Mutation	SNP	T	T	C	rs72816260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:1183612T>C	ENST00000333813.3	+	1	656	c.317T>C	c.(316-318)aTc>aCc	p.I106T		NM_172367.2	NP_758955.2	Q8IXB3	TUSC5_HUMAN	tumor suppressor candidate 5	106					response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|prostate(4)|skin(2)	15				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GATTACCTCATCCTGGCCGTC	0.627													T|||	23	0.00459265	0.0	0.0	5008	,	,		15822	0.0		0.0119	False		,,,				2504	0.0112				p.I106T		Atlas-SNP	.											.	TUSC5	25	.	0			c.T317C						PASS	.	T	THR/ILE	5,3919		0,5,1957	78.0	89.0	85.0		317	5.3	1.0	17	dbSNP_130	85	57,8195		0,57,4069	yes	missense	TUSC5	NM_172367.2	89	0,62,6026	CC,CT,TT		0.6907,0.1274,0.5092	possibly-damaging	106/178	1183612	62,12114	1962	4126	6088	SO:0001583	missense	286753	exon1			ACCTCATCCTGGC	AB090231	CCDS42225.1	17p13.3	2009-10-16			ENSG00000184811	ENSG00000184811			29592	protein-coding gene	gene with protein product	"""located at seventeen p thirteen point three 1"", ""interferon induced transmembrane protein domain containing 3"""	612211				12660825	Standard	NM_172367		Approved	LOST1, IFITMD3	uc002fsi.1	Q8IXB3	OTTHUMG00000132196	ENST00000333813.3:c.317T>C	17.37:g.1183612T>C	ENSP00000329548:p.Ile106Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	127	70	0.551181	NM_172367	A6NMK4	Missense_Mutation	SNP	ENST00000333813.3	37	CCDS42225.1	10	0.004578754578754579	0	0.0	0	0.0	0	0.0	10	0.013192612137203167	T	17.10	3.303222	0.60195	0.001274	0.006907	ENSG00000184811	ENST00000333813	D	0.86297	-2.1	5.28	5.28	0.74379	.	0.222837	0.37669	U	0.001998	D	0.88724	0.6514	M	0.75264	2.295	0.39796	D	0.972507	D	0.58268	0.982	P	0.57620	0.824	D	0.90331	0.4352	10	0.49607	T	0.09	-5.7808	14.0731	0.64872	0.0:0.0:0.0:1.0	.	106	Q8IXB3	TUSC5_HUMAN	T	106	ENSP00000329548:I106T	ENSP00000329548:I106T	I	+	2	0	TUSC5	1130362	1.000000	0.71417	0.998000	0.56505	0.802000	0.45316	3.761000	0.55242	2.022000	0.59522	0.438000	0.28831	ATC	T|0.994;C|0.006	0.006	strong		0.627	TUSC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255249.1	NM_172367	
GLIS3	169792	hgsc.bcm.edu	37	9	4286248	4286248	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:4286248G>T	ENST00000381971.3	-	2	771	c.178C>A	c.(178-180)Ctc>Atc	p.L60I		NM_001042413.1	NP_001035878.1	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	0	Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	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 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)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		GGCATCTTGAGATGGAGGTTG	0.592																																					p.L60I		Atlas-SNP	.											.	GLIS3	152	.	0			c.C178A						PASS	.						64.0	70.0	68.0					9																	4286248		2088	4214	6302	SO:0001583	missense	169792	exon2			TCTTGAGATGGAG	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000381971.3:c.178C>A	9.37:g.4286248G>T	ENSP00000371398:p.Leu60Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	145	55	0.37931	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000381971.3	37	CCDS43784.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.781727	0.49891	.	.	ENSG00000107249	ENST00000381971;ENST00000477901;ENST00000481827	T	0.12361	2.69	5.75	5.75	0.90469	.	.	.	.	.	T	0.19765	0.0475	N	0.24115	0.695	0.29128	N	0.879822	D;P	0.63880	0.993;0.882	P;P	0.61397	0.888;0.477	T	0.06409	-1.0828	9	0.62326	D	0.03	.	8.9189	0.35599	0.1588:0.0:0.8412:0.0	.	60;60	F8WEV9;Q8NEA6-2	.;.	I	60	ENSP00000371398:L60I	ENSP00000371398:L60I	L	-	1	0	GLIS3	4276248	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.698000	0.54771	2.711000	0.92665	0.655000	0.94253	CTC	.	.	none		0.592	GLIS3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354776.1	NM_152629	
DNAH17	8632	hgsc.bcm.edu	37	17	76488794	76488794	+	Silent	SNP	G	G	A	rs76641546	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76488794G>A	ENST00000585328.1	-	42	6571	c.6447C>T	c.(6445-6447)gcC>gcT	p.A2149A	DNAH17_ENST00000586052.1_5'Flank|RP11-559N14.5_ENST00000588565.1_RNA|RP11-559N14.5_ENST00000585969.1_RNA|DNAH17_ENST00000389840.5_Silent_p.A2140A|RP11-559N14.5_ENST00000591373.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2140	AAA 2. {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(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)			CCAGGTCCACGGCGACCGGCT	0.587													G|||	17	0.00339457	0.0	0.0043	5008	,	,		16651	0.0		0.0139	False		,,,				2504	0.0				p.A2154A		Atlas-SNP	.											.	DNAH17	347	.	0			c.C6462T						PASS	.	G		7,3935		0,7,1964	63.0	67.0	66.0		6462	-9.5	0.0	17	dbSNP_133	66	78,8248		1,76,4086	no	coding-synonymous	DNAH17	NM_173628.3		1,83,6050	AA,AG,GG		0.9368,0.1776,0.6929		2154/4463	76488794	85,12183	1971	4163	6134	SO:0001819	synonymous_variant	8632	exon42			GTCCACGGCGACC	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.6447C>T	17.37:g.76488794G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	129	68	0.527132	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.994;A|0.006	0.006	strong		0.587	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
KIAA1407	57577	hgsc.bcm.edu	37	3	113720517	113720517	+	Missense_Mutation	SNP	T	T	A	rs6784095	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113720517T>A	ENST00000295878.3	-	13	2234	c.2088A>T	c.(2086-2088)gaA>gaT	p.E696D	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	696			E -> D (in dbSNP:rs6784095).							endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TTTTCTGACGTTCCTCCTCTT	0.403													T|||	550	0.109824	0.0431	0.1744	5008	,	,		20591	0.1567		0.1362	False		,,,				2504	0.0787				p.E696D		Atlas-SNP	.											.	KIAA1407	80	.	0			c.A2088T						PASS	.	T	ASP/GLU	256,4150	146.9+/-181.5	2,252,1949	248.0	241.0	244.0		2088	-3.1	0.9	3	dbSNP_116	244	1089,7511	227.9+/-263.1	71,947,3282	yes	missense	KIAA1407	NM_020817.1	45	73,1199,5231	AA,AT,TT		12.6628,5.8103,10.3414	probably-damaging	696/937	113720517	1345,11661	2203	4300	6503	SO:0001583	missense	57577	exon13			CTGACGTTCCTCC	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2088A>T	3.37:g.113720517T>A	ENSP00000295878:p.Glu696Asp	Somatic	355	0	0		WXS	Illumina HiSeq	Phase_I	310	310	1	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	277	0.12683150183150182	25	0.0508130081300813	44	0.12154696132596685	97	0.16958041958041958	111	0.14643799472295516	T	20.9	4.062455	0.76187	0.058103	0.126628	ENSG00000163617	ENST00000295878	T	0.34472	1.36	5.19	-3.11	0.05299	.	0.230460	0.43919	N	0.000502	T	0.00109	0.0003	M	0.75447	2.3	0.09310	P	0.999999714946	B	0.33448	0.412	B	0.32583	0.148	T	0.04178	-1.0971	9	0.59425	D	0.04	.	7.3801	0.26851	0.0:0.3389:0.1199:0.5412	rs6784095;rs52804206;rs6784095	696	Q8NCU4	K1407_HUMAN	D	696	ENSP00000295878:E696D	ENSP00000295878:E696D	E	-	3	2	KIAA1407	115203207	0.198000	0.23374	0.939000	0.37840	0.989000	0.77384	-1.312000	0.02720	-0.501000	0.06605	-0.248000	0.11899	GAA	T|0.883;A|0.117	0.117	strong		0.403	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
QSOX1	5768	hgsc.bcm.edu	37	1	180148012	180148012	+	Missense_Mutation	SNP	G	G	C	rs17855475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	131	0	0	1959	WXS	Illumina HiSeq	Phase_I	157	97	0.617834	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	
FAT2	2196	hgsc.bcm.edu	37	5	150945483	150945483	+	Missense_Mutation	SNP	C	C	T	rs3734055	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	160	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	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	
STAB2	55576	hgsc.bcm.edu	37	12	104123911	104123911	+	Silent	SNP	C	C	T	rs10778281	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:104123911C>T	ENST00000388887.2	+	49	5304	c.5100C>T	c.(5098-5100)aaC>aaT	p.N1700N		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						TGTATATAAACAATAAGGCTA	0.338													T|||	1424	0.284345	0.6702	0.2522	5008	,	,		17391	0.0367		0.1511	False		,,,				2504	0.1779				p.N1700N		Atlas-SNP	.											.	STAB2	370	.	0			c.C5100T						PASS	.	T		2627,1779	525.4+/-371.6	785,1057,361	120.0	140.0	134.0		5100	3.4	1.0	12	dbSNP_120	134	1197,7403	763.6+/-407.6	76,1045,3179	no	coding-synonymous	STAB2	NM_017564.9		861,2102,3540	TT,TC,CC		13.9186,40.3768,29.4018		1700/2552	104123911	3824,9182	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon49			TATAAACAATAAG	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.5100C>T	12.37:g.104123911C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.717;T|0.283	0.283	strong		0.338	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
SCARF1	8578	hgsc.bcm.edu	37	17	1538669	1538669	+	Missense_Mutation	SNP	C	C	T	rs36108564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:1538669C>T	ENST00000263071.4	-	11	1925	c.1876G>A	c.(1876-1878)Ggt>Agt	p.G626S	SCARF1_ENST00000571272.1_3'UTR|SCARF1_ENST00000348987.3_Missense_Mutation_p.G540S	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	626	Gly-rich.				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)		CCCTCAGGACCCGACTGCGCC	0.677													C|||	275	0.0549121	0.0076	0.1167	5008	,	,		14353	0.0079		0.1392	False		,,,				2504	0.0368				p.G626S		Atlas-SNP	.											.	SCARF1	46	.	0			c.G1876A						PASS	.	C	SER/GLY,,SER/GLY	131,4275	90.2+/-128.9	0,131,2072	26.0	30.0	29.0		1876,,1618	1.5	0.3	17	dbSNP_126	29	1204,7396	232.8+/-266.3	80,1044,3176	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	56,,56	80,1175,5248	TT,TC,CC		14.0,2.9732,10.2645	benign,,benign	626/831,,540/745	1538669	1335,11671	2203	4300	6503	SO:0001583	missense	8578	exon11			CAGGACCCGACTG	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.1876G>A	17.37:g.1538669C>T	ENSP00000263071:p.Gly626Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	61	59	0.967213	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	165	0.07554945054945054	3	0.006097560975609756	51	0.1408839779005525	4	0.006993006993006993	107	0.14116094986807387	C	8.573	0.880576	0.17467	0.029732	0.14	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.36520	1.25;1.25	5.21	1.48	0.22813	.	0.771440	0.11051	N	0.605086	T	0.00241	0.0007	L	0.47716	1.5	0.80722	P	0.0	B;B	0.19583	0.037;0.027	B;B	0.15484	0.013;0.012	T	0.14035	-1.0487	9	0.22706	T	0.39	-4.2449	10.3537	0.43952	0.0:0.4454:0.403:0.1516	rs36108564	540;626	Q14162-2;Q14162	.;SREC_HUMAN	S	626;540	ENSP00000263071:G626S;ENSP00000323964:G540S	ENSP00000263071:G626S	G	-	1	0	SCARF1	1485419	0.000000	0.05858	0.327000	0.25402	0.015000	0.08874	0.444000	0.21661	0.477000	0.27464	0.555000	0.69702	GGT	C|0.913;T|0.087	0.087	strong		0.677	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
WIPF3	644150	hgsc.bcm.edu	37	7	29927688	29927688	+	Silent	SNP	C	C	T	rs61750796	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:29927688C>T	ENST00000409290.1	+	5	1104	c.1104C>T	c.(1102-1104)gcC>gcT	p.A368A	WIPF3_ENST00000409123.1_Silent_p.A368A|WIPF3_ENST00000242140.5_Silent_p.A368A	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	368					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						TGTAAGGGGCCGGTGGGGGAA	0.522													C|||	115	0.0229633	0.0129	0.0058	5008	,	,		19217	0.0476		0.0179	False		,,,				2504	0.0286				p.A368A		Atlas-SNP	.											.	WIPF3	46	.	0			c.C1104T						PASS	.	C		59,3823		0,59,1882	38.0	39.0	39.0		1104	3.0	0.9	7	dbSNP_129	39	111,8159		1,109,4025	no	coding-synonymous	WIPF3	NM_001080529.2		1,168,5907	TT,TC,CC		1.3422,1.5198,1.3989		368/484	29927688	170,11982	1941	4135	6076	SO:0001819	synonymous_variant	644150	exon6			AGGGGCCGGTGGG	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.1104C>T	7.37:g.29927688C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	79	16	0.202532	NM_001080529	B8ZZV2	Silent	SNP	ENST00000409290.1	37	CCDS56472.1																																																																																			C|0.979;T|0.021	0.021	strong		0.522	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
SP110	3431	hgsc.bcm.edu	37	2	231077110	231077110	+	Missense_Mutation	SNP	C	C	T	rs9061	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231077110C>T	ENST00000358662.4	-	5	697	c.619G>A	c.(619-621)Gaa>Aaa	p.E207K	SP110_ENST00000258381.6_Missense_Mutation_p.E207K|SP110_ENST00000540870.1_Missense_Mutation_p.E213K|SP110_ENST00000258382.5_Missense_Mutation_p.E207K|SP110_ENST00000392048.3_Missense_Mutation_p.E207K|SP110_ENST00000338556.3_5'UTR|SP110_ENST00000486146.2_5'UTR	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	207			E -> K (in dbSNP:rs9061). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16803959, ECO:0000269|PubMed:16816019}.		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)	p.E207K(1)		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)		GAGTCTTCTTCCGCATTCATT	0.473													C|||	654	0.130591	0.0681	0.0476	5008	,	,		21909	0.1726		0.0895	False		,,,				2504	0.273				p.E213K		Atlas-SNP	.											SP110,NS,carcinoma,0,1	SP110	105	1	1	Substitution - Missense(1)	stomach(1)	c.G637A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	342,4064	178.3+/-207.1	16,310,1877	228.0	176.0	194.0		637,619,619,619	-4.6	0.0	2	dbSNP_52	194	807,7793	188.4+/-235.4	36,735,3529	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	56,56,56,56	52,1045,5406	TT,TC,CC		9.3837,7.7621,8.8344	benign,benign,benign,benign	213/556,207/690,207/550,207/714	231077110	1149,11857	2203	4300	6503	SO:0001583	missense	3431	exon6			CTTCTTCCGCATT	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.619G>A	2.37:g.231077110C>T	ENSP00000351488:p.Glu207Lys	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	206	110	0.533981	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	253	0.11584249084249085	39	0.07926829268292683	24	0.06629834254143646	120	0.2097902097902098	70	0.09234828496042216	C	2.728	-0.265138	0.05754	0.077621	0.093837	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000409815	T;T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88;2.88	3.35	-4.55	0.03441	.	1.847310	0.02978	N	0.145246	T	0.00012	0.0000	N	0.02916	-0.46	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.20887	0.02;0.02;0.012;0.049	B;B;B;B	0.12837	0.008;0.008;0.002;0.008	T	0.41288	-0.9517	9	0.14252	T	0.57	.	5.2135	0.15331	0.0:0.2108:0.2935:0.4958	rs9061;rs1047241;rs1804028;rs3172149;rs11556888;rs52833597	207;213;207;207	G5E9C0;F5H1M1;Q9HB58;Q9HB58-6	.;.;SP110_HUMAN;.	K	207;207;207;207;213;207	ENSP00000258381:E207K;ENSP00000351488:E207K;ENSP00000375902:E207K;ENSP00000258382:E207K;ENSP00000439558:E213K;ENSP00000387172:E207K	ENSP00000258381:E207K	E	-	1	0	SP110	230785354	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.451000	0.06795	-1.181000	0.02730	-1.109000	0.02080	GAA	C|0.895;T|0.105	0.105	strong		0.473	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
C12orf71	728858	hgsc.bcm.edu	37	12	27235381	27235381	+	Silent	SNP	G	G	A	rs708168	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:27235381G>A	ENST00000429849.2	-	1	66	c.36C>T	c.(34-36)gaC>gaT	p.D12D		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	12										endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						TGGAGCTGTCGTCCTCTATGT	0.458													G|||	641	0.127995	0.0461	0.121	5008	,	,		19977	0.006		0.329	False		,,,				2504	0.1626				p.D12D		Atlas-SNP	.											.	C12orf71	20	.	0			c.C36T						PASS	.	G		319,3427		19,281,1573	34.0	32.0	32.0		36	-0.2	0.0	12	dbSNP_86	32	2596,5632		421,1754,1939	no	coding-synonymous	C12orf71	NM_001080406.1		440,2035,3512	AA,AG,GG		31.5508,8.5158,24.3444		12/270	27235381	2915,9059	1873	4114	5987	SO:0001819	synonymous_variant	728858	exon1			GCTGTCGTCCTCT		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.36C>T	12.37:g.27235381G>A		Somatic	495	2	0.0040404		WXS	Illumina HiSeq	Phase_I	451	211	0.467849	NM_001080406		Silent	SNP	ENST00000429849.2	37	CCDS44851.1																																																																																			G|0.820;A|0.180	0.180	strong		0.458	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
SPHKAP	80309	hgsc.bcm.edu	37	2	228855866	228855866	+	Missense_Mutation	SNP	G	G	C	rs16824283	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:228855866G>C	ENST00000392056.3	-	11	4855	c.4809C>G	c.(4807-4809)agC>agG	p.S1603R	SPHKAP_ENST00000344657.5_Missense_Mutation_p.S1574R	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1603			S -> R (in dbSNP:rs16824283).			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)		TCCTCTGGGGGCTGGCTGTTC	0.577													G|||	879	0.175519	0.0303	0.1931	5008	,	,		14524	0.2282		0.3022	False		,,,				2504	0.1748				p.S1603R		Atlas-SNP	.											SPHKAP_ENST00000392056,colon,carcinoma,0,2	SPHKAP	750	2	0			c.C4809G						PASS	.	G	ARG/SER,ARG/SER	296,4110	158.9+/-191.5	11,274,1918	43.0	45.0	44.0		4809,4722	-2.2	0.0	2	dbSNP_123	44	2318,6282	381.5+/-340.0	321,1676,2303	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	110,110	332,1950,4221	CC,CG,GG		26.9535,6.7181,20.0984	probably-damaging,probably-damaging	1603/1701,1574/1672	228855866	2614,10392	2203	4300	6503	SO:0001583	missense	80309	exon11			CTGGGGGCTGGCT		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.4809C>G	2.37:g.228855866G>C	ENSP00000375909:p.Ser1603Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	170	70	0.411765	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	435	0.19917582417582416	17	0.034552845528455285	77	0.212707182320442	120	0.2097902097902098	221	0.29155672823219	G	11.64	1.699048	0.30142	0.067181	0.269535	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.06608	3.28;3.28	6.17	-2.19	0.07015	A-kinase anchor 110kDa, C-terminal (1);	0.300797	0.43919	D	0.000501	T	0.00012	0.0000	L	0.48362	1.52	0.80722	P	0.0	D;P	0.54397	0.966;0.935	P;P	0.55923	0.787;0.613	T	0.19614	-1.0300	9	0.59425	D	0.04	.	13.8991	0.63792	0.6506:0.0:0.3494:0.0	rs16824283;rs16824283	1603;1574	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	R	1603;1574	ENSP00000375909:S1603R;ENSP00000339886:S1574R	ENSP00000339886:S1574R	S	-	3	2	SPHKAP	228564110	0.088000	0.21588	0.000000	0.03702	0.090000	0.18270	0.210000	0.17455	-0.511000	0.06514	-0.137000	0.14449	AGC	G|0.803;C|0.197	0.197	strong		0.577	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
SLC9C2	284525	hgsc.bcm.edu	37	1	173516903	173516903	+	Silent	SNP	A	A	G	rs10494490	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:173516903A>G	ENST00000367714.3	-	13	1904	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Silent_p.N392N	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	494					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TCTTCATATCATTATGTGAAA	0.338													G|||	2430	0.485224	0.671	0.3732	5008	,	,		18236	0.6448		0.2147	False		,,,				2504	0.4274				p.N494N		Atlas-SNP	.											SLC9A11,NS,carcinoma,-2,1	.	.	1	0			c.T1482C						PASS	.	G		2607,1799	529.7+/-372.7	790,1027,386	148.0	131.0	137.0		1482	-3.2	0.0	1	dbSNP_119	137	1797,6803	733.2+/-406.9	188,1421,2691	no	coding-synonymous	SLC9A11	NM_178527.3		978,2448,3077	GG,GA,AA		20.8953,40.8307,33.8613		494/1125	173516903	4404,8602	2203	4300	6503	SO:0001819	synonymous_variant	284525	exon13			CATATCATTATGT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1482T>C	1.37:g.173516903A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	207	71	0.342995	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			A|0.637;G|0.363	0.363	strong		0.338	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595802	140595802	+	Missense_Mutation	SNP	T	T	C	rs17844618	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140595802T>C	ENST00000341948.4	+	1	2294	c.2107T>C	c.(2107-2109)Ttt>Ctt	p.F703L		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	703					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)			GCTCTTCCTCTTTTCGGTGCT	0.687													T|||	584	0.116613	0.1233	0.1801	5008	,	,		16903	0.0397		0.159	False		,,,				2504	0.0982				p.F703L		Atlas-SNP	.											.	PCDHB13	142	.	0			c.T2107C						PASS	.	T	LEU/PHE	492,3908		36,420,1744	92.0	98.0	96.0		2107	-7.0	0.0	5	dbSNP_123	96	1344,7238		127,1090,3074	no	missense	PCDHB13	NM_018933.2	22	163,1510,4818	CC,CT,TT		15.6607,11.1818,14.1427	benign	703/799	140595802	1836,11146	2200	4291	6491	SO:0001583	missense	56123	exon1			TTCCTCTTTTCGG	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.2107T>C	5.37:g.140595802T>C	ENSP00000345491:p.Phe703Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_018933	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	269	0.12316849816849818	65	0.13211382113821138	57	0.1574585635359116	25	0.043706293706293704	122	0.16094986807387862	-	2.617	-0.289406	0.05605	0.111818	0.156607	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.07444	3.19	3.5	-6.99	0.01605	.	.	.	.	.	T	0.00012	0.0000	N	0.04335	-0.225	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38067	-0.9678	8	0.02654	T	1	.	2.6993	0.05143	0.1722:0.4218:0.194:0.212	rs17844618	703	Q9Y5F0	PCDBD_HUMAN	L	703;703;649	ENSP00000345491:F703L	ENSP00000345491:F703L	F	+	1	0	PCDHB13	140575986	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-0.846000	0.04336	-1.293000	0.02362	0.248000	0.18094	TTT	T|0.856;C|0.144	0.144	strong		0.687	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
RASL12	51285	hgsc.bcm.edu	37	15	65357558	65357558	+	Silent	SNP	A	A	G	rs36045000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65357558A>G	ENST00000220062.4	-	2	433	c.157T>C	c.(157-159)Ttg>Ctg	p.L53L	RASL12_ENST00000434605.2_Silent_p.L42L|RASL12_ENST00000421977.3_Intron	NM_016563.2	NP_057647.1	Q9NYN1	RASLC_HUMAN	RAS-like, family 12	53					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			lung(1)|ovary(1)|skin(1)|urinary_tract(1)	4						TTCTTACCCAAGTTGGGGTCA	0.562													A|||	47	0.00938498	0.0227	0.0029	5008	,	,		17164	0.0		0.0129	False		,,,				2504	0.002				p.L53L		Atlas-SNP	.											.	RASL12	32	.	0			c.T157C						PASS	.	A		83,4321	68.7+/-106.4	0,83,2119	133.0	97.0	110.0		157	3.4	1.0	15	dbSNP_126	110	115,8481	59.8+/-121.6	2,111,4185	no	coding-synonymous	RASL12	NM_016563.2		2,194,6304	GG,GA,AA		1.3378,1.8847,1.5231		53/267	65357558	198,12802	2202	4298	6500	SO:0001819	synonymous_variant	51285	exon2			TACCCAAGTTGGG	AF233588	CCDS10200.1	15q11.2-q22.33	2014-05-09			ENSG00000103710	ENSG00000103710			30289	protein-coding gene	gene with protein product	"""Ras family member Ris"""					12107412	Standard	NM_016563		Approved	RIS	uc002aoi.1	Q9NYN1	OTTHUMG00000133115	ENST00000220062.4:c.157T>C	15.37:g.65357558A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	101	18	0.178218	NM_016563	B2RC29|B4DJW2|B4DU82	Silent	SNP	ENST00000220062.4	37	CCDS10200.1																																																																																			A|0.987;G|0.013	0.013	strong		0.562	RASL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256782.2	NM_016563	
ZNF345	25850	hgsc.bcm.edu	37	19	37368535	37368535	+	Missense_Mutation	SNP	G	G	C	rs112729744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:37368535G>C	ENST00000529555.1	+	2	1591	c.803G>C	c.(802-804)aGt>aCt	p.S268T	ZNF345_ENST00000589046.1_Missense_Mutation_p.S268T|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000420450.1_Missense_Mutation_p.S268T			Q14585	ZN345_HUMAN	zinc finger protein 345	268					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	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(13)|lung(5)|ovary(2)|prostate(1)	24	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAGGCCTTTAGTTTTGGATCA	0.418													G|||	10	0.00199681	0.0	0.0058	5008	,	,		21427	0.0		0.006	False		,,,				2504	0.0				p.S268T		Atlas-SNP	.											.	ZNF345	68	.	0			c.G803C						PASS	.	G	THR/SER,THR/SER,THR/SER,THR/SER,THR/SER	11,4395	16.8+/-37.8	0,11,2192	84.0	87.0	86.0		803,803,803,803,803	1.6	1.0	19	dbSNP_132	86	106,8494	57.2+/-118.5	1,104,4195	no	missense,missense,missense,missense,missense	ZNF345	NM_001242472.1,NM_001242474.1,NM_001242475.1,NM_001242476.1,NM_003419.4	58,58,58,58,58	1,115,6387	CC,CG,GG		1.2326,0.2497,0.8996	benign,benign,benign,benign,benign	268/489,268/489,268/489,268/489,268/489	37368535	117,12889	2203	4300	6503	SO:0001583	missense	25850	exon4			CCTTTAGTTTTGG	X78933	CCDS12497.1	19q13.12	2013-01-08			ENSG00000251247	ENSG00000251247		"""Zinc fingers, C2H2-type"""	16367	protein-coding gene	gene with protein product						7865130	Standard	NM_003419		Approved	HZF10	uc002oey.4	Q14585	OTTHUMG00000048162	ENST00000529555.1:c.803G>C	19.37:g.37368535G>C	ENSP00000431202:p.Ser268Thr	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	4.013	-0.000126	0.07819	0.002497	0.012326	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.07567	3.18;3.18	3.96	1.58	0.23477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04815	0.0130	L	0.31371	0.925	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33929	-0.9849	9	0.35671	T	0.21	.	11.5634	0.50792	0.0:0.5461:0.4539:0.0	.	268	Q14585	ZN345_HUMAN	T	268;268;32	ENSP00000431216:S268T;ENSP00000431202:S268T	ENSP00000442320:S32T	S	+	2	0	ZNF345	42060375	0.000000	0.05858	1.000000	0.80357	0.994000	0.84299	-0.912000	0.04046	0.347000	0.23924	0.561000	0.74099	AGT	G|0.993;C|0.007	0.007	strong		0.418	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1		
FOXR1	283150	hgsc.bcm.edu	37	11	118851327	118851327	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118851327C>T	ENST00000317011.3	+	5	964	c.739C>T	c.(739-741)Cga>Tga	p.R247*		NM_181721.2	NP_859072.1	Q6PIV2	FOXR1_HUMAN	forkhead box R1	247					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(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16	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)		CACACGGCCTCGATCTTGCCT	0.587																																					p.R247X		Atlas-SNP	.											FOXR1,NS,carcinoma,-1,1	FOXR1	30	1	0			c.C739T						scavenged	.						66.0	67.0	67.0					11																	118851327		2200	4295	6495	SO:0001587	stop_gained	283150	exon5			CGGCCTCGATCTT	AB094092	CCDS31688.1	11q23.3	2008-02-05			ENSG00000176302	ENSG00000176302		"""Forkhead boxes"""	29980	protein-coding gene	gene with protein product		615755				15067358	Standard	XM_005271514		Approved	DLNB13, FOXN5	uc001pui.3	Q6PIV2	OTTHUMG00000166347	ENST00000317011.3:c.739C>T	11.37:g.118851327C>T	ENSP00000314806:p.Arg247*	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	130	4	0.0307692	NM_181721	B0YJ15|Q08AS8|Q86UT9|Q8IXX2	Nonsense_Mutation	SNP	ENST00000317011.3	37	CCDS31688.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.489968	0.84962	.	.	ENSG00000176302	ENST00000317011	.	.	.	5.41	3.52	0.40303	.	0.498913	0.21871	N	0.067892	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	6.9881	0.24739	0.1711:0.7403:0.0:0.0886	.	.	.	.	X	247	.	ENSP00000314806:R247X	R	+	1	2	FOXR1	118356537	0.992000	0.36948	0.715000	0.30552	0.368000	0.29767	2.414000	0.44627	0.633000	0.30452	-0.188000	0.12872	CGA	.	.	none		0.587	FOXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389312.1	NM_181721	
OLA1	29789	hgsc.bcm.edu	37	2	174946760	174946760	+	Missense_Mutation	SNP	T	T	C	rs11558990	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:174946760T>C	ENST00000409546.1	-	8	1451	c.821A>G	c.(820-822)tAt>tGt	p.Y274C	OLA1_ENST00000284719.3_Missense_Mutation_p.Y254C|OLA1_ENST00000392560.2_5'UTR|OLA1_ENST00000428402.2_Intron|OLA1_ENST00000344357.5_Missense_Mutation_p.Y96C					Obg-like ATPase 1											breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						ACCTGGGTCATACTTGTCCAC	0.418													T|||	482	0.096246	0.0703	0.1254	5008	,	,		16705	0.0159		0.1998	False		,,,				2504	0.0869				p.Y254C		Atlas-SNP	.											.	OLA1	37	.	0			c.A761G						PASS	.	T	CYS/TYR,CYS/TYR	426,3980	209.8+/-230.5	23,380,1800	103.0	99.0	101.0		287,761	3.1	1.0	2	dbSNP_120	101	1753,6845	319.0+/-313.9	198,1357,2744	yes	missense,missense	OLA1	NM_001011708.1,NM_013341.3	194,194	221,1737,4544	CC,CT,TT		20.3885,9.6686,16.7564	benign,benign	96/239,254/397	174946760	2179,10825	2203	4299	6502	SO:0001583	missense	29789	exon8			GGGTCATACTTGT		CCDS2255.1, CCDS42779.1	2q31.1	2014-06-24	2007-07-27	2007-07-27	ENSG00000138430	ENSG00000138430			28833	protein-coding gene	gene with protein product		611175	"""GTP-binding protein 9 (putative)"""	GTPBP9		17430889, 24486488	Standard	NM_013341		Approved	PTD004	uc002uih.3	Q9NTK5	OTTHUMG00000132335	ENST00000409546.1:c.821A>G	2.37:g.174946760T>C	ENSP00000386350:p.Tyr274Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_013341		Missense_Mutation	SNP	ENST00000409546.1	37		253	0.11584249084249085	39	0.07926829268292683	56	0.15469613259668508	10	0.017482517482517484	148	0.19525065963060687	T	8.292	0.817935	0.16607	0.096686	0.203885	ENSG00000138430	ENST00000284719;ENST00000344357;ENST00000409546;ENST00000429575	T;T	0.43294	0.95;0.95	5.58	3.11	0.35812	.	0.110120	0.64402	D	0.000010	T	0.00039	0.0001	L	0.27053	0.805	0.28177	P	0.9283201	B;P	0.36010	0.445;0.532	B;B	0.40134	0.32;0.06	T	0.11470	-1.0586	9	0.56958	D	0.05	.	12.6576	0.56795	0.0:0.0:0.2598:0.7402	rs11558990	96;254	Q9NTK5-2;Q9NTK5	.;OLA1_HUMAN	C	254;96;274;96	ENSP00000284719:Y254C;ENSP00000386350:Y274C	ENSP00000284719:Y254C	Y	-	2	0	OLA1	174655006	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.888000	0.48594	0.360000	0.24265	0.533000	0.62120	TAT	T|0.841;C|0.159	0.159	strong		0.418	OLA1-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000333877.1	NM_013341	
HBS1L	10767	hgsc.bcm.edu	37	6	135287533	135287533	+	Silent	SNP	A	A	G	rs13064	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:135287533A>G	ENST00000367837.5	-	17	2183	c.1977T>C	c.(1975-1977)ttT>ttC	p.F659F	HBS1L_ENST00000445176.2_Silent_p.F383F|HBS1L_ENST00000367824.4_Silent_p.F495F|HBS1L_ENST00000367826.2_Silent_p.F617F|HBS1L_ENST00000527578.1_Silent_p.F495F|HBS1L_ENST00000415177.2_Silent_p.F594F	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	659					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)		CCAGCTCTTTAAAGTCTTTAT	0.368													A|||	1299	0.259385	0.1906	0.2378	5008	,	,		16977	0.245		0.3549	False		,,,				2504	0.2843				p.F659F		Atlas-SNP	.											.	HBS1L	75	.	0			c.T1977C						PASS	.	A	,	1011,3395	376.8+/-322.2	113,785,1305	143.0	136.0	138.0		1851,1977	-9.0	0.4	6	dbSNP_52	138	3205,5395	484.5+/-371.4	595,2015,1690	no	coding-synonymous,coding-synonymous	HBS1L	NM_001145158.1,NM_006620.3	,	708,2800,2995	GG,GA,AA		37.2674,22.946,32.4158	,	617/643,659/685	135287533	4216,8790	2203	4300	6503	SO:0001819	synonymous_variant	10767	exon17			CTCTTTAAAGTCT	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.1977T>C	6.37:g.135287533A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	81	0.582734	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1																																																																																			A|0.692;G|0.308	0.308	strong		0.368	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
HDLBP	3069	hgsc.bcm.edu	37	2	242179134	242179134	+	Silent	SNP	G	G	A	rs10153800	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242179134G>A	ENST00000391975.1	-	19	2720	c.2493C>T	c.(2491-2493)ggC>ggT	p.G831G	HDLBP_ENST00000310931.4_Silent_p.G831G|HDLBP_ENST00000391976.2_Silent_p.G831G|HDLBP_ENST00000427183.2_Silent_p.G798G	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	831	KH 10. {ECO:0000255|PROSITE- ProRule:PRU00117}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)			breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|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;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		CCATCACCCCGCCATACTCTT	0.587													G|||	681	0.135982	0.1725	0.1902	5008	,	,		19432	0.001		0.2684	False		,,,				2504	0.0511				p.G831G		Atlas-SNP	.											.	HDLBP	118	.	0			c.C2493T						PASS	.	G	,	774,3632	313.8+/-293.3	58,658,1487	84.0	79.0	80.0		2493,2493	-10.8	0.0	2	dbSNP_119	80	2092,6508	360.6+/-332.0	257,1578,2465	no	coding-synonymous,coding-synonymous	HDLBP	NM_005336.4,NM_203346.3	,	315,2236,3952	AA,AG,GG		24.3256,17.567,22.036	,	831/1269,831/1269	242179134	2866,10140	2203	4300	6503	SO:0001819	synonymous_variant	3069	exon19			CACCCCGCCATAC		CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.2493C>T	2.37:g.242179134G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Silent	SNP	ENST00000391975.1	37	CCDS2547.1	352|352	0.16117216117216118|0.16117216117216118	72|72	0.14634146341463414|0.14634146341463414	78|78	0.2154696132596685|0.2154696132596685	1|1	0.0017482517482517483|0.0017482517482517483	201|201	0.26517150395778366|0.26517150395778366	G|G	6.986|6.986	0.552057|0.552057	0.13374|0.13374	0.17567|0.17567	0.243256|0.243256	ENSG00000115677|ENSG00000115677	ENST00000427487|ENST00000373292	.|.	.|.	.|.	5.41|5.41	-10.8|-10.8	0.00216|0.00216	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999710125|0.999999999710125	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.14839|0.14839	-1.0458|-1.0458	3|3	.|.	.|.	.|.	-18.8764|-18.8764	3.2359|3.2359	0.06765|0.06765	0.2438:0.0884:0.4068:0.2609|0.2438:0.0884:0.4068:0.2609	rs10153800;rs10153800|rs10153800;rs10153800	.|.	.|.	.|.	V|W	233|640	.|.	.|.	A|R	-|-	2|1	0|2	HDLBP|HDLBP	241827807|241827807	0.000000|0.000000	0.05858|0.05858	0.026000|0.026000	0.17262|0.17262	0.604000|0.604000	0.37047|0.37047	-2.605000|-2.605000	0.00889|0.00889	-1.863000|-1.863000	0.01150|0.01150	-1.288000|-1.288000	0.01363|0.01363	GCG|CGG	G|0.800;A|0.200	0.200	strong		0.587	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
PJA2	9867	hgsc.bcm.edu	37	5	108714329	108714329	+	Missense_Mutation	SNP	C	C	T	rs144230886	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:108714329C>T	ENST00000361189.2	-	4	1098	c.859G>A	c.(859-861)Gcc>Acc	p.A287T	PJA2_ENST00000511624.1_5'Flank|PJA2_ENST00000361557.3_Missense_Mutation_p.A287T	NM_014819.4	NP_055634.3	O43164	PJA2_HUMAN	praja ring finger 2, E3 ubiquitin protein ligase	287					long-term memory (GO:0007616)|protein ubiquitination (GO:0016567)|regulation of protein kinase A signaling (GO:0010738)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ligase activity (GO:0016874)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(142;4.4e-06)|all_epithelial(76;8.17e-08)|Prostate(80;0.00676)|Lung NSC(167;0.0436)|Ovarian(225;0.0443)|all_lung(232;0.053)|Colorectal(57;0.0946)|Breast(839;0.151)		OV - Ovarian serous cystadenocarcinoma(64;3.46e-10)|Epithelial(69;6.02e-09)|COAD - Colon adenocarcinoma(37;0.224)		GGACCACAGGCTGCATCTTCA	0.408																																					p.A287T		Atlas-SNP	.											PJA2,NS,carcinoma,+2,1	PJA2	53	1	0			c.G859A						scavenged	.						134.0	146.0	142.0					5																	108714329		2202	4300	6502	SO:0001583	missense	9867	exon4			CACAGGCTGCATC	AB007898	CCDS4099.1	5q22.1	2013-01-09	2012-02-23	2003-06-05	ENSG00000198961	ENSG00000198961		"""RING-type (C3HC4) zinc fingers"""	17481	protein-coding gene	gene with protein product			"""ring finger protein 131"", ""praja ring finger 2"""	RNF131			Standard	NM_014819		Approved	KIAA0438, Neurodap1	uc003kos.4	O43164	OTTHUMG00000128750	ENST00000361189.2:c.859G>A	5.37:g.108714329C>T	ENSP00000354775:p.Ala287Thr	Somatic	180	2	0.0111111		WXS	Illumina HiSeq	Phase_I	173	3	0.017341	NM_014819	A8K6U4|D3DSZ5|Q68D49|Q8N1G5	Missense_Mutation	SNP	ENST00000361189.2	37	CCDS4099.1	.	.	.	.	.	.	.	.	.	.	C	5.549	0.286122	0.10513	.	.	ENSG00000198961	ENST00000361189;ENST00000361557	T;T	0.05513	3.43;3.43	5.61	3.82	0.43975	.	0.726454	0.13281	N	0.399735	T	0.05640	0.0148	L	0.44542	1.39	0.09310	N	1	B	0.26002	0.139	B	0.21546	0.035	T	0.43458	-0.9390	10	0.15952	T	0.53	-0.0644	6.0592	0.19828	0.1498:0.6614:0.0:0.1888	.	287	O43164	PJA2_HUMAN	T	287	ENSP00000354775:A287T;ENSP00000355284:A287T	ENSP00000354775:A287T	A	-	1	0	PJA2	108742228	0.005000	0.15991	0.937000	0.37676	0.130000	0.20726	0.095000	0.15127	0.825000	0.34637	0.655000	0.94253	GCC	C|1.000;A|0.000	.	alt		0.408	PJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250663.1	NM_014819	
SLC16A5	9121	hgsc.bcm.edu	37	17	73089852	73089852	+	Silent	SNP	T	T	C	rs4788863	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73089852T>C	ENST00000450736.2	+	2	536	c.121T>C	c.(121-123)Ttg>Ctg	p.L41L	SLC16A5_ENST00000580123.1_Silent_p.L41L|SLC16A5_ENST00000538213.2_Silent_p.L81L|SLC16A5_ENST00000585293.1_3'UTR|SLC16A5_ENST00000329783.4_Silent_p.L41L			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	41					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	CTTCACTGAATTGCAATGGGA	0.632													C|||	3132	0.625399	0.7186	0.6412	5008	,	,		20101	0.3442		0.7127	False		,,,				2504	0.6881				p.L41L		Atlas-SNP	.											SLC16A5_ENST00000450736,NS,carcinoma,0,2	SLC16A5	80	2	0			c.T121C						PASS	.	C		3245,1161	411.5+/-335.8	1186,873,144	143.0	123.0	130.0		121	4.8	0.2	17	dbSNP_111	130	6255,2345	390.7+/-343.4	2274,1707,319	no	coding-synonymous	SLC16A5	NM_004695.2		3460,2580,463	CC,CT,TT		27.2674,26.3504,26.9568		41/506	73089852	9500,3506	2203	4300	6503	SO:0001819	synonymous_variant	9121	exon3			ACTGAATTGCAAT	U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"""Solute carriers"""	10926	protein-coding gene	gene with protein product		603879	"""solute carrier family 16 (monocarboxylic acid transporters), member 5"", ""solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"""			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.121T>C	17.37:g.73089852T>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_001271765	B4E288	Silent	SNP	ENST00000450736.2	37	CCDS11713.1																																																																																			T|0.323;C|0.677	0.677	strong		0.632	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695	
CDH1	999	hgsc.bcm.edu	37	16	68855966	68855966	+	Missense_Mutation	SNP	G	G	A	rs35187787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:68855966G>A	ENST00000261769.5	+	12	1965	c.1774G>A	c.(1774-1776)Gcc>Acc	p.A592T	RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000422392.2_Missense_Mutation_p.A531T|CDH1_ENST00000562836.1_3'UTR	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	592	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> T (in a thyroid cancer sample; may play a role in colorectal carcinogenesis; dbSNP:rs35187787). {ECO:0000269|PubMed:11562785, ECO:0000269|PubMed:8985087}.		adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.A592T(4)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		GAATGACAACGCCCCCATACC	0.458			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer				G|||	6	0.00119808	0.0008	0.0029	5008	,	,		21048	0.0		0.002	False		,,,				2504	0.001				p.A592T		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	CDH1,NS,carcinoma,0,4	CDH1	535	4	4	Substitution - Missense(4)	breast(2)|thyroid(1)|stomach(1)	c.G1774A	GRCh37	CM994192	CDH1	M	rs35187787	PASS	.	G	THR/ALA	5,4391	9.9+/-24.2	0,5,2193	133.0	121.0	125.0		1774	5.6	0.1	16	dbSNP_126	125	54,8546	34.3+/-88.2	0,54,4246	yes	missense	CDH1	NM_004360.3	58	0,59,6439	AA,AG,GG		0.6279,0.1137,0.454	possibly-damaging	592/883	68855966	59,12937	2198	4300	6498	SO:0001583	missense	999	exon12	Familial Cancer Database	HDGC	GACAACGCCCCCA	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1774G>A	16.37:g.68855966G>A	ENSP00000261769:p.Ala592Thr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	161	21	0.130435	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	15.26	2.781583	0.49891	0.001137	0.006279	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.61627	0.09;0.09	5.56	5.56	0.83823	Cadherin (4);Cadherin conserved site (1);Cadherin-like (2);	0.595783	0.14702	N	0.303477	T	0.45816	0.1361	L	0.45744	1.44	0.34229	D	0.676292	P;P	0.51791	0.948;0.492	B;B	0.38156	0.266;0.092	T	0.68153	-0.5484	10	0.87932	D	0	.	19.1853	0.93641	0.0:0.0:1.0:0.0	rs35187787	531;592	Q9UII8;P12830	.;CADH1_HUMAN	T	592;610;592;531	ENSP00000261769:A592T;ENSP00000414946:A531T	ENSP00000261769:A592T	A	+	1	0	CDH1	67413467	1.000000	0.71417	0.149000	0.22428	0.254000	0.26022	8.900000	0.92551	2.641000	0.89580	0.536000	0.68110	GCC	A|0.003;G|0.997	0.003	strong		0.458	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18504916	18504916	+	Silent	SNP	T	T	A	rs2277160	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:18504916T>A	ENST00000380548.4	+	2	492	c.153T>A	c.(151-153)ggT>ggA	p.G51G	ADAMTSL1_ENST00000431052.2_Silent_p.G51G|ADAMTSL1_ENST00000276935.6_Silent_p.G51G|ADAMTSL1_ENST00000380570.4_Silent_p.G51G|ADAMTSL1_ENST00000327883.7_Silent_p.G51G|ADAMTSL1_ENST00000380566.4_Silent_p.G51G	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	51	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.					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)		CCTGCGGGGGTGGGGCCTCCT	0.627													A|||	2859	0.570887	0.6725	0.5418	5008	,	,		16226	0.4444		0.5755	False		,,,				2504	0.5798				p.G51G		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.T153A						PASS	.	A	,	2876,1530	481.9+/-359.3	952,972,279	41.0	44.0	43.0		153,153	0.1	0.7	9	dbSNP_100	43	4844,3756	530.6+/-381.8	1368,2108,824	no	coding-synonymous,coding-synonymous	ADAMTSL1	NM_001040272.5,NM_052866.4	,	2320,3080,1103	AA,AT,TT		43.6744,34.7254,40.6428	,	51/1763,51/526	18504916	7720,5286	2203	4300	6503	SO:0001819	synonymous_variant	92949	exon2			CGGGGGTGGGGCC	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.153T>A	9.37:g.18504916T>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	43	40	0.930233	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																			T|0.415;A|0.585	0.585	strong		0.627	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331625	21331625	+	Silent	SNP	C	C	T	rs2291075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:21331625C>T	ENST00000256958.2	+	6	693	c.597C>T	c.(595-597)ttC>ttT	p.F199F		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	199					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)	TTGATGATTTCGCTAAAGAAG	0.358													T|||	2081	0.415535	0.5598	0.3314	5008	,	,		15258	0.5109		0.3966	False		,,,				2504	0.2014				p.F199F		Atlas-SNP	.											SLCO1B1,NS,carcinoma,+2,1	SLCO1B1	151	1	0			c.C597T						PASS	.	T		2401,2005	559.9+/-380.3	649,1103,451	122.0	113.0	116.0		597	2.5	1.0	12	dbSNP_100	116	3438,5162	636.0+/-399.1	695,2048,1557	yes	coding-synonymous	SLCO1B1	NM_006446.4		1344,3151,2008	TT,TC,CC		39.9767,45.5061,44.8947		199/692	21331625	5839,7167	2203	4300	6503	SO:0001819	synonymous_variant	10599	exon6			TGATTTCGCTAAA		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.597C>T	12.37:g.21331625C>T		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																			C|0.548;T|0.452	0.452	strong		0.358	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
FREM2	341640	hgsc.bcm.edu	37	13	39424253	39424253	+	Missense_Mutation	SNP	C	C	G	rs35252750|rs9548506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:39424253C>G	ENST00000280481.7	+	9	6674	c.6458C>G	c.(6457-6459)aCt>aGt	p.T2153S	FREM2_ENST00000482551.1_3'UTR	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2153	Calx-beta 4.		T -> S (in dbSNP:rs9548506). {ECO:0000269|PubMed:17974005}.		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)		ATCCATAGGACTGGGGATGTC	0.458													G|||	460	0.091853	0.0802	0.2478	5008	,	,		19704	0.001		0.0885	False		,,,				2504	0.0941				p.T2153S		Atlas-SNP	.											.	FREM2	385	.	0			c.C6458G						PASS	.	G	SER/THR	8,4398		3,2,2198	122.0	110.0	114.0		6458	3.1	0.8	13	dbSNP_119	114	22,8578		4,14,4282	yes	missense	FREM2	NM_207361.4	58	7,16,6480	GG,GC,CC		0.2558,0.1816,0.2307	benign	2153/3170	39424253	30,12976	2203	4300	6503	SO:0001583	missense	341640	exon9			ATAGGACTGGGGA	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.6458C>G	13.37:g.39424253C>G	ENSP00000280481:p.Thr2153Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	125	0.05723443223443223	27	0.054878048780487805	62	0.1712707182320442	1	0.0017482517482517483	35	0.04617414248021108	G	0.174	-1.069032	0.01918	0.001816	0.002558	ENSG00000150893	ENST00000280481	T	0.29917	1.55	5.79	3.13	0.36017	Na-Ca exchanger/integrin-beta4 (2);	0.091594	0.85682	N	0.000000	T	0.00039	0.0001	N	0.00991	-1.07	0.54753	P	1.7000000000044757E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36480	-0.9746	9	0.02654	T	1	.	8.9843	0.35983	0.1235:0.2282:0.6482:0.0	rs9548506;rs9548506	2153;2153	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	S	2153	ENSP00000280481:T2153S	ENSP00000280481:T2153S	T	+	2	0	FREM2	38322253	1.000000	0.71417	0.751000	0.31187	0.013000	0.08279	3.496000	0.53288	0.100000	0.17581	-0.120000	0.15030	ACT	C|0.913;G|0.087	0.087	strong		0.458	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
TYK2	7297	hgsc.bcm.edu	37	19	10463118	10463118	+	Missense_Mutation	SNP	G	G	C	rs34536443	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:10463118G>C	ENST00000525621.1	-	23	3791	c.3310C>G	c.(3310-3312)Ccc>Gcc	p.P1104A	TYK2_ENST00000264818.6_Missense_Mutation_p.P1104A|TYK2_ENST00000524462.1_Missense_Mutation_p.P919A|TYK2_ENST00000529422.1_Intron	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	1104	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> A (in dbSNP:rs34536443). {ECO:0000269|PubMed:17344846}.		cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|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 tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			ACCGTGGGGGGGCTCTGGCTG	0.592													g|||	51	0.0101837	0.0015	0.0202	5008	,	,		14995	0.0		0.0288	False		,,,				2504	0.0061				p.P1104A		Atlas-SNP	.											.	TYK2	126	.	0			c.C3310G	GRCh37	CM070300	TYK2	M	rs34536443	PASS	.	G	ALA/PRO	30,4376	36.0+/-67.5	0,30,2173	69.0	76.0	73.0		3310	4.3	1.0	19	dbSNP_126	73	347,8253	117.0+/-176.6	4,339,3957	yes	missense	TYK2	NM_003331.4	27	4,369,6130	CC,CG,GG		4.0349,0.6809,2.8987	probably-damaging	1104/1188	10463118	377,12629	2203	4300	6503	SO:0001583	missense	7297	exon23			TGGGGGGGCTCTG		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.3310C>G	19.37:g.10463118G>C	ENSP00000431885:p.Pro1104Ala	Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	260	160	0.615385	NM_003331	Q6QB10|Q96CH0	Missense_Mutation	SNP	ENST00000525621.1	37	CCDS12236.1	31	0.014194139194139194	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	23	0.030343007915567283	G	24.3	4.511294	0.85389	0.006809	0.040349	ENSG00000105397	ENST00000524462;ENST00000525621;ENST00000264818;ENST00000543792;ENST00000529739	T;T;T;D	0.82344	-1.32;-1.32;-1.32;-1.6	5.35	4.32	0.51571	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.273195	0.25750	N	0.028545	T	0.71617	0.3361	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.82143	-0.0603	10	0.87932	D	0	-42.3966	11.8328	0.52305	0.0853:0.0:0.9147:0.0	rs34536443	1104	P29597	TYK2_HUMAN	A	919;1104;1104;851;127	ENSP00000433203:P919A;ENSP00000431885:P1104A;ENSP00000264818:P1104A;ENSP00000436155:P127A	ENSP00000264818:P1104A	P	-	1	0	TYK2	10324118	1.000000	0.71417	0.978000	0.43139	0.888000	0.51559	7.317000	0.79018	1.283000	0.44513	0.549000	0.68633	CCC	G|0.975;C|0.025	0.025	strong		0.592	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
VPS53	55275	hgsc.bcm.edu	37	17	534812	534812	+	Missense_Mutation	SNP	G	G	A	rs138639431		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:534812G>A	ENST00000571805.1	-	8	801	c.665C>T	c.(664-666)gCg>gTg	p.A222V	VPS53_ENST00000401468.3_Intron|VPS53_ENST00000574029.1_Intron|VPS53_ENST00000291074.5_Missense_Mutation_p.A193V|VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000437048.2_Missense_Mutation_p.A222V|VPS53_ENST00000446250.2_Missense_Mutation_p.A24V			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	222					protein transport (GO:0015031)	endosome (GO:0005768)|GARP complex (GO:0000938)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(5)|lung(8)|prostate(1)	19				UCEC - Uterine corpus endometrioid carcinoma (25;0.0265)		GGAAGGAAACGCTTCTTCAAA	0.502													G|||	1	0.000199681	0.0	0.0	5008	,	,		21279	0.0		0.001	False		,,,				2504	0.0				p.A222V		Atlas-SNP	.											.	VPS53	109	.	0			c.C665T						PASS	.	G	VAL/ALA,VAL/ALA	0,4406		0,0,2203	153.0	117.0	129.0		665,578	5.8	1.0	17	dbSNP_134	129	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	VPS53	NM_001128159.2,NM_018289.3	64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	222/833,193/671	534812	1,13005	2203	4300	6503	SO:0001583	missense	55275	exon8			GGAAACGCTTCTT		CCDS10995.1, CCDS45558.1	17p13.3	2007-07-13	2006-12-19			ENSG00000141252			25608	protein-coding gene	gene with protein product		615850	"""vacuolar protein sorting 53 (yeast)"""			15878329	Standard	NM_018289		Approved	FLJ10979, HCCS1	uc010cjo.2	Q5VIR6		ENST00000571805.1:c.665C>T	17.37:g.534812G>A	ENSP00000459312:p.Ala222Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	109	47	0.431193	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.9	4.586261	0.86851	0.0	1.16E-4	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074;ENST00000389040	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.82	5.82	0.92795	Vps53-like, N-terminal (1);	0.212444	0.49305	D	0.000142	T	0.42899	0.1223	M	0.61703	1.905	0.80722	D	1	P;P;P;P	0.51537	0.946;0.786;0.821;0.786	P;B;B;B	0.47402	0.546;0.286;0.409;0.286	T	0.33548	-0.9864	10	0.62326	D	0.03	-8.2413	19.0968	0.93255	0.0:0.0:1.0:0.0	.	222;24;222;193	Q5VIR6-4;G3V0H8;Q5VIR6;Q5VIR6-2	.;.;VPS53_HUMAN;.	V	222;24;193;222	ENSP00000401435:A222V;ENSP00000394386:A24V;ENSP00000291074:A193V;ENSP00000373692:A222V	ENSP00000291074:A193V	A	-	2	0	VPS53	481562	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	9.199000	0.95003	2.756000	0.94617	0.563000	0.77884	GCG	G|1.000;A|0.000	0.000	strong		0.502	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289	
PHTF2	57157	hgsc.bcm.edu	37	7	77569559	77569559	+	Silent	SNP	C	C	T	rs1064040	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:77569559C>T	ENST00000248550.7	+	13	1756	c.1680C>T	c.(1678-1680)cgC>cgT	p.R560R	PHTF2_ENST00000424760.1_Silent_p.R522R|PHTF2_ENST00000307305.8_Silent_p.R522R|PHTF2_ENST00000416283.2_Silent_p.R526R|PHTF2_ENST00000275575.7_Silent_p.R522R|PHTF2_ENST00000422959.2_Silent_p.R526R			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	165	0	0		WXS	Illumina HiSeq	Phase_I	178	55	0.308989	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	
MAGI2	9863	hgsc.bcm.edu	37	7	78119109	78119109	+	Silent	SNP	C	C	T	rs3735442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:78119109C>T	ENST00000354212.4	-	6	1267	c.1014G>A	c.(1012-1014)aaG>aaA	p.K338K	MAGI2_ENST00000419488.1_Silent_p.K338K|MAGI2_ENST00000536571.1_Silent_p.K170K|MAGI2_ENST00000522391.1_Silent_p.K338K|MAGI2_ENST00000535697.1_Silent_p.K175K	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	338	Interaction with DDN.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GAGGTTTAGCCTTTTTCGCAA	0.373													C|||	1618	0.323083	0.4864	0.2334	5008	,	,		20046	0.2321		0.2952	False		,,,				2504	0.2883				p.K338K		Atlas-SNP	.											.	MAGI2	246	.	0			c.G1014A						PASS	.	C		1882,2524	542.0+/-375.9	408,1066,729	204.0	207.0	206.0		1014	5.5	1.0	7	dbSNP_107	206	2611,5989	420.6+/-353.4	405,1801,2094	no	coding-synonymous	MAGI2	NM_012301.3		813,2867,2823	TT,TC,CC		30.3605,42.7145,34.5456		338/1456	78119109	4493,8513	2203	4300	6503	SO:0001819	synonymous_variant	9863	exon6			TTTAGCCTTTTTC	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.1014G>A	7.37:g.78119109C>T		Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	259	159	0.6139	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	37	CCDS5594.1																																																																																			C|0.670;T|0.330	0.330	strong		0.373	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301	
COL6A5	256076	hgsc.bcm.edu	37	3	130189719	130189719	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:130189719C>T	ENST00000432398.2	+	39	7976	c.7482C>T	c.(7480-7482)gcC>gcT	p.A2494A	COL6A5_ENST00000265379.6_Silent_p.A2494A	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2494	Nonhelical 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						CTCCAGGTGCCATCAACAAAT	0.443																																					p.A2494A		Atlas-SNP	.											FLJ35880,rectum,carcinoma,+1,4	COL6A5	205	4	0			c.C7482T						scavenged	.						75.0	73.0	74.0					3																	130189719		1887	4121	6008	SO:0001819	synonymous_variant	256076	exon39			AGGTGCCATCAAC	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.7482C>T	3.37:g.130189719C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	93	2	0.0215054	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	C	10.17	1.276981	0.23307	.	.	ENSG00000172752	ENST00000512836	.	.	.	5.35	1.9	0.25705	.	.	.	.	.	T	0.44414	0.1292	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25847	-1.0120	4	.	.	.	.	2.8854	0.05660	0.2656:0.4446:0.0:0.2898	.	.	.	.	Y	746	.	.	H	+	1	0	COL6A5	131672409	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.435000	0.21510	0.498000	0.27948	-0.140000	0.14226	CAT	.	.	none		0.443	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
VPS13A	23230	hgsc.bcm.edu	37	9	79954545	79954545	+	Silent	SNP	T	T	C	rs7025532	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:79954545T>C	ENST00000360280.3	+	48	6752	c.6492T>C	c.(6490-6492)gaT>gaC	p.D2164D	VPS13A_ENST00000376636.3_Silent_p.D2125D|VPS13A_ENST00000376634.4_Silent_p.D2164D|VPS13A_ENST00000357409.5_Silent_p.D2164D	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2164					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						TCAATCACGATTGGAAAAGTG	0.358													T|||	815	0.16274	0.2307	0.1239	5008	,	,		16733	0.0337		0.1958	False		,,,				2504	0.1973				p.D2164D		Atlas-SNP	.											.	VPS13A	735	.	0			c.T6492C						PASS	.	T	,,,	988,3418	368.1+/-318.5	111,766,1326	79.0	67.0	71.0		6375,6492,6492,6492	-0.5	1.0	9	dbSNP_116	71	1727,6873	312.6+/-310.9	175,1377,2748	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	286,2143,4074	CC,CT,TT		20.0814,22.424,20.875	,,,	2125/3136,2164/3070,2164/3096,2164/3175	79954545	2715,10291	2203	4300	6503	SO:0001819	synonymous_variant	23230	exon48			TCACGATTGGAAA	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.6492T>C	9.37:g.79954545T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	107	105	0.981308	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			T|0.818;C|0.182	0.182	strong		0.358	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
ABCA13	154664	hgsc.bcm.edu	37	7	48315930	48315930	+	Missense_Mutation	SNP	G	G	C	rs74859514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:48315930G>C	ENST00000435803.1	+	17	6691	c.6667G>C	c.(6667-6669)Gca>Cca	p.A2223P		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2223					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						TTCTCAGGAAGCAGCTTGGAA	0.343													G|||	156	0.0311502	0.0045	0.0447	5008	,	,		17853	0.001		0.1024	False		,,,				2504	0.0153				p.A2223P		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G6667C						PASS	.	G	PRO/ALA	68,3578		0,68,1755	24.0	23.0	23.0		6667	3.2	0.0	7	dbSNP_132	23	747,7423		27,693,3365	yes	missense	ABCA13	NM_152701.3	27	27,761,5120	CC,CG,GG		9.1432,1.8651,6.8974	possibly-damaging	2223/5059	48315930	815,11001	1823	4085	5908	SO:0001583	missense	154664	exon17			CAGGAAGCAGCTT	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.6667G>C	7.37:g.48315930G>C	ENSP00000411096:p.Ala2223Pro	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	97	0.044413919413919416	7	0.014227642276422764	15	0.04143646408839779	0	0.0	75	0.09894459102902374	G	6.878	0.531385	0.13127	0.018651	0.091432	ENSG00000179869	ENST00000435803	T	0.30981	1.51	5.03	3.19	0.36642	.	0.444772	0.18764	N	0.131819	T	0.00666	0.0022	L	0.50333	1.59	0.49798	P	1.7900000000004024E-4	B	0.21309	0.054	B	0.20767	0.031	T	0.09292	-1.0681	8	.	.	.	.	9.5523	0.39317	0.1537:0.0:0.8463:0.0	.	2223	Q86UQ4	ABCAD_HUMAN	P	2223	ENSP00000411096:A2223P	.	A	+	1	0	ABCA13	48286476	0.930000	0.31532	0.015000	0.15790	0.034000	0.12701	1.981000	0.40628	0.508000	0.28173	0.491000	0.48974	GCA	G|0.939;C|0.061	0.061	strong		0.343	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
OR51Q1	390061	hgsc.bcm.edu	37	11	5444150	5444150	+	Silent	SNP	C	C	T	rs118011081	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5444150C>T	ENST00000300778.4	+	1	810	c.720C>T	c.(718-720)ctC>ctT	p.L240L	HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	240						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(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCCGTGCCCTCAATAACTGCC	0.488													C|||	45	0.00898562	0.0	0.0187	5008	,	,		20993	0.0		0.0278	False		,,,				2504	0.0041				p.L240L		Atlas-SNP	.											.	OR51Q1	79	.	0			c.C720T						PASS	.	C		21,4381	28.1+/-56.4	0,21,2180	137.0	114.0	122.0		720	3.1	0.9	11	dbSNP_132	122	170,8424	79.5+/-142.1	0,170,4127	no	coding-synonymous	OR51Q1	NM_001004757.2		0,191,6307	TT,TC,CC		1.9781,0.4771,1.4697		240/318	5444150	191,12805	2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			TGCCCTCAATAAC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.720C>T	11.37:g.5444150C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	37	CCDS31381.1																																																																																			C|0.985;T|0.015	0.015	strong		0.488	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
FLG	2312	hgsc.bcm.edu	37	1	152280759	152280759	+	Silent	SNP	A	A	G	rs2338554	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280759A>G	ENST00000368799.1	-	3	6638	c.6603T>C	c.(6601-6603)gaT>gaC	p.D2201D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2201	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCTAGAGCCATCTCCTGATT	0.552									Ichthyosis				-|||	1839	0.367212	0.472	0.3501	5008	,	,		27298	0.4454		0.1531	False		,,,				2504	0.3773				p.D2201D		Atlas-SNP	.											FLG,NS,carcinoma,-2,2	FLG	900	2	0			c.T6603C						scavenged	.	G		1706,2700		229,1248,726	444.0	388.0	407.0		6603	-4.9	0.0	1	dbSNP_100	407	945,7655		0,945,3355	no	coding-synonymous	FLG	NM_002016.1		229,2193,4081	GG,GA,AA		10.9884,38.7199,20.3829		2201/4062	152280759	2651,10355	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGAGCCATCTCCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6603T>C	1.37:g.152280759A>G		Somatic	349	2	0.00573066		WXS	Illumina HiSeq	Phase_I	641	104	0.162246	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			A|0.718;G|0.282	0.282	strong		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CEP170B	283638	hgsc.bcm.edu	37	14	105344293	105344293	+	Silent	SNP	C	C	T	rs61995995	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	95	0	0		WXS	Illumina HiSeq	Phase_I	136	82	0.602941	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	
BHLHE40	8553	hgsc.bcm.edu	37	3	5024771	5024771	+	Silent	SNP	T	T	C	rs908078	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:5024771T>C	ENST00000256495.3	+	5	1236	c.633T>C	c.(631-633)ggT>ggC	p.G211G		NM_003670.2	NP_003661.1	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	211					circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|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)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|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 negative regulation of transcription (GO:0001078)|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 negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)	12						CGGCCAAAGGTTCGGAAGGTC	0.592													C|||	791	0.157947	0.0855	0.2435	5008	,	,		17832	0.1915		0.1471	False		,,,				2504	0.1718				p.G211G		Atlas-SNP	.											.	BHLHE40	35	.	0			c.T633C						PASS	.	C		388,4018	786.8+/-414.8	15,358,1830	42.0	46.0	45.0		633	3.8	1.0	3	dbSNP_86	45	1334,7266	752.8+/-407.4	91,1152,3057	no	coding-synonymous	BHLHE40	NM_003670.2		106,1510,4887	CC,CT,TT		15.5116,8.8062,13.24		211/413	5024771	1722,11284	2203	4300	6503	SO:0001819	synonymous_variant	8553	exon5			CAAAGGTTCGGAA	AB004066	CCDS2565.1	3p26	2009-01-12	2009-01-12	2009-01-12	ENSG00000134107	ENSG00000134107		"""Basic helix-loop-helix proteins"""	1046	protein-coding gene	gene with protein product	"""differentially expressed in chondrocytes 1"", "" differentiated embryo chondrocyte expressed gene 1"""	604256	"""basic helix-loop-helix domain containing, class B, 2"""	STRA13, BHLHB2		9240428, 10449910, 18557763	Standard	NM_003670		Approved	DEC1, bHLHe40	uc003bqf.3	O14503	OTTHUMG00000119035	ENST00000256495.3:c.633T>C	3.37:g.5024771T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_003670	Q96TD3	Silent	SNP	ENST00000256495.3	37	CCDS2565.1																																																																																			T|0.855;C|0.145	0.145	strong		0.592	BHLHE40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239244.2	NM_003670	
TMPRSS11E	28983	hgsc.bcm.edu	37	4	69337325	69337325	+	Missense_Mutation	SNP	C	C	G	rs2603188	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:69337325C>G	ENST00000305363.4	+	5	538	c.474C>G	c.(472-474)caC>caG	p.H158Q		NM_014058.3	NP_054777.2	Q9UL52	TM11E_HUMAN	transmembrane protease, serine 11E	158	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.			H -> Q (in Ref. 3; AC019173). {ECO:0000305}.	cognition (GO:0050890)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|lung(19)|pancreas(1)|skin(3)	24						TAGATCCTCACTCAGTTAAAA	0.313													G|||	468	0.0934505	0.1248	0.0778	5008	,	,		13908	0.004		0.1551	False		,,,				2504	0.091				p.H158Q		Atlas-SNP	.											.	TMPRSS11E	40	.	0			c.C474G						PASS	.	G	GLN/HIS	470,3936	776.0+/-414.1	24,422,1757	102.0	107.0	105.0		474	-10.9	0.0	4	dbSNP_100	105	1212,7386	759.5+/-407.6	85,1042,3172	yes	missense	TMPRSS11E	NM_014058.3	24	109,1464,4929	GG,GC,CC		14.0963,10.6673,12.9345	benign	158/424	69337325	1682,11322	2203	4299	6502	SO:0001583	missense	28983	exon5			TCCTCACTCAGTT	AF064819	CCDS33993.1	4q13.2	2010-04-13			ENSG00000087128	ENSG00000087128		"""Serine peptidases / Transmembrane"""	24465	protein-coding gene	gene with protein product		610399	"""transmembrane protease, serine 11E2"""	TMPRSS11E2		15328353	Standard	NM_014058		Approved	DESC1	uc003hdz.4	Q9UL52	OTTHUMG00000160438	ENST00000305363.4:c.474C>G	4.37:g.69337325C>G	ENSP00000307519:p.His158Gln	Somatic	397	1	0.00251889		WXS	Illumina HiSeq	Phase_I	321	156	0.485981	NM_014058	A6NL71|Q14DC8|Q6UW31	Missense_Mutation	SNP	ENST00000305363.4	37	CCDS33993.1	198	0.09065934065934066	56	0.11382113821138211	27	0.07458563535911603	1	0.0017482517482517483	114	0.1503957783641161	G	0.664	-0.804394	0.02819	0.106673	0.140963	ENSG00000087128	ENST00000305363	T	0.32272	1.46	5.83	-10.9	0.00192	.	0.725069	0.12235	N	0.487060	T	0.00073	0.0002	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	0.27082	T	0.32	.	9.7094	0.40236	0.2174:0.3911:0.3915:0.0	.	158	Q9UL52	TM11E_HUMAN	Q	158	ENSP00000307519:H158Q	ENSP00000307519:H158Q	H	+	3	2	TMPRSS11E	69019920	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-2.211000	0.01226	-1.724000	0.01373	-2.686000	0.00141	CAC	C|0.887;G|0.113	0.113	strong		0.313	TMPRSS11E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360584.1	NM_014058	
CNTN4	152330	hgsc.bcm.edu	37	3	3067853	3067853	+	Silent	SNP	G	G	A	rs7639977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:3067853G>A	ENST00000397461.1	+	14	1938	c.1554G>A	c.(1552-1554)ccG>ccA	p.P518P	CNTN4_ENST00000397459.2_Silent_p.P190P|CNTN4_ENST00000418658.1_Silent_p.P518P|CNTN4_ENST00000358480.3_Silent_p.P299P|CNTN4_ENST00000427331.1_Silent_p.P518P|CNTN4_ENST00000448906.2_Silent_p.P190P	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	518	Ig-like C2-type 6.				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)		TTGTTTTACCGTGCCAGGTAA	0.428													G|||	715	0.142772	0.2935	0.0951	5008	,	,		18555	0.0903		0.1034	False		,,,				2504	0.0675				p.P518P		Atlas-SNP	.											.	CNTN4	335	.	0			c.G1554A						PASS	.	G	,,,	1223,3183	424.0+/-340.3	169,885,1149	191.0	160.0	171.0		1554,570,1554,570	-10.0	0.8	3	dbSNP_116	171	855,7745	194.8+/-240.1	36,783,3481	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CNTN4	NM_001206955.1,NM_001206956.1,NM_175607.2,NM_175613.2	,,,	205,1668,4630	AA,AG,GG		9.9419,27.7576,15.9772	,,,	518/1027,190/698,518/1027,190/699	3067853	2078,10928	2203	4300	6503	SO:0001819	synonymous_variant	152330	exon15			TTTACCGTGCCAG	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.1554G>A	3.37:g.3067853G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	191	93	0.486911	NM_175607	B2RAX3|Q8IX14|Q8TC35	Silent	SNP	ENST00000397461.1	37	CCDS43041.1																																																																																			G|0.858;A|0.142	0.142	strong		0.428	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
DNMT3L	29947	hgsc.bcm.edu	37	21	45670770	45670770	+	Missense_Mutation	SNP	T	T	C	rs7354779	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:45670770T>C	ENST00000418993.1	-	10	1315	c.832A>G	c.(832-834)Agg>Ggg	p.R278G	DNMT3L_ENST00000270172.3_Missense_Mutation_p.R278G|AP001059.5_ENST00000442785.1_RNA	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	196	0	0		WXS	Illumina HiSeq	Phase_I	225	138	0.613333	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	
GPR144	347088	hgsc.bcm.edu	37	9	127230891	127230891	+	Missense_Mutation	SNP	G	G	A	rs10760365	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:127230891G>A	ENST00000334810.1	+	14	2248	c.2248G>A	c.(2248-2250)Gtg>Atg	p.V750M				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	750					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						GTGGAGGAAGGTGGTAGCTGT	0.622													G|||	2605	0.520168	0.5371	0.5274	5008	,	,		16910	0.6171		0.4195	False		,,,				2504	0.4959				p.V750M		Atlas-SNP	.											.	GPR144	33	.	0			c.G2248A						PASS	.	G	MET/VAL	661,723		154,353,185	98.0	84.0	88.0		2248	4.9	1.0	9	dbSNP_120	88	1390,1792		305,780,506	yes	missense	GPR144	NM_001161808.1	21	459,1133,691	AA,AG,GG		43.6832,47.7601,44.919	probably-damaging	750/964	127230891	2051,2515	692	1591	2283	SO:0001583	missense	347088	exon14			AGGAAGGTGGTAG	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.2248G>A	9.37:g.127230891G>A	ENSP00000335156:p.Val750Met	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	1132|1132	0.5183150183150184|0.5183150183150184	242|242	0.491869918699187|0.491869918699187	185|185	0.511049723756906|0.511049723756906	381|381	0.666083916083916|0.666083916083916	324|324	0.42744063324538256|0.42744063324538256	G|G	17.72|17.72	3.459464|3.459464	0.63401|0.63401	0.477601|0.477601	0.436832|0.436832	ENSG00000180264|ENSG00000180264	ENST00000446588|ENST00000334810	.|T	.|0.49432	.|0.78	4.94|4.94	4.94|4.94	0.65067|0.65067	.|GPCR, family 2-like (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.72894|0.72894	2.215|2.215	0.22610|0.22610	P|P	0.99893717|0.99893717	D|D	0.63046|0.76494	0.992|0.999	P|D	0.56865|0.87578	0.808|0.998	T|T	0.50311|0.50311	-0.8843|-0.8843	7|8	0.44086|0.72032	T|D	0.13|0.01	.|.	16.7766|16.7766	0.85552|0.85552	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs10760365;rs57939835;rs10760365|rs10760365;rs57939835;rs10760365	18|750	A1E4E8|Q7Z7M1	.|GP144_HUMAN	D|M	18|750	.|ENSP00000335156:V750M	ENSP00000414478:G18D|ENSP00000335156:V750M	G|V	+|+	2|1	0|0	GPR144|GPR144	126270712|126270712	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.233000|0.233000	0.25261|0.25261	8.590000|8.590000	0.90821|0.90821	2.278000|2.278000	0.76064|0.76064	0.561000|0.561000	0.74099|0.74099	GGT|GTG	G|0.465;A|0.535	0.535	strong		0.622	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
TSGA13	114960	hgsc.bcm.edu	37	7	130368440	130368440	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:130368440T>C	ENST00000456951.1	-	4	945	c.94A>G	c.(94-96)Agc>Ggc	p.S32G	TSGA13_ENST00000356588.3_Missense_Mutation_p.S32G			Q96PP4	TSG13_HUMAN	testis specific, 13	32										endometrium(1)|kidney(3)|large_intestine(3)|lung(6)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	18	Melanoma(18;0.0435)					ACCTCTTTGCTATTGACAACC	0.373																																					p.S32G		Atlas-SNP	.											TSGA13,NS,carcinoma,+1,1	TSGA13	35	1	0			c.A94G						scavenged	.						209.0	182.0	191.0					7																	130368440		2203	4299	6502	SO:0001583	missense	114960	exon3			CTTTGCTATTGAC	AK093329	CCDS5824.1	7q32	2008-02-04			ENSG00000213265	ENSG00000213265			12369	protein-coding gene	gene with protein product							Standard	NM_052933		Approved		uc003vqi.3	Q96PP4	OTTHUMG00000154999	ENST00000456951.1:c.94A>G	7.37:g.130368440T>C	ENSP00000406047:p.Ser32Gly	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	135	2	0.0148148	NM_052933	B3KSC9	Missense_Mutation	SNP	ENST00000456951.1	37	CCDS5824.1	.	.	.	.	.	.	.	.	.	.	T	0.905	-0.721010	0.03182	.	.	ENSG00000213265	ENST00000456951;ENST00000418126;ENST00000356588;ENST00000443954;ENST00000438346	.	.	.	4.52	-5.68	0.02436	.	2.548760	0.01875	N	0.037519	T	0.21962	0.0529	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21724	-1.0237	9	0.10902	T	0.67	5.9062	9.2842	0.37746	0.0:0.617:0.1208:0.2622	.	32	Q96PP4	TSG13_HUMAN	G	32	.	ENSP00000348996:S32G	S	-	1	0	TSGA13	130018980	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.619000	0.05572	-1.148000	0.02847	-1.122000	0.02009	AGC	.	.	none		0.373	TSGA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337997.1	NM_052933	
RBM46	166863	hgsc.bcm.edu	37	4	155720274	155720274	+	Silent	SNP	T	T	C	rs156502	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:155720274T>C	ENST00000281722.3	+	4	1195	c.960T>C	c.(958-960)aaT>aaC	p.N320N	RBM46_ENST00000510397.1_Silent_p.N320N|RBM46_ENST00000514866.1_Silent_p.N320N	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	320							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				AGCATCTTAATGGTCAGATTA	0.398													C|||	3424	0.683706	0.9213	0.6787	5008	,	,		17912	0.747		0.4155	False		,,,				2504	0.5767				p.N320N		Atlas-SNP	.											.	RBM46	76	.	0			c.T960C						PASS	.	C		3723,683	283.1+/-276.9	1594,535,74	68.0	71.0	70.0		960	3.8	1.0	4	dbSNP_79	70	3527,5073	630.4+/-398.4	710,2107,1483	no	coding-synonymous	RBM46	NM_144979.3		2304,2642,1557	CC,CT,TT		41.0116,15.5016,44.2565		320/534	155720274	7250,5756	2203	4300	6503	SO:0001819	synonymous_variant	166863	exon4			TCTTAATGGTCAG	BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"""RNA binding motif (RRM) containing"""	28401	protein-coding gene	gene with protein product	"""cancer/testis antigen 68"""					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.960T>C	4.37:g.155720274T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	92	24	0.26087	NM_144979	B3KWU8|B4DZ27	Silent	SNP	ENST00000281722.3	37	CCDS3790.1																																																																																			T|0.395;C|0.605	0.605	strong		0.398	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979	
HRNR	388697	hgsc.bcm.edu	37	1	152188847	152188847	+	Missense_Mutation	SNP	A	A	G	rs145667921		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152188847A>G	ENST00000368801.2	-	3	5333	c.5258T>C	c.(5257-5259)gTc>gCc	p.V1753A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_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	1390	64	0.0460432		WXS	Illumina HiSeq	Phase_I	985	82	0.0832487	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	
BNC2	54796	hgsc.bcm.edu	37	9	16435714	16435714	+	Silent	SNP	T	T	C	rs3739715	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:16435714T>C	ENST00000380672.4	-	6	2535	c.2478A>G	c.(2476-2478)ctA>ctG	p.L826L	BNC2_ENST00000545497.1_Silent_p.L731L|BNC2_ENST00000380667.2_Silent_p.L759L|BNC2_ENST00000380666.2_Silent_p.L826L	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GGCTAGAACATAGGTCACCTT	0.473													C|||	395	0.0788738	0.1551	0.0548	5008	,	,		18864	0.0268		0.0716	False		,,,				2504	0.0542				p.L826L		Atlas-SNP	.											.	BNC2	166	.	0			c.A2478G						PASS	.	C		623,3783	767.9+/-413.5	54,515,1634	71.0	68.0	69.0		2478	5.0	1.0	9	dbSNP_107	69	722,7878	786.7+/-407.6	27,668,3605	no	coding-synonymous	BNC2	NM_017637.5		81,1183,5239	CC,CT,TT		8.3953,14.1398,10.3414		826/1100	16435714	1345,11661	2203	4300	6503	SO:0001819	synonymous_variant	54796	exon6			AGAACATAGGTCA	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.2478A>G	9.37:g.16435714T>C		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_017637		Silent	SNP	ENST00000380672.4	37	CCDS6482.2																																																																																			T|0.903;C|0.097	0.097	strong		0.473	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	
SLC16A8	23539	hgsc.bcm.edu	37	22	38477275	38477275	+	Missense_Mutation	SNP	G	G	A	rs75640043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	94	0	0		WXS	Illumina HiSeq	Phase_I	46	44	0.956522	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	
KRT5	3852	hgsc.bcm.edu	37	12	52911401	52911401	+	Silent	SNP	T	T	G	rs4761924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	108	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	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		
TRIOBP	11078	hgsc.bcm.edu	37	22	38121152	38121152	+	Missense_Mutation	SNP	C	C	A	rs9610841	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	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		
CNKSR3	154043	hgsc.bcm.edu	37	6	154763401	154763401	+	Silent	SNP	G	G	A	rs6557351	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:154763401G>A	ENST00000607772.1	-	3	784	c.240C>T	c.(238-240)aaC>aaT	p.N80N	CNKSR3_ENST00000479339.1_5'UTR	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	80	CRIC. {ECO:0000255|PROSITE- ProRule:PRU00621}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.N80N(1)		breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		AGTTCTTCATGTTATCAGTTT	0.428													A|||	1879	0.3752	0.6203	0.3602	5008	,	,		20916	0.2857		0.2445	False		,,,				2504	0.2812				p.N80N		Atlas-SNP	.											CNKSR3,NS,carcinoma,0,1	CNKSR3	56	1	1	Substitution - coding silent(1)	stomach(1)	c.C240T						PASS	.	A		2556,1850	535.8+/-374.3	725,1106,372	78.0	85.0	83.0		240	-11.1	0.0	6	dbSNP_116	83	1730,6870	736.2+/-407.0	175,1380,2745	no	coding-synonymous	CNKSR3	NM_173515.2		900,2486,3117	AA,AG,GG		20.1163,41.9882,32.954		80/556	154763401	4286,8720	2203	4300	6503	SO:0001819	synonymous_variant	154043	exon3			CTTCATGTTATCA	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"""Sterile alpha motif (SAM) domain containing"""	23034	protein-coding gene	gene with protein product			"""membrane associated guanylate kinase interacting protein-like 1"""	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.240C>T	6.37:g.154763401G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_173515	Q5SGD5|Q96N65	Silent	SNP	ENST00000607772.1	37	CCDS5246.1																																																																																			G|0.660;A|0.340	0.340	strong		0.428	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515	
ANGPT4	51378	hgsc.bcm.edu	37	20	854940	854940	+	Silent	SNP	T	T	C	rs944110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:854940T>C	ENST00000381922.3	-	8	1440	c.1338A>G	c.(1336-1338)caA>caG	p.Q446Q	ANGPT4_ENST00000546022.1_Intron	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	446	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						CAGACATCACTTGGGCACACT	0.612													C|||	2569	0.512979	0.5227	0.4337	5008	,	,		21990	0.6905		0.3191	False		,,,				2504	0.5726				p.Q446Q	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											ANGPT4,colon,carcinoma,0,2	ANGPT4	77	2	0			c.A1338G						PASS	.	C		2205,2201	588.4+/-386.9	537,1131,535	107.0	81.0	90.0		1338	4.2	1.0	20	dbSNP_86	90	2879,5721	672.1+/-402.9	491,1897,1912	no	coding-synonymous	ANGPT4	NM_015985.2		1028,3028,2447	CC,CT,TT		33.4767,49.9546,39.0897		446/504	854940	5084,7922	2203	4300	6503	SO:0001819	synonymous_variant	51378	exon8			CATCACTTGGGCA	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"""Fibrinogen C domain containing"""	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.1338A>G	20.37:g.854940T>C		Somatic	288	1	0.00347222		WXS	Illumina HiSeq	Phase_I	269	132	0.490706	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			T|0.549;C|0.451	0.451	strong		0.612	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985	
ITGA4	3676	hgsc.bcm.edu	37	2	182395345	182395345	+	Missense_Mutation	SNP	G	G	A	rs1143676	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:182395345G>A	ENST00000397033.2	+	24	3063	c.2633G>A	c.(2632-2634)cGg>cAg	p.R878Q		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	878			R -> Q (in dbSNP:rs1143676). {ECO:0000269|PubMed:8643114, ECO:0000269|Ref.5}.		B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	GGCATAGTCCGGTTCTTGTCC	0.403													A|||	3959	0.790535	0.7542	0.8026	5008	,	,		20207	0.8413		0.669	False		,,,				2504	0.9039				p.R878Q		Atlas-SNP	.											.	ITGA4	142	.	0			c.G2633A						PASS	.	A	GLN/ARG	2847,937		1080,687,125	202.0	181.0	188.0		2633	-10.9	0.0	2	dbSNP_86	188	5596,2654		1908,1780,437	yes	missense	ITGA4	NM_000885.4	43	2988,2467,562	AA,AG,GG		32.1697,24.7622,29.8405	benign	878/1033	182395345	8443,3591	1892	4125	6017	SO:0001583	missense	3676	exon24			TAGTCCGGTTCTT		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.2633G>A	2.37:g.182395345G>A	ENSP00000380227:p.Arg878Gln	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	233	229	0.982833	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	1619	0.7413003663003663	362	0.7357723577235772	277	0.7651933701657458	480	0.8391608391608392	500	0.6596306068601583	A	10.58	1.390478	0.25118	0.752378	0.678303	ENSG00000115232	ENST00000397033	T	0.44083	0.93	5.45	-10.9	0.00192	.	1.265470	0.05097	N	0.486427	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22003	0.063	B	0.22753	0.041	T	0.21211	-1.0252	9	0.18276	T	0.48	.	1.4346	0.02341	0.3668:0.2961:0.1653:0.1718	rs1143676;rs2305579;rs4667319;rs17484822;rs52836429;rs58692589;rs4667319	878	P13612	ITA4_HUMAN	Q	878	ENSP00000380227:R878Q	ENSP00000380227:R878Q	R	+	2	0	ITGA4	182103590	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-3.957000	0.00325	-3.283000	0.00196	-0.360000	0.07572	CGG	G|0.258;A|0.742	0.742	strong		0.403	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
KIAA0226	9711	hgsc.bcm.edu	37	3	197432029	197432029	+	Silent	SNP	C	C	A	rs60457064	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:197432029C>A	ENST00000296343.5	-	3	236	c.237G>T	c.(235-237)acG>acT	p.T79T	KIAA0226_ENST00000389665.5_Silent_p.T79T|KIAA0226_ENST00000449205.1_Silent_p.T79T|KIAA0226_ENST00000273582.5_Silent_p.T19T|KIAA0226_ENST00000467303.1_5'UTR	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	79	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				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)		GCCAGTAATCCGTCTGGCGGC	0.537													A|||	768	0.153355	0.3699	0.0692	5008	,	,		20417	0.0308		0.1034	False		,,,				2504	0.0982				p.T79T	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.G237T						PASS	.	A	,	1255,2771		172,911,930	54.0	54.0	54.0		57,237	-1.5	1.0	3	dbSNP_129	54	787,7569		38,711,3429	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	210,1622,4359	AA,AC,CC		9.4184,31.1724,16.4917	,	19/928,79/973	197432029	2042,10340	2013	4178	6191	SO:0001819	synonymous_variant	9711	exon3			GTAATCCGTCTGG	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.237G>T	3.37:g.197432029C>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	68	45	0.661765	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	307	0.14056776556776557	179	0.3638211382113821	27	0.07458563535911603	24	0.04195804195804196	77	0.10158311345646438	A	10.54	1.379884	0.24944	0.311724	0.094184	ENSG00000145016	ENST00000413360	.	.	.	5.63	-1.45	0.08828	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999995791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.7535	0.00994	0.2454:0.3228:0.2227:0.2091	rs60457064;rs61744833	.	.	.	X	58	.	.	G	-	1	0	KIAA0226	198916426	0.045000	0.20229	0.960000	0.40013	0.967000	0.64934	-0.645000	0.05409	-0.430000	0.07318	-0.269000	0.10298	GGA	C|0.877;A|0.123	0.123	strong		0.537	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
ST6GALNAC5	81849	hgsc.bcm.edu	37	1	77510008	77510008	+	Silent	SNP	C	C	A	rs35763299	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:77510008C>A	ENST00000477717.1	+	3	616	c.381C>A	c.(379-381)ccC>ccA	p.P127P		NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	127					glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						ATGACGCCCCCACACGCGGCT	0.622													C|||	75	0.014976	0.0015	0.0331	5008	,	,		20009	0.0		0.0398	False		,,,				2504	0.0102				p.P127P		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.C381A						PASS	.	C		17,4389	22.3+/-47.3	1,15,2187	65.0	59.0	61.0		381	1.6	1.0	1	dbSNP_126	61	232,8368	94.0+/-155.9	5,222,4073	no	coding-synonymous	ST6GALNAC5	NM_030965.1		6,237,6260	AA,AC,CC		2.6977,0.3858,1.9145		127/337	77510008	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	81849	exon3			CGCCCCCACACGC		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"""Sialyltransferases"""	19342	protein-coding gene	gene with protein product		610134	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"""	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	ENST00000477717.1:c.381C>A	1.37:g.77510008C>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	65	19	0.292308	NM_030965	B1AK82	Silent	SNP	ENST00000477717.1	37	CCDS673.1																																																																																			T|0.009;C|0.980;A|0.010	0.010	strong		0.622	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965	
CASP8	841	hgsc.bcm.edu	37	2	202149589	202149589	+	Missense_Mutation	SNP	G	G	C	rs1045485	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:202149589G>C	ENST00000432109.2	+	9	1042	c.853G>C	c.(853-855)Gat>Cat	p.D285H	CASP8_ENST00000323492.7_Missense_Mutation_p.D270H|CASP8_ENST00000358485.4_Missense_Mutation_p.D344H|CASP8_ENST00000264274.9_Missense_Mutation_p.D201H|CASP8_ENST00000392259.2_3'UTR|CASP8_ENST00000392266.3_3'UTR|CASP8_ENST00000264275.5_Missense_Mutation_p.D302H	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	285			D -> H (associated with protection against breast cancer; also associated with a lower risk of cutaneous melanoma; dbSNP:rs1045485). {ECO:0000269|PubMed:11161814, ECO:0000269|PubMed:15601643, ECO:0000269|PubMed:17293864, ECO:0000269|PubMed:18563783, ECO:0000269|PubMed:8755496, ECO:0000269|PubMed:9228018, ECO:0000269|Ref.9}.		activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|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)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						CAAGCCCCACGATGACTGCAC	0.433										HNSCC(4;0.00038)			G|||	264	0.0527157	0.0499	0.0764	5008	,	,		18179	0.001		0.1203	False		,,,				2504	0.0235				p.D344H	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											.	CASP8	272	.	0			c.G1030C	GRCh37	CM043455	CASP8	M	rs1045485	PASS	.	G	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	316,4090	169.1+/-199.8	19,278,1906	99.0	91.0	94.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	808,1030,904,853,808	-3.4	0.0	2	dbSNP_86	94	1111,7489	231.7+/-265.6	68,975,3257	yes	missense,missense,missense,missense,missense	CASP8	NM_001080124.1,NM_001080125.1,NM_001228.4,NM_033355.3,NM_033356.3	81,81,81,81,81	87,1253,5163	CC,CG,GG		12.9186,7.172,10.9719	benign,benign,benign,benign,benign	270/465,344/539,302/497,285/480,270/465	202149589	1427,11579	2203	4300	6503	SO:0001583	missense	841	exon8			CCCCACGATGACT	U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"""Caspases"""	1509	protein-coding gene	gene with protein product		601763	"""caspase 8, apoptosis-related cysteine protease"""			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.853G>C	2.37:g.202149589G>C	ENSP00000412523:p.Asp285His	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	114	29	0.254386	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Missense_Mutation	SNP	ENST00000432109.2	37	CCDS2342.1	148	0.06776556776556776	26	0.052845528455284556	35	0.09668508287292818	0	0.0	87	0.11477572559366754	G	9.874	1.199660	0.22121	0.07172	0.129186	ENSG00000064012	ENST00000392263;ENST00000264274;ENST00000432109;ENST00000264275;ENST00000358485;ENST00000323492;ENST00000444430	T;T;T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68;1.68;1.68	5.6	-3.42	0.04825	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	0.930924	0.09276	N	0.824512	T	0.00144	0.0004	N	0.26162	0.8	0.80722	P	0.0	B;B;B;B;B	0.33103	0.129;0.0;0.002;0.009;0.397	B;B;B;B;B	0.31390	0.052;0.002;0.009;0.012;0.129	T	0.27839	-1.0062	9	0.40728	T	0.16	.	8.7636	0.34689	0.4585:0.1164:0.4251:0.0	rs1045485;rs3185368;rs4134559;rs17649729;rs17860425;rs1045485	201;344;285;270;302	Q14790-3;Q14790-9;Q14790;Q14790-2;Q14790-4	.;.;CASP8_HUMAN;.;.	H	270;201;285;302;344;270;64	ENSP00000376091:D270H;ENSP00000264274:D201H;ENSP00000412523:D285H;ENSP00000264275:D302H;ENSP00000351273:D344H;ENSP00000325722:D270H;ENSP00000394434:D64H	ENSP00000264274:D201H	D	+	1	0	CASP8	201857834	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.532000	0.06164	-0.187000	0.10516	-1.306000	0.01317	GAT	G|0.901;C|0.099	0.099	strong		0.433	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228	
KLHL36	79786	hgsc.bcm.edu	37	16	84695280	84695280	+	Silent	SNP	A	A	G	rs17755815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:84695280A>G	ENST00000564996.1	+	5	1533	c.1392A>G	c.(1390-1392)ctA>ctG	p.L464L	KLHL36_ENST00000258157.5_Silent_p.L401L	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	464					protein ubiquitination (GO:0016567)					endometrium(3)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						AGAACCTGCTATGCTACGACC	0.627													A|||	887	0.177117	0.3714	0.1081	5008	,	,		15033	0.0347		0.2068	False		,,,				2504	0.0798				p.L464L		Atlas-SNP	.											KLHL36,NS,carcinoma,0,1	KLHL36	51	1	0			c.A1392G						PASS	.	A		1570,2828	491.5+/-362.1	277,1016,906	83.0	78.0	80.0		1392	1.4	1.0	16	dbSNP_123	80	1956,6644	344.6+/-325.4	231,1494,2575	no	coding-synonymous	KLHL36	NM_024731.2		508,2510,3481	GG,GA,AA		22.7442,35.698,27.1273		464/617	84695280	3526,9472	2199	4300	6499	SO:0001819	synonymous_variant	79786	exon5			CCTGCTATGCTAC	AK022605	CCDS10948.1	16q24.1	2013-02-22	2013-02-22	2008-07-07	ENSG00000135686	ENSG00000135686		"""Kelch-like"", ""BTB/POZ domain containing"""	17844	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 44"", ""kelch-like 36 (Drosophila)"""	C16orf44			Standard	NM_024731		Approved	FLJ12543	uc002fig.3	Q8N4N3	OTTHUMG00000137642	ENST00000564996.1:c.1392A>G	16.37:g.84695280A>G		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	123	103	0.837398	NM_024731	Q8N5G6|Q9H9U6	Silent	SNP	ENST00000564996.1	37	CCDS10948.1																																																																																			A|0.757;G|0.243	0.243	strong		0.627	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2		
TINAG	27283	hgsc.bcm.edu	37	6	54173413	54173413	+	Missense_Mutation	SNP	A	A	G	rs2297980	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:54173413A>G	ENST00000259782.4	+	1	161	c.65A>G	c.(64-66)cAg>cGg	p.Q22R	TINAG_ENST00000486436.1_3'UTR|TINAG_ENST00000370869.3_Missense_Mutation_p.Q18R|TINAG_ENST00000370864.3_Missense_Mutation_p.Q4R	NM_014464.3	NP_055279.3	Q9UJW2	TINAG_HUMAN	tubulointerstitial nephritis antigen	22			Q -> R (in dbSNP:rs2297980).		cell adhesion (GO:0007155)|immune response (GO:0006955)	basement membrane (GO:0005604)	cysteine-type endopeptidase activity (GO:0004197)|nucleotide binding (GO:0000166)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(1)	34	Lung NSC(77;0.0518)		LUSC - Lung squamous cell carcinoma(124;0.246)			ATGGAGAAGCAGTATTTATCT	0.403													A|||	305	0.0609026	0.0961	0.0418	5008	,	,		20239	0.005		0.0905	False		,,,				2504	0.0542				p.Q22R		Atlas-SNP	.											.	TINAG	102	.	0			c.A65G						PASS	.	A	ARG/GLN	454,3952	217.4+/-235.8	27,400,1776	78.0	75.0	76.0		65	-4.0	0.0	6	dbSNP_100	76	911,7689	201.7+/-245.1	48,815,3437	yes	missense	TINAG	NM_014464.3	43	75,1215,5213	GG,GA,AA		10.593,10.3041,10.4952	benign	22/477	54173413	1365,11641	2203	4300	6503	SO:0001583	missense	27283	exon1			AGAAGCAGTATTT	AB022277	CCDS4955.1	6p12.1	2008-05-15			ENSG00000137251	ENSG00000137251			14599	protein-coding gene	gene with protein product		606749				10652240	Standard	NM_014464		Approved		uc003pcj.2	Q9UJW2	OTTHUMG00000014893	ENST00000259782.4:c.65A>G	6.37:g.54173413A>G	ENSP00000259782:p.Gln22Arg	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	145	77	0.531034	NM_014464	Q5T467|Q9UJW1|Q9ULZ4	Missense_Mutation	SNP	ENST00000259782.4	37	CCDS4955.1	147	0.0673076923076923	49	0.09959349593495935	23	0.06353591160220995	4	0.006993006993006993	71	0.09366754617414248	A	6.649	0.488254	0.12641	0.103041	0.10593	ENSG00000137251	ENST00000370869;ENST00000339741;ENST00000259782;ENST00000370864	T;T;T	0.64618	1.99;-0.11;1.93	5.13	-4.04	0.04010	.	1.522260	0.03689	N	0.246789	T	0.20901	0.0503	L	0.52364	1.645	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.04178	-1.0971	9	0.05959	T	0.93	.	3.7152	0.08435	0.3908:0.0:0.3328:0.2765	rs2297980;rs52793231;rs59264675;rs2297980	22;22	Q9UJW2;Q7Z477	TINAG_HUMAN;.	R	18;22;22;4	ENSP00000359906:Q18R;ENSP00000259782:Q22R;ENSP00000359901:Q4R	ENSP00000259782:Q22R	Q	+	2	0	TINAG	54281372	0.107000	0.21998	0.000000	0.03702	0.868000	0.49771	0.141000	0.16076	-0.930000	0.03752	0.482000	0.46254	CAG	A|0.911;G|0.089	0.089	strong		0.403	TINAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040984.1	NM_014464	
ABHD12B	145447	hgsc.bcm.edu	37	14	51370852	51370852	+	Missense_Mutation	SNP	C	C	G	rs34800262	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:51370852C>G	ENST00000337334.2	+	12	1018	c.1003C>G	c.(1003-1005)Cct>Gct	p.P335A	ABHD12B_ENST00000353130.1_Missense_Mutation_p.P258A|ABHD12B_ENST00000395752.1_Missense_Mutation_p.P228A|PYGL_ENST00000532462.1_Intron	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	335							hydrolase activity (GO:0016787)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					GGTTATCTTTCCTCCTGGCTT	0.443													C|||	596	0.11901	0.0983	0.0865	5008	,	,		21457	0.0913		0.0915	False		,,,				2504	0.227				p.P335A		Atlas-SNP	.											ABHD12B_ENST00000337334,right_upper_lobe,carcinoma,-1,2	ABHD12B	53	2	0			c.C1003G						PASS	.	C	ALA/PRO,ALA/PRO	452,3954	216.8+/-235.3	22,408,1773	213.0	211.0	212.0		1003,772	4.9	1.0	14	dbSNP_126	212	717,7883	175.0+/-225.2	37,643,3620	yes	missense,missense	ABHD12B	NM_001206673.1,NM_181814.1	27,27	59,1051,5393	GG,GC,CC		8.3372,10.2587,8.9882	benign,benign	335/363,258/286	51370852	1169,11837	2203	4300	6503	SO:0001583	missense	145447	exon12			ATCTTTCCTCCTG	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"""Abhydrolase domain containing"""	19837	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 29"""	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.1003C>G	14.37:g.51370852C>G	ENSP00000336693:p.Pro335Ala	Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	336	197	0.58631	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Missense_Mutation	SNP	ENST00000337334.2	37	CCDS55916.1	187	0.08562271062271062	49	0.09959349593495935	18	0.049723756906077346	47	0.08216783216783216	73	0.09630606860158311	C	12.29	1.894362	0.33442	0.102587	0.083372	ENSG00000131969	ENST00000353130;ENST00000337334;ENST00000395752	T;T;T	0.53206	2.25;0.63;2.27	4.94	4.94	0.65067	.	0.426050	0.28589	N	0.014814	T	0.00967	0.0032	L	0.28115	0.83	0.41275	D	0.986877	B;B	0.29085	0.137;0.232	B;B	0.30401	0.115;0.07	T	0.01824	-1.1266	10	0.09843	T	0.71	-19.3759	15.7423	0.77910	0.0:1.0:0.0:0.0	rs34800262	335;258	Q7Z5M8;Q7Z5M8-2	AB12B_HUMAN;.	A	258;335;228	ENSP00000343951:P258A;ENSP00000336693:P335A;ENSP00000379101:P228A	ENSP00000336693:P335A	P	+	1	0	ABHD12B	50440602	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	4.256000	0.58810	2.675000	0.91044	0.655000	0.94253	CCT	C|0.912;G|0.088	0.088	strong		0.443	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1		
AKAP9	10142	hgsc.bcm.edu	37	7	91726927	91726927	+	Silent	SNP	A	A	C	rs1063243	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91726927A>C	ENST00000359028.2	+	42	10663	c.10438A>C	c.(10438-10440)Aga>Cga	p.R3480R	AKAP9_ENST00000356239.3_Silent_p.R3476R|AKAP9_ENST00000358100.2_Silent_p.R3426R			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3480					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)			AACCAGTGATAGAACTAGAAA	0.368			T	BRAF	papillary thyroid								C|||	1890	0.377396	0.5212	0.3573	5008	,	,		18085	0.1617		0.3867	False		,,,				2504	0.41				p.R3476R		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,NS,carcinoma,-1,2	AKAP9	788	2	0			c.A10426C						PASS	.	C	,	2333,2073	560.3+/-380.4	619,1095,489	68.0	69.0	69.0		10426,10402	1.1	0.9	7	dbSNP_86	69	3471,5129	632.1+/-398.6	681,2109,1510	yes	coding-synonymous,coding-synonymous	AKAP9	NM_005751.4,NM_147185.2	,	1300,3204,1999	CC,CA,AA		40.3605,47.0495,44.6256	,	3476/3908,3468/3900	91726927	5804,7202	2203	4300	6503	SO:0001819	synonymous_variant	10142	exon42			AGTGATAGAACTA	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.10438A>C	7.37:g.91726927A>C		Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	263	259	0.984791	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				A|0.588;C|0.412	0.412	strong		0.368	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
ZNF493	284443	hgsc.bcm.edu	37	19	21607253	21607253	+	Missense_Mutation	SNP	A	A	G	rs150159158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21607253A>G	ENST00000355504.4	+	2	1674	c.1408A>G	c.(1408-1410)Aag>Gag	p.K470E	ZNF493_ENST00000392288.2_Missense_Mutation_p.K598E|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	470					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(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						TCATACTGATAAGAAACCCTA	0.338													.|||	3	0.000599042	0.0	0.0	5008	,	,		19874	0.0		0.003	False		,,,				2504	0.0				p.K598E		Atlas-SNP	.											.	ZNF493	178	.	0			c.A1792G						PASS	.						33.0	33.0	33.0					19																	21607253		2201	4298	6499	SO:0001583	missense	284443	exon4			ACTGATAAGAAAC	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1408A>G	19.37:g.21607253A>G	ENSP00000347691:p.Lys470Glu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	11	0.169231	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.049581	0.00394	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.12672	2.66;2.66	1.06	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01940	0.0061	N	0.00191	-1.88	0.38843	D	0.956104	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.50575	-0.8812	9	0.02654	T	1	.	4.9183	0.13856	0.3932:0.1603:0.4464:0.0	.	470;598	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	E	598;470	ENSP00000376110:K598E;ENSP00000347691:K470E	ENSP00000347691:K470E	K	+	1	0	ZNF493	21399093	0.015000	0.18098	0.000000	0.03702	0.000000	0.00434	0.849000	0.27723	-2.911000	0.00308	-2.864000	0.00100	AAG	.	.	weak		0.338	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
ZNF80	7634	hgsc.bcm.edu	37	3	113955753	113955753	+	Missense_Mutation	SNP	C	C	T	rs146464395	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113955753C>T	ENST00000482457.2	-	1	672	c.169G>A	c.(169-171)Gtg>Atg	p.V57M	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	57					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)				TTGTTAAACACGCTCCCACAT	0.478													C|||	53	0.0105831	0.0023	0.0605	5008	,	,		23283	0.0		0.006	False		,,,				2504	0.002				p.V57M	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.G169A						PASS	.	C	MET/VAL	14,4392	21.2+/-45.6	0,14,2189	127.0	111.0	116.0		169	1.9	0.0	3	dbSNP_134	116	79,8521	46.3+/-105.2	0,79,4221	yes	missense	ZNF80	NM_007136.3	21	0,93,6410	TT,TC,CC		0.9186,0.3177,0.7151	possibly-damaging	57/274	113955753	93,12913	2203	4300	6503	SO:0001583	missense	7634	exon1			TAAACACGCTCCC	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.169G>A	3.37:g.113955753C>T	ENSP00000417192:p.Val57Met	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	111	61	0.54955	NM_007136	Q6NSW4|Q6NT14	Missense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	27	0.012362637362637362	3	0.006097560975609756	19	0.052486187845303865	0	0.0	5	0.006596306068601583	C	10.28	1.307049	0.23821	0.003177	0.009186	ENSG00000174255	ENST00000482457	T	0.29917	1.55	2.77	1.87	0.25490	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.06462	0.0166	M	0.62723	1.935	0.09310	N	1	D	0.56746	0.977	P	0.48227	0.571	T	0.06661	-1.0814	9	0.87932	D	0	.	4.3307	0.11062	0.0:0.67:0.0:0.33	.	57	P51504	ZNF80_HUMAN	M	57	ENSP00000417192:V57M	ENSP00000309812:V57M	V	-	1	0	ZNF80	115438443	0.000000	0.05858	0.003000	0.11579	0.068000	0.16541	-0.983000	0.03759	0.708000	0.31955	0.655000	0.94253	GTG	C|0.991;T|0.009	0.009	strong		0.478	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
SRRM2	23524	hgsc.bcm.edu	37	16	2816224	2816224	+	Missense_Mutation	SNP	C	C	T	rs151100831	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2816224C>T	ENST00000301740.8	+	11	6244	c.5695C>T	c.(5695-5697)Cgg>Tgg	p.R1899W		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1899	Arg-rich.|Ser-rich.				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						CAGCCGGAGACGGTCAAGGTC	0.592																																					p.R1899W		Atlas-SNP	.											SRRM2,colon,carcinoma,0,1	SRRM2	263	1	0			c.C5695T						scavenged	.						104.0	100.0	101.0					16																	2816224		2198	4300	6498	SO:0001583	missense	23524	exon11			CGGAGACGGTCAA	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.5695C>T	16.37:g.2816224C>T	ENSP00000301740:p.Arg1899Trp	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	122	2	0.0163934	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	.	.	.	.	.	.	.	.	.	.	C	0.854	-0.737664	0.03111	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.26373	1.74	5.46	3.27	0.37495	.	0.000000	0.56097	D	0.000040	T	0.25717	0.0626	N	0.08118	0	0.31050	N	0.715362	D	0.89917	1.0	D	0.77557	0.99	T	0.10222	-1.0639	10	0.72032	D	0.01	-8.5524	7.212	0.25939	0.3166:0.5967:0.0:0.0867	.	1899	Q9UQ35	SRRM2_HUMAN	W	1899;1899;1151	ENSP00000301740:R1899W	ENSP00000301740:R1899W	R	+	1	2	SRRM2	2756225	0.982000	0.34865	0.993000	0.49108	0.970000	0.65996	1.597000	0.36729	1.280000	0.44463	0.650000	0.86243	CGG	C|0.999;A|0.001	.	alt		0.592	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
ZNF518B	85460	hgsc.bcm.edu	37	4	10447168	10447168	+	Missense_Mutation	SNP	C	C	G	rs66538112	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:10447168C>G	ENST00000326756.3	-	3	1223	c.785G>C	c.(784-786)gGt>gCt	p.G262A		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	262					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(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						GAGAGAGAAACCTGACAGTTG	0.368													C|||	957	0.191094	0.0764	0.2767	5008	,	,		21647	0.2063		0.2435	False		,,,				2504	0.2157				p.G262A		Atlas-SNP	.											.	ZNF518B	116	.	0			c.G785C						PASS	.	C	ALA/GLY	486,3920	228.5+/-243.3	21,444,1738	218.0	213.0	215.0		785	1.2	0.0	4	dbSNP_130	215	2225,6375	379.5+/-339.3	307,1611,2382	yes	missense	ZNF518B	NM_053042.2	60	328,2055,4120	GG,GC,CC		25.8721,11.0304,20.8442	benign	262/1075	10447168	2711,10295	2203	4300	6503	SO:0001583	missense	85460	exon3			GAGAAACCTGACA	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.785G>C	4.37:g.10447168C>G	ENSP00000317614:p.Gly262Ala	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	434	0.1987179487179487	46	0.09349593495934959	83	0.2292817679558011	119	0.20804195804195805	186	0.24538258575197888	C	14.38	2.518259	0.44763	0.110304	0.258721	ENSG00000178163	ENST00000326756	T	0.01414	4.92	6.17	1.25	0.21368	.	0.855383	0.09877	N	0.744208	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	0.34279	-0.9835	9	0.11182	T	0.66	-6.6905	6.0007	0.19519	0.0:0.4868:0.2423:0.2709	.	262	Q9C0D4	Z518B_HUMAN	A	262	ENSP00000317614:G262A	ENSP00000317614:G262A	G	-	2	0	ZNF518B	10056266	0.000000	0.05858	0.027000	0.17364	0.751000	0.42716	0.168000	0.16622	0.486000	0.27676	0.655000	0.94253	GGT	C|0.795;G|0.205	0.205	strong		0.368	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
MUC2	4583	hgsc.bcm.edu	37	11	1075850	1075850	+	Silent	SNP	G	G	A	rs11825969	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1075850G>A	ENST00000441003.2	+	2	303	c.276G>A	c.(274-276)gaG>gaA	p.E92E	MUC2_ENST00000359061.5_Silent_p.E92E	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	92	VWFD 1. {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)	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)	CCGGGGTGGAGTCCATCCTGC	0.647													G|||	582	0.116214	0.2179	0.0821	5008	,	,		16206	0.001		0.2078	False		,,,				2504	0.0276				p.E92E		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G276A						PASS	.	G		840,3090		104,632,1229	23.0	26.0	25.0		276	-0.8	0.0	11	dbSNP_120	25	1728,6528		193,1342,2593	no	coding-synonymous	MUC2	NM_002457.2		297,1974,3822	AA,AG,GG		20.9302,21.374,21.0734		92/2813	1075850	2568,9618	1965	4128	6093	SO:0001819	synonymous_variant	4583	exon2			GGTGGAGTCCATC	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.276G>A	11.37:g.1075850G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	113	63	0.557522	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				G|0.844;A|0.156	0.156	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CLCA2	9635	hgsc.bcm.edu	37	1	86909493	86909493	+	Silent	SNP	C	C	T	rs2390059	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	99	0	0		WXS	Illumina HiSeq	Phase_I	62	14	0.225806	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	
TNS1	7145	hgsc.bcm.edu	37	2	218674614	218674614	+	Silent	SNP	C	C	T	rs13417442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:218674614C>T	ENST00000171887.4	-	30	5345	c.4893G>A	c.(4891-4893)acG>acA	p.T1631T	TNS1_ENST00000419504.1_Silent_p.T1617T|TNS1_ENST00000430930.1_Silent_p.T1610T	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1631					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)		TGGCAGCTGGCGTGGGGTCTG	0.562																																					p.T1631T		Atlas-SNP	.											.	TNS1	251	.	0			c.G4893A						PASS	.			188,4218	120.8+/-158.4	8,172,2023	93.0	84.0	87.0		4893	-5.2	0.9	2	dbSNP_121	87	628,7972	162.5+/-215.2	27,574,3699	yes	coding-synonymous	TNS1	NM_022648.4		35,746,5722	TT,TC,CC		7.3023,4.2669,6.274		1631/1736	218674614	816,12190	2203	4300	6503	SO:0001819	synonymous_variant	7145	exon30			AGCTGGCGTGGGG	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.4893G>A	2.37:g.218674614C>T		Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	188	178	0.946809	NM_022648	Q4ZG71|Q6IPI5	Silent	SNP	ENST00000171887.4	37	CCDS2407.1																																																																																			C|0.934;T|0.066	0.066	strong		0.562	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
ABHD5	51099	hgsc.bcm.edu	37	3	43732496	43732496	+	Silent	SNP	G	G	A	rs141365045	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:43732496G>A	ENST00000458276.2	+	1	135	c.12G>A	c.(10-12)gaG>gaA	p.E4E	ANO10_ENST00000495772.1_Intron	NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	4					cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|negative regulation of sequestering of triglyceride (GO:0010891)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|nucleus (GO:0005634)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|lysophosphatidic acid acyltransferase activity (GO:0042171)			kidney(3)|large_intestine(2)|liver(2)|lung(5)|ovary(1)|skin(1)	14		Renal(3;0.0134)		KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0687)		TGGCGGCGGAGGAGGAGGAGG	0.736													G|||	184	0.0367412	0.0106	0.0303	5008	,	,		10264	0.0258		0.0239	False		,,,				2504	0.1012				p.E4E		Atlas-SNP	.											.	ABHD5	33	.	0			c.G12A						PASS	.	G		38,4310		0,38,2136	14.0	21.0	18.0		12	3.0	1.0	3	dbSNP_134	18	205,8307		2,201,4053	no	coding-synonymous	ABHD5	NM_016006.4		2,239,6189	AA,AG,GG		2.4084,0.874,1.8896		4/350	43732496	243,12617	2174	4256	6430	SO:0001819	synonymous_variant	51099	exon1			GGCGGAGGAGGAG	AF007132	CCDS2711.1	3p21.33	2012-05-16			ENSG00000011198	ENSG00000011198		"""Abhydrolase domain containing"""	21396	protein-coding gene	gene with protein product		604780				11590543, 18606822	Standard	NM_016006		Approved	CGI-58, NCIE2	uc003cmx.3	Q8WTS1	OTTHUMG00000133039	ENST00000458276.2:c.12G>A	3.37:g.43732496G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_016006	B2R9K0|Q9Y369	Silent	SNP	ENST00000458276.2	37	CCDS2711.1																																																																																			G|0.979;A|0.021	0.021	strong		0.736	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006	
GLRX3	10539	hgsc.bcm.edu	37	10	131959150	131959150	+	Missense_Mutation	SNP	C	C	T	rs2274217	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:131959150C>T	ENST00000368644.1	+	4	389	c.367C>T	c.(367-369)Ccc>Tcc	p.P123S	GLRX3_ENST00000331244.5_Missense_Mutation_p.P123S	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	123			P -> S (in dbSNP:rs2274217). {ECO:0000269|PubMed:10636891, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		CTCCTTCCTACCCAGCGCTAA	0.438													C|||	957	0.191094	0.1241	0.1282	5008	,	,		16273	0.1101		0.2853	False		,,,				2504	0.3129				p.P123S		Atlas-SNP	.											TXNL2,colon,carcinoma,0,2	GLRX3	39	2	0			c.C367T						PASS	.	C	SER/PRO,SER/PRO	596,3810	261.9+/-264.6	47,502,1654	114.0	101.0	106.0		367,367	4.4	0.2	10	dbSNP_100	106	2244,6356	381.3+/-340.0	315,1614,2371	yes	missense,missense	GLRX3	NM_001199868.1,NM_006541.4	74,74	362,2116,4025	TT,TC,CC		26.093,13.527,21.8361	benign,benign	123/336,123/336	131959150	2840,10166	2203	4300	6503	SO:0001583	missense	10539	exon4			TTCCTACCCAGCG	AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"""glutaredoxin 4"""	612754	"""thioredoxin-like 2"""	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.367C>T	10.37:g.131959150C>T	ENSP00000357633:p.Pro123Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_006541	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	386	0.17673992673992675	64	0.13008130081300814	53	0.1464088397790055	56	0.0979020979020979	213	0.28100263852242746	C	2.176	-0.388811	0.04932	0.13527	0.26093	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.08546	3.08;3.08	4.39	4.39	0.52855	Thioredoxin-like fold (1);	0.372544	0.26227	N	0.025598	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	0.45249	-0.9274	9	0.08381	T	0.77	-2.8796	10.9948	0.47569	0.0:0.6927:0.3073:0.0	rs2274217;rs17297963;rs2274217	123	O76003	GLRX3_HUMAN	S	123	ENSP00000330836:P123S;ENSP00000357633:P123S	ENSP00000330836:P123S	P	+	1	0	GLRX3	131849140	0.090000	0.21635	0.206000	0.23566	0.141000	0.21300	0.666000	0.25097	2.284000	0.76573	0.655000	0.94253	CCC	C|0.799;T|0.201	0.201	strong		0.438	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541	
F5	2153	hgsc.bcm.edu	37	1	169511555	169511555	+	Missense_Mutation	SNP	T	T	C	rs6032	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:169511555T>C	ENST00000367797.3	-	13	2974	c.2773A>G	c.(2773-2775)Aag>Gag	p.K925E	F5_ENST00000367796.3_Missense_Mutation_p.K930E	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	925	2 X 17 AA tandem repeats.|B.		K -> E (in dbSNP:rs6032). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:11758222, ECO:0000269|PubMed:2827731, ECO:0000269|PubMed:3110773, 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)	GGAGGGTCCTTCCAGGGCCTC	0.478													C|||	1316	0.26278	0.1679	0.3948	5008	,	,		20989	0.248		0.2535	False		,,,				2504	0.3221				p.K925E		Atlas-SNP	.											F5,colon,carcinoma,+2,1	F5	301	1	0			c.A2773G						PASS	.	C	GLU/LYS	812,3594	748.8+/-412.0	67,678,1458	105.0	111.0	109.0		2773	-5.1	0.0	1	dbSNP_52	109	2355,6245	701.7+/-405.2	300,1755,2245	yes	missense	F5	NM_000130.4	56	367,2433,3703	CC,CT,TT		27.3837,18.4294,24.3503	benign	925/2225	169511555	3167,9839	2203	4300	6503	SO:0001583	missense	2153	exon13			GGTCCTTCCAGGG	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.2773A>G	1.37:g.169511555T>C	ENSP00000356771:p.Lys925Glu	Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	237	237	1	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	532	0.24358974358974358	96	0.1951219512195122	130	0.35911602209944754	113	0.19755244755244755	193	0.2546174142480211	C	2.099	-0.406537	0.04832	0.184294	0.273837	ENSG00000198734	ENST00000367797;ENST00000367796	T;T	0.18016	2.24;2.24	5.11	-5.14	0.02875	.	0.944141	0.08852	N	0.884318	T	0.02083	0.0065	N	0.11427	0.14	0.09310	P	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.48502	-0.9030	9	0.02654	T	1	.	17.3504	0.87322	0.0:0.8069:0.0:0.1931	rs6032;rs52829643;rs6032	925	P12259	FA5_HUMAN	E	925;930	ENSP00000356771:K925E;ENSP00000356770:K930E	ENSP00000356770:K930E	K	-	1	0	F5	167778179	0.000000	0.05858	0.002000	0.10522	0.092000	0.18411	-0.987000	0.03743	-1.326000	0.02266	-1.306000	0.01317	AAG	T|0.758;C|0.242	0.242	strong		0.478	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
XPO7	23039	hgsc.bcm.edu	37	8	21847855	21847855	+	Splice_Site	SNP	G	G	C	rs56062629	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:21847855G>C	ENST00000252512.9	+	17	1969	c.1869G>C	c.(1867-1869)ggG>ggC	p.G623G	XPO7_ENST00000434536.1_Splice_Site_p.G632G|XPO7_ENST00000433566.4_Splice_Site_p.G624G	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	623					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)		TTGTCTTCACGTACAGTAGCG	0.448													G|||	203	0.0405351	0.0061	0.0807	5008	,	,		19479	0.0		0.1183	False		,,,				2504	0.0204				p.G623G		Atlas-SNP	.											.	XPO7	79	.	0			c.G1869C						PASS	.	G		73,3799		2,69,1865	205.0	190.0	195.0		1869	-6.2	0.4	8	dbSNP_129	195	838,7454		42,754,3350	yes	coding-synonymous-near-splice	XPO7	NM_015024.4		44,823,5215	CC,CG,GG		10.1061,1.8853,7.4893		623/1088	21847855	911,11253	1936	4146	6082	SO:0001630	splice_region_variant	23039	exon17			CTTCACGTACAGT	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.1869-1G>C	8.37:g.21847855G>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	247	75	0.303644	NM_015024	O94846|Q6PJK9|Q8NEK7	Silent	SNP	ENST00000252512.9	37	CCDS47818.1																																																																																			G|0.938;C|0.062	0.062	strong		0.448	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024	Silent
RIN3	79890	hgsc.bcm.edu	37	14	93118198	93118198	+	Silent	SNP	C	C	T	rs3814830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:93118198C>T	ENST00000216487.7	+	6	963	c.804C>T	c.(802-804)gcC>gcT	p.A268A	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	268	Pro-rich.				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)				CCTCTGATGCCACCTCACCCA	0.682													T|||	1422	0.283946	0.3389	0.2911	5008	,	,		7197	0.2758		0.169	False		,,,				2504	0.3313				p.A268A		Atlas-SNP	.											.	RIN3	81	.	0			c.C804T						PASS	.	T		1418,2988	685.2+/-404.5	229,960,1014	72.0	71.0	71.0		804	3.4	0.5	14	dbSNP_107	71	1253,7347	760.6+/-407.6	84,1085,3131	no	coding-synonymous	RIN3	NM_024832.3		313,2045,4145	TT,TC,CC		14.5698,32.1834,20.5367		268/986	93118198	2671,10335	2203	4300	6503	SO:0001819	synonymous_variant	79890	exon6			TGATGCCACCTCA	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.804C>T	14.37:g.93118198C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	86	55	0.639535	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent	SNP	ENST00000216487.7	37	CCDS32144.1																																																																																			C|0.764;T|0.236	0.236	strong		0.682	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
SIGLEC15	284266	hgsc.bcm.edu	37	18	43422149	43422149	+	Silent	SNP	G	G	A	rs143689799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:43422149G>A	ENST00000389474.3	+	6	1201	c.984G>A	c.(982-984)ccG>ccA	p.P328P	SIGLEC15_ENST00000602118.2_3'UTR|SIGLEC15_ENST00000546268.1_Silent_p.P174P	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	328					cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						TGTGCTCACCGTGAGGAGTCC	0.562													G|||	8	0.00159744	0.0015	0.0	5008	,	,		18230	0.0		0.006	False		,,,				2504	0.0				p.P328P		Atlas-SNP	.											.	SIGLEC15	10	.	0			c.G984A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	73.0	69.0	70.0		984	-8.6	0.0	18	dbSNP_134	70	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	SIGLEC15	NM_213602.2		0,29,6474	AA,AG,GG		0.314,0.0454,0.223		328/329	43422149	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	284266	exon6			CTCACCGTGAGGA	AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27596	protein-coding gene	gene with protein product			"""CD33 antigen-like 3"", ""CD33 molecule-like 3"""	CD33L3		17483134	Standard	NM_213602		Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.984G>A	18.37:g.43422149G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	115	61	0.530435	NM_213602	A8K2Y5|B4DVQ9	Silent	SNP	ENST00000389474.3	37	CCDS32819.1																																																																																			G|0.997;A|0.003	0.003	strong		0.562	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602	
CENPE	1062	hgsc.bcm.edu	37	4	104066461	104066461	+	Missense_Mutation	SNP	A	A	G	rs2615542	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:104066461A>G	ENST00000265148.3	-	32	4692	c.4603T>C	c.(4603-4605)Ttt>Ctt	p.F1535L	CENPE_ENST00000380026.3_Missense_Mutation_p.F1510L	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1535			F -> L (in dbSNP:rs2615542). {ECO:0000269|PubMed:1406971}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.F1535L(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TTTATATTAAATTGTTCCTCT	0.299													G|||	607	0.121206	0.062	0.1153	5008	,	,		16276	0.1409		0.2207	False		,,,				2504	0.0828				p.F1535L		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	1	1	Substitution - Missense(1)	stomach(1)	c.T4603C						PASS	.	G	LEU/PHE	281,4121	778.4+/-414.3	8,265,1928	47.0	46.0	46.0		4603	-2.4	0.0	4	dbSNP_100	46	1768,6828	720.6+/-406.3	195,1378,2725	yes	missense	CENPE	NM_001813.2	22	203,1643,4653	GG,GA,AA		20.5677,6.3835,15.764	benign	1535/2702	104066461	2049,10949	2201	4298	6499	SO:0001583	missense	1062	exon32			TATTAAATTGTTC	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.4603T>C	4.37:g.104066461A>G	ENSP00000265148:p.Phe1535Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	347	0.15888278388278387	39	0.07926829268292683	51	0.1408839779005525	74	0.12937062937062938	183	0.24142480211081793	G	0.006	-2.062430	0.00386	0.063835	0.205677	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.62639	0.01;0.15	4.44	-2.42	0.06542	.	.	.	.	.	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	0.07654	-1.0761	8	0.02654	T	1	.	0.4903	0.00563	0.3766:0.2373:0.1466:0.2394	rs2615542;rs17282727;rs52815493;rs60897952;rs2615542	1510;1535	Q02224-3;Q02224	.;CENPE_HUMAN	L	1535;1535;1510	ENSP00000265148:F1535L;ENSP00000369365:F1510L	ENSP00000265148:F1535L	F	-	1	0	CENPE	104285910	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.886000	0.04157	-0.433000	0.07286	-0.231000	0.12243	TTT	A|0.848;G|0.152	0.152	strong		0.299	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MROH7	374977	hgsc.bcm.edu	37	1	55119144	55119144	+	Missense_Mutation	SNP	A	A	G	rs11206407	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000454855.2_Intron|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000339553.5_Missense_Mutation_p.H182R|MROH7_ENST00000409996.1_Intron|MROH7_ENST00000395690.2_Missense_Mutation_p.H182R	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						PASS	.	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	142	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	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	
PGR	5241	hgsc.bcm.edu	37	11	100998771	100998771	+	Missense_Mutation	SNP	C	C	G	rs3740753	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:100998771C>G	ENST00000325455.5	-	1	2484	c.1031G>C	c.(1030-1032)aGt>aCt	p.S344T	PGR_ENST00000263463.5_Missense_Mutation_p.S344T|PGR_ENST00000534013.1_Intron	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	48	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	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		
XIRP2	129446	hgsc.bcm.edu	37	2	168103304	168103304	+	Missense_Mutation	SNP	G	G	A	rs16853309	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168103304G>A	ENST00000409195.1	+	9	5491	c.5402G>A	c.(5401-5403)cGt>cAt	p.R1801H	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R1579H|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R1801H	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1626					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						CTGGTTGAACGTACTGTTAGT	0.403													G|||	989	0.197484	0.3245	0.1311	5008	,	,		21072	0.12		0.1233	False		,,,				2504	0.229				p.R1801H		Atlas-SNP	.											.	XIRP2	914	.	0			c.G5402A						PASS	.	G	HIS/ARG,HIS/ARG,,,	1080,2776		156,768,1004	180.0	168.0	172.0		4736,5402,,,	2.8	1.0	2	dbSNP_123	172	921,7361		55,811,3275	yes	missense,missense,intron,intron,intron	XIRP2	NM_001199144.1,NM_152381.5,NM_001079810.3,NM_001199143.1,NM_001199145.1	29,29,,,	211,1579,4279	AA,AG,GG		11.1205,28.0083,16.4854	possibly-damaging,possibly-damaging,,,	1579/3328,1801/3550,,,	168103304	2001,10137	1928	4141	6069	SO:0001583	missense	129446	exon9			TTGAACGTACTGT	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.5402G>A	2.37:g.168103304G>A	ENSP00000386840:p.Arg1801His	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	191	83	0.434555	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	384	0.17582417582417584	170	0.34552845528455284	47	0.1298342541436464	72	0.1258741258741259	95	0.12532981530343007	G	10.60	1.396329	0.25205	0.280083	0.111205	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.04502	3.61;3.61;3.61	5.59	2.84	0.33178	.	0.053822	0.85682	D	0.000000	T	0.00012	0.0000	M	0.74258	2.255	0.18873	P	0.999981003	P;P;P	0.41947	0.655;0.766;0.477	B;B;B	0.33121	0.076;0.158;0.081	T	0.49634	-0.8919	9	0.49607	T	0.09	-5.9326	9.9833	0.41826	0.2251:0.0:0.7749:0.0	rs16853309;rs52829936;rs16853309	1626;1626;1579	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	H	1801;1801;1579	ENSP00000386840:R1801H;ENSP00000295237:R1801H;ENSP00000387255:R1579H	ENSP00000295237:R1801H	R	+	2	0	XIRP2	167811550	1.000000	0.71417	1.000000	0.80357	0.350000	0.29205	2.750000	0.47500	0.740000	0.32651	-0.133000	0.14855	CGT	G|0.820;A|0.180	0.180	strong		0.403	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
RNF17	56163	hgsc.bcm.edu	37	13	25440318	25440318	+	Missense_Mutation	SNP	G	G	A	rs9507425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:25440318G>A	ENST00000255324.5	+	30	4190	c.4138G>A	c.(4138-4140)Gaa>Aaa	p.E1380K	RNF17_ENST00000381921.1_Missense_Mutation_p.E1338K|RNF17_ENST00000339524.3_Missense_Mutation_p.E390K	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1380			E -> K (in dbSNP:rs9507425). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		GTATGAAGAGGAACAATGGGA	0.313													G|||	1062	0.212061	0.0847	0.2205	5008	,	,		17485	0.3254		0.2903	False		,,,				2504	0.181				p.E1380K		Atlas-SNP	.											.	RNF17	259	.	0			c.G4138A						PASS	.	G	LYS/GLU,LYS/GLU	539,3867	240.3+/-251.1	35,469,1699	108.0	107.0	107.0		4126,4138	3.9	0.3	13	dbSNP_119	107	2506,6088	405.8+/-348.6	345,1816,2136	yes	missense,missense	RNF17	NM_001184993.1,NM_031277.2	56,56	380,2285,3835	AA,AG,GG		29.1599,12.2333,23.4231	benign,benign	1376/1620,1380/1624	25440318	3045,9955	2203	4297	6500	SO:0001583	missense	56163	exon30			GAAGAGGAACAAT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"""RING-type (C3HC4) zinc fingers"", ""Tudor domain containing"""	10060	protein-coding gene	gene with protein product	"""spermatogenesis associated 23"""	605793	"""tudor domain containing 4"""	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.4138G>A	13.37:g.25440318G>A	ENSP00000255324:p.Glu1380Lys	Somatic	332	1	0.00301205		WXS	Illumina HiSeq	Phase_I	316	160	0.506329	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	489	0.2239010989010989	37	0.07520325203252033	82	0.2265193370165746	155	0.270979020979021	215	0.2836411609498681	G	9.703	1.155106	0.21371	0.122333	0.291599	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000418120;ENST00000339524	T;T;T;T	0.23552	3.52;3.41;2.73;1.9	4.74	3.9	0.45041	.	0.094831	0.46442	D	0.000286	T	0.00012	0.0000	L	0.41236	1.265	0.25451	P	0.988003	B;B;B;B	0.09022	0.001;0.0;0.0;0.002	B;B;B;B	0.09377	0.003;0.0;0.004;0.003	T	0.34354	-0.9832	9	0.07644	T	0.81	-20.6408	9.2271	0.37414	0.0994:0.0:0.9006:0.0	rs9507425;rs17480121;rs52806297;rs59442158;rs9507425	1376;390;1374;1380	B7Z7S1;Q5T6R1;Q9BXT8-5;Q9BXT8	.;.;.;RNF17_HUMAN	K	1380;1338;704;390	ENSP00000255324:E1380K;ENSP00000371346:E1338K;ENSP00000388892:E704K;ENSP00000344776:E390K	ENSP00000255324:E1380K	E	+	1	0	RNF17	24338318	0.968000	0.33430	0.343000	0.25615	0.557000	0.35523	3.135000	0.50546	1.367000	0.46095	-0.254000	0.11334	GAA	G|0.778;A|0.222	0.222	strong		0.313	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
SULT1A2	6799	hgsc.bcm.edu	37	16	28607196	28607196	+	Missense_Mutation	SNP	G	G	A	rs10797300	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:28607196G>A	ENST00000395630.1	-	2	406	c.56C>T	c.(55-57)cCg>cTg	p.P19L	SULT1A2_ENST00000533150.1_Missense_Mutation_p.P19L|SULT1A2_ENST00000335715.4_Missense_Mutation_p.P19L	NM_177528.2	NP_803564	P50226	ST1A2_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 2	19			P -> L (in dbSNP:rs10797300). {ECO:0000269|PubMed:7581483}.		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						CTTGATGAGCGGGACCCCCTT	0.627													.|||	369	0.0736821	0.0666	0.1009	5008	,	,		17319	0.004		0.1233	False		,,,				2504	0.0849				p.P19L		Atlas-SNP	.											.	SULT1A2	27	.	0			c.C56T						PASS	.	G	LEU/PRO,LEU/PRO	336,4058	162.2+/-194.2	27,282,1888	32.0	32.0	32.0		56,56	4.4	1.0	16	dbSNP_120	32	1190,7404	216.0+/-255.2	134,922,3241	no	missense,missense	SULT1A2	NM_001054.3,NM_177528.2	98,98	161,1204,5129	AA,AG,GG		13.8469,7.6468,11.7493	probably-damaging,probably-damaging	19/296,19/296	28607196	1526,11462	2197	4297	6494	SO:0001583	missense	6799	exon2			ATGAGCGGGACCC	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.56C>T	16.37:g.28607196G>A	ENSP00000378992:p.Pro19Leu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	273	137	0.501832	NM_001054	A9QY25|P78393|Q14CJ7	Missense_Mutation	SNP	ENST00000395630.1	37	CCDS10636.1	171	0.0782967032967033	40	0.08130081300813008	43	0.11878453038674033	4	0.006993006993006993	84	0.11081794195250659	g	14.47	2.543663	0.45280	0.076468	0.138469	ENSG00000197165	ENST00000533150;ENST00000335715;ENST00000395630;ENST00000526384	T;T;T;T	0.01560	4.77;4.77;4.77;4.77	4.41	4.41	0.53225	.	0.000000	0.64402	D	0.000001	T	0.00039	0.0001	M	0.69185	2.1	0.09310	P	0.99999051378	D	0.89917	1.0	D	0.97110	1.0	T	0.47749	-0.9093	9	0.06099	T	0.92	.	14.9093	0.70743	0.0:0.0:1.0:0.0	rs10797300	19	P50226	ST1A2_HUMAN	L	19	ENSP00000435271:P19L;ENSP00000338742:P19L;ENSP00000378992:P19L;ENSP00000435358:P19L	ENSP00000338742:P19L	P	-	2	0	SULT1A2	28514697	1.000000	0.71417	0.989000	0.46669	0.700000	0.40528	5.557000	0.67313	2.160000	0.67779	0.556000	0.70494	CCG	G|0.903;A|0.097	0.097	strong		0.627	SULT1A2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109415.2	NM_001054	
ESR2	2100	hgsc.bcm.edu	37	14	64724051	64724051	+	Silent	SNP	C	C	T	rs1256049	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:64724051C>T	ENST00000341099.4	-	6	1401	c.984G>A	c.(982-984)gtG>gtA	p.V328V	ESR2_ENST00000353772.3_Silent_p.V328V|ESR2_ENST00000542956.1_Silent_p.V328V|ESR2_ENST00000557772.1_Silent_p.V328V|ESR2_ENST00000358599.5_Silent_p.V328V|ESR2_ENST00000555278.1_Silent_p.V328V|ESR2_ENST00000554572.1_Silent_p.V328V|ESR2_ENST00000555483.1_5'UTR|ESR2_ENST00000553796.1_Silent_p.V328V|ESR2_ENST00000357782.2_Silent_p.V328V|ESR2_ENST00000267525.6_Intron	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	328	Steroid-binding.				brain development (GO:0007420)|cell-cell signaling (GO:0007267)|epithelial cell maturation involved in prostate gland development (GO:0060743)|extracellular negative regulation of signal transduction (GO:1900116)|gene expression (GO:0010467)|hormone-mediated apoptotic signaling pathway (GO:0008628)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|ovarian follicle development (GO:0001541)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|prostate gland epithelium morphogenesis (GO:0060740)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|uterus development (GO:0060065)|vagina development (GO:0060068)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor antagonist activity (GO:0048019)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.V328V(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	23				all cancers(60;0.00916)|OV - Ovarian serous cystadenocarcinoma(108;0.0111)|BRCA - Breast invasive adenocarcinoma(234;0.0437)	Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estropipate(DB04574)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Trilostane(DB01108)	CCAAGAGCCGCACTTGGTCGA	0.572													C|||	649	0.129593	0.1029	0.0346	5008	,	,		15483	0.4028		0.0358	False		,,,				2504	0.0481				p.V328V		Atlas-SNP	.											ESR2,NS,carcinoma,0,1	ESR2	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G984A	GRCh37	CM010232	ESR2	M	rs1256049	PASS	.	C	,,,,	396,4010	198.7+/-222.5	14,368,1821	105.0	106.0	105.0		984,984,984,984,984	1.7	1.0	14	dbSNP_87	105	297,8303	109.0+/-169.6	5,287,4008	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR2	NM_001040275.1,NM_001040276.1,NM_001214902.1,NM_001214903.1,NM_001437.2	,,,,	19,655,5829	TT,TC,CC		3.4535,8.9877,5.3283	,,,,	328/496,328/496,328/482,328/473,328/531	64724051	693,12313	2203	4300	6503	SO:0001819	synonymous_variant	2100	exon5			GAGCCGCACTTGG	X99101	CCDS9762.1, CCDS32096.1, CCDS55920.1, CCDS61469.1, CCDS61470.1	14q21-q22	2013-01-16			ENSG00000140009	ENSG00000140009		"""Nuclear hormone receptors"""	3468	protein-coding gene	gene with protein product		601663				8769313	Standard	NM_001214902		Approved	NR3A2, Erb	uc001xha.1	Q92731	OTTHUMG00000141306	ENST00000341099.4:c.984G>A	14.37:g.64724051C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	168	57	0.339286	NM_001214902	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Silent	SNP	ENST00000341099.4	37	CCDS9762.1																																																																																			C|0.909;T|0.091	0.091	strong		0.572	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1		
CFHR5	81494	hgsc.bcm.edu	37	1	196967354	196967354	+	Missense_Mutation	SNP	G	G	A	rs35662416	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:196967354G>A	ENST00000256785.4	+	7	1176	c.1067G>A	c.(1066-1068)cGt>cAt	p.R356H	CFHR5_ENST00000367414.5_Missense_Mutation_p.R380H			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	356	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.		R -> H (in dbSNP:rs35662416).		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						TCTAGAATACGTTACAGATGT	0.348													G|||	52	0.0103834	0.0	0.0173	5008	,	,		13940	0.0		0.0328	False		,,,				2504	0.0072				p.R356H		Atlas-SNP	.											CFHR5_ENST00000367414,NS,carcinoma,+1,2	CFHR5	150	2	0			c.G1067A	GRCh37	CM077517	CFHR5	M	rs35662416	PASS	.	G	HIS/ARG	30,4376	35.2+/-66.4	0,30,2173	38.0	37.0	37.0		1067	-6.6	0.0	1	dbSNP_126	37	242,8352	96.3+/-158.1	1,240,4056	yes	missense	CFHR5	NM_030787.3	29	1,270,6229	AA,AG,GG		2.8159,0.6809,2.0923	possibly-damaging	356/570	196967354	272,12728	2203	4297	6500	SO:0001583	missense	81494	exon7			GAATACGTTACAG	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.1067G>A	1.37:g.196967354G>A	ENSP00000256785:p.Arg356His	Somatic	281	1	0.00355872		WXS	Illumina HiSeq	Phase_I	315	204	0.647619	NM_030787	Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	34	0.015567765567765568	0	0.0	9	0.024861878453038673	0	0.0	25	0.032981530343007916	G	12.25	1.882395	0.33255	0.006809	0.028159	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.65916	-0.18;-0.18	3.28	-6.56	0.01848	Complement control module (1);Sushi/SCR/CCP (3);	.	.	.	.	T	0.23532	0.0569	L	0.34521	1.04	0.09310	N	1	P	0.43885	0.82	P	0.48840	0.592	T	0.28202	-1.0051	9	0.28530	T	0.3	.	1.9625	0.03389	0.5098:0.1432:0.2023:0.1447	rs35662416	356	Q9BXR6	FHR5_HUMAN	H	380;356	ENSP00000356384:R380H;ENSP00000256785:R356H	ENSP00000256785:R356H	R	+	2	0	CFHR5	195233977	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-1.428000	0.02439	-1.868000	0.01142	0.289000	0.19496	CGT	G|0.979;A|0.021	0.021	strong		0.348	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787	
TRIM22	10346	hgsc.bcm.edu	37	11	5729419	5729419	+	Silent	SNP	T	T	C	rs112606816	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5729419T>C	ENST00000379965.3	+	6	1067	c.790T>C	c.(790-792)Ttg>Ctg	p.L264L	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	264					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)			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)		AAGCTGGACATTGAAGAAGCC	0.413													T|||	13	0.00259585	0.0008	0.0086	5008	,	,		21253	0.0		0.005	False		,,,				2504	0.001				p.L264L	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.T790C						PASS	.	T	,	13,3775		0,13,1881	126.0	121.0	123.0		778,790	-8.1	0.0	11	dbSNP_132	123	66,8196		0,66,4065	no	coding-synonymous,coding-synonymous	TRIM22	NM_001199573.1,NM_006074.4	,	0,79,5946	CC,CT,TT		0.7988,0.3432,0.6556	,	260/495,264/499	5729419	79,11971	1894	4131	6025	SO:0001819	synonymous_variant	10346	exon6			TGGACATTGAAGA	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.790T>C	11.37:g.5729419T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_006074	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			A|0.000;C|0.006;T|0.993	0.006	strong		0.413	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
SPNS3	201305	hgsc.bcm.edu	37	17	4391152	4391152	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4391152T>C	ENST00000355530.2	+	12	1782	c.1502T>C	c.(1501-1503)cTa>cCa	p.L501P	SPNS3_ENST00000333476.2_Missense_Mutation_p.L374P|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)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						AGACAAGGCCTACTTTCGGGC	0.617																																					p.L501P		Atlas-SNP	.											SPNS3,NS,carcinoma,-1,1	SPNS3	52	1	0			c.T1502C						scavenged	.						115.0	105.0	109.0					17																	4391152		2203	4300	6503	SO:0001583	missense	201305	exon12			AAGGCCTACTTTC		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.1502T>C	17.37:g.4391152T>C	ENSP00000347721:p.Leu501Pro	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	151	3	0.0198676	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	37	CCDS11045.1	.	.	.	.	.	.	.	.	.	.	T	16.61	3.172612	0.57584	.	.	ENSG00000182557	ENST00000355530;ENST00000333476	T;T	0.30981	2.05;1.51	4.45	4.45	0.53987	.	1.232680	0.06377	N	0.714522	T	0.48077	0.1480	M	0.63428	1.95	0.24817	N	0.992601	D;D	0.61080	0.988;0.989	P;P	0.56700	0.804;0.726	T	0.27400	-1.0075	10	0.46703	T	0.11	-7.0686	10.388	0.44152	0.0:0.0:0.0:1.0	.	374;501	Q6ZMD2-2;Q6ZMD2	.;SPNS3_HUMAN	P	501;374	ENSP00000347721:L501P;ENSP00000333207:L374P	ENSP00000333207:L374P	L	+	2	0	SPNS3	4337901	0.614000	0.27017	0.069000	0.20011	0.047000	0.14425	2.121000	0.41977	2.232000	0.73038	0.402000	0.26972	CTA	.	.	none		0.617	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
CDC16	8881	hgsc.bcm.edu	37	13	115004914	115004914	+	Silent	SNP	C	C	T	rs2296971	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:115004914C>T	ENST00000356221.3	+	5	438	c.330C>T	c.(328-330)gaC>gaT	p.D110D	CDC16_ENST00000375312.3_Silent_p.D16D|CDC16_ENST00000252458.6_Silent_p.D16D|CDC16_ENST00000375310.1_Silent_p.D16D|CDC16_ENST00000375308.1_Silent_p.D16D|CDC16_ENST00000360383.3_Silent_p.D110D|CDC16_ENST00000252457.5_Silent_p.D109D			Q13042	CDC16_HUMAN	cell division cycle 16	110					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|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)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|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)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	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)			ACTTGAAGGACGAAAGTGGCT	0.453													T|||	2225	0.444289	0.8464	0.3516	5008	,	,		17472	0.2024		0.3191	False		,,,				2504	0.3446				p.D110D		Atlas-SNP	.											.	CDC16	50	.	0			c.C330T						PASS	.	T	,	3299,1107	398.8+/-331.0	1247,805,151	50.0	56.0	54.0		330,330	3.3	1.0	13	dbSNP_100	54	2451,6149	697.3+/-404.9	369,1713,2218	no	coding-synonymous,coding-synonymous	CDC16	NM_001078645.1,NM_003903.3	,	1616,2518,2369	TT,TC,CC		28.5,25.1248,44.2104	,	110/621,110/621	115004914	5750,7256	2203	4300	6503	SO:0001819	synonymous_variant	8881	exon5			GAAGGACGAAAGT	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.330C>T	13.37:g.115004914C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	76	0.938272	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			C|0.562;T|0.438	0.438	strong		0.453	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	
BANP	54971	hgsc.bcm.edu	37	16	88066717	88066717	+	Missense_Mutation	SNP	C	C	T	rs74992447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88066717C>T	ENST00000393207.1	+	9	1263	c.1042C>T	c.(1042-1044)Ccg>Tcg	p.P348S	BANP_ENST00000355022.4_Missense_Mutation_p.P317S|BANP_ENST00000393208.2_Missense_Mutation_p.P317S|BANP_ENST00000355163.5_Missense_Mutation_p.P323S|BANP_ENST00000286122.7_Missense_Mutation_p.P348S|BANP_ENST00000479780.2_Missense_Mutation_p.P317S|BANP_ENST00000538234.1_Missense_Mutation_p.P356S	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	348	DNA-binding. {ECO:0000250}.|Necessary and sufficient for TP53 activation. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		CCCCACAGAGCCGATGATGAG	0.647													c|||	923	0.184305	0.1672	0.0735	5008	,	,		15135	0.1349		0.1243	False		,,,				2504	0.3988				p.P356S		Atlas-SNP	.											BANP,rectum,carcinoma,-1,1	BANP	67	1	0			c.C1066T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	698,3698	284.9+/-277.9	49,600,1549	28.0	25.0	26.0		1066,967,949,1066,1042,949,949	2.7	1.0	16	dbSNP_131	26	889,7711	194.4+/-239.8	59,771,3470	no	missense,missense,missense,missense,missense,missense,missense	BANP	NM_001173539.1,NM_001173540.1,NM_001173541.1,NM_001173542.1,NM_001173543.1,NM_017869.3,NM_079837.2	74,74,74,74,74,74,74	108,1371,5019	TT,TC,CC		10.3372,15.8781,12.2114	benign,benign,benign,benign,benign,benign,benign	356/506,323/498,317/467,356/509,348/520,317/470,317/492	88066717	1587,11409	2198	4300	6498	SO:0001583	missense	54971	exon9			ACAGAGCCGATGA	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.1042C>T	16.37:g.88066717C>T	ENSP00000376902:p.Pro348Ser	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	287	54	0.188153	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Missense_Mutation	SNP	ENST00000393207.1	37	CCDS54054.1	283	0.1295787545787546	84	0.17073170731707318	37	0.10220994475138122	58	0.10139860139860139	104	0.13720316622691292	C	0.012	-1.671606	0.00758	0.158781	0.103372	ENSG00000172530	ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	.	.	.	3.75	2.65	0.31530	.	0.536094	0.20729	N	0.086754	T	0.00039	0.0001	N	0.03608	-0.345	0.45554	P	0.0014979999999999993	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	0.0;0.0;0.0;0.0;0.0;0.001	T	0.22452	-1.0216	8	0.09338	T	0.73	.	7.0763	0.25207	0.7505:0.2495:0.0:0.0	.	356;323;317;348;317;317	B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4	.;.;.;BANP_HUMAN;.;.	S	348;323;313;317;317;317;317;356;348	.	ENSP00000286122:P348S	P	+	1	0	BANP	86624218	1.000000	0.71417	0.998000	0.56505	0.171000	0.22731	1.255000	0.32909	0.625000	0.30304	0.305000	0.20034	CCG	C|0.875;T|0.125	0.125	strong		0.647	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
JSRP1	126306	hgsc.bcm.edu	37	19	2252990	2252990	+	Missense_Mutation	SNP	C	C	G	rs80043033	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2252990C>G	ENST00000300961.6	-	6	513	c.449G>C	c.(448-450)gGg>gCg	p.G150A	JSRP1_ENST00000586471.2_Missense_Mutation_p.G150A|MIR4321_ENST00000592276.1_RNA	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	150	Pro-rich.		G -> A (polymorphism affecting excitation/contraction coupling in muscle fibers; the sensitivity of CACNA1S voltage sensor is shifted to higher depolarizing voltages in cells carrying this variant; dbSNP:rs80043033). {ECO:0000269|PubMed:22927026}.		protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				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)		TGCTGCCTCCCCAGGGACGGC	0.692													C|||	899	0.179513	0.0091	0.1916	5008	,	,		13576	0.3234		0.2376	False		,,,				2504	0.1933				p.G150A		Atlas-SNP	.											.	JSRP1	18	.	0			c.G449C						PASS	.	C	ALA/GLY	182,4192		3,176,2008	23.0	22.0	22.0		449	2.7	0.0	19	dbSNP_131	22	1727,6863		177,1373,2745	no	missense	JSRP1	NM_144616.3	60	180,1549,4753	GG,GC,CC		20.1048,4.161,14.7254	probably-damaging	150/332	2252990	1909,11055	2187	4295	6482	SO:0001583	missense	126306	exon6			GCCTCCCCAGGGA	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"""homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"""	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.449G>C	19.37:g.2252990C>G	ENSP00000300961:p.Gly150Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	437	0.2000915750915751	5	0.01016260162601626	68	0.1878453038674033	188	0.32867132867132864	176	0.23218997361477572	C	15.49	2.849180	0.51270	0.04161	0.201048	ENSG00000167476	ENST00000300961	T	0.59083	0.29	3.88	2.73	0.32206	.	0.642264	0.13741	N	0.365988	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P	0.36199	0.543	B	0.37387	0.248	T	0.29243	-1.0018	9	0.18276	T	0.48	-30.0495	8.7648	0.34696	0.0:0.767:0.233:0.0	.	150	Q96MG2	JSPR1_HUMAN	A	150	ENSP00000300961:G150A	ENSP00000300961:G150A	G	-	2	0	JSRP1	2203990	0.009000	0.17119	0.007000	0.13788	0.007000	0.05969	1.062000	0.30555	2.169000	0.68431	0.561000	0.74099	GGG	C|0.842;G|0.158	0.158	strong		0.692	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	
ZNF99	7652	hgsc.bcm.edu	37	19	22940659	22940659	+	Silent	SNP	C	C	T	rs59621958	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22940659C>T	ENST00000596209.1	-	4	2142	c.2052G>A	c.(2050-2052)aaG>aaA	p.K684K	CTC-451A6.4_ENST00000442497.2_lincRNA|ZNF99_ENST00000397104.3_Silent_p.K593K	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	684					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(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGTTAAAAGCCTTGCCACATT	0.378													T|||	1087	0.217053	0.4213	0.1326	5008	,	,		20012	0.1726		0.1362	False		,,,				2504	0.1299				p.K684K		Atlas-SNP	.											.	ZNF99	273	.	0			c.G2052A						PASS	.	T		1486,2718		256,974,872	46.0	49.0	48.0		1779	0.2	0.0	19	dbSNP_129	48	980,7520		67,846,3337	no	coding-synonymous	ZNF99	NM_001080409.2		323,1820,4209	TT,TC,CC		11.5294,35.3473,19.4112		593/912	22940659	2466,10238	2102	4250	6352	SO:0001819	synonymous_variant	7652	exon4			AAAAGCCTTGCCA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2052G>A	19.37:g.22940659C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_001080409	M0R335	Silent	SNP	ENST00000596209.1	37	CCDS59369.1																																																																																			C|0.826;T|0.174	0.174	strong		0.378	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
CLRN2	645104	hgsc.bcm.edu	37	4	17524570	17524570	+	Missense_Mutation	SNP	C	C	G	rs13147559	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:17524570C>G	ENST00000511148.2	+	2	439	c.337C>G	c.(337-339)Ctg>Gtg	p.L113V		NM_001079827.2	NP_001073296.1	A0PK11	CLRN2_HUMAN	clarin 2	113			L -> V (in dbSNP:rs13147559).			integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|upper_aerodigestive_tract(1)	15						GGCCCTGGCTCTGGTCAGCAT	0.577													C|||	479	0.095647	0.0053	0.1513	5008	,	,		18490	0.0893		0.1342	False		,,,				2504	0.1452				p.L113V		Atlas-SNP	.											.	CLRN2	40	.	0			c.C337G						PASS	.	C	VAL/LEU	127,4155		0,127,2014	103.0	109.0	107.0		337	4.2	1.0	4	dbSNP_121	107	1141,7363		91,959,3202	yes	missense	CLRN2	NM_001079827.2	32	91,1086,5216	GG,GC,CC		13.4172,2.9659,9.9171	benign	113/233	17524570	1268,11518	2141	4252	6393	SO:0001583	missense	645104	exon2			CTGGCTCTGGTCA		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.337C>G	4.37:g.17524570C>G	ENSP00000424711:p.Leu113Val	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_001079827		Missense_Mutation	SNP	ENST00000511148.2	37	CCDS47032.1	204	0.09340659340659341	6	0.012195121951219513	38	0.10497237569060773	51	0.08916083916083917	109	0.1437994722955145	C	16.71	3.197607	0.58126	0.029659	0.134172	ENSG00000249581	ENST00000511148	D	0.83419	-1.72	5.06	4.22	0.49857	.	0.088467	0.47455	D	0.000233	T	0.02083	0.0065	L	0.38175	1.15	0.22771	P	0.99875403	P	0.47484	0.896	P	0.46758	0.526	T	0.47611	-0.9104	9	0.42905	T	0.14	-13.4468	13.1191	0.59316	0.0:0.9213:0.0:0.0787	rs13147559;rs17518172;rs13147559	113	A0PK11	CLRN2_HUMAN	V	113	ENSP00000424711:L113V	ENSP00000424711:L113V	L	+	1	2	CLRN2	17133668	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.944000	0.56629	1.148000	0.42385	-0.253000	0.11424	CTG	C|0.904;G|0.095	0.095	strong		0.577	CLRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359990.2	NM_001079827	
FREM2	341640	hgsc.bcm.edu	37	13	39263023	39263023	+	Silent	SNP	C	C	T	rs12874397	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	63	37	0.587302	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	
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56704101	56704101	+	Silent	SNP	G	G	A	rs11084427	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	645	1	0.00155039		WXS	Illumina HiSeq	Phase_I	706	272	0.385269	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	
AVL9	23080	hgsc.bcm.edu	37	7	32598656	32598656	+	Silent	SNP	C	C	T	rs2290214	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:32598656C>T	ENST00000318709.4	+	10	1016	c.795C>T	c.(793-795)tcC>tcT	p.S265S	AVL9_ENST00000404479.1_Silent_p.S265S|AVL9_ENST00000409301.1_Silent_p.S265S	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	265					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TTTCTGCATCCACTGCTGATG	0.463													C|||	1206	0.240815	0.3306	0.1744	5008	,	,		18209	0.1319		0.165	False		,,,				2504	0.3569				p.S265S		Atlas-SNP	.											.	AVL9	66	.	0			c.C795T						PASS	.	C		1448,2958	467.9+/-355.0	235,978,990	89.0	85.0	86.0		795	0.1	0.0	7	dbSNP_100	86	1407,7193	270.4+/-288.9	114,1179,3007	no	coding-synonymous	AVL9	NM_015060.1		349,2157,3997	TT,TC,CC		16.3605,32.8643,21.9514		265/649	32598656	2855,10151	2203	4300	6503	SO:0001819	synonymous_variant	23080	exon10			TGCATCCACTGCT	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.795C>T	7.37:g.32598656C>T		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	178	110	0.617977	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	37	CCDS34613.1																																																																																			C|0.781;T|0.219	0.219	strong		0.463	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
SERPINE2	5270	hgsc.bcm.edu	37	2	224866387	224866387	+	Silent	SNP	G	G	A	rs12138	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:224866387G>A	ENST00000258405.4	-	2	473	c.231C>T	c.(229-231)ctC>ctT	p.L77L	SERPINE2_ENST00000409840.3_Silent_p.L77L|SERPINE2_ENST00000447280.2_Silent_p.L89L|SERPINE2_ENST00000409304.1_Silent_p.L77L	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	77					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TCACCATGGCGAGCTGCTTCT	0.577													G|||	1011	0.201877	0.236	0.1744	5008	,	,		17987	0.244		0.0994	False		,,,				2504	0.2372				p.L89L		Atlas-SNP	.											.	SERPINE2	103	.	0			c.C267T						PASS	.	G	,,	949,3457	360.9+/-315.4	90,769,1344	79.0	69.0	73.0		231,267,231	0.6	0.3	2	dbSNP_52	73	835,7765	192.7+/-238.6	36,763,3501	no	coding-synonymous,coding-synonymous,coding-synonymous	SERPINE2	NM_001136528.1,NM_001136530.1,NM_006216.3	,,	126,1532,4845	AA,AG,GG		9.7093,21.5388,13.7167	,,	77/398,89/410,77/399	224866387	1784,11222	2203	4300	6503	SO:0001819	synonymous_variant	5270	exon2			CATGGCGAGCTGC	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"""Serine (or cysteine) peptidase inhibitors"""	8951	protein-coding gene	gene with protein product	"""glial-derived nexin 1"""	177010	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"""	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.231C>T	2.37:g.224866387G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Silent	SNP	ENST00000258405.4	37	CCDS2460.1																																																																																			T|0.040;G|0.683;C|0.156;A|0.120	0.120	strong		0.577	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	
KLRC3	3823	hgsc.bcm.edu	37	12	10573094	10573094	+	Missense_Mutation	SNP	C	C	G	rs2682491	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:10573094C>G	ENST00000396439.2	-	1	100	c.56G>C	c.(55-57)tGg>tCg	p.W19S	KLRC3_ENST00000381904.2_Missense_Mutation_p.W19S|NKG2-E_ENST00000539033.1_Intron|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	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	211	140	0.663507	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	
PTCH1	5727	hgsc.bcm.edu	37	9	98244242	98244242	+	Silent	SNP	T	T	C	rs1805154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:98244242T>C	ENST00000331920.6	-	5	1034	c.735A>G	c.(733-735)acA>acG	p.T245T	PTCH1_ENST00000437951.1_Silent_p.T179T|PTCH1_ENST00000429896.2_Silent_p.T94T|PTCH1_ENST00000421141.1_Silent_p.T94T|PTCH1_ENST00000468211.2_Silent_p.T179T|PTCH1_ENST00000418258.1_Silent_p.T94T|PTCH1_ENST00000430669.2_Silent_p.T179T|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000375274.2_Silent_p.T244T	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	245					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)			NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GGAGGTATGCTGTCCCAGACT	0.388													T|||	47	0.00938498	0.0023	0.0202	5008	,	,		17942	0.0		0.0249	False		,,,				2504	0.0051				p.T245T		Atlas-SNP	.											.	PTCH1	1850	.	0			c.A735G						PASS	.	T	,,,,,,	30,4376	34.3+/-65.2	0,30,2173	84.0	70.0	75.0		735,537,732,282,282,282,282	-2.5	1.0	9	dbSNP_89	75	329,8271	115.2+/-175.0	4,321,3975	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	4,351,6148	CC,CT,TT		3.8256,0.6809,2.7603	,,,,,,	245/1448,179/1382,244/1447,94/1297,94/1297,94/1297,94/1297	98244242	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon5			GTATGCTGTCCCA	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.735A>G	9.37:g.98244242T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			T|0.976;C|0.024	0.024	strong		0.388	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
KRT6C	286887	hgsc.bcm.edu	37	12	52863564	52863564	+	Silent	SNP	C	C	T	rs3894847	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52863564C>T	ENST00000252250.6	-	7	1361	c.1314G>A	c.(1312-1314)aaG>aaA	p.K438K		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	438	Coil 2.|Rod.				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)		CCAGGTCCTGCTTGGCCTTCT	0.607													C|||	1177	0.235024	0.236	0.3429	5008	,	,		21106	0.1558		0.2445	False		,,,				2504	0.229				p.K438K		Atlas-SNP	.											.	KRT6C	55	.	0			c.G1314A						PASS	.	C		1001,3405	372.0+/-320.2	113,775,1315	79.0	67.0	71.0		1314	2.8	1.0	12	dbSNP_108	71	1869,6725	328.0+/-318.1	213,1443,2641	no	coding-synonymous	KRT6C	NM_173086.4		326,2218,3956	TT,TC,CC		21.7477,22.719,22.0769		438/565	52863564	2870,10130	2203	4297	6500	SO:0001819	synonymous_variant	286887	exon7			GTCCTGCTTGGCC	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.1314G>A	12.37:g.52863564C>T		Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	203	92	0.453202	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			C|0.788;T|0.212	0.212	strong		0.607	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
CYP26C1	340665	hgsc.bcm.edu	37	10	94824166	94824166	+	Missense_Mutation	SNP	G	G	A	rs11187265	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:94824166G>A	ENST00000285949.5	+	4	734	c.734G>A	c.(733-735)cGg>cAg	p.R245Q		NM_183374.2	NP_899230.2	Q6V0L0	CP26C_HUMAN	cytochrome P450, family 26, subfamily C, polypeptide 1	245			R -> Q (in dbSNP:rs11187265).		anterior/posterior pattern specification (GO:0009952)|central nervous system development (GO:0007417)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|organelle fusion (GO:0048284)|oxidation-reduction process (GO:0055114)|retinoic acid catabolic process (GO:0034653)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			central_nervous_system(1)|lung(3)|ovary(1)	5		Colorectal(252;0.122)				CAGCTGCATCGGCACCTGGAG	0.602													g|||	370	0.0738818	0.0696	0.1643	5008	,	,		20138	0.001		0.0924	False		,,,				2504	0.0716				p.R245Q		Atlas-SNP	.											.	CYP26C1	25	.	0			c.G734A						PASS	.	A	GLN/ARG	310,4096	165.4+/-196.9	14,282,1907	54.0	52.0	52.0		734	-5.5	0.9	10	dbSNP_120	52	796,7804	186.7+/-234.1	36,724,3540	yes	missense	CYP26C1	NM_183374.2	43	50,1006,5447	AA,AG,GG		9.2558,7.0359,8.5038	benign	245/523	94824166	1106,11900	2203	4300	6503	SO:0001583	missense	340665	exon4			TGCATCGGCACCT		CCDS7425.1	10q23.33	2003-11-20			ENSG00000187553	ENSG00000187553		"""Cytochrome P450s"""	20577	protein-coding gene	gene with protein product		608428					Standard	XR_246086		Approved		uc010qns.2	Q6V0L0	OTTHUMG00000018766	ENST00000285949.5:c.734G>A	10.37:g.94824166G>A	ENSP00000285949:p.Arg245Gln	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	95	29	0.305263	NM_183374	Q5VXH6	Missense_Mutation	SNP	ENST00000285949.5	37	CCDS7425.1	169	0.07738095238095238	42	0.08536585365853659	59	0.16298342541436464	1	0.0017482517482517483	67	0.08839050131926121	g	12.30	1.897735	0.33535	0.070359	0.092558	ENSG00000187553	ENST00000285949	T	0.65916	-0.18	5.33	-5.47	0.02600	.	1.122760	0.06534	N	0.742051	T	0.00210	0.0006	N	0.13043	0.29	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.04103	-1.0977	9	0.31617	T	0.26	-4.0957	16.8136	0.85727	0.8792:0.0:0.1208:0.0	rs11187265;rs58644142	245	Q6V0L0	CP26C_HUMAN	Q	245	ENSP00000285949:R245Q	ENSP00000285949:R245Q	R	+	2	0	CYP26C1	94814156	0.004000	0.15560	0.879000	0.34478	0.768000	0.43524	0.072000	0.14617	-0.815000	0.04346	-2.396000	0.00226	CGG	G|0.914;A|0.086	0.086	strong		0.602	CYP26C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049409.2	NM_183374	
ZNF217	7764	hgsc.bcm.edu	37	20	52193088	52193088	+	Missense_Mutation	SNP	C	C	T	rs6063966	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:52193088C>T	ENST00000371471.2	-	4	2640	c.2215G>A	c.(2215-2217)Gtt>Att	p.V739I	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.V739I			O75362	ZN217_HUMAN	zinc finger protein 217	739			V -> I (in dbSNP:rs6063966).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.V739I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			TTTTTATGAACGTCAGGATTG	0.438													C|||	785	0.156749	0.2602	0.1066	5008	,	,		19555	0.0833		0.1203	False		,,,				2504	0.1656				p.V739I		Atlas-SNP	.											ZNF217,NS,carcinoma,0,1	ZNF217	227	1	1	Substitution - Missense(1)	stomach(1)	c.G2215A						scavenged	.	C	ILE/VAL	931,3475	356.4+/-313.5	107,717,1379	75.0	77.0	76.0		2215	-9.8	0.0	20	dbSNP_114	76	1060,7540	224.1+/-260.6	59,942,3299	yes	missense	ZNF217	NM_006526.2	29	166,1659,4678	TT,TC,CC		12.3256,21.1303,15.3083	benign	739/1049	52193088	1991,11015	2203	4300	6503	SO:0001583	missense	7764	exon3			TATGAACGTCAGG	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2215G>A	20.37:g.52193088C>T	ENSP00000360526:p.Val739Ile	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	115	43	0.373913	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	296	0.13553113553113552	138	0.2804878048780488	41	0.1132596685082873	33	0.057692307692307696	84	0.11081794195250659	C	3.852	-0.031630	0.07543	0.211303	0.123256	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.09445	2.98;2.98	5.45	-9.83	0.00482	.	2.230010	0.01570	N	0.020552	T	0.00012	0.0000	N	0.03967	-0.31	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.36089	-0.9762	9	0.11182	T	0.66	-0.48	4.7667	0.13135	0.0985:0.4318:0.2022:0.2675	rs6063966;rs16998239;rs60939286;rs6063966	739	O75362	ZN217_HUMAN	I	739	ENSP00000360526:V739I;ENSP00000304308:V739I	ENSP00000304308:V739I	V	-	1	0	ZNF217	51626495	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.738000	0.04871	-2.542000	0.00485	-0.300000	0.09419	GTT	C|0.859;T|0.141	0.141	strong		0.438	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
ZNF283	284349	hgsc.bcm.edu	37	19	44351694	44351694	+	Missense_Mutation	SNP	C	C	T	rs2195980	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44351694C>T	ENST00000324461.7	+	7	1238	c.941C>T	c.(940-942)aCt>aTt	p.T314I	ZNF283_ENST00000588797.1_Missense_Mutation_p.T175I	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	314			T -> I (in dbSNP:rs2195980). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7865130}.		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)				AAAATTCATACTGGTGTGAAA	0.398													T|||	4021	0.802915	0.9592	0.6513	5008	,	,		20570	0.5982		0.8638	False		,,,				2504	0.8476				p.T314I		Atlas-SNP	.											.	ZNF283	83	.	0			c.C941T						PASS	.	T	ILE/THR	4114,230		1950,214,8	45.0	52.0	50.0		941	2.0	1.0	19	dbSNP_96	50	7342,1220		3155,1032,94	no	missense	ZNF283	NM_181845.1	89	5105,1246,102	TT,TC,CC		14.249,5.2947,11.2351	benign	314/680	44351694	11456,1450	2172	4281	6453	SO:0001583	missense	284349	exon7			TTCATACTGGTGT	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.941C>T	19.37:g.44351694C>T	ENSP00000327314:p.Thr314Ile	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	133	77	0.578947	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	1723	0.7889194139194139	473	0.9613821138211383	255	0.7044198895027625	337	0.5891608391608392	658	0.8680738786279684	c	9.647	1.140523	0.21205	0.947053	0.85751	ENSG00000167637	ENST00000324461	T	0.25749	1.78	3.0	1.97	0.26223	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.56769	1.78	0.09310	P	0.9999999999999568	B	0.02656	0.0	B	0.06405	0.002	T	0.10382	-1.0632	8	0.51188	T	0.08	.	4.9103	0.13818	0.0:0.415:0.0:0.585	rs2195980;rs52801196;rs58512958;rs2195980	314	Q8N7M2	ZN283_HUMAN	I	314	ENSP00000327314:T314I	ENSP00000327314:T314I	T	+	2	0	ZNF283	49043534	0.087000	0.21565	1.000000	0.80357	0.790000	0.44656	0.064000	0.14437	0.380000	0.24823	-0.360000	0.07572	ACT	C|0.206;T|0.794	0.794	strong		0.398	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
TACC3	10460	hgsc.bcm.edu	37	4	1729958	1729958	+	Missense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1729958G>T	ENST00000313288.4	+	4	935	c.829G>T	c.(829-831)Gcg>Tcg	p.A277S		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	277					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|cytoplasmic sequestering of transcription factor (GO:0042994)|hemopoiesis (GO:0030097)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of cell cycle (GO:0051726)|regulation of microtubule-based process (GO:0032886)|response to hypoxia (GO:0001666)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	25		Breast(71;0.212)|all_epithelial(65;0.241)	OV - Ovarian serous cystadenocarcinoma(23;0.00765)|Epithelial(3;0.0126)			GGGCTGCCCTGCGGGTGTGGG	0.667																																					p.A277S	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.G829T						PASS	.						15.0	17.0	16.0					4																	1729958		2193	4293	6486	SO:0001583	missense	10460	exon4			TGCCCTGCGGGTG	AF093543	CCDS3352.1	4p16.3	2008-07-29			ENSG00000013810	ENSG00000013810			11524	protein-coding gene	gene with protein product		605303				17675670	Standard	NM_006342		Approved	ERIC1	uc003gdo.3	Q9Y6A5	OTTHUMG00000089535	ENST00000313288.4:c.829G>T	4.37:g.1729958G>T	ENSP00000326550:p.Ala277Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	95	59	0.621053	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	.	.	.	.	.	.	.	.	.	.	G	3.044	-0.196772	0.06259	.	.	ENSG00000013810	ENST00000313288	T	0.10477	2.87	3.55	-3.23	0.05109	.	10.642000	0.00481	U	0.000126	T	0.04907	0.0132	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.12837	0.008;0.004	T	0.30736	-0.9968	10	0.10636	T	0.68	0.0017	4.8773	0.13662	0.3038:0.2546:0.4416:0.0	.	277;277	B4DYJ1;Q9Y6A5	.;TACC3_HUMAN	S	277	ENSP00000326550:A277S	ENSP00000326550:A277S	A	+	1	0	TACC3	1699756	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.169000	0.09911	-0.955000	0.03636	0.563000	0.77884	GCG	.	.	none		0.667	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
LTA4H	4048	hgsc.bcm.edu	37	12	96408716	96408716	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:96408716T>C	ENST00000228740.2	-	12	1262	c.1121A>G	c.(1120-1122)gAc>gGc	p.D374G	LTA4H_ENST00000548375.1_5'UTR|LTA4H_ENST00000552789.1_Missense_Mutation_p.D350G|LTA4H_ENST00000413268.2_Missense_Mutation_p.D350G	NM_000895.2	NP_000886.1	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	374					arachidonic acid metabolic process (GO:0019369)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|peptide catabolic process (GO:0043171)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|leukotriene-A4 hydrolase activity (GO:0004463)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(3)|lung(4)|skin(2)|stomach(1)	12					Captopril(DB01197)	TACATCAGGGTCTATATCTGT	0.393																																					p.D374G		Atlas-SNP	.											.	LTA4H	38	.	0			c.A1121G						PASS	.						172.0	157.0	162.0					12																	96408716		2203	4300	6503	SO:0001583	missense	4048	exon12			TCAGGGTCTATAT	BC032528	CCDS9059.1, CCDS58266.1, CCDS58267.1	12q22	2005-10-06				ENSG00000111144	3.3.2.6		6710	protein-coding gene	gene with protein product		151570				7628486	Standard	NM_000895		Approved		uc001ten.2	P09960	OTTHUMG00000170355	ENST00000228740.2:c.1121A>G	12.37:g.96408716T>C	ENSP00000228740:p.Asp374Gly	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	185	8	0.0432432	NM_000895	B4DNQ9|F8VV40|Q6IAT6|Q9UCT7	Missense_Mutation	SNP	ENST00000228740.2	37	CCDS9059.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461791	0.63513	.	.	ENSG00000111144	ENST00000228740;ENST00000552789;ENST00000413268	T;T;T	0.02944	4.1;4.1;4.1	6.07	6.07	0.98685	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.16599	0.0399	M	0.88512	2.96	0.80722	D	1	P;P;D	0.53312	0.502;0.698;0.959	P;P;P	0.57846	0.499;0.736;0.828	T	0.00350	-1.1797	10	0.52906	T	0.07	-23.543	16.6277	0.84984	0.0:0.0:0.0:1.0	.	350;350;374	P09960-3;F8VV40;P09960	.;.;LKHA4_HUMAN	G	374;350;350	ENSP00000228740:D374G;ENSP00000449958:D350G;ENSP00000395051:D350G	ENSP00000228740:D374G	D	-	2	0	LTA4H	94932847	1.000000	0.71417	0.996000	0.52242	0.627000	0.37826	5.728000	0.68531	2.330000	0.79161	0.528000	0.53228	GAC	.	.	none		0.393	LTA4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408655.1	NM_000895	
KDM4B	23030	hgsc.bcm.edu	37	19	5110794	5110794	+	Silent	SNP	A	A	G	rs2613739	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:5110794A>G	ENST00000159111.4	+	10	1298	c.1080A>G	c.(1078-1080)gcA>gcG	p.A360A	KDM4B_ENST00000381759.4_Silent_p.A360A|KDM4B_ENST00000536461.1_Silent_p.A360A	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	360					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CCTGGAGTGCATCCCGGGCCT	0.701													G|||	3178	0.634585	0.6838	0.5706	5008	,	,		14508	0.6677		0.5656	False		,,,				2504	0.6503				p.A360A		Atlas-SNP	.											.	KDM4B	120	.	0			c.A1080G						PASS	.	G		2819,1581		904,1011,285	23.0	22.0	22.0		1080	-2.6	0.9	19	dbSNP_100	22	4747,3847		1318,2111,868	no	coding-synonymous	KDM4B	NM_015015.2		2222,3122,1153	GG,GA,AA		44.7638,35.9318,41.7731		360/1097	5110794	7566,5428	2200	4297	6497	SO:0001819	synonymous_variant	23030	exon10			GAGTGCATCCCGG	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.1080A>G	19.37:g.5110794A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	76	26	0.342105	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																			A|0.406;G|0.594	0.594	strong		0.701	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
TRIM34	53840	hgsc.bcm.edu	37	11	5664831	5664831	+	Silent	SNP	C	C	A	rs3740998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5664831C>A	ENST00000514226.1	+	8	1696	c.1359C>A	c.(1357-1359)ggC>ggA	p.G453G	TRIM6-TRIM34_ENST00000354852.5_Silent_p.G807G|TRIM34_ENST00000429814.2_Silent_p.G453G|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000457787.2_Silent_p.G453G|TRIM34_ENST00000495668.1_3'UTR	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	453	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	17		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;5.72e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CAAGCCATGGCTCCCTCATTT	0.463													C|||	1892	0.377796	0.2103	0.438	5008	,	,		20145	0.6458		0.2306	False		,,,				2504	0.4366				p.G807G		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.C2421A						PASS	.	C	,,	1044,3358	383.2+/-324.8	133,778,1290	150.0	145.0	147.0		2421,1359,1359	-1.6	0.5	11	dbSNP_107	147	2042,6552	354.9+/-329.7	252,1538,2507	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM34,TRIM6-TRIM34	NM_001003819.3,NM_001003827.1,NM_021616.5	,,	385,2316,3797	AA,AC,CC		23.7608,23.7165,23.7458	,,	807/843,453/489,453/489	5664831	3086,9910	2201	4297	6498	SO:0001819	synonymous_variant	445372	exon14			CCATGGCTCCCTC	AB039902	CCDS31391.1	11p15	2013-01-09	2011-01-25	2001-11-23		ENSG00000258659		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10063	protein-coding gene	gene with protein product		605684	"""tripartite motif-containing 34"""	RNF21			Standard	NM_130390		Approved			Q9BYJ4	OTTHUMG00000066892	ENST00000514226.1:c.1359C>A	11.37:g.5664831C>A		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	243	130	0.534979	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Silent	SNP	ENST00000514226.1	37	CCDS31391.1																																																																																			C|0.716;A|0.284	0.284	strong		0.463	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827	
SAMM50	25813	hgsc.bcm.edu	37	22	44372632	44372632	+	Silent	SNP	C	C	T	rs14315	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:44372632C>T	ENST00000350028.4	+	9	937	c.780C>T	c.(778-780)caC>caT	p.H260H	SAMM50_ENST00000396202.3_Silent_p.H50H	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	260					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)		p.H260H(1)		endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TCTTTCAGCACGCCATGGTCA	0.458													C|||	2358	0.470847	0.615	0.3876	5008	,	,		20257	0.4613		0.326	False		,,,				2504	0.4939				p.H260H		Atlas-SNP	.											SAMM50,NS,carcinoma,0,1	SAMM50	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C780T						PASS	.	C		2472,1934	622.5+/-394.0	699,1074,430	117.0	99.0	106.0		780	-5.6	0.9	22	dbSNP_52	106	2330,6270	388.2+/-342.5	329,1672,2299	no	coding-synonymous	SAMM50	NM_015380.4		1028,2746,2729	TT,TC,CC		27.093,43.8947,36.9214		260/470	44372632	4802,8204	2203	4300	6503	SO:0001819	synonymous_variant	25813	exon9			TCAGCACGCCATG	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.780C>T	22.37:g.44372632C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	159	66	0.415094	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Silent	SNP	ENST00000350028.4	37	CCDS14055.1																																																																																			.	.	weak		0.458	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
TENM3	55714	hgsc.bcm.edu	37	4	183721088	183721088	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:183721088C>T	ENST00000511685.1	+	28	7807	c.7684C>T	c.(7684-7686)Ctg>Ttg	p.L2562L	TENM3_ENST00000406950.2_Silent_p.L2562L			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2562					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)										CCTGGGCACGCTGCGGTTGAC	0.632																																					p.L2562L		Atlas-SNP	.											.	.	.	.	0			c.C7684T						PASS	.						23.0	30.0	28.0					4																	183721088		2175	4263	6438	SO:0001819	synonymous_variant	55714	exon27			GGCACGCTGCGGT	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.7684C>T	4.37:g.183721088C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	101	5	0.049505	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																			.	.	none		0.632	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
KIAA1549L	25758	hgsc.bcm.edu	37	11	33581306	33581306	+	Silent	SNP	G	G	A	rs2281380	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:33581306G>A	ENST00000321505.4	+	6	3156	c.2976G>A	c.(2974-2976)acG>acA	p.T992T	KIAA1549L_ENST00000389726.3_Silent_p.T998T|KIAA1549L_ENST00000265654.5_Silent_p.T998T			Q6ZVL6	K154L_HUMAN	KIAA1549-like	992						integral component of membrane (GO:0016021)											TTGTGAGCACGTCCAATGCCT	0.582													G|||	1948	0.388978	0.469	0.3213	5008	,	,		22143	0.3264		0.3887	False		,,,				2504	0.3937				p.T992T		Atlas-SNP	.											.	.	.	.	0			c.G2976A						PASS	.	G		1926,2268		480,966,651	83.0	80.0	81.0		2976	-5.2	1.0	11	dbSNP_100	81	3268,5198		645,1978,1610	no	coding-synonymous	C11orf41	NM_012194.2		1125,2944,2261	AA,AG,GG		38.6015,45.9227,41.0269		992/1850	33581306	5194,7466	2097	4233	6330	SO:0001819	synonymous_variant	25758	exon6			GAGCACGTCCAAT	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.2976G>A	11.37:g.33581306G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	846	0.3873626373626374	227	0.4613821138211382	126	0.34806629834254144	188	0.32867132867132864	305	0.4023746701846966	G	7.557	0.663994	0.14710	0.459227	0.386015	ENSG00000110427	ENST00000526400	.	.	.	5.42	-5.21	0.02815	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999989427	.	.	.	.	.	.	T	0.44697	-0.9311	3	.	.	.	-8.4917	5.8334	0.18593	0.6112:0.1336:0.1659:0.0893	rs2281380;rs59777290;rs2281380	.	.	.	H	390	.	.	R	+	2	0	C11orf41	33537882	0.018000	0.18449	0.951000	0.38953	0.712000	0.41017	-0.872000	0.04219	-0.823000	0.04301	0.573000	0.79308	CGT	G|0.613;A|0.387	0.387	strong		0.582	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
MUC17	140453	hgsc.bcm.edu	37	7	100682094	100682094	+	Missense_Mutation	SNP	C	C	G	rs534020799		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682094C>G	ENST00000306151.4	+	3	7461	c.7397C>G	c.(7396-7398)aCg>aGg	p.T2466R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2466	59 X approximate tandem repeats.|Ser-rich.				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)	p.T2466M(1)		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)					GTCAGCACCACGCCGGTGGTC	0.522																																					p.T2466R		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	1	1	Substitution - Missense(1)	kidney(1)	c.C7397G						scavenged	.						330.0	326.0	327.0					7																	100682094		2203	4300	6503	SO:0001583	missense	140453	exon3			GCACCACGCCGGT	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.7397C>G	7.37:g.100682094C>G	ENSP00000302716:p.Thr2466Arg	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	249	8	0.0321285	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	4.341	0.062759	0.08388	.	.	ENSG00000169876	ENST00000306151	T	0.02472	4.28	1.43	-2.86	0.05717	.	.	.	.	.	T	0.01523	0.0049	L	0.34521	1.04	0.09310	N	1	P	0.39376	0.67	B	0.19946	0.027	T	0.35699	-0.9778	9	0.26408	T	0.33	.	3.3894	0.07283	0.1815:0.4835:0.0:0.335	.	2466	Q685J3	MUC17_HUMAN	R	2466	ENSP00000302716:T2466R	ENSP00000302716:T2466R	T	+	2	0	MUC17	100468814	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.065000	0.14466	-2.607000	0.00447	-3.221000	0.00052	ACG	.	.	none		0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248834	48248834	+	Silent	SNP	T	T	C	rs10404034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48248834T>C	ENST00000246802.5	+	1	56	c.18T>C	c.(16-18)agT>agC	p.S6S	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	6						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)		CAGGAGGCAGTGGCGTTGGTG	0.642													T|||	301	0.0601038	0.0091	0.062	5008	,	,		11421	0.0089		0.1382	False		,,,				2504	0.1002				p.S6S	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.T18C						PASS	.	T		171,4235	114.2+/-152.2	5,161,2037	91.0	103.0	99.0		18	-4.3	0.0	19	dbSNP_119	99	1230,7370	247.2+/-275.4	89,1052,3159	no	coding-synonymous	GLTSCR2	NM_015710.4		94,1213,5196	CC,CT,TT		14.3023,3.8811,10.772		6/479	48248834	1401,11605	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon1			AGGCAGTGGCGTT	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.18T>C	19.37:g.48248834T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	124	58	0.467742	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			A|0.000;C|0.097;T|0.903	0.097	strong		0.642	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
MDN1	23195	hgsc.bcm.edu	37	6	90500067	90500067	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:90500067C>T	ENST00000369393.3	-	6	1024	c.909G>A	c.(907-909)gtG>gtA	p.V303V	MDN1_ENST00000428876.1_Silent_p.V303V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	303					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)		ACTCAACCAGCACATAAGACC	0.478																																					p.V303V		Atlas-SNP	.											.	MDN1	478	.	0			c.G909A						PASS	.						164.0	169.0	167.0					6																	90500067		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon6			AACCAGCACATAA	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.909G>A	6.37:g.90500067C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	130	6	0.0461538	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			.	.	none		0.478	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
NPEPL1	79716	hgsc.bcm.edu	37	20	57282190	57282190	+	Silent	SNP	G	G	A	rs41310841	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:57282190G>A	ENST00000356091.6	+	7	1122	c.834G>A	c.(832-834)ccG>ccA	p.P278P	NPEPL1_ENST00000525817.1_Silent_p.P230P|NPEPL1_ENST00000525967.1_Silent_p.P250P|STX16-NPEPL1_ENST00000530122.1_3'UTR	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	278						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)			CTACCATGCCGGGGATGAAGC	0.692													G|||	179	0.0357428	0.0038	0.0389	5008	,	,		12769	0.1042		0.0358	False		,,,				2504	0.0061				p.P278P		Atlas-SNP	.											NPEPL1,NS,carcinoma,0,1	NPEPL1	36	1	0			c.G834A						scavenged	.	G	,,	27,3877		0,27,1925	11.0	15.0	13.0		750,690,834	-8.9	0.1	20	dbSNP_127	13	240,7886		2,236,3825	no	coding-synonymous,coding-synonymous,coding-synonymous	NPEPL1	NM_001204872.1,NM_001204873.1,NM_024663.3	,,	2,263,5750	AA,AG,GG		2.9535,0.6916,2.2195	,,	250/496,230/476,278/524	57282190	267,11763	1952	4063	6015	SO:0001819	synonymous_variant	79716	exon7			CATGCCGGGGATG	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.834G>A	20.37:g.57282190G>A		Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	182	85	0.467033	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																			G|0.947;A|0.053	0.053	strong		0.692	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
ZCCHC2	54877	hgsc.bcm.edu	37	18	60231851	60231851	+	Silent	SNP	A	A	G	rs12956093	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:60231851A>G	ENST00000269499.5	+	10	2152	c.1734A>G	c.(1732-1734)ggA>ggG	p.G578G	ZCCHC2_ENST00000586834.1_Silent_p.G257G	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	578						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						AGAAGAAAGGAAAGCCACAAA	0.308													A|||	414	0.0826677	0.0068	0.1816	5008	,	,		16285	0.001		0.2386	False		,,,				2504	0.0389				p.G578G		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.A1734G						PASS	.	A		138,3382		3,132,1625	50.0	42.0	44.0		1734	3.6	1.0	18	dbSNP_121	44	1460,6500		123,1214,2643	no	coding-synonymous	ZCCHC2	NM_017742.4		126,1346,4268	GG,GA,AA		18.3417,3.9205,13.9199		578/1179	60231851	1598,9882	1760	3980	5740	SO:0001819	synonymous_variant	54877	exon10			GAAAGGAAAGCCA	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.1734A>G	18.37:g.60231851A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	162	87	0.537037	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Silent	SNP	ENST00000269499.5	37	CCDS45880.1																																																																																			A|0.878;G|0.122	0.122	strong		0.308	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742	
ITIH2	3698	hgsc.bcm.edu	37	10	7759736	7759736	+	Silent	SNP	G	G	A	rs370987991		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:7759736G>A	ENST00000358415.4	+	6	781	c.615G>A	c.(613-615)ctG>ctA	p.L205L	ITIH2_ENST00000480387.1_3'UTR|ITIH2_ENST00000379587.4_Silent_p.L194L	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	205					hyaluronan metabolic process (GO:0030212)|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)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CTGGACGGCTGGCCAAACACT	0.507																																					p.L205L		Atlas-SNP	.											.	ITIH2	144	.	0			c.G615A						PASS	.	G		0,4406		0,0,2203	129.0	125.0	126.0		615	3.3	1.0	10		126	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ITIH2	NM_002216.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		205/947	7759736	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	3698	exon6			ACGGCTGGCCAAA	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.615G>A	10.37:g.7759736G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	122	86	0.704918	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																			.	.	none		0.507	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
ZCCHC11	23318	hgsc.bcm.edu	37	1	52956410	52956410	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:52956410C>T	ENST00000371544.3	-	8	1644	c.1382G>A	c.(1381-1383)cGa>cAa	p.R461Q	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.R461Q|ZCCHC11_ENST00000371541.1_5'UTR	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	461					cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						CAACCTTTTTCGATCTCTGCA	0.294																																					p.R461Q		Atlas-SNP	.											ZCCHC11,NS,carcinoma,0,2	ZCCHC11	151	2	0			c.G1382A						scavenged	.						56.0	57.0	57.0					1																	52956410		2202	4299	6501	SO:0001583	missense	23318	exon8			CTTTTTCGATCTC	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"""Zinc fingers, CCHC domain containing"""	28981	protein-coding gene	gene with protein product	"""TUTase4"""	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.1382G>A	1.37:g.52956410C>T	ENSP00000360599:p.Arg461Gln	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	156	3	0.0192308	NM_015269	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	37	CCDS30716.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.318548	0.40996	.	.	ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000528642;ENST00000484723	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	6.08	2.99	0.34606	.	0.689968	0.13204	N	0.405736	T	0.12092	0.0294	N	0.05487	-0.04	0.80722	D	1	P;B;P	0.45348	0.777;0.414;0.856	B;B;B	0.33254	0.072;0.068;0.16	T	0.07673	-1.0760	10	0.12430	T	0.62	.	4.0377	0.09737	0.2156:0.4506:0.0:0.3338	.	220;461;461	E9PKX1;Q5TAX3-2;Q5TAX3	.;.;TUT4_HUMAN	Q	461;461;461;220	ENSP00000257177:R461Q;ENSP00000360599:R461Q;ENSP00000433486:R461Q;ENSP00000435256:R220Q	ENSP00000257177:R461Q	R	-	2	0	ZCCHC11	52728998	0.951000	0.32395	1.000000	0.80357	0.991000	0.79684	0.396000	0.20867	0.907000	0.36646	0.655000	0.94253	CGA	.	.	none		0.294	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288	
ASTN1	460	hgsc.bcm.edu	37	1	176992553	176992553	+	Silent	SNP	A	A	G	rs172917	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:176992553A>G	ENST00000367654.3	-	7	1636	c.1425T>C	c.(1423-1425)tgT>tgC	p.C475C	ASTN1_ENST00000367657.3_Silent_p.C475C|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000361833.2_Silent_p.C475C|ASTN1_ENST00000424564.2_Silent_p.C475C	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	475	EGF-like 1.				locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TTTCGGGGTCACATTGGTGTT	0.597													G|||	2575	0.514177	0.792	0.4957	5008	,	,		16580	0.2054		0.5895	False		,,,				2504	0.3926				p.C475C		Atlas-SNP	.											.	ASTN1	314	.	0			c.T1425C						PASS	.	G	,	3227,1177		1181,865,156	25.0	24.0	24.0		1425,1425	-2.7	1.0	1	dbSNP_79	24	5122,3478		1535,2052,713	no	coding-synonymous,coding-synonymous	ASTN1	NM_004319.1,NM_207108.1	,	2716,2917,869	GG,GA,AA		40.4419,26.7257,35.7967	,	475/1295,475/1217	176992553	8349,4655	2202	4300	6502	SO:0001819	synonymous_variant	460	exon7			GGGGTCACATTGG	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1425T>C	1.37:g.176992553A>G		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	280	278	0.992857	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																				A|0.423;G|0.577	0.577	strong		0.597	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156027	39156027	+	Missense_Mutation	SNP	G	G	A	rs3829598	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39156027G>A	ENST00000391587.1	-	1	111	c.79C>T	c.(79-81)Cgc>Tgc	p.R27C		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	27	3 X 5 AA repeats of C-C-X(3).		R -> C (in dbSNP:rs3829598).			keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				ACTCCACAGCGGCAGGATTTG	0.612													.|||	872	0.174121	0.0265	0.2709	5008	,	,		18323	0.2629		0.169	False		,,,				2504	0.2188				p.R27C		Atlas-SNP	.											.	KRTAP3-2	11	.	0			c.C79T						PASS	.	G	CYS/ARG	191,4215	120.4+/-158.0	6,179,2018	71.0	81.0	78.0		79	2.6	1.0	17	dbSNP_107	78	1495,7097	281.3+/-295.0	129,1237,2930	no	missense	KRTAP3-2	NM_031959.2	180	135,1416,4948	AA,AG,GG		17.3999,4.335,12.9712	probably-damaging	27/99	39156027	1686,11312	2203	4296	6499	SO:0001583	missense	83897	exon1			CACAGCGGCAGGA	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"""Keratin associated proteins"""	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.79C>T	17.37:g.39156027G>A	ENSP00000375429:p.Arg27Cys	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	245	136	0.555102	NM_031959		Missense_Mutation	SNP	ENST00000391587.1	37	CCDS32644.1	372	0.17032967032967034	13	0.026422764227642278	91	0.2513812154696133	140	0.24475524475524477	128	0.16886543535620052	G	15.53	2.862235	0.51482	0.04335	0.173999	ENSG00000212900	ENST00000391587	T	0.33865	1.39	5.76	2.56	0.30785	.	0.000000	0.51477	D	0.000100	T	0.00039	0.0001	.	.	.	0.22199	P	0.99929956	D	0.89917	1.0	D	0.87578	0.998	T	0.04307	-1.0961	8	0.87932	D	0	.	11.8174	0.52218	0.0:0.0:0.5368:0.4632	rs3829598	27	Q9BYR7	KRA32_HUMAN	C	27	ENSP00000375429:R27C	ENSP00000375429:R27C	R	-	1	0	KRTAP3-2	36409553	1.000000	0.71417	0.959000	0.39883	0.472000	0.32918	2.055000	0.41345	0.312000	0.23038	-0.318000	0.08688	CGC	G|0.865;A|0.135	0.135	strong		0.612	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1		
DDX54	79039	hgsc.bcm.edu	37	12	113600940	113600940	+	Missense_Mutation	SNP	C	C	T	rs11564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113600940C>T	ENST00000306014.5	-	16	2105	c.2078G>A	c.(2077-2079)cGg>cAg	p.R693Q	DDX54_ENST00000314045.7_Missense_Mutation_p.R693Q|DDX54_ENST00000549271.1_5'Flank	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	693			R -> Q (in dbSNP:rs11564).		ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CACTCACCCCCGCTCGCTGTC	0.637													C|||	155	0.0309505	0.025	0.0447	5008	,	,		15348	0.0		0.0805	False		,,,				2504	0.0102				p.R693Q		Atlas-SNP	.											.	DDX54	73	.	0			c.G2078A						PASS	.	C	GLN/ARG,GLN/ARG	115,4291	85.8+/-124.5	1,113,2089	47.0	54.0	52.0		2078,2078	4.2	1.0	12	dbSNP_52	52	501,8099	142.3+/-198.5	14,473,3813	yes	missense,missense	DDX54	NM_001111322.1,NM_024072.3	43,43	15,586,5902	TT,TC,CC		5.8256,2.6101,4.7363	possibly-damaging,possibly-damaging	693/883,693/882	113600940	616,12390	2203	4300	6503	SO:0001583	missense	79039	exon16			CACCCCCGCTCGC	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"""DEAD-boxes"""	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.2078G>A	12.37:g.113600940C>T	ENSP00000304072:p.Arg693Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_024072	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	86	0.039377289377289376	8	0.016260162601626018	16	0.04419889502762431	0	0.0	62	0.08179419525065963	C	17.30	3.355570	0.61293	0.026101	0.058256	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.11277	2.79;2.8	5.1	4.21	0.49690	.	0.112829	0.56097	D	0.000030	T	0.00666	0.0022	M	0.73598	2.24	0.19575	P	0.9999672619	B;B	0.25486	0.127;0.078	B;B	0.18561	0.022;0.01	T	0.10359	-1.0633	9	0.21014	T	0.42	.	13.0042	0.58694	0.0:0.9213:0.0:0.0787	rs11564;rs1130231;rs3188910;rs17296035;rs17354493;rs34797478	693;693	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	Q	693	ENSP00000323858:R693Q;ENSP00000304072:R693Q	ENSP00000304072:R693Q	R	-	2	0	DDX54	112085323	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.529000	0.60588	1.146000	0.42352	0.643000	0.83706	CGG	C|0.954;T|0.046	0.046	strong		0.637	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072	
SERPINF1	5176	hgsc.bcm.edu	37	17	1674429	1674429	+	Silent	SNP	T	T	C	rs8074840	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:1674429T>C	ENST00000254722.4	+	4	553	c.390T>C	c.(388-390)acT>acC	p.T130T	SERPINF1_ENST00000571870.1_3'UTR	NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	130					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						ACACGGTCACTGCCCCCCAGA	0.547													T|||	1504	0.300319	0.1203	0.3631	5008	,	,		15428	0.4067		0.3101	False		,,,				2504	0.3793				p.T130T		Atlas-SNP	.											SERPINF1,NS,carcinoma,0,1	SERPINF1	31	1	0			c.T390C						scavenged	.	T		695,3711	291.8+/-281.7	57,581,1565	76.0	67.0	70.0		390	-8.1	0.5	17	dbSNP_116	70	2530,6070	413.2+/-351.0	357,1816,2127	no	coding-synonymous	SERPINF1	NM_002615.5		414,2397,3692	CC,CT,TT		29.4186,15.7739,24.7962		130/419	1674429	3225,9781	2203	4300	6503	SO:0001819	synonymous_variant	5176	exon4			GGTCACTGCCCCC	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"""Serine (or cysteine) peptidase inhibitors"""	8824	protein-coding gene	gene with protein product	"""pigment epithelium-derived factor"", ""proliferation-inducing protein 35"""	172860	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"""	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.390T>C	17.37:g.1674429T>C		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Silent	SNP	ENST00000254722.4	37	CCDS11012.1																																																																																			T|0.735;C|0.265	0.265	strong		0.547	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615	
KMT2C	58508	hgsc.bcm.edu	37	7	151970797	151970797	+	Silent	SNP	A	A	T	rs141993954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	909	2	0.00220022		WXS	Illumina HiSeq	Phase_I	827	120	0.145103	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		
PTCHD3	374308	hgsc.bcm.edu	37	10	27702169	27702169	+	Silent	SNP	C	C	T	rs6482625	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:27702169C>T	ENST00000438700.3	-	1	1128	c.1011G>A	c.(1009-1011)gtG>gtA	p.V337V		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	337					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						GCTTGCTCTGCACGTCGTACT	0.522													C|||	993	0.198283	0.3805	0.2839	5008	,	,		19255	0.0129		0.2137	False		,,,				2504	0.0665				p.V337V		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G1011A						PASS	.	C		1589,2817	495.1+/-363.2	282,1025,896	132.0	135.0	134.0		1011	-0.2	0.0	10	dbSNP_116	134	1947,6653	341.6+/-324.1	234,1479,2587	no	coding-synonymous	PTCHD3	NM_001034842.3		516,2504,3483	TT,TC,CC		22.6395,36.0645,27.1875		337/768	27702169	3536,9470	2203	4300	6503	SO:0001819	synonymous_variant	374308	exon1			GCTCTGCACGTCG	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.1011G>A	10.37:g.27702169C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	81	18	0.222222	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			C|0.765;T|0.235	0.235	strong		0.522	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
OR1C1	26188	hgsc.bcm.edu	37	1	247921412	247921412	+	Silent	SNP	G	G	C	rs41304163	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247921412G>C	ENST00000408896.2	-	1	570	c.297C>G	c.(295-297)acC>acG	p.T99T		NM_012353.2	NP_036485.2	Q15619	OR1C1_HUMAN	olfactory receptor, family 1, subfamily C, member 1	99					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(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(32)|skin(2)|upper_aerodigestive_tract(1)	46	all_cancers(71;4.34e-05)|all_epithelial(71;1.13e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0786)|Lung NSC(105;0.0858)	all_cancers(173;0.0247)	OV - Ovarian serous cystadenocarcinoma(106;0.0168)			AGAAGAGCTGGGTGAGGCAGC	0.463													g|||	155	0.0309505	0.0197	0.0533	5008	,	,		21292	0.001		0.0626	False		,,,				2504	0.0286				p.T99T		Atlas-SNP	.											.	OR1C1	86	.	0			c.C297G						PASS	.			91,3817		1,89,1864	55.0	52.0	53.0		297	-6.4	0.0	1	dbSNP_127	53	510,7782		18,474,3654	no	coding-synonymous	OR1C1	NM_012353.2		19,563,5518	CC,CG,GG		6.1505,2.3286,4.9262		99/315	247921412	601,11599	1954	4146	6100	SO:0001819	synonymous_variant	26188	exon1			GAGCTGGGTGAGG	X89674	CCDS41481.1	1q44	2012-08-09			ENSG00000221888	ENSG00000221888		"""GPCR / Class A : Olfactory receptors"""	8182	protein-coding gene	gene with protein product						9119360	Standard	NM_012353		Approved	TPCR27, HSTPCR27	uc010pza.2	Q15619	OTTHUMG00000040198	ENST00000408896.2:c.297C>G	1.37:g.247921412G>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	158	94	0.594937	NM_012353	B9EIR9|Q5VVD2|Q6IF97|Q8NGZ1|Q96R83	Silent	SNP	ENST00000408896.2	37	CCDS41481.1																																																																																			G|0.952;C|0.048	0.048	strong		0.463	OR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096855.1		
RNF121	55298	hgsc.bcm.edu	37	11	71701763	71701763	+	Splice_Site	SNP	G	G	A	rs35844388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:71701763G>A	ENST00000361756.3	+	6	988	c.627G>A	c.(625-627)ggG>ggA	p.G209G	RNF121_ENST00000530137.1_Splice_Site_p.G177G|RNF121_ENST00000545854.1_Splice_Site_p.G128G|RNF121_ENST00000490867.1_3'UTR|RNF121_ENST00000393713.3_Splice_Site_p.G177G|RNF121_ENST00000533380.1_Intron	NM_018320.4	NP_060790.2	Q9H920	RN121_HUMAN	ring finger protein 121	209						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|urinary_tract(1)	13						CTACCATAGGGGTAAGTTCAT	0.448													G|||	202	0.0403355	0.0068	0.0403	5008	,	,		21247	0.0833		0.0358	False		,,,				2504	0.046				p.G209G		Atlas-SNP	.											.	RNF121	19	.	0			c.G627A						PASS	.	G		35,4365	39.2+/-71.8	0,35,2165	172.0	179.0	176.0		627	4.2	1.0	11	dbSNP_126	176	237,8349	95.9+/-157.7	4,229,4060	yes	coding-synonymous-near-splice	RNF121	NM_018320.4		4,264,6225	AA,AG,GG		2.7603,0.7955,2.0946		209/328	71701763	272,12714	2200	4293	6493	SO:0001630	splice_region_variant	55298	exon6			CATAGGGGTAAGT	AK001961	CCDS8203.1, CCDS73343.1	11q13.3	2008-02-05			ENSG00000137522	ENSG00000137522		"""RING-type (C3HC4) zinc fingers"""	21070	protein-coding gene	gene with protein product							Standard	NM_018320		Approved	FLJ11099	uc001ora.3	Q9H920	OTTHUMG00000157023	ENST00000361756.3:c.627+1G>A	11.37:g.71701763G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_018320	B3KSW8|Q6IA57|Q6P449|Q96DB4	Silent	SNP	ENST00000361756.3	37	CCDS8203.1																																																																																			G|0.972;A|0.028	0.028	strong		0.448	RNF121-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347132.1	NM_018320	Silent
MLC1	23209	hgsc.bcm.edu	37	22	50502469	50502469	+	Silent	SNP	A	A	G	rs11568189|rs11568190	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50502469A>G	ENST00000311597.5	-	11	1659	c.1053T>C	c.(1051-1053)gcT>gcC	p.A351A	MLC1_ENST00000538737.1_Silent_p.A317A|MLC1_ENST00000395876.2_Silent_p.A351A|MLC1_ENST00000535444.1_Silent_p.A272A|MLC1_ENST00000431262.2_Silent_p.A321A|MLC1_ENST00000450140.2_Silent_p.A299A|MLC1_ENST00000483836.1_5'UTR	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	166	0	0		WXS	Illumina HiSeq	Phase_I	91	12	0.131868	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	
CCDC101	112869	hgsc.bcm.edu	37	16	28602991	28602991	+	Silent	SNP	A	A	G	rs11401	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:28602991A>G	ENST00000317058.3	+	10	1033	c.846A>G	c.(844-846)agA>agG	p.R282R		NM_138414.2	NP_612423.1	Q96ES7	SGF29_HUMAN	coiled-coil domain containing 101	282	SGF29 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00851}.				chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|histone H3 acetylation (GO:0043966)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|SAGA-type complex (GO:0070461)	methylated histone binding (GO:0035064)			central_nervous_system(2)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)	10						TGGCTCAGAGATACGTGGTGG	0.582													.|||	872	0.174121	0.1619	0.2017	5008	,	,		19643	0.2212		0.1571	False		,,,				2504	0.1401				p.R282R		Atlas-SNP	.											.	CCDC101	24	.	0			c.A846G						PASS	.	G		746,3648		59,628,1510	131.0	115.0	121.0		846	2.8	1.0	16	dbSNP_52	121	1497,7103		126,1245,2929	no	coding-synonymous	CCDC101	NM_138414.2		185,1873,4439	GG,GA,AA		17.407,16.9777,17.2618		282/294	28602991	2243,10751	2197	4300	6497	SO:0001819	synonymous_variant	112869	exon10			TCAGAGATACGTG	AK057008	CCDS10635.1	16p11.2	2010-08-03			ENSG00000176476	ENSG00000176476			25156	protein-coding gene	gene with protein product	"""SAGA-associated factor 29 homolog (yeast)"""	613374				17334388	Standard	NM_138414		Approved	FLJ32446, SGF29	uc002dqf.3	Q96ES7	OTTHUMG00000131763	ENST00000317058.3:c.846A>G	16.37:g.28602991A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_138414	Q96MF5	Silent	SNP	ENST00000317058.3	37	CCDS10635.1																																																																																			A|0.832;G|0.168	0.168	strong		0.582	CCDC101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254691.1	NM_138414	
CDC42BPB	9578	hgsc.bcm.edu	37	14	103440473	103440473	+	Silent	SNP	G	G	C	rs8009219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:103440473G>C	ENST00000361246.2	-	12	1809	c.1521C>G	c.(1519-1521)ctC>ctG	p.L507L		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		GCTGTCGCTCGAGCCTGTTTG	0.517													G|||	2959	0.590855	0.4138	0.6758	5008	,	,		19823	0.5764		0.659	False		,,,				2504	0.7147				p.L507L		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.C1521G						PASS	.	G		2049,2357	567.3+/-382.1	495,1059,649	46.0	47.0	47.0		1521	-10.8	0.0	14	dbSNP_116	47	5602,2998	665.3+/-402.3	1855,1892,553	no	coding-synonymous	CDC42BPB	NM_006035.3		2350,2951,1202	CC,CG,GG		34.8605,46.5048,41.1733		507/1712	103440473	7651,5355	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon12			TCGCTCGAGCCTG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.1521C>G	14.37:g.103440473G>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	99	28	0.282828	NM_006035		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			G|0.410;C|0.589	0.589	strong		0.517	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
MUC5B	727897	hgsc.bcm.edu	37	11	1264772	1264772	+	Missense_Mutation	SNP	T	T	C	rs2943500		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1264772T>C	ENST00000529681.1	+	31	6720	c.6662T>C	c.(6661-6663)aTc>aCc	p.I2221T	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.I2224T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2221	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)		p.I2224T(1)		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)		ACCTCGGGCATCTTGGGCACC	0.662																																					p.I2221T		Atlas-SNP	.											MUC5B,NS,neuroblastoma,0,3	MUC5B	473	3	1	Substitution - Missense(1)	skin(1)	c.T6662C						scavenged	.						94.0	111.0	105.0					11																	1264772		2080	4181	6261	SO:0001583	missense	727897	exon31			CGGGCATCTTGGG	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.6662T>C	11.37:g.1264772T>C	ENSP00000436812:p.Ile2221Thr	Somatic	391	1	0.00255754		WXS	Illumina HiSeq	Phase_I	375	15	0.04	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	5.754	0.323450	0.10900	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21191	2.02;2.21	2.39	1.4	0.22301	.	.	.	.	.	T	0.06325	0.0163	N	0.00729	-1.24	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34204	-0.9838	9	0.87932	D	0	.	6.6171	0.22782	0.0:0.7019:0.1804:0.1177	rs2943500	2859;2224	A7Y9J9;E9PBJ0	.;.	T	2221;2224;2222;2236	ENSP00000436812:I2221T;ENSP00000415793:I2224T	ENSP00000343037:I2222T	I	+	2	0	MUC5B	1221348	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.044000	0.13992	-0.095000	0.12351	-0.684000	0.03749	ATC	.	.	weak		0.662	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
OR4L1	122742	hgsc.bcm.edu	37	14	20528496	20528496	+	Missense_Mutation	SNP	T	T	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20528496T>A	ENST00000315683.1	+	1	293	c.293T>A	c.(292-294)gTg>gAg	p.V98E		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	98						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)		TGGGGCTGCGTGACCCAGATG	0.473																																					p.V98E		Atlas-SNP	.											OR4L1,NS,carcinoma,+1,1	OR4L1	98	1	0			c.T293A						scavenged	.						152.0	138.0	143.0					14																	20528496		2203	4300	6503	SO:0001583	missense	122742	exon1			GCTGCGTGACCCA		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.293T>A	14.37:g.20528496T>A	ENSP00000319217:p.Val98Glu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	190	2	0.0105263	NM_001004717	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	.	.	.	.	.	.	.	.	.	.	.	14.00	2.405594	0.42715	.	.	ENSG00000176246	ENST00000315683	T	0.02085	4.46	3.97	2.81	0.32909	GPCR, rhodopsin-like superfamily (1);	0.235104	0.34156	N	0.004208	T	0.02807	0.0084	L	0.48877	1.53	0.25432	N	0.988179	B	0.20780	0.048	B	0.23716	0.048	T	0.35400	-0.9790	10	0.87932	D	0	.	7.7235	0.28746	0.0:0.1044:0.0:0.8956	.	98	Q8NH43	OR4L1_HUMAN	E	98	ENSP00000319217:V98E	ENSP00000319217:V98E	V	+	2	0	OR4L1	19598336	0.048000	0.20356	0.990000	0.47175	0.879000	0.50718	1.746000	0.38288	0.681000	0.31386	0.524000	0.50904	GTG	.	.	none		0.473	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
QSOX2	169714	hgsc.bcm.edu	37	9	139115921	139115921	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139115921C>T	ENST00000358701.5	-	4	553	c.516G>A	c.(514-516)atG>atA	p.M172I		NM_181701.3	NP_859052.3	Q6ZRP7	QSOX2_HUMAN	quiescin Q6 sulfhydryl oxidase 2	172	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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)	p.M172I(1)		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)		GGAAGTCAATCATCGTCTGTC	0.617																																					p.M172I		Atlas-SNP	.											QSOX2,NS,carcinoma,0,1	QSOX2	63	1	1	Substitution - Missense(1)	lung(1)	c.G516A						scavenged	.						124.0	109.0	114.0					9																	139115921		2203	4300	6503	SO:0001583	missense	169714	exon4			GTCAATCATCGTC	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.516G>A	9.37:g.139115921C>T	ENSP00000351536:p.Met172Ile	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	167	4	0.0239521	NM_181701	A2CEE0|A6NLB0|Q5TB37|Q7Z7B6|Q86VV7|Q8N3G2	Missense_Mutation	SNP	ENST00000358701.5	37	CCDS35178.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.85|11.85	1.761210|1.761210	0.31137|0.31137	.|.	.|.	ENSG00000165661|ENSG00000165661	ENST00000455222|ENST00000358701;ENST00000389471	.|T	.|0.67698	.|-0.28	5.18|5.18	5.18|5.18	0.71444|0.71444	.|Thioredoxin-like fold (2);	.|0.043794	.|0.85682	.|D	.|0.000000	T|T	0.58566|0.58566	0.2131|0.2131	N|N	0.20357|0.20357	0.565|0.565	0.54753|0.54753	D|D	0.999989|0.999989	.|P	.|0.42375	.|0.778	.|P	.|0.49332	.|0.607	T|T	0.53301|0.53301	-0.8458|-0.8458	5|10	.|0.16420	.|T	.|0.52	-45.1021|-45.1021	12.7405|12.7405	0.57251|0.57251	0.1642:0.8358:0.0:0.0|0.1642:0.8358:0.0:0.0	.|.	.|172	.|Q6ZRP7	.|QSOX2_HUMAN	N|I	19|172;50	.|ENSP00000351536:M172I	.|ENSP00000351536:M172I	D|M	-|-	1|3	0|0	QSOX2|QSOX2	138255742|138255742	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.511000|0.511000	0.34104|0.34104	4.957000|4.957000	0.63652|0.63652	2.419000|2.419000	0.82065|0.82065	0.467000|0.467000	0.42956|0.42956	GAT|ATG	.	.	none		0.617	QSOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055046.2	NM_181701	
FBN3	84467	hgsc.bcm.edu	37	19	8168545	8168545	+	Missense_Mutation	SNP	C	C	T	rs33967815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:8168545C>T	ENST00000600128.1	-	39	5254	c.4840G>A	c.(4840-4842)Ggc>Agc	p.G1614S	FBN3_ENST00000270509.2_Missense_Mutation_p.G1614S|FBN3_ENST00000601739.1_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	221	0	0		WXS	Illumina HiSeq	Phase_I	199	109	0.547739	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	
TNIP1	10318	hgsc.bcm.edu	37	5	150410219	150410219	+	3'UTR	SNP	C	C	A	rs2233311	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:150410219C>A	ENST00000389378.2	-	0	2554				TNIP1_ENST00000521423.1_5'Flank|TNIP1_ENST00000520931.1_3'UTR|TNIP1_ENST00000521591.1_3'UTR|TNIP1_ENST00000522226.1_3'UTR|TNIP1_ENST00000524280.1_3'UTR|TNIP1_ENST00000523338.1_Missense_Mutation_p.R631I|TNIP1_ENST00000315050.7_3'UTR|TNIP1_ENST00000518977.1_Missense_Mutation_p.R631I	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1						defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTTGGCAATCTGAGATCAGC	0.517													C|||	535	0.106829	0.0673	0.0634	5008	,	,		18524	0.1726		0.0944	False		,,,				2504	0.136				p.R631I		Atlas-SNP	.											.	TNIP1	51	.	0			c.G1892T						PASS	.	C		95,1289		3,89,600	68.0	63.0	65.0			4.8	1.0	5	dbSNP_98	65	372,2810		24,324,1243	no	utr-3	TNIP1	NM_006058.3		27,413,1843	AA,AC,CC		11.6908,6.8642,10.2278			150410219	467,4099	692	1591	2283	SO:0001624	3_prime_UTR_variant	10318	exon18			GGCAATCTGAGAT	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.*55G>T	5.37:g.150410219C>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_001252393	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	37	CCDS34280.1	236	0.10805860805860806	51	0.10365853658536585	22	0.06077348066298342	87	0.1520979020979021	76	0.10026385224274406	C	12.73	2.025598	0.35701	0.068642	0.116908	ENSG00000145901	ENST00000523338;ENST00000518977	T;T	0.11821	2.74;2.74	5.62	4.75	0.60458	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999980101	P;P	0.35628	0.513;0.513	B;B	0.36989	0.238;0.181	T	0.20739	-1.0266	7	0.49607	T	0.09	.	12.5228	0.56069	0.0:0.8324:0.1676:0.0	rs2233311;rs60477588;rs2233311	521;631	A4F1X7;A4F1W9	.;.	I	631	ENSP00000428243:R631I;ENSP00000430971:R631I	ENSP00000430971:R631I	R	-	2	0	TNIP1	150390412	0.996000	0.38824	0.959000	0.39883	0.222000	0.24845	3.585000	0.53943	1.353000	0.45828	0.448000	0.29417	AGA	G|0.000;C|0.890;A|0.109	0.109	strong		0.517	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
ADSSL1	122622	hgsc.bcm.edu	37	14	105211221	105211221	+	Silent	SNP	C	C	T	rs12432802	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105211221C>T	ENST00000330877.2	+	11	1231	c.1146C>T	c.(1144-1146)aaC>aaT	p.N382N	ADSSL1_ENST00000556623.1_5'Flank|ADSSL1_ENST00000554657.1_3'UTR|ADSSL1_ENST00000555674.1_5'Flank|ADSSL1_ENST00000332972.5_Silent_p.N425N	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)		ACAAGCTGAACGGGAAAAGGA	0.532													C|||	1020	0.203674	0.0658	0.2046	5008	,	,		20645	0.5228		0.0656	False		,,,				2504	0.2025				p.N425N		Atlas-SNP	.											.	ADSSL1	37	.	0			c.C1275T						PASS	.	C	,	261,4145	149.2+/-183.4	8,245,1950	84.0	78.0	80.0		1146,1275	-1.4	0.8	14	dbSNP_120	80	559,8041	152.2+/-206.8	16,527,3757	no	coding-synonymous,coding-synonymous	ADSSL1	NM_152328.3,NM_199165.1	,	24,772,5707	TT,TC,CC		6.5,5.9237,6.3048	,	382/458,425/501	105211221	820,12186	2203	4300	6503	SO:0001819	synonymous_variant	122622	exon11			GCTGAACGGGAAA	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.1146C>T	14.37:g.105211221C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	167	43	0.257485	NM_199165		Silent	SNP	ENST00000330877.2	37	CCDS9990.1																																																																																			C|0.882;T|0.118	0.118	strong		0.532	ADSSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410529.1		
C14orf79	122616	hgsc.bcm.edu	37	14	105457923	105457923	+	Missense_Mutation	SNP	T	T	A	rs61745867	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105457923T>A	ENST00000547315.1	+	3	1304	c.665T>A	c.(664-666)tTc>tAc	p.F222Y	C14orf79_ENST00000549240.1_5'UTR|C14orf79_ENST00000549584.1_3'UTR|C14orf79_ENST00000550614.1_5'UTR	NM_174891.3	NP_777551.2	Q96F83	CN079_HUMAN	chromosome 14 open reading frame 79	222										breast(1)|endometrium(1)|lung(1)	3		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00326)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0181)			CAGGAGAACTTCTTTCTTGTT	0.542													T|||	24	0.00479233	0.0015	0.0072	5008	,	,		18114	0.0		0.0099	False		,,,				2504	0.0072				p.F222Y		Atlas-SNP	.											.	C14orf79	13	.	0			c.T665A						PASS	.	T	TYR/PHE	9,3843		0,9,1917	132.0	123.0	126.0		665	2.4	0.0	14	dbSNP_129	126	169,8123		4,161,3981	yes	missense	C14orf79	NM_174891.3	22	4,170,5898	AA,AT,TT		2.0381,0.2336,1.4657	benign	222/326	105457923	178,11966	1926	4146	6072	SO:0001583	missense	122616	exon3			AGAACTTCTTTCT		CCDS42000.1	14q32.33	2012-09-25			ENSG00000140104	ENSG00000140104			20126	protein-coding gene	gene with protein product							Standard	NM_174891		Approved		uc001ypy.1	Q96F83	OTTHUMG00000170474	ENST00000547315.1:c.665T>A	14.37:g.105457923T>A	ENSP00000450114:p.Phe222Tyr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	159	69	0.433962	NM_174891	B2RPK9|Q9BTP4	Missense_Mutation	SNP	ENST00000547315.1	37	CCDS42000.1	11|11	0.005036630036630037|0.005036630036630037	1|1	0.0020325203252032522|0.0020325203252032522	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	T|T	3.056|3.056	-0.194267|-0.194267	0.06259|0.06259	0.002336|0.002336	0.020381|0.020381	ENSG00000140104|ENSG00000140104	ENST00000547315|ENST00000551606	.|.	.|.	.|.	3.62|3.62	2.43|2.43	0.29744|0.29744	.|.	1.254200|.	0.06177|.	N|.	0.678664|.	T|T	0.21103|0.21103	0.0508|0.0508	N|N	0.19112|0.19112	0.55|0.55	0.39067|0.39067	D|D	0.960632|0.960632	B|.	0.14805|.	0.011|.	B|.	0.08055|.	0.003|.	T|T	0.05241|0.05241	-1.0897|-1.0897	9|5	0.29301|.	T|.	0.29|.	-3.7825|-3.7825	6.0924|6.0924	0.20001|0.20001	0.2279:0.0:0.0:0.7721|0.2279:0.0:0.0:0.7721	rs61745867|rs61745867	222|.	Q96F83|.	CN079_HUMAN|.	Y|T	222|116	.|.	ENSP00000450114:F222Y|.	F|S	+|+	2|1	0|0	C14orf79|C14orf79	104528968|104528968	0.021000|0.021000	0.18746|0.18746	0.010000|0.010000	0.14722|0.14722	0.012000|0.012000	0.07955|0.07955	2.128000|2.128000	0.42045|0.42045	0.298000|0.298000	0.22638|0.22638	0.378000|0.378000	0.23410|0.23410	TTC|TCT	T|0.990;A|0.010	0.010	strong		0.542	C14orf79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409318.1	NM_174891	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562836	6562836	+	Silent	SNP	G	G	A	rs2041388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6562836G>A	ENST00000266556.7	+	3	684	c.519G>A	c.(517-519)ccG>ccA	p.P173P	TAPBPL_ENST00000544021.1_Silent_p.P96P|CD27-AS1_ENST00000545339.1_RNA|CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	173					negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						TCTGGCACCCGACGCTGAACT	0.567													G|||	1016	0.202875	0.0136	0.1599	5008	,	,		18787	0.3224		0.2932	False		,,,				2504	0.273				p.P173P		Atlas-SNP	.											.	TAPBPL	21	.	0			c.G519A						PASS	.	G		249,4157	142.7+/-177.9	8,233,1962	31.0	30.0	31.0		519	-0.2	0.0	12	dbSNP_94	31	2499,6101	401.6+/-347.2	364,1771,2165	no	coding-synonymous	TAPBPL	NM_018009.4		372,2004,4127	AA,AG,GG		29.0581,5.6514,21.1287		173/469	6562836	2748,10258	2203	4300	6503	SO:0001819	synonymous_variant	55080	exon3			GCACCCGACGCTG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.519G>A	12.37:g.6562836G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_018009	Q9NWB8	Silent	SNP	ENST00000266556.7	37	CCDS8546.1																																																																																			G|0.800;A|0.200	0.200	strong		0.567	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
BTBD11	121551	hgsc.bcm.edu	37	12	107712880	107712880	+	Silent	SNP	C	C	T	rs10082935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:107712880C>T	ENST00000280758.5	+	1	691	c.163C>T	c.(163-165)Cta>Tta	p.L55L	BTBD11_ENST00000490090.2_Silent_p.L55L|BTBD11_ENST00000420571.2_Silent_p.L55L	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	55						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						CTGGCCGCCTCTAGCTGACTC	0.647													C|||	493	0.0984425	0.0484	0.1758	5008	,	,		12283	0.0		0.1799	False		,,,				2504	0.1288				p.L55L		Atlas-SNP	.											.	BTBD11	122	.	0			c.C163T						PASS	.	C		316,4090		9,298,1896	29.0	30.0	30.0		163	4.0	1.0	12	dbSNP_119	30	1585,7009		143,1299,2855	no	coding-synonymous	BTBD11	NM_001018072.1		152,1597,4751	TT,TC,CC		18.4431,7.172,14.6231		55/1105	107712880	1901,11099	2203	4297	6500	SO:0001819	synonymous_variant	121551	exon1			CCGCCTCTAGCTG	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.163C>T	12.37:g.107712880C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	62	39	0.629032	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			C|0.868;T|0.132	0.132	strong		0.647	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
OR51F1	256892	hgsc.bcm.edu	37	11	4790482	4790482	+	Silent	SNP	T	T	C	rs12792898	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790482T>C	ENST00000380383.1	-	1	686	c.687A>G	c.(685-687)ttA>ttG	p.L229L	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Silent_p.L222L|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	229						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)		AGTGAATAATTAAGATATATG	0.443													T|||	230	0.0459265	0.0061	0.0951	5008	,	,		22294	0.0		0.1412	False		,,,				2504	0.0143				p.L222L		Atlas-SNP	.											OR51F1,NS,carcinoma,-2,1	OR51F1	60	1	0			c.A666G						PASS	.	T		140,4262	98.0+/-136.7	1,138,2062	127.0	125.0	126.0		666	1.1	0.1	11	dbSNP_121	126	1159,7437	238.5+/-269.9	94,971,3233	no	coding-synonymous	OR51F1	NM_001004752.1		95,1109,5295	CC,CT,TT		13.483,3.1804,9.9938		222/313	4790482	1299,11699	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			AATAATTAAGATA	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.687A>G	11.37:g.4790482T>C		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	193	95	0.492228	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				T|0.909;C|0.091	0.091	strong		0.443	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
LRBA	987	hgsc.bcm.edu	37	4	151793903	151793903	+	Missense_Mutation	SNP	T	T	C	rs72719663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:151793903T>C	ENST00000357115.3	-	18	2413	c.2170A>G	c.(2170-2172)Atc>Gtc	p.I724V	LRBA_ENST00000535741.1_Missense_Mutation_p.I724V|LRBA_ENST00000510413.1_Missense_Mutation_p.I724V|LRBA_ENST00000507224.1_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	149	0	0		WXS	Illumina HiSeq	Phase_I	107	22	0.205607	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		
TRIP6	7205	hgsc.bcm.edu	37	7	100465747	100465747	+	Missense_Mutation	SNP	G	G	T	rs139351872	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100465747G>T	ENST00000200457.4	+	3	615	c.255G>T	c.(253-255)agG>agT	p.R85S		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	85					focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTGCAGACAGGGGGGGCCTTC	0.647													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		15814	0.0		0.001	False		,,,				2504	0.0				p.R85S		Atlas-SNP	.											.	TRIP6	45	.	0			c.G255T						PASS	.	G	SER/ARG	2,4404	4.2+/-10.8	0,2,2201	40.0	45.0	43.0		255	-0.6	0.0	7	dbSNP_134	43	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TRIP6	NM_003302.2	110	0,8,6495	TT,TG,GG		0.0698,0.0454,0.0615	probably-damaging	85/477	100465747	8,12998	2203	4300	6503	SO:0001583	missense	7205	exon3			AGACAGGGGGGGC	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.255G>T	7.37:g.100465747G>T	ENSP00000200457:p.Arg85Ser	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	212	71	0.334906	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	7.094	0.572692	0.13623	4.54E-4	6.98E-4	ENSG00000087077	ENST00000200457	T	0.62364	0.03	4.67	-0.581	0.11713	.	0.120807	0.53938	D	0.000055	T	0.51210	0.1661	L	0.47716	1.5	0.23101	N	0.998297	P	0.47762	0.9	P	0.44518	0.452	T	0.49113	-0.8973	10	0.35671	T	0.21	.	7.89	0.29672	0.5076:0.0:0.4924:0.0	.	85	Q15654	TRIP6_HUMAN	S	85	ENSP00000200457:R85S	ENSP00000200457:R85S	R	+	3	2	TRIP6	100303683	0.884000	0.30299	0.018000	0.16275	0.003000	0.03518	0.211000	0.17474	-0.471000	0.06891	-1.022000	0.02435	AGG	C|0.000;G|0.999;T|0.001	0.001	strong		0.647	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
METTL25	84190	hgsc.bcm.edu	37	12	82752559	82752559	+	Missense_Mutation	SNP	T	T	G	rs113882703	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:82752559T>G	ENST00000248306.3	+	1	284	c.215T>G	c.(214-216)cTg>cGg	p.L72R	METTL25_ENST00000547357.1_3'UTR|CCDC59_ENST00000256151.7_5'UTR|CCDC59_ENST00000548126.1_5'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	72							methyltransferase activity (GO:0008168)										ACGGAGGCCCTGCCCTCAGAG	0.657											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	212	0.0423323	0.0182	0.0591	5008	,	,		13342	0.002		0.0805	False		,,,				2504	0.0654				p.L72R		Atlas-SNP	.											.	.	.	.	0			c.T215G						PASS	.	T	ARG/LEU	139,4267	93.0+/-131.7	3,133,2067	42.0	41.0	41.0		215	-5.2	0.0	12	dbSNP_132	41	806,7794	179.0+/-228.3	43,720,3537	yes	missense	C12orf26	NM_032230.2	102	46,853,5604	GG,GT,TT		9.3721,3.1548,7.2659	benign	72/604	82752559	945,12061	2203	4300	6503	SO:0001583	missense	84190	exon1			AGGCCCTGCCCTC	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.215T>G	12.37:g.82752559T>G	ENSP00000248306:p.Leu72Arg	Somatic	293	0	0	1216	WXS	Illumina HiSeq	Phase_I	247	92	0.37247	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	88	0.040293040293040296	11	0.022357723577235773	22	0.06077348066298342	1	0.0017482517482517483	54	0.0712401055408971	T	4.504	0.093403	0.08632	0.031548	0.093721	ENSG00000127720	ENST00000248306;ENST00000548200	T	0.31510	1.49	5.0	-5.17	0.02849	.	1.825470	0.02815	N	0.124811	T	0.00271	0.0008	N	0.00500	-1.43	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12967	-1.0527	10	0.23302	T	0.38	.	1.2997	0.02077	0.4643:0.162:0.1738:0.1999	.	72	Q8N6Q8	CL026_HUMAN	R	72	ENSP00000248306:L72R	ENSP00000248306:L72R	L	+	2	0	C12orf26	81276690	.	.	0.000000	0.03702	0.019000	0.09904	.	.	-0.704000	0.05042	-0.767000	0.03436	CTG	T|0.939;G|0.061	0.061	strong		0.657	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
TMEM86B	255043	hgsc.bcm.edu	37	19	55739689	55739689	+	Silent	SNP	G	G	A	rs10413828	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55739689G>A	ENST00000327042.4	-	2	690	c.168C>T	c.(166-168)ccC>ccT	p.P56P	AC010327.2_ENST00000598855.1_3'UTR	NM_173804.4	NP_776165.3	Q8N661	TM86B_HUMAN	transmembrane protein 86B	56					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)		GGCAGAGGACGGGCAGGCACT	0.652													G|||	2167	0.432708	0.3222	0.4582	5008	,	,		17485	0.5992		0.4175	False		,,,				2504	0.408				p.P56P		Atlas-SNP	.											.	TMEM86B	12	.	0			c.C168T						PASS	.	G		1323,3079		187,949,1065	56.0	49.0	51.0		168	-10.0	0.0	19	dbSNP_119	51	3319,5279		632,2055,1612	no	coding-synonymous	TMEM86B	NM_173804.4		819,3004,2677	AA,AG,GG		38.602,30.0545,35.7077		56/227	55739689	4642,8358	2201	4299	6500	SO:0001819	synonymous_variant	255043	exon2			GAGGACGGGCAGG	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.168C>T	19.37:g.55739689G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	45	0.608108	NM_173804		Silent	SNP	ENST00000327042.4	37	CCDS12920.1																																																																																			G|0.620;A|0.380	0.380	strong		0.652	TMEM86B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452659.1	NM_173804	
CPSF1	29894	hgsc.bcm.edu	37	8	145624559	145624559	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145624559C>T	ENST00000349769.3	-	15	1520	c.1426G>A	c.(1426-1428)Gcc>Acc	p.A476T	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	476					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|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;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GCGGCATTGGCACAGGGTCCA	0.701																																					p.A476T	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.G1426A						PASS	.						8.0	9.0	9.0					8																	145624559		2182	4242	6424	SO:0001583	missense	29894	exon15			CATTGGCACAGGG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1426G>A	8.37:g.145624559C>T	ENSP00000339353:p.Ala476Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	153	36	0.235294	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836638	0.50951	.	.	ENSG00000071894	ENST00000349769	T	0.39406	1.08	5.62	5.62	0.85841	.	0.054386	0.64402	D	0.000001	T	0.34308	0.0893	L	0.32530	0.975	0.58432	D	0.999999	B	0.18310	0.027	B	0.19666	0.026	T	0.09292	-1.0681	10	0.17832	T	0.49	-17.6509	17.1693	0.86825	0.0:1.0:0.0:0.0	.	476	Q10570	CPSF1_HUMAN	T	476	ENSP00000339353:A476T	ENSP00000339353:A476T	A	-	1	0	CPSF1	145595367	1.000000	0.71417	0.995000	0.50966	0.082000	0.17680	5.468000	0.66743	2.658000	0.90341	0.561000	0.74099	GCC	.	.	none		0.701	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
XIRP2	129446	hgsc.bcm.edu	37	2	168104370	168104370	+	Silent	SNP	A	A	C	rs61748715	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168104370A>C	ENST00000409195.1	+	9	6557	c.6468A>C	c.(6466-6468)acA>acC	p.T2156T	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Silent_p.T1934T|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Silent_p.T2156T	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1981	Pro-rich.				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						TAACTGATACACAAAGCTCCA	0.408													A|||	865	0.172724	0.2882	0.1196	5008	,	,		16320	0.12		0.1123	False		,,,				2504	0.1708				p.T2156T		Atlas-SNP	.											.	XIRP2	914	.	0			c.A6468C						PASS	.	A	,,,,	949,2749		133,683,1033	39.0	38.0	38.0		,,5802,,6468	-3.4	0.0	2	dbSNP_129	38	792,7392		43,706,3343	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	176,1389,4376	CC,CA,AA		9.6774,25.6625,14.6524	,,,,	,,1934/3328,,2156/3550	168104370	1741,10141	1849	4092	5941	SO:0001819	synonymous_variant	129446	exon9			TGATACACAAAGC	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.6468A>C	2.37:g.168104370A>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			A|0.860;C|0.140	0.140	strong		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
SCNN1D	6339	hgsc.bcm.edu	37	1	1223385	1223385	+	Missense_Mutation	SNP	G	G	C	rs2228579	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1223385G>C	ENST00000338555.2	+	9	2282	c.1138G>C	c.(1138-1140)Gag>Cag	p.E380Q	SCNN1D_ENST00000379116.5_Missense_Mutation_p.E544Q|SCNN1D_ENST00000325425.8_Missense_Mutation_p.E446Q|SCNN1D_ENST00000400928.3_Missense_Mutation_p.E380Q			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	380			E -> Q (in dbSNP:rs2228579). {ECO:0000269|PubMed:15489334}.		ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	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;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	CGTGGAGGTGGAGCTGCTACA	0.721													G|||	1641	0.327676	0.354	0.2925	5008	,	,		11106	0.6111		0.0229	False		,,,				2504	0.3384				p.E544Q		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G1630C						PASS	.	G	GLN/GLU	1103,2955		124,855,1050	8.0	9.0	9.0		1630	1.4	0.0	1	dbSNP_131	9	139,8021		2,135,3943	yes	missense	SCNN1D	NM_001130413.3	29	126,990,4993	CC,CG,GG		1.7034,27.1809,10.1653	benign	544/803	1223385	1242,10976	2029	4080	6109	SO:0001583	missense	6339	exon12			GAGGTGGAGCTGC	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10601	protein-coding gene	gene with protein product		601328	"""sodium channel, nonvoltage-gated 1, delta"", ""sodium channel, non-voltage-gated 1, delta"""			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.1138G>C	1.37:g.1223385G>C	ENSP00000339504:p.Glu380Gln	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	81	8	0.0987654	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	37		616|616	0.28205128205128205|0.28205128205128205	168|168	0.34146341463414637|0.34146341463414637	83|83	0.2292817679558011|0.2292817679558011	347|347	0.6066433566433567|0.6066433566433567	18|18	0.023746701846965697|0.023746701846965697	G|G	3.550|3.550	-0.091787|-0.091787	0.07053|0.07053	0.271809|0.271809	0.017034|0.017034	ENSG00000162572|ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928|ENST00000379099	T;T;T;T|.	0.68624|.	-0.34;-0.31;-0.32;-0.31|.	3.48|3.48	1.41|1.41	0.22369|0.22369	.|.	2.573000|.	0.02749|.	N|.	0.117187|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04636|0.04636	-0.2|-0.2	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.15930|.	0.015;0.005;0.004|.	B;B;B|.	0.20577|.	0.03;0.01;0.003|.	T|T	0.39563|0.39563	-0.9608|-0.9608	9|4	0.12430|.	T|.	0.62|.	.|.	10.1098|10.1098	0.42555|0.42555	0.1355:0.2843:0.5802:0.0|0.1355:0.2843:0.5802:0.0	rs2228579;rs13306644|rs2228579;rs13306644	202;380;544|.	B1AMF2;P51172;A6NNF7|.	.;SCNND_HUMAN;.|.	Q|A	411;544;380;446;380|196	ENSP00000368411:E544Q;ENSP00000339504:E380Q;ENSP00000321594:E446Q;ENSP00000383717:E380Q|.	ENSP00000321594:E446Q|.	E|G	+|+	1|2	0|0	SCNN1D|SCNN1D	1213248|1213248	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.131000|0.131000	0.20780|0.20780	-0.413000|-0.413000	0.07123|0.07123	0.096000|0.096000	0.17463|0.17463	-0.802000|-0.802000	0.03209|0.03209	GAG|GGA	G|0.717;C|0.283	0.283	strong		0.721	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	
DNAJC25	548645	hgsc.bcm.edu	37	9	114411945	114411945	+	Silent	SNP	G	G	T	rs7019332	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:114411945G>T	ENST00000313525.3	+	3	758	c.702G>T	c.(700-702)ggG>ggT	p.G234G	DNAJC25_ENST00000556107.1_Intron|DNAJC25-GNG10_ENST00000374294.3_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	234						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						ATATAAAGGGGGGCTATCAGA	0.353													G|||	1563	0.312101	0.3517	0.4251	5008	,	,		18464	0.4127		0.2306	False		,,,				2504	0.1585				p.G234G		Atlas-SNP	.											.	DNAJC25	20	.	0			c.G702T						PASS	.	G	,	1147,2465		194,759,853	41.0	42.0	42.0		702,	-0.3	1.0	9	dbSNP_116	42	1718,6410		175,1368,2521	no	coding-synonymous,intron	DNAJC25,DNAJC25-GNG10	NM_001015882.2,NM_004125.3	,	369,2127,3374	TT,TG,GG		21.1368,31.7553,24.4037	,	234/361,	114411945	2865,8875	1806	4064	5870	SO:0001819	synonymous_variant	548645	exon3			AAAGGGGGGCTAT		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"""Heat shock proteins / DNAJ (HSP40)"""	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.702G>T	9.37:g.114411945G>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_001015882	Q5QTD8|Q96BN9	Silent	SNP	ENST00000313525.3	37	CCDS43862.1																																																																																			G|0.691;T|0.309	0.309	strong		0.353	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882	
STPG1	90529	hgsc.bcm.edu	37	1	24706269	24706269	+	Silent	SNP	A	A	G	rs1064842	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:24706269A>G	ENST00000374409.1	-	5	590	c.336T>C	c.(334-336)aaT>aaC	p.N112N	STPG1_ENST00000337248.4_Silent_p.N112N|STPG1_ENST00000003583.8_Silent_p.N65N|STPG1_ENST00000440416.1_Silent_p.N65N|STPG1_ENST00000468303.1_5'UTR	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	112					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											TAGTGTATGCATTCGCTGCAG	0.418													G|||	2099	0.419129	0.4894	0.5101	5008	,	,		20086	0.4444		0.3618	False		,,,				2504	0.2924				p.N112N		Atlas-SNP	.											C1orf201_ENST00000374409,colon,carcinoma,0,2	.	.	2	0			c.T336C						PASS	.	G	,,,	2182,2224	589.8+/-387.2	536,1110,557	100.0	100.0	100.0		336,336,60,195	-7.3	0.0	1	dbSNP_86	100	2936,5664	668.7+/-402.6	467,2002,1831	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C1orf201	NM_001199012.1,NM_001199013.1,NM_001199014.1,NM_178122.4	,,,	1003,3112,2388	GG,GA,AA		34.1395,49.5234,39.3511	,,,	112/335,112/335,20/243,65/288	24706269	5118,7888	2203	4300	6503	SO:0001819	synonymous_variant	90529	exon5			GTATGCATTCGCT	BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 2"""	615826	"""chromosome 1 open reading frame 201"""	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.336T>C	1.37:g.24706269A>G		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	85	55	0.647059	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Silent	SNP	ENST00000374409.1	37	CCDS55581.1	947	0.4336080586080586	241	0.4898373983739837	172	0.47513812154696133	249	0.4353146853146853	285	0.3759894459102902	G	1.081	-0.667099	0.03428	0.495234	0.341395	ENSG00000001460	ENST00000435187	.	.	.	5.9	-7.34	0.01427	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	8.000000000008E-6	.	.	.	.	.	.	T	0.02081	-1.1217	3	.	.	.	-27.1846	18.1247	0.89581	0.3522:0.0:0.6478:0.0	rs1064842;rs3765429;rs10314500;rs59501254;rs1064842	.	.	.	T	89	.	.	M	-	2	0	C1orf201	24578856	0.010000	0.17322	0.000000	0.03702	0.270000	0.26580	-1.203000	0.03019	-1.966000	0.01009	-2.223000	0.00295	ATG	A|0.589;G|0.411	0.411	strong		0.418	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
PTPRU	10076	hgsc.bcm.edu	37	1	29618535	29618535	+	Missense_Mutation	SNP	C	C	T	rs558954146		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:29618535C>T	ENST00000345512.3	+	16	2632	c.2503C>T	c.(2503-2505)Cgg>Tgg	p.R835W	PTPRU_ENST00000356870.3_Missense_Mutation_p.R825W|PTPRU_ENST00000373779.3_Missense_Mutation_p.R825W|PTPRU_ENST00000323874.8_Missense_Mutation_p.R825W|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000428026.2_Missense_Mutation_p.R825W|PTPRU_ENST00000460170.2_Missense_Mutation_p.R825W	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	835	Mediates interaction with CTNNB1. {ECO:0000250}.		R -> W (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R835W(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		CTACAGCACCCGGGGTGAGTG	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		16905	0.0		0.0	False		,,,				2504	0.001				p.R835W		Atlas-SNP	.											PTPRU_ENST00000460170,colon,carcinoma,0,4	PTPRU	374	4	1	Substitution - Missense(1)	large_intestine(1)	c.C2503T						scavenged	.						47.0	47.0	47.0					1																	29618535		2203	4300	6503	SO:0001583	missense	10076	exon16			AGCACCCGGGGTG	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9683	protein-coding gene	gene with protein product	"""pi R-PTP-Psi"""	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.2503C>T	1.37:g.29618535C>T	ENSP00000334941:p.Arg835Trp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	59	2	0.0338983	NM_005704	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.941831	0.73557	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.35421	1.33;1.37;1.37;1.37;1.31;1.37	4.99	1.96	0.26148	.	0.000000	0.85682	D	0.000000	T	0.48624	0.1510	M	0.62723	1.935	0.46874	D	0.999231	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;P;D	0.69479	0.964;0.93;0.964;0.852;0.92	T	0.38499	-0.9658	9	.	.	.	.	6.5859	0.22620	0.3216:0.5948:0.0:0.0836	.	825;825;825;825;835	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	W	835;825;825;825;825;825	ENSP00000334941:R835W;ENSP00000362884:R825W;ENSP00000349333:R825W;ENSP00000314987:R825W;ENSP00000392332:R825W;ENSP00000432906:R825W	.	R	+	1	2	PTPRU	29491122	0.996000	0.38824	1.000000	0.80357	0.987000	0.75469	0.620000	0.24403	0.576000	0.29452	0.655000	0.94253	CGG	.	.	none		0.622	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1		
SSPO	23145	hgsc.bcm.edu	37	7	149521183	149521183	+	RNA	SNP	G	G	A	rs4389841	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149521183G>A	ENST00000378016.2	+	0	13523							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)			AGTGAATGCCGGCGTGGGGAG	0.617													G|||	745	0.148762	0.0537	0.1873	5008	,	,		17753	0.1746		0.1551	False		,,,				2504	0.2168				p.R4508Q		Atlas-SNP	.											.	.	.	.	0			c.G13523A						PASS	.	G		252,3694		14,224,1735	34.0	38.0	37.0		13537	-8.0	0.0	7	dbSNP_111	37	1409,6969		104,1201,2884	yes	coding-notMod3	SSPO	NM_198455.2		118,1425,4619	AA,AG,GG		16.8179,6.3862,13.4778			149521183	1661,10663	1973	4189	6162			23145	exon94			AATGCCGGCGTGG	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.149521183G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	75	9	0.12	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.848;A|0.152	0.152	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
UBE4A	9354	hgsc.bcm.edu	37	11	118253436	118253436	+	Silent	SNP	T	T	C	rs567105943		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118253436T>C	ENST00000431736.2	+	13	2235	c.2163T>C	c.(2161-2163)taT>taC	p.Y721Y	UBE4A_ENST00000545354.1_Silent_p.Y186Y|UBE4A_ENST00000252108.3_Silent_p.Y714Y					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	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;3.28e-05)		ACTTTCAGTATGCACCCCAAC	0.498																																					p.Y721Y		Atlas-SNP	.											.	UBE4A	97	.	0			c.T2163C						PASS	.						180.0	167.0	172.0					11																	118253436		2200	4296	6496	SO:0001819	synonymous_variant	9354	exon13			TCAGTATGCACCC	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"""U-box domain containing"""	12499	protein-coding gene	gene with protein product		603753	"""ubiquitination factor E4A (homologous to yeast UFD2)"", ""ubiquitination factor E4A (UFD2 homolog, yeast)"""			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.2163T>C	11.37:g.118253436T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	110	76	0.690909	NM_004788		Silent	SNP	ENST00000431736.2	37	CCDS8396.1																																																																																			.	.	none		0.498	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788	
MANBA	4126	hgsc.bcm.edu	37	4	103555992	103555992	+	Silent	SNP	A	A	G	rs2272697	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:103555992A>G	ENST00000226578.4	-	16	2467	c.2368T>C	c.(2368-2370)Ttg>Ctg	p.L790L	MANBA_ENST00000505239.1_Silent_p.L733L	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	790					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)	p.L790L(1)		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)		GGTGAGGACAAGAAGTGGTAG	0.567													G|||	2753	0.54972	0.6619	0.6542	5008	,	,		19905	0.5198		0.493	False		,,,				2504	0.4131				p.L790L		Atlas-SNP	.											MANBA,NS,carcinoma,0,2	MANBA	78	2	1	Substitution - coding silent(1)	prostate(1)	c.T2368C						PASS	.	G		2720,1686	511.1+/-367.7	851,1018,334	87.0	79.0	82.0		2368	3.7	1.0	4	dbSNP_100	82	4413,4187	568.4+/-389.0	1120,2173,1007	no	coding-synonymous	MANBA	NM_005908.3		1971,3191,1341	GG,GA,AA		48.686,38.266,45.1561		790/880	103555992	7133,5873	2203	4300	6503	SO:0001819	synonymous_variant	4126	exon16			AGGACAAGAAGTG		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.2368T>C	4.37:g.103555992A>G		Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	182	179	0.983516	NM_005908	Q96BC3|Q9NYX9	Silent	SNP	ENST00000226578.4	37	CCDS3658.1																																																																																			A|0.447;G|0.553	0.553	strong		0.567	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
DISP2	85455	hgsc.bcm.edu	37	15	40660566	40660566	+	Silent	SNP	G	G	A	rs72733420	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	41	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	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	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103152919	103152919	+	Silent	SNP	G	G	A	rs12574626	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:103152919G>A	ENST00000375735.2	+	72	10917	c.10773G>A	c.(10771-10773)acG>acA	p.T3591T	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.T3598T	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3591					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)		AATGGGATACGTTTACAGGTG	0.284													G|||	970	0.19369	0.4198	0.1282	5008	,	,		15088	0.0913		0.1272	False		,,,				2504	0.1084				p.T3598T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G10794A						PASS	.	G	,	1299,2303		234,831,736	87.0	88.0	88.0		10794,10773	-11.7	0.6	11	dbSNP_120	88	952,7168		62,828,3170	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	296,1659,3906	AA,AG,GG		11.7241,36.0633,19.2032	,	3598/4315,3591/4308	103152919	2251,9471	1801	4060	5861	SO:0001819	synonymous_variant	79659	exon73			GGATACGTTTACA	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.10773G>A	11.37:g.103152919G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	73	53	0.726027	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			G|0.808;A|0.192	0.192	strong		0.284	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
CD1C	911	hgsc.bcm.edu	37	1	158261015	158261015	+	Silent	SNP	C	C	T	rs3138099	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158261015C>T	ENST00000368170.3	+	2	432	c.153C>T	c.(151-153)gaC>gaT	p.D51D		NM_001765.2	NP_001756.2	P29017	CD1C_HUMAN	CD1c molecule	51					antigen processing and presentation (GO:0019882)|T cell activation involved in immune response (GO:0002286)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	endogenous lipid antigen binding (GO:0030883)|exogenous lipid antigen binding (GO:0030884)|glycolipid binding (GO:0051861)|lipopeptide binding (GO:0071723)			NS(1)|endometrium(3)|large_intestine(4)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	39	all_hematologic(112;0.0378)					GATGGCTGGACGAGTTGCAGA	0.502													C|||	301	0.0601038	0.1672	0.0331	5008	,	,		19056	0.0		0.0447	False		,,,				2504	0.0123				p.D51D		Atlas-SNP	.											.	CD1C	100	.	0			c.C153T						PASS	.	C		615,3791		46,523,1634	107.0	93.0	98.0		153	-1.9	0.0	1	dbSNP_104	98	413,8187		13,387,3900	no	coding-synonymous	CD1C	NM_001765.2		59,910,5534	TT,TC,CC		4.8023,13.9582,7.904		51/334	158261015	1028,11978	2203	4300	6503	SO:0001819	synonymous_variant	911	exon2			GCTGGACGAGTTG	M28827	CCDS1175.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158481	ENSG00000158481		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1636	protein-coding gene	gene with protein product		188340	"""CD1C antigen, c polypeptide"", ""CD1c antigen"""	CD1		2447586	Standard	NM_001765		Approved		uc001fru.3	P29017	OTTHUMG00000017514	ENST00000368170.3:c.153C>T	1.37:g.158261015C>T		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	400	219	0.5475	NM_001765	Q5TDJ7|Q6IAS4|Q9UMM0|Q9UN96	Silent	SNP	ENST00000368170.3	37	CCDS1175.1																																																																																			C|0.928;T|0.072	0.072	strong		0.502	CD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046351.2	NM_001765	
MGAT4C	25834	hgsc.bcm.edu	37	12	86373221	86373221	+	Missense_Mutation	SNP	G	G	C	rs17855890	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:86373221G>C	ENST00000604798.1	-	8	2487	c.1283C>G	c.(1282-1284)aCt>aGt	p.T428S	MGAT4C_ENST00000549405.2_Missense_Mutation_p.T428S|MGAT4C_ENST00000393205.2_Missense_Mutation_p.T457S|MGAT4C_ENST00000548651.1_Missense_Mutation_p.T428S|MGAT4C_ENST00000552808.2_Missense_Mutation_p.T428S|MGAT4C_ENST00000332156.1_Missense_Mutation_p.T428S			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	428			T -> S (in dbSNP:rs17855890). {ECO:0000269|PubMed:10570912, ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TCTTAAGTAAGTAGAACATTG	0.348													G|||	206	0.0411342	0.0061	0.0793	5008	,	,		17729	0.0		0.1143	False		,,,				2504	0.0286				p.T428S		Atlas-SNP	.											.	MGAT4C	110	.	0			c.C1283G						PASS	.	G	SER/THR	84,4322	73.1+/-111.1	2,80,2121	82.0	81.0	82.0		1283	4.8	0.2	12	dbSNP_123	82	910,7688	204.5+/-247.2	48,814,3437	yes	missense	MGAT4C	NM_013244.3	58	50,894,5558	CC,CG,GG		10.5839,1.9065,7.6438	benign	428/479	86373221	994,12010	2203	4299	6502	SO:0001583	missense	25834	exon7			AAGTAAGTAGAAC		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	30871	protein-coding gene	gene with protein product		607385	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"""			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.1283C>G	12.37:g.86373221G>C	ENSP00000474896:p.Thr428Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_013244	B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	37	CCDS9030.1	107	0.04899267399267399	5	0.01016260162601626	22	0.06077348066298342	0	0.0	80	0.10554089709762533	G	2.671	-0.277587	0.05679	0.019065	0.105839	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651	T;T;T;T;T	0.28895	1.6;1.59;1.6;1.6;1.6	5.76	4.85	0.62838	.	0.180320	0.48767	N	0.000168	T	0.00328	0.0010	N	0.16130	0.375	0.31148	N	0.705815	B;B	0.12630	0.006;0.006	B;B	0.10450	0.005;0.004	T	0.04870	-1.0921	10	0.06494	T	0.89	-19.8644	15.9183	0.79539	0.0:0.0:0.8637:0.1363	rs17855890	457;428	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	S	428;457;428;428;428;428	ENSP00000331664:T428S;ENSP00000376900:T457S;ENSP00000449022:T428S;ENSP00000446647:T428S;ENSP00000447253:T428S	ENSP00000331664:T428S	T	-	2	0	MGAT4C	84897352	1.000000	0.71417	0.163000	0.22734	0.837000	0.47467	4.624000	0.61254	1.366000	0.46076	0.585000	0.79938	ACT	G|0.927;C|0.073	0.073	strong		0.348	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244	
OR2T27	403239	hgsc.bcm.edu	37	1	248813785	248813785	+	Missense_Mutation	SNP	A	A	T	rs200036975	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248813785A>T	ENST00000344889.3	-	1	400	c.401T>A	c.(400-402)gTc>gAc	p.V134D		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	134						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)			GCTCATGAGGACAGGATAGTG	0.557																																					p.V134D		Atlas-SNP	.											OR2T27,bladder,carcinoma,0,1	OR2T27	52	1	0			c.T401A						scavenged	.						88.0	56.0	67.0					1																	248813785		2200	4256	6456	SO:0001583	missense	403239	exon1			ATGAGGACAGGAT		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.401T>A	1.37:g.248813785A>T	ENSP00000342008:p.Val134Asp	Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	610	210	0.344262	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	8.174	0.792423	0.16258	.	.	ENSG00000187701	ENST00000344889	T	0.00892	5.57	2.74	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.441698	0.16541	N	0.209937	T	0.00875	0.0029	.	.	.	0.09310	N	1	B	0.22541	0.071	B	0.22601	0.04	T	0.47761	-0.9092	9	0.72032	D	0.01	.	5.1307	0.14909	0.6126:0.0:0.3874:0.0	rs1782240	134	Q8NH04	O2T27_HUMAN	D	134	ENSP00000342008:V134D	ENSP00000342008:V134D	V	-	2	0	OR2T27	246880408	0.000000	0.05858	0.003000	0.11579	0.051000	0.14879	-0.404000	0.07205	0.438000	0.26450	0.163000	0.16589	GTC	A|0.863;T|0.137	0.137	strong		0.557	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
MUC4	4585	hgsc.bcm.edu	37	3	195506597	195506597	+	Missense_Mutation	SNP	G	G	A	rs200685331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195506597G>A	ENST00000463781.3	-	2	12313	c.11854C>T	c.(11854-11856)Cct>Tct	p.P3952S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3952S	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.P3952S(8)		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)		ACAGGAAGAGGGGTGGTGTCA	0.602													.|||	94	0.01877	0.0068	0.0476	5008	,	,		9784	0.002		0.0467	False		,,,				2504	0.0031				p.P3952S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,9	MUC4	1505	9	8	Substitution - Missense(8)	kidney(4)|skin(2)|stomach(1)|endometrium(1)	c.C11854T						scavenged	.						14.0	11.0	12.0					3																	195506597		651	1454	2105	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGT	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.11854C>T	3.37:g.195506597G>A	ENSP00000417498:p.Pro3952Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	44	10	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	3.614	-0.078859	0.07141	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30981	1.57;1.51	.	.	.	.	.	.	.	.	T	0.14527	0.0351	N	0.19112	0.55	0.09310	N	1	B	0.22080	0.064	B	0.23419	0.046	T	0.25012	-1.0144	7	.	.	.	.	4.6062	0.12378	0.3343:0.0:0.6657:0.0	.	3824	E7ESK3	.	S	3952	ENSP00000417498:P3952S;ENSP00000420243:P3952S	.	P	-	1	0	MUC4	196991376	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	-1.291000	0.02775	-2.068000	0.00884	-2.092000	0.00371	CCT	.	.	weak		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TYMSOS	494514	hgsc.bcm.edu	37	18	658064	658064	+	Missense_Mutation	SNP	G	G	C	rs2853533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:658064G>C	ENST00000323813.3	-	1	276	c.184C>G	c.(184-186)Cgc>Ggc	p.R62G	RP11-806L2.5_ENST00000584679.1_RNA|TYMS_ENST00000323250.5_Intron|C18orf56_ENST00000585033.1_Missense_Mutation_p.R62G|TYMS_ENST00000323224.7_Intron|TYMS_ENST00000323274.10_Intron	NM_001012716.2	NP_001012734.2	Q8TAI1	TYMOS_HUMAN		62			R -> G (in dbSNP:rs2853533). {ECO:0000269|PubMed:15489334}.														TCAATCCTGCGAGGGAGGGGA	0.687													G|||	1698	0.339058	0.3759	0.2176	5008	,	,		13130	0.5476		0.1451	False		,,,				2504	0.3599				p.R62G		Atlas-SNP	.											.	C18orf56	2	.	0			c.C184G						PASS	.	G	GLY/ARG,	1508,2866		292,924,971	12.0	10.0	11.0		184,	1.7	0.0	18	dbSNP_100	11	1107,7425		85,937,3244	yes	missense,intron	TYMS,C18orf56	NM_001012716.2,NM_001071.2	125,	377,1861,4215	CC,CG,GG		12.9747,34.4765,20.2619	probably-damaging,	62/124,	658064	2615,10291	2187	4266	6453	SO:0001583	missense	494514	exon1			TCCTGCGAGGGAG																												ENST00000323813.3:c.184C>G	18.37:g.658064G>C	ENSP00000316465:p.Arg62Gly	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_001012716	A8K1S1	Missense_Mutation	SNP	ENST00000323813.3	37		661	0.30265567765567764	172	0.34959349593495936	70	0.19337016574585636	310	0.541958041958042	109	0.1437994722955145	G	8.524	0.869385	0.17322	0.344765	0.129747	ENSG00000176912	ENST00000323813	T	0.55930	0.49	2.65	1.7	0.24286	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.51233	P	8.399999999997299E-5	D	0.56035	0.974	P	0.51833	0.681	T	0.44221	-0.9342	8	0.87932	D	0	.	8.0251	0.30431	0.0:0.0:0.7558:0.2441	rs2853533;rs3087618;rs17852517;rs58594590;rs2853533	62	Q8TAI1	CR056_HUMAN	G	62	ENSP00000316465:R62G	ENSP00000316465:R62G	R	-	1	0	C18orf56	648064	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.132000	0.15891	0.615000	0.30124	0.555000	0.69702	CGC	G|0.684;C|0.316	0.316	strong		0.687	C18orf56-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000441199.2		
SLC22A16	85413	hgsc.bcm.edu	37	6	110763935	110763935	+	Missense_Mutation	SNP	T	T	C	rs41288594	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:110763935T>C	ENST00000368919.3	-	4	761	c.695A>G	c.(694-696)gAa>gGa	p.E232G	SLC22A16_ENST00000456137.2_3'UTR|RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000439654.1_Missense_Mutation_p.E232G|SLC22A16_ENST00000330550.4_Missense_Mutation_p.E198G	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	232					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	GCCAATGAATTCCATCACATA	0.428													T|||	33	0.00658946	0.003	0.0144	5008	,	,		19307	0.0		0.0099	False		,,,				2504	0.0092				p.E232G		Atlas-SNP	.											.	SLC22A16	81	.	0			c.A695G						PASS	.	T	GLY/GLU	28,4378	31.7+/-61.6	0,28,2175	71.0	69.0	69.0		695	4.7	0.2	6	dbSNP_127	69	186,8414	80.4+/-143.0	1,184,4115	yes	missense	SLC22A16	NM_033125.2	98	1,212,6290	CC,CT,TT		2.1628,0.6355,1.6454	probably-damaging	232/578	110763935	214,12792	2203	4300	6503	SO:0001583	missense	85413	exon4			ATGAATTCCATCA		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.695A>G	6.37:g.110763935T>C	ENSP00000357915:p.Glu232Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	15	0.006868131868131868	4	0.008130081300813009	6	0.016574585635359115	0	0.0	5	0.006596306068601583	T	16.01	3.001806	0.54254	0.006355	0.021628	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949;ENST00000437378	D;D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	4.74	4.74	0.60224	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.95053	0.8398	H	0.97023	3.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.993	D	0.96626	0.9463	10	0.87932	D	0	.	14.2102	0.65759	0.0:0.0:0.0:1.0	rs41288594	232;198	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	G	232;149;198;232;62;189	ENSP00000357915:E232G;ENSP00000395642:E149G;ENSP00000328583:E198G;ENSP00000408799:E232G;ENSP00000409306:E62G;ENSP00000416310:E189G	ENSP00000328583:E198G	E	-	2	0	SLC22A16	110870628	1.000000	0.71417	0.215000	0.23724	0.120000	0.20174	7.301000	0.78850	1.762000	0.52044	0.533000	0.62120	GAA	T|0.985;C|0.015	0.015	strong		0.428	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58350631	58350631	+	Silent	SNP	C	C	T	rs10122	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	90	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	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	
RPE65	6121	hgsc.bcm.edu	37	1	68914353	68914353	+	Silent	SNP	A	A	G	rs62642581		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:68914353A>G	ENST00000262340.5	-	2	101	c.48T>C	c.(46-48)ttT>ttC	p.F16F		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	16					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						CCACAGTTTCAAACAGTTTCT	0.488													A|||	1	0.000199681	0.0	0.0	5008	,	,		14614	0.0		0.001	False		,,,				2504	0.0				p.F16F		Atlas-SNP	.											.	RPE65	87	.	0			c.T48C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	116.0	100.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	48	-4.9	0.9	1	dbSNP_129	106	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	RPE65	NM_000329.2		0,6,6497	GG,GA,AA		0.0581,0.0227,0.0461		16/534	68914353	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	6121	exon2			AGTTTCAAACAGT	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.48T>C	1.37:g.68914353A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	97	25	0.257732	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			A|1.000;G|0.000	0.000	strong		0.488	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
IQCA1	79781	hgsc.bcm.edu	37	2	237300677	237300677	+	Missense_Mutation	SNP	T	T	C	rs10204742	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:237300677T>C	ENST00000409907.3	-	11	1629	c.1355A>G	c.(1354-1356)aAg>aGg	p.K452R	IQCA1_ENST00000465621.1_5'Flank|IQCA1_ENST00000309507.5_Missense_Mutation_p.K448R|IQCA1_ENST00000431676.2_Missense_Mutation_p.K411R|AC019068.2_ENST00000413353.1_RNA	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	452	Lys-rich.		K -> R (in dbSNP:rs10204742).				ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						CACAGCTAGCTTTAAGTTTTT	0.453													T|||	330	0.0658946	0.177	0.0476	5008	,	,		18908	0.0		0.0567	False		,,,				2504	0.0061				p.K459R		Atlas-SNP	.											.	IQCA1	170	.	0			c.A1376G						PASS	.	T	ARG/LYS	590,3144		41,508,1318	175.0	177.0	176.0		1355	5.4	0.6	2	dbSNP_119	176	367,7843		5,357,3743	yes	missense	IQCA1	NM_024726.3	26	46,865,5061	CC,CT,TT		4.4702,15.8007,8.0124	benign	452/823	237300677	957,10987	1867	4105	5972	SO:0001583	missense	79781	exon11			GCTAGCTTTAAGT	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.1355A>G	2.37:g.237300677T>C	ENSP00000387347:p.Lys452Arg	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	167	86	0.51497	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	37	CCDS46549.1	137	0.06272893772893773	79	0.16056910569105692	23	0.06353591160220995	0	0.0	35	0.04617414248021108	T	12.04	1.817829	0.32145	0.158007	0.044702	ENSG00000132321	ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	D;D;D	0.95554	-3.62;-3.58;-3.74	5.45	5.45	0.79879	.	0.104177	0.41823	D	0.000819	T	0.05090	0.0136	L	0.52905	1.665	0.26243	P	0.9788443	B;B;B	0.27656	0.132;0.184;0.132	B;B;B	0.27262	0.034;0.078;0.05	T	0.65327	-0.6195	9	0.15066	T	0.55	.	13.7718	0.63029	0.0:0.0:0.0:1.0	rs10204742;rs52829459;rs10204742	411;459;452	E7EWQ0;E9PH78;Q86XH1	.;.;IQCA1_HUMAN	R	452;459;448;411;448	ENSP00000387347:K452R;ENSP00000311951:K448R;ENSP00000407213:K411R	ENSP00000254653:K452R	K	-	2	0	IQCA1	236965416	0.997000	0.39634	0.598000	0.28837	0.677000	0.39632	2.585000	0.46111	2.064000	0.61679	0.533000	0.62120	AAG	T|0.926;C|0.074	0.074	strong		0.453	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
BTBD16	118663	hgsc.bcm.edu	37	10	124096041	124096041	+	Silent	SNP	T	T	C	rs1129973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124096041T>C	ENST00000260723.4	+	15	1547	c.1296T>C	c.(1294-1296)tcT>tcC	p.S432S	BTBD16_ENST00000495370.2_3'UTR|BTBD16_ENST00000368994.2_Silent_p.S433S	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						scavenged	.	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	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	118	51	0.432203	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	
SHKBP1	92799	hgsc.bcm.edu	37	19	41096189	41096189	+	Silent	SNP	A	A	G	rs396118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41096189A>G	ENST00000291842.5	+	16	1678	c.1629A>G	c.(1627-1629)acA>acG	p.T543T	LTBP4_ENST00000204005.9_5'Flank|LTBP4_ENST00000545697.1_5'Flank|SHKBP1_ENST00000600733.1_Silent_p.T518T|SHKBP1_ENST00000597649.1_3'UTR	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	543					protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CACCCACGACAGCCTTCACAG	0.701													g|||	2894	0.577875	0.8222	0.5	5008	,	,		15016	0.4107		0.501	False		,,,				2504	0.5542				p.T543T		Atlas-SNP	.											SHKBP1,NS,carcinoma,0,2	SHKBP1	68	2	0			c.A1629G						PASS	.			3392,1004		1322,748,128	18.0	20.0	19.0		1629	-5.4	0.8	19	dbSNP_80	19	4266,4324		1080,2106,1109	no	coding-synonymous	SHKBP1	NM_138392.3		2402,2854,1237	GG,GA,AA		49.6624,22.8389,41.0288		543/708	41096189	7658,5328	2198	4295	6493	SO:0001819	synonymous_variant	92799	exon16			CACGACAGCCTTC	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"""WD repeat domain containing"""	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.1629A>G	19.37:g.41096189A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	43	41	0.953488	NM_138392	Q8N2I6|Q8WY93|Q96IB8	Silent	SNP	ENST00000291842.5	37	CCDS12560.1																																																																																			A|0.421;G|0.579	0.579	strong		0.701	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462613.2	NM_138392	
BTNL2	56244	hgsc.bcm.edu	37	6	32363955	32363955	+	Silent	SNP	T	T	C	rs2076529	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32363955T>C	ENST00000374993.1	-	5	938	c.939A>G	c.(937-939)gtA>gtG	p.V313V	BTNL2_ENST00000429232.2_Silent_p.V220V|BTNL2_ENST00000414363.1_Silent_p.V103V|BTNL2_ENST00000544175.1_Silent_p.V36V|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Silent_p.V219V|BTNL2_ENST00000540315.1_Silent_p.V103V|BTNL2_ENST00000454136.3_Silent_p.V313V	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	142	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	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	
ARHGEF12	23365	hgsc.bcm.edu	37	11	120328858	120328858	+	Silent	SNP	T	T	C	rs766894	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:120328858T>C	ENST00000397843.2	+	25	2461	c.2295T>C	c.(2293-2295)gaT>gaC	p.D765D	ARHGEF12_ENST00000532993.1_Silent_p.D662D|ARHGEF12_ENST00000356641.3_Silent_p.D746D	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	765					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|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)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|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(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		TAGAGACAGATCCACCCAACT	0.373			T	MLL	AML								T|||	625	0.1248	0.1823	0.1412	5008	,	,		18458	0.001		0.2237	False		,,,				2504	0.0613				p.D765D		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	ARHGEF12,NS,carcinoma,+2,1	ARHGEF12	133	1	0			c.T2295C						scavenged	.	T	,	726,3020		76,574,1223	120.0	120.0	120.0		2238,2295	-2.3	1.0	11	dbSNP_86	120	1889,6341		221,1447,2447	no	coding-synonymous,coding-synonymous	ARHGEF12	NM_001198665.1,NM_015313.2	,	297,2021,3670	CC,CT,TT		22.9526,19.3807,21.8353	,	746/1526,765/1545	120328858	2615,9361	1873	4115	5988	SO:0001819	synonymous_variant	23365	exon25			GACAGATCCACCC	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"""Rho guanine nucleotide exchange factors"""	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.2295T>C	11.37:g.120328858T>C		Somatic	218	2	0.00917431		WXS	Illumina HiSeq	Phase_I	303	86	0.283828	NM_015313	O15086|Q6P526	Silent	SNP	ENST00000397843.2	37	CCDS41727.1																																																																																			T|0.833;C|0.167	0.167	strong		0.373	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313	
HEG1	57493	hgsc.bcm.edu	37	3	124746347	124746347	+	Silent	SNP	T	T	C	rs4404487	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:124746347T>C	ENST00000311127.4	-	3	682	c.615A>G	c.(613-615)tcA>tcG	p.S205S		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	205					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						GAAGACTTTCTGAGGCTGAAA	0.423													C|||	3851	0.76897	0.7882	0.7248	5008	,	,		21310	0.8889		0.6223	False		,,,				2504	0.8016				p.S205S		Atlas-SNP	.											.	HEG1	109	.	0			c.A615G						PASS	.	C		2804,890		1074,656,117	49.0	44.0	46.0		615	1.2	0.0	3	dbSNP_111	46	4885,3305		1461,1963,671	no	coding-synonymous	HEG1	NM_020733.1		2535,2619,788	CC,CT,TT		40.3541,24.0931,35.2996		205/1382	124746347	7689,4195	1847	4095	5942	SO:0001819	synonymous_variant	57493	exon3			ACTTTCTGAGGCT	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.615A>G	3.37:g.124746347T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	136	61	0.448529	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Silent	SNP	ENST00000311127.4	37	CCDS46898.1																																																																																			T|0.270;C|0.730	0.730	strong		0.423	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
DNAH17	8632	hgsc.bcm.edu	37	17	76455218	76455218	+	Silent	SNP	G	G	A	rs2289754	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76455218G>A	ENST00000585328.1	-	61	9835	c.9711C>T	c.(9709-9711)tgC>tgT	p.C3237C	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.C3228C	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3228	Stalk. {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(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)			TGCACCAGGAGCACAGGCCGG	0.652													G|||	1105	0.220647	0.1392	0.3458	5008	,	,		17683	0.249		0.1382	False		,,,				2504	0.2975				p.C3242C		Atlas-SNP	.											DNAH17,NS,lymphoid_neoplasm,-1,2	DNAH17	347	2	0			c.C9726T						scavenged	.	G		618,3788	268.6+/-268.5	42,534,1627	168.0	180.0	176.0		9726	3.0	1.0	17	dbSNP_100	176	1327,7273	260.3+/-283.2	102,1123,3075	no	coding-synonymous	DNAH17	NM_173628.3		144,1657,4702	AA,AG,GG		15.4302,14.0263,14.9546		3242/4463	76455218	1945,11061	2203	4300	6503	SO:0001819	synonymous_variant	8632	exon61			CCAGGAGCACAGG	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.9711C>T	17.37:g.76455218G>A		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	111	49	0.441441	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.835;A|0.165	0.165	strong		0.652	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
PLXNA1	5361	hgsc.bcm.edu	37	3	126726705	126726705	+	Silent	SNP	A	A	G	rs9876615	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	81	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	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	
MKI67	4288	hgsc.bcm.edu	37	10	129906980	129906980	+	Missense_Mutation	SNP	C	C	T	rs2152143	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129906980C>T	ENST00000368654.3	-	13	3499	c.3124G>A	c.(3124-3126)Ggc>Agc	p.G1042S	MKI67_ENST00000484853.1_5'Flank|MKI67_ENST00000368653.3_Missense_Mutation_p.G682S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1042	16 X 122 AA approximate repeats.		G -> S (in dbSNP:rs2152143).		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)	p.G1042S(1)		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)				GTGAACTTGCCGACTGCTAGG	0.507													C|||	954	0.190495	0.1172	0.3156	5008	,	,		20033	0.1181		0.2704	False		,,,				2504	0.1933				p.G1042S		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	stomach(1)	c.G3124A						scavenged	.	C	SER/GLY,SER/GLY	576,3830	253.7+/-259.5	37,502,1664	381.0	360.0	367.0		2044,3124	-4.1	0.0	10	dbSNP_96	367	2128,6472	366.1+/-334.2	272,1584,2444	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	56,56	309,2086,4108	TT,TC,CC		24.7442,13.0731,20.7904	probably-damaging,probably-damaging	682/2897,1042/3257	129906980	2704,10302	2203	4300	6503	SO:0001583	missense	4288	exon13			ACTTGCCGACTGC	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.3124G>A	10.37:g.129906980C>T	ENSP00000357643:p.Gly1042Ser	Somatic	326	2	0.00613497		WXS	Illumina HiSeq	Phase_I	287	148	0.515679	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	454	0.2078754578754579	49	0.09959349593495935	120	0.3314917127071823	83	0.1451048951048951	202	0.26649076517150394	C	9.554	1.116707	0.20795	0.130731	0.247442	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02015	4.5;4.5	2.17	-4.11	0.03928	.	.	.	.	.	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B;D;P	0.56287	0.401;0.975;0.955	B;P;B	0.47915	0.03;0.561;0.442	T	0.23726	-1.0180	8	0.09338	T	0.73	.	8.0782	0.30729	0.0:0.4907:0.0:0.5093	rs2152143;rs17731451;rs52803099;rs2152143	1041;682;1042	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	S	1042;682;1041	ENSP00000357643:G1042S;ENSP00000357642:G682S	ENSP00000357642:G682S	G	-	1	0	MKI67	129796970	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.344000	0.02639	-1.001000	0.03434	-0.258000	0.10820	GGC	T|0.208;G|0.007	0.208	strong		0.507	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
ELL2	22936	hgsc.bcm.edu	37	5	95234392	95234392	+	Silent	SNP	A	A	C	rs3777202	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:95234392A>C	ENST00000237853.4	-	8	1426	c.1077T>G	c.(1075-1077)tcT>tcG	p.S359S	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	359					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)		GGCCTGCAGCAGATTTTTCAC	0.498													A|||	1930	0.385383	0.5318	0.2464	5008	,	,		15337	0.4325		0.2803	False		,,,				2504	0.3456				p.S359S		Atlas-SNP	.											ELL2,NS,carcinoma,-1,1	ELL2	63	1	0			c.T1077G						PASS	.	A		2118,2282		532,1054,614	85.0	105.0	99.0		1077	-6.7	0.0	5	dbSNP_107	99	2233,6363		292,1649,2357	no	coding-synonymous	ELL2	NM_012081.5		824,2703,2971	CC,CA,AA		25.9772,48.1364,33.4795		359/641	95234392	4351,8645	2200	4298	6498	SO:0001819	synonymous_variant	22936	exon8			TGCAGCAGATTTT	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.1077T>G	5.37:g.95234392A>C		Somatic	408	0	0		WXS	Illumina HiSeq	Phase_I	299	297	0.993311	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			A|0.674;C|0.326	0.326	strong		0.498	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
RBM23	55147	hgsc.bcm.edu	37	14	23371268	23371268	+	Silent	SNP	A	A	G	rs56708790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23371268A>G	ENST00000359890.3	-	12	1362	c.1167T>C	c.(1165-1167)gcT>gcC	p.A389A	RBM23_ENST00000346528.5_Silent_p.A355A|RBM23_ENST00000399922.2_Silent_p.A373A|RBM23_ENST00000542016.2_Silent_p.A219A|RBM23_ENST00000555209.1_Silent_p.A139A	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23	389	Ala-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)		cggcggcggcagcagcagcag	0.552													A|||	195	0.0389377	0.0053	0.0778	5008	,	,		16698	0.0179		0.0676	False		,,,				2504	0.0491				p.A389A		Atlas-SNP	.											RBM23,NS,carcinoma,0,3	RBM23	44	3	0			c.T1167C						PASS	.	A	,,	54,3898		1,52,1923	34.0	35.0	35.0		1167,1065,1119	-2.4	0.4	14	dbSNP_129	35	529,7793		7,515,3639	yes	coding-synonymous,coding-synonymous,coding-synonymous	RBM23	NM_001077351.1,NM_001077352.1,NM_018107.4	,,	8,567,5562	GG,GA,AA		6.3566,1.3664,4.7499	,,	389/440,355/406,373/424	23371268	583,11691	1976	4161	6137	SO:0001819	synonymous_variant	55147	exon12			GGCGGCAGCAGCA	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.1167T>C	14.37:g.23371268A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	47	11	0.234043	NM_001077351	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Silent	SNP	ENST00000359890.3	37	CCDS41921.1	252	0.11538461538461539	8	0.016260162601626018	50	0.13812154696132597	73	0.12762237762237763	121	0.15963060686015831	A	0.768	-0.766868	0.02974	0.013664	0.063566	ENSG00000100461	ENST00000553884	.	.	.	3.36	-2.38	0.06622	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.53005	D	0.999961	.	.	.	.	.	.	T	0.04294	-1.0962	4	.	.	.	.	8.3885	0.32514	0.37:0.0:0.63:0.0	rs56708790;rs61730800	.	.	.	R	164	.	.	C	-	1	0	RBM23	22441108	0.115000	0.22152	0.443000	0.26883	0.195000	0.23768	0.047000	0.14056	-0.453000	0.07076	0.402000	0.26972	TGC	A|0.887;G|0.113	0.113	strong		0.552	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		
PPP1R3C	5507	hgsc.bcm.edu	37	10	93390158	93390158	+	Silent	SNP	C	C	T	rs35530640	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:93390158C>T	ENST00000238994.5	-	2	564	c.480G>A	c.(478-480)gaG>gaA	p.E160E		NM_005398.5	NP_005389.1			protein phosphatase 1, regulatory subunit 3C											breast(1)|endometrium(1)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(1)	12		Colorectal(252;0.235)				ACGAGCAGTTCTCCAGACAGA	0.418													C|||	49	0.00978435	0.0015	0.0144	5008	,	,		21324	0.0		0.0298	False		,,,				2504	0.0072				p.E160E		Atlas-SNP	.											.	PPP1R3C	30	.	0			c.G480A						PASS	.	C		36,4370	40.0+/-72.8	0,36,2167	91.0	89.0	90.0		480	4.9	1.0	10	dbSNP_126	90	321,8279	113.7+/-173.7	7,307,3986	no	coding-synonymous	PPP1R3C	NM_005398.4		7,343,6153	TT,TC,CC		3.7326,0.8171,2.7449		160/318	93390158	357,12649	2203	4300	6503	SO:0001819	synonymous_variant	5507	exon2			GCAGTTCTCCAGA	Y18207	CCDS7416.1	10q23-q24	2012-04-17	2011-10-04	2001-08-01	ENSG00000119938	ENSG00000119938		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9293	protein-coding gene	gene with protein product	"""Phosphatase 1, regulatory inhibitor subunit 5"", ""protein targeting to glycogen"""	602999	"""protein phosphatase 1, regulatory (inhibitor) subunit 3C"""	PPP1R5		8985175	Standard	NM_005398		Approved	PTG	uc001kho.3	Q9UQK1	OTTHUMG00000018745	ENST00000238994.5:c.480G>A	10.37:g.93390158C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	32	27	0.84375	NM_005398		Silent	SNP	ENST00000238994.5	37	CCDS7416.1																																																																																			C|0.974;T|0.026	0.026	strong		0.418	PPP1R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049372.1	NM_005398	
VPS13C	54832	hgsc.bcm.edu	37	15	62254989	62254989	+	Missense_Mutation	SNP	T	T	C	rs3784635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:62254989T>C	ENST00000261517.5	-	33	3467	c.3394A>G	c.(3394-3396)Att>Gtt	p.I1132V	VPS13C_ENST00000249837.3_Missense_Mutation_p.I1089V|VPS13C_ENST00000395898.3_Missense_Mutation_p.I1089V|VPS13C_ENST00000395896.4_Missense_Mutation_p.I1132V	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						GTGACAATAATATTTTCTAGT	0.338													T|||	485	0.096845	0.0038	0.196	5008	,	,		13637	0.2054		0.0298	False		,,,				2504	0.1094				p.I1132V		Atlas-SNP	.											.	VPS13C	506	.	0			c.A3394G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	36,4370	39.2+/-71.8	1,34,2168	74.0	76.0	75.0		3394,3265,3265,3394	3.5	1.0	15	dbSNP_107	75	213,8387	89.2+/-151.4	3,207,4090	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	29,29,29,29	4,241,6258	CC,CT,TT		2.4767,0.8171,1.9145	benign,benign,benign,benign	1132/3629,1089/3711,1089/3586,1132/3754	62254989	249,12757	2203	4300	6503	SO:0001583	missense	54832	exon33			CAATAATATTTTC	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.3394A>G	15.37:g.62254989T>C	ENSP00000261517:p.Ile1132Val	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	130	29	0.223077	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	190	0.08699633699633699	2	0.0040650406504065045	43	0.11878453038674033	116	0.20279720279720279	29	0.03825857519788918	T	9.239	1.037820	0.19669	0.008171	0.024767	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.42900	0.96;0.96;0.96	5.8	3.47	0.39725	.	0.221564	0.38897	N	0.001527	T	0.00039	0.0001	M	0.77486	2.375	0.31812	P	0.627054	B;B;B;B	0.32365	0.124;0.367;0.124;0.048	B;B;B;B	0.28232	0.038;0.087;0.065;0.025	T	0.11446	-1.0587	9	0.20519	T	0.43	.	6.7067	0.23254	0.1147:0.1287:0.0:0.7566	rs3784635;rs17304003;rs52829205;rs57619309;rs3784635	1089;1132;1089;1132	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	V	1089;1132;1132;1132	ENSP00000249837:I1089V;ENSP00000261517:I1132V;ENSP00000379233:I1132V	ENSP00000249837:I1089V	I	-	1	0	VPS13C	60042281	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	1.378000	0.34328	0.444000	0.26612	-0.374000	0.07098	ATT	T|0.948;C|0.052	0.052	strong		0.338	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
GPA33	10223	hgsc.bcm.edu	37	1	167042762	167042762	+	Missense_Mutation	SNP	C	C	T	rs2274531	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:167042762C>T	ENST00000367868.3	-	2	401	c.58G>A	c.(58-60)Gat>Aat	p.D20N	GPA33_ENST00000527955.1_5'UTR	NM_005814.1	NP_005805.1	Q99795	GPA33_HUMAN	glycoprotein A33 (transmembrane)	20			D -> N (in dbSNP:rs2274531).			extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(4)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						GAGATGGCATCGACGGTCACC	0.562													C|||	407	0.08127	0.0333	0.062	5008	,	,		20041	0.1726		0.0944	False		,,,				2504	0.0521				p.D20N		Atlas-SNP	.											.	GPA33	50	.	0			c.G58A						PASS	.	C	ASN/ASP	238,4168	140.0+/-175.5	6,226,1971	76.0	62.0	66.0		58	-10.5	0.0	1	dbSNP_100	66	954,7646	209.7+/-250.8	46,862,3392	yes	missense	GPA33	NM_005814.1	23	52,1088,5363	TT,TC,CC		11.093,5.4017,9.165	benign	20/320	167042762	1192,11814	2203	4300	6503	SO:0001583	missense	10223	exon2			TGGCATCGACGGT	U79725	CCDS1258.1	1q24.1	2013-01-29			ENSG00000143167	ENSG00000143167		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	4445	protein-coding gene	gene with protein product		602171				9012807, 9245713	Standard	NM_005814		Approved	A33	uc001gea.1	Q99795	OTTHUMG00000034435	ENST00000367868.3:c.58G>A	1.37:g.167042762C>T	ENSP00000356842:p.Asp20Asn	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_005814	Q5VZP6	Missense_Mutation	SNP	ENST00000367868.3	37	CCDS1258.1	207	0.09478021978021978	18	0.036585365853658534	27	0.07458563535911603	91	0.1590909090909091	71	0.09366754617414248	C	8.915	0.959717	0.18507	0.054017	0.11093	ENSG00000143167	ENST00000367868	T	0.75589	-0.95	5.26	-10.5	0.00291	Immunoglobulin-like (1);	1.517130	0.03249	N	0.181585	T	0.17408	0.0418	N	0.05124	-0.11	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13150	-1.0520	9	0.17832	T	0.49	.	2.9601	0.05889	0.1411:0.3526:0.3433:0.163	rs2274531;rs52798750;rs58568129;rs2274531	20	Q99795	GPA33_HUMAN	N	20	ENSP00000356842:D20N	ENSP00000356842:D20N	D	-	1	0	GPA33	165309386	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.283000	0.01155	-3.393000	0.00172	-0.797000	0.03246	GAT	C|0.905;T|0.095	0.095	strong		0.562	GPA33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083245.1	NM_005814	
OR6F1	343169	hgsc.bcm.edu	37	1	247875314	247875314	+	Silent	SNP	C	C	A	rs41268353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247875314C>A	ENST00000302084.2	-	1	791	c.744G>T	c.(742-744)gtG>gtT	p.V248V	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005286.1	NP_001005286.1	Q8NGZ6	OR6F1_HUMAN	olfactory receptor, family 6, subfamily F, member 1	248						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)			ACCAAATGAGCACCACGGTGA	0.532													C|||	168	0.0335463	0.0045	0.0634	5008	,	,		21606	0.002		0.0736	False		,,,				2504	0.0429				p.V248V		Atlas-SNP	.											.	OR6F1	88	.	0			c.G744T						PASS	.	C		57,4349	55.5+/-91.7	1,55,2147	109.0	100.0	103.0		744	0.3	0.1	1	dbSNP_127	103	618,7982	161.6+/-214.5	26,566,3708	no	coding-synonymous	OR6F1	NM_001005286.1		27,621,5855	AA,AC,CC		7.186,1.2937,5.1899		248/309	247875314	675,12331	2203	4300	6503	SO:0001819	synonymous_variant	343169	exon1			AATGAGCACCACG	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.744G>T	1.37:g.247875314C>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	77	0.611111	NM_001005286	B2RNV6|Q6IF02|Q96R39	Silent	SNP	ENST00000302084.2	37	CCDS31095.1																																																																																			C|0.948;A|0.052	0.052	strong		0.532	OR6F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096870.1	NM_001005286	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964000	88964000	+	Silent	SNP	C	C	T	rs801839	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:88964000C>T	ENST00000333190.4	+	4	2313	c.1704C>T	c.(1702-1704)ttC>ttT	p.F568F		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	568							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AATATACTTTCAGTGCAAATG	0.353										HNSCC(36;0.09)			T|||	2553	0.509784	0.7345	0.3401	5008	,	,		19433	0.7153		0.2336	False		,,,				2504	0.3988				p.F568F		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C1704T						PASS	.	T		2816,1566		895,1026,270	42.0	45.0	44.0		1704	4.3	0.5	7	dbSNP_86	44	2011,6581		238,1535,2523	no	coding-synonymous	ZNF804B	NM_181646.2		1133,2561,2793	TT,TC,CC		23.4055,35.7371,37.2052		568/1350	88964000	4827,8147	2191	4296	6487	SO:0001819	synonymous_variant	219578	exon4			TACTTTCAGTGCA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1704C>T	7.37:g.88964000C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	101	62	0.613861	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																			C|0.493;T|0.507	0.507	strong		0.353	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
CPEB2	132864	hgsc.bcm.edu	37	4	15005641	15005641	+	Silent	SNP	C	C	T	rs142927413	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:15005641C>T	ENST00000507071.1	+	1	120	c.33C>T	c.(31-33)ggC>ggT	p.G11G	CPEB2_ENST00000538197.1_Silent_p.G448G|RP11-665G4.1_ENST00000513384.1_RNA|CPEB2_ENST00000541112.1_Silent_p.G448G|CPEB2_ENST00000259997.5_Silent_p.G11G|CPEB2_ENST00000382401.3_Silent_p.G11G|CPEB2_ENST00000442003.2_Silent_p.G448G|RP11-665G4.1_ENST00000502344.1_RNA|CPEB2_ENST00000345451.3_Silent_p.G11G|CPEB2_ENST00000382395.3_Silent_p.G11G			Q7Z5Q1	CPEB2_HUMAN	cytoplasmic polyadenylation element binding protein 2	11	Pro-rich.				cellular response to arsenic-containing substance (GO:0071243)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to oxidative stress (GO:0034599)|negative regulation of cytoplasmic translation (GO:2000766)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of GTPase activity (GO:0034260)	cytoplasm (GO:0005737)|messenger ribonucleoprotein complex (GO:1990124)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|ribosome binding (GO:0043022)|translation repressor activity, nucleic acid binding (GO:0000900)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|skin(3)	14						CAGAGAACGGCTTCTACCCCG	0.741													c|||	249	0.0497204	0.0227	0.0144	5008	,	,		4124	0.0268		0.0328	False		,,,				2504	0.1524				p.G448G		Atlas-SNP	.											.	CPEB2	77	.	0			c.C1344T						PASS	.		,,,,,	62,3556		1,60,1748	9.0	10.0	10.0		1344,1344,1344,1344,1344,1344	1.0	1.0	4	dbSNP_134	10	193,7011		2,189,3411	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPEB2	NM_001177381.1,NM_001177382.1,NM_001177383.1,NM_001177384.1,NM_182485.2,NM_182646.2	,,,,,	3,249,5159	TT,TC,CC		2.6791,1.7137,2.3563	,,,,,	448/1008,448/1035,448/1005,448/1000,448/1027,448/997	15005641	255,10567	1809	3602	5411	SO:0001819	synonymous_variant	132864	exon1			GAACGGCTTCTAC	AY247744	CCDS56325.1, CCDS56326.1	4p15.33	2013-02-12			ENSG00000137449	ENSG00000137449		"""RNA binding motif (RRM) containing"""	21745	protein-coding gene	gene with protein product		610605				12672660	Standard	NM_182485		Approved		uc003gnk.2	Q7Z5Q1	OTTHUMG00000090669	ENST00000507071.1:c.33C>T	4.37:g.15005641C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_001177381	E7EPM3|F5H160|Q3B8N6|Q3MI89|Q3MI90|Q3MI92|Q7Z5Q0	Silent	SNP	ENST00000507071.1	37																																																																																				C|0.977;T|0.023	0.023	strong		0.741	CPEB2-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000207349.2	XM_059607	
DHRS12	79758	hgsc.bcm.edu	37	13	52343391	52343391	+	Missense_Mutation	SNP	C	C	T	rs10676	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:52343391C>T	ENST00000444610.2	-	9	758	c.745G>A	c.(745-747)Ggg>Agg	p.G249R	DHRS12_ENST00000490949.1_5'Flank|DHRS12_ENST00000218981.1_Missense_Mutation_p.G200R	NM_001270424.1	NP_001257353.1	A0PJE2	DHR12_HUMAN	dehydrogenase/reductase (SDR family) member 12	249							oxidoreductase activity (GO:0016491)			cervix(1)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	7		Breast(56;0.00173)|Prostate(109;0.00899)|Lung NSC(96;0.0199)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.81e-08)		AGGCGGTCCCCGAACCTGGCG	0.662													T|||	646	0.128994	0.23	0.219	5008	,	,		13794	0.001		0.0596	False		,,,				2504	0.1319				p.G249R		Atlas-SNP	.											.	DHRS12	28	.	0			c.G745A						PASS	.	T	ARG/GLY	858,3526		85,688,1419	12.0	12.0	12.0		598	-4.2	0.0	13	dbSNP_52	12	640,7946		26,588,3679	yes	missense	DHRS12	NM_024705.1	125	111,1276,5098	TT,TC,CC		7.454,19.5712,11.5497		200/243	52343391	1498,11472	2192	4293	6485	SO:0001583	missense	79758	exon9			GGTCCCCGAACCT	AK023701	CCDS9430.1, CCDS31976.1, CCDS58292.1	13q14.3	2013-10-11			ENSG00000102796	ENSG00000102796		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	25832	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 40C, member 1"""					19027726	Standard	NM_001031719		Approved	FLJ13639, SDR40C1	uc001vfq.4	A0PJE2	OTTHUMG00000016952	ENST00000444610.2:c.745G>A	13.37:g.52343391C>T	ENSP00000411565:p.Gly249Arg	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_001270424	Q96GB2|Q9H8H1	Missense_Mutation	SNP	ENST00000444610.2	37	CCDS58292.1	217	0.09935897435897435	104	0.21138211382113822	68	0.1878453038674033	0	0.0	45	0.059366754617414245	T	5.572	0.290416	0.10567	0.195712	0.07454	ENSG00000102796	ENST00000444610;ENST00000218981	D;D	0.90261	-2.02;-2.64	2.99	-4.22	0.03800	NAD(P)-binding domain (1);	.	.	.	.	T	0.00178	0.0005	N	0.11870	0.19	0.80722	P	0.0	B;B	0.16396	0.017;0.001	B;B	0.15052	0.012;0.001	T	0.03863	-1.0997	8	0.23891	T	0.37	.	6.9036	0.24297	0.0:0.5162:0.1436:0.3402	rs10676;rs1052630;rs3193083;rs17342527;rs17350152;rs10676	200;249	A0PJE2-2;A0PJE2	.;DHR12_HUMAN	R	249;200	ENSP00000411565:G249R;ENSP00000218981:G200R	ENSP00000218981:G200R	G	-	1	0	DHRS12	51241392	0.475000	0.25894	0.000000	0.03702	0.001000	0.01503	0.076000	0.14712	-1.374000	0.02131	-1.322000	0.01289	GGG	C|0.885;T|0.115	0.115	strong		0.662	DHRS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045036.3	NM_024705	
NES	10763	hgsc.bcm.edu	37	1	156640308	156640308	+	Silent	SNP	C	C	T	rs3748571	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156640308C>T	ENST00000368223.3	-	4	3804	c.3672G>A	c.(3670-3672)acG>acA	p.T1224T		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1224	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)					TCGGGGTGTACGTTGGGCTGG	0.652													C|||	1123	0.224241	0.0159	0.2882	5008	,	,		17214	0.2946		0.3032	False		,,,				2504	0.3067				p.T1224T		Atlas-SNP	.											NES,rectum,carcinoma,0,1	NES	196	1	0			c.G3672A						scavenged	.	C		278,4128	154.8+/-188.1	8,262,1933	79.0	78.0	79.0		3672	-6.6	0.0	1	dbSNP_107	79	2455,6145	399.5+/-346.5	350,1755,2195	no	coding-synonymous	NES	NM_006617.1		358,2017,4128	TT,TC,CC		28.5465,6.3096,21.0134		1224/1622	156640308	2733,10273	2203	4300	6503	SO:0001819	synonymous_variant	10763	exon4			GGTGTACGTTGGG	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.3672G>A	1.37:g.156640308C>T		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	135	40	0.296296	NM_006617	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	37	CCDS1151.1																																																																																			C|0.788;T|0.212	0.212	strong		0.652	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
CYP2A6	1548	hgsc.bcm.edu	37	19	41354533	41354533	+	Missense_Mutation	SNP	A	A	T	rs1801272	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	110	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	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	
EXOC1	55763	hgsc.bcm.edu	37	4	56737278	56737278	+	Missense_Mutation	SNP	C	C	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:56737278C>G	ENST00000381295.2	+	7	1191	c.843C>G	c.(841-843)gaC>gaG	p.D281E	EXOC1_ENST00000346134.7_Missense_Mutation_p.D281E|EXOC1_ENST00000349598.6_Missense_Mutation_p.D281E	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	281					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					ACCACATGGACTTGGCCAAAG	0.448																																					p.D281E		Atlas-SNP	.											.	EXOC1	103	.	0			c.C843G						PASS	.						98.0	86.0	90.0					4																	56737278		2203	4300	6503	SO:0001583	missense	55763	exon7			CATGGACTTGGCC	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"""SEC3-like 1 (S. cerevisiae)"""	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.843C>G	4.37:g.56737278C>G	ENSP00000370695:p.Asp281Glu	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	158	77	0.487342	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	37	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040304	0.75732	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.97	4.23	0.50019	.	0.043036	0.85682	D	0.000000	T	0.63510	0.2517	L	0.58669	1.825	0.58432	D	0.999993	D;P	0.76494	0.999;0.95	D;P	0.80764	0.994;0.836	T	0.59669	-0.7411	9	0.11182	T	0.66	.	6.0347	0.19699	0.0:0.7065:0.0:0.2935	.	281;281	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	E	281	.	ENSP00000326514:D281E	D	+	3	2	EXOC1	56432035	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.604000	0.36804	2.833000	0.97629	0.585000	0.79938	GAC	.	.	none		0.448	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261	
PLEKHO2	80301	hgsc.bcm.edu	37	15	65158047	65158047	+	Missense_Mutation	SNP	G	G	A	rs77456635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65158047G>A	ENST00000323544.4	+	6	1561	c.1433G>A	c.(1432-1434)cGg>cAg	p.R478Q	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	478										NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						AGGGAGAAGCGGAAGGAGCTG	0.607													G|||	49	0.00978435	0.0008	0.0115	5008	,	,		19769	0.0		0.0239	False		,,,				2504	0.0164				p.R478Q		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.G1433A						PASS	.	G	GLN/ARG,GLN/ARG	33,4371	36.0+/-67.5	0,33,2169	30.0	31.0	31.0		1283,1433	-0.6	1.0	15	dbSNP_132	31	242,8356	95.2+/-157.0	5,232,4062	yes	missense,missense	PLEKHO2	NM_001195059.1,NM_025201.4	43,43	5,265,6231	AA,AG,GG		2.8146,0.7493,2.1151	benign,benign	428/441,478/491	65158047	275,12727	2202	4299	6501	SO:0001583	missense	80301	exon6			AGAAGCGGAAGGA	AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"""Pleckstrin homology (PH) domain containing"""	30026	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family Q member 1"""	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.1433G>A	15.37:g.65158047G>A	ENSP00000326706:p.Arg478Gln	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	17	13	0.764706	NM_025201	Q7L4H4|Q8WYS8	Missense_Mutation	SNP	ENST00000323544.4	37	CCDS10196.1	27	0.012362637362637362	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	21	0.027704485488126648	G	12.58	1.980799	0.34942	0.007493	0.028146	ENSG00000241839	ENST00000323544	T	0.31510	1.49	5.13	-0.638	0.11500	.	0.335637	0.24633	N	0.036878	T	0.04907	0.0132	N	0.19112	0.55	0.28088	N	0.931902	B;B	0.23490	0.086;0.026	B;B	0.16722	0.016;0.004	T	0.22068	-1.0227	10	0.17832	T	0.49	.	8.772	0.34737	0.5539:0.0:0.4461:0.0	.	428;478	Q8TD55-2;Q8TD55	.;PKHO2_HUMAN	Q	478	ENSP00000326706:R478Q	ENSP00000326706:R478Q	R	+	2	0	PLEKHO2	62945100	0.998000	0.40836	0.993000	0.49108	0.988000	0.76386	0.377000	0.20552	-0.025000	0.13918	-0.275000	0.10095	CGG	G|0.982;A|0.018	0.018	strong		0.607	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201	
SVIL	6840	hgsc.bcm.edu	37	10	29747417	29747417	+	Silent	SNP	C	C	T	rs1887465	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:29747417C>T	ENST00000355867.4	-	37	7256	c.6504G>A	c.(6502-6504)ccG>ccA	p.P2168P	PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000535393.1_Silent_p.P1082P|PTCHD3P1_ENST00000446807.1_RNA|SVIL_ENST00000375400.3_Silent_p.P1742P|PTCHD3P1_ENST00000414457.1_RNA|SVIL_ENST00000375398.2_Silent_p.P2168P|PTCHD3P1_ENST00000438202.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000430295.1_RNA|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000445521.1_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	90	0	0		WXS	Illumina HiSeq	Phase_I	56	8	0.142857	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		
EFEMP1	2202	hgsc.bcm.edu	37	2	56144930	56144930	+	Silent	SNP	T	T	C	rs14282	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:56144930T>C	ENST00000394555.2	-	4	822	c.387A>G	c.(385-387)gaA>gaG	p.E129E	EFEMP1_ENST00000394554.1_Silent_p.E129E|EFEMP1_ENST00000355426.3_Silent_p.E129E|EFEMP1_ENST00000424836.2_Silent_p.E71E	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	129					epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CAGTCTGCATTTCAGGGCCTG	0.612													T|||	97	0.019369	0.0008	0.0216	5008	,	,		16856	0.001		0.0239	False		,,,				2504	0.0573				p.E129E	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.A387G						PASS	.	T	,	33,4373	37.6+/-69.7	0,33,2170	56.0	55.0	55.0		387,387	2.2	1.0	2	dbSNP_52	55	231,8369	95.2+/-157.0	3,225,4072	yes	coding-synonymous,coding-synonymous	EFEMP1	NM_001039348.2,NM_001039349.2	,	3,258,6242	CC,CT,TT		2.686,0.749,2.0298	,	129/494,129/494	56144930	264,12742	2203	4300	6503	SO:0001819	synonymous_variant	2202	exon4			CTGCATTTCAGGG	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.387A>G	2.37:g.56144930T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Silent	SNP	ENST00000394555.2	37	CCDS1857.1																																																																																			T|0.979;C|0.021	0.021	strong		0.612	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2		
PLEKHM2	23207	hgsc.bcm.edu	37	1	16056364	16056364	+	Silent	SNP	G	G	A	rs3817269	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16056364G>A	ENST00000375799.3	+	14	2375	c.2148G>A	c.(2146-2148)acG>acA	p.T716T	PLEKHM2_ENST00000477849.1_3'UTR|PLEKHM2_ENST00000375793.2_Silent_p.T696T|RP11-288I21.1_ENST00000453804.1_RNA	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	716					Golgi organization (GO:0007030)	cytoplasm (GO:0005737)	kinesin binding (GO:0019894)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000259)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00057)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;9.18e-07)|COAD - Colon adenocarcinoma(227;4.5e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000133)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|STAD - Stomach adenocarcinoma(313;0.00774)|READ - Rectum adenocarcinoma(331;0.0657)		GCATCCTGACGGATGCCACCA	0.527													G|||	1536	0.306709	0.711	0.2565	5008	,	,		7266	0.0437		0.2087	False		,,,				2504	0.1677				p.T716T		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.G2148A						PASS	.	G		2435,1507		754,927,290	68.0	71.0	70.0		2148	-10.9	0.7	1	dbSNP_107	70	1907,6413		224,1459,2477	no	coding-synonymous	PLEKHM2	NM_015164.2		978,2386,2767	AA,AG,GG		22.9207,38.2293,35.4102		716/1020	16056364	4342,7920	1971	4160	6131	SO:0001819	synonymous_variant	23207	exon14			CCTGACGGATGCC	AB020649	CCDS44063.1	1p36.13	2013-01-10			ENSG00000116786	ENSG00000116786		"""Pleckstrin homology (PH) domain containing"""	29131	protein-coding gene	gene with protein product		609613				10048485	Standard	NM_015164		Approved	KIAA0842	uc010obo.2	Q8IWE5	OTTHUMG00000003062	ENST00000375799.3:c.2148G>A	1.37:g.16056364G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	42	9	0.214286	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	37	CCDS44063.1																																																																																			G|0.678;A|0.322	0.322	strong		0.527	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164	
TTLL6	284076	hgsc.bcm.edu	37	17	46877017	46877017	+	Silent	SNP	C	C	T	rs201225285	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46877017C>T	ENST00000393382.3	-	6	858	c.717G>A	c.(715-717)gtG>gtA	p.V239V		NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TGATTTCTTTCACTGTCCGGG	0.428																																					p.V239V		Atlas-SNP	.											.	TTLL6	113	.	0			c.G717A						PASS	.						173.0	141.0	151.0					17																	46877017		692	1591	2283	SO:0001819	synonymous_variant	284076	exon6			TTCTTTCACTGTC	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.717G>A	17.37:g.46877017C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_001130918		Silent	SNP	ENST00000393382.3	37	CCDS45724.1																																																																																			C|0.996;T|0.004	0.004	strong		0.428	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
COQ9	57017	hgsc.bcm.edu	37	16	57484980	57484980	+	Silent	SNP	G	G	A	rs223864	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57484980G>A	ENST00000262507.6	+	2	171	c.102G>A	c.(100-102)ccG>ccA	p.P34P	COQ9_ENST00000567384.1_3'UTR|COQ9_ENST00000567933.1_Silent_p.P34P|COQ9_ENST00000567072.1_Silent_p.P34P	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN	coenzyme Q9	34					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						CCCTGGTGCCGCGTGCCTTCC	0.547													G|||	102	0.0203674	0.0227	0.0216	5008	,	,		18047	0.002		0.0398	False		,,,				2504	0.0153				p.P34P		Atlas-SNP	.											.	COQ9	30	.	0			c.G102A						PASS	.	G		111,4285	86.3+/-125.0	1,109,2088	60.0	52.0	55.0		102	-1.9	0.3	16	dbSNP_79	55	299,8301	108.4+/-169.1	5,289,4006	no	coding-synonymous	COQ9	NM_020312.3		6,398,6094	AA,AG,GG		3.4767,2.525,3.1548		34/319	57484980	410,12586	2198	4300	6498	SO:0001819	synonymous_variant	57017	exon2			GGTGCCGCGTGCC	BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682			25302	protein-coding gene	gene with protein product		612837	"""chromosome 16 open reading frame 49"", ""coenzyme Q9 homolog (yeast)"", ""coenzyme Q9 homolog (S. cerevisiae)"""	C16orf49		19375058	Standard	NM_020312		Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000262507.6:c.102G>A	16.37:g.57484980G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	98	86	0.877551	NM_020312	A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	Silent	SNP	ENST00000262507.6	37	CCDS32459.1																																																																																			G|0.973;A|0.027	0.027	strong		0.547	COQ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432598.3	NM_020312	
OXR1	55074	hgsc.bcm.edu	37	8	107754473	107754473	+	Silent	SNP	G	G	A	rs1681904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:107754473G>A	ENST00000442977.2	+	14	2442	c.2343G>A	c.(2341-2343)gaG>gaA	p.E781E	OXR1_ENST00000449762.2_Silent_p.E123E|OXR1_ENST00000517566.2_Silent_p.E780E|OXR1_ENST00000521592.1_Silent_p.E26E|OXR1_ENST00000531443.1_Silent_p.E753E|OXR1_ENST00000445937.1_Silent_p.E753E|OXR1_ENST00000312046.6_Silent_p.E746E|OXR1_ENST00000452423.2_Silent_p.E201E|OXR1_ENST00000297447.6_Silent_p.E150E	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	781	TLD.				adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TAGCATCTGAGCCACTGAAAG	0.343													G|||	1911	0.381589	0.2057	0.5216	5008	,	,		16724	0.3492		0.4433	False		,,,				2504	0.4898				p.E781E		Atlas-SNP	.											.	OXR1	190	.	0			c.G2343A						PASS	.	G	,,,,,	1065,3341	388.4+/-326.9	123,819,1261	194.0	180.0	185.0		2343,2340,450,369,2259,2238	4.3	1.0	8	dbSNP_89	185	3733,4867	530.5+/-381.8	804,2125,1371	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OXR1	NM_001198532.1,NM_001198533.1,NM_001198534.1,NM_001198535.1,NM_018002.3,NM_181354.4	,,,,,	927,2944,2632	AA,AG,GG		43.407,24.1716,36.8907	,,,,,	781/875,780/874,150/244,123/217,753/847,746/840	107754473	4798,8208	2203	4300	6503	SO:0001819	synonymous_variant	55074	exon14			ATCTGAGCCACTG	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.2343G>A	8.37:g.107754473G>A		Somatic	230	2	0.00869565		WXS	Illumina HiSeq	Phase_I	289	287	0.99308	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	37	CCDS56548.1	838	0.3836996336996337	100	0.2032520325203252	181	0.5	213	0.3723776223776224	344	0.45382585751978893	G	8.497	0.863313	0.17250	0.241716	0.43407	ENSG00000164830	ENST00000519415	.	.	.	5.46	4.35	0.52113	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.51834	-0.8655	3	.	.	.	-12.3073	6.9569	0.24576	0.2445:0.0:0.7555:0.0	rs1681904;rs11538335;rs17351853;rs1681904	.	.	.	N	425	.	.	S	+	2	0	OXR1	107823649	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.822000	0.39052	2.715000	0.92844	0.563000	0.77884	AGC	G|0.627;A|0.373	0.373	strong		0.343	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	
HPS5	11234	hgsc.bcm.edu	37	11	18303533	18303533	+	Missense_Mutation	SNP	G	G	A	rs61884288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18303533G>A	ENST00000349215.3	-	22	3570	c.3293C>T	c.(3292-3294)aCc>aTc	p.T1098I	HPS5_ENST00000396253.3_Missense_Mutation_p.T984I|HPS5_ENST00000537258.1_Missense_Mutation_p.T205I|HPS5_ENST00000352460.3_5'UTR|HPS5_ENST00000438420.2_Missense_Mutation_p.T984I	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	1098			T -> I (in HPS5; dbSNP:rs61884288). {ECO:0000269|PubMed:15296495}.		blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						GATATCGCAGGTTCTGGTAAA	0.502									Hermansky-Pudlak syndrome				G|||	52	0.0103834	0.0015	0.0086	5008	,	,		23133	0.0		0.0408	False		,,,				2504	0.0031				p.T1098I		Atlas-SNP	.											HPS5,NS,meningioma,0,1	HPS5	70	1	0			c.C3293T	GRCh37	CM045580	HPS5	M	rs61884288	PASS	.	G	ILE/THR,ILE/THR,ILE/THR	34,4364	36.8+/-68.6	0,34,2165	131.0	126.0	128.0		2951,3293,2951	3.9	1.0	11	dbSNP_129	128	320,8266	113.5+/-173.5	3,314,3976	yes	missense,missense,missense	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	89,89,89	3,348,6141	AA,AG,GG		3.727,0.7731,2.7264	benign,benign,benign	984/1016,1098/1130,984/1016	18303533	354,12630	2199	4293	6492	SO:0001583	missense	11234	exon22	Familial Cancer Database	HPS, HPS1-8	TCGCAGGTTCTGG	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.3293C>T	11.37:g.18303533G>A	ENSP00000265967:p.Thr1098Ile	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	185	73	0.394595	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	34	0.015567765567765568	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	29	0.03825857519788918	G	11.52	1.662197	0.29515	0.007731	0.03727	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000537258	T;T;T	0.55930	0.49;0.49;0.53	4.82	3.91	0.45181	.	0.188252	0.45361	N	0.000363	T	0.08714	0.0216	N	0.22421	0.69	0.80722	D	1	P	0.34615	0.459	B	0.30029	0.11	T	0.03103	-1.1072	10	0.36615	T	0.2	.	5.5833	0.17262	0.3361:0.0:0.6639:0.0	rs61884288	1098	Q9UPZ3	HPS5_HUMAN	I	984;984;1098;205	ENSP00000379552:T984I;ENSP00000399590:T984I;ENSP00000265967:T1098I	ENSP00000265967:T1098I	T	-	2	0	HPS5	18260109	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	4.115000	0.57865	1.245000	0.43885	0.650000	0.86243	ACC	G|0.975;A|0.025	0.025	strong		0.502	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21790040	21790040	+	Missense_Mutation	SNP	G	G	T	rs10151259	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21790040G>T	ENST00000400017.2	+	13	1639	c.1639G>T	c.(1639-1641)Gct>Tct	p.A547S	RPGRIP1_ENST00000556336.1_Missense_Mutation_p.A520S|RPGRIP1_ENST00000307974.4_5'Flank|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.A520S|RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000382933.4_Missense_Mutation_p.A189S|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.A547S	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	547			A -> S (in CORD13; dbSNP:rs10151259). {ECO:0000269|PubMed:10958648, ECO:0000269|PubMed:12920076}.		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)		GATGACAAAAGCTGACAATGA	0.393													G|||	838	0.167332	0.2315	0.1412	5008	,	,		20902	0.004		0.2366	False		,,,				2504	0.1963				p.A547S		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.G1639T	GRCh37	CM032029	RPGRIP1	M	rs10151259	PASS	.	G	SER/ALA	775,3007		86,603,1202	80.0	76.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1639	3.0	1.0	14	dbSNP_119	77	2017,6207		230,1557,2325	yes	missense	RPGRIP1	NM_020366.3	99	316,2160,3527	TT,TG,GG		24.5258,20.4918,23.255	probably-damaging	547/1287	21790040	2792,9214	1891	4112	6003	SO:0001583	missense	57096	exon13			ACAAAAGCTGACA	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.1639G>T	14.37:g.21790040G>T	ENSP00000382895:p.Ala547Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	171	56	0.327485	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	352	0.16117216117216118	115	0.23373983739837398	55	0.15193370165745856	0	0.0	182	0.24010554089709762	G	13.80	2.344142	0.41498	0.204918	0.245258	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000555587;ENST00000554303	T;T;T;T;T;T;T	0.79554	-0.1;-0.86;-0.9;-0.9;-0.47;-1.22;-1.28	4.86	3.04	0.35103	.	0.320649	0.34223	N	0.004147	T	0.00073	0.0002	L	0.52266	1.64	0.09310	P	0.99999999479642	D;D;D;D	0.89917	1.0;0.97;1.0;1.0	D;P;D;D	0.91635	0.999;0.747;0.999;0.998	T	0.14117	-1.0484	9	0.29301	T	0.29	-9.0074	5.6994	0.17873	0.1672:0.0:0.6767:0.1561	rs61722408	22;189;163;547	G3V3I7;Q96KN7-4;Q96KN7-5;Q96KN7	.;.;.;RPGR1_HUMAN	S	520;520;547;547;189;22;20	ENSP00000450445:A520S;ENSP00000451219:A520S;ENSP00000382895:A547S;ENSP00000206660:A547S;ENSP00000372391:A189S;ENSP00000451262:A22S;ENSP00000450426:A20S	ENSP00000206660:A547S	A	+	1	0	RPGRIP1	20859880	0.990000	0.36364	0.991000	0.47740	0.402000	0.30811	0.774000	0.26675	0.777000	0.33496	-0.384000	0.06662	GCT	A|0.059;C|0.298	.	strong		0.393	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
FBN3	84467	hgsc.bcm.edu	37	19	8159362	8159362	+	Missense_Mutation	SNP	G	G	T	rs7245429	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	81	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	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	
EML4	27436	hgsc.bcm.edu	37	2	42515437	42515437	+	Missense_Mutation	SNP	A	A	G	rs28651764	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	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	
ATAD3A	55210	hgsc.bcm.edu	37	1	1455652	1455652	+	Missense_Mutation	SNP	G	G	T	rs2767471	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1455652G>T	ENST00000378755.5	+	6	884	c.790G>T	c.(790-792)Gcc>Tcc	p.A264S	ATAD3A_ENST00000378756.3_Missense_Mutation_p.A216S|ATAD3A_ENST00000536055.1_Missense_Mutation_p.A137S	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	264					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.A264S(4)		endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	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;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		CCTGAAGGCGGCCGAGCACCG	0.682																																					p.A264S		Atlas-SNP	.											ATAD3A,NS,carcinoma,0,4	ATAD3A	35	4	4	Substitution - Missense(4)	kidney(4)	c.G790T						scavenged	.						53.0	52.0	52.0					1																	1455652		2203	4300	6503	SO:0001583	missense	55210	exon6			AAGGCGGCCGAGC	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.790G>T	1.37:g.1455652G>T	ENSP00000368030:p.Ala264Ser	Somatic	345	2	0.0057971		WXS	Illumina HiSeq	Phase_I	142	30	0.211268	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Missense_Mutation	SNP	ENST00000378755.5	37	CCDS31.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	9.081|9.081	0.999324|0.999324	0.19121|0.19121	.|.	.|.	ENSG00000197785|ENSG00000197785	ENST00000378756;ENST00000378755;ENST00000536055;ENST00000429957|ENST00000339113	D;T;D|.	0.94457|.	-2.51;1.42;-3.43|.	4.43|4.43	3.44|3.44	0.39384|0.39384	ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523 (1);|.	0.054326|.	0.64402|.	D|.	0.000001|.	T|T	0.48333|0.48333	0.1494|0.1494	N|N	0.20766|0.20766	0.605|0.605	0.52501|0.52501	D|D	0.999956|0.999956	B;B|.	0.14805|.	0.0;0.011|.	B;B|.	0.18263|.	0.007;0.021|.	T|T	0.40997|0.40997	-0.9533|-0.9533	10|5	0.07990|.	T|.	0.79|.	.|.	13.2731|13.2731	0.60172|0.60172	0.0:0.0:0.8418:0.1582|0.0:0.0:0.8418:0.1582	rs2767471|rs2767471	216;264|.	D2K8Q1;Q9NVI7|.	.;ATD3A_HUMAN|.	S|V	216;264;137;98|201	ENSP00000368031:A216S;ENSP00000368030:A264S;ENSP00000439290:A137S|.	ENSP00000368030:A264S|.	A|G	+|+	1|2	0|0	ATAD3A|ATAD3A	1445515|1445515	1.000000|1.000000	0.71417|0.71417	0.501000|0.501000	0.27601|0.27601	0.170000|0.170000	0.22686|0.22686	7.461000|7.461000	0.80834|0.80834	2.162000|2.162000	0.67917|0.67917	0.561000|0.561000	0.74099|0.74099	GCC|GGC	.	.	weak		0.682	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
TP53TG5	27296	hgsc.bcm.edu	37	20	44005936	44005936	+	Missense_Mutation	SNP	C	C	T	rs2231616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44005936C>T	ENST00000372726.3	-	3	326	c.170G>A	c.(169-171)cGc>cAc	p.R57H	TP53TG5_ENST00000537995.1_Missense_Mutation_p.R41H|SYS1-DBNDD2_ENST00000452133.1_Intron|TP53TG5_ENST00000494455.1_5'UTR|SYS1-DBNDD2_ENST00000475242.1_Intron	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	57			R -> H (in dbSNP:rs2231616).		intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						TTGGATCCGGCGGTTTGAGCT	0.502													C|||	1008	0.201278	0.0696	0.2579	5008	,	,		18364	0.2897		0.1123	False		,,,				2504	0.3395				p.R57H		Atlas-SNP	.											.	TP53TG5	36	.	0			c.G170A						PASS	.	C	HIS/ARG	429,3977	208.8+/-229.8	25,379,1799	175.0	168.0	170.0		170	-2.1	0.0	20	dbSNP_98	170	1122,7478	233.2+/-266.6	69,984,3247	yes	missense	TP53TG5	NM_014477.2	29	94,1363,5046	TT,TC,CC		13.0465,9.7367,11.9253	possibly-damaging	57/291	44005936	1551,11455	2203	4300	6503	SO:0001583	missense	27296	exon3			ATCCGGCGGTTTG	AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 10"""	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.170G>A	20.37:g.44005936C>T	ENSP00000361811:p.Arg57His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	81	79	0.975309	NM_014477		Missense_Mutation	SNP	ENST00000372726.3	37	CCDS13352.1	338	0.15476190476190477	32	0.06504065040650407	73	0.20165745856353592	144	0.2517482517482518	89	0.11741424802110818	C	10.75	1.438782	0.25900	0.097367	0.130465	ENSG00000124251	ENST00000372726;ENST00000537995	T;T	0.14022	2.54;2.54	5.52	-2.06	0.07298	.	0.660669	0.14744	N	0.301018	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.22276	0.067	B	0.12837	0.008	T	0.42565	-0.9444	9	0.36615	T	0.2	-0.0354	9.6207	0.39719	0.0:0.4882:0.317:0.1948	rs2231616;rs3746590;rs57771799;rs2231616	57	Q9Y2B4	T53G5_HUMAN	H	57;41	ENSP00000361811:R57H;ENSP00000438374:R41H	ENSP00000361811:R57H	R	-	2	0	TP53TG5	43439350	0.015000	0.18098	0.007000	0.13788	0.771000	0.43674	-1.108000	0.03313	-0.161000	0.10983	-0.176000	0.13171	CGC	C|0.863;T|0.137	0.137	strong		0.502	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477	
SEC16A	9919	hgsc.bcm.edu	37	9	139370217	139370217	+	Silent	SNP	G	G	A	rs76562693	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139370217G>A	ENST00000371706.3	-	1	1350	c.1317C>T	c.(1315-1317)caC>caT	p.H439H	SEC16A_ENST00000431893.2_Silent_p.H439H|SEC16A_ENST00000290037.6_Silent_p.H439H|SEC16A_ENST00000313050.7_Silent_p.H617H			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	439					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		CCCCAACTAAGTGAGATTTTA	0.547													G|||	136	0.0271565	0.003	0.0447	5008	,	,		18314	0.0		0.0696	False		,,,				2504	0.0317				p.H617H		Atlas-SNP	.											SEC16A_NM_014866.1,NS,haematopoietic_neoplasm,0,2	SEC16A	249	2	0			c.C1851T						PASS	.	G		63,4083		0,63,2010	37.0	38.0	38.0		1851	1.2	0.3	9	dbSNP_132	38	592,7816		15,562,3627	yes	coding-synonymous	SEC16A	NM_014866.1		15,625,5637	AA,AG,GG		7.0409,1.5195,5.2175		617/2358	139370217	655,11899	2073	4204	6277	SO:0001819	synonymous_variant	9919	exon3			AACTAAGTGAGAT	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.1317C>T	9.37:g.139370217G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.965;A|0.035	0.035	strong		0.547	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
NF1	4763	hgsc.bcm.edu	37	17	29553485	29553485	+	Silent	SNP	G	G	A	rs2285892	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:29553485G>A	ENST00000358273.4	+	18	2417	c.2034G>A	c.(2032-2034)ccG>ccA	p.P678P	NF1_ENST00000356175.3_Silent_p.P678P	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	678			P -> L (in dbSNP:rs17881753). {ECO:0000269|Ref.7}.		actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.I679fs*21(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GAACCCCCCCGATTTGCCGAC	0.483			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			G|||	2488	0.496805	0.7428	0.4683	5008	,	,		17568	0.5258		0.2803	False		,,,				2504	0.3773				p.P678P		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	13	Whole gene deletion(8)|Unknown(4)|Insertion - Frameshift(1)	soft_tissue(7)|central_nervous_system(3)|autonomic_ganglia(2)|lung(1)	c.G2034A						PASS	.	G	,	2929,1477	677.5+/-403.4	983,963,257	56.0	63.0	61.0		2034,2034	-9.9	0.4	17	dbSNP_100	61	2486,6114	407.2+/-349.1	357,1772,2171	no	coding-synonymous,coding-synonymous	NF1	NM_000267.3,NM_001042492.2	,	1340,2735,2428	AA,AG,GG		28.907,33.5225,41.6346	,	678/2819,678/2840	29553485	5415,7591	2203	4300	6503	SO:0001819	synonymous_variant	4763	exon18	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CCCCCCGATTTGC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2034G>A	17.37:g.29553485G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_000267	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			G|0.568;A|0.432	0.432	strong		0.483	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
RALGPS2	55103	hgsc.bcm.edu	37	1	178861391	178861391	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:178861391C>T	ENST00000367635.3	+	15	1612	c.1274C>T	c.(1273-1275)cCg>cTg	p.P425L	RALGPS2_ENST00000367634.2_Intron|RALGPS2_ENST00000477383.1_Intron	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	425					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TCTCTCGGCCCGGTGACAAGA	0.418																																					p.P425L		Atlas-SNP	.											RALGPS2,NS,carcinoma,-1,1	RALGPS2	69	1	0			c.C1274T						scavenged	.						77.0	82.0	80.0					1																	178861391		2203	4300	6503	SO:0001583	missense	55103	exon15			TCGGCCCGGTGAC	AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.1274C>T	1.37:g.178861391C>T	ENSP00000356607:p.Pro425Leu	Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	498	5	0.0100402	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Missense_Mutation	SNP	ENST00000367635.3	37	CCDS1325.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.134580	0.77662	.	.	ENSG00000116191	ENST00000367635;ENST00000324778;ENST00000535251	T;T	0.24151	1.98;1.87	5.52	5.52	0.82312	.	0.127266	0.53938	D	0.000051	T	0.30198	0.0757	N	0.22421	0.69	0.80722	D	1	D	0.71674	0.998	P	0.51701	0.677	T	0.02676	-1.1125	10	0.51188	T	0.08	.	19.0251	0.92929	0.0:1.0:0.0:0.0	.	425	Q86X27	RGPS2_HUMAN	L	425;390;74	ENSP00000356607:P425L;ENSP00000313613:P390L	ENSP00000313613:P390L	P	+	2	0	RALGPS2	177128014	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.254000	0.78329	2.589000	0.87451	0.591000	0.81541	CCG	.	.	none		0.418	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663	
CYP2A6	1548	hgsc.bcm.edu	37	19	41356246	41356246	+	Missense_Mutation	SNP	C	C	T	rs28399435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41356246C>T	ENST00000301141.5	-	1	106	c.86G>A	c.(85-87)aGc>aAc	p.S29N	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	29			S -> N (in allele CYP2A6*14; dbSNP:rs28399435). {ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15618701, ECO:0000269|PubMed:2726448}.		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)	CTTCCCCTTGCTCTTCCTCTG	0.557													.|||	70	0.0139776	0.0023	0.0173	5008	,	,		17142	0.0		0.0328	False		,,,				2504	0.0225				p.S29N		Atlas-SNP	.											.	CYP2A6	69	.	0			c.G86A						PASS	.	C	ASN/SER	45,4361		2,41,2160	108.0	92.0	98.0		86	-3.7	0.0	19	dbSNP_125	98	350,8248		12,326,3961	no	missense	CYP2A6	NM_000762.5	46	14,367,6121	TT,TC,CC		4.0707,1.0213,3.0375	benign	29/495	41356246	395,12609	2203	4299	6502	SO:0001583	missense	1548	exon1			CCCTTGCTCTTCC	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.86G>A	19.37:g.41356246C>T	ENSP00000301141:p.Ser29Asn	Somatic	341	1	0.00293255		WXS	Illumina HiSeq	Phase_I	330	166	0.50303	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	34	0.015567765567765568	0	0.0	6	0.016574585635359115	0	0.0	28	0.036939313984168866	-	5.795	0.330971	0.10956	0.010213	0.040707	ENSG00000255974	ENST00000301141	T	0.69435	-0.4	2.86	-3.66	0.04489	.	1.227710	0.05870	U	0.624444	T	0.21427	0.0516	L	0.40543	1.245	0.09310	N	1	B	0.20671	0.047	B	0.27262	0.078	T	0.26677	-1.0096	10	0.22706	T	0.39	.	6.2921	0.21065	0.5064:0.3714:0.1222:0.0	rs28399435;rs57299031	29	P11509	CP2A6_HUMAN	N	29	ENSP00000301141:S29N	ENSP00000301141:S29N	S	-	2	0	CYP2A6	46048086	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-2.019000	0.01442	-0.197000	0.10350	0.173000	0.16961	AGC	C|0.975;T|0.025	0.025	strong		0.557	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350044	65350044	+	Silent	SNP	A	A	G	rs35278406	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:65350044A>G	ENST00000284037.5	+	21	3287	c.2898A>G	c.(2896-2898)caA>caG	p.Q966Q	ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000380936.1_Silent_p.Q966Q|ERBB2IP_ENST00000511297.1_Silent_p.Q962Q|ERBB2IP_ENST00000380935.1_Silent_p.Q966Q|ERBB2IP_ENST00000380943.2_Silent_p.Q966Q|ERBB2IP_ENST00000380939.2_Silent_p.Q966Q|ERBB2IP_ENST00000506030.1_Silent_p.Q966Q|ERBB2IP_ENST00000380938.2_Silent_p.Q966Q|ERBB2IP_ENST00000508515.1_Silent_p.Q966Q	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	966					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		GTGGCCCACAATCTGCACCTC	0.398													A|||	87	0.0173722	0.0008	0.0159	5008	,	,		17609	0.0		0.0388	False		,,,				2504	0.0368				p.Q966Q		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.A2898G						PASS	.	A	,	33,4363		0,33,2165	71.0	79.0	76.0		2898,2898	-5.2	0.5	5	dbSNP_126	76	343,8255		5,333,3961	no	coding-synonymous,coding-synonymous	ERBB2IP	NM_001006600.1,NM_018695.2	,	5,366,6126	GG,GA,AA		3.9893,0.7507,2.8936	,	966/1303,966/1372	65350044	376,12618	2198	4299	6497	SO:0001819	synonymous_variant	55914	exon21			CCCACAATCTGCA		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.2898A>G	5.37:g.65350044A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	94	33	0.351064	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	37	CCDS58953.1																																																																																			A|0.974;G|0.026	0.026	strong		0.398	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
PSPH	5723	hgsc.bcm.edu	37	7	56088789	56088789	+	Silent	SNP	G	G	A	rs199851385	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:56088789G>A	ENST00000395471.3	-	4	922	c.117C>T	c.(115-117)ggC>ggT	p.G39G	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Silent_p.G39G			P78330	SERB_HUMAN	phosphoserine phosphatase	39					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CGTCCTCAACGCCACAGATTT	0.423																																					p.G39G		Atlas-SNP	.											.	PSPH	23	.	0			c.C117T						PASS	.						152.0	117.0	129.0					7																	56088789		2203	4300	6503	SO:0001819	synonymous_variant	5723	exon4			CTCAACGCCACAG	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.117C>T	7.37:g.56088789G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	313	90	0.28754	NM_004577	B2RCR5|Q7Z3S5	Silent	SNP	ENST00000395471.3	37	CCDS5522.1																																																																																			G|0.750;A|0.250	0.250	strong		0.423	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
ACTL7B	10880	hgsc.bcm.edu	37	9	111617341	111617341	+	Silent	SNP	A	A	G	rs3750467	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:111617341A>G	ENST00000374667.3	-	1	1898	c.870T>C	c.(868-870)acT>acC	p.T290T		NM_006686.3	NP_006677.1	Q9Y614	ACL7B_HUMAN	actin-like 7B	290						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20						CCTGGCCAATAGTGATGAGTT	0.667													G|||	642	0.128195	0.0469	0.1009	5008	,	,		18533	0.1379		0.1451	False		,,,				2504	0.2301				p.T290T		Atlas-SNP	.											.	ACTL7B	57	.	0			c.T870C						PASS	.	G		257,4141		12,233,1954	47.0	54.0	52.0		870	3.1	1.0	9	dbSNP_107	52	1127,7457		70,987,3235	no	coding-synonymous	ACTL7B	NM_006686.3		82,1220,5189	GG,GA,AA		13.1291,5.8436,10.6609		290/416	111617341	1384,11598	2199	4292	6491	SO:0001819	synonymous_variant	10880	exon1			GCCAATAGTGATG	BC033789	CCDS6771.1	9q31	2009-05-15			ENSG00000148156	ENSG00000148156			162	protein-coding gene	gene with protein product		604304				10373328, 12907721	Standard	NM_006686		Approved	Tact1	uc004bdi.3	Q9Y614	OTTHUMG00000020462	ENST00000374667.3:c.870T>C	9.37:g.111617341A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_006686	B2R9Q2|Q5JSV1	Silent	SNP	ENST00000374667.3	37	CCDS6771.1																																																																																			A|0.890;G|0.110	0.110	strong		0.667	ACTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053571.1	NM_006686	
CLCN7	1186	hgsc.bcm.edu	37	16	1502864	1502864	+	Silent	SNP	A	A	G	rs12926669	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1502864A>G	ENST00000382745.4	-	15	1850	c.1245T>C	c.(1243-1245)atT>atC	p.I415I	CLCN7_ENST00000262318.8_Silent_p.I391I|LA16c-390E6.4_ENST00000563610.1_RNA|CLCN7_ENST00000448525.1_Silent_p.I391I	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	415				I -> V (in Ref. 2; BAG51745). {ECO:0000305}.	chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				GCACGGCCTCAATCACCTGCA	0.672													G|||	311	0.0621006	0.1051	0.0836	5008	,	,		15014	0.0		0.0895	False		,,,				2504	0.0245				p.I415I		Atlas-SNP	.											.	CLCN7	53	.	0			c.T1245C						PASS	.	G	,	496,3848		24,448,1700	14.0	14.0	14.0		1173,1245	-10.3	0.1	16	dbSNP_121	14	846,7700		39,768,3466	no	coding-synonymous,coding-synonymous	CLCN7	NM_001114331.1,NM_001287.4	,	63,1216,5166	GG,GA,AA		9.8994,11.418,10.4112	,	391/782,415/806	1502864	1342,11548	2172	4273	6445	SO:0001819	synonymous_variant	1186	exon15			GGCCTCAATCACC	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.1245T>C	16.37:g.1502864A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			A|0.912;G|0.088	0.088	strong		0.672	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
CCDC67	159989	hgsc.bcm.edu	37	11	93129484	93129484	+	Missense_Mutation	SNP	A	A	G	rs12282288|rs386756254	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	140	0	0		WXS	Illumina HiSeq	Phase_I	250	60	0.24	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	
LATS2	26524	hgsc.bcm.edu	37	13	21562948	21562948	+	Missense_Mutation	SNP	G	G	A	rs558614	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:21562948G>A	ENST00000382592.4	-	4	1376	c.971C>T	c.(970-972)gCg>gTg	p.A324V	LATS2_ENST00000542899.1_Missense_Mutation_p.A324V|LATS2_ENST00000472754.1_5'Flank	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CTGGTGGGCCGCGGGACCGGC	0.726													G|||	3153	0.629593	0.5129	0.6888	5008	,	,		11971	0.5387		0.7972	False		,,,				2504	0.6667				p.A324V		Atlas-SNP	.											LATS2_ENST00000382592,NS,carcinoma,0,2	LATS2	176	2	0			c.C971T						PASS	.	G	VAL/ALA	2514,1854		739,1036,409	17.0	20.0	19.0		971	2.7	0.0	13	dbSNP_83	19	6953,1567		2835,1283,142	no	missense	LATS2	NM_014572.2	64	3574,2319,551	AA,AG,GG		18.392,42.4451,26.5441	benign	324/1089	21562948	9467,3421	2184	4260	6444	SO:0001583	missense	26524	exon4			TGGGCCGCGGGAC	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.971C>T	13.37:g.21562948G>A	ENSP00000372035:p.Ala324Val	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	21	18	0.857143	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	1424	0.652014652014652	248	0.5040650406504065	266	0.7348066298342542	315	0.5506993006993007	595	0.7849604221635884	G	6.803	0.517276	0.13005	0.575549	0.81608	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.59083	0.29;0.29	3.57	2.72	0.32119	.	0.947577	0.08664	N	0.911940	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.28584	0.216	B	0.20184	0.028	T	0.37979	-0.9682	9	0.25751	T	0.34	.	12.1462	0.54024	0.0:0.2164:0.7836:0.0	rs558614;rs3742219;rs57107378;rs558614	324	Q9NRM7	LATS2_HUMAN	V	324	ENSP00000372035:A324V;ENSP00000441817:A324V	ENSP00000372035:A324V	A	-	2	0	LATS2	20460948	1.000000	0.71417	0.001000	0.08648	0.251000	0.25915	6.231000	0.72307	0.682000	0.31407	0.485000	0.47835	GCG	G|0.298;A|0.702	0.702	strong		0.726	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
ACYP1	97	hgsc.bcm.edu	37	14	75520272	75520272	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:75520272C>A	ENST00000238618.3	-	3	278	c.175G>T	c.(175-177)Gtg>Ttg	p.V59L	ACYP1_ENST00000555463.1_Missense_Mutation_p.V89L|MLH3_ENST00000355774.2_5'Flank|ACYP1_ENST00000555694.1_Missense_Mutation_p.V59L|ACYP1_ENST00000357971.3_3'UTR|MLH3_ENST00000238662.7_5'Flank|MLH3_ENST00000380968.2_5'Flank|MLH3_ENST00000556257.1_5'Flank	NM_001107.3	NP_001098.1	P07311	ACYP1_HUMAN	acylphosphatase 1, erythrocyte (common) type	59	Acylphosphatase-like. {ECO:0000255|PROSITE-ProRule:PRU00520}.				phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)	acylphosphatase activity (GO:0003998)			large_intestine(2)	2				BRCA - Breast invasive adenocarcinoma(234;0.00646)		ATATGACGCACCTTGGAGATG	0.478																																					p.V59L		Atlas-SNP	.											ACYP1,NS,carcinoma,+2,1	ACYP1	6	1	0			c.G175T						scavenged	.						249.0	222.0	231.0					14																	75520272		2203	4300	6503	SO:0001583	missense	97	exon3			GACGCACCTTGGA	X84194	CCDS9838.1, CCDS45137.1	14q24.3	2014-08-08			ENSG00000119640	ENSG00000119640	3.6.1.7		179	protein-coding gene	gene with protein product		600875				7796909, 9730610	Standard	NM_001107		Approved		uc001xrg.3	P07311	OTTHUMG00000171767	ENST00000238618.3:c.175G>T	14.37:g.75520272C>A	ENSP00000238618:p.Val59Leu	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	231	5	0.021645	NM_001107	A6NDV8|B2R590	Missense_Mutation	SNP	ENST00000238618.3	37	CCDS9838.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650821	0.87958	.	.	ENSG00000119640	ENST00000238618;ENST00000555463;ENST00000555694	.	.	.	5.73	5.73	0.89815	Acylphosphatase-like (3);	0.130135	0.51477	D	0.000084	T	0.79131	0.4394	.	.	.	0.80722	D	1	P	0.35894	0.526	P	0.52031	0.688	T	0.75164	-0.3414	8	0.39692	T	0.17	-4.3745	19.9568	0.97222	0.0:1.0:0.0:0.0	.	59	P07311	ACYP1_HUMAN	L	59;89;59	.	ENSP00000238618:V59L	V	-	1	0	ACYP1	74590025	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.323000	0.79105	2.729000	0.93468	0.460000	0.39030	GTG	.	.	none		0.478	ACYP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415013.1		
CDC42BPA	8476	hgsc.bcm.edu	37	1	227216775	227216775	+	Missense_Mutation	SNP	C	C	T	rs1929860	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:227216775C>T	ENST00000366769.3	-	29	5201	c.3910G>A	c.(3910-3912)Gta>Ata	p.V1304I	CDC42BPA_ENST00000366767.3_Missense_Mutation_p.V1223I|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.V1284I|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.V1276I|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.V1304I|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.V1339I|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.V1317I	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CCAGAAGTTACGGTTTGACAC	0.473													T|||	1403	0.280152	0.1884	0.33	5008	,	,		18097	0.4028		0.332	False		,,,				2504	0.1892				p.V1304I		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.G3910A						PASS	.	T	ILE/VAL,ILE/VAL	962,3444	733.3+/-410.5	109,744,1350	69.0	56.0	60.0		3910,3667	4.2	1.0	1	dbSNP_92	60	2711,5889	681.9+/-403.8	406,1899,1995	yes	missense,missense	CDC42BPA	NM_003607.3,NM_014826.4	29,29	515,2643,3345	TT,TC,CC		31.5233,21.8339,28.2408	benign,benign	1304/1720,1223/1639	227216775	3673,9333	2203	4300	6503	SO:0001583	missense	8476	exon29			AAGTTACGGTTTG	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.3910G>A	1.37:g.227216775C>T	ENSP00000355731:p.Val1304Ile	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	727|727	0.33287545787545786|0.33287545787545786	105|105	0.21341463414634146|0.21341463414634146	113|113	0.31215469613259667|0.31215469613259667	245|245	0.42832167832167833|0.42832167832167833	264|264	0.3482849604221636|0.3482849604221636	T|T	1.392|1.392	-0.580517|-0.580517	0.03854|0.03854	0.218339|0.218339	0.315233|0.315233	ENSG00000143776|ENSG00000143776	ENST00000448940;ENST00000442054;ENST00000429440;ENST00000441725|ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765	.|T;T;T;T;T;T;T	.|0.04551	.|3.6;3.6;3.6;3.6;3.6;3.6;3.6	5.32|5.32	4.18|4.18	0.49190|0.49190	.|.	.|0.138886	.|0.64402	.|N	.|0.000007	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01705|0.01705	-0.755|-0.755	0.54753|0.54753	P|P	1.799999999996249E-5|1.799999999996249E-5	.|B;B;B;B;B;B;B;B	.|0.06786	.|0.001;0.0;0.001;0.001;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B;B;B	.|0.09377	.|0.001;0.001;0.001;0.004;0.001;0.001;0.0;0.004	T|T	0.45323|0.45323	-0.9269|-0.9269	4|9	.|0.05351	.|T	.|0.99	.|.	8.5234|8.5234	0.33291|0.33291	0.0:0.0681:0.1307:0.8012|0.0:0.0681:0.1307:0.8012	rs1929860;rs3738731;rs57541261;rs1929860|rs1929860;rs3738731;rs57541261;rs1929860	.|1284;1276;619;201;1223;1304;1339;506	.|F5H5N0;Q5VT25-4;E9PEF7;Q5T7A7;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799	.|.;.;.;.;.;.;.;.	H|I	506;632;201;528|1304;1223;1304;1339;1276;619;1284;1317	.|ENSP00000355731:V1304I;ENSP00000355729:V1223I;ENSP00000335341:V1304I;ENSP00000355728:V1339I;ENSP00000355726:V1276I;ENSP00000443275:V1284I;ENSP00000355727:V1317I	.|ENSP00000335341:V1304I	R|V	-|-	2|1	0|0	CDC42BPA|CDC42BPA	225283398|225283398	0.269000|0.269000	0.24143|0.24143	0.994000|0.994000	0.49952|0.49952	0.965000|0.965000	0.64279|0.64279	0.457000|0.457000	0.21875|0.21875	0.411000|0.411000	0.25702|0.25702	-0.352000|-0.352000	0.07741|0.07741	CGT|GTA	T|0.301;C|0.699	0.301	strong		0.473	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
SIX4	51804	hgsc.bcm.edu	37	14	61187111	61187111	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:61187111C>T	ENST00000216513.4	-	2	975	c.916G>A	c.(916-918)Gat>Aat	p.D306N		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	306					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D306N(1)		breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		GGAGATAAATCCTCATGTCCC	0.473																																					p.D306N		Atlas-SNP	.											SIX4,NS,carcinoma,0,1	SIX4	69	1	1	Substitution - Missense(1)	breast(1)	c.G916A						scavenged	.						128.0	122.0	124.0					14																	61187111		2203	4300	6503	SO:0001583	missense	51804	exon2			ATAAATCCTCATG	AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"""Homeoboxes / SINE class"""	10890	protein-coding gene	gene with protein product		606342	"""sine oculis homeobox (Drosophila) homolog 4"", ""sine oculis homeobox homolog 4 (Drosophila)"""			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.916G>A	14.37:g.61187111C>T	ENSP00000216513:p.Asp306Asn	Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	308	4	0.012987	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	C	20.6	4.018991	0.75275	.	.	ENSG00000100625	ENST00000216513;ENST00000556952	D	0.91686	-2.89	5.62	5.62	0.85841	.	0.202710	0.41823	D	0.000814	D	0.93187	0.7830	L	0.29908	0.895	0.47245	D	0.999363	D;D	0.67145	0.974;0.996	P;P	0.62740	0.669;0.906	D	0.93291	0.6668	10	0.51188	T	0.08	.	19.6764	0.95936	0.0:1.0:0.0:0.0	.	298;306	G3V2N2;Q9UIU6	.;SIX4_HUMAN	N	306;298	ENSP00000216513:D306N	ENSP00000216513:D306N	D	-	1	0	SIX4	60256864	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	5.641000	0.67881	2.660000	0.90430	0.655000	0.94253	GAT	.	.	none		0.473	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2		
TTLL12	23170	hgsc.bcm.edu	37	22	43579083	43579083	+	Missense_Mutation	SNP	G	G	A	rs138951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:43579083G>A	ENST00000216129.6	-	2	313	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	84			R -> W (in dbSNP:rs138951).		cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				CGCACCTCCCGGGCTGCCTCG	0.637													G|||	183	0.0365415	0.0038	0.0389	5008	,	,		19228	0.001		0.1302	False		,,,				2504	0.0194				p.R84W		Atlas-SNP	.											.	TTLL12	50	.	0			c.C250T						PASS	.	G	TRP/ARG	103,4303	80.4+/-118.8	0,103,2100	145.0	142.0	143.0		250	-0.8	0.0	22	dbSNP_78	143	988,7612	213.5+/-253.4	57,874,3369	no	missense	TTLL12	NM_015140.3	101	57,977,5469	AA,AG,GG		11.4884,2.3377,8.3884	probably-damaging	84/645	43579083	1091,11915	2203	4300	6503	SO:0001583	missense	23170	exon2			CCTCCCGGGCTGC	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"""Tubulin tyrosine ligase-like family"""	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.250C>T	22.37:g.43579083G>A	ENSP00000216129:p.Arg84Trp	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	214	124	0.579439	NM_015140	Q20WK5|Q9UGU3	Missense_Mutation	SNP	ENST00000216129.6	37	CCDS14047.1	122	0.055860805860805864	6	0.012195121951219513	17	0.04696132596685083	3	0.005244755244755245	96	0.1266490765171504	G	9.569	1.120483	0.20877	0.023377	0.114884	ENSG00000100304	ENST00000216129;ENST00000357017;ENST00000423379	T	0.07800	3.16	5.08	-0.805	0.10879	.	1.539810	0.03716	N	0.251140	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	D;P	0.60160	0.987;0.951	B;B	0.42653	0.394;0.394	T	0.15037	-1.0451	9	0.72032	D	0.01	-31.435	2.5325	0.04706	0.144:0.2853:0.3873:0.1834	rs138951;rs52835787;rs138951	84;84	B1AH89;Q14166	.;TTL12_HUMAN	W	84	ENSP00000216129:R84W	ENSP00000216129:R84W	R	-	1	2	TTLL12	41909027	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.346000	0.19997	-0.339000	0.08401	-0.140000	0.14226	CGG	G|0.927;A|0.073	0.073	strong		0.637	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
OR4X1	390113	hgsc.bcm.edu	37	11	48285906	48285906	+	Missense_Mutation	SNP	C	C	T	rs16905753	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	200	0	0		WXS	Illumina HiSeq	Phase_I	187	85	0.454545	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	
OR9G1	390174	hgsc.bcm.edu	37	11	56468225	56468225	+	Missense_Mutation	SNP	G	G	A	rs148651508	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56468225G>A	ENST00000312153.1	+	1	362	c.362G>A	c.(361-363)cGc>cAc	p.R121H		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R121P(1)		breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GCTTATGACCGCTACGTGGCC	0.527													G|||	5	0.000998403	0.0	0.0	5008	,	,		17980	0.0		0.0	False		,,,				2504	0.0051				p.R121H		Atlas-SNP	.											OR9G1,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	lung(1)	c.G362A						scavenged	.	G	HIS/ARG	6,4396	4.2+/-10.8	0,6,2195	134.0	124.0	127.0		362	0.5	0.7	11	dbSNP_134	127	5,8587	4.3+/-15.6	0,5,4291	yes	missense	OR9G1	NM_001005213.1	29	0,11,6486	AA,AG,GG		0.0582,0.1363,0.0847	benign	121/306	56468225	11,12983	2201	4296	6497	SO:0001583	missense	504191	exon1			ATGACCGCTACGT	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.362G>A	11.37:g.56468225G>A	ENSP00000309012:p.Arg121His	Somatic	289	2	0.00692042		WXS	Illumina HiSeq	Phase_I	298	76	0.255034	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	G	9.545	1.114336	0.20795	0.001363	5.82E-4	ENSG00000174914	ENST00000312153	T	0.77489	-1.1	4.54	0.508	0.16972	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000040	T	0.76147	0.3947	M	0.88842	2.985	0.33993	D	0.649336	B	0.28026	0.198	B	0.26969	0.075	T	0.74272	-0.3719	10	0.72032	D	0.01	-11.8484	5.9681	0.19336	0.2233:0.0:0.6439:0.1329	.	121	Q8NH87	OR9G1_HUMAN	H	121	ENSP00000309012:R121H	ENSP00000309012:R121H	R	+	2	0	OR9G1	56224801	0.996000	0.38824	0.684000	0.30055	0.041000	0.13682	2.226000	0.42963	0.004000	0.14682	-0.203000	0.12734	CGC	G|1.000;A|0.000	0.000	weak		0.527	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
UGT2B4	7363	hgsc.bcm.edu	37	4	70346564	70346564	+	Silent	SNP	G	G	T	rs67904882|rs13142440	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:70346564G>T	ENST00000305107.6	-	6	1421	c.1375C>A	c.(1375-1377)Cga>Aga	p.R459R	AC108078.1_ENST00000583573.1_RNA|UGT2B4_ENST00000381096.3_Silent_p.R323R|UGT2B4_ENST00000512583.1_3'UTR|UGT2B4_ENST00000506580.1_5'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	459					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)	p.R459*(1)		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)	AAGACTGCTCGATCAAGGGGC	0.428													g|||	654	0.130591	0.1362	0.2205	5008	,	,		17789	0.0		0.2266	False		,,,				2504	0.0951				p.R459R		Atlas-SNP	.											UGT2B4,NS,carcinoma,0,1	UGT2B4	105	1	1	Substitution - Nonsense(1)	endometrium(1)	c.C1375A						PASS	.	G		631,3775		44,543,1616	113.0	113.0	113.0		1375	-1.0	0.0	4	dbSNP_121	113	2052,6548		260,1532,2508	no	coding-synonymous	UGT2B4	NM_021139.2		304,2075,4124	TT,TG,GG		23.8605,14.3214,20.6289		459/529	70346564	2683,10323	2203	4300	6503	SO:0001819	synonymous_variant	7363	exon6			CTGCTCGATCAAG	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.1375C>A	4.37:g.70346564G>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	169	83	0.491124	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	CCDS43234.1																																																																																			TT|1.000;|0.000	.	alt		0.428	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
MYEOV	26579	hgsc.bcm.edu	37	11	69063527	69063527	+	Missense_Mutation	SNP	C	C	T	rs150423809	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:69063527C>T	ENST00000308946.3	+	3	1060	c.610C>T	c.(610-612)Cgc>Tgc	p.R204C	MYEOV_ENST00000535407.1_Missense_Mutation_p.R146C|MYEOV_ENST00000441339.2_Missense_Mutation_p.R204C	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	204										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)		TGTGGCTCTGCGCTCACCTGG	0.612													C|||	14	0.00279553	0.0053	0.0014	5008	,	,		17375	0.003		0.001	False		,,,				2504	0.002				p.R204C		Atlas-SNP	.											.	MYEOV	42	.	0			c.C610T						PASS	.	C	CYS/ARG	16,4384	22.3+/-47.3	0,16,2184	119.0	110.0	113.0		610	-2.1	0.0	11	dbSNP_134	113	23,8565	15.3+/-51.7	0,23,4271	yes	missense	MYEOV	NM_138768.2	180	0,39,6455	TT,TC,CC		0.2678,0.3636,0.3003	benign	204/314	69063527	39,12949	2200	4294	6494	SO:0001583	missense	26579	exon3			GCTCTGCGCTCAC	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.610C>T	11.37:g.69063527C>T	ENSP00000308330:p.Arg204Cys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	3.332	-0.136467	0.06711	0.003636	0.002678	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.25912	1.78;1.78;1.77	1.05	-2.1	0.07210	.	.	.	.	.	T	0.10551	0.0258	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19224	-1.0312	9	0.87932	D	0	.	1.8279	0.03125	0.1693:0.4544:0.198:0.1782	.	204	Q96EZ4	MYEOV_HUMAN	C	204;204;146	ENSP00000412482:R204C;ENSP00000308330:R204C;ENSP00000438100:R146C	ENSP00000308330:R204C	R	+	1	0	MYEOV	68820103	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.662000	0.01970	-3.192000	0.00219	-2.087000	0.00375	CGC	C|0.998;T|0.002	0.002	strong		0.612	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789327	117789327	+	Missense_Mutation	SNP	T	T	C	rs201746372|rs58754377|rs61900346	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789327T>C	ENST00000430170.2	-	2	335	c.248A>G	c.(247-249)cAg>cGg	p.Q83R	TMPRSS13_ENST00000445164.2_Missense_Mutation_p.Q83R|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.Q83R|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.Q83R|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.Q83R	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	83	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		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)		TGGAGATGCCTGGGCTGGAGA	0.672													t|||	6	0.00119808	0.0038	0.0	5008	,	,		14227	0.001		0.0	False		,,,				2504	0.0				p.Q83R		Atlas-SNP	.											TMPRSS13_ENST00000445164,NS,carcinoma,0,4	TMPRSS13	75	4	1	Deletion - In frame(1)	urinary_tract(1)	c.A248G						scavenged	.						30.0	37.0	35.0					11																	117789327		1948	4128	6076	SO:0001583	missense	84000	exon2			GATGCCTGGGCTG	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	ENST00000430170.2:c.248A>G	11.37:g.117789327T>C	ENSP00000387702:p.Gln83Arg	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	266	25	0.093985	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	37	CCDS58185.1	408|408	0.18681318681318682|0.18681318681318682	89|89	0.18089430894308944|0.18089430894308944	74|74	0.20441988950276244|0.20441988950276244	90|90	0.15734265734265734|0.15734265734265734	155|155	0.20448548812664907|0.20448548812664907	T|t	0.044|0.044	-1.272742|-1.272742	0.01421|0.01421	.|.	.|.	ENSG00000137747|ENSG00000137747	ENST00000336500|ENST00000528626;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	.|D;D;D;D;D	.|0.87729	.|-2.27;-2.29;-2.29;-2.27;-2.17	3.98|3.98	0.663|0.663	0.17885|0.17885	.|.	.|0.679012	.|0.12584	.|N	.|0.456148	.|T	.|0.00144	.|0.0004	.|.	.|.	.|.	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	.|0.10917	.|-1.0609	.|8	.|0.02654	.|T	.|1	.|.	6.985|6.985	0.24723|0.24723	0.0:0.7178:0.1731:0.1091|0.0:0.7178:0.1731:0.1091	rs61900346|rs61900346	.|78;83	.|Q9BYE2-4;E9PRA0	.|.;.	.|R	-1|83	.|ENSP00000435813:Q83R;ENSP00000434279:Q83R;ENSP00000387702:Q83R;ENSP00000394114:Q83R;ENSP00000436502:Q83R	.|ENSP00000387702:Q83R	.|Q	-|-	.|2	.|0	TMPRSS13|TMPRSS13	117294537|117294537	0.000000|0.000000	0.05858|0.05858	0.014000|0.014000	0.15608|0.15608	0.022000|0.022000	0.10575|0.10575	-1.912000|-1.912000	0.01582|0.01582	0.897000|0.897000	0.36392|0.36392	-0.390000|-0.390000	0.06520|0.06520	.|CAG	T|0.814;C|0.186	0.186	strong		0.672	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
APPL2	55198	hgsc.bcm.edu	37	12	105600935	105600935	+	Silent	SNP	G	G	A	rs2293643	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:105600935G>A	ENST00000258530.3	-	8	750	c.525C>T	c.(523-525)caC>caT	p.H175H	APPL2_ENST00000539978.2_Silent_p.H132H|APPL2_ENST00000551662.1_Silent_p.H181H|APPL2_ENST00000549573.1_5'UTR	NM_001251904.1|NM_018171.3	NP_001238833.1|NP_060641.2	Q06481	APLP2_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 2	0					cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|midbrain development (GO:0030901)|neuromuscular process controlling balance (GO:0050885)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of protein binding (GO:0043393)|suckling behavior (GO:0001967)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GGGAGGAGAGGTGCTGCTTCC	0.532													G|||	919	0.183506	0.0787	0.2421	5008	,	,		19223	0.2599		0.1879	False		,,,				2504	0.2004				p.H181H		Atlas-SNP	.											.	APPL2	69	.	0			c.C543T						PASS	.	G		383,4023	192.6+/-218.0	19,345,1839	89.0	80.0	83.0		525	3.0	1.0	12	dbSNP_100	83	1701,6899	312.7+/-311.0	167,1367,2766	no	coding-synonymous	APPL2	NM_018171.3		186,1712,4605	AA,AG,GG		19.7791,8.6927,16.0234		175/665	105600935	2084,10922	2203	4300	6503	SO:0001819	synonymous_variant	55198	exon8			GGAGAGGTGCTGC	AY113704	CCDS9101.1, CCDS58275.1, CCDS58276.1	12q23.3	2014-08-12			ENSG00000136044	ENSG00000136044		"""Pleckstrin homology (PH) domain containing"""	18242	protein-coding gene	gene with protein product		606231				11431708, 17030088	Standard	NM_001251904		Approved	FLJ10659, DIP13B	uc010swu.1	Q8NEU8	OTTHUMG00000169853	ENST00000258530.3:c.525C>T	12.37:g.105600935G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_001251904	B3KXX9|H7BXI4|Q13861|Q14594|Q14662|Q71U10|Q7M4L3|Q9BT36	Silent	SNP	ENST00000258530.3	37	CCDS9101.1																																																																																			G|0.836;A|0.164	0.164	strong		0.532	APPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406238.3	NM_018171	
SERPINB5	5268	hgsc.bcm.edu	37	18	61170721	61170721	+	Silent	SNP	T	T	C	rs1455556	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	189	0	0		WXS	Illumina HiSeq	Phase_I	192	107	0.557292	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	
BTBD16	118663	hgsc.bcm.edu	37	10	124089075	124089075	+	Missense_Mutation	SNP	G	G	A	rs986178|rs58204486	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124089075G>A	ENST00000260723.4	+	11	1243	c.992G>A	c.(991-993)gGc>gAc	p.G331D	BTBD16_ENST00000368994.2_Missense_Mutation_p.G332D	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	331			G -> D (in dbSNP:rs986178).							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)				CGTCTGCACGGCATCACCAAA	0.612													G|||	480	0.0958466	0.0113	0.0764	5008	,	,		17173	0.1687		0.1044	False		,,,				2504	0.1401				p.G331D		Atlas-SNP	.											BTBD16,NS,carcinoma,0,1	BTBD16	44	1	0			c.G992A						scavenged	.	G	ASP/GLY	116,4290	89.2+/-127.9	3,110,2090	108.0	95.0	99.0		992	1.8	0.2	10	dbSNP_86	99	1093,7507	228.4+/-263.5	69,955,3276	yes	missense	BTBD16	NM_144587.2	94	72,1065,5366	AA,AG,GG		12.7093,2.6328,9.2957	probably-damaging	331/507	124089075	1209,11797	2203	4300	6503	SO:0001583	missense	118663	exon11			TGCACGGCATCAC	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.992G>A	10.37:g.124089075G>A	ENSP00000260723:p.Gly331Asp	Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	52	22	0.423077	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	207	0.09478021978021978	7	0.014227642276422764	33	0.09116022099447514	88	0.15384615384615385	79	0.10422163588390501	G	5.362	0.252126	0.10185	0.026328	0.127093	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.19250	2.16;2.16	5.77	1.79	0.24919	.	0.954977	0.08657	N	0.913061	T	0.00210	0.0006	L	0.56769	1.78	0.35328	P	0.21467999999999998	D;D	0.64830	0.994;0.994	P;P	0.60886	0.88;0.88	T	0.06232	-1.0838	9	0.36615	T	0.2	-4.1952	7.2653	0.26226	0.3742:0.0:0.6258:0.0	rs986178;rs60773779;rs986178	332;331	Q32M84-2;Q32M84	.;BTBDG_HUMAN	D	331;332	ENSP00000260723:G331D;ENSP00000357990:G332D	ENSP00000260723:G331D	G	+	2	0	BTBD16	124079065	0.363000	0.24989	0.161000	0.22692	0.039000	0.13416	0.487000	0.22356	0.062000	0.16340	-0.137000	0.14449	GGC	G|0.902;A|0.098	0.098	strong		0.612	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
PLAT	5327	hgsc.bcm.edu	37	8	42044965	42044965	+	Missense_Mutation	SNP	G	G	A	rs2020921	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:42044965G>A	ENST00000220809.4	-	6	746	c.490C>T	c.(490-492)Cgg>Tgg	p.R164W	PLAT_ENST00000352041.3_Missense_Mutation_p.R118W|PLAT_ENST00000429089.2_Missense_Mutation_p.R164W|PLAT_ENST00000429710.2_Intron|PLAT_ENST00000519510.1_Intron|PLAT_ENST00000270189.6_Missense_Mutation_p.R164W|PLAT_ENST00000524009.1_Intron	NM_000930.3	NP_000921.1	P00750	TPA_HUMAN	plasminogen activator, tissue	164	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.		R -> W (in dbSNP:rs2020921). {ECO:0000269|Ref.12}.		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)	TCTGGCCTCCGCCCGCTGTAG	0.652													G|||	34	0.00678914	0.0038	0.0029	5008	,	,		20354	0.0		0.0229	False		,,,				2504	0.0041				p.R164W		Atlas-SNP	.											PLAT,NS,carcinoma,+1,1	PLAT	62	1	0			c.C490T						PASS	.	G	TRP/ARG,TRP/ARG	22,4384	29.0+/-57.7	0,22,2181	43.0	42.0	43.0		490,352	1.9	0.3	8	dbSNP_94	43	191,8409	83.4+/-145.9	2,187,4111	yes	missense,missense	PLAT	NM_000930.3,NM_033011.2	101,101	2,209,6292	AA,AG,GG		2.2209,0.4993,1.6377	benign,benign	164/563,118/517	42044965	213,12793	2203	4300	6503	SO:0001583	missense	5327	exon6			GCCTCCGCCCGCT		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.490C>T	8.37:g.42044965G>A	ENSP00000220809:p.Arg164Trp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_000930	A8K022|B2R8E8|Q15103|Q503B0|Q6PJA5|Q7Z7N2|Q86YK8|Q9BU99|Q9BZW1	Missense_Mutation	SNP	ENST00000220809.4	37	CCDS6126.1	20	0.009157509157509158	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	11.06	1.529003	0.27387	0.004993	0.022209	ENSG00000104368	ENST00000270189;ENST00000429089;ENST00000220809;ENST00000352041;ENST00000520523	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.95	1.92	0.25849	Kringle (4);Kringle-like fold (1);	0.147675	0.64402	N	0.000015	T	0.33614	0.0869	L	0.35288	1.05	0.34497	D	0.705653	B;B;B	0.24920	0.114;0.036;0.037	B;B;B	0.24848	0.035;0.021;0.056	T	0.47169	-0.9138	10	0.51188	T	0.08	.	5.6142	0.17422	0.0641:0.1146:0.4484:0.3729	rs2020921;rs2020921	164;118;164	B8ZX62;P00750-3;P00750	.;.;TPA_HUMAN	W	164;164;164;118;164	ENSP00000270189:R164W;ENSP00000392045:R164W;ENSP00000220809:R164W;ENSP00000270188:R118W;ENSP00000428797:R164W	ENSP00000220809:R164W	R	-	1	2	PLAT	42164122	0.009000	0.17119	0.283000	0.24790	0.227000	0.25037	1.460000	0.35244	0.376000	0.24707	0.655000	0.94253	CGG	G|0.987;A|0.013	0.013	strong		0.652	PLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377100.1	NM_000930	
UMODL1	89766	hgsc.bcm.edu	37	21	43547873	43547873	+	Missense_Mutation	SNP	G	G	A	rs220159	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43547873G>A	ENST00000408910.2	+	20	3622	c.3622G>A	c.(3622-3624)Gac>Aac	p.D1208N	UMODL1_ENST00000408989.2_Missense_Mutation_p.D1336N|UMODL1_ENST00000400427.1_Missense_Mutation_p.D1264N|UMODL1_ENST00000400424.2_Missense_Mutation_p.D1136N|UMODL1_ENST00000400423.2_3'UTR	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1208	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		D -> N (in dbSNP:rs220159). {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						CTTTATCAACGACTCCATCGT	0.488													A|||	1792	0.357827	0.3253	0.4236	5008	,	,		20774	0.369		0.3499	False		,,,				2504	0.3517				p.D1336N	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											UMODL1_ENST00000408989,colon,carcinoma,0,2	UMODL1	186	2	0			c.G4006A						PASS	.	A	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	1242,2800		217,808,996	127.0	126.0	127.0		3622,3790,3406,4006	2.4	0.9	21	dbSNP_79	127	2939,5417		524,1891,1763	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	23,23,23,23	741,2699,2759	AA,AG,GG		35.1723,30.7274,33.7232	benign,benign,benign,benign	1208/1319,1264/1375,1136/1247,1336/1447	43547873	4181,8217	2021	4178	6199	SO:0001583	missense	89766	exon19			ATCAACGACTCCA		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.3622G>A	21.37:g.43547873G>A	ENSP00000386147:p.Asp1208Asn	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	269	117	0.434944	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	800	0.3663003663003663	161	0.32723577235772355	156	0.430939226519337	219	0.38286713286713286	264	0.3482849604221636	A	0.009	-1.855586	0.00558	0.307274	0.351723	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910;ENST00000434156	D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54	3.56	2.42	0.29668	Zona pellucida sperm-binding protein (3);	0.000000	0.48286	N	0.000200	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.36016	-0.9765	8	.	.	.	-26.8106	6.7343	0.23401	0.7075:0.0:0.2925:0.0	rs220159;rs512994;rs17177620;rs52807694;rs59318415;rs220159	1336;1208	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	N	1264;1136;1336;1208;93	ENSP00000383279:D1264N;ENSP00000383276:D1136N;ENSP00000386126:D1336N;ENSP00000386147:D1208N	.	D	+	1	0	UMODL1	42420942	0.993000	0.37304	0.924000	0.36721	0.050000	0.14768	0.913000	0.28611	0.263000	0.21812	-0.361000	0.07541	GAC	G|0.638;N|0.000	.	strong		0.488	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
ZNF701	55762	hgsc.bcm.edu	37	19	53085813	53085813	+	Silent	SNP	T	T	C	rs3745101	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	185	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	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	
GIT2	9815	hgsc.bcm.edu	37	12	110385079	110385079	+	Silent	SNP	G	G	T	rs2063388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:110385079G>T	ENST00000355312.3	-	15	1622	c.1623C>A	c.(1621-1623)ctC>ctA	p.L541L	GIT2_ENST00000354574.4_Silent_p.L493L|GIT2_ENST00000343646.5_Silent_p.L461L|GIT2_ENST00000553118.1_Intron|GIT2_ENST00000361006.5_Silent_p.L541L|GIT2_ENST00000356259.4_Intron|GIT2_ENST00000551209.1_Silent_p.L490L|GIT2_ENST00000457474.2_Silent_p.L493L|GIT2_ENST00000338373.5_Intron|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000360185.4_Silent_p.L491L	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	541					behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						GGAAGGGCTGGAGTCTCATCC	0.577													G|||	422	0.0842652	0.1596	0.0389	5008	,	,		18604	0.119		0.0378	False		,,,				2504	0.0266				p.L541L		Atlas-SNP	.											.	GIT2	81	.	0			c.C1623A						PASS	.	G	,,,,	685,3721	286.9+/-279.0	46,593,1564	98.0	96.0	97.0		1479,1623,1473,1623,	-1.0	1.0	12	dbSNP_94	97	284,8316	105.2+/-166.2	6,272,4022	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	GIT2	NM_001135213.1,NM_001135214.1,NM_014776.3,NM_057169.3,NM_057170.3	,,,,	52,865,5586	TT,TG,GG		3.3023,15.547,7.4504	,,,,	493/682,541/730,491/680,541/760,	110385079	969,12037	2203	4300	6503	SO:0001819	synonymous_variant	9815	exon15			GGGCTGGAGTCTC	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4273	protein-coding gene	gene with protein product		608564	"""G protein-coupled receptor kinase interactor 2"""			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1623C>A	12.37:g.110385079G>T		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	225	125	0.555556	NM_001135214	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Silent	SNP	ENST00000355312.3	37	CCDS9138.1																																																																																			G|0.922;T|0.078	0.078	strong		0.577	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169	
IDUA	3425	hgsc.bcm.edu	37	4	995919	995919	+	Silent	SNP	G	G	C	rs6830825	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:995919G>C	ENST00000247933.4	+	7	1030	c.942G>C	c.(940-942)gcG>gcC	p.A314A	IDUA_ENST00000514224.1_Silent_p.A182A|IDUA_ENST00000453894.1_Missense_Mutation_p.G301R	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	314					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)			CGTGGAGGGCGGACGTGACCT	0.711													C|||	1095	0.21865	0.2489	0.111	5008	,	,		13585	0.2133		0.169	False		,,,				2504	0.3108				p.A314A		Atlas-SNP	.											IDUA,NS,carcinoma,0,1	IDUA	33	1	0			c.G942C						PASS	.	C		758,3528		75,608,1460	15.0	17.0	16.0		942	-10.3	0.0	4	dbSNP_116	16	1219,7221		94,1031,3095	no	coding-synonymous	IDUA	NM_000203.3		169,1639,4555	CC,CG,GG		14.4431,17.6855,15.5351		314/654	995919	1977,10749	2143	4220	6363	SO:0001819	synonymous_variant	3425	exon7			GAGGGCGGACGTG	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.942G>C	4.37:g.995919G>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	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	0.004	-2.296533	0.00245	0.176855	0.144431	ENSG00000127415	ENST00000453894	D	0.94931	-3.56	5.15	-10.3	0.00346	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.48559	-0.9025	7	0.21014	T	0.42	.	0.4596	0.00514	0.2817:0.2432:0.1416:0.3334	rs6830825;rs60925429	301	B3KWK6	.	R	301	ENSP00000396458:G301R	ENSP00000396458:G301R	G	+	1	0	IDUA	985919	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-4.282000	0.00260	-3.294000	0.00194	-2.305000	0.00258	GGA	G|0.815;C|0.185	0.185	strong		0.711	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
SCRT2	85508	hgsc.bcm.edu	37	20	656181	656181	+	Missense_Mutation	SNP	G	G	A	rs76595598	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:656181G>A	ENST00000246104.6	-	1	642	c.65C>T	c.(64-66)gCc>gTc	p.A22V	RP5-850E9.3_ENST00000488788.2_Missense_Mutation_p.A22V	NM_033129.3	NP_149120.1	Q9NQ03	SCRT2_HUMAN	scratch family zinc finger 2	22					negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of neuron migration (GO:2001222)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			kidney(1)|liver(1)|ovary(1)	3						GTAGGTGGGGGCCGGCACCCC	0.746													G|||	174	0.0347444	0.0219	0.036	5008	,	,		9468	0.001		0.0944	False		,,,				2504	0.0245				p.A22V		Atlas-SNP	.											SCRT2,NS,carcinoma,0,1	SCRT2	16	1	0			c.C65T						PASS	.	G	VAL/ALA	158,4136		5,148,1994	6.0	8.0	8.0		65	2.2	1.0	20	dbSNP_131	8	750,7640		32,686,3477	yes	missense	SCRT2	NM_033129.3	64	37,834,5471	AA,AG,GG		8.9392,3.6796,7.1586	possibly-damaging	22/308	656181	908,11776	2147	4195	6342	SO:0001583	missense	85508	exon1			GTGGGGGCCGGCA		CCDS13006.1	20p13	2013-10-09	2013-10-09		ENSG00000215397	ENSG00000215397		"""Zinc fingers, C2H2-type"""	15952	protein-coding gene	gene with protein product			"""scratch (drosophila homolog) 2, zinc finger protein"", ""scratch homolog 2, zinc finger protein (Drosophila)"""			11274425	Standard	NM_033129		Approved	ZNF898B	uc002wec.3	Q9NQ03	OTTHUMG00000130829	ENST00000246104.6:c.65C>T	20.37:g.656181G>A	ENSP00000246104:p.Ala22Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_033129		Missense_Mutation	SNP	ENST00000246104.6	37	CCDS13006.1	106	0.048534798534798536	7	0.014227642276422764	16	0.04419889502762431	3	0.005244755244755245	80	0.10554089709762533	G	14.23	2.472889	0.43942	0.036796	0.089392	ENSG00000215397	ENST00000246104	T	0.09255	3.0	4.24	2.18	0.27775	.	0.425364	0.19905	U	0.103422	T	0.00178	0.0005	L	0.43152	1.355	0.38947	P	0.04172100000000001	B	0.28470	0.213	B	0.18871	0.023	T	0.23940	-1.0174	9	0.37606	T	0.19	-7.6146	6.9152	0.24355	0.0:0.1932:0.6071:0.1997	.	22	Q9NQ03	SCRT2_HUMAN	V	22	ENSP00000246104:A22V	ENSP00000246104:A22V	A	-	2	0	SCRT2	604181	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.401000	0.44513	0.370000	0.24538	0.484000	0.47621	GCC	G|0.950;A|0.050	0.050	strong		0.746	SCRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253383.2	NM_033129	
SEZ6	124925	hgsc.bcm.edu	37	17	27284443	27284443	+	Missense_Mutation	SNP	A	A	G	rs12941884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:27284443A>G	ENST00000317338.12	-	12	2845	c.2417T>C	c.(2416-2418)aTg>aCg	p.M806T	SEZ6_ENST00000442608.3_Missense_Mutation_p.M806T|SEZ6_ENST00000360295.9_Missense_Mutation_p.M806T|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	806	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.		M -> T (in dbSNP:rs12941884). {ECO:0000269|PubMed:14702039}.		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)			GGAGCTGCCCATCAGCACAAA	0.582													G|||	954	0.190495	0.2224	0.1859	5008	,	,		17489	0.123		0.1213	False		,,,				2504	0.2914				p.M806T		Atlas-SNP	.											.	SEZ6	61	.	0			c.T2417C						PASS	.	G	THR/MET,THR/MET	773,3133		88,597,1268	88.0	98.0	95.0		2417,2417	3.7	1.0	17	dbSNP_121	95	1033,7269		63,907,3181	yes	missense,missense	SEZ6	NM_001098635.1,NM_178860.4	81,81	151,1504,4449	GG,GA,AA		12.4428,19.7901,14.7936	benign,benign	806/994,806/995	27284443	1806,10402	1953	4151	6104	SO:0001583	missense	124925	exon12			CTGCCCATCAGCA	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.2417T>C	17.37:g.27284443A>G	ENSP00000312942:p.Met806Thr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Missense_Mutation	SNP	ENST00000317338.12	37	CCDS45639.1	311	0.1423992673992674	101	0.20528455284552846	56	0.15469613259668508	59	0.10314685314685315	95	0.12532981530343007	G	1.337	-0.595139	0.03771	0.197901	0.124428	ENSG00000063015	ENST00000442608;ENST00000360295;ENST00000317338;ENST00000541381	T;T	0.64618	-0.11;-0.11	5.69	3.65	0.41850	Complement control module (2);Sushi/SCR/CCP (3);	0.060679	0.64402	N	0.000004	T	0.00039	0.0001	N	0.01048	-1.04	0.09310	P	0.9999999999999786	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.08452	-1.0721	9	0.10636	T	0.68	.	8.0263	0.30438	0.1504:0.1309:0.7186:0.0	rs12941884;rs52816964;rs61301981;rs12941884	806;681;806	Q53EL9-3;Q53EL9-2;Q53EL9	.;.;SEZ6_HUMAN	T	806;806;681;806	ENSP00000403784:M806T;ENSP00000353440:M806T	ENSP00000312942:M681T	M	-	2	0	SEZ6	24308569	0.992000	0.36948	0.999000	0.59377	0.783000	0.44284	2.085000	0.41634	0.763000	0.33175	-0.642000	0.03964	ATG	A|0.847;G|0.153	0.153	strong		0.582	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3		
FCGBP	8857	hgsc.bcm.edu	37	19	40392182	40392182	+	Missense_Mutation	SNP	T	T	G	rs202122337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40392182T>G	ENST00000221347.6	-	17	8211	c.8204A>C	c.(8203-8205)cAg>cCg	p.Q2735P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2735	Cys-rich.|TIL 6.					extracellular vesicular exosome (GO:0070062)		p.Q2735P(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)			GTGACTGTTCTGAGGGCATTC	0.652																																					p.Q2735P		Atlas-SNP	.											FCGBP,NS,other,0,1	FCGBP	416	1	1	Substitution - Missense(1)	pancreas(1)	c.A8204C						scavenged	.																																			SO:0001583	missense	8857	exon17			CTGTTCTGAGGGC	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.8204A>C	19.37:g.40392182T>G	ENSP00000221347:p.Gln2735Pro	Somatic	558	15	0.0268817		WXS	Illumina HiSeq	Phase_I	728	28	0.0384615	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	t	0.025	-1.376540	0.01214	.	.	ENSG00000090920	ENST00000221347	D	0.89939	-2.59	2.66	0.187	0.15109	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.660669	0.14170	N	0.336777	T	0.55513	0.1925	N	0.00074	-2.255	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.59731	-0.7399	10	0.21540	T	0.41	.	5.3628	0.16098	0.1062:0.0:0.5459:0.3479	.	2735	Q9Y6R7	FCGBP_HUMAN	P	2735	ENSP00000221347:Q2735P	ENSP00000221347:Q2735P	Q	-	2	0	FCGBP	45084022	0.000000	0.05858	0.004000	0.12327	0.006000	0.05464	0.030000	0.13688	-0.290000	0.09025	-2.537000	0.00180	CAG	T|0.985;G|0.015	0.015	strong		0.652	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ELTD1	64123	hgsc.bcm.edu	37	1	79392756	79392756	+	Missense_Mutation	SNP	C	C	A	rs12754818	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:79392756C>A	ENST00000370742.3	-	8	961	c.898G>T	c.(898-900)Gta>Tta	p.V300L		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	300			V -> L (in dbSNP:rs12754818). {ECO:0000269|PubMed:11050079, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		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)		TTATAATATACAAATGCAACT	0.279													A|||	3108	0.620607	0.4939	0.6844	5008	,	,		16163	0.7044		0.6183	False		,,,				2504	0.6626				p.V300L		Atlas-SNP	.											.	ELTD1	143	.	0			c.G898T						PASS	.	A	LEU/VAL	1884,1704		511,862,421	55.0	51.0	52.0		898	3.7	1.0	1	dbSNP_121	52	5209,2935		1644,1921,507	yes	missense	ELTD1	NM_022159.3	32	2155,2783,928	AA,AC,CC		36.0388,47.4916,39.5414	benign	300/691	79392756	7093,4639	1794	4072	5866	SO:0001583	missense	64123	exon8			AATATACAAATGC	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.898G>T	1.37:g.79392756C>A	ENSP00000359778:p.Val300Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	63	10	0.15873	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	1361	0.6231684981684982	236	0.4796747967479675	243	0.6712707182320442	414	0.7237762237762237	468	0.6174142480211082	a	2.652	-0.281777	0.05642	0.525084	0.639612	ENSG00000162618	ENST00000370742	T	0.11930	2.73	6.02	3.74	0.42951	Domain of unknown function DUF3497 (1);	0.066165	0.64402	N	0.000012	T	0.00815	0.0027	N	0.00483	-1.445	0.53005	P	3.2999999999949736E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46748	-0.9169	8	.	.	.	.	5.2641	0.15589	0.5899:0.1427:0.2674:0.0	rs12754818;rs17845775;rs17858735;rs52801657;rs61009919;rs12754818	300	Q9HBW9	ELTD1_HUMAN	L	300	ENSP00000359778:V300L	.	V	-	1	0	ELTD1	79165344	1.000000	0.71417	0.997000	0.53966	0.909000	0.53808	1.538000	0.36094	0.187000	0.20147	-0.406000	0.06334	GTA	C|0.374;A|0.625	0.625	strong		0.279	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
ARL2	402	hgsc.bcm.edu	37	11	64789194	64789194	+	Splice_Site	SNP	T	T	C	rs664226	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:64789194T>C	ENST00000246747.4	+	5	517	c.422T>C	c.(421-423)gTc>gCc	p.V141A	RP11-399J13.3_ENST00000301886.3_Intron|ARL2_ENST00000533729.1_Splice_Site_p.V114A|ARL2_ENST00000529384.1_Splice_Site_p.V141A	NM_001667.3	NP_001658.2	P36404	ARL2_HUMAN	ADP-ribosylation factor-like 2	141			V -> A (in dbSNP:rs664226). {ECO:0000269|PubMed:15146197, ECO:0000269|PubMed:8415637, ECO:0000269|Ref.3}.		cell cycle (GO:0007049)|centrosome organization (GO:0051297)|GTP catabolic process (GO:0006184)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of GTPase activity (GO:0034260)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of microtubule polymerization (GO:0031116)|regulation of microtubule polymerization (GO:0031113)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)|tubulin complex assembly (GO:0007021)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|GTPase inhibitor activity (GO:0005095)	p.V141A(1)|p.?(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	5						TCCTCCCAGGTCCTGGAGCTG	0.667													C|||	2292	0.457668	0.7088	0.3905	5008	,	,		16560	0.1806		0.6064	False		,,,				2504	0.2986				p.V141A		Atlas-SNP	.											ARL2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ARL2	11	1	2	Substitution - Missense(1)|Unknown(1)	central_nervous_system(2)	c.T422C						PASS	.	C	ALA/VAL,ALA/VAL	3111,1291	423.4+/-340.1	1097,917,187	43.0	35.0	38.0		341,422	3.5	1.0	11	dbSNP_83	38	5392,3200	467.6+/-367.1	1685,2022,589	yes	missense-near-splice,missense-near-splice	ARL2	NM_001199745.1,NM_001667.3	64,64	2782,2939,776	CC,CT,TT		37.2439,29.3276,34.5621	benign,benign	114/158,141/185	64789194	8503,4491	2201	4296	6497	SO:0001630	splice_region_variant	402	exon5			CCCAGGTCCTGGA	AF493888	CCDS8088.1, CCDS55770.1	11q13	2014-05-09			ENSG00000213465	ENSG00000213465		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	693	protein-coding gene	gene with protein product		601175				8415637, 9253601	Standard	NM_001667		Approved	ARFL2	uc001och.4	P36404	OTTHUMG00000165728	ENST00000246747.4:c.421-1T>C	11.37:g.64789194T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_001667	G3V184|Q9BUK8	Missense_Mutation	SNP	ENST00000246747.4	37	CCDS8088.1	1041	0.4766483516483517	331	0.6727642276422764	163	0.45027624309392267	92	0.16083916083916083	455	0.600263852242744	C	2.707	-0.269614	0.05716	0.706724	0.627561	ENSG00000213465	ENST00000246747;ENST00000529384;ENST00000533729	D;D;D	0.81908	-1.55;-1.55;-1.55	4.5	3.5	0.40072	Small GTP-binding protein domain (1);	0.315868	0.28082	N	0.016667	T	0.00012	0.0000	N	0.00666	-1.275	0.09310	P	0.9999999999922409	B	0.02656	0.0	B	0.06405	0.002	T	0.45891	-0.9230	9	0.27785	T	0.31	-11.8565	8.1549	0.31162	0.0:0.7835:0.0:0.2165	rs664226;rs947902;rs2070187;rs2230868;rs11540367;rs61323596;rs664226	141	P36404	ARL2_HUMAN	A	141;141;114	ENSP00000246747:V141A;ENSP00000436021:V141A;ENSP00000432971:V114A	ENSP00000246747:V141A	V	+	2	0	ARL2	64545770	0.998000	0.40836	1.000000	0.80357	0.768000	0.43524	2.192000	0.42649	1.136000	0.42199	-0.338000	0.08134	GTC	T|0.439;C|0.561	0.561	strong		0.667	ARL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385963.1	NM_001667	Missense_Mutation
CELA2B	51032	hgsc.bcm.edu	37	1	15808767	15808767	+	Missense_Mutation	SNP	G	G	A	rs3820071	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15808767G>A	ENST00000375910.3	+	4	260	c.235G>A	c.(235-237)Ggg>Agg	p.G79R	CELA2B_ENST00000494280.1_3'UTR	NM_015849.2	NP_056933	P08218	CEL2B_HUMAN	chymotrypsin-like elastase family, member 2B	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		G -> R (in dbSNP:rs3820071). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3646943}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8						CAGCTCCTCCGGGATCTACCG	0.567													G|||	1635	0.326478	0.2776	0.3473	5008	,	,		14119	0.5685		0.2416	False		,,,				2504	0.2157				p.G79R		Atlas-SNP	.											CELA2B_ENST00000422901,NS,carcinoma,-1,6	CELA2B	37	6	0			c.G235A						PASS	.	G	ARG/GLY	1149,3257	407.5+/-334.3	143,863,1197	61.0	62.0	62.0		235	-6.2	0.2	1	dbSNP_107	62	2113,6487	363.2+/-333.1	270,1573,2457	yes	missense	CELA2B	NM_015849.2	125	413,2436,3654	AA,AG,GG		24.5698,26.0781,25.0807	benign	79/270	15808767	3262,9744	2203	4300	6503	SO:0001583	missense	51032	exon4			TCCTCCGGGATCT		CCDS30605.1	1p36.21	2009-07-09			ENSG00000215704	ENSG00000215704			29995	protein-coding gene	gene with protein product	"""pancreatic elastase IIB"""	609444				3646943, 16327289	Standard	NM_015849		Approved	RP11-265F14.2, ELA2B	uc001awl.3	P08218	OTTHUMG00000002259	ENST00000375910.3:c.235G>A	1.37:g.15808767G>A	ENSP00000365075:p.Gly79Arg	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_015849	Q14D16|Q6ISM5|Q96QV5	Missense_Mutation	SNP	ENST00000375910.3	37	CCDS30605.1	741	0.3392857142857143	121	0.2459349593495935	112	0.30939226519337015	311	0.5437062937062938	197	0.2598944591029024	G	0	-2.798414	0.00076	0.260781	0.245698	ENSG00000215704	ENST00000375910;ENST00000375909;ENST00000422901	D;D	0.90261	-2.35;-2.64	3.08	-6.17	0.02091	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.574111	0.15655	N	0.251153	T	0.00012	0.0000	N	0.12887	0.27	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41484	-0.9506	9	0.02654	T	1	.	0.8149	0.01100	0.2489:0.3212:0.1134:0.3166	rs3820071;rs17214904;rs52801345;rs59821889;rs3820071	79	P08218	CEL2B_HUMAN	R	79;86;98	ENSP00000365075:G79R;ENSP00000399811:G98R	ENSP00000365074:G86R	G	+	1	0	CELA2B	15681354	0.000000	0.05858	0.173000	0.22940	0.003000	0.03518	-1.849000	0.01672	-0.954000	0.03640	-2.217000	0.00297	GGG	G|0.706;A|0.294	0.294	strong		0.567	CELA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006448.1	NM_015849	
OR5H6	79295	hgsc.bcm.edu	37	3	97983602	97983602	+	Silent	SNP	T	T	C	rs75354046	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:97983602T>C	ENST00000383696.2	+	1	515	c.474T>C	c.(472-474)atT>atC	p.I158I	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	158						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AACTATGCATTCAGCTATTAG	0.358																																					p.I158I		Atlas-SNP	.											OR5H6,adrenal_gland,adrenal_cortical_adenoma,0,1	OR5H6	89	1	0			c.T474C						scavenged	.						109.0	102.0	104.0					3																	97983602		2203	4299	6502	SO:0001819	synonymous_variant	79295	exon1			ATGCATTCAGCTA	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.474T>C	3.37:g.97983602T>C		Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	253	8	0.0316206	NM_001005479	Q6IF88	Silent	SNP	ENST00000383696.2	37	CCDS33800.1																																																																																			T|0.898;C|0.102	0.102	strong		0.358	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2		
KIAA0922	23240	hgsc.bcm.edu	37	4	154388363	154388363	+	Splice_Site	SNP	C	C	T	rs78441178	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:154388363C>T	ENST00000409663.3	+	2	177	c.125C>T	c.(124-126)gCg>gTg	p.A42V	KIAA0922_ENST00000440693.1_Splice_Site_p.A42V|KIAA0922_ENST00000409959.3_Splice_Site_p.A42V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	42						integral component of membrane (GO:0016021)				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)				GTTCCTGCAGCGATTGAGCCG	0.577													c|||	2	0.000399361	0.0	0.0	5008	,	,		18938	0.0		0.002	False		,,,				2504	0.0				p.A42V		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C125T						PASS	.		VAL/ALA,VAL/ALA	1,1383		0,1,691	198.0	177.0	183.0		125,125	4.2	1.0	4	dbSNP_131	183	15,3167		0,15,1576	yes	missense-near-splice,missense-near-splice	KIAA0922	NM_001131007.1,NM_015196.3	64,64	0,16,2267	TT,TC,CC		0.4714,0.0723,0.3504	benign,benign	42/1611,42/1610	154388363	16,4550	692	1591	2283	SO:0001630	splice_region_variant	23240	exon2			CTGCAGCGATTGA	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.125-1C>T	4.37:g.154388363C>T		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	137	93	0.678832	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	c	15.31	2.796674	0.50208	7.23E-4	0.004714	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959	T;T;T	0.28255	1.89;1.62;1.9	5.23	4.19	0.49359	.	.	.	.	.	T	0.27798	0.0684	L	0.55481	1.735	0.27301	N	0.957589	B;B	0.32526	0.374;0.257	B;B	0.29942	0.109;0.051	T	0.08827	-1.0703	8	.	.	.	.	10.079	0.42377	0.0:0.8247:0.0:0.1753	.	42;42	A2VDJ0-5;A2VDJ0	.;T131L_HUMAN	V	42	ENSP00000386574:A42V;ENSP00000409663:A42V;ENSP00000386787:A42V	.	A	+	2	0	KIAA0922	154607813	0.991000	0.36638	1.000000	0.80357	0.988000	0.76386	1.197000	0.32211	2.442000	0.82660	0.550000	0.68814	GCG	.	.	weak		0.577	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	Missense_Mutation
ZC3H3	23144	hgsc.bcm.edu	37	8	144620855	144620855	+	Missense_Mutation	SNP	C	C	A	rs4873802	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	29	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	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	
PRX	57716	hgsc.bcm.edu	37	19	40909695	40909695	+	Silent	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40909695T>G	ENST00000324001.7	-	5	372	c.102A>C	c.(100-102)gtA>gtC	p.V34V	PRX_ENST00000291825.7_Silent_p.V34V	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	34	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CGCCGCCCGCTACGTTGATGC	0.692																																					p.V34V		Atlas-SNP	.											.	PRX	151	.	0			c.A102C						PASS	.						15.0	14.0	14.0					19																	40909695		2193	4294	6487	SO:0001819	synonymous_variant	57716	exon5			GCCCGCTACGTTG	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.102A>C	19.37:g.40909695T>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_181882	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	CCDS33028.1																																																																																			.	.	none		0.692	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
PABPC1L	80336	hgsc.bcm.edu	37	20	43566787	43566787	+	Silent	SNP	A	A	G	rs11780	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:43566787A>G	ENST00000217073.2	+	13	1731	c.1731A>G	c.(1729-1731)tcA>tcG	p.S577S	PABPC1L_ENST00000217075.2_Silent_p.S131S|PABPC1L_ENST00000372819.1_Silent_p.S131S|PABPC1L_ENST00000537323.1_3'UTR|PABPC1L_ENST00000372824.1_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	134	63	0.470149	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		
IGF2R	3482	hgsc.bcm.edu	37	6	160453978	160453978	+	Silent	SNP	A	A	G	rs1570070	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160453978A>G	ENST00000356956.1	+	9	1198	c.1050A>G	c.(1048-1050)tcA>tcG	p.S350S		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	350					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTTTAGGTTCATCCTATATTT	0.313													A|||	2123	0.423922	0.2405	0.3545	5008	,	,		20863	0.746		0.3489	False		,,,				2504	0.4663				p.S350S		Atlas-SNP	.											.	IGF2R	251	.	0			c.A1050G						PASS	.	A		1139,3265	378.0+/-322.7	132,875,1195	79.0	88.0	85.0		1050	-7.8	0.0	6	dbSNP_88	85	2790,5810	437.3+/-358.6	463,1864,1973	no	coding-synonymous	IGF2R	NM_000876.2		595,2739,3168	GG,GA,AA		32.4419,25.8629,30.2138		350/2492	160453978	3929,9075	2202	4300	6502	SO:0001819	synonymous_variant	3482	exon9			AGGTTCATCCTAT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1050A>G	6.37:g.160453978A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			A|0.643;G|0.357	0.357	strong		0.313	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887394	9887394	+	Silent	SNP	C	C	T	rs2240910	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:9887394C>T	ENST00000306084.6	+	2	1117	c.918C>T	c.(916-918)gcC>gcT	p.A306A	TXNDC2_ENST00000357775.5_Silent_p.A239A|TXNDC2_ENST00000536353.2_Intron	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	306	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						TAGAGGAAGCCATCCAGCCCA	0.602													-|||	2596	0.518371	0.3623	0.5331	5008	,	,		20966	0.8155		0.4761	False		,,,				2504	0.456				p.A306A		Atlas-SNP	.											TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	0			c.C918T						PASS	.	C	,	1751,2655		357,1037,809	132.0	127.0	128.0		918,717	-0.1	0.0	18	dbSNP_98	128	4210,4390		1043,2124,1133	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	1400,3161,1942	TT,TC,CC		48.9535,39.7413,45.8327	,	306/554,239/487	9887394	5961,7045	2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			GGAAGCCATCCAG	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.918C>T	18.37:g.9887394C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			C|0.531;T|0.469	0.469	strong		0.602	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
BRWD1	54014	hgsc.bcm.edu	37	21	40574434	40574434	+	Missense_Mutation	SNP	T	T	C	rs144295288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:40574434T>C	ENST00000333229.2	-	38	4729	c.4402A>G	c.(4402-4404)Ata>Gta	p.I1468V	BRWD1_ENST00000380800.3_Missense_Mutation_p.I1468V|BRWD1_ENST00000342449.3_Missense_Mutation_p.I1468V	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1468					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TCAGGAATTATTTTTGTCTGA	0.398													T|||	7	0.00139776	0.0	0.0	5008	,	,		18729	0.0		0.007	False		,,,				2504	0.0				p.I1468V	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A4402G						PASS	.	T	VAL/ILE,VAL/ILE	6,4400	9.9+/-24.2	0,6,2197	72.0	67.0	69.0		4402,4402	3.4	0.7	21	dbSNP_134	69	46,8554	29.0+/-79.6	2,42,4256	yes	missense,missense	BRWD1	NM_018963.4,NM_033656.3	29,29	2,48,6453	CC,CT,TT		0.5349,0.1362,0.3998	benign,benign	1468/2321,1468/2270	40574434	52,12954	2203	4300	6503	SO:0001583	missense	54014	exon38			GAATTATTTTTGT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.4402A>G	21.37:g.40574434T>C	ENSP00000330753:p.Ile1468Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	151	55	0.364238	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	T|T	0.007|0.007	-1.938401|-1.938401	0.00484|0.00484	0.001362|0.001362	0.005349|0.005349	ENSG00000185658|ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800;ENST00000380783|ENST00000424441	T;T;T|.	0.52983|.	0.64;0.66;0.73|.	5.27|5.27	3.39|3.39	0.38822|0.38822	.|.	0.692467|.	0.13487|.	N|.	0.384267|.	T|T	0.04815|0.04815	0.0130|0.0130	N|N	0.00436|0.00436	-1.5|-1.5	0.09310|0.09310	N|N	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.04013|.	0.001;0.001;0.0|.	T|T	0.33727|0.33727	-0.9857|-0.9857	10|5	0.24483|.	T|.	0.36|.	-2.138|-2.138	4.6929|4.6929	0.12790|0.12790	0.0:0.5271:0.151:0.3219|0.0:0.5271:0.151:0.3219	.|.	1468;1468;1468|.	Q9NSI6-3;Q9NSI6-2;Q9NSI6|.	.;.;BRWD1_HUMAN|.	V|S	1468;1468;1468;424|405	ENSP00000330753:I1468V;ENSP00000344333:I1468V;ENSP00000370178:I1468V|.	ENSP00000330753:I1468V|.	I|N	-|-	1|2	0|0	BRWD1|BRWD1	39496304|39496304	0.054000|0.054000	0.20591|0.20591	0.729000|0.729000	0.30791|0.30791	0.351000|0.351000	0.29236|0.29236	0.360000|0.360000	0.20250|0.20250	0.608000|0.608000	0.30000|0.30000	-0.177000|-0.177000	0.13119|0.13119	ATA|AAT	T|0.997;C|0.003	0.003	strong		0.398	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
PVR	5817	hgsc.bcm.edu	37	19	45153113	45153113	+	Missense_Mutation	SNP	G	G	C	rs35959395	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45153113G>C	ENST00000425690.3	+	3	759	c.460G>C	c.(460-462)Gtc>Ctc	p.V154L	PVR_ENST00000406449.4_Missense_Mutation_p.V154L|PVR_ENST00000403059.4_Missense_Mutation_p.V154L|PVR_ENST00000344956.4_Missense_Mutation_p.V154L|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	154	Ig-like C2-type 1.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		GGTTCAGAAGGTCCAGCTCAC	0.602													G|||	6	0.00119808	0.0	0.0	5008	,	,		16803	0.0		0.006	False		,,,				2504	0.0				p.V154L		Atlas-SNP	.											.	PVR	23	.	0			c.G460C						PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	2,4404	4.2+/-10.8	0,2,2201	121.0	129.0	126.0		460,460,460,460	-0.5	0.0	19	dbSNP_126	126	19,8581	11.9+/-42.8	0,19,4281	yes	missense,missense,missense,missense	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	32,32,32,32	0,21,6482	CC,CG,GG		0.2209,0.0454,0.1615	probably-damaging,probably-damaging,probably-damaging,probably-damaging	154/373,154/365,154/393,154/418	45153113	21,12985	2203	4300	6503	SO:0001583	missense	5817	exon3			CAGAAGGTCCAGC	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.460G>C	19.37:g.45153113G>C	ENSP00000402060:p.Val154Leu	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.03	2.712862	0.48517	4.54E-4	0.002209	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	4.35	-0.515	0.11954	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);	1.055660	0.07497	N	0.906707	D	0.86493	0.5946	M	0.90309	3.105	0.09310	N	1	P;D;D;D	0.59767	0.842;0.983;0.983;0.986	P;D;D;D	0.74023	0.698;0.957;0.969;0.982	T	0.70328	-0.4902	10	0.20046	T	0.44	.	4.0615	0.09841	0.3186:0.1848:0.4966:0.0	rs35959395	154;154;154;154	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	L	154	ENSP00000340870:V154L;ENSP00000402060:V154L;ENSP00000383907:V154L;ENSP00000385344:V154L	ENSP00000340870:V154L	V	+	1	0	PVR	49844953	0.005000	0.15991	0.000000	0.03702	0.020000	0.10135	0.802000	0.27069	-0.290000	0.09025	-0.339000	0.08088	GTC	G|0.999;C|0.001	0.001	strong		0.602	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
DFNB31	25861	hgsc.bcm.edu	37	9	117266965	117266965	+	Silent	SNP	C	C	T	rs2297815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:117266965C>T	ENST00000362057.3	-	1	285	c.117G>A	c.(115-117)gtG>gtA	p.V39V	DFNB31_ENST00000480518.1_5'Flank|DFNB31_ENST00000374057.3_Silent_p.V39V|DFNB31_ENST00000265134.6_5'Flank	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	39					inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GCAGCTGGCGCACGTTGGCAG	0.736													C|||	1280	0.255591	0.2231	0.3256	5008	,	,		9043	0.1389		0.4016	False		,,,				2504	0.2198				p.V39V		Atlas-SNP	.											.	DFNB31	100	.	0			c.G117A						PASS	.	C	,	1053,3341		130,793,1274	24.0	18.0	20.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	117,117	5.3	1.0	9	dbSNP_100	20	3136,5450		571,1994,1728	no	coding-synonymous,coding-synonymous	DFNB31	NM_001173425.1,NM_015404.3	,	701,2787,3002	TT,TC,CC		36.5246,23.9645,32.2727	,	39/907,39/908	117266965	4189,8791	2197	4293	6490	SO:0001819	synonymous_variant	25861	exon1			CTGGCGCACGTTG	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.117G>A	9.37:g.117266965C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_001173425	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Silent	SNP	ENST00000362057.3	37	CCDS6806.1																																																																																			C|0.706;T|0.294	0.294	strong		0.736	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
DDB1	1642	hgsc.bcm.edu	37	11	61099072	61099072	+	Silent	SNP	G	G	A	rs2230356	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:61099072G>A	ENST00000301764.7	-	2	550	c.153C>T	c.(151-153)ccC>ccT	p.P51P	DAK_ENST00000394900.3_5'Flank|DDB1_ENST00000450997.2_Silent_p.P51P	NM_001923.4	NP_001914.3	Q16531	DDB1_HUMAN	damage-specific DNA binding protein 1, 127kDa	51	Interaction with CDT1.|WD repeat beta-propeller A.				DNA repair (GO:0006281)|histone H2A monoubiquitination (GO:0035518)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of mitotic cell cycle phase transition (GO:1901990)|UV-damage excision repair (GO:0070914)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|Cul4B-RING E3 ubiquitin ligase complex (GO:0031465)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	48						CCTCTTTGACGGGCCGAAGCC	0.512								Nucleotide excision repair (NER)					G|||	237	0.0473243	0.0416	0.0807	5008	,	,		17974	0.0		0.1143	False		,,,				2504	0.0112				p.P51P		Atlas-SNP	.											.	DDB1	100	.	0			c.C153T						PASS	.	G		185,4221	118.4+/-156.1	3,179,2021	109.0	91.0	97.0		153	-4.4	1.0	11	dbSNP_98	97	910,7688	203.0+/-246.1	51,808,3440	no	coding-synonymous	DDB1	NM_001923.3		54,987,5461	AA,AG,GG		10.5839,4.1988,8.4205		51/1141	61099072	1095,11909	2203	4299	6502	SO:0001819	synonymous_variant	1642	exon2			TTTGACGGGCCGA	AJ002955	CCDS31576.1	11q12-q13	2014-09-17	2002-08-29		ENSG00000167986	ENSG00000167986			2717	protein-coding gene	gene with protein product		600045	"""damage-specific DNA binding protein 1 (127kD)"""			8530102, 10574459	Standard	NM_001923		Approved	XPE	uc001nrc.5	Q16531	OTTHUMG00000168209	ENST00000301764.7:c.153C>T	11.37:g.61099072G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	197	96	0.48731	NM_001923	A6NG77|B2R648|B4DG00|O15176|Q13289|Q58F96	Silent	SNP	ENST00000301764.7	37	CCDS31576.1																																																																																			G|0.928;A|0.072	0.072	strong		0.512	DDB1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398816.1	NM_001923	
ABCA8	10351	hgsc.bcm.edu	37	17	66878099	66878099	+	Missense_Mutation	SNP	C	C	T	rs34987539	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:66878099C>T	ENST00000269080.2	-	29	3868	c.3731G>A	c.(3730-3732)tGt>tAt	p.C1244Y	ABCA8_ENST00000586539.1_Missense_Mutation_p.C1284Y|ABCA8_ENST00000430352.2_Missense_Mutation_p.C1284Y	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	1244					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)					CTTGCGTAGACAGCTGGCAAT	0.408													C|||	26	0.00519169	0.0008	0.0029	5008	,	,		23456	0.001		0.0169	False		,,,				2504	0.0051				p.C1244Y		Atlas-SNP	.											.	ABCA8	213	.	0			c.G3731A						PASS	.	C	TYR/CYS	13,4393	19.1+/-41.9	0,13,2190	135.0	126.0	129.0		3731	4.8	1.0	17	dbSNP_126	129	101,8499	56.0+/-117.1	1,99,4200	yes	missense	ABCA8	NM_007168.2	194	1,112,6390	TT,TC,CC		1.1744,0.2951,0.8765	probably-damaging	1244/1582	66878099	114,12892	2203	4300	6503	SO:0001583	missense	10351	exon29			CGTAGACAGCTGG	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.3731G>A	17.37:g.66878099C>T	ENSP00000269080:p.Cys1244Tyr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	118	64	0.542373	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	15	0.006868131868131868	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	13	0.017150395778364115	C	16.93	3.258878	0.59321	0.002951	0.011744	ENSG00000141338	ENST00000269080;ENST00000430352	D;D	0.85629	-2.01;-2.01	4.75	4.75	0.60458	.	0.000000	0.64402	D	0.000018	D	0.88081	0.6341	M	0.89840	3.065	0.39548	D	0.968927	D;D;D	0.89917	1.0;0.993;1.0	D;D;D	0.79784	0.993;0.964;0.984	D	0.90611	0.4552	10	0.62326	D	0.03	.	12.7575	0.57343	0.0:0.9174:0.0:0.0826	rs34987539	1284;1284;1244	A1L3U3;C9JQE6;O94911	.;.;ABCA8_HUMAN	Y	1244;1284	ENSP00000269080:C1244Y;ENSP00000402814:C1284Y	ENSP00000269080:C1244Y	C	-	2	0	ABCA8	64389694	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	0.751000	0.26348	2.623000	0.88846	0.563000	0.77884	TGT	C|0.992;T|0.008	0.008	strong		0.408	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
MAP3K10	4294	hgsc.bcm.edu	37	19	40719076	40719076	+	Silent	SNP	T	T	C	rs1129156	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40719076T>C	ENST00000253055.3	+	8	2106	c.1818T>C	c.(1816-1818)ttT>ttC	p.F606F		NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	606					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						CCCCTGGCTTTGCCAGCCTCA	0.622													C|||	3792	0.757188	0.8011	0.7421	5008	,	,		17049	0.6974		0.7505	False		,,,				2504	0.7771				p.F606F		Atlas-SNP	.											MAP3K10,NS,carcinoma,0,1	MAP3K10	70	1	0			c.T1818C						PASS	.	C		3532,864		1441,650,107	23.0	22.0	22.0		1818	0.5	1.0	19	dbSNP_86	22	6225,2359		2286,1653,353	no	coding-synonymous	MAP3K10	NM_002446.3		3727,2303,460	CC,CT,TT		27.4814,19.6542,24.8305		606/955	40719076	9757,3223	2198	4292	6490	SO:0001819	synonymous_variant	4294	exon8			TGGCTTTGCCAGC	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6849	protein-coding gene	gene with protein product	"""MKN28 kinase"", ""mixed lineage kinase 2"", ""MKN28 derived nonreceptor_type serine/threonine kinase"""	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.1818T>C	19.37:g.40719076T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_002446	Q12761|Q14871	Silent	SNP	ENST00000253055.3	37	CCDS12549.1																																																																																			T|0.250;C|0.750	0.750	strong		0.622	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446	
ZNF646	9726	hgsc.bcm.edu	37	16	31090094	31090094	+	Missense_Mutation	SNP	G	G	A	rs78522165	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:31090094G>A	ENST00000394979.2	+	1	2872	c.2449G>A	c.(2449-2451)Gct>Act	p.A817T	ZNF646_ENST00000300850.5_Missense_Mutation_p.A817T			O15015	ZN646_HUMAN	zinc finger protein 646	817					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						TGGCTGGCAGGCTGGGGCCGC	0.612													G|||	137	0.0273562	0.003	0.0504	5008	,	,		18187	0.0		0.0875	False		,,,				2504	0.0102				p.A817T		Atlas-SNP	.											.	ZNF646	133	.	0			c.G2449A						PASS	.	G	THR/ALA	58,4336	56.8+/-93.2	0,58,2139	70.0	71.0	71.0		2449	-0.9	0.4	16	dbSNP_131	71	619,7981	161.9+/-214.7	17,585,3698	yes	missense	ZNF646	NM_014699.3	58	17,643,5837	AA,AG,GG		7.1977,1.32,5.2101	benign	817/1833	31090094	677,12317	2197	4300	6497	SO:0001583	missense	9726	exon2			TGGCAGGCTGGGG	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.2449G>A	16.37:g.31090094G>A	ENSP00000378429:p.Ala817Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		88	0.040293040293040296	0	0.0	20	0.055248618784530384	0	0.0	68	0.08970976253298153	G	8.689	0.906916	0.17833	0.0132	0.071977	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.08193	3.12;3.18	5.25	-0.882	0.10604	.	.	.	.	.	T	0.00178	0.0005	N	0.11560	0.145	0.20926	N	0.999823	B	0.13145	0.007	B	0.14578	0.011	T	0.47459	-0.9116	9	0.21014	T	0.42	-0.3298	4.8583	0.13570	0.4322:0.0:0.4244:0.1434	.	817	O15015-2	.	T	817	ENSP00000300850:A817T;ENSP00000378429:A817T	ENSP00000300850:A817T	A	+	1	0	ZNF646	30997595	0.001000	0.12720	0.433000	0.26760	0.101000	0.19017	-0.216000	0.09266	-0.019000	0.14055	0.563000	0.77884	GCT	A|0.052;C|0.000;G|0.948	0.052	strong		0.612	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802629	31802629	+	Silent	SNP	C	C	T	rs73356729	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31802629C>T	ENST00000334068.2	+	1	58	c.36C>T	c.(34-36)tcC>tcT	p.S12S		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	12						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						ACTTCTCCTCCCGCTCCTTTG	0.547													-|||	220	0.0439297	0.1581	0.0144	5008	,	,		18637	0.0		0.001	False		,,,				2504	0.0				p.S12S	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.C36T						PASS	.	C		473,3933		25,423,1755	109.0	111.0	110.0		36	0.1	0.1	21	dbSNP_130	110	10,8590		0,10,4290	no	coding-synonymous	KRTAP13-4	NM_181600.1		25,433,6045	TT,TC,CC		0.1163,10.7354,3.7137		12/161	31802629	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	284827	exon1			CTCCTCCCGCTCC	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.36C>T	21.37:g.31802629C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	240	79	0.329167	NM_181600	A2RRL3	Silent	SNP	ENST00000334068.2	37	CCDS13592.1																																																																																			C|0.963;T|0.037	0.037	strong		0.547	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
DEFB129	140881	hgsc.bcm.edu	37	20	210306	210306	+	Missense_Mutation	SNP	C	C	G	rs1053783	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:210306C>G	ENST00000246105.4	+	2	477	c.446C>G	c.(445-447)aCc>aGc	p.T149S		NM_080831.3	NP_543021.1	Q9H1M3	DB129_HUMAN	defensin, beta 129	149			T -> S (in dbSNP:rs1053783).		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				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)			AAGAGTAACACCAAAGAAAGC	0.502													C|||	1248	0.249201	0.469	0.1196	5008	,	,		18729	0.2351		0.0915	False		,,,				2504	0.2209				p.T149S		Atlas-SNP	.											.	DEFB129	24	.	0			c.C446G						PASS	.	C	SER/THR	1840,2566	536.8+/-374.6	389,1062,752	136.0	123.0	127.0		446	2.3	0.0	20	dbSNP_86	127	774,7826	183.5+/-231.7	37,700,3563	yes	missense	DEFB129	NM_080831.3	58	426,1762,4315	GG,GC,CC		9.0,41.7612,20.0984	probably-damaging	149/184	210306	2614,10392	2203	4300	6503	SO:0001583	missense	140881	exon2			GTAACACCAAAGA	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.446C>G	20.37:g.210306C>G	ENSP00000246105:p.Thr149Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_080831	Q8NES7	Missense_Mutation	SNP	ENST00000246105.4	37	CCDS12992.1	459	0.21016483516483517	222	0.45121951219512196	43	0.11878453038674033	127	0.22202797202797203	67	0.08839050131926121	C	14.43	2.533782	0.45073	0.417612	0.09	ENSG00000125903	ENST00000246105	T	0.38401	1.14	4.25	2.27	0.28462	.	0.739381	0.12150	N	0.494997	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.41978	0.767	B	0.33196	0.159	T	0.48175	-0.9058	9	0.49607	T	0.09	-9.4267	6.8928	0.24238	0.0:0.7886:0.0:0.2114	rs1053783;rs3194381;rs52805850;rs59902862;rs1053783	149	Q9H1M3	DB129_HUMAN	S	149	ENSP00000246105:T149S	ENSP00000246105:T149S	T	+	2	0	DEFB129	158306	0.001000	0.12720	0.018000	0.16275	0.084000	0.17831	0.085000	0.14912	0.725000	0.32318	0.462000	0.41574	ACC	C|0.798;G|0.202	0.202	strong		0.502	DEFB129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077430.2	NM_080831	
UHRF1BP1L	23074	hgsc.bcm.edu	37	12	100452832	100452832	+	Silent	SNP	C	C	T	rs11832216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:100452832C>T	ENST00000279907.7	-	14	2435	c.2223G>A	c.(2221-2223)ccG>ccA	p.P741P	UHRF1BP1L_ENST00000545232.2_Silent_p.P391P	NM_015054.1	NP_055869.1	A0JNW5	UH1BL_HUMAN	UHRF1 binding protein 1-like	741										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						TACAAGTCTGCGGCTCTTTTT	0.403													C|||	268	0.0535144	0.0703	0.0591	5008	,	,		18430	0.004		0.0686	False		,,,				2504	0.0624				p.P741P		Atlas-SNP	.											UHRF1BP1L,caecum,carcinoma,-1,1	UHRF1BP1L	144	1	0			c.G2223A						PASS	.	C		336,4066	162.9+/-194.8	14,308,1879	93.0	100.0	98.0		2223	-9.4	0.0	12	dbSNP_120	98	568,8024	151.3+/-206.1	23,522,3751	no	coding-synonymous	UHRF1BP1L	NM_015054.1		37,830,5630	TT,TC,CC		6.6108,7.6329,6.9571		741/1465	100452832	904,12090	2201	4296	6497	SO:0001819	synonymous_variant	23074	exon14			AGTCTGCGGCTCT		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.2223G>A	12.37:g.100452832C>T		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	247	127	0.51417	NM_015054	A0PJE5|O75183|Q8NDL1|Q96C30|Q9BTS5|Q9H0F1	Silent	SNP	ENST00000279907.7	37	CCDS31882.1																																																																																			C|0.936;T|0.064	0.064	strong		0.403	UHRF1BP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407875.1	NM_001006947	
CCDC74A	90557	hgsc.bcm.edu	37	2	132289293	132289293	+	Missense_Mutation	SNP	T	T	C	rs149647165	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:132289293T>C	ENST00000295171.6	+	4	739	c.601T>C	c.(601-603)Tcc>Ccc	p.S201P	CCDC74A_ENST00000409856.3_Missense_Mutation_p.S135P|CCDC74A_ENST00000467992.2_Missense_Mutation_p.S303P	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	203	2	0.00985222		WXS	Illumina HiSeq	Phase_I	114	31	0.27193	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	
C19orf48	84798	hgsc.bcm.edu	37	19	51301456	51301456	+	Missense_Mutation	SNP	G	G	A	rs4802741	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51301456G>A	ENST00000598463.1	-	5	1348	c.250C>T	c.(250-252)Cgc>Tgc	p.R84C	C19orf48_ENST00000596655.1_Missense_Mutation_p.R84C|SNORD88B_ENST00000408454.1_RNA|C19orf48_ENST00000345523.4_Missense_Mutation_p.R84C|SNORD88A_ENST00000408314.1_RNA|C19orf48_ENST00000391812.1_Missense_Mutation_p.R84C|C19orf48_ENST00000595794.1_5'Flank			Q6RUI8	CS048_HUMAN	chromosome 19 open reading frame 48	84			R -> C (in dbSNP:rs4802741).							endometrium(1)|kidney(1)|lung(1)|ovary(1)	4		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00531)|GBM - Glioblastoma multiforme(134;0.0145)		TCACGGTGGCGTATGGACAGC	0.637													G|||	1652	0.329872	0.1309	0.2161	5008	,	,		19818	0.6538		0.3012	False		,,,				2504	0.3753				p.R84C		Atlas-SNP	.											.	C19orf48	11	.	0			c.C250T						PASS	.	G	CYS/ARG,CYS/ARG	682,3724		45,592,1566	110.0	100.0	103.0		250,250	0.9	0.0	19	dbSNP_111	103	2414,6186		350,1714,2236	yes	missense,missense	C19orf48	NM_199250.1,NM_199249.1	180,180	395,2306,3802	AA,AG,GG		28.0698,15.4789,23.8044	benign,benign	84/118,84/118	51301456	3096,9910	2203	4300	6503	SO:0001583	missense	84798	exon5			GGTGGCGTATGGA	BC037227	CCDS12803.1	19q13.33	2012-10-26			ENSG00000167747	ENSG00000167747			29667	protein-coding gene	gene with protein product	"""multidrug resistance-related protein"""					12452007	Standard	NM_001290154		Approved	MGC13170	uc002ptg.3	Q6RUI8		ENST00000598463.1:c.250C>T	19.37:g.51301456G>A	ENSP00000471463:p.Arg84Cys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_199249		Missense_Mutation	SNP	ENST00000598463.1	37	CCDS12803.1	769	0.35210622710622713	71	0.1443089430894309	80	0.22099447513812154	383	0.6695804195804196	235	0.3100263852242744	N	1.803	-0.476478	0.04414	0.154789	0.280698	ENSG00000167747	ENST00000391812;ENST00000345523	T;T	0.32023	1.47;1.47	1.92	0.845	0.18950	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.31779	-0.9931	8	0.44086	T	0.13	.	7.3421	0.26644	0.1625:0.0:0.8375:0.0	rs4802741;rs17657799;rs60128113;rs4802741	84	Q6RUI8	CS048_HUMAN	C	84	ENSP00000375688:R84C;ENSP00000301419:R84C	ENSP00000301419:R84C	R	-	1	0	C19orf48	55993268	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.160000	0.16462	-0.004000	0.14419	-1.786000	0.00637	CGC	G|0.713;A|0.287	0.287	strong		0.637	C19orf48-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464107.1	NM_032712	
PRKD1	5587	hgsc.bcm.edu	37	14	30066929	30066929	+	Silent	SNP	A	A	G	rs2230505	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:30066929A>G	ENST00000331968.5	-	16	2431	c.2202T>C	c.(2200-2202)atT>atC	p.I734I	PRKD1_ENST00000415220.2_Silent_p.I742I	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	734	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to oxidative stress (GO:0034599)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|negative regulation of cell death (GO:0060548)|negative regulation of endocytosis (GO:0045806)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of CREB transcription factor activity (GO:0032793)|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 histone deacetylase activity (GO:1901727)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein autophosphorylation (GO:0046777)|regulation of integrin-mediated signaling pathway (GO:2001044)|regulation of keratinocyte proliferation (GO:0010837)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|lung(32)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	78	Hepatocellular(127;0.0604)		LUAD - Lung adenocarcinoma(48;0.00527)|Lung(238;0.0252)	GBM - Glioblastoma multiforme(265;0.00888)		ACTTCTCTCCAATGATCCGGG	0.478													A|||	2563	0.511781	0.851	0.4568	5008	,	,		14241	0.2113		0.3837	False		,,,				2504	0.5337				p.I734I		Atlas-SNP	.											.	PRKD1	316	.	0			c.T2202C						PASS	.	A		3369,1037	726.8+/-409.8	1298,773,132	58.0	62.0	61.0		2202	2.1	1.0	14	dbSNP_98	61	3258,5342	488.6+/-372.4	595,2068,1637	no	coding-synonymous	PRKD1	NM_002742.2		1893,2841,1769	GG,GA,AA		37.8837,23.5361,49.0466		734/913	30066929	6627,6379	2203	4300	6503	SO:0001819	synonymous_variant	5587	exon16			CTCTCCAATGATC		CCDS9637.1	14q11	2013-01-10	2004-10-28	2004-10-30	ENSG00000184304	ENSG00000184304	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	9407	protein-coding gene	gene with protein product		605435	"""protein kinase C, mu"""	PRKCM		8119958, 10965134	Standard	NM_002742		Approved	PKCM, PKD, PKC-mu	uc001wqh.3	Q15139	OTTHUMG00000140203	ENST00000331968.5:c.2202T>C	14.37:g.30066929A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																			T|0.088;G|0.396;C|0.100;A|0.416	0.396	strong		0.478	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742	
RTTN	25914	hgsc.bcm.edu	37	18	67755252	67755252	+	Missense_Mutation	SNP	C	C	G	rs376382612		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:67755252C>G	ENST00000255674.6	-	31	4561	c.4275G>C	c.(4273-4275)caG>caC	p.Q1425H	RTTN_ENST00000437017.1_Missense_Mutation_p.Q1425H|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1425					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)				TACATTCTGACTGGTCCAGAA	0.483																																					p.Q1425H		Atlas-SNP	.											.	RTTN	184	.	0			c.G4275C						PASS	.	C	HIS/GLN	0,3862		0,0,1931	100.0	98.0	98.0		4275	-1.0	1.0	18		98	1,8241		0,1,4120	no	missense	RTTN	NM_173630.3	24	0,1,6051	GG,GC,CC		0.0121,0.0,0.0083	benign	1425/2227	67755252	1,12103	1931	4121	6052	SO:0001583	missense	25914	exon31			TTCTGACTGGTCC	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.4275G>C	18.37:g.67755252C>G	ENSP00000255674:p.Gln1425His	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.878046	0.33162	0.0	1.21E-4	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.68331	-0.32;-0.32	5.45	-0.961	0.10337	Armadillo-like helical (1);	0.110450	0.64402	D	0.000007	T	0.43389	0.1245	L	0.35414	1.06	0.80722	D	1	P	0.34934	0.476	B	0.26094	0.066	T	0.10428	-1.0630	10	0.40728	T	0.16	.	5.2259	0.15393	0.2225:0.4534:0.0:0.3242	.	1425	Q86VV8	RTTN_HUMAN	H	1425	ENSP00000255674:Q1425H;ENSP00000399520:Q1425H	ENSP00000255674:Q1425H	Q	-	3	2	RTTN	65906232	0.988000	0.35896	0.987000	0.45799	0.968000	0.65278	0.302000	0.19192	0.074000	0.16767	0.484000	0.47621	CAG	.	.	weak		0.483	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
PADI4	23569	hgsc.bcm.edu	37	1	17668563	17668563	+	Missense_Mutation	SNP	G	G	A	rs35903413	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:17668563G>A	ENST00000375448.4	+	7	804	c.778G>A	c.(778-780)Gac>Aac	p.D260N	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	260			D -> N (in dbSNP:rs35903413).		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)	CCCGGACACCGACTTCCCGGG	0.627													G|||	263	0.052516	0.0129	0.0865	5008	,	,		16205	0.001		0.1531	False		,,,				2504	0.0317				p.D260N		Atlas-SNP	.											.	PADI4	70	.	0			c.G778A						PASS	.	G	ASN/ASP	131,4275	96.2+/-134.9	0,131,2072	85.0	80.0	82.0		778	1.3	0.1	1	dbSNP_126	82	1107,7493	231.1+/-265.2	77,953,3270	yes	missense	PADI4	NM_012387.2	23	77,1084,5342	AA,AG,GG		12.8721,2.9732,9.5187	benign	260/664	17668563	1238,11768	2203	4300	6503	SO:0001583	missense	23569	exon7			GACACCGACTTCC	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.778G>A	1.37:g.17668563G>A	ENSP00000364597:p.Asp260Asn	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	107	21	0.196262	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	37	CCDS180.1	156	0.07142857142857142	4	0.008130081300813009	30	0.08287292817679558	1	0.0017482517482517483	121	0.15963060686015831	g	1.634	-0.518326	0.04171	0.029732	0.128721	ENSG00000159339	ENST00000375448	T	0.15372	2.43	4.63	1.27	0.21489	Protein-arginine deiminase (PAD), central domain (2);	0.532611	0.20775	N	0.085903	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.14805	0.011;0.011	B;B	0.12837	0.008;0.008	T	0.37009	-0.9724	9	0.20519	T	0.43	-13.0871	6.2085	0.20615	0.5552:0.0:0.4448:0.0	rs35903413	260;260	A8K392;Q9UM07	.;PADI4_HUMAN	N	260	ENSP00000364597:D260N	ENSP00000364597:D260N	D	+	1	0	PADI4	17541150	0.000000	0.05858	0.069000	0.20011	0.041000	0.13682	0.539000	0.23175	0.345000	0.23873	-0.355000	0.07637	GAC	G|0.908;A|0.092	0.092	strong		0.627	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
MUC16	94025	hgsc.bcm.edu	37	19	9068990	9068990	+	Missense_Mutation	SNP	G	G	T	rs35092547	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9068990G>T	ENST00000397910.4	-	3	18659	c.18456C>A	c.(18454-18456)caC>caA	p.H6152Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6154	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						CGATGGTCTTGTGTGTAGATA	0.507													g|||	49	0.00978435	0.0008	0.0216	5008	,	,		17653	0.001		0.0268	False		,,,				2504	0.0051				p.H6152Q		Atlas-SNP	.											.	MUC16	4315	.	0			c.C18456A						PASS	.	G	GLN/HIS	17,4221		0,17,2102	66.0	70.0	69.0		18456	-2.7	0.0	19	dbSNP_126	69	249,8207		5,239,3984	yes	missense	MUC16	NM_024690.2	24	5,256,6086	TT,TG,GG		2.9447,0.4011,2.0955	benign	6152/14508	9068990	266,12428	2119	4228	6347	SO:0001583	missense	94025	exon3			GGTCTTGTGTGTA	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.18456C>A	19.37:g.9068990G>T	ENSP00000381008:p.His6152Gln	Somatic	620	0	0		WXS	Illumina HiSeq	Phase_I	619	307	0.495961	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	0	0.0	6	0.016574585635359115	1	0.0017482517482517483	21	0.027704485488126648	g	2.171	-0.389912	0.04932	0.004011	0.029447	ENSG00000181143	ENST00000397910	T	0.02525	4.26	1.35	-2.71	0.05986	.	.	.	.	.	T	0.00468	0.0015	N	0.08118	0	.	.	.	B	0.31174	0.311	B	0.20577	0.03	T	0.44452	-0.9327	8	0.87932	D	0	.	2.4961	0.04621	0.3275:0.0:0.4389:0.2335	rs35092547;rs61737587	6152	B5ME49	.	Q	6152	ENSP00000381008:H6152Q	ENSP00000381008:H6152Q	H	-	3	2	MUC16	8929990	0.000000	0.05858	0.000000	0.03702	0.173000	0.22820	-2.276000	0.01161	-1.154000	0.02825	0.163000	0.16589	CAC	G|0.981;T|0.019	0.019	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SLC9C2	284525	hgsc.bcm.edu	37	1	173516871	173516871	+	Missense_Mutation	SNP	G	G	C	rs16846206	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:173516871G>C	ENST00000367714.3	-	13	1936	c.1514C>G	c.(1513-1515)gCt>gGt	p.A505G	SLC9C2_ENST00000466087.1_5'UTR|SLC9C2_ENST00000536496.1_Missense_Mutation_p.A403G	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	505			A -> G (in dbSNP:rs16846206).		sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										CTCCATTAAAGCTTCATCTGT	0.348													G|||	1676	0.334665	0.1293	0.3256	5008	,	,		18034	0.6448		0.2107	False		,,,				2504	0.4264				p.A505G		Atlas-SNP	.											.	.	.	.	0			c.C1514G						PASS	.	G	GLY/ALA	584,3822	256.7+/-261.4	38,508,1657	158.0	142.0	147.0		1514	-0.2	1.0	1	dbSNP_123	147	1771,6829	319.3+/-314.1	183,1405,2712	yes	missense	SLC9A11	NM_178527.3	60	221,1913,4369	CC,CG,GG		20.593,13.2547,18.107	benign	505/1125	173516871	2355,10651	2203	4300	6503	SO:0001583	missense	284525	exon13			ATTAAAGCTTCAT	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1514C>G	1.37:g.173516871G>C	ENSP00000356687:p.Ala505Gly	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	226	80	0.353982	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	700	0.32051282051282054	69	0.1402439024390244	112	0.30939226519337015	355	0.6206293706293706	164	0.21635883905013192	G	10.10	1.258637	0.23051	0.132547	0.20593	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.25414	1.8;1.8	5.5	-0.206	0.13193	.	0.673556	0.13000	N	0.421735	T	0.03053	0.0090	N	0.08118	0	0.46241	P	0.0010580000000000034	B	0.27068	0.167	B	0.21360	0.034	T	0.42068	-0.9473	9	0.30854	T	0.27	-6.9082	4.5975	0.12336	0.3998:0.0:0.0905:0.5097	rs16846206;rs52835556;rs61192359;rs16846206	505	Q5TAH2	S9A11_HUMAN	G	505;403	ENSP00000356687:A505G;ENSP00000445437:A403G	ENSP00000356687:A505G	A	-	2	0	SLC9A11	171783494	0.999000	0.42202	0.997000	0.53966	0.401000	0.30781	0.324000	0.19610	0.035000	0.15519	-0.440000	0.05779	GCT	G|0.763;C|0.237	0.237	strong		0.348	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
MSI2	124540	hgsc.bcm.edu	37	17	55752389	55752389	+	Missense_Mutation	SNP	G	G	A	rs116924898	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:55752389G>A	ENST00000284073.2	+	12	1056	c.847G>A	c.(847-849)Gcc>Acc	p.A283T	MSI2_ENST00000442934.2_Missense_Mutation_p.A222T|MSI2_ENST00000416426.2_Missense_Mutation_p.A279T|MSI2_ENST00000579505.1_3'UTR	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	283						cytoplasm (GO:0005737)|polysome (GO:0005844)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(1)|pancreas(1)|skin(1)	7	Breast(9;1.78e-08)			GBM - Glioblastoma multiforme(1;0.0025)		AGGACCTGTCGCCGATCTCTA	0.687			T	HOXA9	CML								G|||	15	0.00299521	0.0008	0.0043	5008	,	,		15149	0.0		0.0099	False		,,,				2504	0.001				p.A283T		Atlas-SNP	.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2	52	.	0			c.G847A						PASS	.	G	THR/ALA	7,4399	11.4+/-27.6	0,7,2196	47.0	58.0	55.0		847	4.5	1.0	17	dbSNP_132	55	94,8500	49.8+/-109.6	0,94,4203	yes	missense	MSI2	NM_138962.2	58	0,101,6399	AA,AG,GG		1.0938,0.1589,0.7769	probably-damaging	283/329	55752389	101,12899	2203	4297	6500	SO:0001583	missense	124540	exon12			CCTGTCGCCGATC	BC001526	CCDS11596.1, CCDS11597.1	17q23.2	2013-07-16	2012-12-13					"""RNA binding motif (RRM) containing"""	18585	protein-coding gene	gene with protein product		607897	"""musashi homolog 2 (Drosophila)"""			11588182	Standard	NM_138962		Approved		uc002iuz.1	Q96DH6		ENST00000284073.2:c.847G>A	17.37:g.55752389G>A	ENSP00000284073:p.Ala283Thr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_138962	Q7Z6M7|Q8N9T4	Missense_Mutation	SNP	ENST00000284073.2	37	CCDS11596.1	12	0.005494505494505495	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	25.8	4.674614	0.88445	0.001589	0.010938	ENSG00000153944	ENST00000416426;ENST00000284073;ENST00000442934	D;D;D	0.85773	-2.03;-2.03;-2.03	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.87014	0.6072	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71656	0.959;0.974	D	0.85771	0.1355	10	0.15952	T	0.53	.	17.1487	0.86773	0.0:0.0:1.0:0.0	.	279;283	B4DHE8;Q96DH6	.;MSI2H_HUMAN	T	279;283;222	ENSP00000414671:A279T;ENSP00000284073:A283T;ENSP00000392607:A222T	ENSP00000284073:A283T	A	+	1	0	MSI2	53107388	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.418000	0.97395	2.038000	0.60285	0.491000	0.48974	GCC	A|0.007;C|0.000;G|0.992	0.007	strong		0.687	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1		
LRRTM1	347730	hgsc.bcm.edu	37	2	80529918	80529918	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:80529918C>T	ENST00000295057.3	-	2	1683	c.1027G>A	c.(1027-1029)Gcc>Acc	p.A343T	CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000541047.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.A343T|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000361291.4_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	343	LRRCT.				exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						TCCGGGCTGGCGCACTGCAAG	0.677										HNSCC(69;0.2)																											p.A343T		Atlas-SNP	.											LRRTM1_ENST00000295057,colon,carcinoma,+1,2	LRRTM1	251	2	0			c.G1027A						scavenged	.						25.0	23.0	24.0					2																	80529918		2203	4300	6503	SO:0001583	missense	347730	exon2			GGCTGGCGCACTG	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1027G>A	2.37:g.80529918C>T	ENSP00000295057:p.Ala343Thr	Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	135	3	0.0222222	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	11.59	1.682590	0.29872	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.44482	0.92;0.92	5.32	3.48	0.39840	.	0.144128	0.46442	U	0.000283	T	0.30198	0.0757	L	0.42529	1.33	0.44745	D	0.997742	B	0.16603	0.018	B	0.10450	0.005	T	0.07158	-1.0787	9	.	.	.	.	6.4844	0.22081	0.1473:0.7034:0.0:0.1493	.	343	Q86UE6	LRRT1_HUMAN	T	343	ENSP00000295057:A343T;ENSP00000386646:A343T	.	A	-	1	0	LRRTM1	80383429	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.311000	0.51919	0.566000	0.29273	0.655000	0.94253	GCC	.	.	none		0.677	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
MLC1	23209	hgsc.bcm.edu	37	22	50502544	50502544	+	Silent	SNP	G	G	A	rs11568186	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50502544G>A	ENST00000311597.5	-	11	1584	c.978C>T	c.(976-978)tgC>tgT	p.C326C	MLC1_ENST00000538737.1_Silent_p.C292C|MLC1_ENST00000395876.2_Silent_p.C326C|MLC1_ENST00000535444.1_Silent_p.C247C|MLC1_ENST00000431262.2_Silent_p.C296C|MLC1_ENST00000450140.2_Silent_p.C274C|MLC1_ENST00000483836.1_5'UTR	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	185	0	0		WXS	Illumina HiSeq	Phase_I	162	52	0.320988	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	
C1orf52	148423	hgsc.bcm.edu	37	1	85724328	85724328	+	Silent	SNP	C	C	T	rs4949926	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:85724328C>T	ENST00000471115.1	-	2	362	c.354G>A	c.(352-354)ccG>ccA	p.P118P	C1orf52_ENST00000344356.5_Silent_p.P118P|C1orf52_ENST00000294661.4_5'UTR	NM_198077.3	NP_932343.1	Q8N6N3	CA052_HUMAN	chromosome 1 open reading frame 52	118							poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)	10				all cancers(265;0.0105)|Epithelial(280;0.0293)		GCTCTGGAGGCGGAGGCTTCT	0.428													C|||	1126	0.22484	0.1271	0.3156	5008	,	,		13049	0.2956		0.2078	False		,,,				2504	0.2372				p.P118P		Atlas-SNP	.											.	C1orf52	16	.	0			c.G354A						PASS	.	C		598,3808	261.0+/-264.0	36,526,1641	141.0	133.0	135.0		354	-3.8	0.2	1	dbSNP_111	135	1747,6853	319.5+/-314.2	169,1409,2722	no	coding-synonymous	C1orf52	NM_198077.3		205,1935,4363	TT,TC,CC		20.314,13.5724,18.0301		118/183	85724328	2345,10661	2203	4300	6503	SO:0001819	synonymous_variant	148423	exon2			TGGAGGCGGAGGC	BC029538	CCDS703.1	1p22.3	2008-02-05			ENSG00000162642	ENSG00000162642			24871	protein-coding gene	gene with protein product						11891061	Standard	NM_198077		Approved	gm117, FLJ44982	uc001dkv.3	Q8N6N3	OTTHUMG00000009966	ENST00000471115.1:c.354G>A	1.37:g.85724328C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	244	241	0.987705	NM_198077	B3KX89|Q8TDK5|Q8TDK6	Silent	SNP	ENST00000471115.1	37	CCDS703.1																																																																																			C|0.810;T|0.190	0.190	strong		0.428	C1orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027616.2	NM_198077	
OR52E6	390078	hgsc.bcm.edu	37	11	5862532	5862532	+	Missense_Mutation	SNP	A	A	C	rs10742809	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5862532A>C	ENST00000329322.5	-	1	595	c.596T>G	c.(595-597)aTg>aGg	p.M199R	OR52E6_ENST00000379946.2_Missense_Mutation_p.M203R|TRIM5_ENST00000380027.1_Intron	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	199			M -> R (in dbSNP:rs10742809).			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(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAGACCAAACATAATGTTGAC	0.473													A|||	1644	0.328275	0.2224	0.304	5008	,	,		21378	0.4593		0.3439	False		,,,				2504	0.3374				p.M199R		Atlas-SNP	.											.	OR52E6	70	.	0			c.T596G						PASS	.	A	ARG/MET	1031,3371	373.4+/-320.8	122,787,1292	87.0	84.0	85.0		596	3.5	0.0	11	dbSNP_120	85	2800,5792	441.4+/-359.8	448,1904,1944	yes	missense	OR52E6	NM_001005167.1	91	570,2691,3236	CC,CA,AA		32.5885,23.4212,29.4828	benign	199/314	5862532	3831,9163	2201	4296	6497	SO:0001583	missense	390078	exon1			CCAAACATAATGT	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.596T>G	11.37:g.5862532A>C	ENSP00000328878:p.Met199Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	51	0.418033	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	751	0.34386446886446886	102	0.2073170731707317	115	0.31767955801104975	264	0.46153846153846156	270	0.3562005277044855	A	8.103	0.777055	0.16120	0.234212	0.325885	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00084	8.75;8.75	3.45	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	1.217830	0.05771	N	0.606787	T	0.00012	0.0000	N	0.16201	0.385	0.80722	P	0.0	B	0.02656	0.0	B	0.10450	0.005	T	0.13335	-1.0513	9	0.48119	T	0.1	.	10.9113	0.47110	1.0:0.0:0.0:0.0	rs10742809;rs61269500;rs10742809	199	Q96RD3	O52E6_HUMAN	R	199;203	ENSP00000328878:M199R;ENSP00000369279:M203R	ENSP00000328878:M199R	M	-	2	0	OR52E6	5819108	0.000000	0.05858	0.003000	0.11579	0.564000	0.35744	0.650000	0.24858	1.430000	0.47334	0.450000	0.29827	ATG	A|0.670;C|0.330	0.330	strong		0.473	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
PPIG	9360	hgsc.bcm.edu	37	2	170493103	170493103	+	Missense_Mutation	SNP	T	T	A	rs1050354	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:170493103T>A	ENST00000260970.3	+	14	1555	c.1335T>A	c.(1333-1335)gaT>gaA	p.D445E	PPIG_ENST00000409714.3_Missense_Mutation_p.D430E|PPIG_ENST00000482772.1_3'UTR|PPIG_ENST00000448752.2_Missense_Mutation_p.D445E	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	445			D -> E (in dbSNP:rs1050354).		protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)	p.D445E(1)		NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	CAGAAAAAGATGACAAGTATA	0.308													T|||	2926	0.584265	0.7595	0.4625	5008	,	,		17437	0.4296		0.5378	False		,,,				2504	0.6411				p.D445E		Atlas-SNP	.											PPIG,NS,carcinoma,0,1	PPIG	100	1	1	Substitution - Missense(1)	stomach(1)	c.T1335A						PASS	.	T	GLU/ASP	3169,1203		1168,833,185	46.0	48.0	47.0		1335	4.7	1.0	2	dbSNP_86	47	4842,3698		1368,2106,796	yes	missense	PPIG	NM_004792.2	45	2536,2939,981	AA,AT,TT		43.3021,27.516,37.9569	benign	445/755	170493103	8011,4901	2186	4270	6456	SO:0001583	missense	9360	exon14			AAAAGATGACAAG	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.1335T>A	2.37:g.170493103T>A	ENSP00000260970:p.Asp445Glu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	37	CCDS2235.1	1192	0.5457875457875457	350	0.7113821138211383	185	0.511049723756906	244	0.42657342657342656	413	0.5448548812664907	T	7.359	0.624371	0.14193	0.72484	0.566979	ENSG00000138398	ENST00000260970;ENST00000433207;ENST00000409714;ENST00000448752	T;T;T;T	0.21191	2.52;2.02;2.52;2.52	5.92	4.74	0.60224	.	0.101452	0.64402	D	0.000002	T	0.00012	0.0000	N	0.14661	0.345	0.29169	P	0.877258	B;B;B	0.17038	0.0;0.02;0.02	B;B;B	0.12156	0.001;0.007;0.007	T	0.17137	-1.0379	9	0.17369	T	0.5	-9.5082	10.0708	0.42332	0.3831:0.0:0.0:0.6169	rs1050354;rs3190651;rs17621662;rs52823176;rs1050354	438;430;445	C9JM79;E9PG73;Q13427	.;.;PPIG_HUMAN	E	445;438;430;445	ENSP00000260970:D445E;ENSP00000408683:D438E;ENSP00000386245:D430E;ENSP00000407083:D445E	ENSP00000260970:D445E	D	+	3	2	PPIG	170201349	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	0.739000	0.26173	1.028000	0.39785	0.533000	0.62120	GAT	A|0.574;N|0.000	0.574	strong		0.308	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
VPREB1	7441	hgsc.bcm.edu	37	22	22599674	22599674	+	Silent	SNP	C	C	T	rs5995719	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:22599674C>T	ENST00000403807.3	+	2	502	c.363C>T	c.(361-363)agC>agT	p.S121S	VPREB1_ENST00000302273.2_Silent_p.S120S			P12018	VPREB_HUMAN	pre-B lymphocyte 1	121	Ig-like V-type.									large_intestine(1)|liver(1)|lung(6)|skin(1)	9	all_hematologic(9;0.0312)|Acute lymphoblastic leukemia(84;0.155)	all_cancers(3;3.14e-14)|Acute lymphoblastic leukemia(3;2.97e-57)|all_hematologic(3;5.9e-52)		READ - Rectum adenocarcinoma(21;0.145)		GGGCCCGCAGCTCggagaagg	0.572													c|||	798	0.159345	0.3094	0.1009	5008	,	,		16238	0.003		0.1759	False		,,,				2504	0.1421				p.S121S		Atlas-SNP	.											VPREB1,NS,carcinoma,+1,1	VPREB1	20	1	0			c.C363T						scavenged	.	C		1327,3059		210,907,1076	15.0	17.0	16.0		363	3.3	0.0	22	dbSNP_114	16	1647,6935		157,1333,2801	yes	coding-synonymous	VPREB1	NM_007128.2		367,2240,3877	TT,TC,CC		19.1913,30.2554,22.9334		121/146	22599674	2974,9994	2193	4291	6484	SO:0001819	synonymous_variant	7441	exon2			CCGCAGCTCGGAG	M34927	CCDS13798.1	22q11.2	2014-05-16	2008-09-12		ENSG00000169575	ENSG00000169575		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	12709	protein-coding gene	gene with protein product		605141				3139558	Standard	NM_007128		Approved	VpreB, CD179A	uc002zvx.1	P12018	OTTHUMG00000151042	ENST00000403807.3:c.363C>T	22.37:g.22599674C>T		Somatic	17	1	0.0588235		WXS	Illumina HiSeq	Phase_I	18	16	0.888889	NM_007128	B5MCG2	Silent	SNP	ENST00000403807.3	37	CCDS13798.1																																																																																			C|0.808;T|0.192	0.192	strong		0.572	VPREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321101.1		
SYNE2	23224	hgsc.bcm.edu	37	14	64518321	64518321	+	Missense_Mutation	SNP	A	A	G	rs11628107	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:64518321A>G	ENST00000344113.4	+	48	7902	c.7690A>G	c.(7690-7692)Ata>Gta	p.I2564V	SYNE2_ENST00000358025.3_Missense_Mutation_p.I2564V|SYNE2_ENST00000554584.1_Missense_Mutation_p.I2597V|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2564			I -> V (in dbSNP:rs11628107).		centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TAAAAAATTCATAGCATCCAT	0.308													A|||	146	0.0291534	0.0053	0.0677	5008	,	,		18960	0.0556		0.0249	False		,,,				2504	0.0112				p.I2564V		Atlas-SNP	.											.	SYNE2	577	.	0			c.A7690G						PASS	.	A	VAL/ILE,VAL/ILE	40,3546		0,40,1753	43.0	40.0	41.0		7690,7690	4.0	0.4	14	dbSNP_120	41	228,7918		7,214,3852	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	29,29	7,254,5605	GG,GA,AA		2.7989,1.1154,2.2844	benign,benign	2564/6886,2564/6908	64518321	268,11464	1793	4073	5866	SO:0001583	missense	23224	exon48			AAATTCATAGCAT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.7690A>G	14.37:g.64518321A>G	ENSP00000341781:p.Ile2564Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	146	52	0.356164	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	73	0.033424908424908424	1	0.0020325203252032522	23	0.06353591160220995	31	0.05419580419580419	18	0.023746701846965697	A	0.214	-1.034389	0.02029	0.011154	0.027989	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.54071	1.41;1.41;0.59	5.9	4.0	0.46444	.	0.331247	0.22197	N	0.063283	T	0.02156	0.0067	N	0.03608	-0.345	0.44036	D	0.996763	B;B	0.15141	0.007;0.012	B;B	0.09377	0.002;0.004	T	0.04825	-1.0924	10	0.10902	T	0.67	.	1.7505	0.02971	0.2923:0.4147:0.1317:0.1613	rs11628107;rs52797744;rs11628107	2564;2564	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	V	2564;2564;2597;2597	ENSP00000350719:I2564V;ENSP00000341781:I2564V;ENSP00000452570:I2597V	ENSP00000261678:I2597V	I	+	1	0	SYNE2	63588074	0.009000	0.17119	0.431000	0.26735	0.152000	0.21847	0.090000	0.15025	0.747000	0.32809	-0.219000	0.12488	ATA	A|0.970;G|0.030	0.030	strong		0.308	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
WDR62	284403	hgsc.bcm.edu	37	19	36595436	36595436	+	Missense_Mutation	SNP	A	A	C	rs1008328	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36595436A>C	ENST00000270301.7	+	31	4155	c.4155A>C	c.(4153-4155)ttA>ttC	p.L1385F	WDR62_ENST00000401500.2_Missense_Mutation_p.L1390F			O43379	WDR62_HUMAN	WD repeat domain 62	1385			L -> F (in dbSNP:rs1008328). {ECO:0000269|PubMed:15057824, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.L1385F(1)		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)			TTGGTCTGTTACAGGGCAGCC	0.617													C|||	3587	0.716254	0.7035	0.781	5008	,	,		20079	0.752		0.7843	False		,,,				2504	0.5808				p.L1390F		Atlas-SNP	.											WDR62,NS,carcinoma,0,1	WDR62	102	1	1	Substitution - Missense(1)	prostate(1)	c.A4170C						scavenged	.	C	PHE/LEU,PHE/LEU	3066,1340	448.3+/-348.6	1074,918,211	68.0	59.0	62.0		4170,4155	2.0	0.0	19	dbSNP_86	62	6676,1924	339.1+/-323.0	2591,1494,215	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	22,22	3665,2412,426	CC,CA,AA		22.3721,30.4131,25.0961	benign,benign	1390/1524,1385/1519	36595436	9742,3264	2203	4300	6503	SO:0001583	missense	284403	exon31			TCTGTTACAGGGC	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.4155A>C	19.37:g.36595436A>C	ENSP00000270301:p.Leu1385Phe	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	1671	0.7651098901098901	349	0.709349593495935	279	0.7707182320441989	451	0.7884615384615384	592	0.7810026385224275	C	5.933	0.356107	0.11239	0.695869	0.776279	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.47869	0.92;0.83	4.1	1.96	0.26148	.	5.597880	0.00357	N	0.000020	T	0.00012	0.0000	N	0.08118	0	0.58432	P	2.9999999999752447E-6	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.40887	-0.9539	9	0.10111	T	0.7	1.95	2.8656	0.05600	0.1879:0.5308:0.1815:0.0999	rs1008328;rs1140947;rs17845535;rs17858431;rs59629216;rs1008328	1390;1385	O43379-4;O43379	.;WDR62_HUMAN	F	1390;1385	ENSP00000384792:L1390F;ENSP00000270301:L1385F	ENSP00000270301:L1385F	L	+	3	2	WDR62	41287276	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.322000	0.19576	0.303000	0.22785	-0.143000	0.13931	TTA	A|0.255;C|0.745	0.745	strong		0.617	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
KCNK6	9424	hgsc.bcm.edu	37	19	38817876	38817876	+	Missense_Mutation	SNP	G	G	A	rs34989303	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38817876G>A	ENST00000263372.3	+	3	882	c.775G>A	c.(775-777)Gtg>Atg	p.V259M		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	259			V -> M (in dbSNP:rs34989303).		negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	CTTCCGCCACGTGTCCGACCT	0.642													G|||	784	0.15655	0.0507	0.2378	5008	,	,		17801	0.1478		0.1829	False		,,,				2504	0.2239				p.V259M		Atlas-SNP	.											.	KCNK6	37	.	0			c.G775A						PASS	.	G	MET/VAL	327,4079	169.8+/-200.3	21,285,1897	74.0	57.0	63.0		775	0.6	0.0	19	dbSNP_126	63	1314,7286	255.5+/-280.4	101,1112,3087	yes	missense	KCNK6	NM_004823.1	21	122,1397,4984	AA,AG,GG		15.2791,7.4217,12.6173	benign	259/314	38817876	1641,11365	2203	4300	6503	SO:0001583	missense	9424	exon3			CGCCACGTGTCCG	AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.775G>A	19.37:g.38817876G>A	ENSP00000263372:p.Val259Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_004823	Q9HB47	Missense_Mutation	SNP	ENST00000263372.3	37	CCDS12513.1	335	0.1533882783882784	24	0.04878048780487805	88	0.2430939226519337	83	0.1451048951048951	140	0.18469656992084432	G	12.43	1.936680	0.34189	0.074217	0.152791	ENSG00000099337	ENST00000263372	T	0.24350	1.86	5.45	0.581	0.17407	.	0.265585	0.37053	N	0.002279	T	0.00012	0.0000	N	0.11560	0.145	0.58432	P	1.0000000000287557E-6	P	0.43231	0.801	B	0.43658	0.426	T	0.34179	-0.9839	9	0.49607	T	0.09	.	3.8911	0.09119	0.1517:0.1274:0.5898:0.1311	rs34989303	259	Q9Y257	KCNK6_HUMAN	M	259	ENSP00000263372:V259M	ENSP00000263372:V259M	V	+	1	0	KCNK6	43509716	0.003000	0.15002	0.003000	0.11579	0.589000	0.36550	-0.109000	0.10840	0.228000	0.21019	0.561000	0.74099	GTG	G|0.865;A|0.135	0.135	strong		0.642	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823	
DHFRL1	200895	hgsc.bcm.edu	37	3	93780109	93780109	+	Missense_Mutation	SNP	G	G	C	rs61739170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:93780109G>C	ENST00000394221.2	-	2	696	c.247C>G	c.(247-249)Cct>Gct	p.P83A	DHFRL1_ENST00000314636.2_Missense_Mutation_p.P83A|NSUN3_ENST00000314622.4_5'Flank|DHFRL1_ENST00000481631.1_Intron	NM_001195643.1	NP_001182572.1	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	83	DHFR. {ECO:0000255|PROSITE- ProRule:PRU00660}.				glycine biosynthetic process (GO:0006545)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|thymidine biosynthetic process (GO:0046105)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dihydrofolate reductase activity (GO:0004146)|mRNA binding (GO:0003729)|NADP binding (GO:0050661)	p.P83A(1)		kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8						CCTTGTGGAGGTTCCTTGAGT	0.393													G|||	612	0.122204	0.0219	0.2032	5008	,	,		18489	0.1141		0.2306	False		,,,				2504	0.0971				p.P83A		Atlas-SNP	.											DHFRL1,NS,carcinoma,0,1	DHFRL1	25	1	1	Substitution - Missense(1)	stomach(1)	c.C247G						PASS	.	G	ALA/PRO,ALA/PRO	280,4126	151.4+/-185.3	11,258,1934	114.0	117.0	116.0		247,247	0.1	0.4	3	dbSNP_129	116	1978,6622	344.5+/-325.3	216,1546,2538	no	missense,missense	DHFRL1	NM_001195643.1,NM_176815.4	27,27	227,1804,4472	CC,CG,GG		23.0,6.355,17.3612	benign,benign	83/188,83/188	93780109	2258,10748	2203	4300	6503	SO:0001583	missense	200895	exon2			GTGGAGGTTCCTT	AL832912	CCDS2926.1	3q11.2	2005-08-16	2005-02-07		ENSG00000178700	ENSG00000178700			27309	protein-coding gene	gene with protein product			"""dihydrofolate reductase pseudogene 4"""	DHFRP4		12477932	Standard	NM_001195643		Approved	FLJ16119	uc003drj.3	Q86XF0	OTTHUMG00000159014	ENST00000394221.2:c.247C>G	3.37:g.93780109G>C	ENSP00000377768:p.Pro83Ala	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	234	110	0.470085	NM_001195643	D3DN30|Q6P4I9	Missense_Mutation	SNP	ENST00000394221.2	37	CCDS2926.1	329	0.15064102564102563	19	0.03861788617886179	73	0.20165745856353592	68	0.11888111888111888	169	0.22295514511873352	G	0.136	-1.107561	0.01813	0.06355	0.23	ENSG00000178700	ENST00000314636;ENST00000394221;ENST00000496983	T;T;T	0.70869	-0.52;-0.52;-0.52	1.09	0.0854	0.14441	Dihydrofolate reductase domain (2);Dihydrofolate reductase-like domain (2);	0.127127	0.53938	U	0.000053	T	0.00039	0.0001	N	0.20357	0.565	0.34752	P	0.268081	B	0.09022	0.002	B	0.09377	0.004	T	0.05241	-1.0897	9	0.09084	T	0.74	-8.8976	6.8106	0.23802	0.0:0.2956:0.7044:0.0	rs61739170	83	Q86XF0	DYRL1_HUMAN	A	83	ENSP00000319170:P83A;ENSP00000377768:P83A;ENSP00000420810:P83A	ENSP00000319170:P83A	P	-	1	0	DHFRL1	95262799	0.974000	0.33945	0.410000	0.26471	0.620000	0.37586	0.236000	0.17967	0.028000	0.15324	-0.535000	0.04281	CCT	G|0.833;C|0.167	0.167	strong		0.393	DHFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352910.1	NM_176815	
IDUA	3425	hgsc.bcm.edu	37	4	994414	994414	+	Missense_Mutation	SNP	G	G	A	rs3755955	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:994414G>A	ENST00000247933.4	+	3	402	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	IDUA_ENST00000514224.1_5'UTR|IDUA_ENST00000453894.1_Missense_Mutation_p.R58Q	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	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	214	103	0.481308	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	
FAT2	2196	hgsc.bcm.edu	37	5	150945699	150945699	+	Silent	SNP	G	G	A	rs10085060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	295	0	0		WXS	Illumina HiSeq	Phase_I	259	123	0.474903	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	
GPNMB	10457	hgsc.bcm.edu	37	7	23313171	23313171	+	Silent	SNP	T	T	C	rs2268748	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:23313171T>C	ENST00000381990.2	+	10	1658	c.1497T>C	c.(1495-1497)agT>agC	p.S499S	GPNMB_ENST00000258733.4_Silent_p.S487S|GPNMB_ENST00000453162.2_Silent_p.S441S|GPNMB_ENST00000478451.1_3'UTR|GPNMB_ENST00000539136.1_Silent_p.S388S	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	499					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)			TGGCAAACAGTGCCCTGATCT	0.448													T|||	693	0.138379	0.0045	0.2291	5008	,	,		19558	0.3641		0.0417	False		,,,				2504	0.1217				p.S499S		Atlas-SNP	.											.	GPNMB	88	.	0			c.T1497C						PASS	.	T	,	54,4352	53.6+/-89.4	0,54,2149	220.0	168.0	185.0		1497,1461	-0.8	0.0	7	dbSNP_100	185	337,8263	116.6+/-176.3	8,321,3971	no	coding-synonymous,coding-synonymous	GPNMB	NM_001005340.1,NM_002510.2	,	8,375,6120	CC,CT,TT		3.9186,1.2256,3.0063	,	499/573,487/561	23313171	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	10457	exon10			AAACAGTGCCCTG	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.1497T>C	7.37:g.23313171T>C		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	249	163	0.654619	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																			T|0.909;G|0.000	.	strong		0.448	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
TOP3B	8940	hgsc.bcm.edu	37	22	22318538	22318538	+	Missense_Mutation	SNP	C	C	T	rs9610728	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:22318538C>T	ENST00000398793.2	-	10	1527	c.1093G>A	c.(1093-1095)Gac>Aac	p.D365N	TOP3B_ENST00000413067.2_Missense_Mutation_p.D94N|TOP3B_ENST00000357179.5_Missense_Mutation_p.D365N	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	365			D -> N (in dbSNP:rs9610728). {ECO:0000269|PubMed:15489334}.		chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		CTCACCGTGTCGGCCCAGTAG	0.632													C|||	490	0.0978435	0.1362	0.1095	5008	,	,		17067	0.0665		0.1183	False		,,,				2504	0.0491				p.D365N		Atlas-SNP	.											.	TOP3B	107	.	0			c.G1093A						PASS	.	C	ASN/ASP	510,3896	234.2+/-247.1	33,444,1726	89.0	78.0	82.0		1093	2.8	0.9	22	dbSNP_119	82	1060,7540	223.4+/-260.2	74,912,3314	yes	missense	TOP3B	NM_003935.3	23	107,1356,5040	TT,TC,CC		12.3256,11.5751,12.0714	benign	365/863	22318538	1570,11436	2203	4300	6503	SO:0001583	missense	8940	exon10			CCGTGTCGGCCCA	AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.1093G>A	22.37:g.22318538C>T	ENSP00000381773:p.Asp365Asn	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	228	124	0.54386	NM_003935	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	37	CCDS13797.1	234	0.10714285714285714	66	0.13414634146341464	37	0.10220994475138122	36	0.06293706293706294	95	0.12532981530343007	C	10.84	1.463748	0.26335	0.115751	0.123256	ENSG00000100038	ENST00000357179;ENST00000398793;ENST00000413067	T;T;T	0.21543	2.0;2.0;2.0	5.05	2.85	0.33270	DNA topoisomerase, type IA, core domain (1);DNA topoisomerase, type IA, central region, subdomain 3 (1);DNA topoisomerase, type IA, central (1);DNA topoisomerase, type IA, DNA-binding (1);	0.198902	0.52532	N	0.000074	T	0.00144	0.0004	L	0.35249	1.045	0.21950	P	0.999456333	B;B	0.14805	0.011;0.009	B;B	0.11329	0.006;0.005	T	0.18745	-1.0327	9	0.21540	T	0.41	.	12.1463	0.54026	0.0:0.7954:0.1308:0.0737	rs9610728;rs17849583;rs9610728	365;365	O95985;O95985-2	TOP3B_HUMAN;.	N	365;365;94	ENSP00000349705:D365N;ENSP00000381773:D365N;ENSP00000393118:D94N	ENSP00000349705:D365N	D	-	1	0	TOP3B	20648538	0.990000	0.36364	0.947000	0.38551	0.094000	0.18550	2.847000	0.48270	1.359000	0.45940	-0.291000	0.09656	GAC	C|0.880;T|0.120	0.120	strong		0.632	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
DMRT2	10655	hgsc.bcm.edu	37	9	1057204	1057204	+	Silent	SNP	A	A	G	rs4741029	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:1057204A>G	ENST00000358146.2	+	3	1617	c.1617A>G	c.(1615-1617)gaA>gaG	p.E539E	DMRT2_ENST00000302441.6_Silent_p.E539E|DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382251.3_Silent_p.E539E			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	539					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)		CGGTGAATGAACCACTGTCAT	0.393													A|||	1175	0.234625	0.5325	0.1931	5008	,	,		17837	0.1796		0.0537	False		,,,				2504	0.1043				p.E539E		Atlas-SNP	.											.	DMRT2	70	.	0			c.A1617G						PASS	.	A	,,	2057,2349	568.8+/-382.5	487,1083,633	81.0	82.0	81.0		,,1617	1.0	1.0	9	dbSNP_111	81	552,8048	151.0+/-205.8	14,524,3762	no	utr-3,utr-3,coding-synonymous	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,	501,1607,4395	GG,GA,AA		6.4186,46.6863,20.06	,,	,,539/562	1057204	2609,10397	2203	4300	6503	SO:0001819	synonymous_variant	10655	exon4			GAATGAACCACTG	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.1617A>G	9.37:g.1057204A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Silent	SNP	ENST00000358146.2	37	CCDS6444.1																																																																																			A|0.784;G|0.216	0.216	strong		0.393	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
DNAH9	1770	hgsc.bcm.edu	37	17	11511457	11511457	+	Silent	SNP	C	C	T	rs11078022	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:11511457C>T	ENST00000262442.4	+	2	497	c.429C>T	c.(427-429)ccC>ccT	p.P143P	DNAH9_ENST00000454412.2_Silent_p.P143P|DNAH9_ENST00000579828.1_Silent_p.P143P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	143	Stem. {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)		TTGTTCTACCCGTCCTGGCCA	0.483													C|||	2220	0.443291	0.1664	0.5648	5008	,	,		18842	0.5417		0.4235	False		,,,				2504	0.6503				p.P143P		Atlas-SNP	.											.	DNAH9	695	.	0			c.C429T						PASS	.	C		940,3466	357.1+/-313.8	103,734,1366	137.0	136.0	136.0		429	-11.4	0.0	17	dbSNP_120	136	3560,5040	516.7+/-378.9	761,2038,1501	no	coding-synonymous	DNAH9	NM_001372.3		864,2772,2867	TT,TC,CC		41.3953,21.3345,34.5994		143/4487	11511457	4500,8506	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon2			TCTACCCGTCCTG	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.429C>T	17.37:g.11511457C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.626;N|0.000	.	strong		0.483	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ATAD5	79915	hgsc.bcm.edu	37	17	29161503	29161503	+	Missense_Mutation	SNP	A	A	G	rs11080134	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:29161503A>G	ENST00000321990.4	+	2	782	c.404A>G	c.(403-405)gAa>gGa	p.E135G	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	135			E -> G (in dbSNP:rs11080134). {ECO:0000269|PubMed:15489334}.		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)				GCTCCAATTGAAATTAGTAGC	0.289													A|||	759	0.151558	0.0673	0.2594	5008	,	,		19686	0.001		0.327	False		,,,				2504	0.1636				p.E135G		Atlas-SNP	.											.	ATAD5	150	.	0			c.A404G						PASS	.	A	GLY/GLU	482,3924		28,426,1749	118.0	135.0	130.0		404	4.2	1.0	17	dbSNP_120	130	2931,5661		496,1939,1861	yes	missense	ATAD5	NM_024857.3	98	524,2365,3610	GG,GA,AA		34.1131,10.9396,26.2579	possibly-damaging	135/1845	29161503	3413,9585	2203	4296	6499	SO:0001583	missense	79915	exon2			CAATTGAAATTAG		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.404A>G	17.37:g.29161503A>G	ENSP00000313171:p.Glu135Gly	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	380	0.17399267399267399	29	0.05894308943089431	100	0.27624309392265195	1	0.0017482517482517483	250	0.32981530343007914	A	6.597	0.478550	0.12521	0.109396	0.341131	ENSG00000176208	ENST00000321990	T	0.18502	2.21	5.35	4.24	0.50183	.	2.337970	0.01197	N	0.007499	T	0.00012	0.0000	L	0.55481	1.735	0.30194	P	0.799222	D;D	0.56746	0.977;0.961	P;B	0.50659	0.647;0.444	T	0.18713	-1.0328	9	0.38643	T	0.18	.	6.6781	0.23106	0.7905:0.0:0.0723:0.1372	rs11080134;rs17767684;rs58774345;rs11080134	135;135	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	G	135	ENSP00000313171:E135G	ENSP00000313171:E135G	E	+	2	0	ATAD5	26185629	1.000000	0.71417	0.997000	0.53966	0.400000	0.30750	1.536000	0.36072	1.067000	0.40740	0.533000	0.62120	GAA	A|0.786;G|0.214	0.214	strong		0.289	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
GBP1	2633	hgsc.bcm.edu	37	1	89523911	89523911	+	Missense_Mutation	SNP	C	C	T	rs75161612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89523911C>T	ENST00000370473.4	-	6	857	c.638G>A	c.(637-639)aGt>aAt	p.S213N	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	213	GB1/RHD3-type G.|GTPase domain (Globular).				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		ATCTTTTTGACTGGTACCTAG	0.368													.|||	91	0.0181709	0.0053	0.0159	5008	,	,		16962	0.0		0.0298	False		,,,				2504	0.044				p.S213N		Atlas-SNP	.											.	GBP1	68	.	0			c.G638A						PASS	.	C	ASN/SER	30,4374	31.7+/-61.6	0,30,2172	97.0	109.0	105.0		638	-2.4	0.0	1	dbSNP_131	105	220,8380	88.4+/-150.7	1,218,4081	yes	missense	GBP1	NM_002053.2	46	1,248,6253	TT,TC,CC		2.5581,0.6812,1.9225	benign	213/593	89523911	250,12754	2202	4300	6502	SO:0001583	missense	2633	exon6			TTTTGACTGGTAC	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.638G>A	1.37:g.89523911C>T	ENSP00000359504:p.Ser213Asn	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_002053	D3DT26|Q5T8M1	Missense_Mutation	SNP	ENST00000370473.4	37	CCDS718.1	27	0.012362637362637362	4	0.008130081300813009	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	0.084	-1.178538	0.01633	0.006812	0.025581	ENSG00000117228	ENST00000370473;ENST00000542693	T	0.73789	-0.78	4.48	-2.37	0.06643	Guanylate-binding protein, N-terminal (1);	1.837820	0.02201	N	0.062280	T	0.24928	0.0605	N	0.11845	0.185	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15925	-1.0420	10	0.06757	T	0.87	.	5.8264	0.18556	0.0:0.432:0.1405:0.4275	.	213	P32455	GBP1_HUMAN	N	213;176	ENSP00000359504:S213N	ENSP00000359504:S213N	S	-	2	0	GBP1	89296499	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.686000	0.00834	-0.598000	0.05806	0.313000	0.20887	AGT	C|0.981;T|0.019	0.019	strong		0.368	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053	
HSD17B12	51144	hgsc.bcm.edu	37	11	43702530	43702530	+	Silent	SNP	A	A	G	rs56168061	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:43702530A>G	ENST00000278353.4	+	1	272	c.153A>G	c.(151-153)gaA>gaG	p.E51E	HSD17B12_ENST00000395700.4_Silent_p.E51E|HSD17B12_ENST00000529261.1_Intron	NM_016142.2	NP_057226.1	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12	51					cellular lipid metabolic process (GO:0044255)|estrogen biosynthetic process (GO:0006703)|extracellular matrix organization (GO:0030198)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cell-substrate adhesion (GO:0010811)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|heparin binding (GO:0008201)			endometrium(2)|large_intestine(4)|lung(4)	10						GGCTCGGAGAATGGGCAGGTG	0.697													A|||	511	0.102037	0.0817	0.1066	5008	,	,		11188	0.001		0.1938	False		,,,				2504	0.136				p.E51E	Ovarian(58;548 1143 13948 16572 34258)	Atlas-SNP	.											HSD17B12,NS,carcinoma,0,1	HSD17B12	25	1	0			c.A153G						scavenged	.	A		399,3997		19,361,1818	17.0	19.0	18.0		153	1.8	1.0	11	dbSNP_129	18	1843,6753		215,1413,2670	no	coding-synonymous	HSD17B12	NM_016142.2		234,1774,4488	GG,GA,AA		21.4402,9.0764,17.2568		51/313	43702530	2242,10750	2198	4298	6496	SO:0001819	synonymous_variant	51144	exon1			CGGAGAATGGGCA	AF078850	CCDS7905.1	11q11	2011-09-20				ENSG00000149084	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	18646	protein-coding gene	gene with protein product	"""3-ketoacyl-CoA reductase"", ""short chain dehydrogenase/reductase family 12C, member 1"""	609574				12482854, 19027726	Standard	NM_016142		Approved	KAR, SDR12C1	uc001mxq.4	Q53GQ0		ENST00000278353.4:c.153A>G	11.37:g.43702530A>G		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_016142	A8K9B0|D3DR23|Q96EA9|Q96JU2|Q9Y6G8	Silent	SNP	ENST00000278353.4	37	CCDS7905.1																																																																																			A|0.873;G|0.127	0.127	strong		0.697	HSD17B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389594.1		
AQP10	89872	hgsc.bcm.edu	37	1	154296076	154296076	+	Silent	SNP	T	T	C	rs1194610	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154296076T>C	ENST00000324978.3	+	5	541	c.501T>C	c.(499-501)acT>acC	p.T167T	AQP10_ENST00000355197.4_3'UTR|AQP10_ENST00000484864.1_Silent_p.T167T|ATP8B2_ENST00000368487.3_5'Flank	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	167					response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.T167T(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TTCTGGGCACTGGGATGCTGA	0.592													C|||	1378	0.27516	0.503	0.268	5008	,	,		19284	0.1488		0.2306	False		,,,				2504	0.1483				p.T167T		Atlas-SNP	.											AQP10,NS,carcinoma,0,1	AQP10	44	1	1	Substitution - coding silent(1)	stomach(1)	c.T501C						PASS	.	C		2126,2280	599.9+/-389.4	491,1144,568	126.0	135.0	132.0		501	-7.1	0.0	1	dbSNP_87	132	2004,6596	722.3+/-406.4	230,1544,2526	no	coding-synonymous	AQP10	NM_080429.2		721,2688,3094	CC,CT,TT		23.3023,48.2524,31.7546		167/302	154296076	4130,8876	2203	4300	6503	SO:0001819	synonymous_variant	89872	exon5			GGGCACTGGGATG	AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"""Ion channels / Aquaporins"""	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.501T>C	1.37:g.154296076T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	191	190	0.994764	NM_080429	Q5VYD3|Q5VYD4|Q8NG70	Silent	SNP	ENST00000324978.3	37	CCDS1065.1																																																																																			T|0.702;C|0.298	0.298	strong		0.592	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429	
PRDM10	56980	hgsc.bcm.edu	37	11	129785594	129785594	+	Silent	SNP	G	G	A	rs3734073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:129785594G>A	ENST00000360871.3	-	16	2718	c.2487C>T	c.(2485-2487)ccC>ccT	p.P829P	PRDM10_ENST00000358825.5_Silent_p.P833P|PRDM10_ENST00000528746.1_Silent_p.P803P|PRDM10_ENST00000423662.2_Silent_p.P747P|PRDM10_ENST00000304538.6_Silent_p.P743P|PRDM10_ENST00000526082.1_Silent_p.P747P	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	833					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)		GACAGCAGACGGGAGGGGTGG	0.597													G|||	1149	0.229433	0.1218	0.2896	5008	,	,		16915	0.1567		0.3231	False		,,,				2504	0.3108				p.P833P		Atlas-SNP	.											PRDM10,colon,carcinoma,0,1	PRDM10	120	1	0			c.C2499T						PASS	.	G	,,,	726,3676	300.7+/-286.5	64,598,1539	104.0	101.0	102.0		2499,2487,2241,2229	-7.1	0.7	11	dbSNP_107	102	2773,5821	441.1+/-359.7	439,1895,1963	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	503,2493,3502	AA,AG,GG		32.2667,16.4925,26.9237	,,,	833/1161,829/1157,747/1062,743/1024	129785594	3499,9497	2201	4297	6498	SO:0001819	synonymous_variant	56980	exon17			GCAGACGGGAGGG	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.2487C>T	11.37:g.129785594G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	270	80	0.296296	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			G|0.729;A|0.271	0.271	strong		0.597	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
SLC9A9	285195	hgsc.bcm.edu	37	3	143293012	143293012	+	Silent	SNP	A	A	G	rs6763202	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:143293012A>G	ENST00000316549.6	-	8	1126	c.918T>C	c.(916-918)tgT>tgC	p.C306C		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	306					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)			breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						TCGGGAACTCACACAGCTTGG	0.478													G|||	1706	0.340655	0.444	0.3343	5008	,	,		20273	0.251		0.2565	False		,,,				2504	0.3845				p.C306C		Atlas-SNP	.											.	SLC9A9	117	.	0			c.T918C						PASS	.	G		1723,2683	651.1+/-399.2	341,1041,821	61.0	61.0	61.0		918	-3.7	0.4	3	dbSNP_116	61	2111,6489	716.1+/-406.1	251,1609,2440	no	coding-synonymous	SLC9A9	NM_173653.3		592,2650,3261	GG,GA,AA		24.5465,39.1058,29.4787		306/646	143293012	3834,9172	2203	4300	6503	SO:0001819	synonymous_variant	285195	exon8			GAACTCACACAGC	AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"""Solute carriers"""	20653	protein-coding gene	gene with protein product		608396	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 9"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 9"""			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.918T>C	3.37:g.143293012A>G		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	246	124	0.504065	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Silent	SNP	ENST00000316549.6	37	CCDS33872.1																																																																																			A|0.684;G|0.316	0.316	strong		0.478	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653	
HFE	3077	hgsc.bcm.edu	37	6	26091179	26091179	+	Missense_Mutation	SNP	C	C	G	rs1799945	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26091179C>G	ENST00000357618.5	+	2	309	c.187C>G	c.(187-189)Cat>Gat	p.H63D	HFE_ENST00000317896.7_Missense_Mutation_p.H63D|HFE_ENST00000336625.8_Missense_Mutation_p.H63D|HFE_ENST00000353147.5_Intron|HFE_ENST00000397022.3_Missense_Mutation_p.H40D|HFE_ENST00000309234.6_Missense_Mutation_p.H63D|HFE_ENST00000461397.1_Missense_Mutation_p.H63D|HFE_ENST00000470149.1_Missense_Mutation_p.H63D|HFE_ENST00000488199.1_Intron|HFE_ENST00000352392.4_Intron|HFE_ENST00000349999.4_Intron	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	63	Alpha-1.		H -> D (polymorphism associated with hemochromatosis and variegate porphyria; increased frequency among patients with diabetic nephropathy; dbSNP:rs1799945). {ECO:0000269|PubMed:10094552, ECO:0000269|PubMed:10194428, ECO:0000269|PubMed:10401000, ECO:0000269|PubMed:11069625, ECO:0000269|PubMed:11423500, ECO:0000269|PubMed:18157833, ECO:0000269|PubMed:8696333, ECO:0000269|PubMed:9106528, ECO:0000269|PubMed:9425935, ECO:0000269|PubMed:9620340, ECO:0000269|Ref.8}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTTCTATGATCATGAGAGTCG	0.522									Hemochromatosis				C|||	366	0.0730831	0.0113	0.1153	5008	,	,		20637	0.0288		0.172	False		,,,				2504	0.0706				p.H63D		Atlas-SNP	.											.	HFE	37	.	0			c.C187G	GRCh37	CM960827	HFE	M	rs1799945	PASS	.	C	ASP/HIS,ASP/HIS,ASP/HIS,ASP/HIS,,,ASP/HIS,,	139,4267	98.9+/-137.6	2,135,2066	143.0	130.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	187,187,187,187,,,118,,	3.5	0.0	6	dbSNP_89	135	1301,7299	257.7+/-281.7	87,1127,3086	yes	missense,missense,missense,missense,intron,intron,missense,intron,intron	HFE	NM_000410.3,NM_139003.2,NM_139004.2,NM_139006.2,NM_139007.2,NM_139008.2,NM_139009.2,NM_139010.2,NM_139011.2	81,81,81,81,,,81,,	89,1262,5152	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	15.1279,3.1548,11.0718	probably-damaging,probably-damaging,probably-damaging,probably-damaging,,,probably-damaging,,	63/349,63/243,63/257,63/335,,,40/326,,	26091179	1440,11566	2203	4300	6503	SO:0001583	missense	3077	exon2	Familial Cancer Database		TATGATCATGAGA		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"""Immunoglobulin superfamily / C1-set domain containing"""	4886	protein-coding gene	gene with protein product	"""high Fe"""	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.187C>G	6.37:g.26091179C>G	ENSP00000417404:p.His63Asp	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	241	129	0.53527	NM_139006	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	183	0.08379120879120878	9	0.018292682926829267	44	0.12154696132596685	14	0.024475524475524476	116	0.15303430079155672	C	12.44	1.939434	0.34189	0.031548	0.151279	ENSG00000010704	ENST00000397022;ENST00000317896;ENST00000535098;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000309234	D;T;D;D;T;D;D	0.88741	-2.42;5.87;-2.42;-2.42;5.87;-2.42;-2.42	5.3	3.51	0.40186	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.680049	0.14025	N	0.346540	D	0.87954	0.6308	L	0.61036	1.89	0.80722	P	0.0	B;D;D;B;B;B	0.62365	0.142;0.991;0.991;0.117;0.147;0.142	B;P;P;B;B;B	0.61070	0.161;0.883;0.883;0.1;0.083;0.161	D	0.85220	0.1026	9	0.87932	D	0	.	6.6848	0.23138	0.175:0.7358:0.0:0.0892	rs1799945;rs17515604;rs60366842;rs1799945	63;63;63;63;40;63	Q6B0J5;Q30201-7;Q30201-10;Q30201-3;Q30201-5;Q30201	.;.;.;.;.;HFE_HUMAN	D	40;63;63;63;63;63;63;63	ENSP00000380217:H40D;ENSP00000313776:H63D;ENSP00000417404:H63D;ENSP00000419725:H63D;ENSP00000337819:H63D;ENSP00000420802:H63D;ENSP00000311698:H63D	ENSP00000311698:H63D	H	+	1	0	HFE	26199158	0.284000	0.24287	0.002000	0.10522	0.964000	0.63967	0.952000	0.29149	0.785000	0.33685	0.655000	0.94253	CAT	C|0.898;G|0.102	0.102	strong		0.522	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1		
WDR55	54853	hgsc.bcm.edu	37	5	140048707	140048707	+	Missense_Mutation	SNP	A	A	G	rs35983033	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	102	0	0		WXS	Illumina HiSeq	Phase_I	137	71	0.518248	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	
CKM	1158	hgsc.bcm.edu	37	19	45815163	45815163	+	Missense_Mutation	SNP	G	G	A	rs17357122	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45815163G>A	ENST00000221476.3	-	5	671	c.497C>T	c.(496-498)aCg>aTg	p.T166M		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	166	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.		T -> M (in dbSNP:rs17357122).		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)			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)	GAACTCGCCCGTCAGGCTGTT	0.597													G|||	14	0.00279553	0.0015	0.0043	5008	,	,		15490	0.0		0.007	False		,,,				2504	0.002				p.T166M		Atlas-SNP	.											.	CKM	40	.	0			c.C497T						PASS	.	G	MET/THR	12,4394	19.1+/-41.9	0,12,2191	77.0	61.0	67.0		497	4.6	1.0	19	dbSNP_123	67	66,8534	40.8+/-97.7	0,66,4234	yes	missense	CKM	NM_001824.3	81	0,78,6425	AA,AG,GG		0.7674,0.2724,0.5997	possibly-damaging	166/382	45815163	78,12928	2203	4300	6503	SO:0001583	missense	1158	exon5			TCGCCCGTCAGGC	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.497C>T	19.37:g.45815163G>A	ENSP00000221476:p.Thr166Met	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	152	58	0.381579	NM_001824	Q96QL9	Missense_Mutation	SNP	ENST00000221476.3	37	CCDS12659.1	9	0.004120879120879121	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	g	17.70	3.454039	0.63290	0.002724	0.007674	ENSG00000104879	ENST00000221476	T	0.24151	1.87	4.64	4.64	0.57946	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.255179	0.38959	N	0.001515	T	0.32734	0.0839	M	0.84683	2.71	0.42644	D	0.99342	P	0.49185	0.92	P	0.45998	0.5	T	0.51164	-0.8740	10	0.72032	D	0.01	-36.3443	15.0589	0.71936	0.0:0.0:1.0:0.0	rs17357122;rs52824783;rs17357122	166	P06732	KCRM_HUMAN	M	166	ENSP00000221476:T166M	ENSP00000221476:T166M	T	-	2	0	CKM	50507003	0.984000	0.35163	0.997000	0.53966	0.892000	0.51952	2.104000	0.41815	2.421000	0.82119	0.556000	0.70494	ACG	G|0.995;A|0.005	0.005	strong		0.597	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1		
SIPA1L1	26037	hgsc.bcm.edu	37	14	72138078	72138078	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:72138078C>T	ENST00000555818.1	+	8	2846	c.2498C>T	c.(2497-2499)cCg>cTg	p.P833L	SIPA1L1_ENST00000381232.3_Missense_Mutation_p.P833L|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.P833L|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.P308L	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	833					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)		GGCAAGTTTCCGTTCATCTCT	0.532																																					p.P833L		Atlas-SNP	.											SIPA1L1,colon,carcinoma,0,1	SIPA1L1	219	1	0			c.C2498T						scavenged	.						78.0	72.0	74.0					14																	72138078		2203	4300	6503	SO:0001583	missense	26037	exon8			AGTTTCCGTTCAT	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.2498C>T	14.37:g.72138078C>T	ENSP00000450832:p.Pro833Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	165	3	0.0181818	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.002476	0.93227	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.68100	0.2964	M	0.64997	1.995	0.80722	D	1	D;B;D;D;D	0.76494	0.999;0.181;0.995;0.997;0.998	D;B;P;P;P	0.69479	0.964;0.029;0.707;0.886;0.84	T	0.64424	-0.6411	10	0.51188	T	0.08	-19.4596	20.8598	0.99761	0.0:1.0:0.0:0.0	.	308;833;308;833;833	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	L	833;833;833;308	ENSP00000370630:P833L;ENSP00000450832:P833L;ENSP00000351352:P833L;ENSP00000440682:P308L	ENSP00000351352:P833L	P	+	2	0	SIPA1L1	71207831	1.000000	0.71417	0.844000	0.33320	0.822000	0.46500	5.974000	0.70465	2.937000	0.99478	0.650000	0.86243	CCG	.	.	none		0.532	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
TMEM132B	114795	hgsc.bcm.edu	37	12	125900095	125900095	+	Silent	SNP	T	T	A	rs3809261	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:125900095T>A	ENST00000299308.3	+	3	971	c.963T>A	c.(961-963)ggT>ggA	p.G321G		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	321						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)		CGGCAGCAGGTGTGAAGATAA	0.463													T|||	504	0.100639	0.0666	0.0677	5008	,	,		18057	0.1419		0.0994	False		,,,				2504	0.1288				p.G321G		Atlas-SNP	.											.	TMEM132B	207	.	0			c.T963A						PASS	.	T		236,4070		6,224,1923	79.0	92.0	88.0		963	-7.4	0.6	12	dbSNP_107	88	732,7782		34,664,3559	no	coding-synonymous	TMEM132B	NM_052907.2		40,888,5482	AA,AT,TT		8.5976,5.4807,7.5507		321/1079	125900095	968,11852	2153	4257	6410	SO:0001819	synonymous_variant	114795	exon3			AGCAGGTGTGAAG	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.963T>A	12.37:g.125900095T>A		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	113	111	0.982301	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			T|0.901;A|0.099	0.099	strong		0.463	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
CLIP4	79745	hgsc.bcm.edu	37	2	29383256	29383256	+	Missense_Mutation	SNP	G	G	T	rs3100246	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:29383256G>T	ENST00000320081.5	+	12	1712	c.1457G>T	c.(1456-1458)cGc>cTc	p.R486L	CLIP4_ENST00000401605.1_Missense_Mutation_p.R486L|CLIP4_ENST00000401617.2_Missense_Mutation_p.R379L|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	144	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	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	
APOD	347	hgsc.bcm.edu	37	3	195306289	195306289	+	Missense_Mutation	SNP	A	A	G	rs5952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195306289A>G	ENST00000343267.3	-	2	405	c.44T>C	c.(43-45)tTc>tCc	p.F15S		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	15			F -> S (in dbSNP:rs5952). {ECO:0000269|PubMed:10391209}.		aging (GO:0007568)|angiogenesis (GO:0001525)|brain development (GO:0007420)|glucose metabolic process (GO:0006006)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of lipoprotein lipid oxidation (GO:0060588)|negative regulation of monocyte chemotactic protein-1 production (GO:0071638)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of T cell migration (GO:2000405)|peripheral nervous system axon regeneration (GO:0014012)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to reactive oxygen species (GO:0000302)|tissue regeneration (GO:0042246)	cytosolic ribosome (GO:0022626)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	9	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)		TGCCGCACCGAAGAGGCCAGC	0.582													A|||	7	0.00139776	0.0	0.0043	5008	,	,		18597	0.0		0.004	False		,,,				2504	0.0				p.F15S		Atlas-SNP	.											.	APOD	28	.	0			c.T44C						PASS	.	A	SER/PHE	6,4400	9.9+/-24.2	0,6,2197	41.0	44.0	43.0		44	1.6	0.0	3	dbSNP_52	43	54,8546	30.1+/-81.4	0,54,4246	yes	missense	APOD	NM_001647.3	155	0,60,6443	GG,GA,AA		0.6279,0.1362,0.4613	benign	15/190	195306289	60,12946	2203	4300	6503	SO:0001583	missense	347	exon2			GCACCGAAGAGGC		CCDS33925.1	3q29	2013-09-19			ENSG00000189058	ENSG00000189058		"""Lipocalins"", ""Apolipoproteins"""	612	protein-coding gene	gene with protein product		107740				2439269, 3453108	Standard	NM_001647		Approved		uc003fur.2	P05090	OTTHUMG00000155854	ENST00000343267.3:c.44T>C	3.37:g.195306289A>G	ENSP00000345179:p.Phe15Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_001647	B2R579|D3DNW6|Q6IBG6	Missense_Mutation	SNP	ENST00000343267.3	37	CCDS33925.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	A	12.13	1.844610	0.32606	0.001362	0.006279	ENSG00000189058	ENST00000343267;ENST00000421243;ENST00000453131	T;T;T	0.21031	2.03;2.03;2.03	5.68	1.61	0.23674	Calycin (1);	0.701798	0.13384	N	0.391946	T	0.11196	0.0273	L	0.38175	1.15	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.002;0.002	T	0.19976	-1.0289	10	0.62326	D	0.03	-0.2464	7.3764	0.26831	0.7035:0.0:0.2965:0.0	rs5952	15;15	B4DGC3;P05090	.;APOD_HUMAN	S	15;43;15	ENSP00000345179:F15S;ENSP00000415235:F43S;ENSP00000393076:F15S	ENSP00000345179:F15S	F	-	2	0	APOD	196787578	0.127000	0.22367	0.000000	0.03702	0.009000	0.06853	1.338000	0.33873	0.434000	0.26340	0.533000	0.62120	TTC	A|0.996;G|0.004	0.004	strong		0.582	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647	
CEP112	201134	hgsc.bcm.edu	37	17	64025331	64025331	+	Silent	SNP	A	A	G	rs11652766	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:64025331A>G	ENST00000392769.2	-	14	1631	c.1413T>C	c.(1411-1413)aaT>aaC	p.N471N	CEP112_ENST00000541355.1_Silent_p.N106N|CEP112_ENST00000535342.2_Silent_p.N471N|CEP112_ENST00000537949.1_Silent_p.N429N	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	471					receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						GCTCATAATCATTTACAAGAT	0.294													A|||	1907	0.380791	0.5983	0.317	5008	,	,		16744	0.0903		0.5249	False		,,,				2504	0.2832				p.N471N		Atlas-SNP	.											.	CEP112	192	.	0			c.T1413C						PASS	.	A	,	2567,1835	633.9+/-396.1	755,1057,389	194.0	183.0	187.0		1413,1413	-1.7	0.5	17	dbSNP_120	187	4717,3879	604.7+/-394.8	1301,2115,882	no	coding-synonymous,coding-synonymous	CEP112	NM_001199165.1,NM_145036.3	,	2056,3172,1271	GG,GA,AA		45.1256,41.6856,43.9606	,	471/956,471/956	64025331	7284,5714	2201	4298	6499	SO:0001819	synonymous_variant	201134	exon14			ATAATCATTTACA	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.1413T>C	17.37:g.64025331A>G		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	234	115	0.491453	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Silent	SNP	ENST00000392769.2	37	CCDS32710.1																																																																																			A|0.507;G|0.493	0.493	strong		0.294	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84611367	84611367	+	Missense_Mutation	SNP	G	G	C	rs34047645	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:84611367G>C	ENST00000286744.5	+	18	2361	c.2137G>C	c.(2137-2139)Ggg>Cgg	p.G713R	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.G713R	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	713	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.		G -> R (in dbSNP:rs34047645).			proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGGCTCTTGGGGGCCCTGCTC	0.542													G|||	271	0.0541134	0.0076	0.0879	5008	,	,		18592	0.001		0.168	False		,,,				2504	0.0307				p.G713R		Atlas-SNP	.											ADAMTSL3,NS,carcinoma,-2,2	ADAMTSL3	290	2	0			c.G2137C						PASS	.	G	ARG/GLY	161,4245	107.3+/-145.7	3,155,2045	83.0	85.0	84.0		2137	3.6	1.0	15	dbSNP_126	84	1369,7231	264.3+/-285.5	107,1155,3038	yes	missense	ADAMTSL3	NM_207517.2	125	110,1310,5083	CC,CG,GG		15.9186,3.6541,11.7638	benign	713/1692	84611367	1530,11476	2203	4300	6503	SO:0001583	missense	57188	exon18			TCTTGGGGGCCCT	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2137G>C	15.37:g.84611367G>C	ENSP00000286744:p.Gly713Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	33	31	0.939394	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	170	0.07783882783882784	4	0.008130081300813009	34	0.09392265193370165	0	0.0	132	0.1741424802110818	G	10.65	1.410885	0.25465	0.036541	0.159186	ENSG00000156218	ENST00000286744	T	0.53857	0.6	5.7	3.61	0.41365	.	2.009030	0.02079	N	0.052181	T	0.00109	0.0003	N	0.17564	0.495	0.23956	P	0.99635721	B;B	0.18863	0.002;0.031	B;B	0.23419	0.011;0.046	T	0.05886	-1.0858	9	0.33141	T	0.24	.	4.2229	0.10567	0.4509:0.0:0.5491:0.0	rs34047645	713;713	P82987-2;P82987	.;ATL3_HUMAN	R	713	ENSP00000286744:G713R	ENSP00000286744:G713R	G	+	1	0	ADAMTSL3	82402371	1.000000	0.71417	0.993000	0.49108	0.526000	0.34562	3.442000	0.52900	1.409000	0.46915	0.655000	0.94253	GGG	G|0.892;C|0.108	0.108	strong		0.542	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
MUC2	4583	hgsc.bcm.edu	37	11	1093324	1093324	+	Missense_Mutation	SNP	G	G	A	rs201143282		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1093324G>A	ENST00000441003.2	+	30	5170	c.5143G>A	c.(5143-5145)Ggc>Agc	p.G1715S	MUC2_ENST00000359061.5_Missense_Mutation_p.G1682S|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.G3S	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)	aacacccaccggcacacagac	0.637																																					p.G1715S		Atlas-SNP	.											MUC2_ENST00000441003,uveal_tract,malignant_melanoma,0,2	MUC2	614	2	0			c.G5143A						PASS	.						178.0	224.0	208.0					11																	1093324		1930	3651	5581	SO:0001583	missense	4583	exon30			CCCACCGGCACAC	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.5143G>A	11.37:g.1093324G>A	ENSP00000415183:p.Gly1715Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	4	0.0645161	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	G	7.149	0.583420	0.13749	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.16743	3.11;3.17;2.32	1.64	0.221	0.15283	.	155.122000	0.02480	U	0.088379	T	0.09686	0.0238	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.22556	-1.0213	9	0.19147	T	0.46	.	3.4701	0.07563	0.7575:0.0:0.2425:0.0	.	1715	E7EUV1	.	S	1715;1682;3	ENSP00000415183:G1715S;ENSP00000351956:G1682S;ENSP00000331373:G3S	ENSP00000331373:G3S	G	+	1	0	MUC2	1083324	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.131000	0.10482	-0.042000	0.13535	-1.076000	0.02234	GGC	.	.	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR9G1	390174	hgsc.bcm.edu	37	11	56467945	56467945	+	Missense_Mutation	SNP	G	G	T	rs36184181|rs397849604	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56467945G>T	ENST00000312153.1	+	1	82	c.82G>T	c.(82-84)Gtg>Ttg	p.V28L		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GGGCCTCTTCGTGGTGTTCCT	0.502													G|||	4	0.000798722	0.0	0.0	5008	,	,		18770	0.001		0.0	False		,,,				2504	0.0031				p.V28L		Atlas-SNP	.											.	.	.	.	0			c.G82T						PASS	.	G	LEU/VAL	497,3905		0,497,1704	164.0	141.0	149.0		82	2.6	0.0	11	dbSNP_126	149	2528,6064		0,2528,1768	yes	missense	OR9G1	NM_001005213.1	32	0,3025,3472	TT,TG,GG		29.4227,11.2903,23.28	benign	28/306	56467945	3025,9969	2201	4296	6497	SO:0001583	missense	504191	exon1			CTCTTCGTGGTGT	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.82G>T	11.37:g.56467945G>T	ENSP00000309012:p.Val28Leu	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	192	49	0.255208	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	773	0.35393772893772896	65	0.13211382113821138	162	0.44751381215469616	244	0.42657342657342656	302	0.39841688654353563	G	0.022	-1.408655	0.01155	0.112903	0.294227	ENSG00000174914	ENST00000312153	T	0.00448	7.38	4.52	2.63	0.31362	.	0.289314	0.24649	N	0.036723	T	0.00012	0.0000	N	0.11789	0.175	0.09310	N	1	B	0.14012	0.009	B	0.19148	0.024	T	0.31916	-0.9926	10	0.07482	T	0.82	-9.336	9.4573	0.38762	0.2451:0.0:0.7549:0.0	rs36184181	28	Q8NH87	OR9G1_HUMAN	L	28	ENSP00000309012:V28L	ENSP00000309012:V28L	V	+	1	0	OR9G1	56224521	0.000000	0.05858	0.006000	0.13384	0.011000	0.07611	-0.943000	0.03917	0.621000	0.30232	0.573000	0.79308	GTG	G|0.646;T|0.354	0.354	strong		0.502	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
KERA	11081	hgsc.bcm.edu	37	12	91449984	91449984	+	Silent	SNP	C	C	T	rs12320366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:91449984C>T	ENST00000266719.3	-	2	322	c.75G>A	c.(73-75)caG>caA	p.Q25Q		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	25					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)				breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						CTTCATAGACCTGCCTCACAC	0.423													C|||	1130	0.225639	0.5847	0.1412	5008	,	,		17998	0.0804		0.1183	False		,,,				2504	0.0603				p.Q25Q		Atlas-SNP	.											.	KERA	62	.	0			c.G75A						PASS	.	C		2163,2241	576.7+/-384.3	537,1089,576	95.0	75.0	82.0		75	5.1	1.0	12	dbSNP_120	82	1121,7479	230.7+/-264.9	72,977,3251	no	coding-synonymous	KERA	NM_007035.3		609,2066,3827	TT,TC,CC		13.0349,49.1144,25.2538		25/353	91449984	3284,9720	2202	4300	6502	SO:0001819	synonymous_variant	11081	exon2			ATAGACCTGCCTC	AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6309	protein-coding gene	gene with protein product	"""keratocan proteoglycan"""	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.75G>A	12.37:g.91449984C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	80	66	0.825	NM_007035		Silent	SNP	ENST00000266719.3	37	CCDS9037.1																																																																																			C|0.758;T|0.242	0.242	strong		0.423	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035	
STRN	6801	hgsc.bcm.edu	37	2	37152342	37152342	+	Missense_Mutation	SNP	C	C	T	rs200160777	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:37152342C>T	ENST00000263918.4	-	2	252	c.244G>A	c.(244-246)Gcc>Acc	p.A82T	STRN_ENST00000379213.2_Missense_Mutation_p.A70T	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	82					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)	p.A82T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				TGCAGGAAGGCAATCTGGGCC	0.373																																					p.A82T		Atlas-SNP	.											STRN,NS,other,0,2	STRN	71	2	1	Substitution - Missense(1)	pancreas(1)	c.G244A						scavenged	.						46.0	49.0	48.0					2																	37152342		2202	4299	6501	SO:0001583	missense	6801	exon2			GGAAGGCAATCTG	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"""WD repeat domain containing"""	11424	protein-coding gene	gene with protein product		614765	"""striatin, calmodulin-binding protein"""			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.244G>A	2.37:g.37152342C>T	ENSP00000263918:p.Ala82Thr	Somatic	167	14	0.0838323		WXS	Illumina HiSeq	Phase_I	203	14	0.0689655	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Missense_Mutation	SNP	ENST00000263918.4	37	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	C	31	5.066711	0.93898	.	.	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	T;T	0.76060	-0.99;-0.95	5.16	5.16	0.70880	Striatin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87434	0.6176	M	0.85777	2.775	0.80722	D	1	D;D	0.76494	0.996;0.999	D;D	0.74674	0.939;0.984	D	0.88923	0.3367	10	0.56958	D	0.05	-8.9413	17.4167	0.87503	0.0:1.0:0.0:0.0	.	70;82	O43815-2;O43815	.;STRN_HUMAN	T	82;57;70	ENSP00000263918:A82T;ENSP00000368513:A70T	ENSP00000263918:A82T	A	-	1	0	STRN	37005846	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	7.468000	0.80943	2.376000	0.81061	0.650000	0.86243	GCC	C|0.719;T|0.281	0.281	strong		0.373	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1		
OR7A17	26333	hgsc.bcm.edu	37	19	14991963	14991963	+	Missense_Mutation	SNP	C	C	A	rs10404119	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14991963C>A	ENST00000327462.2	-	1	301	c.205G>T	c.(205-207)Gca>Tca	p.A69S		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	69			A -> S (in dbSNP:rs10404119).			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)					CAGATGTCTGCAAAGGACAGG	0.512													.|||	1661	0.331669	0.118	0.3098	5008	,	,		16982	0.6052		0.3161	False		,,,				2504	0.3701				p.A69S		Atlas-SNP	.											.	OR7A17	37	.	0			c.G205T						PASS	.	C	SER/ALA	763,3643	310.0+/-291.3	57,649,1497	99.0	86.0	90.0		205	0.4	0.0	19	dbSNP_119	90	2565,6035	418.0+/-352.6	383,1799,2118	yes	missense	OR7A17	NM_030901.1	99	440,2448,3615	AA,AC,CC		29.8256,17.3173,25.5882	benign	69/310	14991963	3328,9678	2203	4300	6503	SO:0001583	missense	26333	exon1			TGTCTGCAAAGGA	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.205G>T	19.37:g.14991963C>A	ENSP00000328144:p.Ala69Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_030901	Q6IFQ6|Q96R98	Missense_Mutation	SNP	ENST00000327462.2	37	CCDS12319.1	744	0.34065934065934067	53	0.10772357723577236	100	0.27624309392265195	341	0.5961538461538461	250	0.32981530343007914	c	7.921	0.738580	0.15642	0.173173	0.298256	ENSG00000185385	ENST00000327462	T	0.03004	4.08	2.74	0.396	0.16309	GPCR, rhodopsin-like superfamily (1);	1.087770	0.07430	N	0.895552	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.19073	0.033	B	0.26969	0.075	T	0.28586	-1.0039	9	0.51188	T	0.08	.	3.6298	0.08127	0.4309:0.438:0.0:0.1311	rs10404119;rs52793167;rs10404119	69	O14581	OR7AH_HUMAN	S	69	ENSP00000328144:A69S	ENSP00000328144:A69S	A	-	1	0	OR7A17	14852963	0.000000	0.05858	0.010000	0.14722	0.615000	0.37417	-3.279000	0.00529	0.211000	0.20683	0.395000	0.25975	GCA	C|0.711;A|0.289	0.289	strong		0.512	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
SLFN14	342618	hgsc.bcm.edu	37	17	33875262	33875262	+	Missense_Mutation	SNP	T	T	A	rs8073060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33875262T>A	ENST00000415846.3	-	4	2770	c.2735A>T	c.(2734-2736)tAc>tTc	p.Y912F		NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	912			Y -> F (in dbSNP:rs8073060).				ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						TAATTTTCAGTAGGCTGCCCT	0.398													A|||	1755	0.350439	0.4766	0.3069	5008	,	,		20366	0.1815		0.3201	False		,,,				2504	0.4162				p.Y912F		Atlas-SNP	.											.	SLFN14	43	.	0			c.A2735T						PASS	.	A	PHE/TYR	626,758		145,336,211	89.0	84.0	86.0		2735	2.8	0.3	17	dbSNP_116	86	958,2224		147,664,780	yes	missense	SLFN14	NM_001129820.1	22	292,1000,991	AA,AT,TT		30.1069,45.2312,34.6912	benign	912/913	33875262	1584,2982	692	1591	2283	SO:0001583	missense	342618	exon4			TTTCAGTAGGCTG		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.2735A>T	17.37:g.33875262T>A	ENSP00000391101:p.Tyr912Phe	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_001129820	B2RTW9	Missense_Mutation	SNP	ENST00000415846.3	37	CCDS45650.1	688	0.315018315018315	226	0.45934959349593496	110	0.30386740331491713	109	0.19055944055944055	243	0.32058047493403696	A	0.005	-2.218174	0.00286	0.452312	0.301069	ENSG00000236320	ENST00000415846	T	0.01745	4.66	4.97	2.75	0.32379	.	.	.	.	.	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	0.38067	-0.9678	8	0.02654	T	1	.	3.6425	0.08172	0.6653:0.0:0.1751:0.1597	rs8073060;rs52819255;rs8073060	912	P0C7P3	SLN14_HUMAN	F	912	ENSP00000391101:Y912F	ENSP00000391101:Y912F	Y	-	2	0	SLFN14	30899375	0.392000	0.25229	0.343000	0.25615	0.080000	0.17528	0.507000	0.22675	0.132000	0.18615	-0.364000	0.07487	TAC	T|0.694;A|0.306	0.306	strong		0.398	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
CCDC138	165055	hgsc.bcm.edu	37	2	109408208	109408208	+	Missense_Mutation	SNP	G	G	A	rs6740879	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:109408208G>A	ENST00000295124.4	+	4	404	c.344G>A	c.(343-345)aGa>aAa	p.R115K	CCDC138_ENST00000412964.2_Missense_Mutation_p.R115K|CCDC138_ENST00000470608.1_3'UTR	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	115			R -> K (in dbSNP:rs6740879).					p.R115K(1)		endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						AATGATTATAGAGTTAGTACC	0.274													G|||	1302	0.259984	0.3623	0.1888	5008	,	,		15706	0.0913		0.2346	False		,,,				2504	0.3722				p.R115K		Atlas-SNP	.											CCDC138,NS,carcinoma,0,1	CCDC138	49	1	1	Substitution - Missense(1)	stomach(1)	c.G344A						PASS	.	G	LYS/ARG	1502,2894	447.9+/-348.5	259,984,955	71.0	83.0	79.0		344	3.0	0.1	2	dbSNP_116	79	1977,6613	338.9+/-322.9	232,1513,2550	yes	missense	CCDC138	NM_144978.1	26	491,2497,3505	AA,AG,GG		23.0151,34.1674,26.7904	possibly-damaging	115/666	109408208	3479,9507	2198	4295	6493	SO:0001583	missense	165055	exon4			ATTATAGAGTTAG	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.344G>A	2.37:g.109408208G>A	ENSP00000295124:p.Arg115Lys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	486|486	0.22252747252747251|0.22252747252747251	182|182	0.3699186991869919|0.3699186991869919	74|74	0.20441988950276244|0.20441988950276244	53|53	0.09265734265734266|0.09265734265734266	177|177	0.23350923482849603|0.23350923482849603	G|G	11.12|11.12	1.545024|1.545024	0.27652|0.27652	0.341674|0.341674	0.230151|0.230151	ENSG00000163006|ENSG00000163006	ENST00000456512|ENST00000412964;ENST00000295124	.|D;D	.|0.90133	.|-2.62;-2.62	5.77|5.77	2.99|2.99	0.34606|0.34606	.|.	.|0.522350	.|0.19228	.|N	.|0.119493	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	.|B;B	.|0.10296	.|0.003;0.003	.|B;B	.|0.09377	.|0.004;0.004	T|T	0.15521|0.15521	-1.0434|-1.0434	4|9	.|0.05721	.|T	.|0.95	-0.7705|-0.7705	9.3348|9.3348	0.38043|0.38043	0.2322:0.0:0.7678:0.0|0.2322:0.0:0.7678:0.0	rs6740879;rs60240712;rs6740879|rs6740879;rs60240712;rs6740879	.|115;115	.|Q96M89-2;Q96M89	.|.;CC138_HUMAN	K|K	13|115	.|ENSP00000411800:R115K;ENSP00000295124:R115K	.|ENSP00000295124:R115K	E|R	+|+	1|2	0|0	CCDC138|CCDC138	108774640|108774640	0.000000|0.000000	0.05858|0.05858	0.114000|0.114000	0.21550|0.21550	0.749000|0.749000	0.42624|0.42624	0.164000|0.164000	0.16542|0.16542	0.791000|0.791000	0.33826|0.33826	0.655000|0.655000	0.94253|0.94253	GAG|AGA	G|0.747;A|0.253	0.253	strong		0.274	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	
ZNF33A	7581	hgsc.bcm.edu	37	10	38345455	38345455	+	Silent	SNP	A	A	G	rs12242343	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:38345455A>G	ENST00000458705.2	+	5	2558	c.2400A>G	c.(2398-2400)ggA>ggG	p.G800G	ZNF33A_ENST00000374618.3_Silent_p.G801G|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000307441.9_Silent_p.G800G|ZNF33A_ENST00000432900.2_Silent_p.G807G			Q06730	ZN33A_HUMAN	zinc finger protein 33A	800					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						CACACTGTGGAGAAAGCCCTG	0.388													A|||	140	0.0279553	0.0915	0.013	5008	,	,		18836	0.0		0.0099	False		,,,				2504	0.0				p.G801G		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A2403G						PASS	.	A	,	359,4047	175.9+/-205.1	19,321,1863	61.0	59.0	60.0		2403,2400	1.9	0.1	10	dbSNP_120	60	53,8547	32.3+/-84.9	0,53,4247	no	coding-synonymous,coding-synonymous	ZNF33A	NM_006954.1,NM_006974.2	,	19,374,6110	GG,GA,AA		0.6163,8.148,3.1678	,	801/812,800/811	38345455	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	7581	exon5			CTGTGGAGAAAGC	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.2400A>G	10.37:g.38345455A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	66	17	0.257576	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	37	CCDS31182.1																																																																																			A|0.968;G|0.032	0.032	strong		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
ITGA2	3673	hgsc.bcm.edu	37	5	52347369	52347369	+	Silent	SNP	C	C	T	rs1126643	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:52347369C>T	ENST00000296585.5	+	7	902	c.759C>T	c.(757-759)ttC>ttT	p.F253F		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	253	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|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)|virus receptor activity (GO:0001618)			breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				CAAACACATTCGGAGCAATTC	0.328													C|||	1691	0.33766	0.2806	0.4424	5008	,	,		16165	0.2827		0.4026	False		,,,				2504	0.3303				p.F253F		Atlas-SNP	.											.	ITGA2	211	.	0			c.C759T	GRCh37	CM993453	ITGA2	M	rs1126643	PASS	.	C		1343,3063	448.1+/-348.6	209,925,1069	108.0	105.0	106.0		759	4.9	1.0	5	dbSNP_86	106	3414,5186	503.8+/-376.0	651,2112,1537	no	coding-synonymous	ITGA2	NM_002203.3		860,3037,2606	TT,TC,CC		39.6977,30.4812,36.5754		253/1182	52347369	4757,8249	2203	4300	6503	SO:0001819	synonymous_variant	3673	exon7			CACATTCGGAGCA		CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.759C>T	5.37:g.52347369C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			C|0.629;T|0.371	0.371	strong		0.328	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
AMPH	273	hgsc.bcm.edu	37	7	38431511	38431511	+	Silent	SNP	C	C	T	rs2229922	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:38431511C>T	ENST00000356264.2	-	19	1931	c.1716G>A	c.(1714-1716)gcG>gcA	p.A572A	AMPH_ENST00000325590.5_Silent_p.A530A|AMPH_ENST00000471913.1_5'Flank|AMPH_ENST00000428293.2_Silent_p.A530A	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	572					endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CCGGAGGAGCCGCGTCCTCGG	0.607													C|||	368	0.0734824	0.0401	0.0893	5008	,	,		15646	0.004		0.1064	False		,,,				2504	0.1452				p.A572A		Atlas-SNP	.											AMPH,NS,carcinoma,-1,1	AMPH	157	1	0			c.G1716A						PASS	.	C	,	166,4240	110.4+/-148.6	4,158,2041	59.0	56.0	57.0		1716,1590	-9.5	0.0	7	dbSNP_98	57	974,7626	212.0+/-252.4	45,884,3371	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	49,1042,5412	TT,TC,CC		11.3256,3.7676,8.7652	,	572/696,530/654	38431511	1140,11866	2203	4300	6503	SO:0001819	synonymous_variant	273	exon19			AGGAGCCGCGTCC		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1716G>A	7.37:g.38431511C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	37	CCDS5456.1	137	0.06272893772893773	26	0.052845528455284556	30	0.08287292817679558	0	0.0	81	0.10686015831134564	C	7.174	0.588285	0.13812	0.037676	0.113256	ENSG00000078053	ENST00000441628	.	.	.	5.75	-9.5	0.00584	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.17018	-1.0383	3	.	.	.	-0.0635	0.0536	0.00013	0.3054:0.1844:0.2262:0.2839	rs2229922;rs2229922	.	.	.	S	455	.	.	G	-	1	0	AMPH	38398036	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.378000	0.01068	-1.937000	0.01047	-0.229000	0.12294	GGC	C|0.919;T|0.081	0.081	strong		0.607	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
PVRIG	79037	hgsc.bcm.edu	37	7	99817585	99817585	+	Nonsense_Mutation	SNP	G	G	T	rs7786505	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	379	146	0.385224	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	
ELL2	22936	hgsc.bcm.edu	37	5	95236415	95236415	+	Silent	SNP	G	G	A	rs17085249	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:95236415G>A	ENST00000237853.4	-	7	1285	c.936C>T	c.(934-936)gaC>gaT	p.D312D	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	312					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)		p.D312D(1)		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)		AAGATACAGCGTCTCTACTAG	0.413													G|||	1706	0.340655	0.3654	0.2406	5008	,	,		19046	0.4325		0.2793	False		,,,				2504	0.3466				p.D312D		Atlas-SNP	.											ELL2,NS,carcinoma,0,1	ELL2	63	1	1	Substitution - coding silent(1)	prostate(1)	c.C936T						PASS	.	G		1503,2903	478.5+/-358.2	256,991,956	75.0	73.0	73.0		936	-8.4	0.0	5	dbSNP_123	73	2247,6353	380.4+/-339.6	290,1667,2343	no	coding-synonymous	ELL2	NM_012081.5		546,2658,3299	AA,AG,GG		26.1279,34.1126,28.8328		312/641	95236415	3750,9256	2203	4300	6503	SO:0001819	synonymous_variant	22936	exon7			TACAGCGTCTCTA	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.936C>T	5.37:g.95236415G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	177	174	0.983051	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			G|0.697;A|0.303	0.303	strong		0.413	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998004	72998004	+	Silent	SNP	T	T	C	rs3744908	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	86	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	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	
OTOP1	133060	hgsc.bcm.edu	37	4	4199760	4199760	+	Silent	SNP	G	G	A	rs17697262	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:4199760G>A	ENST00000296358.4	-	5	825	c.801C>T	c.(799-801)atC>atT	p.I267I		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	267					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AGAGGTAGTAGATCCCGTGGG	0.537													G|||	431	0.0860623	0.0197	0.1009	5008	,	,		19284	0.0218		0.1899	False		,,,				2504	0.1247				p.I267I		Atlas-SNP	.											OTOP1,NS,carcinoma,-2,1	OTOP1	118	1	0			c.C801T						scavenged	.	G		274,4132	154.8+/-188.1	9,256,1938	73.0	61.0	65.0		801	-3.0	0.3	4	dbSNP_123	65	1940,6660	339.4+/-323.1	222,1496,2582	no	coding-synonymous	OTOP1	NM_177998.1		231,1752,4520	AA,AG,GG		22.5581,6.2188,17.0229		267/613	4199760	2214,10792	2203	4300	6503	SO:0001819	synonymous_variant	133060	exon5			GTAGTAGATCCCG	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.801C>T	4.37:g.4199760G>A		Somatic	262	2	0.00763359		WXS	Illumina HiSeq	Phase_I	244	106	0.434426	NM_177998	A1L476	Silent	SNP	ENST00000296358.4	37	CCDS3372.1																																																																																			G|0.855;A|0.145	0.145	strong		0.537	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
CD6	923	hgsc.bcm.edu	37	11	60776186	60776186	+	Missense_Mutation	SNP	C	C	T	rs11230562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:60776186C>T	ENST00000313421.7	+	4	836	c.650C>T	c.(649-651)aCg>aTg	p.T217M	CD6_ENST00000344028.5_Missense_Mutation_p.T217M|CD6_ENST00000452451.2_Missense_Mutation_p.T217M|CD6_ENST00000352009.5_Missense_Mutation_p.T217M|CD6_ENST00000346437.4_Missense_Mutation_p.T217M|CD6_ENST00000545105.1_Intron	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	217	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		T -> M (in dbSNP:rs11230562). {ECO:0000269|PubMed:17371992}.		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						TTGCACTTCACGCCCGGCCGC	0.692													C|||	442	0.0882588	0.0106	0.1239	5008	,	,		12755	0.0357		0.2386	False		,,,				2504	0.0675				p.T217M	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.C650T						PASS	.	C	MET/THR	238,4154		12,214,1970	26.0	22.0	24.0		650	0.7	0.2	11	dbSNP_120	24	2045,6541		256,1533,2504	yes	missense	CD6	NM_006725.3	81	268,1747,4474	TT,TC,CC		23.8178,5.4189,17.5913	probably-damaging	217/669	60776186	2283,10695	2196	4293	6489	SO:0001583	missense	923	exon4			ACTTCACGCCCGG		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.650C>T	11.37:g.60776186C>T	ENSP00000323280:p.Thr217Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	252|252	0.11538461538461539|0.11538461538461539	8|8	0.016260162601626018|0.016260162601626018	52|52	0.143646408839779|0.143646408839779	12|12	0.02097902097902098|0.02097902097902098	180|180	0.23746701846965698|0.23746701846965698	C|C	12.39|12.39	1.924082|1.924082	0.34002|0.34002	0.054189|0.054189	0.238178|0.238178	ENSG00000013725|ENSG00000013725	ENST00000538611|ENST00000344028;ENST00000346437;ENST00000313421;ENST00000542157;ENST00000433107;ENST00000452451;ENST00000352009	.|T;T;T;T;T;T;T	.|0.29142	.|1.58;1.58;1.58;1.58;1.58;1.58;1.58	4.08|4.08	0.667|0.667	0.17907|0.17907	.|Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.|0.634924	.|0.12753	.|N	.|0.441986	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	P|P	0.0|0.0	.|P;D;D;D;D	.|0.71674	.|0.709;0.998;0.994;0.997;0.996	.|B;P;P;P;P	.|0.61533	.|0.157;0.813;0.729;0.823;0.89	T|T	0.16748|0.16748	-1.0392|-1.0392	4|9	.|0.87932	.|D	.|0	.|.	8.527|8.527	0.33311|0.33311	0.2324:0.2692:0.4984:0.0|0.2324:0.2692:0.4984:0.0	rs11230562|rs11230562	.|217;217;217;217;217	.|E7ER04;P30203-5;P30203-4;P30203;Q8N4Q7	.|.;.;.;CD6_HUMAN;.	C|M	61|217	.|ENSP00000344108:T217M;ENSP00000345566:T217M;ENSP00000323280:T217M;ENSP00000440055:T217M;ENSP00000410638:T217M;ENSP00000390676:T217M;ENSP00000340628:T217M	.|ENSP00000323280:T217M	R|T	+|+	1|2	0|0	CD6|CD6	60532762|60532762	0.000000|0.000000	0.05858|0.05858	0.175000|0.175000	0.22980|0.22980	0.321000|0.321000	0.28281|0.28281	-0.081000|-0.081000	0.11321|0.11321	0.343000|0.343000	0.23821|0.23821	0.561000|0.561000	0.74099|0.74099	CGC|ACG	C|0.852;T|0.148	0.148	strong		0.692	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
WWP2	11060	hgsc.bcm.edu	37	16	69973825	69973825	+	Silent	SNP	G	G	A	rs3748389	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:69973825G>A	ENST00000359154.2	+	24	2696	c.2595G>A	c.(2593-2595)gaG>gaA	p.E865E	WWP2_ENST00000568684.1_Silent_p.E426E|WWP2_ENST00000542271.1_Silent_p.E749E|WWP2_ENST00000448661.1_Silent_p.E865E|WWP2_ENST00000356003.2_Silent_p.E865E|WWP2_ENST00000544162.1_3'UTR	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	865	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|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)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						AGGAGACCGAGGGCTTTGGAC	0.612													G|||	2646	0.528355	0.3994	0.3862	5008	,	,		17241	0.8819		0.3449	False		,,,				2504	0.6278				p.E865E		Atlas-SNP	.											WWP2,NS,carcinoma,0,1	WWP2	88	1	0			c.G2595A						PASS	.	G	,	1633,2763	497.4+/-363.8	305,1023,870	84.0	63.0	70.0		2595,1278	3.4	1.0	16	dbSNP_107	70	3045,5555	462.0+/-365.6	554,1937,1809	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	859,2960,2679	AA,AG,GG		35.407,37.1474,35.9957	,	865/871,426/432	69973825	4678,8318	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon24			GACCGAGGGCTTT	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.2595G>A	16.37:g.69973825G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	93	15	0.16129	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			G|0.572;A|0.428	0.428	strong		0.612	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
ELL	8178	hgsc.bcm.edu	37	19	18562438	18562438	+	Missense_Mutation	SNP	C	C	T	rs2303694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:18562438C>T	ENST00000262809.4	-	7	961	c.890G>A	c.(889-891)aGc>aAc	p.S297N	ELL_ENST00000596124.3_Missense_Mutation_p.S164N	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	297			S -> N (in dbSNP:rs2303694).		gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		GCTGCCAGTGCTCTGTGGCTG	0.692			T	MLL	AL								C|||	761	0.151957	0.2027	0.0922	5008	,	,		16101	0.0774		0.1292	False		,,,				2504	0.226				p.S297N		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.G890A						PASS	.	C	ASN/SER	611,3341		51,509,1416	9.0	10.0	9.0		890	-0.8	0.1	19	dbSNP_100	9	830,6746		38,754,2996	no	missense	ELL	NM_006532.3	46	89,1263,4412	TT,TC,CC		10.9556,15.4605,12.5	benign	297/622	18562438	1441,10087	1976	3788	5764	SO:0001583	missense	8178	exon7			CCAGTGCTCTGTG	U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23114	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 68"""	600284	"""chromosome 19 open reading frame 17"""	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.890G>A	19.37:g.18562438C>T	ENSP00000262809:p.Ser297Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	108	41	0.37963	NM_006532		Missense_Mutation	SNP	ENST00000262809.4	37	CCDS12380.1	295	0.13507326007326007	102	0.2073170731707317	45	0.12430939226519337	46	0.08041958041958042	102	0.1345646437994723	C	1.960	-0.439155	0.04636	0.154605	0.109556	ENSG00000105656	ENST00000262809	T	0.23754	1.89	4.26	-0.837	0.10766	.	0.530492	0.19087	N	0.123064	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33420	-0.9869	9	0.02654	T	1	-5.4715	3.1878	0.06607	0.1855:0.4069:0.0:0.4075	rs2303694	241;297	Q59HG4;P55199	.;ELL_HUMAN	N	297	ENSP00000262809:S297N	ENSP00000262809:S297N	S	-	2	0	ELL	18423438	0.047000	0.20315	0.053000	0.19242	0.173000	0.22820	0.209000	0.17435	0.351000	0.24027	0.549000	0.68633	AGC	C|0.865;T|0.135	0.135	strong		0.692	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532	
GLIS3	169792	hgsc.bcm.edu	37	9	4118111	4118111	+	Missense_Mutation	SNP	G	G	T	rs6415788	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:4118111G>T	ENST00000324333.10	-	3	1095	c.902C>A	c.(901-903)cCa>cAa	p.P301Q	GLIS3_ENST00000381971.3_Missense_Mutation_p.P456Q	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	301	Pro-rich.		P -> Q (in dbSNP:rs6415788). {ECO:0000269|PubMed:15489334}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	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 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)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		tggggggcctgggggcggcgg	0.731													T|||	3386	0.676118	0.6006	0.7622	5008	,	,		9673	0.874		0.6302	False		,,,				2504	0.5603				p.P456Q		Atlas-SNP	.											.	GLIS3	152	.	0			c.C1367A						PASS	.	T	GLN/PRO,GLN/PRO	2499,1143		894,711,216	8.0	11.0	10.0		1367,902	5.4	1.0	9	dbSNP_116	10	4958,2542		1716,1526,508	yes	missense,missense	GLIS3	NM_001042413.1,NM_152629.3	76,76	2610,2237,724	TT,TG,GG		33.8933,31.3839,33.0731	benign,benign	456/931,301/776	4118111	7457,3685	1821	3750	5571	SO:0001583	missense	169792	exon4			GGGCCTGGGGGCG	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.902C>A	9.37:g.4118111G>T	ENSP00000325494:p.Pro301Gln	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	1503	0.6881868131868132	289	0.5873983739837398	261	0.7209944751381215	500	0.8741258741258742	453	0.5976253298153035	T	1.187	-0.636435	0.03557	0.686161	0.661067	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.10192	2.92;2.9	5.37	5.37	0.77165	.	0.000000	0.47852	N	0.000210	T	0.00012	0.0000	N	0.01048	-1.04	0.42193	P	0.008264000000000049	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34576	-0.9823	9	0.02654	T	1	.	12.6151	0.56571	0.0:0.0:0.1388:0.8612	rs6415788;rs13294473;rs59237658;rs6415788	456;301	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	Q	301;456	ENSP00000325494:P301Q;ENSP00000371398:P456Q	ENSP00000325494:P301Q	P	-	2	0	GLIS3	4108111	1.000000	0.71417	0.971000	0.41717	0.160000	0.22226	4.123000	0.57917	0.872000	0.35775	-0.256000	0.11100	CCA	G|0.313;T|0.687	0.687	strong		0.731	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
UMODL1	89766	hgsc.bcm.edu	37	21	43531264	43531264	+	Intron	SNP	C	C	G	rs111772429	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43531264C>G	ENST00000408910.2	+	11	1899				UMODL1_ENST00000408989.2_Missense_Mutation_p.D644E|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400427.1_Missense_Mutation_p.D572E|UMODL1_ENST00000400424.2_Intron	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1						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						TGGGGATGGACCAGGGGAGCC	0.667													C|||	88	0.0175719	0.0015	0.013	5008	,	,		13954	0.0		0.0457	False		,,,				2504	0.0317				p.D644E	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C1932G						PASS	.	C	,GLU/ASP,,GLU/ASP	20,3838		0,20,1909	11.0	16.0	15.0		,1716,,1932	0.3	0.0	21	dbSNP_132	15	346,7926		13,320,3803	yes	intron,missense,intron,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,45,,45	13,340,5712	GG,GC,CC		4.1828,0.5184,3.0173	,benign,,benign	,572/1375,,644/1447	43531264	366,11764	1929	4136	6065	SO:0001627	intron_variant	89766	exon11			GATGGACCAGGGG		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.1899+33C>G	21.37:g.43531264C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	127	47	0.370079	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	C	5.522	0.281200	0.10458	0.005184	0.041828	ENSG00000177398	ENST00000400427;ENST00000408989	T;T	0.70986	-0.53;-0.52	2.29	0.29	0.15728	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.09310	N	1	B	0.20988	0.05	B	0.23419	0.046	T	0.12041	-1.0563	8	0.06891	T	0.86	-4.5992	6.6992	0.23215	0.4928:0.5072:0.0:0.0	.	644	Q5DID0-2	.	E	572;644	ENSP00000383279:D572E;ENSP00000386126:D644E	ENSP00000383279:D572E	D	+	3	2	UMODL1	42404333	0.012000	0.17670	0.002000	0.10522	0.020000	0.10135	0.521000	0.22893	0.056000	0.16144	0.305000	0.20034	GAC	A|0.003;C|0.996;G|0.000	0.000	strong		0.667	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
EPN3	55040	hgsc.bcm.edu	37	17	48608717	48608717	+	5'Flank	SNP	T	T	C	rs1064055	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48608717T>C	ENST00000268933.3	+	0	0				MYCBPAP_ENST00000323776.5_Silent_p.T961T|EPN3_ENST00000537145.1_5'Flank|EPN3_ENST00000541226.1_5'Flank|MYCBPAP_ENST00000436259.2_3'UTR	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3							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)			CCCTGGTGACTGACCTGATGG	0.547													C|||	4081	0.814896	0.9289	0.7003	5008	,	,		17445	0.8859		0.7356	False		,,,				2504	0.7505				p.T961T		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.T2883C						PASS	.	C		3964,442	210.8+/-231.2	1789,386,28	74.0	61.0	66.0		2883	-10.8	0.0	17	dbSNP_86	66	6266,2334	391.1+/-343.5	2295,1676,329	no	coding-synonymous	MYCBPAP	NM_032133.4		4084,2062,357	CC,CT,TT		27.1395,10.0318,21.344		961/985	48608717	10230,2776	2203	4300	6503	SO:0001631	upstream_gene_variant	84073	exon19			GGTGACTGACCTG	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			17.37:g.48608717T>C	Exception_encountered	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_032133	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Silent	SNP	ENST00000268933.3	37	CCDS11570.1																																																																																			T|0.195;C|0.805	0.805	strong		0.547	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
PPM1F	9647	hgsc.bcm.edu	37	22	22288560	22288560	+	Missense_Mutation	SNP	G	G	A	rs9610645	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:22288560G>A	ENST00000263212.5	-	4	499	c.394C>T	c.(394-396)Cgc>Tgc	p.R132C	PPM1F_ENST00000407142.1_5'UTR|PPM1F_ENST00000397495.4_Missense_Mutation_p.R132C|PPM1F_ENST00000486259.1_5'Flank|PPM1F_ENST00000538191.1_Missense_Mutation_p.R28C	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	132			R -> C (in dbSNP:rs9610645).		cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		TCCCAAAGGCGGTTAAAGAAA	0.617													G|||	430	0.0858626	0.0893	0.1081	5008	,	,		16993	0.0655		0.1223	False		,,,				2504	0.0491				p.R132C		Atlas-SNP	.											PPM1F,colon,carcinoma,0,1	PPM1F	34	1	0			c.C394T						PASS	.	G	CYS/ARG	305,4085		14,277,1904	23.0	26.0	25.0		394	0.3	0.6	22	dbSNP_119	25	1017,7559		65,887,3336	yes	missense	PPM1F	NM_014634.3	180	79,1164,5240	AA,AG,GG		11.8587,6.9476,10.1959	benign	132/455	22288560	1322,11644	2195	4288	6483	SO:0001583	missense	9647	exon4			AAAGGCGGTTAAA	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19388	protein-coding gene	gene with protein product	"""partner of PIX 2"", ""Ca(2+)/calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1F (PP2C domain containing)"""			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.394C>T	22.37:g.22288560G>A	ENSP00000263212:p.Arg132Cys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	67	39	0.58209	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Missense_Mutation	SNP	ENST00000263212.5	37	CCDS13796.1	213	0.09752747252747253	48	0.0975609756097561	35	0.09668508287292818	33	0.057692307692307696	97	0.1279683377308707	G	9.196	1.027297	0.19512	0.069476	0.118587	ENSG00000100034	ENST00000263212;ENST00000538191;ENST00000397495;ENST00000424647	T;T;T;T	0.46063	2.5;2.48;1.91;0.88	4.99	0.283	0.15696	.	2.592250	0.00954	N	0.003003	T	0.00241	0.0007	N	0.11560	0.145	0.49213	P	2.3700000000004273E-4	B;B;B	0.15719	0.003;0.014;0.007	B;B;B	0.11329	0.002;0.006;0.004	T	0.15009	-1.0452	9	0.37606	T	0.19	-27.6717	1.284	0.02046	0.1791:0.1235:0.2848:0.4126	rs9610645;rs52834056;rs9610645	28;132;132	B7Z2C3;A8MX49;P49593	.;.;PPM1F_HUMAN	C	132;28;132;28	ENSP00000263212:R132C;ENSP00000439915:R28C;ENSP00000380632:R132C;ENSP00000388350:R28C	ENSP00000263212:R132C	R	-	1	0	PPM1F	20618560	0.148000	0.22702	0.592000	0.28758	0.353000	0.29299	0.430000	0.21428	0.645000	0.30675	0.555000	0.69702	CGC	G|0.900;A|0.100	0.100	strong		0.617	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634	
SLC9B2	133308	hgsc.bcm.edu	37	4	103964529	103964529	+	Missense_Mutation	SNP	A	A	C	rs2276976	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:103964529A>C	ENST00000394785.3	-	9	1701	c.1070T>G	c.(1069-1071)tTt>tGt	p.F357C	SLC9B2_ENST00000503230.1_Missense_Mutation_p.F300C|SLC9B2_ENST00000339611.4_Missense_Mutation_p.F357C|SLC9B2_ENST00000503103.1_Missense_Mutation_p.F300C|SLC9B2_ENST00000362026.3_Missense_Mutation_p.F357C	NM_178833.4	NP_849155.2	Q86UD5	SL9B2_HUMAN	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	357			F -> C (in dbSNP:rs2276976).		ion transmembrane transport (GO:0034220)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	solute:proton antiporter activity (GO:0015299)										AGGGAAACCAAAATGCACACT	0.438													A|||	719	0.14357	0.062	0.1628	5008	,	,		17381	0.1806		0.1064	False		,,,				2504	0.2403				p.F357C		Atlas-SNP	.											.	.	.	.	0			c.T1070G						PASS	.	A	CYS/PHE	264,4142	148.0+/-182.4	6,252,1945	154.0	120.0	131.0		1070	5.9	0.1	4	dbSNP_100	131	996,7604	215.2+/-254.6	62,872,3366	yes	missense	SLC9B2	NM_178833.4	205	68,1124,5311	CC,CA,AA		11.5814,5.9918,9.6878	benign	357/538	103964529	1260,11746	2203	4300	6503	SO:0001583	missense	133308	exon9			AAACCAAAATGCA	AK172823	CCDS3662.1, CCDS75173.1, CCDS75174.1	4q24	2013-05-22	2012-03-22	2011-08-03	ENSG00000164038	ENSG00000164038		"""Solute carriers"""	25143	protein-coding gene	gene with protein product		611789	"""Na+/H+ exchanger domain containing 2"", ""solute carrier family 9, subfamily B (cation proton antiporter 2), member 2"""	NHEDC2		18600791	Standard	XM_005262758		Approved	FLJ23984, NHA2	uc003hwy.3	Q86UD5	OTTHUMG00000131125	ENST00000394785.3:c.1070T>G	4.37:g.103964529A>C	ENSP00000378265:p.Phe357Cys	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_178833	B5ME52|Q6ZMD8|Q96D95	Missense_Mutation	SNP	ENST00000394785.3	37	CCDS3662.1	265	0.12133699633699634	40	0.08130081300813008	59	0.16298342541436464	92	0.16083916083916083	74	0.09762532981530343	A	15.72	2.917232	0.52546	0.059918	0.115814	ENSG00000164038	ENST00000362026;ENST00000506288;ENST00000339611;ENST00000394785;ENST00000503103;ENST00000503230	T;T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33;2.33	5.93	5.93	0.95920	.	0.534116	0.21999	N	0.066029	T	0.00178	0.0005	M	0.70275	2.135	0.24182	P	0.9955815	D;P;D;D	0.65815	0.995;0.909;0.967;0.992	D;P;P;P	0.63113	0.911;0.895;0.818;0.863	T	0.00259	-1.1870	9	0.38643	T	0.18	-14.1416	16.3871	0.83514	1.0:0.0:0.0:0.0	rs2276976;rs52829275;rs57944708;rs2276976	300;300;357;357	B7Z676;E9PE63;Q86UD5-2;Q86UD5	.;.;.;SL9B2_HUMAN	C	357;257;357;357;300;300	ENSP00000354574:F357C;ENSP00000421943:F257C;ENSP00000345241:F357C;ENSP00000378265:F357C;ENSP00000425385:F300C;ENSP00000422477:F300C	ENSP00000345241:F357C	F	-	2	0	SLC9B2	104183978	1.000000	0.71417	0.061000	0.19648	0.991000	0.79684	6.434000	0.73408	2.270000	0.75569	0.482000	0.46254	TTT	A|0.893;C|0.107	0.107	strong		0.438	SLC9B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253805.1	NM_178833	
C15orf52	388115	hgsc.bcm.edu	37	15	40627845	40627845	+	Silent	SNP	G	G	A	rs55641696	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	78	0	0		WXS	Illumina HiSeq	Phase_I	62	50	0.806452	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	
ITGB2	3689	hgsc.bcm.edu	37	21	46330229	46330229	+	Silent	SNP	C	C	T	rs35903905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:46330229C>T	ENST00000397850.2	-	4	569	c.117G>A	c.(115-117)tcG>tcA	p.S39S	ITGB2_ENST00000397852.1_Silent_p.S39S|ITGB2_ENST00000397857.1_Silent_p.S39S|ITGB2_ENST00000302347.5_Silent_p.S39S|ITGB2_ENST00000397846.3_Silent_p.S39S|ITGB2_ENST00000523126.1_5'UTR|ITGB2_ENST00000355153.4_Silent_p.S39S|ITGB2_ENST00000397854.3_Silent_p.S39S			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	39					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)	AGCCGGGCCCCGACTCGATGC	0.672													C|||	101	0.0201677	0.0008	0.0115	5008	,	,		15866	0.0278		0.0229	False		,,,				2504	0.0419				p.S39S		Atlas-SNP	.											.	ITGB2	107	.	0			c.G117A						PASS	.	C	,	12,4394	21.2+/-45.6	0,12,2191	48.0	45.0	46.0		117,117	-2.8	0.1	21	dbSNP_126	46	134,8466	66.7+/-129.0	2,130,4168	no	coding-synonymous,coding-synonymous	ITGB2	NM_000211.3,NM_001127491.1	,	2,142,6359	TT,TC,CC		1.5581,0.2724,1.1226	,	39/770,39/770	46330229	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	3689	exon3			GGGCCCCGACTCG	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.117G>A	21.37:g.46330229C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	218	56	0.256881	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	37	CCDS13716.1																																																																																			C|0.987;T|0.013	0.013	strong		0.672	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211	
CATSPERD	257062	hgsc.bcm.edu	37	19	5749171	5749171	+	Missense_Mutation	SNP	A	A	G	rs72983139	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:5749171A>G	ENST00000381624.3	+	11	1025	c.964A>G	c.(964-966)Atc>Gtc	p.I322V	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	322					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											CAATCTGGGCATCGTGCCAAG	0.438													a|||	398	0.0794728	0.1672	0.036	5008	,	,		19033	0.0119		0.0249	False		,,,				2504	0.1176				p.I322V		Atlas-SNP	.											.	.	.	.	0			c.A964G						PASS	.		VAL/ILE	513,3223		33,447,1388	88.0	88.0	88.0		964	-6.5	0.0	19	dbSNP_130	88	189,8025		0,189,3918	yes	missense	TMEM146	NM_152784.3	29	33,636,5306	GG,GA,AA		2.3009,13.7313,5.8745	benign	322/799	5749171	702,11248	1868	4107	5975	SO:0001583	missense	257062	exon11			CTGGGCATCGTGC	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.964A>G	19.37:g.5749171A>G	ENSP00000371037:p.Ile322Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	120	0.054945054945054944	87	0.17682926829268292	14	0.03867403314917127	2	0.0034965034965034965	17	0.022427440633245383	a	0.139	-1.103923	0.01828	0.137313	0.023009	ENSG00000174898	ENST00000394548;ENST00000381624	T	0.25912	1.77	3.26	-6.52	0.01872	.	2.007800	0.03422	N	0.206446	T	0.00039	0.0001	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.22068	-1.0227	9	0.20046	T	0.44	-0.2315	3.3693	0.07215	0.3218:0.0:0.3244:0.3538	.	322	Q86XM0	TM146_HUMAN	V	248;322	ENSP00000371037:I322V	ENSP00000371037:I322V	I	+	1	0	TMEM146	5700171	0.000000	0.05858	0.000000	0.03702	0.138000	0.21146	-0.433000	0.06948	-1.175000	0.02751	-0.671000	0.03813	ATC	A|0.957;G|0.043	0.043	strong		0.438	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
MUC17	140453	hgsc.bcm.edu	37	7	100678527	100678527	+	Missense_Mutation	SNP	G	G	T	rs73402889	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678527G>T	ENST00000306151.4	+	3	3894	c.3830G>T	c.(3829-3831)aGt>aTt	p.S1277I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1277	59 X approximate tandem repeats.|Ser-rich.				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)					AGTGAAGGAAGTACTCTATTA	0.498																																					p.S1277I		Atlas-SNP	.											MUC17,adrenal_gland,adrenal_cortical_adenoma,0,1	MUC17	804	1	0			c.G3830T						PASS	.	G	ILE/SER	508,3898		0,508,1695	279.0	268.0	272.0		3830	0.4	0.0	7	dbSNP_131	272	744,7856		0,744,3556	yes	missense	MUC17	NM_001040105.1	142	0,1252,5251	TT,TG,GG		8.6512,11.5297,9.6263	possibly-damaging	1277/4494	100678527	1252,11754	2203	4300	6503	SO:0001583	missense	140453	exon3			AAGGAAGTACTCT	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.3830G>T	7.37:g.100678527G>T	ENSP00000302716:p.Ser1277Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	314	109	0.347134	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	209	0.09569597069597069	65	0.13211382113821138	35	0.09668508287292818	26	0.045454545454545456	83	0.10949868073878628	g	0.856	-0.736924	0.03111	0.115297	0.086512	ENSG00000169876	ENST00000306151	T	0.02631	4.22	0.373	0.373	0.16178	.	.	.	.	.	T	0.00039	0.0001	L	0.29908	0.895	0.09310	N	1	P	0.47604	0.898	B	0.36885	0.235	T	0.55224	-0.8174	8	0.42905	T	0.14	.	.	.	.	.	1277	Q685J3	MUC17_HUMAN	I	1277	ENSP00000302716:S1277I	ENSP00000302716:S1277I	S	+	2	0	MUC17	100465247	0.000000	0.05858	0.010000	0.14722	0.017000	0.09413	-1.635000	0.02018	0.472000	0.27344	0.134000	0.15878	AGT	G|0.918;T|0.082	0.082	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MSLN	10232	hgsc.bcm.edu	37	16	816977	816977	+	Missense_Mutation	SNP	G	G	A	rs35935235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:816977G>A	ENST00000382862.3	+	14	1585	c.1490G>A	c.(1489-1491)gGg>gAg	p.G497E	MSLN_ENST00000566549.1_Missense_Mutation_p.G489E|MSLN_ENST00000545450.2_Missense_Mutation_p.G489E|MSLN_ENST00000563941.1_Missense_Mutation_p.G489E	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	497			G -> E (in dbSNP:rs35935235).		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)				AACATGAACGGGTCCGAATAC	0.632													G|||	71	0.0141773	0.0008	0.0274	5008	,	,		18257	0.0		0.0487	False		,,,				2504	0.002				p.G497E		Atlas-SNP	.											.	MSLN	109	.	0			c.G1490A						PASS	.	G	GLU/GLY,GLU/GLY,GLU/GLY	28,4350	35.2+/-66.4	1,26,2162	77.0	78.0	78.0		1466,1466,1490	1.3	0.0	16	dbSNP_126	78	426,8158	131.3+/-189.1	13,400,3879	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	98,98,98	14,426,6041	AA,AG,GG		4.9627,0.6396,3.5025	probably-damaging,probably-damaging,probably-damaging	489/623,489/623,497/631	816977	454,12508	2189	4292	6481	SO:0001583	missense	10232	exon14			TGAACGGGTCCGA	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.1490G>A	16.37:g.816977G>A	ENSP00000372313:p.Gly497Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	115	62	0.53913	NM_013404	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	45	0.020604395604395604	0	0.0	11	0.03038674033149171	0	0.0	34	0.044854881266490766	G	10.49	1.365385	0.24684	0.006396	0.049627	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.22945	1.93;1.93	4.61	1.27	0.21489	.	0.704071	0.13480	N	0.384736	T	0.04048	0.0113	M	0.63843	1.955	0.09310	N	1	P;P;B;P	0.36354	0.493;0.549;0.161;0.493	B;B;B;B	0.40901	0.232;0.343;0.155;0.232	T	0.08146	-1.0736	10	0.33141	T	0.24	-15.5221	3.3382	0.07108	0.224:0.0:0.5571:0.2189	rs35935235;rs62032553	488;497;489;489	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	E	497;489;489;497	ENSP00000442965:G489E;ENSP00000372313:G497E	ENSP00000372313:G497E	G	+	2	0	MSLN	756978	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.178000	0.16820	0.553000	0.29044	0.543000	0.68304	GGG	G|0.968;A|0.032	0.032	strong		0.632	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
ULBP2	80328	hgsc.bcm.edu	37	6	150267527	150267527	+	Silent	SNP	A	A	C	rs2282235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:150267527A>C	ENST00000367351.3	+	3	442	c.369A>C	c.(367-369)gcA>gcC	p.A123A		NM_025217.2	NP_079493.1	Q9BZM5	N2DL2_HUMAN	UL16 binding protein 2	123	MHC class I alpha-2 like.				antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular space (GO:0005615)	natural killer cell lectin-like receptor binding (GO:0046703)			breast(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.58e-12)		CCCTGCAGGCAAGGATGTCTT	0.507													N|||	3467	0.692292	0.8638	0.5922	5008	,	,		20462	0.8046		0.5606	False		,,,				2504	0.5511				p.A123A		Atlas-SNP	.											.	ULBP2	22	.	0			c.A369C						PASS	.						98.0	94.0	95.0					6																	150267527		2203	4297	6500	SO:0001819	synonymous_variant	80328	exon3			GCAGGCAAGGATG	AF304378	CCDS5222.1	6q25	2008-04-11			ENSG00000131015	ENSG00000131015			14894	protein-coding gene	gene with protein product		605698				11239445	Standard	NM_025217		Approved	RAET1H	uc003qno.3	Q9BZM5	OTTHUMG00000015803	ENST00000367351.3:c.369A>C	6.37:g.150267527A>C		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	193	89	0.46114	NM_025217	Q5VUN4	Silent	SNP	ENST00000367351.3	37	CCDS5222.1																																																																																			A|0.889;C|0.111	0.111	strong		0.507	ULBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042669.1		
RIN2	54453	hgsc.bcm.edu	37	20	19970705	19970705	+	Silent	SNP	C	C	T	rs2076584	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:19970705C>T	ENST00000255006.6	+	9	2114	c.1965C>T	c.(1963-1965)caC>caT	p.H655H	RIN2_ENST00000440354.2_Silent_p.H173H|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	606	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						TCAAGGGGCACGTGGAGGCCA	0.522													C|||	2073	0.413938	0.3782	0.4784	5008	,	,		20397	0.6806		0.33	False		,,,				2504	0.228				p.H655H		Atlas-SNP	.											.	RIN2	126	.	0			c.C1965T						PASS	.	C	,	1428,2382		266,896,743	23.0	25.0	24.0		1965,1818	-1.1	1.0	20	dbSNP_96	24	2495,5757		376,1743,2007	yes	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	642,2639,2750	TT,TC,CC		30.2351,37.4803,32.5236	,	655/945,606/896	19970705	3923,8139	1905	4126	6031	SO:0001819	synonymous_variant	54453	exon9			GGGGCACGTGGAG	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.1965C>T	20.37:g.19970705C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	152	69	0.453947	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			C|0.570;T|0.430	0.430	strong		0.522	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
PTPRR	5801	hgsc.bcm.edu	37	12	71029733	71029733	+	IGR	SNP	C	C	T	rs2584021	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:71029733C>T	ENST00000283228.2	-	0	3529				PTPRB_ENST00000551525.1_Missense_Mutation_p.D56N|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000334414.6_Missense_Mutation_p.D57N|PTPRB_ENST00000550358.1_Missense_Mutation_p.D57N|PTPRR_ENST00000537619.2_5'Flank	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R						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)		AGCTTTTCATCCTCAGTCCAC	0.527													C|||	1271	0.253794	0.2436	0.3026	5008	,	,		16560	0.4028		0.0547	False		,,,				2504	0.2843				p.D57N		Atlas-SNP	.											.	PTPRB	676	.	0			c.G169A						PASS	.	C	ASN/ASP	761,3317		68,625,1346	87.0	88.0	88.0		169	3.9	1.0	12	dbSNP_100	88	586,7772		20,546,3613	yes	missense	PTPRB	NM_001109754.2	23	88,1171,4959	TT,TC,CC		7.0112,18.6611,10.8315	possibly-damaging	57/2216	71029733	1347,11089	2039	4179	6218	SO:0001628	intergenic_variant	5787	exon2			TTTCATCCTCAGT	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		12.37:g.71029733C>T		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	335	168	0.501493	NM_001109754	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	484	0.2216117216117216	128	0.2601626016260163	83	0.2292817679558011	234	0.4090909090909091	39	0.051451187335092345	C	15.77	2.930632	0.52866	0.186611	0.070112	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000551525;ENST00000548122	T;T;T;T	0.33654	1.74;1.74;1.74;1.4	5.82	3.92	0.45320	.	.	.	.	.	T	0.00012	0.0000	N	0.17082	0.46	0.09310	P	1.0	B;B;B;B;B	0.24258	0.004;0.1;0.006;0.006;0.006	B;B;B;B;B	0.26094	0.004;0.066;0.009;0.005;0.005	T	0.44467	-0.9326	8	0.46703	T	0.11	.	11.1575	0.48497	0.0:0.8422:0.0:0.1578	rs2584021;rs56726799;rs2584021	57;57;56;57;57	Q6ZR19;Q6ZTX7;F8VSD5;P23467-3;F8VU56	.;.;.;.;.	N	57;57;57;56;57	ENSP00000334928:D57N;ENSP00000448058:D57N;ENSP00000448349:D56N;ENSP00000446982:D57N	ENSP00000334928:D57N	D	-	1	0	PTPRB	69316000	0.717000	0.27966	0.959000	0.39883	0.965000	0.64279	0.943000	0.29030	0.714000	0.32081	0.563000	0.77884	GAT	C|0.773;T|0.227	0.227	strong		0.527	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43636484	43636484	+	Silent	SNP	C	C	G	rs1049276	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43636484C>G	ENST00000236051.2	-	4	531	c.390G>C	c.(388-390)acG>acC	p.T130T	WDR65_ENST00000528956.1_5'Flank|WDR65_ENST00000372492.4_5'Flank|EBNA1BP2_ENST00000472982.1_5'Flank|EBNA1BP2_ENST00000431635.2_Silent_p.T185T	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	150	0	0		WXS	Illumina HiSeq	Phase_I	84	23	0.27381	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		
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56703248	56703248	+	Missense_Mutation	SNP	G	G	A	rs527025	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	122	0	0		WXS	Illumina HiSeq	Phase_I	92	51	0.554348	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	
FAM118A	55007	hgsc.bcm.edu	37	22	45719125	45719125	+	Silent	SNP	C	C	T	rs138980075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:45719125C>T	ENST00000216214.3	+	4	951	c.117C>T	c.(115-117)agC>agT	p.S39S	FAM118A_ENST00000441876.2_Silent_p.S39S|FAM118A_ENST00000405673.1_Silent_p.S39S	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	39						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTGGCGTCAGCGCAGCAGTGG	0.572													C|||	10	0.00199681	0.0	0.0014	5008	,	,		17209	0.0		0.006	False		,,,				2504	0.0031				p.S39S		Atlas-SNP	.											.	FAM118A	32	.	0			c.C117T						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	44.0	49.0	47.0		117,117	-11.3	0.0	22	dbSNP_134	47	36,8564	23.4+/-69.3	0,36,4264	no	coding-synonymous,coding-synonymous	FAM118A	NM_001104595.1,NM_017911.2	,	0,38,6465	TT,TC,CC		0.4186,0.0454,0.2922	,	39/358,39/358	45719125	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	55007	exon3			CGTCAGCGCAGCA	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 8"""	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.117C>T	22.37:g.45719125C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	175	83	0.474286	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Silent	SNP	ENST00000216214.3	37	CCDS14065.1																																																																																			C|0.997;T|0.003	0.003	strong		0.572	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911	
ETS1	2113	hgsc.bcm.edu	37	11	128333503	128333503	+	Silent	SNP	T	T	C	rs2230004	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:128333503T>C	ENST00000319397.6	-	7	1320	c.1011A>G	c.(1009-1011)ctA>ctG	p.L337L	ETS1_ENST00000392668.4_Silent_p.L381L|ETS1_ENST00000531611.1_Intron|ETS1_ENST00000535549.1_Silent_p.L121L|ETS1_ENST00000526145.2_Silent_p.L250L|ETS1_ENST00000345075.4_Silent_p.L250L	NM_005238.3	NP_005229.1	P14921	ETS1_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 1	337				SGPIQL -> RRPPAA (in Ref. 11; AAA52409). {ECO:0000305}.	angiogenesis involved in wound healing (GO:0060055)|cell motility (GO:0048870)|cellular response to hydrogen peroxide (GO:0070301)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|pituitary gland development (GO:0021983)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of apoptotic process (GO:0042981)|regulation of extracellular matrix disassembly (GO:0010715)|response to antibiotic (GO:0046677)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to laminar fluid shear stress (GO:0034616)|response to mechanical stimulus (GO:0009612)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|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)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|pleura(1)|prostate(1)|upper_aerodigestive_tract(3)	35	all_hematologic(175;0.0537)	Lung NSC(97;0.000542)|all_lung(97;0.000665)|Breast(109;0.00765)|all_neural(223;0.0351)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.47e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0174)|LUSC - Lung squamous cell carcinoma(976;0.0815)|Lung(307;0.0833)		GAAACTGCCATAGCTGGATTG	0.468													C|||	2402	0.479633	0.4561	0.3646	5008	,	,		19297	0.5962		0.493	False		,,,				2504	0.4591				p.L381L		Atlas-SNP	.											.	ETS1	123	.	0			c.A1143G						PASS	.	C	,,	2090,2312	603.0+/-390.0	517,1056,628	106.0	104.0	105.0		1143,363,1011	5.9	1.0	11	dbSNP_116	105	4034,4560	596.3+/-393.6	932,2170,1195	no	coding-synonymous,coding-synonymous,coding-synonymous	ETS1	NM_001143820.1,NM_001162422.1,NM_005238.3	,,	1449,3226,1823	CC,CT,TT		46.9397,47.4784,47.1222	,,	381/486,121/226,337/442	128333503	6124,6872	2201	4297	6498	SO:0001819	synonymous_variant	2113	exon9			CTGCCATAGCTGG		CCDS8475.1, CCDS44767.1, CCDS53724.1	11q23.3	2013-07-09	2013-07-09		ENSG00000134954	ENSG00000134954			3488	protein-coding gene	gene with protein product	"""Avian erythroblastosis virus E26 (v-ets) oncogene homolog-1"", ""ets protein"""	164720		EWSR2		1522903	Standard	NM_005238		Approved	FLJ10768, ETS-1	uc001qej.2	P14921	OTTHUMG00000165799	ENST00000319397.6:c.1011A>G	11.37:g.128333503T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	114	77	0.675439	NM_001143820	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Silent	SNP	ENST00000319397.6	37	CCDS8475.1																																																																																			T|0.524;C|0.476	0.476	strong		0.468	ETS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386269.2	NM_005238	
CSPG4	1464	hgsc.bcm.edu	37	15	75982185	75982185	+	Silent	SNP	T	T	C	rs77341302	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	130	4	0.0307692		WXS	Illumina HiSeq	Phase_I	58	29	0.5	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	
MUC17	140453	hgsc.bcm.edu	37	7	100678029	100678029	+	Missense_Mutation	SNP	G	G	C	rs142558659		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678029G>C	ENST00000306151.4	+	3	3396	c.3332G>C	c.(3331-3333)aGg>aCg	p.R1111T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1111	59 X approximate tandem repeats.|Ser-rich.				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)					GTCAGCACCAGGCTGGTGGTC	0.507																																					p.R1111T		Atlas-SNP	.											.	MUC17	804	.	0			c.G3332C						PASS	.						498.0	396.0	431.0					7																	100678029		2203	4300	6503	SO:0001583	missense	140453	exon3			GCACCAGGCTGGT	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.3332G>C	7.37:g.100678029G>C	ENSP00000302716:p.Arg1111Thr	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	766	95	0.124021	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	c	0.065	-1.213913	0.01555	.	.	ENSG00000169876	ENST00000306151	T	0.02812	4.15	0.801	-1.6	0.08426	.	.	.	.	.	T	0.00906	0.0030	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45644	-0.9247	9	0.02654	T	1	.	6.8116	0.23807	0.0:0.6951:0.3049:0.0	.	1111	Q685J3	MUC17_HUMAN	T	1111	ENSP00000302716:R1111T	ENSP00000302716:R1111T	R	+	2	0	MUC17	100464749	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.692000	0.05127	-0.647000	0.05444	-2.911000	0.00091	AGG	.	.	weak		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CNTN5	53942	hgsc.bcm.edu	37	11	99690450	99690450	+	Silent	SNP	T	T	C	rs12222337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:99690450T>C	ENST00000524871.1	+	4	521	c.231T>C	c.(229-231)taT>taC	p.Y77Y	CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000279463.3_Silent_p.Y77Y|CNTN5_ENST00000527185.1_Silent_p.Y77Y|CNTN5_ENST00000528682.1_Silent_p.Y77Y	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	77					cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		AGAATTATTATTCCCCCATCA	0.443																																					p.Y77Y		Atlas-SNP	.											.	CNTN5	324	.	0			c.T231C						PASS	.						61.0	61.0	61.0					11																	99690450		1892	4090	5982	SO:0001819	synonymous_variant	53942	exon3			TTATTATTCCCCC	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.231T>C	11.37:g.99690450T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	209	37	0.177033	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																			C|0.101;T|0.899	0.101	strong		0.443	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168376840	168376840	+	lincRNA	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168376840T>C	ENST00000538528.1	-	0	779																											AGTGTGTGTGTGGGGAGCAGG	0.602																																					p.T165A		Atlas-SNP	.											.	.	.	.	0			c.A493G						PASS	.						31.0	29.0	30.0					6																	168376840		692	1591	2283			0	exon1			TGTGTGTGGGGAG																													6.37:g.168376840T>C		Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	287	30	0.10453	NM_001129895		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																				.	.	none		0.602	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
STAG3	10734	hgsc.bcm.edu	37	7	99778285	99778285	+	Missense_Mutation	SNP	A	A	C	rs2272343	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99778285A>C	ENST00000426455.1	+	2	513	c.106A>C	c.(106-108)Acc>Ccc	p.T36P	STAG3_ENST00000317296.5_Missense_Mutation_p.T36P|STAG3_ENST00000394018.2_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	93	0	0		WXS	Illumina HiSeq	Phase_I	122	36	0.295082	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	
ATP11A	23250	hgsc.bcm.edu	37	13	113508839	113508839	+	Silent	SNP	G	G	C	rs9549573	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:113508839G>C	ENST00000487903.1	+	19	2326	c.2238G>C	c.(2236-2238)ctG>ctC	p.L746L	ATP11A_ENST00000283558.8_Silent_p.L746L|ATP11A_ENST00000375645.3_Silent_p.L746L|ATP11A_ENST00000375630.2_Silent_p.L746L			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	746					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)				GAGACAACCTGTCCGGGTAGG	0.652													C|||	3487	0.696286	0.9644	0.7262	5008	,	,		15382	0.6567		0.6044	False		,,,				2504	0.4479				p.L746L		Atlas-SNP	.											.	ATP11A	225	.	0			c.G2238C						PASS	.	C	,	4036,368		1849,338,15	38.0	39.0	38.0		2238,2238	2.8	0.8	13	dbSNP_119	38	5293,3307		1625,2043,632	no	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	3474,2381,647	CC,CG,GG		38.4535,8.356,28.2605	,	746/1135,746/1192	113508839	9329,3675	2202	4300	6502	SO:0001819	synonymous_variant	23250	exon19			CAACCTGTCCGGG	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.2238G>C	13.37:g.113508839G>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1	1540	0.7051282051282052	473	0.9613821138211383	258	0.712707182320442	356	0.6223776223776224	453	0.5976253298153035	C	0.639	-0.814080	0.02798	0.91644	0.615465	ENSG00000068650	ENST00000418678	.	.	.	4.66	2.84	0.33178	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999997	.	.	.	.	.	.	T	0.16897	-1.0387	3	.	.	.	.	10.7428	0.46162	0.0:0.5688:0.3611:0.0701	rs9549573;rs60929322;rs9549573	.	.	.	S	721	.	.	C	+	2	0	ATP11A	112556840	1.000000	0.71417	0.764000	0.31436	0.011000	0.07611	2.234000	0.43035	0.391000	0.25143	-0.223000	0.12442	TGT	G|0.292;C|0.708	0.708	strong		0.652	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377498	138377498	+	Missense_Mutation	SNP	G	G	T	rs34151777	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:138377498G>T	ENST00000356818.2	+	4	1691	c.1142G>T	c.(1141-1143)cGc>cTc	p.R381L	PPP1R26_ENST00000401470.3_Missense_Mutation_p.R381L|PPP1R26_ENST00000605286.1_Missense_Mutation_p.R381L|PPP1R26_ENST00000605660.1_Missense_Mutation_p.R381L|PPP1R26_ENST00000604351.1_Missense_Mutation_p.R381L|PPP1R26_ENST00000602993.1_Intron	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	381					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CAGAAAACACGCAAGGAGGCC	0.632													G|||	114	0.0227636	0.003	0.0476	5008	,	,		18578	0.0		0.0746	False		,,,				2504	0.002				p.R381L		Atlas-SNP	.											.	.	.	.	0			c.G1142T						PASS	.	G	LEU/ARG	50,4356	47.5+/-82.1	1,48,2154	40.0	45.0	44.0		1142	4.9	0.9	9	dbSNP_126	44	580,8020	146.6+/-202.2	21,538,3741	no	missense	KIAA0649	NM_014811.3	102	22,586,5895	TT,TG,GG		6.7442,1.1348,4.8439	probably-damaging	381/1210	138377498	630,12376	2203	4300	6503	SO:0001583	missense	9858	exon4			AAACACGCAAGGA	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.1142G>T	9.37:g.138377498G>T	ENSP00000349274:p.Arg381Leu	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	77	0.035256410256410256	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	58	0.07651715039577836	G	17.96	3.515599	0.64634	0.011348	0.067442	ENSG00000196422	ENST00000356818	T	0.17054	2.3	4.92	4.92	0.64577	.	0.215951	0.37715	N	0.001969	T	0.02848	0.0085	M	0.68593	2.085	0.23430	P	0.99769767	D	0.89917	1.0	D	0.91635	0.999	T	0.01570	-1.1322	9	0.87932	D	0	-6.0072	17.1139	0.86683	0.0:0.0:1.0:0.0	rs34151777	381	Q5T8A7	PPR26_HUMAN	L	381	ENSP00000349274:R381L	ENSP00000349274:R381L	R	+	2	0	KIAA0649	137517319	0.960000	0.32886	0.921000	0.36526	0.014000	0.08584	2.336000	0.43938	2.262000	0.75019	0.655000	0.94253	CGC	G|0.956;T|0.044	0.044	strong		0.632	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85450426	85450426	+	Missense_Mutation	SNP	G	G	A	rs74720621	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:85450426G>A	ENST00000393217.2	+	8	1916	c.1855G>A	c.(1855-1857)Gaa>Aaa	p.E619K		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	619										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		ACTAACATCAGAAAATTCCAA	0.284													G|||	17	0.00339457	0.0	0.0029	5008	,	,		17719	0.0		0.0149	False		,,,				2504	0.0				p.E619K		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.G1855A						PASS	.	G	LYS/GLU	5,4371		0,5,2183	24.0	25.0	24.0		1855	5.3	0.2	12	dbSNP_132	24	96,8474		0,96,4189	yes	missense	LRRIQ1	NM_001079910.1	56	0,101,6372	AA,AG,GG		1.1202,0.1143,0.7802	possibly-damaging	619/1723	85450426	101,12845	2188	4285	6473	SO:0001583	missense	84125	exon8			ACATCAGAAAATT	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.1855G>A	12.37:g.85450426G>A	ENSP00000376910:p.Glu619Lys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	G	18.93	3.728055	0.69074	0.001143	0.011202	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.53423	0.62	5.32	5.32	0.75619	.	0.664291	0.13539	N	0.380378	T	0.25606	0.0623	L	0.29908	0.895	0.29964	N	0.819151	P;P	0.47350	0.807;0.894	B;B	0.43950	0.294;0.437	T	0.20571	-1.0271	10	0.41790	T	0.15	.	13.6724	0.62434	0.0767:0.0:0.9233:0.0	.	619;594	Q96JM4;C9JI57	LRIQ1_HUMAN;.	K	619;594;619	ENSP00000376910:E619K	ENSP00000256007:E619K	E	+	1	0	LRRIQ1	83974557	1.000000	0.71417	0.163000	0.22734	0.028000	0.11728	3.334000	0.52097	2.640000	0.89533	0.591000	0.81541	GAA	G|0.992;A|0.008	0.008	strong		0.284	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
TBL3	10607	hgsc.bcm.edu	37	16	2028402	2028402	+	Silent	SNP	A	A	C	rs8460	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2028402A>C	ENST00000568546.1	+	21	2351	c.2223A>C	c.(2221-2223)cgA>cgC	p.R741R		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	741					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						TCTTGAGGCGAGAGGCCCCCG	0.677													N|||	2142	0.427716	0.6725	0.3732	5008	,	,		15492	0.3413		0.3062	False		,,,				2504	0.3497				p.R741R	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											TBL3,NS,carcinoma,0,1	TBL3	54	1	0			c.A2223C						PASS	.	G		2661,1735		815,1031,352	45.0	50.0	48.0		2223	-10.3	0.0	16	dbSNP_52	48	2595,6001		389,1817,2092	no	coding-synonymous	TBL3	NM_006453.2		1204,2848,2444	CC,CA,AA		30.1885,39.4677,40.4557		741/809	2028402	5256,7736	2198	4298	6496	SO:0001819	synonymous_variant	10607	exon21			GAGGCGAGAGGCC	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.2223A>C	16.37:g.2028402A>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	43	13	0.302326	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			A|0.592;C|0.408	0.408	strong		0.677	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
SLC12A3	6559	hgsc.bcm.edu	37	16	56919235	56919235	+	Silent	SNP	G	G	A	rs5802	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:56919235G>A	ENST00000563236.1	+	15	1909	c.1884G>A	c.(1882-1884)tcG>tcA	p.S628S	SLC12A3_ENST00000262502.5_Silent_p.S627S|SLC12A3_ENST00000438926.2_Silent_p.S628S|SLC12A3_ENST00000566786.1_Silent_p.S627S			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	628					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)	TCAGCTACTCGGTGGGCCTCA	0.617													G|||	322	0.0642971	0.034	0.072	5008	,	,		19220	0.0437		0.1133	False		,,,				2504	0.0706				p.S628S		Atlas-SNP	.											.	SLC12A3	99	.	0			c.G1884A						PASS	.	G	,,	155,4161		6,143,2009	73.0	59.0	64.0		1884,1881,1884	-10.8	0.0	16	dbSNP_52	64	744,7734		23,698,3518	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC12A3	NM_000339.2,NM_001126107.1,NM_001126108.1	,,	29,841,5527	AA,AG,GG		8.7757,3.5913,7.0267	,,	628/1031,627/1030,628/1022	56919235	899,11895	2158	4239	6397	SO:0001819	synonymous_variant	6559	exon15			CTACTCGGTGGGC		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.1884G>A	16.37:g.56919235G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	57	0.826087	NM_001126108	A8MSJ2|C9JNN9	Silent	SNP	ENST00000563236.1	37	CCDS58464.1																																																																																			A|0.069;C|0.000;G|0.931	0.069	strong		0.617	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		
SH3TC2	79628	hgsc.bcm.edu	37	5	148386525	148386525	+	Silent	SNP	T	T	G	rs6871030	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:148386525T>G	ENST00000515425.1	-	16	3695	c.3594A>C	c.(3592-3594)ccA>ccC	p.P1198P	SH3TC2_ENST00000502274.1_Silent_p.P60P|SH3TC2_ENST00000538184.1_3'UTR|SH3TC2_ENST00000512049.1_Silent_p.P1191P	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1198					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)			TCTGCAGCCATGGTGGACAGA	0.562													G|||	1920	0.383387	0.4902	0.3055	5008	,	,		19946	0.2222		0.4046	False		,,,				2504	0.4387				p.P1198P		Atlas-SNP	.											.	SH3TC2	178	.	0			c.A3594C						PASS	.	G		2477,1929		478,1521,204	122.0	121.0	122.0		3594	-2.6	0.6	5	dbSNP_116	122	3502,5098		681,2140,1479	no	coding-synonymous	SH3TC2	NM_024577.3		1159,3661,1683	GG,GT,TT		40.7209,43.7812,45.9711		1198/1289	148386525	5979,7027	2203	4300	6503	SO:0001819	synonymous_variant	79628	exon16			CAGCCATGGTGGA	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.3594A>C	5.37:g.148386525T>G		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	264	126	0.477273	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Silent	SNP	ENST00000515425.1	37	CCDS4293.1																																																																																			C|0.005;G|0.447;T|0.549	0.447	strong		0.562	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
HEATR5B	54497	hgsc.bcm.edu	37	2	37230734	37230734	+	Silent	SNP	C	C	T	rs17497654	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	122	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	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	
SEMA5A	9037	hgsc.bcm.edu	37	5	9190404	9190404	+	Silent	SNP	G	G	A	rs1806095	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	97	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	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		
WNT8B	7479	hgsc.bcm.edu	37	10	102222957	102222957	+	Missense_Mutation	SNP	G	G	C	rs3793771	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102222957G>C	ENST00000343737.5	+	1	160	c.32G>C	c.(31-33)tGt>tCt	p.C11S		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	11			C -> S (in dbSNP:rs3793771).		cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		GTGTACATCTGTCTTTTCACC	0.428													C|||	933	0.186302	0.2012	0.1873	5008	,	,		18427	0.129		0.2008	False		,,,				2504	0.2096				p.C11S		Atlas-SNP	.											.	WNT8B	31	.	0			c.G32C						PASS	.	C	SER/CYS	894,3512	740.5+/-411.2	80,734,1389	141.0	135.0	137.0		32	4.7	1.0	10	dbSNP_107	137	1950,6650	725.0+/-406.5	222,1506,2572	yes	missense	WNT8B	NM_003393.3	112	302,2240,3961	CC,CG,GG		22.6744,20.2905,21.8668	benign	11/352	102222957	2844,10162	2203	4300	6503	SO:0001583	missense	7479	exon1			ACATCTGTCTTTT	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"""Wingless-type MMTV integration sites"""	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.32G>C	10.37:g.102222957G>C	ENSP00000340677:p.Cys11Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	103	60	0.582524	NM_003393	O00771|Q5VX55|Q8WYK9	Missense_Mutation	SNP	ENST00000343737.5	37	CCDS7494.1	410	0.18772893772893773	85	0.17276422764227642	70	0.19337016574585636	88	0.15384615384615385	167	0.22031662269129287	C	6.745	0.506185	0.12883	0.202905	0.226744	ENSG00000075290	ENST00000343737	T	0.73047	-0.71	5.85	4.72	0.59763	.	0.610680	0.17969	N	0.155936	T	0.00039	0.0001	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06552	-1.0820	9	0.13470	T	0.59	.	8.145	0.31106	0.0:0.0712:0.1356:0.7932	rs3793771;rs17733373;rs3793771	11	Q93098	WNT8B_HUMAN	S	11	ENSP00000340677:C11S	ENSP00000340677:C11S	C	+	2	0	WNT8B	102212947	0.988000	0.35896	0.992000	0.48379	0.703000	0.40648	1.476000	0.35420	0.486000	0.27676	-1.145000	0.01858	TGT	G|0.799;C|0.201	0.201	strong		0.428	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393	
OSMR	9180	hgsc.bcm.edu	37	5	38904082	38904082	+	Missense_Mutation	SNP	T	T	C	rs35117676	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:38904082T>C	ENST00000274276.3	+	8	1492	c.1090T>C	c.(1090-1092)Tat>Cat	p.Y364H		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	364	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					TAATTTCACATATTTGTGTCA	0.328													T|||	18	0.00359425	0.0	0.0072	5008	,	,		18317	0.0		0.0109	False		,,,				2504	0.002				p.Y364H		Atlas-SNP	.											.	OSMR	133	.	0			c.T1090C						PASS	.	T	HIS/TYR	16,4390	24.3+/-50.5	0,16,2187	61.0	63.0	62.0		1090	-1.3	0.0	5	dbSNP_126	62	124,8474	64.9+/-127.2	1,122,4176	yes	missense	OSMR	NM_003999.2	83	1,138,6363	CC,CT,TT		1.4422,0.3631,1.0766	benign	364/980	38904082	140,12864	2203	4299	6502	SO:0001583	missense	9180	exon8			TTCACATATTTGT	U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"""Fibronectin type III domain containing"""	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1090T>C	5.37:g.38904082T>C	ENSP00000274276:p.Tyr364His	Somatic	387	1	0.00258398		WXS	Illumina HiSeq	Phase_I	365	171	0.468493	NM_003999	Q6P4E8|Q96QJ6	Missense_Mutation	SNP	ENST00000274276.3	37	CCDS3928.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	T	12.79	2.044954	0.36085	0.003631	0.014422	ENSG00000145623	ENST00000274276	T	0.53640	0.61	5.75	-1.26	0.09376	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.457709	0.22766	N	0.055885	T	0.19644	0.0472	N	0.22421	0.69	0.09310	N	1	P	0.48640	0.913	B	0.37601	0.254	T	0.25222	-1.0138	10	0.87932	D	0	.	9.3318	0.38027	0.0:0.32:0.0:0.68	rs35117676	364	Q99650	OSMR_HUMAN	H	364	ENSP00000274276:Y364H	ENSP00000274276:Y364H	Y	+	1	0	OSMR	38939839	0.001000	0.12720	0.002000	0.10522	0.020000	0.10135	-0.039000	0.12124	-0.126000	0.11682	-0.408000	0.06270	TAT	T|0.991;C|0.009	0.009	strong		0.328	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999	
AS3MT	57412	hgsc.bcm.edu	37	10	104638723	104638723	+	Missense_Mutation	SNP	T	T	C	rs11191439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:104638723T>C	ENST00000369880.3	+	9	937	c.860T>C	c.(859-861)aTg>aCg	p.M287T	C10orf32-ASMT_ENST00000299353.6_3'UTR	NM_020682.3	NP_065733.2	Q9HBK9	AS3MT_HUMAN	arsenite methyltransferase	287			M -> T (common polymorphism; frequency in African-Americans 0.108 and Caucasian- Americans 0.100; enzyme activity is 350% of wild-type; dbSNP:rs11191439). {ECO:0000269|PubMed:16407288, ECO:0000269|PubMed:18334919}.		arsonoacetate metabolic process (GO:0018872)|toxin metabolic process (GO:0009404)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	arsenite methyltransferase activity (GO:0030791)|methylarsonite methyltransferase activity (GO:0030792)			large_intestine(1)|lung(6)	7		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)		AAAGAACTAATGTTTGATGCC	0.368													T|||	386	0.0770767	0.0938	0.1009	5008	,	,		20509	0.0218		0.1133	False		,,,				2504	0.0573				p.M287T		Atlas-SNP	.											.	AS3MT	17	.	0			c.T860C	GRCh37	CM081161	AS3MT	M	rs11191439	PASS	.	T	THR/MET	434,3340		27,380,1480	132.0	121.0	124.0		860	2.9	0.1	10	dbSNP_120	124	843,7359		38,767,3296	yes	missense	AS3MT	NM_020682.3	81	65,1147,4776	CC,CT,TT		10.278,11.4997,10.663	benign	287/376	104638723	1277,10699	1887	4101	5988	SO:0001583	missense	57412	exon9			AACTAATGTTTGA	AF226730	CCDS41567.1	10q24.33	2014-05-09	2014-05-09		ENSG00000214435	ENSG00000214435	2.1.1.137		17452	protein-coding gene	gene with protein product		611806	"""arsenic (+3 oxidation state) methyltransferase"""			11790780	Standard	NM_020682		Approved	CYT19	uc001kwk.3	Q9HBK9	OTTHUMG00000018972	ENST00000369880.3:c.860T>C	10.37:g.104638723T>C	ENSP00000358896:p.Met287Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	75	54	0.72	NM_020682	A6NP79|Q0VDK3|Q0VDK4|Q5PZ02	Missense_Mutation	SNP	ENST00000369880.3	37	CCDS41567.1	179	0.08195970695970696	48	0.0975609756097561	31	0.0856353591160221	14	0.024475524475524476	86	0.11345646437994723	T	0.012	-1.669566	0.00758	0.114997	0.10278	ENSG00000214435	ENST00000369880	T	0.21932	1.98	5.4	2.9	0.33743	.	0.531595	0.19599	N	0.110423	T	0.00144	0.0004	N	0.04508	-0.205	0.24058	P	0.996029	B;B;B	0.13594	0.008;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.0	T	0.31696	-0.9934	9	0.14252	T	0.57	-1.7851	5.5404	0.17036	0.2478:0.0856:0.0:0.6667	rs11191439;rs17725209;rs17884200;rs17885947;rs11191439	287;287;287	Q0VDK3;Q9HBK9;Q0VDK4	.;AS3MT_HUMAN;.	T	287	ENSP00000358896:M287T	ENSP00000358896:M287T	M	+	2	0	AS3MT	104628713	1.000000	0.71417	0.113000	0.21522	0.025000	0.11179	2.096000	0.41738	0.977000	0.38444	-0.441000	0.05720	ATG	T|0.914;C|0.086	0.086	strong		0.368	AS3MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050107.1	NM_020682	
RHPN2	85415	hgsc.bcm.edu	37	19	33493201	33493201	+	Missense_Mutation	SNP	C	C	T	rs201601538	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:33493201C>T	ENST00000254260.3	-	9	1092	c.1057G>A	c.(1057-1059)Gcg>Acg	p.A353T	RHPN2_ENST00000400226.4_Missense_Mutation_p.A202T	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	353	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.A353T(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)					GCCAGGGCCGCGTAGTGGTGG	0.642																																					p.A353T		Atlas-SNP	.											RHPN2,caecum,carcinoma,0,17	RHPN2	107	17	2	Substitution - Missense(2)	central_nervous_system(2)	c.G1057A						scavenged	.						51.0	48.0	49.0					19																	33493201		2203	4300	6503	SO:0001583	missense	85415	exon9			GGGCCGCGTAGTG	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.1057G>A	19.37:g.33493201C>T	ENSP00000254260:p.Ala353Thr	Somatic	167	3	0.0179641		WXS	Illumina HiSeq	Phase_I	177	20	0.112994	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	6.623	0.483344	0.12581	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.17691	2.26;2.26	4.61	-0.585	0.11698	BRO1 domain (3);	1.055030	0.07227	N	0.861852	T	0.07279	0.0184	N	0.11560	0.145	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.41378	-0.9512	10	0.13853	T	0.58	0.2931	3.9219	0.09247	0.1643:0.3914:0.0:0.4443	.	353	Q8IUC4	RHPN2_HUMAN	T	353;83;202	ENSP00000254260:A353T;ENSP00000402244:A202T	ENSP00000254260:A353T	A	-	1	0	RHPN2	38185041	0.000000	0.05858	0.006000	0.13384	0.362000	0.29581	-0.172000	0.09868	0.142000	0.18901	-0.373000	0.07131	GCG	C|0.929;T|0.070	0.070	strong		0.642	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209168942	209168942	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:209168942C>T	ENST00000264380.4	+	11	1526	c.1368C>T	c.(1366-1368)aaC>aaT	p.N456N	PIKFYVE_ENST00000308862.6_Silent_p.N370N|PIKFYVE_ENST00000407449.1_Silent_p.N456N|PIKFYVE_ENST00000392202.3_Silent_p.N359N	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	456					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						ACTCAGTGAACTCCGTGGAAG	0.443																																					p.N456N		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.C1368T						PASS	.						125.0	120.0	122.0					2																	209168942		2203	4300	6503	SO:0001819	synonymous_variant	200576	exon11			AGTGAACTCCGTG	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.1368C>T	2.37:g.209168942C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	59	42	0.711864	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																			.	.	none		0.443	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
TMEM132B	114795	hgsc.bcm.edu	37	12	126137060	126137060	+	Missense_Mutation	SNP	C	C	T	rs61021440	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:126137060C>T	ENST00000299308.3	+	8	1981	c.1973C>T	c.(1972-1974)gCg>gTg	p.A658V	TMEM132B_ENST00000535886.1_Missense_Mutation_p.A170V	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	658			A -> V (in dbSNP:rs16919359). {ECO:0000269|PubMed:15489334}.			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)		GTCACCATCGCGGAGCTGGGA	0.587													C|||	1715	0.342452	0.5008	0.451	5008	,	,		21676	0.2768		0.2505	False		,,,				2504	0.2137				p.A658V		Atlas-SNP	.											TMEM132B,NS,carcinoma,-1,1	TMEM132B	207	1	0			c.C1973T						PASS	.						47.0	51.0	50.0					12																	126137060		2106	4242	6348	SO:0001583	missense	114795	exon8			CCATCGCGGAGCT	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.1973C>T	12.37:g.126137060C>T	ENSP00000299308:p.Ala658Val	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	263	112	0.425856	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Missense_Mutation	SNP	ENST00000299308.3	37	CCDS41859.1	613	0.2806776556776557	182	0.3699186991869919	135	0.3729281767955801	121	0.21153846153846154	175	0.23087071240105542	C	12.01	1.810105	0.32053	.	.	ENSG00000139364	ENST00000299308;ENST00000535886	T;T	0.46063	0.88;0.88	5.53	4.64	0.57946	.	0.589970	0.16854	N	0.196801	T	0.00012	0.0000	N	0.12746	0.255	0.39908	P	0.02601500000000001	B	0.09022	0.002	B	0.06405	0.002	T	0.38134	-0.9675	9	0.40728	T	0.16	.	10.7695	0.46314	0.0:0.8542:0.0:0.1458	rs61021440;rs61748700	658	Q14DG7	T132B_HUMAN	V	658;170	ENSP00000299308:A658V;ENSP00000440436:A170V	ENSP00000299308:A658V	A	+	2	0	TMEM132B	124703013	0.003000	0.15002	0.256000	0.24389	0.132000	0.20833	1.919000	0.40015	1.317000	0.45149	0.655000	0.94253	GCG	C|0.759;T|0.241	0.241	strong		0.587	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
OR10S1	219873	hgsc.bcm.edu	37	11	123848121	123848121	+	Missense_Mutation	SNP	T	T	C	rs17686210	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:123848121T>C	ENST00000531945.1	-	1	367	c.278A>G	c.(277-279)aAg>aGg	p.K93R		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	93			K -> R (in dbSNP:rs17686210).			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(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		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)		TGCCATGACCTTGGGCACTGT	0.552													T|||	902	0.180112	0.1558	0.2161	5008	,	,		23775	0.1171		0.2903	False		,,,				2504	0.1391				p.K93R		Atlas-SNP	.											.	OR10S1	78	.	0			c.A278G						PASS	.	T	ARG/LYS	739,3665	302.4+/-287.4	65,609,1528	84.0	67.0	73.0		278	3.7	1.0	11	dbSNP_123	73	2217,6381	373.0+/-336.8	297,1623,2379	yes	missense	OR10S1	NM_001004474.1	26	362,2232,3907	CC,CT,TT		25.7851,16.7802,22.735	benign	93/332	123848121	2956,10046	2202	4299	6501	SO:0001583	missense	219873	exon1			ATGACCTTGGGCA	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.278A>G	11.37:g.123848121T>C	ENSP00000431914:p.Lys93Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	174	99	0.568965	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	449	0.20558608058608058	81	0.16463414634146342	87	0.24033149171270718	73	0.12762237762237763	208	0.27440633245382584	T	11.00	1.511627	0.27036	0.167802	0.257851	ENSG00000196248	ENST00000531945	T	0.06768	3.26	4.84	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.195670	0.24750	U	0.035919	T	0.00012	0.0000	L	0.28458	0.855	0.44373	P	0.00273000000000001	D	0.60575	0.988	P	0.51657	0.676	T	0.50734	-0.8793	9	0.48119	T	0.1	-9.7909	11.6588	0.51334	0.0:0.0:0.1488:0.8512	rs17686210;rs52830816;rs17686210	93	Q8NGN2	O10S1_HUMAN	R	93	ENSP00000431914:K93R	ENSP00000431914:K93R	K	-	2	0	OR10S1	123353331	0.335000	0.24748	1.000000	0.80357	0.953000	0.61014	0.933000	0.28897	0.877000	0.35895	-0.340000	0.08031	AAG	T|0.785;C|0.215	0.215	strong		0.552	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
OR7A17	26333	hgsc.bcm.edu	37	19	14992045	14992045	+	Silent	SNP	C	C	T	rs10404335	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14992045C>T	ENST00000327462.2	-	1	219	c.123G>A	c.(121-123)ggG>ggA	p.G41G		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	41						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)					TGAGCAGATTCCCGAGCACAG	0.498													.|||	1703	0.340056	0.118	0.3271	5008	,	,		13957	0.6121		0.338	False		,,,				2504	0.3712				p.G41G		Atlas-SNP	.											.	OR7A17	37	.	0			c.G123A						PASS	.	C		758,3648		64,630,1509	58.0	50.0	53.0		123	-1.5	0.4	19	dbSNP_119	53	2702,5896		460,1782,2057	no	coding-synonymous	OR7A17	NM_030901.1		524,2412,3566	TT,TC,CC		31.4259,17.2038,26.6072		41/310	14992045	3460,9544	2203	4299	6502	SO:0001819	synonymous_variant	26333	exon1			CAGATTCCCGAGC	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.123G>A	19.37:g.14992045C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			C|0.713;T|0.287	0.287	strong		0.498	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
RNF43	54894	hgsc.bcm.edu	37	17	56436109	56436109	+	Missense_Mutation	SNP	C	C	T	rs34523089	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:56436109C>T	ENST00000584437.1	-	8	2983	c.1028G>A	c.(1027-1029)cGc>cAc	p.R343H	RNF43_ENST00000577625.1_Missense_Mutation_p.R216H|RNF43_ENST00000500597.2_Missense_Mutation_p.R302H|RNF43_ENST00000583753.1_Missense_Mutation_p.R302H|RNF43_ENST00000407977.2_Missense_Mutation_p.R343H|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	57	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	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	
MYBPC3	4607	hgsc.bcm.edu	37	11	47370041	47370041	+	Missense_Mutation	SNP	T	T	C	rs3729989	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47370041T>C	ENST00000545968.1	-	6	760	c.706A>G	c.(706-708)Agc>Ggc	p.S236G	MYBPC3_ENST00000256993.4_Missense_Mutation_p.S236G|MYBPC3_ENST00000399249.2_Missense_Mutation_p.S236G	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	236	Ig-like C2-type 1.		S -> G (in dbSNP:rs3729989). {ECO:0000269|PubMed:12379228, ECO:0000269|PubMed:12974739, ECO:0000269|PubMed:15519027, ECO:0000269|PubMed:15582318, ECO:0000269|PubMed:18403758, ECO:0000269|Ref.4}.		cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		CAGCGGTAGCTGCCAGTGAAG	0.617													C|||	336	0.0670927	0.0431	0.0836	5008	,	,		18193	0.0268		0.1412	False		,,,				2504	0.0532				p.S236G		Atlas-SNP	.											.	MYBPC3	102	.	0			c.A706G	GRCh37	CM043536	MYBPC3	M	rs3729989	PASS	.	C	GLY/SER	239,3925		8,223,1851	46.0	57.0	53.0		706	5.1	0.9	11	dbSNP_107	53	1060,7334		69,922,3206	yes	missense	MYBPC3	NM_000256.3	56	77,1145,5057	CC,CT,TT		12.6281,5.7397,10.344	benign	236/1275	47370041	1299,11259	2082	4197	6279	SO:0001583	missense	4607	exon6			GGTAGCTGCCAGT	X84075	CCDS53621.1	11p11.2	2014-09-17	2001-11-28			ENSG00000134571		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7551	protein-coding gene	gene with protein product		600958	"""myosin-binding protein C, cardiac"""	CMH4		7744002, 8358441	Standard	NM_000256		Approved	MYBP-C, FHC	uc021qis.1	Q14896		ENST00000545968.1:c.706A>G	11.37:g.47370041T>C	ENSP00000442795:p.Ser236Gly	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	137	75	0.547445	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	189	0.08653846153846154	32	0.06504065040650407	38	0.10497237569060773	14	0.024475524475524476	105	0.13852242744063326	C	4.342	0.062968	0.08388	0.057397	0.126281	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.68025	-0.3;-0.3;-0.3	5.12	5.12	0.69794	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00210	0.0006	N	0.00317	-1.655	0.47659	P	5.169999999999897E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.12319	-1.0552	8	0.02654	T	1	.	13.8315	0.63384	0.0:0.9259:0.0:0.0741	rs3729989;rs57344110;rs3729989	236	Q14896	MYPC3_HUMAN	G	236	ENSP00000442795:S236G;ENSP00000382193:S236G;ENSP00000256993:S236G	ENSP00000256993:S236G	S	-	1	0	MYBPC3	47326617	0.252000	0.23972	0.859000	0.33776	0.579000	0.36224	2.559000	0.45888	1.170000	0.42753	-0.215000	0.12644	AGC	T|0.916;C|0.084	0.084	strong		0.617	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
SLC35G6	643664	hgsc.bcm.edu	37	17	7386217	7386217	+	Missense_Mutation	SNP	T	T	C	rs200349946	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7386217T>C	ENST00000412468.2	+	2	1029	c.914T>C	c.(913-915)gTg>gCg	p.V305A	POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	305	EamA 2.					integral component of membrane (GO:0016021)		p.V305A(1)									CATGAGACTGTGGCACCTTCT	0.587																																					p.V305A		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,0,3	.	.	3	1	Substitution - Missense(1)	lung(1)	c.T914C						PASS	.						152.0	140.0	144.0					17																	7386217		2203	4300	6503	SO:0001583	missense	643664	exon2			AGACTGTGGCACC		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.914T>C	17.37:g.7386217T>C	ENSP00000396523:p.Val305Ala	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	278	44	0.158273	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	T	9.097	1.003182	0.19121	.	.	ENSG00000181222	ENST00000412468	T	0.52526	0.66	4.38	4.38	0.52667	.	.	.	.	.	T	0.29588	0.0738	N	0.08118	0	0.28830	N	0.897226	P	0.45634	0.863	P	0.45538	0.484	T	0.03662	-1.1015	9	0.23891	T	0.37	-5.5045	7.8045	0.29193	0.0:0.0972:0.0:0.9028	.	305	P0C7Q6	S35G6_HUMAN	A	305	ENSP00000396523:V305A	ENSP00000396523:V305A	V	+	2	0	SLC35G6	7326941	1.000000	0.71417	0.967000	0.41034	0.203000	0.24098	2.735000	0.47377	1.756000	0.51951	0.482000	0.46254	GTG	T|0.734;C|0.266	0.266	strong		0.587	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
EIF2B3	8891	hgsc.bcm.edu	37	1	45444038	45444038	+	Silent	SNP	G	G	A	rs11556200	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:45444038G>A	ENST00000360403.2	-	3	369	c.243C>T	c.(241-243)gaC>gaT	p.D81D	EIF2B3_ENST00000480675.1_5'UTR|EIF2B3_ENST00000372183.3_Silent_p.D81D	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	81					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|positive regulation of GTPase activity (GO:0043547)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	guanyl-nucleotide exchange factor activity (GO:0005085)|nucleotidyltransferase activity (GO:0016779)|translation initiation factor activity (GO:0003743)			endometrium(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	17	Acute lymphoblastic leukemia(166;0.155)					CCATGTCAGCGTCATCAGGAA	0.363													A|||	1485	0.296526	0.4032	0.4265	5008	,	,		17307	0.2758		0.1998	False		,,,				2504	0.181				p.D81D	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											.	EIF2B3	43	.	0			c.C243T						PASS	.	A	,	1705,2701	653.0+/-399.5	345,1015,843	215.0	210.0	211.0		243,243	-4.9	0.8	1	dbSNP_120	211	1990,6610	723.2+/-406.4	234,1522,2544	no	coding-synonymous,coding-synonymous	EIF2B3	NM_001166588.1,NM_020365.3	,	579,2537,3387	AA,AG,GG		23.1395,38.6972,28.41	,	81/413,81/453	45444038	3695,9311	2203	4300	6503	SO:0001819	synonymous_variant	8891	exon3			GTCAGCGTCATCA	AF257077	CCDS517.1, CCDS53313.1, CCDS72775.1	1p34.1	2008-02-05	2002-08-29		ENSG00000070785	ENSG00000070785			3259	protein-coding gene	gene with protein product		606273	"""eukaryotic translation initiation factor 2B, subunit 3 (gamma, 58kD)"""			10900014	Standard	NM_020365		Approved	EIF2Bgamma, EIF-2B	uc001cmt.3	Q9NR50	OTTHUMG00000008585	ENST00000360403.2:c.243C>T	1.37:g.45444038G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	96	22	0.229167	NM_020365	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Silent	SNP	ENST00000360403.2	37	CCDS517.1																																																																																			G|0.714;A|0.286	0.286	strong		0.363	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365	
UTP20	27340	hgsc.bcm.edu	37	12	101685852	101685852	+	Silent	SNP	G	G	A	rs11110737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:101685852G>A	ENST00000261637.4	+	10	1317	c.1143G>A	c.(1141-1143)ccG>ccA	p.P381P		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	381					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						TTTCCTTGCCGGAGACCCTCA	0.383													G|||	441	0.0880591	0.0219	0.111	5008	,	,		16923	0.0278		0.165	False		,,,				2504	0.1442				p.P381P		Atlas-SNP	.											.	UTP20	222	.	0			c.G1143A						PASS	.	G		187,4219	118.4+/-156.1	5,177,2021	149.0	143.0	145.0		1143	-2.9	0.9	12	dbSNP_120	145	1422,7178	274.5+/-291.2	121,1180,2999	no	coding-synonymous	UTP20	NM_014503.2		126,1357,5020	AA,AG,GG		16.5349,4.2442,12.3712		381/2786	101685852	1609,11397	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon10			CTTGCCGGAGACC	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.1143G>A	12.37:g.101685852G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	89	51	0.573034	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			G|0.888;A|0.112	0.112	strong		0.383	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
CAPN2	824	hgsc.bcm.edu	37	1	223954080	223954080	+	Missense_Mutation	SNP	A	A	C	rs17599	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:223954080A>C	ENST00000295006.5	+	16	2011	c.1702A>C	c.(1702-1704)Aag>Cag	p.K568Q	CAPN2_ENST00000433674.2_Missense_Mutation_p.K490Q|CAPN2_ENST00000474026.1_3'UTR	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	568	Domain IV.		K -> Q (in dbSNP:rs17599). {ECO:0000269|Ref.4}.		blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)	p.K568Q(1)		breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CCAAGATATCAAGTCAGATGG	0.403													A|||	1038	0.207268	0.0983	0.2493	5008	,	,		22375	0.2698		0.2425	False		,,,				2504	0.2239				p.K568Q		Atlas-SNP	.											CAPN2,NS,carcinoma,0,1	CAPN2	69	1	1	Substitution - Missense(1)	stomach(1)	c.A1702C						scavenged	.	A	GLN/LYS,GLN/LYS	554,3852	249.3+/-256.8	38,478,1687	142.0	126.0	132.0		1468,1702	5.5	1.0	1	dbSNP_63	132	2104,6496	362.6+/-332.8	269,1566,2465	yes	missense,missense	CAPN2	NM_001146068.1,NM_001748.4	53,53	307,2044,4152	CC,CA,AA		24.4651,12.5738,20.4367	probably-damaging,probably-damaging	490/623,568/701	223954080	2658,10348	2203	4300	6503	SO:0001583	missense	824	exon16			GATATCAAGTCAG	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"""EF-hand domain containing"""	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.1702A>C	1.37:g.223954080A>C	ENSP00000295006:p.Lys568Gln	Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	193	75	0.388601	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	466	0.21336996336996336	51	0.10365853658536585	91	0.2513812154696133	132	0.23076923076923078	192	0.2532981530343008	A	16.47	3.132564	0.56828	0.125738	0.244651	ENSG00000162909	ENST00000433674;ENST00000295006;ENST00000366869	T;T	0.32988	1.43;1.43	5.47	5.47	0.80525	EF-hand-like domain (1);	0.154834	0.56097	D	0.000021	T	0.00012	0.0000	M	0.77712	2.385	0.09310	P	0.999999146384	B;B;B	0.17465	0.007;0.022;0.007	B;B;B	0.27796	0.032;0.083;0.02	T	0.07424	-1.0773	9	0.59425	D	0.04	.	15.5473	0.76112	1.0:0.0:0.0:0.0	rs17599;rs1130849;rs3190187;rs3738372;rs11547592;rs17318843;rs17398495;rs52809008;rs59544343;rs3738372	490;151;568	B7ZA96;B3KUH9;P17655	.;.;CAN2_HUMAN	Q	490;568;597	ENSP00000413158:K490Q;ENSP00000295006:K568Q	ENSP00000295006:K568Q	K	+	1	0	CAPN2	222020703	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.158000	0.77470	2.069000	0.61940	0.459000	0.35465	AAG	A|0.649;C|0.175;G|0.031;T|0.145	0.175	strong		0.403	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748	
UTP20	27340	hgsc.bcm.edu	37	12	101732655	101732655	+	Silent	SNP	C	C	T	rs56265469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:101732655C>T	ENST00000261637.4	+	31	4107	c.3933C>T	c.(3931-3933)agC>agT	p.S1311S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1311					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						AGTATCTCAGCAAAACCACAA	0.328													C|||	1285	0.256589	0.1536	0.317	5008	,	,		17124	0.375		0.2376	False		,,,				2504	0.2505				p.S1311S		Atlas-SNP	.											.	UTP20	222	.	0			c.C3933T						PASS	.	C		768,3638	310.2+/-291.5	64,640,1499	95.0	94.0	95.0		3933	4.4	1.0	12	dbSNP_129	95	2074,6522	356.5+/-330.3	268,1538,2492	no	coding-synonymous	UTP20	NM_014503.2		332,2178,3991	TT,TC,CC		24.1275,17.4308,21.8582		1311/2786	101732655	2842,10160	2203	4298	6501	SO:0001819	synonymous_variant	27340	exon31			TCTCAGCAAAACC	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.3933C>T	12.37:g.101732655C>T		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	223	108	0.484305	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			C|0.766;T|0.234	0.234	strong		0.328	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
MED12	9968	hgsc.bcm.edu	37	X	70349947	70349947	+	Silent	SNP	A	A	C	rs5030619	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:70349947A>C	ENST00000374080.3	+	28	3962	c.3930A>C	c.(3928-3930)ccA>ccC	p.P1310P	MED12_ENST00000374102.1_Silent_p.P1310P|MED12_ENST00000333646.6_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	456	1	0.00219298		WXS	Illumina HiSeq	Phase_I	230	224	0.973913	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	
BCAM	4059	hgsc.bcm.edu	37	19	45316588	45316588	+	Missense_Mutation	SNP	G	G	A	rs28399654	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45316588G>A	ENST00000270233.6	+	5	608	c.586G>A	c.(586-588)Gta>Ata	p.V196I	BCAM_ENST00000589651.1_Missense_Mutation_p.V196I	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	196	Ig-like V-type 2.		V -> I (in dbSNP:rs28399654). {ECO:0000269|Ref.2}.		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)				GGAGGTGCCCGTAGAGATGAA	0.687													G|||	44	0.00878594	0.0015	0.0173	5008	,	,		15655	0.0		0.0288	False		,,,				2504	0.001				p.V196I		Atlas-SNP	.											.	BCAM	53	.	0			c.G586A						PASS	.	G	ILE/VAL,ILE/VAL	21,4385		0,21,2182	35.0	37.0	36.0		586,586	-4.5	0.7	19	dbSNP_125	36	290,8300		7,276,4012	yes	missense,missense	BCAM	NM_001013257.1,NM_005581.3	29,29	7,297,6194	AA,AG,GG		3.376,0.4766,2.393	benign,benign	196/589,196/629	45316588	311,12685	2203	4295	6498	SO:0001583	missense	4059	exon5			GTGCCCGTAGAGA	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.586G>A	19.37:g.45316588G>A	ENSP00000270233:p.Val196Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	31	0.014194139194139194	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	22	0.029023746701846966	.	1.290	-0.607948	0.03717	0.004766	0.03376	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.58940	0.3;0.33	4.48	-4.49	0.03504	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.08980	0.0222	N	0.05124	-0.11	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09530	-1.0670	9	0.23302	T	0.38	-7.0325	0.2649	0.00223	0.2385:0.2871:0.1925:0.2819	rs28399654	196	P50895	BCAM_HUMAN	I	196	ENSP00000270233:V196I;ENSP00000375817:V196I	ENSP00000270233:V196I	V	+	1	0	BCAM	50008428	0.001000	0.12720	0.739000	0.30968	0.211000	0.24417	-0.426000	0.07008	-0.826000	0.04284	-0.379000	0.06801	GTA	G|0.983;A|0.017	0.017	strong		0.687	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
PPT1	5538	hgsc.bcm.edu	37	1	40557033	40557033	+	Missense_Mutation	SNP	A	A	G	rs1800205	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:40557033A>G	ENST00000433473.3	-	4	865	c.401T>C	c.(400-402)aTc>aCc	p.I134T	PPT1_ENST00000449045.2_Intron	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1	134			I -> T (in dbSNP:rs1800205). {ECO:0000269|PubMed:9664077}.		adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|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;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			GATCAGATTGATCATGGGAGG	0.433													A|||	370	0.0738818	0.0068	0.036	5008	,	,		19738	0.1052		0.0746	False		,,,				2504	0.1585				p.I134T		Atlas-SNP	.											.	PPT1	18	.	0			c.T401C						PASS	.	A	THR/ILE,	46,4360	48.2+/-83.0	0,46,2157	102.0	85.0	91.0		401,	2.4	1.0	1	dbSNP_89	91	408,8192	128.8+/-187.0	12,384,3904	yes	missense,intron	PPT1	NM_000310.3,NM_001142604.1	89,	12,430,6061	GG,GA,AA		4.7442,1.044,3.4907	benign,	134/307,	40557033	454,12552	2203	4300	6503	SO:0001583	missense	5538	exon4			AGATTGATCATGG	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 1, infantile"""	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495	ENST00000433473.3:c.401T>C	1.37:g.40557033A>G	ENSP00000394863:p.Ile134Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	51	7	0.137255	NM_000310	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	37	CCDS447.1	151	0.06913919413919414	4	0.008130081300813009	17	0.04696132596685083	68	0.11888111888111888	62	0.08179419525065963	A	10.71	1.425899	0.25726	0.01044	0.047442	ENSG00000131238	ENST00000433473;ENST00000439754;ENST00000372779;ENST00000526547	D;D;D;D	0.96522	-4.04;-4.04;-4.04;-4.04	4.82	2.39	0.29439	.	0.738450	0.13506	N	0.382876	T	0.17662	0.0424	N	0.25890	0.77	0.09310	P	0.999999863687	B;B	0.15930	0.001;0.015	B;B	0.23419	0.004;0.046	T	0.66256	-0.5969	9	0.23302	T	0.38	-17.087	8.6687	0.34137	0.5085:0.0:0.0:0.4915	rs1800205;rs52825618	84;134	B4DWU3;P50897	.;PPT1_HUMAN	T	134;29;163;84	ENSP00000394863:I134T;ENSP00000403207:I29T;ENSP00000361865:I163T;ENSP00000436481:I84T	ENSP00000361865:I163T	I	-	2	0	PPT1	40329620	0.982000	0.34865	0.956000	0.39512	0.964000	0.63967	0.574000	0.23714	0.294000	0.22547	0.528000	0.53228	ATC	A|0.952;G|0.048	0.048	strong		0.433	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310	
DNAH14	127602	hgsc.bcm.edu	37	1	225586274	225586274	+	Missense_Mutation	SNP	G	G	T	rs41304131	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225586274G>T	ENST00000445597.2	+	60	10214	c.10214G>T	c.(10213-10215)gGg>gTg	p.G3405V	DNAH14_ENST00000430092.1_Missense_Mutation_p.G4413V|DNAH14_ENST00000439375.2_Missense_Mutation_p.G4413V			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	3405					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						TTCATCGAGGGGGCAAGATGG	0.473													G|||	49	0.00978435	0.0008	0.0101	5008	,	,		18877	0.0		0.0338	False		,,,				2504	0.0072				p.G4413V		Atlas-SNP	.											.	DNAH14	300	.	0			c.G13238T						PASS	.	G	VAL/GLY	4,1380		0,4,688	210.0	179.0	189.0		13238	5.2	1.0	1	dbSNP_127	189	106,3076		4,98,1489	yes	missense	DNAH14	NM_001373.1	109	4,102,2177	TT,TG,GG		3.3312,0.289,2.4091	probably-damaging	4413/4516	225586274	110,4456	692	1591	2283	SO:0001583	missense	127602	exon83			TCGAGGGGGCAAG	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.10214G>T	1.37:g.225586274G>T	ENSP00000409472:p.Gly3405Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	234	77	0.32906	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		30	0.013736263736263736	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	25	0.032981530343007916	G	15.77	2.931346	0.52866	0.00289	0.033312	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.20069	2.1;2.1;2.1	5.24	5.24	0.73138	.	.	.	.	.	T	0.29684	0.0741	M	0.89030	3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.52555	-0.8560	9	0.87932	D	0	.	16.5995	0.84807	0.0:0.0:1.0:0.0	rs41304131	4413	Q0VDD8-4	.	V	3405;4413;4413	ENSP00000409472:G3405V;ENSP00000414402:G4413V;ENSP00000392061:G4413V	ENSP00000414402:G4413V	G	+	2	0	DNAH14	223652897	1.000000	0.71417	0.968000	0.41197	0.153000	0.21895	5.025000	0.64097	2.834000	0.97654	0.557000	0.71058	GGG	G|0.985;T|0.015	0.015	strong		0.473	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
CNOT4	4850	hgsc.bcm.edu	37	7	135098310	135098310	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:135098310C>T	ENST00000315544.5	-	6	893	c.614G>A	c.(613-615)tGt>tAt	p.C205Y	CNOT4_ENST00000541284.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000428680.2_Missense_Mutation_p.C205Y|CNOT4_ENST00000361528.4_Missense_Mutation_p.C205Y|CNOT4_ENST00000451834.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000414802.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000423368.2_Missense_Mutation_p.C205Y|CNOT4_ENST00000356162.4_Missense_Mutation_p.C205Y	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	205					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)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						AGGTTTTGGACACTGCATATT	0.418																																					p.C205Y	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.G614A						PASS	.						130.0	118.0	122.0					7																	135098310		1876	4110	5986	SO:0001583	missense	4850	exon6			TTTGGACACTGCA	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.614G>A	7.37:g.135098310C>T	ENSP00000326731:p.Cys205Tyr	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	133	72	0.541353	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.043251	0.75732	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;T;D;T;T;D;D	0.82619	-1.52;-1.57;-1.44;-1.51;-1.38;-1.38;-1.63;-1.56	5.95	5.07	0.68467	Zinc finger, CCCH-type (1);	0.000000	0.85682	D	0.000000	D	0.92756	0.7697	M	0.91612	3.225	0.80722	D	1	D;D;D;D;B;D	0.89917	1.0;1.0;1.0;1.0;0.16;0.997	D;D;D;D;B;D	0.97110	0.999;1.0;0.999;1.0;0.051;0.991	D	0.94292	0.7529	10	0.87932	D	0	-12.3216	15.3196	0.74112	0.0:0.9329:0.0:0.0671	.	205;205;205;205;205;205	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	Y	205	ENSP00000445508:C205Y;ENSP00000388491:C205Y;ENSP00000406777:C205Y;ENSP00000354673:C205Y;ENSP00000416532:C205Y;ENSP00000348485:C205Y;ENSP00000399108:C205Y;ENSP00000326731:C205Y	ENSP00000262563:C205Y	C	-	2	0	CNOT4	134748850	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.506000	0.81665	1.527000	0.49086	0.563000	0.77884	TGT	.	.	none		0.418	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
LAMC1	3915	hgsc.bcm.edu	37	1	183079729	183079729	+	Missense_Mutation	SNP	C	C	T	rs142614579	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:183079729C>T	ENST00000258341.4	+	4	1218	c.961C>T	c.(961-963)Cct>Tct	p.P321S		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	321	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|endoderm development (GO:0007492)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|positive regulation of epithelial cell proliferation (GO:0050679)|protein complex assembly (GO:0006461)|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-11 complex (GO:0043260)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(27)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	76						AAAGTGTCTTCCTTTCTTCAA	0.473																																					p.P321S		Atlas-SNP	.											.	LAMC1	176	.	0			c.C961T						PASS	.	C	SER/PRO	3,4403	6.2+/-15.9	0,3,2200	188.0	184.0	186.0		961	4.9	0.3	1	dbSNP_134	186	4,8596	3.7+/-12.6	0,4,4296	yes	missense	LAMC1	NM_002293.3	74	0,7,6496	TT,TC,CC		0.0465,0.0681,0.0538	probably-damaging	321/1610	183079729	7,12999	2203	4300	6503	SO:0001583	missense	3915	exon4			TGTCTTCCTTTCT	J03202	CCDS1351.1	1q31	2013-03-01			ENSG00000135862	ENSG00000135862		"""Laminins"""	6492	protein-coding gene	gene with protein product		150290		LAMB2		3234037	Standard	NM_002293		Approved		uc001gpy.4	P11047	OTTHUMG00000035418	ENST00000258341.4:c.961C>T	1.37:g.183079729C>T	ENSP00000258341:p.Pro321Ser	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	203	122	0.600985	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382348	0.82792	6.81E-4	4.65E-4	ENSG00000135862	ENST00000258341	T	0.62498	0.02	4.87	4.87	0.63330	EGF-like, laminin (4);	0.054481	0.85682	D	0.000000	T	0.76026	0.3930	M	0.79475	2.455	0.80722	D	1	P	0.46142	0.873	P	0.54026	0.74	T	0.80443	-0.1380	10	0.87932	D	0	.	17.9961	0.89184	0.0:1.0:0.0:0.0	.	321	P11047	LAMC1_HUMAN	S	321	ENSP00000258341:P321S	ENSP00000258341:P321S	P	+	1	0	LAMC1	181346352	0.998000	0.40836	0.254000	0.24359	0.975000	0.68041	3.714000	0.54889	2.239000	0.73571	0.305000	0.20034	CCT	C|0.999;T|0.001	0.001	strong		0.473	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293	
MYO5A	4644	hgsc.bcm.edu	37	15	52635394	52635394	+	Splice_Site	SNP	T	T	A	rs61731219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52635394T>A	ENST00000399231.3	-	31	4203	c.3960A>T	c.(3958-3960)agA>agT	p.R1320S	MYO5A_ENST00000553916.1_Intron|MYO5A_ENST00000399233.2_Splice_Site_p.R1317S|MYO5A_ENST00000356338.6_Intron|MYO5A_ENST00000358212.6_Splice_Site_p.R1320S	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1320					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)		GAGCAGATGATCTTCCATGCA	0.408													T|||	58	0.0115815	0.0023	0.0072	5008	,	,		19797	0.0		0.0437	False		,,,				2504	0.0061				p.R1320S		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3960T						PASS	.	T	SER/ARG,	24,3884		0,24,1930	92.0	85.0	87.0		3960,	5.9	1.0	15	dbSNP_129	87	339,7997		6,327,3835	yes	missense-near-splice,intron	MYO5A	NM_000259.3,NM_001142495.1	110,	6,351,5765	AA,AT,TT		4.0667,0.6141,2.9647	benign,	1320/1856,	52635394	363,11881	1954	4168	6122	SO:0001630	splice_region_variant	4644	exon31			AGATGATCTTCCA		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.3960-1A>T	15.37:g.52635394T>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	56	48	0.857143	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	T	15.01	2.706322	0.48412	0.006141	0.040667	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000358212;ENST00000399228	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	5.87	5.87	0.94306	.	0.059846	0.64402	D	0.000003	T	0.02807	0.0084	L	0.43152	1.355	0.80722	D	1	D;D;P	0.61080	0.989;0.989;0.495	D;D;B	0.75020	0.985;0.985;0.034	T	0.05566	-1.0877	10	0.38643	T	0.18	.	10.8931	0.47006	0.0:0.0783:0.0:0.9217	rs61731219	110;113;1320	Q9UES5;O95317;Q9Y4I1	.;.;MYO5A_HUMAN	S	1320;1317;1320;110	ENSP00000382177:R1320S;ENSP00000382179:R1317S;ENSP00000350945:R1320S;ENSP00000382174:R110S	ENSP00000350945:R1320S	R	-	3	2	MYO5A	50422686	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.751000	0.55165	2.236000	0.73375	0.528000	0.53228	AGA	T|0.955;A|0.045	0.045	strong		0.408	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	Missense_Mutation
PDILT	204474	hgsc.bcm.edu	37	16	20371972	20371972	+	Missense_Mutation	SNP	A	A	C	rs4500734	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:20371972A>C	ENST00000302451.4	-	11	1672	c.1424T>G	c.(1423-1425)cTg>cGg	p.L475R		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	475			L -> R (in dbSNP:rs4500734).		cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						TCCCTTATACAGGACAGCCTA	0.488													A|||	86	0.0171725	0.031	0.0115	5008	,	,		20637	0.002		0.0149	False		,,,				2504	0.0204				p.L475R		Atlas-SNP	.											.	PDILT	120	.	0			c.T1424G						PASS	.	A	ARG/LEU	171,4235	113.3+/-151.4	2,167,2034	146.0	133.0	138.0		1424	-4.0	0.0	16	dbSNP_111	138	143,8457	70.3+/-132.9	0,143,4157	yes	missense	PDILT	NM_174924.1	102	2,310,6191	CC,CA,AA		1.6628,3.8811,2.4143	benign	475/585	20371972	314,12692	2203	4300	6503	SO:0001583	missense	204474	exon11			TTATACAGGACAG		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"""Protein disulfide isomerases"""	27338	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 7"", ""protein disulfide isomerase-like protein of the testis"""					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.1424T>G	16.37:g.20371972A>C	ENSP00000305465:p.Leu475Arg	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	232	111	0.478448	NM_174924	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	30	0.013736263736263736	15	0.03048780487804878	5	0.013812154696132596	0	0.0	10	0.013192612137203167	A	2.551	-0.303994	0.05495	0.038811	0.016628	ENSG00000169340	ENST00000302451	T	0.03094	4.05	4.58	-4.03	0.04021	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.670897	0.15388	N	0.264943	T	0.00328	0.0010	N	0.02391	-0.57	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.42932	-0.9422	10	0.19147	T	0.46	.	3.8562	0.08976	0.2633:0.0:0.2602:0.4765	rs4500734;rs52825116;rs60405183;rs4500734	475	Q8N807	PDILT_HUMAN	R	475	ENSP00000305465:L475R	ENSP00000305465:L475R	L	-	2	0	PDILT	20279473	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.772000	0.04694	-0.854000	0.04131	-0.280000	0.10049	CTG	A|0.975;C|0.025	0.025	strong		0.488	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924	
FRG1	2483	hgsc.bcm.edu	37	4	190883051	190883051	+	Missense_Mutation	SNP	G	G	A	rs1803593		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:190883051G>A	ENST00000226798.4	+	8	926	c.704G>A	c.(703-705)cGg>cAg	p.R235Q		NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	235					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)		AAAAAGGCTCGGAAAGATGGA	0.328																																					p.R235Q		Atlas-SNP	.											FRG1,NS,carcinoid-endocrine_tumour,0,1	FRG1	76	1	0			c.G704A						scavenged	.						81.0	99.0	93.0					4																	190883051		2158	4213	6371	SO:0001583	missense	2483	exon8			AGGCTCGGAAAGA	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.704G>A	4.37:g.190883051G>A	ENSP00000226798:p.Arg235Gln	Somatic	241	40	0.165975		WXS	Illumina HiSeq	Phase_I	169	45	0.266272	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	15.68	2.904307	0.52333	.	.	ENSG00000109536	ENST00000226798	T	0.34472	1.36	4.07	3.23	0.37069	.	0.049801	0.85682	D	0.000000	T	0.27967	0.0689	.	.	.	0.58432	D	0.999998	B	0.30439	0.279	B	0.28385	0.089	T	0.07404	-1.0774	9	0.48119	T	0.1	1.7828	10.172	0.42915	0.1019:0.0:0.8981:0.0	rs1803593;rs3202757;rs17435102	235	Q14331	FRG1_HUMAN	Q	235	ENSP00000226798:R235Q	ENSP00000226798:R235Q	R	+	2	0	FRG1	191120045	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.403000	0.79983	0.849000	0.35215	-0.359000	0.07587	CGG	G|1.000;|0.000	.	weak		0.328	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
RASSF7	8045	hgsc.bcm.edu	37	11	562219	562219	+	Missense_Mutation	SNP	C	C	G	rs2242183	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:562219C>G	ENST00000397583.3	+	3	698	c.265C>G	c.(265-267)Ccc>Gcc	p.P89A	C11orf35_ENST00000329451.3_5'Flank|RP11-496I9.1_ENST00000527620.1_RNA|RASSF7_ENST00000397582.3_Missense_Mutation_p.P89A|RASSF7_ENST00000344375.4_Missense_Mutation_p.P89A|RASSF7_ENST00000454668.2_Missense_Mutation_p.P89A|RASSF7_ENST00000524468.1_3'UTR|RP11-496I9.1_ENST00000527113.1_RNA|RASSF7_ENST00000431809.1_Missense_Mutation_p.P89A	NM_003475.3	NP_003466.1	Q02833	RASF7_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	89	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.		P -> A (in dbSNP:rs2242183). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(3)	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)		GCGCACAGGGCCCAGCCTAGC	0.657													C|||	537	0.107228	0.0053	0.0648	5008	,	,		17268	0.3016		0.0656	False		,,,				2504	0.1176				p.P89A	Pancreas(184;1170 3913 7268)	Atlas-SNP	.											.	RASSF7	22	.	0			c.C265G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	64,4342	57.4+/-93.9	0,64,2139	47.0	46.0	47.0		265,265,265	3.8	1.0	11	dbSNP_98	47	465,8135	128.5+/-186.7	7,451,3842	yes	missense,missense,missense	RASSF7	NM_001143993.1,NM_001143994.1,NM_003475.3	27,27,27	7,515,5981	GG,GC,CC		5.407,1.4526,4.0674	probably-damaging,probably-damaging,probably-damaging	89/338,89/321,89/374	562219	529,12477	2203	4300	6503	SO:0001583	missense	8045	exon3			ACAGGGCCCAGCC	M91083	CCDS7702.1, CCDS44505.1, CCDS44506.1	11p15.5	2008-02-22	2008-02-22	2005-09-14	ENSG00000099849	ENSG00000099849			1166	protein-coding gene	gene with protein product		143023	"""chromosome 11 open reading frame 13"""	C11orf13		1339391	Standard	NM_001143993		Approved	HRC1, HRAS1	uc001lqc.3	Q02833	OTTHUMG00000132004	ENST00000397583.3:c.265C>G	11.37:g.562219C>G	ENSP00000380713:p.Pro89Ala	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_001143994	G5E9N9|Q3KP41|Q3KP42	Missense_Mutation	SNP	ENST00000397583.3	37	CCDS7702.1	264	0.12087912087912088	4	0.008130081300813009	23	0.06353591160220995	183	0.31993006993006995	54	0.0712401055408971	C	22.7	4.318867	0.81469	0.014526	0.05407	ENSG00000099849	ENST00000431809;ENST00000397582;ENST00000344375;ENST00000397583;ENST00000454668	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	3.81	3.81	0.43845	Ras-association (2);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.72894	2.215	0.09310	P	0.99999999876555	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.997	T	0.11792	-1.0573	9	0.30078	T	0.28	-3.5329	15.8892	0.79279	0.0:1.0:0.0:0.0	rs2242183;rs2242183	89;89;89	G5E9N9;Q02833;Q02833-2	.;RASF7_HUMAN;.	A	89	ENSP00000403068:P89A;ENSP00000380712:P89A;ENSP00000344226:P89A;ENSP00000380713:P89A;ENSP00000405606:P89A	ENSP00000344226:P89A	P	+	1	0	RASSF7	552219	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	4.717000	0.61923	1.975000	0.57531	0.561000	0.74099	CCC	C|0.930;G|0.070	0.070	strong		0.657	RASSF7-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254972.2	NM_003475	
OR52E8	390079	hgsc.bcm.edu	37	11	5878458	5878458	+	Silent	SNP	G	G	A	rs549924845	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5878458G>A	ENST00000537935.1	-	1	506	c.475C>T	c.(475-477)Ctg>Ttg	p.L159L	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	159						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(3)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCATGTACAGGCTCCTCAGG	0.507													G|||	10	0.00199681	0.0068	0.0	5008	,	,		18808	0.0		0.0	False		,,,				2504	0.001				p.L159L		Atlas-SNP	.											OR52E8,NS,carcinoma,0,1	OR52E8	54	1	0			c.C475T						scavenged	.						135.0	147.0	143.0					11																	5878458		2154	4296	6450	SO:0001819	synonymous_variant	390079	exon1			TGTACAGGCTCCT	BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269		"""GPCR / Class A : Olfactory receptors"""	15217	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily E, member 8 pseudogene"""				Standard	NM_001005168		Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.475C>T	11.37:g.5878458G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	194	4	0.0206186	NM_001005168	B9EH38	Silent	SNP	ENST00000537935.1	37	CCDS31400.1																																																																																			.	.	none		0.507	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401145.1	NM_001005168	
ATN1	1822	hgsc.bcm.edu	37	12	7047143	7047143	+	Silent	SNP	C	C	A	rs7969685	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	36	0	0	638	WXS	Illumina HiSeq	Phase_I	29	28	0.965517	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	
PRRC2C	23215	hgsc.bcm.edu	37	1	171486912	171486912	+	Missense_Mutation	SNP	G	G	A	rs10913157	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171486912G>A	ENST00000338920.4	+	6	940	c.703G>A	c.(703-705)Gct>Act	p.A235T	PRRC2C_ENST00000392078.3_Missense_Mutation_p.A237T|RNU6-773P_ENST00000364256.1_RNA|PRRC2C_ENST00000426496.2_Missense_Mutation_p.A235T|PRRC2C_ENST00000367742.3_Missense_Mutation_p.A237T|PRRC2C_ENST00000476522.1_3'UTR	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	235			A -> T (in dbSNP:rs10913157).		hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										TGGACAGCAGGCTGCTCTCGC	0.448													G|||	653	0.130391	0.0628	0.1081	5008	,	,		19825	0.2371		0.1342	False		,,,				2504	0.1237				p.A235T		Atlas-SNP	.											.	.	.	.	0			c.G703A						PASS	.	G	THR/ALA	330,4076	174.4+/-204.0	13,304,1886	80.0	76.0	78.0		703	2.3	0.4	1	dbSNP_120	78	1150,7450	236.9+/-269.0	82,986,3232	yes	missense	PRRC2C	NM_015172.3	58	95,1290,5118	AA,AG,GG		13.3721,7.4898,11.3794	benign	235/2818	171486912	1480,11526	2203	4300	6503	SO:0001583	missense	23215	exon6			CAGCAGGCTGCTC	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.703G>A	1.37:g.171486912G>A	ENSP00000343629:p.Ala235Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	138	94	0.681159	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	311	0.1423992673992674	24	0.04878048780487805	39	0.10773480662983426	142	0.24825174825174826	106	0.13984168865435356	G	12.38	1.921855	0.33908	0.074898	0.133721	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920	T;T;T;T	0.01854	4.6;4.6;4.6;4.6	5.38	2.34	0.29019	.	0.475392	0.17610	N	0.168118	T	0.00552	0.0018	N	0.08118	0	0.48696	P	3.069999999999462E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.48885	-0.8995	9	0.42905	T	0.14	.	11.0083	0.47649	0.145:0.6035:0.2515:0.0	rs10913157;rs52814203;rs58301963;rs10913157	235;237	Q9Y520-4;E7EPN9	.;.	T	237;235;235;237;235	ENSP00000375928:A237T;ENSP00000410219:A235T;ENSP00000356716:A237T;ENSP00000343629:A235T	ENSP00000343629:A235T	A	+	1	0	PRRC2C	169753536	0.998000	0.40836	0.431000	0.26735	0.964000	0.63967	1.014000	0.29950	0.183000	0.20059	-0.302000	0.09304	GCT	G|0.869;A|0.131	0.131	strong		0.448	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
WRN	7486	hgsc.bcm.edu	37	8	31024638	31024638	+	Silent	SNP	C	C	T	rs1801196	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:31024638C>T	ENST00000298139.5	+	34	4332	c.4083C>T	c.(4081-4083)agC>agT	p.S1361S	RP11-363L24.3_ENST00000521252.1_RNA	NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1361					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)		GTCCTGACAGCGGACTTCAAC	0.398			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				C|||	1370	0.273562	0.2632	0.2536	5008	,	,		17102	0.2282		0.2942	False		,,,				2504	0.3272				p.S1361S	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.C4083T						PASS	.	C		1189,3217	417.2+/-337.8	157,875,1171	124.0	108.0	113.0		4083	2.9	0.0	8	dbSNP_89	113	2480,6120	407.5+/-349.2	370,1740,2190	no	coding-synonymous	WRN	NM_000553.4		527,2615,3361	TT,TC,CC		28.8372,26.9859,28.2101		1361/1433	31024638	3669,9337	2203	4300	6503	SO:0001819	synonymous_variant	7486	exon34	Familial Cancer Database	WS, Adult Progeria	TGACAGCGGACTT		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.4083C>T	8.37:g.31024638C>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	310	172	0.554839	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	37	CCDS6082.1																																																																																			C|0.728;T|0.272	0.272	strong		0.398	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
MUC17	140453	hgsc.bcm.edu	37	7	100681917	100681917	+	Missense_Mutation	SNP	T	T	G	rs111633703	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681917T>G	ENST00000306151.4	+	3	7284	c.7220T>G	c.(7219-7221)aTg>aGg	p.M2407R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2407	59 X approximate tandem repeats.|Ser-rich.				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)					GTCAGCACCATGCCGGTGGTC	0.507																																					p.M2407R		Atlas-SNP	.											.	MUC17	804	.	0			c.T7220G						PASS	.						383.0	363.0	370.0					7																	100681917		2203	4300	6503	SO:0001583	missense	140453	exon3			GCACCATGCCGGT	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.7220T>G	7.37:g.100681917T>G	ENSP00000302716:p.Met2407Arg	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	326	16	0.0490798	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.009	-1.819708	0.00595	.	.	ENSG00000169876	ENST00000306151	T	0.02216	4.39	0.679	-1.36	0.09085	.	.	.	.	.	T	0.01156	0.0038	N	0.14661	0.345	0.09310	N	1	P	0.35139	0.486	B	0.22601	0.04	T	0.50311	-0.8843	9	0.17832	T	0.49	.	7.4277	0.27109	0.0:0.7775:0.0:0.2225	.	2407	Q685J3	MUC17_HUMAN	R	2407	ENSP00000302716:M2407R	ENSP00000302716:M2407R	M	+	2	0	MUC17	100468637	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.128000	0.10531	-1.293000	0.02362	-1.602000	0.00811	ATG	T|0.996;C|0.004	.	alt		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FLG	2312	hgsc.bcm.edu	37	1	152276626	152276626	+	Missense_Mutation	SNP	G	G	C	rs3126075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152276626G>C	ENST00000368799.1	-	3	10771	c.10736C>G	c.(10735-10737)aCg>aGg	p.T3579R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3579	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGATGGGACGTGGGGTGTCT	0.567									Ichthyosis				C|||	2393	0.477835	0.6074	0.4395	5008	,	,		15943	0.6498		0.1561	False		,,,				2504	0.4836				p.T3579R		Atlas-SNP	.											FLG,colon,carcinoma,-1,1	FLG	900	1	0			c.C10736G						scavenged	.	C	ARG/THR	1117,3267		429,259,1504	128.0	213.0	184.0		10736	-2.5	0.0	1	dbSNP_103	184	149,8435		32,85,4175	no	missense	FLG	NM_002016.1	71	461,344,5679	CC,CG,GG		1.7358,25.479,9.7625	benign	3579/4062	152276626	1266,11702	2192	4292	6484	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGACGTGGGGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10736C>G	1.37:g.152276626G>C	ENSP00000357789:p.Thr3579Arg	Somatic	483	3	0.00621118		WXS	Illumina HiSeq	Phase_I	413	46	0.11138	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	619	0.2834249084249084	182	0.3699186991869919	94	0.2596685082872928	272	0.4755244755244755	71	0.09366754617414248	C	1.750	-0.489390	0.04352	0.25479	0.017358	ENSG00000143631	ENST00000368799	T	0.01705	4.68	2.29	-2.52	0.06346	.	.	.	.	.	T	0.00178	0.0005	N	0.00538	-1.39	0.09310	N	1	B	0.14438	0.01	B	0.01281	0.0	T	0.26189	-1.0110	9	0.12430	T	0.62	.	4.0484	0.09783	0.0:0.2359:0.3609:0.4032	rs3126075;rs12072880;rs60733655	3579	P20930	FILA_HUMAN	R	3579	ENSP00000357789:T3579R	ENSP00000357789:T3579R	T	-	2	0	FLG	150543250	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.448000	0.00121	-0.991000	0.03476	-0.521000	0.04368	ACG	G|0.716;C|0.284	0.284	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC2	4583	hgsc.bcm.edu	37	11	1093344	1093344	+	Silent	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1093344G>T	ENST00000441003.2	+	30	5190	c.5163G>T	c.(5161-5163)ccG>ccT	p.P1721P	MUC2_ENST00000359061.5_Silent_p.P1688P|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Silent_p.P9P	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.P1688P(1)|p.P1721P(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)	ccccaaccccgacacccatct	0.642																																					p.P1721P		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - coding silent(2)	lung(2)	c.G5163T						PASS	.						231.0	269.0	256.0					11																	1093344		1975	3757	5732	SO:0001819	synonymous_variant	4583	exon30			AACCCCGACACCC	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.5163G>T	11.37:g.1093344G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	77	7	0.0909091	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389005	1389005	+	Missense_Mutation	SNP	T	T	C	rs71614970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	121	0	0		WXS	Illumina HiSeq	Phase_I	13	8	0.615385	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	
KCNH3	23416	hgsc.bcm.edu	37	12	49951528	49951528	+	Missense_Mutation	SNP	C	C	T	rs144397719	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:49951528C>T	ENST00000257981.6	+	15	3304	c.3044C>T	c.(3043-3045)cCt>cTt	p.P1015L	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	1015	Pro-rich.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						CCCAGCACCCCTGCCTCCCCT	0.662													C|||	37	0.00738818	0.0023	0.0159	5008	,	,		17441	0.0		0.0159	False		,,,				2504	0.0072				p.P1015L		Atlas-SNP	.											.	KCNH3	88	.	0			c.C3044T						PASS	.	C	LEU/PRO	30,4376	32.6+/-62.9	0,30,2173	32.0	33.0	33.0		3044	4.1	0.9	12	dbSNP_134	33	293,8307	104.4+/-165.4	6,281,4013	yes	missense	KCNH3	NM_012284.1	98	6,311,6186	TT,TC,CC		3.407,0.6809,2.4835	probably-damaging	1015/1084	49951528	323,12683	2203	4300	6503	SO:0001583	missense	23416	exon15			GCACCCCTGCCTC	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.3044C>T	12.37:g.49951528C>T	ENSP00000257981:p.Pro1015Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	37	CCDS8786.1	25	0.011446886446886446	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	13.07	2.127869	0.37533	0.006809	0.03407	ENSG00000135519	ENST00000257981	D	0.98777	-5.13	5.02	4.12	0.48240	.	0.000000	0.41396	D	0.000899	D	0.86851	0.6032	N	0.08118	0	0.80722	D	1	B	0.27498	0.18	B	0.19391	0.025	D	0.87871	0.2671	10	0.37606	T	0.19	.	11.2615	0.49085	0.0:0.8159:0.1841:0.0	.	1015	Q9ULD8	KCNH3_HUMAN	L	1015	ENSP00000257981:P1015L	ENSP00000257981:P1015L	P	+	2	0	KCNH3	48237795	0.397000	0.25270	0.941000	0.38009	0.990000	0.78478	3.676000	0.54612	1.319000	0.45190	0.561000	0.74099	CCT	C|0.982;T|0.018	0.018	strong		0.662	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
POPDC2	64091	hgsc.bcm.edu	37	3	119379186	119379186	+	Missense_Mutation	SNP	C	C	T	rs4688023	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:119379186C>T	ENST00000264231.3	-	1	251	c.85G>A	c.(85-87)Gtc>Atc	p.V29I	POPDC2_ENST00000468801.1_Missense_Mutation_p.V29I|POPDC2_ENST00000493094.1_Missense_Mutation_p.V29I|POPDC2_ENST00000538678.1_Missense_Mutation_p.V29I|POPDC2_ENST00000474523.1_Intron	NM_022135.2	NP_071418.2	Q9HBU9	POPD2_HUMAN	popeye domain containing 2	29			V -> I (in dbSNP:rs4688023).		regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sinoatrial node cell development (GO:0060931)	integral component of membrane (GO:0016021)	cAMP binding (GO:0030552)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.242)		AGGTGGTAGACAGCCCCTTCC	0.557													C|||	2012	0.401757	0.2935	0.4611	5008	,	,		15446	0.3323		0.4304	False		,,,				2504	0.5481				p.V29I		Atlas-SNP	.											.	POPDC2	36	.	0			c.G85A						PASS	.	C	ILE/VAL	1404,3002	459.6+/-352.3	226,952,1025	89.0	83.0	85.0		85	-5.6	0.5	3	dbSNP_111	85	3806,4794	537.6+/-383.2	840,2126,1334	yes	missense	POPDC2	NM_022135.2	29	1066,3078,2359	TT,TC,CC		44.2558,31.8656,40.0584	benign	29/365	119379186	5210,7796	2203	4300	6503	SO:0001583	missense	64091	exon1			GGTAGACAGCCCC	AF204173	CCDS2992.1	3q13.33	2004-01-15			ENSG00000121577	ENSG00000121577			17648	protein-coding gene	gene with protein product		605823				10882522	Standard	NM_022135		Approved	POP2	uc031sbc.1	Q9HBU9	OTTHUMG00000159438	ENST00000264231.3:c.85G>A	3.37:g.119379186C>T	ENSP00000264231:p.Val29Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	110	45	0.409091	NM_022135	Q86UE7	Missense_Mutation	SNP	ENST00000264231.3	37	CCDS2992.1	820	0.37545787545787546	130	0.26422764227642276	170	0.4696132596685083	197	0.34440559440559443	323	0.4261213720316623	C	1.924	-0.447524	0.04572	0.318656	0.442558	ENSG00000121577	ENST00000264231;ENST00000493094;ENST00000468801;ENST00000538678	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.66	-5.63	0.02474	.	1.223450	0.05589	N	0.574411	T	0.00012	0.0000	N	0.25060	0.705	0.40670	P	0.017796000000000034	B;B	0.18166	0.026;0.009	B;B	0.16289	0.015;0.01	T	0.42050	-0.9474	9	0.06236	T	0.91	.	10.9218	0.47169	0.1494:0.2332:0.5606:0.0568	rs4688023;rs52810037;rs59425816;rs4688023	29;29	Q9HBU9-2;Q9HBU9	.;POPD2_HUMAN	I	29	ENSP00000264231:V29I;ENSP00000417250:V29I;ENSP00000420715:V29I;ENSP00000438271:V29I	ENSP00000264231:V29I	V	-	1	0	POPDC2	120861876	0.000000	0.05858	0.478000	0.27316	0.573000	0.36030	-0.433000	0.06948	-0.985000	0.03503	-0.309000	0.09137	GTC	C|0.615;T|0.385	0.385	strong		0.557	POPDC2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355378.1	NM_022135	
PER2	8864	hgsc.bcm.edu	37	2	239157721	239157721	+	Silent	SNP	G	G	A	rs35873326	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:239157721G>A	ENST00000254657.3	-	22	3879	c.3600C>T	c.(3598-3600)ccC>ccT	p.P1200P	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	1200	CRY binding domain. {ECO:0000250|UniProtKB:Q9Z301}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		CGATGGCTGCGGGCAGGCCGC	0.562													G|||	244	0.048722	0.1505	0.0245	5008	,	,		12948	0.0		0.0209	False		,,,				2504	0.0072				p.P1200P		Atlas-SNP	.											.	PER2	85	.	0			c.C3600T						PASS	.	G		529,3877	239.0+/-250.2	28,473,1702	113.0	125.0	121.0		3600	0.0	0.0	2	dbSNP_126	121	152,8448	72.3+/-134.9	1,150,4149	no	coding-synonymous	PER2	NM_022817.2		29,623,5851	AA,AG,GG		1.7674,12.0064,5.236		1200/1256	239157721	681,12325	2203	4300	6503	SO:0001819	synonymous_variant	8864	exon22			GGCTGCGGGCAGG	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"""period (Drosophila) homolog 2"", ""period homolog 2 (Drosophila)"""			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.3600C>T	2.37:g.239157721G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	37	CCDS2528.1																																																																																			G|0.950;A|0.050	0.050	strong		0.562	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48597114	48597114	+	Silent	SNP	C	C	T	rs28498091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48597114C>T	ENST00000323776.5	+	7	1173	c.1011C>T	c.(1009-1011)caC>caT	p.H337H	MYCBPAP_ENST00000468821.1_3'UTR|MYCBPAP_ENST00000436259.2_Silent_p.H300H	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)			CCATCACTCACATCAGGAAGC	0.577													C|||	832	0.166134	0.3631	0.0937	5008	,	,		21016	0.0496		0.1421	False		,,,				2504	0.0961				p.H337H		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C1011T						PASS	.	C		1566,2840	487.6+/-361.0	285,996,922	74.0	62.0	66.0		1011	2.3	0.0	17	dbSNP_125	66	1235,7365	245.8+/-274.5	90,1055,3155	no	coding-synonymous	MYCBPAP	NM_032133.4		375,2051,4077	TT,TC,CC		14.3605,35.5424,21.5362		337/985	48597114	2801,10205	2203	4300	6503	SO:0001819	synonymous_variant	84073	exon7			CACTCACATCAGG	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.1011C>T	17.37:g.48597114C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_032133		Silent	SNP	ENST00000323776.5	37	CCDS32680.2																																																																																			C|0.802;T|0.198	0.198	strong		0.577	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
DMKN	93099	hgsc.bcm.edu	37	19	36002421	36002421	+	Silent	SNP	A	A	G	rs72334573	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36002421A>G	ENST00000339686.3	-	5	986	c.810T>C	c.(808-810)ggT>ggC	p.G270G	DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000418261.1_Silent_p.G270G|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000440396.1_Silent_p.G270G|DMKN_ENST00000424570.2_Silent_p.G270G|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000447113.2_Silent_p.G270G|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000451297.2_Silent_p.G270G|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000402589.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	270	Gly-rich.					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)			tgctgctgccaccactgctgc	0.652																																					p.G270G		Atlas-SNP	.											DMKN,colon,carcinoma,0,1	DMKN	116	1	0			c.T810C						PASS	.						30.0	23.0	25.0					19																	36002421		2166	4245	6411	SO:0001819	synonymous_variant	93099	exon5			GCTGCCACCACTG	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.810T>C	19.37:g.36002421A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	72	6	0.0833333	NM_001126058	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																																																																																			.	.	none		0.652	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461116	141461116	+	Silent	SNP	C	C	T	rs34457678	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:141461116C>T	ENST00000438773.2	-	2	490	c.357G>A	c.(355-357)ggG>ggA	p.G119G	TRAPPC9_ENST00000389327.3_Silent_p.G119G|TRAPPC9_ENST00000389328.4_Silent_p.G217G	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	119					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						CCCCCTGCAGCCCGAAGACAA	0.587													C|||	321	0.0640974	0.1036	0.072	5008	,	,		19353	0.004		0.0785	False		,,,				2504	0.0521				p.G217G		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.G651A						PASS	.	C	,	493,3913	224.6+/-240.7	28,437,1738	65.0	58.0	61.0		357,651	5.3	1.0	8	dbSNP_126	61	726,7874	176.9+/-226.6	34,658,3608	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	62,1095,5346	TT,TC,CC		8.4419,11.1893,9.3726	,	119/1149,217/1247	141461116	1219,11787	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon2			CTGCAGCCCGAAG	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.357G>A	8.37:g.141461116C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	130	62	0.476923	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1																																																																																			C|0.912;T|0.088	0.088	strong		0.587	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
SERPINE2	5270	hgsc.bcm.edu	37	2	224866576	224866576	+	Silent	SNP	C	C	A	rs12436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:224866576C>A	ENST00000258405.4	-	2	284	c.42G>T	c.(40-42)acG>acT	p.T14T	SERPINE2_ENST00000409840.3_Silent_p.T14T|SERPINE2_ENST00000447280.2_Silent_p.T26T|SERPINE2_ENST00000409304.1_Silent_p.T14T	NM_001136528.1|NM_006216.3	NP_001130000.1|NP_006207.1	P07093	GDN_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	14					blood coagulation (GO:0007596)|cerebellar granular layer morphogenesis (GO:0021683)|detection of mechanical stimulus involved in sensory perception (GO:0050974)|innervation (GO:0060384)|long-term synaptic potentiation (GO:0060291)|mating plug formation (GO:0042628)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein processing (GO:0010955)|negative regulation of proteolysis (GO:0045861)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of sodium ion transport (GO:0010766)|positive regulation of astrocyte differentiation (GO:0048711)|regulation of cell migration (GO:0030334)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of timing of cell differentiation (GO:0048505)|secretion by cell (GO:0032940)|secretory granule organization (GO:0033363)|seminal vesicle epithelium development (GO:0061108)	cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|neuromuscular junction (GO:0031594)|platelet alpha granule (GO:0031091)|vesicle (GO:0031982)	glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	17		Renal(207;0.025)|all_lung(227;0.0586)|Lung NSC(271;0.0682)|all_hematologic(139;0.0797)		Epithelial(121;5.68e-10)|all cancers(144;1.9e-07)|Lung(261;0.0088)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TGGAAGGCAGCGTCACAGAGG	0.478													C|||	1189	0.23742	0.351	0.1844	5008	,	,		17072	0.244		0.1123	False		,,,				2504	0.2434				p.T26T		Atlas-SNP	.											SERPINE2_ENST00000447280,NS,carcinoma,-1,2	SERPINE2	103	2	0			c.G78T						scavenged	.	C	,,	1318,3088	442.9+/-346.8	186,946,1071	100.0	112.0	108.0		42,78,42	-2.0	0.2	2	dbSNP_52	108	905,7695	202.4+/-245.7	41,823,3436	no	coding-synonymous,coding-synonymous,coding-synonymous	SERPINE2	NM_001136528.1,NM_001136530.1,NM_006216.3	,,	227,1769,4507	AA,AC,CC		10.5233,29.9138,17.0921	,,	14/398,26/410,14/399	224866576	2223,10783	2203	4300	6503	SO:0001819	synonymous_variant	5270	exon2			AGGCAGCGTCACA	M17783	CCDS2460.1, CCDS46525.1, CCDS46526.1	2q36.1	2014-02-18	2005-08-18		ENSG00000135919	ENSG00000135919		"""Serine (or cysteine) peptidase inhibitors"""	8951	protein-coding gene	gene with protein product	"""glial-derived nexin 1"""	177010	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2"""	PI7		7665170, 24172014	Standard	NM_006216		Approved	PN1, GDN, PNI, nexin	uc002vnu.2	P07093	OTTHUMG00000133163	ENST00000258405.4:c.42G>T	2.37:g.224866576C>A		Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_001136530	B2R6A4|B4DIF2|Q53S15|Q5D0C4	Silent	SNP	ENST00000258405.4	37	CCDS2460.1																																																																																			C|0.805;A|0.195	0.195	strong		0.478	SERPINE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256865.2	NM_006216	
B3GNTL1	146712	hgsc.bcm.edu	37	17	80992932	80992932	+	Silent	SNP	A	A	C	rs16940609	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80992932A>C	ENST00000320865.3	-	4	334	c.321T>G	c.(319-321)tcT>tcG	p.S107S	B3GNTL1_ENST00000576599.1_5'UTR|B3GNTL1_ENST00000571954.1_5'UTR	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	107							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)			AGCAAAGGTAAGACCCTGAGC	0.343													A|||	874	0.174521	0.1301	0.17	5008	,	,		16864	0.2093		0.2286	False		,,,				2504	0.1462				p.S107S		Atlas-SNP	.											.	B3GNTL1	40	.	0			c.T321G						PASS	.	A		609,3797	267.1+/-267.6	45,519,1639	102.0	103.0	103.0		321	4.2	1.0	17	dbSNP_123	103	2164,6436	370.3+/-335.8	277,1610,2413	no	coding-synonymous	B3GNTL1	NM_001009905.1		322,2129,4052	CC,CA,AA		25.1628,13.8221,21.3209		107/362	80992932	2773,10233	2203	4300	6503	SO:0001819	synonymous_variant	146712	exon4			AAGGTAAGACCCT	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.321T>G	17.37:g.80992932A>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_001009905	Q6GV30|Q8WUT3	Silent	SNP	ENST00000320865.3	37	CCDS32778.1																																																																																			A|0.794;C|0.206	0.206	strong		0.343	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
P4HA3	283208	hgsc.bcm.edu	37	11	73988167	73988167	+	Missense_Mutation	SNP	C	C	T	rs2282488	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:73988167C>T	ENST00000331597.4	-	9	1243	c.1198G>A	c.(1198-1200)Gac>Aac	p.D400N	P4HA3_ENST00000427714.2_Missense_Mutation_p.D400N	NM_182904.3	NP_878907.1	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha polypeptide III	400			D -> N (in dbSNP:rs2282488). {ECO:0000269|PubMed:15489334}.			endoplasmic reticulum (GO:0005783)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)|procollagen-proline 4-dioxygenase activity (GO:0004656)			NS(1)|biliary_tract(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(1)	15	Breast(11;2.31e-05)					AGTTTTGGGTCAACAGTGTCC	0.488													C|||	887	0.177117	0.0991	0.1225	5008	,	,		20531	0.2808		0.161	False		,,,				2504	0.2311				p.D400N		Atlas-SNP	.											.	P4HA3	43	.	0			c.G1198A						PASS	.	C	ASN/ASP	453,3947	217.4+/-235.8	19,415,1766	204.0	154.0	171.0		1198	5.2	1.0	11	dbSNP_100	171	1235,7351	248.7+/-276.3	94,1047,3152	yes	missense	P4HA3	NM_182904.3	23	113,1462,4918	TT,TC,CC		14.3839,10.2955,12.9986	probably-damaging	400/545	73988167	1688,11298	2200	4293	6493	SO:0001583	missense	283208	exon9			TTGGGTCAACAGT	AY327887	CCDS8230.1, CCDS73347.1	11q13	2008-12-09	2008-12-09			ENSG00000149380			30135	protein-coding gene	gene with protein product	"""collagen prolyl 4-hydroxylase alpha(III)"""	608987	"""procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III"""			14500733	Standard	XM_005273924		Approved	C-P4Halpha(III)	uc001ouz.3	Q7Z4N8		ENST00000331597.4:c.1198G>A	11.37:g.73988167C>T	ENSP00000332170:p.Asp400Asn	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	175	172	0.982857	NM_182904	A0AV13|B4DUD3|Q5EBL3|Q5JPA9	Missense_Mutation	SNP	ENST00000331597.4	37	CCDS8230.1	392	0.1794871794871795	46	0.09349593495934959	45	0.12430939226519337	169	0.29545454545454547	132	0.1741424802110818	C	12.61	1.989270	0.35131	0.102955	0.143839	ENSG00000149380	ENST00000331597;ENST00000427714	T;T	0.60548	1.0;0.18	5.2	5.2	0.72013	Prolyl 4-hydroxylase, alpha subunit (1);	0.193816	0.53938	D	0.000051	T	0.00012	0.0000	L	0.47190	1.495	0.36285	P	0.143988	P;B	0.52842	0.956;0.25	P;B	0.45071	0.468;0.067	T	0.21999	-1.0229	9	0.25751	T	0.34	-27.1451	11.8802	0.52571	0.0:0.8246:0.1753:0.0	rs2282488;rs52799645;rs58071724;rs2282488	400;400	B4DUD3;Q7Z4N8	.;P4HA3_HUMAN	N	400	ENSP00000332170:D400N;ENSP00000401749:D400N	ENSP00000332170:D400N	D	-	1	0	P4HA3	73665815	0.989000	0.36119	0.998000	0.56505	0.964000	0.63967	2.442000	0.44873	2.691000	0.91804	0.655000	0.94253	GAC	C|0.847;T|0.153	0.153	strong		0.488	P4HA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382988.1	NM_182904	
ZNF99	7652	hgsc.bcm.edu	37	19	22941617	22941617	+	Missense_Mutation	SNP	T	T	C	rs58653025	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22941617T>C	ENST00000596209.1	-	4	1184	c.1094A>G	c.(1093-1095)gAa>gGa	p.E365G	ZNF99_ENST00000397104.3_Missense_Mutation_p.E274G	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	365					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.E274G(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGGTTTCTCTTCAGTATGAAT	0.368													C|||	1087	0.217053	0.4206	0.1326	5008	,	,		19505	0.1746		0.1362	False		,,,				2504	0.1288				p.E365G		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	1	1	Substitution - Missense(1)	stomach(1)	c.A1094G						scavenged	.	C	GLY/GLU	1432,2612		250,932,840	69.0	77.0	74.0		821	0.3	0.0	19	dbSNP_129	74	994,7436		67,860,3288	no	missense	ZNF99	NM_001080409.2	98	317,1792,4128	CC,CT,TT		11.7912,35.4105,19.4485	benign	274/912	22941617	2426,10048	2022	4215	6237	SO:0001583	missense	7652	exon4			TTCTCTTCAGTAT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1094A>G	19.37:g.22941617T>C	ENSP00000472969:p.Glu365Gly	Somatic	62	2	0.0322581		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	454	0.2078754578754579	203	0.41260162601626016	54	0.14917127071823205	104	0.18181818181818182	93	0.12269129287598944	-	0.008	-1.877054	0.00537	0.354105	0.117912	ENSG00000213973	ENST00000397104	T	0.11821	2.74	1.46	0.302	0.15786	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00496	-1.435	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.44498	-0.9324	8	0.02654	T	1	.	6.1729	0.20427	0.0:0.6931:0.0:0.3069	rs58653025	274	A8MXY4	ZNF99_HUMAN	G	274	ENSP00000380293:E274G	ENSP00000380293:E274G	E	-	2	0	ZNF99	22733457	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.130000	0.10498	-0.501000	0.06605	-0.526000	0.04340	GAA	T|0.811;C|0.189	0.189	strong		0.368	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
ITSN2	50618	hgsc.bcm.edu	37	2	24426581	24426581	+	Missense_Mutation	SNP	G	G	A	rs140804905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:24426581G>A	ENST00000355123.4	-	40	5451	c.5008C>T	c.(5008-5010)Cgc>Tgc	p.R1670C	ITSN2_ENST00000361999.3_Missense_Mutation_p.R1643C|AC008073.9_ENST00000429717.1_RNA	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1670					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)					AGCAGTCGGCGGGTCATAGGG	0.507													G|||	4	0.000798722	0.0023	0.0	5008	,	,		16966	0.0		0.001	False		,,,				2504	0.0				p.R1670C		Atlas-SNP	.											.	ITSN2	224	.	0			c.C5008T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	82.0	83.0	83.0		5008,4927	4.5	1.0	2	dbSNP_134	83	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ITSN2	NM_006277.2,NM_019595.3	180,180	0,6,6497	AA,AG,GG		0.0465,0.0454,0.0461	probably-damaging,probably-damaging	1670/1698,1643/1671	24426581	6,13000	2203	4300	6503	SO:0001583	missense	50618	exon40			GTCGGCGGGTCAT	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.5008C>T	2.37:g.24426581G>A	ENSP00000347244:p.Arg1670Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	5	0.0022893772893772895	4	0.008130081300813009	0	0.0	0	0.0	1	0.0013192612137203166	G	16.42	3.118003	0.56505	4.54E-4	4.65E-4	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868	T;T;T	0.67523	-0.27;-0.27;-0.27	5.46	4.52	0.55395	C2 calcium/lipid-binding domain, CaLB (1);	0.412335	0.15639	U	0.251972	T	0.69611	0.3130	L	0.54323	1.7	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;P	0.65773	0.938;0.869	T	0.73877	-0.3844	10	0.87932	D	0	.	11.956	0.52981	0.0:0.0:0.6677:0.3323	.	1643;1670	Q9NZM3-2;Q9NZM3	.;ITSN2_HUMAN	C	1643;1670;1643	ENSP00000354561:R1643C;ENSP00000347244:R1670C;ENSP00000370250:R1643C	ENSP00000347244:R1670C	R	-	1	0	ITSN2	24280085	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.498000	0.60373	2.735000	0.93741	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.507	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
CCND1	595	hgsc.bcm.edu	37	11	69457987	69457987	+	Silent	SNP	C	C	T	rs371689281		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:69457987C>T	ENST00000227507.2	+	2	614	c.387C>T	c.(385-387)gaC>gaT	p.D129D	CCND1_ENST00000536559.1_Intron	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	129	Cyclin N-terminal.				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)	TCTACACCGACAACTCCATCC	0.687			T	"""IGH@, FSTL3"""	"""CLL, B-ALL, breast"""					Multiple Myeloma(6;0.086)																											p.D129D	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"""L, E"""	.	CCND1	107	.	0			c.C387T						PASS	.	C		0,4378		0,0,2189	38.0	36.0	37.0		387	3.7	1.0	11		37	2,8578		0,2,4288	no	coding-synonymous	CCND1	NM_053056.2		0,2,6477	TT,TC,CC		0.0233,0.0,0.0154		129/296	69457987	2,12956	2189	4290	6479	SO:0001819	synonymous_variant	595	exon2			CACCGACAACTCC	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.387C>T	11.37:g.69457987C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_053056	Q6LEF0	Silent	SNP	ENST00000227507.2	37	CCDS8191.1																																																																																			.	.	weak		0.687	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056	
SMTN	6525	hgsc.bcm.edu	37	22	31487146	31487146	+	Silent	SNP	C	C	T	rs143316150		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:31487146C>T	ENST00000347557.2	+	10	1355	c.1137C>T	c.(1135-1137)agC>agT	p.S379S	SMTN_ENST00000333137.7_Silent_p.S379S|SMTN_ENST00000404574.1_5'Flank|SMTN_ENST00000358743.1_Silent_p.S379S	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	379					muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						CCTCCTCCAGCGGCTCCTCCT	0.697																																					p.S435S		Atlas-SNP	.											SMTN_ENST00000404496,NS,carcinoma,0,3	SMTN	219	3	0			c.C1305T						scavenged	.	C	,,,,	0,4406		0,0,2203	31.0	36.0	35.0		1299,1305,1137,1137,1137	-6.1	0.0	22	dbSNP_134	35	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SMTN	NM_001207017.1,NM_001207018.1,NM_006932.4,NM_134269.2,NM_134270.2	,,,,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,,,,	433/1003,435/972,379/918,379/916,379/941	31487146	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	6525	exon9			CTCCAGCGGCTCC	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.1137C>T	22.37:g.31487146C>T		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	208	4	0.0192308	NM_001207018	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Silent	SNP	ENST00000347557.2	37	CCDS13886.1	.	.	.	.	.	.	.	.	.	.	C	5.911	0.352092	0.11182	0.0	1.16E-4	ENSG00000183963	ENST00000329852	.	.	.	5.1	-6.13	0.02118	.	.	.	.	.	T	0.24736	0.0600	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.40627	-0.9553	5	0.72032	D	0.01	3.8243	0.8931	0.01258	0.1774:0.275:0.2592:0.2885	.	.	.	.	W	379	.	ENSP00000329393:R379W	R	+	1	2	SMTN	29817146	0.000000	0.05858	0.010000	0.14722	0.874000	0.50279	-0.802000	0.04545	-0.864000	0.04078	-0.658000	0.03865	CGG	C|1.000;T|0.000	0.000	weak		0.697	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270	
KCNH2	3757	hgsc.bcm.edu	37	7	150645534	150645534	+	Missense_Mutation	SNP	T	T	G	rs1805123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	46	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	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	
CEP170	9859	hgsc.bcm.edu	37	1	243329211	243329211	+	Missense_Mutation	SNP	G	G	T	rs2728430		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:243329211G>T	ENST00000366542.1	-	13	2102	c.2051C>A	c.(2050-2052)aCa>aAa	p.T684K	CEP170_ENST00000366544.1_Missense_Mutation_p.T586K|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Missense_Mutation_p.T586K	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	221	0	0		WXS	Illumina HiSeq	Phase_I	329	42	0.12766	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	
COQ4	51117	hgsc.bcm.edu	37	9	131094453	131094453	+	Missense_Mutation	SNP	G	G	A	rs34043652	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:131094453G>A	ENST00000300452.3	+	5	747	c.424G>A	c.(424-426)Gca>Aca	p.A142T	COQ4_ENST00000461102.1_3'UTR	NM_016035.3	NP_057119			coenzyme Q4											endometrium(4)|large_intestine(1)|lung(4)	9						AGACACCCGAGCACCCACCCG	0.602													G|||	46	0.0091853	0.0015	0.0014	5008	,	,		18056	0.0		0.003	False		,,,				2504	0.0409				p.A142T		Atlas-SNP	.											.	COQ4	20	.	0			c.G424A						PASS	.	G	THR/ALA	1,4403		0,1,2201	75.0	50.0	58.0		424	5.8	0.7	9	dbSNP_126	58	32,8566		0,32,4267	yes	missense	COQ4	NM_016035.3	58	0,33,6468	AA,AG,GG		0.3722,0.0227,0.2538	probably-damaging	142/266	131094453	33,12969	2202	4299	6501	SO:0001583	missense	51117	exon5			ACCCGAGCACCCA	AF151850	CCDS6898.1	9q34.2	2013-10-18	2013-10-18		ENSG00000167113	ENSG00000167113			19693	protein-coding gene	gene with protein product		612898	"""coenzyme Q4 homolog (yeast)"", ""coenzyme Q4 homolog (S. cerevisiae)"""			11469793, 18474229	Standard	NM_016035		Approved	CGI-92	uc004bur.4	Q9Y3A0	OTTHUMG00000020743	ENST00000300452.3:c.424G>A	9.37:g.131094453G>A	ENSP00000300452:p.Ala142Thr	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_016035		Missense_Mutation	SNP	ENST00000300452.3	37	CCDS6898.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	13.72	2.321269	0.41096	2.27E-4	0.003722	ENSG00000167113	ENST00000300452	T	0.46063	0.88	5.85	5.85	0.93711	.	0.267657	0.42682	D	0.000670	T	0.47135	0.1429	M	0.61703	1.905	0.32752	N	0.506265	D	0.58268	0.982	P	0.55055	0.767	T	0.54016	-0.8356	10	0.14252	T	0.57	-14.8437	6.6755	0.23092	0.1447:0.1546:0.7007:0.0	rs34043652;rs34043652	142	Q9Y3A0	COQ4_HUMAN	T	142	ENSP00000300452:A142T	ENSP00000300452:A142T	A	+	1	0	COQ4	130134274	1.000000	0.71417	0.694000	0.30210	0.972000	0.66771	4.765000	0.62271	2.771000	0.95319	0.561000	0.74099	GCA	G|0.995;A|0.005	0.005	strong		0.602	COQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054427.1	NM_016035	
MUC17	140453	hgsc.bcm.edu	37	7	100680939	100680939	+	Missense_Mutation	SNP	C	C	A	rs36120435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680939C>A	ENST00000306151.4	+	3	6306	c.6242C>A	c.(6241-6243)gCc>gAc	p.A2081D		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2081	59 X approximate tandem repeats.|Ser-rich.				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)					TCTACTGAAGCCAGTTCATCT	0.498													C|||	612	0.122204	0.1997	0.0821	5008	,	,		26174	0.0665		0.1173	False		,,,				2504	0.1084				p.A2081D		Atlas-SNP	.											.	MUC17	804	.	0			c.C6242A						PASS	.	C	ASP/ALA	775,3631	314.9+/-293.9	64,647,1492	172.0	170.0	171.0		6242	-1.2	0.0	7	dbSNP_126	171	983,7617	213.1+/-253.2	56,871,3373	no	missense	MUC17	NM_001040105.1	126	120,1518,4865	AA,AC,CC		11.4302,17.5897,13.5168	benign	2081/4494	100680939	1758,11248	2203	4300	6503	SO:0001583	missense	140453	exon3			CTGAAGCCAGTTC	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.6242C>A	7.37:g.100680939C>A	ENSP00000302716:p.Ala2081Asp	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	220	0.10073260073260074	70	0.14227642276422764	34	0.09392265193370165	29	0.050699300699300696	87	0.11477572559366754	c	3.462	-0.109758	0.06924	0.175897	0.114302	ENSG00000169876	ENST00000306151	T	0.02787	4.16	0.589	-1.18	0.09617	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.49483	P	2.0900000000001473E-4	B	0.14438	0.01	B	0.08055	0.003	T	0.46735	-0.9170	8	0.21540	T	0.41	.	5.2138	0.15332	0.3336:0.6663:0.0:0.0	.	2081	Q685J3	MUC17_HUMAN	D	2081	ENSP00000302716:A2081D	ENSP00000302716:A2081D	A	+	2	0	MUC17	100467659	0.000000	0.05858	0.003000	0.11579	0.020000	0.10135	-0.240000	0.08952	-0.374000	0.07967	0.134000	0.15878	GCC	C|0.880;A|0.120	0.120	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
DHRS4	10901	hgsc.bcm.edu	37	14	24423007	24423007	+	Missense_Mutation	SNP	G	G	A	rs17099455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24423007G>A	ENST00000313250.5	+	1	213	c.10G>A	c.(10-12)Gcg>Acg	p.A4T	DHRS4_ENST00000397075.3_Missense_Mutation_p.A4T|DHRS4_ENST00000558581.1_Missense_Mutation_p.A4T|DHRS4_ENST00000421831.1_5'UTR|DHRS4_ENST00000397073.2_5'UTR|DHRS4_ENST00000308178.8_5'UTR|DHRS4_ENST00000559632.1_Missense_Mutation_p.A4T|DHRS4_ENST00000543741.2_Missense_Mutation_p.A4T|DHRS4_ENST00000558263.1_Missense_Mutation_p.A4T|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000382761.3_5'UTR|DHRS4_ENST00000397074.3_Missense_Mutation_p.A4T	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	4					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CATGCACAAGGCGGGGCTGCT	0.662													.|||	988	0.197284	0.6135	0.1023	5008	,	,		16663	0.0099		0.0517	False		,,,				2504	0.045				p.A4T		Atlas-SNP	.											.	DHRS4	22	.	0			c.G10A						PASS	.	A	THR/ALA	2359,2047		647,1065,491	49.0	54.0	52.0		10	1.8	0.0	14	dbSNP_123	52	456,8144		13,430,3857	yes	missense	DHRS4	NM_021004.2	58	660,1495,4348	AA,AG,GG		5.3023,46.4594,21.6439	benign	4/279	24423007	2815,10191	2203	4300	6503	SO:0001583	missense	10901	exon1			CACAAGGCGGGGC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.10G>A	14.37:g.24423007G>A	ENSP00000326219:p.Ala4Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	393	0.17994505494505494	312	0.6341463414634146	36	0.09944751381215469	8	0.013986013986013986	37	0.048812664907651716	.	10.41	1.343665	0.24339	0.535406	0.053023	ENSG00000157326	ENST00000313250;ENST00000397075;ENST00000397074;ENST00000543741	D;T;T;T	0.84298	-1.83;1.85;0.42;1.63	2.71	1.81	0.25067	.	0.882556	0.09474	N	0.797291	T	0.00012	0.0000	L	0.60455	1.87	0.48571	P	3.300000000000525E-4	B;B;B;B;B;B	0.16603	0.011;0.001;0.0;0.018;0.003;0.001	B;B;B;B;B;B	0.17722	0.009;0.003;0.002;0.019;0.003;0.002	T	0.44390	-0.9331	9	0.42905	T	0.14	.	5.8712	0.18805	0.149:0.0:0.851:0.0	rs17099455;rs52815329;rs17099455	4;4;4;4;4;4	Q9BTZ2-5;F5GWZ1;Q9BTZ2-2;Q9BTZ2-7;Q9BTZ2-4;Q9BTZ2	.;.;.;.;.;DHRS4_HUMAN	T	4	ENSP00000326219:A4T;ENSP00000380265:A4T;ENSP00000380264:A4T;ENSP00000440508:A4T	ENSP00000326219:A4T	A	+	1	0	DHRS4	23492847	0.004000	0.15560	0.001000	0.08648	0.005000	0.04900	1.198000	0.32223	0.744000	0.32741	-0.346000	0.07831	GCG	G|0.795;A|0.205	0.205	strong		0.662	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
ALS2CR12	130540	hgsc.bcm.edu	37	2	202154200	202154200	+	Silent	SNP	C	C	T	rs17468277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:202154200C>T	ENST00000286190.5	-	13	1237	c.1191G>A	c.(1189-1191)acG>acA	p.T397T	ALS2CR12_ENST00000439709.1_Silent_p.T374T|ALS2CR12_ENST00000405148.2_Silent_p.T397T|ALS2CR12_ENST00000392257.3_Silent_p.T374T			Q96Q35	AL2SB_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 12	397					regulation of GTPase activity (GO:0043087)	outer dense fiber (GO:0001520)|sperm fibrous sheath (GO:0035686)|sperm flagellum (GO:0036126)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)	21						TGTTCTCTTCCGTCAGGATCT	0.423													C|||	254	0.0507188	0.0431	0.0749	5008	,	,		22722	0.001		0.1203	False		,,,				2504	0.0235				p.T397T		Atlas-SNP	.											.	ALS2CR12	54	.	0			c.G1191A						PASS	.	C	,	294,4112	161.1+/-193.3	18,258,1927	149.0	148.0	148.0		1122,1191	-7.1	0.0	2	dbSNP_123	148	1110,7490	230.8+/-265.0	67,976,3257	no	coding-synonymous,coding-synonymous	ALS2CR12	NM_001127391.1,NM_139163.2	,	85,1234,5184	TT,TC,CC		12.907,6.6727,10.795	,	374/423,397/446	202154200	1404,11602	2203	4300	6503	SO:0001819	synonymous_variant	130540	exon14			CTCTTCCGTCAGG	AB053314	CCDS2346.1, CCDS46488.1	2q33.1	2009-10-06			ENSG00000155749	ENSG00000155749			14439	protein-coding gene	gene with protein product							Standard	XM_006712272		Approved		uc002uya.4	Q96Q35	OTTHUMG00000132824	ENST00000286190.5:c.1191G>A	2.37:g.202154200C>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	139	40	0.28777	NM_139163	G5E9S3|Q53TT6|Q8N1B6	Silent	SNP	ENST00000286190.5	37	CCDS2346.1																																																																																			C|0.910;T|0.090	0.090	strong		0.423	ALS2CR12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256286.1	NM_139163	
CSHL1	1444	hgsc.bcm.edu	37	17	61987576	61987576	+	Silent	SNP	G	G	A	rs2246207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:61987576G>A	ENST00000309894.5	-	4	416	c.417C>T	c.(415-417)agC>agT	p.S139S	CSHL1_ENST00000346606.6_Silent_p.S45S|CSHL1_ENST00000438387.2_Silent_p.S56S|CSHL1_ENST00000450719.3_Silent_p.S45S|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000259003.10_Silent_p.S77S|CSHL1_ENST00000392824.4_3'UTR|CSHL1_ENST00000561003.1_Silent_p.S56S	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	139						extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						GATAGTCATCGCTGTCCGAGG	0.587													G|||	1952	0.389776	0.4637	0.3501	5008	,	,		19398	0.4196		0.4225	False		,,,				2504	0.2536				p.S139S		Atlas-SNP	.											CSHL1_ENST00000561003,NS,adenoma,0,2	CSHL1	42	2	0			c.C417T						scavenged	.	G	,,,	2165,2241	583.4+/-385.8	538,1089,576	88.0	76.0	80.0		135,417,168,348	-4.3	0.0	17	dbSNP_100	80	3571,5029	517.8+/-379.1	751,2069,1480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSHL1	NM_001318.2,NM_022579.1,NM_022580.1,NM_022581.1	,,,	1289,3158,2056	AA,AG,GG		41.5233,49.1375,44.1027	,,,	45/129,139/223,56/140,116/200	61987576	5736,7270	2203	4300	6503	SO:0001819	synonymous_variant	1444	exon4			GTCATCGCTGTCC	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.417C>T	17.37:g.61987576G>A		Somatic	591	4	0.00676819		WXS	Illumina HiSeq	Phase_I	436	165	0.37844	NM_022579	D3DU26|D3DU27|Q0VDB2	Silent	SNP	ENST00000309894.5	37	CCDS11652.1																																																																																			G|0.566;A|0.434	0.434	strong		0.587	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579	
CUEDC2	79004	hgsc.bcm.edu	37	10	104184081	104184081	+	Silent	SNP	G	G	A	rs1044476	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:104184081G>A	ENST00000369937.4	-	5	496	c.351C>T	c.(349-351)ccC>ccT	p.P117P	CUEDC2_ENST00000465409.1_5'Flank|PSD_ENST00000492902.2_5'Flank	NM_024040.2	NP_076945.2	Q9H467	CUED2_HUMAN	CUE domain containing 2	117						cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)		p.P117P(1)		autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(1)|stomach(1)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.122)		Epithelial(162;9.17e-09)|all cancers(201;2.16e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		TGAGCATTTCGGGCCGCTGCA	0.582													G|||	416	0.0830671	0.0121	0.0821	5008	,	,		17467	0.0923		0.1461	False		,,,				2504	0.1053				p.P117P		Atlas-SNP	.											CUEDC2,NS,carcinoma,0,1	CUEDC2	22	1	1	Substitution - coding silent(1)	stomach(1)	c.C351T						PASS	.	G		127,3617		1,125,1746	77.0	81.0	80.0		351	-7.9	0.7	10	dbSNP_86	80	992,7210		61,870,3170	no	coding-synonymous	CUEDC2	NM_024040.2		62,995,4916	AA,AG,GG		12.0946,3.3921,9.3672		117/288	104184081	1119,10827	1872	4101	5973	SO:0001819	synonymous_variant	79004	exon5			CATTTCGGGCCGC	BC000262	CCDS41566.1	10q24.32	2008-10-23	2004-03-04	2004-03-05	ENSG00000107874	ENSG00000107874			28352	protein-coding gene	gene with protein product		614142	"""chromosome 10 open reading frame 66"""	C10orf66		12477932	Standard	NM_024040		Approved	MGC2491	uc001kvn.2	Q9H467	OTTHUMG00000018958	ENST00000369937.4:c.351C>T	10.37:g.104184081G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	83	79	0.951807	NM_024040	D3DR88|Q9BWG8	Silent	SNP	ENST00000369937.4	37	CCDS41566.1																																																																																			G|0.898;A|0.102	0.102	strong		0.582	CUEDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050060.1	NM_024040	
FER	2241	hgsc.bcm.edu	37	5	108133967	108133967	+	Silent	SNP	A	A	G	rs2229085	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:108133967A>G	ENST00000281092.4	+	3	468	c.84A>G	c.(82-84)gtA>gtG	p.V28V	FER_ENST00000536402.1_Silent_p.V28V|FER_ENST00000502752.1_3'UTR|FER_ENST00000438717.2_5'UTR	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	28	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.|Important for interaction with membranes containing phosphoinositides.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TGGAAACAGTAAAGAAATTTA	0.363													A|||	891	0.177915	0.2988	0.17	5008	,	,		17170	0.0575		0.167	False		,,,				2504	0.1554				p.V28V	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.A84G						PASS	.	A		1242,3162	427.0+/-341.4	179,884,1139	87.0	90.0	89.0		84	1.1	1.0	5	dbSNP_98	89	1534,7066	288.9+/-299.0	135,1264,2901	no	coding-synonymous	FER	NM_005246.2		314,2148,4040	GG,GA,AA		17.8372,28.2016,21.3473		28/823	108133967	2776,10228	2202	4300	6502	SO:0001819	synonymous_variant	2241	exon3			AACAGTAAAGAAA	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	3655	protein-coding gene	gene with protein product	"""phosphoprotein NCP94"", ""protein phosphatase 1, regulatory subunit 74"""	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.84A>G	5.37:g.108133967A>G		Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	288	287	0.996528	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			A|0.801;G|0.199	0.199	strong		0.363	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
AOX1	316	hgsc.bcm.edu	37	2	201526330	201526330	+	Missense_Mutation	SNP	A	A	G	rs55754655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:201526330A>G	ENST00000374700.2	+	30	3645	c.3404A>G	c.(3403-3405)aAc>aGc	p.N1135S	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	1135			N -> S (increases homodimerization and turnover number with phenanthridine as substrate; nearly no effect on kinetic parameters with benzaldehyde, phtalazine and chloroquinazolinone as substrate; dbSNP:rs55754655). {ECO:0000269|PubMed:22279051}.		inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)			breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	GAAAGCATTAACCTTTCAGCT	0.408													G|||	550	0.109824	0.2678	0.072	5008	,	,		22079	0.003		0.1213	False		,,,				2504	0.0215				p.N1135S		Atlas-SNP	.											.	AOX1	152	.	0			c.A3404G						PASS	.	G	SER/ASN	1137,3269	715.8+/-408.5	161,815,1227	141.0	134.0	136.0		3404	5.3	0.3	2	dbSNP_129	136	1116,7484	767.4+/-407.6	71,974,3255	yes	missense	AOX1	NM_001159.3	46	232,1789,4482	GG,GA,AA		12.9767,25.8057,17.3228	benign	1135/1339	201526330	2253,10753	2203	4300	6503	SO:0001583	missense	316	exon30			GCATTAACCTTTC	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.3404A>G	2.37:g.201526330A>G	ENSP00000363832:p.Asn1135Ser	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	99	23	0.232323	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	37	CCDS33360.1	233	0.10668498168498168	125	0.2540650406504065	21	0.058011049723756904	2	0.0034965034965034965	85	0.11213720316622691	G	6.479	0.456545	0.12283	0.258057	0.129767	ENSG00000138356	ENST00000374700;ENST00000260930	T;T	0.35421	1.31;1.31	5.35	5.35	0.76521	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.167012	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00760	-1.21	0.51233	P	9.00000000000345E-5	B	0.02656	0.0	B	0.06405	0.002	T	0.23583	-1.0184	9	0.02654	T	1	-36.2148	14.7385	0.69434	0.0692:0.0:0.9308:0.0	rs55754655;rs60972007;rs61737010	1135	Q06278	ADO_HUMAN	S	1135;21	ENSP00000363832:N1135S;ENSP00000260930:N21S	ENSP00000260930:N21S	N	+	2	0	AOX1	201234575	1.000000	0.71417	0.251000	0.24312	0.054000	0.15201	3.173000	0.50839	1.644000	0.50603	-0.119000	0.15052	AAC	A|0.848;G|0.152	0.152	strong		0.408	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
CNGA2	1260	hgsc.bcm.edu	37	X	150909307	150909307	+	Missense_Mutation	SNP	G	G	T	rs35350051	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:150909307G>T	ENST00000329903.4	+	4	449	c.416G>T	c.(415-417)tGg>tTg	p.W139L		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	139			W -> L (in dbSNP:rs35350051).		phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					GCTGGGGATTGGTACTACTGC	0.552													G|||	457	0.12106	0.0068	0.1081	3775	,	,		13777	0.1974		0.0954	False		,,,				2504	0.0798				p.W139L		Atlas-SNP	.											.	CNGA2	136	.	0			c.G416T						PASS	.	G	LEU/TRP	108,3727		1,91,15,1540,556	212.0	183.0	193.0		416	5.4	1.0	X	dbSNP_126	193	986,5742		59,595,273,1774,1599	yes	missense	CNGA2	NM_005140.1	61	60,686,288,3314,2155	TT,TG,T,GG,G		14.6552,2.8162,10.3569	benign	139/665	150909307	1094,9469	2203	4300	6503	SO:0001583	missense	1260	exon5			GGGATTGGTACTA	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.416G>T	X.37:g.150909307G>T	ENSP00000328478:p.Trp139Leu	Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	196	0.11814345991561181	5	0.01020408163265306	25	0.07352941176470588	58	0.11372549019607843	50	0.06868131868131869	G	1.518	-0.547556	0.04024	0.028162	0.146552	ENSG00000183862	ENST00000329903	D	0.97161	-4.27	5.44	5.44	0.79542	.	0.329033	0.34133	N	0.004228	T	0.05273	0.0140	N	0.04724	-0.175	0.32707	P	0.512141	B	0.06786	0.001	B	0.06405	0.002	T	0.68678	-0.5345	9	0.09843	T	0.71	.	15.5522	0.76161	0.0:0.0:1.0:0.0	rs35350051	139	Q16280	CNGA2_HUMAN	L	139	ENSP00000328478:W139L	ENSP00000328478:W139L	W	+	2	0	CNGA2	150659963	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	2.216000	0.42871	2.267000	0.75376	0.544000	0.68410	TGG	G|0.898;T|0.102	0.102	strong		0.552	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140	
MBD3L3	653657	hgsc.bcm.edu	37	19	7056590	7056590	+	Missense_Mutation	SNP	C	C	T	rs201052967	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:7056590C>T	ENST00000333843.4	-	2	404	c.370G>A	c.(370-372)Ggt>Agt	p.G124S		NM_001164425.1	NP_001157897.1	A6NE82	MB3L3_HUMAN	methyl-CpG binding domain protein 3-like 3	124					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					central_nervous_system(1)|lung(5)|stomach(1)	7						AGAGATTCACCGGCCGTCCCC	0.642																																					p.G124S		Atlas-SNP	.											MBD3L3,NS,haematopoietic_neoplasm,0,1	MBD3L3	12	1	0			c.G370A						scavenged	.						37.0	47.0	44.0					19																	7056590		692	1591	2283	SO:0001583	missense	653657	exon2			ATTCACCGGCCGT		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.370G>A	19.37:g.7056590C>T	ENSP00000333183:p.Gly124Ser	Somatic	349	6	0.017192		WXS	Illumina HiSeq	Phase_I	314	57	0.181529	NM_001164425		Missense_Mutation	SNP	ENST00000333843.4	37	CCDS45944.1	.	.	.	.	.	.	.	.	.	.	.	6.048	0.377169	0.11466	.	.	ENSG00000182315	ENST00000333843	.	.	.	0.742	0.742	0.18341	.	.	.	.	.	T	0.39937	0.1097	L	0.54323	1.7	0.80722	P	0.0	.	.	.	.	.	.	T	0.42155	-0.9468	5	0.13853	T	0.58	-14.6112	4.8637	0.13598	0.0:1.0:0.0:0.0	.	.	.	.	S	124	.	ENSP00000333183:G124S	G	-	1	0	MBD3L3	7007590	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.055000	0.14229	0.683000	0.31428	0.392000	0.25879	GGT	.	.	weak		0.642	MBD3L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458500.1	NM_001164425	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561316	32561316	+	Nonsense_Mutation	SNP	G	G	T	rs200628183	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:32561316G>T	ENST00000345122.3	+	2	1756	c.1441G>T	c.(1441-1443)Gaa>Taa	p.E481*	ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.E481*|ARHGAP5_ENST00000396582.2_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	481	FF 3.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		GCATCAGCGAGAAATAGTTGA	0.373																																					p.E481X	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											ARHGAP5,uveal_tract,malignant_melanoma,0,1	ARHGAP5	166	1	0			c.G1441T						PASS	.						69.0	70.0	70.0					14																	32561316		2203	4297	6500	SO:0001587	stop_gained	394	exon2			CAGCGAGAAATAG	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1441G>T	14.37:g.32561316G>T	ENSP00000371897:p.Glu481*	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	130	7	0.0538462	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Nonsense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	G	40	8.091676	0.98648	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	.	.	.	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	20.547	0.99278	0.0:0.0:1.0:0.0	.	.	.	.	X	481	.	ENSP00000371897:E481X	E	+	1	0	ARHGAP5	31631067	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.850000	0.98022	0.650000	0.86243	GAA	G|0.996;T|0.004	0.004	strong		0.373	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
TPP1	1200	hgsc.bcm.edu	37	11	6637577	6637577	+	Silent	SNP	G	G	A	rs35706972	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6637577G>A	ENST00000299427.6	-	8	1104	c.1044C>T	c.(1042-1044)gcC>gcT	p.A348A	TPP1_ENST00000533371.1_Silent_p.A105A|TPP1_ENST00000534644.1_5'Flank|RP11-732A19.9_ENST00000545572.1_RNA	NM_000391.3	NP_000382.3	P49638	TTPA_HUMAN	tripeptidyl peptidase I	0					embryonic placenta development (GO:0001892)|intermembrane transport (GO:0046909)|intracellular pH reduction (GO:0051452)|lipid metabolic process (GO:0006629)|negative regulation of cell death (GO:0060548)|negative regulation of establishment of blood-brain barrier (GO:0090212)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|response to toxic substance (GO:0009636)|transport (GO:0006810)|vitamin E metabolic process (GO:0042360)|vitamin transport (GO:0051180)	cytosol (GO:0005829)|late endosome (GO:0005770)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|transporter activity (GO:0005215)|vitamin E binding (GO:0008431)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;3.45e-09)|BRCA - Breast invasive adenocarcinoma(625;0.131)	Vitamin E(DB00163)	GACCCCGAGCGGCAGCCTTCA	0.567													G|||	26	0.00519169	0.0	0.0058	5008	,	,		17941	0.0		0.0129	False		,,,				2504	0.0092				p.A348A		Atlas-SNP	.											.	TPP1	71	.	0			c.C1044T						PASS	.	G		11,4391	16.8+/-37.8	0,11,2190	106.0	107.0	107.0		1044	-6.7	0.0	11	dbSNP_126	107	114,8478	60.2+/-122.0	1,112,4183	no	coding-synonymous	TPP1	NM_000391.3		1,123,6373	AA,AG,GG		1.3268,0.2499,0.962		348/564	6637577	125,12869	2201	4296	6497	SO:0001819	synonymous_variant	1200	exon8			CCGAGCGGCAGCC	AF017456	CCDS7770.1	11p15.4	2014-09-17	2004-12-09	2004-12-10	ENSG00000166340	ENSG00000166340			2073	protein-coding gene	gene with protein product	"""TPP I"""	607998	"""ceroid-lipofuscinosis, neuronal 2, late infantile (Jansky-Bielschowsky disease)"", ""spinocerebellar ataxia, autosomal recessive 7"""	CLN2, SCAR7		9653647, 23418007	Standard	NM_000391		Approved		uc001mel.1	O14773	OTTHUMG00000133404	ENST00000299427.6:c.1044C>T	11.37:g.6637577G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_000391	Q71V64	Silent	SNP	ENST00000299427.6	37	CCDS7770.1																																																																																			G|0.992;A|0.008	0.008	strong		0.567	TPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257261.2		
ZNF493	284443	hgsc.bcm.edu	37	19	21606719	21606719	+	Missense_Mutation	SNP	C	C	G	rs10414834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21606719C>G	ENST00000355504.4	+	2	1140	c.874C>G	c.(874-876)Ctt>Gtt	p.L292V	ZNF493_ENST00000392288.2_Missense_Mutation_p.L420V|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	292			L -> V (in dbSNP:rs10414834). {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)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						GTCTTCACACCTTACTACACA	0.333													.|||	453	0.0904553	0.0386	0.1023	5008	,	,		19313	0.0179		0.1998	False		,,,				2504	0.1145				p.L420V		Atlas-SNP	.											.	ZNF493	178	.	0			c.C1258G						PASS	.	C	VAL/LEU,VAL/LEU	290,4106		13,264,1921	33.0	36.0	35.0		1258,874	1.0	0.0	19	dbSNP_119	35	1747,6839		186,1375,2732	no	missense,missense	ZNF493	NM_001076678.2,NM_175910.6	32,32	199,1639,4653	GG,GC,CC		20.3471,6.5969,15.691	possibly-damaging,possibly-damaging	420/775,292/647	21606719	2037,10945	2198	4293	6491	SO:0001583	missense	284443	exon4			TCACACCTTACTA	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.874C>G	19.37:g.21606719C>G	ENSP00000347691:p.Leu292Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	228	0.1043956043956044	22	0.044715447154471545	46	0.1270718232044199	15	0.026223776223776224	145	0.19129287598944592	N	6.277	0.419191	0.11870	0.065969	0.203471	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.52983	0.64;0.64	1.03	1.03	0.20045	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00109	0.0003	M	0.91354	3.2	0.38251	P	0.058401999999999954	P;P	0.46621	0.881;0.654	P;P	0.52627	0.669;0.704	T	0.04522	-1.0945	8	0.66056	D	0.02	.	5.1005	0.14756	0.0:0.7687:0.0:0.2313	rs10414834;rs52820517;rs61566728;rs10414834	292;420	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	V	420;292	ENSP00000376110:L420V;ENSP00000347691:L292V	ENSP00000347691:L292V	L	+	1	0	ZNF493	21398559	0.771000	0.28555	0.010000	0.14722	0.010000	0.07245	1.364000	0.34171	0.447000	0.26695	0.454000	0.30748	CTT	.	.	weak		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
SLC10A2	6555	hgsc.bcm.edu	37	13	103705050	103705050	+	Silent	SNP	G	G	A	rs41281678	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:103705050G>A	ENST00000245312.3	-	3	1101	c.505C>T	c.(505-507)Ctg>Ttg	p.L169L		NM_000452.2	NP_000443	Q12908	NTCP2_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 2	169					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	bile acid:sodium symporter activity (GO:0008508)			breast(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_neural(89;0.0662)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)				Aciclovir(DB00787)|Cyclosporine(DB00091)|Ursodeoxycholic acid(DB01586)|Valaciclovir(DB00577)	AGAGAAACCAGAGATGTACCT	0.403													G|||	106	0.0211661	0.0484	0.013	5008	,	,		17622	0.0		0.0229	False		,,,				2504	0.0102				p.L169L		Atlas-SNP	.											.	SLC10A2	67	.	0			c.C505T	GRCh37	CM014220	SLC10A2	M	rs41281678	PASS	.	G		161,4245	111.2+/-149.4	2,157,2044	160.0	145.0	150.0		505	0.2	1.0	13	dbSNP_127	150	212,8388	91.1+/-153.3	0,212,4088	no	coding-synonymous	SLC10A2	NM_000452.2		2,369,6132	AA,AG,GG		2.4651,3.6541,2.8679		169/349	103705050	373,12633	2203	4300	6503	SO:0001819	synonymous_variant	6555	exon3			AAACCAGAGATGT	U10417	CCDS9506.1	13q33	2013-07-18	2013-07-18		ENSG00000125255	ENSG00000125255		"""Solute carriers"""	10906	protein-coding gene	gene with protein product		601295		ASBT, ISBT		8661017	Standard	NM_000452		Approved		uc001vpy.4	Q12908	OTTHUMG00000017313	ENST00000245312.3:c.505C>T	13.37:g.103705050G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	124	51	0.41129	NM_000452	A1L4F4|Q13839	Silent	SNP	ENST00000245312.3	37	CCDS9506.1																																																																																			G|0.972;A|0.028	0.028	strong		0.403	SLC10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045716.1		
R3HCC1	203069	hgsc.bcm.edu	37	8	23148940	23148940	+	Missense_Mutation	SNP	G	G	A	rs2272761	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:23148940G>A	ENST00000411463.1	+	6	1039	c.1039G>A	c.(1039-1041)Gtg>Atg	p.V347M	R3HCC1_ENST00000522012.1_3'UTR|R3HCC1_ENST00000518454.1_Missense_Mutation_p.V120M|R3HCC1_ENST00000265806.6_Missense_Mutation_p.V120M			Q9Y3T6	R3HC1_HUMAN	R3H domain and coiled-coil containing 1	347			V -> M (in dbSNP:rs2272761).				nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)			central_nervous_system(1)|skin(2)	3						ATCCTCCTTCGTGGAGGAGCT	0.517													G|||	2772	0.553514	0.4312	0.4553	5008	,	,		21586	0.7996		0.5408	False		,,,				2504	0.5481				p.V120M		Atlas-SNP	.											.	R3HCC1	11	.	0			c.G358A						PASS	.	G	MET/VAL	623,761		142,339,211	123.0	112.0	115.0		358	-0.3	0.0	8	dbSNP_100	115	1809,1373		505,799,287	yes	missense	R3HCC1	NM_001136108.1	21	647,1138,498	AA,AG,GG		43.149,45.0145,46.7367	benign	120/254	23148940	2432,2134	692	1591	2283	SO:0001583	missense	203069	exon5			TCCTTCGTGGAGG		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.1039G>A	8.37:g.23148940G>A	ENSP00000397555:p.Val347Met	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_001136108	B7ZLI1	Missense_Mutation	SNP	ENST00000411463.1	37		1277	0.5847069597069597	219	0.4451219512195122	178	0.49171270718232046	459	0.8024475524475524	421	0.5554089709762533	G	5.465	0.270928	0.10349	0.450145	0.56851	ENSG00000104679	ENST00000518454;ENST00000265806;ENST00000411463;ENST00000519952;ENST00000520480	T;T;T;T;T	0.44482	2.31;2.31;2.31;0.92;2.31	5.78	-0.354	0.12591	.	2.071810	0.01906	N	0.039493	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.26081	0.141	B	0.12156	0.007	T	0.47711	-0.9096	9	0.46703	T	0.11	1.107	9.6153	0.39687	0.4609:0.0:0.5391:0.0	rs2272761;rs3186282;rs17840551;rs56703251;rs2272761	347	Q9Y3T6	R3HC1_HUMAN	M	120;120;347;120;42	ENSP00000430607:V120M;ENSP00000265806:V120M;ENSP00000397555:V347M;ENSP00000429417:V120M;ENSP00000430339:V42M	ENSP00000265806:V120M	V	+	1	0	R3HCC1	23204885	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.514000	0.06298	-0.394000	0.07727	0.563000	0.77884	GTG	G|0.401;A|0.599	0.599	strong		0.517	R3HCC1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001136108	
LEPRE1	64175	hgsc.bcm.edu	37	1	43212926	43212926	+	Intron	SNP	G	G	A	rs67014447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43212926G>A	ENST00000296388.5	-	14	2107				LEPRE1_ENST00000236040.4_Missense_Mutation_p.A691V|LEPRE1_ENST00000462474.1_5'UTR|LEPRE1_ENST00000397054.3_Missense_Mutation_p.A691V			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1						bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	GCTCTCACCCGCTCGAGCTGC	0.627											OREG0013422	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	-|||	310	0.061901	0.1384	0.0389	5008	,	,		19053	0.001		0.0398	False		,,,				2504	0.0603				p.A691V		Atlas-SNP	.											.	LEPRE1	130	.	0			c.C2072T						PASS	.	-	VAL/ALA,	584,3822		33,518,1652	61.0	61.0	61.0		2072,		0.0	1	dbSNP_130	61	378,8222		7,364,3929	yes	missense,intron	LEPRE1	NM_001146289.1,NM_022356.3	64,	40,882,5581	AA,AG,GG		4.3953,13.2547,7.3966	,	691/698,	43212926	962,12044	2203	4300	6503	SO:0001627	intron_variant	64175	exon14			TCACCCGCTCGAG	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.2055+16C>T	1.37:g.43212926G>A		Somatic	65	0	0	914	WXS	Illumina HiSeq	Phase_I	45	11	0.244444	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	112	0.05128205128205128	61	0.12398373983739837	19	0.052486187845303865	0	0.0	32	0.04221635883905013	-	0.009	-1.803442	0.00611	0.132547	0.043953	ENSG00000117385	ENST00000397054;ENST00000236040	T;T	0.37411	1.2;1.28	.	.	.	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.19224	-1.0312	4	0.21540	T	0.41	.	.	.	.	.	691	Q32P28-3	.	V	691	ENSP00000380245:A691V;ENSP00000236040:A691V	ENSP00000236040:A691V	A	-	2	0	LEPRE1	42985513	0.009000	0.17119	0.014000	0.15608	0.025000	0.11179	-0.234000	0.09028	0.000000	0.14550	0.000000	0.15137	GCG	G|0.936;A|0.064	0.064	strong		0.627	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
TRPV4	59341	hgsc.bcm.edu	37	12	110252569	110252569	+	Silent	SNP	C	C	A	rs56092423	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:110252569C>A	ENST00000418703.2	-	1	127	c.33G>T	c.(31-33)ggG>ggT	p.G11G	TRPV4_ENST00000536838.1_Silent_p.G11G|TRPV4_ENST00000346520.2_Silent_p.G11G|TRPV4_ENST00000541794.1_Silent_p.G11G|TRPV4_ENST00000544971.1_Silent_p.G11G|TRPV4_ENST00000392719.2_Silent_p.G11G|TRPV4_ENST00000261740.2_Silent_p.G11G|TRPV4_ENST00000536570.1_5'UTR|TRPV4_ENST00000537083.1_Silent_p.G11G	NM_001177431.1	NP_001170902.1	Q9HBA0	TRPV4_HUMAN	transient receptor potential cation channel, subfamily V, member 4	11					actin cytoskeleton reorganization (GO:0031532)|actin filament organization (GO:0007015)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cell death (GO:0008219)|cell volume homeostasis (GO:0006884)|cell-cell junction assembly (GO:0007043)|cellular calcium ion homeostasis (GO:0006874)|cellular hypotonic response (GO:0071476)|cellular response to heat (GO:0034605)|cellular response to osmotic stress (GO:0071470)|cortical microtubule organization (GO:0043622)|hyperosmotic salinity response (GO:0042538)|ion transmembrane transport (GO:0034220)|microtubule polymerization (GO:0046785)|negative regulation of neuron projection development (GO:0010977)|osmosensory signaling pathway (GO:0007231)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule depolymerization (GO:0031117)|regulation of response to osmotic stress (GO:0047484)|response to mechanical stimulus (GO:0009612)|transmembrane transport (GO:0055085)|vasopressin secretion (GO:0030103)	adherens junction (GO:0005912)|cell surface (GO:0009986)|cilium (GO:0005929)|cortical actin cytoskeleton (GO:0030864)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|alpha-tubulin binding (GO:0043014)|ATP binding (GO:0005524)|beta-tubulin binding (GO:0048487)|calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)|cation channel activity (GO:0005261)|microtubule binding (GO:0008017)|osmosensor activity (GO:0005034)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(2)|skin(4)|stomach(1)	35						CCTccccgggccccgcgcggg	0.677													c|||	12	0.00239617	0.0008	0.0	5008	,	,		15170	0.0		0.0089	False		,,,				2504	0.002				p.G11G		Atlas-SNP	.											.	TRPV4	88	.	0			c.G33T						PASS	.	C	,,,,	9,4291		0,9,2141	8.0	8.0	8.0		33,33,33,33,33	-1.7	0.2	12	dbSNP_129	8	103,8301		0,103,4099	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV4	NM_001177428.1,NM_001177431.1,NM_001177433.1,NM_021625.4,NM_147204.2	,,,,	0,112,6240	AA,AC,CC		1.2256,0.2093,0.8816	,,,,	11/825,11/838,11/765,11/872,11/812	110252569	112,12592	2150	4202	6352	SO:0001819	synonymous_variant	59341	exon1			CCCGGGCCCCGCG	AF263523	CCDS9134.1, CCDS9135.1, CCDS53827.1, CCDS53828.1, CCDS53829.1	12q24.1	2014-09-17				ENSG00000111199		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18083	protein-coding gene	gene with protein product	"""osmosensitive transient receptor potential channel 4"""	605427				11025659, 11081638, 16382100, 20037587	Standard	NM_147204		Approved	OTRPC4, TRP12, VROAC, VRL-2, VR-OAC, CMT2C	uc001tpk.2	Q9HBA0		ENST00000418703.2:c.33G>T	12.37:g.110252569C>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	16	7	0.4375	NM_001177433	B7ZKQ6|Q17R79|Q2Y122|Q2Y123|Q2Y124|Q86YZ6|Q8NDY7|Q8NG64|Q96Q92|Q96RS7|Q9HBC0	Silent	SNP	ENST00000418703.2	37	CCDS9134.1																																																																																			C|0.996;A|0.004	0.004	strong		0.677	TRPV4-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403270.1	NM_021625	
TRPM6	140803	hgsc.bcm.edu	37	9	77377410	77377410	+	Missense_Mutation	SNP	C	C	T	rs3750425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:77377410C>T	ENST00000360774.1	-	26	4414	c.4177G>A	c.(4177-4179)Gtt>Att	p.V1393I	TRPM6_ENST00000376864.4_Missense_Mutation_p.V1393I|TRPM6_ENST00000361255.3_Missense_Mutation_p.V1388I|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Missense_Mutation_p.V1388I|TRPM6_ENST00000451710.3_Missense_Mutation_p.V1393I|TRPM6_ENST00000376871.3_Intron	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	100	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	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	
CEP170B	283638	hgsc.bcm.edu	37	14	105346632	105346632	+	Silent	SNP	G	G	A	rs72700176	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105346632G>A	ENST00000414716.3	+	6	570	c.342G>A	c.(340-342)aaG>aaA	p.K114K	CEP170B_ENST00000453495.1_Silent_p.K114K|CEP170B_ENST00000556508.1_Silent_p.K44K|CEP170B_ENST00000418279.1_Silent_p.K44K	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	114						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGCATGAAAAGTACACCAGCC	0.657													G|||	146	0.0291534	0.0015	0.0216	5008	,	,		18700	0.0357		0.0447	False		,,,				2504	0.0491				p.K114K		Atlas-SNP	.											.	.	.	.	0			c.G342A						PASS	.	G	,	30,4140		0,30,2055	32.0	40.0	38.0		342,132	2.4	1.0	14	dbSNP_130	38	281,8113		2,277,3918	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	2,307,5973	AA,AG,GG		3.3476,0.7194,2.4753	,	114/1555,44/1520	105346632	311,12253	2085	4197	6282	SO:0001819	synonymous_variant	283638	exon6			TGAAAAGTACACC	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.342G>A	14.37:g.105346632G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	39	0.375	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																			G|0.971;A|0.029	0.029	strong		0.657	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
CNTNAP4	85445	hgsc.bcm.edu	37	16	76482747	76482747	+	Missense_Mutation	SNP	C	C	G	rs34251012	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:76482747C>G	ENST00000476707.1	+	5	974	c.835C>G	c.(835-837)Ctc>Gtc	p.L279V	CNTNAP4_ENST00000478060.1_Missense_Mutation_p.L251V|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.L275V|CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.L275V			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	276	Laminin G-like 1. {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)				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						GCATTCAGTGCTCATCCAGCG	0.473													C|||	162	0.0323482	0.0598	0.0202	5008	,	,		17949	0.005		0.0159	False		,,,				2504	0.0491				p.L251V		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.C751G						PASS	.	C	VAL/LEU,VAL/LEU	267,4129	151.8+/-185.6	9,249,1940	142.0	108.0	119.0		825,751	4.4	1.0	16	dbSNP_126	119	161,8439	76.3+/-139.0	0,161,4139	yes	missense,missense	CNTNAP4	NM_033401.3,NM_138994.3	32,32	9,410,6079	GG,GC,CC		1.8721,6.0737,3.2933	possibly-damaging,possibly-damaging	276/1309,251/1236	76482747	428,12568	2198	4300	6498	SO:0001583	missense	85445	exon6			TCAGTGCTCATCC	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.835C>G	16.37:g.76482747C>G	ENSP00000417628:p.Leu279Val	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	247	39	0.157895	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		56	0.02564102564102564	38	0.07723577235772358	7	0.019337016574585635	1	0.0017482517482517483	10	0.013192612137203167	C	14.10	2.433919	0.43224	0.060737	0.018721	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11	5.34	4.37	0.52481	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.33419	N	0.004929	T	0.12603	0.0306	.	.	.	0.27364	N	0.955881	B;B;B;B	0.34226	0.05;0.443;0.003;0.399	B;B;B;B	0.39465	0.14;0.3;0.088;0.256	T	0.29058	-1.0024	9	0.32370	T	0.25	.	11.0366	0.47804	0.1455:0.7144:0.1401:0.0	rs34251012	251;279;251;276	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	V	275;275;251;279	ENSP00000306893:L275V;ENSP00000439733:L275V;ENSP00000418741:L251V;ENSP00000417628:L279V	ENSP00000306893:L275V	L	+	1	0	CNTNAP4	75040248	0.999000	0.42202	0.994000	0.49952	0.972000	0.66771	2.155000	0.42301	1.447000	0.47661	0.655000	0.94253	CTC	C|0.967;G|0.033	0.033	strong		0.473	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
SLC3A1	6519	hgsc.bcm.edu	37	2	44502977	44502977	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:44502977C>T	ENST00000260649.6	+	1	379	c.303C>T	c.(301-303)atC>atT	p.I101I	SLC3A1_ENST00000409387.1_Silent_p.I101I|SLC3A1_ENST00000409229.3_Silent_p.I101I|SLC3A1_ENST00000409741.1_Silent_p.I101I|SLC3A1_ENST00000410056.3_Silent_p.I101I	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1	101					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)	TGGTGCTCATCGCGGCCACCA	0.582																																					p.I101I		Atlas-SNP	.											SLC3A1,NS,carcinoma,0,1	SLC3A1	62	1	0			c.C303T						scavenged	.						60.0	57.0	58.0					2																	44502977		2203	4300	6503	SO:0001819	synonymous_variant	6519	exon1			GCTCATCGCGGCC		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.303C>T	2.37:g.44502977C>T		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	170	2	0.0117647	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Silent	SNP	ENST00000260649.6	37	CCDS1819.1																																																																																			.	.	none		0.582	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	
CD93	22918	hgsc.bcm.edu	37	20	23065879	23065879	+	Silent	SNP	G	G	A	rs34170527	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	213	117	0.549296	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	
HK3	3101	hgsc.bcm.edu	37	5	176314459	176314459	+	Silent	SNP	G	G	A	rs2278492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	112	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	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		
NOBOX	135935	hgsc.bcm.edu	37	7	144096068	144096068	+	Missense_Mutation	SNP	C	C	T	rs2525702	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	329	1	0.00303951		WXS	Illumina HiSeq	Phase_I	224	64	0.285714	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	
OR13D1	286365	hgsc.bcm.edu	37	9	107456763	107456763	+	Missense_Mutation	SNP	T	T	C	rs10991359	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:107456763T>C	ENST00000318763.5	+	1	104	c.61T>C	c.(61-63)Ttc>Ctc	p.F21L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	21			F -> L (in dbSNP:rs10991359).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F21L(1)		large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						TCATGTCCTTTTCTATACTAC	0.368													T|||	1099	0.219449	0.0106	0.3631	5008	,	,		18835	0.4484		0.2425	False		,,,				2504	0.1401				p.F21L		Atlas-SNP	.											OR13D1,NS,carcinoma,0,1	OR13D1	42	1	1	Substitution - Missense(1)	prostate(1)	c.T61C						PASS	.	T	LEU/PHE	238,4166	140.0+/-175.5	6,226,1970	65.0	61.0	63.0		61	-5.4	0.0	9	dbSNP_120	63	1834,6766	327.2+/-317.7	209,1416,2675	yes	missense	OR13D1	NM_001004484.1	22	215,1642,4645	CC,CT,TT		21.3256,5.4042,15.9336	benign	21/347	107456763	2072,10932	2202	4300	6502	SO:0001583	missense	286365	exon1			GTCCTTTTCTATA		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.61T>C	9.37:g.107456763T>C	ENSP00000317357:p.Phe21Leu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_001004484	B9EIS1|Q6IFL1	Missense_Mutation	SNP	ENST00000318763.5	37	CCDS35094.1	582	0.2664835164835165	7	0.014227642276422764	117	0.32320441988950277	261	0.4562937062937063	197	0.2598944591029024	T	10.34	1.323824	0.24080	0.054042	0.213256	ENSG00000179055	ENST00000318763	T	0.00003	9.83	4.08	-5.42	0.02640	.	.	.	.	.	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	0.04165	-1.0972	8	0.27785	T	0.31	.	1.5599	0.02593	0.5009:0.1979:0.1347:0.1665	rs10991359;rs52837362;rs10991359	21	Q8NGV5	O13D1_HUMAN	L	21	ENSP00000317357:F21L	ENSP00000317357:F21L	F	+	1	0	OR13D1	106496584	0.000000	0.05858	0.000000	0.03702	0.520000	0.34377	-1.980000	0.01492	-0.946000	0.03677	0.533000	0.62120	TTC	T|0.800;C|0.200	0.200	strong		0.368	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
SLC5A4	6527	hgsc.bcm.edu	37	22	32631021	32631021	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:32631021A>G	ENST00000266086.4	-	8	735	c.724T>C	c.(724-726)Tcc>Ccc	p.S242P	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	242					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TCGACTACGGATGGGGTGGCA	0.483																																					p.S242P		Atlas-SNP	.											SLC5A4,NS,carcinoma,+2,2	SLC5A4	82	2	0			c.T724C						scavenged	.						201.0	182.0	188.0					22																	32631021		2203	4300	6503	SO:0001583	missense	6527	exon8			CTACGGATGGGGT	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"""Solute carriers"""	11039	protein-coding gene	gene with protein product			"""solute carrier family 5 (low affinity glucose cotransporter), member 4"""			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.724T>C	22.37:g.32631021A>G	ENSP00000266086:p.Ser242Pro	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	140	3	0.0214286	NM_014227	O15279	Missense_Mutation	SNP	ENST00000266086.4	37	CCDS13903.1	.	.	.	.	.	.	.	.	.	.	.	5.548	0.286036	0.10513	.	.	ENSG00000100191	ENST00000266086	D	0.88509	-2.39	4.64	2.39	0.29439	.	0.341722	0.35320	N	0.003289	D	0.91798	0.7405	M	0.76574	2.34	0.19775	N	0.999957	P	0.49307	0.922	P	0.59948	0.866	D	0.84495	0.0613	10	0.72032	D	0.01	.	8.3072	0.32049	0.6847:0.0:0.0:0.3153	.	242	Q9NY91	SC5A4_HUMAN	P	242	ENSP00000266086:S242P	ENSP00000266086:S242P	S	-	1	0	SLC5A4	30961021	0.000000	0.05858	0.008000	0.14137	0.019000	0.09904	-0.337000	0.07852	0.330000	0.23485	0.528000	0.53228	TCC	.	.	none		0.483	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	
DEFA3	1668	hgsc.bcm.edu	37	8	6873603	6873603	+	Missense_Mutation	SNP	T	T	G	rs145076681		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	1031	19	0.0184287		WXS	Illumina HiSeq	Phase_I	328	31	0.0945122	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	
HCAR3	8843	hgsc.bcm.edu	37	12	123200354	123200354	+	Missense_Mutation	SNP	G	G	A	rs200905183	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:123200354G>A	ENST00000528880.2	-	1	1085	c.931C>T	c.(931-933)Cgc>Tgc	p.R311C	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	311					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)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9					Niacin(DB00627)	TGGAGGCAGCGGTTGATCAAA	0.542																																					p.R311C		Atlas-SNP	.											HCAR3_ENST00000528880,colon,carcinoma,+1,3	HCAR3	49	3	0			c.C931T						scavenged	.	G	CYS/ARG	141,4177		11,119,2029	38.0	52.0	47.0		931	2.0	0.9	12	dbSNP_134	47	1417,7167		82,1253,2957	no	missense	HCAR3	NM_006018.2	180	93,1372,4986	AA,AG,GG		16.5075,3.2654,12.0756	benign	311/388	123200354	1558,11344	2159	4292	6451	SO:0001583	missense	8843	exon1			GGCAGCGGTTGAT	D10923	CCDS53842.1	12q24.31	2012-08-08	2011-05-30	2011-05-30		ENSG00000255398		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	16824	protein-coding gene	gene with protein product		606039	"""G protein-coupled receptor 109B"""	GPR109B		7505609, 9205127, 18983141, 21454438	Standard	NM_006018		Approved	HCA3, HM74	uc001ucy.4	P49019		ENST00000528880.2:c.931C>T	12.37:g.123200354G>A	ENSP00000436714:p.Arg311Cys	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	258	92	0.356589	NM_006018	A8K4G5|B2R830|E9PI97|Q8NGE4	Missense_Mutation	SNP	ENST00000528880.2	37	CCDS53842.1	.	.	.	.	.	.	.	.	.	.	g	5.415	0.261672	0.10239	0.032654	0.165075	ENSG00000255398	ENST00000528880	T	0.35048	1.33	3.26	1.96	0.26148	.	.	.	.	.	T	0.00073	0.0002	N	0.25332	0.735	0.09310	N	1	B	0.23377	0.084	B	0.16722	0.016	T	0.16394	-1.0404	9	0.28530	T	0.3	.	3.6353	0.08146	0.4011:0.0:0.5989:0.0	.	311	E9PI97	.	C	311	ENSP00000436714:R311C	ENSP00000436714:R311C	R	-	1	0	HCAR3	121766307	0.352000	0.24895	0.927000	0.36925	0.456000	0.32438	1.250000	0.32850	1.514000	0.48869	0.184000	0.17185	CGC	G|0.884;A|0.116	0.116	strong		0.542	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387549.2	NM_006018	
MED12L	116931	hgsc.bcm.edu	37	3	151150568	151150568	+	Silent	SNP	G	G	A	rs142871635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151150568G>A	ENST00000474524.1	+	43	6452	c.6414G>A	c.(6412-6414)ccG>ccA	p.P2138P	MED12L_ENST00000273432.4_Silent_p.P1802P	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	2138						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GAGTGACTCCGTATGGGCATC	0.393													G|||	4	0.000798722	0.0	0.0029	5008	,	,		20900	0.0		0.002	False		,,,				2504	0.0				p.P2138P		Atlas-SNP	.											.	MED12L	271	.	0			c.G6414A						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	111.0	98.0	102.0		6414	-3.0	1.0	3	dbSNP_134	102	37,8563	24.6+/-71.5	0,37,4263	no	coding-synonymous	MED12L	NM_053002.4		0,40,6463	AA,AG,GG		0.4302,0.0681,0.3076		2138/2146	151150568	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon43			GACTCCGTATGGG	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.6414G>A	3.37:g.151150568G>A		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	166	90	0.542169	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			G|0.997;A|0.003	0.003	strong		0.393	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
POLE	5426	hgsc.bcm.edu	37	12	133253180	133253180	+	Missense_Mutation	SNP	A	A	T	rs139075637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:133253180A>T	ENST00000320574.5	-	9	904	c.861T>A	c.(859-861)gaT>gaA	p.D287E	POLE_ENST00000535270.1_Missense_Mutation_p.D260E	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	287					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)	CTGTCTCAGCATCAGGAAACT	0.498								DNA polymerases (catalytic subunits)					A|||	2	0.000399361	0.0	0.0	5008	,	,		20902	0.0		0.002	False		,,,				2504	0.0				p.D287E		Atlas-SNP	.											.	POLE	416	.	0			c.T861A						PASS	.	A	GLU/ASP	1,4405	2.1+/-5.4	0,1,2202	115.0	99.0	105.0		861	1.9	1.0	12	dbSNP_134	105	11,8589	8.4+/-32.0	0,11,4289	yes	missense	POLE	NM_006231.2	45	0,12,6491	TT,TA,AA		0.1279,0.0227,0.0923	probably-damaging	287/2287	133253180	12,12994	2203	4300	6503	SO:0001583	missense	5426	exon9			CTCAGCATCAGGA		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.861T>A	12.37:g.133253180A>T	ENSP00000322570:p.Asp287Glu	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	167	91	0.54491	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	22.2	4.257395	0.80246	2.27E-4	0.001279	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577	T;T;T;T	0.48201	3.07;3.07;3.07;0.82	5.49	1.9	0.25705	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.62841	0.2461	M	0.71206	2.165	0.51233	D	0.999917	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.62469	-0.6848	10	0.87932	D	0	.	8.9216	0.35615	0.718:0.0:0.282:0.0	.	260;287	F5H1D6;Q07864	.;DPOE1_HUMAN	E	287;298;260;67;222	ENSP00000322570:D287E;ENSP00000406383:D298E;ENSP00000445753:D260E;ENSP00000442519:D67E	ENSP00000322570:D287E	D	-	3	2	POLE	131763253	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.156000	0.31712	0.376000	0.24707	-0.441000	0.05720	GAT	A|0.999;T|0.001	0.001	strong		0.498	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
PKD1L1	168507	hgsc.bcm.edu	37	7	47968927	47968927	+	Missense_Mutation	SNP	C	C	A	rs2686817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:47968927C>A	ENST00000289672.2	-	7	984	c.934G>T	c.(934-936)Gtt>Ttt	p.V312F		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	312			V -> F (in dbSNP:rs2686817).		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						GCCATATGAACACGGAATCCC	0.498													C|||	2428	0.484824	0.5136	0.5072	5008	,	,		19692	0.5089		0.505	False		,,,				2504	0.3845				p.V312F		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G934T						PASS	.	C	PHE/VAL	2182,2224	586.2+/-386.4	556,1070,577	156.0	162.0	160.0		934	2.0	0.0	7	dbSNP_100	160	4220,4380	571.8+/-389.6	1029,2162,1109	yes	missense	PKD1L1	NM_138295.3	50	1585,3232,1686	AA,AC,CC		49.0698,49.5234,49.2234	probably-damaging	312/2850	47968927	6402,6604	2203	4300	6503	SO:0001583	missense	168507	exon7			TATGAACACGGAA	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.934G>T	7.37:g.47968927C>A	ENSP00000289672:p.Val312Phe	Somatic	273	2	0.00732601		WXS	Illumina HiSeq	Phase_I	249	243	0.975904	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	1075	0.49221611721611724	230	0.46747967479674796	174	0.48066298342541436	279	0.48776223776223776	392	0.5171503957783641	C	13.77	2.335500	0.41398	0.495234	0.490698	ENSG00000158683	ENST00000289672	T	0.42131	0.98	3.97	2.03	0.26663	.	3.865810	0.00589	N	0.000357	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D	0.89917	1.0	D	0.80764	0.994	T	0.42882	-0.9425	9	0.87932	D	0	-11.5068	5.4202	0.16396	0.0:0.68:0.2049:0.1151	rs2686817;rs2686817	312	Q8TDX9	PK1L1_HUMAN	F	312	ENSP00000289672:V312F	ENSP00000289672:V312F	V	-	1	0	PKD1L1	47935452	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	0.448000	0.21726	0.395000	0.25257	0.579000	0.79373	GTT	C|0.513;A|0.487	0.487	strong		0.498	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
LILRA3	11026	hgsc.bcm.edu	37	19	54804167	54804167	+	Missense_Mutation	SNP	G	G	A	rs11574606	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54804167G>A	ENST00000251390.3	-	1	98	c.7C>T	c.(7-9)Ccc>Tcc	p.P3S	LILRA3_ENST00000391744.3_Missense_Mutation_p.P3S|LILRA3_ENST00000391745.1_Missense_Mutation_p.P20S	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	3			P -> S (in dbSNP:rs11574606). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9278324, ECO:0000269|PubMed:9548455}.		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)		GTGAGGATGGGGGTCATGGCG	0.592													G|||	314	0.0626997	0.0129	0.111	5008	,	,		14210	0.003		0.1829	False		,,,				2504	0.0337				p.P3S		Atlas-SNP	.											.	LILRA3	65	.	0			c.C7T						PASS	.	G	SER/PRO,SER/PRO	124,4266		18,88,2089	129.0	98.0	109.0		7,7	-3.9	0.0	19	dbSNP_120	109	1433,6907		320,793,3057	yes	missense,missense	LILRA3	NM_001172654.1,NM_006865.3	74,74	338,881,5146	AA,AG,GG		17.1823,2.8246,12.231	,	3/376,3/440	54804167	1557,11173	2195	4170	6365	SO:0001583	missense	11026	exon1			GGATGGGGGTCAT	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.7C>T	19.37:g.54804167G>A	ENSP00000251390:p.Pro3Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	203	115	0.566502	NM_001172654	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	172	0.07875457875457875	10	0.02032520325203252	38	0.10497237569060773	2	0.0034965034965034965	122	0.16094986807387862	G	12.13	1.845588	0.32606	0.028246	0.171823	ENSG00000170866	ENST00000251390;ENST00000391744;ENST00000391745	T;T;T	0.00745	5.75;5.79;5.77	1.96	-3.93	0.04143	.	1.147850	0.06558	N	0.746265	T	0.00012	0.0000	L	0.53617	1.68	0.80722	P	0.0	B;B;B	0.30542	0.106;0.284;0.027	B;B;B	0.32805	0.098;0.153;0.001	T	0.37197	-0.9716	9	0.45353	T	0.12	.	0.1575	0.00099	0.3149:0.1943:0.2667:0.2242	rs11574606;rs17852512	3;3;3	E7EU74;Q8N6C8;B5ME96	.;LIRA3_HUMAN;.	S	3;3;20	ENSP00000251390:P3S;ENSP00000375624:P3S;ENSP00000375625:P20S	ENSP00000251390:P3S	P	-	1	0	LILRA3	59495979	0.000000	0.05858	0.000000	0.03702	0.197000	0.23852	-0.321000	0.08018	-0.876000	0.04017	0.485000	0.47835	CCC	G|0.907;A|0.093	0.093	strong		0.592	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
FLG	2312	hgsc.bcm.edu	37	1	152285930	152285930	+	Missense_Mutation	SNP	G	G	A	rs11584340	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152285930G>A	ENST00000368799.1	-	3	1467	c.1432C>T	c.(1432-1434)Cct>Tct	p.P478S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	478	Ser-rich.		P -> S (in dbSNP:rs11584340).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCAGAGTCAGGCTGTTCATGA	0.612									Ichthyosis				-|||	1726	0.344649	0.1286	0.4222	5008	,	,		18652	0.6062		0.171	False		,,,				2504	0.4908				p.P478S		Atlas-SNP	.											.	FLG	900	.	0			c.C1432T	GRCh37	CM084968	FLG	M	rs11584340	PASS	.	A	SER/PRO	615,3791		44,527,1632	220.0	210.0	214.0		1432	-3.1	0.0	1	dbSNP_120	214	1444,7156		124,1196,2980	yes	missense	FLG	NM_002016.1	74	168,1723,4612	AA,AG,GG		16.7907,13.9582,15.8312	benign	478/4062	152285930	2059,10947	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGTCAGGCTGTTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1432C>T	1.37:g.152285930G>A	ENSP00000357789:p.Pro478Ser	Somatic	313	1	0.00319489		WXS	Illumina HiSeq	Phase_I	440	172	0.390909	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	684	0.3131868131868132	72	0.14634146341463414	125	0.3453038674033149	355	0.6206293706293706	132	0.1741424802110818	-	4.251	0.045625	0.08196	0.139582	0.167907	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.00873	5.59	3.05	-3.12	0.05282	.	.	.	.	.	T	0.00073	0.0002	N	0.00260	-1.75	0.80722	P	0.0	B	0.17038	0.02	B	0.21360	0.034	T	0.30149	-0.9988	8	0.02654	T	1	.	3.0665	0.06217	0.3181:0.0:0.3425:0.3394	rs11584340;rs52819317;rs11584340	478	P20930	FILA_HUMAN	S	478;10	ENSP00000357789:P478S	ENSP00000357789:P478S	P	-	1	0	FLG	150552554	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.893000	0.01609	-1.350000	0.02199	-1.441000	0.01070	CCT	G|0.785;A|0.215	0.215	strong		0.612	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SLC17A3	10786	hgsc.bcm.edu	37	6	25850845	25850845	+	Missense_Mutation	SNP	C	C	T	rs56027330	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:25850845C>T	ENST00000360657.3	-	7	886	c.601G>A	c.(601-603)Ggg>Agg	p.G201R	SLC17A3_ENST00000397060.4_Missense_Mutation_p.G279R|SLC17A3_ENST00000361703.6_Missense_Mutation_p.G201R			O00476	NPT4_HUMAN	solute carrier family 17 (organic anion transporter), member 3	201			G -> R (in dbSNP:rs56027330). {ECO:0000269|PubMed:15505377}.		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						TTAGAAGACCCGACCTGAAAA	0.423													T|||	348	0.0694888	0.0136	0.0793	5008	,	,		19531	0.0238		0.1362	False		,,,				2504	0.1166				p.G279R		Atlas-SNP	.											SLC17A3,NS,carcinoma,+1,1	SLC17A3	95	1	0			c.G835A	GRCh37	CM043093	SLC17A3	M	rs56027330	PASS	.	T	ARG/GLY,ARG/GLY	144,4262	812.9+/-416.1	4,136,2063	106.0	103.0	104.0		835,601	2.3	0.0	6	dbSNP_129	104	1082,7518	768.9+/-407.6	73,936,3291	yes	missense,missense	SLC17A3	NM_001098486.1,NM_006632.3	125,125	77,1072,5354	TT,TC,CC		12.5814,3.2683,9.4264	benign,benign	279/499,201/421	25850845	1226,11780	2203	4300	6503	SO:0001583	missense	10786	exon8			AAGACCCGACCTG	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.601G>A	6.37:g.25850845C>T	ENSP00000353873:p.Gly201Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	63	38	0.603175	NM_001098486	B7WNJ5|B7Z511|Q8WWC7|Q9H533	Missense_Mutation	SNP	ENST00000360657.3	37	CCDS4566.2	153	0.07005494505494506	11	0.022357723577235773	33	0.09116022099447514	9	0.015734265734265736	100	0.13192612137203166	T	12.48	1.949222	0.34377	0.032683	0.125814	ENSG00000124564	ENST00000397060;ENST00000360657;ENST00000361703	T;T;T	0.57273	0.41;0.41;0.41	3.53	2.32	0.28847	Major facilitator superfamily domain, general substrate transporter (1);	4.308840	0.00481	N	0.000127	T	0.13970	0.0338	N	0.16130	0.375	0.80722	P	0.0	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.10450	0.005;0.003;0.0	T	0.06917	-1.0800	9	0.25751	T	0.34	.	3.7929	0.08728	0.0:0.1185:0.2204:0.6611	rs56027330;rs61745238	201;279;201	B7Z531;B7Z511;O00476	.;.;NPT4_HUMAN	R	279;201;201	ENSP00000380250:G279R;ENSP00000353873:G201R;ENSP00000355307:G201R	ENSP00000353873:G201R	G	-	1	0	SLC17A3	25958824	0.011000	0.17503	0.009000	0.14445	0.675000	0.39556	0.386000	0.20702	0.204000	0.20548	-0.352000	0.07741	GGG	C|0.910;T|0.090	0.090	strong		0.423	SLC17A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040070.2		
ATP13A1	57130	hgsc.bcm.edu	37	19	19758522	19758522	+	Silent	SNP	T	T	C	rs142259293	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	161	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	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	
DNAH14	127602	hgsc.bcm.edu	37	1	225393787	225393787	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225393787T>G	ENST00000445597.2	+	27	4811	c.4811T>G	c.(4810-4812)aTa>aGa	p.I1604R	DNAH14_ENST00000430092.1_Missense_Mutation_p.I2009R|DNAH14_ENST00000439375.2_Missense_Mutation_p.I2009R			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1604					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						AGTGAGAGAATAGCTTTAACT	0.423																																					p.I2009R		Atlas-SNP	.											.	DNAH14	300	.	0			c.T6026G						PASS	.						96.0	84.0	87.0					1																	225393787		692	1591	2283	SO:0001583	missense	127602	exon39			AGAGAATAGCTTT	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.4811T>G	1.37:g.225393787T>G	ENSP00000409472:p.Ile1604Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	103	34	0.330097	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		.	.	.	.	.	.	.	.	.	.	T	23.2	4.387882	0.82902	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	D;D;D	0.94280	-3.39;-3.39;-3.39	5.44	5.44	0.79542	.	.	.	.	.	D	0.97920	0.9316	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99250	1.0887	9	0.87932	D	0	.	14.4654	0.67480	0.0:0.0:0.0:1.0	.	2009	Q0VDD8-4	.	R	1604;2009;2009	ENSP00000409472:I1604R;ENSP00000414402:I2009R;ENSP00000392061:I2009R	ENSP00000414402:I2009R	I	+	2	0	DNAH14	223460410	1.000000	0.71417	0.908000	0.35775	0.995000	0.86356	6.910000	0.75741	2.063000	0.61619	0.481000	0.45027	ATA	.	.	none		0.423	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PLA2G7	7941	hgsc.bcm.edu	37	6	46672943	46672943	+	Missense_Mutation	SNP	A	A	G	rs1051931	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:46672943A>G	ENST00000274793.7	-	11	1332	c.1136T>C	c.(1135-1137)gTa>gCa	p.V379A	PLA2G7_ENST00000537365.1_Missense_Mutation_p.V379A	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	379			V -> A (common polymorphism; dbSNP:rs1051931). {ECO:0000269|PubMed:10733466, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		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)			ATCAATAGCTACATTTGAATC	0.353													A|||	4058	0.810304	0.7239	0.8458	5008	,	,		18249	0.9087		0.7565	False		,,,				2504	0.8558				p.V379A		Atlas-SNP	.											.	PLA2G7	49	.	0			c.T1136C	GRCh37	CM001309	PLA2G7	M	rs1051931	PASS	.	A	ALA/VAL,ALA/VAL	3294,1112	717.3+/-408.7	1238,818,147	100.0	90.0	94.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1136,1136	5.9	0.8	6	dbSNP_86	94	6914,1686	737.8+/-407.0	2783,1348,169	yes	missense,missense	PLA2G7	NM_001168357.1,NM_005084.3	64,64	4021,2166,316	GG,GA,AA		19.6047,25.2383,21.5131	probably-damaging,probably-damaging	379/442,379/442	46672943	10208,2798	2203	4300	6503	SO:0001583	missense	7941	exon11			ATAGCTACATTTG	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.1136T>C	6.37:g.46672943A>G	ENSP00000274793:p.Val379Ala	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_005084	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Missense_Mutation	SNP	ENST00000274793.7	37	CCDS4917.1	1731	0.7925824175824175	335	0.6808943089430894	307	0.8480662983425414	515	0.9003496503496503	574	0.7572559366754618	A	15.75	2.924347	0.52653	0.747617	0.803953	ENSG00000146070	ENST00000274793;ENST00000537365	T;T	0.53206	0.63;0.63	5.87	5.87	0.94306	.	0.391798	0.25660	N	0.029152	T	0.43122	0.1233	M	0.65975	2.015	0.09310	P	0.999999999535277	D	0.61697	0.99	P	0.57152	0.814	T	0.47812	-0.9088	9	0.09338	T	0.73	.	11.8741	0.52537	0.8693:0.0:0.0:0.1307	rs1051931;rs3192320;rs17853835;rs52828849;rs57815470;rs1051931	379	Q13093	PAFA_HUMAN	A	379	ENSP00000274793:V379A;ENSP00000445666:V379A	ENSP00000274793:V379A	V	-	2	0	PLA2G7	46780902	0.980000	0.34600	0.775000	0.31657	0.901000	0.52897	6.861000	0.75478	2.247000	0.74100	0.482000	0.46254	GTA	A|0.223;G|0.777	0.777	strong		0.353	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1		
UBE2U	148581	hgsc.bcm.edu	37	1	64672525	64672525	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:64672525C>T	ENST00000371076.3	+	3	471	c.227C>T	c.(226-228)cCg>cTg	p.P76L		NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	76					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)	p.P76L(1)		large_intestine(3)|lung(2)|skin(1)	6						ATAACAATTCCGTTTCATCCA	0.294																																					p.P76L		Atlas-SNP	.											UBE2U,caecum,carcinoma,0,2	UBE2U	16	2	1	Substitution - Missense(1)	large_intestine(1)	c.C227T						scavenged	.						46.0	47.0	47.0					1																	64672525		2201	4293	6494	SO:0001583	missense	148581	exon3			CAATTCCGTTTCA	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.227C>T	1.37:g.64672525C>T	ENSP00000360116:p.Pro76Leu	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	189	3	0.015873	NM_152489	Q8N1D4	Missense_Mutation	SNP	ENST00000371076.3	37	CCDS627.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.151028	0.57151	.	.	ENSG00000177414	ENST00000371077;ENST00000371076	T;T	0.34667	1.35;1.35	5.87	5.87	0.94306	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.64402	D	0.000009	T	0.31136	0.0787	L	0.33710	1.025	0.58432	D	0.999995	D	0.89917	1.0	D	0.97110	1.0	T	0.09271	-1.0682	10	0.02654	T	1	.	15.7051	0.77573	0.0:1.0:0.0:0.0	.	76	Q5VVX9	UBE2U_HUMAN	L	76	ENSP00000360117:P76L;ENSP00000360116:P76L	ENSP00000360116:P76L	P	+	2	0	UBE2U	64445113	1.000000	0.71417	1.000000	0.80357	0.288000	0.27193	3.824000	0.55723	2.777000	0.95525	0.591000	0.81541	CCG	.	.	none		0.294	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489	
SPAG17	200162	hgsc.bcm.edu	37	1	118530796	118530796	+	Silent	SNP	C	C	T	rs12040811	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:118530796C>T	ENST00000336338.5	-	39	5618	c.5553G>A	c.(5551-5553)caG>caA	p.Q1851Q		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1851						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)		TAGCCAAAGACTGCTTGAATA	0.363													c|||	693	0.138379	0.0522	0.0461	5008	,	,		19230	0.3403		0.0626	False		,,,				2504	0.1902				p.Q1851Q		Atlas-SNP	.											.	SPAG17	263	.	0			c.G5553A						PASS	.	T		216,4190	131.0+/-167.6	3,210,1990	65.0	62.0	63.0		5553	-3.5	0.1	1	dbSNP_120	63	496,8104	142.3+/-198.5	16,464,3820	no	coding-synonymous	SPAG17	NM_206996.2		19,674,5810	TT,TC,CC		5.7674,4.9024,5.4744		1851/2224	118530796	712,12294	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon39			CAAAGACTGCTTG		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.5553G>A	1.37:g.118530796C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	92	56	0.608696	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			C|0.915;T|0.085	0.085	strong		0.363	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
SEZ6	124925	hgsc.bcm.edu	37	17	27284515	27284515	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:27284515C>T	ENST00000317338.12	-	12	2773	c.2345G>A	c.(2344-2346)cGc>cAc	p.R782H	SEZ6_ENST00000442608.3_Missense_Mutation_p.R782H|SEZ6_ENST00000360295.9_Missense_Mutation_p.R782H|PIPOX_ENST00000583215.1_Intron|SEZ6_ENST00000335960.6_Intron			Q53EL9	SEZ6_HUMAN	seizure related 6 homolog (mouse)	782	Sushi 4. {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)			GGATATGAGGCGTCGGCTGTG	0.567																																					p.R782H		Atlas-SNP	.											SEZ6,colon,carcinoma,0,1	SEZ6	61	1	0			c.G2345A						scavenged	.						45.0	52.0	50.0					17																	27284515		1955	4144	6099	SO:0001583	missense	124925	exon12			ATGAGGCGTCGGC	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.2345G>A	17.37:g.27284515C>T	ENSP00000312942:p.Arg782His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	127	2	0.015748	NM_001098635	B6ZDN1|Q8N701|Q8NB57|Q8ND50|Q8TD25|Q96NI5|Q96NQ3	Missense_Mutation	SNP	ENST00000317338.12	37	CCDS45639.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064473	0.76187	.	.	ENSG00000063015	ENST00000442608;ENST00000360295;ENST00000317338;ENST00000541381	T;T;T	0.64803	-0.12;-0.12;1.3	5.39	5.39	0.77823	Complement control module (2);Sushi/SCR/CCP (3);	0.066575	0.56097	D	0.000023	T	0.78084	0.4228	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.79543	-0.1760	10	0.72032	D	0.01	.	16.9908	0.86353	0.0:1.0:0.0:0.0	.	782;782	Q53EL9-3;Q53EL9	.;SEZ6_HUMAN	H	782;782;657;782	ENSP00000403784:R782H;ENSP00000353440:R782H;ENSP00000312942:R657H	ENSP00000312942:R657H	R	-	2	0	SEZ6	24308641	0.013000	0.17824	1.000000	0.80357	0.967000	0.64934	2.324000	0.43831	2.693000	0.91896	0.313000	0.20887	CGC	.	.	none		0.567	SEZ6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397475.3		
CD3EAP	10849	hgsc.bcm.edu	37	19	45912343	45912343	+	Missense_Mutation	SNP	A	A	G	rs762562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45912343A>G	ENST00000309424.3	+	3	1605	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CD3EAP_ENST00000589804.1_Missense_Mutation_p.K375E|PPP1R13L_ENST00000418234.2_5'Flank|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000423698.2_3'UTR|ERCC1_ENST00000588738.1_5'Flank	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	373			K -> E (in dbSNP:rs762562).		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)		AGAAGGAGCGAAGCCTCAGGC	0.617													G|||	1436	0.286741	0.3109	0.2233	5008	,	,		16994	0.4613		0.1322	False		,,,				2504	0.2781				p.K373E		Atlas-SNP	.											CD3EAP,NS,carcinoma,0,1	CD3EAP	27	1	0			c.A1117G						PASS	.	G	,,GLU/LYS	1183,3221		168,847,1187	39.0	48.0	45.0		,,1117	1.6	0.0	19	dbSNP_86	45	1150,7450		79,992,3229	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,56	247,1839,4416	GG,GA,AA		13.3721,26.8619,17.9406	,,benign	,,373/511	45912343	2333,10671	2202	4300	6502	SO:0001583	missense	10849	exon3			GGAGCGAAGCCTC	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.1117A>G	19.37:g.45912343A>G	ENSP00000310966:p.Lys373Glu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	570	0.260989010989011	131	0.266260162601626	72	0.19889502762430938	259	0.4527972027972028	108	0.1424802110817942	G	1.401	-0.578050	0.03854	0.268619	0.133721	ENSG00000117877	ENST00000309424	T	0.09911	2.93	5.4	1.59	0.23543	.	0.794983	0.10950	N	0.616167	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	0.47071	-0.9145	9	0.02654	T	1	-2.1051	5.1222	0.14865	0.3446:0.1515:0.5039:0.0	rs762562;rs56437955;rs60195558;rs762562	375;373	O15446-2;O15446	.;RPA34_HUMAN	E	373	ENSP00000310966:K373E	ENSP00000310966:K373E	K	+	1	0	CD3EAP	50604183	0.005000	0.15991	0.000000	0.03702	0.013000	0.08279	0.970000	0.29383	0.267000	0.21916	-0.215000	0.12644	AAG	A|0.774;G|0.226	0.226	strong		0.617	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
RFPL4A	342931	hgsc.bcm.edu	37	19	56274453	56274453	+	Missense_Mutation	SNP	G	G	A	rs75239380	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56274453G>A	ENST00000434937.2	+	3	947	c.776G>A	c.(775-777)gGa>gAa	p.G259E		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	259	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.G259E(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						CATAAACGTGGAAGTCAAGAT	0.438																																					p.G259E		Atlas-SNP	.											ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	1	Substitution - Missense(1)	stomach(1)	c.G776A						scavenged	.						18.0	22.0	21.0					19																	56274453		691	1590	2281	SO:0001583	missense	342931	exon3			AACGTGGAAGTCA		CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.776G>A	19.37:g.56274453G>A	ENSP00000392936:p.Gly259Glu	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	192	46	0.239583	NM_001145014		Missense_Mutation	SNP	ENST00000434937.2	37	CCDS46201.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.580299	0.00879	.	.	ENSG00000223638	ENST00000434937	T	0.62498	0.02	2.78	-5.56	0.02529	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.24928	0.0605	N	0.01751	-0.74	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.10776	-1.0615	8	0.25751	T	0.34	-12.9296	1.2915	0.02061	0.279:0.1414:0.3715:0.2082	.	259	A6NLU0	RFPLA_HUMAN	E	259	ENSP00000392936:G259E	ENSP00000392936:G259E	G	+	2	0	RFPL4A	60966265	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.179000	0.03090	-1.696000	0.01421	-1.408000	0.01128	GGA	G|0.760;A|0.240	0.240	strong		0.438	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1	XM_292796	
OR52J3	119679	hgsc.bcm.edu	37	11	5068431	5068431	+	Missense_Mutation	SNP	G	G	A	rs17350764	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5068431G>A	ENST00000380370.1	+	1	676	c.676G>A	c.(676-678)Gtc>Atc	p.V226I		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	226			V -> I (in dbSNP:rs17350764).			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(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTCCGTGCTGTCTTCCGCCT	0.443													G|||	1114	0.222444	0.2519	0.3372	5008	,	,		21888	0.1081		0.1829	False		,,,				2504	0.2597				p.V226I		Atlas-SNP	.											OR52J3,right_upper_lobe,carcinoma,-2,1	OR52J3	77	1	0			c.G676A						scavenged	.	G	ILE/VAL	1079,3323	392.8+/-328.6	139,801,1261	338.0	302.0	314.0		676	3.3	0.9	11	dbSNP_123	314	1605,6991	298.6+/-304.0	159,1287,2852	yes	missense	OR52J3	NM_001001916.2	29	298,2088,4113	AA,AG,GG		18.6715,24.5116,20.6493	probably-damaging	226/312	5068431	2684,10314	2201	4298	6499	SO:0001583	missense	119679	exon1			CGTGCTGTCTTCC	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.676G>A	11.37:g.5068431G>A	ENSP00000369728:p.Val226Ile	Somatic	518	4	0.00772201		WXS	Illumina HiSeq	Phase_I	444	230	0.518018	NM_001001916	Q6IFE4	Missense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	431	0.19734432234432234	124	0.25203252032520324	104	0.287292817679558	71	0.12412587412587413	132	0.1741424802110818	G	12.36	1.915057	0.33815	0.245116	0.186715	ENSG00000205495	ENST00000380370	T	0.00224	8.51	4.19	3.28	0.37604	GPCR, rhodopsin-like superfamily (1);	0.163104	0.28393	N	0.015504	T	0.00012	0.0000	M	0.69463	2.115	0.80722	P	0.0	D	0.57899	0.981	P	0.61070	0.883	T	0.52335	-0.8589	9	0.66056	D	0.02	.	7.7255	0.28757	0.1939:0.0:0.8061:0.0	rs17350764;rs57530495;rs17350764	226	Q8NH60	O52J3_HUMAN	I	226	ENSP00000369728:V226I	ENSP00000369728:V226I	V	+	1	0	OR52J3	5025007	0.109000	0.22037	0.924000	0.36721	0.042000	0.13812	0.668000	0.25127	0.970000	0.38263	-0.126000	0.14955	GTC	G|0.792;A|0.208	0.208	strong		0.443	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
PCDH7	5099	hgsc.bcm.edu	37	4	30725987	30725987	+	Silent	SNP	G	G	A	rs977931	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:30725987G>A	ENST00000361762.2	+	1	3951	c.2943G>A	c.(2941-2943)agG>agA	p.R981R	PCDH7_ENST00000543491.1_Silent_p.R981R	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	981					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						GGCGATACAGGTCCGTTAATG	0.522													A|||	1055	0.210663	0.1982	0.1571	5008	,	,		17125	0.3204		0.1133	False		,,,				2504	0.2526				p.R981R		Atlas-SNP	.											.	PCDH7	215	.	0			c.G2943A						PASS	.	A	,,,	759,3647	754.8+/-412.5	77,605,1521	89.0	90.0	90.0		2943,2943,2943,2943	0.0	1.0	4	dbSNP_86	90	1061,7539	770.5+/-407.7	61,939,3300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCDH7	NM_001173523.1,NM_002589.2,NM_032456.2,NM_032457.3	,,,	138,1544,4821	AA,AG,GG		12.3372,17.2265,13.9935	,,,	981/1256,981/1070,981/1073,981/1248	30725987	1820,11186	2203	4300	6503	SO:0001819	synonymous_variant	5099	exon1			ATACAGGTCCGTT	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2943G>A	4.37:g.30725987G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_032457	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000361762.2	37	CCDS33971.1	417	0.19093406593406592	91	0.18495934959349594	62	0.1712707182320442	177	0.3094405594405594	87	0.11477572559366754	A	0.011	-1.710468	0.00712	0.172265	0.123372	ENSG00000169851	ENST00000511884	.	.	.	5.08	9.99E-4	0.14044	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999997651	.	.	.	.	.	.	T	0.38394	-0.9663	3	.	.	.	.	3.2835	0.06924	0.3811:0.1117:0.3868:0.1204	rs977931;rs1047013;rs3775329;rs977931	.	.	.	I	671	.	.	V	+	1	0	PCDH7	30335085	0.589000	0.26807	0.991000	0.47740	0.219000	0.24729	-0.023000	0.12456	-0.116000	0.11893	-1.214000	0.01621	GTC	A|0.158;C|0.004	0.158	strong		0.522	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589	
SLIT1	6585	hgsc.bcm.edu	37	10	98806512	98806512	+	Silent	SNP	G	G	C	rs17112342	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:98806512G>C	ENST00000266058.4	-	18	1997	c.1752C>G	c.(1750-1752)gcC>gcG	p.A584A	SLIT1_ENST00000371070.4_Silent_p.A584A|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	584					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)		CGCCCTCGAAGGCCCCATCTT	0.607													G|||	337	0.0672923	0.0204	0.0288	5008	,	,		18144	0.1012		0.0477	False		,,,				2504	0.1431				p.A584A		Atlas-SNP	.											.	SLIT1	154	.	0			c.C1752G						PASS	.	G		86,4320	72.0+/-110.0	1,84,2118	63.0	62.0	63.0		1752	2.8	1.0	10	dbSNP_123	63	378,8222	124.1+/-182.9	19,340,3941	no	coding-synonymous	SLIT1	NM_003061.2		20,424,6059	CC,CG,GG		4.3953,1.9519,3.5676		584/1535	98806512	464,12542	2203	4300	6503	SO:0001819	synonymous_variant	6585	exon18			CTCGAAGGCCCCA	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.1752C>G	10.37:g.98806512G>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	28	4	0.142857	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	37	CCDS7453.1																																																																																			G|0.955;C|0.045	0.045	strong		0.607	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
ZNF385A	25946	hgsc.bcm.edu	37	12	54767812	54767812	+	Silent	SNP	G	G	A	rs2887875	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:54767812G>A	ENST00000338010.5	-	4	419	c.366C>T	c.(364-366)gaC>gaT	p.D122D	ZNF385A_ENST00000394313.2_Silent_p.D102D|ZNF385A_ENST00000552382.1_5'UTR|ZNF385A_ENST00000352268.6_Silent_p.D122D|ZNF385A_ENST00000551109.1_Silent_p.D102D|ZNF385A_ENST00000551771.1_Silent_p.D102D|RP11-753H16.3_ENST00000550474.1_RNA|RP11-753H16.5_ENST00000552785.1_RNA|ZNF385A_ENST00000546970.1_Silent_p.D102D	NM_001130967.1	NP_001124439.1	Q96PM9	Z385A_HUMAN	zinc finger protein 385A	122					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|hemostasis (GO:0007599)|learning or memory (GO:0007611)|locomotory behavior (GO:0007626)|megakaryocyte development (GO:0035855)|mRNA localization resulting in posttranscriptional regulation of gene expression (GO:0010609)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)|positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:1902164)|positive regulation of fat cell differentiation (GO:0045600)|regulation of cytoplasmic translation (GO:2000765)|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)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|urinary_tract(1)	15						GGGGAGCTGGGTCTCCAGGTT	0.587													G|||	1202	0.240016	0.1029	0.3674	5008	,	,		16152	0.3075		0.165	False		,,,				2504	0.3425				p.D122D		Atlas-SNP	.											.	ZNF385A	45	.	0			c.C366T						PASS	.	G	,,	570,3836	254.3+/-259.9	42,486,1675	84.0	74.0	78.0		366,366,306	0.9	1.0	12	dbSNP_101	78	1534,7066	289.2+/-299.1	133,1268,2899	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF385A	NM_001130967.1,NM_001130968.1,NM_015481.1	,,	175,1754,4574	AA,AG,GG		17.8372,12.9369,16.1771	,,	122/387,122/306,102/367	54767812	2104,10902	2203	4300	6503	SO:0001819	synonymous_variant	25946	exon4			AGCTGGGTCTCCA	AF304052	CCDS8879.1, CCDS44910.1, CCDS44911.1	12q13.13	2012-10-05	2007-12-06	2007-12-06		ENSG00000161642			17521	protein-coding gene	gene with protein product		609124	"""zinc finger protein 385"""	ZNF385			Standard	XM_005268785		Approved	DKFZp586G1122, Hzf, ZFP385	uc001sfy.3	Q96PM9	OTTHUMG00000169840	ENST00000338010.5:c.366C>T	12.37:g.54767812G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	94	54	0.574468	NM_001130967	B2RDN5|B4DKH2|F1T0F1|J3KNS3|Q5VH53|Q9H7R6|Q9UFU3	Silent	SNP	ENST00000338010.5	37	CCDS44911.1																																																																																			G|0.827;C|0.000;A|0.173	0.173	strong		0.587	ZNF385A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406162.1	NM_015481	
UTP6	55813	hgsc.bcm.edu	37	17	30200750	30200750	+	Missense_Mutation	SNP	G	G	A	rs267604797		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:30200750G>A	ENST00000261708.4	-	15	1465	c.1328C>T	c.(1327-1329)tCc>tTc	p.S443F	CTC-542B22.2_ENST00000583236.1_lincRNA	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	443					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)				CTCTGCCCAGGAAATCCACAA	0.428																																					p.S443F		Atlas-SNP	.											.	UTP6	46	.	0			c.C1328T						PASS	.						199.0	189.0	192.0					17																	30200750		2203	4300	6503	SO:0001583	missense	55813	exon15			GCCCAGGAAATCC	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.1328C>T	17.37:g.30200750G>A	ENSP00000261708:p.Ser443Phe	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	51	4	0.0784314	NM_018428	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	37	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.626443	0.28978	.	.	ENSG00000108651	ENST00000261708	T	0.34859	1.34	5.1	2.71	0.32032	Tetratricopeptide-like helical (1);	0.326861	0.31301	N	0.007891	T	0.18841	0.0452	L	0.29908	0.895	0.29239	N	0.872766	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.15636	-1.0430	10	0.08837	T	0.75	-7.7125	4.5063	0.11889	0.3816:0.0:0.6184:0.0	.	443;443	B3KQ21;Q9NYH9	.;UTP6_HUMAN	F	443	ENSP00000261708:S443F	ENSP00000261708:S443F	S	-	2	0	UTP6	27224863	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.107000	0.57811	1.291000	0.44653	0.650000	0.86243	TCC	.	.	none		0.428	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428	
SIGLEC12	89858	hgsc.bcm.edu	37	19	52004878	52004878	+	Missense_Mutation	SNP	C	C	T	rs148809065	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52004878C>T	ENST00000291707.3	-	1	165	c.110G>A	c.(109-111)gGc>gAc	p.G37D	SIGLEC12_ENST00000598614.1_5'Flank	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	37	Ig-like V-type 1.				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)		GACACACAGGCCCTCCTGCAC	0.582													c|||	37	0.00738818	0.0008	0.0115	5008	,	,		18708	0.0		0.0199	False		,,,				2504	0.0082				p.G37D		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.G110A						PASS	.	C	ASP/GLY	18,4388		0,18,2185	111.0	82.0	92.0		110	2.1	1.0	19	dbSNP_134	92	178,8422		3,172,4125	yes	missense	SIGLEC12	NM_053003.2	94	3,190,6310	TT,TC,CC		2.0698,0.4085,1.507	probably-damaging	37/596	52004878	196,12810	2203	4300	6503	SO:0001583	missense	89858	exon1			CACAGGCCCTCCT	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.110G>A	19.37:g.52004878C>T	ENSP00000291707:p.Gly37Asp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	21	0.009615384615384616	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	15	0.01978891820580475	.	19.94	3.919078	0.73098	0.004085	0.020698	ENSG00000254521	ENST00000291707	T	0.80393	-1.37	2.09	2.09	0.27110	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.85729	0.5764	H	0.96080	3.765	0.25507	N	0.987498	D	0.89917	1.0	D	0.91635	0.999	T	0.76745	-0.2846	9	0.87932	D	0	.	7.6643	0.28421	0.0:1.0:0.0:0.0	.	37	Q96PQ1	SIG12_HUMAN	D	37	ENSP00000291707:G37D	ENSP00000291707:G37D	G	-	2	0	SIGLEC12	56696690	0.981000	0.34729	0.979000	0.43373	0.737000	0.42083	2.505000	0.45424	1.173000	0.42796	0.503000	0.49774	GGC	C|0.988;T|0.012	0.012	strong		0.582	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
PAK2	5062	hgsc.bcm.edu	37	3	196529917	196529917	+	Silent	SNP	A	A	G	rs183020057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:196529917A>G	ENST00000327134.3	+	4	640	c.318A>G	c.(316-318)ctA>ctG	p.L106L		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	106	Autoregulatory region. {ECO:0000250}.|GTPase-binding. {ECO:0000250}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		CTCGATTACTACAGACCTCCA	0.378													A|||	5	0.000998403	0.0008	0.0	5008	,	,		19631	0.001		0.001	False		,,,				2504	0.002				p.L106L		Atlas-SNP	.											.	PAK2	113	.	0			c.A318G						PASS	.						93.0	81.0	85.0					3																	196529917		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon4			ATTACTACAGACC	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.318A>G	3.37:g.196529917A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	214	10	0.046729	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																			A|1.000;G|0.000	0.000	strong		0.378	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
CAPN1	823	hgsc.bcm.edu	37	11	64981853	64981853	+	IGR	SNP	G	G	T	rs239259	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:64981853G>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)		CCGTCTACATGGCCGGGGTGC	0.667													G|||	1489	0.297324	0.1082	0.268	5008	,	,		14644	0.3889		0.4115	False		,,,				2504	0.362				p.M146I		Atlas-SNP	.											SLC22A20,NS,carcinoma,0,4	SLC22A20	36	4	0			c.G438T						scavenged	.	G	ILE/MET	617,3463		55,507,1478	30.0	34.0	33.0		438	4.5	1.0	11	dbSNP_79	33	3571,4793		742,2087,1353	yes	missense	SLC22A20	NM_001004326.4	10	797,2594,2831	TT,TG,GG		42.6949,15.1225,33.6548	probably-damaging	146/350	64981853	4188,8256	2040	4182	6222	SO:0001628	intergenic_variant	440044	exon2			CTACATGGCCGGG	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.64981853G>T		Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	76	45	0.592105	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			G|0.667;T|0.333	0.333	strong		0.667	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
ME3	10873	hgsc.bcm.edu	37	11	86159223	86159223	+	Silent	SNP	C	C	T	rs34662182	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:86159223C>T	ENST00000393324.3	-	10	1459	c.1206G>A	c.(1204-1206)gtG>gtA	p.V402V	RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000359636.2_Silent_p.V402V|ME3_ENST00000543262.1_Silent_p.V402V	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	402					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)			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)				CCAGCCTCACCACCTCCTCCA	0.552													C|||	180	0.0359425	0.003	0.0591	5008	,	,		18896	0.001		0.0855	False		,,,				2504	0.0491				p.V402V		Atlas-SNP	.											ME3,NS,carcinoma,0,1	ME3	70	1	0			c.G1206A						PASS	.	C	,,	68,4336	62.3+/-99.4	1,66,2135	149.0	106.0	121.0		1206,1206,1206	3.7	1.0	11	dbSNP_126	121	684,7914	170.4+/-221.6	23,638,3638	no	coding-synonymous,coding-synonymous,coding-synonymous	ME3	NM_001014811.1,NM_001161586.1,NM_006680.2	,,	24,704,5773	TT,TC,CC		7.9553,1.5441,5.7837	,,	402/605,402/605,402/605	86159223	752,12250	2202	4299	6501	SO:0001819	synonymous_variant	10873	exon11			CCTCACCACCTCC	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.1206G>A	11.37:g.86159223C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	174	117	0.672414	NM_006680	B7Z6V0|Q8TBJ0	Silent	SNP	ENST00000393324.3	37	CCDS8277.1																																																																																			C|0.946;T|0.054	0.054	strong		0.552	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2		
TUBA3E	112714	hgsc.bcm.edu	37	2	130951488	130951488	+	Silent	SNP	A	A	G	rs2443644	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:130951488A>G	ENST00000312988.7	-	4	1027	c.927T>C	c.(925-927)caT>caC	p.H309H		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	309					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)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					TGTACTTGCCATGGCGAGGGT	0.577																																					p.H309H		Atlas-SNP	.											TUBA3E,right_upper_lobe,carcinoma,-1,1	TUBA3E	73	1	0			c.T927C						scavenged	.						155.0	139.0	145.0					2																	130951488		2203	4300	6503	SO:0001819	synonymous_variant	112714	exon4			CTTGCCATGGCGA	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.927T>C	2.37:g.130951488A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	248	58	0.233871	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			A|0.985;G|0.015	0.015	strong		0.577	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
RSPH3	83861	hgsc.bcm.edu	37	6	159398700	159398700	+	Missense_Mutation	SNP	C	C	T	rs3756987	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159398700C>T	ENST00000252655.1	-	8	1742	c.1553G>A	c.(1552-1554)gGc>gAc	p.G518D	RSPH3_ENST00000297262.3_Missense_Mutation_p.G422D|RSPH3_ENST00000367069.2_Missense_Mutation_p.G376D|RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000449822.1_Missense_Mutation_p.G280D	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	518			G -> D (in dbSNP:rs3756987).					p.G518D(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		TTGTAGGTAGCCTCCATCTAA	0.488													T|||	1064	0.21246	0.0651	0.3746	5008	,	,		16377	0.3919		0.1034	False		,,,				2504	0.2239				p.G518D		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - Missense(1)	stomach(1)	c.G1553A						PASS	.	T	ASP/GLY	404,4002	788.9+/-415.0	12,380,1811	198.0	185.0	190.0		1553	2.8	0.0	6	dbSNP_107	190	926,7674	777.0+/-407.7	61,804,3435	yes	missense	RSPH3	NM_031924.4	94	73,1184,5246	TT,TC,CC		10.7674,9.1693,10.226	benign	518/561	159398700	1330,11676	2203	4300	6503	SO:0001583	missense	83861	exon8			AGGTAGCCTCCAT	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1553G>A	6.37:g.159398700C>T	ENSP00000252655:p.Gly518Asp	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	166	74	0.445783	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	469	0.21474358974358973	33	0.06707317073170732	109	0.3011049723756906	244	0.42657342657342656	83	0.10949868073878628	T	0.023	-1.405423	0.01155	0.091693	0.107674	ENSG00000130363	ENST00000367069;ENST00000449822;ENST00000252655;ENST00000297262	T;T;T;T	0.10382	2.91;2.92;2.89;2.88	3.96	2.75	0.32379	.	0.930568	0.08825	N	0.888160	T	0.00695	0.0023	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	0.47235	-0.9133	9	0.05833	T	0.94	-0.913	3.7359	0.08510	0.1874:0.109:0.0:0.7036	rs3756987;rs59000492;rs3756987	422;518	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	D	376;280;518;422	ENSP00000356036:G376D;ENSP00000393195:G280D;ENSP00000252655:G518D;ENSP00000297262:G422D	ENSP00000252655:G518D	G	-	2	0	RSPH3	159318688	0.005000	0.15991	0.000000	0.03702	0.002000	0.02628	1.408000	0.34668	0.060000	0.16281	-0.893000	0.02921	GGC	C|0.842;T|0.158	0.158	strong		0.488	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
C10orf90	118611	hgsc.bcm.edu	37	10	128193368	128193368	+	Missense_Mutation	SNP	C	C	T	rs11245008	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:128193368C>T	ENST00000284694.7	-	3	521	c.401G>A	c.(400-402)cGc>cAc	p.R134H	C10orf90_ENST00000454341.1_Missense_Mutation_p.R134H|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000392694.1_Missense_Mutation_p.R87H|C10orf90_ENST00000544758.1_Missense_Mutation_p.R231H|C10orf90_ENST00000356858.3_Missense_Mutation_p.R87H	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	134	Required for interaction with HDAC1. {ECO:0000250}.		R -> H (in dbSNP:rs11245008).		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)		AAACCCTCTGCGGGGGCCCCC	0.672											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1077	0.215056	0.4592	0.1599	5008	,	,		14007	0.129		0.1153	False		,,,				2504	0.1155				p.R134H		Atlas-SNP	.											.	C10orf90	121	.	0			c.G401A						PASS	.	C	HIS/ARG	1634,2730		321,992,869	28.0	33.0	32.0		401	-9.9	0.0	10	dbSNP_120	32	1103,7457		75,953,3252	yes	missense	C10orf90	NM_001004298.2	29	396,1945,4121	TT,TC,CC		12.8855,37.4427,21.1777	benign	134/700	128193368	2737,10187	2182	4280	6462	SO:0001583	missense	118611	exon3			CCTCTGCGGGGGC	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.401G>A	10.37:g.128193368C>T	ENSP00000284694:p.Arg134His	Somatic	104	0	0	1563	WXS	Illumina HiSeq	Phase_I	94	57	0.606383	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	449	0.20558608058608058	217	0.4410569105691057	59	0.16298342541436464	85	0.1486013986013986	88	0.11609498680738786	C	9.636	1.137739	0.21123	0.374427	0.128855	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.26810	2.01;2.01;2.03;2.02;1.71	4.97	-9.93	0.00452	.	1.535690	0.03830	N	0.268998	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B;B;B;B;B	0.18741	0.003;0.008;0.03;0.008;0.008	B;B;B;B;B	0.14578	0.003;0.002;0.011;0.003;0.003	T	0.31052	-0.9957	9	0.30078	T	0.28	-0.0577	11.4554	0.50179	0.0:0.2321:0.1567:0.6112	rs11245008;rs60449744;rs11245008	231;231;87;134;134	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	H	87;134;134;231;134;87;87	ENSP00000284694:R134H;ENSP00000398786:R134H;ENSP00000444369:R231H;ENSP00000405995:R134H;ENSP00000376459:R87H	ENSP00000284694:R134H	R	-	2	0	C10orf90	128183358	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-2.225000	0.01212	-3.872000	0.00096	-1.421000	0.01109	CGC	C|0.781;T|0.219	0.219	strong		0.672	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067099	79067099	+	Silent	SNP	G	G	C	rs142017909	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	71	0	0		WXS	Illumina HiSeq	Phase_I	74	9	0.121622	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	
MPDZ	8777	hgsc.bcm.edu	37	9	13150531	13150531	+	Silent	SNP	T	T	C	rs10756457	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:13150531T>C	ENST00000319217.7	-	25	3856	c.3609A>G	c.(3607-3609)aaA>aaG	p.K1203K	MPDZ_ENST00000447879.1_Silent_p.K1203K|MPDZ_ENST00000536827.1_Silent_p.K1203K|MPDZ_ENST00000541718.1_Silent_p.K1203K|MPDZ_ENST00000538841.1_Silent_p.K95K|MPDZ_ENST00000381022.2_Silent_p.K1203K|MPDZ_ENST00000381015.4_Silent_p.K1203K|MPDZ_ENST00000546205.1_Silent_p.K1217K	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1203	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)		TATCTCCAGGTTTCAAGGTTC	0.368													T|||	2392	0.477636	0.6982	0.3473	5008	,	,		13929	0.496		0.33	False		,,,				2504	0.4049				p.K1203K		Atlas-SNP	.											.	MPDZ	324	.	0			c.A3609G						PASS	.	T		2224,1466		675,874,296	164.0	162.0	163.0		3609	0.9	1.0	9	dbSNP_120	163	2645,5529		442,1761,1884	no	coding-synonymous	MPDZ	NM_003829.3		1117,2635,2180	CC,CT,TT		32.3587,39.729,41.0401		1203/2042	13150531	4869,6995	1845	4087	5932	SO:0001819	synonymous_variant	8777	exon25			TCCAGGTTTCAAG	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.3609A>G	9.37:g.13150531T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	140	59	0.421429	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				T|0.540;C|0.460	0.460	strong		0.368	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
FAT3	120114	hgsc.bcm.edu	37	11	92257991	92257991	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:92257991C>A	ENST00000298047.6	+	2	3501	c.3484C>A	c.(3484-3486)Cca>Aca	p.P1162T	FAT3_ENST00000525166.1_Missense_Mutation_p.P1012T|FAT3_ENST00000541502.1_Missense_Mutation_p.P1162T|FAT3_ENST00000409404.2_Missense_Mutation_p.P1162T			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1162	Cadherin 11. {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)				GGAAAACTCTCCAAAGGACGT	0.418										TCGA Ovarian(4;0.039)																											p.P1162T		Atlas-SNP	.											.	FAT3	1822	.	0			c.C3484A						PASS	.						58.0	58.0	58.0					11																	92257991		1968	4167	6135	SO:0001583	missense	120114	exon2			AACTCTCCAAAGG	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.3484C>A	11.37:g.92257991C>A	ENSP00000298047:p.Pro1162Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	200	123	0.615	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	21.8	4.197532	0.79015	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.66	5.66	0.87406	.	.	.	.	.	T	0.68933	0.3055	L	0.58925	1.835	0.51482	D	0.999922	D	0.89917	1.0	D	0.91635	0.999	T	0.68969	-0.5269	9	0.54805	T	0.06	.	15.2581	0.73601	0.0:0.8603:0.1397:0.0	.	1162	Q8TDW7-3	.	T	1162;1162;1162;1012	ENSP00000298047:P1162T;ENSP00000387040:P1162T;ENSP00000443786:P1162T;ENSP00000432586:P1012T	ENSP00000298047:P1162T	P	+	1	0	FAT3	91897639	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	5.946000	0.70234	2.682000	0.91365	0.650000	0.86243	CCA	.	.	none		0.418	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
SCAMP5	192683	hgsc.bcm.edu	37	15	75308976	75308976	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75308976C>T	ENST00000361900.6	+	5	386	c.179C>T	c.(178-180)gCg>gTg	p.A60V	SCAMP5_ENST00000425597.3_Missense_Mutation_p.A60V|SCAMP5_ENST00000545456.1_Intron|SCAMP5_ENST00000562212.1_Missense_Mutation_p.A60V|SCAMP5_ENST00000565923.1_3'UTR|SCAMP5_ENST00000568081.1_5'Flank	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	60					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)				large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						GGCTGTCTCGCGTGGCTGATC	0.612																																					p.A60V		Atlas-SNP	.											.	SCAMP5	34	.	0			c.C179T						PASS	.						107.0	111.0	109.0					15																	75308976		2165	4255	6420	SO:0001583	missense	192683	exon5			GTCTCGCGTGGCT	AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"""Secretory carrier membrane proteins"""	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.179C>T	15.37:g.75308976C>T	ENSP00000355387:p.Ala60Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Missense_Mutation	SNP	ENST00000361900.6	37	CCDS45306.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087901	0.94100	.	.	ENSG00000198794	ENST00000361900;ENST00000425597	T;T	0.18016	2.24;2.24	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.33118	0.0852	L	0.45352	1.415	0.80722	D	1	P;D	0.71674	0.842;0.998	B;D	0.63793	0.214;0.918	T	0.03443	-1.1036	10	0.59425	D	0.04	-8.1334	17.2941	0.87166	0.0:1.0:0.0:0.0	.	60;60	Q8TAC9-2;Q8TAC9	.;SCAM5_HUMAN	V	60	ENSP00000355387:A60V;ENSP00000406547:A60V	ENSP00000355387:A60V	A	+	2	0	SCAMP5	73096029	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.681000	0.84073	2.391000	0.81399	0.561000	0.74099	GCG	.	.	none		0.612	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967	
DRG2	1819	hgsc.bcm.edu	37	17	18003919	18003919	+	Missense_Mutation	SNP	G	G	A	rs143296623	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:18003919G>A	ENST00000225729.3	+	7	715	c.577G>A	c.(577-579)Gtc>Atc	p.V193I	DRG2_ENST00000395726.4_Missense_Mutation_p.V193I|DRG2_ENST00000583355.1_Intron	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	193	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)	p.V193fs*2(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					TAACTCGACAGTCACGCTGAC	0.562													G|||	13	0.00259585	0.0	0.0086	5008	,	,		22449	0.0		0.006	False		,,,				2504	0.001				p.V193I		Atlas-SNP	.											.	DRG2	27	.	1	Deletion - Frameshift(1)	ovary(1)	c.G577A						PASS	.	G	ILE/VAL	4,4402	8.1+/-20.4	0,4,2199	91.0	78.0	82.0		577	5.3	1.0	17	dbSNP_134	82	47,8553	30.1+/-81.4	0,47,4253	yes	missense	DRG2	NM_001388.3	29	0,51,6452	AA,AG,GG		0.5465,0.0908,0.3921	benign	193/365	18003919	51,12955	2203	4300	6503	SO:0001583	missense	1819	exon7			TCGACAGTCACGC	X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591			3030	protein-coding gene	gene with protein product		602986	"""developmentally regulated GTP-binding protein 2"""			9605870, 7929244	Standard	NM_001388		Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000225729.3:c.577G>A	17.37:g.18003919G>A	ENSP00000225729:p.Val193Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_001388	B2R8G5|Q53Y50|Q9BWB2	Missense_Mutation	SNP	ENST00000225729.3	37	CCDS11191.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	G	14.49	2.551381	0.45383	9.08E-4	0.005465	ENSG00000108591	ENST00000395726;ENST00000225729	T;T	0.30182	1.54;1.54	5.29	5.29	0.74685	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.29491	0.0735	M	0.66378	2.025	0.80722	D	1	B;B	0.18310	0.027;0.015	B;B	0.12837	0.008;0.008	T	0.16305	-1.0407	10	0.59425	D	0.04	-21.1669	18.9395	0.92600	0.0:0.0:1.0:0.0	.	193;193	A8MZF9;P55039	.;DRG2_HUMAN	I	193	ENSP00000379076:V193I;ENSP00000225729:V193I	ENSP00000225729:V193I	V	+	1	0	DRG2	17944644	1.000000	0.71417	0.952000	0.39060	0.257000	0.26127	7.764000	0.85297	2.484000	0.83849	0.462000	0.41574	GTC	G|0.996;A|0.004	0.004	strong		0.562	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	NM_001388	
HSDL1	83693	hgsc.bcm.edu	37	16	84158248	84158248	+	Missense_Mutation	SNP	G	G	C	rs4378600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:84158248G>C	ENST00000219439.4	-	6	1156	c.980C>G	c.(979-981)tCc>tGc	p.S327C	HSDL1_ENST00000565275.1_5'Flank|HSDL1_ENST00000434463.3_Missense_Mutation_p.S272C	NM_001146051.1|NM_031463.4	NP_001139523.1|NP_113651.4	Q3SXM5	HSDL1_HUMAN	hydroxysteroid dehydrogenase like 1	327			S -> C (in dbSNP:rs4378600). {ECO:0000269|PubMed:14702039}.			mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7						GGCTGTGCAGGATAAGGCTTC	0.428													G|||	1238	0.247204	0.236	0.1729	5008	,	,		21727	0.2331		0.3161	False		,,,				2504	0.2587				p.S327C		Atlas-SNP	.											.	HSDL1	23	.	0			c.C980G						PASS	.	G	CYS/SER,CYS/SER	1021,3379	378.0+/-322.7	118,785,1297	112.0	98.0	103.0		815,980	5.6	1.0	16	dbSNP_111	103	2505,6095	410.7+/-350.2	346,1813,2141	yes	missense,missense	HSDL1	NM_001146051.1,NM_031463.4	112,112	464,2598,3438	CC,CG,GG		29.1279,23.2045,27.1231	benign,benign	272/276,327/331	84158248	3526,9474	2200	4300	6500	SO:0001583	missense	83693	exon6			GTGCAGGATAAGG	AF237684	CCDS10942.1, CCDS54046.1	16q24	2011-09-20			ENSG00000103160	ENSG00000103160		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	16475	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 3"""					12153137, 19027726	Standard	NM_031463		Approved	SDR12C3	uc002fhk.2	Q3SXM5	OTTHUMG00000137635	ENST00000219439.4:c.980C>G	16.37:g.84158248G>C	ENSP00000219439:p.Ser327Cys	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	160	19	0.11875	NM_031463	B4DSL2|D3DUL4|Q3SXM4|Q8NC98|Q9BY22	Missense_Mutation	SNP	ENST00000219439.4	37	CCDS10942.1	546	0.25	115	0.23373983739837398	71	0.19613259668508287	123	0.21503496503496503	237	0.31266490765171506	G	13.14	2.147509	0.37923	0.232045	0.291279	ENSG00000103160	ENST00000434463;ENST00000219439	T;D	0.83673	-1.12;-1.75	5.6	5.6	0.85130	.	0.580099	0.17534	N	0.170776	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	P;P	0.50710	0.726;0.938	B;B	0.40101	0.319;0.319	T	0.03619	-1.1019	9	0.56958	D	0.05	-30.9015	12.4939	0.55916	0.077:0.0:0.923:0.0	rs4378600;rs17652812;rs52833604;rs4378600	272;327	B4DSL2;Q3SXM5	.;HSDL1_HUMAN	C	272;327	ENSP00000407437:S272C;ENSP00000219439:S327C	ENSP00000219439:S327C	S	-	2	0	HSDL1	82715749	0.982000	0.34865	0.993000	0.49108	0.401000	0.30781	4.775000	0.62346	2.808000	0.96608	0.650000	0.86243	TCC	G|0.737;C|0.263	0.263	strong		0.428	HSDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269076.3	NM_031463	
DEPDC5	9681	hgsc.bcm.edu	37	22	32205632	32205632	+	Splice_Site	SNP	A	A	C	rs5998135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:32205632A>C	ENST00000382112.3	+	18	1393	c.1323A>C	c.(1321-1323)acA>acC	p.T441T	DEPDC5_ENST00000382111.2_Splice_Site_p.T441T|DEPDC5_ENST00000400246.1_Splice_Site_p.T441T|DEPDC5_ENST00000400242.3_Splice_Site_p.T441T|DEPDC5_ENST00000535622.1_Splice_Site_p.T441T|DEPDC5_ENST00000536766.1_Splice_Site_p.T413T|DEPDC5_ENST00000266091.3_Splice_Site_p.T441T|DEPDC5_ENST00000400248.2_Splice_Site_p.T441T|DEPDC5_ENST00000400249.2_Splice_Site_p.T441T|DEPDC5_ENST00000382105.2_Splice_Site_p.T441T	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	441					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GCCGTGATACATGTGAGTATT	0.413													a|||	448	0.0894569	0.1097	0.1859	5008	,	,		18696	0.0347		0.0984	False		,,,				2504	0.0409				p.T441T		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A1323C						PASS	.	G	,,,,	469,3189		39,391,1399	90.0	86.0	87.0		1323,1323,1323,1323,1323	-10.8	0.6	22	dbSNP_114	87	814,7356		41,732,3312	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	DEPDC5	NM_001007188.2,NM_001136029.2,NM_001242896.1,NM_001242897.1,NM_014662.3	,,,,	80,1123,4711	CC,CA,AA		9.9633,12.8212,10.8471	,,,,	441/560,441/1595,441/1604,441/1504,441/1573	32205632	1283,10545	1829	4085	5914	SO:0001630	splice_region_variant	9681	exon19			TGATACATGTGAG	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1324+1A>C	22.37:g.32205632A>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	14	0.264151	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382112.3	37	CCDS46692.1																																																																																			A|0.906;C|0.094	0.094	strong		0.413	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	Silent
SDK1	221935	hgsc.bcm.edu	37	7	4172006	4172006	+	Silent	SNP	C	C	T	rs13224870	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	104	0	0		WXS	Illumina HiSeq	Phase_I	121	80	0.661157	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	
POLN	353497	hgsc.bcm.edu	37	4	2176454	2176454	+	Missense_Mutation	SNP	G	G	A	rs9328764	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:2176454G>A	ENST00000511885.2	-	10	1626	c.1273C>T	c.(1273-1275)Cgt>Tgt	p.R425C	POLN_ENST00000382865.1_Missense_Mutation_p.R425C|POLN_ENST00000515357.1_5'UTR			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	425			R -> C (in dbSNP:rs9328764). {ECO:0000269|PubMed:14702039, 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)			TCCAAAGTACGAAATAGTTGC	0.333								DNA polymerases (catalytic subunits)					A|||	1612	0.321885	0.5703	0.2435	5008	,	,		20717	0.373		0.1243	False		,,,				2504	0.1922				p.R425C		Atlas-SNP	.											.	POLN	82	.	0			c.C1273T						PASS	.	A	CYS/ARG	2220,2186	583.8+/-385.9	580,1060,563	63.0	68.0	66.0		1273	4.5	1.0	4	dbSNP_119	66	995,7605	772.9+/-407.7	59,877,3364	yes	missense	POLN	NM_181808.2	180	639,1937,3927	AA,AG,GG		11.5698,49.6142,24.7194	benign	425/901	2176454	3215,9791	2203	4300	6503	SO:0001583	missense	353497	exon8			AAGTACGAAATAG	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.1273C>T	4.37:g.2176454G>A	ENSP00000435506:p.Arg425Cys	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	178	87	0.488764	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	37	CCDS3360.1	678	0.31043956043956045	282	0.573170731707317	91	0.2513812154696133	210	0.36713286713286714	95	0.12532981530343007	A	12.38	1.919595	0.33908	0.503858	0.115698	ENSG00000130997	ENST00000511885;ENST00000382865;ENST00000253313;ENST00000382857	T;T	0.09255	3.0;3.0	5.64	4.48	0.54585	.	0.376286	0.31246	N	0.007983	T	0.00012	0.0000	N	0.25426	0.745	0.47547	P	5.439999999999889E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.36553	-0.9743	9	0.27785	T	0.31	0.361	6.7108	0.23276	0.8195:0.0:0.1805:0.0	rs9328764;rs52794301;rs57613484;rs9328764	425;15;425	E7ERY2;C9JDP8;Q7Z5Q5	.;.;DPOLN_HUMAN	C	425;425;116;15	ENSP00000435506:R425C;ENSP00000372316:R425C	ENSP00000253313:R116C	R	-	1	0	POLN	2146252	1.000000	0.71417	0.997000	0.53966	0.909000	0.53808	1.365000	0.34182	0.984000	0.38629	-0.521000	0.04368	CGT	G|0.682;A|0.318	0.318	strong		0.333	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808	
BRAT1	221927	hgsc.bcm.edu	37	7	2577809	2577809	+	Missense_Mutation	SNP	G	G	A	rs375916445		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:2577809G>A	ENST00000340611.4	-	14	2616	c.2360C>T	c.(2359-2361)aCg>aTg	p.T787M	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	787					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						CTCGGCCAGCGTGCTCCGCAG	0.701																																					p.T787M		Atlas-SNP	.											.	BRAT1	57	.	0			c.C2360T						PASS	.						22.0	22.0	22.0					7																	2577809		2187	4272	6459	SO:0001583	missense	221927	exon14			GCCAGCGTGCTCC	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.2360C>T	7.37:g.2577809G>A	ENSP00000339637:p.Thr787Met	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	72	53	0.736111	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	G	9.550	1.115689	0.20795	.	.	ENSG00000106009	ENST00000340611	T	0.30981	1.51	5.42	4.53	0.55603	.	0.648485	0.17239	N	0.181608	T	0.24851	0.0603	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	P	0.50490	0.642	T	0.05209	-1.0899	10	0.34782	T	0.22	-11.8434	10.0764	0.42362	0.0:0.189:0.6795:0.1314	.	787	Q6PJG6	BRAT1_HUMAN	M	787	ENSP00000339637:T787M	ENSP00000339637:T787M	T	-	2	0	BRAT1	2544335	0.005000	0.15991	0.006000	0.13384	0.041000	0.13682	1.359000	0.34113	1.239000	0.43787	0.561000	0.74099	ACG	.	.	weak		0.701	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
MFGE8	4240	hgsc.bcm.edu	37	15	89450003	89450003	+	Silent	SNP	G	G	A	rs2271714	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:89450003G>A	ENST00000566497.1	-	4	455	c.394C>T	c.(394-396)Ctg>Ttg	p.L132L	MFGE8_ENST00000268150.8_Silent_p.L132L|MFGE8_ENST00000268151.7_Silent_p.L132L|MFGE8_ENST00000559997.1_5'UTR|MFGE8_ENST00000539437.1_Silent_p.L124L|MFGE8_ENST00000542878.1_Silent_p.L88L			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	132	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)	p.L132L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					CTCCGCAGCAGGTTCACCTGG	0.587													G|||	1047	0.209065	0.4002	0.1787	5008	,	,		18372	0.2798		0.0398	False		,,,				2504	0.0736				p.L132L		Atlas-SNP	.											MFGE8,NS,carcinoma,0,1	MFGE8	60	1	1	Substitution - coding silent(1)	stomach(1)	c.C394T						PASS	.	G	,	1517,2883	481.0+/-359.0	264,989,947	95.0	76.0	83.0		394,394	4.1	1.0	15	dbSNP_100	83	357,8241	119.2+/-178.6	9,339,3951	no	coding-synonymous,coding-synonymous	MFGE8	NM_001114614.1,NM_005928.2	,	273,1328,4898	AA,AG,GG		4.1521,34.4773,14.4176	,	132/336,132/388	89450003	1874,11124	2200	4299	6499	SO:0001819	synonymous_variant	4240	exon4			GCAGCAGGTTCAC	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"""sperm surface protein hP47"""	602281	"""sperm associated antigen 10"""	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.394C>T	15.37:g.89450003G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	78	15	0.192308	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Silent	SNP	ENST00000566497.1	37	CCDS10347.1																																																																																			G|0.826;A|0.174	0.174	strong		0.587	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
VWDE	221806	hgsc.bcm.edu	37	7	12391319	12391319	+	Missense_Mutation	SNP	G	G	T	rs6967385	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:12391319G>T	ENST00000275358.3	-	19	3954	c.3766C>A	c.(3766-3768)Caa>Aaa	p.Q1256K		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1256			Q -> K (in dbSNP:rs6967385). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						GTAGTAAATTGATTTACAAAC	0.328													T|||	3139	0.626797	0.9281	0.5893	5008	,	,		17726	0.5942		0.4125	False		,,,				2504	0.5				p.Q1256K		Atlas-SNP	.											.	VWDE	123	.	0			c.C3766A						PASS	.						129.0	123.0	125.0					7																	12391319		692	1590	2282	SO:0001583	missense	221806	exon19			TAAATTGATTTAC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.3766C>A	7.37:g.12391319G>T	ENSP00000275358:p.Gln1256Lys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	1325	0.6066849816849816	458	0.9308943089430894	205	0.5662983425414365	356	0.6223776223776224	306	0.40369393139841686	T	0.008	-1.919281	0.00498	.	.	ENSG00000146530	ENST00000275358;ENST00000536307	T	0.65732	-0.17	3.06	-1.11	0.09840	.	1.313100	0.05006	N	0.470136	T	0.00012	0.0000	N	0.02721	-0.515	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40701	-0.9549	9	0.05721	T	0.95	.	0.5757	0.00703	0.1747:0.3048:0.1715:0.3489	rs6967385;rs10334388;rs58096598;rs6967385	1256	Q8N2E2	VWDE_HUMAN	K	1256;710	ENSP00000275358:Q1256K	ENSP00000275358:Q1256K	Q	-	1	0	VWDE	12357844	0.003000	0.15002	0.001000	0.08648	0.006000	0.05464	-0.133000	0.10451	-0.579000	0.05952	-1.202000	0.01658	CAA	G|0.378;T|0.622	0.622	strong		0.328	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
CRACR2A	84766	hgsc.bcm.edu	37	12	3789452	3789452	+	Missense_Mutation	SNP	C	C	T	rs17836273	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:3789452C>T	ENST00000252322.1	-	5	760	c.292G>A	c.(292-294)Gct>Act	p.A98T	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.A98T|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.A98T	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		98	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		A -> T (in dbSNP:rs17836273).		activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TTGCCATCAGCATCCAGGGCA	0.507													C|||	778	0.155351	0.1331	0.2262	5008	,	,		21101	0.128		0.1123	False		,,,				2504	0.2076				p.A98T		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.G292A						PASS	.	C	THR/ALA,THR/ALA	589,3817	259.2+/-262.9	48,493,1662	134.0	108.0	116.0		292,292	3.8	1.0	12	dbSNP_123	116	971,7629	211.4+/-252.0	54,863,3383	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	58,58	102,1356,5045	TT,TC,CC		11.2907,13.3681,11.9945	benign,benign	98/732,98/396	3789452	1560,11446	2203	4300	6503	SO:0001583	missense	84766	exon5			CATCAGCATCCAG																												ENST00000252322.1:c.292G>A	12.37:g.3789452C>T	ENSP00000252322:p.Ala98Thr	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	177	89	0.502825	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	313	0.1433150183150183	71	0.1443089430894309	79	0.21823204419889503	81	0.14160839160839161	82	0.10817941952506596	C	11.90	1.776639	0.31411	0.133681	0.112907	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.75704	-0.96;-0.36;-0.96	4.69	3.79	0.43588	EF-hand-like domain (1);	0.248943	0.41097	N	0.000946	T	0.00039	0.0001	L	0.28694	0.88	0.24654	P	0.99350352	B;B;B	0.29378	0.243;0.011;0.1	B;B;B	0.27262	0.078;0.027;0.077	T	0.04946	-1.0916	9	0.13108	T	0.6	-4.6645	10.8966	0.47025	0.0:0.9068:0.0:0.0932	rs17836273;rs60176556;rs17836273	98;98;98	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	T	98	ENSP00000409382:A98T;ENSP00000412496:A98T;ENSP00000252322:A98T	ENSP00000252322:A98T	A	-	1	0	EFCAB4B	3659713	0.982000	0.34865	1.000000	0.80357	0.995000	0.86356	0.198000	0.17217	1.194000	0.43101	0.561000	0.74099	GCT	C|0.866;T|0.134	0.134	strong		0.507	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
SLC2A4	6517	hgsc.bcm.edu	37	17	7187123	7187123	+	Silent	SNP	T	T	C	rs5435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7187123T>C	ENST00000317370.8	+	4	658	c.390T>C	c.(388-390)aaT>aaC	p.N130N	SLC2A4_ENST00000571308.1_Silent_p.N130N|RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000424875.2_Silent_p.N120N	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	130					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						GCCTGGCCAATGCTGCTGCCT	0.602													C|||	3493	0.697484	0.913	0.6081	5008	,	,		19792	0.625		0.6064	False		,,,				2504	0.638				p.N130N		Atlas-SNP	.											.	SLC2A4	44	.	0			c.T390C						PASS	.	C		3716,690	288.1+/-279.7	1576,564,63	68.0	61.0	63.0		390	-11.5	0.0	17	dbSNP_52	63	5363,3237	487.6+/-372.2	1696,1971,633	no	coding-synonymous	SLC2A4	NM_001042.2		3272,2535,696	CC,CT,TT		37.6395,15.6605,30.1938		130/510	7187123	9079,3927	2203	4300	6503	SO:0001819	synonymous_variant	6517	exon4			GGCCAATGCTGCT	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"""Solute carriers"""	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.390T>C	17.37:g.7187123T>C		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001042	Q05BQ3|Q14CX2	Silent	SNP	ENST00000317370.8	37	CCDS11097.1																																																																																			C|0.701;N|0.001	0.701	strong		0.602	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3		
CUL4A	8451	hgsc.bcm.edu	37	13	113909008	113909008	+	Splice_Site	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:113909008G>A	ENST00000375440.4	+	17	1838	c.1754G>A	c.(1753-1755)gGg>gAg	p.G585E	CUL4A_ENST00000326335.4_Splice_Site_p.G485E|CUL4A_ENST00000375441.3_Splice_Site_p.G485E|CUL4A_ENST00000451881.1_Splice_Site_p.G485E	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	585					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)			CTCTTCCAGGGGAAGAAGGAA	0.443																																					p.G585E		Atlas-SNP	.											.	CUL4A	50	.	0			c.G1754A						PASS	.						138.0	130.0	133.0					13																	113909008		2203	4300	6503	SO:0001630	splice_region_variant	8451	exon17			TCCAGGGGAAGAA	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.1753-1G>A	13.37:g.113909008G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598067	0.66332	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81	5.3	5.3	0.74995	Cullin, N-terminal (1);Cullin homology (2);	0.000000	0.85682	D	0.000000	T	0.72203	0.3431	M	0.61703	1.905	0.80722	D	1	P;P	0.42161	0.772;0.772	B;B	0.41036	0.346;0.346	T	0.74077	-0.3781	10	0.46703	T	0.11	-31.6571	12.6463	0.56735	0.0762:0.0:0.9238:0.0	.	585;585	Q13619;A8MSH7	CUL4A_HUMAN;.	E	485;485;485;585	ENSP00000364590:G485E;ENSP00000389118:G485E;ENSP00000322132:G485E;ENSP00000364589:G585E	ENSP00000322132:G485E	G	+	2	0	CUL4A	112957009	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	7.668000	0.83897	2.627000	0.88993	0.561000	0.74099	GGG	.	.	none		0.443	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589	Missense_Mutation
ARHGEF40	55701	hgsc.bcm.edu	37	14	21542753	21542753	+	Silent	SNP	G	G	A	rs1243472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21542753G>A	ENST00000298694.4	+	3	991	c.864G>A	c.(862-864)gcG>gcA	p.A288A	ARHGEF40_ENST00000298693.3_Silent_p.A288A			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	288	Gly-rich.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GACACCGGGCGTGGATGCACC	0.721													G|||	1212	0.242013	0.1452	0.1369	5008	,	,		16369	0.4762		0.2117	False		,,,				2504	0.2372				p.A288A		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.G864A						PASS	.	G		628,3730		45,538,1596	9.0	12.0	11.0		864	-10.2	0.1	14	dbSNP_87	11	1636,6912		158,1320,2796	no	coding-synonymous	ARHGEF40	NM_018071.3		203,1858,4392	AA,AG,GG		19.139,14.4103,17.5422		288/1520	21542753	2264,10642	2179	4274	6453	SO:0001819	synonymous_variant	55701	exon3			CCGGGCGTGGATG		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.864G>A	14.37:g.21542753G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	33	22	0.666667	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	37	CCDS32041.1																																																																																			G|0.741;A|0.259	0.259	strong		0.721	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29910693	29910693	+	Missense_Mutation	SNP	A	A	G	rs41559716	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29910693A>G	ENST00000396634.1	+	4	574	c.233A>G	c.(232-234)cAg>cGg	p.Q78R	HLA-A_ENST00000376806.5_Missense_Mutation_p.Q78R|HLA-A_ENST00000376802.2_Missense_Mutation_p.Q78R|HLA-A_ENST00000376809.5_Missense_Mutation_p.Q78R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	78	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)	p.Q78R(2)		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						TGGATAGAGCAGGAGGGGCCG	0.657									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.Q78R		Atlas-SNP	.											HLA-A,bladder,carcinoma,0,8	HLA-A	89	8	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.A233G						PASS	.						54.0	57.0	56.0					6																	29910693		2203	4299	6502	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TAGAGCAGGAGGG	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.233A>G	6.37:g.29910693A>G	ENSP00000379873:p.Gln78Arg	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	205	14	0.0682927	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.798	1.179669	0.21787	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00784	5.7;5.7;5.7;5.7	3.72	-4.39	0.03611	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	1.398580	0.06189	N	0.681068	T	0.00815	0.0027	L	0.56280	1.765	0.09310	N	1	B;P;B;P;B	0.42483	0.0;0.781;0.0;0.781;0.0	B;D;B;D;B	0.71184	0.006;0.972;0.01;0.972;0.01	T	0.44952	-0.9294	10	0.87932	D	0	.	0.9552	0.01384	0.3504:0.1689:0.3159:0.1647	rs41559716	78;78;78;78;78	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	R	78	ENSP00000379873:Q78R;ENSP00000366002:Q78R;ENSP00000366005:Q78R;ENSP00000365998:Q78R	ENSP00000348012:Q78R	Q	+	2	0	HLA-A	30018672	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-0.990000	0.03732	-0.910000	0.03847	-0.450000	0.05554	CAG	A|0.979;G|0.021	0.021	strong		0.657	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
DCAF12	25853	hgsc.bcm.edu	37	9	34107505	34107505	+	Missense_Mutation	SNP	C	C	T	rs11557154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34107505C>T	ENST00000361264.4	-	3	733	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	DCAF12_ENST00000463286.1_5'UTR	NM_015397.3	NP_056212.1	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	131			R -> Q (in dbSNP:rs11557154). {ECO:0000269|PubMed:15489334}.		protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						TCCAGGCTCCCGGTCTTTCAG	0.483													C|||	1137	0.227037	0.0106	0.2147	5008	,	,		19495	0.6012		0.1372	False		,,,				2504	0.2352				p.R131Q		Atlas-SNP	.											DCAF12,colon,carcinoma,+1,1	DCAF12	37	1	0			c.G392A						PASS	.	C	GLN/ARG	151,4255	103.8+/-142.4	3,145,2055	104.0	100.0	102.0		392	4.2	1.0	9	dbSNP_120	102	1064,7536	222.9+/-259.8	78,908,3314	yes	missense	DCAF12	NM_015397.3	43	81,1053,5369	TT,TC,CC		12.3721,3.4271,9.3418	probably-damaging	131/454	34107505	1215,11791	2203	4300	6503	SO:0001583	missense	25853	exon3			GGCTCCCGGTCTT	AB067479	CCDS6549.1	9p11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000198876	ENSG00000198876		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	19911	protein-coding gene	gene with protein product	"""cancer/testis antigen 102"""		"""KIAA1892"", ""WD repeat domain 40A"""	KIAA1892, WDR40A		11572484, 9110174	Standard	NM_015397		Approved	DKFZP434O125, MGC1058, CT102, TCC52	uc003ztt.2	Q5T6F0	OTTHUMG00000019806	ENST00000361264.4:c.392G>A	9.37:g.34107505C>T	ENSP00000355114:p.Arg131Gln	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	176	79	0.448864	NM_015397	A8KA70|D3DRL6|Q5T6E9|Q5T6F1|Q6P3V0|Q7L4F8|Q96PZ5|Q9NXA9|Q9UFJ1	Missense_Mutation	SNP	ENST00000361264.4	37	CCDS6549.1	532	0.24358974358974358	10	0.02032520325203252	76	0.20994475138121546	335	0.5856643356643356	111	0.14643799472295516	C	22.7	4.325631	0.81580	0.034271	0.123721	ENSG00000198876	ENST00000361264;ENST00000396990;ENST00000450964	T;T;T	0.30182	1.54;1.54;1.54	5.07	4.17	0.49024	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.58101	1.795	0.20489	P	0.999890017	D	0.64830	0.994	P	0.47376	0.545	T	0.46735	-0.9170	9	0.31617	T	0.26	-22.0702	11.837	0.52330	0.0:0.9192:0.0:0.0808	rs11557154;rs17855881;rs11557154	131	Q5T6F0	DCA12_HUMAN	Q	131;113;110	ENSP00000355114:R131Q;ENSP00000380187:R113Q;ENSP00000415833:R110Q	ENSP00000355114:R131Q	R	-	2	0	DCAF12	34097505	1.000000	0.71417	0.976000	0.42696	0.769000	0.43574	7.287000	0.78681	1.368000	0.46115	0.655000	0.94253	CGG	C|0.846;T|0.154	0.154	strong		0.483	DCAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052133.2	NM_015397	
COG8	84342	hgsc.bcm.edu	37	16	69373414	69373414	+	Silent	SNP	T	T	C	rs11542583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:69373414T>C	ENST00000306875.4	-	1	156	c.42A>G	c.(40-42)acA>acG	p.T14T	RP11-343C2.7_ENST00000564737.1_Intron|NIP7_ENST00000254941.6_5'Flank|NIP7_ENST00000569637.2_5'Flank|COG8_ENST00000562081.1_Silent_p.T14T|NIP7_ENST00000254940.5_5'UTR|RP11-343C2.9_ENST00000563634.1_Intron	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	14					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						GAGCCGCTGCTGTGGCCGTGG	0.677													C|||	1290	0.257588	0.3192	0.2161	5008	,	,		14793	0.0833		0.2853	False		,,,				2504	0.3548				p.T14T		Atlas-SNP	.											.	COG8	32	.	0			c.A42G						PASS	.	C		1459,2839		233,993,923	15.0	15.0	15.0		42	-1.1	0.0	16	dbSNP_120	15	2691,5805		446,1799,2003	no	coding-synonymous	COG8	NM_032382.4		679,2792,2926	CC,CT,TT		31.6737,33.946,32.4371		14/613	69373414	4150,8644	2149	4248	6397	SO:0001819	synonymous_variant	84342	exon1			CGCTGCTGTGGCC	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"""Components of oligomeric golgi complex"""	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.42A>G	16.37:g.69373414T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Silent	SNP	ENST00000306875.4	37	CCDS10876.1																																																																																			T|0.711;C|0.289	0.289	strong		0.677	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382	
IRS1	3667	hgsc.bcm.edu	37	2	227660544	227660544	+	Missense_Mutation	SNP	C	C	T	rs1801278	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:227660544C>T	ENST00000305123.5	-	1	3931	c.2911G>A	c.(2911-2913)Ggg>Agg	p.G971R	IRS1_ENST00000498335.1_5'Flank	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	971			G -> R (in dbSNP:rs1801278). {ECO:0000269|PubMed:14671192, ECO:0000269|PubMed:14707024, ECO:0000269|PubMed:15590636, ECO:0000269|PubMed:8104271}.		cellular response to insulin stimulus (GO:0032869)|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)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		CTAGCAGCCCCGGGAGGTGCA	0.652													C|||	266	0.053115	0.0635	0.0317	5008	,	,		17610	0.0228		0.0855	False		,,,				2504	0.0521				p.G971R		Atlas-SNP	.											.	IRS1	141	.	0			c.G2911A	GRCh37	CM930444	IRS1	M	rs1801278	PASS	.	C	ARG/GLY	255,4151		9,237,1957	41.0	48.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2911	5.4	0.6	2	dbSNP_89	46	566,8034		27,512,3761	yes	missense	IRS1	NM_005544.2	125	36,749,5718	TT,TC,CC		6.5814,5.7876,6.3125	probably-damaging	971/1243	227660544	821,12185	2203	4300	6503	SO:0001583	missense	3667	exon1			CAGCCCCGGGAGG		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.2911G>A	2.37:g.227660544C>T	ENSP00000304895:p.Gly971Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	54	40	0.740741	NM_005544		Missense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	117	0.05357142857142857	36	0.07317073170731707	10	0.027624309392265192	15	0.026223776223776224	56	0.07387862796833773	C	14.51	2.556395	0.45487	0.057876	0.065814	ENSG00000169047	ENST00000305123	T	0.57273	0.41	5.39	5.39	0.77823	.	0.244505	0.30639	N	0.009181	T	0.02455	0.0075	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	P	0.40360	0.714	B	0.21151	0.033	T	0.14392	-1.0474	9	0.23302	T	0.38	-19.979	18.0965	0.89492	0.0:1.0:0.0:0.0	rs1801278;rs3769648;rs1801278	971	P35568	IRS1_HUMAN	R	971	ENSP00000304895:G971R	ENSP00000304895:G971R	G	-	1	0	IRS1	227368788	0.144000	0.22641	0.575000	0.28536	0.839000	0.47603	1.352000	0.34033	2.804000	0.96469	0.655000	0.94253	GGG	T|0.061;C|0.939	0.061	strong		0.652	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544	
SH3PXD2B	285590	hgsc.bcm.edu	37	5	171849471	171849471	+	Silent	SNP	G	G	A	rs17074773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	25	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	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	
NR0B1	190	hgsc.bcm.edu	37	X	30326983	30326983	+	Silent	SNP	C	C	T	rs2269345	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:30326983C>T	ENST00000378970.4	-	1	732	c.498G>A	c.(496-498)cgG>cgA	p.R166R	NR0B1_ENST00000378963.1_5'Flank|NR0B1_ENST00000453287.1_Silent_p.R166R	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	166	4 X 67 AA tandem repeats.				adrenal gland development (GO:0030325)|gene expression (GO:0010467)|gonad development (GO:0008406)|hypothalamus development (GO:0021854)|intracellular receptor signaling pathway (GO:0030522)|Leydig cell differentiation (GO:0033327)|male gonad development (GO:0008584)|male sex determination (GO:0030238)|negative regulation of cell differentiation (GO:0045596)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|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)|pituitary gland development (GO:0021983)|protein localization (GO:0008104)|response to immobilization stress (GO:0035902)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)|steroid biosynthetic process (GO:0006694)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	AF-2 domain binding (GO:0050682)|DNA binding (GO:0003677)|DNA hairpin binding (GO:0032448)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|steroid hormone receptor binding (GO:0035258)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	24					Dexamethasone(DB01234)|Tretinoin(DB00755)	CGCCCCCTGGCCGTGCCTCGG	0.677											OREG0019719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1799	0.476556	0.3669	0.2983	3775	,	,		10783	0.5506		0.1252	False		,,,				2504	0.4356				p.R166R		Atlas-SNP	.											.	NR0B1	61	.	0			c.G498A						PASS	.	C		1657,2162		310,798,239,518,328	14.0	12.0	13.0		498	0.3	0.0	X	dbSNP_100	13	1320,5388		111,746,352,1565,1512	no	coding-synonymous	NR0B1	NM_000475.4		421,1544,591,2083,1840	TT,TC,T,CC,C		19.678,43.3883,28.2797		166/471	30326983	2977,7550	2193	4286	6479	SO:0001819	synonymous_variant	190	exon1			CCCTGGCCGTGCC	S74720	CCDS14223.1	Xp21.3	2014-06-28			ENSG00000169297	ENSG00000169297		"""Nuclear hormone receptors"""	7960	protein-coding gene	gene with protein product		300473	"""dosage-sensitive sex reversal"""	AHC, DSS		1301166, 10412368	Standard	NM_000475		Approved	DAX1, AHCH	uc004dcf.4	P51843	OTTHUMG00000021323	ENST00000378970.4:c.498G>A	X.37:g.30326983C>T		Somatic	66	0	0	816	WXS	Illumina HiSeq	Phase_I	28	26	0.928571	NM_000475	Q96F69	Silent	SNP	ENST00000378970.4	37	CCDS14223.1																																																																																			C|0.621;T|0.379	0.379	strong		0.677	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	NM_000475	
SLC23A2	9962	hgsc.bcm.edu	37	20	4880308	4880308	+	Silent	SNP	G	G	A	rs1776964	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:4880308G>A	ENST00000379333.1	-	6	767	c.375C>T	c.(373-375)gcC>gcT	p.A125A	SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000424750.2_Silent_p.A125A|SLC23A2_ENST00000338244.1_Silent_p.A125A	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	125					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						ACATGGCATCGGCCAACAGGA	0.532													G|||	2256	0.450479	0.3638	0.4236	5008	,	,		19147	0.5446		0.4622	False		,,,				2504	0.4775				p.A125A		Atlas-SNP	.											.	SLC23A2	62	.	0			c.C375T						PASS	.	G	,	1723,2683	519.1+/-369.9	334,1055,814	163.0	140.0	148.0		375,375	-10.2	0.0	20	dbSNP_89	148	3934,4666	548.9+/-385.4	890,2154,1256	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	1224,3209,2070	AA,AG,GG		45.7442,39.1058,43.4953	,	125/651,125/651	4880308	5657,7349	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon6			GGCATCGGCCAAC	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.375C>T	20.37:g.4880308G>A		Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1																																																																																			G|0.545;A|0.455	0.455	strong		0.532	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
FSIP2	401024	hgsc.bcm.edu	37	2	186678633	186678633	+	Missense_Mutation	SNP	C	C	T	rs17826666	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	246	0	0		WXS	Illumina HiSeq	Phase_I	230	112	0.486957	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	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487265	32487265	+	Missense_Mutation	SNP	C	C	G	rs139485758	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32487265C>G	ENST00000374975.3	-	3	596	c.534G>C	c.(532-534)caG>caC	p.Q178H		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5									p.Q178H(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						AGTCTCCATTCTGAATCAGGC	0.552													C|||	836	0.166933	0.2224	0.1326	5008	,	,		15097	0.1667		0.1531	False		,,,				2504	0.1309				p.Q178H		Atlas-SNP	.											HLA-DRB5,NS,NS,0,1	HLA-DRB5	31	1	1	Substitution - Missense(1)	NS(1)	c.G534C						scavenged	.						61.0	68.0	65.0					6																	32487265		1933	3889	5822	SO:0001583	missense	3127	exon3			TCCATTCTGAATC		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.534G>C	6.37:g.32487265C>G	ENSP00000364114:p.Gln178His	Somatic	91	9	0.0989011		WXS	Illumina HiSeq	Phase_I	113	18	0.159292	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	2.451	-0.326294	0.05350	.	.	ENSG00000198502	ENST00000374975	T	0.14391	2.51	4.6	-9.19	0.00685	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	1.115120	0.06656	N	0.763651	T	0.02193	0.0068	L	0.35487	1.065	0.80722	P	0.0	B;B	0.19445	0.036;0.003	B;B	0.33690	0.168;0.014	T	0.35871	-0.9771	9	0.35671	T	0.21	.	1.7649	0.03000	0.2235:0.402:0.1926:0.1818	.	105;178	Q29973;Q30154	.;DRB5_HUMAN	H	178	ENSP00000364114:Q178H	ENSP00000364114:Q178H	Q	-	3	2	HLA-DRB5	32595243	0.000000	0.05858	0.000000	0.03702	0.495000	0.33615	-4.437000	0.00234	-3.808000	0.00104	-0.273000	0.10243	CAG	A|0.003;C|0.930;G|0.067	0.067	strong		0.552	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
LAMA1	284217	hgsc.bcm.edu	37	18	7033037	7033037	+	Silent	SNP	G	G	A	rs621993	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:7033037G>A	ENST00000389658.3	-	15	2202	c.2109C>T	c.(2107-2109)gcC>gcT	p.A703A		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	703	Laminin IV type A 1. {ECO:0000255|PROSITE-ProRule:PRU00458}.				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)				CCACATCAGCGGCCACCACCA	0.512													G|||	2036	0.40655	0.708	0.3905	5008	,	,		18010	0.1319		0.4036	False		,,,				2504	0.2965				p.A703A		Atlas-SNP	.											LAMA1,brain,glioma,-1,1	LAMA1	458	1	0			c.C2109T						scavenged	.	G		2823,1583	657.4+/-400.2	894,1035,274	107.0	78.0	88.0		2109	-0.5	0.0	18	dbSNP_83	88	3478,5122	495.4+/-374.0	690,2098,1512	no	coding-synonymous	LAMA1	NM_005559.3		1584,3133,1786	AA,AG,GG		40.4419,35.9283,48.4469		703/3076	7033037	6301,6705	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon15			ATCAGCGGCCACC	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.2109C>T	18.37:g.7033037G>A		Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.542;A|0.458	0.458	strong		0.512	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
OR13C9	286362	hgsc.bcm.edu	37	9	107380396	107380396	+	Silent	SNP	T	T	G	rs36091517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:107380396T>G	ENST00000259362.1	-	1	89	c.90A>C	c.(88-90)ctA>ctC	p.L30L		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	30						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						TTATGAAGATTAGCACAAAAA	0.408													G|||	1140	0.227636	0.0552	0.3588	5008	,	,		18148	0.3819		0.2445	False		,,,				2504	0.1912				p.L30L		Atlas-SNP	.											.	OR13C9	42	.	0			c.A90C						PASS	.	G		463,3943	783.2+/-414.6	34,395,1774	148.0	139.0	142.0		90	-9.8	0.0	9	dbSNP_126	142	1977,6623	722.5+/-406.4	235,1507,2558	no	coding-synonymous	OR13C9	NM_001001956.1		269,1902,4332	GG,GT,TT		22.9884,10.5084,18.7606		30/319	107380396	2440,10566	2203	4300	6503	SO:0001819	synonymous_variant	286362	exon1			GAAGATTAGCACA		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.90A>C	9.37:g.107380396T>G		Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	371	162	0.436658	NM_001001956	Q6IFL2	Silent	SNP	ENST00000259362.1	37	CCDS35093.1																																																																																			T|0.792;G|0.208	0.208	strong		0.408	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
THBS4	7060	hgsc.bcm.edu	37	5	79351852	79351852	+	Silent	SNP	A	A	T	rs71594659|rs438042	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79351852A>T	ENST00000350881.2	+	3	727	c.537A>T	c.(535-537)ccA>ccT	p.P179P	THBS4_ENST00000511733.1_Silent_p.P88P|CTD-2201I18.1_ENST00000503007.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	179	Laminin G-like.				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)	p.P179P(1)		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)		AGAGGAAGCCACAGGTAGGAA	0.537													A|||	2852	0.569489	0.6536	0.5476	5008	,	,		17271	0.5139		0.5527	False		,,,				2504	0.546				p.P179P		Atlas-SNP	.											THBS4,NS,carcinoma,0,1	THBS4	82	1	1	Substitution - coding silent(1)	stomach(1)	c.A537T						PASS	.	A		2744,1660		894,956,352	20.0	24.0	23.0		537	-3.2	1.0	5	dbSNP_80	23	4236,4362		1063,2110,1126	no	coding-synonymous	THBS4	NM_003248.4		1957,3066,1478	TT,TA,AA		49.2673,37.693,46.316		179/962	79351852	6980,6022	2202	4299	6501	SO:0001819	synonymous_variant	7060	exon3			GAAGCCACAGGTA		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.537A>T	5.37:g.79351852A>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_003248	B2R909|Q86TG2	Silent	SNP	ENST00000350881.2	37	CCDS4049.1																																																																																			ACAGGTAGG|0.500;TCAGGTAAA|0.500	.	alt		0.537	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
RAD9B	144715	hgsc.bcm.edu	37	12	110960196	110960196	+	Missense_Mutation	SNP	G	G	A	rs34513555	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:110960196G>A	ENST00000409778.3	+	8	922	c.898G>A	c.(898-900)Ggg>Agg	p.G300R	RAD9B_ENST00000409425.1_Missense_Mutation_p.G297R|RAD9B_ENST00000409246.1_Missense_Mutation_p.G297R|RAD9B_ENST00000392672.4_Missense_Mutation_p.G369R|RAD9B_ENST00000409300.1_Missense_Mutation_p.G369R			Q6WBX8	RAD9B_HUMAN	RAD9 homolog B (S. pombe)	366					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	checkpoint clamp complex (GO:0030896)|nucleoplasm (GO:0005654)				endometrium(1)|large_intestine(2)|lung(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	7						GGAAGTGCCAGGGTCTCTGTG	0.468													G|||	385	0.076877	0.1513	0.0346	5008	,	,		16243	0.0685		0.0378	False		,,,				2504	0.0552				p.G369R		Atlas-SNP	.											.	RAD9B	50	.	0			c.G1105A						PASS	.	G	ARG/GLY	644,3762	261.9+/-264.6	53,538,1612	68.0	52.0	57.0		1105	1.3	0.0	12	dbSNP_126	57	282,8318	100.1+/-161.6	6,270,4024	yes	missense	RAD9B	NM_152442.3	125	59,808,5636	AA,AG,GG		3.2791,14.6164,7.1198	benign	369/430	110960196	926,12080	2203	4300	6503	SO:0001583	missense	144715	exon10			GTGCCAGGGTCTC		CCDS9148.2, CCDS66469.1, CCDS73526.1, CCDS73527.1	12q24.13	2008-12-15	2008-12-15		ENSG00000151164	ENSG00000151164			21700	protein-coding gene	gene with protein product		608368					Standard	NM_152442		Approved	FLJ40346	uc001trf.4	Q6WBX8	OTTHUMG00000152952	ENST00000409778.3:c.898G>A	12.37:g.110960196G>A	ENSP00000386697:p.Gly300Arg	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	213	113	0.530516	NM_152442	Q5U5K0|Q6NVJ1|Q6ZVT7|Q8N7T9|Q96LI8	Missense_Mutation	SNP	ENST00000409778.3	37		144	0.06593406593406594	66	0.13414634146341464	13	0.03591160220994475	34	0.05944055944055944	31	0.040897097625329816	G	10.62	1.402734	0.25291	0.146164	0.032791	ENSG00000151164	ENST00000409246;ENST00000392672;ENST00000409300;ENST00000409425;ENST00000409778	T;T;T;T;T	0.22945	1.93;2.25;2.27;1.93;2.1	5.26	1.29	0.21616	.	1.349910	0.04442	N	0.371039	T	0.00144	0.0004	L	0.44542	1.39	0.09310	N	1	B;B;B	0.31125	0.025;0.309;0.294	B;B;B	0.32289	0.019;0.143;0.078	T	0.21552	-1.0242	10	0.51188	T	0.08	-0.1357	7.6457	0.28318	0.3825:0.0:0.6175:0.0	rs34513555;rs34513555	300;369;366	B4DYM6;B4DX60;Q6WBX8	.;.;RAD9B_HUMAN	R	297;369;369;297;300	ENSP00000387329:G297R;ENSP00000376440:G369R;ENSP00000386434:G369R;ENSP00000386629:G297R;ENSP00000386697:G300R	ENSP00000376440:G369R	G	+	1	0	RAD9B	109444579	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.018000	0.13422	0.300000	0.22699	-0.140000	0.14226	GGG	G|0.924;A|0.076	0.076	strong		0.468	RAD9B-009	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404634.1	NM_152442	
ESYT2	57488	hgsc.bcm.edu	37	7	158536334	158536334	+	Silent	SNP	G	G	A	rs2305474	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:158536334G>A	ENST00000251527.5	-	16	1826	c.1761C>T	c.(1759-1761)aaC>aaT	p.N587N	ESYT2_ENST00000435514.2_Silent_p.N22N	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	615	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						GGACCTTCAGGTTCCCCAGGG	0.542													G|||	1287	0.256989	0.2829	0.1326	5008	,	,		17626	0.5417		0.0656	False		,,,				2504	0.2137				p.N587N		Atlas-SNP	.											.	ESYT2	70	.	0			c.C1761T						PASS	.			1021,3385	377.3+/-322.4	128,765,1310	79.0	64.0	69.0		1761	1.3	0.0	7	dbSNP_100	69	552,8048	150.7+/-205.6	14,524,3762	no	coding-synonymous	ESYT2	NM_020728.2		142,1289,5072	AA,AG,GG		6.4186,23.1729,12.0944		587/894	158536334	1573,11433	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon16			CTTCAGGTTCCCC	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1761C>T	7.37:g.158536334G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	67	46	0.686567	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			G|0.846;A|0.154	0.154	strong		0.542	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
F5	2153	hgsc.bcm.edu	37	1	169512027	169512027	+	Silent	SNP	T	T	C	rs6021	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:169512027T>C	ENST00000367797.3	-	13	2502	c.2301A>G	c.(2299-2301)tcA>tcG	p.S767S	F5_ENST00000367796.3_Silent_p.S772S	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	767	B.				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)	TATCTGTGTTTGAAGAAACGA	0.393													C|||	1316	0.26278	0.1679	0.3948	5008	,	,		21933	0.248		0.2535	False		,,,				2504	0.3221				p.S767S		Atlas-SNP	.											.	F5	301	.	0			c.A2301G						PASS	.	C		813,3593	750.9+/-412.2	68,677,1458	165.0	159.0	161.0		2301	0.8	0.0	1	dbSNP_52	161	2355,6245	702.6+/-405.3	299,1757,2244	no	coding-synonymous	F5	NM_000130.4		367,2434,3702	CC,CT,TT		27.3837,18.4521,24.358		767/2225	169512027	3168,9838	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			TGTGTTTGAAGAA	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.2301A>G	1.37:g.169512027T>C		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			T|0.763;C|0.237	0.237	strong		0.393	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
C1orf53	388722	hgsc.bcm.edu	37	1	197874949	197874949	+	Silent	SNP	T	T	C	rs2270763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	290	2	0.00689655		WXS	Illumina HiSeq	Phase_I	363	362	0.997245	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	
FAM178A	55719	hgsc.bcm.edu	37	10	102716222	102716222	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102716222A>G	ENST00000238961.4	+	18	3887	c.3345A>G	c.(3343-3345)ctA>ctG	p.L1115L	FAM178A_ENST00000370269.3_Silent_p.L1115L	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	1115						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											ACTTTGTGCTACTCTGTGGGG	0.328																																					p.L1115L		Atlas-SNP	.											.	FAM178A	9	.	0			c.A3345G						PASS	.						145.0	143.0	144.0					10																	102716222		2203	4300	6503	SO:0001819	synonymous_variant	55719	exon18			TGTGCTACTCTGT	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.3345A>G	10.37:g.102716222A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	98	4	0.0408163	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Silent	SNP	ENST00000238961.4	37	CCDS7500.1																																																																																			.	.	none		0.328	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3		
GPER1	2852	hgsc.bcm.edu	37	7	1131411	1131411	+	Missense_Mutation	SNP	C	C	T	rs11544331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:1131411C>T	ENST00000297469.3	+	2	738	c.47C>T	c.(46-48)cCa>cTa	p.P16L	GPER1_ENST00000397092.1_Missense_Mutation_p.P16L|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron|GPER1_ENST00000401670.1_Missense_Mutation_p.P16L|GPER1_ENST00000397088.3_Missense_Mutation_p.P16L|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_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	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	191	121	0.633508	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	
NLRP2	55655	hgsc.bcm.edu	37	19	55485899	55485899	+	Silent	SNP	G	G	A	rs2217659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55485899G>A	ENST00000543010.1	+	3	455	c.312G>A	c.(310-312)aaG>aaA	p.K104K	NLRP2_ENST00000391721.4_Silent_p.K104K|NLRP2_ENST00000339757.7_Silent_p.K104K|NLRP2_ENST00000427260.2_Silent_p.K81K|NLRP2_ENST00000263437.6_Silent_p.K104K|NLRP2_ENST00000537859.1_Silent_p.K104K|NLRP2_ENST00000538819.1_Silent_p.K104K|NLRP2_ENST00000448584.2_Silent_p.K104K	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	104					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)		ATAAAAGGAAGCCTCTATCAT	0.358													.|||	887	0.177117	0.093	0.1542	5008	,	,		17526	0.3512		0.1779	False		,,,				2504	0.1268				p.K104K		Atlas-SNP	.											.	NLRP2	161	.	0			c.G312A						PASS	.	G	,,,	502,3902	229.8+/-244.2	31,440,1731	99.0	102.0	101.0		312,312,243,312	-2.6	0.0	19	dbSNP_96	101	1525,7075	285.7+/-297.3	145,1235,2920	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	176,1675,4651	AA,AG,GG		17.7326,11.3987,15.5875	,,,	104/1063,104/1041,81/1040,104/1063	55485899	2027,10977	2202	4300	6502	SO:0001819	synonymous_variant	55655	exon3			AAGGAAGCCTCTA	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.312G>A	19.37:g.55485899G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_001174082	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			G|0.829;A|0.171	0.171	strong		0.358	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
HHLA3	11147	hgsc.bcm.edu	37	1	70820880	70820880	+	Silent	SNP	G	G	A	rs55863806	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:70820880G>A	ENST00000359875.5	+	1	386	c.246G>A	c.(244-246)gcG>gcA	p.A82A	HHLA3_ENST00000361764.4_Intron|HHLA3_ENST00000370940.5_Intron|ANKRD13C_ENST00000370944.4_5'Flank|HHLA3_ENST00000531950.1_Silent_p.A82A|ANKRD13C_ENST00000262346.6_5'Flank|HHLA3_ENST00000486110.1_3'UTR|HHLA3_ENST00000432224.1_Silent_p.A82A	NM_001036645.1	NP_001031722.1	Q9XRX5	HHLA3_HUMAN	HERV-H LTR-associating 3	82										large_intestine(3)|lung(1)	4						aattaaaAGCGGAGGCGGGGA	0.453													G|||	467	0.0932508	0.0325	0.0908	5008	,	,		19262	0.0605		0.1044	False		,,,				2504	0.1994				p.A82A		Atlas-SNP	.											.	HHLA3	11	.	0			c.G246A						PASS	.	G	,,	175,4231	111.6+/-149.8	5,165,2033	36.0	38.0	37.0		,246,	-3.4	0.0	1	dbSNP_129	37	788,7812	183.6+/-231.8	27,734,3539	no	intron,coding-synonymous,intron	HHLA3	NM_001031693.2,NM_001036645.1,NM_001036646.1	,,	32,899,5572	AA,AG,GG		9.1628,3.9719,7.4043	,,	,82/115,	70820880	963,12043	2203	4300	6503	SO:0001819	synonymous_variant	11147	exon1			AAAAGCGGAGGCG	AF126164	CCDS649.1, CCDS30752.1, CCDS30753.1	1p31.1	2008-02-05			ENSG00000197568	ENSG00000197568			4906	protein-coding gene	gene with protein product		604372				10444326	Standard	NR_027404		Approved		uc001dfa.3	Q9XRX5	OTTHUMG00000009346	ENST00000359875.5:c.246G>A	1.37:g.70820880G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	44	8	0.181818	NM_001036645	D3DQ74|Q5VZP2|Q96FH5|Q9XRX4	Silent	SNP	ENST00000359875.5	37	CCDS30753.1																																																																																			G|0.926;A|0.074	0.074	strong		0.453	HHLA3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025911.2	NM_007071	
SEL1L2	80343	hgsc.bcm.edu	37	20	13912309	13912309	+	Missense_Mutation	SNP	G	G	A	rs41275404	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:13912309G>A	ENST00000284951.5	-	3	297	c.223C>T	c.(223-225)Cgt>Tgt	p.R75C	SEL1L2_ENST00000378072.5_Missense_Mutation_p.R75C|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	75						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						CTTATTTTACGTTGATTCTTC	0.249													G|||	271	0.0541134	0.0083	0.0922	5008	,	,		15442	0.001		0.1471	False		,,,				2504	0.0481				p.R75C		Atlas-SNP	.											SEL1L2,colon,carcinoma,0,1	SEL1L2	103	1	0			c.C223T						PASS	.	G	CYS/ARG	99,3455		1,97,1679	59.0	52.0	54.0		223	1.9	0.0	20	dbSNP_127	54	1041,7023		65,911,3056	yes	missense	SEL1L2	NM_025229.1	180	66,1008,4735	AA,AG,GG		12.9092,2.7856,9.8124	possibly-damaging	75/689	13912309	1140,10478	1777	4032	5809	SO:0001583	missense	80343	exon3			TTTTACGTTGATT	AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.223C>T	20.37:g.13912309G>A	ENSP00000284951:p.Arg75Cys	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	154	65	0.422078	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		151	0.06913919413919414	7	0.014227642276422764	34	0.09392265193370165	0	0.0	110	0.14511873350923482	G	6.852	0.526474	0.13066	0.027856	0.129092	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.24723	1.84;2.16	5.11	1.92	0.25849	.	1.668320	0.03077	N	0.157986	T	0.00073	0.0002	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	0.21861	-1.0233	9	0.37606	T	0.19	3.976	2.2167	0.03962	0.1072:0.1386:0.4371:0.3171	rs41275404	75;75	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	C	75	ENSP00000367312:R75C;ENSP00000284951:R75C	ENSP00000284951:R75C	R	-	1	0	SEL1L2	13860309	0.627000	0.27129	0.000000	0.03702	0.309000	0.27889	1.730000	0.38125	0.222000	0.20900	0.655000	0.94253	CGT	G|0.910;A|0.090	0.090	strong		0.249	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
GLMN	11146	hgsc.bcm.edu	37	1	92754667	92754667	+	Missense_Mutation	SNP	C	C	T	rs61754623	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:92754667C>T	ENST00000370360.3	-	6	517	c.436G>A	c.(436-438)Gca>Aca	p.A146T	GLMN_ENST00000534881.1_Missense_Mutation_p.A146T	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein	146					muscle cell differentiation (GO:0042692)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of T cell proliferation (GO:0042130)|neural tube closure (GO:0001843)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of phosphorylation (GO:0042327)|regulation of gene expression, epigenetic (GO:0040029)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|vasculogenesis (GO:0001570)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul3-RING ubiquitin ligase complex (GO:0031463)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|cullin-RING ubiquitin ligase complex (GO:0031461)|intracellular (GO:0005622)	hepatocyte growth factor receptor binding (GO:0005171)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase inhibitor activity (GO:0055105)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	17		all_lung(203;0.00827)|Lung NSC(277;0.0295)		all cancers(265;0.00702)|GBM - Glioblastoma multiforme(16;0.0381)|Epithelial(280;0.0989)		GTAGACAATGCTAATCCAATT	0.383									Multiple Glomus Tumors (of the Skin), Familial				C|||	10	0.00199681	0.0008	0.0058	5008	,	,		21197	0.0		0.005	False		,,,				2504	0.0				p.A146T		Atlas-SNP	.											.	GLMN	37	.	0			c.G436A						PASS	.	C	THR/ALA	11,4395	17.9+/-39.9	0,11,2192	105.0	97.0	99.0		436	3.8	1.0	1	dbSNP_129	99	60,8540	37.4+/-92.8	0,60,4240	yes	missense	GLMN	NM_053274.2	58	0,71,6432	TT,TC,CC		0.6977,0.2497,0.5459	possibly-damaging	146/595	92754667	71,12935	2203	4300	6503	SO:0001583	missense	11146	exon6	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	ACAATGCTAATCC	U73704	CCDS738.1	1p22.1	2008-02-05	2004-07-01		ENSG00000174842	ENSG00000174842			14373	protein-coding gene	gene with protein product		601749	"""venous malformation with glomus cells"""	VMGLOM		8955134	Standard	XM_005270400		Approved	FAP48, GLML, GVM, FKBPAP	uc001dor.3	Q92990	OTTHUMG00000010283	ENST00000370360.3:c.436G>A	1.37:g.92754667C>T	ENSP00000359385:p.Ala146Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	58	49	0.844828	NM_053274	Q5VVC3|Q9BVE8	Missense_Mutation	SNP	ENST00000370360.3	37	CCDS738.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	15.94	2.981941	0.53827	0.002497	0.006977	ENSG00000174842	ENST00000370360;ENST00000534881	T;T	0.52754	0.65;0.65	5.69	3.8	0.43715	.	0.217361	0.48767	N	0.000163	T	0.17662	0.0424	L	0.39633	1.23	0.40000	D	0.975158	B;B	0.24426	0.064;0.103	B;B	0.22152	0.038;0.038	T	0.06180	-1.0841	10	0.25106	T	0.35	-9.4675	6.2615	0.20903	0.2337:0.6103:0.0:0.156	rs61754623	146;146	B4DJ85;Q92990	.;GLMN_HUMAN	T	146	ENSP00000359385:A146T;ENSP00000440156:A146T	ENSP00000359385:A146T	A	-	1	0	GLMN	92527255	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.288000	0.33296	1.399000	0.46721	0.585000	0.79938	GCA	C|0.996;T|0.004	0.004	strong		0.383	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	NM_007070	
CAMKMT	79823	hgsc.bcm.edu	37	2	44942450	44942450	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:44942450A>G	ENST00000378494.3	+	7	625	c.581A>G	c.(580-582)aAt>aGt	p.N194S		NM_024766.4	NP_079042.1	Q7Z624	CMKMT_HUMAN	calmodulin-lysine N-methyltransferase	194						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	calmodulin-lysine N-methyltransferase activity (GO:0018025)			breast(2)|large_intestine(3)|lung(5)	10						ATCACAAGGAATCAGAAGGCT	0.363																																					p.N194S		Atlas-SNP	.											.	CAMKMT	20	.	0			c.A581G						PASS	.						87.0	92.0	90.0					2																	44942450		2203	4300	6503	SO:0001583	missense	79823	exon7			CAAGGAATCAGAA		CCDS1820.1	2p21	2011-06-22	2011-03-10	2011-03-10	ENSG00000143919	ENSG00000143919	2.1.1.60		26276	protein-coding gene	gene with protein product	"""CaM KMT"""	609559	"""chromosome 2 open reading frame 34"""	C2orf34		20975703	Standard	NM_024766		Approved	CLNMT	uc002rum.3	Q7Z624	OTTHUMG00000128761	ENST00000378494.3:c.581A>G	2.37:g.44942450A>G	ENSP00000367755:p.Asn194Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_024766	Q4ZG15|Q53SS6|Q8N6P5|Q9H5G8	Missense_Mutation	SNP	ENST00000378494.3	37	CCDS1820.1	.	.	.	.	.	.	.	.	.	.	A	17.82	3.482904	0.63962	.	.	ENSG00000143919	ENST00000378494	T	0.12879	2.64	5.52	5.52	0.82312	.	0.086330	0.85682	D	0.000000	T	0.39279	0.1072	M	0.89478	3.035	0.80722	D	1	D	0.56746	0.977	P	0.61874	0.895	T	0.42050	-0.9474	10	0.72032	D	0.01	-12.628	10.9403	0.47270	0.8434:0.1566:0.0:0.0	.	194	Q7Z624	CMKMT_HUMAN	S	194	ENSP00000367755:N194S	ENSP00000367755:N194S	N	+	2	0	CAMKMT	44795954	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.066000	0.64351	2.104000	0.64026	0.528000	0.53228	AAT	.	.	none		0.363	CAMKMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250678.2	NM_024766	
CEP135	9662	hgsc.bcm.edu	37	4	56874517	56874517	+	Missense_Mutation	SNP	A	A	C	rs3214045	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:56874517A>C	ENST00000257287.4	+	18	2429	c.2305A>C	c.(2305-2307)Ata>Cta	p.I769L		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	769			I -> L (in dbSNP:rs3214045).		centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					TCAAATGAAGATAATGATCTC	0.289													a|||	697	0.139177	0.087	0.1182	5008	,	,		18162	0.0913		0.2714	False		,,,				2504	0.138				p.I769L		Atlas-SNP	.											.	CEP135	115	.	0			c.A2305C						PASS	.	C	LEU/ILE	529,3877	237.1+/-249.0	28,473,1702	77.0	80.0	79.0		2305	-6.1	0.0	4	dbSNP_106	79	2212,6386	373.7+/-337.1	267,1678,2354	yes	missense	CEP135	NM_025009.3	5	295,2151,4056	CC,CA,AA		25.7269,12.0064,21.0781	benign	769/1141	56874517	2741,10263	2203	4299	6502	SO:0001583	missense	9662	exon18			ATGAAGATAATGA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"""KIAA0635"", ""centrosomal protein 4"""	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.2305A>C	4.37:g.56874517A>C	ENSP00000257287:p.Ile769Leu	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	85	83	0.976471	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	360	0.16483516483516483	40	0.08130081300813008	45	0.12430939226519337	63	0.11013986013986014	212	0.2796833773087071	a	0.064	-1.216297	0.01542	0.120064	0.257269	ENSG00000174799	ENST00000257287	T	0.16597	2.33	5.62	-6.14	0.02111	.	0.837336	0.11284	N	0.580002	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	0.48525	-0.9028	9	0.27082	T	0.32	.	7.6315	0.28243	0.3133:0.323:0.3638:0.0	rs3214045;rs52815254;rs61495232;rs3214045	769	Q66GS9	CP135_HUMAN	L	769	ENSP00000257287:I769L	ENSP00000257287:I769L	I	+	1	0	CEP135	56569274	0.062000	0.20869	0.003000	0.11579	0.010000	0.07245	-1.014000	0.03641	-0.994000	0.03463	-3.568000	0.00029	ATA	A|0.815;C|0.185;G|0.000	0.185	strong		0.289	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	
FARP2	9855	hgsc.bcm.edu	37	2	242407588	242407588	+	Missense_Mutation	SNP	G	G	A	rs41342147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242407588G>A	ENST00000264042.3	+	18	2097	c.1927G>A	c.(1927-1929)Gtc>Atc	p.V643I		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	643	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		V -> I (in dbSNP:rs41342147).		actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		ACATGACGAGGTCCTAACAGA	0.522													G|||	422	0.0842652	0.0938	0.0893	5008	,	,		20182	0.0258		0.1153	False		,,,				2504	0.0961				p.V643I		Atlas-SNP	.											FARP2,rectum,carcinoma,-2,1	FARP2	92	1	0			c.G1927A						PASS	.	G	ILE/VAL	376,4030	188.1+/-214.6	19,338,1846	167.0	169.0	169.0		1927	5.0	1.0	2	dbSNP_127	169	1140,7460	235.3+/-267.9	72,996,3232	yes	missense	FARP2	NM_014808.2	29	91,1334,5078	AA,AG,GG		13.2558,8.5338,11.6562	probably-damaging	643/1055	242407588	1516,11490	2203	4300	6503	SO:0001583	missense	9855	exon18			GACGAGGTCCTAA	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1927G>A	2.37:g.242407588G>A	ENSP00000264042:p.Val643Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	185	0.08470695970695971	43	0.08739837398373984	28	0.07734806629834254	21	0.03671328671328671	93	0.12269129287598944	G	21.3	4.129199	0.77549	0.085338	0.132558	ENSG00000006607	ENST00000264042	T	0.63417	-0.04	4.96	4.96	0.65561	Dbl homology (DH) domain (5);	0.000000	0.64402	D	0.000001	T	0.01523	0.0049	L	0.31804	0.96	0.09310	P	1.0	D	0.76494	0.999	D	0.85130	0.997	T	0.13229	-1.0517	9	0.12766	T	0.61	.	18.2382	0.89957	0.0:0.0:1.0:0.0	rs41342147;rs61752501;rs41342147	643	O94887	FARP2_HUMAN	I	643	ENSP00000264042:V643I	ENSP00000264042:V643I	V	+	1	0	FARP2	242056261	1.000000	0.71417	0.975000	0.42487	0.898000	0.52572	9.096000	0.94182	2.290000	0.77057	0.655000	0.94253	GTC	G|0.892;A|0.108	0.108	strong		0.522	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
PEX11G	92960	hgsc.bcm.edu	37	19	7542118	7542118	+	Silent	SNP	G	G	A	rs7256275	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:7542118G>A	ENST00000221480.1	-	5	704	c.696C>T	c.(694-696)gcC>gcT	p.A232A	PEX11G_ENST00000593942.1_Silent_p.A162A|PEX11G_ENST00000599519.1_5'UTR	NM_001270539.1|NM_080662.3	NP_001257468.1|NP_542393.1	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	232					peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						CCTGGCCGCCGGCCCGGGCCG	0.711													G|||	708	0.141374	0.2254	0.1383	5008	,	,		13753	0.1389		0.0706	False		,,,				2504	0.1053				p.A232A		Atlas-SNP	.											.	PEX11G	16	.	0			c.C696T						PASS	.	G		835,3479		79,677,1401	7.0	11.0	10.0		696	-7.8	0.0	19	dbSNP_116	10	555,7895		21,513,3691	no	coding-synonymous	PEX11G	NM_080662.2		100,1190,5092	AA,AG,GG		6.568,19.3556,10.89		232/242	7542118	1390,11374	2157	4225	6382	SO:0001819	synonymous_variant	92960	exon5			GCCGCCGGCCCGG	BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883			20208	protein-coding gene	gene with protein product		607583				12417726	Standard	NM_080662		Approved		uc002mgk.2	Q96HA9		ENST00000221480.1:c.696C>T	19.37:g.7542118G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_080662	Q8NDM0	Silent	SNP	ENST00000221480.1	37	CCDS12178.1																																																																																			G|0.870;A|0.130	0.130	strong		0.711	PEX11G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458965.1	NM_080662	
OPN4	94233	hgsc.bcm.edu	37	10	88422028	88422028	+	Missense_Mutation	SNP	C	C	G	rs34191521	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:88422028C>G	ENST00000241891.5	+	8	1260	c.1093C>G	c.(1093-1095)Ctg>Gtg	p.L365V	OPN4_ENST00000372071.2_Missense_Mutation_p.L376V	NM_033282.3	NP_150598.1	Q9UHM6	OPN4_HUMAN	opsin 4	365					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						TGCCCAGCACCTGCCCTGCCT	0.677													C|||	197	0.0393371	0.003	0.1556	5008	,	,		18411	0.001		0.0298	False		,,,				2504	0.0552				p.L376V		Atlas-SNP	.											.	OPN4	61	.	0			c.C1126G						PASS	.	C	VAL/LEU,VAL/LEU	25,4381		0,25,2178	26.0	22.0	23.0		1126,1093	-0.4	1.0	10	dbSNP_126	23	221,8377		2,217,4080	yes	missense,missense	OPN4	NM_001030015.2,NM_033282.3	32,32	2,242,6258	GG,GC,CC		2.5704,0.5674,1.8917	benign,benign	376/490,365/479	88422028	246,12758	2203	4299	6502	SO:0001583	missense	94233	exon9			CAGCACCTGCCCT	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.1093C>G	10.37:g.88422028C>G	ENSP00000241891:p.Leu365Val	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	107	84	0.785047	NM_001030015	B7ZLB3|Q14D01|Q2PP22|Q8NGQ9	Missense_Mutation	SNP	ENST00000241891.5	37	CCDS7376.1	76	0.0347985347985348	3	0.006097560975609756	49	0.13535911602209943	1	0.0017482517482517483	23	0.030343007915567283	C	2.901	-0.227540	0.06022	0.005674	0.025704	ENSG00000122375	ENST00000372071;ENST00000241891;ENST00000443292	T;T;T	0.48836	0.8;0.8;0.8	5.39	-0.368	0.12537	.	0.337294	0.22598	N	0.057994	T	0.00210	0.0006	L	0.39566	1.225	0.34048	D	0.655787	B;B;B	0.22800	0.031;0.016;0.075	B;B;B	0.29440	0.034;0.019;0.102	T	0.14364	-1.0475	10	0.02654	T	1	.	1.4865	0.02447	0.191:0.3918:0.1123:0.3048	rs34191521	376;365;376	C9JWU6;Q9UHM6;Q9UHM6-2	.;OPN4_HUMAN;.	V	376;365;376	ENSP00000361141:L376V;ENSP00000241891:L365V;ENSP00000393132:L376V	ENSP00000241891:L365V	L	+	1	2	OPN4	88412008	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	0.953000	0.29162	0.249000	0.21456	0.655000	0.94253	CTG	C|0.977;G|0.023	0.023	strong		0.677	OPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049158.2	NM_033282	
MUC17	140453	hgsc.bcm.edu	37	7	100677556	100677556	+	Silent	SNP	A	A	C	rs4373459	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677556A>C	ENST00000306151.4	+	3	2923	c.2859A>C	c.(2857-2859)acA>acC	p.T953T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	953	59 X approximate tandem repeats.|Ser-rich.				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)					ACACCAGCACACCTGTGACCA	0.498																																					p.T953T		Atlas-SNP	.											MUC17,colon,carcinoma,0,1	MUC17	804	1	0			c.A2859C						scavenged	.	A		426,3980	162.9+/-194.8	0,426,1777	317.0	293.0	301.0		2859	-0.2	0.0	7	dbSNP_111	301	518,8082	119.5+/-178.9	0,518,3782	no	coding-synonymous	MUC17	NM_001040105.1		0,944,5559	CC,CA,AA		6.0233,9.6686,7.2582		953/4494	100677556	944,12062	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAGCACACCTGTG	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.2859A>C	7.37:g.100677556A>C		Somatic	176	2	0.0113636		WXS	Illumina HiSeq	Phase_I	534	174	0.325843	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			A|0.947;C|0.053	0.053	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
OR2L8	391190	hgsc.bcm.edu	37	1	248112915	248112915	+	Silent	SNP	A	A	G	rs10888280	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248112915A>G	ENST00000357191.3	+	1	756	c.756A>G	c.(754-756)gcA>gcG	p.A252A	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	252						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(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	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)			TCTACTATGCACCTTTTGTCT	0.478													A|||	1552	0.309904	0.1354	0.3458	5008	,	,		21316	0.4216		0.2952	False		,,,				2504	0.4202				p.A252A		Atlas-SNP	.											OR2L8,right_upper_lobe,carcinoma,+1,1	OR2L8	92	1	0			c.A756G						scavenged	.	A	,	673,3733		48,577,1578	142.0	102.0	115.0		756,	0.6	0.2	1	dbSNP_120	115	2622,5974		396,1830,2072	no	coding-synonymous,intron	OR2L13,OR2L8	NM_001001963.1,NM_175911.2	,	444,2407,3650	GG,GA,AA		30.5026,15.2746,25.3423	,	252/313,	248112915	3295,9707	2203	4298	6501	SO:0001819	synonymous_variant	391190	exon1			CTATGCACCTTTT	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.756A>G	1.37:g.248112915A>G		Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	372	120	0.322581	NM_001001963	Q6IF03	Silent	SNP	ENST00000357191.3	37	CCDS31101.1																																																																																			.	.	weak		0.478	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
FAM126A	84668	hgsc.bcm.edu	37	7	23015831	23015831	+	Silent	SNP	T	T	C	rs3735231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:23015831T>C	ENST00000432176.2	-	7	856	c.624A>G	c.(622-624)tcA>tcG	p.S208S	FAM126A_ENST00000409923.1_Silent_p.S208S	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	208					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						TACTTTACCTTGAACAAATTT	0.318													T|||	1877	0.3748	0.3578	0.33	5008	,	,		18391	0.4663		0.3628	False		,,,				2504	0.3476				p.S208S		Atlas-SNP	.											FAM126A,NS,carcinoma,-1,1	FAM126A	53	1	0			c.A624G						PASS	.	T		1514,2892	479.2+/-358.4	276,962,965	86.0	84.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	624	5.5	1.0	7	dbSNP_107	85	2966,5632	460.2+/-365.1	518,1930,1851	no	coding-synonymous	FAM126A	NM_032581.3		794,2892,2816	CC,CT,TT		34.4964,34.3622,34.4509		208/522	23015831	4480,8524	2203	4299	6502	SO:0001819	synonymous_variant	84668	exon7			TTACCTTGAACAA	BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"""down regulated by Ctnnb1, a"""	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.624A>G	7.37:g.23015831T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Silent	SNP	ENST00000432176.2	37	CCDS5377.1	823	0.3768315018315018	154	0.3130081300813008	130	0.35911602209944754	269	0.47027972027972026	270	0.3562005277044855	T	12.31	1.900832	0.33535	0.343622	0.344964	ENSG00000122591	ENST00000440481	.	.	.	5.49	5.49	0.81192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43653	-0.9378	3	.	.	.	-16.156	15.587	0.76491	0.0:0.0:0.0:1.0	rs3735231;rs10368120;rs17147509;rs58350469;rs3735231	.	.	.	R	260	.	.	Q	-	2	0	FAM126A	22982356	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	1.643000	0.37217	2.092000	0.63282	0.374000	0.22700	CAA	T|0.643;C|0.357	0.357	strong		0.318	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581	
ZNF16	7564	hgsc.bcm.edu	37	8	146157339	146157339	+	Silent	SNP	T	T	C	rs3735787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:146157339T>C	ENST00000276816.4	-	4	1020	c.834A>G	c.(832-834)tcA>tcG	p.S278S	ZNF16_ENST00000394909.2_Silent_p.S278S	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	278	Required for nuclear localization.				cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|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(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		TAGAAAAGTCTGAGTGCCCTC	0.473													T|||	1127	0.22504	0.1263	0.2104	5008	,	,		20473	0.3383		0.2535	False		,,,				2504	0.2229				p.S278S		Atlas-SNP	.											ZNF16,NS,adenoma,0,1	ZNF16	80	1	0			c.A834G						PASS	.	T	,	570,3836	254.0+/-259.7	39,492,1672	116.0	114.0	115.0		834,834	-0.6	0.0	8	dbSNP_107	115	2091,6509	362.5+/-332.8	220,1651,2429	no	coding-synonymous,coding-synonymous	ZNF16	NM_001029976.2,NM_006958.2	,	259,2143,4101	CC,CT,TT		24.314,12.9369,20.4598	,	278/683,278/683	146157339	2661,10345	2203	4300	6503	SO:0001819	synonymous_variant	7564	exon3			AAAGTCTGAGTGC	X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"""Zinc fingers, C2H2-type"""	12947	protein-coding gene	gene with protein product		601262	"""zinc finger protein 16 (KOX 9)"""				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.834A>G	8.37:g.146157339T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	186	47	0.252688	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Silent	SNP	ENST00000276816.4	37	CCDS6437.1																																																																																			T|0.784;C|0.216	0.216	strong		0.473	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958	
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959776	45959776	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:45959776C>A	ENST00000400375.1	-	1	302	c.258G>T	c.(256-258)caG>caT	p.Q86H	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	86	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.Q86H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						agcaagccggctggcagctag	0.672																																					p.Q86H		Atlas-SNP	.											KRTAP10-1,NS,carcinoma,0,1	KRTAP10-1	34	1	1	Substitution - Missense(1)	prostate(1)	c.G258T						scavenged	.						37.0	43.0	41.0					21																	45959776		2181	4262	6443	SO:0001583	missense	386677	exon1			AGCCGGCTGGCAG	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.258G>T	21.37:g.45959776C>A	ENSP00000383226:p.Gln86His	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	141	10	0.070922	NM_198691	Q0VAR0|Q0VAR1	Missense_Mutation	SNP	ENST00000400375.1	37	CCDS42954.1	.	.	.	.	.	.	.	.	.	.	c	3.333	-0.136213	0.06711	.	.	ENSG00000215455	ENST00000400375;ENST00000545982	T	0.01043	5.41	3.32	2.42	0.29668	.	.	.	.	.	T	0.08358	0.0208	M	0.93763	3.455	0.20196	N	0.99992	D	0.71674	0.998	D	0.75020	0.985	T	0.04593	-1.0940	9	0.87932	D	0	.	7.939	0.29946	0.0:0.871:0.0:0.129	.	86	P60331	KR101_HUMAN	H	86	ENSP00000383226:Q86H	ENSP00000383226:Q86H	Q	-	3	2	KRTAP10-1	44784204	0.957000	0.32711	0.990000	0.47175	0.259000	0.26198	1.028000	0.30128	1.856000	0.53863	0.491000	0.48974	CAG	.	.	none		0.672	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1		
DTX2	113878	hgsc.bcm.edu	37	7	76126737	76126737	+	Missense_Mutation	SNP	C	C	T	rs145964625		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76126737C>T	ENST00000324432.5	+	7	1603	c.1093C>T	c.(1093-1095)Cgt>Tgt	p.R365C	DTX2_ENST00000430490.2_Missense_Mutation_p.R365C|DTX2_ENST00000413936.2_Missense_Mutation_p.R365C|DTX2_ENST00000307569.8_Intron|DTX2_ENST00000446820.2_Intron|DTX2_ENST00000446600.1_Missense_Mutation_p.R274C	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	365					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)	p.R365C(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						TCCCGCCTCCCGTCTGGCTTC	0.557																																					p.R365C		Atlas-SNP	.											DTX2,NS,haematopoietic_neoplasm,0,3	DTX2	64	3	1	Substitution - Missense(1)	large_intestine(1)	c.C1093T						scavenged	.						34.0	34.0	34.0					7																	76126737		2199	4273	6472	SO:0001583	missense	113878	exon6			GCCTCCCGTCTGG		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.1093C>T	7.37:g.76126737C>T	ENSP00000322885:p.Arg365Cys	Somatic	477	1	0.00209644		WXS	Illumina HiSeq	Phase_I	632	91	0.143987	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	37	CCDS5587.1	.	.	.	.	.	.	.	.	.	.	.	13.40	2.224425	0.39300	.	.	ENSG00000091073	ENST00000324432;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000430490	T;T;T;T	0.12147	2.72;2.71;2.72;2.72	5.41	-3.71	0.04424	.	1.247470	0.05079	N	0.483163	T	0.07188	0.0182	N	0.04203	-0.255	0.80722	D	1	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.22243	-1.0222	10	0.42905	T	0.14	-0.0088	12.0171	0.53319	0.1235:0.6798:0.0:0.1966	.	274;274;365	F5GX89;E7ET89;Q86UW9	.;.;DTX2_HUMAN	C	365;274;274;365;365	ENSP00000322885:R365C;ENSP00000397648:R274C;ENSP00000390218:R365C;ENSP00000411986:R365C	ENSP00000322885:R365C	R	+	1	0	AC005522.1	75964673	0.878000	0.30173	0.971000	0.41717	0.991000	0.79684	-0.087000	0.11215	-0.633000	0.05545	-0.302000	0.09304	CGT	.	.	weak		0.557	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
USP34	9736	hgsc.bcm.edu	37	2	61415492	61415492	+	Silent	SNP	A	A	G	rs14170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:61415492A>G	ENST00000398571.2	-	80	10462	c.10386T>C	c.(10384-10386)gcT>gcC	p.A3462A	AHSA2_ENST00000394457.3_3'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3462					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ATTCTTCCTCAGCTAGGGTAG	0.453													A|||	2062	0.411741	0.4781	0.4164	5008	,	,		21759	0.3929		0.4901	False		,,,				2504	0.2577				p.A3462A		Atlas-SNP	.											.	USP34	334	.	0			c.T10386C						PASS	.	A		1798,1958		455,888,535	85.0	79.0	80.0		10386	-0.6	1.0	2	dbSNP_52	80	4028,4222		984,2060,1081	no	coding-synonymous	USP34	NM_014709.3		1439,2948,1616	GG,GA,AA		48.8242,47.8701,48.5257		3462/3547	61415492	5826,6180	1878	4125	6003	SO:0001819	synonymous_variant	9736	exon80			TTCCTCAGCTAGG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.10386T>C	2.37:g.61415492A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1	1003	0.4592490842490842	240	0.4878048780487805	165	0.4558011049723757	217	0.3793706293706294	381	0.5026385224274407	.	4.254	0.046111	0.08243	0.478701	0.488242	ENSG00000115464	ENST00000411912	.	.	.	5.52	-0.572	0.11745	.	.	.	.	.	.	.	.	.	.	.	0.18873	P	0.999985041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.133	0.06430	0.3824:0.1165:0.3872:0.1138	rs14170;rs3205597;rs3814034;rs11548862;rs17540386;rs17846593;rs17859675;rs61060947	.	.	.	R	1139	.	.	X	-	1	0	USP34	61268996	0.078000	0.21339	0.957000	0.39632	0.987000	0.75469	-0.555000	0.05999	0.049000	0.15920	0.482000	0.46254	TGA	A|0.525;G|0.475	0.475	strong		0.453	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
CEP128	145508	hgsc.bcm.edu	37	14	80971261	80971261	+	Missense_Mutation	SNP	C	C	T	rs61744330	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	54	0	0		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	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	
ADAMTS6	11174	hgsc.bcm.edu	37	5	64756136	64756136	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:64756136C>T	ENST00000536360.1	-	4	1305	c.492G>A	c.(490-492)gaG>gaA	p.E164E				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	164						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		CGATAAAATACTCTTCATCTT	0.308																																					p.E164E		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.G492A						PASS	.						109.0	114.0	112.0					5																	64756136		2203	4300	6503	SO:0001819	synonymous_variant	11174	exon4			AAAATACTCTTCA	AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	222	protein-coding gene	gene with protein product	"""a disintegrin and metalloproteinase with thrombospondin motifs 6"""	605008	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"""			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.492G>A	5.37:g.64756136C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	8	0.0701754	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Silent	SNP	ENST00000536360.1	37																																																																																				.	.	none		0.308	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941	
SAMD4A	23034	hgsc.bcm.edu	37	14	55226987	55226987	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:55226987C>T	ENST00000554335.1	+	7	1948	c.1285C>T	c.(1285-1287)Cgc>Tgc	p.R429C	SAMD4A_ENST00000555192.1_Missense_Mutation_p.R20C|SAMD4A_ENST00000251091.5_Missense_Mutation_p.R341C|SAMD4A_ENST00000392067.3_Missense_Mutation_p.R429C|SAMD4A_ENST00000357634.3_Missense_Mutation_p.R428C			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	429					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						CGAGGCTCGCCGCCGGGAGCC	0.716																																					p.R429C		Atlas-SNP	.											.	SAMD4A	68	.	0			c.C1285T						PASS	.																																			SO:0001583	missense	23034	exon6			GCTCGCCGCCGGG	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1285C>T	14.37:g.55226987C>T	ENSP00000452535:p.Arg429Cys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	46	32	0.695652	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	13.96	2.391816	0.42410	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634;ENST00000555192	.	.	.	5.07	3.07	0.35406	.	0.889887	0.09934	N	0.736892	T	0.23451	0.0567	N	0.14661	0.345	0.24451	N	0.994482	B;D;P	0.53151	0.012;0.958;0.474	B;P;B	0.50617	0.002;0.646;0.093	T	0.09271	-1.0682	9	0.51188	T	0.08	-15.041	3.4091	0.07352	0.288:0.5045:0.1175:0.09	.	20;341;429	G3V2R1;Q9UPU9-3;Q9UPU9	.;.;SMAG1_HUMAN	C	429;429;341;340;428;20	.	ENSP00000251091:R58C	R	+	1	0	SAMD4A	54296737	0.921000	0.31238	0.318000	0.25279	0.343000	0.28985	1.821000	0.39041	1.331000	0.45412	0.609000	0.83330	CGC	.	.	none		0.716	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
NLRP5	126206	hgsc.bcm.edu	37	19	56572832	56572832	+	Missense_Mutation	SNP	G	G	A	rs10409555	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56572832G>A	ENST00000390649.3	+	15	3541	c.3541G>A	c.(3541-3543)Gtc>Atc	p.V1181I		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	1181			V -> I (in dbSNP:rs10409555).		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)		CAAGCCCCGAGTCGTAATTGA	0.517													A|||	1797	0.358826	0.466	0.2277	5008	,	,		19130	0.4415		0.2575	False		,,,				2504	0.3262				p.V1181I		Atlas-SNP	.											.	NLRP5	217	.	0			c.G3541A						PASS	.	A	ILE/VAL	1683,2261		356,971,645	133.0	130.0	131.0		3541	-6.7	0.0	19	dbSNP_119	131	2146,6148		278,1590,2279	yes	missense	NLRP5	NM_153447.4	29	634,2561,2924	AA,AG,GG		25.8741,42.6724,31.2878	benign	1181/1201	56572832	3829,8409	1972	4147	6119	SO:0001583	missense	126206	exon15			CCCCGAGTCGTAA	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.3541G>A	19.37:g.56572832G>A	ENSP00000375063:p.Val1181Ile	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	213	120	0.56338	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	744	0.34065934065934067	220	0.44715447154471544	83	0.2292817679558011	247	0.4318181818181818	194	0.2559366754617414	A	0.009	-1.828455	0.00584	0.426724	0.258741	ENSG00000171487	ENST00000390649	T	0.72394	-0.65	3.33	-6.66	0.01789	.	.	.	.	.	T	0.00012	0.0000	L	0.28274	0.84	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.04153	-1.0973	8	0.09843	T	0.71	.	8.169	0.31243	0.1062:0.2707:0.5272:0.0958	rs10409555;rs52789679;rs56800517;rs10409555	1181	P59047	NALP5_HUMAN	I	1181	ENSP00000375063:V1181I	ENSP00000375063:V1181I	V	+	1	0	NLRP5	61264644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.531000	0.02219	-4.845000	0.00029	-3.614000	0.00027	GTC	G|0.645;A|0.355	0.355	strong		0.517	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
C2orf71	388939	hgsc.bcm.edu	37	2	29294754	29294754	+	Missense_Mutation	SNP	G	G	C	rs17744093	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	99	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	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	
MKI67	4288	hgsc.bcm.edu	37	10	129900918	129900918	+	Silent	SNP	C	C	A	rs201914667	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129900918C>A	ENST00000368654.3	-	13	9561	c.9186G>T	c.(9184-9186)gcG>gcT	p.A3062A	MKI67_ENST00000368653.3_Silent_p.A2702A	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3062					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)				TCAGCTCTTCCGCAGGTTCAA	0.458																																					p.A3062A		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	0			c.G9186T						scavenged	.						244.0	222.0	230.0					10																	129900918		2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			CTCTTCCGCAGGT	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.9186G>T	10.37:g.129900918C>A		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	274	3	0.0109489	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			C|1.000;T|0.000	.	alt		0.458	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
OR4D1	26689	hgsc.bcm.edu	37	17	56233234	56233234	+	Silent	SNP	C	C	T	rs62636635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:56233234C>T	ENST00000268912.5	+	1	741	c.720C>T	c.(718-720)tgC>tgT	p.C240C		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	240					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)			kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						CTTCCACCTGCACCACCCACA	0.507													C|||	166	0.033147	0.0023	0.0231	5008	,	,		17040	0.001		0.0596	False		,,,				2504	0.0879				p.C240C		Atlas-SNP	.											.	OR4D1	48	.	0			c.C720T						PASS	.	C		40,4366	43.1+/-76.7	0,40,2163	117.0	106.0	110.0		720	0.9	1.0	17	dbSNP_129	110	476,8124	139.5+/-196.2	11,454,3835	no	coding-synonymous	OR4D1	NM_012374.1		11,494,5998	TT,TC,CC		5.5349,0.9079,3.9674		240/311	56233234	516,12490	2203	4300	6503	SO:0001819	synonymous_variant	26689	exon1			CACCTGCACCACC	X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"""GPCR / Class A : Olfactory receptors"""	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.720C>T	17.37:g.56233234C>T		Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	287	143	0.498258	NM_012374	B2RN14|Q8NGB1|Q96R76	Silent	SNP	ENST00000268912.5	37	CCDS42365.1																																																																																			C|0.961;T|0.039	0.039	strong		0.507	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1		
FAM71F2	346653	hgsc.bcm.edu	37	7	128315889	128315889	+	Missense_Mutation	SNP	A	A	T	rs6971819	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:128315889A>T	ENST00000480462.1	+	2	447	c.341A>T	c.(340-342)gAc>gTc	p.D114V	FAM71F2_ENST00000378704.3_Missense_Mutation_p.D105V|FAM71F2_ENST00000477515.1_Missense_Mutation_p.D114V|FAM71F2_ENST00000460349.1_3'UTR			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	114			D -> V (in dbSNP:rs6971819). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334}.							NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						ACACCTGGTGACGCCCCAGTC	0.562													.|||	567	0.113219	0.2186	0.0677	5008	,	,		15377	0.0278		0.1203	False		,,,				2504	0.0838				p.D114V		Atlas-SNP	.											.	FAM71F2	19	.	0			c.A341T						PASS	.	A	VAL/ASP,VAL/ASP	755,3051		85,585,1233	43.0	41.0	41.0		341,314	0.5	0.0	7	dbSNP_116	41	957,7289		62,833,3228	yes	missense,missense	FAM71F2	NM_001012454.3,NM_001128926.1	152,152	147,1418,4461	TT,TA,AA		11.6056,19.8371,14.2051	benign,benign	114/310,105/301	128315889	1712,10340	1903	4123	6026	SO:0001583	missense	346653	exon2			CTGGTGACGCCCC	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member B"""	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.341A>T	7.37:g.128315889A>T	ENSP00000420140:p.Asp114Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	235	0.10760073260073261	90	0.18292682926829268	28	0.07734806629834254	18	0.03146853146853147	99	0.13060686015831136	A	2.983	-0.209937	0.06140	0.198371	0.116056	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001;ENST00000477515	T;T;T;T;T	0.30714	2.2;2.2;2.2;2.2;1.52	4.16	0.475	0.16774	.	2.399370	0.01787	N	0.032075	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;0.001	T	0.25152	-1.0140	9	0.33940	T	0.23	-6.2876	0.5566	0.00672	0.2287:0.3575:0.2032:0.2107	rs6971819;rs6971819	105;114	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	V	105;114;105;105;114	ENSP00000418907:D105V;ENSP00000420140:D114V;ENSP00000367976:D105V;ENSP00000401654:D105V;ENSP00000419649:D114V	ENSP00000367976:D105V	D	+	2	0	FAM71F2	128103125	0.005000	0.15991	0.025000	0.17156	0.320000	0.28249	-0.094000	0.11094	-0.021000	0.14009	0.455000	0.32223	GAC	A|0.892;T|0.108	0.108	strong		0.562	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
KRTAP24-1	643803	hgsc.bcm.edu	37	21	31654809	31654809	+	Missense_Mutation	SNP	C	C	T	rs77638540	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31654809C>T	ENST00000340345.4	-	1	467	c.442G>A	c.(442-444)Ggt>Agt	p.G148S		NM_001085455.1	NP_001078924.1	Q3LI83	KR241_HUMAN	keratin associated protein 24-1	148						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|large_intestine(3)|lung(7)|urinary_tract(3)	14						CAGTTGGAACCGTTGCGGAGG	0.483													C|||	358	0.0714856	0.1513	0.0389	5008	,	,		20814	0.0069		0.0368	False		,,,				2504	0.089				p.G148S		Atlas-SNP	.											.	KRTAP24-1	44	.	0			c.G442A						PASS	.	C	SER/GLY	450,3458		23,404,1527	126.0	127.0	127.0		442	0.9	0.0	21	dbSNP_131	127	331,7989		9,313,3838	yes	missense	KRTAP24-1	NM_001085455.1	56	32,717,5365	TT,TC,CC		3.9784,11.5148,6.387	benign	148/255	31654809	781,11447	1954	4160	6114	SO:0001583	missense	643803	exon1			TGGAACCGTTGCG	AB096935	CCDS42915.1	21q22.11	2007-11-23			ENSG00000188694	ENSG00000188694		"""Keratin associated proteins"""	33902	protein-coding gene	gene with protein product							Standard	NM_001085455		Approved	KAP24.1	uc002ynv.3	Q3LI83	OTTHUMG00000125483	ENST00000340345.4:c.442G>A	21.37:g.31654809C>T	ENSP00000339238:p.Gly148Ser	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	277	155	0.559567	NM_001085455	Q1XDX0	Missense_Mutation	SNP	ENST00000340345.4	37	CCDS42915.1	114	0.0521978021978022	68	0.13821138211382114	17	0.04696132596685083	3	0.005244755244755245	26	0.03430079155672823	C	11.26	1.587728	0.28268	0.115148	0.039784	ENSG00000188694	ENST00000340345	T	0.03607	3.87	4.96	0.877	0.19145	.	0.655352	0.12549	N	0.459217	T	0.00039	0.0001	L	0.57536	1.79	0.09310	N	1	P	0.52316	0.952	B	0.43225	0.412	T	0.34403	-0.9830	10	0.11794	T	0.64	-0.8583	2.2788	0.04109	0.1556:0.5163:0.1511:0.1771	.	148	Q3LI83	KR241_HUMAN	S	148	ENSP00000339238:G148S	ENSP00000339238:G148S	G	-	1	0	KRTAP24-1	30576680	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.057000	0.14279	0.034000	0.15491	-0.218000	0.12543	GGT	C|0.951;T|0.049	0.049	strong		0.483	KRTAP24-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246806.2	NM_001085455	
CCDC176	80127	hgsc.bcm.edu	37	14	74516497	74516497	+	Silent	SNP	G	G	A	rs34076068	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:74516497G>A	ENST00000394009.3	+	8	1008	c.885G>A	c.(883-885)ttG>ttA	p.L295L	AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000553773.1_Silent_p.L20L	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	295					motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											TAGTAAACTTGGAGACTGCTC	0.398													G|||	480	0.0958466	0.0076	0.232	5008	,	,		21736	0.0873		0.1312	False		,,,				2504	0.091				p.L295L		Atlas-SNP	.											.	.	.	.	0			c.G885A						PASS	.	G		145,4261	95.7+/-134.4	3,139,2061	60.0	61.0	60.0		885	4.9	1.0	14	dbSNP_126	60	1266,7332	245.6+/-274.3	82,1102,3115	no	coding-synonymous	C14orf45	NM_025057.2		85,1241,5176	AA,AG,GG		14.7244,3.291,10.8505		295/530	74516497	1411,11593	2203	4299	6502	SO:0001819	synonymous_variant	80127	exon8			AAACTTGGAGACT	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.885G>A	14.37:g.74516497G>A		Somatic	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	279	187	0.670251	NM_025057	Q0P604|Q9H5P8	Silent	SNP	ENST00000394009.3	37	CCDS32119.2																																																																																			G|0.885;A|0.115	0.115	strong		0.398	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
ZNF142	7701	hgsc.bcm.edu	37	2	219513782	219513782	+	Silent	SNP	T	T	C	rs4674322	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219513782T>C	ENST00000449707.1	-	6	1270	c.849A>G	c.(847-849)ccA>ccG	p.P283P	ZNF142_ENST00000411696.2_Silent_p.P283P	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	283					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)		GAAGGGGTAATGGCTCTGCTG	0.617											OREG0015202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	434	0.0866613	0.0151	0.1441	5008	,	,		19362	0.0		0.2704	False		,,,				2504	0.0429				p.P283P	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A849G						PASS	.	C		185,3867		3,179,1844	29.0	32.0	31.0		849	-10.4	0.0	2	dbSNP_111	31	2169,6219		310,1549,2335	no	coding-synonymous	ZNF142	NM_001105537.1		313,1728,4179	CC,CT,TT		25.8584,4.5656,18.9228		283/1688	219513782	2354,10086	2026	4194	6220	SO:0001819	synonymous_variant	7701	exon6			GGGTAATGGCTCT	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.849A>G	2.37:g.219513782T>C		Somatic	62	0	0	2259	WXS	Illumina HiSeq	Phase_I	42	12	0.285714	NM_001105537	Q92510	Silent	SNP	ENST00000449707.1	37	CCDS42817.1																																																																																			T|0.861;C|0.139	0.139	strong		0.617	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
PPAP2C	8612	hgsc.bcm.edu	37	19	282753	282753	+	Splice_Site	SNP	G	G	A	rs1138439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:282753G>A	ENST00000269812.3	-	4	588	c.539C>T	c.(538-540)gCg>gTg	p.A180V	PPAP2C_ENST00000434325.2_Splice_Site_p.A124V|PPAP2C_ENST00000327790.3_Splice_Site_p.A201V	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	180			A -> V (in dbSNP:rs1138439).		dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		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)		CAGACTCACCGCCAAGAACAC	0.537													.|||	1826	0.364617	0.4682	0.4323	5008	,	,		16201	0.1181		0.4602	False		,,,				2504	0.3323				p.A201V		Atlas-SNP	.											PPAP2C_ENST00000269812,caecum,carcinoma,0,5	PPAP2C	38	5	0			c.C602T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	2049,2357		479,1091,633	121.0	103.0	109.0		539,371,602	-0.1	0.4	19	dbSNP_86	109	3724,4876		824,2076,1400	yes	missense-near-splice,missense-near-splice,missense-near-splice	PPAP2C	NM_003712.2,NM_177526.1,NM_177543.1	64,64,64	1303,3167,2033	AA,AG,GG		43.3023,46.5048,44.3872	benign,benign,benign	180/289,124/233,201/310	282753	5773,7233	2203	4300	6503	SO:0001630	splice_region_variant	8612	exon4			CTCACCGCCAAGA	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.540+1C>T	19.37:g.282753G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	56	19	0.339286	NM_177543	A6NLV0|E9PAY8	Missense_Mutation	SNP	ENST00000269812.3	37	CCDS12023.1	815	0.3731684981684982	210	0.4268292682926829	153	0.42265193370165743	88	0.15384615384615385	364	0.48021108179419525	.	6.371	0.436500	0.12104	0.465048	0.433023	ENSG00000141934	ENST00000269812;ENST00000327790;ENST00000434325	T;T;T	0.75367	-0.93;-0.93;-0.93	4.73	-0.069	0.13753	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.209140	0.39687	N	0.001299	T	0.00012	0.0000	L	0.42581	1.335	0.22479	P	0.999061563	B;B	0.21309	0.032;0.054	B;B	0.24006	0.05;0.033	T	0.43147	-0.9409	9	0.33141	T	0.24	-21.5272	8.9489	0.35776	0.3281:0.0:0.6719:0.0	rs1138439;rs1802137;rs3202329;rs10407115;rs52811693;rs57859690;rs10407115	180;201	O43688;O43688-2	LPP2_HUMAN;.	V	180;201;124	ENSP00000269812:A180V;ENSP00000329697:A201V;ENSP00000388565:A124V	ENSP00000269812:A180V	A	-	2	0	PPAP2C	233753	1.000000	0.71417	0.424000	0.26647	0.000000	0.00434	6.075000	0.71261	-0.160000	0.11002	-1.008000	0.02478	GCG	T|0.071;G|0.466;C|0.124;A|0.339	0.339	strong		0.537	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2		Missense_Mutation
PHYH	5264	hgsc.bcm.edu	37	10	13330402	13330402	+	Silent	SNP	T	T	C	rs473407	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:13330402T>C	ENST00000263038.4	-	6	694	c.636A>G	c.(634-636)acA>acG	p.T212T	PHYH_ENST00000396913.2_Silent_p.T112T|PHYH_ENST00000396920.3_Silent_p.T195T	NM_006214.3	NP_006205.1	O14832	PAHX_HUMAN	phytanoyl-CoA 2-hydroxylase	212					cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|isoprenoid metabolic process (GO:0006720)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	cofactor binding (GO:0048037)|electron carrier activity (GO:0009055)|L-ascorbic acid binding (GO:0031418)|metal ion binding (GO:0046872)|phytanoyl-CoA dioxygenase activity (GO:0048244)			NS(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	25		Ovarian(717;0.0448)			Antihemophilic Factor(DB00025)|Vitamin C(DB00126)	AGCCCTTGTGTGTGCCTGGGA	0.587													T|||	1197	0.239018	0.4312	0.1686	5008	,	,		16570	0.124		0.2286	False		,,,				2504	0.1585				p.T212T		Atlas-SNP	.											.	PHYH	50	.	0			c.A636G						PASS	.	T	,	1709,2697	509.9+/-367.4	339,1031,833	57.0	55.0	56.0		336,636	-5.6	0.3	10	dbSNP_83	56	2192,6408	372.2+/-336.6	278,1636,2386	no	coding-synonymous,coding-synonymous	PHYH	NM_001037537.1,NM_006214.3	,	617,2667,3219	CC,CT,TT		25.4884,38.788,29.9938	,	112/239,212/339	13330402	3901,9105	2203	4300	6503	SO:0001819	synonymous_variant	5264	exon6			CTTGTGTGTGCCT		CCDS7097.1, CCDS41489.1	10p13	2010-04-27	2006-01-09		ENSG00000107537	ENSG00000107537	1.14.11.18		8940	protein-coding gene	gene with protein product	"""Refsum disease"", ""phytanoyl-CoA dioxygenase"""	602026	"""phytanoyl-CoA hydroxylase (Refsum disease)"", ""phytanoyl-CoA hydroxylase"""			9326939	Standard	XM_005252469		Approved	PAHX, RD, PHYH1	uc001imf.3	O14832	OTTHUMG00000017693	ENST00000263038.4:c.636A>G	10.37:g.13330402T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	61	12	0.196721	NM_006214	A8MTS8|B1ALH5	Silent	SNP	ENST00000263038.4	37	CCDS7097.1																																																																																			T|0.728;C|0.272	0.272	strong		0.587	PHYH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046845.2		
RNF39	80352	hgsc.bcm.edu	37	6	30039240	30039240	+	Missense_Mutation	SNP	G	G	T	rs2301753	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:30039240G>T	ENST00000244360.6	-	4	1008	c.911C>A	c.(910-912)gCg>gAg	p.A304E	RNF39_ENST00000376751.3_Missense_Mutation_p.A304E	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	304	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		A -> E (in dbSNP:rs2301753). {ECO:0000269|PubMed:14574404}.			cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										CTCGTCGTCCGCATCCTCCCC	0.706													t|||	958	0.191294	0.2988	0.1744	5008	,	,		12945	0.1905		0.0954	False		,,,				2504	0.1575				p.A304E	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											.	RNF39	27	.	0			c.C911A						PASS	.		GLU/ALA,GLU/ALA	753,2251		92,569,841	12.0	9.0	10.0		911,911	4.5	0.0	6	dbSNP_100	10	637,4757		52,533,2112	yes	missense,missense	RNF39	NM_025236.3,NM_170769.2	107,107	144,1102,2953	TT,TG,GG		11.8094,25.0666,16.5516	benign,benign	304/421,304/355	30039240	1390,7008	1502	2697	4199	SO:0001583	missense	80352	exon4			TCGTCCGCATCCT	AF238315	CCDS4673.1, CCDS4674.1	6p21.3	2013-01-09			ENSG00000204618	ENSG00000204618		"""RING-type (C3HC4) zinc fingers"""	18064	protein-coding gene	gene with protein product		607524				11130983, 11716498	Standard	NM_170769		Approved	HZFw1, LIRF	uc003npe.3	Q9H2S5	OTTHUMG00000031288	ENST00000244360.6:c.911C>A	6.37:g.30039240G>T	ENSP00000244360:p.Ala304Glu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	37	CCDS4673.1	404	0.184981684981685	146	0.2967479674796748	72	0.19889502762430938	115	0.20104895104895104	71	0.09366754617414248	t	1.410	-0.575640	0.03882	0.250666	0.118094	ENSG00000204618	ENST00000376751;ENST00000244360	T;T	0.69306	0.03;-0.39	4.54	4.54	0.55810	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.151026	0.29653	N	0.011551	T	0.10637	0.0260	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	0.15925	-1.0420	9	0.02654	T	1	-14.7253	9.8189	0.40869	0.0:0.0:0.1737:0.8263	rs2301753;rs60004051;rs2301753	304;304	Q9H2S5;Q9H2S5-2	RNF39_HUMAN;.	E	304	ENSP00000365942:A304E;ENSP00000244360:A304E	ENSP00000244360:A304E	A	-	2	0	RNF39	30147219	0.020000	0.18652	0.045000	0.18777	0.578000	0.36192	0.703000	0.25646	0.706000	0.31912	-1.106000	0.02097	GCG	G|0.804;T|0.196	0.196	strong		0.706	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769	
CMYA5	202333	hgsc.bcm.edu	37	5	79095417	79095417	+	Missense_Mutation	SNP	C	C	T	rs10043986	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79095417C>T	ENST00000446378.2	+	13	12219	c.12188C>T	c.(12187-12189)cCg>cTg	p.P4063L	CTC-431G16.2_ENST00000421252.2_RNA	NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	4063	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		P -> L (in dbSNP:rs10043986). {ECO:0000269|PubMed:17974005}.		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)		ATAGAGCCCCCGGATTCTGTA	0.483													C|||	234	0.0467252	0.0038	0.0692	5008	,	,		17507	0.0		0.1262	False		,,,				2504	0.0552				p.P4063L		Atlas-SNP	.											.	CMYA5	643	.	0			c.C12188T						PASS	.	C	LEU/PRO	94,3600		1,92,1754	52.0	51.0	51.0		12188	6.0	1.0	5	dbSNP_119	51	978,7216		56,866,3175	yes	missense	CMYA5	NM_153610.3	98	57,958,4929	TT,TC,CC		11.9356,2.5447,9.0175	possibly-damaging	4063/4070	79095417	1072,10816	1847	4097	5944	SO:0001583	missense	202333	exon13			AGCCCCCGGATTC	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.12188C>T	5.37:g.79095417C>T	ENSP00000394770:p.Pro4063Leu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	137	72	0.525547	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	128	0.05860805860805861	3	0.006097560975609756	32	0.08839779005524862	0	0.0	93	0.12269129287598944	C	34	5.327759	0.95733	0.025447	0.119356	ENSG00000164309	ENST00000446378	D	0.86164	-2.08	5.99	5.99	0.97316	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.27027	0.0662	M	0.79693	2.465	0.09310	P	0.999999999560952	D	0.89917	1.0	D	0.91635	0.999	T	0.68116	-0.5494	8	0.87932	D	0	.	20.4777	0.99188	0.0:1.0:0.0:0.0	rs10043986;rs52815654;rs60366119;rs10043986	4063	Q8N3K9	CMYA5_HUMAN	L	4063	ENSP00000394770:P4063L	ENSP00000394770:P4063L	P	+	2	0	CMYA5	79131173	1.000000	0.71417	0.969000	0.41365	0.987000	0.75469	6.620000	0.74224	2.840000	0.97914	0.655000	0.94253	CCG	C|0.938;T|0.062	0.062	strong		0.483	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
TACC2	10579	hgsc.bcm.edu	37	10	123846252	123846252	+	Missense_Mutation	SNP	G	G	A	rs201709460		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:123846252G>A	ENST00000369005.1	+	4	4577	c.4237G>A	c.(4237-4239)Gcc>Acc	p.A1413T	TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.A1413T|TACC2_ENST00000453444.2_Missense_Mutation_p.A1413T|TACC2_ENST00000334433.3_Missense_Mutation_p.A1413T|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.A1413T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1413					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)				GGAGCACATCGCCAAGATCTT	0.592													G|||	0	0.0	0.0	0.0	5008	,	,		19162	0.0		0.0	False		,,,				2504	0.0				p.A1413T		Atlas-SNP	.											.	TACC2	271	.	0			c.G4237A						PASS	.	G	,THR/ALA	0,4406		0,0,2203	70.0	67.0	68.0		,4237	4.2	1.0	10		68	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,benign	,1413/2949	123846252	1,13005	2203	4300	6503	SO:0001583	missense	10579	exon4			CACATCGCCAAGA	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.4237G>A	10.37:g.123846252G>A	ENSP00000358001:p.Ala1413Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	51	0.428571	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	3.835	-0.035002	0.07543	0.0	1.16E-4	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.02301	4.35;4.46;4.37;4.35;4.46	5.27	4.15	0.48705	.	0.234704	0.22121	N	0.064340	T	0.00936	0.0031	N	0.02539	-0.55	0.22280	N	0.999238	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.01281	0.0;0.0;0.0	T	0.47724	-0.9095	10	0.02654	T	1	-6.9253	7.1361	0.25529	0.8892:0.0:0.1108:0.0	.	1413;1413;1413	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1413;1413;1413;1413;1413;1403	ENSP00000358001:A1413T;ENSP00000424467:A1413T;ENSP00000427618:A1413T;ENSP00000334280:A1413T;ENSP00000395048:A1413T	ENSP00000334280:A1413T	A	+	1	0	TACC2	123836242	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	3.191000	0.50981	0.855000	0.35359	0.549000	0.68633	GCC	G|0.999;A|0.001	0.001	strong		0.592	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
MMAB	326625	hgsc.bcm.edu	37	12	110011229	110011229	+	Silent	SNP	G	G	T	rs10774774|rs36013132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:110011229G>T	ENST00000545712.2	-	1	450	c.57C>A	c.(55-57)cgC>cgA	p.R19R	MVK_ENST00000541384.1_5'Flank|MVK_ENST00000539696.1_5'Flank|MVK_ENST00000539575.1_5'Flank|MMAB_ENST00000266839.5_5'UTR|MVK_ENST00000228510.3_5'Flank|MVK_ENST00000535044.1_3'UTR|MVK_ENST00000392727.3_5'Flank|MMAB_ENST00000540016.1_Silent_p.R19R	NM_052845.3	NP_443077.1	Q96EY8	MMAB_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblB type	19			R -> H (in dbSNP:rs10774775).|R -> Q (in dbSNP:rs36013132). {ECO:0000269|PubMed:12471062, ECO:0000269|PubMed:12514191, ECO:0000269|PubMed:15489334}.		cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|cob(I)yrinic acid a,c-diamide adenosyltransferase activity (GO:0008817)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CGAAGCACCCGCGCAGGCCAA	0.711													G|||	1427	0.284944	0.438	0.2939	5008	,	,		13025	0.1607		0.2853	False		,,,				2504	0.1994				p.R19R		Atlas-SNP	.											.	MMAB	16	.	0			c.C57A						PASS	.	G		1718,2668		356,1006,831	16.0	17.0	16.0		57	2.0	0.4	12	dbSNP_120	16	2294,6298		372,1550,2374	no	coding-synonymous	MMAB	NM_052845.3		728,2556,3205	TT,TG,GG		26.6993,39.1701,30.9139		19/251	110011229	4012,8966	2193	4296	6489	SO:0001819	synonymous_variant	326625	exon1			GCACCCGCGCAGG	AF550404	CCDS9131.1	12q24	2014-07-18	2005-07-11		ENSG00000139428	ENSG00000139428			19331	protein-coding gene	gene with protein product	"""ATP:cob(I)alamin adenosyltransferase"", ""cilia and flagella associated protein 23"""	607568	"""methylmalonic aciduria (cobalamin deficiency) type B"""			12471062, 12514191	Standard	NM_052845		Approved	cblB, CFAP23	uc001tou.3	Q96EY8	OTTHUMG00000169255	ENST00000545712.2:c.57C>A	12.37:g.110011229G>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	NM_052845	C5HU05|Q9BSH0	Silent	SNP	ENST00000545712.2	37	CCDS9131.1																																																																																			.	.	alt		0.711	MMAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403128.2		
SYNRG	11276	hgsc.bcm.edu	37	17	35896123	35896123	+	Silent	SNP	T	T	C	rs1045000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:35896123T>C	ENST00000339208.6	-	19	3764	c.3624A>G	c.(3622-3624)gtA>gtG	p.V1208V	SYNRG_ENST00000345615.4_Silent_p.V1130V|SYNRG_ENST00000591288.1_Silent_p.V1002V|SYNRG_ENST00000585472.1_Silent_p.V1129V|SYNRG_ENST00000502449.2_Silent_p.V1085V|SYNRG_ENST00000394378.2_Silent_p.V1130V|SYNRG_ENST00000346661.4_Silent_p.V1208V	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	1208					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						GGTTATTCCATACTTTATCGA	0.468													T|||	1174	0.234425	0.1793	0.366	5008	,	,		22803	0.255		0.2197	False		,,,				2504	0.2096				p.V1208V		Atlas-SNP	.											.	SYNRG	101	.	0			c.A3624G						PASS	.	T	,,,,,,	870,3536	340.2+/-306.1	99,672,1432	196.0	163.0	174.0		3390,3387,3255,3006,3624,3390,3390	-11.3	0.2	17	dbSNP_86	174	1928,6672	341.2+/-323.9	215,1498,2587	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNRG	NM_001163544.1,NM_001163545.1,NM_001163546.1,NM_001163547.1,NM_007247.4,NM_080550.3,NM_198882.1	,,,,,,	314,2170,4019	CC,CT,TT		22.4186,19.7458,21.5131	,,,,,,	1130/1237,1129/1236,1085/1180,1002/1109,1208/1315,1130/1225,1130/1260	35896123	2798,10208	2203	4300	6503	SO:0001819	synonymous_variant	11276	exon19			ATTCCATACTTTA	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.3624A>G	17.37:g.35896123T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	135	58	0.42963	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Silent	SNP	ENST00000339208.6	37	CCDS11321.1																																																																																			T|0.778;C|0.222	0.222	strong		0.468	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	
RBM6	10180	hgsc.bcm.edu	37	3	50005855	50005855	+	Missense_Mutation	SNP	G	G	A	rs143972186	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:50005855G>A	ENST00000266022.4	+	3	1256	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K	RBM6_ENST00000442092.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.E201K|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000539992.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	333					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)		TCAGAAGGGAGAATTTGAGCA	0.423													G|||	5	0.000998403	0.0	0.0014	5008	,	,		21143	0.0		0.003	False		,,,				2504	0.001				p.E333K		Atlas-SNP	.											.	RBM6	85	.	0			c.G997A						PASS	.	G	,LYS/GLU	7,4399	12.9+/-30.5	0,7,2196	81.0	72.0	75.0		,997	6.0	1.0	3	dbSNP_134	75	37,8563	25.1+/-72.6	0,37,4263	yes	intron,missense	RBM6	NM_001167582.1,NM_005777.2	,56	0,44,6459	AA,AG,GG		0.4302,0.1589,0.3383	,probably-damaging	,333/1124	50005855	44,12962	2203	4300	6503	SO:0001583	missense	10180	exon3			AAGGGAGAATTTG	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.997G>A	3.37:g.50005855G>A	ENSP00000266022:p.Glu333Lys	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	205	106	0.517073	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	16.90	3.249072	0.59103	0.001589	0.004302	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.38887	1.11;1.15	6.04	6.04	0.98038	.	0.128334	0.51477	D	0.000098	T	0.49695	0.1572	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.35574	-0.9783	9	.	.	.	-13.7992	13.7331	0.62802	0.0698:0.0:0.9302:0.0	.	333	P78332	RBM6_HUMAN	K	333;201	ENSP00000266022:E333K;ENSP00000396466:E201K	.	E	+	1	0	RBM6	49980859	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	4.840000	0.62817	2.873000	0.98535	0.561000	0.74099	GAA	G|0.997;A|0.003	0.003	strong		0.423	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
GTF2A1	2957	hgsc.bcm.edu	37	14	81662494	81662494	+	Silent	SNP	T	T	C	rs34999597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:81662494T>C	ENST00000553612.1	-	6	973	c.570A>G	c.(568-570)ccA>ccG	p.P190P	GTF2A1_ENST00000434192.2_Silent_p.P151P	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa	190					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(234;0.0287)		GCTGCATTTGTGGTATAACCT	0.428													T|||	5	0.000998403	0.0	0.0	5008	,	,		18335	0.0		0.002	False		,,,				2504	0.0031				p.P190P		Atlas-SNP	.											.	GTF2A1	34	.	0			c.A570G						PASS	.	T	,	2,4404	4.2+/-10.8	0,2,2201	180.0	162.0	168.0		570,453	4.2	1.0	14	dbSNP_126	168	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous,coding-synonymous	GTF2A1	NM_015859.2,NM_201595.1	,	0,27,6476	CC,CT,TT		0.2907,0.0454,0.2076	,	190/377,151/338	81662494	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	2957	exon6			CATTTGTGGTATA	X75383	CCDS9873.1, CCDS9874.1	14q31	2010-03-23	2002-08-29					"""General transcription factors"""	4646	protein-coding gene	gene with protein product		600520	"""glucose regulated protein, 58kD pseudogene"""			8224848	Standard	NM_015859		Approved	TFIIA	uc001xvf.2	P52655		ENST00000553612.1:c.570A>G	14.37:g.81662494T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	212	107	0.504717	NM_015859	Q3KNQ9	Silent	SNP	ENST00000553612.1	37	CCDS9873.1																																																																																			T|0.998;C|0.002	0.002	strong		0.428	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859	
ZNF215	7762	hgsc.bcm.edu	37	11	6962879	6962879	+	Missense_Mutation	SNP	C	C	T	rs141940336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6962879C>T	ENST00000278319.5	+	4	1066	c.478C>T	c.(478-480)Cca>Tca	p.P160S	ZNF215_ENST00000414517.2_Missense_Mutation_p.P160S|ZNF215_ENST00000529903.1_Missense_Mutation_p.P160S|ZNF215_ENST00000527171.1_3'UTR	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	160					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)		AACAGGCAAACCACAGGTGAA	0.413																																					p.P160S		Atlas-SNP	.											.	ZNF215	72	.	0			c.C478T						PASS	.	C	SER/PRO	0,4402		0,0,2201	90.0	86.0	87.0		478	1.1	0.0	11	dbSNP_134	87	2,8590	2.2+/-6.3	0,2,4294	yes	missense	ZNF215	NM_013250.2	74	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	benign	160/518	6962879	2,12992	2201	4296	6497	SO:0001583	missense	7762	exon4			GGCAAACCACAGG	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.478C>T	11.37:g.6962879C>T	ENSP00000278319:p.Pro160Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	C	0.861	-0.735158	0.03111	0.0	2.33E-4	ENSG00000149054	ENST00000278319;ENST00000414517;ENST00000529903	T;T;T	0.00768	5.72;5.72;5.72	4.32	1.07	0.20283	Krueppel-associated box (1);	0.585459	0.14355	N	0.324834	T	0.00328	0.0010	N	0.01705	-0.755	0.34821	D	0.738729	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.31998	-0.9923	10	0.02654	T	1	4.8197	5.2224	0.15375	0.0:0.4366:0.0:0.5634	.	160;160;160	B4DYW9;Q96C84;Q9UL58	.;.;ZN215_HUMAN	S	160	ENSP00000278319:P160S;ENSP00000393202:P160S;ENSP00000432306:P160S	ENSP00000278319:P160S	P	+	1	0	ZNF215	6919455	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	0.273000	0.18662	0.419000	0.25927	0.591000	0.81541	CCA	C|1.000;T|0.000	0.000	strong		0.413	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
POLR1B	84172	hgsc.bcm.edu	37	2	113308516	113308516	+	Silent	SNP	T	T	A	rs2304555	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:113308516T>A	ENST00000263331.5	+	5	1279	c.699T>A	c.(697-699)acT>acA	p.T233T	POLR1B_ENST00000537335.1_Silent_p.T22T|POLR1B_ENST00000417433.2_Silent_p.T177T|POLR1B_ENST00000541869.1_Silent_p.T271T|POLR1B_ENST00000409894.3_Silent_p.T233T	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	233					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)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						AAAATGGCACTGTTATGTTGA	0.353													T|||	2775	0.554113	0.5015	0.5562	5008	,	,		21138	0.4038		0.6938	False		,,,				2504	0.635				p.T233T	Ovarian(16;256 576 9537 23969 41147)	Atlas-SNP	.											POLR1B,NS,carcinoma,+1,1	POLR1B	95	1	0			c.T699A						PASS	.	T	,	2453,1953	620.2+/-393.5	701,1051,451	228.0	214.0	219.0		531,699	-10.0	0.3	2	dbSNP_100	219	6370,2230	709.9+/-405.7	2353,1664,283	no	coding-synonymous,coding-synonymous	POLR1B	NM_001137604.1,NM_019014.4	,	3054,2715,734	AA,AT,TT		25.9302,44.3259,32.1621	,	177/1080,233/1136	113308516	8823,4183	2203	4300	6503	SO:0001819	synonymous_variant	84172	exon5			TGGCACTGTTATG	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"""RNA polymerase subunits"""	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.699T>A	2.37:g.113308516T>A		Somatic	366	0	0		WXS	Illumina HiSeq	Phase_I	278	273	0.982014	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Silent	SNP	ENST00000263331.5	37	CCDS2097.1																																																																																			T|0.369;A|0.631	0.631	strong		0.353	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014	
CENPF	1063	hgsc.bcm.edu	37	1	214805928	214805928	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:214805928C>T	ENST00000366955.3	+	10	1597	c.1429C>T	c.(1429-1431)Ctg>Ttg	p.L477L		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0	Interaction with SNAP25 and required for localization to the cytoplasm. {ECO:0000250}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GGAGAATGAGCTGAGGAGAAG	0.433																																					p.L477L	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,colon,carcinoma,-1,1	CENPF	321	1	0			c.C1429T						scavenged	.						73.0	63.0	67.0					1																	214805928		2203	4300	6503	SO:0001819	synonymous_variant	1063	exon10			AATGAGCTGAGGA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.1429C>T	1.37:g.214805928C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	158	2	0.0126582	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			.	.	none		0.433	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
POLN	353497	hgsc.bcm.edu	37	4	2195024	2195024	+	Missense_Mutation	SNP	T	T	G	rs10018786	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	227	0	0		WXS	Illumina HiSeq	Phase_I	192	83	0.432292	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	
TNXB	7148	hgsc.bcm.edu	37	6	32029431	32029431	+	Missense_Mutation	SNP	G	G	A	rs12524664	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32029431G>A	ENST00000375244.3	-	21	7436	c.7235C>T	c.(7234-7236)cCg>cTg	p.P2412L	TNXB_ENST00000375247.2_Missense_Mutation_p.P2412L			P22105	TENX_HUMAN	tenascin XB	2472	Fibronectin type-III 16. {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						CCCCAGGAGCGGCTCCTCAGG	0.647													G|||	527	0.105232	0.2012	0.0749	5008	,	,		14003	0.0823		0.0934	False		,,,				2504	0.0327				p.P2412L		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,+1,2	TNXB	553	2	0			c.C7235T						scavenged	.	G	LEU/PRO	367,1871		29,309,781	46.0	53.0	51.0		7235	4.0	1.0	6	dbSNP_120	51	312,4646		6,300,2173	no	missense	TNXB	NM_019105.6	98	35,609,2954	AA,AG,GG		6.2929,16.3986,9.4358	benign	2412/4243	32029431	679,6517	1119	2479	3598	SO:0001583	missense	7148	exon21			AGGAGCGGCTCCT	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.7235C>T	6.37:g.32029431G>A	ENSP00000364393:p.Pro2412Leu	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	99	2	0.020202	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		269	0.12316849816849818	98	0.1991869918699187	38	0.10497237569060773	60	0.1048951048951049	73	0.09630606860158311	G	18.44	3.624587	0.66901	0.163986	0.062929	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.61980	0.22;0.06	4.0	4.0	0.46444	.	0.104175	0.43416	D	0.000567	T	0.78947	0.4364	M	0.93150	3.385	0.26478	P	0.9751589	D	0.76494	0.999	D	0.67103	0.949	D	0.85220	0.1026	9	0.87932	D	0	.	13.1106	0.59270	0.0:0.0:1.0:0.0	rs12524664;rs17201532	2412	P22105-3	.	L	2412	ENSP00000364393:P2412L;ENSP00000364396:P2412L	ENSP00000364393:P2412L	P	-	2	0	TNXB	32137409	0.990000	0.36364	0.999000	0.59377	0.792000	0.44763	2.762000	0.47597	2.038000	0.60285	0.591000	0.81541	CCG	G|0.894;A|0.106	0.106	strong		0.647	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
SYNGR4	23546	hgsc.bcm.edu	37	19	48879375	48879375	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48879375C>T	ENST00000344846.2	+	5	755	c.505C>T	c.(505-507)Cga>Tga	p.R169*	SYNGR4_ENST00000601610.1_Missense_Mutation_p.P145L|SYNGR4_ENST00000595322.1_Missense_Mutation_p.P73L	NM_012451.3	NP_036583.2	O95473	SNG4_HUMAN	synaptogyrin 4	169	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		CCAGGACCTCCGAAATGATGC	0.602																																					p.R169X		Atlas-SNP	.											SYNGR4,NS,carcinoma,-2,3	SYNGR4	31	3	0			c.C505T						PASS	.						104.0	98.0	100.0					19																	48879375		2203	4300	6503	SO:0001587	stop_gained	23546	exon5			GACCTCCGAAATG	AJ011733	CCDS12717.1	19q13.3	2008-07-04				ENSG00000105467			11502	protein-coding gene	gene with protein product		608373					Standard	NM_012451		Approved		uc002piz.3	O95473		ENST00000344846.2:c.505C>T	19.37:g.48879375C>T	ENSP00000344041:p.Arg169*	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	147	38	0.258503	NM_012451	Q3KP58	Nonsense_Mutation	SNP	ENST00000344846.2	37	CCDS12717.1	.	.	.	.	.	.	.	.	.	.	C	36	5.676643	0.96764	.	.	ENSG00000105467	ENST00000344846	.	.	.	5.61	4.55	0.56014	.	0.948152	0.08692	N	0.907770	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.6799	7.5531	0.27808	0.1663:0.7504:0.0:0.0833	.	.	.	.	X	169	.	ENSP00000344041:R169X	R	+	1	2	SYNGR4	53571187	0.522000	0.26266	0.855000	0.33649	0.846000	0.48090	0.827000	0.27421	1.480000	0.48289	0.555000	0.69702	CGA	.	.	none		0.602	SYNGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465704.1		
MAMLD1	10046	hgsc.bcm.edu	37	X	149638920	149638920	+	Missense_Mutation	SNP	C	C	T	rs41313406	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000455522.2_5'Flank|MAMLD1_ENST00000262858.5_Missense_Mutation_p.P359S|MAMLD1_ENST00000426613.2_Missense_Mutation_p.P334S			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	106	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	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	
MMP14	4323	hgsc.bcm.edu	37	14	23312594	23312594	+	Missense_Mutation	SNP	G	G	A	rs1042704	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23312594G>A	ENST00000311852.6	+	5	1078	c.817G>A	c.(817-819)Gat>Aat	p.D273N	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	273			D -> N (in dbSNP:rs1042704). {ECO:0000269|Ref.8}.		angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	TGTGCTGCCCGATGATGACCG	0.597													G|||	550	0.109824	0.0091	0.1311	5008	,	,		17770	0.0258		0.1988	False		,,,				2504	0.226				p.D273N		Atlas-SNP	.											.	MMP14	40	.	0			c.G817A						PASS	.	G	ASN/ASP	197,4209	122.5+/-159.9	2,193,2008	106.0	108.0	107.0		817	5.6	1.0	14	dbSNP_86	107	1747,6853	317.6+/-313.3	167,1413,2720	yes	missense	MMP14	NM_004995.2	23	169,1606,4728	AA,AG,GG		20.314,4.4712,14.9469	benign	273/583	23312594	1944,11062	2203	4300	6503	SO:0001583	missense	4323	exon5			CTGCCCGATGATG		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"""membrane type 1 metalloprotease"""	600754	"""matrix metalloproteinase 14 (membrane-inserted)"""			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.817G>A	14.37:g.23312594G>A	ENSP00000308208:p.Asp273Asn	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	72	49	0.680556	NM_004995	A8K5L0|Q6GSF3|Q92678	Missense_Mutation	SNP	ENST00000311852.6	37	CCDS9577.1	231	0.10576923076923077	8	0.016260162601626018	53	0.1464088397790055	13	0.022727272727272728	157	0.20712401055408972	G	9.413	1.081018	0.20309	0.044712	0.20314	ENSG00000157227	ENST00000311852	T	0.20598	2.06	5.6	5.6	0.85130	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.143577	0.64402	D	0.000009	T	0.00012	0.0000	L	0.35414	1.06	0.18873	P	0.9999895192	B	0.12013	0.005	B	0.09377	0.004	T	0.29579	-1.0007	9	0.32370	T	0.25	.	18.3853	0.90464	0.0:0.0:1.0:0.0	rs1042704;rs3182168;rs17881628;rs52820031;rs60437546;rs1042704	273	P50281	MMP14_HUMAN	N	273	ENSP00000308208:D273N	ENSP00000308208:D273N	D	+	1	0	MMP14	22382434	1.000000	0.71417	0.979000	0.43373	0.140000	0.21249	4.763000	0.62257	2.644000	0.89710	0.563000	0.77884	GAT	G|0.873;A|0.127	0.127	strong		0.597	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
YIPF7	285525	hgsc.bcm.edu	37	4	44652030	44652030	+	Missense_Mutation	SNP	C	C	T	rs2348353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:44652030C>T	ENST00000332990.5	-	2	176	c.160G>A	c.(160-162)Gcc>Acc	p.A54T	YIPF7_ENST00000415895.4_Missense_Mutation_p.A30T	NM_182592.2	NP_872398.2	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	54			A -> T (in dbSNP:rs2348353). {ECO:0000269|PubMed:14702039}.			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(1)	12						TTTCCATAGGCATTAGAGTCA	0.308													C|||	676	0.134984	0.0567	0.1758	5008	,	,		15827	0.251		0.1034	False		,,,				2504	0.1247				p.A54T		Atlas-SNP	.											.	YIPF7	33	.	0			c.G160A						PASS	.	C	THR/ALA	252,3364		7,238,1563	48.0	44.0	45.0		160	1.8	0.0	4	dbSNP_100	45	579,7581		24,531,3525	yes	missense	YIPF7	NM_182592.2	58	31,769,5088	TT,TC,CC		7.0956,6.969,7.0567	benign	54/281	44652030	831,10945	1808	4080	5888	SO:0001583	missense	285525	exon2			CATAGGCATTAGA	AK096895	CCDS54766.1	4p13	2008-08-07			ENSG00000177752	ENSG00000177752		"""Yip1 domain family"""	26825	protein-coding gene	gene with protein product							Standard	NM_182592		Approved	FLJ39576, FinGER9	uc021xnx.1	Q8N8F6	OTTHUMG00000160467	ENST00000332990.5:c.160G>A	4.37:g.44652030C>T	ENSP00000332772:p.Ala54Thr	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	152	87	0.572368	NM_182592	Q3SY21|Q3SY22	Missense_Mutation	SNP	ENST00000332990.5	37	CCDS54766.1	324|324	0.14835164835164835|0.14835164835164835	26|26	0.052845528455284556|0.052845528455284556	56|56	0.15469613259668508|0.15469613259668508	155|155	0.270979020979021|0.270979020979021	87|87	0.11477572559366754|0.11477572559366754	C|C	6.390|6.390	0.440160|0.440160	0.12104|0.12104	0.06969|0.06969	0.070956|0.070956	ENSG00000177752|ENSG00000177752	ENST00000332990|ENST00000415895	T|.	0.44482|.	0.92|.	5.45|5.45	1.76|1.76	0.24704|0.24704	.|.	0.760435|.	0.11681|.	N|.	0.539804|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.25563|.	0.129;0.002|.	B;B|.	0.23419|.	0.046;0.004|.	T|T	0.17868|0.17868	-1.0355|-1.0355	9|4	0.30078|.	T|.	0.28|.	-9.8831|-9.8831	4.8351|4.8351	0.13460|0.13460	0.1552:0.6455:0.0:0.1993|0.1552:0.6455:0.0:0.1993	rs2348353;rs17600948;rs52793322;rs58123416;rs2348353|rs2348353;rs17600948;rs52793322;rs58123416;rs2348353	54;54|.	Q8N8F6-4;Q8N8F6|.	.;YIPF7_HUMAN|.	T|Y	54|30	ENSP00000332772:A54T|.	ENSP00000332772:A54T|.	A|C	-|-	1|2	0|0	YIPF7|YIPF7	44346787|44346787	0.004000|0.004000	0.15560|0.15560	0.004000|0.004000	0.12327|0.12327	0.035000|0.035000	0.12851|0.12851	0.362000|0.362000	0.20284|0.20284	0.119000|0.119000	0.18210|0.18210	0.644000|0.644000	0.83932|0.83932	GCC|TGC	C|0.816;T|0.184	0.184	strong		0.308	YIPF7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_182592	
SP2	6668	hgsc.bcm.edu	37	17	45994154	45994154	+	Silent	SNP	G	G	A	rs2229358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45994154G>A	ENST00000376741.4	+	3	854	c.717G>A	c.(715-717)ccG>ccA	p.P239P	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	239					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						CCCCAACCCCGCTGTCTAAGA	0.607													G|||	2473	0.49381	0.3457	0.4625	5008	,	,		17625	0.7748		0.4602	False		,,,				2504	0.4611				p.P239P		Atlas-SNP	.											.	SP2	38	.	0			c.G717A						PASS	.	G		1622,2784	498.8+/-364.2	303,1016,884	82.0	87.0	85.0		717	-10.8	0.0	17	dbSNP_98	85	3732,4868	531.3+/-382.0	811,2110,1379	no	coding-synonymous	SP2	NM_003110.5		1114,3126,2263	AA,AG,GG		43.3953,36.8134,41.1656		239/614	45994154	5354,7652	2203	4300	6503	SO:0001819	synonymous_variant	6668	exon3			AACCCCGCTGTCT		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.717G>A	17.37:g.45994154G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_003110	A6NK74	Silent	SNP	ENST00000376741.4	37	CCDS11521.2																																																																																			G|0.545;A|0.455	0.455	strong		0.607	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
CEP68	23177	hgsc.bcm.edu	37	2	65298839	65298839	+	Silent	SNP	A	A	G	rs17849707	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:65298839A>G	ENST00000377990.2	+	3	812	c.609A>G	c.(607-609)acA>acG	p.T203T	CEP68_ENST00000546106.1_Silent_p.T203T|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000260569.4_Silent_p.T203T|CEP68_ENST00000537589.1_5'UTR|RAB1A_ENST00000494188.1_Intron	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	96	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	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	
ZNF721	170960	hgsc.bcm.edu	37	4	438067	438067	+	Silent	SNP	C	C	T	rs73070365	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:438067C>T	ENST00000338977.5	-	2	201	c.153G>A	c.(151-153)aaG>aaA	p.K51K	ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000511833.2_Silent_p.K63K|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	51					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(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						TATAAACTCCCTTCTGCACTT	0.308													T|||	350	0.0698882	0.1967	0.0591	5008	,	,		20712	0.0		0.0358	False		,,,				2504	0.0133				p.V63V		Atlas-SNP	.											.	ZNF721	205	.	0			c.A189A						PASS	.	T		620,3442		45,530,1456	65.0	73.0	70.0		189	0.0	0.0	4	dbSNP_130	70	305,8181		2,301,3940	no	coding-synonymous	ZNF721	NM_133474.2		47,831,5396	TT,TC,CC		3.5942,15.2634,7.3717		63/924	438067	925,11623	2031	4243	6274	SO:0001819	synonymous_variant	170960	exon3			AACTCCCTTCTGC	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.153G>A	4.37:g.438067C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	155	69	0.445161	NM_133474	Q69YG7	Silent	SNP	ENST00000338977.5	37																																																																																				C|0.943;T|0.057	0.057	strong		0.308	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
CTTNBP2NL	55917	hgsc.bcm.edu	37	1	112991698	112991698	+	Silent	SNP	T	T	C	rs2256883	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:112991698T>C	ENST00000271277.6	+	4	459	c.234T>C	c.(232-234)aaT>aaC	p.N78N		NM_018704.2	NP_061174.1	Q9P2B4	CT2NL_HUMAN	CTTNBP2 N-terminal like	78					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)	p.N78N(1)		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)		TCTGCACAAATCCACTCTCTA	0.458													C|||	2631	0.525359	0.3238	0.5692	5008	,	,		18306	0.4464		0.66	False		,,,				2504	0.7096				p.N78N		Atlas-SNP	.											CTTNBP2NL,NS,carcinoma,0,1	CTTNBP2NL	65	1	1	Substitution - coding silent(1)	stomach(1)	c.T234C						PASS	.	C		1698,2708	653.7+/-399.6	320,1058,825	73.0	70.0	71.0		234	3.8	1.0	1	dbSNP_100	71	5574,3026	465.3+/-366.5	1786,2002,512	no	coding-synonymous	CTTNBP2NL	NM_018704.2		2106,3060,1337	CC,CT,TT		35.186,38.5384,44.0873		78/640	112991698	7272,5734	2203	4300	6503	SO:0001819	synonymous_variant	55917	exon4			CACAAATCCACTC	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.234T>C	1.37:g.112991698T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	NM_018704	B3KMS5|Q96B40	Silent	SNP	ENST00000271277.6	37	CCDS845.1																																																																																			T|0.457;C|0.543	0.543	strong		0.458	CTTNBP2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030686.1	NM_018704	
ZNRF4	148066	hgsc.bcm.edu	37	19	5455976	5455976	+	Silent	SNP	C	C	T	rs386806230|rs61740902	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:5455976C>T	ENST00000222033.4	+	1	551	c.474C>T	c.(472-474)atC>atT	p.I158I		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	158	PA.			AIV -> SIA (in Ref. 4; AAH17592). {ECO:0000305}.		cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			NS(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (162;0.0002)		TGGGCGCCATCGTGCTGATCC	0.682													C|||	596	0.11901	0.0477	0.1729	5008	,	,		15731	0.004		0.2296	False		,,,				2504	0.182				p.I158I		Atlas-SNP	.											.	ZNRF4	59	.	0			c.C474T						PASS	.	C		259,3999		8,243,1878	28.0	31.0	30.0		474	-9.3	0.0	19	dbSNP_129	30	1616,6844		228,1160,2842	no	coding-synonymous	ZNRF4	NM_181710.3		236,1403,4720	TT,TC,CC		19.1017,6.0827,14.7429		158/430	5455976	1875,10843	2129	4230	6359	SO:0001819	synonymous_variant	148066	exon1			CGCCATCGTGCTG	AK098722	CCDS42475.1	19p13.3	2013-01-09				ENSG00000105428		"""RING-type (C3HC4) zinc fingers"""	17726	protein-coding gene	gene with protein product		612063					Standard	NM_181710		Approved	spzn, Ssrzf1, RNF204	uc002mca.4	Q8WWF5		ENST00000222033.4:c.474C>T	19.37:g.5455976C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	NM_181710	A8K886|O75866	Silent	SNP	ENST00000222033.4	37	CCDS42475.1																																																																																			C|0.851;T|0.149	0.149	strong		0.682	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710	
MUC16	94025	hgsc.bcm.edu	37	19	9082514	9082514	+	Missense_Mutation	SNP	C	C	A	rs17000871	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9082514C>A	ENST00000397910.4	-	1	9504	c.9301G>T	c.(9301-9303)Gca>Tca	p.A3101S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3102	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						TCTTCTTCTGCAATGGTCTGG	0.483													c|||	863	0.172324	0.2496	0.1167	5008	,	,		17683	0.2292		0.0855	False		,,,				2504	0.138				p.A3101S		Atlas-SNP	.											.	MUC16	4315	.	0			c.G9301T						PASS	.	T	SER/ALA	843,3065		125,593,1236	267.0	276.0	273.0		9301	-1.1	0.0	19	dbSNP_123	273	635,7667		26,583,3542	yes	missense	MUC16	NM_024690.2	99	151,1176,4778	AA,AC,CC		7.6488,21.5711,12.1048	benign	3101/14508	9082514	1478,10732	1954	4151	6105	SO:0001583	missense	94025	exon1			CTTCTGCAATGGT	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.9301G>T	19.37:g.9082514C>A	ENSP00000381008:p.Ala3101Ser	Somatic	419	0	0		WXS	Illumina HiSeq	Phase_I	387	190	0.490956	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	359	0.16437728937728938	106	0.21544715447154472	39	0.10773480662983426	146	0.25524475524475526	68	0.08970976253298153	t	0.394	-0.922017	0.02396	0.215711	0.076488	ENSG00000181143	ENST00000397910	T	0.02631	4.22	0.541	-1.08	0.09936	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.18166	0.026	B	0.15052	0.012	T	0.49762	-0.8905	7	0.87932	D	0	.	.	.	.	rs17000871;rs52804859;rs59318309;rs17000871	3101	B5ME49	.	S	3101	ENSP00000381008:A3101S	ENSP00000381008:A3101S	A	-	1	0	MUC16	8943514	0.019000	0.18553	0.001000	0.08648	0.005000	0.04900	-0.707000	0.05041	-2.646000	0.00426	-2.410000	0.00221	GCA	A|0.158;C|0.841;T|0.000	0.158	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GGT1	2678	hgsc.bcm.edu	37	22	25016911	25016911	+	Missense_Mutation	SNP	C	C	T	rs199703506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:25016911C>T	ENST00000400382.1	+	9	1362	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	GGT1_ENST00000400383.1_Missense_Mutation_p.R203W|GGT1_ENST00000406383.2_Missense_Mutation_p.R203W|GGT1_ENST00000248923.4_Missense_Mutation_p.R203W|GGT1_ENST00000400380.1_Missense_Mutation_p.R203W|GGT1_ENST00000466310.1_Intron			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	203					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.R203W(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)	AAAGGTGCTTCGGGAGGGGGA	0.652																																					p.R203W		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	breast(1)	c.C607T						scavenged	.						20.0	22.0	21.0					22																	25016911		1981	4142	6123	SO:0001583	missense	2678	exon9			GTGCTTCGGGAGG	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.607C>T	22.37:g.25016911C>T	ENSP00000383232:p.Arg203Trp	Somatic	378	0	0		WXS	Illumina HiSeq	Phase_I	429	17	0.039627	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	16.88	3.244872	0.59103	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12;3.12	3.94	1.51	0.23008	.	0.465560	0.21948	U	0.066770	T	0.18841	0.0452	M	0.62016	1.91	0.29917	N	0.823045	D	0.76494	0.999	P	0.58970	0.849	T	0.03121	-1.1070	10	0.87932	D	0	-23.2527	10.8877	0.46976	0.3395:0.6605:0.0:0.0	.	203	P19440	GGT1_HUMAN	W	203	ENSP00000248923:R203W;ENSP00000393537:R203W;ENSP00000383232:R203W;ENSP00000383233:R203W;ENSP00000383231:R203W;ENSP00000385975:R203W	ENSP00000248923:R203W	R	+	1	2	GGT1	23346911	0.047000	0.20315	0.042000	0.18584	0.549000	0.35272	1.263000	0.33004	0.735000	0.32537	0.555000	0.69702	CGG	C|0.996;T|0.004	0.004	strong		0.652	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
MAN2B2	23324	hgsc.bcm.edu	37	4	6610889	6610889	+	Missense_Mutation	SNP	G	G	A	rs61733402	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:6610889G>A	ENST00000285599.3	+	12	1906	c.1870G>A	c.(1870-1872)Ggg>Agg	p.G624R	MAN2B2_ENST00000504248.1_Missense_Mutation_p.G573R|MAN2B2_ENST00000504960.1_3'UTR	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	624					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CCACGTCAACGGGGATGTGAA	0.572													G|||	181	0.0361422	0.0061	0.0389	5008	,	,		21881	0.001		0.0885	False		,,,				2504	0.0573				p.G624R		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G1870A						PASS	.	G	ARG/GLY	79,4327	69.2+/-107.0	0,79,2124	102.0	90.0	94.0		1870	0.3	0.0	4	dbSNP_129	94	818,7782	190.0+/-236.6	46,726,3528	yes	missense	MAN2B2	NM_015274.1	125	46,805,5652	AA,AG,GG		9.5116,1.793,6.8968	probably-damaging	624/1010	6610889	897,12109	2203	4300	6503	SO:0001583	missense	23324	exon12			GTCAACGGGGATG	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1870G>A	4.37:g.6610889G>A	ENSP00000285599:p.Gly624Arg	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	160	74	0.4625	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	92	0.04212454212454213	6	0.012195121951219513	15	0.04143646408839779	0	0.0	71	0.09366754617414248	G	23.1	4.376100	0.82682	0.01793	0.095116	ENSG00000013288	ENST00000285599;ENST00000504248	T;T	0.79141	-1.24;-1.24	4.36	0.289	0.15723	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.520725	0.20150	N	0.098165	T	0.11580	0.0282	L	0.60455	1.87	0.09310	N	1	D;D;D	0.76494	0.999;0.998;0.991	D;D;P	0.68353	0.957;0.936;0.763	T	0.48502	-0.9030	10	0.62326	D	0.03	-0.1459	5.3779	0.16176	0.1494:0.0:0.579:0.2715	rs61733402	573;624;624	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	R	624;573	ENSP00000285599:G624R;ENSP00000423129:G573R	ENSP00000285599:G624R	G	+	1	0	MAN2B2	6661790	0.985000	0.35326	0.000000	0.03702	0.904000	0.53231	2.922000	0.48860	-0.356000	0.08187	0.313000	0.20887	GGG	G|0.936;A|0.064	0.064	strong		0.572	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
NLRX1	79671	hgsc.bcm.edu	37	11	119052826	119052826	+	Missense_Mutation	SNP	C	C	A	rs4245191	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:119052826C>A	ENST00000409109.1	+	9	2965	c.2378C>A	c.(2377-2379)gCg>gAg	p.A793E	NLRX1_ENST00000292199.2_Missense_Mutation_p.A793E|NLRX1_ENST00000525863.1_Missense_Mutation_p.A793E|NLRX1_ENST00000409991.1_Missense_Mutation_p.A793E|NLRX1_ENST00000409265.4_Missense_Mutation_p.A793E	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	793	Required for the repression of MAVS- induced interferon signaling.		A -> E (in dbSNP:rs4245191). {ECO:0000269|PubMed:12766759, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		innate immune response (GO:0045087)|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 interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CCGCTGACGGCGGCAGGTGTT	0.632													C|||	3447	0.688299	0.708	0.4179	5008	,	,		18563	0.8839		0.5477	False		,,,				2504	0.7965				p.A793E		Atlas-SNP	.											.	NLRX1	128	.	0			c.C2378A						PASS	.	C	GLU/ALA,GLU/ALA	2971,1429	652.9+/-399.5	1024,923,253	124.0	118.0	120.0		2378,2378	2.9	0.0	11	dbSNP_111	120	4477,4113	565.2+/-388.4	1172,2133,990	yes	missense,missense	NLRX1	NM_024618.2,NM_170722.1	107,107	2196,3056,1243	AA,AC,CC		47.8813,32.4773,42.6636	benign,benign	793/976,793/922	119052826	7448,5542	2200	4295	6495	SO:0001583	missense	79671	exon9			TGACGGCGGCAGG	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.2378C>A	11.37:g.119052826C>A	ENSP00000387334:p.Ala793Glu	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	182	119	0.653846	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	1419	0.6497252747252747	349	0.709349593495935	166	0.4585635359116022	496	0.8671328671328671	408	0.5382585751978892	C	0.006	-2.091840	0.00364	0.675227	0.521187	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	4.78	2.91	0.33838	.	0.152719	0.40640	N	0.001049	T	0.00012	0.0000	N	0.03115	-0.41	0.54753	P	1.799999999996249E-5	B;B	0.15719	0.014;0.007	B;B	0.17979	0.02;0.006	T	0.40590	-0.9555	9	0.02654	T	1	.	6.5557	0.22460	0.1759:0.6611:0.0:0.163	rs4245191;rs17627663;rs17845376;rs17858230;rs61333211;rs4245191	793;793	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	E	793	ENSP00000386851:A793E;ENSP00000292199:A793E;ENSP00000386858:A793E;ENSP00000387334:A793E;ENSP00000433442:A793E	ENSP00000292199:A793E	A	+	2	0	NLRX1	118558036	0.979000	0.34478	0.018000	0.16275	0.003000	0.03518	2.559000	0.45888	0.628000	0.30357	0.609000	0.83330	GCG	C|0.378;A|0.622	0.622	strong		0.632	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
PRKAA1	5562	hgsc.bcm.edu	37	5	40765280	40765280	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:40765280A>G	ENST00000397128.2	-	7	890	c.882T>C	c.(880-882)taT>taC	p.Y294Y	PRKAA1_ENST00000354209.3_Silent_p.Y309Y	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	294					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to glucose starvation (GO:0042149)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|cholesterol biosynthetic process (GO:0006695)|cold acclimation (GO:0009631)|fatty acid biosynthetic process (GO:0006633)|fatty acid homeostasis (GO:0055089)|fatty acid oxidation (GO:0019395)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of glucosylceramide biosynthetic process (GO:0046318)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of TOR signaling (GO:0032007)|positive regulation of autophagy (GO:0010508)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of gene expression (GO:0010628)|positive regulation of glycolytic process (GO:0045821)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of circadian rhythm (GO:0042752)|regulation of energy homeostasis (GO:2000505)|regulation of transcription, DNA-templated (GO:0006355)|regulation of vesicle-mediated transport (GO:0060627)|response to activity (GO:0014823)|response to caffeine (GO:0031000)|response to camptothecin (GO:1901563)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	AMP-activated protein kinase complex (GO:0031588)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)	[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)|cAMP-dependent protein kinase activity (GO:0004691)|chromatin binding (GO:0003682)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|tau-protein kinase activity (GO:0050321)			breast(1)	1					Acetylsalicylic acid(DB00945)|Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)|Phenformin(DB00914)	TGGTTGAACTATATGATGGAT	0.388																																					p.Y309Y		Atlas-SNP	.											.	PRKAA1	27	.	0			c.T927C						PASS	.						126.0	115.0	118.0					5																	40765280		1838	4091	5929	SO:0001819	synonymous_variant	5562	exon8			TGAACTATATGAT		CCDS3932.2, CCDS3933.2	5p13.1	2012-10-03			ENSG00000132356	ENSG00000132356			9376	protein-coding gene	gene with protein product	"""AMPK, alpha, 1"""	602739				8557660	Standard	XM_006714481		Approved	AMPKa1	uc003jmb.3	Q13131	OTTHUMG00000162269	ENST00000397128.2:c.882T>C	5.37:g.40765280A>G		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	306	131	0.428105	NM_206907	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Silent	SNP	ENST00000397128.2	37	CCDS3932.2																																																																																			.	.	none		0.388	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251	
DEFB104A	140596	hgsc.bcm.edu	37	8	7694034	7694034	+	Missense_Mutation	SNP	A	A	G	rs202183310		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	2087	5	0.00239578		WXS	Illumina HiSeq	Phase_I	1448	369	0.254834	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	
VSIG10	54621	hgsc.bcm.edu	37	12	118509191	118509191	+	Missense_Mutation	SNP	G	G	A	rs7307331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:118509191G>A	ENST00000359236.5	-	6	1579	c.1303C>T	c.(1303-1305)Cat>Tat	p.H435Y		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	435			H -> Y (in dbSNP:rs7307331). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GGGCTATAATGCAACAGAAGC	0.502													A|||	2714	0.541933	0.7337	0.5072	5008	,	,		19367	0.7808		0.2813	False		,,,				2504	0.3292				p.H435Y		Atlas-SNP	.											.	VSIG10	41	.	0			c.C1303T						PASS	.	A	TYR/HIS	2457,1341		789,879,231	112.0	118.0	116.0		1303	5.2	1.0	12	dbSNP_116	116	2364,5868		343,1678,2095	yes	missense	VSIG10	NM_019086.5	83	1132,2557,2326	AA,AG,GG		28.7172,35.3081,40.0748	benign	435/541	118509191	4821,7209	1899	4116	6015	SO:0001583	missense	54621	exon6			TATAATGCAACAG		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1303C>T	12.37:g.118509191G>A	ENSP00000352172:p.His435Tyr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	151	66	0.437086	NM_019086	Q9NWQ7	Missense_Mutation	SNP	ENST00000359236.5	37	CCDS44992.1	1150	0.5265567765567766	348	0.7073170731707317	165	0.4558011049723757	433	0.756993006993007	204	0.2691292875989446	A	0.457	-0.890959	0.02491	0.646919	0.287172	ENSG00000176834	ENST00000359236	T	0.47528	0.84	5.15	5.15	0.70609	.	0.000000	0.38272	N	0.001751	T	0.00012	0.0000	N	0.00104	-2.125	0.48395	P	3.5799999999996945E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.40590	-0.9555	9	0.06625	T	0.88	-8.5865	11.2621	0.49089	0.928:0.0:0.072:0.0	rs7307331;rs59386576;rs7307331	435	Q8N0Z9	VSI10_HUMAN	Y	435	ENSP00000352172:H435Y	ENSP00000352172:H435Y	H	-	1	0	VSIG10	116993574	0.999000	0.42202	0.959000	0.39883	0.215000	0.24574	3.890000	0.56220	0.926000	0.37118	-0.535000	0.04281	CAT	G|0.472;A|0.528	0.528	strong		0.502	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
MYO1G	64005	hgsc.bcm.edu	37	7	45005795	45005795	+	Silent	SNP	G	G	A	rs2269969	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	86	0	0		WXS	Illumina HiSeq	Phase_I	116	70	0.603448	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		
FBXO30	84085	hgsc.bcm.edu	37	6	146126419	146126419	+	Missense_Mutation	SNP	C	C	T	rs9373475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:146126419C>T	ENST00000237281.4	-	2	1289	c.1123G>A	c.(1123-1125)Gtg>Atg	p.V375M		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	375	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.		V -> M (in dbSNP:rs9373475). {ECO:0000269|Ref.3}.				ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		ACATTCTTCACGTCCCCTAAG	0.398													c|||	1649	0.329273	0.2549	0.232	5008	,	,		23522	0.2341		0.4105	False		,,,				2504	0.5133				p.V375M		Atlas-SNP	.											.	FBXO30	56	.	0			c.G1123A						PASS	.	T	MET/VAL	1117,3289	401.0+/-331.8	152,813,1238	159.0	151.0	153.0		1123	-3.2	0.2	6	dbSNP_119	153	3553,5047	516.6+/-378.9	728,2097,1475	yes	missense	FBXO30	NM_032145.4	21	880,2910,2713	TT,TC,CC		41.314,25.3518,35.9065	benign	375/746	146126419	4670,8336	2203	4300	6503	SO:0001583	missense	84085	exon2			TCTTCACGTCCCC	AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"""F-boxes /  ""other"""""	15600	protein-coding gene	gene with protein product		609101	"""F-box only protein, helicase, 18"""				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.1123G>A	6.37:g.146126419C>T	ENSP00000237281:p.Val375Met	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	192	94	0.489583	NM_032145	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	37	CCDS5208.1	674	0.3086080586080586	125	0.2540650406504065	90	0.24861878453038674	149	0.26048951048951047	310	0.40897097625329815	c	4.167	0.029502	0.08054	0.253518	0.41314	ENSG00000118496	ENST00000237281	T	0.18810	2.19	5.46	-3.18	0.05186	.	0.133607	0.51477	N	0.000086	T	0.02193	0.0068	N	0.08118	0	0.80722	P	0.0	B	0.20261	0.043	B	0.12156	0.007	T	0.33650	-0.9860	9	0.56958	D	0.05	-0.0044	2.7703	0.05332	0.2489:0.2465:0.3853:0.1193	rs9373475;rs17822286;rs52794580;rs57120223;rs9373475	375	Q8TB52	FBX30_HUMAN	M	375	ENSP00000237281:V375M	ENSP00000237281:V375M	V	-	1	0	FBXO30	146168112	0.104000	0.21937	0.186000	0.23195	0.512000	0.34134	-0.321000	0.08018	-0.720000	0.04935	-1.033000	0.02402	GTG	C|0.663;N|0.000	.	strong		0.398	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2		
TECPR2	9895	hgsc.bcm.edu	37	14	102901023	102901023	+	Silent	SNP	G	G	A	rs45605932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102901023G>A	ENST00000359520.7	+	9	2095	c.1869G>A	c.(1867-1869)ggG>ggA	p.G623G	TECPR2_ENST00000558678.1_Silent_p.G623G	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	623					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						GCTCTCCTGGGGCGCATGATG	0.562													G|||	517	0.103235	0.2753	0.0519	5008	,	,		21086	0.001		0.0775	False		,,,				2504	0.0389				p.G623G		Atlas-SNP	.											.	TECPR2	114	.	0			c.G1869A						PASS	.	G	,	1086,3320	391.9+/-328.3	123,840,1240	72.0	51.0	58.0		1869,1869	2.8	0.0	14	dbSNP_127	58	696,7904	172.3+/-223.0	28,640,3632	no	coding-synonymous,coding-synonymous	TECPR2	NM_001172631.1,NM_014844.3	,	151,1480,4872	AA,AG,GG		8.093,24.6482,13.7014	,	623/1268,623/1412	102901023	1782,11224	2203	4300	6503	SO:0001819	synonymous_variant	9895	exon9			TCCTGGGGCGCAT	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.1869G>A	14.37:g.102901023G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	114	32	0.280702	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Silent	SNP	ENST00000359520.7	37	CCDS32162.1																																																																																			G|0.880;A|0.120	0.120	strong		0.562	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
GRIN3B	116444	hgsc.bcm.edu	37	19	1003374	1003374	+	Silent	SNP	G	G	A	rs34585248	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1003374G>A	ENST00000234389.3	+	2	691	c.672G>A	c.(670-672)gcG>gcA	p.A224A	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	224					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)	CGATGGCGGCGCCAGTGGGGG	0.746													g|||	158	0.0315495	0.0015	0.0173	5008	,	,		11320	0.0754		0.0338	False		,,,				2504	0.0348				p.A224A		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G672A						PASS	.	G		37,3905		0,37,1934	4.0	6.0	5.0		672	-8.1	0.0	19	dbSNP_126	5	211,7611		3,205,3703	no	coding-synonymous	GRIN3B	NM_138690.1		3,242,5637	AA,AG,GG		2.6975,0.9386,2.1081		224/1044	1003374	248,11516	1971	3911	5882	SO:0001819	synonymous_variant	116444	exon2			GGCGGCGCCAGTG		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.672G>A	19.37:g.1003374G>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			G|0.966;A|0.034	0.034	strong		0.746	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
LRRC15	131578	hgsc.bcm.edu	37	3	194080696	194080696	+	Silent	SNP	G	G	A	rs9682541	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:194080696G>A	ENST00000347624.3	-	2	1162	c.1077C>T	c.(1075-1077)aaC>aaT	p.N359N	LRRC15_ENST00000439944.2_Silent_p.N365N|LRRC15_ENST00000428839.1_Silent_p.N365N	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	359					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)		TGCGGAAGACGTTCCCGTCCA	0.587													A|||	582	0.116214	0.093	0.1052	5008	,	,		19476	0.0685		0.2107	False		,,,				2504	0.1074				p.N365N		Atlas-SNP	.											.	LRRC15	137	.	0			c.C1095T						PASS	.	A	,	432,3974	786.5+/-414.8	16,400,1787	67.0	64.0	65.0		1095,1077	-9.8	0.0	3	dbSNP_119	65	2013,6587	721.4+/-406.4	240,1533,2527	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	256,1933,4314	AA,AG,GG		23.407,9.8048,18.799	,	365/588,359/582	194080696	2445,10561	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			GAAGACGTTCCCG	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.1077C>T	3.37:g.194080696G>A		Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	241	131	0.543568	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			G|0.844;A|0.156	0.156	strong		0.587	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
CASP10	843	hgsc.bcm.edu	37	2	202074207	202074207	+	Missense_Mutation	SNP	A	A	G	rs17860405	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:202074207A>G	ENST00000272879.5	+	9	1521	c.1337A>G	c.(1336-1338)tAt>tGt	p.Y446C	CASP10_ENST00000346817.5_Missense_Mutation_p.Y403C|CASP10_ENST00000286186.6_Missense_Mutation_p.Y446C|CASP10_ENST00000360132.3_3'UTR|CASP10_ENST00000492363.1_3'UTR|CASP10_ENST00000313728.7_Missense_Mutation_p.Y379C|CASP10_ENST00000448480.1_Missense_Mutation_p.Y403C	NM_032974.4	NP_116756.2	Q92851	CASPA_HUMAN	caspase 10, apoptosis-related cysteine peptidase	446			Y -> C (associated with ALPS2A; does not interfere with apoptosis in a dominant negative manner; dbSNP:rs17860405). {ECO:0000269|PubMed:16446975}.		apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|innate immune response (GO:0045087)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of apoptotic process (GO:0042981)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|death effector domain binding (GO:0035877)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	27						GTCCCAGGCTATGTATCCTTT	0.507													A|||	64	0.0127796	0.0008	0.0231	5008	,	,		17367	0.0		0.0417	False		,,,				2504	0.0051				p.Y446C		Atlas-SNP	.											.	CASP10	95	.	0			c.A1337G	GRCh37	CM060890	CASP10	M	rs17860405	PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,,CYS/TYR	31,4375	35.2+/-66.4	0,31,2172	108.0	102.0	104.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1136,1208,1208,1337,,1337	1.0	0.0	2	dbSNP_123	104	322,8278	114.2+/-174.2	6,310,3984	yes	missense,missense,missense,missense,utr-3,missense	CASP10	NM_001206524.1,NM_001206542.1,NM_001230.4,NM_032974.4,NM_032976.3,NM_032977.3	194,194,194,194,,194	6,341,6156	GG,GA,AA		3.7442,0.7036,2.7141	benign,benign,benign,benign,,benign	379/456,403/479,403/480,446/522,,446/523	202074207	353,12653	2203	4300	6503	SO:0001583	missense	843	exon9			CAGGCTATGTATC	U60519	CCDS2338.1, CCDS2339.1, CCDS2340.1, CCDS56159.1, CCDS56160.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000003400	ENSG00000003400	3.4.22.63	"""Caspases"""	1500	protein-coding gene	gene with protein product		601762	"""caspase 10, apoptosis-related cysteine protease"""			8755496	Standard	NM_032974		Approved	MCH4	uc002uxj.1	Q92851	OTTHUMG00000132818	ENST00000272879.5:c.1337A>G	2.37:g.202074207A>G	ENSP00000272879:p.Tyr446Cys	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	77	7	0.0909091	NM_032977	Q68HC0|Q6KF62|Q6KF63|Q8IUP5|Q8WYQ8|Q99845|Q9Y2U6|Q9Y2U7	Missense_Mutation	SNP	ENST00000272879.5	37	CCDS2338.1	49	0.022435897435897436	0	0.0	11	0.03038674033149171	0	0.0	38	0.05013192612137203	A	10.66	1.413801	0.25465	0.007036	0.037442	ENSG00000003400	ENST00000286186;ENST00000272879;ENST00000346817;ENST00000313728;ENST00000448480	T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97	5.05	1.01	0.19927	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.208989	0.44285	N	0.000473	T	0.06371	0.0164	M	0.76938	2.355	0.80722	D	1	P;B;P;P;P	0.52692	0.501;0.439;0.955;0.69;0.735	P;B;P;B;B	0.51701	0.482;0.231;0.677;0.411;0.414	T	0.01124	-1.1444	10	0.46703	T	0.11	.	10.3166	0.43740	0.6892:0.0:0.3108:0.0	rs17860405	379;403;446;403;446	Q92851-6;Q92851-5;Q92851;Q92851-2;Q92851-4	.;.;CASPA_HUMAN;.;.	C	446;446;403;379;403	ENSP00000286186:Y446C;ENSP00000272879:Y446C;ENSP00000237865:Y403C;ENSP00000314599:Y379C;ENSP00000396835:Y403C	ENSP00000272879:Y446C	Y	+	2	0	CASP10	201782452	0.018000	0.18449	0.010000	0.14722	0.115000	0.19883	0.456000	0.21859	0.301000	0.22738	-0.263000	0.10527	TAT	A|0.973;G|0.027	0.027	strong		0.507	CASP10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256273.1	NM_032977	
SRMS	6725	hgsc.bcm.edu	37	20	62172244	62172244	+	Missense_Mutation	SNP	C	C	G	rs33933649	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62172244C>G	ENST00000217188.1	-	8	1434	c.1394G>C	c.(1393-1395)aGc>aCc	p.S465T		NM_080823.2	NP_543013.1	Q9H3Y6	SRMS_HUMAN	src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites	465	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> T (in dbSNP:rs33933649). {ECO:0000269|PubMed:17344846}.		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)			CTCGGGGCTGCTCCTCCAGCA	0.682													C|||	42	0.00838658	0.0038	0.013	5008	,	,		16998	0.0		0.0229	False		,,,				2504	0.0051				p.S465T		Atlas-SNP	.											.	SRMS	48	.	0			c.G1394C						PASS	.	C	THR/SER	32,4372	36.8+/-68.6	1,30,2171	91.0	86.0	88.0		1394	-3.8	0.0	20	dbSNP_126	88	253,8347	99.3+/-160.8	1,251,4048	yes	missense	SRMS	NM_080823.2	58	2,281,6219	GG,GC,CC		2.9419,0.7266,2.1916	benign	465/489	62172244	285,12719	2202	4300	6502	SO:0001583	missense	6725	exon8			GGGCTGCTCCTCC		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.1394G>C	20.37:g.62172244C>G	ENSP00000217188:p.Ser465Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_080823		Missense_Mutation	SNP	ENST00000217188.1	37	CCDS13525.1	24	0.01098901098901099	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	5.972	0.363358	0.11296	0.007266	0.029419	ENSG00000125508	ENST00000217188	D	0.82803	-1.65	5.17	-3.81	0.04294	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.880119	0.09801	N	0.754091	T	0.42921	0.1224	N	0.13299	0.325	0.09310	N	1	B	0.17465	0.022	B	0.26416	0.069	T	0.49031	-0.8981	10	0.44086	T	0.13	.	7.2562	0.26177	0.0:0.2938:0.4425:0.2637	rs33933649	465	Q9H3Y6	SRMS_HUMAN	T	465	ENSP00000217188:S465T	ENSP00000217188:S465T	S	-	2	0	SRMS	61642688	0.000000	0.05858	0.008000	0.14137	0.033000	0.12548	-0.195000	0.09546	-0.615000	0.05679	-0.955000	0.02649	AGC	C|0.979;G|0.021	0.021	strong		0.682	SRMS-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080148.1	NM_080823	
DOCK2	1794	hgsc.bcm.edu	37	5	169174484	169174484	+	Silent	SNP	A	A	G	rs13155521	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:169174484A>G	ENST00000256935.8	+	23	2432	c.2352A>G	c.(2350-2352)caA>caG	p.Q784Q	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000520908.1_Silent_p.Q276Q	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	118	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	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	
TCEB2	6923	hgsc.bcm.edu	37	16	2821525	2821525	+	3'UTR	SNP	G	G	A	rs4036	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2821525G>A	ENST00000409906.4	-	0	880				TCEB2_ENST00000262306.7_Missense_Mutation_p.T145M|TCEB2_ENST00000409477.1_3'UTR|AC092117.2_ENST00000581119.1_RNA	NM_007108.3	NP_009039.1	Q15370	ELOB_HUMAN	transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)						cellular response to hypoxia (GO:0071456)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|elongin complex (GO:0070449)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|prostate(1)	3						GGGTTCCCTCGTTGAACATGC	0.577													A|||	943	0.188299	0.466	0.1138	5008	,	,		16029	0.0754		0.1044	False		,,,				2504	0.0685				p.T145M	GBM(141;5215 5962)	Atlas-SNP	.											.	TCEB2	6	.	0			c.C434T						PASS	.	A	,MET/THR	1714,2682	650.5+/-399.1	334,1046,818	117.0	108.0	111.0		,434	0.1	0.0	16	dbSNP_36	111	788,7812	783.7+/-407.6	37,714,3549	yes	utr-3,missense	TCEB2	NM_007108.3,NM_207013.2	,81	371,1760,4367	AA,AG,GG		9.1628,38.99,19.2521	,benign	,145/162	2821525	2502,10494	2198	4300	6498	SO:0001624	3_prime_UTR_variant	6923	exon5			TCCCTCGTTGAAC	L42856	CCDS32374.1, CCDS45387.1	16p12.3	2008-02-05	2002-08-29		ENSG00000103363	ENSG00000103363			11619	protein-coding gene	gene with protein product		600787	"""transcription elongation factor B (SIII), polypeptide 2 (18kD, elongin B)"""			7638163	Standard	NM_007108		Approved	SIII	uc002crm.3	Q15370	OTTHUMG00000154125	ENST00000409906.4:c.*466C>T	16.37:g.2821525G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	162	75	0.462963	NM_207013	B7WPD3	Missense_Mutation	SNP	ENST00000409906.4	37	CCDS45387.1	384	0.17582417582417584	224	0.45528455284552843	42	0.11602209944751381	38	0.06643356643356643	80	0.10554089709762533	A	5.944	0.358230	0.11239	0.3899	0.091628	ENSG00000103363	ENST00000262306	.	.	.	2.58	0.106	0.14540	.	.	.	.	.	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	0.44143	-0.9347	7	0.02654	T	1	.	2.9225	0.05773	0.4589:0.2437:0.2974:0.0	rs4036;rs57537347;rs4036	145	B7WPD3	.	M	145	.	ENSP00000262306:T145M	T	-	2	0	TCEB2	2761526	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.772000	0.04694	-0.315000	0.08703	-0.254000	0.11334	ACG	G|0.812;A|0.188	0.188	strong		0.577	TCEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333975.2	NM_007108	
FAM13A	10144	hgsc.bcm.edu	37	4	89772301	89772301	+	Missense_Mutation	SNP	C	C	A	rs7680970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:89772301C>A	ENST00000264344.5	-	7	1084	c.877G>T	c.(877-879)Gcc>Tcc	p.A293S	FAM13A_ENST00000511976.1_Intron|FAM13A_ENST00000502459.1_5'UTR	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	293					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						ACTCTGTGGGCCTGAATAGAT	0.428													C|||	360	0.071885	0.208	0.0202	5008	,	,		15473	0.0		0.0398	False		,,,				2504	0.0317				p.A293S		Atlas-SNP	.											.	FAM13A	181	.	0			c.G877T						PASS	.	C	SER/ALA	877,3529	342.5+/-307.2	84,709,1410	104.0	110.0	108.0		877	-8.6	0.0	4	dbSNP_116	108	372,8228	122.5+/-181.5	7,358,3935	yes	missense	FAM13A	NM_014883.2	99	91,1067,5345	AA,AC,CC		4.3256,19.9047,9.6033	benign	293/1024	89772301	1249,11757	2203	4300	6503	SO:0001583	missense	10144	exon7			TGTGGGCCTGAAT	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.877G>T	4.37:g.89772301C>A	ENSP00000264344:p.Ala293Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	64	41	0.640625	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Missense_Mutation	SNP	ENST00000264344.5	37	CCDS34029.1	131	0.059981684981684984	92	0.18699186991869918	8	0.022099447513812154	0	0.0	31	0.040897097625329816	C	0.266	-0.996427	0.02145	0.199047	0.043256	ENSG00000138640	ENST00000264344	T	0.17528	2.27	4.33	-8.65	0.00870	.	1.727690	0.03193	N	0.173561	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.28681	-1.0036	9	0.09843	T	0.71	.	1.8154	0.03099	0.2605:0.2239:0.0863:0.4293	rs7680970;rs7680970	293	O94988	FA13A_HUMAN	S	293	ENSP00000264344:A293S	ENSP00000264344:A293S	A	-	1	0	FAM13A	89991324	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-2.226000	0.01211	-2.955000	0.00292	-0.813000	0.03139	GCC	C|0.918;A|0.082	0.082	strong		0.428	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
JADE1	79960	hgsc.bcm.edu	37	4	129792787	129792787	+	Silent	SNP	A	A	G	rs6850940	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:129792787A>G	ENST00000226319.6	+	11	2179	c.1899A>G	c.(1897-1899)ttA>ttG	p.L633L	PHF17_ENST00000512960.1_Silent_p.L633L|PHF17_ENST00000452328.2_Silent_p.L621L	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TTTTGGGTTTAGAAAAGACCT	0.483													G|||	111	0.0221645	0.0734	0.0144	5008	,	,		18630	0.0		0.002	False		,,,				2504	0.002				p.L633L		Atlas-SNP	.											.	PHF17	63	.	0			c.A1899G						PASS	.	G		329,4077	793.1+/-415.2	13,303,1887	62.0	66.0	65.0		1899	-4.7	0.1	4	dbSNP_116	65	10,8590	817.4+/-406.9	0,10,4290	no	coding-synonymous	PHF17	NM_199320.2		13,313,6177	GG,GA,AA		0.1163,7.4671,2.6065		633/843	129792787	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	79960	exon11			GGGTTTAGAAAAG																												ENST00000226319.6:c.1899A>G	4.37:g.129792787A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	86	22	0.255814	NM_199320		Silent	SNP	ENST00000226319.6	37	CCDS34062.1																																																																																			A|0.972;G|0.028	0.028	strong		0.483	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1		
HDHD1	8226	hgsc.bcm.edu	37	X	6995438	6995438	+	Silent	SNP	C	C	T	rs1803675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:6995438C>T	ENST00000381077.5	-	3	409	c.333G>A	c.(331-333)ctG>ctA	p.L111L	HDHD1_ENST00000412827.2_Silent_p.L68L|HDHD1_ENST00000540122.1_Silent_p.L111L|HDHD1_ENST00000424830.2_Silent_p.L134L	NM_001178136.1|NM_012080.4	NP_001171607.1|NP_036212.3	Q08623	HDHD1_HUMAN	haloacid dehalogenase-like hydrolase domain containing 1	111					nucleotide metabolic process (GO:0009117)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)			breast(2)|large_intestine(1)|lung(3)	6						AGCTGGTGGCCAGTGCAAAGG	0.597													C|||	1051	0.278411	0.1074	0.3473	3775	,	,		12574	0.2153		0.1909	False		,,,				2504	0.2648				p.L134L		Atlas-SNP	.											.	HDHD1	21	.	0			c.G402A						PASS	.	C	,,,	645,2938		57,424,107,1025,464	51.0	51.0	51.0		402,333,204,333	-7.8	0.0	X	dbSNP_89	51	1700,4864		172,894,462,1310,1350	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDHD1	NM_001135565.1,NM_001178135.1,NM_001178136.1,NM_012080.4	,,,	229,1318,569,2335,1814	TT,TC,T,CC,C		25.8988,18.0017,23.1103	,,,	134/252,111/209,68/186,111/229	6995438	2345,7802	2077	4188	6265	SO:0001819	synonymous_variant	8226	exon4			GGTGGCCAGTGCA	M86934	CCDS48075.1, CCDS48076.1, CCDS55366.1, CCDS55367.1	Xp22.32	2010-07-21	2010-07-21	2010-07-21	ENSG00000130021	ENSG00000130021			16818	protein-coding gene	gene with protein product		306480	"""family with sequence similarity 16, member A, X-linked"", ""haloacid dehalogenase-like hydrolase domain containing 1A"""	FAM16AX, HDHD1A		1734713, 1284467	Standard	NM_012080		Approved	DXF68S1E, GS1	uc011mhm.1	Q08623	OTTHUMG00000021101	ENST00000381077.5:c.333G>A	X.37:g.6995438C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_001135565	B2R7X6|B4DV93|B7Z6Q3|E9PAV8|F5GWZ2|Q53F84|Q96EB8	Silent	SNP	ENST00000381077.5	37	CCDS48075.1																																																																																			C|0.723;T|0.277	0.277	strong		0.597	HDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055683.2	NM_012080	
TSPAN6	7105	hgsc.bcm.edu	37	X	99890204	99890204	+	Missense_Mutation	SNP	C	C	T	rs1802288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:99890204C>T	ENST00000373020.4	-	3	433	c.322G>A	c.(322-324)Gcc>Acc	p.A108T	TSPAN6_ENST00000496771.1_5'UTR	NM_001278740.1|NM_001278741.1|NM_003270.2	NP_001265669.1|NP_001265670.1|NP_003261.1	O43657	TSN6_HUMAN	tetraspanin 6	108			A -> T (in dbSNP:rs1802288). {ECO:0000269|PubMed:12761501}.		negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway (GO:0039532)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|ovary(1)	12						CCTACGATGGCAGCGACCAGT	0.378													C|||	201	0.053245	0.003	0.0562	3775	,	,		13734	0.0		0.1461	False		,,,				2504	0.0112				p.A108T		Atlas-SNP	.											.	TSPAN6	23	.	0			c.G322A						PASS	.	C	THR/ALA	126,3706		2,102,20,1528,548	83.0	60.0	68.0		322	4.0	1.0	X	dbSNP_89	68	1147,5573		63,699,322,1666,1542	yes	missense	TSPAN6	NM_003270.2	58	65,801,342,3194,2090	TT,TC,T,CC,C		17.0685,3.2881,12.0641	possibly-damaging	108/246	99890204	1273,9279	2200	4292	6492	SO:0001583	missense	7105	exon3			CGATGGCAGCGAC	AF043906	CCDS14470.1, CCDS76001.1	Xq22	2013-02-14	2005-03-21	2005-03-21	ENSG00000000003	ENSG00000000003		"""Tetraspanins"""	11858	protein-coding gene	gene with protein product		300191	"""transmembrane 4 superfamily member 6"""	TM4SF6		9782095	Standard	NM_003270		Approved	T245, TSPAN-6	uc004ega.1	O43657	OTTHUMG00000022002	ENST00000373020.4:c.322G>A	X.37:g.99890204C>T	ENSP00000362111:p.Ala108Thr	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	107	103	0.962617	NM_003270	Q54A42|Q6IAN9	Missense_Mutation	SNP	ENST00000373020.4	37	CCDS14470.1	137	0.08257986738999397	2	0.0040650406504065045	20	0.056179775280898875	0	0.0	81	0.11637931034482758	C	28.0	4.883948	0.91814	0.032881	0.170685	ENSG00000000003	ENST00000373020;ENST00000431386	T	0.81415	-1.49	4.93	4.03	0.46877	.	0.270215	0.41605	D	0.000842	T	0.01189	0.0039	M	0.62154	1.92	0.21256	P	0.999745475	D	0.59357	0.985	P	0.62298	0.9	T	0.31194	-0.9952	8	.	.	.	.	12.7618	0.57370	0.1637:0.8363:0.0:0.0	rs1802288;rs2234090;rs17323283;rs52820290;rs57629276;rs1802288	108	O43657	TSN6_HUMAN	T	108;90	ENSP00000362111:A108T	.	A	-	1	0	TSPAN6	99776860	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	5.520000	0.67080	2.298000	0.77334	0.523000	0.50628	GCC	0|0.015;T|0.099	0.099	strong		0.378	TSPAN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057483.1		
SPARCL1	8404	hgsc.bcm.edu	37	4	88412806	88412806	+	Missense_Mutation	SNP	T	T	C	rs1130643	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:88412806T>C	ENST00000282470.6	-	5	1725	c.1255A>G	c.(1255-1257)Acg>Gcg	p.T419A	SPARCL1_ENST00000418378.1_Missense_Mutation_p.T419A|SPARCL1_ENST00000503414.1_Missense_Mutation_p.T294A	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	419			T -> A (in dbSNP:rs1130643).		signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		TCACTTGACGTTTCCTCCTCA	0.393													T|||	1101	0.219848	0.5061	0.1311	5008	,	,		19417	0.1538		0.1243	False		,,,				2504	0.0624				p.T419A		Atlas-SNP	.											.	SPARCL1	59	.	0			c.A1255G						PASS	.	T	ALA/THR,ALA/THR	1998,2408	558.6+/-380.0	441,1116,646	298.0	237.0	258.0		1255,1255	-4.3	0.0	4	dbSNP_86	258	1118,7482	231.4+/-265.4	67,984,3249	yes	missense,missense	SPARCL1	NM_001128310.1,NM_004684.4	58,58	508,2100,3895	CC,CT,TT		13.0,45.3473,23.9582	benign,benign	419/665,419/665	88412806	3116,9890	2203	4300	6503	SO:0001583	missense	8404	exon5			TTGACGTTTCCTC	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1255A>G	4.37:g.88412806T>C	ENSP00000282470:p.Thr419Ala	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_004684	B4E2Z0|E7ESU2|Q14800	Missense_Mutation	SNP	ENST00000282470.6	37	CCDS3622.1	429	0.19642857142857142	211	0.42886178861788615	52	0.143646408839779	66	0.11538461538461539	100	0.13192612137203166	T	4.774	0.143962	0.09134	0.453473	0.13	ENSG00000152583	ENST00000282470;ENST00000418378;ENST00000438050;ENST00000503414	D;D;D	0.89343	-2.5;-2.5;-2.5	5.18	-4.28	0.03732	.	1.245570	0.04943	N	0.459008	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.19257	-1.0311	9	0.07644	T	0.81	3.0442	1.8177	0.03104	0.1153:0.2416:0.3399:0.3033	rs1130643;rs2219682;rs3189727;rs52819302;rs60236995;rs1130643	419	Q14515	SPRL1_HUMAN	A	419;419;294;294	ENSP00000282470:T419A;ENSP00000414856:T419A;ENSP00000422903:T294A	ENSP00000282470:T419A	T	-	1	0	SPARCL1	88631830	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.309000	0.08145	-0.779000	0.04560	-0.327000	0.08410	ACG	T|0.777;C|0.223	0.223	strong		0.393	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
AMICA1	120425	hgsc.bcm.edu	37	11	118074337	118074337	+	Missense_Mutation	SNP	A	A	G	rs1793174	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118074337A>G	ENST00000356289.5	-	6	751	c.578T>C	c.(577-579)gTg>gCg	p.V193A	AMICA1_ENST00000533261.1_Missense_Mutation_p.V182A|AMICA1_ENST00000292067.7_Missense_Mutation_p.V183A|AMICA1_ENST00000526620.1_Missense_Mutation_p.V154A	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	193	Ig-like V-type 2.		V -> A (in dbSNP:rs1793174). {ECO:0000269|PubMed:12869515, 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.V183A(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)		GGAGTACTCCACAGACATCCT	0.498													G|||	4019	0.802516	0.9251	0.7954	5008	,	,		20180	0.6736		0.7356	False		,,,				2504	0.8436				p.V193A		Atlas-SNP	.											AMICA1,NS,carcinoma,0,1	AMICA1	49	1	1	Substitution - Missense(1)	stomach(1)	c.T578C						PASS	.	G	ALA/VAL,ALA/VAL	3972,428	206.5+/-228.1	1795,382,23	101.0	100.0	100.0		578,548	-8.3	0.0	11	dbSNP_89	100	6517,2075	359.8+/-331.7	2474,1569,253	yes	missense,missense	AMICA1	NM_001098526.1,NM_153206.2	64,64	4269,1951,276	GG,GA,AA		24.1504,9.7273,19.2657	benign,benign	193/395,183/385	118074337	10489,2503	2200	4296	6496	SO:0001583	missense	120425	exon6			TACTCCACAGACA	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.578T>C	11.37:g.118074337A>G	ENSP00000348635:p.Val193Ala	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	243	61	0.251029	NM_001098526	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Missense_Mutation	SNP	ENST00000356289.5	37	CCDS41723.1	1696	0.7765567765567766	451	0.9166666666666666	283	0.7817679558011049	403	0.7045454545454546	559	0.737467018469657	G	0.014	-1.604930	0.00842	0.902727	0.758496	ENSG00000160593	ENST00000356289;ENST00000292067;ENST00000533261;ENST00000526620;ENST00000537867	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	4.16	-8.32	0.00996	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.939970	0.02665	N	0.107954	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;B;B;B	0.17667	0.0;0.016;0.016;0.023	B;B;B;B	0.19391	0.003;0.015;0.025;0.009	T	0.48570	-0.9024	9	0.05351	T	0.99	1.2069	1.4872	0.02449	0.2602:0.3525:0.1345:0.2528	rs1793174;rs17531584;rs52816574;rs57924556;rs1793174	154;193;182;183	E9PKK2;Q86YT9;E9PR26;Q86YT9-2	.;JAML1_HUMAN;.;.	A	193;183;182;154;154	ENSP00000348635:V193A;ENSP00000292067:V183A;ENSP00000436117:V182A;ENSP00000431218:V154A	ENSP00000292067:V183A	V	-	2	0	AMICA1	117579547	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.995000	0.01472	-5.640000	0.00011	-3.383000	0.00040	GTG	A|0.202;G|0.798	0.798	strong		0.498	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206	
COX6C	1345	hgsc.bcm.edu	37	8	100899793	100899793	+	Silent	SNP	G	G	A	rs1130569	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:100899793G>A	ENST00000520468.2	-	3	622	c.168C>T	c.(166-168)taC>taT	p.Y56Y	COX6C_ENST00000522940.1_Silent_p.Y56Y|COX6C_ENST00000518171.1_Silent_p.Y56Y|COX6C_ENST00000297564.2_Silent_p.Y56Y|COX6C_ENST00000517682.2_Silent_p.Y56Y|COX6C_ENST00000523016.1_Silent_p.Y56Y|COX6C_ENST00000520271.1_Silent_p.Y56Y|COX6C_ENST00000524245.1_Silent_p.Y56Y	NM_004374.3	NP_004365.1	P09669	COX6C_HUMAN	cytochrome c oxidase subunit VIc	56					cellular metabolic process (GO:0044237)|generation of precursor metabolites and energy (GO:0006091)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	cytochrome-c oxidase activity (GO:0004129)	p.Y56Y(1)	HMGA2/COX6C(2)	liver(1)|lung(2)	3			all cancers(13;8.32e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TCATGACATCGTAGTTTCTGT	0.343			T	HMGA2	uterine leiomyoma								A|||	1249	0.249401	0.5265	0.1758	5008	,	,		17900	0.13		0.1819	False		,,,				2504	0.1196				p.Y56Y	NSCLC(46;1123 1136 1705 23767 45086)	Atlas-SNP	.		Dom	yes		8	8q22-q23	1345	cytochrome c oxidase subunit VIc		M	COX6C_ENST00000520468,NS,carcinoma,0,1	COX6C	25	1	1	Substitution - coding silent(1)	stomach(1)	c.C168T						PASS	.	A		2157,2249	592.6+/-387.8	520,1117,566	59.0	60.0	60.0		168	4.4	1.0	8	dbSNP_86	60	1546,7050	744.5+/-407.2	123,1300,2875	no	coding-synonymous	COX6C	NM_004374.3		643,2417,3441	AA,AG,GG		17.9851,48.956,28.4802		56/76	100899793	3703,9299	2203	4298	6501	SO:0001819	synonymous_variant	1345	exon3			GACATCGTAGTTT	X13238	CCDS6284.1	8q22.2	2011-07-04			ENSG00000164919	ENSG00000164919	1.9.3.1	"""Mitochondrial respiratory chain complex / Complex IV"""	2285	protein-coding gene	gene with protein product		124090				10072584	Standard	NM_004374		Approved		uc003yiy.2	P09669	OTTHUMG00000164703	ENST00000520468.2:c.168C>T	8.37:g.100899793G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_004374	B2R4D7	Silent	SNP	ENST00000520468.2	37	CCDS6284.1																																																																																			G|0.733;A|0.267	0.267	strong		0.343	COX6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379834.3	NM_004374	
OR4A5	81318	hgsc.bcm.edu	37	11	51411918	51411918	+	Missense_Mutation	SNP	C	C	T	rs150995059	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:51411918C>T	ENST00000319760.6	-	1	530	c.478G>A	c.(478-480)Gtg>Atg	p.V160M		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	160						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(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				AGACTGTACACAACAATTTGA	0.448													.|||	15	0.00299521	0.0008	0.0014	5008	,	,		21527	0.0		0.0089	False		,,,				2504	0.0041				p.V160M		Atlas-SNP	.											.	OR4A5	116	.	0			c.G478A						PASS	.	C	MET/VAL	10,4392		0,10,2191	79.0	71.0	74.0		478	1.0	0.1	11	dbSNP_134	74	109,8483		1,107,4188	no	missense	OR4A5	NM_001005272.3	21	1,117,6379	TT,TC,CC		1.2686,0.2272,0.9158	benign	160/316	51411918	119,12875	2201	4296	6497	SO:0001583	missense	81318	exon1			TGTACACAACAAT	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.478G>A	11.37:g.51411918C>T	ENSP00000367664:p.Val160Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	148	72	0.486486	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	.	2.005	-0.428430	0.04701	0.002272	0.012686	ENSG00000221840	ENST00000319760	T	0.00130	8.69	1.93	0.984	0.19773	GPCR, rhodopsin-like superfamily (1);	0.547041	0.15102	N	0.280442	T	0.00073	0.0002	N	0.11673	0.155	0.09310	N	0.999999	B	0.33739	0.422	B	0.41666	0.363	T	0.03493	-1.1031	10	0.33141	T	0.24	.	4.1454	0.10214	0.0:0.6238:0.0:0.3762	.	160	Q8NH83	OR4A5_HUMAN	M	160	ENSP00000367664:V160M	ENSP00000367664:V160M	V	-	1	0	OR4A5	51268494	0.000000	0.05858	0.070000	0.20053	0.214000	0.24535	-0.808000	0.04515	0.371000	0.24564	0.162000	0.16502	GTG	C|0.993;T|0.007	0.007	strong		0.448	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
ZNF75D	7626	hgsc.bcm.edu	37	X	134421168	134421168	+	Silent	SNP	C	C	T	rs1129093	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:134421168C>T	ENST00000370766.3	-	7	4143	c.1434G>A	c.(1432-1434)acG>acA	p.T478T	ZNF75D_ENST00000494295.1_Intron|ZNF75D_ENST00000370764.1_Silent_p.T383T	NM_007131.3	NP_009062.2	P51815	ZN75D_HUMAN	zinc finger protein 75D	478					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)			autonomic_ganglia(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(14)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						ATAAGCTACACGTATAAGGCT	0.433													C|||	559	0.148079	0.0166	0.1772	3775	,	,		14789	0.0367		0.3201	False		,,,				2504	0.0562				p.T478T		Atlas-SNP	.											.	ZNF75D	65	.	0			c.G1434A						PASS	.	C	,	270,3565		10,209,41,1413,530	144.0	127.0	133.0		1149,1434	-6.5	0.0	X	dbSNP_86	133	2851,3877		445,1201,760,782,1112	no	coding-synonymous,coding-synonymous	ZNF75D	NM_001185063.1,NM_007131.3	,	455,1410,801,2195,1642	TT,TC,T,CC,C		42.3751,7.0404,29.5465	,	383/416,478/511	134421168	3121,7442	2203	4300	6503	SO:0001819	synonymous_variant	7626	exon6			GCTACACGTATAA	S43109	CCDS14648.1, CCDS55503.1	Xq26	2013-01-09	2008-06-11	2008-06-11	ENSG00000186376	ENSG00000186376		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13145	protein-coding gene	gene with protein product		314997	"""zinc finger protein 75 (D8C6)"""	ZNF82, ZNF75		1505955	Standard	XM_005262469		Approved	ZKSCAN24, D8C6, ZSCAN28	uc004eyo.3	P51815	OTTHUMG00000022482	ENST00000370766.3:c.1434G>A	X.37:g.134421168C>T		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_007131	A6NK62|B3KRI7|Q5JPG0|Q6LDE0	Silent	SNP	ENST00000370766.3	37	CCDS14648.1																																																																																			0|0.005;T|0.219	0.219	strong		0.433	ZNF75D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058415.1	NM_007131	
MOV10L1	54456	hgsc.bcm.edu	37	22	50572473	50572473	+	Missense_Mutation	SNP	G	G	A	rs2340601	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50572473G>A	ENST00000262794.5	+	14	2031	c.1948G>A	c.(1948-1950)Gtc>Atc	p.V650I	MOV10L1_ENST00000545383.1_Missense_Mutation_p.V650I|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000540615.1_Missense_Mutation_p.V630I|MOV10L1_ENST00000395858.3_Missense_Mutation_p.V650I	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	153	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	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	
MAP6	4135	hgsc.bcm.edu	37	11	75298468	75298468	+	Missense_Mutation	SNP	A	A	C	rs61895095	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:75298468A>C	ENST00000304771.3	-	4	2828	c.2078T>G	c.(2077-2079)gTt>gGt	p.V693G	MAP6_ENST00000526689.1_5'Flank|CTD-2530H12.4_ENST00000527803.1_RNA|MAP6_ENST00000526740.1_Missense_Mutation_p.V364G	NM_033063.1	NP_149052.1	Q96JE9	MAP6_HUMAN	microtubule-associated protein 6	693	Pro-rich.				dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|microtubule cytoskeleton organization (GO:0000226)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	19	Ovarian(111;0.11)					AGAATCGTGAACCTTTGCATG	0.478													A|||	163	0.0325479	0.0272	0.036	5008	,	,		23172	0.0278		0.0636	False		,,,				2504	0.0102				p.V693G	Esophageal Squamous(181;1115 2007 8647 17065 22697)	Atlas-SNP	.											.	MAP6	45	.	0			c.T2078G						PASS	.	A	GLY/VAL	110,4290	86.3+/-125.0	1,108,2091	178.0	173.0	175.0		2078	-8.9	0.0	11	dbSNP_129	175	409,8177	129.3+/-187.4	10,389,3894	yes	missense	MAP6	NM_033063.1	109	11,497,5985	CC,CA,AA		4.7636,2.5,3.9966	benign	693/814	75298468	519,12467	2200	4293	6493	SO:0001583	missense	4135	exon4			TCGTGAACCTTTG	AK123340	CCDS31641.1, CCDS44686.1	11q13.5	2005-10-11			ENSG00000171533	ENSG00000171533			6868	protein-coding gene	gene with protein product		601783				10516426, 12231625	Standard	NM_207577		Approved	KIAA1878, STOP, FLJ41346	uc001owu.3	Q96JE9	OTTHUMG00000165343	ENST00000304771.3:c.2078T>G	11.37:g.75298468A>C	ENSP00000307093:p.Val693Gly	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	174	87	0.5	NM_033063	A7E2A1|Q6P3T0|Q6ZWB8	Missense_Mutation	SNP	ENST00000304771.3	37	CCDS31641.1	90	0.04120879120879121	15	0.03048780487804878	13	0.03591160220994475	15	0.026223776223776224	47	0.06200527704485488	A	8.664	0.901288	0.17760	0.025	0.047636	ENSG00000171533	ENST00000304771;ENST00000526740;ENST00000545476	T	0.40476	1.03	4.79	-8.93	0.00771	.	0.894418	0.09480	N	0.796476	T	0.01222	0.0040	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13415	-1.0510	10	0.21540	T	0.41	1.4208	4.0634	0.09849	0.1076:0.4295:0.3:0.1628	rs61895095	693	Q96JE9	MAP6_HUMAN	G	693;364;364	ENSP00000307093:V693G	ENSP00000307093:V693G	V	-	2	0	MAP6	74976116	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-1.691000	0.01920	-1.340000	0.02227	0.533000	0.62120	GTT	A|0.960;C|0.040	0.040	strong		0.478	MAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383527.1	NM_033063	
C2orf74	339804	hgsc.bcm.edu	37	2	61389737	61389737	+	Missense_Mutation	SNP	T	T	G	rs1729674	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:61389737T>G	ENST00000432605.1	+	1	109	c.109T>G	c.(109-111)Tat>Gat	p.Y37D	C2orf74_ENST00000426997.1_Intron|RP11-493E12.1_ENST00000605902.1_lincRNA	NM_001143959.1	NP_001137431.1	A8MZ97	CB074_HUMAN	chromosome 2 open reading frame 74	37						integral component of membrane (GO:0016021)				endometrium(1)	1						GGTTTTTTTATATAAATGGTA	0.318													T|||	1972	0.39377	0.4455	0.389	5008	,	,		20712	0.3968		0.4533	False		,,,				2504	0.2628				p.Y37D		Atlas-SNP	.											.	C2orf74	22	.	0			c.T109G						PASS	.						218.0	173.0	187.0					2																	61389737		692	1591	2283	SO:0001583	missense	339804	exon1			TTTTTATATAAAT			2p15	2012-08-06			ENSG00000237651	ENSG00000237651			34439	protein-coding gene	gene with protein product							Standard	NM_001143959		Approved	LOC339804	uc010ypm.1	A8MZ97		ENST00000432605.1:c.109T>G	2.37:g.61389737T>G	ENSP00000402915:p.Tyr37Asp	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	167	95	0.568862	NM_001143959	C9JP62	Missense_Mutation	SNP	ENST00000432605.1	37		938	0.42948717948717946	210	0.4268292682926829	158	0.43646408839779005	223	0.38986013986013984	347	0.4577836411609499	T	12.42	1.933117	0.34096	.	.	ENSG00000237651	ENST00000432605	.	.	.	4.9	2.31	0.28768	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	1.0000000000287557E-6	D	0.54207	0.965	P	0.54312	0.748	T	0.45190	-0.9278	7	0.87932	D	0	.	1.6236	0.02719	0.1687:0.0969:0.1747:0.5597	rs1729674;rs52790424;rs56837693;rs1729674	37	A8MZ97	CB074_HUMAN	D	37	.	ENSP00000402915:Y37D	Y	+	1	0	C2orf74	61243241	0.829000	0.29322	0.939000	0.37840	0.582000	0.36321	1.552000	0.36244	0.831000	0.34780	0.254000	0.18369	TAT	T|0.583;G|0.417	0.417	strong		0.318	C2orf74-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001143959	
RXRG	6258	hgsc.bcm.edu	37	1	165389129	165389129	+	Silent	SNP	G	G	A	rs1128977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	186	115	0.61828	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	
SLC26A6	65010	hgsc.bcm.edu	37	3	48669447	48669447	+	Missense_Mutation	SNP	C	C	T	rs13324142	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48669447C>T	ENST00000395550.2	-	6	663	c.616G>A	c.(616-618)Gtg>Atg	p.V206M	SLC26A6_ENST00000482282.1_5'UTR|SLC26A6_ENST00000455886.2_Missense_Mutation_p.R171H|SLC26A6_ENST00000337000.8_Intron|SLC26A6_ENST00000358747.6_Missense_Mutation_p.V185M|SLC26A6_ENST00000420764.2_Missense_Mutation_p.V206M|SLC26A6_ENST00000383733.3_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	179	0	0		WXS	Illumina HiSeq	Phase_I	172	73	0.424419	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	
ZNF99	7652	hgsc.bcm.edu	37	19	22941591	22941591	+	Missense_Mutation	SNP	A	A	T	rs62119159	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22941591A>T	ENST00000596209.1	-	4	1210	c.1120T>A	c.(1120-1122)Tgc>Agc	p.C374S	ZNF99_ENST00000397104.3_Missense_Mutation_p.C283S	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	374					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.C283S(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GCTTTGCCGCATTCTTCATAT	0.363													A|||	448	0.0894569	0.0681	0.0879	5008	,	,		19708	0.0933		0.0934	False		,,,				2504	0.1115				p.C374S		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	1	1	Substitution - Missense(1)	stomach(1)	c.T1120A						PASS	.	A	SER/CYS	265,3805		9,247,1779	87.0	94.0	92.0		847	1.1	0.0	19	dbSNP_129	92	767,7637		39,689,3474	no	missense	ZNF99	NM_001080409.2	112	48,936,5253	TT,TA,AA		9.1266,6.5111,8.2732	probably-damaging	283/912	22941591	1032,11442	2035	4202	6237	SO:0001583	missense	7652	exon4			TGCCGCATTCTTC	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1120T>A	19.37:g.22941591A>T	ENSP00000472969:p.Cys374Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	30	0.357143	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	191	0.08745421245421245	35	0.07113821138211382	39	0.10773480662983426	52	0.09090909090909091	65	0.08575197889182058	N	9.311	1.055510	0.19907	0.065111	0.091266	ENSG00000213973	ENST00000397104	D	0.85861	-2.04	1.12	1.12	0.20585	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31167	0.0788	H	0.96996	3.92	0.33547	P	0.40431799999999996	D	0.89917	1.0	D	0.97110	1.0	T	0.72394	-0.4307	8	0.72032	D	0.01	.	5.689	0.17819	1.0:0.0:0.0:0.0	rs62119159	283	A8MXY4	ZNF99_HUMAN	S	283	ENSP00000380293:C283S	ENSP00000380293:C283S	C	-	1	0	ZNF99	22733431	0.899000	0.30636	0.032000	0.17829	0.031000	0.12232	4.564000	0.60830	0.465000	0.27167	0.325000	0.21440	TGC	A|0.911;T|0.089	0.089	strong		0.363	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
ACOX1	51	hgsc.bcm.edu	37	17	73949540	73949540	+	Missense_Mutation	SNP	G	G	C	rs1135640	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73949540G>C	ENST00000301608.4	-	7	996	c.936C>G	c.(934-936)atC>atG	p.I312M	ACOX1_ENST00000537812.1_Missense_Mutation_p.I274M|ACOX1_ENST00000293217.5_Missense_Mutation_p.I312M|ACOX1_ENST00000591857.1_5'Flank	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	312			I -> M (in dbSNP:rs1135640). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:8040306, ECO:0000269|PubMed:8117268}.		alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	ACCCTGGCTTGATTTCAGACT	0.507													G|||	2758	0.550719	0.1589	0.6729	5008	,	,		19337	0.7877		0.6402	False		,,,				2504	0.6575				p.I312M		Atlas-SNP	.											.	ACOX1	85	.	0			c.C936G						PASS	.	G	MET/ILE,MET/ILE,MET/ILE	1034,3372	380.4+/-323.7	122,790,1291	106.0	87.0	94.0		822,936,936	5.2	1.0	17	dbSNP_86	94	5582,3018	663.4+/-402.1	1825,1932,543	yes	missense,missense,missense	ACOX1	NM_001185039.1,NM_004035.6,NM_007292.5	10,10,10	1947,2722,1834	CC,CG,GG		35.093,23.468,49.1312	benign,benign,benign	274/623,312/661,312/661	73949540	6616,6390	2203	4300	6503	SO:0001583	missense	51	exon7			TGGCTTGATTTCA	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"""acyl-Coenzyme A oxidase 1, palmitoyl"""			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.936C>G	17.37:g.73949540G>C	ENSP00000301608:p.Ile312Met	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	222	97	0.436937	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	1251	0.5728021978021978	85	0.17276422764227642	229	0.6325966850828729	433	0.756993006993007	504	0.6649076517150396	G	13.17	2.156848	0.38119	0.23468	0.64907	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.70282	-0.47;-0.47;-0.47	6.17	5.2	0.72013	Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.200754	0.50627	D	0.000111	T	0.00012	0.0000	L	0.28458	0.855	0.23351	P	0.99785757	B;B;B;B	0.13145	0.003;0.0;0.0;0.007	B;B;B;B	0.09377	0.004;0.004;0.002;0.004	T	0.47086	-0.9144	9	0.35671	T	0.21	-22.5782	7.546	0.27768	0.0666:0.167:0.6551:0.1114	rs1135640;rs1137582;rs3198449;rs3201363;rs11550765;rs17420148;rs17583121;rs17850378;rs17850653;rs52804397;rs56586913;rs1137582	244;274;312;312	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	M	312;312;274;312;244	ENSP00000301608:I312M;ENSP00000293217:I312M;ENSP00000441257:I274M	ENSP00000293217:I312M	I	-	3	3	ACOX1	71461135	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.086000	0.30853	2.941000	0.99782	0.655000	0.94253	ATC	G|0.477;C|0.523	0.523	strong		0.507	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1		
SLC26A7	115111	hgsc.bcm.edu	37	8	92364100	92364100	+	Silent	SNP	T	T	C	rs10109254	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:92364100T>C	ENST00000276609.3	+	10	1442	c.1203T>C	c.(1201-1203)ctT>ctC	p.L401L	SLC26A7_ENST00000309536.2_Silent_p.L401L|SLC26A7_ENST00000520249.1_3'UTR|SLC26A7_ENST00000523719.1_Silent_p.L401L	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			GACCTTTGCTTTACTGGCTGC	0.343													T|||	1107	0.221046	0.32	0.2233	5008	,	,		18150	0.0357		0.2823	False		,,,				2504	0.2137				p.L401L		Atlas-SNP	.											.	SLC26A7	207	.	0			c.T1203C						PASS	.	T	,	1372,3034	452.8+/-350.1	220,932,1051	204.0	186.0	192.0		1203,1203	2.0	1.0	8	dbSNP_119	192	2541,6059	413.3+/-351.1	372,1797,2131	no	coding-synonymous,coding-synonymous	SLC26A7	NM_052832.2,NM_134266.1	,	592,2729,3182	CC,CT,TT		29.5465,31.1394,30.0861	,	401/657,401/664	92364100	3913,9093	2203	4300	6503	SO:0001819	synonymous_variant	115111	exon10			TTTGCTTTACTGG	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"""Solute carriers"""	14467	protein-coding gene	gene with protein product		608479	"""solute carrier family 26, member 7"""			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.1203T>C	8.37:g.92364100T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	162	51	0.314815	NM_134266		Silent	SNP	ENST00000276609.3	37	CCDS6254.1																																																																																			T|0.739;C|0.261	0.261	strong		0.343	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1		
ZNF492	57615	hgsc.bcm.edu	37	19	22846623	22846623	+	Missense_Mutation	SNP	G	G	A	rs71355986	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22846623G>A	ENST00000456783.2	+	4	396	c.152G>A	c.(151-153)cGa>cAa	p.R51Q	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	51					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.R51Q(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				TATTTTGCCCGAGACCTTTGG	0.284													N|||	1067	0.213059	0.4054	0.134	5008	,	,		14205	0.1736		0.1362	False		,,,				2504	0.1288				p.R51Q		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,0,1	ZNF492	129	1	1	Substitution - Missense(1)	stomach(1)	c.G152A						scavenged	.						18.0	20.0	20.0					19																	22846623		1801	4095	5896	SO:0001583	missense	57615	exon4			TTGCCCGAGACCT	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.152G>A	19.37:g.22846623G>A	ENSP00000413660:p.Arg51Gln	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	55	10	0.181818	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	409	0.18727106227106227	166	0.33739837398373984	54	0.14917127071823205	99	0.17307692307692307	90	0.11873350923482849	.	0.007	-1.940811	0.00479	.	.	ENSG00000229676	ENST00000456783	T	0.06687	3.27	1.12	-0.367	0.12541	.	.	.	.	.	T	0.00012	0.0000	N	0.00014	-2.9	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36986	-0.9725	8	0.02654	T	1	.	4.7284	0.12952	0.4846:0.0:0.5154:0.0	.	51	Q9P255	ZN492_HUMAN	Q	51	ENSP00000413660:R51Q	ENSP00000413660:R51Q	R	+	2	0	ZNF492	22638463	0.000000	0.05858	0.053000	0.19242	0.052000	0.14988	-0.921000	0.04008	-0.964000	0.03595	-0.974000	0.02594	CGA	G|0.827;A|0.173	0.173	strong		0.284	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
KIAA1522	57648	hgsc.bcm.edu	37	1	33235651	33235651	+	Missense_Mutation	SNP	A	A	G	rs12730560	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:33235651A>G	ENST00000373480.1	+	6	797	c.694A>G	c.(694-696)Atg>Gtg	p.M232V	KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000373481.3_Missense_Mutation_p.M243V|KIAA1522_ENST00000401073.2_Missense_Mutation_p.M291V	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	232			M -> V (in dbSNP:rs12730560).							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)				GACAGAGGCCATGCTGCAGCG	0.701													A|||	732	0.146166	0.2738	0.2291	5008	,	,		14565	0.002		0.1342	False		,,,				2504	0.0757				p.M291V		Atlas-SNP	.											KIAA1522,colon,carcinoma,0,1	KIAA1522	68	1	0			c.A871G						PASS	.	A	,VAL/MET,VAL/MET	954,3190		115,724,1233	24.0	30.0	28.0		,871,694	-3.4	0.9	1	dbSNP_121	28	1100,7316		70,960,3178	yes	intron,missense,missense	KIAA1522	NM_001198973.1,NM_020888.2,NM_001198972.1	,21,21	185,1684,4411	GG,GA,AA		13.0703,23.0212,16.3535	,benign,benign	,291/1095,232/1036	33235651	2054,10506	2072	4208	6280	SO:0001583	missense	57648	exon6			GAGGCCATGCTGC	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.694A>G	1.37:g.33235651A>G	ENSP00000362579:p.Met232Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	70	14	0.2	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	318	0.14560439560439561	135	0.27439024390243905	75	0.20718232044198895	0	0.0	108	0.1424802110817942	A	8.480	0.859501	0.17178	0.230212	0.130703	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.27557	1.66;1.66;1.66	4.47	-3.42	0.04825	.	1.518330	0.03681	N	0.245441	T	0.00012	0.0000	N	0.22421	0.69	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	0.24440	-1.0160	9	0.02654	T	1	-0.0856	6.5649	0.22507	0.3748:0.144:0.4812:0.0	rs12730560;rs61225963;rs12730560	243;232;291	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	V	291;243;232	ENSP00000383851:M291V;ENSP00000362580:M243V;ENSP00000362579:M232V	ENSP00000362579:M232V	M	+	1	0	KIAA1522	33008238	0.010000	0.17322	0.905000	0.35620	0.935000	0.57460	-0.197000	0.09518	-0.456000	0.07043	0.402000	0.26972	ATG	A|0.838;G|0.162	0.162	strong		0.701	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1		
VPS39	23339	hgsc.bcm.edu	37	15	42459034	42459034	+	Silent	SNP	T	T	C	rs1619030	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42459034T>C	ENST00000348544.4	-	15	1487	c.1488A>G	c.(1486-1488)ctA>ctG	p.L496L	VPS39_ENST00000318006.5_Silent_p.L485L			Q96JC1	VPS39_HUMAN	vacuolar protein sorting 39 homolog (S. cerevisiae)	496					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	small GTPase regulator activity (GO:0005083)			breast(2)|kidney(5)|large_intestine(4)|lung(8)|ovary(1)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_cancers(109;6.78e-16)|all_epithelial(112;1.81e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;3.05e-06)		GAGCCTTCTTTAGCACGTGCT	0.547													C|||	1995	0.398363	0.739	0.4942	5008	,	,		20631	0.1815		0.1332	False		,,,				2504	0.3661				p.L485L		Atlas-SNP	.											.	VPS39	53	.	0			c.A1455G						PASS	.	C		2756,1650	505.1+/-366.0	893,970,340	145.0	128.0	134.0		1455	4.9	1.0	15	dbSNP_89	134	1201,7397	762.9+/-407.6	97,1007,3195	no	coding-synonymous	VPS39	NM_015289.2		990,1977,3535	CC,CT,TT		13.9684,37.4489,30.4291		485/876	42459034	3957,9047	2203	4299	6502	SO:0001819	synonymous_variant	23339	exon14			CTTCTTTAGCACG	AF280814	CCDS10083.1, CCDS73710.1	15q14	2008-02-05	2006-12-19		ENSG00000166887	ENSG00000166887			20593	protein-coding gene	gene with protein product		612188	"""vacuolar protein sorting 39 (yeast)"""			11448994	Standard	XM_005254259		Approved	KIAA0770, VAM6	uc001zpc.3	Q96JC1	OTTHUMG00000130467	ENST00000348544.4:c.1488A>G	15.37:g.42459034T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	79	21	0.265823	NM_015289	O94869|Q71SQ6|Q7Z3V3|Q96B93|Q96RM0	Silent	SNP	ENST00000348544.4	37	CCDS10083.1																																																																																			T|0.694;C|0.306	0.306	strong		0.547	VPS39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000420472.1	NM_015289	
DDX60L	91351	hgsc.bcm.edu	37	4	169348435	169348435	+	Silent	SNP	T	T	C	rs2712120	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:169348435T>C	ENST00000511577.1	-	14	1963	c.1716A>G	c.(1714-1716)aaA>aaG	p.K572K	DDX60L_ENST00000505890.1_Silent_p.K572K|DDX60L_ENST00000260184.7_Silent_p.K572K			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	572							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)	p.K572K(1)		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)		GAAATGACTTTTTCTTACTCT	0.328													T|||	1035	0.206669	0.5401	0.1441	5008	,	,		19157	0.006		0.1272	False		,,,				2504	0.089				p.K572K		Atlas-SNP	.											DDX60L,NS,carcinoma,0,1	DDX60L	116	1	1	Substitution - coding silent(1)	stomach(1)	c.A1716G						PASS	.	T		1644,1996		393,858,569	121.0	103.0	109.0		1716	-6.5	0.0	4	dbSNP_100	109	1050,7118		81,888,3115	no	coding-synonymous	DDX60L	NM_001012967.1		474,1746,3684	CC,CT,TT		12.855,45.1648,22.815		572/1707	169348435	2694,9114	1820	4084	5904	SO:0001819	synonymous_variant	91351	exon14			TGACTTTTTCTTA	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.1716A>G	4.37:g.169348435T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	131	97	0.740458	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				T|0.783;C|0.217	0.217	strong		0.328	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
EP400	57634	hgsc.bcm.edu	37	12	132547096	132547096	+	Silent	SNP	G	G	A	rs74479394|rs113304321	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:132547096G>A	ENST00000333577.4	+	48	8401	c.8292G>A	c.(8290-8292)caG>caA	p.Q2764Q	EP400_ENST00000389562.2_Silent_p.Q2727Q|EP400_ENST00000332482.4_Silent_p.Q2691Q|EP400_ENST00000330386.6_Silent_p.Q2647Q|EP400_ENST00000389561.2_Silent_p.Q2728Q			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)			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)		agcaacaacagcagcagcagc	0.567													G|||	734	0.146565	0.3215	0.0432	5008	,	,		15582	0.1111		0.0417	False		,,,				2504	0.1278				p.Q2728Q		Atlas-SNP	.											EP400,colon,carcinoma,0,3	EP400	370	3	0			c.G8184A						scavenged	.	G		0,4324		0,0,2162	24.0	29.0	27.0		8184	0.5	0.9	12	dbSNP_131	27	1,8349		0,1,4174	no	coding-synonymous	EP400	NM_015409.4		0,1,6336	AA,AG,GG		0.012,0.0,0.0079		2728/3124	132547096	1,12673	2162	4175	6337	SO:0001819	synonymous_variant	57634	exon47			ACAACAGCAGCAG	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.8292G>A	12.37:g.132547096G>A		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	143	4	0.027972	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				.	.	weak		0.567	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
HIP1	3092	hgsc.bcm.edu	37	7	75171262	75171262	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:75171262G>A	ENST00000336926.6	-	29	2954	c.2928C>T	c.(2926-2928)atC>atT	p.I976I	HIP1_ENST00000434438.2_Silent_p.I925I	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	976	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CTTGGCGTTTGATCTGTGTCA	0.463			T	PDGFRB	CMML																																p.I976I		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	HIP1,NS,carcinoma,-2,1	HIP1	91	1	0			c.C2928T						PASS	.						180.0	162.0	168.0					7																	75171262		2203	4300	6503	SO:0001819	synonymous_variant	3092	exon29			GCGTTTGATCTGT	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.2928C>T	7.37:g.75171262G>A		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	317	72	0.227129	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			.	.	none		0.463	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
FAM171A1	221061	hgsc.bcm.edu	37	10	15256368	15256368	+	Missense_Mutation	SNP	C	C	T	rs143772901	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:15256368C>T	ENST00000378116.4	-	8	1225	c.1219G>A	c.(1219-1221)Gaa>Aaa	p.E407K	FAM171A1_ENST00000477161.1_5'UTR	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	407						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(6)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	52						AGGTCCCCTTCGCCGCCCGGA	0.622													C|||	2	0.000399361	0.0	0.0	5008	,	,		16253	0.0		0.0	False		,,,				2504	0.002				p.E407K		Atlas-SNP	.											.	FAM171A1	252	.	0			c.G1219A						PASS	.	C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	58.0	62.0	61.0		1219	5.1	0.1	10	dbSNP_134	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FAM171A1	NM_001010924.1	56	0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461	probably-damaging	407/891	15256368	6,13000	2203	4300	6503	SO:0001583	missense	221061	exon8			CCCCTTCGCCGCC	AK022946	CCDS31154.1	10p13	2008-06-16	2008-06-16	2008-06-16	ENSG00000148468	ENSG00000148468			23522	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 38"""	C10orf38			Standard	NM_001010924		Approved	FLJ12884	uc001iob.3	Q5VUB5	OTTHUMG00000017732	ENST00000378116.4:c.1219G>A	10.37:g.15256368C>T	ENSP00000367356:p.Glu407Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.213121	0.58452	2.27E-4	5.81E-4	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.35421	1.31	5.14	5.14	0.70334	.	0.101232	0.64402	D	0.000003	T	0.51092	0.1654	M	0.72894	2.215	0.80722	D	1	D	0.54397	0.966	P	0.51101	0.659	T	0.51965	-0.8638	10	0.45353	T	0.12	-22.4632	18.8133	0.92068	0.0:1.0:0.0:0.0	.	407	Q5VUB5	F1711_HUMAN	K	407;408	ENSP00000367356:E407K	ENSP00000367356:E407K	E	-	1	0	FAM171A1	15296374	1.000000	0.71417	0.106000	0.21319	0.055000	0.15305	7.103000	0.77014	2.667000	0.90743	0.563000	0.77884	GAA	C|1.000;T|0.000	0.000	weak		0.622	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709	
MUC17	140453	hgsc.bcm.edu	37	7	100677625	100677625	+	Silent	SNP	G	G	A	rs115078078	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677625G>A	ENST00000306151.4	+	3	2992	c.2928G>A	c.(2926-2928)tcG>tcA	p.S976S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	976	59 X approximate tandem repeats.|Ser-rich.				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)					TACCAACCTCGACTCCTAGTG	0.507																																					p.S976S		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.G2928A						scavenged	.	A		154,4252	793.6+/-415.2	0,154,2049	352.0	328.0	336.0		2928	-1.5	0.0	7	dbSNP_133	336	106,8494	808.3+/-407.2	0,106,4194	no	coding-synonymous	MUC17	NM_001040105.1		0,260,6243	AA,AG,GG		1.2326,3.4952,1.9991		976/4494	100677625	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACCTCGACTCCT	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.2928G>A	7.37:g.100677625G>A		Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	625	151	0.2416	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.964;A|0.036	0.036	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ATXN1	6310	hgsc.bcm.edu	37	6	16327906	16327906	+	Missense_Mutation	SNP	C	C	A	rs376233432		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	83	19	0.228916	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	
IGFALS	3483	hgsc.bcm.edu	37	16	1838703	1838703	+	IGR	SNP	G	G	A	rs11540961	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1838703G>A	ENST00000215539.3	-	0	2116				NUBP2_ENST00000262302.9_Silent_p.A268A|NUBP2_ENST00000568706.1_Silent_p.A127A|NUBP2_ENST00000565987.1_Silent_p.A208A|NUBP2_ENST00000543305.1_Silent_p.A127A			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit						cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						CGACGCCCGCGTGCCTCCCCT	0.657													G|||	144	0.028754	0.0061	0.0591	5008	,	,		15636	0.002		0.0716	False		,,,				2504	0.0215				p.A268A		Atlas-SNP	.											NUBP2,NS,carcinoma,+2,2	NUBP2	25	2	0			c.G804A						PASS	.	G		87,4307	69.8+/-107.6	2,83,2112	26.0	26.0	26.0		804	-9.9	0.0	16	dbSNP_120	26	624,7968	158.0+/-211.6	20,584,3692	no	coding-synonymous	NUBP2	NM_012225.2		22,667,5804	AA,AG,GG		7.2626,1.98,5.4751		268/272	1838703	711,12275	2197	4296	6493	SO:0001628	intergenic_variant	10101	exon7			GCCCGCGTGCCTC	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638		16.37:g.1838703G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_012225	B4DZY8|E9PGU3	Silent	SNP	ENST00000215539.3	37	CCDS10446.1																																																																																			G|0.949;A|0.051	0.051	strong		0.657	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
TRIM4	89122	hgsc.bcm.edu	37	7	99490190	99490190	+	Missense_Mutation	SNP	G	G	A	rs35432946	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99490190G>A	ENST00000355947.2	-	7	1228	c.1099C>T	c.(1099-1101)Ccc>Tcc	p.P367S	TRIM4_ENST00000349062.2_Missense_Mutation_p.P341S	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	367	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		P -> S (in dbSNP:rs35432946).		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)				AGAACACAGGGTAAGTGCTGA	0.468													G|||	242	0.0483227	0.0711	0.0418	5008	,	,		21802	0.002		0.0577	False		,,,				2504	0.0603				p.P367S		Atlas-SNP	.											.	TRIM4	33	.	0			c.C1099T						PASS	.	G	SER/PRO,SER/PRO	300,4106	162.5+/-194.5	16,268,1919	108.0	103.0	105.0		1099,1021	2.4	1.0	7	dbSNP_126	105	618,7982	161.0+/-214.0	18,582,3700	yes	missense,missense	TRIM4	NM_033017.3,NM_033091.2	74,74	34,850,5619	AA,AG,GG		7.186,6.8089,7.0583	probably-damaging,probably-damaging	367/501,341/475	99490190	918,12088	2203	4300	6503	SO:0001583	missense	89122	exon7			CACAGGGTAAGTG	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.1099C>T	7.37:g.99490190G>A	ENSP00000348216:p.Pro367Ser	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	186	59	0.317204	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Missense_Mutation	SNP	ENST00000355947.2	37	CCDS5679.1	91	0.041666666666666664	30	0.06097560975609756	14	0.03867403314917127	2	0.0034965034965034965	45	0.059366754617414245	G	15.87	2.959568	0.53400	0.068089	0.07186	ENSG00000146833	ENST00000355947;ENST00000349062;ENST00000542799	T;T	0.62232	0.04;0.04	2.42	2.42	0.29668	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.17152	0.0412	M	0.62723	1.935	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.68943	0.961;0.915	T	0.49818	-0.8899	9	0.48119	T	0.1	.	7.2255	0.26012	0.0:0.2787:0.7213:0.0	rs35432946	341;367	Q9C037-2;Q9C037	.;TRIM4_HUMAN	S	367;341;197	ENSP00000348216:P367S;ENSP00000275736:P341S	ENSP00000275736:P341S	P	-	1	0	TRIM4	99328126	0.001000	0.12720	0.986000	0.45419	0.844000	0.47949	0.272000	0.18644	1.689000	0.51079	0.655000	0.94253	CCC	G|0.942;A|0.058	0.058	strong		0.468	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017	
APOB	338	hgsc.bcm.edu	37	2	21232804	21232804	+	Silent	SNP	G	G	A	rs386643884|rs1041968	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	156	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	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		
MUC17	140453	hgsc.bcm.edu	37	7	100680017	100680017	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680017A>G	ENST00000306151.4	+	3	5384	c.5320A>G	c.(5320-5322)Att>Gtt	p.I1774V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1774	59 X approximate tandem repeats.|Ser-rich.				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)					AGCAACTCCTATTGACACCAG	0.493																																					p.I1774V		Atlas-SNP	.											MUC17,right_lower_lobe,carcinoma,-1,1	MUC17	804	1	0			c.A5320G						scavenged	.						279.0	291.0	287.0					7																	100680017		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTCCTATTGACA	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.5320A>G	7.37:g.100680017A>G	ENSP00000302716:p.Ile1774Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	205	11	0.0536585	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	0.003	-2.528736	0.00147	.	.	ENSG00000169876	ENST00000306151	T	0.01933	4.55	0.932	-1.86	0.07760	.	.	.	.	.	T	0.01124	0.0037	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42982	-0.9419	9	0.11794	T	0.64	.	4.2197	0.10552	0.2353:0.4114:0.3533:0.0	.	1774	Q685J3	MUC17_HUMAN	V	1774	ENSP00000302716:I1774V	ENSP00000302716:I1774V	I	+	1	0	MUC17	100466737	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.563000	0.00430	-4.292000	0.00058	-3.891000	0.00017	ATT	.	.	none		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FRMPD1	22844	hgsc.bcm.edu	37	9	37733752	37733752	+	Missense_Mutation	SNP	G	G	A	rs140800271	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:37733752G>A	ENST00000539465.1	+	12	1741	c.1148G>A	c.(1147-1149)cGt>cAt	p.R383H	FRMPD1_ENST00000377765.3_Missense_Mutation_p.R383H|RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000536622.1_Missense_Mutation_p.R205H|FRMPD1_ENST00000541302.1_Missense_Mutation_p.R252H			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	383	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		GCCCAGCTACGTTTAAATTAT	0.343													G|||	16	0.00319489	0.0015	0.0101	5008	,	,		20643	0.0		0.007	False		,,,				2504	0.0				p.R383H		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G1148A						PASS	.	G	HIS/ARG	4,4402	8.1+/-20.4	0,4,2199	143.0	146.0	145.0		1148	5.2	1.0	9	dbSNP_134	145	29,8571	21.0+/-64.5	0,29,4271	yes	missense	FRMPD1	NM_014907.2	29	0,33,6470	AA,AG,GG		0.3372,0.0908,0.2537	probably-damaging	383/1579	37733752	33,12973	2203	4300	6503	SO:0001583	missense	22844	exon12			AGCTACGTTTAAA	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.1148G>A	9.37:g.37733752G>A	ENSP00000444411:p.Arg383His	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	11	0.005036630036630037	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	5	0.006596306068601583	G	25.5	4.643088	0.87859	9.08E-4	0.003372	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.16	5.16	0.70880	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);	0.000000	0.85682	D	0.000000	T	0.81049	0.4742	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.64687	0.923;0.928	D	0.84554	0.0646	10	0.66056	D	0.02	-11.2075	16.1394	0.81513	0.0:0.0:1.0:0.0	.	252;383	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	H	383;383;205;252	ENSP00000366995:R383H;ENSP00000444411:R383H;ENSP00000437762:R205H;ENSP00000444804:R252H	ENSP00000366995:R383H	R	+	2	0	FRMPD1	37723752	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.626000	0.83164	2.400000	0.81607	0.609000	0.83330	CGT	G|0.997;A|0.003	0.003	strong		0.343	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
TIAM1	7074	hgsc.bcm.edu	37	21	32638549	32638549	+	Missense_Mutation	SNP	C	C	A	rs386817934|rs2070417	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:32638549C>A	ENST00000286827.3	-	5	1211	c.740G>T	c.(739-741)gGg>gTg	p.G247V	TIAM1_ENST00000541036.1_Missense_Mutation_p.G247V|TIAM1_ENST00000469412.1_Intron	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	247			G -> R (in dbSNP:rs2070418).|G -> V (in dbSNP:rs2070417).	G -> M (in Ref. 1; AAA98443). {ECO:0000305}.	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						CCCCGGCCCCCCGTTTGCTGT	0.532													C|||	1069	0.213458	0.0159	0.2594	5008	,	,		16243	0.4107		0.1133	False		,,,				2504	0.3476				p.G247V		Atlas-SNP	.											.	TIAM1	522	.	0			c.G740T						PASS	.	C	VAL/GLY	145,4261	86.3+/-125.0	6,133,2064	69.0	73.0	72.0		740	4.4	1.0	21	dbSNP_96	72	711,7889	137.1+/-194.1	38,635,3627	yes	missense	TIAM1	NM_003253.2	109	44,768,5691	AA,AC,CC		8.2674,3.291,6.5816	probably-damaging	247/1592	32638549	856,12150	2203	4300	6503	SO:0001583	missense	7074	exon5			GGCCCCCCGTTTG		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.740G>T	21.37:g.32638549C>A	ENSP00000286827:p.Gly247Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	49	0.401639	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	353	0.16163003663003664	7	0.014227642276422764	80	0.22099447513812154	196	0.34265734265734266	70	0.09234828496042216	C	16.56	3.156271	0.57259	0.03291	0.082674	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.41065	1.03;1.01	5.4	4.45	0.53987	.	0.367039	0.30869	N	0.008718	T	0.00012	0.0000	L	0.36672	1.1	0.09310	P	0.999999663474	B;B;B	0.30281	0.275;0.18;0.18	B;B;B	0.30646	0.118;0.055;0.055	T	0.33803	-0.9854	9	0.52906	T	0.07	.	14.725	0.69339	0.0:0.9206:0.0:0.0794	rs2070417;rs59059207;rs2070417	247;247;247	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	V	247;88;247	ENSP00000286827:G247V;ENSP00000441570:G247V	ENSP00000286827:G247V	G	-	2	0	TIAM1	31560420	0.938000	0.31826	1.000000	0.80357	0.994000	0.84299	4.159000	0.58157	2.803000	0.96430	0.585000	0.79938	GGG	C|0.874;A|0.119	0.119	strong		0.532	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
ARID4B	51742	hgsc.bcm.edu	37	1	235383742	235383742	+	Missense_Mutation	SNP	C	C	G	rs148132837		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:235383742C>G	ENST00000264183.3	-	15	1779	c.1282G>C	c.(1282-1284)Gtt>Ctt	p.V428L	ARID4B_ENST00000349213.3_Missense_Mutation_p.V428L|ARID4B_ENST00000366603.2_Missense_Mutation_p.V428L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	428	Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TCCTCCTTAACTTTTATTTCT	0.348													C|||	1	0.000199681	0.0	0.0	5008	,	,		14311	0.0		0.001	False		,,,				2504	0.0				p.V428L		Atlas-SNP	.											.	ARID4B	142	.	0			c.G1282C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	0,4406		0,0,2203	128.0	118.0	121.0		1282,1282,1282	-0.5	1.0	1	dbSNP_134	121	9,8585	7.1+/-27.0	0,9,4288	yes	missense,missense,missense	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	32,32,32	0,9,6491	GG,GC,CC		0.1047,0.0,0.0692	benign,benign,benign	428/1313,428/1313,428/1227	235383742	9,12991	2203	4297	6500	SO:0001583	missense	51742	exon15			CCTTAACTTTTAT	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1282G>C	1.37:g.235383742C>G	ENSP00000264183:p.Val428Leu	Somatic	405	0	0		WXS	Illumina HiSeq	Phase_I	487	158	0.324435	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Missense_Mutation	SNP	ENST00000264183.3	37	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	C	5.309	0.242397	0.10077	0.0	0.001047	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183;ENST00000439834;ENST00000418304	T;T;T;T	0.22945	1.95;1.93;1.93;1.97	5.29	-0.47	0.12131	.	0.806611	0.11942	N	0.514583	T	0.13586	0.0329	N	0.19112	0.55	0.25879	N	0.983618	B;B;B;B	0.12013	0.005;0.005;0.005;0.003	B;B;B;B	0.15052	0.007;0.012;0.007;0.003	T	0.36986	-0.9725	10	0.09084	T	0.74	-3.7761	10.6262	0.45508	0.0:0.4311:0.0:0.5689	.	109;428;428;428	Q4LE39-4;Q4LE39-3;Q4LE39-2;Q4LE39	.;.;.;ARI4B_HUMAN	L	428	ENSP00000264184:V428L;ENSP00000355562:V428L;ENSP00000264183:V428L;ENSP00000391497:V428L	ENSP00000264183:V428L	V	-	1	0	ARID4B	233450365	0.953000	0.32496	0.997000	0.53966	0.690000	0.40134	-0.041000	0.12084	-0.034000	0.13713	0.609000	0.83330	GTT	C|0.999;G|0.001	0.001	strong		0.348	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
ELMOD1	55531	hgsc.bcm.edu	37	11	107535758	107535758	+	Silent	SNP	G	G	A	rs647756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:107535758G>A	ENST00000265840.7	+	12	1105	c.840G>A	c.(838-840)ttG>ttA	p.L280L	ELMOD1_ENST00000531234.1_Silent_p.L274L|ELMOD1_ENST00000443271.2_Silent_p.L272L	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	280	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)			endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		CAGGCTATTTGATGCATGAAT	0.378													G|||	1440	0.28754	0.6445	0.17	5008	,	,		18636	0.3234		0.0437	False		,,,				2504	0.1022				p.L280L		Atlas-SNP	.											.	ELMOD1	40	.	0			c.G840A						PASS	.	G	,	2085,1625		577,931,347	116.0	122.0	121.0		816,840	6.0	1.0	11	dbSNP_83	121	476,7728		17,442,3643	no	coding-synonymous,coding-synonymous	ELMOD1	NM_001130037.1,NM_018712.3	,	594,1373,3990	AA,AG,GG		5.802,43.8005,21.4957	,	272/327,280/335	107535758	2561,9353	1855	4102	5957	SO:0001819	synonymous_variant	55531	exon12			CTATTTGATGCAT	AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"""ELMO domain containing 1"""			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.840G>A	11.37:g.107535758G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	134	41	0.30597	NM_018712	B4E167|G5E9S5|Q9NPW3	Silent	SNP	ENST00000265840.7	37	CCDS44723.1																																																																																			G|0.697;A|0.303	0.303	strong		0.378	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712	
ACTRT2	140625	hgsc.bcm.edu	37	1	2938989	2938989	+	Missense_Mutation	SNP	G	G	A	rs3795263	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:2938989G>A	ENST00000378404.2	+	1	944	c.739G>A	c.(739-741)Ggg>Agg	p.G247R		NM_080431.4	NP_536356.3	Q8TDY3	ACTT2_HUMAN	actin-related protein T2	247			G -> R (in dbSNP:rs3795263).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_cancers(77;0.00205)|all_epithelial(69;0.0011)|Ovarian(185;0.0634)|Lung NSC(156;0.0893)|all_lung(157;0.0909)	all_epithelial(116;2.66e-20)|all_lung(118;1.56e-08)|Lung NSC(185;2.54e-06)|Breast(487;0.00156)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;7.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.15e-22)|GBM - Glioblastoma multiforme(42;1.1e-12)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000329)|BRCA - Breast invasive adenocarcinoma(365;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.125)		GCTGCCCGACGGGAACATCAT	0.652													G|||	611	0.122005	0.0106	0.121	5008	,	,		16197	0.1607		0.2584	False		,,,				2504	0.093				p.G247R		Atlas-SNP	.											.	ACTRT2	69	.	0			c.G739A						PASS	.	G	ARG/GLY	218,4188		11,196,1996	36.0	41.0	40.0		739	4.8	0.9	1	dbSNP_107	40	2009,6589		245,1519,2535	yes	missense	ACTRT2	NM_080431.4	125	256,1715,4531	AA,AG,GG		23.3659,4.9478,17.1255	probably-damaging	247/378	2938989	2227,10777	2203	4299	6502	SO:0001583	missense	140625	exon1			CCCGACGGGAACA	AF440740, AB057364	CCDS45.1	1p36.3	2008-02-05	2005-11-22		ENSG00000169717	ENSG00000169717			24026	protein-coding gene	gene with protein product		608535				11750065, 12243744	Standard	NM_080431		Approved	Arp-T2, ARPM2, FLJ25424	uc001ajz.3	Q8TDY3	OTTHUMG00000000562	ENST00000378404.2:c.739G>A	1.37:g.2938989G>A	ENSP00000367658:p.Gly247Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	47	35	0.744681	NM_080431	B1AN52|Q8NHS6|Q8TDG1	Missense_Mutation	SNP	ENST00000378404.2	37	CCDS45.1	348	0.15934065934065933	4	0.008130081300813009	57	0.1574585635359116	96	0.16783216783216784	191	0.2519788918205805	G	16.11	3.029664	0.54790	0.049478	0.233659	ENSG00000169717	ENST00000378404;ENST00000543312	D	0.97089	-4.24	4.85	4.85	0.62838	.	0.000000	0.56097	D	0.000026	T	0.01254	0.0041	M	0.94142	3.5	0.09310	P	0.99999892596	D	0.89917	1.0	D	0.83275	0.996	T	0.00000	-1.6286	9	0.87932	D	0	.	11.1701	0.48567	0.0907:0.0:0.9093:0.0	rs3795263;rs17390011;rs60765657;rs3795263	247	Q8TDY3	ACTT2_HUMAN	R	247	ENSP00000367658:G247R	ENSP00000367658:G247R	G	+	1	0	ACTRT2	2928849	1.000000	0.71417	0.915000	0.36163	0.341000	0.28922	6.582000	0.74049	2.228000	0.72767	0.561000	0.74099	GGG	G|0.842;A|0.158	0.158	strong		0.652	ACTRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001331.1	NM_080431	
NLRX1	79671	hgsc.bcm.edu	37	11	119050906	119050906	+	Missense_Mutation	SNP	G	G	A	rs45450295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:119050906G>A	ENST00000409109.1	+	7	2763	c.2176G>A	c.(2176-2178)Gcc>Acc	p.A726T	NLRX1_ENST00000292199.2_Missense_Mutation_p.A726T|NLRX1_ENST00000525863.1_Missense_Mutation_p.A726T|NLRX1_ENST00000409991.1_Missense_Mutation_p.A726T|NLRX1_ENST00000409265.4_Missense_Mutation_p.A726T	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	726	Required for the repression of MAVS- induced interferon signaling.				innate immune response (GO:0045087)|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 interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CGGAAGGCATGCCCTGGATGA	0.637													G|||	45	0.00898562	0.0295	0.0043	5008	,	,		18736	0.0		0.002	False		,,,				2504	0.001				p.A726T		Atlas-SNP	.											.	NLRX1	128	.	0			c.G2176A						PASS	.	G	THR/ALA,THR/ALA	162,4238	104.3+/-142.8	2,158,2040	51.0	47.0	49.0		2176,2176	-0.9	0.9	11	dbSNP_127	49	41,8549	26.3+/-74.7	0,41,4254	yes	missense,missense	NLRX1	NM_024618.2,NM_170722.1	58,58	2,199,6294	AA,AG,GG		0.4773,3.6818,1.5627	benign,benign	726/976,726/922	119050906	203,12787	2200	4295	6495	SO:0001583	missense	79671	exon7			AGGCATGCCCTGG	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.2176G>A	11.37:g.119050906G>A	ENSP00000387334:p.Ala726Thr	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	428	99	0.231308	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	13	0.005952380952380952	11	0.022357723577235773	0	0.0	0	0.0	2	0.002638522427440633	G	5.185	0.219615	0.09863	0.036818	0.004773	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73	5.17	-0.941	0.10402	.	0.788838	0.11541	N	0.553714	T	0.04588	0.0125	N	0.08118	0	0.18873	N	0.999983	B;B	0.15473	0.013;0.0	B;B	0.12156	0.007;0.002	T	0.16867	-1.0388	10	0.13108	T	0.6	.	3.8077	0.08783	0.1544:0.3464:0.3861:0.1131	rs45450295	726;726	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	T	726	ENSP00000386851:A726T;ENSP00000292199:A726T;ENSP00000386858:A726T;ENSP00000387334:A726T;ENSP00000433442:A726T	ENSP00000292199:A726T	A	+	1	0	NLRX1	118556116	0.000000	0.05858	0.911000	0.35937	0.797000	0.45037	-0.202000	0.09451	0.162000	0.19483	0.313000	0.20887	GCC	G|0.988;A|0.012	0.012	strong		0.637	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
KIAA0319L	79932	hgsc.bcm.edu	37	1	35972375	35972375	+	Silent	SNP	A	A	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:35972375A>T	ENST00000325722.3	-	3	738	c.504T>A	c.(502-504)gcT>gcA	p.A168A		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	168						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTCTGAGTGCAGCTCTGGGTG	0.502																																					p.A168A		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.T504A						PASS	.						121.0	117.0	118.0					1																	35972375		2203	4300	6503	SO:0001819	synonymous_variant	79932	exon3			GAGTGCAGCTCTG	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.504T>A	1.37:g.35972375A>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	103	29	0.281553	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Silent	SNP	ENST00000325722.3	37	CCDS390.1	.	.	.	.	.	.	.	.	.	.	A	0.044	-1.271484	0.01421	.	.	ENSG00000142687	ENST00000431916	.	.	.	5.78	-1.12	0.09808	.	.	.	.	.	T	0.22166	0.0534	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.28459	-1.0043	4	.	.	.	-0.4253	4.2445	0.10665	0.5279:0.2944:0.0697:0.108	.	.	.	.	S	32	.	.	C	-	1	0	KIAA0319L	35744962	0.905000	0.30787	0.001000	0.08648	0.083000	0.17756	0.332000	0.19751	0.104000	0.17725	0.533000	0.62120	TGC	.	.	none		0.502	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
SMYD3	64754	hgsc.bcm.edu	37	1	246021858	246021858	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:246021858A>G	ENST00000388985.4	-	10	1015	c.1016T>C	c.(1015-1017)aTc>aCc	p.I339T	SMYD3_ENST00000490107.1_Missense_Mutation_p.I280T|SMYD3_ENST00000541742.1_Missense_Mutation_p.I280T|SMYD3_ENST00000366517.1_5'UTR			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	339					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)		GCCGAGGTTGATGCAGGCATC	0.552																																					p.I339T		Atlas-SNP	.											SMYD3_ENST00000388985,right_lower_lobe,carcinoma,+1,2	SMYD3	77	2	0			c.T1016C						scavenged	.						145.0	119.0	128.0					1																	246021858		2203	4300	6503	SO:0001583	missense	64754	exon10			AGGTTGATGCAGG	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.1016T>C	1.37:g.246021858A>G	ENSP00000373637:p.Ile339Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	219	3	0.0136986	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Missense_Mutation	SNP	ENST00000388985.4	37	CCDS53486.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.385062	0.82792	.	.	ENSG00000185420	ENST00000541742;ENST00000490107;ENST00000544586;ENST00000388985	T;T;T	0.25250	1.81;1.81;1.81	5.57	5.57	0.84162	.	0.125689	0.52532	D	0.000071	T	0.33990	0.0882	L	0.56199	1.76	0.58432	D	0.999998	P;P	0.45474	0.859;0.6	P;B	0.47915	0.561;0.345	T	0.02950	-1.1090	10	0.30078	T	0.28	-18.4157	15.7313	0.77807	1.0:0.0:0.0:0.0	.	339;150	Q9H7B4;B3KN46	SMYD3_HUMAN;.	T	280;280;169;339	ENSP00000444184:I280T;ENSP00000419184:I280T;ENSP00000373637:I339T	ENSP00000373637:I339T	I	-	2	0	SMYD3	244088481	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.113000	0.77095	2.119000	0.64992	0.533000	0.62120	ATC	.	.	none		0.552	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743	
SLC39A12	221074	hgsc.bcm.edu	37	10	18254606	18254606	+	Silent	SNP	C	C	A	rs691513	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:18254606C>A	ENST00000377369.2	+	4	1011	c.738C>A	c.(736-738)acC>acA	p.T246T	SLC39A12_ENST00000539911.1_Silent_p.T112T|SLC39A12_ENST00000377374.4_Silent_p.T246T|SLC39A12_ENST00000377371.3_Silent_p.T246T	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	246					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						GTACGAATACCCTCCGCCTAT	0.418													C|||	1660	0.33147	0.2443	0.4006	5008	,	,		18941	0.3889		0.3608	False		,,,				2504	0.3108				p.T246T		Atlas-SNP	.											.	SLC39A12	181	.	0			c.C738A						PASS	.	C	,	1136,3270	404.2+/-333.0	147,842,1214	48.0	46.0	47.0		738,738	0.9	0.5	10	dbSNP_83	47	2935,5665	453.3+/-363.2	502,1931,1867	no	coding-synonymous,coding-synonymous	SLC39A12	NM_001145195.1,NM_152725.3	,	649,2773,3081	AA,AC,CC		34.1279,25.783,31.3009	,	246/692,246/655	18254606	4071,8935	2203	4300	6503	SO:0001819	synonymous_variant	221074	exon4			GAATACCCTCCGC		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.738C>A	10.37:g.18254606C>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	54	39	0.722222	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Silent	SNP	ENST00000377369.2	37	CCDS44362.1																																																																																			C|0.672;A|0.328	0.328	strong		0.418	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
GPR162	27239	hgsc.bcm.edu	37	12	6935977	6935977	+	Missense_Mutation	SNP	A	A	G	rs11612427	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6935977A>G	ENST00000311268.3	+	5	2162	c.1375A>G	c.(1375-1377)Aga>Gga	p.R459G	GPR162_ENST00000382315.3_Missense_Mutation_p.R155G|LEPREL2_ENST00000251761.8_RNA|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000428545.2_Missense_Mutation_p.R175G|LEPREL2_ENST00000396725.2_RNA	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	459			R -> G (in dbSNP:rs11612427). {ECO:0000269|PubMed:15489334}.			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						CCTGGGACAAAGACACAGGTT	0.632													A|||	527	0.105232	0.0151	0.2104	5008	,	,		-128	0.002		0.3012	False		,,,				2504	0.0573				p.R459G		Atlas-SNP	.											.	GPR162	55	.	0			c.A1375G						PASS	.	A	GLY/ARG,GLY/ARG	280,4126	152.2+/-185.9	10,260,1933	48.0	58.0	55.0		523,1375	3.1	0.1	12	dbSNP_120	55	2698,5902	427.2+/-355.5	436,1826,2038	no	missense,missense	GPR162	NM_014449.1,NM_019858.1	125,125	446,2086,3971	GG,GA,AA		31.3721,6.355,22.8971	benign,benign	175/305,459/589	6935977	2978,10028	2203	4300	6503	SO:0001583	missense	27239	exon5			GGACAAAGACACA	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.1375A>G	12.37:g.6935977A>G	ENSP00000311528:p.Arg459Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	37	CCDS8563.1	319	0.14606227106227107	6	0.012195121951219513	84	0.23204419889502761	0	0.0	229	0.3021108179419525	A	11.06	1.529094	0.27387	0.06355	0.313721	ENSG00000250510	ENST00000311268;ENST00000428545;ENST00000382315	T;T;T	0.44881	3.07;0.91;0.92	4.24	3.13	0.36017	.	.	.	.	.	T	0.00012	0.0000	L	0.43923	1.385	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.19943	-1.0290	8	0.72032	D	0.01	.	10.9424	0.47281	0.6818:0.3182:0.0:0.0	rs11612427;rs11612427	175;459	Q16538-2;Q16538	.;GP162_HUMAN	G	459;175;155	ENSP00000311528:R459G;ENSP00000399670:R175G;ENSP00000371752:R155G	ENSP00000311528:R459G	R	+	1	2	GPR162	6806238	0.074000	0.21230	0.100000	0.21137	0.758000	0.43043	1.813000	0.38962	1.006000	0.39211	0.459000	0.35465	AGA	A|0.801;G|0.199	0.199	strong		0.632	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
ARFGAP2	84364	hgsc.bcm.edu	37	11	47188411	47188411	+	Missense_Mutation	SNP	C	C	T	rs3740691	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47188411C>T	ENST00000524782.1	-	13	1460	c.1232G>A	c.(1231-1233)aGc>aAc	p.S411N	ARFGAP2_ENST00000319543.6_Missense_Mutation_p.S142N|ARFGAP2_ENST00000395449.3_5'UTR|RP11-390K5.6_ENST00000524412.1_RNA|ARFGAP2_ENST00000419701.2_Missense_Mutation_p.S304N|ARFGAP2_ENST00000426335.2_Missense_Mutation_p.S275N	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2	411	Required for interaction with coatomer.		S -> N (in dbSNP:rs3740691). {ECO:0000269|PubMed:12880961}.		protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						TGAGCTCCGGCTCTCCACTTC	0.562													C|||	1946	0.388578	0.6853	0.2435	5008	,	,		22014	0.124		0.335	False		,,,				2504	0.4182				p.S411N		Atlas-SNP	.											.	ARFGAP2	43	.	0			c.G1232A						PASS	.	C	ASN/SER,ASN/SER	2697,1705	651.6+/-399.3	837,1023,341	121.0	125.0	123.0		1148,1232	3.8	0.9	11	dbSNP_107	123	2729,5869	435.0+/-357.9	432,1865,2002	no	missense,missense	ARFGAP2	NM_001242832.1,NM_032389.4	46,46	1269,2888,2343	TT,TC,CC		31.7399,38.7324,41.7385	benign,benign	383/494,411/522	47188411	5426,7574	2201	4299	6500	SO:0001583	missense	84364	exon13			CTCCGGCTCTCCA	AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"""ADP-ribosylation factor GTPase activating proteins"""	13504	protein-coding gene	gene with protein product		606908	"""zinc finger protein 289, ID1 regulated"""	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773	ENST00000524782.1:c.1232G>A	11.37:g.47188411C>T	ENSP00000434442:p.Ser411Asn	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_032389	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Missense_Mutation	SNP	ENST00000524782.1	37	CCDS7926.1	747	0.34203296703296704	319	0.6483739837398373	94	0.2596685082872928	81	0.14160839160839161	253	0.3337730870712401	C	11.84	1.757403	0.31137	0.612676	0.317399	ENSG00000149182	ENST00000426335;ENST00000524782;ENST00000319543;ENST00000419701;ENST00000526342	T;T;T;T;T	0.18016	3.37;3.5;3.1;3.22;2.24	5.67	3.76	0.43208	.	0.420602	0.32106	N	0.006579	T	0.00012	0.0000	L	0.28192	0.835	0.39789	P	0.027595000000000036	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.28744	-1.0034	9	0.25751	T	0.34	-1.2283	6.6827	0.23129	0.1396:0.6627:0.1237:0.074	rs3740691;rs57763298;rs3740691	304;275;411	B4DX29;G5E9L0;Q8N6H7	.;.;ARFG2_HUMAN	N	275;411;142;304;118	ENSP00000400226:S275N;ENSP00000434442:S411N;ENSP00000327309:S142N;ENSP00000389264:S304N;ENSP00000437305:S118N	ENSP00000327309:S142N	S	-	2	0	ARFGAP2	47144987	0.994000	0.37717	0.864000	0.33941	0.722000	0.41435	0.616000	0.24344	0.703000	0.31848	0.655000	0.94253	AGC	C|0.607;T|0.393	0.393	strong		0.562	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389	
SSPN	8082	hgsc.bcm.edu	37	12	26377232	26377232	+	Silent	SNP	T	T	C	rs34624361	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:26377232T>C	ENST00000242729.2	+	2	463	c.286T>C	c.(286-288)Tta>Cta	p.L96L	SSPN_ENST00000540266.1_5'UTR|RP11-283G6.4_ENST00000540392.1_RNA|SSPN_ENST00000422622.2_5'UTR|SSPN_ENST00000535504.1_Silent_p.L96L	NM_005086.4	NP_005077.2	Q14714	SSPN_HUMAN	sarcospan	96					cell adhesion (GO:0007155)|muscle contraction (GO:0006936)	cell junction (GO:0030054)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)		p.L96L(1)		kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	10	Colorectal(261;0.0847)					GCAGGTCTGCTTAGTGGCCTA	0.413													T|||	358	0.0714856	0.0915	0.098	5008	,	,		21111	0.0357		0.0686	False		,,,				2504	0.0654				p.L96L		Atlas-SNP	.											SSPN,NS,carcinoma,0,1	SSPN	19	1	1	Substitution - coding silent(1)	stomach(1)	c.T286C						scavenged	.	T	,	452,3954	216.8+/-235.3	22,408,1773	349.0	327.0	335.0		,286	-7.1	0.4	12	dbSNP_126	335	625,7975	161.9+/-214.7	29,567,3704	no	utr-5,coding-synonymous	SSPN	NM_001135823.1,NM_005086.4	,	51,975,5477	CC,CT,TT		7.2674,10.2587,8.2808	,	,96/244	26377232	1077,11929	2203	4300	6503	SO:0001819	synonymous_variant	8082	exon2			GTCTGCTTAGTGG	AF016028	CCDS8707.1, CCDS44850.1	12p11.2	2014-09-17	2012-03-14			ENSG00000123096			11322	protein-coding gene	gene with protein product		601599	"""Kras oncogene-associated gene"""	KRAG		9395445, 8661122	Standard	NM_005086		Approved	SPN1, SPN2	uc001rhe.3	Q14714		ENST00000242729.2:c.286T>C	12.37:g.26377232T>C		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	205	92	0.44878	NM_005086	B3KS67	Silent	SNP	ENST00000242729.2	37	CCDS8707.1																																																																																			T|0.919;C|0.081	0.081	strong		0.413	SSPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402654.2	NM_005086	
SLC25A23	79085	hgsc.bcm.edu	37	19	6458240	6458240	+	Silent	SNP	G	G	C	rs2289784	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	51	0	0		WXS	Illumina HiSeq	Phase_I	36	11	0.305556	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	
RBBP7	5931	hgsc.bcm.edu	37	X	16887655	16887655	+	Intron	SNP	C	C	T	rs67984110		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:16887655C>T	ENST00000380087.2	-	2	377				RBBP7_ENST00000380084.4_Missense_Mutation_p.R37H|RBBP7_ENST00000404022.1_Intron			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7						cell proliferation (GO:0008283)|cellular heat acclimation (GO:0070370)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	RNA binding (GO:0003723)			biliary_tract(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	25	Hepatocellular(33;0.0997)					AGGGGCTGCGCGACCCAGTCG	0.572													C|||	989	0.261987	0.1157	0.1556	3775	,	,		10610	0.0437		0.3201	False		,,,				2504	0.3701				p.R37H		Atlas-SNP	.											.	RBBP7	58	.	0			c.G110A						PASS	.																																			SO:0001627	intron_variant	5931	exon1			GCTGCGCGACCCA	U35143	CCDS14179.1, CCDS56598.1	Xp22.22	2013-01-10	2001-11-28		ENSG00000102054	ENSG00000102054		"""WD repeat domain containing"""	9890	protein-coding gene	gene with protein product	"""G1/S transition control protein-binding protein RbAp46"", ""retinoblastoma-binding protein 7"", ""retinoblastoma-binding protein RbAp46"", ""histone acetyltransferase type B subunit 2"", ""retinoblastoma-binding protein p46"""	300825	"""retinoblastoma-binding protein 7"""			7503932	Standard	NM_002893		Approved	RbAp46	uc004cxs.2	Q16576	OTTHUMG00000021198	ENST00000380087.2:c.17-312G>A	X.37:g.16887655C>T		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	148	143	0.966216	NM_001198719	Q5JP00	Missense_Mutation	SNP	ENST00000380087.2	37	CCDS14179.1	383	0.23086196503918022	43	0.09347826086956522	41	0.12654320987654322	10	0.017793594306049824	165	0.2796610169491525	C	15.32	2.798641	0.50208	.	.	ENSG00000102054	ENST00000380084	T	0.74106	-0.81	3.88	3.88	0.44766	.	0.540328	0.16034	N	0.232734	T	0.00012	0.0000	.	.	.	0.23978	P	0.996286	P	0.47841	0.901	B	0.26864	0.074	T	0.10200	-1.0640	8	0.59425	D	0.04	-11.0168	10.2474	0.43350	0.0:1.0:0.0:0.0	.	37	Q5JP00	.	H	37	ENSP00000369424:R37H	ENSP00000369424:R37H	R	-	2	0	RBBP7	16797576	0.004000	0.15560	0.250000	0.24296	0.009000	0.06853	1.149000	0.31626	2.173000	0.68751	0.594000	0.82650	CGC	C|0.769;T|0.231	0.231	strong		0.572	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893	
PEAR1	375033	hgsc.bcm.edu	37	1	156877797	156877797	+	Silent	SNP	C	C	A	rs77235035	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156877797C>A	ENST00000338302.3	+	9	1081	c.856C>A	c.(856-858)Cga>Aga	p.R286R	PEAR1_ENST00000292357.7_Silent_p.R286R			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	286	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)					CCTCTGTGACCGATTCACTGG	0.692													C|||	1140	0.227636	0.2383	0.1931	5008	,	,		12560	0.3502		0.1223	False		,,,				2504	0.2198				p.R286R		Atlas-SNP	.											PEAR1,NS,carcinoma,0,2	PEAR1	118	2	0			c.C856A						scavenged	.	C		972,3404		115,742,1331	13.0	14.0	14.0		856	3.6	1.0	1	dbSNP_131	14	1050,7512		71,908,3302	no	coding-synonymous	PEAR1	NM_001080471.1		186,1650,4633	AA,AC,CC		12.2635,22.2121,15.6284		286/1038	156877797	2022,10916	2188	4281	6469	SO:0001819	synonymous_variant	375033	exon8			TGTGACCGATTCA	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.856C>A	1.37:g.156877797C>A		Somatic	218	2	0.00917431		WXS	Illumina HiSeq	Phase_I	286	90	0.314685	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			C|0.810;A|0.190	0.190	strong		0.692	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
PKD1L2	114780	hgsc.bcm.edu	37	16	81208515	81208515	+	RNA	SNP	G	G	A	rs12596941	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:81208515G>A	ENST00000527937.1	-	0	469				PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000525539.1_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	65	0	0		WXS	Illumina HiSeq	Phase_I	65	16	0.246154	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		
DCHS2	54798	hgsc.bcm.edu	37	4	155241572	155241572	+	Missense_Mutation	SNP	G	G	A	rs11935573	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:155241572G>A	ENST00000357232.4	-	14	3613	c.3614C>T	c.(3613-3615)tCa>tTa	p.S1205L		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1205	Cadherin 10. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> L (in dbSNP:rs11935573).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S1205L(2)		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)		TTCATTTCCTGAGAGGATGCT	0.393													G|||	1317	0.262979	0.0613	0.2997	5008	,	,		22015	0.3552		0.3161	False		,,,				2504	0.3599				p.S1205L		Atlas-SNP	.											DCHS2,NS,carcinoma,0,2	DCHS2	594	2	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.C3614T						PASS	.	G	LEU/SER	461,3945	219.1+/-236.9	25,411,1767	186.0	168.0	174.0		3614	5.6	1.0	4	dbSNP_120	174	2792,5808	442.8+/-360.2	457,1878,1965	yes	missense	DCHS2	NM_017639.3	145	482,2289,3732	AA,AG,GG		32.4651,10.463,25.0115	probably-damaging	1205/2917	155241572	3253,9753	2203	4300	6503	SO:0001583	missense	54798	exon14			TTTCCTGAGAGGA	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.3614C>T	4.37:g.155241572G>A	ENSP00000349768:p.Ser1205Leu	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	158	31	0.196203	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	597	0.2733516483516483	25	0.0508130081300813	115	0.31767955801104975	210	0.36713286713286714	247	0.3258575197889182	G	24.6	4.548489	0.86127	0.10463	0.324651	ENSG00000197410	ENST00000357232	T	0.43294	0.95	5.56	5.56	0.83823	Cadherin (4);Cadherin-like (1);	0.455087	0.18369	N	0.143322	T	0.00012	0.0000	M	0.76328	2.33	0.09310	P	1.0	D	0.71674	0.998	P	0.61592	0.891	T	0.26643	-1.0097	9	0.54805	T	0.06	.	14.3837	0.66929	0.0:0.0:0.8522:0.1478	rs11935573;rs52822939;rs61644114;rs11935573	1205	Q6V1P9	PCD23_HUMAN	L	1205	ENSP00000349768:S1205L	ENSP00000349768:S1205L	S	-	2	0	DCHS2	155461022	0.953000	0.32496	1.000000	0.80357	0.965000	0.64279	4.281000	0.58965	2.619000	0.88677	0.467000	0.42956	TCA	G|0.746;A|0.254	0.254	strong		0.393	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
FZD8	8325	hgsc.bcm.edu	37	10	35929131	35929131	+	Silent	SNP	G	G	A	rs74989785	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:35929131G>A	ENST00000374694.1	-	1	1231	c.1227C>T	c.(1225-1227)gcC>gcT	p.A409A	MIR4683_ENST00000579659.1_RNA	NM_031866.2	NP_114072.1	Q9H461	FZD8_HUMAN	frizzled class receptor 8	409					axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|gonad development (GO:0008406)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|T cell differentiation in thymus (GO:0033077)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	11						AGATGGAGCTGGCCATGCCGA	0.637													G|||	370	0.0738818	0.0832	0.0706	5008	,	,		9437	0.1468		0.007	False		,,,				2504	0.0573				p.A409A		Atlas-SNP	.											.	FZD8	41	.	0			c.C1227T						PASS	.	G		295,4111	159.2+/-191.8	18,259,1926	58.0	57.0	58.0		1227	2.9	1.0	10	dbSNP_131	58	55,8545	35.9+/-90.5	1,53,4246	no	coding-synonymous	FZD8	NM_031866.2		19,312,6172	AA,AG,GG		0.6395,6.6954,2.6911		409/695	35929131	350,12656	2203	4300	6503	SO:0001819	synonymous_variant	8325	exon1			GGAGCTGGCCATG	AB043703	CCDS7192.1	10p11.2	2014-01-29	2014-01-29		ENSG00000177283	ENSG00000177283		"""GPCR / Class F : Frizzled receptors"""	4046	protein-coding gene	gene with protein product		606146	"""frizzled (Drosophila) homolog 8"", ""frizzled homolog 8 (Drosophila)"", ""frizzled 8, seven transmembrane spanning receptor"", ""frizzled family receptor 8"""			11295046	Standard	NM_031866		Approved		uc001iyz.1	Q9H461	OTTHUMG00000017956	ENST00000374694.1:c.1227C>T	10.37:g.35929131G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	39	30	0.769231	NM_031866		Silent	SNP	ENST00000374694.1	37	CCDS7192.1																																																																																			G|0.962;A|0.038	0.038	strong		0.637	FZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047575.2	NM_031866	
POLN	353497	hgsc.bcm.edu	37	4	2194953	2194953	+	Silent	SNP	G	G	A	rs10002583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	246	0	0		WXS	Illumina HiSeq	Phase_I	188	88	0.468085	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	
MMP19	4327	hgsc.bcm.edu	37	12	56236136	56236136	+	Splice_Site	SNP	C	C	T	rs145293054		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:56236136C>T	ENST00000322569.4	-	2	265		c.e2+1		MMP19_ENST00000548629.1_Splice_Site|MMP19_ENST00000409200.3_Splice_Site|MMP19_ENST00000547487.1_Splice_Site	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19						angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|luteolysis (GO:0001554)|ovarian follicle development (GO:0001541)|ovulation from ovarian follicle (GO:0001542)|proteolysis (GO:0006508)|response to cAMP (GO:0051591)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	26					Marimastat(DB00786)	TAGCTTCTCACCTCAGAGCCT	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		19637	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.											.	MMP19	61	.	0			c.173+1G>A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	154.0	119.0	131.0			6.1	1.0	12	dbSNP_134	131	17,8583	12.6+/-44.7	0,17,4283	yes	splice-5	MMP19	NM_002429.4		0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384			56236136	18,12988	2203	4300	6503	SO:0001630	splice_region_variant	4327	exon3			TTCTCACCTCAGA	X92521	CCDS8895.1, CCDS61146.1	12q14	2005-08-08	2005-08-08			ENSG00000123342			7165	protein-coding gene	gene with protein product		601807	"""matrix metalloproteinase 19"""	MMP18		9232430	Standard	NM_002429		Approved	RASI-1	uc001sib.4	Q99542	OTTHUMG00000170216	ENST00000322569.4:c.173+1G>A	12.37:g.56236136C>T		Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	230	117	0.508696	NM_002429	B4E030|O15278|O95606|Q99580	Splice_Site	SNP	ENST00000322569.4	37	CCDS8895.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	24.7	4.564157	0.86335	2.27E-4	0.001977	ENSG00000123342	ENST00000322569;ENST00000548629;ENST00000409200	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4349	0.94788	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MMP19	54522403	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.839000	0.62810	2.894000	0.99253	0.655000	0.94253	.	C|0.999;T|0.001	0.001	strong		0.498	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429	Intron
SCN2A	6326	hgsc.bcm.edu	37	2	166245230	166245230	+	Silent	SNP	T	T	A	rs2060198	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:166245230T>A	ENST00000375437.2	+	27	5204	c.4914T>A	c.(4912-4914)cgT>cgA	p.R1638R	SCN2A_ENST00000375427.2_Silent_p.R1638R|SCN2A_ENST00000283256.6_Silent_p.R1638R|SCN2A_ENST00000357398.3_Silent_p.R1638R	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1638					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)	GAATCCTACGTCTGATCAAAG	0.483													T|||	1249	0.249401	0.1551	0.2478	5008	,	,		19642	0.253		0.2913	False		,,,				2504	0.3313				p.R1638R		Atlas-SNP	.											SCN2A_ENST00000375437,colon,carcinoma,+2,2	SCN2A	589	2	0			c.T4914A						PASS	.	T	,,	743,3663	306.3+/-289.4	60,623,1520	108.0	109.0	109.0		4914,4914,4914	0.2	1.0	2	dbSNP_94	109	2395,6199	398.2+/-346.0	317,1761,2219	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN2A	NM_001040142.1,NM_001040143.1,NM_021007.2	,,	377,2384,3739	AA,AT,TT		27.8683,16.8634,24.1385	,,	1638/2006,1638/2006,1638/2006	166245230	3138,9862	2203	4297	6500	SO:0001819	synonymous_variant	6326	exon26			CCTACGTCTGATC	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.4914T>A	2.37:g.166245230T>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	180	84	0.466667	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	37	CCDS33314.1																																																																																			.	.	weak		0.483	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
MAD2L1BP	9587	hgsc.bcm.edu	37	6	43608220	43608220	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43608220G>A	ENST00000372171.4	+	3	832	c.775G>A	c.(775-777)Gac>Aac	p.D259N	MAD2L1BP_ENST00000451025.2_Missense_Mutation_p.D291N	NM_014628.2	NP_055443.1	Q15013	MD2BP_HUMAN	MAD2L1 binding protein	259					mitotic cell cycle checkpoint (GO:0007093)|regulation of exit from mitosis (GO:0007096)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|large_intestine(1)|lung(3)	5	all_cancers(18;9.36e-06)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000351)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GGCTTGGGAAGACTACATTTG	0.493																																					p.D291N		Atlas-SNP	.											.	MAD2L1BP	12	.	0			c.G871A						PASS	.						51.0	48.0	49.0					6																	43608220		2203	4300	6503	SO:0001583	missense	9587	exon4			TGGGAAGACTACA	BC002904	CCDS4904.1, CCDS47431.1	6p21.1	2003-06-23			ENSG00000124688	ENSG00000124688			21059	protein-coding gene	gene with protein product						7788527, 12456649	Standard	NM_014628		Approved	CMT2, KIAA0110, dJ261G23.1	uc003ovu.3	Q15013	OTTHUMG00000014747	ENST00000372171.4:c.775G>A	6.37:g.43608220G>A	ENSP00000361244:p.Asp259Asn	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	101	30	0.29703	NM_001003690	B4DLV3|E9PAT7|Q6IBB1	Missense_Mutation	SNP	ENST00000372171.4	37	CCDS4904.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831484	0.91036	.	.	ENSG00000124688	ENST00000451025;ENST00000372171	T	0.57752	0.38	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62511	-0.6839	10	0.72032	D	0.01	-18.5445	16.7112	0.85386	0.0:0.0:1.0:0.0	.	259;291	Q15013;E9PAT7	MD2BP_HUMAN;.	N	291;259	ENSP00000410818:D291N	ENSP00000361244:D259N	D	+	1	0	MAD2L1BP	43716198	1.000000	0.71417	0.997000	0.53966	0.568000	0.35870	6.281000	0.72632	2.365000	0.80145	0.555000	0.69702	GAC	.	.	none		0.493	MAD2L1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040692.2	NM_014628	
FN1	2335	hgsc.bcm.edu	37	2	216242917	216242917	+	Silent	SNP	T	T	A	rs1132741	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000354785.4_Silent_p.G1897G|FN1_ENST00000323926.6_Silent_p.G1897G|FN1_ENST00000432072.2_Silent_p.G1807G|FN1_ENST00000336916.4_Silent_p.G1806G|FN1_ENST00000357009.2_Silent_p.G1806G|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000346544.3_Silent_p.G1806G|FN1_ENST00000421182.1_Silent_p.G1716G|FN1_ENST00000345488.5_Silent_p.G1806G|FN1_ENST00000357867.4_Silent_p.G1716G|FN1_ENST00000446046.1_Silent_p.G1806G|FN1_ENST00000443816.1_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	67	0	0		WXS	Illumina HiSeq	Phase_I	33	31	0.939394	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	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388350	1388350	+	Silent	SNP	G	G	A	rs77782813		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1388350G>A	ENST00000324803.4	+	1	3011	c.51G>A	c.(49-51)acG>acA	p.T17T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	17					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)			CTGCTCACACGTGCCCATGTG	0.577																																					p.T17T		Atlas-SNP	.											.	CRIPAK	185	.	0			c.G51A						PASS	.	G		1231,3175		0,1231,972	148.0	151.0	150.0		51	-0.8	0.0	4	dbSNP_131	150	2931,5669		0,2931,1369	no	coding-synonymous	CRIPAK	NM_175918.3		0,4162,2341	AA,AG,GG		34.0814,27.9392,32.0006		17/447	1388350	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	285464	exon1			TCACACGTGCCCA	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.51G>A	4.37:g.1388350G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	204	83	0.406863	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																			G|0.858;A|0.142	0.142	strong		0.577	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
ISOC1	51015	hgsc.bcm.edu	37	5	128430757	128430757	+	Silent	SNP	T	T	C	rs1127827	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:128430757T>C	ENST00000173527.5	+	1	314	c.298T>C	c.(298-300)Ttg>Ctg	p.L100L	MIR4633_ENST00000584064.1_RNA	NM_016048.2	NP_057132.2	Q96CN7	ISOC1_HUMAN	isochorismatase domain containing 1	100						extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	catalytic activity (GO:0003824)			kidney(2)|lung(7)	9		all_cancers(142;0.0813)|Prostate(80;0.0865)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.138)|OV - Ovarian serous cystadenocarcinoma(64;0.164)		CCTCGTGCCGTTGCAGATCCA	0.692													C|||	4039	0.80651	0.9682	0.7464	5008	,	,		11507	0.8661		0.6004	False		,,,				2504	0.7812				p.L100L		Atlas-SNP	.											.	ISOC1	26	.	0			c.T298C						PASS	.	C		3754,388		1706,342,23	17.0	21.0	20.0		298	3.4	1.0	5	dbSNP_86	20	5111,3281		1551,2009,636	no	coding-synonymous	ISOC1	NM_016048.2		3257,2351,659	CC,CT,TT		39.0968,9.3675,29.2724		100/299	128430757	8865,3669	2071	4196	6267	SO:0001819	synonymous_variant	51015	exon1			GTGCCGTTGCAGA	AF151869	CCDS43357.1	5q22.1-q33.3	2010-03-19			ENSG00000066583	ENSG00000066583			24254	protein-coding gene	gene with protein product						10810093, 18566572	Standard	NM_016048		Approved	CGI-111	uc003kva.3	Q96CN7	OTTHUMG00000163144	ENST00000173527.5:c.298T>C	5.37:g.128430757T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	30	10	0.333333	NM_016048	Q7Z770	Silent	SNP	ENST00000173527.5	37	CCDS43357.1																																																																																			T|0.232;C|0.768	0.768	strong		0.692	ISOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371826.1	NM_016048	
TYW1	55253	hgsc.bcm.edu	37	7	66648157	66648157	+	Silent	SNP	C	C	T	rs4145350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:66648157C>T	ENST00000359626.5	+	14	1907	c.1743C>T	c.(1741-1743)aaC>aaT	p.N581N		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	581					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				AAGCATGGAACGTGGACGAGC	0.527																																					p.N581N		Atlas-SNP	.											.	TYW1	71	.	0			c.C1743T						PASS	.	C		1517,2889		140,1237,826	93.0	69.0	77.0		1743	-4.6	1.0	7	dbSNP_110	77	2010,6590		167,1676,2457	no	coding-synonymous	TYW1	NM_018264.2		307,2913,3283	TT,TC,CC		23.3721,34.4303,27.1183		581/733	66648157	3527,9479	2203	4300	6503	SO:0001819	synonymous_variant	55253	exon14			ATGGAACGTGGAC	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1743C>T	7.37:g.66648157C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	128	82	0.640625	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																			C|0.778;T|0.222	0.222	strong		0.527	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
ZNF16	7564	hgsc.bcm.edu	37	8	146171437	146171437	+	Silent	SNP	A	A	G	rs3735785	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:146171437A>G	ENST00000276816.4	-	3	342	c.156T>C	c.(154-156)gaT>gaC	p.D52D	ZNF16_ENST00000394909.2_Silent_p.D52D	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	52					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to sodium dodecyl sulfate (GO:0072707)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell cycle phase transition (GO:1901989)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of kinase activity (GO:0033674)|positive regulation of megakaryocyte differentiation (GO:0045654)|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(4)|large_intestine(5)|lung(9)|ovary(5)|prostate(1)|skin(1)|urinary_tract(1)	29	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.136)	Epithelial(56;3.45e-38)|all cancers(56;3.04e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0424)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.02)|KIRC - Kidney renal clear cell carcinoma(644;0.0486)		CCAGCTCAGTATCACTACAGC	0.582													A|||	1178	0.235224	0.171	0.2061	5008	,	,		20324	0.3284		0.2535	False		,,,				2504	0.228				p.D52D		Atlas-SNP	.											.	ZNF16	80	.	0			c.T156C						PASS	.	A	,	751,3655	306.6+/-289.6	69,613,1521	83.0	79.0	80.0		156,156	-1.5	0.0	8	dbSNP_107	80	2088,6512	362.0+/-332.6	218,1652,2430	no	coding-synonymous,coding-synonymous	ZNF16	NM_001029976.2,NM_006958.2	,	287,2265,3951	GG,GA,AA		24.2791,17.0449,21.8284	,	52/683,52/683	146171437	2839,10167	2203	4300	6503	SO:0001819	synonymous_variant	7564	exon2			CTCAGTATCACTA	X52340	CCDS6437.1	8q24	2013-01-08	2006-05-10		ENSG00000170631	ENSG00000170631		"""Zinc fingers, C2H2-type"""	12947	protein-coding gene	gene with protein product		601262	"""zinc finger protein 16 (KOX 9)"""				Standard	NM_006958		Approved	KOX9	uc003zeu.3	P17020	OTTHUMG00000165253	ENST00000276816.4:c.156T>C	8.37:g.146171437A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	146	38	0.260274	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Silent	SNP	ENST00000276816.4	37	CCDS6437.1																																																																																			A|0.773;G|0.227	0.227	strong		0.582	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958	
KIF5C	3800	hgsc.bcm.edu	37	2	149799216	149799216	+	Silent	SNP	T	T	C	rs61734995	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:149799216T>C	ENST00000435030.1	+	7	899	c.531T>C	c.(529-531)ccT>ccC	p.P177P	KIF5C_ENST00000414838.2_Silent_p.P82P			O60282	KIF5C_HUMAN	kinesin family member 5C	177	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		TGTCGAGCCCTGAGGAAGTCA	0.488													C|||	750	0.14976	0.3427	0.1037	5008	,	,		19701	0.0347		0.1064	False		,,,				2504	0.0849				p.P177P		Atlas-SNP	.											.	KIF5C	166	.	0			c.T531C						PASS	.	C		1115,2823		164,787,1018	74.0	73.0	73.0		242	-11.0	0.0	2	dbSNP_129	73	765,7533		44,677,3428	no	coding-synonymous	KIF5C	NM_004522.1		208,1464,4446	CC,CT,TT		9.2191,28.3139,15.3645		177/958	149799216	1880,10356	1969	4149	6118	SO:0001819	synonymous_variant	3800	exon7			GAGCCCTGAGGAA	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.531T>C	2.37:g.149799216T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	192	88	0.458333	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				T|0.860;C|0.140	0.140	strong		0.488	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
KIF26B	55083	hgsc.bcm.edu	37	1	245772617	245772617	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:245772617C>T	ENST00000407071.2	+	8	2141	c.1701C>T	c.(1699-1701)ggC>ggT	p.G567G	KIF26B_ENST00000366518.4_Silent_p.G186G	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	567	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)			AGAACCTGGGCATCATTCCCT	0.517																																					p.G567G		Atlas-SNP	.											KIF26B_ENST00000407071,NS,carcinoma,0,2	KIF26B	343	2	0			c.C1701T						scavenged	.						40.0	41.0	41.0					1																	245772617		1932	4139	6071	SO:0001819	synonymous_variant	55083	exon8			CCTGGGCATCATT	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.1701C>T	1.37:g.245772617C>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	283	3	0.0106007	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			.	.	none		0.517	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
VPS13A	23230	hgsc.bcm.edu	37	9	79891006	79891006	+	Missense_Mutation	SNP	T	T	C	rs78048112	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:79891006T>C	ENST00000360280.3	+	26	2953	c.2693T>C	c.(2692-2694)gTt>gCt	p.V898A	VPS13A_ENST00000376636.3_Missense_Mutation_p.V898A|VPS13A_ENST00000376634.4_Missense_Mutation_p.V898A|VPS13A_ENST00000357409.5_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	53	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	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	
GXYLT1	283464	hgsc.bcm.edu	37	12	42503467	42503467	+	Silent	SNP	T	T	C	rs7312933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	91	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	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	
DCAF6	55827	hgsc.bcm.edu	37	1	167973976	167973976	+	Silent	SNP	C	C	T	rs1060041	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:167973976C>T	ENST00000312263.6	+	10	1527	c.1323C>T	c.(1321-1323)gaC>gaT	p.D441D	DCAF6_ENST00000367843.3_Silent_p.D441D|DCAF6_ENST00000432587.2_Silent_p.D410D|DCAF6_ENST00000367840.3_Silent_p.D441D	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	441					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						CTTCTCCAGACAGTGAACAAA	0.448													C|||	841	0.167931	0.0401	0.3876	5008	,	,		18740	0.1339		0.2266	False		,,,				2504	0.1595				p.D441D		Atlas-SNP	.											.	DCAF6	99	.	0			c.C1323T						PASS	.	C	,,,	395,4011	194.0+/-219.0	12,371,1820	101.0	97.0	98.0		1323,1323,1230,1323	2.2	1.0	1	dbSNP_86	98	2042,6556	355.6+/-330.0	246,1550,2503	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCAF6	NM_001017977.2,NM_001198956.1,NM_001198957.1,NM_018442.3	,,,	258,1921,4323	TT,TC,CC		23.7497,8.965,18.7404	,,,	441/861,441/952,410/921,441/881	167973976	2437,10567	2203	4299	6502	SO:0001819	synonymous_variant	55827	exon10			TCCAGACAGTGAA	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.1323C>T	1.37:g.167973976C>T		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	221	130	0.588235	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Silent	SNP	ENST00000312263.6	37	CCDS30933.1																																																																																			C|0.821;T|0.179	0.179	strong		0.448	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	
R3HDM2	22864	hgsc.bcm.edu	37	12	57649840	57649840	+	Silent	SNP	C	C	T	rs4075325	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:57649840C>T	ENST00000347140.3	-	23	2913	c.2523G>A	c.(2521-2523)aaG>aaA	p.K841K	R3HDM2_ENST00000546843.1_5'Flank|R3HDM2_ENST00000403821.2_Silent_p.K875K|RP11-123K3.4_ENST00000548184.1_3'UTR|R3HDM2_ENST00000402412.1_Silent_p.K855K|R3HDM2_ENST00000441731.2_Silent_p.K536K|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	295	2	0.00677966		WXS	Illumina HiSeq	Phase_I	285	284	0.996491	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	
MUC16	94025	hgsc.bcm.edu	37	19	9088722	9088722	+	Silent	SNP	G	G	A	rs17000948	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9088722G>A	ENST00000397910.4	-	1	3296	c.3093C>T	c.(3091-3093)ggC>ggT	p.G1031G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1031	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						CAGCCATAGAGCCTGGGCCAT	0.478													G|||	720	0.14377	0.1437	0.1124	5008	,	,		22388	0.2282		0.0855	False		,,,				2504	0.1391				p.G1031G		Atlas-SNP	.											.	MUC16	4315	.	0			c.C3093T						PASS	.	G		509,3445		39,431,1507	158.0	152.0	154.0		3093	1.5	0.0	19	dbSNP_123	154	628,7686		25,578,3554	no	coding-synonymous	MUC16	NM_024690.2		64,1009,5061	AA,AG,GG		7.5535,12.873,9.268		1031/14508	9088722	1137,11131	1977	4157	6134	SO:0001819	synonymous_variant	94025	exon1			CATAGAGCCTGGG	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.3093C>T	19.37:g.9088722G>A		Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	242	117	0.483471	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.860;A|0.140	0.140	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SCAF4	57466	hgsc.bcm.edu	37	21	33044408	33044408	+	Silent	SNP	A	A	G	rs73201506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:33044408A>G	ENST00000286835.7	-	20	3130	c.2748T>C	c.(2746-2748)gtT>gtC	p.V916V	SCAF4_ENST00000434667.3_Silent_p.V901V|SCAF4_ENST00000399804.1_Silent_p.V894V	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	916						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						CACCAGGCCTAACAAAGGGGC	0.662													A|||	83	0.0165735	0.0008	0.0187	5008	,	,		15066	0.003		0.0596	False		,,,				2504	0.0061				p.V916V		Atlas-SNP	.											.	SCAF4	142	.	0			c.T2748C						PASS	.	A	,,	41,4365	40.0+/-72.8	0,41,2162	33.0	33.0	33.0		2703,2682,2748	-1.9	0.8	21	dbSNP_130	33	392,8206	117.7+/-177.3	14,364,3921	no	coding-synonymous,coding-synonymous,coding-synonymous	SCAF4	NM_001145444.1,NM_001145445.1,NM_020706.2	,,	14,405,6083	GG,GA,AA		4.5592,0.9305,3.3297	,,	901/1133,894/1126,916/1148	33044408	433,12571	2203	4299	6502	SO:0001819	synonymous_variant	57466	exon20			AGGCCTAACAAAG	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.2748T>C	21.37:g.33044408A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	82	24	0.292683	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	37	CCDS33537.1																																																																																			A|0.972;G|0.028	0.028	strong		0.662	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
CLCN3	1182	hgsc.bcm.edu	37	4	170634390	170634390	+	Silent	SNP	C	C	T	rs1058868	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:170634390C>T	ENST00000513761.1	+	12	2869	c.2310C>T	c.(2308-2310)atC>atT	p.I770I	CLCN3_ENST00000360642.3_Silent_p.I743I|CLCN3_ENST00000504131.2_Silent_p.I753I|CLCN3_ENST00000347613.4_Silent_p.I770I	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	770	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)	p.I770I(1)		breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		CAATGGAGATCGTGGTGGATA	0.483													T|||	589	0.117612	0.1021	0.098	5008	,	,		19300	0.1766		0.1213	False		,,,				2504	0.0879				p.I770I		Atlas-SNP	.											CLCN3,NS,carcinoma,+1,2	CLCN3	85	2	1	Substitution - coding silent(1)	stomach(1)	c.C2310T						PASS	.	T	,	391,4015	790.6+/-415.0	12,367,1824	111.0	99.0	103.0		2310,2310	-6.9	0.8	4	dbSNP_123	103	1095,7505	769.0+/-407.6	78,939,3283	no	coding-synonymous,coding-synonymous	CLCN3	NM_001829.3,NM_173872.3	,	90,1306,5107	TT,TC,CC		12.7326,8.8743,11.4255	,	770/819,770/867	170634390	1486,11520	2203	4300	6503	SO:0001819	synonymous_variant	1182	exon12			GGAGATCGTGGTG	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"""Ion channels / Chloride channels : Voltage-sensitive"""	2021	protein-coding gene	gene with protein product		600580	"""chloride channel 3"""				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.2310C>T	4.37:g.170634390C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	146	49	0.335616	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Silent	SNP	ENST00000513761.1	37	CCDS34101.1																																																																																			C|0.879;T|0.121	0.121	strong		0.483	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2		
GOLIM4	27333	hgsc.bcm.edu	37	3	167747022	167747022	+	Missense_Mutation	SNP	C	C	T	rs61743591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:167747022C>T	ENST00000470487.1	-	11	2191	c.1502G>A	c.(1501-1503)gGa>gAa	p.G501E	GOLIM4_ENST00000309027.4_Missense_Mutation_p.G473E	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	501	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						TCCTTCCTCTCCTTGGATTCC	0.373													T|||	134	0.0267572	0.0068	0.0115	5008	,	,		15771	0.0308		0.0537	False		,,,				2504	0.0327				p.G501E		Atlas-SNP	.											GOLIM4,NS,carcinoma,-1,1	GOLIM4	71	1	0			c.G1502A						PASS	.	T	GLU/GLY	89,4317	818.1+/-416.3	0,89,2114	130.0	112.0	118.0		1502	5.0	1.0	3	dbSNP_129	118	556,8044	794.4+/-407.5	23,510,3767	yes	missense	GOLIM4	NM_014498.3	98	23,599,5881	TT,TC,CC		6.4651,2.02,4.9592	benign	501/697	167747022	645,12361	2203	4300	6503	SO:0001583	missense	27333	exon11			TCCTCTCCTTGGA	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.1502G>A	3.37:g.167747022C>T	ENSP00000417354:p.Gly501Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	63	0.028846153846153848	5	0.01016260162601626	4	0.011049723756906077	10	0.017482517482517484	44	0.05804749340369393	T	5.739	0.320877	0.10845	0.0202	0.064651	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	4.97	4.97	0.65823	.	0.222920	0.47455	N	0.000232	T	0.00552	0.0018	N	0.00069	-2.28	0.18873	N	0.999988	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33777	-0.9855	9	0.02654	T	1	-10.1009	10.7675	0.46303	0.0:0.0753:0.0:0.9246	.	473;501	F8W785;O00461	.;GOLI4_HUMAN	E	501;473	.	ENSP00000309893:G473E	G	-	2	0	GOLIM4	169229716	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	4.289000	0.59013	0.758000	0.33059	-0.391000	0.06502	GGA	C|0.956;T|0.044	0.044	strong		0.373	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2		
NKAIN3	286183	hgsc.bcm.edu	37	8	63659635	63659635	+	Missense_Mutation	SNP	G	G	A	rs4739003	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:63659635G>A	ENST00000523211.1	+	4	550	c.418G>A	c.(418-420)Gtt>Att	p.V140I	NKAIN3_ENST00000519049.1_3'UTR|NKAIN3_ENST00000328472.5_Missense_Mutation_p.V140I	NM_173688.2	NP_775959.1	Q8N8D7	NKAI3_HUMAN	Na+/K+ transporting ATPase interacting 3	140			V -> I (in dbSNP:rs4739003).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(3)|large_intestine(2)|lung(8)	13	Breast(64;0.127)	Lung NSC(129;0.187)				AGGCTGCATCGTTGACTTCCA	0.488													G|||	1180	0.235623	0.2519	0.2104	5008	,	,		20558	0.3304		0.1421	False		,,,				2504	0.2301				p.V140I		Atlas-SNP	.											.	NKAIN3	32	.	0			c.G418A						PASS	.	G	ILE/VAL	784,3352		79,626,1363	117.0	118.0	118.0		418	2.3	0.3	8	dbSNP_111	118	1090,7344		69,952,3196	yes	missense	NKAIN3	NM_173688.2	29	148,1578,4559	AA,AG,GG		12.9239,18.9555,14.9085	benign	140/198	63659635	1874,10696	2068	4217	6285	SO:0001583	missense	286183	exon4			TGCATCGTTGACT	AK096949	CCDS55239.1	8q12.3	2014-08-12	2007-10-04	2007-10-04	ENSG00000185942	ENSG00000185942		"""Na+/K+ transporting ATPase interacting"""	26829	protein-coding gene	gene with protein product		612872	"""family with sequence similarity 77, member D"""	FAM77D		17606467	Standard	NM_173688		Approved	FLJ39630	uc010lyq.1	Q8N8D7	OTTHUMG00000164361	ENST00000523211.1:c.418G>A	8.37:g.63659635G>A	ENSP00000429073:p.Val140Ile	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	73	13	0.178082	NM_173688		Missense_Mutation	SNP	ENST00000523211.1	37	CCDS55239.1	504	0.23076923076923078	129	0.2621951219512195	70	0.19337016574585636	193	0.3374125874125874	112	0.14775725593667546	G	13.69	2.311959	0.40895	0.189555	0.129239	ENSG00000185942	ENST00000545532;ENST00000523211;ENST00000328472	T;T	0.12879	2.64;2.64	5.49	2.28	0.28536	.	0.355782	0.26492	N	0.024075	T	0.00012	0.0000	N	0.13235	0.315	0.58432	P	4.000000000004E-6	B	0.14012	0.009	B	0.10450	0.005	T	0.47911	-0.9080	9	0.41790	T	0.15	-15.1687	6.993	0.24765	0.4394:0.0:0.5606:0.0	rs4739003;rs59573623;rs4739003	140	Q8N8D7	NKAI3_HUMAN	I	140	ENSP00000429073:V140I;ENSP00000333627:V140I	ENSP00000333627:V140I	V	+	1	0	NKAIN3	63822189	0.182000	0.23173	0.265000	0.24526	0.954000	0.61252	0.641000	0.24720	0.698000	0.31739	0.650000	0.86243	GTT	G|0.768;A|0.231	0.231	strong		0.488	NKAIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378447.2	NM_173688	
METTL25	84190	hgsc.bcm.edu	37	12	82792666	82792666	+	Silent	SNP	C	C	T	rs10506872	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:82792666C>T	ENST00000248306.3	+	4	693	c.624C>T	c.(622-624)acC>acT	p.T208T	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	208							methyltransferase activity (GO:0008168)										CTTCAAATACCAATACTCATG	0.363													C|||	212	0.0423323	0.0189	0.0591	5008	,	,		13940	0.002		0.0805	False		,,,				2504	0.0644				p.T208T		Atlas-SNP	.											.	.	.	.	0			c.C624T						PASS	.	C		147,4259	99.4+/-138.0	3,141,2059	48.0	47.0	47.0		624	0.9	0.9	12	dbSNP_119	47	818,7780	186.0+/-233.6	43,732,3524	no	coding-synonymous	C12orf26	NM_032230.2		46,873,5583	TT,TC,CC		9.5138,3.3364,7.4208		208/604	82792666	965,12039	2203	4299	6502	SO:0001819	synonymous_variant	84190	exon4			AAATACCAATACT	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.624C>T	12.37:g.82792666C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_032230	Q9H5Y3	Silent	SNP	ENST00000248306.3	37	CCDS9024.1	89	0.04075091575091575	11	0.022357723577235773	22	0.06077348066298342	1	0.0017482517482517483	55	0.07255936675461741	C	7.250	0.603078	0.13939	0.033364	0.095138	ENSG00000127720	ENST00000550058	.	.	.	5.3	0.871	0.19107	.	.	.	.	.	T	0.02342	0.0072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00896	-1.1523	4	.	.	.	-0.1742	7.0117	0.24865	0.1109:0.5787:0.0:0.3105	rs10506872;rs17774639;rs10506872	.	.	.	L	167	.	.	P	+	2	0	C12orf26	81316797	1.000000	0.71417	0.941000	0.38009	0.953000	0.61014	0.943000	0.29030	-0.274000	0.09232	-1.128000	0.01989	CCA	C|0.955;T|0.045	0.045	strong		0.363	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855647	12855647	+	Silent	SNP	C	C	T	rs200536957		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:12855647C>T	ENST00000332296.7	+	4	1030	c.927C>T	c.(925-927)gaC>gaT	p.D309D	PRAMEF1_ENST00000400814.3_Silent_p.D64D	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	309					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)		TGGAAGAAGACATGAAGTGTC	0.498																																					p.D309D		Atlas-SNP	.											PRAMEF1,NS,carcinoma,+2,2	PRAMEF1	78	2	0			c.C927T						scavenged	.						43.0	48.0	46.0					1																	12855647		2197	4275	6472	SO:0001819	synonymous_variant	65121	exon4			AGAAGACATGAAG	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.927C>T	1.37:g.12855647C>T		Somatic	442	29	0.0656109		WXS	Illumina HiSeq	Phase_I	234	26	0.111111	NM_023013	Q9UQP2	Silent	SNP	ENST00000332296.7	37	CCDS148.1																																																																																			C|0.999;T|0.001	0.001	weak		0.498	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
MUC5B	727897	hgsc.bcm.edu	37	11	1264767	1264767	+	Silent	SNP	G	G	A	rs2943501	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1264767G>A	ENST00000529681.1	+	31	6715	c.6657G>A	c.(6655-6657)tcG>tcA	p.S2219S	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.S2222S	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2219	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)		CGGCCACCTCGGGCATCTTGG	0.652																																					p.S2219S		Atlas-SNP	.											MUC5B,NS,neuroblastoma,0,2	MUC5B	473	2	0			c.G6657A						scavenged	.						86.0	102.0	97.0					11																	1264767		2068	4181	6249	SO:0001819	synonymous_variant	727897	exon31			CACCTCGGGCATC	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.6657G>A	11.37:g.1264767G>A		Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	366	14	0.0382514	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	weak		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
IVD	3712	hgsc.bcm.edu	37	15	40705225	40705225	+	Silent	SNP	C	C	T	rs2229312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	148	0	0		WXS	Illumina HiSeq	Phase_I	100	68	0.68	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			
UPK3BL	100134938	hgsc.bcm.edu	37	7	102279621	102279621	+	Missense_Mutation	SNP	C	C	T	rs56365279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:102279621C>T	ENST00000340457.8	-	4	560	c.511G>A	c.(511-513)Gaa>Aaa	p.E171K	POLR2J2_ENST00000476151.1_3'UTR|RP11-514P8.6_ENST00000519541.1_Missense_Mutation_p.E171K|POLR2J2_ENST00000591000.1_3'UTR	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	576	4	0.00694444		WXS	Illumina HiSeq	Phase_I	1349	294	0.217939	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	
ORC4	5000	hgsc.bcm.edu	37	2	148730367	148730367	+	Missense_Mutation	SNP	G	G	C	rs2307397	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:148730367G>C	ENST00000392857.5	-	4	273	c.166C>G	c.(166-168)Ctc>Gtc	p.L56V	ORC4_ENST00000536575.1_Intron|ORC4_ENST00000264169.2_Missense_Mutation_p.L56V|ORC4_ENST00000392858.1_Missense_Mutation_p.L56V|ORC4_ENST00000540442.1_5'UTR|ORC4_ENST00000542387.1_5'UTR|ORC4_ENST00000535373.1_Missense_Mutation_p.L56V	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	56			L -> V (in dbSNP:rs2307397). {ECO:0000269|Ref.4}.		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						TCTCCATGGAGAGCAGTTCTT	0.358													G|||	86	0.0171725	0.0045	0.0288	5008	,	,		13467	0.0		0.0447	False		,,,				2504	0.0153				p.L56V		Atlas-SNP	.											.	ORC4	40	.	0			c.C166G						PASS	.	G	VAL/LEU,,,VAL/LEU,VAL/LEU,VAL/LEU	51,4355	51.6+/-87.1	1,49,2153	73.0	75.0	74.0		166,,,166,166,166	2.3	1.0	2	dbSNP_100	74	464,8136	138.3+/-195.1	13,438,3849	yes	missense,intron,utr-5,missense,missense,missense	ORC4	NM_001190879.2,NM_001190881.2,NM_001190882.2,NM_002552.4,NM_181741.3,NM_181742.3	32,,,32,32,32	14,487,6002	CC,CG,GG		5.3953,1.1575,3.9597	benign,,,benign,benign,benign	56/437,,,56/437,56/437,56/437	148730367	515,12491	2203	4300	6503	SO:0001583	missense	5000	exon4			CATGGAGAGCAGT	AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"""ATPases / AAA-type"""	8490	protein-coding gene	gene with protein product		603056	"""origin recognition complex, subunit 4 (yeast homolog)-like"", ""origin recognition complex, subunit 4-like (yeast)"", ""origin recognition complex, subunit 4-like (S. cerevisiae)"", ""origin recognition complex, subunit 4 homolog (S. cerevisiae)"""	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.166C>G	2.37:g.148730367G>C	ENSP00000376597:p.Leu56Val	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	206	122	0.592233	NM_002552	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	56	0.02564102564102564	6	0.012195121951219513	14	0.03867403314917127	0	0.0	36	0.047493403693931395	G	9.786	1.176749	0.21704	0.011575	0.053953	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000392857;ENST00000416719;ENST00000457954;ENST00000440042	T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15	5.88	2.28	0.28536	.	0.171869	0.51477	N	0.000088	T	0.03608	0.0103	N	0.01257	-0.925	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.01961	-1.1239	10	0.26408	T	0.33	-4.2923	4.915	0.13842	0.0:0.2245:0.1536:0.6219	rs2307397;rs17219015;rs56449945;rs2307397	56;56;56	B7Z2M4;A8K7H4;O43929	.;.;ORC4_HUMAN	V	56	ENSP00000264169:L56V;ENSP00000441953:L56V;ENSP00000376598:L56V;ENSP00000376597:L56V;ENSP00000413939:L56V;ENSP00000391484:L56V;ENSP00000403105:L56V	ENSP00000264169:L56V	L	-	1	0	ORC4	148446837	0.997000	0.39634	1.000000	0.80357	0.885000	0.51271	0.434000	0.21494	0.487000	0.27698	-0.266000	0.10368	CTC	G|0.964;C|0.036	0.036	strong		0.358	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742	
MADCAM1	8174	hgsc.bcm.edu	37	19	501900	501900	+	Missense_Mutation	SNP	C	C	A	rs3745925	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:501900C>A	ENST00000215637.3	+	4	945	c.899C>A	c.(898-900)cCc>cAc	p.P300H	MADCAM1_ENST00000382683.4_Intron|MADCAM1_ENST00000346144.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000587541.1_Missense_Mutation_p.P81H	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	300	Mucin-like.		P -> H (in dbSNP:rs3745925).		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)		CAGGCTGGGCCCACGCAGGGA	0.667													C|||	1088	0.217252	0.2103	0.2017	5008	,	,		11442	0.3224		0.2386	False		,,,				2504	0.1074				p.P300H		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C899A						PASS	.	C	HIS/PRO,	870,3470		95,680,1395	8.0	9.0	8.0		899,	-0.8	0.0	19	dbSNP_107	8	1715,6805		191,1333,2736	yes	missense,intron	MADCAM1	NM_130760.2,NM_130762.2	77,	286,2013,4131	AA,AC,CC		20.1291,20.0461,20.1011	probably-damaging,	300/383,	501900	2585,10275	2170	4260	6430	SO:0001583	missense	8174	exon4			CTGGGCCCACGCA	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.899C>A	19.37:g.501900C>A	ENSP00000215637:p.Pro300His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	566	0.2591575091575092	102	0.2073170731707317	82	0.2265193370165746	192	0.3356643356643357	190	0.25065963060686014	c	0.244	-1.011721	0.02095	0.200461	0.201291	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10382	2.88	1.75	-0.825	0.10809	.	1.969940	0.03219	U	0.177235	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.67145	0.996	P	0.46172	0.506	T	0.28964	-1.0027	9	0.46703	T	0.11	.	0.5786	0.00708	0.2459:0.3319:0.2439:0.1782	rs3745925;rs58652856;rs3745925	300	Q13477	MADCA_HUMAN	H	324;316;308;300	ENSP00000215637:P300H	ENSP00000215637:P300H	P	+	2	0	MADCAM1	452900	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.049000	0.14099	-0.143000	0.11334	0.650000	0.86243	CCC	C|0.760;A|0.240	0.240	strong		0.667	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
PCDHB7	56129	hgsc.bcm.edu	37	5	140552558	140552558	+	Silent	SNP	T	T	C	rs17096945	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140552558T>C	ENST00000231137.3	+	1	316	c.142T>C	c.(142-144)Ttg>Ctg	p.L48L		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	48	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)			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)			TCTTACCAACTTGGCAAAAGA	0.488													T|||	543	0.108427	0.1029	0.1744	5008	,	,		16638	0.0407		0.1531	False		,,,				2504	0.093				p.L48L		Atlas-SNP	.											PCDHB7,NS,carcinoma,-2,1	PCDHB7	231	1	0			c.T142C						scavenged	.	T		496,3910	231.0+/-245.0	28,440,1735	96.0	96.0	96.0		142	-3.6	0.5	5	dbSNP_123	96	1419,7181	273.5+/-290.7	122,1175,3003	no	coding-synonymous	PCDHB7	NM_018940.2		150,1615,4738	CC,CT,TT		16.5,11.2574,14.724		48/794	140552558	1915,11091	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			ACCAACTTGGCAA	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.142T>C	5.37:g.140552558T>C		Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	180	90	0.5	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			T|0.860;C|0.140	0.140	strong		0.488	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
A1CF	29974	hgsc.bcm.edu	37	10	52573698	52573698	+	Silent	SNP	G	G	A	rs41274048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:52573698G>A	ENST00000373993.1	-	8	1310	c.1266C>T	c.(1264-1266)ctC>ctT	p.L422L	A1CF_ENST00000373995.3_Silent_p.L422L|A1CF_ENST00000373997.3_Silent_p.L414L|A1CF_ENST00000395495.1_Silent_p.L367L|A1CF_ENST00000493415.1_5'UTR|A1CF_ENST00000282641.2_Silent_p.L422L|A1CF_ENST00000374001.2_Silent_p.L414L|A1CF_ENST00000395489.2_Silent_p.L415L|ASAH2B_ENST00000483649.1_Intron			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	422					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						AAATGTCATAGAGTTTGTCTT	0.507													G|||	531	0.10603	0.1498	0.0432	5008	,	,		16897	0.0883		0.0865	False		,,,				2504	0.1299				p.L430L		Atlas-SNP	.											.	A1CF	190	.	0			c.C1290T						PASS	.	G	,,,,,	561,3845	252.1+/-258.6	33,495,1675	156.0	154.0	155.0		1242,1290,1266,1242,1266,1266	5.0	1.0	10	dbSNP_127	155	646,7954	165.2+/-217.4	22,602,3676	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	A1CF	NM_001198818.1,NM_001198819.1,NM_001198820.1,NM_014576.3,NM_138932.2,NM_138933.2	,,,,,	55,1097,5351	AA,AG,GG		7.5116,12.7326,9.2803	,,,,,	414/587,430/603,422/595,414/587,422/595,422/595	52573698	1207,11799	2203	4300	6503	SO:0001819	synonymous_variant	29974	exon12			GTCATAGAGTTTG	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.1266C>T	10.37:g.52573698G>A		Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	190	134	0.705263	NM_001198819	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Silent	SNP	ENST00000373993.1	37	CCDS7242.1																																																																																			G|0.908;A|0.092	0.092	strong		0.507	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576	
P2RY11	5032	hgsc.bcm.edu	37	19	10224526	10224526	+	Silent	SNP	C	C	T	rs3745600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:10224526C>T	ENST00000321826.4	+	2	421	c.237C>T	c.(235-237)gcC>gcT	p.A79A	PPAN-P2RY11_ENST00000393796.4_Silent_p.A499A|PPAN_ENST00000556468.1_Silent_p.A499A|PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.P520L	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	79					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)			TGCTCTGCGCCCTGACGCTGC	0.687											OREG0025230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1830	0.365415	0.149	0.5144	5008	,	,		16363	0.3462		0.4901	False		,,,				2504	0.4438				p.P520L		Atlas-SNP	.											PPAN-P2RY11,caecum,carcinoma,+2,2	PPAN-P2RY11	81	2	0			c.C1559T						PASS	.	C	,LEU/PRO,	972,3434	355.6+/-313.1	100,772,1331	34.0	32.0	33.0		1497,1559,237	-4.4	0.6	19	dbSNP_107	33	3890,4706	534.7+/-382.6	888,2114,1296	yes	coding-synonymous,missense,coding-synonymous	P2RY11,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_002566.4	,98,	988,2886,2627	TT,TC,CC		45.2536,22.0608,37.3942	,,	499/795,520/521,79/375	10224526	4862,8140	2203	4298	6501	SO:0001819	synonymous_variant	692312	exon13			CTGCGCCCTGACG	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	ENST00000321826.4:c.237C>T	19.37:g.10224526C>T		Somatic	112	0	0	663	WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_001198690	B2R8X9|O43190|Q9BYU4|Q9H170	Missense_Mutation	SNP	ENST00000321826.4	37	CCDS12226.1	821	0.3759157509157509	82	0.16666666666666666	184	0.5082872928176796	193	0.3374125874125874	362	0.47757255936675463	C	16.94	3.261297	0.59431	0.220608	0.452536	ENSG00000243207	ENST00000428358	T	0.33865	1.39	4.33	-4.37	0.03633	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999716189	B	0.02656	0.0	B	0.06405	0.002	T	0.49293	-0.8955	7	0.87932	D	0	.	3.5462	0.07829	0.1206:0.3738:0.3544:0.1512	rs3745600	520	C9J3F9	.	L	520	ENSP00000411918:P520L	ENSP00000411918:P520L	P	+	2	0	PPAN-P2RY11	10085526	0.000000	0.05858	0.553000	0.28255	0.283000	0.27025	-0.364000	0.07583	-0.519000	0.06444	0.561000	0.74099	CCC	C|0.631;T|0.369	0.369	strong		0.687	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
GPR18	2841	hgsc.bcm.edu	37	13	99907341	99907341	+	Silent	SNP	G	G	A	rs3742130	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:99907341G>A	ENST00000340807.3	-	3	1342	c.786C>T	c.(784-786)aaC>aaT	p.N262N	GPR18_ENST00000397473.2_Silent_p.N262N|UBAC2_ENST00000376440.2_Intron|GPR18_ENST00000397470.2_Silent_p.N262N|UBAC2_ENST00000403766.3_Intron			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	262					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)			endometrium(2)|large_intestine(2)|lung(6)	10	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Glycine(DB00145)	GATTGTAACTGTTCTCCCCCG	0.498													G|||	543	0.108427	0.0401	0.1499	5008	,	,		19549	0.0595		0.2217	False		,,,				2504	0.1053				p.N262N		Atlas-SNP	.											.	GPR18	23	.	0			c.C786T						PASS	.	G	,,,	362,4044	184.7+/-212.0	13,336,1854	193.0	148.0	163.0		786,,786,	0.1	0.0	13	dbSNP_107	163	1891,6709	336.9+/-322.1	223,1445,2632	no	coding-synonymous,intron,coding-synonymous,intron	GPR18,UBAC2	NM_001098200.1,NM_001144072.1,NM_005292.3,NM_177967.3	,,,	236,1781,4486	AA,AG,GG		21.9884,8.2161,17.3228	,,,	262/332,,262/332,	99907341	2253,10753	2203	4300	6503	SO:0001819	synonymous_variant	2841	exon2			GTAACTGTTCTCC	L42324	CCDS9491.1	13q32	2014-01-30			ENSG00000125245	ENSG00000125245		"""GPCR / Class A : Orphans"""	4472	protein-coding gene	gene with protein product		602042				9205118	Standard	NM_005292		Approved		uc010afv.3	Q14330	OTTHUMG00000017266	ENST00000340807.3:c.786C>T	13.37:g.99907341G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	180	88	0.488889	NM_001098200	Q6GTM3|Q96HI6|Q9H2L2	Silent	SNP	ENST00000340807.3	37	CCDS9491.1																																																																																			G|0.849;A|0.151	0.151	strong		0.498	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1		
SPECC1	92521	hgsc.bcm.edu	37	17	20013802	20013802	+	Silent	SNP	G	G	A	rs3764436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:20013802G>A	ENST00000261503.5	+	3	261	c.210G>A	c.(208-210)gtG>gtA	p.V70V	SPECC1_ENST00000395527.4_Silent_p.V70V|SPECC1_ENST00000395529.3_Silent_p.V70V|SPECC1_ENST00000472876.1_Intron	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	70					cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		CATCGGGGGTGGTTCGCCTGA	0.627													G|||	545	0.108826	0.0787	0.1369	5008	,	,		16233	0.0962		0.1223	False		,,,				2504	0.1288				p.V70V		Atlas-SNP	.											.	SPECC1	100	.	0			c.G210A						PASS	.	G	,	387,4019	191.6+/-217.2	19,349,1835	43.0	45.0	45.0		210,210	-9.5	0.0	17	dbSNP_107	45	1148,7452	234.9+/-267.6	85,978,3237	no	coding-synonymous,coding-synonymous	SPECC1	NM_001033553.2,NM_152904.4	,	104,1327,5072	AA,AG,GG		13.3488,8.7835,11.8022	,	70/1069,70/791	20013802	1535,11471	2203	4300	6503	SO:0001819	synonymous_variant	92521	exon3			GGGGGTGGTTCGC	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.210G>A	17.37:g.20013802G>A		Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	284	127	0.447183	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Silent	SNP	ENST00000261503.5	37	CCDS32590.1																																																																																			G|0.892;A|0.108	0.108	strong		0.627	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
EPHA4	2043	hgsc.bcm.edu	37	2	222301160	222301160	+	Silent	SNP	G	G	T	rs56159060		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:222301160G>T	ENST00000281821.2	-	13	2346	c.2305C>A	c.(2305-2307)Cga>Aga	p.R769R	EPHA4_ENST00000409938.1_Silent_p.R769R|EPHA4_ENST00000409854.1_Silent_p.R769R|EPHA4_ENST00000392071.4_Silent_p.R718R	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	769	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|cell adhesion (GO:0007155)|corticospinal tract morphogenesis (GO:0021957)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|glial cell migration (GO:0008347)|motor neuron axon guidance (GO:0008045)|negative regulation of axon regeneration (GO:0048681)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001108)|protein autophosphorylation (GO:0046777)|regulation of astrocyte differentiation (GO:0048710)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rac GTPase activity (GO:0032314)|regulation of Rap GTPase activity (GO:0032317)	axon (GO:0030424)|axon terminus (GO:0043679)|axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuromuscular junction (GO:0031594)|perikaryon (GO:0043204)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|DH domain binding (GO:0097161)|GPI-linked ephrin receptor activity (GO:0005004)|PH domain binding (GO:0042731)|protein kinase activity (GO:0004672)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|liver(1)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Renal(207;0.0183)		Epithelial(121;5.38e-09)|all cancers(144;2.47e-06)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(261;0.0154)		TCAAGCACTCGGGACATGCCA	0.488																																					p.R769R		Atlas-SNP	.											.	EPHA4	263	.	0			c.C2305A						PASS	.						101.0	83.0	89.0					2																	222301160		2203	4300	6503	SO:0001819	synonymous_variant	2043	exon13			GCACTCGGGACAT	L36645	CCDS2447.1	2q36.3	2013-02-11	2004-10-28		ENSG00000116106	ENSG00000116106	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3388	protein-coding gene	gene with protein product		602188	"""EphA4"""	TYRO1		9267020	Standard	NM_004438		Approved	Hek8	uc002vmq.3	P54764	OTTHUMG00000133142	ENST00000281821.2:c.2305C>A	2.37:g.222301160G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	71	16	0.225352	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Silent	SNP	ENST00000281821.2	37	CCDS2447.1																																																																																			.	.	weak		0.488	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3		
CEP170	9859	hgsc.bcm.edu	37	1	243329075	243329075	+	Silent	SNP	T	T	C	rs61833876		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:243329075T>C	ENST00000366542.1	-	13	2238	c.2187A>G	c.(2185-2187)aaA>aaG	p.K729K	CEP170_ENST00000366544.1_Silent_p.K631K|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Silent_p.K631K	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	206	0	0		WXS	Illumina HiSeq	Phase_I	322	42	0.130435	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	
SLC37A2	219855	hgsc.bcm.edu	37	11	124949044	124949044	+	Silent	SNP	C	C	T	rs33932952|rs373958961	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:124949044C>T	ENST00000403796.2	+	5	652	c.351C>T	c.(349-351)taC>taT	p.Y117Y	SLC37A2_ENST00000407458.1_Silent_p.Y117Y|SLC37A2_ENST00000308074.4_Silent_p.Y117Y|SLC37A2_ENST00000298280.5_Silent_p.Y117Y	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	117					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.Y117Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		TCCGTTACTACCTCTCAGCTG	0.542													C|||	664	0.132588	0.18	0.1023	5008	,	,		20435	0.0605		0.1918	False		,,,				2504	0.1033				p.Y117Y	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											SLC37A2,NS,carcinoma,0,1	SLC37A2	105	1	1	Substitution - coding silent(1)	stomach(1)	c.C351T						PASS	.	C	,	887,3515	344.1+/-307.9	92,703,1406	153.0	147.0	149.0		351,351	4.6	1.0	11	dbSNP_126	149	1719,6879	314.6+/-311.9	172,1375,2752	no	coding-synonymous,coding-synonymous	SLC37A2	NM_001145290.1,NM_198277.2	,	264,2078,4158	TT,TC,CC		19.993,20.1499,20.0462	,	117/502,117/506	124949044	2606,10394	2201	4299	6500	SO:0001819	synonymous_variant	219855	exon5			TTACTACCTCTCA	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.351C>T	11.37:g.124949044C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	354	233	0.658192	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Silent	SNP	ENST00000403796.2	37	CCDS44757.1																																																																																			C|0.814;T|0.186	0.186	strong		0.542	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
SPATA18	132671	hgsc.bcm.edu	37	4	52946023	52946023	+	Silent	SNP	G	G	A	rs79854970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:52946023G>A	ENST00000295213.4	+	9	1667	c.1293G>A	c.(1291-1293)caG>caA	p.Q431Q	SPATA18_ENST00000419395.2_Silent_p.Q399Q	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	431					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)			TTGCAATGCAGGCCTTAGAAC	0.428													G|||	44	0.00878594	0.0008	0.0	5008	,	,		21066	0.0377		0.001	False		,,,				2504	0.0041				p.Q431Q		Atlas-SNP	.											SPATA18_ENST00000295213,NS,carcinoma,0,2	SPATA18	222	2	0			c.G1293A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	245.0	230.0	235.0		1293	4.4	1.0	4	dbSNP_131	235	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SPATA18	NM_145263.2		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		431/539	52946023	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	132671	exon9			AATGCAGGCCTTA	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.1293G>A	4.37:g.52946023G>A		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	221	98	0.443439	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Silent	SNP	ENST00000295213.4	37	CCDS3489.1																																																																																			G|0.995;A|0.005	0.005	strong		0.428	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263	
LMNTD2	256329	hgsc.bcm.edu	37	11	556584	556584	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:556584G>A	ENST00000329451.3	-	9	1043	c.981C>T	c.(979-981)ctC>ctT	p.L327L	RP11-496I9.1_ENST00000527620.1_RNA|RP11-496I9.1_ENST00000527113.1_RNA	NM_173573.2	NP_775844.2	Q8IXW0	LMTD2_HUMAN		327										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)		GGGTTTTCTGGAGATCTAGAG	0.657																																					p.L327L		Atlas-SNP	.											.	C11orf35	22	.	0			c.C981T						PASS	.						20.0	20.0	20.0					11																	556584		2172	4248	6420	SO:0001819	synonymous_variant	256329	exon9			TTTCTGGAGATCT																												ENST00000329451.3:c.981C>T	11.37:g.556584G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	45	28	0.622222	NM_173573		Silent	SNP	ENST00000329451.3	37	CCDS7701.1																																																																																			.	.	none		0.657	C11orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254973.2		
OR10G2	26534	hgsc.bcm.edu	37	14	22102439	22102439	+	Missense_Mutation	SNP	C	C	G	rs35963889	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	473	4	0.00845666		WXS	Illumina HiSeq	Phase_I	429	154	0.358974	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		
JAK1	3716	hgsc.bcm.edu	37	1	65312342	65312342	+	Silent	SNP	G	G	A	rs17127063	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:65312342G>A	ENST00000342505.4	-	14	2225	c.1977C>T	c.(1975-1977)cgC>cgT	p.R659R	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	659	Protein kinase 1. {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)	TCTCCACGTCGCGGACACAGA	0.582			Mis		ALL								G|||	233	0.0465256	0.1309	0.0274	5008	,	,		19095	0.0		0.0298	False		,,,				2504	0.0112				p.R659R		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	JAK1,NS,malignant_melanoma,-1,1	JAK1	209	1	0			c.C1977T						PASS	.	G		461,3823		28,405,1709	83.0	90.0	88.0		1977	-8.6	0.5	1	dbSNP_123	88	231,8311		2,227,4042	no	coding-synonymous	JAK1	NM_002227.2		30,632,5751	AA,AG,GG		2.7043,10.761,5.3953		659/1155	65312342	692,12134	2142	4271	6413	SO:0001819	synonymous_variant	3716	exon14			CACGTCGCGGACA	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.1977C>T	1.37:g.65312342G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	82	56	0.682927	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			G|0.944;A|0.056	0.056	strong		0.582	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
SPECC1	92521	hgsc.bcm.edu	37	17	20108184	20108184	+	Missense_Mutation	SNP	C	C	G	rs9908032	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:20108184C>G	ENST00000261503.5	+	4	873	c.822C>G	c.(820-822)agC>agG	p.S274R	AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000395527.4_Missense_Mutation_p.S274R|SPECC1_ENST00000395529.3_Missense_Mutation_p.S274R|SPECC1_ENST00000395530.2_Missense_Mutation_p.S193R|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395525.3_Missense_Mutation_p.S193R|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395522.2_Missense_Mutation_p.S193R	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	274	Ser-rich.		S -> R (in dbSNP:rs9908032). {ECO:0000269|Ref.1}.		cell adhesion (GO:0007155)	nucleus (GO:0005634)				breast(1)|large_intestine(3)|ovary(4)	8				KIRC - Kidney renal clear cell carcinoma(2;0.166)|Kidney(2;0.196)		GCGACAGCAGCTGCCCAACAT	0.463													C|||	569	0.113618	0.093	0.1455	5008	,	,		18010	0.0942		0.1223	False		,,,				2504	0.1299				p.S274R		Atlas-SNP	.											.	SPECC1	100	.	0			c.C822G						PASS	.	C	ARG/SER,ARG/SER,ARG/SER,ARG/SER	506,3900	223.6+/-240.1	34,438,1731	66.0	75.0	72.0		822,579,579,822	5.4	1.0	17	dbSNP_119	72	1154,7446	234.6+/-267.5	86,982,3232	yes	missense,missense,missense,missense	SPECC1	NM_001033553.2,NM_001033554.2,NM_001033555.2,NM_152904.4	110,110,110,110	120,1420,4963	GG,GC,CC		13.4186,11.4843,12.7633	probably-damaging,probably-damaging,probably-damaging,probably-damaging	274/1069,193/710,193/988,274/791	20108184	1660,11346	2203	4300	6503	SO:0001583	missense	92521	exon4			CAGCAGCTGCCCA	AY816329, AB041533	CCDS32590.1, CCDS42280.1, CCDS42281.1, CCDS45628.1, CCDS58531.1	17p11.2	2012-11-19	2010-09-17	2010-09-17	ENSG00000128487	ENSG00000128487			30615	protein-coding gene	gene with protein product	"""sperm antigen HCMOGT 1"", ""cytokinesis and spindle organization B"", ""cytospin B"""	608793				15602574, 18763323, 15087372	Standard	NM_001033553		Approved	HCMOGT-1, FLJ36955, NSP, CYTSB	uc002gwq.3	Q5M775	OTTHUMG00000179808	ENST00000261503.5:c.822C>G	17.37:g.20108184C>G	ENSP00000261503:p.Ser274Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Missense_Mutation	SNP	ENST00000261503.5	37	CCDS32590.1	229	0.10485347985347986	43	0.08739837398373984	43	0.11878453038674033	47	0.08216783216783216	96	0.1266490765171504	C	20.7	4.031537	0.75504	0.114843	0.134186	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	T;T;T;T	0.67171	-0.25;2.74;2.77;2.76	5.38	5.38	0.77491	.	0.136950	0.64402	D	0.000004	T	0.03477	0.0100	M	0.65498	2.005	0.09310	P	1.0	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.961;0.999;0.999;0.999;0.979	T	0.39542	-0.9609	9	0.59425	D	0.04	-17.4801	17.0048	0.86390	0.0:1.0:0.0:0.0	rs9908032	274;193;193;274;274	A8MV89;Q5M775-4;Q5M775-3;Q5M775-2;Q5M775	.;.;.;.;CYTSB_HUMAN	R	274;274;274;193;193;193	ENSP00000261503:S274R;ENSP00000378900:S274R;ENSP00000378893:S193R;ENSP00000378896:S193R	ENSP00000261503:S274R	S	+	3	2	SPECC1	20048776	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.068000	0.50018	2.698000	0.92095	0.655000	0.94253	AGC	C|0.883;G|0.117	0.117	strong		0.463	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
GNAI1	2770	hgsc.bcm.edu	37	7	79842157	79842157	+	Silent	SNP	T	T	C	rs10241877	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:79842157T>C	ENST00000351004.3	+	7	1219	c.846T>C	c.(844-846)ccT>ccC	p.P282P	GNAI1_ENST00000457358.2_Silent_p.P230P	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	282					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)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						AAAAGAGCCCTCTCACTATAT	0.333													T|||	533	0.10643	0.0098	0.1196	5008	,	,		16091	0.0843		0.1233	False		,,,				2504	0.2331				p.P282P		Atlas-SNP	.											.	GNAI1	44	.	0			c.T846C						PASS	.	T		129,4277	87.8+/-126.4	1,127,2075	66.0	74.0	71.0		846	-1.8	1.0	7	dbSNP_119	71	888,7698	189.4+/-236.2	40,808,3445	no	coding-synonymous	GNAI1	NM_002069.5		41,935,5520	CC,CT,TT		10.3424,2.9278,7.8279		282/355	79842157	1017,11975	2203	4293	6496	SO:0001819	synonymous_variant	2770	exon7			GAGCCCTCTCACT	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"""Gi1 protein alpha subunit"""	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.846T>C	7.37:g.79842157T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	204	65	0.318627	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	37	CCDS5595.1																																																																																			T|0.917;C|0.083	0.083	strong		0.333	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069	
ZNF469	84627	hgsc.bcm.edu	37	16	88502208	88502208	+	Missense_Mutation	SNP	A	A	T	rs3812954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88502208A>T	ENST00000437464.1	+	2	8246	c.8246A>T	c.(8245-8247)gAc>gTc	p.D2749V	ZNF469_ENST00000565624.1_Missense_Mutation_p.D2777V	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2749			D -> V (in dbSNP:rs3812954).		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						CCTGCGGAGGACAGCAGCAGG	0.652													A|||	218	0.0435304	0.0068	0.0432	5008	,	,		16230	0.0427		0.0984	False		,,,				2504	0.0378				p.D2749V		Atlas-SNP	.											.	ZNF469	121	.	0			c.A8246T						PASS	.	A	VAL/ASP	16,1368		1,14,677	45.0	62.0	57.0		8246	2.2	0.0	16	dbSNP_107	57	239,2943		7,225,1359	yes	missense	ZNF469	NM_001127464.1	152	8,239,2036	TT,TA,AA		7.511,1.1561,5.5848	possibly-damaging	2749/3926	88502208	255,4311	692	1591	2283	SO:0001583	missense	84627	exon2			CGGAGGACAGCAG	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.8246A>T	16.37:g.88502208A>T	ENSP00000402343:p.Asp2749Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	63	54	0.857143	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	123	0.05631868131868132	6	0.012195121951219513	23	0.06353591160220995	27	0.0472027972027972	67	0.08839050131926121	A	11.24	1.580640	0.28180	0.011561	0.07511	ENSG00000225614	ENST00000437464	T	0.07567	3.18	4.56	2.24	0.28232	.	.	.	.	.	T	0.00210	0.0006	N	0.19112	0.55	0.80722	P	0.0	P	0.46512	0.879	B	0.37943	0.261	T	0.38887	-0.9640	8	0.62326	D	0.03	.	5.1164	0.14836	0.544:0.3576:0.0984:0.0	rs3812954	2749	Q96JG9	ZN469_HUMAN	V	2749	ENSP00000402343:D2749V	ENSP00000402343:D2749V	D	+	2	0	ZNF469	87029709	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.155000	0.10115	0.136000	0.18733	0.459000	0.35465	GAC	A|0.944;T|0.056	0.056	strong		0.652	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
STT3A	3703	hgsc.bcm.edu	37	11	125479363	125479363	+	Silent	SNP	G	G	A	rs2241502	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125479363G>A	ENST00000529196.1	+	11	1202	c.996G>A	c.(994-996)tcG>tcA	p.S332S	STT3A_ENST00000531491.1_Silent_p.S240S|STT3A_ENST00000392708.4_Silent_p.S332S			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	332					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|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)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		GTTTCTACTCGCTGCTGGATC	0.453													A|||	2100	0.419329	0.5227	0.2752	5008	,	,		19315	0.4335		0.3787	False		,,,				2504	0.409				p.S332S		Atlas-SNP	.											STT3A,NS,carcinoma,+1,1	STT3A	52	1	0			c.G996A						PASS	.	A		2208,2194	588.4+/-386.9	570,1068,563	200.0	189.0	193.0		996	-4.4	0.9	11	dbSNP_98	193	3157,5441	655.5+/-401.3	583,1991,1725	no	coding-synonymous	STT3A	NM_152713.3		1153,3059,2288	AA,AG,GG		36.7178,49.841,41.2692		332/706	125479363	5365,7635	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon10			CTACTCGCTGCTG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.996G>A	11.37:g.125479363G>A		Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	438	291	0.664384	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1	893	0.4088827838827839	280	0.5691056910569106	114	0.3149171270718232	220	0.38461538461538464	279	0.36807387862796836	A	20.3	3.961505	0.74016	0.50159	0.367178	ENSG00000134910	ENST00000526726	.	.	.	5.4	-4.43	0.03568	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47484	-0.9114	3	.	.	.	-7.8117	0.9414	0.01356	0.2588:0.3186:0.2101:0.2125	rs2241502;rs17720009;rs59721461;rs2241502	.	.	.	T	75	.	.	A	+	1	0	STT3A	124984573	0.016000	0.18221	0.950000	0.38849	0.919000	0.55068	-0.694000	0.05115	-0.923000	0.03785	-1.905000	0.00526	GCT	G|0.582;A|0.418	0.418	strong		0.453	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
MLC1	23209	hgsc.bcm.edu	37	22	50502491	50502491	+	Missense_Mutation	SNP	T	T	C	rs11568188	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50502491T>C	ENST00000311597.5	-	11	1637	c.1031A>G	c.(1030-1032)aAc>aGc	p.N344S	MLC1_ENST00000538737.1_Missense_Mutation_p.N310S|MLC1_ENST00000395876.2_Missense_Mutation_p.N344S|MLC1_ENST00000535444.1_Missense_Mutation_p.N265S|MLC1_ENST00000431262.2_Missense_Mutation_p.N314S|MLC1_ENST00000450140.2_Missense_Mutation_p.N292S|MLC1_ENST00000483836.1_5'UTR	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	186	0	0		WXS	Illumina HiSeq	Phase_I	120	14	0.116667	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	
PARD3	56288	hgsc.bcm.edu	37	10	34620220	34620220	+	Silent	SNP	C	C	T	rs3781128	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:34620220C>T	ENST00000374789.3	-	19	2992	c.2667G>A	c.(2665-2667)tcG>tcA	p.S889S	PARD3_ENST00000374790.3_Silent_p.S829S|PARD3_ENST00000466092.1_5'UTR|PARD3_ENST00000374776.1_Silent_p.S843S|PARD3_ENST00000374788.3_Silent_p.S886S|PARD3_ENST00000374794.3_Silent_p.S814S|PARD3_ENST00000350537.4_Silent_p.S843S|PARD3_ENST00000346874.4_Silent_p.S889S|PARD3_ENST00000545260.1_Silent_p.S799S|PARD3_ENST00000545693.1_Silent_p.S873S|PARD3_ENST00000544292.1_Silent_p.S602S|PARD3_ENST00000340077.5_Silent_p.S886S|PARD3_ENST00000374773.1_Silent_p.S856S	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	889	Interacts with PRKCI and PRKCZ. {ECO:0000250}.				apical constriction (GO:0003383)|asymmetric cell division (GO:0008356)|axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|centrosome localization (GO:0051642)|establishment of epithelial cell polarity (GO:0090162)|establishment or maintenance of cell polarity (GO:0007163)|microtubule cytoskeleton organization (GO:0000226)|myelination in peripheral nervous system (GO:0022011)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein targeting to membrane (GO:0006612)|regulation of actin filament-based process (GO:0032970)|regulation of cellular localization (GO:0060341)|tight junction assembly (GO:0070830)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing, spreading of cells (GO:0044319)	apical part of cell (GO:0045177)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|internode region of axon (GO:0033269)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spindle (GO:0005819)|tight junction (GO:0005923)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	63		Breast(68;0.0707)				GACTCTCCAACGAGCTTGACT	0.493													T|||	2753	0.54972	0.7254	0.5173	5008	,	,		15913	0.3919		0.4761	False		,,,				2504	0.5736				p.S889S		Atlas-SNP	.											.	PARD3	131	.	0			c.G2667A						PASS	.	T	,,,,,,,,,,	3105,1301	440.8+/-346.1	1111,883,209	72.0	67.0	69.0		2658,2619,2667,2529,2529,2397,2442,2658,2565,2529,2667	-10.9	0.0	10	dbSNP_107	69	4031,4569	596.6+/-393.6	926,2179,1195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PARD3	NM_001184785.1,NM_001184786.1,NM_001184787.1,NM_001184788.1,NM_001184789.1,NM_001184790.1,NM_001184791.1,NM_001184792.1,NM_001184793.1,NM_001184794.1,NM_019619.3	,,,,,,,,,,	2037,3062,1404	TT,TC,CC		46.8721,29.5279,45.133	,,,,,,,,,,	886/1354,873/1341,889/1320,843/1311,843/1274,799/1267,814/1245,886/1032,855/1001,843/989,889/1357	34620220	7136,5870	2203	4300	6503	SO:0001819	synonymous_variant	56288	exon19			CTCCAACGAGCTT	AF252293	CCDS7178.1, CCDS53509.1, CCDS53510.1, CCDS53511.1, CCDS53512.1, CCDS53513.1, CCDS53514.1, CCDS53515.1, CCDS53516.1	10p11.22	2014-06-13	2013-08-28		ENSG00000148498	ENSG00000148498			16051	protein-coding gene	gene with protein product	"""atypical PKC isotype-specific interacting protein"", ""par-3 family cell polarity regulator alpha"", ""protein phosphatase 1, regulatory subunit 118"""	606745	"""par-3 (partitioning defective 3, C.elegans) homolog"", ""par-3 partitioning defective 3 homolog (C. elegans)"""			10934474	Standard	NM_001184790		Approved	PAR3, PARD3A, Bazooka, Baz, ASIP, PPP1R118	uc010qej.2	Q8TEW0	OTTHUMG00000017948	ENST00000374789.3:c.2667G>A	10.37:g.34620220C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	49	35	0.714286	NM_001184787	F5H5T0|Q5T2U1|Q5VUA2|Q5VUA3|Q5VWV0|Q5VWV1|Q5VWV3|Q5VWV4|Q5VWV5|Q6IQ47|Q8TCZ9|Q8TEW1|Q8TEW2|Q8TEW3|Q96K28|Q96RM6|Q96RM7|Q9BY57|Q9BY58|Q9HC48|Q9NWL4|Q9NYE6	Silent	SNP	ENST00000374789.3	37	CCDS7178.1																																																																																			C|0.459;T|0.541	0.541	strong		0.493	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619	
FAT3	120114	hgsc.bcm.edu	37	11	92568149	92568149	+	Missense_Mutation	SNP	A	A	G	rs75651194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:92568149A>G	ENST00000298047.6	+	14	10002	c.9985A>G	c.(9985-9987)Atc>Gtc	p.I3329V	FAT3_ENST00000525166.1_Missense_Mutation_p.I3179V|FAT3_ENST00000409404.2_Missense_Mutation_p.I3329V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3329	Cadherin 30. {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)				CACTGTCAACATCAACCTCAC	0.498										TCGA Ovarian(4;0.039)			A|||	27	0.00539137	0.0008	0.0115	5008	,	,		16819	0.0		0.0119	False		,,,				2504	0.0061				p.I3329V		Atlas-SNP	.											.	FAT3	1822	.	0			c.A9985G						PASS	.	A	VAL/ILE	2,3912		0,2,1955	50.0	51.0	51.0		9985	3.2	1.0	11	dbSNP_133	51	113,8195		2,109,4043	yes	missense	FAT3	NM_001008781.2	29	2,111,5998	GG,GA,AA		1.3601,0.0511,0.9409	benign	3329/4558	92568149	115,12107	1957	4154	6111	SO:0001583	missense	120114	exon14			GTCAACATCAACC	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.9985A>G	11.37:g.92568149A>G	ENSP00000298047:p.Ile3329Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	183	50	0.273224	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	A	3.371	-0.128480	0.06753	5.11E-4	0.013601	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.35421	1.31;1.31;1.31	5.46	3.17	0.36434	.	.	.	.	.	T	0.15652	0.0377	N	0.20574	0.59	0.80722	D	1	B	0.13594	0.008	B	0.18263	0.021	T	0.04128	-1.0975	9	0.28530	T	0.3	.	8.4034	0.32601	0.7733:0.0:0.2267:0.0	.	3329	Q8TDW7-3	.	V	3329;3329;3179	ENSP00000298047:I3329V;ENSP00000387040:I3329V;ENSP00000432586:I3179V	ENSP00000298047:I3329V	I	+	1	0	FAT3	92207797	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	1.781000	0.38644	0.897000	0.36392	-0.256000	0.11100	ATC	A|0.991;G|0.009	0.009	strong		0.498	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
EHD4	30844	hgsc.bcm.edu	37	15	42235316	42235316	+	Missense_Mutation	SNP	C	C	T	rs11549015	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42235316C>T	ENST00000220325.4	-	3	543	c.460G>A	c.(460-462)Gtc>Atc	p.V154I		NM_139265.3	NP_644670.1	Q9H223	EHD4_HUMAN	EH-domain containing 4	154	Dynamin-type G.		V -> I (in dbSNP:rs11549015).		cellular response to growth factor stimulus (GO:0071363)|endocytic recycling (GO:0032456)|pinocytosis (GO:0006907)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein homooligomerization (GO:0051260)|regulation of endocytosis (GO:0030100)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|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)	p.V154I(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(7)|ovary(2)|stomach(1)|urinary_tract(1)	20		all_cancers(109;2.54e-12)|all_epithelial(112;6.59e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		OV - Ovarian serous cystadenocarcinoma(18;1.6e-19)|GBM - Glioblastoma multiforme(94;3.77e-06)|COAD - Colon adenocarcinoma(120;0.0474)|Colorectal(105;0.0538)		CTGTCGATGACGCTGATGCTC	0.602													T|||	416	0.0830671	0.0113	0.1052	5008	,	,		19426	0.0099		0.174	False		,,,				2504	0.1462				p.V154I		Atlas-SNP	.											EHD4,NS,carcinoma,0,1	EHD4	46	1	1	Substitution - Missense(1)	stomach(1)	c.G460A						PASS	.	T	ILE/VAL	152,4252		6,140,2056	73.0	60.0	65.0		460	4.2	1.0	15	dbSNP_120	65	1432,7162		121,1190,2986	yes	missense	EHD4	NM_139265.3	29	127,1330,5042	TT,TC,CC		16.6628,3.4514,12.1865	benign	154/542	42235316	1584,11414	2202	4297	6499	SO:0001583	missense	30844	exon3			CGATGACGCTGAT	AF181265	CCDS10081.1	15q11.1	2013-01-10			ENSG00000103966	ENSG00000103966		"""EF-hand domain containing"""	3245	protein-coding gene	gene with protein product		605892		PAST4		10673336, 11533061	Standard	NM_139265		Approved		uc001zot.3	Q9H223	OTTHUMG00000130370	ENST00000220325.4:c.460G>A	15.37:g.42235316C>T	ENSP00000220325:p.Val154Ile	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	50	12	0.24	NM_139265	Q9HAR1|Q9NZN2	Missense_Mutation	SNP	ENST00000220325.4	37	CCDS10081.1	187	0.08562271062271062	8	0.016260162601626018	43	0.11878453038674033	5	0.008741258741258742	131	0.17282321899736147	T	6.270	0.417981	0.11870	0.034514	0.166628	ENSG00000103966	ENST00000220325	D	0.94828	-3.53	5.31	4.18	0.49190	Dynamin, GTPase domain (1);	0.050763	0.85682	N	0.000000	T	0.00608	0.0020	N	0.00496	-1.435	0.47341	P	6.070000000000242E-4	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.50189	-0.8857	9	0.02654	T	1	-14.2989	9.7155	0.40272	0.0:0.144:0.0:0.856	rs11549015;rs17739185;rs52802765;rs11549015	154;154	A8K9B9;Q9H223	.;EHD4_HUMAN	I	154	ENSP00000220325:V154I	ENSP00000220325:V154I	V	-	1	0	EHD4	40022608	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.535000	0.45685	0.330000	0.23485	-0.360000	0.07572	GTC	C|0.899;T|0.101	0.101	strong		0.602	EHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252737.2	NM_139265	
PSORS1C2	170680	hgsc.bcm.edu	37	6	31106065	31106065	+	Missense_Mutation	SNP	C	C	T	rs2233950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31106065C>T	ENST00000259845.4	-	2	397	c.74G>A	c.(73-75)gGc>gAc	p.G25D	PSORS1C1_ENST00000547221.1_Intron|PSORS1C1_ENST00000259881.9_Intron|PSORS1C1_ENST00000481450.2_5'Flank	NM_014069.2	NP_054788.2	Q9UIG4	PS1C2_HUMAN	psoriasis susceptibility 1 candidate 2	25			G -> D (in dbSNP:rs2233950). {ECO:0000269|PubMed:12930300}.			extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						AGAGGGGTGGCCCTCGCTGCC	0.677													T|||	252	0.0503195	0.0363	0.049	5008	,	,		11976	0.0734		0.0567	False		,,,				2504	0.0399				p.G25D		Atlas-SNP	.											.	PSORS1C2	11	.	0			c.G74A						PASS	.	T	,ASP/GLY	111,2887		2,107,1390	13.0	13.0	13.0		,74	4.4	0.9	6	dbSNP_98	13	174,5226		3,168,2529	yes	intron,missense	PSORS1C1,PSORS1C2	NM_014068.2,NM_014069.2	,94	5,275,3919	TT,TC,CC		3.2222,3.7025,3.3937	,benign	,25/137	31106065	285,8113	1499	2700	4199	SO:0001583	missense	170680	exon2			GGGTGGCCCTCGC	AB031480	CCDS4694.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204538	ENSG00000204538			17199	protein-coding gene	gene with protein product		613526	"""chromosome 6 open reading frame 17"""	C6orf17			Standard	NM_014069		Approved	SPR1	uc003nso.4	Q9UIG4	OTTHUMG00000031081	ENST00000259845.4:c.74G>A	6.37:g.31106065C>T	ENSP00000259845:p.Gly25Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_014069	Q5STD0	Missense_Mutation	SNP	ENST00000259845.4	37	CCDS4694.1	113	0.051739926739926737	17	0.034552845528455285	11	0.03038674033149171	38	0.06643356643356643	47	0.06200527704485488	T	0.016	-1.538190	0.00942	0.037025	0.032222	ENSG00000204538	ENST00000259845	T	0.16897	2.31	4.43	4.43	0.53597	.	0.139304	0.32671	N	0.005797	T	0.01061	0.0035	N	0.01168	-0.975	0.22292	N	0.999222	B	0.02656	0.0	B	0.01281	0.0	T	0.48445	-0.9035	10	0.02654	T	1	-3.5661	6.8292	0.23900	0.0:0.1072:0.0:0.8928	rs2233950;rs2233950	25	Q9UIG4	PS1C2_HUMAN	D	25	ENSP00000259845:G25D	ENSP00000259845:G25D	G	-	2	0	PSORS1C2	31214044	1.000000	0.71417	0.947000	0.38551	0.032000	0.12392	2.056000	0.41355	0.729000	0.32403	-0.629000	0.03991	GGC	C|0.957;T|0.043	0.043	strong		0.677	PSORS1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076115.3		
ZNF33B	7582	hgsc.bcm.edu	37	10	43089278	43089278	+	Missense_Mutation	SNP	T	T	C	rs71505624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:43089278T>C	ENST00000359467.3	-	5	1234	c.1120A>G	c.(1120-1122)Aaa>Gaa	p.K374E	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	374					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						CTCTGATGTTTAGTGAGGTTT	0.433													t|||	7	0.00139776	0.0	0.0014	5008	,	,		20809	0.0		0.004	False		,,,				2504	0.002				p.K374E	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A1120G						PASS	.	T	GLU/LYS	2,4404	4.2+/-10.8	0,2,2201	117.0	117.0	117.0		1120	2.3	1.0	10	dbSNP_130	117	20,8580	14.6+/-50.1	0,20,4280	yes	missense	ZNF33B	NM_006955.1	56	0,22,6481	CC,CT,TT		0.2326,0.0454,0.1692	probably-damaging	374/779	43089278	22,12984	2203	4300	6503	SO:0001583	missense	7582	exon5			GATGTTTAGTGAG	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.1120A>G	10.37:g.43089278T>C	ENSP00000352444:p.Lys374Glu	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	174	33	0.189655	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	5.009	0.187437	0.09547	4.54E-4	0.002326	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.19394	2.15	2.28	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38548	N	0.001658	T	0.17959	0.0431	N	0.12569	0.235	0.09310	N	1	D	0.76494	0.999	D	0.69479	0.964	T	0.13548	-1.0505	10	0.02654	T	1	.	8.5071	0.33195	0.0:0.0:0.0:1.0	.	374	Q06732	ZN33B_HUMAN	E	374;340	ENSP00000352444:K374E	ENSP00000352444:K374E	K	-	1	0	ZNF33B	42409284	0.000000	0.05858	1.000000	0.80357	0.981000	0.71138	-0.059000	0.11731	1.324000	0.45282	0.341000	0.21757	AAA	T|0.998;C|0.002	0.002	strong		0.433	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955	
DAPK1	1612	hgsc.bcm.edu	37	9	90265015	90265015	+	Silent	SNP	C	C	T	rs3818584	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:90265015C>T	ENST00000408954.3	+	16	1943	c.1608C>T	c.(1606-1608)gaC>gaT	p.D536D	DAPK1_ENST00000469640.2_Silent_p.D536D|DAPK1_ENST00000491893.1_Silent_p.D536D|DAPK1_ENST00000358077.5_Silent_p.D536D|DAPK1_ENST00000472284.1_Silent_p.D536D	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	536					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						ATGGAGCCGACCTTAATGCTT	0.552									Chronic Lymphocytic Leukemia, Familial Clustering of				C|||	1773	0.354034	0.1241	0.5432	5008	,	,		16292	0.5784		0.3748	False		,,,				2504	0.2781				p.D536D		Atlas-SNP	.											DAPK1_ENST00000408954,NS,carcinoma,0,4	DAPK1	329	4	0			c.C1608T						PASS	.	C		603,3323		46,511,1406	50.0	50.0	50.0		1608	1.6	0.9	9	dbSNP_107	50	3141,5141		587,1967,1587	no	coding-synonymous	DAPK1	NM_004938.2		633,2478,2993	TT,TC,CC		37.9256,15.3591,30.6684		536/1431	90265015	3744,8464	1963	4141	6104	SO:0001819	synonymous_variant	1612	exon16	Familial Cancer Database	Familial CLL	AGCCGACCTTAAT	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.1608C>T	9.37:g.90265015C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			C|0.634;T|0.365	0.365	strong		0.552	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
LLGL2	3993	hgsc.bcm.edu	37	17	73566561	73566561	+	Silent	SNP	G	G	A	rs2305525	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	43	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	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	
SEC31B	25956	hgsc.bcm.edu	37	10	102247526	102247526	+	Silent	SNP	G	G	C	rs2298074	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102247526G>C	ENST00000370345.3	-	26	3484	c.3387C>G	c.(3385-3387)ctC>ctG	p.L1129L		NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	1129					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CAACCTCATGGAGCCCAGCCA	0.597													G|||	713	0.142372	0.0401	0.1772	5008	,	,		20066	0.129		0.1998	False		,,,				2504	0.2106				p.L1129L		Atlas-SNP	.											.	SEC31B	84	.	0			c.C3387G						PASS	.	G		263,4143	148.8+/-183.1	11,241,1951	39.0	38.0	39.0		3387	0.7	0.8	10	dbSNP_100	39	1940,6660	332.8+/-320.3	222,1496,2582	no	coding-synonymous	SEC31B	NM_015490.3		233,1737,4533	CC,CG,GG		22.5581,5.9691,16.9383		1129/1180	102247526	2203,10803	2203	4300	6503	SO:0001819	synonymous_variant	25956	exon26			CTCATGGAGCCCA	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.3387C>G	10.37:g.102247526G>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	37	CCDS7495.1																																																																																			G|0.833;C|0.167	0.167	strong		0.597	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
BTN2A2	10385	hgsc.bcm.edu	37	6	26384092	26384092	+	Missense_Mutation	SNP	C	C	T	rs546542545		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26384092C>T	ENST00000356709.4	+	2	154	c.43C>T	c.(43-45)Ctc>Ttc	p.L15F	BTN2A2_ENST00000469230.1_Missense_Mutation_p.L15F|BTN2A2_ENST00000416795.2_Missense_Mutation_p.L15F|BTN2A2_ENST00000432533.2_Missense_Mutation_p.L15F|BTN2A2_ENST00000482536.1_Missense_Mutation_p.L15F|BTN2A2_ENST00000352867.2_Missense_Mutation_p.L15F	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	15					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						GCCAGCCTCcctcctcctcct	0.587																																					p.L15F		Atlas-SNP	.											BTN2A2_ENST00000432533,bladder,carcinoma,-1,2	BTN2A2	87	2	0			c.C43T						scavenged	.						191.0	138.0	156.0					6																	26384092		2203	4300	6503	SO:0001583	missense	10385	exon2			GCCTCCCTCCTCC	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.43C>T	6.37:g.26384092C>T	ENSP00000349143:p.Leu15Phe	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	125	6	0.048	NM_181531	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Missense_Mutation	SNP	ENST00000356709.4	37	CCDS4606.1	.	.	.	.	.	.	.	.	.	.	c	14.03	2.412871	0.42817	.	.	ENSG00000124508	ENST00000469230;ENST00000356709;ENST00000352867;ENST00000493275;ENST00000472507;ENST00000482536;ENST00000432533;ENST00000416795;ENST00000494184;ENST00000483410	T;T;T;T;T;T;D;T;T;T	0.90444	3.76;1.1;0.43;4.24;3.36;-0.21;-2.67;1.1;2.29;3.8	2.01	1.1	0.20463	.	0.656368	0.12607	N	0.454165	T	0.62085	0.2399	N	0.08118	0	0.21675	N	0.999591	B;B;B;B;B;B	0.24132	0.003;0.008;0.098;0.014;0.003;0.003	B;B;B;B;B;B	0.15052	0.002;0.003;0.012;0.006;0.002;0.002	T	0.57562	-0.7790	10	0.87932	D	0	.	4.8159	0.13367	0.0:0.8071:0.0:0.1929	.	15;15;15;15;15;15	E9PH07;B4DQ01;B4E3J1;Q8WVV5-2;A6NM84;Q8WVV5	.;.;.;.;.;BT2A2_HUMAN	F	15	ENSP00000417472:L15F;ENSP00000349143:L15F;ENSP00000337117:L15F;ENSP00000418857:L15F;ENSP00000419226:L15F;ENSP00000419451:L15F;ENSP00000394241:L15F;ENSP00000399308:L15F;ENSP00000417511:L15F;ENSP00000418176:L15F	ENSP00000337117:L15F	L	+	1	0	BTN2A2	26492071	0.000000	0.05858	0.368000	0.25939	0.580000	0.36256	-0.390000	0.07332	0.383000	0.24910	0.298000	0.19748	CTC	.	.	none		0.587	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1		
NOX5	79400	hgsc.bcm.edu	37	15	69328226	69328226	+	Missense_Mutation	SNP	C	C	T	rs12907196	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:69328226C>T	ENST00000388866.3	+	7	1179	c.1138C>T	c.(1138-1140)Ctc>Ttc	p.L380F	NOX5_ENST00000455873.3_Missense_Mutation_p.L345F|NOX5_ENST00000448182.3_Missense_Mutation_p.L334F|NOX5_ENST00000530406.2_Missense_Mutation_p.L352F|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	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	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	
RNF151	146310	hgsc.bcm.edu	37	16	2018554	2018554	+	Silent	SNP	G	G	T	rs114840677	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2018554G>T	ENST00000569714.1	+	4	374	c.366G>T	c.(364-366)gtG>gtT	p.V122V	RNF151_ENST00000569210.2_3'UTR|RNF151_ENST00000321392.3_Silent_p.V121V	NM_174903.4	NP_777563.2	Q2KHN1	RN151_HUMAN	ring finger protein 151	122					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2						CCTCGCAGGTGCCGCGTGGGA	0.706													G|||	191	0.038139	0.0961	0.0187	5008	,	,		15259	0.0		0.0149	False		,,,				2504	0.0368				p.V122V		Atlas-SNP	.											.	RNF151	12	.	0			c.G366T						PASS	.	G		333,3687		13,307,1690	13.0	14.0	13.0		366	1.0	0.0	16	dbSNP_132	13	188,8108		2,184,3962	no	coding-synonymous	RNF151	NM_174903.4		15,491,5652	TT,TG,GG		2.2662,8.2836,4.2303		122/246	2018554	521,11795	2010	4148	6158	SO:0001819	synonymous_variant	146310	exon4			GCAGGTGCCGCGT	BC029501	CCDS58405.1	16p13.3	2013-01-09			ENSG00000179580	ENSG00000179580		"""RING-type (C3HC4) zinc fingers"""	23235	protein-coding gene	gene with protein product						12477932	Standard	NM_174903		Approved		uc002cnt.1	Q2KHN1	OTTHUMG00000176852	ENST00000569714.1:c.366G>T	16.37:g.2018554G>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_174903	Q8NHS5	Silent	SNP	ENST00000569714.1	37	CCDS58405.1																																																																																			G|0.970;T|0.030	0.030	strong		0.706	RNF151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434030.1	NM_174903	
SLC17A9	63910	hgsc.bcm.edu	37	20	61595636	61595636	+	Silent	SNP	C	C	T	rs2248900	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:61595636C>T	ENST00000370351.4	+	8	1010	c.879C>T	c.(877-879)agC>agT	p.S293S	SLC17A9_ENST00000370349.3_Silent_p.S287S|SLC17A9_ENST00000488738.1_3'UTR	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	307	0	0		WXS	Illumina HiSeq	Phase_I	292	150	0.513699	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	
ASIC4	55515	hgsc.bcm.edu	37	2	220399951	220399951	+	Silent	SNP	A	A	G	rs2276643	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220399951A>G	ENST00000347842.3	+	5	1472	c.1458A>G	c.(1456-1458)acA>acG	p.T486T	ASIC4_ENST00000358078.4_Silent_p.T505T	NM_182847.2	NP_878267.2	Q96FT7	ASIC4_HUMAN	acid-sensing (proton-gated) ion channel family member 4	486					ion transmembrane transport (GO:0034220)|sodium ion transmembrane transport (GO:0035725)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)	ion channel activity (GO:0005216)|sodium channel activity (GO:0005272)|sodium ion transmembrane transporter activity (GO:0015081)										GCAACCTGACACGCTATGGGA	0.607													G|||	1297	0.258986	0.466	0.2723	5008	,	,		16038	0.1468		0.2008	False		,,,				2504	0.1452				p.T486T		Atlas-SNP	.											.	.	.	.	0			c.A1458G						PASS	.	G	,	1906,2500	626.8+/-394.8	412,1082,709	57.0	50.0	52.0		1515,1458	-8.9	0.1	2	dbSNP_100	52	1724,6876	736.5+/-407.0	185,1354,2761	no	coding-synonymous,coding-synonymous	ACCN4	NM_018674.4,NM_182847.2	,	597,2436,3470	GG,GA,AA		20.0465,43.2592,27.9102	,	505/667,486/648	220399951	3630,9376	2203	4300	6503	SO:0001819	synonymous_variant	55515	exon5			CCTGACACGCTAT	AJ271643	CCDS2442.1	2q36.1	2012-02-22	2012-02-22	2012-02-22	ENSG00000072182	ENSG00000072182		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	21263	protein-coding gene	gene with protein product		606715	"""amiloride-sensitive cation channel 4, pituitary"", ""amiloride-sensitive cation channel family member 4, pituitary"""	ACCN4		10852210	Standard	NM_182847		Approved	BNAC4	uc002vma.3	Q96FT7	OTTHUMG00000058928	ENST00000347842.3:c.1458A>G	2.37:g.220399951A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	58	49	0.844828	NM_182847	Q53SB7|Q6GMS1|Q6PIN9|Q9NQA4	Silent	SNP	ENST00000347842.3	37	CCDS2442.1																																																																																			A|0.731;G|0.268	0.268	strong		0.607	ASIC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130263.1	NM_018674	
ST3GAL1	6482	hgsc.bcm.edu	37	8	134488007	134488007	+	Silent	SNP	G	G	A	rs2230542	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:134488007G>A	ENST00000319914.5	-	4	1288	c.261C>T	c.(259-261)acC>acT	p.T87T	ST3GAL1_ENST00000399640.2_Silent_p.T87T|ST3GAL1_ENST00000519435.1_5'Flank|ST3GAL1_ENST00000522652.1_Silent_p.T87T|ST3GAL1_ENST00000521180.1_Silent_p.T87T			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	87					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein phosphorylation (GO:0006468)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)	p.T87T(1)		endometrium(3)|large_intestine(2)|lung(11)|prostate(1)	17	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			CGTTCTGGGCGGTCAGCAGCG	0.627													G|||	2206	0.440495	0.5893	0.4308	5008	,	,		18010	0.1657		0.501	False		,,,				2504	0.4673				p.T87T		Atlas-SNP	.											ST3GAL1,NS,carcinoma,0,1	ST3GAL1	39	1	1	Substitution - coding silent(1)	prostate(1)	c.C261T						PASS	.	G	,	2535,1871	627.4+/-394.9	754,1027,422	54.0	42.0	46.0		261,261	-10.9	0.0	8	dbSNP_98	46	4686,3914	600.9+/-394.3	1272,2142,886	no	coding-synonymous,coding-synonymous	ST3GAL1	NM_003033.3,NM_173344.2	,	2026,3169,1308	AA,AG,GG		45.5116,42.4648,44.4795	,	87/341,87/341	134488007	7221,5785	2203	4300	6503	SO:0001819	synonymous_variant	6482	exon5			CTGGGCGGTCAGC	L29555	CCDS6373.1	8q24.22	2013-03-01	2003-01-14	2005-02-07	ENSG00000008513	ENSG00000008513	2.4.99.4	"""Sialyltransferases"""	10862	protein-coding gene	gene with protein product	"""ST3Gal I"""	607187	"""sialyltransferase 4A (beta-galactosidase alpha-2,3-sialytransferase)"""	SIAT4A		10504389, 7655169	Standard	NM_003033		Approved	ST3O, SIATFL, ST3GalA.1	uc003yuk.2	Q11201	OTTHUMG00000164534	ENST00000319914.5:c.261C>T	8.37:g.134488007G>A		Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_173344	O60677|Q9UN51	Silent	SNP	ENST00000319914.5	37	CCDS6373.1																																																																																			G|0.495;A|0.505	0.505	strong		0.627	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379132.1	NM_003033	
NLRP4	147945	hgsc.bcm.edu	37	19	56392875	56392875	+	Silent	SNP	T	T	G	rs302456	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56392875T>G	ENST00000301295.6	+	10	3329	c.2907T>G	c.(2905-2907)ctT>ctG	p.L969L	NLRP4_ENST00000587891.1_Silent_p.L894L|NLRP4_ENST00000346986.5_Silent_p.L913L	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						PASS	.	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	61	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	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	
HEG1	57493	hgsc.bcm.edu	37	3	124739892	124739892	+	Silent	SNP	G	G	A	rs6438874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:124739892G>A	ENST00000311127.4	-	4	1063	c.996C>T	c.(994-996)gcC>gcT	p.A332A	HEG1_ENST00000477536.1_5'Flank	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	332					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						TGAACACGGTGGCAACATGCA	0.498													G|||	2552	0.509585	0.4561	0.4769	5008	,	,		20452	0.4772		0.5437	False		,,,				2504	0.6033				p.A332A		Atlas-SNP	.											.	HEG1	109	.	0			c.C996T						PASS	.	G		1752,2302		373,1006,648	67.0	67.0	67.0		996	-4.2	0.0	3	dbSNP_116	67	4254,4152		1058,2138,1007	no	coding-synonymous	HEG1	NM_020733.1		1431,3144,1655	AA,AG,GG		49.3933,43.2166,48.2022		332/1382	124739892	6006,6454	2027	4203	6230	SO:0001819	synonymous_variant	57493	exon4			CACGGTGGCAACA	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.996C>T	3.37:g.124739892G>A		Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	223	106	0.475336	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Silent	SNP	ENST00000311127.4	37	CCDS46898.1																																																																																			G|0.510;A|0.490	0.490	strong		0.498	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
ZNF813	126017	hgsc.bcm.edu	37	19	53995004	53995004	+	Silent	SNP	G	G	A	rs2708845	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53995004G>A	ENST00000396403.4	+	4	1646	c.1518G>A	c.(1516-1518)cgG>cgA	p.R506R	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	506					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)		GTTTTAATCGGAAAACACACC	0.403													.|||	3921	0.782947	0.9304	0.8084	5008	,	,		24042	0.6498		0.7485	False		,,,				2504	0.7382				p.R506R		Atlas-SNP	.											ZNF813_ENST00000396403,colon,carcinoma,+1,1	ZNF813	81	1	0			c.G1518A						scavenged	.	G		3949,449		1780,389,30	49.0	53.0	52.0		1518	-2.6	0.0	19	dbSNP_100	52	6290,2308		2323,1644,332	no	coding-synonymous	ZNF813	NM_001004301.3		4103,2033,362	AA,AG,GG		26.8435,10.2092,21.2142		506/618	53995004	10239,2757	2199	4299	6498	SO:0001819	synonymous_variant	126017	exon4			TAATCGGAAAACA	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.1518G>A	19.37:g.53995004G>A		Somatic	202	3	0.0148515		WXS	Illumina HiSeq	Phase_I	170	73	0.429412	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			G|0.248;A|0.752	0.752	strong		0.403	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
HGFAC	3083	hgsc.bcm.edu	37	4	3446132	3446132	+	Missense_Mutation	SNP	C	C	G	rs111368413|rs1987546	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:3446132C>G	ENST00000382774.3	+	6	808	c.693C>G	c.(691-693)ttC>ttG	p.F231L	HGFAC_ENST00000511533.1_Missense_Mutation_p.F231L	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	231	Fibronectin type-I. {ECO:0000255|PROSITE- ProRule:PRU00478}.		F -> L (in dbSNP:rs1987546). {ECO:0000269|PubMed:15489334}.		proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|rough endoplasmic reticulum (GO:0005791)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GCGAGTGCTTCGGGGGCCGGA	0.677													G|||	3676	0.734026	0.6619	0.7262	5008	,	,		15879	0.9236		0.7197	False		,,,				2504	0.6564				p.F231L		Atlas-SNP	.											.	HGFAC	69	.	0			c.C693G						PASS	.	G	LEU/PHE	2876,1482		989,898,292	11.0	13.0	12.0		693	-2.2	0.0	4	dbSNP_92	12	5811,2755		2018,1775,490	no	missense	HGFAC	NM_001528.2	22	3007,2673,782	GG,GC,CC		32.162,34.0064,32.784	benign	231/656	3446132	8687,4237	2179	4283	6462	SO:0001583	missense	3083	exon6			GTGCTTCGGGGGC	D14012	CCDS3369.1, CCDS75098.1	4p16	2008-02-07			ENSG00000109758	ENSG00000109758	3.4.21.-		4894	protein-coding gene	gene with protein product		604552				7683665, 8226803	Standard	XM_005247966		Approved	HGFAP, HGFA	uc003ghc.3	Q04756	OTTHUMG00000090281	ENST00000382774.3:c.693C>G	4.37:g.3446132C>G	ENSP00000372224:p.Phe231Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	74	0.973684	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	1683	0.7706043956043956	326	0.6626016260162602	263	0.7265193370165746	536	0.9370629370629371	558	0.7361477572559367	G	0.365	-0.937015	0.02340	0.659936	0.67838	ENSG00000109758	ENST00000382774;ENST00000511533	T;T	0.37584	1.19;1.19	3.61	-2.24	0.06909	Fibronectin, type I (4);	2.027680	0.02261	N	0.067530	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;0.001	T	0.36089	-0.9762	9	0.26408	T	0.33	.	8.6734	0.34165	0.0:0.4709:0.1813:0.3478	rs1987546;rs60554660	231;231	D6RAR4;Q04756	.;HGFA_HUMAN	L	231	ENSP00000372224:F231L;ENSP00000421801:F231L	ENSP00000372224:F231L	F	+	3	2	HGFAC	3415930	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-3.770000	0.00371	-0.409000	0.07553	-0.647000	0.03941	TTC	C|0.293;G|0.707	0.707	strong		0.677	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
DPYD	1806	hgsc.bcm.edu	37	1	97915624	97915624	+	Silent	SNP	A	A	G	rs17376848	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:97915624A>G	ENST00000370192.3	-	14	1996	c.1896T>C	c.(1894-1896)ttT>ttC	p.F632F		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	632					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)	CGTTGTCTGGAAAGTCAGCCT	0.363													A|||	261	0.0521166	0.0136	0.0821	5008	,	,		17356	0.1141		0.0368	False		,,,				2504	0.0348				p.F632F		Atlas-SNP	.											.	DPYD	219	.	0			c.T1896C						PASS	.	A		91,4315	76.8+/-115.0	1,89,2113	153.0	142.0	146.0		1896	-2.6	1.0	1	dbSNP_123	146	387,8213	123.9+/-182.7	6,375,3919	no	coding-synonymous	DPYD	NM_000110.3		7,464,6032	GG,GA,AA		4.5,2.0654,3.6752		632/1026	97915624	478,12528	2203	4300	6503	SO:0001819	synonymous_variant	1806	exon14			GTCTGGAAAGTCA	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.1896T>C	1.37:g.97915624A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	96	67	0.697917	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Silent	SNP	ENST00000370192.3	37	CCDS30777.1																																																																																			A|0.951;G|0.049	0.049	strong		0.363	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259822	71259822	+	Missense_Mutation	SNP	A	A	G	rs10792769	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:71259822A>G	ENST00000528743.2	+	1	357	c.119A>G	c.(118-120)tAc>tGc	p.Y40C		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	40	8 X 4 AA repeats of C-C-X-P.		Y -> C (in dbSNP:rs10792769). {ECO:0000269|Ref.3}.		epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						GCACCCGTCTACTGCTGCAAG	0.662													N|||	989	0.197484	0.4062	0.1455	5008	,	,		17872	0.1329		0.1362	False		,,,				2504	0.0818				p.Y40C		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.A119G						PASS	.	G	CYS/TYR	1598,2802		316,966,918	83.0	94.0	90.0		119	1.6	0.9	11	dbSNP_120	90	1063,7525		68,927,3299	no	missense	KRTAP5-9	NM_005553.3	194	384,1893,4217	GG,GA,AA		12.3777,36.3182,20.4881	benign	40/170	71259822	2661,10327	2200	4294	6494	SO:0001583	missense	3846	exon1			CCGTCTACTGCTG	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.119A>G	11.37:g.71259822A>G	ENSP00000431443:p.Tyr40Cys	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	242	120	0.495868	NM_005553	Q14564|Q3MIP8	Missense_Mutation	SNP	ENST00000528743.2	37	CCDS53677.1	400	0.18315018315018314	178	0.3617886178861789	51	0.1408839779005525	70	0.12237762237762238	101	0.13324538258575197	N	6.676	0.493371	0.12702	0.363182	0.123777	ENSG00000254997	ENST00000528743	T	0.02579	4.24	1.57	1.57	0.23409	.	.	.	.	.	T	0.00012	0.0000	N	0.00004	-3.37	0.48236	P	3.8800000000005497E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.42982	-0.9419	8	0.02654	T	1	.	4.1148	0.10076	0.3975:0.0:0.6025:0.0	rs10792769;rs10792769	40	P26371	KRA59_HUMAN	C	40	ENSP00000431443:Y40C	ENSP00000431443:Y40C	Y	+	2	0	KRTAP5-9	70937470	0.994000	0.37717	0.931000	0.37212	0.616000	0.37450	0.754000	0.26390	0.236000	0.21180	-0.391000	0.06502	TAC	A|0.819;G|0.181	0.181	strong		0.662	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
MUC17	140453	hgsc.bcm.edu	37	7	100678407	100678407	+	Missense_Mutation	SNP	G	G	A	rs4729649	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678407G>A	ENST00000306151.4	+	3	3774	c.3710G>A	c.(3709-3711)aGc>aAc	p.S1237N		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1237	59 X approximate tandem repeats.|Ser-rich.				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)					TCTGAGGCTAGCACCCTTTCA	0.527													G|||	989	0.197484	0.2663	0.0893	5008	,	,		29474	0.2212		0.1083	False		,,,				2504	0.2485				p.S1237N		Atlas-SNP	.											MUC17,caecum,carcinoma,0,1	MUC17	804	1	0			c.G3710A						scavenged	.	G	ASN/SER	354,4052	149.2+/-183.4	0,354,1849	303.0	291.0	295.0		3710	-1.7	0.0	7	dbSNP_111	295	220,8380	66.0+/-128.3	0,220,4080	no	missense	MUC17	NM_001040105.1	46	0,574,5929	AA,AG,GG		2.5581,8.0345,4.4133	benign	1237/4494	100678407	574,12432	2203	4300	6503	SO:0001583	missense	140453	exon3			AGGCTAGCACCCT	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.3710G>A	7.37:g.100678407G>A	ENSP00000302716:p.Ser1237Asn	Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	244	68	0.278689	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.984	-0.696233	0.03279	0.080345	0.025581	ENSG00000169876	ENST00000306151	T	0.02606	4.23	0.838	-1.68	0.08212	.	.	.	.	.	T	0.00144	0.0004	L	0.29908	0.895	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.47235	-0.9133	9	0.26408	T	0.33	.	2.9027	0.05711	0.0:0.3166:0.4155:0.2679	rs4729649	1237	Q685J3	MUC17_HUMAN	N	1237	ENSP00000302716:S1237N	ENSP00000302716:S1237N	S	+	2	0	MUC17	100465127	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-2.728000	0.00807	-1.139000	0.02881	0.134000	0.15878	AGC	G|0.948;A|0.052	0.052	strong		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MUC17	140453	hgsc.bcm.edu	37	7	100681345	100681345	+	Missense_Mutation	SNP	T	T	G	rs142097516		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681345T>G	ENST00000306151.4	+	3	6712	c.6648T>G	c.(6646-6648)agT>agG	p.S2216R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2216	59 X approximate tandem repeats.|Ser-rich.				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)					CAACTCCTAGTGAAGGAAGCA	0.507																																					p.S2216R		Atlas-SNP	.											.	MUC17	804	.	0			c.T6648G						PASS	.						343.0	338.0	340.0					7																	100681345		2203	4300	6503	SO:0001583	missense	140453	exon3			TCCTAGTGAAGGA	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.6648T>G	7.37:g.100681345T>G	ENSP00000302716:p.Ser2216Arg	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	249	23	0.0923695	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	T	2.901	-0.227411	0.06022	.	.	ENSG00000169876	ENST00000306151	T	0.02606	4.23	1.11	-2.01	0.07410	.	.	.	.	.	T	0.01489	0.0048	N	0.14661	0.345	0.09310	N	1	B	0.24963	0.115	B	0.13407	0.009	T	0.49351	-0.8949	9	0.18710	T	0.47	.	4.0824	0.09932	0.3049:0.0:0.0:0.695	.	2216	Q685J3	MUC17_HUMAN	R	2216	ENSP00000302716:S2216R	ENSP00000302716:S2216R	S	+	3	2	MUC17	100468065	0.013000	0.17824	0.006000	0.13384	0.003000	0.03518	-0.741000	0.04855	0.459000	0.27016	0.113000	0.15668	AGT	.	.	weak		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PTPRN	5798	hgsc.bcm.edu	37	2	220162015	220162015	+	Silent	SNP	C	C	G	rs17847406	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220162015C>G	ENST00000295718.2	-	14	2268	c.2028G>C	c.(2026-2028)ccG>ccC	p.P676P	PTPRN_ENST00000423636.2_Silent_p.P586P|PTPRN_ENST00000497977.1_5'Flank|PTPRN_ENST00000409251.3_Silent_p.P647P|AC114803.3_ENST00000417355.1_RNA	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	676					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)		CGCACCAGGACGGGGTGCTGC	0.662													C|||	320	0.0638978	0.0234	0.072	5008	,	,		16733	0.0437		0.0895	False		,,,				2504	0.1074				p.P676P		Atlas-SNP	.											PTPRN,NS,carcinoma,-1,1	PTPRN	138	1	0			c.G2028C						PASS	.	C	,,	153,4253	99.4+/-138.0	3,147,2053	53.0	52.0	52.0		1941,1758,2028	-7.8	0.1	2	dbSNP_123	52	870,7730	190.3+/-236.8	51,768,3481	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN	NM_001199763.1,NM_001199764.1,NM_002846.3	,,	54,915,5534	GG,GC,CC		10.1163,3.4725,7.8656	,,	647/951,586/890,676/980	220162015	1023,11983	2203	4300	6503	SO:0001819	synonymous_variant	5798	exon14			CCAGGACGGGGTG		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.2028G>C	2.37:g.220162015C>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	128	31	0.242188	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Silent	SNP	ENST00000295718.2	37	CCDS2440.1																																																																																			C|0.921;G|0.079	0.079	strong		0.662	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2		
COL9A3	1299	hgsc.bcm.edu	37	20	61463522	61463522	+	Missense_Mutation	SNP	C	C	A	rs751557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:61463522C>A	ENST00000343916.3	+	25	1307	c.1304C>A	c.(1303-1305)gCa>gAa	p.A435E		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	435	Triple-helical region 3 (COL3).		A -> E (in dbSNP:rs751557). {ECO:0000269|PubMed:11565064, ECO:0000269|PubMed:8586434}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					GGAGGTGCCGCAGGCCCTAAG	0.602													C|||	1066	0.212859	0.447	0.1729	5008	,	,		20947	0.0496		0.2177	False		,,,				2504	0.0879				p.A435E		Atlas-SNP	.											COL9A3,caecum,carcinoma,0,1	COL9A3	70	1	0			c.C1304A						scavenged	.	C	GLU/ALA	1747,2659	513.9+/-368.5	338,1071,794	58.0	61.0	60.0		1304	4.2	0.4	20	dbSNP_86	60	1774,6826	317.9+/-313.4	185,1404,2711	yes	missense	COL9A3	NM_001853.3	107	523,2475,3505	AA,AC,CC		20.6279,39.6505,27.0721	probably-damaging	435/685	61463522	3521,9485	2203	4300	6503	SO:0001583	missense	1299	exon25			GTGCCGCAGGCCC	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.1304C>A	20.37:g.61463522C>A	ENSP00000341640:p.Ala435Glu	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_001853	Q13681|Q9H4G9|Q9UPE2	Missense_Mutation	SNP	ENST00000343916.3	37	CCDS13505.1	464	0.21245421245421245	204	0.4146341463414634	66	0.18232044198895028	32	0.055944055944055944	162	0.21372031662269128	C	10.51	1.371130	0.24771	0.396505	0.206279	ENSG00000092758	ENST00000343916	D	0.93712	-3.27	5.2	4.23	0.50019	.	0.843935	0.10592	N	0.656672	T	0.00012	0.0000	N	0.05078	-0.115	0.80722	P	0.0	B	0.23185	0.081	B	0.25506	0.061	T	0.04664	-1.0935	9	0.07325	T	0.83	.	12.5103	0.56002	0.0:0.868:0.0:0.132	rs751557;rs59729765;rs751557	435	Q14050	CO9A3_HUMAN	E	435	ENSP00000341640:A435E	ENSP00000341640:A435E	A	+	2	0	COL9A3	60933967	0.003000	0.15002	0.425000	0.26659	0.227000	0.25037	0.934000	0.28910	2.584000	0.87258	0.462000	0.41574	GCA	T|0.003;G|0.006	.	strong		0.602	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
OR10Z1	128368	hgsc.bcm.edu	37	1	158577109	158577109	+	Missense_Mutation	SNP	A	A	C	rs857685	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158577109A>C	ENST00000361284.1	+	1	881	c.881A>C	c.(880-882)aAt>aCt	p.N294T		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	294			N -> T (in dbSNP:rs857685). {ECO:0000269|Ref.3}.			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(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					AGTCTAAGGAATAGGGCTATA	0.468													A|||	1213	0.242212	0.0658	0.2983	5008	,	,		21019	0.495		0.2634	False		,,,				2504	0.1585				p.N294T		Atlas-SNP	.											.	OR10Z1	99	.	0			c.A881C						PASS	.	A	THR/ASN	432,3974	210.2+/-230.7	16,400,1787	181.0	183.0	182.0		881	5.2	0.9	1	dbSNP_86	182	2170,6430	370.0+/-335.7	290,1590,2420	yes	missense	OR10Z1	NM_001004478.1	65	306,1990,4207	CC,CA,AA		25.2326,9.8048,20.0062	probably-damaging	294/314	158577109	2602,10404	2203	4300	6503	SO:0001583	missense	128368	exon1			TAAGGAATAGGGC	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"""GPCR / Class A : Olfactory receptors"""	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.881A>C	1.37:g.158577109A>C	ENSP00000354707:p.Asn294Thr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	224	129	0.575893	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	595	0.2724358974358974	38	0.07723577235772358	101	0.27900552486187846	252	0.4405594405594406	204	0.2691292875989446	A	12.87	2.067421	0.36470	0.098048	0.252326	ENSG00000198967	ENST00000361284	T	0.47528	0.84	5.19	5.19	0.71726	.	0.000000	0.40818	N	0.001014	T	0.48607	0.1509	L	0.34521	1.04	0.53688	P	2.6999999999999247E-5	D	0.89917	1.0	D	0.78314	0.991	T	0.57382	-0.7821	9	0.87932	D	0	.	14.1654	0.65473	1.0:0.0:0.0:0.0	rs857685;rs52811497;rs857685	294	Q8NGY1	O10Z1_HUMAN	T	294	ENSP00000354707:N294T	ENSP00000354707:N294T	N	+	2	0	OR10Z1	156843733	1.000000	0.71417	0.901000	0.35422	0.564000	0.35744	5.936000	0.70153	2.170000	0.68504	0.528000	0.53228	AAT	A|0.766;C|0.234	0.234	strong		0.468	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
TMEM52B	120939	hgsc.bcm.edu	37	12	10339178	10339178	+	Silent	SNP	C	C	T	rs4764308	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:10339178C>T	ENST00000381923.2	+	5	701	c.297C>T	c.(295-297)agC>agT	p.S99S	TMEM52B_ENST00000298530.3_Silent_p.S79S|TMEM52B_ENST00000536952.1_Silent_p.S99S			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	99						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CTCTCCAGAGCACTATCACAT	0.507													C|||	67	0.0133786	0.0023	0.013	5008	,	,		14362	0.0		0.0477	False		,,,				2504	0.0072				p.S79S		Atlas-SNP	.											.	.	.	.	0			c.C237T						PASS	.	C		44,4362	47.5+/-82.1	1,42,2160	82.0	76.0	78.0		237	2.4	0.9	12	dbSNP_111	78	392,8208	125.8+/-184.4	15,362,3923	no	coding-synonymous	C12orf59	NM_153022.2		16,404,6083	TT,TC,CC		4.5581,0.9986,3.3523		79/164	10339178	436,12570	2203	4300	6503	SO:0001819	synonymous_variant	120939	exon3			CCAGAGCACTATC	AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 59"""	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.297C>T	12.37:g.10339178C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	92	33	0.358696	NM_153022	Q96NA7	Silent	SNP	ENST00000381923.2	37																																																																																				C|0.970;T|0.030	0.030	strong		0.507	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022	
FAM189A1	23359	hgsc.bcm.edu	37	15	29421054	29421054	+	Missense_Mutation	SNP	C	C	T	rs2306933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:29421054C>T	ENST00000261275.4	-	8	940	c.941G>A	c.(940-942)gGt>gAt	p.G314D		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	314	Pro-rich.		G -> D (in dbSNP:rs2306933).			integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						CACCTGCTGACCTATACTTGT	0.552													T|||	677	0.135184	0.1263	0.1138	5008	,	,		16994	0.2093		0.0706	False		,,,				2504	0.1524				p.G314D		Atlas-SNP	.											.	FAM189A1	20	.	0			c.G941A						PASS	.	T	ASP/GLY	160,1224		10,140,542	53.0	54.0	54.0		941	2.7	0.0	15	dbSNP_100	54	230,2952		11,208,1372	yes	missense	FAM189A1	NM_015307.1	94	21,348,1914	TT,TC,CC		7.2282,11.5607,8.5414	benign	314/540	29421054	390,4176	692	1591	2283	SO:0001583	missense	23359	exon8			TGCTGACCTATAC		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.941G>A	15.37:g.29421054C>T	ENSP00000261275:p.Gly314Asp	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	45	29	0.644444	NM_015307	A0PK09	Missense_Mutation	SNP	ENST00000261275.4	37	CCDS45198.1	260	0.11904761904761904	56	0.11382113821138211	35	0.09668508287292818	121	0.21153846153846154	48	0.0633245382585752	T	0.011	-1.701260	0.00725	0.115607	0.072282	ENSG00000104059	ENST00000261275	T	0.02737	4.18	5.07	2.73	0.32206	.	0.239743	0.41001	N	0.000968	T	0.00012	0.0000	N	0.00159	-1.955	0.53005	P	3.2999999999949736E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.42582	-0.9443	9	0.02654	T	1	-16.8578	7.6984	0.28608	0.0:0.2482:0.0:0.7518	rs2306933;rs59289923;rs2306933	314	O60320	F1891_HUMAN	D	314	ENSP00000261275:G314D	ENSP00000261275:G314D	G	-	2	0	FAM189A1	27208346	0.944000	0.32072	0.004000	0.12327	0.014000	0.08584	1.419000	0.34793	0.048000	0.15891	-0.254000	0.11334	GGT	C|0.877;T|0.123	0.123	strong		0.552	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
CNGB1	1258	hgsc.bcm.edu	37	16	57996932	57996932	+	Silent	SNP	G	G	A	rs17821448	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57996932G>A	ENST00000251102.8	-	5	387	c.327C>T	c.(325-327)ggC>ggT	p.G109G	CNGB1_ENST00000311183.4_Silent_p.G109G|CNGB1_ENST00000564448.1_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	95	0	0		WXS	Illumina HiSeq	Phase_I	77	74	0.961039	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	
PRR5L	79899	hgsc.bcm.edu	37	11	36472800	36472800	+	Silent	SNP	A	A	G	rs3740958	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:36472800A>G	ENST00000378867.3	+	9	982	c.627A>G	c.(625-627)caA>caG	p.Q209Q	PRR5L_ENST00000527487.1_Intron|PRR5L_ENST00000311599.5_Silent_p.Q136Q|PRR5L_ENST00000389693.3_3'UTR|PRR5L_ENST00000530639.1_Silent_p.Q209Q	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	209					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)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						GTTATTTGCAACTGGAGGAGC	0.537													A|||	1025	0.204673	0.1679	0.111	5008	,	,		23939	0.377		0.1282	False		,,,				2504	0.2219				p.Q209Q		Atlas-SNP	.											.	PRR5L	35	.	0			c.A627G						PASS	.	A	,,,	720,3684	296.4+/-284.2	46,628,1528	185.0	160.0	168.0		627,243,,627	2.2	1.0	11	dbSNP_107	168	1111,7485	229.3+/-264.0	77,957,3264	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	PRR5L	NM_001160167.1,NM_001160168.1,NM_001160169.1,NM_024841.4	,,,	123,1585,4792	GG,GA,AA		12.9246,16.3488,14.0846	,,,	209/369,81/241,,209/369	36472800	1831,11169	2202	4298	6500	SO:0001819	synonymous_variant	79899	exon9			TTTGCAACTGGAG		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.627A>G	11.37:g.36472800A>G		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	278	134	0.482014	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Silent	SNP	ENST00000378867.3	37	CCDS31463.1																																																																																			A|0.833;G|0.167	0.167	strong		0.537	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841	
TBPL2	387332	hgsc.bcm.edu	37	14	55907172	55907172	+	Missense_Mutation	SNP	C	C	G	rs8019270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:55907172C>G	ENST00000247219.5	-	1	162	c.92G>C	c.(91-93)cGg>cCg	p.R31P		NM_199047.2	NP_950248.1			TATA box binding protein like 2											endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8						CTCCATGGACCGTAATCCCAC	0.662													G|||	3429	0.684704	0.8079	0.7291	5008	,	,		14117	0.6349		0.5984	False		,,,				2504	0.6268				p.R31P		Atlas-SNP	.											TBPL2,NS,carcinoma,0,2	TBPL2	27	2	0			c.G92C						PASS	.	G	PRO/ARG	3369,971		1333,703,134	38.0	40.0	40.0		92	-4.0	0.0	14	dbSNP_116	40	4943,3589		1495,1953,818	yes	missense	TBPL2	NM_199047.2	103	2828,2656,952	GG,GC,CC		42.0652,22.3733,35.4257	benign	31/376	55907172	8312,4560	2170	4266	6436	SO:0001583	missense	387332	exon1			ATGGACCGTAATC	AY457923	CCDS9724.1	14q22.2	2004-06-03			ENSG00000182521	ENSG00000182521			19841	protein-coding gene	gene with protein product		608964				14634207	Standard	NM_199047		Approved	TRF3, TBP2	uc001xby.3	Q6SJ96	OTTHUMG00000140313	ENST00000247219.5:c.92G>C	14.37:g.55907172C>G	ENSP00000247219:p.Arg31Pro	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	134	54	0.402985	NM_199047		Missense_Mutation	SNP	ENST00000247219.5	37	CCDS9724.1	1477	0.6762820512820513	387	0.7865853658536586	272	0.7513812154696132	366	0.6398601398601399	452	0.5963060686015831	G	5.876	0.345715	0.11126	0.776267	0.579348	ENSG00000182521	ENST00000247219	T	0.45276	0.9	3.12	-3.98	0.04082	.	1.197560	0.06202	N	0.683464	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	0.33523	-0.9865	9	0.38643	T	0.18	8.6782	6.0453	0.19755	0.2829:0.2463:0.4707:0.0	rs8019270;rs52821151;rs8019270	31	Q6SJ96	TBPL2_HUMAN	P	31	ENSP00000247219:R31P	ENSP00000247219:R31P	R	-	2	0	TBPL2	54976925	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.407000	0.07178	-1.351000	0.02197	-1.567000	0.00876	CGG	C|0.350;G|0.650	0.650	strong		0.662	TBPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276916.1	NM_199047	
RRM1	6240	hgsc.bcm.edu	37	11	4154851	4154851	+	Missense_Mutation	SNP	T	T	C	rs145770432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4154851T>C	ENST00000300738.5	+	17	2168	c.1964T>C	c.(1963-1965)aTg>aCg	p.M655T	RRM1_ENST00000534285.1_Missense_Mutation_p.M433T|RRM1_ENST00000423050.2_Missense_Mutation_p.M558T|RRM1_ENST00000537197.1_Missense_Mutation_p.M317T	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	655					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)	CATGAAGAGATGAAAAACCAG	0.403													T|||	2	0.000399361	0.0	0.0	5008	,	,		20309	0.0		0.002	False		,,,				2504	0.0				p.M655T	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.T1964C						PASS	.	T	THR/MET	1,4401	2.1+/-5.4	0,1,2200	111.0	103.0	106.0		1964	5.5	1.0	11	dbSNP_134	106	2,8594	2.2+/-6.3	0,2,4296	yes	missense	RRM1	NM_001033.3	81	0,3,6496	CC,CT,TT		0.0233,0.0227,0.0231	benign	655/793	4154851	3,12995	2201	4298	6499	SO:0001583	missense	6240	exon17			AAGAGATGAAAAA	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.1964T>C	11.37:g.4154851T>C	ENSP00000300738:p.Met655Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	112	40	0.357143	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	37	CCDS7750.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	17.36	3.368737	0.61624	2.27E-4	2.33E-4	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.52	5.52	0.82312	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.45736	0.1357	M	0.75884	2.315	0.80722	D	1	P	0.42757	0.789	B	0.38264	0.269	T	0.55179	-0.8181	10	0.87932	D	0	-17.4615	14.8104	0.69992	0.0:0.0:0.0:1.0	.	655	P23921	RIR1_HUMAN	T	655;558;568;433;433;317	ENSP00000300738:M655T;ENSP00000390539:M558T;ENSP00000431464:M433T;ENSP00000442148:M317T	ENSP00000300738:M655T	M	+	2	0	RRM1	4111427	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	2.092000	0.63282	0.533000	0.62120	ATG	T|0.999;C|0.001	0.001	strong		0.403	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136287582	136287582	+	Missense_Mutation	SNP	C	C	T	rs34024143	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000371916.1_Missense_Mutation_p.R7W|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.R7W|ADAMTS13_ENST00000356589.2_Missense_Mutation_p.R7W|ADAMTS13_ENST00000485925.1_Intron	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						scavenged	.	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	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	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	
ZNF99	7652	hgsc.bcm.edu	37	19	22940694	22940694	+	Missense_Mutation	SNP	C	C	T	rs62119157	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22940694C>T	ENST00000596209.1	-	4	2107	c.2017G>A	c.(2017-2019)Gaa>Aaa	p.E673K	ZNF99_ENST00000397104.3_Missense_Mutation_p.E582K	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	673					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.E582K(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGTTTCTCTTCAGTATGAATT	0.363													C|||	449	0.0896565	0.0681	0.0879	5008	,	,		20352	0.0933		0.0934	False		,,,				2504	0.1125				p.E673K		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	1	1	Substitution - Missense(1)	stomach(1)	c.G2017A						PASS	.	T	LYS/GLU	270,3994		9,252,1871	48.0	51.0	50.0		1744	-2.6	0.0	19	dbSNP_129	50	761,7751		38,685,3533	no	missense	ZNF99	NM_001080409.2	56	47,937,5404	TT,TC,CC		8.9403,6.3321,8.0698	benign	582/912	22940694	1031,11745	2132	4256	6388	SO:0001583	missense	7652	exon4			TCTCTTCAGTATG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.2017G>A	19.37:g.22940694C>T	ENSP00000472969:p.Glu673Lys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	186	0.08516483516483517	35	0.07113821138211382	39	0.10773480662983426	52	0.09090909090909091	60	0.079155672823219	c	9.496	1.101957	0.20632	0.063321	0.089403	ENSG00000213973	ENST00000397104	T	0.15834	2.39	1.29	-2.57	0.06248	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00178	0.0005	N	0.11154	0.105	0.58432	P	2.9999999999752447E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.31833	-0.9929	8	0.62326	D	0.03	.	6.0523	0.19792	0.0:0.6058:0.0:0.3942	rs62119157	582	A8MXY4	ZNF99_HUMAN	K	582	ENSP00000380293:E582K	ENSP00000380293:E582K	E	-	1	0	ZNF99	22732534	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.218000	0.17622	-0.701000	0.05063	-2.083000	0.00378	GAA	C|0.913;T|0.087	0.087	strong		0.363	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
ZNF217	7764	hgsc.bcm.edu	37	20	52192637	52192637	+	Missense_Mutation	SNP	T	T	C	rs34323943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:52192637T>C	ENST00000371471.2	-	4	3091	c.2666A>G	c.(2665-2667)gAc>gGc	p.D889G	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.D889G			O75362	ZN217_HUMAN	zinc finger protein 217	889			D -> G (in dbSNP:rs34323943).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			CCACGGGCTGTCGTTCTTGGC	0.527													T|||	435	0.086861	0.0023	0.0951	5008	,	,		18538	0.0833		0.1203	False		,,,				2504	0.1646				p.D889G		Atlas-SNP	.											.	ZNF217	227	.	0			c.A2666G						PASS	.	T	GLY/ASP	103,4303	80.4+/-118.8	1,101,2101	74.0	70.0	71.0		2666	3.9	0.0	20	dbSNP_126	71	1043,7557	218.1+/-256.6	58,927,3315	yes	missense	ZNF217	NM_006526.2	94	59,1028,5416	CC,CT,TT		12.1279,2.3377,8.8113	benign	889/1049	52192637	1146,11860	2203	4300	6503	SO:0001583	missense	7764	exon3			GGGCTGTCGTTCT	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2666A>G	20.37:g.52192637T>C	ENSP00000360526:p.Asp889Gly	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	143	84	0.587413	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	161	0.07371794871794872	5	0.01016260162601626	39	0.10773480662983426	33	0.057692307692307696	84	0.11081794195250659	T	8.423	0.846730	0.16963	0.023377	0.121279	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.08102	3.13;3.13	5.06	3.94	0.45596	.	1.338930	0.04449	N	0.372289	T	0.00178	0.0005	L	0.40543	1.245	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.39014	-0.9634	10	0.66056	D	0.02	-17.0378	11.513	0.50504	0.0:0.0:0.4757:0.5243	rs34323943	889	O75362	ZN217_HUMAN	G	889;889;49	ENSP00000360526:D889G;ENSP00000304308:D889G	ENSP00000304308:D889G	D	-	2	0	ZNF217	51626044	0.003000	0.15002	0.003000	0.11579	0.011000	0.07611	1.316000	0.33620	0.741000	0.32674	0.528000	0.53228	GAC	T|0.918;C|0.082;A|0.000	0.082	strong		0.527	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
RANBP17	64901	hgsc.bcm.edu	37	5	170626735	170626735	+	Silent	SNP	A	A	G	rs35724654	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:170626735A>G	ENST00000523189.1	+	19	2264	c.2100A>G	c.(2098-2100)gtA>gtG	p.V700V	RANBP17_ENST00000521759.1_3'UTR	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	700					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTGAAACAGTATTACAAATAT	0.333			T	TRD@	ALL								A|||	323	0.0644968	0.0098	0.0634	5008	,	,		18777	0.001		0.173	False		,,,				2504	0.093				p.V700V		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.A2100G						PASS	.	A		141,4265	98.9+/-137.6	4,133,2066	122.0	121.0	121.0		2100	-3.7	0.9	5	dbSNP_126	121	1398,7202	269.3+/-288.3	138,1122,3040	no	coding-synonymous	RANBP17	NM_022897.3		142,1255,5106	GG,GA,AA		16.2558,3.2002,11.833		700/1089	170626735	1539,11467	2203	4300	6503	SO:0001819	synonymous_variant	64901	exon19			AACAGTATTACAA	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.2100A>G	5.37:g.170626735A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	73	35	0.479452	NM_022897	Q8IU74	Silent	SNP	ENST00000523189.1	37	CCDS34287.1																																																																																			A|0.890;G|0.110	0.110	strong		0.333	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319488	21319488	+	Silent	SNP	C	C	T	rs77176173	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:21319488C>T	ENST00000583088.1	+	3	1729	c.834C>T	c.(832-834)agC>agT	p.S278S	KCNJ12_ENST00000331718.5_Silent_p.S278S	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	278					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)	p.S278S(1)		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)	ACGAGGCCAGCCCGCTCTTCG	0.607										Prostate(3;0.18)																											p.S278S		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.C834T						scavenged	.						104.0	85.0	91.0					17																	21319488		2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			GGCCAGCCCGCTC	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.834C>T	17.37:g.21319488C>T		Somatic	220	28	0.127273		WXS	Illumina HiSeq	Phase_I	190	25	0.131579	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			C|0.625;T|0.375	0.375	strong		0.607	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
IMPG1	3617	hgsc.bcm.edu	37	6	76640781	76640781	+	Missense_Mutation	SNP	C	C	T	rs3734313	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:76640781C>T	ENST00000369950.3	-	15	2321	c.2132G>A	c.(2131-2133)cGc>cAc	p.R711H	IMPG1_ENST00000369963.3_3'UTR|Y_RNA_ENST00000363170.1_RNA	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)				TGGTTTGCAGCGACACTCCGC	0.567													C|||	962	0.192093	0.1293	0.2032	5008	,	,		18124	0.254		0.1809	False		,,,				2504	0.2168				p.R711H	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											IMPG1,NS,carcinoma,-1,1	IMPG1	143	1	0			c.G2132A						PASS	.	C	HIS/ARG	553,3853	249.3+/-256.8	36,481,1686	119.0	95.0	103.0		2132	1.2	1.0	6	dbSNP_107	103	1460,7140	278.6+/-293.5	118,1224,2958	yes	missense	IMPG1	NM_001563.2	29	154,1705,4644	TT,TC,CC		16.9767,12.5511,15.4775	probably-damaging	711/798	76640781	2013,10993	2203	4300	6503	SO:0001583	missense	3617	exon15			TTGCAGCGACACT	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.2132G>A	6.37:g.76640781C>T	ENSP00000358966:p.Arg711His	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	442	0.20238095238095238	66	0.13414634146341464	68	0.1878453038674033	165	0.28846153846153844	143	0.18865435356200527	C	13.01	2.108235	0.37242	0.125511	0.169767	ENSG00000112706	ENST00000369950;ENST00000369952	T;T	0.20463	2.07;2.15	5.45	1.18	0.20946	Epidermal growth factor-like, type 3 (1);	0.353536	0.24280	N	0.039906	T	0.04543	0.0124	L	0.46157	1.445	0.09310	P	0.9999999898373	P	0.52316	0.952	B	0.35770	0.21	T	0.33369	-0.9871	9	0.34782	T	0.22	.	3.7999	0.08754	0.2697:0.437:0.0:0.2933	rs3734313;rs52816738;rs61241500;rs3734313	711	Q17R60	IMPG1_HUMAN	H	711;72	ENSP00000358966:R711H;ENSP00000358968:R72H	ENSP00000358966:R711H	R	-	2	0	IMPG1	76697501	0.112000	0.22096	0.992000	0.48379	0.274000	0.26718	0.372000	0.20467	0.283000	0.22279	0.461000	0.40582	CGC	C|0.826;T|0.174	0.174	strong		0.567	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
TRPM8	79054	hgsc.bcm.edu	37	2	234905078	234905078	+	Silent	SNP	C	C	T	rs11563208	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:234905078C>T	ENST00000324695.4	+	22	3088	c.3048C>T	c.(3046-3048)atC>atT	p.I1016I	TRPM8_ENST00000433712.2_Silent_p.I594I	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	1016					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	TCCCCTTCATCGTCTTCGCTT	0.507													C|||	795	0.158746	0.0802	0.3184	5008	,	,		21633	0.0823		0.2525	False		,,,				2504	0.1339				p.I1016I		Atlas-SNP	.											.	TRPM8	146	.	0			c.C3048T						PASS	.	C		480,3926	227.2+/-242.5	31,418,1754	159.0	149.0	153.0		3048	-11.2	0.1	2	dbSNP_120	153	2394,6206	398.8+/-346.2	337,1720,2243	no	coding-synonymous	TRPM8	NM_024080.4		368,2138,3997	TT,TC,CC		27.8372,10.8942,22.0975		1016/1105	234905078	2874,10132	2203	4300	6503	SO:0001819	synonymous_variant	79054	exon22			CTTCATCGTCTTC	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.3048C>T	2.37:g.234905078C>T		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	250	140	0.56	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Silent	SNP	ENST00000324695.4	37	CCDS33407.1																																																																																			C|0.795;N|0.000	.	strong		0.507	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733164	52733164	+	Missense_Mutation	SNP	G	G	C	rs149898988		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:52733164G>C	ENST00000360540.5	-	7	1227	c.821C>G	c.(820-822)cCc>cGc	p.P274R	PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Missense_Mutation_p.P274R|PCMTD1_ENST00000544451.1_Missense_Mutation_p.P198R	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	274						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)				TTTCCTTTTGGGTGGAGCCCT	0.408																																					p.P274R		Atlas-SNP	.											PCMTD1,NS,carcinoma,0,3	PCMTD1	73	3	0			c.C821G						PASS	.						130.0	136.0	134.0					8																	52733164		2203	4300	6503	SO:0001583	missense	115294	exon6			CTTTTGGGTGGAG		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.821C>G	8.37:g.52733164G>C	ENSP00000353739:p.Pro274Arg	Somatic	458	0	0		WXS	Illumina HiSeq	Phase_I	579	27	0.0466321	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.691913	0.30052	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.48201	0.82;0.82;0.82	5.97	5.97	0.96955	.	0.058223	0.64402	D	0.000001	T	0.61652	0.2364	L	0.55990	1.75	0.58432	D	0.999998	P;D;P	0.89917	0.875;1.0;0.855	B;D;P	0.74674	0.307;0.984;0.448	T	0.52646	-0.8548	10	0.02654	T	1	-6.8456	20.4238	0.99064	0.0:0.0:1.0:0.0	.	144;198;274	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	R	274;198;274	ENSP00000353739:P274R;ENSP00000444026:P198R;ENSP00000428099:P274R	ENSP00000353739:P274R	P	-	2	0	PCMTD1	52895717	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.412000	0.66392	2.828000	0.97474	0.655000	0.94253	CCC	.	.	weak		0.408	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
CENPE	1062	hgsc.bcm.edu	37	4	104102563	104102563	+	Silent	SNP	T	T	C	rs17217250	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:104102563T>C	ENST00000265148.3	-	12	1103	c.1014A>G	c.(1012-1014)gtA>gtG	p.V338V	CENPE_ENST00000380026.3_Silent_p.V338V|CENPE_ENST00000509120.1_5'UTR	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	338					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.V338V(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CATCAGTTGATACCTCATTAA	0.294													T|||	599	0.119609	0.0552	0.1153	5008	,	,		14600	0.1419		0.2207	False		,,,				2504	0.0828				p.V338V		Atlas-SNP	.											CENPE,NS,carcinoma,0,1	CENPE	253	1	1	Substitution - coding silent(1)	stomach(1)	c.A1014G						scavenged	.	T		250,4146	142.3+/-177.5	8,234,1956	62.0	62.0	62.0		1014	-3.2	1.0	4	dbSNP_123	62	1770,6810	313.0+/-311.1	193,1384,2713	no	coding-synonymous	CENPE	NM_001813.2		201,1618,4669	CC,CT,TT		20.6294,5.687,15.5672		338/2702	104102563	2020,10956	2198	4290	6488	SO:0001819	synonymous_variant	1062	exon12			AGTTGATACCTCA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.1014A>G	4.37:g.104102563T>C		Somatic	443	3	0.00677201		WXS	Illumina HiSeq	Phase_I	423	178	0.420804	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																			T|0.840;C|0.160	0.160	strong		0.294	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PDE6A	5145	hgsc.bcm.edu	37	5	149242788	149242788	+	Silent	SNP	G	G	A	rs4705390	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149242788G>A	ENST00000255266.5	-	21	2519	c.2400C>T	c.(2398-2400)gaC>gaT	p.D800D		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	800					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	TGGTGATCCCGTCCAACATTG	0.552													G|||	132	0.0263578	0.0038	0.0793	5008	,	,		24054	0.002		0.0268	False		,,,				2504	0.044				p.D800D		Atlas-SNP	.											PDE6A,NS,carcinoma,-2,1	PDE6A	98	1	0			c.C2400T						scavenged	.	G		31,4375	38.4+/-70.7	0,31,2172	221.0	182.0	195.0		2400	-10.1	0.7	5	dbSNP_111	195	316,8284	113.5+/-173.5	6,304,3990	no	coding-synonymous	PDE6A	NM_000440.2		6,335,6162	AA,AG,GG		3.6744,0.7036,2.668		800/861	149242788	347,12659	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon21			GATCCCGTCCAAC		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.2400C>T	5.37:g.149242788G>A		Somatic	218	2	0.00917431		WXS	Illumina HiSeq	Phase_I	220	95	0.431818	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			A|0.027;G|0.973;T|0.000	0.027	strong		0.552	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
TUBB8	347688	hgsc.bcm.edu	37	10	93987	93987	+	Silent	SNP	T	T	C	rs61839057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:93987T>C	ENST00000309812.4	-	4	407	c.345A>G	c.(343-345)tcA>tcG	p.S115S	TUBB8_ENST00000332708.5_3'UTR|TUBB8_ENST00000447903.2_Silent_p.S43S|TUBB8_ENST00000413237.3_5'UTR	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	115					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)			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)		CGTCCATCACTGACTCCATCA	0.617																																					p.S115S	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.A345G						PASS	.						57.0	50.0	53.0					10																	93987		2203	4300	6503	SO:0001819	synonymous_variant	347688	exon4			CATCACTGACTCC	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.345A>G	10.37:g.93987T>C		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	221	42	0.190045	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			T|0.500;C|0.500	0.500	weak		0.617	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
GPR1	2825	hgsc.bcm.edu	37	2	207041602	207041602	+	Missense_Mutation	SNP	T	T	C	rs138365581	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:207041602T>C	ENST00000407325.2	-	3	732	c.370A>G	c.(370-372)Agt>Ggt	p.S124G	GPR1_ENST00000437420.1_Missense_Mutation_p.S124G	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	124					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		AAAAAAACACTGGCAAACATG	0.483													T|||	8	0.00159744	0.0008	0.0014	5008	,	,		21149	0.0		0.006	False		,,,				2504	0.0				p.S124G		Atlas-SNP	.											.	GPR1	38	.	0			c.A370G						PASS	.	T	GLY/SER,GLY/SER	6,4400	11.4+/-27.6	0,6,2197	114.0	106.0	109.0		370,370	5.8	1.0	2	dbSNP_134	109	77,8523	44.9+/-103.4	0,77,4223	yes	missense,missense	GPR1	NM_001098199.1,NM_005279.3	56,56	0,83,6420	CC,CT,TT		0.8953,0.1362,0.6382	probably-damaging,probably-damaging	124/356,124/356	207041602	83,12923	2203	4300	6503	SO:0001583	missense	2825	exon3			AAACACTGGCAAA		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.370A>G	2.37:g.207041602T>C	ENSP00000384345:p.Ser124Gly	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	95	24	0.252632	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Missense_Mutation	SNP	ENST00000407325.2	37	CCDS2368.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	24.7	4.558336	0.86231	0.001362	0.008953	ENSG00000183671	ENST00000407325;ENST00000437420;ENST00000442134;ENST00000451790;ENST00000447845	T;T;T;T;T	0.54071	0.59;0.59;0.59;0.59;0.59	5.84	5.84	0.93424	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.68229	0.2978	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76302	-0.3009	10	0.87932	D	0	.	16.2311	0.82343	0.0:0.0:0.0:1.0	.	124	P46091	GPR1_HUMAN	G	124	ENSP00000384345:S124G;ENSP00000397535:S124G;ENSP00000414836:S124G;ENSP00000391146:S124G;ENSP00000414524:S124G	ENSP00000384345:S124G	S	-	1	0	GPR1	206749847	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.907000	0.87430	2.234000	0.73211	0.528000	0.53228	AGT	T|0.996;C|0.004	0.004	strong		0.483	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
SP2	6668	hgsc.bcm.edu	37	17	45994094	45994094	+	Silent	SNP	T	T	C	rs2228251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45994094T>C	ENST00000376741.4	+	3	794	c.657T>C	c.(655-657)ctT>ctC	p.L219L	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	219					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						TCAACAACCTTGTGAACGCCA	0.597													C|||	2845	0.568091	0.615	0.4813	5008	,	,		18037	0.7758		0.4622	False		,,,				2504	0.4611				p.L219L		Atlas-SNP	.											.	SP2	38	.	0			c.T657C						PASS	.	C		2581,1825	534.4+/-373.9	743,1095,365	76.0	75.0	75.0		657	-9.3	0.3	17	dbSNP_98	75	3755,4845	616.9+/-396.6	825,2105,1370	no	coding-synonymous	SP2	NM_003110.5		1568,3200,1735	CC,CT,TT		43.6628,41.4208,48.716		219/614	45994094	6336,6670	2203	4300	6503	SO:0001819	synonymous_variant	6668	exon3			CAACCTTGTGAAC		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.657T>C	17.37:g.45994094T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_003110	A6NK74	Silent	SNP	ENST00000376741.4	37	CCDS11521.2																																																																																			T|0.467;C|0.533	0.533	strong		0.597	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
TULP2	7288	hgsc.bcm.edu	37	19	49391404	49391404	+	Missense_Mutation	SNP	C	C	T	rs8112811	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49391404C>T	ENST00000221399.3	-	8	895	c.751G>A	c.(751-753)Gac>Aac	p.D251N		NM_003323.2	NP_003314.2	O00295	TULP2_HUMAN	tubby like protein 2	251			D -> N (in dbSNP:rs8112811).		visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	protein complex binding (GO:0032403)			NS(1)|breast(2)|central_nervous_system(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	22		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;0.000259)|all cancers(93;0.000435)|Epithelial(262;0.0221)|GBM - Glioblastoma multiforme(486;0.0234)		CTCATATGGTCGCTGTCCGTG	0.622													C|||	1076	0.214856	0.41	0.2017	5008	,	,		19229	0.0665		0.1262	False		,,,				2504	0.2045				p.D251N		Atlas-SNP	.											.	TULP2	60	.	0			c.G751A						PASS	.	C	ASN/ASP	1491,2915	474.6+/-357.0	251,989,963	94.0	63.0	73.0		751	-7.8	0.0	19	dbSNP_116	73	1028,7572	219.0+/-257.2	61,906,3333	yes	missense	TULP2	NM_003323.2	23	312,1895,4296	TT,TC,CC		11.9535,33.8402,19.368	benign	251/521	49391404	2519,10487	2203	4300	6503	SO:0001583	missense	7288	exon8			TATGGTCGCTGTC	U82469	CCDS12739.1	19q13.1	2009-08-06			ENSG00000104804	ENSG00000104804			12424	protein-coding gene	gene with protein product	"""cancer/testis antigen 65"""	602309				9096357	Standard	NM_003323		Approved	TUBL2, CT65	uc002pkz.2	O00295	OTTHUMG00000164406	ENST00000221399.3:c.751G>A	19.37:g.49391404C>T	ENSP00000221399:p.Asp251Asn	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	130	70	0.538462	NM_003323	Q8TC50	Missense_Mutation	SNP	ENST00000221399.3	37	CCDS12739.1	423	0.1936813186813187	203	0.41260162601626016	74	0.20441988950276244	42	0.07342657342657342	104	0.13720316622691292	C	0.828	-0.746256	0.03065	0.338402	0.119535	ENSG00000104804	ENST00000221399;ENST00000518572	D;T	0.82433	-1.61;2.26	3.9	-7.8	0.01214	.	21.342800	0.00166	N	0.000000	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	P	0.34615	0.459	B	0.18871	0.023	T	0.08764	-1.0706	9	0.14656	T	0.56	5.8448	4.3174	0.11000	0.1014:0.4134:0.3042:0.181	rs8112811;rs17847565;rs52800287;rs59119925;rs8112811	251	O00295	TULP2_HUMAN	N	251;205	ENSP00000221399:D251N;ENSP00000428420:D205N	ENSP00000221399:D251N	D	-	1	0	TULP2	54083216	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.866000	0.01647	-2.765000	0.00368	-1.113000	0.02065	GAC	C|0.790;T|0.210	0.210	strong		0.622	TULP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378633.1	NM_003323	
BTNL2	56244	hgsc.bcm.edu	37	6	32362669	32362669	+	Silent	SNP	T	T	G	rs41449245	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32362669T>G	ENST00000374993.1	-	6	1211	c.1212A>C	c.(1210-1212)tcA>tcC	p.S404S	BTNL2_ENST00000429232.2_3'UTR|BTNL2_ENST00000414363.1_Silent_p.S194S|BTNL2_ENST00000544175.1_Silent_p.S127S|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Silent_p.S310S|BTNL2_ENST00000540315.1_Silent_p.S194S|BTNL2_ENST00000454136.3_Silent_p.S404S	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	404						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						CCTGGGAAGATGATGGTATCG	0.552													t|||	821	0.163938	0.1422	0.1599	5008	,	,		20290	0.1587		0.163	False		,,,				2504	0.2025				p.S404S		Atlas-SNP	.											.	BTNL2	50	.	0			c.A1212C						PASS	.			551,3855	248.1+/-256.1	28,495,1680	233.0	221.0	225.0		1212	-10.2	0.0	6	dbSNP_127	225	1241,7359	248.3+/-276.0	92,1057,3151	no	coding-synonymous	BTNL2	NM_019602.1		120,1552,4831	GG,GT,TT		14.4302,12.5057,13.7783		404/456	32362669	1792,11214	2203	4300	6503	SO:0001819	synonymous_variant	56244	exon6			GGAAGATGATGGT	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.1212A>C	6.37:g.32362669T>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	142	64	0.450704	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|0.859;G|0.141	0.141	strong		0.552	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
CHMP4C	92421	hgsc.bcm.edu	37	8	82670412	82670412	+	Silent	SNP	G	G	A	rs62514262	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:82670412G>A	ENST00000297265.4	+	4	712	c.519G>A	c.(517-519)caG>caA	p.Q173Q		NM_152284.3	NP_689497.1	Q96CF2	CHM4C_HUMAN	charged multivesicular body protein 4C	173	Intramolecular interaction with N- terminus. {ECO:0000250}.				abscission (GO:0009838)|cytokinesis checkpoint (GO:0031565)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of cytokinesis (GO:0032466)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|membrane (GO:0016020)|midbody (GO:0030496)	protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	10						AATTGGAACAGGAGGAATTAA	0.428													G|||	92	0.0183706	0.0023	0.0375	5008	,	,		19447	0.001		0.0447	False		,,,				2504	0.0174				p.Q173Q		Atlas-SNP	.											CHMP4C,NS,carcinoma,0,1	CHMP4C	28	1	0			c.G519A						scavenged	.	G		41,4365	43.8+/-77.6	0,41,2162	109.0	108.0	108.0		519	3.5	1.0	8	dbSNP_129	108	417,8183	129.8+/-187.9	14,389,3897	no	coding-synonymous	CHMP4C	NM_152284.3		14,430,6059	AA,AG,GG		4.8488,0.9305,3.5215		173/234	82670412	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	92421	exon4			GGAACAGGAGGAA	AK000049	CCDS6233.1	8q21.13	2011-09-21	2011-09-21		ENSG00000164695	ENSG00000164695		"""Charged multivesicular body proteins"""	30599	protein-coding gene	gene with protein product	"""Snf7 homologue associated with Alix 3"""	610899	"""chromatin modifying protein 4C"""			12860994 , 14678797	Standard	NM_152284		Approved	MGC22825, Shax3, VPS32C	uc003ycl.3	Q96CF2	OTTHUMG00000164726	ENST00000297265.4:c.519G>A	8.37:g.82670412G>A		Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	165	92	0.557576	NM_152284	B2RBZ1	Silent	SNP	ENST00000297265.4	37	CCDS6233.1																																																																																			G|0.966;A|0.034	0.034	strong		0.428	CHMP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379927.1	NM_152284	
PPP1R9A	55607	hgsc.bcm.edu	37	7	94539536	94539536	+	Silent	SNP	C	C	T	rs12536183	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:94539536C>T	ENST00000433881.1	+	2	643	c.111C>T	c.(109-111)ccC>ccT	p.P37P	PPP1R9A_ENST00000456331.2_Silent_p.P37P|PPP1R9A_ENST00000424654.1_Silent_p.P37P|PPP1R9A_ENST00000289495.5_Silent_p.P37P|PPP1R9A_ENST00000433360.1_Silent_p.P37P|PPP1R9A_ENST00000340694.4_Silent_p.P37P			Q9ULJ8	NEB1_HUMAN	protein phosphatase 1, regulatory subunit 9A	37	Actin-binding.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|neuron projection development (GO:0031175)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|dendritic spine (GO:0043197)|filopodium (GO:0030175)|growth cone (GO:0030426)|synapse (GO:0045202)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(11)|liver(2)|lung(22)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(8)|urinary_tract(5)	71	all_cancers(62;9.12e-11)|all_epithelial(64;4.34e-09)		STAD - Stomach adenocarcinoma(171;0.0031)			TTGACAAACCCAAGTCAGATG	0.453										HNSCC(28;0.073)			C|||	549	0.109625	0.0182	0.2248	5008	,	,		19522	0.1448		0.0964	False		,,,				2504	0.1288				p.P37P		Atlas-SNP	.											.	PPP1R9A	264	.	0			c.C111T						PASS	.	C	,,,,	154,4252	105.2+/-143.6	4,146,2053	51.0	50.0	50.0		111,111,111,111,111	4.6	1.0	7	dbSNP_120	50	731,7869	177.8+/-227.3	31,669,3600	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP1R9A	NM_001166160.1,NM_001166161.1,NM_001166162.1,NM_001166163.1,NM_017650.2	,,,,	35,815,5653	TT,TC,CC		8.5,3.4952,6.8046	,,,,	37/1375,37/1297,37/1254,37/1091,37/1099	94539536	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	55607	exon2			CAAACCCAAGTCA	AB033048	CCDS34683.1, CCDS55127.1, CCDS55128.1	7q21.3	2013-01-10	2011-10-04		ENSG00000158528	ENSG00000158528		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Sterile alpha motif (SAM) domain containing"""	14946	protein-coding gene	gene with protein product		602468	"""protein phosphatase 1, regulatory (inhibitor) subunit 9A"""			10574462	Standard	NM_001166160		Approved	Neurabin-I, KIAA1222, FLJ20068	uc010lfj.3	Q9ULJ8	OTTHUMG00000155566	ENST00000433881.1:c.111C>T	7.37:g.94539536C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	177	78	0.440678	NM_017650	A1L494|B2RWQ1|E9PCA0|E9PCK6|E9PDX1|F8W7J9|O76059|Q9NXT2	Silent	SNP	ENST00000433881.1	37	CCDS34683.1																																																																																			C|0.915;T|0.085	0.085	strong		0.453	PPP1R9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340662.1	NM_001166160	
FRG2	448831	hgsc.bcm.edu	37	4	190947916	190947916	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:190947916C>T	ENST00000378763.1	-	2	235	c.183G>A	c.(181-183)tcG>tcA	p.S61S	FRG2_ENST00000504750.1_Silent_p.S62S	NM_001005217.1|NM_001199232.1	NP_001005217.1|NP_001186161.1	Q64ET8	FRG2_HUMAN	FSHD region gene 2	61						nucleus (GO:0005634)				large_intestine(1)|lung(3)|ovary(2)|skin(1)	7		all_cancers(14;1.01e-50)|all_epithelial(14;6.7e-35)|all_lung(41;2.17e-14)|Lung NSC(41;4.95e-14)|Breast(6;3.4e-05)|Melanoma(20;0.000539)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|all_hematologic(60;0.0489)|Prostate(90;0.0513)		all cancers(3;3.83e-31)|Epithelial(3;1.36e-30)|OV - Ovarian serous cystadenocarcinoma(60;1.99e-15)|BRCA - Breast invasive adenocarcinoma(30;8.54e-06)|Lung(3;3.23e-05)|STAD - Stomach adenocarcinoma(60;8.24e-05)|LUSC - Lung squamous cell carcinoma(40;0.000184)|GBM - Glioblastoma multiforme(59;0.00831)|READ - Rectum adenocarcinoma(43;0.155)		GATTGGGCTCCGATCCTGCTG	0.488																																					p.S61S		Atlas-SNP	.											FRG2,NS,carcinoma,0,1	FRG2	12	1	0			c.G183A						scavenged	.						1.0	1.0	1.0					4																	190947916		10	29	39	SO:0001819	synonymous_variant	448831	exon2			GGGCTCCGATCCT		CCDS34123.1, CCDS68834.1	4q35.2	2014-09-04			ENSG00000205097	ENSG00000205097			19136	protein-coding gene	gene with protein product		609032				12176321, 15520407	Standard	NM_001005217		Approved	FRG2A		Q64ET8	OTTHUMG00000160339	ENST00000378763.1:c.183G>A	4.37:g.190947916C>T		Somatic	265	34	0.128302		WXS	Illumina HiSeq	Phase_I	213	50	0.234742	NM_001005217	B7ZMJ1|E7EN36	Silent	SNP	ENST00000378763.1	37	CCDS34123.1																																																																																			.	.	weak		0.488	FRG2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360294.1	NM_001005217	
ELP2	55250	hgsc.bcm.edu	37	18	33725931	33725931	+	Missense_Mutation	SNP	G	G	A	rs1785928	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:33725931G>A	ENST00000358232.6	+	10	976	c.913G>A	c.(913-915)Gtg>Atg	p.V305M	ELP2_ENST00000351393.6_Missense_Mutation_p.V279M|ELP2_ENST00000350494.6_Missense_Mutation_p.V344M|ELP2_ENST00000542824.1_Missense_Mutation_p.V279M|ELP2_ENST00000442325.2_Missense_Mutation_p.V370M|ELP2_ENST00000423854.2_Missense_Mutation_p.V235M	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	305			V -> M (in dbSNP:rs1785928). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						ACAGCAGCCAGTGAGATTATT	0.368													A|||	1611	0.321685	0.3865	0.3847	5008	,	,		18633	0.2014		0.3797	False		,,,				2504	0.2536				p.V370M		Atlas-SNP	.											ELP2,colon,carcinoma,0,1	ELP2	70	1	0			c.G1108A						PASS	.	A	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1626,2780	657.6+/-400.3	300,1026,877	163.0	177.0	172.0		1108,1030,835,835,703,913	-1.7	1.0	18	dbSNP_89	172	3192,5408	652.7+/-401.0	583,2026,1691	no	missense,missense,missense,missense,missense,missense	ELP2	NM_001242875.1,NM_001242876.1,NM_001242877.1,NM_001242878.1,NM_001242879.1,NM_018255.2	21,21,21,21,21,21	883,3052,2568	AA,AG,GG		37.1163,36.9042,37.0444	benign,benign,benign,benign,benign,benign	370/892,344/822,279/801,279/757,235/757,305/827	33725931	4818,8188	2203	4300	6503	SO:0001583	missense	55250	exon11			CAGCCAGTGAGAT	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"""Elongator acetyltransferase complex subunits"", ""WD repeat domain containing"""	18248	protein-coding gene	gene with protein product			"""signal transducer and activator of transcription 3 interacting protein 1"", ""elongation protein 2 homolog (S. cerevisiae)"""	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.913G>A	18.37:g.33725931G>A	ENSP00000350967:p.Val305Met	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	235	107	0.455319	NM_001242875	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Missense_Mutation	SNP	ENST00000358232.6	37	CCDS11918.1	759	0.3475274725274725	193	0.39227642276422764	154	0.425414364640884	111	0.19405594405594406	301	0.3970976253298153	A	3.309	-0.141116	0.06669	0.369042	0.371163	ENSG00000134759	ENST00000358232;ENST00000351393;ENST00000442325;ENST00000423854;ENST00000350494;ENST00000542824	T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24	5.37	-1.7	0.08159	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);WD40-repeat-containing domain (1);	0.259165	0.46145	N	0.000307	T	0.00012	0.0000	N	0.02247	-0.625	0.48571	P	3.300000000000525E-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	0.09377	0.004;0.004;0.001;0.001;0.001;0.001	T	0.46582	-0.9181	9	0.42905	T	0.14	-4.6675	7.0425	0.25029	0.4848:0.1249:0.3903:0.0	rs1785928;rs17846001;rs17858985;rs56552971;rs60807235;rs1785928	344;370;235;279;279;305	B4DTG0;E7EP23;E9PCX0;Q6IA86-2;Q6IA86-3;Q6IA86	.;.;.;.;.;ELP2_HUMAN	M	305;279;370;235;344;279	ENSP00000350967:V305M;ENSP00000257191:V279M;ENSP00000414851:V370M;ENSP00000391202:V235M;ENSP00000316051:V344M;ENSP00000443800:V279M	ENSP00000316051:V344M	V	+	1	0	ELP2	31979929	0.979000	0.34478	0.997000	0.53966	0.868000	0.49771	0.248000	0.18198	-0.180000	0.10637	-0.893000	0.02921	GTG	G|0.656;A|0.344	0.344	strong		0.368	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255	
SLC1A4	6509	hgsc.bcm.edu	37	2	65217089	65217089	+	Silent	SNP	G	G	C	rs7559202	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:65217089G>C	ENST00000234256.3	+	1	555	c.312G>C	c.(310-312)tcG>tcC	p.S104S	SLC1A4_ENST00000493121.1_Intron|SLC1A4_ENST00000531327.1_Intron	NM_003038.4	NP_003029.2	P43007	SATT_HUMAN	solute carrier family 1 (glutamate/neutral amino acid transporter), member 4	104					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)	GCGCCGCCTCGCTCGATGCCA	0.682													C|||	881	0.175919	0.1778	0.1167	5008	,	,		13619	0.2401		0.169	False		,,,				2504	0.1564				p.S104S		Atlas-SNP	.											.	SLC1A4	33	.	0			c.G312C						PASS	.	C	,	717,3669		70,577,1546	9.0	10.0	10.0		,312	-1.5	0.8	2	dbSNP_116	10	1187,7369		91,1005,3182	no	intron,coding-synonymous	SLC1A4	NM_001193493.1,NM_003038.4	,	161,1582,4728	CC,CG,GG		13.8733,16.3475,14.7118	,	,104/533	65217089	1904,11038	2193	4278	6471	SO:0001819	synonymous_variant	6509	exon1			CGCCTCGCTCGAT		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.312G>C	2.37:g.65217089G>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_003038	B7Z3C0|D6W5F0	Silent	SNP	ENST00000234256.3	37	CCDS1879.1																																																																																			G|0.815;C|0.185	0.185	strong		0.682	SLC1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251726.2	NM_003038	
DQX1	165545	hgsc.bcm.edu	37	2	74746757	74746757	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:74746757A>G	ENST00000404568.3	-	10	1951	c.1732T>C	c.(1732-1734)Tcc>Ccc	p.S578P	DQX1_ENST00000393951.2_Missense_Mutation_p.S578P	NM_133637.2	NP_598376.2	Q8TE96	DQX1_HUMAN	DEAQ box RNA-dependent ATPase 1	578						nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	18						GCTGGTAGGGACAAGGGAAGT	0.522																																					p.S578P		Atlas-SNP	.											DQX1_ENST00000404568,NS,malignant_melanoma,+1,2	DQX1	95	2	0			c.T1732C						scavenged	.						148.0	143.0	145.0					2																	74746757		2203	4300	6503	SO:0001583	missense	165545	exon10			GTAGGGACAAGGG	AK074337	CCDS1949.2	2p12	2010-04-20	2009-01-15		ENSG00000144045	ENSG00000144045			20410	protein-coding gene	gene with protein product			"""DEAQ box polypeptide 1 (RNA-dependent ATPase)"""				Standard	NM_133637		Approved	FLJ23757	uc010yrw.2	Q8TE96	OTTHUMG00000129965	ENST00000404568.3:c.1732T>C	2.37:g.74746757A>G	ENSP00000384621:p.Ser578Pro	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	181	3	0.0165746	NM_133637	Q6B017|Q8NAM8	Missense_Mutation	SNP	ENST00000404568.3	37	CCDS1949.2	.	.	.	.	.	.	.	.	.	.	A	21.3	4.122542	0.77436	.	.	ENSG00000144045	ENST00000393951;ENST00000404568	T;T	0.03212	4.01;4.01	5.69	5.69	0.88448	Domain of unknown function DUF1605 (1);	0.000000	0.64402	D	0.000002	T	0.15392	0.0371	M	0.79475	2.455	0.45108	D	0.998126	D	0.89917	1.0	D	0.77557	0.99	T	0.01030	-1.1475	10	0.35671	T	0.21	-16.7963	9.2335	0.37453	0.8387:0.0:0.0:0.1613	.	578	Q8TE96	DQX1_HUMAN	P	578	ENSP00000377523:S578P;ENSP00000384621:S578P	ENSP00000377523:S578P	S	-	1	0	DQX1	74600265	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.627000	0.67784	2.157000	0.67596	0.533000	0.62120	TCC	.	.	none		0.522	DQX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252230.3	NM_133637	
ZNF28	7576	hgsc.bcm.edu	37	19	53303890	53303890	+	Missense_Mutation	SNP	C	C	G	rs57548937	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53303890C>G	ENST00000457749.2	-	4	1327	c.1208G>C	c.(1207-1209)aGg>aCg	p.R403T	ZNF28_ENST00000414252.2_Missense_Mutation_p.R350T|ZNF28_ENST00000360272.4_Missense_Mutation_p.R350T|ZNF28_ENST00000438150.2_Missense_Mutation_p.R350T	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	403				R -> T (in Ref. 1; BAD18706 and 2; CAI46258). {ECO:0000305}.	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)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		AGTATGAATCCTCTTATGTCT	0.378													-|||	981	0.195887	0.0045	0.0764	5008	,	,		22502	0.5774		0.0845	False		,,,				2504	0.2607				p.R403T		Atlas-SNP	.											.	ZNF28	191	.	0			c.G1208C						PASS	.	C	THR/ARG	105,4301		1,103,2099	104.0	110.0	108.0		1208	-2.9	0.0	19	dbSNP_129	108	781,7819		38,705,3557	no	missense	ZNF28	NM_006969.3	71	39,808,5656	GG,GC,CC		9.0814,2.3831,6.8122	possibly-damaging	403/719	53303890	886,12120	2203	4300	6503	SO:0001583	missense	7576	exon4			TGAATCCTCTTAT	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"""Zinc fingers, C2H2-type"", ""-"""	13073	protein-coding gene	gene with protein product			"""zinc finger protein 28 (KOX 24)"""				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.1208G>C	19.37:g.53303890C>G	ENSP00000397693:p.Arg403Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	37	CCDS33093.2	437	0.2000915750915751	4	0.008130081300813009	29	0.08011049723756906	335	0.5856643356643356	69	0.09102902374670185	-	10.32	1.317047	0.23908	0.023831	0.090814	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8	1.75	-2.87	0.05700	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.74647	2.275	0.80722	P	0.0	B	0.31274	0.317	B	0.27170	0.077	T	0.39461	-0.9613	8	0.51188	T	0.08	.	4.3917	0.11343	0.0:0.4204:0.1714:0.4082	rs57548937	403	P17035	ZNF28_HUMAN	T	350;403;350;350;350	ENSP00000412143:R350T;ENSP00000397693:R403T;ENSP00000353410:R350T;ENSP00000444965:R350T;ENSP00000375661:R350T	ENSP00000353410:R350T	R	-	2	0	ZNF28	57995702	0.000000	0.05858	0.008000	0.14137	0.148000	0.21650	-1.266000	0.02842	-0.737000	0.04824	0.196000	0.17591	AGG	C|0.898;G|0.102	0.102	strong		0.378	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969	
PAPD7	11044	hgsc.bcm.edu	37	5	6753013	6753013	+	Silent	SNP	C	C	T	rs28381429	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:6753013C>T	ENST00000230859.6	+	12	1426	c.1297C>T	c.(1297-1299)Cta>Tta	p.L433L		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	663	PAP-associated.				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)			cervix(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TCCACCGACCCTAGGGGTTGC	0.532													C|||	74	0.0147764	0.0	0.0159	5008	,	,		17117	0.0		0.0288	False		,,,				2504	0.0348				p.L433L	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											.	PAPD7	69	.	0			c.C1297T						PASS	.	C	,,	25,4381	32.6+/-62.9	0,25,2178	103.0	97.0	99.0		1297,757,1297	2.2	1.0	5	dbSNP_125	99	247,8353	97.0+/-158.7	3,241,4056	no	coding-synonymous,coding-synonymous,coding-synonymous	PAPD7	NM_001171805.1,NM_001171806.1,NM_006999.4	,,	3,266,6234	TT,TC,CC		2.8721,0.5674,2.0913	,,	433/542,253/363,433/543	6753013	272,12734	2203	4300	6503	SO:0001819	synonymous_variant	11044	exon12			CCGACCCTAGGGG	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.1297C>T	5.37:g.6753013C>T		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	210	89	0.42381	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Silent	SNP	ENST00000230859.6	37	CCDS3871.1																																																																																			C|0.979;T|0.021	0.021	strong		0.532	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999	
PRSS57	400668	hgsc.bcm.edu	37	19	687112	687112	+	Missense_Mutation	SNP	G	G	A	rs72618588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:687112G>A	ENST00000329267.7	-	4	487	c.458C>T	c.(457-459)gCg>gTg	p.A153V		NM_214710.3	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine, 57	153	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(5)	6						CCGTGTCCCCGCTGTGGGGGG	0.687													G|||	521	0.104034	0.0726	0.0317	5008	,	,		16352	0.2738		0.0567	False		,,,				2504	0.0716				p.A153V		Atlas-SNP	.											.	PRSS57	18	.	0			c.C458T						PASS	.	G	VAL/ALA	308,4090		9,290,1900	20.0	22.0	21.0		458	1.9	0.0	19	dbSNP_130	21	448,8148		17,414,3867	yes	missense	PRSS57	NM_214710.3	64	26,704,5767	AA,AG,GG		5.2117,7.0032,5.8181	benign	153/284	687112	756,12238	2199	4298	6497	SO:0001583	missense	400668	exon4			GTCCCCGCTGTGG	AY358594	CCDS12041.1	19p13.3	2012-03-26	2011-03-07	2011-03-07		ENSG00000185198		"""Serine peptidases / Serine peptidases"""	31397	protein-coding gene	gene with protein product			"""protease, serine-like 1"""	PRSSL1		12975309	Standard	NM_214710		Approved	UNQ782	uc002lpl.1	Q6UWY2		ENST00000329267.7:c.458C>T	19.37:g.687112G>A	ENSP00000327386:p.Ala153Val	Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	184	99	0.538043	NM_214710	B2RNW8	Missense_Mutation	SNP	ENST00000329267.7	37	CCDS12041.1	238	0.10897435897435898	38	0.07723577235772358	14	0.03867403314917127	148	0.25874125874125875	38	0.05013192612137203	G	10.28	1.306360	0.23736	0.070032	0.052117	ENSG00000185198	ENST00000329267	D	0.87650	-2.28	4.38	1.91	0.25777	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.674599	0.12248	N	0.485869	T	0.00039	0.0001	L	0.28192	0.835	0.80722	P	0.0	B;B	0.24533	0.105;0.105	B;B	0.28011	0.059;0.085	T	0.08269	-1.0730	9	0.52906	T	0.07	.	9.4911	0.38960	0.0879:0.0:0.7611:0.151	.	152;153	B7ZMF6;Q6UWY2	.;PRS57_HUMAN	V	153	ENSP00000327386:A153V	ENSP00000327386:A153V	A	-	2	0	PRSS57	638112	0.000000	0.05858	0.002000	0.10522	0.046000	0.14306	-0.237000	0.08990	0.840000	0.34995	0.462000	0.41574	GCG	G|0.929;A|0.071	0.071	strong		0.687	PRSS57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452480.2	NM_214710	
MKI67	4288	hgsc.bcm.edu	37	10	129903016	129903016	+	Missense_Mutation	SNP	T	T	C	rs7071768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129903016T>C	ENST00000368654.3	-	13	7463	c.7088A>G	c.(7087-7089)aAc>aGc	p.N2363S	MKI67_ENST00000368653.3_Missense_Mutation_p.N2003S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2363	16 X 122 AA approximate repeats.		N -> S (in dbSNP:rs7071768).		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)				TTTCCTGAGGTTTCTCTTGGG	0.488													C|||	2322	0.463658	0.4607	0.6095	5008	,	,		20346	0.381		0.5219	False		,,,				2504	0.3896				p.N2363S		Atlas-SNP	.											.	MKI67	363	.	0			c.A7088G						PASS	.	C	SER/ASN,SER/ASN	2025,2381	613.1+/-392.1	473,1079,651	363.0	374.0	370.0		6008,7088	-5.4	0.0	10	dbSNP_116	370	4474,4126	564.3+/-388.3	1162,2150,988	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	46,46	1635,3229,1639	CC,CT,TT		47.9767,45.9601,49.9692	benign,benign	2003/2897,2363/3257	129903016	6499,6507	2203	4300	6503	SO:0001583	missense	4288	exon13			CTGAGGTTTCTCT	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.7088A>G	10.37:g.129903016T>C	ENSP00000357643:p.Asn2363Ser	Somatic	364	1	0.00274725		WXS	Illumina HiSeq	Phase_I	346	167	0.482659	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	1041	0.4766483516483517	198	0.4024390243902439	210	0.580110497237569	236	0.4125874125874126	397	0.5237467018469657	C	0.302	-0.973252	0.02215	0.459601	0.520233	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01629	4.72;4.72	3.21	-5.36	0.02689	.	6.543270	0.00531	N	0.000217	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	0.43925	-0.9361	9	0.05959	T	0.93	.	9.3918	0.38378	0.0:0.1286:0.5136:0.3578	rs7071768;rs16907865;rs7071768	2362;2003;2363	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	S	2363;2003;2362	ENSP00000357643:N2363S;ENSP00000357642:N2003S	ENSP00000357642:N2003S	N	-	2	0	MKI67	129793006	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.572000	0.05881	-1.763000	0.01307	-1.147000	0.01851	AAC	T|0.519;C|0.481	0.481	strong		0.488	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
DHRS9	10170	hgsc.bcm.edu	37	2	169952233	169952233	+	Silent	SNP	T	T	C	rs1059261	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:169952233T>C	ENST00000327239.4	+	8	2420	c.916T>C	c.(916-918)Ttg>Ctg	p.L306L	DHRS9_ENST00000412271.1_Silent_p.L306L|DHRS9_ENST00000357546.2_Silent_p.L306L|DHRS9_ENST00000421653.1_Silent_p.L159L|DHRS9_ENST00000428522.1_Silent_p.L306L|DHRS9_ENST00000602501.1_Silent_p.L306L|DHRS9_ENST00000432060.2_Silent_p.L366L|DHRS9_ENST00000436483.2_Silent_p.L306L	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	306					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						AGACTTTTTATTGTTGAAACA	0.438													T|||	1376	0.27476	0.4221	0.2522	5008	,	,		20683	0.3214		0.1799	False		,,,				2504	0.1411				p.L306L		Atlas-SNP	.											.	DHRS9	29	.	0			c.T916C						PASS	.	T	,,,	1618,2788	501.5+/-365.0	296,1026,881	81.0	80.0	80.0		916,916,916,916	0.8	1.0	2	dbSNP_86	80	1728,6872	315.3+/-312.2	178,1372,2750	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DHRS9	NM_001142270.1,NM_001142271.1,NM_005771.4,NM_199204.1	,,,	474,2398,3631	CC,CT,TT		20.093,36.7227,25.7266	,,,	306/320,306/320,306/320,306/320	169952233	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	10170	exon8			TTTTTATTGTTGA	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	16888	protein-coding gene	gene with protein product	"""NADP-dependent retinol dehydrogenase/reductase"", ""3-alpha hydroxysteroid dehydrogenase"", ""retinol dehydrogenase homolog"", ""short chain dehydrogenase/reductase family 9C, member 4"""	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.916T>C	2.37:g.169952233T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	162	74	0.45679	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Silent	SNP	ENST00000327239.4	37	CCDS2231.1																																																																																			T|0.732;C|0.268	0.268	strong		0.438	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771	
WDR27	253769	hgsc.bcm.edu	37	6	170058374	170058374	+	Missense_Mutation	SNP	C	C	T	rs3800544	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170058374C>T	ENST00000448612.1	-	13	1509	c.1400G>A	c.(1399-1401)cGt>cAt	p.R467H	WDR27_ENST00000333572.6_Missense_Mutation_p.R467H|WDR27_ENST00000423258.1_Missense_Mutation_p.R340H|WDR27_ENST00000546525.1_5'UTR	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	437						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		GTACTGACCACGTCGCTGTTC	0.483													C|||	400	0.0798722	0.1014	0.049	5008	,	,		20160	0.0903		0.0716	False		,,,				2504	0.0706				p.R467H		Atlas-SNP	.											.	WDR27	129	.	0			c.G1400A						PASS	.	C	HIS/ARG,HIS/ARG	364,3848		17,330,1759	78.0	78.0	78.0		1400,1019	1.5	0.0	6	dbSNP_107	78	604,7838		23,558,3640	yes	missense,missense	WDR27	NM_182552.4,NM_001202550.1	29,29	40,888,5399	TT,TC,CC		7.1547,8.642,7.6498	benign,benign	467/896,340/731	170058374	968,11686	2106	4221	6327	SO:0001583	missense	253769	exon13			TGACCACGTCGCT	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"""WD repeat domain containing"""	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.1400G>A	6.37:g.170058374C>T	ENSP00000416289:p.Arg467His	Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	182	101	0.554945	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	37	CCDS47520.2	184|184	0.08424908424908426|0.08424908424908426	48|48	0.0975609756097561|0.0975609756097561	21|21	0.058011049723756904|0.058011049723756904	61|61	0.10664335664335664|0.10664335664335664	54|54	0.0712401055408971|0.0712401055408971	C|C	4.979|4.979	0.181740|0.181740	0.09495|0.09495	0.08642|0.08642	0.071547|0.071547	ENSG00000184465|ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258|ENST00000441385	T;T;T|.	0.24538|.	1.92;2.17;1.85|.	4.56|4.56	1.5|1.5	0.22942|0.22942	.|.	1.649040|.	0.03431|.	N|.	0.207806|.	T|T	0.10121|0.10121	0.0248|0.0248	N|N	0.14661|0.14661	0.345|0.345	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B;B;B|.	0.06786|.	0.001;0.0;0.001;0.001|.	B;B;B;B|.	0.08055|.	0.0;0.0;0.003;0.001|.	T|T	0.26815|0.26815	-1.0092|-1.0092	9|4	0.14252|.	T|.	0.57|.	-13.7184|-13.7184	7.3373|7.3373	0.26617|0.26617	0.0:0.3557:0.4646:0.1796|0.0:0.3557:0.4646:0.1796	rs3800544;rs52796940;rs58816624;rs3800544|rs3800544;rs52796940;rs58816624;rs3800544	467;437;340;467|.	F2Z2U5;A2RRH5;A2RRH5-2;C9JGV0|.	.;WDR27_HUMAN;.;.|.	H|M	467;467;340|101	ENSP00000416289:R467H;ENSP00000330265:R467H;ENSP00000397869:R340H|.	ENSP00000330265:R467H|.	R|V	-|-	2|1	0|0	WDR27|WDR27	169800299|169800299	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	0.443000|0.443000	0.21644|0.21644	0.049000|0.049000	0.15920|0.15920	-0.344000|-0.344000	0.07964|0.07964	CGT|GTG	C|0.910;T|0.090	0.090	strong		0.483	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
VILL	50853	hgsc.bcm.edu	37	3	38047680	38047680	+	Silent	SNP	G	G	A	rs11707277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38047680G>A	ENST00000283713.6	+	18	2408	c.2142G>A	c.(2140-2142)ccG>ccA	p.P714P	VILL_ENST00000383759.2_Silent_p.P714P|VILL_ENST00000465644.1_Silent_p.P432P			O15195	VILL_HUMAN	villin-like	714					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)	p.P714P(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		AGAGCCACCCGTCCCACAAGG	0.617													G|||	546	0.109026	0.0545	0.098	5008	,	,		18268	0.0843		0.1252	False		,,,				2504	0.1994				p.P714P		Atlas-SNP	.											VILL,NS,carcinoma,+1,2	VILL	61	2	1	Substitution - coding silent(1)	stomach(1)	c.G2142A						PASS	.	G		430,3976	208.5+/-229.5	29,372,1802	78.0	83.0	82.0		2142	2.6	0.1	3	dbSNP_120	82	1299,7301	257.3+/-281.4	99,1101,3100	no	coding-synonymous	VILL	NM_015873.3		128,1473,4902	AA,AG,GG		15.1047,9.7594,13.2939		714/857	38047680	1729,11277	2203	4300	6503	SO:0001819	synonymous_variant	50853	exon17			CCACCCGTCCCAC		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.2142G>A	3.37:g.38047680G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	112	63	0.5625	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Silent	SNP	ENST00000283713.6	37	CCDS2670.2																																																																																			G|0.881;A|0.119	0.119	strong		0.617	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
TNS1	7145	hgsc.bcm.edu	37	2	218682757	218682757	+	Missense_Mutation	SNP	G	G	A	rs140104262	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:218682757G>A	ENST00000171887.4	-	24	4438	c.3986C>T	c.(3985-3987)cCg>cTg	p.P1329L	TNS1_ENST00000419504.1_Missense_Mutation_p.P1316L|TNS1_ENST00000430930.1_Missense_Mutation_p.P1308L	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1329					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)		CCGATCCTCCGGGGTAGAATA	0.662													G|||	4	0.000798722	0.0	0.0	5008	,	,		15504	0.0		0.003	False		,,,				2504	0.001				p.P1329L		Atlas-SNP	.											TNS1,NS,carcinoma,+1,1	TNS1	251	1	0			c.C3986T						PASS	.	G	LEU/PRO	1,4405		0,1,2202	22.0	23.0	23.0		3986	4.6	1.0	2	dbSNP_134	23	21,8577		0,21,4278	yes	missense	TNS1	NM_022648.4	98	0,22,6480	AA,AG,GG		0.2442,0.0227,0.1692	possibly-damaging	1329/1736	218682757	22,12982	2203	4299	6502	SO:0001583	missense	7145	exon24			TCCTCCGGGGTAG	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.3986C>T	2.37:g.218682757G>A	ENSP00000171887:p.Pro1329Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	39	37	0.948718	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.68	3.675106	0.67928	2.27E-4	0.002442	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.94138	-3.36;1.7;-3.36;-3.36	4.57	4.57	0.56435	.	0.605025	0.15502	N	0.258967	D	0.94853	0.8337	L	0.50333	1.59	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	P;P;P	0.58721	0.844;0.754;0.826	D	0.95184	0.8302	10	0.87932	D	0	.	17.5631	0.87912	0.0:0.0:1.0:0.0	.	1329;1308;1316	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	L	1329;467;1316;1308	ENSP00000171887:P1329L;ENSP00000394171:P467L;ENSP00000408724:P1316L;ENSP00000406016:P1308L	ENSP00000171887:P1329L	P	-	2	0	TNS1	218391002	1.000000	0.71417	0.989000	0.46669	0.311000	0.27955	6.993000	0.76245	2.368000	0.80403	0.563000	0.77884	CCG	G|0.999;A|0.001	0.001	strong		0.662	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
QDPR	5860	hgsc.bcm.edu	37	4	17506042	17506042	+	Silent	SNP	G	G	A	rs12645938	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:17506042G>A	ENST00000281243.5	-	3	434	c.255C>T	c.(253-255)tgC>tgT	p.C85C	QDPR_ENST00000513615.1_Silent_p.C85C|QDPR_ENST00000508623.1_Silent_p.C85C|QDPR_ENST00000428702.2_Silent_p.C54C	NM_000320.2	NP_000311.2	P09417	DHPR_HUMAN	quinoid dihydropteridine reductase	85					cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|dihydrobiopterin metabolic process (GO:0051066)|L-phenylalanine catabolic process (GO:0006559)|liver development (GO:0001889)|response to aluminum ion (GO:0010044)|response to glucagon (GO:0033762)|response to lead ion (GO:0010288)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	6,7-dihydropteridine reductase activity (GO:0004155)|electron carrier activity (GO:0009055)|NADH binding (GO:0070404)|NADPH binding (GO:0070402)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	13						CTCCAGCAACGCAAAGAATTG	0.468													G|||	165	0.0329473	0.0023	0.0375	5008	,	,		19684	0.0536		0.0477	False		,,,				2504	0.0348				p.C85C		Atlas-SNP	.											.	QDPR	22	.	0			c.C255T						PASS	.	G		43,4363	46.0+/-80.4	1,41,2161	142.0	131.0	135.0		255	4.3	1.0	4	dbSNP_120	135	398,8202	126.8+/-185.2	11,376,3913	no	coding-synonymous	QDPR	NM_000320.2		12,417,6074	AA,AG,GG		4.6279,0.9759,3.3907		85/245	17506042	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	5860	exon3			AGCAACGCAAAGA	AB053170	CCDS3421.1	4p15.31	2014-04-01			ENSG00000151552	ENSG00000151552	1.5.1.34	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	9752	protein-coding gene	gene with protein product	"""6,7-dihydropteridine reductase"", ""short chain dehydrogenase/reductase family 33C, member 1"""	612676				19027726	Standard	NM_000320		Approved	DHPR, PKU2, SDR33C1	uc003gpd.3	P09417	OTTHUMG00000128537	ENST00000281243.5:c.255C>T	4.37:g.17506042G>A		Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	209	98	0.4689	NM_000320	A8K158|B3KW71|Q53F52|Q9H3M5	Silent	SNP	ENST00000281243.5	37	CCDS3421.1	92	0.04212454212454213	1	0.0020325203252032522	15	0.04143646408839779	38	0.06643356643356643	38	0.05013192612137203	G	8.489	0.861623	0.17178	0.009759	0.046279	ENSG00000151552	ENST00000505710	.	.	.	5.5	4.33	0.51752	.	.	.	.	.	T	0.06645	0.0170	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41998	-0.9477	3	.	.	.	-9.7047	7.9524	0.30023	0.8281:0.0:0.1719:0.0	rs12645938;rs59248207;rs12645938	.	.	.	V	61	.	.	A	-	2	0	QDPR	17115140	0.985000	0.35326	1.000000	0.80357	0.804000	0.45430	0.330000	0.19715	0.926000	0.37118	-0.471000	0.05019	GCG	G|0.963;A|0.037	0.037	strong		0.468	QDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250372.1	NM_000320	
MAP3K10	4294	hgsc.bcm.edu	37	19	40712040	40712040	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40712040G>A	ENST00000253055.3	+	5	1699	c.1411G>A	c.(1411-1413)Ggc>Agc	p.G471S	AC118344.1_ENST00000408124.1_RNA	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	471				G -> S (in Ref. 2; CAA88531). {ECO:0000305}.|LKLREGGSHISLPSGF -> AQAAGRRQPHQPALWL (in Ref. 3). {ECO:0000305}.	activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)	p.G471C(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GCGGGAAGGCGGCAGCCACAT	0.657																																					p.G471S		Atlas-SNP	.											.	MAP3K10	70	.	1	Substitution - Missense(1)	lung(1)	c.G1411A						PASS	.						16.0	19.0	18.0					19																	40712040		2094	4126	6220	SO:0001583	missense	4294	exon5			GAAGGCGGCAGCC	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6849	protein-coding gene	gene with protein product	"""MKN28 kinase"", ""mixed lineage kinase 2"", ""MKN28 derived nonreceptor_type serine/threonine kinase"""	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.1411G>A	19.37:g.40712040G>A	ENSP00000253055:p.Gly471Ser	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	144	80	0.555556	NM_002446	Q12761|Q14871	Missense_Mutation	SNP	ENST00000253055.3	37	CCDS12549.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.649911	0.47362	.	.	ENSG00000130758	ENST00000253055	T	0.73469	-0.75	4.53	-1.14	0.09741	.	0.279022	0.41097	N	0.000942	T	0.56790	0.2009	L	0.28192	0.835	0.31735	N	0.636552	B	0.15930	0.015	B	0.21917	0.037	T	0.51568	-0.8689	10	0.41790	T	0.15	.	8.6882	0.34251	0.5148:0.0:0.4852:0.0	.	471	Q02779	M3K10_HUMAN	S	471	ENSP00000253055:G471S	ENSP00000253055:G471S	G	+	1	0	MAP3K10	45403880	0.376000	0.25098	0.585000	0.28666	0.988000	0.76386	-0.143000	0.10296	-0.078000	0.12730	0.491000	0.48974	GGC	.	.	none		0.657	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446	
CBS	875	hgsc.bcm.edu	37	21	44485590	44485590	+	Silent	SNP	C	C	T	rs73906420	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:44485590C>T	ENST00000398165.3	-	7	832	c.573G>A	c.(571-573)acG>acA	p.T191T	CBS_ENST00000352178.5_Silent_p.T191T|CBS_ENST00000544202.1_Silent_p.T103T|CBS_ENST00000398158.1_Silent_p.T191T|CBS_ENST00000470912.1_5'Flank|CBS_ENST00000359624.3_Silent_p.T191T|CBS_ENST00000398168.1_Silent_p.T191T	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	191			T -> M (in CBSD; moderate and severe forms; exhibits an activity lower than 4% of the wild-type enzyme; absent capacity to form multimeric quaternary structure). {ECO:0000269|PubMed:12815602, ECO:0000269|PubMed:15993874}.		cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)	p.T191T(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	CATTGGTGGGCGTCCTCACAA	0.647													C|||	22	0.00439297	0.0091	0.0	5008	,	,		16325	0.0		0.005	False		,,,				2504	0.0051				p.T191T		Atlas-SNP	.											CBS_ENST00000398168,NS,carcinoma,0,2	CBS	85	2	2	Substitution - coding silent(2)	endometrium(2)	c.G573A						scavenged	.	C	,,	25,4381	30.8+/-60.4	0,25,2178	43.0	46.0	45.0		573,573,573	-2.3	1.0	21	dbSNP_130	45	64,8536	39.8+/-96.3	1,62,4237	no	coding-synonymous,coding-synonymous,coding-synonymous	CBS	NM_000071.2,NM_001178008.1,NM_001178009.1	,,	1,87,6415	TT,TC,CC		0.7442,0.5674,0.6843	,,	191/552,191/552,191/552	44485590	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	875	exon7			GGTGGGCGTCCTC	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.573G>A	21.37:g.44485590C>T		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	134	55	0.410448	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Silent	SNP	ENST00000398165.3	37	CCDS13693.1																																																																																			C|0.993;T|0.007	0.007	strong		0.647	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
PLK3	1263	hgsc.bcm.edu	37	1	45270024	45270024	+	Silent	SNP	G	G	C	rs11211036	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	171	0	0		WXS	Illumina HiSeq	Phase_I	107	30	0.280374	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	
YIF1B	90522	hgsc.bcm.edu	37	19	38800165	38800165	+	Silent	SNP	C	C	T	rs3900981	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38800165C>T	ENST00000339413.6	-	2	222	c.177G>A	c.(175-177)ctG>ctA	p.L59L	YIF1B_ENST00000592694.1_Silent_p.L28L|YIF1B_ENST00000337679.8_Silent_p.L56L|YIF1B_ENST00000591784.1_Silent_p.L28L|YIF1B_ENST00000591755.1_Silent_p.L56L|YIF1B_ENST00000329420.8_Silent_p.L44L|YIF1B_ENST00000587361.1_5'UTR|YIF1B_ENST00000392124.3_Silent_p.L28L|YIF1B_ENST00000592246.1_Silent_p.L28L	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	59						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAGGATAACTCAGGCCACCAG	0.672													T|||	1112	0.222045	0.1407	0.3213	5008	,	,		14481	0.2331		0.2296	False		,,,				2504	0.2423				p.L59L		Atlas-SNP	.											.	YIF1B	47	.	0			c.G177A						PASS	.	T	,,,,,,	723,3679		50,623,1528	26.0	30.0	28.0		132,177,168,126,84,168,84	1.0	1.0	19	dbSNP_108	28	1697,6897		156,1385,2756	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YIF1B	NM_001039671.2,NM_001039672.2,NM_001039673.2,NM_001145461.1,NM_001145462.1,NM_001145463.1,NM_033557.3	,,,,,,	206,2008,4284	TT,TC,CC		19.7463,16.4244,18.6211	,,,,,,	44/300,59/315,56/312,42/298,28/284,56/292,28/284	38800165	2420,10576	2201	4297	6498	SO:0001819	synonymous_variant	90522	exon2			ATAACTCAGGCCA	AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.177G>A	19.37:g.38800165C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	182	78	0.428571	NM_001039672	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Silent	SNP	ENST00000339413.6	37	CCDS33010.1																																																																																			C|0.803;T|0.197	0.197	strong		0.672	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411619	105411619	+	Missense_Mutation	SNP	T	T	C	rs200461684		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105411619T>C	ENST00000333244.5	-	7	10288	c.10169A>G	c.(10168-10170)cAc>cGc	p.H3390R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3390						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)			CTTGGGCAGGTGCCCTTTGAG	0.627													.|||	1	0.000199681	0.0	0.0	5008	,	,		17915	0.0		0.001	False		,,,				2504	0.0				p.H3390R		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A10169G						PASS	.	T	ARG/HIS	1,3791		0,1,1895	149.0	161.0	157.0		10169	4.2	0.8	14		157	10,8194		0,10,4092	no	missense	AHNAK2	NM_138420.2	29	0,11,5987	CC,CT,TT		0.1219,0.0264,0.0917	probably-damaging	3390/5796	105411619	11,11985	1896	4102	5998	SO:0001583	missense	113146	exon7			GGCAGGTGCCCTT	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.10169A>G	14.37:g.105411619T>C	ENSP00000353114:p.His3390Arg	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	246	96	0.390244	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	2.101	-0.406153	0.04832	2.64E-4	0.001219	ENSG00000185567	ENST00000333244	T	0.01902	4.57	4.22	4.22	0.49857	.	.	.	.	.	T	0.07007	0.0178	M	0.82923	2.615	0.09310	N	1	D	0.59357	0.985	P	0.52109	0.69	T	0.24977	-1.0145	9	0.17832	T	0.49	.	8.3292	0.32175	0.0:0.0:0.2686:0.7314	.	3390	Q8IVF2	AHNK2_HUMAN	R	3390	ENSP00000353114:H3390R	ENSP00000353114:H3390R	H	-	2	0	AHNAK2	104482664	0.865000	0.29922	0.833000	0.33012	0.077000	0.17291	3.174000	0.50847	1.792000	0.52537	0.402000	0.26972	CAC	T|0.999;C|0.001	0.001	weak		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MT-ND1	4535	hgsc.bcm.edu	37	M	4153	4153	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrM:4153G>A	ENST00000361390.2	+	1	847	c.847G>A	c.(847-849)Gac>Aac	p.D283N	MT-RNR1_ENST00000389680.2_RNA|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-CO1_ENST00000361624.2_5'Flank			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	283					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 membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GATTCCGCTACGACCAACTCA	0.443																																					p.D283N		Atlas-SNP	.											.	.	.	.	0			c.G847A						PASS	.																																			SO:0001583	missense	10625	exon1			CGCTACGACCAAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.847G>A	M.37:g.4153G>A	ENSP00000354687:p.Asp283Asn	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	ENST00000361390	C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	37																																																																																				.	.	none		0.443	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
SNAP23	8773	hgsc.bcm.edu	37	15	42820589	42820589	+	Silent	SNP	G	G	A	rs1060291	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42820589G>A	ENST00000249647.3	+	6	864	c.396G>A	c.(394-396)acG>acA	p.T132T	SNAP23_ENST00000397138.1_Intron|SNAP23_ENST00000349777.1_Intron|SNAP23_ENST00000564153.1_Intron	NM_003825.3	NP_003816.2	O00161	SNP23_HUMAN	synaptosomal-associated protein, 23kDa	132					exocytosis (GO:0006887)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	azurophil granule (GO:0042582)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|specific granule (GO:0042581)|synapse (GO:0045202)				large_intestine(1)|lung(1)	2		all_cancers(109;7.14e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;1.18e-08)|all_lung(180;4.2e-08)|Melanoma(134;0.0179)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;2.62e-06)		AACCAACAACGGGAGCAGCCA	0.458													A|||	1416	0.282748	0.6611	0.2061	5008	,	,		14604	0.0079		0.2227	False		,,,				2504	0.1708				p.T132T		Atlas-SNP	.											SNAP23,colon,carcinoma,+1,1	SNAP23	15	1	0			c.G396A						PASS	.	A	,	2567,1839	535.6+/-374.3	751,1065,387	76.0	64.0	68.0		396,	-3.2	0.0	15	dbSNP_86	68	2086,6512	716.4+/-406.1	277,1532,2490	no	coding-synonymous,intron	SNAP23	NM_003825.3,NM_130798.2	,	1028,2597,2877	AA,AG,GG		24.2615,41.7385,35.7813	,	132/212,	42820589	4653,8351	2203	4299	6502	SO:0001819	synonymous_variant	8773	exon6			AACAACGGGAGCA	Y09567	CCDS10087.1, CCDS10088.1	15q14	2004-01-19	2002-08-29		ENSG00000092531	ENSG00000092531			11131	protein-coding gene	gene with protein product		602534	"""synaptosomal-associated protein, 23kD"""			9070898, 8663154	Standard	NM_003825		Approved	SNAP23A, SNAP23B, HsT17016	uc001zpz.2	O00161	OTTHUMG00000130625	ENST00000249647.3:c.396G>A	15.37:g.42820589G>A		Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_003825	O00162|Q13602|Q6IAE3	Silent	SNP	ENST00000249647.3	37	CCDS10087.1																																																																																			G|0.678;A|0.322	0.322	strong		0.458	SNAP23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253111.4	NM_003825	
HERC5	51191	hgsc.bcm.edu	37	4	89390360	89390360	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:89390360T>C	ENST00000264350.3	+	9	1340	c.1187T>C	c.(1186-1188)gTa>gCa	p.V396A	HERC5_ENST00000508159.1_Missense_Mutation_p.V34A	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	396					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of defense response to virus (GO:0050688)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ISG15 ligase activity (GO:0042296)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|liver(2)|lung(17)|ovary(4)|prostate(1)|skin(4)	53		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000209)		GAAGGGACTGTAAAGAGATGG	0.383																																					p.V396A	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											HERC5,NS,carcinoma,+1,1	HERC5	114	1	0			c.T1187C						scavenged	.						141.0	130.0	134.0					4																	89390360		2203	4300	6503	SO:0001583	missense	51191	exon9			GGACTGTAAAGAG	AB027289	CCDS3630.1	4q22.1-q23	2012-02-23	2012-02-23		ENSG00000138646	ENSG00000138646			24368	protein-coding gene	gene with protein product		608242	"""hect domain and RLD 5"""			10581175	Standard	NM_016323		Approved	CEB1	uc003hrt.4	Q9UII4	OTTHUMG00000130953	ENST00000264350.3:c.1187T>C	4.37:g.89390360T>C	ENSP00000264350:p.Val396Ala	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	159	2	0.0125786	NM_016323	B2RTQ1|Q69G20	Missense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	.	.	.	.	.	.	.	.	.	.	T	6.319	0.426866	0.11987	.	.	ENSG00000138646	ENST00000264350;ENST00000508159	T;T	0.40225	1.04;1.06	3.79	2.62	0.31277	.	0.405775	0.20080	N	0.099677	T	0.29458	0.0734	L	0.44542	1.39	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.14172	-1.0482	10	0.26408	T	0.33	.	5.2059	0.15291	0.0:0.2306:0.0:0.7694	.	396	Q9UII4	HERC5_HUMAN	A	396;34	ENSP00000264350:V396A;ENSP00000424129:V34A	ENSP00000264350:V396A	V	+	2	0	HERC5	89609383	0.651000	0.27340	0.166000	0.22797	0.492000	0.33523	1.920000	0.40025	0.832000	0.34804	0.459000	0.35465	GTA	.	.	none		0.383	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323	
TTN	7273	hgsc.bcm.edu	37	2	179395554	179395554	+	Missense_Mutation	SNP	G	G	A	rs66961115	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179395554G>A	ENST00000591111.1	-	308	101089	c.100865C>T	c.(100864-100866)gCc>gTc	p.A33622V	TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.A35263V|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A32695V|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A26198V|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A26323V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A26390V|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590040.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33622					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)			GGGTGATACGGCTTTCGGGTG	0.498													G|||	26	0.00519169	0.0	0.0043	5008	,	,		17466	0.0		0.0229	False		,,,				2504	0.0				p.A35263V		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+1,5	TTN	18412	5	0			c.C105788T						scavenged	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	8,3810		0,8,1901	125.0	124.0	125.0		79169,78968,98084,78593	4.1	1.0	2	dbSNP_130	125	118,8112		0,118,3997	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	64,64,64,64	0,126,5898	AA,AG,GG		1.4338,0.2095,1.0458	benign,benign,benign,benign	26390/27119,26323/27052,32695/33424,26198/26927	179395554	126,11922	1909	4115	6024	SO:0001583	missense	7273	exon358			GATACGGCTTTCG	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.100865C>T	2.37:g.179395554G>A	ENSP00000465570:p.Ala33622Val	Somatic	387	2	0.00516796		WXS	Illumina HiSeq	Phase_I	323	130	0.402477	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		11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	G	15.84	2.951848	0.53293	0.002095	0.014338	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.61510	0.1;0.26;0.24;0.23	4.99	4.11	0.48088	Ribonuclease H-like (1);	.	.	.	.	T	0.37461	0.1004	N	0.24115	0.695	0.28112	N	0.930973	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	0.42565	-0.9444	9	0.87932	D	0	.	13.4254	0.61022	0.0763:0.0:0.9237:0.0	.	26198;26323;26390;33622	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	32695;26198;26390;26323;26195	ENSP00000343764:A32695V;ENSP00000434586:A26198V;ENSP00000340554:A26390V;ENSP00000352154:A26323V	ENSP00000340554:A26390V	A	-	2	0	TTN	179103800	0.994000	0.37717	0.980000	0.43619	0.775000	0.43874	2.328000	0.43867	1.101000	0.41535	0.455000	0.32223	GCC	G|0.993;A|0.007	0.007	strong		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RBM6	10180	hgsc.bcm.edu	37	3	50005373	50005373	+	Missense_Mutation	SNP	C	C	T	rs142246877	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:50005373C>T	ENST00000266022.4	+	3	774	c.515C>T	c.(514-516)cCa>cTa	p.P172L	RBM6_ENST00000442092.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.P40L|RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000539992.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	172					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)		GATGCTCCTCCATCTGACTTC	0.473													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17453	0.0		0.003	False		,,,				2504	0.001				p.P172L		Atlas-SNP	.											.	RBM6	85	.	0			c.C515T						PASS	.	C	,LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	61.0	63.0	62.0		,515	5.9	1.0	3	dbSNP_134	62	37,8563	25.7+/-73.6	0,37,4263	yes	intron,missense	RBM6	NM_001167582.1,NM_005777.2	,98	0,44,6459	TT,TC,CC		0.4302,0.1589,0.3383	,probably-damaging	,172/1124	50005373	44,12962	2203	4300	6503	SO:0001583	missense	10180	exon3			CTCCTCCATCTGA	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.515C>T	3.37:g.50005373C>T	ENSP00000266022:p.Pro172Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	14.30	2.493001	0.44352	0.001589	0.004302	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.34472	1.43;1.36	5.88	5.88	0.94601	.	0.109289	0.41396	D	0.000894	T	0.32315	0.0825	L	0.40543	1.245	0.80722	D	1	B	0.31383	0.321	B	0.25614	0.062	T	0.03910	-1.0993	9	.	.	.	-3.6177	20.2405	0.98372	0.0:1.0:0.0:0.0	.	172	P78332	RBM6_HUMAN	L	172;40	ENSP00000266022:P172L;ENSP00000396466:P40L	.	P	+	2	0	RBM6	49980377	0.965000	0.33210	0.985000	0.45067	0.994000	0.84299	4.345000	0.59360	2.797000	0.96272	0.561000	0.74099	CCA	C|0.997;T|0.003	0.003	strong		0.473	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
ADGB	79747	hgsc.bcm.edu	37	6	147038089	147038089	+	Missense_Mutation	SNP	G	G	T	rs61748896	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:147038089G>T	ENST00000397944.3	+	15	1888	c.1812G>T	c.(1810-1812)gaG>gaT	p.E604D	ADGB_ENST00000367493.3_Missense_Mutation_p.E23D	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	604					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						TGGAAAGAGAGATAGTCAGCC	0.378													T|||	425	0.0848642	0.2995	0.0288	5008	,	,		15968	0.004		0.002	False		,,,				2504	0.0031				p.E604D		Atlas-SNP	.											.	ADGB	93	.	0			c.G1812T						PASS	.	T	ASP/GLU	344,1040		44,256,392	122.0	111.0	115.0		1812	-1.0	0.0	6	dbSNP_129	115	8,3174		0,8,1583	yes	missense	C6orf103	NM_024694.3	45	44,264,1975	TT,TG,GG		0.2514,24.8555,7.7092	benign	604/1668	147038089	352,4214	692	1591	2283	SO:0001583	missense	79747	exon15			AAGAGAGATAGTC	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.1812G>T	6.37:g.147038089G>T	ENSP00000381036:p.Glu604Asp	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_024694	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	37		162	0.07417582417582418	146	0.2967479674796748	11	0.03038674033149171	4	0.006993006993006993	1	0.0013192612137203166	T	0.671	-0.801848	0.02841	0.248555	0.002514	ENSG00000118492	ENST00000397944;ENST00000367493	T	0.29917	1.55	4.87	-0.985	0.10256	Peptidase C2, calpain, catalytic domain (1);	0.461581	0.22279	N	0.062150	T	0.01124	0.0037	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28902	-1.0029	9	0.08837	T	0.75	-15.0076	1.0124	0.01500	0.1439:0.1814:0.2969:0.3777	rs61748896	604	Q8N7X0	CAN7L_HUMAN	D	604;23	ENSP00000381036:E604D	ENSP00000356463:E23D	E	+	3	2	C6orf103	147079782	0.564000	0.26602	0.007000	0.13788	0.002000	0.02628	-0.080000	0.11339	-0.519000	0.06444	-0.525000	0.04345	GAG	G|0.941;T|0.059	0.059	strong		0.378	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
STK36	27148	hgsc.bcm.edu	37	2	219555262	219555262	+	Missense_Mutation	SNP	G	G	A	rs1344642	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219555262G>A	ENST00000295709.3	+	14	2027	c.1748G>A	c.(1747-1749)cGg>cAg	p.R583Q	STK36_ENST00000392105.3_Missense_Mutation_p.R583Q|STK36_ENST00000392106.2_Missense_Mutation_p.R583Q|STK36_ENST00000440309.1_Missense_Mutation_p.R583Q	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)		CAGACTTTGCGGAGGGACAGC	0.522													G|||	2112	0.421725	0.7095	0.4107	5008	,	,		18563	0.1429		0.4235	False		,,,				2504	0.3262				p.R583Q		Atlas-SNP	.											.	STK36	111	.	0			c.G1748A						PASS	.	G	GLN/ARG	2804,1602	665.1+/-401.5	886,1032,285	69.0	67.0	68.0		1748	2.4	0.0	2	dbSNP_88	68	3775,4825	536.2+/-383.0	840,2095,1365	yes	missense	STK36	NM_015690.4	43	1726,3127,1650	AA,AG,GG		43.8953,36.3595,49.4157	possibly-damaging	583/1316	219555262	6579,6427	2203	4300	6503	SO:0001583	missense	27148	exon14			CTTTGCGGAGGGA	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.1748G>A	2.37:g.219555262G>A	ENSP00000295709:p.Arg583Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	94	23	0.244681	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	921	0.4217032967032967	371	0.7540650406504065	146	0.40331491712707185	90	0.15734265734265734	314	0.41424802110817943	G	10.15	1.270143	0.23221	0.636405	0.438953	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.73681	-0.77;-0.77;0.56;-0.77	5.14	2.42	0.29668	Armadillo-like helical (1);	0.366067	0.19209	N	0.119992	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.26258	0.145;0.041	B;B	0.12837	0.008;0.002	T	0.41179	-0.9523	9	0.32370	T	0.25	-4.1498	8.0229	0.30419	0.2473:0.0:0.7527:0.0	rs1344642;rs17463680;rs52819602;rs59588577;rs1344642	583;583	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	Q	583	ENSP00000295709:R583Q;ENSP00000375955:R583Q;ENSP00000375954:R583Q;ENSP00000394095:R583Q	ENSP00000295709:R583Q	R	+	2	0	STK36	219263506	0.309000	0.24518	0.046000	0.18839	0.720000	0.41350	1.646000	0.37249	0.356000	0.24157	-0.136000	0.14681	CGG	G|0.530;A|0.470	0.470	strong		0.522	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
FAM21A	387680	hgsc.bcm.edu	37	10	47909792	47909792	+	Missense_Mutation	SNP	C	C	T	rs201373575	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	827	1	0.00120919		WXS	Illumina HiSeq	Phase_I	148	9	0.0608108	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		
MUC17	140453	hgsc.bcm.edu	37	7	100684550	100684550	+	Missense_Mutation	SNP	A	A	G	rs35090328	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100684550A>G	ENST00000306151.4	+	3	9917	c.9853A>G	c.(9853-9855)Agt>Ggt	p.S3285G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3285	59 X approximate tandem repeats.|Ser-rich.				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)					TCCATTAACAAGTATGCCTGT	0.507													A|||	483	0.0964457	0.1188	0.0764	5008	,	,		28559	0.0615		0.1133	False		,,,				2504	0.0992				p.S3285G		Atlas-SNP	.											.	MUC17	804	.	0			c.A9853G						PASS	.	A	GLY/SER	470,3936		9,452,1742	342.0	338.0	339.0		9853	-2.2	0.0	7	dbSNP_126	339	950,7650		23,904,3373	no	missense	MUC17	NM_001040105.1	56	32,1356,5115	GG,GA,AA		11.0465,10.6673,10.918	possibly-damaging	3285/4494	100684550	1420,11586	2203	4300	6503	SO:0001583	missense	140453	exon3			TTAACAAGTATGC	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.9853A>G	7.37:g.100684550A>G	ENSP00000302716:p.Ser3285Gly	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	218	185	0.848624	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	180	0.08241758241758242	39	0.07926829268292683	31	0.0856353591160221	28	0.04895104895104895	82	0.10817941952506596	a	3.445	-0.113248	0.06881	0.106673	0.110465	ENSG00000169876	ENST00000306151	T	0.02579	4.24	1.46	-2.19	0.07015	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.09310	N	1	P	0.37985	0.613	B	0.37047	0.24	T	0.43212	-0.9405	9	0.20519	T	0.43	.	2.3573	0.04299	0.342:0.0:0.4041:0.2539	rs35090328;rs58812832	3285	Q685J3	MUC17_HUMAN	G	3285	ENSP00000302716:S3285G	ENSP00000302716:S3285G	S	+	1	0	MUC17	100471270	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.627000	0.05521	-0.483000	0.06772	0.165000	0.16767	AGT	A|0.904;G|0.096	0.096	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TNN	63923	hgsc.bcm.edu	37	1	175105996	175105996	+	Missense_Mutation	SNP	C	C	T	rs2072036	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:175105996C>T	ENST00000239462.4	+	17	3580	c.3467C>T	c.(3466-3468)gCg>gTg	p.A1156V		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1156	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		A -> V (in dbSNP:rs2072036).		axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GGCACTCCAGCGCGGTATGAG	0.453													C|||	608	0.121406	0.0961	0.1052	5008	,	,		19829	0.2123		0.0905	False		,,,				2504	0.1053				p.A1156V		Atlas-SNP	.											TNN,bladder,carcinoma,-1,1	TNN	297	1	0			c.C3467T						PASS	.	C	VAL/ALA	405,4001	201.8+/-224.7	22,361,1820	84.0	78.0	80.0		3467	1.9	0.0	1	dbSNP_96	80	770,7830	183.2+/-231.5	26,718,3556	yes	missense	TNN	NM_022093.1	64	48,1079,5376	TT,TC,CC		8.9535,9.192,9.0343	benign	1156/1300	175105996	1175,11831	2203	4300	6503	SO:0001583	missense	63923	exon17			CTCCAGCGCGGTA	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.3467C>T	1.37:g.175105996C>T	ENSP00000239462:p.Ala1156Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	121	81	0.669421	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	293	0.13415750915750915	55	0.11178861788617886	34	0.09392265193370165	136	0.23776223776223776	68	0.08970976253298153	C	2.604	-0.292295	0.05568	0.09192	0.089535	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.26223	1.75	5.27	1.92	0.25849	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.397573	0.29730	N	0.011357	T	0.00012	0.0000	L	0.33624	1.015	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.26573	-1.0099	9	0.52906	T	0.07	.	4.2092	0.10503	0.0:0.5171:0.1689:0.314	rs2072036;rs52836593;rs2072036	1156	Q9UQP3	TENN_HUMAN	V	1156;979	ENSP00000239462:A1156V	ENSP00000239462:A1156V	A	+	2	0	TNN	173372619	0.000000	0.05858	0.020000	0.16555	0.006000	0.05464	0.590000	0.23954	0.750000	0.32877	-0.710000	0.03640	GCG	C|0.889;T|0.111	0.111	strong		0.453	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
CLGN	1047	hgsc.bcm.edu	37	4	141313500	141313500	+	Silent	SNP	G	G	A	rs34492995	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:141313500G>A	ENST00000325617.5	-	13	1964	c.1524C>T	c.(1522-1524)acC>acT	p.T508T	CLGN_ENST00000537281.1_Silent_p.T508T|CLGN_ENST00000414773.1_Silent_p.T508T	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	508					binding of sperm to zona pellucida (GO:0007339)|protein complex assembly (GO:0006461)|protein folding (GO:0006457)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)	calcium ion binding (GO:0005509)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(5)|ovary(2)|prostate(3)|skin(4)|urinary_tract(1)	25	all_hematologic(180;0.162)					TACATATGTCGGTTTTTTTAT	0.333													G|||	19	0.00379393	0.0008	0.0043	5008	,	,		16252	0.0		0.0139	False		,,,				2504	0.001				p.T508T		Atlas-SNP	.											.	CLGN	76	.	0			c.C1524T						PASS	.	G	,	10,4396	16.8+/-37.8	0,10,2193	129.0	123.0	125.0		1524,1524	-9.4	0.0	4	dbSNP_126	125	131,8469	66.7+/-129.0	3,125,4172	no	coding-synonymous,coding-synonymous	CLGN	NM_001130675.1,NM_004362.2	,	3,135,6365	AA,AG,GG		1.5233,0.227,1.0841	,	508/611,508/611	141313500	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	1047	exon14			TATGTCGGTTTTT	D86322	CCDS3751.1	4q28.3-q31.1	2008-02-05			ENSG00000153132	ENSG00000153132			2060	protein-coding gene	gene with protein product		601858					Standard	NM_004362		Approved		uc003iii.3	O14967	OTTHUMG00000133414	ENST00000325617.5:c.1524C>T	4.37:g.141313500G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	163	117	0.717791	NM_001130675	B3KS90|B4DXV8|D3DNY8	Silent	SNP	ENST00000325617.5	37	CCDS3751.1																																																																																			G|0.992;A|0.008	0.008	strong		0.333	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	
HIVEP1	3096	hgsc.bcm.edu	37	6	12164308	12164308	+	Missense_Mutation	SNP	G	G	A	rs181056704		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:12164308G>A	ENST00000379388.2	+	9	8103	c.7771G>A	c.(7771-7773)Gca>Aca	p.A2591T	HIVEP1_ENST00000541134.1_Missense_Mutation_p.A456T	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2591					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)				TGTAGCCAGCGCAAACCAGGT	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		21442	0.0		0.001	False		,,,				2504	0.0				p.A2591T		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G7771A						PASS	.	G	THR/ALA	3,4009		0,3,2003	70.0	78.0	76.0		7771	3.3	0.0	6		76	31,8333		0,31,4151	yes	missense	HIVEP1	NM_002114.2	58	0,34,6154	AA,AG,GG		0.3706,0.0748,0.2747	benign	2591/2719	12164308	34,12342	2006	4182	6188	SO:0001583	missense	3096	exon9			GCCAGCGCAAACC	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.7771G>A	6.37:g.12164308G>A	ENSP00000368698:p.Ala2591Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.33	3.092661	0.56075	7.48E-4	0.003706	ENSG00000095951	ENST00000379388;ENST00000541134;ENST00000542327	T;T	0.31769	2.99;1.48	5.23	3.27	0.37495	.	0.224672	0.22869	N	0.054645	T	0.07007	0.0178	L	0.38175	1.15	0.09310	N	1	P	0.35155	0.487	B	0.20955	0.032	T	0.13098	-1.0522	10	0.37606	T	0.19	-6.4409	6.6498	0.22955	0.0763:0.2109:0.5992:0.1136	.	2591	P15822	ZEP1_HUMAN	T	2591;456;573	ENSP00000368698:A2591T;ENSP00000445617:A456T	ENSP00000368698:A2591T	A	+	1	0	HIVEP1	12272294	0.000000	0.05858	0.005000	0.12908	0.319000	0.28217	0.217000	0.17603	1.173000	0.42796	0.580000	0.79431	GCA	G|0.999;A|0.001	0.001	strong		0.537	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
AIM1	202	hgsc.bcm.edu	37	6	106967185	106967185	+	Missense_Mutation	SNP	A	A	C	rs1159148	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:106967185A>C	ENST00000369066.3	+	2	1365	c.878A>C	c.(877-879)cAa>cCa	p.Q293P		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		ATTCGAGGCCAAAGGAATACT	0.428													C|||	1034	0.20647	0.1974	0.1945	5008	,	,		19009	0.0536		0.2366	False		,,,				2504	0.3538				p.Q293P		Atlas-SNP	.											.	AIM1	161	.	0			c.A878C						PASS	.	C	PRO/GLN	925,3481	733.5+/-410.5	84,757,1362	55.0	55.0	55.0		878	2.6	0.0	6	dbSNP_87	55	2232,6368	704.2+/-405.4	297,1638,2365	yes	missense	AIM1	NM_001624.2	76	381,2395,3727	CC,CA,AA		25.9535,20.9941,24.2734	benign	293/1724	106967185	3157,9849	2203	4300	6503	SO:0001583	missense	202	exon2			GAGGCCAAAGGAA	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.878A>C	6.37:g.106967185A>C	ENSP00000358062:p.Gln293Pro	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	373	0.1707875457875458	98	0.1991869918699187	73	0.20165745856353592	27	0.0472027972027972	175	0.23087071240105542	C	2.681	-0.275346	0.05679	0.209941	0.259535	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.71103	-0.54	5.73	2.58	0.30949	.	1.852350	0.03052	N	0.154645	T	0.22820	0.0551	N	0.02011	-0.69	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.03184	-1.1063	9	0.25106	T	0.35	.	8.426	0.32729	0.1137:0.6849:0.0:0.2014	rs1159148;rs17495353;rs56550327;rs58077185;rs1159148	293	Q9Y4K1	AIM1_HUMAN	P	701;293	ENSP00000358062:Q293P	ENSP00000285105:Q701P	Q	+	2	0	AIM1	107073878	0.001000	0.12720	0.000000	0.03702	0.018000	0.09664	1.127000	0.31357	0.381000	0.24851	-0.121000	0.15023	CAA	A|0.787;C|0.213	0.213	strong		0.428	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
ALDH1L1	10840	hgsc.bcm.edu	37	3	125865766	125865766	+	Missense_Mutation	SNP	C	C	A	rs2886059	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:125865766C>A	ENST00000393434.2	-	9	1337	c.988G>T	c.(988-990)Gtt>Ttt	p.V330F	ALDH1L1_ENST00000273450.3_Missense_Mutation_p.V340F|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.V330F|ALDH1L1_ENST00000393431.2_Missense_Mutation_p.V330F|ALDH1L1_ENST00000452905.2_Missense_Mutation_p.V229F|ALDH1L1_ENST00000413612.1_5'UTR	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	330	Acyl carrier. {ECO:0000255|PROSITE- ProRule:PRU00258}.		V -> F (in dbSNP:rs2886059).		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)	CGCTGCCAAACACTCTGCAAA	0.577													C|||	1188	0.23722	0.4206	0.1859	5008	,	,		19510	0.2302		0.165	False		,,,				2504	0.1074				p.V340F		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.G1018T						PASS	.	C	PHE/VAL	1587,2819	485.7+/-360.4	283,1021,899	38.0	38.0	38.0		988	0.6	0.0	3	dbSNP_101	38	1412,7188	265.3+/-286.1	124,1164,3012	yes	missense	ALDH1L1	NM_012190.2	50	407,2185,3911	AA,AC,CC		16.4186,36.0191,23.0586	benign	330/903	125865766	2999,10007	2203	4300	6503	SO:0001583	missense	10840	exon9			GCCAAACACTCTG	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.988G>T	3.37:g.125865766C>A	ENSP00000377083:p.Val330Phe	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	51	49	0.960784	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	521	0.23855311355311357	190	0.3861788617886179	74	0.20441988950276244	128	0.22377622377622378	129	0.17018469656992086	C	11.17	1.560641	0.27827	0.360191	0.164186	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434;ENST00000393431	T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92	4.69	0.561	0.17285	Acyl carrier protein-like (3);Phosphopantetheine-binding (1);	0.582604	0.16840	N	0.197367	T	0.00012	0.0000	L	0.50333	1.59	0.45979	P	0.0012020000000000364	P;P;B	0.48407	0.91;0.752;0.248	P;P;B	0.54590	0.756;0.477;0.353	T	0.36335	-0.9752	9	0.87932	D	0	.	4.42	0.11476	0.1543:0.5856:0.0:0.26	rs2886059;rs52826531;rs2886059	229;382;330	E9PBX3;Q59G10;O75891	.;.;AL1L1_HUMAN	F	340;330;229;330;330	ENSP00000273450:V340F;ENSP00000420293:V330F;ENSP00000395881:V229F;ENSP00000377083:V330F;ENSP00000377081:V330F	ENSP00000273450:V340F	V	-	1	0	ALDH1L1	127348456	0.000000	0.05858	0.041000	0.18516	0.041000	0.13682	0.133000	0.15912	-0.088000	0.12506	-0.469000	0.05056	GTT	C|0.771;N|0.000	.	strong		0.577	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
RNASET2	8635	hgsc.bcm.edu	37	6	167344583	167344583	+	Silent	SNP	A	A	G	rs13213697	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:167344583A>G	ENST00000508775.1	-	8	1035	c.516T>C	c.(514-516)ctT>ctC	p.L172L	RNASET2_ENST00000366855.6_Silent_p.L134L|RNASET2_ENST00000476238.2_Silent_p.L172L|RP11-514O12.4_ENST00000507747.1_Intron|RNASET2_ENST00000496851.2_5'Flank	NM_003730.4	NP_003721.2	O00584	RNT2_HUMAN	ribonuclease T2	172					RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	ribonuclease activity (GO:0004540)|ribonuclease T2 activity (GO:0033897)|RNA binding (GO:0003723)			large_intestine(4)|lung(4)	8		Breast(66;1.53e-05)|Ovarian(120;0.0606)		OV - Ovarian serous cystadenocarcinoma(33;1.53e-19)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00665)		ATACTCTGGCAAGGGCATCTT	0.388													A|||	924	0.184505	0.3608	0.1513	5008	,	,		25713	0.0069		0.1948	False		,,,				2504	0.1421				p.L172L		Atlas-SNP	.											.	RNASET2	18	.	0			c.T516C						PASS	.	A		1524,2882	481.7+/-359.2	274,976,953	162.0	158.0	160.0		516	-5.7	0.6	6	dbSNP_121	160	1597,7003	297.0+/-303.2	139,1319,2842	no	coding-synonymous	RNASET2	NM_003730.4		413,2295,3795	GG,GA,AA		18.5698,34.5892,23.9966		172/257	167344583	3121,9885	2203	4300	6503	SO:0001819	synonymous_variant	8635	exon8			TCTGGCAAGGGCA	AJ419866	CCDS5295.1	6q27	2014-05-20			ENSG00000026297	ENSG00000026297			21686	protein-coding gene	gene with protein product		612944				9192857	Standard	NM_003730		Approved	RNASE6PL, FLJ10907, bA514O12.3	uc003qve.3	O00584	OTTHUMG00000016009	ENST00000508775.1:c.516T>C	6.37:g.167344583A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_003730	B2RDA7|E1P5C3|Q5T8Q0|Q8TCU2|Q9BZ46|Q9BZ47	Silent	SNP	ENST00000508775.1	37	CCDS5295.1																																																																																			A|0.780;G|0.220	0.220	strong		0.388	RNASET2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043089.2	NM_003730	
CPT2	1376	hgsc.bcm.edu	37	1	53679229	53679229	+	Missense_Mutation	SNP	A	A	G	rs1799822	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:53679229A>G	ENST00000371486.3	+	5	2454	c.1939A>G	c.(1939-1941)Atg>Gtg	p.M647V	RP5-1024G6.2_ENST00000452466.1_RNA|C1orf123_ENST00000470385.1_5'Flank	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	647			M -> V (common polymorphism; confirmed at protein level; dbSNP:rs1799822). {ECO:0000269|PubMed:14605500, ECO:0000269|PubMed:1528846, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17488105, ECO:0000269|PubMed:18306170, ECO:0000269|PubMed:9600456, ECO:0000269|PubMed:9758712}.		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	CTTAGAAGACATGTTTGATGC	0.483													A|||	503	0.100439	0.0227	0.1542	5008	,	,		20518	0.0853		0.2068	False		,,,				2504	0.0736				p.M647V		Atlas-SNP	.											.	CPT2	34	.	0			c.A1939G						PASS	.	A	VAL/MET	240,4166	140.8+/-176.2	7,226,1970	88.0	80.0	83.0		1939	5.9	1.0	1	dbSNP_89	83	1937,6663	341.9+/-324.3	208,1521,2571	yes	missense	CPT2	NM_000098.2	21	215,1747,4541	GG,GA,AA		22.5233,5.4471,16.7384	benign	647/659	53679229	2177,10829	2203	4300	6503	SO:0001583	missense	1376	exon5			GAAGACATGTTTG	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.1939A>G	1.37:g.53679229A>G	ENSP00000360541:p.Met647Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	42	0.711864	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	280	0.1282051282051282	14	0.028455284552845527	68	0.1878453038674033	54	0.0944055944055944	144	0.18997361477572558	A	17.02	3.280726	0.59758	0.054471	0.225233	ENSG00000157184	ENST00000371486	D	0.90133	-2.62	5.9	5.9	0.94986	.	0.189419	0.56097	D	0.000031	T	0.00178	0.0005	L	0.31752	0.955	0.23371	P	0.99781582	B	0.09022	0.002	B	0.13407	0.009	T	0.11665	-1.0578	9	0.44086	T	0.13	-32.7754	16.3322	0.83039	1.0:0.0:0.0:0.0	rs1799822;rs17377870;rs17848486;rs17849929;rs17857680;rs52797123;rs1799822	647	P23786	CPT2_HUMAN	V	647	ENSP00000360541:M647V	ENSP00000360541:M647V	M	+	1	0	CPT2	53451817	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.445000	0.80570	2.251000	0.74343	0.528000	0.53228	ATG	A|0.854;G|0.146	0.146	strong		0.483	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098	
FAM47A	158724	hgsc.bcm.edu	37	X	34148882	34148882	+	Missense_Mutation	SNP	C	C	T	rs5973089		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:34148882C>T	ENST00000346193.3	-	1	1565	c.1514G>A	c.(1513-1515)cGc>cAc	p.R505H		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	505			Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.					p.R505H(2)		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						AGGCTCCGAGCGGAGACTGGA	0.647																																					p.R505H		Atlas-SNP	.											.	FAM47A	249	.	2	Substitution - Missense(2)	kidney(1)|endometrium(1)	c.G1514A						PASS	.						30.0	31.0	31.0					X																	34148882		2183	4272	6455	SO:0001583	missense	158724	exon1			TCCGAGCGGAGAC	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.1514G>A	X.37:g.34148882C>T	ENSP00000345029:p.Arg505His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	54	7	0.12963	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	0.583	-0.836375	0.02692	.	.	ENSG00000185448	ENST00000346193	T	0.21191	2.02	0.513	-0.53	0.11898	.	.	.	.	.	T	0.11623	0.0283	N	0.21097	0.63	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.28106	-1.0054	8	0.40728	T	0.16	.	.	.	.	rs5973089	505	Q5JRC9	FA47A_HUMAN	H	505	ENSP00000345029:R505H	ENSP00000345029:R505H	R	-	2	0	FAM47A	34058803	0.076000	0.21285	0.002000	0.10522	0.006000	0.05464	-0.425000	0.07017	-0.338000	0.08413	-0.722000	0.03604	CGC	C|1.000;T|0.000	0.000	strong		0.647	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408	
NMT1	4836	hgsc.bcm.edu	37	17	43176804	43176804	+	Silent	SNP	C	C	T	rs2239923	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	315	0	0	914	WXS	Illumina HiSeq	Phase_I	324	149	0.459877	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	
DIS3L	115752	hgsc.bcm.edu	37	15	66618342	66618342	+	Missense_Mutation	SNP	A	A	G	rs3803412	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:66618342A>G	ENST00000319212.4	+	12	1891	c.1841A>G	c.(1840-1842)gAt>gGt	p.D614G	DIS3L_ENST00000319194.5_Missense_Mutation_p.D531G|RP11-352G18.2_ENST00000565993.1_RNA	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	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	87	87	1	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29910335	29910335	+	Missense_Mutation	SNP	C	C	T	rs200058378		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29910335C>T	ENST00000396634.1	+	3	346	c.5C>T	c.(4-6)gCc>gTc	p.A2V	HLA-A_ENST00000376806.5_Missense_Mutation_p.A2V|HLA-A_ENST00000376802.2_Missense_Mutation_p.A2V|HLA-A_ENST00000376809.5_Missense_Mutation_p.A2V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	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						CCGAGGATGGCCGTCATGGCG	0.672									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.A2V		Atlas-SNP	.											HLA-A,NS,carcinoma,-1,1	HLA-A	89	1	0			c.C5T						scavenged	.						36.0	38.0	37.0					6																	29910335		2201	4296	6497	SO:0001583	missense	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGATGGCCGTCAT	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.5C>T	6.37:g.29910335C>T	ENSP00000379873:p.Ala2Val	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	155	5	0.0322581	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.183	0.794292	0.16327	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00662	5.94;5.93;5.94;5.94	2.6	-4.04	0.04010	.	.	.	.	.	T	0.00552	0.0018	L	0.27053	0.805	0.09310	N	1	D;B;D;B	0.76494	0.999;0.003;0.997;0.001	D;B;D;B	0.75484	0.986;0.014;0.986;0.014	T	0.50065	-0.8871	9	0.56958	D	0.05	.	4.6272	0.12484	0.4071:0.1733:0.4196:0.0	.	2;2;2;2	Q5SRN7;P16188;Q5SRN5;P04439	.;1A30_HUMAN;.;1A03_HUMAN	V	2	ENSP00000379873:A2V;ENSP00000366002:A2V;ENSP00000366005:A2V;ENSP00000365998:A2V	ENSP00000348012:A2V	A	+	2	0	HLA-A	30018314	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.890000	0.01613	-0.952000	0.03649	-0.531000	0.04308	GCC	C|0.999;T|0.001	0.001	weak		0.672	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
IPO11	51194	hgsc.bcm.edu	37	5	61772535	61772535	+	Silent	SNP	G	G	T	rs26635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	475	4	0.00842105		WXS	Illumina HiSeq	Phase_I	352	351	0.997159	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	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84651057	84651057	+	Missense_Mutation	SNP	G	G	A	rs140206840	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:84651057G>A	ENST00000286744.5	+	21	2901	c.2677G>A	c.(2677-2679)Gag>Aag	p.E893K	ADAMTSL3_ENST00000567716.1_3'UTR|ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.E893K	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	893						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AAAACTTGGTGAGCAGGGTCC	0.393													G|||	44	0.00878594	0.0008	0.0216	5008	,	,		18861	0.0		0.0249	False		,,,				2504	0.0031				p.E893K		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.G2677A						PASS	.	G	LYS/GLU	27,4379	31.7+/-61.6	0,27,2176	89.0	83.0	85.0		2677	3.2	0.2	15	dbSNP_134	85	214,8386	90.6+/-152.8	2,210,4088	yes	missense	ADAMTSL3	NM_207517.2	56	2,237,6264	AA,AG,GG		2.4884,0.6128,1.853	benign	893/1692	84651057	241,12765	2203	4300	6503	SO:0001583	missense	57188	exon21			CTTGGTGAGCAGG	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2677G>A	15.37:g.84651057G>A	ENSP00000286744:p.Glu893Lys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	63	53	0.84127	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	29	0.013278388278388278	0	0.0	11	0.03038674033149171	0	0.0	18	0.023746701846965697	G	9.622	1.134225	0.21123	0.006128	0.024884	ENSG00000156218	ENST00000286744	T	0.62941	-0.01	5.05	3.17	0.36434	.	0.159829	0.29551	N	0.011831	T	0.14874	0.0359	N	0.24115	0.695	0.09310	N	1	B;B	0.29716	0.002;0.255	B;B	0.27262	0.012;0.078	T	0.20042	-1.0287	10	0.02654	T	1	.	4.5348	0.12022	0.2957:0.0:0.5527:0.1516	.	893;893	P82987-2;P82987	.;ATL3_HUMAN	K	893	ENSP00000286744:E893K	ENSP00000286744:E893K	E	+	1	0	ADAMTSL3	82442061	0.235000	0.23794	0.248000	0.24265	0.960000	0.62799	1.422000	0.34826	1.121000	0.41925	0.563000	0.77884	GAG	G|0.980;A|0.020	0.020	strong		0.393	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
ARHGEF25	115557	hgsc.bcm.edu	37	12	58005682	58005682	+	Missense_Mutation	SNP	G	G	A	rs60586224	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:58005682G>A	ENST00000286494.4	+	1	465	c.5G>A	c.(4-6)cGg>cAg	p.R2Q	ARHGEF25_ENST00000333972.7_Intron|AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000356672.3_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	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						ggcgccATGCGGGGGGGGCAC	0.766													G|||	1020	0.203674	0.2564	0.1585	5008	,	,		6274	0.1657		0.2366	False		,,,				2504	0.1697				p.R2Q		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.G5A						PASS	.	G	,GLN/ARG	1060,2980		158,744,1118	8.0	10.0	9.0		,5	2.6	1.0	12	dbSNP_129	9	1844,6144		237,1370,2387	yes	intron,missense	ARHGEF25	NM_001111270.1,NM_182947.2	,43	395,2114,3505	AA,AG,GG		23.0846,26.2376,24.1437	,	,2/581	58005682	2904,9124	2020	3994	6014	SO:0001583	missense	115557	exon1			CCATGCGGGGGGG		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.5G>A	12.37:g.58005682G>A	ENSP00000286494:p.Arg2Gln	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	13	7	0.538462	NM_182947	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	37	CCDS8947.1	480	0.21978021978021978	132	0.2682926829268293	58	0.16022099447513813	106	0.1853146853146853	184	0.24274406332453827	g	16.49	3.137243	0.56936	0.262376	0.230846	ENSG00000240771	ENST00000286494	T	0.47528	0.84	2.62	2.62	0.31277	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.39530	P	0.031360000000000054	D	0.58620	0.983	P	0.61201	0.885	T	0.17379	-1.0371	8	0.62326	D	0.03	.	11.0356	0.47799	0.0:0.0:1.0:0.0	rs60586224	2	Q86VW2	ARHGP_HUMAN	Q	2	ENSP00000286494:R2Q	ENSP00000286494:R2Q	R	+	2	0	ARHGEF25	56291949	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.044000	0.49830	1.767000	0.52121	0.289000	0.19496	CGG	G|0.777;A|0.223	0.223	strong		0.766	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483	
INTS2	57508	hgsc.bcm.edu	37	17	59969000	59969000	+	Silent	SNP	T	T	C	rs753765	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	134	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	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	
ADGB	79747	hgsc.bcm.edu	37	6	146993392	146993392	+	Silent	SNP	A	A	G	rs77104188	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:146993392A>G	ENST00000397944.3	+	8	952	c.876A>G	c.(874-876)aaA>aaG	p.K292K	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	292	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				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						AGCTCCTGAAAGAAATATTGC	0.378													A|||	111	0.0221645	0.003	0.0274	5008	,	,		17411	0.0		0.0437	False		,,,				2504	0.045				p.K292K		Atlas-SNP	.											.	ADGB	93	.	0			c.A876G						PASS	.	A		13,1371		0,13,679	57.0	51.0	53.0		876	1.3	1.0	6	dbSNP_132	53	206,2976		9,188,1394	no	coding-synonymous	C6orf103	NM_024694.3		9,201,2073	GG,GA,AA		6.4739,0.9393,4.7963		292/1668	146993392	219,4347	692	1591	2283	SO:0001819	synonymous_variant	79747	exon8			CCTGAAAGAAATA	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.876A>G	6.37:g.146993392A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	182	92	0.505495	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				A|0.976;G|0.024	0.024	strong		0.378	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
MYH9	4627	hgsc.bcm.edu	37	22	36689434	36689434	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:36689434C>T	ENST00000216181.5	-	30	4266	c.4036G>A	c.(4036-4038)Gag>Aag	p.E1346K		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1346					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						TCCTCCTCCTCCAGCTGCTCC	0.637			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.E1346K		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.G4036A						PASS	.						80.0	76.0	77.0					22																	36689434		2203	4300	6503	SO:0001583	missense	4627	exon30	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CCTCCTCCAGCTG		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.4036G>A	22.37:g.36689434C>T	ENSP00000216181:p.Glu1346Lys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	100	4	0.04	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.763943	0.89932	.	.	ENSG00000100345	ENST00000216181	D	0.84070	-1.8	5.0	2.88	0.33553	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.90974	0.7162	M	0.88906	2.99	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.90771	0.4672	10	0.87932	D	0	.	10.4603	0.44575	0.0:0.7922:0.1347:0.0731	.	1346	P35579	MYH9_HUMAN	K	1346	ENSP00000216181:E1346K	ENSP00000216181:E1346K	E	-	1	0	MYH9	35019380	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.997000	0.70646	0.607000	0.29982	0.491000	0.48974	GAG	.	.	none		0.637	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
CDC16	8881	hgsc.bcm.edu	37	13	115030714	115030714	+	Splice_Site	SNP	T	T	C	rs8809	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:115030714T>C	ENST00000356221.3	+	17	1710	c.1602T>C	c.(1600-1602)atT>atC	p.I534I	CDC16_ENST00000375312.3_Splice_Site_p.I389I|CDC16_ENST00000252458.6_Splice_Site_p.I389I|CDC16_ENST00000375310.1_Splice_Site_p.I440I|CDC16_ENST00000375308.1_Splice_Site_p.I440I|CDC16_ENST00000360383.3_Splice_Site_p.I534I|CDC16_ENST00000461716.1_3'UTR|CDC16_ENST00000252457.5_Splice_Site_p.I533I			Q13042	CDC16_HUMAN	cell division cycle 16	534					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|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)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|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)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	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)			AAGCTTATATTGGTAAGATAA	0.358													C|||	1850	0.369409	0.6868	0.2853	5008	,	,		19363	0.1567		0.2565	False		,,,				2504	0.3354				p.I534I		Atlas-SNP	.											.	CDC16	50	.	0			c.T1602C						PASS	.	C	,	2645,1761	524.3+/-371.3	796,1053,354	283.0	264.0	270.0		1602,1602	-4.7	0.7	13	dbSNP_116	270	1962,6638	724.1+/-406.5	227,1508,2565	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CDC16	NM_001078645.1,NM_003903.3	,	1023,2561,2919	CC,CT,TT		22.814,39.9682,35.4221	,	534/621,534/621	115030714	4607,8399	2203	4300	6503	SO:0001630	splice_region_variant	8881	exon17			TTATATTGGTAAG	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.1603+1T>C	13.37:g.115030714T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			T|0.661;C|0.339	0.339	strong		0.358	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	Silent
MUC4	4585	hgsc.bcm.edu	37	3	195512302	195512302	+	Missense_Mutation	SNP	G	G	A	rs201164821	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195512302G>A	ENST00000463781.3	-	2	6608	c.6149C>T	c.(6148-6150)cCt>cTt	p.P2050L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2050L	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)		GCTGGTGACAGGAAGAGGGGT	0.572																																					p.P2050L		Atlas-SNP	.											MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	0			c.C6149T						scavenged	.						23.0	21.0	22.0					3																	195512302		687	1578	2265	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.6149C>T	3.37:g.195512302G>A	ENSP00000417498:p.Pro2050Leu	Somatic	296	4	0.0135135		WXS	Illumina HiSeq	Phase_I	405	52	0.128395	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	2.749	-0.260440	0.05791	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29397	1.58;1.57	.	.	.	.	.	.	.	.	T	0.14399	0.0348	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.27365	-1.0076	6	.	.	.	.	.	.	.	.	2050	E7ESK3	.	L	2050	ENSP00000417498:P2050L;ENSP00000420243:P2050L	.	P	-	2	0	MUC4	196996697	0.014000	0.17966	0.001000	0.08648	0.017000	0.09413	1.130000	0.31393	-0.833000	0.04245	0.064000	0.15345	CCT	A|0.008;G|0.989;T|0.002	0.008	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BRAT1	221927	hgsc.bcm.edu	37	7	2577781	2577781	+	Silent	SNP	T	T	C	rs1043291	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:2577781T>C	ENST00000340611.4	-	14	2644	c.2388A>G	c.(2386-2388)gaA>gaG	p.E796E	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	796					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						GGGGACTCTTTTCCACGTGGT	0.667													C|||	2311	0.461462	0.7352	0.4121	5008	,	,		17797	0.3661		0.3519	False		,,,				2504	0.3374				p.E796E		Atlas-SNP	.											BRAT1,NS,carcinoma,0,4	BRAT1	57	4	0			c.A2388G						PASS	.	C		2809,1561		929,951,305	26.0	25.0	25.0		2388	3.6	1.0	7	dbSNP_86	25	2832,5676		502,1828,1924	yes	coding-synonymous	BRAT1	NM_152743.3		1431,2779,2229	CC,CT,TT		33.2863,35.7208,43.8034		796/822	2577781	5641,7237	2185	4254	6439	SO:0001819	synonymous_variant	221927	exon14			ACTCTTTTCCACG	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.2388A>G	7.37:g.2577781T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	21	0.259259	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Silent	SNP	ENST00000340611.4	37	CCDS5334.1																																																																																			T|0.555;C|0.445	0.445	strong		0.667	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
ANKEF1	63926	hgsc.bcm.edu	37	20	10030188	10030188	+	Missense_Mutation	SNP	T	T	A	rs652633	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:10030188T>A	ENST00000378380.3	+	6	1300	c.971T>A	c.(970-972)cTg>cAg	p.L324Q	ANKEF1_ENST00000488991.1_3'UTR|SNAP25-AS1_ENST00000603542.1_RNA|SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.L324Q	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	324			L -> Q (in dbSNP:rs652633).				calcium ion binding (GO:0005509)										CCAAATCCACTGTGGGCCCTT	0.517													T|||	990	0.197684	0.2685	0.1571	5008	,	,		16990	0.0069		0.2744	False		,,,				2504	0.2485				p.L324Q		Atlas-SNP	.											.	.	.	.	0			c.T971A						PASS	.	T	GLN/LEU,GLN/LEU	1128,3278	405.1+/-333.4	145,838,1220	77.0	80.0	79.0		971,971	3.2	0.0	20	dbSNP_83	79	2417,6183	401.6+/-347.2	345,1727,2228	yes	missense,missense	ANKRD5	NM_022096.4,NM_198798.1	113,113	490,2565,3448	AA,AT,TT		28.1047,25.6015,27.2567	benign,benign	324/777,324/777	10030188	3545,9461	2203	4300	6503	SO:0001583	missense	63926	exon6			ATCCACTGTGGGC	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.971T>A	20.37:g.10030188T>A	ENSP00000367631:p.Leu324Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_198798	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	391	0.17902930402930403	116	0.23577235772357724	65	0.17955801104972377	5	0.008741258741258742	205	0.2704485488126649	T	3.673	-0.067203	0.07273	0.256015	0.281047	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.68331	-0.32;-0.32	5.6	3.19	0.36642	Ankyrin repeat-containing domain (1);	0.632290	0.16702	N	0.203072	T	0.00012	0.0000	L	0.38531	1.155	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.08953	-1.0697	9	0.29301	T	0.29	0.0049	3.4295	0.07422	0.1276:0.108:0.1193:0.645	rs652633;rs52838052;rs652633	324	Q9NU02	ANKR5_HUMAN	Q	324	ENSP00000367644:L324Q;ENSP00000367631:L324Q	ENSP00000367631:L324Q	L	+	2	0	ANKRD5	9978188	0.000000	0.05858	0.017000	0.16124	0.073000	0.16967	-0.618000	0.05578	1.044000	0.40200	0.528000	0.53228	CTG	T|0.761;A|0.239	0.239	strong		0.517	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562823	6562823	+	Missense_Mutation	SNP	C	C	T	rs2041387	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6562823C>T	ENST00000266556.7	+	3	671	c.506C>T	c.(505-507)gCg>gTg	p.A169V	TAPBPL_ENST00000544021.1_Missense_Mutation_p.A92V|CD27-AS1_ENST00000545339.1_RNA|CD27-AS1_ENST00000399492.2_RNA|TAPBPL_ENST00000545700.1_3'UTR	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	169			A -> V (in dbSNP:rs2041387). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						AAGAATGAGGCGCTCTGGCAC	0.572													C|||	1293	0.258187	0.1846	0.1744	5008	,	,		18472	0.3224		0.3042	False		,,,				2504	0.3037				p.A169V		Atlas-SNP	.											.	TAPBPL	21	.	0			c.C506T						PASS	.	C	VAL/ALA	825,3581	324.8+/-298.8	84,657,1462	37.0	35.0	36.0		506	4.6	0.0	12	dbSNP_94	36	2622,5978	419.4+/-353.1	407,1808,2085	yes	missense	TAPBPL	NM_018009.4	64	491,2465,3547	TT,TC,CC		30.4884,18.7245,26.5032	benign	169/469	6562823	3447,9559	2203	4300	6503	SO:0001583	missense	55080	exon3			ATGAGGCGCTCTG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.506C>T	12.37:g.6562823C>T	ENSP00000266556:p.Ala169Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	562	0.2573260073260073	88	0.17886178861788618	63	0.17403314917127072	188	0.32867132867132864	223	0.2941952506596306	C	9.385	1.073965	0.20147	0.187245	0.304884	ENSG00000139192	ENST00000544021;ENST00000266556	T;T	0.48201	0.82;3.02	4.56	4.56	0.56223	.	0.481446	0.23317	N	0.049484	T	0.00012	0.0000	L	0.56769	1.78	0.58432	P	2.9999999999752447E-6	B	0.10296	0.003	B	0.08055	0.003	T	0.25012	-1.0144	9	0.21014	T	0.42	-5.8199	12.8579	0.57897	0.0:1.0:0.0:0.0	rs2041387;rs3168617;rs16932609;rs17196801;rs17845451;rs17858324;rs57407101;rs2041387	169	Q9BX59	TPSNR_HUMAN	V	92;169	ENSP00000445341:A92V;ENSP00000266556:A169V	ENSP00000266556:A169V	A	+	2	0	TAPBPL	6433084	0.179000	0.23135	0.022000	0.16811	0.002000	0.02628	1.069000	0.30641	2.097000	0.63578	0.609000	0.83330	GCG	C|0.744;N|0.000	.	strong		0.572	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
ERMAP	114625	hgsc.bcm.edu	37	1	43296195	43296195	+	Missense_Mutation	SNP	C	C	T	rs33953680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43296195C>T	ENST00000372517.2	+	3	320	c.76C>T	c.(76-78)Cat>Tat	p.H26Y	ERMAP_ENST00000487556.1_Intron|ERMAP_ENST00000328249.3_5'UTR|ERMAP_ENST00000372514.3_Missense_Mutation_p.H26Y	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	26			H -> Y (in dbSNP:rs33953680). {ECO:0000269|PubMed:12393480, ECO:0000269|Ref.5}.			cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCTGTCTGTGCATGTGTCAGG	0.527													C|||	713	0.142372	0.0234	0.2723	5008	,	,		19084	0.0099		0.2952	False		,,,				2504	0.1902				p.H26Y		Atlas-SNP	.											.	ERMAP	30	.	0			c.C76T						PASS	.	C	TYR/HIS,TYR/HIS	307,4099	167.3+/-198.3	11,285,1907	127.0	102.0	110.0		76,76	0.7	0.0	1	dbSNP_126	110	2391,6209	397.5+/-345.8	337,1717,2246	yes	missense,missense	ERMAP	NM_001017922.1,NM_018538.3	83,83	348,2002,4153	TT,TC,CC		27.8023,6.9678,20.7443	benign,benign	26/476,26/476	43296195	2698,10308	2203	4300	6503	SO:0001583	missense	114625	exon3			TCTGTGCATGTGT	AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010		"""Blood group antigens"", ""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	15743	protein-coding gene	gene with protein product		609017	"""Radin blood group"", ""Scianna blood group"", ""erythroblast membrane-associated protein"", ""erythroblast membrane-associated protein (RD and SC blood groups)"""	RD, SC		11549310	Standard	XM_005270415		Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.76C>T	1.37:g.43296195C>T	ENSP00000361595:p.His26Tyr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	81	60	0.740741	NM_001017922	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	Missense_Mutation	SNP	ENST00000372517.2	37	CCDS475.1	347	0.15888278388278387	15	0.03048780487804878	108	0.2983425414364641	4	0.006993006993006993	220	0.29023746701846964	C	8.207	0.799368	0.16397	0.069678	0.278023	ENSG00000164010	ENST00000372517;ENST00000372514	T;T	0.45276	0.9;0.9	5.32	0.706	0.18133	Immunoglobulin-like (1);	1.705140	0.03691	N	0.247099	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	D;B	0.59357	0.985;0.386	P;B	0.51055	0.657;0.063	T	0.19192	-1.0313	9	0.02654	T	1	.	8.39	0.32522	0.2569:0.4622:0.2809:0.0	rs33953680	87;26	B7Z3C6;Q96PL5	.;ERMAP_HUMAN	Y	26	ENSP00000361595:H26Y;ENSP00000361592:H26Y	ENSP00000361592:H26Y	H	+	1	0	ERMAP	43068782	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.089000	0.11180	0.192000	0.20272	-0.291000	0.09656	CAT	C|0.807;T|0.193	0.193	strong		0.527	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020180.1	NM_018538	
EXT1	2131	hgsc.bcm.edu	37	8	118847782	118847782	+	Silent	SNP	G	G	A	rs11546829	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:118847782G>A	ENST00000378204.2	-	3	1871	c.1065C>T	c.(1063-1065)tgC>tgT	p.C355C		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	355					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)	p.C355C(1)		breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			TCACAGGGACGCAGGCAGCCT	0.478			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Langer-Giedion syndrome;Hereditary Multiple Exostoses				G|||	871	0.173922	0.0908	0.3069	5008	,	,		19602	0.0853		0.2684	False		,,,				2504	0.1861				p.C355C		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	EXT1,NS,carcinoma,0,1	EXT1	98	1	1	Substitution - coding silent(1)	stomach(1)	c.C1065T						PASS	.	G		556,3850	250.0+/-257.2	32,492,1679	93.0	80.0	85.0		1065	1.4	1.0	8	dbSNP_120	85	2644,5956	427.4+/-355.6	415,1814,2071	no	coding-synonymous	EXT1	NM_000127.2		447,2306,3750	AA,AG,GG		30.7442,12.6192,24.604		355/747	118847782	3200,9806	2203	4300	6503	SO:0001819	synonymous_variant	2131	exon3	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	AGGGACGCAGGCA	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3512	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608177	"""Langer-Giedion syndrome chromosome region"", ""exostoses (multiple) 1"", ""exostosin 1"""	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1065C>T	8.37:g.118847782G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	116	43	0.37069	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	37	CCDS6324.1	421	0.19276556776556777	46	0.09349593495934959	113	0.31215469613259667	50	0.08741258741258741	212	0.2796833773087071	g	10.46	1.356943	0.24598	0.126192	0.307442	ENSG00000182197	ENST00000436216	.	.	.	5.77	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.24905	-1.0147	3	.	.	.	-14.1796	10.3835	0.44125	0.6261:0.0:0.3739:0.0	rs11546829;rs17439875;rs17474651;rs17439875	.	.	.	C	145	.	.	R	-	1	0	EXT1	118916963	0.906000	0.30813	0.998000	0.56505	0.986000	0.74619	0.094000	0.15107	0.002000	0.14630	-0.137000	0.14449	CGT	G|0.774;A|0.226	0.226	strong		0.478	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127	
HDGFL1	154150	hgsc.bcm.edu	37	6	22570064	22570064	+	Missense_Mutation	SNP	C	C	T	rs2076506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:22570064C>T	ENST00000230012.3	+	1	387	c.260C>T	c.(259-261)aCg>aTg	p.T87M	HDGFL1_ENST00000510882.2_Missense_Mutation_p.T87M	NM_138574.2	NP_612641.2	Q5TGJ6	HDGL1_HUMAN	hepatoma derived growth factor-like 1	87			T -> M (in dbSNP:rs2076506).							kidney(1)|large_intestine(3)|lung(7)	11	Ovarian(93;0.163)					AACAACCCCACGGTCCAGGCC	0.652													C|||	955	0.190695	0.0567	0.2493	5008	,	,		12678	0.3879		0.0865	False		,,,				2504	0.2342				p.T87M		Atlas-SNP	.											.	HDGFL1	33	.	0			c.C260T						PASS	.	C	MET/THR	301,4105		13,275,1915	27.0	26.0	26.0		260	1.4	0.0	6	dbSNP_96	26	711,7887		27,657,3615	yes	missense	HDGFL1	NM_138574.2	81	40,932,5530	TT,TC,CC		8.2694,6.8316,7.7822	possibly-damaging	87/252	22570064	1012,11992	2203	4299	6502	SO:0001583	missense	154150	exon1			ACCCCACGGTCCA	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.260C>T	6.37:g.22570064C>T	ENSP00000230012:p.Thr87Met	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_138574	Q96MJ6	Missense_Mutation	SNP	ENST00000230012.3	37	CCDS34347.1	375	0.1717032967032967	29	0.05894308943089431	70	0.19337016574585636	213	0.3723776223776224	63	0.08311345646437995	C	10.33	1.320124	0.23994	0.068316	0.082694	ENSG00000112273	ENST00000230012;ENST00000510882	T;T	0.70749	-0.51;-0.51	3.28	1.38	0.22167	.	0.258413	0.37261	N	0.002180	T	0.33673	0.0871	L	0.42245	1.32	0.80722	P	0.0	D	0.53745	0.962	B	0.38378	0.272	T	0.31779	-0.9931	9	0.51188	T	0.08	-40.4351	1.6909	0.02852	0.2123:0.453:0.2077:0.127	rs2076506;rs56879815;rs2076506	87	Q5TGJ6	HDGL1_HUMAN	M	87	ENSP00000230012:T87M;ENSP00000442129:T87M	ENSP00000230012:T87M	T	+	2	0	HDGFL1	22678043	0.000000	0.05858	0.007000	0.13788	0.424000	0.31475	-0.161000	0.10026	0.352000	0.24053	0.491000	0.48974	ACG	C|0.862;T|0.138	0.138	strong		0.652	HDGFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043500.1	NM_138574	
WRAP73	49856	hgsc.bcm.edu	37	1	3551792	3551792	+	Silent	SNP	G	G	A	rs2296034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:3551792G>A	ENST00000270708.7	-	7	743	c.670C>T	c.(670-672)Ctg>Ttg	p.L224L	WRAP73_ENST00000378322.3_Silent_p.L224L	NM_017818.3	NP_060288.3	Q9P2S5	WRP73_HUMAN	WD repeat containing, antisense to TP73	224						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)	12						TTGATGCCCAGGGACCACTCG	0.522													G|||	394	0.0786741	0.0045	0.0634	5008	,	,		18738	0.1915		0.0388	False		,,,				2504	0.1145				p.L224L		Atlas-SNP	.											.	WRAP73	43	.	0			c.C670T						PASS	.	G		41,4365	43.1+/-76.7	0,41,2162	77.0	77.0	77.0		670	4.7	1.0	1	dbSNP_100	77	365,8235	121.5+/-180.6	13,339,3948	no	coding-synonymous	WRAP73	NM_017818.3		13,380,6110	AA,AG,GG		4.2442,0.9305,3.1216		224/461	3551792	406,12600	2203	4300	6503	SO:0001819	synonymous_variant	49856	exon7			TGCCCAGGGACCA	AB034912, EF494669	CCDS48.1	1p36.3	2013-05-21	2011-04-13	2011-04-13	ENSG00000116213	ENSG00000116213		"""WD repeat domain containing"""	12759	protein-coding gene	gene with protein product		606040	"""WD repeat domain 8"""	WDR8			Standard	NM_017818		Approved		uc001ako.3	Q9P2S5	OTTHUMG00000000612	ENST00000270708.7:c.670C>T	1.37:g.3551792G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	110	69	0.627273	NM_017818	Q5T0D6|Q9BUH7|Q9NTK7|Q9NX56	Silent	SNP	ENST00000270708.7	37	CCDS48.1																																																																																			G|0.949;A|0.051	0.051	strong		0.522	WRAP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001470.1		
SIDT1	54847	hgsc.bcm.edu	37	3	113320477	113320477	+	Missense_Mutation	SNP	C	C	T	rs33990195	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113320477C>T	ENST00000264852.4	+	11	1814	c.1088C>T	c.(1087-1089)aCa>aTa	p.T363I	SIDT1_ENST00000393830.3_Missense_Mutation_p.T363I	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	363			T -> I (in dbSNP:rs33990195).		dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						GCTGCCAGCACACCCGAAGGG	0.418													C|||	227	0.0453275	0.0068	0.0605	5008	,	,		19620	0.0407		0.0994	False		,,,				2504	0.0358				p.T363I		Atlas-SNP	.											SIDT1,colon,carcinoma,-1,1	SIDT1	99	1	0			c.C1088T						PASS	.	C	ILE/THR	64,4342	60.5+/-97.4	2,60,2141	118.0	104.0	109.0		1088	6.1	1.0	3	dbSNP_126	109	872,7728	197.6+/-242.2	52,768,3480	yes	missense	SIDT1	NM_017699.2	89	54,828,5621	TT,TC,CC		10.1395,1.4526,7.1967	possibly-damaging	363/828	113320477	936,12070	2203	4300	6503	SO:0001583	missense	54847	exon11			CCAGCACACCCGA	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.1088C>T	3.37:g.113320477C>T	ENSP00000264852:p.Thr363Ile	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	184	88	0.478261	NM_017699	Q17RR4	Missense_Mutation	SNP	ENST00000264852.4	37	CCDS2974.1	122	0.055860805860805864	6	0.012195121951219513	23	0.06353591160220995	26	0.045454545454545456	67	0.08839050131926121	C	16.59	3.166585	0.57476	0.014526	0.101395	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.23348	1.91;1.91	6.07	6.07	0.98685	.	0.083258	0.52532	D	0.000080	T	0.00666	0.0022	L	0.34521	1.04	0.54753	D	0.999988	B;B	0.30727	0.248;0.292	B;B	0.33846	0.136;0.171	T	0.01993	-1.1233	10	0.32370	T	0.25	-16.7075	20.6593	0.99626	0.0:1.0:0.0:0.0	rs33990195	363;363	Q9NXL6-2;Q9NXL6	.;SIDT1_HUMAN	I	363	ENSP00000264852:T363I;ENSP00000377416:T363I	ENSP00000264852:T363I	T	+	2	0	SIDT1	114803167	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	5.080000	0.64437	2.885000	0.99019	0.655000	0.94253	ACA	C|0.924;T|0.076	0.076	strong		0.418	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
FAM32A	26017	hgsc.bcm.edu	37	19	16301759	16301759	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:16301759C>T	ENST00000263384.7	+	4	357	c.332C>T	c.(331-333)aCg>aTg	p.T111M	FAM32A_ENST00000588367.1_Missense_Mutation_p.T93M|CTD-2562J15.4_ENST00000591038.1_RNA|FAM32A_ENST00000589852.1_Missense_Mutation_p.T91M	NM_014077.2	NP_054796.1	Q9Y421	FA32A_HUMAN	family with sequence similarity 32, member A	111					apoptotic process (GO:0006915)|cell cycle (GO:0007049)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.T111M(1)		lung(1)	1						GTCAGCTGGACGAAGTAGCCG	0.557																																					p.T111M		Atlas-SNP	.											FAM32A,NS,carcinoma,0,1	FAM32A	6	1	1	Substitution - Missense(1)	lung(1)	c.C332T						PASS	.						73.0	61.0	65.0					19																	16301759		2203	4300	6503	SO:0001583	missense	26017	exon4			GCTGGACGAAGTA	BC000639	CCDS12341.1	19p13.12-p13.11	2013-09-19			ENSG00000105058	ENSG00000105058			24563	protein-coding gene	gene with protein product		614554				11230166, 10810093	Standard	NM_014077		Approved	DKFZP586O0120	uc002ndt.3	Q9Y421	OTTHUMG00000182279	ENST00000263384.7:c.332C>T	19.37:g.16301759C>T	ENSP00000263384:p.Thr111Met	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	131	53	0.40458	NM_014077	Q9BT02	Missense_Mutation	SNP	ENST00000263384.7	37	CCDS12341.1	.	.	.	.	.	.	.	.	.	.	C	16.01	2.999969	0.54147	.	.	ENSG00000105058	ENST00000263384	.	.	.	3.99	2.94	0.34122	.	0.000000	0.85682	D	0.000000	T	0.44307	0.1287	M	0.72576	2.205	0.80722	D	1	P	0.40144	0.704	B	0.28465	0.09	T	0.48747	-0.9008	9	0.66056	D	0.02	-16.2628	9.4497	0.38719	0.0:0.8985:0.0:0.1015	.	111	Q9Y421	FA32A_HUMAN	M	111	.	ENSP00000263384:T111M	T	+	2	0	FAM32A	16162759	1.000000	0.71417	0.841000	0.33234	0.578000	0.36192	5.807000	0.69157	0.793000	0.33875	0.462000	0.41574	ACG	.	.	none		0.557	FAM32A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460346.1	NM_014077	
OR12D2	26529	hgsc.bcm.edu	37	6	29364838	29364838	+	Missense_Mutation	SNP	C	C	G	rs2073152	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29364838C>G	ENST00000383555.2	+	1	423	c.362C>G	c.(361-363)tCt>tGt	p.S121C	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	121			S -> C (in dbSNP:rs2073152).			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(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						TTTGACCTCTCTGTGGCTATC	0.498													C|||	873	0.174321	0.1044	0.1455	5008	,	,		21158	0.2381		0.3052	False		,,,				2504	0.089				p.S121C		Atlas-SNP	.											.	OR12D2	42	.	0			c.C362G						PASS	.	C	CYS/SER	400,2622		27,346,1138	95.0	95.0	95.0		362	1.4	1.0	6	dbSNP_96	95	1588,3830		251,1086,1372	no	missense	OR12D2	NM_013936.3	112	278,1432,2510	GG,GC,CC		29.3097,13.2363,23.5545	benign	121/308	29364838	1988,6452	1511	2709	4220	SO:0001583	missense	26529	exon1			ACCTCTCTGTGGC		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.362C>G	6.37:g.29364838C>G	ENSP00000373047:p.Ser121Cys	Somatic	304	1	0.00328947		WXS	Illumina HiSeq	Phase_I	225	220	0.977778	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	500	0.22893772893772893	62	0.12601626016260162	56	0.15469613259668508	146	0.25524475524475526	236	0.3113456464379947	C	3.829	-0.036169	0.07497	0.132363	0.293097	ENSG00000168787	ENST00000383555	T	0.01369	4.97	3.94	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	0.312384	0.27807	N	0.017778	T	0.00210	0.0006	N	0.01257	-0.925	0.48901	P	2.7800000000000047E-4	B	0.24186	0.099	B	0.14578	0.011	T	0.47249	-0.9132	9	0.72032	D	0.01	.	4.3245	0.11034	0.4926:0.0982:0.0:0.4092	rs2073152;rs52828595;rs57122758;rs2073152	121	P58182	O12D2_HUMAN	C	121	ENSP00000373047:S121C	ENSP00000373047:S121C	S	+	2	0	OR12D2	29472817	0.118000	0.22208	0.954000	0.39281	0.013000	0.08279	0.184000	0.16939	0.093000	0.17368	-1.328000	0.01277	TCT	C|0.763;G|0.237	0.237	strong		0.498	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
TUBB1	81027	hgsc.bcm.edu	37	20	57598808	57598808	+	Missense_Mutation	SNP	G	G	A	rs41303899	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:57598808G>A	ENST00000217133.1	+	4	595	c.326G>A	c.(325-327)gGa>gAa	p.G109E		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	109					'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)	TACACGGAGGGAGCCGAGCTG	0.592													G|||	4	0.000798722	0.0	0.0029	5008	,	,		16838	0.0		0.002	False		,,,				2504	0.0				p.G109E		Atlas-SNP	.											TUBB1,mucosal,malignant_melanoma,+1,1	TUBB1	42	1	0			c.G326A						PASS	.	G	GLU/GLY	2,4404	4.2+/-10.8	0,2,2201	83.0	91.0	89.0		326	5.4	1.0	20	dbSNP_127	89	12,8588	9.1+/-34.3	0,12,4288	yes	missense	TUBB1	NM_030773.3	98	0,14,6489	AA,AG,GG		0.1395,0.0454,0.1076	probably-damaging	109/452	57598808	14,12992	2203	4300	6503	SO:0001583	missense	81027	exon4			CGGAGGGAGCCGA	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.326G>A	20.37:g.57598808G>A	ENSP00000217133:p.Gly109Glu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	59	0.475806	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	37	CCDS13475.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	17.48	3.399586	0.62177	4.54E-4	0.001395	ENSG00000101162	ENST00000217133	T	0.75821	-0.97	5.39	5.39	0.77823	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.94374	0.8191	H	0.99993	5.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97591	1.0117	10	0.87932	D	0	.	18.1143	0.89546	0.0:0.0:1.0:0.0	rs41303899	109	Q9H4B7	TBB1_HUMAN	E	109	ENSP00000217133:G109E	ENSP00000217133:G109E	G	+	2	0	TUBB1	57032203	1.000000	0.71417	0.952000	0.39060	0.158000	0.22134	9.824000	0.99380	2.537000	0.85549	0.655000	0.94253	GGA	G|0.999;A|0.001	0.001	strong		0.592	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773	
TRIM58	25893	hgsc.bcm.edu	37	1	248023966	248023966	+	Silent	SNP	C	C	T	rs3737277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248023966C>T	ENST00000366481.3	+	2	516	c.468C>T	c.(466-468)gaC>gaT	p.D156D		NM_015431.3	NP_056246.3	Q8NG06	TRI58_HUMAN	tripartite motif containing 58	156						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(39)|ovary(4)|pancreas(1)|skin(7)|stomach(1)	63	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)	all_cancers(173;0.0286)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			AGTTGGAGGACGCCTTGACTC	0.483													C|||	1288	0.257188	0.3298	0.268	5008	,	,		19154	0.1885		0.2744	False		,,,				2504	0.2045				p.D156D		Atlas-SNP	.											.	TRIM58	143	.	0			c.C468T						PASS	.	C		1463,2943	471.7+/-356.1	243,977,983	106.0	103.0	104.0		468	-7.8	0.0	1	dbSNP_107	104	2429,6171	402.2+/-347.4	345,1739,2216	no	coding-synonymous	TRIM58	NM_015431.3		588,2716,3199	TT,TC,CC		28.2442,33.2047,29.9247		156/487	248023966	3892,9114	2203	4300	6503	SO:0001819	synonymous_variant	25893	exon2			GGAGGACGCCTTG	AF327057	CCDS1636.1	1q44	2013-01-09	2011-01-25		ENSG00000162722	ENSG00000162722		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	24150	protein-coding gene	gene with protein product			"""tripartite motif-containing 58"""				Standard	NM_015431		Approved	BIA2	uc001ido.3	Q8NG06	OTTHUMG00000040203	ENST00000366481.3:c.468C>T	1.37:g.248023966C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	159	52	0.327044	NM_015431	Q6B0H9	Silent	SNP	ENST00000366481.3	37	CCDS1636.1																																																																																			C|0.716;T|0.284	0.284	strong		0.483	TRIM58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096860.1	NM_015431	
AKAP13	11214	hgsc.bcm.edu	37	15	86287867	86287867	+	Missense_Mutation	SNP	G	G	A	rs2614668	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:86287867G>A	ENST00000394518.2	+	37	8496	c.8401G>A	c.(8401-8403)Gcg>Acg	p.A2801T	AKAP13_ENST00000560579.1_3'UTR|RP11-158M2.3_ENST00000558375.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.A2805T|AKAP13_ENST00000394510.2_Missense_Mutation_p.A1046T	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	2801	Interaction with ESR1.		A -> T (in dbSNP:rs2614668).		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						AGATGGTCCCGCGTCAGAAGT	0.493													G|||	944	0.188498	0.2005	0.0677	5008	,	,		19457	0.3085		0.0746	False		,,,				2504	0.2515				p.A2805T	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.G8413A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	960,3444	364.1+/-316.8	103,754,1345	140.0	147.0	145.0		8413,8401,3136	1.3	0.0	15	dbSNP_100	145	744,7854	180.2+/-229.2	32,680,3587	yes	missense,missense,missense	AKAP13	NM_006738.4,NM_007200.3,NM_144767.3	58,58,58	135,1434,4932	AA,AG,GG		8.6532,21.7984,13.1057	benign,benign,benign	2805/2818,2801/2814,1046/1059	86287867	1704,11298	2202	4299	6501	SO:0001583	missense	11214	exon37			GGTCCCGCGTCAG	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.8401G>A	15.37:g.86287867G>A	ENSP00000378026:p.Ala2801Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	67	50	0.746269	NM_006738	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	381	0.17445054945054944	104	0.21138211382113822	31	0.0856353591160221	196	0.34265734265734266	50	0.06596306068601583	G	8.788	0.929971	0.18131	0.217984	0.086532	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540;ENST00000394510	T;T;T	0.44083	0.93;0.93;0.93	5.64	1.26	0.21427	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.13145	0.004;0.007	B;B	0.09377	0.002;0.004	T	0.37641	-0.9697	8	0.33940	T	0.23	.	6.2305	0.20732	0.1819:0.0:0.6152:0.2029	rs2614668;rs52833278;rs58410149;rs2614668	2801;2805	Q12802;Q12802-2	AKP13_HUMAN;.	T	2805;2801;2804;2780;1046	ENSP00000354718:A2805T;ENSP00000378026:A2801T;ENSP00000378018:A1046T	ENSP00000354718:A2805T	A	+	1	0	AKAP13	84088871	0.001000	0.12720	0.016000	0.15963	0.126000	0.20510	0.331000	0.19733	0.325000	0.23359	-1.149000	0.01842	GCG	G|0.842;A|0.158	0.158	strong		0.493	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
YTHDC2	64848	hgsc.bcm.edu	37	5	112889374	112889374	+	Missense_Mutation	SNP	G	G	A	rs10071816	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:112889374G>A	ENST00000161863.4	+	14	2168	c.1955G>A	c.(1954-1956)aGt>aAt	p.S652N	YTHDC2_ENST00000515883.1_Missense_Mutation_p.S652N	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	652	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		S -> N (in dbSNP:rs10071816).		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)		TTTGCTGACAGTACACATAGG	0.398													A|||	1672	0.333866	0.6172	0.4265	5008	,	,		15678	0.2083		0.1909	False		,,,				2504	0.1616				p.S652N		Atlas-SNP	.											.	YTHDC2	118	.	0			c.G1955A						PASS	.	A	ASN/SER	2532,1872	539.9+/-375.4	746,1040,416	141.0	141.0	141.0		1955	1.6	0.2	5	dbSNP_119	141	1581,7019	743.6+/-407.2	140,1301,2859	yes	missense	YTHDC2	NM_022828.3	46	886,2341,3275	AA,AG,GG		18.3837,42.5068,31.6287	benign	652/1431	112889374	4113,8891	2202	4300	6502	SO:0001583	missense	64848	exon14			CTGACAGTACACA	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.1955G>A	5.37:g.112889374G>A	ENSP00000161863:p.Ser652Asn	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	725	0.33195970695970695	324	0.6585365853658537	134	0.3701657458563536	123	0.21503496503496503	144	0.18997361477572558	A	0	-2.651789	0.00109	0.574932	0.183837	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000511372	T;T	0.06933	4.22;3.24	5.38	1.65	0.23941	Helicase, C-terminal (2);	0.343223	0.32836	N	0.005589	T	0.00012	0.0000	N	0.11927	0.2	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.42498	-0.9448	9	0.02654	T	1	.	12.1875	0.54247	0.7907:0.0:0.2093:0.0	rs10071816;rs57240370;rs10071816	652	Q9H6S0	YTDC2_HUMAN	N	652;652;562	ENSP00000161863:S652N;ENSP00000423101:S652N	ENSP00000161863:S652N	S	+	2	0	YTHDC2	112917273	0.970000	0.33590	0.154000	0.22540	0.067000	0.16453	1.347000	0.33975	-0.510000	0.06523	-2.276000	0.00273	AGT	G|0.681;A|0.319	0.319	strong		0.398	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
CNNM2	54805	hgsc.bcm.edu	37	10	104678801	104678801	+	Silent	SNP	C	C	T	rs117691462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:104678801C>T	ENST00000369878.4	+	1	752	c.564C>T	c.(562-564)tcC>tcT	p.S188S	CNNM2_ENST00000369875.3_Silent_p.S188S|CNNM2_ENST00000433628.2_Silent_p.S188S	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	188					magnesium ion homeostasis (GO:0010960)|magnesium ion transport (GO:0015693)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	adenyl nucleotide binding (GO:0030554)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19		Colorectal(252;0.103)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;7.89e-09)|all cancers(201;1.82e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)		AGAGCAAGTCCTATTACCTGT	0.652													C|||	8	0.00159744	0.0008	0.0	5008	,	,		13685	0.0		0.007	False		,,,				2504	0.0				p.S188S		Atlas-SNP	.											.	CNNM2	119	.	0			c.C564T						PASS	.	C	,,	2,4402		0,2,2200	96.0	104.0	102.0		564,564,564	2.6	1.0	10	dbSNP_132	102	46,8548		0,46,4251	no	coding-synonymous,coding-synonymous,coding-synonymous	CNNM2	NM_017649.3,NM_199076.1,NM_199077.1	,,	0,48,6451	TT,TC,CC		0.5353,0.0454,0.3693	,,	188/876,188/854,188/553	104678801	48,12950	2202	4297	6499	SO:0001819	synonymous_variant	54805	exon1			CAAGTCCTATTAC	AF216962	CCDS7543.1, CCDS44474.1, CCDS44475.1	10q24.32	2014-08-08	2014-08-07		ENSG00000148842	ENSG00000148842			103	protein-coding gene	gene with protein product		607803	"""cyclin M2"""	ACDP2		21393841, 24699222	Standard	NM_017649		Approved		uc001kwm.3	Q9H8M5	OTTHUMG00000018976	ENST00000369878.4:c.564C>T	10.37:g.104678801C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	75	62	0.826667	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	37	CCDS44474.1																																																																																			C|0.996;T|0.004	0.004	strong		0.652	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649	
TEP1	7011	hgsc.bcm.edu	37	14	20837033	20837033	+	Missense_Mutation	SNP	T	T	C	rs2104978	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20837033T>C	ENST00000262715.5	-	54	7725	c.7685A>G	c.(7684-7686)cAt>cGt	p.H2562R	TEP1_ENST00000556935.1_Missense_Mutation_p.H2454R	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2562			H -> R (in dbSNP:rs2104978).		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)		AGGTAGCACATGGAGGGCTGT	0.527													T|||	173	0.0345447	0.003	0.0317	5008	,	,		16457	0.002		0.0656	False		,,,				2504	0.0808				p.H2562R		Atlas-SNP	.											.	TEP1	224	.	0			c.A7685G						PASS	.	T	ARG/HIS	62,4344	60.5+/-97.4	0,62,2141	87.0	67.0	74.0		7685	5.8	1.0	14	dbSNP_96	74	570,8030	153.6+/-207.9	17,536,3747	yes	missense	TEP1	NM_007110.4	29	17,598,5888	CC,CT,TT		6.6279,1.4072,4.8593	probably-damaging	2562/2628	20837033	632,12374	2203	4300	6503	SO:0001583	missense	7011	exon54			AGCACATGGAGGG		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.7685A>G	14.37:g.20837033T>C	ENSP00000262715:p.His2562Arg	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	260	155	0.596154	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	63	0.028846153846153848	0	0.0	12	0.03314917127071823	0	0.0	51	0.06728232189973615	T	21.4	4.151048	0.78001	0.014072	0.066279	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.58210	0.35;0.35	5.81	5.81	0.92471	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.181219	0.42964	D	0.000629	T	0.10594	0.0259	L	0.39898	1.24	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.72338	0.961;0.977	T	0.22556	-1.0213	10	0.13108	T	0.6	-17.9579	13.6839	0.62504	0.0:0.0:0.0:1.0	rs2104978;rs2228033;rs17277305;rs52818387;rs2104978	2454;2562	G3V5X7;Q99973	.;TEP1_HUMAN	R	2562;2554;2454	ENSP00000262715:H2562R;ENSP00000452574:H2454R	ENSP00000262715:H2562R	H	-	2	0	TEP1	19906873	0.998000	0.40836	1.000000	0.80357	0.986000	0.74619	3.917000	0.56424	2.226000	0.72624	0.482000	0.46254	CAT	T|0.957;C|0.043	0.043	strong		0.527	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
ZNF304	57343	hgsc.bcm.edu	37	19	57863052	57863052	+	Missense_Mutation	SNP	T	T	C	rs117111481	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57863052T>C	ENST00000282286.5	+	1	193	c.20T>C	c.(19-21)aTg>aCg	p.M7T	ZNF304_ENST00000443917.2_Missense_Mutation_p.M7T|ZNF304_ENST00000391705.3_Missense_Mutation_p.M7T|ZNF304_ENST00000598744.1_5'UTR|CTC-444N24.13_ENST00000597973.1_RNA			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	7					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)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		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;0.0265)		GCGGTGCTGATGGACCGGGTT	0.662													T|||	37	0.00738818	0.0008	0.0072	5008	,	,		14774	0.0		0.0308	False		,,,				2504	0.0				p.M7T		Atlas-SNP	.											.	ZNF304	74	.	0			c.T20C						PASS	.	T	THR/MET	16,4390	23.3+/-48.9	0,16,2187	98.0	76.0	83.0		20	-4.4	0.0	19	dbSNP_132	83	226,8374	93.3+/-155.3	5,216,4079	yes	missense	ZNF304	NM_020657.2	81	5,232,6266	CC,CT,TT		2.6279,0.3631,1.8607	possibly-damaging	7/660	57863052	242,12764	2203	4300	6503	SO:0001583	missense	57343	exon1			TGCTGATGGACCG	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"""Zinc fingers, C2H2-type"", ""-"""	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.20T>C	19.37:g.57863052T>C	ENSP00000282286:p.Met7Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	37	CCDS12950.1	26	0.011904761904761904	0	0.0	2	0.0055248618784530384	0	0.0	24	0.0316622691292876	T	0.005	-2.125450	0.00342	0.003631	0.026279	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.06528	3.29;3.29;3.35	2.49	-4.43	0.03568	Krueppel-associated box (1);	.	.	.	.	T	0.01287	0.0042	L	0.31926	0.97	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47586	-0.9106	9	0.06757	T	0.87	.	10.8558	0.46798	0.0:0.7312:0.0:0.2688	.	7;7	Q9HCX3;E7EQD3	ZN304_HUMAN;.	T	7	ENSP00000282286:M7T;ENSP00000375586:M7T;ENSP00000401642:M7T	ENSP00000282286:M7T	M	+	2	0	ZNF304	62554864	0.001000	0.12720	0.000000	0.03702	0.036000	0.12997	-1.136000	0.03222	-1.491000	0.01840	-0.314000	0.08810	ATG	T|0.985;C|0.015	0.015	strong		0.662	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		
CTH	1491	hgsc.bcm.edu	37	1	70904800	70904800	+	Missense_Mutation	SNP	G	G	T	rs1021737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:70904800G>T	ENST00000370938.3	+	12	1352	c.1208G>T	c.(1207-1209)aGt>aTt	p.S403I	CTH_ENST00000346806.2_Missense_Mutation_p.S359I|CTH_ENST00000411986.2_Missense_Mutation_p.S371I	NM_001902.5	NP_001893.2	Q96IQ7	VSIG2_HUMAN	cystathionine gamma-lyase	0						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						CCAAGTGGAAGTCACAGCTAG	0.373													G|||	1028	0.205272	0.0628	0.3703	5008	,	,		17108	0.2173		0.2584	False		,,,				2504	0.2137				p.S403I		Atlas-SNP	.											.	CTH	48	.	0			c.G1208T	GRCh37	CM041751	CTH	M	rs1021737	PASS	.	G	ILE/SER,ILE/SER,ILE/SER	476,3930	222.6+/-239.4	32,412,1759	122.0	126.0	125.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1112,1208,1076	0.8	0.0	1	dbSNP_86	125	2617,5983	423.1+/-354.3	402,1813,2085	yes	missense,missense,missense	CTH	NM_001190463.1,NM_001902.5,NM_153742.4	142,142,142	434,2225,3844	TT,TG,GG		30.4302,10.8034,23.7813	benign,benign,benign	371/374,403/406,359/362	70904800	3093,9913	2203	4300	6503	SO:0001583	missense	1491	exon12			GTGGAAGTCACAG	BC015807	CCDS650.1, CCDS651.1, CCDS53333.1	1p31.1	2014-06-24	2014-06-24		ENSG00000116761	ENSG00000116761	4.4.1.1		2501	protein-coding gene	gene with protein product		607657	"""cystathionase (cystathionine gamma-lyase)"""			1339280	Standard	NM_001902		Approved		uc001dfd.3	P32929	OTTHUMG00000009352	ENST00000370938.3:c.1208G>T	1.37:g.70904800G>T	ENSP00000359976:p.Ser403Ile	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	136	92	0.676471	NM_001902	O95791|Q9NX42	Missense_Mutation	SNP	ENST00000370938.3	37	CCDS650.1	496	0.2271062271062271	38	0.07723577235772358	130	0.35911602209944754	125	0.21853146853146854	203	0.2678100263852243	G	3.230	-0.157730	0.06544	0.108034	0.304302	ENSG00000116761	ENST00000411986;ENST00000370938;ENST00000346806	T;T;T	0.72505	-0.65;-0.65;-0.66	4.79	0.838	0.18902	.	0.641097	0.14202	N	0.334609	T	0.29321	0.0730	N	0.08118	0	0.80722	P	0.0	B;B;B	0.31859	0.232;0.343;0.232	B;B;B	0.35607	0.102;0.206;0.102	T	0.04467	-1.0949	9	0.45353	T	0.12	-20.7361	6.4403	0.21847	0.3992:0.0:0.6008:0.0	rs1021737;rs1128455;rs3185428;rs17407754;rs17531503;rs52829078;rs61639407;rs1021737	371;359;403	E9PDV0;P32929-2;P32929	.;.;CGL_HUMAN	I	371;403;359	ENSP00000413407:S371I;ENSP00000359976:S403I;ENSP00000311554:S359I	ENSP00000311554:S359I	S	+	2	0	CTH	70677388	0.000000	0.05858	0.035000	0.18076	0.023000	0.10783	0.035000	0.13797	0.308000	0.22923	-0.156000	0.13503	AGT	G|0.779;T|0.221	0.221	strong		0.373	CTH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025918.1	NM_001902	
NUP133	55746	hgsc.bcm.edu	37	1	229623338	229623338	+	Missense_Mutation	SNP	T	T	C	rs1065674	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:229623338T>C	ENST00000261396.3	-	10	1308	c.1217A>G	c.(1216-1218)cAg>cGg	p.Q406R	NUP133_ENST00000537506.1_Missense_Mutation_p.Q390R	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	406			Q -> R (in dbSNP:rs1065674).		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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GACCGTCAACTGACACAAAAT	0.338													C|||	1519	0.303315	0.5802	0.3271	5008	,	,		16738	0.1607		0.2097	False		,,,				2504	0.1554				p.Q406R		Atlas-SNP	.											.	NUP133	111	.	0			c.A1217G						PASS	.	C	ARG/GLN	2321,2085	571.2+/-383.0	600,1121,482	83.0	85.0	84.0		1217	2.2	0.4	1	dbSNP_86	84	1863,6737	729.6+/-406.7	201,1461,2638	yes	missense	NUP133	NM_018230.2	43	801,2582,3120	CC,CT,TT		21.6628,47.3218,32.1698	benign	406/1157	229623338	4184,8822	2203	4300	6503	SO:0001583	missense	55746	exon10			GTCAACTGACACA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1217A>G	1.37:g.229623338T>C	ENSP00000261396:p.Gln406Arg	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	82	30	0.365854	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	612	0.2802197802197802	275	0.5589430894308943	100	0.27624309392265195	80	0.13986013986013987	157	0.20712401055408972	C	0.017	-1.505721	0.00992	0.526782	0.216628	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.35605	1.3;1.3;1.3	5.07	2.2	0.27929	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.167226	0.56097	N	0.000039	T	0.00012	0.0000	N	0.01015	-1.05	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48525	-0.9028	9	0.02654	T	1	-5.5753	9.3235	0.37980	0.0:0.583:0.0:0.417	rs1065674;rs17355666;rs60689296;rs1065674	406	Q8WUM0	NU133_HUMAN	R	406;406;406;390	ENSP00000261396:Q406R;ENSP00000355640:Q406R;ENSP00000443496:Q390R	ENSP00000261396:Q406R	Q	-	2	0	NUP133	227689961	0.910000	0.30920	0.355000	0.25773	0.580000	0.36256	1.748000	0.38308	0.029000	0.15352	-1.952000	0.00485	CAG	T|0.691;C|0.309	0.309	strong		0.338	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
CPSF6	11052	hgsc.bcm.edu	37	12	69646914	69646914	+	Silent	SNP	G	G	A	rs2305641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:69646914G>A	ENST00000435070.2	+	3	464	c.354G>A	c.(352-354)cgG>cgA	p.R118R	CPSF6_ENST00000266679.8_Silent_p.R118R|CPSF6_ENST00000551516.1_Intron|CPSF6_ENST00000456847.3_Silent_p.R118R|CPSF6_ENST00000550987.1_3'UTR	NM_007007.2	NP_008938.2	Q16630	CPSF6_HUMAN	cleavage and polyadenylation specific factor 6, 68kDa	118	Necessary for interaction with NUDT21/CPSF5.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA polyadenylation (GO:0006378)|mRNA processing (GO:0006397)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleus (GO:0005634)|paraspeckles (GO:0042382)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(7)|lung(8)	16	all_epithelial(5;2.47e-36)|Lung NSC(4;1.1e-32)|all_lung(4;6.26e-31)|Breast(13;1.59e-06)|Esophageal squamous(21;0.187)		Epithelial(6;4.89e-17)|BRCA - Breast invasive adenocarcinoma(5;8.5e-10)|Lung(24;6.04e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|LUSC - Lung squamous cell carcinoma(43;0.171)|Kidney(9;0.241)			TTGAAAATCGGGCAAATGGCC	0.318													G|||	2147	0.428714	0.4607	0.4236	5008	,	,		17172	0.4395		0.4284	False		,,,				2504	0.3783				p.R118R		Atlas-SNP	.											.	CPSF6	96	.	0			c.G354A						PASS	.	G		1972,2432	536.2+/-374.4	456,1060,686	58.0	62.0	61.0		354	0.3	1.0	12	dbSNP_100	61	3769,4827	527.8+/-381.2	826,2117,1355	no	coding-synonymous	CPSF6	NM_007007.2		1282,3177,2041	AA,AG,GG		43.846,44.7775,44.1615		118/552	69646914	5741,7259	2202	4298	6500	SO:0001819	synonymous_variant	11052	exon3			AAATCGGGCAAAT	X67336	CCDS8988.1, CCDS73494.1	12q15	2013-06-18	2002-08-29			ENSG00000111605		"""RNA binding motif (RRM) containing"""	13871	protein-coding gene	gene with protein product	"""cleavage factor Im complex 68 kDa subunit"""	604979	"""cleavage and polyadenylation specific factor 6, 68kD subunit"""			9659921, 17267687	Standard	NM_007007		Approved	CFIM, HPBRII-4, HPBRII-7, CFIM68	uc001sut.4	Q16630		ENST00000435070.2:c.354G>A	12.37:g.69646914G>A		Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	300	136	0.453333	NM_007007	A8K7K9|Q53ES1|Q9BSJ7|Q9BW18	Silent	SNP	ENST00000435070.2	37	CCDS8988.1																																																																																			G|0.568;A|0.432	0.432	strong		0.318	CPSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403609.1	NM_007007	
ZP3	7784	hgsc.bcm.edu	37	7	76069811	76069811	+	Missense_Mutation	SNP	T	T	C	rs2906999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76069811T>C	ENST00000394857.3	+	7	1001	c.943T>C	c.(943-945)Tcg>Ccg	p.S315P	ZP3_ENST00000336517.4_Missense_Mutation_p.S264P|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Missense_Mutation_p.S139P	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	315			S -> P (in dbSNP:rs2906999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1478648, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2385582}.		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						AGTGGAAGGCTCGGCTGACAT	0.493													C|||	2960	0.591054	0.6558	0.5908	5008	,	,		21316	0.5427		0.5209	False		,,,				2504	0.6258				p.S315P		Atlas-SNP	.											.	ZP3	32	.	0			c.T943C						PASS	.	C	PRO/SER,PRO/SER	2642,1764		883,876,444	87.0	95.0	92.0		943,790	-7.7	0.0	7	dbSNP_101	92	4353,4247		1072,2209,1019	no	missense,missense	ZP3	NM_001110354.1,NM_007155.5	74,74	1955,3085,1463	CC,CT,TT		49.3837,40.0363,46.2171	benign,benign	315/425,264/374	76069811	6995,6011	2203	4300	6503	SO:0001583	missense	7784	exon7			GAAGGCTCGGCTG	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.943T>C	7.37:g.76069811T>C	ENSP00000378326:p.Ser315Pro	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	288	182	0.631944	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	1102	0.5045787545787546	290	0.5894308943089431	189	0.5220994475138122	273	0.4772727272727273	350	0.46174142480211083	N	0.087	-1.174174	0.01646	0.599637	0.506163	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	T;T;T	0.22336	2.54;2.77;1.96	4.96	-7.74	0.01241	.	1.184840	0.06001	N	0.647710	T	0.00012	0.0000	N	0.01431	-0.87	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40040	-0.9584	9	0.06099	T	0.92	0.1283	1.1308	0.01745	0.3458:0.3118:0.1128:0.2297	rs2906999;rs2906999	264;315	P21754-3;P21754	.;ZP3_HUMAN	P	264;315;315;139	ENSP00000337310:S264P;ENSP00000378326:S315P;ENSP00000411955:S139P	ENSP00000337310:S264P	S	+	1	0	ZP3	75907747	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.059000	0.03479	-2.339000	0.00626	-1.329000	0.01275	TCG	T|0.444;C|0.556	0.556	strong		0.493	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
CLEC4D	338339	hgsc.bcm.edu	37	12	8667897	8667897	+	Missense_Mutation	SNP	A	A	G	rs4304840	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:8667897A>G	ENST00000299665.2	+	2	287	c.94A>G	c.(94-96)Agt>Ggt	p.S32G		NM_080387.4	NP_525126.2	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D	32			S -> G (in dbSNP:rs4304840). {ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Lung SC(5;0.184)					CTTACTTCTCAGTGTCTGTTT	0.378													A|||	1504	0.300319	0.5923	0.1844	5008	,	,		-128	0.122		0.2475	False		,,,				2504	0.226				p.S32G		Atlas-SNP	.											.	CLEC4D	46	.	0			c.A94G						PASS	.	A	GLY/SER	2420,1986	618.2+/-393.1	668,1084,451	232.0	197.0	209.0		94	-0.3	0.3	12	dbSNP_111	209	1987,6613	348.8+/-327.2	249,1489,2562	yes	missense	CLEC4D	NM_080387.4	56	917,2573,3013	GG,GA,AA		23.1047,45.0749,33.8844	benign	32/216	8667897	4407,8599	2203	4300	6503	SO:0001583	missense	338339	exon2			CTTCTCAGTGTCT	AF411850	CCDS8593.1	12p13.31	2005-09-21	2005-02-09	2005-02-11		ENSG00000166527		"""C-type lectin domain containing"""	14554	protein-coding gene	gene with protein product		609964	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8"""	CLECSF8			Standard	NM_080387		Approved	Mpcl	uc001qun.3	Q8WXI8		ENST00000299665.2:c.94A>G	12.37:g.8667897A>G	ENSP00000299665:p.Ser32Gly	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	286	120	0.41958	NM_080387	Q8N5J5	Missense_Mutation	SNP	ENST00000299665.2	37	CCDS8593.1	621	0.28434065934065933	279	0.5670731707317073	66	0.18232044198895028	88	0.15384615384615385	188	0.24802110817941952	a	0.126	-1.119811	0.01785	0.549251	0.231047	ENSG00000166527	ENST00000382064;ENST00000299665	T;T	0.05513	3.43;3.7	3.36	-0.299	0.12808	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.52501	P	4.199999999998649E-5	B	0.10296	0.003	B	0.04013	0.001	T	0.29518	-1.0009	8	0.36615	T	0.2	.	7.1227	0.25454	0.7959:0.0:0.2041:0.0	rs4304840;rs60537162;rs4304840	32	Q8WXI8	CLC4D_HUMAN	G	32	ENSP00000371496:S32G;ENSP00000299665:S32G	ENSP00000299665:S32G	S	+	1	0	CLEC4D	8559164	0.031000	0.19500	0.321000	0.25320	0.003000	0.03518	-0.178000	0.09782	-0.089000	0.12484	-1.335000	0.01260	AGT	A|0.678;G|0.322	0.322	strong		0.378	CLEC4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400565.1	NM_080387	
NIN	51199	hgsc.bcm.edu	37	14	51227000	51227000	+	Silent	SNP	A	A	G	rs4901055	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:51227000A>G	ENST00000382041.3	-	17	2164	c.1974T>C	c.(1972-1974)caT>caC	p.H658H	NIN_ENST00000389868.3_Silent_p.H658H|NIN_ENST00000324330.9_Silent_p.H658H|NIN_ENST00000245441.5_Silent_p.H658H|NIN_ENST00000382043.4_Silent_p.H658H|NIN_ENST00000453196.1_Silent_p.H658H|NIN_ENST00000530997.2_Silent_p.H658H	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	658					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)					TTTCGTTCTCATGCCTTTGCT	0.478			T	PDGFRB	MPD								A|||	743	0.148363	0.3775	0.1138	5008	,	,		21891	0.004		0.1243	False		,,,				2504	0.0368				p.H658H		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.T1974C						PASS	.	A	,,,	1517,2889	444.3+/-347.3	258,1001,944	73.0	79.0	77.0		1974,1974,1974,1974	-0.7	0.6	14	dbSNP_111	77	1259,7341	243.5+/-273.1	111,1037,3152	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,,,	369,2038,4096	GG,GA,AA		14.6395,34.4303,21.344	,,,	658/1378,658/2134,658/2047,658/2091	51227000	2776,10230	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon17			GTTCTCATGCCTT	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.1974T>C	14.37:g.51227000A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	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	341	0.15613553113553114	195	0.39634146341463417	48	0.13259668508287292	3	0.005244755244755245	95	0.12532981530343007	A	0.227	-1.023764	0.02061	0.344303	0.146395	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.93	-0.694	0.11294	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999822304	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.5257	13.3399	0.60538	0.6236:0.0:0.3764:0.0	rs4901055;rs59513340;rs4901055	.	.	.	R	149	.	.	X	-	1	0	NIN	50296750	0.002000	0.14202	0.582000	0.28627	0.047000	0.14425	-0.071000	0.11505	-0.332000	0.08489	-1.431000	0.01090	TGA	A|0.812;G|0.188	0.188	strong		0.478	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
FLG	2312	hgsc.bcm.edu	37	1	152279729	152279729	+	Missense_Mutation	SNP	C	C	T	rs3126072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152279729C>T	ENST00000368799.1	-	3	7668	c.7633G>A	c.(7633-7635)Gga>Aga	p.G2545R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2545	Ser-rich.		G -> R (in dbSNP:rs3126072).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCGAGTGTCCAGAGCTGTCG	0.577									Ichthyosis				T|||	2378	0.47484	0.5658	0.451	5008	,	,		19229	0.6548		0.173	False		,,,				2504	0.4939				p.G2545R		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.G7633A						scavenged	.	T	ARG/GLY	2198,2202	581.0+/-385.3	593,1012,595	204.0	228.0	220.0		7633	0.8	0.0	1	dbSNP_103	220	1457,7143	750.7+/-407.4	126,1205,2969	no	missense	FLG	NM_002016.1	125	719,2217,3564	TT,TC,CC		16.9419,49.9545,28.1154	benign	2545/4062	152279729	3655,9345	2200	4300	6500	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGTGTCCAGAGCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7633G>A	1.37:g.152279729C>T	ENSP00000357789:p.Gly2545Arg	Somatic	295	2	0.00677966		WXS	Illumina HiSeq	Phase_I	401	151	0.376559	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	882	0.40384615384615385	256	0.5203252032520326	135	0.3729281767955801	358	0.6258741258741258	133	0.17546174142480211	T	2.868	-0.234541	0.05983	0.499545	0.169419	ENSG00000143631	ENST00000368799	T	0.01705	4.68	1.97	0.755	0.18415	.	.	.	.	.	T	0.00144	0.0004	N	0.00265	-1.74	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.12656	-1.0539	8	0.14252	T	0.57	.	4.4439	0.11588	0.0:0.4317:0.0:0.5682	.	2545	P20930	FILA_HUMAN	R	2545	ENSP00000357789:G2545R	ENSP00000357789:G2545R	G	-	1	0	FLG	150546353	0.408000	0.25360	0.001000	0.08648	0.010000	0.07245	-0.243000	0.08915	-0.360000	0.08138	-0.848000	0.03037	GGA	C|0.682;T|0.318	0.318	strong		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
RBM5	10181	hgsc.bcm.edu	37	3	50153356	50153356	+	Silent	SNP	T	T	C	rs1138536	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:50153356T>C	ENST00000347869.3	+	22	2212	c.2037T>C	c.(2035-2037)taT>taC	p.Y679Y	RP11-493K19.3_ENST00000425674.1_RNA|RP11-493K19.3_ENST00000437204.1_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	101	0	0		WXS	Illumina HiSeq	Phase_I	86	55	0.639535	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	
USP31	57478	hgsc.bcm.edu	37	16	23091371	23091371	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:23091371G>A	ENST00000219689.7	-	13	2071	c.2072C>T	c.(2071-2073)cCg>cTg	p.P691L		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	333	DUSP 2. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CCGTCTCCACGGGGACCAATG	0.562																																					p.P691L		Atlas-SNP	.											.	USP31	122	.	0			c.C2072T						PASS	.						126.0	109.0	114.0					16																	23091371		2197	4300	6497	SO:0001583	missense	57478	exon13			CTCCACGGGGACC	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.2072C>T	16.37:g.23091371G>A	ENSP00000219689:p.Pro691Leu	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	264	15	0.0568182	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.393555	0.83011	.	.	ENSG00000103404	ENST00000219689	T	0.10005	2.92	4.91	3.96	0.45880	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	U	0.000000	T	0.25791	0.0628	L	0.50993	1.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00641	-1.1631	10	0.59425	D	0.04	-16.8435	12.2435	0.54558	0.0829:0.0:0.9171:0.0	.	691	Q70CQ4	UBP31_HUMAN	L	691	ENSP00000219689:P691L	ENSP00000219689:P691L	P	-	2	0	USP31	22998872	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.471000	0.97696	1.058000	0.40530	0.557000	0.71058	CCG	.	.	none		0.562	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
FLG	2312	hgsc.bcm.edu	37	1	152277822	152277822	+	Silent	SNP	T	T	C	rs3126069	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152277822T>C	ENST00000368799.1	-	3	9575	c.9540A>G	c.(9538-9540)tcA>tcG	p.S3180S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3180	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CATGGTGACGTGACACTGAGT	0.557									Ichthyosis				C|||	1121	0.223842	0.0378	0.2709	5008	,	,		17239	0.4831		0.0944	False		,,,				2504	0.3078				p.S3180S		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.A9540G						scavenged	.						291.0	281.0	285.0					1																	152277822		2201	4293	6494	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGACGTGACACT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.9540A>G	1.37:g.152277822T>C		Somatic	479	0	0		WXS	Illumina HiSeq	Phase_I	442	22	0.0497738	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.777;C|0.223	0.223	strong		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792093	8792093	+	Silent	SNP	G	G	A	rs16957702	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8792093G>A	ENST00000447110.1	-	10	1135	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D	PIK3R5_ENST00000584803.1_Silent_p.D337D|PIK3R5_ENST00000581552.1_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	51	0	0		WXS	Illumina HiSeq	Phase_I	38	37	0.973684	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	
TDG	6996	hgsc.bcm.edu	37	12	104373829	104373829	+	Silent	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:104373829C>A	ENST00000392872.3	+	3	621	c.387C>A	c.(385-387)acC>acA	p.T129T	TDG_ENST00000542036.1_5'UTR|TDG_ENST00000266775.9_Silent_p.T125T|TDG_ENST00000544861.1_5'UTR	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	129					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.T129T(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		ATATTTTGACCTTCAATCTGG	0.358								Base excision repair (BER), DNA glycosylases																													p.T129T		Atlas-SNP	.											TDG,pharynx,carcinoma,0,1	TDG	43	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C387A						scavenged	.						48.0	47.0	47.0					12																	104373829		2203	4300	6503	SO:0001819	synonymous_variant	6996	exon3			TTTGACCTTCAAT	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.387C>A	12.37:g.104373829C>A		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	284	8	0.028169	NM_003211	Q8IUZ6|Q8IZM3	Silent	SNP	ENST00000392872.3	37	CCDS9095.1																																																																																			.	.	weak		0.358	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
CAPN10	11132	hgsc.bcm.edu	37	2	241526428	241526428	+	Missense_Mutation	SNP	C	C	G	rs138005500	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241526428C>G	ENST00000391984.2	+	1	296	c.100C>G	c.(100-102)Ctg>Gtg	p.L34V	CAPN10_ENST00000391982.2_Missense_Mutation_p.L34V|CAPN10_ENST00000352879.4_Missense_Mutation_p.L34V|CAPN10_ENST00000404753.3_Missense_Mutation_p.L34V|CAPN10_ENST00000270364.7_Missense_Mutation_p.L34V|CAPN10_ENST00000354082.4_Missense_Mutation_p.L34V|CAPN10-AS1_ENST00000567819.1_RNA	NM_023083.3	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10	34	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				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)		GTCTACGCCGCTGGCCCAGTT	0.726													C|||	18	0.00359425	0.0	0.0014	5008	,	,		11190	0.0		0.0169	False		,,,				2504	0.0				p.L34V		Atlas-SNP	.											.	CAPN10	105	.	0			c.C100G						PASS	.	C	VAL/LEU,VAL/LEU	4,4070		0,4,2033	5.0	5.0	5.0		100,100	2.5	1.0	2	dbSNP_134	5	46,8054		0,46,4004	yes	missense,missense	CAPN10	NM_023083.3,NM_023085.3	32,32	0,50,6037	GG,GC,CC		0.5679,0.0982,0.4107	probably-damaging,probably-damaging	34/673,34/518	241526428	50,12124	2037	4050	6087	SO:0001583	missense	11132	exon1			ACGCCGCTGGCCC	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.100C>G	2.37:g.241526428C>G	ENSP00000375844:p.Leu34Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	94	55	0.585106	NM_023085	A8MVS7|Q4ZFV1|Q8NCD4|Q96IG4|Q96JI2|Q9HC89|Q9HC90|Q9HC91|Q9HC92|Q9HC93|Q9HC94|Q9HC95	Missense_Mutation	SNP	ENST00000391984.2	37	CCDS42838.1	20	0.009157509157509158	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	17	0.022427440633245383	C	14.30	2.493770	0.44352	9.82E-4	0.005679	ENSG00000142330	ENST00000391984;ENST00000391982;ENST00000404753;ENST00000270364;ENST00000352879;ENST00000354082	T;T;T;T;T;T	0.42513	2.39;2.39;2.39;0.97;0.97;2.39	3.44	2.55	0.30701	Peptidase C2, calpain, catalytic domain (3);	0.273086	0.30704	N	0.009053	T	0.29491	0.0735	L	0.42581	1.335	0.41081	D	0.985527	D;P;D;D;P	0.69078	0.997;0.909;0.987;0.994;0.955	D;P;P;P;P	0.66196	0.942;0.455;0.735;0.904;0.843	T	0.24012	-1.0172	10	0.17369	T	0.5	.	6.6983	0.23211	0.0:0.8657:0.0:0.1343	.	34;34;34;34;34	B7Z6G3;Q9HC96-7;Q9HC96-8;Q9HC96-3;Q9HC96	.;.;.;.;CAN10_HUMAN	V	34	ENSP00000375844:L34V;ENSP00000375842:L34V;ENSP00000384422:L34V;ENSP00000270364:L34V;ENSP00000289381:L34V;ENSP00000270362:L34V	ENSP00000270361:L34V	L	+	1	2	CAPN10	241175101	0.818000	0.29161	1.000000	0.80357	0.952000	0.60782	1.288000	0.33296	0.655000	0.30866	0.655000	0.94253	CTG	C|0.991;G|0.009	0.009	strong		0.726	CAPN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257191.3	NM_023083	
SOAT1	6646	hgsc.bcm.edu	37	1	179312752	179312752	+	Silent	SNP	C	C	T	rs10753191	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:179312752C>T	ENST00000367619.3	+	10	1112	c.969C>T	c.(967-969)gtC>gtT	p.V323V	SOAT1_ENST00000535686.1_Silent_p.V59V|SOAT1_ENST00000540564.1_Silent_p.V265V|SOAT1_ENST00000539888.1_Silent_p.V258V	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	323					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	GGGGTTATGTCGCTATGAAGT	0.313													C|||	1315	0.26258	0.3472	0.2882	5008	,	,		16006	0.3542		0.1302	False		,,,				2504	0.1718				p.V323V		Atlas-SNP	.											.	SOAT1	53	.	0			c.C969T						PASS	.	C		1388,3018	446.7+/-348.1	218,952,1033	137.0	135.0	136.0		969	-10.6	0.6	1	dbSNP_120	136	1210,7390	242.9+/-272.7	89,1032,3179	no	coding-synonymous	SOAT1	NM_003101.4		307,1984,4212	TT,TC,CC		14.0698,31.5025,19.9754		323/551	179312752	2598,10408	2203	4300	6503	SO:0001819	synonymous_variant	6646	exon10			TTATGTCGCTATG	L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	2.3.1.26		11177	protein-coding gene	gene with protein product	"""acyl-Coenzyme A: cholesterol acyltransferase"""	102642	"""sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1"""	SOAT, STAT		8407899	Standard	NM_003101		Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.969C>T	1.37:g.179312752C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Silent	SNP	ENST00000367619.3	37	CCDS1330.1																																																																																			C|0.768;N|0.000	.	strong		0.313	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101	
ANKRD33	341405	hgsc.bcm.edu	37	12	52284500	52284500	+	Missense_Mutation	SNP	A	A	G	rs34494292	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52284500A>G	ENST00000340970.4	+	5	766	c.395A>G	c.(394-396)cAg>cGg	p.Q132R	ANKRD33_ENST00000301190.6_Missense_Mutation_p.Q257R|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Missense_Mutation_p.Q63R			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	27	0	0		WXS	Illumina HiSeq	Phase_I	27	26	0.962963	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	
OR6Q1	219952	hgsc.bcm.edu	37	11	57798942	57798942	+	Missense_Mutation	SNP	A	A	G	rs2513726	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:57798942A>G	ENST00000302622.3	+	1	541	c.518A>G	c.(517-519)tAt>tGt	p.Y173C	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	173				Y -> C (in Ref. 1; BAC05958, 3; AAI51148 and 4; AAK95094). {ECO:0000305}.		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)				CTAACATTTTATGGCCCAAAT	0.522													G|||	2044	0.408147	0.3238	0.2651	5008	,	,		23219	0.6825		0.2913	False		,,,				2504	0.4611				p.Y173C		Atlas-SNP	.											.	OR6Q1	58	.	0			c.A518G						PASS	.	G	CYS/TYR	1482,2920	677.5+/-403.4	247,988,966	228.0	203.0	212.0		518	5.0	1.0	11	dbSNP_100	212	2565,6027	690.1+/-404.4	395,1775,2126	yes	missense	OR6Q1	NM_001005186.2	194	642,2763,3092	GG,GA,AA		29.8534,33.6665,31.1451	benign	173/318	57798942	4047,8947	2201	4296	6497	SO:0001583	missense	219952	exon1			CATTTTATGGCCC	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.518A>G	11.37:g.57798942A>G	ENSP00000307734:p.Tyr173Cys	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	245	103	0.420408	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Missense_Mutation	SNP	ENST00000302622.3	37	CCDS31541.1	840	0.38461538461538464	154	0.3130081300813008	96	0.26519337016574585	376	0.6573426573426573	214	0.28232189973614774	G	1.599	-0.527015	0.04141	0.336665	0.298534	ENSG00000172381	ENST00000302622	T	0.00020	9.05	5.04	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41712	N	0.000822	T	0.00012	0.0000	N	0.00006	-3.245	0.44162	P	0.003037999999999985	B	0.02656	0.0	B	0.01281	0.0	T	0.31833	-0.9929	9	0.02654	T	1	.	9.7534	0.40490	0.1681:0.0:0.8319:0.0	rs2513726;rs57387147;rs2513726	173	Q8NGQ2	OR6Q1_HUMAN	C	173	ENSP00000307734:Y173C	ENSP00000307734:Y173C	Y	+	2	0	OR6Q1	57555518	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.148000	0.64857	1.136000	0.42199	-0.131000	0.14894	TAT	A|0.653;G|0.347	0.347	strong		0.522	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
SLC26A9	115019	hgsc.bcm.edu	37	1	205884508	205884508	+	Missense_Mutation	SNP	C	C	T	rs147005854		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:205884508C>T	ENST00000367135.3	-	21	2466	c.2353G>A	c.(2353-2355)Gca>Aca	p.A785T	SLC26A9_ENST00000367134.2_Missense_Mutation_p.A785T|SLC26A9_ENST00000340781.4_Missense_Mutation_p.A785T	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	785					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)			AGGGTCTCTGCGTGAAACATG	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		19734	0.0		0.001	False		,,,				2504	0.0				p.A785T		Atlas-SNP	.											.	SLC26A9	176	.	0			c.G2353A						PASS	.	C	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	108.0	98.0	102.0		2353,2353	-10.9	0.0	1	dbSNP_134	102	8,8592	5.7+/-21.5	0,8,4292	yes	missense,missense	SLC26A9	NM_052934.3,NM_134325.2	58,58	0,9,6494	TT,TC,CC		0.093,0.0227,0.0692	benign,benign	785/792,785/888	205884508	9,12997	2203	4300	6503	SO:0001583	missense	115019	exon21			TCTCTGCGTGAAA	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.2353G>A	1.37:g.205884508C>T	ENSP00000356103:p.Ala785Thr	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	254	88	0.346457	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	3.411	-0.120195	0.06838	2.27E-4	9.3E-4	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.92699	-3.09;-2.98;-3.09	5.44	-10.9	0.00192	.	1.255410	0.05466	N	0.552214	T	0.76772	0.4034	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.65307	-0.6200	10	0.11794	T	0.64	.	10.9011	0.47051	0.2271:0.5876:0.0:0.1853	.	785;785	Q7LBE3;B1AVM8	S26A9_HUMAN;.	T	785	ENSP00000341682:A785T;ENSP00000356103:A785T;ENSP00000356102:A785T	ENSP00000341682:A785T	A	-	1	0	SLC26A9	204151131	0.000000	0.05858	0.035000	0.18076	0.935000	0.57460	-2.719000	0.00812	-3.835000	0.00101	-1.327000	0.01280	GCA	C|0.999;T|0.001	0.001	strong		0.577	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934	
FBXO47	494188	hgsc.bcm.edu	37	17	37093510	37093510	+	Missense_Mutation	SNP	T	T	C	rs113358400	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:37093510T>C	ENST00000378079.2	-	11	1476	c.1277A>G	c.(1276-1278)aAt>aGt	p.N426S		NM_001008777.2	NP_001008777.2	Q5MNV8	FBX47_HUMAN	F-box protein 47	426										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	20						ATGGAACAAATTCAAAAAGCT	0.363													T|||	35	0.00698882	0.0008	0.0144	5008	,	,		15990	0.0		0.0239	False		,,,				2504	0.0				p.N426S		Atlas-SNP	.											.	FBXO47	34	.	0			c.A1277G						PASS	.	T	SER/ASN	36,4370	40.0+/-72.8	0,36,2167	127.0	111.0	116.0		1277	4.8	1.0	17	dbSNP_132	116	256,8344	99.9+/-161.4	3,250,4047	yes	missense	FBXO47	NM_001008777.2	46	3,286,6214	CC,CT,TT		2.9767,0.8171,2.2451	benign	426/453	37093510	292,12714	2203	4300	6503	SO:0001583	missense	494188	exon11			AACAAATTCAAAA		CCDS32639.1	17q12	2014-08-12			ENSG00000204952	ENSG00000204952		"""F-boxes /  ""other"""""	31969	protein-coding gene	gene with protein product		609498				15723337	Standard	NM_001008777		Approved		uc002hrc.2	Q5MNV8	OTTHUMG00000178945	ENST00000378079.2:c.1277A>G	17.37:g.37093510T>C	ENSP00000367319:p.Asn426Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_001008777	B2RTZ4	Missense_Mutation	SNP	ENST00000378079.2	37	CCDS32639.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	T	14.00	2.405097	0.42613	0.008171	0.029767	ENSG00000204952	ENST00000378079	T	0.59502	0.26	5.88	4.81	0.61882	.	0.203730	0.50627	N	0.000112	T	0.19366	0.0465	L	0.29908	0.895	0.40423	D	0.979864	B	0.28350	0.208	B	0.20577	0.03	T	0.10965	-1.0607	10	0.33940	T	0.23	-5.6902	10.6903	0.45867	0.0:0.0748:0.0:0.9252	.	426	Q5MNV8	FBX47_HUMAN	S	426	ENSP00000367319:N426S	ENSP00000367319:N426S	N	-	2	0	FBXO47	34347036	1.000000	0.71417	0.984000	0.44739	0.974000	0.67602	3.816000	0.55658	1.066000	0.40716	0.528000	0.53228	AAT	T|0.981;C|0.019	0.019	strong		0.363	FBXO47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444073.1	NM_001008777	
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43630156	43630156	+	Silent	SNP	A	A	C	rs11559311	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43630156A>C	ENST00000236051.2	-	9	1020	c.879T>G	c.(877-879)ccT>ccG	p.P293P	EBNA1BP2_ENST00000431635.2_Silent_p.P348P	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	293					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)				TTCGTTTTCCAGGTCTCTTCT	0.443													A|||	410	0.081869	0.2405	0.0605	5008	,	,		19601	0.001		0.0368	False		,,,				2504	0.0123				p.P348P		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.T1044G						PASS	.	A	,	913,3493	351.1+/-311.1	102,709,1392	176.0	155.0	162.0		1044,879	-0.3	1.0	1	dbSNP_120	162	356,8244	119.7+/-179.0	6,344,3950	no	coding-synonymous,coding-synonymous	EBNA1BP2	NM_001159936.1,NM_006824.2	,	108,1053,5342	CC,CA,AA		4.1395,20.7217,9.757	,	348/362,293/307	43630156	1269,11737	2203	4300	6503	SO:0001819	synonymous_variant	10969	exon10			TTTTCCAGGTCTC	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.879T>G	1.37:g.43630156A>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	119	87	0.731092	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	37	CCDS478.1																																																																																			A|0.912;C|0.088	0.088	strong		0.443	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1		
SLC14A2	8170	hgsc.bcm.edu	37	18	43246156	43246156	+	Missense_Mutation	SNP	G	G	A	rs9960464	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:43246156G>A	ENST00000255226.6	+	12	2345	c.1529G>A	c.(1528-1530)cGa>cAa	p.R510Q	SLC14A2_ENST00000589658.1_5'UTR|SLC14A2_ENST00000586448.1_Missense_Mutation_p.R510Q	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	510			R -> Q (in dbSNP:rs9960464). {ECO:0000269|PubMed:11502588, ECO:0000269|PubMed:14702039, 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.R510Q(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						TTTCCCTATCGATACCGGAAG	0.512											OREG0024946	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	1870	0.373403	0.2867	0.4712	5008	,	,		17597	0.3423		0.4314	False		,,,				2504	0.3937				p.R510Q		Atlas-SNP	.											SLC14A2,NS,carcinoma,0,1	SLC14A2	121	1	1	Substitution - Missense(1)	stomach(1)	c.G1529A						PASS	.	G	GLN/ARG,GLN/ARG	1446,2960	469.2+/-355.4	225,996,982	160.0	126.0	138.0		1529,1529	-11.7	0.0	18	dbSNP_119	138	3848,4752	541.7+/-384.0	826,2196,1278	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	43,43	1051,3192,2260	AA,AG,GG		44.7442,32.8189,40.7043	benign,benign	510/921,510/921	43246156	5294,7712	2203	4300	6503	SO:0001583	missense	8170	exon13			CCTATCGATACCG	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.1529G>A	18.37:g.43246156G>A	ENSP00000255226:p.Arg510Gln	Somatic	135	0	0	914	WXS	Illumina HiSeq	Phase_I	106	59	0.556604	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	839	0.3841575091575092	138	0.2804878048780488	175	0.48342541436464087	192	0.3356643356643357	334	0.44063324538258575	g	7.576	0.667826	0.14710	0.328189	0.447442	ENSG00000132874	ENST00000255226	T	0.32515	1.45	6.04	-11.7	0.00046	.	1.340750	0.04528	N	0.385873	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	0.40924	-0.9537	9	0.13108	T	0.6	3.2061	6.7344	0.23401	0.1347:0.579:0.0671:0.2192	rs9960464;rs52828182;rs59892831;rs9960464	510	Q15849	UT2_HUMAN	Q	510	ENSP00000255226:R510Q	ENSP00000255226:R510Q	R	+	2	0	SLC14A2	41500154	0.000000	0.05858	0.000000	0.03702	0.146000	0.21551	-0.763000	0.04740	-1.612000	0.01579	-0.405000	0.06341	CGA	G|0.615;A|0.385	0.385	strong		0.512	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
N4BP2	55728	hgsc.bcm.edu	37	4	40138676	40138676	+	Missense_Mutation	SNP	A	A	G	rs2271395	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:40138676A>G	ENST00000261435.6	+	14	5175	c.4759A>G	c.(4759-4761)Act>Gct	p.T1587A		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1587			T -> A (in dbSNP:rs2271395).		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						CACATCTCATACTGGCCAGAA	0.343													A|||	644	0.128594	0.0076	0.0403	5008	,	,		16869	0.3998		0.0517	False		,,,				2504	0.1544				p.T1587A		Atlas-SNP	.											.	N4BP2	166	.	0			c.A4759G						PASS	.	A	ALA/THR	85,4321	73.6+/-111.7	0,85,2118	73.0	72.0	72.0		4759	2.9	1.0	4	dbSNP_100	72	395,8205	127.2+/-185.5	14,367,3919	yes	missense	N4BP2	NM_018177.4	58	14,452,6037	GG,GA,AA		4.593,1.9292,3.6906	benign	1587/1771	40138676	480,12526	2203	4300	6503	SO:0001583	missense	55728	exon14			TCTCATACTGGCC	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.4759A>G	4.37:g.40138676A>G	ENSP00000261435:p.Thr1587Ala	Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	207	110	0.531401	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	317|317	0.14514652014652016|0.14514652014652016	5|5	0.01016260162601626|0.01016260162601626	16|16	0.04419889502762431|0.04419889502762431	260|260	0.45454545454545453|0.45454545454545453	36|36	0.047493403693931395|0.047493403693931395	A|A	9.740|9.740	1.164654|1.164654	0.21538|0.21538	0.019292|0.019292	0.04593|0.04593	ENSG00000078177|ENSG00000078177	ENST00000261435;ENST00000381804|ENST00000513269	T|.	0.17691|.	2.26|.	5.41|5.41	2.91|2.91	0.33838|0.33838	.|.	0.397696|.	0.24141|.	N|.	0.041178|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.19112|0.19112	0.55|0.55	0.44927|0.44927	P|P	0.002055000000000029|0.002055000000000029	B;B|.	0.33171|.	0.4;0.278|.	B;B|.	0.33960|.	0.173;0.084|.	T|T	0.48536|0.48536	-0.9027|-0.9027	9|4	0.33940|.	T|.	0.23|.	-12.4649|-12.4649	5.2482|5.2482	0.15508|0.15508	0.6522:0.0:0.0747:0.2731|0.6522:0.0:0.0747:0.2731	rs2271395;rs52816843;rs2271395|rs2271395;rs52816843;rs2271395	1587;1587|.	Q86UW6-2;Q86UW6|.	.;N4BP2_HUMAN|.	A|C	1587;1507|1233	ENSP00000261435:T1587A|.	ENSP00000261435:T1587A|.	T|Y	+|+	1|2	0|0	N4BP2|N4BP2	39815071|39815071	0.313000|0.313000	0.24554|0.24554	0.994000|0.994000	0.49952|0.49952	0.462000|0.462000	0.32619|0.32619	1.060000|1.060000	0.30530|0.30530	0.329000|0.329000	0.23460|0.23460	0.460000|0.460000	0.39030|0.39030	ACT|TAC	A|0.918;G|0.082	0.082	strong		0.343	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
TECPR1	25851	hgsc.bcm.edu	37	7	97847040	97847040	+	Silent	SNP	G	G	A	rs2279676	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:97847040G>A	ENST00000447648.2	-	25	3647	c.3348C>T	c.(3346-3348)caC>caT	p.H1116H	TECPR1_ENST00000379795.3_Silent_p.H1118H			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	1116					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CCTTGGGCTCGTGAGGCTGCA	0.667													G|||	1040	0.207668	0.2156	0.2882	5008	,	,		16670	0.2589		0.1879	False		,,,				2504	0.1074				p.H1116H		Atlas-SNP	.											TECPR1,colon,carcinoma,0,1	TECPR1	77	1	0			c.C3348T						scavenged	.	G		632,3406		41,550,1428	12.0	16.0	15.0		3348	-9.1	0.0	7	dbSNP_100	15	1048,6808		57,934,2937	no	coding-synonymous	TECPR1	NM_015395.1		98,1484,4365	AA,AG,GG		13.3401,15.6513,14.1248		1116/1166	97847040	1680,10214	2019	3928	5947	SO:0001819	synonymous_variant	25851	exon25			GGGCTCGTGAGGC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.3348C>T	7.37:g.97847040G>A		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	94	67	0.712766	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			G|0.772;A|0.228	0.228	strong		0.667	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
FAM131C	348487	hgsc.bcm.edu	37	1	16384999	16384999	+	Missense_Mutation	SNP	G	G	A	rs1807284	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16384999G>A	ENST00000375662.4	-	7	959	c.776C>T	c.(775-777)cCc>cTc	p.P259L	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	259	Pro-rich.									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)		GGAGCCCGGGGGGTGGGTCCC	0.721													A|||	1887	0.376797	0.4032	0.2795	5008	,	,		19329	0.4315		0.336	False		,,,				2504	0.3957				p.P259L		Atlas-SNP	.											FAM131C,NS,carcinoma,0,2	FAM131C	21	2	0			c.C776T						scavenged	.						2.0	3.0	3.0					1																	16384999		1408	3137	4545	SO:0001583	missense	348487	exon7			CCCGGGGGGTGGG		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.776C>T	1.37:g.16384999G>A	ENSP00000364814:p.Pro259Leu	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	9	4	0.444444	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	618	0.28296703296703296	170	0.34552845528455284	94	0.2596685082872928	168	0.2937062937062937	186	0.24538258575197888	A	0.006	-2.029401	0.00410	.	.	ENSG00000185519	ENST00000375662	T	0.11821	2.74	4.65	-2.16	0.07080	.	1.628260	0.03484	N	0.215578	T	0.00012	0.0000	N	0.00972	-1.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43605	-0.9381	10	0.02654	T	1	.	10.8536	0.46784	0.4433:0.0:0.5567:0.0	rs1807284;rs3884147	259	Q96AQ9	F131C_HUMAN	L	259	ENSP00000364814:P259L	ENSP00000364814:P259L	P	-	2	0	FAM131C	16257586	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.041000	0.12084	-1.034000	0.03295	-1.271000	0.01417	CCC	G|0.717;A|0.283	0.283	strong		0.721	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
SORT1	6272	hgsc.bcm.edu	37	1	109878903	109878903	+	Missense_Mutation	SNP	C	C	G	rs2228606	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109878903C>G	ENST00000256637.6	-	11	1388	c.1330G>C	c.(1330-1332)Gaa>Caa	p.E444Q	SORT1_ENST00000538502.1_Missense_Mutation_p.E307Q	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	444					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)		TCACTGTTTTCAGGCTTCCTC	0.428													C|||	22	0.00439297	0.0	0.0029	5008	,	,		21131	0.0		0.0199	False		,,,				2504	0.0				p.E444Q		Atlas-SNP	.											.	SORT1	48	.	0			c.G1330C						PASS	.	C	GLN/GLU,GLN/GLU	15,4391	21.2+/-45.6	0,15,2188	223.0	184.0	197.0		919,1330	5.7	1.0	1	dbSNP_130	197	152,8448	73.5+/-136.2	2,148,4150	yes	missense,missense	SORT1	NM_001205228.1,NM_002959.5	29,29	2,163,6338	GG,GC,CC		1.7674,0.3404,1.284	benign,benign	307/695,444/832	109878903	167,12839	2203	4300	6503	SO:0001583	missense	6272	exon11			TGTTTTCAGGCTT	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.1330G>C	1.37:g.109878903C>G	ENSP00000256637:p.Glu444Gln	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	130	102	0.784615	NM_002959	B4DWI3|C0JYZ0|Q8IZ49	Missense_Mutation	SNP	ENST00000256637.6	37	CCDS798.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	C	11.19	1.566647	0.28003	0.003404	0.017674	ENSG00000134243	ENST00000256637;ENST00000538502	T;T	0.30182	1.54;1.54	5.69	5.69	0.88448	VPS10 (1);	0.261908	0.35805	N	0.002977	T	0.17450	0.0419	L	0.45581	1.43	0.43714	D	0.996188	B;B	0.16396	0.001;0.017	B;B	0.10450	0.001;0.005	T	0.03514	-1.1029	10	0.22706	T	0.39	-17.0522	18.5855	0.91188	0.0:1.0:0.0:0.0	.	307;444	B4DWI3;Q99523	.;SORT_HUMAN	Q	444;307	ENSP00000256637:E444Q;ENSP00000438597:E307Q	ENSP00000256637:E444Q	E	-	1	0	SORT1	109680426	0.991000	0.36638	0.995000	0.50966	0.144000	0.21451	1.857000	0.39399	2.673000	0.90976	0.655000	0.94253	GAA	C|0.986;G|0.014	0.014	strong		0.428	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959	
CCDC180	100499483	hgsc.bcm.edu	37	9	100105735	100105735	+	Silent	SNP	T	T	C	rs1947717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100105735T>C	ENST00000357054.1	+	33	3872	c.2937T>C	c.(2935-2937)tgT>tgC	p.C979C	CCDC180_ENST00000395220.1_3'UTR|CCDC180_ENST00000411667.2_Silent_p.C837C|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Silent_p.C840C|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000375202.2_Silent_p.C840C			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	979						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											AAGAGCATTGTAGGAAGTCCC	0.423													C|||	2973	0.59365	0.7458	0.6628	5008	,	,		17941	0.5843		0.3936	False		,,,				2504	0.5542				p.C840C		Atlas-SNP	.											.	.	.	.	0			c.T2520C						PASS	.	C		3195,1211	420.2+/-338.9	1154,887,162	123.0	113.0	116.0		2520	2.3	0.0	9	dbSNP_92	116	3980,4620	600.2+/-394.2	912,2156,1232	no	coding-synonymous	C9orf174	NM_020893.2		2066,3043,1394	CC,CT,TT		46.2791,27.4852,44.8332		840/1702	100105735	7175,5831	2203	4300	6503	SO:0001819	synonymous_variant	0	exon19			GCATTGTAGGAAG	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.2937T>C	9.37:g.100105735T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	107	104	0.971963	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				T|0.445;C|0.555	0.555	strong		0.423	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
POM121L2	94026	hgsc.bcm.edu	37	6	27279852	27279852	+	Missense_Mutation	SNP	T	T	C	rs2235233	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:27279852T>C	ENST00000444565.1	-	1	97	c.98A>G	c.(97-99)cAg>cGg	p.Q33R	POM121L2_ENST00000377451.2_Missense_Mutation_p.Q33R	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	33										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						GTGAAGGGGCTGAGGTGGCCG	0.632													T|||	1084	0.216454	0.0144	0.2622	5008	,	,		14287	0.379		0.2008	False		,,,				2504	0.3057				p.Q33R		Atlas-SNP	.											.	POM121L2	61	.	0			c.A98G						PASS	.	T	ARG/GLN	76,1308		1,74,617	21.0	27.0	25.0		98	-0.4	0.0	6	dbSNP_98	25	752,2430		92,568,931	yes	missense	POM121L2	NM_033482.3	43	93,642,1548	CC,CT,TT		23.6329,5.4913,18.134	benign	33/1036	27279852	828,3738	692	1591	2283	SO:0001583	missense	94026	exon1			AGGGGCTGAGGTG	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.98A>G	6.37:g.27279852T>C	ENSP00000392726:p.Gln33Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	87	82	0.942529	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	490	0.22435897435897437	10	0.02032520325203252	97	0.26795580110497236	227	0.3968531468531469	156	0.20580474934036938	T	0.003	-2.507600	0.00155	0.054913	0.236329	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.13307	2.6;2.62	3.19	-0.415	0.12355	.	.	.	.	.	T	0.01870	0.0059	L	0.29908	0.895	0.80722	P	0.0	B	0.16603	0.018	B	0.18871	0.023	T	0.47018	-0.9149	8	0.08837	T	0.75	.	3.1692	0.06546	0.0:0.2608:0.2664:0.4728	rs2235233;rs52826507;rs59279970;rs2235233	33	C9J1I7	.	R	33	ENSP00000366671:Q33R;ENSP00000392726:Q33R	ENSP00000366671:Q33R	Q	-	2	0	POM121L2	27387831	0.415000	0.25416	0.004000	0.12327	0.012000	0.07955	0.398000	0.20899	-0.078000	0.12730	0.459000	0.35465	CAG	T|0.762;C|0.238	0.238	strong		0.632	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
SERPINA6	866	hgsc.bcm.edu	37	14	94776219	94776219	+	Silent	SNP	C	C	T	rs2228542	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:94776219C>T	ENST00000341584.3	-	3	884	c.738G>A	c.(736-738)tcG>tcA	p.S246S		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	246			S -> A (in dbSNP:rs2228541). {ECO:0000269|PubMed:15489334}.		glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	AGGGGAGCTCCGAGTCATGAA	0.542													C|||	901	0.179912	0.2284	0.1484	5008	,	,		21531	0.0595		0.3012	False		,,,				2504	0.136				p.S246S		Atlas-SNP	.											SERPINA6_ENST00000341584,NS,adenoma,0,1	SERPINA6	102	1	0			c.G738A						scavenged	.	C		1032,3374	380.2+/-323.6	124,784,1295	138.0	112.0	121.0		738	-7.6	0.0	14	dbSNP_98	121	2335,6265	390.8+/-343.4	363,1609,2328	no	coding-synonymous	SERPINA6	NM_001756.3		487,2393,3623	TT,TC,CC		27.1512,23.4226,25.8881		246/406	94776219	3367,9639	2203	4300	6503	SO:0001819	synonymous_variant	866	exon3			GAGCTCCGAGTCA	J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"""Serine (or cysteine) peptidase inhibitors"""	1540	protein-coding gene	gene with protein product	"""corticosteroid binding globulin"", ""transcortin"""	122500	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"""	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.738G>A	14.37:g.94776219C>T		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	149	89	0.597315	NM_001756	A8K456|Q7Z2Q9	Silent	SNP	ENST00000341584.3	37	CCDS9924.1																																																																																			C|0.758;T|0.242	0.242	strong		0.542	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756	
PIAS1	8554	hgsc.bcm.edu	37	15	68479959	68479959	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:68479959T>C	ENST00000249636.6	+	14	1890	c.1742T>C	c.(1741-1743)tTc>tCc	p.F581S	PIAS1_ENST00000545237.1_Missense_Mutation_p.F583S	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	581	4 X 4 AA repeats of N-T-S-L.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						TCTCGGTTTTTCCCGTATACC	0.498																																					p.F581S		Atlas-SNP	.											PIAS1,NS,carcinoma,-1,1	PIAS1	42	1	0			c.T1742C						PASS	.						87.0	84.0	85.0					15																	68479959		1919	4137	6056	SO:0001583	missense	8554	exon14			GGTTTTTCCCGTA	AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800		"""Zinc fingers, MIZ-type"""	2752	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 3"""	603566	"""DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1"""	DDXBP1		9724754, 9177271	Standard	XM_005254735		Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.1742T>C	15.37:g.68479959T>C	ENSP00000249636:p.Phe581Ser	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	171	16	0.0935673	NM_016166	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Missense_Mutation	SNP	ENST00000249636.6	37	CCDS45290.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.317953	0.60524	.	.	ENSG00000033800	ENST00000249636;ENST00000545237	T;T	0.33216	1.43;1.42	5.74	5.74	0.90152	.	0.103576	0.64402	D	0.000002	T	0.26011	0.0634	L	0.39898	1.24	0.51233	D	0.999913	P	0.40000	0.698	B	0.32211	0.142	T	0.07233	-1.0783	10	0.87932	D	0	-15.7775	16.0292	0.80564	0.0:0.0:0.0:1.0	.	581	O75925	PIAS1_HUMAN	S	581;583	ENSP00000249636:F581S;ENSP00000438574:F583S	ENSP00000249636:F581S	F	+	2	0	PIAS1	66267013	1.000000	0.71417	0.918000	0.36340	0.518000	0.34316	7.420000	0.80191	2.187000	0.69744	0.533000	0.62120	TTC	.	.	none		0.498	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2		
KLC1	3831	hgsc.bcm.edu	37	14	104143806	104143806	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104143806C>T	ENST00000348520.6	+	12	1753	c.1434C>T	c.(1432-1434)ggC>ggT	p.G478G	KLC1_ENST00000347839.6_Silent_p.G478G|KLC1_ENST00000555836.1_Silent_p.G478G|KLC1_ENST00000389744.4_Silent_p.G478G|KLC1_ENST00000246489.7_Silent_p.G478G|KLC1_ENST00000452929.2_Silent_p.G478G|KLC1_ENST00000334553.6_Silent_p.G478G|KLC1_ENST00000557450.1_Silent_p.G478G|KLC1_ENST00000445352.4_Silent_p.G476G|KLC1_ENST00000554280.1_Silent_p.G478G|KLC1_ENST00000553286.1_Silent_p.G478G|KLC1_ENST00000380038.3_Silent_p.G478G|RP11-73M18.2_ENST00000472726.2_Silent_p.G650G|KLC1_ENST00000557575.1_Silent_p.G478G	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1	478					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|stress granule disassembly (GO:0035617)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|growth cone (GO:0030426)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)|motor activity (GO:0003774)		KLC1/ALK(2)	NS(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	12		Melanoma(154;0.155)|all_epithelial(191;0.19)				GACGTCAAGGCAAATTTGAAG	0.418																																					p.G478G		Atlas-SNP	.											.	KLC1	54	.	0			c.C1434T						PASS	.						145.0	141.0	143.0					14																	104143806		2203	4300	6503	SO:0001819	synonymous_variant	3831	exon12			TCAAGGCAAATTT	AF267530	CCDS32165.1, CCDS41996.1, CCDS45168.1	14q32.3	2013-01-10	2007-03-09	2007-03-09	ENSG00000126214	ENSG00000126214		"""Tetratricopeptide (TTC) repeat domain containing"""	6387	protein-coding gene	gene with protein product		600025	"""kinesin 2 60/70kDa"", ""kinesin 2"""	KNS2		8274221, 11106729	Standard	NM_005552		Approved	KNS2A, KLC, hKLC1S, hKLC1N, hKLC1P, hKLC1G, hKLC1R, hKLC1J, hKLC1B	uc010tyf.2	Q07866	OTTHUMG00000169227	ENST00000348520.6:c.1434C>T	14.37:g.104143806C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	126	35	0.277778	NM_182923	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Silent	SNP	ENST00000348520.6	37	CCDS41996.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.60|10.60	1.396952|1.396952	0.25205|0.25205	.|.	.|.	ENSG00000126214|ENSG00000126214	ENST00000553325;ENST00000553436;ENST00000555856|ENST00000537046	.|.	.|.	.|.	5.52|5.52	2.56|2.56	0.30785|0.30785	.|.	.|.	.|.	.|.	.|.	T|.	0.72350|.	0.3449|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.71869|.	-0.4462|.	4|.	.|.	.|.	.|.	-15.9577|-15.9577	17.9404|17.9404	0.89025|0.89025	0.0:0.7802:0.2198:0.0|0.0:0.7802:0.2198:0.0	.|.	.|.	.|.	.|.	V|X	58;54;52|84	.|.	.|.	A|Q	+|+	2|1	0|0	KLC1|KLC1	103213559|103213559	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.964000|0.964000	0.63967|0.63967	1.666000|1.666000	0.37460|0.37460	0.313000|0.313000	0.23062|0.23062	0.655000|0.655000	0.94253|0.94253	GCA|CAA	.	.	none		0.418	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552	
MTL5	9633	hgsc.bcm.edu	37	11	68512543	68512543	+	Missense_Mutation	SNP	A	A	G	rs12365708	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68512543A>G	ENST00000255087.5	-	4	850	c.667T>C	c.(667-669)Tgt>Cgt	p.C223R	MTL5_ENST00000544963.1_Missense_Mutation_p.C223R|MTL5_ENST00000540869.1_Intron|MTL5_ENST00000443940.2_Missense_Mutation_p.C223R	NM_004923.3	NP_004914.2	Q9Y4I5	MTL5_HUMAN	metallothionein-like 5, testis-specific (tesmin)	223			C -> R (in dbSNP:rs12365708). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|cellular metal ion homeostasis (GO:0006875)|multicellular organismal development (GO:0007275)|response to metal ion (GO:0010038)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	15	Esophageal squamous(3;4.37e-12)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.185)			TTGTCTATACATAGCATTTGT	0.313													A|||	236	0.0471246	0.0204	0.0706	5008	,	,		15602	0.0188		0.1193	False		,,,				2504	0.0215				p.C223R		Atlas-SNP	.											.	MTL5	37	.	0			c.T667C						PASS	.	A	ARG/CYS,ARG/CYS	139,4261	97.1+/-135.8	6,127,2067	142.0	137.0	139.0		667,667	5.3	1.0	11	dbSNP_120	139	904,7682	202.0+/-245.4	55,794,3444	yes	missense,missense	MTL5	NM_001039656.1,NM_004923.3	180,180	61,921,5511	GG,GA,AA		10.5288,3.1591,8.0317	probably-damaging,probably-damaging	223/307,223/509	68512543	1043,11943	2200	4293	6493	SO:0001583	missense	9633	exon4			CTATACATAGCAT	U86074	CCDS8184.1, CCDS44661.1	11q13.2-q13.3	2007-01-03			ENSG00000132749	ENSG00000132749			7446	protein-coding gene	gene with protein product	"""CXC domain containing 2"""	604374				1091092	Standard	XR_428932		Approved	CXCDC2	uc001ooc.3	Q9Y4I5	OTTHUMG00000167891	ENST00000255087.5:c.667T>C	11.37:g.68512543A>G	ENSP00000255087:p.Cys223Arg	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	160	84	0.525	NM_001039656	A8K8J3|Q4G182|Q6P2E2|Q8NCC8	Missense_Mutation	SNP	ENST00000255087.5	37	CCDS8184.1	149	0.06822344322344322	12	0.024390243902439025	26	0.0718232044198895	17	0.02972027972027972	94	0.12401055408970976	A	14.03	2.413044	0.42817	0.031591	0.105288	ENSG00000132749	ENST00000255087;ENST00000443940;ENST00000544963	T;T;T	0.67698	0.75;-0.28;0.31	5.35	5.35	0.76521	.	0.000000	0.56097	D	0.000026	T	0.02888	0.0086	L	0.34521	1.04	0.09310	P	0.9999968072	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.45934	-0.9227	9	0.36615	T	0.2	-11.1037	13.5671	0.61824	1.0:0.0:0.0:0.0	rs12365708;rs52818299;rs61464222;rs12365708	223;223	Q9Y4I5-3;Q9Y4I5	.;MTL5_HUMAN	R	223	ENSP00000255087:C223R;ENSP00000403086:C223R;ENSP00000440968:C223R	ENSP00000255087:C223R	C	-	1	0	MTL5	68269119	0.990000	0.36364	1.000000	0.80357	0.978000	0.69477	1.869000	0.39519	2.006000	0.58801	0.533000	0.62120	TGT	A|0.925;G|0.075	0.075	strong		0.313	MTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396844.1	NM_004923	
ZBTB45	84878	hgsc.bcm.edu	37	19	59028407	59028407	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:59028407C>T	ENST00000594051.1	-	2	1114	c.634G>A	c.(634-636)Gag>Aag	p.E212K	ZBTB45_ENST00000600990.1_Missense_Mutation_p.E212K|ZBTB45_ENST00000354590.3_Missense_Mutation_p.E212K			Q96K62	ZBT45_HUMAN	zinc finger and BTB domain containing 45	212					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.E212K(1)		breast(2)|endometrium(3)|lung(5)|urinary_tract(1)	11		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0165)|Lung(386;0.18)		TCACTTTCCTCGTCATCCTCG	0.652											OREG0025700	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E212K	NSCLC(164;1383 2017 5233 27540 46677)	Atlas-SNP	.											ZBTB45,NS,carcinoma,0,1	ZBTB45	37	1	1	Substitution - Missense(1)	endometrium(1)	c.G634A						scavenged	.						175.0	180.0	178.0					19																	59028407		2203	4300	6503	SO:0001583	missense	84878	exon2			TTTCCTCGTCATC	AK027392	CCDS12984.1	19q13.43	2013-10-10	2006-09-19	2006-09-19	ENSG00000119574	ENSG00000119574		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	23715	protein-coding gene	gene with protein product			"""zinc finger protein 499"""	ZNF499			Standard	NM_032792		Approved	FLJ14486	uc002qtd.3	Q96K62	OTTHUMG00000183545	ENST00000594051.1:c.634G>A	19.37:g.59028407C>T	ENSP00000469089:p.Glu212Lys	Somatic	165	0	0	1035	WXS	Illumina HiSeq	Phase_I	178	2	0.011236	NM_032792		Missense_Mutation	SNP	ENST00000594051.1	37	CCDS12984.1	.	.	.	.	.	.	.	.	.	.	c	10.52	1.374128	0.24857	.	.	ENSG00000119574	ENST00000354590	T	0.09073	3.02	3.23	3.23	0.37069	.	1.242270	0.06052	U	0.656755	T	0.05135	0.0137	N	0.08118	0	0.32825	D	0.503304	B	0.31519	0.327	B	0.19946	0.027	T	0.15350	-1.0440	10	0.27082	T	0.32	.	12.7123	0.57096	0.0:1.0:0.0:0.0	.	212	Q96K62	ZBT45_HUMAN	K	212	ENSP00000346603:E212K	ENSP00000346603:E212K	E	-	1	0	ZBTB45	63720219	0.046000	0.20272	0.400000	0.26346	0.030000	0.12068	1.067000	0.30616	2.122000	0.65172	0.467000	0.42956	GAG	.	.	none		0.652	ZBTB45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467067.1	NM_032792	
RBM44	375316	hgsc.bcm.edu	37	2	238742968	238742968	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238742968G>A	ENST00000409864.1	+	15	3337	c.3083G>A	c.(3082-3084)gGt>gAt	p.G1028D	RBM44_ENST00000316997.4_Missense_Mutation_p.G1028D			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	1027						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		AGACATAAAGGTTTTCTGAAT	0.318																																					p.G1028D		Atlas-SNP	.											.	RBM44	167	.	0			c.G3083A						PASS	.						38.0	37.0	37.0					2																	238742968		1804	4054	5858	SO:0001583	missense	375316	exon15			ATAAAGGTTTTCT	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.3083G>A	2.37:g.238742968G>A	ENSP00000386727:p.Gly1028Asp	Somatic	297	1	0.003367		WXS	Illumina HiSeq	Phase_I	262	128	0.48855	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962568	0.74016	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.69561	-0.41;-0.41	4.96	4.96	0.65561	.	.	.	.	.	T	0.81351	0.4804	M	0.74881	2.28	0.43275	D	0.995234	D	0.89917	1.0	D	0.91635	0.999	D	0.83952	0.0317	9	0.87932	D	0	-15.9804	15.6834	0.77391	0.0:0.0:1.0:0.0	.	1027	Q6ZP01	RBM44_HUMAN	D	1028	ENSP00000321179:G1028D;ENSP00000386727:G1028D	ENSP00000321179:G1028D	G	+	2	0	RBM44	238407707	1.000000	0.71417	0.812000	0.32479	0.977000	0.68977	6.062000	0.71155	2.297000	0.77311	0.484000	0.47621	GGT	.	.	none		0.318	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
SFN	2810	hgsc.bcm.edu	37	1	27190196	27190196	+	Missense_Mutation	SNP	A	A	T	rs77755255		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:27190196A>T	ENST00000339276.4	+	1	564	c.493A>T	c.(493-495)Acc>Tcc	p.T165S		NM_006142.3	NP_006133.1	Q9Y3B8	ORN_HUMAN	stratifin	0	Exonuclease.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide metabolic process (GO:0009117)	focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	9		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.1e-52)|Epithelial(14;2.31e-52)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)|GBM - Glioblastoma multiforme(114;0.0767)|Lung(427;0.215)		GATGCCGCCCACCAACCCCAT	0.617																																					p.T165S		Atlas-SNP	.											.	SFN	20	.	0			c.A493T						PASS	.						90.0	84.0	86.0					1																	27190196		2203	4300	6503	SO:0001583	missense	2810	exon1			CCGCCCACCAACC	BC023552	CCDS288.1	1p36.11	2008-02-05			ENSG00000175793	ENSG00000175793			10773	protein-coding gene	gene with protein product	"""14-3-3 sigma"""	601290				8515476	Standard	NM_006142		Approved	YWHAS	uc001bnc.1	P31947	OTTHUMG00000004093	ENST00000339276.4:c.493A>T	1.37:g.27190196A>T	ENSP00000340989:p.Thr165Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	37	6	0.162162	NM_006142	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Missense_Mutation	SNP	ENST00000339276.4	37	CCDS288.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.919577	0.92249	.	.	ENSG00000175793	ENST00000339276;ENST00000538651	T	0.46819	0.86	5.91	5.91	0.95273	14-3-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.73938	0.3651	M	0.89715	3.055	0.36736	D	0.881953	D	0.53885	0.963	D	0.65443	0.935	T	0.83349	-0.0004	10	0.87932	D	0	-45.3648	16.0112	0.80404	1.0:0.0:0.0:0.0	.	165	P31947	1433S_HUMAN	S	165;133	ENSP00000340989:T165S	ENSP00000340989:T165S	T	+	1	0	SFN	27062783	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.335000	0.96500	2.255000	0.74692	0.533000	0.62120	ACC	.	.	weak		0.617	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011709.1	NM_006142	
LAD1	3898	hgsc.bcm.edu	37	1	201355522	201355522	+	Missense_Mutation	SNP	T	T	C	rs4128458	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201355522T>C	ENST00000391967.2	-	3	1268	c.967A>G	c.(967-969)Aag>Gag	p.K323E	LAD1_ENST00000367313.3_Missense_Mutation_p.K337E|LAD1_ENST00000488842.1_5'Flank	NM_005558.3	NP_005549.2	O00515	LAD1_HUMAN	ladinin 1	323			K -> E (in dbSNP:rs4128458).			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						GCCCCCTGCTTTGCCAAAGAG	0.677													C|||	2770	0.553115	0.8775	0.3847	5008	,	,		15336	0.5188		0.4612	False		,,,				2504	0.364				p.K323E		Atlas-SNP	.											.	LAD1	42	.	0			c.A967G						PASS	.	C	GLU/LYS	3531,871		1427,677,97	29.0	28.0	28.0		967	1.6	0.0	1	dbSNP_108	28	4209,4391		1011,2187,1102	yes	missense	LAD1	NM_005558.3	56	2438,2864,1199	CC,CT,TT		48.9419,19.7865,40.4707	benign	323/518	201355522	7740,5262	2201	4300	6501	SO:0001583	missense	3898	exon3			CCTGCTTTGCCAA	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.967A>G	1.37:g.201355522T>C	ENSP00000375829:p.Lys323Glu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	155	51	0.329032	NM_005558	O95614|Q96GD8	Missense_Mutation	SNP	ENST00000391967.2	37	CCDS1410.1	1219	0.5581501831501832	437	0.8882113821138211	153	0.42265193370165743	282	0.493006993006993	347	0.4577836411609499	C	1.003	-0.690442	0.03303	0.802135	0.489419	ENSG00000159166	ENST00000391967;ENST00000367313	T;T	0.10477	2.88;2.87	4.6	1.65	0.23941	.	1.051530	0.07467	N	0.901672	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24657	-1.0154	9	0.02654	T	1	-17.1114	6.8142	0.23820	0.0:0.5957:0.0:0.4043	rs4128458;rs4342880;rs59727181;rs4128458	337;323	E9PDI4;O00515	.;LAD1_HUMAN	E	323;337	ENSP00000375829:K323E;ENSP00000356282:K337E	ENSP00000356282:K337E	K	-	1	0	LAD1	199622145	0.267000	0.24122	0.000000	0.03702	0.095000	0.18619	1.124000	0.31320	0.206000	0.20587	-0.166000	0.13349	AAG	T|0.405;C|0.595	0.595	strong		0.677	LAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086946.1	NM_005558	
TNFAIP6	7130	hgsc.bcm.edu	37	2	152226570	152226570	+	Missense_Mutation	SNP	A	A	G	rs1046668	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:152226570A>G	ENST00000243347.3	+	4	506	c.431A>G	c.(430-432)cAa>cGa	p.Q144R	MIR4773-1_ENST00000585225.1_RNA|RN7SL124P_ENST00000498656.2_RNA	NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	144	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.		Q -> R (in dbSNP:rs1046668). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1730767}.		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	GATCCAAAGCAAATTTTTAAA	0.383													G|||	887	0.177117	0.3033	0.1138	5008	,	,		17071	0.1329		0.1382	False		,,,				2504	0.137				p.Q144R		Atlas-SNP	.											.	TNFAIP6	98	.	0			c.A431G						PASS	.	G	ARG/GLN	1301,3105	695.6+/-406.0	199,903,1101	112.0	113.0	113.0		431	3.5	1.0	2	dbSNP_86	113	1188,7412	763.4+/-407.6	77,1034,3189	yes	missense	TNFAIP6	NM_007115.3	43	276,1937,4290	GG,GA,AA		13.814,29.5279,19.1373	benign	144/278	152226570	2489,10517	2203	4300	6503	SO:0001583	missense	7130	exon4			CAAAGCAAATTTT		CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.431A>G	2.37:g.152226570A>G	ENSP00000243347:p.Gln144Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_007115	Q53TI7|Q8WWI9	Missense_Mutation	SNP	ENST00000243347.3	37	CCDS2193.1	389	0.17811355311355312	144	0.2926829268292683	39	0.10773480662983426	96	0.16783216783216784	110	0.14511873350923482	G	0.071	-1.201428	0.01581	0.295279	0.13814	ENSG00000123610	ENST00000243347	T	0.28255	1.62	5.27	3.46	0.39613	CUB (5);	0.247185	0.38436	N	0.001692	T	0.00012	0.0000	N	0.05383	-0.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41342	-0.9514	9	0.42905	T	0.14	.	5.9954	0.19491	0.2722:0.1359:0.592:0.0	rs1046668;rs3186656;rs17411793;rs56445941;rs61444688;rs1046668	144	P98066	TSG6_HUMAN	R	144	ENSP00000243347:Q144R	ENSP00000243347:Q144R	Q	+	2	0	TNFAIP6	151934816	0.990000	0.36364	0.963000	0.40424	0.230000	0.25150	1.071000	0.30666	0.225000	0.20959	-0.227000	0.12334	CAA	A|0.810;G|0.190	0.190	strong		0.383	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115	
FAT2	2196	hgsc.bcm.edu	37	5	150947719	150947719	+	Silent	SNP	C	C	T	rs3734060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	147	68	0.462585	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	
SYVN1	84447	hgsc.bcm.edu	37	11	64898226	64898226	+	Silent	SNP	C	C	T	rs9971407	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:64898226C>T	ENST00000377190.3	-	11	1105	c.1011G>A	c.(1009-1011)tcG>tcA	p.S337S	SYVN1_ENST00000526060.1_Silent_p.S337S|SYVN1_ENST00000294256.8_Silent_p.S337S|SYVN1_ENST00000307289.6_Silent_p.S286S|SYVN1_ENST00000526121.1_5'UTR	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	337					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)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)	p.S337S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						GCGCTGGCAGCGATGCACGAA	0.692													c|||	657	0.13119	0.1051	0.1556	5008	,	,		10257	0.0615		0.2266	False		,,,				2504	0.1227				p.S337S		Atlas-SNP	.											SYVN1,NS,lymphoid_neoplasm,0,1	SYVN1	55	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1011A						PASS	.	C	,	524,3876		36,452,1712	21.0	25.0	24.0		1011,1011	-10.4	0.1	11	dbSNP_119	24	2025,6561		255,1515,2523	no	coding-synonymous,coding-synonymous	SYVN1	NM_032431.2,NM_172230.2	,	291,1967,4235	TT,TC,CC		23.5849,11.9091,19.6288	,	337/617,337/618	64898226	2549,10437	2200	4293	6493	SO:0001819	synonymous_variant	84447	exon11			TGGCAGCGATGCA	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"""RING-type (C3HC4) zinc fingers"""	20738	protein-coding gene	gene with protein product	"""HMG-coA reductase degradation 1 homolog (S. cerevisiae)"""	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.1011G>A	11.37:g.64898226C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	24	6	0.25	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Silent	SNP	ENST00000377190.3	37	CCDS31605.1																																																																																			C|0.844;T|0.156	0.156	strong		0.692	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	
DYX1C1	161582	hgsc.bcm.edu	37	15	55722882	55722882	+	Nonsense_Mutation	SNP	C	C	A	rs57809907	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:55722882C>A	ENST00000321149.3	-	10	1616	c.1249G>T	c.(1249-1251)Gaa>Taa	p.E417*	DYX1C1_ENST00000457155.2_3'UTR|DYX1C1_ENST00000380679.1_Intron|DYX1C1_ENST00000348518.3_3'UTR|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000448430.2_Intron	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	417					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)		GATTTTAGTTCTGTTCCTTGA	0.338													C|||	879	0.175519	0.4818	0.0706	5008	,	,		13441	0.0089		0.0865	False		,,,				2504	0.0992				p.E417X		Atlas-SNP	.											DYX1C1,NS,carcinoma,+2,1	DYX1C1	54	1	0			c.G1249T	GRCh37	CM035520	DYX1C1	M	rs57809907	PASS	.	C	,,stop/GLU	1825,2559	532.5+/-373.5	383,1059,750	107.0	107.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,1249	4.7	1.0	15	dbSNP_129	107	765,7809	181.3+/-230.0	28,709,3550	yes	utr-3,intron,stop-gained	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	,,	411,1768,4300	AA,AC,CC		8.9223,41.6286,19.9877	,,	,,417/421	55722882	2590,10368	2192	4287	6479	SO:0001587	stop_gained	161582	exon10			TTAGTTCTGTTCC		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.1249G>T	15.37:g.55722882C>A	ENSP00000323275:p.Glu417*	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_130810	Q6P5Y9|Q8N1S6	Nonsense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	344	0.1575091575091575	243	0.49390243902439024	26	0.0718232044198895	6	0.01048951048951049	69	0.09102902374670185	C	38	7.101446	0.98063	0.416286	0.089223	ENSG00000256061	ENST00000321149	.	.	.	5.6	4.68	0.58851	.	0.670270	0.13414	U	0.389654	.	.	.	.	.	.	0.09310	P	0.9999999862604	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	7.7377	0.28823	0.0:0.717:0.1348:0.1483	rs57809907	.	.	.	X	417	.	ENSP00000323275:E417X	E	-	1	0	DYX1C1	53510174	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	-0.079000	0.11357	1.350000	0.45770	0.558000	0.71614	GAA	C|0.819;A|0.181	0.181	strong		0.338	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
UBAP2	55833	hgsc.bcm.edu	37	9	33971740	33971740	+	Silent	SNP	A	A	G	rs3739690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:33971740A>G	ENST00000379238.1	-	8	705	c.588T>C	c.(586-588)ccT>ccC	p.P196P	UBAP2_ENST00000539807.1_Intron|UBAP2_ENST00000449054.1_Silent_p.P196P|UBAP2_ENST00000360802.1_Silent_p.P196P|UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000418786.2_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	91	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	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	
LTK	4058	hgsc.bcm.edu	37	15	41805237	41805237	+	Missense_Mutation	SNP	C	C	T	rs2305030	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:41805237C>T	ENST00000263800.6	-	2	221	c.125G>A	c.(124-126)cGg>cAg	p.R42Q	LTK_ENST00000355166.5_Missense_Mutation_p.R42Q|LTK_ENST00000453182.2_Missense_Mutation_p.R42Q|LTK_ENST00000561619.1_Intron	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	42			R -> Q (in dbSNP:rs2305030). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7685902}.		cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TTTCGGGTCCCGGGGGCTGGG	0.627										TSP Lung(18;0.14)			C|||	781	0.15595	0.0893	0.1354	5008	,	,		13698	0.4038		0.0825	False		,,,				2504	0.0808				p.R42Q		Atlas-SNP	.											.	LTK	117	.	0			c.G125A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	405,3993		20,365,1814	19.0	24.0	23.0		125,125,125	-6.4	0.0	15	dbSNP_100	23	917,7675		39,839,3418	yes	missense,missense,missense	LTK	NM_001135685.1,NM_002344.5,NM_206961.3	43,43,43	59,1204,5232	TT,TC,CC		10.6727,9.2087,10.1771	benign,benign,benign	42/735,42/865,42/804	41805237	1322,11668	2199	4296	6495	SO:0001583	missense	4058	exon2			GGGTCCCGGGGGC	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"""leukocyte tyrosine kinase"""			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.125G>A	15.37:g.41805237C>T	ENSP00000263800:p.Arg42Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	44	29	0.659091	NM_001135685	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	37	CCDS10077.1	371	0.16987179487179488	38	0.07723577235772358	53	0.1464088397790055	223	0.38986013986013984	57	0.07519788918205805	C	10.85	1.466746	0.26335	0.092087	0.106727	ENSG00000062524	ENST00000360087;ENST00000355166;ENST00000263800;ENST00000453182	T;T;T	0.75367	-0.93;-0.71;-0.88	4.31	-6.41	0.01938	.	1.621950	0.04291	N	0.345471	T	0.00012	0.0000	N	0.03115	-0.41	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04128	-1.0975	9	0.20046	T	0.44	.	3.33	0.07080	0.106:0.3338:0.1054:0.4549	rs2305030;rs52810035;rs59038632;rs2305030	42;42;42	E9PFX4;P29376-4;P29376	.;.;LTK_HUMAN	Q	42	ENSP00000347293:R42Q;ENSP00000263800:R42Q;ENSP00000392196:R42Q	ENSP00000263800:R42Q	R	-	2	0	LTK	39592529	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-0.907000	0.04067	-1.564000	0.01678	-2.614000	0.00158	CGG	C|0.858;T|0.142	0.142	strong		0.627	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
AGAP11	119385	hgsc.bcm.edu	37	10	88768423	88768423	+	RNA	SNP	A	A	G	rs2641562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:88768423A>G	ENST00000444431.1	+	0	3023				RP11-96C23.10_ENST00000451760.1_RNA|RP11-96C23.14_ENST00000444180.3_RNA|RP11-96C23.5_ENST00000433214.2_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	102	0	0		WXS	Illumina HiSeq	Phase_I	93	73	0.784946	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	
ELMSAN1	91748	hgsc.bcm.edu	37	14	74205878	74205878	+	Silent	SNP	C	C	T	rs17782128	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:74205878C>T	ENST00000286523.5	-	2	1616	c.834G>A	c.(832-834)ccG>ccA	p.P278P	ELMSAN1_ENST00000486739.1_5'Flank|ELMSAN1_ENST00000394071.2_Silent_p.P278P	NM_194278.3	NP_919254.2	Q6PJG2	EMSA1_HUMAN	ELM2 and Myb/SANT-like domain containing 1	278	Gln-rich.|Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGGGTTGCTGCGGCATGGAAT	0.627													c|||	760	0.151757	0.0469	0.1182	5008	,	,		15558	0.1409		0.1839	False		,,,				2504	0.2955				p.P278P		Atlas-SNP	.											C14orf43,bladder,carcinoma,-1,1	.	.	1	0			c.G834A						PASS	.	A	,	275,4131	149.5+/-183.7	12,251,1940	29.0	31.0	30.0		834,834	-1.0	0.9	14	dbSNP_123	30	1666,6934	297.9+/-303.7	162,1342,2796	no	coding-synonymous,coding-synonymous	C14orf43	NM_001043318.1,NM_194278.3	,	174,1593,4736	TT,TC,CC		19.3721,6.2415,14.9239	,	278/1046,278/1046	74205878	1941,11065	2203	4300	6503	SO:0001819	synonymous_variant	91748	exon2			TTGCTGCGGCATG	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.834G>A	14.37:g.74205878C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	168	59	0.35119	NM_194278	Q6PK13|Q6PK59|Q6ZS23	Silent	SNP	ENST00000286523.5	37	CCDS9819.1																																																																																			C|0.861;T|0.139	0.139	strong		0.627	ELMSAN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317793.1	NM_194278	
KIF26A	26153	hgsc.bcm.edu	37	14	104641612	104641612	+	Silent	SNP	T	T	C	rs4906422	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104641612T>C	ENST00000423312.2	+	12	2487	c.2487T>C	c.(2485-2487)ggT>ggC	p.G829G	KIF26A_ENST00000315264.7_Silent_p.G690G	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	829					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CCTCCAAGGGTCCCCGAGACG	0.682													C|||	1475	0.294529	0.1127	0.3545	5008	,	,		14159	0.3998		0.3022	False		,,,				2504	0.3814				p.G829G		Atlas-SNP	.											KIF26A,NS,carcinoma,0,1	KIF26A	84	1	0			c.T2487C						PASS	.	C		495,3585		34,427,1579	15.0	18.0	17.0		2487	-2.1	0.0	14	dbSNP_111	17	2411,5939		389,1633,2153	no	coding-synonymous	KIF26A	NM_015656.1		423,2060,3732	CC,CT,TT		28.8743,12.1324,23.3789		829/1883	104641612	2906,9524	2040	4175	6215	SO:0001819	synonymous_variant	26153	exon12			CAAGGGTCCCCGA	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.2487T>C	14.37:g.104641612T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	45	0.714286	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			T|0.708;C|0.292	0.292	strong		0.682	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
STAC	6769	hgsc.bcm.edu	37	3	36422216	36422216	+	Silent	SNP	T	T	C	rs73052248	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:36422216T>C	ENST00000273183.3	+	1	381	c.81T>C	c.(79-81)tcT>tcC	p.S27S	STAC_ENST00000457375.2_Silent_p.S27S|STAC_ENST00000476388.1_3'UTR	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	27					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)	p.S27S(1)		endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						AACCGCCCTCTCCTGCATCCA	0.662													T|||	867	0.173123	0.031	0.2579	5008	,	,		14453	0.1994		0.2475	False		,,,				2504	0.2014				p.S27S		Atlas-SNP	.											STAC,caecum,carcinoma,0,1	STAC	78	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T81C						PASS	.	T		266,4128		12,242,1943	26.0	21.0	23.0		81	-0.7	1.0	3	dbSNP_130	23	1974,6604		238,1498,2553	no	coding-synonymous	STAC	NM_003149.1		250,1740,4496	CC,CT,TT		23.0124,6.0537,17.268		27/403	36422216	2240,10732	2197	4289	6486	SO:0001819	synonymous_variant	6769	exon1			GCCCTCTCCTGCA	D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"""src homology three (SH3) and cysteine rich domain"""			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.81T>C	3.37:g.36422216T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_003149	B2R8S8	Silent	SNP	ENST00000273183.3	37	CCDS2662.1																																																																																			T|0.823;C|0.177	0.177	strong		0.662	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149	
CCDC170	80129	hgsc.bcm.edu	37	6	151939181	151939181	+	Missense_Mutation	SNP	G	G	A	rs3734804	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:151939181G>A	ENST00000239374.7	+	11	2146	c.2047G>A	c.(2047-2049)Gtc>Atc	p.V683I	RNU6-813P_ENST00000384691.1_RNA|CCDC170_ENST00000367290.5_Missense_Mutation_p.V690I	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	683			V -> I (in dbSNP:rs3734804). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.														TGAAAGATTGGTCCATTCACA	0.488													A|||	2662	0.53155	0.7564	0.3804	5008	,	,		19217	0.4276		0.504	False		,,,				2504	0.4703				p.V683I		Atlas-SNP	.											.	.	.	.	0			c.G2047A						PASS	.	A	ILE/VAL	3060,990		1164,732,129	127.0	129.0	128.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2047	3.5	1.0	6	dbSNP_107	128	4451,3891		1199,2053,919	yes	missense	C6orf97	NM_025059.3	29	2363,2785,1048	AA,AG,GG		46.6435,24.4444,39.3883	benign	683/716	151939181	7511,4881	2025	4171	6196	SO:0001583	missense	80129	exon11			AGATTGGTCCATT	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.2047G>A	6.37:g.151939181G>A	ENSP00000239374:p.Val683Ile	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	203	75	0.369458	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	1098	0.5027472527472527	356	0.7235772357723578	146	0.40331491712707185	229	0.40034965034965037	367	0.4841688654353562	A	2.969	-0.212916	0.06140	0.755556	0.533565	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.04809	3.56;3.55	5.96	3.55	0.40652	.	0.220933	0.41396	N	0.000881	T	0.00271	0.0008	N	0.00119	-2.075	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.41928	-0.9481	9	0.02654	T	1	-11.5196	7.4255	0.27096	0.7528:0.1208:0.1264:0.0	rs3734804;rs17855719;rs52806953;rs57580983;rs3734804	683	Q8IYT3	CF097_HUMAN	I	683;690	ENSP00000239374:V683I;ENSP00000356259:V690I	ENSP00000239374:V683I	V	+	1	0	C6orf97	151980874	1.000000	0.71417	0.998000	0.56505	0.637000	0.38172	1.248000	0.32827	0.146000	0.19002	-0.254000	0.11334	GTC	G|0.473;A|0.527	0.527	strong		0.488	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
FAM179A	165186	hgsc.bcm.edu	37	2	29274704	29274704	+	Silent	SNP	C	C	T	rs61749512	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:29274704C>T	ENST00000379558.4	+	20	3156	c.2805C>T	c.(2803-2805)acC>acT	p.T935T	FAM179A_ENST00000403861.2_Silent_p.T880T|FAM179A_ENST00000465300.1_3'UTR	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	935										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						TCCTGAACACCGCCACCAGGA	0.642													C|||	1129	0.225439	0.1694	0.1859	5008	,	,		16173	0.5099		0.0915	False		,,,				2504	0.1738				p.T935T		Atlas-SNP	.											.	FAM179A	106	.	0			c.C2805T						PASS	.	C		560,3498		30,500,1499	16.0	19.0	18.0		2805	2.8	0.0	2	dbSNP_129	18	756,7610		34,688,3461	no	coding-synonymous	FAM179A	NM_199280.2		64,1188,4960	TT,TC,CC		9.0366,13.7999,10.5924		935/1020	29274704	1316,11108	2029	4183	6212	SO:0001819	synonymous_variant	165186	exon20			GAACACCGCCACC	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.2805C>T	2.37:g.29274704C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	167	73	0.437126	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			C|0.785;T|0.215	0.215	strong		0.642	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
MYO7A	4647	hgsc.bcm.edu	37	11	76922868	76922868	+	Silent	SNP	C	C	T	rs41298757	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:76922868C>T	ENST00000409709.3	+	46	6512	c.6240C>T	c.(6238-6240)tcC>tcT	p.S2080S	MYO7A_ENST00000409619.2_Silent_p.S2031S|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000458637.2_Silent_p.S2042S	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2080	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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						CCCCATAGTCCATCGTCGCCT	0.627													C|||	80	0.0159744	0.0038	0.0173	5008	,	,		19295	0.0		0.0507	False		,,,				2504	0.0123				p.S2080S		Atlas-SNP	.											.	MYO7A	164	.	0			c.C6240T						PASS	.	C	,	39,4353	38.4+/-70.7	1,37,2158	46.0	47.0	47.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6240,6126	0.5	0.9	11	dbSNP_127	47	371,8199	119.7+/-179.0	11,349,3925	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	12,386,6083	TT,TC,CC		4.3291,0.888,3.1631	,	2080/2216,2042/2176	76922868	410,12552	2196	4285	6481	SO:0001819	synonymous_variant	4647	exon46			ATAGTCCATCGTC	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.6240C>T	11.37:g.76922868C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			C|0.975;T|0.025	0.025	strong		0.627	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
MICA	100507436	hgsc.bcm.edu	37	6	31379794	31379794	+	Silent	SNP	C	C	T	rs1051797|rs386699191	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31379794C>T	ENST00000449934.2	+	4	738	c.684C>T	c.(682-684)tcC>tcT	p.S228S	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)				GCAGGGCTTCCAGCTTCTATC	0.587													t|||	1823	0.364018	0.4773	0.4063	5008	,	,		19466	0.2996		0.3141	False		,,,				2504	0.2986				p.S228S		Atlas-SNP	.											.	MICA	21	.	0			c.C684T						PASS	.						21.0	25.0	24.0					6																	31379794		692	1591	2283	SO:0001819	synonymous_variant	100507436	exon4			GGCTTCCAGCTTC	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.684C>T	6.37:g.31379794C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	118	39	0.330508	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.698;T|0.302	0.302	strong		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
SPRY4	81848	hgsc.bcm.edu	37	5	141693948	141693948	+	Silent	SNP	G	G	A	rs145360326	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:141693948G>A	ENST00000434127.2	-	2	969	c.726C>T	c.(724-726)tcC>tcT	p.S242S	SPRY4_ENST00000344120.4_Silent_p.S265S|SPRY4_ENST00000503582.1_5'Flank	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	242	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.S265S(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGCACCACGGAGAGAGCAC	0.682									Testicular Cancer, Familial Clustering of																												p.S265S		Atlas-SNP	.											SPRY4,rectum,carcinoma,0,2	SPRY4	31	2	3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	c.C795T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	60.0	60.0	60.0		726,795	0.7	1.0	5	dbSNP_134	60	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	SPRY4	NM_001127496.1,NM_030964.3	,	0,7,6496	AA,AG,GG		0.0581,0.0454,0.0538	,	242/300,265/323	141693948	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	81848	exon3	Familial Cancer Database		CACCACGGAGAGA	AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.726C>T	5.37:g.141693948G>A		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	229	108	0.471616	NM_030964	A4FVB2|A4FVB3|Q6QIX2|Q9C003	Silent	SNP	ENST00000434127.2	37	CCDS47296.1																																																																																			G|0.999;A|0.001	0.001	strong		0.682	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1		
MEF2A	4205	hgsc.bcm.edu	37	15	100250918	100250918	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:100250918G>A	ENST00000557785.1	+	10	1414	c.1065G>A	c.(1063-1065)tcG>tcA	p.S355S	MEF2A_ENST00000449277.2_Silent_p.S287S|MEF2A_ENST00000557942.1_Silent_p.S363S|MEF2A_ENST00000558812.1_Silent_p.S295S|MEF2A_ENST00000453228.2_Silent_p.S355S|MEF2A_ENST00000338042.6_Silent_p.S364S|MEF2A_ENST00000354410.5_Silent_p.S357S	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	365					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)			GACAGGTGTCGGCCTGGCAGC	0.537																																					p.S357S		Atlas-SNP	.											.	MEF2A	138	.	0			c.G1071A						PASS	.						51.0	53.0	53.0					15																	100250918		2046	4203	6249	SO:0001819	synonymous_variant	4205	exon10			GGTGTCGGCCTGG		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.1065G>A	15.37:g.100250918G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	97	71	0.731959	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																			.	.	none		0.537	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
GAS8	2622	hgsc.bcm.edu	37	16	90106746	90106746	+	Silent	SNP	C	C	T	rs61734731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:90106746C>T	ENST00000268699.4	+	9	1172	c.1050C>T	c.(1048-1050)acC>acT	p.T350T	GAS8_ENST00000540721.1_3'UTR|GAS8_ENST00000536122.1_Silent_p.T325T|URAHP_ENST00000517889.1_RNA	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	350					cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		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;0.029)		GGAAGTTCACCGCAGCCATCC	0.627													c|||	136	0.0271565	0.0091	0.0115	5008	,	,		19539	0.0446		0.0487	False		,,,				2504	0.0225				p.T350T		Atlas-SNP	.											GAS8,NS,carcinoma,0,1	GAS8	29	1	0			c.C1050T						PASS	.	C		65,4323		0,65,2129	61.0	45.0	51.0		1050	-11.6	0.0	16	dbSNP_129	51	507,8091		15,477,3807	no	coding-synonymous	GAS8	NM_001481.2		15,542,5936	TT,TC,CC		5.8967,1.4813,4.4047		350/479	90106746	572,12414	2194	4299	6493	SO:0001819	synonymous_variant	2622	exon9			GTTCACCGCAGCC	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.1050C>T	16.37:g.90106746C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	46	5	0.108696	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			C|0.963;T|0.037	0.037	strong		0.627	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
PRSS57	400668	hgsc.bcm.edu	37	19	687078	687078	+	Silent	SNP	G	G	A	rs72618587	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:687078G>A	ENST00000329267.7	-	4	521	c.492C>T	c.(490-492)ttC>ttT	p.F164F		NM_214710.3	NP_999875	Q6UWY2	PRS57_HUMAN	protease, serine, 57	164	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|lung(5)	6						AGTCAGACACGAAGCCCCAGC	0.692													G|||	527	0.105232	0.0719	0.0317	5008	,	,		16125	0.2738		0.0557	False		,,,				2504	0.0798				p.F164F		Atlas-SNP	.											.	PRSS57	18	.	0			c.C492T						PASS	.	G		305,4099	162.2+/-194.2	8,289,1905	36.0	36.0	36.0		492	-2.5	0.0	19	dbSNP_130	36	453,8147	134.1+/-191.5	16,421,3863	no	coding-synonymous	PRSS57	NM_214710.3		24,710,5768	AA,AG,GG		5.2674,6.9255,5.829		164/284	687078	758,12246	2202	4300	6502	SO:0001819	synonymous_variant	400668	exon4			AGACACGAAGCCC	AY358594	CCDS12041.1	19p13.3	2012-03-26	2011-03-07	2011-03-07		ENSG00000185198		"""Serine peptidases / Serine peptidases"""	31397	protein-coding gene	gene with protein product			"""protease, serine-like 1"""	PRSSL1		12975309	Standard	NM_214710		Approved	UNQ782	uc002lpl.1	Q6UWY2		ENST00000329267.7:c.492C>T	19.37:g.687078G>A		Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	262	130	0.496183	NM_214710	B2RNW8	Silent	SNP	ENST00000329267.7	37	CCDS12041.1																																																																																			G|0.928;A|0.072	0.072	strong		0.692	PRSS57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452480.2	NM_214710	
TEKT3	64518	hgsc.bcm.edu	37	17	15215660	15215660	+	Silent	SNP	T	T	C	rs2286516	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:15215660T>C	ENST00000395930.1	-	7	1203	c.1017A>G	c.(1015-1017)caA>caG	p.Q339Q	TEKT3_ENST00000338696.2_Silent_p.Q339Q|RNU6-799P_ENST00000363567.1_RNA	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	339					cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		CTTTGTTGAATTGATTCCACA	0.448													T|||	1174	0.234425	0.1445	0.2896	5008	,	,		21481	0.252		0.2793	False		,,,				2504	0.2526				p.Q339Q		Atlas-SNP	.											.	TEKT3	64	.	0			c.A1017G						PASS	.	T		744,3662	306.0+/-289.3	64,616,1523	130.0	113.0	118.0		1017	2.2	1.0	17	dbSNP_100	118	2224,6376	377.6+/-338.6	274,1676,2350	no	coding-synonymous	TEKT3	NM_031898.2		338,2292,3873	CC,CT,TT		25.8605,16.8861,22.8202		339/491	15215660	2968,10038	2203	4300	6503	SO:0001819	synonymous_variant	64518	exon7			GTTGAATTGATTC	AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.1017A>G	17.37:g.15215660T>C		Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	225	97	0.431111	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Silent	SNP	ENST00000395930.1	37	CCDS11169.1																																																																																			T|0.770;C|0.230	0.230	strong		0.448	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769276	43769276	+	Silent	SNP	T	T	C	rs10880473	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:43769276T>C	ENST00000389420.3	-	36	5351	c.5352A>G	c.(5350-5352)agA>agG	p.R1784R		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1784	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		AGTCTTCCCTTCTACTCCCAT	0.348													C|||	1121	0.223842	0.4266	0.1239	5008	,	,		18065	0.1002		0.1998	False		,,,				2504	0.1728				p.R1784R		Atlas-SNP	.											ADAMTS20_ENST00000389420,neck,malignant_melanoma,-2,1	ADAMTS20	635	1	0			c.A5352G						scavenged	.	C		1647,2759	659.9+/-400.6	316,1015,872	156.0	153.0	154.0		5352	2.0	1.0	12	dbSNP_120	154	1768,6832	734.1+/-406.9	182,1404,2714	no	coding-synonymous	ADAMTS20	NM_025003.3		498,2419,3586	CC,CT,TT		20.5581,37.3808,26.2571		1784/1911	43769276	3415,9591	2203	4300	6503	SO:0001819	synonymous_variant	80070	exon36			TTCCCTTCTACTC	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5352A>G	12.37:g.43769276T>C		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	157	61	0.388535	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																			T|0.747;C|0.253	0.253	strong		0.348	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
ABCF2	10061	hgsc.bcm.edu	37	7	150912750	150912750	+	Silent	SNP	G	G	T	rs12538823	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:150912750G>T	ENST00000287844.2	-	13	1579	c.1470C>A	c.(1468-1470)atC>atA	p.I490I	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Silent_p.I490I	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	490	ABC transporter 2. {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)		CCTTCTCCTTGATCTCTGGGT	0.488													G|||	250	0.0499201	0.0197	0.1138	5008	,	,		20679	0.0159		0.0775	False		,,,				2504	0.0521				p.I490I		Atlas-SNP	.											.	ABCF2	54	.	0			c.C1470A						PASS	.	G	,	154,4252	105.2+/-143.6	0,154,2049	245.0	209.0	221.0		1470,1470	3.8	1.0	7	dbSNP_120	221	822,7778	191.4+/-237.6	45,732,3523	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	45,886,5572	TT,TG,GG		9.5581,3.4952,7.5042	,	490/635,490/624	150912750	976,12030	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon13			CTCCTTGATCTCT	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.1470C>A	7.37:g.150912750G>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	123	22	0.178862	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			G|0.939;T|0.061	0.061	strong		0.488	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
MYO1C	4641	hgsc.bcm.edu	37	17	1373518	1373518	+	Missense_Mutation	SNP	T	T	C	rs9905106	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:1373518T>C	ENST00000575158.1	-	24	2548	c.2372A>G	c.(2371-2373)cAg>cGg	p.Q791R	MYO1C_ENST00000545534.2_Missense_Mutation_p.Q802R|MYO1C_ENST00000359786.5_Missense_Mutation_p.Q826R|MYO1C_ENST00000438665.2_Missense_Mutation_p.Q807R|MYO1C_ENST00000361007.2_Missense_Mutation_p.Q791R			Q12965	MYO1E_HUMAN	myosin IC	0	Myosin tail. {ECO:0000255}.				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)		CAGGACATTCTGGGGCAGCTG	0.637													C|||	3564	0.711661	0.9183	0.7017	5008	,	,		12609	0.4196		0.7008	False		,,,				2504	0.7515				p.Q826R		Atlas-SNP	.											MYO1C,NS,carcinoma,0,2	MYO1C	57	2	0			c.A2477G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN	3834,498		1699,436,31	14.0	15.0	15.0		2477,2420,2372	4.9	1.0	17	dbSNP_119	15	6265,2185		2341,1583,301	yes	missense,missense,missense	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	43,43,43	4040,2019,332	CC,CT,TT		25.858,11.4958,20.9905	benign,benign,benign	826/1064,807/1045,791/1029	1373518	10099,2683	2166	4225	6391	SO:0001583	missense	4641	exon24			ACATTCTGGGGCA	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.2372A>G	17.37:g.1373518T>C	ENSP00000459174:p.Gln791Arg	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_001080779	Q14778	Missense_Mutation	SNP	ENST00000575158.1	37	CCDS11003.1	1440	0.6593406593406593	441	0.8963414634146342	256	0.7071823204419889	226	0.3951048951048951	517	0.6820580474934037	C	5.871	0.344923	0.11126	0.885042	0.74142	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534	D;D;D;D	0.87029	-2.19;-2.2;-2.2;-2.2	4.95	4.95	0.65309	.	0.106416	0.64402	N	0.000009	T	0.00012	0.0000	N	0.03608	-0.345	0.53005	P	3.500000000000725E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41124	-0.9526	9	0.15952	T	0.53	.	6.3336	0.21285	0.0:0.7213:0.0:0.2787	rs9905106;rs57897716	826;807	O00159;O00159-3	MYO1C_HUMAN;.	R	826;807;807;791;802	ENSP00000352834:Q826R;ENSP00000412197:Q807R;ENSP00000354283:Q791R;ENSP00000437685:Q802R	ENSP00000352834:Q826R	Q	-	2	0	MYO1C	1320268	0.998000	0.40836	0.999000	0.59377	0.215000	0.24574	1.400000	0.34577	1.334000	0.45468	-0.215000	0.12644	CAG	T|0.270;C|0.730	0.730	strong		0.637	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
MAD1L1	8379	hgsc.bcm.edu	37	7	2020125	2020125	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:2020125T>C	ENST00000406869.1	-	15	2025	c.1468A>G	c.(1468-1470)Agc>Ggc	p.S490G	MAD1L1_ENST00000265854.7_Missense_Mutation_p.S490G|MAD1L1_ENST00000402746.1_Missense_Mutation_p.S398G|MAD1L1_ENST00000399654.2_Missense_Mutation_p.S490G			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)	490	Necessary for interaction with NEK2.				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)		p.S490G(1)		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)		AACAGGAAGCTCTGTTCGGCA	0.612																																					p.S490G		Atlas-SNP	.											MAD1L1,NS,carcinoma,0,1	MAD1L1	81	1	1	Substitution - Missense(1)	endometrium(1)	c.A1468G						scavenged	.						32.0	35.0	34.0					7																	2020125		2028	4167	6195	SO:0001583	missense	8379	exon15			GGAAGCTCTGTTC	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.1468A>G	7.37:g.2020125T>C	ENSP00000385334:p.Ser490Gly	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	98	3	0.0306122	NM_003550	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Missense_Mutation	SNP	ENST00000406869.1	37	CCDS43539.1	.	.	.	.	.	.	.	.	.	.	T	9.739	1.164308	0.21538	.	.	ENSG00000002822	ENST00000402746;ENST00000399654;ENST00000406869;ENST00000442131;ENST00000265854;ENST00000450235;ENST00000438959;ENST00000444373	T;T;T;T;T;T	0.78364	2.12;2.12;2.12;2.12;2.12;-1.17	5.09	2.71	0.32032	.	0.120467	0.85682	N	0.000000	T	0.73575	0.3604	L	0.52126	1.63	0.27055	N	0.963692	D;D;P	0.61697	0.99;0.99;0.943	P;P;B	0.50708	0.595;0.648;0.372	T	0.63699	-0.6578	10	0.27785	T	0.31	-21.3733	6.4918	0.22119	0.0:0.1967:0.0:0.8033	.	489;398;490	A4D218;B3KR41;Q9Y6D9	.;.;MD1L1_HUMAN	G	398;490;490;41;490;41;157;80	ENSP00000384155:S398G;ENSP00000382562:S490G;ENSP00000385334:S490G;ENSP00000265854:S490G;ENSP00000394886:S41G;ENSP00000414877:S157G	ENSP00000265854:S490G	S	-	1	0	MAD1L1	1986651	0.837000	0.29446	0.357000	0.25798	0.170000	0.22686	1.032000	0.30178	0.291000	0.22468	0.533000	0.62120	AGC	.	.	none		0.612	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
METTL21A	151194	hgsc.bcm.edu	37	2	208478055	208478055	+	Silent	SNP	A	A	G	rs17520056	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:208478055A>G	ENST00000411432.1	-	4	588	c.372T>C	c.(370-372)acT>acC	p.T124T	METTL21A_ENST00000426075.1_Silent_p.T124T|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000442521.1_Silent_p.T124T|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000432416.1_Intron|METTL21A_ENST00000406927.2_Silent_p.T124T|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000448007.2_Silent_p.T124T|METTL21A_ENST00000272839.3_Silent_p.T142T	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	124					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)	p.T124T(1)		endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						TTTGTCCCCAAGTCAGCTCCT	0.368													A|||	1741	0.347644	0.233	0.3617	5008	,	,		20308	0.372		0.3072	False		,,,				2504	0.5092				p.T124T		Atlas-SNP	.											METTL21A,NS,carcinoma,0,1	METTL21A	24	1	1	Substitution - coding silent(1)	stomach(1)	c.T372C						PASS	.	A	,	1099,3307	392.8+/-328.6	138,823,1242	83.0	83.0	83.0		372,372	-5.0	0.9	2	dbSNP_123	83	2724,5876	432.7+/-357.2	427,1870,2003	no	coding-synonymous,coding-synonymous	METTL21A	NM_001127395.1,NM_145280.4	,	565,2693,3245	GG,GA,AA		31.6744,24.9433,29.3941	,	124/219,124/219	208478055	3823,9183	2203	4300	6503	SO:0001819	synonymous_variant	151194	exon4			TCCCCAAGTCAGC	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 557b"", ""heat shock protein 70kDa lysine (K) methyltransferase"""	615257	"""family with sequence similarity 119, member A"""	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.372T>C	2.37:g.208478055A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	61	43	0.704918	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Silent	SNP	ENST00000411432.1	37	CCDS2376.1																																																																																			A|0.705;G|0.295	0.295	strong		0.368	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280	
LRRC42	115353	hgsc.bcm.edu	37	1	54432019	54432019	+	Silent	SNP	G	G	A	rs2294514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:54432019G>A	ENST00000371370.3	+	8	1499	c.978G>A	c.(976-978)gaG>gaA	p.E326E	LRRC42_ENST00000319223.4_Silent_p.E326E|LRRC42_ENST00000477905.1_3'UTR	NM_001256409.1	NP_001243338.1	Q9Y546	LRC42_HUMAN	leucine rich repeat containing 42	326										breast(2)|kidney(1)|large_intestine(1)|lung(5)	9						AGCCACGGGAGACCTCGGAGC	0.443													A|||	1301	0.259784	0.7163	0.1254	5008	,	,		19363	0.0605		0.1451	False		,,,				2504	0.0613				p.E326E		Atlas-SNP	.											.	LRRC42	29	.	0			c.G978A						PASS	.	A		2618,1788	526.7+/-371.9	781,1056,366	90.0	95.0	93.0		978	1.2	0.0	1	dbSNP_100	93	1291,7309	759.0+/-407.5	105,1081,3114	yes	coding-synonymous	LRRC42	NM_052940.3		886,2137,3480	AA,AG,GG		15.0116,40.581,30.0554		326/429	54432019	3909,9097	2203	4300	6503	SO:0001819	synonymous_variant	115353	exon7			ACGGGAGACCTCG	AK075201	CCDS585.1	1p33-p32.1	2014-02-12			ENSG00000116212	ENSG00000116212			28792	protein-coding gene	gene with protein product						12477932	Standard	NM_001256409		Approved	MGC8974	uc001cwj.2	Q9Y546	OTTHUMG00000008436	ENST00000371370.3:c.978G>A	1.37:g.54432019G>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	103	70	0.679612	NM_052940	D3DQ46|Q8N2Q8	Silent	SNP	ENST00000371370.3	37	CCDS585.1																																																																																			G|0.708;A|0.292	0.292	strong		0.443	LRRC42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023250.1	NM_052940	
SAMD9	54809	hgsc.bcm.edu	37	7	92734358	92734358	+	Silent	SNP	G	G	A	rs200454238		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:92734358G>A	ENST00000379958.2	-	3	1322	c.1053C>T	c.(1051-1053)gaC>gaT	p.D351D		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	351						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.S348fs*47(1)		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)			TTTTCGTAATGTCCTTAGAGC	0.323																																					p.D351D		Atlas-SNP	.											.	SAMD9	239	.	1	Deletion - Frameshift(1)	breast(1)	c.C1053T						PASS	.	G	,	0,4402		0,0,2201	97.0	95.0	96.0		1053,1053	2.4	0.1	7		96	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous	SAMD9	NM_001193307.1,NM_017654.3	,	0,4,6496	AA,AG,GG		0.0465,0.0,0.0308	,	351/1590,351/1590	92734358	4,12996	2201	4299	6500	SO:0001819	synonymous_variant	54809	exon2			CGTAATGTCCTTA	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.1053C>T	7.37:g.92734358G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	198	68	0.343434	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																			G|0.999;A|0.001	0.001	weak		0.323	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
CFAP74	85452	hgsc.bcm.edu	37	1	1887245	1887245	+	IGR	SNP	G	G	A	rs28575980	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:1887245G>A								TMEM52 (36533 upstream) : C1orf222 (32317 downstream)																							AGCTGGTGGCGGCTTTGTCAT	0.562													G|||	908	0.18131	0.1044	0.219	5008	,	,		17542	0.2292		0.2316	False		,,,				2504	0.1575				p.A687A		Atlas-SNP	.											KIAA1751,NS,carcinoma,0,1	KIAA1751	92	1	0			c.C2061T						PASS	.	G		517,3601		38,441,1580	44.0	48.0	47.0		2061	-1.6	0.0	1	dbSNP_125	47	2075,6339		258,1559,2390	no	coding-synonymous	KIAA1751	NM_001080484.1		296,2000,3970	AA,AG,GG		24.6613,12.5546,20.6831		687/763	1887245	2592,9940	2059	4207	6266	SO:0001628	intergenic_variant	85452	exon18			GGTGGCGGCTTTG																													1.37:g.1887245G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001080484		Silent	SNP		37		480	0.21978021978021978	59	0.11991869918699187	82	0.2265193370165746	159	0.27797202797202797	180	0.23746701846965698	G	3.005	-0.205185	0.06180	0.125546	0.246613	ENSG00000142609	ENST00000493316	.	.	.	2.8	-1.58	0.08479	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.35724	-0.9777	3	.	.	.	-1.4405	5.1203	0.14856	0.3205:0.1589:0.5206:0.0	rs28575980;rs61496843	.	.	.	L	93	.	.	P	-	2	0	C1orf222	1877105	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.129000	0.15830	-0.723000	0.04915	-1.119000	0.02030	CCG	G|0.777;A|0.223	0.223	strong	0	0.562								
ADH4	127	hgsc.bcm.edu	37	4	100047812	100047812	+	Silent	SNP	G	G	A	rs1126672	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:100047812G>A	ENST00000265512.7	-	8	1125	c.1051C>T	c.(1051-1053)Ctg>Ttg	p.L351L	ADH4_ENST00000508393.1_Silent_p.L370L|ADH4_ENST00000505590.1_Silent_p.L370L|ADH4_ENST00000423445.1_Silent_p.L370L|RP11-696N14.1_ENST00000500358.2_RNA	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	351					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)	p.L351L(2)		NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		TGGGTCACCAGTGCATCCAGA	0.363													A|||	587	0.117212	0.0696	0.1729	5008	,	,		15373	0.0		0.2773	False		,,,				2504	0.0982				p.L351L		Atlas-SNP	.											ADH4,NS,carcinoma,0,1	ADH4	35	1	2	Substitution - coding silent(2)	prostate(2)	c.C1051T						PASS	.	A		484,3922	781.9+/-414.5	21,442,1740	142.0	138.0	139.0		1051	-3.5	0.0	4	dbSNP_86	139	2481,6119	696.0+/-404.8	343,1795,2162	no	coding-synonymous	ADH4	NM_000670.3		364,2237,3902	AA,AG,GG		28.8488,10.985,22.7972		351/381	100047812	2965,10041	2203	4300	6503	SO:0001819	synonymous_variant	127	exon8			TCACCAGTGCATC	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.1051C>T	4.37:g.100047812G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	139	59	0.42446	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	37	CCDS34032.1																																																																																			G|0.824;A|0.176	0.176	strong		0.363	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	
KISS1	3814	hgsc.bcm.edu	37	1	204159922	204159922	+	Missense_Mutation	SNP	T	T	C	rs35431622	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:204159922T>C	ENST00000367194.4	-	3	255	c.107A>G	c.(106-108)cAg>cGg	p.Q36R		NM_002256.3	NP_002247.3	Q15726	KISS1_HUMAN	KiSS-1 metastasis-suppressor	36			Q -> R (in dbSNP:rs35431622). {ECO:0000269|PubMed:15598687}.		cytoskeleton organization (GO:0007010)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of luteinizing hormone secretion (GO:0033686)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of synaptic transmission (GO:0050806)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				large_intestine(1)|lung(1)|ovary(1)	3	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)	Breast(1374;9.42e-05)	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.069)|Kidney(21;0.0934)|Epithelial(59;0.239)	Colorectal(1306;0.0129)		TTCTAGCTGCTGGCCTAGGAC	0.627													T|||	376	0.0750799	0.2118	0.0461	5008	,	,		13089	0.0		0.0437	False		,,,				2504	0.0204				p.Q36R		Atlas-SNP	.											.	KISS1	6	.	0			c.A107G						PASS	.	T	ARG/GLN	492,2418		35,422,998	10.0	12.0	11.0		107	-2.8	0.0	1	dbSNP_126	11	258,6504		10,238,3133	yes	missense	KISS1	NM_002256.3	43	45,660,4131	CC,CT,TT		3.8154,16.9072,7.7543	benign	36/139	204159922	750,8922	1455	3381	4836	SO:0001583	missense	3814	exon3			AGCTGCTGGCCTA	U43527	CCDS41454.1	1q32	2014-01-30			ENSG00000170498	ENSG00000170498		"""Endogenous ligands"""	6341	protein-coding gene	gene with protein product	"""prepro-kisspeptin"", ""kisspeptin"""	603286				9192814, 9806840	Standard	NM_002256		Approved		uc001har.3	Q15726	OTTHUMG00000036060	ENST00000367194.4:c.107A>G	1.37:g.204159922T>C	ENSP00000356162:p.Gln36Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	127	26	0.204724	NM_002256	A8K6N0|Q9HBP1	Missense_Mutation	SNP	ENST00000367194.4	37	CCDS41454.1	140	0.0641025641025641	90	0.18292682926829268	21	0.058011049723756904	0	0.0	29	0.03825857519788918	T	6.208	0.406493	0.11754	0.169072	0.038154	ENSG00000170498	ENST00000367194	T	0.70869	-0.52	4.46	-2.78	0.05859	.	0.506089	0.16641	N	0.205660	T	0.00073	0.0002	N	0.12746	0.255	0.80722	P	0.0	B	0.24258	0.1	B	0.15052	0.012	T	0.04128	-1.0975	9	0.20046	T	0.44	-1.2884	1.3061	0.02088	0.1365:0.1816:0.3428:0.3391	rs35431622;rs59402757	36	Q15726	KISS1_HUMAN	R	36	ENSP00000356162:Q36R	ENSP00000356162:Q36R	Q	-	2	0	KISS1	202426545	0.001000	0.12720	0.039000	0.18376	0.011000	0.07611	-0.160000	0.10041	-0.610000	0.05716	-0.250000	0.11733	CAG	T|0.941;C|0.059	0.059	strong		0.627	KISS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087892.1	NM_002256	
TBC1D26	353149	hgsc.bcm.edu	37	17	15640806	15640806	+	Missense_Mutation	SNP	A	A	C	rs200208182	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:15640806A>C	ENST00000437605.2	+	5	417	c.167A>C	c.(166-168)gAg>gCg	p.E56A	AC005324.6_ENST00000433873.1_RNA|AC005324.6_ENST00000434017.1_RNA|TBC1D26_ENST00000579428.1_Missense_Mutation_p.E56A|ZNF286A_ENST00000593105.1_3'UTR|ZNF286A_ENST00000413242.2_3'UTR	NM_178571.4	NP_848666	Q86UD7	TBC26_HUMAN	TBC1 domain family, member 26	56							Rab GTPase activator activity (GO:0005097)	p.E56A(1)		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)		AGTGAGATGGAGCTGCCCCAC	0.647																																					p.E56A		Atlas-SNP	.											TBC1D26,trunk,malignant_melanoma,0,1	TBC1D26	16	1	1	Substitution - Missense(1)	skin(1)	c.A167C						scavenged	.						35.0	39.0	37.0					17																	15640806		1942	4099	6041	SO:0001583	missense	353149	exon5			AGATGGAGCTGCC		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.167A>C	17.37:g.15640806A>C	ENSP00000410111:p.Glu56Ala	Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	323	20	0.0619195	NM_178571	A8K929|Q4G172	Missense_Mutation	SNP	ENST00000437605.2	37	CCDS42265.1	.	.	.	.	.	.	.	.	.	.	a	8.747	0.920269	0.17982	.	.	ENSG00000214946	ENST00000437605	T	0.44881	0.91	0.888	-1.78	0.07957	.	0.321547	0.28187	U	0.016280	T	0.40067	0.1102	M	0.81682	2.555	0.09310	N	1	P;P	0.41710	0.76;0.481	B;B	0.44163	0.443;0.347	T	0.39292	-0.9621	10	0.51188	T	0.08	.	1.5879	0.02648	0.3144:0.2682:0.0:0.4174	.	56;56	Q86UD7;Q86UD7-2	TBC26_HUMAN;.	A	56	ENSP00000410111:E56A	ENSP00000410111:E56A	E	+	2	0	TBC1D26	15581531	0.176000	0.23096	0.000000	0.03702	0.001000	0.01503	0.354000	0.20146	-1.189000	0.02702	-0.811000	0.03165	GAG	A|0.500;C|0.500	0.500	strong		0.647	TBC1D26-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178571	
RHBDF2	79651	hgsc.bcm.edu	37	17	74473329	74473329	+	Missense_Mutation	SNP	C	C	T	rs140433374		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:74473329C>T	ENST00000313080.4	-	8	1213	c.940G>A	c.(940-942)Gcc>Acc	p.A314T	RHBDF2_ENST00000592378.1_5'Flank|RHBDF2_ENST00000591885.1_Missense_Mutation_p.A285T|RHBDF2_ENST00000389760.4_Missense_Mutation_p.A285T	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	314					negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						AAGTAGCTGGCAGAGAGTGGG	0.582													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.A314T		Atlas-SNP	.											.	RHBDF2	57	.	0			c.G940A						PASS	.	C	THR/ALA,THR/ALA	0,4404		0,0,2202	30.0	35.0	33.0		853,940	5.5	1.0	17	dbSNP_134	33	9,8591	6.4+/-24.3	0,9,4291	yes	missense,missense	RHBDF2	NM_001005498.3,NM_024599.5	58,58	0,9,6493	TT,TC,CC		0.1047,0.0,0.0692	possibly-damaging,possibly-damaging	285/828,314/857	74473329	9,12995	2202	4300	6502	SO:0001583	missense	79651	exon8			AGCTGGCAGAGAG	BC016034	CCDS32743.1, CCDS32744.1	17q25.3	2014-09-17	2006-02-22	2006-02-22		ENSG00000129667			20788	protein-coding gene	gene with protein product		614404	"""rhomboid, veinlet-like 6 (Drosophila)"", ""tylosis with oesophageal cancer"""	RHBDL6, TOC		12838346, 22265016	Standard	NM_024599		Approved	FLJ22341, RHBDL5, TOCG	uc002jrq.2	Q6PJF5		ENST00000313080.4:c.940G>A	17.37:g.74473329C>T	ENSP00000322775:p.Ala314Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	138	74	0.536232	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	37	CCDS32743.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	27.4	4.830924	0.91036	0.0	0.001047	ENSG00000129667	ENST00000313080;ENST00000389760;ENST00000389762	T;T	0.69561	-0.41;-0.41	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.78566	0.4303	L	0.56769	1.78	0.50632	D	0.999886	D;P;P;P	0.69078	0.997;0.866;0.891;0.799	D;P;B;P	0.67548	0.952;0.507;0.439;0.615	T	0.73920	-0.3830	10	0.26408	T	0.33	-38.8792	19.4819	0.95013	0.0:1.0:0.0:0.0	.	285;260;314;285	B7Z8H4;Q6ZWP8;Q6PJF5;Q6PJF5-2	.;.;RHDF2_HUMAN;.	T	314;285;260	ENSP00000322775:A314T;ENSP00000374410:A285T	ENSP00000322775:A314T	A	-	1	0	RHBDF2	71984924	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.534000	0.67167	2.595000	0.87683	0.655000	0.94253	GCC	C|0.999;T|0.001	0.001	strong		0.582	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599	
VILL	50853	hgsc.bcm.edu	37	3	38047954	38047954	+	Missense_Mutation	SNP	G	G	C	rs9816693	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38047954G>C	ENST00000283713.6	+	19	2486	c.2220G>C	c.(2218-2220)ttG>ttC	p.L740F	VILL_ENST00000383759.2_Missense_Mutation_p.L740F|VILL_ENST00000465644.1_Missense_Mutation_p.L458F			O15195	VILL_HUMAN	villin-like	740			L -> F (in dbSNP:rs9816693).		actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)	p.L740F(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		TCAACAACTTGCGGCTATCCA	0.617													C|||	1164	0.232428	0.4168	0.1383	5008	,	,		17942	0.0863		0.1441	False		,,,				2504	0.2914				p.L740F		Atlas-SNP	.											VILL,NS,carcinoma,0,1	VILL	61	1	1	Substitution - Missense(1)	stomach(1)	c.G2220C						scavenged	.	C	PHE/LEU	1635,2753		309,1017,868	74.0	88.0	83.0		2220	2.3	0.5	3	dbSNP_119	83	1448,7118		121,1206,2956	yes	missense	VILL	NM_015873.3	22	430,2223,3824	CC,CG,GG		16.904,37.2607,23.7996	benign	740/857	38047954	3083,9871	2194	4283	6477	SO:0001583	missense	50853	exon18			CAACTTGCGGCTA		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.2220G>C	3.37:g.38047954G>C	ENSP00000283713:p.Leu740Phe	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	190	67	0.352632	NM_015873	A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	37	CCDS2670.2	389	0.17811355311355312	194	0.3943089430894309	44	0.12154696132596685	45	0.07867132867132867	106	0.13984168865435356	C	0.885	-0.727332	0.03158	0.372607	0.16904	ENSG00000136059	ENST00000283713;ENST00000383759;ENST00000356246;ENST00000465644	T;T;T	0.14516	2.58;2.58;2.5	3.14	2.26	0.28386	.	0.479810	0.20403	N	0.093008	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	0.45716	-0.9242	9	0.44086	T	0.13	-11.3814	4.5018	0.11867	0.0:0.6389:0.2314:0.1297	rs9816693;rs58692772;rs9816693	740	O15195	VILL_HUMAN	F	740;740;726;458	ENSP00000283713:L740F;ENSP00000373266:L740F;ENSP00000422096:L458F	ENSP00000283713:L740F	L	+	3	2	VILL	38022958	0.001000	0.12720	0.499000	0.27577	0.691000	0.40173	-0.005000	0.12855	0.379000	0.24794	-0.357000	0.07601	TTG	G|0.800;C|0.200	0.200	strong		0.617	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34824107	34824107	+	Missense_Mutation	SNP	A	A	C	rs16894945	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	148	0	0		WXS	Illumina HiSeq	Phase_I	155	62	0.4	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	
SLC15A4	121260	hgsc.bcm.edu	37	12	129293346	129293346	+	Silent	SNP	C	C	T	rs11059924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:129293346C>T	ENST00000266771.5	-	5	1284	c.1245G>A	c.(1243-1245)tcG>tcA	p.S415S	SLC15A4_ENST00000544112.1_Silent_p.S78S|SLC15A4_ENST00000539703.1_5'Flank	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	130	0	0		WXS	Illumina HiSeq	Phase_I	89	33	0.370787	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	
PRDM10	56980	hgsc.bcm.edu	37	11	129830796	129830796	+	Missense_Mutation	SNP	C	C	T	rs11221912	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:129830796C>T	ENST00000360871.3	-	2	295	c.64G>A	c.(64-66)Gca>Aca	p.A22T	PRDM10_ENST00000358825.5_Missense_Mutation_p.A22T|PRDM10_ENST00000528746.1_Missense_Mutation_p.A22T	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	22			A -> T (in dbSNP:rs11221912).		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)	p.A22T(1)		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)		TTCACCTGTGCGGCATTCTGT	0.493													C|||	1397	0.278954	0.3949	0.1758	5008	,	,		18326	0.5417		0.0557	False		,,,				2504	0.1544				p.A22T		Atlas-SNP	.											PRDM10,NS,carcinoma,0,1	PRDM10	120	1	1	Substitution - Missense(1)	stomach(1)	c.G64A						PASS	.	C	THR/ALA,THR/ALA	1553,2849	487.6+/-361.0	272,1009,920	139.0	124.0	129.0		64,64	-0.9	0.0	11	dbSNP_120	129	475,8119	139.5+/-196.2	13,449,3835	yes	missense,missense	PRDM10	NM_020228.2,NM_199437.1	58,58	285,1458,4755	TT,TC,CC		5.5271,35.2794,15.6048	benign,benign	22/1161,22/1157	129830796	2028,10968	2201	4297	6498	SO:0001583	missense	56980	exon2			CCTGTGCGGCATT	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.64G>A	11.37:g.129830796C>T	ENSP00000354118:p.Ala22Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	133	34	0.255639	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	37	CCDS8484.1	594	0.27197802197802196	196	0.3983739837398374	54	0.14917127071823205	308	0.5384615384615384	36	0.047493403693931395	C	11.92	1.781863	0.31502	0.352794	0.055271	ENSG00000170325	ENST00000358825;ENST00000360871;ENST00000528746;ENST00000527581;ENST00000531431	T;T;T;T;T	0.52295	2.76;2.75;2.76;0.67;0.68	5.39	-0.936	0.10419	.	0.349382	0.28871	N	0.013866	T	0.00012	0.0000	L	0.27053	0.805	0.22342	P	0.999180817	B;B;B	0.14438	0.01;0.006;0.001	B;B;B	0.12156	0.007;0.002;0.0	T	0.48175	-0.9058	9	0.51188	T	0.08	-3.0822	10.3723	0.44062	0.0:0.611:0.0:0.389	rs11221912;rs58525085;rs11221912	22;22;22	Q9NQV6-4;G3XAE5;Q9NQV6	.;.;PRD10_HUMAN	T	22	ENSP00000351686:A22T;ENSP00000354118:A22T;ENSP00000431262:A22T;ENSP00000432093:A22T;ENSP00000436681:A22T	ENSP00000351686:A22T	A	-	1	0	PRDM10	129336006	0.041000	0.20044	0.002000	0.10522	0.116000	0.19942	0.163000	0.16520	-0.364000	0.08088	-0.143000	0.13931	GCA	C|0.776;T|0.224	0.224	strong		0.493	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
PLEKHA1	59338	hgsc.bcm.edu	37	10	124189197	124189197	+	Missense_Mutation	SNP	A	A	G	rs1045216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124189197A>G	ENST00000368990.3	+	12	1089	c.958A>G	c.(958-960)Acc>Gcc	p.T320A	PLEKHA1_ENST00000538022.1_3'UTR|PLEKHA1_ENST00000368989.2_Silent_p.P333P|PLEKHA1_ENST00000433307.1_Missense_Mutation_p.T320A|PLEKHA1_ENST00000368988.1_Silent_p.P333P	NM_001001974.2	NP_001001974.1	Q9HB21	PKHA1_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	320			T -> A (in dbSNP:rs1045216). {ECO:0000269|PubMed:11001876, ECO:0000269|Ref.4}.		androgen metabolic process (GO:0008209)|B cell receptor signaling pathway (GO:0050853)|cellular response to hydrogen peroxide (GO:0070301)|establishment of protein localization (GO:0045184)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|multicellular organism growth (GO:0035264)|negative regulation of protein kinase B signaling (GO:0051898)|palate development (GO:0060021)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|ruffle organization (GO:0031529)|skeletal system morphogenesis (GO:0048705)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CAACGCAGCCACCGCCACCTC	0.542													G|||	3740	0.746805	0.8321	0.745	5008	,	,		17071	0.8155		0.5895	False		,,,				2504	0.7239				p.T320A		Atlas-SNP	.											.	PLEKHA1	33	.	0			c.A958G						PASS	.	G	ALA/THR,,ALA/THR	3495,911	349.0+/-310.2	1396,703,104	86.0	77.0	80.0		958,,958	4.8	0.1	10	dbSNP_86	80	5183,3417	504.5+/-376.2	1558,2067,675	yes	missense,utr-3,missense	PLEKHA1	NM_001001974.2,NM_001195608.1,NM_021622.4	58,,58	2954,2770,779	GG,GA,AA		39.7326,20.6764,33.2769	benign,,benign	320/405,,320/405	124189197	8678,4328	2203	4300	6503	SO:0001583	missense	59338	exon12			GCAGCCACCGCCA	AF286160	CCDS7629.1, CCDS55730.1	10q26.3	2013-01-10	2002-01-14		ENSG00000107679	ENSG00000107679		"""Pleckstrin homology (PH) domain containing"""	14335	protein-coding gene	gene with protein product	"""tandem PH domain containing protein-1"""	607772	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 1"""			11001876, 15485858	Standard	NM_001001974		Approved	TAPP1	uc001lge.2	Q9HB21	OTTHUMG00000019184	ENST00000368990.3:c.958A>G	10.37:g.124189197A>G	ENSP00000357986:p.Thr320Ala	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_021622	B3KQ55|D3DRE2|Q9BVK0	Missense_Mutation	SNP	ENST00000368990.3	37	CCDS7629.1	1571	0.7193223443223443	395	0.8028455284552846	265	0.7320441988950276	457	0.798951048951049	454	0.5989445910290238	G	1.391	-0.580748	0.03854	0.793236	0.602674	ENSG00000107679	ENST00000368990;ENST00000409427;ENST00000433307	T;T	0.05319	3.46;3.46	5.71	4.81	0.61882	.	0.968694	0.08615	N	0.919389	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999999927212	B	0.02656	0.0	B	0.01281	0.0	T	0.28106	-1.0054	9	0.02654	T	1	-2.568	6.7268	0.23361	0.2111:0.1282:0.6607:0.0	rs1045216;rs3185078;rs52798853;rs60697358;rs1045216	320	Q9HB21	PKHA1_HUMAN	A	320	ENSP00000357986:T320A;ENSP00000394416:T320A	ENSP00000357986:T320A	T	+	1	0	PLEKHA1	124179187	0.913000	0.31002	0.134000	0.22075	0.197000	0.23852	1.192000	0.32150	0.899000	0.36444	-0.128000	0.14901	ACC	A|0.314;G|0.686	0.686	strong		0.542	PLEKHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050783.1	NM_001001974	
RNF121	55298	hgsc.bcm.edu	37	11	71706544	71706544	+	Silent	SNP	A	A	G	rs34075366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:71706544A>G	ENST00000361756.3	+	8	1171	c.810A>G	c.(808-810)caA>caG	p.Q270Q	RNF121_ENST00000530137.1_Silent_p.Q238Q|RNF121_ENST00000545854.1_Silent_p.Q189Q|RNF121_ENST00000393713.3_Missense_Mutation_p.K197R|RNF121_ENST00000533380.1_Silent_p.Q110Q	NM_018320.4	NP_060790.2	Q9H920	RN121_HUMAN	ring finger protein 121	270						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|urinary_tract(1)	13						GAAAGAAGCAAACGTGTCCCT	0.552													G|||	245	0.0489217	0.0287	0.0432	5008	,	,		20900	0.0883		0.0388	False		,,,				2504	0.0501				p.Q270Q		Atlas-SNP	.											.	RNF121	19	.	0			c.A810G						PASS	.	G		97,4303		0,97,2103	160.0	122.0	135.0		810	6.1	1.0	11	dbSNP_126	135	257,8329		3,251,4039	no	coding-synonymous	RNF121	NM_018320.4		3,348,6142	GG,GA,AA		2.9932,2.2045,2.726		270/328	71706544	354,12632	2200	4293	6493	SO:0001819	synonymous_variant	55298	exon8			GAAGCAAACGTGT	AK001961	CCDS8203.1, CCDS73343.1	11q13.3	2008-02-05			ENSG00000137522	ENSG00000137522		"""RING-type (C3HC4) zinc fingers"""	21070	protein-coding gene	gene with protein product							Standard	NM_018320		Approved	FLJ11099	uc001ora.3	Q9H920	OTTHUMG00000157023	ENST00000361756.3:c.810A>G	11.37:g.71706544A>G		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	219	108	0.493151	NM_018320	B3KSW8|Q6IA57|Q6P449|Q96DB4	Silent	SNP	ENST00000361756.3	37	CCDS8203.1	116	0.05311355311355311	24	0.04878048780487805	15	0.04143646408839779	53	0.09265734265734266	24	0.0316622691292876	G	19.36	3.813521	0.70912	0.022045	0.029932	ENSG00000137522	ENST00000393713	T	0.48201	0.82	6.06	6.06	0.98353	.	.	.	.	.	T	0.02047	0.0064	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.00591	-1.1655	8	0.54805	T	0.06	-5.8447	14.5636	0.68159	0.0708:0.0:0.9292:0.0	rs34075366	197	C9JQY5	.	R	197	ENSP00000377316:K197R	ENSP00000377316:K197R	K	+	2	0	RNF121	71384192	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.411000	0.80078	1.593000	0.50029	-0.119000	0.15052	AAA	A|0.964;G|0.036	0.036	strong		0.552	RNF121-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347132.1	NM_018320	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87493737	87493737	+	Splice_Site	SNP	T	T	C	rs11648852	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	174	0	0		WXS	Illumina HiSeq	Phase_I	157	115	0.732484	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
MYOM2	9172	hgsc.bcm.edu	37	8	2092803	2092803	+	Silent	SNP	A	A	G	rs1063523	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:2092803A>G	ENST00000262113.4	+	37	4437	c.4296A>G	c.(4294-4296)acA>acG	p.T1432T	MYOM2_ENST00000520298.1_3'UTR|MYOM2_ENST00000523438.1_Silent_p.T857T	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1432	Ig-like C2-type 5.				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)		TCGACGTGACAGTGAGCGTGT	0.587													G|||	1206	0.240815	0.2481	0.2435	5008	,	,		13751	0.2292		0.2883	False		,,,				2504	0.1922				p.T1432T		Atlas-SNP	.											.	MYOM2	251	.	0			c.A4296G						PASS	.	G		1137,3269	716.8+/-408.6	130,877,1196	108.0	92.0	98.0		4296	-9.3	0.1	8	dbSNP_86	98	2274,6326	707.3+/-405.6	301,1672,2327	no	coding-synonymous	MYOM2	NM_003970.2		431,2549,3523	GG,GA,AA		26.4419,25.8057,26.2264		1432/1466	2092803	3411,9595	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon37			CGTGACAGTGAGC		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.4296A>G	8.37:g.2092803A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	29	0.367089	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			A|0.741;G|0.259	0.259	strong		0.587	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
SESTD1	91404	hgsc.bcm.edu	37	2	179979930	179979930	+	Silent	SNP	T	T	C	rs2289993	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179979930T>C	ENST00000428443.3	-	16	2017	c.1701A>G	c.(1699-1701)caA>caG	p.Q567Q		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	567							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			AGCGCAAAGATTGGCATAACA	0.388													T|||	972	0.194089	0.2882	0.1081	5008	,	,		17715	0.0645		0.166	False		,,,				2504	0.2904				p.Q567Q		Atlas-SNP	.											.	SESTD1	66	.	0			c.A1701G						PASS	.	T		1082,3324	391.7+/-328.2	128,826,1249	71.0	63.0	66.0		1701	0.9	1.0	2	dbSNP_100	66	1358,7242	265.8+/-286.4	112,1134,3054	no	coding-synonymous	SESTD1	NM_178123.4		240,1960,4303	CC,CT,TT		15.7907,24.5574,18.7606		567/697	179979930	2440,10566	2203	4300	6503	SO:0001819	synonymous_variant	91404	exon16			CAAAGATTGGCAT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1701A>G	2.37:g.179979930T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	180	98	0.544444	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	37	CCDS33338.1																																																																																			T|0.810;C|0.190	0.190	strong		0.388	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123	
MTHFSD	64779	hgsc.bcm.edu	37	16	86585743	86585743	+	Missense_Mutation	SNP	G	G	C	rs34005514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:86585743G>C	ENST00000360900.6	-	3	158	c.133C>G	c.(133-135)Ctg>Gtg	p.L45V	MTHFSD_ENST00000322911.6_Missense_Mutation_p.L44V|MTHFSD_ENST00000543303.2_Intron|MTHFSD_ENST00000568037.1_Intron|MTHFSD_ENST00000546093.1_Intron|MTHFSD_ENST00000381214.5_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	130	0	0		WXS	Illumina HiSeq	Phase_I	142	113	0.795775	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	
SUSD4	55061	hgsc.bcm.edu	37	1	223465859	223465859	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:223465859T>C	ENST00000343846.3	-	2	916	c.283A>G	c.(283-285)Aca>Gca	p.T95A	SUSD4_ENST00000366878.4_Missense_Mutation_p.T95A|SUSD4_ENST00000454695.2_5'UTR|SUSD4_ENST00000478605.1_5'UTR|SUSD4_ENST00000494793.2_Missense_Mutation_p.T95A|SUSD4_ENST00000484758.2_Intron|SUSD4_ENST00000344029.6_Missense_Mutation_p.T95A			Q5VX71	SUSD4_HUMAN	sushi domain containing 4	95	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|skin(1)	17				GBM - Glioblastoma multiforme(131;0.0611)		AGTCTCTTTGTAGCGCCCTTC	0.493																																					p.T95A		Atlas-SNP	.											SUSD4_ENST00000343846,NS,carcinoma,+2,2	SUSD4	82	2	0			c.A283G						scavenged	.						132.0	135.0	134.0					1																	223465859		2203	4300	6503	SO:0001583	missense	55061	exon3			TCTTTGTAGCGCC	AK096265	CCDS31034.1, CCDS41471.1	1q41	2008-05-14			ENSG00000143502	ENSG00000143502			25470	protein-coding gene	gene with protein product		615827				12477932	Standard	NM_017982		Approved	FLJ10052	uc001hny.4	Q5VX71	OTTHUMG00000037936	ENST00000343846.3:c.283A>G	1.37:g.223465859T>C	ENSP00000344219:p.Thr95Ala	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	296	3	0.0101351	NM_017982	D3DTB9|Q6UX62|Q9BSR0|Q9NWG0	Missense_Mutation	SNP	ENST00000343846.3	37	CCDS41471.1	.	.	.	.	.	.	.	.	.	.	T	2.652	-0.281825	0.05642	.	.	ENSG00000143502	ENST00000343846;ENST00000366878;ENST00000271787;ENST00000344029	T;T;T	0.62498	0.02;0.02;0.02	5.36	-3.62	0.04543	Complement control module (2);Sushi/SCR/CCP (3);	0.456706	0.18584	N	0.136948	T	0.25754	0.0627	N	0.02674	-0.535	0.18873	N	0.999988	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.09662	-1.0664	10	0.48119	T	0.1	-2.0298	2.4371	0.04485	0.5152:0.0772:0.2039:0.2037	.	95;95	Q5VX71-3;Q5VX71	.;SUSD4_HUMAN	A	95	ENSP00000344219:T95A;ENSP00000355843:T95A;ENSP00000339926:T95A	ENSP00000271787:T95A	T	-	1	0	SUSD4	221532482	0.012000	0.17670	0.015000	0.15790	0.262000	0.26303	0.061000	0.14366	-0.276000	0.09206	-0.411000	0.06167	ACA	.	.	none		0.493	SUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092592.2	NM_017982	
LPAR2	9170	hgsc.bcm.edu	37	19	19737992	19737992	+	Silent	SNP	G	G	A	rs150741448	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19737992G>A	ENST00000542587.1	-	5	1004	c.102C>T	c.(100-102)gtC>gtT	p.V34V	LPAR2_ENST00000589311.1_5'Flank|LPAR2_ENST00000407877.3_Silent_p.V34V|LPAR2_ENST00000586703.1_Silent_p.V34V			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	34					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						GTGCCACCACGACCACATCCT	0.592													G|||	7	0.00139776	0.0	0.0029	5008	,	,		18269	0.0		0.005	False		,,,				2504	0.0				p.V34V		Atlas-SNP	.											.	LPAR2	28	.	0			c.C102T						PASS	.	G		4,4400	6.2+/-15.9	0,4,2198	33.0	32.0	33.0		102	-8.9	0.4	19	dbSNP_134	33	39,8561	24.0+/-70.4	0,39,4261	no	coding-synonymous	LPAR2	NM_004720.5		0,43,6459	AA,AG,GG		0.4535,0.0908,0.3307		34/352	19737992	43,12961	2202	4300	6502	SO:0001819	synonymous_variant	9170	exon2			CACCACGACCACA	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.102C>T	19.37:g.19737992G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_004720	O00543|O43431	Silent	SNP	ENST00000542587.1	37	CCDS12407.1																																																																																			G|0.997;A|0.003	0.003	strong		0.592	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720	
ZNF283	284349	hgsc.bcm.edu	37	19	44352665	44352665	+	Missense_Mutation	SNP	T	T	C	rs2356437|rs386809609|rs371852581	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44352665T>C	ENST00000324461.7	+	7	2209	c.1912T>C	c.(1912-1914)Tgt>Cgt	p.C638R	ZNF283_ENST00000588797.1_Missense_Mutation_p.C499R	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	638			C -> R (in dbSNP:rs2356437).|C -> Y (in dbSNP:rs1061769).	C -> H (in Ref. 1; BAC05251/BAG57956 and 4; AAS55109). {ECO:0000305}.	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)				GACCTTTACTTGTGGCTCAAA	0.398													C|||	3417	0.682308	0.8533	0.536	5008	,	,		19701	0.374		0.7684	False		,,,				2504	0.7843				p.C638R		Atlas-SNP	.											ZNF283_ENST00000324461,colon,carcinoma,0,1	ZNF283	83	1	0			c.T1912C						PASS	.	C	ARG/CYS	3346,690		1429,488,101	98.0	106.0	103.0		1912	-1.7	0.0	19	dbSNP_100	103	6268,2114		2464,1340,387	yes	missense	ZNF283	NM_181845.1	180	3893,1828,488	CC,CT,TT		25.2207,17.0961,22.5801	benign	638/680	44352665	9614,2804	2018	4191	6209	SO:0001583	missense	284349	exon7			TTTACTTGTGGCT	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.1912T>C	19.37:g.44352665T>C	ENSP00000327314:p.Cys638Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	1338	0.6126373626373627	387	0.7865853658536586	205	0.5662983425414365	191	0.3339160839160839	555	0.7321899736147758	C	2.444	-0.327973	0.05314	0.829039	0.747793	ENSG00000167637	ENST00000324461	T	0.06608	3.28	2.6	-1.72	0.08107	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.03194	-0.395	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.14783	-1.0460	8	0.08179	T	0.78	.	3.364	0.07197	0.3032:0.2499:0.0:0.4469	rs2356437;rs57860916;rs2356437	638	Q8N7M2	ZN283_HUMAN	R	638	ENSP00000327314:C638R	ENSP00000327314:C638R	C	+	1	0	ZNF283	49044505	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-4.778000	0.00187	-0.926000	0.03770	-0.226000	0.12346	TGT	T|0.341;C|0.659	0.659	strong		0.398	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
INF2	64423	hgsc.bcm.edu	37	14	105180785	105180785	+	Missense_Mutation	SNP	C	C	T	rs34251364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105180785C>T	ENST00000392634.4	+	21	3398	c.3286C>T	c.(3286-3288)Ccc>Tcc	p.P1096S	INF2_ENST00000330634.7_Missense_Mutation_p.P1096S	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	1096			P -> S (in dbSNP:rs34251364).		actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		GTGCCCCCAGCCCTTGGAGGG	0.642													C|||	229	0.0457268	0.0113	0.0461	5008	,	,		16564	0.0159		0.0835	False		,,,				2504	0.0838				p.P1096S		Atlas-SNP	.											.	INF2	148	.	0			c.C3286T						PASS	.	C	SER/PRO,SER/PRO	86,3762		1,84,1839	27.0	34.0	32.0		3286,3286	1.1	0.0	14	dbSNP_126	32	619,7613		27,565,3524	yes	missense,missense	INF2	NM_022489.3,NM_001031714.3	74,74	28,649,5363	TT,TC,CC		7.5194,2.2349,5.8361	benign,benign	1096/1250,1096/1241	105180785	705,11375	1924	4116	6040	SO:0001583	missense	64423	exon21			CCCCAGCCCTTGG	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.3286C>T	14.37:g.105180785C>T	ENSP00000376410:p.Pro1096Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	125	75	0.6	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	37	CCDS9989.2	98	0.04487179487179487	4	0.008130081300813009	24	0.06629834254143646	11	0.019230769230769232	59	0.07783641160949868	C	11.75	1.732891	0.30684	0.022349	0.075194	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.79940	-1.31;-1.32	4.29	1.1	0.20463	.	0.960665	0.08440	U	0.945563	T	0.09642	0.0237	L	0.34521	1.04	0.80722	P	0.0	B;B	0.33807	0.426;0.3	B;B	0.29077	0.098;0.045	T	0.38156	-0.9674	9	0.22109	T	0.4	.	5.9086	0.19014	0.3824:0.431:0.1866:0.0	rs34251364	1096;1096	Q27J81-2;Q27J81	.;INF2_HUMAN	S	1096	ENSP00000376406:P1096S;ENSP00000376410:P1096S	ENSP00000252527:P564S	P	+	1	0	INF2	104251830	0.649000	0.27322	0.012000	0.15200	0.031000	0.12232	2.003000	0.40844	0.890000	0.36211	-0.500000	0.04577	CCC	C|0.946;T|0.054	0.054	strong		0.642	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
PI4KA	5297	hgsc.bcm.edu	37	22	21066897	21066897	+	Silent	SNP	G	G	A	rs1135929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:21066897G>A	ENST00000572273.1	-	50	5735	c.5505C>T	c.(5503-5505)tgC>tgT	p.C1835C	PI4KA_ENST00000255882.6_Silent_p.C1893C|PI4KA_ENST00000414196.3_Silent_p.C645C			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1835	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.C1835C(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-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)			CGATCACCCCGCACTAGGAGG	0.652													g|||	2170	0.433307	0.5083	0.4683	5008	,	,		12263	0.4752		0.3976	False		,,,				2504	0.3006				p.C1893C	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,2	PI4KA	313	2	2	Substitution - coding silent(2)	stomach(2)	c.C5679T						scavenged	.						20.0	24.0	23.0					22																	21066897		2111	4203	6314	SO:0001819	synonymous_variant	5297	exon50			CACCCCGCACTAG	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.5505C>T	22.37:g.21066897G>A		Somatic	432	1	0.00231481		WXS	Illumina HiSeq	Phase_I	285	56	0.196491	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				A|1.000;|0.000	1.000	weak		0.652	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
GGT1	2678	hgsc.bcm.edu	37	22	25023459	25023459	+	Missense_Mutation	SNP	G	G	C	rs138813205	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:25023459G>C	ENST00000400382.1	+	12	1836	c.1081G>C	c.(1081-1083)Gac>Cac	p.D361H	GGT1_ENST00000400383.1_Missense_Mutation_p.D361H|GGT1_ENST00000401885.1_Missense_Mutation_p.D17H|GGT1_ENST00000406383.2_Missense_Mutation_p.D361H|GGT1_ENST00000404532.1_Missense_Mutation_p.D17H|GGT1_ENST00000248923.4_Missense_Mutation_p.D361H|GGT1_ENST00000403838.1_Missense_Mutation_p.D17H|GGT1_ENST00000400380.1_Missense_Mutation_p.D361H|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404223.1_Missense_Mutation_p.D17H|GGT1_ENST00000404920.1_Missense_Mutation_p.D17H			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	322	0	0		WXS	Illumina HiSeq	Phase_I	338	27	0.0798817	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	
LRRC16B	90668	hgsc.bcm.edu	37	14	24534270	24534270	+	Missense_Mutation	SNP	C	C	T	rs117833529	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24534270C>T	ENST00000342740.5	+	33	3338	c.3184C>T	c.(3184-3186)Cgg>Tgg	p.R1062W	LRRC16B_ENST00000334420.7_Missense_Mutation_p.R158W	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1062				R -> W (in Ref. 2; CAD38886). {ECO:0000305}.		cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TCGCCGGCCCCGGAGCTTCAA	0.716													C|||	108	0.0215655	0.0015	0.0418	5008	,	,		8025	0.0		0.0368	False		,,,				2504	0.0409				p.R1062W		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C3184T						PASS	.	C	TRP/ARG	23,3751		0,23,1864	19.0	24.0	22.0		3184	2.8	1.0	14	dbSNP_132	22	255,7637		2,251,3693	yes	missense	LRRC16B	NM_138360.3	101	2,274,5557	TT,TC,CC		3.2311,0.6094,2.383	probably-damaging	1062/1373	24534270	278,11388	1887	3946	5833	SO:0001583	missense	90668	exon33			CGGCCCCGGAGCT	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.3184C>T	14.37:g.24534270C>T	ENSP00000340467:p.Arg1062Trp	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	46	0.021062271062271064	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	25	0.032981530343007916	C	12.56	1.973870	0.34848	0.006094	0.032311	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.60797	1.2;0.16	4.66	2.77	0.32553	.	0.254810	0.20948	N	0.082818	T	0.29389	0.0732	L	0.59436	1.845	0.28233	N	0.926034	D;D	0.89917	1.0;0.999	D;P	0.80764	0.994;0.876	T	0.48725	-0.9010	10	0.87932	D	0	-13.2657	9.764	0.40550	0.3756:0.6244:0.0:0.0	.	158;1062	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	W	1062;158	ENSP00000340467:R1062W;ENSP00000334701:R158W	ENSP00000334701:R158W	R	+	1	2	LRRC16B	23604110	0.999000	0.42202	1.000000	0.80357	0.602000	0.36980	1.625000	0.37029	0.375000	0.24679	-0.348000	0.07805	CGG	C|0.976;T|0.024	0.024	strong		0.716	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
MCM10	55388	hgsc.bcm.edu	37	10	13239651	13239651	+	Missense_Mutation	SNP	A	A	G	rs2274110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	101	0	0		WXS	Illumina HiSeq	Phase_I	49	36	0.734694	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	
TPX2	22974	hgsc.bcm.edu	37	20	30382315	30382315	+	Silent	SNP	A	A	G	rs3203770	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:30382315A>G	ENST00000300403.6	+	15	2325	c.1797A>G	c.(1795-1797)agA>agG	p.R599R	TPX2_ENST00000340513.4_Silent_p.R635R	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	599					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			AGACTGACAGAAGAGGTGCTC	0.488													A|||	1122	0.224042	0.5454	0.1599	5008	,	,		18629	0.0		0.2346	False		,,,				2504	0.0552				p.R599R		Atlas-SNP	.											.	TPX2	61	.	0			c.A1797G						PASS	.	A		2046,2360	566.7+/-382.0	471,1104,628	111.0	104.0	107.0		1797	0.3	0.6	20	dbSNP_105	107	1814,6786	326.8+/-317.6	191,1432,2677	no	coding-synonymous	TPX2	NM_012112.4		662,2536,3305	GG,GA,AA		21.093,46.4367,29.6786		599/748	30382315	3860,9146	2203	4300	6503	SO:0001819	synonymous_variant	22974	exon15			TGACAGAAGAGGT	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.1797A>G	20.37:g.30382315A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Silent	SNP	ENST00000300403.6	37	CCDS13190.1																																																																																			A|0.722;G|0.278	0.278	strong		0.488	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
HYI	81888	hgsc.bcm.edu	37	1	43917637	43917637	+	Silent	SNP	G	G	A	rs2251802	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43917637G>A	ENST00000372425.4	-	4	669	c.474C>T	c.(472-474)gaC>gaT	p.D158D	SZT2_ENST00000562955.1_3'UTR|HYI_ENST00000372432.1_Silent_p.D158D|HYI_ENST00000372434.1_Silent_p.D183D|HYI_ENST00000486909.1_Silent_p.D158D|SZT2_ENST00000372442.1_3'UTR|HYI-AS1_ENST00000444386.1_RNA|HYI_ENST00000583037.1_Silent_p.D85D|HYI_ENST00000372426.1_Silent_p.D110D			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	183	0	0		WXS	Illumina HiSeq	Phase_I	129	32	0.248062	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	
GIT2	9815	hgsc.bcm.edu	37	12	110383141	110383141	+	Missense_Mutation	SNP	G	G	A	rs11068997	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:110383141G>A	ENST00000355312.3	-	16	1654	c.1655C>T	c.(1654-1656)gCa>gTa	p.A552V	GIT2_ENST00000354574.4_Intron|GIT2_ENST00000343646.5_Intron|GIT2_ENST00000553118.1_Intron|GIT2_ENST00000361006.5_Intron|GIT2_ENST00000356259.4_Intron|GIT2_ENST00000551209.1_Missense_Mutation_p.A501V|GIT2_ENST00000457474.2_Intron|GIT2_ENST00000338373.5_Missense_Mutation_p.A454V|TCHP_ENST00000550780.1_Intron|GIT2_ENST00000360185.4_Missense_Mutation_p.A502V	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	552			A -> V (in dbSNP:rs11068997).		behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						GGTCACAAGTGCACTCCTCCC	0.493													G|||	325	0.0648962	0.0961	0.0274	5008	,	,		20549	0.119		0.0328	False		,,,				2504	0.0266				p.A552V		Atlas-SNP	.											.	GIT2	81	.	0			c.C1655T						PASS	.	G	,,,VAL/ALA,	427,3979	202.1+/-225.0	16,395,1792	62.0	58.0	59.0		,,,1655,	5.7	1.0	12	dbSNP_120	59	268,8332	100.3+/-161.8	5,258,4037	yes	intron,intron,intron,missense,intron	GIT2	NM_001135213.1,NM_001135214.1,NM_014776.3,NM_057169.3,NM_057170.3	,,,64,	21,653,5829	AA,AG,GG		3.1163,9.6913,5.3437	,,,benign,	,,,552/760,	110383141	695,12311	2203	4300	6503	SO:0001583	missense	9815	exon16			ACAAGTGCACTCC	AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4273	protein-coding gene	gene with protein product		608564	"""G protein-coupled receptor kinase interactor 2"""			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.1655C>T	12.37:g.110383141G>A	ENSP00000347464:p.Ala552Val	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_057169	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Missense_Mutation	SNP	ENST00000355312.3	37	CCDS9138.1	131	0.059981684981684984	47	0.09552845528455285	14	0.03867403314917127	43	0.07517482517482517	27	0.03562005277044855	G	15.86	2.959123	0.53400	0.096913	0.031163	ENSG00000139436	ENST00000355312;ENST00000360185;ENST00000338373;ENST00000551209	T;T;T;T	0.72725	-0.62;-0.65;-0.55;-0.68	5.69	5.69	0.88448	.	0.153604	0.56097	D	0.000022	T	0.04724	0.0128	L	0.51422	1.61	0.09310	P	1.0	P	0.45044	0.849	B	0.40165	0.321	T	0.38866	-0.9641	9	0.30854	T	0.27	.	18.8027	0.92025	0.0:0.0:1.0:0.0	rs11068997;rs52812275;rs11068997	552	Q14161	GIT2_HUMAN	V	552;502;454;501	ENSP00000347464:A552V;ENSP00000353312:A502V;ENSP00000340342:A454V;ENSP00000448832:A501V	ENSP00000340342:A454V	A	-	2	0	GIT2	108867524	1.000000	0.71417	0.997000	0.53966	0.611000	0.37282	7.568000	0.82369	2.683000	0.91414	0.563000	0.77884	GCA	G|0.941;A|0.059	0.059	strong		0.493	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169	
FAM21A	387680	hgsc.bcm.edu	37	10	51827934	51827934	+	Missense_Mutation	SNP	G	G	A	rs55875820	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:51827934G>A	ENST00000282633.5	+	2	118	c.73G>A	c.(73-75)Gtg>Atg	p.V25M	RP11-324H6.5_ENST00000456967.1_RNA|FAM21A_ENST00000351071.6_Missense_Mutation_p.V25M|FAM21A_ENST00000314664.7_Missense_Mutation_p.V25M	NM_001005751.1	NP_001005751.1	Q641Q2	FA21A_HUMAN	family with sequence similarity 21, member A	25					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)				breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	15						GCCGTGGTCGGTGGAGGAGAT	0.701													.|||	1540	0.307508	0.0681	0.3213	5008	,	,		12321	0.3304		0.5189	False		,,,				2504	0.3804				p.V25M		Atlas-SNP	.											FAM21A,NS,carcinoma,0,1	FAM21A	32	1	0			c.G73A						PASS	.	G	MET/VAL	488,3032		88,312,1360	8.0	12.0	11.0		73	1.6	1.0	10	dbSNP_129	11	3767,4229		1086,1595,1317	no	missense	FAM21A	NM_001005751.1	21	1174,1907,2677	AA,AG,GG		47.1111,13.8636,36.9486	benign	25/1342	51827934	4255,7261	1760	3998	5758	SO:0001583	missense	387680	exon2			TGGTCGGTGGAGG	BC082258	CCDS41527.1	10q11.23	2014-06-19			ENSG00000099290	ENSG00000099290			23416	protein-coding gene	gene with protein product			"""family with sequence similarity 21, member B"""	FAM21B			Standard	XM_005269805		Approved	bA56A21.1, bA98I6.1, FLJ10824	uc001jjb.3	Q641Q2	OTTHUMG00000018225	ENST00000282633.5:c.73G>A	10.37:g.51827934G>A	ENSP00000282633:p.Val25Met	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	56	54	0.964286	NM_001005751	A2A3S2|A2A3U6|Q6DHY0	Missense_Mutation	SNP	ENST00000282633.5	37	CCDS41527.1	677	0.309981684981685	36	0.07317073170731707	112	0.30939226519337015	189	0.3304195804195804	340	0.44854881266490765	G	13.62	2.291169	0.40494	0.138636	0.471111	ENSG00000099290	ENST00000351071;ENST00000314664;ENST00000434114;ENST00000282633	.	.	.	2.71	1.65	0.23941	.	0.156736	0.42821	D	0.000653	T	0.00012	0.0000	L	0.59912	1.85	0.09310	P	0.9999999999999996	B;B;B	0.30634	0.181;0.288;0.181	B;B;B	0.34722	0.136;0.136;0.188	T	0.46803	-0.9165	8	0.72032	D	0.01	-9.0815	6.6531	0.22973	0.0:0.0:0.5652:0.4347	rs55875820	25;25;25	E7ESD2;Q641Q2-2;Q641Q2	.;.;FA21A_HUMAN	M	25;25;24;25	.	ENSP00000282633:V25M	V	+	1	0	FAM21A	51497940	1.000000	0.71417	1.000000	0.80357	0.689000	0.40095	2.625000	0.46452	1.523000	0.49018	0.194000	0.17425	GTG	G|0.689;A|0.311	0.311	strong		0.701	FAM21A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276917.2	NM_001005751	
IBTK	25998	hgsc.bcm.edu	37	6	82933309	82933309	+	Silent	SNP	C	C	T	rs111957007|rs9361904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:82933309C>T	ENST00000306270.7	-	8	1521	c.972G>A	c.(970-972)aaG>aaA	p.K324K	IBTK_ENST00000510291.1_Silent_p.K324K|IBTK_ENST00000503631.1_Silent_p.K324K	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	324					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)	p.K324K(1)		central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		CAGTTACACACTTTTCTCCAT	0.413													C|||	1285	0.256589	0.2912	0.3055	5008	,	,		19622	0.2014		0.2266	False		,,,				2504	0.2628				p.K324K		Atlas-SNP	.											IBTK,NS,carcinoma,0,1	IBTK	128	1	1	Substitution - coding silent(1)	stomach(1)	c.G972A						PASS	.	C		1215,3191	414.8+/-337.0	181,853,1169	71.0	67.0	68.0		972	1.5	1.0	6	dbSNP_119	68	1761,6839	314.1+/-311.6	172,1417,2711	no	coding-synonymous	IBTK	NM_015525.2		353,2270,3880	TT,TC,CC		20.4767,27.576,22.8817		324/1354	82933309	2976,10030	2203	4300	6503	SO:0001819	synonymous_variant	25998	exon8			TACACACTTTTCT	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.972G>A	6.37:g.82933309C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Silent	SNP	ENST00000306270.7	37	CCDS34490.1																																																																																			C|0.756;T|0.244	0.244	strong		0.413	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	
SCFD2	152579	hgsc.bcm.edu	37	4	54011576	54011576	+	Silent	SNP	T	T	C	rs79628372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:54011576T>C	ENST00000401642.3	-	5	1618	c.1485A>G	c.(1483-1485)gaA>gaG	p.E495E	SCFD2_ENST00000388940.4_Silent_p.E495E	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	495					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)			p.E495E(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	30			GBM - Glioblastoma multiforme(3;1.07e-26)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TGACTTTTTCTTCTGCTTCAC	0.443													T|||	253	0.0505192	0.0023	0.0663	5008	,	,		19321	0.0853		0.0835	False		,,,				2504	0.0348				p.E495E		Atlas-SNP	.											SCFD2,NS,carcinoma,0,1	SCFD2	78	1	1	Substitution - coding silent(1)	prostate(1)	c.A1485G						PASS	.	T		63,4343	58.7+/-95.3	0,63,2140	146.0	130.0	135.0		1485	0.8	1.0	4	dbSNP_131	135	646,7954	164.6+/-216.9	28,590,3682	no	coding-synonymous	SCFD2	NM_152540.3		28,653,5822	CC,CT,TT		7.5116,1.4299,5.4513		495/685	54011576	709,12297	2203	4300	6503	SO:0001819	synonymous_variant	152579	exon5			TTTTTCTTCTGCT	AY299407	CCDS33984.1	4q12	2004-01-15			ENSG00000184178	ENSG00000184178			30676	protein-coding gene	gene with protein product						12477932	Standard	NM_152540		Approved	STXBP1L1, FLJ39514	uc003gzu.3	Q8WU76	OTTHUMG00000160588	ENST00000401642.3:c.1485A>G	4.37:g.54011576T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	151	84	0.556291	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Silent	SNP	ENST00000401642.3	37	CCDS33984.1																																																																																			T|0.942;C|0.058	0.058	strong		0.443	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540	
ZNF808	388558	hgsc.bcm.edu	37	19	53057479	53057479	+	Missense_Mutation	SNP	G	G	A	rs61746334	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53057479G>A	ENST00000359798.4	+	5	1490	c.1310G>A	c.(1309-1311)aGt>aAt	p.S437N		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	437					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(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		AAAGTTTTCAGTCAGAAATCA	0.373													A|||	347	0.0692891	0.1551	0.0648	5008	,	,		22149	0.0079		0.0706	False		,,,				2504	0.0184				p.S437N		Atlas-SNP	.											.	ZNF808	81	.	0			c.G1310A						PASS	.	A	ASN/SER	521,3861		27,467,1697	45.0	50.0	48.0		1310	-2.8	0.0	19	dbSNP_129	48	596,7990		17,562,3714	no	missense	ZNF808	NM_001039886.3	46	44,1029,5411	AA,AG,GG		6.9415,11.8895,8.6135	benign	437/904	53057479	1117,11851	2191	4293	6484	SO:0001583	missense	388558	exon5			TTTTCAGTCAGAA	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"""Zinc fingers, C2H2-type"", ""-"""	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.1310G>A	19.37:g.53057479G>A	ENSP00000352846:p.Ser437Asn	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	160	0.07326007326007326	75	0.1524390243902439	27	0.07458563535911603	7	0.012237762237762238	51	0.06728232189973615	.	0.011	-1.702933	0.00719	0.118895	0.069415	ENSG00000198482	ENST00000359798	T	0.19394	2.15	1.4	-2.81	0.05805	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	L	0.55743	1.74	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.28776	-1.0033	8	0.25751	T	0.34	.	1.1063	0.01694	0.2943:0.139:0.3979:0.1688	rs61746334	437	Q8N4W9	ZN808_HUMAN	N	437	ENSP00000352846:S437N	ENSP00000352846:S437N	S	+	2	0	ZNF808	57749291	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-9.386000	0.00011	-4.610000	0.00040	-3.754000	0.00022	AGT	G|0.924;A|0.076	0.076	strong		0.373	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886	
SPEN	23013	hgsc.bcm.edu	37	1	16256007	16256007	+	Missense_Mutation	SNP	T	T	C	rs848209|rs386628859	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16256007T>C	ENST00000375759.3	+	11	3476	c.3272T>C	c.(3271-3273)cTa>cCa	p.L1091P		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1091			L -> P (in dbSNP:rs848209). {ECO:0000269|PubMed:14702039}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|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)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CTGGGAGAACTAGCAGGTGAA	0.478													C|||	3250	0.648962	0.9758	0.7118	5008	,	,		18084	0.3214		0.5577	False		,,,				2504	0.5941				p.L1091P		Atlas-SNP	.											.	SPEN	374	.	0			c.T3272C						PASS	.	C	PRO/LEU	3989,417	198.4+/-222.2	1827,335,41	42.0	45.0	44.0		3272	3.5	0.5	1	dbSNP_86	44	4956,3644	522.8+/-380.2	1426,2104,770	yes	missense	SPEN	NM_015001.2	98	3253,2439,811	CC,CT,TT		42.3721,9.4644,31.2241	benign	1091/3665	16256007	8945,4061	2203	4300	6503	SO:0001583	missense	23013	exon11			GAGAACTAGCAGG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3272T>C	1.37:g.16256007T>C	ENSP00000364912:p.Leu1091Pro	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	147	42	0.285714	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	1320	0.6043956043956044	469	0.9532520325203252	252	0.6961325966850829	174	0.3041958041958042	425	0.5606860158311345	C	0.188	-1.056057	0.01965	0.905356	0.576279	ENSG00000065526	ENST00000375759	T	0.07327	3.2	5.39	3.51	0.40186	.	.	.	.	.	T	0.00012	0.0000	N	0.02142	-0.665	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.19778	-1.0295	8	0.20519	T	0.43	-0.1843	11.1582	0.48499	0.0:0.7988:0.0:0.2012	rs848209;rs17387129;rs52796232;rs57983056;rs848209	1091	Q96T58	MINT_HUMAN	P	1091	ENSP00000364912:L1091P	ENSP00000364912:L1091P	L	+	2	0	SPEN	16128594	0.064000	0.20934	0.520000	0.27837	0.397000	0.30659	1.031000	0.30165	0.411000	0.25702	-0.128000	0.14901	CTA	T|0.347;C|0.653	0.653	strong		0.478	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
OR4N2	390429	hgsc.bcm.edu	37	14	20295779	20295779	+	Missense_Mutation	SNP	C	C	G	rs11621884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	645	0	0		WXS	Illumina HiSeq	Phase_I	281	152	0.540925	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		
MYO3A	53904	hgsc.bcm.edu	37	10	26357747	26357747	+	Silent	SNP	C	C	T	rs35379457|rs386742102	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	100	0	0		WXS	Illumina HiSeq	Phase_I	76	20	0.263158	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	
ZFAT	57623	hgsc.bcm.edu	37	8	135602581	135602581	+	Silent	SNP	A	A	G	rs3739425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:135602581A>G	ENST00000377838.3	-	8	2667	c.2493T>C	c.(2491-2493)tcT>tcC	p.S831S	ZFAT_ENST00000517307.1_5'UTR|ZFAT_ENST00000520356.1_Silent_p.S819S|ZFAT_ENST00000520727.1_Silent_p.S819S|ZFAT_ENST00000520214.1_Silent_p.S819S|ZFAT_ENST00000429442.2_Silent_p.S819S|ZFAT_ENST00000523399.1_Silent_p.S769S	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	831					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			AAACAGGACAAGAATAACTCC	0.348																																					p.S831S		Atlas-SNP	.											.	ZFAT	265	.	0			c.T2493C						PASS	.	A	,,,,	694,3070		52,590,1240	90.0	91.0	91.0		2457,2457,2307,2457,2493	3.7	1.0	8	dbSNP_107	91	1444,6764		113,1218,2773	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	,,,,	165,1808,4013	GG,GA,AA		17.5926,18.4378,17.8583	,,,,	819/1232,819/1232,769/1182,819/1146,831/1244	135602581	2138,9834	1882	4104	5986	SO:0001819	synonymous_variant	57623	exon8			AGGACAAGAATAA	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2493T>C	8.37:g.135602581A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Silent	SNP	ENST00000377838.3	37	CCDS47924.1																																																																																			A|0.709;G|0.291	0.291	strong		0.348	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
DNAJB8	165721	hgsc.bcm.edu	37	3	128181537	128181537	+	Silent	SNP	C	C	T	rs2953129	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:128181537C>T	ENST00000469083.1	-	2	3109	c.552G>A	c.(550-552)tcG>tcA	p.S184S	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Silent_p.S184S			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	184	Ser-rich.				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)		TCTCGGTGGACGACATCACCG	0.627													C|||	995	0.198682	0.0136	0.2291	5008	,	,		16918	0.4008		0.2008	False		,,,				2504	0.2168				p.S184S		Atlas-SNP	.											.	DNAJB8	34	.	0			c.G552A						PASS	.	C		220,4186	131.8+/-168.3	7,206,1990	115.0	100.0	105.0		552	-1.9	0.9	3	dbSNP_101	105	1612,6988	300.5+/-305.0	169,1274,2857	no	coding-synonymous	DNAJB8	NM_153330.2		176,1480,4847	TT,TC,CC		18.7442,4.9932,14.0858		184/233	128181537	1832,11174	2203	4300	6503	SO:0001819	synonymous_variant	165721	exon3			GGTGGACGACATC		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.552G>A	3.37:g.128181537C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	147	64	0.435374	NM_153330	B3KWV7	Silent	SNP	ENST00000469083.1	37	CCDS3048.1																																																																																			C|0.820;T|0.180	0.180	strong		0.627	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256807	140256807	+	Missense_Mutation	SNP	T	T	A	rs199811254		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140256807T>A	ENST00000398631.2	+	1	1750	c.1750T>A	c.(1750-1752)Tcg>Acg	p.S584T	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	584	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)			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)			GGTACCGCGGTCGGTGGGTGC	0.682													.|||	1	0.000199681	0.0	0.0	5008	,	,		17689	0.0		0.001	False		,,,				2504	0.0				p.S584T	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,carcinoma,-1,2	PCDHA12	196	2	0			c.T1750A						PASS	.	T	,,,THR/SER,,,,,,,,,,,,THR/SER	1,4405	2.1+/-5.4	0,1,2202	221.0	209.0	213.0		,,,1750,,,,,,,,,,,,1750	-1.4	0.0	5		213	5,8591	4.3+/-15.6	0,5,4293	no	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	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	,,,58,,,,,,,,,,,,58	0,6,6495	AA,AT,TT		0.0582,0.0227,0.0461	,,,,,,,,,,,,,,,	,,,584/942,,,,,,,,,,,,584/793	140256807	6,12996	2203	4298	6501	SO:0001583	missense	56137	exon1			CCGCGGTCGGTGG	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.1750T>A	5.37:g.140256807T>A	ENSP00000381628:p.Ser584Thr	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	224	117	0.522321	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	4.945	0.175589	0.09391	2.27E-4	5.82E-4	ENSG00000251664	ENST00000398631	T	0.39229	1.09	4.71	-1.37	0.09056	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.33760	0.0874	M	0.69185	2.1	0.09310	N	1	B;B	0.33212	0.232;0.402	B;B	0.32762	0.152;0.082	T	0.37549	-0.9701	9	0.59425	D	0.04	.	1.4327	0.02337	0.276:0.0817:0.2678:0.3745	.	584;584	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	T	584	ENSP00000381628:S584T	ENSP00000381628:S584T	S	+	1	0	PCDHA12	140236991	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.529000	0.06186	-0.138000	0.11434	-0.516000	0.04426	TCG	T|0.999;A|0.001	0.001	strong		0.682	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
OR5AN1	390195	hgsc.bcm.edu	37	11	59132798	59132798	+	Missense_Mutation	SNP	G	G	C	rs7941190	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:59132798G>C	ENST00000313940.2	+	1	914	c.867G>C	c.(865-867)ttG>ttC	p.L289F		NM_001004729.1	NP_001004729.1	Q8NGI8	O5AN1_HUMAN	olfactory receptor, family 5, subfamily AN, member 1	289			L -> F (in dbSNP:rs7941190). {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)			breast(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	21						TAAATCCCTTGATTTACAGTT	0.378													G|||	3372	0.673323	0.5061	0.7363	5008	,	,		21663	0.744		0.7227	False		,,,				2504	0.7311				p.L289F		Atlas-SNP	.											.	OR5AN1	49	.	0			c.G867C						PASS	.	G	PHE/LEU	2340,2062	605.2+/-390.5	629,1082,490	73.0	70.0	71.0		867	1.4	0.8	11	dbSNP_116	71	5971,2619	682.4+/-403.8	2075,1821,399	yes	missense	OR5AN1	NM_001004729.1	22	2704,2903,889	CC,CG,GG		30.4889,46.8423,36.0299	probably-damaging	289/312	59132798	8311,4681	2201	4295	6496	SO:0001583	missense	390195	exon1			TCCCTTGATTTAC	AB065806	CCDS31559.1	11q12.1	2012-08-09			ENSG00000176495	ENSG00000176495		"""GPCR / Class A : Olfactory receptors"""	15255	protein-coding gene	gene with protein product		615702					Standard	NM_001004729		Approved		uc010rks.2	Q8NGI8	OTTHUMG00000167337	ENST00000313940.2:c.867G>C	11.37:g.59132798G>C	ENSP00000320302:p.Leu289Phe	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_001004729	B9EIS2|Q6IEV4	Missense_Mutation	SNP	ENST00000313940.2	37	CCDS31559.1	1452	0.6648351648351648	257	0.5223577235772358	256	0.7071823204419889	403	0.7045454545454546	536	0.7071240105540897	G	14.55	2.568337	0.45798	0.531577	0.695111	ENSG00000176495	ENST00000313940	T	0.38887	1.11	4.51	1.4	0.22301	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38326	N	0.001735	T	0.00012	0.0000	M	0.67517	2.055	0.42638	P	0.0065990000000000215	D	0.89917	1.0	D	0.91635	0.999	T	0.44406	-0.9330	9	0.62326	D	0.03	-19.1172	4.6162	0.12428	0.0866:0.4254:0.3431:0.145	rs7941190;rs52831590;rs7941190	289	Q8NGI8	O5AN1_HUMAN	F	289	ENSP00000320302:L289F	ENSP00000320302:L289F	L	+	3	2	OR5AN1	58889374	0.923000	0.31300	0.751000	0.31187	0.984000	0.73092	0.022000	0.13511	0.184000	0.20083	-0.140000	0.14226	TTG	G|0.358;C|0.642	0.642	strong		0.378	OR5AN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394231.1	NM_001004729	
MYH6	4624	hgsc.bcm.edu	37	14	23874507	23874507	+	Silent	SNP	G	G	T	rs2277473	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23874507G>T	ENST00000356287.3	-	4	456	c.427C>A	c.(427-429)Cgg>Agg	p.R143R	MYH6_ENST00000405093.3_Silent_p.R143R			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	143	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)		TTCTTGCCCCGGTAGGCGGCC	0.612													G|||	389	0.0776757	0.0129	0.085	5008	,	,		18374	0.0675		0.1044	False		,,,				2504	0.1431				p.R143R		Atlas-SNP	.											.	MYH6	274	.	0			c.C427A						PASS	.	G		110,4296		1,108,2094	108.0	110.0	110.0		427	1.2	1.0	14	dbSNP_100	110	942,7658		54,834,3412	no	coding-synonymous	MYH6	NM_002471.3		55,942,5506	TT,TG,GG		10.9535,2.4966,8.0886		143/1940	23874507	1052,11954	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon5			TGCCCCGGTAGGC	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.427C>A	14.37:g.23874507G>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	216	131	0.606481	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			A|0.000;C|0.007	.	strong		0.612	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
CYLC1	1538	hgsc.bcm.edu	37	X	83116204	83116204	+	Missense_Mutation	SNP	G	G	C	rs142474490	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:83116204G>C	ENST00000329312.4	+	1	51	c.14G>C	c.(13-15)aGg>aCg	p.R5T		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	5					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						TCTCTTCCAAGGTTGTAAGTC	0.318													G|||	54	0.0143046	0.0	0.0014	3775	,	,		11318	0.0		0.0139	False		,,,				2504	0.0399				p.R5T		Atlas-SNP	.											.	CYLC1	272	.	0			c.G14C						PASS	.	G	THR/ARG	3,3830		0,2,1,1629,570	90.0	81.0	84.0		14	1.5	0.0	X	dbSNP_134	84	90,6638		0,63,27,2365,1845	yes	missense	CYLC1	NM_021118.1	71	0,65,28,3994,2415	CC,CG,C,GG,G		1.3377,0.0783,0.8806	probably-damaging	5/652	83116204	93,10468	2202	4300	6502	SO:0001583	missense	1538	exon1			TTCCAAGGTTGTA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"""cylicin 1"""	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.14G>C	X.37:g.83116204G>C	ENSP00000331556:p.Arg5Thr	Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	13	0.007836045810729355	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010666666666666666	g	5.026	0.190461	0.09547	7.83E-4	0.013377	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.49432	0.78	3.33	1.49	0.22878	.	.	.	.	.	T	0.28665	0.0710	N	0.24115	0.695	0.09310	N	1	D;P	0.58268	0.982;0.884	P;P	0.51135	0.66;0.541	T	0.09907	-1.0653	9	0.27082	T	0.32	5.8543	4.5828	0.12267	0.3301:0.0:0.6699:0.0	.	5;5	P35663;F5H4V5	CYLC1_HUMAN;.	T	5	ENSP00000331556:R5T	ENSP00000331556:R5T	R	+	2	0	CYLC1	83002860	0.109000	0.22037	0.029000	0.17559	0.328000	0.28507	0.304000	0.19228	0.259000	0.21709	0.449000	0.29647	AGG	G|0.992;C|0.008	0.008	strong		0.318	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118	
KIF2C	11004	hgsc.bcm.edu	37	1	45226084	45226084	+	Silent	SNP	G	G	A	rs1140279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:45226084G>A	ENST00000372224.4	+	15	1613	c.1500G>A	c.(1498-1500)gcG>gcA	p.A500A	KIF2C_ENST00000372222.3_Silent_p.A387A|KIF2C_ENST00000372217.1_Silent_p.A446A|KIF2C_ENST00000372218.4_Silent_p.A459A|RP11-269F19.2_ENST00000428791.1_RNA|RP11-269F19.2_ENST00000440985.1_RNA	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	106	0	0		WXS	Illumina HiSeq	Phase_I	49	10	0.204082	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	
ZNF451	26036	hgsc.bcm.edu	37	6	57012930	57012930	+	Silent	SNP	C	C	T	rs3734738	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:57012930C>T	ENST00000370706.4	+	10	2291	c.2047C>T	c.(2047-2049)Ctg>Ttg	p.L683L	RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|RP11-203B9.4_ENST00000589263.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000586466.1_RNA|ZNF451_ENST00000491832.2_Silent_p.L683L|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|ZNF451_ENST00000357489.3_Silent_p.L683L	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	683					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AGAAGCATTTCTGAGTCATTA	0.348													T|||	1096	0.21885	0.3669	0.1888	5008	,	,		21558	0.131		0.2416	False		,,,				2504	0.1074				p.L683L		Atlas-SNP	.											.	ZNF451	181	.	0			c.C2047T						PASS	.	T	,	1498,2908	649.1+/-398.8	247,1004,952	52.0	54.0	53.0		2047,2047	0.5	0.2	6	dbSNP_107	53	1952,6646	704.1+/-405.4	215,1522,2562	no	coding-synonymous,coding-synonymous	ZNF451	NM_001031623.2,NM_015555.2	,	462,2526,3514	TT,TC,CC		22.703,33.9991,26.5303	,	683/1062,683/1014	57012930	3450,9554	2203	4299	6502	SO:0001819	synonymous_variant	26036	exon10			GCATTTCTGAGTC	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"""Zinc fingers, C2H2-type"""	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.2047C>T	6.37:g.57012930C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	158	65	0.411392	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Silent	SNP	ENST00000370706.4	37	CCDS43477.1																																																																																			C|0.753;T|0.247	0.247	strong		0.348	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555	
MUC17	140453	hgsc.bcm.edu	37	7	100682117	100682117	+	Missense_Mutation	SNP	G	G	A	rs555953599	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682117G>A	ENST00000306151.4	+	3	7484	c.7420G>A	c.(7420-7422)Ggc>Agc	p.G2474S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2474	59 X approximate tandem repeats.|Ser-rich.				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)					TTCTGAGGCTGGCACCCTTTC	0.522													N|||	3	0.000599042	0.0	0.0	5008	,	,		27478	0.0		0.0	False		,,,				2504	0.0031				p.G2474S		Atlas-SNP	.											MUC17,right_upper_lobe,carcinoma,-2,1	MUC17	804	1	0			c.G7420A						scavenged	.																																			SO:0001583	missense	140453	exon3			GAGGCTGGCACCC	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.7420G>A	7.37:g.100682117G>A	ENSP00000302716:p.Gly2474Ser	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	238	15	0.0630252	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	2.617	-0.289370	0.05605	.	.	ENSG00000169876	ENST00000306151	T	0.03468	3.92	0.869	-0.297	0.12820	.	.	.	.	.	T	0.01254	0.0041	N	0.02916	-0.46	0.09310	N	1	B	0.27286	0.174	B	0.19148	0.024	T	0.45131	-0.9282	9	0.02654	T	1	.	5.8185	0.18514	0.4085:0.0:0.5915:0.0	.	2474	Q685J3	MUC17_HUMAN	S	2474	ENSP00000302716:G2474S	ENSP00000302716:G2474S	G	+	1	0	MUC17	100468837	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.476000	0.06591	-0.655000	0.05387	-1.616000	0.00795	GGC	.	.	none		0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110510964	110510964	+	Missense_Mutation	SNP	A	A	C	rs191412861	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:110510964A>C	ENST00000378402.5	+	67	10896	c.10792A>C	c.(10792-10794)Agt>Cgt	p.S3598R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3598					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AGGAATCATGAGTTACAATGC	0.408										HNSCC(38;0.096)			A|||	28	0.00559105	0.0008	0.0072	5008	,	,		16193	0.0		0.005	False		,,,				2504	0.0174				p.S3598R		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A10792C						PASS	.	A	ARG/SER	2,3744		0,2,1871	81.0	77.0	78.0		10792	6.0	1.0	8		78	48,8134		1,46,4044	yes	missense	PKHD1L1	NM_177531.4	110	1,48,5915	CC,CA,AA		0.5867,0.0534,0.4192	probably-damaging	3598/4244	110510964	50,11878	1873	4091	5964	SO:0001583	missense	93035	exon67			ATCATGAGTTACA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.10792A>C	8.37:g.110510964A>C	ENSP00000367655:p.Ser3598Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	217	73	0.336406	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	A	26.4	4.731514	0.89390	5.34E-4	0.005867	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.86865	-2.18;-1.99	6.02	6.02	0.97574	.	0.109105	0.64402	D	0.000010	D	0.83723	0.5316	M	0.78637	2.42	0.40619	D	0.981744	B	0.25719	0.132	B	0.22601	0.04	D	0.84175	0.0436	10	0.59425	D	0.04	.	14.5014	0.67724	1.0:0.0:0.0:0.0	.	3598	Q86WI1	PKHL1_HUMAN	R	3598;526	ENSP00000367655:S3598R;ENSP00000437376:S526R	ENSP00000367655:S3598R	S	+	1	0	PKHD1L1	110580140	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.683000	0.84093	2.299000	0.77371	0.528000	0.53228	AGT	A|0.997;C|0.003	0.003	strong		0.408	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
POM121	9883	hgsc.bcm.edu	37	7	72413874	72413874	+	Silent	SNP	T	T	C	rs199633193	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:72413874T>C	ENST00000434423.2	+	11	3342	c.3342T>C	c.(3340-3342)aaT>aaC	p.N1114N	POM121_ENST00000395270.1_Silent_p.N849N|POM121_ENST00000358357.3_Silent_p.N849N|POM121_ENST00000257622.4_Silent_p.N849N|POM121_ENST00000446813.1_Silent_p.N849N			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1114	Pore side. {ECO:0000255}.				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)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				TTGGGATCAATGTGGCCACCC	0.642																																					p.N849N		Atlas-SNP	.											POM121_ENST00000395270,bladder,carcinoma,+1,2	POM121	131	2	0			c.T2547C						scavenged	.						28.0	23.0	24.0					7																	72413874		2164	4162	6326	SO:0001819	synonymous_variant	9883	exon11			GATCAATGTGGCC	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.3342T>C	7.37:g.72413874T>C		Somatic	492	6	0.0121951		WXS	Illumina HiSeq	Phase_I	360	148	0.411111	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000434423.2	37																																																																																				T|0.500;C|0.500	0.500	weak		0.642	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
GP6	51206	hgsc.bcm.edu	37	19	55525818	55525818	+	3'UTR	SNP	C	C	T	rs41275822	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55525818C>T	ENST00000417454.1	-	0	1518				GP6_ENST00000310373.3_Missense_Mutation_p.G499S|CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.7_ENST00000586845.1_RNA|GP6_ENST00000333884.2_3'UTR	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)		TTTGTTAGACCGCAGTGGGAG	0.507													C|||	64	0.0127796	0.0023	0.0288	5008	,	,		21622	0.0		0.0378	False		,,,				2504	0.0031				p.G499S		Atlas-SNP	.											GP6,caecum,carcinoma,+2,1	GP6	55	1	0			c.G1495A						PASS	.	C	,SER/GLY	19,3893		0,19,1937	106.0	105.0	105.0		,1495	0.5	0.0	19	dbSNP_127	105	287,8009		5,277,3866	yes	utr-3,missense	GP6	NM_016363.4,NM_001083899.1	,56	5,296,5803	TT,TC,CC		3.4595,0.4857,2.5066	,benign	,499/621	55525818	306,11902	1956	4148	6104	SO:0001624	3_prime_UTR_variant	51206	exon8			TTAGACCGCAGTG	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.*471G>A	19.37:g.55525818C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_001083899	Q9HCN7|Q9UIF2	Missense_Mutation	SNP	ENST00000417454.1	37	CCDS46184.1	40	0.018315018315018316	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	26	0.03430079155672823	c	2.827	-0.243411	0.05906	0.004857	0.034595	ENSG00000088053	ENST00000310373	T	0.00581	6.42	1.56	0.493	0.16878	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48007	-0.9072	8	0.87932	D	0	.	3.5713	0.07918	0.0:0.2251:0.0:0.7749	rs41275822	499	Q9HCN6-3	.	S	499	ENSP00000308782:G499S	ENSP00000308782:G499S	G	-	1	0	GP6	60217630	0.000000	0.05858	0.004000	0.12327	0.006000	0.05464	-0.243000	0.08915	0.059000	0.16252	-0.415000	0.06103	GGT	C|0.977;T|0.023	0.023	strong		0.507	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
MYO3A	53904	hgsc.bcm.edu	37	10	26446312	26446312	+	Missense_Mutation	SNP	G	G	A	rs3758449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	118	21	0.177966	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	
CACNA1S	779	hgsc.bcm.edu	37	1	201009182	201009182	+	Missense_Mutation	SNP	A	A	G	rs12139527	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201009182A>G	ENST00000362061.3	-	44	5625	c.5399T>C	c.(5398-5400)tTg>tCg	p.L1800S	RP11-168O16.2_ENST00000415359.1_RNA|CACNA1S_ENST00000367338.3_Missense_Mutation_p.L1781S	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1800			L -> S (in dbSNP:rs12139527). {ECO:0000269|PubMed:15489334}.		axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ATCAGCTGCCAAGGTGCCCAG	0.602													A|||	1148	0.229233	0.6059	0.1023	5008	,	,		20196	0.1091		0.1054	False		,,,				2504	0.0613				p.L1800S		Atlas-SNP	.											.	CACNA1S	249	.	0			c.T5399C						PASS	.	A	SER/LEU	2385,2021		660,1065,478	74.0	73.0	73.0		5399	4.9	1.0	1	dbSNP_120	73	1124,7476		60,1004,3236	yes	missense	CACNA1S	NM_000069.2	145	720,2069,3714	GG,GA,AA		13.0698,45.8693,26.9799	probably-damaging	1800/1874	201009182	3509,9497	2203	4300	6503	SO:0001583	missense	779	exon44			GCTGCCAAGGTGC	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.5399T>C	1.37:g.201009182A>G	ENSP00000355192:p.Leu1800Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	211	78	0.369668	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	464	0.21245421245421245	280	0.5691056910569106	37	0.10220994475138122	65	0.11363636363636363	82	0.10817941952506596	.	18.77	3.695757	0.68386	0.541307	0.130698	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.54675	0.56;0.56	4.93	4.93	0.64822	.	.	.	.	.	T	0.00012	0.0000	M	0.61703	1.905	0.29257	P	0.871619	D	0.76494	0.999	D	0.80764	0.994	T	0.51529	-0.8694	8	0.66056	D	0.02	.	8.9075	0.35532	0.8334:0.0:0.0:0.1666	rs12139527;rs12139527	1800	Q13698	CAC1S_HUMAN	S	1800;1781	ENSP00000355192:L1800S;ENSP00000356307:L1781S	ENSP00000355192:L1800S	L	-	2	0	CACNA1S	199275805	1.000000	0.71417	0.994000	0.49952	0.930000	0.56654	5.618000	0.67722	1.851000	0.53745	0.332000	0.21555	TTG	A|0.756;G|0.244	0.244	strong		0.602	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
PTPRB	5787	hgsc.bcm.edu	37	12	70928616	70928616	+	Silent	SNP	G	G	A	rs3752703	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:70928616G>A	ENST00000261266.5	-	28	5576	c.5547C>T	c.(5545-5547)tgC>tgT	p.C1849C	PTPRB_ENST00000538708.1_Silent_p.C1759C|RP11-588H23.3_ENST00000546836.1_RNA|RP11-588H23.3_ENST00000547656.1_RNA|RP11-588H23.3_ENST00000548687.1_RNA|PTPRB_ENST00000334414.6_Silent_p.C2067C|RP11-588H23.3_ENST00000551438.1_RNA|PTPRB_ENST00000550857.1_Silent_p.C1759C|PTPRB_ENST00000451516.2_Silent_p.C1759C|PTPRB_ENST00000550358.1_Silent_p.C1979C|RP11-588H23.3_ENST00000549460.1_RNA	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	1849	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)			AACATACACCGCATATCTTAA	0.527													G|||	1961	0.391573	0.4539	0.3357	5008	,	,		19377	0.5278		0.3062	False		,,,				2504	0.2945				p.C2067C		Atlas-SNP	.											PTPRB_ENST00000334414,colon,carcinoma,0,3	PTPRB	676	3	0			c.C6201T						PASS	.	G	,,,	1625,2281		339,947,667	64.0	63.0	63.0		6201,5277,5277,5547	5.5	1.0	12	dbSNP_107	63	2611,5703		423,1765,1969	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	,,,	762,2712,2636	AA,AG,GG		31.4049,41.6027,34.6645	,,,	2067/2216,1759/1908,1759/1908,1849/1998	70928616	4236,7984	1953	4157	6110	SO:0001819	synonymous_variant	5787	exon30			TACACCGCATATC	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.5547C>T	12.37:g.70928616G>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1																																																																																			G|0.613;A|0.387	0.387	strong		0.527	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
JAG2	3714	hgsc.bcm.edu	37	14	105617042	105617042	+	Missense_Mutation	SNP	C	C	T	rs1057744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105617042C>T	ENST00000331782.3	-	12	1904	c.1501G>A	c.(1501-1503)Gag>Aag	p.E501K	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Missense_Mutation_p.E463K	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	501	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.		E -> K (in dbSNP:rs1057744). {ECO:0000269|PubMed:10079256, ECO:0000269|PubMed:10662552, ECO:0000269|PubMed:9315665}.		auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|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)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CTGGCACACTCGTCTCGTTCC	0.701													C|||	2605	0.520168	0.8238	0.4107	5008	,	,		14114	0.3185		0.5417	False		,,,				2504	0.3732				p.E501K		Atlas-SNP	.											JAG2,NS,carcinoma,0,1	JAG2	69	1	0			c.G1501A						PASS	.	C	LYS/GLU,LYS/GLU	3254,1012		1278,698,157	17.0	15.0	16.0		1501,1387	1.4	0.1	14	dbSNP_86	16	4465,3887		1284,1897,995	yes	missense,missense	JAG2	NM_002226.3,NM_145159.1	56,56	2562,2595,1152	TT,TC,CC		46.5398,23.7225,38.8255	benign,benign	501/1239,463/1201	105617042	7719,4899	2133	4176	6309	SO:0001583	missense	3714	exon12			CACACTCGTCTCG	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.1501G>A	14.37:g.105617042C>T	ENSP00000328169:p.Glu501Lys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	100	64	0.64	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	1182	0.5412087912087912	397	0.806910569105691	168	0.46408839779005523	196	0.34265734265734266	421	0.5554089709762533	C	10.53	1.376496	0.24857	0.762775	0.534602	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.87412	-2.25;-2.25	3.37	1.36	0.22044	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.823265	0.10860	N	0.626157	T	0.00012	0.0000	M	0.68728	2.09	0.58432	P	9.99999999995449E-6	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.41161	-0.9524	9	0.39692	T	0.17	.	2.7873	0.05377	0.24:0.4941:0.0:0.2659	rs1057744;rs61261226;rs1057744	463;501	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	K	501;463	ENSP00000328169:E501K;ENSP00000328566:E463K	ENSP00000328169:E501K	E	-	1	0	JAG2	104688087	0.000000	0.05858	0.068000	0.19968	0.763000	0.43281	0.056000	0.14256	0.035000	0.15519	0.297000	0.19635	GAG	C|0.423;T|0.577	0.577	strong		0.701	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
LSG1	55341	hgsc.bcm.edu	37	3	194387253	194387253	+	Missense_Mutation	SNP	A	A	G	rs34423045	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:194387253A>G	ENST00000265245.5	-	3	589	c.275T>C	c.(274-276)cTg>cCg	p.L92P	AC046143.1_ENST00000408791.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	92			L -> P (in dbSNP:rs34423045).		GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		CTCGAAAGACAGTAGTCCAGT	0.383													A|||	408	0.0814696	0.0938	0.0965	5008	,	,		17073	0.0734		0.0507	False		,,,				2504	0.0941				p.L92P		Atlas-SNP	.											.	LSG1	38	.	0			c.T275C						PASS	.	A	PRO/LEU	338,4068	179.0+/-207.6	14,310,1879	88.0	89.0	89.0		275	3.0	0.6	3	dbSNP_126	89	411,8189	128.7+/-186.9	10,391,3899	yes	missense	LSG1	NM_018385.2	98	24,701,5778	GG,GA,AA		4.7791,7.6714,5.7589	benign	92/659	194387253	749,12257	2203	4300	6503	SO:0001583	missense	55341	exon3			AAAGACAGTAGTC		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"""large subunit GTPase 1 homolog (S. cerevisiae)"""			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.275T>C	3.37:g.194387253A>G	ENSP00000265245:p.Leu92Pro	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	146	75	0.513699	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	37	CCDS33922.1	157	0.07188644688644688	45	0.09146341463414634	33	0.09116022099447514	41	0.07167832167832168	38	0.05013192612137203	A	8.622	0.891674	0.17613	0.076714	0.047791	ENSG00000041802	ENST00000265245	D	0.85484	-1.99	5.34	2.97	0.34412	.	0.226280	0.36303	N	0.002679	T	0.19406	0.0466	M	0.64630	1.985	0.27522	P	0.9513762	P	0.43024	0.798	P	0.44518	0.452	T	0.64879	-0.6303	9	0.48119	T	0.1	.	8.5746	0.33590	0.8397:0.0:0.1603:0.0	rs34423045	92	Q9H089	LSG1_HUMAN	P	92	ENSP00000265245:L92P	ENSP00000265245:L92P	L	-	2	0	LSG1	195868542	0.998000	0.40836	0.635000	0.29338	0.268000	0.26511	6.510000	0.73729	0.363000	0.24346	0.533000	0.62120	CTG	A|0.940;G|0.060	0.060	strong		0.383	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	
CPNE6	9362	hgsc.bcm.edu	37	14	24543808	24543808	+	Silent	SNP	G	G	C	rs2070343	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24543808G>C	ENST00000397016.2	+	7	878	c.567G>C	c.(565-567)ctG>ctC	p.L189L	CPNE6_ENST00000537691.1_Silent_p.L244L|CPNE6_ENST00000216775.2_Silent_p.L189L	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	189	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		GTGATCAGCTGGTCTGGAGAA	0.517													G|||	1337	0.266973	0.0862	0.1671	5008	,	,		21595	0.5714		0.175	False		,,,				2504	0.363				p.L189L		Atlas-SNP	.											.	CPNE6	40	.	0			c.G567C						PASS	.	G		386,4020	195.0+/-219.7	18,350,1835	97.0	98.0	98.0		567	2.2	1.0	14	dbSNP_96	98	1588,7012	297.3+/-303.3	138,1312,2850	no	coding-synonymous	CPNE6	NM_006032.2		156,1662,4685	CC,CG,GG		18.4651,8.7608,15.1776		189/558	24543808	1974,11032	2203	4300	6503	SO:0001819	synonymous_variant	9362	exon6			TCAGCTGGTCTGG	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.567G>C	14.37:g.24543808G>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	126	123	0.97619	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																			G|0.789;C|0.211	0.211	strong		0.517	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5		
ZNF366	167465	hgsc.bcm.edu	37	5	71756670	71756670	+	Silent	SNP	C	C	T	rs2278600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:71756670C>T	ENST00000318442.5	-	2	1144	c.654G>A	c.(652-654)gaG>gaA	p.E218E		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	218					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TCTCCTGGGGCTCGGCTTTCC	0.647													C|||	1385	0.276558	0.3775	0.2046	5008	,	,		18159	0.4077		0.1332	False		,,,				2504	0.2035				p.E218E		Atlas-SNP	.											ZNF366,NS,carcinoma,-2,1	ZNF366	108	1	0			c.G654A						PASS	.	C		1601,2805	491.7+/-362.2	310,981,912	73.0	75.0	74.0		654	3.1	0.4	5	dbSNP_100	74	1198,7402	242.2+/-272.3	85,1028,3187	no	coding-synonymous	ZNF366	NM_152625.1		395,2009,4099	TT,TC,CC		13.9302,36.3368,21.5208		218/745	71756670	2799,10207	2203	4300	6503	SO:0001819	synonymous_variant	167465	exon2			CTGGGGCTCGGCT	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.654G>A	5.37:g.71756670C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	119	49	0.411765	NM_152625	Q5HYI9|Q7RTV4	Silent	SNP	ENST00000318442.5	37	CCDS4015.1																																																																																			C|0.757;T|0.243	0.243	strong		0.647	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
SERPINE1	5054	hgsc.bcm.edu	37	7	100771717	100771717	+	Missense_Mutation	SNP	G	G	A	rs6092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100771717G>A	ENST00000223095.4	+	2	200	c.43G>A	c.(43-45)Gcc>Acc	p.A15T	SERPINE1_ENST00000445463.2_Missense_Mutation_p.A15T	NM_000602.4	NP_000593.1	P05121	PAI1_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	15			A -> T (in dbSNP:rs6092). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:9194591, ECO:0000269|Ref.8}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to lipopolysaccharide (GO:0071222)|chronological cell aging (GO:0001300)|defense response to Gram-negative bacterium (GO:0050829)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|gene expression (GO:0010467)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of endopeptidase activity (GO:0010951)|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 fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell-matrix adhesion (GO:2000098)|negative regulation of vascular wound healing (GO:0061044)|negative regulation of wound healing (GO:0061045)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukotriene production involved in inflammatory response (GO:0035491)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of receptor activity (GO:0010469)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(3)	20	Lung NSC(181;0.136)|all_lung(186;0.182)				Alteplase(DB00009)|Anistreplase(DB00029)|Drotrecogin alfa(DB00055)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	CCTGGGCCTGGCCCTTGTCTT	0.607													G|||	358	0.0714856	0.0023	0.0807	5008	,	,		20984	0.0972		0.0984	False		,,,				2504	0.1043				p.A15T		Atlas-SNP	.											.	SERPINE1	60	.	0			c.G43A	GRCh37	CM055540	SERPINE1	M	rs6092	PASS	.	G	THR/ALA,THR/ALA	101,4305	80.4+/-118.8	1,99,2103	126.0	97.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	43,43	3.9	1.0	7	dbSNP_52	107	1008,7592	216.6+/-255.6	59,890,3351	yes	missense,missense	SERPINE1	NM_000602.3,NM_001165413.1	58,58	60,989,5454	AA,AG,GG		11.7209,2.2923,8.5268	benign,benign	15/403,15/388	100771717	1109,11897	2203	4300	6503	SO:0001583	missense	5054	exon2			GGCCTGGCCCTTG	M16006	CCDS5711.1	7q22.1	2014-02-18	2005-08-18		ENSG00000106366	ENSG00000106366		"""Serine (or cysteine) peptidase inhibitors"""	8583	protein-coding gene	gene with protein product	"""plasminogen activator inhibitor, type I"""	173360	"""serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1"""	PLANH1, PAI1		3097076, 2891140, 24172014	Standard	NM_000602		Approved	PAI	uc003uxt.4	P05121	OTTHUMG00000157107	ENST00000223095.4:c.43G>A	7.37:g.100771717G>A	ENSP00000223095:p.Ala15Thr	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	83	51	0.614458	NM_000602	B7Z4S0|F8WD53	Missense_Mutation	SNP	ENST00000223095.4	37	CCDS5711.1	157	0.07188644688644688	2	0.0040650406504065045	31	0.0856353591160221	55	0.09615384615384616	69	0.09102902374670185	G	10.79	1.450758	0.26074	0.022923	0.117209	ENSG00000106366	ENST00000223095;ENST00000445463;ENST00000441467	D;D	0.85629	-1.83;-2.01	4.84	3.88	0.44766	Serpin domain (1);	0.549688	0.17694	N	0.165180	T	0.02533	0.0077	N	0.08118	0	0.46849	P	7.789999999999742E-4	P;B	0.36633	0.562;0.281	B;B	0.38500	0.275;0.06	T	0.48103	-0.9064	9	0.30854	T	0.27	.	9.6714	0.40015	0.0:0.0:0.7929:0.2071	rs6092;rs11553531;rs52825313;rs6092	15;15	F8WD53;P05121	.;PAI1_HUMAN	T	15	ENSP00000223095:A15T;ENSP00000396766:A15T	ENSP00000223095:A15T	A	+	1	0	SERPINE1	100558437	1.000000	0.71417	0.999000	0.59377	0.110000	0.19582	0.686000	0.25392	2.622000	0.88805	0.655000	0.94253	GCC	G|0.914;A|0.086	0.086	strong		0.607	SERPINE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347458.1	NM_000602	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289721	98289721	+	Missense_Mutation	SNP	C	C	T	rs118032326	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:98289721C>T	ENST00000322128.3	-	1	455	c.352G>A	c.(352-354)Gca>Aca	p.A118T		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	118					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					ACAGTGTCTGCGGCCAGGCGC	0.731													C|||	21	0.00419329	0.0008	0.0101	5008	,	,		11818	0.001		0.0109	False		,,,				2504	0.001				p.A118T		Atlas-SNP	.											.	TSPYL5	48	.	0			c.G352A						PASS	.	C	THR/ALA	11,4217		0,11,2103	9.0	10.0	10.0		352	-3.3	0.0	8	dbSNP_132	10	100,8066		0,100,3983	yes	missense	TSPYL5	NM_033512.2	58	0,111,6086	TT,TC,CC		1.2246,0.2602,0.8956	benign	118/418	98289721	111,12283	2114	4083	6197	SO:0001583	missense	85453	exon1			TGTCTGCGGCCAG	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.352G>A	8.37:g.98289721C>T	ENSP00000322802:p.Ala118Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	C	8.533	0.871456	0.17322	0.002602	0.012246	ENSG00000180543	ENST00000322128	T	0.18338	2.22	4.16	-3.35	0.04928	.	2.452570	0.02423	N	0.082796	T	0.06050	0.0157	N	0.12961	0.28	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22382	-1.0218	10	0.39692	T	0.17	4.9426	1.6446	0.02759	0.1614:0.3902:0.1656:0.2828	.	118	Q86VY4	TSYL5_HUMAN	T	118	ENSP00000322802:A118T	ENSP00000322802:A118T	A	-	1	0	TSPYL5	98358897	0.000000	0.05858	0.000000	0.03702	0.140000	0.21249	-2.322000	0.01118	-0.639000	0.05502	-1.275000	0.01399	GCA	C|0.994;T|0.006	0.006	strong		0.731	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
SIRPA	140885	hgsc.bcm.edu	37	20	1895965	1895965	+	Missense_Mutation	SNP	C	C	A	rs17855614|rs373583167|rs386811662	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1895965C>A	ENST00000358771.4	+	2	452	c.300C>A	c.(298-300)aaC>aaA	p.N100K	SIRPA_ENST00000356025.3_Missense_Mutation_p.N100K|SIRPA_ENST00000400068.3_Missense_Mutation_p.N100K	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	100	Ig-like V-type.		N -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CAAAGAGAAACAACATGGACT	0.517													C|||	480	0.0958466	0.0386	0.1095	5008	,	,		14804	0.1835		0.0537	False		,,,				2504	0.1166				p.N100K	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,brain,glioma,0,4	SIRPA	83	4	0			c.C300A						scavenged	.																																			SO:0001583	missense	140885	exon3			GAGAAACAACATG	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.300C>A	20.37:g.1895965C>A	ENSP00000351621:p.Asn100Lys	Somatic	669	0	0		WXS	Illumina HiSeq	Phase_I	360	15	0.0416667	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.533326	0.27387	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02158	4.42;4.42;4.42	5.11	0.771	0.18504	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.743450	0.02696	N	0.111247	T	0.04634	0.0126	M	0.65975	2.015	0.09310	N	1	B;B;B	0.33299	0.003;0.407;0.039	B;B;B	0.31812	0.056;0.136;0.082	T	0.44345	-0.9334	10	0.72032	D	0.01	.	8.1767	0.31285	0.0:0.4423:0.4696:0.0881	rs17855614	80;100;100	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	K	100	ENSP00000382941:N100K;ENSP00000348307:N100K;ENSP00000351621:N100K	ENSP00000348307:N100K	N	+	3	2	SIRPA	1843965	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.328000	0.07945	0.028000	0.15324	-0.315000	0.08773	AAC	.	.	weak		0.517	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
PADI2	11240	hgsc.bcm.edu	37	1	17410253	17410253	+	Nonsense_Mutation	SNP	G	G	A	rs142403504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:17410253G>A	ENST00000375486.4	-	9	1081	c.1018C>T	c.(1018-1020)Cag>Tag	p.Q340*	PADI2_ENST00000444885.2_Nonsense_Mutation_p.Q224*|PADI2_ENST00000375481.1_Nonsense_Mutation_p.Q340*|PADI2_ENST00000466151.1_5'Flank	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	340					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)	TTTAGGTACTGGAAGCAGACC	0.522													G|||	4	0.000798722	0.0	0.0	5008	,	,		20901	0.0		0.001	False		,,,				2504	0.0031				p.Q340X		Atlas-SNP	.											.	PADI2	72	.	0			c.C1018T						PASS	.	G	stop/GLN	1,4405	2.1+/-5.4	0,1,2202	140.0	133.0	135.0		1018	5.8	1.0	1	dbSNP_134	135	30,8570	21.0+/-64.5	0,30,4270	yes	stop-gained	PADI2	NM_007365.2		0,31,6472	AA,AG,GG		0.3488,0.0227,0.2384		340/666	17410253	31,12975	2203	4300	6503	SO:0001587	stop_gained	11240	exon9			GGTACTGGAAGCA	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.1018C>T	1.37:g.17410253G>A	ENSP00000364635:p.Gln340*	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	121	35	0.289256	NM_007365	Q96DA7|Q9UPN2	Nonsense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	38	7.248142	0.98161	2.27E-4	0.003488	ENSG00000117115	ENST00000375486;ENST00000444885;ENST00000375481	.	.	.	5.77	5.77	0.91146	.	0.267496	0.41605	D	0.000847	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-37.1678	13.5666	0.61822	0.0:0.2539:0.7461:0.0	.	.	.	.	X	340;224;340	.	ENSP00000364630:Q340X	Q	-	1	0	PADI2	17282840	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.120000	0.64685	2.724000	0.93272	0.561000	0.74099	CAG	G|0.998;A|0.002	0.002	strong		0.522	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
SEMG1	6406	hgsc.bcm.edu	37	20	43837278	43837278	+	Missense_Mutation	SNP	G	G	A	rs79500955	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:43837278G>A	ENST00000372781.3	+	2	1397	c.1340G>A	c.(1339-1341)cGt>cAt	p.R447H	SEMG1_ENST00000244069.6_Missense_Mutation_p.R387H	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	447					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)				GACAGTGATCGTCATTTGGCA	0.398													g|||	14	0.00279553	0.0	0.0029	5008	,	,		21943	0.0		0.0099	False		,,,				2504	0.002				p.R447H		Atlas-SNP	.											SEMG1,colon,carcinoma,+1,1	SEMG1	71	1	0			c.G1340A						PASS	.	A	HIS/ARG	16,4390	23.3+/-48.9	0,16,2187	128.0	119.0	122.0		1340	1.5	0.0	20	dbSNP_131	122	59,8541	36.4+/-91.3	1,57,4242	yes	missense	SEMG1	NM_003007.3	29	1,73,6429	AA,AG,GG		0.686,0.3631,0.5767		447/463	43837278	75,12931	2203	4300	6503	SO:0001583	missense	6406	exon2			GTGATCGTCATTT		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.1340G>A	20.37:g.43837278G>A	ENSP00000361867:p.Arg447His	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	260	127	0.488462	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	g	0.027	-1.359398	0.01245	0.003631	0.00686	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.06449	3.3;3.3	1.47	1.47	0.22746	.	.	.	.	.	T	0.01627	0.0052	N	0.02539	-0.55	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	0.45026	-0.9289	9	0.39692	T	0.17	.	3.4522	0.07502	0.7668:0.0:0.2332:0.0	.	387;447;387	P04279-2;P04279;E7EPD3	.;SEMG1_HUMAN;.	H	387;447	ENSP00000244069:R387H;ENSP00000361867:R447H	ENSP00000244069:R387H	R	+	2	0	SEMG1	43270692	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.261000	0.08694	0.052000	0.16007	-0.381000	0.06696	CGT	G|0.996;A|0.004	0.004	strong		0.398	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
XIRP2	129446	hgsc.bcm.edu	37	2	168115158	168115158	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168115158A>C	ENST00000409728.1	+	11	2290	c.2201A>C	c.(2200-2202)aAa>aCa	p.K734T	XIRP2_ENST00000409605.1_Missense_Mutation_p.K479T|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.K701T|XIRP2_ENST00000409043.1_Missense_Mutation_p.K701T|XIRP2_ENST00000420519.1_Missense_Mutation_p.K734T|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409195.1_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					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						GAAAATCATAAAGAAAATTTG	0.294																																					p.K734T		Atlas-SNP	.											.	XIRP2	914	.	0			c.A2201C						PASS	.						28.0	27.0	27.0					2																	168115158		1807	4068	5875	SO:0001583	missense	129446	exon11			ATCATAAAGAAAA	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	ENST00000409728.1:c.2201A>C	2.37:g.168115158A>C	ENSP00000386619:p.Lys734Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.463028	0.43736	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	D;D;D;D;D	0.82167	-1.54;-1.54;-1.54;-1.54;-1.58	5.61	3.21	0.36854	.	.	.	.	.	D	0.87597	0.6217	.	.	.	0.80722	D	1	D;D	0.67145	0.996;0.996	P;P	0.62298	0.9;0.9	D	0.85431	0.1149	8	0.87932	D	0	.	5.8857	0.18880	0.7743:0.0:0.0791:0.1466	.	701;734	A4UGR9-4;A4UGR9-6	.;.	T	701;734;701;734;479	ENSP00000386454:K701T;ENSP00000386619:K734T;ENSP00000386724:K701T;ENSP00000415541:K734T;ENSP00000386981:K479T	ENSP00000386454:K701T	K	+	2	0	XIRP2	167823404	1.000000	0.71417	0.366000	0.25914	0.381000	0.30169	2.375000	0.44283	0.407000	0.25591	0.418000	0.28097	AAA	.	.	none		0.294	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
BAIAP2	10458	hgsc.bcm.edu	37	17	79089590	79089590	+	Missense_Mutation	SNP	A	A	G	rs4969391	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:79089590A>G	ENST00000321300.6	+	14	1649	c.1556A>G	c.(1555-1557)cAg>cGg	p.Q519R	BAIAP2_ENST00000392411.3_Missense_Mutation_p.Q441R|BAIAP2_ENST00000435091.3_3'UTR|BAIAP2_ENST00000428708.2_Missense_Mutation_p.Q519R|BAIAP2_ENST00000575245.1_3'UTR	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	519			Q -> R (in dbSNP:rs4969391).		actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GCCCACGTCCAGCTGAAGCCG	0.582													A|||	863	0.172324	0.1059	0.3631	5008	,	,		17328	0.1478		0.1561	False		,,,				2504	0.1687				p.Q519R		Atlas-SNP	.											BAIAP2_ENST00000321300,colon,carcinoma,0,1	BAIAP2	74	1	0			c.A1556G						PASS	.	A	ARG/GLN,,ARG/GLN	516,3890	234.6+/-247.4	35,446,1722	90.0	91.0	91.0		1556,,1556	5.0	1.0	17	dbSNP_111	91	1330,7270	259.8+/-282.9	98,1134,3068	yes	missense,utr-3,missense	BAIAP2	NM_001144888.1,NM_006340.2,NM_017451.2	43,,43	133,1580,4790	GG,GA,AA		15.4651,11.7113,14.1934	benign,,benign	519/535,,519/553	79089590	1846,11160	2203	4300	6503	SO:0001583	missense	10458	exon14			ACGTCCAGCTGAA	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.1556A>G	17.37:g.79089590A>G	ENSP00000316338:p.Gln519Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Missense_Mutation	SNP	ENST00000321300.6	37	CCDS11775.1	410	0.18772893772893773	84	0.17073170731707318	112	0.30939226519337015	92	0.16083916083916083	122	0.16094986807387862	A	13.79	2.343165	0.41498	0.117113	0.154651	ENSG00000175866	ENST00000321300;ENST00000428708;ENST00000392411	T;T;T	0.38560	1.13;1.13;1.13	4.96	4.96	0.65561	.	1.320840	0.04637	N	0.404645	T	0.00012	0.0000	N	0.04508	-0.205	0.43761	P	0.0037289999999999823	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.18935	-1.0321	9	0.30854	T	0.27	-1.4439	8.529	0.33321	0.9135:0.0:0.0865:0.0	rs4969391;rs52805958;rs56955834;rs4969391	441;519;519	F8W878;Q9UQB8;Q9UQB8-2	.;BAIP2_HUMAN;.	R	519;519;441	ENSP00000316338:Q519R;ENSP00000401022:Q519R;ENSP00000376211:Q441R	ENSP00000316338:Q519R	Q	+	2	0	BAIAP2	76704185	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	4.516000	0.60496	1.862000	0.54008	0.379000	0.24179	CAG	A|0.843;G|0.157	0.157	strong		0.582	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
DMPK	1760	hgsc.bcm.edu	37	19	46273740	46273740	+	3'UTR	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46273740T>C	ENST00000291270.4	-	0	2021				DMPK_ENST00000600757.1_Nonstop_Mutation_p.*636W|AC074212.6_ENST00000586251.1_RNA|AC074212.6_ENST00000590076.1_RNA|AC074212.6_ENST00000586498.1_RNA|DMPK_ENST00000354227.5_3'UTR|AC074212.5_ENST00000592217.2_RNA|SIX5_ENST00000317578.6_5'Flank|DMPK_ENST00000458663.2_Nonstop_Mutation_p.*626W|AC074212.5_ENST00000559756.1_RNA|DMPK_ENST00000343373.4_3'UTR|DMPK_ENST00000447742.2_3'UTR|SIX5_ENST00000560168.1_5'Flank|AC074212.6_ENST00000591530.1_RNA	NM_004409.3	NP_004400.4	Q09013	DMPK_HUMAN	dystrophia myotonica-protein kinase						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)		AAGACAGTTCTAGGGTTCAGG	0.716											OREG0025561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.X626W	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											.	DMPK	74	.	0			c.A1877G						PASS	.						7.0	8.0	8.0					19																	46273740		1840	3549	5389	SO:0001624	3_prime_UTR_variant	1760	exon15			CAGTTCTAGGGTT	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.*6A>G	19.37:g.46273740T>C		Somatic	157	0	0	938	WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_001081562	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	37	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	t	17.91	3.504333	0.64410	.	.	ENSG00000104936	ENST00000458663	.	.	.	4.05	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3258	0.37993	0.0:0.0:0.0:1.0	.	.	.	.	W	626	.	.	X	-	2	0	DMPK	50965580	1.000000	0.71417	0.967000	0.41034	0.514000	0.34195	1.865000	0.39479	1.712000	0.51347	0.454000	0.30748	TAG	.	.	none		0.716	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409	
CACNA2D1	781	hgsc.bcm.edu	37	7	81635083	81635083	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:81635083T>C	ENST00000356253.5	-	17	1768	c.1513A>G	c.(1513-1515)Aca>Gca	p.T505A	CACNA2D1_ENST00000464354.1_5'UTR|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.T505A			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	505	Cache.				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)	CATCTTACTGTAAAACGTGGT	0.358																																					p.T505A		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A1513G						PASS	.						123.0	117.0	119.0					7																	81635083		2203	4299	6502	SO:0001583	missense	781	exon17			TTACTGTAAAACG	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.1513A>G	7.37:g.81635083T>C	ENSP00000348589:p.Thr505Ala	Somatic	380	0	0		WXS	Illumina HiSeq	Phase_I	475	107	0.225263	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	T	17.74	3.464121	0.63513	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.06608	3.28;3.28	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.10165	0.0249	L	0.58669	1.825	0.80722	D	1	B	0.19445	0.036	B	0.20384	0.029	T	0.02885	-1.1098	10	0.56958	D	0.05	-20.1301	15.0578	0.71927	0.0:0.0:0.0:1.0	.	505	P54289-2	.	A	505	ENSP00000349320:T505A;ENSP00000348589:T505A	ENSP00000284088:T505A	T	-	1	0	CACNA2D1	81473019	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.672000	0.83956	2.040000	0.60383	0.482000	0.46254	ACA	.	.	none		0.358	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
CNOT1	23019	hgsc.bcm.edu	37	16	58616984	58616984	+	Silent	SNP	T	T	C	rs17854029	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:58616984T>C	ENST00000317147.5	-	9	1241	c.909A>G	c.(907-909)ggA>ggG	p.G303G	CNOT1_ENST00000441024.2_Silent_p.G303G|CNOT1_ENST00000569240.1_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	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	209	209	1	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	
MXRA5	25878	hgsc.bcm.edu	37	X	3248333	3248333	+	Silent	SNP	T	T	C	rs372395776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:3248333T>C	ENST00000217939.6	-	4	589	c.435A>G	c.(433-435)caA>caG	p.Q145Q		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	145						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CGTTGAAAGCTTGAGGGTGGA	0.488																																					p.Q145Q		Atlas-SNP	.											.	MXRA5	815	.	0			c.A435G						PASS	.	T		1,3834		0,0,1,1632,570	118.0	96.0	103.0		435	-7.1	0.0	X		103	1,6727		0,0,1,2428,1871	no	coding-synonymous	MXRA5	NM_015419.3		0,0,2,4060,2441	CC,CT,C,TT,T		0.0149,0.0261,0.0189		145/2829	3248333	2,10561	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon4			GAAAGCTTGAGGG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.435A>G	X.37:g.3248333T>C		Somatic	397	2	0.00503778		WXS	Illumina HiSeq	Phase_I	176	171	0.971591	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			.	.	weak		0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
TSPAN13	27075	hgsc.bcm.edu	37	7	16816000	16816000	+	Silent	SNP	T	T	C	rs2290837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:16816000T>C	ENST00000262067.4	+	2	661	c.228T>C	c.(226-228)ttT>ttC	p.F76F	TSPAN13_ENST00000466195.1_3'UTR	NM_014399.3	NP_055214.1	O95857	TSN13_HUMAN	tetraspanin 13	76						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	7	Lung NSC(10;0.0494)|all_lung(11;0.109)			UCEC - Uterine corpus endometrioid carcinoma (126;0.188)		TGTTGCTATTTTTTGTATCCT	0.363													T|||	1694	0.338259	0.4766	0.3487	5008	,	,		18343	0.2024		0.3926	False		,,,				2504	0.228				p.F76F		Atlas-SNP	.											.	TSPAN13	13	.	0			c.T228C						PASS	.	T		2009,2397	555.4+/-379.2	450,1109,644	166.0	150.0	155.0		228	2.5	1.0	7	dbSNP_100	155	3279,5321	482.4+/-370.9	629,2021,1650	no	coding-synonymous	TSPAN13	NM_014399.3		1079,3130,2294	CC,CT,TT		38.1279,45.5969,40.6582		76/205	16816000	5288,7718	2203	4300	6503	SO:0001819	synonymous_variant	27075	exon2			GCTATTTTTTGTA	AF100759	CCDS5363.1	7p21.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000106537	ENSG00000106537		"""Tetraspanins"""	21643	protein-coding gene	gene with protein product		613139	"""transmembrane 4 superfamily member 13"""	TM4SF13			Standard	NM_014399		Approved	NET-6	uc003stq.3	O95857	OTTHUMG00000022968	ENST00000262067.4:c.228T>C	7.37:g.16816000T>C		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	266	166	0.62406	NM_014399		Silent	SNP	ENST00000262067.4	37	CCDS5363.1																																																																																			T|0.608;C|0.392	0.392	strong		0.363	TSPAN13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250178.2	NM_014399	
SSPO	23145	hgsc.bcm.edu	37	7	149484798	149484798	+	RNA	SNP	C	C	T	rs62490656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	57	0	0		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	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			
APOBEC3F	200316	hgsc.bcm.edu	37	22	39438955	39438955	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:39438955C>T	ENST00000308521.5	+	2	388	c.31C>T	c.(31-33)Cga>Tga	p.R11*	APOBEC3F_ENST00000381565.2_Nonsense_Mutation_p.R11*|APOBEC3F_ENST00000491387.1_3'UTR|APOBEC3G_ENST00000452957.2_Intron	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	11					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|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)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|skin(2)	16	Melanoma(58;0.04)					CACAGTGGAGCGAATGTATCG	0.502																																					p.R11X		Atlas-SNP	.											APOBEC3F_ENST00000381565,brain,glioma,0,2	APOBEC3F	37	2	0			c.C31T						scavenged	.						52.0	50.0	51.0					22																	39438955		2203	4297	6500	SO:0001587	stop_gained	200316	exon2			GTGGAGCGAATGT	BC038808	CCDS33648.1, CCDS33649.1	22q13.1-q13.2	2008-05-15			ENSG00000128394	ENSG00000128394		"""Apolipoprotein B mRNA editing enzymes"""	17356	protein-coding gene	gene with protein product		608993				11863358, 17121840	Standard	NM_145298		Approved	ARP8, BK150C2.4.MRNA, KA6	uc003aww.3	Q8IUX4	OTTHUMG00000151080	ENST00000308521.5:c.31C>T	22.37:g.39438955C>T	ENSP00000309749:p.Arg11*	Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	318	4	0.0125786	NM_145298	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Nonsense_Mutation	SNP	ENST00000308521.5	37	CCDS33648.1	.	.	.	.	.	.	.	.	.	.	.	13.42	2.232238	0.39498	.	.	ENSG00000128394	ENST00000308521;ENST00000381565	.	.	.	1.96	-1.51	0.08664	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.034	0.24983	0.4145:0.5855:0.0:0.0	.	.	.	.	X	11	.	ENSP00000309749:R11X	R	+	1	2	APOBEC3F	37768901	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.371000	0.02573	-0.323000	0.08602	0.561000	0.74099	CGA	.	.	none		0.502	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298	
MS4A13	503497	hgsc.bcm.edu	37	11	60291413	60291413	+	Missense_Mutation	SNP	C	C	T	rs6591595	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:60291413C>T	ENST00000378186.2	+	4	496	c.173C>T	c.(172-174)cCg>cTg	p.P58L	MS4A13_ENST00000437058.2_Intron|MS4A13_ENST00000527948.1_Intron|MS4A13_ENST00000378185.2_Missense_Mutation_p.P58L	NM_001012417.2	NP_001012417.2	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 13	104						integral component of membrane (GO:0016021)				endometrium(3)|large_intestine(1)|lung(2)|skin(2)	8						ACAAAGTATCCGACTCGATCT	0.289													C|||	3650	0.728834	0.6059	0.6859	5008	,	,		17015	0.7242		0.8787	False		,,,				2504	0.7761				p.P58L		Atlas-SNP	.											.	MS4A13	27	.	0			c.C173T						PASS	.	C	LEU/PRO,LEU/PRO	2822,1582	657.1+/-400.2	906,1010,286	84.0	86.0	85.0		173,173	1.3	0.0	11	dbSNP_116	85	7444,1138	760.4+/-407.6	3231,982,78	yes	missense,missense	MS4A13	NM_001012417.2,NM_001100909.1	98,98	4137,1992,364	TT,TC,CC		13.2603,35.9219,20.9456	probably-damaging,probably-damaging	58/153,58/113	60291413	10266,2720	2202	4291	6493	SO:0001583	missense	503497	exon4			AGTATCCGACTCG	AY324188	CCDS31571.1, CCDS41653.1, CCDS60801.1	11q12.2	2005-12-05	2005-12-05		ENSG00000204979	ENSG00000204979			16674	protein-coding gene	gene with protein product							Standard	NM_001012417		Approved		uc001nps.3	Q5J8X5	OTTHUMG00000167615	ENST00000378186.2:c.173C>T	11.37:g.60291413C>T	ENSP00000367428:p.Pro58Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001100909	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000378186.2	37	CCDS31571.1	1622	0.7426739926739927	293	0.5955284552845529	253	0.6988950276243094	410	0.7167832167832168	666	0.8786279683377308	C	12.74	2.027638	0.35797	0.640781	0.867397	ENSG00000204979	ENST00000378186;ENST00000378185	T;T	0.23552	4.19;1.9	4.29	1.32	0.21799	.	1.169620	0.06367	N	0.712834	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P;D	0.53745	0.953;0.962	B;P	0.48488	0.343;0.579	T	0.36261	-0.9755	9	0.66056	D	0.02	-4.2807	6.8654	0.24091	0.3573:0.4696:0.1731:0.0	rs6591595;rs59009772;rs6591595	58;58	Q5J8X5-2;Q5J8X5	.;M4A13_HUMAN	L	58	ENSP00000367428:P58L;ENSP00000367427:P58L	ENSP00000367427:P58L	P	+	2	0	MS4A13	60047989	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.211000	0.09332	0.316000	0.23135	-0.188000	0.12872	CCG	C|0.236;T|0.764	0.764	strong		0.289	MS4A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395408.1	NM_001012417	
PLXNB2	23654	hgsc.bcm.edu	37	22	50722408	50722408	+	Missense_Mutation	SNP	T	T	C	rs79966207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50722408T>C	ENST00000449103.1	-	14	2415	c.2275A>G	c.(2275-2277)Aac>Gac	p.N759D	PLXNB2_ENST00000359337.4_Missense_Mutation_p.N759D|PLXNB2_ENST00000496720.1_5'UTR			O15031	PLXB2_HUMAN	plexin B2	759					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)	p.N802D(1)		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)		AAGGAGCAGTTGTAGAGGGTC	0.706													t|||	373	0.0744808	0.0061	0.0893	5008	,	,		8236	0.0694		0.175	False		,,,				2504	0.0583				p.N759D		Atlas-SNP	.											PLXNB2,brain,glioma,0,1	PLXNB2	172	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2275G						PASS	.		ASP/ASN	101,3857		1,99,1879	13.0	19.0	17.0		2275	4.5	1.0	22	dbSNP_131	17	1264,6886		91,1082,2902	yes	missense	PLXNB2	NM_012401.3	23	92,1181,4781	CC,CT,TT		15.5092,2.5518,11.2735	probably-damaging	759/1839	50722408	1365,10743	1979	4075	6054	SO:0001583	missense	23654	exon14			AGCAGTTGTAGAG		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.2275A>G	22.37:g.50722408T>C	ENSP00000409171:p.Asn759Asp	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	199	0.09111721611721611	3	0.006097560975609756	31	0.0856353591160221	38	0.06643356643356643	127	0.16754617414248021	t	10.59	1.392764	0.25118	0.025518	0.155092	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.03242	4.0;4.0	4.52	4.52	0.55395	.	0.092327	0.46758	D	0.000272	T	0.00012	0.0000	L	0.38953	1.18	0.09310	P	0.99999717682	P	0.45126	0.851	B	0.41332	0.354	T	0.59392	-0.7463	9	0.19590	T	0.45	.	11.8308	0.52295	0.0:0.0:0.0:1.0	.	759	O15031	PLXB2_HUMAN	D	759	ENSP00000409171:N759D;ENSP00000352288:N759D	ENSP00000352288:N759D	N	-	1	0	PLXNB2	49064535	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	3.062000	0.49971	1.899000	0.54978	0.398000	0.26397	AAC	T|0.908;C|0.092	0.092	strong		0.706	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
TBC1D25	4943	hgsc.bcm.edu	37	X	48418659	48418659	+	Missense_Mutation	SNP	G	G	A	rs235836	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:48418659G>A	ENST00000376771.4	+	6	1704	c.1363G>A	c.(1363-1365)Gct>Act	p.A455T	TBC1D25_ENST00000537536.1_Missense_Mutation_p.A201T|snoU13_ENST00000459609.1_RNA	NM_002536.2	NP_002527.1	Q3MII6	TBC25_HUMAN	TBC1 domain family, member 25	455				A -> T (in Ref. 2; AAI01818/AAI01820/ AAI25089). {ECO:0000305}.	autophagy (GO:0006914)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of autophagic vacuole maturation (GO:1901096)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)	Rab GTPase activator activity (GO:0005097)			large_intestine(1)|lung(1)|ovary(1)|pancreas(1)	4						AGTGGCAGACGCTGGTTTTGG	0.607													A|||	2101	0.556556	0.6089	0.3285	3775	,	,		14249	0.4127		0.3082	False		,,,				2504	0.3497				p.A455T		Atlas-SNP	.											.	TBC1D25	70	.	0			c.G1363A						PASS	.	A	THR/ALA	2926,909		957,587,425,88,146	28.0	23.0	25.0		1363	-7.3	0.0	X	dbSNP_79	25	2876,3852		481,1133,781,814,1091	yes	missense	TBC1D25	NM_002536.2	58	1438,1720,1206,902,1237	AA,AG,A,GG,G		42.7467,23.7027,45.0724	benign	455/689	48418659	5802,4761	2203	4300	6503	SO:0001583	missense	4943	exon6			GCAGACGCTGGTT	L08240	CCDS35242.1	Xp11.23	2014-01-28	2007-01-12	2007-01-12	ENSG00000068354	ENSG00000068354			8092	protein-coding gene	gene with protein product		311240	"""ornithine aminotransferase-like 1"""	OATL1		21383079	Standard	NM_002536		Approved		uc004dka.1	Q3MII6	OTTHUMG00000024123	ENST00000376771.4:c.1363G>A	X.37:g.48418659G>A	ENSP00000365962:p.Ala455Thr	Somatic	227	2	0.00881057		WXS	Illumina HiSeq	Phase_I	109	105	0.963303	NM_002536	Q08AN9|Q3MII4|Q8TAR9	Missense_Mutation	SNP	ENST00000376771.4	37	CCDS35242.1	892	0.5376732971669681	208	0.6459627329192547	80	0.28169014084507044	157	0.3866995073891626	162	0.2691029900332226	A	0.018	-1.479371	0.01035	0.762973	0.427467	ENSG00000068354	ENST00000376771;ENST00000537536	T;T	0.21543	2.0;2.0	4.05	-7.34	0.01427	Rab-GAP/TBC domain (2);	2.072600	0.01690	N	0.026624	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	0.34825	-0.9813	9	0.02654	T	1	2.5694	3.1069	0.06345	0.2791:0.2206:0.3908:0.1095	rs235836	459;397;455	B4DF03;B4DGU3;Q3MII6	.;.;TBC25_HUMAN	T	455;201	ENSP00000365962:A455T;ENSP00000444091:A201T	ENSP00000365962:A455T	A	+	1	0	TBC1D25	48303603	0.000000	0.05858	0.015000	0.15790	0.736000	0.42039	-1.130000	0.03241	-2.436000	0.00553	-0.573000	0.04149	GCT	G|0.441;A|0.559	0.559	strong		0.607	TBC1D25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060764.2	NM_002536	
OR12D2	26529	hgsc.bcm.edu	37	6	29365241	29365241	+	Silent	SNP	T	T	C	rs2073150	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29365241T>C	ENST00000383555.2	+	1	826	c.765T>C	c.(763-765)ctT>ctC	p.L255L	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	255						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(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CACCTGTTCTTTTCACCTATA	0.458													C|||	1651	0.329673	0.2254	0.3588	5008	,	,		21296	0.3641		0.4533	False		,,,				2504	0.2873				p.L255L		Atlas-SNP	.											.	OR12D2	42	.	0			c.T765C						PASS	.	C		768,2254		96,576,839	212.0	210.0	210.0		765	-1.6	0.0	6	dbSNP_96	210	2419,2997		538,1343,827	no	coding-synonymous	OR12D2	NM_013936.3		634,1919,1666	CC,CT,TT		44.664,25.4136,37.7696		255/308	29365241	3187,5251	1511	2708	4219	SO:0001819	synonymous_variant	26529	exon1			TGTTCTTTTCACC		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.765T>C	6.37:g.29365241T>C		Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	280	280	1	NM_013936	B0S862|Q5SUN9|Q6IET9	Silent	SNP	ENST00000383555.2	37	CCDS4659.1																																																																																			T|0.623;C|0.377	0.377	strong		0.458	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
DVL2	1856	hgsc.bcm.edu	37	17	7133162	7133162	+	Silent	SNP	G	G	A	rs222836	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	78	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	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	
ISLR	3671	hgsc.bcm.edu	37	15	74467856	74467856	+	Silent	SNP	G	G	A	rs1052622	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:74467856G>A	ENST00000249842.3	+	2	1014	c.657G>A	c.(655-657)acG>acA	p.T219T	ISLR_ENST00000395118.1_Silent_p.T219T|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	219	LRRCT.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						TCAAGGGTACGCCGCTGAGCC	0.667													G|||	2933	0.585663	0.407	0.7104	5008	,	,		15910	0.5615		0.6988	False		,,,				2504	0.6472				p.T219T		Atlas-SNP	.											ISLR,NS,carcinoma,0,1	ISLR	49	1	0			c.G657A						PASS	.	G	,	2058,2338	542.2+/-376.0	503,1052,643	39.0	36.0	37.0		657,657	-8.4	0.1	15	dbSNP_86	37	5860,2734	654.2+/-401.1	2005,1850,442	no	coding-synonymous,coding-synonymous	ISLR	NM_005545.3,NM_201526.1	,	2508,2902,1085	AA,AG,GG		31.8129,46.8153,39.0454	,	219/429,219/429	74467856	7918,5072	2198	4297	6495	SO:0001819	synonymous_variant	3671	exon2			GGGTACGCCGCTG	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"""Immunoglobulin superfamily / I-set domain containing"""	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.657G>A	15.37:g.74467856G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_201526		Silent	SNP	ENST00000249842.3	37	CCDS10260.1																																																																																			G|0.400;A|0.600	0.600	strong		0.667	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545	
TMEM132D	121256	hgsc.bcm.edu	37	12	129566469	129566469	+	Silent	SNP	C	C	T	rs77363876	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:129566469C>T	ENST00000422113.2	-	7	2084	c.1758G>A	c.(1756-1758)gaG>gaA	p.E586E	TMEM132D_ENST00000389441.4_Silent_p.E124E	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	586					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)		GGCCGGCCGCCTCAGCCACAA	0.647													C|||	372	0.0742812	0.0038	0.2046	5008	,	,		14998	0.1548		0.0209	False		,,,				2504	0.0491				p.E586E		Atlas-SNP	.											TMEM132D,NS,carcinoma,-2,1	TMEM132D	299	1	0			c.G1758A						scavenged	.	C		23,4383	27.2+/-55.0	0,23,2180	39.0	42.0	41.0		1758	0.8	0.3	12	dbSNP_131	41	131,8467	64.2+/-126.4	1,129,4169	no	coding-synonymous	TMEM132D	NM_133448.2		1,152,6349	TT,TC,CC		1.5236,0.522,1.1843		586/1100	129566469	154,12850	2203	4299	6502	SO:0001819	synonymous_variant	121256	exon7			GGCCGCCTCAGCC	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.1758G>A	12.37:g.129566469C>T		Somatic	221	2	0.00904977		WXS	Illumina HiSeq	Phase_I	195	108	0.553846	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																			C|0.970;T|0.030	0.030	strong		0.647	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
PDE8A	5151	hgsc.bcm.edu	37	15	85610349	85610349	+	Silent	SNP	C	C	T	rs35666574	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:85610349C>T	ENST00000310298.4	+	4	600	c.348C>T	c.(346-348)gtC>gtT	p.V116V	PDE8A_ENST00000394553.1_Silent_p.V116V|PDE8A_ENST00000557819.2_3'UTR|PDE8A_ENST00000557957.1_Silent_p.V44V|PDE8A_ENST00000339708.5_Silent_p.V116V			O60658	PDE8A_HUMAN	phosphodiesterase 8A	116					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|phosphorelay signal transduction system (GO:0000160)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	25	Colorectal(223;0.227)		BRCA - Breast invasive adenocarcinoma(143;0.0608)		Caffeine(DB00201)|Ketotifen(DB00920)	CTCAGGCTGTCCTTGCCTGTT	0.448													C|||	64	0.0127796	0.0098	0.0058	5008	,	,		19685	0.0		0.0408	False		,,,				2504	0.0061				p.V116V		Atlas-SNP	.											.	PDE8A	50	.	0			c.C348T						PASS	.	C	,	60,4346	58.1+/-94.6	0,60,2143	164.0	138.0	147.0		348,348	0.2	1.0	15	dbSNP_126	147	280,8318	105.6+/-166.5	7,266,4026	no	coding-synonymous,coding-synonymous	PDE8A	NM_002605.2,NM_173454.1	,	7,326,6169	TT,TC,CC		3.2566,1.3618,2.6146	,	116/830,116/784	85610349	340,12664	2203	4299	6502	SO:0001819	synonymous_variant	5151	exon3			GGCTGTCCTTGCC	AF056490	CCDS10336.1, CCDS10337.1, CCDS58397.1	15q25.3	2008-05-14			ENSG00000073417	ENSG00000073417	3.1.4.17	"""Phosphodiesterases"""	8793	protein-coding gene	gene with protein product		602972				9618252	Standard	NM_001243137		Approved	HsT19550	uc002blh.3	O60658	OTTHUMG00000148670	ENST00000310298.4:c.348C>T	15.37:g.85610349C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	73	62	0.849315	NM_173454	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Silent	SNP	ENST00000310298.4	37	CCDS10336.1																																																																																			C|0.976;T|0.024	0.024	strong		0.448	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605	
FBXO16	157574	hgsc.bcm.edu	37	8	28309958	28309958	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:28309958A>G	ENST00000380254.2	-	6	691	c.543T>C	c.(541-543)gtT>gtC	p.V181V	FBXO16_ENST00000346498.2_Silent_p.V169V|FBXO16_ENST00000517436.1_Intron|FBXO16_ENST00000518734.1_Silent_p.V169V|RP11-181B11.2_ENST00000518819.1_RNA|RP11-181B11.2_ENST00000523935.1_RNA	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	181										large_intestine(2)|ovary(1)	3		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.121)|Kidney(114;0.144)|Colorectal(74;0.249)		TAACTAGTTGAACGTCAGCGA	0.428																																					p.V181V		Atlas-SNP	.											FBXO16_ENST00000380254,lower_third,carcinoma,-2,1	FBXO16	29	1	0			c.T543C						scavenged	.						71.0	75.0	74.0					8																	28309958		2203	4300	6503	SO:0001819	synonymous_variant	157574	exon6			TAGTTGAACGTCA	AF453435	CCDS6068.1, CCDS59099.1	8p21.1	2008-02-05	2004-06-15		ENSG00000214050	ENSG00000214050		"""F-boxes /  ""other"""""	13618	protein-coding gene	gene with protein product		608519	"""F-box only protein 16"""			12243353	Standard	NM_172366		Approved	FBX16	uc003xgu.4	Q8IX29	OTTHUMG00000102147	ENST00000380254.2:c.543T>C	8.37:g.28309958A>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	225	3	0.0133333	NM_172366	Q3T1B2|Q3T1B3|Q3T1B4	Silent	SNP	ENST00000380254.2	37	CCDS6068.1	.	.	.	.	.	.	.	.	.	.	A	0.326	-0.958961	0.02267	.	.	ENSG00000214050	ENST00000518248	.	.	.	5.49	0.443	0.16587	.	.	.	.	.	T	0.50837	0.1639	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	T	0.36553	-0.9743	4	.	.	.	-6.6615	4.9362	0.13941	0.4866:0.2783:0.2351:0.0	.	.	.	.	S	26	.	.	F	-	2	0	FBXO16	28365877	0.948000	0.32251	0.117000	0.21633	0.045000	0.14185	0.154000	0.16343	0.054000	0.16065	0.482000	0.46254	TTC	.	.	none		0.428	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366	
ARHGAP29	9411	hgsc.bcm.edu	37	1	94643531	94643531	+	Silent	SNP	T	T	C	rs1048854	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:94643531T>C	ENST00000260526.6	-	21	2855	c.2673A>G	c.(2671-2673)caA>caG	p.Q891Q	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	891					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)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		CATCTTGTGGTTGTAGGGACC	0.428													T|||	682	0.136182	0.0318	0.2147	5008	,	,		17432	0.002		0.2962	False		,,,				2504	0.1953				p.Q891Q		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.A2673G						PASS	.	T		304,4102	166.9+/-198.0	10,284,1909	138.0	131.0	133.0		2673	3.6	1.0	1	dbSNP_86	133	2275,6325	383.2+/-340.6	324,1627,2349	no	coding-synonymous	ARHGAP29	NM_004815.3		334,1911,4258	CC,CT,TT		26.4535,6.8997,19.8293		891/1262	94643531	2579,10427	2203	4300	6503	SO:0001819	synonymous_variant	9411	exon21			TTGTGGTTGTAGG		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"""Rho GTPase activating proteins"""	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.2673A>G	1.37:g.94643531T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	92	72	0.782609	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Silent	SNP	ENST00000260526.6	37	CCDS748.1																																																																																			T|0.826;C|0.174	0.174	strong		0.428	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815	
RHOBTB3	22836	hgsc.bcm.edu	37	5	95115959	95115959	+	Missense_Mutation	SNP	C	C	T	rs41276257	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:95115959C>T	ENST00000379982.3	+	9	1794	c.1286C>T	c.(1285-1287)aCg>aTg	p.T429M	GLRX_ENST00000508780.1_Intron|RHOBTB3_ENST00000504179.1_Missense_Mutation_p.T60M|GLRX_ENST00000507605.1_5'Flank	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	429	BTB 2. {ECO:0000255|PROSITE- ProRule:PRU00037}.|Interaction with Rab9.				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)		CTTTCAGGTACGACAGTGCCA	0.463													C|||	202	0.0403355	0.0091	0.049	5008	,	,		18769	0.0		0.1153	False		,,,				2504	0.0409				p.T429M		Atlas-SNP	.											RHOBTB3,NS,carcinoma,-1,1	RHOBTB3	43	1	0			c.C1286T						PASS	.	C	MET/THR	102,4304	80.4+/-118.8	2,98,2103	59.0	56.0	57.0		1286	5.2	0.3	5	dbSNP_127	57	821,7779	190.1+/-236.7	49,723,3528	yes	missense	RHOBTB3	NM_014899.3	81	51,821,5631	TT,TC,CC		9.5465,2.315,7.0967	possibly-damaging	429/612	95115959	923,12083	2203	4300	6503	SO:0001583	missense	22836	exon9			CAGGTACGACAGT	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.1286C>T	5.37:g.95115959C>T	ENSP00000369318:p.Thr429Met	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	260	120	0.461538	NM_014899	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	37	CCDS4077.1	102|102	0.046703296703296704|0.046703296703296704	7|7	0.014227642276422764|0.014227642276422764	20|20	0.055248618784530384|0.055248618784530384	0|0	0.0|0.0	75|75	0.09894459102902374|0.09894459102902374	C|C	16.64|16.64	3.179423|3.179423	0.57800|0.57800	0.02315|0.02315	0.095465|0.095465	ENSG00000164292|ENSG00000164292	ENST00000510313|ENST00000379982;ENST00000504179	.|T;T	.|0.68025	.|-0.3;-0.3	5.24|5.24	5.24|5.24	0.73138|0.73138	.|BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	.|0.398328	.|0.29348	.|N	.|0.012408	.|T	.|0.04679	.|0.0127	L|L	0.45352|0.45352	1.415|1.415	0.24529|0.24529	P|P	0.99412356|0.99412356	.|D	.|0.58970	.|0.984	.|P	.|0.51833	.|0.681	.|T	.|0.51379	.|-0.8713	.|9	.|0.49607	.|T	.|0.09	-4.4503|-4.4503	12.2008|12.2008	0.54323|0.54323	0.0:0.9207:0.0:0.0793|0.0:0.9207:0.0:0.0793	rs41276257;rs61749616|rs41276257;rs61749616	.|429	.|O94955	.|RHBT3_HUMAN	X|M	11|429;60	.|ENSP00000369318:T429M;ENSP00000422360:T60M	.|ENSP00000369318:T429M	R|T	+|+	1|2	2|0	RHOBTB3|RHOBTB3	95141715|95141715	0.288000|0.288000	0.24324|0.24324	0.251000|0.251000	0.24312|0.24312	0.243000|0.243000	0.25628|0.25628	3.640000|3.640000	0.54350|0.54350	2.597000|2.597000	0.87782|0.87782	0.655000|0.655000	0.94253|0.94253	CGA|ACG	C|0.934;T|0.066	0.066	strong		0.463	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
TSHZ3	57616	hgsc.bcm.edu	37	19	31768416	31768416	+	Silent	SNP	A	A	G	rs3745784	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:31768416A>G	ENST00000240587.4	-	2	2610	c.2283T>C	c.(2281-2283)gcT>gcC	p.A761A		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	761					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					TGGCCACAGCAGCCTTCTCCG	0.592													G|||	1558	0.311102	0.5923	0.2637	5008	,	,		15913	0.249		0.1133	False		,,,				2504	0.2321				p.A761A		Atlas-SNP	.											.	TSHZ3	549	.	0			c.T2283C						PASS	.	G		2295,2111	570.4+/-382.8	610,1075,518	63.0	64.0	64.0		2283	-8.5	0.7	19	dbSNP_107	64	1147,7453	759.6+/-407.6	79,989,3232	no	coding-synonymous	TSHZ3	NM_020856.2		689,2064,3750	GG,GA,AA		13.3372,47.9119,26.4647		761/1082	31768416	3442,9564	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CACAGCAGCCTTC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2283T>C	19.37:g.31768416A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	56	0.421053	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			A|0.717;G|0.283	0.283	strong		0.592	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
CNGB1	1258	hgsc.bcm.edu	37	16	57937788	57937788	+	Missense_Mutation	SNP	T	T	C	rs2303785	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57937788T>C	ENST00000251102.8	-	27	2792	c.2732A>G	c.(2731-2733)aAg>aGg	p.K911R	CNGB1_ENST00000564448.1_Missense_Mutation_p.K905R	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	911			K -> R (in dbSNP:rs2303785).		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						CTGCACGGACTTGGGGATCTT	0.587													T|||	386	0.0770767	0.0091	0.1441	5008	,	,		20179	0.0843		0.1203	False		,,,				2504	0.0695				p.K911R	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.A2732G						PASS	.	T	ARG/LYS	123,4069		0,123,1973	125.0	135.0	131.0		2732	1.5	1.0	16	dbSNP_100	131	922,7488		43,836,3326	yes	missense	CNGB1	NM_001297.4	26	43,959,5299	CC,CT,TT		10.9631,2.9342,8.2923	benign	911/1252	57937788	1045,11557	2096	4205	6301	SO:0001583	missense	1258	exon27			ACGGACTTGGGGA	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.2732A>G	16.37:g.57937788T>C	ENSP00000251102:p.Lys911Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	174	145	0.833333	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	195	0.08928571428571429	2	0.0040650406504065045	50	0.13812154696132597	50	0.08741258741258741	93	0.12269129287598944	T	6.169	0.399308	0.11696	0.029342	0.109631	ENSG00000070729	ENST00000251102	D	0.96774	-4.12	4.82	1.45	0.22620	Cyclic nucleotide-binding-like (1);	0.194559	0.43579	N	0.000550	T	0.07954	0.0199	L	0.46157	1.445	0.09310	P	0.9999999887751	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.62101	-0.6925	9	0.07325	T	0.83	.	5.705	0.17903	0.0:0.6616:0.1562:0.1822	rs2303785;rs17240987;rs56435449;rs59336536;rs2303785	283;911	Q14028-2;Q14028	.;CNGB1_HUMAN	R	911	ENSP00000251102:K911R	ENSP00000251102:K911R	K	-	2	0	CNGB1	56495289	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	-0.330000	0.07925	0.389000	0.25086	0.460000	0.39030	AAG	T|0.922;C|0.078	0.078	strong		0.587	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
ZNF607	84775	hgsc.bcm.edu	37	19	38189555	38189555	+	Missense_Mutation	SNP	T	T	C	rs61910733	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38189555T>C	ENST00000355202.4	-	5	2072	c.1477A>G	c.(1477-1479)Act>Gct	p.T493A	ZNF607_ENST00000395835.3_Missense_Mutation_p.T492A|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	493					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)			CGATGTATAGTGAGTTTATGG	0.393													T|||	25	0.00499201	0.0	0.0115	5008	,	,		21521	0.0		0.0119	False		,,,				2504	0.0051				p.T493A		Atlas-SNP	.											ZNF607,bladder,carcinoma,+1,1	ZNF607	82	1	0			c.A1477G						PASS	.	T	ALA/THR,ALA/THR	9,4397	16.8+/-37.8	0,9,2194	103.0	100.0	101.0		1474,1477	1.3	0.0	19	dbSNP_129	101	123,8477	64.2+/-126.4	0,123,4177	yes	missense,missense	ZNF607	NM_001172677.1,NM_032689.4	58,58	0,132,6371	CC,CT,TT		1.4302,0.2043,1.0149	possibly-damaging,possibly-damaging	492/696,493/697	38189555	132,12874	2203	4300	6503	SO:0001583	missense	84775	exon5			GTATAGTGAGTTT	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.1477A>G	19.37:g.38189555T>C	ENSP00000347338:p.Thr493Ala	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	T	0.022	-1.408887	0.01155	0.002043	0.014302	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.35421	1.31;1.31	2.38	1.34	0.21922	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13970	0.0338	N	0.25380	0.74	0.09310	N	1	B;B	0.28350	0.0;0.208	B;B	0.29663	0.001;0.105	T	0.22173	-1.0224	9	0.12103	T	0.63	.	3.5898	0.07985	0.0:0.4651:0.0:0.5349	.	493;492	Q96SK3;F5H141	ZN607_HUMAN;.	A	493;492	ENSP00000347338:T493A;ENSP00000438015:T492A	ENSP00000347338:T493A	T	-	1	0	ZNF607	42881395	0.000000	0.05858	0.008000	0.14137	0.966000	0.64601	-0.066000	0.11598	1.086000	0.41228	0.459000	0.35465	ACT	T|0.992;C|0.008	0.008	strong		0.393	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689	
MYOT	9499	hgsc.bcm.edu	37	5	137221770	137221770	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:137221770A>G	ENST00000239926.4	+	8	1432	c.1058A>G	c.(1057-1059)tAc>tGc	p.Y353C	MYOT_ENST00000509812.1_3'UTR|RP11-381K20.2_ENST00000508281.2_RNA|MYOT_ENST00000515645.1_Missense_Mutation_p.Y238C|MYOT_ENST00000421631.2_Missense_Mutation_p.Y169C|RP11-381K20.2_ENST00000514616.1_RNA	NM_006790.2	NP_006781	Q9UBF9	MYOTI_HUMAN	myotilin	353	Ig-like C2-type 2.|Necessary for interaction with ACTA1.|Necessary for interaction with FLNC.				muscle contraction (GO:0006936)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	structural constituent of muscle (GO:0008307)			cervix(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			ATGTTTATCTACAAACCACAG	0.303																																					p.Y353C		Atlas-SNP	.											MYOT,NS,carcinoma,-1,1	MYOT	50	1	0			c.A1058G						scavenged	.						58.0	64.0	62.0					5																	137221770		2203	4300	6503	SO:0001583	missense	9499	exon8			TTATCTACAAACC	AF133820	CCDS4194.1, CCDS47268.1, CCDS75309.1	5q31.2	2014-09-17	2005-09-07	2005-09-07	ENSG00000120729	ENSG00000120729		"""Immunoglobulin superfamily / I-set domain containing"""	12399	protein-coding gene	gene with protein product		604103	"""titin immunoglobulin domain protein (myotilin)"", ""limb-girdle muscular dystrophy 1A (autosomal dominant)"""	TTID, LGMD1A, LGMD1		10486214, 10369880	Standard	NM_006790		Approved		uc003lbv.3	Q9UBF9	OTTHUMG00000129154	ENST00000239926.4:c.1058A>G	5.37:g.137221770A>G	ENSP00000239926:p.Tyr353Cys	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	175	2	0.0114286	NM_006790	A0A4R6|B4DT79	Missense_Mutation	SNP	ENST00000239926.4	37	CCDS4194.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.315795	0.60524	.	.	ENSG00000120729	ENST00000239926;ENST00000421631;ENST00000515645	T;T;T	0.66815	-0.23;-0.23;-0.23	5.1	-3.07	0.05363	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.814724	0.10978	N	0.613057	T	0.54983	0.1892	L	0.39898	1.24	0.25734	N	0.985234	P	0.46327	0.876	B	0.44085	0.44	T	0.53337	-0.8453	10	0.66056	D	0.02	.	7.6241	0.28202	0.3697:0.0:0.0726:0.5577	.	353	Q9UBF9	MYOTI_HUMAN	C	353;169;238	ENSP00000239926:Y353C;ENSP00000391185:Y169C;ENSP00000426281:Y238C	ENSP00000239926:Y353C	Y	+	2	0	MYOT	137249669	0.997000	0.39634	0.986000	0.45419	0.995000	0.86356	1.259000	0.32956	-0.273000	0.09246	0.482000	0.46254	TAC	.	.	none		0.303	MYOT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251219.2	NM_006790	
PSME4	23198	hgsc.bcm.edu	37	2	54133744	54133744	+	Silent	SNP	T	T	C	rs805316	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:54133744T>C	ENST00000404125.1	-	26	2989	c.2934A>G	c.(2932-2934)tcA>tcG	p.S978S	PSME4_ENST00000421748.2_Silent_p.S122S	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	978					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)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|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)|spermatogenesis, exchange of chromosomal proteins (GO:0035093)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)|spermatoproteasome complex (GO:1990111)	lysine-acetylated histone binding (GO:0070577)|peptidase activator activity (GO:0016504)	p.S864S(1)		breast(5)|endometrium(8)|kidney(1)|large_intestine(11)|lung(26)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(2)	60			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			CCTGACTGTATGAACTTGTAG	0.363													T|||	1071	0.213858	0.1082	0.2205	5008	,	,		18843	0.1558		0.2664	False		,,,				2504	0.3579				p.S978S		Atlas-SNP	.											PSME4,NS,carcinoma,0,1	PSME4	247	1	1	Substitution - coding silent(1)	stomach(1)	c.A2934G						scavenged	.	T		581,3825	258.6+/-262.5	38,505,1660	165.0	163.0	164.0		2934	-3.0	1.0	2	dbSNP_86	164	2403,6197	399.1+/-346.3	332,1739,2229	no	coding-synonymous	PSME4	NM_014614.2		370,2244,3889	CC,CT,TT		27.9419,13.1866,22.9433		978/1844	54133744	2984,10022	2203	4300	6503	SO:0001819	synonymous_variant	23198	exon26			ACTGTATGAACTT	D38521	CCDS33197.2	2p16.1	2003-04-14			ENSG00000068878	ENSG00000068878		"""Proteasome (prosome, macropain) subunits"""	20635	protein-coding gene	gene with protein product		607705				7584044, 12093752	Standard	NM_014614		Approved	PA200, KIAA0077	uc002rxp.2	Q14997	OTTHUMG00000151852	ENST00000404125.1:c.2934A>G	2.37:g.54133744T>C		Somatic	195	2	0.0102564		WXS	Illumina HiSeq	Phase_I	207	89	0.429952	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			T|0.784;C|0.216	0.216	strong		0.363	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158	
PLCB3	5331	hgsc.bcm.edu	37	11	64026685	64026685	+	Silent	SNP	C	C	T	rs28395882	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:64026685C>T	ENST00000540288.1	+	13	1597	c.1494C>T	c.(1492-1494)tcC>tcT	p.S498S	PLCB3_ENST00000279230.6_Silent_p.S498S|PLCB3_ENST00000325234.5_Silent_p.S431S	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	498					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						GCGAGAGCTCCGCGGCCACCG	0.706													C|||	865	0.172724	0.0234	0.147	5008	,	,		12937	0.1339		0.3012	False		,,,				2504	0.3006				p.S498S		Atlas-SNP	.											PLCB3,NS,carcinoma,0,1	PLCB3	103	1	0			c.C1494T						PASS	.	C	,	242,4066		8,226,1920	9.0	11.0	11.0		1494,1293	-9.8	0.0	11	dbSNP_126	11	2553,5907		423,1707,2100	no	coding-synonymous,coding-synonymous	PLCB3	NM_000932.2,NM_001184883.1	,	431,1933,4020	TT,TC,CC		30.1773,5.6175,21.8907	,	498/1235,431/1168	64026685	2795,9973	2154	4230	6384	SO:0001819	synonymous_variant	5331	exon13			GAGCTCCGCGGCC	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.1494C>T	11.37:g.64026685C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																			C|0.817;T|0.183	0.183	strong		0.706	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
PRDM7	11105	hgsc.bcm.edu	37	16	90130136	90130136	+	Missense_Mutation	SNP	C	C	T	rs2078478	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	307	0	0		WXS	Illumina HiSeq	Phase_I	270	26	0.0962963	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		
VWDE	221806	hgsc.bcm.edu	37	7	12376811	12376811	+	Missense_Mutation	SNP	A	A	C	rs2192828	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:12376811A>C	ENST00000275358.3	-	25	4642	c.4454T>G	c.(4453-4455)tTc>tGc	p.F1485C		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1485	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.		F -> C (in dbSNP:rs2192828). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						ACTTTTTTGGAATCTCCTACC	0.393													C|||	3497	0.698283	0.9448	0.7017	5008	,	,		20755	0.6151		0.5885	False		,,,				2504	0.5613				p.F1485C		Atlas-SNP	.											.	VWDE	123	.	0			c.T4454G						PASS	.	C	CYS/PHE	1222,162		539,144,9	198.0	156.0	169.0		4454	4.9	1.0	7	dbSNP_96	169	1802,1380		514,774,303	yes	missense	VWDE	NM_001135924.1	205	1053,918,312	CC,CA,AA		43.369,11.7052,33.7714	benign	1485/1591	12376811	3024,1542	692	1591	2283	SO:0001583	missense	221806	exon25			TTTTGGAATCTCC		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.4454T>G	7.37:g.12376811A>C	ENSP00000275358:p.Phe1485Cys	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	231	125	0.541126	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	1539	0.7046703296703297	464	0.943089430894309	254	0.7016574585635359	371	0.6486013986013986	450	0.5936675461741425	C	6.674	0.492883	0.12702	0.882948	0.56631	ENSG00000146530	ENST00000275358;ENST00000536307	T	0.57907	0.37	4.86	4.86	0.63082	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00000	-4.73	0.37090	P	0.10061900000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.50608	-0.8808	9	0.02654	T	1	.	14.8064	0.69959	0.1453:0.8546:0.0:0.0	rs2192828;rs10382186;rs17670328;rs52819048;rs2192828	1485	Q8N2E2	VWDE_HUMAN	C	1485;939	ENSP00000275358:F1485C	ENSP00000275358:F1485C	F	-	2	0	VWDE	12343336	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.640000	0.67875	1.281000	0.44480	-0.127000	0.14921	TTC	A|0.306;C|0.694	0.694	strong		0.393	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
ANKEF1	63926	hgsc.bcm.edu	37	20	10030452	10030452	+	Missense_Mutation	SNP	G	G	A	rs524625	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:10030452G>A	ENST00000378380.3	+	6	1564	c.1235G>A	c.(1234-1236)gGa>gAa	p.G412E	ANKEF1_ENST00000488991.1_3'UTR|SNAP25-AS1_ENST00000603542.1_RNA|SNAP25-AS1_ENST00000421143.2_RNA|ANKEF1_ENST00000378392.1_Missense_Mutation_p.G412E	NM_198798.1	NP_942093.1	Q9NU02	ANKE1_HUMAN	ankyrin repeat and EF-hand domain containing 1	412			G -> E (in dbSNP:rs524625).				calcium ion binding (GO:0005509)										GGATCGTATGGACCTAAGAAA	0.413													G|||	980	0.195687	0.2799	0.1556	5008	,	,		19334	0.0069		0.2604	False		,,,				2504	0.2382				p.G412E		Atlas-SNP	.											.	.	.	.	0			c.G1235A						PASS	.	G	GLU/GLY,GLU/GLY	1155,3247		155,845,1201	45.0	53.0	50.0		1235,1235	5.9	1.0	20	dbSNP_83	50	2224,6370		292,1640,2365	yes	missense,missense	ANKRD5	NM_022096.4,NM_198798.1	98,98	447,2485,3566	AA,AG,GG		25.8785,26.2381,26.0003	probably-damaging,probably-damaging	412/777,412/777	10030452	3379,9617	2201	4297	6498	SO:0001583	missense	63926	exon6			CGTATGGACCTAA	AK025322	CCDS13108.1	20p12.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000132623	ENSG00000132623		"""EF-hand domain containing"", ""Ankyrin repeat domain containing"""	15803	protein-coding gene	gene with protein product			"""ankyrin repeat domain 5"""	ANKRD5		17142250	Standard	NM_022096		Approved	FLJ21669, dJ839B4.6	uc002wnp.3	Q9NU02	OTTHUMG00000031860	ENST00000378380.3:c.1235G>A	20.37:g.10030452G>A	ENSP00000367631:p.Gly412Glu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_198798	B3KUQ0|Q9H6Y9	Missense_Mutation	SNP	ENST00000378380.3	37	CCDS13108.1	387	0.1771978021978022	122	0.24796747967479674	65	0.17955801104972377	5	0.008741258741258742	195	0.25725593667546176	G	12.66	2.005879	0.35415	0.262381	0.258785	ENSG00000132623	ENST00000378392;ENST00000378380	T;T	0.64991	-0.13;-0.13	5.86	5.86	0.93980	Ankyrin repeat-containing domain (1);	0.194693	0.53938	D	0.000057	T	0.00039	0.0001	L	0.52011	1.625	0.09310	P	0.999999164682	D	0.89917	1.0	D	0.71414	0.973	T	0.00294	-1.1840	9	0.26408	T	0.33	-20.6073	20.5632	0.99335	0.0:0.0:1.0:0.0	rs524625;rs52809150;rs58343015;rs524625	412	Q9NU02	ANKR5_HUMAN	E	412	ENSP00000367644:G412E;ENSP00000367631:G412E	ENSP00000367631:G412E	G	+	2	0	ANKRD5	9978452	0.997000	0.39634	0.995000	0.50966	0.044000	0.14063	1.841000	0.39240	2.937000	0.99478	0.650000	0.86243	GGA	G|0.769;A|0.231	0.231	strong		0.413	ANKEF1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077968.2	NM_022096	
HMOX2	3163	hgsc.bcm.edu	37	16	4556911	4556911	+	Silent	SNP	G	G	A	rs25685	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4556911G>A	ENST00000570646.1	+	3	707	c.102G>A	c.(100-102)tcG>tcA	p.S34S	HMOX2_ENST00000219700.6_Silent_p.S34S|HMOX2_ENST00000398595.3_Silent_p.S34S|HMOX2_ENST00000406590.2_Silent_p.S34S|HMOX2_ENST00000575120.1_Silent_p.S5S|HMOX2_ENST00000414777.1_Silent_p.S34S|HMOX2_ENST00000458134.3_Silent_p.S34S	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	34					cellular iron ion homeostasis (GO:0006879)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|porphyrin-containing compound metabolic process (GO:0006778)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	8						CTGACCTCTCGGAGCTCCTGA	0.493											OREG0023582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	411	0.0820687	0.2103	0.1081	5008	,	,		19674	0.003		0.0457	False		,,,				2504	0.0092				p.S34S		Atlas-SNP	.											.	HMOX2	22	.	0			c.G102A						PASS	.	G	,,,	718,3676	297.3+/-284.7	54,610,1533	142.0	151.0	148.0		102,102,102,102	-8.3	0.9	16	dbSNP_72	148	315,8285	111.4+/-171.7	3,309,3988	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HMOX2	NM_001127204.1,NM_001127205.1,NM_001127206.1,NM_002134.3	,,,	57,919,5521	AA,AG,GG		3.6628,16.3405,7.9498	,,,	34/317,34/317,34/317,34/317	4556911	1033,11961	2197	4300	6497	SO:0001819	synonymous_variant	3163	exon3			CCTCTCGGAGCTC		CCDS10517.1, CCDS66931.1, CCDS73818.1	16p13.3	2008-02-05			ENSG00000103415	ENSG00000103415	1.14.99.3		5014	protein-coding gene	gene with protein product		141251				1575508	Standard	NM_002134		Approved	HO-2	uc002cwq.4	P30519	OTTHUMG00000129473	ENST00000570646.1:c.102G>A	16.37:g.4556911G>A		Somatic	117	0	0	619	WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_001127205	A8MT35|D3DUD5|I3L430|O60605	Silent	SNP	ENST00000570646.1	37	CCDS10517.1																																																																																			G|0.921;A|0.079	0.079	strong		0.493	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2		
C15orf59	388135	hgsc.bcm.edu	37	15	74032783	74032783	+	Silent	SNP	A	A	G	rs28594180	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:74032783A>G	ENST00000569673.1	-	3	1561	c.357T>C	c.(355-357)tcT>tcC	p.S119S	C15orf59_ENST00000558834.1_5'UTR|C15orf59_ENST00000379822.4_Silent_p.S119S			Q2T9L4	CO059_HUMAN	chromosome 15 open reading frame 59	119										breast(1)|endometrium(2)|large_intestine(2)|lung(6)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CCGAGGGGGTAGAGACGTCCA	0.642													A|||	2244	0.448083	0.2761	0.4669	5008	,	,		17151	0.5853		0.4056	False		,,,				2504	0.5695				p.S119S		Atlas-SNP	.											C15orf59,NS,carcinoma,0,1	C15orf59	38	1	0			c.T357C						PASS	.	A		1346,3050	435.1+/-344.2	218,910,1070	82.0	85.0	84.0		357	-3.5	0.7	15	dbSNP_125	84	3473,5119	490.6+/-372.9	712,2049,1535	no	coding-synonymous	C15orf59	NM_001039614.1		930,2959,2605	GG,GA,AA		40.4213,30.6187,37.1035		119/294	74032783	4819,8169	2198	4296	6494	SO:0001819	synonymous_variant	388135	exon2			GGGGGTAGAGACG		CCDS32289.1	15q24.1	2012-09-27			ENSG00000205363	ENSG00000205363			33753	protein-coding gene	gene with protein product							Standard	XM_005254369		Approved	MGC131524, LOC388135	uc002avy.3	Q2T9L4	OTTHUMG00000172556	ENST00000569673.1:c.357T>C	15.37:g.74032783A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	44	43	0.977273	NM_001039614		Silent	SNP	ENST00000569673.1	37	CCDS32289.1																																																																																			A|0.610;G|0.390;T|0.000	0.390	strong		0.642	C15orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419077.2	NM_001039614	
PPL	5493	hgsc.bcm.edu	37	16	4933907	4933907	+	Silent	SNP	T	T	C	rs17137389	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4933907T>C	ENST00000345988.2	-	22	4838	c.4749A>G	c.(4747-4749)caA>caG	p.Q1583Q	PPL_ENST00000590782.2_Silent_p.Q1581Q	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1583					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						TGATTTCCGATTGGAGCCTTC	0.532													T|||	351	0.0700879	0.1604	0.036	5008	,	,		19681	0.006		0.0775	False		,,,				2504	0.0307				p.Q1583Q		Atlas-SNP	.											.	PPL	168	.	0			c.A4749G						PASS	.	T		668,3726	281.9+/-276.2	42,584,1571	120.0	119.0	119.0		4749	-3.7	0.7	16	dbSNP_123	119	665,7935	167.1+/-218.9	29,607,3664	no	coding-synonymous	PPL	NM_002705.4		71,1191,5235	CC,CT,TT		7.7326,15.2025,10.2586		1583/1757	4933907	1333,11661	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			TTCCGATTGGAGC	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.4749A>G	16.37:g.4933907T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	164	90	0.548781	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			T|0.902;C|0.098	0.098	strong		0.532	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
ATXN3	4287	hgsc.bcm.edu	37	14	92537387	92537387	+	Missense_Mutation	SNP	T	T	G	rs12896588|rs141993435		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:92537387T>G	ENST00000532032.1	-	10	892	c.883A>C	c.(883-885)Aag>Cag	p.K295Q	ATXN3_ENST00000503767.1_Missense_Mutation_p.K280Q|ATXN3_ENST00000545170.1_Missense_Mutation_p.K304Q|ATXN3_ENST00000429774.2_Missense_Mutation_p.K288Q|ATXN3_ENST00000393287.5_Missense_Mutation_p.K295Q|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000340660.6_Missense_Mutation_p.K240Q|ATXN3_ENST00000502250.1_Missense_Mutation_p.K116Q			P54252	ATX3_HUMAN	ataxin 3	295	Poly-Gln.				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)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		tgttgctgcttttgctgctgT	0.413																																					p.K295Q	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											.	ATXN3	46	.	0			c.A883C						PASS	.																																			SO:0001583	missense	4287	exon10			GCTGCTTTTGCTG	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.883A>C	14.37:g.92537387T>G	ENSP00000437157:p.Lys295Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37		173	0.07921245421245421	65	0.13211382113821138	33	0.09116022099447514	30	0.05244755244755245	45	0.059366754617414245	T	0.020	-1.441768	0.01098	.	.	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	0.52057	1.3;1.3;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68;0.68	4.91	3.01	0.34805	.	0.480369	0.23780	N	0.044638	T	0.00210	0.0006	.	.	.	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.10450	0.003;0.001;0.005;0.005;0.001	T	0.15009	-1.0452	9	0.02654	T	1	.	7.7843	0.29083	0.0:0.1935:0.6301:0.1764	rs12896588	295;280;306;240;295	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	Q	311;308;306;304;304;303;300;288;309;295;116;280;240;295;225;116;294;197;244;189	ENSP00000445618:K304Q;ENSP00000389376:K288Q;ENSP00000376965:K295Q;ENSP00000425322:K116Q;ENSP00000426697:K280Q;ENSP00000339110:K240Q;ENSP00000437157:K295Q;ENSP00000451001:K225Q;ENSP00000450642:K116Q;ENSP00000451385:K294Q;ENSP00000451417:K197Q;ENSP00000451996:K244Q;ENSP00000450641:K189Q	ENSP00000339110:K240Q	K	-	1	0	ATXN3	91607140	0.125000	0.22332	0.997000	0.53966	0.114000	0.19823	-0.495000	0.06443	0.464000	0.27142	-1.018000	0.02450	AAG	T|0.921;G|0.079	0.079	strong		0.413	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
HMHA1	23526	hgsc.bcm.edu	37	19	1079959	1079959	+	Missense_Mutation	SNP	G	G	A	rs36084354	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1079959G>A	ENST00000313093.2	+	13	1776	c.1545G>A	c.(1543-1545)atG>atA	p.M515I	HMHA1_ENST00000590577.1_Missense_Mutation_p.M150I|HMHA1_ENST00000586866.1_Missense_Mutation_p.M519I|HMHA1_ENST00000590214.1_Missense_Mutation_p.M542I|HMHA1_ENST00000539243.2_Missense_Mutation_p.M531I|HMHA1_ENST00000543365.1_Missense_Mutation_p.M398I|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	109	0	0		WXS	Illumina HiSeq	Phase_I	86	52	0.604651	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		
ZNF781	163115	hgsc.bcm.edu	37	19	38160565	38160565	+	Missense_Mutation	SNP	C	C	T	rs113316386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38160565C>T	ENST00000590008.1	-	5	1337	c.485G>A	c.(484-486)aGc>aAc	p.S162N	ZNF781_ENST00000358582.4_Missense_Mutation_p.S162N|ZNF781_ENST00000593040.1_5'Flank|ZFP30_ENST00000586732.1_Intron			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	162					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)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						TTCTCTGATGCTGAATAAGAG	0.378													C|||	48	0.00958466	0.0008	0.0144	5008	,	,		21916	0.0		0.0358	False		,,,				2504	0.001				p.S162N		Atlas-SNP	.											.	ZNF781	66	.	0			c.G485A						PASS	.	C	ASN/SER	37,4369	41.6+/-74.8	0,37,2166	109.0	107.0	108.0		485	-2.0	0.0	19	dbSNP_132	108	299,8301	109.2+/-169.8	5,289,4006	yes	missense	ZNF781	NM_152605.3	46	5,326,6172	TT,TC,CC		3.4767,0.8398,2.5834	benign	162/328	38160565	336,12670	2203	4300	6503	SO:0001583	missense	163115	exon4			CTGATGCTGAATA	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"""Zinc fingers, C2H2-type"""	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.485G>A	19.37:g.38160565C>T	ENSP00000466370:p.Ser162Asn	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_152605	Q2VPJ8	Missense_Mutation	SNP	ENST00000590008.1	37	CCDS12507.1	36	0.016483516483516484	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	27	0.03562005277044855	C	0.010	-1.792237	0.00623	0.008398	0.034767	ENSG00000196381	ENST00000358582;ENST00000545586	T	0.07021	3.23	1.74	-1.98	0.07480	.	.	.	.	.	T	0.00580	0.0019	N	0.01809	-0.71	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43909	-0.9362	9	0.30078	T	0.28	10.144	3.4274	0.07416	0.0:0.3161:0.2144:0.4694	.	162	Q8N8C0	ZN781_HUMAN	N	162	ENSP00000351391:S162N	ENSP00000351391:S162N	S	-	2	0	ZNF781	42852405	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-5.038000	0.00157	-0.482000	0.06782	-0.474000	0.04947	AGC	C|0.977;T|0.023	0.023	strong		0.378	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605	
USP53	54532	hgsc.bcm.edu	37	4	120181724	120181724	+	Silent	SNP	A	A	G	rs35372126	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:120181724A>G	ENST00000274030.6	+	11	1917	c.738A>G	c.(736-738)acA>acG	p.T246T	USP53_ENST00000450251.1_Silent_p.T246T	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											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						AGATTGTTACAATTGGTTTAG	0.353													A|||	1190	0.23762	0.0666	0.3372	5008	,	,		15472	0.2629		0.2724	False		,,,				2504	0.3364				p.T246T		Atlas-SNP	.											.	USP53	69	.	0			c.A738G						PASS	.	A		347,3325		17,313,1506	144.0	132.0	136.0		738	-0.9	1.0	4	dbSNP_126	136	2141,6027		293,1555,2236	no	coding-synonymous	USP53	NM_019050.2		310,1868,3742	GG,GA,AA		26.212,9.4499,21.0135		246/1074	120181724	2488,9352	1836	4084	5920	SO:0001819	synonymous_variant	54532	exon10			TGTTACAATTGGT	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.738A>G	4.37:g.120181724A>G		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	123	30	0.243902	NM_019050		Silent	SNP	ENST00000274030.6	37	CCDS43265.1																																																																																			A|0.753;G|0.247	0.247	strong		0.353	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
UGT1A1	54658	hgsc.bcm.edu	37	2	234526871	234526871	+	Missense_Mutation	SNP	C	C	G	rs1042597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:234526871C>G	ENST00000373450.4	+	1	581	c.518C>G	c.(517-519)gCt>gGt	p.A173G		NM_019076.4	NP_061949.3	P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	176					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	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)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	AGGGGAATAGCTTGCCACTAT	0.473													-|||	1282	0.25599	0.0325	0.2954	5008	,	,		17737	0.506		0.2495	False		,,,				2504	0.2791				p.A173G		Atlas-SNP	.											.	UGT1A8	69	.	0			c.C518G						PASS	.	C	GLY/ALA	345,4061	178.0+/-206.8	12,321,1870	182.0	183.0	183.0		518	-0.2	0.0	2	dbSNP_86	183	2127,6473	367.0+/-334.5	269,1589,2442	no	missense	UGT1A8	NM_019076.4	60	281,1910,4312	GG,GC,CC		24.7326,7.8302,19.0066		173/531	234526871	2472,10534	2203	4300	6503	SO:0001583	missense	54576	exon1			GAATAGCTTGCCA	M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"""UDP glucuronosyltransferases"""	12530	other	complex locus constituent		191740	"""UDP glycosyltransferase 1 family, polypeptide A1"""	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000373450.4:c.518C>G	2.37:g.234526871C>G	ENSP00000362549:p.Ala173Gly	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	185	97	0.524324	NM_019076	A6NJC3|B8K286	Missense_Mutation	SNP	ENST00000373450.4	37	CCDS33402.1	625	0.28617216117216115	23	0.046747967479674794	110	0.30386740331491713	292	0.5104895104895105	200	0.2638522427440633	C	2.320	-0.355915	0.05138	0.078302	0.247326	ENSG00000242366	ENST00000373450	T	0.66460	-0.21	3.96	-0.18	0.13295	.	.	.	.	.	T	0.00012	0.0000	N	0.04373	-0.215	0.80722	P	0.0	B;B	0.20368	0.044;0.044	B;B	0.30495	0.116;0.116	T	0.45234	-0.9275	8	0.51188	T	0.08	.	6.5183	0.22260	0.0:0.4965:0.1616:0.3419	rs1042597;rs2071043;rs13387262;rs17862843;rs56696602	173;173	Q5DSZ6;Q9HAW9	.;UD18_HUMAN	G	173	ENSP00000362549:A173G	ENSP00000362549:A173G	A	+	2	0	UGT1A8	234191610	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.056000	0.14256	-0.052000	0.13311	-1.422000	0.01108	GCT	C|0.755;G|0.245	0.245	strong		0.473	UGT1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130994.1		
MUC16	94025	hgsc.bcm.edu	37	19	9074265	9074265	+	Missense_Mutation	SNP	G	G	A	rs10406209	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9074265G>A	ENST00000397910.4	-	3	13384	c.13181C>T	c.(13180-13182)aCt>aTt	p.T4394I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4396	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						TGCAGCTCCAGTAGGACCTGT	0.468													G|||	768	0.153355	0.1142	0.183	5008	,	,		23652	0.0089		0.2634	False		,,,				2504	0.2209				p.T4394I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C13181T						PASS	.	G	ILE/THR	502,3590		32,438,1576	145.0	141.0	142.0		13181	0.5	0.0	19	dbSNP_119	142	2429,5961		370,1689,2136	yes	missense	MUC16	NM_024690.2	89	402,2127,3712	AA,AG,GG		28.9511,12.2678,23.4818	possibly-damaging	4394/14508	9074265	2931,9551	2046	4195	6241	SO:0001583	missense	94025	exon3			GCTCCAGTAGGAC	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.13181C>T	19.37:g.9074265G>A	ENSP00000381008:p.Thr4394Ile	Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	372	187	0.502688	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	334	0.15293040293040294	53	0.10772357723577236	73	0.20165745856353592	5	0.008741258741258742	203	0.2678100263852243	g	3.708	-0.060188	0.07317	0.122678	0.289511	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.67	0.509	0.16977	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	P	0.46020	0.871	B	0.34346	0.18	T	0.52170	-0.8611	8	0.87932	D	0	.	5.6254	0.17480	0.0:0.3493:0.6507:0.0	rs10406209;rs17515888;rs52837265;rs59614183;rs10406209	4394	B5ME49	.	I	4394	ENSP00000381008:T4394I	ENSP00000381008:T4394I	T	-	2	0	MUC16	8935265	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	0.366000	0.20365	0.231000	0.21079	0.305000	0.20034	ACT	G|0.826;A|0.174	0.174	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TMC5	79838	hgsc.bcm.edu	37	16	19451987	19451987	+	Silent	SNP	C	C	T	rs148052684	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:19451987C>T	ENST00000396229.2	+	3	1376	c.627C>T	c.(625-627)ggC>ggT	p.G209G	TMC5_ENST00000542583.2_Silent_p.G209G|TMC5_ENST00000381414.4_Silent_p.G209G|TMC5_ENST00000541464.1_Silent_p.G209G	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	209					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						ATTATCCAGGCGCTGACATTC	0.463													C|||	26	0.00519169	0.0015	0.0101	5008	,	,		20856	0.0		0.0159	False		,,,				2504	0.001				p.G209G		Atlas-SNP	.											.	TMC5	169	.	0			c.C627T						PASS	.	C	,	9,3985		0,9,1988	70.0	69.0	70.0		627,627	-3.4	0.8	16	dbSNP_134	70	131,8235		2,127,4054	no	coding-synonymous,coding-synonymous	TMC5	NM_001105248.1,NM_001105249.1	,	2,136,6042	TT,TC,CC		1.5659,0.2253,1.1327	,	209/1007,209/949	19451987	140,12220	1997	4183	6180	SO:0001819	synonymous_variant	79838	exon3			TCCAGGCGCTGAC	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.627C>T	16.37:g.19451987C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Silent	SNP	ENST00000396229.2	37	CCDS45431.1																																																																																			C|0.992;T|0.008	0.008	strong		0.463	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	
MUC17	140453	hgsc.bcm.edu	37	7	100678988	100678988	+	Missense_Mutation	SNP	G	G	A	rs71286276		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678988G>A	ENST00000306151.4	+	3	4355	c.4291G>A	c.(4291-4293)Gct>Act	p.A1431T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1431	59 X approximate tandem repeats.|Ser-rich.				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)	p.A1431T(1)		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)					GACCACTTCTGCTGAAGCCAC	0.488																																					p.A1431T		Atlas-SNP	.											MUC17,NS,carcinoma,0,2	MUC17	804	2	1	Substitution - Missense(1)	kidney(1)	c.G4291A						scavenged	.						207.0	222.0	217.0					7																	100678988		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTTCTGCTGAAG	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.4291G>A	7.37:g.100678988G>A	ENSP00000302716:p.Ala1431Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	205	12	0.0585366	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	3.722	-0.057377	0.07317	.	.	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.982	-0.425	0.12317	.	.	.	.	.	T	0.01558	0.0050	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48779	-0.9005	9	0.02654	T	1	.	4.4511	0.11621	0.488:0.0:0.512:0.0	.	1431	Q685J3	MUC17_HUMAN	T	1431	ENSP00000302716:A1431T	ENSP00000302716:A1431T	A	+	1	0	MUC17	100465708	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-2.968000	0.00669	-0.790000	0.04492	-1.616000	0.00795	GCT	.	.	none		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PRR32	100130613	hgsc.bcm.edu	37	X	125954753	125954753	+	Silent	SNP	C	C	T	rs41309538		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:125954753C>T	ENST00000371125.3	+	2	212	c.132C>T	c.(130-132)gaC>gaT	p.D44D		NM_001122716.1	NP_001116188.1	B1ATL7	PRR32_HUMAN		44																	CAGAGGATGACGCAGAGCCCT	0.547													C|||	195	0.0516556	0.0189	0.0216	3775	,	,		13679	0.0248		0.0487	False		,,,				2504	0.0828				p.D44D		Atlas-SNP	.											.	.	.	.	0			c.C132T						PASS	.	C		32,1177		1,23,7,493,168	86.0	68.0	73.0		132	-2.3	0.0	X	dbSNP_127	73	164,2227		4,93,63,703,728	no	coding-synonymous	CXorf64	NM_001122716.1		5,116,70,1196,896	TT,TC,T,CC,C		6.8591,2.6468,5.4444		44/299	125954753	196,3404	692	1591	2283	SO:0001819	synonymous_variant	100130613	exon2			GGATGACGCAGAG																												ENST00000371125.3:c.132C>T	X.37:g.125954753C>T		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	136	132	0.970588	NM_001122716		Silent	SNP	ENST00000371125.3	37	CCDS48163.1																																																																																			C|0.953;T|0.047	0.047	strong		0.547	CXorf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058188.1		
SYNJ2	8871	hgsc.bcm.edu	37	6	158502527	158502527	+	Silent	SNP	C	C	T	rs1744177	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000367122.2_Silent_p.D950D|SYNJ2_ENST00000367121.3_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	172	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	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		
TXNDC16	57544	hgsc.bcm.edu	37	14	52937255	52937255	+	Missense_Mutation	SNP	C	C	T	rs7155490	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:52937255C>T	ENST00000281741.4	-	15	1827	c.1456G>A	c.(1456-1458)Gaa>Aaa	p.E486K	TXNDC16_ENST00000554399.1_Intron	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	486	Thioredoxin.		E -> K (in dbSNP:rs7155490). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(3)|skin(1)	21	Breast(41;0.0716)					AGGAGATCTTCGGTTCCTAAC	0.348													C|||	1105	0.220647	0.1989	0.2363	5008	,	,		16669	0.3125		0.168	False		,,,				2504	0.1984				p.E486K		Atlas-SNP	.											.	TXNDC16	59	.	0			c.G1456A						PASS	.	C	LYS/GLU,LYS/GLU	918,3488	349.8+/-310.5	93,732,1378	77.0	78.0	77.0		1441,1456	2.2	1.0	14	dbSNP_116	77	1415,7185	272.6+/-290.2	117,1181,3002	yes	missense,missense	TXNDC16	NM_001160047.1,NM_020784.2	56,56	210,1913,4380	TT,TC,CC		16.4535,20.8352,17.9379	benign,benign	481/821,486/826	52937255	2333,10673	2203	4300	6503	SO:0001583	missense	57544	exon15			GATCTTCGGTTCC	AB037765	CCDS32083.1	14q22.1	2007-08-16	2007-08-16	2007-08-16		ENSG00000087301			19965	protein-coding gene	gene with protein product			"""KIAA1344"""	KIAA1344			Standard	NM_020784		Approved		uc001wzs.3	Q9P2K2		ENST00000281741.4:c.1456G>A	14.37:g.52937255C>T	ENSP00000281741:p.Glu486Lys	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	197	69	0.350254	NM_020784	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Missense_Mutation	SNP	ENST00000281741.4	37	CCDS32083.1	490	0.22435897435897437	108	0.21951219512195122	81	0.22375690607734808	169	0.29545454545454547	132	0.1741424802110818	C	4.653	0.121429	0.08881	0.208352	0.164535	ENSG00000087301	ENST00000281741	T	0.44881	0.91	5.03	2.16	0.27623	Thioredoxin domain (1);Thioredoxin-like fold (2);	0.215706	0.47093	N	0.000247	T	0.00012	0.0000	L	0.31120	0.905	0.37658	P	0.07732899999999998	B;B	0.29766	0.256;0.165	B;B	0.25291	0.059;0.024	T	0.41070	-0.9529	9	0.16420	T	0.52	-23.5327	10.616	0.45451	0.0:0.749:0.0:0.251	rs7155490;rs17350947;rs52793553;rs60140637;rs7155490	481;486	B7ZME4;Q9P2K2	.;TXD16_HUMAN	K	486	ENSP00000281741:E486K	ENSP00000281741:E486K	E	-	1	0	TXNDC16	52007005	0.775000	0.28604	0.964000	0.40570	0.063000	0.16089	1.241000	0.32743	-0.007000	0.14345	-1.119000	0.02030	GAA	C|0.787;N|0.000	.	strong		0.348	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580941	140580941	+	Missense_Mutation	SNP	G	G	A	rs138686663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140580941G>A	ENST00000354757.3	+	1	1594	c.1594G>A	c.(1594-1596)Ggc>Agc	p.G532S	PCDHB11_ENST00000536699.1_Missense_Mutation_p.G167S	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	532	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)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.G532S(2)		NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTCCGCGTGGGCGCCACAGA	0.677																																					p.G532S		Atlas-SNP	.											PCDHB11,NS,carcinoma,0,3	PCDHB11	162	3	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G1594A						PASS	.						51.0	67.0	62.0					5																	140580941		2202	4300	6502	SO:0001583	missense	56125	exon1			CGCGTGGGCGCCA	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1594G>A	5.37:g.140580941G>A	ENSP00000346802:p.Gly532Ser	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	204	46	0.22549	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	g	11.84	1.758724	0.31137	.	.	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.01647	4.71;4.71	2.51	-5.02	0.02982	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.01695	0.0054	N	0.11845	0.185	0.09310	N	0.999999	B	0.26081	0.141	B	0.40375	0.327	T	0.50056	-0.8872	9	0.34782	T	0.22	.	8.9541	0.35807	0.3349:0.5322:0.1329:0.0	.	532	Q9Y5F2	PCDBB_HUMAN	S	167;532	ENSP00000440344:G167S;ENSP00000346802:G532S	ENSP00000346802:G532S	G	+	1	0	PCDHB11	140561125	0.000000	0.05858	0.010000	0.14722	0.109000	0.19521	-4.241000	0.00268	-1.731000	0.01360	0.298000	0.19748	GGC	G|0.970;A|0.030	0.030	strong		0.677	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
KCNQ4	9132	hgsc.bcm.edu	37	1	41296828	41296828	+	Missense_Mutation	SNP	T	T	G	rs34287852	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	311	2	0.00643087		WXS	Illumina HiSeq	Phase_I	205	138	0.673171	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	
FARSA	2193	hgsc.bcm.edu	37	19	13035006	13035006	+	Silent	SNP	G	G	A	rs1045913	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13035006G>A	ENST00000314606.4	-	12	1365	c.1347C>T	c.(1345-1347)ccC>ccT	p.P449P	FARSA_ENST00000588025.1_Silent_p.P489P|FARSA_ENST00000423140.2_Silent_p.P418P	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	449					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	20					L-Phenylalanine(DB00120)	ACACGTTCTCGGGAAGCCCCA	0.597													G|||	401	0.0800719	0.0053	0.1542	5008	,	,		17317	0.0962		0.0944	False		,,,				2504	0.0971				p.P449P		Atlas-SNP	.											.	FARSA	46	.	0			c.C1347T						PASS	.	G		116,4290	86.8+/-125.4	2,112,2089	80.0	83.0	82.0		1347	-10.2	0.3	19	dbSNP_86	82	960,7640	210.3+/-251.2	55,850,3395	no	coding-synonymous	FARSA	NM_004461.2		57,962,5484	AA,AG,GG		11.1628,2.6328,8.2731		449/509	13035006	1076,11930	2203	4300	6503	SO:0001819	synonymous_variant	2193	exon12			GTTCTCGGGAAGC	U07424	CCDS12287.1	19p13.2	2014-05-06	2007-02-23	2007-02-23	ENSG00000179115	ENSG00000179115	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	3592	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, alpha, cytoplasmic"""	602918	"""phenylalanine-tRNA synthetase-like"", ""phenylalanyl-tRNA synthetase-like, alpha subunit"""	FARSL, FARSLA		9177188	Standard	NM_004461		Approved	CML33	uc002mvs.2	Q9Y285	OTTHUMG00000180569	ENST00000314606.4:c.1347C>T	19.37:g.13035006G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	32	23	0.71875	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Silent	SNP	ENST00000314606.4	37	CCDS12287.1																																																																																			G|0.920;A|0.080	0.080	strong		0.597	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461	
CCDC51	79714	hgsc.bcm.edu	37	3	48474249	48474249	+	Silent	SNP	A	A	G	rs2279077	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48474249A>G	ENST00000395694.2	-	4	890	c.805T>C	c.(805-807)Ttg>Ctg	p.L269L	CCDC51_ENST00000447018.1_Silent_p.L160L|CCDC51_ENST00000412398.2_Silent_p.L160L|PLXNB1_ENST00000448774.2_5'Flank|CCDC51_ENST00000442740.1_Silent_p.L160L|PLXNB1_ENST00000296440.6_5'Flank|CCDC51_ENST00000395696.1_Silent_p.L269L	NM_001256964.1	NP_001243893.1	Q96ER9	CCD51_HUMAN	coiled-coil domain containing 51	269						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				endometrium(4)|kidney(4)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		AGGCCCCTCAAGTCCACCATG	0.607													A|||	1602	0.319888	0.2413	0.2882	5008	,	,		19801	0.3135		0.4632	False		,,,				2504	0.3078				p.L269L		Atlas-SNP	.											.	CCDC51	34	.	0			c.T805C						PASS	.	A		1061,2881		145,771,1055	70.0	74.0	73.0		805	2.3	1.0	3	dbSNP_100	73	3858,4428		901,2056,1186	no	coding-synonymous	CCDC51	NM_024661.3		1046,2827,2241	GG,GA,AA		46.5605,26.9153,40.2273		269/412	48474249	4919,7309	1971	4143	6114	SO:0001819	synonymous_variant	79714	exon4			CCCTCAAGTCCAC	AK022498	CCDS2766.2, CCDS58830.1	3p21.31	2005-12-30			ENSG00000164051	ENSG00000164051			25714	protein-coding gene	gene with protein product						12477932	Standard	NM_001256964		Approved	FLJ12436	uc003ctc.3	Q96ER9	OTTHUMG00000133534	ENST00000395694.2:c.805T>C	3.37:g.48474249A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_024661	Q9HA01	Silent	SNP	ENST00000395694.2	37	CCDS2766.2																																																																																			A|0.636;G|0.364	0.364	strong		0.607	CCDC51-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344599.2	NM_024661	
VAMP1	6843	hgsc.bcm.edu	37	12	6575044	6575044	+	Silent	SNP	G	G	T	rs2072375	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6575044G>T	ENST00000396308.3	-	3	397	c.252C>A	c.(250-252)gcC>gcA	p.A84A	VAMP1_ENST00000400911.3_Silent_p.A84A|VAMP1_ENST00000544432.1_5'UTR|TAPBPL_ENST00000545700.1_3'UTR|VAMP1_ENST00000361716.3_Silent_p.A84A|VAMP1_ENST00000535180.1_Silent_p.A84A	NM_014231.3|NM_199245.1	NP_055046.1|NP_954740.1	P23763	VAMP1_HUMAN	vesicle-associated membrane protein 1 (synaptobrevin 1)	84	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				neurotransmitter secretion (GO:0007269)|SNARE complex assembly (GO:0035493)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|mitochondrial outer membrane (GO:0005741)|neuron projection (GO:0043005)|synapse (GO:0045202)				endometrium(1)|large_intestine(1)|prostate(1)	3					Botulinum Toxin Type B(DB00042)	TCTTTAGCTTGGCAGCACTGC	0.512											OREG0021627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1364	0.272364	0.2095	0.1859	5008	,	,		18976	0.3284		0.3241	False		,,,				2504	0.3078				p.A84A		Atlas-SNP	.											.	VAMP1	6	.	0			c.C252A						PASS	.	T	,,	886,3520	742.2+/-411.3	89,708,1406	134.0	114.0	121.0		252,252,252	1.7	1.0	12	dbSNP_96	121	2759,5841	679.6+/-403.6	450,1859,1991	no	coding-synonymous,coding-synonymous,coding-synonymous	VAMP1	NM_014231.3,NM_016830.2,NM_199245.1	,,	539,2567,3397	TT,TG,GG		32.0814,20.1089,28.0255	,,	84/119,84/117,84/118	6575044	3645,9361	2203	4300	6503	SO:0001819	synonymous_variant	6843	exon3			TAGCTTGGCAGCA		CCDS31731.1, CCDS41740.1, CCDS44809.1, CCDS73422.1	12p	2013-02-13			ENSG00000139190	ENSG00000139190		"""Vesicle-associated membrane proteins"""	12642	protein-coding gene	gene with protein product		185880		SYB1		1976629	Standard	XM_006719011		Approved	VAMP-1	uc001qok.3	P23763	OTTHUMG00000168269	ENST00000396308.3:c.252C>A	12.37:g.6575044G>T		Somatic	140	0	0	635	WXS	Illumina HiSeq	Phase_I	124	69	0.556452	NM_014231	A8MVP3|D3DUR3|O75468|Q15857|Q6FG94|Q8IVC9	Silent	SNP	ENST00000396308.3	37	CCDS41740.1																																																																																			G|0.728;T|0.272	0.272	strong		0.512	VAMP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399078.1		
KANK2	25959	hgsc.bcm.edu	37	19	11305161	11305161	+	Silent	SNP	A	A	G	rs754529	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11305161A>G	ENST00000586659.1	-	3	341	c.27T>C	c.(25-27)gcT>gcC	p.A9A	KANK2_ENST00000589359.1_Silent_p.A9A|KANK2_ENST00000432929.2_Silent_p.A9A|KANK2_ENST00000589894.1_Silent_p.A9A|KANK2_ENST00000355150.5_Silent_p.A9A			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	9	Interaction with AIFM1.				apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CTGGGAAGGGAGCAGGCACGT	0.632													G|||	258	0.0515176	0.0499	0.1066	5008	,	,		15242	0.0129		0.0706	False		,,,				2504	0.0348				p.A9A		Atlas-SNP	.											.	KANK2	47	.	0			c.T27C						PASS	.	G	,	252,4154	800.1+/-415.6	5,242,1956	73.0	60.0	64.0		27,27	-0.2	1.0	19	dbSNP_86	64	719,7881	784.9+/-407.6	28,663,3609	no	coding-synonymous,coding-synonymous	KANK2	NM_001136191.2,NM_015493.6	,	33,905,5565	GG,GA,AA		8.3605,5.7195,7.4658	,	9/852,9/860	11305161	971,12035	2203	4300	6503	SO:0001819	synonymous_variant	25959	exon1			GAAGGGAGCAGGC	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.27T>C	19.37:g.11305161A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Silent	SNP	ENST00000586659.1	37	CCDS12255.1																																																																																			A|0.932;G|0.068	0.068	strong		0.632	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
SLC29A3	55315	hgsc.bcm.edu	37	10	73082563	73082563	+	Missense_Mutation	SNP	A	A	G	rs2277257	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:73082563A>G	ENST00000373189.5	+	2	104	c.52A>G	c.(52-54)Aga>Gga	p.R18G	snoU13_ENST00000459444.1_RNA	NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	18			R -> G (in dbSNP:rs2277257). {ECO:0000269|PubMed:12975309}.		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						CTCCACCTACAGAACCACAAG	0.587													A|||	2350	0.469249	0.7005	0.3444	5008	,	,		19962	0.3601		0.4006	False		,,,				2504	0.4284				p.R18G	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											.	SLC29A3	51	.	0			c.A52G						PASS	.	A	GLY/ARG,GLY/ARG	2802,1604	663.8+/-401.3	894,1014,295	128.0	129.0	129.0		52,52	1.2	0.4	10	dbSNP_100	129	3537,5063	515.4+/-378.6	725,2087,1488	yes	missense,missense	SLC29A3	NM_001174098.1,NM_018344.5	125,125	1619,3101,1783	GG,GA,AA		41.1279,36.4049,48.739	possibly-damaging,possibly-damaging	18/259,18/476	73082563	6339,6667	2203	4300	6503	SO:0001583	missense	55315	exon2			ACCTACAGAACCA	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.52A>G	10.37:g.73082563A>G	ENSP00000362285:p.Arg18Gly	Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	104	77	0.740385	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Missense_Mutation	SNP	ENST00000373189.5	37	CCDS7310.1	983	0.4500915750915751	334	0.6788617886178862	132	0.36464088397790057	219	0.38286713286713286	298	0.39313984168865435	A	6.233	0.411183	0.11812	0.635951	0.411279	ENSG00000198246	ENST00000373189	T	0.68331	-0.32	5.15	1.21	0.21127	.	0.644976	0.15117	N	0.279597	T	0.00012	0.0000	M	0.63428	1.95	0.26705	P	0.971088	B	0.06786	0.001	B	0.06405	0.002	T	0.41627	-0.9498	9	0.39692	T	0.17	-3.3134	7.3753	0.26825	0.5473:0.3726:0.0801:0.0	rs2277257;rs17629116;rs52808361;rs56776781;rs2277257	18	Q9BZD2	S29A3_HUMAN	G	18	ENSP00000362285:R18G	ENSP00000362285:R18G	R	+	1	2	SLC29A3	72752569	0.324000	0.24652	0.394000	0.26270	0.007000	0.05969	0.728000	0.26013	0.363000	0.24346	-0.321000	0.08615	AGA	A|0.527;G|0.473	0.473	strong		0.587	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344	
COL6A3	1293	hgsc.bcm.edu	37	2	238277573	238277573	+	Silent	SNP	C	C	A	rs2645774	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238277573C>A	ENST00000295550.4	-	10	4985	c.4533G>T	c.(4531-4533)ggG>ggT	p.G1511G	COL6A3_ENST00000472056.1_Silent_p.G904G|COL6A3_ENST00000353578.4_Silent_p.G1305G|COL6A3_ENST00000347401.3_Silent_p.G1310G|COL6A3_ENST00000346358.4_Silent_p.G1311G|COL6A3_ENST00000409809.1_Silent_p.G1305G	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1511	Nonhelical region.|VWFA 8. {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)		TCAGTGGGGACCCCCCTCTGA	0.562													C|||	1330	0.265575	0.295	0.3084	5008	,	,		18618	0.256		0.2177	False		,,,				2504	0.2546				p.G1511G		Atlas-SNP	.											.	COL6A3	608	.	0			c.G4533T						PASS	.	C	,,	1224,3182	421.5+/-339.4	163,898,1142	47.0	48.0	48.0		4533,2712,3915	-5.6	0.0	2	dbSNP_100	48	1824,6776	321.3+/-315.0	208,1408,2684	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	371,2306,3826	AA,AC,CC		21.2093,27.7803,23.4353	,,	1511/3178,904/2571,1305/2972	238277573	3048,9958	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon10			TGGGGACCCCCCT	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.4533G>T	2.37:g.238277573C>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.757;A|0.243	0.243	strong		0.562	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
NUP160	23279	hgsc.bcm.edu	37	11	47833936	47833936	+	Silent	SNP	C	C	T	rs61756071	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47833936C>T	ENST00000378460.2	-	16	2044	c.1998G>A	c.(1996-1998)agG>agA	p.R666R	NUP160_ENST00000530326.1_Silent_p.R552R|NUP160_ENST00000528501.1_Silent_p.R230R|NUP160_ENST00000528071.1_Silent_p.R552R|NUP160_ENST00000531016.1_5'Flank	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	666					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)|protein transport (GO:0015031)|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 pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						GGATTGGGTTCCTAATCTCTT	0.363													C|||	45	0.00898562	0.0023	0.0014	5008	,	,		20408	0.0238		0.0119	False		,,,				2504	0.0051				p.R666R		Atlas-SNP	.											.	NUP160	116	.	0			c.G1998A						PASS	.	C		19,4383	28.1+/-56.4	0,19,2182	164.0	155.0	158.0		1998	-0.1	1.0	11	dbSNP_129	158	143,8453	70.7+/-133.2	1,141,4156	no	coding-synonymous	NUP160	NM_015231.1		1,160,6338	TT,TC,CC		1.6636,0.4316,1.2463		666/1437	47833936	162,12836	2201	4298	6499	SO:0001819	synonymous_variant	23279	exon16			TGGGTTCCTAATC	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"""nucleoporin 160kD"""			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.1998G>A	11.37:g.47833936C>T		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	216	97	0.449074	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Silent	SNP	ENST00000378460.2	37	CCDS31484.1																																																																																			C|0.989;T|0.011	0.011	strong		0.363	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231	
EEF1B2	1933	hgsc.bcm.edu	37	2	207025366	207025366	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:207025366G>A	ENST00000392222.2	+	2	510	c.135G>A	c.(133-135)ccG>ccA	p.P45P	NDUFS1_ENST00000432169.1_5'Flank|NDUFS1_ENST00000423725.1_5'Flank|SNORA41_ENST00000384675.1_RNA|NDUFS1_ENST00000455934.2_5'Flank|NDUFS1_ENST00000233190.6_5'Flank|EEF1B2_ENST00000392221.1_Silent_p.P45P|NDUFS1_ENST00000440274.1_5'Flank|NDUFS1_ENST00000457011.1_5'Flank|SNORD51_ENST00000384320.2_RNA|NDUFS1_ENST00000449699.1_5'Flank|EEF1B2_ENST00000236957.5_Silent_p.P45P	NM_001959.3	NP_001950.1	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta 2	45	GST C-terminal.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)	translation elongation factor activity (GO:0003746)	p.P45P(5)		breast(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(6)	16						CCAGCCCACCGCCTGCCGACT	0.448																																					p.P45P		Atlas-SNP	.											EEF1B2,NS,carcinoma,0,19	EEF1B2	58	19	5	Substitution - coding silent(5)	kidney(2)|endometrium(2)|lung(1)	c.G135A						scavenged	.						109.0	99.0	102.0					2																	207025366		2203	4300	6503	SO:0001819	synonymous_variant	1933	exon3			CCCACCGCCTGCC	X60489	CCDS2367.1	2q33.3	2011-04-28			ENSG00000114942	ENSG00000114942			3208	protein-coding gene	gene with protein product		600655				8250921	Standard	NM_001959		Approved		uc002vbf.1	P24534	OTTHUMG00000132891	ENST00000392222.2:c.135G>A	2.37:g.207025366G>A		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	165	3	0.0181818	NM_021121	A8K795|Q6IBH9	Silent	SNP	ENST00000392222.2	37	CCDS2367.1																																																																																			.	.	none		0.448	EEF1B2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336436.1	NM_001037663	
OR4N2	390429	hgsc.bcm.edu	37	14	20295763	20295763	+	Silent	SNP	C	C	T	rs11621854	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20295763C>T	ENST00000315947.1	+	1	156	c.156C>T	c.(154-156)gaC>gaT	p.D52D	OR4N2_ENST00000568211.1_Silent_p.D52D	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, 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)			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)		TAAAGTCAGACCCTGGGCTCA	0.463																																					p.D52D		Atlas-SNP	.											.	OR4N2	125	.	0			c.C156T						PASS	.	C		1466,2940		210,1046,947	182.0	219.0	206.0		156	-0.9	0.9	14	dbSNP_120	206	1721,6879		148,1425,2727	no	coding-synonymous	OR4N2	NM_001004723.1		358,2471,3674	TT,TC,CC		20.0116,33.2728,24.5041		52/308	20295763	3187,9819	2203	4300	6503	SO:0001819	synonymous_variant	390429	exon1			GTCAGACCCTGGG		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.156C>T	14.37:g.20295763C>T		Somatic	663	0	0		WXS	Illumina HiSeq	Phase_I	316	186	0.588608	NM_001004723	Q6IEY9|Q6IFA2	Silent	SNP	ENST00000315947.1	37	CCDS32022.1																																																																																			C|0.764;T|0.236	0.236	strong		0.463	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
KCNK6	9424	hgsc.bcm.edu	37	19	38817486	38817486	+	Silent	SNP	T	T	C	rs3745951	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38817486T>C	ENST00000263372.3	+	2	683	c.576T>C	c.(574-576)ttT>ttC	p.F192F		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	192					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	CTGTGATCTTTGCCCACCTCG	0.652													C|||	896	0.178914	0.0673	0.2507	5008	,	,		16393	0.1518		0.2217	False		,,,				2504	0.2628				p.F192F		Atlas-SNP	.											.	KCNK6	37	.	0			c.T576C						PASS	.	C		389,4017	791.1+/-415.1	28,333,1842	144.0	138.0	140.0		576	-3.4	0.0	19	dbSNP_107	140	1603,6997	742.8+/-407.2	149,1305,2846	no	coding-synonymous	KCNK6	NM_004823.1		177,1638,4688	CC,CT,TT		18.6395,8.8289,15.316		192/314	38817486	1992,11014	2203	4300	6503	SO:0001819	synonymous_variant	9424	exon2			GATCTTTGCCCAC	AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.576T>C	19.37:g.38817486T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_004823	Q9HB47	Silent	SNP	ENST00000263372.3	37	CCDS12513.1																																																																																			T|0.836;C|0.164	0.164	strong		0.652	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823	
SPEF2	79925	hgsc.bcm.edu	37	5	35641582	35641582	+	Missense_Mutation	SNP	A	A	C	rs6897513	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:35641582A>C	ENST00000356031.3	+	3	365	c.211A>C	c.(211-213)Aac>Cac	p.N71H	SPEF2_ENST00000509059.1_Missense_Mutation_p.N71H|SPEF2_ENST00000282469.6_Missense_Mutation_p.N71H|SPEF2_ENST00000440995.2_Missense_Mutation_p.N71H	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	71	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.		N -> H (in dbSNP:rs6897513). {ECO:0000269|PubMed:15489334}.		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)			GCCAACACTTAACCTTCTGGG	0.383													C|||	3401	0.679113	0.7194	0.6873	5008	,	,		17171	0.7401		0.5278	False		,,,				2504	0.7117				p.N71H		Atlas-SNP	.											.	SPEF2	324	.	0			c.A211C						PASS	.	C	HIS/ASN,HIS/ASN	3041,1365	453.0+/-350.2	1032,977,194	89.0	90.0	90.0		211,211	5.9	1.0	5	dbSNP_116	90	4707,3893	544.2+/-384.5	1257,2193,850	yes	missense,missense	SPEF2	NM_024867.3,NM_144722.3	68,68	2289,3170,1044	CC,CA,AA		45.2674,30.9805,40.4275	benign,benign	71/1823,71/515	35641582	7748,5258	2203	4300	6503	SO:0001583	missense	79925	exon3			ACACTTAACCTTC	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.211A>C	5.37:g.35641582A>C	ENSP00000348314:p.Asn71His	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	1448	0.663003663003663	375	0.7621951219512195	245	0.6767955801104972	421	0.736013986013986	407	0.5369393139841688	C	9.414	1.081246	0.20309	0.690195	0.547326	ENSG00000152582	ENST00000282469;ENST00000356031;ENST00000509059;ENST00000510777;ENST00000440995	T;T;T;T;T	0.23552	1.9;1.9;1.9;1.9;1.9	5.93	5.93	0.95920	Calponin homology domain (1);	0.317648	0.33834	N	0.004513	T	0.00012	0.0000	N	0.00210	-1.845	0.09310	P	1.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.41484	-0.9506	9	0.02654	T	1	.	16.7419	0.85461	0.1305:0.8695:0.0:0.0	rs6897513;rs17267978;rs57065583;rs6897513	71;71;71	D6REZ4;Q9C093;Q9C093-3	.;SPEF2_HUMAN;.	H	71	ENSP00000282469:N71H;ENSP00000348314:N71H;ENSP00000421593:N71H;ENSP00000426259:N71H;ENSP00000412125:N71H	ENSP00000282469:N71H	N	+	1	0	SPEF2	35677339	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.407000	0.44565	1.534000	0.49203	-0.121000	0.15023	AAC	A|0.372;C|0.621	0.621	strong		0.383	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
KIAA0408	9729	hgsc.bcm.edu	37	6	127768762	127768762	+	Silent	SNP	G	G	A	rs6902288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:127768762G>A	ENST00000483725.3	-	5	1038	c.702C>T	c.(700-702)aaC>aaT	p.N234N	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	234										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)		GATTCTTCCTGTTTTTCTGTT	0.368													A|||	2071	0.413538	0.5787	0.415	5008	,	,		18533	0.0655		0.5606	False		,,,				2504	0.3967				p.N234N		Atlas-SNP	.											.	KIAA0408	61	.	0			c.C702T						PASS	.	A	,	2548,1858	534.4+/-373.9	724,1100,379	55.0	54.0	54.0		,702	-5.0	0.0	6	dbSNP_116	54	5115,3485	499.2+/-374.9	1515,2085,700	no	utr-3,coding-synonymous	KIAA0408,C6orf174	NM_001012279.2,NM_014702.4	,	2239,3185,1079	AA,AG,GG		40.5233,42.1698,41.081	,	,234/695	127768762	7663,5343	2203	4300	6503	SO:0001819	synonymous_variant	9729	exon5			CTTCCTGTTTTTC	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.702C>T	6.37:g.127768762G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_014702	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Silent	SNP	ENST00000483725.3	37	CCDS34531.1																																																																																			G|0.483;A|0.517	0.517	strong		0.368	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702	
CPAMD8	27151	hgsc.bcm.edu	37	19	17100550	17100550	+	Missense_Mutation	SNP	A	A	T	rs61744414	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17100550A>T	ENST00000443236.1	-	13	1470	c.1439T>A	c.(1438-1440)gTg>gAg	p.V480E	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	433						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						CTGAGCCCCCACAGGCTTCCC	0.602													A|||	51	0.0101837	0.0008	0.0086	5008	,	,		16513	0.0		0.0179	False		,,,				2504	0.0266				p.V480E		Atlas-SNP	.											.	CPAMD8	192	.	0			c.T1439A						PASS	.	A	GLU/VAL	13,3901		0,13,1944	32.0	42.0	39.0		1439	-1.4	0.4	19	dbSNP_129	39	162,8114		1,160,3977	no	missense	CPAMD8	NM_015692.2	121	1,173,5921	TT,TA,AA		1.9575,0.3321,1.4356	possibly-damaging	480/1933	17100550	175,12015	1957	4138	6095	SO:0001583	missense	27151	exon13			GCCCCCACAGGCT	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.1439T>A	19.37:g.17100550A>T	ENSP00000402505:p.Val480Glu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	18|18	0.008241758241758242|0.008241758241758242	0|0	0.0|0.0	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	13|13	0.017150395778364115|0.017150395778364115	A|A	4.384|4.384	0.070842|0.070842	0.08436|0.08436	0.003321|0.003321	0.019575|0.019575	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	2.87|2.87	-1.4|-1.4	0.08968|0.08968	.|.	0.467573|.	0.18364|.	U|.	0.143477|.	T|T	0.14184|0.14184	0.0343|0.0343	N|N	0.19112|0.19112	0.55|0.55	0.29616|0.29616	N|N	0.846543|0.846543	P|.	0.38922|.	0.651|.	B|.	0.32805|.	0.153|.	T|T	0.30794|0.30794	-0.9966|-0.9966	9|5	0.39692|.	T|.	0.17|.	.|.	8.9973|8.9973	0.36061|0.36061	0.2239:0.0:0.7761:0.0|0.2239:0.0:0.7761:0.0	rs61744414|rs61744414	433|.	Q8IZJ3|.	CPMD8_HUMAN|.	E|R	480|491	.|.	ENSP00000291440:V480E|.	V|W	-|-	2|1	0|0	CPAMD8|CPAMD8	16961550|16961550	0.936000|0.936000	0.31750|0.31750	0.360000|0.360000	0.25837|0.25837	0.007000|0.007000	0.05969|0.05969	3.004000|3.004000	0.49513|0.49513	-0.173000|-0.173000	0.10761|0.10761	-0.451000|-0.451000	0.05528|0.05528	GTG|TGG	A|0.967;T|0.033	0.033	strong		0.602	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
SPATA3	130560	hgsc.bcm.edu	37	2	231861056	231861056	+	Silent	SNP	A	A	C	rs72362780		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231861056A>C	ENST00000452881.1	+	1	216	c.108A>C	c.(106-108)acA>acC	p.T36T	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000433428.2_Silent_p.T36T|SPATA3_ENST00000424440.1_Silent_p.T36T|SPATA3_ENST00000455816.1_Silent_p.T36T			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	36										endometrium(2)|lung(1)	3						CTGAATCCACACCACAGCAGC	0.577																																					p.T36T		Atlas-SNP	.											SPATA3,rectum,carcinoma,0,1	SPATA3	52	1	0			c.A108C						scavenged	.						133.0	139.0	137.0					2																	231861056		692	1591	2283	SO:0001819	synonymous_variant	130560	exon1			ATCCACACCACAG	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.108A>C	2.37:g.231861056A>C		Somatic	157	6	0.0382166		WXS	Illumina HiSeq	Phase_I	84	13	0.154762	NM_139073	Q86WX5|Q8N9Y6	Silent	SNP	ENST00000452881.1	37	CCDS2481.1																																																																																			.	.	none		0.577	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
TBK1	29110	hgsc.bcm.edu	37	12	64849716	64849716	+	Silent	SNP	T	T	C	rs41292019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:64849716T>C	ENST00000331710.5	+	2	405	c.66T>C	c.(64-66)aaT>aaC	p.N22N		NM_013254.3	NP_037386.1	Q9UHD2	TBK1_HUMAN	TANK-binding kinase 1	22	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|dendritic cell proliferation (GO:0044565)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of gene expression (GO:0010629)|negative regulation of type I interferon production (GO:0032480)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|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 peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to virus (GO:0009615)|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)|type I interferon production (GO:0032606)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)	ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)|phosphoprotein binding (GO:0051219)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)	20				GBM - Glioblastoma multiforme(28;0.0386)		CTACTGCAAATGTCTTTCGTG	0.378													T|||	60	0.0119808	0.0015	0.0115	5008	,	,		19971	0.0		0.0318	False		,,,				2504	0.0184				p.N22N		Atlas-SNP	.											.	TBK1	149	.	0			c.T66C						PASS	.	T		44,4362	47.5+/-82.1	0,44,2159	84.0	79.0	81.0		66	5.0	1.0	12	dbSNP_127	81	410,8190	128.8+/-187.0	12,386,3902	no	coding-synonymous	TBK1	NM_013254.3		12,430,6061	CC,CT,TT		4.7674,0.9986,3.4907		22/730	64849716	454,12552	2203	4300	6503	SO:0001819	synonymous_variant	29110	exon2			TGCAAATGTCTTT	AF191838	CCDS8968.1	12q14.2	2006-06-10			ENSG00000183735	ENSG00000183735			11584	protein-coding gene	gene with protein product		604834				10581243, 10783893	Standard	NM_013254		Approved	NAK	uc001ssc.2	Q9UHD2	OTTHUMG00000168796	ENST00000331710.5:c.66T>C	12.37:g.64849716T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	151	64	0.423841	NM_013254	A8K4S4|Q8IYV3|Q9NUJ5	Silent	SNP	ENST00000331710.5	37	CCDS8968.1																																																																																			T|0.970;C|0.030	0.030	strong		0.378	TBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401130.1	NM_013254	
CSMD3	114788	hgsc.bcm.edu	37	8	114186003	114186003	+	Missense_Mutation	SNP	T	T	C	rs2219898	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:114186003T>C	ENST00000297405.5	-	4	901	c.657A>G	c.(655-657)atA>atG	p.I219M	CSMD3_ENST00000343508.3_Missense_Mutation_p.I179M|CSMD3_ENST00000352409.3_Missense_Mutation_p.I219M|CSMD3_ENST00000455883.2_Missense_Mutation_p.I219M|CSMD3_ENST00000519485.1_5'UTR	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	219	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> M (in dbSNP:rs2219898). {ECO:0000269|PubMed:12943675}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTGAATTGGCTATGCAGGTGA	0.428										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			T|||	2334	0.466054	0.4365	0.611	5008	,	,		17045	0.6766		0.2674	False		,,,				2504	0.3906				p.I219M		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A657G						PASS	.	T	MET/ILE,MET/ILE,MET/ILE	1761,2645	524.6+/-371.4	368,1025,810	134.0	125.0	128.0		657,657,537	1.1	1.0	8	dbSNP_96	128	2303,6297	387.9+/-342.4	309,1685,2306	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	10,10,10	677,2710,3116	CC,CT,TT		26.7791,39.9682,31.2471	possibly-damaging,possibly-damaging,possibly-damaging	219/3539,219/3708,179/3668	114186003	4064,8942	2203	4300	6503	SO:0001583	missense	114788	exon4			ATTGGCTATGCAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.657A>G	8.37:g.114186003T>C	ENSP00000297405:p.Ile219Met	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	261	143	0.547893	NM_052900	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	1012	0.4633699633699634	229	0.4654471544715447	195	0.5386740331491713	395	0.6905594405594405	193	0.2546174142480211	T	7.868	0.727602	0.15439	0.399682	0.267791	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	5.09	1.06	0.20224	Complement control module (2);Sushi/SCR/CCP (3);	0.186890	0.33631	N	0.004715	T	0.00012	0.0000	N	0.25245	0.725	0.44643	P	0.0023729999999999585	P;P;P;P	0.51653	0.828;0.571;0.947;0.708	B;B;P;P	0.52159	0.392;0.168;0.691;0.622	T	0.25745	-1.0123	9	0.37606	T	0.19	.	7.6324	0.28247	0.1313:0.0:0.2743:0.5944	rs2219898;rs52789540;rs58255477;rs2219898	219;219;219;179	Q7Z407-3;Q7Z407-4;Q7Z407;Q7Z407-2	.;.;CSMD3_HUMAN;.	M	179;219;219;219	ENSP00000345799:I179M;ENSP00000297405:I219M;ENSP00000412263:I219M;ENSP00000343124:I219M	ENSP00000297405:I219M	I	-	3	3	CSMD3	114255179	0.994000	0.37717	0.999000	0.59377	0.996000	0.88848	0.054000	0.14205	0.003000	0.14656	0.528000	0.53228	ATA	T|0.622;C|0.378	0.378	strong		0.428	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
MTX3	345778	hgsc.bcm.edu	37	5	79286042	79286042	+	Missense_Mutation	SNP	T	T	A	rs371364933		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79286042T>A	ENST00000512528.1	-	3	189	c.169A>T	c.(169-171)Aca>Tca	p.T57S	MTX3_ENST00000509852.1_Missense_Mutation_p.T57S|MTX3_ENST00000512560.1_5'UTR			Q5HYI7	MTX3_HUMAN	metaxin 3	57					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)		TCTTCAGTTGTCAAAATTGGT	0.358																																					p.T57S		Atlas-SNP	.											.	MTX3	29	.	0			c.A169T						PASS	.	T	SER/THR,	0,3672		0,0,1836	86.0	78.0	81.0		169,	4.7	1.0	5		81	2,8158		0,2,4078	no	missense,utr-5	MTX3	NM_001010891.4,NM_001167741.1	58,	0,2,5914	AA,AT,TT		0.0245,0.0,0.0169	benign,	57/249,	79286042	2,11830	1836	4080	5916	SO:0001583	missense	345778	exon3			CAGTTGTCAAAAT	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.169A>T	5.37:g.79286042T>A	ENSP00000424798:p.Thr57Ser	Somatic	380	0	0		WXS	Illumina HiSeq	Phase_I	349	162	0.464183	NM_001010891	B4DL65|E9PB57|Q7Z380|Q8NB92	Missense_Mutation	SNP	ENST00000512528.1	37		.	.	.	.	.	.	.	.	.	.	T	8.983	0.975725	0.18736	0.0	2.45E-4	ENSG00000177034	ENST00000328496;ENST00000509852;ENST00000512528;ENST00000418095	T;T	0.42513	0.97;0.97	5.86	4.69	0.59074	.	0.541563	0.21589	N	0.072127	T	0.30885	0.0779	L	0.35644	1.08	0.28755	N	0.901208	B;B	0.10296	0.003;0.001	B;B	0.09377	0.002;0.004	T	0.18116	-1.0347	10	0.33141	T	0.24	-2.1085	8.1501	0.31134	0.1203:0.0663:0.0:0.8134	.	57;57	Q5HYI7-4;Q5HYI7	.;MTX3_HUMAN	S	57	ENSP00000423302:T57S;ENSP00000424798:T57S	ENSP00000331672:T57S	T	-	1	0	MTX3	79321798	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.676000	0.37565	1.036000	0.39998	-0.290000	0.09829	ACA	.	.	weak		0.358	MTX3-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372567.1	XM_293971	
CHTF18	63922	hgsc.bcm.edu	37	16	841238	841238	+	Silent	SNP	G	G	A	rs151271197	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:841238G>A	ENST00000262315.9	+	8	1035	c.972G>A	c.(970-972)aaG>aaA	p.K324K	RPUSD1_ENST00000565809.1_5'Flank|CHTF18_ENST00000491530.1_3'UTR|RPUSD1_ENST00000007264.2_5'Flank|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000455171.2_Silent_p.K352K|CHTF18_ENST00000317063.6_Silent_p.K519K	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	324					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CTTCCCGGAAGCCCAGGCCCA	0.642													G|||	27	0.00539137	0.0	0.0058	5008	,	,		18196	0.0		0.008	False		,,,				2504	0.0153				p.K324K		Atlas-SNP	.											.	CHTF18	52	.	0			c.G972A						PASS	.	G		5,4119		0,5,2057	19.0	24.0	22.0		972	1.3	1.0	16	dbSNP_134	22	86,8280		1,84,4098	no	coding-synonymous	CHTF18	NM_022092.2		1,89,6155	AA,AG,GG		1.028,0.1212,0.7286		324/976	841238	91,12399	2062	4183	6245	SO:0001819	synonymous_variant	63922	exon8			CCGGAAGCCCAGG	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.972G>A	16.37:g.841238G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	1.548	-0.540090	0.04053	0.001212	0.01028	ENSG00000127586	ENST00000426047	.	.	.	4.85	1.28	0.21552	.	.	.	.	.	T	0.43787	0.1263	.	.	.	0.41571	D	0.988681	.	.	.	.	.	.	T	0.36768	-0.9734	4	.	.	.	-39.2725	5.5091	0.16870	0.4904:0.0:0.5096:0.0	.	.	.	.	T	220	.	.	A	+	1	0	CHTF18	781239	0.890000	0.30428	0.994000	0.49952	0.848000	0.48234	0.510000	0.22723	0.579000	0.29504	0.579000	0.79373	GCC	G|0.995;A|0.005	0.005	strong		0.642	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
HSPH1	10808	hgsc.bcm.edu	37	13	31725260	31725260	+	Silent	SNP	A	A	G	rs11556147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:31725260A>G	ENST00000320027.5	-	7	1076	c.732T>C	c.(730-732)ttT>ttC	p.F244F	HSPH1_ENST00000429785.2_Silent_p.F63F|HSPH1_ENST00000445273.2_Silent_p.F246F|HSPH1_ENST00000380406.5_Silent_p.F203F|HSPH1_ENST00000380405.4_Silent_p.F244F	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	244					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		ATTCTGCACAAAAATGTTCCA	0.348													A|||	1131	0.225839	0.2451	0.2723	5008	,	,		18635	0.0109		0.4642	False		,,,				2504	0.1431				p.F244F		Atlas-SNP	.											.	HSPH1	65	.	0			c.T732C						PASS	.	A		1261,3145	427.4+/-341.5	171,919,1113	101.0	100.0	100.0		732	-2.6	1.0	13	dbSNP_120	100	4061,4539	553.7+/-386.4	951,2159,1190	no	coding-synonymous	HSPH1	NM_006644.2		1122,3078,2303	GG,GA,AA		47.2209,28.6201,40.9196		244/859	31725260	5322,7684	2203	4300	6503	SO:0001819	synonymous_variant	10808	exon7			TGCACAAAAATGT	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"""Heat shock proteins / HSP70"""	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.732T>C	13.37:g.31725260A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	180	96	0.533333	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Silent	SNP	ENST00000320027.5	37	CCDS9340.1																																																																																			A|0.653;G|0.347	0.347	strong		0.348	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1		
TOR1A	1861	hgsc.bcm.edu	37	9	132585058	132585058	+	Silent	SNP	G	G	A	rs2296793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:132585058G>A	ENST00000351698.4	-	2	294	c.246C>T	c.(244-246)gcC>gcT	p.A82A	TOR1A_ENST00000473084.1_5'UTR	NM_000113.2	NP_000104.1	O14656	TOR1A_HUMAN	torsin family 1, member A (torsin A)	82					ATP catabolic process (GO:0006200)|cell adhesion (GO:0007155)|chaperone mediated protein folding requiring cofactor (GO:0051085)|chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|ER-associated misfolded protein catabolic process (GO:0071712)|intermediate filament cytoskeleton organization (GO:0045104)|neuron projection development (GO:0031175)|nuclear envelope organization (GO:0006998)|nuclear membrane organization (GO:0071763)|organelle organization (GO:0006996)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|protein deneddylation (GO:0000338)|protein homooligomerization (GO:0051260)|protein localization to nucleus (GO:0034504)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of protein localization to cell surface (GO:2000008)|response to oxidative stress (GO:0006979)|synaptic vesicle transport (GO:0048489)|wound healing, spreading of cells (GO:0044319)	cell junction (GO:0030054)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cytoskeletal protein binding (GO:0008092)|kinesin binding (GO:0019894)|unfolded protein binding (GO:0051082)	p.A82A(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	20		Ovarian(14;0.00556)				AACCAAACACGGCATTTAAGA	0.488													A|||	1133	0.226238	0.2179	0.2118	5008	,	,		21361	0.2133		0.2753	False		,,,				2504	0.2106				p.A82A		Atlas-SNP	.											TOR1A,NS,carcinoma,0,1	TOR1A	36	1	1	Substitution - coding silent(1)	stomach(1)	c.C246T						PASS	.	A		981,3425	733.0+/-410.4	107,767,1329	167.0	152.0	157.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	246	-10.4	0.0	9	dbSNP_100	157	2066,6534	718.9+/-406.2	263,1540,2497	no	coding-synonymous	TOR1A	NM_000113.2		370,2307,3826	AA,AG,GG		24.0233,22.2651,23.4276		82/333	132585058	3047,9959	2203	4300	6503	SO:0001819	synonymous_variant	1861	exon2			AAACACGGCATTT	AF007871	CCDS6930.1	9q32-q34	2008-07-21	2004-11-24	2004-11-26	ENSG00000136827	ENSG00000136827			3098	protein-coding gene	gene with protein product		605204	"""dystonia 1, torsion (autosomal dominant; torsin A)"""	DYT1		10644435	Standard	NM_000113		Approved	DQ2	uc004byl.3	O14656	OTTHUMG00000020794	ENST00000351698.4:c.246C>T	9.37:g.132585058G>A		Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	233	107	0.459227	NM_000113	B2RB58|Q53Y64|Q96CA0	Silent	SNP	ENST00000351698.4	37	CCDS6930.1																																																																																			G|0.763;A|0.237	0.237	strong		0.488	TOR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054611.1	NM_000113	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376119	113376119	+	Silent	SNP	C	C	T	rs62265538|rs112313093|rs59601191		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113376119C>T	ENST00000478658.1	-	5	4427	c.4410G>A	c.(4408-4410)caG>caA	p.Q1470Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1470Q			Q68DE3	K2018_HUMAN	KIAA2018	1470	Gln-rich.					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						gttgctgctgctgctgctgct	0.493																																					p.Q1470Q		Atlas-SNP	.											KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	0			c.G4410A						PASS	.						58.0	65.0	63.0					3																	113376119		2185	4279	6464	SO:0001819	synonymous_variant	205717	exon7			CTGCTGCTGCTGC	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.4410G>A	3.37:g.113376119C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	16	0.131148	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			C|0.500;T|0.500	0.500	weak		0.493	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
FAM19A3	284467	hgsc.bcm.edu	37	1	113264930	113264930	+	Silent	SNP	C	C	G	rs35995150	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:113264930C>G	ENST00000361886.3	+	2	134	c.75C>G	c.(73-75)acC>acG	p.T25T	FAM19A3_ENST00000369630.3_Silent_p.T25T	NM_001004440.1|NM_182759.2	NP_001004440.1|NP_877436.1	Q7Z5A8	F19A3_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A3	25						extracellular region (GO:0005576)				lung(4)|ovary(1)	5	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		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)		GGCTGTGGACCCACCTGACCT	0.662													C|||	276	0.0551118	0.0045	0.049	5008	,	,		16390	0.001		0.1302	False		,,,				2504	0.1063				p.T25T		Atlas-SNP	.											.	FAM19A3	10	.	0			c.C75G						PASS	.	C	,	121,4285	88.2+/-126.9	2,117,2084	67.0	65.0	66.0		75,75	-3.3	0.0	1	dbSNP_126	66	1179,7421	239.6+/-270.6	77,1025,3198	no	coding-synonymous,coding-synonymous	FAM19A3	NM_001004440.1,NM_182759.2	,	79,1142,5282	GG,GC,CC		13.7093,2.7463,9.9954	,	25/170,25/134	113264930	1300,11706	2203	4300	6503	SO:0001819	synonymous_variant	284467	exon2			GTGGACCCACCTG	AY325119	CCDS856.1, CCDS30806.1	1p13.2	2008-02-05			ENSG00000184599	ENSG00000184599			21590	protein-coding gene	gene with protein product						15028294	Standard	NM_182759		Approved	TAFA-3	uc001ecu.3	Q7Z5A8	OTTHUMG00000012020	ENST00000361886.3:c.75C>G	1.37:g.113264930C>G		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	102	84	0.823529	NM_001004440	B7ZLU0|Q2M1P9|Q7Z5A6	Silent	SNP	ENST00000361886.3	37	CCDS856.1																																																																																			C|0.909;G|0.091	0.091	strong		0.662	FAM19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033255.1	NM_182759	
MOV10L1	54456	hgsc.bcm.edu	37	22	50584201	50584201	+	Silent	SNP	A	A	C	rs2272838	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50584201A>C	ENST00000262794.5	+	19	2672	c.2589A>C	c.(2587-2589)acA>acC	p.T863T	MOV10L1_ENST00000545383.1_Silent_p.T863T|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395852.1_5'Flank|MOV10L1_ENST00000540615.1_Silent_p.T843T|MOV10L1_ENST00000395858.3_Silent_p.T863T	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	66	34	0.515152	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	
P2RY11	5032	hgsc.bcm.edu	37	19	10226256	10226256	+	IGR	SNP	A	A	G	rs7710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:10226256A>G	ENST00000321826.4	+	0	1943				EIF3G_ENST00000253108.4_Silent_p.F282F	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)			TGATGAAGGCAAAGCCCTGTG	0.667													G|||	2273	0.453874	0.407	0.5303	5008	,	,		14409	0.371		0.494	False		,,,				2504	0.5072				p.F282F		Atlas-SNP	.											.	EIF3G	16	.	0			c.T846C						PASS	.	G		1779,2627	638.1+/-396.9	350,1079,774	49.0	49.0	49.0		846	-1.9	1.0	19	dbSNP_52	49	3911,4687	602.8+/-394.6	895,2121,1283	no	coding-synonymous	EIF3G	NM_003755.3		1245,3200,2057	GG,GA,AA		45.4873,40.3768,43.7558		282/321	10226256	5690,7314	2203	4299	6502	SO:0001628	intergenic_variant	8666	exon10			GAAGGCAAAGCCC	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.10226256A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_003755	B2R8X9|O43190|Q9BYU4|Q9H170	Silent	SNP	ENST00000321826.4	37	CCDS12226.1																																																																																			A|0.564;G|0.436	0.436	strong		0.667	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
TMCC3	57458	hgsc.bcm.edu	37	12	94972290	94972290	+	Silent	SNP	C	C	T	rs2270893	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:94972290C>T	ENST00000261226.4	-	3	1142	c.1011G>A	c.(1009-1011)gaG>gaA	p.E337E	TMCC3_ENST00000551457.1_Silent_p.E306E	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	337						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						GCAGCTGGTCCTCCAGTCGCT	0.542													C|||	2604	0.519968	0.5234	0.5634	5008	,	,		16768	0.4653		0.5378	False		,,,				2504	0.5225				p.E337E		Atlas-SNP	.											TMCC3,NS,carcinoma,0,1	TMCC3	63	1	0			c.G1011A						scavenged	.	C		2276,2130	598.6+/-389.1	590,1096,517	71.0	57.0	62.0		1011	-1.1	1.0	12	dbSNP_100	62	4626,3974	600.1+/-394.2	1263,2100,937	no	coding-synonymous	TMCC3	NM_020698.2		1853,3196,1454	TT,TC,CC		46.2093,48.3432,46.9322		337/478	94972290	6902,6104	2203	4300	6503	SO:0001819	synonymous_variant	57458	exon3			CTGGTCCTCCAGT	AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.1011G>A	12.37:g.94972290C>T		Somatic	99	1	0.010101		WXS	Illumina HiSeq	Phase_I	67	21	0.313433	NM_020698	Q8IWB2	Silent	SNP	ENST00000261226.4	37	CCDS31877.1																																																																																			C|0.474;T|0.526	0.526	strong		0.542	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
PKDREJ	10343	hgsc.bcm.edu	37	22	46652959	46652959	+	Silent	SNP	A	A	G	rs4508712	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46652959A>G	ENST00000253255.5	-	1	6260	c.6261T>C	c.(6259-6261)ccT>ccC	p.P2087P		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	2087					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		GGCAGATGCCAGGGAGGGCAG	0.478													G|||	1855	0.370407	0.9244	0.2147	5008	,	,		20978	0.0516		0.2893	False		,,,				2504	0.1442				p.P2087P		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T6261C						PASS	.	G		3673,733	287.8+/-279.5	1544,585,74	36.0	40.0	38.0		6261	-11.8	0.0	22	dbSNP_111	38	2476,6124	689.2+/-404.3	354,1768,2178	no	coding-synonymous	PKDREJ	NM_006071.1		1898,2353,2252	GG,GA,AA		28.7907,16.6364,47.2782		2087/2254	46652959	6149,6857	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			GATGCCAGGGAGG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.6261T>C	22.37:g.46652959A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.593;G|0.407;T|0.000	0.407	strong		0.478	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
SLC41A3	54946	hgsc.bcm.edu	37	3	125726048	125726048	+	Silent	SNP	G	G	C	rs2279819	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:125726048G>C	ENST00000315891.6	-	11	1513	c.1275C>G	c.(1273-1275)ctC>ctG	p.L425L	SLC41A3_ENST00000360370.4_Silent_p.L425L|SLC41A3_ENST00000508835.1_Silent_p.L308L|SLC41A3_ENST00000383598.2_Silent_p.L399L|SLC41A3_ENST00000346785.5_Silent_p.L389L	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	425						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		TCACTTCTGCGAGGTACAGCA	0.552													C|||	3334	0.665735	0.9395	0.5461	5008	,	,		21833	0.503		0.6203	False		,,,				2504	0.5951				p.L425L		Atlas-SNP	.											.	SLC41A3	80	.	0			c.C1275G						PASS	.	C	,,,,	3927,479	223.6+/-240.1	1749,429,25	63.0	58.0	60.0		1275,1167,1197,924,1275	4.6	1.0	3	dbSNP_100	60	5407,3193	483.1+/-371.0	1711,1985,604	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC41A3	NM_001008485.1,NM_001008486.1,NM_001008487.1,NM_001164475.1,NM_017836.3	,,,,	3460,2414,629	CC,CG,GG		37.1279,10.8715,28.2331	,,,,	425/508,389/472,399/462,308/371,425/488	125726048	9334,3672	2203	4300	6503	SO:0001819	synonymous_variant	54946	exon11			TTCTGCGAGGTAC		CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"""Solute carriers"""	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.1275C>G	3.37:g.125726048G>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_017836	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Silent	SNP	ENST00000315891.6	37	CCDS33843.1																																																																																			G|0.309;C|0.691	0.691	strong		0.552	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836	
ZDHHC19	131540	hgsc.bcm.edu	37	3	195938177	195938177	+	Silent	SNP	A	A	G	rs1522394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195938177A>G	ENST00000296326.3	-	1	89	c.10T>C	c.(10-12)Tta>Cta	p.L4L	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	4						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)		GCATCCGTTAAGAGTGTCATG	0.647													A|||	1350	0.269569	0.0537	0.3098	5008	,	,		16359	0.5248		0.2704	False		,,,				2504	0.2689				p.L4L		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.T10C						PASS	.	A		357,3821		19,319,1751	96.0	121.0	113.0		10	-6.1	0.0	3	dbSNP_88	113	2005,6435		224,1557,2439	no	coding-synonymous	ZDHHC19	NM_001039617.1		243,1876,4190	GG,GA,AA		23.7559,8.5448,18.7193		4/310	195938177	2362,10256	2089	4220	6309	SO:0001819	synonymous_variant	131540	exon1			CCGTTAAGAGTGT	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.10T>C	3.37:g.195938177A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_001039617	A8MSY6|B3KVI1	Silent	SNP	ENST00000296326.3	37	CCDS43190.1																																																																																			A|0.742;G|0.258	0.258	strong		0.647	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637	
ATRN	8455	hgsc.bcm.edu	37	20	3624830	3624830	+	Silent	SNP	G	G	A	rs2246808	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	233	0	0		WXS	Illumina HiSeq	Phase_I	192	86	0.447917	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	
C9orf72	203228	hgsc.bcm.edu	37	9	27561628	27561628	+	Missense_Mutation	SNP	T	T	C	rs113299382|rs17769294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:27561628T>C	ENST00000380003.3	-	5	683	c.620A>G	c.(619-621)aAt>aGt	p.N207S	C9orf72_ENST00000379997.3_Missense_Mutation_p.N207S|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	207			N -> S (in dbSNP:rs17769294).		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)	p.N207I(1)		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)		ATCATCATCATTGAGTACTGT	0.318													T|||	246	0.0491214	0.0189	0.0735	5008	,	,		18348	0.001		0.1083	False		,,,				2504	0.0613				p.N207S		Atlas-SNP	.											.	C9orf72	48	.	1	Substitution - Missense(1)	lung(1)	c.A620G						PASS	.	T	SER/ASN,SER/ASN	150,4256	101.6+/-140.2	0,150,2053	60.0	57.0	58.0		620,620	4.9	1.0	9	dbSNP_123	58	1085,7513	225.1+/-261.3	74,937,3288	yes	missense,missense	C9orf72	NM_018325.2,NM_145005.4	46,46	74,1087,5341	CC,CT,TT		12.6192,3.4044,9.4971	possibly-damaging,possibly-damaging	207/482,207/223	27561628	1235,11769	2203	4299	6502	SO:0001583	missense	203228	exon5			TCATCATTGAGTA	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.620A>G	9.37:g.27561628T>C	ENSP00000369339:p.Asn207Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	37	CCDS6522.1	113	0.051739926739926737	9	0.018292682926829267	24	0.06629834254143646	0	0.0	80	0.10554089709762533	T	14.66	2.602228	0.46423	0.034044	0.126192	ENSG00000147894	ENST00000380003;ENST00000379997;ENST00000379995	T;T;T	0.42900	0.96;0.96;0.96	6.07	4.95	0.65309	.	0.042329	0.85682	D	0.000000	T	0.00384	0.0012	L	0.54323	1.7	0.09310	P	0.99999873259	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.06409	-1.0828	8	.	.	.	.	9.7079	0.40227	0.0:0.1306:0.0:0.8694	rs17769294;rs52789634;rs17769294	207;207	Q96LT7-2;Q96LT7	.;CI072_HUMAN	S	207	ENSP00000369339:N207S;ENSP00000369333:N207S;ENSP00000369331:N207S	.	N	-	2	0	C9orf72	27551628	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	1.986000	0.40677	2.330000	0.79161	0.477000	0.44152	AAT	T|0.919;C|0.081	0.081	strong		0.318	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325	
KMO	8564	hgsc.bcm.edu	37	1	241695792	241695792	+	Silent	SNP	T	T	C	rs3819976	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:241695792T>C	ENST00000366559.4	+	1	359	c.48T>C	c.(46-48)ggT>ggC	p.G16G	KMO_ENST00000484628.1_3'UTR|KMO_ENST00000366558.3_Silent_p.G16G|KMO_ENST00000366557.4_Silent_p.G16G	NM_003679.4	NP_003670.2			kynurenine 3-monooxygenase (kynurenine 3-hydroxylase)											NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Ovarian(103;0.103)|all_lung(81;0.23)		OV - Ovarian serous cystadenocarcinoma(106;0.0176)			TCATTGGTGGTGGCTTGGTAA	0.333													T|||	550	0.109824	0.1808	0.0692	5008	,	,		16107	0.1359		0.0318	False		,,,				2504	0.0961				p.G16G		Atlas-SNP	.											.	KMO	69	.	0			c.T48C						PASS	.	T		752,3654	308.3+/-290.5	69,614,1520	227.0	232.0	230.0		48	1.5	1.0	1	dbSNP_107	230	191,8409	85.0+/-147.5	6,179,4115	no	coding-synonymous	KMO	NM_003679.3		75,793,5635	CC,CT,TT		2.2209,17.0676,7.2505		16/487	241695792	943,12063	2203	4300	6503	SO:0001819	synonymous_variant	8564	exon1			TGGTGGTGGCTTG	AF056032	CCDS1618.1	1q42-q44	2010-11-23			ENSG00000117009	ENSG00000117009	1.14.13.9		6381	protein-coding gene	gene with protein product		603538				9237672	Standard	NM_003679		Approved		uc009xgp.3	O15229	OTTHUMG00000039635	ENST00000366559.4:c.48T>C	1.37:g.241695792T>C		Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	237	160	0.675106	NM_003679		Silent	SNP	ENST00000366559.4	37	CCDS1618.1																																																																																			T|0.910;C|0.090	0.090	strong		0.333	KMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095612.1	NM_003679	
OR5H1	26341	hgsc.bcm.edu	37	3	97851645	97851645	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:97851645A>G	ENST00000354565.2	+	1	104	c.104A>G	c.(103-105)tAt>tGt	p.Y35C	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	35						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						TTGGTAATATATCTCATCACC	0.408																																					p.Y35C		Atlas-SNP	.											OR5H1,NS,carcinoma,+1,1	OR5H1	71	1	0			c.A104G						scavenged	.						44.0	48.0	46.0					3																	97851645		2156	4222	6378	SO:0001583	missense	26341	exon1			TAATATATCTCAT	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.104A>G	3.37:g.97851645A>G	ENSP00000346575:p.Tyr35Cys	Somatic	691	0	0		WXS	Illumina HiSeq	Phase_I	657	16	0.0243531	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.634358	0.29068	.	.	ENSG00000231192	ENST00000354565	T	0.04706	3.57	3.63	3.63	0.41609	.	0.000000	0.38837	N	0.001559	T	0.25568	0.0622	M	0.93016	3.37	0.26808	N	0.96907	D	0.89917	1.0	D	0.75484	0.986	T	0.10520	-1.0626	10	0.87932	D	0	.	10.2248	0.43218	1.0:0.0:0.0:0.0	.	35	A6NKK0	OR5H1_HUMAN	C	35	ENSP00000346575:Y35C	ENSP00000346575:Y35C	Y	+	2	0	OR5H1	99334335	0.980000	0.34600	0.019000	0.16419	0.184000	0.23303	2.621000	0.46418	1.511000	0.48818	0.164000	0.16699	TAT	.	.	none		0.408	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
CFAP44	55779	hgsc.bcm.edu	37	3	113128051	113128051	+	Silent	SNP	G	G	T	rs13059888	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113128051G>T	ENST00000295868.2	-	7	954	c.792C>A	c.(790-792)ccC>ccA	p.P264P	WDR52_ENST00000393845.2_Silent_p.P264P|WDR52-AS1_ENST00000498480.1_RNA|WDR52-AS1_ENST00000473329.1_RNA	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TCCTTAGTATGGGTTGTTCTT	0.423													G|||	248	0.0495208	0.0136	0.0807	5008	,	,		16702	0.001		0.1412	False		,,,				2504	0.0317				p.P264P		Atlas-SNP	.											.	WDR52	151	.	0			c.C792A						PASS	.	G	,	98,4308	79.3+/-117.8	1,96,2106	144.0	139.0	141.0		792,792	2.0	1.0	3	dbSNP_121	141	1129,7471	232.8+/-266.3	80,969,3251	no	coding-synonymous,coding-synonymous	WDR52	NM_001164496.1,NM_018338.3	,	81,1065,5357	TT,TG,GG		13.1279,2.2242,9.4341	,	264/1855,264/983	113128051	1227,11779	2203	4300	6503	SO:0001819	synonymous_variant	55779	exon7			TAGTATGGGTTGT																												ENST00000295868.2:c.792C>A	3.37:g.113128051G>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	111	45	0.405405	NM_001164496		Silent	SNP	ENST00000295868.2	37	CCDS2972.1																																																																																			G|0.919;T|0.081	0.081	strong		0.423	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
PRRG2	5639	hgsc.bcm.edu	37	19	50093248	50093248	+	Missense_Mutation	SNP	A	A	T	rs144521999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50093248A>T	ENST00000246794.5	+	6	698	c.529A>T	c.(529-531)Acc>Tcc	p.T177S	PRRG2_ENST00000596700.1_3'UTR|PRR12_ENST00000418929.2_5'Flank	NM_000951.2	NP_000942.1	O14669	TMG2_HUMAN	proline rich Gla (G-carboxyglutamic acid) 2	177						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			lung(1)|skin(1)|soft_tissue(1)	3		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0121)		aGGCCTCCCCACCTATGAGCA	0.711													A|||	186	0.0371406	0.003	0.0548	5008	,	,		4918	0.003		0.1133	False		,,,				2504	0.0276				p.T177S		Atlas-SNP	.											.	PRRG2	13	.	0			c.A529T						PASS	.	A	SER/THR	46,2892		1,44,1424	2.0	2.0	2.0		529	3.7	1.0	19	dbSNP_134	2	490,5602		6,478,2562	yes	missense	PRRG2	NM_000951.2	58	7,522,3986	TT,TA,AA		8.0433,1.5657,5.9358	possibly-damaging	177/203	50093248	536,8494	1469	3046	4515	SO:0001583	missense	5639	exon6			CTCCCCACCTATG		CCDS12773.1	19q13.33	2008-02-05	2004-05-27						9470	protein-coding gene	gene with protein product		604429	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 2"""			9256434	Standard	NM_000951		Approved	PRGP2	uc002pon.3	O14669		ENST00000246794.5:c.529A>T	19.37:g.50093248A>T	ENSP00000246794:p.Thr177Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_000951	Q6IBF8	Missense_Mutation	SNP	ENST00000246794.5	37	CCDS12773.1	132	0.06043956043956044	1	0.0020325203252032522	33	0.09116022099447514	1	0.0017482517482517483	97	0.1279683377308707	A	10.89	1.478535	0.26511	0.015657	0.080433	ENSG00000126460	ENST00000246794;ENST00000543867	D	0.96396	-4.0	4.75	3.65	0.41850	.	0.117120	0.52532	D	0.000078	T	0.19087	0.0458	N	0.21373	0.66	0.34516	P	0.29237	D;D	0.67145	0.996;0.993	D;D	0.73380	0.98;0.978	T	0.79152	-0.1921	9	0.02654	T	1	-30.9692	7.2004	0.25877	0.8017:0.0:0.0:0.1983	.	154;177	F5GZ13;O14669	.;TMG2_HUMAN	S	177;154	ENSP00000246794:T177S	ENSP00000246794:T177S	T	+	1	0	PRRG2	54785060	0.968000	0.33430	1.000000	0.80357	0.983000	0.72400	2.130000	0.42064	1.902000	0.55061	0.374000	0.22700	ACC	A|0.939;T|0.061	0.061	strong		0.711	PRRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465257.1	NM_000951	
MUC4	4585	hgsc.bcm.edu	37	3	195507262	195507262	+	Missense_Mutation	SNP	T	T	G	rs74187968|rs367631576		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195507262T>G	ENST00000463781.3	-	2	11648	c.11189A>C	c.(11188-11190)cAt>cCt	p.H3730P	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3730P	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)		GCTGGTGACATGAAGAGGGGT	0.567																																					p.H3730P		Atlas-SNP	.											MUC4_ENST00000463781,NS,haematopoietic_neoplasm,0,1	MUC4	1505	1	0			c.A11189C						scavenged	.						63.0	58.0	59.0					3																	195507262		615	1586	2201	SO:0001583	missense	4585	exon2			GTGACATGAAGAG	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.11189A>C	3.37:g.195507262T>G	ENSP00000417498:p.His3730Pro	Somatic	329	7	0.0212766		WXS	Illumina HiSeq	Phase_I	453	54	0.119205	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	3.238	-0.155985	0.06544	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.51;1.48	.	.	.	.	.	.	.	.	T	0.13157	0.0319	N	0.14661	0.345	0.49483	P	2.0600000000003948E-4	.	.	.	.	.	.	T	0.21827	-1.0234	4	.	.	.	.	5.3635	0.16101	0.0:0.0:0.5708:0.4292	.	3602	E7ESK3	.	P	3730	ENSP00000417498:H3730P;ENSP00000420243:H3730P	.	H	-	2	0	MUC4	196992041	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-2.571000	0.00913	-2.418000	0.00566	-2.418000	0.00219	CAT	.	.	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RSPRY1	89970	hgsc.bcm.edu	37	16	57261339	57261339	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57261339C>T	ENST00000537866.1	+	11	2120	c.1247C>T	c.(1246-1248)cCt>cTt	p.P416L	RSPRY1_ENST00000394420.4_Missense_Mutation_p.P416L|RSPRY1_ENST00000563073.1_3'UTR			Q96DX4	RSPRY_HUMAN	ring finger and SPRY domain containing 1	416	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular region (GO:0005576)	zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|urinary_tract(3)	27						AGAAGTAAGCCTCACATACAC	0.433																																					p.P416L		Atlas-SNP	.											RSPRY1,colon,carcinoma,-1,2	RSPRY1	49	2	0			c.C1247T						scavenged	.						121.0	104.0	109.0					16																	57261339		2198	4300	6498	SO:0001583	missense	89970	exon11			GTAAGCCTCACAT	AB075852	CCDS10775.1	16q13	2014-02-12			ENSG00000159579	ENSG00000159579		"""RING-type (C3HC4) zinc fingers"""	29420	protein-coding gene	gene with protein product						11853319	Standard	NM_133368		Approved	KIAA1972	uc002elb.3	Q96DX4	OTTHUMG00000133462	ENST00000537866.1:c.1247C>T	16.37:g.57261339C>T	ENSP00000443176:p.Pro416Leu	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	164	3	0.0182927	NM_133368	Q6UX21|Q8ND53	Missense_Mutation	SNP	ENST00000537866.1	37	CCDS10775.1	.	.	.	.	.	.	.	.	.	.	C	32	5.170621	0.94807	.	.	ENSG00000159579	ENST00000394420;ENST00000537866	T;T	0.69306	-0.39;-0.39	6.16	6.16	0.99307	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.75715	0.3887	M	0.72894	2.215	0.80722	D	1	P	0.45986	0.87	P	0.48166	0.569	T	0.75969	-0.3130	10	0.59425	D	0.04	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	416	Q96DX4	RSPRY_HUMAN	L	416	ENSP00000377942:P416L;ENSP00000443176:P416L	ENSP00000377942:P416L	P	+	2	0	RSPRY1	55818840	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	CCT	.	.	none		0.433	RSPRY1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432953.1	NM_133368	
TREML4	285852	hgsc.bcm.edu	37	6	41196169	41196169	+	Missense_Mutation	SNP	G	G	T	rs112680060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:41196169G>T	ENST00000341495.2	+	1	108	c.4G>T	c.(4-6)Gcc>Tcc	p.A2S	TREML4_ENST00000448827.2_Missense_Mutation_p.A2S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	2						extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					GGCTGGAATGGCCTGGGGTGG	0.607													G|||	141	0.028155	0.0	0.0159	5008	,	,		17102	0.006		0.0129	False		,,,				2504	0.1135				p.A2S		Atlas-SNP	.											.	TREML4	25	.	0			c.G4T						PASS	.	G	SER/ALA	7,4399		0,7,2196	37.0	37.0	37.0		4	2.0	0.3	6	dbSNP_132	37	57,8543		0,57,4243	yes	missense	TREML4	NM_198153.2	99	0,64,6439	TT,TG,GG		0.6628,0.1589,0.4921	possibly-damaging	2/201	41196169	64,12942	2203	4300	6503	SO:0001583	missense	285852	exon1			GGAATGGCCTGGG	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.4G>T	6.37:g.41196169G>T	ENSP00000342570:p.Ala2Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_198153	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	37	CCDS34446.1	16	0.007326007326007326	0	0.0	6	0.016574585635359115	0	0.0	10	0.013192612137203167	.	12.79	2.044341	0.36085	0.001589	0.006628	ENSG00000188056	ENST00000341495;ENST00000445267;ENST00000448827	T;T	0.09445	2.98;2.98	3.94	2.05	0.26809	.	.	.	.	.	T	0.05273	0.0140	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	D	0.63381	0.914	T	0.22800	-1.0206	9	0.72032	D	0.01	-18.3792	4.7235	0.12929	0.1155:0.0:0.6718:0.2127	.	2	Q6UXN2	TRML4_HUMAN	S	2	ENSP00000342570:A2S;ENSP00000418078:A2S	ENSP00000342570:A2S	A	+	1	0	TREML4	41304147	0.595000	0.26857	0.269000	0.24586	0.017000	0.09413	0.825000	0.27393	0.395000	0.25257	0.591000	0.81541	GCC	G|0.995;T|0.005	0.005	strong		0.607	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
CDC16	8881	hgsc.bcm.edu	37	13	115002305	115002305	+	Silent	SNP	G	G	A	rs8002514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:115002305G>A	ENST00000356221.3	+	3	243	c.135G>A	c.(133-135)caG>caA	p.Q45Q	CDC16_ENST00000375312.3_5'UTR|CDC16_ENST00000252458.6_5'UTR|CDC16_ENST00000375310.1_5'UTR|CDC16_ENST00000375308.1_5'UTR|CDC16_ENST00000360383.3_Silent_p.Q45Q|CDC16_ENST00000252457.5_Silent_p.Q44Q			Q13042	CDC16_HUMAN	cell division cycle 16	45					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|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)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|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)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	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)			GGTTGGCTCAGTGTCTTTACC	0.413													A|||	1711	0.341653	0.5825	0.2767	5008	,	,		14511	0.1587		0.2584	False		,,,				2504	0.3364				p.Q45Q		Atlas-SNP	.											.	CDC16	50	.	0			c.G135A						PASS	.	A	,	2277,2129	579.4+/-384.9	577,1123,503	118.0	116.0	117.0		135,135	2.4	1.0	13	dbSNP_116	117	1991,6609	722.8+/-406.4	230,1531,2539	no	coding-synonymous,coding-synonymous	CDC16	NM_001078645.1,NM_003903.3	,	807,2654,3042	AA,AG,GG		23.1512,48.3205,32.8156	,	45/621,45/621	115002305	4268,8738	2203	4300	6503	SO:0001819	synonymous_variant	8881	exon3			GGCTCAGTGTCTT	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.135G>A	13.37:g.115002305G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			G|0.678;A|0.322	0.322	strong		0.413	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610504	38610504	+	Silent	SNP	G	G	A	rs59185302	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38610504G>A	ENST00000222345.6	+	9	3359	c.2850G>A	c.(2848-2850)gaG>gaA	p.E950E		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	950					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			ACATAAGGGAGATAGTGCAGA	0.532													G|||	711	0.141973	0.2224	0.1455	5008	,	,		19812	0.0893		0.1342	False		,,,				2504	0.093				p.E950E		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.G2850A						PASS	.	G		783,3621		85,613,1504	25.0	27.0	26.0		2850	-5.9	0.4	19	dbSNP_129	26	1113,7485		87,939,3273	no	coding-synonymous	SIPA1L3	NM_015073.1		172,1552,4777	AA,AG,GG		12.9449,17.7793,14.5824		950/1782	38610504	1896,11106	2202	4299	6501	SO:0001819	synonymous_variant	23094	exon9			AAGGGAGATAGTG	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2850G>A	19.37:g.38610504G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	37	CCDS33007.1																																																																																			G|0.866;A|0.134	0.134	strong		0.532	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
BRD3	8019	hgsc.bcm.edu	37	9	136901254	136901254	+	Silent	SNP	G	G	A	rs448698	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136901254G>A	ENST00000303407.7	-	10	2021	c.1836C>T	c.(1834-1836)gaC>gaT	p.D612D	LINC00094_ENST00000605164.1_RNA|BRD3_ENST00000371834.2_3'UTR|BRD3_ENST00000473349.1_5'UTR	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	612	NET. {ECO:0000255|PROSITE- ProRule:PRU00857}.				chromatin modification (GO:0016568)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|lysine-acetylated histone binding (GO:0070577)		BRD3/C15orf55(3)	kidney(1)|skin(1)|stomach(4)	6				OV - Ovarian serous cystadenocarcinoma(145;1.43e-08)|Epithelial(140;8.41e-08)|all cancers(34;5.21e-07)		TTTCTATCTCGTCGGGGTTGG	0.527			T	C15orf55	lethal midline carcinoma of young people								G|||	55	0.0109824	0.003	0.0245	5008	,	,		19407	0.0		0.0258	False		,,,				2504	0.0082				p.D612D		Atlas-SNP	.		Dom	yes		9	9q34	8019	bromodomain containing 3		E	.	BRD3	82	.	0			c.C1836T						PASS	.	G		34,4372	39.2+/-71.8	2,30,2171	81.0	82.0	82.0		1836	-3.3	0.9	9	dbSNP_80	82	283,8317	105.0+/-166.0	6,271,4023	no	coding-synonymous	BRD3	NM_007371.3		8,301,6194	AA,AG,GG		3.2907,0.7717,2.4373		612/727	136901254	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	8019	exon10			TATCTCGTCGGGG		CCDS6980.1	9q34	2010-12-23	2002-01-14		ENSG00000169925	ENSG00000169925			1104	protein-coding gene	gene with protein product	"""RING3-like"""	601541	"""bromodomain-containing 3"""			7584044, 8781126	Standard	NM_007371		Approved	RING3L, ORFX, KIAA0043	uc004cew.3	Q15059	OTTHUMG00000021004	ENST00000303407.7:c.1836C>T	9.37:g.136901254G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	201	107	0.532338	NM_007371	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Silent	SNP	ENST00000303407.7	37	CCDS6980.1																																																																																			G|0.979;A|0.021	0.021	strong		0.527	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3483205	3483205	+	Silent	SNP	C	C	T	rs6767	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:3483205C>T	ENST00000324266.5	+	12	2376	c.2181C>T	c.(2179-2181)ttC>ttT	p.F727F	TRAPPC12-AS1_ENST00000453806.1_RNA|TRAPPC12_ENST00000382110.2_Silent_p.F727F	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	214	0	0		WXS	Illumina HiSeq	Phase_I	216	101	0.467593	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	
PNPLA7	375775	hgsc.bcm.edu	37	9	140357943	140357943	+	Silent	SNP	G	G	A	rs78550888	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:140357943G>A	ENST00000277531.4	-	28	3378	c.3192C>T	c.(3190-3192)tcC>tcT	p.S1064S	PNPLA7_ENST00000492278.1_5'UTR|PNPLA7_ENST00000406427.1_Silent_p.S1089S|PNPLA7_ENST00000371457.1_Silent_p.S670S	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	1064	Patatin.				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)		GCATGTAACCGGACAGGGACA	0.667													G|||	164	0.0327476	0.0023	0.0403	5008	,	,		15314	0.0		0.0696	False		,,,				2504	0.0644				p.S1089S		Atlas-SNP	.											.	PNPLA7	124	.	0			c.C3267T						PASS	.	G	,	71,4321		0,71,2125	73.0	50.0	58.0		3267,3192	-9.2	0.7	9	dbSNP_132	58	577,8009		26,525,3742	no	coding-synonymous,coding-synonymous	PNPLA7	NM_001098537.1,NM_152286.3	,	26,596,5867	AA,AG,GG		6.7202,1.6166,4.9931	,	1089/1343,1064/1318	140357943	648,12330	2196	4293	6489	SO:0001819	synonymous_variant	375775	exon29			GTAACCGGACAGG	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.3192C>T	9.37:g.140357943G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Silent	SNP	ENST00000277531.4	37	CCDS7045.1																																																																																			G|0.958;A|0.042	0.042	strong		0.667	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
CNOT4	4850	hgsc.bcm.edu	37	7	135082953	135082953	+	Missense_Mutation	SNP	G	G	C	rs77841106	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:135082953G>C	ENST00000315544.5	-	8	1126	c.847C>G	c.(847-849)Ctc>Gtc	p.L283V	CNOT4_ENST00000541284.1_Missense_Mutation_p.L283V|CNOT4_ENST00000428680.2_Missense_Mutation_p.L280V|CNOT4_ENST00000361528.4_Missense_Mutation_p.L280V|CNOT4_ENST00000451834.1_Missense_Mutation_p.L280V|CNOT4_ENST00000414802.1_Missense_Mutation_p.L283V|CNOT4_ENST00000423368.2_Missense_Mutation_p.L283V|CNOT4_ENST00000356162.4_Missense_Mutation_p.L283V	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	283					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)|protein autoubiquitination (GO:0051865)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)	22						CCTATACTGAGAGAATCTGAA	0.348													G|||	216	0.043131	0.0318	0.0346	5008	,	,		17001	0.001		0.1054	False		,,,				2504	0.044				p.L283V	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.C847G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	148,3458		3,142,1658	95.0	88.0	90.0		838,847,847,838,847,838	5.2	1.0	7	dbSNP_131	90	814,7332		37,740,3296	yes	missense,missense,missense,missense,missense,missense	CNOT4	NM_001008225.2,NM_001190847.1,NM_001190848.1,NM_001190849.1,NM_001190850.1,NM_013316.3	32,32,32,32,32,32	40,882,4954	CC,CG,GG		9.9926,4.1043,8.1858	benign,benign,benign,benign,benign,benign	280/573,283/643,283/576,280/711,283/714,280/640	135082953	962,10790	1803	4073	5876	SO:0001583	missense	4850	exon8			TACTGAGAGAATC	AF180475	CCDS43650.1, CCDS47719.1, CCDS55164.1, CCDS55165.1, CCDS55166.1, CCDS55167.1	7q33	2013-09-19			ENSG00000080802	ENSG00000080802		"""RNA binding motif (RRM) containing"""	7880	protein-coding gene	gene with protein product		604911		NOT4		10637334	Standard	NM_013316		Approved	CLONE243, NOT4H	uc011kpy.2	O95628	OTTHUMG00000155568	ENST00000315544.5:c.847C>G	7.37:g.135082953G>C	ENSP00000326731:p.Leu283Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	56	45	0.803571	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	121	0.0554029304029304	21	0.042682926829268296	19	0.052486187845303865	0	0.0	81	0.10686015831134564	G	11.93	1.786225	0.31593	0.041043	0.099926	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	T;T;T;T;T;T;T;T	0.60424	0.19;0.19;0.19;0.19;0.19;0.19;0.19;0.19	5.22	5.22	0.72569	.	0.112601	0.64402	D	0.000019	T	0.00845	0.0028	N	0.24115	0.695	0.22581	P	0.99896632	B;B;B;B;B;B	0.27932	0.062;0.102;0.012;0.02;0.076;0.194	B;B;B;B;B;B	0.24848	0.015;0.033;0.004;0.009;0.056;0.056	T	0.11251	-1.0595	9	0.18276	T	0.48	-13.0679	11.2538	0.49041	0.0851:0.0:0.9149:0.0	.	280;283;283;280;283;280	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	V	283;280;283;283;280;283;283;280;283	ENSP00000445508:L283V;ENSP00000388491:L280V;ENSP00000406777:L283V;ENSP00000354673:L280V;ENSP00000416532:L283V;ENSP00000348485:L283V;ENSP00000399108:L280V;ENSP00000326731:L283V	ENSP00000262563:L283V	L	-	1	0	CNOT4	134733493	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.578000	0.67450	2.588000	0.87417	0.650000	0.86243	CTC	G|0.933;C|0.067	0.067	strong		0.348	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68257352	68257352	+	Missense_Mutation	SNP	T	T	A	rs17192170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:68257352T>A	ENST00000347230.4	-	15	2830	c.2692A>T	c.(2692-2694)Acc>Tcc	p.T898S	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.T898S	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	898			T -> S (in dbSNP:rs17192170).		cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CTCCGAATGGTGCTGCTACCC	0.547													T|||	215	0.0429313	0.0061	0.0648	5008	,	,		20189	0.0		0.1153	False		,,,				2504	0.047				p.T898S		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A2692T						PASS	.	T	SER/THR	122,4284	91.6+/-130.3	4,114,2085	149.0	118.0	128.0		2692	2.4	1.0	14	dbSNP_123	128	1032,7568	219.9+/-257.8	61,910,3329	yes	missense	ZFYVE26	NM_015346.3	58	65,1024,5414	AA,AT,TT		12.0,2.769,8.8728	benign	898/2540	68257352	1154,11852	2203	4300	6503	SO:0001583	missense	23503	exon15			GAATGGTGCTGCT	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.2692A>T	14.37:g.68257352T>A	ENSP00000251119:p.Thr898Ser	Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	356	218	0.61236	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	102	0.046703296703296704	1	0.0020325203252032522	27	0.07458563535911603	0	0.0	74	0.09762532981530343	T	12.54	1.967920	0.34754	0.02769	0.12	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.28895	1.73;1.59	5.95	2.38	0.29361	.	0.540708	0.19473	N	0.113394	T	0.00300	0.0009	M	0.65975	2.015	0.34490	P	0.29508900000000005	B;B	0.23128	0.041;0.08	B;B	0.19946	0.027;0.023	T	0.18461	-1.0336	9	0.06494	T	0.89	-15.8916	2.4765	0.04577	0.1242:0.1348:0.1296:0.6114	rs17192170;rs52807491;rs17192170	898;898	G3V2D8;Q68DK2	.;ZFY26_HUMAN	S	898;877;898	ENSP00000251119:T898S;ENSP00000450603:T898S	ENSP00000251119:T898S	T	-	1	0	ZFYVE26	67327105	1.000000	0.71417	0.991000	0.47740	0.836000	0.47400	1.256000	0.32921	0.504000	0.28082	-0.336000	0.08194	ACC	T|0.932;A|0.068	0.068	strong		0.547	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
EPHA5	2044	hgsc.bcm.edu	37	4	66509085	66509085	+	Missense_Mutation	SNP	T	T	G	rs33932471	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:66509085T>G	ENST00000273854.3	-	2	842	c.242A>C	c.(241-243)aAt>aCt	p.N81T	EPHA5_ENST00000432638.2_Missense_Mutation_p.N81T|EPHA5_ENST00000511294.1_Missense_Mutation_p.N81T|EPHA5_ENST00000354839.4_Missense_Mutation_p.N81T	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	81	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.		N -> T (in dbSNP:rs33932471). {ECO:0000269|PubMed:17344846}.		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						ACTTACCCCATTTTTTGGAAA	0.338										TSP Lung(17;0.13)			T|||	133	0.0265575	0.0038	0.0303	5008	,	,		15740	0.001		0.0726	False		,,,				2504	0.0337				p.N81T		Atlas-SNP	.											.	EPHA5	315	.	0			c.A242C						PASS	.	T	THR/ASN,THR/ASN	61,4345	54.2+/-90.2	1,59,2143	54.0	55.0	54.0		242,242	5.4	1.0	4	dbSNP_126	54	550,8048	147.1+/-202.6	18,514,3767	yes	missense,missense	EPHA5	NM_004439.5,NM_182472.2	65,65	19,573,5910	GG,GT,TT		6.3968,1.3845,4.6986	possibly-damaging,possibly-damaging	81/1038,81/1016	66509085	611,12393	2203	4299	6502	SO:0001583	missense	2044	exon2			ACCCCATTTTTTG	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.242A>C	4.37:g.66509085T>G	ENSP00000273854:p.Asn81Thr	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	179	83	0.463687	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	69	0.03159340659340659	2	0.0040650406504065045	11	0.03038674033149171	1	0.0017482517482517483	55	0.07255936675461741	T	19.81	3.897453	0.72639	0.013845	0.063968	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.03607	3.87;3.87;3.87;3.87	5.4	5.4	0.78164	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.64402	D	0.000006	T	0.00552	0.0018	L	0.28694	0.88	0.49687	D	0.999813	P;P;P;P	0.49358	0.875;0.772;0.713;0.923	P;B;P;P	0.52672	0.676;0.439;0.547;0.706	T	0.46624	-0.9178	10	0.54805	T	0.06	.	15.7089	0.77609	0.0:0.0:0.0:1.0	rs33932471	81;81;81;81	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	T	81	ENSP00000273854:N81T;ENSP00000389208:N81T;ENSP00000346899:N81T;ENSP00000427638:N81T	ENSP00000273854:N81T	N	-	2	0	EPHA5	66191680	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	6.320000	0.72876	2.162000	0.67917	0.377000	0.23210	AAT	T|0.959;G|0.041	0.041	strong		0.338	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
GNAO1	2775	hgsc.bcm.edu	37	16	56377748	56377748	+	Intron	SNP	A	A	G	rs1799917	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:56377748A>G	ENST00000262493.6	+	6	1569				GNAO1_ENST00000262494.7_Silent_p.K317K	NM_020988.2	NP_066268.1	P09471	GNAO_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O						adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|dopamine receptor signaling pathway (GO:0007212)|forebrain development (GO:0030900)|locomotory behavior (GO:0007626)|muscle contraction (GO:0006936)|negative regulation of calcium ion transport (GO:0051926)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|regulation of heart contraction (GO:0008016)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to morphine (GO:0043278)	heterotrimeric G-protein complex (GO:0005834)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	corticotropin-releasing hormone receptor 1 binding (GO:0051430)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|mu-type opioid receptor binding (GO:0031852)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)	17		all_neural(199;0.159)				CAGCCCACAAAGAGATCTACA	0.562													G|||	2053	0.409944	0.6286	0.2435	5008	,	,		13508	0.2242		0.326	False		,,,				2504	0.5102				p.K317K		Atlas-SNP	.											.	GNAO1	95	.	0			c.A951G						PASS	.	G	,	2506,1890	541.3+/-375.7	701,1104,393	203.0	128.0	153.0		,951	4.4	1.0	16	dbSNP_89	153	2997,5603	664.4+/-402.2	532,1933,1835	no	intron,coding-synonymous	GNAO1	NM_020988.2,NM_138736.2	,	1233,3037,2228	GG,GA,AA		34.8488,42.9936,42.3438	,	,317/355	56377748	5503,7493	2198	4300	6498	SO:0001627	intron_variant	2775	exon8			CCACAAAGAGATC		CCDS10756.1, CCDS10757.1	16q13	2008-08-01			ENSG00000087258	ENSG00000087258			4389	protein-coding gene	gene with protein product		139311				1899283, 11395521	Standard	NM_020988		Approved	G-ALPHA-o	uc002eit.4	P09471	OTTHUMG00000133241	ENST00000262493.6:c.723+6976A>G	16.37:g.56377748A>G		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	120	99	0.825	NM_138736	P29777|Q8TD72|Q9UMV4	Silent	SNP	ENST00000262493.6	37	CCDS10756.1																																																																																			A|0.609;G|0.391	0.391	strong		0.562	GNAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256981.2	NM_020988	
ARSD	414	hgsc.bcm.edu	37	X	2833631	2833631	+	Silent	SNP	A	A	G	rs377542415		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	192	0	0		WXS	Illumina HiSeq	Phase_I	94	26	0.276596	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		
TSC2	7249	hgsc.bcm.edu	37	16	2138269	2138269	+	Silent	SNP	T	T	C	rs137854091|rs1748	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2138269T>C	ENST00000219476.3	+	41	5832	c.5202T>C	c.(5200-5202)gaT>gaC	p.D1734D	TSC2_ENST00000382538.6_Silent_p.D1619D|TSC2_ENST00000568454.1_Silent_p.D1678D|TSC2_ENST00000353929.4_Silent_p.D1691D|MIR1225_ENST00000408729.1_RNA|TSC2_ENST00000439673.2_Silent_p.D1631D|TSC2_ENST00000401874.2_Silent_p.D1667D|TSC2_ENST00000350773.4_Silent_p.D1711D	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1734	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				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)				ACCCCACCGATATCTACCCCT	0.652			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				C|||	1384	0.276358	0.7481	0.1988	5008	,	,		14957	0.0		0.1839	False		,,,				2504	0.0736				p.D1734D		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.T5202C						PASS	.	C	,,	2789,1607	496.0+/-363.4	885,1019,294	96.0	103.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5202,5001,5133	3.2	1.0	16	dbSNP_36	101	1531,7067	745.9+/-407.3	140,1251,2908	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	1025,2270,3202	CC,CT,TT		17.8065,36.556,33.2461	,,	1734/1808,1667/1741,1711/1785	2138269	4320,8674	2198	4299	6497	SO:0001819	synonymous_variant	7249	exon41	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CACCGATATCTAC	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.5202T>C	16.37:g.2138269T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	118	71	0.601695	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			T|0.695;G|0.000;C|0.305;A|0.000	0.305	strong		0.652	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
FAM205A	259308	hgsc.bcm.edu	37	9	34724987	34724987	+	Silent	SNP	A	A	G	rs1697617	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34724987A>G	ENST00000378788.3	-	4	2289	c.2250T>C	c.(2248-2250)gcT>gcC	p.A750A		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	750						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						TACCTGGTAAAGCCTGTTGCT	0.527																																					p.A750A		Atlas-SNP	.											FAM205A_ENST00000378788,colon,carcinoma,-1,2	FAM205A	45	2	0			c.T2250C						scavenged	.						50.0	37.0	41.0					9																	34724987		692	1591	2283	SO:0001819	synonymous_variant	259308	exon4			TGGTAAAGCCTGT		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.2250T>C	9.37:g.34724987A>G		Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	363	97	0.267218	NM_001141917	A8MVW7	Silent	SNP	ENST00000378788.3	37	CCDS55305.1																																																																																			A|0.870;G|0.130	0.130	strong		0.527	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
TBC1D15	64786	hgsc.bcm.edu	37	12	72307637	72307637	+	Silent	SNP	C	C	G	rs11178983	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:72307637C>G	ENST00000550746.1	+	13	1447	c.1383C>G	c.(1381-1383)tcC>tcG	p.S461S	TBC1D15_ENST00000548679.1_3'UTR|TBC1D15_ENST00000485960.2_Silent_p.S444S|TBC1D15_ENST00000319106.8_Silent_p.S452S|TBC1D15_ENST00000393309.3_Silent_p.S215S	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	461	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)|regulation of Rab GTPase activity (GO:0032313)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	Rab GTPase activator activity (GO:0005097)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ATTTACTTTCCCCTCTTTTAT	0.353													C|||	315	0.0628994	0.003	0.0346	5008	,	,		16596	0.0734		0.0606	False		,,,				2504	0.1554				p.S461S		Atlas-SNP	.											.	TBC1D15	99	.	0			c.C1383G						PASS	.	C	,,	81,4325	67.6+/-105.2	0,81,2122	131.0	136.0	134.0		1332,1356,1383	-6.5	0.6	12	dbSNP_120	134	661,7939	166.5+/-218.5	26,609,3665	no	coding-synonymous,coding-synonymous,coding-synonymous	TBC1D15	NM_001146213.1,NM_001146214.1,NM_022771.4	,,	26,690,5787	GG,GC,CC		7.686,1.8384,5.7051	,,	444/675,452/683,461/692	72307637	742,12264	2203	4300	6503	SO:0001819	synonymous_variant	64786	exon13			ACTTTCCCCTCTT	AL157464	CCDS31858.1, CCDS53814.1, CCDS55849.1	12q15	2013-07-09			ENSG00000121749	ENSG00000121749			25694	protein-coding gene	gene with protein product		612662				16055087	Standard	NM_022771		Approved	FLJ12085, DKFZp761D0223	uc001swu.3	Q8TC07	OTTHUMG00000158553	ENST00000550746.1:c.1383C>G	12.37:g.72307637C>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	33	0.354839	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Silent	SNP	ENST00000550746.1	37	CCDS31858.1																																																																																			C|0.947;G|0.053	0.053	strong		0.353	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	
SPACA3	124912	hgsc.bcm.edu	37	17	31322691	31322691	+	Missense_Mutation	SNP	A	A	G	rs28963	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:31322691A>G	ENST00000269053.3	+	2	369	c.299A>G	c.(298-300)cAt>cGt	p.H100R	SPACA3_ENST00000394638.1_Intron|SPACA3_ENST00000580599.1_Missense_Mutation_p.H31R|SPACA3_ENST00000394637.2_3'UTR	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	100			H -> R (in dbSNP:rs28963).		cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			AGAGTGCTACATGACTTCGGG	0.612																																					p.H100R		Atlas-SNP	.											.	SPACA3	35	.	0			c.A299G						PASS	.	A	ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	102.0	67.0	79.0		299	-1.0	0.0	17	dbSNP_76	79	14,8586	10.5+/-38.8	0,14,4286	yes	missense	SPACA3	NM_173847.3	29	0,15,6488	GG,GA,AA		0.1628,0.0227,0.1153	benign	100/216	31322691	15,12991	2203	4300	6503	SO:0001583	missense	124912	exon2			TGCTACATGACTT	AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316			16260	protein-coding gene	gene with protein product	"""cancer/testis antigen 54"", ""sperm lyzozyme-like acrosomal protein 1"""	612749				12606493	Standard	NM_173847		Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000269053.3:c.299A>G	17.37:g.31322691A>G	ENSP00000269053:p.His100Arg	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	203	101	0.497537	NM_173847	Q7Z4Y5	Missense_Mutation	SNP	ENST00000269053.3	37	CCDS11275.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	2.934|2.934	-0.220387|-0.220387	0.06061|0.06061	2.27E-4|2.27E-4	0.001628|0.001628	ENSG00000141316|ENSG00000141316	ENST00000269053;ENST00000394637|ENST00000411740	T|.	0.67345|.	-0.26|.	3.82|3.82	-0.968|-0.968	0.10313|0.10313	Lysozyme-like domain (1);|.	0.660523|.	0.13489|.	N|.	0.384114|.	T|T	0.16642|0.16642	0.0400|0.0400	N|N	0.05230|0.05230	-0.09|-0.09	0.09310|0.09310	N|N	1|1	B|.	0.06786|.	0.001|.	B|.	0.08055|.	0.003|.	T|T	0.20739|0.20739	-1.0266|-1.0266	10|6	0.39692|0.87932	T|D	0.17|0	-7.1977|-7.1977	3.9109|3.9109	0.09202|0.09202	0.4882:0.1912:0.3206:0.0|0.4882:0.1912:0.3206:0.0	rs28963;rs52826872;rs28963|rs28963;rs52826872;rs28963	100|.	Q8IXA5|.	SACA3_HUMAN|.	R|V	100;101|1	ENSP00000269053:H100R|.	ENSP00000269053:H100R|ENSP00000392807:M1V	H|M	+|+	2|1	0|0	SPACA3|SPACA3	28346804|28346804	0.026000|0.026000	0.19158|0.19158	0.000000|0.000000	0.03702|0.03702	0.607000|0.607000	0.37147|0.37147	2.419000|2.419000	0.44671|0.44671	-0.692000|-0.692000	0.05128|0.05128	-0.443000|-0.443000	0.05667|0.05667	CAT|ATG	A|0.998;G|0.002	0.002	strong		0.612	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786440	75786440	+	Silent	SNP	C	C	T	rs145944373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:75786440C>T	ENST00000478296.1	-	4	2460	c.2184G>A	c.(2182-2184)ggG>ggA	p.G728G	ZNF717_ENST00000422325.1_Silent_p.G778G|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000400845.3_Silent_p.G771G			Q9BY31	ZN717_HUMAN	zinc finger protein 717	768					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)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CTGAGTGAGTCCCCTGATGCG	0.413													c|||	3116	0.622204	0.3684	0.7133	5008	,	,		10213	0.8204		0.7167	False		,,,				2504	0.5992				p.G778G		Atlas-SNP	.											ZNF717,NS,carcinoma,0,1	ZNF717	160	1	0			c.G2334A						scavenged	.						7.0	7.0	7.0					3																	75786440		648	1313	1961	SO:0001819	synonymous_variant	100131827	exon5			GTGAGTCCCCTGA	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.2184G>A	3.37:g.75786440C>T		Somatic	57	5	0.0877193		WXS	Illumina HiSeq	Phase_I	43	33	0.767442	NM_001128223		Silent	SNP	ENST00000478296.1	37																																																																																				C|0.603;T|0.397	0.397	strong		0.413	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
ASPA	443	hgsc.bcm.edu	37	17	3397702	3397702	+	Silent	SNP	C	C	T	rs12948217	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:3397702C>T	ENST00000263080.2	+	5	851	c.693C>T	c.(691-693)taC>taT	p.Y231Y	ASPA_ENST00000456349.2_Silent_p.Y231Y|SPATA22_ENST00000541913.1_Intron	NM_000049.2	NP_000040.1	P45381	ACY2_HUMAN	aspartoacylase	231			Y -> C (in CAND). {ECO:0000269|PubMed:10564886}.		aspartate catabolic process (GO:0006533)|central nervous system myelination (GO:0022010)|positive regulation of oligodendrocyte differentiation (GO:0048714)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminoacylase activity (GO:0004046)|aspartoacylase activity (GO:0019807)|hydrolase activity, acting on ester bonds (GO:0016788)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(6)|lung(5)|stomach(1)|urinary_tract(1)	17					L-Aspartic Acid(DB00128)	AAGTTGATTACCCCCGGGATG	0.343													t|||	1020	0.203674	0.2345	0.1844	5008	,	,		20080	0.0496		0.3101	False		,,,				2504	0.2249				p.Y231Y		Atlas-SNP	.											.	ASPA	37	.	0			c.C693T	GRCh37	CM940123	ASPA	M	rs12948217	PASS	.	T	,	1075,3331	722.2+/-409.3	127,821,1255	179.0	200.0	192.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	693,693	3.5	1.0	17	dbSNP_121	192	2687,5913	683.3+/-403.9	446,1795,2059	no	coding-synonymous,coding-synonymous	ASPA	NM_000049.2,NM_001128085.1	,	573,2616,3314	TT,TC,CC		31.2442,24.3985,28.9251	,	231/314,231/314	3397702	3762,9244	2203	4300	6503	SO:0001819	synonymous_variant	443	exon5			TGATTACCCCCGG	S67156	CCDS11028.1	17p13.3	2010-06-24	2010-06-24		ENSG00000108381	ENSG00000108381	3.5.1.15		756	protein-coding gene	gene with protein product	"""aminoacylase 2"", ""Canavan disease"""	608034	"""aspartoacylase (aminoacylase 2, Canavan disease)"""			8252036	Standard	NM_001128085		Approved	ASP, ACY2	uc002fvq.3	P45381	OTTHUMG00000090655	ENST00000263080.2:c.693C>T	17.37:g.3397702C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	125	52	0.416	NM_000049		Silent	SNP	ENST00000263080.2	37	CCDS11028.1																																																																																			C|0.732;T|0.268	0.268	strong		0.343	ASPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207315.1	NM_000049	
KRT84	3890	hgsc.bcm.edu	37	12	52777439	52777439	+	Silent	SNP	A	A	G	rs1614888	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52777439A>G	ENST00000257951.3	-	2	756	c.690T>C	c.(688-690)agT>agC	p.S230S	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	230	Coil 1B.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGGCCTGATCACTGACCAGCA	0.557													a|||	1663	0.332069	0.6172	0.3199	5008	,	,		20368	0.1954		0.2058	False		,,,				2504	0.226				p.S230S		Atlas-SNP	.											.	KRT84	61	.	0			c.T690C						PASS	.	G		2467,1939	621.9+/-393.8	717,1033,453	70.0	67.0	68.0		690	-10.6	0.0	12	dbSNP_89	68	1804,6796	324.3+/-316.4	180,1444,2676	no	coding-synonymous	KRT84	NM_033045.3		897,2477,3129	GG,GA,AA		20.9767,44.0082,32.8387		230/601	52777439	4271,8735	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			CTGATCACTGACC	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.690T>C	12.37:g.52777439A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.686;G|0.314	0.314	strong		0.557	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
MRGPRF	116535	hgsc.bcm.edu	37	11	68772925	68772925	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68772925T>C	ENST00000309099.6	-	3	1235	c.853A>G	c.(853-855)Agc>Ggc	p.S285G	MRGPRF_ENST00000441623.1_Missense_Mutation_p.S285G|RP11-554A11.5_ENST00000562506.1_RNA	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	285						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GGCTTGGCGCTGCTGTTGATG	0.642																																					p.S285G		Atlas-SNP	.											MRGPRF,rectum,carcinoma,+2,1	MRGPRF	22	1	0			c.A853G						scavenged	.						34.0	27.0	29.0					11																	68772925		2195	4289	6484	SO:0001583	missense	116535	exon3			TGGCGCTGCTGTT	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"""GPCR / Class A : Orphans"""	24828	protein-coding gene	gene with protein product		607233	"""G protein-coupled receptor 168"", ""G protein-coupled receptor 140"""	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.853A>G	11.37:g.68772925T>C	ENSP00000309782:p.Ser285Gly	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	137	2	0.0145985	NM_001098515	B3KV43|Q8NBK8	Missense_Mutation	SNP	ENST00000309099.6	37	CCDS8188.1	.	.	.	.	.	.	.	.	.	.	T	14.28	2.489496	0.44249	.	.	ENSG00000172935	ENST00000441623;ENST00000309099;ENST00000421543	T;T	0.37915	1.17;1.17	5.25	-3.55	0.04639	GPCR, rhodopsin-like superfamily (1);	0.246864	0.28933	N	0.013663	T	0.29716	0.0742	M	0.78916	2.43	0.32093	N	0.591644	B	0.06786	0.001	B	0.01281	0.0	T	0.10019	-1.0648	10	0.59425	D	0.04	-10.9422	3.3026	0.06988	0.4245:0.2545:0.0:0.321	.	285	Q96AM1	MRGRF_HUMAN	G	285;285;257	ENSP00000403660:S285G;ENSP00000309782:S285G	ENSP00000309782:S285G	S	-	1	0	MRGPRF	68529501	0.811000	0.29063	0.981000	0.43875	0.977000	0.68977	-0.343000	0.07791	-0.570000	0.06022	0.459000	0.35465	AGC	.	.	none		0.642	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015	
CYFIP1	23191	hgsc.bcm.edu	37	15	22969232	22969232	+	Missense_Mutation	SNP	G	G	A	rs7170637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:22969232G>A	ENST00000313077.7	+	22	2583	c.2458G>A	c.(2458-2460)Ggc>Agc	p.G820S	CYFIP1_ENST00000435939.2_Missense_Mutation_p.G389S|CYFIP1_ENST00000560848.1_Missense_Mutation_p.G820S	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		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;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GACGCTGGACGGCTTCGACGC	0.607													A|||	1331	0.265775	0.6906	0.1484	5008	,	,		20818	0.004		0.1769	False		,,,				2504	0.136				p.G820S		Atlas-SNP	.											CYFIP1_ENST00000435939,colon,carcinoma,0,2	CYFIP1	159	2	0			c.G2458A						scavenged	.	A	SER/GLY,SER/GLY	2625,1781	527.9+/-372.3	787,1051,365	137.0	101.0	113.0		1165,2458	5.4	1.0	15	dbSNP_116	113	1407,7193	753.6+/-407.5	124,1159,3017	yes	missense,missense	CYFIP1	NM_001033028.1,NM_014608.2	56,56	911,2210,3382	AA,AG,GG		16.3605,40.4222,31.0011	benign,benign	389/823,820/1254	22969232	4032,8974	2203	4300	6503	SO:0001583	missense	23191	exon22			CTGGACGGCTTCG	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.2458G>A	15.37:g.22969232G>A	ENSP00000324549:p.Gly820Ser	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	62	44	0.709677	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	37	CCDS10009.1	532	0.24358974358974358	340	0.6910569105691057	51	0.1408839779005525	3	0.005244755244755245	138	0.1820580474934037	A	9.988	1.229904	0.22542	0.595778	0.163605	ENSG00000068793	ENST00000313077;ENST00000412127;ENST00000435939	T;T	0.20332	2.08;2.08	5.41	5.41	0.78517	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00210	-1.845	0.41978	P	0.009217999999999948	B;B;B	0.13145	0.002;0.007;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.33701	-0.9858	9	0.08381	T	0.77	-23.3927	11.3522	0.49594	0.9287:0.0:0.0713:0.0	rs7170637;rs17844900;rs17857620;rs7170637	848;389;820	E7EQ04;Q7L576-2;Q7L576	.;.;CYFP1_HUMAN	S	820;848;389	ENSP00000324549:G820S;ENSP00000405956:G389S	ENSP00000324549:G820S	G	+	1	0	CYFIP1	20520673	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	6.190000	0.72057	0.901000	0.36495	-0.361000	0.07541	GGC	G|0.704;A|0.296	0.296	strong		0.607	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
USP4	7375	hgsc.bcm.edu	37	3	49343175	49343175	+	Silent	SNP	G	G	A	rs2230929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49343175G>A	ENST00000265560.4	-	9	1147	c.1101C>T	c.(1099-1101)gaC>gaT	p.D367D	USP4_ENST00000351842.4_Silent_p.D320D|USP4_ENST00000488520.1_5'UTR	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	227	0	0		WXS	Illumina HiSeq	Phase_I	219	112	0.511416	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	
SLC12A5	57468	hgsc.bcm.edu	37	20	44680412	44680412	+	Silent	SNP	C	C	T	rs3746522	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44680412C>T	ENST00000454036.2	+	18	2398	c.2349C>T	c.(2347-2349)tcC>tcT	p.S783S	SLC12A5_ENST00000243964.3_Silent_p.S760S	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	783					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)	TGATCCAGTCCGGGGGCCTCG	0.592													C|||	866	0.172923	0.0121	0.1816	5008	,	,		13847	0.3393		0.2197	False		,,,				2504	0.1646				p.S783S		Atlas-SNP	.											SLC12A5,caecum,carcinoma,0,1	SLC12A5	181	1	0			c.C2349T						PASS	.	C	,	193,4213	120.0+/-157.7	6,181,2016	86.0	83.0	84.0		2349,2280	-8.4	0.8	20	dbSNP_107	84	1978,6622	347.9+/-326.8	223,1532,2545	no	coding-synonymous,coding-synonymous	SLC12A5	NM_001134771.1,NM_020708.4	,	229,1713,4561	TT,TC,CC		23.0,4.3804,16.6923	,	783/1140,760/1117	44680412	2171,10835	2203	4300	6503	SO:0001819	synonymous_variant	57468	exon18			CCAGTCCGGGGGC	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.2349C>T	20.37:g.44680412C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	37	CCDS46610.1																																																																																			C|0.824;T|0.176	0.176	strong		0.592	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
HHIPL1	84439	hgsc.bcm.edu	37	14	100129327	100129327	+	Silent	SNP	G	G	A	rs34890784	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	249	172	0.690763	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	
BTBD16	118663	hgsc.bcm.edu	37	10	124066731	124066731	+	Silent	SNP	T	T	G	rs7100442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124066731T>G	ENST00000260723.4	+	10	1070	c.819T>G	c.(817-819)ctT>ctG	p.L273L	BTBD16_ENST00000368994.2_Silent_p.L274L	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	273										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)				AATTCCATCTTCTGAAAACAA	0.348													T|||	648	0.129393	0.1263	0.2118	5008	,	,		20692	0.248		0.0338	False		,,,				2504	0.0511				p.L273L		Atlas-SNP	.											.	BTBD16	44	.	0			c.T819G						PASS	.	T		556,3850	247.5+/-255.7	41,474,1688	116.0	118.0	117.0		819	-1.2	0.9	10	dbSNP_116	117	247,8353	97.7+/-159.3	4,239,4057	no	coding-synonymous	BTBD16	NM_144587.2		45,713,5745	GG,GT,TT		2.8721,12.6192,6.1741		273/507	124066731	803,12203	2203	4300	6503	SO:0001819	synonymous_variant	118663	exon10			CCATCTTCTGAAA	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.819T>G	10.37:g.124066731T>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	149	70	0.469799	NM_144587	A6NM63|Q4VXL1|Q96LN0	Silent	SNP	ENST00000260723.4	37	CCDS31301.1																																																																																			T|0.906;G|0.094	0.094	strong		0.348	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
FCRLA	84824	hgsc.bcm.edu	37	1	161681780	161681780	+	Missense_Mutation	SNP	A	A	G	rs2275603	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161681780A>G	ENST00000236938.6	+	4	849	c.607A>G	c.(607-609)Agc>Ggc	p.S203G	FCRLA_ENST00000367950.1_Intron|FCRLA_ENST00000294796.4_Missense_Mutation_p.S52G|FCRLA_ENST00000540521.1_Missense_Mutation_p.S69G|FCRLA_ENST00000546024.1_Missense_Mutation_p.S114G|FCRLA_ENST00000367957.2_Missense_Mutation_p.S63G|FCRLA_ENST00000350710.3_Intron|FCRLA_ENST00000540926.1_Missense_Mutation_p.S192G|FCRLA_ENST00000349527.4_Intron|FCRLA_ENST00000309691.6_Missense_Mutation_p.S97G|FCRLA_ENST00000367959.2_Missense_Mutation_p.S209G|FCRLA_ENST00000367949.2_Intron|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000367953.3_Missense_Mutation_p.S192G	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	186	Ig-like C2-type 2.				cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)				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)			CCAAGCAGGAAGCCCCATGAC	0.522													G|||	2389	0.477037	0.764	0.4553	5008	,	,		17754	0.5734		0.2078	False		,,,				2504	0.2822				p.S209G		Atlas-SNP	.											.	FCRLA	101	.	0			c.A625G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER,,GLY/SER,,GLY/SER	2903,1503	477.0+/-357.8	980,943,280	116.0	145.0	135.0		625,340,205,,187,,607	-8.4	0.0	1	dbSNP_100	135	1882,6718	726.9+/-406.6	220,1442,2638	yes	missense,missense,missense,intron,missense,intron,missense	FCRLA	NM_001184866.1,NM_001184867.1,NM_001184870.1,NM_001184871.1,NM_001184872.1,NM_001184873.1,NM_032738.3	56,56,56,,56,,56	1200,2385,2918	GG,GA,AA		21.8837,34.1126,36.7907	benign,benign,benign,,benign,,benign	209/383,114/288,69/243,,63/237,,203/377	161681780	4785,8221	2203	4300	6503	SO:0001583	missense	84824	exon5			GCAGGAAGCCCCA	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.607A>G	1.37:g.161681780A>G	ENSP00000236938:p.Ser203Gly	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	208	76	0.365385	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	977	0.44734432234432236	357	0.725609756097561	143	0.39502762430939226	317	0.5541958041958042	160	0.21108179419525067	G	0.009	-1.843804	0.00568	0.658874	0.218837	ENSG00000132185	ENST00000236938;ENST00000367959;ENST00000546024;ENST00000540521;ENST00000540926;ENST00000367957;ENST00000309691;ENST00000294796;ENST00000367953	T;T;T;T;T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77;2.77	5.57	-8.4	0.00965	.	0.922351	0.09125	N	0.845187	T	0.02610	0.0079	L	0.41356	1.27	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.15484	0.001;0.013;0.001;0.0;0.001	T	0.46105	-0.9215	9	0.08837	T	0.75	.	20.1836	0.98210	0.8865:0.0:0.1135:0.0	rs2275603;rs60711230;rs2275603	69;63;114;209;203	F5H720;Q5VXB1;G3V1J2;A6NC03;Q7L513-9	.;.;.;.;.	G	203;209;114;69;192;63;97;52;192	ENSP00000236938:S203G;ENSP00000356936:S209G;ENSP00000439838:S114G;ENSP00000442870:S69G;ENSP00000446380:S192G;ENSP00000356934:S63G;ENSP00000309596:S97G;ENSP00000294796:S52G;ENSP00000356930:S192G	ENSP00000236938:S203G	S	+	1	0	FCRLA	159948404	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.373000	0.07494	-2.199000	0.00748	-0.930000	0.02707	AGC	A|0.595;G|0.405	0.405	strong		0.522	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	
NCOR1	9611	hgsc.bcm.edu	37	17	16068463	16068463	+	Missense_Mutation	SNP	C	C	T	rs74453660		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:16068463C>T	ENST00000268712.3	-	5	705	c.448G>A	c.(448-450)Gga>Aga	p.G150R	NCOR1_ENST00000395848.1_Missense_Mutation_p.G41R|NCOR1_ENST00000395851.1_Missense_Mutation_p.G150R	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	150	Interaction with ZBTB33 and HEXIM1.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|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)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)	p.G150R(2)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		TGTTTGCCTCCGAATGCTGGA	0.373																																					p.G150R		Atlas-SNP	.											NCOR1,NS,carcinoma,0,2	NCOR1	240	2	2	Substitution - Missense(2)	urinary_tract(1)|kidney(1)	c.G448A						PASS	.						108.0	100.0	103.0					17																	16068463		2203	4300	6503	SO:0001583	missense	9611	exon4			TGCCTCCGAATGC	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.448G>A	17.37:g.16068463C>T	ENSP00000268712:p.Gly150Arg	Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	488	66	0.135246	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.536088	0.27475	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000458113;ENST00000395848;ENST00000411510;ENST00000436828	T;T;T	0.44083	0.93;1.51;0.98	5.04	5.04	0.67666	.	0.436377	0.26792	N	0.022465	T	0.49490	0.1560	L	0.40543	1.245	0.80722	D	1	P;P;D;P;D;D;D	0.69078	0.569;0.702;0.957;0.702;0.997;0.994;0.964	B;B;P;B;P;P;P	0.58928	0.071;0.071;0.487;0.071;0.848;0.685;0.591	T	0.42716	-0.9435	10	0.41790	T	0.15	-8.2798	13.2054	0.59793	0.0:0.8401:0.1599:0.0	.	150;150;150;150;41;150;150	E7EU93;E7EV02;Q3B773;E7EW50;E9PGV6;O75376;O75376-2	.;.;.;.;.;NCOR1_HUMAN;.	R	150;150;41;150;41;150;150	ENSP00000268712:G150R;ENSP00000379192:G150R;ENSP00000379189:G41R	ENSP00000268712:G150R	G	-	1	0	NCOR1	16009188	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	2.110000	0.41873	2.349000	0.79799	0.478000	0.44815	GGA	.	.	weak		0.373	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
RASGRP1	10125	hgsc.bcm.edu	37	15	38794566	38794566	+	Silent	SNP	A	A	G	rs12324402	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:38794566A>G	ENST00000310803.5	-	12	1662	c.1485T>C	c.(1483-1485)ttT>ttC	p.F495F	RASGRP1_ENST00000450598.2_Silent_p.F460F|RASGRP1_ENST00000559830.1_Silent_p.F460F|RP11-102L12.2_ENST00000560231.1_RNA|RASGRP1_ENST00000558164.1_Silent_p.F460F|RASGRP1_ENST00000539159.1_Silent_p.F447F|RASGRP1_ENST00000561180.1_Silent_p.F546F	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	495	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		CAATCTTTTCAAATTCTTCCT	0.403													A|||	863	0.172324	0.1853	0.1787	5008	,	,		18857	0.006		0.2624	False		,,,				2504	0.229				p.F495F		Atlas-SNP	.											.	RASGRP1	50	.	0			c.T1485C						PASS	.	A	,	721,2949		69,583,1183	90.0	81.0	84.0		1380,1485	5.0	1.0	15	dbSNP_120	84	2142,6046		282,1578,2234	no	coding-synonymous,coding-synonymous	RASGRP1	NM_001128602.1,NM_005739.3	,	351,2161,3417	GG,GA,AA		26.1602,19.6458,24.144	,	460/763,495/798	38794566	2863,8995	1835	4094	5929	SO:0001819	synonymous_variant	10125	exon12			CTTTTCAAATTCT	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"""EF-hand domain containing"""	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.1485T>C	15.37:g.38794566A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	80	61	0.7625	NM_005739	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Silent	SNP	ENST00000310803.5	37	CCDS45222.1																																																																																			A|0.833;G|0.167	0.167	strong		0.403	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739	
CHST13	166012	hgsc.bcm.edu	37	3	126260995	126260995	+	Silent	SNP	C	C	T	rs7614066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126260995C>T	ENST00000319340.2	+	3	650	c.600C>T	c.(598-600)taC>taT	p.Y200Y		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	200					carbohydrate biosynthetic process (GO:0016051)|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 membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		AGAGGCGCTACGGTGCACGCA	0.721													C|||	273	0.0545128	0.1248	0.0288	5008	,	,		7896	0.002		0.0258	False		,,,				2504	0.0613				p.Y200Y		Atlas-SNP	.											.	CHST13	21	.	0			c.C600T						PASS	.	C		331,3793		10,311,1741	6.0	7.0	6.0		600	-5.3	0.2	3	dbSNP_116	6	189,7819		2,185,3817	no	coding-synonymous	CHST13	NM_152889.2		12,496,5558	TT,TC,CC		2.3601,8.0262,4.2862		200/342	126260995	520,11612	2062	4004	6066	SO:0001819	synonymous_variant	166012	exon3			GCGCTACGGTGCA	AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"""Sulfotransferases, membrane-bound"""	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.600C>T	3.37:g.126260995C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_152889	Q3SYA3|Q3SYA5	Silent	SNP	ENST00000319340.2	37	CCDS3039.1																																																																																			C|0.956;T|0.044	0.044	strong		0.721	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889	
TRIO	7204	hgsc.bcm.edu	37	5	14304588	14304588	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:14304588T>G	ENST00000344204.4	+	8	1411	c.1387T>G	c.(1387-1389)Tca>Gca	p.S463A	TRIO_ENST00000537187.1_Missense_Mutation_p.S463A|TRIO_ENST00000509967.2_Missense_Mutation_p.S414A	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	463					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)					CAACGTGGATTCATGGTGTAA	0.373																																					p.S463A		Atlas-SNP	.											.	TRIO	305	.	0			c.T1387G						PASS	.						177.0	160.0	166.0					5																	14304588		2203	4300	6503	SO:0001583	missense	7204	exon8			GTGGATTCATGGT	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.1387T>G	5.37:g.14304588T>G	ENSP00000339299:p.Ser463Ala	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	168	81	0.482143	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.816676	0.32145	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.65178	-0.14;-0.11;0.53	5.18	5.18	0.71444	.	0.080894	0.56097	D	0.000034	T	0.43366	0.1244	N	0.12831	0.26	0.48135	D	0.999591	B;B;B	0.22983	0.0;0.078;0.004	B;B;B	0.27380	0.002;0.079;0.001	T	0.35351	-0.9792	10	0.08599	T	0.76	.	15.0541	0.71897	0.0:0.0:0.0:1.0	.	414;463;463	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	A	463;463;414;150	ENSP00000339299:S463A;ENSP00000446348:S463A;ENSP00000445592:S414A	ENSP00000339299:S463A	S	+	1	0	TRIO	14357588	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	2.719000	0.47244	1.966000	0.57179	0.528000	0.53228	TCA	.	.	none		0.373	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
PKD1L2	114780	hgsc.bcm.edu	37	16	81232294	81232294	+	RNA	SNP	T	T	C	rs61734110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	122	0	0		WXS	Illumina HiSeq	Phase_I	109	88	0.807339	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		
TIFA	92610	hgsc.bcm.edu	37	4	113199075	113199075	+	Silent	SNP	A	A	G	rs701759|rs386678484	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:113199075A>G	ENST00000361717.3	-	2	779	c.498T>C	c.(496-498)taT>taC	p.Y166Y	TIFA_ENST00000500655.2_Silent_p.Y166Y	NM_052864.2	NP_443096.1	Q96CG3	TIFA_HUMAN	TRAF-interacting protein with forkhead-associated domain	166					I-kappaB kinase/NF-kappaB signaling (GO:0007249)					breast(2)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)	6		Ovarian(17;0.0443)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00172)		AGCAGAGCGAATAAGTGCCAT	0.423													A|||	3256	0.65016	0.8926	0.634	5008	,	,		18519	0.751		0.508	False		,,,				2504	0.3763				p.Y166Y		Atlas-SNP	.											.	TIFA	15	.	0			c.T498C						PASS	.	A		3697,709	757.8+/-412.8	1554,589,60	90.0	91.0	91.0		498	-11.2	0.0	4	dbSNP_86	91	4495,4105	590.0+/-392.6	1201,2093,1006	no	coding-synonymous	TIFA	NM_052864.2		2755,2682,1066	GG,GA,AA		47.7326,16.0917,37.0137		166/185	113199075	8192,4814	2203	4300	6503	SO:0001819	synonymous_variant	92610	exon2			GAGCGAATAAGTG	BC008294	CCDS34051.1	4q25	2008-03-17				ENSG00000145365			19075	protein-coding gene	gene with protein product	"""TRAF2 binding protein"", ""TRAF6 binding protein"""	609028				1179819	Standard	NM_052864		Approved	MGC20791, T2BP, T6BP, TIFAA	uc003ial.3	Q96CG3		ENST00000361717.3:c.498T>C	4.37:g.113199075A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_052864		Silent	SNP	ENST00000361717.3	37	CCDS34051.1																																																																																			A|0.344;G|0.656	0.656	strong		0.423	TIFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363647.2	NM_052864	
RHPN1	114822	hgsc.bcm.edu	37	8	144462841	144462841	+	Silent	SNP	G	G	A	rs117282246	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144462841G>A	ENST00000289013.6	+	11	1400	c.1299G>A	c.(1297-1299)gtG>gtA	p.V433V		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	458	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			TGCGCGAGGTGGACCTGCTTC	0.687													g|||	20	0.00399361	0.0	0.0	5008	,	,		17518	0.0		0.0129	False		,,,				2504	0.0072				p.V433V		Atlas-SNP	.											.	RHPN1	76	.	0			c.G1299A						PASS	.	G		7,4217		0,7,2105	19.0	23.0	21.0		1299	2.5	0.9	8	dbSNP_132	21	71,8371		0,71,4150	no	coding-synonymous	RHPN1	NM_052924.2		0,78,6255	AA,AG,GG		0.841,0.1657,0.6158		433/671	144462841	78,12588	2112	4221	6333	SO:0001819	synonymous_variant	114822	exon11			CGAGGTGGACCTG	AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.1299G>A	8.37:g.144462841G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	210	95	0.452381	NM_052924	Q8TAV1|Q96PV9	Silent	SNP	ENST00000289013.6	37	CCDS47927.1																																																																																			G|0.994;A|0.006	0.006	strong		0.687	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1		
AGMAT	79814	hgsc.bcm.edu	37	1	15909850	15909850	+	Missense_Mutation	SNP	C	C	G	rs6429757	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15909850C>G	ENST00000375826.3	-	2	455	c.313G>C	c.(313-315)Ggg>Cgg	p.G105R	DNAJC16_ENST00000483270.1_Intron|RP4-680D5.2_ENST00000428945.1_RNA	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	105			G -> R (in dbSNP:rs6429757). {ECO:0000269|PubMed:11804860, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		TTGACTGTCCCAAGCATCACT	0.527													G|||	3171	0.633187	0.9017	0.5274	5008	,	,		18672	0.6359		0.5288	False		,,,				2504	0.4499				p.G105R	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.G313C						PASS	.	G	ARG/GLY	3749,657	279.0+/-274.6	1598,553,52	63.0	57.0	59.0		313	-1.4	0.0	1	dbSNP_116	59	4755,3845	541.2+/-384.0	1338,2079,883	yes	missense	AGMAT	NM_024758.4	125	2936,2632,935	GG,GC,CC		44.7093,14.9115,34.6148	benign	105/353	15909850	8504,4502	2203	4300	6503	SO:0001583	missense	79814	exon2			CTGTCCCAAGCAT	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.313G>C	1.37:g.15909850C>G	ENSP00000364986:p.Gly105Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	1383	0.6332417582417582	428	0.8699186991869918	193	0.5331491712707183	344	0.6013986013986014	418	0.5514511873350924	G	0.008	-1.909524	0.00508	0.850885	0.552907	ENSG00000116771	ENST00000375826	D	0.84800	-1.9	5.13	-1.41	0.08941	Ureohydrolase domain (1);	0.051023	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00405	-1.535	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.34900	-0.9810	9	0.02654	T	1	-8.5468	3.7841	0.08692	0.0764:0.1895:0.3075:0.4267	rs6429757;rs17856129;rs56615894;rs6429757	105	Q9BSE5	SPEB_HUMAN	R	105	ENSP00000364986:G105R	ENSP00000364986:G105R	G	-	1	0	AGMAT	15782437	0.997000	0.39634	0.010000	0.14722	0.138000	0.21146	0.598000	0.24074	-0.321000	0.08627	-0.986000	0.02555	GGG	C|0.348;G|0.652	0.652	strong		0.527	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
PRND	23627	hgsc.bcm.edu	37	20	4705718	4705718	+	Missense_Mutation	SNP	C	C	T	rs2245220	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:4705718C>T	ENST00000305817.2	+	2	592	c.521C>T	c.(520-522)aCg>aTg	p.T174M		NM_012409.2	NP_036541.2	Q9UKY0	PRND_HUMAN	prion protein 2 (dublet)	174			T -> M (common polymorphism; dbSNP:rs2245220). {ECO:0000269|PubMed:10525406, ECO:0000269|PubMed:10825657, ECO:0000269|PubMed:11702213, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		protein homooligomerization (GO:0051260)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	13						ATCTGGCTCACGGTGAAATAA	0.577													T|||	2480	0.495208	0.6702	0.3646	5008	,	,		19250	0.253		0.4871	False		,,,				2504	0.6094				p.T174M		Atlas-SNP	.											PRND,caecum,carcinoma,0,1	PRND	34	1	0			c.C521T	GRCh37	CM014824	PRND	M	rs2245220	PASS	.	T	MET/THR	2798,1608		897,1004,302	22.0	21.0	21.0		521	2.2	0.0	20	dbSNP_100	21	4200,4392		1030,2140,1126	yes	missense	PRND	NM_012409.2	81	1927,3144,1428	TT,TC,CC		48.8827,36.4957,46.1609	benign	174/177	4705718	6998,6000	2203	4296	6499	SO:0001583	missense	23627	exon2			GGCTCACGGTGAA	AF106918	CCDS13081.1	20p13	2013-09-19			ENSG00000171864	ENSG00000171864			15748	protein-coding gene	gene with protein product	"""prion-like protein doppel"""	604263				10525406, 10577243	Standard	NM_012409		Approved	DPL, dJ1068H6.4, DOPPEL, PrPLP	uc002wkz.3	Q9UKY0	OTTHUMG00000031789	ENST00000305817.2:c.521C>T	20.37:g.4705718C>T	ENSP00000306900:p.Thr174Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_012409	A7U7M5|Q9H311|Q9H312|Q9NTM4	Missense_Mutation	SNP	ENST00000305817.2	37	CCDS13081.1	1004	0.4597069597069597	345	0.7012195121951219	140	0.3867403314917127	151	0.263986013986014	368	0.48548812664907653	T	8.922	0.961269	0.18583	0.635043	0.488827	ENSG00000171864	ENST00000305817	D	0.88664	-2.41	4.7	2.23	0.28157	Prion/Doppel protein, beta-ribbon domain (1);	0.787074	0.11050	N	0.605177	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	0.43766	-0.9371	9	0.38643	T	0.18	-13.5917	3.7704	0.08639	0.0:0.2044:0.1882:0.6074	rs2245220;rs17736407;rs17846360;rs17859396;rs52805311;rs61599564;rs2245220	174	Q9UKY0	PRND_HUMAN	M	174	ENSP00000306900:T174M	ENSP00000306900:T174M	T	+	2	0	PRND	4653718	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.864000	0.27926	0.253000	0.21552	-0.381000	0.06696	ACG	C|0.492;T|0.508	0.508	strong		0.577	PRND-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077827.2	NM_012409	
ADAMTSL1	92949	hgsc.bcm.edu	37	9	18777422	18777422	+	Silent	SNP	G	G	A	rs45579937	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	81	0	0		WXS	Illumina HiSeq	Phase_I	91	57	0.626374	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		
KAT2A	2648	hgsc.bcm.edu	37	17	40265751	40265751	+	Silent	SNP	C	C	T	rs147642400	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:40265751C>T	ENST00000225916.5	-	18	2483	c.2430G>A	c.(2428-2430)ccG>ccA	p.P810P	DHX58_ENST00000251642.3_5'Flank	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	810	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ACTCGCTGTCCGGGGGGTTGT	0.612													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		17799	0.0		0.004	False		,,,				2504	0.0				p.P810P		Atlas-SNP	.											.	KAT2A	54	.	0			c.G2430A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	34.0	35.0	34.0		2430	-10.1	0.6	17	dbSNP_134	34	54,8546	32.3+/-84.9	0,54,4246	no	coding-synonymous	KAT2A	NM_021078.2		0,55,6448	TT,TC,CC		0.6279,0.0227,0.4229		810/838	40265751	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	2648	exon18			GCTGTCCGGGGGG	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"""Chromatin-modifying enzymes / K-acetyltransferases"""	4201	protein-coding gene	gene with protein product		602301	"""GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"""	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.2430G>A	17.37:g.40265751C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	54	15	0.277778	NM_021078	Q8N1A2|Q9UCW1	Silent	SNP	ENST00000225916.5	37	CCDS11417.1																																																																																			C|0.998;T|0.002	0.002	strong		0.612	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204434438	204434438	+	Missense_Mutation	SNP	G	G	A	rs45492196	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:204434438G>A	ENST00000367187.3	-	4	1499	c.943C>T	c.(943-945)Cgg>Tgg	p.R315W	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.R315W	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	315					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)			GTGTGGGGCCGGGAGCCCACC	0.502													G|||	92	0.0183706	0.0038	0.0202	5008	,	,		16995	0.001		0.0537	False		,,,				2504	0.0184				p.R315W		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C943T						PASS	.	G	TRP/ARG	46,4360	47.5+/-82.1	0,46,2157	91.0	95.0	94.0		943	3.3	1.0	1	dbSNP_127	94	459,8141	136.2+/-193.3	12,435,3853	yes	missense	PIK3C2B	NM_002646.3	101	12,481,6010	AA,AG,GG		5.3372,1.044,3.8828	probably-damaging	315/1635	204434438	505,12501	2203	4300	6503	SO:0001583	missense	5287	exon4			GGGGCCGGGAGCC	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.943C>T	1.37:g.204434438G>A	ENSP00000356155:p.Arg315Trp	Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	513	306	0.596491	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	37	CCDS1446.1	53	0.024267399267399268	4	0.008130081300813009	10	0.027624309392265192	0	0.0	39	0.051451187335092345	G	18.81	3.704108	0.68615	0.01044	0.053372	ENSG00000133056	ENST00000367187;ENST00000424712;ENST00000438854;ENST00000367184	T;T	0.62232	0.04;0.11	5.24	3.35	0.38373	.	0.728159	0.12772	N	0.440488	T	0.19805	0.0476	L	0.44542	1.39	0.37785	D	0.927165	D;P	0.71674	0.998;0.83	P;B	0.52856	0.711;0.23	T	0.51325	-0.8720	10	0.87932	D	0	.	2.2963	0.04151	0.1668:0.1537:0.5205:0.159	rs45492196;rs61749328	315;315	F5GWN5;O00750	.;P3C2B_HUMAN	W	315;315;93;93	ENSP00000356155:R315W;ENSP00000400561:R315W	ENSP00000356152:R93W	R	-	1	2	PIK3C2B	202701061	0.999000	0.42202	0.990000	0.47175	0.941000	0.58515	1.269000	0.33074	0.586000	0.29626	0.655000	0.94253	CGG	G|0.963;A|0.037	0.037	strong		0.502	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
TBC1D2B	23102	hgsc.bcm.edu	37	15	78369815	78369815	+	Silent	SNP	G	G	A	rs9047	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:78369815G>A	ENST00000300584.3	-	1	179	c.180C>T	c.(178-180)ttC>ttT	p.F60F	SH2D7_ENST00000409568.2_5'Flank|TBC1D2B_ENST00000409931.3_Silent_p.F60F	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	38	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	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	
RNF123	63891	hgsc.bcm.edu	37	3	49749976	49749976	+	Missense_Mutation	SNP	G	G	A	rs34823813	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49749976G>A	ENST00000327697.6	+	27	2705	c.2561G>A	c.(2560-2562)cGc>cAc	p.R854H	RNF123_ENST00000433785.1_5'Flank|RNF123_ENST00000432042.1_Missense_Mutation_p.R708H	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	177	0	0		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	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	
IGSF10	285313	hgsc.bcm.edu	37	3	151161112	151161112	+	Missense_Mutation	SNP	A	A	G	rs12487205	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	123	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	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	
WDR27	253769	hgsc.bcm.edu	37	6	170047902	170047902	+	Missense_Mutation	SNP	T	T	A	rs61740334	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170047902T>A	ENST00000448612.1	-	16	1733	c.1624A>T	c.(1624-1626)Acc>Tcc	p.T542S	WDR27_ENST00000333572.6_Missense_Mutation_p.T542S|WDR27_ENST00000423258.1_Missense_Mutation_p.T415S|WDR27_ENST00000546525.1_5'UTR	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	512						nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		CGTGTGCAGGTGGGGGCGGCA	0.617													T|||	287	0.0573083	0.0121	0.0418	5008	,	,		13579	0.0992		0.0726	False		,,,				2504	0.0706				p.T542S		Atlas-SNP	.											.	WDR27	129	.	0			c.A1624T						PASS	.	T	SER/THR,SER/THR	72,3958		0,72,1943	9.0	13.0	12.0		1624,1243	-7.6	0.0	6	dbSNP_129	12	578,7746		16,546,3600	yes	missense,missense	WDR27	NM_182552.4,NM_001202550.1	58,58	16,618,5543	AA,AT,TT		6.9438,1.7866,5.2615	benign,benign	542/896,415/731	170047902	650,11704	2015	4162	6177	SO:0001583	missense	253769	exon16			TGCAGGTGGGGGC	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"""WD repeat domain containing"""	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.1624A>T	6.37:g.170047902T>A	ENSP00000416289:p.Thr542Ser	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	227	120	0.528634	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	37	CCDS47520.2	141	0.06456043956043957	8	0.016260162601626018	16	0.04419889502762431	62	0.10839160839160839	55	0.07255936675461741	T	1.713	-0.498641	0.04291	0.017866	0.069438	ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000423258	T;T;D	0.95724	1.94;1.09;-3.79	3.79	-7.58	0.01313	.	3.278270	0.00991	N	0.003520	T	0.67924	0.2945	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.20887	0.013;0.009;0.049	B;B;B	0.18263	0.004;0.014;0.021	T	0.75079	-0.3444	9	0.08599	T	0.76	1.0724	8.3339	0.32202	0.0:0.5217:0.2596:0.2187	rs61740334	542;415;542	F2Z2U5;A2RRH5-2;C9JGV0	.;.;.	S	542;542;415	ENSP00000416289:T542S;ENSP00000330265:T542S;ENSP00000397869:T415S	ENSP00000330265:T542S	T	-	1	0	WDR27	169789827	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.815000	0.00096	-2.957000	0.00291	-0.959000	0.02639	ACC	T|0.912;A|0.088	0.088	strong		0.617	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
TCF25	22980	hgsc.bcm.edu	37	16	89965055	89965055	+	Silent	SNP	G	G	A	rs11648433	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:89965055G>A	ENST00000263346.8	+	10	1169	c.1113G>A	c.(1111-1113)ctG>ctA	p.L371L	TCF25_ENST00000263347.7_Silent_p.L136L	NM_014972.2	NP_055787.1	Q9BQ70	TCF25_HUMAN	transcription factor 25 (basic helix-loop-helix)	371					heart development (GO:0007507)|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)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|ovary(3)|skin(1)|urinary_tract(2)	18		all_cancers(9;4.71e-08)|Lung NSC(15;0.000192)|all_lung(18;0.000319)|all_neural(9;0.0122)|all_hematologic(23;0.027)		BRCA - Breast invasive adenocarcinoma(80;0.0288)		AGCTCATCCTGAGGTGAGTGT	0.622													G|||	393	0.0784744	0.0045	0.0231	5008	,	,		17571	0.2837		0.0666	False		,,,				2504	0.0184				p.L371L		Atlas-SNP	.											.	TCF25	61	.	0			c.G1113A						PASS	.	G		89,4307	72.5+/-110.5	0,89,2109	64.0	70.0	68.0		1113	-0.7	1.0	16	dbSNP_120	68	746,7854	179.6+/-228.7	34,678,3588	no	coding-synonymous	TCF25	NM_014972.2		34,767,5697	AA,AG,GG		8.6744,2.0246,6.4251		371/677	89965055	835,12161	2198	4300	6498	SO:0001819	synonymous_variant	22980	exon10			CATCCTGAGGTGA	AF322111	CCDS10987.1	16q24.3	2008-02-05			ENSG00000141002	ENSG00000141002			29181	protein-coding gene	gene with protein product		612326				12107429, 16574069	Standard	NM_014972		Approved	Nulp1, KIAA1049	uc002fpb.2	Q9BQ70	OTTHUMG00000138986	ENST00000263346.8:c.1113G>A	16.37:g.89965055G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	15	0.254237	NM_014972	Q2MK75|Q9UPV3	Silent	SNP	ENST00000263346.8	37	CCDS10987.1																																																																																			G|0.932;A|0.068	0.068	strong		0.622	TCF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272875.2	NM_014972	
TBC1D32	221322	hgsc.bcm.edu	37	6	121642851	121642851	+	Missense_Mutation	SNP	C	C	T	rs7767455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	315	1	0.0031746		WXS	Illumina HiSeq	Phase_I	281	128	0.455516	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	
FANCA	2175	hgsc.bcm.edu	37	16	89857935	89857935	+	Missense_Mutation	SNP	G	G	A	rs11646374	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:89857935G>A	ENST00000389301.3	-	14	1265	c.1235C>T	c.(1234-1236)gCg>gTg	p.A412V	FANCA_ENST00000568369.1_Missense_Mutation_p.A412V	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	412			A -> V (in dbSNP:rs11646374). {ECO:0000269|PubMed:18987736}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		CATCAAACGCGCCACCCAGTC	0.567			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	353	0.0704872	0.0038	0.0187	5008	,	,		19935	0.254		0.0626	False		,,,				2504	0.0164				p.A412V		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C1235T						PASS	.	G	VAL/ALA	76,4320	64.7+/-102.0	0,76,2122	65.0	51.0	56.0		1235	5.1	0.1	16	dbSNP_120	56	698,7902	172.5+/-223.2	26,646,3628	yes	missense	FANCA	NM_000135.2	64	26,722,5750	AA,AG,GG		8.1163,1.7288,5.9557	possibly-damaging	412/1456	89857935	774,12222	2198	4300	6498	SO:0001583	missense	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAACGCGCCACCC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1235C>T	16.37:g.89857935G>A	ENSP00000373952:p.Ala412Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	21	0.247059	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	180	0.08241758241758242	3	0.006097560975609756	10	0.027624309392265192	117	0.20454545454545456	50	0.06596306068601583	G	14.47	2.546014	0.45383	0.017288	0.081163	ENSG00000187741	ENST00000389301	D	0.98585	-5.01	5.13	5.13	0.70059	.	0.801903	0.11032	N	0.607099	T	0.03220	0.0094	M	0.65975	2.015	0.09310	P	0.9999999999981521	P;P	0.52316	0.952;0.952	B;B	0.41174	0.349;0.349	T	0.11155	-1.0599	9	0.46703	T	0.11	-1.967	12.244	0.54560	0.0:0.1854:0.8146:0.0	rs11646374;rs17226204;rs52813493;rs58856001;rs11646374	412;412	B4DRI7;O15360	.;FANCA_HUMAN	V	412	ENSP00000373952:A412V	ENSP00000373952:A412V	A	-	2	0	FANCA	88385436	1.000000	0.71417	0.128000	0.21923	0.016000	0.09150	4.990000	0.63876	2.417000	0.82017	0.650000	0.86243	GCG	G|0.932;A|0.068	0.068	strong		0.567	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
MKI67	4288	hgsc.bcm.edu	37	10	129899778	129899778	+	Missense_Mutation	SNP	G	G	C	rs11106	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129899778G>C	ENST00000368654.3	-	14	9824	c.9449C>G	c.(9448-9450)aCt>aGt	p.T3150S	MKI67_ENST00000368653.3_Missense_Mutation_p.T2790S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3150			T -> S (in dbSNP:rs11106).		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)				TTTGTTCTCAGTGACTTTGTC	0.498													C|||	2123	0.423922	0.4561	0.5432	5008	,	,		18870	0.3859		0.4264	False		,,,				2504	0.3323				p.T3150S		Atlas-SNP	.											.	MKI67	363	.	0			c.C9449G						PASS	.	C	SER/THR,SER/THR	1961,2445	621.5+/-393.8	446,1069,688	178.0	169.0	172.0		8369,9449	-1.5	0.0	10	dbSNP_52	172	3659,4941	623.1+/-397.4	781,2097,1422	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	58,58	1227,3166,2110	CC,CG,GG		42.5465,44.5075,43.2108	benign,benign	2790/2897,3150/3257	129899778	5620,7386	2203	4300	6503	SO:0001583	missense	4288	exon14			TTCTCAGTGACTT	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.9449C>G	10.37:g.129899778G>C	ENSP00000357643:p.Thr3150Ser	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	217	103	0.474654	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	941	0.4308608058608059	190	0.3861788617886179	187	0.5165745856353591	239	0.4178321678321678	325	0.4287598944591029	C	0.019	-1.458143	0.01071	0.445075	0.425465	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01178	5.27;5.22	2.91	-1.54	0.08584	.	1.520690	0.03664	N	0.243062	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	0.30765	-0.9967	9	0.07644	T	0.81	.	3.3231	0.07057	0.1586:0.2004:0.513:0.1281	rs11106;rs3191123;rs17804362;rs52813625;rs58399763;rs11106	2790;3150	P46013-2;P46013	.;KI67_HUMAN	S	3150;2790;3149	ENSP00000357643:T3150S;ENSP00000357642:T2790S	ENSP00000357642:T2790S	T	-	2	0	MKI67	129789768	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.919000	0.01572	-0.713000	0.04981	-0.215000	0.12644	ACT	G|0.569;C|0.431	0.431	strong		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
MYT1L	23040	hgsc.bcm.edu	37	2	1893133	1893133	+	Silent	SNP	C	C	T	rs75247762	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:1893133C>T	ENST00000399161.2	-	16	3147	c.2400G>A	c.(2398-2400)caG>caA	p.Q800Q	MYT1L_ENST00000428368.2_Silent_p.Q798Q	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	800					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)		TCACTGCCTGCTGCTGGGGGG	0.617													C|||	321	0.0640974	0.0015	0.0504	5008	,	,		15516	0.1994		0.0457	False		,,,				2504	0.0378				p.Q798Q		Atlas-SNP	.											.	MYT1L	241	.	0			c.G2394A						PASS	.	C		40,4030		0,40,1995	59.0	65.0	63.0		2394	2.7	1.0	2	dbSNP_132	63	441,7897		15,411,3743	no	coding-synonymous	MYT1L	NM_015025.2		15,451,5738	TT,TC,CC		5.289,0.9828,3.8765		798/1185	1893133	481,11927	2035	4169	6204	SO:0001819	synonymous_variant	23040	exon16			TGCCTGCTGCTGG	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.2400G>A	2.37:g.1893133C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																				C|0.930;T|0.070	0.070	strong		0.617	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
TNN	63923	hgsc.bcm.edu	37	1	175087729	175087729	+	Missense_Mutation	SNP	T	T	C	rs6696455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:175087729T>C	ENST00000239462.4	+	11	2532	c.2419T>C	c.(2419-2421)Tgg>Cgg	p.W807R		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	807	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.		W -> R (in dbSNP:rs6696455).		axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GGTCACTGACTGGGTGACAGA	0.517													C|||	2370	0.473243	0.91	0.3818	5008	,	,		18720	0.0704		0.4513	False		,,,				2504	0.3855				p.W807R		Atlas-SNP	.											.	TNN	297	.	0			c.T2419C						PASS	.	C	ARG/TRP	3632,774	310.5+/-291.6	1501,630,72	55.0	60.0	58.0		2419	0.9	0.0	1	dbSNP_116	58	3790,4810	611.1+/-395.8	827,2136,1337	yes	missense	TNN	NM_022093.1	101	2328,2766,1409	CC,CT,TT		44.0698,17.567,42.934	benign	807/1300	175087729	7422,5584	2203	4300	6503	SO:0001583	missense	63923	exon11			ACTGACTGGGTGA	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.2419T>C	1.37:g.175087729T>C	ENSP00000239462:p.Trp807Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	181	179	0.98895	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	929	0.42536630036630035	418	0.8495934959349594	139	0.3839779005524862	44	0.07692307692307693	328	0.43271767810026385	C	0.009	-1.837943	0.00573	0.82433	0.440698	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.55588	0.51	5.17	0.856	0.19019	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.988879	0.08265	N	0.972365	T	0.00012	0.0000	N	0.00185	-1.9	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32508	-0.9904	9	0.32370	T	0.25	.	4.7145	0.12889	0.3345:0.2723:0.3273:0.0659	rs6696455;rs52819008;rs56969638;rs6696455	807	Q9UQP3	TENN_HUMAN	R	807;630	ENSP00000239462:W807R	ENSP00000239462:W807R	W	+	1	0	TNN	173354352	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.030000	0.12308	-0.249000	0.09569	-1.619000	0.00793	TGG	T|0.488;C|0.512	0.512	strong		0.517	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
CASP1	834	hgsc.bcm.edu	37	11	104900488	104900488	+	Silent	SNP	G	G	A	rs580253	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:104900488G>A	ENST00000533400.1	-	6	801	c.766C>T	c.(766-768)Cta>Tta	p.L256L	CASP1_ENST00000598974.1_Silent_p.L256L|CASP1_ENST00000446369.1_Silent_p.L163L|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000415981.2_Intron|CASP1_ENST00000436863.3_Silent_p.L256L|CASP1_ENST00000534497.1_Silent_p.L163L|CASP1_ENST00000525825.1_Silent_p.L235L|CASP1_ENST00000527979.1_Silent_p.L219L|CASP1_ENST00000526568.1_Silent_p.L163L|CASP1_ENST00000393136.4_Silent_p.L235L|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000593315.1_Silent_p.L235L|CASP1_ENST00000528974.1_Silent_p.L217L|CASP1_ENST00000594519.1_Silent_p.L163L	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	256					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	TTGAGTTGTAGTATATCTGGG	0.468													.|||	580	0.115815	0.0893	0.2464	5008	,	,		19797	0.006		0.1759	False		,,,				2504	0.1104				p.L256L	NSCLC(41;1246 1743 4934)	Atlas-SNP	.											.	CASP1	53	.	0			c.C766T						PASS	.	A	,,,,	420,3984		18,384,1800	140.0	125.0	130.0		703,766,487,487,	1.1	0.0	11	dbSNP_83	130	1409,7189		125,1159,3015	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	CASP1	NM_001223.3,NM_033292.2,NM_033293.2,NM_033294.2,NM_033295.2	,,,,	143,1543,4815	AA,AG,GG		16.3875,9.5368,14.0671	,,,,	235/384,256/405,163/312,163/264,	104900488	1829,11173	2202	4299	6501	SO:0001819	synonymous_variant	834	exon6			GTTGTAGTATATC	U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"""Caspases"""	1499	protein-coding gene	gene with protein product	"""caspase-1"", ""interleukin 1, beta, convertase"""	147678	"""caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)"", ""caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"""	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.766C>T	11.37:g.104900488G>A		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	492	137	0.278455	NM_001257118	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Silent	SNP	ENST00000533400.1	37	CCDS8330.1																																																																																			G|0.867;A|0.133	0.133	strong		0.468	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292	
SPAG17	200162	hgsc.bcm.edu	37	1	118629599	118629599	+	Silent	SNP	G	G	A	rs12142616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:118629599G>A	ENST00000336338.5	-	11	1457	c.1392C>T	c.(1390-1392)ccC>ccT	p.P464P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	464						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)		CCCGCAGACTGGGTGGGACGA	0.522													G|||	660	0.131789	0.0749	0.0461	5008	,	,		17193	0.2847		0.0596	False		,,,				2504	0.1861				p.P464P		Atlas-SNP	.											.	SPAG17	263	.	0			c.C1392T						PASS	.	G		339,4067	175.1+/-204.6	12,315,1876	126.0	123.0	124.0		1392	-10.1	0.0	1	dbSNP_120	124	489,8111	143.0+/-199.1	16,457,3827	no	coding-synonymous	SPAG17	NM_206996.2		28,772,5703	AA,AG,GG		5.686,7.6941,6.3663		464/2224	118629599	828,12178	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon11			CAGACTGGGTGGG		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.1392C>T	1.37:g.118629599G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	67	52	0.776119	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			G|0.923;A|0.077	0.077	strong		0.522	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
C5orf64	285668	hgsc.bcm.edu	37	5	60999768	60999768	+	Missense_Mutation	SNP	C	C	T	rs436696	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:60999768C>T	ENST00000505642.1	+	4	376	c.301C>T	c.(301-303)Cgg>Tgg	p.R101W	C5orf64_ENST00000313303.7_Missense_Mutation_p.R101W|C5orf64_ENST00000510414.1_3'UTR	NM_173667.2	NP_775938.1	Q2M2E5	CE064_HUMAN	chromosome 5 open reading frame 64	101			R -> W (in dbSNP:rs436696). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				breast(1)	1						AATAGAGGAACGGAAAGTTTT	0.388													C|||	1094	0.21845	0.3411	0.2061	5008	,	,		21113	0.003		0.329	False		,,,				2504	0.1697				p.R101W		Atlas-SNP	.											C5orf64,caecum,carcinoma,0,2	C5orf64	9	2	0			c.C301T						PASS	.	C	TRP/ARG	1219,2651		187,845,903	105.0	101.0	102.0		301	1.6	0.0	5	dbSNP_80	102	2880,5384		484,1912,1736	yes	missense	C5orf64	NM_173667.2	101	671,2757,2639	TT,TC,CC		34.85,31.4987,33.7811	possibly-damaging	101/131	60999768	4099,8035	1935	4132	6067	SO:0001583	missense	285668	exon4			GAGGAACGGAAAG		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.301C>T	5.37:g.60999768C>T	ENSP00000423157:p.Arg101Trp	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	190	89	0.468421	NM_173667	Q2M2H1|Q8N1U8	Missense_Mutation	SNP	ENST00000505642.1	37	CCDS54860.1	488	0.22344322344322345	161	0.32723577235772355	84	0.23204419889502761	1	0.0017482517482517483	242	0.31926121372031663	C	4.794	0.147611	0.09134	0.314987	0.3485	ENSG00000178722	ENST00000505642;ENST00000313303	T;T	0.40476	1.03;1.03	4.16	1.61	0.23674	.	0.996198	0.08121	N	0.994721	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	0.37267	-0.9713	9	0.87932	D	0	9.0349	5.6444	0.17582	0.0:0.2226:0.0:0.7774	rs436696;rs61432002;rs436696	101	Q2M2E5	CE064_HUMAN	W	101	ENSP00000423157:R101W;ENSP00000318395:R101W	ENSP00000318395:R101W	R	+	1	2	C5orf64	61035525	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.239000	0.18023	0.398000	0.25338	-0.290000	0.09829	CGG	C|0.769;T|0.231	0.231	strong		0.388	C5orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368790.1	NM_173667	
IGF1R	3480	hgsc.bcm.edu	37	15	99456369	99456369	+	Silent	SNP	G	G	A	rs2228531	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:99456369G>A	ENST00000268035.6	+	8	2297	c.1686G>A	c.(1684-1686)gtG>gtA	p.V562V	IGF1R_ENST00000558762.1_Silent_p.V562V	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	562	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	ACAAGGACGTGGAGCCCGGCA	0.567													G|||	22	0.00439297	0.0008	0.0072	5008	,	,		19039	0.0		0.0149	False		,,,				2504	0.001				p.V562V		Atlas-SNP	.											.	IGF1R	147	.	0			c.G1686A						PASS	.	G		12,4382	19.1+/-41.9	0,12,2185	99.0	78.0	85.0		1686	-9.1	0.0	15	dbSNP_98	85	117,8477	61.7+/-123.6	0,117,4180	no	coding-synonymous	IGF1R	NM_000875.3		0,129,6365	AA,AG,GG		1.3614,0.2731,0.9932		562/1368	99456369	129,12859	2197	4297	6494	SO:0001819	synonymous_variant	3480	exon8			GGACGTGGAGCCC	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.1686G>A	15.37:g.99456369G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	65	22	0.338462	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																			G|0.990;A|0.010	0.010	strong		0.567	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
PRRC2B	84726	hgsc.bcm.edu	37	9	134351770	134351770	+	Silent	SNP	G	G	A	rs78591540	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:134351770G>A	ENST00000357304.4	+	15	4309	c.4254G>A	c.(4252-4254)aaG>aaA	p.K1418K	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron|PRRC2B_ENST00000405995.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1418							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						AGCTGGCCAAGAGGAGCTTCT	0.652											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	487	0.0972444	0.1778	0.0735	5008	,	,		13836	0.004		0.163	False		,,,				2504	0.0337				p.K1418K		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G4254A						PASS	.	G		504,3354		23,458,1448	15.0	17.0	16.0		4254	4.9	1.0	9	dbSNP_132	16	1094,7126		70,954,3086	no	coding-synonymous	PRRC2B	NM_013318.3		93,1412,4534	AA,AG,GG		13.309,13.0638,13.2307		1418/2230	134351770	1598,10480	1929	4110	6039	SO:0001819	synonymous_variant	84726	exon15			GGCCAAGAGGAGC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.4254G>A	9.37:g.134351770G>A		Somatic	70	0	0	1610	WXS	Illumina HiSeq	Phase_I	67	63	0.940298	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1	219	0.10027472527472528	68	0.13821138211382114	29	0.08011049723756906	1	0.0017482517482517483	121	0.15963060686015831	G	7.262	0.605446	0.14002	0.130638	0.13309	ENSG00000130723	ENST00000451855	.	.	.	5.93	4.94	0.65067	.	.	.	.	.	T	0.00412	0.0013	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06463	-1.0825	3	.	.	.	.	12.4476	0.55659	0.1081:0.0:0.8919:0.0	.	.	.	.	K	152	.	.	E	+	1	0	PRRC2B	133341591	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	3.787000	0.55439	2.814000	0.96858	0.655000	0.94253	GAG	A|0.104;C|0.000;G|0.895	0.104	strong		0.652	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OMG	4974	hgsc.bcm.edu	37	17	29623288	29623288	+	Missense_Mutation	SNP	C	C	T	rs11080149	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:29623288C>T	ENST00000247271.4	-	2	323	c.62G>A	c.(61-63)gGt>gAt	p.G21D	NF1_ENST00000356175.3_Intron|NF1_ENST00000358273.4_Intron	NM_002544.4	NP_002535.3	P23515	OMGP_HUMAN	oligodendrocyte myelin glycoprotein	21			G -> D (in dbSNP:rs11080149).		cell adhesion (GO:0007155)|negative regulation of axonogenesis (GO:0050771)|neuron projection regeneration (GO:0031102)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|regulation of collateral sprouting of intact axon in response to injury (GO:0048683)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.0?(8)|p.?(3)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|stomach(1)	13		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;1.81e-13)|Epithelial(4;4.04e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.49e-12)|GBM - Glioblastoma multiforme(4;0.121)		GCATAAAATACCAGGTGTGAG	0.403													C|||	205	0.0409345	0.0076	0.0735	5008	,	,		20869	0.0		0.1054	False		,,,				2504	0.0389				p.G21D		Atlas-SNP	.											.	OMG	30	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.G62A						PASS	.	C	,,ASP/GLY	113,4293	86.3+/-125.0	0,113,2090	78.0	75.0	76.0		,,62	3.2	1.0	17	dbSNP_120	76	1032,7568	218.4+/-256.8	67,898,3335	yes	intron,intron,missense	NF1,OMG	NM_000267.3,NM_001042492.2,NM_002544.4	,,94	67,1011,5425	TT,TC,CC		12.0,2.5647,8.8036	,,possibly-damaging	,,21/441	29623288	1145,11861	2203	4300	6503	SO:0001583	missense	4974	exon2			AAAATACCAGGTG		CCDS11265.1	17q11-q12	2008-07-18			ENSG00000126861	ENSG00000126861			8135	protein-coding gene	gene with protein product		164345				1899288, 2277079	Standard	NM_002544		Approved	OMGP	uc002hgj.3	P23515	OTTHUMG00000132870	ENST00000247271.4:c.62G>A	17.37:g.29623288C>T	ENSP00000247271:p.Gly21Asp	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	NM_002544	E1P659	Missense_Mutation	SNP	ENST00000247271.4	37	CCDS11265.1	109	0.04990842490842491	6	0.012195121951219513	20	0.055248618784530384	0	0.0	83	0.10949868073878628	C	9.393	1.075892	0.20227	0.025647	0.12	ENSG00000126861	ENST00000247271	T	0.61392	0.11	5.23	3.15	0.36227	.	0.309106	0.27696	N	0.018239	T	0.00637	0.0021	L	0.27053	0.805	0.38132	P	0.06181199999999998	B	0.16802	0.019	B	0.16289	0.015	T	0.09640	-1.0665	9	0.66056	D	0.02	-1.5116	7.3305	0.26580	0.0:0.4951:0.3546:0.1503	rs11080149;rs17767990;rs17878280;rs56581348;rs57667724;rs11080149	21	P23515	OMGP_HUMAN	D	21	ENSP00000247271:G21D	ENSP00000247271:G21D	G	-	2	0	OMG	26647414	0.972000	0.33761	1.000000	0.80357	0.996000	0.88848	1.113000	0.31184	1.314000	0.45095	0.557000	0.71058	GGT	C|0.931;T|0.069	0.069	strong		0.403	OMG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256350.2	NM_002544	
GUCY2D	3000	hgsc.bcm.edu	37	17	7918754	7918754	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7918754G>A	ENST00000254854.4	+	15	3028	c.2878G>A	c.(2878-2880)Gtg>Atg	p.V960M		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	960	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.				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)				CCTCAGTGCCGTGGGCACTTT	0.637																																					p.V960M		Atlas-SNP	.											GUCY2D_ENST00000254854,NS,carcinoma,0,2	GUCY2D	82	2	0			c.G2878A						scavenged	.						50.0	42.0	45.0					17																	7918754		2203	4300	6503	SO:0001583	missense	3000	exon15			AGTGCCGTGGGCA	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.2878G>A	17.37:g.7918754G>A	ENSP00000254854:p.Val960Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	2	0.0204082	NM_000180	Q6LEA7	Missense_Mutation	SNP	ENST00000254854.4	37	CCDS11127.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.139257	0.77775	.	.	ENSG00000132518	ENST00000254854	D	0.84944	-1.92	4.92	4.92	0.64577	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.45126	D	0.000385	D	0.88489	0.6450	L	0.33624	1.015	0.43036	D	0.99461	D	0.89917	1.0	D	0.80764	0.994	D	0.89672	0.3884	10	0.62326	D	0.03	.	17.0538	0.86527	0.0:0.0:1.0:0.0	.	960	Q02846	GUC2D_HUMAN	M	960	ENSP00000254854:V960M	ENSP00000254854:V960M	V	+	1	0	GUCY2D	7859479	1.000000	0.71417	0.954000	0.39281	0.944000	0.59088	4.781000	0.62389	2.546000	0.85860	0.467000	0.42956	GTG	.	.	none		0.637	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2		
SCN4A	6329	hgsc.bcm.edu	37	17	62020348	62020348	+	Missense_Mutation	SNP	T	T	C	rs2058194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:62020348T>C	ENST00000435607.1	-	23	4202	c.4126A>G	c.(4126-4128)Aac>Gac	p.N1376D	SCN4A_ENST00000578147.1_Missense_Mutation_p.N1376D	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1376			N -> D (in dbSNP:rs2058194). {ECO:0000269|PubMed:1315496}.		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.N1376D(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TGGCTCTGGTTGTCTGTCTCC	0.532													C|||	2812	0.561502	0.7837	0.4697	5008	,	,		24608	0.5377		0.5557	False		,,,				2504	0.3569				p.N1376D		Atlas-SNP	.											SCN4A,NS,carcinoma,0,1	SCN4A	205	1	1	Substitution - Missense(1)	stomach(1)	c.A4126G						scavenged	.	C	ASP/ASN	3221,1185	414.6+/-336.9	1193,835,175	224.0	209.0	214.0		4126	3.9	1.0	17	dbSNP_94	214	4574,4026	556.3+/-386.8	1265,2044,991	yes	missense	SCN4A	NM_000334.4	23	2458,2879,1166	CC,CT,TT		46.814,26.8951,40.0661	benign	1376/1837	62020348	7795,5211	2203	4300	6503	SO:0001583	missense	6329	exon23			TCTGGTTGTCTGT	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.4126A>G	17.37:g.62020348T>C	ENSP00000396320:p.Asn1376Asp	Somatic	406	4	0.00985222		WXS	Illumina HiSeq	Phase_I	413	183	0.443099	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	1282	0.586996336996337	387	0.7865853658536586	184	0.5082872928176796	289	0.5052447552447552	422	0.5567282321899736	C	8.322	0.824528	0.16678	0.731049	0.53186	ENSG00000007314	ENST00000435607	D	0.97328	-4.34	3.87	3.87	0.44632	.	0.050633	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00045	-2.445	0.48288	P	3.769999999999607E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47100	-0.9143	9	0.02654	T	1	.	11.0601	0.47942	0.0:0.9087:0.0:0.0913	rs2058194;rs52833416;rs56720134;rs2058194	1376	P35499	SCN4A_HUMAN	D	1376	ENSP00000396320:N1376D	ENSP00000396320:N1376D	N	-	1	0	SCN4A	59374080	1.000000	0.71417	0.988000	0.46212	0.969000	0.65631	4.799000	0.62517	0.993000	0.38866	-0.355000	0.07637	AAC	T|0.407;C|0.593	0.593	strong		0.532	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
FAM160B2	64760	hgsc.bcm.edu	37	8	21955116	21955116	+	Silent	SNP	C	C	T	rs11352	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:21955116C>T	ENST00000289921.7	+	4	433	c.387C>T	c.(385-387)gtC>gtT	p.V129V		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	129										endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						ACCTCAGCGTCCACAGGCCTG	0.657													.|||	1855	0.370407	0.3601	0.2594	5008	,	,		16790	0.374		0.3946	False		,,,				2504	0.4346				p.V129V		Atlas-SNP	.											.	FAM160B2	35	.	0			c.C387T						PASS	.	C		1385,2707		248,889,909	24.0	29.0	27.0		387	2.3	1.0	8	dbSNP_52	27	3416,4960		701,2014,1473	no	coding-synonymous	FAM160B2	NM_022749.5		949,2903,2382	TT,TC,CC		40.7832,33.8465,38.5066		129/744	21955116	4801,7667	2046	4188	6234	SO:0001819	synonymous_variant	64760	exon4			CAGCGTCCACAGG	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.387C>T	8.37:g.21955116C>T		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	281	161	0.572954	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Silent	SNP	ENST00000289921.7	37	CCDS6021.2																																																																																			C|0.639;T|0.361	0.361	strong		0.657	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2		
MICA	100507436	hgsc.bcm.edu	37	6	31379795	31379795	+	Missense_Mutation	SNP	A	A	G	rs1131898|rs386699191	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31379795A>G	ENST00000449934.2	+	4	739	c.685A>G	c.(685-687)Agc>Ggc	p.S229G	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)				CAGGGCTTCCAGCTTCTATCC	0.587													g|||	1823	0.364018	0.4773	0.4063	5008	,	,		19594	0.2996		0.3141	False		,,,				2504	0.2986				p.S229G		Atlas-SNP	.											.	MICA	21	.	0			c.A685G						PASS	.						20.0	24.0	23.0					6																	31379795		692	1591	2283	SO:0001583	missense	100507436	exon4			GCTTCCAGCTTCT	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.685A>G	6.37:g.31379795A>G	ENSP00000413079:p.Ser229Gly	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	118	37	0.313559	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	664	0.304029304029304	188	0.3821138211382114	147	0.40607734806629836	134	0.23426573426573427	195	0.25725593667546176	N	0.013	-1.630927	0.00813	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.09163	3.01;3.01	2.52	-1.92	0.07618	.	1.300610	0.05734	N	0.600057	T	0.00967	0.0032	.	.	.	0.80722	P	0.0	B;B	0.14012	0.009;0.003	B;B	0.08055	0.003;0.001	T	0.43310	-0.9399	8	0.02654	T	1	.	8.8893	0.35423	0.6127:0.0:0.3873:0.0	rs1131898;rs3192173;rs17206701;rs17883642	91;229	Q5SS58;Q96QC4	.;.	G	91;229;186;229;120	ENSP00000413079:S229G;ENSP00000402410:S120G	ENSP00000365394:S229G	S	+	1	0	MICA	31487774	0.015000	0.18098	0.001000	0.08648	0.014000	0.08584	0.171000	0.16685	-0.782000	0.04541	-1.366000	0.01203	AGC	A|0.700;G|0.300	0.300	strong		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
KRT84	3890	hgsc.bcm.edu	37	12	52774305	52774305	+	Silent	SNP	A	A	G	rs1732293	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52774305A>G	ENST00000257951.3	-	7	1332	c.1266T>C	c.(1264-1266)gaT>gaC	p.D422D	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	422	Coil 2.|Rod.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TGCATTTGGCATCACTGAGGG	0.632											OREG0021848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1686	0.336661	0.6369	0.3184	5008	,	,		20415	0.2004		0.2068	False		,,,				2504	0.2178				p.D422D		Atlas-SNP	.											.	KRT84	61	.	0			c.T1266C						PASS	.	G		2537,1869	537.0+/-374.6	756,1025,422	46.0	38.0	41.0		1266	-10.1	0.0	12	dbSNP_89	41	1804,6796	726.4+/-406.6	180,1444,2676	no	coding-synonymous	KRT84	NM_033045.3		936,2469,3098	GG,GA,AA		20.9767,42.4194,33.3769		422/601	52774305	4341,8665	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon7			TTTGGCATCACTG	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.1266T>C	12.37:g.52774305A>G		Somatic	127	0	0	987	WXS	Illumina HiSeq	Phase_I	117	55	0.470085	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.682;G|0.318	0.318	strong		0.632	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
ATRN	8455	hgsc.bcm.edu	37	20	3564672	3564672	+	Silent	SNP	C	C	T	rs235540	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	235	134	0.570213	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	
ACOT8	10005	hgsc.bcm.edu	37	20	44483868	44483868	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44483868C>T	ENST00000217455.4	-	2	282	c.192G>A	c.(190-192)ctG>ctA	p.L64L	ZSWIM3_ENST00000255152.2_5'Flank|ZSWIM3_ENST00000454862.2_5'Flank	NM_005469.3	NP_005460.2	O14734	ACOT8_HUMAN	acyl-CoA thioesterase 8	64					acyl-CoA metabolic process (GO:0006637)|alpha-linolenic acid metabolic process (GO:0036109)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|dicarboxylic acid catabolic process (GO:0043649)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|peroxisome fission (GO:0016559)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|viral process (GO:0016032)	mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|choloyl-CoA hydrolase activity (GO:0033882)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			kidney(2)|large_intestine(3)|lung(4)|skin(1)	10		Myeloproliferative disorder(115;0.0122)				CTGCAGCCACCAGGGCCTGGC	0.587																																					p.L64L		Atlas-SNP	.											ACOT8,NS,carcinoma,-2,1	ACOT8	29	1	0			c.G192A						scavenged	.						110.0	105.0	106.0					20																	44483868		2203	4300	6503	SO:0001819	synonymous_variant	10005	exon2			AGCCACCAGGGCC	AF014404	CCDS13378.1	20q13.12	2012-05-16	2005-09-19	2005-09-19	ENSG00000101473	ENSG00000101473	3.1.2.27	"""Acyl CoA thioesterases"""	15919	protein-coding gene	gene with protein product	"""choloyl-CoA hydrolase"""	608123	"""peroxisomal acyl-CoA thioesterase"", ""peroxisomal acyl-CoA thioesterase 1"""	PTE1		10092594, 9153233, 16103133, 16940157	Standard	NM_005469		Approved	hACTE-III, hTE, PTE-2	uc002xqa.2	O14734	OTTHUMG00000033045	ENST00000217455.4:c.192G>A	20.37:g.44483868C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	2	0.0363636	NM_005469	O15261|Q17RX4	Silent	SNP	ENST00000217455.4	37	CCDS13378.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.844|9.844	1.191853|1.191853	0.21954|0.21954	.|.	.|.	ENSG00000101473|ENSG00000101473	ENST00000457981|ENST00000487205	.|.	.|.	.|.	4.98|4.98	4.98|4.98	0.66077|0.66077	.|.	.|.	.|.	.|.	.|.	T|.	0.74374|.	0.3708|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.73414|.	-0.3990|.	4|.	.|.	.|.	.|.	.|.	18.4349|18.4349	0.90642|0.90642	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	S|X	25|19	.|.	.|.	G|W	-|-	1|2	0|0	ACOT8|ACOT8	43917275|43917275	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	2.025000|2.025000	0.41059|0.41059	2.588000|2.588000	0.87417|0.87417	0.561000|0.561000	0.74099|0.74099	GGT|TGG	.	.	none		0.587	ACOT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080338.2	NM_183386	
TMPRSS11A	339967	hgsc.bcm.edu	37	4	68810246	68810246	+	Silent	SNP	G	G	A	rs1370840	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:68810246G>A	ENST00000334830.7	-	3	989	c.243C>T	c.(241-243)acC>acT	p.T81T	TMPRSS11A_ENST00000508048.1_Silent_p.T80T|UBA6-AS1_ENST00000500538.2_RNA|TMPRSS11A_ENST00000396188.2_Silent_p.T81T			Q6ZMR5	TM11A_HUMAN	transmembrane protease, serine 11A	81	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell cycle (GO:0007049)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.T81T(1)		breast(1)|cervix(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	29						CCAAATTTTCGGTCGTCTCTC	0.338													g|||	1638	0.327077	0.5537	0.3761	5008	,	,		18399	0.1885		0.2157	False		,,,				2504	0.2434				p.T81T	NSCLC(26;2 894 10941 14480 22546)	Atlas-SNP	.											TMPRSS11A,NS,carcinoma,0,1	TMPRSS11A	74	1	1	Substitution - coding silent(1)	stomach(1)	c.C243T						PASS	.	A	,	2178,2228	586.0+/-386.4	526,1126,551	164.0	168.0	166.0		243,243	-10.6	0.0	4	dbSNP_88	166	1451,7149	276.4+/-292.3	117,1217,2966	no	coding-synonymous,coding-synonymous	TMPRSS11A	NM_001114387.1,NM_182606.3	,	643,2343,3517	AA,AG,GG		16.8721,49.4326,27.9025	,	81/419,81/422	68810246	3629,9377	2203	4300	6503	SO:0001819	synonymous_variant	339967	exon3			ATTTTCGGTCGTC	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.243C>T	4.37:g.68810246G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_001114387	J3KNQ8|Q2NKI9|Q6JE90|Q7RTY4|Q86TK8	Silent	SNP	ENST00000334830.7	37	CCDS3519.1																																																																																			G|0.710;A|0.290	0.290	strong		0.338	TMPRSS11A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251433.3	NM_182606	
ZNF17	7565	hgsc.bcm.edu	37	19	57931553	57931553	+	Silent	SNP	C	C	T	rs10417533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57931553C>T	ENST00000601808.1	+	3	906	c.693C>T	c.(691-693)tcC>tcT	p.S231S	AC004076.7_ENST00000597410.1_Intron|ZNF17_ENST00000307658.7_Silent_p.S233S	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	231					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(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		GGTACAACTCCGACCTTATTA	0.413													C|||	1133	0.226238	0.3449	0.2176	5008	,	,		23816	0.0794		0.2694	False		,,,				2504	0.1789				p.S231S	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.C693T						PASS	.	C		1306,3092	411.3+/-335.7	195,916,1088	87.0	89.0	89.0		693	-3.5	0.0	19	dbSNP_119	89	2171,6427	363.7+/-333.3	274,1623,2402	no	coding-synonymous	ZNF17	NM_006959.2		469,2539,3490	TT,TC,CC		25.2501,29.6953,26.7544		231/663	57931553	3477,9519	2199	4299	6498	SO:0001819	synonymous_variant	7565	exon3			CAACTCCGACCTT	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"""Zinc fingers, C2H2-type"", ""-"""	12958	protein-coding gene	gene with protein product			"""zinc finger protein 17 (HPF3, KOX 10)"""			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.693C>T	19.37:g.57931553C>T		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Silent	SNP	ENST00000601808.1	37	CCDS42636.1																																																																																			C|0.772;T|0.228	0.228	strong		0.413	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959	
EXO5	64789	hgsc.bcm.edu	37	1	40980731	40980731	+	Missense_Mutation	SNP	G	G	T	rs11208299	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:40980731G>T	ENST00000372703.1	+	2	1589	c.515G>T	c.(514-516)gGg>gTg	p.G172V	RP11-656D10.6_ENST00000437060.1_RNA|EXO5_ENST00000296380.4_Missense_Mutation_p.G172V|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000358527.2_Missense_Mutation_p.G172V			Q9H790	EXO5_HUMAN	exonuclease 5	172			G -> V (polymorphism that does not affect exonuclease activity; dbSNP:rs11208299). {ECO:0000269|PubMed:15489334}.		DNA catabolic process, exonucleolytic (GO:0000738)|interstrand cross-link repair (GO:0036297)	cytosol (GO:0005829)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)										TTTGGGGAAGGGGAGGGTGTA	0.502													T|||	2715	0.542133	0.6997	0.536	5008	,	,		20246	0.5		0.3757	False		,,,				2504	0.5481				p.G172V		Atlas-SNP	.											.	.	.	.	0			c.G515T						PASS	.	T	VAL/GLY	2811,1595	493.4+/-362.7	897,1017,289	82.0	88.0	86.0		515	4.0	1.0	1	dbSNP_120	86	3196,5404	651.2+/-400.8	582,2032,1686	yes	missense	DEM1	NM_022774.1	109	1479,3049,1975	TT,TG,GG		37.1628,36.2006,46.1864	benign	172/374	40980731	6007,6999	2203	4300	6503	SO:0001583	missense	64789	exon3			GGGAAGGGGAGGG	AK024797	CCDS453.1	1p34.2	2012-11-02	2012-10-30	2012-10-30	ENSG00000164002	ENSG00000164002			26115	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 176"", ""defects in morphology 1 homolog (S. cerevisiae)"""	C1orf176, DEM1		23095756	Standard	NM_022774		Approved	FLJ21144	uc001cfp.3	Q9H790	OTTHUMG00000007305	ENST00000372703.1:c.515G>T	1.37:g.40980731G>T	ENSP00000361788:p.Gly172Val	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	127	33	0.259843	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Missense_Mutation	SNP	ENST00000372703.1	37	CCDS453.1	1122	0.5137362637362637	357	0.725609756097561	185	0.511049723756906	295	0.5157342657342657	285	0.3759894459102902	T	0.127	-1.118333	0.01785	0.637994	0.371628	ENSG00000164002	ENST00000358527;ENST00000372703;ENST00000420209;ENST00000296380;ENST00000418186;ENST00000443729;ENST00000419161	T;T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83;1.83	5.09	3.96	0.45880	.	0.692054	0.12336	N	0.477953	T	0.00012	0.0000	N	0.00025	-2.675	0.38200	P	0.059826999999999964	B	0.02656	0.0	B	0.01281	0.0	T	0.41431	-0.9509	9	0.02654	T	1	-5.5314	5.3966	0.16273	0.0:0.0896:0.1772:0.7333	rs11208299;rs17845666;rs17858602;rs52798759;rs60314009;rs11208299	172	Q9H790	EXO5_HUMAN	V	172	ENSP00000351328:G172V;ENSP00000361788:G172V;ENSP00000398437:G172V;ENSP00000296380:G172V;ENSP00000391240:G172V;ENSP00000409715:G172V;ENSP00000392115:G172V	ENSP00000296380:G172V	G	+	2	0	DEM1	40753318	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.213000	0.42844	0.504000	0.28082	-0.264000	0.10439	GGG	G|0.508;T|0.492	0.492	strong		0.502	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774	
CSF3R	1441	hgsc.bcm.edu	37	1	36937106	36937106	+	Missense_Mutation	SNP	C	C	T	rs3918019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:36937106C>T	ENST00000373106.1	-	10	1760	c.1213G>A	c.(1213-1215)Gag>Aag	p.E405K	CSF3R_ENST00000373103.1_Missense_Mutation_p.E405K|CSF3R_ENST00000418048.2_Missense_Mutation_p.E405K|CSF3R_ENST00000373104.1_Missense_Mutation_p.E405K|CSF3R_ENST00000338937.5_Missense_Mutation_p.E405K|CSF3R_ENST00000331941.5_Missense_Mutation_p.E405K|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000440588.2_Missense_Mutation_p.E405K|CSF3R_ENST00000361632.4_Missense_Mutation_p.E405K	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	405	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> K (in dbSNP:rs3918019). {ECO:0000269|Ref.4}.		cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	AGGGCCACCTCCTGGGCTTCT	0.612													C|||	8	0.00159744	0.0	0.0014	5008	,	,		17751	0.0		0.007	False		,,,				2504	0.0				p.E405K		Atlas-SNP	.											.	CSF3R	157	.	0			c.G1213A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	103.0	111.0	108.0		1213,1213,1213	3.3	0.9	1	dbSNP_108	108	37,8563	25.7+/-73.6	1,35,4264	yes	missense,missense,missense	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	56,56,56	1,38,6464	TT,TC,CC		0.4302,0.0681,0.3076	possibly-damaging,possibly-damaging,possibly-damaging	405/837,405/864,405/784	36937106	40,12966	2203	4300	6503	SO:0001583	missense	1441	exon10			CCACCTCCTGGGC	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1213G>A	1.37:g.36937106C>T	ENSP00000362198:p.Glu405Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	73	50	0.684932	NM_156039		Missense_Mutation	SNP	ENST00000373106.1	37	CCDS413.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	15.35	2.808248	0.50421	6.81E-4	0.004302	ENSG00000119535	ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000338937;ENST00000440588	T;T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.2	3.3	0.37823	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.580572	0.20168	N	0.097787	T	0.05686	0.0149	L	0.33485	1.01	0.25352	N	0.988858	P;P;P;B	0.48764	0.915;0.902;0.651;0.028	B;B;B;B	0.36092	0.217;0.194;0.057;0.038	T	0.14952	-1.0454	10	0.06236	T	0.91	-11.2121	7.3658	0.26772	0.0:0.7939:0.0:0.2061	rs3918019;rs3918019	405;405;405;405	E1B6W6;Q99062-3;Q99062;Q99062-4	.;.;CSF3R_HUMAN;.	K	405	ENSP00000362198:E405K;ENSP00000362196:E405K;ENSP00000362195:E405K;ENSP00000355406:E405K;ENSP00000332180:E405K;ENSP00000401588:E405K;ENSP00000345013:E405K;ENSP00000397568:E405K	ENSP00000332180:E405K	E	-	1	0	CSF3R	36709693	0.102000	0.21896	0.923000	0.36655	0.788000	0.44548	1.384000	0.34396	0.561000	0.29186	-0.258000	0.10820	GAG	C|0.996;T|0.004	0.004	strong		0.612	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039	
OR2AK2	391191	hgsc.bcm.edu	37	1	248128929	248128929	+	Missense_Mutation	SNP	G	G	A	rs6664332	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248128929G>A	ENST00000366480.3	+	1	395	c.296G>A	c.(295-297)aGc>aAc	p.S99N	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	99			S -> N (in dbSNP:rs6664332).			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)			ATGGCAGTCAGCTTCCTCTCA	0.483													.|||	1861	0.371605	0.2882	0.3646	5008	,	,		20363	0.4633		0.328	False		,,,				2504	0.4397				p.S99N	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.G296A						PASS	.	A	ASN/SER,	1281,3125		189,903,1111	232.0	204.0	214.0		296,	1.9	0.0	1	dbSNP_116	214	2872,5728		471,1930,1899	yes	missense,intron	OR2L13,OR2AK2	NM_001004491.1,NM_175911.2	46,	660,2833,3010	AA,AG,GG		33.3953,29.074,31.9314	benign,	99/336,	248128929	4153,8853	2203	4300	6503	SO:0001583	missense	391191	exon1			CAGTCAGCTTCCT	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.296G>A	1.37:g.248128929G>A	ENSP00000355436:p.Ser99Asn	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	225	84	0.373333	NM_001004491	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	37	CCDS31102.1	776	0.3553113553113553	131	0.266260162601626	140	0.3867403314917127	252	0.4405594405594406	253	0.3337730870712401	.	0.010	-1.794300	0.00617	0.29074	0.333953	ENSG00000187080	ENST00000366480	T	0.01126	5.3	3.15	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00337	-1.62	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17349	-1.0372	8	0.07813	T	0.8	.	2.7483	0.05273	0.4798:0.0:0.1224:0.3979	rs6664332;rs58317680;rs6664332	99	Q8NG84	O2AK2_HUMAN	N	99	ENSP00000355436:S99N	ENSP00000355436:S99N	S	+	2	0	OR2AK2	246195552	0.000000	0.05858	0.002000	0.10522	0.030000	0.12068	0.001000	0.13038	-0.026000	0.13895	-0.556000	0.04195	AGC	G|0.663;A|0.337	0.337	strong		0.483	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491	
IDUA	3425	hgsc.bcm.edu	37	4	995305	995305	+	Silent	SNP	T	T	C	rs6815946	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:995305T>C	ENST00000247933.4	+	5	631	c.543T>C	c.(541-543)aaT>aaC	p.N181N	IDUA_ENST00000514224.1_Silent_p.N49N|IDUA_ENST00000453894.1_Silent_p.N134N	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	86	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	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	
CNDP1	84735	hgsc.bcm.edu	37	18	72238472	72238472	+	Missense_Mutation	SNP	C	C	A	rs73973908	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	372	3	0.00806452		WXS	Illumina HiSeq	Phase_I	349	344	0.985673	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	
TEP1	7011	hgsc.bcm.edu	37	14	20847202	20847202	+	Silent	SNP	A	A	G	rs938887	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20847202A>G	ENST00000262715.5	-	36	5230	c.5190T>C	c.(5188-5190)gaT>gaC	p.D1730D	TEP1_ENST00000556935.1_Silent_p.D1622D|TEP1_ENST00000545983.1_Silent_p.D68D	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	170	0	0		WXS	Illumina HiSeq	Phase_I	187	64	0.342246	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	
SLC16A13	201232	hgsc.bcm.edu	37	17	6943266	6943266	+	Silent	SNP	G	G	A	rs4796576	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	58	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	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		
OSCP1	127700	hgsc.bcm.edu	37	1	36898067	36898067	+	Missense_Mutation	SNP	T	T	C	rs34409118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:36898067T>C	ENST00000356637.5	-	4	484	c.421A>G	c.(421-423)Acc>Gcc	p.T141A	OSCP1_ENST00000433045.2_Missense_Mutation_p.T86A|OSCP1_ENST00000354267.3_Missense_Mutation_p.T131A|OSCP1_ENST00000315643.9_Missense_Mutation_p.T141A|OSCP1_ENST00000235532.5_Missense_Mutation_p.T131A			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	141			T -> A (in dbSNP:rs34409118). {ECO:0000269|PubMed:16006562}.		transport (GO:0006810)	plasma membrane (GO:0005886)		p.T141A(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						TGCAGGATGGTTGGGGAGTCT	0.502													T|||	1042	0.208067	0.1604	0.1369	5008	,	,		21091	0.2599		0.2048	False		,,,				2504	0.273				p.T131A		Atlas-SNP	.											OSCP1_ENST00000354267,colon,carcinoma,0,4	OSCP1	48	4	2	Substitution - Missense(2)	stomach(1)|pancreas(1)	c.A391G						PASS	.	T	ALA/THR,ALA/THR	794,3612	317.4+/-295.1	67,660,1476	128.0	113.0	118.0		391,391	-1.4	1.0	1	dbSNP_126	118	1836,6764	329.8+/-318.9	202,1432,2666	yes	missense,missense	OSCP1	NM_145047.4,NM_206837.2	58,58	269,2092,4142	CC,CT,TT		21.3488,18.0209,20.2214	benign,benign	131/380,131/224	36898067	2630,10376	2203	4300	6503	SO:0001583	missense	127700	exon3			GGATGGTTGGGGA		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"""oxidored nitro domain containing protein"""	608854	"""chromosome 1 open reading frame 102"""	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.421A>G	1.37:g.36898067T>C	ENSP00000349052:p.Thr141Ala	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	100	80	0.8	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	37		420	0.19230769230769232	65	0.13211382113821138	58	0.16022099447513813	144	0.2517482517482518	153	0.20184696569920843	T	1.622	-0.521352	0.04171	0.180209	0.213488	ENSG00000116885	ENST00000235532;ENST00000356637;ENST00000433045;ENST00000445843;ENST00000315643;ENST00000354267	T;T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64;1.64	5.6	-1.39	0.08997	.	0.615809	0.16766	N	0.200427	T	0.00012	0.0000	N	0.01228	-0.945	0.45914	P	0.0012499999999999734	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.37619	-0.9698	9	0.05620	T	0.96	.	7.0272	0.24946	0.0:0.3174:0.1172:0.5655	rs34409118	131;131;141	Q8WVF1-4;Q8WVF1-3;Q8WVF1	.;.;OSCP1_HUMAN	A	131;141;86;101;141;131	ENSP00000235532:T131A;ENSP00000349052:T141A;ENSP00000390820:T86A;ENSP00000396417:T101A;ENSP00000314541:T141A;ENSP00000346216:T131A	ENSP00000235532:T131A	T	-	1	0	OSCP1	36670654	0.980000	0.34600	0.993000	0.49108	0.462000	0.32619	0.340000	0.19892	-0.153000	0.11137	0.533000	0.62120	ACC	T|0.800;C|0.200	0.200	strong		0.502	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
SSPO	23145	hgsc.bcm.edu	37	7	149515103	149515103	+	RNA	SNP	C	C	T	rs10250401	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149515103C>T	ENST00000378016.2	+	0	11493							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)			GAGGGCTGGGCACCCGTACCC	0.697													C|||	1017	0.203075	0.2496	0.2003	5008	,	,		13910	0.1746		0.1551	False		,,,				2504	0.2209				p.G3831G		Atlas-SNP	.											.	.	.	.	0			c.C11493T						PASS	.	C		791,3127		104,583,1272	18.0	23.0	21.0		11503	-3.3	0.9	7	dbSNP_119	21	1369,6887		106,1157,2865	yes	coding-notMod3	SSPO	NM_198455.2		210,1740,4137	TT,TC,CC		16.5819,20.1889,17.7427			149515103	2160,10014	1959	4128	6087			23145	exon80			GCTGGGCACCCGT	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.149515103C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	44	5	0.113636	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.840;T|0.160	0.160	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
OR13G1	441933	hgsc.bcm.edu	37	1	247835779	247835779	+	Missense_Mutation	SNP	C	C	G	rs56096718	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247835779C>G	ENST00000359688.2	-	1	586	c.565G>C	c.(565-567)Gta>Cta	p.V189L	RP11-634B7.4_ENST00000449298.1_RNA	NM_001005487.1	NP_001005487.1	Q8NGZ3	O13G1_HUMAN	olfactory receptor, family 13, subfamily G, 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)|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)			TTGATTCTTACAGGGCTACAG	0.448													C|||	118	0.0235623	0.0045	0.0447	5008	,	,		23401	0.001		0.0517	False		,,,				2504	0.0286				p.V189L		Atlas-SNP	.											.	OR13G1	78	.	0			c.G565C						PASS	.	C	LEU/VAL	45,4361	47.5+/-82.1	1,43,2159	87.0	86.0	86.0		565	0.0	0.0	1	dbSNP_129	86	423,8177	131.3+/-189.1	12,399,3889	yes	missense	OR13G1	NM_001005487.1	32	13,442,6048	GG,GC,CC		4.9186,1.0213,3.5983	possibly-damaging	189/308	247835779	468,12538	2203	4300	6503	SO:0001583	missense	441933	exon1			TTCTTACAGGGCT	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.565G>C	1.37:g.247835779C>G	ENSP00000352717:p.Val189Leu	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	229	130	0.567686	NM_001005487	B2RN80|Q5T2T2|Q6IF86	Missense_Mutation	SNP	ENST00000359688.2	37	CCDS31094.1	60	0.027472527472527472	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	38	0.05013192612137203	C	11.76	1.733440	0.30684	0.010213	0.049186	ENSG00000197437	ENST00000359688	T	0.00084	8.75	4.2	0.00648	0.14067	GPCR, rhodopsin-like superfamily (1);	0.394146	0.18431	N	0.141430	T	0.00012	0.0000	N	0.20807	0.61	0.09310	N	1	B	0.34290	0.447	B	0.43194	0.411	T	0.26292	-1.0107	10	0.87932	D	0	-29.6394	5.3384	0.15971	0.0:0.5834:0.1476:0.269	rs56096718;rs61997175	189	Q8NGZ3	O13G1_HUMAN	L	189	ENSP00000352717:V189L	ENSP00000352717:V189L	V	-	1	0	OR13G1	245902402	0.000000	0.05858	0.000000	0.03702	0.701000	0.40568	-0.056000	0.11787	-0.080000	0.12685	0.563000	0.77884	GTA	C|0.956;G|0.044	0.044	strong		0.448	OR13G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096869.1	NM_001005487	
DLG4	1742	hgsc.bcm.edu	37	17	7099811	7099811	+	Silent	SNP	G	G	A	rs17203281	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7099811G>A	ENST00000399506.2	-	10	1358	c.1167C>T	c.(1165-1167)atC>atT	p.I389I	DLG4_ENST00000399510.2_Silent_p.I432I|DLG4_ENST00000302955.6_Silent_p.I386I			P78352	DLG4_HUMAN	discs, large homolog 4 (Drosophila)	389	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|axon guidance (GO:0007411)|dendritic spine morphogenesis (GO:0060997)|establishment of protein localization (GO:0045184)|learning (GO:0007612)|locomotory exploration behavior (GO:0035641)|negative regulation of receptor internalization (GO:0002091)|nervous system development (GO:0007399)|neuromuscular process controlling balance (GO:0050885)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synaptic transmission (GO:0050806)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|receptor localization to synapse (GO:0097120)|regulation of grooming behavior (GO:2000821)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|signal transduction (GO:0007165)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vocalization behavior (GO:0071625)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|juxtaparanode region of axon (GO:0044224)|neuron projection terminus (GO:0044306)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	acetylcholine receptor binding (GO:0033130)|beta-1 adrenergic receptor binding (GO:0031697)|D1 dopamine receptor binding (GO:0031748)|ionotropic glutamate receptor binding (GO:0035255)|P2Y1 nucleotide receptor binding (GO:0031812)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein phosphatase binding (GO:0019903)|scaffold protein binding (GO:0097110)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)	18					Guanidine(DB00536)	TATACTGAGCGATGATCGTGA	0.542													G|||	1232	0.246006	0.1831	0.2349	5008	,	,		22199	0.3155		0.331	False		,,,				2504	0.18				p.I432I		Atlas-SNP	.											.	DLG4	110	.	0			c.C1296T						PASS	.	G	,	781,3401		71,639,1381	76.0	72.0	74.0		1158,1296	-2.8	1.0	17	dbSNP_123	74	2570,5840		396,1778,2031	no	coding-synonymous,coding-synonymous	DLG4	NM_001128827.1,NM_001365.3	,	467,2417,3412	AA,AG,GG		30.5589,18.6753,26.6121	,	386/722,432/768	7099811	3351,9241	2091	4205	6296	SO:0001819	synonymous_variant	1742	exon12			CTGAGCGATGATC	U83192	CCDS45599.1, CCDS45600.1	17p13.1	2008-12-15	2001-12-04		ENSG00000132535	ENSG00000132535			2903	protein-coding gene	gene with protein product		602887				9286702	Standard	NM_001128827		Approved	PSD-95, PSD95, SAP90, SAP-90	uc010cly.3	P78352	OTTHUMG00000134327	ENST00000399506.2:c.1167C>T	17.37:g.7099811G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_001365	B7Z1S1|G5E939|Q92941|Q9UKK8	Silent	SNP	ENST00000399506.2	37																																																																																				G|0.742;A|0.258	0.258	strong		0.542	DLG4-002	KNOWN	non_canonical_TEC|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000259419.2	NM_001365	
MYO7A	4647	hgsc.bcm.edu	37	11	76918411	76918411	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:76918411A>G	ENST00000409709.3	+	42	6092	c.5820A>G	c.(5818-5820)tcA>tcG	p.S1940S	MYO7A_ENST00000409619.2_Silent_p.S1891S|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000458637.2_Silent_p.S1902S	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1940	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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						TCAAGTCCTCAGAGGGATTCA	0.572																																					p.S1940S		Atlas-SNP	.											.	MYO7A	164	.	0			c.A5820G						PASS	.						40.0	45.0	43.0					11																	76918411		2062	4191	6253	SO:0001819	synonymous_variant	4647	exon42			GTCCTCAGAGGGA	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.5820A>G	11.37:g.76918411A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	118	72	0.610169	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			.	.	none		0.572	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
PDGFD	80310	hgsc.bcm.edu	37	11	103780455	103780455	+	Silent	SNP	A	A	G	rs10791649	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:103780455A>G	ENST00000393158.2	-	7	1259	c.1080T>C	c.(1078-1080)tgT>tgC	p.C360C	PDGFD_ENST00000302251.5_Silent_p.C354C			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	360					cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		AGATACAATCACATCGTTCAT	0.453													G|||	2311	0.461462	0.5106	0.3487	5008	,	,		22084	0.4603		0.4523	False		,,,				2504	0.4857				p.C360C		Atlas-SNP	.											.	PDGFD	125	.	0			c.T1080C						PASS	.	G	,	2120,2284	600.3+/-389.5	509,1102,591	324.0	263.0	284.0		1080,1062	-5.4	0.3	11	dbSNP_120	284	4117,4481	591.2+/-392.8	999,2119,1181	no	coding-synonymous,coding-synonymous	PDGFD	NM_025208.4,NM_033135.3	,	1508,3221,1772	GG,GA,AA		47.8832,48.1381,47.9695	,	360/371,354/365	103780455	6237,6765	2202	4299	6501	SO:0001819	synonymous_variant	80310	exon7			ACAATCACATCGT	AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"""spinal cord derived growth factor B"""	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.1080T>C	11.37:g.103780455A>G		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	296	204	0.689189	NM_025208	A8K9T6|Q9BWV5	Silent	SNP	ENST00000393158.2	37	CCDS41703.1																																																																																			A|0.527;G|0.473	0.473	strong		0.453	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208	
NAT2	10	hgsc.bcm.edu	37	8	18258316	18258316	+	Missense_Mutation	SNP	G	G	A	rs1208	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	42	0	0		WXS	Illumina HiSeq	Phase_I	49	47	0.959184	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	
ANKZF1	55139	hgsc.bcm.edu	37	2	220100787	220100787	+	Missense_Mutation	SNP	C	C	T	rs2293079	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220100787C>T	ENST00000323348.5	+	13	2201	c.2027C>T	c.(2026-2028)cCa>cTa	p.P676L	ANKZF1_ENST00000409849.1_Missense_Mutation_p.P466L|GLB1L_ENST00000497855.1_5'Flank|ANKZF1_ENST00000410034.3_Missense_Mutation_p.P676L	NM_018089.2	NP_060559.2	Q9H8Y5	ANKZ1_HUMAN	ankyrin repeat and zinc finger domain containing 1	676			P -> L (in dbSNP:rs2293079).			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)		CCTACCTCTCCAATCCCTGAC	0.577													c|||	382	0.076278	0.0499	0.0951	5008	,	,		19304	0.0397		0.1163	False		,,,				2504	0.0951				p.P676L		Atlas-SNP	.											.	ANKZF1	45	.	0			c.C2027T						PASS	.	C	LEU/PRO,LEU/PRO	218,3816		5,208,1804	62.0	64.0	63.0		2027,2027	0.4	0.0	2	dbSNP_100	63	1046,7320		73,900,3210	yes	missense,missense	ANKZF1	NM_001042410.1,NM_018089.2	98,98	78,1108,5014	TT,TC,CC		12.503,5.4041,10.1935	benign,benign	676/727,676/727	220100787	1264,11136	2017	4183	6200	SO:0001583	missense	55139	exon13			CCTCTCCAATCCC	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.2027C>T	2.37:g.220100787C>T	ENSP00000321617:p.Pro676Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	70	15	0.214286	NM_001042410	Q9NVZ4	Missense_Mutation	SNP	ENST00000323348.5	37	CCDS42821.1	178	0.0815018315018315	28	0.056910569105691054	42	0.11602209944751381	24	0.04195804195804196	84	0.11081794195250659	C	1.822	-0.472009	0.04445	0.054041	0.12503	ENSG00000163516	ENST00000323348;ENST00000409849;ENST00000410034	T;T;T	0.27402	1.67;1.87;1.67	5.05	0.449	0.16619	.	1.098760	0.06643	N	0.761364	T	0.00210	0.0006	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22661	-1.0210	9	0.59425	D	0.04	-1.8475	5.0328	0.14419	0.2545:0.515:0.0:0.2305	rs2293079;rs59264444;rs2293079	676	Q9H8Y5	ANKZ1_HUMAN	L	676;466;676	ENSP00000321617:P676L;ENSP00000386815:P466L;ENSP00000386337:P676L	ENSP00000321617:P676L	P	+	2	0	ANKZF1	219809031	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.168000	0.09925	0.260000	0.21731	0.655000	0.94253	CCA	C|0.912;T|0.088	0.088	strong		0.577	ANKZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335790.1	NM_018089	
MUC17	140453	hgsc.bcm.edu	37	7	100679136	100679136	+	Missense_Mutation	SNP	T	T	C	rs7780935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100679136T>C	ENST00000306151.4	+	3	4503	c.4439T>C	c.(4438-4440)gTt>gCt	p.V1480A		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1480	59 X approximate tandem repeats.|Ser-rich.		V -> A (in dbSNP:rs7780935). {ECO:0000269|PubMed:9299468}.		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)					ACAACTCCTGTTGACTCTAAC	0.483													T|||	657	0.13119	0.2322	0.085	5008	,	,		25204	0.0665		0.1173	False		,,,				2504	0.1084				p.V1480A		Atlas-SNP	.											.	MUC17	804	.	0			c.T4439C						PASS	.	T	ALA/VAL	909,3497	350.0+/-310.6	93,723,1387	157.0	165.0	162.0		4439	-2.2	0.0	7	dbSNP_116	162	987,7609	213.4+/-253.3	57,873,3368	no	missense	MUC17	NM_001040105.1	64	150,1596,4755	CC,CT,TT		11.4821,20.631,14.5824	benign	1480/4494	100679136	1896,11106	2203	4298	6501	SO:0001583	missense	140453	exon3			CTCCTGTTGACTC	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.4439T>C	7.37:g.100679136T>C	ENSP00000302716:p.Val1480Ala	Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	215	208	0.967442	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	237	0.10851648351648352	87	0.17682926829268292	34	0.09392265193370165	30	0.05244755244755245	86	0.11345646437994723	t	1.397	-0.579307	0.03854	0.20631	0.114821	ENSG00000169876	ENST00000306151	T	0.02631	4.22	1.09	-2.18	0.07037	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.14438	0.01	B	0.08055	0.003	T	0.41928	-0.9481	8	0.07644	T	0.81	.	2.0054	0.03476	0.2509:0.0:0.3084:0.4408	rs7780935	1480	Q685J3	MUC17_HUMAN	A	1480	ENSP00000302716:V1480A	ENSP00000302716:V1480A	V	+	2	0	MUC17	100465856	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.010000	0.03656	-1.218000	0.02601	0.113000	0.15668	GTT	T|0.875;C|0.125	0.125	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
DNAH1	25981	hgsc.bcm.edu	37	3	52409421	52409421	+	Missense_Mutation	SNP	A	A	G	rs56002041	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:52409421A>G	ENST00000420323.2	+	45	7412	c.7151A>G	c.(7150-7152)aAc>aGc	p.N2384S		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2384	AAA 3. {ECO:0000250}.		N -> S (in dbSNP:rs56002041).		cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATCCTGGGCAACTGGTTGGGT	0.582													A|||	212	0.0423323	0.0023	0.0706	5008	,	,		22405	0.0		0.1044	False		,,,				2504	0.0562				p.N2384S		Atlas-SNP	.											.	DNAH1	534	.	0			c.A7151G						PASS	.	A	SER/ASN	76,4074		2,72,2001	48.0	48.0	48.0		7151	2.9	0.0	3	dbSNP_129	48	1026,7384		62,902,3241	yes	missense	DNAH1	NM_015512.4	46	64,974,5242	GG,GA,AA		12.1998,1.8313,8.7739	benign	2384/4266	52409421	1102,11458	2075	4205	6280	SO:0001583	missense	25981	exon45			TGGGCAACTGGTT	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.7151A>G	3.37:g.52409421A>G	ENSP00000401514:p.Asn2384Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	106	0.048534798534798536	2	0.0040650406504065045	29	0.08011049723756906	0	0.0	75	0.09894459102902374	A	0.045	-1.270904	0.01421	0.018313	0.121998	ENSG00000114841	ENST00000420323	T	0.34859	1.34	5.71	2.9	0.33743	.	0.342659	0.24601	N	0.037132	T	0.00144	0.0004	N	0.00793	-1.18	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.17930	-1.0353	9	0.20519	T	0.43	.	8.3407	0.32241	0.1424:0.1287:0.7289:0.0	rs56002041;rs61734635	2384	C9JXH6	.	S	2384	ENSP00000401514:N2384S	ENSP00000401514:N2384S	N	+	2	0	DNAH1	52384461	0.958000	0.32768	0.016000	0.15963	0.362000	0.29581	3.673000	0.54591	0.324000	0.23333	-0.375000	0.07067	AAC	A|0.943;G|0.057	0.057	strong		0.582	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
BFSP1	631	hgsc.bcm.edu	37	20	17475217	17475217	+	Silent	SNP	C	C	T	rs6136118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:17475217C>T	ENST00000377873.3	-	8	1539	c.1500G>A	c.(1498-1500)gcG>gcA	p.A500A	BFSP1_ENST00000377868.2_Silent_p.A375A|BFSP1_ENST00000536626.1_Silent_p.A361A|BFSP1_ENST00000544874.1_Silent_p.A361A	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	180	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	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	
SYT10	341359	hgsc.bcm.edu	37	12	33538179	33538179	+	Silent	SNP	C	C	T	rs11052670	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:33538179C>T	ENST00000228567.3	-	4	1421	c.1125G>A	c.(1123-1125)ccG>ccA	p.P375P	SYT10_ENST00000535526.1_Silent_p.P194P	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	375	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)					GCCCAGCCGTCGGTAGGTAAC	0.438													C|||	134	0.0267572	0.0015	0.0202	5008	,	,		16837	0.001		0.0606	False		,,,				2504	0.0573				p.P375P		Atlas-SNP	.											.	SYT10	109	.	0			c.G1125A						PASS	.	C		71,4335	64.7+/-102.0	0,71,2132	136.0	113.0	121.0		1125	-9.0	0.3	12	dbSNP_120	121	557,8043	152.5+/-207.1	14,529,3757	no	coding-synonymous	SYT10	NM_198992.3		14,600,5889	TT,TC,CC		6.4767,1.6114,4.8285		375/524	33538179	628,12378	2203	4300	6503	SO:0001819	synonymous_variant	341359	exon4			AGCCGTCGGTAGG	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.1125G>A	12.37:g.33538179C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_198992	Q495U2	Silent	SNP	ENST00000228567.3	37	CCDS8732.1																																																																																			C|0.958;T|0.042	0.042	strong		0.438	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992	
PSG8	440533	hgsc.bcm.edu	37	19	43269704	43269704	+	Silent	SNP	T	T	C	rs71337226|rs34129574|rs62112127	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43269704T>C	ENST00000306511.4	-	1	127	c.30A>G	c.(28-30)acA>acG	p.T10T	PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Silent_p.T10T|PSG8_ENST00000406636.3_Silent_p.T10T	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	10				TQR -> MQH (in Ref. 2; CAH18672). {ECO:0000305}.		extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				TGATGCGCTGTGTGCAGGGAG	0.597													.|||	1834	0.366214	0.7322	0.2781	5008	,	,		17082	0.0933		0.3241	False		,,,				2504	0.2587				p.T10T		Atlas-SNP	.											.	PSG8	101	.	0			c.A30G						PASS	.	C	,,	1742,1280		670,402,439	120.0	120.0	120.0		30,30,30	-1.0	0.0	19	dbSNP_129	120	1357,4061		286,785,1638	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	,,	956,1187,2077	CC,CT,TT		25.0461,42.3561,36.718	,,	10/420,10/298,10/427	43269704	3099,5341	1511	2709	4220	SO:0001819	synonymous_variant	440533	exon1			GCGCTGTGTGCAG	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.30A>G	19.37:g.43269704T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Silent	SNP	ENST00000306511.4	37	CCDS33037.1																																																																																			T|0.624;C|0.376	0.376	strong		0.597	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
HEATR6	63897	hgsc.bcm.edu	37	17	58156228	58156228	+	Silent	SNP	C	C	T	rs116476597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:58156228C>T	ENST00000184956.6	-	1	64	c.48G>A	c.(46-48)cgG>cgA	p.R16R	HEATR6_ENST00000585976.1_Silent_p.R16R|CTD-2319I12.2_ENST00000589740.1_lincRNA|HEATR6_ENST00000585712.1_5'UTR	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	16							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			GCGGTGCCTCCCGCGGCTGCA	0.662													C|||	16	0.00319489	0.0	0.0086	5008	,	,		7336	0.0		0.0099	False		,,,				2504	0.0				p.R16R		Atlas-SNP	.											.	HEATR6	98	.	0			c.G48A						PASS	.	C		10,4394		0,10,2192	22.0	20.0	21.0		48	-5.8	0.0	17	dbSNP_132	21	61,8535		0,61,4237	no	coding-synonymous	HEATR6	NM_022070.4		0,71,6429	TT,TC,CC		0.7096,0.2271,0.5462		16/1182	58156228	71,12929	2202	4298	6500	SO:0001819	synonymous_variant	63897	exon1			TGCCTCCCGCGGC	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.48G>A	17.37:g.58156228C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	88	52	0.590909	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Silent	SNP	ENST00000184956.6	37	CCDS11623.1																																																																																			C|0.996;T|0.004	0.004	strong		0.662	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070	
HEG1	57493	hgsc.bcm.edu	37	3	124731485	124731485	+	Missense_Mutation	SNP	C	C	G	rs10804567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:124731485C>G	ENST00000311127.4	-	6	3005	c.2938G>C	c.(2938-2940)Gtg>Ctg	p.V980L	HEG1_ENST00000477536.1_5'Flank	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	980			V -> L (in dbSNP:rs10804567). {ECO:0000269|PubMed:15489334}.		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						GAAGAGGACACTGTTGTTGGT	0.522													G|||	3737	0.746206	0.6596	0.7363	5008	,	,		20780	0.9286		0.6262	False		,,,				2504	0.8057				p.V980L		Atlas-SNP	.											.	HEG1	109	.	0			c.G2938C						PASS	.	G	LEU/VAL	2824,1414		952,920,247	72.0	83.0	79.0		2938	-9.0	0.0	3	dbSNP_120	79	5148,3376		1556,2036,670	yes	missense	HEG1	NM_020733.1	32	2508,2956,917	GG,GC,CC		39.6058,33.3648,37.5333	benign	980/1382	124731485	7972,4790	2119	4262	6381	SO:0001583	missense	57493	exon6			AGGACACTGTTGT	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.2938G>C	3.37:g.124731485C>G	ENSP00000311502:p.Val980Leu	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	230	104	0.452174	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	1585	0.7257326007326007	322	0.6544715447154471	246	0.6795580110497238	524	0.916083916083916	493	0.6503957783641161	G	0.188	-1.056212	0.01965	0.666352	0.603942	ENSG00000173706	ENST00000311127	D	0.87334	-2.24	4.51	-9.01	0.00744	.	1.618810	0.04775	N	0.428701	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	0.40232	-0.9574	9	0.05525	T	0.97	.	4.6055	0.12376	0.1528:0.3258:0.4141:0.1073	rs10804567;rs52819187;rs56613990;rs10804567	980;980	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	L	980	ENSP00000311502:V980L	ENSP00000311502:V980L	V	-	1	0	HEG1	126214175	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.876000	0.01633	-2.011000	0.00952	-1.077000	0.02231	GTG	C|0.293;G|0.707	0.707	strong		0.522	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
PALD1	27143	hgsc.bcm.edu	37	10	72291172	72291172	+	Missense_Mutation	SNP	G	G	A	rs61737673	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72291172G>A	ENST00000263563.6	+	5	863	c.595G>A	c.(595-597)Gtc>Atc	p.V199I		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	199						cytosol (GO:0005829)											TGGACCCGGGGTCCGGGTGGA	0.602													G|||	67	0.0133786	0.003	0.0216	5008	,	,		18858	0.0		0.0388	False		,,,				2504	0.0092				p.V199I		Atlas-SNP	.											.	.	.	.	0			c.G595A						PASS	.	G	ILE/VAL	38,4368	41.6+/-74.8	0,38,2165	64.0	58.0	60.0		595	1.1	0.0	10	dbSNP_129	60	276,8324	104.2+/-165.2	3,270,4027	yes	missense	KIAA1274	NM_014431.2	29	3,308,6192	AA,AG,GG		3.2093,0.8625,2.4143	benign	199/857	72291172	314,12692	2203	4300	6503	SO:0001583	missense	27143	exon5			CCCGGGGTCCGGG	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.595G>A	10.37:g.72291172G>A	ENSP00000263563:p.Val199Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	54	13	0.240741	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	33	0.01510989010989011	0	0.0	10	0.027624309392265192	0	0.0	23	0.030343007915567283	G	2.180	-0.387703	0.04932	0.008625	0.032093	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.21932	1.98	5.08	1.08	0.20341	.	0.896709	0.09766	N	0.758599	T	0.04588	0.0125	L	0.33753	1.03	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.37033	-0.9723	10	0.18710	T	0.47	-16.1671	6.6817	0.23123	0.2174:0.3405:0.442:0.0	rs61737673	199	Q9ULE6	PALD_HUMAN	I	199	ENSP00000263563:V199I	ENSP00000263563:V199I	V	+	1	0	KIAA1274	71961178	0.013000	0.17824	0.003000	0.11579	0.070000	0.16714	0.778000	0.26732	0.091000	0.17302	0.655000	0.94253	GTC	G|0.979;A|0.021	0.021	strong		0.602	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
CSPG4	1464	hgsc.bcm.edu	37	15	75982119	75982119	+	Silent	SNP	G	G	T	rs199778089	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75982119G>T	ENST00000308508.5	-	3	1379	c.1287C>A	c.(1285-1287)acC>acA	p.T429T		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	429	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						TCAGCAGCTGGGTGAAATTGG	0.642																																					p.T429T		Atlas-SNP	.											CSPG4,NS,neuroblastoma,0,1	CSPG4	175	1	0			c.C1287A						PASS	.						34.0	34.0	34.0					15																	75982119		2197	4291	6488	SO:0001819	synonymous_variant	1464	exon3			CAGCTGGGTGAAA	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.1287C>A	15.37:g.75982119G>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	88	15	0.170455	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			G|0.997;T|0.003	0.003	strong		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
TENM3	55714	hgsc.bcm.edu	37	4	183549831	183549831	+	Silent	SNP	T	T	G	rs74199039	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:183549831T>G	ENST00000511685.1	+	5	900	c.777T>G	c.(775-777)ggT>ggG	p.G259G	TENM3_ENST00000406950.2_Silent_p.G259G|RN7SKP67_ENST00000515905.1_RNA			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	259	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				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)										CAGGAACAGGTACAACGCCAC	0.423													G|||	424	0.0846645	0.0166	0.0677	5008	,	,		18152	0.1359		0.0785	False		,,,				2504	0.1421				p.G259G		Atlas-SNP	.											.	.	.	.	0			c.T777G						PASS	.	G		103,3855		3,97,1879	45.0	43.0	44.0		777	3.5	1.0	4	dbSNP_130	44	651,7683		27,597,3543	no	coding-synonymous	ODZ3	NM_001080477.1		30,694,5422	GG,GT,TT		7.8114,2.6023,6.1341		259/2700	183549831	754,11538	1979	4167	6146	SO:0001819	synonymous_variant	55714	exon4			AACAGGTACAACG	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.777T>G	4.37:g.183549831T>G		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	130	91	0.7	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																			T|0.912;G|0.088	0.088	strong		0.423	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
COQ3	51805	hgsc.bcm.edu	37	6	99825348	99825348	+	Missense_Mutation	SNP	T	T	C	rs11548336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:99825348T>C	ENST00000254759.3	-	4	424	c.400A>G	c.(400-402)Aaa>Gaa	p.K134E	COQ3_ENST00000369240.1_5'Flank|COQ3_ENST00000479163.1_5'UTR|COQ3_ENST00000369242.1_5'UTR	NM_017421.3	NP_059117.3	Q9NZJ6	COQ3_HUMAN	coenzyme Q3 methyltransferase	134			K -> E (in dbSNP:rs11548336). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		glycerol metabolic process (GO:0006071)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	2-polyprenyl-6-methoxy-1,4-benzoquinone methyltransferase activity (GO:0008425)|3-demethylubiquinone-9 3-O-methyltransferase activity (GO:0008689)|hexaprenyldihydroxybenzoate methyltransferase activity (GO:0004395)|O-methyltransferase activity (GO:0008171)			cervix(1)|lung(5)|upper_aerodigestive_tract(2)	8		all_cancers(76;1.24e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.00716)|Colorectal(196;0.0691)|Lung NSC(302;0.186)		BRCA - Breast invasive adenocarcinoma(108;0.0625)		GGAATTGTTTTCAGAAGATTG	0.348													T|||	1594	0.318291	0.2428	0.2017	5008	,	,		12394	0.496		0.3151	False		,,,				2504	0.3231				p.K134E		Atlas-SNP	.											.	COQ3	19	.	0			c.A400G						PASS	.	T	GLU/LYS	1205,3201	401.9+/-332.2	174,857,1172	76.0	67.0	70.0		400	5.6	1.0	6	dbSNP_120	70	2586,6014	400.1+/-346.7	406,1774,2120	yes	missense	COQ3	NM_017421.3	56	580,2631,3292	CC,CT,TT		30.0698,27.3491,29.1481	benign	134/370	99825348	3791,9215	2203	4300	6503	SO:0001583	missense	51805	exon4			TTGTTTTCAGAAG	AF193016	CCDS5042.1	6q21	2013-05-01	2013-05-01		ENSG00000132423	ENSG00000132423	2.1.1.114		18175	protein-coding gene	gene with protein product	"""polyprenyldihydroxybenzoate methyltransferase"""	605196	"""coenzyme Q3 homolog, methyltransferase (yeast)"", ""coenzyme Q3 homolog, methyltransferase (S. cerevisiae)"""			10777520	Standard	NM_017421		Approved	bA9819.1	uc003ppk.3	Q9NZJ6	OTTHUMG00000015264	ENST00000254759.3:c.400A>G	6.37:g.99825348T>C	ENSP00000254759:p.Lys134Glu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_017421	B3KPX0|Q5T061|Q6P4F0|Q8IXG6|Q96BG1|Q9H0N1	Missense_Mutation	SNP	ENST00000254759.3	37	CCDS5042.1	704	0.32234432234432236	122	0.24796747967479674	79	0.21823204419889503	253	0.4423076923076923	250	0.32981530343007914	T	15.33	2.802452	0.50315	0.273491	0.300698	ENSG00000132423	ENST00000254759	T	0.13420	2.59	5.61	5.61	0.85477	.	0.196194	0.51477	D	0.000085	T	0.04137	0.0115	N	0.21617	0.685	0.09310	P	1.0	B	0.21821	0.061	B	0.20184	0.028	T	0.34925	-0.9809	9	0.22109	T	0.4	-30.8554	14.3797	0.66902	0.0:0.0:0.0:1.0	rs11548336;rs17355554;rs45447894;rs58257605	134	Q9NZJ6	COQ3_HUMAN	E	134	ENSP00000254759:K134E	ENSP00000254759:K134E	K	-	1	0	COQ3	99932069	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.681000	0.74523	2.147000	0.66899	0.477000	0.44152	AAA	T|0.701;C|0.299	0.299	strong		0.348	COQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041602.1	NM_017421	
CAPN1	823	hgsc.bcm.edu	37	11	64981472	64981472	+	IGR	SNP	G	G	C	rs239258	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:64981472G>C	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)	p.T43T(2)		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)		AGAACTTCACGGCCGCTGTCC	0.687													G|||	1736	0.346645	0.233	0.2939	5008	,	,		12972	0.3929		0.4553	False		,,,				2504	0.3783				p.T43T		Atlas-SNP	.											SLC22A20,NS,carcinoma,0,6	SLC22A20	36	6	2	Substitution - coding silent(2)	prostate(2)	c.G129C						PASS	.	G		845,3041		105,635,1203	10.0	15.0	13.0		129	-4.7	0.8	11	dbSNP_79	13	3702,4532		877,1948,1292	no	coding-synonymous	SLC22A20	NM_001004326.4		982,2583,2495	CC,CG,GG		44.9599,21.7447,37.5165		43/350	64981472	4547,7573	1943	4117	6060	SO:0001628	intergenic_variant	440044	exon1			CTTCACGGCCGCT	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.64981472G>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_001004326	Q2TTR0|Q6DHV4	Silent	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			G|0.614;C|0.386	0.386	strong		0.687	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
CPAMD8	27151	hgsc.bcm.edu	37	19	17091368	17091368	+	Silent	SNP	T	T	G	rs8103646	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17091368T>G	ENST00000443236.1	-	14	1696	c.1665A>C	c.(1663-1665)cgA>cgC	p.R555R	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	508						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						CCCGCTTGCTTCGCTGCTGGG	0.587													T|||	2373	0.473842	0.6475	0.3559	5008	,	,		17983	0.5506		0.3509	False		,,,				2504	0.3701				p.R555R		Atlas-SNP	.											CPAMD8,NS,carcinoma,-1,1	CPAMD8	192	1	0			c.A1665C						PASS	.	T		2244,1706		634,976,365	58.0	65.0	63.0		1665	0.6	1.0	19	dbSNP_116	63	2636,5682		401,1834,1924	no	coding-synonymous	CPAMD8	NM_015692.2		1035,2810,2289	GG,GT,TT		31.6903,43.1899,39.7783		555/1933	17091368	4880,7388	1975	4159	6134	SO:0001819	synonymous_variant	27151	exon14			CTTGCTTCGCTGC	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.1665A>C	19.37:g.17091368T>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	1035	0.4739010989010989	317	0.6443089430894309	133	0.3674033149171271	312	0.5454545454545454	273	0.36015831134564646	T	7.048	0.563842	0.13498	0.568101	0.316903	ENSG00000160111	ENST00000443236	.	.	.	2.9	0.633	0.17712	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999769414	.	.	.	.	.	.	T	0.43572	-0.9383	3	.	.	.	.	7.1737	0.25732	0.0:0.4272:0.0:0.5728	rs8103646	.	.	.	A	566	.	.	E	-	2	0	CPAMD8	16952368	0.968000	0.33430	0.972000	0.41901	0.565000	0.35776	-0.114000	0.10757	0.105000	0.17753	0.383000	0.25322	GAA	T|0.601;G|0.399	0.399	strong		0.587	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388324	1388324	+	Missense_Mutation	SNP	A	A	C	rs74377230		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	178	23	0.129213	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	
ESPNL	339768	hgsc.bcm.edu	37	2	239036270	239036270	+	Silent	SNP	C	C	T	rs13382446	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:239036270C>T	ENST00000343063.3	+	7	1373	c.1110C>T	c.(1108-1110)tcC>tcT	p.S370S	ESPNL_ENST00000409506.1_Silent_p.S2S|ESPNL_ENST00000409169.1_Silent_p.S326S	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	370	Pro-rich.									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)		CAGCCATGTCCCTCAGCCCGG	0.667													C|||	613	0.122404	0.1346	0.121	5008	,	,		14389	0.1042		0.1362	False		,,,				2504	0.1115				p.S370S		Atlas-SNP	.											.	ESPNL	63	.	0			c.C1110T						PASS	.	C		555,3849		43,469,1690	39.0	34.0	36.0		1110	-0.8	0.3	2	dbSNP_121	36	1380,7216		123,1134,3041	no	coding-synonymous	ESPNL	NM_194312.2		166,1603,4731	TT,TC,CC		16.054,12.6022,14.8846		370/1006	239036270	1935,11065	2202	4298	6500	SO:0001819	synonymous_variant	339768	exon7			CATGTCCCTCAGC	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.1110C>T	2.37:g.239036270C>T		Somatic	381	1	0.00262467		WXS	Illumina HiSeq	Phase_I	374	200	0.534759	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			C|0.861;T|0.139	0.139	strong		0.667	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
SLC22A16	85413	hgsc.bcm.edu	37	6	110777962	110777962	+	Silent	SNP	A	A	G	rs6907567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:110777962A>G	ENST00000368919.3	-	2	378	c.312T>C	c.(310-312)aaT>aaC	p.N104N	SLC22A16_ENST00000456137.2_Silent_p.N104N|SLC22A16_ENST00000439654.1_Silent_p.N104N|SLC22A16_ENST00000461487.1_5'UTR|SLC22A16_ENST00000330550.4_Silent_p.N70N	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	104					acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	TCTCCCTCTTATTCCTGCTAC	0.473													G|||	1573	0.314097	0.3888	0.2406	5008	,	,		19928	0.4107		0.2207	False		,,,				2504	0.2618				p.N104N		Atlas-SNP	.											.	SLC22A16	81	.	0			c.T312C						PASS	.	G		1600,2806	663.6+/-401.2	281,1038,884	241.0	238.0	239.0		312	0.3	0.0	6	dbSNP_116	239	1917,6683	726.4+/-406.6	180,1557,2563	no	coding-synonymous	SLC22A16	NM_033125.2		461,2595,3447	GG,GA,AA		22.2907,36.3141,27.0414		104/578	110777962	3517,9489	2203	4300	6503	SO:0001819	synonymous_variant	85413	exon2			CCTCTTATTCCTG		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.312T>C	6.37:g.110777962A>G		Somatic	354	0	0		WXS	Illumina HiSeq	Phase_I	307	135	0.439739	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Silent	SNP	ENST00000368919.3	37	CCDS5084.1																																																																																			A|0.716;G|0.284	0.284	strong		0.473	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
CCR6	1235	hgsc.bcm.edu	37	6	167549775	167549775	+	Silent	SNP	T	T	C	rs3093007	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:167549775T>C	ENST00000341935.5	+	3	609	c.57T>C	c.(55-57)ttT>ttC	p.F19F	RP11-517H2.6_ENST00000609590.1_RNA|CCR6_ENST00000349984.4_Silent_p.F19F|CCR6_ENST00000400926.2_Silent_p.F19F	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	111	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	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		
RNF17	56163	hgsc.bcm.edu	37	13	25378476	25378476	+	Missense_Mutation	SNP	A	A	G	rs9511451	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:25378476A>G	ENST00000255324.5	+	15	2052	c.2000A>G	c.(1999-2001)cAc>cGc	p.H667R	RNF17_ENST00000381921.1_Missense_Mutation_p.H667R|RNF17_ENST00000255325.6_Intron	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	667			H -> R (in dbSNP:rs9511451).		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		ACTACTTTACACTATCATCCA	0.348													A|||	1064	0.21246	0.0847	0.2219	5008	,	,		20210	0.3244		0.2913	False		,,,				2504	0.182				p.H667R		Atlas-SNP	.											RNF17_ENST00000255324,NS,carcinoma,+1,1	RNF17	259	1	0			c.A2000G						PASS	.	A	ARG/HIS,ARG/HIS	526,3874	239.0+/-250.2	34,458,1708	92.0	91.0	91.0		2000,2000	0.3	0.1	13	dbSNP_119	91	2517,6083	409.5+/-349.8	346,1825,2129	yes	missense,missense	RNF17	NM_001184993.1,NM_031277.2	29,29	380,2283,3837	GG,GA,AA		29.2674,11.9545,23.4077	benign,benign	667/1620,667/1624	25378476	3043,9957	2200	4300	6500	SO:0001583	missense	56163	exon15			CTTTACACTATCA	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"""RING-type (C3HC4) zinc fingers"", ""Tudor domain containing"""	10060	protein-coding gene	gene with protein product	"""spermatogenesis associated 23"""	605793	"""tudor domain containing 4"""	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.2000A>G	13.37:g.25378476A>G	ENSP00000255324:p.His667Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	493	0.22573260073260074	40	0.08130081300813008	82	0.2265193370165746	155	0.270979020979021	216	0.2849604221635884	A	0.018	-1.480284	0.01027	0.119545	0.292674	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047	T;T	0.20069	2.1;2.1	5.5	0.308	0.15815	.	1.211800	0.05578	N	0.572397	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43782	-0.9370	9	0.11485	T	0.65	.	5.0512	0.14508	0.3981:0.1682:0.4338:0.0	rs9511451;rs9511451	667;667	B7Z7S1;Q9BXT8	.;RNF17_HUMAN	R	667;667;526	ENSP00000255324:H667R;ENSP00000371346:H667R	ENSP00000255324:H667R	H	+	2	0	RNF17	24276476	0.001000	0.12720	0.054000	0.19295	0.249000	0.25844	0.214000	0.17541	0.061000	0.16311	0.482000	0.46254	CAC	A|0.776;G|0.224	0.224	strong		0.348	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
ZNF337	26152	hgsc.bcm.edu	37	20	25666737	25666737	+	Missense_Mutation	SNP	C	C	T	rs926487	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:25666737C>T	ENST00000376436.1	-	2	588	c.49G>A	c.(49-51)Gtc>Atc	p.V17I	ZNF337_ENST00000538750.1_Missense_Mutation_p.V17I|ZNF337_ENST00000481610.1_5'UTR|ZNF337_ENST00000252979.5_Missense_Mutation_p.V17I			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	17	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> I (in dbSNP:rs926487).		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(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TCCACAGTGACATCCCCAAAT	0.552													C|||	832	0.166134	0.4478	0.0821	5008	,	,		20528	0.0734		0.0606	False		,,,				2504	0.0491				p.V17I		Atlas-SNP	.											.	ZNF337	65	.	0			c.G49A						PASS	.	C	ILE/VAL	1674,2732		305,1064,834	113.0	111.0	112.0		49	1.0	0.0	20	dbSNP_86	112	408,8192		7,394,3899	yes	missense	ZNF337	NM_015655.2	29	312,1458,4733	TT,TC,CC		4.7442,37.9936,16.008	probably-damaging	17/752	25666737	2082,10924	2203	4300	6503	SO:0001583	missense	26152	exon3			CAGTGACATCCCC		CCDS13174.1	20p11.1	2013-09-20			ENSG00000130684	ENSG00000130684		"""Zinc fingers, C2H2-type"", ""-"""	15809	protein-coding gene	gene with protein product							Standard	XM_005260702		Approved	dJ694B14.1	uc002wuz.3	Q9Y3M9	OTTHUMG00000032131	ENST00000376436.1:c.49G>A	20.37:g.25666737C>T	ENSP00000365619:p.Val17Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_015655	B4DSM2|Q9Y3Y5	Missense_Mutation	SNP	ENST00000376436.1	37	CCDS13174.1	315	0.14423076923076922	203	0.41260162601626016	32	0.08839779005524862	34	0.05944055944055944	46	0.06068601583113457	.	15.97	2.989929	0.54041	0.379936	0.047442	ENSG00000130684	ENST00000376436;ENST00000252979;ENST00000376412;ENST00000538750	T;T;T	0.08720	3.06;3.06;3.06	2.02	1.05	0.20165	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	M	0.78285	2.405	0.80722	P	0.0	D;D	0.56968	0.978;0.978	D;D	0.63793	0.918;0.918	T	0.44862	-0.9300	8	0.87932	D	0	.	6.0643	0.19854	0.0:0.8238:0.0:0.1762	rs926487;rs52820675;rs926487	17;17	B4DSM2;Q9Y3M9	.;ZN337_HUMAN	I	17	ENSP00000365619:V17I;ENSP00000252979:V17I;ENSP00000442181:V17I	ENSP00000252979:V17I	V	-	1	0	ZNF337	25614737	0.403000	0.25319	0.009000	0.14445	0.959000	0.62525	1.441000	0.35035	0.074000	0.16767	0.461000	0.40582	GTC	C|0.838;T|0.162	0.162	strong		0.552	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1		
PLD2	5338	hgsc.bcm.edu	37	17	4722876	4722876	+	Splice_Site	SNP	G	G	A	rs3764897	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4722876G>A	ENST00000263088.6	+	23	2592	c.2461G>A	c.(2461-2463)Ggt>Agt	p.G821S	PLD2_ENST00000572940.1_Intron	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	821			G -> R (in dbSNP:rs3764897).|G -> S (in dbSNP:rs3764897). {ECO:0000269|Ref.3}.		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)	GCACTGCTTCGGGTAGAGCTG	0.617													A|||	918	0.183307	0.3033	0.1671	5008	,	,		16910	0.1071		0.168	False		,,,				2504	0.1268				p.G821S		Atlas-SNP	.											.	PLD2	138	.	0			c.G2461A						PASS	.	A	SER/GLY	1198,3208	707.7+/-407.5	167,864,1172	68.0	51.0	57.0		2461	3.8	1.0	17	dbSNP_107	57	1363,7237	754.6+/-407.5	111,1141,3048	yes	missense-near-splice	PLD2	NM_002663.4	56	278,2005,4220	AA,AG,GG		15.8488,27.1902,19.6909	benign	821/934	4722876	2561,10445	2203	4300	6503	SO:0001630	splice_region_variant	5338	exon23			TGCTTCGGGTAGA	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.2462+1G>A	17.37:g.4722876G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_002663	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	384	0.17582417582417584	162	0.32926829268292684	53	0.1464088397790055	55	0.09615384615384616	114	0.1503957783641161	A	11.54	1.668938	0.29604	0.271902	0.158488	ENSG00000129219	ENST00000263088	T	0.06142	3.34	3.82	3.82	0.43975	.	0.048535	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00128	-2.045	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40664	-0.9551	9	0.21540	T	0.41	-2.6275	7.5853	0.27989	0.893:0.0:0.107:0.0	rs3764897;rs3764897	821	O14939	PLD2_HUMAN	S	821	ENSP00000263088:G821S	ENSP00000263088:G821S	G	+	1	0	PLD2	4669842	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	3.580000	0.53907	0.645000	0.30675	-0.521000	0.04368	GGT	G|0.804;A|0.196	0.196	strong		0.617	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	Missense_Mutation
USHBP1	83878	hgsc.bcm.edu	37	19	17367435	17367435	+	Missense_Mutation	SNP	T	T	C	rs9676419	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17367435T>C	ENST00000252597.3	-	9	1488	c.1315A>G	c.(1315-1317)Atg>Gtg	p.M439V	AC010646.3_ENST00000594059.1_5'Flank|USHBP1_ENST00000431146.2_Missense_Mutation_p.M375V	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1									p.M439V(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						AGAATCTTCATTAGAGAACGG	0.612													C|||	1650	0.329473	0.4735	0.3098	5008	,	,		18737	0.2758		0.2336	False		,,,				2504	0.3027				p.M439V		Atlas-SNP	.											USHBP1,NS,carcinoma,0,2	USHBP1	85	2	1	Substitution - Missense(1)	prostate(1)	c.A1315G						PASS	.	C	VAL/MET	1957,2449	622.4+/-393.9	428,1101,674	73.0	73.0	73.0		1315	-0.3	0.9	19	dbSNP_119	73	1879,6721	729.3+/-406.7	189,1501,2610	yes	missense	USHBP1	NM_031941.3	21	617,2602,3284	CC,CT,TT		21.8488,44.4167,29.4941	benign	439/704	17367435	3836,9170	2203	4300	6503	SO:0001583	missense	83878	exon9			TCTTCATTAGAGA	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.1315A>G	19.37:g.17367435T>C	ENSP00000252597:p.Met439Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_031941		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	689	0.31547619047619047	264	0.5365853658536586	103	0.2845303867403315	150	0.26223776223776224	172	0.22691292875989447	C	0.006	-2.114278	0.00349	0.444167	0.218488	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.10192	2.9;2.91	4.9	-0.346	0.12620	.	0.309917	0.24128	N	0.041292	T	0.00012	0.0000	N	0.00170	-1.935	0.09310	P	0.99999999854739	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36817	-0.9732	9	0.02654	T	1	-9.9883	6.3927	0.21595	0.0:0.4031:0.4212:0.1757	rs9676419;rs59052683;rs9676419	375;439	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	V	439;375	ENSP00000252597:M439V;ENSP00000407902:M375V	ENSP00000252597:M439V	M	-	1	0	USHBP1	17228435	0.875000	0.30112	0.886000	0.34754	0.011000	0.07611	-0.030000	0.12308	-0.123000	0.11745	-0.119000	0.15052	ATG	T|0.693;C|0.307	0.307	strong		0.612	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
BDP1	55814	hgsc.bcm.edu	37	5	70800475	70800475	+	Missense_Mutation	SNP	C	C	T	rs3761966	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:70800475C>T	ENST00000358731.4	+	16	2532	c.2269C>T	c.(2269-2271)Cgt>Tgt	p.R757C	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	757			R -> C (in dbSNP:rs3761966). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:15489334}.		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)		AGATCAATCGCGTAAAGATTT	0.343													C|||	1621	0.323682	0.1067	0.4928	5008	,	,		16692	0.505		0.335	False		,,,				2504	0.2986				p.R757C		Atlas-SNP	.											.	BDP1	204	.	0			c.C2269T						PASS	.	C	CYS/ARG	547,3127		37,473,1327	89.0	81.0	84.0		2269	-0.2	0.0	5	dbSNP_107	84	2808,5364		507,1794,1785	yes	missense	BDP1	NM_018429.2	180	544,2267,3112	TT,TC,CC		34.3612,14.8884,28.3218	benign	757/2625	70800475	3355,8491	1837	4086	5923	SO:0001583	missense	55814	exon16			CAATCGCGTAAAG	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.2269C>T	5.37:g.70800475C>T	ENSP00000351575:p.Arg757Cys	Somatic	320	2	0.00625		WXS	Illumina HiSeq	Phase_I	263	262	0.996198	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	750	0.3434065934065934	49	0.09959349593495935	159	0.43922651933701656	291	0.5087412587412588	251	0.3311345646437995	C	0.484	-0.878384	0.02550	0.148884	0.343612	ENSG00000145734	ENST00000358731;ENST00000437938;ENST00000451951;ENST00000444711	T	0.09445	2.98	4.92	-0.211	0.13172	.	0.828507	0.10896	N	0.622116	T	0.00012	0.0000	N	0.01003	-1.06	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37709	-0.9694	9	0.35671	T	0.21	.	3.227	0.06735	0.1743:0.2987:0.0:0.527	rs3761966;rs58491588;rs3761966	757;757;757	A6H8Y1;A6H8Y1-2;A6H8Y1-4	BDP1_HUMAN;.;.	C	757;757;337;757	ENSP00000351575:R757C	ENSP00000351575:R757C	R	+	1	0	BDP1	70836231	0.000000	0.05858	0.004000	0.12327	0.005000	0.04900	-0.258000	0.08733	-0.150000	0.11195	-0.247000	0.11927	CGT	C|0.667;T|0.333	0.333	strong		0.343	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573719	140573719	+	Missense_Mutation	SNP	G	G	A	rs148484995	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140573719G>A	ENST00000239446.4	+	1	1778	c.1594G>A	c.(1594-1596)Ggc>Agc	p.G532S		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	532	Cadherin 5. {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)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTTCCGCGTGGGCGCCACAGA	0.692																																					p.G532S		Atlas-SNP	.											PCDHB10,NS,lymphoid_neoplasm,-2,1	PCDHB10	177	1	0			c.G1594A						scavenged	.						64.0	82.0	76.0					5																	140573719		2203	4300	6503	SO:0001583	missense	56126	exon1			CGCGTGGGCGCCA	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1594G>A	5.37:g.140573719G>A	ENSP00000239446:p.Gly532Ser	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	141	3	0.0212766	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	121	0.0554029304029304	49	0.09959349593495935	14	0.03867403314917127	4	0.006993006993006993	54	0.0712401055408971	g	13.25	2.180349	0.38511	.	.	ENSG00000120324	ENST00000239446	T	0.01647	4.71	3.53	-1.46	0.08800	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00073	0.0002	N	0.04787	-0.16	0.09310	N	1	P	0.40578	0.722	P	0.50162	0.633	T	0.53781	-0.8390	9	0.34782	T	0.22	.	6.5285	0.22314	0.1851:0.6244:0.1905:0.0	.	532	Q9UN67	PCDBA_HUMAN	S	532	ENSP00000239446:G532S	ENSP00000239446:G532S	G	+	1	0	PCDHB10	140553903	0.000000	0.05858	0.997000	0.53966	0.972000	0.66771	-1.808000	0.01732	-0.175000	0.10725	0.549000	0.68633	GGC	G|0.961;A|0.039	0.039	strong		0.692	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
PRR21	643905	hgsc.bcm.edu	37	2	240982052	240982052	+	Silent	SNP	C	C	G	rs77588089		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:240982052C>G	ENST00000408934.1	-	1	347	c.348G>C	c.(346-348)tcG>tcC	p.S116S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	116	Pro-rich.							p.S116S(2)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GAGGCATGGACGAAGGGCCGT	0.627																																					p.S116S		Atlas-SNP	.											PRR21,pharynx,carcinoma,0,4	PRR21	53	4	2	Substitution - coding silent(2)	upper_aerodigestive_tract(2)	c.G348C						scavenged	.						5.0	6.0	6.0					2																	240982052		1363	2884	4247	SO:0001819	synonymous_variant	643905	exon1			CATGGACGAAGGG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.348G>C	2.37:g.240982052C>G		Somatic	100	2	0.02		WXS	Illumina HiSeq	Phase_I	82	19	0.231707	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			C|0.250;G|0.750	0.750	weak		0.627	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
NUDT12	83594	hgsc.bcm.edu	37	5	102895124	102895124	+	Silent	SNP	G	G	A	rs7723689	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:102895124G>A	ENST00000230792.2	-	3	348	c.252C>T	c.(250-252)gaC>gaT	p.D84D	NUDT12_ENST00000507423.1_Silent_p.D66D	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	84					NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		ATACAGCAATGTCCAGTGCAG	0.373													A|||	501	0.10004	0.1407	0.1513	5008	,	,		17726	0.0129		0.1561	False		,,,				2504	0.0409				p.D84D		Atlas-SNP	.											.	NUDT12	27	.	0			c.C252T						PASS	.	A		533,3835		26,481,1677	49.0	51.0	51.0		252	3.5	1.0	5	dbSNP_116	51	1428,7160		109,1210,2975	no	coding-synonymous	NUDT12	NM_031438.2		135,1691,4652	AA,AG,GG		16.6279,12.2024,15.1358		84/463	102895124	1961,10995	2184	4294	6478	SO:0001819	synonymous_variant	83594	exon3			AGCAATGTCCAGT	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"""Nudix motif containing"", ""Ankyrin repeat domain containing"""	18826	protein-coding gene	gene with protein product	"""nucleoside diphosphate linked moiety X-type motif 12"""	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.252C>T	5.37:g.102895124G>A		Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	170	84	0.494118	NM_031438	B3KUW2|Q8TAL7	Silent	SNP	ENST00000230792.2	37	CCDS4096.1																																																																																			G|0.869;A|0.131	0.131	strong		0.373	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438	
CACNA1C	775	hgsc.bcm.edu	37	12	2694638	2694638	+	Silent	SNP	C	C	T	rs215976	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:2694638C>T	ENST00000347598.4	+	17	2436	c.2436C>T	c.(2434-2436)gaC>gaT	p.D812D	CACNA1C_ENST00000399597.1_Silent_p.D812D|CACNA1C_ENST00000399637.1_Silent_p.D812D|CACNA1C_ENST00000480911.1_Silent_p.D812D|CACNA1C_ENST00000399606.1_Silent_p.D812D|CACNA1C_ENST00000344100.3_Silent_p.D812D|CACNA1C_ENST00000399617.1_Silent_p.D812D|CACNA1C_ENST00000399634.1_Silent_p.D812D|CACNA1C_ENST00000399641.1_Silent_p.D812D|CACNA1C_ENST00000399644.1_Silent_p.D812D|CACNA1C_ENST00000399629.1_Silent_p.D812D|CACNA1C_ENST00000399621.1_Silent_p.D812D|CACNA1C_ENST00000399591.1_Silent_p.D812D|CACNA1C_ENST00000399601.1_Silent_p.D812D|CACNA1C_ENST00000406454.3_Silent_p.D812D|CACNA1C_ENST00000399638.1_Silent_p.D812D|CACNA1C_ENST00000327702.7_Silent_p.D812D|CACNA1C_ENST00000335762.5_Silent_p.D837D|CACNA1C_ENST00000402845.3_Silent_p.D812D|CACNA1C_ENST00000399603.1_Silent_p.D812D|CACNA1C_ENST00000399649.1_Silent_p.D812D|CACNA1C_ENST00000399655.1_Silent_p.D812D|CACNA1C_ENST00000399595.1_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	87	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	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	
MYO1H	283446	hgsc.bcm.edu	37	12	109883374	109883374	+	Missense_Mutation	SNP	T	T	C	rs3825393	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:109883374T>C	ENST00000431443.2	+	30	3032	c.3032T>C	c.(3031-3033)cTg>cCg	p.L1011P	MYO1H_ENST00000310903.5_Missense_Mutation_p.L1001P|RP11-256L11.3_ENST00000539987.1_RNA	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	1011	Myosin tail. {ECO:0000255}.		L -> P (in dbSNP:rs3825393).			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						GACACTGGACTGGAAGAACAA	0.353													C|||	3529	0.704673	0.9803	0.5591	5008	,	,		19581	0.4821		0.6491	False		,,,				2504	0.7219				p.L1001P		Atlas-SNP	.											.	MYO1H	98	.	0			c.T3002C						PASS	.	C	PRO/LEU	3399,295		1562,275,10	109.0	104.0	106.0		3002	2.8	0.5	12	dbSNP_107	106	5268,2914		1690,1888,513	yes	missense	MYO1H	NM_001101421.3	98	3252,2163,523	CC,CT,TT		35.6148,7.9859,27.0209	benign	1001/1023	109883374	8667,3209	1847	4091	5938	SO:0001583	missense	283446	exon30			CTGGACTGGAAGA		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.3032T>C	12.37:g.109883374T>C	ENSP00000444076:p.Leu1011Pro	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	37		1454	0.6657509157509157	475	0.9654471544715447	209	0.5773480662983426	274	0.479020979020979	496	0.6543535620052771	C	10.73	1.432156	0.25813	0.920141	0.643852	ENSG00000174527	ENST00000310903;ENST00000431443;ENST00000542268	T;T	0.34472	1.36;1.36	5.97	2.79	0.32731	Myosin tail 2 (1);	.	.	.	.	T	0.00012	0.0000	N	0.00210	-1.845	0.45342	P	0.0016659999999999453	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32929	-0.9888	8	0.02654	T	1	.	8.4305	0.32755	0.2336:0.6344:0.0:0.132	rs3825393;rs59454453;rs3825393	1011;1001	Q8N1T3;F5H3C6	MYO1H_HUMAN;.	P	1001;1011;192	ENSP00000439182:L1001P;ENSP00000444076:L1011P	ENSP00000439182:L1001P	L	+	2	0	MYO1H	108367757	0.001000	0.12720	0.491000	0.27477	0.450000	0.32258	0.012000	0.13287	0.402000	0.25451	-0.128000	0.14901	CTG	T|0.322;C|0.678	0.678	strong		0.353	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
LRRC71	149499	hgsc.bcm.edu	37	1	156890672	156890672	+	Missense_Mutation	SNP	T	T	C	rs41273221	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156890672T>C	ENST00000337428.7	+	1	231	c.77T>C	c.(76-78)gTg>gCg	p.V26A		NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	26										endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						TCTGGCGCGGTGACCAAAAAG	0.697													T|||	945	0.188698	0.1604	0.1628	5008	,	,		13847	0.2847		0.174	False		,,,				2504	0.1616				p.V26A		Atlas-SNP	.											.	LRRC71	33	.	0			c.T77C						PASS	.						10.0	17.0	15.0					1																	156890672		690	1587	2277	SO:0001583	missense	149499	exon1			GCGCGGTGACCAA	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.77T>C	1.37:g.156890672T>C	ENSP00000336661:p.Val26Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	457	0.20924908424908426	79	0.16056910569105692	69	0.19060773480662985	185	0.32342657342657344	124	0.16358839050131926	T	10.69	1.421957	0.25639	.	.	ENSG00000160838	ENST00000337428	T	0.25250	1.81	4.97	-2.03	0.07365	.	0.956381	0.08632	N	0.916908	T	0.04952	0.0133	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40346	-0.9568	9	0.56958	D	0.05	-9.6466	4.4224	0.11486	0.1486:0.3411:0.0:0.5104	rs41273221;rs62640956	26	Q8N4P6	LRC71_HUMAN	A	26	ENSP00000336661:V26A	ENSP00000336661:V26A	V	+	2	0	LRRC71	155157296	0.440000	0.25618	0.020000	0.16555	0.172000	0.22775	0.040000	0.13905	-0.554000	0.06150	0.397000	0.26171	GTG	T|0.793;C|0.207	0.207	strong		0.697	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
POTEH	23784	hgsc.bcm.edu	37	22	16287562	16287562	+	Missense_Mutation	SNP	G	G	C	rs202187764	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:16287562G>C	ENST00000343518.6	-	1	375	c.324C>G	c.(322-324)tgC>tgG	p.C108W		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	108										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						TCCCCCTGCAGCAGGGGAAGC	0.587																																					p.C108W		Atlas-SNP	.											POTEH,NS,carcinoma,0,1	POTEH	114	1	0			c.C324G						scavenged	.						97.0	113.0	107.0					22																	16287562		2057	3890	5947	SO:0001583	missense	23784	exon1			CCTGCAGCAGGGG	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	133	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 7"""	608913	"""actin, beta-like 1"", ""ANKRD26-like family C, member 3"""	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.324C>G	22.37:g.16287562G>C	ENSP00000340610:p.Cys108Trp	Somatic	467	7	0.0149893		WXS	Illumina HiSeq	Phase_I	159	16	0.100629	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Missense_Mutation	SNP	ENST00000343518.6	37	CCDS46658.1	.	.	.	.	.	.	.	.	.	.	.	4.136	0.023586	0.08006	.	.	ENSG00000198062	ENST00000343518;ENST00000355872	T	0.37411	1.2	.	.	.	.	.	.	.	.	T	0.40297	0.1111	L	0.53249	1.67	0.09310	N	1	P	0.46578	0.88	P	0.51615	0.675	T	0.21314	-1.0249	7	0.38643	T	0.18	.	.	.	.	.	108	Q6S545	POTEH_HUMAN	W	108	ENSP00000340610:C108W	ENSP00000340610:C108W	C	-	3	2	POTEH	14667562	0.075000	0.21258	0.021000	0.16686	0.022000	0.10575	0.263000	0.18478	0.269000	0.21961	0.274000	0.19336	TGC	G|0.975;C|0.025	0.025	strong		0.587	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213	
TUBB8	347688	hgsc.bcm.edu	37	10	94025	94025	+	Missense_Mutation	SNP	T	T	C	rs143154682	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:94025T>C	ENST00000309812.4	-	4	369	c.307A>G	c.(307-309)Aag>Gag	p.K103E	TUBB8_ENST00000332708.5_Silent_p.P66P|TUBB8_ENST00000447903.2_Missense_Mutation_p.K31E|TUBB8_ENST00000413237.3_5'UTR	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	103					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)			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)		TAGTGTCCCTTGGCCCAGTTG	0.577																																					p.K103E	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.A307G						PASS	.						69.0	57.0	61.0					10																	94025		2203	4300	6503	SO:0001583	missense	347688	exon4			GTCCCTTGGCCCA	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.307A>G	10.37:g.94025T>C	ENSP00000311042:p.Lys103Glu	Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	237	56	0.236287	NM_177987	Q5SQX9|Q8WZ78	Missense_Mutation	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	T	13.76	2.332365	0.41297	.	.	ENSG00000173876	ENST00000447903;ENST00000272035;ENST00000440680;ENST00000328974	T	0.70399	-0.48	.	.	.	Tubulin/FtsZ, GTPase domain (4);	0.078738	0.47455	U	0.000224	D	0.83700	0.5311	H	0.96805	3.885	0.33195	D	0.551322	P;D	0.56968	0.646;0.978	P;P	0.59221	0.621;0.854	T	0.83158	-0.0100	9	0.87932	D	0	.	4.5487	0.12098	0.0:6.0E-4:0.0:0.9994	.	66;103	C9JAA5;Q3ZCM7	.;TBB8_HUMAN	E	31;69;66;103	ENSP00000403895:K31E	ENSP00000272035:K69E	K	-	1	0	RP11-631M21.2	84025	1.000000	0.71417	0.357000	0.25798	0.361000	0.29550	5.418000	0.66429	0.103000	0.17682	0.102000	0.15555	AAG	T|0.998;C|0.002	0.002	strong		0.577	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
PCOLCE	5118	hgsc.bcm.edu	37	7	100205706	100205706	+	Missense_Mutation	SNP	G	G	C	rs61739556	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100205706G>C	ENST00000223061.5	+	9	1610	c.1330G>C	c.(1330-1332)Gct>Cct	p.A444P		NM_002593.3	NP_002584.2	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	444					multicellular organismal development (GO:0007275)|positive regulation of peptidase activity (GO:0010952)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					ACCTGTGCGGGCTGCTGCGTC	0.572													G|||	22	0.00439297	0.0008	0.0043	5008	,	,		15040	0.0		0.0119	False		,,,				2504	0.0061				p.A444P		Atlas-SNP	.											.	PCOLCE	37	.	0			c.G1330C						PASS	.	G	PRO/ALA	12,4394	19.1+/-41.9	0,12,2191	34.0	39.0	37.0		1330	2.5	0.0	7	dbSNP_129	37	129,8471	56.8+/-118.0	1,127,4172	no	missense	PCOLCE	NM_002593.3	27	1,139,6363	CC,CG,GG		1.5,0.2724,1.0841	probably-damaging	444/450	100205706	141,12865	2203	4300	6503	SO:0001583	missense	5118	exon9			GTGCGGGCTGCTG	L33799	CCDS5700.1	7q22	2008-07-18			ENSG00000106333	ENSG00000106333			8738	protein-coding gene	gene with protein product	"""procollagen, type 1, COOH-terminal proteinase enhancer"", ""procollagen C-proteinase enhancer 1"""	600270				8824813, 9799793	Standard	NM_002593		Approved	PCPE, PCPE1	uc003uvo.3	Q15113	OTTHUMG00000156675	ENST00000223061.5:c.1330G>C	7.37:g.100205706G>C	ENSP00000223061:p.Ala444Pro	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	86	28	0.325581	NM_002593	B2R9E1|O14550	Missense_Mutation	SNP	ENST00000223061.5	37	CCDS5700.1	14	0.00641025641025641	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	15.79	2.937936	0.52972	0.002724	0.015	ENSG00000106333	ENST00000223061	T	0.24723	1.84	4.31	2.47	0.30058	.	0.335919	0.21418	N	0.074877	T	0.08626	0.0214	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.19484	-1.0304	10	0.56958	D	0.05	-1.0701	7.9729	0.30138	0.0943:0.1628:0.7429:0.0	rs61739556	444	Q15113	PCOC1_HUMAN	P	444	ENSP00000223061:A444P	ENSP00000223061:A444P	A	+	1	0	PCOLCE	100043642	0.957000	0.32711	0.003000	0.11579	0.099000	0.18886	1.804000	0.38873	0.521000	0.28445	0.462000	0.41574	GCT	G|0.992;C|0.008	0.008	strong		0.572	PCOLCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345285.1	NM_002593	
PIK3C3	5289	hgsc.bcm.edu	37	18	39623783	39623783	+	Splice_Site	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:39623783T>C	ENST00000262039.4	+	20	2274		c.e20+2		PIK3C3_ENST00000589056.1_Splice_Site|PIK3C3_ENST00000593098.1_Splice_Site|PIK3C3_ENST00000587402.1_Splice_Site|PIK3C3_ENST00000398870.3_Splice_Site	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3						autophagic vacuole assembly (GO:0000045)|cytokinesis (GO:0000910)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein processing (GO:0016485)|regulation of protein secretion (GO:0050708)|response to leucine (GO:0043201)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)|midbody (GO:0030496)|phagocytic vesicle (GO:0045335)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(25)|ovary(1)|skin(2)|urinary_tract(1)	49						AAAGCTGTGGTAAGTTTTTCA	0.343										TSP Lung(28;0.18)																											.	NSCLC(37;552 1060 2683 16430 37914)	Atlas-SNP	.											PIK3C3,NS,carcinoma,+2,1	PIK3C3	138	1	0			c.2188+2T>C						scavenged	.						153.0	135.0	141.0					18																	39623783		2203	4300	6503	SO:0001630	splice_region_variant	5289	exon20			CTGTGGTAAGTTT	Z46973	CCDS11920.1	18q12.3	2012-07-13	2012-07-13		ENSG00000078142	ENSG00000078142	2.7.1.137		8974	protein-coding gene	gene with protein product		602609	"""phosphoinositide-3-kinase, class 3"""			7628435	Standard	NM_002647		Approved	Vps34	uc002lap.3	Q8NEB9	OTTHUMG00000132593	ENST00000262039.4:c.2188+2T>C	18.37:g.39623783T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	119	3	0.0252101	NM_002647	Q15134	Splice_Site	SNP	ENST00000262039.4	37	CCDS11920.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.511025	0.85389	.	.	ENSG00000078142	ENST00000262039;ENST00000398870	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4058	0.74877	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	PIK3C3	37877781	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.552000	0.82192	2.105000	0.64084	0.528000	0.53228	.	.	.	none		0.343	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647	Intron
SDK1	221935	hgsc.bcm.edu	37	7	4026944	4026944	+	Silent	SNP	C	C	G	rs7785899	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:4026944C>G	ENST00000404826.2	+	14	2260	c.2121C>G	c.(2119-2121)ctC>ctG	p.L707L	SDK1_ENST00000389531.3_Silent_p.L707L	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	707	Fibronectin type-III 1. {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)		TCGTGGAGCTCTCTGAAAACA	0.458													G|||	2114	0.422125	0.7451	0.3718	5008	,	,		20231	0.1647		0.2942	False		,,,				2504	0.4182				p.L707L		Atlas-SNP	.											.	SDK1	361	.	0			c.C2121G						PASS	.	G		3069,1337	446.7+/-348.1	1081,907,215	130.0	132.0	131.0		2121	1.2	0.9	7	dbSNP_116	131	2946,5654	668.5+/-402.6	533,1880,1887	no	coding-synonymous	SDK1	NM_152744.3		1614,2787,2102	GG,GC,CC		34.2558,30.345,46.2479		707/2214	4026944	6015,6991	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon14			GGAGCTCTCTGAA	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.2121C>G	7.37:g.4026944C>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	165	163	0.987879	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			C|0.566;G|0.434	0.434	strong		0.458	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
DLEC1	9940	hgsc.bcm.edu	37	3	38125704	38125704	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38125704C>T	ENST00000308059.6	+	7	1250	c.1229C>T	c.(1228-1230)cCg>cTg	p.P410L	DLEC1_ENST00000469151.1_3'UTR|DLEC1_ENST00000346219.3_Missense_Mutation_p.P410L|DLEC1_ENST00000452631.2_Missense_Mutation_p.P410L					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)		CGAGTCCTCCCGCCTTCCACG	0.453																																					p.P410L		Atlas-SNP	.											.	DLEC1	278	.	0			c.C1229T						PASS	.						110.0	121.0	117.0					3																	38125704		2083	4217	6300	SO:0001583	missense	9940	exon7			TCCTCCCGCCTTC	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.1229C>T	3.37:g.38125704C>T	ENSP00000308597:p.Pro410Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	178	89	0.5	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	c	23.3	4.394599	0.83011	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.08984	3.03;3.05;3.27	5.4	5.4	0.78164	.	0.060013	0.64402	D	0.000002	T	0.32882	0.0844	M	0.80422	2.495	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.998;0.999	T	0.03545	-1.1026	10	0.56958	D	0.05	-17.7606	17.9203	0.88964	0.0:1.0:0.0:0.0	.	410;410;410;410	A1L305;F8W6T4;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	410	ENSP00000308597:P410L;ENSP00000315914:P410L;ENSP00000410427:P410L	ENSP00000308597:P410L	P	+	2	0	DLEC1	38100708	0.999000	0.42202	0.891000	0.34965	0.768000	0.43524	5.469000	0.66749	2.532000	0.85374	0.524000	0.50904	CCG	.	.	none		0.453	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
MUC2	4583	hgsc.bcm.edu	37	11	1093094	1093094	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1093094T>G	ENST00000441003.2	+	30	4940	c.4913T>G	c.(4912-4914)gTg>gGg	p.V1638G	MUC2_ENST00000359061.5_Missense_Mutation_p.V1605G|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	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.V1605G(1)|p.V1638G(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)	accactacggtgaccccaacc	0.627																																					p.V1638G		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	2	Substitution - Missense(2)	lung(2)	c.T4913G						PASS	.						70.0	127.0	107.0					11																	1093094		1817	3454	5271	SO:0001583	missense	4583	exon30			CTACGGTGACCCC	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.4913T>G	11.37:g.1093094T>G	ENSP00000415183:p.Val1638Gly	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	60	13	0.216667	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	T	2.324	-0.355023	0.05138	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14022	2.54;3.16	1.66	-3.31	0.04988	.	0.262594	0.13470	U	0.385509	T	0.06462	0.0166	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.29822	-0.9999	9	0.41790	T	0.15	.	0.1958	0.00139	0.2143:0.1839:0.2436:0.3582	.	1638	E7EUV1	.	G	1638;1605	ENSP00000415183:V1638G;ENSP00000351956:V1605G	ENSP00000351956:V1605G	V	+	2	0	MUC2	1083094	0.003000	0.15002	0.000000	0.03702	0.171000	0.22731	1.577000	0.36515	-1.792000	0.01259	0.102000	0.15555	GTG	.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
GALNT14	79623	hgsc.bcm.edu	37	2	31135184	31135184	+	Missense_Mutation	SNP	G	G	T	rs2288101	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:31135184G>T	ENST00000349752.5	-	14	2044	c.1405C>A	c.(1405-1407)Cag>Aag	p.Q469K	GALNT14_ENST00000356174.3_Missense_Mutation_p.Q436K|GALNT14_ENST00000406653.1_Missense_Mutation_p.Q449K|GALNT14_ENST00000420311.2_Missense_Mutation_p.Q434K|GALNT14_ENST00000324589.5_Missense_Mutation_p.Q474K|GALNT14_ENST00000486564.1_5'UTR	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	469	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		Q -> K (in dbSNP:rs2288101).		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	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)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					TGGAGGATCTGCTGGGTGTAT	0.547													G|||	993	0.198283	0.1407	0.1844	5008	,	,		19413	0.1984		0.2614	False		,,,				2504	0.2209				p.Q474K		Atlas-SNP	.											.	GALNT14	103	.	0			c.C1420A						PASS	.	G	LYS/GLN	722,3684	298.7+/-285.4	62,598,1543	89.0	88.0	89.0		1405	5.0	1.0	2	dbSNP_100	89	2081,6519	360.9+/-332.1	253,1575,2472	yes	missense	GALNT14	NM_024572.2	53	315,2173,4015	TT,TG,GG		24.1977,16.3867,21.5516	benign	469/553	31135184	2803,10203	2203	4300	6503	SO:0001583	missense	79623	exon15			GGATCTGCTGGGT	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.1405C>A	2.37:g.31135184G>T	ENSP00000288988:p.Gln469Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	CCDS1773.2	440	0.20146520146520147	58	0.11788617886178862	60	0.16574585635359115	120	0.2097902097902098	202	0.26649076517150394	G	12.20	1.867597	0.32977	0.163867	0.241977	ENSG00000158089	ENST00000349752;ENST00000324589;ENST00000406653;ENST00000356174;ENST00000420311	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.04	5.04	0.67666	Ricin B-related lectin (1);Ricin B lectin (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.82056	2.57	0.09310	P	0.999999763259	B;D;B;P	0.53745	0.336;0.962;0.1;0.896	B;P;B;P	0.53313	0.268;0.723;0.14;0.649	T	0.02059	-1.1221	9	0.45353	T	0.12	.	17.1769	0.86844	0.0:0.0:1.0:0.0	rs2288101;rs52827502;rs57335829;rs2288101	434;474;469;449	F5H263;Q96FL9-3;Q96FL9;B3KV89	.;.;GLT14_HUMAN;.	K	469;474;449;436;434	ENSP00000288988:Q469K;ENSP00000314500:Q474K;ENSP00000385435:Q449K;ENSP00000348497:Q436K;ENSP00000415514:Q434K	ENSP00000314500:Q474K	Q	-	1	0	GALNT14	30988688	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	6.095000	0.71439	2.349000	0.79799	0.563000	0.77884	CAG	G|0.797;T|0.203	0.203	strong		0.547	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
MUC17	140453	hgsc.bcm.edu	37	7	100695138	100695138	+	Missense_Mutation	SNP	G	G	A	rs73168398	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100695138G>A	ENST00000306151.4	+	9	13062	c.12998G>A	c.(12997-12999)cGg>cAg	p.R4333Q		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4333					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)					GTGGAGTACCGGGACCAGAAG	0.572													G|||	536	0.107029	0.1021	0.0778	5008	,	,		19865	0.124		0.1143	False		,,,				2504	0.1094				p.R4333Q		Atlas-SNP	.											.	MUC17	804	.	0			c.G12998A						PASS	.	G	GLN/ARG	479,3927	226.2+/-241.8	25,429,1749	160.0	143.0	149.0		12998	0.1	0.0	7	dbSNP_130	149	936,7664	206.8+/-248.7	54,828,3418	yes	missense	MUC17	NM_001040105.1	43	79,1257,5167	AA,AG,GG		10.8837,10.8715,10.8796	benign	4333/4494	100695138	1415,11591	2203	4300	6503	SO:0001583	missense	140453	exon9			AGTACCGGGACCA	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.12998G>A	7.37:g.100695138G>A	ENSP00000302716:p.Arg4333Gln	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	184	182	0.98913	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	217	0.09935897435897435	32	0.06504065040650407	27	0.07458563535911603	70	0.12237762237762238	88	0.11609498680738786	G	7.977	0.750437	0.15778	0.108715	0.108837	ENSG00000169876	ENST00000306151	T	0.43294	0.95	4.17	0.0575	0.14323	.	.	.	.	.	T	0.00144	0.0004	N	0.00926	-1.1	0.80722	P	0.0	B	0.32203	0.36	B	0.15052	0.012	T	0.23904	-1.0175	8	0.18710	T	0.47	.	6.1801	0.20465	0.6597:0.0:0.3403:0.0	.	4333	Q685J3	MUC17_HUMAN	Q	4333	ENSP00000302716:R4333Q	ENSP00000302716:R4333Q	R	+	2	0	MUC17	100481858	0.001000	0.12720	0.043000	0.18650	0.012000	0.07955	-0.054000	0.11826	-0.016000	0.14127	-0.658000	0.03865	CGG	G|0.898;A|0.102	0.102	strong		0.572	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CDH19	28513	hgsc.bcm.edu	37	18	64172434	64172434	+	Missense_Mutation	SNP	C	C	G	rs55874520	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:64172434C>G	ENST00000262150.2	-	12	2226	c.1934G>C	c.(1933-1935)gGg>gCg	p.G645A	CDH19_ENST00000540086.1_3'UTR	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	0	Cadherin 6. {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)				TTCTCCACCCCCTTCATCATC	0.403													c|||	35	0.00698882	0.0015	0.0101	5008	,	,		14403	0.0		0.0258	False		,,,				2504	0.0				p.G645A		Atlas-SNP	.											.	CDH19	141	.	0			c.G1934C						PASS	.	C	ALA/GLY	26,4380	29.0+/-57.7	0,26,2177	169.0	169.0	169.0		1934	5.2	0.8	18	dbSNP_129	169	219,8381	83.1+/-145.7	3,213,4084	yes	missense	CDH19	NM_021153.2	60	3,239,6261	GG,GC,CC		2.5465,0.5901,1.8837	probably-damaging	645/773	64172434	245,12761	2203	4300	6503	SO:0001583	missense	28513	exon12			CCACCCCCTTCAT	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.1934G>C	18.37:g.64172434C>G	ENSP00000262150:p.Gly645Ala	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	201	97	0.482587	NM_021153	O15098	Missense_Mutation	SNP	ENST00000262150.2	37	CCDS11994.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	c	19.92	3.917129	0.73098	0.005901	0.025465	ENSG00000071991	ENST00000262150	D	0.85556	-2.0	5.18	5.18	0.71444	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.87030	0.6076	M	0.91717	3.235	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.90204	0.4259	10	0.87932	D	0	.	19.0693	0.93126	0.0:1.0:0.0:0.0	rs55874520	645	Q9H159	CAD19_HUMAN	A	645	ENSP00000262150:G645A	ENSP00000262150:G645A	G	-	2	0	CDH19	62323414	1.000000	0.71417	0.759000	0.31340	0.423000	0.31445	7.284000	0.78650	2.564000	0.86499	0.650000	0.86243	GGG	C|0.983;G|0.017	0.017	strong		0.403	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
XIRP2	129446	hgsc.bcm.edu	37	2	168104199	168104199	+	Silent	SNP	C	C	T	rs7581190	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168104199C>T	ENST00000409195.1	+	9	6386	c.6297C>T	c.(6295-6297)gaC>gaT	p.D2099D	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Silent_p.D1877D|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Silent_p.D2099D	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1924					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						AAGAATCAGACAGGGCAGTGA	0.383													C|||	865	0.172724	0.2882	0.1196	5008	,	,		18181	0.12		0.1123	False		,,,				2504	0.1708				p.D2099D		Atlas-SNP	.											.	XIRP2	914	.	0			c.C6297T						PASS	.	C	,,,,	971,2885		131,709,1088	56.0	52.0	53.0		,,5631,,6297	4.1	0.9	2	dbSNP_116	53	800,7504		42,716,3394	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	173,1425,4482	TT,TC,CC		9.6339,25.1815,14.5641	,,,,	,,1877/3328,,2099/3550	168104199	1771,10389	1928	4152	6080	SO:0001819	synonymous_variant	129446	exon9			ATCAGACAGGGCA	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.6297C>T	2.37:g.168104199C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			C|0.840;T|0.160	0.160	strong		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
FGD2	221472	hgsc.bcm.edu	37	6	36988364	36988364	+	Silent	SNP	C	C	T	rs831504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:36988364C>T	ENST00000274963.8	+	10	1341	c.1170C>T	c.(1168-1170)tcC>tcT	p.S390S		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	390	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)|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)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|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)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						TCCTGGTGTCCGGGAAGCAGC	0.642													C|||	2793	0.557708	0.612	0.5548	5008	,	,		16624	0.4831		0.492	False		,,,				2504	0.6309				p.S390S		Atlas-SNP	.											.	FGD2	65	.	0			c.C1170T						PASS	.	C		2604,1802	611.4+/-391.8	773,1058,372	33.0	31.0	32.0		1170	-10.9	0.2	6	dbSNP_86	32	4259,4341	548.0+/-385.3	1058,2143,1099	no	coding-synonymous	FGD2	NM_173558.3		1831,3201,1471	TT,TC,CC		49.5233,40.8988,47.232		390/656	36988364	6863,6143	2203	4300	6503	SO:0001819	synonymous_variant	221472	exon10			GGTGTCCGGGAAG	AK097230	CCDS4829.1	6p21.2	2013-01-10	2004-08-24		ENSG00000146192	ENSG00000146192		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	3664	protein-coding gene	gene with protein product		605091	"""FGD1 family, member 2"""			10458911	Standard	NM_173558		Approved	ZFYVE4	uc010jwp.1	Q7Z6J4	OTTHUMG00000014616	ENST00000274963.8:c.1170C>T	6.37:g.36988364C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Silent	SNP	ENST00000274963.8	37	CCDS4829.1																																																																																			C|0.467;T|0.533	0.533	strong		0.642	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558	
CEP164	22897	hgsc.bcm.edu	37	11	117266312	117266312	+	Missense_Mutation	SNP	C	C	G	rs2305830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117266312C>G	ENST00000278935.3	+	24	3110	c.2963C>G	c.(2962-2964)aCc>aGc	p.T988S	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	988			T -> S (in dbSNP:rs2305830). {ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		AAGGAGCACACCCACCTGTTG	0.567													C|||	1392	0.277955	0.267	0.2089	5008	,	,		18904	0.3046		0.3211	False		,,,				2504	0.2699				p.T991S		Atlas-SNP	.											.	CEP164	121	.	0			c.C2972G						PASS	.	C	SER/THR	1176,3226	411.3+/-335.7	155,866,1180	56.0	57.0	57.0		2963	0.9	0.0	11	dbSNP_100	57	2658,5934	425.8+/-355.1	405,1848,2043	yes	missense	CEP164	NM_014956.4	58	560,2714,3223	GG,GC,CC		30.9358,26.7151,29.5059	benign	988/1461	117266312	3834,9160	2201	4296	6497	SO:0001583	missense	22897	exon23			AGCACACCCACCT	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.2963C>G	11.37:g.117266312C>G	ENSP00000278935:p.Thr988Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	260	259	0.996154	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	635	0.2907509157509158	139	0.28252032520325204	87	0.24033149171270718	168	0.2937062937062937	241	0.3179419525065963	C	10.78	1.445822	0.25987	0.267151	0.309358	ENSG00000110274	ENST00000278935;ENST00000529538	T	0.27104	1.69	5.02	0.953	0.19590	.	0.702415	0.12990	N	0.422568	T	0.00012	0.0000	L	0.50919	1.6	0.80722	P	0.0	B;B;B;B	0.10296	0.002;0.003;0.003;0.003	B;B;B;B	0.10450	0.002;0.005;0.005;0.005	T	0.40664	-0.9551	9	0.29301	T	0.29	-0.0052	3.8141	0.08808	0.1203:0.3898:0.353:0.1368	rs2305830;rs17500832;rs52823446;rs2305830	962;762;988;991	E9PI34;Q9NTH6;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	S	988;962	ENSP00000278935:T988S	ENSP00000278935:T988S	T	+	2	0	CEP164	116771522	0.000000	0.05858	0.003000	0.11579	0.953000	0.61014	-0.116000	0.10724	-0.075000	0.12798	0.491000	0.48974	ACC	C|0.709;G|0.291	0.291	strong		0.567	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
GTF3C4	9329	hgsc.bcm.edu	37	9	135546021	135546021	+	Silent	SNP	G	G	A	rs146201597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:135546021G>A	ENST00000372146.4	+	1	600	c.36G>A	c.(34-36)gcG>gcA	p.A12A	DDX31_ENST00000480876.1_5'Flank|DDX31_ENST00000372153.1_5'Flank|DDX31_ENST00000310532.2_5'Flank|DDX31_ENST00000372159.3_5'Flank|GTF3C4_ENST00000483873.2_Silent_p.A12A|DDX31_ENST00000544003.1_5'Flank	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	12					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|positive regulation of catalytic activity (GO:0043085)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)|enzyme activator activity (GO:0008047)|histone acetyltransferase activity (GO:0004402)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;8.15e-07)|Epithelial(140;2.6e-05)		TGGGGCCCGCGGACGACGGGC	0.771													G|||	81	0.0161741	0.0045	0.0202	5008	,	,		9102	0.0		0.0338	False		,,,				2504	0.0276				p.A12A	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											.	GTF3C4	53	.	0			c.G36A						PASS	.	G		13,2385		0,13,1186	3.0	4.0	4.0		36	2.4	0.9	9	dbSNP_134	4	168,5390		0,168,2611	no	coding-synonymous	GTF3C4	NM_012204.2		0,181,3797	AA,AG,GG		3.0227,0.5421,2.275		12/823	135546021	181,7775	1199	2779	3978	SO:0001819	synonymous_variant	9329	exon1			GCCCGCGGACGAC	AF142328	CCDS6953.1	9q34.3	2011-07-01	2002-08-29		ENSG00000125484	ENSG00000125484		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""General transcription factors"""	4667	protein-coding gene	gene with protein product		604892	"""general transcription factor IIIC, polypeptide 4 (90kD)"""			10523658	Standard	NM_012204		Approved	TFIIIC90, KAT12	uc010mzv.3	Q9UKN8	OTTHUMG00000020842	ENST00000372146.4:c.36G>A	9.37:g.135546021G>A		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	9	8	0.888889	NM_012204	Q5VZJ7	Silent	SNP	ENST00000372146.4	37	CCDS6953.1																																																																																			G|0.986;A|0.014	0.014	strong		0.771	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1		
ZNF470	388566	hgsc.bcm.edu	37	19	57085769	57085769	+	Missense_Mutation	SNP	G	G	C	rs10421285	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57085769G>C	ENST00000330619.8	+	4	753	c.67G>C	c.(67-69)Gtg>Ctg	p.V23L	ZNF470_ENST00000391709.3_Missense_Mutation_p.V23L|ZNF470_ENST00000601902.1_Missense_Mutation_p.V23L	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	23	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		V -> L (in dbSNP:rs10421285). {ECO:0000269|PubMed:15302581}.		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.V23L(1)		endometrium(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		TTAGGGTTCAGTGACTTTCAC	0.403													G|||	2123	0.423922	0.6657	0.3357	5008	,	,		20025	0.2788		0.3698	False		,,,				2504	0.365				p.V23L		Atlas-SNP	.											ZNF470,NS,carcinoma,0,1	ZNF470	103	1	1	Substitution - Missense(1)	stomach(1)	c.G67C						PASS	.	G	LEU/VAL	2705,1701	652.9+/-399.5	827,1051,325	182.0	166.0	171.0		67	-3.1	0.0	19	dbSNP_119	171	3139,5461	478.2+/-369.8	605,1929,1766	yes	missense	ZNF470	NM_001001668.3	32	1432,2980,2091	CC,CG,GG		36.5,38.6064,44.9331	benign	23/718	57085769	5844,7162	2203	4300	6503	SO:0001583	missense	388566	exon4			GGTTCAGTGACTT	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"""Zinc fingers, C2H2-type"", ""-"""	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.67G>C	19.37:g.57085769G>C	ENSP00000333223:p.Val23Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	162	88	0.54321	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Missense_Mutation	SNP	ENST00000330619.8	37	CCDS33122.1	867	0.39697802197802196	317	0.6443089430894309	127	0.35082872928176795	147	0.256993006993007	276	0.3641160949868074	G	7.600	0.672565	0.14776	0.613936	0.365	ENSG00000197016	ENST00000391709;ENST00000330619	T;T	0.04862	3.54;3.54	3.58	-3.06	0.05379	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	L	0.53671	1.685	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31364	-0.9946	8	0.21540	T	0.41	.	4.4059	0.11409	0.4026:0.3162:0.2812:0.0	rs10421285;rs56621387;rs10421285	23	Q6ECI4	ZN470_HUMAN	L	23	ENSP00000375590:V23L;ENSP00000333223:V23L	ENSP00000333223:V23L	V	+	1	0	ZNF470	61777581	0.661000	0.27430	0.034000	0.17996	0.830000	0.47004	0.740000	0.26188	-0.621000	0.05633	-0.182000	0.12963	GTG	G|0.566;C|0.434	0.434	strong		0.403	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
AKAP9	10142	hgsc.bcm.edu	37	7	91713972	91713972	+	Intron	SNP	C	C	T	rs10228334	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91713972C>T	ENST00000359028.2	+	35	8947				AKAP9_ENST00000356239.3_Silent_p.L2889L|AKAP9_ENST00000358100.2_Intron			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9						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)			AATTCCTGAGCTAGCACATTC	0.289			T	BRAF	papillary thyroid								T|||	1872	0.373802	0.5076	0.3573	5008	,	,		15836	0.1617		0.3867	False		,,,				2504	0.41				p.L2889L		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C8665T						PASS	.	T	,	2271,2135	553.6+/-378.8	579,1113,511	42.0	45.0	44.0		8665,8641	0.7	0.9	7	dbSNP_119	44	3458,5128	618.1+/-396.7	681,2096,1516	no	coding-synonymous,coding-synonymous	AKAP9	NM_005751.4,NM_147185.2	,	1260,3209,2027	TT,TC,CC		40.2749,48.4567,44.0964	,	2889/3908,2881/3900	91713972	5729,7263	2203	4293	6496	SO:0001627	intron_variant	10142	exon34			CCTGAGCTAGCAC	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.8723-161C>T	7.37:g.91713972C>T		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	251	251	1	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				C|0.593;T|0.407	0.407	strong		0.289	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
MUC4	4585	hgsc.bcm.edu	37	3	195506603	195506603	+	Missense_Mutation	SNP	T	T	C	rs201602653		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195506603T>C	ENST00000463781.3	-	2	12307	c.11848A>G	c.(11848-11850)Acc>Gcc	p.T3950A	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3950A	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.T3950A(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	0.592																																					p.T3950A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.A11848G						scavenged	.						14.0	12.0	13.0					3																	195506603		630	1408	2038	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.11848A>G	3.37:g.195506603T>C	ENSP00000417498:p.Thr3950Ala	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	45	13	0.288889	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	1.026	-0.683487	0.03353	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28666	1.6;1.8	.	.	.	.	.	.	.	.	T	0.11281	0.0275	N	0.08118	0	0.09310	N	0.999999	P	0.44006	0.824	B	0.37047	0.24	T	0.11817	-1.0572	7	.	.	.	.	2.8304	0.05498	3.0E-4:2.0E-4:0.4983:0.5012	.	3822	E7ESK3	.	A	3950	ENSP00000417498:T3950A;ENSP00000420243:T3950A	.	T	-	1	0	MUC4	196991382	0.070000	0.21116	0.015000	0.15790	0.013000	0.08279	1.182000	0.32029	0.056000	0.16144	0.055000	0.15244	ACC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GBGT1	26301	hgsc.bcm.edu	37	9	136029138	136029138	+	Silent	SNP	G	G	A	rs35902535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136029138G>A	ENST00000372040.3	-	7	1181	c.870C>T	c.(868-870)ggC>ggT	p.G290G	GBGT1_ENST00000540636.1_Silent_p.G273G|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000372043.3_Missense_Mutation_p.A284V|RALGDS_ENST00000542690.1_Intron	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	290					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		CAGCCATGATGCCATTGGCCT	0.587													G|||	210	0.0419329	0.0333	0.0403	5008	,	,		17659	0.002		0.0795	False		,,,				2504	0.0573				p.G290G		Atlas-SNP	.											.	GBGT1	25	.	0			c.C870T						PASS	.	G		200,4206	124.9+/-162.1	8,184,2011	121.0	113.0	116.0		870	2.3	1.0	9	dbSNP_126	116	618,7982	160.3+/-213.4	16,586,3698	no	coding-synonymous	GBGT1	NM_021996.4		24,770,5709	AA,AG,GG		7.186,4.5393,6.2894		290/348	136029138	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	26301	exon7			CATGATGCCATTG	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.870C>T	9.37:g.136029138G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	105	0.04807692307692308	21	0.042682926829268296	15	0.04143646408839779	2	0.0034965034965034965	67	0.08839050131926121	G	12.72	2.022220	0.35701	0.045393	0.07186	ENSG00000148288	ENST00000372043	T	0.23348	1.91	5.38	2.31	0.28768	.	.	.	.	.	T	0.01287	0.0042	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00460	-1.1726	6	0.87932	D	0	-15.1162	5.0909	0.14708	0.2677:0.3054:0.4269:0.0	rs35902535;rs62638711	.	.	.	V	284	ENSP00000361113:A284V	ENSP00000361113:A284V	A	-	2	0	GBGT1	135018959	0.629000	0.27146	0.992000	0.48379	0.929000	0.56500	0.761000	0.26489	0.542000	0.28846	0.561000	0.74099	GCA	G|0.944;A|0.056	0.056	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
Unknown	0	hgsc.bcm.edu	37	14	20181502	20181502	+	IGR	SNP	C	C	T	rs201024081		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	1699	1	0.000588581		WXS	Illumina HiSeq	Phase_I	911	521	0.571899	NM_001197287		Missense_Mutation	SNP		37																																																																																				.	.	weak	0	0.443								
MGARP	84709	hgsc.bcm.edu	37	4	140188094	140188094	+	Missense_Mutation	SNP	C	C	T	rs3208941	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:140188094C>T	ENST00000398955.1	-	4	561	c.382G>A	c.(382-384)Gct>Act	p.A128T		NM_032623.3	NP_116012.2	Q8TDB4	HUMMR_HUMAN	mitochondria-localized glutamic acid-rich protein	128			A -> T (in dbSNP:rs3208941).		anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cellular response to gonadotropin-releasing hormone (GO:0097211)|cellular response to hypoxia (GO:0071456)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of mitochondrion organization (GO:0010822)|protein targeting to mitochondrion (GO:0006626)|retrograde axon cargo transport (GO:0008090)	integral component of mitochondrial outer membrane (GO:0031307)|mitochondrion (GO:0005739)											ACAACTGTAGCACTGGGACTT	0.517													C|||	261	0.0521166	0.0318	0.0476	5008	,	,		17941	0.1052		0.0507	False		,,,				2504	0.0297				p.A128T		Atlas-SNP	.											.	.	.	.	0			c.G382A						PASS	.	C	THR/ALA	175,3857		4,167,1845	166.0	159.0	161.0		382	5.3	0.0	4	dbSNP_105	161	567,7815		15,537,3639	yes	missense	C4orf49	NM_032623.3	58	19,704,5484	TT,TC,CC		6.7645,4.3403,5.9771	possibly-damaging	128/241	140188094	742,11672	2016	4191	6207	SO:0001583	missense	84709	exon4			CTGTAGCACTGGG	AF484960	CCDS43269.1	4q31.1	2014-02-19	2014-02-19	2012-04-17	ENSG00000137463	ENSG00000137463			29969	protein-coding gene	gene with protein product	"""ovary-specific acidic protein"", ""corneal endothelium-specific protein 1"", ""hypoxia up-regulated mitochondrial movement regulator"""		"""chromosome 4 open reading frame 49"""	C4orf49			Standard	NM_032623		Approved	OSAP, CESP-1, HUMMR	uc003ihr.1	Q8TDB4	OTTHUMG00000161325	ENST00000398955.1:c.382G>A	4.37:g.140188094C>T	ENSP00000381928:p.Ala128Thr	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	139	23	0.165468	NM_032623	Q9BZC3	Missense_Mutation	SNP	ENST00000398955.1	37	CCDS43269.1	110	0.05036630036630037	17	0.034552845528455285	10	0.027624309392265192	49	0.08566433566433566	34	0.044854881266490766	C	14.42	2.528927	0.44969	0.043403	0.067645	ENSG00000137463	ENST00000398955	T	0.49432	0.78	5.31	5.31	0.75309	.	0.559675	0.18543	N	0.138136	T	0.02047	0.0064	L	0.41710	1.295	0.80722	D	1	P	0.35745	0.518	B	0.36504	0.226	T	0.02059	-1.1221	10	0.87932	D	0	-11.2069	14.4853	0.67614	0.0:1.0:0.0:0.0	rs3208941;rs52834247;rs3208941	128	Q8TDB4	CD049_HUMAN	T	128	ENSP00000381928:A128T	ENSP00000381928:A128T	A	-	1	0	C4orf49	140407544	0.000000	0.05858	0.020000	0.16555	0.004000	0.04260	0.517000	0.22832	2.481000	0.83766	0.467000	0.42956	GCT	C|0.944;T|0.056	0.056	strong		0.517	MGARP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364536.1	NM_032623	
TEKT5	146279	hgsc.bcm.edu	37	16	10788200	10788200	+	Missense_Mutation	SNP	C	C	G	rs148185751	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:10788200C>G	ENST00000283025.2	-	1	602	c.531G>C	c.(529-531)gaG>gaC	p.E177D	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	177						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						TGGCCGCGCACTCCAGCCGCC	0.587													C|||	13	0.00259585	0.0015	0.0058	5008	,	,		17641	0.0		0.006	False		,,,				2504	0.001				p.E177D		Atlas-SNP	.											.	TEKT5	66	.	0			c.G531C						PASS	.	C	ASP/GLU	5,4389	9.9+/-24.2	0,5,2192	137.0	151.0	147.0		531	4.7	1.0	16	dbSNP_134	147	29,8571	21.0+/-64.5	1,27,4272	yes	missense	TEKT5	NM_144674.1	45	1,32,6464	GG,GC,CC		0.3372,0.1138,0.2617	probably-damaging	177/486	10788200	34,12960	2197	4300	6497	SO:0001583	missense	146279	exon1			CGCGCACTCCAGC		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.531G>C	16.37:g.10788200C>G	ENSP00000283025:p.Glu177Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	12.33	1.905042	0.33628	0.001138	0.003372	ENSG00000153060	ENST00000283025	T	0.03330	3.97	5.63	4.68	0.58851	.	0.190679	0.36234	N	0.002712	T	0.11281	0.0275	M	0.86343	2.81	0.44380	D	0.997282	B	0.31318	0.319	B	0.41691	0.364	T	0.00458	-1.1727	10	0.66056	D	0.02	-35.8279	8.0289	0.30453	0.0:0.7616:0.0:0.2384	.	177	Q96M29	TEKT5_HUMAN	D	177	ENSP00000283025:E177D	ENSP00000283025:E177D	E	-	3	2	TEKT5	10695701	0.989000	0.36119	0.991000	0.47740	0.036000	0.12997	0.283000	0.18846	1.368000	0.46115	0.650000	0.86243	GAG	C|0.998;G|0.002	0.002	strong		0.587	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
SLC1A5	6510	hgsc.bcm.edu	37	19	47282162	47282162	+	Silent	SNP	G	G	A	rs2070246	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:47282162G>A	ENST00000542575.2	-	5	1456	c.828C>T	c.(826-828)taC>taT	p.Y276Y	SLC1A5_ENST00000412532.2_Silent_p.Y48Y|SLC1A5_ENST00000594991.1_Silent_p.Y100Y|SLC1A5_ENST00000434726.2_Silent_p.Y74Y	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	276					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)	CCACAGGGGCGTACCTGATCA	0.582													G|||	1673	0.334065	0.4463	0.4294	5008	,	,		17783	0.2629		0.2177	False		,,,				2504	0.3078				p.Y276Y		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C828T						PASS	.	G	,,	1896,2510	542.8+/-376.1	408,1080,715	132.0	111.0	118.0		144,222,828	-2.2	0.8	19	dbSNP_96	118	1778,6822	320.3+/-314.5	199,1380,2721	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC1A5	NM_001145144.1,NM_001145145.1,NM_005628.2	,,	607,2460,3436	AA,AG,GG		20.6744,43.0322,28.2485	,,	48/314,74/340,276/542	47282162	3674,9332	2203	4300	6503	SO:0001819	synonymous_variant	6510	exon5			AGGGGCGTACCTG	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.828C>T	19.37:g.47282162G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Silent	SNP	ENST00000542575.2	37	CCDS12692.1																																																																																			G|0.704;A|0.296	0.296	strong		0.582	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
LACC1	144811	hgsc.bcm.edu	37	13	44457984	44457984	+	Silent	SNP	A	A	G	rs9533673	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:44457984A>G	ENST00000441843.1	+	4	1304	c.819A>G	c.(817-819)agA>agG	p.R273R	LACC1_ENST00000325686.6_Silent_p.R273R	NM_001128303.1	NP_001121775.1	Q8IV20	LACC1_HUMAN	laccase (multicopper oxidoreductase) domain containing 1	273																	CAAATCAGAGAGGAGTCACAA	0.413													A|||	324	0.0646965	0.1029	0.0793	5008	,	,		15921	0.0		0.1014	False		,,,				2504	0.0317				p.R273R		Atlas-SNP	.											.	.	.	.	0			c.A819G						PASS	.	A	,	476,3930	222.3+/-239.2	25,426,1752	115.0	109.0	111.0		819,819	1.7	1.0	13	dbSNP_119	111	871,7729	196.5+/-241.4	51,769,3480	no	coding-synonymous,coding-synonymous	LACC1	NM_001128303.1,NM_153218.2	,	76,1195,5232	GG,GA,AA		10.1279,10.8034,10.3568	,	273/431,273/431	44457984	1347,11659	2203	4300	6503	SO:0001819	synonymous_variant	144811	exon4			TCAGAGAGGAGTC	AK096044	CCDS9391.1	13q14.11	2012-05-11	2011-08-09	2011-08-09	ENSG00000179630	ENSG00000179630			26789	protein-coding gene	gene with protein product		613409	"""chromosome 13 open reading frame 31"""	C13orf31		16740638, 22504414	Standard	NM_153218		Approved	FLJ38725	uc010acg.3	Q8IV20	OTTHUMG00000016826	ENST00000441843.1:c.819A>G	13.37:g.44457984A>G		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	200	98	0.49	NM_001128303	A2A3Z6|Q8N8X5	Silent	SNP	ENST00000441843.1	37	CCDS9391.1																																																																																			A|0.903;G|0.097	0.097	strong		0.413	LACC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044726.3	NM_153218	
OR51F1	256892	hgsc.bcm.edu	37	11	4790605	4790605	+	Silent	SNP	A	A	G	rs112024216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790605A>G	ENST00000380383.1	-	1	563	c.564T>C	c.(562-564)tgT>tgC	p.C188C	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Silent_p.C181C|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	188						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)		CTGGATGGTAACAATAGGAGT	0.388													A|||	77	0.0153754	0.0008	0.0389	5008	,	,		23784	0.0		0.0487	False		,,,				2504	0.0				p.C181C		Atlas-SNP	.											.	OR51F1	60	.	0			c.T543C						PASS	.	A		37,4365	41.6+/-74.8	0,37,2164	144.0	138.0	140.0		543	-5.1	0.3	11	dbSNP_132	140	331,8265	115.3+/-175.2	6,319,3973	no	coding-synonymous	OR51F1	NM_001004752.1		6,356,6137	GG,GA,AA		3.8506,0.8405,2.8312		181/313	4790605	368,12630	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			ATGGTAACAATAG	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.564T>C	11.37:g.4790605A>G		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	248	126	0.508065	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.971;G|0.029	0.029	strong		0.388	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
RPS6KA2	6196	hgsc.bcm.edu	37	6	167040463	167040463	+	Silent	SNP	A	A	G	rs10946179	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:167040463A>G	ENST00000265678.4	-	1	268	c.45T>C	c.(43-45)tcT>tcC	p.S15S	RPS6KA2_ENST00000510118.1_Intron|RPS6KA2_ENST00000503859.1_Intron|RPS6KA2_ENST00000366863.2_5'UTR	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	15					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)		GCAGGTACACAGAGAAGAACC	0.711													g|||	874	0.174521	0.1536	0.1369	5008	,	,		9611	0.2609		0.1889	False		,,,				2504	0.1258				p.S15S		Atlas-SNP	.											RPS6KA2,brain,glioma,0,2	RPS6KA2	212	2	0			c.T45C						PASS	.		,	643,3735		46,551,1592	14.0	13.0	13.0		,45	-9.4	0.9	6	dbSNP_120	13	1454,7112		127,1200,2956	no	intron,coding-synonymous	RPS6KA2	NM_001006932.1,NM_021135.4	,	173,1751,4548	GG,GA,AA		16.9741,14.6871,16.2006	,	,15/734	167040463	2097,10847	2189	4283	6472	SO:0001819	synonymous_variant	6196	exon1			GTACACAGAGAAG	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.45T>C	6.37:g.167040463A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_021135	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Silent	SNP	ENST00000265678.4	37	CCDS5294.1																																																																																			A|0.834;G|0.166	0.166	strong		0.711	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
SHC1	6464	hgsc.bcm.edu	37	1	154938235	154938235	+	Silent	SNP	G	G	C	rs1131397	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154938235G>C	ENST00000368445.5	-	11	1621	c.1407C>G	c.(1405-1407)cgC>cgG	p.R469R	SHC1_ENST00000448116.2_Silent_p.R470R|SHC1_ENST00000368453.4_Silent_p.R360R|SHC1_ENST00000490667.1_5'UTR|PYGO2_ENST00000483463.1_5'Flank|SHC1_ENST00000368449.4_Silent_p.R240R|SHC1_ENST00000606391.1_Silent_p.R270R|SHC1_ENST00000368450.1_Silent_p.R359R	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	469	CH1.|Pro-rich.				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)			GTGGAGGCACGCGAAGAGCAT	0.622													C|||	793	0.158347	0.5061	0.0576	5008	,	,		19439	0.002		0.0278	False		,,,				2504	0.0552				p.R470R	NSCLC(4;32 234 1864 2492 3259 13747 17376)	Atlas-SNP	.											SHC1_ENST00000448116,NS,carcinoma,-2,2	SHC1	91	2	0			c.C1410G						PASS	.	C	,,,,	1977,2429		479,1019,705	32.0	35.0	34.0		1410,1077,942,1080,1407	-0.8	1.0	1	dbSNP_86	34	302,8298		5,292,4003	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SHC1	NM_001130040.1,NM_001130041.1,NM_001202859.1,NM_003029.4,NM_183001.4	,,,,	484,1311,4708	CC,CG,GG		3.5116,44.8706,17.5227	,,,,	470/585,359/474,314/429,360/475,469/584	154938235	2279,10727	2203	4300	6503	SO:0001819	synonymous_variant	6464	exon11			AGGCACGCGAAGA	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.1407C>G	1.37:g.154938235G>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	168	115	0.684524	NM_001130040	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Silent	SNP	ENST00000368445.5	37	CCDS30881.1	306	0.1401098901098901	260	0.5284552845528455	25	0.06906077348066299	1	0.0017482517482517483	20	0.026385224274406333	C	8.197	0.797373	0.16327	0.448706	0.035116	ENSG00000160691	ENST00000444664	T	0.47528	0.84	4.76	-0.804	0.10882	.	0.315155	0.29376	N	0.012336	T	0.19406	0.0466	.	.	.	0.09310	P	0.99999999397811	.	.	.	.	.	.	T	0.10823	-1.0613	6	0.49607	T	0.09	.	1.8226	0.03114	0.3253:0.3188:0.2166:0.1393	rs1131397;rs3191299;rs12080731;rs16990832;rs58820991;rs1131397	.	.	.	G	133	ENSP00000396333:R133G	ENSP00000396333:R133G	R	-	1	0	SHC1	153204859	0.014000	0.17966	0.981000	0.43875	0.930000	0.56654	-0.357000	0.07651	-0.231000	0.09825	-0.990000	0.02549	CGT	G|0.847;C|0.153	0.153	strong		0.622	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001	
WDR27	253769	hgsc.bcm.edu	37	6	170070723	170070723	+	Missense_Mutation	SNP	A	A	G	rs4236176	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170070723A>G	ENST00000448612.1	-	4	507	c.398T>C	c.(397-399)cTg>cCg	p.L133P	WDR27_ENST00000333572.6_Missense_Mutation_p.L133P|WDR27_ENST00000423258.1_Intron|WDR27_ENST00000420344.2_Missense_Mutation_p.L133P	NM_182552.4	NP_872358.4	A2RRH5	WDR27_HUMAN	WD repeat domain 27	133			L -> P (in dbSNP:rs4236176). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	12		Breast(66;1.53e-05)|Ovarian(120;0.216)		OV - Ovarian serous cystadenocarcinoma(33;6.48e-20)|BRCA - Breast invasive adenocarcinoma(81;3.56e-07)|GBM - Glioblastoma multiforme(31;0.00168)		ATGATCATCCAGGCTCAACTG	0.468													a|||	2691	0.53734	0.4803	0.5548	5008	,	,		16862	0.9365		0.2922	False		,,,				2504	0.4427				p.L133P		Atlas-SNP	.											.	WDR27	129	.	0			c.T398C						PASS	.	A	,PRO/LEU	1677,2209		358,961,624	123.0	123.0	123.0		,398	0.7	0.0	6	dbSNP_111	123	2170,6136		294,1582,2277	yes	intron,missense	WDR27	NM_001202550.1,NM_182552.4	,98	652,2543,2901	GG,GA,AA		26.1257,43.1549,31.5535	,benign	,133/896	170070723	3847,8345	1943	4153	6096	SO:0001583	missense	253769	exon4			TCATCCAGGCTCA	AK131435	CCDS47520.1, CCDS47520.2, CCDS56459.1	6q27	2013-01-09	2003-06-18		ENSG00000184465	ENSG00000184465		"""WD repeat domain containing"""	21248	protein-coding gene	gene with protein product							Standard	NM_182552		Approved	MGC43690	uc003qwx.3	A2RRH5	OTTHUMG00000016061	ENST00000448612.1:c.398T>C	6.37:g.170070723A>G	ENSP00000416289:p.Leu133Pro	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_182552	A5PLM8|C9JGV0|Q5T066	Missense_Mutation	SNP	ENST00000448612.1	37	CCDS47520.2	1132	0.5183150183150184	202	0.4105691056910569	179	0.494475138121547	524	0.916083916083916	227	0.2994722955145119	a	0.086	-1.174843	0.01646	0.431549	0.261257	ENSG00000184465	ENST00000448612;ENST00000333572;ENST00000420344	T;T;T	0.60299	1.73;2.37;0.2	5.52	0.661	0.17874	.	0.643068	0.15332	N	0.267927	T	0.05410	0.0143	N	0.00419	-1.52	0.51012	P	9.40000000000385E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38607	-0.9653	9	0.02654	T	1	-7.9112	9.8422	0.41006	0.3536:0.0:0.6464:0.0	rs4236176;rs17854047;rs17860914;rs61562734;rs4236176	133;133	F2Z2U5;C9JGV0	.;.	P	133	ENSP00000416289:L133P;ENSP00000330265:L133P;ENSP00000406114:L133P	ENSP00000330265:L133P	L	-	2	0	WDR27	169812648	0.509000	0.26163	0.000000	0.03702	0.050000	0.14768	0.527000	0.22987	-0.185000	0.10550	-0.362000	0.07510	CTG	A|0.485;G|0.515	0.515	strong		0.468	WDR27-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407334.1	NM_182552	
GLRA1	2741	hgsc.bcm.edu	37	5	151208500	151208500	+	Silent	SNP	C	C	T	rs75463357	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:151208500C>T	ENST00000455880.2	-	8	1327	c.1041G>A	c.(1039-1041)agG>agA	p.R347R	GLRA1_ENST00000274576.4_Silent_p.R347R|GLRA1_ENST00000545569.1_Silent_p.R264R			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	347					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GTCTCCGCTTCCTCCTGAATC	0.468													C|||	42	0.00838658	0.0008	0.0159	5008	,	,		21283	0.0		0.0258	False		,,,				2504	0.0041				p.R347R		Atlas-SNP	.											.	GLRA1	61	.	0			c.G1041A						PASS	.	C	,	23,4383	30.8+/-60.4	0,23,2180	172.0	167.0	169.0		1041,1041	4.2	1.0	5	dbSNP_132	169	209,8391	89.2+/-151.4	5,199,4096	no	coding-synonymous,coding-synonymous	GLRA1	NM_000171.3,NM_001146040.1	,	5,222,6276	TT,TC,CC		2.4302,0.522,1.7838	,	347/450,347/458	151208500	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	2741	exon8			CCGCTTCCTCCTG		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"""Ligand-gated ion channels / Glycine receptors"""	4326	protein-coding gene	gene with protein product	"""startle disease/hyperekplexia"", ""stiff person syndrome"""	138491	"""glycine receptor, alpha 1 (startle disease/hyperekplexia)"""	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.1041G>A	5.37:g.151208500C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_000171	B2R6T3|Q14C77|Q6DJV9	Silent	SNP	ENST00000455880.2	37	CCDS54942.1																																																																																			C|0.983;T|0.017	0.017	strong		0.468	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1		
SPATA6	54558	hgsc.bcm.edu	37	1	48865121	48865121	+	Missense_Mutation	SNP	C	C	T	rs77303590	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:48865121C>T	ENST00000371847.3	-	7	846	c.682G>A	c.(682-684)Gag>Aag	p.E228K	SPATA6_ENST00000371843.3_Missense_Mutation_p.E228K|SPATA6_ENST00000463938.1_5'UTR|SPATA6_ENST00000396199.3_Missense_Mutation_p.E156K	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	228					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						TCAGATAGCTCACACATGCGT	0.403													C|||	35	0.00698882	0.0008	0.0086	5008	,	,		15414	0.0		0.0219	False		,,,				2504	0.0061				p.E228K		Atlas-SNP	.											.	SPATA6	45	.	0			c.G682A						PASS	.	C	LYS/GLU	26,4380	32.6+/-62.9	0,26,2177	217.0	221.0	220.0		682	5.7	1.0	1	dbSNP_131	220	213,8387	90.4+/-152.6	5,203,4092	yes	missense	SPATA6	NM_019073.2	56	5,229,6269	TT,TC,CC		2.4767,0.5901,1.8376	probably-damaging	228/489	48865121	239,12767	2203	4300	6503	SO:0001583	missense	54558	exon7			ATAGCTCACACAT	AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"""spermatogenesis-related factor-1"""	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.682G>A	1.37:g.48865121C>T	ENSP00000360913:p.Glu228Lys	Somatic	318	1	0.00314465		WXS	Illumina HiSeq	Phase_I	221	159	0.719457	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	21	0.009615384615384616	0	0.0	4	0.011049723756906077	0	0.0	17	0.022427440633245383	C	25.7	4.660228	0.88154	0.005901	0.024767	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199;ENST00000371841	T;T;T;T	0.53640	2.61;2.59;2.59;0.61	5.68	5.68	0.88126	.	0.112377	0.64402	D	0.000013	T	0.46541	0.1398	L	0.40543	1.245	0.42181	D	0.991682	D;D;D;D	0.71674	0.989;0.998;0.996;0.996	D;D;D;D	0.80764	0.915;0.994;0.917;0.917	T	0.58645	-0.7600	10	0.66056	D	0.02	.	18.7846	0.91949	0.0:1.0:0.0:0.0	.	156;156;228;228	B4DX17;A8MU33;Q9NWH7-2;Q9NWH7	.;.;.;SPAT6_HUMAN	K	228;228;156;69	ENSP00000360913:E228K;ENSP00000360909:E228K;ENSP00000379502:E156K;ENSP00000360907:E69K	ENSP00000360907:E69K	E	-	1	0	SPATA6	48637708	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.807000	0.55591	2.683000	0.91414	0.555000	0.69702	GAG	C|0.983;T|0.017	0.017	strong		0.403	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073	
GUCY1B3	2983	hgsc.bcm.edu	37	4	156721198	156721198	+	Silent	SNP	C	C	T	rs2229202	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:156721198C>T	ENST00000264424.8	+	9	1229	c.1147C>T	c.(1147-1149)Ctg>Ttg	p.L383L	GUCY1B3_ENST00000503520.1_Silent_p.L383L|GUCY1B3_ENST00000505764.1_Silent_p.L363L|GUCY1B3_ENST00000505154.1_Silent_p.L315L|GUCY1B3_ENST00000507146.1_Silent_p.L315L|GUCY1B3_ENST00000502959.1_Silent_p.L405L|GUCY1B3_ENST00000513437.1_Silent_p.L315L	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	383					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.L383L(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		GTTAAGAGCCCTGGAAGATGA	0.398													C|||	801	0.159944	0.2156	0.111	5008	,	,		19760	0.123		0.1531	False		,,,				2504	0.1646				p.L383L		Atlas-SNP	.											GUCY1B3,NS,carcinoma,0,1	GUCY1B3	65	1	1	Substitution - coding silent(1)	prostate(1)	c.C1147T						PASS	.	C		722,3066		78,566,1250	90.0	89.0	90.0		1147	1.0	0.9	4	dbSNP_98	90	1241,6983		96,1049,2967	no	coding-synonymous	GUCY1B3	NM_000857.2		174,1615,4217	TT,TC,CC		15.09,19.0602,16.342		383/620	156721198	1963,10049	1894	4112	6006	SO:0001819	synonymous_variant	2983	exon9			AGAGCCCTGGAAG	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.1147C>T	4.37:g.156721198C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	47	43	0.914894	NM_000857	B7Z426|Q86WY5	Silent	SNP	ENST00000264424.8	37	CCDS47154.1																																																																																			C|0.851;T|0.149	0.149	strong		0.398	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2		
STK31	56164	hgsc.bcm.edu	37	7	23811795	23811795	+	Missense_Mutation	SNP	T	T	G	rs10263079	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:23811795T>G	ENST00000355870.3	+	15	1982	c.1863T>G	c.(1861-1863)aaT>aaG	p.N621K	STK31_ENST00000354639.3_Missense_Mutation_p.N598K|STK31_ENST00000428484.1_Missense_Mutation_p.N598K|STK31_ENST00000433467.2_Missense_Mutation_p.N621K|STK31_ENST00000405627.3_3'UTR	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	621			N -> K (in dbSNP:rs10263079). {ECO:0000269|PubMed:17344846}.	NKS -> KKI (in Ref. 1; AAK31978). {ECO:0000305}.		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						AATATTTAAATAAGAGTCCCA	0.289													T|||	484	0.0966454	0.0454	0.1297	5008	,	,		16803	0.0575		0.2117	False		,,,				2504	0.0644				p.N621K		Atlas-SNP	.											.	STK31	175	.	0			c.T1863G						PASS	.	T	LYS/ASN,LYS/ASN,LYS/ASN	305,4097	154.4+/-187.8	14,277,1910	42.0	44.0	43.0		1794,1863,1794	1.5	1.0	7	dbSNP_119	43	1823,6755	318.2+/-313.6	179,1465,2645	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	94,94,94	193,1742,4555	GG,GT,TT		21.252,6.9287,16.3945	possibly-damaging,possibly-damaging,possibly-damaging	598/997,621/1020,598/997	23811795	2128,10852	2201	4289	6490	SO:0001583	missense	56164	exon15			TTTAAATAAGAGT	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.1863T>G	7.37:g.23811795T>G	ENSP00000348132:p.Asn621Lys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	201	109	0.542289	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	284	0.13003663003663005	28	0.056910569105691054	61	0.1685082872928177	31	0.05419580419580419	164	0.21635883905013192	T	17.51	3.408289	0.62399	0.069287	0.21252	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.70045	-0.45;1.29;-0.44;-0.44	5.19	1.51	0.23008	.	0.121725	0.53938	D	0.000050	T	0.00073	0.0002	M	0.64997	1.995	0.29422	P	0.860491	P;P	0.52842	0.956;0.956	P;P	0.45071	0.468;0.468	T	0.03259	-1.1055	9	0.51188	T	0.08	-16.6838	8.6987	0.34312	0.0:0.2245:0.0:0.7755	rs10263079;rs10263079	621;621	B4DZ06;Q9BXU1	.;STK31_HUMAN	K	621;621;598;598	ENSP00000348132:N621K;ENSP00000411852:N621K;ENSP00000346660:N598K;ENSP00000406146:N598K	ENSP00000346660:N598K	N	+	3	2	STK31	23778320	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	1.330000	0.33781	0.024000	0.15214	-0.379000	0.06801	AAT	T|0.843;G|0.157	0.157	strong		0.289	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
MYH10	4628	hgsc.bcm.edu	37	17	8396176	8396176	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8396176T>C	ENST00000269243.4	-	31	4421	c.4283A>G	c.(4282-4284)gAg>gGg	p.E1428G	MYH10_ENST00000379980.4_Missense_Mutation_p.E1444G|MYH10_ENST00000396239.1_Missense_Mutation_p.E1449G|MYH10_ENST00000360416.3_Missense_Mutation_p.E1459G	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1428					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)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						GTCGTCCAGCTCCTGCTGCAG	0.607																																					p.E1459G		Atlas-SNP	.											.	MYH10	148	.	0			c.A4376G						PASS	.						80.0	71.0	74.0					17																	8396176		2203	4300	6503	SO:0001583	missense	4628	exon33			TCCAGCTCCTGCT	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.4283A>G	17.37:g.8396176T>C	ENSP00000269243:p.Glu1428Gly	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	91	4	0.043956	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	31	5.091155	0.94149	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01	5.31	5.31	0.75309	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.94820	0.8327	H	0.95917	3.74	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	0.96370	0.9273	10	0.87932	D	0	.	15.4317	0.75105	0.0:0.0:0.0:1.0	.	1437;1459;1428	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	G	1428;1459;1449;1444	ENSP00000269243:E1428G;ENSP00000353590:E1459G;ENSP00000379539:E1449G;ENSP00000369315:E1444G	ENSP00000269243:E1428G	E	-	2	0	MYH10	8336901	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.825000	0.86693	2.224000	0.72417	0.528000	0.53228	GAG	.	.	none		0.607	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
DNAH6	1768	hgsc.bcm.edu	37	2	84926756	84926756	+	Silent	SNP	G	G	A	rs74514752	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:84926756G>A	ENST00000237449.6	+	47	7724	c.7716G>A	c.(7714-7716)ctG>ctA	p.L2572L	DNAH6_ENST00000389394.3_Silent_p.L2572L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2572	AAA 4. {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						GTCAGAAGCTGCACATTGTTC	0.408													G|||	23	0.00459265	0.0023	0.0101	5008	,	,		20442	0.0		0.0109	False		,,,				2504	0.002				p.L2572L		Atlas-SNP	.											.	DNAH6	194	.	0			c.G7716A						PASS	.	G		3,1381		0,3,689	113.0	92.0	99.0		7716	-0.2	1.0	2	dbSNP_132	99	43,3139		1,41,1549	no	coding-synonymous	DNAH6	NM_001370.1		1,44,2238	AA,AG,GG		1.3514,0.2168,1.0074		2572/4159	84926756	46,4520	692	1591	2283	SO:0001819	synonymous_variant	1768	exon48			GAAGCTGCACATT	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.7716G>A	2.37:g.84926756G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			G|0.994;A|0.006	0.006	strong		0.408	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
ANK1	286	hgsc.bcm.edu	37	8	41559609	41559609	+	Silent	SNP	G	G	A	rs2304880	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:41559609G>A	ENST00000347528.4	-	21	2432	c.2349C>T	c.(2347-2349)acC>acT	p.T783T	ANK1_ENST00000379758.2_Silent_p.T783T|ANK1_ENST00000289734.7_Silent_p.T783T|ANK1_ENST00000352337.4_Silent_p.T783T|ANK1_ENST00000396945.1_Silent_p.T783T|ANK1_ENST00000265709.8_Silent_p.T816T|ANK1_ENST00000396942.1_Silent_p.T783T	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	783	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TGAGCACGTCGGTGACAGAAA	0.607											OREG0018740	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	905	0.180711	0.0159	0.2954	5008	,	,		18368	0.0794		0.2843	False		,,,				2504	0.32				p.T816T		Atlas-SNP	.											.	ANK1	497	.	0			c.C2448T						PASS	.	G	,,,,	250,4156	145.4+/-180.2	7,236,1960	122.0	110.0	114.0		2349,2448,2349,2349,2349	-3.0	0.7	8	dbSNP_100	114	2302,6298	387.0+/-342.0	319,1664,2317	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	326,1900,4277	AA,AG,GG		26.7674,5.6741,19.6217	,,,,	783/1881,816/1898,783/1857,783/1882,783/1720	41559609	2552,10454	2203	4300	6503	SO:0001819	synonymous_variant	286	exon21			CACGTCGGTGACA	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2349C>T	8.37:g.41559609G>A		Somatic	120	0	0	902	WXS	Illumina HiSeq	Phase_I	128	73	0.570312	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	370	0.16941391941391942	11	0.022357723577235773	100	0.27624309392265195	37	0.06468531468531469	222	0.2928759894459103	G	1.954	-0.440462	0.04636	0.056741	0.267674	ENSG00000029534	ENST00000520299	.	.	.	5.96	-2.95	0.05564	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.0165	0.06061	0.0902:0.1696:0.3084:0.4317	rs2304880;rs2304880	.	.	.	X	97	.	.	R	-	1	2	ANK1	41678766	0.006000	0.16342	0.704000	0.30370	0.001000	0.01503	-1.166000	0.03129	-0.110000	0.12022	-0.885000	0.02943	CGA	G|0.820;A|0.180	0.180	strong		0.607	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
CR1	1378	hgsc.bcm.edu	37	1	207787796	207787796	+	Missense_Mutation	SNP	T	T	C	rs61822976		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:207787796T>C	ENST00000367049.4	+	40	6623	c.6623T>C	c.(6622-6624)aTg>aCg	p.M2208T	CR1_ENST00000367052.1_Missense_Mutation_p.M1758T|CR1_ENST00000400960.2_Missense_Mutation_p.M1758T|CR1_ENST00000367053.1_Missense_Mutation_p.M1758T|CR1_ENST00000367051.1_Missense_Mutation_p.M1758T	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1758					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.M1758T(1)|p.M2208T(1)|p.M1763T(1)		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						TTGGCTGGAATGAAAGCCCTT	0.408																																					p.M2208T		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,0,4	CR1	354	4	3	Substitution - Missense(3)	prostate(3)	c.T6623C						PASS	.						128.0	121.0	123.0					1																	207787796		1882	4112	5994	SO:0001583	missense	1378	exon40			CTGGAATGAAAGC	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.6623T>C	1.37:g.207787796T>C	ENSP00000356016:p.Met2208Thr	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	394	36	0.0913706	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	T	3.803	-0.041226	0.07452	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96	4.29	-5.87	0.02297	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.09335	0.0230	N	0.20986	0.625	0.09310	N	1	B;P	0.46457	0.043;0.878	B;B	0.42422	0.009;0.387	T	0.19614	-1.0300	9	0.18276	T	0.48	.	1.2481	0.01977	0.4109:0.0944:0.2677:0.2271	rs61822976	1758;2208	P17927;E9PDY4	CR1_HUMAN;.	T	1758;1758;1758;1758;2208	ENSP00000356019:M1758T;ENSP00000356018:M1758T;ENSP00000356020:M1758T;ENSP00000383744:M1758T;ENSP00000356016:M2208T	ENSP00000356016:M2208T	M	+	2	0	CR1	205854419	0.002000	0.14202	0.000000	0.03702	0.554000	0.35429	-0.327000	0.07955	-0.793000	0.04475	0.358000	0.22013	ATG	.	.	weak		0.408	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
NLRP5	126206	hgsc.bcm.edu	37	19	56543982	56543982	+	Missense_Mutation	SNP	G	G	T	rs17713875	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56543982G>T	ENST00000390649.3	+	8	2282	c.2282G>T	c.(2281-2283)cGg>cTg	p.R761L		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	761			R -> L (in dbSNP:rs17713875).		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)		CATAGGATGCGGGATAAGACC	0.577													G|||	67	0.0133786	0.0008	0.0202	5008	,	,		19693	0.0		0.0477	False		,,,				2504	0.0041				p.R761L		Atlas-SNP	.											NLRP5,NS,carcinoma,+1,1	NLRP5	217	1	0			c.G2282T						scavenged	.	G	LEU/ARG	32,4022		0,32,1995	45.0	46.0	46.0		2282	-7.4	0.0	19	dbSNP_123	46	290,8130		12,266,3932	yes	missense	NLRP5	NM_153447.4	102	12,298,5927	TT,TG,GG		3.4442,0.7893,2.5814	benign	761/1201	56543982	322,12152	2027	4210	6237	SO:0001583	missense	126206	exon8			GGATGCGGGATAA	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.2282G>T	19.37:g.56543982G>T	ENSP00000375063:p.Arg761Leu	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	43	0.019688644688644688	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	35	0.04617414248021108	G	5.886	0.347609	0.11126	0.007893	0.034442	ENSG00000171487	ENST00000390649	D	0.88586	-2.4	3.68	-7.36	0.01417	.	1.568660	0.04523	N	0.384938	T	0.42291	0.1196	L	0.33245	0.995	0.09310	N	1	B	0.18610	0.029	B	0.17433	0.018	T	0.58109	-0.7694	10	0.30078	T	0.28	.	3.4915	0.07639	0.2015:0.4832:0.201:0.1144	rs17713875;rs52815477;rs17713875	761	P59047	NALP5_HUMAN	L	761	ENSP00000375063:R761L	ENSP00000375063:R761L	R	+	2	0	NLRP5	61235794	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.931000	0.03967	-2.119000	0.00827	-0.858000	0.03015	CGG	G|0.978;T|0.022	0.022	strong		0.577	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
GRB10	2887	hgsc.bcm.edu	37	7	50660787	50660787	+	Silent	SNP	G	G	A	rs3807550	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:50660787G>A	ENST00000401949.1	-	19	2116	c.1647C>T	c.(1645-1647)gaC>gaT	p.D549D	GRB10_ENST00000398812.2_Silent_p.D549D|GRB10_ENST00000439599.1_Silent_p.D543D|GRB10_ENST00000402578.1_Silent_p.D491D|GRB10_ENST00000406641.1_Silent_p.D491D|GRB10_ENST00000398810.2_Silent_p.D491D|GRB10_ENST00000407526.1_Silent_p.D491D|GRB10_ENST00000402497.1_Silent_p.D491D|GRB10_ENST00000357271.5_Silent_p.D503D|GRB10_ENST00000335866.3_Silent_p.D491D|GRB10_ENST00000403097.1_Silent_p.D543D			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	549	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					TCTGCCCGTCGTCCTCGCACT	0.557									Russell-Silver syndrome				G|||	389	0.0776757	0.0053	0.0965	5008	,	,		20589	0.0565		0.1113	False		,,,				2504	0.1493				p.D549D		Atlas-SNP	.											.	GRB10	155	.	0			c.C1647T						PASS	.	G	,,,	101,4069		1,99,1985	97.0	99.0	98.0		1509,1473,1473,1647	-7.3	0.5	7	dbSNP_107	98	746,7696		31,684,3506	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRB10	NM_001001549.2,NM_001001550.2,NM_001001555.2,NM_005311.4	,,,	32,783,5491	AA,AG,GG		8.8368,2.4221,6.7158	,,,	503/549,491/537,491/537,549/595	50660787	847,11765	2085	4221	6306	SO:0001819	synonymous_variant	2887	exon16	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	CCCGTCGTCCTCG		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.1647C>T	7.37:g.50660787G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Silent	SNP	ENST00000401949.1	37	CCDS43582.1																																																																																			T|0.000;G|0.913;A|0.087	0.087	strong		0.557	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1		
PCDHB16	57717	hgsc.bcm.edu	37	5	140564214	140564214	+	Silent	SNP	T	T	C	rs61739446	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140564214T>C	ENST00000361016.2	+	1	3235	c.2080T>C	c.(2080-2082)Ttg>Ctg	p.L694L		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	694					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)			GGTGGTGGCGTTGGCCTCGGT	0.692													T|||	547	0.109225	0.1029	0.1744	5008	,	,		16254	0.0407		0.1571	False		,,,				2504	0.093				p.L694L		Atlas-SNP	.											.	PCDHB16	159	.	0			c.T2080C						PASS	.	T		498,3908		29,440,1734	68.0	72.0	71.0		2080	-6.2	0.0	5	dbSNP_129	71	1450,7148		130,1190,2979	no	coding-synonymous	PCDHB16	NM_020957.1		159,1630,4713	CC,CT,TT		16.8644,11.3028,14.98		694/777	140564214	1948,11056	2203	4299	6502	SO:0001819	synonymous_variant	57717	exon1			GTGGCGTTGGCCT	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.2080T>C	5.37:g.140564214T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																			T|0.863;C|0.137	0.137	strong		0.692	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
VWCE	220001	hgsc.bcm.edu	37	11	61053895	61053895	+	Silent	SNP	G	G	A	rs146572904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:61053895G>A	ENST00000335613.5	-	5	818	c.432C>T	c.(430-432)gaC>gaT	p.D144D		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	144	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						TTACACATTCGTCAATGTCTG	0.547													g|||	6	0.00119808	0.0	0.0014	5008	,	,		23016	0.0		0.005	False		,,,				2504	0.0				p.D144D		Atlas-SNP	.											.	VWCE	84	.	0			c.C432T						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	89.0	77.0	81.0		432	-10.6	0.0	11	dbSNP_134	81	22,8576	16.6+/-54.9	0,22,4277	no	coding-synonymous	VWCE	NM_152718.2		0,24,6478	AA,AG,GG		0.2559,0.0454,0.1846		144/956	61053895	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	220001	exon5			ACATTCGTCAATG	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.432C>T	11.37:g.61053895G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	37	CCDS8002.1																																																																																			G|0.998;A|0.002	0.002	strong		0.547	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718	
CYP2F1	1572	hgsc.bcm.edu	37	19	41622481	41622481	+	Missense_Mutation	SNP	G	G	C	rs57670668	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41622481G>C	ENST00000331105.2	+	3	365	c.293G>C	c.(292-294)cGc>cCc	p.R98P		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	98			R -> P (in allele CYP2F1*6; dbSNP:rs57670668).		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						TTTAGTGGCCGCGGTGACTAC	0.587													G|||	25	0.00499201	0.003	0.0058	5008	,	,		18879	0.0		0.0149	False		,,,				2504	0.002				p.R98P		Atlas-SNP	.											.	CYP2F1	60	.	0			c.G293C						PASS	.	G	PRO/ARG	12,4394	17.9+/-39.9	0,12,2191	86.0	85.0	85.0		293	2.9	0.9	19	dbSNP_129	85	147,8453	70.3+/-132.9	0,147,4153	no	missense	CYP2F1	NM_000774.3	103	0,159,6344	CC,CG,GG		1.7093,0.2724,1.2225	probably-damaging	98/492	41622481	159,12847	2203	4300	6503	SO:0001583	missense	1572	exon3			GTGGCCGCGGTGA	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.293G>C	19.37:g.41622481G>C	ENSP00000333534:p.Arg98Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	14.36	2.512521	0.44660	0.002724	0.017093	ENSG00000197446	ENST00000331105	T	0.72167	-0.63	3.91	2.87	0.33458	.	0.207943	0.36200	U	0.002721	T	0.77432	0.4129	H	0.94698	3.57	0.51233	D	0.999912	D;D	0.63880	0.993;0.993	D;D	0.66979	0.948;0.914	D	0.84263	0.0484	10	0.87932	D	0	.	10.5264	0.44952	0.0996:0.0:0.9004:0.0	rs57670668;rs61736450	98;98	Q32MN5;P24903	.;CP2F1_HUMAN	P	98	ENSP00000333534:R98P	ENSP00000333534:R98P	R	+	2	0	CYP2F1	46314321	0.942000	0.31987	0.882000	0.34594	0.163000	0.22366	3.127000	0.50484	0.859000	0.35456	-0.282000	0.10007	CGC	G|0.992;C|0.008	0.008	strong		0.587	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
COL5A1	1289	hgsc.bcm.edu	37	9	137734084	137734084	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:137734084A>G	ENST00000371817.3	+	66	5866	c.5452A>G	c.(5452-5454)Aat>Gat	p.N1818D		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1818	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		CATCATGTTCAATGACTTCGG	0.577																																					p.N1818D		Atlas-SNP	.											.	COL5A1	323	.	0			c.A5452G						PASS	.						129.0	125.0	126.0					9																	137734084		2203	4300	6503	SO:0001583	missense	1289	exon66			ATGTTCAATGACT	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.5452A>G	9.37:g.137734084A>G	ENSP00000360882:p.Asn1818Asp	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	A	16.41	3.114962	0.56505	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	T	0.73152	-0.72	4.72	4.72	0.59763	Fibrillar collagen, C-terminal (4);	0.069214	0.53938	U	0.000046	T	0.69278	0.3093	M	0.70595	2.14	0.42323	D	0.992266	P	0.38280	0.625	B	0.37508	0.252	T	0.70575	-0.4834	10	0.33940	T	0.23	.	14.1846	0.65598	1.0:0.0:0.0:0.0	.	1818	P20908	CO5A1_HUMAN	D	1818;355	ENSP00000360882:N1818D	ENSP00000347458:N355D	N	+	1	0	COL5A1	136873905	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	9.057000	0.93889	1.765000	0.52091	0.460000	0.39030	AAT	.	.	none		0.577	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489754	32489754	+	Missense_Mutation	SNP	T	T	C	rs41551116|rs201925120	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489754T>C	ENST00000374975.3	-	2	360	c.298A>G	c.(298-300)Agg>Ggg	p.R100G		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						GCGGCGCGCCTGTCTTCCAGG	0.667													T|||	280	0.0559105	0.084	0.0605	5008	,	,		4296	0.0317		0.0626	False		,,,				2504	0.0327				p.R100G		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.A298G						PASS	.						36.0	32.0	33.0					6																	32489754		1942	3732	5674	SO:0001583	missense	3127	exon2			CGCGCCTGTCTTC		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.298A>G	6.37:g.32489754T>C	ENSP00000364114:p.Arg100Gly	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	29	27	0.931035	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	10.39	1.336269	0.24253	.	.	ENSG00000198502	ENST00000374975	T	0.00349	7.99	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);	5.372110	0.00166	N	0.000006	T	0.00300	0.0009	H	0.95950	3.745	0.09310	N	1	P;B	0.35155	0.487;0.304	B;P	0.58266	0.344;0.836	T	0.48536	-0.9027	10	0.66056	D	0.02	.	0.4687	0.00528	0.2086:0.2516:0.2378:0.302	rs41551116	27;100	Q29973;Q30154	.;DRB5_HUMAN	G	100	ENSP00000364114:R100G	ENSP00000364114:R100G	R	-	1	2	HLA-DRB5	32597732	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.530000	0.00062	-5.722000	0.00010	-3.428000	0.00037	AGG	T|0.952;C|0.047	0.047	strong		0.667	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
CA14	23632	hgsc.bcm.edu	37	1	150234657	150234657	+	Silent	SNP	G	G	T	rs34714364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	101	0	0		WXS	Illumina HiSeq	Phase_I	159	90	0.566038	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	
HMHA1	23526	hgsc.bcm.edu	37	19	1085993	1085993	+	Silent	SNP	G	G	A	rs34721728	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1085993G>A	ENST00000313093.2	+	23	3630	c.3399G>A	c.(3397-3399)ccG>ccA	p.P1133P	HMHA1_ENST00000590577.1_Silent_p.P768P|HMHA1_ENST00000586866.1_Silent_p.P1137P|HMHA1_ENST00000590214.1_Silent_p.P1160P|HMHA1_ENST00000539243.2_Silent_p.P1149P|HMHA1_ENST00000543365.1_Silent_p.P1016P|HMHA1_ENST00000536472.1_Silent_p.P1001P|HMHA1_ENST00000591169.1_3'UTR|POLR2E_ENST00000585838.1_5'Flank	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	1133					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)		AAAGGCAGCCGGAATTCGTGT	0.647													g|||	80	0.0159744	0.003	0.0346	5008	,	,		13378	0.0		0.0417	False		,,,				2504	0.0102				p.P1149P		Atlas-SNP	.											.	HMHA1	78	.	0			c.G3447A						PASS	.	G		51,4329		0,51,2139	35.0	37.0	36.0		3399	-9.2	0.0	19	dbSNP_126	36	441,8127		15,411,3858	no	coding-synonymous	HMHA1	NM_012292.2		15,462,5997	AA,AG,GG		5.1471,1.1644,3.7998		1133/1137	1085993	492,12456	2190	4284	6474	SO:0001819	synonymous_variant	23526	exon23			GCAGCCGGAATTC	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.3399G>A	19.37:g.1085993G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			G|0.963;A|0.037	0.037	strong		0.647	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
C12orf29	91298	hgsc.bcm.edu	37	12	88440676	88440676	+	Missense_Mutation	SNP	G	G	C	rs9262	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:88440676G>C	ENST00000356891.3	+	6	915	c.712G>C	c.(712-714)Gtg>Ctg	p.V238L	C12orf29_ENST00000548757.2_3'UTR	NM_001009894.2	NP_001009894.2	Q8N999	CL029_HUMAN	chromosome 12 open reading frame 29	238			V -> L (in dbSNP:rs9262). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		hematopoietic progenitor cell differentiation (GO:0002244)					large_intestine(3)|lung(1)|ovary(1)	5						CAATGATCTCGTGTCCTGGTT	0.393													G|||	2557	0.510583	0.1528	0.562	5008	,	,		19449	0.7361		0.6083	False		,,,				2504	0.6247				p.V238L		Atlas-SNP	.											.	C12orf29	18	.	0			c.G712C						PASS	.	G	LEU/VAL	1038,3368	382.1+/-324.3	140,758,1305	195.0	181.0	186.0		712	-4.2	0.5	12	dbSNP_52	186	5064,3536	630.8+/-398.4	1472,2120,708	yes	missense	C12orf29	NM_001009894.2	32	1612,2878,2013	CC,CG,GG		41.1163,23.5588,46.9168	benign	238/326	88440676	6102,6904	2203	4300	6503	SO:0001583	missense	91298	exon6			GATCTCGTGTCCT	AL137488	CCDS31866.1	12q21.32	2012-05-30			ENSG00000133641	ENSG00000133641			25322	protein-coding gene	gene with protein product						14702039	Standard	NM_001009894		Approved	DKFZp434N2030	uc001tao.3	Q8N999	OTTHUMG00000169870	ENST00000356891.3:c.712G>C	12.37:g.88440676G>C	ENSP00000349358:p.Val238Leu	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	194	94	0.484536	NM_001009894	Q569K5|Q6AWA8|Q6PEK5|Q8IYQ5|Q9NT75	Missense_Mutation	SNP	ENST00000356891.3	37	CCDS31866.1	1113	0.5096153846153846	60	0.12195121951219512	199	0.5497237569060773	408	0.7132867132867133	446	0.5883905013192612	G	8.664	0.901337	0.17760	0.235588	0.588837	ENSG00000133641	ENST00000356891	T	0.27890	1.64	5.53	-4.2	0.03823	.	0.572548	0.18487	N	0.139750	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	0.29852	-0.9998	9	0.15499	T	0.54	-21.6581	9.2016	0.37263	0.0:0.4575:0.2107:0.3319	rs9262;rs1127464;rs3183491;rs17334013;rs17846127;rs17859132;rs52814303;rs9262	238	Q8N999	CL029_HUMAN	L	238	ENSP00000349358:V238L	ENSP00000349358:V238L	V	+	1	0	C12orf29	86964807	0.000000	0.05858	0.503000	0.27626	0.990000	0.78478	-1.166000	0.03129	-0.739000	0.04809	-0.346000	0.07831	GTG	G|0.510;C|0.490	0.490	strong		0.393	C12orf29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406335.1	NM_001009894	
ESPNL	339768	hgsc.bcm.edu	37	2	239025630	239025630	+	Silent	SNP	T	T	C	rs11904159	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:239025630T>C	ENST00000343063.3	+	5	1205	c.942T>C	c.(940-942)caT>caC	p.H314H	ESPNL_ENST00000409169.1_Intron	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	314										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)		CGGAGTACCATGGACACCGGG	0.687													C|||	983	0.196286	0.2867	0.1412	5008	,	,		17120	0.2302		0.1322	False		,,,				2504	0.1442				p.H314H		Atlas-SNP	.											.	ESPNL	63	.	0			c.T942C						PASS	.	C		1121,3279	705.9+/-407.3	174,773,1253	69.0	55.0	59.0		942	-2.8	0.9	2	dbSNP_120	59	1415,7177	748.6+/-407.3	129,1157,3010	no	coding-synonymous	ESPNL	NM_194312.2		303,1930,4263	CC,CT,TT		16.4688,25.4773,19.5197		314/1006	239025630	2536,10456	2200	4296	6496	SO:0001819	synonymous_variant	339768	exon5			GTACCATGGACAC	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.942T>C	2.37:g.239025630T>C		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	159	80	0.503145	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			T|0.803;C|0.197	0.197	strong		0.687	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
LHX2	9355	hgsc.bcm.edu	37	9	126783433	126783433	+	Silent	SNP	G	G	C	rs1042486	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	87	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	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		
CLHC1	130162	hgsc.bcm.edu	37	2	55404883	55404883	+	Silent	SNP	T	T	C	rs13032294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:55404883T>C	ENST00000401408.1	-	12	1764	c.1419A>G	c.(1417-1419)caA>caG	p.Q473Q	CLHC1_ENST00000406437.2_Silent_p.Q24Q|CLHC1_ENST00000407122.1_Silent_p.Q473Q|CLHC1_ENST00000494539.1_5'UTR|CLHC1_ENST00000406076.1_Silent_p.Q351Q	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	473								p.Q473Q(2)									TTAATTCAACTTGGGGACATG	0.343													T|||	374	0.0746805	0.09	0.0288	5008	,	,		18576	0.1181		0.0497	False		,,,				2504	0.0675				p.Q473Q		Atlas-SNP	.											C2orf63_ENST00000407122,NS,carcinoma,0,2	.	.	2	2	Substitution - coding silent(2)	stomach(2)	c.A1419G						PASS	.	T	,	372,4034	188.1+/-214.6	18,336,1849	86.0	83.0	84.0		1053,1419	-0.8	0.0	2	dbSNP_121	84	468,8130	137.1+/-194.1	17,434,3848	no	coding-synonymous,coding-synonymous	C2orf63	NM_001135598.1,NM_152385.2	,	35,770,5697	CC,CT,TT		5.4431,8.443,6.4596	,	351/465,473/587	55404883	840,12164	2203	4299	6502	SO:0001819	synonymous_variant	130162	exon12			TTCAACTTGGGGA		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.1419A>G	2.37:g.55404883T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_152385	B2RDV1|Q53R93|Q8N403	Silent	SNP	ENST00000401408.1	37	CCDS33201.1																																																																																			T|0.932;C|0.068	0.068	strong		0.343	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
PI3	5266	hgsc.bcm.edu	37	20	43804522	43804522	+	Missense_Mutation	SNP	A	A	C	rs2664581	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	127	0	0		WXS	Illumina HiSeq	Phase_I	125	52	0.416	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	
TPH2	121278	hgsc.bcm.edu	37	12	72372862	72372862	+	Silent	SNP	A	A	G	rs7305115	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:72372862A>G	ENST00000333850.3	+	7	1077	c.936A>G	c.(934-936)ccA>ccG	p.P312P		NM_173353.3	NP_775489.2	Q8IWU9	TPH2_HUMAN	tryptophan hydroxylase 2	312					aromatic amino acid family metabolic process (GO:0009072)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to lithium ion (GO:0071285)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|response to activity (GO:0014823)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to nutrient levels (GO:0031667)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	41					L-Tryptophan(DB00150)	TCTACACCCCAGAACCGTGAG	0.512													G|||	2713	0.541733	0.6044	0.4856	5008	,	,		17921	0.4494		0.5825	False		,,,				2504	0.5501				p.P312P		Atlas-SNP	.											TPH2,colon,carcinoma,+1,1	TPH2	81	1	0			c.A936G	GRCh37	CM077900	TPH2	M	rs7305115	PASS	.	G		2591,1815	531.5+/-373.2	766,1059,378	126.0	126.0	126.0		936	-10.5	0.1	12	dbSNP_116	126	4977,3623	522.3+/-380.1	1439,2099,762	no	coding-synonymous	TPH2	NM_173353.3		2205,3158,1140	GG,GA,AA		42.1279,41.1938,41.8115		312/491	72372862	7568,5438	2203	4300	6503	SO:0001819	synonymous_variant	121278	exon7			CACCCCAGAACCG	AY098914	CCDS31859.1	12q15	2008-02-07				ENSG00000139287	1.14.16.4		20692	protein-coding gene	gene with protein product		607478				12511643	Standard	NM_173353		Approved	NTPH, FLJ37295	uc009zrw.1	Q8IWU9		ENST00000333850.3:c.936A>G	12.37:g.72372862A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_173353	A6NGA4|Q14CB0	Silent	SNP	ENST00000333850.3	37	CCDS31859.1																																																																																			A|0.439;G|0.561	0.561	strong		0.512	TPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405234.1	NM_173353	
TBC1D1	23216	hgsc.bcm.edu	37	4	38016395	38016395	+	Missense_Mutation	SNP	T	T	G	rs10501	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:38016395T>G	ENST00000261439.4	+	3	1038	c.683T>G	c.(682-684)gTg>gGg	p.V228G	TBC1D1_ENST00000508802.1_Missense_Mutation_p.V228G	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	228			V -> G (in dbSNP:rs10501).		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						CAGGAGCCTGTGCGCAGGCCC	0.692													G|||	2897	0.578474	0.6422	0.487	5008	,	,		11341	0.7093		0.4284	False		,,,				2504	0.5767				p.V228G		Atlas-SNP	.											TBC1D1,NS,carcinoma,0,1	TBC1D1	94	1	0			c.T683G						PASS	.	G	GLY/VAL	2525,1759		779,967,396	12.0	15.0	14.0		683	0.3	0.0	4	dbSNP_52	14	3573,4971		790,1993,1489	no	missense	TBC1D1	NM_015173.2	109	1569,2960,1885	GG,GT,TT		41.8188,41.0598,47.5366	benign	228/1169	38016395	6098,6730	2142	4272	6414	SO:0001583	missense	23216	exon3			AGCCTGTGCGCAG	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.683T>G	4.37:g.38016395T>G	ENSP00000261439:p.Val228Gly	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_015173	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Missense_Mutation	SNP	ENST00000261439.4	37	CCDS33972.1	1227	0.5618131868131868	307	0.6239837398373984	174	0.48066298342541436	426	0.7447552447552448	320	0.42216358839050133	G	0.134	-1.110455	0.01813	0.589402	0.418188	ENSG00000065882	ENST00000508802;ENST00000261439;ENST00000446803	T;T;T	0.17213	3.65;4.04;2.29	5.22	0.314	0.15847	Phosphotyrosine interaction domain (1);	0.609127	0.15462	N	0.261076	T	0.00012	0.0000	N	0.08118	0	0.51012	P	9.40000000000385E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.12293	-1.0553	9	0.22109	T	0.4	-0.0107	4.0723	0.09887	0.0774:0.1785:0.3923:0.3518	rs10501;rs3188894;rs13113776;rs58439251	228;228;228	B9A6J6;E9PGH8;Q86TI0	.;.;TBCD1_HUMAN	G	228;228;99	ENSP00000423651:V228G;ENSP00000261439:V228G;ENSP00000396877:V99G	ENSP00000261439:V228G	V	+	2	0	TBC1D1	37692790	0.138000	0.22547	0.000000	0.03702	0.023000	0.10783	1.416000	0.34759	-0.122000	0.11766	-0.323000	0.08544	GTG	T|0.448;G|0.552	0.552	strong		0.692	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349037	65349037	+	Silent	SNP	G	G	A	rs74684453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65349037G>A	ENST00000309295.4	+	9	1159	c.894G>A	c.(892-894)acG>acA	p.T298T		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	298						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						CCCAGGACACGGCCCCCACCC	0.677													G|||	34	0.00678914	0.0008	0.0086	5008	,	,		13897	0.0		0.0239	False		,,,				2504	0.0031				p.T298T		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G894A						PASS	.	G		13,3719		0,13,1853	8.0	9.0	9.0		894	3.0	0.8	11	dbSNP_134	9	194,7914		2,190,3862	no	coding-synonymous	EHBP1L1	NM_001099409.1		2,203,5715	AA,AG,GG		2.3927,0.3483,1.7483		298/1524	65349037	207,11633	1866	4054	5920	SO:0001819	synonymous_variant	254102	exon9			GGACACGGCCCCC	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.894G>A	11.37:g.65349037G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	209	92	0.440191	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																			G|0.989;A|0.011	0.011	strong		0.677	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
TTC7A	57217	hgsc.bcm.edu	37	2	47278901	47278901	+	Silent	SNP	G	G	A	rs3739100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:47278901G>A	ENST00000319190.5	+	18	2402	c.2034G>A	c.(2032-2034)tcG>tcA	p.S678S	TTC7A_ENST00000394850.2_Silent_p.S702S|TTC7A_ENST00000263737.6_Silent_p.S324S|TTC7A_ENST00000409245.1_Silent_p.S644S	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	678					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)			GGCGGGCTTCGTCCATCGCCG	0.657													G|||	921	0.183906	0.1566	0.1398	5008	,	,		16415	0.4435		0.0378	False		,,,				2504	0.135				p.S678S		Atlas-SNP	.											.	TTC7A	80	.	0			c.G2034A						PASS	.	G		691,3693		63,565,1564	45.0	47.0	47.0		2034	-10.4	0.1	2	dbSNP_107	47	261,8305		4,253,4026	no	coding-synonymous	TTC7A	NM_020458.2		67,818,5590	AA,AG,GG		3.0469,15.7619,7.3514		678/859	47278901	952,11998	2192	4283	6475	SO:0001819	synonymous_variant	57217	exon18			GGCTTCGTCCATC	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.2034G>A	2.37:g.47278901G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	159	81	0.509434	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			G|0.870;A|0.130	0.130	strong		0.657	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
CACNA1E	777	hgsc.bcm.edu	37	1	181725110	181725110	+	Silent	SNP	T	T	C	rs4652678	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:181725110T>C	ENST00000367573.2	+	29	4008	c.4008T>C	c.(4006-4008)caT>caC	p.H1336H	CACNA1E_ENST00000360108.3_Silent_p.H1317H|CACNA1E_ENST00000358338.5_Silent_p.H1268H|CACNA1E_ENST00000367570.1_Silent_p.H1336H|CACNA1E_ENST00000357570.5_Silent_p.H1287H|CACNA1E_ENST00000367567.4_Silent_p.H943H|CACNA1E_ENST00000526775.1_Silent_p.H1317H	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1336					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						ATGTAGATCATGAGAAAAACA	0.483													T|||	1594	0.318291	0.4856	0.3256	5008	,	,		18946	0.0754		0.2863	False		,,,				2504	0.3701				p.H1336H		Atlas-SNP	.											.	CACNA1E	778	.	0			c.T4008C						PASS	.	T	,,	1605,2223		339,927,648	79.0	80.0	80.0		4008,4008,3951	0.3	1.0	1	dbSNP_111	80	2240,6028		299,1642,2193	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	,,	638,2569,2841	CC,CT,TT		27.0924,41.9279,31.7874	,,	1336/2271,1336/2314,1317/2252	181725110	3845,8251	1914	4134	6048	SO:0001819	synonymous_variant	777	exon29			AGATCATGAGAAA	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.4008T>C	1.37:g.181725110T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	74	0.601626	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																			T|0.710;C|0.290	0.290	strong		0.483	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
AAAS	8086	hgsc.bcm.edu	37	12	53708910	53708910	+	Silent	SNP	A	A	G	rs11540353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53708910A>G	ENST00000209873.4	-	5	579	c.414T>C	c.(412-414)gaT>gaC	p.D138D	AAAS_ENST00000550286.1_Silent_p.D14D|AAAS_ENST00000394384.3_Silent_p.D138D|AAAS_ENST00000549983.1_5'UTR	NM_015665.5	NP_056480.1	Q9NRG9	AAAS_HUMAN	achalasia, adrenocortical insufficiency, alacrimia	138					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nucleocytoplasmic transport (GO:0006913)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of nucleocytoplasmic transport (GO:0046822)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	20						CAGCGATCAGATCTTCGCTCC	0.498													A|||	182	0.0363419	0.0038	0.085	5008	,	,		20660	0.0		0.1113	False		,,,				2504	0.0061				p.D138D		Atlas-SNP	.											.	AAAS	46	.	0			c.T414C						PASS	.	A	,	104,4302	82.4+/-120.9	2,100,2101	94.0	87.0	89.0		414,414	4.9	1.0	12	dbSNP_120	89	881,7719	199.0+/-243.2	53,775,3472	no	coding-synonymous,coding-synonymous	AAAS	NM_001173466.1,NM_015665.5	,	55,875,5573	GG,GA,AA		10.2442,2.3604,7.5734	,	138/514,138/547	53708910	985,12021	2203	4300	6503	SO:0001819	synonymous_variant	8086	exon5			GATCAGATCTTCG	AJ289841	CCDS8856.1, CCDS53797.1	12q13	2013-06-27	2010-06-24		ENSG00000094914	ENSG00000094914		"""WD repeat domain containing"""	13666	protein-coding gene	gene with protein product	"""aladin"", ""Allgrove, triple-A"""	605378	"""achalasia, adrenocortical insufficiency, alacrimia (Allgrove, triple-A)"""			11062474	Standard	NM_015665		Approved		uc001scr.4	Q9NRG9	OTTHUMG00000169729	ENST00000209873.4:c.414T>C	12.37:g.53708910A>G		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	223	117	0.524664	NM_015665	Q5JB47|Q9NWI6|Q9UG19	Silent	SNP	ENST00000209873.4	37	CCDS8856.1																																																																																			A|0.931;G|0.069	0.069	strong		0.498	AAAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405632.1		
CHEK2	11200	hgsc.bcm.edu	37	22	29130458	29130458	+	Silent	SNP	T	T	C	rs1805129	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:29130458T>C	ENST00000405598.1	-	3	443	c.252A>G	c.(250-252)gaA>gaG	p.E84E	CHEK2_ENST00000328354.6_Silent_p.E84E|CHEK2_ENST00000382566.1_Silent_p.E84E|CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000382565.1_Silent_p.E84E|CHEK2_ENST00000403642.1_Silent_p.E84E|CHEK2_ENST00000348295.3_Silent_p.E84E|CHEK2_ENST00000382578.1_Silent_p.E84E|CHEK2_ENST00000404276.1_Silent_p.E84E|CHEK2_ENST00000382580.2_Silent_p.E84E|CHEK2_ENST00000402731.1_Silent_p.E84E			O96017	CHK2_HUMAN	checkpoint kinase 2	84					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)	p.E84E(1)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						GCTCCTCAGGTTCTTGGTCCT	0.512			F			breast		Direct reversal of damage;Other conserved DNA damage response genes					T|||	214	0.0427316	0.0545	0.0144	5008	,	,		18034	0.0863		0.0169	False		,,,				2504	0.0286				p.E84E		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	CHEK2,NS,carcinoma,0,1	CHEK2	438	1	1	Substitution - coding silent(1)	stomach(1)	c.A252G						PASS	.	T	,,	270,4136	150.3+/-184.3	8,254,1941	65.0	70.0	68.0		252,252,252	-0.8	1.0	22	dbSNP_89	68	237,8363	95.6+/-157.4	2,233,4065	no	coding-synonymous,coding-synonymous,coding-synonymous	CHEK2	NM_001005735.1,NM_007194.3,NM_145862.2	,,	10,487,6006	CC,CT,TT		2.7558,6.128,3.8982	,,	84/587,84/544,84/515	29130458	507,12499	2203	4300	6503	SO:0001819	synonymous_variant	11200	exon2			CTCAGGTTCTTGG	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.252A>G	22.37:g.29130458T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	51	18	0.352941	NM_145862	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	CCDS13843.1																																																																																			T|0.954;C|0.046	0.046	strong		0.512	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735	
WDR17	116966	hgsc.bcm.edu	37	4	177100644	177100644	+	Missense_Mutation	SNP	G	G	A	rs11736872	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:177100644G>A	ENST00000280190.4	+	31	4039	c.3883G>A	c.(3883-3885)Gct>Act	p.A1295T	WDR17_ENST00000508596.1_Missense_Mutation_p.A1256T|WDR17_ENST00000507824.2_Missense_Mutation_p.A1270T|WDR17_ENST00000393643.2_Missense_Mutation_p.A1271T			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	330	0	0		WXS	Illumina HiSeq	Phase_I	170	131	0.770588	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		
LILRA6	79168	hgsc.bcm.edu	37	19	54743824	54743824	+	Missense_Mutation	SNP	T	T	G	rs199826565	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54743824T>G	ENST00000396365.2	-	7	1301	c.1262A>C	c.(1261-1263)cAc>cCc	p.H421P	LILRA6_ENST00000419410.2_Missense_Mutation_p.H421P|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000245621.5_Intron|LILRA6_ENST00000391735.3_3'UTR	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	421					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)		GCCTCCAGAGTGTCCTGGAAG	0.697													.|||	342	0.0682907	0.0008	0.0288	5008	,	,		19291	0.0169		0.0338	False		,,,				2504	0.2761				p.H421P		Atlas-SNP	.											LILRA6,NS,carcinoma,0,1	LILRA6	75	1	0			c.A1262C						scavenged	.	G	PRO/HIS	15,3271		0,15,1628	4.0	6.0	5.0		1262	1.2	0.0	19		5	185,6449		1,183,3133	no	missense	LILRA6	NM_024318.2	77	1,198,4761	GG,GT,TT		2.7887,0.4565,2.0161		421/482	54743824	200,9720	1643	3317	4960	SO:0001583	missense	79168	exon7			CCAGAGTGTCCTG	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.1262A>C	19.37:g.54743824T>G	ENSP00000379651:p.His421Pro	Somatic	128	3	0.0234375		WXS	Illumina HiSeq	Phase_I	142	55	0.387324	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	t	0.027	-1.364083	0.01235	0.004565	0.027887	ENSG00000244482	ENST00000419410;ENST00000396365	T;T	0.00497	7.19;6.98	2.31	1.2	0.21068	.	18.772200	0.00166	N	0.000002	T	0.00073	0.0002	N	0.01668	-0.77	0.19775	N	0.999958	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41124	-0.9526	10	0.02654	T	1	.	2.942	0.05834	0.1669:0.0:0.5667:0.2663	.	421;421	Q6PI73;D3YTC4	LIRA6_HUMAN;.	P	421	ENSP00000411227:H421P;ENSP00000379651:H421P	ENSP00000379651:H421P	H	-	2	0	LILRA6	59435636	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.743000	0.04845	-0.068000	0.12953	-1.415000	0.01116	CAC	.	.	weak		0.697	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789314	117789314	+	Silent	SNP	G	G	A	rs201746372|rs58754377		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789314G>A	ENST00000430170.2	-	2	348	c.261C>T	c.(259-261)gcC>gcT	p.A87A	TMPRSS13_ENST00000445164.2_Silent_p.A87A|TMPRSS13_ENST00000526090.1_Silent_p.A87A|TMPRSS13_ENST00000528626.1_Silent_p.A87A|TMPRSS13_ENST00000524993.1_Silent_p.A87A	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	87	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		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)		GAGATGCCCGGGCTGGAGATG	0.647																																					p.A87A		Atlas-SNP	.											TMPRSS13,colon,carcinoma,0,2	TMPRSS13	75	2	1	Deletion - In frame(1)	urinary_tract(1)	c.C261T						scavenged	.						35.0	42.0	40.0					11																	117789314		1958	4138	6096	SO:0001819	synonymous_variant	84000	exon2			TGCCCGGGCTGGA	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	ENST00000430170.2:c.261C>T	11.37:g.117789314G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	264	10	0.0378788	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	37	CCDS58185.1																																																																																			.	.	none		0.647	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
GUCY2D	3000	hgsc.bcm.edu	37	17	7906519	7906519	+	Missense_Mutation	SNP	G	G	T	rs61749665	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	23	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	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		
PPP1R3A	5506	hgsc.bcm.edu	37	7	113519637	113519637	+	Missense_Mutation	SNP	C	C	G	rs371962450		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:113519637C>G	ENST00000284601.3	-	4	1578	c.1510G>C	c.(1510-1512)Gga>Cga	p.G504R		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	504					glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						TTAGAAGATCCTTCTTCTGTT	0.318																																					p.G504R		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G1510C						PASS	.						63.0	60.0	61.0					7																	113519637		2203	4299	6502	SO:0001583	missense	5506	exon4			AAGATCCTTCTTC	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9291	protein-coding gene	gene with protein product	"""glycogen-associated regulatory subunit of protein phosphatase-1"", ""protein phosphatase 1 regulatory subunit GM"""	600917	"""protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)"", ""protein phosphatase 1, regulatory (inhibitor) subunit 3A"""	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1510G>C	7.37:g.113519637C>G	ENSP00000284601:p.Gly504Arg	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	181	53	0.292818	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	C	9.621	1.133935	0.21123	.	.	ENSG00000154415	ENST00000284601;ENST00000449795	T;T	0.29655	2.51;1.56	6.02	2.73	0.32206	.	0.930568	0.09052	N	0.855709	T	0.19604	0.0471	N	0.25144	0.715	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28586	-1.0039	10	0.13853	T	0.58	-0.2141	9.1988	0.37244	0.0:0.6562:0.0:0.3437	.	504	Q16821	PPR3A_HUMAN	R	504;183	ENSP00000284601:G504R;ENSP00000401278:G183R	ENSP00000284601:G504R	G	-	1	0	PPP1R3A	113306873	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.331000	0.19733	0.826000	0.34661	0.655000	0.94253	GGA	.	.	none		0.318	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711	
DRC7	84229	hgsc.bcm.edu	37	16	57732012	57732012	+	Missense_Mutation	SNP	G	G	A	rs55645458	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57732012G>A	ENST00000360716.3	+	3	372	c.151G>A	c.(151-153)Gac>Aac	p.D51N	CCDC135_ENST00000394337.4_Missense_Mutation_p.D51N|RP11-405F3.4_ENST00000563062.1_RNA|CCDC135_ENST00000336825.8_Missense_Mutation_p.D51N			Q8IY82	CC135_HUMAN		51			D -> N (in dbSNP:rs55645458).		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30						GACGCTCAGAGACCTGGAGAA	0.607													g|||	54	0.0107827	0.0	0.0072	5008	,	,		18158	0.0		0.0398	False		,,,				2504	0.0092				p.D51N		Atlas-SNP	.											.	CCDC135	97	.	0			c.G151A						PASS	.	G	ASN/ASP	47,4349	50.2+/-85.5	0,47,2151	100.0	91.0	94.0		151	4.2	1.0	16	dbSNP_129	94	422,8178	130.8+/-188.7	10,402,3888	yes	missense	CCDC135	NM_032269.5	23	10,449,6039	AA,AG,GG		4.907,1.0692,3.6088	possibly-damaging	51/875	57732012	469,12527	2198	4300	6498	SO:0001583	missense	84229	exon2			CTCAGAGACCTGG																												ENST00000360716.3:c.151G>A	16.37:g.57732012G>A	ENSP00000353942:p.Asp51Asn	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	106	18	0.169811	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	35	0.016025641025641024	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	32	0.04221635883905013	G	15.87	2.961520	0.53400	0.010692	0.04907	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.10573	3.1;2.86;3.1	4.18	4.18	0.49190	.	0.477501	0.21157	N	0.079231	T	0.03434	0.0099	M	0.63843	1.955	0.32197	N	0.578329	D;D	0.59357	0.985;0.967	P;P	0.54270	0.747;0.718	T	0.00899	-1.1522	10	0.62326	D	0.03	-34.8223	12.3248	0.55005	0.0:0.0:1.0:0.0	rs55645458	51;51	Q8IY82-2;Q8IY82	.;CC135_HUMAN	N	51	ENSP00000377869:D51N;ENSP00000338938:D51N;ENSP00000353942:D51N	ENSP00000338938:D51N	D	+	1	0	CCDC135	56289513	0.994000	0.37717	0.997000	0.53966	0.030000	0.12068	2.049000	0.41288	2.613000	0.88420	0.549000	0.68633	GAC	G|0.971;A|0.029	0.029	strong		0.607	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
OPN3	23596	hgsc.bcm.edu	37	1	241755348	241755348	+	IGR	SNP	C	C	T	rs1053230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:241755348C>T	ENST00000366554.2	-	0	2620				KMO_ENST00000366558.3_Missense_Mutation_p.R439C|OPN3_ENST00000469376.1_5'Flank|KMO_ENST00000366559.4_Missense_Mutation_p.R452C|KMO_ENST00000366557.4_Missense_Mutation_p.R418C	NM_014322.2	NP_055137.2	Q9H1Y3	OPN3_HUMAN	opsin 3						detection of light stimulus (GO:0009583)|detection of visible light (GO:0009584)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(1)|large_intestine(5)|lung(5)	11	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			ATCTTTCCTCCGCTTGAGAAG	0.448													C|||	582	0.116214	0.0091	0.1282	5008	,	,		19206	0.0526		0.2237	False		,,,				2504	0.2076				p.R452C		Atlas-SNP	.											KMO,NS,adenoma,0,1	KMO	69	1	0			c.C1354T						scavenged	.	C	CYS/ARG	192,4214	121.3+/-158.8	2,188,2013	174.0	148.0	157.0		1354	0.3	0.0	1	dbSNP_86	157	1945,6655	343.5+/-324.9	212,1521,2567	yes	missense	KMO	NM_003679.3	180	214,1709,4580	TT,TC,CC		22.6163,4.3577,16.4309	benign	452/487	241755348	2137,10869	2203	4300	6503	SO:0001628	intergenic_variant	8564	exon15			TTCCTCCGCTTGA	AF140242	CCDS31072.1	1q43	2014-06-13	2008-04-16		ENSG00000054277	ENSG00000054277		"""GPCR / Class A : Opsin receptors"""	14007	protein-coding gene	gene with protein product	"""panopsin"", ""protein phosphatase 1, regulatory subunit 116"""	606695	"""encephalopsin"""	ECPN		10234000, 11401433	Standard	NM_014322		Approved	ERO, NMO-1, encephalopsin, PPP1R116	uc001hza.3	Q9H1Y3	OTTHUMG00000039691		1.37:g.241755348C>T		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_003679	Q8IX08|Q9Y344	Missense_Mutation	SNP	ENST00000366554.2	37	CCDS31072.1	271|271	0.12408424908424909|0.12408424908424909	5|5	0.01016260162601626|0.01016260162601626	55|55	0.15193370165745856|0.15193370165745856	37|37	0.06468531468531469|0.06468531468531469	174|174	0.22955145118733508|0.22955145118733508	C|C	4.393|4.393	0.072607|0.072607	0.08436|0.08436	0.043577|0.043577	0.226163|0.226163	ENSG00000117009|ENSG00000117009	ENST00000366555|ENST00000366559;ENST00000366558;ENST00000366557	.|T;T;T	.|0.44482	.|0.92;0.92;0.95	5.4|5.4	0.337|0.337	0.15966|0.15966	.|.	.|1.582250	.|0.02739	.|N	.|0.116117	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	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.12372|0.12372	-1.0550|-1.0550	4|9	.|0.38643	.|T	.|0.18	.|.	7.3222|7.3222	0.26533|0.26533	0.0:0.3956:0.0:0.6044|0.0:0.3956:0.0:0.6044	rs1053230;rs58727153;rs1053230|rs1053230;rs58727153;rs1053230	.|452	.|O15229	.|KMO_HUMAN	L|C	137|452;439;418	.|ENSP00000355517:R452C;ENSP00000355516:R439C;ENSP00000355515:R418C	.|ENSP00000355515:R418C	P|R	+|+	2|1	0|0	KMO|KMO	239821971|239821971	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.265000|0.265000	0.18515|0.18515	0.139000|0.139000	0.18822|0.18822	-0.247000|-0.247000	0.11927|0.11927	CCG|CGC	C|0.853;T|0.147	0.147	strong		0.448	OPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095713.1	NM_014322	
MYO3B	140469	hgsc.bcm.edu	37	2	171240249	171240249	+	Silent	SNP	C	C	T	rs11675394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:171240249C>T	ENST00000408978.4	+	12	1358	c.1215C>T	c.(1213-1215)cgC>cgT	p.R405R	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.R405R|MYO3B_ENST00000334231.6_Silent_p.R414R	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	405	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)	p.S397_A406del(1)		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						GGGTGAAACGCGCCTCCAATC	0.453													C|||	1079	0.215455	0.0303	0.2493	5008	,	,		20601	0.2887		0.325	False		,,,				2504	0.2536				p.R405R		Atlas-SNP	.											MYO3B_ENST00000408978,rectum,carcinoma,0,6	MYO3B	320	6	1	Deletion - In frame(1)	ovary(1)	c.C1215T						PASS	.	C	,,	327,3487		13,301,1593	120.0	112.0	114.0		1215,1215,1215	-2.5	1.0	2	dbSNP_120	114	2679,5543		437,1805,1869	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	450,2106,3462	TT,TC,CC		32.5833,8.5737,24.9751	,,	405/1315,405/1276,405/1342	171240249	3006,9030	1907	4111	6018	SO:0001819	synonymous_variant	140469	exon12			GAAACGCGCCTCC		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.1215C>T	2.37:g.171240249C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																			C|0.732;T|0.268	0.268	strong		0.453	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
LRRC37A3	374819	hgsc.bcm.edu	37	17	62892159	62892159	+	Missense_Mutation	SNP	G	G	T	rs17857225		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:62892159G>T	ENST00000584306.1	-	3	1747	c.1217C>A	c.(1216-1218)gCt>gAt	p.A406D	RP11-927P21.1_ENST00000584959.1_RNA|RP11-927P21.1_ENST00000577938.1_RNA|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.A406D|LRRC37A3_ENST00000577487.1_5'Flank|LRRC37A3_ENST00000339474.5_Intron|RP11-927P21.1_ENST00000584131.1_RNA|LRRC37A3_ENST00000400877.3_Intron	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	406						integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						ACTGGGTGAAGCTAAATGATG	0.537																																					p.A406D		Atlas-SNP	.											LRRC37A3,NS,carcinoma,0,1	LRRC37A3	75	1	0			c.C1217A						scavenged	.						1.0	1.0	1.0					17																	62892159		292	887	1179	SO:0001583	missense	374819	exon3			GGTGAAGCTAAAT	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.1217C>A	17.37:g.62892159G>T	ENSP00000464535:p.Ala406Asp	Somatic	923	3	0.00325027		WXS	Illumina HiSeq	Phase_I	830	59	0.0710843	NM_199340	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.581395	0.00129	.	.	ENSG00000176809	ENST00000319651	T	0.59772	0.24	2.63	-5.25	0.02781	.	.	.	.	.	T	0.16342	0.0393	N	0.00483	-1.445	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11108	-1.0601	9	0.11794	T	0.64	.	2.8545	0.05568	0.2063:0.2804:0.3945:0.1188	.	406	O60309	L37A3_HUMAN	D	406	ENSP00000325713:A406D	ENSP00000325713:A406D	A	-	2	0	LRRC37A3	60322621	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.921000	0.01569	-5.806000	0.00009	-2.171000	0.00323	GCT	.	.	weak		0.537	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
SEC31B	25956	hgsc.bcm.edu	37	10	102247408	102247408	+	Missense_Mutation	SNP	C	C	A	rs2298075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102247408C>A	ENST00000370345.3	-	26	3602	c.3505G>T	c.(3505-3507)Gct>Tct	p.A1169S		NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	1169			A -> S (in dbSNP:rs2298075).		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		ATGAGGACAGCCTTCAGGATA	0.562													C|||	946	0.188898	0.2088	0.1888	5008	,	,		20238	0.129		0.2018	False		,,,				2504	0.2106				p.A1169S		Atlas-SNP	.											SEC31B,NS,carcinoma,0,2	SEC31B	84	2	0			c.G3505T						scavenged	.	C	SER/ALA	908,3498	347.2+/-309.4	82,744,1377	49.0	41.0	44.0		3505	1.2	0.9	10	dbSNP_100	44	1955,6645	338.2+/-322.6	225,1505,2570	yes	missense	SEC31B	NM_015490.3	99	307,2249,3947	AA,AC,CC		22.7326,20.6083,22.0129	benign	1169/1180	102247408	2863,10143	2203	4300	6503	SO:0001583	missense	25956	exon26			GGACAGCCTTCAG	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.3505G>T	10.37:g.102247408C>A	ENSP00000359370:p.Ala1169Ser	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	50	38	0.76	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	415	0.190018315018315	89	0.18089430894308944	71	0.19613259668508287	88	0.15384615384615385	167	0.22031662269129287	C	7.962	0.747208	0.15710	0.206083	0.227326	ENSG00000075826	ENST00000370345	T	0.49432	0.78	4.45	1.23	0.21249	.	0.487653	0.22268	N	0.062301	T	0.00012	0.0000	N	0.03050	-0.425	0.09310	P	0.9999999999717782	B;B	0.17038	0.02;0.012	B;B	0.16289	0.015;0.007	T	0.20438	-1.0275	9	0.45353	T	0.12	-2.4525	7.7526	0.28907	0.2984:0.6126:0.0:0.089	rs2298075;rs17672195;rs52835061;rs59609476;rs2298075	1168;1169	Q9NQW1-5;Q9NQW1	.;SC31B_HUMAN	S	1169	ENSP00000359370:A1169S	ENSP00000359370:A1169S	A	-	1	0	SEC31B	102237398	1.000000	0.71417	0.924000	0.36721	0.103000	0.19146	3.426000	0.52778	0.477000	0.27464	0.561000	0.74099	GCT	C|0.795;A|0.205	0.205	strong		0.562	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
DNAH14	127602	hgsc.bcm.edu	37	1	225528189	225528189	+	Silent	SNP	C	C	T	rs115148958	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225528189C>T	ENST00000445597.2	+	47	7776	c.7776C>T	c.(7774-7776)ccC>ccT	p.P2592P	DNAH14_ENST00000430092.1_Silent_p.P3395P|DNAH14_ENST00000439375.2_Silent_p.P3395P			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2592					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						TAGACAACCCCCATTTTCTTC	0.328													C|||	52	0.0103834	0.0008	0.0101	5008	,	,		17560	0.001		0.0288	False		,,,				2504	0.0143				p.P3395P		Atlas-SNP	.											.	DNAH14	300	.	0			c.C10185T						PASS	.	C		3,1381		0,3,689	119.0	104.0	109.0		10185	-1.4	0.1	1	dbSNP_132	109	72,3110		0,72,1519	no	coding-synonymous	DNAH14	NM_001373.1		0,75,2208	TT,TC,CC		2.2627,0.2168,1.6426		3395/4516	225528189	75,4491	692	1591	2283	SO:0001819	synonymous_variant	127602	exon67			CAACCCCCATTTT	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.7776C>T	1.37:g.225528189C>T		Somatic	391	0	0		WXS	Illumina HiSeq	Phase_I	383	189	0.493473	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Silent	SNP	ENST00000445597.2	37																																																																																				C|0.988;T|0.012	0.012	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PSG2	5670	hgsc.bcm.edu	37	19	43575905	43575905	+	Missense_Mutation	SNP	C	C	T	rs77035666	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43575905C>T	ENST00000406487.1	-	4	1009	c.911G>A	c.(910-912)cGt>cAt	p.R304H		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	304	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.R304H(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				GGCTGAGTTACGAACAGAGCA	0.453													C|||	484	0.0966454	0.0651	0.2061	5008	,	,		19273	0.004		0.1103	False		,,,				2504	0.1431				p.R304H		Atlas-SNP	.											PSG2,NS,carcinoma,0,1	PSG2	84	1	1	Substitution - Missense(1)	pancreas(1)	c.G911A						scavenged	.	C	HIS/ARG	322,4082	171.9+/-202.1	23,276,1903	176.0	180.0	179.0		911	-2.5	0.0	19	dbSNP_131	179	942,7656	206.8+/-248.7	57,828,3414	yes	missense	PSG2	NM_031246.3	29	80,1104,5317	TT,TC,CC		10.956,7.3115,9.7216		304/336	43575905	1264,11738	2202	4299	6501	SO:0001583	missense	5670	exon4			GAGTTACGAACAG		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.911G>A	19.37:g.43575905C>T	ENSP00000385706:p.Arg304His	Somatic	227	2	0.00881057		WXS	Illumina HiSeq	Phase_I	234	121	0.517094	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	188	0.08608058608058608	32	0.06504065040650407	63	0.17403314917127072	2	0.0034965034965034965	91	0.12005277044854881	c	0.004	-2.267055	0.00259	0.073115	0.10956	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.12774	2.65	1.26	-2.53	0.06326	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00039	0.0001	L	0.33710	1.025	0.80722	P	0.0	B;B	0.24368	0.021;0.102	B;B	0.18263	0.009;0.021	T	0.43196	-0.9406	8	0.09843	T	0.71	.	2.1681	0.03843	0.0:0.2749:0.324:0.4011	.	304;304	B5MCM8;P11465	.;PSG2_HUMAN	H	304	ENSP00000385706:R304H	ENSP00000332984:R304H	R	-	2	0	PSG2	48267745	0.000000	0.05858	0.015000	0.15790	0.005000	0.04900	-0.559000	0.05971	-0.279000	0.09167	-0.507000	0.04495	CGT	C|0.904;T|0.096	0.096	strong		0.453	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
FLG	2312	hgsc.bcm.edu	37	1	152280032	152280032	+	Missense_Mutation	SNP	T	T	C	rs71625200	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280032T>C	ENST00000368799.1	-	3	7365	c.7330A>G	c.(7330-7332)Aag>Gag	p.K2444E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2444	Ser-rich.			K -> Q (in Ref. 3; AAA52454). {ECO:0000305}.	establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGTGCCTGCTTGTGGTGGGAT	0.592									Ichthyosis				C|||	1718	0.343051	0.1218	0.4222	5008	,	,		21032	0.6071		0.171	False		,,,				2504	0.4908				p.K2444E		Atlas-SNP	.											FLG,larynx,carcinoma,+2,1	FLG	900	1	0			c.A7330G						PASS	.	C	GLU/LYS	599,3807	766.7+/-413.5	43,513,1647	304.0	277.0	286.0		7330	2.1	0.0	1	dbSNP_130	286	1407,7191	749.4+/-407.4	123,1161,3015	no	missense	FLG	NM_002016.1	56	166,1674,4662	CC,CT,TT		16.3643,13.5951,15.426	benign	2444/4062	152280032	2006,10998	2203	4299	6502	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTGCTTGTGGTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7330A>G	1.37:g.152280032T>C	ENSP00000357789:p.Lys2444Glu	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	421	170	0.4038	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	586	0.2683150183150183	51	0.10365853658536585	107	0.2955801104972376	319	0.5576923076923077	109	0.1437994722955145	C	7.499	0.652241	0.14580	0.135951	0.163643	ENSG00000143631	ENST00000368799	T	0.01647	4.71	4.1	2.1	0.27182	.	.	.	.	.	T	0.00109	0.0003	N	0.00036	-2.535	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26710	-1.0095	8	0.02654	T	1	.	3.9847	0.09511	0.0:0.5744:0.1996:0.226	.	2444	P20930	FILA_HUMAN	E	2444	ENSP00000357789:K2444E	ENSP00000357789:K2444E	K	-	1	0	FLG	150546656	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-0.889000	0.04144	0.313000	0.23062	-0.330000	0.08379	AAG	T|0.803;C|0.197	0.197	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
B4GALNT1	2583	hgsc.bcm.edu	37	12	58023981	58023981	+	Silent	SNP	C	C	A	rs715930	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:58023981C>A	ENST00000341156.4	-	6	1250	c.666G>T	c.(664-666)ctG>ctT	p.L222L	B4GALNT1_ENST00000418555.2_Silent_p.L167L|B4GALNT1_ENST00000552350.1_Silent_p.L222L|B4GALNT1_ENST00000550943.1_5'Flank|B4GALNT1_ENST00000449184.3_Silent_p.L222L|B4GALNT1_ENST00000550764.1_Silent_p.L222L	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	222					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid metabolic process (GO:0006687)|lipid glycosylation (GO:0030259)|lipid storage (GO:0019915)|protein glycosylation (GO:0006486)|spermatogenesis (GO:0007283)	integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|plasma membrane (GO:0005886)	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity (GO:0003947)	p.L222L(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|urinary_tract(1)	20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			TGTAAGTGACCAGTTGTAGTT	0.572													C|||	1067	0.213059	0.2776	0.281	5008	,	,		20016	0.1319		0.2058	False		,,,				2504	0.1687				p.Q222H		Atlas-SNP	.											B4GALNT1,NS,carcinoma,0,1	B4GALNT1	53	1	1	Substitution - coding silent(1)	stomach(1)	c.G666T						scavenged	.	C		1156,3250		141,874,1188	125.0	97.0	107.0		666	3.8	1.0	12	dbSNP_86	107	1821,6779		205,1411,2684	no	coding-synonymous	B4GALNT1	NM_001478.3		346,2285,3872	AA,AC,CC		21.1744,26.2369,22.8894		222/534	58023981	2977,10029	2203	4300	6503	SO:0001819	synonymous_variant	2583	exon6			AGTGACCAGTTGT	M83651	CCDS8950.1, CCDS61170.1, CCDS61171.1	12q13.3	2013-09-11	2006-01-08	2006-01-08	ENSG00000135454	ENSG00000135454	2.4.1.92	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	4117	protein-coding gene	gene with protein product	"""GD2 synthase, GM2 synthase"""	601873	"""UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (GalNAc-T)"", ""UDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1"", ""spastic paraplegia 26"""	GALGT, SPG26		1601877, 23746551	Standard	NM_001478		Approved	beta1-4GalNAc-T	uc001spg.2	Q00973	OTTHUMG00000170190	ENST00000341156.4:c.666G>T	12.37:g.58023981C>A		Somatic	323	2	0.00619195		WXS	Illumina HiSeq	Phase_I	295	150	0.508475	NM_001478	B4DE26|Q8N636	Missense_Mutation	SNP	ENST00000341156.4	37	CCDS8950.1																																																																																			C|0.771;A|0.229	0.229	strong		0.572	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	NM_001478	
LRRN1	57633	hgsc.bcm.edu	37	3	3886919	3886919	+	Silent	SNP	C	C	T	rs3749348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:3886919C>T	ENST00000319331.3	+	2	1355	c.594C>T	c.(592-594)atC>atT	p.I198I	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	198						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)		TTCTCATGATCGGAGAAAACC	0.393													C|||	1060	0.211661	0.2943	0.1455	5008	,	,		18416	0.2619		0.1024	False		,,,				2504	0.2076				p.I198I		Atlas-SNP	.											.	LRRN1	82	.	0			c.C594T						PASS	.	C		1036,3370	371.2+/-319.9	112,812,1279	117.0	126.0	123.0		594	1.8	1.0	3	dbSNP_107	123	1051,7549	220.8+/-258.4	61,929,3310	no	coding-synonymous	LRRN1	NM_020873.5		173,1741,4589	TT,TC,CC		12.2209,23.5134,16.0464		198/717	3886919	2087,10919	2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			CATGATCGGAGAA	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.594C>T	3.37:g.3886919C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			C|0.817;T|0.183	0.183	strong		0.393	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
COL9A3	1299	hgsc.bcm.edu	37	20	61460124	61460124	+	Silent	SNP	G	G	A	rs2249903	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:61460124G>A	ENST00000343916.3	+	18	912	c.909G>A	c.(907-909)ccG>ccA	p.P303P		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	303	Triple-helical region 3 (COL3).				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female gonad development (GO:0008585)|male gonad development (GO:0008584)	collagen type IX trimer (GO:0005594)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(1)|endometrium(3)|large_intestine(1)|lung(18)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	28	Breast(26;5.68e-08)					AGGGCATGCCGGGCAAGGACG	0.682													G|||	422	0.0842652	0.0363	0.1167	5008	,	,		19021	0.0308		0.1889	False		,,,				2504	0.0736				p.P303P		Atlas-SNP	.											COL9A3,right_lower_lobe,carcinoma,+1,1	COL9A3	70	1	0			c.G909A						PASS	.	G		276,4126	150.3+/-184.3	11,254,1936	51.0	47.0	48.0		909	-7.8	1.0	20	dbSNP_100	48	1507,7091	281.8+/-295.3	135,1237,2927	no	coding-synonymous	COL9A3	NM_001853.3		146,1491,4863	AA,AG,GG		17.5273,6.2699,13.7154		303/685	61460124	1783,11217	2201	4299	6500	SO:0001819	synonymous_variant	1299	exon18			CATGCCGGGCAAG	AK075240	CCDS13505.1	20q13.3	2013-01-16			ENSG00000092758	ENSG00000092758		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2219	protein-coding gene	gene with protein product	"""collagen type IX proteoglycan"""	120270				8586434, 1429648	Standard	NM_001853		Approved	IDD, MED, EDM3, FLJ90759, DJ885L7.4.1	uc002ydm.3	Q14050	OTTHUMG00000032938	ENST00000343916.3:c.909G>A	20.37:g.61460124G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_001853	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																			G|0.833;A|0.167	0.167	strong		0.682	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853	
SULT1C4	27233	hgsc.bcm.edu	37	2	108994808	108994808	+	Missense_Mutation	SNP	C	C	G	rs1402467	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:108994808C>G	ENST00000272452.2	+	1	341	c.15C>G	c.(13-15)gaC>gaG	p.D5E	SULT1C4_ENST00000409309.3_Missense_Mutation_p.D5E	NM_006588.2	NP_006579.2	O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 4	5			D -> E (in dbSNP:rs1402467). {ECO:0000269|PubMed:9852044, ECO:0000269|Ref.4}.		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						CCTTACACGACATGGAGGATT	0.443													G|||	2092	0.417732	0.8752	0.1801	5008	,	,		22504	0.1081		0.2634	False		,,,				2504	0.4458				p.D5E		Atlas-SNP	.											.	SULT1C4	41	.	0			c.C15G						PASS	.	G	GLU/ASP	3378,1028	377.1+/-322.3	1306,766,131	162.0	169.0	167.0		15	-1.8	0.0	2	dbSNP_88	167	2118,6482	716.6+/-406.1	254,1610,2436	yes	missense	SULT1C4	NM_006588.2	45	1560,2376,2567	GG,GC,CC		24.6279,23.3318,42.2574	benign	5/303	108994808	5496,7510	2203	4300	6503	SO:0001583	missense	27233	exon1			ACACGACATGGAG	AF055584	CCDS2077.1	2q12.3	2008-09-04	2007-03-16	2007-03-16	ENSG00000198075	ENSG00000198075		"""Sulfotransferases, cytosolic"""	11457	protein-coding gene	gene with protein product		608357	"""sulfotransferase family, cytosolic, 1C, member 2"""	SULT1C2		10783263, 9852044	Standard	NM_006588		Approved	SULT1C	uc002tea.1	O75897	OTTHUMG00000130958	ENST00000272452.2:c.15C>G	2.37:g.108994808C>G	ENSP00000272452:p.Asp5Glu	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_006588	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000272452.2	37	CCDS2077.1	776	0.3553113553113553	444	0.9024390243902439	70	0.19337016574585636	62	0.10839160839160839	200	0.2638522427440633	G	1.450	-0.565305	0.03939	0.766682	0.246279	ENSG00000198075	ENST00000272452;ENST00000409309	T;T	0.01745	5.01;4.66	4.88	-1.75	0.08031	.	7739.210000	0.00166	N	0.000000	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	0.26950	-1.0088	9	0.02654	T	1	.	6.7063	0.23252	0.4812:0.3766:0.1422:0.0	rs1402467;rs52816974;rs61392346;rs1402467	5;5;5	Q08AS5;O75897;Q6PD90	.;ST1C4_HUMAN;.	E	5	ENSP00000272452:D5E;ENSP00000387225:D5E	ENSP00000272452:D5E	D	+	3	2	SULT1C4	108361240	0.281000	0.24258	0.007000	0.13788	0.136000	0.21042	-0.691000	0.05133	-0.973000	0.03555	-0.167000	0.13348	GAC	C|0.602;G|0.398	0.398	strong		0.443	SULT1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253561.1	NM_006588	
ZNF286A	57335	hgsc.bcm.edu	37	17	15620481	15620481	+	Silent	SNP	C	C	T	rs2530064	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:15620481C>T	ENST00000464847.2	+	5	1996	c.1443C>T	c.(1441-1443)ctC>ctT	p.L481L	ZNF286A_ENST00000421016.1_Silent_p.L481L|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000395894.2_3'UTR|ZNF286A_ENST00000583566.1_Silent_p.L481L|ZNF286A_ENST00000593105.1_Silent_p.L471L|ZNF286A_ENST00000413242.2_Silent_p.L481L			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	481					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.L481L(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)		CATCAGCTCTCATTCAACATC	0.403													T|||	1613	0.322085	0.3215	0.3473	5008	,	,		18041	0.25		0.327	False		,,,				2504	0.3742				p.L481L		Atlas-SNP	.											ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	1	Substitution - coding silent(1)	stomach(1)	c.C1443T						PASS	.						57.0	60.0	59.0					17																	15620481		2200	4294	6494	SO:0001819	synonymous_variant	57335	exon6			AGCTCTCATTCAA	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.1443C>T	17.37:g.15620481C>T		Somatic	359	0	0		WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_020652	B4DKF9|Q96JF3	Silent	SNP	ENST00000464847.2	37	CCDS11172.1																																																																																			C|0.250;T|0.750	0.750	weak		0.403	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
TOP2A	7153	hgsc.bcm.edu	37	17	38564363	38564363	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38564363G>A	ENST00000423485.1	-	12	1514	c.1356C>T	c.(1354-1356)tcC>tcT	p.S452S		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	452					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)	TACACTCAGTGGAGTTTCGGC	0.403																																					p.S452S		Atlas-SNP	.											.	TOP2A	124	.	0			c.C1356T						PASS	.						39.0	37.0	37.0					17																	38564363		1832	4080	5912	SO:0001819	synonymous_variant	7153	exon12			CTCAGTGGAGTTT		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.1356C>T	17.37:g.38564363G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			.	.	none		0.403	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
NOL4L	140688	hgsc.bcm.edu	37	20	31044059	31044059	+	Silent	SNP	G	G	A	rs570929204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:31044059G>A	ENST00000359676.5	-	3	391	c.249C>T	c.(247-249)gcC>gcT	p.A83A	RP5-1184F4.5_ENST00000442179.1_RNA|C20orf112_ENST00000475781.1_5'UTR	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		83						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						GATCCTCGGCGGCCGTGGTGA	0.687													G|||	4	0.000798722	0.0	0.0	5008	,	,		17312	0.0		0.0	False		,,,				2504	0.0041				p.A327A		Atlas-SNP	.											.	C20orf112	39	.	0			c.C981T						PASS	.						43.0	40.0	41.0					20																	31044059		2203	4298	6501	SO:0001819	synonymous_variant	140688	exon6			CTCGGCGGCCGTG																												ENST00000359676.5:c.249C>T	20.37:g.31044059G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	152	71	0.467105	NM_001256798	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Silent	SNP	ENST00000359676.5	37	CCDS13202.1																																																																																			.	.	none		0.687	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2		
C8orf22	492307	hgsc.bcm.edu	37	8	49987801	49987801	+	3'UTR	SNP	A	A	G	rs72641628	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:49987801A>G	ENST00000303202.8	+	0	1139				C8orf22_ENST00000522267.1_3'UTR|C8orf22_ENST00000399653.4_Missense_Mutation_p.S81G|C8orf22_ENST00000517663.1_3'UTR	NM_001256598.1	NP_001243527.1	Q8WWR9	PDPFL_HUMAN	chromosome 8 open reading frame 22						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)					large_intestine(1)|lung(7)|prostate(1)	9		all_cancers(86;0.0452)|all_epithelial(80;0.000863)|Lung NSC(129;0.0019)|all_lung(136;0.00502)				TAGCATGAACAGTTGATTCTG	0.468													A|||	43	0.00858626	0.0	0.0086	5008	,	,		17149	0.0		0.0328	False		,,,				2504	0.0041				p.S81G		Atlas-SNP	.											.	C8orf22	20	.	0			c.A241G						PASS	.	A	GLY/SER	24,4014		0,24,1995	183.0	177.0	179.0		241	2.3	0.0	8	dbSNP_130	179	204,8170		5,194,3988	yes	missense	C8orf22	NM_001007176.3	56	5,218,5983	GG,GA,AA		2.4361,0.5944,1.8369	benign	81/82	49987801	228,12184	2019	4187	6206	SO:0001624	3_prime_UTR_variant	492307	exon5			ATGAACAGTTGAT	BC017981	CCDS47854.1, CCDS59101.1, CCDS59102.1	8q11.21	2012-04-11			ENSG00000168333	ENSG00000168333			31745	protein-coding gene	gene with protein product							Standard	NM_001007176		Approved		uc031tba.1	Q8WWR9	OTTHUMG00000164217	ENST00000303202.8:c.*711A>G	8.37:g.49987801A>G		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	313	115	0.367412	NM_001007176	G3V137|Q8WVI1	Missense_Mutation	SNP	ENST00000303202.8	37	CCDS59101.1	31	0.014194139194139194	0	0.0	4	0.011049723756906077	0	0.0	27	0.03562005277044855	A	11.78	1.741160	0.30865	0.005944	0.024361	ENSG00000168333	ENST00000399653	.	.	.	3.53	2.29	0.28610	.	.	.	.	.	T	0.04634	0.0126	.	.	.	0.09310	N	1	B	0.30281	0.275	B	0.24269	0.052	T	0.12192	-1.0557	6	.	.	.	.	6.1636	0.20378	0.7409:0.0:0.0:0.2591	.	81	Q8WWR9-2	.	G	81	.	.	S	+	1	0	C8orf22	50150354	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	0.597000	0.24059	0.461000	0.27071	0.533000	0.62120	AGT	A|0.985;G|0.015	0.015	strong		0.468	C8orf22-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377837.1	NM_001007176	
TOP1MT	116447	hgsc.bcm.edu	37	8	144406705	144406705	+	Missense_Mutation	SNP	C	C	T	rs11544484	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144406705C>T	ENST00000329245.4	-	6	800	c.766G>A	c.(766-768)Gtt>Att	p.V256I	TOP1MT_ENST00000521193.1_Missense_Mutation_p.V158I|TOP1MT_ENST00000519148.1_Missense_Mutation_p.V158I|TOP1MT_ENST00000523676.1_Missense_Mutation_p.V158I	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	256			V -> I (in dbSNP:rs11544484). {ECO:0000269|PubMed:15489334}.		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)	GAGTTCTGAACGCTCTCGGTC	0.627													C|||	1381	0.275759	0.5015	0.1873	5008	,	,		18410	0.0754		0.3121	False		,,,				2504	0.2025				p.V256I		Atlas-SNP	.											.	TOP1MT	63	.	0			c.G766A						PASS	.	C	ILE/VAL	2179,2227	584.9+/-386.1	549,1081,573	133.0	112.0	119.0		766	-7.1	0.0	8	dbSNP_120	119	2426,6174	402.5+/-347.5	368,1690,2242	yes	missense	TOP1MT	NM_052963.1	29	917,2771,2815	TT,TC,CC		28.2093,49.4553,35.4067	benign	256/602	144406705	4605,8401	2203	4300	6503	SO:0001583	missense	116447	exon6			TCTGAACGCTCTC	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.766G>A	8.37:g.144406705C>T	ENSP00000328835:p.Val256Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	176	62	0.352273	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	37	CCDS6400.1	593	0.2715201465201465	252	0.5121951219512195	73	0.20165745856353592	39	0.06818181818181818	229	0.3021108179419525	C	0.012	-1.660811	0.00772	0.494553	0.282093	ENSG00000184428	ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676;ENST00000522041;ENST00000519591	T;T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24;1.24	3.55	-7.1	0.01547	DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, DNA binding, mixed alpha/beta motif, eukaryotic-type (1);DNA topoisomerase I, DNA binding, eukaryotic-type (2);	0.581986	0.13931	N	0.352874	T	0.00012	0.0000	N	0.01656	-0.775	0.46678	P	8.439999999999559E-4	B;B	0.20164	0.042;0.01	B;B	0.19666	0.026;0.02	T	0.16041	-1.0416	9	0.02654	T	1	.	9.912	0.41411	0.0:0.4416:0.0:0.5584	rs11544484;rs61685599;rs11544484	51;256	E7ESI1;Q969P6	.;TOP1M_HUMAN	I	256;158;158;158;158;158	ENSP00000328835:V256I;ENSP00000428369:V158I;ENSP00000429169:V158I;ENSP00000429181:V158I;ENSP00000427998:V158I;ENSP00000429177:V158I	ENSP00000328835:V256I	V	-	1	0	TOP1MT	144478080	1.000000	0.71417	0.013000	0.15412	0.002000	0.02628	1.413000	0.34725	-1.752000	0.01325	-1.077000	0.02231	GTT	C|0.689;T|0.311	0.311	strong		0.627	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
PRDM7	11105	hgsc.bcm.edu	37	16	90124871	90124871	+	Missense_Mutation	SNP	G	G	T	rs7206111	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:90124871G>T	ENST00000449207.2	-	10	1324	c.1305C>A	c.(1303-1305)aaC>aaA	p.N435K	PRDM7_ENST00000407825.1_Missense_Mutation_p.T135K|PRDM7_ENST00000325921.6_Missense_Mutation_p.T135K	NM_001098173.1	NP_001091643.1	Q9NQW5	PRDM7_HUMAN	PR domain containing 7	435			N -> K (in dbSNP:rs7206111).		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)	p.T135K(1)		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)		CGTTCCACATGTTGACTGAGA	0.483													.|||	436	0.0870607	0.1225	0.0259	5008	,	,		19923	0.1776		0.0517	False		,,,				2504	0.0256				p.N435K		Atlas-SNP	.											PRDM7,NS,carcinoma,0,1	PRDM7	53	1	1	Substitution - Missense(1)	stomach(1)	c.C1305A						PASS	.	G	LYS/ASN,LYS/THR	491,3905	229.1+/-243.8	22,447,1729	151.0	143.0	146.0		1305,404	2.7	0.1	16	dbSNP_116	146	512,8088	145.4+/-201.1	13,486,3801	no	missense,missense	PRDM7	NM_001098173.1,NM_052996.2	94,78	35,933,5530	TT,TG,GG		5.9535,11.1692,7.7178	possibly-damaging,possibly-damaging	435/493,135/172	90124871	1003,11993	2198	4300	6498	SO:0001583	missense	11105	exon10			CCACATGTTGACT	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.1305C>A	16.37:g.90124871G>T	ENSP00000396732:p.Asn435Lys	Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	329	51	0.155015	NM_001098173	A4Q9G8|Q08EM4|Q9NQW4	Missense_Mutation	SNP	ENST00000449207.2	37	CCDS45557.1	180|180	0.08241758241758242|0.08241758241758242	57|57	0.11585365853658537|0.11585365853658537	11|11	0.03038674033149171|0.03038674033149171	68|68	0.11888111888111888|0.11888111888111888	44|44	0.05804749340369393|0.05804749340369393	G|G	12.21|12.21	1.869148|1.869148	0.32977|0.32977	0.111692|0.111692	0.059535|0.059535	ENSG00000126856|ENSG00000126856	ENST00000449207|ENST00000325921;ENST00000407825	T|T;T	0.12879|0.50277	2.64|0.75;0.75	2.69|2.69	2.69|2.69	0.31865|0.31865	.|.	.|.	.|.	.|.	.|.	T|T	0.01454|0.01454	0.0047|0.0047	.|.	.|.	.|.	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B|D	0.23316|0.76494	0.083|0.999	B|D	0.19391|0.69142	0.025|0.962	T|T	0.32214|0.32214	-0.9915|-0.9915	6|6	.|.	.|.	.|.	0.1464|0.1464	7.4136|7.4136	0.27032|0.27032	0.0:0.0:0.7407:0.2593|0.0:0.0:0.7407:0.2593	rs7206111;rs52835907;rs7206111|rs7206111;rs52835907;rs7206111	435|135	Q9NQW5|Q9NQW5-2	PRDM7_HUMAN|.	K|K	435|135	ENSP00000396732:N435K|ENSP00000315512:T135K;ENSP00000385121:T135K	.|.	N|T	-|-	3|2	2|0	PRDM7|PRDM7	88652372|88652372	0.981000|0.981000	0.34729|0.34729	0.100000|0.100000	0.21137|0.21137	0.502000|0.502000	0.33828|0.33828	3.065000|3.065000	0.49994|0.49994	1.471000|1.471000	0.48121|0.48121	0.467000|0.467000	0.42956|0.42956	AAC|ACA	G|0.923;T|0.077	0.077	strong		0.483	PRDM7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420560.1		
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39465094	39465094	+	Missense_Mutation	SNP	C	C	T	rs12453338	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39465094C>T	ENST00000391352.1	-	1	411	c.412G>A	c.(412-414)Gtt>Att	p.V138I		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	138	11 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						GGCTCACAAACGGTGGCCTCA	0.562													T|||	1153	0.230232	0.2806	0.147	5008	,	,		24905	0.3204		0.1849	False		,,,				2504	0.1748				p.V138I		Atlas-SNP	.											KRTAP16-1,NS,carcinoma,+2,1	KRTAP16-1	12	1	0			c.G412A						scavenged	.																																			SO:0001583	missense	100505753	exon1			CACAAACGGTGGC	AP001708	CCDS56032.1	17q21.2	2012-07-04			ENSG00000212657	ENSG00000212657		"""Keratin associated proteins"""	18916	protein-coding gene	gene with protein product							Standard	NM_001146182		Approved	KAP16.1	uc021txi.1	A8MUX0	OTTHUMG00000133640	ENST00000391352.1:c.412G>A	17.37:g.39465094C>T	ENSP00000375147:p.Val138Ile	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	259	6	0.023166	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	493	0.22573260073260074	124	0.25203252032520324	56	0.15469613259668508	175	0.30594405594405594	138	0.1820580474934037	T	0.005	-2.230228	0.00280	.	.	ENSG00000212657	ENST00000391352	T	0.01335	5.0	3.88	-7.76	0.01232	.	.	.	.	.	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	.	.	.	.	.	.	T	0.51395	-0.8711	6	0.39692	T	0.17	.	10.9678	0.47422	0.0:0.6171:0.225:0.1579	rs12453338;rs12453338	.	.	.	I	138	ENSP00000375147:V138I	ENSP00000375147:V138I	V	-	1	0	KRTAP16-1	36718620	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-1.707000	0.01893	-2.488000	0.00518	-1.265000	0.01443	GTT	C|0.771;T|0.229	0.229	strong		0.562	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
PTGIS	5740	hgsc.bcm.edu	37	20	48140682	48140682	+	Silent	SNP	C	C	T	rs5628	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:48140682C>T	ENST00000244043.4	-	6	797	c.768G>A	c.(766-768)ctG>ctA	p.L256L	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	256					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	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 (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)	p.L256L(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	GGTAACTCTCCAGCCATTTGC	0.627													C|||	620	0.123802	0.2027	0.121	5008	,	,		19573	0.1002		0.0646	False		,,,				2504	0.1043				p.L256L		Atlas-SNP	.											PTGIS,NS,carcinoma,0,1	PTGIS	60	1	1	Substitution - coding silent(1)	stomach(1)	c.G768A						PASS	.	C		679,3727	286.0+/-278.5	48,583,1572	127.0	105.0	113.0		768	4.3	1.0	20	dbSNP_52	113	525,8075	147.4+/-202.8	11,503,3786	no	coding-synonymous	PTGIS	NM_000961.3		59,1086,5358	TT,TC,CC		6.1047,15.4108,9.2573		256/501	48140682	1204,11802	2203	4300	6503	SO:0001819	synonymous_variant	5740	exon6			ACTCTCCAGCCAT		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.768G>A	20.37:g.48140682C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	195	90	0.461538	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																			C|0.897;T|0.103	0.103	strong		0.627	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
ISM2	145501	hgsc.bcm.edu	37	14	77942316	77942316	+	Silent	SNP	G	G	A	rs3742732	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77942316G>A	ENST00000342219.4	-	7	1394	c.1338C>T	c.(1336-1338)gaC>gaT	p.D446D	ISM2_ENST00000493585.1_3'UTR|ISM2_ENST00000429906.1_Silent_p.D365D|ISM2_ENST00000393684.3_Silent_p.D358D|ISM2_ENST00000412904.1_Silent_p.D365D	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	446	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.					extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						CCTGGTGCTCGTCCTGTAGGC	0.652													G|||	322	0.0642971	0.0363	0.1571	5008	,	,		17437	0.0149		0.0765	False		,,,				2504	0.0746				p.D446D		Atlas-SNP	.											.	ISM2	68	.	0			c.C1338T						PASS	.	G	,	210,4196	127.8+/-164.7	6,198,1999	36.0	38.0	37.0		,1338	-3.0	0.3	14	dbSNP_107	37	775,7825	179.2+/-228.4	32,711,3557	no	utr-3,coding-synonymous	ISM2	NM_182509.3,NM_199296.2	,	38,909,5556	AA,AG,GG		9.0116,4.7662,7.5734	,	,446/572	77942316	985,12021	2203	4300	6503	SO:0001819	synonymous_variant	145501	exon7			GTGCTCGTCCTGT	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"""thrombospondin and AMOP containing isthmin-like 1"""	612684	"""thrombospondin, type I domain-containing 3"", ""thrombospondin, type I, domain containing 3"", ""isthmin 2 homolog (zebrafish)"""	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.1338C>T	14.37:g.77942316G>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Silent	SNP	ENST00000342219.4	37	CCDS9864.1																																																																																			G|0.930;A|0.070	0.070	strong		0.652	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509	
MYO7A	4647	hgsc.bcm.edu	37	11	76922946	76922946	+	Silent	SNP	G	G	A	rs11237123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:76922946G>A	ENST00000409709.3	+	46	6590	c.6318G>A	c.(6316-6318)aaG>aaA	p.K2106K	MYO7A_ENST00000409619.2_Silent_p.K2057K|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000458637.2_Silent_p.K2068K	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2106	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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						TCATCTTCAAGTGGCCCACCT	0.562													G|||	980	0.195687	0.3994	0.147	5008	,	,		15615	0.0635		0.2227	False		,,,				2504	0.0634				p.K2106K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6318A						PASS	.	G	,	1490,2892		279,932,980	57.0	60.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6318,6204	4.6	1.0	11	dbSNP_120	59	1705,6857		175,1355,2751	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	454,2287,3731	AA,AG,GG		19.9136,34.0027,24.6833	,	2106/2216,2068/2176	76922946	3195,9749	2191	4281	6472	SO:0001819	synonymous_variant	4647	exon46			CTTCAAGTGGCCC	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.6318G>A	11.37:g.76922946G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			G|0.785;A|0.215	0.215	strong		0.562	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
NACAD	23148	hgsc.bcm.edu	37	7	45122324	45122324	+	Missense_Mutation	SNP	C	C	A	rs3735493	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:45122324C>A	ENST00000490531.2	-	2	3474	c.3455G>T	c.(3454-3456)tGc>tTc	p.C1152F		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1152			C -> F (in dbSNP:rs3735493).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						AGACTCTGGGCAGGAGTCCAG	0.662													C|||	553	0.110423	0.0166	0.1657	5008	,	,		15349	0.121		0.174	False		,,,				2504	0.1217				p.C1152F		Atlas-SNP	.											.	NACAD	44	.	0			c.G3455T						PASS	.						19.0	28.0	25.0					7																	45122324		692	1590	2282	SO:0001583	missense	23148	exon2			TCTGGGCAGGAGT	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.3455G>T	7.37:g.45122324C>A	ENSP00000420477:p.Cys1152Phe	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	153	61	0.398693	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	262	0.11996336996336997	8	0.016260162601626018	64	0.17679558011049723	59	0.10314685314685315	131	0.17282321899736147	c	14.82	2.649534	0.47362	.	.	ENSG00000136274	ENST00000490531	T	0.12984	2.63	3.08	2.16	0.27623	.	.	.	.	.	T	0.00039	0.0001	L	0.32530	0.975	0.80722	P	0.0	D	0.65815	0.995	P	0.57911	0.829	T	0.24333	-1.0163	8	0.42905	T	0.14	-2.9206	9.0995	0.36660	0.0:0.557:0.443:0.0	rs3735493;rs10377947;rs3735493	1152	O15069	NACAD_HUMAN	F	1152	ENSP00000420477:C1152F	ENSP00000420477:C1152F	C	-	2	0	NACAD	45088849	0.000000	0.05858	0.319000	0.25293	0.438000	0.31896	-0.135000	0.10420	0.576000	0.29452	0.290000	0.19541	TGC	C|0.891;A|0.109	0.109	strong		0.662	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
C3orf62	375341	hgsc.bcm.edu	37	3	49313978	49313978	+	Missense_Mutation	SNP	C	C	T	rs13077498	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	273	0	0		WXS	Illumina HiSeq	Phase_I	189	82	0.433862	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	
ADCY10	55811	hgsc.bcm.edu	37	1	167839578	167839578	+	Silent	SNP	G	G	A	rs67878347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:167839578G>A	ENST00000367851.4	-	14	1717	c.1533C>T	c.(1531-1533)gtC>gtT	p.V511V	ADCY10_ENST00000545172.1_Silent_p.V358V|ADCY10_ENST00000367848.1_Silent_p.V419V	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	511					cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CATACATTAAGACTTGGCTGC	0.343													G|||	629	0.125599	0.0356	0.2161	5008	,	,		18173	0.126		0.2068	False		,,,				2504	0.0992				p.V511V		Atlas-SNP	.											ADCY10,brain,glioma,0,1	ADCY10	175	1	0			c.C1533T						PASS	.	G	,	321,4085	168.3+/-199.2	12,297,1894	112.0	107.0	108.0		1074,1533	0.7	0.4	1	dbSNP_130	108	1775,6825	320.4+/-314.6	204,1367,2729	no	coding-synonymous,coding-synonymous	ADCY10	NM_001167749.1,NM_018417.4	,	216,1664,4623	AA,AG,GG		20.6395,7.2855,16.1156	,	358/1458,511/1611	167839578	2096,10910	2203	4300	6503	SO:0001819	synonymous_variant	55811	exon14			CATTAAGACTTGG	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"""Adenylate cyclases"""	21285	protein-coding gene	gene with protein product	"""soluble adenylyl cyclase"", ""Hypercalciuria, absorptive, 2"""	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.1533C>T	1.37:g.167839578G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	169	103	0.609467	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Silent	SNP	ENST00000367851.4	37	CCDS1265.1																																																																																			G|0.835;A|0.165	0.165	strong		0.343	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
OR6M1	390261	hgsc.bcm.edu	37	11	123676388	123676388	+	Missense_Mutation	SNP	G	G	A	rs76301014	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:123676388G>A	ENST00000309154.2	-	1	707	c.670C>T	c.(670-672)Cgt>Tgt	p.R224C		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, 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)			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)		GAGGGGATACGCAGGATGGTA	0.493													G|||	617	0.123203	0.0605	0.121	5008	,	,		20252	0.0516		0.1968	False		,,,				2504	0.2076				p.R224C		Atlas-SNP	.											.	OR6M1	60	.	0			c.C670T						PASS	.	G	CYS/ARG	350,4054	181.9+/-209.8	11,328,1863	75.0	65.0	68.0		670	-0.9	0.0	11	dbSNP_131	68	1592,7006	295.0+/-302.2	138,1316,2845	yes	missense	OR6M1	NM_001005325.1	180	149,1644,4708	AA,AG,GG		18.5159,7.9473,14.9362	benign	224/314	123676388	1942,11060	2202	4299	6501	SO:0001583	missense	390261	exon1			GGATACGCAGGAT	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.670C>T	11.37:g.123676388G>A	ENSP00000311038:p.Arg224Cys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	95	66	0.694737	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	283	0.1295787545787546	33	0.06707317073170732	53	0.1464088397790055	40	0.06993006993006994	157	0.20712401055408972	G	1.766	-0.485686	0.04352	0.079473	0.185159	ENSG00000196099	ENST00000309154	T	0.00267	8.38	3.48	-0.874	0.10631	GPCR, rhodopsin-like superfamily (1);	1.150030	0.06870	U	0.800580	T	0.00012	0.0000	M	0.85777	2.775	0.80722	P	0.0	B	0.16802	0.019	B	0.20955	0.032	T	0.29882	-0.9997	9	0.87932	D	0	.	3.6471	0.08189	0.2078:0.0:0.301:0.4912	.	224	Q8NGM8	OR6M1_HUMAN	C	224	ENSP00000311038:R224C	ENSP00000311038:R224C	R	-	1	0	OR6M1	123181598	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.461000	0.06712	-0.456000	0.07043	-0.768000	0.03414	CGT	G|0.859;A|0.141	0.141	strong		0.493	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325	
MUC17	140453	hgsc.bcm.edu	37	7	100678075	100678075	+	Silent	SNP	C	C	T	rs147945988	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678075C>T	ENST00000306151.4	+	3	3442	c.3378C>T	c.(3376-3378)gtC>gtT	p.V1126V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1126	59 X approximate tandem repeats.|Ser-rich.				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)					CAACTCCTGTCGACACCAGCA	0.517													T|||	163	0.0325479	0.0333	0.013	5008	,	,		37322	0.0734		0.0229	False		,,,				2504	0.0133				p.V1126V		Atlas-SNP	.											.	MUC17	804	.	0			c.C3378T						PASS	.						403.0	345.0	365.0					7																	100678075		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TCCTGTCGACACC	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.3378C>T	7.37:g.100678075C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	529	80	0.151229	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			C|0.998;T|0.002	0.002	strong		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PEX11G	92960	hgsc.bcm.edu	37	19	7547074	7547074	+	Missense_Mutation	SNP	A	A	C	rs2303146	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:7547074A>C	ENST00000221480.1	-	3	281	c.273T>G	c.(271-273)tgT>tgG	p.C91W	PEX11G_ENST00000593942.1_Missense_Mutation_p.C21W|PEX11G_ENST00000599519.1_5'UTR	NM_001270539.1|NM_080662.3	NP_001257468.1|NP_542393.1	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	91			C -> W (in dbSNP:rs2303146).		peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						GGACGGAGACACAGCGGACAA	0.632													C|||	2291	0.457468	0.7201	0.3055	5008	,	,		18080	0.4435		0.326	False		,,,				2504	0.3599				p.C91W		Atlas-SNP	.											.	PEX11G	16	.	0			c.T273G						PASS	.	C	TRP/CYS	2773,1611		888,997,307	35.0	31.0	33.0		273	-3.5	0.0	19	dbSNP_100	33	2669,5909		450,1769,2070	yes	missense	PEX11G	NM_080662.2	215	1338,2766,2377	CC,CA,AA		31.1145,36.7473,41.9843	benign	91/242	7547074	5442,7520	2192	4289	6481	SO:0001583	missense	92960	exon3			GGAGACACAGCGG	BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883			20208	protein-coding gene	gene with protein product		607583				12417726	Standard	NM_080662		Approved		uc002mgk.2	Q96HA9		ENST00000221480.1:c.273T>G	19.37:g.7547074A>C	ENSP00000221480:p.Cys91Trp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_001270539	Q8NDM0	Missense_Mutation	SNP	ENST00000221480.1	37	CCDS12178.1	922	0.42216117216117216	336	0.6829268292682927	101	0.27900552486187846	243	0.42482517482517484	242	0.31926121372031663	C	0.007	-1.998520	0.00435	0.632527	0.311145	ENSG00000104883	ENST00000221480	T	0.40476	1.03	4.76	-3.55	0.04639	.	0.407958	0.31438	N	0.007641	T	0.00012	0.0000	N	0.03891	-0.335	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.39231	-0.9624	9	0.26408	T	0.33	0.2335	9.6386	0.39824	0.5017:0.2648:0.2335:0.0	rs2303146;rs61461499;rs2303146	91	Q96HA9	PX11C_HUMAN	W	91	ENSP00000221480:C91W	ENSP00000221480:C91W	C	-	3	2	PEX11G	7453074	0.004000	0.15560	0.000000	0.03702	0.023000	0.10783	-0.078000	0.11375	-1.121000	0.02949	-0.217000	0.12591	TGT	A|0.557;C|0.443	0.443	strong		0.632	PEX11G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458965.1	NM_080662	
KNCN	148930	hgsc.bcm.edu	37	1	47013431	47013431	+	Missense_Mutation	SNP	G	G	A	rs61735709	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:47013431G>A	ENST00000481882.2	-	4	657	c.346C>T	c.(346-348)Ccg>Tcg	p.P116S	KNCN_ENST00000396314.3_Missense_Mutation_p.P93S|MKNK1-AS1_ENST00000602433.1_RNA|KNCN_ENST00000524908.1_5'UTR			A6PVL3	KNCN_HUMAN	kinocilin	116						apical plasma membrane (GO:0016324)|ciliary basal body (GO:0036064)|cuticular plate (GO:0032437)|integral component of membrane (GO:0016021)|kinocilium (GO:0060091)|neuronal cell body (GO:0043025)				central_nervous_system(1)|endometrium(1)|lung(1)|ovary(1)	4	Acute lymphoblastic leukemia(166;0.155)					CGGGTCCCCGGCTTCAGCTTC	0.667													G|||	9	0.00179712	0.0	0.0014	5008	,	,		15347	0.0		0.008	False		,,,				2504	0.0				p.P93S		Atlas-SNP	.											.	KNCN	7	.	0			c.C277T						PASS	.	G	SER/PRO	6,4274		0,6,2134	9.0	10.0	10.0		277	0.7	1.0	1	dbSNP_129	10	87,8313		0,87,4113	yes	missense	KNCN	NM_001097611.1	74	0,93,6247	AA,AG,GG		1.0357,0.1402,0.7334	benign	93/102	47013431	93,12587	2140	4200	6340	SO:0001583	missense	148930	exon3			TCCCCGGCTTCAG	AK056573	CCDS44133.1	1p33	2014-02-12	2006-10-26		ENSG00000162456	ENSG00000162456			26488	protein-coding gene	gene with protein product		611455				15855039	Standard	NM_001097611		Approved	FLJ32011, KINO, L5	uc001cpy.2	A6PVL3	OTTHUMG00000007987	ENST00000481882.2:c.346C>T	1.37:g.47013431G>A	ENSP00000419705:p.Pro116Ser	Somatic	389	0	0		WXS	Illumina HiSeq	Phase_I	273	61	0.223443	NM_001097611	A8MXE3	Missense_Mutation	SNP	ENST00000481882.2	37		9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	13.21	2.168955	0.38315	0.001402	0.010357	ENSG00000162456	ENST00000481882;ENST00000396314	.	.	.	3.73	0.731	0.18277	.	.	.	.	.	T	0.19886	0.0478	.	.	.	0.27084	N	0.963004	B	0.02656	0.0	B	0.08055	0.003	T	0.23190	-1.0195	7	0.59425	D	0.04	-1.3298	2.4743	0.04572	0.1074:0.1882:0.5104:0.194	.	93	A6PVL3-2	.	S	116;93	.	ENSP00000379607:P93S	P	-	1	0	KNCN	46786018	1.000000	0.71417	0.975000	0.42487	0.225000	0.24961	1.216000	0.32443	0.175000	0.19841	-0.314000	0.08810	CCG	G|0.995;A|0.005	0.005	strong		0.667	KNCN-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000316334.2	NM_182516	
AKAP9	10142	hgsc.bcm.edu	37	7	91632306	91632306	+	Silent	SNP	C	C	T	rs1989779	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91632306C>T	ENST00000359028.2	+	9	3336	c.3111C>T	c.(3109-3111)acC>acT	p.T1037T	AKAP9_ENST00000356239.3_Silent_p.T1025T|AKAP9_ENST00000358100.2_Silent_p.T1037T			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1037					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)			GAGTTGTGACCATGACAAGCA	0.343			T	BRAF	papillary thyroid								T|||	4687	0.935903	0.9894	0.9409	5008	,	,		19914	0.9673		0.8787	False		,,,				2504	0.8865				p.T1025T		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C3075T						PASS	.	T	,	4283,123	90.6+/-129.3	2082,119,2	78.0	79.0	79.0		3075,3075	-5.9	0.0	7	dbSNP_92	79	7505,1095	227.9+/-263.1	3277,951,72	no	coding-synonymous,coding-synonymous	AKAP9	NM_005751.4,NM_147185.2	,	5359,1070,74	TT,TC,CC		12.7326,2.7916,9.3649	,	1025/3908,1025/3900	91632306	11788,1218	2203	4300	6503	SO:0001819	synonymous_variant	10142	exon8			TGTGACCATGACA	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.3111C>T	7.37:g.91632306C>T		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	229	229	1	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				C|0.082;T|0.918	0.918	strong		0.343	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
CSPG4	1464	hgsc.bcm.edu	37	15	75982186	75982186	+	Missense_Mutation	SNP	G	G	A	rs199819221	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	131	5	0.0381679		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	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	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65350374	65350374	+	Silent	SNP	A	A	G	rs36303	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:65350374A>G	ENST00000284037.5	+	21	3617	c.3228A>G	c.(3226-3228)cgA>cgG	p.R1076R	ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000380936.1_Silent_p.R1076R|ERBB2IP_ENST00000511297.1_Silent_p.R1072R|ERBB2IP_ENST00000380935.1_Silent_p.R1076R|ERBB2IP_ENST00000380943.2_Silent_p.R1076R|ERBB2IP_ENST00000380939.2_Silent_p.R1076R|ERBB2IP_ENST00000506030.1_Silent_p.R1076R|ERBB2IP_ENST00000380938.2_Silent_p.R1076R|ERBB2IP_ENST00000508515.1_Silent_p.R1076R	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1076					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		CAATCCAGCGACAAAGTAGTG	0.473													A|||	1050	0.209665	0.09	0.2968	5008	,	,		19190	0.4623		0.1203	False		,,,				2504	0.1411				p.R1076R		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.A3228G						PASS	.	A	,	418,3988	205.2+/-227.1	11,396,1796	128.0	123.0	125.0		3228,3228	0.3	1.0	5	dbSNP_76	125	1191,7409	241.0+/-271.5	84,1023,3193	no	coding-synonymous,coding-synonymous	ERBB2IP	NM_001006600.1,NM_018695.2	,	95,1419,4989	GG,GA,AA		13.8488,9.4871,12.3712	,	1076/1303,1076/1372	65350374	1609,11397	2203	4300	6503	SO:0001819	synonymous_variant	55914	exon21			CCAGCGACAAAGT		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.3228A>G	5.37:g.65350374A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	37	CCDS58953.1																																																																																			A|0.830;G|0.170	0.170	strong		0.473	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058090	79058090	+	Missense_Mutation	SNP	A	A	G	rs2929158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	62	15	0.241935	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	
LURAP1L	286343	hgsc.bcm.edu	37	9	12821695	12821695	+	Missense_Mutation	SNP	T	T	C	rs61755264	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:12821695T>C	ENST00000319264.3	+	2	1318	c.623T>C	c.(622-624)aTa>aCa	p.I208T		NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	211																	AGCTCCCTCATAGAGGACTCA	0.493													T|||	33	0.00658946	0.0008	0.0144	5008	,	,		18761	0.0		0.0129	False		,,,				2504	0.0092				p.I208T		Atlas-SNP	.											.	.	.	.	0			c.T623C						PASS	.	T	THR/ILE	7,4399	12.9+/-30.5	0,7,2196	182.0	164.0	170.0		623	4.4	0.4	9	dbSNP_129	170	78,8522	45.8+/-104.6	0,78,4222	yes	missense	C9orf150	NM_203403.1	89	0,85,6418	CC,CT,TT		0.907,0.1589,0.6535	benign	208/229	12821695	85,12921	2203	4300	6503	SO:0001583	missense	286343	exon2			CCCTCATAGAGGA	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.623T>C	9.37:g.12821695T>C	ENSP00000321026:p.Ile208Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Missense_Mutation	SNP	ENST00000319264.3	37	CCDS6473.1	17	0.007783882783882784	0	0.0	7	0.019337016574585635	0	0.0	10	0.013192612137203167	T	8.760	0.923302	0.18056	0.001589	0.00907	ENSG00000153714	ENST00000319264	T	0.47528	0.84	5.59	4.45	0.53987	.	1.264020	0.05579	N	0.572551	T	0.20659	0.0497	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.17899	-1.0354	10	0.44086	T	0.13	.	6.1872	0.20503	0.0:0.1423:0.1354:0.7223	rs61755264	211	Q8IV03	CI150_HUMAN	T	208	ENSP00000321026:I208T	ENSP00000321026:I208T	I	+	2	0	C9orf150	12811695	0.131000	0.22433	0.357000	0.25798	0.813000	0.45954	1.783000	0.38664	0.956000	0.37904	0.460000	0.39030	ATA	T|0.992;C|0.008	0.008	strong		0.493	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
LENG9	94059	hgsc.bcm.edu	37	19	54973280	54973280	+	Missense_Mutation	SNP	C	C	G	rs10423424	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54973280C>G	ENST00000333834.4	-	1	1614	c.1496G>C	c.(1495-1497)cGc>cCc	p.R499P		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	499			R -> P (in dbSNP:rs10423424).				catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		TCACTCCAGGCGGATCTCAGC	0.602													G|||	2900	0.579073	0.77	0.464	5008	,	,		16629	0.3651		0.5626	False		,,,				2504	0.6401				p.R499P		Atlas-SNP	.											.	LENG9	46	.	0			c.G1496C						PASS	.	G	PRO/ARG	3282,1124		1235,812,156	59.0	68.0	65.0		1496	3.9	0.0	19	dbSNP_119	65	4680,3914		1273,2134,890	yes	missense	LENG9	NM_198988.1	103	2508,2946,1046	GG,GC,CC		45.5434,25.5107,38.7538	benign	499/502	54973280	7962,5038	2203	4297	6500	SO:0001583	missense	94059	exon1			TCCAGGCGGATCT	AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.1496G>C	19.37:g.54973280C>G	ENSP00000331647:p.Arg499Pro	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	55	54	0.981818	NM_198988	B2VAM3	Missense_Mutation	SNP	ENST00000333834.4	37	CCDS12895.2	1226	0.5613553113553114	408	0.8292682926829268	193	0.5331491712707183	201	0.3513986013986014	424	0.5593667546174143	G	0.689	-0.795374	0.02862	0.744893	0.544566	ENSG00000182909	ENST00000333834	T	0.37584	1.19	4.98	3.9	0.45041	RNA ligase/cyclic nucleotide phosphodiesterase (1);	1.097220	0.07030	N	0.828234	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	0.39396	-0.9616	9	0.02654	T	1	-10.4024	8.3798	0.32463	0.0:0.1707:0.6521:0.1772	rs10423424;rs57017426;rs10423424	499	Q96B70	LENG9_HUMAN	P	499	ENSP00000331647:R499P	ENSP00000331647:R499P	R	-	2	0	LENG9	59665092	0.003000	0.15002	0.008000	0.14137	0.023000	0.10783	1.083000	0.30815	0.581000	0.29539	-0.120000	0.15030	CGC	C|0.414;G|0.586	0.586	strong		0.602	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988	
PTPRT	11122	hgsc.bcm.edu	37	20	40714479	40714479	+	Silent	SNP	G	G	A	rs2016647	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:40714479G>A	ENST00000373187.1	-	28	3860	c.3861C>T	c.(3859-3861)taC>taT	p.Y1287Y	PTPRT_ENST00000373190.1_Silent_p.Y1286Y|PTPRT_ENST00000373184.1_Silent_p.Y1297Y|PTPRT_ENST00000373198.4_Silent_p.Y1306Y|PTPRT_ENST00000356100.2_Silent_p.Y1296Y|PTPRT_ENST00000373201.1_Silent_p.Y1277Y|PTPRT_ENST00000373193.3_Silent_p.Y1290Y			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1287	Tyrosine-protein phosphatase 2. {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)				TCTCAGGCCAGTACTGCATAC	0.498													G|||	721	0.14397	0.115	0.1671	5008	,	,		17005	0.0734		0.2425	False		,,,				2504	0.138				p.Y1306Y		Atlas-SNP	.											.	PTPRT	372	.	0			c.C3918T						PASS	.	G	,	518,3350		36,446,1452	67.0	69.0	68.0		3861,3918	4.3	1.0	20	dbSNP_92	68	2056,6218		232,1592,2313	no	coding-synonymous,coding-synonymous	PTPRT	NM_007050.5,NM_133170.3	,	268,2038,3765	AA,AG,GG		24.8489,13.3919,21.1991	,	1287/1442,1306/1461	40714479	2574,9568	1934	4137	6071	SO:0001819	synonymous_variant	11122	exon29			AGGCCAGTACTGC	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.3861C>T	20.37:g.40714479G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	124	64	0.516129	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																			G|0.823;A|0.177	0.177	strong		0.498	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507379	195507379	+	Missense_Mutation	SNP	G	G	C	rs371423143		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195507379G>C	ENST00000463781.3	-	2	11531	c.11072C>G	c.(11071-11073)aCa>aGa	p.T3691R	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3691R	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	120	0	0		WXS	Illumina HiSeq	Phase_I	164	19	0.115854	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	
ITGA11	22801	hgsc.bcm.edu	37	15	68606192	68606192	+	Missense_Mutation	SNP	C	C	T	rs368307734		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:68606192C>T	ENST00000315757.7	-	23	2893	c.2807G>A	c.(2806-2808)cGg>cAg	p.R936Q	ITGA11_ENST00000423218.2_Missense_Mutation_p.R936Q	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	936					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						GGTGCTGTCCCGCTCATTACT	0.637																																					p.R936Q		Atlas-SNP	.											.	ITGA11	110	.	0			c.G2807A						PASS	.	C	GLN/ARG	0,4316		0,0,2158	80.0	84.0	83.0		2807	2.6	1.0	15		83	2,8508		0,2,4253	no	missense	ITGA11	NM_001004439.1	43	0,2,6411	TT,TC,CC		0.0235,0.0,0.0156	benign	936/1189	68606192	2,12824	2158	4255	6413	SO:0001583	missense	22801	exon23			CTGTCCCGCTCAT	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.2807G>A	15.37:g.68606192C>T	ENSP00000327290:p.Arg936Gln	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	100	78	0.78	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386513	0.25031	0.0	2.35E-4	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.39997	1.05;1.05	4.94	2.58	0.30949	Integrin alpha-2 (1);	0.362684	0.31071	N	0.008308	T	0.14657	0.0354	N	0.02539	-0.55	0.22581	N	0.998964	B;B	0.09022	0.002;0.0	B;B	0.13407	0.009;0.001	T	0.24297	-1.0164	10	0.15499	T	0.54	.	5.5239	0.16947	0.1525:0.0858:0.0:0.7617	.	936;936	A8K8T0;Q9UKX5	.;ITA11_HUMAN	Q	936;936;571	ENSP00000327290:R936Q;ENSP00000403392:R936Q	ENSP00000327290:R936Q	R	-	2	0	ITGA11	66393246	0.984000	0.35163	0.987000	0.45799	0.698000	0.40448	2.853000	0.48317	0.228000	0.21019	-0.367000	0.07326	CGG	.	.	weak		0.637	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
CCDC110	256309	hgsc.bcm.edu	37	4	186380846	186380846	+	Missense_Mutation	SNP	A	A	T	rs7698680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:186380846A>T	ENST00000307588.3	-	6	970	c.895T>A	c.(895-897)Ttg>Atg	p.L299M	CCDC110_ENST00000510617.1_Missense_Mutation_p.L299M|CCDC110_ENST00000507501.1_5'Flank|CCDC110_ENST00000393540.3_Missense_Mutation_p.L262M	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	299			L -> M (in dbSNP:rs7698680).			nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		TTACCGTCCAAGTTTTCTTCC	0.338													T|||	1931	0.385583	0.2837	0.3631	5008	,	,		18589	0.2827		0.5378	False		,,,				2504	0.4888				p.L299M		Atlas-SNP	.											CCDC110,NS,carcinoma,0,1	CCDC110	78	1	0			c.T895A						PASS	.	T	MET/LEU,MET/LEU	1477,2927	660.9+/-400.8	242,993,967	70.0	71.0	71.0		784,895	2.0	0.2	4	dbSNP_116	71	4852,3744	523.4+/-380.3	1373,2106,819	yes	missense,missense	CCDC110	NM_001145411.1,NM_152775.3	15,15	1615,3099,1786	TT,TA,AA		43.5551,33.5377,48.6846	benign,benign	262/797,299/834	186380846	6329,6671	2202	4298	6500	SO:0001583	missense	256309	exon6			CGTCCAAGTTTTC	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.895T>A	4.37:g.186380846A>T	ENSP00000306776:p.Leu299Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	74	16	0.216216	NM_152775	Q86YI9|Q8N7W0	Missense_Mutation	SNP	ENST00000307588.3	37	CCDS3843.1	857	0.3923992673992674	151	0.30691056910569103	147	0.40607734806629836	159	0.27797202797202797	400	0.5277044854881267	T	0.001	-3.256225	0.00021	0.335377	0.564449	ENSG00000168491	ENST00000393540;ENST00000307588;ENST00000510617	T;T;T	0.06068	3.35;3.36;3.37	5.8	2.03	0.26663	.	0.991008	0.08207	N	0.981349	T	0.00012	0.0000	N	0.01048	-1.04	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	0.42682	-0.9437	9	0.02654	T	1	-0.03	3.8067	0.08780	0.2471:0.2772:0.0:0.4757	rs7698680;rs17224991;rs52809202;rs59414924;rs7698680	299;262;299	B4DZA2;Q8TBZ0-2;Q8TBZ0	.;.;CC110_HUMAN	M	262;299;299	ENSP00000377172:L262M;ENSP00000306776:L299M;ENSP00000427246:L299M	ENSP00000306776:L299M	L	-	1	2	CCDC110	186617840	0.000000	0.05858	0.183000	0.23137	0.020000	0.10135	-0.753000	0.04792	0.139000	0.18822	-1.071000	0.02255	TTG	A|0.555;T|0.445	0.445	strong		0.338	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
AVL9	23080	hgsc.bcm.edu	37	7	32598630	32598630	+	Missense_Mutation	SNP	T	T	A	rs2290213	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:32598630T>A	ENST00000318709.4	+	10	990	c.769T>A	c.(769-771)Tgt>Agt	p.C257S	AVL9_ENST00000404479.1_Missense_Mutation_p.C257S|AVL9_ENST00000409301.1_Missense_Mutation_p.C257S	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	257			C -> S (in dbSNP:rs2290213).		cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AAGTAACCCATGTGCAGATGA	0.443													T|||	780	0.155751	0.1793	0.1066	5008	,	,		18083	0.129		0.1243	False		,,,				2504	0.2188				p.C257S		Atlas-SNP	.											.	AVL9	66	.	0			c.T769A						PASS	.	T	SER/CYS	794,3612	314.7+/-293.7	89,616,1498	97.0	94.0	95.0		769	-1.3	0.0	7	dbSNP_100	95	1098,7502	228.0+/-263.2	64,970,3266	yes	missense	AVL9	NM_015060.1	112	153,1586,4764	AA,AT,TT		12.7674,18.0209,14.5471	benign	257/649	32598630	1892,11114	2203	4300	6503	SO:0001583	missense	23080	exon10			AACCCATGTGCAG	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.769T>A	7.37:g.32598630T>A	ENSP00000315568:p.Cys257Ser	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	177	117	0.661017	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	37	CCDS34613.1	327	0.14972527472527472	98	0.1991869918699187	39	0.10773480662983426	91	0.1590909090909091	99	0.13060686015831136	T	0.014	-1.585371	0.00872	0.180209	0.127674	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000404479;ENST00000446718	T;T;T;T	0.39787	1.11;1.11;1.07;1.06	5.31	-1.29	0.09288	.	0.871343	0.10468	N	0.671197	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	0.01281	0.0;0.0;0.0	T	0.31916	-0.9926	9	0.08381	T	0.77	-28.4598	6.015	0.19598	0.1203:0.42:0.0:0.4597	rs2290213;rs52798277;rs2290213	257;257;257	Q8N6Z3;Q8NBF6-2;Q8NBF6	.;.;AVL9_HUMAN	S	257;257;257;257;188	ENSP00000315568:C257S;ENSP00000387011:C257S;ENSP00000385242:C257S;ENSP00000395134:C188S	ENSP00000315568:C257S	C	+	1	0	AVL9	32565155	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-0.114000	0.10757	-0.455000	0.07054	-0.326000	0.08463	TGT	A|0.150;C|0.000;T|0.850	0.150	strong		0.443	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
OR2T27	403239	hgsc.bcm.edu	37	1	248813271	248813271	+	Silent	SNP	C	C	A	rs2802081	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248813271C>A	ENST00000344889.3	-	1	914	c.915G>T	c.(913-915)gtG>gtT	p.V305V		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	305						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)			CACACCTCCCCACAACCTTCT	0.443													c|||	332	0.0662939	0.025	0.0749	5008	,	,		20910	0.0615		0.1074	False		,,,				2504	0.0787				p.V305V		Atlas-SNP	.											.	OR2T27	52	.	0			c.G915T						PASS	.						65.0	69.0	68.0					1																	248813271		2180	4274	6454	SO:0001819	synonymous_variant	403239	exon1			CCTCCCCACAACC		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.915G>T	1.37:g.248813271C>A		Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	399	59	0.14787	NM_001001824		Silent	SNP	ENST00000344889.3	37	CCDS31124.1																																																																																			C|0.779;A|0.221	0.221	strong		0.443	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
ZNF142	7701	hgsc.bcm.edu	37	2	219508372	219508372	+	Missense_Mutation	SNP	A	A	T	rs3770213	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219508372A>T	ENST00000449707.1	-	8	3288	c.2867T>A	c.(2866-2868)cTt>cAt	p.L956H	ZNF142_ENST00000411696.2_Missense_Mutation_p.L956H	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	956			L -> H (in dbSNP:rs3770213).		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)		GACTGTGGCAAGAGGCTCTTC	0.562													A|||	959	0.191494	0.028	0.3271	5008	,	,		18398	0.0556		0.3757	False		,,,				2504	0.2669				p.L956H	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.T2867A						PASS	.	A	HIS/LEU	298,3464		9,280,1592	199.0	203.0	202.0		2867	-1.6	0.0	2	dbSNP_107	202	3128,5106		625,1878,1614	yes	missense	ZNF142	NM_001105537.1	99	634,2158,3206	TT,TA,AA		37.9888,7.9213,28.5595	possibly-damaging	956/1688	219508372	3426,8570	1881	4117	5998	SO:0001583	missense	7701	exon8			GTGGCAAGAGGCT	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.2867T>A	2.37:g.219508372A>T	ENSP00000408643:p.Leu956His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	99	29	0.292929	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	459	0.21016483516483517	26	0.052845528455284556	114	0.3149171270718232	36	0.06293706293706294	283	0.3733509234828496	A	15.87	2.960372	0.53400	0.079213	0.379888	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.14144	2.53;2.53	3.93	-1.58	0.08479	.	2.400410	0.01281	N	0.009736	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D;D	0.57257	0.979;0.979	P;P	0.46975	0.533;0.533	T	0.39396	-0.9616	9	0.15499	T	0.54	-14.8295	5.5057	0.16852	0.4894:0.1476:0.363:0.0	rs3770213;rs17463262;rs52792951;rs3770213	956;793	P52746;A8MWU9	ZN142_HUMAN;.	H	956	ENSP00000408643:L956H;ENSP00000398798:L956H	ENSP00000398798:L956H	L	-	2	0	ZNF142	219216616	0.000000	0.05858	0.000000	0.03702	0.484000	0.33280	0.104000	0.15313	-0.052000	0.13311	0.459000	0.35465	CTT	A|0.741;N|0.000	.	strong		0.562	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
EIF4G2	1982	hgsc.bcm.edu	37	11	10825093	10825093	+	Silent	SNP	C	C	T	rs35388213	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:10825093C>T	ENST00000526148.1	-	9	1257	c.747G>A	c.(745-747)gaG>gaA	p.E249E	SNORD97_ENST00000459187.1_RNA|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000339995.5_Silent_p.E249E|EIF4G2_ENST00000396525.2_Silent_p.E249E|EIF4G2_ENST00000525995.1_5'Flank|EIF4G2_ENST00000525681.1_Silent_p.E249E	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		ACTCCAAATCCTCTCCCATAT	0.428													C|||	34	0.00678914	0.0	0.0231	5008	,	,		20421	0.0		0.0159	False		,,,				2504	0.002				p.E249E		Atlas-SNP	.											.	EIF4G2	89	.	0			c.G747A						PASS	.	C	,,	17,4385	24.3+/-50.5	0,17,2184	161.0	147.0	152.0		747,747,747	6.1	1.0	11	dbSNP_126	152	204,8384	88.4+/-150.7	2,200,4092	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4G2	NM_001042559.2,NM_001172705.1,NM_001418.3	,,	2,217,6276	TT,TC,CC		2.3754,0.3862,1.7013	,,	249/870,249/908,249/908	10825093	221,12769	2201	4294	6495	SO:0001819	synonymous_variant	1982	exon9			CAAATCCTCTCCC	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.747G>A	11.37:g.10825093C>T		Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	199	92	0.462312	NM_001172705		Silent	SNP	ENST00000526148.1	37	CCDS31428.1																																																																																			C|0.984;T|0.016	0.016	strong		0.428	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
HDHD3	81932	hgsc.bcm.edu	37	9	116136262	116136262	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116136262G>A	ENST00000238379.5	-	2	1270	c.373C>T	c.(373-375)Cgc>Tgc	p.R125C	HDHD3_ENST00000374180.3_Missense_Mutation_p.R125C|HDHD3_ENST00000485934.1_5'UTR	NM_031219.2	NP_112496.1	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain containing 3	125						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			large_intestine(2)|liver(1)	3						CCCCGTGTGCGGCACTCCCTC	0.597																																					p.R125C		Atlas-SNP	.											.	HDHD3	10	.	0			c.C373T						PASS	.						120.0	127.0	125.0					9																	116136262		2203	4300	6503	SO:0001583	missense	81932	exon2			GTGTGCGGCACTC	AK097067	CCDS6793.1	9q33.1	2006-04-12	2004-08-09	2004-08-12	ENSG00000119431	ENSG00000119431			28171	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 158"""	C9orf158		12477932	Standard	NM_031219		Approved	MGC12904	uc004bhi.1	Q9BSH5	OTTHUMG00000020524	ENST00000238379.5:c.373C>T	9.37:g.116136262G>A	ENSP00000238379:p.Arg125Cys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	145	75	0.517241	NM_031219	B2RD47	Missense_Mutation	SNP	ENST00000238379.5	37	CCDS6793.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529009	0.44969	.	.	ENSG00000119431	ENST00000238379;ENST00000374180	T;T	0.06687	3.27;3.27	5.76	5.76	0.90799	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.421114	0.26963	N	0.021610	T	0.34861	0.0912	M	0.92507	3.315	0.53688	D	0.999974	D	0.89917	1.0	P	0.62089	0.898	T	0.34775	-0.9815	10	0.87932	D	0	-14.3793	13.8598	0.63552	0.0:0.0:0.8475:0.1525	.	125	Q9BSH5	HDHD3_HUMAN	C	125	ENSP00000238379:R125C;ENSP00000363295:R125C	ENSP00000238379:R125C	R	-	1	0	HDHD3	115176083	0.955000	0.32602	0.998000	0.56505	0.238000	0.25445	1.482000	0.35486	2.721000	0.93114	0.655000	0.94253	CGC	.	.	none		0.597	HDHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053731.1	NM_031219	
SLCO1B7	338821	hgsc.bcm.edu	37	12	21201663	21201663	+	Missense_Mutation	SNP	G	G	A	rs11045689	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:21201663G>A	ENST00000421593.2	+	8	1012	c.1012G>A	c.(1012-1014)Gct>Act	p.A338T	LST3_ENST00000540229.1_Intron|LST3_ENST00000381541.3_Missense_Mutation_p.A385T|SLCO1B3_ENST00000553473.1_Intron|SLCO1B7_ENST00000554957.1_Missense_Mutation_p.A385T	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	141	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	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	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978210	45978210	+	Missense_Mutation	SNP	G	G	C	rs200250794		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:45978210G>C	ENST00000391620.1	-	1	433	c.389C>G	c.(388-390)tCt>tGt	p.S130C	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	130	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGAAGCCCCAGAgcagacggg	0.657																																					p.S130C		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C389G						PASS	.	G	,CYS/SER	0,4406		0,0,2203	154.0	157.0	156.0		,389	0.3	0.9	21		156	4,8596	3.7+/-12.6	0,4,4296	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,112	0,4,6499	CC,CG,GG		0.0465,0.0,0.0308	,benign	,130/222	45978210	4,13002	2203	4300	6503	SO:0001583	missense	386682	exon1			GCCCCAGAGCAGA	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.389C>G	21.37:g.45978210G>C	ENSP00000375478:p.Ser130Cys	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	199	118	0.592965	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	.	.	.	.	.	.	.	.	.	.	g	0.926	-0.714347	0.03206	0.0	4.65E-4	ENSG00000212935	ENST00000391620	T	0.00672	5.89	3.53	0.295	0.15752	.	.	.	.	.	T	0.00496	0.0016	N	0.13168	0.305	0.24401	N	0.994705	B	0.09022	0.002	B	0.12156	0.007	T	0.43972	-0.9358	9	0.02654	T	1	.	7.3519	0.26695	0.0:0.4413:0.4219:0.1367	.	130	P60369	KR103_HUMAN	C	130	ENSP00000375478:S130C	ENSP00000375478:S130C	S	-	2	0	KRTAP10-3	44802638	0.172000	0.23043	0.877000	0.34402	0.106000	0.19336	1.422000	0.34826	0.267000	0.21916	0.561000	0.74099	TCT	G|0.999;C|0.001	0.001	weak		0.657	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
SLC39A12	221074	hgsc.bcm.edu	37	10	18254595	18254595	+	Missense_Mutation	SNP	C	C	T	rs62619938	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:18254595C>T	ENST00000377369.2	+	4	1000	c.727C>T	c.(727-729)Cgt>Tgt	p.R243C	SLC39A12_ENST00000539911.1_Missense_Mutation_p.R109C|SLC39A12_ENST00000377374.4_Missense_Mutation_p.R243C|SLC39A12_ENST00000377371.3_Missense_Mutation_p.R243C	NM_001145195.1|NM_001282733.1|NM_001282734.1	NP_001138667.1|NP_001269662.1|NP_001269663.1	Q504Y0	S39AC_HUMAN	solute carrier family 39 (zinc transporter), member 12	243					regulation of microtubule polymerization (GO:0031113)|regulation of neuron projection development (GO:0010975)|signal transduction (GO:0007165)|zinc ion transmembrane import (GO:0071578)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(5)|lung(38)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						TTCCTTGAATCGTACGAATAC	0.418													C|||	130	0.0259585	0.0068	0.0403	5008	,	,		18927	0.0		0.0875	False		,,,				2504	0.0051				p.R243C		Atlas-SNP	.											SLC39A12,NS,carcinoma,-1,1	SLC39A12	181	1	0			c.C727T						PASS	.	C	CYS/ARG,CYS/ARG	50,4356	50.2+/-85.5	2,46,2155	53.0	52.0	52.0		727,727	3.5	0.6	10	dbSNP_129	52	582,8018	155.5+/-209.5	20,542,3738	yes	missense,missense	SLC39A12	NM_001145195.1,NM_152725.3	180,180	22,588,5893	TT,TC,CC		6.7674,1.1348,4.8593	possibly-damaging,possibly-damaging	243/692,243/655	18254595	632,12374	2203	4300	6503	SO:0001583	missense	221074	exon4			TTGAATCGTACGA		CCDS7124.1, CCDS44362.1, CCDS60493.1, CCDS60494.1	10p12.33	2013-05-22			ENSG00000148482	ENSG00000148482		"""Solute carriers"""	20860	protein-coding gene	gene with protein product		608734	"""solute carrier family 39 (metal ion transporter), member 12"""			12659941	Standard	NM_152725		Approved	FLJ30499	uc001ipo.2	Q504Y0	OTTHUMG00000017759	ENST00000377369.2:c.727C>T	10.37:g.18254595C>T	ENSP00000366586:p.Arg243Cys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	61	14	0.229508	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Missense_Mutation	SNP	ENST00000377369.2	37	CCDS44362.1	83	0.038003663003663	5	0.01016260162601626	18	0.049723756906077346	0	0.0	60	0.079155672823219	C	6.711	0.499822	0.12762	0.011348	0.067674	ENSG00000148482	ENST00000377369;ENST00000377374;ENST00000377371;ENST00000539911;ENST00000425219	T;T;T;T	0.62364	0.15;0.03;0.15;0.04	5.81	3.49	0.39957	.	0.362650	0.35838	N	0.002960	T	0.05502	0.0145	L	0.53249	1.67	0.42390	D	0.992526	B;B;B	0.12013	0.005;0.002;0.002	B;B;B	0.14578	0.011;0.003;0.002	T	0.09530	-1.0670	10	0.56958	D	0.05	-1.9829	8.7303	0.34494	0.7981:0.1345:0.0674:0.0	rs62619938	243;243;243	Q504Y0-4;Q504Y0;Q504Y0-3	.;S39AC_HUMAN;.	C	243;243;243;109;163	ENSP00000366586:R243C;ENSP00000366591:R243C;ENSP00000366588:R243C;ENSP00000440445:R109C	ENSP00000366586:R243C	R	+	1	0	SLC39A12	18294601	1.000000	0.71417	0.560000	0.28344	0.007000	0.05969	2.918000	0.48829	0.476000	0.27440	-0.262000	0.10625	CGT	C|0.956;T|0.044	0.044	strong		0.418	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
FLG	2312	hgsc.bcm.edu	37	1	152280347	152280347	+	Missense_Mutation	SNP	C	C	T	rs139476473	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280347C>T	ENST00000368799.1	-	3	7050	c.7015G>A	c.(7015-7017)Gac>Aac	p.D2339N	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2339	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.D2339N(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGGAGCTGTCTGCTGACTGC	0.557									Ichthyosis																												p.D2339N		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	1	Substitution - Missense(1)	stomach(1)	c.G7015A						scavenged	.	C	ASN/ASP	81,4309		0,81,2114	193.0	265.0	240.0		7015	4.1	0.1	1	dbSNP_134	240	282,8314		22,238,4038	no	missense	FLG	NM_002016.1	23	22,319,6152	TT,TC,CC		3.2806,1.8451,2.7953	probably-damaging	2339/4062	152280347	363,12623	2195	4298	6493	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	AGCTGTCTGCTGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7015G>A	1.37:g.152280347C>T	ENSP00000357789:p.Asp2339Asn	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	295	45	0.152542	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	432	0.1978021978021978	6	0.012195121951219513	90	0.24861878453038674	245	0.42832167832167833	91	0.12005277044854881	C	13.82	2.350104	0.41599	0.018451	0.032806	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.08008	3.14	4.12	4.12	0.48240	.	.	.	.	.	T	0.14570	0.0352	M	0.62723	1.935	0.80722	P	0.0	D	0.69078	0.997	D	0.66196	0.942	T	0.00619	-1.1641	8	0.66056	D	0.02	.	12.0996	0.53776	0.0:1.0:0.0:0.0	.	2339	P20930	FILA_HUMAN	N	2339;249	ENSP00000357789:D2339N	ENSP00000271820:D249N	D	-	1	0	FLG	150546971	0.223000	0.23663	0.097000	0.21041	0.004000	0.04260	1.691000	0.37721	2.287000	0.76781	0.430000	0.28490	GAC	.	.	weak		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC17	140453	hgsc.bcm.edu	37	7	100680438	100680438	+	Missense_Mutation	SNP	G	G	C	rs112926140		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680438G>C	ENST00000306151.4	+	3	5805	c.5741G>C	c.(5740-5742)aGc>aCc	p.S1914T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1914	59 X approximate tandem repeats.|Ser-rich.				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)					GCTGACGGTAGCAGCATGCCA	0.493																																					p.S1914T		Atlas-SNP	.											MUC17,right_upper_lobe,carcinoma,+1,1	MUC17	804	1	0			c.G5741C						scavenged	.						249.0	250.0	250.0					7																	100680438		2203	4300	6503	SO:0001583	missense	140453	exon3			ACGGTAGCAGCAT	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.5741G>C	7.37:g.100680438G>C	ENSP00000302716:p.Ser1914Thr	Somatic	167	2	0.011976		WXS	Illumina HiSeq	Phase_I	209	16	0.076555	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.074	-1.195664	0.01594	.	.	ENSG00000169876	ENST00000306151	T	0.02498	4.27	1.18	-2.36	0.06663	.	.	.	.	.	T	0.00998	0.0033	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41610	-0.9499	9	0.02654	T	1	.	1.2251	0.01932	0.1506:0.3181:0.2997:0.2316	.	1914	Q685J3	MUC17_HUMAN	T	1914	ENSP00000302716:S1914T	ENSP00000302716:S1914T	S	+	2	0	MUC17	100467158	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	-0.876000	0.04201	-3.962000	0.00087	-1.848000	0.00571	AGC	A|0.001;G|0.999	.	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ST8SIA3	51046	hgsc.bcm.edu	37	18	55021725	55021725	+	Missense_Mutation	SNP	A	A	C	rs3745060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:55021725A>C	ENST00000324000.3	+	2	2306	c.272A>C	c.(271-273)aAa>aCa	p.K91T		NM_015879.2	NP_056963.2	O43173	SIA8C_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3	91			K -> T (in dbSNP:rs3745060).		cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycoprotein metabolic process (GO:0009100)|glycosphingolipid biosynthetic process (GO:0006688)|N-glycan processing (GO:0006491)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialic acid binding (GO:0033691)			breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(16)|prostate(1)|skin(3)	36				READ - Rectum adenocarcinoma(59;0.19)|Colorectal(16;0.205)		TCTAAGTGGAAATTTAATCGG	0.403													C|||	1846	0.36861	0.5204	0.3199	5008	,	,		18792	0.495		0.159	False		,,,				2504	0.2832				p.K91T		Atlas-SNP	.											.	ST8SIA3	73	.	0			c.A272C						PASS	.	C	THR/LYS	1999,2407	616.4+/-392.8	455,1089,659	110.0	109.0	109.0		272	2.0	1.0	18	dbSNP_107	109	1365,7235	755.4+/-407.5	100,1165,3035	yes	missense	ST8SIA3	NM_015879.2	78	555,2254,3694	CC,CA,AA		15.8721,45.37,25.865	benign	91/381	55021725	3364,9642	2203	4300	6503	SO:0001583	missense	51046	exon2			AGTGGAAATTTAA	AF004668	CCDS32834.1	18q21.31	2013-03-01	2005-02-07	2005-02-07	ENSG00000177511	ENSG00000177511		"""Sialyltransferases"""	14269	protein-coding gene	gene with protein product	"""ST8Sia III"""	609478	"""sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)"""	SIAT8C			Standard	NM_015879		Approved		uc002lgn.3	O43173	OTTHUMG00000180101	ENST00000324000.3:c.272A>C	18.37:g.55021725A>C	ENSP00000320431:p.Lys91Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	49	0.563218	NM_015879	A8K0F2|Q6B085|Q9NS41	Missense_Mutation	SNP	ENST00000324000.3	37	CCDS32834.1	763	0.34935897435897434	240	0.4878048780487805	102	0.281767955801105	306	0.534965034965035	115	0.1517150395778364	C	2.834	-0.241904	0.05906	0.4537	0.158721	ENSG00000177511	ENST00000541833;ENST00000324000	T	0.39997	1.05	4.88	2.02	0.26589	.	0.387780	0.31495	N	0.007546	T	0.00012	0.0000	N	0.14661	0.345	0.49798	P	1.7400000000000748E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47302	-0.9128	9	0.08837	T	0.75	-6.3465	2.5347	0.04711	0.2854:0.336:0.2786:0.1	rs3745060;rs52812069;rs56693866;rs3745060	91	O43173	SIA8C_HUMAN	T	198;91	ENSP00000320431:K91T	ENSP00000320431:K91T	K	+	2	0	ST8SIA3	53172723	0.043000	0.20138	0.987000	0.45799	0.979000	0.70002	-0.004000	0.12878	-0.039000	0.13602	-0.352000	0.07741	AAA	A|0.692;C|0.308	0.308	strong		0.403	ST8SIA3-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449765.1	NM_015879	
USP45	85015	hgsc.bcm.edu	37	6	99883694	99883694	+	Silent	SNP	T	T	C	rs9402791	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:99883694T>C	ENST00000327681.6	-	18	2875	c.2343A>G	c.(2341-2343)gcA>gcG	p.A781A	USP45_ENST00000539675.1_Silent_p.A74A|USP45_ENST00000500704.2_Silent_p.A781A|USP45_ENST00000369233.2_Silent_p.A733A|USP45_ENST00000392738.2_Silent_p.A461A	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	781	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.A781A(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)		CCCACTGGCCTGCTGATTCAT	0.363													T|||	1462	0.291933	0.112	0.3184	5008	,	,		14521	0.503		0.2207	False		,,,				2504	0.3722				p.A781A		Atlas-SNP	.											USP45,NS,carcinoma,0,1	USP45	56	1	1	Substitution - coding silent(1)	stomach(1)	c.A2343G						PASS	.	T		582,3824	256.4+/-261.2	29,524,1650	111.0	111.0	111.0		2343	1.7	0.8	6	dbSNP_119	111	1625,6975	301.7+/-305.6	147,1331,2822	no	coding-synonymous	USP45	NM_001080481.1		176,1855,4472	CC,CT,TT		18.8953,13.2093,16.9691		781/815	99883694	2207,10799	2203	4300	6503	SO:0001819	synonymous_variant	85015	exon18			CTGGCCTGCTGAT	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.2343A>G	6.37:g.99883694T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Silent	SNP	ENST00000327681.6	37	CCDS34501.1																																																																																			T|0.786;C|0.214	0.214	strong		0.363	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
OR51S1	119692	hgsc.bcm.edu	37	11	4870261	4870261	+	Missense_Mutation	SNP	G	G	C	rs11602499	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4870261G>C	ENST00000322101.2	-	1	253	c.178C>G	c.(178-180)Cag>Gag	p.Q60E	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	60			Q -> E (in dbSNP:rs11602499).			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)		AGGGCGGGCTGCAGGGCAATG	0.567													C|||	1373	0.274161	0.2352	0.2579	5008	,	,		20052	0.0675		0.4066	False		,,,				2504	0.4151				p.Q60E		Atlas-SNP	.											.	OR51S1	83	.	0			c.C178G						PASS	.	C	GLU/GLN	1237,3165	705.5+/-407.3	183,871,1147	109.0	88.0	95.0		178	4.8	0.2	11	dbSNP_120	95	3700,4896	619.9+/-397.0	805,2090,1403	yes	missense	OR51S1	NM_001004758.1	29	988,2961,2550	CC,CG,GG		43.0433,28.1009,37.9828	benign	60/324	4870261	4937,8061	2201	4298	6499	SO:0001583	missense	119692	exon1			CGGGCTGCAGGGC	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.178C>G	11.37:g.4870261G>C	ENSP00000322754:p.Gln60Glu	Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	290	290	1	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	573	0.2623626373626374	121	0.2459349593495935	118	0.3259668508287293	32	0.055944055944055944	302	0.39841688654353563	C	0.003	-2.537173	0.00143	0.281009	0.430433	ENSG00000176922	ENST00000322101	T	0.02709	4.19	4.85	4.85	0.62838	GPCR, rhodopsin-like superfamily (1);	0.173223	0.27460	N	0.019276	T	0.00012	0.0000	N	0.00157	-1.96	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42447	-0.9451	9	0.02654	T	1	-1.7637	14.1463	0.65353	0.0:0.8486:0.1514:0.0	rs11602499;rs17328866;rs61047571;rs11602499	60	Q8NGJ8	O51S1_HUMAN	E	60	ENSP00000322754:Q60E	ENSP00000322754:Q60E	Q	-	1	0	OR51S1	4826837	0.000000	0.05858	0.205000	0.23548	0.102000	0.19082	0.343000	0.19944	1.277000	0.44412	-0.215000	0.12644	CAG	G|0.673;C|0.327	0.327	strong		0.567	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
SEC16B	89866	hgsc.bcm.edu	37	1	177935050	177935050	+	Silent	SNP	T	T	A	rs1889981	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:177935050T>A	ENST00000308284.6	-	3	479	c.390A>T	c.(388-390)ccA>ccT	p.P130P	SEC16B_ENST00000464631.2_Silent_p.P130P|RP4-798P15.3_ENST00000354921.3_RNA	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						PASS	.	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	116	0	0		WXS	Illumina HiSeq	Phase_I	171	111	0.649123	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	
MAN2A1	4124	hgsc.bcm.edu	37	5	109110537	109110537	+	Silent	SNP	T	T	A	rs6894260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:109110537T>A	ENST00000261483.4	+	8	2297	c.1245T>A	c.(1243-1245)cgT>cgA	p.R415R		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	415					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		AGCTTTTTCGTACCAAAGTTC	0.363													T|||	1683	0.336062	0.5552	0.3314	5008	,	,		14466	0.2609		0.3489	False		,,,				2504	0.1074				p.R415R		Atlas-SNP	.											MAN2A1,extremity,malignant_melanoma,+2,1	MAN2A1	136	1	0			c.T1245A						scavenged	.	T		2462,1942	621.9+/-393.8	701,1060,441	77.0	76.0	76.0		1245	-3.9	0.5	5	dbSNP_116	76	2914,5686	454.3+/-363.5	522,1870,1908	no	coding-synonymous	MAN2A1	NM_002372.2		1223,2930,2349	AA,AT,TT		33.8837,44.0963,41.3411		415/1145	109110537	5376,7628	2202	4300	6502	SO:0001819	synonymous_variant	4124	exon8			TTTTCGTACCAAA		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.1245T>A	5.37:g.109110537T>A		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_002372	Q16767	Silent	SNP	ENST00000261483.4	37	CCDS34209.1																																																																																			A|0.390;N|0.000	0.390	strong		0.363	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
SLC39A8	64116	hgsc.bcm.edu	37	4	103225513	103225513	+	Silent	SNP	T	T	C	rs11097773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:103225513T>C	ENST00000394833.2	-	5	1277	c.801A>G	c.(799-801)ggA>ggG	p.G267G	SLC39A8_ENST00000424970.2_Silent_p.G267G|SLC39A8_ENST00000356736.4_Silent_p.G267G|SLC39A8_ENST00000510255.1_5'Flank	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	267					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)			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)		AATGGATATGTCCATTAGCTT	0.358													T|||	726	0.144968	0.0915	0.1772	5008	,	,		18835	0.1181		0.1541	False		,,,				2504	0.2127				p.G267G		Atlas-SNP	.											.	SLC39A8	24	.	0			c.A801G						PASS	.	T	,,,	416,3990	204.5+/-226.7	12,392,1799	160.0	139.0	146.0		801,801,600,801	4.8	1.0	4	dbSNP_120	146	1513,7087	285.1+/-297.0	122,1269,2909	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A8	NM_001135146.1,NM_001135147.1,NM_001135148.1,NM_022154.5	,,,	134,1661,4708	CC,CT,TT		17.593,9.4417,14.8316	,,,	267/461,267/445,200/394,267/461	103225513	1929,11077	2203	4300	6503	SO:0001819	synonymous_variant	64116	exon5			GATATGTCCATTA		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.801A>G	4.37:g.103225513T>C		Somatic	196	1	0.00510204		WXS	Illumina HiSeq	Phase_I	182	103	0.565934	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Silent	SNP	ENST00000394833.2	37	CCDS3656.1																																																																																			T|0.860;C|0.140	0.140	strong		0.358	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
TRAP1	10131	hgsc.bcm.edu	37	16	3708193	3708193	+	Silent	SNP	G	G	A	rs1059857	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3708193G>A	ENST00000246957.5	-	18	2140	c.2052C>T	c.(2050-2052)gaC>gaT	p.D684D	TRAP1_ENST00000538171.1_Silent_p.D631D|DNASE1_ENST00000414110.2_Intron|TRAP1_ENST00000575671.1_Silent_p.D475D	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	684					chaperone-mediated protein folding (GO:0061077)|negative regulation of cellular respiration (GO:1901856)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to stress (GO:0006950)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|tumor necrosis factor receptor binding (GO:0005164)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Ovarian(90;0.0261)				CCCTAGGGTCGTCAACAAGTC	0.527													G|||	475	0.0948482	0.1989	0.0418	5008	,	,		18260	0.0228		0.0437	False		,,,				2504	0.1186				p.D684D		Atlas-SNP	.											.	TRAP1	53	.	0			c.C2052T						PASS	.	G		818,3576	325.0+/-298.9	74,670,1453	61.0	59.0	59.0		2052	-10.8	0.0	16	dbSNP_86	59	358,8242	120.6+/-179.8	6,346,3948	no	coding-synonymous	TRAP1	NM_016292.2		80,1016,5401	AA,AG,GG		4.1628,18.6163,9.0503		684/705	3708193	1176,11818	2197	4300	6497	SO:0001819	synonymous_variant	10131	exon18			AGGGTCGTCAACA	AF154108	CCDS10508.1, CCDS61824.1	16p13.3	2011-09-02			ENSG00000126602	ENSG00000126602		"""Heat shock proteins / HSPC"""	16264	protein-coding gene	gene with protein product		606219				10652318, 7876093	Standard	NM_016292		Approved	HSP75, HSP90L	uc002cvt.4	Q12931	OTTHUMG00000129427	ENST00000246957.5:c.2052C>T	16.37:g.3708193G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Silent	SNP	ENST00000246957.5	37	CCDS10508.1																																																																																			G|0.912;A|0.088	0.088	strong		0.527	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
ACSM5	54988	hgsc.bcm.edu	37	16	20432605	20432605	+	Missense_Mutation	SNP	A	A	G	rs59025904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:20432605A>G	ENST00000331849.4	+	5	796	c.649A>G	c.(649-651)Atg>Gtg	p.M217V		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	217			M -> V (in dbSNP:rs59025904).		fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						GCACAACTGCATGAGGACAAA	0.517													G|||	684	0.136581	0.3079	0.0605	5008	,	,		14543	0.0615		0.0487	False		,,,				2504	0.1268				p.M217V		Atlas-SNP	.											.	ACSM5	101	.	0			c.A649G						PASS	.	G	VAL/MET	1224,3182	706.7+/-407.4	172,880,1151	61.0	60.0	60.0		649	1.2	0.0	16	dbSNP_129	60	496,8104	797.0+/-407.5	13,470,3817	yes	missense	ACSM5	NM_017888.2	21	185,1350,4968	GG,GA,AA		5.7674,27.7803,13.2247	benign	217/580	20432605	1720,11286	2203	4300	6503	SO:0001583	missense	54988	exon5			AACTGCATGAGGA		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.649A>G	16.37:g.20432605A>G	ENSP00000327916:p.Met217Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	250	0.11446886446886446	145	0.29471544715447157	27	0.07458563535911603	37	0.06468531468531469	41	0.05408970976253298	G	0.001	-3.144640	0.00029	0.277803	0.057674	ENSG00000183549	ENST00000331849	T	0.42513	0.97	4.43	1.23	0.21249	AMP-dependent synthetase/ligase (1);	0.373188	0.22389	N	0.060709	T	0.00012	0.0000	N	0.00113	-2.09	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41052	-0.9530	9	0.02654	T	1	-3.0733	9.1067	0.36703	0.1418:0.3348:0.5234:0.0	rs59025904	217	Q6NUN0	ACSM5_HUMAN	V	217	ENSP00000327916:M217V	ENSP00000327916:M217V	M	+	1	0	ACSM5	20340106	0.004000	0.15560	0.023000	0.16930	0.055000	0.15305	-0.147000	0.10234	-0.295000	0.08960	-2.208000	0.00301	ATG	A|0.875;G|0.125	0.125	strong		0.517	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
WDR5	11091	hgsc.bcm.edu	37	9	137017126	137017126	+	Silent	SNP	A	A	G	rs34523253	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:137017126A>G	ENST00000358625.3	+	9	777	c.606A>G	c.(604-606)tcA>tcG	p.S202S	WDR5_ENST00000425041.1_Silent_p.S202S	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	202					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)		ACACCGCCTCAGGCCAGTGCC	0.562													G|||	394	0.0786741	0.2489	0.0375	5008	,	,		18445	0.0		0.0328	False		,,,				2504	0.0061				p.S202S		Atlas-SNP	.											WDR5,NS,carcinoma,+1,1	WDR5	29	1	0			c.A606G						PASS	.	G	,	925,3481	737.9+/-410.9	90,745,1368	158.0	157.0	157.0		606,606	-7.5	0.0	9	dbSNP_126	157	247,8353	808.4+/-407.2	4,239,4057	no	coding-synonymous,coding-synonymous	WDR5	NM_017588.2,NM_052821.3	,	94,984,5425	GG,GA,AA		2.8721,20.9941,9.0112	,	202/335,202/335	137017126	1172,11834	2203	4300	6503	SO:0001819	synonymous_variant	11091	exon8			CGCCTCAGGCCAG	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.606A>G	9.37:g.137017126A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	NM_052821	Q91VA5|Q9NWX7|Q9UGP9	Silent	SNP	ENST00000358625.3	37	CCDS6981.1																																																																																			A|0.920;G|0.080	0.080	strong		0.562	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1	NM_052821	
SYNE2	23224	hgsc.bcm.edu	37	14	64612858	64612858	+	Missense_Mutation	SNP	C	C	A	rs10151658	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:64612858C>A	ENST00000344113.4	+	84	15768	c.15556C>A	c.(15556-15558)Ctg>Atg	p.L5186M	SYNE2_ENST00000358025.3_Missense_Mutation_p.L5186M|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Missense_Mutation_p.L5103M|SYNE2_ENST00000357395.3_Missense_Mutation_p.L1571M|SYNE2_ENST00000394768.2_Missense_Mutation_p.L1571M|SYNE2_ENST00000555002.1_Missense_Mutation_p.L1820M	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5186			L -> M (in dbSNP:rs10151658). {ECO:0000269|PubMed:12118075, ECO:0000269|PubMed:14702039}.		centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.L5186M(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		GAACAACTGGCTGGAAGCACA	0.383													A|||	3164	0.631789	0.9168	0.513	5008	,	,		17217	0.6429		0.4553	False		,,,				2504	0.501				p.L5186M		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	1	1	Substitution - Missense(1)	prostate(1)	c.C15556A						scavenged	.	A	MET/LEU,MET/LEU	3745,661	281.4+/-275.9	1603,539,61	68.0	73.0	71.0		15556,15556	-2.1	1.0	14	dbSNP_119	71	3771,4829	614.9+/-396.3	832,2107,1361	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	15,15	2435,2646,1422	AA,AC,CC		43.8488,15.0023,42.2113	benign,benign	5186/6886,5186/6908	64612858	7516,5490	2203	4300	6503	SO:0001583	missense	23224	exon84			AACTGGCTGGAAG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.15556C>A	14.37:g.64612858C>A	ENSP00000341781:p.Leu5186Met	Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	324	98	0.302469	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	1340	0.6135531135531136	448	0.9105691056910569	184	0.5082872928176796	368	0.6433566433566433	340	0.44854881266490765	A	2.298	-0.360858	0.05103	0.849977	0.438488	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;3.78;0.71	5.63	-2.1	0.07210	.	0.647372	0.14331	N	0.326332	T	0.00012	0.0000	N	0.05510	-0.035	0.09310	P	0.9999999999999748	B;B;B;B	0.18310	0.002;0.027;0.002;0.006	B;B;B;B	0.17098	0.01;0.017;0.01;0.012	T	0.27020	-1.0086	9	0.15952	T	0.53	.	12.0809	0.53669	0.1859:0.6107:0.0:0.2034	rs10151658;rs17179138;rs58728365;rs10151658	1571;5103;5186;5186	Q8WXH0-7;G3V5X4;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	M	5186;1571;5186;5103;5109;1820;1571	ENSP00000350719:L5186M;ENSP00000349969:L1571M;ENSP00000341781:L5186M;ENSP00000452570:L5103M;ENSP00000450831:L1820M;ENSP00000378249:L1571M	ENSP00000261678:L5109M	L	+	1	2	SYNE2	63682611	0.060000	0.20803	0.953000	0.39169	0.324000	0.28378	-0.595000	0.05727	-1.072000	0.03141	-1.140000	0.01884	CTG	C|0.386;A|0.614	0.614	strong		0.383	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
SSPO	23145	hgsc.bcm.edu	37	7	149489540	149489540	+	RNA	SNP	G	G	A	rs199795943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149489540G>A	ENST00000378016.2	+	0	5693							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)			GGACGGCCCCGACGCTGCCGA	0.692													G|||	7	0.00139776	0.0	0.0014	5008	,	,		15662	0.0		0.005	False		,,,				2504	0.001				p.R1898Q		Atlas-SNP	.											.	.	.	.	0			c.G5693A						PASS	.	G		2,4260		0,2,2129	14.0	21.0	19.0		5697	-0.2	0.1	7		19	30,8422		0,30,4196	no	coding-notMod3	SSPO	NM_198455.2		0,32,6325	AA,AG,GG		0.3549,0.0469,0.2517			149489540	32,12682	2131	4226	6357			23145	exon37			GGCCCCGACGCTG	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.149489540G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.998;A|0.002	0.002	weak		0.692	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
OR52J3	119679	hgsc.bcm.edu	37	11	5068662	5068662	+	Nonsense_Mutation	SNP	C	C	T	rs386750099|rs57026471	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5068662C>T	ENST00000380370.1	+	1	907	c.907C>T	c.(907-909)Cga>Tga	p.R303*		NM_001001916.2	NP_001001916.2	Q8NH60	O52J3_HUMAN	olfactory receptor, family 52, subfamily J, member 3	303						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(1)|kidney(6)|large_intestine(6)|lung(19)|ovary(1)|skin(2)	36		Medulloblastoma(188;0.00131)|all_neural(188;0.0189)|Breast(177;0.0204)		Epithelial(150;9.29e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATTCGAGAACGAGTGCTCTA	0.383													C|||	567	0.113219	0.0673	0.2853	5008	,	,		21243	0.0863		0.1372	False		,,,				2504	0.0562				p.R303X		Atlas-SNP	.											.	OR52J3	77	.	0			c.C907T						PASS	.	C	stop/ARG	265,4137		9,247,1945	57.0	54.0	55.0		907	-5.8	0.0	11	dbSNP_129	55	810,7786		65,680,3553	yes	stop-gained	OR52J3	NM_001001916.2		74,927,5498	TT,TC,CC		9.423,6.02,8.2705		303/312	5068662	1075,11923	2201	4298	6499	SO:0001587	stop_gained	119679	exon1			CGAGAACGAGTGC	AB065530	CCDS31370.1	11p15.4	2012-08-09			ENSG00000205495	ENSG00000205495		"""GPCR / Class A : Olfactory receptors"""	14799	protein-coding gene	gene with protein product							Standard	NM_001001916		Approved		uc010qyv.2	Q8NH60	OTTHUMG00000066600	ENST00000380370.1:c.907C>T	11.37:g.5068662C>T	ENSP00000369728:p.Arg303*	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	39	0.590909	NM_001001916	Q6IFE4	Nonsense_Mutation	SNP	ENST00000380370.1	37	CCDS31370.1	249	0.11401098901098901	27	0.054878048780487805	70	0.19337016574585636	59	0.10314685314685315	93	0.12269129287598944	C	9.770	1.172462	0.21704	0.0602	0.09423	ENSG00000205495	ENST00000380370	.	.	.	4.19	-5.75	0.02384	.	1.063770	0.07513	N	0.909200	.	.	.	.	.	.	0.40923	P	0.015674999999999994	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.0031	0.14275	0.3115:0.1927:0.0:0.4958	rs57026471;rs61747641	.	.	.	X	303	.	ENSP00000369728:R303X	R	+	1	2	OR52J3	5025238	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.028000	0.00639	-0.806000	0.04398	-1.808000	0.00615	CGA	C|0.886;T|0.114	0.114	strong		0.383	OR52J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142807.1	NM_001001916	
ZNF33A	7581	hgsc.bcm.edu	37	10	38344895	38344895	+	Missense_Mutation	SNP	G	G	A	rs12256916	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:38344895G>A	ENST00000458705.2	+	5	1998	c.1840G>A	c.(1840-1842)Gga>Aga	p.G614R	ZNF33A_ENST00000374618.3_Missense_Mutation_p.G615R|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000307441.9_Missense_Mutation_p.G614R|ZNF33A_ENST00000432900.2_Missense_Mutation_p.G621R			Q06730	ZN33A_HUMAN	zinc finger protein 33A	614			G -> R (in dbSNP:rs12256916).		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						TAATGAATGTGGAAAAGCCTT	0.368													G|||	140	0.0279553	0.0915	0.013	5008	,	,		20194	0.0		0.0099	False		,,,				2504	0.0				p.G615R		Atlas-SNP	.											.	ZNF33A	103	.	0			c.G1843A						PASS	.	G	ARG/GLY,ARG/GLY	363,4043	184.7+/-212.0	19,325,1859	75.0	74.0	74.0		1843,1840	1.7	1.0	10	dbSNP_120	74	54,8546	34.3+/-88.2	0,54,4246	no	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	125,125	19,379,6105	AA,AG,GG		0.6279,8.2388,3.2062	probably-damaging,probably-damaging	615/812,614/811	38344895	417,12589	2203	4300	6503	SO:0001583	missense	7581	exon5			GAATGTGGAAAAG	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.1840G>A	10.37:g.38344895G>A	ENSP00000387713:p.Gly614Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	48	10	0.208333	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	50	0.022893772893772892	35	0.07113821138211382	7	0.019337016574585635	0	0.0	8	0.010554089709762533	G	14.71	2.615327	0.46631	0.082388	0.006279	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.01484	4.84;4.84;4.84;4.84	1.69	1.69	0.24217	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34386	N	0.004010	T	0.00468	0.0015	M	0.85373	2.75	0.31075	N	0.712553	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.77004	0.981;0.989;0.859	T	0.00756	-1.1579	10	0.56958	D	0.05	.	8.8982	0.35479	0.0:0.0:1.0:0.0	rs12256916;rs52814973;rs12256916	621;614;615	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	R	615;621;614;614	ENSP00000363747:G615R;ENSP00000402467:G621R;ENSP00000387713:G614R;ENSP00000304268:G614R	ENSP00000304268:G614R	G	+	1	0	ZNF33A	38384901	1.000000	0.71417	0.998000	0.56505	0.725000	0.41563	4.320000	0.59203	0.902000	0.36520	0.313000	0.20887	GGA	G|0.970;A|0.030	0.030	strong		0.368	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
CCDC9	26093	hgsc.bcm.edu	37	19	47774358	47774358	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:47774358G>C	ENST00000221922.6	+	11	1327	c.1105G>C	c.(1105-1107)Gag>Cag	p.E369Q		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	369							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)		TGACCGCTGGGAGACAAAAGA	0.622																																					p.E369Q		Atlas-SNP	.											.	CCDC9	37	.	0			c.G1105C						PASS	.						35.0	35.0	35.0					19																	47774358		2198	4285	6483	SO:0001583	missense	26093	exon11			CGCTGGGAGACAA	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.1105G>C	19.37:g.47774358G>C	ENSP00000221922:p.Glu369Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	145	72	0.496552	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	.	13.05	2.122654	0.37436	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.58358	0.34	4.34	4.34	0.51931	.	0.059852	0.64402	D	0.000005	T	0.69043	0.3067	M	0.69823	2.125	0.45025	D	0.998043	D	0.67145	0.996	D	0.75484	0.986	T	0.72080	-0.4398	10	0.62326	D	0.03	-22.8191	12.1997	0.54317	0.0:0.0:1.0:0.0	.	369	Q9Y3X0	CCDC9_HUMAN	Q	369;351	ENSP00000221922:E369Q	ENSP00000221922:E369Q	E	+	1	0	CCDC9	52466198	1.000000	0.71417	1.000000	0.80357	0.463000	0.32649	2.962000	0.49176	2.213000	0.71641	0.305000	0.20034	GAG	.	.	none		0.622	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
F8	2157	hgsc.bcm.edu	37	X	154158285	154158285	+	Missense_Mutation	SNP	G	G	C	rs1800291	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:154158285G>C	ENST00000360256.4	-	14	3980	c.3780C>G	c.(3778-3780)gaC>gaG	p.D1260E		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1260	B.		D -> E (in dbSNP:rs1800291). {ECO:0000269|PubMed:12195713, ECO:0000269|PubMed:8644728, ECO:0000269|Ref.6}.		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)	CATATGCCCCGTCATATGAAC	0.373													C|||	968	0.256424	0.5408	0.1282	3775	,	,		13663	0.0327		0.1004	False		,,,				2504	0.0307				p.D1260E		Atlas-SNP	.											.	F8	646	.	0			c.C3780G	GRCh37	CM960556	F8	M	rs1800291	PASS	.	C	GLU/ASP	2492,1343		702,712,376,218,195	93.0	80.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3780	0.8	0.0	X	dbSNP_89	84	1168,5559		77,709,305,1642,1566	yes	missense	F8	NM_000132.3	45	779,1421,681,1860,1761	CC,CG,C,GG,G		17.3629,35.0196,34.6525	benign	1260/2352	154158285	3660,6902	2203	4299	6502	SO:0001583	missense	2157	exon14			TGCCCCGTCATAT	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.3780C>G	X.37:g.154158285G>C	ENSP00000353393:p.Asp1260Glu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	408	0.24593128390596744	167	0.5030120481927711	34	0.10303030303030303	21	0.03804347826086957	57	0.0800561797752809	c	0.001	-2.940936	0.00052	0.649804	0.173629	ENSG00000185010	ENST00000360256	D	0.98777	-5.13	5.0	0.78	0.18556	.	0.229900	0.30311	N	0.009907	T	0.00012	0.0000	N	0.00104	-2.125	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48525	-0.9028	9	0.02654	T	1	-0.5074	4.356	0.11178	0.0:0.3526:0.1713:0.476	rs1800291;rs12857528;rs52807479;rs1800291	1260	P00451	FA8_HUMAN	E	1260	ENSP00000353393:D1260E	ENSP00000353393:D1260E	D	-	3	2	F8	153811479	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.490000	0.06482	-0.282000	0.09128	-0.260000	0.10688	GAC	G|0.649;0|0.032	.	strong		0.373	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
METTL2B	55798	hgsc.bcm.edu	37	7	128140982	128140982	+	Silent	SNP	T	T	C	rs10257897	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:128140982T>C	ENST00000262432.8	+	8	979	c.942T>C	c.(940-942)taT>taC	p.Y314Y	METTL2B_ENST00000480046.1_Silent_p.Y249Y	NM_018396.2	NP_060866.2	Q6P1Q9	MET2B_HUMAN	methyltransferase like 2B	314					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(1)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GAAATTTCTATGTGAGAGGTG	0.398													C|||	1794	0.358227	0.4145	0.3055	5008	,	,		20144	0.2877		0.3827	False		,,,				2504	0.3671				p.Y314Y		Atlas-SNP	.											.	METTL2B	34	.	0			c.T942C						PASS	.	C		1772,2634	643.2+/-397.8	347,1078,778	216.0	214.0	215.0		942	2.1	1.0	7	dbSNP_119	215	3414,5184	638.8+/-399.4	679,2056,1564	no	coding-synonymous	METTL2B	NM_018396.2		1026,3134,2342	CC,CT,TT		39.7069,40.2179,39.88		314/379	128140982	5186,7818	2203	4299	6502	SO:0001819	synonymous_variant	55798	exon8			TTTCTATGTGAGA	AK002212	CCDS5803.2	7q32.2	2012-06-12	2006-02-09	2006-02-09	ENSG00000165055	ENSG00000165055			18272	protein-coding gene	gene with protein product		607846	"""methyltransferase like 2"""	METTL2		11738826	Standard	NM_018396		Approved	METL, FLJ11350	uc003vnf.3	Q6P1Q9	OTTHUMG00000143738	ENST00000262432.8:c.942T>C	7.37:g.128140982T>C		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	177	137	0.774011	NM_018396	B4DZ68|Q0IJ54|Q3B7J1	Silent	SNP	ENST00000262432.8	37	CCDS5803.2																																																																																			.	.	weak		0.398	METTL2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289817.1	NM_018396	
CTCFL	140690	hgsc.bcm.edu	37	20	56090779	56090779	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:56090779T>C	ENST00000608263.1	-	5	1832	c.1171A>G	c.(1171-1173)Acg>Gcg	p.T391A	CTCFL_ENST00000539382.1_Missense_Mutation_p.T186A|CTCFL_ENST00000502686.2_Missense_Mutation_p.T129A|CTCFL_ENST00000429804.3_Missense_Mutation_p.T391A|CTCFL_ENST00000609232.1_Missense_Mutation_p.T391A|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000243914.3_Missense_Mutation_p.T391A|CTCFL_ENST00000422869.2_Missense_Mutation_p.T391A|CTCFL_ENST00000433949.3_Missense_Mutation_p.T186A|CTCFL_ENST00000608440.1_Missense_Mutation_p.T391A|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000608425.1_Missense_Mutation_p.T391A|CTCFL_ENST00000423479.3_Missense_Mutation_p.T391A|CTCFL_ENST00000608903.1_Missense_Mutation_p.T129A|CTCFL_ENST00000371196.2_Missense_Mutation_p.T391A	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	391					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)			CCTGAGTGCGTTCTCATGTGG	0.478																																					p.T391A		Atlas-SNP	.											CTCFL,colon,carcinoma,+2,2	CTCFL	97	2	0			c.A1171G						scavenged	.						168.0	157.0	161.0					20																	56090779		2203	4300	6503	SO:0001583	missense	140690	exon5			AGTGCGTTCTCAT		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.1171A>G	20.37:g.56090779T>C	ENSP00000476783:p.Thr391Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	2	0.027027	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	.	.	.	.	.	.	.	.	.	.	T	21.8	4.203477	0.79127	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T	0.30448	2.08;2.08;2.08;1.53;2.08;2.08;1.53;2.08;2.08;2.08	5.24	5.24	0.73138	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45867	D	0.000328	T	0.48390	0.1497	L	0.56199	1.76	0.42311	D	0.992219	D;D;D;D;D	0.71674	0.975;0.998;0.98;0.998;0.998	P;D;P;D;D	0.69654	0.854;0.965;0.881;0.965;0.965	T	0.38993	-0.9635	10	0.33940	T	0.23	-29.2685	14.4174	0.67160	0.0:0.0:0.0:1.0	.	391;391;391;391;391	A6XGM9;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;CTCFL_HUMAN	A	391;391;391;391;391;129;391;391;186;391	ENSP00000415579:T391A;ENSP00000243914:T391A;ENSP00000360239:T391A;ENSP00000415329:T391A;ENSP00000392034:T391A;ENSP00000437999:T129A;ENSP00000413713:T391A;ENSP00000403369:T391A;ENSP00000439998:T186A;ENSP00000399061:T391A	ENSP00000243914:T391A	T	-	1	0	CTCFL	55524185	1.000000	0.71417	0.587000	0.28692	0.538000	0.34931	7.706000	0.84615	2.108000	0.64289	0.528000	0.53228	ACG	.	.	none		0.478	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
ZNF708	7562	hgsc.bcm.edu	37	19	21477403	21477403	+	Missense_Mutation	SNP	T	T	G	rs1781872	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21477403T>G	ENST00000356929.3	-	4	562	c.365A>C	c.(364-366)aAa>aCa	p.K122T		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	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)|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						GTGACCTCCTTTGTGCAACTT	0.363													T|||	492	0.0982428	0.0651	0.1037	5008	,	,		17875	0.0069		0.1978	False		,,,				2504	0.1309				p.K122T		Atlas-SNP	.											.	ZNF708	66	.	0			c.A365C						PASS	.	T	THR/LYS	429,3977		24,381,1798	172.0	154.0	161.0		365	-0.8	0.0	19	dbSNP_89	161	1799,6801		204,1391,2705	yes	missense	ZNF708	NM_021269.2	78	228,1772,4503	GG,GT,TT		20.9186,9.7367,17.1306	benign	122/564	21477403	2228,10778	2203	4300	6503	SO:0001583	missense	7562	exon4			CCTCCTTTGTGCA	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.365A>C	19.37:g.21477403T>G	ENSP00000349401:p.Lys122Thr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	58	0.43609	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	227	0.10393772893772894	34	0.06910569105691057	45	0.12430939226519337	5	0.008741258741258742	143	0.18865435356200527	.	7.383	0.629218	0.14257	0.097367	0.209186	ENSG00000182141	ENST00000356929	T	0.06687	3.27	1.07	-0.782	0.10961	.	.	.	.	.	T	0.00012	0.0000	M	0.86651	2.83	0.80722	P	0.0	P	0.39748	0.686	B	0.34242	0.178	T	0.21415	-1.0246	8	0.48119	T	0.1	.	4.6273	0.12484	0.0:0.0:0.317:0.683	rs1781872;rs17680541;rs52800300;rs1781872	122	P17019	ZN708_HUMAN	T	122	ENSP00000349401:K122T	ENSP00000349401:K122T	K	-	2	0	ZNF708	21269243	0.000000	0.05858	0.026000	0.17262	0.025000	0.11179	-0.456000	0.06754	0.402000	0.25451	0.391000	0.25812	AAA	T|0.851;G|0.149	0.149	strong		0.363	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269	
RPS24	6229	hgsc.bcm.edu	37	10	79814612	79814612	+	Silent	SNP	T	T	C	rs2257155	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:79814612T>C	ENST00000440692.1	+	5	856	c.714T>C	c.(712-714)ggT>ggC	p.G238G	RPS24_ENST00000476545.1_3'UTR	NM_001142285.1	NP_001135757.1	P62847	RS24_HUMAN	ribosomal protein S24	0					cellular protein metabolic process (GO:0044267)|erythrocyte homeostasis (GO:0034101)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|translation initiation factor binding (GO:0031369)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(2)|skin(1)	5	all_cancers(46;0.0343)|all_epithelial(25;0.000959)|Breast(12;0.00113)|Prostate(51;0.0095)		Epithelial(14;0.00128)|OV - Ovarian serous cystadenocarcinoma(4;0.00248)|all cancers(16;0.00428)			ctgtggacggtgacttggtcc	0.572													T|||	3	0.000599042	0.0	0.0014	5008	,	,		17704	0.0		0.002	False		,,,				2504	0.0				p.G238G		Atlas-SNP	.											.	RPS24	23	.	0			c.T714C						PASS	.	T		0,1384		0,0,692	105.0	103.0	104.0		714	-1.1	0.0	10	dbSNP_100	104	10,3172		0,10,1581	no	coding-synonymous	RPS24	NM_001142285.1		0,10,2273	CC,CT,TT		0.3143,0.0,0.219		238/290	79814612	10,4556	692	1591	2283	SO:0001819	synonymous_variant	6229	exon5			GGACGGTGACTTG	AB007159	CCDS7355.1, CCDS7356.1, CCDS44443.1	10q22	2011-04-06			ENSG00000138326	ENSG00000138326		"""S ribosomal proteins"""	10411	protein-coding gene	gene with protein product		602412				9027498, 9582194	Standard	NM_001142283		Approved	S24	uc001jzs.3	P62847	OTTHUMG00000018549	ENST00000440692.1:c.714T>C	10.37:g.79814612T>C		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	94	67	0.712766	NM_001142285	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Silent	SNP	ENST00000440692.1	37	CCDS44443.1																																																																																			T|1.000;|0.000	.	weak		0.572	RPS24-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001026	
HEG1	57493	hgsc.bcm.edu	37	3	124746182	124746182	+	Silent	SNP	C	C	A	rs2333041	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:124746182C>A	ENST00000311127.4	-	3	847	c.780G>T	c.(778-780)ccG>ccT	p.P260P		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	260					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						GAAGAAAGGACGGGCTCCAAG	0.557													c|||	2572	0.513578	0.469	0.4755	5008	,	,		18354	0.4782		0.5457	False		,,,				2504	0.6043				p.P260P		Atlas-SNP	.											HEG1,NS,carcinoma,-1,1	HEG1	109	1	0			c.G780T						scavenged	.	T		1785,2205		387,1011,597	61.0	64.0	63.0		780	0.7	0.0	3	dbSNP_100	63	4203,4105		1043,2117,994	no	coding-synonymous	HEG1	NM_020733.1		1430,3128,1591	AA,AC,CC		49.4102,44.7368,48.6908		260/1382	124746182	5988,6310	1995	4154	6149	SO:0001819	synonymous_variant	57493	exon3			AAAGGACGGGCTC	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.780G>T	3.37:g.124746182C>A		Somatic	201	2	0.00995025		WXS	Illumina HiSeq	Phase_I	210	102	0.485714	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Silent	SNP	ENST00000311127.4	37	CCDS46898.1																																																																																			A|0.503;C|0.497;T|0.000	0.503	strong		0.557	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
ZDHHC11	79844	hgsc.bcm.edu	37	5	843815	843815	+	Silent	SNP	C	C	T	rs71591190	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:843815C>T	ENST00000283441.8	-	4	911	c.528G>A	c.(526-528)tcG>tcA	p.S176S	ZDHHC11_ENST00000424784.2_Silent_p.S176S|ZDHHC11_ENST00000511539.1_5'UTR|ZDHHC11_ENST00000503758.2_5'Flank	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	176						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)			CAGCTGTGGCCGAGGCCACAG	0.667																																					p.S176S		Atlas-SNP	.											ZDHHC11_ENST00000424784,rectum,carcinoma,0,2	ZDHHC11	97	2	0			c.G528A						scavenged	.						27.0	22.0	23.0					5																	843815		2199	4276	6475	SO:0001819	synonymous_variant	79844	exon4			TGTGGCCGAGGCC	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.528G>A	5.37:g.843815C>T		Somatic	487	3	0.00616016		WXS	Illumina HiSeq	Phase_I	451	136	0.301552	NM_024786	Q6UWR9	Silent	SNP	ENST00000283441.8	37	CCDS3857.1																																																																																			C|0.856;T|0.144	0.144	strong		0.667	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062065	64062065	+	Missense_Mutation	SNP	T	T	C	rs10878075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:64062065T>C	ENST00000324472.4	-	1	292	c.109A>G	c.(109-111)Atg>Gtg	p.M37V	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	37			M -> V (in dbSNP:rs10878075). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GACTTTTCCATCTCCTCCTCT	0.642													C|||	1980	0.395367	0.4433	0.2565	5008	,	,		14843	0.5714		0.1978	False		,,,				2504	0.4509				p.M37V		Atlas-SNP	.											.	DPY19L2	97	.	0			c.A109G						PASS	.	C	VAL/MET	1659,2729		308,1043,843	28.0	36.0	34.0		109	0.6	0.0	12	dbSNP_120	34	1695,6897		179,1337,2780	no	missense	DPY19L2	NM_173812.4	21	487,2380,3623	CC,CT,TT		19.7277,37.8077,25.8398	benign	37/759	64062065	3354,9626	2194	4296	6490	SO:0001583	missense	283417	exon1			TTTCCATCTCCTC		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.109A>G	12.37:g.64062065T>C	ENSP00000315988:p.Met37Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	140	52	0.371429	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	767	0.35119047619047616	189	0.38414634146341464	99	0.27348066298342544	331	0.5786713286713286	148	0.19525065963060687	C	1.696	-0.502757	0.04261	0.378077	0.197277	ENSG00000177990	ENST00000324472;ENST00000542209	T;T	0.34072	1.38;1.99	1.61	0.65	0.17812	.	1.705710	0.04502	N	0.381454	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	0.45086	-0.9285	8	.	.	.	.	2.3121	0.04189	0.2942:0.512:0.0:0.1938	rs10878075;rs10878075	37	Q6NUT2	D19L2_HUMAN	V	37	ENSP00000315988:M37V;ENSP00000444932:M37V	.	M	-	1	0	DPY19L2	62348332	0.000000	0.05858	0.007000	0.13788	0.027000	0.11550	-1.353000	0.02617	-0.139000	0.11414	-1.063000	0.02288	ATG	T|0.711;C|0.289	0.289	strong		0.642	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
MUC2	4583	hgsc.bcm.edu	37	11	1092926	1092926	+	Missense_Mutation	SNP	C	C	G	rs377100070		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1092926C>G	ENST00000441003.2	+	30	4772	c.4745C>G	c.(4744-4746)aCa>aGa	p.T1582R	MUC2_ENST00000359061.5_Missense_Mutation_p.T1583R|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	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.T1582R(1)|p.T1583R(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)	cagaccccaacatcgacaccc	0.632																																					p.T1582R		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - Missense(2)	prostate(2)	c.C4745G						PASS	.	C	ARG/THR	24,3818		0,24,1897	77.0	115.0	102.0		4742	0.5	0.0	11		102	140,6992		0,140,3426	no	missense	MUC2	NM_002457.2	71	0,164,5323	GG,GC,CC		1.963,0.6247,1.4944	benign	1581/2813	1092926	164,10810	1921	3566	5487	SO:0001583	missense	4583	exon30			CCCCAACATCGAC	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.4745C>G	11.37:g.1092926C>G	ENSP00000415183:p.Thr1582Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	67	9	0.134328	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.792	-0.251014	0.05867	0.006247	0.01963	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.14144	2.53;2.91	1.75	0.53	0.17102	.	18.926900	0.00496	U	0.000153	T	0.05227	0.0139	.	.	.	0.09310	N	1	B	0.16802	0.019	B	0.11329	0.006	T	0.28364	-1.0046	9	0.45353	T	0.12	.	7.5493	0.27786	0.0:0.7315:0.2684:0.0	.	1582	E7EUV1	.	R	1582;1583	ENSP00000415183:T1582R;ENSP00000351956:T1583R	ENSP00000351956:T1583R	T	+	2	0	MUC2	1082926	0.001000	0.12720	0.001000	0.08648	0.035000	0.12851	0.551000	0.23361	1.016000	0.39470	0.121000	0.15741	ACA	.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
NEK1	4750	hgsc.bcm.edu	37	4	170428901	170428901	+	Missense_Mutation	SNP	C	C	T	rs33933790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:170428901C>T	ENST00000439128.2	-	20	2432	c.1792G>A	c.(1792-1794)Gct>Act	p.A598T	NEK1_ENST00000512193.1_Missense_Mutation_p.A529T|NEK1_ENST00000507142.1_Missense_Mutation_p.A626T|NEK1_ENST00000510533.1_Missense_Mutation_p.A554T|NEK1_ENST00000511633.1_Missense_Mutation_p.A582T	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	598			A -> T (in dbSNP:rs33933790). {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)		CTCATGTCAGCCTCTTCACTT	0.348													C|||	119	0.023762	0.0038	0.0346	5008	,	,		14938	0.0		0.0795	False		,,,				2504	0.0102				p.A626T		Atlas-SNP	.											.	NEK1	203	.	0			c.G1876A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	63,3621		1,61,1780	122.0	112.0	115.0		1876,1744,1585,1660,1792	1.8	1.0	4	dbSNP_126	115	655,7525		31,593,3466	yes	missense,missense,missense,missense,missense	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	58,58,58,58,58	32,654,5246	TT,TC,CC		8.0073,1.7101,6.0519	benign,benign,benign,benign,benign	626/1287,582/1243,529/1190,554/1215,598/1259	170428901	718,11146	1842	4090	5932	SO:0001583	missense	4750	exon22			TGTCAGCCTCTTC	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.1792G>A	4.37:g.170428901C>T	ENSP00000408020:p.Ala598Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	77	58	0.753247	NM_001199397	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	78	0.03571428571428571	3	0.006097560975609756	10	0.027624309392265192	0	0.0	65	0.08575197889182058	C	15.63	2.889056	0.52014	0.017101	0.080073	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.72282	-0.6;-0.6;-0.53;-0.64;-0.57	5.53	1.79	0.24919	.	0.307929	0.27495	N	0.019103	T	0.04318	0.0119	L	0.39397	1.21	0.38085	D	0.936805	B;B;B;B;B	0.26318	0.146;0.069;0.146;0.069;0.09	B;B;B;B;B	0.31337	0.128;0.056;0.128;0.056;0.06	T	0.06127	-1.0844	10	0.28530	T	0.3	.	7.5477	0.27777	0.1188:0.6787:0.0:0.2025	rs33933790;rs57604515	529;582;626;554;598	Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;NEK1_HUMAN	T	598;582;554;626;529	ENSP00000408020:A598T;ENSP00000423332:A582T;ENSP00000427653:A554T;ENSP00000424757:A626T;ENSP00000424938:A529T	ENSP00000408020:A598T	A	-	1	0	NEK1	170665476	0.151000	0.22747	0.998000	0.56505	0.884000	0.51177	0.194000	0.17135	0.363000	0.24346	0.655000	0.94253	GCT	C|0.961;T|0.039	0.039	strong		0.348	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
CECR1	51816	hgsc.bcm.edu	37	22	17662874	17662874	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:17662874T>C	ENST00000399839.1	-	9	1548	c.1278A>G	c.(1276-1278)gtA>gtG	p.V426V	CECR1_ENST00000399837.2_Silent_p.V426V|CECR1_ENST00000330232.4_Silent_p.V185V|CECR1_ENST00000449907.2_Silent_p.V384V|CECR1_ENST00000262607.3_Silent_p.V426V	NM_001282227.1|NM_001282228.1	NP_001269156.1|NP_001269157.1	Q9NZK5	CECR1_HUMAN	cat eye syndrome chromosome region, candidate 1	426					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)				TCAGAGTGGCTACAGGGTGGT	0.498																																					p.V426V		Atlas-SNP	.											CECR1_ENST00000330232,NS,lymphoid_neoplasm,-2,4	CECR1	77	4	0			c.A1278G						scavenged	.						83.0	73.0	77.0					22																	17662874		2203	4300	6503	SO:0001819	synonymous_variant	51816	exon8			AGTGGCTACAGGG	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.1278A>G	22.37:g.17662874T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	124	2	0.016129	NM_017424	A8K9H4|Q6ICF1|Q86UB6|Q8NCJ2|Q96K41	Silent	SNP	ENST00000399839.1	37	CCDS13742.1																																																																																			.	.	none		0.498	CECR1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316079.1		
KIRREL2	84063	hgsc.bcm.edu	37	19	36351935	36351935	+	Silent	SNP	G	G	T	rs35854130	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36351935G>T	ENST00000360202.5	+	8	1251	c.1053G>T	c.(1051-1053)gcG>gcT	p.A351A	NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000592409.1_Silent_p.A351A|KIRREL2_ENST00000347900.6_Silent_p.A301A|KIRREL2_ENST00000262625.7_Silent_p.A351A	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	351	Ig-like C2-type 4.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	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)			GCGGTGGCGCGCAGGTACAGC	0.677													G|||	895	0.178714	0.2042	0.1527	5008	,	,		15275	0.0139		0.2296	False		,,,				2504	0.2802				p.A351A		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G1053T						PASS	.	G	,,	915,3469		114,687,1391	12.0	14.0	13.0		1053,903,1053	-4.8	0.2	19	dbSNP_126	13	1946,6610		222,1502,2554	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	336,2189,3945	TT,TG,GG		22.7443,20.8714,22.1097	,,	351/634,301/584,351/709	36351935	2861,10079	2192	4278	6470	SO:0001819	synonymous_variant	84063	exon8			TGGCGCGCAGGTA	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1053G>T	19.37:g.36351935G>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			G|0.811;T|0.189	0.189	strong		0.677	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2883588	2883588	+	Missense_Mutation	SNP	C	C	A	rs17762452	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:2883588C>A	ENST00000254695.8	+	9	694	c.604C>A	c.(604-606)Ctg>Atg	p.L202M	RAP1GAP2_ENST00000366401.4_Missense_Mutation_p.L187M|RAP1GAP2_ENST00000542807.1_Missense_Mutation_p.L202M|RAP1GAP2_ENST00000540393.2_Missense_Mutation_p.L183M	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	202			L -> M (in dbSNP:rs17762452).		negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CAGGTCCAAACTGAAGACGGT	0.547													C|||	1488	0.297125	0.1104	0.3112	5008	,	,		1167	0.3313		0.2972	False		,,,				2504	0.5041				p.L202M		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C604A						PASS	.	C	MET/LEU,MET/LEU	530,3480		43,444,1518	87.0	84.0	85.0		559,604	4.0	1.0	17	dbSNP_123	85	2656,5676		444,1768,1954	yes	missense,missense	RAP1GAP2	NM_001100398.1,NM_015085.4	15,15	487,2212,3472	AA,AC,CC		31.8771,13.217,25.8143	benign,benign	187/716,202/731	2883588	3186,9156	2005	4166	6171	SO:0001583	missense	23108	exon9			TCCAAACTGAAGA	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.604C>A	17.37:g.2883588C>A	ENSP00000254695:p.Leu202Met	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	188	97	0.515957	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Missense_Mutation	SNP	ENST00000254695.8	37	CCDS45573.1	594	0.27197802197802196	58	0.11788617886178862	105	0.2900552486187845	204	0.35664335664335667	227	0.2994722955145119	C	11.10	1.540719	0.27563	0.13217	0.318771	ENSG00000132359	ENST00000254695;ENST00000366401;ENST00000540393;ENST00000542807	D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36	4.99	4.02	0.46733	.	0.484343	0.21364	N	0.075741	T	0.00012	0.0000	N	0.08118	0	0.46149	P	0.0011100000000000554	B;B	0.27264	0.173;0.108	B;B	0.34038	0.174;0.084	T	0.03433	-1.1037	9	0.31617	T	0.26	-8.9204	9.9318	0.41528	0.0:0.3971:0.6029:0.0	rs17762452;rs52833255;rs17762452	187;202	Q684P5-2;Q684P5	.;RPGP2_HUMAN	M	202;187;183;202	ENSP00000254695:L202M;ENSP00000389824:L187M;ENSP00000439688:L183M;ENSP00000444890:L202M	ENSP00000254695:L202M	L	+	1	2	RAP1GAP2	2830338	0.999000	0.42202	1.000000	0.80357	0.953000	0.61014	0.540000	0.23191	1.113000	0.41760	0.555000	0.69702	CTG	C|0.737;A|0.263	0.263	strong		0.547	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
SLC26A8	116369	hgsc.bcm.edu	37	6	35960390	35960390	+	Missense_Mutation	SNP	C	C	T	rs17707331	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:35960390C>T	ENST00000490799.1	-	6	1042	c.689G>A	c.(688-690)aGt>aAt	p.S230N	SLC26A8_ENST00000355574.2_Missense_Mutation_p.S230N|SLC26A8_ENST00000394602.2_Intron	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						CAGGTAAGCACTCATTGCAGA	0.478													C|||	448	0.0894569	0.0325	0.1383	5008	,	,		20612	0.0506		0.1402	False		,,,				2504	0.1196				p.S230N		Atlas-SNP	.											.	SLC26A8	95	.	0			c.G689A						PASS	.	C	ASN/SER,ASN/SER,	188,4218	118.8+/-156.5	3,182,2018	133.0	125.0	128.0		689,689,	3.3	0.7	6	dbSNP_123	128	1143,7457	234.3+/-267.3	89,965,3246	yes	missense,missense,intron	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	46,46,	92,1147,5264	TT,TC,CC		13.2907,4.2669,10.2337	benign,benign,	230/971,230/971,	35960390	1331,11675	2203	4300	6503	SO:0001583	missense	116369	exon6			TAAGCACTCATTG	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.689G>A	6.37:g.35960390C>T	ENSP00000417638:p.Ser230Asn	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	221	0.10119047619047619	22	0.044715447154471545	60	0.16574585635359115	34	0.05944055944055944	105	0.13852242744063326	C	0.032	-1.328172	0.01309	0.042669	0.132907	ENSG00000112053	ENST00000490799;ENST00000355574	D;D	0.93859	-3.3;-3.3	5.26	3.26	0.37387	Sulphate transporter (1);	0.337905	0.28790	N	0.014127	T	0.75635	0.3876	L	0.28054	0.825	0.38754	P	0.04583300000000001	B	0.18863	0.031	B	0.19946	0.027	T	0.61083	-0.7134	9	0.28530	T	0.3	.	4.1904	0.10417	0.0:0.4915:0.0:0.5085	rs17707331;rs52836854;rs17707331	230	Q96RN1	S26A8_HUMAN	N	230	ENSP00000417638:S230N;ENSP00000347778:S230N	ENSP00000347778:S230N	S	-	2	0	SLC26A8	36068368	0.310000	0.24527	0.680000	0.29994	0.068000	0.16541	-0.214000	0.09292	0.501000	0.28013	0.655000	0.94253	AGT	C|0.898;N|0.000	.	strong		0.478	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
MUC17	140453	hgsc.bcm.edu	37	7	100681303	100681303	+	Silent	SNP	T	T	C	rs143516283		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681303T>C	ENST00000306151.4	+	3	6670	c.6606T>C	c.(6604-6606)ccT>ccC	p.P2202P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2202	59 X approximate tandem repeats.|Ser-rich.				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)					GTTCATCTCCTACAACTTCTG	0.507																																					p.P2202P		Atlas-SNP	.											MUC17,rectum,carcinoma,0,1	MUC17	804	1	0			c.T6606C						PASS	.						311.0	311.0	311.0					7																	100681303		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			ATCTCCTACAACT	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.6606T>C	7.37:g.100681303T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	245	40	0.163265	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.	.	weak		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CCNA1	8900	hgsc.bcm.edu	37	13	37012830	37012830	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:37012830C>T	ENST00000255465.4	+	5	983	c.719C>T	c.(718-720)aCg>aTg	p.T240M	CCNA1_ENST00000440264.1_Missense_Mutation_p.T196M|CCNA1_ENST00000418263.1_Missense_Mutation_p.T239M|CCNA1_ENST00000449823.1_Missense_Mutation_p.T196M			P78396	CCNA1_HUMAN	cyclin A1	240					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)		p.T240M(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		CCAGACATCACGGAAGGCATG	0.468																																					p.T240M		Atlas-SNP	.											CCNA1,NS,carcinoma,0,1	CCNA1	91	1	1	Substitution - Missense(1)	endometrium(1)	c.C719T						scavenged	.						114.0	100.0	105.0					13																	37012830		2203	4300	6503	SO:0001583	missense	8900	exon5			ACATCACGGAAGG	U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.719C>T	13.37:g.37012830C>T	ENSP00000255465:p.Thr240Met	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	216	4	0.0185185	NM_003914	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Missense_Mutation	SNP	ENST00000255465.4	37	CCDS9357.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689414	0.88735	.	.	ENSG00000133101	ENST00000440264;ENST00000449823;ENST00000418263;ENST00000255465	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	5.33	5.33	0.75918	Cyclin, N-terminal (1);Cyclin-like (2);	0.000000	0.85682	D	0.000000	T	0.50684	0.1630	M	0.93939	3.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.64127	-0.6480	10	0.87932	D	0	.	19.3924	0.94590	0.0:1.0:0.0:0.0	.	239;240	P78396-2;P78396	.;CCNA1_HUMAN	M	196;196;239;240	ENSP00000400666:T196M;ENSP00000409873:T196M;ENSP00000396479:T239M;ENSP00000255465:T240M	ENSP00000255465:T240M	T	+	2	0	CCNA1	35910830	1.000000	0.71417	0.957000	0.39632	0.791000	0.44710	7.493000	0.81493	2.641000	0.89580	0.650000	0.86243	ACG	.	.	none		0.468	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914	
DPP10	57628	hgsc.bcm.edu	37	2	116510817	116510817	+	Missense_Mutation	SNP	G	G	C	rs2053724	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:116510817G>C	ENST00000410059.1	+	11	1498	c.1018G>C	c.(1018-1020)Gct>Cct	p.A340P	DPP10_ENST00000393147.2_Missense_Mutation_p.A344P|DPP10_ENST00000409163.1_Missense_Mutation_p.A290P|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						scavenged	.	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	257	2	0.0077821		WXS	Illumina HiSeq	Phase_I	186	84	0.451613	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	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011298	46011298	+	Silent	SNP	G	G	A	rs113437209	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:46011298G>A	ENST00000400368.1	-	1	1088	c.1068C>T	c.(1066-1068)agC>agT	p.S356S	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	356						keratin filament (GO:0045095)		p.S356S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CAGAGCAGAGGCTGTAGCAGG	0.677																																					p.S356S		Atlas-SNP	.											KRTAP10-6,NS,carcinoma,0,1	KRTAP10-6	57	1	1	Substitution - coding silent(1)	stomach(1)	c.C1068T						scavenged	.						29.0	38.0	35.0					21																	46011298		2194	4298	6492	SO:0001819	synonymous_variant	386674	exon1			GCAGAGGCTGTAG	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.1068C>T	21.37:g.46011298G>A		Somatic	251	9	0.0358566		WXS	Illumina HiSeq	Phase_I	303	14	0.0462046	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			A|1.000;|0.000	1.000	weak		0.677	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
FTCD	10841	hgsc.bcm.edu	37	21	47557222	47557222	+	Silent	SNP	G	G	A	rs10432965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:47557222G>A	ENST00000291670.5	-	13	1513	c.1470C>T	c.(1468-1470)ggC>ggT	p.G490G	FTCD_ENST00000355384.2_Missense_Mutation_p.R476C|FTCD_ENST00000397743.1_Missense_Mutation_p.R476C|FTCD_ENST00000397746.3_Silent_p.G490G|FTCD_ENST00000359679.2_Silent_p.G490G|FTCD_ENST00000498355.2_5'UTR|FTCD_ENST00000397748.1_Silent_p.G490G	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	490	Cyclodeaminase/cyclohydrolase. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|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)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	CGCCAAACACGCCCATCTCCA	0.602													G|||	839	0.167532	0.2103	0.0951	5008	,	,		18852	0.3512		0.0338	False		,,,				2504	0.1094				p.G490G		Atlas-SNP	.											.	FTCD	59	.	0			c.C1470T						PASS	.	G	,	840,3566	331.0+/-301.8	82,676,1445	142.0	132.0	135.0		1470,1470	-8.2	0.2	21	dbSNP_119	135	352,8248	118.1+/-177.6	1,350,3949	no	coding-synonymous,coding-synonymous	FTCD	NM_006657.2,NM_206965.1	,	83,1026,5394	AA,AG,GG		4.093,19.0649,9.165	,	490/542,490/542	47557222	1192,11814	2203	4300	6503	SO:0001819	synonymous_variant	10841	exon13			AAACACGCCCATC	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"""formiminotransferase cyclodeaminase"""			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.1470C>T	21.37:g.47557222G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Silent	SNP	ENST00000291670.5	37	CCDS13731.1	377|377	0.17261904761904762|0.17261904761904762	97|97	0.19715447154471544|0.19715447154471544	27|27	0.07458563535911603|0.07458563535911603	227|227	0.3968531468531469|0.3968531468531469	26|26	0.03430079155672823|0.03430079155672823	G|G	0.542|0.542	-0.853002|-0.853002	0.02630|0.02630	0.190649|0.190649	0.04093|0.04093	ENSG00000160282|ENSG00000160282	ENST00000446405|ENST00000355384;ENST00000397743	.|D;D	.|0.84800	.|-1.9;-1.9	4.12|4.12	-8.25|-8.25	0.01025|0.01025	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.52501|0.52501	P|P	4.300000000001525E-5|4.300000000001525E-5	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.24621|0.24621	-1.0155|-1.0155	3|7	.|0.72032	.|D	.|0.01	.|.	2.3273|2.3273	0.04226|0.04226	0.2715:0.0919:0.3691:0.2676|0.2715:0.0919:0.3691:0.2676	rs10432965;rs10432965|rs10432965;rs10432965	.|476	.|B7WPK3	.|.	V|C	31|476	.|ENSP00000347545:R476C;ENSP00000380851:R476C	.|ENSP00000347545:R476C	A|R	-|-	2|1	0|0	FTCD|FTCD	46381650|46381650	0.000000|0.000000	0.05858|0.05858	0.210000|0.210000	0.23637|0.23637	0.100000|0.100000	0.18952|0.18952	-4.192000|-4.192000	0.00277|0.00277	-1.093000|-1.093000	0.03058|0.03058	-1.360000|-1.360000	0.01215|0.01215	GCG|CGT	G|0.872;A|0.128	0.128	strong		0.602	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657	
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526406	150526406	+	Silent	SNP	C	C	T	rs6681639	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:150526406C>T	ENST00000369038.2	+	4	1140	c.939C>T	c.(937-939)ggC>ggT	p.G313G	ADAMTSL4_ENST00000271643.4_Silent_p.G313G|ADAMTSL4_ENST00000369041.5_Silent_p.G313G|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000369039.5_Silent_p.G313G|MIR4257_ENST00000581735.1_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	313					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)			GCCAGCAGGGCCAAGGGCCTT	0.716													C|||	1739	0.347244	0.5832	0.2666	5008	,	,		13904	0.3056		0.2853	False		,,,				2504	0.1922				p.G313G		Atlas-SNP	.											ADAMTSL4,NS,carcinoma,0,1	ADAMTSL4	101	1	0			c.C939T						PASS	.	C	,	2293,2099		603,1087,506	13.0	16.0	15.0		939,939	1.3	0.5	1	dbSNP_116	15	2315,6257		329,1657,2300	no	coding-synonymous,coding-synonymous	ADAMTSL4	NM_019032.4,NM_025008.3	,	932,2744,2806	TT,TC,CC		27.0065,47.7914,35.5446	,	313/1075,313/878	150526406	4608,8356	2196	4286	6482	SO:0001819	synonymous_variant	54507	exon6			GCAGGGCCAAGGG	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.939C>T	1.37:g.150526406C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	137	84	0.613139	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Silent	SNP	ENST00000369038.2	37	CCDS955.1																																																																																			C|0.647;T|0.353	0.353	strong		0.716	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
FNDC1	84624	hgsc.bcm.edu	37	6	159653544	159653544	+	Missense_Mutation	SNP	G	G	A	rs139265083	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159653544G>A	ENST00000297267.9	+	11	2200	c.2000G>A	c.(1999-2001)cGg>cAg	p.R667Q	FNDC1_ENST00000340366.6_Missense_Mutation_p.R604Q	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	667					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)		GCCCAGCCCCGGCCAGCCCTG	0.697													G|||	67	0.0133786	0.0015	0.0317	5008	,	,		12156	0.001		0.0278	False		,,,				2504	0.0143				p.R667Q		Atlas-SNP	.											FNDC1,NS,haematopoietic_neoplasm,+1,2	FNDC1	250	2	0			c.G2000A						PASS	.	G	GLN/ARG	28,3892		0,28,1932	13.0	18.0	16.0		2000	2.7	0.0	6	dbSNP_134	16	307,7885		10,287,3799	no	missense	FNDC1	NM_032532.2	43	10,315,5731	AA,AG,GG		3.7476,0.7143,2.7659	possibly-damaging	667/1895	159653544	335,11777	1960	4096	6056	SO:0001583	missense	84624	exon11			AGCCCCGGCCAGC	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.2000G>A	6.37:g.159653544G>A	ENSP00000297267:p.Arg667Gln	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	42	30	0.714286	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	36	0.016483516483516484	0	0.0	13	0.03591160220994475	0	0.0	23	0.030343007915567283	G	12.96	2.094516	0.36952	0.007143	0.037476	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.07567	3.18;3.98	4.64	2.74	0.32292	.	1.268200	0.05190	N	0.502856	T	0.01489	0.0048	N	0.14661	0.345	0.09310	N	1	B;B	0.30021	0.265;0.105	B;B	0.23852	0.049;0.009	T	0.46911	-0.9157	10	0.30854	T	0.27	-3.1622	6.7573	0.23520	0.2381:0.0:0.7619:0.0	.	604;667	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	Q	667;604	ENSP00000297267:R667Q;ENSP00000342460:R604Q	ENSP00000297267:R667Q	R	+	2	0	FNDC1	159573534	0.000000	0.05858	0.029000	0.17559	0.073000	0.16967	-0.331000	0.07914	0.330000	0.23485	-0.345000	0.07892	CGG	G|0.979;A|0.021	0.021	strong		0.697	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
MUC17	140453	hgsc.bcm.edu	37	7	100678560	100678560	+	Missense_Mutation	SNP	C	C	A	rs77199586	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678560C>A	ENST00000306151.4	+	3	3927	c.3863C>A	c.(3862-3864)aCg>aAg	p.T1288K		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1288	59 X approximate tandem repeats.|Ser-rich.				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)					GTCAGCACCACGCTGGTGACC	0.473																																					p.T1288K		Atlas-SNP	.											MUC17,NS,carcinoma,-1,2	MUC17	804	2	0			c.C3863A						PASS	.	C	LYS/THR	768,3638		0,768,1435	272.0	261.0	265.0		3863	-0.9	0.0	7	dbSNP_131	265	553,8047		0,553,3747	no	missense	MUC17	NM_001040105.1	78	0,1321,5182	AA,AC,CC		6.4302,17.4308,10.1569	possibly-damaging	1288/4494	100678560	1321,11685	2203	4300	6503	SO:0001583	missense	140453	exon3			GCACCACGCTGGT	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.3863C>A	7.37:g.100678560C>A	ENSP00000302716:p.Thr1288Lys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	263	85	0.323194	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.025	-1.376343	0.01214	0.174308	0.064302	ENSG00000169876	ENST00000306151	T	0.02421	4.3	0.471	-0.942	0.10398	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	N	1	P	0.47302	0.893	B	0.35727	0.209	T	0.40683	-0.9550	8	0.25106	T	0.35	.	.	.	.	.	1288	Q685J3	MUC17_HUMAN	K	1288	ENSP00000302716:T1288K	ENSP00000302716:T1288K	T	+	2	0	MUC17	100465280	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.039000	0.13884	-1.561000	0.01684	-2.053000	0.00404	ACG	C|0.936;A|0.064	0.064	strong		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MTRR	4552	hgsc.bcm.edu	37	5	7885959	7885959	+	Missense_Mutation	SNP	A	A	G	rs162036	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:7885959A>G	ENST00000264668.2	+	7	1160	c.1130A>G	c.(1129-1131)aAg>aGg	p.K377R	MTRR_ENST00000440940.2_Missense_Mutation_p.K350R|MTRR_ENST00000341013.6_3'UTR	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	377	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		K -> R (in dbSNP:rs162036).		cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|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, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GCAGACACAAAGAAGAAAGGT	0.493													A|||	1268	0.253195	0.4365	0.3516	5008	,	,		16390	0.1687		0.1362	False		,,,				2504	0.1431				p.K377R		Atlas-SNP	.											.	MTRR	74	.	0			c.A1130G						PASS	.	A	ARG/LYS,ARG/LYS	1662,2744	504.4+/-365.8	324,1014,865	85.0	85.0	85.0		1049,1130	-2.2	0.1	5	dbSNP_79	85	1019,7581	218.0+/-256.5	63,893,3344	yes	missense,missense	MTRR	NM_002454.2,NM_024010.2	26,26	387,1907,4209	GG,GA,AA		11.8488,37.7213,20.6136	benign,benign	350/699,377/726	7885959	2681,10325	2203	4300	6503	SO:0001583	missense	4552	exon7			ACACAAAGAAGAA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1130A>G	5.37:g.7885959A>G	ENSP00000264668:p.Lys377Arg	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	159	157	0.987421	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	504	0.23076923076923078	194	0.3943089430894309	111	0.30662983425414364	103	0.18006993006993008	96	0.1266490765171504	A	11.42	1.634585	0.29068	0.377213	0.118488	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.32515	1.45;1.45	5.83	-2.24	0.06909	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.374649	0.32753	N	0.005698	T	0.00012	0.0000	M	0.67700	2.07	0.19775	P	0.9999567659	B	0.30482	0.281	B	0.32022	0.139	T	0.43097	-0.9412	9	0.25106	T	0.35	-7.9558	11.3763	0.49730	0.6606:0.0:0.3394:0.0	rs162036;rs327619;rs329836;rs696311;rs1189017;rs16879313;rs52821116;rs61092918;rs162036	377	Q9UBK8	MTRR_HUMAN	R	377;350	ENSP00000264668:K377R;ENSP00000402510:K350R	ENSP00000264668:K377R	K	+	2	0	MTRR	7938959	0.995000	0.38212	0.055000	0.19348	0.522000	0.34438	1.230000	0.32612	-0.619000	0.05648	-0.263000	0.10527	AAG	A|0.774;G|0.226	0.226	strong		0.493	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
MUS81	80198	hgsc.bcm.edu	37	11	65631361	65631361	+	Missense_Mutation	SNP	C	C	T	rs34891773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65631361C>T	ENST00000308110.4	+	10	1397	c.1048C>T	c.(1048-1050)Cgg>Tgg	p.R350W	CFL1_ENST00000534769.1_5'Flank|MUS81_ENST00000533035.1_Missense_Mutation_p.R275W|EFEMP2_ENST00000532648.1_5'Flank	NM_025128.4	NP_079404.3	Q96NY9	MUS81_HUMAN	MUS81 structure-specific endonuclease subunit	350	ERCC4.		R -> W (in dbSNP:rs34891773).		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)		CGGCCGCTTCCGGGAGCAGAA	0.587								Homologous recombination					C|||	62	0.0123802	0.0197	0.0159	5008	,	,		18549	0.0		0.0239	False		,,,				2504	0.001				p.R350W		Atlas-SNP	.											.	MUS81	68	.	0			c.C1048T						PASS	.	C	TRP/ARG	59,4343	58.1+/-94.6	1,57,2143	62.0	69.0	67.0		1048	4.9	1.0	11	dbSNP_126	67	245,8347	97.7+/-159.3	3,239,4054	yes	missense	MUS81	NM_025128.4	101	4,296,6197	TT,TC,CC		2.8515,1.3403,2.3395	probably-damaging	350/552	65631361	304,12690	2201	4296	6497	SO:0001583	missense	80198	exon10			CGCTTCCGGGAGC		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.1048C>T	11.37:g.65631361C>T	ENSP00000307853:p.Arg350Trp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_025128	Q9H7D9	Missense_Mutation	SNP	ENST00000308110.4	37	CCDS8115.1	32|32	0.014652014652014652|0.014652014652014652	13|13	0.026422764227642278|0.026422764227642278	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	14|14	0.018469656992084433|0.018469656992084433	C|C	24.3|24.3	4.513249|4.513249	0.85389|0.85389	0.013403|0.013403	0.028515|0.028515	ENSG00000172732|ENSG00000172732	ENST00000529374|ENST00000533035;ENST00000308110;ENST00000437855	.|T;T	.|0.23754	.|1.89;1.89	5.8|5.8	4.89|4.89	0.63831|0.63831	.|DNA repair nuclease, XPF-type/Helicase (1);Restriction endonuclease, type II-like (1);ERCC4 domain (2);	.|0.177713	.|0.45126	.|D	.|0.000400	T|T	0.17066|0.17066	0.0410|0.0410	L|L	0.45228|0.45228	1.405|1.405	0.52501|0.52501	D|D	0.999959|0.999959	.|D	.|0.89917	.|1.0	.|D	.|0.64877	.|0.93	T|T	0.01298|0.01298	-1.1392|-1.1392	5|10	.|0.37606	.|T	.|0.19	-12.1179|-12.1179	12.8651|12.8651	0.57936|0.57936	0.0:0.9207:0.0:0.0793|0.0:0.9207:0.0:0.0793	rs34891773;rs61893866|rs34891773;rs61893866	.|350	.|Q96NY9	.|MUS81_HUMAN	L|W	275|275;350;350	.|ENSP00000432287:R275W;ENSP00000307853:R350W	.|ENSP00000307853:R350W	P|R	+|+	2|1	0|2	MUS81|MUS81	65387937|65387937	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.971000|0.971000	0.66376|0.66376	2.194000|2.194000	0.42668|0.42668	1.453000|1.453000	0.47775|0.47775	0.655000|0.655000	0.94253|0.94253	CCG|CGG	C|0.979;T|0.021	0.021	strong		0.587	MUS81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390941.3	NM_025128	
C10orf71	118461	hgsc.bcm.edu	37	10	50531606	50531606	+	Missense_Mutation	SNP	C	C	A	rs386743566|rs55780106	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50531606C>A	ENST00000374144.3	+	3	1304	c.1016C>A	c.(1015-1017)gCa>gAa	p.A339E	C10orf71_ENST00000323868.4_Missense_Mutation_p.A339E			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	339				A -> E (in Ref. 2; AL833265 and 4; AAI26414). {ECO:0000305}.						endometrium(1)	1						AACAGACTTGCAGCAGGGGCT	0.572													C|||	881	0.175919	0.1021	0.2594	5008	,	,		17311	0.3085		0.1481	False		,,,				2504	0.1084				p.A339E		Atlas-SNP	.											.	C10orf71	179	.	0			c.C1016A						PASS	.	C	GLU/ALA,GLU/ALA	499,3421		25,449,1486	47.0	51.0	49.0		1016,1016	1.1	0.0	10	dbSNP_129	49	1338,6972		106,1126,2923	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	107,107	131,1575,4409	AA,AC,CC		16.1011,12.7296,15.0204	benign,benign	339/1436,339/720	50531606	1837,10393	1960	4155	6115	SO:0001583	missense	118461	exon3			GACTTGCAGCAGG	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.1016C>A	10.37:g.50531606C>A	ENSP00000363259:p.Ala339Glu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	42	32	0.761905	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	474	0.21703296703296704	68	0.13821138211382114	90	0.24861878453038674	199	0.3479020979020979	117	0.15435356200527706	C	1.477	-0.558277	0.03967	0.127296	0.161011	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.14391	2.51;3.63	5.4	1.13	0.20643	.	1.118300	0.06816	N	0.791357	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.24043	0.096	B	0.28638	0.092	T	0.46034	-0.9220	9	0.08837	T	0.75	.	7.5024	0.27526	0.0:0.6013:0.2534:0.1452	rs55780106	339	Q711Q0-3	.	E	339	ENSP00000318713:A339E;ENSP00000363259:A339E	ENSP00000318713:A339E	A	+	2	0	C10orf71	50201612	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.095000	0.15127	0.658000	0.30925	0.655000	0.94253	GCA	C|0.803;A|0.197	0.197	strong		0.572	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
MUC17	140453	hgsc.bcm.edu	37	7	100678013	100678013	+	Missense_Mutation	SNP	G	G	A	rs75312831	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678013G>A	ENST00000306151.4	+	3	3380	c.3316G>A	c.(3316-3318)Gtg>Atg	p.V1106M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1106	59 X approximate tandem repeats.|Ser-rich.				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)					ACTAACAAGTGTGCCTGTCAG	0.507																																					p.V1106M		Atlas-SNP	.											MUC17,NS,carcinoma,-2,1	MUC17	804	1	0			c.G3316A						scavenged	.	A	MET/VAL	242,4164	121.3+/-158.8	0,242,1961	496.0	393.0	428.0		3316	-1.6	0.0	7	dbSNP_131	428	151,8449	62.8+/-124.8	0,151,4149	no	missense	MUC17	NM_001040105.1	21	0,393,6110	AA,AG,GG		1.7558,5.4925,3.0217	benign	1106/4494	100678013	393,12613	2203	4300	6503	SO:0001583	missense	140453	exon3			ACAAGTGTGCCTG	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.3316G>A	7.37:g.100678013G>A	ENSP00000302716:p.Val1106Met	Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	848	181	0.213443	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	0.067	-1.211056	0.01555	0.054925	0.017558	ENSG00000169876	ENST00000306151	T	0.02763	4.17	0.801	-1.6	0.08426	.	.	.	.	.	T	0.00241	0.0007	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.01281	0.0	T	0.43475	-0.9389	9	0.28530	T	0.3	.	0.7416	0.00975	0.3295:0.1734:0.324:0.173	.	1106	Q685J3	MUC17_HUMAN	M	1106	ENSP00000302716:V1106M	ENSP00000302716:V1106M	V	+	1	0	MUC17	100464733	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.810000	0.01729	-2.966000	0.00288	-1.214000	0.01621	GTG	A|0.022;G|0.978	0.022	strong		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ITIH5	80760	hgsc.bcm.edu	37	10	7618501	7618501	+	Silent	SNP	A	A	G	rs2275068	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:7618501A>G	ENST00000256861.6	-	10	1971	c.1893T>C	c.(1891-1893)gaT>gaC	p.D631D	ITIH5_ENST00000446830.2_Silent_p.D413D|ITIH5_ENST00000397145.2_Silent_p.D631D|ITIH5_ENST00000298441.6_Silent_p.D417D|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397146.2_Silent_p.D631D	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	631					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						CCTCCAGGCCATCCATGCGTG	0.692													G|||	2660	0.53115	0.3646	0.5461	5008	,	,		16089	0.7679		0.5219	False		,,,				2504	0.5112				p.D631D		Atlas-SNP	.											ITIH5_ENST00000397145,caecum,carcinoma,0,6	ITIH5	343	6	0			c.T1893C						scavenged	.	G	,,	1793,2613		363,1067,773	29.0	30.0	30.0		1893,1893,1251	-3.0	0.0	10	dbSNP_100	30	4619,3979		1269,2081,949	no	coding-synonymous,coding-synonymous,coding-synonymous	ITIH5	NM_001001851.2,NM_030569.6,NM_032817.5	,,	1632,3148,1722	GG,GA,AA		46.2782,40.6945,49.3079	,,	631/703,631/943,417/729	7618501	6412,6592	2203	4299	6502	SO:0001819	synonymous_variant	80760	exon10			CAGGCCATCCATG			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.1893T>C	10.37:g.7618501A>G		Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	51	50	0.980392	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																				A|0.494;G|0.506	0.506	strong		0.692	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
CEP55	55165	hgsc.bcm.edu	37	10	95259979	95259979	+	Missense_Mutation	SNP	C	C	G	rs3740370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:95259979C>G	ENST00000371485.3	+	2	475	c.171C>G	c.(169-171)caC>caG	p.H57Q		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	57			H -> Q (in dbSNP:rs3740370). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16406728}.		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)				AAGAGAGACACAGACTTTTGG	0.383													C|||	1345	0.26857	0.3238	0.1715	5008	,	,		18932	0.2887		0.2207	False		,,,				2504	0.2914				p.H57Q		Atlas-SNP	.											.	CEP55	35	.	0			c.C171G						PASS	.	C	GLN/HIS,GLN/HIS	1263,3143	430.1+/-342.5	192,879,1132	117.0	128.0	124.0		171,171	-1.1	0.9	10	dbSNP_107	124	1955,6645	345.8+/-325.9	210,1535,2555	yes	missense,missense	CEP55	NM_001127182.1,NM_018131.4	24,24	402,2414,3687	GG,GC,CC		22.7326,28.6655,24.7424	benign,benign	57/465,57/465	95259979	3218,9788	2203	4300	6503	SO:0001583	missense	55165	exon2			GAGACACAGACTT	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.171C>G	10.37:g.95259979C>G	ENSP00000360540:p.His57Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Missense_Mutation	SNP	ENST00000371485.3	37	CCDS7428.1	540	0.24725274725274726	160	0.3252032520325203	64	0.17679558011049723	161	0.28146853146853146	155	0.20448548812664907	C	4.002	-0.002321	0.07819	0.286655	0.227326	ENSG00000138180	ENST00000371485;ENST00000358339	T	0.15952	2.38	5.39	-1.15	0.09709	.	0.772035	0.12648	N	0.450712	T	0.00012	0.0000	L	0.47716	1.5	0.50632	P	1.1099999999997223E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.46386	-0.9195	9	0.10377	T	0.69	-0.1339	2.9794	0.05948	0.2209:0.3378:0.3252:0.1162	rs3740370;rs11546296;rs52801109;rs3740370	57	Q53EZ4	CEP55_HUMAN	Q	57	ENSP00000360540:H57Q	ENSP00000351102:H57Q	H	+	3	2	CEP55	95249969	0.799000	0.28903	0.864000	0.33941	0.730000	0.41778	-0.508000	0.06344	-0.016000	0.14127	-1.121000	0.02013	CAC	C|0.756;G|0.244	0.244	strong		0.383	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
NLRP5	126206	hgsc.bcm.edu	37	19	56538832	56538832	+	Silent	SNP	C	C	T	rs1808663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56538832C>T	ENST00000390649.3	+	7	1233	c.1233C>T	c.(1231-1233)gaC>gaT	p.D411D		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	411	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)		CCGTCAGAGACGTGGGCACAG	0.562													C|||	210	0.0419329	0.0696	0.0735	5008	,	,		21053	0.0		0.0616	False		,,,				2504	0.0051				p.D411D		Atlas-SNP	.											NLRP5_ENST00000390649,NS,carcinoma,0,1	NLRP5	217	1	0			c.C1233T						scavenged	.	C		300,3898		10,280,1809	47.0	48.0	47.0		1233	2.3	0.0	19	dbSNP_92	47	445,7985		23,399,3793	no	coding-synonymous	NLRP5	NM_153447.4		33,679,5602	TT,TC,CC		5.2788,7.1463,5.8996		411/1201	56538832	745,11883	2099	4215	6314	SO:0001819	synonymous_variant	126206	exon7			CAGAGACGTGGGC	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.1233C>T	19.37:g.56538832C>T		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			C|0.950;T|0.050	0.050	strong		0.562	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
DFNB31	25861	hgsc.bcm.edu	37	9	117166206	117166206	+	Missense_Mutation	SNP	G	G	T	rs2274158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:117166206G>T	ENST00000362057.3	-	10	2556	c.2388C>A	c.(2386-2388)aaC>aaA	p.N796K	DFNB31_ENST00000265134.6_Missense_Mutation_p.N413K|DFNB31_ENST00000374059.3_Missense_Mutation_p.N445K	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	796			N -> K (in dbSNP:rs2274158).		inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGGGCCTCTCGTTCCGAGGCA	0.652													G|||	1114	0.222444	0.0507	0.3213	5008	,	,		18204	0.3472		0.2167	False		,,,				2504	0.2618				p.N796K		Atlas-SNP	.											.	DFNB31	100	.	0			c.C2388A						PASS	.	G	LYS/ASN,LYS/ASN,LYS/ASN	353,4053	182.6+/-210.3	11,331,1861	115.0	100.0	105.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1239,2385,2388	-7.5	0.0	9	dbSNP_100	105	1987,6613	346.0+/-326.0	213,1561,2526	yes	missense,missense,missense	DFNB31	NM_001083885.2,NM_001173425.1,NM_015404.3	94,94,94	224,1892,4387	TT,TG,GG		23.1047,8.0118,17.9917	benign,benign,benign	413/525,795/907,796/908	117166206	2340,10666	2203	4300	6503	SO:0001583	missense	25861	exon10			CCTCTCGTTCCGA	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.2388C>A	9.37:g.117166206G>T	ENSP00000354623:p.Asn796Lys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_015404	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Missense_Mutation	SNP	ENST00000362057.3	37	CCDS6806.1	512	0.23443223443223443	31	0.06300813008130081	109	0.3011049723756906	207	0.3618881118881119	165	0.21767810026385223	G	2.127	-0.399968	0.04865	0.080118	0.231047	ENSG00000095397	ENST00000265134;ENST00000374059;ENST00000362057	T;T;T	0.06371	4.2;4.18;3.31	5.03	-7.49	0.01355	PDZ/DHR/GLGF (1);	0.596241	0.16860	N	0.196549	T	0.00012	0.0000	L	0.29908	0.895	0.27905	P	0.9388432	B;B;B	0.17667	0.01;0.013;0.023	B;B;B	0.24155	0.005;0.005;0.051	T	0.43893	-0.9363	9	0.16420	T	0.52	-6.4945	4.6597	0.12636	0.5065:0.2391:0.1757:0.0786	rs2274158;rs58851791;rs2274158	795;796;445	B9EGE6;Q9P202;Q9P202-4	.;WHRN_HUMAN;.	K	413;445;796	ENSP00000265134:N413K;ENSP00000363172:N445K;ENSP00000354623:N796K	ENSP00000265134:N413K	N	-	3	2	DFNB31	116206027	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-2.700000	0.00824	-1.629000	0.01546	-1.523000	0.00931	AAC	G|0.796;T|0.204	0.204	strong		0.652	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
KHSRP	8570	hgsc.bcm.edu	37	19	6415735	6415735	+	Silent	SNP	A	A	G	rs145698454	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6415735A>G	ENST00000398148.3	-	17	1790	c.1698T>C	c.(1696-1698)gcT>gcC	p.A566A	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	566	Ala/Gly/Pro-rich.				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)	p.A566A(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CGGCCGCTGCAGCTGCTTTGC	0.706													A|||	32	0.00638978	0.0008	0.0144	5008	,	,		11509	0.0		0.0139	False		,,,				2504	0.0072				p.A566A	Colon(55;593 1006 2067 9135 22980)	Atlas-SNP	.											KHSRP,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	KHSRP	51	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.T1698C						PASS	.	A		3,3369		0,3,1683	4.0	6.0	5.0		1698	-10.1	0.0	19	dbSNP_134	5	31,7415		0,31,3692	no	coding-synonymous	KHSRP	NM_003685.2		0,34,5375	GG,GA,AA		0.4163,0.089,0.3143		566/712	6415735	34,10784	1686	3723	5409	SO:0001819	synonymous_variant	8570	exon17			CGCTGCAGCTGCT	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		ENST00000398148.3:c.1698T>C	19.37:g.6415735A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	31	10	0.322581	NM_003685	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Silent	SNP	ENST00000398148.3	37	CCDS45936.1																																																																																			A|0.994;G|0.006	0.006	strong		0.706	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1		
BOD1L1	259282	hgsc.bcm.edu	37	4	13601337	13601337	+	Missense_Mutation	SNP	G	G	A	rs3733557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	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	
DUSP19	142679	hgsc.bcm.edu	37	2	183951796	183951796	+	Missense_Mutation	SNP	G	G	A	rs368865344		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:183951796G>A	ENST00000354221.4	+	3	477	c.302G>A	c.(301-303)gGa>gAa	p.G101E	AC064871.3_ENST00000444562.1_RNA|DUSP19_ENST00000342619.6_Intron|DUSP19_ENST00000469344.1_Intron	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	101					inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						GTTGCATATGGAGTTGAAAAT	0.333																																					p.G101E		Atlas-SNP	.											.	DUSP19	41	.	0			c.G302A						PASS	.		GLU/GLY,	0,4404		0,0,2202	112.0	111.0	111.0		302,	5.4	1.0	2		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	DUSP19	NM_080876.3,NM_001142314.1	98,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,	101/218,	183951796	1,13003	2202	4300	6502	SO:0001583	missense	142679	exon3			CATATGGAGTTGA	AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.302G>A	2.37:g.183951796G>A	ENSP00000346160:p.Gly101Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_080876	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	g	18.99	3.739002	0.69304	0.0	1.16E-4	ENSG00000162999	ENST00000354221	D	0.83506	-1.73	5.38	5.38	0.77491	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.199838	0.53938	D	0.000058	T	0.79106	0.4390	L	0.35341	1.055	0.80722	D	1	P	0.42908	0.793	P	0.46885	0.53	T	0.74284	-0.3715	10	0.02654	T	1	.	19.5054	0.95113	0.0:0.0:1.0:0.0	.	101	Q8WTR2	DUS19_HUMAN	E	101	ENSP00000346160:G101E	ENSP00000346160:G101E	G	+	2	0	DUSP19	183660041	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.691000	0.91279	2.674000	0.91012	0.651000	0.88453	GGA	.	.	weak		0.333	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1		
MUC17	140453	hgsc.bcm.edu	37	7	100676409	100676409	+	Missense_Mutation	SNP	C	C	T	rs34834039	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100676409C>T	ENST00000306151.4	+	3	1776	c.1712C>T	c.(1711-1713)cCa>cTa	p.P571L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	571	59 X approximate tandem repeats.|Ser-rich.		P -> L (in dbSNP:rs34834039).		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)					GGAAGCACTCCATTAACAAAC	0.493													C|||	602	0.120208	0.1967	0.0821	5008	,	,		27512	0.0645		0.1173	False		,,,				2504	0.1043				p.P571L		Atlas-SNP	.											.	MUC17	804	.	0			c.C1712T						PASS	.	C	LEU/PRO	773,3633	314.4+/-293.6	63,647,1493	287.0	298.0	294.0		1712	0.4	0.0	7	dbSNP_126	294	982,7618	212.9+/-253.1	56,870,3374	yes	missense	MUC17	NM_001040105.1	98	119,1517,4867	TT,TC,CC		11.4186,17.5443,13.4938	benign	571/4494	100676409	1755,11251	2203	4300	6503	SO:0001583	missense	140453	exon3			GCACTCCATTAAC	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.1712C>T	7.37:g.100676409C>T	ENSP00000302716:p.Pro571Leu	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	222	222	1	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	221	0.10119047619047619	69	0.1402439024390244	34	0.09392265193370165	29	0.050699300699300696	89	0.11741424802110818	C	2.299	-0.360703	0.05103	0.175443	0.114186	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.401	0.401	0.16338	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	1.0000000000287557E-6	B	0.24963	0.115	B	0.09377	0.004	T	0.46816	-0.9164	8	0.16420	T	0.52	.	6.7501	0.23482	0.0:0.9999:0.0:1.0E-4	rs34834039	571	Q685J3	MUC17_HUMAN	L	571	ENSP00000302716:P571L	ENSP00000302716:P571L	P	+	2	0	MUC17	100463129	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	0.756000	0.26419	0.496000	0.27904	0.501000	0.49751	CCA	C|0.880;T|0.120	0.120	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ZNF33A	7581	hgsc.bcm.edu	37	10	38345409	38345409	+	Missense_Mutation	SNP	A	A	G	rs71491230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:38345409A>G	ENST00000458705.2	+	5	2512	c.2354A>G	c.(2353-2355)cAg>cGg	p.Q785R	ZNF33A_ENST00000374618.3_Missense_Mutation_p.Q786R|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000307441.9_Missense_Mutation_p.Q785R|ZNF33A_ENST00000432900.2_Missense_Mutation_p.Q792R			Q06730	ZN33A_HUMAN	zinc finger protein 33A	785					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.Q785R(1)		cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AGAAATTTCCAGCCACAAGTC	0.383													A|||	3	0.000599042	0.0	0.0	5008	,	,		18653	0.0		0.003	False		,,,				2504	0.0				p.Q786R		Atlas-SNP	.											ZNF33A,NS,carcinoma,0,1	ZNF33A	103	1	1	Substitution - Missense(1)	lung(1)	c.A2357G						PASS	.	A	ARG/GLN,ARG/GLN	2,4404	4.2+/-10.8	0,2,2201	61.0	61.0	61.0		2357,2354	0.6	0.0	10	dbSNP_130	61	25,8575	17.3+/-56.4	0,25,4275	yes	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	43,43	0,27,6476	GG,GA,AA		0.2907,0.0454,0.2076	benign,benign	786/812,785/811	38345409	27,12979	2203	4300	6503	SO:0001583	missense	7581	exon5			ATTTCCAGCCACA	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.2354A>G	10.37:g.38345409A>G	ENSP00000387713:p.Gln785Arg	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	95	24	0.252632	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	7.459	0.644218	0.14451	4.54E-4	0.002907	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.07327	3.2;3.46;3.2;3.2	1.92	0.561	0.17285	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.09310	N	1	B;B;B	0.15141	0.012;0.007;0.012	B;B;B	0.09377	0.004;0.002;0.004	T	0.40961	-0.9535	9	0.87932	D	0	.	2.6079	0.04883	0.4659:0.2692:0.0:0.2649	.	792;785;786	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	R	786;792;785;785	ENSP00000363747:Q786R;ENSP00000402467:Q792R;ENSP00000387713:Q785R;ENSP00000304268:Q785R	ENSP00000304268:Q785R	Q	+	2	0	ZNF33A	38385415	0.000000	0.05858	0.007000	0.13788	0.142000	0.21351	-0.152000	0.10159	-0.018000	0.14079	0.260000	0.18958	CAG	A|0.998;G|0.002	0.002	strong		0.383	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
BMP2	650	hgsc.bcm.edu	37	20	6759706	6759706	+	Silent	SNP	C	C	T	rs13037675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:6759706C>T	ENST00000378827.4	+	3	2380	c.1161C>T	c.(1159-1161)gaC>gaT	p.D387D		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	387			D -> G (in dbSNP:rs11545591).		activation of MAPK activity (GO:0000187)|atrioventricular valve morphogenesis (GO:0003181)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|bone mineralization (GO:0030282)|bone mineralization involved in bone maturation (GO:0035630)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiocyte differentiation (GO:0035051)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to BMP stimulus (GO:0071773)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation (GO:0002062)|corticotropin hormone secreting cell differentiation (GO:0060128)|embryo development (GO:0009790)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion morphogenesis (GO:0003203)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|inflammatory response (GO:0006954)|inner ear development (GO:0048839)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchyme development (GO:0060485)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of calcium-independent cell-cell adhesion (GO:0051042)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|pericardium development (GO:0060039)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of odontogenesis (GO:0042482)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of phosphatase activity (GO:0010922)|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 involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of Wnt signaling pathway by BMP signaling pathway (GO:0060804)|protein destabilization (GO:0031648)|protein phosphorylation (GO:0006468)|proteoglycan metabolic process (GO:0006029)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	BMP receptor binding (GO:0070700)|phosphatase activator activity (GO:0019211)|protein heterodimerization activity (GO:0046982)|receptor binding (GO:0005102)|retinol dehydrogenase activity (GO:0004745)|SMAD binding (GO:0046332)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)	13						ACTATCAGGACATGGTTGTGG	0.348													C|||	226	0.0451278	0.0386	0.1225	5008	,	,		12726	0.0		0.0706	False		,,,				2504	0.0194				p.D387D		Atlas-SNP	.											.	BMP2	45	.	0			c.C1161T						PASS	.	C		215,4191	131.0+/-167.6	7,201,1995	67.0	65.0	65.0		1161	4.6	1.0	20	dbSNP_121	65	577,8023	154.0+/-208.3	19,539,3742	no	coding-synonymous	BMP2	NM_001200.2		26,740,5737	TT,TC,CC		6.7093,4.8797,6.0895		387/397	6759706	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	650	exon3			TCAGGACATGGTT		CCDS13099.1	20p12	2014-01-30			ENSG00000125845	ENSG00000125845		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1069	protein-coding gene	gene with protein product		112261		BMP2A		2376592	Standard	NM_001200		Approved		uc002wmu.1	P12643	OTTHUMG00000031833	ENST00000378827.4:c.1161C>T	20.37:g.6759706C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_001200		Silent	SNP	ENST00000378827.4	37	CCDS13099.1																																																																																			C|0.943;T|0.057	0.057	strong		0.348	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3		
ABCC3	8714	hgsc.bcm.edu	37	17	48761053	48761053	+	Missense_Mutation	SNP	G	G	A	rs11568591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48761053G>A	ENST00000285238.8	+	27	3970	c.3890G>A	c.(3889-3891)cGc>cAc	p.R1297H		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1297	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> H (in dbSNP:rs11568591).		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|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)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TATTCTGTGCGCTACCGGCCG	0.662													g|||	99	0.0197684	0.0045	0.0476	5008	,	,		18448	0.0		0.0557	False		,,,				2504	0.0041				p.R1297H		Atlas-SNP	.											ABCC3,NS,carcinoma,+1,2	ABCC3	138	2	0			c.G3890A						PASS	.		HIS/ARG	75,4331	65.8+/-103.3	3,69,2131	124.0	112.0	116.0		3890	5.9	1.0	17	dbSNP_123	116	542,8058	149.2+/-204.3	10,522,3768	yes	missense	ABCC3	NM_003786.3	29	13,591,5899	AA,AG,GG		6.3023,1.7022,4.744	probably-damaging	1297/1528	48761053	617,12389	2203	4300	6503	SO:0001583	missense	8714	exon27			CTGTGCGCTACCG	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.3890G>A	17.37:g.48761053G>A	ENSP00000285238:p.Arg1297His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	67	0.030677655677655676	3	0.006097560975609756	22	0.06077348066298342	0	0.0	42	0.055408970976253295	g	35	5.496309	0.96355	0.017022	0.063023	ENSG00000108846	ENST00000285238	D	0.90788	-2.73	5.94	5.94	0.96194	ABC transporter-like (1);	0.000000	0.85682	D	0.000000	T	0.78947	0.4364	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84861	0.0819	10	0.87932	D	0	-23.8467	20.3705	0.98891	0.0:0.0:1.0:0.0	rs11568591;rs17643133;rs52818811;rs61701650;rs11568591	1297	O15438	MRP3_HUMAN	H	1297	ENSP00000285238:R1297H	ENSP00000285238:R1297H	R	+	2	0	ABCC3	46116052	1.000000	0.71417	1.000000	0.80357	0.666000	0.39218	9.790000	0.99075	2.821000	0.97095	0.651000	0.88453	CGC	G|0.964;A|0.036	0.036	strong		0.662	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
SIM2	6493	hgsc.bcm.edu	37	21	38117505	38117505	+	Intron	SNP	C	C	T	rs2073602	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:38117505C>T	ENST00000290399.6	+	10	2189				SIM2_ENST00000430056.3_Silent_p.G548G	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2						cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						GCAGCCATGGCGGTGGGTGGC	0.602													C|||	1395	0.278554	0.3865	0.1787	5008	,	,		20123	0.2292		0.2276	False		,,,				2504	0.3067				p.G548G		Atlas-SNP	.											.	SIM2	55	.	0			c.C1644T						PASS	.	C	,	980,1668		181,618,525	46.0	55.0	52.0		,1644	-1.5	0.0	21	dbSNP_96	52	1030,3582		116,798,1392	no	intron,coding-synonymous	SIM2	NM_005069.3,NM_009586.2	,	297,1416,1917	TT,TC,CC		22.333,37.0091,27.686	,	,548/571	38117505	2010,5250	1324	2306	3630	SO:0001627	intron_variant	6493	exon10			CCATGGCGGTGGG		CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"""Basic helix-loop-helix proteins"""	10883	protein-coding gene	gene with protein product	"""transcription factor SIM2"""	600892	"""single-minded (Drosophila) homolog 2"", ""single-minded homolog 2 (Drosophila)"""	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.1576+68C>T	21.37:g.38117505C>T		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	383	120	0.313316	NM_009586	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Silent	SNP	ENST00000290399.6	37	CCDS13646.1																																																																																			C|0.739;T|0.261	0.261	strong		0.602	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
ARHGAP12	94134	hgsc.bcm.edu	37	10	32128611	32128611	+	Missense_Mutation	SNP	A	A	G	rs2808096	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:32128611A>G	ENST00000344936.2	-	8	1559	c.1325T>C	c.(1324-1326)tTt>tCt	p.F442S	ARHGAP12_ENST00000375245.4_Missense_Mutation_p.F395S|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.F442S|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.F395S|ARHGAP12_ENST00000375250.5_Intron	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	59	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	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		
NOC3L	64318	hgsc.bcm.edu	37	10	96106240	96106240	+	Missense_Mutation	SNP	G	G	C	rs11187895	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:96106240G>C	ENST00000371361.3	-	11	1431	c.1331C>G	c.(1330-1332)cCa>cGa	p.P444R	NOC3L_ENST00000543788.1_Missense_Mutation_p.P182R|NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Missense_Mutation_p.P444R	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	444			P -> R (in dbSNP:rs11187895).		fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.P444R(1)		endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				AAATTTTTTTGGTTTATTAAT	0.254													G|||	391	0.0780751	0.0061	0.0576	5008	,	,		15494	0.2093		0.0895	False		,,,				2504	0.0429				p.P444R		Atlas-SNP	.											NOC3L,NS,carcinoma,0,1	NOC3L	67	1	1	Substitution - Missense(1)	stomach(1)	c.C1331G						PASS	.	G	ARG/PRO	78,4296	64.7+/-102.0	0,78,2109	61.0	60.0	61.0		1331	2.8	1.0	10	dbSNP_120	61	785,7765	179.8+/-228.8	26,733,3516	yes	missense	NOC3L	NM_022451.9	103	26,811,5625	CC,CG,GG		9.1813,1.7833,6.6775	benign	444/801	96106240	863,12061	2187	4275	6462	SO:0001583	missense	64318	exon11			TTTTTTGGTTTAT	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.1331C>G	10.37:g.96106240G>C	ENSP00000360412:p.Pro444Arg	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	69	44	0.637681	NM_022451	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	175	0.08012820512820513	3	0.006097560975609756	24	0.06629834254143646	82	0.14335664335664336	66	0.0870712401055409	G	6.558	0.471202	0.12461	0.017833	0.091813	ENSG00000173145	ENST00000543788;ENST00000371361;ENST00000371350	T;T;T	0.14893	2.47;2.66;2.66	5.83	2.82	0.32997	.	0.224065	0.42420	D	0.000717	T	0.00073	0.0002	N	0.12569	0.235	0.31587	P	0.6543559999999999	B	0.27450	0.179	B	0.24974	0.057	T	0.38714	-0.9648	9	0.20046	T	0.44	-2.7874	7.8049	0.29195	0.078:0.0:0.447:0.475	rs11187895;rs60469249;rs11187895	444	Q8WTT2	NOC3L_HUMAN	R	182;444;444	ENSP00000437838:P182R;ENSP00000360412:P444R;ENSP00000360401:P444R	ENSP00000360401:P444R	P	-	2	0	NOC3L	96096230	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.740000	0.62087	0.810000	0.34279	0.655000	0.94253	CCA	G|0.928;C|0.072	0.072	strong		0.254	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	
CPS1	1373	hgsc.bcm.edu	37	2	211481257	211481257	+	Silent	SNP	C	C	G	rs2287599	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:211481257C>G	ENST00000233072.5	+	21	2875	c.2679C>G	c.(2677-2679)ggC>ggG	p.G893G	CPS1_ENST00000430249.2_Silent_p.G899G|CPS1_ENST00000451903.2_Silent_p.G442G	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	893					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)	CACTGAAAGGCCTCAACAGGT	0.393													G|||	3251	0.649161	0.9107	0.4885	5008	,	,		17249	0.5248		0.5537	False		,,,				2504	0.636				p.G899G		Atlas-SNP	.											.	CPS1	485	.	0			c.C2697G						PASS	.	G	,,	3783,623	269.2+/-268.9	1624,535,44	144.0	146.0	146.0		2697,1326,2679	-0.1	1.0	2	dbSNP_100	146	4830,3770	531.5+/-382.0	1333,2164,803	no	coding-synonymous,coding-synonymous,coding-synonymous	CPS1	NM_001122633.2,NM_001122634.2,NM_001875.4	,,	2957,2699,847	GG,GC,CC		43.8372,14.1398,33.7767	,,	899/1507,442/1050,893/1501	211481257	8613,4393	2203	4300	6503	SO:0001819	synonymous_variant	1373	exon22			GAAAGGCCTCAAC	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.2679C>G	2.37:g.211481257C>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	45	6	0.133333	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	37	CCDS2393.1																																																																																			C|0.357;G|0.643	0.643	strong		0.393	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
KRT80	144501	hgsc.bcm.edu	37	12	52579294	52579294	+	Silent	SNP	G	G	A	rs17704675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52579294G>A	ENST00000394815.2	-	2	475	c.378C>T	c.(376-378)ttC>ttT	p.F126F	KRT80_ENST00000313234.5_Silent_p.F126F	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80	126	Linker 1.|Rod.					cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(2)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.108)		GCCCGAGGTCGAAGATGGCTG	0.642													G|||	248	0.0495208	0.0666	0.0648	5008	,	,		17453	0.0		0.1083	False		,,,				2504	0.0061				p.F126F	GBM(178;2309 2916 15678 35873)	Atlas-SNP	.											.	KRT80	68	.	0			c.C378T						PASS	.	G	,	351,4055	180.1+/-208.5	12,327,1864	53.0	52.0	52.0		378,378	-0.7	0.0	12	dbSNP_123	52	861,7739	195.6+/-240.8	43,775,3482	no	coding-synonymous,coding-synonymous	KRT80	NM_001081492.1,NM_182507.2	,	55,1102,5346	AA,AG,GG		10.0116,7.9664,9.3188	,	126/423,126/453	52579294	1212,11794	2203	4300	6503	SO:0001819	synonymous_variant	144501	exon2			GAGGTCGAAGATG	BX537567	CCDS8821.2, CCDS41784.1	12q13.13	2013-01-16			ENSG00000167767	ENSG00000167767		"""-"", ""Intermediate filaments type II, keratins (basic)"""	27056	protein-coding gene	gene with protein product		611161				16831889	Standard	NM_001081492		Approved	KB20	uc001rzx.3	Q6KB66	OTTHUMG00000150193	ENST00000394815.2:c.378C>T	12.37:g.52579294G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_182507	Q6P1A5|Q7Z3Q0	Silent	SNP	ENST00000394815.2	37	CCDS8821.2																																																																																			G|0.920;A|0.080	0.080	strong		0.642	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	NM_182507	
RASSF4	83937	hgsc.bcm.edu	37	10	45478092	45478092	+	Missense_Mutation	SNP	A	A	G	rs870957	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:45478092A>G	ENST00000340258.5	+	4	375	c.262A>G	c.(262-264)Aga>Gga	p.R88G	RASSF4_ENST00000472561.1_3'UTR|RASSF4_ENST00000374417.2_Missense_Mutation_p.R88G|RASSF4_ENST00000334940.6_Missense_Mutation_p.R70G	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	624					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						ATGGATGCCCAGACGGCCTAG	0.667													.|||	1406	0.280751	0.3782	0.1412	5008	,	,		19294	0.3194		0.171	False		,,,				2504	0.3211				p.R88G		Atlas-SNP	.											.	RASSF4	33	.	0			c.A262G						PASS	.	G	GLY/ARG	1484,2922	676.9+/-403.3	254,976,973	72.0	70.0	71.0		262	1.4	0.0	10	dbSNP_86	71	1499,7101	747.6+/-407.3	120,1259,2921	yes	missense	RASSF4	NM_032023.3	125	374,2235,3894	GG,GA,AA		17.4302,33.6813,22.9356	benign	88/322	45478092	2983,10023	2203	4300	6503	SO:0001583	missense	83937	exon4			ATGCCCAGACGGC	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.262A>G	10.37:g.45478092A>G	ENSP00000339692:p.Arg88Gly	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	121	24	0.198347	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000340258.5	37	CCDS7208.1	575	0.2632783882783883	189	0.38414634146341464	62	0.1712707182320442	196	0.34265734265734266	128	0.16886543535620052	G	0.027	-1.361971	0.01235	0.336813	0.174302	ENSG00000107551	ENST00000334940;ENST00000374417;ENST00000374414;ENST00000340258;ENST00000427758;ENST00000428466;ENST00000374411	T;T;T;T;T	0.30448	2.54;1.54;2.56;1.53;1.53	4.39	1.39	0.22231	.	0.619583	0.14038	N	0.345633	T	0.00012	0.0000	N	0.00621	-1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47156	-0.9139	9	0.22109	T	0.4	-1.7041	5.0423	0.14465	0.1868:0.3279:0.4853:0.0	rs870957;rs11540202;rs56589186;rs57926736;rs870957	88	Q9H2L5	RASF4_HUMAN	G	70;88;88;88;88;81;179	ENSP00000334543:R70G;ENSP00000363538:R88G;ENSP00000339692:R88G;ENSP00000409767:R88G;ENSP00000413468:R81G	ENSP00000334543:R70G	R	+	1	2	RASSF4	44798098	0.087000	0.21565	0.000000	0.03702	0.002000	0.02628	0.681000	0.25320	0.069000	0.16605	-0.119000	0.15052	AGA	A|0.750;G|0.250	0.250	strong		0.667	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023	
OR10S1	219873	hgsc.bcm.edu	37	11	123848212	123848212	+	Missense_Mutation	SNP	C	C	T	rs17759513	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:123848212C>T	ENST00000531945.1	-	1	276	c.187G>A	c.(187-189)Ggc>Agc	p.G63S		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	63			G -> S (in dbSNP:rs17759513).			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(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		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)		GAGTCAGAGCCCACAGTTAGG	0.527													C|||	867	0.173123	0.1301	0.2147	5008	,	,		22925	0.1171		0.2903	False		,,,				2504	0.1391				p.G63S		Atlas-SNP	.											.	OR10S1	78	.	0			c.G187A						PASS	.	C	SER/GLY	660,3744	281.1+/-275.7	45,570,1587	71.0	63.0	66.0		187	1.9	1.0	11	dbSNP_123	66	2219,6379	374.8+/-337.5	296,1627,2376	yes	missense	OR10S1	NM_001004474.1	56	341,2197,3963	TT,TC,CC		25.8083,14.9864,22.1427	benign	63/332	123848212	2879,10123	2202	4299	6501	SO:0001583	missense	219873	exon1			CAGAGCCCACAGT	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.187G>A	11.37:g.123848212C>T	ENSP00000431914:p.Gly63Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	138	77	0.557971	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	433	0.19826007326007325	65	0.13211382113821138	87	0.24033149171270718	73	0.12762237762237763	208	0.27440633245382584	C	9.701	1.154552	0.21371	0.149864	0.258083	ENSG00000196248	ENST00000531945	T	0.01076	5.37	4.84	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	1.379400	0.05329	U	0.527956	T	0.00012	0.0000	N	0.03930	-0.32	0.52099	P	5.900000000003125E-5	B	0.14438	0.01	B	0.08055	0.003	T	0.41680	-0.9495	9	0.22109	T	0.4	-6.4442	4.5215	0.11960	0.1454:0.5349:0.0:0.3197	rs17759513;rs52797693;rs60266391;rs17759513	63	Q8NGN2	O10S1_HUMAN	S	63	ENSP00000431914:G63S	ENSP00000431914:G63S	G	-	1	0	OR10S1	123353422	0.000000	0.05858	0.998000	0.56505	0.996000	0.88848	-0.391000	0.07323	0.668000	0.31126	0.638000	0.83543	GGC	C|0.792;N|0.000	.	strong		0.527	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
MLLT4	4301	hgsc.bcm.edu	37	6	168343838	168343838	+	Silent	SNP	T	T	C	rs1132306	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168343838T>C	ENST00000447894.2	+	23	3108	c.3108T>C	c.(3106-3108)taT>taC	p.Y1036Y	MLLT4_ENST00000366806.2_Silent_p.Y1036Y|MLLT4_ENST00000344191.4_Silent_p.Y1036Y|MLLT4_ENST00000351017.4_Silent_p.Y1043Y|MLLT4_ENST00000400822.3_Silent_p.Y1035Y|MLLT4_ENST00000507679.1_3'UTR|MLLT4_ENST00000392108.3_Silent_p.Y1036Y|MLLT4_ENST00000392112.1_Silent_p.Y1020Y			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1036	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(13)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65		Breast(66;1.07e-05)|Ovarian(120;0.024)		Epithelial(4;2.38e-32)|OV - Ovarian serous cystadenocarcinoma(33;9.99e-23)|BRCA - Breast invasive adenocarcinoma(4;1.2e-11)|GBM - Glioblastoma multiforme(31;0.00117)		TAGGAATCTATGTGAAGTCGG	0.378			T	MLL	AL								T|||	2786	0.55631	0.4138	0.5605	5008	,	,		22196	0.7927		0.4066	False		,,,				2504	0.6564				p.Y1036Y		Atlas-SNP	.		Dom	yes		6	6q27	4301	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4 (AF6)"""		L	.	MLLT4	351	.	0			c.T3108C						PASS	.	T	,	1842,2564	536.8+/-374.6	379,1084,740	179.0	162.0	168.0		3108,3060	-4.9	0.9	6	dbSNP_86	168	3657,4943	525.8+/-380.8	771,2115,1414	no	coding-synonymous,coding-synonymous	MLLT4	NM_001040000.2,NM_001207008.1	,	1150,3199,2154	CC,CT,TT		42.5233,41.8066,42.2805	,	1036/1652,1020/1744	168343838	5499,7507	2203	4300	6503	SO:0001819	synonymous_variant	4301	exon23			AATCTATGTGAAG	AB011399	CCDS47517.1, CCDS75553.1	6q27	2008-02-05	2001-11-28		ENSG00000130396	ENSG00000130396			7137	protein-coding gene	gene with protein product		159559	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 4"""			8242616	Standard	NM_001040000		Approved	AF-6, AF6	uc021zij.1	P55196	OTTHUMG00000016031	ENST00000447894.2:c.3108T>C	6.37:g.168343838T>C		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	185	93	0.502703	NM_001040000	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Silent	SNP	ENST00000447894.2	37																																																																																				T|0.525;C|0.475	0.475	strong		0.378	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936	
EIF5B	9669	hgsc.bcm.edu	37	2	99992822	99992822	+	Missense_Mutation	SNP	A	A	C	rs7558074	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:99992822A>C	ENST00000289371.6	+	10	1767	c.1565A>C	c.(1564-1566)aAa>aCa	p.K522T		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	522			K -> T (in dbSNP:rs7558074). {ECO:0000269|PubMed:10200264, ECO:0000269|PubMed:10432305, ECO:0000269|PubMed:21269460}.		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						GAAGGAAACAAAGTTCATATA	0.343													C|||	2964	0.591853	0.7678	0.7032	5008	,	,		16798	0.3671		0.5686	False		,,,				2504	0.5307				p.K522T	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											.	EIF5B	95	.	0			c.A1565C						PASS	.	C	THR/LYS	2951,933		1154,643,145	8.0	8.0	8.0		1565	5.3	0.5	2	dbSNP_116	8	4651,3555		1372,1907,824	yes	missense	EIF5B	NM_015904.3	78	2526,2550,969	CC,CA,AA		43.322,24.0216,37.1216	benign	522/1221	99992822	7602,4488	1942	4103	6045	SO:0001583	missense	9669	exon10			GAAACAAAGTTCA	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.1565A>C	2.37:g.99992822A>C	ENSP00000289371:p.Lys522Thr	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	26	11	0.423077	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Missense_Mutation	SNP	ENST00000289371.6	37	CCDS42721.1	1287	0.5892857142857143	378	0.7682926829268293	254	0.7016574585635359	212	0.3706293706293706	443	0.5844327176781002	C	4.458	0.084868	0.08583	0.759784	0.56678	ENSG00000158417	ENST00000289371	T	0.48522	0.81	6.17	5.29	0.74685	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.45452	P	0.0015760000000000218	B	0.02656	0.0	B	0.01281	0.0	T	0.28681	-1.0036	7	.	.	.	-4.241	10.7971	0.46466	0.1323:0.7994:0.0:0.0683	rs7558074;rs17856952;rs52796323;rs61100948;rs7558074	522	O60841	IF2P_HUMAN	T	522	ENSP00000289371:K522T	.	K	+	2	0	EIF5B	99359254	0.992000	0.36948	0.545000	0.28153	0.444000	0.32077	2.998000	0.49465	0.933000	0.37291	-0.121000	0.15023	AAA	A|0.436;C|0.564;G|0.000;T|0.000	0.564	strong		0.343	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904	
TRERF1	55809	hgsc.bcm.edu	37	6	42233518	42233518	+	Silent	SNP	C	C	T	rs17704222	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:42233518C>T	ENST00000372922.4	-	6	2017	c.1455G>A	c.(1453-1455)ggG>ggA	p.G485G	TRERF1_ENST00000541110.1_Silent_p.G485G|TRERF1_ENST00000372917.4_Silent_p.G485G|TRERF1_ENST00000340840.2_Silent_p.G485G|TRERF1_ENST00000354325.2_Silent_p.G485G	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	485	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCTGGGCTCTCCCATCAGGTA	0.493													C|||	178	0.0355431	0.0045	0.0375	5008	,	,		19050	0.004		0.0726	False		,,,				2504	0.0706				p.G485G		Atlas-SNP	.											.	TRERF1	124	.	0			c.G1455A						PASS	.	C		79,4327	67.6+/-105.2	1,77,2125	57.0	55.0	56.0		1455	3.8	1.0	6	dbSNP_123	56	764,7836	180.8+/-229.6	32,700,3568	no	coding-synonymous	TRERF1	NM_033502.2		33,777,5693	TT,TC,CC		8.8837,1.793,6.4816		485/1201	42233518	843,12163	2203	4300	6503	SO:0001819	synonymous_variant	55809	exon6			GGCTCTCCCATCA	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1455G>A	6.37:g.42233518C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																			C|0.950;T|0.050	0.050	strong		0.493	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
CNKSR1	10256	hgsc.bcm.edu	37	1	26515956	26515956	+	Missense_Mutation	SNP	C	C	A	rs1045105	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:26515956C>A	ENST00000374253.5	+	21	2119	c.2080C>A	c.(2080-2082)Cac>Aac	p.H694N	CNKSR1_ENST00000531191.1_Missense_Mutation_p.H429N|CNKSR1_ENST00000361530.6_Missense_Mutation_p.H687N|CATSPER4_ENST00000456354.2_5'Flank	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	694				H -> N (in Ref. 1; AAC80558). {ECO:0000305}.	Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)	p.H687Y(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGTCCCCCCACTCCCTGCC	0.637													C|||	591	0.118011	0.0779	0.0821	5008	,	,		17563	0.0962		0.1223	False		,,,				2504	0.2157				p.H687N	NSCLC(180;1396 2109 28270 30756 34275)	Atlas-SNP	.											CNKSR1,colon,carcinoma,0,3	CNKSR1	66	3	1	Substitution - Missense(1)	kidney(1)	c.C2059A						PASS	.	C	ASN/HIS	384,4022	191.6+/-217.2	38,308,1857	132.0	134.0	133.0		2059	2.8	0.0	1	dbSNP_86	133	1162,7438	237.9+/-269.6	87,988,3225	yes	missense	CNKSR1	NM_006314.2	68	125,1296,5082	AA,AC,CC		13.5116,8.7154,11.8868	benign	687/714	26515956	1546,11460	2203	4300	6503	SO:0001583	missense	10256	exon21			TCCCCCCACTCCC	AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.2080C>A	1.37:g.26515956C>A	ENSP00000363371:p.His694Asn	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	162	31	0.191358	NM_006314	B1AMW9|O95381	Missense_Mutation	SNP	ENST00000374253.5	37		212	0.09706959706959707	41	0.08333333333333333	31	0.0856353591160221	57	0.09965034965034965	83	0.10949868073878628	C	4.741	0.137816	0.09032	0.087154	0.135116	ENSG00000142675	ENST00000361530;ENST00000374253;ENST00000531191	T;T;T	0.13538	2.59;2.6;2.58	4.66	2.77	0.32553	.	1.288580	0.04684	N	0.412844	T	0.00109	0.0003	L	0.44542	1.39	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31308	-0.9948	9	0.27082	T	0.32	-0.9495	6.9902	0.24751	0.1255:0.6606:0.1346:0.0793	rs1045105;rs3184920;rs57946802;rs1045105	694;687	Q969H4;Q53GM7	CNKR1_HUMAN;.	N	687;694;429	ENSP00000354609:H687N;ENSP00000363371:H694N;ENSP00000431817:H429N	ENSP00000354609:H687N	H	+	1	0	CNKSR1	26388543	0.000000	0.05858	0.005000	0.12908	0.007000	0.05969	0.030000	0.13688	0.660000	0.30964	-0.808000	0.03180	CAC	A|0.120;C|0.880;T|0.000	0.120	strong		0.637	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314	
MROH9	80133	hgsc.bcm.edu	37	1	171033252	171033252	+	Missense_Mutation	SNP	T	T	C	rs190157737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171033252T>C	ENST00000367759.4	+	22	2511	c.2357T>C	c.(2356-2358)cTg>cCg	p.L786P		NM_001163629.1	NP_001157101.1	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	0																	ATTGAACGACTGCTCCGAGAT	0.378													T|||	7	0.00139776	0.0	0.0014	5008	,	,		17701	0.0		0.005	False		,,,				2504	0.001				p.L786P		Atlas-SNP	.											.	.	.	.	0			c.T2357C						PASS	.						33.0	30.0	31.0					1																	171033252		692	1591	2283	SO:0001583	missense	80133	exon22			AACGACTGCTCCG	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367759.4:c.2357T>C	1.37:g.171033252T>C	ENSP00000356733:p.Leu786Pro	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_001163629	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367759.4	37	CCDS53429.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	13.37	2.216312	0.39201	.	.	ENSG00000117501	ENST00000367759	T	0.72167	-0.63	4.98	1.22	0.21188	.	.	.	.	.	T	0.43700	0.1259	N	0.24115	0.695	0.09310	N	0.999997	D	0.54964	0.969	P	0.51016	0.656	T	0.32666	-0.9898	9	0.87932	D	0	.	3.7455	0.08547	0.3354:0.0915:0.0:0.5731	.	786	F5GWX6	.	P	786	ENSP00000356733:L786P	ENSP00000356733:L786P	L	+	2	0	C1orf129	169299876	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.324000	0.19610	0.094000	0.17404	-0.333000	0.08304	CTG	T|0.998;C|0.002	0.002	strong		0.378	MROH9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_025063	
GPR98	84059	hgsc.bcm.edu	37	5	89979698	89979698	+	Missense_Mutation	SNP	C	C	T	rs4916685	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	163	163	1	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	
SNTB2	6645	hgsc.bcm.edu	37	16	69221510	69221510	+	Silent	SNP	C	C	G	rs10650	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:69221510C>G	ENST00000336278.4	+	1	479	c.441C>G	c.(439-441)ccC>ccG	p.P147P		NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	147	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		AGATCTTCCCCGGGCTGGCTG	0.716													G|||	905	0.180711	0.3003	0.1671	5008	,	,		5567	0.0417		0.2296	False		,,,				2504	0.1217				p.P147P	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.C441G						PASS	.	G		1114,3104		166,782,1161	7.0	9.0	8.0		441	2.9	1.0	16	dbSNP_52	8	1807,6475		241,1325,2575	no	coding-synonymous	SNTB2	NM_006750.3		407,2107,3736	GG,GC,CC		21.8184,26.4106,23.368		147/541	69221510	2921,9579	2109	4141	6250	SO:0001819	synonymous_variant	6645	exon1			CTTCCCCGGGCTG	U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807			11169	protein-coding gene	gene with protein product		600027	"""syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)"""	SNT2B2, SNTL, D16S2531E		8576247, 8183929	Standard	NM_006750		Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000336278.4:c.441C>G	16.37:g.69221510C>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	26	20	0.769231	NM_006750	Q9BY09	Silent	SNP	ENST00000336278.4	37	CCDS10873.1	400	0.18315018315018314	144	0.2926829268292683	62	0.1712707182320442	30	0.05244755244755245	164	0.21635883905013192	G	13.11	2.137905	0.37728	0.264106	0.218184	ENSG00000168807	ENST00000525632;ENST00000360496	T	0.31510	1.49	4.91	2.86	0.33363	.	0.067858	0.64402	N	0.000013	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17992	-1.0351	6	0.87932	D	0	3.495	8.6306	0.33917	0.1548:0.1286:0.7166:0.0	rs10650;rs1136061;rs1136064;rs3169308;rs17354236	.	.	.	R	16;8	ENSP00000432201:P16R	ENSP00000353686:P8R	P	+	2	0	SNTB2	67779011	0.942000	0.31987	1.000000	0.80357	0.953000	0.61014	0.499000	0.22546	0.564000	0.29238	-0.215000	0.12644	CCG	C|0.815;G|0.185	0.185	strong		0.716	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1		
NUMA1	4926	hgsc.bcm.edu	37	11	71717106	71717106	+	Silent	SNP	G	G	A	rs61745941	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:71717106G>A	ENST00000393695.3	-	22	5998	c.5667C>T	c.(5665-5667)gcC>gcT	p.A1889A	NUMA1_ENST00000351960.6_Silent_p.A753A|NUMA1_ENST00000358965.6_Silent_p.A1875A	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						TGGACACCCCGGCCTGGGAAC	0.597			T	RARA	APL								G|||	219	0.04373	0.0189	0.0447	5008	,	,		18923	0.0823		0.0348	False		,,,				2504	0.046				p.A1889A		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.C5667T						PASS	.	G		80,4320	67.0+/-104.6	1,78,2121	58.0	69.0	65.0		5667	-10.2	0.1	11	dbSNP_129	65	235,8351	93.1+/-155.1	4,227,4062	no	coding-synonymous	NUMA1	NM_006185.2		5,305,6183	AA,AG,GG		2.737,1.8182,2.4257		1889/2116	71717106	315,12671	2200	4293	6493	SO:0001819	synonymous_variant	4926	exon22			CACCCCGGCCTGG	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.5667C>T	11.37:g.71717106G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1	104	0.047619047619047616	17	0.034552845528455285	15	0.04143646408839779	49	0.08566433566433566	23	0.030343007915567283	G	6.573	0.474061	0.12521	0.018182	0.02737	ENSG00000137497	ENST00000541584	.	.	.	5.11	-10.2	0.00374	.	.	.	.	.	T	0.02767	0.0083	.	.	.	0.43271	D	0.995225	.	.	.	.	.	.	T	0.56505	-0.7968	4	.	.	.	.	10.9463	0.47301	0.1966:0.0869:0.6301:0.0864	rs61745941	.	.	.	L	738	.	.	P	-	2	0	NUMA1	71394754	0.055000	0.20627	0.086000	0.20670	0.764000	0.43329	-1.306000	0.02735	-2.382000	0.00593	-1.202000	0.01658	CCG	G|0.969;A|0.031	0.031	strong		0.597	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
ZNF813	126017	hgsc.bcm.edu	37	19	53990002	53990002	+	Silent	SNP	G	G	A	rs12974996	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	92	0	0		WXS	Illumina HiSeq	Phase_I	119	30	0.252101	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	
COL6A5	256076	hgsc.bcm.edu	37	3	130129322	130129322	+	Missense_Mutation	SNP	G	G	C	rs35886424	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:130129322G>C	ENST00000432398.2	+	20	5110	c.4616G>C	c.(4615-4617)aGt>aCt	p.S1539T	COL6A5_ENST00000265379.6_Missense_Mutation_p.S1539T	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1539	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						TAGGGTAGAAGTGGACAGAAA	0.388													C|||	549	0.109625	0.0953	0.1037	5008	,	,		18486	0.1081		0.1123	False		,,,				2504	0.1319				p.S1539T		Atlas-SNP	.											.	COL6A5	205	.	0			c.G4616C						PASS	.	C	THR/SER	143,1241		8,127,557	114.0	90.0	97.0		4616	4.8	0.6	3	dbSNP_126	97	431,2751		27,377,1187	yes	missense	COL6A5	NM_153264.5	58	35,504,1744	CC,CG,GG		13.5449,10.3324,12.5712	benign	1539/2527	130129322	574,3992	692	1591	2283	SO:0001583	missense	256076	exon20			GTAGAAGTGGACA	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.4616G>C	3.37:g.130129322G>C	ENSP00000390895:p.Ser1539Thr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		241	0.11034798534798534	40	0.08130081300813008	44	0.12154696132596685	69	0.12062937062937062	88	0.11609498680738786	C	4.952	0.176814	0.09443	0.103324	0.135449	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.93604	-3.2;-3.25	5.73	4.84	0.62591	.	.	.	.	.	T	0.02230	0.0069	N	0.01091	-1.02	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.54173	-0.8333	8	0.23302	T	0.38	.	12.913	0.58190	0.0:0.5405:0.4595:0.0	rs35886424	1539	A8TX70-2	.	T	1539	ENSP00000390895:S1539T;ENSP00000265379:S1539T	ENSP00000265379:S1539T	S	+	2	0	COL6A5	131612012	0.049000	0.20398	0.606000	0.28943	0.230000	0.25150	1.005000	0.29834	1.445000	0.47624	-0.127000	0.14921	AGT	G|0.888;C|0.112	0.112	strong		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
CD300C	10871	hgsc.bcm.edu	37	17	72541052	72541052	+	Silent	SNP	C	C	T	rs2292107	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:72541052C>T	ENST00000330793.1	-	2	456	c.96G>A	c.(94-96)gcG>gcA	p.A32A		NM_006678.3	NP_006669.1	Q08708	CLM6_HUMAN	CD300c molecule	32	Ig-like V-type.				cellular defense response (GO:0006968)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|kidney(1)|large_intestine(4)|lung(11)|skin(2)|upper_aerodigestive_tract(1)	21						CCACGGGGCCCGCCACGGTCA	0.567													C|||	297	0.0593051	0.0219	0.0951	5008	,	,		19241	0.005		0.1163	False		,,,				2504	0.0818				p.A32A	Esophageal Squamous(66;421 1121 20537 25337 27468)	Atlas-SNP	.											CD300C,NS,carcinoma,-2,1	CD300C	41	1	0			c.G96A						PASS	.	C		145,4261	93.4+/-132.2	2,141,2060	42.0	47.0	45.0		96	-8.7	0.0	17	dbSNP_100	45	1132,7468	218.8+/-257.1	73,986,3241	no	coding-synonymous	CD300C	NM_006678.3		75,1127,5301	TT,TC,CC		13.1628,3.291,9.8185		32/225	72541052	1277,11729	2203	4300	6503	SO:0001819	synonymous_variant	10871	exon2			GGGGCCCGCCACG	BC022279	CCDS11701.1	17q25.2	2014-05-15	2006-03-28		ENSG00000167850	ENSG00000167850		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	19320	protein-coding gene	gene with protein product		606786	"""CD300c antigen"""			1349532, 10746781	Standard	NM_006678		Approved	CMRF35, LIR, CMRF-35A, CMRF35A, IGSF16	uc002jky.2	Q08708	OTTHUMG00000067608	ENST00000330793.1:c.96G>A	17.37:g.72541052C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	49	0.521277	NM_006678		Silent	SNP	ENST00000330793.1	37	CCDS11701.1																																																																																			C|0.911;T|0.089	0.089	strong		0.567	CD300C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145084.1	NM_006678	
SF3B4	10262	hgsc.bcm.edu	37	1	149895866	149895866	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:149895866G>A	ENST00000271628.8	-	5	1538	c.954C>T	c.(952-954)ggC>ggT	p.G318G		NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	318					gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)	17	Breast(34;0.0009)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			GATGTCCTAAGCCATGAGGGC	0.542																																					p.G318G		Atlas-SNP	.											.	SF3B4	37	.	0			c.C954T						PASS	.						12.0	13.0	13.0					1																	149895866		2197	4296	6493	SO:0001819	synonymous_variant	10262	exon5			TCCTAAGCCATGA	L35013	CCDS72900.1	1q21.2	2013-02-12	2002-08-29		ENSG00000143368	ENSG00000143368		"""RNA binding motif (RRM) containing"""	10771	protein-coding gene	gene with protein product		605593	"""splicing factor 3b, subunit 4, 49kD"""			7958871	Standard	NM_005850		Approved	SAP49, SF3b49, Hsh49	uc001etk.2	Q15427	OTTHUMG00000012208	ENST00000271628.8:c.954C>T	1.37:g.149895866G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	120	31	0.258333	NM_005850	Q5SZ63	Silent	SNP	ENST00000271628.8	37	CCDS941.1																																																																																			.	.	none		0.542	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850	
MAK16	84549	hgsc.bcm.edu	37	8	33356074	33356074	+	Missense_Mutation	SNP	A	A	G	rs6468171	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:33356074A>G	ENST00000360128.6	+	10	1287	c.830A>G	c.(829-831)cAg>cGg	p.Q277R	TTI2_ENST00000519356.1_Intron	NM_032509.3	NP_115898.2	Q9BXY0	MAK16_HUMAN	MAK16 homolog (S. cerevisiae)	277			Q -> R (in dbSNP:rs6468171). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	8						GGACCACTGCAGAGAAAACGA	0.483													A|||	2771	0.553315	0.6762	0.4914	5008	,	,		15259	0.4851		0.6322	False		,,,				2504	0.4202				p.Q277R		Atlas-SNP	.											.	MAK16	25	.	0			c.A830G						PASS	.	A	ARG/GLN	3005,1401	687.6+/-404.9	1028,949,226	77.0	78.0	78.0		830	-7.7	0.0	8	dbSNP_116	78	5362,3238	650.8+/-400.8	1667,2028,605	yes	missense	MAK16	NM_032509.3	43	2695,2977,831	GG,GA,AA		37.6512,31.7975,35.6682	benign	277/301	33356074	8367,4639	2203	4300	6503	SO:0001583	missense	84549	exon10			CACTGCAGAGAAA	AF251062	CCDS6089.1	8p12	2011-10-13	2008-06-04	2008-06-04	ENSG00000198042	ENSG00000198042		"""RNA binding motif (RRM) containing"""	13703	protein-coding gene	gene with protein product			"""RNA binding motif protein 13"""	RBM13			Standard	NM_032509		Approved	MAK16L	uc003xjj.3	Q9BXY0	OTTHUMG00000163957	ENST00000360128.6:c.830A>G	8.37:g.33356074A>G	ENSP00000353246:p.Gln277Arg	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	210	134	0.638095	NM_032509	B2RB44|Q5U5T1|Q86UC4|Q96SY6	Missense_Mutation	SNP	ENST00000360128.6	37	CCDS6089.1	1275	0.5837912087912088	338	0.6869918699186992	181	0.5	283	0.49475524475524474	473	0.6240105540897097	A	0.008	-1.880408	0.00537	0.682025	0.623488	ENSG00000198042	ENST00000360128	T	0.40225	1.04	5.5	-7.74	0.01241	.	0.671566	0.14962	N	0.288291	T	0.00012	0.0000	N	0.00642	-1.3	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27262	-1.0079	9	0.02654	T	1	1.1579	11.6164	0.51092	0.5923:0.0:0.3273:0.0804	rs6468171;rs56555602;rs60555743;rs6468171	277	Q9BXY0	MAK16_HUMAN	R	277	ENSP00000353246:Q277R	ENSP00000353246:Q277R	Q	+	2	0	MAK16	33475616	0.012000	0.17670	0.026000	0.17262	0.024000	0.10985	0.068000	0.14531	-1.724000	0.01373	-2.367000	0.00236	CAG	A|0.389;G|0.611	0.611	strong		0.483	MAK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376559.3	NM_032509	
USH2A	7399	hgsc.bcm.edu	37	1	216172380	216172380	+	Missense_Mutation	SNP	A	A	G	rs10864219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:216172380A>G	ENST00000307340.3	-	34	6892	c.6506T>C	c.(6505-6507)aTa>aCa	p.I2169T	USH2A_ENST00000366943.2_Missense_Mutation_p.I2169T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2169	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T (in dbSNP:rs10864219). {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)		AATCCCACTTATTTTTCTTGG	0.313										HNSCC(13;0.011)			A|||	2972	0.59345	0.4206	0.6513	5008	,	,		16630	0.8343		0.497	False		,,,				2504	0.637				p.I2169T		Atlas-SNP	.											.	USH2A	1168	.	0			c.T6506C						PASS	.	A	THR/ILE	1932,2474	549.4+/-377.8	449,1034,720	127.0	120.0	123.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6506	5.8	0.9	1	dbSNP_120	123	4323,4277	576.9+/-390.5	1088,2147,1065	yes	missense	USH2A	NM_206933.2	89	1537,3181,1785	GG,GA,AA		49.7326,43.8493,48.0932	benign	2169/5203	216172380	6255,6751	2203	4300	6503	SO:0001583	missense	7399	exon34			CCACTTATTTTTC	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.6506T>C	1.37:g.216172380A>G	ENSP00000305941:p.Ile2169Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	1296	0.5934065934065934	210	0.4268292682926829	224	0.6187845303867403	484	0.8461538461538461	378	0.49868073878627966	A	8.510	0.866247	0.17250	0.438493	0.502674	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.52526	0.66;0.66	5.77	5.77	0.91146	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.730054	0.11203	N	0.588593	T	0.00012	0.0000	N	0.02539	-0.55	0.48901	P	2.729999999999677E-4	B	0.23937	0.094	B	0.16722	0.016	T	0.34279	-0.9835	9	0.11485	T	0.65	.	11.5472	0.50700	0.7261:0.2738:0.0:0.0	rs10864219;rs17584229;rs52809712;rs56928409;rs10864219	2169	O75445	USH2A_HUMAN	T	2169	ENSP00000305941:I2169T;ENSP00000355910:I2169T	ENSP00000305941:I2169T	I	-	2	0	USH2A	214239003	0.984000	0.35163	0.921000	0.36526	0.472000	0.32918	2.395000	0.44459	2.199000	0.70637	0.533000	0.62120	ATA	A|0.470;G|0.530	0.530	strong		0.313	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
ZNF85	7639	hgsc.bcm.edu	37	19	21133078	21133078	+	Missense_Mutation	SNP	A	A	G	rs142868740	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21133078A>G	ENST00000328178.8	+	4	1871	c.1758A>G	c.(1756-1758)atA>atG	p.I586M	ZNF85_ENST00000345030.6_Missense_Mutation_p.I553M|ZNF85_ENST00000601023.1_Missense_Mutation_p.I527M	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	586					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						AACATAAGATAATTCATACCG	0.284													.|||	2	0.000399361	0.0	0.0	5008	,	,		18633	0.0		0.001	False		,,,				2504	0.001				p.I616M		Atlas-SNP	.											.	ZNF85	72	.	0			c.A1848G						PASS	.	A	MET/ILE	0,4396		0,0,2198	18.0	19.0	19.0		1758	1.3	0.0	19	dbSNP_134	19	12,8550		0,12,4269	yes	missense	ZNF85	NM_003429.4	10	0,12,6467	GG,GA,AA		0.1402,0.0,0.0926	benign	586/596	21133078	12,12946	2198	4281	6479	SO:0001583	missense	7639	exon5			TAAGATAATTCAT	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"""Zinc fingers, C2H2-type"", ""-"""	13160	protein-coding gene	gene with protein product		603899	"""zinc finger protein 85 (HPF4, HTF1)"""			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.1758A>G	19.37:g.21133078A>G	ENSP00000329793:p.Ile586Met	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	0.029	-1.346964	0.01266	0.0	0.001402	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.07444	3.19;3.19	1.27	1.27	0.21489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04407	0.0121	N	0.12471	0.22	0.80722	D	1	P;B;P	0.44816	0.478;0.082;0.844	B;B;B	0.40165	0.272;0.002;0.321	T	0.48906	-0.8993	9	0.72032	D	0.01	.	5.3151	0.15850	0.7085:0.2915:0.0:0.0	.	553;527;586	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	M	586;553;461	ENSP00000329793:I586M;ENSP00000342340:I553M	ENSP00000329793:I586M	I	+	3	3	ZNF85	20924918	0.001000	0.12720	0.044000	0.18714	0.048000	0.14542	0.031000	0.13710	0.528000	0.28580	0.329000	0.21502	ATA	A|0.999;G|0.001	0.001	strong		0.284	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
C4orf19	55286	hgsc.bcm.edu	37	4	37592128	37592128	+	Missense_Mutation	SNP	G	G	A	rs2973275	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:37592128G>A	ENST00000284437.6	+	3	629	c.451G>A	c.(451-453)Gcc>Acc	p.A151T	RP11-36B15.1_ENST00000503034.1_RNA|C4orf19_ENST00000381980.4_Missense_Mutation_p.A151T|C4orf19_ENST00000508175.1_Intron	NM_018302.2	NP_060772.2	Q8IY42	CD019_HUMAN	chromosome 4 open reading frame 19	151			A -> T (in dbSNP:rs2973275).							large_intestine(1)|lung(3)|skin(3)|stomach(1)|urinary_tract(1)	9						TGTGCTGCTGGCCTCAGAAGG	0.542													G|||	642	0.128195	0.0469	0.1499	5008	,	,		21033	0.0784		0.2545	False		,,,				2504	0.1442				p.A151T		Atlas-SNP	.											.	C4orf19	17	.	0			c.G451A						PASS	.	G	THR/ALA,THR/ALA	386,4020	192.3+/-217.7	7,372,1824	73.0	76.0	75.0		451,451	2.3	0.0	4	dbSNP_101	75	2126,6474	366.1+/-334.2	261,1604,2435	yes	missense,missense	C4orf19	NM_001104629.1,NM_018302.2	58,58	268,1976,4259	AA,AG,GG		24.7209,8.7608,19.3142	benign,benign	151/315,151/315	37592128	2512,10494	2203	4300	6503	SO:0001583	missense	55286	exon3			CTGCTGGCCTCAG	BC037906	CCDS3442.1	4p14	2008-02-05			ENSG00000154274	ENSG00000154274			25618	protein-coding gene	gene with protein product						12477932	Standard	NM_001104629		Approved	FLJ11017	uc003gsw.4	Q8IY42	OTTHUMG00000128580	ENST00000284437.6:c.451G>A	4.37:g.37592128G>A	ENSP00000284437:p.Ala151Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_018302	Q9NV03	Missense_Mutation	SNP	ENST00000284437.6	37	CCDS3442.1	364	0.16666666666666666	45	0.09146341463414634	61	0.1685082872928177	63	0.11013986013986014	195	0.25725593667546176	G	9.098	1.003456	0.19121	0.087608	0.247209	ENSG00000154274	ENST00000381980;ENST00000284437	T;T	0.34667	1.35;1.35	5.03	2.33	0.28932	.	0.879757	0.09877	N	0.744153	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.21753	0.06	B	0.27715	0.082	T	0.34675	-0.9819	9	0.06757	T	0.87	-3.985	6.4018	0.21642	0.3087:0.0:0.6913:0.0	rs2973275;rs3733499;rs61356581;rs2973275	151	Q8IY42	CD019_HUMAN	T	151	ENSP00000371408:A151T;ENSP00000284437:A151T	ENSP00000284437:A151T	A	+	1	0	C4orf19	37268523	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.494000	0.22467	0.381000	0.24851	0.655000	0.94253	GCC	G|0.830;A|0.170	0.170	strong		0.542	C4orf19-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250432.1	NM_018302	
SNX16	64089	hgsc.bcm.edu	37	8	82727569	82727569	+	Silent	SNP	T	T	C	rs16909651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:82727569T>C	ENST00000345957.4	-	5	950	c.672A>G	c.(670-672)gaA>gaG	p.E224E	SNX16_ENST00000353788.4_Silent_p.E195E|RP13-923O23.6_ENST00000524337.1_RNA|SNX16_ENST00000396330.2_Silent_p.E224E	NM_152836.2	NP_690049.1	P57768	SNX16_HUMAN	sorting nexin 16	224					early endosome to late endosome transport (GO:0045022)|endosome to lysosome transport (GO:0008333)|protein targeting to lysosome (GO:0006622)	early endosome (GO:0005769)|extrinsic component of endosome membrane (GO:0031313)|late endosome (GO:0005770)|lysosome (GO:0005764)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			large_intestine(1)|ovary(1)|pancreas(1)|skin(2)	5						CCCTGCTTTCTTCTAGGCTAT	0.353													T|||	786	0.156949	0.0144	0.147	5008	,	,		16427	0.1974		0.1978	False		,,,				2504	0.273				p.E224E		Atlas-SNP	.											SNX16,caecum,carcinoma,0,1	SNX16	21	1	0			c.A672G						PASS	.	T	,,	192,4214	121.3+/-158.8	4,184,2015	101.0	90.0	94.0		672,672,585	4.6	1.0	8	dbSNP_123	94	1600,7000	297.7+/-303.5	165,1270,2865	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX16	NM_022133.3,NM_152836.2,NM_152837.2	,,	169,1454,4880	CC,CT,TT		18.6047,4.3577,13.7783	,,	224/345,224/345,195/316	82727569	1792,11214	2203	4300	6503	SO:0001819	synonymous_variant	64089	exon5			GCTTTCTTCTAGG	AF305779	CCDS6234.1, CCDS6235.1	8q21.13	2011-05-03			ENSG00000104497	ENSG00000104497		"""Sorting nexins"""	14980	protein-coding gene	gene with protein product		614903				12461558, 12813048	Standard	NM_152837		Approved		uc003ycn.3	P57768	OTTHUMG00000164727	ENST00000345957.4:c.672A>G	8.37:g.82727569T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	137	76	0.554745	NM_152836	A8K4D8|Q658L0|Q8N4U3	Silent	SNP	ENST00000345957.4	37	CCDS6234.1																																																																																			T|0.855;C|0.145	0.145	strong		0.353	SNX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379929.1	NM_022133	
TFDP2	7029	hgsc.bcm.edu	37	3	141692893	141692893	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:141692893C>T	ENST00000489671.1	-	8	1090	c.660G>A	c.(658-660)ctG>ctA	p.L220L	TFDP2_ENST00000499676.2_Silent_p.L160L|TFDP2_ENST00000467072.1_Silent_p.L160L|TFDP2_ENST00000310282.6_Silent_p.L160L|TFDP2_ENST00000317104.7_Silent_p.L144L|TFDP2_ENST00000479040.1_Silent_p.L159L|TFDP2_ENST00000397991.4_Silent_p.L192L|TFDP2_ENST00000486111.1_Silent_p.L160L|TFDP2_ENST00000477292.1_Silent_p.L84L|TFDP2_ENST00000495310.1_Silent_p.L123L			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	220	Dimerization. {ECO:0000255}.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)|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 cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						CACTTACCTCCAGATTCTGAC	0.303																																					p.L220L		Atlas-SNP	.											TFDP2_ENST00000489671,rectum,carcinoma,0,3	TFDP2	44	3	0			c.G660A						scavenged	.						86.0	80.0	82.0					3																	141692893		1843	4118	5961	SO:0001819	synonymous_variant	7029	exon8			TACCTCCAGATTC	U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.660G>A	3.37:g.141692893C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	197	3	0.0152284	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Silent	SNP	ENST00000489671.1	37	CCDS54650.1																																																																																			.	.	none		0.303	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286	
FLG2	388698	hgsc.bcm.edu	37	1	152329369	152329369	+	Missense_Mutation	SNP	C	C	G	rs2282302	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152329369C>G	ENST00000388718.5	-	3	965	c.893G>C	c.(892-894)tGt>tCt	p.C298S	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	298	Ser-rich.		C -> S (in dbSNP:rs2282302).		establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGTGACTGACAAGAACTTGA	0.463													C|||	684	0.136581	0.0061	0.2305	5008	,	,		23480	0.1875		0.2117	False		,,,				2504	0.1166				p.C298S		Atlas-SNP	.											.	FLG2	431	.	0			c.G893C						PASS	.	C	SER/CYS	184,4222	118.8+/-156.5	6,172,2025	207.0	194.0	198.0		893	2.4	1.0	1	dbSNP_100	198	1689,6911	309.3+/-309.3	167,1355,2778	yes	missense	FLG2	NM_001014342.2	112	173,1527,4803	GG,GC,CC		19.6395,4.1761,14.401	probably-damaging	298/2392	152329369	1873,11133	2203	4300	6503	SO:0001583	missense	388698	exon3			GACTGACAAGAAC	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.893G>C	1.37:g.152329369C>G	ENSP00000373370:p.Cys298Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	144	83	0.576389	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	361	0.1652930402930403	3	0.006097560975609756	84	0.23204419889502761	118	0.2062937062937063	156	0.20580474934036938	C	8.079	0.771974	0.16051	0.041761	0.196395	ENSG00000143520	ENST00000388718	T	0.00832	5.64	5.32	2.4	0.29515	.	.	.	.	.	T	0.00468	0.0015	L	0.44542	1.39	0.39373	P	0.033887	D	0.54207	0.965	P	0.51016	0.656	T	0.31194	-0.9952	8	0.05525	T	0.97	-8.9525	7.6768	0.28490	0.0:0.73:0.0:0.27	rs2282302;rs56511827;rs2282302	298	Q5D862	FILA2_HUMAN	S	298	ENSP00000373370:C298S	ENSP00000373370:C298S	C	-	2	0	FLG2	150595993	0.974000	0.33945	0.998000	0.56505	0.134000	0.20937	-0.065000	0.11617	0.319000	0.23209	0.557000	0.71058	TGT	C|0.848;G|0.152	0.152	strong		0.463	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
C10orf12	26148	hgsc.bcm.edu	37	10	98742750	98742750	+	Missense_Mutation	SNP	A	A	C	rs3829856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:98742750A>C	ENST00000286067.2	+	1	1710	c.1603A>C	c.(1603-1605)Atc>Ctc	p.I535L		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	535			I -> L (in dbSNP:rs3829856).							NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		TTGTCTTGAAATCAAAGTTCC	0.453													A|||	509	0.101637	0.0832	0.0476	5008	,	,		18675	0.1915		0.0646	False		,,,				2504	0.1104				p.I535L		Atlas-SNP	.											.	C10orf12	94	.	0			c.A1603C						PASS	.	A	LEU/ILE	333,4073	160.7+/-193.0	9,315,1879	71.0	80.0	77.0		1603	-2.5	0.4	10	dbSNP_107	77	503,8095	141.1+/-197.5	16,471,3812	yes	missense	C10orf12	NM_015652.2	5	25,786,5691	CC,CA,AA		5.8502,7.5579,6.4288	benign	535/1248	98742750	836,12168	2203	4299	6502	SO:0001583	missense	26148	exon1			CTTGAAATCAAAG	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.1603A>C	10.37:g.98742750A>C	ENSP00000286067:p.Ile535Leu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	63	13	0.206349	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	37	CCDS7452.1	212	0.09706959706959707	40	0.08130081300813008	20	0.055248618784530384	104	0.18181818181818182	48	0.0633245382585752	A	10.88	1.475286	0.26511	0.075579	0.058502	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.10382	2.88	5.82	-2.46	0.06461	.	0.278980	0.24499	U	0.037985	T	0.00012	0.0000	N	0.19112	0.55	0.41806	P	0.01005900000000004	B	0.14805	0.011	B	0.16289	0.015	T	0.41124	-0.9526	9	0.36615	T	0.2	-0.0766	6.6806	0.23117	0.5194:0.1323:0.3484:0.0	rs3829856;rs52834733;rs61155862;rs3829856	535	Q8N655	CJ012_HUMAN	L	535;369	ENSP00000286067:I535L	ENSP00000286067:I535L	I	+	1	0	C10orf12	98732740	0.995000	0.38212	0.426000	0.26672	0.191000	0.23601	0.418000	0.21230	-0.712000	0.04988	-0.396000	0.06452	ATC	A|0.918;C|0.082	0.082	strong		0.453	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
HK3	3101	hgsc.bcm.edu	37	5	176314639	176314639	+	Silent	SNP	G	G	A	rs6875296	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	151	0	0		WXS	Illumina HiSeq	Phase_I	141	83	0.588652	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		
ANKMY1	51281	hgsc.bcm.edu	37	2	241463453	241463453	+	Missense_Mutation	SNP	C	C	A	rs3821348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241463453C>A	ENST00000272972.3	-	7	1628	c.1414G>T	c.(1414-1416)Gtg>Ttg	p.V472L	ANKMY1_ENST00000403283.1_Missense_Mutation_p.V410L|ANKMY1_ENST00000462004.1_5'Flank|ANKMY1_ENST00000401804.1_Missense_Mutation_p.V561L|ANKMY1_ENST00000405523.3_Missense_Mutation_p.V331L|ANKMY1_ENST00000391987.1_Missense_Mutation_p.V472L|ANKMY1_ENST00000373320.4_Missense_Mutation_p.V242L|ANKMY1_ENST00000405002.1_Missense_Mutation_p.V242L|ANKMY1_ENST00000373318.2_Missense_Mutation_p.V331L|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000361678.4_Missense_Mutation_p.V331L|ANKMY1_ENST00000536462.1_Missense_Mutation_p.V284L	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	472			V -> L (in dbSNP:rs3821348). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039}.				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)		CACACACACACGTTGGACTCA	0.597													C|||	818	0.163339	0.1089	0.1412	5008	,	,		21397	0.0992		0.1769	False		,,,				2504	0.3047				p.V472L		Atlas-SNP	.											.	ANKMY1	112	.	0			c.G1414T						PASS	.	C	LEU/VAL,LEU/VAL	509,3897	235.8+/-248.2	33,443,1727	142.0	124.0	130.0		1414,991	-8.1	0.0	2	dbSNP_107	130	1367,7233	264.6+/-285.7	99,1169,3032	yes	missense,missense	ANKMY1	NM_016552.2,NM_017844.2	32,32	132,1612,4759	AA,AC,CC		15.8953,11.5524,14.4241	benign,benign	472/942,331/718	241463453	1876,11130	2203	4300	6503	SO:0001583	missense	51281	exon7			CACACACGTTGGA	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.1414G>T	2.37:g.241463453C>A	ENSP00000272972:p.Val472Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_016552	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	334	0.15293040293040294	62	0.12601626016260162	55	0.15193370165745856	65	0.11363636363636363	152	0.20052770448548812	C	0.659	-0.806463	0.02819	0.115524	0.158953	ENSG00000144504	ENST00000373318;ENST00000272972;ENST00000361678;ENST00000391987;ENST00000373320;ENST00000403283;ENST00000401804;ENST00000536462;ENST00000405523;ENST00000405002	T;T;T;T;T;T;T;T;T;T	0.54071	3.02;0.6;2.35;0.6;4.48;2.58;0.59;2.4;2.36;2.65	4.06	-8.12	0.01078	Ankyrin repeat-containing domain (1);	11.972400	0.00166	N	0.000000	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B;B;B	0.09022	0.0;0.0;0.002;0.0;0.002;0.0	B;B;B;B;B;B	0.06405	0.0;0.001;0.002;0.001;0.002;0.0	T	0.03315	-1.1049	9	0.27785	T	0.31	-50.1229	11.6405	0.51230	0.0:0.1362:0.6239:0.24	rs3821348;rs17442610;rs61619400;rs3821348	472;284;242;331;331;472	Q4ZFV3;F5H558;Q9P2S6-4;Q6GPI0;Q9P2S6-2;Q9P2S6	.;.;.;.;.;ANKY1_HUMAN	L	331;472;331;472;242;410;561;284;331;242	ENSP00000362415:V331L;ENSP00000272972:V472L;ENSP00000355097:V331L;ENSP00000375847:V472L;ENSP00000362417:V242L;ENSP00000383968:V410L;ENSP00000385887:V561L;ENSP00000444707:V284L;ENSP00000385635:V331L;ENSP00000385145:V242L	ENSP00000272972:V472L	V	-	1	0	ANKMY1	241112126	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.542000	0.00935	-2.329000	0.00634	-0.327000	0.08410	GTG	C|0.846;A|0.147	0.147	strong		0.597	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2	NM_017844	
KDM5A	5927	hgsc.bcm.edu	37	12	427575	427575	+	Missense_Mutation	SNP	A	A	G	rs11062385	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:427575A>G	ENST00000399788.2	-	19	2956	c.2594T>C	c.(2593-2595)aTg>aCg	p.M865T	KDM5A_ENST00000382815.4_Missense_Mutation_p.M865T	NM_001042603.1	NP_001036068.1	P29375	KDM5A_HUMAN	lysine (K)-specific demethylase 5A	865			M -> T (in dbSNP:rs11062385).		chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|multicellular organismal development (GO:0007275)|negative regulation of histone deacetylase activity (GO:1901726)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			NS(2)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(29)|ovary(1)|prostate(5)|skin(6)|stomach(1)|urinary_tract(2)	77						GGTTTCATCCATCATGGCCTC	0.393			T	NUP98	AML								A|||	1768	0.353035	0.3321	0.3199	5008	,	,		21745	0.5109		0.2326	False		,,,				2504	0.3661				p.M865T		Atlas-SNP	.		Dom	yes		12	12p11	5927	"""lysine (K)-specific demethylase 5A, JARID1A"""		L	.	KDM5A	307	.	0			c.T2594C						PASS	.	A	THR/MET	1180,2546		203,774,886	108.0	105.0	106.0		2594	4.0	1.0	12	dbSNP_120	106	2085,6131		276,1533,2299	yes	missense	KDM5A	NM_001042603.1	81	479,2307,3185	GG,GA,AA		25.3773,31.6694,27.3405	benign	865/1691	427575	3265,8677	1863	4108	5971	SO:0001583	missense	5927	exon19			TCATCCATCATGG		CCDS41736.1	12p13.33	2013-01-28	2009-04-06	2009-04-06	ENSG00000073614	ENSG00000073614		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	9886	protein-coding gene	gene with protein product		180202	"""retinoblastoma-binding protein 2"", ""Jumonji, AT rich interactive domain 1A (RBBP2-like)"", ""jumonji, AT rich interactive domain 1A"""	RBBP2, JARID1A		1857421	Standard	NM_001042603		Approved		uc001qif.1	P29375	OTTHUMG00000168055	ENST00000399788.2:c.2594T>C	12.37:g.427575A>G	ENSP00000382688:p.Met865Thr	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_001042603	A8MV76|Q4LE72|Q86XZ1	Missense_Mutation	SNP	ENST00000399788.2	37	CCDS41736.1	768	0.3516483516483517	181	0.3678861788617886	116	0.32044198895027626	289	0.5052447552447552	182	0.24010554089709762	A	6.591	0.477457	0.12521	0.316694	0.253773	ENSG00000073614	ENST00000261253;ENST00000399787;ENST00000399788;ENST00000382815;ENST00000544760	T;T;T	0.39997	1.05;1.05;1.05	5.18	3.99	0.46301	Lysine-specific demethylase-like domain (1);	0.270105	0.38217	N	0.001762	T	0.00012	0.0000	N	0.01874	-0.695	0.32953	P	0.479989	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.09377	0.001;0.001;0.004	T	0.46965	-0.9153	9	0.21014	T	0.42	-7.7721	6.1802	0.20468	0.7533:0.1572:0.0895:0.0	rs11062385;rs52835808;rs60765971;rs11062385	865;865;865	F5H1F7;P29375;P29375-2	.;KDM5A_HUMAN;.	T	484;824;865;865;484	ENSP00000382688:M865T;ENSP00000372265:M865T;ENSP00000440622:M484T	ENSP00000261253:M484T	M	-	2	0	KDM5A	297836	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.908000	0.56355	0.760000	0.33108	0.482000	0.46254	ATG	A|0.651;G|0.349	0.349	strong		0.393	KDM5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397812.1	NM_005056	
NOP58	51602	hgsc.bcm.edu	37	2	203139844	203139844	+	Silent	SNP	T	T	C	rs80282360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:203139844T>C	ENST00000264279.5	+	2	280	c.54T>C	c.(52-54)aaT>aaC	p.N18N	SNORD70_ENST00000391007.1_RNA|SNORD70_ENST00000391232.1_RNA|NOP58_ENST00000467734.1_Intron	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	18					cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						AGGTTCTAAATGAGAAGAAAC	0.284													T|||	618	0.123403	0.0045	0.1427	5008	,	,		17571	0.123		0.1362	False		,,,				2504	0.2577				p.N18N		Atlas-SNP	.											NOP58,NS,carcinoma,0,1	NOP58	41	1	0			c.T54C						PASS	.	T		106,4286	72.0+/-110.0	4,98,2094	32.0	35.0	34.0		54	5.1	1.0	2	dbSNP_131	34	1007,7561	207.3+/-249.1	55,897,3332	no	coding-synonymous	NOP58	NM_015934.3		59,995,5426	CC,CT,TT		11.753,2.4135,8.588		18/530	203139844	1113,11847	2196	4284	6480	SO:0001819	synonymous_variant	51602	exon2			TCTAAATGAGAAG		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"""NOP58 ribonucleoprotein homolog (yeast)"""			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.54T>C	2.37:g.203139844T>C		Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	186	150	0.806452	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	37	CCDS2353.1																																																																																			T|0.904;C|0.096	0.096	strong		0.284	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934	
TJP1	7082	hgsc.bcm.edu	37	15	30026582	30026582	+	Missense_Mutation	SNP	T	T	C	rs2229517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:30026582T>C	ENST00000346128.6	-	12	1886	c.1412A>G	c.(1411-1413)aAc>aGc	p.N471S	TJP1_ENST00000545208.2_Missense_Mutation_p.N471S|TJP1_ENST00000356107.6_Missense_Mutation_p.N471S|TJP1_ENST00000400011.2_Missense_Mutation_p.N475S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	471	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.		N -> S (in dbSNP:rs2229517). {ECO:0000269|Ref.3}.		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)		ATCTACGTTGTTTACCTAATA	0.348													T|||	24	0.00479233	0.003	0.0014	5008	,	,		17609	0.0		0.0109	False		,,,				2504	0.0082				p.N471S	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.A1412G						PASS	.	T	SER/ASN,SER/ASN	7,3635		0,7,1814	99.0	89.0	92.0		1412,1412	5.4	1.0	15	dbSNP_98	92	108,8050		0,108,3971	yes	missense,missense	TJP1	NM_003257.3,NM_175610.2	46,46	0,115,5785	CC,CT,TT		1.3239,0.1922,0.9746	benign,benign	471/1749,471/1669	30026582	115,11685	1821	4079	5900	SO:0001583	missense	7082	exon12			ACGTTGTTTACCT		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.1412A>G	15.37:g.30026582T>C	ENSP00000281537:p.Asn471Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	61	43	0.704918	NM_175610	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	16	0.007326007326007326	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	T	16.63	3.176786	0.57692	0.001922	0.013239	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.36	5.36	0.76844	Src homology-3 domain (1);PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.72550	0.3474	M	0.85945	2.785	0.80722	D	1	B;D;B;D	0.89917	0.009;1.0;0.009;0.998	B;D;B;D	0.87578	0.04;0.998;0.04;0.994	T	0.79434	-0.1805	9	.	.	.	.	15.6385	0.76977	0.0:0.0:0.0:1.0	rs2229517;rs45612033	464;471;471;475	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	S	471;475;471;471;471	ENSP00000281537:N471S;ENSP00000382890:N475S;ENSP00000441202:N471S;ENSP00000348416:N471S	.	N	-	2	0	TJP1	27813874	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	7.997000	0.88414	2.147000	0.66899	0.477000	0.44152	AAC	T|0.991;C|0.009	0.009	strong		0.348	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257	
N4BP3	23138	hgsc.bcm.edu	37	5	177547336	177547336	+	Missense_Mutation	SNP	G	G	A	rs3812082	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:177547336G>A	ENST00000274605.5	+	3	847	c.488G>A	c.(487-489)cGg>cAg	p.R163Q		NM_015111.1	NP_055926.1	O15049	N4BP3_HUMAN	NEDD4 binding protein 3	163				R -> Q (in Ref. 3; AAH53323). {ECO:0000305}.		cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)				breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	9	all_cancers(89;0.00294)|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)			CCCGGGCCCCGGGCCAGCCAG	0.706													G|||	741	0.147963	0.0121	0.2176	5008	,	,		12060	0.1389		0.2058	False		,,,				2504	0.2321				p.R163Q		Atlas-SNP	.											N4BP3,NS,carcinoma,0,2	N4BP3	25	2	0			c.G488A						scavenged	.	G	GLN/ARG	185,4175		8,169,2003	13.0	17.0	16.0		488	0.0	0.9	5	dbSNP_107	16	1968,6542		246,1476,2533	no	missense	N4BP3	NM_015111.1	43	254,1645,4536	AA,AG,GG		23.1257,4.2431,16.7288	benign	163/545	177547336	2153,10717	2180	4255	6435	SO:0001583	missense	23138	exon3			GGCCCCGGGCCAG	AB002339	CCDS34307.1	5q35.3	2012-05-17				ENSG00000145911			29852	protein-coding gene	gene with protein product						9205841, 11717310	Standard	XM_006714834		Approved	LZTS4	uc003mik.1	O15049		ENST00000274605.5:c.488G>A	5.37:g.177547336G>A	ENSP00000274605:p.Arg163Gln	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_015111	B4DIL3|D3DWP3|Q6ZSQ6|Q7Z6I3	Missense_Mutation	SNP	ENST00000274605.5	37	CCDS34307.1	330	0.1510989010989011	13	0.026422764227642278	78	0.2154696132596685	77	0.1346153846153846	162	0.21372031662269128	G	2.203	-0.382529	0.04966	0.042431	0.231257	ENSG00000145911	ENST00000274605	T	0.00518	6.86	5.13	0.0071	0.14069	.	0.846391	0.10796	N	0.633194	T	0.00012	0.0000	N	0.00926	-1.1	0.47778	P	4.8199999999998244E-4	B	0.14438	0.01	B	0.06405	0.002	T	0.03566	-1.1024	9	0.10636	T	0.68	-17.7226	4.3863	0.11318	0.427:0.0:0.4229:0.1501	rs3812082;rs17846503;rs17859572	163	O15049	N4BP3_HUMAN	Q	163	ENSP00000274605:R163Q	ENSP00000274605:R163Q	R	+	2	0	N4BP3	177479942	1.000000	0.71417	0.896000	0.35187	0.056000	0.15407	1.348000	0.33987	0.079000	0.16929	-1.686000	0.00732	CGG	G|0.832;A|0.168	0.168	strong		0.706	N4BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373552.2	NM_015111	
PSPH	5723	hgsc.bcm.edu	37	7	56088786	56088786	+	Silent	SNP	A	A	T	rs202027697	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:56088786A>T	ENST00000395471.3	-	4	925	c.120T>A	c.(118-120)gtT>gtA	p.V40V	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Silent_p.V40V			P78330	SERB_HUMAN	phosphoserine phosphatase	40					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CCGCGTCCTCAACGCCACAGA	0.423																																					p.V40V		Atlas-SNP	.											.	PSPH	23	.	0			c.T120A						PASS	.						151.0	116.0	128.0					7																	56088786		2203	4300	6503	SO:0001819	synonymous_variant	5723	exon4			GTCCTCAACGCCA	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.120T>A	7.37:g.56088786A>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	302	86	0.284768	NM_004577	B2RCR5|Q7Z3S5	Silent	SNP	ENST00000395471.3	37	CCDS5522.1																																																																																			A|0.749;T|0.251	0.251	strong		0.423	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
ZP3	7784	hgsc.bcm.edu	37	7	76069886	76069886	+	Missense_Mutation	SNP	A	A	G	rs2906997	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76069886A>G	ENST00000394857.3	+	7	1076	c.1018A>G	c.(1018-1020)Atg>Gtg	p.M340V	ZP3_ENST00000336517.4_Missense_Mutation_p.M289V|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Missense_Mutation_p.M164V	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	340			M -> V (in dbSNP:rs2906997).		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						GCCTCATGTCATGAGCCAGTG	0.542																																					p.M340V		Atlas-SNP	.											.	ZP3	32	.	0			c.A1018G						PASS	.						134.0	129.0	131.0					7																	76069886		2203	4300	6503	SO:0001583	missense	7784	exon7			CATGTCATGAGCC	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.1018A>G	7.37:g.76069886A>G	ENSP00000378326:p.Met340Val	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	342	32	0.0935673	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	.	.	.	.	.	.	.	.	.	.	N	2.901	-0.227591	0.06022	.	.	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	T;T;T	0.20463	2.66;2.88;2.07	4.27	-5.46	0.02608	.	2.545950	0.01889	N	0.038399	T	0.04952	0.0133	N	0.00483	-1.445	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23368	-1.0190	10	0.29301	T	0.29	1.7081	2.1536	0.03806	0.4579:0.2402:0.1865:0.1154	rs2906997;rs2906997	289;340	P21754-3;P21754	.;ZP3_HUMAN	V	289;340;340;164	ENSP00000337310:M289V;ENSP00000378326:M340V;ENSP00000411955:M164V	ENSP00000337310:M289V	M	+	1	0	ZP3	75907822	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.029000	0.01430	-1.516000	0.01782	-1.163000	0.01768	ATG	A|0.912;G|0.088	0.088	strong		0.542	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
SFN	2810	hgsc.bcm.edu	37	1	27190149	27190149	+	Missense_Mutation	SNP	C	C	T	rs78707984		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:27190149C>T	ENST00000339276.4	+	1	517	c.446C>T	c.(445-447)tCa>tTa	p.S149L		NM_006142.3	NP_006133.1	Q9Y3B8	ORN_HUMAN	stratifin	0	Exonuclease.				nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide metabolic process (GO:0009117)	focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	9		all_cancers(24;1.23e-26)|all_epithelial(13;1.19e-23)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Breast(348;0.00017)|Renal(390;0.0007)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.1e-52)|Epithelial(14;2.31e-52)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)|GBM - Glioblastoma multiforme(114;0.0767)|Lung(427;0.215)		TCAGCCCGGTCAGCCTACCAG	0.602																																					p.S149L		Atlas-SNP	.											.	SFN	20	.	0			c.C446T						PASS	.	C	LEU/SER	0,4406		0,0,2203	85.0	83.0	84.0		446	5.1	0.7	1	dbSNP_131	84	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SFN	NM_006142.3	145	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	149/249	27190149	2,13004	2203	4300	6503	SO:0001583	missense	2810	exon1			CCCGGTCAGCCTA	BC023552	CCDS288.1	1p36.11	2008-02-05			ENSG00000175793	ENSG00000175793			10773	protein-coding gene	gene with protein product	"""14-3-3 sigma"""	601290				8515476	Standard	NM_006142		Approved	YWHAS	uc001bnc.1	P31947	OTTHUMG00000004093	ENST00000339276.4:c.446C>T	1.37:g.27190149C>T	ENSP00000340989:p.Ser149Leu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	41	11	0.268293	NM_006142	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Missense_Mutation	SNP	ENST00000339276.4	37	CCDS288.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.858571	0.32791	0.0	2.33E-4	ENSG00000175793	ENST00000339276;ENST00000538651	T	0.43688	0.94	6.06	5.1	0.69264	14-3-3 domain (4);	0.906876	0.09400	N	0.807339	T	0.20780	0.0500	N	0.02368	-0.58	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.05402	-1.0887	10	0.25751	T	0.34	-0.5242	11.3178	0.49403	0.1716:0.7101:0.1183:0.0	.	149	P31947	1433S_HUMAN	L	149;117	ENSP00000340989:S149L	ENSP00000340989:S149L	S	+	2	0	SFN	27062736	0.144000	0.22641	0.733000	0.30861	0.993000	0.82548	2.150000	0.42254	2.871000	0.98454	0.655000	0.94253	TCA	.	.	weak		0.602	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011709.1	NM_006142	
SCN7A	6332	hgsc.bcm.edu	37	2	167262169	167262169	+	Missense_Mutation	SNP	T	T	C	rs35344714	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:167262169T>C	ENST00000409855.1	-	25	5096	c.4970A>G	c.(4969-4971)gAc>gGc	p.D1657G		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1657			D -> G (in dbSNP:rs35344714).		membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	AACATCTCTGTCACCATCTAT	0.378													T|||	266	0.053115	0.031	0.0288	5008	,	,		19281	0.0129		0.0775	False		,,,				2504	0.1166				p.D1657G		Atlas-SNP	.											.	SCN7A	410	.	0			c.A4970G						PASS	.	T	GLY/ASP	158,3554		3,152,1701	256.0	240.0	245.0		4970	0.9	0.0	2	dbSNP_126	245	807,7383		38,731,3326	yes	missense	SCN7A	NM_002976.3	94	41,883,5027	CC,CT,TT		9.8535,4.2565,8.1079	benign	1657/1683	167262169	965,10937	1856	4095	5951	SO:0001583	missense	6332	exon25			TCTCTGTCACCAT	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.4970A>G	2.37:g.167262169T>C	ENSP00000386796:p.Asp1657Gly	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	236	106	0.449153	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	87	0.03983516483516483	9	0.018292682926829267	10	0.027624309392265192	12	0.02097902097902098	56	0.07387862796833773	T	6.169	0.399411	0.11696	0.042565	0.098535	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.96802	-4.13	4.62	0.936	0.19488	.	0.625902	0.14359	N	0.324601	T	0.21801	0.0525	N	0.13235	0.315	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.64892	-0.6300	9	0.06891	T	0.86	.	6.3668	0.21459	0.0:0.3025:0.0:0.6975	rs35344714	1657	Q01118	SCN7A_HUMAN	G	1657	ENSP00000386796:D1657G	ENSP00000259060:D1657G	D	-	2	0	SCN7A	166970415	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.973000	0.29422	0.074000	0.16767	0.459000	0.35465	GAC	T|0.949;C|0.051	0.051	strong		0.378	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
UNC80	285175	hgsc.bcm.edu	37	2	210705348	210705348	+	Silent	SNP	C	C	G	rs10178675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:210705348C>G	ENST00000439458.1	+	20	3419	c.3339C>G	c.(3337-3339)ctC>ctG	p.L1113L	UNC80_ENST00000272845.6_Silent_p.L1108L	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	1113					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						TGGACCGACTCTCTTTCATCA	0.458													C|||	971	0.19389	0.3714	0.1095	5008	,	,		17314	0.0079		0.1223	False		,,,				2504	0.2791				p.L1113L		Atlas-SNP	.											.	UNC80	280	.	0			c.C3339G						PASS	.	C	,	435,949		71,293,328	137.0	116.0	123.0		3339,3324	2.0	1.0	2	dbSNP_119	123	378,2804		23,332,1236	no	coding-synonymous,coding-synonymous	UNC80	NM_032504.1,NM_182587.3	,	94,625,1564	GG,GC,CC		11.8793,31.4306,17.8055	,	1113/3259,1108/3235	210705348	813,3753	692	1591	2283	SO:0001819	synonymous_variant	285175	exon20			CCGACTCTCTTTC	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.3339C>G	2.37:g.210705348C>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	135	93	0.688889	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Silent	SNP	ENST00000439458.1	37	CCDS46504.1																																																																																			C|0.831;G|0.169	0.169	strong		0.458	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
DNHD1	144132	hgsc.bcm.edu	37	11	6588553	6588553	+	Silent	SNP	C	C	T	rs56313830	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6588553C>T	ENST00000527990.2	+	34	11814	c.11814C>T	c.(11812-11814)ggC>ggT	p.G3938G	DNHD1_ENST00000254579.6_Silent_p.G3938G			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3938					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)		GTGCATTGGGCGCTTTGGCTC	0.597													C|||	967	0.193091	0.531	0.1239	5008	,	,		21235	0.0149		0.0417	False		,,,				2504	0.1247				p.G3938G		Atlas-SNP	.											.	DNHD1	198	.	0			c.C11814T						PASS	.	C		1869,2321		424,1021,650	54.0	62.0	59.0		11814	0.7	1.0	11	dbSNP_129	59	384,8054		6,372,3841	no	coding-synonymous	DNHD1	NM_144666.2		430,1393,4491	TT,TC,CC		4.5508,44.6062,17.8413		3938/4754	6588553	2253,10375	2095	4219	6314	SO:0001819	synonymous_variant	144132	exon36			ATTGGGCGCTTTG	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.11814C>T	11.37:g.6588553C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			C|0.870;T|0.130	0.130	strong		0.597	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
NBPF14	25832	hgsc.bcm.edu	37	1	148010987	148010987	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	783	8	0.0102171		WXS	Illumina HiSeq	Phase_I	1403	20	0.0142552	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	
SMC4	10051	hgsc.bcm.edu	37	3	160146646	160146646	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:160146646A>G	ENST00000357388.3	+	18	3162	c.2711A>G	c.(2710-2712)gAc>gGc	p.D904G	RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000469762.1_Missense_Mutation_p.D879G|SMC4_ENST00000462787.1_Missense_Mutation_p.D904G|SMC4_ENST00000344722.5_Missense_Mutation_p.D904G|SMC4_ENST00000360111.2_Missense_Mutation_p.D904G	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	904					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GCCCAACAAGACAAACTTGAT	0.378																																					p.D904G		Atlas-SNP	.											SMC4,bladder,carcinoma,+1,1	SMC4	135	1	0			c.A2711G						scavenged	.						126.0	120.0	122.0					3																	160146646		2203	4300	6503	SO:0001583	missense	10051	exon17			AACAAGACAAACT	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"""Structural maintenance of chromosomes proteins"""	14013	protein-coding gene	gene with protein product		605575	"""SMC4 (structural maintenance of chromosomes 4, yeast)-like 1"", ""SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"""	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.2711A>G	3.37:g.160146646A>G	ENSP00000349961:p.Asp904Gly	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	263	4	0.0152091	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	37	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502369	0.85176	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000469762;ENST00000462787;ENST00000344722;ENST00000545277	T;T;T;T;T	0.77750	-1.12;-1.12;-0.86;-1.12;-1.12	6.07	6.07	0.98685	RecF/RecN/SMC (1);	0.039653	0.85682	D	0.000000	D	0.83216	0.5206	M	0.79805	2.47	0.80722	D	1	P;B;P;B	0.40398	0.532;0.009;0.716;0.109	B;B;P;B	0.45610	0.423;0.065;0.487;0.174	D	0.83591	0.0123	10	0.44086	T	0.13	-19.3703	16.6406	0.85098	1.0:0.0:0.0:0.0	.	904;879;879;904	Q9NTJ3-2;B3KXX5;E9PD53;Q9NTJ3	.;.;.;SMC4_HUMAN	G	904;904;879;904;904;498	ENSP00000349961:D904G;ENSP00000353225:D904G;ENSP00000417964:D879G;ENSP00000420734:D904G;ENSP00000341382:D904G	ENSP00000341382:D904G	D	+	2	0	SMC4	161629340	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.142000	0.94618	2.326000	0.78906	0.533000	0.62120	GAC	.	.	none		0.378	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1		
PKD1L2	114780	hgsc.bcm.edu	37	16	81241100	81241100	+	RNA	SNP	G	G	C	rs386792899|rs11150370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	81	0	0		WXS	Illumina HiSeq	Phase_I	80	11	0.1375	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		
SYNE2	23224	hgsc.bcm.edu	37	14	64612845	64612845	+	Silent	SNP	C	C	T	rs11629287	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:64612845C>T	ENST00000344113.4	+	84	15755	c.15543C>T	c.(15541-15543)atC>atT	p.I5181I	SYNE2_ENST00000358025.3_Silent_p.I5181I|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Silent_p.I5098I|SYNE2_ENST00000357395.3_Silent_p.I1566I|SYNE2_ENST00000394768.2_Silent_p.I1566I|SYNE2_ENST00000555002.1_Silent_p.I1815I	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	5181					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.I5181I(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAATACAGATCTTGAACAACT	0.353													T|||	2213	0.441893	0.5726	0.3977	5008	,	,		17561	0.504		0.3469	False		,,,				2504	0.3303				p.I5181I		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	1	1	Substitution - coding silent(1)	prostate(1)	c.C15543T						PASS	.	T	,	2373,2033	561.1+/-380.6	642,1089,472	59.0	65.0	63.0		15543,15543	-1.2	0.8	14	dbSNP_120	63	2918,5682	668.0+/-402.5	502,1914,1884	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	1144,3003,2356	TT,TC,CC		33.9302,46.1416,40.6812	,	5181/6886,5181/6908	64612845	5291,7715	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon84			ACAGATCTTGAAC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.15543C>T	14.37:g.64612845C>T		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	308	91	0.295455	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.567;T|0.433	0.433	strong		0.353	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
MUC4	4585	hgsc.bcm.edu	37	3	195506147	195506147	+	Missense_Mutation	SNP	G	G	A	rs200473856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195506147G>A	ENST00000463781.3	-	2	12763	c.12304C>T	c.(12304-12306)Ctt>Ttt	p.L4102F	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L4102F	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	30	6	0.2		WXS	Illumina HiSeq	Phase_I	38	10	0.263158	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	
PRDM4	11108	hgsc.bcm.edu	37	12	108140191	108140191	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:108140191C>T	ENST00000228437.5	-	6	1596	c.1137G>A	c.(1135-1137)ctG>ctA	p.L379L	RP11-864J10.4_ENST00000546714.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	379					cell proliferation (GO:0008283)|negative regulation of cell cycle (GO:0045786)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|methyltransferase activity (GO:0008168)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	20						CGCGGTCACACAGAGTACACC	0.458																																					p.L379L		Atlas-SNP	.											PRDM4,bladder,carcinoma,-1,1	PRDM4	64	1	0			c.G1137A						PASS	.						86.0	83.0	84.0					12																	108140191		2203	4300	6503	SO:0001819	synonymous_variant	11108	exon6			GTCACACAGAGTA	AF144757	CCDS9115.1	12q23-q24.1	2013-01-08				ENSG00000110851		"""Zinc fingers, C2H2-type"""	9348	protein-coding gene	gene with protein product		605780				10552934	Standard	NM_012406		Approved	PFM1	uc001tmp.3	Q9UKN5	OTTHUMG00000169914	ENST00000228437.5:c.1137G>A	12.37:g.108140191C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_012406	Q9UFA6	Silent	SNP	ENST00000228437.5	37	CCDS9115.1																																																																																			.	.	none		0.458	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406	
PIGB	9488	hgsc.bcm.edu	37	15	55647492	55647492	+	Silent	SNP	C	C	T	rs8043415	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:55647492C>T	ENST00000164305.5	+	12	1818	c.1527C>T	c.(1525-1527)agC>agT	p.S509S	PIGB_ENST00000539642.1_Silent_p.S314S|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000310958.6_3'UTR|CCPG1_ENST00000442196.3_3'UTR	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	509					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)		AGGAAATAAGCGCTTTCCTAA	0.348													C|||	488	0.0974441	0.2254	0.0519	5008	,	,		17133	0.001		0.0696	False		,,,				2504	0.0849				p.S509S		Atlas-SNP	.											PIGB,NS,carcinoma,+1,1	PIGB	36	1	0			c.C1527T						PASS	.	C	,,,,	728,2880		68,592,1144	46.0	45.0	45.0		,,,1527,	1.0	0.2	15	dbSNP_116	45	603,7529		17,569,3480	no	utr-3,utr-3,utr-3,coding-synonymous,utr-3	CCPG1,PIGB	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_004855.4,NM_020739.3	,,,,	85,1161,4624	TT,TC,CC		7.4152,20.1774,11.3373	,,,,	,,,509/555,	55647492	1331,10409	1804	4066	5870	SO:0001819	synonymous_variant	9488	exon12			AATAAGCGCTTTC	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.1527C>T	15.37:g.55647492C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_004855	Q53FF9|Q8WVN7	Silent	SNP	ENST00000164305.5	37																																																																																				C|0.909;T|0.091	0.091	strong		0.348	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855	
MFI2	4241	hgsc.bcm.edu	37	3	196746629	196746629	+	Intron	SNP	T	T	C	rs1056664	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:196746629T>C	ENST00000296350.5	-	6	826				MFI2_ENST00000296351.4_Silent_p.E252E	NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5						cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-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;0.00536)		ACTCGCCTTCTTCCTCCTCAG	0.488													C|||	1334	0.266374	0.2844	0.3444	5008	,	,		20384	0.2847		0.2266	False		,,,				2504	0.2086				p.E252E		Atlas-SNP	.											.	MFI2	88	.	0			c.A756G						PASS	.	C	,	1202,3204	708.8+/-407.7	167,868,1168	112.0	87.0	96.0		,756	-2.4	0.0	3	dbSNP_86	96	1912,6688	726.6+/-406.6	216,1480,2604	no	intron,coding-synonymous	MFI2	NM_005929.5,NM_033316.3	,	383,2348,3772	CC,CT,TT		22.2326,27.281,23.9428	,	,252/303	196746629	3114,9892	2203	4300	6503	SO:0001627	intron_variant	4241	exon7			GCCTTCTTCCTCC		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.712+1645A>G	3.37:g.196746629T>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	153	76	0.496732	NM_033316	Q9BQE2	Silent	SNP	ENST00000296350.5	37	CCDS3325.1																																																																																			T|0.742;C|0.258	0.258	strong		0.488	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
HOXB1	3211	hgsc.bcm.edu	37	17	46607958	46607958	+	Missense_Mutation	SNP	T	T	A	rs12939811	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	45	0	0		WXS	Illumina HiSeq	Phase_I	35	11	0.314286	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		
IGFN1	91156	hgsc.bcm.edu	37	1	201190732	201190732	+	Silent	SNP	G	G	A	rs3738269	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201190732G>A	ENST00000335211.4	+	19	10189	c.10059G>A	c.(10057-10059)gtG>gtA	p.V3353V	IGFN1_ENST00000295591.8_Silent_p.V513V|RP11-567E21.3_ENST00000453155.1_RNA	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	896						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						CGTGCCATGTGGGCACCGTGC	0.637													G|||	1105	0.220647	0.1135	0.2464	5008	,	,		18470	0.255		0.2694	False		,,,				2504	0.2618				p.V3353V		Atlas-SNP	.											IGFN1_ENST00000335211,NS,carcinoma,0,4	IGFN1	220	4	0			c.G10059A						PASS	.	G		663,3743	277.5+/-273.7	53,557,1593	51.0	42.0	45.0		10059	-2.2	0.1	1	dbSNP_107	45	2373,6227	388.2+/-342.5	339,1695,2266	no	coding-synonymous	IGFN1	NM_001164586.1		392,2252,3859	AA,AG,GG		27.593,15.0477,23.3431		3353/3709	201190732	3036,9970	2203	4300	6503	SO:0001819	synonymous_variant	91156	exon19			CCATGTGGGCACC	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.10059G>A	1.37:g.201190732G>A		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	293	101	0.34471	NM_001164586	F8WAI1|Q9NT72	Silent	SNP	ENST00000335211.4	37	CCDS53455.1	528	0.24175824175824176	64	0.13008130081300814	90	0.24861878453038674	151	0.263986013986014	223	0.2941952506596306	G	5.257	0.232928	0.09969	0.150477	0.27593	ENSG00000163395	ENST00000412892	.	.	.	4.64	-2.23	0.06930	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41142	-0.9525	3	.	.	.	.	1.0589	0.01596	0.4369:0.1254:0.2305:0.2072	rs3738269;rs3738269	.	.	.	R	771	.	.	G	+	1	0	IGFN1	199457355	0.000000	0.05858	0.070000	0.20053	0.049000	0.14656	-1.111000	0.03303	0.082000	0.17018	-0.727000	0.03589	GGG	G|0.775;A|0.225	0.225	strong		0.637	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
TRPV2	51393	hgsc.bcm.edu	37	17	16325968	16325968	+	Silent	SNP	A	A	G	rs8121	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:16325968A>G	ENST00000338560.7	+	4	789	c.390A>G	c.(388-390)ggA>ggG	p.G130G	TRPV2_ENST00000577397.1_5'UTR	NM_016113.4	NP_057197.2	Q9Y5S1	TRPV2_HUMAN	transient receptor potential cation channel, subfamily V, member 2	130	Required for interaction with SLC50A1. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|positive regulation of axon extension (GO:0045773)|positive regulation of calcium ion import (GO:0090280)|response to heat (GO:0009408)|response to temperature stimulus (GO:0009266)|sensory perception (GO:0007600)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|growth cone membrane (GO:0032584)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|ion channel activity (GO:0005216)|ion transmembrane transporter activity (GO:0015075)	p.G130G(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|stomach(3)	28				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		TTAAGGACGGAGTCAATGCCT	0.572													G|||	1960	0.391374	0.6475	0.3818	5008	,	,		18556	0.2321		0.3877	False		,,,				2504	0.2198				p.G130G		Atlas-SNP	.											TRPV2,right_upper_lobe,carcinoma,+1,2	TRPV2	74	2	1	Substitution - coding silent(1)	stomach(1)	c.A390G						scavenged	.	G		2586,1820	532.3+/-373.4	765,1056,382	82.0	67.0	72.0		390	-5.9	0.0	17	dbSNP_52	72	3364,5236	641.2+/-399.7	648,2068,1584	no	coding-synonymous	TRPV2	NM_016113.4		1413,3124,1966	GG,GA,AA		39.1163,41.3073,45.7481		130/765	16325968	5950,7056	2203	4300	6503	SO:0001819	synonymous_variant	51393	exon4			GGACGGAGTCAAT	AF129112	CCDS32576.1	17p11.2	2013-01-10			ENSG00000187688	ENSG00000187688		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	18082	protein-coding gene	gene with protein product		606676				10201375, 16382100	Standard	NM_016113		Approved	VRL, VRL-1, VRL1	uc002gpy.3	Q9Y5S1	OTTHUMG00000058989	ENST00000338560.7:c.390A>G	17.37:g.16325968A>G		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_016113	A6NML2|A8K0Z0|Q9Y670	Silent	SNP	ENST00000338560.7	37	CCDS32576.1	889	0.40705128205128205	301	0.6117886178861789	153	0.42265193370165743	148	0.25874125874125875	287	0.3786279683377309	G	0.717	-0.784796	0.02907	0.586927	0.391163	ENSG00000187688	ENST00000455666	.	.	.	5.24	-5.94	0.02247	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999865	.	.	.	.	.	.	T	0.46569	-0.9182	3	.	.	.	-7.0661	0.4381	0.00482	0.2267:0.1978:0.2647:0.3108	rs8121;rs1129232;rs3186904;rs60740001;rs8121	.	.	.	G	88	.	.	S	+	1	0	TRPV2	16266693	0.000000	0.05858	0.029000	0.17559	0.089000	0.18198	-1.548000	0.02184	-1.326000	0.02266	-0.812000	0.03155	AGT	A|0.561;G|0.439	0.439	strong		0.572	TRPV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130464.2	NM_016113	
NUP85	79902	hgsc.bcm.edu	37	17	73205976	73205976	+	Silent	SNP	T	T	C	rs34126097	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73205976T>C	ENST00000245544.4	+	3	257	c.186T>C	c.(184-186)gaT>gaC	p.D62D	NUP85_ENST00000579298.1_Silent_p.D62D|NUP85_ENST00000541827.1_Silent_p.D16D|NUP85_ENST00000449421.2_3'UTR|NUP85_ENST00000579324.1_5'UTR|NUP85_ENST00000447371.2_5'UTR	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	62					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|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)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			AGGATGTAGATGTTTACTCTC	0.353													T|||	256	0.0511182	0.0053	0.0331	5008	,	,		18261	0.0685		0.1103	False		,,,				2504	0.047				p.D62D		Atlas-SNP	.											.	NUP85	44	.	0			c.T186C						PASS	.	T		79,4327	68.1+/-105.8	0,79,2124	68.0	73.0	72.0		186	0.9	0.9	17	dbSNP_126	72	851,7749	193.7+/-239.3	48,755,3497	no	coding-synonymous	NUP85	NM_024844.3		48,834,5621	CC,CT,TT		9.8953,1.793,7.1505		62/657	73205976	930,12076	2203	4300	6503	SO:0001819	synonymous_variant	79902	exon3			TGTAGATGTTTAC	AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.186T>C	17.37:g.73205976T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_024844	B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Silent	SNP	ENST00000245544.4	37	CCDS32730.1																																																																																			T|0.929;C|0.071	0.071	strong		0.353	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1	NM_024844	
SCAF1	58506	hgsc.bcm.edu	37	19	50154607	50154607	+	Missense_Mutation	SNP	C	C	T	rs146455893	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50154607C>T	ENST00000360565.3	+	7	1085	c.961C>T	c.(961-963)Cgc>Tgc	p.R321C		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	321					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		CGAGAGCCCCCGCCCGGACGC	0.697																																					p.R321C		Atlas-SNP	.											.	SCAF1	78	.	0			c.C961T						PASS	.	C	CYS/ARG	2,4400		0,2,2199	18.0	19.0	19.0		961	0.7	0.2	19	dbSNP_134	19	5,8591		0,5,4293	no	missense	SCAF1	NM_021228.2	180	0,7,6492	TT,TC,CC		0.0582,0.0454,0.0539	possibly-damaging	321/1313	50154607	7,12991	2201	4298	6499	SO:0001583	missense	58506	exon7			AGCCCCCGCCCGG	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.961C>T	19.37:g.50154607C>T	ENSP00000353769:p.Arg321Cys	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	16	0.842105	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.595518	0.46318	4.54E-4	5.82E-4	ENSG00000126461	ENST00000360565	T	0.34275	1.37	4.47	0.683	0.17998	.	1.130880	0.06849	N	0.797016	T	0.19685	0.0473	N	0.08118	0	0.09310	N	0.999999	P	0.44281	0.831	B	0.36186	0.219	T	0.23547	-1.0185	9	.	.	.	-2.8823	14.2469	0.65995	0.0:0.4311:0.5689:0.0	.	321	Q9H7N4	SFR19_HUMAN	C	321	ENSP00000353769:R321C	.	R	+	1	0	SCAF1	54846419	0.000000	0.05858	0.200000	0.23457	0.964000	0.63967	-0.197000	0.09518	0.401000	0.25424	0.591000	0.81541	CGC	A|0.000;C|0.999;T|0.001	0.001	strong		0.697	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
OR6P1	128366	hgsc.bcm.edu	37	1	158533224	158533224	+	Silent	SNP	A	A	G	rs12081915	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158533224A>G	ENST00000334632.1	-	1	170	c.171T>C	c.(169-171)cgT>cgC	p.R57R		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	57						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(4)|lung(1)	6						AGTACATGGGACGATGAAGGC	0.448													G|||	2637	0.526558	0.6611	0.4193	5008	,	,		19703	0.5863		0.4742	False		,,,				2504	0.4131				p.R57R		Atlas-SNP	.											OR6P1,NS,carcinoma,-1,1	OR6P1	47	1	0			c.T171C						PASS	.	G		891,493		278,335,79	43.0	49.0	47.0		171	0.9	1.0	1	dbSNP_120	47	1456,1726		348,760,483	no	coding-synonymous	OR6P1	NM_001160325.1		626,1095,562	GG,GA,AA		45.7574,35.6214,48.5983		57/318	158533224	2347,2219	692	1591	2283	SO:0001819	synonymous_variant	128366	exon1			CATGGGACGATGA	BK004193	CCDS53391.1	1q23.1	2012-08-09			ENSG00000186440	ENSG00000186440		"""GPCR / Class A : Olfactory receptors"""	15036	protein-coding gene	gene with protein product							Standard	NM_001160325		Approved		uc010pim.2	Q8NGX9	OTTHUMG00000019633	ENST00000334632.1:c.171T>C	1.37:g.158533224A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	135	82	0.607407	NM_001160325	Q6IFR9	Silent	SNP	ENST00000334632.1	37	CCDS53391.1																																																																																			A|0.441;G|0.558	0.558	strong		0.448	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
TRIOBP	11078	hgsc.bcm.edu	37	22	38119894	38119894	+	Missense_Mutation	SNP	G	G	A	rs35105846	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:38119894G>A	ENST00000406386.3	+	7	1586	c.1331G>A	c.(1330-1332)aGt>aAt	p.S444N		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	444					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.S444N(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)					TCCTCTCCCAGTAGAGCTACA	0.587																																					p.S444N		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	1	Substitution - Missense(1)	prostate(1)	c.G1331A						scavenged	.						70.0	74.0	73.0					22																	38119894		1882	4104	5986	SO:0001583	missense	11078	exon7			CTCCCAGTAGAGC	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.1331G>A	22.37:g.38119894G>A	ENSP00000384312:p.Ser444Asn	Somatic	204	6	0.0294118		WXS	Illumina HiSeq	Phase_I	222	7	0.0315315	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	3.506	-0.100772	0.06967	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19938	2.11	3.02	-0.653	0.11447	.	.	.	.	.	T	0.04003	0.0112	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33266	-0.9875	9	0.15952	T	0.53	.	0.3565	0.00358	0.3833:0.1916:0.2386:0.1864	rs35105846	444	Q9H2D6	TARA_HUMAN	N	444	ENSP00000384312:S444N	ENSP00000384312:S444N	S	+	2	0	TRIOBP	36449840	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.155000	0.03163	-0.991000	0.03476	-3.651000	0.00026	AGT	G|0.500;A|0.500	0.500	strong		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
FLG2	388698	hgsc.bcm.edu	37	1	152328222	152328222	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152328222A>G	ENST00000388718.5	-	3	2112	c.2040T>C	c.(2038-2040)ggT>ggC	p.G680G	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	680	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTTGTCCAAAACCAGAGGATT	0.478																																					p.G680G		Atlas-SNP	.											FLG2,NS,carcinoma,0,3	FLG2	431	3	0			c.T2040C						scavenged	.						291.0	292.0	292.0					1																	152328222		2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			TCCAAAACCAGAG	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.2040T>C	1.37:g.152328222A>G		Somatic	256	4	0.015625		WXS	Illumina HiSeq	Phase_I	369	10	0.0271003	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			.	.	none		0.478	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
SPAM1	6677	hgsc.bcm.edu	37	7	123594206	123594206	+	Silent	SNP	G	G	A	rs2285996	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:123594206G>A	ENST00000439500.1	+	4	1195	c.582G>A	c.(580-582)aaG>aaA	p.K194K	SPAM1_ENST00000460182.1_Silent_p.K194K|SPAM1_ENST00000402183.2_Silent_p.K194K|SPAM1_ENST00000223028.7_Silent_p.K194K|SPAM1_ENST00000340011.5_Silent_p.K194K	NM_001174045.1|NM_001174046.1	NP_001167516.1|NP_001167517.1	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	194					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|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)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	hyalurononglucosaminidase activity (GO:0004415)			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						AATTTGAAAAGGCAGGGAAGG	0.373													G|||	1237	0.247005	0.1271	0.379	5008	,	,		18479	0.3006		0.2753	False		,,,				2504	0.2311				p.K194K		Atlas-SNP	.											.	SPAM1	195	.	0			c.G582A						PASS	.	G	,,,,	694,3712	273.4+/-271.3	61,572,1570	66.0	70.0	69.0		582,582,582,582,582	0.8	0.1	7	dbSNP_100	69	2407,6193	390.9+/-343.5	325,1757,2218	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPAM1	NM_001174044.1,NM_001174045.1,NM_001174046.1,NM_003117.4,NM_153189.2	,,,,	386,2329,3788	AA,AG,GG		27.9884,15.7512,23.8428	,,,,	194/510,194/510,194/510,194/512,194/510	123594206	3101,9905	2203	4300	6503	SO:0001819	synonymous_variant	6677	exon3			TGAAAAGGCAGGG	L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304			11217	protein-coding gene	gene with protein product		600930				8282124, 8575780	Standard	NM_153189		Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000439500.1:c.582G>A	7.37:g.123594206G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_153189	Q8TC30	Silent	SNP	ENST00000439500.1	37	CCDS5791.1																																																																																			G|0.754;T|0.001	.	strong		0.373	SPAM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348309.1		
ARID4B	51742	hgsc.bcm.edu	37	1	235392546	235392546	+	Splice_Site	SNP	T	T	C	rs17846600|rs12731746	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:235392546T>C	ENST00000264183.3	-	11	1394	c.897A>G	c.(895-897)gaA>gaG	p.E299E	ARID4B_ENST00000349213.3_Splice_Site_p.E299E|ARID4B_ENST00000366603.2_Splice_Site_p.E299E	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	299	Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			TTTCACTTACTTCTTCTTCAC	0.348													C|||	2247	0.448682	0.4342	0.5086	5008	,	,		17805	0.251		0.4791	False		,,,				2504	0.5982				p.E299E		Atlas-SNP	.											.	ARID4B	142	.	0			c.A897G						PASS	.	C	,,	2060,2346	605.0+/-390.5	474,1112,617	95.0	88.0	90.0		897,897,897	4.0	1.0	1	dbSNP_121	90	3983,4617	598.5+/-393.9	920,2143,1237	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	,,	1394,3255,1854	CC,CT,TT		46.314,46.7544,46.4632	,,	299/1313,299/1313,299/1227	235392546	6043,6963	2203	4300	6503	SO:0001630	splice_region_variant	51742	exon11			ACTTACTTCTTCT	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.897+1A>G	1.37:g.235392546T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	214	126	0.588785	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	37	CCDS31061.1																																																																																			T|0.545;C|0.455	0.455	strong		0.348	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	Silent
PSG2	5670	hgsc.bcm.edu	37	19	43579679	43579679	+	Missense_Mutation	SNP	T	T	A	rs1058086	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43579679T>A	ENST00000406487.1	-	3	634	c.536A>T	c.(535-537)cAg>cTg	p.Q179L		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	179	Ig-like C2-type 1.		Q -> L (in dbSNP:rs1058086).		cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CATCCACCACTGGTAGCTTGT	0.502													T|||	609	0.121605	0.056	0.2017	5008	,	,		19263	0.0893		0.1103	False		,,,				2504	0.1984				p.Q179L		Atlas-SNP	.											.	PSG2	84	.	0			c.A536T						PASS	.	T	LEU/GLN	303,4101		21,261,1920	245.0	247.0	246.0		536	-2.7	0.0	19	dbSNP_86	246	964,7630		57,850,3390	no	missense	PSG2	NM_031246.3	113	78,1111,5310	AA,AT,TT		11.2171,6.8801,9.7477		179/336	43579679	1267,11731	2202	4297	6499	SO:0001583	missense	5670	exon3			CACCACTGGTAGC		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.536A>T	19.37:g.43579679T>A	ENSP00000385706:p.Gln179Leu	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	284	121	0.426056	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	231	0.10576923076923077	30	0.06097560975609756	61	0.1685082872928177	49	0.08566433566433566	91	0.12005277044854881	N	0	-2.587248	0.00128	0.068801	0.112171	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.14516	2.5	1.33	-2.66	0.06077	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.01076	-1.035	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.29305	-1.0016	8	0.02654	T	1	.	3.0717	0.06233	0.2961:0.4666:0.0:0.2373	rs1058086;rs3198696;rs16976416;rs57294777	179;179	B5MCM8;P11465	.;PSG2_HUMAN	L	179	ENSP00000385706:Q179L	ENSP00000332984:Q179L	Q	-	2	0	PSG2	48271519	0.001000	0.12720	0.005000	0.12908	0.005000	0.04900	-3.566000	0.00429	-1.108000	0.03000	-0.589000	0.04120	CAG	T|0.897;A|0.103	0.103	strong		0.502	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
NEB	4703	hgsc.bcm.edu	37	2	152432311	152432311	+	Silent	SNP	T	T	C	rs33988153	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:152432311T>C	ENST00000172853.10	-	79	11955	c.11808A>G	c.(11806-11808)ccA>ccG	p.P3936P	NEB_ENST00000604864.1_Silent_p.P5637P|NEB_ENST00000427231.2_Silent_p.P5637P|NEB_ENST00000603639.1_Silent_p.P5637P|NEB_ENST00000397345.3_Silent_p.P5637P|NEB_ENST00000409198.1_Silent_p.P3936P			P20929	NEBU_HUMAN	nebulin	3936					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)		CTCTGTACTTTGGCTGTGGAA	0.333													T|||	552	0.110224	0.0113	0.1282	5008	,	,		17816	0.004		0.2406	False		,,,				2504	0.2065				p.P5637P		Atlas-SNP	.											.	NEB	1697	.	0			c.A16911G						PASS	.	T	,,	166,3456		7,152,1652	243.0	237.0	239.0		16911,16911,11808	2.5	1.0	2	dbSNP_126	239	2064,6090		264,1536,2277	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	271,1688,3929	CC,CT,TT		25.3127,4.5831,18.9368	,,	5637/8526,5637/8526,3936/6670	152432311	2230,9546	1811	4077	5888	SO:0001819	synonymous_variant	4703	exon107			GTACTTTGGCTGT	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.11808A>G	2.37:g.152432311T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				T|0.853;C|0.147	0.147	strong		0.333	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
AGGF1	55109	hgsc.bcm.edu	37	5	76332463	76332463	+	Missense_Mutation	SNP	C	C	A	rs78273685		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	216	0	0		WXS	Illumina HiSeq	Phase_I	240	8	0.0333333	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	
OR5T2	219464	hgsc.bcm.edu	37	11	56000451	56000451	+	Silent	SNP	G	G	A	rs11227598	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56000451G>A	ENST00000313264.4	-	1	286	c.211C>T	c.(211-213)Cta>Tta	p.L71L		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	71						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L71L(1)		endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TAGATTGCTAGAAACAGGAAG	0.388													g|||	511	0.102037	0.062	0.1009	5008	,	,		21549	0.125		0.1173	False		,,,				2504	0.1176				p.L71L		Atlas-SNP	.											OR5T2,colon,carcinoma,0,2	OR5T2	107	2	1	Substitution - coding silent(1)	stomach(1)	c.C211T						PASS	.	G		277,4125	152.5+/-186.2	9,259,1933	72.0	65.0	67.0		211	-0.9	0.0	11	dbSNP_120	67	998,7594	214.3+/-254.0	54,890,3352	no	coding-synonymous	OR5T2	NM_001004746.1		63,1149,5285	AA,AG,GG		11.6155,6.2926,9.8122		71/360	56000451	1275,11719	2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			TTGCTAGAAACAG	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.211C>T	11.37:g.56000451G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	37	CCDS31523.1																																																																																			G|0.901;A|0.099	0.099	strong		0.388	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964196	88964196	+	Missense_Mutation	SNP	T	T	A	rs801840	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:88964196T>A	ENST00000333190.4	+	4	2509	c.1900T>A	c.(1900-1902)Ttt>Att	p.F634I		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	634			F -> I (in dbSNP:rs801840). {ECO:0000269|PubMed:12690205}.				metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			CATCTCTAGGTTTAAAAAGCA	0.418										HNSCC(36;0.09)			A|||	2607	0.520567	0.7738	0.3415	5008	,	,		19885	0.7153		0.2346	False		,,,				2504	0.3988				p.F634I		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T1900A						PASS	.	A	ILE/PHE	3011,1395	456.1+/-351.2	1021,969,213	80.0	84.0	83.0		1900	4.3	0.7	7	dbSNP_86	83	2036,6564	719.1+/-406.2	234,1568,2498	yes	missense	ZNF804B	NM_181646.2	21	1255,2537,2711	AA,AT,TT		23.6744,31.6614,38.8052	benign	634/1350	88964196	5047,7959	2203	4300	6503	SO:0001583	missense	219578	exon4			TCTAGGTTTAAAA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1900T>A	7.37:g.88964196T>A	ENSP00000329638:p.Phe634Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	154	98	0.636364	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	1073	0.4913003663003663	374	0.7601626016260162	130	0.35911602209944754	390	0.6818181818181818	179	0.23614775725593667	A	6.795	0.515659	0.12944	0.683386	0.236744	ENSG00000182348	ENST00000333190	T	0.04015	3.73	5.48	4.33	0.51752	.	0.169739	0.42294	D	0.000738	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	0.06643	-1.0815	9	0.51188	T	0.08	-4.6357	7.8499	0.29448	0.8102:0.0:0.0666:0.1232	rs801840;rs1721758;rs56634318;rs801840	634	A4D1E1	Z804B_HUMAN	I	634	ENSP00000329638:F634I	ENSP00000329638:F634I	F	+	1	0	ZNF804B	88802132	1.000000	0.71417	0.702000	0.30337	0.028000	0.11728	3.085000	0.50151	0.518000	0.28383	-0.265000	0.10407	TTT	T|0.483;A|0.517	0.517	strong		0.418	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
CACNA1A	773	hgsc.bcm.edu	37	19	13414594	13414594	+	Silent	SNP	C	C	T	rs16016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13414594C>T	ENST00000360228.5	-	16	2090	c.2091G>A	c.(2089-2091)acG>acA	p.T697T	CACNA1A_ENST00000573710.2_Silent_p.T698T	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	698					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)	TCCCAAAGAGCGTCAGTACAA	0.567													c|||	927	0.185104	0.0673	0.2205	5008	,	,		13056	0.2887		0.1203	False		,,,				2504	0.2791				p.T698T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G2094A						PASS	.	T	,,,,	328,3650		13,302,1674	149.0	151.0	150.0		2094,2094,2091,2094,2094	-9.2	0.1	19	dbSNP_54	150	1076,7250		71,934,3158	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	,,,,	84,1236,4832	TT,TC,CC		12.9234,8.2453,11.4109	,,,,	698/2267,698/2262,697/2507,698/2264,698/2513	13414594	1404,10900	1989	4163	6152	SO:0001819	synonymous_variant	773	exon16			AAAGAGCGTCAGT	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.2091G>A	19.37:g.13414594C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.834;T|0.166	0.166	strong		0.567	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
C10orf111	221060	hgsc.bcm.edu	37	10	15138696	15138696	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:15138696C>T	ENST00000378207.3	-	2	401	c.128G>A	c.(127-129)aGa>aAa	p.R43K	RPP38_ENST00000378202.5_5'Flank|RPP38_ENST00000378197.4_5'Flank	NM_153244.1	NP_694976.1	Q8N326	CJ111_HUMAN	chromosome 10 open reading frame 111	43						integral component of membrane (GO:0016021)				lung(5)|upper_aerodigestive_tract(1)	6						CAAGGCAACTCTTACTGCCTT	0.498																																					p.R43K		Atlas-SNP	.											C10orf111,NS,malignant_melanoma,0,1	C10orf111	11	1	0			c.G128A						scavenged	.						164.0	152.0	156.0					10																	15138696		2203	4300	6503	SO:0001583	missense	221060	exon2			GCAACTCTTACTG	BC029034	CCDS7107.1	10p13	2004-04-20			ENSG00000176236	ENSG00000176236			28582	protein-coding gene	gene with protein product						12477932	Standard	NM_153244		Approved	MGC35468, bA455B2.4	uc001inw.3	Q8N326	OTTHUMG00000017727	ENST00000378207.3:c.128G>A	10.37:g.15138696C>T	ENSP00000367449:p.Arg43Lys	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	246	3	0.0121951	NM_153244	B2RAC4	Missense_Mutation	SNP	ENST00000378207.3	37	CCDS7107.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.283991	0.23392	.	.	ENSG00000176236	ENST00000378207	T	0.53857	0.6	3.27	2.27	0.28462	.	.	.	.	.	T	0.28499	0.0705	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.18650	-1.0330	9	0.87932	D	0	.	3.4725	0.07573	0.0:0.7033:0.0:0.2967	.	43	Q8N326	CJ111_HUMAN	K	43	ENSP00000367449:R43K	ENSP00000367449:R43K	R	-	2	0	C10orf111	15178702	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.190000	0.17057	0.805000	0.34159	0.561000	0.74099	AGA	.	.	none		0.498	C10orf111-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046975.1	NM_153244	
C3	718	hgsc.bcm.edu	37	19	6702157	6702157	+	Silent	SNP	C	C	G	rs428453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6702157C>G	ENST00000245907.6	-	19	2513	c.2421G>C	c.(2419-2421)gtG>gtC	p.V807V		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	807					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)	CCGACATGCTCACAGCCAGAA	0.493													C|||	3668	0.732428	0.7103	0.7695	5008	,	,		19845	0.8512		0.6272	False		,,,				2504	0.7219				p.V807V		Atlas-SNP	.											.	C3	192	.	0			c.G2421C						PASS	.	C		3093,1313	696.4+/-406.1	1081,931,191	69.0	67.0	68.0		2421	1.5	1.0	19	dbSNP_80	68	5322,3278	647.4+/-400.4	1635,2052,613	no	coding-synonymous	C3	NM_000064.2		2716,2983,804	GG,GC,CC		38.1163,29.8003,35.2991		807/1664	6702157	8415,4591	2203	4300	6503	SO:0001819	synonymous_variant	718	exon19			CATGCTCACAGCC	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.2421G>C	19.37:g.6702157C>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	33	31	0.939394	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																			C|0.332;G|0.668	0.668	strong		0.493	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
FCGR3A	2214	hgsc.bcm.edu	37	1	161599571	161599571	+	Intron	SNP	T	T	C	rs2290834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161599571T>C	ENST00000540048.1	-	2	94				FCGR3B_ENST00000294800.3_Missense_Mutation_p.I106V|FCGR3B_ENST00000531221.1_Missense_Mutation_p.I142V|FCGR3B_ENST00000367964.2_Missense_Mutation_p.I106V|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000403078.3_Intron			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						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)	AACTCACCGATATGGACTTCT	0.478																																					p.I142V		Atlas-SNP	.											FCGR3B,NS,carcinoma,+2,1	FCGR3B	35	1	0			c.A424G						scavenged	.						24.0	26.0	25.0					1																	161599571		2124	4279	6403	SO:0001627	intron_variant	2215	exon3			CACCGATATGGAC	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	ENST00000540048.1:c.61+586A>G	1.37:g.161599571T>C		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	359	40	0.111421	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	1.794|1.794	-0.478839|-0.478839	0.04414|0.04414	.|.	.|.	ENSG00000162747|ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221;ENST00000534776|ENST00000421702	T;T;T;T|.	0.02787|.	4.91;4.91;5.01;4.16|.	2.79|2.79	-5.57|-5.57	0.02521|0.02521	.|.	4.037030|.	0.00559|.	N|.	0.000262|.	T|T	0.02727|0.02727	0.0082|0.0082	N|N	0.04508|0.04508	-0.205|-0.205	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.16660|0.16660	-1.0395|-1.0395	9|4	0.20046|.	T|.	0.44|.	.|.	3.2984|3.2984	0.06974|0.06974	0.1208:0.478:0.2427:0.1584|0.1208:0.478:0.2427:0.1584	.|.	106|.	O75015|.	FCG3B_HUMAN|.	V|C	106;106;142;89|126	ENSP00000356941:I106V;ENSP00000294800:I106V;ENSP00000433642:I142V;ENSP00000437084:I89V|.	ENSP00000294800:I106V|.	I|Y	-|-	1|2	0|0	FCGR3B|FCGR3B	159866195|159866195	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	-7.325000|-7.325000	0.00039|0.00039	-3.260000|-3.260000	0.00202|0.00202	0.319000|0.319000	0.21371|0.21371	ATC|TAT	.	.	weak		0.478	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
PLEC	5339	hgsc.bcm.edu	37	8	144993324	144993324	+	Silent	SNP	C	C	T	rs6984820	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144993324C>T	ENST00000322810.4	-	32	11245	c.11076G>A	c.(11074-11076)acG>acA	p.T3692T	PLEC_ENST00000398774.2_Silent_p.T3523T|PLEC_ENST00000527096.1_Silent_p.T3578T|PLEC_ENST00000357649.2_Silent_p.T3559T|PLEC_ENST00000345136.3_Silent_p.T3555T|PLEC_ENST00000356346.3_Silent_p.T3541T|PLEC_ENST00000436759.2_Silent_p.T3582T|PLEC_ENST00000354958.2_Silent_p.T3533T|PLEC_ENST00000354589.3_Silent_p.T3555T	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	121	0	0		WXS	Illumina HiSeq	Phase_I	161	90	0.559006	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	
CLDN19	149461	hgsc.bcm.edu	37	1	43201614	43201614	+	Silent	SNP	C	C	T	rs9660973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43201614C>T	ENST00000296387.1	-	4	751	c.561G>A	c.(559-561)ccG>ccA	p.P187P	CLDN19_ENST00000372539.3_Silent_p.P187P|CLDN19_ENST00000539749.1_Missense_Mutation_p.R159Q	NM_001123395.1|NM_148960.2	NP_001116867.1|NP_683763.2	Q8N6F1	CLD19_HUMAN	claudin 19	187					apical junction assembly (GO:0043297)|calcium-independent cell-cell adhesion (GO:0016338)|neuronal action potential propagation (GO:0019227)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	apical junction complex (GO:0043296)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			breast(2)|large_intestine(1)|lung(2)|skin(1)	6	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TCTCTGGCTCCGGGCATGTGC	0.677													c|||	260	0.0519169	0.1006	0.0389	5008	,	,		16585	0.001		0.0398	False		,,,				2504	0.0603				p.R159Q		Atlas-SNP	.											.	CLDN19	21	.	0			c.G476A						PASS	.		,GLN/ARG,	396,3984		9,378,1803	30.0	28.0	29.0		561,476,561	-8.6	0.0	1	dbSNP_119	29	351,8217		5,341,3938	yes	coding-synonymous,missense,coding-synonymous	CLDN19	NM_001123395.1,NM_001185117.1,NM_148960.2	,43,	14,719,5741	TT,TC,CC		4.0966,9.0411,5.7692	,,	187/212,159/219,187/225	43201614	747,12201	2190	4284	6474	SO:0001819	synonymous_variant	149461	exon3			TGGCTCCGGGCAT	AK096063	CCDS471.1, CCDS44125.1, CCDS53306.1	1p34.2	2008-05-14			ENSG00000164007	ENSG00000164007		"""Claudins"""	2040	protein-coding gene	gene with protein product		610036					Standard	NM_148960		Approved		uc001cht.1	Q8N6F1	OTTHUMG00000007524	ENST00000296387.1:c.561G>A	1.37:g.43201614C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	134	45	0.335821	NM_001185117	B7Z5I2|F5H5P9|Q5QT57|Q8N8X0	Missense_Mutation	SNP	ENST00000296387.1	37	CCDS471.1	98	0.04487179487179487	48	0.0975609756097561	19	0.052486187845303865	0	0.0	31	0.040897097625329816	c	11.52	1.664047	0.29604	0.090411	0.040966	ENSG00000164007	ENST00000539749	D	0.86627	-2.15	4.31	-8.62	0.00881	.	.	.	.	.	T	0.07458	0.0188	.	.	.	0.23260	N	0.998023	B	0.10296	0.003	B	0.04013	0.001	T	0.48714	-0.9011	8	0.72032	D	0.01	.	2.721	0.05201	0.2173:0.0855:0.367:0.3302	rs9660973;rs9660973	159	F5H5P9	.	Q	159	ENSP00000443229:R159Q	ENSP00000443229:R159Q	R	-	2	0	CLDN19	42974201	0.000000	0.05858	0.016000	0.15963	0.624000	0.37722	-2.658000	0.00852	-3.151000	0.00230	-0.516000	0.04426	CGG	C|0.945;T|0.055	0.055	strong		0.677	CLDN19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019788.1	NM_148960	
TEP1	7011	hgsc.bcm.edu	37	14	20852770	20852770	+	Silent	SNP	G	G	T	rs1713458	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20852770G>T	ENST00000262715.5	-	22	3250	c.3210C>A	c.(3208-3210)atC>atA	p.I1070I	TEP1_ENST00000556935.1_Silent_p.I962I|TEP1_ENST00000545983.1_5'Flank	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1070					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)		TGCGGCAGGTGATCCCTTTCT	0.557													G|||	1343	0.268171	0.4244	0.304	5008	,	,		17233	0.2698		0.1282	False		,,,				2504	0.1738				p.I1070I		Atlas-SNP	.											.	TEP1	224	.	0			c.C3210A						PASS	.	G		1584,2822	494.1+/-362.9	291,1002,910	140.0	150.0	147.0		3210	-3.4	0.1	14	dbSNP_89	147	1085,7515	227.3+/-262.8	71,943,3286	no	coding-synonymous	TEP1	NM_007110.4		362,1945,4196	TT,TG,GG		12.6163,35.951,20.5213		1070/2628	20852770	2669,10337	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon22			GCAGGTGATCCCT		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.3210C>A	14.37:g.20852770G>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	178	57	0.320225	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			G|0.769;T|0.231	0.231	strong		0.557	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
ALOXE3	59344	hgsc.bcm.edu	37	17	7999957	7999957	+	Silent	SNP	G	G	A	rs3809881	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7999957G>A	ENST00000448843.2	-	16	2464	c.2124C>T	c.(2122-2124)agC>agT	p.S708S	ALOXE3_ENST00000318227.3_Silent_p.S840S|ALOXE3_ENST00000380149.1_Silent_p.S864S	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	708	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				arachidonic acid metabolic process (GO:0019369)|ceramide biosynthetic process (GO:0046513)|establishment of skin barrier (GO:0061436)|fat cell differentiation (GO:0045444)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipoxygenase pathway (GO:0019372)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|sensory perception of pain (GO:0019233)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)	hepoxilin A3 synthase activity (GO:0051120)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	31						AGATGGAGACGCTGTTCTCAA	0.582													G|||	2127	0.42472	0.2504	0.5735	5008	,	,		18332	0.6022		0.4205	False		,,,				2504	0.3763				p.S840S		Atlas-SNP	.											ALOXE3_ENST00000318227,NS,carcinoma,0,2	ALOXE3	145	2	0			c.C2520T						scavenged	.	G	,	1211,3195	419.8+/-338.8	161,889,1153	183.0	167.0	172.0		2520,2124	-9.0	0.2	17	dbSNP_107	172	3581,5019	518.5+/-379.3	754,2073,1473	no	coding-synonymous,coding-synonymous	ALOXE3	NM_001165960.1,NM_021628.2	,	915,2962,2626	AA,AG,GG		41.6395,27.4852,36.8445	,	840/844,708/712	7999957	4792,8214	2203	4300	6503	SO:0001819	synonymous_variant	59344	exon16			GGAGACGCTGTTC	AJ269499	CCDS11130.1, CCDS54084.1	17p13.1	2009-07-10			ENSG00000179148	ENSG00000179148	1.13.11.-	"""Arachidonate lipoxygenases"""	13743	protein-coding gene	gene with protein product		607206					Standard	NM_021628		Approved	eLOX3, E-LOX	uc010vuo.2	Q9BYJ1	OTTHUMG00000108179	ENST00000448843.2:c.2124C>T	17.37:g.7999957G>A		Somatic	330	3	0.00909091		WXS	Illumina HiSeq	Phase_I	330	162	0.490909	NM_001165960	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Silent	SNP	ENST00000448843.2	37	CCDS11130.1																																																																																			G|0.593;A|0.407	0.407	strong		0.582	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1		
DOCK9	23348	hgsc.bcm.edu	37	13	99575568	99575568	+	Silent	SNP	G	G	A	rs12428661	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:99575568G>A	ENST00000376460.1	-	5	554	c.474C>T	c.(472-474)gtC>gtT	p.V158V	DOCK9_ENST00000442173.1_Silent_p.V158V|DOCK9_ENST00000448493.2_Silent_p.V170V|DOCK9_ENST00000339416.2_Silent_p.V159V	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	97	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	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	
TPCN1	53373	hgsc.bcm.edu	37	12	113733830	113733830	+	Silent	SNP	C	C	T	rs61943642	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113733830C>T	ENST00000335509.6	+	28	2714	c.2400C>T	c.(2398-2400)ccC>ccT	p.P800P	TPCN1_ENST00000392569.4_Silent_p.P732P|TPCN1_ENST00000541517.1_Silent_p.P872P|TPCN1_ENST00000550785.1_Silent_p.P872P	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	800					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|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)|voltage-gated calcium channel activity (GO:0005245)			cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(1)	40						GTGCAGCCCCCGCCGCCCAGC	0.617													C|||	123	0.0245607	0.0023	0.0461	5008	,	,		11380	0.0		0.0775	False		,,,				2504	0.0102				p.P872P		Atlas-SNP	.											.	TPCN1	109	.	0			c.C2616T						PASS	.	C	,	60,4340	48.9+/-83.8	2,56,2142	27.0	32.0	30.0		2616,2400	0.7	0.0	12	dbSNP_129	30	498,8102	133.3+/-190.8	13,472,3815	no	coding-synonymous,coding-synonymous	TPCN1	NM_001143819.1,NM_017901.4	,	15,528,5957	TT,TC,CC		5.7907,1.3636,4.2923	,	872/889,800/817	113733830	558,12442	2200	4300	6500	SO:0001819	synonymous_variant	53373	exon29			AGCCCCCGCCGCC	AB032995	CCDS31908.1, CCDS44985.1	12q24.21	2011-07-05			ENSG00000186815	ENSG00000186815		"""Voltage-gated ion channels / Two-pore channels"""	18182	protein-coding gene	gene with protein product		609666				10574461, 10753632, 16382101	Standard	XM_005253905		Approved	KIAA1169, FLJ20612, TPC1	uc001tux.3	Q9ULQ1	OTTHUMG00000169625	ENST00000335509.6:c.2400C>T	12.37:g.113733830C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_001143819	A7E258|Q86XS9|Q8NC20	Silent	SNP	ENST00000335509.6	37	CCDS31908.1																																																																																			C|0.958;T|0.042	0.042	strong		0.617	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901	
CPVL	54504	hgsc.bcm.edu	37	7	29152371	29152371	+	Silent	SNP	G	G	A	rs323182	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:29152371G>A	ENST00000409850.1	-	7	883	c.237C>T	c.(235-237)acC>acT	p.T79T	CPVL_ENST00000488891.2_5'UTR|CPVL_ENST00000396276.3_Silent_p.T79T|CPVL_ENST00000265394.5_Silent_p.T79T			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	79						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						TCTTATTCACGGTGAGGAAGC	0.478													G|||	400	0.0798722	0.1513	0.0778	5008	,	,		15771	0.0337		0.0984	False		,,,				2504	0.0133				p.T79T		Atlas-SNP	.											.	CPVL	60	.	0			c.C237T						PASS	.	G	,	612,3794	267.4+/-267.8	48,516,1639	108.0	98.0	101.0		237,237	-11.7	0.4	7	dbSNP_79	101	1011,7589	216.3+/-255.4	63,885,3352	no	coding-synonymous,coding-synonymous	CPVL	NM_019029.2,NM_031311.3	,	111,1401,4991	AA,AG,GG		11.7558,13.8901,12.4789	,	79/477,79/477	29152371	1623,11383	2203	4300	6503	SO:0001819	synonymous_variant	54504	exon3			ATTCACGGTGAGG	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"""carboxypeptidase WUG"", ""vitellogenic carboxypeptidase-like protein"", ""CP-Mac carboxypeptidase"""	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.237C>T	7.37:g.29152371G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	207	72	0.347826	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Silent	SNP	ENST00000409850.1	37	CCDS5419.1																																																																																			G|0.887;A|0.113	0.113	strong		0.478	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
OR8H3	390152	hgsc.bcm.edu	37	11	55889895	55889895	+	Missense_Mutation	SNP	C	C	T	rs61751933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						PASS	.	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	186	0	0		WXS	Illumina HiSeq	Phase_I	199	123	0.61809	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	
DNASE1	1773	hgsc.bcm.edu	37	16	3707747	3707747	+	Missense_Mutation	SNP	G	G	A	rs1053874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3707747G>A	ENST00000246949.5	+	8	3940	c.731G>A	c.(730-732)cGa>cAa	p.R244Q	DNASE1_ENST00000414110.2_Missense_Mutation_p.R127Q|DNASE1_ENST00000407479.1_Missense_Mutation_p.R244Q	NM_005223.3	NP_005214.2	P24855	DNAS1_HUMAN	deoxyribonuclease I	244			R -> Q (in allele DNASE1*1; dbSNP:rs1053874). {ECO:0000269|PubMed:7762978}.		apoptotic process (GO:0006915)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	deoxyribonuclease I activity (GO:0004530)			lung(1)	1		Ovarian(90;0.0261)		Kidney(780;0.0556)		ATGCTGCTCCGAGGCGCCGTT	0.567													A|||	2475	0.494209	0.8177	0.3473	5008	,	,		20043	0.4286		0.3032	False		,,,				2504	0.4254				p.R244Q		Atlas-SNP	.											.	DNASE1	16	.	0			c.G731A	GRCh37	CM042698	DNASE1	M	rs1053874	PASS	.	A	GLN/ARG	3251,1143	405.3+/-333.4	1206,839,152	79.0	67.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	731	4.5	0.3	16	dbSNP_86	71	2606,5994	688.3+/-404.3	405,1796,2099	yes	missense	DNASE1	NM_005223.3	43	1611,2635,2251	AA,AG,GG		30.3023,26.0127,45.0746	benign	244/283	3707747	5857,7137	2197	4300	6497	SO:0001583	missense	1773	exon8			TGCTCCGAGGCGC		CCDS10507.1	16p13.3	2008-02-05			ENSG00000213918	ENSG00000213918	3.1.21.1		2956	protein-coding gene	gene with protein product		125505		DNL1		2349940	Standard	XM_005255148		Approved		uc002cvr.3	P24855	OTTHUMG00000129426	ENST00000246949.5:c.731G>A	16.37:g.3707747G>A	ENSP00000246949:p.Arg244Gln	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_005223	B4DV35|Q14UU9|Q14UV0	Missense_Mutation	SNP	ENST00000246949.5	37	CCDS10507.1	1062	0.48626373626373626	414	0.8414634146341463	141	0.38950276243093923	273	0.4772727272727273	234	0.3087071240105541	A	5.843	0.339737	0.11069	0.739873	0.303023	ENSG00000213918	ENST00000407479;ENST00000246949;ENST00000414110	T;T;T	0.32272	1.46;1.46;1.46	4.5	4.5	0.54988	Endonuclease/exonuclease/phosphatase (2);	0.225509	0.42172	N	0.000756	T	0.00012	0.0000	N	0.01424	-0.875	0.28650	P	0.9067025	B	0.12630	0.006	B	0.04013	0.001	T	0.32613	-0.9900	9	0.07813	T	0.8	-9.4549	5.216	0.15342	0.7586:0.0:0.0848:0.1566	rs1053874;rs1801110;rs3169473;rs17255932;rs17418314;rs59499103;rs1053874	244	P24855	DNAS1_HUMAN	Q	244;244;127	ENSP00000385905:R244Q;ENSP00000246949:R244Q;ENSP00000416699:R127Q	ENSP00000246949:R244Q	R	+	2	0	DNASE1	3647748	0.000000	0.05858	0.315000	0.25238	0.004000	0.04260	0.033000	0.13754	0.875000	0.35847	-0.361000	0.07541	CGA	G|0.520;A|0.480	0.480	strong		0.567	DNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251585.2		
PER2	8864	hgsc.bcm.edu	37	2	239161957	239161957	+	Missense_Mutation	SNP	C	C	T	rs35333999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:239161957C>T	ENST00000254657.3	-	19	2986	c.2707G>A	c.(2707-2709)Gtc>Atc	p.V903I	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	903	Interaction with PPARG. {ECO:0000250|UniProtKB:O54943}.|Pro-rich.		V -> I (in dbSNP:rs35333999).		circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		AATGCCATGACAGGCGCCAAA	0.642													C|||	85	0.0169728	0.003	0.0288	5008	,	,		16468	0.0		0.0596	False		,,,				2504	0.001				p.V903I		Atlas-SNP	.											.	PER2	85	.	0			c.G2707A						PASS	.	C	ILE/VAL	36,4370	40.0+/-72.8	0,36,2167	43.0	46.0	45.0		2707	2.4	0.2	2	dbSNP_126	45	392,8208	122.9+/-181.8	4,384,3912	yes	missense	PER2	NM_022817.2	29	4,420,6079	TT,TC,CC		4.5581,0.8171,3.2908	possibly-damaging	903/1256	239161957	428,12578	2203	4300	6503	SO:0001583	missense	8864	exon19			CCATGACAGGCGC	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"""period (Drosophila) homolog 2"", ""period homolog 2 (Drosophila)"""			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.2707G>A	2.37:g.239161957C>T	ENSP00000254657:p.Val903Ile	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	CCDS2528.1	49	0.022435897435897436	0	0.0	13	0.03591160220994475	0	0.0	36	0.047493403693931395	C	9.693	1.152364	0.21371	0.008171	0.045581	ENSG00000132326	ENST00000254657	T	0.12465	2.68	4.3	2.41	0.29592	.	0.357292	0.30142	N	0.010304	T	0.03739	0.0106	L	0.59436	1.845	0.19300	N	0.999971	D;D	0.58970	0.984;0.984	D;D	0.70016	0.956;0.967	T	0.04551	-1.0943	10	0.23302	T	0.38	-28.5715	3.5113	0.07709	0.1737:0.557:0.1692:0.1001	rs35333999	903;903	B4DH14;O15055	.;PER2_HUMAN	I	903	ENSP00000254657:V903I	ENSP00000254657:V903I	V	-	1	0	PER2	238826696	0.003000	0.15002	0.171000	0.22900	0.078000	0.17371	0.082000	0.14847	0.909000	0.36697	0.561000	0.74099	GTC	C|0.970;T|0.030	0.030	strong		0.642	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	
BRAT1	221927	hgsc.bcm.edu	37	7	2583328	2583328	+	Silent	SNP	C	C	T	rs61753095	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	130	0	0		WXS	Illumina HiSeq	Phase_I	154	59	0.383117	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	
LINS	55180	hgsc.bcm.edu	37	15	101109683	101109683	+	Silent	SNP	T	T	C	rs1047320	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:101109683T>C	ENST00000314742.8	-	7	2256	c.2034A>G	c.(2032-2034)ccA>ccG	p.P678P	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	678										central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						GAGGCCTTGATGGAGGCTCAA	0.423													T|||	45	0.00898562	0.0015	0.0216	5008	,	,		18428	0.0		0.0258	False		,,,				2504	0.002				p.P678P		Atlas-SNP	.											.	LINS	62	.	0			c.A2034G						PASS	.	T		16,4390	23.3+/-48.9	0,16,2187	85.0	86.0	86.0		2034	-4.4	0.0	15	dbSNP_86	86	219,8381	89.9+/-152.1	3,213,4084	no	coding-synonymous	LINS	NM_001040616.2		3,229,6271	CC,CT,TT		2.5465,0.3631,1.8069		678/758	101109683	235,12771	2203	4300	6503	SO:0001819	synonymous_variant	55180	exon7			CCTTGATGGAGGC	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.2034A>G	15.37:g.101109683T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	56	53	0.946429	NM_001040616	Q96FW2|Q9NVQ3	Silent	SNP	ENST00000314742.8	37	CCDS10385.1																																																																																			T|0.982;C|0.018	0.018	strong		0.423	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
KIF6	221458	hgsc.bcm.edu	37	6	39325078	39325078	+	Missense_Mutation	SNP	A	A	G	rs20455	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:39325078A>G	ENST00000287152.7	-	19	2249	c.2155T>C	c.(2155-2157)Tgg>Cgg	p.W719R	KIF6_ENST00000373216.3_Missense_Mutation_p.W719R|KIF6_ENST00000394362.1_Missense_Mutation_p.W170R|KIF6_ENST00000229913.5_Missense_Mutation_p.W170R|KIF6_ENST00000373213.4_Missense_Mutation_p.W558R|KIF6_ENST00000541946.1_Missense_Mutation_p.W170R|KIF6_ENST00000538893.1_Missense_Mutation_p.W663R|KIF6_ENST00000373215.3_Missense_Mutation_p.W702R	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	719			W -> R (in dbSNP:rs20455). {ECO:0000269|PubMed:14702039}.		ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.W719R(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						AGTTGGGACCATTCATGCTGG	0.473													G|||	2703	0.539736	0.854	0.3343	5008	,	,		15961	0.5238		0.3628	False		,,,				2504	0.4591				p.W719R		Atlas-SNP	.											KIF6_ENST00000287152,NS,carcinoma,0,1	KIF6	233	1	1	Substitution - Missense(1)	stomach(1)	c.T2155C	GRCh37	CM074911	KIF6	M	rs20455	scavenged	.	G	ARG/TRP	3444,962	362.4+/-316.1	1365,714,124	162.0	150.0	154.0		2155	0.5	0.0	6	dbSNP_67	154	3078,5522	660.5+/-401.8	573,1932,1795	yes	missense	KIF6	NM_145027.4	101	1938,2646,1919	GG,GA,AA		35.7907,21.8339,49.8539	benign	719/815	39325078	6522,6484	2203	4300	6503	SO:0001583	missense	221458	exon19			GGGACCATTCATG	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"""Kinesins"""	21202	protein-coding gene	gene with protein product		613919	"""chromosome 6 open reading frame 102"""	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.2155T>C	6.37:g.39325078A>G	ENSP00000287152:p.Trp719Arg	Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	171	80	0.467836	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	1071	0.49038461538461536	400	0.8130081300813008	132	0.36464088397790057	278	0.486013986013986	261	0.34432717678100266	G	0.234	-1.018519	0.02078	0.781661	0.357907	ENSG00000164627	ENST00000287152;ENST00000394362;ENST00000373216;ENST00000373213;ENST00000229913;ENST00000373215;ENST00000538893;ENST00000541946	T;T;T;T;T;T;T;T	0.70045	-0.39;1.63;-0.43;-0.21;1.71;-0.4;-0.45;1.68	4.56	0.525	0.17072	.	.	.	.	.	T	0.09335	0.0230	N	0.01352	-0.895	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	0.11012	-1.0605	8	0.11485	T	0.65	.	0.7034	0.00911	0.3077:0.1367:0.3643:0.1913	rs20455;rs16891985;rs56572561;rs58306844;rs20455	702;663;719;719	E7EUN7;F6VGH2;Q6ZMV9-3;Q6ZMV9	.;.;.;KIF6_HUMAN	R	719;170;719;558;170;702;663;170	ENSP00000287152:W719R;ENSP00000377889:W170R;ENSP00000362312:W719R;ENSP00000362309:W558R;ENSP00000229913:W170R;ENSP00000362311:W702R;ENSP00000441435:W663R;ENSP00000439064:W170R	ENSP00000229913:W170R	W	-	1	0	KIF6	39433056	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.021000	0.13489	-0.250000	0.09555	-0.735000	0.03563	TGG	A|0.497;G|0.503	0.503	strong		0.473	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	
GPATCH1	55094	hgsc.bcm.edu	37	19	33600764	33600764	+	Missense_Mutation	SNP	T	T	C	rs2287679	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:33600764T>C	ENST00000170564.2	+	11	1741	c.1427T>C	c.(1426-1428)cTc>cCc	p.L476P		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	476			L -> P (in dbSNP:rs2287679). {ECO:0000269|PubMed:17974005}.		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)					AGAGCCCAGCTCTCCCCTGCA	0.552													C|||	2672	0.533546	0.8003	0.2867	5008	,	,		16368	0.5079		0.2416	False		,,,				2504	0.6748				p.L476P	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.T1427C						PASS	.	C	PRO/LEU	3203,1203	401.0+/-331.8	1159,885,159	39.0	40.0	40.0		1427	5.7	0.1	19	dbSNP_100	40	2297,6303	678.3+/-403.4	281,1735,2284	yes	missense	GPATCH1	NM_018025.2	98	1440,2620,2443	CC,CT,TT		26.7093,27.3037,42.2882	benign	476/932	33600764	5500,7506	2203	4300	6503	SO:0001583	missense	55094	exon11			CCCAGCTCTCCCC	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.1427T>C	19.37:g.33600764T>C	ENSP00000170564:p.Leu476Pro	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	37	CCDS12428.1	970	0.4441391941391941	386	0.7845528455284553	107	0.2955801104972376	285	0.4982517482517482	192	0.2532981530343008	C	2.963	-0.214135	0.06101	0.726963	0.267093	ENSG00000076650	ENST00000170564	T	0.30182	1.54	5.74	5.74	0.90152	.	0.773566	0.12715	N	0.445174	T	0.00012	0.0000	N	0.01081	-1.03	0.41672	P	0.010757000000000017	B	0.02656	0.0	B	0.04013	0.001	T	0.30679	-0.9970	9	0.30078	T	0.28	-0.2351	9.4371	0.38646	0.0:0.7817:0.0:0.2183	rs2287679;rs57097144;rs2287679	476	Q9BRR8	GPTC1_HUMAN	P	476	ENSP00000170564:L476P	ENSP00000170564:L476P	L	+	2	0	GPATCH1	38292604	0.001000	0.12720	0.127000	0.21898	0.004000	0.04260	1.138000	0.31491	1.454000	0.47793	-0.119000	0.15052	CTC	T|0.541;C|0.459	0.459	strong		0.552	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
FLG	2312	hgsc.bcm.edu	37	1	152282267	152282267	+	Missense_Mutation	SNP	G	G	A	rs12405278	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152282267G>A	ENST00000368799.1	-	3	5130	c.5095C>T	c.(5095-5097)Cgc>Tgc	p.R1699C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1699	Ser-rich.		R -> C (in dbSNP:rs12405278).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCTTGTCTGCGCCCAGTGCCT	0.572									Ichthyosis				g|||	1441	0.28774	0.0121	0.3905	5008	,	,		20090	0.5843		0.1421	False		,,,				2504	0.4315				p.R1699C		Atlas-SNP	.											FLG,colon,carcinoma,+1,1	FLG	900	1	0			c.C5095T						PASS	.	C	CYS/ARG	161,4245	108.2+/-146.6	2,157,2044	256.0	259.0	258.0		5095	1.8	0.0	1	dbSNP_120	258	1240,7360	249.0+/-276.5	97,1046,3157	yes	missense	FLG	NM_002016.1	180	99,1203,5201	AA,AG,GG		14.4186,3.6541,10.772	probably-damaging	1699/4062	152282267	1401,11605	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCTGCGCCCAGT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5095C>T	1.37:g.152282267G>A	ENSP00000357789:p.Arg1699Cys	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	277	109	0.393502	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	573	0.2623626373626374	9	0.018292682926829267	118	0.3259668508287293	335	0.5856643356643356	111	0.14643799472295516	g	3.096	-0.185843	0.06340	0.036541	0.144186	ENSG00000143631	ENST00000368799	T	0.04275	3.66	2.69	1.76	0.24704	.	.	.	.	.	T	0.05823	0.0152	L	0.54323	1.7	0.80722	P	0.0	D	0.76494	0.999	D	0.63192	0.912	T	0.21484	-1.0244	8	0.54805	T	0.06	.	7.611	0.28131	0.0:0.2659:0.7341:0.0	rs56401605;rs58569216	1699	P20930	FILA_HUMAN	C	1699	ENSP00000357789:R1699C	ENSP00000357789:R1699C	R	-	1	0	FLG	150548891	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.137000	0.15995	0.482000	0.27582	-0.672000	0.03802	CGC	G|0.811;A|0.189	0.189	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LMNA	4000	hgsc.bcm.edu	37	1	156105059	156105059	+	Missense_Mutation	SNP	C	C	T	rs59885338		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156105059C>T	ENST00000368300.4	+	5	1104	c.892C>T	c.(892-894)Cgc>Tgc	p.R298C	LMNA_ENST00000392353.3_Missense_Mutation_p.R217C|LMNA_ENST00000368297.1_Missense_Mutation_p.R217C|LMNA_ENST00000347559.2_Missense_Mutation_p.R298C|LMNA_ENST00000361308.4_Missense_Mutation_p.R298C|LMNA_ENST00000368299.3_Missense_Mutation_p.R298C|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000368301.2_Missense_Mutation_p.R298C|LMNA_ENST00000473598.2_Missense_Mutation_p.R199C|LMNA_ENST00000448611.2_Missense_Mutation_p.R186C	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	298	Coil 2.|Rod.		R -> C (in CMT2B1). {ECO:0000269|PubMed:11799477}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					GTCGCGCATCCGCATCGACAG	0.647									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												p.R298C		Atlas-SNP	.											LMNA,colon,carcinoma,0,1	LMNA	31	1	0			c.C892T	GRCh37	CM020461	LMNA	M	rs59885338	scavenged	.						32.0	34.0	33.0					1																	156105059		2203	4300	6503	SO:0001583	missense	4000	exon5	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	CGCATCCGCATCG	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.892C>T	1.37:g.156105059C>T	ENSP00000357283:p.Arg298Cys	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	339	4	0.0117994	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Missense_Mutation	SNP	ENST00000368300.4	37	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.333499	0.81801	.	.	ENSG00000160789	ENST00000368301;ENST00000347559;ENST00000361308;ENST00000368300;ENST00000368299;ENST00000292302;ENST00000392355;ENST00000448611;ENST00000368297;ENST00000473598;ENST00000392353	D;D;D;D;D;D;D;D;D	0.89552	-2.53;-2.53;-2.53;-2.53;-2.53;-2.53;-2.53;-2.53;-2.53	5.6	5.6	0.85130	Filament (1);	0.000000	0.56097	D	0.000024	D	0.95617	0.8575	M	0.93283	3.4	0.80722	A	1	P;D;D;D;D;P;D	0.89917	0.93;1.0;0.995;0.997;0.973;0.873;1.0	P;D;D;P;P;P;D	0.75020	0.632;0.985;0.932;0.857;0.616;0.71;0.975	D	0.96329	0.9242	9	0.87932	D	0	.	17.1117	0.86676	0.0:1.0:0.0:0.0	rs59885338	186;298;199;217;298;298;298	E7EUI9;Q6UYC3;D6RAQ3;Q5TCI8;P02545;P02545-3;P02545-2	.;.;.;.;LMNA_HUMAN;.;.	C	298;298;298;298;298;298;298;186;217;199;217	ENSP00000357284:R298C;ENSP00000292304:R298C;ENSP00000355292:R298C;ENSP00000357283:R298C;ENSP00000357282:R298C;ENSP00000395597:R186C;ENSP00000357280:R217C;ENSP00000421821:R199C;ENSP00000376164:R217C	ENSP00000292302:R298C	R	+	1	0	LMNA	154371683	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	3.090000	0.50191	2.653000	0.90120	0.563000	0.77884	CGC	.	.	weak		0.647	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	
ITIH1	3697	hgsc.bcm.edu	37	3	52825912	52825912	+	Silent	SNP	C	C	A	rs7549	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:52825912C>A	ENST00000273283.2	+	22	2745	c.2721C>A	c.(2719-2721)gtC>gtA	p.V907V	ITIH3_ENST00000449956.2_5'Flank|ITIH3_ENST00000416872.2_5'Flank|ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000540715.1_Silent_p.V765V|ITIH1_ENST00000405128.3_Silent_p.V273V|ITIH1_ENST00000537050.1_Silent_p.V619V	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	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	264	126	0.477273	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	
FLG	2312	hgsc.bcm.edu	37	1	152276660	152276660	+	Missense_Mutation	SNP	G	G	C	rs7540123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152276660G>C	ENST00000368799.1	-	3	10737	c.10702C>G	c.(10702-10704)Cag>Gag	p.Q3568E	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3568	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACTGCTCCTGAGCAGATCCA	0.572									Ichthyosis				G|||	1035	0.206669	0.2133	0.1916	5008	,	,		17873	0.3403		0.0696	False		,,,				2504	0.2117				p.Q3568E		Atlas-SNP	.											FLG,NS,carcinoma,+2,1	FLG	900	1	0			c.C10702G						PASS	.						149.0	201.0	183.0					1																	152276660		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTCCTGAGCAGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10702C>G	1.37:g.152276660G>C	ENSP00000357789:p.Gln3568Glu	Somatic	395	0	0		WXS	Illumina HiSeq	Phase_I	375	31	0.0826667	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	3.450	-0.112146	0.06881	.	.	ENSG00000143631	ENST00000368799	T	0.01629	4.72	3.16	1.14	0.20703	.	.	.	.	.	T	0.00412	0.0013	L	0.44542	1.39	0.09310	N	1	P	0.41080	0.737	B	0.36504	0.226	T	0.32402	-0.9908	9	0.02654	T	1	.	3.1883	0.06608	0.1468:0.0:0.5899:0.2633	rs7540123;rs57866496;rs7540123	3568	P20930	FILA_HUMAN	E	3568	ENSP00000357789:Q3568E	ENSP00000357789:Q3568E	Q	-	1	0	FLG	150543284	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	1.365000	0.34182	0.608000	0.30000	0.398000	0.26397	CAG	G|0.995;C|0.005	0.005	strong		0.572	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CEP170	9859	hgsc.bcm.edu	37	1	243328887	243328887	+	Nonsense_Mutation	SNP	G	G	T	rs2728433		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:243328887G>T	ENST00000366542.1	-	13	2426	c.2375C>A	c.(2374-2376)tCa>tAa	p.S792*	CEP170_ENST00000366544.1_Nonsense_Mutation_p.S694*|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Nonsense_Mutation_p.S694*	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	96	0	0		WXS	Illumina HiSeq	Phase_I	165	11	0.0666667	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	
C19orf53	28974	hgsc.bcm.edu	37	19	13885484	13885484	+	Missense_Mutation	SNP	A	A	G	rs10104	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13885484A>G	ENST00000588234.1	+	2	426	c.116A>G	c.(115-117)aAg>aGg	p.K39R	C19orf53_ENST00000593274.1_5'Flank|CTB-5E10.3_ENST00000586297.1_RNA|CTB-5E10.3_ENST00000586894.1_RNA|CTB-5E10.3_ENST00000591826.1_RNA	NM_014047.2	NP_054766.1	Q9UNZ5	L10K_HUMAN	chromosome 19 open reading frame 53	39			K -> R (in dbSNP:rs10104).							breast(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	6			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			ATCGCTCCCAAGAAGGCGCGC	0.677													A|||	1891	0.377596	0.4032	0.3184	5008	,	,		16120	0.4266		0.2555	False		,,,				2504	0.4601				p.K39R		Atlas-SNP	.											.	C19orf53	14	.	0			c.A116G						PASS	.	A	ARG/LYS	1770,2636	506.7+/-366.5	349,1072,782	72.0	83.0	79.0		116	5.2	1.0	19	dbSNP_52	79	2227,6371	364.9+/-333.7	305,1617,2377	yes	missense	C19orf53	NM_014047.2	26	654,2689,3159	GG,GA,AA		25.9014,40.1725,30.7367	probably-damaging	39/100	13885484	3997,9007	2203	4299	6502	SO:0001583	missense	28974	exon2			CTCCCAAGAAGGC	AF078852	CCDS12298.1	19p13.2	2011-11-24			ENSG00000104979	ENSG00000104979			24991	protein-coding gene	gene with protein product	"""leydig cell tumor 10 kDa protein homolog"""					11042152	Standard	NM_014047		Approved	HSPC023, LYDG10	uc002mxg.3	Q9UNZ5		ENST00000588234.1:c.116A>G	19.37:g.13885484A>G	ENSP00000465432:p.Lys39Arg	Somatic	334	0	0		WXS	Illumina HiSeq	Phase_I	287	147	0.512195	NM_014047	B2R4J9	Missense_Mutation	SNP	ENST00000588234.1	37	CCDS12298.1	738	0.33791208791208793	210	0.4268292682926829	103	0.2845303867403315	233	0.40734265734265734	192	0.2532981530343008	A	34	5.402346	0.96030	0.401725	0.259014	ENSG00000104979	ENST00000221576	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	D	0.69078	0.997	D	0.80764	0.994	T	0.27706	-1.0066	7	0.87932	D	0	.	13.346	0.60573	1.0:0.0:0.0:0.0	rs10104;rs1128778;rs1559148;rs11557473;rs17112907;rs17295622;rs59089349;rs10104	39	Q9UNZ5	L10K_HUMAN	R	39	.	ENSP00000221576:K39R	K	+	2	0	C19orf53	13746484	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.204000	0.65180	2.102000	0.63906	0.524000	0.50904	AAG	A|0.669;G|0.331	0.331	strong		0.677	C19orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453621.1	NM_014047	
SAE1	10055	hgsc.bcm.edu	37	19	47700542	47700542	+	Silent	SNP	T	T	C	rs117605411	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:47700542T>C	ENST00000270225.7	+	7	854	c.786T>C	c.(784-786)taT>taC	p.Y262Y	SAE1_ENST00000392776.3_Intron|SAE1_ENST00000540850.1_Silent_p.Y88Y|SAE1_ENST00000413379.3_Intron|SAE1_ENST00000598840.1_Silent_p.Y181Y	NM_005500.2	NP_005491.1	Q9UBE0	SAE1_HUMAN	SUMO1 activating enzyme subunit 1	262					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitotic cell cycle (GO:0007346)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP-dependent protein binding (GO:0043008)|enzyme activator activity (GO:0008047)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|ubiquitin activating enzyme activity (GO:0004839)			endometrium(3)|large_intestine(5)|lung(4)|ovary(1)	13		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		CTGATACATATGAGGAAGATT	0.408													T|||	23	0.00459265	0.0	0.0014	5008	,	,		19443	0.001		0.005	False		,,,				2504	0.0164				p.Y262Y		Atlas-SNP	.											.	SAE1	50	.	0			c.T786C						PASS	.	T	,,	9,4397	14.3+/-33.2	0,9,2194	213.0	193.0	200.0		,,786	-4.8	0.0	19	dbSNP_132	200	27,8573	19.2+/-60.6	0,27,4273	no	intron,intron,coding-synonymous	SAE1	NM_001145713.1,NM_001145714.1,NM_005500.2	,,	0,36,6467	CC,CT,TT		0.314,0.2043,0.2768	,,	,,262/347	47700542	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	10055	exon7			TACATATGAGGAA	BC018271	CCDS12696.1, CCDS54284.1, CCDS54285.1	19q13.32	2013-09-26				ENSG00000142230		"""Ubiquitin-like modifier activating enzymes"""	30660	protein-coding gene	gene with protein product	"""activator Of sumo 1"""	613294				10187858, 9920803, 10217437	Standard	NM_005500		Approved	AOS1, FLJ3091, Sua1	uc002pgc.3	Q9UBE0		ENST00000270225.7:c.786T>C	19.37:g.47700542T>C		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	190	74	0.389474	NM_005500	B2RDP5|B3KMQ2|F5GXX7|G3XAK6|O95717|Q9P020	Silent	SNP	ENST00000270225.7	37	CCDS12696.1																																																																																			T|0.997;C|0.003	0.003	strong		0.408	SAE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466775.1	NM_005500	
FAM171B	165215	hgsc.bcm.edu	37	2	187558960	187558960	+	Silent	SNP	G	G	A	rs2276562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187558960G>A	ENST00000304698.5	+	1	263	c.60G>A	c.(58-60)ctG>ctA	p.L20L	AC017101.10_ENST00000453665.1_RNA	NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	20						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						CCGTGGTGCTGCTGAAAGCGC	0.687													G|||	1446	0.288738	0.0598	0.2939	5008	,	,		12251	0.7153		0.2624	False		,,,				2504	0.182				p.L20L		Atlas-SNP	.											.	FAM171B	146	.	0			c.G60A						PASS	.	G		333,3951		10,313,1819	12.0	14.0	13.0		60	2.0	1.0	2	dbSNP_100	13	1773,6647		180,1413,2617	no	coding-synonymous	FAM171B	NM_177454.3		190,1726,4436	AA,AG,GG		21.057,7.7731,16.5775		20/827	187558960	2106,10598	2142	4210	6352	SO:0001819	synonymous_variant	165215	exon1			GGTGCTGCTGAAA	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.60G>A	2.37:g.187558960G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Silent	SNP	ENST00000304698.5	37	CCDS33347.1																																																																																			G|0.763;A|0.237	0.237	strong		0.687	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493809	77493809	+	Silent	SNP	C	C	T	rs61991638		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77493809C>T	ENST00000238647.3	-	1	1225	c.327G>A	c.(325-327)caG>caA	p.Q109Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	109	Poly-Gln.				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						gctgctgctgctgctgttgct	0.687																																					p.Q109Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.G327A						PASS	.						2.0	2.0	2.0					14																	77493809		1179	2145	3324	SO:0001819	synonymous_variant	64207	exon1			CTGCTGCTGCTGT	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.327G>A	14.37:g.77493809C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	13	4	0.307692	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			C|0.978;T|0.022	0.022	strong		0.687	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496	
MLPH	79083	hgsc.bcm.edu	37	2	238434249	238434249	+	Silent	SNP	C	C	T	rs2292881	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238434249C>T	ENST00000264605.3	+	7	975	c.681C>T	c.(679-681)ctC>ctT	p.L227L	MLPH_ENST00000410032.1_Intron|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Silent_p.L227L|MLPH_ENST00000338530.4_Silent_p.L227L|MLPH_ENST00000409373.1_Silent_p.L187L	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	227					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)			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)		CTTAGTCCCTCACAGATGAGT	0.607													C|||	737	0.147165	0.0741	0.1988	5008	,	,		17998	0.1935		0.0676	False		,,,				2504	0.2434				p.L227L		Atlas-SNP	.											.	MLPH	41	.	0			c.C681T						PASS	.	C	,	410,3996	200.1+/-223.5	12,386,1805	43.0	46.0	45.0		681,681	2.4	0.7	2	dbSNP_100	45	734,7866	177.3+/-227.0	22,690,3588	no	coding-synonymous,coding-synonymous	MLPH	NM_001042467.1,NM_024101.5	,	34,1076,5393	TT,TC,CC		8.5349,9.3055,8.7959	,	227/573,227/601	238434249	1144,11862	2203	4300	6503	SO:0001819	synonymous_variant	79083	exon7			GTCCCTCACAGAT	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.681C>T	2.37:g.238434249C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Silent	SNP	ENST00000264605.3	37	CCDS2518.1	260	0.11904761904761904	43	0.08739837398373984	55	0.15193370165745856	111	0.19405594405594406	51	0.06728232189973615	C	8.698	0.909104	0.17833	0.093055	0.085349	ENSG00000115648	ENST00000437893	T	0.28454	1.61	3.35	2.43	0.29744	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.99999854391	.	.	.	.	.	.	T	0.17349	-1.0372	4	.	.	.	-15.6364	8.4894	0.33091	0.0:0.7609:0.2391:0.0	rs2292881;rs2292881	.	.	.	L	34	ENSP00000412438:S34L	.	S	+	2	0	MLPH	238098988	0.637000	0.27216	0.748000	0.31131	0.727000	0.41649	1.310000	0.33551	0.955000	0.37878	0.563000	0.77884	TCA	C|0.895;T|0.105	0.105	strong		0.607	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
SPG11	80208	hgsc.bcm.edu	37	15	44943757	44943757	+	Missense_Mutation	SNP	A	A	G	rs3759871	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:44943757A>G	ENST00000261866.7	-	6	1404	c.1388T>C	c.(1387-1389)tTt>tCt	p.F463S	SPG11_ENST00000559193.1_Missense_Mutation_p.F463S|SPG11_ENST00000427534.2_Missense_Mutation_p.F463S|SPG11_ENST00000558319.1_Missense_Mutation_p.F463S|SPG11_ENST00000535302.2_Missense_Mutation_p.F463S	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	463			F -> S (in dbSNP:rs3759871). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.F463S(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GCCAAGGGAAAAACACTGCAT	0.463													A|||	2378	0.47484	0.5234	0.5893	5008	,	,		20546	0.4653		0.4513	False		,,,				2504	0.362				p.F463S		Atlas-SNP	.											SPG11,NS,carcinoma,0,1	SPG11	207	1	1	Substitution - Missense(1)	stomach(1)	c.T1388C						PASS	.	A	SER/PHE,SER/PHE	2310,2086	603.0+/-390.0	609,1092,497	118.0	110.0	113.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1388,1388	4.9	0.9	15	dbSNP_107	113	3917,4679	547.6+/-385.2	924,2069,1305	yes	missense,missense	SPG11	NM_001160227.1,NM_025137.3	155,155	1533,3161,1802	GG,GA,AA		45.5677,47.4522,47.9295	benign,benign	463/2331,463/2444	44943757	6227,6765	2198	4298	6496	SO:0001583	missense	80208	exon6			AGGGAAAAACACT		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.1388T>C	15.37:g.44943757A>G	ENSP00000261866:p.Phe463Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	124	24	0.193548	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	1075	0.49221611721611724	254	0.516260162601626	206	0.569060773480663	283	0.49475524475524474	332	0.43799472295514513	A	10.01	1.234381	0.22626	0.525478	0.455677	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.76060	-0.99;-0.73;-0.73	6.06	4.93	0.64822	.	0.209291	0.42053	D	0.000773	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B;B;B	0.22211	0.021;0.066;0.053;0.021	B;B;B;B	0.18561	0.009;0.02;0.022;0.008	T	0.48514	-0.9029	9	0.26408	T	0.33	.	3.1014	0.06327	0.6352:0.1486:0.0744:0.1418	rs3759871;rs52807288;rs59538210;rs3759871	463;463;463;463	C4B7M2;F5H3N6;B9EK60;Q96JI7	.;.;.;SPTCS_HUMAN	S	463	ENSP00000261866:F463S;ENSP00000445278:F463S;ENSP00000396110:F463S	ENSP00000261866:F463S	F	-	2	0	SPG11	42731049	0.042000	0.20092	0.856000	0.33681	0.991000	0.79684	1.226000	0.32563	1.092000	0.41356	0.533000	0.62120	TTT	A|0.523;G|0.477	0.477	strong		0.463	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
ARHGEF10	9639	hgsc.bcm.edu	37	8	1857548	1857548	+	Silent	SNP	T	T	C	rs2294038	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:1857548T>C	ENST00000398564.1	+	18	2130	c.2130T>C	c.(2128-2130)taT>taC	p.Y710Y	ARHGEF10_ENST00000520359.1_Silent_p.Y647Y|ARHGEF10_ENST00000262112.6_Silent_p.Y710Y|ARHGEF10_ENST00000349830.3_Silent_p.Y685Y|ARHGEF10_ENST00000518288.1_Silent_p.Y709Y			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	710					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)		CCATCGAGTATGGCAGCAGCG	0.602													T|||	786	0.156949	0.115	0.2248	5008	,	,		18080	0.1746		0.171	False		,,,				2504	0.1329				p.Y685Y		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.T2055C						PASS	.	T		572,3834	254.0+/-259.7	35,502,1666	126.0	113.0	117.0		2055	-3.9	0.0	8	dbSNP_100	117	1328,7272	260.6+/-283.4	105,1118,3077	no	coding-synonymous	ARHGEF10	NM_014629.2		140,1620,4743	CC,CT,TT		15.4419,12.9823,14.6086		685/1345	1857548	1900,11106	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon18			CGAGTATGGCAGC	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.2130T>C	8.37:g.1857548T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	136	47	0.345588	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				T|0.853;C|0.147	0.147	strong		0.602	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
TJP3	27134	hgsc.bcm.edu	37	19	3728609	3728609	+	Missense_Mutation	SNP	G	G	A	rs2067019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3728609G>A	ENST00000541714.2	+	3	518	c.56G>A	c.(55-57)cGc>cAc	p.R19H	TJP3_ENST00000539908.2_5'UTR|TJP3_ENST00000589378.1_Missense_Mutation_p.R28H|TJP3_ENST00000262968.9_Missense_Mutation_p.R38H|TJP3_ENST00000587686.1_Missense_Mutation_p.R38H|TJP3_ENST00000382008.3_Missense_Mutation_p.R19H	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	19	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.			R -> H (in Ref. 4; AAI08907). {ECO:0000305}.	regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGACCCCCGCCGGGGCTTT	0.627													G|||	1440	0.28754	0.1626	0.3847	5008	,	,		16938	0.3482		0.1948	False		,,,				2504	0.4202				p.R28H		Atlas-SNP	.											TJP3,colon,carcinoma,0,1	TJP3	79	1	0			c.G83A						scavenged	.	G	HIS/ARG	766,3638	282.2+/-276.4	73,620,1509	21.0	26.0	25.0		113	4.0	1.0	19	dbSNP_96	25	1634,6966	283.9+/-296.4	173,1288,2839	yes	missense	TJP3	NM_014428.1	29	246,1908,4348	AA,AG,GG		19.0,17.3933,18.4559	probably-damaging	38/953	3728609	2400,10604	2202	4300	6502	SO:0001583	missense	27134	exon3			ACCCCCGCCGGGG	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.56G>A	19.37:g.3728609G>A	ENSP00000439278:p.Arg19His	Somatic	72	2	0.0277778		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	572	0.2619047619047619	76	0.15447154471544716	123	0.3397790055248619	225	0.39335664335664333	148	0.19525065963060687	G	16.41	3.114745	0.56505	0.173933	0.19	ENSG00000105289	ENST00000541714;ENST00000382008;ENST00000262968	T;T;T	0.29917	1.55;1.55;2.28	4.02	4.02	0.46733	PDZ/DHR/GLGF (3);	0.147473	0.46758	D	0.000274	T	0.00012	0.0000	N	0.21545	0.675	0.28643	P	0.9070552000000001	D;D;D;D	0.89917	0.991;1.0;1.0;0.991	P;D;D;P	0.81914	0.72;0.995;0.984;0.72	T	0.40384	-0.9566	9	0.46703	T	0.11	.	9.3472	0.38115	0.1135:0.0:0.8865:0.0	rs2067019;rs59188659;rs2067019	38;38;19;19	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	H	19;19;38	ENSP00000439278:R19H;ENSP00000371438:R19H;ENSP00000262968:R38H	ENSP00000262968:R38H	R	+	2	0	TJP3	3679609	0.999000	0.42202	0.991000	0.47740	0.664000	0.39144	3.676000	0.54612	2.253000	0.74438	0.456000	0.33151	CGC	G|0.787;A|0.213	0.213	strong		0.627	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
SLC12A6	9990	hgsc.bcm.edu	37	15	34551082	34551082	+	Silent	SNP	G	G	A	rs7164902	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:34551082G>A	ENST00000354181.3	-	5	967	c.475C>T	c.(475-477)Ctg>Ttg	p.L159L	SLC12A6_ENST00000558589.1_Silent_p.L150L|SLC12A6_ENST00000560164.1_Silent_p.L20L|SLC12A6_ENST00000451844.2_Silent_p.L20L|SLC12A6_ENST00000397707.2_Silent_p.L144L|RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000558667.1_Silent_p.L159L|SLC12A6_ENST00000458406.2_Silent_p.L100L|SLC12A6_ENST00000397702.2_Silent_p.L100L|SLC12A6_ENST00000560611.1_Silent_p.L159L|SLC12A6_ENST00000290209.5_Silent_p.L108L			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	159					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)	CCTTGAGTCAGATTAGTGTAA	0.448													G|||	1386	0.276757	0.1982	0.2161	5008	,	,		18454	0.3542		0.2406	False		,,,				2504	0.3834				p.L159L		Atlas-SNP	.											.	SLC12A6	205	.	0			c.C475T						PASS	.	G	,,,,,	951,3451	361.4+/-315.7	105,741,1355	231.0	217.0	222.0		298,298,448,430,322,475	2.8	1.0	15	dbSNP_116	222	2092,6504	361.6+/-332.4	259,1574,2465	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	,,,,,	364,2315,3820	AA,AG,GG		24.3369,21.6038,23.4113	,,,,,	100/1092,100/1092,150/1142,144/1136,108/1100,159/1151	34551082	3043,9955	2201	4298	6499	SO:0001819	synonymous_variant	9990	exon4			GAGTCAGATTAGT	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.475C>T	15.37:g.34551082G>A		Somatic	439	1	0.0022779		WXS	Illumina HiSeq	Phase_I	237	185	0.780591	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Silent	SNP	ENST00000354181.3	37	CCDS58352.1																																																																																			G|0.751;A|0.249	0.249	strong		0.448	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
SLC7A8	23428	hgsc.bcm.edu	37	14	23598976	23598976	+	Silent	SNP	G	G	A	rs17183863	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23598976G>A	ENST00000316902.7	-	9	1871	c.1146C>T	c.(1144-1146)agC>agT	p.S382S	SLC7A8_ENST00000422941.2_Silent_p.S158S|SLC7A8_ENST00000469263.1_Intron|SLC7A8_ENST00000529705.2_Silent_p.S277S|SLC7A8_ENST00000453702.1_Silent_p.S179S	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	382					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)	TGTACATGTCGCTGGTGACCA	0.498													G|||	524	0.104633	0.1331	0.0778	5008	,	,		20700	0.1438		0.0606	False		,,,				2504	0.09				p.S382S		Atlas-SNP	.											.	SLC7A8	54	.	0			c.C1146T						PASS	.	G	,	598,3808	262.2+/-264.8	43,512,1648	226.0	195.0	206.0		1146,537	-9.6	0.6	14	dbSNP_123	206	578,8022	154.9+/-209.1	19,540,3741	no	coding-synonymous,coding-synonymous	SLC7A8	NM_012244.2,NM_182728.1	,	62,1052,5389	AA,AG,GG		6.7209,13.5724,9.042	,	382/536,179/333	23598976	1176,11830	2203	4300	6503	SO:0001819	synonymous_variant	23428	exon9			CATGTCGCTGGTG	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.1146C>T	14.37:g.23598976G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	176	67	0.380682	NM_012244	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Silent	SNP	ENST00000316902.7	37	CCDS9590.1	235	0.10760073260073261	78	0.15853658536585366	26	0.0718232044198895	87	0.1520979020979021	44	0.05804749340369393	G	9.529	1.110304	0.20714	0.135724	0.067209	ENSG00000092068	ENST00000334354	.	.	.	5.86	-9.58	0.00559	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	20.7128	0.99707	0.8442:0.0:0.1558:0.0	rs17183863;rs17854736;rs52824765;rs58569778;rs17183863	.	.	.	X	179	.	ENSP00000334744:R179X	R	-	1	2	SLC7A8	22668816	0.000000	0.05858	0.616000	0.29078	0.953000	0.61014	-2.118000	0.01325	-2.000000	0.00965	-1.727000	0.00703	CGA	G|0.901;A|0.099	0.099	strong		0.498	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3		
EIF2B4	8890	hgsc.bcm.edu	37	2	27590666	27590666	+	Silent	SNP	C	C	T	rs41288829	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:27590666C>T	ENST00000347454.4	-	8	900	c.729G>A	c.(727-729)ccG>ccA	p.P243P	SNX17_ENST00000537606.1_5'Flank|AC074117.10_ENST00000412749.1_RNA|SNX17_ENST00000233575.2_5'Flank|EIF2B4_ENST00000451130.2_Silent_p.P263P|SNX17_ENST00000543024.1_5'Flank|EIF2B4_ENST00000493344.2_Silent_p.P264P|EIF2B4_ENST00000445933.2_Silent_p.P242P	NM_001034116.1|NM_015636.3	NP_001029288.1|NP_056451.3	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	243					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation (GO:0045947)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translation (GO:0006417)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(5)|skin(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCATTAGGCGGTGTTGTGT	0.458													C|||	50	0.00998403	0.0015	0.0144	5008	,	,		2100	0.0		0.0328	False		,,,				2504	0.0051				p.P263P		Atlas-SNP	.											.	EIF2B4	48	.	0			c.G789A						PASS	.	C	,,	27,4379	32.6+/-62.9	0,27,2176	101.0	92.0	95.0		729,726,789	-7.1	0.9	2	dbSNP_127	95	213,8387	90.4+/-152.6	2,209,4089	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF2B4	NM_001034116.1,NM_015636.3,NM_172195.3	,,	2,236,6265	TT,TC,CC		2.4767,0.6128,1.8453	,,	243/524,242/523,263/544	27590666	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	8890	exon7			ATTAGGCGGTGTT	AJ011306	CCDS33164.1, CCDS46244.1, CCDS46245.1	2p23.3	2008-02-05	2002-08-29		ENSG00000115211	ENSG00000115211			3260	protein-coding gene	gene with protein product		606687	"""eukaryotic translation initiation factor 2B, subunit 4 (delta, 67kD)"""			8929216, 7982969	Standard	NM_172195		Approved	EIF2Bdelta, EIF-2B, DKFZP586J0119, EIF2B	uc002rjz.3	Q9UI10	OTTHUMG00000151927	ENST00000347454.4:c.729G>A	2.37:g.27590666C>T		Somatic	345	0	0		WXS	Illumina HiSeq	Phase_I	291	137	0.47079	NM_172195	Q53RY7|Q5BJF4|Q9BUV9|Q9UBG4|Q9UIQ9|Q9UJ95	Silent	SNP	ENST00000347454.4	37	CCDS33164.1																																																																																			C|0.981;T|0.019	0.019	strong		0.458	EIF2B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324448.1		
C8orf34	116328	hgsc.bcm.edu	37	8	69699756	69699756	+	Missense_Mutation	SNP	G	G	A	rs16935065	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:69699756G>A	ENST00000539993.1	+	12	1825	c.1276G>A	c.(1276-1278)Gca>Aca	p.A426T	C8orf34_ENST00000518698.1_Missense_Mutation_p.A512T|C8orf34_ENST00000337103.4_Missense_Mutation_p.A401T|C8orf34_ENST00000325233.3_Missense_Mutation_p.A170T			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	426			A -> T (in dbSNP:rs16935065). {ECO:0000269|PubMed:15489334}.							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)			AGGAGTGGAAGCAGAACAAGA	0.353													G|||	843	0.168331	0.2784	0.0965	5008	,	,		17608	0.124		0.1521	False		,,,				2504	0.1329				p.A512T		Atlas-SNP	.											.	C8orf34	170	.	0			c.G1534A						PASS	.	G	THR/ALA	1040,3364	379.7+/-323.4	130,780,1292	110.0	99.0	102.0		1534	-0.3	1.0	8	dbSNP_123	102	1339,7261	258.4+/-282.1	99,1141,3060	yes	missense	C8orf34	NM_052958.2	58	229,1921,4352	AA,AG,GG		15.5698,23.6149,18.2944	benign	512/539	69699756	2379,10625	2202	4300	6502	SO:0001583	missense	116328	exon12			GTGGAAGCAGAAC	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.1276G>A	8.37:g.69699756G>A	ENSP00000438159:p.Ala426Thr	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	119	82	0.689076	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Missense_Mutation	SNP	ENST00000539993.1	37		356	0.163003663003663	124	0.25203252032520324	34	0.09392265193370165	72	0.1258741258741259	126	0.1662269129287599	G	17.35	3.368334	0.61513	0.236149	0.155698	ENSG00000165084	ENST00000518698;ENST00000539993;ENST00000337103;ENST00000325233	T;T;T;T	0.54675	0.58;0.65;0.64;0.56	5.36	-0.339	0.12647	.	0.700302	0.12960	N	0.425071	T	0.00012	0.0000	N	0.19112	0.55	0.38403	P	0.05427199999999999	B	0.02656	0.0	B	0.06405	0.002	T	0.25916	-1.0118	8	.	.	.	-3.0872	5.0911	0.14708	0.3637:0.2059:0.4304:0.0	rs16935065;rs52799884;rs16935065	426	Q49A92	CH034_HUMAN	T	512;426;401;170	ENSP00000427820:A512T;ENSP00000438159:A426T;ENSP00000337174:A401T;ENSP00000319532:A170T	.	A	+	1	0	C8orf34	69862310	0.998000	0.40836	0.956000	0.39512	0.994000	0.84299	0.396000	0.20867	0.006000	0.14734	0.655000	0.94253	GCA	G|0.813;A|0.187	0.187	strong		0.353	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958	
AP3D1	8943	hgsc.bcm.edu	37	19	2110746	2110746	+	Silent	SNP	G	G	A	rs20567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2110746G>A	ENST00000345016.5	-	25	3180	c.2949C>T	c.(2947-2949)tcC>tcT	p.S983S	AP3D1_ENST00000356926.4_Silent_p.S942S|AP3D1_ENST00000350812.6_Silent_p.S814S|AP3D1_ENST00000355272.6_Silent_p.S1045S	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	983					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)		CATCGTGGACGGAGGAGCCCT	0.672													A|||	1628	0.32508	0.4879	0.2075	5008	,	,		16934	0.3333		0.1968	False		,,,				2504	0.3119				p.S1045S		Atlas-SNP	.											.	AP3D1	81	.	0			c.C3135T						PASS	.	A	,	1968,2386		426,1116,635	22.0	28.0	26.0		2826,2949	-9.6	0.0	19	dbSNP_67	26	1888,6670		219,1450,2610	no	coding-synonymous,coding-synonymous	AP3D1	NM_001077523.1,NM_003938.5	,	645,2566,3245	AA,AG,GG		22.0612,45.1998,29.8637	,	942/1113,983/1154	2110746	3856,9056	2177	4279	6456	SO:0001819	synonymous_variant	8943	exon27			GTGGACGGAGGAG	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.2949C>T	19.37:g.2110746G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																			G|0.672;N|0.000	.	strong		0.672	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
ZSWIM2	151112	hgsc.bcm.edu	37	2	187692983	187692983	+	Missense_Mutation	SNP	T	T	C	rs17856918	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187692983T>C	ENST00000295131.2	-	9	1669	c.1630A>G	c.(1630-1632)Atg>Gtg	p.M544V		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	544				M -> V (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			CCTTTGGTCATCCGGCTTAGA	0.398													T|||	873	0.174321	0.4213	0.1066	5008	,	,		14139	0.0218		0.1103	False		,,,				2504	0.1115				p.M544V		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A1630G						PASS	.	T	VAL/MET	1752,2654	511.2+/-367.7	346,1060,797	97.0	92.0	94.0		1630	5.5	0.0	2	dbSNP_123	94	977,7623	209.8+/-250.9	44,889,3367	yes	missense	ZSWIM2	NM_182521.2	21	390,1949,4164	CC,CT,TT		11.3605,39.764,20.9826	benign	544/634	187692983	2729,10277	2203	4300	6503	SO:0001583	missense	151112	exon9			TGGTCATCCGGCT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1630A>G	2.37:g.187692983T>C	ENSP00000295131:p.Met544Val	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	250	139	0.556	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	T	1.692	-0.503653	0.04261	0.39764	0.113605	ENSG00000163012	ENST00000295131	T	0.21361	2.01	5.46	5.46	0.80206	.	0.613366	0.15829	N	0.242594	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.12630	0.006	B	0.08055	0.003	T	0.45352	-0.9267	9	0.26408	T	0.33	0.2554	11.9266	0.52823	0.0:0.0:0.0:1.0	rs17856918;rs17856918	544	Q8NEG5	ZSWM2_HUMAN	V	544	ENSP00000295131:M544V	ENSP00000295131:M544V	M	-	1	0	ZSWIM2	187401228	0.950000	0.32346	0.013000	0.15412	0.031000	0.12232	2.484000	0.45242	2.088000	0.63022	0.402000	0.26972	ATG	T|0.813;C|0.187	0.187	strong		0.398	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
KNG1	3827	hgsc.bcm.edu	37	3	186437944	186437944	+	Silent	SNP	T	T	C	rs5029980	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:186437944T>C	ENST00000265023.4	+	2	458	c.246T>C	c.(244-246)gaT>gaC	p.D82D	KNG1_ENST00000447445.1_Silent_p.D82D|RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000287611.2_Silent_p.D82D	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	82	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)	p.D82D(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)		AGGAGGGGGATTGTCCTGTTC	0.468													T|||	488	0.0974441	0.0567	0.1455	5008	,	,		17100	0.0595		0.1272	False		,,,				2504	0.1268				p.D82D		Atlas-SNP	.											KNG1_ENST00000265023,NS,carcinoma,0,2	KNG1	129	2	2	Substitution - coding silent(2)	stomach(2)	c.T246C						PASS	.	T	,,	302,4104	165.8+/-197.2	9,284,1910	129.0	118.0	122.0		246,246,246	-3.3	0.1	3	dbSNP_113	122	960,7640	210.0+/-251.0	60,840,3400	no	coding-synonymous,coding-synonymous,coding-synonymous	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,,	69,1124,5310	CC,CT,TT		11.1628,6.8543,9.7032	,,	82/428,82/645,82/392	186437944	1262,11744	2203	4300	6503	SO:0001819	synonymous_variant	3827	exon2			GGGGGATTGTCCT		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.246T>C	3.37:g.186437944T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_000893	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Silent	SNP	ENST00000265023.4	37	CCDS43183.1																																																																																			T|0.907;C|0.093	0.093	strong		0.468	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
FCN2	2220	hgsc.bcm.edu	37	9	137775155	137775155	+	Silent	SNP	T	T	C	rs4520243	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	100	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	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	
POGLUT1	56983	hgsc.bcm.edu	37	3	119196166	119196166	+	Silent	SNP	T	T	C	rs3732420	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:119196166T>C	ENST00000295588.4	+	4	411	c.327T>C	c.(325-327)agT>agC	p.S109S		NM_152305.2	NP_689518.1	Q8NBL1	PGLT1_HUMAN	protein O-glucosyltransferase 1	109					cardiovascular system development (GO:0072358)|Notch signaling pathway (GO:0007219)|protein O-linked glycosylation (GO:0006493)|regulation of Notch signaling pathway (GO:0008593)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	glucosyltransferase activity (GO:0046527)|protein xylosyltransferase activity (GO:0030158)|UDP-glucosyltransferase activity (GO:0035251)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(1)	16						ACAGGTGTAGTGGTGTTGAGC	0.468													T|||	596	0.11901	0.0136	0.2305	5008	,	,		21369	0.123		0.169	False		,,,				2504	0.1268				p.S109S		Atlas-SNP	.											.	POGLUT1	32	.	0			c.T327C						PASS	.	T		188,4218	118.0+/-155.7	6,176,2021	183.0	178.0	180.0		327	1.6	1.0	3	dbSNP_107	180	1636,6964	303.2+/-306.3	163,1310,2827	no	coding-synonymous	POGLUT1	NM_152305.2		169,1486,4848	CC,CT,TT		19.0233,4.2669,14.0243		109/393	119196166	1824,11182	2203	4300	6503	SO:0001819	synonymous_variant	56983	exon4			GTGTAGTGGTGTT	BC030614	CCDS2988.1	3q13.33	2010-09-29	2010-09-29	2010-09-29	ENSG00000163389	ENSG00000163389			22954	protein-coding gene	gene with protein product	"""KDELC family like 1"""	615618	"""chromosome 3 open reading frame 9"", ""KTEL (Lys-Tyr-Glu-Leu) containing 1"""	C3orf9, KTELC1		16524674	Standard	NM_152305		Approved	MDS010, MGC32995, 9630046K23Rik, MDSRP, hCLP46, KDELCL1, Rumi	uc003ecm.3	Q8NBL1	OTTHUMG00000159379	ENST00000295588.4:c.327T>C	3.37:g.119196166T>C		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	207	95	0.458937	NM_152305	B2RD13|Q53GJ4|Q8N2T1	Silent	SNP	ENST00000295588.4	37	CCDS2988.1	279	0.12774725274725274	10	0.02032520325203252	65	0.17955801104972377	79	0.1381118881118881	125	0.16490765171503957	T	10.66	1.412246	0.25465	0.042669	0.190233	ENSG00000163389	ENST00000476573	.	.	.	5.26	1.57	0.23409	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11108	-1.0601	3	.	.	.	-7.4987	6.8594	0.24058	0.0:0.2755:0.0:0.7245	rs3732420;rs17852786;rs3732420	.	.	.	R	96	.	.	W	+	1	0	POGLUT1	120678856	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.215000	0.32431	0.479000	0.27511	0.533000	0.62120	TGG	T|0.860;C|0.140	0.140	strong		0.468	POGLUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355034.2	NM_152305	
PEX5	5830	hgsc.bcm.edu	37	12	7343153	7343153	+	Intron	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7343153A>G	ENST00000455147.2	+	3	727				RP11-273B20.3_ENST00000545794.1_RNA|PEX5_ENST00000420616.2_Intron|PEX5_ENST00000266564.3_Intron|PEX5_ENST00000412720.2_Intron|PEX5_ENST00000434354.2_Silent_p.A60A|PEX5_ENST00000266563.5_Intron|PEX5_ENST00000545220.1_Intron|RP11-273B20.3_ENST00000543061.1_RNA	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5						cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						GCCCAGGTGCAGCCTCTGAGG	0.627																																					p.A60A		Atlas-SNP	.											PEX5_ENST00000434354,colon,carcinoma,0,3	PEX5	63	3	0			c.A180G						scavenged	.						9.0	11.0	11.0					12																	7343153		2154	4209	6363	SO:0001627	intron_variant	5830	exon2			AGGTGCAGCCTCT	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"""Tetratricopeptide (TTC) repeat domain containing"""	9719	protein-coding gene	gene with protein product		600414	"""peroxisome receptor 1"""	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.147+33A>G	12.37:g.7343153A>G		Somatic	49	2	0.0408163		WXS	Illumina HiSeq	Phase_I	61	6	0.0983607	NM_001131023	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Silent	SNP	ENST00000455147.2	37	CCDS44823.1																																																																																			.	.	none		0.627	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319	
AOC3	8639	hgsc.bcm.edu	37	17	41004625	41004625	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:41004625C>T	ENST00000308423.2	+	1	1425	c.1265C>T	c.(1264-1266)cCc>cTc	p.P422L	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	422					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)	TCCCAGGCCCCCAAGACAATA	0.582																																					p.P422L	NSCLC(3;192 220 10664 11501 16477)	Atlas-SNP	.											AOC3,NS,neuroblastoma,0,1	AOC3	88	1	0			c.C1265T						scavenged	.						85.0	76.0	79.0					17																	41004625		2203	4300	6503	SO:0001583	missense	8639	exon1			AGGCCCCCAAGAC	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.1265C>T	17.37:g.41004625C>T	ENSP00000312326:p.Pro422Leu	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	316	4	0.0126582	NM_003734	B2RCI5|K7ESB3|L0L8N9|Q45F94	Missense_Mutation	SNP	ENST00000308423.2	37	CCDS11444.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.142695	0.57044	.	.	ENSG00000131471	ENST00000308423	T	0.04015	3.73	4.64	4.64	0.57946	Copper amine oxidase, C-terminal (3);	0.191114	0.45867	D	0.000325	T	0.18635	0.0447	M	0.87381	2.88	0.80722	D	1	P	0.50528	0.936	P	0.54629	0.757	T	0.00277	-1.1854	10	0.59425	D	0.04	.	13.0901	0.59162	0.1604:0.8396:0.0:0.0	.	422	Q16853	AOC3_HUMAN	L	422	ENSP00000312326:P422L	ENSP00000312326:P422L	P	+	2	0	AOC3	38258151	0.030000	0.19436	0.913000	0.36048	0.485000	0.33311	1.933000	0.40153	2.591000	0.87537	0.591000	0.81541	CCC	.	.	none		0.582	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734	
ABCC11	85320	hgsc.bcm.edu	37	16	48226458	48226458	+	Silent	SNP	C	C	T	rs144318062		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:48226458C>T	ENST00000394747.1	-	19	3028	c.2679G>A	c.(2677-2679)acG>acA	p.T893T	ABCC11_ENST00000356608.2_Silent_p.T893T|ABCC11_ENST00000537808.1_3'UTR|ABCC11_ENST00000394748.1_Silent_p.T893T|ABCC11_ENST00000353782.5_Silent_p.T893T	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	893	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|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)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TGTGCAGGGCCGTGGATGCCT	0.552																																					p.T893T		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2679A						PASS	.	C	,,	0,4402		0,0,2201	90.0	82.0	85.0		2679,2679,2679	-9.9	0.0	16	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,,	893/1383,893/1383,893/1345	48226458	1,13001	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon19			CAGGGCCGTGGAT	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2679G>A	16.37:g.48226458C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	141	116	0.822695	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			C|1.000;T|0.000	0.000	weak		0.552	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
C1QA	712	hgsc.bcm.edu	37	1	22965438	22965438	+	Silent	SNP	A	A	G	rs172378	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:22965438A>G	ENST00000374642.3	+	3	480	c.276A>G	c.(274-276)ggA>ggG	p.G92G	C1QA_ENST00000402322.1_Silent_p.G92G	NM_015991.2	NP_057075.1	P02745	C1QA_HUMAN	complement component 1, q subcomponent, A chain	92	Collagen-like.				cell-cell signaling (GO:0007267)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|liver(1)|lung(3)|skin(1)	6		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;6.41e-27)|Colorectal(126;1.52e-07)|COAD - Colon adenocarcinoma(152;1.12e-05)|GBM - Glioblastoma multiforme(114;1.63e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000541)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.197)	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)	GCCCCCTCGGAGCCCGTGGCA	0.662													G|||	3087	0.616414	0.7905	0.5965	5008	,	,		14379	0.6111		0.3956	False		,,,				2504	0.6278				p.G92G		Atlas-SNP	.											.	C1QA	31	.	0			c.A276G						PASS	.	G		3110,1270		1153,804,233	11.0	15.0	14.0		276	-2.6	0.0	1	dbSNP_79	14	3215,5367		655,1905,1731	no	coding-synonymous	C1QA	NM_015991.2		1808,2709,1964	GG,GA,AA		37.4621,28.9954,48.7965		92/246	22965438	6325,6637	2190	4291	6481	SO:0001819	synonymous_variant	712	exon3			CCTCGGAGCCCGT	AF135157	CCDS226.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173372	ENSG00000173372		"""Complement system"""	1241	protein-coding gene	gene with protein product		120550	"""complement component 1, q subcomponent, alpha polypeptide"""			1537612	Standard	NM_015991		Approved		uc001bfy.3	P02745	OTTHUMG00000002893	ENST00000374642.3:c.276A>G	1.37:g.22965438A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	57	9	0.157895	NM_015991	B2R4X2|Q5T963	Silent	SNP	ENST00000374642.3	37	CCDS226.1	1278	0.5851648351648352	396	0.8048780487804879	211	0.5828729281767956	367	0.6416083916083916	304	0.40105540897097625	G	0.191	-1.053646	0.01965	0.710046	0.374621	ENSG00000173372	ENST00000339353	.	.	.	5.48	-2.62	0.06152	.	0.948505	0.08607	N	0.920650	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999274	.	.	.	.	.	.	T	0.43653	-0.9378	5	0.02654	T	1	0.056	0.3476	0.00343	0.2294:0.1928:0.2583:0.3196	rs172378;rs647404;rs3767552;rs17852737;rs17886668;rs60395382	.	.	.	G	90	.	ENSP00000341271:E90G	E	+	2	0	C1QA	22838025	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.296000	0.08287	-0.601000	0.05783	-0.215000	0.12644	GAG	A|0.431;C|0.013	.	strong		0.662	C1QA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008087.2	NM_015991	
SSPO	23145	hgsc.bcm.edu	37	7	149485557	149485557	+	RNA	SNP	C	C	T	rs73168056	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149485557C>T	ENST00000378016.2	+	0	3963							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)			CTCTGCTGCACGGTGTGTAGA	0.652													C|||	65	0.0129792	0.0008	0.0548	5008	,	,		20320	0.0		0.0209	False		,,,				2504	0.0051				p.H1321H		Atlas-SNP	.											.	.	.	.	0			c.C3963T						PASS	.	C		18,4176		1,16,2080	34.0	41.0	39.0		3967	-6.3	0.6	7	dbSNP_130	39	136,8306		1,134,4086	yes	coding-notMod3-near-splice	SSPO	NM_198455.2		2,150,6166	TT,TC,CC		1.611,0.4292,1.2187			149485557	154,12482	2097	4221	6318			23145	exon27			GCTGCACGGTGTG	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.149485557C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	86	15	0.174419	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.986;T|0.014	0.014	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
IHH	3549	hgsc.bcm.edu	37	2	219920565	219920565	+	Silent	SNP	C	C	T	rs3731878	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219920565C>T	ENST00000295731.6	-	3	599	c.600G>A	c.(598-600)acG>acA	p.T200T	MIR3131_ENST00000583592.1_RNA	NM_002181.3	NP_002172.2	Q14623	IHH_HUMAN	indian hedgehog	200					bone resorption (GO:0045453)|camera-type eye photoreceptor cell fate commitment (GO:0060220)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|chondrocyte proliferation (GO:0035988)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint development (GO:0072498)|epithelial cell morphogenesis (GO:0003382)|epithelial cell-cell adhesion (GO:0090136)|head morphogenesis (GO:0060323)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intein-mediated protein splicing (GO:0016539)|maternal process involved in female pregnancy (GO:0060135)|multicellular organism growth (GO:0035264)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of eye pigmentation (GO:0048074)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell differentiation in thymus (GO:0033085)|neuron development (GO:0048666)|osteoblast differentiation (GO:0001649)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of growth (GO:0040008)|response to estradiol (GO:0032355)|retinal pigment epithelium development (GO:0003406)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|somite development (GO:0061053)|vitelline membrane formation (GO:0030704)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|patched binding (GO:0005113)|peptidase activity (GO:0008233)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCAGCCGCCCGTCTTGGCTG	0.672													C|||	551	0.110024	0.1104	0.0951	5008	,	,		16118	0.1617		0.0865	False		,,,				2504	0.091				p.T200T		Atlas-SNP	.											.	IHH	33	.	0			c.G600A						PASS	.	C		421,3975		30,361,1807	16.0	18.0	18.0		600	-5.4	1.0	2	dbSNP_107	18	670,7918		28,614,3652	no	coding-synonymous	IHH	NM_002181.3		58,975,5459	TT,TC,CC		7.8016,9.5769,8.4026		200/412	219920565	1091,11893	2198	4294	6492	SO:0001819	synonymous_variant	3549	exon3			GCCGCCCGTCTTG	L38517	CCDS33380.1	2q33-q35	2013-02-15	2013-02-15		ENSG00000163501	ENSG00000163501			5956	protein-coding gene	gene with protein product		600726	"""Indian hedgehog (Drosophila) homolog"", ""Indian hedgehog homolog (Drosophila)"""			7590746, 14770182	Standard	NM_002181		Approved	HHG2, BDA1	uc002vjo.2	Q14623	OTTHUMG00000154631	ENST00000295731.6:c.600G>A	2.37:g.219920565C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_002181	B9EGM5|O43322|Q8N4B9	Silent	SNP	ENST00000295731.6	37	CCDS33380.1																																																																																			C|0.902;T|0.098	0.098	strong		0.672	IHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336408.2	NM_002181	
CHD6	84181	hgsc.bcm.edu	37	20	40080586	40080586	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:40080586G>A	ENST00000373233.3	-	22	3580	c.3403C>T	c.(3403-3405)Cgt>Tgt	p.R1135C	CHD6_ENST00000309279.7_Missense_Mutation_p.R618C	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1135					ATP catabolic process (GO:0006200)|chromatin modification (GO:0016568)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|transcription cofactor binding (GO:0001221)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(24)|lung(53)|ovary(8)|prostate(5)|skin(8)|stomach(1)|urinary_tract(9)	129		Myeloproliferative disorder(115;0.00425)				AGGAGGGCACGGCAAATCATC	0.512																																					p.R1135C		Atlas-SNP	.											CHD6,NS,lymphoid_neoplasm,+1,3	CHD6	312	3	0			c.C3403T						scavenged	.						190.0	155.0	167.0					20																	40080586		2203	4300	6503	SO:0001583	missense	84181	exon22			GGGCACGGCAAAT	AF525085	CCDS13317.1	20q12	2003-03-07			ENSG00000124177	ENSG00000124177			19057	protein-coding gene	gene with protein product						11889561	Standard	NM_032221		Approved	KIAA1335, FLJ22369, dJ620E11.1, CHD5, RIGB	uc002xka.1	Q8TD26	OTTHUMG00000032487	ENST00000373233.3:c.3403C>T	20.37:g.40080586G>A	ENSP00000362330:p.Arg1135Cys	Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	346	4	0.0115607	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.174118	0.78452	.	.	ENSG00000124177	ENST00000373233;ENST00000309279	D;D	0.87256	-2.23;-2.23	5.79	4.83	0.62350	.	0.000000	0.56097	D	0.000032	D	0.93638	0.7968	M	0.86268	2.805	0.42403	D	0.992574	D	0.89917	1.0	D	0.91635	0.999	D	0.94319	0.7552	10	0.59425	D	0.04	-14.5265	14.1103	0.65118	0.0:0.0:0.7278:0.2722	.	1135	Q8TD26	CHD6_HUMAN	C	1135;618	ENSP00000362330:R1135C;ENSP00000308684:R618C	ENSP00000308684:R618C	R	-	1	0	CHD6	39514000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.229000	0.58625	1.421000	0.47157	0.650000	0.86243	CGT	.	.	none		0.512	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1		
KLHL30	377007	hgsc.bcm.edu	37	2	239059610	239059610	+	Silent	SNP	C	C	T	rs61736173	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:239059610C>T	ENST00000409223.1	+	8	1748	c.1641C>T	c.(1639-1641)ggC>ggT	p.G547G	KLHL30_ENST00000305959.4_Silent_p.G529G			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	547										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)		CCCGCCACGGCGCCCTGCCCC	0.682													c|||	172	0.034345	0.0711	0.0317	5008	,	,		13240	0.0		0.0517	False		,,,				2504	0.0041				p.G547G		Atlas-SNP	.											.	KLHL30	79	.	0			c.C1641T						PASS	.	T		255,3769		9,237,1766	8.0	14.0	12.0		1641	-0.5	1.0	2	dbSNP_129	12	387,7855		11,365,3745	no	coding-synonymous	KLHL30	NM_198582.3		20,602,5511	TT,TC,CC		4.6955,6.337,5.234		547/579	239059610	642,11624	2012	4121	6133	SO:0001819	synonymous_variant	377007	exon8			CCACGGCGCCCTG		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.1641C>T	2.37:g.239059610C>T		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	191	115	0.602094	NM_198582	Q6ZUS1	Silent	SNP	ENST00000409223.1	37	CCDS46555.2																																																																																			C|0.961;T|0.039	0.039	strong		0.682	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
CGRRF1	10668	hgsc.bcm.edu	37	14	55005083	55005083	+	Silent	SNP	C	C	T	rs202061859		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:55005083C>T	ENST00000216420.7	+	6	1113	c.981C>T	c.(979-981)gaC>gaT	p.D327D		NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1	327					cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|lung(5)|ovary(2)|stomach(1)	13						AAGATAAAGACAAACCGAAGA	0.383																																					p.D327D		Atlas-SNP	.											.	CGRRF1	30	.	0			c.C981T						PASS	.	C		0,4406		0,0,2203	71.0	67.0	69.0		981	1.5	0.2	14		69	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CGRRF1	NM_006568.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		327/333	55005083	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10668	exon6			TAAAGACAAACCG	BC015063	CCDS9719.1	14q22.2	2013-09-20			ENSG00000100532	ENSG00000100532		"""RING-type (C3HC4) zinc fingers"""	15528	protein-coding gene	gene with protein product		606138				8968090	Standard	NM_006568		Approved	CGR19, RNF197	uc001xay.3	Q99675	OTTHUMG00000140308	ENST00000216420.7:c.981C>T	14.37:g.55005083C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	32	0.326531	NM_006568	Q96BX2	Silent	SNP	ENST00000216420.7	37	CCDS9719.1																																																																																			C|0.999;T|0.001	0.001	weak		0.383	CGRRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276905.2	NM_006568	
DHRS13	147015	hgsc.bcm.edu	37	17	27228198	27228198	+	Silent	SNP	G	G	A	rs4795474	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:27228198G>A	ENST00000378895.4	-	4	618	c.492C>T	c.(490-492)cgC>cgT	p.R164R	DHRS13_ENST00000426464.2_Silent_p.R83R|RP11-20B24.4_ENST00000579187.1_RNA|RP11-20B24.4_ENST00000580603.1_RNA|DHRS13_ENST00000581974.1_5'Flank|DHRS13_ENST00000394901.3_Silent_p.R114R	NM_144683.3	NP_653284.2	Q6UX07	DHR13_HUMAN	dehydrogenase/reductase (SDR family) member 13	164						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)			CCACCACCACGCGGCTAGGGG	0.627													G|||	702	0.140176	0.0794	0.1801	5008	,	,		17429	0.0754		0.1163	False		,,,				2504	0.2853				p.R164R		Atlas-SNP	.											DHRS13,NS,carcinoma,-1,1	DHRS13	22	1	0			c.C492T						PASS	.	G		430,3976	206.5+/-228.1	31,368,1804	79.0	80.0	80.0		492	-10.6	0.2	17	dbSNP_111	80	1064,7536	223.1+/-260.0	71,922,3307	no	coding-synonymous	DHRS13	NM_144683.3		102,1290,5111	AA,AG,GG		12.3721,9.7594,11.487		164/378	27228198	1494,11512	2203	4300	6503	SO:0001819	synonymous_variant	147015	exon4			CACCACGCGGCTA	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.492C>T	17.37:g.27228198G>A		Somatic	283	1	0.00353357		WXS	Illumina HiSeq	Phase_I	281	145	0.516014	NM_144683	Q96BH7	Silent	SNP	ENST00000378895.4	37	CCDS11246.2																																																																																			G|0.885;A|0.115	0.115	strong		0.627	DHRS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255952.1	NM_144683	
TPSAB1	7177	hgsc.bcm.edu	37	16	1291621	1291621	+	Silent	SNP	C	C	T	rs372314315	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1291621C>T	ENST00000338844.3	+	4	453	c.420C>T	c.(418-420)gtC>gtT	p.V140V	TPSAB1_ENST00000461509.2_Silent_p.V147V	NM_003294.3	NP_003285.2	Q15661	TRYB1_HUMAN	tryptase alpha/beta 1	140	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				defense response (GO:0006952)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|skin(1)	10		Hepatocellular(780;0.00369)				TCCACACGGTCACCCTGCCCC	0.657													C|||	141	0.028155	0.0045	0.0303	5008	,	,		17950	0.0119		0.0427	False		,,,				2504	0.0603				p.V140V		Atlas-SNP	.											TPSAB1,NS,carcinoma,0,1	TPSAB1	24	1	0			c.C420T						PASS	.						29.0	24.0	25.0					16																	1291621		2198	4297	6495	SO:0001819	synonymous_variant	7177	exon4			CACGGTCACCCTG	M33494	CCDS10431.1	16p13.3	2009-11-13	2004-10-14	2004-10-15	ENSG00000172236	ENSG00000172236			12019	protein-coding gene	gene with protein product	"""tryptase alpha II"", ""tryptase beta I"", ""tryptase-I"", ""tryptase-II"", ""tryptase-III"""	191080	"""tryptase beta 1"""	TPSB1, TPS1, TPS2		2203827, 9920877	Standard	NM_003294		Approved		uc002ckz.3	Q15661	OTTHUMG00000090467	ENST00000338844.3:c.420C>T	16.37:g.1291621C>T		Somatic	417	1	0.00239808		WXS	Illumina HiSeq	Phase_I	708	173	0.24435	NM_003294	D2E6R9|D2E6S1|P15157|Q15663|Q6B052|Q9H2Y4|Q9H2Y5|Q9UQI1	Silent	SNP	ENST00000338844.3	37	CCDS10431.1																																																																																			.	.	weak		0.657	TPSAB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000206914.1	NM_003294	
SSPO	23145	hgsc.bcm.edu	37	7	149519742	149519742	+	RNA	SNP	G	G	A	rs201102091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149519742G>A	ENST00000378016.2	+	0	13232							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)			GGCCACTTCCGGCCTTGCCTT	0.687													G|||	6	0.00119808	0.0	0.0029	5008	,	,		15642	0.0		0.003	False		,,,				2504	0.001				p.R4411Q		Atlas-SNP	.											.	.	.	.	0			c.G13232A						PASS	.	G		5,3807		0,5,1901	6.0	8.0	8.0		13246	4.0	1.0	7		8	36,8100		0,36,4032	yes	coding-notMod3	SSPO	NM_198455.2		0,41,5933	AA,AG,GG		0.4425,0.1312,0.3432			149519742	41,11907	1906	4068	5974			23145	exon91			ACTTCCGGCCTTG	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.149519742G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	48	11	0.229167	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.	.	weak		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CXXC1	30827	hgsc.bcm.edu	37	18	47810351	47810351	+	Silent	SNP	A	A	G	rs7228084	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:47810351A>G	ENST00000285106.6	-	10	2040	c.1326T>C	c.(1324-1326)acT>acC	p.T442T	MBD1_ENST00000269468.5_5'Flank|CXXC1_ENST00000412036.2_Silent_p.T446T|MBD1_ENST00000398493.1_5'Flank|MBD1_ENST00000436910.1_5'Flank|MBD1_ENST00000353909.3_5'Flank|MBD1_ENST00000269471.5_5'Flank|MBD1_ENST00000424334.2_5'Flank|CXXC1_ENST00000589940.1_Silent_p.T442T|MBD1_ENST00000457839.2_5'Flank|MBD1_ENST00000585595.1_5'Flank|MBD1_ENST00000347968.3_5'Flank|MBD1_ENST00000585672.1_5'Flank|MBD1_ENST00000382948.5_5'Flank|MBD1_ENST00000590208.1_5'Flank|MBD1_ENST00000591416.1_5'Flank|CXXC1_ENST00000587396.1_5'Flank|MBD1_ENST00000339998.6_5'Flank|MBD1_ENST00000587605.1_5'Flank|MBD1_ENST00000349085.2_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	442					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						CCTGAAGGCGAGTGCGGGCAC	0.602													A|||	3578	0.714457	0.5953	0.7709	5008	,	,		21331	0.7907		0.7396	False		,,,				2504	0.7311				p.T446T		Atlas-SNP	.											.	CXXC1	50	.	0			c.T1338C						PASS	.	A	,	2734,1672	655.2+/-399.9	847,1040,316	107.0	97.0	100.0		1338,1326	-5.3	1.0	18	dbSNP_116	100	6192,2408	698.7+/-405.0	2230,1732,338	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	3077,2772,654	GG,GA,AA		28.0,37.9483,31.3701	,	446/661,442/657	47810351	8926,4080	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon10			AAGGCGAGTGCGG	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.1326T>C	18.37:g.47810351A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			A|0.305;G|0.695	0.695	strong		0.602	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593	
MAP2K1	5604	hgsc.bcm.edu	37	15	66727483	66727483	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:66727483G>A	ENST00000307102.5	+	2	730	c.199G>A	c.(199-201)Gac>Aac	p.D67N		NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	67					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|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)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|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)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|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)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)	p.D67N(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	GAAGGATGACGACTTTGAGAA	0.547																																					p.D67N		Atlas-SNP	.											MAP2K1,NS,lymphoid_neoplasm,0,5	MAP2K1	115	5	1	Substitution - Missense(1)	large_intestine(1)	c.G199A	GRCh37	CM076269	MAP2K1	M		PASS	.						188.0	174.0	179.0					15																	66727483		2201	4299	6500	SO:0001583	missense	5604	exon2			GATGACGACTTTG	L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.199G>A	15.37:g.66727483G>A	ENSP00000302486:p.Asp67Asn	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_002755		Missense_Mutation	SNP	ENST00000307102.5	37	CCDS10216.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.691697|5.691697	0.96793|0.96793	.|.	.|.	ENSG00000169032|ENSG00000169032	ENST00000307102|ENST00000425818	D|.	0.93859|.	-3.3|.	5.24|5.24	5.24|5.24	0.73138|0.73138	Protein kinase-like domain (1);|.	0.091006|.	0.85682|.	D|.	0.000000|.	T|T	0.76133|0.76133	0.3945|0.3945	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.993|.	D;P|.	0.64687|.	0.928;0.638|.	T|T	0.76211|0.76211	-0.3042|-0.3042	10|5	0.72032|.	D|.	0.01|.	-32.7633|-32.7633	17.8302|17.8302	0.88680|0.88680	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	45;67|.	B4DFY5;Q02750|.	.;MP2K1_HUMAN|.	N|Q	67|6	ENSP00000302486:D67N|.	ENSP00000302486:D67N|.	D|R	+|+	1|2	0|0	MAP2K1|MAP2K1	64514537|64514537	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.983000|0.983000	0.72400|0.72400	9.723000|9.723000	0.98772|0.98772	2.443000|2.443000	0.82685|0.82685	0.591000|0.591000	0.81541|0.81541	GAC|CGA	.	.	none		0.547	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4		
OR9G1	390174	hgsc.bcm.edu	37	11	56468440	56468440	+	Missense_Mutation	SNP	G	G	T	rs397849038|rs12421330		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56468440G>T	ENST00000312153.1	+	1	577	c.577G>T	c.(577-579)Ggc>Tgc	p.G193C		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						CGAGAAGGGCGGCTATAAAAT	0.478																																					p.G193C		Atlas-SNP	.											.	.	.	.	0			c.G577T						PASS	.						117.0	118.0	118.0					11																	56468440		2201	4296	6497	SO:0001583	missense	504191	exon1			AAGGGCGGCTATA	AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.577G>T	11.37:g.56468440G>T	ENSP00000309012:p.Gly193Cys	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	146	31	0.212329	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	G	5.488	0.275107	0.10403	.	.	ENSG00000174914	ENST00000312153	T	0.00091	8.74	4.52	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.649761	0.14366	N	0.324095	T	0.00241	0.0007	L	0.28400	0.85	0.09310	N	1	P	0.46859	0.885	P	0.62184	0.899	T	0.56208	-0.8017	10	0.72032	D	0.01	-12.3577	8.9994	0.36072	0.2548:0.0:0.7452:0.0	rs12421330	193	Q8NH87	OR9G1_HUMAN	C	193	ENSP00000309012:G193C	ENSP00000309012:G193C	G	+	1	0	OR9G1	56225016	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	-1.080000	0.03407	0.630000	0.30394	-1.202000	0.01658	GGC	G|0.625;T|0.375	0.375	strong		0.478	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213	
OR11H6	122748	hgsc.bcm.edu	37	14	20691888	20691888	+	Missense_Mutation	SNP	C	C	A	rs10140652	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20691888C>A	ENST00000315519.2	+	1	98	c.20C>A	c.(19-21)tCt>tAt	p.S7Y		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	7			S -> Y (in dbSNP:rs10140652).			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)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		attattCATTCTTTGGTTACT	0.373													c|||	498	0.0994409	0.121	0.049	5008	,	,		21282	0.0903		0.0815	False		,,,				2504	0.1339				p.S7Y		Atlas-SNP	.											.	OR11H6	60	.	0			c.C20A						PASS	.	C	TYR/SER	427,3979	198.7+/-222.5	18,391,1794	70.0	75.0	73.0		20	-4.8	0.0	14	dbSNP_119	73	620,7980	153.0+/-207.5	34,552,3714	yes	missense	OR11H6	NM_001004480.1	144	52,943,5508	AA,AC,CC		7.2093,9.6913,8.0501	benign	7/331	20691888	1047,11959	2203	4300	6503	SO:0001583	missense	122748	exon1			TTCATTCTTTGGT		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.20C>A	14.37:g.20691888C>A	ENSP00000319071:p.Ser7Tyr	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	245	84	0.342857	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	204	0.09340659340659341	72	0.14634146341463414	17	0.04696132596685083	53	0.09265734265734266	62	0.08179419525065963	c	8.427	0.847651	0.17034	0.096913	0.072093	ENSG00000176219	ENST00000315519	T	0.00554	6.64	4.53	-4.82	0.03171	.	2.033520	0.02979	U	0.145446	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.20671	0.047	B	0.16289	0.015	T	0.39461	-0.9613	9	0.38643	T	0.18	.	7.818	0.29271	0.0:0.2525:0.129:0.6185	rs10140652;rs52838202;rs58829059;rs10140652	7	Q8NGC7	O11H6_HUMAN	Y	7	ENSP00000319071:S7Y	ENSP00000319071:S7Y	S	+	2	0	OR11H6	19761728	0.000000	0.05858	0.001000	0.08648	0.129000	0.20672	-1.346000	0.02634	-0.847000	0.04168	-0.417000	0.06048	TCT	C|0.909;A|0.091	0.091	strong		0.373	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
ABCA4	24	hgsc.bcm.edu	37	1	94476467	94476467	+	Missense_Mutation	SNP	T	T	A	rs1801466	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:94476467T>A	ENST00000370225.3	-	40	5689	c.5603A>T	c.(5602-5604)aAt>aTt	p.N1868I	ABCA4_ENST00000535881.1_5'UTR|ABCA4_ENST00000465352.1_5'UTR|ABCA4_ENST00000536513.1_Missense_Mutation_p.N138I	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1868			N -> I (slightly reduced retinal- stimulated ATP hydrolysis; dbSNP:rs1801466). {ECO:0000269|PubMed:10958763, ECO:0000269|PubMed:11379881, ECO:0000269|PubMed:11384574, ECO:0000269|PubMed:11527935, ECO:0000269|PubMed:11594993}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		GTGGAACGGATTTGCAGAGTG	0.592													T|||	104	0.0207668	0.0045	0.0274	5008	,	,		19038	0.0		0.0646	False		,,,				2504	0.0143				p.N1868I		Atlas-SNP	.											.	ABCA4	275	.	0			c.A5603T	GRCh37	CM015091	ABCA4	M	rs1801466	PASS	.	T	ILE/ASN	49,4357	50.9+/-86.3	0,49,2154	171.0	129.0	143.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5603	4.8	0.1	1	dbSNP_89	143	572,8028	153.1+/-207.6	16,540,3744	yes	missense	ABCA4	NM_000350.2	149	16,589,5898	AA,AT,TT		6.6512,1.1121,4.7747	possibly-damaging	1868/2274	94476467	621,12385	2203	4300	6503	SO:0001583	missense	24	exon40			AACGGATTTGCAG	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.5603A>T	1.37:g.94476467T>A	ENSP00000359245:p.Asn1868Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	82	12	0.146341	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	63	0.028846153846153848	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	50	0.06596306068601583	T	12.15	1.852683	0.32699	0.011121	0.066512	ENSG00000198691	ENST00000546054;ENST00000370225;ENST00000536513	D;D	0.91631	-2.88;-2.37	4.76	4.76	0.60689	.	0.321128	0.36665	N	0.002461	D	0.91389	0.7283	M	0.81497	2.545	0.80722	D	1	P;P	0.37525	0.598;0.459	B;B	0.42593	0.392;0.175	D	0.93225	0.6612	10	0.87932	D	0	.	14.708	0.69206	0.0:0.0:0.0:1.0	rs1801466;rs52819278	138;1868	B4DWY6;P78363	.;ABCA4_HUMAN	I	660;1868;138	ENSP00000359245:N1868I;ENSP00000439707:N138I	ENSP00000359245:N1868I	N	-	2	0	ABCA4	94249055	0.987000	0.35691	0.139000	0.22197	0.062000	0.15995	3.348000	0.52209	2.111000	0.64477	0.477000	0.44152	AAT	T|0.956;A|0.044	0.044	strong		0.592	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
MOV10L1	54456	hgsc.bcm.edu	37	22	50546666	50546666	+	Missense_Mutation	SNP	C	C	T	rs3810971	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50546666C>T	ENST00000262794.5	+	4	627	c.544C>T	c.(544-546)Cgc>Tgc	p.R182C	MOV10L1_ENST00000545383.1_Missense_Mutation_p.R182C|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000540615.1_Missense_Mutation_p.R162C|MOV10L1_ENST00000395858.3_Missense_Mutation_p.R182C	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	143	0	0		WXS	Illumina HiSeq	Phase_I	157	81	0.515924	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	
TTC7A	57217	hgsc.bcm.edu	37	2	47251469	47251469	+	Missense_Mutation	SNP	G	G	C	rs2304290	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:47251469G>C	ENST00000319190.5	+	14	1980	c.1612G>C	c.(1612-1614)Gtc>Ctc	p.V538L	TTC7A_ENST00000394850.2_Missense_Mutation_p.V538L|TTC7A_ENST00000263737.6_Missense_Mutation_p.V184L|TTC7A_ENST00000461601.1_3'UTR|TTC7A_ENST00000409245.1_Missense_Mutation_p.V504L	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	538			V -> L (in dbSNP:rs2304290). {ECO:0000269|PubMed:17974005}.		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)			CATCCTCTATGTCTCGCTGCA	0.632													G|||	1353	0.270168	0.2156	0.196	5008	,	,		2519	0.6032		0.1332	False		,,,				2504	0.1943				p.V538L		Atlas-SNP	.											.	TTC7A	80	.	0			c.G1612C						PASS	.	G	LEU/VAL	1008,3398	373.4+/-320.8	121,766,1316	93.0	82.0	86.0		1612	2.6	1.0	2	dbSNP_100	86	1215,7385	244.6+/-273.7	93,1029,3178	yes	missense	TTC7A	NM_020458.2	32	214,1795,4494	CC,CG,GG		14.1279,22.8779,17.0921	benign	538/859	47251469	2223,10783	2203	4300	6503	SO:0001583	missense	57217	exon14			CTCTATGTCTCGC	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.1612G>C	2.37:g.47251469G>C	ENSP00000316699:p.Val538Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	164	80	0.487805	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Missense_Mutation	SNP	ENST00000319190.5	37	CCDS33193.1	598	0.27380952380952384	87	0.17682926829268292	71	0.19613259668508287	335	0.5856643356643356	105	0.13852242744063326	G	0.029	-1.344233	0.01277	0.228779	0.141279	ENSG00000068724	ENST00000409245;ENST00000319190;ENST00000394850;ENST00000263737;ENST00000434093	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.43	2.57	0.30868	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.211356	0.41001	N	0.000969	T	0.00012	0.0000	N	0.00793	-1.18	0.31108	P	0.71029	B;B;B;B;B	0.09022	0.002;0.0;0.0;0.0;0.0	B;B;B;B;B	0.08055	0.003;0.001;0.003;0.002;0.001	T	0.45934	-0.9227	9	0.02654	T	1	-29.6049	1.9777	0.03419	0.1736:0.1587:0.5039:0.1638	rs2304290;rs12995476;rs56747692;rs2304290	538;504;538;366;504	Q2T9J9;B3KPK7;Q9ULT0;Q6P0M3;G5E9G4	.;.;TTC7A_HUMAN;.;.	L	504;538;538;184;365	ENSP00000386307:V504L;ENSP00000316699:V538L;ENSP00000378320:V538L;ENSP00000263737:V184L	ENSP00000263737:V184L	V	+	1	0	TTC7A	47104973	0.998000	0.40836	0.996000	0.52242	0.051000	0.14879	1.360000	0.34125	0.626000	0.30322	0.563000	0.77884	GTC	G|0.779;C|0.221	0.221	strong		0.632	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
CATIP	375307	hgsc.bcm.edu	37	2	219221846	219221846	+	Silent	SNP	G	G	A	rs4324314	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	97	0	0		WXS	Illumina HiSeq	Phase_I	76	22	0.289474	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		
NPR3	4883	hgsc.bcm.edu	37	5	32786389	32786389	+	Missense_Mutation	SNP	A	A	G	rs2270915	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:32786389A>G	ENST00000265074.8	+	8	1907	c.1564A>G	c.(1564-1566)Aac>Gac	p.N522D	NPR3_ENST00000415167.2_Missense_Mutation_p.N521D|NPR3_ENST00000434067.2_Missense_Mutation_p.N306D|NPR3_ENST00000415685.2_Missense_Mutation_p.N305D|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	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	265	115	0.433962	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	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388378	1388378	+	Missense_Mutation	SNP	T	T	C	rs55884223	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	209	7	0.0334928		WXS	Illumina HiSeq	Phase_I	190	48	0.252632	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	
ZNF835	90485	hgsc.bcm.edu	37	19	57176304	57176304	+	Missense_Mutation	SNP	T	T	G	rs12460400	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57176304T>G	ENST00000537055.2	-	2	494	c.263A>C	c.(262-264)gAg>gCg	p.E88A		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	88			E -> A (in dbSNP:rs12460400). {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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CTTCGGGCTCTCCCCAGGCGC	0.637													.|||	2007	0.400759	0.4123	0.3732	5008	,	,		15470	0.4702		0.3121	False		,,,				2504	0.4243				p.E88A		Atlas-SNP	.											.	ZNF835	106	.	0			c.A263C						PASS	.	T	ALA/GLU	1630,2550		347,936,807	54.0	59.0	57.0		263	-1.0	0.0	19	dbSNP_120	57	2524,5938		380,1764,2087	no	missense	ZNF835	NM_001005850.2	107	727,2700,2894	GG,GT,TT		29.8275,38.9952,32.8587	benign	88/538	57176304	4154,8488	2090	4231	6321	SO:0001583	missense	90485	exon2			GGGCTCTCCCCAG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.263A>C	19.37:g.57176304T>G	ENSP00000444747:p.Glu88Ala	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	847	0.38782051282051283	215	0.4369918699186992	127	0.35082872928176795	264	0.46153846153846156	241	0.3179419525065963	T	6.640	0.486634	0.12641	0.389952	0.298275	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.06849	3.25	2.58	-1.04	0.10068	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.12837	0.008	T	0.44605	-0.9317	8	0.72032	D	0.01	.	2.9659	0.05908	0.0:0.2978:0.2397:0.4625	rs12460400	110	Q9Y2P0	ZN835_HUMAN	A	110;88	ENSP00000444747:E88A	ENSP00000341756:E110A	E	-	2	0	ZNF835	61868116	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.149000	0.10204	-0.483000	0.06772	0.459000	0.35465	GAG	T|0.628;G|0.372	0.372	strong		0.637	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
TRAF3IP2	10758	hgsc.bcm.edu	37	6	111913070	111913070	+	Missense_Mutation	SNP	G	G	A	rs13190932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:111913070G>A	ENST00000340026.6	-	3	841	c.247C>T	c.(247-249)Cgg>Tgg	p.R83W	TRAF3IP2_ENST00000359831.4_Missense_Mutation_p.R74W|TRAF3IP2_ENST00000368761.5_Missense_Mutation_p.R74W|TRAF3IP2_ENST00000392556.4_5'UTR|TRAF3IP2-AS1_ENST00000532353.1_RNA			O43734	CIKS_HUMAN	TRAF3 interacting protein 2	83	Mediates interaction with TRAF6.		R -> W (in dbSNP:rs13190932).		B cell apoptotic process (GO:0001783)|humoral immune response (GO:0006959)|immunoglobulin secretion (GO:0048305)|intracellular signal transduction (GO:0035556)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)					central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	18		all_cancers(87;7.87e-06)|Acute lymphoblastic leukemia(125;3.61e-09)|all_hematologic(75;2.63e-07)|all_epithelial(87;0.0024)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.033)|all cancers(137;0.0412)|Epithelial(106;0.0732)		GATACAGGCCGCTGGTGATTT	0.547													G|||	182	0.0363419	0.0295	0.0591	5008	,	,		19031	0.0		0.0676	False		,,,				2504	0.0348				p.R74W		Atlas-SNP	.											.	TRAF3IP2	35	.	0			c.C220T						PASS	.	G	TRP/ARG,TRP/ARG	159,4247	108.6+/-147.0	3,153,2047	88.0	89.0	89.0		220,220	-5.7	0.0	6	dbSNP_121	89	513,8087	145.9+/-201.5	15,483,3802	yes	missense,missense	TRAF3IP2	NM_001164281.1,NM_147686.2	101,101	18,636,5849	AA,AG,GG		5.9651,3.6087,5.1668	benign,benign	74/565,74/566	111913070	672,12334	2203	4300	6503	SO:0001583	missense	10758	exon2			CAGGCCGCTGGTG	AF136405	CCDS5093.1, CCDS55049.1, CCDS55050.1	6q21	2008-09-05	2002-06-20	2005-04-13	ENSG00000056972	ENSG00000056972			1343	protein-coding gene	gene with protein product		607043	"""chromosome 6 open reading frame 5"", ""chromosome 6 open reading frame 2"""	C6orf4, C6orf5, C6orf6, C6orf2		10962033, 10962024	Standard	NR_028338		Approved	DKFZP586G0522, ACT1, CIKS	uc003pvf.4	O43734	OTTHUMG00000015379	ENST00000340026.6:c.247C>T	6.37:g.111913070G>A	ENSP00000345984:p.Arg83Trp	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	197	116	0.588832	NM_147686	B2RAY9|E1P555|Q5R3A3|Q7Z6Q1|Q7Z6Q2|Q7Z6Q3|Q9H5W2|Q9H6Y3|Q9NS14|Q9UG72	Missense_Mutation	SNP	ENST00000340026.6	37		82	0.037545787545787544	10	0.02032520325203252	21	0.058011049723756904	0	0.0	51	0.06728232189973615	G	6.895	0.534567	0.13188	0.036087	0.059651	ENSG00000056972	ENST00000392555;ENST00000368761;ENST00000340026;ENST00000359831	T;T;T	0.31769	1.48;1.48;1.48	5.55	-5.66	0.02451	.	1.101480	0.06841	N	0.795720	T	0.05960	0.0155	N	0.14661	0.345	0.20638	N	0.999874	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.0	T	0.45011	-0.9290	10	0.62326	D	0.03	-27.0216	9.5888	0.39532	0.6324:0.1093:0.2582:0.0	rs13190932;rs57477005;rs13190932	83;74;74	O43734;O43734-2;Q7Z6Q1	CIKS_HUMAN;.;.	W	83;74;83;74	ENSP00000357750:R74W;ENSP00000345984:R83W;ENSP00000352889:R74W	ENSP00000345984:R83W	R	-	1	2	TRAF3IP2	112019763	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-0.970000	0.03810	-1.092000	0.03062	-0.254000	0.11334	CGG	G|0.954;A|0.046	0.046	strong		0.547	TRAF3IP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000041841.2		
GPR158	57512	hgsc.bcm.edu	37	10	25888180	25888180	+	Missense_Mutation	SNP	A	A	G	rs10828833	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:25888180A>G	ENST00000376351.3	+	11	3984	c.3625A>G	c.(3625-3627)Atc>Gtc	p.I1209V	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1209			I -> V (in dbSNP:rs10828833).		protein localization to plasma membrane (GO:0072659)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|cervix(1)|endometrium(9)|kidney(10)|large_intestine(20)|lung(56)|ovary(4)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	119						GAAAGAAGAGATCTGGGATAG	0.438													G|||	3323	0.663538	0.9652	0.5144	5008	,	,		18834	0.7579		0.3956	False		,,,				2504	0.5399				p.I1209V		Atlas-SNP	.											GPR158,right_upper_lobe,carcinoma,-2,1	GPR158	255	1	0			c.A3625G						PASS	.	G	VAL/ILE	3819,587		1656,507,40	43.0	51.0	48.0		3625	3.1	0.1	10	dbSNP_120	48	3647,4951		764,2119,1416	yes	missense	GPR158	NM_020752.2	29	2420,2626,1456	GG,GA,AA		42.4168,13.3227,42.5869	benign	1209/1216	25888180	7466,5538	2203	4299	6502	SO:0001583	missense	57512	exon11			GAAGAGATCTGGG	AB032962	CCDS31166.1	10p12.31	2012-08-21			ENSG00000151025	ENSG00000151025		"""GPCR / Class C : Orphans"""	23689	protein-coding gene	gene with protein product		614573					Standard	NM_020752		Approved	KIAA1136	uc001isj.3	Q5T848	OTTHUMG00000017832	ENST00000376351.3:c.3625A>G	10.37:g.25888180A>G	ENSP00000365529:p.Ile1209Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	36	29	0.805556	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	1407	0.6442307692307693	467	0.9491869918699187	199	0.5497237569060773	432	0.7552447552447552	309	0.4076517150395778	G	0.009	-1.856044	0.00558	0.866773	0.424168	ENSG00000151025	ENST00000376351	T	0.59083	0.29	5.92	3.1	0.35709	.	1.738420	0.03741	N	0.255005	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	0.40079	-0.9582	9	0.02654	T	1	.	10.728	0.46079	0.2544:0.0:0.7456:0.0	rs10828833;rs17639060;rs52832343;rs58605179;rs10828833	1209	Q5T848	GP158_HUMAN	V	1209	ENSP00000365529:I1209V	ENSP00000365529:I1209V	I	+	1	0	GPR158	25928186	0.991000	0.36638	0.145000	0.22337	0.573000	0.36030	2.214000	0.42853	0.136000	0.18733	-0.119000	0.15052	ATC	A|0.388;G|0.612	0.612	strong		0.438	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110	
MTL5	9633	hgsc.bcm.edu	37	11	68514791	68514791	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68514791G>A	ENST00000255087.5	-	3	698	c.515C>T	c.(514-516)cCg>cTg	p.P172L	MTL5_ENST00000544963.1_Missense_Mutation_p.P172L|MTL5_ENST00000540869.1_5'UTR|MTL5_ENST00000443940.2_Missense_Mutation_p.P172L	NM_004923.3	NP_004914.2	Q9Y4I5	MTL5_HUMAN	metallothionein-like 5, testis-specific (tesmin)	172					cell differentiation (GO:0030154)|cellular metal ion homeostasis (GO:0006875)|multicellular organismal development (GO:0007275)|response to metal ion (GO:0010038)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.P172Q(1)		breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	15	Esophageal squamous(3;4.37e-12)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.185)			TGCTTCTTCCGGATTATTACT	0.423																																					p.P172L		Atlas-SNP	.											MTL5,NS,carcinoma,0,1	MTL5	37	1	1	Substitution - Missense(1)	lung(1)	c.C515T						scavenged	.						134.0	128.0	130.0					11																	68514791		2200	4294	6494	SO:0001583	missense	9633	exon3			TCTTCCGGATTAT	U86074	CCDS8184.1, CCDS44661.1	11q13.2-q13.3	2007-01-03			ENSG00000132749	ENSG00000132749			7446	protein-coding gene	gene with protein product	"""CXC domain containing 2"""	604374				1091092	Standard	XR_428932		Approved	CXCDC2	uc001ooc.3	Q9Y4I5	OTTHUMG00000167891	ENST00000255087.5:c.515C>T	11.37:g.68514791G>A	ENSP00000255087:p.Pro172Leu	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	157	2	0.0127389	NM_001039656	A8K8J3|Q4G182|Q6P2E2|Q8NCC8	Missense_Mutation	SNP	ENST00000255087.5	37	CCDS8184.1	.	.	.	.	.	.	.	.	.	.	G	1.720	-0.496866	0.04291	.	.	ENSG00000132749	ENST00000255087;ENST00000443940;ENST00000544963	T;T;T	0.42131	1.59;0.98;1.57	5.1	-2.27	0.06846	.	1.095660	0.06919	N	0.809035	T	0.20700	0.0498	N	0.12746	0.255	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.0	T	0.19943	-1.0290	10	0.26408	T	0.33	-1.9232	4.6009	0.12352	0.3337:0.0:0.385:0.2813	.	172;155;172	Q9Y4I5-3;Q6PHY4;Q9Y4I5	.;.;MTL5_HUMAN	L	172	ENSP00000255087:P172L;ENSP00000403086:P172L;ENSP00000440968:P172L	ENSP00000255087:P172L	P	-	2	0	MTL5	68271367	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.165000	0.09968	-0.189000	0.10482	-0.215000	0.12644	CCG	.	.	none		0.423	MTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396844.1	NM_004923	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331549	21331549	+	Missense_Mutation	SNP	T	T	C	rs4149056	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:21331549T>C	ENST00000256958.2	+	6	617	c.521T>C	c.(520-522)gTg>gCg	p.V174A		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	174			V -> A (decreased transport activity; dbSNP:rs4149056). {ECO:0000269|PubMed:11477075, ECO:0000269|PubMed:12130747}.		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)	TGGATATATGTGTTCATGGGT	0.343													T|||	439	0.0876597	0.0136	0.134	5008	,	,		15111	0.123		0.161	False		,,,				2504	0.0429				p.V174A		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.T521C	GRCh37	CM043777	SLCO1B1	M	rs4149056	PASS	.	T	ALA/VAL	159,4247	108.6+/-147.0	3,153,2047	144.0	135.0	138.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	521	3.6	0.1	12	dbSNP_110	138	1336,7264	261.4+/-283.8	119,1098,3083	yes	missense	SLCO1B1	NM_006446.4	64	122,1251,5130	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	15.5349,3.6087,11.4947	probably-damaging	174/692	21331549	1495,11511	2203	4300	6503	SO:0001583	missense	10599	exon6			TATATGTGTTCAT		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.521T>C	12.37:g.21331549T>C	ENSP00000256958:p.Val174Ala	Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	253	149	0.588933	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	268	0.1227106227106227	13	0.026422764227642278	50	0.13812154696132597	73	0.12762237762237763	132	0.1741424802110818	T	12.39	1.923669	0.34002	0.036087	0.155349	ENSG00000134538	ENST00000256958	T	0.43294	0.95	3.62	3.62	0.41486	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.163062	0.39687	N	0.001300	T	0.00440	0.0014	M	0.92833	3.35	0.54753	P	1.4999999999987246E-5	D	0.89917	1.0	D	0.83275	0.996	T	0.43196	-0.9406	9	0.87932	D	0	.	12.6758	0.56893	0.0:0.0:0.0:1.0	rs4149056;rs52816141;rs60037639;rs4149056	174	Q9Y6L6	SO1B1_HUMAN	A	174	ENSP00000256958:V174A	ENSP00000256958:V174A	V	+	2	0	SLCO1B1	21222816	1.000000	0.71417	0.058000	0.19502	0.015000	0.08874	7.326000	0.79133	1.641000	0.50575	0.260000	0.18958	GTG	T|0.890;C|0.110	0.110	strong		0.343	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
ABCA3	21	hgsc.bcm.edu	37	16	2329071	2329071	+	Missense_Mutation	SNP	G	G	A	rs146709251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2329071G>A	ENST00000301732.5	-	29	5120	c.4420C>T	c.(4420-4422)Cgg>Tgg	p.R1474W	ABCA3_ENST00000382381.3_Missense_Mutation_p.R1416W	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1474	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|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)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	AGCATCTCCCGGCCTGTCATG	0.677													G|||	11	0.00219649	0.0	0.0	5008	,	,		18482	0.0		0.0109	False		,,,				2504	0.0				p.R1474W		Atlas-SNP	.											.	ABCA3	176	.	0			c.C4420T						PASS	.	G	TRP/ARG	1,4395	2.1+/-5.4	0,1,2197	56.0	57.0	57.0		4420	3.3	1.0	16	dbSNP_134	57	31,8569	22.2+/-67.0	0,31,4269	yes	missense	ABCA3	NM_001089.2	101	0,32,6466	AA,AG,GG		0.3605,0.0227,0.2462	probably-damaging	1474/1705	2329071	32,12964	2198	4300	6498	SO:0001583	missense	21	exon29			TCTCCCGGCCTGT	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.4420C>T	16.37:g.2329071G>A	ENSP00000301732:p.Arg1474Trp	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	143	67	0.468531	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	13.04	2.118520	0.37436	2.27E-4	0.003605	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.94613	-3.47	5.35	3.32	0.38043	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.057559	0.64402	N	0.000002	D	0.92414	0.7592	M	0.76328	2.33	0.80722	D	1	P;P	0.43024	0.798;0.689	P;P	0.47573	0.55;0.466	D	0.90607	0.4549	10	0.56958	D	0.05	.	9.1349	0.36868	0.0781:0.0:0.7721:0.1498	.	1478;1474	Q4LE27;Q99758	.;ABCA3_HUMAN	W	1474;1478	ENSP00000301732:R1474W	ENSP00000301732:R1474W	R	-	1	2	ABCA3	2269072	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	2.466000	0.45084	0.580000	0.29522	0.561000	0.74099	CGG	G|0.997;A|0.003	0.003	strong		0.677	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
NLRP2	55655	hgsc.bcm.edu	37	19	55496494	55496494	+	Silent	SNP	C	C	T	rs61733928	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55496494C>T	ENST00000543010.1	+	7	2253	c.2110C>T	c.(2110-2112)Cta>Tta	p.L704L	NLRP2_ENST00000391721.4_Silent_p.L680L|NLRP2_ENST00000339757.7_Silent_p.L682L|NLRP2_ENST00000427260.2_Silent_p.L681L|NLRP2_ENST00000263437.6_Silent_p.L701L|NLRP2_ENST00000537859.1_Silent_p.L682L|NLRP2_ENST00000538819.1_Silent_p.L680L|NLRP2_ENST00000448584.2_Silent_p.L704L	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	704					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)		TCTGATGGGTCTAGCAATCAA	0.448													c|||	61	0.0121805	0.0113	0.0216	5008	,	,		19099	0.001		0.0278	False		,,,				2504	0.002				p.L704L		Atlas-SNP	.											.	NLRP2	161	.	0			c.C2110T						PASS	.	T	,,,	36,4370	40.8+/-73.8	0,36,2167	198.0	170.0	179.0		2110,2044,2041,2110	1.4	0.0	19	dbSNP_129	179	255,8345	100.6+/-161.9	2,251,4047	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	2,287,6214	TT,TC,CC		2.9651,0.8171,2.2374	,,,	704/1063,682/1041,681/1040,704/1063	55496494	291,12715	2203	4300	6503	SO:0001819	synonymous_variant	55655	exon7			ATGGGTCTAGCAA	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.2110C>T	19.37:g.55496494C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	154	73	0.474026	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			C|0.980;T|0.020	0.020	strong		0.448	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
PKDREJ	10343	hgsc.bcm.edu	37	22	46655779	46655779	+	Missense_Mutation	SNP	G	G	C	rs36125344	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46655779G>C	ENST00000253255.5	-	1	3440	c.3441C>G	c.(3439-3441)atC>atG	p.I1147M		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1147			I -> M (in dbSNP:rs36125344).		acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CCGTGAGTCCGATTGTGCCCA	0.507													G|||	319	0.0636981	0.0802	0.0663	5008	,	,		20273	0.001		0.1233	False		,,,				2504	0.0429				p.I1147M		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C3441G						PASS	.	G	MET/ILE	337,4069	177.3+/-206.3	19,299,1885	184.0	160.0	168.0		3441	-8.8	0.0	22	dbSNP_126	168	905,7695	202.5+/-245.8	52,801,3447	yes	missense	PKDREJ	NM_006071.1	10	71,1100,5332	CC,CG,GG		10.5233,7.6487,9.5494	benign	1147/2254	46655779	1242,11764	2203	4300	6503	SO:0001583	missense	10343	exon1			GAGTCCGATTGTG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.3441C>G	22.37:g.46655779G>C	ENSP00000253255:p.Ile1147Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	164	0.07509157509157509	36	0.07317073170731707	31	0.0856353591160221	0	0.0	97	0.1279683377308707	G	3.363	-0.130048	0.06753	0.076487	0.105233	ENSG00000130943	ENST00000253255	T	0.36878	1.23	4.38	-8.75	0.00834	GPS domain (1);	13.660900	0.00166	N	0.000001	T	0.00241	0.0007	L	0.36672	1.1	0.80722	P	0.0	B	0.17465	0.022	B	0.06405	0.002	T	0.04178	-1.0971	9	0.32370	T	0.25	-0.189	2.8003	0.05412	0.1299:0.3542:0.1808:0.3351	rs36125344	1147	Q9NTG1	PKDRE_HUMAN	M	1147	ENSP00000253255:I1147M	ENSP00000253255:I1147M	I	-	3	3	PKDREJ	45034443	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.473000	0.00459	-3.170000	0.00225	-1.036000	0.02392	ATC	G|0.912;C|0.088	0.088	strong		0.507	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
PRB3	5544	hgsc.bcm.edu	37	12	11421004	11421004	+	Missense_Mutation	SNP	C	C	T	rs71455364		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:11421004C>T	ENST00000279573.7	-	3	314	c.179G>A	c.(178-180)cGa>cAa	p.R60Q	PRB3_ENST00000381842.3_Missense_Mutation_p.R60Q|PRB3_ENST00000538488.1_Missense_Mutation_p.R60Q|PRB3_ENST00000440870.3_5'UTR			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	60	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.			R -> P (in Ref. 1; CAA30728). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			TTGTGGGGGTCGTCCTTCTGG	0.627																																					p.R60Q		Atlas-SNP	.											.	PRB3	84	.	0			c.G179A						PASS	.						160.0	173.0	168.0					12																	11421004		2198	4296	6494	SO:0001583	missense	5544	exon3			GGGGGTCGTCCTT			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.179G>A	12.37:g.11421004C>T	ENSP00000279573:p.Arg60Gln	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		.	.	.	.	.	.	.	.	.	.	.	3.985	-0.005638	0.07773	.	.	ENSG00000197870	ENST00000381842;ENST00000538488	T;T	0.04119	3.7;3.7	0.763	-1.53	0.08611	.	0.242690	0.19335	U	0.116811	T	0.02610	0.0079	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46233	-0.9206	9	0.13470	T	0.59	.	5.5053	0.16850	0.0:0.3072:0.4664:0.2265	.	60	Q04118	PRB3_HUMAN	Q	60	ENSP00000371264:R60Q;ENSP00000442626:R60Q	ENSP00000279573:R60Q	R	-	2	0	PRB3	11312271	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.005000	0.00315	-4.132000	0.00071	-2.937000	0.00087	CGA	C|0.500;G|0.500	.	alt		0.627	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
LGR6	59352	hgsc.bcm.edu	37	1	202287813	202287813	+	Silent	SNP	T	T	C	rs788793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	229	226	0.9869	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	
PKDREJ	10343	hgsc.bcm.edu	37	22	46652737	46652737	+	Silent	SNP	G	G	A	rs6008362	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46652737G>A	ENST00000253255.5	-	1	6482	c.6483C>T	c.(6481-6483)tgC>tgT	p.C2161C		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	2161					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TGATCAAGACGCAGATCATCA	0.438													G|||	1202	0.240016	0.6604	0.1297	5008	,	,		22415	0.001		0.16	False		,,,				2504	0.0787				p.C2161C		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C6483T						PASS	.	G		2569,1837	635.7+/-396.4	749,1071,383	68.0	65.0	66.0		6483	-2.1	0.2	22	dbSNP_114	66	1256,7344	251.2+/-277.8	88,1080,3132	no	coding-synonymous	PKDREJ	NM_006071.1		837,2151,3515	AA,AG,GG		14.6047,41.6931,29.4095		2161/2254	46652737	3825,9181	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			CAAGACGCAGATC	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.6483C>T	22.37:g.46652737G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			G|0.737;A|0.263	0.263	strong		0.438	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
ZSWIM5	57643	hgsc.bcm.edu	37	1	45504720	45504720	+	Silent	SNP	G	G	C	rs7551698	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:45504720G>C	ENST00000359600.5	-	8	1987	c.1782C>G	c.(1780-1782)acC>acG	p.T594T		NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	594						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)					GGTTTGTGATGGTTGTGGTTC	0.512													G|||	2556	0.510383	0.3805	0.4337	5008	,	,		17531	0.4544		0.6183	False		,,,				2504	0.6871				p.T594T		Atlas-SNP	.											ZSWIM5,NS,carcinoma,-1,1	ZSWIM5	72	1	0			c.C1782G						scavenged	.	G		1507,2257		326,855,701	72.0	75.0	74.0		1782	2.0	1.0	1	dbSNP_116	74	4900,3320		1473,1954,683	no	coding-synonymous	ZSWIM5	NM_020883.1		1799,2809,1384	CC,CG,GG		40.3893,40.0372,46.537		594/1186	45504720	6407,5577	1882	4110	5992	SO:0001819	synonymous_variant	57643	exon8			TGTGATGGTTGTG	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.1782C>G	1.37:g.45504720G>C		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	47	37	0.787234	NM_020883	Q5SXQ9	Silent	SNP	ENST00000359600.5	37	CCDS41319.1																																																																																			G|0.462;C|0.538	0.538	strong		0.512	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581	
OR12D2	26529	hgsc.bcm.edu	37	6	29364643	29364643	+	Missense_Mutation	SNP	T	T	C	rs4987411	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29364643T>C	ENST00000383555.2	+	1	228	c.167T>C	c.(166-168)cTt>cCt	p.L56P	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	56			L -> P (in dbSNP:rs4987411).			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(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CTCCATTCCCTTATGTATTTC	0.453													C|||	1597	0.31889	0.1921	0.3458	5008	,	,		21557	0.3641		0.4523	False		,,,				2504	0.2873				p.L56P		Atlas-SNP	.											.	OR12D2	42	.	0			c.T167C						PASS	.	C	PRO/LEU	663,2357		75,513,922	113.0	115.0	114.0		167	3.2	0.1	6	dbSNP_113	114	2407,3011		535,1337,837	yes	missense	OR12D2	NM_013936.3	98	610,1850,1759	CC,CT,TT		44.426,21.9536,36.383	benign	56/308	29364643	3070,5368	1510	2709	4219	SO:0001583	missense	26529	exon1			ATTCCCTTATGTA		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.167T>C	6.37:g.29364643T>C	ENSP00000373047:p.Leu56Pro	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	260	257	0.988462	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	787	0.36034798534798534	101	0.20528455284552846	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	C	0.008	-1.929605	0.00488	0.219536	0.44426	ENSG00000168787	ENST00000383555	T	0.00000	10.38	4.07	3.2	0.36748	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000019	T	0.00012	0.0000	N	0.00002	-3.6	0.20307	P	0.9999180459	B	0.02656	0.0	B	0.01281	0.0	T	0.48885	-0.8995	9	0.02654	T	1	.	9.8586	0.41101	0.0:0.8292:0.0:0.1708	rs4987411;rs56924123;rs4987411	56	P58182	O12D2_HUMAN	P	56	ENSP00000373047:L56P	ENSP00000373047:L56P	L	+	2	0	OR12D2	29472622	1.000000	0.71417	0.108000	0.21378	0.018000	0.09664	5.299000	0.65716	0.387000	0.25024	-0.473000	0.04963	CTT	T|0.630;C|0.370	0.370	strong		0.453	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
RERE	473	hgsc.bcm.edu	37	1	8425900	8425900	+	Silent	SNP	T	T	C	rs3753275	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:8425900T>C	ENST00000337907.3	-	14	2053	c.1419A>G	c.(1417-1419)acA>acG	p.T473T	RERE_ENST00000476556.1_5'UTR|RERE_ENST00000400907.2_Silent_p.T473T|RERE_ENST00000377464.1_Silent_p.T205T|RERE_ENST00000460659.1_5'Flank|RERE_ENST00000400908.2_Silent_p.T473T	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	473					chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GTCTGGAGGGTGTGTTGACGG	0.642													T|||	1243	0.248203	0.413	0.1945	5008	,	,		16536	0.0575		0.1978	False		,,,				2504	0.3119				p.T473T		Atlas-SNP	.											.	RERE	129	.	0			c.A1419G						PASS	.	T	,,	1601,2805	496.7+/-363.6	285,1031,887	90.0	94.0	93.0		1419,,1419	-5.1	1.0	1	dbSNP_107	93	1644,6956	303.8+/-306.6	157,1330,2813	no	coding-synonymous,utr-5,coding-synonymous	RERE	NM_001042681.1,NM_001042682.1,NM_012102.3	,,	442,2361,3700	CC,CT,TT		19.1163,36.3368,24.95	,,	473/1567,,473/1567	8425900	3245,9761	2203	4300	6503	SO:0001819	synonymous_variant	473	exon14			GGAGGGTGTGTTG	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.1419A>G	1.37:g.8425900T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	68	53	0.779412	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																			T|0.771;C|0.229	0.229	strong		0.642	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
NEK2	4751	hgsc.bcm.edu	37	1	211846876	211846876	+	Silent	SNP	A	A	G	rs701929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:211846876A>G	ENST00000366999.4	-	3	642	c.504T>C	c.(502-504)caT>caC	p.H168H	NEK2_ENST00000462283.1_5'Flank|NEK2_ENST00000540251.1_Silent_p.H125H|NEK2_ENST00000366998.3_Silent_p.H168H|RP11-122M14.1_ENST00000415202.1_RNA	NM_002497.3	NP_002488.1	P51955	NEK2_HUMAN	NIMA-related kinase 2	168	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blastocyst development (GO:0001824)|centrosome separation (GO:0051299)|chromosome segregation (GO:0007059)|G2/M transition of mitotic cell cycle (GO:0000086)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of centriole-centriole cohesion (GO:1903126)|negative regulation of DNA binding (GO:0043392)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of mitosis (GO:0007088)|regulation of mitotic centrosome separation (GO:0046602)|spindle assembly (GO:0051225)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|microtubule (GO:0005874)|midbody (GO:0030496)|nucleus (GO:0005634)|protein complex (GO:0043234)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|stomach(1)	3				OV - Ovarian serous cystadenocarcinoma(81;0.00203)|all cancers(67;0.0339)|Epithelial(68;0.0546)		AACTCGTGTCATGGTTTAATA	0.368													G|||	3020	0.603035	0.5454	0.6671	5008	,	,		19471	0.7252		0.4732	False		,,,				2504	0.6431				p.H168H		Atlas-SNP	.											.	NEK2	49	.	0			c.T504C						PASS	.	G	,,	2353,2053	566.7+/-382.0	640,1073,490	86.0	88.0	87.0		504,504,504	-10.5	0.2	1	dbSNP_86	87	4169,4431	586.8+/-392.1	1022,2125,1153	no	coding-synonymous,coding-synonymous,coding-synonymous	NEK2	NM_001204182.1,NM_001204183.1,NM_002497.3	,,	1662,3198,1643	GG,GA,AA		48.4767,46.5956,49.8539	,,	168/389,168/385,168/446	211846876	6522,6484	2203	4300	6503	SO:0001819	synonymous_variant	4751	exon3			CGTGTCATGGTTT	U11050	CCDS1500.1, CCDS55682.1, CCDS73024.1	1q32.3	2014-06-12	2012-11-15		ENSG00000117650	ENSG00000117650			7745	protein-coding gene	gene with protein product	"""HsPK 21"", ""protein phosphatase 1, regulatory subunit 111"""	604043	"""NIMA (never in mitosis gene a)-related kinase 2"""			8274451, 24043777	Standard	NM_002497		Approved	NLK1, NEK2A, RP67, PPP1R111	uc001hir.2	P51955	OTTHUMG00000037121	ENST00000366999.4:c.504T>C	1.37:g.211846876A>G		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	266	94	0.353383	NM_002497	Q53FD6|Q5I1Z9|Q5VXZ1|Q6NZX8|Q7Z634|Q86XH2|Q96QN9	Silent	SNP	ENST00000366999.4	37	CCDS1500.1																																																																																			A|0.463;G|0.537	0.537	strong		0.368	NEK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090154.1	NM_002497	
HES7	84667	hgsc.bcm.edu	37	17	8026364	8026364	+	Silent	SNP	C	C	T	rs61731639	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8026364C>T	ENST00000317814.4	-	2	122	c.123G>A	c.(121-123)gaG>gaA	p.E41E	HES7_ENST00000541682.2_Silent_p.E41E			Q9BYE0	HES7_HUMAN	hes family bHLH transcription factor 7	41	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				mesoderm development (GO:0007498)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|post-anal tail morphogenesis (GO:0036342)|regulation of somitogenesis (GO:0014807)|rhythmic process (GO:0048511)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)										CCCGGGTCCGCTCCAGCAGCA	0.662													C|||	702	0.140176	0.0068	0.2709	5008	,	,		14642	0.375		0.0437	False		,,,				2504	0.0849				p.E41E		Atlas-SNP	.											.	.	.	.	0			c.G123A						PASS	.	C	,	53,3827		1,51,1888	10.0	13.0	12.0		123,123	4.3	1.0	17	dbSNP_129	12	332,7902		8,316,3793	no	coding-synonymous,coding-synonymous	HES7	NM_001165967.1,NM_032580.3	,	9,367,5681	TT,TC,CC		4.0321,1.366,3.1781	,	41/231,41/226	8026364	385,11729	1940	4117	6057	SO:0001819	synonymous_variant	84667	exon2			GGTCCGCTCCAGC	AB049064	CCDS42258.1, CCDS54085.1	17p13.1	2013-10-17	2013-10-17			ENSG00000179111		"""Basic helix-loop-helix proteins"""	15977	protein-coding gene	gene with protein product	"""bHLH factor Hes7"""	608059	"""hairy and enhancer of split 7 (Drosophila)"""			11260262	Standard	NM_032580		Approved	bHLHb37	uc002gkb.2	Q9BYE0		ENST00000317814.4:c.123G>A	17.37:g.8026364C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	216	114	0.527778	NM_001165967	F8VPC9	Silent	SNP	ENST00000317814.4	37	CCDS42258.1																																																																																			C|0.854;T|0.146	0.146	strong		0.662	HES7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441479.1	NM_032580	
MACROD1	28992	hgsc.bcm.edu	37	11	63767186	63767186	+	Silent	SNP	A	A	G	rs709594	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:63767186A>G	ENST00000255681.6	-	6	780	c.714T>C	c.(712-714)agT>agC	p.S238S	OTUB1_ENST00000535715.1_Intron	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1	238	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				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						CGGCAGCCTGACTGGCGCTGG	0.726													G|||	2143	0.427915	0.736	0.2493	5008	,	,		10778	0.1379		0.4463	False		,,,				2504	0.4182				p.S238S		Atlas-SNP	.											.	MACROD1	17	.	0			c.T714C						PASS	.	G		2959,1321		1069,821,250	10.0	13.0	12.0		714	3.8	1.0	11	dbSNP_86	12	3770,4672		906,1958,1357	no	coding-synonymous	MACROD1	NM_014067.3		1975,2779,1607	GG,GA,AA		44.6577,30.8645,47.1074		238/326	63767186	6729,5993	2140	4221	6361	SO:0001819	synonymous_variant	28992	exon6			AGCCTGACTGGCG	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.714T>C	11.37:g.63767186A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	NM_014067	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			A|0.619;G|0.381	0.381	strong		0.726	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
SLC41A2	84102	hgsc.bcm.edu	37	12	105199038	105199038	+	Silent	SNP	G	G	A	rs11112201	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:105199038G>A	ENST00000258538.3	-	10	1741	c.1614C>T	c.(1612-1614)tcC>tcT	p.S538S	SLC41A2_ENST00000549713.1_5'UTR	NM_032148.3	NP_115524.3	Q96JW4	S41A2_HUMAN	solute carrier family 41 (magnesium transporter), member 2	538					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)	p.S455S(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	22						GGTAGGGGATGGAGAAACTAT	0.453													G|||	418	0.0834665	0.0658	0.072	5008	,	,		18623	0.0883		0.0845	False		,,,				2504	0.1094				p.S538S	Esophageal Squamous(195;176 2919 4272 35572)	Atlas-SNP	.											SLC41A2,NS,carcinoma,0,1	SLC41A2	66	1	1	Substitution - coding silent(1)	stomach(1)	c.C1614T						PASS	.	G		378,4028	191.6+/-217.2	18,342,1843	196.0	200.0	199.0		1614	1.9	1.0	12	dbSNP_120	199	776,7824	184.5+/-232.4	38,700,3562	no	coding-synonymous	SLC41A2	NM_032148.3		56,1042,5405	AA,AG,GG		9.0233,8.5792,8.8728		538/574	105199038	1154,11852	2203	4300	6503	SO:0001819	synonymous_variant	84102	exon10			GGGGATGGAGAAA	BC036734	CCDS9100.2	12q24.11	2013-07-17	2013-07-17		ENSG00000136052	ENSG00000136052		"""Solute carriers"""	31045	protein-coding gene	gene with protein product		610802	"""solute carrier family 41, member 2"""				Standard	NM_032148		Approved	DKFZP434K0427	uc001tla.3	Q96JW4	OTTHUMG00000156965	ENST00000258538.3:c.1614C>T	12.37:g.105199038G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_032148	Q3KP68|Q9H0E5	Silent	SNP	ENST00000258538.3	37	CCDS9100.2																																																																																			G|0.919;A|0.081	0.081	strong		0.453	SLC41A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346850.3	NM_032148	
FAM198A	729085	hgsc.bcm.edu	37	3	43073761	43073761	+	Silent	SNP	G	G	A	rs658958	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:43073761G>A	ENST00000430121.2	+	2	101	c.6G>A	c.(4-6)gcG>gcA	p.A2A	KRBOX1_ENST00000443313.1_Intron|KRBOX1_ENST00000418093.2_3'UTR	NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	2						extracellular region (GO:0005576)				endometrium(1)	1						TCTCTCAGGCGTCTTGGCTCC	0.527													G|||	2195	0.438299	0.3404	0.5331	5008	,	,		20480	0.6518		0.4066	False		,,,				2504	0.316				p.A2A		Atlas-SNP	.											FAM198A_ENST00000430121,caecum,carcinoma,0,1	FAM198A	23	1	0			c.G6A						scavenged	.	G		454,930		72,310,310	27.0	26.0	27.0		6	-5.3	0.8	3	dbSNP_83	27	1298,1884		269,760,562	no	coding-synonymous	FAM198A	NM_001129908.2		341,1070,872	AA,AG,GG		40.792,32.8035,38.3706		2/576	43073761	1752,2814	692	1591	2283	SO:0001819	synonymous_variant	729085	exon2			TCAGGCGTCTTGG	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.6G>A	3.37:g.43073761G>A		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	112	106	0.946429	NM_001129908	B3KR48	Silent	SNP	ENST00000430121.2	37	CCDS46808.1																																																																																			G|0.533;A|0.467	0.467	strong		0.527	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
CCDC170	80129	hgsc.bcm.edu	37	6	151936677	151936677	+	Missense_Mutation	SNP	G	G	A	rs6929137	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:151936677G>A	ENST00000239374.7	+	10	1909	c.1810G>A	c.(1810-1812)Gtc>Atc	p.V604I	RNU6-813P_ENST00000384691.1_RNA|CCDC170_ENST00000367290.5_Missense_Mutation_p.V611I	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	604			V -> I (in dbSNP:rs6929137). {ECO:0000269|PubMed:14702039}.														GCTCATGTCTGTCAAGTCAGA	0.393													G|||	1750	0.349441	0.4962	0.245	5008	,	,		18841	0.3333		0.2952	False		,,,				2504	0.2975				p.V604I		Atlas-SNP	.											.	.	.	.	0			c.G1810A						PASS	.	G	ILE/VAL	1842,1882		458,926,478	149.0	144.0	145.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1810	3.4	0.5	6	dbSNP_116	145	2695,5513		467,1761,1876	yes	missense	C6orf97	NM_025059.3	29	925,2687,2354	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	32.8338,49.4629,38.0238	benign	604/716	151936677	4537,7395	1862	4104	5966	SO:0001583	missense	80129	exon10			ATGTCTGTCAAGT	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1810G>A	6.37:g.151936677G>A	ENSP00000239374:p.Val604Ile	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	174	82	0.471264	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	744	0.34065934065934067	251	0.5101626016260162	97	0.26795580110497236	181	0.31643356643356646	215	0.2836411609498681	G	10.50	1.368391	0.24771	0.494629	0.328338	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.76060	3.03;-0.99	6.16	3.37	0.38596	.	0.296403	0.31392	N	0.007735	T	0.45875	0.1364	L	0.42686	1.345	0.28753	P	0.9013056	B	0.18166	0.026	B	0.16289	0.015	T	0.28073	-1.0055	9	0.24483	T	0.36	-5.1069	9.8684	0.41160	0.126:0.1149:0.7591:0.0	rs6929137;rs57948778;rs6929137	604	Q8IYT3	CF097_HUMAN	I	604;611	ENSP00000239374:V604I;ENSP00000356259:V611I	ENSP00000239374:V604I	V	+	1	0	C6orf97	151978370	0.662000	0.27439	0.486000	0.27416	0.575000	0.36095	1.023000	0.30065	0.910000	0.36722	-0.145000	0.13849	GTC	G|0.655;A|0.345	0.345	strong		0.393	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
PML	5371	hgsc.bcm.edu	37	15	74328206	74328206	+	Intron	SNP	G	G	C	rs743582	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:74328206G>C	ENST00000268058.3	+	7	1806				PML_ENST00000565898.1_Intron|PML_ENST00000564428.1_Intron|PML_ENST00000395135.3_Intron|PML_ENST00000268059.6_Missense_Mutation_p.A802P|PML_ENST00000354026.6_Missense_Mutation_p.A754P|PML_ENST00000359928.4_Intron|PML_ENST00000395132.2_Intron|PML_ENST00000435786.2_3'UTR|PML_ENST00000563500.1_3'UTR|PML_ENST00000569965.1_Intron|PML_ENST00000436891.3_3'UTR	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia						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						GCCTCTGGAAGCCTCTCCAAT	0.622			T	"""RARA, PAX5"""	"""APL, ALL"""								G|||	785	0.156749	0.1127	0.0591	5008	,	,		14618	0.2371		0.0964	False		,,,				2504	0.2648				p.A802P		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.G2404C						PASS	.	G	,,PRO/ALA,,,,,,PRO/ALA	441,3955	196.0+/-220.5	18,405,1775	82.0	101.0	95.0		,,2404,,,,,,2260	1.2	0.0	15	dbSNP_86	95	815,7779	185.0+/-232.9	37,741,3519	yes	intron,intron,missense,utr-3,utr-3,intron,intron,intron,missense	PML	NM_002675.3,NM_033238.2,NM_033239.2,NM_033240.2,NM_033244.3,NM_033246.2,NM_033247.2,NM_033249.2,NM_033250.2	,,27,,,,,,27	55,1146,5294	CC,CG,GG		9.4834,10.0318,9.669	,,,,,,,,	,,802/830,,,,,,754/782	74328206	1256,11734	2198	4297	6495	SO:0001627	intron_variant	5371	exon8			CTGGAAGCCTCTC	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.1710+1335G>C	15.37:g.74328206G>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	35	11	0.314286	NM_033239	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	258	0.11813186813186813	47	0.09552845528455285	24	0.06629834254143646	120	0.2097902097902098	67	0.08839050131926121	G	9.783	1.175788	0.21704	0.100318	0.094834	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	3.17	1.22	0.21188	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.10450	0.005;0.005	T	0.19192	-1.0313	7	0.54805	T	0.06	.	4.5986	0.12341	0.1275:0.2266:0.6459:0.0	rs743582;rs743582	754;802	P29590-13;P29590-8	.;.	P	802;754	.	ENSP00000268059:A802P	A	+	1	0	PML	72115259	0.000000	0.05858	0.000000	0.03702	0.146000	0.21551	0.631000	0.24568	0.355000	0.24131	0.456000	0.33151	GCC	G|0.888;C|0.112	0.112	strong		0.622	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
SOCS6	9306	hgsc.bcm.edu	37	18	67993227	67993227	+	Silent	SNP	C	C	T	rs112244149	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:67993227C>T	ENST00000397942.3	+	2	1639	c.1323C>T	c.(1321-1323)agC>agT	p.S441S	SOCS6_ENST00000582322.1_Silent_p.S441S	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	441	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				GTAGGTTTAGCTTTTATGAAC	0.413													C|||	12	0.00239617	0.0008	0.0029	5008	,	,		22146	0.0		0.005	False		,,,				2504	0.0041				p.S441S	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											.	SOCS6	54	.	0			c.C1323T						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	116.0	112.0	113.0		1323	4.8	1.0	18	dbSNP_132	113	60,8540	37.4+/-92.8	0,60,4240	no	coding-synonymous	SOCS6	NM_004232.3		0,67,6436	TT,TC,CC		0.6977,0.1589,0.5151		441/536	67993227	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	9306	exon2			GTTTAGCTTTTAT	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16833	protein-coding gene	gene with protein product		605118	"""suppressor of cytokine signaling 4"""	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.1323C>T	18.37:g.67993227C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	181	66	0.364641	NM_004232	Q8WUM3	Silent	SNP	ENST00000397942.3	37	CCDS11998.1																																																																																			C|0.995;T|0.005	0.005	strong		0.413	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2		
VPS4A	27183	hgsc.bcm.edu	37	16	69354963	69354963	+	Silent	SNP	A	A	G	rs1127231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:69354963A>G	ENST00000254950.11	+	9	1017	c.861A>G	c.(859-861)aaA>aaG	p.K287K	COG8_ENST00000564419.1_Intron	NM_013245.2	NP_037377.1			vacuolar protein sorting 4 homolog A (S. cerevisiae)											NS(1)|central_nervous_system(1)|large_intestine(2)|lung(3)	7		Ovarian(137;0.101)				GGTTTGAAAAACGAATTTATA	0.552													G|||	1357	0.270966	0.3714	0.2147	5008	,	,		18592	0.0833		0.2863	False		,,,				2504	0.3528				p.K287K		Atlas-SNP	.											.	VPS4A	18	.	0			c.A861G						PASS	.	G		1673,2713		327,1019,847	38.0	42.0	41.0		861	4.5	1.0	16	dbSNP_86	41	2682,5914		427,1828,2043	no	coding-synonymous	VPS4A	NM_013245.2		754,2847,2890	GG,GA,AA		31.2006,38.1441,33.5464		287/438	69354963	4355,8627	2193	4298	6491	SO:0001819	synonymous_variant	27183	exon9			TGAAAAACGAATT	AF112215	CCDS45517.1	16q23.1	2010-04-21	2006-04-04		ENSG00000132612	ENSG00000132612		"""ATPases / AAA-type"""	13488	protein-coding gene	gene with protein product		609982	"""vacuolar protein sorting 4A (yeast homolog)"", ""vacuolar protein sorting 4A (yeast)"""			10637304, 11563910	Standard	NM_013245		Approved	VPS4, VPS4-1, FLJ22197, SKD2, SKD1, SKD1A	uc002eww.3	Q9UN37		ENST00000254950.11:c.861A>G	16.37:g.69354963A>G		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	141	139	0.985816	NM_013245		Silent	SNP	ENST00000254950.11	37	CCDS45517.1																																																																																			A|0.722;G|0.278	0.278	strong		0.552	VPS4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430563.3	NM_013245	
GLRX3	10539	hgsc.bcm.edu	37	10	131934747	131934747	+	Missense_Mutation	SNP	G	G	C	rs13991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:131934747G>C	ENST00000368644.1	+	1	85	c.63G>C	c.(61-63)caG>caC	p.Q21H	GLRX3_ENST00000331244.5_Missense_Mutation_p.Q21H	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	21	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.		Q -> H (in dbSNP:rs13991). {ECO:0000269|PubMed:10636891, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		CAGCCGGGCAGTTTGAGGAGC	0.726													G|||	814	0.16254	0.1233	0.0893	5008	,	,		9451	0.1091		0.2326	False		,,,				2504	0.2505				p.Q21H		Atlas-SNP	.											TXNL2,NS,carcinoma,0,2	GLRX3	39	2	0			c.G63C						PASS	.	G	HIS/GLN,HIS/GLN	308,2812		15,278,1267	7.0	10.0	9.0		63,63	2.9	1.0	10	dbSNP_52	9	885,4637		75,735,1951	no	missense,missense	GLRX3	NM_001199868.1,NM_006541.4	24,24	90,1013,3218	CC,CG,GG		16.0268,9.8718,13.8047	possibly-damaging,possibly-damaging	21/336,21/336	131934747	1193,7449	1560	2761	4321	SO:0001583	missense	10539	exon1			CGGGCAGTTTGAG	AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"""glutaredoxin 4"""	612754	"""thioredoxin-like 2"""	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.63G>C	10.37:g.131934747G>C	ENSP00000357633:p.Gln21His	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	27	10	0.37037	NM_006541	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	334	0.15293040293040294	64	0.13008130081300814	39	0.10773480662983426	52	0.09090909090909091	179	0.23614775725593667	G	16.20	3.054661	0.55325	0.098718	0.160268	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.14893	2.47;2.47	3.85	2.92	0.33932	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.077404	0.53938	D	0.000052	T	0.00012	0.0000	L	0.50993	1.605	0.20307	P	0.999915407	P	0.39862	0.692	P	0.50590	0.645	T	0.33954	-0.9848	9	0.24483	T	0.36	-2.8845	8.5365	0.33366	0.0:0.0:0.7694:0.2306	rs13991;rs1047395;rs3187400;rs13991	21	O76003	GLRX3_HUMAN	H	21	ENSP00000330836:Q21H;ENSP00000357633:Q21H	ENSP00000330836:Q21H	Q	+	3	2	GLRX3	131824737	0.996000	0.38824	0.997000	0.53966	0.810000	0.45777	0.140000	0.16056	0.802000	0.34089	0.313000	0.20887	CAG	G|0.849;C|0.151	0.151	strong		0.726	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541	
YAP1	10413	hgsc.bcm.edu	37	11	102094424	102094424	+	Silent	SNP	C	C	T	rs61749258	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102094424C>T	ENST00000282441.5	+	7	1492	c.1104C>T	c.(1102-1104)ccC>ccT	p.P368P	YAP1_ENST00000537274.1_Silent_p.P356P|YAP1_ENST00000526343.1_Silent_p.P314P|YAP1_ENST00000345877.2_Silent_p.P318P|YAP1_ENST00000524575.1_Silent_p.P190P|YAP1_ENST00000531439.1_Silent_p.P352P	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	368	Transactivation domain.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|contact inhibition (GO:0060242)|embryonic heart tube morphogenesis (GO:0003143)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|keratinocyte differentiation (GO:0030216)|lateral mesoderm development (GO:0048368)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|notochord development (GO:0030903)|paraxial mesoderm development (GO:0048339)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of keratinocyte proliferation (GO:0010837)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of stem cell proliferation (GO:0072091)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4	all_cancers(8;0.000575)|all_epithelial(12;0.00564)	Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.00936)	Lung(13;0.245)	BRCA - Breast invasive adenocarcinoma(274;0.0189)		TGTCTTCTCCCGGGATGTCTC	0.438													C|||	15	0.00299521	0.0	0.0029	5008	,	,		20533	0.0		0.008	False		,,,				2504	0.0051				p.P368P	Colon(50;247 1103 7861 28956)	Atlas-SNP	.											.	YAP1	45	.	0			c.C1104T						PASS	.	C	,,,	13,4393	20.2+/-43.8	0,13,2190	108.0	97.0	101.0		1104,1056,570,942	-11.0	0.2	11	dbSNP_129	101	81,8517	46.7+/-105.8	0,81,4218	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YAP1	NM_001130145.2,NM_001195044.1,NM_001195045.1,NM_006106.4	,,,	0,94,6408	TT,TC,CC		0.9421,0.2951,0.7229	,,,	368/505,352/489,190/327,314/451	102094424	94,12910	2203	4299	6502	SO:0001819	synonymous_variant	10413	exon7			TTCTCCCGGGATG		CCDS8314.1, CCDS44716.1, CCDS8314.2, CCDS53699.1, CCDS53700.1, CCDS60944.1, CCDS73373.1, CCDS73374.1	11q13	2010-03-19	2010-03-19		ENSG00000137693	ENSG00000137693			16262	protein-coding gene	gene with protein product		606608	"""Yes-associated protein 1, 65kDa"""			7782338	Standard	NM_001130145		Approved	YAP65	uc001pgt.3	P46937	OTTHUMG00000167322	ENST00000282441.5:c.1104C>T	11.37:g.102094424C>T		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	316	209	0.661392	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Silent	SNP	ENST00000282441.5	37	CCDS44716.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	8.228	0.803942	0.16467	0.002951	0.009421	ENSG00000137693	ENST00000529029	.	.	.	5.49	-11.0	0.00169	.	0.114641	0.64402	D	0.000010	T	0.27866	0.0686	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56019	-0.8048	6	0.39692	T	0.17	.	1.2473	0.01975	0.1961:0.1395:0.2166:0.4477	rs61749258	.	.	.	L	122	.	ENSP00000431626:P122L	P	+	2	0	YAP1	101599634	0.700000	0.27796	0.231000	0.23993	0.968000	0.65278	-0.459000	0.06728	-2.745000	0.00377	-1.083000	0.02208	CCG	C|0.995;T|0.005	0.005	strong		0.438	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106	
GCAT	23464	hgsc.bcm.edu	37	22	38204089	38204089	+	Missense_Mutation	SNP	C	C	T	rs397839522|rs710187	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:38204089C>T	ENST00000248924.6	+	1	171	c.115C>T	c.(115-117)Cgc>Tgc	p.R39C	GCAT_ENST00000415371.1_3'UTR|GCAT_ENST00000323205.6_Missense_Mutation_p.R39C	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	39			R -> C (in dbSNP:rs710187).		biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	GGAAGGCATCCGCGGAGCTGG	0.711													.|||	2990	0.597045	0.6407	0.6023	5008	,	,		14234	0.6815		0.5437	False		,,,				2504	0.502				p.R39C		Atlas-SNP	.											GCAT,NS,carcinoma,0,1	GCAT	27	1	0			c.C115T						PASS	.	C	CYS/ARG,CYS/ARG	2693,1695		856,981,357	28.0	19.0	22.0		115,115	4.6	1.0	22	dbSNP_86	22	4680,3894		1284,2112,891	yes	missense,missense	GCAT	NM_001171690.1,NM_014291.3	180,180	2140,3093,1248	TT,TC,CC		45.4164,38.6281,43.1183	probably-damaging,probably-damaging	39/446,39/420	38204089	7373,5589	2194	4287	6481	SO:0001583	missense	23464	exon1			GGCATCCGCGGAG	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"""2-amino-3-ketobutyrate coenzyme A ligase"""	607422	"""glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"""				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.115C>T	22.37:g.38204089C>T	ENSP00000248924:p.Arg39Cys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	37	CCDS13957.1	1303	0.5966117216117216	313	0.6361788617886179	203	0.5607734806629834	374	0.6538461538461539	413	0.5448548812664907	c	21.7	4.190764	0.78789	0.613719	0.545836	ENSG00000100116	ENST00000323205;ENST00000248924;ENST00000445195;ENST00000394944	D;D;D	0.96104	-3.91;-3.69;-1.9	4.6	4.6	0.57074	Pyridoxal phosphate-dependent transferase, major domain (1);	0.053451	0.85682	D	0.000000	T	0.00012	0.0000	L	0.58810	1.83	0.09310	P	0.9999999999986385	B;B	0.24043	0.016;0.096	B;B	0.11329	0.002;0.006	T	0.46133	-0.9213	9	0.87932	D	0	-12.1151	17.9807	0.89140	0.0:1.0:0.0:0.0	rs710187;rs3171658;rs17851163;rs710187	39;39	E2QC23;O75600	.;KBL_HUMAN	C	39	ENSP00000371110:R39C;ENSP00000248924:R39C;ENSP00000406719:R39C	ENSP00000248924:R39C	R	+	1	0	GCAT	36534035	1.000000	0.71417	0.999000	0.59377	0.736000	0.42039	6.794000	0.75135	2.545000	0.85829	0.655000	0.94253	CGC	C|0.420;T|0.580	0.580	strong		0.711	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	
GPR180	160897	hgsc.bcm.edu	37	13	95273447	95273447	+	Silent	SNP	G	G	A	rs12429818	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	169	0	0		WXS	Illumina HiSeq	Phase_I	152	78	0.513158	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	
KLK4	9622	hgsc.bcm.edu	37	19	51412666	51412666	+	Silent	SNP	C	C	A	rs1654552	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	129	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	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	
CLCN7	1186	hgsc.bcm.edu	37	16	1502857	1502857	+	Missense_Mutation	SNP	C	C	T	rs12926089	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1502857C>T	ENST00000382745.4	-	15	1857	c.1252G>A	c.(1252-1254)Gtg>Atg	p.V418M	CLCN7_ENST00000262318.8_Missense_Mutation_p.V394M|LA16c-390E6.4_ENST00000563610.1_RNA|CLCN7_ENST00000448525.1_Missense_Mutation_p.V394M	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	418			V -> M (in dbSNP:rs12926089). {ECO:0000269|PubMed:14584882}.		chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				GCCACCAGCACGGCCTCAATC	0.677													T|||	395	0.0788738	0.1604	0.0951	5008	,	,		15111	0.0		0.0924	False		,,,				2504	0.0245				p.V418M		Atlas-SNP	.											.	CLCN7	53	.	0			c.G1252A	GRCh37	CM057585	CLCN7	M	rs12926089	PASS	.	T	MET/VAL,MET/VAL	711,3631		63,585,1523	14.0	14.0	14.0		1180,1252	2.9	1.0	16	dbSNP_121	14	887,7653		48,791,3431	yes	missense,missense	CLCN7	NM_001114331.1,NM_001287.4	21,21	111,1376,4954	TT,TC,CC		10.3864,16.3749,12.4049	benign,benign	394/782,418/806	1502857	1598,11284	2171	4270	6441	SO:0001583	missense	1186	exon15			CCAGCACGGCCTC	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.1252G>A	16.37:g.1502857C>T	ENSP00000372193:p.Val418Met	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	37	CCDS32361.1	200	0.09157509157509157	83	0.16869918699186992	38	0.10497237569060773	0	0.0	79	0.10422163588390501	T	0.173	-1.069814	0.01918	0.163749	0.103864	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.94723	-3.5;-3.5	5.15	2.86	0.33363	Chloride channel, core (2);	0.115098	0.85682	N	0.000000	T	0.01320	0.0043	N	0.16862	0.45	0.53005	P	3.799999999998249E-5	B;B	0.16603	0.018;0.005	B;B	0.17722	0.019;0.007	T	0.44267	-0.9339	9	0.23302	T	0.38	-20.2438	8.1552	0.31165	0.0:0.2533:0.0:0.7467	rs12926089;rs59307144;rs12926089	394;418	E9PDB9;P51798	.;CLCN7_HUMAN	M	394;371;418;360	ENSP00000410907:V394M;ENSP00000372193:V418M	ENSP00000262318:V371M	V	-	1	0	CLCN7	1442858	1.000000	0.71417	0.997000	0.53966	0.326000	0.28443	1.084000	0.30828	0.005000	0.14708	-0.361000	0.07541	GTG	C|0.889;T|0.111	0.111	strong		0.677	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
ZNF469	84627	hgsc.bcm.edu	37	16	88504850	88504850	+	Missense_Mutation	SNP	G	G	C	rs1105066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88504850G>C	ENST00000437464.1	+	2	10888	c.10888G>C	c.(10888-10890)Gag>Cag	p.E3630Q	ZNF469_ENST00000565624.1_Missense_Mutation_p.E3658Q	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	3630			E -> Q (in dbSNP:rs1105066). {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						CATGGTGTCTGAGGGGGGGCC	0.642													G|||	1958	0.390974	0.531	0.3818	5008	,	,		13825	0.38		0.3926	False		,,,				2504	0.2178				p.E3630Q		Atlas-SNP	.											.	ZNF469	121	.	0			c.G10888C						PASS	.	G	GLN/GLU	729,639		200,329,155	7.0	11.0	10.0		10888	1.3	0.1	16	dbSNP_86	10	1311,1845		287,737,554	yes	missense	ZNF469	NM_001127464.1	29	487,1066,709	CC,CG,GG		41.5399,46.7105,45.0928	benign	3630/3926	88504850	2040,2484	684	1578	2262	SO:0001583	missense	84627	exon2			GTGTCTGAGGGGG	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.10888G>C	16.37:g.88504850G>C	ENSP00000402343:p.Glu3630Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	56	7	0.125	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	886	0.4056776556776557	265	0.5386178861788617	133	0.3674033149171271	195	0.3409090909090909	293	0.3865435356200528	G	9.407	1.079583	0.20309	0.532895	0.415399	ENSG00000225614	ENST00000437464	T	0.09911	2.93	4.65	1.33	0.21861	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	P	0.34724	0.465	B	0.30572	0.117	T	0.38972	-0.9636	8	0.49607	T	0.09	-3.6085	6.1191	0.20144	0.1901:0.1577:0.6522:0.0	rs1105066;rs3812952;rs57863012;rs1105066	3630	Q96JG9	ZN469_HUMAN	Q	3630	ENSP00000402343:E3630Q	ENSP00000402343:E3630Q	E	+	1	0	ZNF469	87032351	0.000000	0.05858	0.122000	0.21767	0.019000	0.09904	-0.519000	0.06260	0.950000	0.37743	0.561000	0.74099	GAG	G|0.601;C|0.399	0.399	strong		0.642	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
CNTROB	116840	hgsc.bcm.edu	37	17	7843053	7843053	+	Silent	SNP	C	C	T	rs11078719	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7843053C>T	ENST00000563694.1	+	8	2075	c.1150C>T	c.(1150-1152)Ctg>Ttg	p.L384L	CNTROB_ENST00000380262.3_Silent_p.L384L|CNTROB_ENST00000380255.3_Silent_p.L384L|CNTROB_ENST00000565740.1_Silent_p.L384L	NM_053051.3	NP_444279.2	Q8N137	CNTRB_HUMAN	centrobin, centrosomal BRCA2 interacting protein	384	Required for centrosome localization.				centriole replication (GO:0007099)|centrosome separation (GO:0051299)|cytokinesis (GO:0000910)	centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)	25		Prostate(122;0.173)				CCAGGCTCAGCTGGAAAGGGA	0.522													T|||	2979	0.594848	0.4433	0.6398	5008	,	,		20015	0.8016		0.4274	False		,,,				2504	0.727				p.L384L		Atlas-SNP	.											.	CNTROB	61	.	0			c.C1150T						PASS	.	T	,	2044,2362	578.7+/-384.7	482,1080,641	45.0	48.0	47.0		1150,1150	-6.8	0.2	17	dbSNP_120	47	3745,4853	586.7+/-392.1	829,2087,1383	no	coding-synonymous,coding-synonymous	CNTROB	NM_001037144.5,NM_053051.3	,	1311,3167,2024	TT,TC,CC		43.5566,46.3913,44.5171	,	384/926,384/904	7843053	5789,7215	2203	4299	6502	SO:0001819	synonymous_variant	116840	exon8			GCTCAGCTGGAAA	AF331638	CCDS32557.1, CCDS11126.1	17p13.1	2006-03-15				ENSG00000170037			29616	protein-coding gene	gene with protein product	"""centrobin"""	611425				11984006, 16275750	Standard	NM_001037144		Approved	LIP8, PP1221	uc002gjp.3	Q8N137		ENST00000563694.1:c.1150C>T	17.37:g.7843053C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001037144	A6NHQ1|Q331K3|Q69YV7|Q8NCB8|Q8WXV3|Q96CQ7|Q9C060	Silent	SNP	ENST00000563694.1	37	CCDS11126.1																																																																																			C|0.506;T|0.494	0.494	strong		0.522	CNTROB-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421372.1	NM_053051	
GBGT1	26301	hgsc.bcm.edu	37	9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	rs35898523	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136029645G>T	ENST00000372040.3	-	7	674	c.363C>A	c.(361-363)taC>taA	p.Y121*	GBGT1_ENST00000540636.1_Nonsense_Mutation_p.Y104*|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000372038.3_Missense_Mutation_p.H134N|GBGT1_ENST00000372043.3_Intron|RALGDS_ENST00000542690.1_Intron	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	121					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		TGAAATGAGTGTACCTAGTGA	0.587													G|||	215	0.0429313	0.034	0.0418	5008	,	,		18455	0.002		0.0815	False		,,,				2504	0.0583				p.Y121X		Atlas-SNP	.											GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	0			c.C363A						PASS	.	G	stop/TYR	199,4207	121.7+/-159.2	8,183,2012	39.0	40.0	39.0		363	1.5	0.9	9	dbSNP_126	39	629,7971	155.7+/-209.7	18,593,3689	yes	stop-gained	GBGT1	NM_021996.4		26,776,5701	TT,TG,GG		7.314,4.5166,6.3663		121/348	136029645	828,12178	2203	4300	6503	SO:0001587	stop_gained	26301	exon7			ATGAGTGTACCTA	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.363C>A	9.37:g.136029645G>T	ENSP00000361110:p.Tyr121*	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	23	7	0.304348	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Nonsense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	108|108	0.04945054945054945|0.04945054945054945	23|23	0.046747967479674794|0.046747967479674794	16|16	0.04419889502762431|0.04419889502762431	2|2	0.0034965034965034965|0.0034965034965034965	67|67	0.08839050131926121|0.08839050131926121	G|G	17.35|17.35	3.367115|3.367115	0.61513|0.61513	0.045166|0.045166	0.07314|0.07314	ENSG00000148288|ENSG00000148288	ENST00000372038|ENST00000372040;ENST00000540636	T|.	0.36157|.	1.27|.	5.38|5.38	1.47|1.47	0.22746|0.22746	.|.	.|0.137701	.|0.50627	.|D	.|0.000106	T|.	0.01156|.	0.0038|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.02358|.	-1.1171|.	6|.	0.05833|0.07813	T|T	0.94|0.8	-15.2709|-15.2709	6.0904|6.0904	0.19991|0.19991	0.2143:0.0:0.6535:0.1322|0.2143:0.0:0.6535:0.1322	rs35898523;rs62638704|rs35898523;rs62638704	.|.	.|.	.|.	N|X	134|121;104	ENSP00000361108:H134N|.	ENSP00000361108:H134N|ENSP00000361110:Y121X	H|Y	-|-	1|3	0|2	GBGT1|GBGT1	135019466|135019466	0.883000|0.883000	0.30277|0.30277	0.900000|0.900000	0.35374|0.35374	0.243000|0.243000	0.25628|0.25628	0.687000|0.687000	0.25407|0.25407	0.008000|0.008000	0.14787|0.14787	0.491000|0.491000	0.48974|0.48974	CAC|TAC	G|0.941;T|0.059	0.059	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
KDM7A	80853	hgsc.bcm.edu	37	7	139801777	139801777	+	Silent	SNP	T	T	G	rs1062277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:139801777T>G	ENST00000397560.2	-	12	1709	c.1612A>C	c.(1612-1614)Aga>Cga	p.R538R	JHDM1D_ENST00000006967.5_Silent_p.R538R	NM_030647.1	NP_085150.1	Q6ZMT4	KDM7A_HUMAN		538					histone H3-K27 demethylation (GO:0071557)|histone H3-K36 demethylation (GO:0070544)|histone H3-K9 demethylation (GO:0033169)|histone H4-K20 demethylation (GO:0035574)|midbrain development (GO:0030901)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K27 specific) (GO:0071558)|histone demethylase activity (H3-K36 specific) (GO:0051864)|histone demethylase activity (H3-K9 specific) (GO:0032454)|histone demethylase activity (H4-K20 specific) (GO:0035575)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|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)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)	22	Melanoma(164;0.0142)					ATCTCTAATCTTTTGAGGACC	0.398													T|||	1670	0.333466	0.416	0.281	5008	,	,		20517	0.245		0.335	False		,,,				2504	0.3487				p.R538R		Atlas-SNP	.											.	JHDM1D	54	.	0			c.A1612C						PASS	.	T		1448,2302		272,904,699	191.0	171.0	178.0		1612	5.9	0.8	7	dbSNP_86	178	2794,5418		479,1836,1791	no	coding-synonymous	JHDM1D	NM_030647.1		751,2740,2490	GG,GT,TT		34.0234,38.6133,35.4623		538/942	139801777	4242,7720	1875	4106	5981	SO:0001819	synonymous_variant	80853	exon12			CTAATCTTTTGAG																												ENST00000397560.2:c.1612A>C	7.37:g.139801777T>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	154	108	0.701299	NM_030647	A4D1S9|C9JJH9|C9JQU2|Q6MZL8|Q9C0E5	Silent	SNP	ENST00000397560.2	37	CCDS43658.1																																																																																			T|0.659;G|0.341	0.341	strong		0.398	JHDM1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348460.1		
CTSB	1508	hgsc.bcm.edu	37	8	11710174	11710174	+	Missense_Mutation	SNP	T	T	C	rs1803250	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:11710174T>C	ENST00000353047.6	-	3	410	c.157A>G	c.(157-159)Agc>Ggc	p.S53G	CTSB_ENST00000534510.1_Missense_Mutation_p.S53G|CTSB_ENST00000531089.1_Missense_Mutation_p.S53G|CTSB_ENST00000530640.2_Missense_Mutation_p.S53G|CTSB_ENST00000434271.1_Missense_Mutation_p.S53G|CTSB_ENST00000345125.3_Missense_Mutation_p.S53G|CTSB_ENST00000525076.1_5'UTR|CTSB_ENST00000415599.2_Missense_Mutation_p.S53G|CTSB_ENST00000453527.2_Missense_Mutation_p.S53G|CTSB_ENST00000533455.1_Missense_Mutation_p.S53G	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	53			S -> G (in dbSNP:rs1803250). {ECO:0000269|PubMed:15489334}.		cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		TTCAAGTAGCTCATGTCCACG	0.612													T|||	288	0.057508	0.0325	0.0879	5008	,	,		17881	0.0		0.1511	False		,,,				2504	0.0327				p.S53G		Atlas-SNP	.											.	CTSB	24	.	0			c.A157G						PASS	.	T	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	219,4187	131.0+/-167.6	6,207,1990	139.0	106.0	117.0		157,157,157,157,157	5.8	1.0	8	dbSNP_89	117	1196,7404	242.5+/-272.5	87,1022,3191	yes	missense,missense,missense,missense,missense	CTSB	NM_001908.3,NM_147780.2,NM_147781.2,NM_147782.2,NM_147783.2	56,56,56,56,56	93,1229,5181	CC,CT,TT		13.907,4.9705,10.8796	benign,benign,benign,benign,benign	53/340,53/340,53/340,53/340,53/340	11710174	1415,11591	2203	4300	6503	SO:0001583	missense	1508	exon5			AGTAGCTCATGTC	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"""Cathepsins"""	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.157A>G	8.37:g.11710174T>C	ENSP00000345672:p.Ser53Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_147780	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	176	0.08058608058608059	21	0.042682926829268296	36	0.09944751381215469	0	0.0	119	0.15699208443271767	T	13.56	2.272847	0.40194	0.049705	0.13907	ENSG00000164733	ENST00000434271;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000415599;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000534636;ENST00000533572;ENST00000530296;ENST00000526195;ENST00000527243;ENST00000534149;ENST00000526645;ENST00000530573;ENST00000505496;ENST00000524500;ENST00000531502;ENST00000527215;ENST00000532656;ENST00000534382;ENST00000528965	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34;1.34	5.85	5.85	0.93711	Peptidase C1A, propeptide (1);	0.071971	0.85682	D	0.000000	T	0.00144	0.0004	L	0.47190	1.495	0.22034	P	0.999404319	B	0.21753	0.06	B	0.15052	0.012	T	0.05666	-1.0871	9	0.38643	T	0.18	.	11.4166	0.49956	0.0:0.0:0.1508:0.8492	rs1803250;rs2230068;rs11548598;rs17757721;rs17855418;rs52837364;rs61727982	53	P07858	CATB_HUMAN	G	53	ENSP00000415889:S53G;ENSP00000345672:S53G;ENSP00000435105:S53G;ENSP00000433215:S53G;ENSP00000409917:S53G;ENSP00000411254:S53G;ENSP00000342070:S53G;ENSP00000432244:S53G;ENSP00000434217:S53G;ENSP00000436159:S53G;ENSP00000433995:S53G;ENSP00000435074:S53G;ENSP00000436627:S53G;ENSP00000434725:S53G;ENSP00000436122:S53G;ENSP00000431518:S53G;ENSP00000435650:S53G;ENSP00000436074:S53G;ENSP00000435886:S53G;ENSP00000431143:S53G;ENSP00000435260:S53G;ENSP00000433929:S53G	ENSP00000342070:S53G	S	-	1	0	CTSB	11747583	1.000000	0.71417	0.994000	0.49952	0.560000	0.35617	3.402000	0.52608	2.233000	0.73108	0.533000	0.62120	AGC	T|0.896;C|0.103;A|0.000	0.103	strong		0.612	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187698707	187698707	+	Missense_Mutation	SNP	C	C	T	rs6434197	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187698707C>T	ENST00000295131.2	-	6	833	c.794G>A	c.(793-795)tGc>tAc	p.C265Y		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	265				C -> Y (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			AAGATGGCAGCAGCTATCAAA	0.358													C|||	871	0.173922	0.4213	0.1066	5008	,	,		19180	0.0208		0.1103	False		,,,				2504	0.1104				p.C265Y		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.G794A						PASS	.	C	TYR/CYS	1761,2645	522.3+/-370.8	345,1071,787	139.0	120.0	127.0		794	2.9	0.6	2	dbSNP_116	127	978,7622	211.8+/-252.3	44,890,3366	yes	missense	ZSWIM2	NM_182521.2	194	389,1961,4153	TT,TC,CC		11.3721,39.9682,21.0595	possibly-damaging	265/634	187698707	2739,10267	2203	4300	6503	SO:0001583	missense	151112	exon6			TGGCAGCAGCTAT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.794G>A	2.37:g.187698707C>T	ENSP00000295131:p.Cys265Tyr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	C	14.90	2.672216	0.47781	0.399682	0.113721	ENSG00000163012	ENST00000295131	D	0.87103	-2.21	5.78	2.94	0.34122	Zinc finger, ZZ-type (1);	0.203889	0.35495	N	0.003173	T	0.00012	0.0000	L	0.54323	1.7	0.34988	P	0.24524800000000002	D	0.56287	0.975	P	0.55011	0.766	T	0.17107	-1.0380	9	0.31617	T	0.26	-0.3472	3.1443	0.06466	0.1403:0.5685:0.1362:0.155	rs6434197;rs17852919;rs52810898;rs58561796;rs6434197	265	Q8NEG5	ZSWM2_HUMAN	Y	265	ENSP00000295131:C265Y	ENSP00000295131:C265Y	C	-	2	0	ZSWIM2	187406952	0.004000	0.15560	0.630000	0.29268	0.581000	0.36288	0.540000	0.23191	0.797000	0.33971	0.467000	0.42956	TGC	C|0.806;T|0.194	0.194	strong		0.358	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
RFC4	5984	hgsc.bcm.edu	37	3	186509517	186509517	+	Silent	SNP	G	G	A	rs187868	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:186509517G>A	ENST00000392481.2	-	8	1079	c.798C>T	c.(796-798)gcC>gcT	p.A266A	RFC4_ENST00000433496.1_Silent_p.A266A|RFC4_ENST00000296273.2_Silent_p.A266A	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	266					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|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)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		CTCTTACCCCGGCAATGTCTG	0.388													A|||	2423	0.483826	0.4402	0.4942	5008	,	,		17459	0.5		0.494	False		,,,				2504	0.5082				p.A266A		Atlas-SNP	.											RFC4,colon,carcinoma,0,1	RFC4	54	1	0			c.C798T						PASS	.	A	,	2040,2366	609.3+/-391.3	467,1106,630	124.0	123.0	123.0		798,798	4.6	1.0	3	dbSNP_79	123	4135,4465	588.7+/-392.4	1011,2113,1176	no	coding-synonymous,coding-synonymous	RFC4	NM_002916.3,NM_181573.2	,	1478,3219,1806	AA,AG,GG		48.0814,46.3005,47.4781	,	266/364,266/364	186509517	6175,6831	2203	4300	6503	SO:0001819	synonymous_variant	5984	exon8			TACCCCGGCAATG		CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"""ATPases / AAA-type"""	9972	protein-coding gene	gene with protein product	"""A1 37 kDa subunit"", ""activator 1 37 kDa subunit"", ""RFC 37 kDa subunit"""	102577	"""replication factor C (activator 1) 4 (37kD)"""			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.798C>T	3.37:g.186509517G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_181573	B4DM41|D3DNV2|Q6FHX7	Silent	SNP	ENST00000392481.2	37	CCDS3283.1																																																																																			G|0.516;A|0.484	0.484	strong		0.388	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916	
OTUD3	23252	hgsc.bcm.edu	37	1	20224152	20224152	+	Silent	SNP	G	G	A	rs61769077	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:20224152G>A	ENST00000375120.3	+	4	604	c.603G>A	c.(601-603)acG>acA	p.T201T	OTUD3_ENST00000466697.1_3'UTR	NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	201					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)		ATCTCCAGACGGATGTGAGTG	0.502													G|||	222	0.0443291	0.0681	0.036	5008	,	,		16019	0.0		0.0557	False		,,,				2504	0.0521				p.T201T		Atlas-SNP	.											.	OTUD3	25	.	0			c.G603A						PASS	.	G		253,3697		15,223,1737	93.0	92.0	92.0		603	-11.1	0.2	1	dbSNP_129	92	446,7872		12,422,3725	no	coding-synonymous	OTUD3	NM_015207.1		27,645,5462	AA,AG,GG		5.3619,6.4051,5.6978		201/399	20224152	699,11569	1975	4159	6134	SO:0001819	synonymous_variant	23252	exon4			CCAGACGGATGTG	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.603G>A	1.37:g.20224152G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	58	10	0.172414	NM_015207	O75047	Silent	SNP	ENST00000375120.3	37	CCDS41279.1																																																																																			G|0.950;A|0.050	0.050	strong		0.502	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1		
MLC1	23209	hgsc.bcm.edu	37	22	50515270	50515270	+	Splice_Site	SNP	T	T	C	rs267607236|rs6010164	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50515270T>C	ENST00000311597.5	-	7	1203	c.597A>G	c.(595-597)tcA>tcG	p.S199S	MLC1_ENST00000538737.1_Splice_Site_p.S165S|MLC1_ENST00000395876.2_Splice_Site_p.S199S|MLC1_ENST00000535444.1_Splice_Site_p.S120S|MLC1_ENST00000431262.2_Splice_Site_p.S169S|MLC1_ENST00000450140.2_Splice_Site_p.S147S	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	84	51	0.607143	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
XIRP2	129446	hgsc.bcm.edu	37	2	168115797	168115797	+	Missense_Mutation	SNP	G	G	C	rs75758327	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168115797G>C	ENST00000409728.1	+	11	2929	c.2840G>C	c.(2839-2841)aGa>aCa	p.R947T	XIRP2_ENST00000409605.1_Missense_Mutation_p.R692T|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.R914T|XIRP2_ENST00000409043.1_Missense_Mutation_p.R914T|XIRP2_ENST00000420519.1_Missense_Mutation_p.R947T|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409195.1_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					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						TTGTTTCCCAGAGTGGAGGTG	0.448													G|||	466	0.0930511	0.1838	0.049	5008	,	,		18315	0.0129		0.0845	False		,,,				2504	0.093				p.R947T		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2840C						PASS	.	G	THR/ARG,THR/ARG,,THR/ARG,	646,3228		53,540,1344	79.0	73.0	75.0		2741,2840,,2075,	-1.6	0.0	2	dbSNP_131	75	606,7688		26,554,3567	yes	missense,missense,utr-3,missense,utr-3	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	71,71,,71,	79,1094,4911	CC,CG,GG		7.3065,16.6753,10.2893	,,,,	914/939,947/972,,692/717,	168115797	1252,10916	1937	4147	6084	SO:0001583	missense	129446	exon11			TTCCCAGAGTGGA	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	ENST00000409728.1:c.2840G>C	2.37:g.168115797G>C	ENSP00000386619:p.Arg947Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	191	0.08745421245421245	88	0.17886178861788618	21	0.058011049723756904	14	0.024475524475524476	68	0.08970976253298153	G	13.02	2.113098	0.37339	0.166753	0.073065	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13	5.7	-1.62	0.08372	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.80722	P	0.0	B;B	0.16802	0.004;0.019	B;B	0.15052	0.008;0.012	T	0.06023	-1.0850	7	0.54805	T	0.06	.	1.9647	0.03393	0.2847:0.2083:0.4003:0.1066	.	914;947	A4UGR9-4;A4UGR9-6	.;.	T	914;947;914;947;692	ENSP00000386454:R914T;ENSP00000386619:R947T;ENSP00000386724:R914T;ENSP00000415541:R947T;ENSP00000386981:R692T	ENSP00000386454:R914T	R	+	2	0	XIRP2	167824043	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	0.318000	0.19504	-0.318000	0.08665	0.650000	0.86243	AGA	G|0.922;C|0.078	0.078	strong		0.448	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238671328	238671328	+	Silent	SNP	A	A	G	rs868119	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238671328A>G	ENST00000392000.4	+	11	1089	c.972A>G	c.(970-972)gaA>gaG	p.E324E	LRRFIP1_ENST00000308482.9_Intron|LRRFIP1_ENST00000289175.6_Silent_p.E268E|LRRFIP1_ENST00000244815.5_Silent_p.E300E	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	324					innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		CTGAGAAAGAACAACACACAG	0.458													A|||	1647	0.328874	0.3533	0.2723	5008	,	,		21928	0.4444		0.1998	False		,,,				2504	0.3497				p.E324E		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.A972G						PASS	.	A	,,,,	1576,2830	491.3+/-362.1	296,984,923	82.0	74.0	77.0		,,972,804,900	-9.9	0.0	2	dbSNP_86	77	1617,6983	300.5+/-305.0	144,1329,2827	no	intron,intron,coding-synonymous,coding-synonymous,coding-synonymous	LRRFIP1	NM_001137550.1,NM_001137551.1,NM_001137552.1,NM_001137553.1,NM_004735.3	,,,,	440,2313,3750	GG,GA,AA		18.8023,35.7694,24.5502	,,,,	,,324/809,268/753,300/785	238671328	3193,9813	2203	4300	6503	SO:0001819	synonymous_variant	9208	exon11			GAAAGAACAACAC	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"""GC-binding factor 2"""	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.972A>G	2.37:g.238671328A>G		Somatic	385	1	0.0025974		WXS	Illumina HiSeq	Phase_I	413	200	0.484262	NM_001137552	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Silent	SNP	ENST00000392000.4	37	CCDS46552.1																																																																																			A|0.732;G|0.268	0.268	strong		0.458	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
ABCC1	4363	hgsc.bcm.edu	37	16	16162039	16162039	+	Silent	SNP	C	C	T	rs8187858	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:16162039C>T	ENST00000399410.3	+	13	1879	c.1704C>T	c.(1702-1704)taC>taT	p.Y568Y	ABCC1_ENST00000345148.5_Silent_p.Y568Y|ABCC1_ENST00000351154.5_Silent_p.Y568Y|ABCC1_ENST00000399408.2_Silent_p.Y568Y|ABCC1_ENST00000349029.5_Silent_p.Y568Y|ABCC1_ENST00000346370.5_Silent_p.Y568Y	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	568	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	TTGCCGTCTACGTGACCATTG	0.562													C|||	179	0.0357428	0.0053	0.0504	5008	,	,		19559	0.001		0.0984	False		,,,				2504	0.0378				p.Y568Y		Atlas-SNP	.											.	ABCC1	156	.	0			c.C1704T						PASS	.	C	,,,,	66,4202		0,66,2068	182.0	177.0	179.0		1704,1704,1704,1704,1704	0.1	1.0	16	dbSNP_123	179	791,7693		41,709,3492	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	,,,,	41,775,5560	TT,TC,CC		9.3234,1.5464,6.7205	,,,,	568/1532,568/1473,568/1476,568/1417,568/1467	16162039	857,11895	2134	4242	6376	SO:0001819	synonymous_variant	4363	exon13			CGTCTACGTGACC	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.1704C>T	16.37:g.16162039C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	182	83	0.456044	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			C|0.953;T|0.047	0.047	strong		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
TECPR2	9895	hgsc.bcm.edu	37	14	102909991	102909991	+	Silent	SNP	C	C	T	rs17100923	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102909991C>T	ENST00000359520.7	+	12	2986	c.2760C>T	c.(2758-2760)agC>agT	p.S920S	TECPR2_ENST00000558678.1_Silent_p.S920S	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	920					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						CAGGTCTGAGCGTGGATCGCC	0.532													C|||	431	0.0860623	0.2383	0.0403	5008	,	,		15922	0.001		0.0616	False		,,,				2504	0.0256				p.S920S		Atlas-SNP	.											.	TECPR2	114	.	0			c.C2760T						PASS	.	C	,	930,3476	351.1+/-311.1	87,756,1360	79.0	58.0	65.0		2760,2760	-10.0	0.1	14	dbSNP_123	65	505,8095	143.1+/-199.2	17,471,3812	no	coding-synonymous,coding-synonymous	TECPR2	NM_001172631.1,NM_014844.3	,	104,1227,5172	TT,TC,CC		5.8721,21.1076,11.0334	,	920/1268,920/1412	102909991	1435,11571	2203	4300	6503	SO:0001819	synonymous_variant	9895	exon12			TCTGAGCGTGGAT	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.2760C>T	14.37:g.102909991C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Silent	SNP	ENST00000359520.7	37	CCDS32162.1																																																																																			C|0.899;T|0.101	0.101	strong		0.532	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
GNB5	10681	hgsc.bcm.edu	37	15	52446200	52446200	+	Silent	SNP	G	G	A	rs6493537	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52446200G>A	ENST00000261837.7	-	4	377	c.312C>T	c.(310-312)caC>caT	p.H104H	GNB5_ENST00000396335.4_Silent_p.H62H|GNB5_ENST00000560116.1_Silent_p.H62H|GNB5_ENST00000358784.7_Silent_p.H62H	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	104					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		CTTTGTTCCCGTGGCCTTTGA	0.562													A|||	650	0.129792	0.3442	0.1167	5008	,	,		19422	0.0258		0.0417	False		,,,				2504	0.047				p.H104H		Atlas-SNP	.											.	GNB5	28	.	0			c.C312T						PASS	.	A	,	1362,3028	690.6+/-405.3	225,912,1058	152.0	129.0	137.0		186,312	-6.0	0.9	15	dbSNP_116	137	334,8252	803.8+/-407.3	5,324,3964	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	230,1236,5022	AA,AG,GG		3.8901,31.0251,13.0703	,	62/354,104/396	52446200	1696,11280	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			GTTCCCGTGGCCT	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"""WD repeat domain containing"""	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.312C>T	15.37:g.52446200G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	35	7	0.2	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			G|0.873;A|0.127	0.127	strong		0.562	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
MYRF	745	hgsc.bcm.edu	37	11	61553284	61553284	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:61553284C>T	ENST00000278836.5	+	26	3409	c.3313C>T	c.(3313-3315)Cgg>Tgg	p.R1105W	MYRF_ENST00000265460.5_Missense_Mutation_p.R1065W|MYRF_ENST00000389602.4_Missense_Mutation_p.R491W|TMEM258_ENST00000535042.1_Intron	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	1105					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)										CACCTCTCACCGGTGGCCAAT	0.622																																					p.R1105W		Atlas-SNP	.											C11orf9,right_upper_lobe,carcinoma,-1,1	.	.	1	0			c.C3313T						scavenged	.						81.0	75.0	77.0					11																	61553284		2202	4299	6501	SO:0001583	missense	745	exon26			TCTCACCGGTGGC		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.3313C>T	11.37:g.61553284C>T	ENSP00000278836:p.Arg1105Trp	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	228	3	0.0131579	NM_001127392	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	37	CCDS44622.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.618976	0.46736	.	.	ENSG00000124920	ENST00000278836;ENST00000265460;ENST00000389602	T;T;T	0.45276	0.9;0.9;0.9	5.08	5.08	0.68730	.	0.301612	0.31734	N	0.007144	T	0.37210	0.0995	N	0.22421	0.69	0.80722	D	1	D;P;D	0.55605	0.972;0.956;0.964	P;P;P	0.49597	0.616;0.502;0.536	T	0.20174	-1.0283	10	0.62326	D	0.03	-16.2016	11.3429	0.49543	0.0:0.9167:0.0:0.0833	.	491;1065;1105	B4DHB2;Q9Y2G1-2;Q9Y2G1	.;.;MRF_HUMAN	W	1105;1065;491	ENSP00000278836:R1105W;ENSP00000265460:R1065W;ENSP00000374253:R491W	ENSP00000265460:R1065W	R	+	1	2	C11orf9	61309860	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	2.065000	0.41442	2.537000	0.85549	0.561000	0.74099	CGG	.	.	none		0.622	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279	
TARBP1	6894	hgsc.bcm.edu	37	1	234541801	234541801	+	Silent	SNP	A	A	G	rs12073170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:234541801A>G	ENST00000040877.1	-	24	3836	c.3837T>C	c.(3835-3837)tgT>tgC	p.C1279C	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1279					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TGTGATTGAAACACCACTGCA	0.373													A|||	569	0.113618	0.146	0.1744	5008	,	,		21750	0.0853		0.0885	False		,,,				2504	0.0818				p.C1279C		Atlas-SNP	.											.	TARBP1	111	.	0			c.T3837C						PASS	.	A		579,3827	259.2+/-262.9	48,483,1672	117.0	113.0	114.0		3837	-4.3	0.1	1	dbSNP_120	114	773,7827	183.0+/-231.3	39,695,3566	no	coding-synonymous	TARBP1	NM_005646.3		87,1178,5238	GG,GA,AA		8.9884,13.1412,10.3952		1279/1622	234541801	1352,11654	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon24			ATTGAAACACCAC		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"""tRNA methyltransferase 3 homolog (S. cerevisiae)"""	605052	"""Tar (HIV-1) RNA binding protein 1"""			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.3837T>C	1.37:g.234541801A>G		Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	328	327	0.996951	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			A|0.897;G|0.103	0.103	strong		0.373	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
ELL2	22936	hgsc.bcm.edu	37	5	95234350	95234350	+	Silent	SNP	A	A	G	rs3777204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:95234350A>G	ENST00000237853.4	-	8	1468	c.1119T>C	c.(1117-1119)ccT>ccC	p.P373P	ELL2_ENST00000431061.2_Intron	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	373					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)		GTGGAGGGGTAGGGATGGCAG	0.552													G|||	2237	0.446685	0.6263	0.3314	5008	,	,		14177	0.4643		0.2863	False		,,,				2504	0.4325				p.P373P		Atlas-SNP	.											.	ELL2	63	.	0			c.T1119C						PASS	.	G		2505,1901		720,1065,418	57.0	70.0	66.0		1119	-3.4	0.2	5	dbSNP_107	66	2316,6284		308,1700,2292	yes	coding-synonymous	ELL2	NM_012081.5		1028,2765,2710	GG,GA,AA		26.9302,43.1457,37.0675		373/641	95234350	4821,8185	2203	4300	6503	SO:0001819	synonymous_variant	22936	exon8			AGGGGTAGGGATG	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.1119T>C	5.37:g.95234350A>G		Somatic	292	2	0.00684932		WXS	Illumina HiSeq	Phase_I	230	228	0.991304	NM_012081	B4DNK7	Silent	SNP	ENST00000237853.4	37	CCDS4080.1																																																																																			A|0.626;G|0.374	0.374	strong		0.552	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656479	46656479	+	Missense_Mutation	SNP	A	A	G	rs6519993	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46656479A>G	ENST00000253255.5	-	1	2740	c.2741T>C	c.(2740-2742)cTc>cCc	p.L914P		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	914			L -> P (in dbSNP:rs6519993).		acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CCAAGGAAAGAGGTCATTTGT	0.418													G|||	1229	0.245407	0.6785	0.134	5008	,	,		22048	0.001		0.16	False		,,,				2504	0.0787				p.L914P		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T2741C						PASS	.	G	PRO/LEU	2650,1756	517.3+/-369.4	793,1064,346	106.0	111.0	109.0		2741	5.3	1.0	22	dbSNP_116	109	1256,7344	758.5+/-407.5	88,1080,3132	yes	missense	PKDREJ	NM_006071.1	98	881,2144,3478	GG,GA,AA		14.6047,39.8547,30.0323	benign	914/2254	46656479	3906,9100	2203	4300	6503	SO:0001583	missense	10343	exon1			GGAAAGAGGTCAT	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2741T>C	22.37:g.46656479A>G	ENSP00000253255:p.Leu914Pro	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	477	0.2184065934065934	309	0.6280487804878049	55	0.15193370165745856	0	0.0	113	0.14907651715039577	G	1.467	-0.560725	0.03939	0.601453	0.146047	ENSG00000130943	ENST00000253255	T	0.30714	1.52	5.33	5.33	0.75918	.	0.307994	0.28398	N	0.015492	T	0.00012	0.0000	N	0.00392	-1.555	0.30026	P	0.813909	B	0.02656	0.0	B	0.01281	0.0	T	0.41610	-0.9499	9	0.02654	T	1	-28.6325	13.3236	0.60447	0.0774:0.0:0.9226:0.0	rs6519993;rs52835982;rs61529203;rs6519993	914	Q9NTG1	PKDRE_HUMAN	P	914	ENSP00000253255:L914P	ENSP00000253255:L914P	L	-	2	0	PKDREJ	45035143	1.000000	0.71417	0.965000	0.40720	0.372000	0.29890	4.073000	0.57570	1.411000	0.46957	-0.119000	0.15052	CTC	A|0.724;G|0.276	0.276	strong		0.418	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
CATSPERG	57828	hgsc.bcm.edu	37	19	38847431	38847431	+	Silent	SNP	T	T	C	rs2286475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38847431T>C	ENST00000409235.3	+	11	1360	c.1245T>C	c.(1243-1245)acT>acC	p.T415T	CATSPERG_ENST00000215069.4_Silent_p.T408T|CATSPERG_ENST00000410018.1_Intron	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	415					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						GTGAGTATACTCTACTGCTGC	0.532													C|||	1648	0.329073	0.1573	0.3948	5008	,	,		19875	0.4544		0.2873	False		,,,				2504	0.4284				p.T415T		Atlas-SNP	.											.	CATSPERG	121	.	0			c.T1245C						PASS	.	C		779,3627	753.3+/-412.4	75,629,1499	204.0	184.0	191.0		1245	-8.2	0.0	19	dbSNP_100	191	2029,6571	720.5+/-406.3	239,1551,2510	no	coding-synonymous	CATSPERG	NM_021185.4		314,2180,4009	CC,CT,TT		23.593,17.6804,21.59		415/1160	38847431	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	57828	exon11			GTATACTCTACTG	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"""chromosome 19 open reading frame 15"", ""cation channel, sperm-associated, gamma"""	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.1245T>C	19.37:g.38847431T>C		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	220	96	0.436364	NM_021185	A6NEG6|Q659E1	Silent	SNP	ENST00000409235.3	37	CCDS12514.2																																																																																			T|0.735;C|0.265	0.265	strong		0.532	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	
FAM189A1	23359	hgsc.bcm.edu	37	15	29421014	29421014	+	Silent	SNP	G	G	C	rs2306934	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:29421014G>C	ENST00000261275.4	-	8	980	c.981C>G	c.(979-981)acC>acG	p.T327T		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	327	Pro-rich.					integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						AGCCAGCACTGGTGTTTGGGT	0.537													G|||	690	0.13778	0.1271	0.1196	5008	,	,		18171	0.2103		0.0805	False		,,,				2504	0.1493				p.T327T		Atlas-SNP	.											.	FAM189A1	20	.	0			c.C981G						PASS	.	G		160,1224		9,142,541	60.0	62.0	61.0		981	1.8	0.0	15	dbSNP_100	61	249,2933		12,225,1354	no	coding-synonymous	FAM189A1	NM_015307.1		21,367,1895	CC,CG,GG		7.8253,11.5607,8.9575		327/540	29421014	409,4157	692	1591	2283	SO:0001819	synonymous_variant	23359	exon8			AGCACTGGTGTTT		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.981C>G	15.37:g.29421014G>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	54	35	0.648148	NM_015307	A0PK09	Silent	SNP	ENST00000261275.4	37	CCDS45198.1																																																																																			G|0.869;C|0.131	0.131	strong		0.537	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
EIF5B	9669	hgsc.bcm.edu	37	2	99995804	99995804	+	Silent	SNP	T	T	C	rs1376443	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:99995804T>C	ENST00000289371.6	+	12	2176	c.1974T>C	c.(1972-1974)gaT>gaC	p.D658D		NM_015904.3	NP_056988.3	O60841	IF2P_HUMAN	eukaryotic translation initiation factor 5B	658	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				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						ATGTACAAGATGGTGAAGCAG	0.363													C|||	3024	0.603834	0.7602	0.7104	5008	,	,		17893	0.3681		0.5865	False		,,,				2504	0.5777				p.D658D	Colon(162;2388 2567 2705 3444)	Atlas-SNP	.											.	EIF5B	95	.	0			c.T1974C						PASS	.	C		2839,941		1071,697,122	90.0	83.0	85.0		1974	2.0	1.0	2	dbSNP_88	85	4694,3514		1343,2008,753	no	coding-synonymous	EIF5B	NM_015904.3		2414,2705,875	CC,CT,TT		42.8119,24.8942,37.1622		658/1221	99995804	7533,4455	1890	4104	5994	SO:0001819	synonymous_variant	9669	exon12			ACAAGATGGTGAA	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.1974T>C	2.37:g.99995804T>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	231	115	0.497835	NM_015904	O95805|Q53RV7|Q53SI8|Q9UF81|Q9UMN7	Silent	SNP	ENST00000289371.6	37	CCDS42721.1																																																																																			T|0.415;C|0.585	0.585	strong		0.363	EIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330364.2	NM_015904	
SLC6A12	6539	hgsc.bcm.edu	37	12	311949	311949	+	Silent	SNP	A	A	G	rs216250	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:311949A>G	ENST00000428720.1	-	5	1190	c.447T>C	c.(445-447)acT>acC	p.T149T	SLC6A12_ENST00000359674.4_Silent_p.T149T|RP11-283I3.2_ENST00000539568.1_RNA|SLC6A12_ENST00000536824.1_Silent_p.T149T|SLC6A12_ENST00000424061.2_Silent_p.T149T|SLC6A12_ENST00000538272.1_5'UTR|SLC6A12_ENST00000397296.2_Silent_p.T149T	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	149					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)			GCAGCTCAGAAGTGAAGGAGC	0.517													G|||	3085	0.616014	0.767	0.5908	5008	,	,		20019	0.6339		0.4632	False		,,,				2504	0.5685				p.T149T		Atlas-SNP	.											.	SLC6A12	60	.	0			c.T447C						PASS	.	G	,,,	3065,1341	447.9+/-348.5	1074,917,212	117.0	103.0	108.0		447,447,447,447	5.5	1.0	12	dbSNP_79	108	3811,4789	613.3+/-396.1	866,2079,1355	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC6A12	NM_001122847.2,NM_001122848.2,NM_001206931.1,NM_003044.4	,,,	1940,2996,1567	GG,GA,AA		44.314,30.4358,47.1321	,,,	149/615,149/615,149/615,149/615	311949	6876,6130	2203	4300	6503	SO:0001819	synonymous_variant	6539	exon5			CTCAGAAGTGAAG	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.447T>C	12.37:g.311949A>G		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	90	86	0.955556	NM_001122848	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	37	CCDS8501.1																																																																																			A|0.437;G|0.563	0.563	strong		0.517	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
ARSD	414	hgsc.bcm.edu	37	X	2835964	2835964	+	Silent	SNP	G	G	A	rs73632972	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:2835964G>A	ENST00000381154.1	-	5	819	c.744C>T	c.(742-744)ttC>ttT	p.F248F	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	248					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)				GCACAAACCCGAAGGAGGAGT	0.557																																					p.F248F		Atlas-SNP	.											.	ARSD	47	.	0			c.C744T						PASS	.						35.0	38.0	37.0					X																	2835964		2203	4300	6503	SO:0001819	synonymous_variant	414	exon5			AAACCCGAAGGAG	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.744C>T	X.37:g.2835964G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	140	55	0.392857	NM_001669	Q9UHJ8	Silent	SNP	ENST00000381154.1	37	CCDS35196.1																																																																																			G|0.500;A|0.500	0.500	strong		0.557	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
GJB3	2707	hgsc.bcm.edu	37	1	35250720	35250720	+	Silent	SNP	C	C	T	rs41310442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:35250720C>T	ENST00000373366.2	+	2	972	c.357C>T	c.(355-357)aaC>aaT	p.N119N	RP1-34M23.5_ENST00000542839.1_RNA|GJB3_ENST00000373362.3_Silent_p.N119N	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	186	0	0		WXS	Illumina HiSeq	Phase_I	147	99	0.673469	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	
EPB41L2	2037	hgsc.bcm.edu	37	6	131190838	131190838	+	Silent	SNP	G	G	A	rs17059736	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:131190838G>A	ENST00000337057.3	-	15	2653	c.2472C>T	c.(2470-2472)ccC>ccT	p.P824P	EPB41L2_ENST00000530481.1_Intron|EPB41L2_ENST00000525271.1_Intron|EPB41L2_ENST00000528282.1_Intron|EPB41L2_ENST00000368128.2_Silent_p.P824P|EPB41L2_ENST00000445890.2_Intron|EPB41L2_ENST00000530757.1_Intron|EPB41L2_ENST00000527411.1_Silent_p.P754P|EPB41L2_ENST00000524581.1_Silent_p.P202P|EPB41L2_ENST00000525193.1_Intron|EPB41L2_ENST00000529208.1_Silent_p.P754P|EPB41L2_ENST00000392427.3_Intron|EPB41L2_ENST00000531410.1_Intron|EPB41L2_ENST00000527659.1_Intron	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	824					cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		TCTTCTCTCCGGGTATCTTTT	0.507													G|||	799	0.159545	0.2489	0.2104	5008	,	,		19065	0.0873		0.1262	False		,,,				2504	0.1115				p.P824P		Atlas-SNP	.											.	EPB41L2	96	.	0			c.C2472T						PASS	.	G	,,,,	1149,3257	408.4+/-334.6	155,839,1209	266.0	248.0	254.0		,,,,2472	-0.6	0.6	6	dbSNP_123	254	988,7612	212.5+/-252.8	51,886,3363	no	intron,intron,intron,intron,coding-synonymous	EPB41L2	NM_001135554.1,NM_001135555.2,NM_001199388.1,NM_001199389.1,NM_001431.3	,,,,	206,1725,4572	AA,AG,GG		11.4884,26.0781,16.4309	,,,,	,,,,824/1006	131190838	2137,10869	2203	4300	6503	SO:0001819	synonymous_variant	2037	exon15			CTCTCCGGGTATC	AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.2472C>T	6.37:g.131190838G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	260	112	0.430769	NM_001431	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Silent	SNP	ENST00000337057.3	37	CCDS5141.1	336	0.15384615384615385	110	0.22357723577235772	71	0.19613259668508287	61	0.10664335664335664	94	0.12401055408970976	G	0.169	-1.073530	0.01918	0.260781	0.114884	ENSG00000079819	ENST00000456097	.	.	.	5.71	-0.641	0.11490	.	.	.	.	.	T	0.31389	0.0795	.	.	.	0.09310	P	0.9999999765644	.	.	.	.	.	.	T	0.18053	-1.0349	3	.	.	.	.	10.824	0.46620	0.5978:0.0:0.4022:0.0	rs17059736;rs17059736	.	.	.	W	367	.	.	R	-	1	2	EPB41L2	131232531	0.003000	0.15002	0.625000	0.29200	0.157000	0.22087	-0.125000	0.10579	-0.095000	0.12351	-1.587000	0.00848	CGG	G|0.841;A|0.159	0.159	strong		0.507	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3		
WRAP73	49856	hgsc.bcm.edu	37	1	3551828	3551828	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:3551828G>A	ENST00000270708.7	-	7	707	c.634C>T	c.(634-636)Cgg>Tgg	p.R212W	WRAP73_ENST00000378322.3_Missense_Mutation_p.R212W	NM_017818.3	NP_060288.3	Q9P2S5	WRP73_HUMAN	WD repeat containing, antisense to TP73	212						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)	12						GACAACAACCGGCCATCCAAT	0.542																																					p.R212W		Atlas-SNP	.											WRAP73,NS,carcinoma,+1,1	WRAP73	43	1	0			c.C634T						PASS	.						80.0	80.0	80.0					1																	3551828		2203	4300	6503	SO:0001583	missense	49856	exon7			ACAACCGGCCATC	AB034912, EF494669	CCDS48.1	1p36.3	2013-05-21	2011-04-13	2011-04-13	ENSG00000116213	ENSG00000116213		"""WD repeat domain containing"""	12759	protein-coding gene	gene with protein product		606040	"""WD repeat domain 8"""	WDR8			Standard	NM_017818		Approved		uc001ako.3	Q9P2S5	OTTHUMG00000000612	ENST00000270708.7:c.634C>T	1.37:g.3551828G>A	ENSP00000270708:p.Arg212Trp	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_017818	Q5T0D6|Q9BUH7|Q9NTK7|Q9NX56	Missense_Mutation	SNP	ENST00000270708.7	37	CCDS48.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.168380	0.57584	.	.	ENSG00000116213	ENST00000270708;ENST00000378322;ENST00000419924	T;T	0.49139	3.34;0.79	5.65	5.65	0.86999	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.77226	0.4099	H	0.94423	3.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83414	0.0029	10	0.87932	D	0	-63.099	15.1585	0.72761	0.0:0.0:0.8584:0.1416	.	212	Q9P2S5	WRP73_HUMAN	W	212;212;183	ENSP00000270708:R212W;ENSP00000367573:R212W	ENSP00000270708:R212W	R	-	1	2	WRAP73	3541688	1.000000	0.71417	1.000000	0.80357	0.053000	0.15095	5.938000	0.70170	2.652000	0.90054	0.655000	0.94253	CGG	.	.	none		0.542	WRAP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001470.1		
ADAMTS20	80070	hgsc.bcm.edu	37	12	43769228	43769228	+	Silent	SNP	A	A	C	rs10506226	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:43769228A>C	ENST00000389420.3	-	36	5399	c.5400T>G	c.(5398-5400)acT>acG	p.T1800T		NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1800	GON. {ECO:0000255|PROSITE- ProRule:PRU00383}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TGCTGAAAACAGTGTATCCAG	0.338													A|||	1114	0.222444	0.4213	0.1239	5008	,	,		17947	0.1002		0.1998	False		,,,				2504	0.1728				p.T1800T		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.T5400G						PASS	.	A		1633,2773	500.1+/-364.6	310,1013,880	137.0	133.0	134.0		5400	-3.6	0.2	12	dbSNP_119	134	1768,6832	319.5+/-314.2	182,1404,2714	no	coding-synonymous	ADAMTS20	NM_025003.3		492,2417,3594	CC,CA,AA		20.5581,37.0631,26.1495		1800/1911	43769228	3401,9605	2203	4300	6503	SO:0001819	synonymous_variant	80070	exon36			GAAAACAGTGTAT	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.5400T>G	12.37:g.43769228A>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	144	56	0.388889	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																			A|0.790;C|0.210	0.210	strong		0.338	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
KRT81	3887	hgsc.bcm.edu	37	12	52681080	52681080	+	Silent	SNP	G	G	A	rs4761784	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52681080G>A	ENST00000327741.5	-	7	1121	c.1053C>T	c.(1051-1053)gcC>gcT	p.A351A	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	351	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		GCTCAGACTGGGCCACCGCGG	0.607													.|||	1476	0.294728	0.1082	0.3386	5008	,	,		18323	0.4296		0.332	False		,,,				2504	0.3384				p.A351A		Atlas-SNP	.											.	KRT81	46	.	0			c.C1053T						PASS	.	G		607,3799		60,487,1656	25.0	28.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1053	1.0	0.7	12	dbSNP_111	27	2649,5951		396,1857,2047	no	coding-synonymous	KRT81	NM_002281.3		456,2344,3703	AA,AG,GG		30.8023,13.7767,25.0346		351/506	52681080	3256,9750	2203	4300	6503	SO:0001819	synonymous_variant	3887	exon7			AGACTGGGCCACC	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6458	protein-coding gene	gene with protein product	"""hard keratin type II 1"""	602153	"""keratin, hair, basic, 1"""	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.1053C>T	12.37:g.52681080G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Silent	SNP	ENST00000327741.5	37	CCDS31805.1																																																																																			G|0.744;A|0.256	0.256	strong		0.607	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	
HOXD4	3233	hgsc.bcm.edu	37	2	177016728	177016728	+	Missense_Mutation	SNP	T	T	C	rs34727427	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:177016728T>C	ENST00000306324.3	+	1	779	c.367T>C	c.(367-369)Tcc>Ccc	p.S123P	HOXD3_ENST00000468418.3_5'UTR|MIR10B_ENST00000385011.1_RNA	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	123			S -> P (in dbSNP:rs34727427). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1975093}.		multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		GCAGCCGCCCTCCGGGACGGC	0.687													C|||	1184	0.236422	0.4054	0.1916	5008	,	,		9977	0.0228		0.3082	False		,,,				2504	0.1861				p.S123P		Atlas-SNP	.											HOXD4,NS,carcinoma,-1,1	HOXD4	32	1	0			c.T367C						PASS	.	C	PRO/SER	1451,2795		252,947,924	28.0	35.0	33.0		367	2.9	1.0	2	dbSNP_126	33	2576,5950		397,1782,2084	yes	missense	HOXD4	NM_014621.2	74	649,2729,3008	CC,CT,TT		30.2135,34.1733,31.5299	benign	123/256	177016728	4027,8745	2123	4263	6386	SO:0001583	missense	3233	exon1			CCGCCCTCCGGGA		CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"""Homeoboxes / ANTP class : HOXL subclass"""	5138	protein-coding gene	gene with protein product		142981	"""homeo box D4"""	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.367T>C	2.37:g.177016728T>C	ENSP00000302548:p.Ser123Pro	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_014621	B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	37	CCDS2269.1	511	0.23397435897435898	195	0.39634146341463417	80	0.22099447513812154	8	0.013986013986013986	228	0.3007915567282322	C	6.670	0.492176	0.12702	0.341733	0.302135	ENSG00000170166	ENST00000306324	D	0.91464	-2.85	3.98	2.91	0.33838	.	1.788980	0.03345	N	0.195361	T	0.00012	0.0000	N	0.11560	0.145	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.09574	-1.0668	9	0.14656	T	0.56	.	8.922	0.35617	0.2134:0.6905:0.0:0.0961	rs34727427;rs61746914;rs34727427	123	P09016	HXD4_HUMAN	P	123	ENSP00000302548:S123P	ENSP00000302548:S123P	S	+	1	0	HOXD4	176724974	0.994000	0.37717	1.000000	0.80357	0.953000	0.61014	0.663000	0.25053	0.784000	0.33661	-0.119000	0.15052	TCC	T|0.722;C|0.278	0.278	strong		0.687	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2		
PCM1	5108	hgsc.bcm.edu	37	8	17847418	17847418	+	Silent	SNP	A	A	G	rs145539051	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17847418A>G	ENST00000519253.1	+	27	4712	c.4461A>G	c.(4459-4461)caA>caG	p.Q1487Q	PCM1_ENST00000325083.8_Silent_p.Q1487Q|PCM1_ENST00000327578.8_Silent_p.Q186Q|PCM1_ENST00000524226.1_Silent_p.Q1433Q			Q15154	PCM1_HUMAN	pericentriolar material 1	1487	Interaction with HAP1.				centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TAAGTGAGCAAAATGATGCTG	0.308			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""								A|||	18	0.00359425	0.0015	0.0058	5008	,	,		18234	0.0		0.0099	False		,,,				2504	0.002				p.Q1487Q		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.A4461G						PASS	.	A		13,3403		0,13,1695	86.0	80.0	82.0		4461	-1.6	1.0	8	dbSNP_134	82	106,7508		0,106,3701	no	coding-synonymous	PCM1	NM_006197.3		0,119,5396	GG,GA,AA		1.3922,0.3806,1.0789		1487/2025	17847418	119,10911	1708	3807	5515	SO:0001819	synonymous_variant	5108	exon27			TGAGCAAAATGAT		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.4461A>G	8.37:g.17847418A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Silent	SNP	ENST00000519253.1	37		13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	A	5.205	0.223287	0.09863	0.003806	0.013922	ENSG00000078674	ENST00000522275	.	.	.	5.17	-1.58	0.08479	.	.	.	.	.	T	0.33498	0.0865	.	.	.	0.52099	D	0.999945	.	.	.	.	.	.	T	0.24476	-1.0159	4	.	.	.	-4.1258	2.8152	0.05454	0.5136:0.1104:0.2686:0.1075	.	.	.	.	R	227	.	.	K	+	2	0	PCM1	17891698	0.998000	0.40836	0.990000	0.47175	0.774000	0.43823	0.689000	0.25437	-0.140000	0.11394	-2.258000	0.00281	AAA	A|0.991;G|0.009	0.009	strong		0.308	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
ALDH9A1	223	hgsc.bcm.edu	37	1	165648709	165648709	+	Silent	SNP	C	C	T	rs1143661	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:165648709C>T	ENST00000354775.4	-	6	1204	c.900G>A	c.(898-900)gcG>gcA	p.A300A	ALDH9A1_ENST00000538148.1_Silent_p.A206A|ALDH9A1_ENST00000461664.1_5'Flank	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	276					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TGGCCATCAGCGCCCCCTTTA	0.468													C|||	397	0.0792732	0.1702	0.0447	5008	,	,		18744	0.0179		0.0616	False		,,,				2504	0.0624				p.A300A	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.G900A						PASS	.	C		637,3769	274.9+/-272.2	55,527,1621	124.0	103.0	110.0		900	-10.7	0.3	1	dbSNP_120	110	615,7985	160.8+/-213.9	24,567,3709	no	coding-synonymous	ALDH9A1	NM_000696.3		79,1094,5330	TT,TC,CC		7.1512,14.4576,9.6263		300/519	165648709	1252,11754	2203	4300	6503	SO:0001819	synonymous_variant	223	exon6			CATCAGCGCCCCC	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.900G>A	1.37:g.165648709C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	258	253	0.98062	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Silent	SNP	ENST00000354775.4	37	CCDS1250.2																																																																																			C|0.910;T|0.090	0.090	strong		0.468	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
SIRPA	140885	hgsc.bcm.edu	37	20	1895963	1895963	+	Missense_Mutation	SNP	A	A	G	rs373583167|rs386811662|rs17855613	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1895963A>G	ENST00000358771.4	+	2	450	c.298A>G	c.(298-300)Aac>Gac	p.N100D	SIRPA_ENST00000356025.3_Missense_Mutation_p.N100D|SIRPA_ENST00000400068.3_Missense_Mutation_p.N100D	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	100	Ig-like V-type.		N -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CACAAAGAGAAACAACATGGA	0.522																																					p.N100D	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,brain,glioma,-2,4	SIRPA	83	4	0			c.A298G						scavenged	.																																			SO:0001583	missense	140885	exon3			AAGAGAAACAACA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.298A>G	20.37:g.1895963A>G	ENSP00000351621:p.Asn100Asp	Somatic	673	0	0		WXS	Illumina HiSeq	Phase_I	360	15	0.0416667	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.430951	0.25726	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02236	4.38;4.38;4.38	5.11	-5.69	0.02428	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.743450	0.02696	N	0.111247	T	0.03651	0.0104	L	0.55481	1.735	0.09310	N	1	B;B;B	0.17465	0.0;0.022;0.0	B;B;B	0.24701	0.004;0.055;0.007	T	0.41875	-0.9484	10	0.51188	T	0.08	.	10.2665	0.43457	0.2384:0.1377:0.6239:0.0	rs17855613	80;100;100	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	D	100	ENSP00000382941:N100D;ENSP00000348307:N100D;ENSP00000351621:N100D	ENSP00000348307:N100D	N	+	1	0	SIRPA	1843963	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.479000	0.02327	-1.294000	0.02360	-0.388000	0.06559	AAC	.	.	weak		0.522	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
LIG4	3981	hgsc.bcm.edu	37	13	108863609	108863609	+	Missense_Mutation	SNP	G	G	A	rs1805389	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:108863609G>A	ENST00000356922.4	-	2	280	c.8C>T	c.(7-9)gCc>gTc	p.A3V	LIG4_ENST00000405925.1_Missense_Mutation_p.A3V|LIG4_ENST00000442234.1_Missense_Mutation_p.A3V	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	3			A -> V (associated with resistance to multiple myeloma; dbSNP:rs1805389). {ECO:0000269|PubMed:12471202}.		cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					AGTTTGTGAGGCAGCCATCAA	0.328								Non-homologous end-joining					G|||	271	0.0541134	0.0015	0.0793	5008	,	,		17139	0.1002		0.0586	False		,,,				2504	0.0552				p.A3V		Atlas-SNP	.											.	LIG4	91	.	0			c.C8T	GRCh37	CM023642	LIG4	M	rs1805389	PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	53,4315		0,53,2131	27.0	28.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	8,8,8	5.8	1.0	13	dbSNP_92	27	429,7989		10,409,3790	yes	missense,missense,missense	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	64,64,64	10,462,5921	AA,AG,GG		5.0962,1.2134,3.7697	benign,benign,benign	3/912,3/912,3/912	108863609	482,12304	2184	4209	6393	SO:0001583	missense	3981	exon3			TGTGAGGCAGCCA	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"""polydeoxyribonucleotide synthase [ATP] 4"", ""polynucleotide ligase"", ""sealase"", ""DNA repair enzyme"", ""DNA joinase"""	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.8C>T	13.37:g.108863609G>A	ENSP00000349393:p.Ala3Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	124	0.056776556776556776	4	0.008130081300813009	21	0.058011049723756904	54	0.0944055944055944	45	0.059366754617414245	G	15.10	2.732522	0.48939	0.012134	0.050962	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.61980	0.06;0.06;0.06	5.82	5.82	0.92795	DNA ligase, ATP-dependent, N-terminal (1);	0.448521	0.24037	N	0.042138	T	0.02267	0.0070	N	0.08118	0	0.38382	P	0.054835999999999996	B	0.32573	0.376	B	0.28465	0.09	T	0.29458	-1.0011	9	0.59425	D	0.04	.	19.0813	0.93182	0.0:0.0:1.0:0.0	rs1805389;rs1805389	3	P49917	DNLI4_HUMAN	V	3	ENSP00000385955:A3V;ENSP00000402030:A3V;ENSP00000349393:A3V	ENSP00000349393:A3V	A	-	2	0	LIG4	107661610	0.991000	0.36638	0.997000	0.53966	0.436000	0.31835	4.221000	0.58574	2.761000	0.94854	0.643000	0.83706	GCC	G|0.955;A|0.045	0.045	strong		0.328	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
CBS	875	hgsc.bcm.edu	37	21	44483101	44483101	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:44483101T>C	ENST00000398165.3	-	10	1175	c.916A>G	c.(916-918)Atc>Gtc	p.I306V	CBS_ENST00000352178.5_Missense_Mutation_p.I306V|CBS_ENST00000544202.1_Missense_Mutation_p.I218V|CBS_ENST00000398158.1_Missense_Mutation_p.I306V|CBS_ENST00000359624.3_Missense_Mutation_p.I306V|CBS_ENST00000398168.1_Missense_Mutation_p.I306V	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	306					cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	TCGTAGCCGATCCCTTCCACC	0.632																																					p.I306V		Atlas-SNP	.											.	CBS	85	.	0			c.A916G						PASS	.						145.0	121.0	129.0					21																	44483101		2203	4300	6503	SO:0001583	missense	875	exon10			AGCCGATCCCTTC	L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.916A>G	21.37:g.44483101T>C	ENSP00000381231:p.Ile306Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	27	0.225	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	37	CCDS13693.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494781	0.64186	.	.	ENSG00000160200	ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202	D;D;D;D;D;D	0.97066	-4.23;-4.23;-4.23;-4.23;-4.23;-4.23	4.67	4.67	0.58626	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	D	0.97766	0.9267	M	0.82056	2.57	0.49798	D	0.99982	P;P	0.46784	0.573;0.884	P;P	0.57720	0.775;0.826	D	0.97377	0.9980	10	0.38643	T	0.18	-21.5015	12.3672	0.55234	0.0:0.0:0.0:1.0	.	306;263	P35520;B7Z2D6	CBS_HUMAN;.	V	306;306;306;306;306;263;218	ENSP00000381225:I306V;ENSP00000381231:I306V;ENSP00000352643:I306V;ENSP00000344460:I306V;ENSP00000381234:I306V;ENSP00000439332:I218V	ENSP00000344460:I306V	I	-	1	0	CBS	43356170	1.000000	0.71417	0.122000	0.21767	0.415000	0.31203	6.807000	0.75201	1.740000	0.51718	0.482000	0.46254	ATC	.	.	none		0.632	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
MACF1	23499	hgsc.bcm.edu	37	1	39549983	39549983	+	Silent	SNP	G	G	A	rs3736890	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39549983G>A	ENST00000372915.3	+	1	180	c.93G>A	c.(91-93)tcG>tcA	p.S31S	MACF1_ENST00000484793.1_Silent_p.S31S|MACF1_ENST00000317713.7_Silent_p.S31S|MACF1_ENST00000602421.1_Silent_p.S31S|MACF1_ENST00000361689.2_Silent_p.S31S|MACF1_ENST00000567887.1_Silent_p.S31S|MACF1_ENST00000539005.1_Silent_p.S31S|MACF1_ENST00000545844.1_Silent_p.S31S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	31	Actin-binding.				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)			GCGAGCGGTCGGGGAGCCTGT	0.607													A|||	492	0.0982428	0.0522	0.111	5008	,	,		17702	0.0456		0.2058	False		,,,				2504	0.0951				p.S31S		Atlas-SNP	.											.	MACF1	909	.	0			c.G93A						PASS	.	A		331,4075	792.9+/-415.2	18,295,1890	63.0	55.0	58.0		93	-0.0	1.0	1	dbSNP_107	58	1609,6991	740.1+/-407.1	160,1289,2851	no	coding-synonymous	MACF1	NM_012090.4		178,1584,4741	AA,AG,GG		18.7093,7.5125,14.9162		31/5431	39549983	1940,11066	2203	4300	6503	SO:0001819	synonymous_variant	23499	exon3			GCGGTCGGGGAGC	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.93G>A	1.37:g.39549983G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	60	16	0.266667	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																				G|0.867;A|0.133	0.133	strong		0.607	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
QSOX1	5768	hgsc.bcm.edu	37	1	180144485	180144485	+	Silent	SNP	G	G	A	rs10913939	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	355	221	0.622535	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	
FTL	2512	hgsc.bcm.edu	37	19	49469087	49469087	+	Silent	SNP	T	T	C	rs2230267	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49469087T>C	ENST00000331825.6	+	2	370	c.163T>C	c.(163-165)Ttg>Ctg	p.L55L	CTD-2639E6.9_ENST00000599784.1_lincRNA	NM_000146.3	NP_000137.2	P02792	FRIL_HUMAN	ferritin, light polypeptide	55	Catalytic site for iron oxidation.|Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular ferritin complex (GO:0008043)|membrane (GO:0016020)	ferric iron binding (GO:0008199)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)			cervix(1)|kidney(3)|lung(5)	9		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;0.000152)|all cancers(93;0.000435)|GBM - Glioblastoma multiforme(486;0.0171)|Epithelial(262;0.0267)	Iron Dextran(DB00893)	CTTCCGCGAATTGGCCGAGGA	0.582													T|||	2307	0.460663	0.4849	0.5	5008	,	,		19910	0.4246		0.5398	False		,,,				2504	0.3558				p.L55L		Atlas-SNP	.											.	FTL	19	.	0			c.T163C						PASS	.	T		2088,2318	571.8+/-383.2	512,1064,627	56.0	60.0	58.0		163	-2.2	0.8	19	dbSNP_98	58	4669,3931	602.4+/-394.5	1278,2113,909	no	coding-synonymous	FTL	NM_000146.3		1790,3177,1536	CC,CT,TT		45.7093,47.3899,48.0471		55/176	49469087	6757,6249	2203	4300	6503	SO:0001819	synonymous_variant	2512	exon2			CGCGAATTGGCCG	AY207005	CCDS33070.1	19q13.33	2014-05-19			ENSG00000087086	ENSG00000087086			3999	protein-coding gene	gene with protein product	"""ferritin light polypeptide-like 3"", ""L apoferritin"", ""ferritin L subunit"", ""ferritin light chain"", ""ferritin L-chain"", ""neurodegeneration with brain iron accumulation 3"""	134790				3000916, 9526618	Standard	NM_000146		Approved	MGC71996, NBIA3	uc002plo.3	P02792		ENST00000331825.6:c.163T>C	19.37:g.49469087T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	51	0.566667	NM_000146	B2R4B9|Q6IBT7|Q7Z2W1|Q86WI9|Q8WU07|Q96AU9|Q96CU0|Q9BTZ8	Silent	SNP	ENST00000331825.6	37	CCDS33070.1																																																																																			T|0.480;C|0.520	0.520	strong		0.582	FTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466233.1	NM_000146	
CHAMP1	283489	hgsc.bcm.edu	37	13	115091399	115091399	+	Silent	SNP	T	T	C	rs9525332	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:115091399T>C	ENST00000361283.1	+	3	2391	c.2082T>C	c.(2080-2082)tcT>tcC	p.S694S		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	694	Mediates localization to the chromosome and the spindle and negatively regulates chromosome alignment.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										CTTTTATCTCTGAAGAGGAGA	0.353													.|||	606	0.121006	0.1452	0.1455	5008	,	,		21177	0.1062		0.0785	False		,,,				2504	0.1299				p.S694S		Atlas-SNP	.											.	.	.	.	0			c.T2082C						PASS	.	C	,,	514,3892	233.9+/-246.9	30,454,1719	80.0	82.0	81.0		2082,2082,2082	0.6	1.0	13	dbSNP_119	81	576,8024	155.2+/-209.3	21,534,3745	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF828	NM_001164144.1,NM_001164145.1,NM_032436.2	,,	51,988,5464	CC,CT,TT		6.6977,11.6659,8.3807	,,	694/813,694/813,694/813	115091399	1090,11916	2203	4300	6503	SO:0001819	synonymous_variant	283489	exon3			TATCTCTGAAGAG	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"""Zinc fingers, C2H2-type"""	20311	protein-coding gene	gene with protein product	"""chromosome alignment-maintaining phosphoprotein"""		"""chromosome 13 open reading frame 8"", ""zinc finger protein 828"""	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.2082T>C	13.37:g.115091399T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_001164144	B3KU06|Q6P181|Q8NC88|Q9BST0	Silent	SNP	ENST00000361283.1	37	CCDS9545.1																																																																																			T|0.893;C|0.107	0.107	strong		0.353	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436	
ZC3H3	23144	hgsc.bcm.edu	37	8	144621084	144621084	+	Missense_Mutation	SNP	T	T	G	rs3750207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144621084T>G	ENST00000262577.5	-	2	484	c.453A>C	c.(451-453)gaA>gaC	p.E151D		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	151			E -> D (in dbSNP:rs3750207). {ECO:0000269|PubMed:8590280}.		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)			TCCAGGGGGTTTCCTCAAATT	0.612													G|||	2086	0.416534	0.5779	0.4654	5008	,	,		15931	0.2133		0.3479	False		,,,				2504	0.4438				p.E151D		Atlas-SNP	.											.	ZC3H3	75	.	0			c.A453C						PASS	.	G	ASP/GLU	2318,2086		622,1074,506	27.0	31.0	30.0		453	-2.4	0.0	8	dbSNP_107	30	2719,5873		441,1837,2018	yes	missense	ZC3H3	NM_015117.2	45	1063,2911,2524	GG,GT,TT		31.6457,47.366,38.7581	benign	151/949	144621084	5037,7959	2202	4296	6498	SO:0001583	missense	23144	exon2			GGGGGTTTCCTCA	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.453A>C	8.37:g.144621084T>G	ENSP00000262577:p.Glu151Asp	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	108	28	0.259259	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	852	0.3901098901098901	277	0.5630081300813008	158	0.43646408839779005	136	0.23776223776223776	281	0.370712401055409	G	0.004	-2.250215	0.00268	0.52634	0.316457	ENSG00000014164	ENST00000262577	T	0.02525	4.26	4.88	-2.42	0.06542	.	0.554792	0.16290	N	0.220921	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	0.25433	-1.0132	9	0.02654	T	1	-4.8995	2.0717	0.03615	0.4945:0.1384:0.226:0.141	rs3750207;rs59595990;rs3750207	151	Q8IXZ2	ZC3H3_HUMAN	D	151	ENSP00000262577:E151D	ENSP00000262577:E151D	E	-	3	2	ZC3H3	144692227	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.351000	0.01092	-0.336000	0.08438	-0.737000	0.03537	GAA	T|0.601;G|0.399	0.399	strong		0.612	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
DFNA5	1687	hgsc.bcm.edu	37	7	24789386	24789386	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:24789386G>A	ENST00000342947.3	-	2	433	c.8C>T	c.(7-9)gCc>gTc	p.A3V	DFNA5_ENST00000409775.3_Missense_Mutation_p.A3V|DFNA5_ENST00000419307.1_Intron|DFNA5_ENST00000409970.1_Intron|DFNA5_ENST00000545231.1_5'UTR	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	3					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						GGTTGCTTTGGCAAACATTTT	0.333																																					p.A3V	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.C8T						PASS	.						79.0	85.0	83.0					7																	24789386		2203	4300	6503	SO:0001583	missense	1687	exon2			GCTTTGGCAAACA	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.8C>T	7.37:g.24789386G>A	ENSP00000339587:p.Ala3Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	114	29	0.254386	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	37	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.670665	0.88348	.	.	ENSG00000105928	ENST00000342947;ENST00000409775	T;T	0.25414	1.8;1.8	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.54498	0.1862	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.57230	-0.7847	10	0.59425	D	0.04	-24.0835	16.4772	0.84135	0.0:0.1308:0.8692:0.0	.	3;3	A4FTY0;O60443	.;DFNA5_HUMAN	V	3	ENSP00000339587:A3V;ENSP00000386670:A3V	ENSP00000339587:A3V	A	-	2	0	DFNA5	24755911	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.414000	0.66405	2.606000	0.88127	0.655000	0.94253	GCC	.	.	none		0.333	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
ZNF286A	57335	hgsc.bcm.edu	37	17	15604485	15604485	+	Silent	SNP	T	T	C	rs78494624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:15604485T>C	ENST00000464847.2	+	2	610	c.57T>C	c.(55-57)tcT>tcC	p.S19S	ZNF286A_ENST00000421016.1_Silent_p.S19S|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000472486.1_Silent_p.S9S|ZNF286A_ENST00000395894.2_Silent_p.S19S|ZNF286A_ENST00000395893.2_Silent_p.S19S|ZNF286A_ENST00000585194.1_Silent_p.S19S|ZNF286A_ENST00000581529.1_Silent_p.S9S|ZNF286A_ENST00000583566.1_Silent_p.S19S|ZNF286A_ENST00000593105.1_Silent_p.S9S|ZNF286A_ENST00000413242.2_Silent_p.S19S|ZNF286A_ENST00000580259.1_Silent_p.S19S			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	250	0	0		WXS	Illumina HiSeq	Phase_I	317	74	0.233438	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	
DHRS4	10901	hgsc.bcm.edu	37	14	24435538	24435538	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24435538C>A	ENST00000313250.5	+	6	781	c.578C>A	c.(577-579)aCc>aAc	p.T193N	DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000558581.1_Missense_Mutation_p.T159N|DHRS4_ENST00000421831.1_Missense_Mutation_p.T141N|DHRS4_ENST00000397073.2_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000382761.3_Intron|DHRS4_ENST00000397074.3_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	193					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)	p.T193N(1)		central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	CTGGGCCTGACCAAGACCCTG	0.502																																					p.T193N		Atlas-SNP	.											DHRS4,NS,carcinoma,0,1	DHRS4	22	1	1	Substitution - Missense(1)	kidney(1)	c.C578A						scavenged	.						181.0	156.0	165.0					14																	24435538		2200	4300	6500	SO:0001583	missense	10901	exon6			GCCTGACCAAGAC	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.578C>A	14.37:g.24435538C>A	ENSP00000326219:p.Thr193Asn	Somatic	1014	1	0.000986193		WXS	Illumina HiSeq	Phase_I	1334	116	0.0869565	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	c	11.36	1.615720	0.28801	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	T;T	0.32023	1.47;1.47	3.53	2.63	0.31362	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.115238	0.56097	N	0.000021	T	0.47691	0.1459	H	0.95504	3.68	0.80722	D	1	B;B	0.25105	0.118;0.023	B;B	0.32342	0.073;0.144	T	0.52155	-0.8613	10	0.54805	T	0.06	.	10.3016	0.43656	0.1993:0.8007:0.0:0.0	.	159;193	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	N	193;141	ENSP00000326219:T193N;ENSP00000404147:T141N	ENSP00000326219:T193N	T	+	2	0	DHRS4	23505378	1.000000	0.71417	0.992000	0.48379	0.683000	0.39861	3.158000	0.50723	0.608000	0.30000	-0.202000	0.12741	ACC	.	.	none		0.502	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
YIPF5	81555	hgsc.bcm.edu	37	5	143539969	143539969	+	Missense_Mutation	SNP	C	C	T	rs147304369	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:143539969C>T	ENST00000274496.5	-	6	900	c.766G>A	c.(766-768)Gtc>Atc	p.V256I	YIPF5_ENST00000448443.2_Missense_Mutation_p.V256I|YIPF5_ENST00000513112.1_Missense_Mutation_p.V202I	NM_001271732.1|NM_030799.7	NP_001258661.1|NP_110426.4	Q969M3	YIPF5_HUMAN	Yip1 domain family, member 5	256					protein transport (GO:0015031)|regulation of ER to Golgi vesicle-mediated transport (GO:0060628)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum exit site (GO:0070971)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)				large_intestine(2)|lung(5)|ovary(1)|skin(1)	9		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			TTTCAAAAGACGGAAATCAGG	0.413													C|||	11	0.00219649	0.0008	0.0043	5008	,	,		18492	0.0		0.007	False		,,,				2504	0.0				p.V256I		Atlas-SNP	.											.	YIPF5	17	.	0			c.G766A						PASS	.	C	ILE/VAL,ILE/VAL	4,4402	8.1+/-20.4	0,4,2199	98.0	104.0	102.0		766,766	2.4	0.6	5	dbSNP_134	102	97,8503	53.6+/-114.3	0,97,4203	yes	missense,missense	YIPF5	NM_001024947.2,NM_030799.7	29,29	0,101,6402	TT,TC,CC		1.1279,0.0908,0.7766	benign,benign	256/258,256/258	143539969	101,12905	2203	4300	6503	SO:0001583	missense	81555	exon6			AAAAGACGGAAAT	AF318329	CCDS4279.1, CCDS64277.1	5q31.3	2009-01-12			ENSG00000145817	ENSG00000145817		"""Yip1 domain family"""	24877	protein-coding gene	gene with protein product		611483				12975309, 18718466	Standard	NM_001024947		Approved	SMAP-5, FinGER5	uc003lnl.5	Q969M3	OTTHUMG00000129679	ENST00000274496.5:c.766G>A	5.37:g.143539969C>T	ENSP00000274496:p.Val256Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001024947	D3DQF5|Q4VSN6|Q53EX4|Q8NHE5|Q9H338|Q9H3U4	Missense_Mutation	SNP	ENST00000274496.5	37	CCDS4279.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	7.832	0.720141	0.15372	9.08E-4	0.011279	ENSG00000145817	ENST00000274496;ENST00000448443;ENST00000513112	T;T;T	0.36699	1.88;1.88;1.24	5.6	2.42	0.29668	.	.	.	.	.	T	0.08582	0.0213	N	0.03967	-0.31	0.53005	D	0.999962	P	0.35527	0.507	B	0.28385	0.089	T	0.19353	-1.0308	9	0.02654	T	1	.	12.1691	0.54148	0.0:0.7814:0.0:0.2186	.	256	Q969M3	YIPF5_HUMAN	I	256;256;202	ENSP00000274496:V256I;ENSP00000397704:V256I;ENSP00000425422:V202I	ENSP00000274496:V256I	V	-	1	0	YIPF5	143520162	0.306000	0.24490	0.615000	0.29064	0.944000	0.59088	0.969000	0.29370	0.730000	0.32425	-0.140000	0.14226	GTC	C|0.993;T|0.007	0.007	strong		0.413	YIPF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251882.1	NM_030799	
DHX15	1665	hgsc.bcm.edu	37	4	24550580	24550580	+	Silent	SNP	G	G	A	rs33972724	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:24550580G>A	ENST00000336812.4	-	6	1302	c.1146C>T	c.(1144-1146)gaC>gaT	p.D382D		NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	382	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	30		Breast(46;0.0503)				TGATTTTAATGTCACCAACTT	0.393													G|||	25	0.00499201	0.0015	0.013	5008	,	,		15491	0.0		0.0139	False		,,,				2504	0.0				p.D382D		Atlas-SNP	.											.	DHX15	69	.	0			c.C1146T						PASS	.	G		11,4395	17.9+/-39.9	0,11,2192	124.0	111.0	115.0		1146	3.2	1.0	4	dbSNP_126	115	108,8492	59.1+/-120.7	0,108,4192	no	coding-synonymous	DHX15	NM_001358.2		0,119,6384	AA,AG,GG		1.2558,0.2497,0.915		382/796	24550580	119,12887	2203	4300	6503	SO:0001819	synonymous_variant	1665	exon6			TTTAATGTCACCA	AB001636	CCDS33966.1	4p15.3	2013-05-13	2013-05-13	2003-06-20	ENSG00000109606	ENSG00000109606		"""DEAH-boxes"""	2738	protein-coding gene	gene with protein product		603403	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 15"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 15"""	DDX15		9388478	Standard	NM_001358		Approved	HRH2, DBP1, PRP43, PrPp43p, PRPF43	uc003gqx.3	O43143	OTTHUMG00000160304	ENST00000336812.4:c.1146C>T	4.37:g.24550580G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	NM_001358	Q9NQT7	Silent	SNP	ENST00000336812.4	37	CCDS33966.1																																																																																			G|0.991;A|0.009	0.009	strong		0.393	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358	
MTTP	4547	hgsc.bcm.edu	37	4	100510903	100510903	+	Missense_Mutation	SNP	A	A	G	rs3792683	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:100510903A>G	ENST00000265517.5	+	4	700	c.497A>G	c.(496-498)aAt>aGt	p.N166S	MTTP_ENST00000457717.1_Missense_Mutation_p.N166S|MTTP_ENST00000511045.1_Missense_Mutation_p.N193S			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	166	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		N -> S (in dbSNP:rs3792683).		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)	GGAACCACCAATGAGGTACTT	0.348													A|||	573	0.114417	0.1929	0.0692	5008	,	,		17528	0.2143		0.0159	False		,,,				2504	0.0389				p.N166S		Atlas-SNP	.											MTTP,NS,carcinoma,-1,1	MTTP	127	1	0			c.A497G						PASS	.	A	SER/ASN	763,3643	309.1+/-290.9	69,625,1509	76.0	78.0	77.0		497	4.1	0.9	4	dbSNP_107	77	351,8249	118.1+/-177.6	5,341,3954	yes	missense	MTTP	NM_000253.2	46	74,966,5463	GG,GA,AA		4.0814,17.3173,8.5653	benign	166/895	100510903	1114,11892	2203	4300	6503	SO:0001583	missense	4547	exon5			CCACCAATGAGGT		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.497A>G	4.37:g.100510903A>G	ENSP00000265517:p.Asn166Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	268	0.1227106227106227	91	0.18495934959349594	20	0.055248618784530384	142	0.24825174825174826	15	0.01978891820580475	A	2.852	-0.238086	0.05944	0.173173	0.040814	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T;T	0.14022	2.54;3.56;3.56;3.56	5.35	4.13	0.48395	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.639345	0.17178	N	0.183997	T	0.00012	0.0000	L	0.29908	0.895	0.45194	P	0.0017930000000000446	B;B	0.33777	0.013;0.425	B;B	0.31946	0.03;0.138	T	0.37820	-0.9689	9	0.09338	T	0.73	-25.0927	3.6587	0.08230	0.607:0.2013:0.1916:0.0	rs3792683;rs52834225;rs3792683	193;166	E9PBP6;P55157	.;MTP_HUMAN	S	176;193;166;166;166	ENSP00000426755:N176S;ENSP00000427679:N193S;ENSP00000400821:N166S;ENSP00000265517:N166S	ENSP00000265517:N166S	N	+	2	0	MTTP	100729926	0.014000	0.17966	0.944000	0.38274	0.988000	0.76386	0.371000	0.20450	0.833000	0.34828	0.533000	0.62120	AAT	A|0.901;G|0.099	0.099	strong		0.348	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
TNKS2	80351	hgsc.bcm.edu	37	10	93608142	93608142	+	Silent	SNP	G	G	A	rs3758499	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	73	0	0		WXS	Illumina HiSeq	Phase_I	50	38	0.76	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	
SLC16A13	201232	hgsc.bcm.edu	37	17	6942108	6942108	+	Silent	SNP	C	C	T	rs11078663	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	102	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	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		
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150284	39150284	+	Silent	SNP	A	A	G	rs2010201	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39150284A>G	ENST00000391586.1	-	1	101	c.66T>C	c.(64-66)tcT>tcC	p.S22S		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	22	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			lung(2)|prostate(2)	4		Breast(137;0.00043)				AGGATTTGTCAGAGGAGCAGA	0.582													A|||	2379	0.47504	0.6377	0.4784	5008	,	,		17574	0.5		0.2913	False		,,,				2504	0.4162				p.S22S		Atlas-SNP	.											.	KRTAP3-3	11	.	0			c.T66C						PASS	.	A		2510,1896	625.1+/-394.5	720,1070,413	90.0	90.0	90.0		66	-11.2	0.0	17	dbSNP_92	90	2274,6318	374.7+/-337.5	295,1684,2317	no	coding-synonymous	KRTAP3-3	NM_033185.2		1015,2754,2730	GG,GA,AA		26.4665,43.0322,36.8057		22/99	39150284	4784,8214	2203	4296	6499	SO:0001819	synonymous_variant	85293	exon1			TTTGTCAGAGGAG	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.66T>C	17.37:g.39150284A>G		Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	224	119	0.53125	NM_033185	Q52LP0|Q6NTD4	Silent	SNP	ENST00000391586.1	37	CCDS32643.1																																																																																			A|0.598;G|0.402	0.402	strong		0.582	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1		
KIFC1	3833	hgsc.bcm.edu	37	6	33374422	33374422	+	Silent	SNP	T	T	C	rs371316441		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:33374422T>C	ENST00000428849.2	+	9	2331	c.1881T>C	c.(1879-1881)tcT>tcC	p.S627S		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	627	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|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)|minus-end-directed microtubule motor activity (GO:0008569)	p.S627S(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						TGCAGAACTCTCTGGGTGGTA	0.527																																					p.S627S		Atlas-SNP	.											KIFC1,rectum,carcinoma,0,1	KIFC1	47	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T1881C						scavenged	.	T		2,4404	4.2+/-10.8	0,2,2201	141.0	131.0	135.0		1881	0.1	1.0	6		135	0,8600		0,0,4300	no	coding-synonymous	KIFC1	NM_002263.3		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		627/674	33374422	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3833	exon9			GAACTCTCTGGGT	D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"""Kinesins"""	6389	protein-coding gene	gene with protein product		603763	"""kinesin-like 2"""	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.1881T>C	6.37:g.33374422T>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	231	3	0.012987	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Silent	SNP	ENST00000428849.2	37	CCDS34430.1																																																																																			.	.	weak		0.527	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263	
SLC16A10	117247	hgsc.bcm.edu	37	6	111493953	111493953	+	Silent	SNP	C	C	T	rs33965856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:111493953C>T	ENST00000368851.5	+	2	574	c.399C>T	c.(397-399)agC>agT	p.S133S	SLC16A10_ENST00000465319.1_3'UTR	NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	133					amino acid transport (GO:0006865)|aromatic amino acid transport (GO:0015801)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)	12		all_cancers(87;0.00172)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0313)|Colorectal(196;0.0466)		OV - Ovarian serous cystadenocarcinoma(136;0.0703)|Epithelial(106;0.12)|all cancers(137;0.132)	Droxidopa(DB06262)|Glycine(DB00145)|L-Alanine(DB00160)|L-Arginine(DB00125)|L-Asparagine(DB00174)|L-Aspartic Acid(DB00128)|L-Cysteine(DB00151)|L-Cystine(DB00138)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Histidine(DB00117)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Lysine(DB00123)|L-Methionine(DB00134)|L-Phenylalanine(DB00120)|L-Proline(DB00172)|L-Serine(DB00133)|L-Threonine(DB00156)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|L-Valine(DB00161)|Liothyronine(DB00279)|Liotrix(DB01583)|Pyruvic acid(DB00119)	CAATAGTCAGCGTCTTCACAG	0.468													C|||	150	0.0299521	0.0008	0.0605	5008	,	,		15158	0.002		0.0666	False		,,,				2504	0.0389				p.S133S		Atlas-SNP	.											.	SLC16A10	33	.	0			c.C399T						PASS	.	C		59,4347	56.8+/-93.2	1,57,2145	216.0	199.0	205.0		399	-8.6	0.4	6	dbSNP_126	205	588,8012	156.9+/-210.6	16,556,3728	no	coding-synonymous	SLC16A10	NM_018593.4		17,613,5873	TT,TC,CC		6.8372,1.3391,4.9746		133/516	111493953	647,12359	2203	4300	6503	SO:0001819	synonymous_variant	117247	exon2			AGTCAGCGTCTTC	AF116652	CCDS5089.1	6q21-q22	2014-01-28	2013-07-18		ENSG00000112394	ENSG00000112394		"""Solute carriers"""	17027	protein-coding gene	gene with protein product		607550	"""solute carrier family 16 (monocarboxylic acid transporters), member 10"""			11278508, 11827462	Standard	NM_018593		Approved	TAT1, MCT10	uc003pus.3	Q8TF71	OTTHUMG00000015371	ENST00000368851.5:c.399C>T	6.37:g.111493953C>T		Somatic	311	1	0.00321543		WXS	Illumina HiSeq	Phase_I	332	165	0.496988	NM_018593	B3KWY0|Q6ZMG0|Q8WVI5	Silent	SNP	ENST00000368851.5	37	CCDS5089.1	70	0.03205128205128205	0	0.0	21	0.058011049723756904	1	0.0017482517482517483	48	0.0633245382585752	C	10.27	1.304606	0.23736	0.013391	0.068372	ENSG00000112394	ENST00000419619;ENST00000439288	.	.	.	5.65	-8.6	0.00889	.	.	.	.	.	T	0.60064	0.2240	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73151	-0.4073	4	.	.	.	.	20.5759	0.99371	0.0:0.6994:0.0:0.3006	rs33965856;rs33965856	.	.	.	V	19	.	.	A	+	2	0	SLC16A10	111600646	0.239000	0.23836	0.384000	0.26145	0.972000	0.66771	-0.137000	0.10389	-2.098000	0.00850	-0.339000	0.08088	GCG	C|0.952;T|0.048	0.048	strong		0.468	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041822.2		
EXO1	9156	hgsc.bcm.edu	37	1	242035438	242035438	+	Missense_Mutation	SNP	G	G	A	rs4149965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	296	0	0		WXS	Illumina HiSeq	Phase_I	379	202	0.532982	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	
FAM188B	84182	hgsc.bcm.edu	37	7	30868352	30868352	+	Splice_Site	SNP	C	C	T	rs201645679		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:30868352C>T	ENST00000265299.6	+	6	1208	c.1131C>T	c.(1129-1131)ctC>ctT	p.L377L	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	377										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCCTGCGGCTCGGTAGGTGCA	0.582																																					p.L377L		Atlas-SNP	.											.	FAM188B	62	.	0			c.C1131T						PASS	.	C		0,4054		0,0,2027	115.0	119.0	118.0		1131	-6.6	0.3	7		118	1,8369		0,1,4184	yes	coding-synonymous-near-splice	FAM188B	NM_032222.2		0,1,6211	TT,TC,CC		0.0119,0.0,0.0080		377/758	30868352	1,12423	2027	4185	6212	SO:0001630	splice_region_variant	84182	exon6			GCGGCTCGGTAGG	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1132+1C>T	7.37:g.30868352C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																			C|0.999;T|0.001	0.001	weak		0.582	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	Silent
IKBKB	3551	hgsc.bcm.edu	37	8	42174380	42174380	+	Silent	SNP	G	G	A	rs56230731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:42174380G>A	ENST00000520810.1	+	11	1269	c.1083G>A	c.(1081-1083)ttG>ttA	p.L361L	IKBKB_ENST00000416505.2_Silent_p.L302L|IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000379708.3_Silent_p.L138L|IKBKB_ENST00000520835.1_Silent_p.L359L	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	361					B cell homeostasis (GO:0001782)|cellular response to tumor necrosis factor (GO:0071356)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|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)|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)|positive regulation of cation channel activity (GO:2001259)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)|serine phosphorylation of STAT protein (GO:0042501)|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)|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)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|scaffold protein binding (GO:0097110)			breast(4)|lung(1)|ovary(2)|skin(1)	8	all_cancers(6;1.42e-24)|all_epithelial(6;1.02e-25)|all_lung(13;6.21e-12)|Lung NSC(13;1.04e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Colorectal(14;0.0468)|Lung SC(25;0.211)	all_lung(54;0.000434)|Lung NSC(58;0.00161)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	BRCA - Breast invasive adenocarcinoma(8;1.37e-10)|Colorectal(10;0.00102)|OV - Ovarian serous cystadenocarcinoma(14;0.00168)|Lung(22;0.00467)|LUSC - Lung squamous cell carcinoma(45;0.024)|COAD - Colon adenocarcinoma(11;0.0264)		Acetylcysteine(DB06151)|Acetylsalicylic acid(DB00945)|Arsenic trioxide(DB01169)|Auranofin(DB00995)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	GCCTGGCGTTGATCCCCGATA	0.582													G|||	19	0.00379393	0.0008	0.0014	5008	,	,		17740	0.0		0.0169	False		,,,				2504	0.0				p.L361L		Atlas-SNP	.											.	IKBKB	88	.	0			c.G1083A						PASS	.	G	,,	14,4392	21.2+/-45.6	0,14,2189	82.0	76.0	78.0		1077,906,1083	4.6	1.0	8	dbSNP_129	78	128,8472	65.6+/-127.9	1,126,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	IKBKB	NM_001190720.2,NM_001242778.1,NM_001556.2	,,	1,140,6362	AA,AG,GG		1.4884,0.3177,1.0918	,,	359/755,302/698,361/757	42174380	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	3551	exon11			GGCGTTGATCCCC	AF029684	CCDS6128.1, CCDS55228.1, CCDS56535.1	8p11.2	2008-08-18			ENSG00000104365	ENSG00000104365			5960	protein-coding gene	gene with protein product		603258				9878263, 9763654	Standard	NM_001556		Approved	IKK2, NFKBIKB, IKK-beta, IKKB	uc003xow.2	O14920	OTTHUMG00000164092	ENST00000520810.1:c.1083G>A	8.37:g.42174380G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	115	37	0.321739	NM_001556	B4DZ30|B4E0U4|O75327	Silent	SNP	ENST00000520810.1	37	CCDS6128.1																																																																																			G|0.991;A|0.009	0.009	strong		0.582	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1		
TRPM2	7226	hgsc.bcm.edu	37	21	45811343	45811343	+	Missense_Mutation	SNP	T	T	G	rs1556314	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:45811343T>G	ENST00000397928.1	+	11	2074	c.1629T>G	c.(1627-1629)gaT>gaG	p.D543E	TRPM2_ENST00000300481.9_Intron|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.D543E|TRPM2_ENST00000300482.5_Missense_Mutation_p.D543E	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	543			D -> E (in dbSNP:rs1556314). {ECO:0000269|Ref.6}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						TGGTGGAGGATCCCGAGCGCC	0.662													G|||	1024	0.204473	0.3064	0.2089	5008	,	,		11261	0.1567		0.1769	False		,,,				2504	0.1411				p.D543E		Atlas-SNP	.											.	TRPM2	196	.	0			c.T1629G						PASS	.	G	GLU/ASP	1254,3152	703.0+/-406.9	184,886,1133	65.0	50.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1629	2.8	0.0	21	dbSNP_88	55	1717,6883	736.6+/-407.0	166,1385,2749	yes	missense	TRPM2	NM_003307.3	45	350,2271,3882	GG,GT,TT		19.9651,28.4612,22.8433	benign	543/1504	45811343	2971,10035	2203	4300	6503	SO:0001583	missense	7226	exon11			GGAGGATCCCGAG	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.1629T>G	21.37:g.45811343T>G	ENSP00000381023:p.Asp543Glu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	461	0.21108058608058608	161	0.32723577235772355	69	0.19060773480662985	95	0.1660839160839161	136	0.17941952506596306	G	0.007	-2.007743	0.00426	0.284612	0.199651	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000397932	T;T;T	0.26373	1.74;1.74;1.74	4.71	2.82	0.32997	.	0.638554	0.16045	N	0.232236	T	0.00012	0.0000	N	0.00077	-2.24	0.19945	P	0.9999431249	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.47381	-0.9122	9	0.02654	T	1	-21.0034	10.0415	0.42162	0.1367:0.0:0.7476:0.1157	rs1556314;rs58121890;rs1556314	543;329;543	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	E	543	ENSP00000300482:D543E;ENSP00000381023:D543E;ENSP00000381026:D543E	ENSP00000300482:D543E	D	+	3	2	TRPM2	44635771	0.016000	0.18221	0.036000	0.18154	0.001000	0.01503	-0.011000	0.12721	-0.135000	0.11495	-1.945000	0.00491	GAT	T|0.777;G|0.223	0.223	strong		0.662	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17934319	17934319	+	Silent	SNP	C	C	T	rs114551094	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:17934319C>T	ENST00000361221.3	+	7	615	c.456C>T	c.(454-456)taC>taT	p.Y152Y	ARHGEF10L_ENST00000434513.1_Silent_p.Y152Y|ARHGEF10L_ENST00000375420.3_5'UTR|ARHGEF10L_ENST00000375415.1_Silent_p.Y152Y|ARHGEF10L_ENST00000452522.1_Silent_p.Y152Y	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	152						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)		ACCTGCTCTACGAGGATGCGC	0.667													C|||	100	0.0199681	0.003	0.0086	5008	,	,		13360	0.0		0.0338	False		,,,				2504	0.0573				p.Y152Y		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.C456T						PASS	.	C	,	24,4364		0,24,2170	14.0	18.0	17.0		456,456	-6.4	0.0	1	dbSNP_132	17	322,8234		7,308,3963	no	coding-synonymous,coding-synonymous	ARHGEF10L	NM_001011722.2,NM_018125.3	,	7,332,6133	TT,TC,CC		3.7634,0.5469,2.6731	,	152/1241,152/1280	17934319	346,12598	2194	4278	6472	SO:0001819	synonymous_variant	55160	exon7			GCTCTACGAGGAT	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.456C>T	1.37:g.17934319C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	93	28	0.301075	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Silent	SNP	ENST00000361221.3	37	CCDS182.1																																																																																			C|0.981;T|0.019	0.019	strong		0.667	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
SLC22A1	6580	hgsc.bcm.edu	37	6	160560845	160560845	+	Missense_Mutation	SNP	A	A	G	rs628031	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160560845A>G	ENST00000366963.4	+	7	1369	c.1222A>G	c.(1222-1224)Atg>Gtg	p.M408V	SLC22A1_ENST00000324965.4_Missense_Mutation_p.M408V|SLC22A1_ENST00000457470.2_Missense_Mutation_p.M408V	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	408			M -> V (no changes in the MPP uptake. No changes in the MPP uptake; when associated with F-14. No changes in the MPP uptake; when associated with F-85. No changes in the MPP uptake; when associated with L-189. No changes in the MPP uptake; when associated with His-342. No changes in the MPP uptake; when associated with M-420 del. No changes in the MPP uptake; when associated with I- 440. No changes in the MPP uptake; when associated with I-461. No changes in the MPP uptake; when associated with M-488. Reduction of the MPP uptake; when associated with C-61. No MPP uptake; when associated with V-220. Reduction of the MPP uptake; when associated with L-341. No MPP uptake; when associated with S- 401. No MPP uptake; when associated with R-465; dbSNP:rs628031). {ECO:0000269|PubMed:12719534, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15499200}.		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)	CCCCATGGCCATGTCAAATTT	0.527													G|||	3444	0.6877	0.7307	0.7839	5008	,	,		14343	0.7411		0.5865	False		,,,				2504	0.6104				p.M408V		Atlas-SNP	.											.	SLC22A1	69	.	0			c.A1222G						PASS	.	G	VAL/MET,VAL/MET	3200,1206	418.9+/-338.5	1173,854,176	67.0	67.0	67.0		1222,1222	-9.1	0.0	6	dbSNP_83	67	5093,3507	511.4+/-377.7	1516,2061,723	yes	missense,missense	SLC22A1	NM_003057.2,NM_153187.1	21,21	2689,2915,899	GG,GA,AA		40.7791,27.3718,36.2371	benign,benign	408/555,408/507	160560845	8293,4713	2203	4300	6503	SO:0001583	missense	6580	exon7			ATGGCCATGTCAA	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.1222A>G	6.37:g.160560845A>G	ENSP00000355930:p.Met408Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	63	61	0.968254	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Missense_Mutation	SNP	ENST00000366963.4	37	CCDS5274.1	1524	0.6978021978021978	368	0.7479674796747967	279	0.7707182320441989	435	0.7604895104895105	442	0.58311345646438	G	0.022	-1.406937	0.01155	0.726282	0.592209	ENSG00000175003	ENST00000366963;ENST00000324965;ENST00000457470	T;T;T	0.73047	-0.71;0.48;0.48	5.08	-9.1	0.00714	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.244500	0.05468	N	0.552535	T	0.06917	0.0176	N	0.00569	-1.365	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.04165	-1.0972	9	0.07175	T	0.84	.	1.367	0.02203	0.3768:0.2354:0.2283:0.1594	rs628031;rs1086277;rs17202481;rs60990824;rs628031	408;408	O15245-2;O15245	.;S22A1_HUMAN	V	408	ENSP00000355930:M408V;ENSP00000318103:M408V;ENSP00000409557:M408V	ENSP00000318103:M408V	M	+	1	0	SLC22A1	160480835	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.590000	0.00899	-2.233000	0.00716	-0.994000	0.02522	ATG	A|0.330;G|0.669	0.669	strong		0.527	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
ZFYVE1	53349	hgsc.bcm.edu	37	14	73440864	73440864	+	Silent	SNP	C	C	T	rs12931	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:73440864C>T	ENST00000556143.1	-	11	2745	c.2025G>A	c.(2023-2025)acG>acA	p.T675T	ZFYVE1_ENST00000555072.1_Silent_p.T260T|ZFYVE1_ENST00000554145.1_5'Flank|ZFYVE1_ENST00000553891.1_Silent_p.T675T|ZFYVE1_ENST00000318876.5_Silent_p.T661T|ZFYVE1_ENST00000394207.2_Silent_p.T260T	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	675					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		GAGCAATGAGCGTTCCACCTT	0.537													T|||	2400	0.479233	0.5877	0.4049	5008	,	,		20915	0.371		0.4781	False		,,,				2504	0.498				p.T675T		Atlas-SNP	.											.	ZFYVE1	67	.	0			c.G2025A						PASS	.	T	,	2386,2020	562.1+/-380.9	628,1130,445	157.0	121.0	133.0		2025,780	-9.5	0.2	14	dbSNP_52	133	4175,4425	586.6+/-392.1	1029,2117,1154	yes	coding-synonymous,coding-synonymous	ZFYVE1	NM_021260.2,NM_178441.1	,	1657,3247,1599	TT,TC,CC		48.5465,45.8466,49.5541	,	675/778,260/363	73440864	6561,6445	2203	4300	6503	SO:0001819	synonymous_variant	53349	exon11			AATGAGCGTTCCA	AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.2025G>A	14.37:g.73440864C>T		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	143	140	0.979021	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Silent	SNP	ENST00000556143.1	37	CCDS9811.1																																																																																			C|0.501;T|0.499	0.499	strong		0.537	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
MUC4	4585	hgsc.bcm.edu	37	3	195506983	195506983	+	Missense_Mutation	SNP	G	G	A	rs541438739	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195506983G>A	ENST00000463781.3	-	2	11927	c.11468C>T	c.(11467-11469)aCc>aTc	p.T3823I	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	156	6	0.0384615	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	
HIST1H2AH	85235	hgsc.bcm.edu	37	6	27115084	27115084	+	Silent	SNP	G	G	C	rs147640519	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:27115084G>C	ENST00000377459.1	+	1	224	c.177G>C	c.(175-177)ctG>ctC	p.L59L	MIR3143_ENST00000584253.1_RNA|HIST1H2BK_ENST00000396891.4_5'Flank|HIST1H2BK_ENST00000356950.1_5'Flank	NM_080596.1	NP_542163.1	Q96KK5	H2A1H_HUMAN	histone cluster 1, H2ah	59						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|prostate(1)|skin(1)	12						TGGAGTACCTGACCGCTGAGA	0.657													G|||	7	0.00139776	0.0	0.0014	5008	,	,		16644	0.0		0.005	False		,,,				2504	0.001				p.L59L		Atlas-SNP	.											.	HIST1H2AH	26	.	0			c.G177C						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	59.0	59.0	59.0		177	1.0	1.0	6	dbSNP_134	59	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	HIST1H2AH	NM_080596.1		0,92,6411	CC,CG,GG		1.0116,0.1135,0.7074		59/129	27115084	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	85235	exon1			GTACCTGACCGCT	AY131988	CCDS4622.1	6p22.1	2011-01-27	2006-10-11			ENSG00000274997		"""Histones / Replication-dependent"""	13671	protein-coding gene	gene with protein product		615013	"""histone 1, H2ah"""			12408966	Standard	NM_080596		Approved	H2AFALii, dJ86C11.1, H2A/S	uc003niz.4	Q96KK5		ENST00000377459.1:c.177G>C	6.37:g.27115084G>C		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	218	113	0.518349	NM_080596		Silent	SNP	ENST00000377459.1	37	CCDS4622.1																																																																																			G|0.994;C|0.006	0.006	strong		0.657	HIST1H2AH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040136.1	NM_080596	
CRELD1	78987	hgsc.bcm.edu	37	3	9985096	9985096	+	Silent	SNP	G	G	A	rs76764016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:9985096G>A	ENST00000383811.3	+	9	1544	c.945G>A	c.(943-945)ccG>ccA	p.P315P	CRELD1_ENST00000397170.3_Silent_p.P315P|CRELD1_ENST00000326434.5_Silent_p.P315P|CRELD1_ENST00000489674.1_Intron|CRELD1_ENST00000452070.1_Silent_p.P315P	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1	315	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cardiac septum development (GO:0003279)|endocardial cushion development (GO:0003197)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|urinary_tract(1)	14						AGGTGTGTCCGGGAGAGAACA	0.582													G|||	18	0.00359425	0.0008	0.0029	5008	,	,		19869	0.001		0.0129	False		,,,				2504	0.001				p.P315P		Atlas-SNP	.											.	CRELD1	48	.	0			c.G945A						PASS	.	G	,,	16,4390	23.3+/-48.9	0,16,2187	119.0	116.0	117.0		945,945,945	-6.8	1.0	3	dbSNP_132	117	150,8450	72.6+/-135.2	3,144,4153	no	coding-synonymous,coding-synonymous,coding-synonymous	CRELD1	NM_001031717.3,NM_001077415.2,NM_015513.4	,,	3,160,6340	AA,AG,GG		1.7442,0.3631,1.2763	,,	315/423,315/421,315/421	9985096	166,12840	2203	4300	6503	SO:0001819	synonymous_variant	78987	exon10			GTGTCCGGGAGAG	AF452623	CCDS2593.1, CCDS33693.1	3p25.3	2005-12-08	2004-02-13		ENSG00000163703	ENSG00000163703			14630	protein-coding gene	gene with protein product		607170	"""atrioventricular septal defect 2"""	AVSD2		10922384, 12137942	Standard	NM_015513		Approved		uc003buf.3	Q96HD1	OTTHUMG00000128653	ENST00000383811.3:c.945G>A	3.37:g.9985096G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	229	110	0.480349	NM_001077415	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Silent	SNP	ENST00000383811.3	37	CCDS2593.1																																																																																			G|0.991;A|0.009	0.009	strong		0.582	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513	
HEMGN	55363	hgsc.bcm.edu	37	9	100692648	100692648	+	Silent	SNP	G	G	T	rs35527067	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100692648G>T	ENST00000259456.3	-	4	1172	c.1029C>A	c.(1027-1029)atC>atA	p.I343I		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	343					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)				GTGTTTCTTGGATTGTTTTAT	0.363													G|||	11	0.00219649	0.0	0.0	5008	,	,		19044	0.0		0.0099	False		,,,				2504	0.001				p.I343I		Atlas-SNP	.											.	HEMGN	55	.	0			c.C1029A						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	189.0	195.0	193.0		1029,1029	3.3	1.0	9	dbSNP_126	193	108,8492	57.5+/-118.9	1,106,4193	no	coding-synonymous,coding-synonymous	HEMGN	NM_018437.3,NM_197978.1	,	1,120,6382	TT,TG,GG		1.2558,0.3177,0.938	,	343/485,343/485	100692648	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	55363	exon3			TTCTTGGATTGTT	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.1029C>A	9.37:g.100692648G>T		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	267	119	0.445693	NM_197978	Q6XAR3|Q86XY5|Q9NPC0	Silent	SNP	ENST00000259456.3	37	CCDS6731.1																																																																																			G|0.992;T|0.008	0.008	strong		0.363	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978	
OR51F1	256892	hgsc.bcm.edu	37	11	4790951	4790951	+	Missense_Mutation	SNP	A	A	G	rs11033801	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4790951A>G	ENST00000380383.1	-	1	217	c.218T>C	c.(217-219)tTc>tCc	p.F73S	MMP26_ENST00000380390.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.F66S|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	73			F -> S (in dbSNP:rs11033801).			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)		TGATAGCCTGAAGAGGAAATA	0.443													G|||	1080	0.215655	0.4569	0.2017	5008	,	,		21639	0.0		0.2704	False		,,,				2504	0.0654				p.F66S		Atlas-SNP	.											.	OR51F1	60	.	0			c.T197C						PASS	.	G	SER/PHE	1966,2436	617.7+/-393.0	443,1080,678	67.0	63.0	65.0		197	4.8	1.0	11	dbSNP_120	65	2164,6432	712.0+/-405.9	286,1592,2420	yes	missense	OR51F1	NM_001004752.1	155	729,2672,3098	GG,GA,AA		25.1745,44.6615,31.7741	benign	66/313	4790951	4130,8868	2201	4298	6499	SO:0001583	missense	256892	exon1			AGCCTGAAGAGGA	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.218T>C	11.37:g.4790951A>G	ENSP00000369744:p.Phe73Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	43	0.413462	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		494	0.2261904761904762	225	0.4573170731707317	82	0.2265193370165746	0	0.0	187	0.24670184696569922	G	0.026	-1.367725	0.01225	0.446615	0.251745	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00449	7.37;7.37	4.81	4.81	0.61882	GPCR, rhodopsin-like superfamily (1);	0.133054	0.34580	N	0.003857	T	0.00012	0.0000	N	0.00186	-1.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06643	-1.0815	9	0.02654	T	1	.	7.3933	0.26921	0.0863:0.0:0.7488:0.1649	rs11033801;rs52802475;rs58778978;rs11033801	73	A6NGY5	O51F1_HUMAN	S	66;73	ENSP00000345163:F66S;ENSP00000369744:F73S	ENSP00000345163:F66S	F	-	2	0	OR51F1	4747527	0.352000	0.24895	0.965000	0.40720	0.712000	0.41017	0.483000	0.22292	1.271000	0.44313	-0.197000	0.12766	TTC	A|0.702;G|0.298	0.298	strong		0.443	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
IMMT	10989	hgsc.bcm.edu	37	2	86400824	86400824	+	Missense_Mutation	SNP	G	G	A	rs1050301	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000409051.2_Missense_Mutation_p.P124S|IMMT_ENST00000442664.2_Missense_Mutation_p.P124S|IMMT_ENST00000490238.1_5'Flank	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	148	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	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	
LIPA	3988	hgsc.bcm.edu	37	10	91007360	91007360	+	Missense_Mutation	SNP	T	T	G	rs1051338	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:91007360T>G	ENST00000336233.5	-	2	368	c.46A>C	c.(46-48)Acc>Ccc	p.T16P	LIPA_ENST00000456827.1_Missense_Mutation_p.T16P|LIPA_ENST00000371837.1_Intron			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	16			T -> P (in dbSNP:rs1051338). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1718995}.		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)		GAATGCAGGGTCCAGAGAACC	0.373													T|||	1433	0.286142	0.1082	0.3545	5008	,	,		11907	0.3085		0.327	False		,,,				2504	0.4131				p.T16P		Atlas-SNP	.											.	LIPA	29	.	0			c.A46C						PASS	.	T	PRO/THR,PRO/THR	568,3838	254.6+/-260.1	41,486,1676	109.0	106.0	107.0		46,46	3.7	1.0	10	dbSNP_86	107	2566,6034	416.2+/-352.0	393,1780,2127	yes	missense,missense	LIPA	NM_000235.2,NM_001127605.1	38,38	434,2266,3803	GG,GT,TT		29.8372,12.8915,24.0966	benign,benign	16/400,16/400	91007360	3134,9872	2203	4300	6503	SO:0001583	missense	3988	exon2			GCAGGGTCCAGAG	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.46A>C	10.37:g.91007360T>G	ENSP00000337354:p.Thr16Pro	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	36	23	0.638889	NM_000235	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Missense_Mutation	SNP	ENST00000336233.5	37	CCDS7401.1	599	0.2742673992673993	54	0.10975609756097561	118	0.3259668508287293	166	0.2902097902097902	261	0.34432717678100266	T	11.49	1.652821	0.29336	0.128915	0.298372	ENSG00000107798	ENST00000336233;ENST00000371829;ENST00000541980;ENST00000456827;ENST00000542307;ENST00000428800;ENST00000282673	T;T;T;T	0.77750	-0.51;-0.51;-0.39;-1.12	4.93	3.72	0.42706	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.47153	P	6.650000000000267E-4	B	0.09022	0.002	B	0.06405	0.002	T	0.06391	-1.0829	8	0.35671	T	0.21	-1.309	7.5127	0.27583	0.1911:0.0:0.0:0.8089	rs1051338;rs2229254;rs3191715;rs17845330;rs17858173;rs52817712;rs1051338	16	P38571	LICH_HUMAN	P	16	ENSP00000337354:T16P;ENSP00000413019:T16P;ENSP00000388415:T16P;ENSP00000282673:T16P	ENSP00000282673:T16P	T	-	1	0	LIPA	90997340	0.000000	0.05858	0.997000	0.53966	0.146000	0.21551	-0.090000	0.11163	2.216000	0.71823	0.454000	0.30748	ACC	T|0.740;G|0.254	0.254	strong		0.373	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235	
EFCAB3	146779	hgsc.bcm.edu	37	17	60469289	60469289	+	Silent	SNP	T	T	C	rs61764063	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:60469289T>C	ENST00000305286.3	+	4	336	c.258T>C	c.(256-258)caT>caC	p.H86H	EFCAB3_ENST00000450662.2_Silent_p.H138H	NM_173503.3	NP_775774.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	86	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			TGACCAAGCATGATGTCTATA	0.358													.|||	21	0.00419329	0.0	0.0086	5008	,	,		16329	0.0		0.0119	False		,,,				2504	0.0031				p.H138H		Atlas-SNP	.											.	EFCAB3	71	.	0			c.T414C						PASS	.	T	,	9,4397	15.5+/-35.6	0,9,2194	238.0	203.0	215.0		414,258	-0.3	0.9	17	dbSNP_129	215	98,8502	55.2+/-116.2	1,96,4203	no	coding-synonymous,coding-synonymous	EFCAB3	NM_001144933.1,NM_173503.3	,	1,105,6397	CC,CT,TT		1.1395,0.2043,0.8227	,	138/491,86/439	60469289	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	146779	exon6			CAAGCATGATGTC	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"""EF-hand domain containing"""	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000305286.3:c.258T>C	17.37:g.60469289T>C		Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	323	113	0.349845	NM_001144933	J3KQM8	Silent	SNP	ENST00000305286.3	37	CCDS11632.1																																																																																			T|0.993;C|0.007	0.007	strong		0.358	EFCAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379114.1	NM_173503	
MUC17	140453	hgsc.bcm.edu	37	7	100678616	100678616	+	Missense_Mutation	SNP	G	G	A	rs113959201	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678616G>A	ENST00000306151.4	+	3	3983	c.3919G>A	c.(3919-3921)Ggt>Agt	p.G1307S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1307	59 X approximate tandem repeats.|Ser-rich.				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)					TGACACTAAAGGTCCTGTGGT	0.453																																					p.G1307S		Atlas-SNP	.											.	MUC17	804	.	0			c.G3919A						PASS	.						238.0	228.0	231.0					7																	100678616		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTAAAGGTCCTG	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.3919G>A	7.37:g.100678616G>A	ENSP00000302716:p.Gly1307Ser	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	256	92	0.359375	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	2.077	-0.411605	0.04799	.	.	ENSG00000169876	ENST00000306151	T	0.03468	3.92	0.471	-0.942	0.10398	.	.	.	.	.	T	0.01029	0.0034	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39761	-0.9598	8	0.06757	T	0.87	.	.	.	.	.	1307	Q685J3	MUC17_HUMAN	S	1307	ENSP00000302716:G1307S	ENSP00000302716:G1307S	G	+	1	0	MUC17	100465336	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.794000	0.04584	-2.345000	0.00621	-1.616000	0.00795	GGT	G|0.941;A|0.059	0.059	strong		0.453	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ZNF317	57693	hgsc.bcm.edu	37	19	9267319	9267319	+	Missense_Mutation	SNP	G	G	T	rs3752199	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	67	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	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	
CCPG1	9236	hgsc.bcm.edu	37	15	55664110	55664110	+	Missense_Mutation	SNP	G	G	C	rs117236526	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:55664110G>C	ENST00000310958.6	-	6	885	c.587C>G	c.(586-588)gCt>gGt	p.A196G	CCPG1_ENST00000425574.3_Missense_Mutation_p.A196G|MIR628_ENST00000385229.1_RNA|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000442196.3_Missense_Mutation_p.A196G|CCPG1_ENST00000569205.1_Missense_Mutation_p.A196G	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	196	Interaction with MCF2L and SRC. {ECO:0000250}.			A -> G (in Ref. 1; BAA86568). {ECO:0000305}.	cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TTCTTGTTCAGCAACTAGCCG	0.448													G|||	182	0.0363419	0.0015	0.0389	5008	,	,		17926	0.001		0.0696	False		,,,				2504	0.0838				p.A196G		Atlas-SNP	.											.	CCPG1	74	.	0			c.C587G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	67,3689		0,67,1811	96.0	90.0	92.0		587,587,587,587	1.4	0.0	15	dbSNP_132	92	607,7603		18,571,3516	yes	missense,missense,missense,missense	CCPG1	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_020739.3	60,60,60,60	18,638,5327	CC,CG,GG		7.3934,1.7838,5.6326	benign,benign,benign,benign	196/808,196/425,196/758,196/758	55664110	674,11292	1878	4105	5983	SO:0001583	missense	9236	exon6			TGTTCAGCAACTA	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.587C>G	15.37:g.55664110G>C	ENSP00000311656:p.Ala196Gly	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	105	99	0.942857	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	37	CCDS42039.1	73	0.033424908424908424	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	56	0.07387862796833773	G	6.652	0.488778	0.12641	0.017838	0.073934	ENSG00000256061	ENST00000310958;ENST00000442196;ENST00000425574	T;T;T	0.32515	3.78;3.78;1.45	5.74	1.42	0.22433	.	1.328530	0.04456	N	0.373577	T	0.01905	0.0060	L	0.51422	1.61	0.09310	N	1	B;B;B;B	0.16166	0.002;0.016;0.002;0.001	B;B;B;B	0.16289	0.004;0.015;0.006;0.004	T	0.13980	-1.0489	10	0.19590	T	0.45	.	3.2974	0.06971	0.1161:0.1212:0.4335:0.3291	.	196;196;196;52	A8K9T0;Q9ULG6-3;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	G	196	ENSP00000311656:A196G;ENSP00000403400:A196G;ENSP00000415128:A196G	ENSP00000311656:A196G	A	-	2	0	DYX1C1	53451402	0.000000	0.05858	0.021000	0.16686	0.364000	0.29643	-0.006000	0.12833	0.719000	0.32188	0.655000	0.94253	GCT	G|0.947;C|0.053	0.053	strong		0.448	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
PARP3	10039	hgsc.bcm.edu	37	3	51981769	51981769	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:51981769G>A	ENST00000417220.2	+	11	1778	c.1290G>A	c.(1288-1290)aaG>aaA	p.K430K	PARP3_ENST00000431474.1_Silent_p.K430K|PARP3_ENST00000486510.1_3'UTR|PARP3_ENST00000398755.3_Silent_p.K437K			Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	430	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|positive regulation of DNA ligation (GO:0051106)|protein ADP-ribosylation (GO:0006471)|protein localization to site of double-strand break (GO:1990166)|regulation of mitotic spindle organization (GO:0060236)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	catalytic activity (GO:0003824)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		TTGGCATGAAGTGTGGGGCCC	0.602																																					p.K437K		Atlas-SNP	.											.	PARP3	90	.	0			c.G1311A						PASS	.						95.0	100.0	98.0					3																	51981769		2053	4189	6242	SO:0001819	synonymous_variant	10039	exon10			CATGAAGTGTGGG	AF083068	CCDS43097.1, CCDS46839.1	3p22.2-p21.1	2010-07-14	2004-08-20	2004-08-26	ENSG00000041880	ENSG00000041880	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	273	protein-coding gene	gene with protein product	"""poly(ADP-ribose) synthetase-3"", ""NAD+ ADP-ribosyltransferase 3"", ""poly(ADP-ribose) polymerase 3"""	607726	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 3"""	ADPRTL3		10329013	Standard	NM_001003931		Approved	ADPRT3, IRT1, hPARP-3, pADPRT-3	uc003dbz.3	Q9Y6F1	OTTHUMG00000156931	ENST00000417220.2:c.1290G>A	3.37:g.51981769G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_001003931	Q8NER9|Q96CG2|Q9UG81	Silent	SNP	ENST00000417220.2	37	CCDS43097.1																																																																																			.	.	none		0.602	PARP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348612.2	NM_005485.4	
MACROD1	28992	hgsc.bcm.edu	37	11	63884747	63884747	+	Intron	SNP	C	C	T	rs35247680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:63884747C>T	ENST00000255681.6	-	3	584				FLRT1_ENST00000246841.3_Silent_p.L336L|RP11-21A7A.3_ENST00000543817.1_RNA	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						GCTGCAACCTCATGTGGCTGC	0.657													C|||	67	0.0133786	0.003	0.0173	5008	,	,		17278	0.0		0.0447	False		,,,				2504	0.0061				p.L336L		Atlas-SNP	.											.	FLRT1	46	.	0			c.C1008T						PASS	.	C	,	29,4373	35.2+/-66.4	0,29,2172	54.0	57.0	56.0		1008,	5.2	1.0	11	dbSNP_126	56	359,8235	120.6+/-179.8	7,345,3945	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	7,374,6117	TT,TC,CC		4.1773,0.6588,2.9855	,	336/675,	63884747	388,12608	2201	4297	6498	SO:0001627	intron_variant	23769	exon2			CAACCTCATGTGG	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+33963G>A	11.37:g.63884747C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	165	163	0.987879	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			C|0.975;T|0.025	0.025	strong		0.657	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
SCYL1	57410	hgsc.bcm.edu	37	11	65293819	65293819	+	Silent	SNP	G	G	A	rs75169347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000524944.1_Silent_p.K200K|SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000420247.2_Silent_p.K200K|SCYL1_ENST00000527009.1_Silent_p.K57K|SCYL1_ENST00000279270.6_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	141	0	0		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	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	
MUC17	140453	hgsc.bcm.edu	37	7	100680463	100680463	+	Missense_Mutation	SNP	G	G	T	rs368849364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680463G>T	ENST00000306151.4	+	3	5830	c.5766G>T	c.(5764-5766)agG>agT	p.R1922S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1922	59 X approximate tandem repeats.|Ser-rich.				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)					CAACTCCTAGGGAAGGAAGGC	0.507																																					p.R1922S		Atlas-SNP	.											.	MUC17	804	.	0			c.G5766T						PASS	.						242.0	242.0	242.0					7																	100680463		2203	4300	6503	SO:0001583	missense	140453	exon3			TCCTAGGGAAGGA	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.5766G>T	7.37:g.100680463G>T	ENSP00000302716:p.Arg1922Ser	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	204	19	0.0931373	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.015	-1.561399	0.00903	.	.	ENSG00000169876	ENST00000306151	T	0.02787	4.16	0.932	-1.86	0.07760	.	.	.	.	.	T	0.00998	0.0033	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39210	-0.9625	9	0.06494	T	0.89	.	3.4094	0.07353	0.2058:0.0:0.3687:0.4255	.	1922	Q685J3	MUC17_HUMAN	S	1922	ENSP00000302716:R1922S	ENSP00000302716:R1922S	R	+	3	2	MUC17	100467183	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.905000	0.00338	-2.952000	0.00293	-2.056000	0.00403	AGG	.	.	alt		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SCUBE1	80274	hgsc.bcm.edu	37	22	43607040	43607040	+	Silent	SNP	G	G	A	rs138988	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:43607040G>A	ENST00000360835.4	-	18	2397	c.2271C>T	c.(2269-2271)atC>atT	p.I757I	Z82214.3_ENST00000420269.1_RNA	NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	757					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CGGGGCAGCGGATGCAGCGGT	0.647													G|||	252	0.0503195	0.0552	0.036	5008	,	,		15874	0.0		0.1352	False		,,,				2504	0.0184				p.I757I		Atlas-SNP	.											.	SCUBE1	105	.	0			c.C2271T						PASS	.	G		307,4093	165.4+/-196.9	9,289,1902	172.0	136.0	148.0		2271	1.7	1.0	22	dbSNP_78	148	976,7622	211.4+/-252.0	53,870,3376	no	coding-synonymous	SCUBE1	NM_173050.3		62,1159,5278	AA,AG,GG		11.3515,6.9773,9.8707		757/989	43607040	1283,11715	2200	4299	6499	SO:0001819	synonymous_variant	80274	exon18			GCAGCGGATGCAG		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2271C>T	22.37:g.43607040G>A		Somatic	483	1	0.00207039		WXS	Illumina HiSeq	Phase_I	446	208	0.466368	NM_173050	Q5R336	Silent	SNP	ENST00000360835.4	37	CCDS14048.1																																																																																			G|0.910;A|0.090	0.090	strong		0.647	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
PANX2	56666	hgsc.bcm.edu	37	22	50617671	50617671	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50617671G>A	ENST00000395842.2	+	3	1999	c.1999G>A	c.(1999-2001)Gag>Aag	p.E667K	PANX2_ENST00000159647.5_Silent_p.T638T	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	667					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		CACCTTCGACGAGCCGAGAAC	0.697																																					p.E667K		Atlas-SNP	.											.	PANX2	69	.	0			c.G1999A						PASS	.						49.0	43.0	45.0					22																	50617671		2203	4297	6500	SO:0001583	missense	56666	exon3			TTCGACGAGCCGA		CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"""Ion channels / Pannexins"""	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.1999G>A	22.37:g.50617671G>A	ENSP00000379183:p.Glu667Lys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	127	44	0.346457	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	37	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	G	22.1	4.250501	0.80024	.	.	ENSG00000073150	ENST00000395842;ENST00000401643	T	0.33216	1.42	3.72	3.72	0.42706	.	0.000000	0.37304	U	0.002153	T	0.55529	0.1926	.	.	.	0.46279	D	0.998968	D	0.76494	0.999	D	0.68621	0.959	T	0.64744	-0.6335	9	0.87932	D	0	-23.7117	15.9969	0.80256	0.0:0.0:1.0:0.0	.	667	Q96RD6	PANX2_HUMAN	K	667;344	ENSP00000379183:E667K	ENSP00000379183:E667K	E	+	1	0	PANX2	48959798	1.000000	0.71417	0.946000	0.38457	0.282000	0.26991	6.495000	0.73665	2.081000	0.62600	0.313000	0.20887	GAG	.	.	none		0.697	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839	
KANK2	25959	hgsc.bcm.edu	37	19	11303943	11303943	+	Silent	SNP	A	A	G	rs3745681	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11303943A>G	ENST00000586659.1	-	4	1127	c.813T>C	c.(811-813)gtT>gtC	p.V271V	KANK2_ENST00000589359.1_Silent_p.V271V|KANK2_ENST00000432929.2_Silent_p.V271V|KANK2_ENST00000589894.1_Silent_p.V271V|KANK2_ENST00000355150.5_Silent_p.V271V			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	271					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CCCGTTCTCGAACCCAGGTGC	0.692													G|||	2531	0.505391	0.6483	0.4265	5008	,	,		15958	0.4514		0.3787	False		,,,				2504	0.5542				p.V271V		Atlas-SNP	.											KANK2,NS,carcinoma,0,1	KANK2	47	1	0			c.T813C						PASS	.	G	,	2625,1773		791,1043,365	26.0	28.0	27.0		813,813	-2.5	0.9	19	dbSNP_107	27	3333,5259		652,2029,1615	no	coding-synonymous,coding-synonymous	KANK2	NM_001136191.2,NM_015493.6	,	1443,3072,1980	GG,GA,AA		38.7919,40.3138,45.8661	,	271/852,271/860	11303943	5958,7032	2199	4296	6495	SO:0001819	synonymous_variant	25959	exon2			TTCTCGAACCCAG	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.813T>C	19.37:g.11303943A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Silent	SNP	ENST00000586659.1	37	CCDS12255.1																																																																																			A|0.544;G|0.456	0.456	strong		0.692	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
C1orf105	92346	hgsc.bcm.edu	37	1	172431333	172431333	+	Missense_Mutation	SNP	A	A	G	rs16844498	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:172431333A>G	ENST00000367727.4	+	5	487	c.289A>G	c.(289-291)Atg>Gtg	p.M97V	C1orf105_ENST00000367725.4_Missense_Mutation_p.M87V|C1orf105_ENST00000367726.1_3'UTR	NM_139240.3	NP_640333.3	O95561	CA105_HUMAN	chromosome 1 open reading frame 105	97			M -> V (in dbSNP:rs16844498).							large_intestine(1)|lung(12)|prostate(1)|skin(1)	15						ACCAAGAACAATGAAAATCCC	0.318													A|||	220	0.0439297	0.0272	0.049	5008	,	,		20279	0.0		0.0875	False		,,,				2504	0.0634				p.M97V		Atlas-SNP	.											.	C1orf105	24	.	0			c.A289G						PASS	.	A	VAL/MET	137,4269	98.5+/-137.1	2,133,2068	97.0	91.0	93.0		289	-8.5	0.0	1	dbSNP_123	93	515,8085	145.4+/-201.1	19,477,3804	yes	missense	C1orf105	NM_139240.3	21	21,610,5872	GG,GA,AA		5.9884,3.1094,5.0131	benign	97/184	172431333	652,12354	2203	4300	6503	SO:0001583	missense	92346	exon5			AGAACAATGAAAA	AL035295	CCDS1301.1, CCDS72983.1	1q24.3	2012-06-26			ENSG00000180999	ENSG00000180999			29591	protein-coding gene	gene with protein product						12477932	Standard	NM_139240		Approved		uc001gik.3	O95561	OTTHUMG00000034750	ENST00000367727.4:c.289A>G	1.37:g.172431333A>G	ENSP00000356700:p.Met97Val	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	338	114	0.337278	NM_139240	Q8IY02	Missense_Mutation	SNP	ENST00000367727.4	37	CCDS1301.1	102	0.046703296703296704	14	0.028455284552845527	17	0.04696132596685083	0	0.0	71	0.09366754617414248	A	0.006	-2.077666	0.00375	0.031094	0.059884	ENSG00000180999	ENST00000367727;ENST00000488100;ENST00000367725	T;T;T	0.33438	1.41;1.41;1.41	4.26	-8.53	0.00916	.	1.919010	0.02269	N	0.068313	T	0.03390	0.0098	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06162	-1.0842	10	0.33141	T	0.24	0.3528	0.2515	0.00206	0.3358:0.2407:0.1748:0.2487	rs16844498;rs52830958;rs16844498	97	O95561	CA105_HUMAN	V	97;68;87	ENSP00000356700:M97V;ENSP00000431442:M68V;ENSP00000356698:M87V	ENSP00000356698:M87V	M	+	1	0	C1orf105	170697956	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.598000	0.00419	-4.449000	0.00048	-1.937000	0.00501	ATG	A|0.949;G|0.051	0.051	strong		0.318	C1orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084062.2	NM_139240	
GNPDA1	10007	hgsc.bcm.edu	37	5	141391532	141391532	+	Silent	SNP	G	G	A	rs164080	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:141391532G>A	ENST00000508177.1	-	1	827	c.69C>T	c.(67-69)cgC>cgT	p.R23R	GNPDA1_ENST00000513454.1_Silent_p.R23R|GNPDA1_ENST00000500692.2_Silent_p.R23R|GNPDA1_ENST00000542860.1_Silent_p.R23R|GNPDA1_ENST00000311337.6_Silent_p.R23R|GNPDA1_ENST00000458112.2_Silent_p.R23R|GNPDA1_ENST00000503794.1_Silent_p.R23R			P46926	GNPI1_HUMAN	glucosamine-6-phosphate deaminase 1	23					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucosamine catabolic process (GO:0006043)|N-acetylglucosamine metabolic process (GO:0006044)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	glucosamine-6-phosphate deaminase activity (GO:0004342)|hydrolase activity (GO:0016787)	p.R23R(1)		central_nervous_system(1)|lung(1)|skin(3)|stomach(1)	6		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACTGGATGATGCGGTTCCTGA	0.567											OREG0016880	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2728	0.544728	0.671	0.4352	5008	,	,		19378	0.625		0.4612	False		,,,				2504	0.455				p.R23R		Atlas-SNP	.											GNPDA1,NS,carcinoma,0,1	GNPDA1	16	1	1	Substitution - coding silent(1)	stomach(1)	c.C69T						PASS	.	G		2771,1635	659.9+/-400.6	883,1005,315	113.0	106.0	108.0		69	-0.2	1.0	5	dbSNP_79	108	3927,4673	547.6+/-385.2	889,2149,1262	no	coding-synonymous	GNPDA1	NM_005471.4		1772,3154,1577	AA,AG,GG		45.6628,37.1085,48.5007		23/290	141391532	6698,6308	2203	4300	6503	SO:0001819	synonymous_variant	10007	exon2			GATGATGCGGTTC	AF048826	CCDS4272.1	5q21	2008-02-05	2003-10-17	2003-10-22	ENSG00000113552	ENSG00000113552	3.5.99.6		4417	protein-coding gene	gene with protein product	"""glucosamine-6-phosphate deaminase"", ""oscillin"""	601798	"""glucosamine-6-phosphate isomerase"""	GNPI		9714720, 9438414	Standard	NM_005471		Approved	GNPDA, HLN, GPI, KIAA0060	uc010jgh.3	P46926	OTTHUMG00000129657	ENST00000508177.1:c.69C>T	5.37:g.141391532G>A		Somatic	241	0	0	1663	WXS	Illumina HiSeq	Phase_I	245	107	0.436735	NM_005471	B7Z3X4|D3DQE7	Silent	SNP	ENST00000508177.1	37	CCDS4272.1																																																																																			G|0.454;A|0.546	0.546	strong		0.567	GNPDA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370631.1	NM_005471	
TGM4	7047	hgsc.bcm.edu	37	3	44948563	44948563	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:44948563A>G	ENST00000296125.4	+	10	1266	c.1198A>G	c.(1198-1200)Atg>Gtg	p.M400V		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	400					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)			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)	GTTGGTGAAGATGGTGAATGG	0.498																																					p.M400V		Atlas-SNP	.											.	TGM4	82	.	0			c.A1198G						PASS	.						140.0	128.0	132.0					3																	44948563		2203	4300	6503	SO:0001583	missense	7047	exon10			GTGAAGATGGTGA	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.1198A>G	3.37:g.44948563A>G	ENSP00000296125:p.Met400Val	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	230	117	0.508696	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	A	5.841	0.339412	0.11069	.	.	ENSG00000163810	ENST00000296125	T	0.20738	2.05	2.03	-4.07	0.03975	.	0.468908	0.16456	U	0.213616	T	0.04048	0.0113	N	0.01048	-1.04	0.09310	N	1	B	0.19073	0.033	B	0.08055	0.003	T	0.22765	-1.0207	10	0.33141	T	0.24	.	0.4585	0.00512	0.3471:0.1383:0.2793:0.2353	.	400	P49221	TGM4_HUMAN	V	400	ENSP00000296125:M400V	ENSP00000296125:M400V	M	+	1	0	TGM4	44923567	0.002000	0.14202	0.000000	0.03702	0.112000	0.19704	-0.168000	0.09925	-1.271000	0.02430	-0.710000	0.03640	ATG	.	.	none		0.498	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
IGF2R	3482	hgsc.bcm.edu	37	6	160493834	160493834	+	Silent	SNP	G	G	A	rs2230044	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160493834G>A	ENST00000356956.1	+	33	4756	c.4608G>A	c.(4606-4608)gcG>gcA	p.A1536A		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1536					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GTGGCAGGGCGGGATTCACAG	0.552													G|||	298	0.0595048	0.0749	0.0187	5008	,	,		21061	0.0933		0.0109	False		,,,				2504	0.0828				p.A1536A		Atlas-SNP	.											.	IGF2R	251	.	0			c.G4608A						PASS	.	G		334,4072	177.3+/-206.3	12,310,1881	168.0	140.0	150.0		4608	-10.2	0.2	6	dbSNP_98	150	119,8481	62.4+/-124.4	2,115,4183	no	coding-synonymous	IGF2R	NM_000876.2		14,425,6064	AA,AG,GG		1.3837,7.5806,3.483		1536/2492	160493834	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon33			CAGGGCGGGATTC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4608G>A	6.37:g.160493834G>A		Somatic	286	1	0.0034965		WXS	Illumina HiSeq	Phase_I	235	111	0.47234	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			G|0.958;A|0.042	0.042	strong		0.552	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
PRR21	643905	hgsc.bcm.edu	37	2	240982131	240982131	+	Missense_Mutation	SNP	A	A	G	rs79839275	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:240982131A>G	ENST00000408934.1	-	1	268	c.269T>C	c.(268-270)aTg>aCg	p.M90T		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	90	Pro-rich.							p.S86fs*291(2)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GTGAAGAGGCATGGATGAAGG	0.617													-|||	1342	0.267971	0.3094	0.2378	5008	,	,		13820	0.3591		0.2167	False		,,,				2504	0.1922				p.M90T		Atlas-SNP	.											PRR21,NS,carcinoma,0,2	PRR21	53	2	2	Deletion - Frameshift(2)	upper_aerodigestive_tract(2)	c.T269C						scavenged	.	A	THR/MET	623,3545		160,303,1621	145.0	139.0	141.0		269	-3.6	0.0	2	dbSNP_131	141	921,7389		239,443,3473	no	missense	PRR21	NM_001080835.1	81	399,746,5094	GG,GA,AA		11.083,14.9472,12.3738	benign	90/390	240982131	1544,10934	2084	4155	6239	SO:0001583	missense	643905	exon1			AGAGGCATGGATG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.269T>C	2.37:g.240982131A>G	ENSP00000386166:p.Met90Thr	Somatic	211	3	0.014218		WXS	Illumina HiSeq	Phase_I	190	94	0.494737	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	573	0.2623626373626374	126	0.25609756097560976	81	0.22375690607734808	202	0.3531468531468531	164	0.21635883905013192	-	0.001	-3.069052	0.00036	0.149472	0.11083	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13196	2.61;2.61	1.79	-3.59	0.04583	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.48103	-0.9064	8	0.21014	T	0.42	.	6.6332	0.22869	0.1723:0.4441:0.3836:0.0	.	90	Q8WXC7	PRR21_HUMAN	T	90	ENSP00000386166:M90T;ENSP00000418240:M90T	ENSP00000386166:M90T	M	-	2	0	PRR21	240630804	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.360000	0.20250	-2.294000	0.00663	-0.489000	0.04712	ATG	A|0.737;G|0.263	0.263	strong		0.617	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
SLCO1A2	6579	hgsc.bcm.edu	37	12	21487544	21487544	+	Missense_Mutation	SNP	A	A	G	rs10841795	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:21487544A>G	ENST00000307378.6	-	3	758	c.38T>C	c.(37-39)aTa>aCa	p.I13T	SLCO1A2_ENST00000390670.3_5'UTR|SLCO1A2_ENST00000458504.1_5'UTR|SLCO1A2_ENST00000537524.1_5'UTR|SLCO1A2_ENST00000452078.1_Missense_Mutation_p.I13T|SLCO1A2_ENST00000473830.1_5'UTR	NM_134431.3	NP_602307.1	P46721	SO1A2_HUMAN	solute carrier organic anion transporter family, member 1A2	13			I -> T (in dbSNP:rs10841795). {ECO:0000269|PubMed:15632119}.		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 membrane (GO:0016021)|plasma membrane (GO:0005886)	organic anion transmembrane transporter activity (GO:0008514)			breast(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(6)|upper_aerodigestive_tract(1)	48					Aminohippurate(DB00345)|Atorvastatin(DB01076)|Bumetanide(DB00887)|Chlorambucil(DB00291)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dexamethasone(DB01234)|Digitoxin(DB01396)|Digoxin(DB00390)|Dinoprostone(DB00917)|Enalapril(DB00584)|Erythromycin(DB00199)|Estradiol(DB00783)|Estriol(DB04573)|Estrone(DB00655)|Fexofenadine(DB00950)|Glyburide(DB01016)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Indinavir(DB00224)|Indomethacin(DB00328)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Methyltestosterone(DB06710)|Mirabegron(DB08893)|Naloxone(DB01183)|Naproxen(DB00788)|Nelfinavir(DB00220)|Ouabain(DB01092)|Pravastatin(DB00175)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rocuronium(DB00728)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Simvastatin(DB00641)|Spironolactone(DB00421)|Sumatriptan(DB00669)|Tauroursodeoxycholic acid(DB08834)|Testosterone(DB00624)|Tolbutamide(DB01124)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)	AAGACATCTTATTCTATGGGT	0.348													A|||	258	0.0515176	0.0045	0.072	5008	,	,		18017	0.003		0.1272	False		,,,				2504	0.0726				p.I13T		Atlas-SNP	.											SLCO1A2,NS,carcinoma,0,1	SLCO1A2	107	1	0			c.T38C						scavenged	.	A	THR/ILE,THR/ILE	113,4293	85.8+/-124.5	3,107,2093	223.0	207.0	213.0		38,38	3.7	0.8	12	dbSNP_120	213	1169,7425	238.9+/-270.2	96,977,3224	yes	missense,missense	SLCO1A2	NM_021094.3,NM_134431.3	89,89	99,1084,5317	GG,GA,AA		13.6025,2.5647,9.8615	benign,benign	13/671,13/671	21487544	1282,11718	2203	4297	6500	SO:0001583	missense	6579	exon3			CATCTTATTCTAT		CCDS8686.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000084453	ENSG00000084453		"""Solute carriers"""	10956	protein-coding gene	gene with protein product		602883	"""solute carrier family 21 (organic anion transporter), member 3"""	SLC21A3		9007731	Standard	NM_134431		Approved	OATP, OATP1A2, OATP-A	uc001rer.3	P46721	OTTHUMG00000156259	ENST00000307378.6:c.38T>C	12.37:g.21487544A>G	ENSP00000305974:p.Ile13Thr	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	177	90	0.508475	NM_134431	Q9UGP7|Q9UL38	Missense_Mutation	SNP	ENST00000307378.6	37	CCDS8686.1	132	0.06043956043956044	6	0.012195121951219513	27	0.07458563535911603	1	0.0017482517482517483	98	0.12928759894459102	A	2.680	-0.275492	0.05679	0.025647	0.136025	ENSG00000084453	ENST00000307378;ENST00000452078;ENST00000422327;ENST00000453443;ENST00000421294;ENST00000450590;ENST00000435179;ENST00000421287;ENST00000416627	T;T;T;T;T;T;T;T	0.58060	1.2;1.2;1.37;1.37;0.38;0.37;0.36;0.92	4.89	3.74	0.42951	Major facilitator superfamily domain, general substrate transporter (1);	0.445107	0.23581	N	0.046652	T	0.00210	0.0006	N	0.05441	-0.05	0.09310	P	0.99999273965	B	0.09022	0.002	B	0.09377	0.004	T	0.08493	-1.0719	9	0.17832	T	0.49	.	7.4597	0.27287	0.9023:0.0:0.0977:0.0	rs10841795;rs52792469;rs57921276;rs10841795	13	P46721	SO1A2_HUMAN	T	13	ENSP00000305974:I13T;ENSP00000393973:I13T;ENSP00000416190:I13T;ENSP00000409314:I13T;ENSP00000390572:I13T;ENSP00000407462:I13T;ENSP00000401195:I13T;ENSP00000390672:I13T	ENSP00000305974:I13T	I	-	2	0	SLCO1A2	21378811	0.990000	0.36364	0.849000	0.33467	0.977000	0.68977	2.454000	0.44979	0.995000	0.38917	0.528000	0.53228	ATA	A|0.924;G|0.076	0.076	strong		0.348	SLCO1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343648.3	NM_021094	
HNRNPA1	3178	hgsc.bcm.edu	37	12	54676630	54676630	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:54676630G>A	ENST00000340913.6	+	7	776	c.723G>A	c.(721-723)ggG>ggA	p.G241G	HNRNPA1_ENST00000547276.1_Intron|HNRNPA1_ENST00000330752.8_Silent_p.G228G|HNRNPA1_ENST00000546500.1_Silent_p.G241G|RP11-968A15.8_ENST00000553061.1_RNA|CBX5_ENST00000209875.4_5'Flank	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	241	Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|nuclear export (GO:0051168)|nuclear import (GO:0051170)|RNA export from nucleus (GO:0006405)|RNA splicing (GO:0008380)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20						gtggcagtggggatggctata	0.398																																					p.G241G	Colon(83;502 1289 8436 16406 24870)	Atlas-SNP	.											.	HNRNPA1	72	.	0			c.G723A						PASS	.						34.0	33.0	34.0					12																	54676630		2008	3945	5953	SO:0001819	synonymous_variant	3178	exon7			CAGTGGGGATGGC	BC009600	CCDS41793.1, CCDS44909.1	12q13.1	2013-10-11		2007-08-16	ENSG00000135486	ENSG00000135486		"""RNA binding motif (RRM) containing"""	5031	protein-coding gene	gene with protein product		164017		HNRPA1		1733858	Standard	XR_245923		Approved	hnRNPA1, hnRNP-A1	uc001sfl.3	P09651		ENST00000340913.6:c.723G>A	12.37:g.54676630G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	104	38	0.365385	NM_002136	A8K4Z8|Q3MIB7|Q6PJZ7	Silent	SNP	ENST00000340913.6	37	CCDS44909.1																																																																																			.	.	none		0.398	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157	
BSN	8927	hgsc.bcm.edu	37	3	49690496	49690496	+	Silent	SNP	C	C	T	rs11709525	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:49690496C>T	ENST00000296452.4	+	5	3621	c.3507C>T	c.(3505-3507)tcC>tcT	p.S1169S		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1169					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AGACACCCTCCGGCAGCTCCA	0.602													C|||	1039	0.207468	0.2632	0.1657	5008	,	,		19657	0.0565		0.3241	False		,,,				2504	0.1973				p.S1169S		Atlas-SNP	.											BSN,NS,carcinoma,0,1	BSN	272	1	0			c.C3507T						scavenged	.	C		1179,3227	381.6+/-324.1	150,879,1174	33.0	35.0	35.0		3507	-9.8	0.0	3	dbSNP_120	35	2556,6044	384.5+/-341.1	405,1746,2149	no	coding-synonymous	BSN	NM_003458.3		555,2625,3323	TT,TC,CC		29.7209,26.759,28.7175		1169/3927	49690496	3735,9271	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon5			ACCCTCCGGCAGC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3507C>T	3.37:g.49690496C>T		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	103	59	0.572816	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			C|0.731;G|0.000;T|0.269	0.269	strong		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
TMEM45A	55076	hgsc.bcm.edu	37	3	100274090	100274090	+	Missense_Mutation	SNP	C	C	A	rs200878698		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:100274090C>A	ENST00000323523.4	+	2	348	c.35C>A	c.(34-36)aCc>aAc	p.T12N	TMEM45A_ENST00000462884.1_3'UTR|TMEM45A_ENST00000403410.1_Missense_Mutation_p.T28N	NM_018004.1	NP_060474.1	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	12						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)	11						CTCCCTGGAACCTTCTTTTTT	0.368																																					p.T12N		Atlas-SNP	.											TMEM45A,NS,carcinoma,+1,1	TMEM45A	35	1	0			c.C35A						PASS	.	C	ASN/THR	0,4406		0,0,2203	166.0	176.0	172.0		35	-0.4	0.6	3		172	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEM45A	NM_018004.1	65	0,2,6501	AA,AC,CC		0.0233,0.0,0.0154	benign	12/276	100274090	2,13004	2203	4300	6503	SO:0001583	missense	55076	exon2			CTGGAACCTTCTT	AK000996	CCDS2937.1	3q12.2	2005-02-04			ENSG00000181458	ENSG00000181458			25480	protein-coding gene	gene with protein product						12477932	Standard	XM_005247568		Approved	FLJ10134, DERP7	uc003dtz.1	Q9NWC5	OTTHUMG00000150327	ENST00000323523.4:c.35C>A	3.37:g.100274090C>A	ENSP00000319009:p.Thr12Asn	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	156	68	0.435897	NM_018004	Q53YW5	Missense_Mutation	SNP	ENST00000323523.4	37	CCDS2937.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740553	0.30865	0.0	2.33E-4	ENSG00000181458	ENST00000323523;ENST00000403410;ENST00000449609	T;T;T	0.50001	1.39;1.38;0.76	5.84	-0.364	0.12553	.	0.370601	0.35349	N	0.003273	T	0.45135	0.1327	M	0.62723	1.935	0.25270	N	0.989529	B;P	0.47106	0.22;0.89	B;B	0.39876	0.036;0.312	T	0.52711	-0.8539	10	0.59425	D	0.04	0.3845	17.6844	0.88253	0.0:0.1546:0.7715:0.0738	.	28;12	C9J9Z5;Q9NWC5	.;TM45A_HUMAN	N	12;28;28	ENSP00000319009:T12N;ENSP00000385089:T28N;ENSP00000405597:T28N	ENSP00000319009:T12N	T	+	2	0	TMEM45A	101756780	1.000000	0.71417	0.567000	0.28434	0.432000	0.31715	0.710000	0.25748	-0.406000	0.07588	-0.150000	0.13652	ACC	.	.	weak		0.368	TMEM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317571.1	NM_018004	
VANGL2	57216	hgsc.bcm.edu	37	1	160385934	160385934	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:160385934C>T	ENST00000368061.2	+	3	628	c.154C>T	c.(154-156)Ccc>Tcc	p.P52S		NM_020335.2	NP_065068.1	Q9ULK5	VANG2_HUMAN	VANGL planar cell polarity protein 2	52					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|cell migration involved in kidney development (GO:0035787)|cochlea morphogenesis (GO:0090103)|convergent extension involved in axis elongation (GO:0060028)|convergent extension involved in neural plate elongation (GO:0022007)|digestive tract morphogenesis (GO:0048546)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity involved in neural tube closure (GO:0090177)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|glomerulus development (GO:0032835)|hair follicle development (GO:0001942)|heart looping (GO:0001947)|inner ear receptor stereocilium organization (GO:0060122)|kidney morphogenesis (GO:0060993)|lateral sprouting involved in lung morphogenesis (GO:0060490)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|neural tube closure (GO:0001843)|nonmotile primary cilium assembly (GO:0035058)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in axis elongation (GO:0003402)|planar cell polarity pathway involved in heart morphogenesis (GO:0061346)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|positive regulation of JUN kinase activity (GO:0043507)|post-anal tail morphogenesis (GO:0036342)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Wnt signaling pathway (GO:0030111)|Rho protein signal transduction (GO:0007266)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell pole (GO:0060187)|cell-cell junction (GO:0005911)|ER to Golgi transport vesicle (GO:0030134)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)				biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	37	all_cancers(52;1.08e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TCCCGGGGAGCCCCTGCTGGA	0.657																																					p.P52S		Atlas-SNP	.											VANGL2,NS,carcinoma,-2,1	VANGL2	83	1	0			c.C154T						scavenged	.						37.0	44.0	41.0					1																	160385934		2203	4299	6502	SO:0001583	missense	57216	exon3			GGGGAGCCCCTGC	AB033041	CCDS30915.1	1q22-q23	2013-03-05	2013-03-05		ENSG00000162738	ENSG00000162738			15511	protein-coding gene	gene with protein product	"""vang, van gogh-like 2"", ""loop-tail-associated protein"", ""strabismus"""	600533	"""vang (van gogh, Drosophila)-like 2, vang, van gogh-like 2 (Drosophila)"", ""vang-like 2 (van gogh, Drosophila)"""			11431695	Standard	NM_020335		Approved	KIAA1215, LTAP, LPP1, STBM, STB1, STBM1, MGC119403, MGC119404	uc001fwc.2	Q9ULK5	OTTHUMG00000033122	ENST00000368061.2:c.154C>T	1.37:g.160385934C>T	ENSP00000357040:p.Pro52Ser	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	267	5	0.0187266	NM_020335	D3DVE9|Q5T212	Missense_Mutation	SNP	ENST00000368061.2	37	CCDS30915.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.677009	0.88445	.	.	ENSG00000162738	ENST00000368061	D	0.81579	-1.51	4.55	4.55	0.56014	.	0.069721	0.56097	D	0.000024	T	0.63954	0.2555	L	0.49350	1.555	0.58432	D	0.999998	B	0.20261	0.043	B	0.22386	0.039	T	0.61978	-0.6951	10	0.17369	T	0.5	-36.3007	14.8376	0.70194	0.0:1.0:0.0:0.0	.	52	Q9ULK5	VANG2_HUMAN	S	52	ENSP00000357040:P52S	ENSP00000357040:P52S	P	+	1	0	VANGL2	158652558	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.398000	0.66308	2.354000	0.79902	0.461000	0.40582	CCC	.	.	none		0.657	VANGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080677.1	NM_020335	
MICA	100507436	hgsc.bcm.edu	37	6	31382882	31382882	+	3'UTR	SNP	C	C	A	rs9266825	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31382882C>A	ENST00000449934.2	+	0	1176				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)				CTGATGTCAGCTCTTGGGTCC	0.572													t|||	1717	0.342851	0.4372	0.3516	5008	,	,		14470	0.2996		0.2992	False		,,,				2504	0.2986				p.A373D		Atlas-SNP	.											.	MICA	21	.	0			c.C1118A						PASS	.	C		524,860		108,308,276	173.0	157.0	162.0			-1.5	0.0	6	dbSNP_118	162	821,2361		97,627,867	yes	utr-3	MICA	NM_001177519.1		205,935,1143	AA,AC,CC		25.8014,37.8613,29.4569			31382882	1345,3221	692	1591	2283	SO:0001624	3_prime_UTR_variant	100507436	exon7			TGTCAGCTCTTGG	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.*123C>A	6.37:g.31382882C>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	162	68	0.419753	NM_000247		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.666;A|0.334	0.334	strong		0.572	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
COPE	11316	hgsc.bcm.edu	37	19	19011244	19011244	+	Silent	SNP	T	T	C	rs1127821	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19011244T>C	ENST00000262812.4	-	8	798	c.750A>G	c.(748-750)ccA>ccG	p.P250P	COPE_ENST00000351079.4_Silent_p.P199P|COPE_ENST00000600932.1_Silent_p.P273P|COPE_ENST00000598969.1_5'UTR|COPE_ENST00000349893.4_Silent_p.P198P	NM_007263.3	NP_009194.2	O14579	COPE_HUMAN	coatomer protein complex, subunit epsilon	250					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|membrane organization (GO:0061024)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	11						CCAGCGTCTCTGGGTAGCCAC	0.662													C|||	1815	0.36242	0.3654	0.5994	5008	,	,		15588	0.1915		0.4841	False		,,,				2504	0.2413				p.P250P		Atlas-SNP	.											.	COPE	26	.	0			c.A750G						PASS	.	C	,,	1321,2265		262,797,734	31.0	26.0	28.0		750,597,594	-9.9	0.2	19	dbSNP_86	28	2857,3705		650,1557,1074	no	coding-synonymous,coding-synonymous,coding-synonymous	COPE	NM_007263.3,NM_199442.1,NM_199444.1	,,	912,2354,1808	CC,CT,TT		43.5386,36.8377,41.1707	,,	250/309,199/258,198/257	19011244	4178,5970	1793	3281	5074	SO:0001819	synonymous_variant	11316	exon8			CGTCTCTGGGTAG	AJ131182	CCDS12387.1, CCDS12388.1, CCDS12389.1	19p13.11	2008-02-05				ENSG00000105669			2234	protein-coding gene	gene with protein product		606942				10469566	Standard	NM_007263		Approved	epsilon-COP	uc002nkk.3	O14579		ENST00000262812.4:c.750A>G	19.37:g.19011244T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_007263	A6NE29|A6NKA3|O76097|Q6IBB8|Q9UGP6	Silent	SNP	ENST00000262812.4	37	CCDS12387.1																																																																																			T|0.421;G|0.095;C|0.305;A|0.179	0.305	strong		0.662	COPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464801.1	NM_007263	
PKD1	5310	hgsc.bcm.edu	37	16	2160973	2160973	+	Missense_Mutation	SNP	A	A	G	rs116092985	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2160973A>G	ENST00000262304.4	-	15	4403	c.4195T>C	c.(4195-4197)Tgg>Cgg	p.W1399R	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.W1399R	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1399	PKD 9. {ECO:0000255|PROSITE- ProRule:PRU00151}.		W -> R (in dbSNP:rs116092985). {ECO:0000269|PubMed:10364515, ECO:0000269|PubMed:10577909, ECO:0000269|PubMed:11857740, ECO:0000269|PubMed:11967008, ECO:0000269|PubMed:12070253, ECO:0000269|PubMed:18837007}.		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						GCCACCAGCCAGGCCTCGTCC	0.667													g|||	234	0.0467252	0.0484	0.0879	5008	,	,		16393	0.0		0.0944	False		,,,				2504	0.0143				p.W1399R		Atlas-SNP	.											.	PKD1	184	.	0			c.T4195C						PASS	.						38.0	39.0	39.0					16																	2160973		2194	4294	6488	SO:0001583	missense	5310	exon15			CCAGCCAGGCCTC	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.4195T>C	16.37:g.2160973A>G	ENSP00000262304:p.Trp1399Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	107	34	0.317757	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	117	0.05357142857142857	19	0.03861788617886179	35	0.09668508287292818	0	0.0	63	0.08311345646437995	g	0.018	-1.486396	0.01018	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.59224	0.28;0.28	5.58	3.39	0.38822	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (2);	1.582370	0.03389	N	0.201594	T	0.00552	0.0018	N	0.00170	-1.935	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.06058	-1.0848	10	0.25106	T	0.35	.	5.7645	0.18219	0.3067:0.0:0.5246:0.1687	.	1399;1399	P98161-3;P98161	.;PKD1_HUMAN	R	1399;1399;1080	ENSP00000262304:W1399R;ENSP00000399501:W1399R	ENSP00000262304:W1399R	W	-	1	0	PKD1	2100974	0.031000	0.19500	0.051000	0.19133	0.001000	0.01503	0.221000	0.17680	0.711000	0.32018	-0.404000	0.06349	TGG	A|0.943;G|0.057	0.057	strong		0.667	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
IRF2	3660	hgsc.bcm.edu	37	4	185310218	185310218	+	Silent	SNP	C	C	T	rs1131553	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:185310218C>T	ENST00000393593.3	-	9	951	c.744G>A	c.(742-744)ggG>ggA	p.G248G		NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	248					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G248G(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	22		all_lung(41;7.86e-14)|Lung NSC(41;1.87e-13)|Colorectal(36;0.00146)|Hepatocellular(41;0.00826)|Renal(120;0.00992)|Prostate(90;0.0115)|all_neural(102;0.0573)|all_hematologic(60;0.0592)		all cancers(43;3.94e-27)|Epithelial(43;5.3e-24)|OV - Ovarian serous cystadenocarcinoma(60;1.06e-10)|Colorectal(24;7.98e-07)|STAD - Stomach adenocarcinoma(60;3.95e-05)|GBM - Glioblastoma multiforme(59;8.3e-05)|COAD - Colon adenocarcinoma(29;0.000106)|BRCA - Breast invasive adenocarcinoma(30;0.000311)|LUSC - Lung squamous cell carcinoma(40;0.0128)|READ - Rectum adenocarcinoma(43;0.0419)		AGTGTGGCCGCCCCTTTCAAG	0.498													C|||	2119	0.423123	0.3548	0.5245	5008	,	,		20139	0.4216		0.3598	False		,,,				2504	0.5102				p.G248G		Atlas-SNP	.											IRF2,NS,carcinoma,0,1	IRF2	53	1	1	Substitution - coding silent(1)	stomach(1)	c.G744A						PASS	.	C		1525,2881	483.3+/-359.7	262,1001,940	129.0	111.0	117.0		744	-4.0	0.9	4	dbSNP_107	117	3376,5224	500.1+/-375.1	677,2022,1601	no	coding-synonymous	IRF2	NM_002199.3		939,3023,2541	TT,TC,CC		39.2558,34.6119,37.6826		248/350	185310218	4901,8105	2203	4300	6503	SO:0001819	synonymous_variant	3660	exon9			TGGCCGCCCCTTT		CCDS3835.1	4q34.1-q35.1	2008-07-29				ENSG00000168310			6117	protein-coding gene	gene with protein product		147576				2475256	Standard	NM_002199		Approved		uc003iwf.4	P14316		ENST00000393593.3:c.744G>A	4.37:g.185310218C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	104	84	0.807692	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Silent	SNP	ENST00000393593.3	37	CCDS3835.1	869	0.39789377289377287	184	0.37398373983739835	192	0.5303867403314917	211	0.3688811188811189	282	0.3720316622691293	C	4.681	0.126624	0.08931	0.346119	0.392558	ENSG00000168310	ENST00000505067	.	.	.	5.31	-4.03	0.04021	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999610463	.	.	.	.	.	.	T	0.48151	-0.9060	3	.	.	.	.	1.1333	0.01749	0.3733:0.1003:0.2741:0.2523	rs3775543;rs17417214;rs3775543	.	.	.	T	182	.	.	A	-	1	0	IRF2	185547212	0.073000	0.21202	0.901000	0.35422	0.846000	0.48090	-1.266000	0.02842	-0.699000	0.05077	-0.324000	0.08512	GCG	C|0.617;T|0.383	0.383	strong		0.498	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1		
TMED6	146456	hgsc.bcm.edu	37	16	69381769	69381769	+	Silent	SNP	C	C	T	rs16958777	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:69381769C>T	ENST00000288025.3	-	3	466	c.411G>A	c.(409-411)ggG>ggA	p.G137G	RP11-343C2.7_ENST00000564737.1_Missense_Mutation_p.G130S|RP11-343C2.9_ENST00000563634.1_Intron	NM_144676.3	NP_653277.2	Q8WW62	TMED6_HUMAN	transmembrane emp24 protein transport domain containing 6	137	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.				transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	9						CATAGAAGACCCCAAAGTTGA	0.403													T|||	382	0.076278	0.1324	0.0692	5008	,	,		18822	0.0258		0.0547	False		,,,				2504	0.0798				p.G137G		Atlas-SNP	.											.	TMED6	19	.	0			c.G411A						PASS	.	T		598,3798	769.6+/-413.7	48,502,1648	246.0	235.0	238.0		411	4.2	1.0	16	dbSNP_123	238	541,8059	795.0+/-407.5	15,511,3774	no	coding-synonymous	TMED6	NM_144676.3		63,1013,5422	TT,TC,CC		6.2907,13.6033,8.7642		137/241	69381769	1139,11857	2198	4300	6498	SO:0001819	synonymous_variant	146456	exon3			GAAGACCCCAAAG	BC020827	CCDS10878.1	16q22.1	2008-02-05			ENSG00000157315	ENSG00000157315			28331	protein-coding gene	gene with protein product						12477932	Standard	NM_144676		Approved	MGC23911	uc002exc.2	Q8WW62	OTTHUMG00000137571	ENST00000288025.3:c.411G>A	16.37:g.69381769C>T		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	275	34	0.123636	NM_144676	Q6UXN5	Silent	SNP	ENST00000288025.3	37	CCDS10878.1																																																																																			C|0.926;T|0.074	0.074	strong		0.403	TMED6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268951.1	NM_144676	
LAMA5	3911	hgsc.bcm.edu	37	20	60892538	60892538	+	Silent	SNP	G	G	A	rs146174815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:60892538G>A	ENST00000252999.3	-	55	7440	c.7374C>T	c.(7372-7374)gcC>gcT	p.A2458A		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2458	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)			CCAGGCTGGCGGCGAGGCGCT	0.672													.|||	11	0.00219649	0.0	0.0072	5008	,	,		16528	0.0		0.005	False		,,,				2504	0.001				p.A2458A		Atlas-SNP	.											.	LAMA5	268	.	0			c.C7374T						PASS	.			7,4333		0,7,2163	21.0	23.0	22.0		7374	-7.1	0.8	20	dbSNP_134	22	70,8470		1,68,4201	no	coding-synonymous	LAMA5	NM_005560.3		1,75,6364	AA,AG,GG		0.8197,0.1613,0.5978		2458/3696	60892538	77,12803	2170	4270	6440	SO:0001819	synonymous_variant	3911	exon55			GCTGGCGGCGAGG	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.7374C>T	20.37:g.60892538G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.994;A|0.006	0.006	strong		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
RP1L1	94137	hgsc.bcm.edu	37	8	10467124	10467124	+	Missense_Mutation	SNP	G	G	C	rs4841399	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:10467124G>C	ENST00000382483.3	-	4	4707	c.4484C>G	c.(4483-4485)cCc>cGc	p.P1495R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1575					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)		CCCCTGGGTGGGTTGGGCCTG	0.642													G|||	1411	0.281749	0.2511	0.353	5008	,	,		16131	0.3938		0.2555	False		,,,				2504	0.184				p.P1495R		Atlas-SNP	.											RP1L1,NS,carcinoma,0,1	RP1L1	453	1	0			c.C4484G						PASS	.	G	ARG/PRO	982,2946		128,726,1110	33.0	38.0	36.0		4484	-5.1	0.0	8	dbSNP_111	36	2003,6307		241,1521,2393	yes	missense	RP1L1	NM_178857.5	103	369,2247,3503	CC,CG,GG		24.1035,25.0,24.3912	possibly-damaging	1495/2401	10467124	2985,9253	1964	4155	6119	SO:0001583	missense	94137	exon4			TGGGTGGGTTGGG	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.4484C>G	8.37:g.10467124G>C	ENSP00000371923:p.Pro1495Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	643	0.2944139194139194	100	0.2032520325203252	107	0.2955801104972376	242	0.4230769230769231	194	0.2559366754617414	G	9.308	1.054817	0.19907	0.25	0.241035	ENSG00000183638	ENST00000382483	T	0.04156	3.69	4.69	-5.06	0.02946	.	2.449500	0.02245	N	0.066177	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.45126	0.851	B	0.39935	0.314	T	0.37549	-0.9701	9	0.56958	D	0.05	3.2668	1.9854	0.03435	0.3306:0.2097:0.3541:0.1056	rs4841399	1495	A6NKC6	.	R	1495	ENSP00000371923:P1495R	ENSP00000371923:P1495R	P	-	2	0	RP1L1	10504534	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.416000	0.02467	-1.450000	0.01936	-0.339000	0.08088	CCC	G|0.722;C|0.278	0.278	strong		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
FCGR3A	2214	hgsc.bcm.edu	37	1	161518314	161518314	+	Silent	SNP	C	C	T	rs114535887	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161518314C>T	ENST00000436743.1	-	4	370	c.216G>A	c.(214-216)tcG>tcA	p.S72S	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000443193.1_Silent_p.S107S|FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000367969.3_Silent_p.S108S|FCGR3A_ENST00000540048.1_Silent_p.S72S	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)	72	Ig-like C2-type 1.				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)	TGAAGTAGCTCGAGGCCTGGC	0.547													C|||	95	0.0189696	0.003	0.0216	5008	,	,		33212	0.0		0.0497	False		,,,				2504	0.0266				p.S108S		Atlas-SNP	.											.	FCGR3A	38	.	0			c.G324A						PASS	.	C	,,,,	50,4356	48.9+/-83.8	0,50,2153	301.0	287.0	292.0		324,321,216,216,213	-1.1	0.0	1	dbSNP_132	292	454,8146	135.1+/-192.4	0,454,3846	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCGR3A	NM_000569.6,NM_001127592.1,NM_001127593.1,NM_001127595.1,NM_001127596.1	,,,,	0,504,5999	TT,TC,CC		5.2791,1.1348,3.8751	,,,,	108/291,107/290,72/255,72/255,71/254	161518314	504,12502	2203	4300	6503	SO:0001819	synonymous_variant	2214	exon3			GTAGCTCGAGGCC	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.216G>A	1.37:g.161518314C>T		Somatic	590	1	0.00169492		WXS	Illumina HiSeq	Phase_I	952	246	0.258403	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Silent	SNP	ENST00000436743.1	37	CCDS44266.1	50	0.022893772893772892	3	0.006097560975609756	9	0.024861878453038673	0	0.0	38	0.05013192612137203	C	3.603	-0.081182	0.07141	0.011348	0.052791	ENSG00000203747	ENST00000426740	.	.	.	4.43	-1.09	0.09904	.	.	.	.	.	T	0.08133	0.0203	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35251	-0.9796	4	.	.	.	.	3.0365	0.06123	0.0953:0.4015:0.2855:0.2177	.	.	.	.	Q	89	.	.	R	-	2	0	FCGR3A	159784938	0.066000	0.20996	0.048000	0.18961	0.003000	0.03518	0.274000	0.18680	-0.010000	0.14271	-0.964000	0.02622	CGA	C|0.960;T|0.040	0.040	strong		0.547	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
B3GALTL	145173	hgsc.bcm.edu	37	13	31891746	31891746	+	Missense_Mutation	SNP	G	G	A	rs1041073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:31891746G>A	ENST00000343307.4	+	13	1257	c.1108G>A	c.(1108-1110)Gag>Aag	p.E370K		NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	370			E -> K (in dbSNP:rs1041073). {ECO:0000269|PubMed:12943678, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16899492, ECO:0000269|Ref.5}.		fucose metabolic process (GO:0006004)|protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		TGACTCCGGCGAGCCTGTGTT	0.507													G|||	3339	0.666733	0.3873	0.7579	5008	,	,		17221	0.7798		0.7575	False		,,,				2504	0.7699				p.E370K		Atlas-SNP	.											.	B3GALTL	48	.	0			c.G1108A						PASS	.	G	LYS/GLU	1833,2573	535.3+/-374.2	397,1039,767	122.0	118.0	120.0		1108	3.2	0.0	13	dbSNP_86	120	6691,1909	727.8+/-406.7	2586,1519,195	yes	missense	B3GALTL	NM_194318.3	56	2983,2558,962	AA,AG,GG		22.1977,41.6024,34.461	benign	370/499	31891746	8524,4482	2203	4300	6503	SO:0001583	missense	145173	exon13			TCCGGCGAGCCTG	AB101481	CCDS9341.1	13q12.3	2014-03-24			ENSG00000187676	ENSG00000187676		"""Beta 3-glycosyltransferases"""	20207	protein-coding gene	gene with protein product		610308				12943678, 16899492, 17032646	Standard	NM_194318		Approved	B3GTL, B3Glc-T	uc010aaz.3	Q6Y288	OTTHUMG00000016688	ENST00000343307.4:c.1108G>A	13.37:g.31891746G>A	ENSP00000343002:p.Glu370Lys	Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_194318	A8K5F8|Q5W0H2|Q6NUI3	Missense_Mutation	SNP	ENST00000343307.4	37	CCDS9341.1	1500	0.6868131868131868	193	0.39227642276422764	287	0.7928176795580111	443	0.7744755244755245	577	0.7612137203166227	G	18.40	3.616191	0.66672	0.416024	0.778023	ENSG00000187676	ENST00000343307	D	0.84944	-1.92	4.93	3.21	0.36854	.	0.160355	0.53938	N	0.000047	T	0.00012	0.0000	L	0.28014	0.82	0.22185	P	0.999307048	D	0.54047	0.964	P	0.45167	0.472	T	0.47262	-0.9131	9	0.30078	T	0.28	-8.7626	7.087	0.25264	0.1525:0.1406:0.7069:0.0	rs1041073;rs52822546;rs59155765;rs1041073	370	Q6Y288	B3GLT_HUMAN	K	370	ENSP00000343002:E370K	ENSP00000343002:E370K	E	+	1	0	B3GALTL	30789746	1.000000	0.71417	0.002000	0.10522	0.489000	0.33432	5.974000	0.70465	0.602000	0.29896	0.650000	0.86243	GAG	G|0.337;A|0.663	0.663	strong		0.507	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318	
MUC4	4585	hgsc.bcm.edu	37	3	195515304	195515304	+	Silent	SNP	T	T	A	rs202019266		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195515304T>A	ENST00000463781.3	-	2	3606	c.3147A>T	c.(3145-3147)gcA>gcT	p.A1049A	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	178	17	0.0955056	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	
EYA2	2139	hgsc.bcm.edu	37	20	45717954	45717954	+	Silent	SNP	C	C	T	rs866937	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:45717954C>T	ENST00000327619.5	+	8	1112	c.738C>T	c.(736-738)gaC>gaT	p.D246D	EYA2_ENST00000357410.3_Silent_p.D246D|EYA2_ENST00000317304.6_Silent_p.D246D	NM_005244.4	NP_005235.3	O00167	EYA2_HUMAN	EYA transcriptional coactivator and phosphatase 2	246					DNA repair (GO:0006281)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|histone dephosphorylation (GO:0016576)|mesodermal cell fate specification (GO:0007501)|mitochondrial outer membrane permeabilization (GO:0097345)|peptidyl-tyrosine dephosphorylation (GO:0035335)|regulation of transcription, DNA-templated (GO:0006355)|striated muscle tissue development (GO:0014706)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|protein tyrosine phosphatase activity (GO:0004725)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0241)				GGGCCTCCGACGGGAAGCTCC	0.582													C|||	1262	0.251997	0.1445	0.3329	5008	,	,		18244	0.253		0.2575	False		,,,				2504	0.3333				p.D246D	Pancreas(120;56 1725 18501 25218 43520)	Atlas-SNP	.											.	EYA2	85	.	0			c.C738T						PASS	.	C	,	719,3687	299.8+/-286.0	60,599,1544	74.0	75.0	75.0		738,738	-4.2	0.9	20	dbSNP_86	75	2328,6272	390.8+/-343.4	320,1688,2292	no	coding-synonymous,coding-synonymous	EYA2	NM_005244.4,NM_172110.3	,	380,2287,3836	TT,TC,CC		27.0698,16.3187,23.4276	,	246/539,246/460	45717954	3047,9959	2203	4300	6503	SO:0001819	synonymous_variant	2139	exon8			CTCCGACGGGAAG		CCDS13403.1, CCDS54471.1	20q13.1	2014-06-19	2014-06-19		ENSG00000064655	ENSG00000064655		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3520	protein-coding gene	gene with protein product		601654	"""eyes absent (Drosophila) homolog 2"", ""eyes absent homolog 2 (Drosophila)"""			9020840	Standard	NM_005244		Approved	EAB1	uc002xsm.3	O00167	OTTHUMG00000033041	ENST00000327619.5:c.738C>T	20.37:g.45717954C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	121	51	0.421488	NM_172110	Q5JSW8|Q86U84|Q96CV6|Q96H97|Q99503|Q99812|Q9BWF6|Q9H4S3|Q9H4S9|Q9NPZ4|Q9UIX7	Silent	SNP	ENST00000327619.5	37	CCDS13403.1																																																																																			C|0.768;T|0.232	0.232	strong		0.582	EYA2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080326.2	NM_005244	
CPNE3	8895	hgsc.bcm.edu	37	8	87567193	87567193	+	Missense_Mutation	SNP	C	C	T	rs2304789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:87567193C>T	ENST00000521271.1	+	15	1397	c.1235C>T	c.(1234-1236)aCg>aTg	p.T412M	CPNE3_ENST00000198765.4_Missense_Mutation_p.T412M	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	412	VWFA.		T -> M (in dbSNP:rs2304789). {ECO:0000269|PubMed:14702039}.		lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						GCTGCAGCCACGCAACAGCAG	0.463													C|||	1066	0.212859	0.2829	0.17	5008	,	,		17111	0.0139		0.332	False		,,,				2504	0.2311				p.T412M		Atlas-SNP	.											.	CPNE3	65	.	0			c.C1235T						PASS	.	C	MET/THR	1380,3026	454.0+/-350.5	217,946,1040	110.0	102.0	105.0		1235	5.7	1.0	8	dbSNP_100	105	2740,5860	437.5+/-358.6	427,1886,1987	yes	missense	CPNE3	NM_003909.3	81	644,2832,3027	TT,TC,CC		31.8605,31.3209,31.6777	benign	412/538	87567193	4120,8886	2203	4300	6503	SO:0001583	missense	8895	exon15			CAGCCACGCAACA	AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.1235C>T	8.37:g.87567193C>T	ENSP00000430934:p.Thr412Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	137	45	0.328467	NM_003909	A8KA47|Q8IYA1	Missense_Mutation	SNP	ENST00000521271.1	37	CCDS6243.1	479	0.21932234432234432	155	0.3150406504065041	69	0.19060773480662985	10	0.017482517482517484	245	0.3232189973614776	C	14.49	2.550189	0.45383	0.313209	0.318605	ENSG00000085719	ENST00000198765;ENST00000521271	T;T	0.23348	1.91;1.91	5.66	5.66	0.87406	von Willebrand factor, type A (1);Copine (1);	0.224009	0.46758	D	0.000267	T	0.00012	0.0000	L	0.38649	1.16	0.09310	P	1.0	P	0.34826	0.471	B	0.32624	0.149	T	0.44832	-0.9302	9	0.42905	T	0.14	-22.0502	20.1115	0.97913	0.0:1.0:0.0:0.0	rs2304789;rs59566172;rs2304789	412	O75131	CPNE3_HUMAN	M	412	ENSP00000198765:T412M;ENSP00000430934:T412M	ENSP00000198765:T412M	T	+	2	0	CPNE3	87636309	0.936000	0.31750	0.998000	0.56505	0.958000	0.62258	3.088000	0.50175	2.814000	0.96858	0.655000	0.94253	ACG	C|0.730;T|0.270	0.270	strong		0.463	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1		
DNAH14	127602	hgsc.bcm.edu	37	1	225534219	225534219	+	Missense_Mutation	SNP	T	T	C	rs7527925	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225534219T>C	ENST00000445597.2	+	49	8471	c.8471T>C	c.(8470-8472)gTa>gCa	p.V2824A	DNAH14_ENST00000430092.1_Missense_Mutation_p.V3627A|DNAH14_ENST00000439375.2_Missense_Mutation_p.V3627A			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2824					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						CTTTGCACTGTAATCATGCAA	0.323													C|||	2650	0.529153	0.6407	0.4697	5008	,	,		17450	0.5089		0.4046	False		,,,				2504	0.5695				p.V3627A		Atlas-SNP	.											.	DNAH14	300	.	0			c.T10880C						PASS	.	C	ALA/VAL	842,542		268,306,118	70.0	60.0	63.0		10880	3.5	0.2	1	dbSNP_116	63	1404,1770		323,758,506	yes	missense	DNAH14	NM_001373.1	64	591,1064,624	CC,CT,TT		44.2344,39.1618,49.276	benign	3627/4516	225534219	2246,2312	692	1587	2279	SO:0001583	missense	127602	exon69			GCACTGTAATCAT	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.8471T>C	1.37:g.225534219T>C	ENSP00000409472:p.Val2824Ala	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	356	215	0.603933	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	C	2.312	-0.357714	0.05138	0.608382	0.442344	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.50001	0.76;0.76;0.76	5.48	3.53	0.40419	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.45086	-0.9285	7	0.15066	T	0.55	.	3.7279	0.08481	0.1327:0.5895:0.1289:0.1488	rs7527925;rs52797267;rs56543759;rs61045802;rs7527925	3627	Q0VDD8-4	.	A	2824;3627;3627	ENSP00000409472:V2824A;ENSP00000414402:V3627A;ENSP00000392061:V3627A	ENSP00000414402:V3627A	V	+	2	0	DNAH14	223600842	0.000000	0.05858	0.155000	0.22561	0.949000	0.60115	0.067000	0.14510	0.662000	0.31006	-0.294000	0.09567	GTA	T|0.500;C|0.500	0.500	strong		0.323	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
RP1	6101	hgsc.bcm.edu	37	8	55542540	55542540	+	Missense_Mutation	SNP	G	G	A	rs61739567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	189	0	0		WXS	Illumina HiSeq	Phase_I	94	74	0.787234	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	
HENMT1	113802	hgsc.bcm.edu	37	1	109200108	109200108	+	Missense_Mutation	SNP	C	C	T	rs36100901	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109200108C>T	ENST00000370032.5	-	3	535	c.115G>A	c.(115-117)Gtt>Att	p.V39I	HENMT1_ENST00000493676.1_5'UTR|HENMT1_ENST00000402983.1_Missense_Mutation_p.V39I|HENMT1_ENST00000370031.1_Missense_Mutation_p.V39I	NM_144584.2	NP_653185.2	Q5T8I9	HENMT_HUMAN	HEN1 methyltransferase homolog 1 (Arabidopsis)	39					gene silencing by RNA (GO:0031047)|piRNA metabolic process (GO:0034587)|RNA methylation (GO:0001510)	P granule (GO:0043186)	metal ion binding (GO:0046872)|O-methyltransferase activity (GO:0008171)|RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	16						AAATTTTTAACGAACTGGTAC	0.383													C|||	62	0.0123802	0.0053	0.0202	5008	,	,		17554	0.0		0.0288	False		,,,				2504	0.0123				p.V39I		Atlas-SNP	.											.	HENMT1	38	.	0			c.G115A						PASS	.	C	ILE/VAL,ILE/VAL	22,4384	29.0+/-57.7	0,22,2181	112.0	113.0	113.0		115,115	3.7	0.2	1	dbSNP_126	113	219,8381	91.4+/-153.5	2,215,4083	yes	missense,missense	HENMT1	NM_001102592.1,NM_144584.2	29,29	2,237,6264	TT,TC,CC		2.5465,0.4993,1.853	possibly-damaging,possibly-damaging	39/394,39/394	109200108	241,12765	2203	4300	6503	SO:0001583	missense	113802	exon3			TTTTAACGAACTG		CCDS787.1	1p13.3	2011-01-28	2011-01-28	2011-01-28	ENSG00000162639	ENSG00000162639			26400	protein-coding gene	gene with protein product	"""HEN1 methyltransferase homolog (Arabidopsis)"""	612178	"""chromosome 1 open reading frame 59"""	C1orf59			Standard	NM_144584		Approved	FLJ30525, HEN1	uc001dvt.4	Q5T8I9	OTTHUMG00000011123	ENST00000370032.5:c.115G>A	1.37:g.109200108C>T	ENSP00000359049:p.Val39Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	69	53	0.768116	NM_144584	A8MRR6|B1AM16|B1AM17|Q96EJ7|Q96NN0	Missense_Mutation	SNP	ENST00000370032.5	37	CCDS787.1	29	0.013278388278388278	4	0.008130081300813009	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	15.44	2.833273	0.50951	0.004993	0.025465	ENSG00000162639	ENST00000402983;ENST00000370031;ENST00000370032;ENST00000420055	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	5.62	3.68	0.42216	.	0.067024	0.64402	D	0.000015	T	0.31327	0.0793	L	0.41573	1.285	0.48185	D	0.999609	D	0.76494	0.999	D	0.66979	0.948	T	0.05733	-1.0867	10	0.32370	T	0.25	.	8.5831	0.33642	0.0:0.813:0.0:0.187	rs36100901	39	Q5T8I9	HENMT_HUMAN	I	39	ENSP00000385655:V39I;ENSP00000359048:V39I;ENSP00000359049:V39I;ENSP00000403953:V39I	ENSP00000359048:V39I	V	-	1	0	HENMT1	109001631	0.607000	0.26958	0.229000	0.23960	0.264000	0.26372	0.956000	0.29202	1.292000	0.44672	0.655000	0.94253	GTT	C|0.984;T|0.016	0.016	strong		0.383	HENMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030592.1	NM_144584	
MCPH1	79648	hgsc.bcm.edu	37	8	6479178	6479178	+	Silent	SNP	C	C	A	rs2912016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:6479178C>A	ENST00000344683.5	+	13	2494	c.2418C>A	c.(2416-2418)gcC>gcA	p.A806A	CTD-2541M15.1_ENST00000522897.1_RNA|CTD-2541M15.1_ENST00000515608.1_RNA|MCPH1_ENST00000521175.1_3'UTR	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	806	BRCT 3. {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)		AGAAGAAAGCCACAGTCAAGT	0.577													A|||	1972	0.39377	0.4304	0.2925	5008	,	,		18838	0.4375		0.3618	False		,,,				2504	0.4039				p.A806A	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											.	MCPH1	65	.	0			c.C2418A						PASS	.	A		1695,2457		376,943,757	70.0	82.0	78.0		2418	-6.4	0.0	8	dbSNP_101	78	2862,5554		475,1912,1821	no	coding-synonymous	MCPH1	NM_024596.3		851,2855,2578	AA,AC,CC		34.0067,40.8237,36.2588		806/836	6479178	4557,8011	2076	4208	6284	SO:0001819	synonymous_variant	79648	exon13			GAAAGCCACAGTC	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.2418C>A	8.37:g.6479178C>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	121	68	0.561983	NM_024596	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	37	CCDS43689.1																																																																																			C|0.615;A|0.385	0.385	strong		0.577	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
EIF3D	8664	hgsc.bcm.edu	37	22	36912630	36912630	+	Silent	SNP	A	A	G	rs11558519	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:36912630A>G	ENST00000216190.8	-	12	1471	c.1101T>C	c.(1099-1101)gaT>gaC	p.D367D	EIF3D_ENST00000405442.1_Silent_p.D367D|EIF3D_ENST00000541106.1_Silent_p.D318D	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D											cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						GGTCAATATCATCTCCAAGCT	0.498													G|||	364	0.0726837	0.1271	0.0576	5008	,	,		20490	0.002		0.0646	False		,,,				2504	0.091				p.D367D		Atlas-SNP	.											.	EIF3D	37	.	0			c.T1101C						PASS	.	G		568,3838	773.3+/-413.9	36,496,1671	286.0	264.0	271.0		1101	-7.3	0.1	22	dbSNP_120	271	669,7931	789.1+/-407.6	15,639,3646	no	coding-synonymous	EIF3D	NM_003753.3		51,1135,5317	GG,GA,AA		7.7791,12.8915,9.511		367/549	36912630	1237,11769	2203	4300	6503	SO:0001819	synonymous_variant	8664	exon12			AATATCATCTCCA	U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"""eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"""	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.1101T>C	22.37:g.36912630A>G		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	181	80	0.441989	NM_003753		Silent	SNP	ENST00000216190.8	37	CCDS13930.1																																																																																			A|0.914;G|0.086	0.086	strong		0.498	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1		
PROM1	8842	hgsc.bcm.edu	37	4	16077515	16077515	+	Silent	SNP	G	G	A	rs10033189	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:16077515G>A	ENST00000510224.1	-	2	263	c.15C>T	c.(13-15)ctC>ctT	p.L5L	PROM1_ENST00000539194.1_Silent_p.L5L|PROM1_ENST00000508167.1_Silent_p.L5L|PROM1_ENST00000543373.1_Silent_p.L5L|PROM1_ENST00000505450.1_Silent_p.L5L|PROM1_ENST00000540805.1_Silent_p.L5L|PROM1_ENST00000447510.2_Silent_p.L5L			O43490	PROM1_HUMAN	prominin 1	5					camera-type eye photoreceptor cell differentiation (GO:0060219)|glomerular parietal epithelial cell differentiation (GO:0072139)|glomerular visceral epithelial cell differentiation (GO:0072112)|photoreceptor cell maintenance (GO:0045494)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|retina layer formation (GO:0010842)|retina morphogenesis in camera-type eye (GO:0060042)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actinin binding (GO:0042805)|cadherin binding (GO:0045296)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|liver(1)|lung(11)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(2)	35						ACAGGGAGCCGAGTACGAGGG	0.547													G|||	276	0.0551118	0.1581	0.0274	5008	,	,		18625	0.0		0.0388	False		,,,				2504	0.0092				p.L5L		Atlas-SNP	.											.	PROM1	91	.	0			c.C15T						PASS	.	G	,,,,,,	558,3540		43,472,1534	29.0	30.0	29.0		15,15,15,15,15,15,15	-4.3	0.0	4	dbSNP_119	29	196,8194		1,194,4000	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PROM1	NM_001145847.1,NM_001145848.1,NM_001145849.1,NM_001145850.1,NM_001145851.1,NM_001145852.1,NM_006017.2	,,,,,,	44,666,5534	AA,AG,GG		2.3361,13.6164,6.0378	,,,,,,	5/857,5/857,5/843,5/835,5/834,5/826,5/866	16077515	754,11734	2049	4195	6244	SO:0001819	synonymous_variant	8842	exon2			GGAGCCGAGTACG	AF027208	CCDS47029.1, CCDS54746.1, CCDS54747.1, CCDS54748.1	4p15	2013-06-06	2001-11-28	2003-03-28	ENSG00000007062	ENSG00000007062		"""CD molecules"""	9454	protein-coding gene	gene with protein product		604365	"""prominin (mouse)-like 1"", ""macular dystrophy, retinal 2"", ""Stargardt disease 4 (autosomal dominant)"""	PROML1, MCDR2, STGD4		11467842	Standard	NM_006017		Approved	AC133, CD133, RP41, CORD12	uc003goo.2	O43490	OTTHUMG00000160180	ENST00000510224.1:c.15C>T	4.37:g.16077515G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	87	56	0.643678	NM_001145847	Q6SV49|Q6SV50|Q6SV51|Q6SV52|Q6SV53|Q96EN6	Silent	SNP	ENST00000510224.1	37	CCDS47029.1																																																																																			G|0.945;A|0.055	0.055	strong		0.547	PROM1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359595.2	NM_006017	
B3GNTL1	146712	hgsc.bcm.edu	37	17	80923536	80923536	+	Silent	SNP	C	C	T	rs4986144	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80923536C>T	ENST00000320865.3	-	7	604	c.591G>A	c.(589-591)gaG>gaA	p.E197E	B3GNTL1_ENST00000576599.1_Silent_p.E86E|B3GNTL1_ENST00000571954.1_5'UTR	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	197							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)			CCTGACCTCCCTCGTTAAAGG	0.612													C|||	1117	0.223043	0.233	0.1974	5008	,	,		16277	0.3214		0.2336	False		,,,				2504	0.1155				p.E197E		Atlas-SNP	.											B3GNTL1,NS,malignant_melanoma,0,2	B3GNTL1	40	2	0			c.G591A						PASS	.	C		1013,3393	349.0+/-310.2	129,755,1319	37.0	34.0	35.0		591	2.8	1.0	17	dbSNP_111	35	2503,6095	374.9+/-337.6	338,1827,2134	no	coding-synonymous	B3GNTL1	NM_001009905.1		467,2582,3453	TT,TC,CC		29.1114,22.9914,27.0378		197/362	80923536	3516,9488	2203	4299	6502	SO:0001819	synonymous_variant	146712	exon7			ACCTCCCTCGTTA	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.591G>A	17.37:g.80923536C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_001009905	Q6GV30|Q8WUT3	Silent	SNP	ENST00000320865.3	37	CCDS32778.1																																																																																			C|0.739;T|0.261	0.261	strong		0.612	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
AGBL2	79841	hgsc.bcm.edu	37	11	47711820	47711820	+	Missense_Mutation	SNP	A	A	G	rs76215382	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47711820A>G	ENST00000525123.1	-	10	1724	c.1439T>C	c.(1438-1440)cTt>cCt	p.L480P	AGBL2_ENST00000298861.4_Missense_Mutation_p.L480P|AGBL2_ENST00000529712.1_5'UTR|AGBL2_ENST00000528244.1_Missense_Mutation_p.L442P|AGBL2_ENST00000357610.3_Missense_Mutation_p.L480P	NM_024783.3	NP_079059.2	Q5U5Z8	CBPC2_HUMAN	ATP/GTP binding protein-like 2	480						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						GGAGTTGCTAAGGATGAAGTC	0.473													A|||	38	0.00758786	0.0008	0.0014	5008	,	,		19580	0.0198		0.0109	False		,,,				2504	0.0051				p.L480P		Atlas-SNP	.											.	AGBL2	73	.	0			c.T1439C						PASS	.	A	PRO/LEU	20,4382	27.2+/-55.0	0,20,2181	90.0	93.0	92.0		1439	6.0	1.0	11	dbSNP_131	92	141,8455	68.7+/-131.2	1,139,4158	yes	missense	AGBL2	NM_024783.3	98	1,159,6339	GG,GA,AA		1.6403,0.4543,1.2387	probably-damaging	480/903	47711820	161,12837	2201	4298	6499	SO:0001583	missense	79841	exon10			TTGCTAAGGATGA		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.1439T>C	11.37:g.47711820A>G	ENSP00000435582:p.Leu480Pro	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	246	108	0.439024	NM_024783	A8MPX2|Q53FV5|Q8IV57|Q9H5C0	Missense_Mutation	SNP	ENST00000525123.1	37	CCDS7944.1	18	0.008241758241758242	0	0.0	0	0.0	9	0.015734265734265736	9	0.011873350923482849	A	13.74	2.327068	0.41197	0.004543	0.016403	ENSG00000165923	ENST00000525123;ENST00000357610;ENST00000298861;ENST00000528244	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	5.96	5.96	0.96718	Peptidase M14, carboxypeptidase A (1);	0.000000	0.85682	D	0.000000	T	0.33789	0.0875	H	0.94658	3.565	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.997	D;D;D	0.74348	0.983;0.979;0.979	T	0.60193	-0.7311	10	0.87932	D	0	-16.6469	16.4484	0.83959	1.0:0.0:0.0:0.0	.	442;442;480	F6U0I4;B4DZS1;Q5U5Z8	.;.;CBPC2_HUMAN	P	480;480;480;442	ENSP00000435582:L480P;ENSP00000350228:L480P;ENSP00000298861:L480P;ENSP00000436630:L442P	ENSP00000298861:L480P	L	-	2	0	AGBL2	47668396	1.000000	0.71417	0.973000	0.42090	0.984000	0.73092	8.748000	0.91615	2.285000	0.76669	0.533000	0.62120	CTT	A|0.990;G|0.010	0.010	strong		0.473	AGBL2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383726.2	NM_024783	
NRP1	8829	hgsc.bcm.edu	37	10	33475282	33475282	+	Missense_Mutation	SNP	C	C	T	rs2228638	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:33475282C>T	ENST00000265371.4	-	15	2722	c.2197G>A	c.(2197-2199)Gtc>Atc	p.V733I	NRP1_ENST00000374867.2_Missense_Mutation_p.V733I|NRP1_ENST00000374875.1_Missense_Mutation_p.V545I|NRP1_ENST00000395995.1_Missense_Mutation_p.V733I			O14786	NRP1_HUMAN	neuropilin 1	733	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.		V -> I (in dbSNP:rs2228638).		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)	AGTGTGCCGACGTGGGACCCA	0.557													C|||	548	0.109425	0.0083	0.245	5008	,	,		19265	0.128		0.1083	False		,,,				2504	0.1319				p.V733I	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											NRP1,NS,carcinoma,+2,1	NRP1	126	1	0			c.G2197A						scavenged	.	C	ILE/VAL	110,4296	86.3+/-125.0	1,108,2094	132.0	92.0	105.0		2197	5.9	1.0	10	dbSNP_98	105	918,7682	204.1+/-246.9	36,846,3418	yes	missense	NRP1	NM_003873.5	29	37,954,5512	TT,TC,CC		10.6744,2.4966,7.904	benign	733/924	33475282	1028,11978	2203	4300	6503	SO:0001583	missense	8829	exon14			TGCCGACGTGGGA	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.2197G>A	10.37:g.33475282C>T	ENSP00000265371:p.Val733Ile	Somatic	165	2	0.0121212		WXS	Illumina HiSeq	Phase_I	114	86	0.754386	NM_003873	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Missense_Mutation	SNP	ENST00000265371.4	37	CCDS7177.1	210	0.09615384615384616	5	0.01016260162601626	74	0.20441988950276244	54	0.0944055944055944	77	0.10158311345646438	C	7.352	0.623167	0.14193	0.024966	0.106744	ENSG00000099250	ENST00000265371;ENST00000374875;ENST00000374867;ENST00000395995	T;T;T;T	0.02015	4.5;4.5;4.5;4.5	5.91	5.91	0.95273	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.049762	0.85682	D	0.000000	T	0.00012	0.0000	N	0.04636	-0.2	0.09310	P	1.0	B;P;B;B;B	0.38863	0.364;0.65;0.364;0.364;0.209	B;B;B;B;B	0.29440	0.102;0.068;0.102;0.102;0.018	T	0.73372	-0.4003	9	0.33940	T	0.23	-25.0873	20.2985	0.98592	0.0:1.0:0.0:0.0	rs2228638;rs59659881;rs2228638	727;733;733;545;733	A8K9V7;Q68DN3;O14786;Q5JWQ6;E9PEP6	.;.;NRP1_HUMAN;.;.	I	733;545;733;733	ENSP00000265371:V733I;ENSP00000364009:V545I;ENSP00000364001:V733I;ENSP00000379317:V733I	ENSP00000265371:V733I	V	-	1	0	NRP1	33515288	1.000000	0.71417	0.989000	0.46669	0.828000	0.46876	4.322000	0.59215	2.793000	0.96121	0.655000	0.94253	GTC	C|0.910;T|0.090	0.090	strong		0.557	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
TGS1	96764	hgsc.bcm.edu	37	8	56698801	56698801	+	Missense_Mutation	SNP	C	C	T	rs76064957	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:56698801C>T	ENST00000260129.5	+	4	821	c.344C>T	c.(343-345)tCt>tTt	p.S115F		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	115					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			ATATAGGTATCTATGAATACT	0.219													C|||	16	0.00319489	0.0008	0.0029	5008	,	,		15987	0.0		0.0129	False		,,,				2504	0.0				p.S115F	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.C344T						PASS	.	C	PHE/SER	9,3903		0,9,1947	7.0	7.0	7.0		344	3.9	0.8	8	dbSNP_133	7	89,8121		1,87,4017	yes	missense	TGS1	NM_024831.6	155	1,96,5964	TT,TC,CC		1.084,0.2301,0.8084	possibly-damaging	115/854	56698801	98,12024	1956	4105	6061	SO:0001583	missense	96764	exon4			AGGTATCTATGAA	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.344C>T	8.37:g.56698801C>T	ENSP00000260129:p.Ser115Phe	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	14	0.00641025641025641	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	15.71	2.914765	0.52546	0.002301	0.01084	ENSG00000137574	ENST00000260129	T	0.17691	2.26	5.69	3.87	0.44632	.	0.827624	0.10980	N	0.612788	T	0.28632	0.0709	M	0.72479	2.2	0.26676	N	0.971621	D;D	0.71674	0.998;0.998	D;D	0.65573	0.921;0.936	T	0.10894	-1.0610	10	0.72032	D	0.01	-3.8428	6.7135	0.23290	0.0:0.6958:0.1484:0.1557	.	115;115	B2RBJ7;Q96RS0	.;TGS1_HUMAN	F	115	ENSP00000260129:S115F	ENSP00000260129:S115F	S	+	2	0	TGS1	56861355	0.840000	0.29493	0.793000	0.32043	0.913000	0.54294	2.008000	0.40893	0.732000	0.32470	0.655000	0.94253	TCT	C|0.992;T|0.008	0.008	strong		0.219	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
CEP170	9859	hgsc.bcm.edu	37	1	243329049	243329049	+	Missense_Mutation	SNP	G	G	A	rs3766664	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:243329049G>A	ENST00000366542.1	-	13	2264	c.2213C>T	c.(2212-2214)aCt>aTt	p.T738I	CEP170_ENST00000366544.1_Missense_Mutation_p.T640I|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Missense_Mutation_p.T640I	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	738						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)			TACCAAAGAAGTTTCCTTATC	0.393																																					p.T738I		Atlas-SNP	.											.	CEP170	153	.	0			c.C2213T						PASS	.						211.0	204.0	206.0					1																	243329049		1864	4090	5954	SO:0001583	missense	9859	exon13			AAAGAAGTTTCCT	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.2213C>T	1.37:g.243329049G>A	ENSP00000355500:p.Thr738Ile	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	336	54	0.160714	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.512|9.512	1.106068|1.106068	0.20632|0.20632	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000336415|ENST00000366542;ENST00000366544;ENST00000366543	.|T;T;T	.|0.46819	.|0.87;0.86;0.86	5.25|5.25	3.25|3.25	0.37280|0.37280	.|.	.|1.055560	.|0.07311	.|N	.|0.875849	T|T	0.34106|0.34106	0.0886|0.0886	N|N	0.19112|0.19112	0.55|0.55	0.26599|0.26599	N|N	0.973053|0.973053	.|B;B;B;B	.|0.34200	.|0.068;0.096;0.441;0.07	.|B;B;B;B	.|0.35312	.|0.093;0.067;0.2;0.043	T|T	0.28808|0.28808	-1.0032|-1.0032	5|10	.|0.44086	.|T	.|0.13	0.1048|0.1048	7.1054|7.1054	0.25360|0.25360	0.0872:0.0:0.7427:0.1701|0.0872:0.0:0.7427:0.1701	rs3766664|rs3766664	.|701;640;640;738	.|B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.|.;.;.;CE170_HUMAN	F|I	702|738;640;640	.|ENSP00000355500:T738I;ENSP00000355502:T640I;ENSP00000355501:T640I	.|ENSP00000355500:T738I	L|T	-|-	1|2	0|0	CEP170|CEP170	241395672|241395672	0.174000|0.174000	0.23070|0.23070	0.502000|0.502000	0.27614|0.27614	0.868000|0.868000	0.49771|0.49771	1.630000|1.630000	0.37081|0.37081	1.208000|1.208000	0.43306|0.43306	0.484000|0.484000	0.47621|0.47621	CTT|ACT	G|0.167;A|0.833	0.833	weak		0.393	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
LRRC15	131578	hgsc.bcm.edu	37	3	194081179	194081179	+	Silent	SNP	G	G	A	rs11715737	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:194081179G>A	ENST00000347624.3	-	2	679	c.594C>T	c.(592-594)aaC>aaT	p.N198N	LRRC15_ENST00000439944.2_Silent_p.N204N|LRRC15_ENST00000428839.1_Silent_p.N204N	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	198					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)		GGACCTGGAGGTTGCCCAGGT	0.572													G|||	584	0.116613	0.093	0.1052	5008	,	,		19872	0.0685		0.2107	False		,,,				2504	0.1094				p.N204N		Atlas-SNP	.											.	LRRC15	137	.	0			c.C612T						PASS	.	G	,	432,3974	208.5+/-229.5	16,400,1787	177.0	178.0	178.0		612,594	4.1	1.0	3	dbSNP_120	178	2013,6587	352.5+/-328.7	240,1533,2527	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	256,1933,4314	AA,AG,GG		23.407,9.8048,18.799	,	204/588,198/582	194081179	2445,10561	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			CTGGAGGTTGCCC	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.594C>T	3.37:g.194081179G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	114	67	0.587719	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			G|0.830;A|0.170	0.170	strong		0.572	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
FAM161B	145483	hgsc.bcm.edu	37	14	74402693	74402693	+	Silent	SNP	C	C	T	rs17182699	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:74402693C>T	ENST00000534936.1	-	8	1869	c.1764G>A	c.(1762-1764)cgG>cgA	p.R588R	FAM161B_ENST00000286544.3_Silent_p.R651R|RP5-1021I20.5_ENST00000555916.1_RNA			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	588										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						CTTGAACAGCCCGGGTGCCTT	0.468													C|||	219	0.04373	0.0083	0.0648	5008	,	,		18871	0.0		0.1123	False		,,,				2504	0.0511				p.R651R		Atlas-SNP	.											.	FAM161B	67	.	0			c.G1953A						PASS	.	C		96,4310	78.3+/-116.7	2,92,2109	144.0	133.0	137.0		1953	-4.7	0.0	14	dbSNP_123	137	887,7713	199.4+/-243.5	56,775,3469	no	coding-synonymous	FAM161B	NM_152445.2		58,867,5578	TT,TC,CC		10.314,2.1788,7.5581		651/711	74402693	983,12023	2203	4300	6503	SO:0001819	synonymous_variant	145483	exon8			AACAGCCCGGGTG	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 44"""	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.1764G>A	14.37:g.74402693C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	229	92	0.401747	NM_152445	B7Z882|J3KNA2	Silent	SNP	ENST00000534936.1	37		119	0.05448717948717949	1	0.0020325203252032522	29	0.08011049723756906	0	0.0	89	0.11741424802110818	C	3.048	-0.196076	0.06259	0.021788	0.10314	ENSG00000156050	ENST00000556794	.	.	.	4.86	-4.65	0.03339	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.22487	-1.0215	3	.	.	.	20.474	1.6237	0.02719	0.2691:0.1841:0.099:0.4477	rs17182699;rs60311174;rs17182699	.	.	.	S	116	.	.	G	-	1	0	FAM161B	73472446	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.111000	0.01333	-0.712000	0.04988	-0.768000	0.03414	GGC	C|0.935;T|0.065	0.065	strong		0.468	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445	
RAD54B	25788	hgsc.bcm.edu	37	8	95419698	95419698	+	Silent	SNP	A	A	G	rs2291439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:95419698A>G	ENST00000336148.5	-	5	874	c.750T>C	c.(748-750)aaT>aaC	p.N250N		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	250					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			GTGGTTTGCAATTTTGGAAAT	0.328								Direct reversal of damage;Homologous recombination					A|||	2094	0.418131	0.3517	0.536	5008	,	,		18131	0.4663		0.3777	False		,,,				2504	0.4162				p.N250N		Atlas-SNP	.											.	RAD54B	88	.	0			c.T750C						PASS	.	A	,	1557,2849	487.4+/-360.9	261,1035,907	76.0	74.0	75.0		198,750	2.7	0.6	8	dbSNP_100	75	3140,5460	476.8+/-369.5	549,2042,1709	yes	coding-synonymous,coding-synonymous	RAD54B	NM_001205263.1,NM_012415.3	,	810,3077,2616	GG,GA,AA		36.5116,35.3382,36.1141	,	66/727,250/911	95419698	4697,8309	2203	4300	6503	SO:0001819	synonymous_variant	25788	exon5			TTTGCAATTTTGG	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.750T>C	8.37:g.95419698A>G		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	368	219	0.595109	NM_012415	F6WBS8	Silent	SNP	ENST00000336148.5	37	CCDS6262.1																																																																																			A|0.610;C|0.003	.	strong		0.328	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
CRISP3	10321	hgsc.bcm.edu	37	6	49701523	49701523	+	Missense_Mutation	SNP	A	A	G	rs495335	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:49701523A>G	ENST00000393666.1	-	4	322	c.316T>C	c.(316-318)Tcc>Ccc	p.S106P	CRISP3_ENST00000433368.2_Missense_Mutation_p.S129P|CRISP3_ENST00000371159.4_Missense_Mutation_p.S137P|CRISP3_ENST00000423399.2_Missense_Mutation_p.S16P|CRISP3_ENST00000263045.4_Missense_Mutation_p.S119P			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	106	SCP.		S -> P (in dbSNP:rs495335). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		defense response (GO:0006952)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|specific granule (GO:0042581)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(14)|skin(6)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			CATGAGCTGGAGGCACTTGAC	0.433													G|||	3381	0.67512	0.7383	0.7594	5008	,	,		18918	0.5476		0.6948	False		,,,				2504	0.6411				p.S129P		Atlas-SNP	.											.	CRISP3	67	.	0			c.T385C						PASS	.	G	PRO/SER,PRO/SER	3280,1126	401.5+/-332.0	1205,870,128	149.0	139.0	142.0		385,355	5.1	0.0	6	dbSNP_83	142	5784,2816	445.5+/-361.0	1947,1890,463	yes	missense,missense	CRISP3	NM_001190986.1,NM_006061.2	74,74	3152,2760,591	GG,GA,AA		32.7442,25.5561,30.3091	benign,benign	129/269,119/259	49701523	9064,3942	2203	4300	6503	SO:0001583	missense	10321	exon5			AGCTGGAGGCACT	X94323	CCDS4929.1, CCDS4929.2, CCDS55019.1	6p12.3	2008-02-05			ENSG00000096006	ENSG00000096006			16904	protein-coding gene	gene with protein product						8665901, 12223513	Standard	NM_006061		Approved	SGP28, CRISP-3, CRS3, dJ442L6.3, Aeg2	uc003ozs.3	P54108	OTTHUMG00000014823	ENST00000393666.1:c.316T>C	6.37:g.49701523A>G	ENSP00000377274:p.Ser106Pro	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	133	131	0.984962	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	37		1478	0.6767399267399268	372	0.7560975609756098	273	0.7541436464088398	310	0.541958041958042	523	0.6899736147757256	G	1.963	-0.438361	0.04636	0.744439	0.672558	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000423399;ENST00000371159;ENST00000354620	T;T;T;T;T;T	0.44881	3.06;3.06;3.06;0.91;3.06;3.06	5.1	5.1	0.69264	CAP domain (3);	0.182430	0.34291	N	0.004100	T	0.03305	0.0096	N	0.00500	-1.43	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35101	-0.9802	9	0.02654	T	1	.	9.8183	0.40867	0.0963:0.0:0.9037:0.0	rs495335;rs1771237;rs13192493;rs16879714;rs52821725;rs495335	106	P54108	CRIS3_HUMAN	P	119;129;106;16;137;129	ENSP00000263045:S119P;ENSP00000389026:S129P;ENSP00000377274:S106P;ENSP00000410469:S16P;ENSP00000360201:S137P;ENSP00000346636:S129P	ENSP00000263045:S119P	S	-	1	0	CRISP3	49809482	0.021000	0.18746	0.003000	0.11579	0.001000	0.01503	1.944000	0.40263	1.156000	0.42514	-0.197000	0.12766	TCC	A|0.322;G|0.678	0.678	strong		0.433	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061	
FLG	2312	hgsc.bcm.edu	37	1	152279019	152279019	+	Silent	SNP	G	G	A	rs57670307	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152279019G>A	ENST00000368799.1	-	3	8378	c.8343C>T	c.(8341-8343)gaC>gaT	p.D2781D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2781	Ser-rich.		D -> Y (in dbSNP:rs2065958).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCCTGACCGTCTTGGGATG	0.607									Ichthyosis																												p.D2781D		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.C8343T						scavenged	.	C		87,4307		0,87,2110	459.0	597.0	550.0		8343	-6.8	0.0	1	dbSNP_129	550	660,7940		0,660,3640	no	coding-synonymous	FLG	NM_002016.1		0,747,5750	AA,AG,GG		7.6744,1.98,5.7488		2781/4062	152279019	747,12247	2197	4300	6497	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCGTCTTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.8343C>T	1.37:g.152279019G>A		Somatic	679	4	0.00589102		WXS	Illumina HiSeq	Phase_I	1422	244	0.171589	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			G|0.939;A|0.061	0.061	strong		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MUC2	4583	hgsc.bcm.edu	37	11	1092954	1092954	+	Splice_Site	SNP	G	G	A	rs56352686		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank			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						scavenged	.						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	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	67	3	0.0447761	NM_002457	Q14878	Silent	SNP	ENST00000359061.5	37																																																																																				.	.	none		0.627	MUC2-202	KNOWN	basic	protein_coding	protein_coding		NM_002457	Silent
OR8J3	81168	hgsc.bcm.edu	37	11	55904828	55904828	+	Missense_Mutation	SNP	A	A	G	rs11227321	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	214	0	0		WXS	Illumina HiSeq	Phase_I	218	97	0.444954	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	
XKR9	389668	hgsc.bcm.edu	37	8	71646201	71646201	+	Missense_Mutation	SNP	C	C	T	rs61734026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:71646201C>T	ENST00000408926.3	+	5	1198	c.664C>T	c.(664-666)Ctt>Ttt	p.L222F	XKR9_ENST00000520273.1_Intron|XKR9_ENST00000520030.1_Missense_Mutation_p.L222F	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	222						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)			GAGTGTTGTACTTCTACTATT	0.313													C|||	24	0.00479233	0.0	0.0101	5008	,	,		16387	0.0		0.0149	False		,,,				2504	0.002				p.L222F		Atlas-SNP	.											.	XKR9	43	.	0			c.C664T						PASS	.	C	PHE/LEU	7,4399	15.5+/-35.6	0,7,2196	189.0	188.0	188.0		664	4.7	1.0	8	dbSNP_129	188	110,8486	57.5+/-118.9	1,108,4189	yes	missense	XKR9	NM_001011720.1	22	1,115,6385	TT,TC,CC		1.2797,0.1589,0.8999	possibly-damaging	222/374	71646201	117,12885	2203	4298	6501	SO:0001583	missense	389668	exon5			GTTGTACTTCTAC	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.664C>T	8.37:g.71646201C>T	ENSP00000386141:p.Leu222Phe	Somatic	365	0	0		WXS	Illumina HiSeq	Phase_I	461	266	0.577007	NM_001011720	B2RNS9|B9EH74	Missense_Mutation	SNP	ENST00000408926.3	37	CCDS34905.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.17	2.456518	0.43634	0.001589	0.012797	ENSG00000221947	ENST00000408926;ENST00000520030	T;T	0.70749	-0.51;-0.51	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.57975	0.2090	M	0.62723	1.935	0.53688	D	0.999976	P	0.42993	0.797	B	0.39840	0.311	T	0.66097	-0.6008	10	0.49607	T	0.09	-22.2782	9.9909	0.41870	0.0:0.8431:0.0:0.1569	rs61734026	222	Q5GH70	XKR9_HUMAN	F	222	ENSP00000386141:L222F;ENSP00000431088:L222F	ENSP00000386141:L222F	L	+	1	0	XKR9	71808755	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	1.792000	0.38754	2.597000	0.87782	0.563000	0.77884	CTT	C|0.990;T|0.010	0.010	strong		0.313	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720	
SLC35G6	643664	hgsc.bcm.edu	37	17	7386272	7386272	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7386272C>T	ENST00000412468.2	+	2	1084	c.969C>T	c.(967-969)atC>atT	p.I323I	POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	323	EamA 2.					integral component of membrane (GO:0016021)		p.I323I(1)									TTGCCATCATCACAGCCTGGA	0.557																																					p.I323I		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	prostate(1)	c.C969T						scavenged	.																																			SO:0001819	synonymous_variant	643664	exon2			CATCATCACAGCC		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.969C>T	17.37:g.7386272C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	149	5	0.033557	NM_001102614		Silent	SNP	ENST00000412468.2	37	CCDS45603.1																																																																																			.	.	none		0.557	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
KMT2C	58508	hgsc.bcm.edu	37	7	151845972	151845972	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:151845972G>A	ENST00000262189.6	-	52	13258	c.13040C>T	c.(13039-13041)cCg>cTg	p.P4347L	KMT2C_ENST00000355193.2_Missense_Mutation_p.P4404L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	4347					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)										TTTATTGAGCGGCCTGCAATC	0.468																																					p.P4347L		Atlas-SNP	.											MLL3_ENST00000355193,rectum,carcinoma,-1,7	MLL3	1564	7	0			c.C13040T						scavenged	.						65.0	61.0	62.0					7																	151845972		2203	4300	6503	SO:0001583	missense	58508	exon52			TTGAGCGGCCTGC	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.13040C>T	7.37:g.151845972G>A	ENSP00000262189:p.Pro4347Leu	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	147	3	0.0204082	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	10.48	1.361301	0.24684	.	.	ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877	D;D;D	0.88896	-1.78;-1.76;-2.44	5.67	5.67	0.87782	.	0.159293	0.29212	U	0.012816	D	0.91362	0.7275	L	0.56769	1.78	0.80722	D	1	D;D;D	0.63880	0.993;0.993;0.993	P;P;P	0.51701	0.632;0.605;0.677	D	0.91980	0.5594	10	0.87932	D	0	.	19.7589	0.96306	0.0:0.0:1.0:0.0	.	4347;3465;4404	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3	MLL3_HUMAN;.;.	L	4347;4404;964	ENSP00000262189:P4347L;ENSP00000347325:P4404L;ENSP00000410411:P964L	ENSP00000262189:P4347L	P	-	2	0	MLL3	151476905	1.000000	0.71417	0.466000	0.27168	0.026000	0.11368	6.961000	0.76042	2.670000	0.90874	0.650000	0.86243	CCG	.	.	none		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
C9orf172	389813	hgsc.bcm.edu	37	9	139740436	139740436	+	Missense_Mutation	SNP	G	G	A	rs375030600		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139740436G>A	ENST00000436881.1	+	1	1570	c.1570G>A	c.(1570-1572)Ggc>Agc	p.G524S	PHPT1_ENST00000371661.1_5'Flank|PHPT1_ENST00000545326.1_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	524										endometrium(2)|large_intestine(1)|lung(6)	9						CGAGGGCCTGGGCCGCAACTG	0.711																																					p.G524S		Atlas-SNP	.											.	C9orf172	23	.	0			c.G1570A						PASS	.	G	SER/GLY	0,3880		0,0,1940	7.0	8.0	8.0		1570	1.4	1.0	9		8	1,8013		0,1,4006	no	missense	C9orf172	NM_001080482.2	56	0,1,5946	AA,AG,GG		0.0125,0.0,0.0084	possibly-damaging	524/977	139740436	1,11893	1940	4007	5947	SO:0001583	missense	389813	exon1			GGCCTGGGCCGCA		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.1570G>A	9.37:g.139740436G>A	ENSP00000412388:p.Gly524Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	37	0.587302	NM_001080482		Missense_Mutation	SNP	ENST00000436881.1	37	CCDS48059.1	.	.	.	.	.	.	.	.	.	.	.	7.729	0.698804	0.15106	0.0	1.25E-4	ENSG00000232434	ENST00000436881	.	.	.	3.54	1.41	0.22369	.	.	.	.	.	T	0.18718	0.0449	N	0.12746	0.255	0.26736	N	0.970498	P	0.36683	0.565	B	0.34385	0.181	T	0.12319	-1.0552	8	0.30078	T	0.28	-13.7135	9.0585	0.36421	0.2261:0.0:0.7739:0.0	.	524	C9J069	CI172_HUMAN	S	524	.	ENSP00000412388:G524S	G	+	1	0	C9orf172	138860257	0.337000	0.24766	0.990000	0.47175	0.802000	0.45316	0.645000	0.24782	0.670000	0.31165	0.472000	0.43445	GGC	.	.	weak		0.711	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482	
SCRN3	79634	hgsc.bcm.edu	37	2	175289259	175289259	+	Missense_Mutation	SNP	G	G	T	rs41270195	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:175289259G>T	ENST00000272732.6	+	7	1056	c.974G>T	c.(973-975)aGt>aTt	p.S325I	SCRN3_ENST00000409673.3_Missense_Mutation_p.S318I|SCRN3_ENST00000548921.1_3'UTR	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	325							dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			TTGGATACCAGTTCACCAACA	0.313													G|||	53	0.0105831	0.0	0.0115	5008	,	,		19014	0.0		0.0408	False		,,,				2504	0.0041				p.S325I		Atlas-SNP	.											.	SCRN3	76	.	0			c.G974T						PASS	.	G	ILE/SER,ILE/SER	42,4364	46.7+/-81.2	0,42,2161	71.0	67.0	68.0		953,974	-0.7	0.3	2	dbSNP_127	68	376,8224	122.7+/-181.7	8,360,3932	yes	missense,missense	SCRN3	NM_001193528.1,NM_024583.4	142,142	8,402,6093	TT,TG,GG		4.3721,0.9532,3.2139	benign,benign	318/418,325/425	175289259	418,12588	2203	4300	6503	SO:0001583	missense	79634	exon7			ATACCAGTTCACC	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.974G>T	2.37:g.175289259G>T	ENSP00000272732:p.Ser325Ile	Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	271	148	0.546125	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	37	CCDS2258.1	34	0.015567765567765568	0	0.0	5	0.013812154696132596	0	0.0	29	0.03825857519788918	G	3.398	-0.122847	0.06795	0.009532	0.043721	ENSG00000144306	ENST00000409673;ENST00000272732	T;T	0.08546	3.08;3.08	4.91	-0.677	0.11357	.	0.409489	0.27253	N	0.020212	T	0.00936	0.0031	L	0.31294	0.92	0.09310	N	1	B;B	0.12013	0.005;0.004	B;B	0.12156	0.007;0.002	T	0.34650	-0.9820	10	0.35671	T	0.21	-2.0764	1.0261	0.01528	0.2119:0.2024:0.3628:0.2229	rs41270195	318;325	B4DI11;Q0VDG4	.;SCRN3_HUMAN	I	318;325	ENSP00000387142:S318I;ENSP00000272732:S325I	ENSP00000272732:S325I	S	+	2	0	SCRN3	174997505	0.000000	0.05858	0.267000	0.24556	0.187000	0.23431	0.068000	0.14531	0.103000	0.17682	-0.266000	0.10368	AGT	G|0.971;T|0.029	0.029	strong		0.313	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583	
CATSPERG	57828	hgsc.bcm.edu	37	19	38827960	38827960	+	Missense_Mutation	SNP	T	T	C	rs2302182	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38827960T>C	ENST00000409235.3	+	2	201	c.86T>C	c.(85-87)cTc>cCc	p.L29P	CATSPERG_ENST00000215069.4_Missense_Mutation_p.L45P|CATSPERG_ENST00000410018.1_Missense_Mutation_p.L29P	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	29			L -> P (in dbSNP:rs2302182). {ECO:0000269|PubMed:17974005}.		cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						CTGGCAGTGCTCCTGGCGTCG	0.622													t|||	751	0.14996	0.0348	0.2378	5008	,	,		16010	0.1339		0.1849	False		,,,				2504	0.2239				p.L29P		Atlas-SNP	.											.	CATSPERG	121	.	0			c.T86C						PASS	.		PRO/LEU	94,1290		4,86,602	132.0	118.0	122.0		86	3.3	0.0	19	dbSNP_100	122	494,2688		39,416,1136	yes	missense	CATSPERG	NM_021185.4	98	43,502,1738	CC,CT,TT		15.5248,6.7919,12.8778	probably-damaging	29/1160	38827960	588,3978	692	1591	2283	SO:0001583	missense	57828	exon2			CAGTGCTCCTGGC	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"""chromosome 19 open reading frame 15"", ""cation channel, sperm-associated, gamma"""	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.86T>C	19.37:g.38827960T>C	ENSP00000386962:p.Leu29Pro	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	331	0.15155677655677655	17	0.034552845528455285	87	0.24033149171270718	85	0.1486013986013986	142	0.18733509234828497	t	14.33	2.502586	0.44455	0.067919	0.155248	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410;ENST00000215069	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	3.3	3.3	0.37823	.	0.000000	0.32736	N	0.005711	T	0.00039	0.0001	L	0.56769	1.78	0.45427	P	0.001595000000000013	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.05289	-1.0894	9	0.59425	D	0.04	-9.8134	8.3357	0.32213	0.0:0.0:0.0:1.0	rs2302182;rs52832791;rs2302182	29;29	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	P	29;29;29;45	ENSP00000387057:L29P;ENSP00000386962:L29P;ENSP00000386950:L29P;ENSP00000215069:L45P	ENSP00000215069:L45P	L	+	2	0	CATSPERG	43519800	0.190000	0.23276	0.025000	0.17156	0.004000	0.04260	1.135000	0.31454	1.760000	0.52011	0.370000	0.22315	CTC	T|0.855;C|0.145	0.145	strong		0.622	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	
ZNF816	125893	hgsc.bcm.edu	37	19	53454543	53454543	+	Missense_Mutation	SNP	G	G	A	rs11084210	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53454543G>A	ENST00000357666.4	-	5	785	c.485C>T	c.(484-486)tCg>tTg	p.S162L	ZNF816_ENST00000444460.2_Missense_Mutation_p.S162L|ZNF816_ENST00000434371.2_Intron|ZNF321P_ENST00000391777.3_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	162			S -> L (in dbSNP:rs11084210). {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)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						AGGCAGATGCGAATGAAAGCT	0.403													a|||	732	0.146166	0.2466	0.085	5008	,	,		19862	0.2163		0.0437	False		,,,				2504	0.0869				p.S162L		Atlas-SNP	.											.	ZNF816	73	.	0			c.C485T						PASS	.	G	LEU/SER,LEU/SER,LEU/SER,	855,3551		77,701,1425	161.0	170.0	167.0		485,485,485,	0.1	0.0	19	dbSNP_120	167	397,8203		9,379,3912	yes	missense,missense,missense,intron	ZNF816,ZNF816-ZNF321P	NM_001031665.2,NM_001202456.1,NM_001202457.1,NM_001202473.1	145,145,145,	86,1080,5337	AA,AG,GG		4.6163,19.4054,9.6263	benign,benign,benign,	162/652,162/652,162/652,	53454543	1252,11754	2203	4300	6503	SO:0001583	missense	125893	exon4			AGATGCGAATGAA	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"""Zinc fingers, C2H2-type"", ""-"""	26995	protein-coding gene	gene with protein product			"""zinc finger protein 816A"""	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.485C>T	19.37:g.53454543G>A	ENSP00000350295:p.Ser162Leu	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_001202457	A8K7H5|Q3KR39|Q659B3	Missense_Mutation	SNP	ENST00000357666.4	37	CCDS33096.1	298	0.13644688644688643	115	0.23373983739837398	29	0.08011049723756906	122	0.21328671328671328	32	0.04221635883905013	-	4.247	0.044860	0.08196	0.194054	0.046163	ENSG00000180257	ENST00000357666;ENST00000444460	T;T	0.06068	3.35;3.35	1.3	0.084	0.14436	.	.	.	.	.	T	0.00012	0.0000	L	0.58354	1.805	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.37709	-0.9694	8	0.46703	T	0.11	.	3.8846	0.09093	0.2687:0.0:0.7313:0.0	rs11084210;rs60109951;rs11084210	162	Q0VGE8	ZN816_HUMAN	L	162	ENSP00000350295:S162L;ENSP00000403266:S162L	ENSP00000350295:S162L	S	-	2	0	ZNF816	58146355	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.626000	0.05527	-0.141000	0.11374	-1.026000	0.02426	TCG	A|0.112;C|0.000;G|0.888	0.112	strong		0.403	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665	
NUP210	23225	hgsc.bcm.edu	37	3	13368892	13368892	+	Silent	SNP	G	G	A	rs2271509	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	159	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	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	
SSPO	23145	hgsc.bcm.edu	37	7	149513560	149513560	+	RNA	SNP	T	T	C	rs12674102	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149513560T>C	ENST00000378016.2	+	0	11181							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)			GCTGCTTCTCTGAGGGCTGCG	0.706													C|||	1992	0.397764	0.5287	0.3746	5008	,	,		12159	0.4127		0.2982	False		,,,				2504	0.3241				p.S3727S		Atlas-SNP	.											.	.	.	.	0			c.T11181C						PASS	.	C		1846,2182		464,918,632	10.0	14.0	13.0		11191	-6.0	0.0	7	dbSNP_120	13	2594,5680		455,1684,1998	yes	coding-notMod3	SSPO	NM_198455.2		919,2602,2630	CC,CT,TT		31.3512,45.8292,36.0917			149513560	4440,7862	2014	4137	6151			23145	exon78			CTTCTCTGAGGGC	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.149513560T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	49	7	0.142857	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				T|0.614;C|0.386	0.386	strong		0.706	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
FREM2	341640	hgsc.bcm.edu	37	13	39422624	39422624	+	Missense_Mutation	SNP	C	C	T	rs9548505	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:39422624C>T	ENST00000280481.7	+	8	6412	c.6196C>T	c.(6196-6198)Cgt>Tgt	p.R2066C	FREM2_ENST00000482551.1_3'UTR	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2066	Calx-beta 3.		R -> C (in dbSNP:rs9548505). {ECO:0000269|PubMed:17974005}.		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)		GGGCATCAGCCGTAATTTAGA	0.378													C|||	549	0.109625	0.1445	0.2522	5008	,	,		15477	0.001		0.0895	False		,,,				2504	0.0941				p.R2066C		Atlas-SNP	.											.	FREM2	385	.	0			c.C6196T						PASS	.	C	CYS/ARG	624,3782	272.5+/-270.8	46,532,1625	146.0	142.0	144.0		6196	5.7	0.8	13	dbSNP_119	144	938,7662	208.0+/-249.6	67,804,3429	yes	missense	FREM2	NM_207361.4	180	113,1336,5054	TT,TC,CC		10.907,14.1625,12.0098	probably-damaging	2066/3170	39422624	1562,11444	2203	4300	6503	SO:0001583	missense	341640	exon8			ATCAGCCGTAATT	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.6196C>T	13.37:g.39422624C>T	ENSP00000280481:p.Arg2066Cys	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	120	68	0.566667	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	190	0.08699633699633699	61	0.12398373983739837	73	0.20165745856353592	1	0.0017482517482517483	55	0.07255936675461741	C	25.2	4.614809	0.87359	0.141625	0.10907	ENSG00000150893	ENST00000280481	T	0.27557	1.66	5.66	5.66	0.87406	Na-Ca exchanger/integrin-beta4 (2);	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	M	0.86028	2.79	0.09310	P	0.9999999980019	D;D	0.76494	0.999;0.999	P;D	0.64595	0.906;0.927	T	0.00114	-1.2041	9	0.72032	D	0.01	.	19.7538	0.96281	0.0:1.0:0.0:0.0	rs9548505;rs52831056;rs59917479;rs9548505	2066;2066	Q5SZK8-2;Q5SZK8	.;FREM2_HUMAN	C	2066	ENSP00000280481:R2066C	ENSP00000280481:R2066C	R	+	1	0	FREM2	38320624	1.000000	0.71417	0.774000	0.31636	0.993000	0.82548	4.804000	0.62554	2.690000	0.91761	0.655000	0.94253	CGT	C|0.894;G|0.000;T|0.106	0.106	strong		0.378	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
NUP133	55746	hgsc.bcm.edu	37	1	229622162	229622162	+	Silent	SNP	A	A	G	rs1065675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:229622162A>G	ENST00000261396.3	-	11	1547	c.1456T>C	c.(1456-1458)Ttg>Ctg	p.L486L	NUP133_ENST00000537506.1_Silent_p.L470L	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	486					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 organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.L486L(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GACCCTTCCAAGTCTTCTGCC	0.378													G|||	1521	0.303714	0.5809	0.3285	5008	,	,		19446	0.1607		0.2097	False		,,,				2504	0.1554				p.L486L		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - coding silent(1)	stomach(1)	c.T1456C						PASS	.	G		2316,2090	569.8+/-382.7	600,1116,487	105.0	110.0	108.0		1456	-1.6	0.1	1	dbSNP_86	108	1864,6736	729.8+/-406.7	201,1462,2637	no	coding-synonymous	NUP133	NM_018230.2		801,2578,3124	GG,GA,AA		21.6744,47.4353,32.139		486/1157	229622162	4180,8826	2203	4300	6503	SO:0001819	synonymous_variant	55746	exon11			CTTCCAAGTCTTC		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1456T>C	1.37:g.229622162A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	173	54	0.312139	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	37	CCDS1579.1																																																																																			A|0.690;G|0.310	0.310	strong		0.378	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
KIF26A	26153	hgsc.bcm.edu	37	14	104643409	104643409	+	Silent	SNP	A	A	G	rs2487303	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104643409A>G	ENST00000423312.2	+	12	4284	c.4284A>G	c.(4282-4284)gcA>gcG	p.A1428A	KIF26A_ENST00000315264.7_Silent_p.A1289A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1428					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		AGGTAGAAGCAGCACACCGTC	0.706													G|||	3872	0.773163	0.826	0.7176	5008	,	,		14740	0.7827		0.7048	False		,,,				2504	0.8016				p.A1428A		Atlas-SNP	.											KIF26A,NS,carcinoma,0,1	KIF26A	84	1	0			c.A4284G						scavenged	.	G		3386,734		1393,600,67	11.0	16.0	14.0		4284	-7.2	0.0	14	dbSNP_100	14	6044,2232		2231,1582,325	no	coding-synonymous	KIF26A	NM_015656.1		3624,2182,392	GG,GA,AA		26.9696,17.8155,23.9271		1428/1883	104643409	9430,2966	2060	4138	6198	SO:0001819	synonymous_variant	26153	exon12			AGAAGCAGCACAC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.4284A>G	14.37:g.104643409A>G		Somatic	2	1	0.5		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			A|0.242;G|0.758	0.758	strong		0.706	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
MBD1	4152	hgsc.bcm.edu	37	18	47796399	47796399	+	3'UTR	SNP	A	A	C	rs183864846	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:47796399A>C	ENST00000591416.1	-	0	3721				MBD1_ENST00000269468.5_Intron|MBD1_ENST00000436910.1_Intron|MBD1_ENST00000353909.3_Intron|MBD1_ENST00000269471.5_Intron|MBD1_ENST00000424334.2_Intron|MBD1_ENST00000585595.1_Intron|MBD1_ENST00000347968.3_Intron|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000382948.5_Intron|MBD1_ENST00000590208.1_Intron|MBD1_ENST00000339998.6_Missense_Mutation_p.I545M|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000349085.2_Intron|MBD1_ENST00000588937.1_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						CAATCAAATAAATTTCATATA	0.378													A|||	14	0.00279553	0.0	0.0029	5008	,	,		20091	0.0		0.006	False		,,,				2504	0.0061				p.I545M		Atlas-SNP	.											MBD1_ENST00000339998,NS,carcinoma,-1,1	MBD1	228	1	0			c.T1635G						scavenged	.	A	,,,MET/ILE,,,,,,	2,1750		0,2,874	110.0	109.0	110.0		,,,1635,,,,,,	1.4	0.0	18		110	31,3951		0,31,1960	yes	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron	MBD1	NM_001204136.1,NM_001204139.1,NM_001204141.1,NM_001204142.1,NM_001204143.1,NM_002384.2,NM_015844.2,NM_015845.3,NM_015846.3,NM_015847.3	,,,10,,,,,,	0,33,2834	CC,CA,AA		0.7785,0.1142,0.5755	,,,,,,,,,	,,,545/551,,,,,,	47796399	33,5701	876	1991	2867	SO:0001624	3_prime_UTR_variant	4152	exon14			CAAATAAATTTCA	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.*1472T>G	18.37:g.47796399A>C		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_001204142	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Missense_Mutation	SNP	ENST00000591416.1	37	CCDS11943.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	A	9.230	1.035529	0.19590	0.001142	0.007785	ENSG00000141644	ENST00000339998	D	0.95756	-3.8	4.03	1.44	0.22558	.	.	.	.	.	D	0.87981	0.6315	.	.	.	0.18873	N	0.999987	B	0.24368	0.102	B	0.18561	0.022	T	0.81816	-0.0759	8	0.87932	D	0	.	4.6182	0.12437	0.5301:0.2952:0.0:0.1746	.	545	Q9UIS9-6	.	M	545	ENSP00000339546:I545M	ENSP00000339546:I545M	I	-	3	3	MBD1	46050397	0.000000	0.05858	0.010000	0.14722	0.703000	0.40648	-0.694000	0.05115	0.273000	0.22049	0.482000	0.46254	ATT	A|0.993;C|0.007	0.007	strong		0.378	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
RSPH3	83861	hgsc.bcm.edu	37	6	159399348	159399348	+	Missense_Mutation	SNP	A	A	G	rs768994	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159399348A>G	ENST00000252655.1	-	7	1505	c.1316T>C	c.(1315-1317)aTg>aCg	p.M439T	RSPH3_ENST00000297262.3_Missense_Mutation_p.M343T|RSPH3_ENST00000367069.2_Missense_Mutation_p.M297T|RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000449822.1_Missense_Mutation_p.M201T	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	439			M -> T (in dbSNP:rs768994).					p.M439T(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		AACTTCATTCATTAGCCATGG	0.299													A|||	981	0.195887	0.0492	0.3429	5008	,	,		14515	0.3919		0.0765	False		,,,				2504	0.2106				p.M439T		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - Missense(1)	stomach(1)	c.T1316C						PASS	.	A	THR/MET	307,4095	164.4+/-196.0	9,289,1903	58.0	56.0	57.0		1316	5.6	1.0	6	dbSNP_86	57	712,7862	171.7+/-222.6	37,638,3612	yes	missense	RSPH3	NM_031924.4	81	46,927,5515	GG,GA,AA		8.3042,6.9741,7.853	probably-damaging	439/561	159399348	1019,11957	2201	4287	6488	SO:0001583	missense	83861	exon7			TCATTCATTAGCC	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1316T>C	6.37:g.159399348A>G	ENSP00000252655:p.Met439Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	422	0.19322344322344323	24	0.04878048780487805	94	0.2596685082872928	244	0.42657342657342656	60	0.079155672823219	A	19.24	3.789284	0.70337	0.069741	0.083042	ENSG00000130363	ENST00000367069;ENST00000449822;ENST00000252655;ENST00000297262	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	5.57	5.57	0.84162	.	0.083199	0.85682	D	0.000000	T	0.20088	0.0483	M	0.73430	2.235	0.09310	P	0.99999176289	P;P	0.41232	0.724;0.743	B;P	0.47075	0.376;0.536	T	0.02333	-1.1175	9	0.41790	T	0.15	-24.6425	15.3989	0.74823	1.0:0.0:0.0:0.0	rs768994;rs52797265;rs60633343;rs768994	343;439	Q86UC2-2;Q86UC2	.;RSPH3_HUMAN	T	297;201;439;343	ENSP00000356036:M297T;ENSP00000393195:M201T;ENSP00000252655:M439T;ENSP00000297262:M343T	ENSP00000252655:M439T	M	-	2	0	RSPH3	159319336	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.445000	0.90326	2.124000	0.65301	0.477000	0.44152	ATG	A|0.862;G|0.138	0.138	strong		0.299	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
CDH7	1005	hgsc.bcm.edu	37	18	63477206	63477206	+	Silent	SNP	G	G	A	rs17075229	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:63477206G>A	ENST00000397968.2	+	3	903	c.477G>A	c.(475-477)acG>acA	p.T159T	CDH7_ENST00000323011.3_Silent_p.T159T|CDH7_ENST00000536984.2_Silent_p.T159T	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	159	Cadherin 2. {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)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)				GCCCATACACGGCAGGAGTTC	0.443													G|||	83	0.0165735	0.0008	0.0778	5008	,	,		16186	0.0		0.0199	False		,,,				2504	0.0082				p.T159T		Atlas-SNP	.											CDH7_ENST00000323011,NS,carcinoma,+2,2	CDH7	362	2	0			c.G477A						scavenged	.	G	,	23,4383	30.8+/-60.4	0,23,2180	88.0	87.0	87.0		477,477	-11.7	0.3	18	dbSNP_123	87	153,8447	74.2+/-136.8	1,151,4148	no	coding-synonymous,coding-synonymous	CDH7	NM_004361.2,NM_033646.1	,	1,174,6328	AA,AG,GG		1.7791,0.522,1.3532	,	159/786,159/786	63477206	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	1005	exon3			ATACACGGCAGGA	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.477G>A	18.37:g.63477206G>A		Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	125	52	0.416	NM_004361	Q9H157	Silent	SNP	ENST00000397968.2	37	CCDS11993.1																																																																																			G|0.984;A|0.016	0.016	strong		0.443	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
ANKRD34C	390616	hgsc.bcm.edu	37	15	79586361	79586361	+	Silent	SNP	T	T	C	rs8038778	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	45	8	0.177778	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	
HDGFL1	154150	hgsc.bcm.edu	37	6	22570245	22570245	+	Silent	SNP	G	G	A	rs6900627	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	102	0	0		WXS	Illumina HiSeq	Phase_I	58	20	0.344828	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	
FAM134A	79137	hgsc.bcm.edu	37	2	220046155	220046155	+	Silent	SNP	C	C	T	rs548711754		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220046155C>T	ENST00000430297.2	+	7	985	c.849C>T	c.(847-849)agC>agT	p.S283S		NM_024293.4	NP_077269.3	Q8NC44	F134A_HUMAN	family with sequence similarity 134, member A	283						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	19		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAGTGAAAGCGAGGCAGAGC	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		18963	0.0		0.0	False		,,,				2504	0.001				p.S283S		Atlas-SNP	.											FAM134A,colon,carcinoma,0,1	FAM134A	34	1	0			c.C849T						PASS	.						56.0	57.0	57.0					2																	220046155		2203	4300	6503	SO:0001819	synonymous_variant	79137	exon7			TGAAAGCGAGGCA	AK074983	CCDS2434.1	2q36.1	2008-02-05	2007-05-01	2007-05-01	ENSG00000144567	ENSG00000144567			28450	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 17"""	C2orf17			Standard	NM_024293		Approved	MGC3035	uc002vjw.4	Q8NC44	OTTHUMG00000154577	ENST00000430297.2:c.849C>T	2.37:g.220046155C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	18	0.243243	NM_024293	Q6P1P5|Q9H0K7	Silent	SNP	ENST00000430297.2	37	CCDS2434.1																																																																																			.	.	none		0.542	FAM134A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336147.2	NM_024293	
MUC4	4585	hgsc.bcm.edu	37	3	195513285	195513285	+	Silent	SNP	G	G	T	rs200293322	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195513285G>T	ENST00000463781.3	-	2	5625	c.5166C>A	c.(5164-5166)tcC>tcA	p.S1722S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.S1722S	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.S1722S(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)		TGTCACCTGTGGATACTGAGG	0.582																																					p.S1722S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.C5166A						scavenged	.						22.0	24.0	23.0					3																	195513285		683	1583	2266	SO:0001819	synonymous_variant	4585	exon2			ACCTGTGGATACT	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.5166C>A	3.37:g.195513285G>T		Somatic	444	7	0.0157658		WXS	Illumina HiSeq	Phase_I	531	12	0.0225989	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|0.988;T|0.013	0.013	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KCNG4	93107	hgsc.bcm.edu	37	16	84256103	84256103	+	Missense_Mutation	SNP	C	C	T	rs35649980	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:84256103C>T	ENST00000308251.4	-	3	1348	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H		NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	427			R -> H (in dbSNP:rs35649980).		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)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						TGGCACACTGCGGGGCACCAT	0.632													C|||	321	0.0640974	0.0159	0.0375	5008	,	,		19028	0.1002		0.0855	False		,,,				2504	0.089				p.R427H		Atlas-SNP	.											.	KCNG4	71	.	0			c.G1280A						PASS	.	C	HIS/ARG	104,4296	81.4+/-119.9	1,102,2097	53.0	50.0	51.0		1280	5.6	1.0	16	dbSNP_126	51	649,7951	163.5+/-216.0	19,611,3670	yes	missense	KCNG4	NM_172347.2	29	20,713,5767	TT,TC,CC		7.5465,2.3636,5.7923	benign	427/520	84256103	753,12247	2200	4300	6500	SO:0001583	missense	93107	exon3			ACACTGCGGGGCA	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.1280G>A	16.37:g.84256103C>T	ENSP00000312129:p.Arg427His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	126	111	0.880952	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	149	0.06822344322344322	11	0.022357723577235773	20	0.055248618784530384	55	0.09615384615384616	63	0.08311345646437995	C	26.8	4.771200	0.90108	0.023636	0.075465	ENSG00000168418	ENST00000308251	T	0.44881	0.91	5.61	5.61	0.85477	Ion transport (1);	0.165528	0.48286	D	0.000200	T	0.01092	0.0036	L	0.31207	0.915	0.80722	D	1	P	0.47191	0.891	B	0.42282	0.382	T	0.00374	-1.1780	10	0.56958	D	0.05	.	18.6265	0.91342	0.0:1.0:0.0:0.0	rs35649980	427	Q8TDN1	KCNG4_HUMAN	H	427	ENSP00000312129:R427H	ENSP00000312129:R427H	R	-	2	0	KCNG4	82813604	0.899000	0.30636	0.999000	0.59377	0.974000	0.67602	4.934000	0.63491	2.631000	0.89168	0.655000	0.94253	CGC	C|0.935;T|0.065	0.065	strong		0.632	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
MEP1B	4225	hgsc.bcm.edu	37	18	29782953	29782953	+	Missense_Mutation	SNP	A	A	G	rs71361372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:29782953A>G	ENST00000269202.6	+	6	395	c.348A>G	c.(346-348)atA>atG	p.I116M	MEP1B_ENST00000581447.1_Missense_Mutation_p.I116M	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	116	Metalloprotease.				digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CAAACTATATATCAGTGTTCA	0.413													A|||	36	0.0071885	0.0015	0.0086	5008	,	,		20162	0.0		0.0129	False		,,,				2504	0.0153				p.I116M		Atlas-SNP	.											.	MEP1B	54	.	0			c.A348G						PASS	.	A	MET/ILE	13,3787		0,13,1887	83.0	81.0	82.0		348	1.2	1.0	18	dbSNP_130	82	141,8103		3,135,3984	yes	missense	MEP1B	NM_005925.2	10	3,148,5871	GG,GA,AA		1.7103,0.3421,1.2786	probably-damaging	116/702	29782953	154,11890	1900	4122	6022	SO:0001583	missense	4225	exon6			CTATATATCAGTG	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.348A>G	18.37:g.29782953A>G	ENSP00000269202:p.Ile116Met	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	A	18.72	3.684857	0.68157	0.003421	0.017103	ENSG00000141434	ENST00000269202	T	0.70749	-0.51	5.72	1.22	0.21188	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.74199	0.3685	M	0.91972	3.26	0.38390	D	0.945362	D	0.89917	1.0	D	0.81914	0.995	T	0.80837	-0.1204	10	0.87932	D	0	-18.6302	8.2453	0.31684	0.5426:0.3346:0.0:0.1228	.	116	Q16820	MEP1B_HUMAN	M	116	ENSP00000269202:I116M	ENSP00000269202:I116M	I	+	3	3	MEP1B	28036951	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	1.052000	0.30429	0.376000	0.24707	0.533000	0.62120	ATA	A|0.992;G|0.008	0.008	strong		0.413	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
NUF2	83540	hgsc.bcm.edu	37	1	163313539	163313539	+	Missense_Mutation	SNP	C	C	T	rs11802875	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:163313539C>T	ENST00000271452.3	+	10	965	c.686C>T	c.(685-687)tCg>tTg	p.S229L	NUF2_ENST00000367900.3_Missense_Mutation_p.S229L|NUF2_ENST00000524800.1_Missense_Mutation_p.S229L	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	229	Interaction with the N-terminus of NDC80.		S -> L (in dbSNP:rs11802875). {ECO:0000269|PubMed:11266451, ECO:0000269|PubMed:11685532}.		chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					CTAAAATTGTCGGTGGTTTCT	0.274													C|||	621	0.124002	0.1664	0.1671	5008	,	,		14112	0.0228		0.1928	False		,,,				2504	0.0695				p.S229L		Atlas-SNP	.											NUF2_ENST00000271452,NS,carcinoma,0,2	NUF2	138	2	0			c.C686T						PASS	.	C	LEU/SER,LEU/SER	582,3586		39,504,1541	20.0	22.0	21.0		686,686	3.0	0.5	1	dbSNP_120	21	1469,7027		127,1215,2906	yes	missense,missense	NUF2	NM_031423.3,NM_145697.2	145,145	166,1719,4447	TT,TC,CC		17.2905,13.9635,16.1955	possibly-damaging,possibly-damaging	229/465,229/465	163313539	2051,10613	2084	4248	6332	SO:0001583	missense	83540	exon10			AATTGTCGGTGGT	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"""cancer/testis antigen 106"""	611772	"""cell division cycle associated 1"", ""NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.686C>T	1.37:g.163313539C>T	ENSP00000271452:p.Ser229Leu	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	168	90	0.535714	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	310	0.14194139194139194	76	0.15447154471544716	63	0.17403314917127072	14	0.024475524475524476	157	0.20712401055408972	C	10.29	1.308613	0.23821	0.139635	0.172905	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.31247	1.54;1.5;1.5	4.83	2.96	0.34315	.	0.474249	0.23149	N	0.051374	T	0.06872	0.0175	L	0.47716	1.5	0.30934	P	0.726526	P;P	0.45569	0.861;0.861	B;B	0.25614	0.062;0.062	T	0.21177	-1.0253	9	0.28530	T	0.3	-1.4962	6.7062	0.23252	0.0:0.7141:0.0:0.2859	rs11802875;rs56525990;rs59877163;rs11802875	229;229	E9PQC4;Q9BZD4	.;NUF2_HUMAN	L	229	ENSP00000436888:S229L;ENSP00000356875:S229L;ENSP00000271452:S229L	ENSP00000271452:S229L	S	+	2	0	NUF2	161580163	0.477000	0.25909	0.455000	0.27031	0.560000	0.35617	1.227000	0.32576	0.763000	0.33175	0.585000	0.79938	TCG	C|0.865;N|0.000	.	strong		0.274	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	
QSER1	79832	hgsc.bcm.edu	37	11	32996805	32996805	+	Silent	SNP	C	C	T	rs11032076	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	80	32	0.4	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	
LEPRE1	64175	hgsc.bcm.edu	37	1	43223489	43223489	+	Missense_Mutation	SNP	C	C	T	rs6700677	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43223489C>T	ENST00000296388.5	-	5	1096	c.1045G>A	c.(1045-1047)Gga>Aga	p.G349R	LEPRE1_ENST00000236040.4_Missense_Mutation_p.G349R|LEPRE1_ENST00000397054.3_Missense_Mutation_p.G349R			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	349			G -> R (in dbSNP:rs6700677).		bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TGTTCTTCTCCAAGCATAGCT	0.498											OREG0013423	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	275	0.0549121	0.112	0.0389	5008	,	,		22023	0.001		0.0388	False		,,,				2504	0.0613				p.G349R		Atlas-SNP	.											LEPRE1_ENST00000296388,colon,carcinoma,0,8	LEPRE1	130	8	0			c.G1045A						PASS	.	C	ARG/GLY,ARG/GLY	478,3928	223.9+/-240.3	18,442,1743	253.0	211.0	225.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1045,1045	5.8	1.0	1	dbSNP_116	225	374,8226	122.0+/-181.0	6,362,3932	yes	missense,missense	LEPRE1	NM_001146289.1,NM_022356.3	125,125	24,804,5675	TT,TC,CC		4.3488,10.8488,6.5508	probably-damaging,probably-damaging	349/698,349/737	43223489	852,12154	2203	4300	6503	SO:0001583	missense	64175	exon5			CTTCTCCAAGCAT	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.1045G>A	1.37:g.43223489C>T	ENSP00000296388:p.Gly349Arg	Somatic	170	0	0	914	WXS	Illumina HiSeq	Phase_I	98	20	0.204082	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	97	0.044413919413919416	48	0.0975609756097561	19	0.052486187845303865	0	0.0	30	0.0395778364116095	C	23.0	4.365718	0.82463	0.108488	0.043488	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	D;D;D	0.82893	-1.66;-1.66;-1.66	5.84	5.84	0.93424	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.27384	0.0672	M	0.87547	2.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.68618	-0.5361	10	0.87932	D	0	-19.1499	17.6432	0.88142	0.0:1.0:0.0:0.0	rs6700677;rs52814052;rs56872967;rs6700677	349;214;349	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	R	349;349;349;214	ENSP00000380245:G349R;ENSP00000236040:G349R;ENSP00000296388:G349R	ENSP00000236040:G349R	G	-	1	0	LEPRE1	42996076	1.000000	0.71417	0.993000	0.49108	0.473000	0.32948	7.487000	0.81328	2.769000	0.95229	0.462000	0.41574	GGA	C|0.940;T|0.060	0.060	strong		0.498	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
TRPM6	140803	hgsc.bcm.edu	37	9	77415284	77415284	+	Silent	SNP	A	A	C	rs7859201	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:77415284A>C	ENST00000360774.1	-	17	2361	c.2124T>G	c.(2122-2124)ctT>ctG	p.L708L	TRPM6_ENST00000376864.4_Silent_p.L708L|RN7SKP47_ENST00000365347.1_RNA|TRPM6_ENST00000361255.3_Silent_p.L703L|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000449912.2_Silent_p.L703L|TRPM6_ENST00000451710.3_Silent_p.L708L|TRPM6_ENST00000376871.3_Intron	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	708			L -> P (in HOMG1; loss of function; no effect on cell membrane localization). {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						CGGCCAGTTTAAGGCAGGTCG	0.498													C|||	2308	0.460863	0.7436	0.3415	5008	,	,		18117	0.3482		0.3728	False		,,,				2504	0.3701				p.L708L		Atlas-SNP	.											.	TRPM6	377	.	0			c.T2124G						PASS	.	C	,,	2924,1482	475.3+/-357.3	973,978,252	130.0	106.0	114.0		2109,2109,2124	3.2	0.8	9	dbSNP_116	114	3264,5336	648.3+/-400.5	607,2050,1643	no	coding-synonymous,coding-synonymous,coding-synonymous	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	,,	1580,3028,1895	CC,CA,AA		37.9535,33.636,47.578	,,	703/2018,703/2018,708/2023	77415284	6188,6818	2203	4300	6503	SO:0001819	synonymous_variant	140803	exon17			CAGTTTAAGGCAG	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.2124T>G	9.37:g.77415284A>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Silent	SNP	ENST00000360774.1	37	CCDS6647.1																																																																																			A|0.532;C|0.468	0.468	strong		0.498	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	
CHSY1	22856	hgsc.bcm.edu	37	15	101717888	101717888	+	Missense_Mutation	SNP	C	C	T	rs62621399	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:101717888C>T	ENST00000254190.3	-	3	2589	c.2114G>A	c.(2113-2115)cGa>cAa	p.R705Q	CHSY1_ENST00000543813.1_5'UTR	NM_014918.4	NP_055733.2	Q86X52	CHSS1_HUMAN	chondroitin sulfate synthase 1	705					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|negative regulation of ossification (GO:0030279)|response to nutrient levels (GO:0031667)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	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)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(5)|skin(1)	24	Lung NSC(78;0.00217)|all_lung(78;0.00271)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			GCCACCCACTCGGACAAGATC	0.478													C|||	262	0.0523163	0.0061	0.0663	5008	,	,		19215	0.002		0.1561	False		,,,				2504	0.0501				p.R705Q		Atlas-SNP	.											CHSY1,colon,carcinoma,-1,1	CHSY1	60	1	0			c.G2114A						scavenged	.	C	GLN/ARG	121,4285	90.6+/-129.3	1,119,2083	103.0	113.0	109.0		2114	4.7	0.9	15	dbSNP_129	109	1221,7379	246.0+/-274.6	96,1029,3175	yes	missense	CHSY1	NM_014918.4	43	97,1148,5258	TT,TC,CC		14.1977,2.7463,10.3183	benign	705/803	101717888	1342,11664	2203	4300	6503	SO:0001583	missense	22856	exon3			CCCACTCGGACAA	AB023207	CCDS10390.1	15q26.3	2013-02-19	2008-01-24	2008-01-24	ENSG00000131873	ENSG00000131873	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	17198	protein-coding gene	gene with protein product		608183	"""carbohydrate (chondroitin) synthase 1"""			11514575	Standard	NM_014918		Approved	KIAA0990, CSS1	uc021sxt.1	Q86X52	OTTHUMG00000149873	ENST00000254190.3:c.2114G>A	15.37:g.101717888C>T	ENSP00000254190:p.Arg705Gln	Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	79	22	0.278481	NM_014918	Q6UX38|Q7LFU5|Q9Y2J5	Missense_Mutation	SNP	ENST00000254190.3	37	CCDS10390.1	154	0.07051282051282051	5	0.01016260162601626	29	0.08011049723756906	1	0.0017482517482517483	119	0.15699208443271767	C	11.62	1.693241	0.30052	0.027463	0.141977	ENSG00000131873	ENST00000254190;ENST00000543813	T	0.35048	1.33	5.6	4.69	0.59074	.	0.069705	0.56097	D	0.000021	T	0.00109	0.0003	N	0.25647	0.755	0.21147	P	0.999773402	P	0.48016	0.904	B	0.39771	0.309	T	0.12502	-1.0545	9	0.12103	T	0.63	-20.3917	14.5886	0.68347	0.0:0.9297:0.0:0.0703	rs62621399	705	Q86X52	CHSS1_HUMAN	Q	705;433	ENSP00000254190:R705Q	ENSP00000254190:R705Q	R	-	2	0	CHSY1	99535411	0.939000	0.31865	0.923000	0.36655	0.963000	0.63663	1.711000	0.37930	1.365000	0.46057	0.561000	0.74099	CGA	C|0.907;G|0.000;T|0.093	0.093	strong		0.478	CHSY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313624.1	NM_014918	
MACROD1	28992	hgsc.bcm.edu	37	11	63885704	63885704	+	Intron	SNP	C	C	T	rs677447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:63885704C>T	ENST00000255681.6	-	3	584				FLRT1_ENST00000246841.3_Silent_p.Y655Y|RP11-21A7A.3_ENST00000543817.1_RNA	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	142	0	0		WXS	Illumina HiSeq	Phase_I	146	145	0.993151	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	
FAM155B	27112	hgsc.bcm.edu	37	X	68725640	68725640	+	Missense_Mutation	SNP	T	T	C	rs1171942	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:68725640T>C	ENST00000252338.4	+	1	557	c.515T>C	c.(514-516)cTt>cCt	p.L172P	AL158069.1_ENST00000579664.1_RNA	NM_015686.2	NP_056501.2	O75949	F155B_HUMAN	family with sequence similarity 155, member B	172			L -> P (in dbSNP:rs1171942). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|endometrium(4)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)	16						CCTGACTCCCTTTCCCGTGCC	0.592													c|||	2428	0.643179	0.6664	0.5029	3775	,	,		7543	0.6111		0.2336	False		,,,				2504	0.3548				p.L172P		Atlas-SNP	.											.	FAM155B	44	.	0			c.T515C						PASS	.		PRO/LEU	3216,615		1162,411,481,58,88	24.0	30.0	28.0		515	1.7	0.9	X	dbSNP_87	28	2199,4526		270,1044,615,1113,1256	yes	missense	FAM155B	NM_015686.2	98	1432,1455,1096,1171,1344	CC,CT,C,TT,T		32.6989,16.0532,48.7022	benign	172/473	68725640	5415,5141	2200	4298	6498	SO:0001583	missense	27112	exon1			ACTCCCTTTCCCG	AF087142	CCDS35317.1	Xq13.1	2008-04-15	2008-04-15	2008-04-15	ENSG00000130054	ENSG00000130054			30701	protein-coding gene	gene with protein product			"""transmembrane protein 28"", ""chromosome X open reading frame 63"""	TMEM28, CXorf63			Standard	NM_015686		Approved	TED	uc004dxk.3	O75949	OTTHUMG00000021756	ENST00000252338.4:c.515T>C	X.37:g.68725640T>C	ENSP00000252338:p.Leu172Pro	Somatic	265	2	0.00754717		WXS	Illumina HiSeq	Phase_I	125	119	0.952	NM_015686	B1ALV6|B9EGK1|D3DVU1	Missense_Mutation	SNP	ENST00000252338.4	37	CCDS35317.1	1017	0.6130198915009042	214	0.722972972972973	115	0.4637096774193548	234	0.6964285714285714	127	0.19538461538461538	C	0.003	-2.570916	0.00133	0.839468	0.326989	ENSG00000130054	ENST00000252338	T	0.42131	0.98	4.7	1.72	0.24424	.	0.680336	0.13754	N	0.365088	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	0.16897	-1.0387	9	0.22109	T	0.4	2.301	4.9816	0.14168	0.0:0.5568:0.1525:0.2907	rs1171942;rs16989158	172	O75949-2	.	P	172	ENSP00000252338:L172P	ENSP00000252338:L172P	L	+	2	0	FAM155B	68642365	0.067000	0.21026	0.877000	0.34402	0.392000	0.30506	1.452000	0.35156	-0.005000	0.14395	-1.324000	0.01287	CTT	T|0.456;C|0.544	0.544	strong		0.592	FAM155B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057037.1	NM_015686	
MUC4	4585	hgsc.bcm.edu	37	3	195509378	195509378	+	Missense_Mutation	SNP	G	G	C	rs199889138		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195509378G>C	ENST00000463781.3	-	2	9532	c.9073C>G	c.(9073-9075)Ctt>Gtt	p.L3025V	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L3025V	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)		GTGACATGAAGAGGGGTGGCG	0.582																																					p.L3025V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C9073G						PASS	.						25.0	19.0	21.0					3																	195509378		663	1544	2207	SO:0001583	missense	4585	exon2			CATGAAGAGGGGT	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.9073C>G	3.37:g.195509378G>C	ENSP00000417498:p.Leu3025Val	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	363	71	0.195592	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	3.681	-0.065503	0.07273	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.5;1.41	.	.	.	.	.	.	.	.	T	0.14270	0.0345	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.12156	0.007	T	0.27872	-1.0061	7	.	.	.	.	2.745	0.05264	0.0:0.4482:0.2987:0.2531	.	2897	E7ESK3	.	V	3025	ENSP00000417498:L3025V;ENSP00000420243:L3025V	.	L	-	1	0	MUC4	196994157	0.073000	0.21202	0.014000	0.15608	0.000000	0.00434	0.211000	0.17474	-0.893000	0.03930	0.000000	0.15137	CTT	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR8D2	283160	hgsc.bcm.edu	37	11	124189306	124189306	+	Missense_Mutation	SNP	G	G	A	rs2466620	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:124189306G>A	ENST00000357438.2	-	1	878	c.788C>T	c.(787-789)cCt>cTt	p.P263L		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	263			P -> L (in dbSNP:rs2466620).			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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		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;0.0525)		AGTGCTGGAAGGGGGCTTGAA	0.448													G|||	1390	0.277556	0.4531	0.2003	5008	,	,		18104	0.1895		0.1292	False		,,,				2504	0.3384				p.P263L		Atlas-SNP	.											.	OR8D2	65	.	0			c.C788T						PASS	.	G	LEU/PRO	1863,2539	538.7+/-375.1	384,1095,722	135.0	142.0	140.0		788	1.4	0.0	11	dbSNP_100	140	1278,7320	250.7+/-277.5	112,1054,3133	yes	missense	OR8D2	NM_001002918.1	98	496,2149,3855	AA,AG,GG		14.8639,42.3217,24.1615	benign	263/312	124189306	3141,9859	2201	4299	6500	SO:0001583	missense	283160	exon1			CTGGAAGGGGGCT	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"""GPCR / Class A : Olfactory receptors"""	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.788C>T	11.37:g.124189306G>A	ENSP00000350022:p.Pro263Leu	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	227	67	0.295154	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	37	CCDS31707.1	520	0.23809523809523808	224	0.45528455284552843	71	0.19613259668508287	124	0.21678321678321677	101	0.13324538258575197	g	14.01	2.407143	0.42715	0.423217	0.148639	ENSG00000197263	ENST00000357438	T	0.00164	8.64	3.34	1.41	0.22369	GPCR, rhodopsin-like superfamily (1);	0.294224	0.24506	N	0.037940	T	0.00012	0.0000	N	0.26162	0.8	0.80722	P	0.0	P	0.40000	0.698	B	0.43413	0.419	T	0.00001	-1.2671	9	0.66056	D	0.02	.	8.25	0.31712	0.0937:0.4291:0.4772:0.0	rs2466620;rs52820798;rs59068946;rs2466620	263	Q9GZM6	OR8D2_HUMAN	L	263	ENSP00000350022:P263L	ENSP00000350022:P263L	P	-	2	0	OR8D2	123694516	0.008000	0.16893	0.003000	0.11579	0.975000	0.68041	1.552000	0.36244	0.435000	0.26365	0.530000	0.56133	CCT	G|0.761;A|0.239	0.239	strong		0.448	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918	
PEX10	5192	hgsc.bcm.edu	37	1	2340212	2340212	+	Silent	SNP	G	G	A	rs1143016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:2340212G>A	ENST00000447513.2	-	3	347	c.279C>T	c.(277-279)ggC>ggT	p.G93G	PEX10_ENST00000507596.1_Silent_p.G93G|PEX10_ENST00000288774.3_Silent_p.G93G|PEX10_ENST00000515760.1_5'UTR	NM_002617.3	NP_002608.1	O60683	PEX10_HUMAN	peroxisomal biogenesis factor 10	93					peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)	integral component of peroxisomal membrane (GO:0005779)|intracellular (GO:0005622)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)	p.G93G(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	7	all_cancers(77;0.000247)|all_epithelial(69;9.96e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;5.35e-20)|all_lung(118;2.78e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00102)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0169)|Lung(427;0.199)		TCACCAGCACGCCACGGCGCA	0.662													G|||	100	0.0199681	0.0053	0.0115	5008	,	,		18508	0.001		0.0596	False		,,,				2504	0.0245				p.G93G	GBM(12;9 508 1649 13619)	Atlas-SNP	.											.	PEX10	18	.	1	Substitution - coding silent(1)	lung(1)	c.C279T						PASS	.	G	,	65,4341	61.1+/-98.1	1,63,2139	97.0	96.0	97.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	279,279	-9.2	0.0	1	dbSNP_86	97	539,8061	148.8+/-204.0	20,499,3781	no	coding-synonymous,coding-synonymous	PEX10	NM_002617.3,NM_153818.1	,	21,562,5920	AA,AG,GG		6.2674,1.4753,4.644	,	93/327,93/347	2340212	604,12402	2203	4300	6503	SO:0001819	synonymous_variant	5192	exon3			CAGCACGCCACGG	AF060502	CCDS41.1, CCDS44045.1	1p36.32	2013-01-09	2008-08-26		ENSG00000157911	ENSG00000157911		"""RING-type (C3HC4) zinc fingers"""	8851	protein-coding gene	gene with protein product		602859	"""peroxisome biogenesis factor 10"""			9683594	Standard	NM_002617		Approved	RNF69	uc001ajg.3	O60683	OTTHUMG00000001637	ENST00000447513.2:c.279C>T	1.37:g.2340212G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	104	77	0.740385	NM_002617	B3KWD8|Q5T095|Q9BW90	Silent	SNP	ENST00000447513.2	37	CCDS44045.1																																																																																			G|0.960;A|0.040	0.040	strong		0.662	PEX10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367454.1	NM_153818	
PTH1R	5745	hgsc.bcm.edu	37	3	46939456	46939456	+	Splice_Site	SNP	G	G	C	rs201472450		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46939456G>C	ENST00000313049.5	+	4	627		c.e4+1		PTH1R_ENST00000449590.1_Splice_Site|PTH1R_ENST00000490109.1_Splice_Site|PTH1R_ENST00000430002.2_Splice_Site|PTH1R_ENST00000418619.1_Splice_Site			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor						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)			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)	AATCACAAAGGTGAGGCCTGC	0.612																																					.		Atlas-SNP	.											.	PTH1R	49	.	0			c.424+1G>C						PASS	.						61.0	63.0	62.0					3																	46939456		2203	4300	6503	SO:0001630	splice_region_variant	5745	exon6			ACAAAGGTGAGGC		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.424+1G>C	3.37:g.46939456G>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	147	49	0.333333	NM_000316	Q2M1U3	Splice_Site	SNP	ENST00000313049.5	37	CCDS2747.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.198211	0.79015	.	.	ENSG00000160801	ENST00000449590;ENST00000418619;ENST00000427125;ENST00000430002;ENST00000313049	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3295	0.83004	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTH1R	46914460	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.292000	0.96076	2.448000	0.82819	0.561000	0.74099	.	.	.	weak		0.612	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	Intron
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789345	117789345	+	Missense_Mutation	SNP	G	G	C	rs61900347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789345G>C	ENST00000430170.2	-	2	317	c.230C>G	c.(229-231)gCc>gGc	p.A77G	TMPRSS13_ENST00000445164.2_Missense_Mutation_p.A77G|TMPRSS13_ENST00000526090.1_Missense_Mutation_p.A77G|TMPRSS13_ENST00000528626.1_Missense_Mutation_p.A77G|TMPRSS13_ENST00000524993.1_Missense_Mutation_p.A77G	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	77	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					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)		AGATGCCTGGGCTGGAGATGC	0.672													G|||	2	0.000399361	0.0	0.0	5008	,	,		14255	0.002		0.0	False		,,,				2504	0.0				p.A77G		Atlas-SNP	.											TMPRSS13_ENST00000445164,NS,carcinoma,0,2	TMPRSS13	75	2	0			c.C230G						PASS	.						39.0	48.0	45.0					11																	117789345		1921	4109	6030	SO:0001583	missense	84000	exon2			GCCTGGGCTGGAG	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	ENST00000430170.2:c.230C>G	11.37:g.117789345G>C	ENSP00000387702:p.Ala77Gly	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	243	27	0.111111	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Missense_Mutation	SNP	ENST00000430170.2	37	CCDS58185.1	219|219	0.10027472527472528|0.10027472527472528	67|67	0.13617886178861788|0.13617886178861788	52|52	0.143646408839779|0.143646408839779	45|45	0.07867132867132867|0.07867132867132867	55|55	0.07255936675461741|0.07255936675461741	G|G	4.978|4.978	0.181711|0.181711	0.09495|0.09495	.|.	.|.	ENSG00000137747|ENSG00000137747	ENST00000336500|ENST00000528626;ENST00000524993;ENST00000430170;ENST00000445164;ENST00000526090	.|D;D;D;D;D	.|0.88431	.|-2.38;-2.36;-2.36;-2.34;-2.24	3.11|3.11	1.04|1.04	0.20106|0.20106	.|.	.|1.049680	.|0.07486	.|N	.|0.904837	.|T	.|0.02380	.|0.0073	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	.|T	.|0.28776	.|-1.0033	.|9	.|0.20046	.|T	.|0.44	.|.	6.0296|6.0296	0.19673|0.19673	0.1228:0.2258:0.6514:0.0|0.1228:0.2258:0.6514:0.0	rs61900347|rs61900347	.|77	.|E9PRA0	.|.	.|G	-1|77	.|ENSP00000435813:A77G;ENSP00000434279:A77G;ENSP00000387702:A77G;ENSP00000394114:A77G;ENSP00000436502:A77G	.|ENSP00000387702:A77G	.|A	-|-	.|2	.|0	TMPRSS13|TMPRSS13	117294555|117294555	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.105000|0.105000	0.15333|0.15333	-0.045000|-0.045000	0.13468|0.13468	-0.189000|-0.189000	0.12847|0.12847	.|GCC	G|0.899;C|0.101	0.101	strong		0.672	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
SACS	26278	hgsc.bcm.edu	37	13	23908034	23908034	+	Silent	SNP	A	A	G	rs2737700	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	115	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	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	
GTPBP10	85865	hgsc.bcm.edu	37	7	89982132	89982132	+	Silent	SNP	T	T	C	rs6972561	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:89982132T>C	ENST00000222511.6	+	2	102	c.36T>C	c.(34-36)taT>taC	p.Y12Y	GTPBP10_ENST00000257659.8_Silent_p.Y12Y	NM_033107.3	NP_149098.2	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 (putative)	12					ribosome biogenesis (GO:0042254)	chromosome (GO:0005694)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)	10						TTTTTAAGTATGGAAATTTCA	0.368											OREG0003797	type=REGULATORY REGION|Gene=BC021573|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	T|||	1370	0.273562	0.3979	0.2536	5008	,	,		15695	0.244		0.2366	False		,,,				2504	0.1881				p.Y12Y		Atlas-SNP	.											.	GTPBP10	31	.	0			c.T36C						PASS	.	T	,	1521,2885	481.0+/-359.0	269,983,951	81.0	82.0	82.0		36,36	6.1	1.0	7	dbSNP_116	82	1671,6929	307.2+/-308.3	156,1359,2785	no	coding-synonymous,coding-synonymous	GTPBP10	NM_001042717.2,NM_033107.3	,	425,2342,3736	CC,CT,TT		19.4302,34.5211,24.5425	,	12/309,12/388	89982132	3192,9814	2203	4300	6503	SO:0001819	synonymous_variant	85865	exon2			TAAGTATGGAAAT		CCDS5617.1, CCDS43614.1	7q21.13	2006-08-15			ENSG00000105793	ENSG00000105793			25106	protein-coding gene	gene with protein product		610920				12477932	Standard	NM_001042717		Approved	DKFZP686A10121, FLJ38242	uc003ukm.2	A4D1E9	OTTHUMG00000023655	ENST00000222511.6:c.36T>C	7.37:g.89982132T>C		Somatic	39	0	0	1271	WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_001042717	B4DFY6|Q3B7A6|Q5H9V2|Q8IXG8|Q8N982|Q8WU16|Q9BSP1|Q9Y6T6	Silent	SNP	ENST00000222511.6	37	CCDS5617.1																																																																																			T|0.731;C|0.269	0.269	strong		0.368	GTPBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059976.3	NM_033107	
EPHA3	2042	hgsc.bcm.edu	37	3	89521725	89521725	+	Silent	SNP	T	T	C	rs1054750	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	157	2	0.0127389		WXS	Illumina HiSeq	Phase_I	127	65	0.511811	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	
CCL24	6369	hgsc.bcm.edu	37	7	75442730	75442730	+	Missense_Mutation	SNP	T	T	G	rs2302006	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:75442730T>G	ENST00000416943.1	-	3	178	c.85A>C	c.(85-87)Atc>Ctc	p.I29L	CCL24_ENST00000222902.2_Missense_Mutation_p.I29L	NM_002991.2	NP_002982.2	O00175	CCL24_HUMAN	chemokine (C-C motif) ligand 24	29			I -> L (in dbSNP:rs2302006). {ECO:0000269|PubMed:14702039}.		cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of inflammatory response (GO:0050729)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|lung(2)	3						GGAGAGGGGATGACCACAGAG	0.562													T|||	1733	0.346046	0.2685	0.4063	5008	,	,		17705	0.5595		0.1839	False		,,,				2504	0.3548				p.I29L		Atlas-SNP	.											.	CCL24	11	.	0			c.A85C						PASS	.	T	LEU/ILE	1230,3176		173,884,1146	69.0	72.0	71.0		85	-0.4	0.0	7	dbSNP_100	71	1725,6875		170,1385,2745	yes	missense	CCL24	NM_002991.2	5	343,2269,3891	GG,GT,TT		20.0581,27.9165,22.7203	benign	29/120	75442730	2955,10051	2203	4300	6503	SO:0001583	missense	6369	exon2			AGGGGATGACCAC	U85768	CCDS34670.1	7q11.23	2013-02-25	2002-08-22	2002-08-23	ENSG00000106178	ENSG00000106178		"""Chemokine ligands"", ""Endogenous ligands"""	10623	protein-coding gene	gene with protein product	"""CK-beta-6"", ""myeloid progenitor inhibitory factor 2"", ""eotaxin-2"""	602495	"""small inducible cytokine subfamily A (Cys-Cys), member 24"""	SCYA24		9104803, 9598329	Standard	NM_002991		Approved	Ckb-6, MPIF-2, eotaxin-2, MPIF2	uc011kga.2	O00175	OTTHUMG00000156635	ENST00000416943.1:c.85A>C	7.37:g.75442730T>G	ENSP00000400533:p.Ile29Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_002991	B2R5K2	Missense_Mutation	SNP	ENST00000416943.1	37	CCDS34670.1	739	0.3383699633699634	141	0.2865853658536585	125	0.3453038674033149	325	0.5681818181818182	148	0.19525065963060687	.	6.304	0.424243	0.11928	0.279165	0.200581	ENSG00000106178	ENST00000222902;ENST00000416943	T;T	0.03689	3.84;3.84	3.61	-0.408	0.12381	Chemokine interleukin-8-like domain (1);	1.308000	0.05150	N	0.495911	T	0.00012	0.0000	L	0.37800	1.135	0.80722	P	0.0	B	0.11235	0.004	B	0.14023	0.01	T	0.35895	-0.9770	9	0.16420	T	0.52	.	9.5265	0.39167	0.0:0.0:0.5652:0.4348	rs2302006;rs11465292;rs60968338;rs2302006	29	O00175	CCL24_HUMAN	L	29	ENSP00000222902:I29L;ENSP00000400533:I29L	ENSP00000222902:I29L	I	-	1	0	CCL24	75280666	0.696000	0.27757	0.004000	0.12327	0.004000	0.04260	0.260000	0.18424	-0.058000	0.13177	-0.291000	0.09656	ATC	T|0.714;G|0.286	0.286	strong		0.562	CCL24-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344886.1	NM_002991	
PSD3	23362	hgsc.bcm.edu	37	8	18729459	18729459	+	Silent	SNP	T	T	C	rs13273954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:18729459T>C	ENST00000327040.8	-	3	1017	c.915A>G	c.(913-915)gaA>gaG	p.E305E	PSD3_ENST00000440756.2_Silent_p.E305E|PSD3_ENST00000523619.1_Silent_p.E240E	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	305					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		TCCACAGTATTTCCACTCCTT	0.522													C|||	1473	0.294129	0.3691	0.2406	5008	,	,		18807	0.3095		0.171	False		,,,				2504	0.3415				p.E305E		Atlas-SNP	.											.	PSD3	142	.	0			c.A915G						PASS	.	C		1275,2735		222,831,952	110.0	114.0	113.0		915	1.8	1.0	8	dbSNP_121	113	1336,6992		112,1112,2940	no	coding-synonymous	PSD3	NM_015310.3		334,1943,3892	CC,CT,TT		16.0423,31.7955,21.1623		305/1048	18729459	2611,9727	2005	4164	6169	SO:0001819	synonymous_variant	23362	exon3			CAGTATTTCCACT	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"""Pleckstrin homology (PH) domain containing"""	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.915A>G	8.37:g.18729459T>C		Somatic	314	1	0.00318471		WXS	Illumina HiSeq	Phase_I	377	136	0.360743	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Silent	SNP	ENST00000327040.8	37	CCDS43720.1																																																																																			C|0.267;N|0.001	0.267	strong		0.522	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310	
ANAPC15	25906	hgsc.bcm.edu	37	11	71821236	71821236	+	Silent	SNP	A	A	G	rs17161980	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:71821236A>G	ENST00000227618.4	-	5	441	c.216T>C	c.(214-216)gaT>gaC	p.D72D	ANAPC15_ENST00000538393.1_Silent_p.D72D|ANAPC15_ENST00000538919.1_Silent_p.D72D|ANAPC15_ENST00000542531.1_Silent_p.D72D|ANAPC15_ENST00000543050.1_Silent_p.D72D|ANAPC15_ENST00000535503.1_Silent_p.D72D|ANAPC15_ENST00000535234.1_Silent_p.D72D|LRTOMT_ENST00000419228.1_3'UTR|ANAPC15_ENST00000543587.1_Silent_p.D72D|ANAPC15_ENST00000545680.1_Silent_p.D72D|ANAPC15_ENST00000543015.1_5'UTR|ANAPC15_ENST00000502597.2_5'UTR|LRTOMT_ENST00000435085.1_3'UTR|LRTOMT_ENST00000307198.7_3'UTR|ANAPC15_ENST00000545944.1_Silent_p.D72D	NM_001278487.1|NM_001278491.1|NM_014042.2	NP_001265416.1|NP_001265420.1|NP_054761.1	P60006	APC15_HUMAN	anaphase promoting complex subunit 15	72	Asp-rich.				mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	anaphase-promoting complex (GO:0005680)|intracellular (GO:0005622)											tatcctcatcatcttcatcat	0.498													g|||	873	0.174321	0.208	0.1974	5008	,	,		23194	0.2242		0.0596	False		,,,				2504	0.1789				p.D72D		Atlas-SNP	.											.	.	.	.	0			c.T216C						PASS	.	G	,	819,3581	749.0+/-412.0	71,677,1452	329.0	281.0	297.0		,216	-5.3	0.5	11	dbSNP_123	297	451,8135	798.5+/-407.4	13,425,3855	no	utr-3,coding-synonymous	C11orf51,LRTOMT	NM_001145308.2,NM_014042.2	,	84,1102,5307	GG,GA,AA		5.2527,18.6136,9.7798	,	,72/122	71821236	1270,11716	2200	4293	6493	SO:0001819	synonymous_variant	25906	exon5			CTCATCATCTTCA	AL080071	CCDS8210.1, CCDS60880.1	11q13.4	2012-10-17	2012-05-31	2012-05-31	ENSG00000110200	ENSG00000110200		"""Anaphase promoting complex subunits"""	24531	protein-coding gene	gene with protein product		614717	"""chromosome 11 open reading frame 51"""	C11orf51		21926987	Standard	NM_014042		Approved	HSPC020, DKFZP564M082, APC15	uc001orw.3	P60006	OTTHUMG00000167865	ENST00000227618.4:c.216T>C	11.37:g.71821236A>G		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	190	84	0.442105	NM_014042	G3V1Q3|Q9CXK2|Q9Y269	Silent	SNP	ENST00000227618.4	37	CCDS8210.1																																																																																			A|0.864;G|0.136	0.136	strong		0.498	ANAPC15-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396695.1	NM_014042	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626724	140626724	+	Silent	SNP	T	T	G	rs3776091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140626724T>G	ENST00000231173.3	+	1	1578	c.1578T>G	c.(1576-1578)gcT>gcG	p.A526A		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	526	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)			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)			CCCTGCAGGCTTTCGAGTTCC	0.682													t|||	593	0.118411	0.1324	0.1787	5008	,	,		16249	0.0397		0.1561	False		,,,				2504	0.0992				p.A526A		Atlas-SNP	.											.	PCDHB15	138	.	0			c.T1578G						PASS	.	T		591,3815	766.0+/-413.4	51,489,1663	66.0	77.0	73.0		1578	-4.0	0.1	5	dbSNP_107	73	1397,7203	749.7+/-407.4	126,1145,3029	no	coding-synonymous	PCDHB15	NM_018935.2		177,1634,4692	GG,GT,TT		16.2442,13.4135,15.2853		526/788	140626724	1988,11018	2203	4300	6503	SO:0001819	synonymous_variant	56121	exon1			GCAGGCTTTCGAG	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.1578T>G	5.37:g.140626724T>G		Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	186	82	0.44086	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			T|0.852;G|0.148	0.148	strong		0.682	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
ADCK4	79934	hgsc.bcm.edu	37	19	41220529	41220529	+	Silent	SNP	C	C	T	rs11673492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	154	72	0.467532	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	
CUL9	23113	hgsc.bcm.edu	37	6	43182906	43182906	+	Silent	SNP	C	C	T	rs76552409	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43182906C>T	ENST00000252050.4	+	30	5862	c.5778C>T	c.(5776-5778)gtC>gtT	p.V1926V	CUL9_ENST00000372647.2_Silent_p.V1898V|CUL9_ENST00000354495.3_Silent_p.V1816V|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1926					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						GTACAGATGTCCTCTCTTGCA	0.612													C|||	43	0.00858626	0.0015	0.013	5008	,	,		18847	0.0		0.0278	False		,,,				2504	0.0041				p.V1926V		Atlas-SNP	.											.	CUL9	248	.	0			c.C5778T						PASS	.	C		31,4375	36.8+/-68.6	0,31,2172	107.0	105.0	106.0		5778	3.5	1.0	6	dbSNP_132	106	256,8344	100.1+/-161.6	3,250,4047	no	coding-synonymous	CUL9	NM_015089.2		3,281,6219	TT,TC,CC		2.9767,0.7036,2.2067		1926/2518	43182906	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon30			AGATGTCCTCTCT	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.5778C>T	6.37:g.43182906C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	110	0.973451	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.981;T|0.019	0.019	strong		0.612	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
MSRB2	22921	hgsc.bcm.edu	37	10	23408278	23408278	+	Silent	SNP	C	C	T	rs7427	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:23408278C>T	ENST00000376510.3	+	4	445	c.342C>T	c.(340-342)tcC>tcT	p.S114S	MSRB2_ENST00000468633.1_3'UTR	NM_012228.3	NP_036360.3	Q9Y3D2	MSRB2_HUMAN	methionine sulfoxide reductase B2	114					actin filament polymerization (GO:0030041)|protein repair (GO:0030091)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)	actin binding (GO:0003779)|peptide-methionine (R)-S-oxide reductase activity (GO:0033743)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	9					L-Methionine(DB00134)	CTTCGTTTTCCGAGGCTCATG	0.502													C|||	1130	0.225639	0.2315	0.1571	5008	,	,		20241	0.123		0.327	False		,,,				2504	0.2679				p.S114S	Esophageal Squamous(89;1240 1363 4973 30188 42299)	Atlas-SNP	.											.	MSRB2	21	.	0			c.C342T						PASS	.	C		906,3100		97,712,1194	106.0	107.0	107.0		342	-10.5	0.6	10	dbSNP_52	107	2897,5443		477,1943,1750	no	coding-synonymous	MSRB2	NM_012228.3		574,2655,2944	TT,TC,CC		34.7362,22.6161,30.8035		114/183	23408278	3803,8543	2003	4170	6173	SO:0001819	synonymous_variant	22921	exon4			GTTTTCCGAGGCT	AF122004	CCDS41495.1	10p12	2004-12-07	2004-12-06	2004-12-07	ENSG00000148450	ENSG00000148450			17061	protein-coding gene	gene with protein product		613782	"""methionine sulfoxide reductase B"""	MSRB		8749308, 10375640	Standard	NM_012228		Approved	PILB, CGI-131, CBS1, CBS-1	uc001iro.3	Q9Y3D2	OTTHUMG00000017812	ENST00000376510.3:c.342C>T	10.37:g.23408278C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	68	50	0.735294	NM_012228	Q17R44|Q4G1C7|Q9Y5W6	Silent	SNP	ENST00000376510.3	37	CCDS41495.1																																																																																			C|0.746;T|0.254	0.254	strong		0.502	MSRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047205.1	NM_012228	
ZNF181	339318	hgsc.bcm.edu	37	19	35232368	35232368	+	Missense_Mutation	SNP	G	G	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:35232368G>C	ENST00000492450.1	+	4	1171	c.1082G>C	c.(1081-1083)aGg>aCg	p.R361T	ZNF181_ENST00000459757.2_Missense_Mutation_p.R360T|ZNF181_ENST00000392232.3_Missense_Mutation_p.R405T			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	361					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.R297T(1)		endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TTCATTCATAGGTCATCTCTC	0.393																																					p.R361T		Atlas-SNP	.											ZNF181,NS,carcinoma,0,1	ZNF181	65	1	1	Substitution - Missense(1)	endometrium(1)	c.G1082C						scavenged	.						58.0	58.0	58.0					19																	35232368		2203	4300	6503	SO:0001583	missense	339318	exon4			TTCATAGGTCATC	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"""Zinc fingers, C2H2-type"", ""-"""	12971	protein-coding gene	gene with protein product		606741	"""zinc finger protein 181 (HHZ181)"""				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.1082G>C	19.37:g.35232368G>C	ENSP00000420727:p.Arg361Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	140	6	0.0428571	NM_001029997	B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	37	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	G	4.274	0.050021	0.08243	.	.	ENSG00000197841	ENST00000392232;ENST00000425140;ENST00000492450;ENST00000459757	T;T;T	0.07114	3.22;3.22;3.22	2.84	2.84	0.33178	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05731	0.0150	L	0.37897	1.145	0.09310	N	1	B;B	0.31790	0.34;0.288	B;B	0.24269	0.052;0.045	T	0.31998	-0.9923	9	0.22109	T	0.4	.	5.8316	0.18584	0.1455:0.0:0.8545:0.0	.	360;361	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	T	405;360;361;360	ENSP00000376065:R405T;ENSP00000420727:R361T;ENSP00000419435:R360T	ENSP00000376065:R405T	R	+	2	0	ZNF181	39924208	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-0.914000	0.04038	1.876000	0.54355	0.561000	0.74099	AGG	.	.	none		0.393	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997	
TEKT5	146279	hgsc.bcm.edu	37	16	10775932	10775932	+	Missense_Mutation	SNP	A	A	G	rs138988373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:10775932A>G	ENST00000283025.2	-	4	852	c.781T>C	c.(781-783)Tgt>Cgt	p.C261R		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	261						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						TCATCGATACACTGGGCCGAG	0.532													A|||	11	0.00219649	0.0	0.0058	5008	,	,		22117	0.0		0.006	False		,,,				2504	0.001				p.C261R		Atlas-SNP	.											.	TEKT5	66	.	0			c.T781C						PASS	.	A	ARG/CYS	3,4391	4.2+/-10.8	0,3,2194	277.0	214.0	235.0		781	3.9	0.7	16	dbSNP_134	235	29,8571	21.0+/-64.5	1,27,4272	yes	missense	TEKT5	NM_144674.1	180	1,30,6466	GG,GA,AA		0.3372,0.0683,0.2463	benign	261/486	10775932	32,12962	2197	4300	6497	SO:0001583	missense	146279	exon4			CGATACACTGGGC		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.781T>C	16.37:g.10775932A>G	ENSP00000283025:p.Cys261Arg	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	205	85	0.414634	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	1.395	-0.579606	0.03854	6.83E-4	0.003372	ENSG00000153060	ENST00000283025	T	0.02140	4.43	5.05	3.88	0.44766	.	0.349267	0.24492	N	0.038046	T	0.00754	0.0025	N	0.00661	-1.28	0.37910	D	0.931338	B	0.02656	0.0	B	0.01281	0.0	T	0.51655	-0.8678	10	0.15952	T	0.53	-5.2887	5.513	0.16890	0.7338:0.1763:0.0899:0.0	.	261	Q96M29	TEKT5_HUMAN	R	261	ENSP00000283025:C261R	ENSP00000283025:C261R	C	-	1	0	TEKT5	10683433	0.249000	0.23941	0.748000	0.31131	0.005000	0.04900	1.120000	0.31271	1.889000	0.54706	0.533000	0.62120	TGT	A|0.998;G|0.002	0.002	strong		0.532	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178634683	178634683	+	Missense_Mutation	SNP	C	C	T	rs11750821	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:178634683C>T	ENST00000251582.7	-	4	823	c.722G>A	c.(721-723)cGc>cAc	p.R241H	ADAMTS2_ENST00000274609.5_Missense_Mutation_p.R241H	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	241			R -> H (in dbSNP:rs11750821).		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)		GCCCAGGGCGCGGCTGAGGCT	0.672													c|||	360	0.071885	0.0106	0.0937	5008	,	,		14961	0.1052		0.1044	False		,,,				2504	0.0716				p.R241H		Atlas-SNP	.											ADAMTS2,right_upper_lobe,carcinoma,+1,1	ADAMTS2	190	1	0			c.G722A						PASS	.	T	HIS/ARG,HIS/ARG	87,4319	72.5+/-110.5	3,81,2119	71.0	63.0	66.0		722,722	-4.9	0.0	5	dbSNP_120	66	835,7765	191.7+/-237.8	33,769,3498	yes	missense,missense	ADAMTS2	NM_014244.4,NM_021599.2	29,29	36,850,5617	TT,TC,CC		9.7093,1.9746,7.089	benign,benign	241/1212,241/567	178634683	922,12084	2203	4300	6503	SO:0001583	missense	9509	exon4			AGGGCGCGGCTGA	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.722G>A	5.37:g.178634683C>T	ENSP00000251582:p.Arg241His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_021599		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	166	0.076007326007326	4	0.008130081300813009	28	0.07734806629834254	55	0.09615384615384616	79	0.10422163588390501	c	2.950	-0.216993	0.06101	0.019746	0.097093	ENSG00000087116	ENST00000251582;ENST00000274609	T;T	0.62105	0.12;0.05	5.49	-4.94	0.03057	.	1.174200	0.06781	N	0.785253	T	0.01124	0.0037	N	0.16478	0.41	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.07578	-1.0765	10	0.11794	T	0.64	.	7.9908	0.30239	0.101:0.3896:0.0:0.5094	rs11750821;rs11750821	241;241	O95450-2;O95450	.;ATS2_HUMAN	H	241	ENSP00000251582:R241H;ENSP00000274609:R241H	ENSP00000251582:R241H	R	-	2	0	ADAMTS2	178567289	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.826000	0.04429	-1.704000	0.01407	-3.259000	0.00049	CGC	C|0.931;T|0.069	0.069	strong		0.672	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
LRRC71	149499	hgsc.bcm.edu	37	1	156902281	156902281	+	Missense_Mutation	SNP	T	T	G	rs822431	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156902281T>G	ENST00000337428.7	+	14	1661	c.1507T>G	c.(1507-1509)Tcc>Gcc	p.S503A	LRRC71_ENST00000490146.1_3'UTR|ARHGEF11_ENST00000487682.1_5'Flank	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	503			S -> A (in dbSNP:rs822431).					p.S503A(1)		endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						GATGCAGTTCTCCAAGGCCAA	0.597													T|||	1417	0.282947	0.447	0.2997	5008	,	,		17869	0.2917		0.175	False		,,,				2504	0.1513				p.S503A		Atlas-SNP	.											LRRC71,NS,carcinoma,0,1	LRRC71	33	1	1	Substitution - Missense(1)	stomach(1)	c.T1507G						PASS	.	T	ALA/SER	1753,2541		395,963,789	65.0	75.0	72.0		1507	0.6	1.0	1	dbSNP_86	72	1468,7064		128,1212,2926	yes	missense	LRRC71	NM_144702.2	99	523,2175,3715	GG,GT,TT		17.2058,40.8244,25.1131	benign	503/560	156902281	3221,9605	2147	4266	6413	SO:0001583	missense	149499	exon14			CAGTTCTCCAAGG	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1507T>G	1.37:g.156902281T>G	ENSP00000336661:p.Ser503Ala	Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	247	241	0.975708	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	631	0.2889194139194139	204	0.4146341463414634	113	0.31215469613259667	188	0.32867132867132864	126	0.1662269129287599	T	9.430	1.085354	0.20390	0.408244	0.172058	ENSG00000160838	ENST00000337428	T	0.20598	2.06	4.59	0.602	0.17535	.	0.698180	0.12516	N	0.462092	T	0.03305	0.0096	L	0.29908	0.895	0.42428	P	0.007337999999999956	B;B	0.09022	0.0;0.002	B;B	0.09377	0.001;0.004	T	0.41645	-0.9497	9	0.23891	T	0.37	-17.0122	0.4647	0.00522	0.1848:0.2001:0.1681:0.4469	rs822431;rs60893033;rs822431	503;289	Q8N4P6;Q8N4P6-2	LRC71_HUMAN;.	A	503	ENSP00000336661:S503A	ENSP00000336661:S503A	S	+	1	0	LRRC71	155168905	0.114000	0.22134	0.998000	0.56505	0.956000	0.61745	-0.154000	0.10130	0.265000	0.21872	0.460000	0.39030	TCC	T|0.706;G|0.294	0.294	strong		0.597	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
PAX8	7849	hgsc.bcm.edu	37	2	113976146	113976146	+	Silent	SNP	T	T	C	rs368201100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:113976146T>C	ENST00000429538.3	-	12	1511	c.1317A>G	c.(1315-1317)gcA>gcG	p.A439A	AC016683.6_ENST00000456685.1_RNA|PAX8_ENST00000348715.5_3'UTR|PAX8_ENST00000397647.3_3'UTR|PAX8_ENST00000263335.7_3'UTR	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	439					anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						TGGTGGGCGGTGCACTCGGCC	0.517			T	PPARG	follicular thyroid		Thyroid dysgenesis						T|||	8	0.00159744	0.0	0.0014	5008	,	,		17403	0.0		0.006	False		,,,				2504	0.001				p.A439A	Ovarian(188;7 2067 9084 29802 29892)	Atlas-SNP	.		Dom	yes		2	2q12-q14	7849	paired box gene 8	yes	E	.	PAX8	42	.	0			c.A1317G						PASS	.	T	,,,	6,3874		0,6,1934	34.0	40.0	38.0		1317,,,	-6.1	0.0	2		38	37,8203		0,37,4083	no	coding-synonymous,utr-3,utr-3,utr-3	PAX8	NM_003466.3,NM_013952.3,NM_013953.3,NM_013992.3	,,,	0,43,6017	CC,CT,TT		0.449,0.1546,0.3548	,,,	439/451,,,	113976146	43,12077	1940	4120	6060	SO:0001819	synonymous_variant	7849	exon12			GGGCGGTGCACTC	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"""Paired boxes"", ""Homeoboxes / PRD class"""	8622	protein-coding gene	gene with protein product		167415	"""paired box gene 8"""			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.1317A>G	2.37:g.113976146T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_003466	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Silent	SNP	ENST00000429538.3	37	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	T	0.123	-1.122781	0.01785	0.001546	0.00449	ENSG00000125618	ENST00000468980	.	.	.	5.34	-6.12	0.02124	.	.	.	.	.	T	0.51907	0.1702	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56056	-0.8042	4	.	.	.	.	10.6988	0.45915	0.1148:0.5796:0.0:0.3056	.	.	.	.	A	162	.	.	T	-	1	0	PAX8	113692617	0.000000	0.05858	0.014000	0.15608	0.065000	0.16274	-4.294000	0.00258	-0.902000	0.03886	-1.054000	0.02325	ACC	.	.	weak		0.517	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5		
FKBP15	23307	hgsc.bcm.edu	37	9	115950156	115950156	+	Missense_Mutation	SNP	G	G	A	rs10465129	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:115950156G>A	ENST00000238256.3	-	14	1417	c.1300C>T	c.(1300-1302)Ctc>Ttc	p.L434F		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	434			L -> F (in dbSNP:rs10465129).		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.L434F(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GGTGCCTGGAGCCCAGTAACA	0.458													G|||	611	0.122005	0.0091	0.1138	5008	,	,		23480	0.2183		0.0736	False		,,,				2504	0.2311				p.L434F		Atlas-SNP	.											FKBP15_ENST00000238256,NS,carcinoma,0,1	FKBP15	128	1	1	Substitution - Missense(1)	stomach(1)	c.C1300T						PASS	.	G	PHE/LEU	67,3965		0,67,1949	81.0	85.0	84.0		1300	4.1	1.0	9	dbSNP_119	84	549,7817		17,515,3651	yes	missense	FKBP15	NM_015258.1	22	17,582,5600	AA,AG,GG		6.5623,1.6617,4.9685	probably-damaging	434/1220	115950156	616,11782	2016	4183	6199	SO:0001583	missense	23307	exon14			CCTGGAGCCCAGT	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.1300C>T	9.37:g.115950156G>A	ENSP00000238256:p.Leu434Phe	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	209	103	0.492823	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	231	0.10576923076923077	8	0.016260162601626018	33	0.09116022099447514	137	0.2395104895104895	53	0.06992084432717678	.	14.88	2.666880	0.47677	0.016617	0.065623	ENSG00000119321	ENST00000446284;ENST00000238256;ENST00000414250	T;T;T	0.32988	1.83;1.84;1.43	5.97	4.05	0.47172	.	.	.	.	.	T	0.00012	0.0000	L	0.52364	1.645	0.30854	P	0.7343189999999999	B;B;B;B	0.18610	0.029;0.016;0.016;0.009	B;B;B;B	0.20955	0.032;0.014;0.014;0.007	T	0.06006	-1.0851	8	0.45353	T	0.12	-10.9534	10.3509	0.43934	0.0:0.144:0.7077:0.1482	rs10465129;rs11558692;rs52793569;rs10465129	15;434;434;434	B4DVS2;Q5T1M5-2;Q5T1M5-3;Q5T1M5	.;.;.;FKB15_HUMAN	F	459;434;459	ENSP00000416158:L459F;ENSP00000238256:L434F;ENSP00000415733:L459F	ENSP00000238256:L434F	L	-	1	0	FKBP15	114989977	0.980000	0.34600	1.000000	0.80357	0.993000	0.82548	1.709000	0.37909	2.828000	0.97474	0.655000	0.94253	CTC	G|0.890;A|0.110	0.110	strong		0.458	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
OR51D1	390038	hgsc.bcm.edu	37	11	4661285	4661285	+	Missense_Mutation	SNP	A	A	G	rs905871	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	332	1	0.00301205		WXS	Illumina HiSeq	Phase_I	330	153	0.463636	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	
AKR1B15	441282	hgsc.bcm.edu	37	7	134261174	134261174	+	Missense_Mutation	SNP	A	A	G	rs2458502	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:134261174A>G	ENST00000457545.2	+	9	1077	c.817A>G	c.(817-819)Aca>Gca	p.T273A	AKR1B15_ENST00000423958.1_Missense_Mutation_p.T245A	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	273							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						CAAAAAAACCACAGCCCAGGT	0.448													A|||	5	0.000998403	0.0	0.0029	5008	,	,		21387	0.0		0.003	False		,,,				2504	0.0				p.T273A		Atlas-SNP	.											.	AKR1B15	105	.	0			c.A817G						PASS	.	A	ALA/THR	7,4399	12.9+/-30.5	0,7,2196	64.0	71.0	68.0		817	-6.9	0.0	7	dbSNP_100	68	48,8552	31.2+/-83.2	0,48,4252	no	missense	AKR1B15	NM_001080538.2	58	0,55,6448	GG,GA,AA		0.5581,0.1589,0.4229	benign	273/345	134261174	55,12951	2203	4300	6503	SO:0001583	missense	441282	exon9			AAAACCACAGCCC		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"""Aldo-keto reductases"""	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.817A>G	7.37:g.134261174A>G	ENSP00000389289:p.Thr273Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	77	17	0.220779	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	a	0.028	-1.354403	0.01256	0.001589	0.005581	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.16324	2.35;2.35	3.46	-6.91	0.01649	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.03178	0.0093	N	0.03071	-0.42	0.09310	N	0.999998	B;B	0.10296	0.0;0.003	B;B	0.12156	0.001;0.007	T	0.33904	-0.9850	9	0.33141	T	0.24	.	2.4069	0.04414	0.2716:0.2406:0.3777:0.1102	rs2458502	245;273	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	A	273;245	ENSP00000389289:T273A;ENSP00000397009:T245A	ENSP00000397009:T245A	T	+	1	0	AKR1B15	133911714	0.000000	0.05858	0.001000	0.08648	0.157000	0.22087	-5.815000	0.00096	-2.183000	0.00763	-1.140000	0.01884	ACA	A|0.998;G|0.002	0.002	strong		0.448	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
TNR	7143	hgsc.bcm.edu	37	1	175335234	175335234	+	Silent	SNP	C	C	T	rs1385541	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	284	0	0		WXS	Illumina HiSeq	Phase_I	308	114	0.37013	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	
CCDC178	374864	hgsc.bcm.edu	37	18	30928852	30928852	+	Splice_Site	SNP	A	A	G	rs140419270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:30928852A>G	ENST00000383096.3	-	8	640		c.e8+1		CCDC178_ENST00000579947.1_Splice_Site|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000402325.1_Splice_Site|CCDC178_ENST00000406524.2_Splice_Site|CCDC178_ENST00000403303.1_Splice_Site|CCDC178_ENST00000300227.8_Splice_Site|CCDC178_ENST00000583930.1_Splice_Site			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178									p.?(2)									GAACAACTTTACCTCTCTTTT	0.323													A|||	8	0.00159744	0.0	0.0029	5008	,	,		15391	0.0		0.005	False		,,,				2504	0.001				.		Atlas-SNP	.											.	.	.	.	2	Unknown(2)	lung(2)	c.457+2T>C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	132.0	111.0	118.0		,	4.2	0.8	18	dbSNP_134	118	31,8569	21.6+/-65.8	0,31,4269	yes	splice-5,splice-5	C18orf34	NM_001105528.1,NM_198995.2	,	0,36,6467	GG,GA,AA		0.3605,0.1135,0.2768	,	,	30928852	36,12970	2203	4300	6503	SO:0001630	splice_region_variant	374864	exon8			AACTTTACCTCTC	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.457+1T>C	18.37:g.30928852A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Splice_Site	SNP	ENST00000383096.3	37	CCDS42424.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	12.87	2.068210	0.36470	0.001135	0.003605	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0289	0.42087	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C18orf34	29182850	0.994000	0.37717	0.791000	0.31998	0.061000	0.15899	3.552000	0.53705	2.144000	0.66660	0.533000	0.62120	.	A|0.997;G|0.003	0.003	strong		0.323	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	Intron
PDE1C	5137	hgsc.bcm.edu	37	7	31855569	31855569	+	Silent	SNP	G	G	A	rs2302450	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000396184.3_Silent_p.A594A|PDE1C_ENST00000321453.7_Silent_p.A594A|PDE1C_ENST00000396182.2_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	282	0	0		WXS	Illumina HiSeq	Phase_I	372	106	0.284946	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		
FAM69B	138311	hgsc.bcm.edu	37	9	139617836	139617836	+	Silent	SNP	C	C	T	rs6874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139617836C>T	ENST00000371692.4	+	5	1002	c.906C>T	c.(904-906)aaC>aaT	p.N302N	SNHG7_ENST00000416970.1_RNA|FAM69B_ENST00000371691.1_Silent_p.N215N|SNHG7_ENST00000362567.2_RNA|SNHG7_ENST00000436596.1_RNA|SNHG7_ENST00000414282.1_RNA|SNHG7_ENST00000447221.1_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	88	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	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	
F5	2153	hgsc.bcm.edu	37	1	169498975	169498975	+	Missense_Mutation	SNP	T	T	C	rs6030	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:169498975T>C	ENST00000367797.3	-	16	5491	c.5290A>G	c.(5290-5292)Atg>Gtg	p.M1764V	F5_ENST00000367796.3_Missense_Mutation_p.M1769V	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1764	F5/8 type A 3.|Plastocyanin-like 6.		M -> V (in dbSNP:rs6030). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:3110773, ECO:0000269|PubMed:7874144}.		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)	CTCATGTCCATAGGCATGTTG	0.393													C|||	1546	0.308706	0.1732	0.4885	5008	,	,		19732	0.2837		0.3111	False		,,,				2504	0.3875				p.M1764V		Atlas-SNP	.											.	F5	301	.	0			c.A5290G	GRCh37	CM070090	F5	M	rs6030	PASS	.	C	VAL/MET	878,3528	744.5+/-411.6	87,704,1412	154.0	148.0	150.0		5290	-2.9	0.2	1	dbSNP_52	150	2886,5714	672.0+/-402.9	453,1980,1867	yes	missense	F5	NM_000130.4	21	540,2684,3279	CC,CT,TT		33.5581,19.9274,28.9405	benign	1764/2225	169498975	3764,9242	2203	4300	6503	SO:0001583	missense	2153	exon16			TGTCCATAGGCAT	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.5290A>G	1.37:g.169498975T>C	ENSP00000356771:p.Met1764Val	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	205	203	0.990244	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	639	0.2925824175824176	102	0.2073170731707317	161	0.4447513812154696	137	0.2395104895104895	239	0.3153034300791557	C	0.020	-1.433840	0.01108	0.199274	0.335581	ENSG00000198734	ENST00000367797;ENST00000367796	D;D	0.98602	-5.02;-5.02	5.32	-2.86	0.05717	Cupredoxin (2);	0.908379	0.09456	N	0.799742	T	0.78729	0.4329	N	0.03608	-0.345	0.19945	P	0.999945	B	0.02656	0.0	B	0.01281	0.0	T	0.72293	-0.4336	9	0.02654	T	1	-0.243	3.2522	0.06819	0.0923:0.1961:0.2724:0.4392	rs6030;rs3830171;rs17579170;rs61682329;rs6030	1764	P12259	FA5_HUMAN	V	1764;1769	ENSP00000356771:M1764V;ENSP00000356770:M1769V	ENSP00000356770:M1769V	M	-	1	0	F5	167765599	0.000000	0.05858	0.189000	0.23252	0.981000	0.71138	-2.414000	0.01037	-0.913000	0.03832	-0.226000	0.12346	ATG	T|0.711;C|0.288	0.288	strong		0.393	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
PAGE5	90737	hgsc.bcm.edu	37	X	55247817	55247817	+	Missense_Mutation	SNP	T	T	C	rs61745114	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:55247817T>C	ENST00000289619.5	+	2	307	c.62T>C	c.(61-63)aTg>aCg	p.M21T	PAGE5_ENST00000374955.3_Start_Codon_SNP_p.M1T|PAGE5_ENST00000374952.1_Start_Codon_SNP_p.M1T	NM_130467.3	NP_569734.2	Q96GU1	PAGE5_HUMAN	P antigen family, member 5 (prostate associated)	21										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8						GTGAGAGATATGAGTGAGCAT	0.363													T|||	7	0.0018543	0.0	0.0	3775	,	,		11913	0.0		0.006	False		,,,				2504	0.001				p.M21T		Atlas-SNP	.											.	PAGE5	20	.	0			c.T62C						PASS	.	T	THR/MET,THR/MET	11,3824		0,11,0,1621,571	98.0	80.0	86.0		2,62	1.1	0.0	X	dbSNP_129	86	80,6648		0,52,28,2376,1844	yes	missense,missense	PAGE5	NM_001013435.1,NM_130467.3	81,81	0,63,28,3997,2415	CC,CT,C,TT,T		1.1891,0.2868,0.8615	probably-damaging,probably-damaging	1/111,21/131	55247817	91,10472	2203	4300	6503	SO:0001583	missense	90737	exon2			GAGATATGAGTGA	AJ344352	CCDS14368.1, CCDS35306.1	Xp11.22	2009-08-18			ENSG00000158639	ENSG00000158639			29992	protein-coding gene	gene with protein product	"""cancer/testis antigen family 16, member 1"", ""cancer/testis antigen family 16, member 2"""					11920606, 11992404	Standard	XM_006724613		Approved	PAGE-5, CT16.1, CT16.2	uc004duk.3	Q96GU1	OTTHUMG00000021650	ENST00000289619.5:c.62T>C	X.37:g.55247817T>C	ENSP00000289619:p.Met21Thr	Somatic	622	0	0		WXS	Illumina HiSeq	Phase_I	278	272	0.978417	NM_130467	Q2NL97|Q5JUL0|Q8WWL9	Missense_Mutation	SNP	ENST00000289619.5	37	CCDS14368.1	4	0.0024110910186859553	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	.	9.512	1.106093	0.20632	0.002868	0.011891	ENSG00000158639	ENST00000289619;ENST00000374955;ENST00000374952	T;T;T	0.50813	1.66;1.75;0.73	1.09	1.09	0.20402	.	.	.	.	.	T	0.49081	0.1536	M	0.67397	2.05	0.54753	D	0.999989	D	0.60160	0.987	D	0.66196	0.942	T	0.55205	-0.8177	9	0.87932	D	0	.	4.0529	0.09803	0.0:0.0:0.0:1.0	rs61745114	21	Q96GU1	GGEE1_HUMAN	T	21;1;1	ENSP00000289619:M21T;ENSP00000364093:M1T;ENSP00000364090:M1T	ENSP00000289619:M21T	M	+	2	0	PAGE5	55264542	0.381000	0.25140	0.020000	0.16555	0.069000	0.16628	0.969000	0.29370	0.677000	0.31305	0.231000	0.17811	ATG	T|0.994;C|0.006	0.006	strong		0.363	PAGE5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056861.1	NM_130467	
TCEAL4	79921	hgsc.bcm.edu	37	X	102842041	102842041	+	Silent	SNP	T	T	C	rs11010	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:102842041T>C	ENST00000472745.1	+	3	990	c.438T>C	c.(436-438)caT>caC	p.H146H	TCEAL4_ENST00000468024.1_Silent_p.H146H|TCEAL4_ENST00000415568.2_Silent_p.H146H|TCEAL4_ENST00000472484.1_Silent_p.H146H|TCEAL4_ENST00000494801.1_Silent_p.H146H|TCEAL4_ENST00000372629.4_Silent_p.H289H			Q96EI5	TCAL4_HUMAN	transcription elongation factor A (SII)-like 4	146					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(2)|skin(2)	6						AGGCCATACATGATATGAATT	0.423													C|||	977	0.258808	0.357	0.1686	3775	,	,		16721	0.0308		0.2515	False		,,,				2504	0.1063				p.H146H		Atlas-SNP	.											.	TCEAL4	18	.	0			c.T438C						PASS	.	C	,,	1737,2098		333,820,251,479,320	122.0	125.0	124.0		438,438,438	-8.0	0.0	X	dbSNP_52	124	2459,4269		343,1084,689,1001,1183	no	coding-synonymous,coding-synonymous,coding-synonymous	TCEAL4	NM_001006935.1,NM_001006937.1,NM_024863.4	,,	676,1904,940,1480,1503	CC,CT,C,TT,T		36.5488,45.2934,39.7236	,,	146/216,146/216,146/216	102842041	4196,6367	2203	4300	6503	SO:0001819	synonymous_variant	79921	exon3			CATACATGATATG	AF314542	CCDS14510.2, CCDS76004.1	Xq22.2	2014-03-21			ENSG00000133142	ENSG00000133142			26121	protein-coding gene	gene with protein product						14702039, 16221301	Standard	XM_005262192		Approved	FLJ21174, WEX7	uc004ekn.3	Q96EI5	OTTHUMG00000022103	ENST00000472745.1:c.438T>C	X.37:g.102842041T>C		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001006935	Q8WY12|Q9H2H1|Q9H775	Silent	SNP	ENST00000472745.1	37	CCDS14510.2																																																																																			0|0.006;C|0.292	0.292	strong		0.423	TCEAL4-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252339.2	NM_024863	
HERC2	8924	hgsc.bcm.edu	37	15	28517454	28517454	+	Silent	SNP	G	G	T	rs28457230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:28517454G>T	ENST00000261609.7	-	9	1098	c.990C>A	c.(988-990)gcC>gcA	p.A330A		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)		TGGTGCCCTGGGCGGAACGCT	0.547																																					p.A330A		Atlas-SNP	.											.	HERC2	501	.	0			c.C990A						PASS	.	G		269,4137	118.4+/-156.1	0,269,1934	69.0	55.0	59.0		990	0.8	1.0	15	dbSNP_125	59	333,8267	99.3+/-160.8	0,333,3967	no	coding-synonymous	HERC2	NM_004667.4		0,602,5901	TT,TG,GG		3.8721,6.1053,4.6286		330/4835	28517454	602,12404	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon9			GCCCTGGGCGGAA	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.990C>A	15.37:g.28517454G>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	118	43	0.364407	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.938;T|0.062	0.062	strong		0.547	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
AKR7A3	22977	hgsc.bcm.edu	37	1	19612477	19612477	+	Missense_Mutation	SNP	C	C	T	rs2231198	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19612477C>T	ENST00000361640.4	-	3	952	c.412G>A	c.(412-414)Gtg>Atg	p.V138M		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	138			V -> M (in dbSNP:rs2231198). {ECO:0000269|PubMed:10383892, ECO:0000269|PubMed:15489334}.		cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		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;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCAAGCTCCACGAACTTGCCC	0.612													C|||	2320	0.463259	0.3646	0.5432	5008	,	,		19169	0.6905		0.3817	False		,,,				2504	0.3896				p.V138M		Atlas-SNP	.											.	AKR7A3	30	.	0			c.G412A						PASS	.	C	MET/VAL	1614,2784		319,976,904	58.0	54.0	55.0		412	3.0	1.0	1	dbSNP_98	55	3110,5490		564,1982,1754	no	missense	AKR7A3	NM_012067.2	21	883,2958,2658	TT,TC,CC		36.1628,36.6985,36.3441	benign	138/332	19612477	4724,8274	2199	4300	6499	SO:0001583	missense	22977	exon3			GCTCCACGAACTT	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"""Aldo-keto reductases"""	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.412G>A	1.37:g.19612477C>T	ENSP00000355377:p.Val138Met	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	132	32	0.242424	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Missense_Mutation	SNP	ENST00000361640.4	37	CCDS193.1	1072	0.4908424908424908	187	0.3800813008130081	194	0.5359116022099447	411	0.7185314685314685	280	0.36939313984168864	.	6.831	0.522560	0.13066	0.366985	0.361628	ENSG00000162482	ENST00000361640	T	0.23348	1.91	3.04	3.04	0.35103	NADP-dependent oxidoreductase domain (3);	0.240515	0.40640	N	0.001046	T	0.00012	0.0000	M	0.82823	2.61	0.41505	P	0.011692999999999953	B	0.32543	0.375	B	0.24974	0.057	T	0.34453	-0.9828	9	0.41790	T	0.15	.	5.9087	0.19016	0.0:0.8521:0.0:0.1479	rs2231198;rs11539611;rs13374777;rs17852954;rs59246333	138	O95154	ARK73_HUMAN	M	138	ENSP00000355377:V138M	ENSP00000355377:V138M	V	-	1	0	AKR7A3	19485064	1.000000	0.71417	1.000000	0.80357	0.263000	0.26337	2.346000	0.44027	1.542000	0.49330	0.194000	0.17425	GTG	C|0.603;T|0.397	0.397	strong		0.612	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
ZNF184	7738	hgsc.bcm.edu	37	6	27425185	27425185	+	Missense_Mutation	SNP	C	C	A	rs386698292|rs1883216	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	111	62	0.558559	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	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383137	41383137	+	Silent	SNP	C	C	T	rs148915421	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	243	1	0.00411523		WXS	Illumina HiSeq	Phase_I	173	67	0.387283	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	
KCNA6	3742	hgsc.bcm.edu	37	12	4920767	4920767	+	Silent	SNP	T	T	C	rs34642709	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:4920767T>C	ENST00000280684.3	+	1	2426	c.1560T>C	c.(1558-1560)taT>taC	p.Y520Y	KCNA6_ENST00000433855.1_Silent_p.Y520Y|RP11-234B24.4_ENST00000542988.1_lincRNA			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	520					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)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|endometrium(5)|large_intestine(6)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(5)	49					Dalfampridine(DB06637)	ATCGGGCCTATGCAGAGAAAA	0.577										HNSCC(72;0.22)			T|||	67	0.0133786	0.0015	0.0043	5008	,	,		20418	0.0		0.0189	False		,,,				2504	0.044				p.Y520Y		Atlas-SNP	.											.	KCNA6	122	.	0			c.T1560C						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	55.0	59.0	58.0		1560	1.4	0.1	12	dbSNP_126	58	154,8446	72.6+/-135.2	2,150,4148	no	coding-synonymous	KCNA6	NM_002235.3		2,157,6344	CC,CT,TT		1.7907,0.1589,1.2379		520/530	4920767	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	3742	exon1			GGCCTATGCAGAG	X17622	CCDS8534.1	12p13	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6225	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 96"""	176257				16382104	Standard	NM_002235		Approved	Kv1.6, HBK2, PPP1R96	uc001qng.3	P17658		ENST00000280684.3:c.1560T>C	12.37:g.4920767T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_002235		Silent	SNP	ENST00000280684.3	37	CCDS8534.1																																																																																			T|0.987;C|0.013	0.013	strong		0.577	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235	
UMODL1	89766	hgsc.bcm.edu	37	21	43557698	43557698	+	Missense_Mutation	SNP	A	A	C	rs3819142	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43557698A>C	ENST00000408910.2	+	22	3925	c.3925A>C	c.(3925-3927)Aac>Cac	p.N1309H	UMODL1_ENST00000408989.2_Missense_Mutation_p.N1437H|UMODL1_ENST00000400427.1_Missense_Mutation_p.N1365H|UMODL1_ENST00000400424.2_Missense_Mutation_p.N1237H|UMODL1_ENST00000400423.2_3'UTR	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	175	0	0		WXS	Illumina HiSeq	Phase_I	162	59	0.364198	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		
SCYL2	55681	hgsc.bcm.edu	37	12	100709420	100709420	+	Silent	SNP	C	C	T	rs10860577	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:100709420C>T	ENST00000360820.2	+	9	1617	c.1180C>T	c.(1180-1182)Cta>Tta	p.L394L		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	394					endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						GCCCAATGTTCTACTTATTGC	0.398													C|||	553	0.110423	0.1263	0.1239	5008	,	,		15891	0.003		0.1998	False		,,,				2504	0.0982				p.L394L		Atlas-SNP	.											SCYL2,colon,carcinoma,-1,1	SCYL2	99	1	0			c.C1180T						PASS	.	C		536,3870	242.1+/-252.3	39,458,1706	110.0	102.0	105.0		1180	2.4	1.0	12	dbSNP_120	105	1541,7059	289.8+/-299.5	135,1271,2894	no	coding-synonymous	SCYL2	NM_017988.4		174,1729,4600	TT,TC,CC		17.9186,12.1652,15.9696		394/930	100709420	2077,10929	2203	4300	6503	SO:0001819	synonymous_variant	55681	exon9			AATGTTCTACTTA	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.1180C>T	12.37:g.100709420C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Silent	SNP	ENST00000360820.2	37	CCDS9076.1																																																																																			C|0.853;T|0.147	0.147	strong		0.398	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988	
TOPAZ1	375337	hgsc.bcm.edu	37	3	44283817	44283817	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:44283817C>T	ENST00000309765.4	+	1	440	c.272C>T	c.(271-273)cCg>cTg	p.P91L		NM_001145030.1	NP_001138502.1	Q8N9V7	TOPZ1_HUMAN	testis and ovary specific PAZ domain containing 1	91						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)	p.P91L(1)									CCGGTGAGCCCGTCAGACTCG	0.602																																					p.P91L		Atlas-SNP	.											C3orf77_ENST00000309765,NS,carcinoma,-1,3	.	.	3	1	Substitution - Missense(1)	breast(1)	c.C272T						scavenged	.						61.0	60.0	60.0					3																	44283817		692	1591	2283	SO:0001583	missense	375337	exon1			TGAGCCCGTCAGA	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.272C>T	3.37:g.44283817C>T	ENSP00000310303:p.Pro91Leu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	154	2	0.012987	NM_001145030		Missense_Mutation	SNP	ENST00000309765.4	37	CCDS46809.1	.	.	.	.	.	.	.	.	.	.	c	6.072	0.381524	0.11524	.	.	ENSG00000173769	ENST00000309765	T	0.10763	2.84	2.7	-1.29	0.09288	.	1.573250	0.04556	N	0.390834	T	0.07007	0.0178	N	0.24115	0.695	0.09310	N	1	B	0.17465	0.022	B	0.06405	0.002	T	0.38023	-0.9680	10	0.41790	T	0.15	1.7087	2.7521	0.05284	0.2061:0.4131:0.0:0.3808	.	91	Q8N9V7	CC077_HUMAN	L	91	ENSP00000310303:P91L	ENSP00000310303:P91L	P	+	2	0	C3orf77	44258821	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.294000	0.02767	-0.314000	0.08716	-0.701000	0.03672	CCG	.	.	none		0.602	TOPAZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343247.1	NM_001145030	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489753	32489753	+	Missense_Mutation	SNP	C	C	T	rs41544215	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489753C>T	ENST00000374975.3	-	2	361	c.299G>A	c.(298-300)aGg>aAg	p.R100K		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						CGCGGCGCGCCTGTCTTCCAG	0.662																																					p.R100K		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.G299A						PASS	.	C	LYS/ARG	193,3701		62,69,1816	36.0	32.0	33.0		299	-9.4	0.0	6	dbSNP_127	33	210,7310		48,114,3598	no	missense	HLA-DRB5	NM_002125.3	26	110,183,5414	TT,TC,CC		2.7926,4.9563,3.5308	benign	100/267	32489753	403,11011	1947	3760	5707	SO:0001583	missense	3127	exon2			GCGCGCCTGTCTT		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.299G>A	6.37:g.32489753C>T	ENSP00000364114:p.Arg100Lys	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	27	25	0.925926	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	92	0.04212454212454213	32	0.06504065040650407	21	0.058011049723756904	9	0.015734265734265736	30	0.0395778364116095	.	4.604	0.112185	0.08831	0.049563	0.027926	ENSG00000198502	ENST00000374975	T	0.00314	8.14	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);	5.372110	0.00166	N	0.000006	T	0.00039	0.0001	N	0.11756	0.17	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.29942	0.006;0.109	T	0.39014	-0.9634	10	0.10636	T	0.68	.	2.9021	0.05709	0.1516:0.3667:0.2298:0.2519	.	27;100	Q29973;Q30154	.;DRB5_HUMAN	K	100	ENSP00000364114:R100K	ENSP00000364114:R100K	R	-	2	0	HLA-DRB5	32597731	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-12.951000	0.00001	-4.402000	0.00051	-2.111000	0.00353	AGG	T|0.078;C|0.922	0.078	strong		0.662	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
HRNR	388697	hgsc.bcm.edu	37	1	152191082	152191082	+	Missense_Mutation	SNP	C	C	G	rs139947063	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152191082C>G	ENST00000368801.2	-	3	3098	c.3023G>C	c.(3022-3024)aGc>aCc	p.S1008T	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1008					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)			ACGGCTAGGGCTAGGAGACTG	0.597													C|||	5	0.000998403	0.0	0.0	5008	,	,		23723	0.0		0.003	False		,,,				2504	0.002				p.S1008T		Atlas-SNP	.											.	HRNR	403	.	0			c.G3023C						PASS	.						116.0	125.0	122.0					1																	152191082		2203	4298	6501	SO:0001583	missense	388697	exon3			CTAGGGCTAGGAG	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.3023G>C	1.37:g.152191082C>G	ENSP00000357791:p.Ser1008Thr	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	229	100	0.436681	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	9.293	1.051238	0.19827	.	.	ENSG00000197915	ENST00000368801	T	0.01647	4.71	3.45	3.45	0.39498	.	.	.	.	.	T	0.00695	0.0023	N	0.19112	0.55	0.09310	N	1	D	0.53885	0.963	P	0.46825	0.528	T	0.53535	-0.8425	9	0.13108	T	0.6	.	10.7277	0.46079	0.0:1.0:0.0:0.0	.	1008	Q86YZ3	HORN_HUMAN	T	1008	ENSP00000357791:S1008T	ENSP00000357791:S1008T	S	-	2	0	HRNR	150457706	0.001000	0.12720	0.004000	0.12327	0.211000	0.24417	1.099000	0.31013	1.957000	0.56846	0.551000	0.68910	AGC	A|0.002;C|0.998;G|0.000	0.000	strong		0.597	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
GPATCH1	55094	hgsc.bcm.edu	37	19	33605300	33605300	+	Missense_Mutation	SNP	A	A	G	rs10416265	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:33605300A>G	ENST00000170564.2	+	15	2485	c.2171A>G	c.(2170-2172)cAt>cGt	p.H724R		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	724			H -> R (in dbSNP:rs10416265). {ECO:0000269|PubMed:17974005}.		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)					GAGGAAGAGCATGCACCAGAA	0.438													G|||	2967	0.592452	0.7239	0.3386	5008	,	,		18961	0.8433		0.2475	False		,,,				2504	0.6912				p.H724R	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.A2171G						PASS	.	G	ARG/HIS	2963,1443	466.2+/-354.4	998,967,238	70.0	77.0	75.0		2171	-8.9	0.0	19	dbSNP_119	75	2340,6260	703.4+/-405.3	294,1752,2254	yes	missense	GPATCH1	NM_018025.2	29	1292,2719,2492	GG,GA,AA		27.2093,32.7508,40.7735	benign	724/932	33605300	5303,7703	2203	4300	6503	SO:0001583	missense	55094	exon15			AAGAGCATGCACC	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.2171A>G	19.37:g.33605300A>G	ENSP00000170564:p.His724Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Missense_Mutation	SNP	ENST00000170564.2	37	CCDS12428.1	1164	0.532967032967033	358	0.7276422764227642	116	0.32044198895027626	493	0.8618881118881119	197	0.2598944591029024	G	3.646	-0.072520	0.07228	0.672492	0.272093	ENSG00000076650	ENST00000170564	T	0.20332	2.08	5.32	-8.87	0.00792	.	1.955520	0.02032	N	0.048608	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	0.24764	-1.0151	9	0.14656	T	0.56	4.8647	9.3731	0.38266	0.2957:0.3351:0.3692:0.0	rs10416265;rs60644468;rs10416265	724;724	B2RDX4;Q9BRR8	.;GPTC1_HUMAN	R	724	ENSP00000170564:H724R	ENSP00000170564:H724R	H	+	2	0	GPATCH1	38297140	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.933000	0.01553	-2.702000	0.00398	-0.748000	0.03510	CAT	A|0.517;G|0.483	0.483	strong		0.438	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
PDE6A	5145	hgsc.bcm.edu	37	5	149245754	149245754	+	Silent	SNP	A	A	G	rs17110644	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149245754A>G	ENST00000255266.5	-	20	2456	c.2337T>C	c.(2335-2337)ttT>ttC	p.F779F		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	779					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	AGGTGCAAACAAAGTCAATGA	0.458													A|||	274	0.0547125	0.1044	0.0865	5008	,	,		20697	0.005		0.0278	False		,,,				2504	0.044				p.F779F		Atlas-SNP	.											.	PDE6A	98	.	0			c.T2337C						PASS	.	A		404,4002	201.5+/-224.5	22,360,1821	161.0	147.0	152.0		2337	-6.7	0.4	5	dbSNP_123	152	318,8282	113.7+/-173.7	6,306,3988	no	coding-synonymous	PDE6A	NM_000440.2		28,666,5809	GG,GA,AA		3.6977,9.1693,5.5513		779/861	149245754	722,12284	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon20			GCAAACAAAGTCA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.2337T>C	5.37:g.149245754A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	89	32	0.359551	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			A|0.946;G|0.054	0.054	strong		0.458	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
PLEKHG2	64857	hgsc.bcm.edu	37	19	39905888	39905888	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:39905888C>T	ENST00000409794.3	+	3	1216	c.366C>T	c.(364-366)cgC>cgT	p.R122R	PLEKHG2_ENST00000425673.1_Silent_p.R122R|PLEKHG2_ENST00000409797.2_Silent_p.R122R|PLEKHG2_ENST00000378550.1_Silent_p.R122R|PLEKHG2_ENST00000458508.2_Silent_p.R63R	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	122	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)			GGGACCTCCGCAGCATCGTGG	0.647																																					p.R122R		Atlas-SNP	.											PLEKHG2_ENST00000409794,colon,carcinoma,+1,2	PLEKHG2	329	2	0			c.C366T						scavenged	.						37.0	34.0	35.0					19																	39905888		2198	4297	6495	SO:0001819	synonymous_variant	64857	exon3			CCTCCGCAGCATC	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.366C>T	19.37:g.39905888C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	2	0.025	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	C	8.701	0.909832	0.17833	.	.	ENSG00000090924	ENST00000205135	.	.	.	4.63	1.05	0.20165	.	.	.	.	.	T	0.43188	0.1236	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26710	-1.0095	4	.	.	.	.	2.4055	0.04412	0.187:0.4957:0.2082:0.1091	.	.	.	.	V	19	.	.	A	+	2	0	PLEKHG2	44597728	0.983000	0.35010	0.995000	0.50966	0.653000	0.38743	0.021000	0.13489	0.559000	0.29153	0.491000	0.48974	GCA	.	.	none		0.647	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
PZP	5858	hgsc.bcm.edu	37	12	9315209	9315209	+	Silent	SNP	A	A	G	rs10771381	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:9315209A>G	ENST00000261336.2	-	22	2800	c.2772T>C	c.(2770-2772)tcT>tcC	p.S924S	PZP_ENST00000381997.2_Silent_p.S710S|PZP_ENST00000539983.1_5'UTR	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	924					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						CACAGGTCATAGAACTGAAAG	0.388													G|||	2036	0.40655	0.3933	0.366	5008	,	,		-128	0.4226		0.3966	False		,,,				2504	0.4468				p.S924S	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.T2772C						PASS	.	G		1870,2536	630.9+/-395.5	405,1060,738	151.0	134.0	140.0		2772	-4.4	0.0	12	dbSNP_120	140	3698,4902	620.1+/-397.0	802,2094,1404	no	coding-synonymous	PZP	NM_002864.2		1207,3154,2142	GG,GA,AA		43.0,42.4421,42.811		924/1483	9315209	5568,7438	2203	4300	6503	SO:0001819	synonymous_variant	5858	exon22			GGTCATAGAACTG	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.2772T>C	12.37:g.9315209A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																			A|0.580;G|0.420	0.420	strong		0.388	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
DHX37	57647	hgsc.bcm.edu	37	12	125453115	125453115	+	Missense_Mutation	SNP	C	C	T	rs11057939	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	48	0	0		WXS	Illumina HiSeq	Phase_I	46	15	0.326087	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	
JAKMIP3	282973	hgsc.bcm.edu	37	10	133950642	133950642	+	Silent	SNP	T	T	C	rs75996870	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:133950642T>C	ENST00000298622.4	+	6	1374	c.1236T>C	c.(1234-1236)gaT>gaC	p.D412D		NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	412						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)		ACCTCATAGATGAACTGTCTA	0.522													T|||	402	0.0802716	0.0023	0.0101	5008	,	,		18350	0.3016		0.0308	False		,,,				2504	0.0583				p.D412D		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.T1236C						PASS	.			29,3789		0,29,1880	97.0	100.0	99.0		1236	-9.4	0.2	10	dbSNP_132	99	281,7953		3,275,3839	no	coding-synonymous	JAKMIP3	NM_001105521.2		3,304,5719	CC,CT,TT		3.4127,0.7596,2.5722		412/845	133950642	310,11742	1909	4117	6026	SO:0001819	synonymous_variant	282973	exon6			CATAGATGAACTG	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.1236T>C	10.37:g.133950642T>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	162	79	0.487654	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			T|0.912;C|0.088	0.088	strong		0.522	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303	
FAM98C	147965	hgsc.bcm.edu	37	19	38893856	38893856	+	Silent	SNP	G	G	C	rs3745957	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38893856G>C	ENST00000252530.5	+	1	82	c.63G>C	c.(61-63)ctG>ctC	p.L21L	FAM98C_ENST00000343358.7_Silent_p.L21L|FAM98C_ENST00000588262.1_Silent_p.L21L	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	21										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)			TGCTGGCTCTGGGGTAAAAGG	0.701													G|||	654	0.130591	0.0227	0.1398	5008	,	,		10294	0.2857		0.0785	False		,,,				2504	0.1636				p.L21L		Atlas-SNP	.											.	FAM98C	39	.	0			c.G63C						PASS	.	G		104,4036		1,102,1967	14.0	21.0	19.0		63	-5.1	0.2	19	dbSNP_107	19	454,7934		9,436,3749	no	coding-synonymous	FAM98C	NM_174905.3		10,538,5716	CC,CG,GG		5.4125,2.5121,4.454		21/350	38893856	558,11970	2070	4194	6264	SO:0001819	synonymous_variant	147965	exon1			GGCTCTGGGGTAA		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.63G>C	19.37:g.38893856G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	73	28	0.383562	NM_174905	A6NMW3|Q66K45	Silent	SNP	ENST00000252530.5	37	CCDS42562.1																																																																																			G|0.900;C|0.100	0.100	strong		0.701	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905	
C10orf71	118461	hgsc.bcm.edu	37	10	50532588	50532588	+	Missense_Mutation	SNP	C	C	G	rs10857469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	84	0	0		WXS	Illumina HiSeq	Phase_I	59	17	0.288136	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	
MADD	8567	hgsc.bcm.edu	37	11	47306585	47306585	+	Missense_Mutation	SNP	G	G	A	rs1051006	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47306585G>A	ENST00000311027.5	+	13	2416	c.2251G>A	c.(2251-2253)Gtg>Atg	p.V751M	MADD_ENST00000395344.3_Missense_Mutation_p.V751M|MADD_ENST00000402799.1_Missense_Mutation_p.V751M|MADD_ENST00000406482.1_Missense_Mutation_p.V751M|MADD_ENST00000342922.4_Missense_Mutation_p.V751M|MADD_ENST00000407859.3_Missense_Mutation_p.V751M|MADD_ENST00000402192.2_Missense_Mutation_p.V751M|MADD_ENST00000349238.3_Missense_Mutation_p.V751M|MADD_ENST00000395336.3_Missense_Mutation_p.V751M	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)		CAAATCGAACGTGGACAGACG	0.552													G|||	1678	0.335064	0.3873	0.2608	5008	,	,		19647	0.622		0.162	False		,,,				2504	0.1994				p.V751M		Atlas-SNP	.											.	MADD	172	.	0			c.G2251A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1517,2885	481.4+/-359.1	266,985,950	91.0	88.0	89.0		2251,2251,2251,2251,2251,2251,2251,2251,2251,2251	-5.5	0.0	11	dbSNP_86	89	1414,7182	271.7+/-289.7	118,1178,3002	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	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	21,21,21,21,21,21,21,21,21,21	384,2163,3952	AA,AG,GG		16.4495,34.4616,22.5496	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	751/1545,751/1542,751/1648,751/1589,751/1566,751/1546,751/1609,751/1480,751/1582,751/1588	47306585	2931,10067	2201	4298	6499	SO:0001583	missense	8567	exon13			TCGAACGTGGACA	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.2251G>A	11.37:g.47306585G>A	ENSP00000310933:p.Val751Met	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_130474		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	711	0.32554945054945056	153	0.31097560975609756	100	0.27624309392265195	331	0.5786713286713286	127	0.16754617414248021	G	11.28	1.593369	0.28357	0.344616	0.164495	ENSG00000110514	ENST00000342922;ENST00000395342;ENST00000402799;ENST00000406482;ENST00000349238;ENST00000311027;ENST00000407859;ENST00000395344;ENST00000395336;ENST00000402192	T;T;T;T;T;T;T;T;T	0.06068	3.42;3.35;3.35;3.41;3.4;3.36;3.36;3.4;3.42	5.88	-5.48	0.02592	.	0.643077	0.16526	N	0.210600	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	1.999999999946489E-6	B;B;B;B;B;B;B;B;B;B	0.27932	0.122;0.008;0.006;0.013;0.062;0.194;0.002;0.006;0.003;0.003	B;B;B;B;B;B;B;B;B;B	0.20577	0.014;0.001;0.005;0.004;0.012;0.03;0.002;0.004;0.002;0.005	T	0.37549	-0.9701	9	0.35671	T	0.21	0.0134	4.5741	0.12225	0.5719:0.1332:0.1482:0.1467	rs1051006;rs3736103;rs17702266;rs58641924;rs1051006	751;751;751;751;751;751;751;751;751;751	B5MEE5;A8K8S7;Q8WXG6-7;F8W9P9;Q8WXG6-6;Q8WXG6-5;Q8WXG6-2;Q8WXG6-4;Q8WXG6;Q8WXG6-3	.;.;.;.;.;.;.;.;MADD_HUMAN;.	M	751	ENSP00000343902:V751M;ENSP00000385585:V751M;ENSP00000384435:V751M;ENSP00000304505:V751M;ENSP00000310933:V751M;ENSP00000384204:V751M;ENSP00000378753:V751M;ENSP00000378745:V751M;ENSP00000384287:V751M	ENSP00000310933:V751M	V	+	1	0	MADD	47263161	0.000000	0.05858	0.000000	0.03702	0.994000	0.84299	-0.823000	0.04443	-0.592000	0.05851	0.655000	0.94253	GTG	G|0.733;A|0.267	0.267	strong		0.552	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
MYOF	26509	hgsc.bcm.edu	37	10	95093619	95093619	+	Missense_Mutation	SNP	G	G	A	rs61861290	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:95093619G>A	ENST00000359263.4	-	42	4614	c.4615C>T	c.(4615-4617)Ccc>Tcc	p.P1539S	MYOF_ENST00000371502.4_Missense_Mutation_p.P1558S|MYOF_ENST00000371501.4_Missense_Mutation_p.P1539S|MYOF_ENST00000358334.5_Missense_Mutation_p.P1526S	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1539	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)	p.P1539A(1)		NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						AACTGTCTGGGAGGGGCTGGC	0.572													G|||	31	0.0061901	0.0008	0.0144	5008	,	,		15295	0.0		0.0189	False		,,,				2504	0.001				p.P1539S		Atlas-SNP	.											MYOF,trunk,malignant_melanoma,0,1	MYOF	177	1	1	Substitution - Missense(1)	skin(1)	c.C4615T						scavenged	.	G	SER/PRO,SER/PRO	14,4096		0,14,2041	51.0	54.0	53.0		4615,4576	5.2	1.0	10	dbSNP_129	53	142,8288		0,142,4073	yes	missense,missense	MYOF	NM_013451.3,NM_133337.2	74,74	0,156,6114	AA,AG,GG		1.6845,0.3406,1.244	possibly-damaging,possibly-damaging	1539/2062,1526/2049	95093619	156,12384	2055	4215	6270	SO:0001583	missense	26509	exon42			GTCTGGGAGGGGC	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4615C>T	10.37:g.95093619G>A	ENSP00000352208:p.Pro1539Ser	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	75	20	0.266667	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	37	CCDS41551.1	24	0.01098901098901099	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	15	0.01978891820580475	G	27.1	4.797467	0.90538	0.003406	0.016845	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	5.23	5.23	0.72850	C2 membrane targeting protein (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.38188	0.1031	L	0.53249	1.67	0.80722	D	1	P;D	0.55800	0.918;0.973	P;P	0.54346	0.749;0.685	T	0.40942	-0.9536	10	0.45353	T	0.12	-14.1993	18.9988	0.92824	0.0:0.0:1.0:0.0	rs61861290	1526;1539	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	S	1526;1539;1539;1558	ENSP00000351094:P1526S;ENSP00000352208:P1539S;ENSP00000360556:P1539S;ENSP00000360557:P1558S	ENSP00000351094:P1526S	P	-	1	0	MYOF	95083609	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.263000	0.95617	2.721000	0.93114	0.650000	0.86243	CCC	G|0.988;A|0.012	0.012	strong		0.572	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
MLXIP	22877	hgsc.bcm.edu	37	12	122618131	122618131	+	Silent	SNP	A	A	G	rs36045144	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:122618131A>G	ENST00000319080.7	+	9	1461	c.1329A>G	c.(1327-1329)ccA>ccG	p.P443P	MLXIP_ENST00000377037.2_Silent_p.P33P|MLXIP_ENST00000538698.1_Silent_p.P50P					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		GCCCCGCCCCACCGCCCATCT	0.652													A|||	1128	0.22524	0.2042	0.1974	5008	,	,		10846	0.2738		0.2306	False		,,,				2504	0.2178				p.P443P	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.A1329G						PASS	.	A		753,3347		82,589,1379	17.0	19.0	19.0		919	-10.0	0.0	12	dbSNP_126	19	1468,6918		136,1196,2861	no	coding-synonymous	MLXIP	NM_014938.3		218,1785,4240	GG,GA,AA		17.5054,18.3659,17.7879		443/920	122618131	2221,10265	2050	4193	6243	SO:0001819	synonymous_variant	22877	exon9			CGCCCCACCGCCC	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1329A>G	12.37:g.122618131A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	115	62	0.53913	NM_014938		Silent	SNP	ENST00000319080.7	37																																																																																				A|0.784;G|0.216;T|0.000	0.216	strong		0.652	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296423	39296423	+	Missense_Mutation	SNP	C	C	T	rs349790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39296423C>T	ENST00000345847.4	-	1	316	c.317G>A	c.(316-318)cGt>cAt	p.R106H		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	106	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GCAGCTGGGACGGCAGCAAGT	0.652													C|||	64	0.0127796	0.0023	0.0303	5008	,	,		18713	0.006		0.0149	False		,,,				2504	0.0194				p.R106H		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,0,2	KRTAP4-6	46	2	0			c.G317A						scavenged	.																																			SO:0001583	missense	81871	exon1			CTGGGACGGCAGC	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.317G>A	17.37:g.39296423C>T	ENSP00000328270:p.Arg106His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	152	11	0.0723684	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	31	0.014194139194139194	5	0.01016260162601626	4	0.011049723756906077	6	0.01048951048951049	16	0.021108179419525065	.	11.71	1.719810	0.30503	.	.	ENSG00000198090	ENST00000345847	T	0.01505	4.82	5.0	-8.28	0.01013	.	209.318000	0.00520	U	0.000185	T	0.01695	0.0054	M	0.76838	2.35	0.09310	N	1	.	.	.	.	.	.	T	0.38373	-0.9664	8	0.38643	T	0.18	.	4.1396	0.10188	0.0982:0.3223:0.0969:0.4827	.	.	.	.	H	106	ENSP00000328270:R106H	ENSP00000328270:R106H	R	-	2	0	KRTAP4-6	36549949	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.922000	0.04004	-1.133000	0.02903	-2.248000	0.00284	CGT	C|0.988;T|0.012	0.012	strong		0.652	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
QPCTL	54814	hgsc.bcm.edu	37	19	46202131	46202131	+	Missense_Mutation	SNP	C	C	T	rs145016874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46202131C>T	ENST00000012049.5	+	5	1080	c.859C>T	c.(859-861)Cgc>Tgc	p.R287C	QPCTL_ENST00000366382.4_Missense_Mutation_p.R193C	NM_017659.3	NP_060129.2	Q9NXS2	QPCTL_HUMAN	glutaminyl-peptide cyclotransferase-like	287					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(1)|lung(5)|skin(1)|stomach(1)	11		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)		TCGCACGGTCCGCTGGTTCCA	0.617													C|||	3	0.000599042	0.0	0.0	5008	,	,		15872	0.0		0.002	False		,,,				2504	0.001				p.R287C		Atlas-SNP	.											.	QPCTL	24	.	0			c.C859T						PASS	.	C	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	81.0	80.0	81.0		577,859	3.8	1.0	19	dbSNP_134	81	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	QPCTL	NM_001163377.1,NM_017659.3	180,180	0,13,6490	TT,TC,CC		0.1279,0.0454,0.1	probably-damaging,probably-damaging	193/289,287/383	46202131	13,12993	2203	4300	6503	SO:0001583	missense	54814	exon5			ACGGTCCGCTGGT	AK000091	CCDS12672.1, CCDS54282.1	19q13.32	2014-09-04			ENSG00000011478	ENSG00000011478			25952	protein-coding gene	gene with protein product	"""glutaminyl cyclase-like"""						Standard	NM_017659		Approved	FLJ20084	uc010xxr.2	Q9NXS2	OTTHUMG00000182131	ENST00000012049.5:c.859C>T	19.37:g.46202131C>T	ENSP00000012049:p.Arg287Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_017659	Q53HE4|Q96F74	Missense_Mutation	SNP	ENST00000012049.5	37	CCDS12672.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.33	3.362347	0.61403	4.54E-4	0.001279	ENSG00000011478	ENST00000012049;ENST00000366382	T;T	0.51071	0.72;0.72	5.93	3.83	0.44106	Peptidase M28 (1);	0.342596	0.33772	N	0.004570	T	0.63212	0.2492	M	0.88450	2.955	0.58432	D	0.999993	D	0.71674	0.998	P	0.56700	0.804	T	0.64580	-0.6374	10	0.39692	T	0.17	-1.3625	8.816	0.34996	0.0:0.8542:0.0:0.1458	.	287	Q9NXS2	QPCTL_HUMAN	C	287;193	ENSP00000012049:R287C;ENSP00000387944:R193C	ENSP00000012049:R287C	R	+	1	0	QPCTL	50893971	0.932000	0.31603	0.997000	0.53966	0.627000	0.37826	1.506000	0.35747	2.826000	0.97356	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.617	QPCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459656.1	NM_017659	
MUC6	4588	hgsc.bcm.edu	37	11	1017068	1017068	+	Silent	SNP	C	C	T	rs78992004		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1017068C>T	ENST00000421673.2	-	31	5783	c.5733G>A	c.(5731-5733)acG>acA	p.T1911T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1911	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)		AAGTTTTGGCCGTGCTAAATG	0.552																																					p.T1911T		Atlas-SNP	.											MUC6,NS,carcinoma,-1,1	MUC6	408	1	0			c.G5733A						scavenged	.																																			SO:0001819	synonymous_variant	4588	exon31			TTTGGCCGTGCTA	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.5733G>A	11.37:g.1017068C>T		Somatic	801	61	0.0761548		WXS	Illumina HiSeq	Phase_I	690	58	0.084058	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			C|0.500;T|0.500	0.500	weak		0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ERCC6L2	375748	hgsc.bcm.edu	37	9	98691137	98691137	+	Missense_Mutation	SNP	T	T	C	rs2274654	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	47	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	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	
ARHGEF37	389337	hgsc.bcm.edu	37	5	149008467	149008467	+	Missense_Mutation	SNP	C	C	A	rs3733662	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149008467C>A	ENST00000333677.6	+	12	1919	c.1756C>A	c.(1756-1758)Ccc>Acc	p.P586T		NM_001001669.2	NP_001001669.2	A1IGU5	ARH37_HUMAN	Rho guanine nucleotide exchange factor (GEF) 37	586			P -> T (in dbSNP:rs3733662).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(5)|lung(6)|ovary(1)|prostate(2)|stomach(3)	17						GAACAAAGACCCCCGATGTCT	0.602													C|||	803	0.160343	0.0189	0.1412	5008	,	,		17591	0.3333		0.1501	False		,,,				2504	0.1973				p.P586T		Atlas-SNP	.											.	ARHGEF37	45	.	0			c.C1756A						PASS	.	C	THR/PRO	154,3812		0,154,1829	49.0	54.0	52.0		1756	2.9	0.0	5	dbSNP_107	52	1277,7041		87,1103,2969	yes	missense	ARHGEF37	NM_001001669.2	38	87,1257,4798	AA,AC,CC		15.3522,3.883,11.6493	benign	586/676	149008467	1431,10853	1983	4159	6142	SO:0001583	missense	389337	exon12			AAAGACCCCCGAT	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.1756C>A	5.37:g.149008467C>A	ENSP00000328083:p.Pro586Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_001001669	Q6ZW51	Missense_Mutation	SNP	ENST00000333677.6	37	CCDS43385.1	364	0.16666666666666666	9	0.018292682926829267	59	0.16298342541436464	179	0.3129370629370629	117	0.15435356200527706	C	5.285	0.237941	0.10023	0.03883	0.153522	ENSG00000183111	ENST00000333677	T	0.55052	0.54	5.4	2.86	0.33363	.	0.980252	0.08377	N	0.955147	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.34551	-0.9824	9	0.22706	T	0.39	-0.6438	3.7967	0.08743	0.2349:0.1019:0.0:0.6632	rs3733662;rs58657387;rs3733662	586	A1IGU5	ARH37_HUMAN	T	586	ENSP00000328083:P586T	ENSP00000328083:P586T	P	+	1	0	ARHGEF37	148988660	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	0.583000	0.23849	0.267000	0.21916	-0.339000	0.08088	CCC	C|0.839;A|0.161	0.161	strong		0.602	ARHGEF37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373763.1	NM_001001669	
MMP27	64066	hgsc.bcm.edu	37	11	102562700	102562700	+	Missense_Mutation	SNP	C	C	T	rs2509010	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102562700C>T	ENST00000260229.4	-	10	1430	c.1339G>A	c.(1339-1341)Gac>Aac	p.D447N		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	447			D -> N (in dbSNP:rs2509010). {ECO:0000269|PubMed:12975309}.		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GTCTTAATGTCGTATTCAAAT	0.333													C|||	820	0.163738	0.0696	0.2435	5008	,	,		17366	0.1081		0.2744	False		,,,				2504	0.1779				p.D447N		Atlas-SNP	.											.	MMP27	84	.	0			c.G1339A						PASS	.	C	ASN/ASP	475,3931	223.6+/-240.1	26,423,1754	89.0	80.0	83.0		1339	3.9	1.0	11	dbSNP_100	83	2437,6155	402.7+/-347.6	353,1731,2212	yes	missense	MMP27	NM_022122.2	23	379,2154,3966	TT,TC,CC		28.3636,10.7808,22.4034	benign	447/514	102562700	2912,10086	2203	4296	6499	SO:0001583	missense	64066	exon10			TAATGTCGTATTC	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.1339G>A	11.37:g.102562700C>T	ENSP00000260229:p.Asp447Asn	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	136	34	0.25	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	393	0.17994505494505494	32	0.06504065040650407	78	0.2154696132596685	60	0.1048951048951049	223	0.2941952506596306	C	14.06	2.422247	0.43020	0.107808	0.283636	ENSG00000137675	ENST00000260229	T	0.14144	2.53	5.96	3.86	0.44501	Hemopexin/matrixin (2);	0.085303	0.50627	D	0.000108	T	0.00012	0.0000	L	0.41079	1.255	0.30645	P	0.75601	P	0.36974	0.576	B	0.20767	0.031	T	0.48514	-0.9029	9	0.18710	T	0.47	.	10.2161	0.43168	0.0:0.7788:0.1407:0.0804	rs2509010;rs52836586;rs2509010	447	Q9H306	MMP27_HUMAN	N	447	ENSP00000260229:D447N	ENSP00000260229:D447N	D	-	1	0	MMP27	102067910	0.990000	0.36364	0.980000	0.43619	0.808000	0.45660	1.080000	0.30779	2.819000	0.97034	0.585000	0.79938	GAC	C|0.800;T|0.200	0.200	strong		0.333	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
C17orf77	146723	hgsc.bcm.edu	37	17	72588806	72588806	+	Nonsense_Mutation	SNP	C	C	A	rs545652	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:72588806C>A	ENST00000392620.1	+	3	983	c.621C>A	c.(619-621)tgC>tgA	p.C207*	C17orf77_ENST00000328023.2_Nonsense_Mutation_p.C207*|CD300LD_ENST00000375352.1_5'Flank	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	207						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						AAAGCCCATGCCCCAGGCTTC	0.607													C|||	1120	0.223642	0.5189	0.1441	5008	,	,		19490	0.0476		0.1392	False		,,,				2504	0.1493				p.C207X		Atlas-SNP	.											C17orf77,colon,carcinoma,0,1	C17orf77	31	1	0			c.C621A						PASS	.	C	stop/CYS	1969,2437	555.4+/-379.2	435,1099,669	79.0	80.0	79.0		621	2.4	0.0	17	dbSNP_83	79	1485,7115	280.5+/-294.5	138,1209,2953	yes	stop-gained	C17orf77	NM_152460.2		573,2308,3622	AA,AC,CC		17.2674,44.6891,26.557		207/244	72588806	3454,9552	2203	4300	6503	SO:0001587	stop_gained	146723	exon3			CCCATGCCCCAGG		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.621C>A	17.37:g.72588806C>A	ENSP00000376396:p.Cys207*	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	133	75	0.56391	NM_152460		Nonsense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	453	0.20741758241758243	256	0.5203252032520326	67	0.1850828729281768	22	0.038461538461538464	108	0.1424802110817942	C	22.9	4.351629	0.82132	0.446891	0.172674	ENSG00000182352	ENST00000392620;ENST00000328023	.	.	.	2.38	2.38	0.29361	.	.	.	.	.	.	.	.	.	.	.	0.37000	P	0.10478399999999999	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3461	0.32275	0.0:1.0:0.0:0.0	rs545652;rs545652	.	.	.	X	207	.	.	C	+	3	2	C17orf77	70100401	0.000000	0.05858	0.007000	0.13788	0.031000	0.12232	-0.036000	0.12185	1.642000	0.50584	0.511000	0.50034	TGC	C|0.751;A|0.249	0.249	strong		0.607	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
DPY19L2	283417	hgsc.bcm.edu	37	12	64062132	64062132	+	Silent	SNP	G	G	A	rs11175111	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:64062132G>A	ENST00000324472.4	-	1	225	c.42C>T	c.(40-42)tcC>tcT	p.S14S	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	14					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		GGCTGCGGCCGGAAGATTGCA	0.617													G|||	457	0.091254	0.121	0.0231	5008	,	,		14854	0.1329		0.0119	False		,,,				2504	0.138				p.S14S		Atlas-SNP	.											.	DPY19L2	97	.	0			c.C42T						PASS	.	G		338,3996		13,312,1842	12.0	15.0	14.0		42	0.5	0.0	12	dbSNP_120	14	130,8398		1,128,4135	no	coding-synonymous	DPY19L2	NM_173812.4		14,440,5977	AA,AG,GG		1.5244,7.7988,3.6386		14/759	64062132	468,12394	2167	4264	6431	SO:0001819	synonymous_variant	283417	exon1			GCGGCCGGAAGAT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.42C>T	12.37:g.64062132G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	64	18	0.28125	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Silent	SNP	ENST00000324472.4	37	CCDS31851.1																																																																																			G|0.957;A|0.043	0.043	strong		0.617	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
F2RL3	9002	hgsc.bcm.edu	37	19	17000632	17000632	+	Missense_Mutation	SNP	G	G	A	rs773902	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17000632G>A	ENST00000248076.3	+	2	688	c.358G>A	c.(358-360)Gct>Act	p.A120T	F2RL3_ENST00000599210.1_3'UTR	NM_003950.2	NP_003941.2	Q96RI0	PAR4_HUMAN	coagulation factor II (thrombin) receptor-like 3	120			A -> T (in dbSNP:rs773902). {ECO:0000269|PubMed:9618465, ECO:0000269|PubMed:9716134, ECO:0000269|PubMed:9722561}.		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						GAACCTCGCGGCTGCTGACCT	0.741													G|||	1713	0.342053	0.615	0.2911	5008	,	,		14611	0.2371		0.2058	False		,,,				2504	0.2577				p.A120T		Atlas-SNP	.											.	F2RL3	20	.	0			c.G358A						PASS	.	G	THR/ALA	2354,1990		672,1010,490	11.0	10.0	11.0		358	0.9	0.0	19	dbSNP_86	11	1691,6781		190,1311,2735	yes	missense	F2RL3	NM_003950.2	58	862,2321,3225	AA,AG,GG		19.9599,45.8103,31.5621	benign	120/386	17000632	4045,8771	2172	4236	6408	SO:0001583	missense	9002	exon2			CTCGCGGCTGCTG	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		ENST00000248076.3:c.358G>A	19.37:g.17000632G>A	ENSP00000248076:p.Ala120Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_003950	O76067|Q6DK42	Missense_Mutation	SNP	ENST00000248076.3	37	CCDS12350.1	647	0.29624542124542125	263	0.5345528455284553	108	0.2983425414364641	130	0.22727272727272727	146	0.19261213720316622	G	8.642	0.896247	0.17686	0.541897	0.199599	ENSG00000127533	ENST00000248076	T	0.37752	1.18	4.3	0.917	0.19380	GPCR, rhodopsin-like superfamily (1);	0.571113	0.15977	U	0.235519	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.33135	0.399	B	0.40782	0.34	T	0.45920	-0.9228	9	0.36615	T	0.2	.	5.4574	0.16598	0.244:0.0:0.6162:0.1398	rs773902;rs936378;rs58632682;rs773902	120	Q96RI0	PAR4_HUMAN	T	120	ENSP00000248076:A120T	ENSP00000248076:A120T	A	+	1	0	F2RL3	16861632	0.002000	0.14202	0.001000	0.08648	0.142000	0.21351	1.267000	0.33050	0.003000	0.14656	-0.336000	0.08194	GCT	G|0.677;A|0.323	0.323	strong		0.741	F2RL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462875.1		
ASXL1	171023	hgsc.bcm.edu	37	20	31024274	31024274	+	Silent	SNP	T	T	C	rs4911231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	53	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	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	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151121915	151121915	+	Silent	SNP	G	G	A	rs2073061	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:151121915G>A	ENST00000358517.2	+	6	901	c.690G>A	c.(688-690)gaG>gaA	p.E230E	PLEKHG1_ENST00000367328.1_Silent_p.E230E			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	230	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						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)		TCTTCAGGGAGCGTCAGGAAA	0.453													A|||	3269	0.652756	0.8011	0.5216	5008	,	,		19189	0.8046		0.4841	False		,,,				2504	0.5624				p.E230E		Atlas-SNP	.											PLEKHG1,NS,adenoma,0,1	PLEKHG1	97	1	0			c.G690A						PASS	.	A		3297,1109	399.0+/-331.0	1245,807,151	126.0	124.0	124.0		690	-6.9	0.6	6	dbSNP_96	124	4075,4525	594.4+/-393.3	1008,2059,1233	no	coding-synonymous	PLEKHG1	NM_001029884.1		2253,2866,1384	AA,AG,GG		47.3837,25.1702,43.3185		230/1386	151121915	7372,5634	2203	4300	6503	SO:0001819	synonymous_variant	57480	exon7			CAGGGAGCGTCAG	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.690G>A	6.37:g.151121915G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	166	87	0.524096	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																			G|0.393;A|0.607	0.607	strong		0.453	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
MLPH	79083	hgsc.bcm.edu	37	2	238449023	238449023	+	Silent	SNP	T	T	C	rs3817363	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238449023T>C	ENST00000264605.3	+	10	1431	c.1137T>C	c.(1135-1137)gaT>gaC	p.D379D	MLPH_ENST00000410032.1_Silent_p.D236D|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Silent_p.D379D|MLPH_ENST00000338530.4_Silent_p.D351D|MLPH_ENST00000409373.1_Silent_p.D311D	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	134	0	0		WXS	Illumina HiSeq	Phase_I	149	46	0.308725	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	
POLD1	5424	hgsc.bcm.edu	37	19	50905074	50905074	+	Missense_Mutation	SNP	G	G	A	rs1726801	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50905074G>A	ENST00000440232.2	+	4	409	c.356G>A	c.(355-357)cGc>cAc	p.R119H	POLD1_ENST00000599857.1_Missense_Mutation_p.R119H|POLD1_ENST00000595904.1_Missense_Mutation_p.R119H	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	119			R -> H (in dbSNP:rs1726801). {ECO:0000269|PubMed:1542570, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|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)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CCACCATCCCGCGGCTCCGTG	0.677								DNA polymerases (catalytic subunits)					G|||	943	0.188299	0.3222	0.1023	5008	,	,		12711	0.1607		0.0706	False		,,,				2504	0.2178				p.R119H		Atlas-SNP	.											.	POLD1	174	.	0			c.G356A						PASS	.	G	HIS/ARG	1305,3099	415.7+/-337.3	206,893,1103	36.0	40.0	39.0		356	-8.1	0.0	19	dbSNP_89	39	619,7977	153.7+/-208.1	22,575,3701	yes	missense	POLD1	NM_002691.2	29	228,1468,4804	AA,AG,GG		7.201,29.6322,14.8	benign	119/1108	50905074	1924,11076	2202	4298	6500	SO:0001583	missense	5424	exon4			CATCCCGCGGCTC		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.356G>A	19.37:g.50905074G>A	ENSP00000406046:p.Arg119His	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	83	50	0.60241	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	37	CCDS12795.1	354	0.1620879120879121	149	0.30284552845528456	40	0.11049723756906077	110	0.19230769230769232	55	0.07255936675461741	G	9.914	1.210250	0.22289	0.296322	0.07201	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.22743	1.94	4.04	-8.08	0.01094	Ribonuclease H-like (1);	1.185790	0.05994	N	0.646591	T	0.00012	0.0000	L	0.39898	1.24	0.58432	P	1.0000000000287557E-6	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.41233	-0.9520	9	0.13108	T	0.6	-1.863	6.6121	0.22757	0.4495:0.3218:0.2288:0.0	rs1726801;rs2230241;rs17850396;rs58282823;rs1726801	119;119	E7EVW0;P28340	.;DPOD1_HUMAN	H	119;120	ENSP00000406046:R119H	ENSP00000366129:R120H	R	+	2	0	POLD1	55596886	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.860000	0.04272	-1.701000	0.01413	-1.576000	0.00868	CGC	G|0.838;A|0.162	0.162	strong		0.677	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
CYP2D6	1565	hgsc.bcm.edu	37	22	42526775	42526775	+	Missense_Mutation	SNP	C	C	T	rs72549358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:42526775C>T	ENST00000360608.5	-	1	133	c.19G>A	c.(19-21)Gtg>Atg	p.V7M	CYP2D6_ENST00000389970.3_Missense_Mutation_p.V7M|NDUFA6-AS1_ENST00000608288.1_RNA|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.V7M|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	7					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)	GCCAGGGGCACCAGTGCTTCT	0.652													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19268	0.0		0.005	False		,,,				2504	0.0				p.V7M		Atlas-SNP	.											.	CYP2D6	104	.	0			c.G19A						PASS	.	C	MET/VAL,MET/VAL	6,4376		0,6,2185	37.0	37.0	37.0		19,19	0.1	0.0	22	dbSNP_130	37	27,8549		0,27,4261	no	missense,missense	CYP2D6	NM_001025161.1,NM_000106.4	21,21	0,33,6446	TT,TC,CC		0.3148,0.1369,0.2547	benign,benign	7/447,7/498	42526775	33,12925	2191	4288	6479	SO:0001583	missense	1565	exon1			GGGGCACCAGTGC	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.19G>A	22.37:g.42526775C>T	ENSP00000353820:p.Val7Met	Somatic	308	1	0.00324675		WXS	Illumina HiSeq	Phase_I	289	154	0.532872	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	C	1.817	-0.473201	0.04445	0.001369	0.003148	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000359033	T;T;T	0.37058	1.22;1.22;1.22	3.46	0.0648	0.14354	.	3.717790	0.00802	N	0.001421	T	0.18964	0.0455	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.08055	0.003;0.002	T	0.12578	-1.0542	10	0.34782	T	0.22	.	2.8284	0.05491	0.2852:0.448:0.0:0.2668	.	7;7	Q6NXU8;Q6NWU0	.;.	M	7	ENSP00000353820:V7M;ENSP00000374620:V7M;ENSP00000351927:V7M	ENSP00000351927:V7M	V	-	1	0	CYP2D6	40856719	0.001000	0.12720	0.013000	0.15412	0.004000	0.04260	-0.451000	0.06795	0.050000	0.15949	-0.350000	0.07774	GTG	C|0.996;T|0.004	0.004	strong		0.652	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
CDH7	1005	hgsc.bcm.edu	37	18	63511176	63511176	+	Silent	SNP	T	T	C	rs2306675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:63511176T>C	ENST00000397968.2	+	7	1536	c.1110T>C	c.(1108-1110)gaT>gaC	p.D370D	CDH7_ENST00000323011.3_Silent_p.D370D|CDH7_ENST00000536984.2_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	297	0	0		WXS	Illumina HiSeq	Phase_I	276	123	0.445652	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	
PLIN3	10226	hgsc.bcm.edu	37	19	4847868	4847868	+	Silent	SNP	G	G	A	rs10406652	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4847868G>A	ENST00000221957.4	-	6	845	c.669C>T	c.(667-669)gtC>gtT	p.V223V	PLIN3_ENST00000592528.1_Silent_p.V211V|PLIN3_ENST00000585479.1_Silent_p.V223V	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	223					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GCACGGACGCGACGTCAAAGC	0.617													G|||	581	0.116014	0.1604	0.1484	5008	,	,		17332	0.0685		0.1312	False		,,,				2504	0.0665				p.V223V		Atlas-SNP	.											.	PLIN3	36	.	0			c.C669T						PASS	.	G	,,	696,3710	277.2+/-273.6	47,602,1554	44.0	35.0	38.0		669,633,669	0.9	0.2	19	dbSNP_119	38	1163,7437	226.6+/-262.3	74,1015,3211	no	coding-synonymous,coding-synonymous,coding-synonymous	PLIN3	NM_001164189.1,NM_001164194.1,NM_005817.4	,,	121,1617,4765	AA,AG,GG		13.5233,15.7966,14.2934	,,	223/434,211/423,223/435	4847868	1859,11147	2203	4300	6503	SO:0001819	synonymous_variant	10226	exon6			GGACGCGACGTCA	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.669C>T	19.37:g.4847868G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	141	69	0.489362	NM_001164189	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Silent	SNP	ENST00000221957.4	37	CCDS12137.1																																																																																			G|0.867;A|0.132	0.132	strong		0.617	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817	
TMC7	79905	hgsc.bcm.edu	37	16	19041595	19041595	+	Missense_Mutation	SNP	G	G	A	rs28583298	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	176	0	0		WXS	Illumina HiSeq	Phase_I	150	144	0.96	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	
GRIN3A	116443	hgsc.bcm.edu	37	9	104335682	104335682	+	Missense_Mutation	SNP	C	C	T	rs3739722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:104335682C>T	ENST00000361820.3	-	9	3722	c.3122G>A	c.(3121-3123)cGg>cAg	p.R1041Q		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	1041			R -> Q (in dbSNP:rs3739722). {ECO:0000269|PubMed:11853319, ECO:0000269|PubMed:15489334}.		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)	CTGGTGGATCCGGATGCCCAG	0.522													C|||	933	0.186302	0.2171	0.2046	5008	,	,		20654	0.2579		0.1173	False		,,,				2504	0.1288				p.R1041Q		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G3122A						PASS	.	C	GLN/ARG	933,3473	356.9+/-313.7	104,725,1374	152.0	139.0	144.0		3122	-4.0	0.0	9	dbSNP_107	144	1126,7474	233.0+/-266.5	88,950,3262	yes	missense	GRIN3A	NM_133445.2	43	192,1675,4636	TT,TC,CC		13.093,21.1757,15.8312	benign	1041/1116	104335682	2059,10947	2203	4300	6503	SO:0001583	missense	116443	exon9			TGGATCCGGATGC		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.3122G>A	9.37:g.104335682C>T	ENSP00000355155:p.Arg1041Gln	Somatic	279	1	0.00358423		WXS	Illumina HiSeq	Phase_I	233	118	0.506438	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	421	0.19276556776556777	111	0.22560975609756098	63	0.17403314917127072	150	0.26223776223776224	97	0.1279683377308707	C	10.40	1.340250	0.24339	0.211757	0.13093	ENSG00000198785	ENST00000361820	T	0.09911	2.93	5.46	-3.96	0.04106	.	0.924765	0.09105	N	0.847883	T	0.00012	0.0000	M	0.66939	2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42155	-0.9468	9	0.18710	T	0.47	.	13.8051	0.63225	0.0:0.3847:0.0:0.6153	rs3739722;rs52800836;rs59648517;rs3739722	1041	Q8TCU5	NMD3A_HUMAN	Q	1041	ENSP00000355155:R1041Q	ENSP00000355155:R1041Q	R	-	2	0	GRIN3A	103375503	0.000000	0.05858	0.000000	0.03702	0.866000	0.49608	-1.991000	0.01478	-0.711000	0.04995	-0.136000	0.14681	CGG	C|0.831;T|0.169	0.169	strong		0.522	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
ACTR3B	57180	hgsc.bcm.edu	37	7	152511706	152511706	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:152511706A>G	ENST00000256001.8	+	5	542	c.408A>G	c.(406-408)gtA>gtG	p.V136V	ACTR3B_ENST00000537264.1_Silent_p.V48V|ACTR3B_ENST00000377776.3_Silent_p.V136V|ACTR3B_ENST00000397282.2_Silent_p.V48V|ACTR3B_ENST00000488782.1_3'UTR	NM_020445.5	NP_065178.1	Q9P1U1	ARP3B_HUMAN	ARP3 actin-related protein 3 homolog B (yeast)	136						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)		CATTTAACGTACCAGGACTCT	0.383																																					p.V136V		Atlas-SNP	.											ACTR3B,brain,glioma,0,13	ACTR3B	50	13	0			c.A408G						scavenged	.						149.0	139.0	142.0					7																	152511706		2203	4300	6503	SO:0001819	synonymous_variant	57180	exon5			TAACGTACCAGGA		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.408A>G	7.37:g.152511706A>G		Somatic	519	0	0		WXS	Illumina HiSeq	Phase_I	356	4	0.011236	NM_020445	A8MTG1|B4DFW4|Q7Z526|Q96BT2	Silent	SNP	ENST00000256001.8	37	CCDS5934.1																																																																																			.	.	alt		0.383	ACTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322803.1	NM_020445	
HIST1H2AA	221613	hgsc.bcm.edu	37	6	25726621	25726621	+	Silent	SNP	C	C	T	rs9467583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	93	0	0		WXS	Illumina HiSeq	Phase_I	97	32	0.329897	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	
SOAT1	6646	hgsc.bcm.edu	37	1	179320578	179320578	+	Missense_Mutation	SNP	A	A	G	rs13306731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:179320578A>G	ENST00000367619.3	+	15	1720	c.1577A>G	c.(1576-1578)cAg>cGg	p.Q526R	SOAT1_ENST00000535686.1_Missense_Mutation_p.Q262R|SOAT1_ENST00000540564.1_Missense_Mutation_p.Q468R|SOAT1_ENST00000539888.1_Missense_Mutation_p.Q461R	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	526			Q -> R (in dbSNP:rs13306731). {ECO:0000269|PubMed:8407899}.		cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	TATGCACGTCAGCACTGTCCT	0.438													A|||	626	0.125	0.0053	0.1499	5008	,	,		17986	0.3016		0.0736	False		,,,				2504	0.1401				p.Q526R		Atlas-SNP	.											.	SOAT1	53	.	0			c.A1577G						PASS	.	A	ARG/GLN	76,4330	67.0+/-104.6	1,74,2128	193.0	179.0	184.0		1577	5.6	1.0	1	dbSNP_121	184	632,7968	163.5+/-216.0	22,588,3690	yes	missense	SOAT1	NM_003101.4	43	23,662,5818	GG,GA,AA		7.3488,1.7249,5.4436	benign	526/551	179320578	708,12298	2203	4300	6503	SO:0001583	missense	6646	exon15			CACGTCAGCACTG	L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	2.3.1.26		11177	protein-coding gene	gene with protein product	"""acyl-Coenzyme A: cholesterol acyltransferase"""	102642	"""sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1"""	SOAT, STAT		8407899	Standard	NM_003101		Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.1577A>G	1.37:g.179320578A>G	ENSP00000356591:p.Gln526Arg	Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	316	309	0.977848	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Missense_Mutation	SNP	ENST00000367619.3	37	CCDS1330.1	270	0.12362637362637363	4	0.008130081300813009	35	0.09668508287292818	173	0.30244755244755245	58	0.07651715039577836	A	3.499	-0.102232	0.06967	0.017249	0.073488	ENSG00000057252	ENST00000539888;ENST00000540564;ENST00000535686;ENST00000367619	T;T;T;T	0.30182	1.56;1.56;1.59;1.54	5.58	5.58	0.84498	.	0.226336	0.43747	D	0.000530	T	0.00012	0.0000	N	0.04746	-0.17	0.29657	P	0.843493	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30179	-0.9987	9	0.02654	T	1	-4.7383	8.2832	0.31913	0.9124:0.0:0.0876:0.0	rs13306731;rs52792572;rs61194290;rs13306731	468;526	A8K3P4;P35610	.;SOAT1_HUMAN	R	461;468;262;526	ENSP00000441356:Q461R;ENSP00000445315:Q468R;ENSP00000442503:Q262R;ENSP00000356591:Q526R	ENSP00000356591:Q526R	Q	+	2	0	SOAT1	177587201	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	1.970000	0.40520	2.117000	0.64856	0.460000	0.39030	CAG	A|0.904;G|0.095	0.095	strong		0.438	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101	
OR7A17	26333	hgsc.bcm.edu	37	19	14991643	14991643	+	Silent	SNP	G	G	A	rs10401818	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14991643G>A	ENST00000327462.2	-	1	621	c.525C>T	c.(523-525)ccC>ccT	p.P175P		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	175						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)					AGAAAAAGTGGGGGATTTCCA	0.483													.|||	1390	0.277556	0.438	0.2349	5008	,	,		21572	0.2867		0.2356	False		,,,				2504	0.1247				p.P175P		Atlas-SNP	.											.	OR7A17	37	.	0			c.C525T						PASS	.	G		1723,2683	516.7+/-369.2	350,1023,830	91.0	86.0	88.0		525	-2.2	0.6	19	dbSNP_119	88	1945,6655	341.3+/-324.0	215,1515,2570	no	coding-synonymous	OR7A17	NM_030901.1		565,2538,3400	AA,AG,GG		22.6163,39.1058,28.2024		175/310	14991643	3668,9338	2203	4300	6503	SO:0001819	synonymous_variant	26333	exon1			AAAGTGGGGGATT	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.525C>T	19.37:g.14991643G>A		Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			G|0.709;A|0.291	0.291	strong		0.483	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
HNRNPA2B1	3181	hgsc.bcm.edu	37	7	26236961	26236961	+	Missense_Mutation	SNP	C	C	T	rs542884101		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:26236961C>T	ENST00000354667.4	-	4	442	c.274G>A	c.(274-276)Gag>Aag	p.E92K	HNRNPA2B1_ENST00000356674.7_Missense_Mutation_p.E80K	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	92	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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 transcription from RNA polymerase II promoter (GO:0000122)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|RNA binding (GO:0003723)|single-stranded telomeric DNA binding (GO:0043047)	p.E80Q(1)|p.E92Q(1)	HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22						CGTTTTGGCTCAACTACTCTC	0.423			T	ETV1	prostate																																p.E92K		Atlas-SNP	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	HNRNPA2B1_ENST00000354667,NS,carcinoma,0,2	HNRNPA2B1	70	2	2	Substitution - Missense(2)	lung(2)	c.G274A						scavenged	.						217.0	190.0	199.0					7																	26236961		2203	4300	6503	SO:0001583	missense	3181	exon4			TTGGCTCAACTAC	D28877	CCDS5397.1, CCDS43557.1	7p15	2013-02-12		2007-08-16	ENSG00000122566	ENSG00000122566		"""RNA binding motif (RRM) containing"""	5033	protein-coding gene	gene with protein product		600124		HNRPA2B1		8029005	Standard	NM_002137		Approved		uc003sxr.4	P22626	OTTHUMG00000023471	ENST00000354667.4:c.274G>A	7.37:g.26236961C>T	ENSP00000346694:p.Glu92Lys	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	292	3	0.010274	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	Missense_Mutation	SNP	ENST00000354667.4	37	CCDS43557.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.794710	0.90453	.	.	ENSG00000122566	ENST00000354667;ENST00000356674;ENST00000409814	D;D	0.91894	-2.93;-2.93	6.07	6.07	0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.64402	D	0.000001	D	0.94518	0.8235	M	0.70275	2.135	0.53688	D	0.999973	D;P	0.63046	0.992;0.86	P;P	0.52554	0.702;0.607	D	0.94378	0.7602	10	0.87932	D	0	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	80;92	P22626-2;P22626	.;ROA2_HUMAN	K	92;80;80	ENSP00000346694:E92K;ENSP00000349101:E80K	ENSP00000346694:E92K	E	-	1	0	HNRNPA2B1	26203486	1.000000	0.71417	1.000000	0.80357	0.164000	0.22412	7.747000	0.85070	2.885000	0.99019	0.655000	0.94253	GAG	.	.	none		0.423	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137	
CAPN10	11132	hgsc.bcm.edu	37	2	241531479	241531479	+	Silent	SNP	A	A	G	rs3792269	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241531479A>G	ENST00000391984.2	+	4	796	c.600A>G	c.(598-600)ccA>ccG	p.P200P	CAPN10_ENST00000391982.2_Silent_p.P200P|CAPN10_ENST00000352879.4_Intron|CAPN10_ENST00000404753.3_Silent_p.P200P|CAPN10_ENST00000270364.7_Intron|CAPN10_ENST00000354082.4_Silent_p.P200P	NM_023083.3	NP_075571	Q9HC96	CAN10_HUMAN	calpain 10	200	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		P -> T (in dbSNP:rs3792268). {ECO:0000269|PubMed:11017071}.		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)		AGGACAGGCCAGGCCGCTGGG	0.667													G|||	589	0.117612	0.0287	0.1254	5008	,	,		20411	0.0972		0.159	False		,,,				2504	0.2106				p.P200P		Atlas-SNP	.											.	CAPN10	105	.	0			c.A600G						PASS	.	G	,	229,4173		4,221,1976	27.0	29.0	29.0		600,600	-8.8	0.0	2	dbSNP_107	29	1388,7206		117,1154,3026	no	coding-synonymous,coding-synonymous	CAPN10	NM_023083.3,NM_023085.3	,	121,1375,5002	GG,GA,AA		16.1508,5.2022,12.4423	,	200/673,200/518	241531479	1617,11379	2201	4297	6498	SO:0001819	synonymous_variant	11132	exon4			CAGGCCAGGCCGC	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.600A>G	2.37:g.241531479A>G		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	228	106	0.464912	NM_023085	A8MVS7|Q4ZFV1|Q8NCD4|Q96IG4|Q96JI2|Q9HC89|Q9HC90|Q9HC91|Q9HC92|Q9HC93|Q9HC94|Q9HC95	Silent	SNP	ENST00000391984.2	37	CCDS42838.1																																																																																			A|0.886;G|0.114	0.114	strong		0.667	CAPN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257191.3	NM_023083	
SRP14	6727	hgsc.bcm.edu	37	15	40330518	40330518	+	Silent	SNP	T	T	G	rs1059395	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:40330518T>G	ENST00000267884.6	-	3	246	c.175A>C	c.(175-177)Aga>Cga	p.R59R	SRP14-AS1_ENST00000504245.1_lincRNA|SRP14_ENST00000560773.1_5'UTR|SRP14_ENST00000558720.1_5'UTR|SRP14_ENST00000558527.1_5'UTR|SRP14_ENST00000559081.1_Silent_p.R59R	NM_003134.4	NP_003125.3	P37108	SRP14_HUMAN	signal recognition particle 14kDa (homologous Alu RNA binding protein)	59					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)		TCGGTAGCTCTTAACAGACAC	0.463													T|||	489	0.0976438	0.0953	0.1023	5008	,	,		19815	0.0248		0.175	False		,,,				2504	0.093				p.R59R		Atlas-SNP	.											.	SRP14	11	.	0			c.A175C						PASS	.	T		430,3368		21,388,1490	122.0	115.0	117.0		175	3.7	1.0	15	dbSNP_86	117	1465,6767		122,1221,2773	no	coding-synonymous	SRP14	NM_003134.4		143,1609,4263	GG,GT,TT		17.7964,11.3217,15.7523		59/137	40330518	1895,10135	1899	4116	6015	SO:0001819	synonymous_variant	6727	exon3			TAGCTCTTAACAG		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.175A>C	15.37:g.40330518T>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_003134	B5BUF5|Q6B0K5|Q96Q14	Silent	SNP	ENST00000267884.6	37	CCDS42017.1																																																																																			T|0.867;G|0.133	0.133	strong		0.463	SRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418262.2	NM_003134	
EDDM3A	10876	hgsc.bcm.edu	37	14	21215923	21215923	+	Missense_Mutation	SNP	G	G	T	rs34552133	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21215923G>T	ENST00000326842.2	+	2	311	c.184G>T	c.(184-186)Ggc>Tgc	p.G62C		NM_006683.4	NP_006674.2	Q14507	EP3A_HUMAN	epididymal protein 3A	62			G -> C (in dbSNP:rs34552133).		sperm displacement (GO:0007321)	extracellular space (GO:0005615)				breast(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						GGCTCTGAAAGGCAAGAGCTT	0.378													G|||	566	0.113019	0.062	0.0519	5008	,	,		21696	0.1627		0.1064	False		,,,				2504	0.181				p.G62C		Atlas-SNP	.											.	EDDM3A	15	.	0			c.G184T						PASS	.	G	CYS/GLY	286,4120	157.0+/-190.0	12,262,1929	106.0	107.0	107.0		184	0.2	0.0	14	dbSNP_126	107	922,7678	204.8+/-247.4	49,824,3427	yes	missense	EDDM3A	NM_006683.4	159	61,1086,5356	TT,TG,GG		10.7209,6.4911,9.288	probably-damaging	62/148	21215923	1208,11798	2203	4300	6503	SO:0001583	missense	10876	exon2			CTGAAAGGCAAGA	X76383	CCDS9556.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181562	ENSG00000181562			16978	protein-coding gene	gene with protein product		611580	"""family with sequence similarity 12, member A"""	FAM12A		7514008	Standard	NM_006683		Approved	HE3-ALPHA	uc001vyc.3	Q14507	OTTHUMG00000029581	ENST00000326842.2:c.184G>T	14.37:g.21215923G>T	ENSP00000315098:p.Gly62Cys	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	261	161	0.616858	NM_006683	Q4KN33	Missense_Mutation	SNP	ENST00000326842.2	37	CCDS9556.1	225	0.10302197802197802	27	0.054878048780487805	26	0.0718232044198895	94	0.16433566433566432	78	0.10290237467018469	G	11.97	1.797746	0.31777	0.064911	0.107209	ENSG00000181562	ENST00000326842	T	0.41758	0.99	2.46	0.182	0.15077	Ribonuclease A, domain (2);	1.031530	0.07726	N	0.944462	T	0.00241	0.0007	L	0.40543	1.245	0.80722	P	0.0	D	0.67145	0.996	P	0.62813	0.907	T	0.05225	-1.0898	9	0.62326	D	0.03	.	3.8521	0.08959	0.1757:0.3849:0.4394:0.0	rs34552133	62	Q14507	EP3A_HUMAN	C	62	ENSP00000315098:G62C	ENSP00000315098:G62C	G	+	1	0	EDDM3A	20285763	0.001000	0.12720	0.000000	0.03702	0.129000	0.20672	0.484000	0.22308	-0.138000	0.11434	0.313000	0.20887	GGC	T|0.100;G|0.900;A|0.000	0.100	strong		0.378	EDDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073742.3		
KCNQ3	3786	hgsc.bcm.edu	37	8	133192521	133192521	+	Silent	SNP	A	A	G	rs41272389	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:133192521A>G	ENST00000388996.4	-	4	1080	c.660T>C	c.(658-660)aaT>aaC	p.N220N	KCNQ3_ENST00000519445.1_Silent_p.N220N|KCNQ3_ENST00000521134.1_Silent_p.N100N	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	220					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TGGCCAGAACATTGCCTTGGT	0.592													A|||	121	0.0241613	0.003	0.0303	5008	,	,		20790	0.0		0.0835	False		,,,				2504	0.0123				p.N220N		Atlas-SNP	.											.	KCNQ3	164	.	0			c.T660C						PASS	.	A	,	65,4341	62.3+/-99.4	0,65,2138	107.0	93.0	98.0		300,660	3.2	1.0	8	dbSNP_127	98	607,7993	158.8+/-212.2	27,553,3720	no	coding-synonymous,coding-synonymous	KCNQ3	NM_001204824.1,NM_004519.3	,	27,618,5858	GG,GA,AA		7.0581,1.4753,5.1668	,	100/753,220/873	133192521	672,12334	2203	4300	6503	SO:0001819	synonymous_variant	3786	exon4			CAGAACATTGCCT	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.660T>C	8.37:g.133192521A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	17	0.223684	NM_004519	A2VCT8|B4DJY4|E7EQ89	Silent	SNP	ENST00000388996.4	37	CCDS34943.1																																																																																			A|0.951;G|0.049	0.049	strong		0.592	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
PEAR1	375033	hgsc.bcm.edu	37	1	156882996	156882996	+	Silent	SNP	G	G	C	rs822441	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156882996G>C	ENST00000338302.3	+	20	2658	c.2433G>C	c.(2431-2433)ccG>ccC	p.P811P	PEAR1_ENST00000292357.7_Silent_p.P811P			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	811	Pro-rich.				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)					ATGTCCCTCCGAGCTACAGTC	0.597													G|||	1599	0.319289	0.5477	0.147	5008	,	,		18610	0.3323		0.159	False		,,,				2504	0.2843				p.P811P		Atlas-SNP	.											PEAR1,NS,carcinoma,+2,1	PEAR1	118	1	0			c.G2433C						scavenged	.	G		2121,2285	577.1+/-384.4	487,1147,569	124.0	117.0	120.0		2433	-10.6	0.0	1	dbSNP_86	120	1372,7228	267.2+/-287.2	116,1140,3044	no	coding-synonymous	PEAR1	NM_001080471.1		603,2287,3613	CC,CG,GG		15.9535,48.1389,26.8568		811/1038	156882996	3493,9513	2203	4300	6503	SO:0001819	synonymous_variant	375033	exon19			CCCTCCGAGCTAC	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.2433G>C	1.37:g.156882996G>C		Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	204	58	0.284314	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																			G|0.714;C|0.285	0.285	strong		0.597	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
RBMS3	27303	hgsc.bcm.edu	37	3	30032626	30032626	+	Silent	SNP	C	C	G	rs114278295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:30032626C>G	ENST00000383767.2	+	14	1569	c.1233C>G	c.(1231-1233)acC>acG	p.T411T	RBMS3_ENST00000456853.1_Silent_p.T408T|RBMS3_ENST00000273139.9_Silent_p.T395T|RBMS3_ENST00000383766.2_Silent_p.T393T|RBMS3_ENST00000396583.3_Silent_p.T408T|RBMS3_ENST00000434693.2_Silent_p.T410T|RBMS3_ENST00000452462.1_Silent_p.T395T|RBMS3_ENST00000473799.1_3'UTR			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	411					positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)	mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|large_intestine(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	11		Ovarian(412;0.0956)				CCCAGGACACCAGTGGTCAGC	0.478													C|||	59	0.0117812	0.0	0.0231	5008	,	,		21432	0.0		0.0278	False		,,,				2504	0.0153				p.T411T		Atlas-SNP	.											.	RBMS3	62	.	0			c.C1233G						PASS	.	C	,,,,	21,4385	29.0+/-57.7	0,21,2182	233.0	178.0	196.0		1179,1233,1185,1224,1185	3.5	1.0	3	dbSNP_132	196	224,8376	93.3+/-155.3	0,224,4076	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RBMS3	NM_001003792.2,NM_001003793.2,NM_001177711.1,NM_001177712.1,NM_014483.3	,,,,	0,245,6258	GG,GC,CC		2.6047,0.4766,1.8837	,,,,	393/420,411/438,395/422,408/434,395/421	30032626	245,12761	2203	4300	6503	SO:0001819	synonymous_variant	27303	exon14			GGACACCAGTGGT	AF023259	CCDS33724.1, CCDS33725.1, CCDS33726.1, CCDS54557.1, CCDS54558.1	3p24-p23	2013-02-12	2010-04-20		ENSG00000144642	ENSG00000144642		"""RNA binding motif (RRM) containing"""	13427	protein-coding gene	gene with protein product	"""RNA-binding protein"""	605786	"""RNA binding motif, single stranded interacting protein"""			10675610	Standard	NM_001003793		Approved		uc003cel.3	Q6XE24	OTTHUMG00000155699	ENST00000383767.2:c.1233C>G	3.37:g.30032626C>G		Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	294	127	0.431973	NM_001003793	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Silent	SNP	ENST00000383767.2	37	CCDS33724.1																																																																																			C|0.982;G|0.018	0.018	strong		0.478	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792	
CFTR	1080	hgsc.bcm.edu	37	7	117199533	117199533	+	Missense_Mutation	SNP	G	G	A	rs213950|rs397508204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:117199533G>A	ENST00000003084.6	+	11	1540	c.1408G>A	c.(1408-1410)Gtg>Atg	p.V470M	AC000111.3_ENST00000441019.1_RNA|CFTR_ENST00000454343.1_Missense_Mutation_p.V409M	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	470	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		V -> M (in dbSNP:rs213950). {ECO:0000269|PubMed:10651488, ECO:0000269|PubMed:1710598, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:2475911, ECO:0000269|Ref.3}.		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)	ACTTCTAATGGTGATTATGGG	0.393									Cystic Fibrosis				A|||	2915	0.582069	0.9349	0.513	5008	,	,		17643	0.3869		0.4384	False		,,,				2504	0.5031				p.V470M		Atlas-SNP	.											.	CFTR	171	.	0			c.G1408A	GRCh37	CM034388	CFTR	M	rs213950	PASS	.	A	MET/VAL	3747,659		1586,575,42	102.0	111.0	108.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1408	3.0	1.0	7	dbSNP_79	108	4026,4574		1025,1976,1299	yes	missense	CFTR	NM_000492.3	21	2611,2551,1341	AA,AG,GG		46.814,14.9569,40.2353	benign	470/1481	117199533	7773,5233	2203	4300	6503	SO:0001583	missense	1080	exon11	Familial Cancer Database	CF	CTAATGGTGATTA	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.1408G>A	7.37:g.117199533G>A	ENSP00000003084:p.Val470Met	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Missense_Mutation	SNP	ENST00000003084.6	37	CCDS5773.1	1180	0.5402930402930403	449	0.9126016260162602	192	0.5303867403314917	202	0.3531468531468531	337	0.4445910290237467	A	2.095	-0.407418	0.04832	0.850431	0.46814	ENSG00000001626	ENST00000003084;ENST00000454343;ENST00000426809	D;D;D	0.94280	-3.39;-3.39;-3.39	5.47	3.05	0.35203	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.113641	0.85682	N	0.000000	T	0.00012	0.0000	N	0.11341	0.13	0.46279	P	0.0010339999999999794	B	0.02656	0.0	B	0.06405	0.002	T	0.42032	-0.9475	9	0.16420	T	0.52	-17.102	2.8388	0.05523	0.5314:0.1098:0.0703:0.2886	rs213950;rs10360044;rs34570734;rs52833540;rs57055567;rs213950	470	P13569	CFTR_HUMAN	M	470;409;440	ENSP00000003084:V470M;ENSP00000403677:V409M;ENSP00000389119:V440M	ENSP00000003084:V470M	V	+	1	0	CFTR	116986769	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.608000	0.46308	0.103000	0.17682	-0.269000	0.10298	GTG	G|0.436;A|0.564	0.564	strong		0.393	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	
RPL10L	140801	hgsc.bcm.edu	37	14	47120423	47120423	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:47120423A>G	ENST00000298283.3	-	1	605	c.517T>C	c.(517-519)Ttc>Ctc	p.F173L		NM_080746.2	NP_542784.1	Q96L21	RL10L_HUMAN	ribosomal protein L10-like	173					spermatogenesis (GO:0007283)|translation (GO:0006412)	cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)	structural constituent of ribosome (GO:0003735)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(20)|ovary(1)	27						AACTTCGTGAAGCCCCACTTC	0.507																																					p.F173L		Atlas-SNP	.											RPL10L,bladder,carcinoma,+2,1	RPL10L	64	1	0			c.T517C						scavenged	.						100.0	99.0	100.0					14																	47120423		2203	4300	6503	SO:0001583	missense	140801	exon1			TCGTGAAGCCCCA	AB063608	CCDS32071.1	14q21.2	2011-09-15			ENSG00000165496	ENSG00000165496		"""L ribosomal proteins"""	17976	protein-coding gene	gene with protein product						19123937	Standard	NM_080746		Approved		uc001wwg.3	Q96L21	OTTHUMG00000157869	ENST00000298283.3:c.517T>C	14.37:g.47120423A>G	ENSP00000298283:p.Phe173Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	171	2	0.0116959	NM_080746	Q8IUD1	Missense_Mutation	SNP	ENST00000298283.3	37	CCDS32071.1	.	.	.	.	.	.	.	.	.	.	A	17.96	3.515022	0.64634	.	.	ENSG00000165496	ENST00000298283	T	0.75704	-0.96	4.57	4.57	0.56435	Ribosomal protein L10e/L16 (1);	0.000000	0.85682	D	0.000000	T	0.76407	0.3983	M	0.84433	2.695	0.80722	D	1	B	0.13594	0.008	B	0.12156	0.007	T	0.77474	-0.2574	10	0.87932	D	0	-23.7482	12.5486	0.56214	1.0:0.0:0.0:0.0	.	173	Q96L21	RL10L_HUMAN	L	173	ENSP00000298283:F173L	ENSP00000298283:F173L	F	-	1	0	RPL10L	46190173	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	6.588000	0.74076	2.279000	0.76181	0.533000	0.62120	TTC	.	.	none		0.507	RPL10L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349819.1		
C7orf72	100130988	hgsc.bcm.edu	37	7	50180972	50180972	+	Missense_Mutation	SNP	C	C	T	rs1456908	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:50180972C>T	ENST00000297001.6	+	7	1123	c.1073C>T	c.(1072-1074)aCa>aTa	p.T358I	AC020743.2_ENST00000454877.1_RNA	NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72	358				T -> I (in Ref. 2; EAL23902). {ECO:0000305}.						NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						CCTCTTTATACAAACACAAGT	0.398													C|||	1658	0.33107	0.3147	0.2651	5008	,	,		17515	0.1974		0.3986	False		,,,				2504	0.4683				p.T358I		Atlas-SNP	.											.	C7orf72	26	.	0			c.C1073T						PASS	.	C	ILE/THR	477,907		75,327,290	125.0	105.0	111.0		1073	5.8	0.1	7	dbSNP_88	111	1344,1838		292,760,539	yes	missense	C7orf72	NM_001161834.2	89	367,1087,829	TT,TC,CC		42.2376,34.4653,39.8817	probably-damaging	358/439	50180972	1821,2745	692	1591	2283	SO:0001583	missense	100130988	exon7			TTTATACAAACAC		CCDS47585.1	7p12.2	2009-10-15			ENSG00000164500	ENSG00000164500			22564	protein-coding gene	gene with protein product							Standard	NM_001161834		Approved		uc011kcj.2	A4D263	OTTHUMG00000155883	ENST00000297001.6:c.1073C>T	7.37:g.50180972C>T	ENSP00000297001:p.Thr358Ile	Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	233	232	0.995708	NM_001161834	A6NDX9	Missense_Mutation	SNP	ENST00000297001.6	37	CCDS47585.1	666	0.30494505494505497	167	0.3394308943089431	102	0.281767955801105	94	0.16433566433566432	303	0.3997361477572559	C	13.81	2.348928	0.41599	0.344653	0.422376	ENSG00000164500	ENST00000297001	.	.	.	5.78	5.78	0.91487	.	.	.	.	.	T	0.00012	0.0000	L	0.48642	1.525	0.40751	P	0.01708900000000002	D	0.89917	1.0	D	0.87578	0.998	T	0.35051	-0.9804	7	0.52906	T	0.07	.	15.5045	0.75728	0.0:1.0:0.0:0.0	rs1456908;rs60427088;rs1456908	358	A4D263	CG072_HUMAN	I	358	.	ENSP00000297001:T358I	T	+	2	0	C7orf72	50151518	0.180000	0.23148	0.104000	0.21259	0.597000	0.36814	3.850000	0.55918	2.714000	0.92807	0.650000	0.86243	ACA	C|0.671;T|0.329	0.329	strong		0.398	C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	
POLN	353497	hgsc.bcm.edu	37	4	2194946	2194946	+	Missense_Mutation	SNP	C	C	T	rs10011549	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	219	0	0		WXS	Illumina HiSeq	Phase_I	178	83	0.466292	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	
MUC17	140453	hgsc.bcm.edu	37	7	100675376	100675376	+	Missense_Mutation	SNP	A	A	C	rs10229731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100675376A>C	ENST00000306151.4	+	3	743	c.679A>C	c.(679-681)Aag>Cag	p.K227Q		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	227	59 X approximate tandem repeats.|Ser-rich.		K -> Q (in dbSNP:rs10229731).		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)					CAGCACCATGAAGGTGGCCAG	0.478													C|||	1179	0.235423	0.3396	0.1009	5008	,	,		23835	0.254		0.1213	False		,,,				2504	0.2883				p.K227Q		Atlas-SNP	.											.	MUC17	804	.	0			c.A679C						PASS	.	C	GLN/LYS	1330,3076	695.0+/-405.9	209,912,1082	174.0	177.0	176.0		679	-0.6	0.0	7	dbSNP_119	176	998,7602	773.4+/-407.7	56,886,3358	yes	missense	MUC17	NM_001040105.1	53	265,1798,4440	CC,CA,AA		11.6047,30.1861,17.8994	benign	227/4494	100675376	2328,10678	2203	4300	6503	SO:0001583	missense	140453	exon3			ACCATGAAGGTGG	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.679A>C	7.37:g.100675376A>C	ENSP00000302716:p.Lys227Gln	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	210	206	0.980952	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	411	0.18818681318681318	142	0.2886178861788618	41	0.1132596685082873	139	0.243006993006993	89	0.11741424802110818	C	0.851	-0.738688	0.03111	0.301861	0.116047	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.533	-0.628	0.11537	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15719	0.014	B	0.01281	0.0	T	0.42155	-0.9468	7	0.13470	T	0.59	.	.	.	.	rs10229731;rs52834675;rs59400468;rs10229731	227	Q685J3	MUC17_HUMAN	Q	227	ENSP00000302716:K227Q	ENSP00000302716:K227Q	K	+	1	0	MUC17	100462096	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-4.063000	0.00302	-1.118000	0.02961	-1.116000	0.02052	AAG	A|0.825;C|0.175	0.175	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SLC26A1	10861	hgsc.bcm.edu	37	4	983868	983868	+	Missense_Mutation	SNP	G	G	A	rs201572215		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:983868G>A	ENST00000361661.2	-	4	1236	c.859C>T	c.(859-861)Cgc>Tgc	p.R287C	SLC26A1_ENST00000398516.2_Missense_Mutation_p.R287C|SLC26A1_ENST00000398520.2_Intron|SLC26A1_ENST00000513138.1_5'Flank|IDUA_ENST00000247933.4_Intron|IDUA_ENST00000453894.1_Intron	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	287					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			ACCCTCAGGCGGTGTCGGTAG	0.697													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17070	0.0		0.0	False		,,,				2504	0.0				p.R287C		Atlas-SNP	.											SLC26A1,colon,carcinoma,0,2	SLC26A1	44	2	0			c.C859T						scavenged	.	G	,CYS/ARG,,CYS/ARG	0,4366		0,0,2183	27.0	21.0	23.0		,859,,859	3.0	0.8	4		23	2,8578		0,2,4288	yes	intron,missense,intron,missense	IDUA,SLC26A1	NM_000203.3,NM_022042.2,NM_134425.1,NM_213613.2	,180,,180	0,2,6471	AA,AG,GG		0.0233,0.0,0.0154	,possibly-damaging,,possibly-damaging	,287/702,,287/702	983868	2,12944	2183	4290	6473	SO:0001583	missense	10861	exon3			TCAGGCGGTGTCG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"""Solute carriers"""	10993	protein-coding gene	gene with protein product		610130	"""solute carrier family 26 (sulfate transporter), member 1"""				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.859C>T	4.37:g.983868G>A	ENSP00000354721:p.Arg287Cys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	73	2	0.0273973	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Missense_Mutation	SNP	ENST00000361661.2	37	CCDS33934.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.44	1.937885	0.34189	0.0	2.33E-4	ENSG00000145217	ENST00000361661;ENST00000398516	D;D	0.93366	-3.21;-3.21	4.97	2.97	0.34412	Sulphate transporter (1);	0.622270	0.17478	N	0.172846	D	0.94928	0.8360	M	0.80982	2.52	0.09310	N	1	D	0.56746	0.977	P	0.58077	0.832	D	0.88360	0.2987	10	0.87932	D	0	.	7.2805	0.26308	0.0961:0.0:0.6662:0.2377	.	287	Q9H2B4	S26A1_HUMAN	C	287	ENSP00000354721:R287C;ENSP00000381528:R287C	ENSP00000354721:R287C	R	-	1	0	SLC26A1	973868	0.001000	0.12720	0.780000	0.31762	0.053000	0.15095	0.610000	0.24253	1.054000	0.40438	0.561000	0.74099	CGC	G|1.000;A|0.000	0.000	strong		0.697	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425	
MFSD1	64747	hgsc.bcm.edu	37	3	158538056	158538056	+	Silent	SNP	T	T	C	rs4680469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:158538056T>C	ENST00000264266.8	+	9	866	c.804T>C	c.(802-804)ctT>ctC	p.L268L	MFSD1_ENST00000392813.4_Silent_p.L278L|MFSD1_ENST00000415822.2_Silent_p.L317L			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	246	0	0		WXS	Illumina HiSeq	Phase_I	219	113	0.515982	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	
LY6H	4062	hgsc.bcm.edu	37	8	144239859	144239859	+	Silent	SNP	A	A	G	rs10109061	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144239859A>G	ENST00000430474.2	-	4	396	c.231T>C	c.(229-231)tgT>tgC	p.C77C	LY6H_ENST00000342752.4_Silent_p.C98C|LY6H_ENST00000414417.2_Silent_p.C98C	NM_002347.4	NP_002338.3	O94772	LY6H_HUMAN	lymphocyte antigen 6 complex, locus H	77	UPAR/Ly6.				nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.C77C(1)		endometrium(1)|lung(1)|stomach(2)	4	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)					TAACGAAGTCACAGGAGGAGG	0.537													G|||	2194	0.438099	0.7156	0.3343	5008	,	,		20246	0.2827		0.4036	False		,,,				2504	0.3323				p.C98C		Atlas-SNP	.											LY6H,NS,carcinoma,0,1	LY6H	12	1	1	Substitution - coding silent(1)	stomach(1)	c.T294C						scavenged	.	G	,,	2878,1528	484.6+/-360.1	947,984,272	107.0	106.0	107.0		294,294,231	-6.0	0.4	8	dbSNP_119	107	3756,4844	616.1+/-396.5	813,2130,1357	no	coding-synonymous,coding-synonymous,coding-synonymous	LY6H	NM_001130478.1,NM_001135655.1,NM_002347.4	,,	1760,3114,1629	GG,GA,AA		43.6744,34.68,48.9928	,,	98/162,98/162,77/141	144239859	6634,6372	2203	4300	6503	SO:0001819	synonymous_variant	4062	exon4			GAAGTCACAGGAG	AB012293	CCDS6396.1, CCDS47926.1	8q24.3	2008-08-01			ENSG00000176956	ENSG00000176956			6728	protein-coding gene	gene with protein product		603625				9799603	Standard	NM_001130478		Approved	NMLY6	uc011lkb.2	O94772	OTTHUMG00000154890	ENST00000430474.2:c.231T>C	8.37:g.144239859A>G		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_001135655	B2RAD2|J3KQI0|Q6IAX0	Silent	SNP	ENST00000430474.2	37	CCDS6396.1																																																																																			A|0.509;G|0.491	0.491	strong		0.537	LY6H-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337535.1		
TTN	7273	hgsc.bcm.edu	37	2	179440955	179440955	+	Missense_Mutation	SNP	C	C	T	rs190421400	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179440955C>T	ENST00000591111.1	-	276	65205	c.64981G>A	c.(64981-64983)Gtt>Att	p.V21661I	TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V23302I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V20734I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V14237I|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V14362I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592750.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V14429I			Q8WZ42	TITIN_HUMAN	titin	21661	Fibronectin type-III 57. {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)	p.V14429I(1)|p.V14237I(1)|p.V14362I(1)|p.V20732I(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)			TCAGGAACAACGAACTGAGTG	0.458													c|||	4	0.000798722	0.003	0.0	5008	,	,		19570	0.0		0.0	False		,,,				2504	0.0				p.V23302I		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,0,4	TTN	18412	4	4	Substitution - Missense(4)	prostate(4)	c.G69904A						scavenged	.	T	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	5,3791		0,5,1893	72.0	71.0	71.0		43285,43084,62200,42709	4.1	0.9	2		71	1,8261		0,1,4130	no	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	0,6,6023	TT,TC,CC		0.0121,0.1317,0.0498	benign,benign,benign,benign	14429/27119,14362/27052,20734/33424,14237/26927	179440955	6,12052	1898	4131	6029	SO:0001583	missense	7273	exon326			GAACAACGAACTG	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.64981G>A	2.37:g.179440955C>T	ENSP00000465570:p.Val21661Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	126	3	0.0238095	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		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	12.24	1.880041	0.33162	0.001317	1.21E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.87	4.08	0.47627	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.47451	0.1446	L	0.60904	1.88	0.37679	D	0.923431	P;P;P;B	0.36086	0.536;0.536;0.536;0.383	B;B;B;B	0.30495	0.116;0.116;0.116;0.082	T	0.56129	-0.8030	9	0.87932	D	0	.	13.1755	0.59624	0.0:0.8695:0.0:0.1305	.	14237;14362;14429;21661	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	20734;14237;14429;14362;14235	ENSP00000343764:V20734I;ENSP00000434586:V14237I;ENSP00000340554:V14429I;ENSP00000352154:V14362I	ENSP00000340554:V14429I	V	-	1	0	TTN	179149201	1.000000	0.71417	0.944000	0.38274	0.937000	0.57800	4.075000	0.57584	0.823000	0.34589	-0.119000	0.15052	GTT	C|1.000;T|0.000	0.000	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CSMD1	64478	hgsc.bcm.edu	37	8	3267108	3267108	+	Silent	SNP	A	A	G	rs190257069	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:3267108A>G	ENST00000520002.1	-	14	2139	c.1584T>C	c.(1582-1584)tgT>tgC	p.C528C	CSMD1_ENST00000400186.3_Silent_p.C528C|CSMD1_ENST00000602557.1_Silent_p.C528C|CSMD1_ENST00000537824.1_Silent_p.C527C|CSMD1_ENST00000542608.1_Silent_p.C527C|CSMD1_ENST00000602723.1_Silent_p.C528C|CSMD1_ENST00000539096.1_Silent_p.C527C			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	528	Sushi 3. {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)		CAGGATCCCCACACCCTCCCT	0.453													A|||	3	0.000599042	0.0008	0.0014	5008	,	,		16262	0.0		0.001	False		,,,				2504	0.0				p.C527C		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T1581C						PASS	.	A		1,3679		0,1,1839	23.0	24.0	24.0		1581	-0.3	0.9	8		24	17,8143		0,17,4063	no	coding-synonymous	CSMD1	NM_033225.5		0,18,5902	GG,GA,AA		0.2083,0.0272,0.152		527/3565	3267108	18,11822	1840	4080	5920	SO:0001819	synonymous_variant	64478	exon13			ATCCCCACACCCT			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.1584T>C	8.37:g.3267108A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	102	38	0.372549	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	10.20	1.285284	0.23478	2.72E-4	0.002083	ENSG00000183117	ENST00000335551	.	.	.	5.26	-0.303	0.12792	.	.	.	.	.	T	0.56804	0.2010	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49725	-0.8909	4	.	.	.	.	9.8509	0.41057	0.7465:0.0:0.2535:0.0	.	.	.	.	R	8	.	.	W	-	1	0	CSMD1	3254516	0.997000	0.39634	0.924000	0.36721	0.977000	0.68977	0.529000	0.23019	-0.300000	0.08895	0.467000	0.42956	TGG	A|0.999;G|0.001	0.001	strong		0.453	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79057989	79057989	+	Missense_Mutation	SNP	C	C	T	rs200769684		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	111	19	0.171171	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	
MR1	3140	hgsc.bcm.edu	37	1	181018236	181018236	+	Missense_Mutation	SNP	A	A	G	rs2236410	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:181018236A>G	ENST00000367580.5	+	2	121	c.116A>G	c.(115-117)cAt>cGt	p.H39R	MR1_ENST00000434571.2_Missense_Mutation_p.H39R|MR1_ENST00000282990.6_Missense_Mutation_p.H39R|MR1_ENST00000438435.2_3'UTR|MR1_ENST00000367579.3_Missense_Mutation_p.H39R	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	39	Alpha-1.|Ligand-binding.		H -> R (in dbSNP:rs2236410). {ECO:0000269|Ref.10}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)	p.H39R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	GATCCCATCCATGGGGTCCCT	0.542													A|||	966	0.192891	0.1263	0.2161	5008	,	,		17473	0.3502		0.1372	False		,,,				2504	0.1616				p.H39R	Colon(174;1412 1962 45296 46549 47110)	Atlas-SNP	.											MR1,NS,carcinoma,0,1	MR1	46	1	1	Substitution - Missense(1)	stomach(1)	c.A116G						PASS	.	A	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	593,3813	258.3+/-262.4	44,505,1654	50.0	51.0	50.0		116,116,116,116	-6.8	0.0	1	dbSNP_98	50	1339,7261	262.1+/-284.2	97,1145,3058	no	missense,missense,missense,missense	MR1	NM_001194999.1,NM_001195000.1,NM_001195035.1,NM_001531.2	29,29,29,29	141,1650,4712	GG,GA,AA		15.5698,13.4589,14.8547	benign,benign,benign,benign	39/297,39/250,39/215,39/342	181018236	1932,11074	2203	4300	6503	SO:0001583	missense	3140	exon3			CCATCCATGGGGT	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"""Immunoglobulin superfamily / C1-set domain containing"""	4975	protein-coding gene	gene with protein product		600764	"""major histocompatibility complex, class I-like sequence"""	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.116A>G	1.37:g.181018236A>G	ENSP00000356552:p.His39Arg	Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	362	140	0.38674	NM_001195035	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Missense_Mutation	SNP	ENST00000367580.5	37	CCDS1342.1	450	0.20604395604395603	68	0.13821138211382114	73	0.20165745856353592	207	0.3618881118881119	102	0.1345646437994723	A	7.426	0.637720	0.14386	0.134589	0.155698	ENSG00000153029	ENST00000434571;ENST00000367580;ENST00000282990;ENST00000367579	T;T;T;D	0.88741	9.51;9.51;9.51;-2.42	4.78	-6.85	0.01681	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.135970	0.06552	N	0.745148	T	0.00012	0.0000	N	0.02120	-0.675	0.22601	P	0.998948	B;P;P;P;B	0.37276	0.158;0.589;0.589;0.473;0.0	B;B;B;B;B	0.38106	0.067;0.083;0.173;0.265;0.001	T	0.04153	-1.0973	9	0.02654	T	1	.	3.7899	0.08716	0.2244:0.5:0.1585:0.117	rs2236410;rs2236410	39;39;39;39;39	B4E3B1;Q95460-3;Q95460-2;Q95460;Q95460-4	.;.;.;HMR1_HUMAN;.	R	39	ENSP00000388504:H39R;ENSP00000356552:H39R;ENSP00000282990:H39R;ENSP00000356551:H39R	ENSP00000282990:H39R	H	+	2	0	MR1	179284859	0.000000	0.05858	0.000000	0.03702	0.213000	0.24496	0.431000	0.21444	-1.392000	0.02082	-0.425000	0.05940	CAT	A|0.833;G|0.167	0.167	strong		0.542	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531	
TTI2	80185	hgsc.bcm.edu	37	8	33369994	33369994	+	Silent	SNP	A	A	G	rs3098657	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:33369994A>G	ENST00000431156.2	-	2	756	c.138T>C	c.(136-138)aaT>aaC	p.N46N	TTI2_ENST00000519356.1_5'Flank|TTI2_ENST00000360742.5_Silent_p.N46N|TTI2_ENST00000520636.1_Silent_p.N46N|SNORD13_ENST00000459299.1_RNA	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	46																	CATCTTTTACATTGCCTCGTC	0.507													G|||	2899	0.578874	0.6702	0.4957	5008	,	,		17050	0.5565		0.6551	False		,,,				2504	0.4591				p.N46N		Atlas-SNP	.											.	.	.	.	0			c.T138C						PASS	.	G	,	2955,1451	468.9+/-355.3	999,957,247	72.0	73.0	73.0		138,138	0.2	0.0	8	dbSNP_103	73	5578,3022	463.9+/-366.1	1807,1964,529	yes	coding-synonymous,coding-synonymous	TTI2	NM_001102401.1,NM_025115.2	,	2806,2921,776	GG,GA,AA		35.1395,32.9324,34.3918	,	46/509,46/509	33369994	8533,4473	2203	4300	6503	SO:0001819	synonymous_variant	80185	exon2			TTTTACATTGCCT	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.138T>C	8.37:g.33369994A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	126	69	0.547619	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	37	CCDS6090.1																																																																																			A|0.369;G|0.631	0.631	strong		0.507	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	
MYO19	80179	hgsc.bcm.edu	37	17	34884029	34884029	+	Missense_Mutation	SNP	T	T	C	rs61738887	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:34884029T>C	ENST00000431794.3	-	4	539	c.17A>G	c.(16-18)aAt>aGt	p.N6S	MYO19_ENST00000268852.9_Missense_Mutation_p.N6S|MYO19_ENST00000586007.1_Missense_Mutation_p.N6S|MYO19_ENST00000544606.1_Intron	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	6						cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		ATTGTGGCCATTGACCTGGAA	0.577													T|||	444	0.0886581	0.1142	0.072	5008	,	,		18846	0.1062		0.0278	False		,,,				2504	0.1104				p.N6S		Atlas-SNP	.											.	MYO19	130	.	0			c.A17G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	417,3487		31,355,1566	32.0	33.0	32.0		17,17,17	2.1	1.0	17	dbSNP_129	32	227,8043		1,225,3909	yes	missense,missense,missense	MYO19	NM_001033580.2,NM_001163735.1,NM_025109.5	46,46,46	32,580,5475	CC,CT,TT		2.7449,10.6814,5.29	benign,benign,benign	6/318,6/971,6/771	34884029	644,11530	1952	4135	6087	SO:0001583	missense	80179	exon5			TGGCCATTGACCT	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.17A>G	17.37:g.34884029T>C	ENSP00000409936:p.Asn6Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	166	0.076007326007326	56	0.11382113821138211	26	0.0718232044198895	65	0.11363636363636363	19	0.025065963060686015	T	14.05	2.420349	0.42918	0.106814	0.027449	ENSG00000141140	ENST00000431794;ENST00000268852	D;D	0.89196	-2.3;-2.48	5.46	2.12	0.27331	.	0.152848	0.30356	N	0.009820	T	0.08133	0.0203	L	0.29908	0.895	0.09310	P	0.999999999818922	B;B;B	0.20671	0.028;0.047;0.047	B;B;B	0.20767	0.007;0.031;0.015	T	0.57510	-0.7799	9	0.87932	D	0	.	8.6507	0.34033	0.0:0.2172:0.0:0.7828	.	6;6;6	Q96H55;Q96H55-2;Q96H55-4	MYO19_HUMAN;.;.	S	6	ENSP00000409936:N6S;ENSP00000268852:N6S	ENSP00000268852:N6S	N	-	2	0	MYO19	31958142	1.000000	0.71417	0.983000	0.44433	0.931000	0.56810	3.346000	0.52190	0.177000	0.19895	-0.250000	0.11733	AAT	T|0.931;C|0.069	0.069	strong		0.577	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
CCDC180	100499483	hgsc.bcm.edu	37	9	100074446	100074446	+	Silent	SNP	C	C	T	rs3747504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100074446C>T	ENST00000357054.1	+	18	1796	c.861C>T	c.(859-861)atC>atT	p.I287I	CCDC180_ENST00000395220.1_Silent_p.I287I|CCDC180_ENST00000411667.2_Silent_p.I148I|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000529487.1_Silent_p.I148I|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						scavenged	.	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	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	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	
SEC14L6	730005	hgsc.bcm.edu	37	22	30921371	30921371	+	Silent	SNP	T	T	C	rs6518698	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:30921371T>C	ENST00000402034.2	-	11	1046	c.1047A>G	c.(1045-1047)gaA>gaG	p.E349E		NM_001193336.2	NP_001180265.2	B5MCN3	S14L6_HUMAN	SEC14-like 6 (S. cerevisiae)	349	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			lung(3)	3						GAATCCCATCTTCAGGCACCA	0.602													C|||	1449	0.289337	0.4811	0.3329	5008	,	,		18972	0.1399		0.2565	False		,,,				2504	0.1871				p.E349E		Atlas-SNP	.											.	SEC14L6	6	.	0			c.A1047G						PASS	.																																			SO:0001819	synonymous_variant	730005	exon11			CCCATCTTCAGGC		CCDS54518.1	22q12.2	2011-05-06			ENSG00000214491	ENSG00000214491			40047	protein-coding gene	gene with protein product							Standard	NM_001193336		Approved		uc021wnu.1	B5MCN3	OTTHUMG00000151267	ENST00000402034.2:c.1047A>G	22.37:g.30921371T>C		Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	204	203	0.995098	NM_001193336		Silent	SNP	ENST00000402034.2	37	CCDS54518.1																																																																																			C|0.290;N|0.001	0.290	strong		0.602	SEC14L6-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000322022.2		
KIAA0895	23366	hgsc.bcm.edu	37	7	36366404	36366404	+	Missense_Mutation	SNP	C	C	T	rs191576648		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:36366404C>T	ENST00000297063.6	-	7	1578	c.1528G>A	c.(1528-1530)Gaa>Aaa	p.E510K	KIAA0895_ENST00000436884.1_Missense_Mutation_p.E407K|KIAA0895_ENST00000453212.1_Missense_Mutation_p.E265K|KIAA0895_ENST00000338533.5_Missense_Mutation_p.E497K|KIAA0895_ENST00000440378.1_Missense_Mutation_p.E507K|KIAA0895_ENST00000317020.6_Missense_Mutation_p.E459K	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	510										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						TCAGTCAGTTCATTCACTTCC	0.418													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16857	0.0		0.0	False		,,,				2504	0.0				p.E510K		Atlas-SNP	.											.	KIAA0895	89	.	0			c.G1528A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,3788		0,0,1894	180.0	169.0	172.0		1528,1519,1489,1219,1375	5.6	1.0	7		172	1,8201		0,1,4100	no	missense,missense,missense,missense,missense	KIAA0895	NM_001100425.1,NM_001199706.1,NM_001199707.1,NM_001199708.1,NM_015314.2	56,56,56,56,56	0,1,5994	TT,TC,CC		0.0122,0.0,0.0083	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	510/521,507/518,497/508,407/418,459/470	36366404	1,11989	1894	4101	5995	SO:0001583	missense	23366	exon7			TCAGTTCATTCAC	BC028678	CCDS43570.1, CCDS47573.1, CCDS56482.1, CCDS56483.1, CCDS56484.1, CCDS75583.1	7p14.2	2008-11-27			ENSG00000164542	ENSG00000164542			22206	protein-coding gene	gene with protein product							Standard	NM_015314		Approved		uc003tfd.2	Q8NCT3	OTTHUMG00000154939	ENST00000297063.6:c.1528G>A	7.37:g.36366404C>T	ENSP00000297063:p.Glu510Lys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	246	100	0.406504	NM_001100425	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.36	2.811535	0.50527	0.0	1.22E-4	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000453212	.	.	.	5.6	5.6	0.85130	.	0.205140	0.51477	D	0.000096	T	0.45856	0.1363	L	0.33485	1.01	0.80722	D	1	B;B;B;B;B	0.31548	0.018;0.019;0.009;0.328;0.001	B;B;B;B;B	0.30495	0.023;0.023;0.015;0.116;0.004	T	0.43310	-0.9399	9	0.02654	T	1	-22.975	19.9925	0.97371	0.0:1.0:0.0:0.0	.	507;407;510;497;459	B7ZLT4;B4DF35;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;K0895_HUMAN;.;.	K	510;497;459;507;407;265	.	ENSP00000297063:E510K	E	-	1	0	KIAA0895	36332929	0.998000	0.40836	0.990000	0.47175	0.994000	0.84299	1.435000	0.34969	2.818000	0.97014	0.655000	0.94253	GAA	C|1.000;T|0.000	0.000	strong		0.418	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314	
OXTR	5021	hgsc.bcm.edu	37	3	8809184	8809184	+	Silent	SNP	G	G	A	rs237902	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:8809184G>A	ENST00000316793.3	-	3	1314	c.690C>T	c.(688-690)aaC>aaT	p.N230N	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	230					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	TGAGCCGCAAGTTCTGCCAGA	0.667													G|||	1240	0.247604	0.3124	0.2305	5008	,	,		14583	0.0546		0.327	False		,,,				2504	0.2894				p.N230N		Atlas-SNP	.											OXTR,NS,carcinoma,0,1	OXTR	31	1	0			c.C690T						PASS	.	G		1325,3073		208,909,1082	21.0	20.0	21.0		690	-1.7	0.0	3	dbSNP_79	21	2954,5642		522,1910,1866	no	coding-synonymous	OXTR	NM_000916.3		730,2819,2948	AA,AG,GG		34.3648,30.1273,32.9306		230/390	8809184	4279,8715	2199	4298	6497	SO:0001819	synonymous_variant	5021	exon3			CCGCAAGTTCTGC		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.690C>T	3.37:g.8809184G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	100	70	0.7	NM_000916	Q15071	Silent	SNP	ENST00000316793.3	37	CCDS2570.1																																																																																			G|0.714;A|0.286	0.286	strong		0.667	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2		
SCN10A	6336	hgsc.bcm.edu	37	3	38766701	38766701	+	Silent	SNP	C	C	T	rs6791171	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	163	0	0		WXS	Illumina HiSeq	Phase_I	156	57	0.365385	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	
SPEF2	79925	hgsc.bcm.edu	37	5	35654711	35654711	+	Silent	SNP	C	C	T	rs2270558	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:35654711C>T	ENST00000356031.3	+	7	1015	c.861C>T	c.(859-861)gaC>gaT	p.D287D	SPEF2_ENST00000509059.1_Silent_p.D287D|SPEF2_ENST00000282469.6_Silent_p.D287D|SPEF2_ENST00000440995.2_Silent_p.D287D	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	287					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)			ACTCAGATGACGAGTACATTA	0.368													C|||	3391	0.677117	0.7194	0.683	5008	,	,		16471	0.7401		0.5229	False		,,,				2504	0.7096				p.D287D		Atlas-SNP	.											SPEF2,NS,carcinoma,+2,1	SPEF2	324	1	0			c.C861T						PASS	.	C	,	3037,1369	672.6+/-402.7	1029,979,195	73.0	75.0	74.0		861,861	-3.9	1.0	5	dbSNP_100	74	4662,3938	602.0+/-394.5	1232,2198,870	no	coding-synonymous,coding-synonymous	SPEF2	NM_024867.3,NM_144722.3	,	2261,3177,1065	TT,TC,CC		45.7907,31.0713,40.8042	,	287/1823,287/515	35654711	7699,5307	2203	4300	6503	SO:0001819	synonymous_variant	79925	exon7			AGATGACGAGTAC	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.861C>T	5.37:g.35654711C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	139	136	0.978417	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Silent	SNP	ENST00000356031.3	37	CCDS43309.1																																																																																			C|0.379;A|0.004	.	strong		0.368	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
SFTA2	389376	hgsc.bcm.edu	37	6	30899571	30899571	+	Splice_Site	SNP	C	C	T	rs2286656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:30899571C>T	ENST00000359086.3	-	2	141	c.63G>A	c.(61-63)ggG>ggA	p.G21G	Y_RNA_ENST00000516952.1_RNA	NM_205854.2	NP_995326.1	Q6UW10	SFTA2_HUMAN	surfactant associated 2	21						extracellular region (GO:0005576)				lung(2)	2						TCATACCCGGCCCTGCGGATC	0.517													C|||	1414	0.282348	0.1203	0.366	5008	,	,		19919	0.3641		0.1839	False		,,,				2504	0.4591				p.G21G		Atlas-SNP	.											.	SFTA2	6	.	0			c.G63A						PASS	.	C		397,2623		33,331,1146	58.0	70.0	66.0		63	2.1	0.9	6	dbSNP_100	66	810,4608		62,686,1961	yes	coding-synonymous-near-splice	SFTA2	NM_205854.2		95,1017,3107	TT,TC,CC		14.9502,13.1457,14.3043		21/79	30899571	1207,7231	1510	2709	4219	SO:0001630	splice_region_variant	389376	exon2			ACCCGGCCCTGCG	AY102070	CCDS4691.1	6p21.3	2008-08-26	2008-08-26	2008-08-26	ENSG00000196260	ENSG00000196260			18386	protein-coding gene	gene with protein product			"""surfactant associated protein G"""	SFTPG			Standard	NM_205854		Approved		uc003nsf.3	Q6UW10	OTTHUMG00000031183	ENST00000359086.3:c.62-1G>A	6.37:g.30899571C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	90	28	0.311111	NM_205854	A2ABK7|A2ACH1|B7ZCJ7	Silent	SNP	ENST00000359086.3	37	CCDS4691.1																																																																																			C|0.811;T|0.189	0.189	strong		0.517	SFTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076360.2	NM_205854	Silent
OSGIN1	29948	hgsc.bcm.edu	37	16	83999548	83999548	+	Missense_Mutation	SNP	T	T	C	rs62640905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	76	0	0		WXS	Illumina HiSeq	Phase_I	53	43	0.811321	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	
COPZ1	22818	hgsc.bcm.edu	37	12	54734289	54734289	+	Intron	SNP	A	A	G	rs11170877	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:54734289A>G	ENST00000262061.2	+	2	55				COPZ1_ENST00000552362.1_Intron|COPZ1_ENST00000548753.1_Intron|COPZ1_ENST00000551779.1_Intron|COPZ1_ENST00000548281.1_Intron|COPZ1_ENST00000416254.2_Intron|COPZ1_ENST00000553231.1_Intron|RP11-968A15.8_ENST00000553061.1_RNA|COPZ1_ENST00000549116.1_Intron|COPZ1_ENST00000549043.1_Start_Codon_SNP_p.M1V|COPZ1_ENST00000552218.1_Intron|COPZ1_ENST00000455864.2_Intron	NM_001271734.1|NM_001271736.1|NM_016057.1	NP_001258663.1|NP_001258665.1|NP_057141.1	P61923	COPZ1_HUMAN	coatomer protein complex, subunit zeta 1						COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)				kidney(1)|lung(4)	5						ACCAGTGGTGATGGGAGGCTT	0.488													G|||	1008	0.201278	0.2413	0.2349	5008	,	,		18652	0.2222		0.1252	False		,,,				2504	0.18				p.M1V		Atlas-SNP	.											.	COPZ1	10	.	0			c.A1G						PASS	.	G		1016,3390	728.6+/-410.0	136,744,1323	149.0	123.0	132.0			2.5	0.0	12	dbSNP_120	132	958,7642	775.2+/-407.7	58,842,3400	no	intron	COPZ1	NM_016057.1		194,1586,4723	GG,GA,AA		11.1395,23.0595,15.1776			54734289	1974,11032	2203	4300	6503	SO:0001627	intron_variant	22818	exon2			GTGGTGATGGGAG	AF151878	CCDS8877.1, CCDS61137.1, CCDS61138.1, CCDS61139.1	12q13.2-q13.3	2008-02-05		2003-07-23					2243	protein-coding gene	gene with protein product		615472	"""coatomer protein complex, subunit zeta"""	COPZ			Standard	NM_001271734		Approved	CGI-120	uc009znm.2	P61923		ENST00000262061.2:c.19-42A>G	12.37:g.54734289A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	155	73	0.470968	NM_001271736	B4DDX8|B4DHZ0|F8VS17|F8VWL5|Q549N6|Q9Y3C3	Missense_Mutation	SNP	ENST00000262061.2	37	CCDS8877.1	371	0.16987179487179488	80	0.16260162601626016	76	0.20994475138121546	126	0.2202797202797203	89	0.11741424802110818	G	7.333	0.619402	0.14129	0.230595	0.111395	ENSG00000111481	ENST00000549043;ENST00000550713	.	.	.	4.35	2.49	0.30216	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10800	-1.0614	6	0.87932	D	0	.	4.024	0.09678	0.1994:0.0:0.6156:0.185	rs11170877;rs58661926;rs11170877	1	F8VWL5	.	V	1	.	ENSP00000449270:M1V	M	+	1	0	COPZ1	53020556	0.000000	0.05858	0.000000	0.03702	0.252000	0.25951	0.266000	0.18534	0.206000	0.20587	-0.213000	0.12676	ATG	A|0.825;G|0.175	0.175	strong		0.488	COPZ1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405753.1	NM_016057	
GAB3	139716	hgsc.bcm.edu	37	X	153925443	153925443	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:153925443T>C	ENST00000369575.3	-	7	1419	c.1388A>G	c.(1387-1389)gAa>gGa	p.E463G	GAB3_ENST00000424127.2_Missense_Mutation_p.E464G|GAB3_ENST00000496390.1_5'UTR	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	463					macrophage differentiation (GO:0030225)					NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|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)					AGATGCATGTTCCCGGATGAT	0.537																																					p.E464G		Atlas-SNP	.											.	GAB3	73	.	0			c.A1391G						PASS	.						146.0	123.0	131.0					X																	153925443		2203	4300	6503	SO:0001583	missense	139716	exon7			GCATGTTCCCGGA	AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219		"""Pleckstrin homology (PH) domain containing"""	17515	protein-coding gene	gene with protein product	"""DOS/Gab family member 3"", ""Gab3 scaffolding protein"""	300482				11739737	Standard	XM_005274648		Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000369575.3:c.1388A>G	X.37:g.153925443T>C	ENSP00000358588:p.Glu463Gly	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	74	4	0.0540541	NM_001081573	A6NHF8|E9PB44	Missense_Mutation	SNP	ENST00000369575.3	37	CCDS14760.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.675913	0.47886	.	.	ENSG00000160219	ENST00000369575;ENST00000369568;ENST00000424127	T;T;T	0.30448	1.53;1.53;1.53	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	M	0.88031	2.925	0.39665	D	0.970665	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.997;0.996	T	0.69884	-0.5024	10	0.87932	D	0	-15.0336	12.0037	0.53246	0.0:0.0:0.0:1.0	.	464;464;463	A6NHF8;E9PB44;Q8WWW8	.;.;GAB3_HUMAN	G	463;464;464	ENSP00000358588:E463G;ENSP00000358581:E464G;ENSP00000399588:E464G	ENSP00000358581:E464G	E	-	2	0	GAB3	153578637	1.000000	0.71417	0.875000	0.34327	0.065000	0.16274	5.325000	0.65869	1.808000	0.52836	0.486000	0.48141	GAA	.	.	none		0.537	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573	
MOV10L1	54456	hgsc.bcm.edu	37	22	50582626	50582626	+	Missense_Mutation	SNP	A	A	G	rs2272837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50582626A>G	ENST00000262794.5	+	18	2542	c.2459A>G	c.(2458-2460)cAg>cGg	p.Q820R	MOV10L1_ENST00000545383.1_Missense_Mutation_p.Q820R|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395852.1_5'Flank|MOV10L1_ENST00000540615.1_Missense_Mutation_p.Q800R|MOV10L1_ENST00000395858.3_Missense_Mutation_p.Q820R	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	820			Q -> R (in dbSNP:rs2272837). {ECO:0000269|PubMed:14702039, 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)		AAGGTGCTACAGCCGGCCACC	0.617													G|||	1690	0.33746	0.1717	0.402	5008	,	,		20265	0.5734		0.2237	False		,,,				2504	0.3896				p.Q820R		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A2459G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN	851,3555	745.6+/-411.7	83,685,1435	115.0	99.0	104.0		2459,2399,2459	-4.2	0.0	22	dbSNP_100	104	2062,6538	718.2+/-406.2	257,1548,2495	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	43,43,43	340,2233,3930	GG,GA,AA		23.9767,19.3146,22.3974	benign,benign,benign	820/1166,800/1166,820/1212	50582626	2913,10093	2203	4300	6503	SO:0001583	missense	54456	exon18			TGCTACAGCCGGC	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.2459A>G	22.37:g.50582626A>G	ENSP00000262794:p.Gln820Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	724	0.3315018315018315	81	0.16463414634146342	128	0.35359116022099446	343	0.5996503496503497	172	0.22691292875989447	G	1.424	-0.572018	0.03882	0.193146	0.239767	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.52	-4.18	0.03846	.	0.946793	0.08938	N	0.872037	T	0.00012	0.0000	N	0.01817	-0.705	0.58432	P	6.999999999979245E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.36138	-0.9760	9	0.15499	T	0.54	-13.6798	8.6847	0.34229	0.6308:0.225:0.1443:0.0	rs2272837;rs5771079;rs17248126;rs2272837	800;820;820	F5H403;A8MXC6;Q9BXT6	.;.;M10L1_HUMAN	R	820;820;820;800	ENSP00000438978:Q820R;ENSP00000262794:Q820R;ENSP00000379199:Q820R;ENSP00000438542:Q800R	ENSP00000262794:Q820R	Q	+	2	0	MOV10L1	48924753	0.437000	0.25593	0.000000	0.03702	0.008000	0.06430	1.697000	0.37784	-0.519000	0.06444	-0.735000	0.03563	CAG	A|0.738;G|0.262	0.262	strong		0.617	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
AVPR1B	553	hgsc.bcm.edu	37	1	206230986	206230986	+	Silent	SNP	G	G	A	rs28676508	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:206230986G>A	ENST00000367126.4	+	2	1584	c.1119G>A	c.(1117-1119)tcG>tcA	p.S373S		NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	373					activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protein kinase C binding (GO:0005080)|vasopressin receptor activity (GO:0005000)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(3)|prostate(1)|skin(2)	20			BRCA - Breast invasive adenocarcinoma(75;0.0312)		Desmopressin(DB00035)|Terlipressin(DB02638)|Vasopressin(DB00067)	GCAGCCTCTCGAGCCGCCACA	0.701													G|||	1203	0.240216	0.4962	0.1225	5008	,	,		12235	0.0923		0.1312	False		,,,				2504	0.2423				p.S373S		Atlas-SNP	.											AVPR1B,rectum,carcinoma,0,1	AVPR1B	47	1	0			c.G1119A						scavenged	.	G		1866,2526		424,1018,754	13.0	15.0	14.0		1119	-4.5	0.2	1	dbSNP_125	14	1019,7549		71,877,3336	no	coding-synonymous	AVPR1B	NM_000707.3		495,1895,4090	AA,AG,GG		11.8931,42.4863,22.2608		373/425	206230986	2885,10075	2196	4284	6480	SO:0001819	synonymous_variant	553	exon2			CCTCTCGAGCCGC	D31833	CCDS73015.1	1q32	2014-05-06			ENSG00000198049	ENSG00000198049		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	896	protein-coding gene	gene with protein product		600264		AVPR3		7929452, 8586456	Standard	NM_000707		Approved		uc001hds.2	P47901	OTTHUMG00000184377	ENST00000367126.4:c.1119G>A	1.37:g.206230986G>A		Somatic	43	1	0.0232558		WXS	Illumina HiSeq	Phase_I	65	40	0.615385	NM_000707	B0M0J6|Q5TZ00	Silent	SNP	ENST00000367126.4	37	CCDS30994.1																																																																																			G|0.775;A|0.225	0.225	strong		0.701	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707	
TNK1	8711	hgsc.bcm.edu	37	17	7286326	7286326	+	Silent	SNP	T	T	A	rs1554948	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7286326T>A	ENST00000576812.1	+	2	450	c.81T>A	c.(79-81)ctT>ctA	p.L27L	TNK1_ENST00000570896.1_Silent_p.L27L|TNK1_ENST00000311668.2_Silent_p.L27L	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)				GGCCCATCCTTGAGGAGCTTA	0.592													.|||	1926	0.384585	0.2965	0.3314	5008	,	,		19751	0.2579		0.4533	False		,,,				2504	0.6012				p.L27L		Atlas-SNP	.											.	TNK1	31	.	0			c.T81A						PASS	.	T		1350,2944		239,872,1036	58.0	62.0	61.0		81	-10.1	0.4	17	dbSNP_88	61	3920,4584		935,2050,1267	no	coding-synonymous	TNK1	NM_003985.3		1174,2922,2303	AA,AT,TT		46.096,31.4392,41.1783		27/662	7286326	5270,7528	2147	4252	6399	SO:0001819	synonymous_variant	8711	exon2			CATCCTTGAGGAG	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.81T>A	17.37:g.7286326T>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_003985		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			T|0.623;A|0.377	0.377	strong		0.592	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	
LRP2	4036	hgsc.bcm.edu	37	2	170163816	170163816	+	Silent	SNP	G	G	T	rs34104660	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:170163816G>T	ENST00000263816.3	-	4	687	c.402C>A	c.(400-402)ccC>ccA	p.P134P	LRP2_ENST00000443831.1_Silent_p.P134P	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	134	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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)"""	CAGCTCCATCGGGGCAGTCTC	0.453													T|||	238	0.047524	0.0666	0.0476	5008	,	,		18149	0.0		0.0815	False		,,,				2504	0.0358				p.P134P		Atlas-SNP	.											.	LRP2	751	.	0			c.C402A						PASS	.	T		264,4142	802.7+/-415.7	6,252,1945	150.0	112.0	125.0		402	-10.5	0.0	2	dbSNP_126	125	688,7912	788.3+/-407.6	33,622,3645	no	coding-synonymous	LRP2	NM_004525.2		39,874,5590	TT,TG,GG		8.0,5.9918,7.3197		134/4656	170163816	952,12054	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon4			TCCATCGGGGCAG		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.402C>A	2.37:g.170163816G>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.934;T|0.066	0.066	strong		0.453	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
EPHA8	2046	hgsc.bcm.edu	37	1	22919904	22919904	+	Silent	SNP	C	C	T	rs209696	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	178	0	0		WXS	Illumina HiSeq	Phase_I	143	34	0.237762	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	
MYO16	23026	hgsc.bcm.edu	37	13	109777503	109777503	+	Missense_Mutation	SNP	A	A	G	rs157024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:109777503A>G	ENST00000357550.2	+	29	3554	c.3513A>G	c.(3511-3513)atA>atG	p.I1171M	MYO16_ENST00000457511.2_Missense_Mutation_p.I683M|MYO16_ENST00000356711.2_Missense_Mutation_p.I1171M	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)			TTCAGAGAATAAGCATCAGAC	0.423													G|||	665	0.132788	0.093	0.1902	5008	,	,		19256	0.1141		0.1441	False		,,,				2504	0.1534				p.I1193M		Atlas-SNP	.											.	MYO16	285	.	0			c.A3579G						PASS	.	G	MET/ILE,MET/ILE	474,3932	782.5+/-414.6	17,440,1746	71.0	69.0	69.0		3579,3513	3.7	1.0	13	dbSNP_79	69	1189,7411	764.2+/-407.6	79,1031,3190	yes	missense,missense	MYO16	NM_001198950.1,NM_015011.1	10,10	96,1471,4936	GG,GA,AA		13.8256,10.7581,12.7864	benign,benign	1193/1881,1171/1859	109777503	1663,11343	2203	4300	6503	SO:0001583	missense	23026	exon30			GAGAATAAGCATC		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.3513A>G	13.37:g.109777503A>G	ENSP00000350160:p.Ile1171Met	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	301	135	0.448505	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	283	0.1295787545787546	43	0.08739837398373984	59	0.16298342541436464	75	0.13111888111888112	106	0.13984168865435356	G	3.681	-0.065551	0.07273	0.107581	0.138256	ENSG00000041515	ENST00000356711;ENST00000357550;ENST00000457511	D;D;D	0.95518	-3.73;-3.73;-3.73	5.51	3.68	0.42216	.	0.277746	0.24573	N	0.037361	T	0.01592	0.0051	N	0.02539	-0.55	0.54753	P	1.3000000000040757E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49244	-0.8960	8	.	.	.	.	9.7733	0.40603	0.2358:0.0:0.7642:0.0	rs157024;rs17393560;rs52818809;rs56579413;rs57240489;rs157024	683;1171	F8W883;Q9Y6X6	.;MYO16_HUMAN	M	1171;1171;683	ENSP00000349145:I1171M;ENSP00000350160:I1171M;ENSP00000401633:I683M	.	I	+	3	3	MYO16	108575504	1.000000	0.71417	0.976000	0.42696	0.311000	0.27955	2.054000	0.41335	0.247000	0.21414	-0.699000	0.03677	ATA	A|0.869;G|0.131	0.131	strong		0.423	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
KIAA1586	57691	hgsc.bcm.edu	37	6	56919443	56919443	+	Missense_Mutation	SNP	A	A	G	rs61740375	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56919443A>G	ENST00000370733.4	+	4	2353	c.2146A>G	c.(2146-2148)Ata>Gta	p.I716V	KIAA1586_ENST00000545356.1_Missense_Mutation_p.I689V	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	716							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			tttaatgaacataatttgtac	0.318													a|||	462	0.0922524	0.1142	0.0865	5008	,	,		16956	0.0893		0.0944	False		,,,				2504	0.0675				p.I716V		Atlas-SNP	.											.	KIAA1586	59	.	0			c.A2146G						PASS	.	A	VAL/ILE	440,3944		20,400,1772	25.0	25.0	25.0		2146	2.0	1.0	6	dbSNP_129	25	678,7904		29,620,3642	yes	missense	KIAA1586	NM_020931.2	29	49,1020,5414	GG,GA,AA		7.9003,10.0365,8.6226	possibly-damaging	716/788	56919443	1118,11848	2192	4291	6483	SO:0001583	missense	57691	exon4			ATGAACATAATTT	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.2146A>G	6.37:g.56919443A>G	ENSP00000359768:p.Ile716Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	185	0.08470695970695971	43	0.08739837398373984	30	0.08287292817679558	39	0.06818181818181818	73	0.09630606860158311	a	6.156	0.397023	0.11638	0.100365	0.079003	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.21361	2.01;2.01	3.23	2.04	0.26737	Ribonuclease H-like (1);	.	.	.	.	T	0.02418	0.0074	N	0.08118	0	0.53005	P	4.0000000000040004E-5	B;B	0.21381	0.055;0.055	B;B	0.22386	0.039;0.039	T	0.47275	-0.9130	8	0.11794	T	0.64	.	5.301	0.15778	0.8611:0.0:0.1389:0.0	rs61740375	689;716	F5H2N6;Q9HCI6	.;K1586_HUMAN	V	716;689	ENSP00000359768:I716V;ENSP00000445507:I689V	ENSP00000359768:I716V	I	+	1	0	KIAA1586	57027402	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.205000	0.32308	0.431000	0.26258	-0.290000	0.09829	ATA	A|0.917;G|0.083	0.083	strong		0.318	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	
LATS1	9113	hgsc.bcm.edu	37	6	149983216	149983216	+	Silent	SNP	G	G	A	rs3924871	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	145	0	0		WXS	Illumina HiSeq	Phase_I	132	57	0.431818	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	
BCL7A	605	hgsc.bcm.edu	37	12	122497001	122497001	+	Silent	SNP	T	T	C	rs28629903	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:122497001T>C	ENST00000261822.4	+	6	771	c.565T>C	c.(565-567)Ttg>Ctg	p.L189L	BCL7A_ENST00000538010.1_Silent_p.L210L	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	189					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)		CCCCAAGGATTTGGAAGGAGT	0.522			T	MYC	BNHL								T|||	2531	0.505391	0.3487	0.6196	5008	,	,		19418	0.4921		0.5795	False		,,,				2504	0.5736				p.L210L	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.T628C						PASS	.	T	,	1667,2739	506.6+/-366.4	313,1041,849	75.0	71.0	72.0		565,628	1.6	1.0	12	dbSNP_125	72	4817,3783	614.2+/-396.2	1332,2153,815	no	coding-synonymous,coding-synonymous	BCL7A	NM_001024808.1,NM_020993.3	,	1645,3194,1664	CC,CT,TT		43.9884,37.8348,49.8539	,	189/211,210/232	122497001	6484,6522	2203	4300	6503	SO:0001819	synonymous_variant	605	exon6			AAGGATTTGGAAG	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.565T>C	12.37:g.122497001T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	110	106	0.963636	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Silent	SNP	ENST00000261822.4	37	CCDS53841.1																																																																																			T|0.501;C|0.499	0.499	strong		0.522	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1		
CYP27A1	1593	hgsc.bcm.edu	37	2	219678877	219678877	+	Missense_Mutation	SNP	C	C	T	rs41272687	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219678877C>T	ENST00000258415.4	+	6	1578	c.1151C>T	c.(1150-1152)cCg>cTg	p.P384L		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	384	Sterol-binding. {ECO:0000255}.				bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cholestanetriol 26-monooxygenase activity (GO:0047749)|cholesterol 26-hydroxylase activity (GO:0031073)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(3)|urinary_tract(1)	26		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Chenodeoxycholic acid(DB06777)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Pegvisomant(DB00082)	GCCCACATGCCGTTGCTCAAA	0.577													C|||	43	0.00858626	0.0015	0.0086	5008	,	,		20653	0.0		0.0209	False		,,,				2504	0.0143				p.P384L		Atlas-SNP	.											.	CYP27A1	52	.	0			c.C1151T	GRCh37	CM005424	CYP27A1	M	rs41272687	PASS	.	C	LEU/PRO	18,4388	26.2+/-53.5	0,18,2185	79.0	69.0	72.0		1151	5.8	1.0	2	dbSNP_127	72	223,8377	92.3+/-154.4	2,219,4079	yes	missense	CYP27A1	NM_000784.3	98	2,237,6264	TT,TC,CC		2.593,0.4085,1.853	probably-damaging	384/532	219678877	241,12765	2203	4300	6503	SO:0001583	missense	1593	exon6			ACATGCCGTTGCT	BC017044	CCDS2423.1	2q35	2013-09-19	2003-01-14		ENSG00000135929	ENSG00000135929		"""Cytochrome P450s"""	2605	protein-coding gene	gene with protein product	"""cerebrotendinous xanthomatosis"""	606530	"""cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1"""	CYP27		2019602	Standard	NM_000784		Approved	CTX, CP27	uc002viz.4	Q02318	OTTHUMG00000048238	ENST00000258415.4:c.1151C>T	2.37:g.219678877C>T	ENSP00000258415:p.Pro384Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	87	62	0.712644	NM_000784	A8K303|Q6LDB4|Q86YQ6	Missense_Mutation	SNP	ENST00000258415.4	37	CCDS2423.1	18	0.008241758241758242	0	0.0	1	0.0027624309392265192	0	0.0	17	0.022427440633245383	C	25.5	4.649480	0.87958	0.004085	0.02593	ENSG00000135929	ENST00000258415	T	0.74947	-0.89	5.76	5.76	0.90799	.	0.107590	0.64402	D	0.000004	T	0.76863	0.4047	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.85215	0.1023	10	0.87932	D	0	-28.2801	18.9739	0.92728	0.0:1.0:0.0:0.0	rs41272687;rs59907267;rs61733620	384	Q02318	CP27A_HUMAN	L	384	ENSP00000258415:P384L	ENSP00000258415:P384L	P	+	2	0	CYP27A1	219387121	1.000000	0.71417	0.969000	0.41365	0.460000	0.32559	7.629000	0.83207	2.706000	0.92434	0.655000	0.94253	CCG	C|0.985;T|0.015	0.015	strong		0.577	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4		
ZP3	7784	hgsc.bcm.edu	37	7	76069881	76069881	+	Missense_Mutation	SNP	A	A	G	rs2906998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76069881A>G	ENST00000394857.3	+	7	1071	c.1013A>G	c.(1012-1014)cAt>cGt	p.H338R	ZP3_ENST00000336517.4_Missense_Mutation_p.H287R|ZP3_ENST00000467555.1_3'UTR|ZP3_ENST00000416245.1_Missense_Mutation_p.H162R	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	338					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						AGGCAGCCTCATGTCATGAGC	0.537																																					p.H338R		Atlas-SNP	.											.	ZP3	32	.	0			c.A1013G						PASS	.						132.0	128.0	130.0					7																	76069881		2203	4300	6503	SO:0001583	missense	7784	exon7			AGCCTCATGTCAT	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.1013A>G	7.37:g.76069881A>G	ENSP00000378326:p.His338Arg	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	335	31	0.0925373	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	9.044|9.044	0.990333|0.990333	0.18966|0.18966	.|.	.|.	ENSG00000188372|ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245|ENST00000394860	T;T;T|.	0.21031|.	2.61;2.82;2.03|.	4.68|4.68	-7.24|-7.24	0.01475|0.01475	.|.	1.306680|.	0.05708|.	N|.	0.595475|.	T|T	0.32912|0.32912	0.0845|0.0845	L|L	0.53249|0.53249	1.67|1.67	0.09310|0.09310	N|N	1|1	B;B|.	0.12013|.	0.005;0.001|.	B;B|.	0.13407|.	0.009;0.001|.	T|T	0.38908|0.38908	-0.9639|-0.9639	10|5	0.23891|.	T|.	0.37|.	2.8954|2.8954	3.3471|3.3471	0.07139|0.07139	0.1819:0.4453:0.2607:0.1121|0.1819:0.4453:0.2607:0.1121	rs2906998|rs2906998	287;338|.	P21754-3;P21754|.	.;ZP3_HUMAN|.	R|V	287;338;338;162|172	ENSP00000337310:H287R;ENSP00000378326:H338R;ENSP00000411955:H162R|.	ENSP00000337310:H287R|.	H|M	+|+	2|1	0|0	ZP3|ZP3	75907817|75907817	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.016000|0.016000	0.09150|0.09150	-1.122000|-1.122000	0.03267|0.03267	-1.144000|-1.144000	0.02862|0.02862	0.459000|0.459000	0.35465|0.35465	CAT|ATG	A|0.885;G|0.115	0.115	strong		0.537	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587185	15587185	+	Missense_Mutation	SNP	C	C	T	rs733731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:15587185C>T	ENST00000340880.4	-	2	776	c.296G>A	c.(295-297)cGa>cAa	p.R99Q	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.R99Q	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	99			R -> Q (in dbSNP:rs733731). {ECO:0000269|PubMed:12975309}.		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.R99fs*10(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						TACGTCATGTCGGGCCACCTC	0.622													C|||	1759	0.351238	0.3457	0.3401	5008	,	,		19780	0.3631		0.4056	False		,,,				2504	0.2986				p.R99Q		Atlas-SNP	.											PGLYRP2_ENST00000292609,NS,carcinoma,0,4	PGLYRP2	116	4	2	Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(2)	c.G296A						PASS	.	C	GLN/ARG	1516,2890	482.6+/-359.5	259,998,946	154.0	107.0	123.0		296	-5.8	0.0	19	dbSNP_86	123	3316,5284	494.8+/-373.9	672,1972,1656	yes	missense	PGLYRP2	NM_052890.3	43	931,2970,2602	TT,TC,CC		38.5581,34.4076,37.1521	benign	99/577	15587185	4832,8174	2203	4300	6503	SO:0001583	missense	114770	exon2			TCATGTCGGGCCA	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.296G>A	19.37:g.15587185C>T	ENSP00000345968:p.Arg99Gln	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	254	112	0.440945	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	788	0.3608058608058608	162	0.32926829268292684	113	0.31215469613259667	209	0.36538461538461536	304	0.40105540897097625	C	3.013	-0.203499	0.06180	0.344076	0.385581	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.04706	3.6;3.57	5.27	-5.85	0.02311	.	0.940554	0.08756	N	0.898418	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.18741	0.03;0.002	B;B	0.10450	0.005;0.002	T	0.47058	-0.9146	9	0.09843	T	0.71	-8.6097	14.0632	0.64812	0.0:0.6294:0.0:0.3706	rs733731;rs3813134;rs17721949;rs52810675;rs58606529;rs733731	99;99	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	Q	99	ENSP00000345968:R99Q;ENSP00000292609:R99Q	ENSP00000292609:R99Q	R	-	2	0	PGLYRP2	15448185	0.012000	0.17670	0.001000	0.08648	0.004000	0.04260	-0.461000	0.06712	-1.182000	0.02727	-1.264000	0.01445	CGA	C|0.637;T|0.363	0.363	strong		0.622	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
DNTTIP2	30836	hgsc.bcm.edu	37	1	94342564	94342564	+	Missense_Mutation	SNP	C	C	A	rs3747965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:94342564C>A	ENST00000436063.2	-	2	984	c.927G>T	c.(925-927)gaG>gaT	p.E309D	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	309			E -> D (in dbSNP:rs3747965). {ECO:0000269|PubMed:12786946, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TTTCTTTCCCCTCATCTGTTA	0.378													C|||	1727	0.344848	0.0817	0.33	5008	,	,		19818	0.5565		0.325	False		,,,				2504	0.5133				p.E309D		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.G927T						PASS	.	C	ASP/GLU	505,3149		34,437,1356	65.0	54.0	58.0		927	0.4	0.0	1	dbSNP_107	58	2741,5429		446,1849,1790	yes	missense	DNTTIP2	NM_014597.4	45	480,2286,3146	AA,AC,CC		33.5496,13.8205,27.4526	possibly-damaging	309/757	94342564	3246,8578	1827	4085	5912	SO:0001583	missense	30836	exon2			TTTCCCCTCATCT	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.927G>T	1.37:g.94342564C>A	ENSP00000411010:p.Glu309Asp	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	84	81	0.964286	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	741	0.3392857142857143	44	0.08943089430894309	124	0.3425414364640884	325	0.5681818181818182	248	0.32717678100263853	C	7.180	0.589308	0.13812	0.138205	0.335496	ENSG00000067334	ENST00000436063	T	0.22134	1.97	4.83	0.373	0.16178	.	1.095520	0.06942	N	0.813102	T	0.07324	0.0185	L	0.56769	1.78	0.80722	P	0.0	B	0.12630	0.006	B	0.10450	0.005	T	0.35943	-0.9768	9	0.38643	T	0.18	.	4.5422	0.12064	0.2991:0.529:0.0:0.1719	rs3747965;rs17846411;rs17859454;rs52797280;rs59636660;rs3747965	309	Q5QJE6	TDIF2_HUMAN	D	309	ENSP00000411010:E309D	ENSP00000352137:E309D	E	-	3	2	DNTTIP2	94115152	0.000000	0.05858	0.001000	0.08648	0.292000	0.27327	-1.753000	0.01818	-0.083000	0.12618	-0.345000	0.07892	GAG	C|0.661;A|0.339	0.339	strong		0.378	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
HAS1	3036	hgsc.bcm.edu	37	19	52220351	52220351	+	Silent	SNP	G	G	A	rs11084111	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52220351G>A	ENST00000222115.1	-	3	832	c.798C>T	c.(796-798)gaC>gaT	p.D266D	HAS1_ENST00000540069.2_Silent_p.D265D|HAS1_ENST00000594621.1_Silent_p.D120D|HAS1_ENST00000601714.1_Silent_p.D273D	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	266					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GGATCCGCACGTCCCCACCAA	0.607													g|||	893	0.178315	0.1263	0.098	5008	,	,		17074	0.4435		0.1123	False		,,,				2504	0.1002				p.D266D	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.C798T						PASS	.			578,3828	257.4+/-261.8	43,492,1668	101.0	96.0	98.0		798	-2.1	0.9	19	dbSNP_120	98	772,7828	182.6+/-231.0	22,728,3550	no	coding-synonymous	HAS1	NM_001523.2		65,1220,5218	AA,AG,GG		8.9767,13.1185,10.3798		266/579	52220351	1350,11656	2203	4300	6503	SO:0001819	synonymous_variant	3036	exon3			CCGCACGTCCCCA	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.798C>T	19.37:g.52220351G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																			G|0.855;A|0.145	0.145	strong		0.607	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
ANK1	286	hgsc.bcm.edu	37	8	41553928	41553928	+	Silent	SNP	C	C	G	rs504574	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:41553928C>G	ENST00000347528.4	-	26	2996	c.2913G>C	c.(2911-2913)ctG>ctC	p.L971L	ANK1_ENST00000379758.2_Silent_p.L971L|ANK1_ENST00000289734.7_Silent_p.L971L|ANK1_ENST00000352337.4_Silent_p.L971L|ANK1_ENST00000396945.1_Silent_p.L971L|ANK1_ENST00000265709.8_Silent_p.L1012L|ANK1_ENST00000396942.1_Silent_p.L971L	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	971	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TCCTGCTGGCCAGGCCCTCCT	0.716													C|||	2039	0.407149	0.1082	0.5461	5008	,	,		16503	0.5079		0.494	False		,,,				2504	0.5194				p.L1012L		Atlas-SNP	.											ANK1_ENST00000265709,NS,carcinoma,0,4	ANK1	497	4	0			c.G3036C						PASS	.	C	,,,,	646,3758		49,548,1605	34.0	37.0	36.0		2913,3036,2913,2913,2913	2.7	1.0	8	dbSNP_83	36	4071,4525		973,2125,1200	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	1022,2673,2805	GG,GC,CC		47.3592,14.6685,36.2846	,,,,	971/1881,1012/1898,971/1857,971/1882,971/1720	41553928	4717,8283	2202	4298	6500	SO:0001819	synonymous_variant	286	exon27			GCTGGCCAGGCCC	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2913G>C	8.37:g.41553928C>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	96	59	0.614583	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	908	0.4157509157509158	54	0.10975609756097561	191	0.5276243093922652	281	0.49125874125874125	382	0.503957783641161	C	9.971	1.225504	0.22457	0.146685	0.473592	ENSG00000029534	ENST00000520299	.	.	.	5.53	2.7	0.31948	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48833	-0.9000	3	.	.	.	.	7.5449	0.27761	0.1353:0.72:0.0:0.1447	rs504574;rs504574	.	.	.	R	293	.	.	G	-	1	0	ANK1	41673085	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.076000	0.41548	0.267000	0.21916	0.561000	0.74099	GGC	C|0.627;G|0.373	0.373	strong		0.716	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
GFAP	2670	hgsc.bcm.edu	37	17	42992714	42992714	+	Silent	SNP	C	C	T	rs2229011	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:42992714C>T	ENST00000253408.5	-	1	206	c.141G>A	c.(139-141)ccG>ccA	p.P47P	GFAP_ENST00000435360.2_Silent_p.P47P|GFAP_ENST00000586793.1_Silent_p.P47P|GFAP_ENST00000588735.1_Intron|GFAP_ENST00000591327.1_5'UTR	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	47	Head.		P -> L (in dbSNP:rs57474185). {ECO:0000269|PubMed:11138011, ECO:0000269|PubMed:15732097}.		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)				CCACCCGGGTCGGGAGTGGAG	0.662													C|||	103	0.0205671	0.0008	0.0375	5008	,	,		15949	0.0		0.0586	False		,,,				2504	0.0174				p.P47P		Atlas-SNP	.											.	GFAP	88	.	0			c.G141A						PASS	.	C	,,	40,4366		0,40,2163	22.0	26.0	25.0		141,141,141	-9.6	0.0	17	dbSNP_98	25	428,8170		9,410,3880	no	coding-synonymous,coding-synonymous,coding-synonymous	GFAP	NM_001131019.2,NM_001242376.1,NM_002055.4	,,	9,450,6043	TT,TC,CC		4.9779,0.9079,3.5989	,,	47/432,47/439,47/433	42992714	468,12536	2203	4299	6502	SO:0001819	synonymous_variant	2670	exon1			CCGGGTCGGGAGT	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.141G>A	17.37:g.42992714C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_001131019	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Silent	SNP	ENST00000253408.5	37	CCDS11491.1																																																																																			C|0.969;T|0.031	0.031	strong		0.662	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055	
LILRA2	11027	hgsc.bcm.edu	37	19	55086873	55086873	+	Nonsense_Mutation	SNP	G	G	A	rs575246367	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55086873G>A	ENST00000251377.3	+	6	939	c.806G>A	c.(805-807)tGg>tAg	p.W269*	LILRA2_ENST00000251376.3_Nonsense_Mutation_p.W269*|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRA2_ENST00000391738.3_Nonsense_Mutation_p.W269*|LILRB1_ENST00000396321.2_Intron|LILRA2_ENST00000391737.1_Nonsense_Mutation_p.W257*			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	269	Ig-like C2-type 3.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.W269L(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		CGCCCTGGTTGGCAGCCCCAG	0.622													g|||	24	0.00479233	0.0	0.0	5008	,	,		15852	0.0		0.001	False		,,,				2504	0.0235				p.W269X		Atlas-SNP	.											LILRA2,NS,carcinoma,0,1	LILRA2	99	1	1	Substitution - Missense(1)	lung(1)	c.G806A						scavenged	.						75.0	74.0	74.0					19																	55086873		2203	4300	6503	SO:0001587	stop_gained	11027	exon5			CTGGTTGGCAGCC	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.806G>A	19.37:g.55086873G>A	ENSP00000251377:p.Trp269*	Somatic	296	5	0.0168919		WXS	Illumina HiSeq	Phase_I	248	7	0.0282258	NM_001130917	O75020	Nonsense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.154944	0.38021	.	.	ENSG00000239998	ENST00000439534;ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	.	.	.	2.26	-4.53	0.03462	.	3.839380	0.00628	N	0.000462	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	0.3518	0.00350	0.3906:0.152:0.2111:0.2464	.	.	.	.	X	269;269;269;269;257	.	ENSP00000251376:W269X	W	+	2	0	LILRA2	59778685	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.564000	0.00918	-1.647000	0.01511	-0.527000	0.04329	TGG	.	.	none		0.622	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2		
NDST3	9348	hgsc.bcm.edu	37	4	118975189	118975189	+	Nonsense_Mutation	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:118975189G>T	ENST00000296499.5	+	2	527	c.124G>T	c.(124-126)Gaa>Taa	p.E42*	NDST3_ENST00000433996.2_Nonsense_Mutation_p.E42*	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	42	Heparan sulfate N-deacetylase 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)			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						ACAGGAAAATGAACTCTCTGA	0.423																																					p.E42X		Atlas-SNP	.											.	NDST3	107	.	0			c.G124T						PASS	.						122.0	119.0	120.0					4																	118975189		2203	4300	6503	SO:0001587	stop_gained	9348	exon2			GAAAATGAACTCT	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.124G>T	4.37:g.118975189G>T	ENSP00000296499:p.Glu42*	Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	123	60	0.487805	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Nonsense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	G	36	5.624220	0.96660	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	.	.	.	5.82	4.98	0.66077	.	0.262983	0.39083	N	0.001477	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	11.9424	0.52909	0.0:0.1318:0.7311:0.1371	.	.	.	.	X	42	.	ENSP00000296499:E42X	E	+	1	0	NDST3	119194637	1.000000	0.71417	0.305000	0.25099	0.920000	0.55202	7.237000	0.78164	1.441000	0.47550	0.650000	0.86243	GAA	.	.	none		0.423	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	
MYO9B	4650	hgsc.bcm.edu	37	19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	rs112900956	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17306074G>A	ENST00000594824.1	+	22	3985	c.3838G>A	c.(3838-3840)Ggc>Agc	p.G1280S	MYO9B_ENST00000595618.1_Missense_Mutation_p.G1280S|MYO9B_ENST00000397274.2_Missense_Mutation_p.G1280S			Q13459	MYO9B_HUMAN	myosin IXB	1280	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						CAAACCATGTGGCAGCCCAAG	0.701													G|||	19	0.00379393	0.0008	0.0029	5008	,	,		13079	0.0		0.0129	False		,,,				2504	0.0031				p.G1280S		Atlas-SNP	.											MYO9B_ENST00000319396,adrenal_gland,adrenal_cortical_adenoma,0,2	MYO9B	264	2	0			c.G3838A						PASS	.	G	SER/GLY,SER/GLY	11,3783		0,11,1886	20.0	27.0	25.0		3838,3838	-3.2	0.0	19	dbSNP_132	25	119,8027		0,119,3954	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	56,56	0,130,5840	AA,AG,GG		1.4608,0.2899,1.0888	benign,benign	1280/2023,1280/2158	17306074	130,11810	1897	4073	5970	SO:0001583	missense	4650	exon22			CCATGTGGCAGCC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.3838G>A	19.37:g.17306074G>A	ENSP00000471367:p.Gly1280Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	65	40	0.615385	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	5.753	0.323409	0.10900	0.002899	0.014608	ENSG00000099331	ENST00000397274	D	0.83673	-1.75	5.28	-3.16	0.05217	.	1.740110	0.03022	N	0.150866	T	0.65123	0.2661	L	0.34521	1.04	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.0;0.002	T	0.56932	-0.7897	10	0.07030	T	0.85	.	10.5091	0.44851	0.645:0.0:0.355:0.0	.	1280;1280;1286	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	S	1280	ENSP00000380444:G1280S	ENSP00000380444:G1280S	G	+	1	0	MYO9B	17167074	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.479000	0.06567	-0.339000	0.08401	-0.367000	0.07326	GGC	G|0.994;A|0.006	0.006	strong		0.701	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
ATXN3	4287	hgsc.bcm.edu	37	14	92537379	92537379	+	Silent	SNP	T	T	C	rs12896583		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:92537379T>C	ENST00000532032.1	-	10	900	c.891A>G	c.(889-891)caA>caG	p.Q297Q	ATXN3_ENST00000503767.1_Silent_p.Q282Q|ATXN3_ENST00000545170.1_Silent_p.Q306Q|ATXN3_ENST00000429774.2_Silent_p.Q290Q|ATXN3_ENST00000393287.5_Silent_p.Q297Q|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000340660.6_Silent_p.Q242Q|ATXN3_ENST00000502250.1_Silent_p.Q118Q			P54252	ATX3_HUMAN	ataxin 3	297	Poly-Gln.				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)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		gctgctgctgttgctgctttt	0.423																																					p.T136A	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											ATXN3,NS,carcinoma,0,1	ATXN3	46	1	0			c.A406G						PASS	.						46.0	45.0	45.0					14																	92537379		2203	4300	6503	SO:0001819	synonymous_variant	4287	exon6			CTGCTGTTGCTGC	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.891A>G	14.37:g.92537379T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	53	0.697368	NM_001164778	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37																																																																																				T|1.000;|0.000	.	strong		0.423	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
ZNF618	114991	hgsc.bcm.edu	37	9	116810204	116810204	+	Silent	SNP	G	G	A	rs12378906	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116810204G>A	ENST00000374126.5	+	14	1377	c.1278G>A	c.(1276-1278)caG>caA	p.Q426Q	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Silent_p.Q333Q			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	426					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						CCTCCAACCAGTCCCGATCGC	0.532													G|||	329	0.0656949	0.1203	0.0605	5008	,	,		21014	0.0		0.0885	False		,,,				2504	0.0399				p.Q333Q		Atlas-SNP	.											.	ZNF618	184	.	0			c.G999A						PASS	.	G		467,3649		17,433,1608	75.0	78.0	77.0		999	3.6	1.0	9	dbSNP_120	77	715,7715		33,649,3533	yes	coding-synonymous	ZNF618	NM_133374.2		50,1082,5141	AA,AG,GG		8.4816,11.346,9.4213		333/862	116810204	1182,11364	2058	4215	6273	SO:0001819	synonymous_variant	114991	exon13			CAACCAGTCCCGA	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.1278G>A	9.37:g.116810204G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				G|0.927;A|0.073	0.073	strong		0.532	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
SEMA5A	9037	hgsc.bcm.edu	37	5	9108333	9108333	+	Silent	SNP	C	C	T	rs34874986	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:9108333C>T	ENST00000382496.5	-	16	2657	c.1992G>A	c.(1990-1992)cgG>cgA	p.R664R		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	664	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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						GGGCTGTGCACCGTTCCCAAG	0.522													C|||	923	0.184305	0.208	0.1513	5008	,	,		20825	0.3333		0.0557	False		,,,				2504	0.1544				p.R664R		Atlas-SNP	.											SEMA5A,NS,carcinoma,-2,1	SEMA5A	236	1	0			c.G1992A						PASS	.	C		891,3515	344.9+/-308.3	98,695,1410	79.0	71.0	73.0		1992	1.9	1.0	5	dbSNP_126	73	420,8180	131.0+/-188.9	7,406,3887	no	coding-synonymous	SEMA5A	NM_003966.2		105,1101,5297	TT,TC,CC		4.8837,20.2224,10.08		664/1075	9108333	1311,11695	2203	4300	6503	SO:0001819	synonymous_variant	9037	exon16			TGTGCACCGTTCC	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.1992G>A	5.37:g.9108333C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	211	105	0.49763	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			C|0.879;T|0.121	0.121	strong		0.522	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
FLG	2312	hgsc.bcm.edu	37	1	152286032	152286032	+	Missense_Mutation	SNP	C	C	T	rs11588170	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152286032C>T	ENST00000368799.1	-	3	1365	c.1330G>A	c.(1330-1332)Ggg>Agg	p.G444R	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	444	Ser-rich.		G -> R (in dbSNP:rs11588170).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCTCAGCCCAGCCTTTCCG	0.582									Ichthyosis				-|||	1438	0.287141	0.0113	0.3905	5008	,	,		19918	0.5823		0.1421	False		,,,				2504	0.4315				p.G444R		Atlas-SNP	.											.	FLG	900	.	0			c.G1330A						PASS	.	C	ARG/GLY	161,4245		2,157,2044	201.0	196.0	198.0		1330	-0.6	0.0	1	dbSNP_120	198	1241,7359		97,1047,3156	yes	missense	FLG	NM_002016.1	125	99,1204,5200	TT,TC,CC		14.4302,3.6541,10.7796	probably-damaging	444/4062	152286032	1402,11604	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCAGCCCAGCCTT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1330G>A	1.37:g.152286032C>T	ENSP00000357789:p.Gly444Arg	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	364	134	0.368132	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	571	0.26144688644688646	9	0.018292682926829267	118	0.3259668508287293	333	0.5821678321678322	111	0.14643799472295516	-	9.564	1.119273	0.20877	0.036541	0.144302	ENSG00000143631	ENST00000368799	T	0.00768	5.72	2.5	-0.615	0.11587	.	.	.	.	.	T	0.00552	0.0018	L	0.53671	1.685	0.80722	P	0.0	P	0.51147	0.942	P	0.57244	0.816	T	0.48175	-0.9058	8	0.14252	T	0.57	.	3.0061	0.06028	0.0:0.467:0.2361:0.2968	rs11588170	444	P20930	FILA_HUMAN	R	444	ENSP00000357789:G444R	ENSP00000357789:G444R	G	-	1	0	FLG	150552656	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.639000	0.05446	-0.107000	0.12088	-0.458000	0.05436	GGG	C|0.839;T|0.161	0.161	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32489766	32489766	+	Missense_Mutation	SNP	A	A	T	rs41562819		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489766A>T	ENST00000374975.3	-	2	348	c.286T>A	c.(286-288)Ttc>Atc	p.F96I		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						TCTTCCAGGAAGTCCTTCTGG	0.647																																					p.F96I		Atlas-SNP	.											HLA-DRB5,brain,glioma,0,2	HLA-DRB5	31	2	0			c.T286A						PASS	.						39.0	34.0	36.0					6																	32489766		2125	4114	6239	SO:0001583	missense	3127	exon2			CCAGGAAGTCCTT		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.286T>A	6.37:g.32489766A>T	ENSP00000364114:p.Phe96Ile	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	32	28	0.875	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	2.149	-0.394867	0.04899	.	.	ENSG00000198502	ENST00000374975	T	0.00302	8.2	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);	1.726360	0.03614	N	0.235269	T	0.00012	0.0000	N	0.03154	-0.405	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42344	-0.9457	10	0.06099	T	0.92	.	2.9274	0.05788	0.4968:0.1765:0.2165:0.1102	rs41562819	23;96	Q29973;Q30154	.;DRB5_HUMAN	I	96	ENSP00000364114:F96I	ENSP00000364114:F96I	F	-	1	0	HLA-DRB5	32597744	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-11.144000	0.00004	-5.435000	0.00014	-4.131000	0.00010	TTC	G|0.474;A|0.526	.	strong		0.647	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
AURKC	6795	hgsc.bcm.edu	37	19	57742489	57742489	+	5'UTR	SNP	C	C	T	rs58264281	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57742489C>T	ENST00000302804.7	+	0	59				AURKC_ENST00000599062.1_5'Flank|AURKC_ENST00000598785.1_5'Flank|AURKC_ENST00000415300.2_Intron|AURKC_ENST00000448930.1_Splice_Site	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C						attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		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;0.0122)		ATCAGTGAGGCTGCAGGACGA	0.627													c|||	3845	0.767772	0.5719	0.8184	5008	,	,		13065	0.8492		0.835	False		,,,				2504	0.8436				.		Atlas-SNP	.											.	AURKC	97	.	0			.						PASS	.						23.0	28.0	26.0					19																	57742489		1762	3049	4811	SO:0001623	5_prime_UTR_variant	6795	.			GTGAGGCTGCAGG		CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"""serine/threonine kinase 13 (aurora/IPL1-like)"""	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.-128C>T	19.37:g.57742489C>T		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	39	35	0.897436	.	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Splice_Site	SNP	ENST00000302804.7	37	CCDS33128.1																																																																																			C|0.239;T|0.761	0.761	strong		0.627	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160	
PNPLA1	285848	hgsc.bcm.edu	37	6	36238357	36238357	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:36238357C>T	ENST00000394571.2	+	1	121	c.121C>T	c.(121-123)Cgg>Tgg	p.R41W	PNPLA1_ENST00000388715.3_Intron|PNPLA1_ENST00000312917.5_Intron	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	41	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						CCTGGCCCCCCGGATGCTGGA	0.662																																					p.R41W		Atlas-SNP	.											PNPLA1_ENST00000394571,NS,carcinoma,0,2	PNPLA1	92	2	0			c.C121T						scavenged	.						18.0	23.0	21.0					6																	36238357		692	1591	2283	SO:0001583	missense	285848	exon1			GCCCCCCGGATGC		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.121C>T	6.37:g.36238357C>T	ENSP00000378072:p.Arg41Trp	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	229	3	0.0131004	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	C	17.70	3.454761	0.63290	.	.	ENSG00000180316	ENST00000457797;ENST00000394571	T;T	0.80824	-1.42;-1.42	4.42	3.51	0.40186	Acyl transferase/acyl hydrolase/lysophospholipase (1);Patatin/Phospholipase A2-related (1);	0.150937	0.27147	U	0.020715	T	0.64972	0.2647	M	0.62723	1.935	0.30069	N	0.810181	P	0.44478	0.836	B	0.43867	0.434	T	0.59284	-0.7483	10	0.38643	T	0.18	-15.4586	7.1262	0.25473	0.2038:0.6141:0.1821:0.0	.	41	Q8N8W4	PLPL1_HUMAN	W	41	ENSP00000391868:R41W;ENSP00000378072:R41W	ENSP00000378072:R41W	R	+	1	2	PNPLA1	36346335	0.232000	0.23762	1.000000	0.80357	0.971000	0.66376	0.223000	0.17719	0.790000	0.33803	0.467000	0.42956	CGG	.	.	none		0.662	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
NDUFAF1	51103	hgsc.bcm.edu	37	15	41679685	41679685	+	Missense_Mutation	SNP	G	G	C	rs12900702	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:41679685G>C	ENST00000260361.4	-	5	1322	c.941C>G	c.(940-942)gCc>gGc	p.A314G		NM_016013.3	NP_057097.2	Q9Y375	CIA30_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 1	314			A -> G (in dbSNP:rs12900702). {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)		ATTTTCATAGGCAAATTCTTC	0.358													G|||	361	0.0720847	0.0121	0.111	5008	,	,		15415	0.0		0.1849	False		,,,				2504	0.0838				p.A314G		Atlas-SNP	.											.	NDUFAF1	39	.	0			c.C941G						PASS	.	G	GLY/ALA	163,4243	108.2+/-146.6	5,153,2045	78.0	87.0	84.0		941	5.6	1.0	15	dbSNP_121	84	1634,6966	299.4+/-304.4	153,1328,2819	yes	missense	NDUFAF1	NM_016013.2	60	158,1481,4864	CC,CG,GG		19.0,3.6995,13.8167	probably-damaging	314/328	41679685	1797,11209	2203	4300	6503	SO:0001583	missense	51103	exon5			TCATAGGCAAATT	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.941C>G	15.37:g.41679685G>C	ENSP00000260361:p.Ala314Gly	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	100	27	0.27	NM_016013	Q9BVZ5	Missense_Mutation	SNP	ENST00000260361.4	37	CCDS10075.1	193	0.08836996336996338	5	0.01016260162601626	47	0.1298342541436464	0	0.0	141	0.18601583113456466	G	32	5.189559	0.94923	0.036995	0.19	ENSG00000137806	ENST00000260361	T	0.65178	-0.14	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	M	0.71871	2.18	0.09310	P	0.99999999756846	P	0.52316	0.952	P	0.51895	0.683	T	0.00403	-1.1761	9	0.72032	D	0.01	-22.3975	19.5923	0.95520	0.0:0.0:1.0:0.0	rs12900702;rs52792714;rs12900702	314	Q9Y375	CIA30_HUMAN	G	314	ENSP00000260361:A314G	ENSP00000260361:A314G	A	-	2	0	NDUFAF1	39466977	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.859000	0.92264	2.644000	0.89710	0.557000	0.71058	GCC	G|0.873;C|0.127	0.127	strong		0.358	NDUFAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252692.2	NM_016013	
SIDT2	51092	hgsc.bcm.edu	37	11	117052532	117052532	+	Silent	SNP	C	C	A	rs61729990	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117052532C>A	ENST00000324225.4	+	3	846	c.315C>A	c.(313-315)cgC>cgA	p.R105R	SIDT2_ENST00000530948.1_3'UTR|SIDT2_ENST00000431081.2_Silent_p.R105R	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	105					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		GGTTTCAGCGCAAGTACCTCT	0.592											OREG0021368	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	23	0.00459265	0.0008	0.0072	5008	,	,		18191	0.0		0.0139	False		,,,				2504	0.0031				p.R105R		Atlas-SNP	.											SIDT2,colon,carcinoma,+1,1	SIDT2	82	1	0			c.C315A						PASS	.	C		17,4385	25.3+/-52.1	0,17,2184	87.0	87.0	87.0		315	-0.1	1.0	11	dbSNP_129	87	141,8451	70.7+/-133.2	0,141,4155	no	coding-synonymous	SIDT2	NM_001040455.1		0,158,6339	AA,AC,CC		1.6411,0.3862,1.2159		105/833	117052532	158,12836	2201	4296	6497	SO:0001819	synonymous_variant	51092	exon3			TCAGCGCAAGTAC	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.315C>A	11.37:g.117052532C>A		Somatic	98	0	0	1478	WXS	Illumina HiSeq	Phase_I	183	54	0.295082	NM_001040455	Q8NBY7|Q9Y357	Silent	SNP	ENST00000324225.4	37	CCDS31682.1																																																																																			C|0.991;A|0.009	0.009	strong		0.592	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
REXO4	57109	hgsc.bcm.edu	37	9	136279935	136279935	+	Missense_Mutation	SNP	C	C	T	rs6597630	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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|REXO4_ENST00000478037.1_5'UTR|ADAMTS13_ENST00000485925.1_Intron	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	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	190	101	0.531579	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		
ZNF214	7761	hgsc.bcm.edu	37	11	7022360	7022360	+	Missense_Mutation	SNP	A	A	C	rs2239734	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:7022360A>C	ENST00000278314.4	-	3	869	c.554T>G	c.(553-555)aTa>aGa	p.I185R	ZNF214_ENST00000536068.1_Missense_Mutation_p.I185R|ZNF214_ENST00000531083.1_5'Flank	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	185			I -> R (in dbSNP:rs2239734).		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)		ATGCTGAACTATGAGCTTCTG	0.433													A|||	522	0.104233	0.0378	0.1542	5008	,	,		18495	0.128		0.1083	False		,,,				2504	0.1299				p.I185R	Ovarian(22;251 657 736 21522 46864)	Atlas-SNP	.											.	ZNF214	65	.	0			c.T554G						PASS	.	A	ARG/ILE	262,4138	146.1+/-180.8	6,250,1944	105.0	105.0	105.0		554	3.1	0.9	11	dbSNP_98	105	843,7745	192.7+/-238.6	44,755,3495	yes	missense	ZNF214	NM_013249.2	97	50,1005,5439	CC,CA,AA		9.816,5.9545,8.5079	possibly-damaging	185/607	7022360	1105,11883	2200	4294	6494	SO:0001583	missense	7761	exon3			TGAACTATGAGCT	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.554T>G	11.37:g.7022360A>C	ENSP00000278314:p.Ile185Arg	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	173	89	0.514451	NM_013249	B2R8Q1	Missense_Mutation	SNP	ENST00000278314.4	37	CCDS31418.1	241	0.11034798534798534	13	0.026422764227642278	56	0.15469613259668508	89	0.1555944055944056	83	0.10949868073878628	A	6.532	0.466409	0.12402	0.059545	0.09816	ENSG00000149050	ENST00000278314;ENST00000536068	T;T	0.08008	3.14;3.14	4.29	3.12	0.35913	.	0.444056	0.19246	N	0.119042	T	0.00012	0.0000	N	0.08118	0	0.58432	P	4.000000000004E-6	B	0.09022	0.002	B	0.04013	0.001	T	0.43556	-0.9384	9	0.25106	T	0.35	.	7.7734	0.29021	0.7869:0.2131:0.0:0.0	rs2239734;rs17278329;rs52798655;rs57682570;rs2239734	185	Q9UL59	ZN214_HUMAN	R	185	ENSP00000278314:I185R;ENSP00000445373:I185R	ENSP00000278314:I185R	I	-	2	0	ZNF214	6978936	0.000000	0.05858	0.916000	0.36221	0.940000	0.58332	0.082000	0.14847	0.759000	0.33084	0.533000	0.62120	ATA	A|0.909;C|0.091	0.091	strong		0.433	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
UPF3A	65110	hgsc.bcm.edu	37	13	115047305	115047305	+	Missense_Mutation	SNP	G	G	A	rs3752105	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:115047305G>A	ENST00000375299.3	+	1	247	c.191G>A	c.(190-192)aGg>aAg	p.R64K	UPF3A_ENST00000351487.5_Missense_Mutation_p.R64K	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	64			R -> K (in dbSNP:rs3752105).		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)		GAGGAGAAGAGGACGGCCCTG	0.721													g|||	1524	0.304313	0.5416	0.17	5008	,	,		6771	0.1032		0.2584	False		,,,				2504	0.3333				p.R64K		Atlas-SNP	.											UPF3A,NS,carcinoma,0,1	UPF3A	47	1	0			c.G191A						PASS	.		LYS/ARG,LYS/ARG	1665,2487		352,961,763	6.0	7.0	6.0		191,191	0.4	0.3	13	dbSNP_107	6	1559,6677		178,1203,2737	yes	missense,missense	UPF3A	NM_023011.3,NM_080687.2	26,26	530,2164,3500	AA,AG,GG		18.9291,40.1012,26.0252	benign,benign	64/477,64/444	115047305	3224,9164	2076	4118	6194	SO:0001583	missense	65110	exon1			AGAAGAGGACGGC	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.191G>A	13.37:g.115047305G>A	ENSP00000364448:p.Arg64Lys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_080687	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Missense_Mutation	SNP	ENST00000375299.3	37	CCDS9543.1	596	0.27289377289377287	268	0.5447154471544715	69	0.19060773480662985	67	0.11713286713286714	192	0.2532981530343008	g	0.059	-1.228239	0.01518	0.401012	0.189291	ENSG00000169062	ENST00000375299;ENST00000351487	T;T	0.61980	0.06;0.06	3.1	0.383	0.16239	Regulator of nonsense-mediated decay, UPF3 (1);	0.193157	0.44902	N	0.000402	T	0.00012	0.0000	N	0.00841	-1.15	0.80722	P	0.0	B;B;B	0.18461	0.001;0.004;0.028	B;B;B	0.18263	0.006;0.006;0.021	T	0.45833	-0.9234	8	.	.	.	-6.5893	7.2758	0.26283	0.425:0.0:0.575:0.0	rs3752105	64;64;64	B4DGE0;Q9H1J1-2;Q9H1J1	.;.;REN3A_HUMAN	K	64	ENSP00000364448:R64K;ENSP00000329592:R64K	.	R	+	2	0	UPF3A	114065407	0.085000	0.21516	0.350000	0.25708	0.233000	0.25261	0.005000	0.13129	0.041000	0.15688	0.479000	0.44913	AGG	G|0.728;A|0.272	0.272	strong		0.721	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		
ZNF208	7757	hgsc.bcm.edu	37	19	22155918	22155918	+	Missense_Mutation	SNP	T	T	C	rs10425763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22155918T>C	ENST00000397126.4	-	4	2066	c.1918A>G	c.(1918-1920)Aaa>Gaa	p.K640E	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_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	108	0	0		WXS	Illumina HiSeq	Phase_I	86	28	0.325581	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	
RNPEP	6051	hgsc.bcm.edu	37	1	201973565	201973565	+	Missense_Mutation	SNP	G	G	A	rs3820439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201973565G>A	ENST00000295640.4	+	10	1778	c.1735G>A	c.(1735-1737)Gtc>Atc	p.V579I	RNPEP_ENST00000471105.1_3'UTR|RNPEP_ENST00000367286.3_Missense_Mutation_p.V540I|RP11-465N4.4_ENST00000419190.1_RNA	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	579			V -> I (in dbSNP:rs3820439).		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)			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)		GGGCCAAATCGTCCTTAAGAA	0.517													G|||	1658	0.33107	0.2224	0.2435	5008	,	,		19561	0.3968		0.2942	False		,,,				2504	0.5102				p.V579I	GBM(19;39 479 7473 13131 19462)	Atlas-SNP	.											.	RNPEP	39	.	0			c.G1735A						PASS	.	G	ILE/VAL	1130,3276	404.6+/-333.2	125,880,1198	112.0	119.0	117.0		1735	2.5	0.2	1	dbSNP_107	117	2440,6160	403.3+/-347.8	354,1732,2214	yes	missense	RNPEP	NM_020216.3	29	479,2612,3412	AA,AG,GG		28.3721,25.6468,27.4489	benign	579/651	201973565	3570,9436	2203	4300	6503	SO:0001583	missense	6051	exon10			CAAATCGTCCTTA	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.1735G>A	1.37:g.201973565G>A	ENSP00000295640:p.Val579Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	83	22	0.26506	NM_020216	Q9BVM9|Q9H1D4|Q9NPT7	Missense_Mutation	SNP	ENST00000295640.4	37	CCDS1418.1	673	0.30815018315018317	111	0.22560975609756098	105	0.2900552486187845	225	0.39335664335664333	232	0.30606860158311344	G	8.411	0.844100	0.16963	0.256468	0.283721	ENSG00000176393	ENST00000295640;ENST00000367286	T;T	0.43688	0.94;0.94	5.58	2.54	0.30619	Peptidase M1, leukotriene A4 hydrolase, aminopeptidase C-terminal (1);Armadillo-type fold (1);	0.292841	0.31495	N	0.007542	T	0.00012	0.0000	L	0.46741	1.465	0.58432	P	1.999999999946489E-6	B;B	0.16603	0.018;0.015	B;B	0.19946	0.02;0.027	T	0.40421	-0.9564	9	0.35671	T	0.21	-19.6368	6.1407	0.20259	0.2522:0.1335:0.6143:0.0	rs3820439;rs58505075;rs3820439	587;579	Q7RU04;Q9H4A4	.;AMPB_HUMAN	I	579;540	ENSP00000295640:V579I;ENSP00000356255:V540I	ENSP00000295640:V579I	V	+	1	0	RNPEP	200240188	0.891000	0.30450	0.193000	0.23327	0.508000	0.34012	1.254000	0.32897	0.635000	0.30488	0.655000	0.94253	GTC	G|0.707;A|0.293	0.293	strong		0.517	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216	
POU4F2	5458	hgsc.bcm.edu	37	4	147561804	147561804	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:147561804C>T	ENST00000281321.3	+	2	1322	c.1074C>T	c.(1072-1074)cgC>cgT	p.R358R	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	358					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)					CAGAGAAGCGCTCGCTCGAAG	0.602																																					p.R358R		Atlas-SNP	.											POU4F2,caecum,carcinoma,+1,1	POU4F2	83	1	0			c.C1074T						scavenged	.						74.0	77.0	76.0					4																	147561804		2203	4300	6503	SO:0001819	synonymous_variant	5458	exon2			GAAGCGCTCGCTC	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.1074C>T	4.37:g.147561804C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	55	3	0.0545455	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	37	CCDS34074.1																																																																																			.	.	none		0.602	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575	
GBGT1	26301	hgsc.bcm.edu	37	9	136037742	136037742	+	Missense_Mutation	SNP	G	G	A	rs2073924	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136037742G>A	ENST00000372040.3	-	2	369	c.58C>T	c.(58-60)Ctc>Ttc	p.L20F	GBGT1_ENST00000540636.1_Missense_Mutation_p.L20F|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000372038.3_Missense_Mutation_p.L20F|GBGT1_ENST00000372043.3_Missense_Mutation_p.L20F|RALGDS_ENST00000542690.1_Missense_Mutation_p.L20F|GBGT1_ENST00000372036.3_Missense_Mutation_p.L20F	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	20			L -> F (in dbSNP:rs2073924). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		AGGACACTGAGGCTTGTGCCC	0.657													G|||	1586	0.316693	0.2579	0.2954	5008	,	,		11531	0.5288		0.1829	False		,,,				2504	0.3303				p.L20F		Atlas-SNP	.											GBGT1,NS,carcinoma,0,1	GBGT1	25	1	0			c.C58T						scavenged	.	G	PHE/LEU	1215,3189		158,899,1145	36.0	33.0	34.0		58	0.9	0.0	9	dbSNP_96	34	1652,6948		167,1318,2815	yes	missense	GBGT1	NM_021996.4	22	325,2217,3960	AA,AG,GG		19.2093,27.5886,22.0471		20/348	136037742	2867,10137	2202	4300	6502	SO:0001583	missense	26301	exon2			CACTGAGGCTTGT	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.58C>T	9.37:g.136037742G>A	ENSP00000361110:p.Leu20Phe	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	146	68	0.465753	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	678	0.31043956043956045	139	0.28252032520325204	99	0.27348066298342544	298	0.5209790209790209	142	0.18733509234828497	G	16.05	3.014065	0.54468	0.275886	0.192093	ENSG00000160271;ENSG00000148288;ENSG00000148288;ENSG00000148288;ENSG00000148288;ENSG00000148288	ENST00000542690;ENST00000372043;ENST00000372040;ENST00000540636;ENST00000372038;ENST00000372036	T;T;T;T;T;T	0.44083	1.32;5.03;5.03;4.78;0.93;0.99	2.86	0.886	0.19194	.	1.329470	0.04963	N	0.462367	T	0.00012	0.0000	L	0.47190	1.495	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.19073	0.002;0.018;0.033;0.002	B;B;B;B	0.19946	0.014;0.018;0.027;0.014	T	0.46048	-0.9219	9	0.51188	T	0.08	0.216	3.2144	0.06694	0.146:0.0:0.5942:0.2597	rs2073924;rs17853057;rs58898475;rs2073924	20;20;20;20	B7Z8S5;F5H6M6;Q8N5D6-2;Q8N5D6	.;.;.;GBGT1_HUMAN	F	20	ENSP00000437518:L20F;ENSP00000361113:L20F;ENSP00000361110:L20F;ENSP00000437663:L20F;ENSP00000361108:L20F;ENSP00000361106:L20F	ENSP00000361106:L20F	L	-	1	0	GBGT1;RALGDS	135027563	0.202000	0.23423	0.042000	0.18584	0.580000	0.36256	0.412000	0.21131	0.218000	0.20820	0.563000	0.77884	CTC	G|0.741;A|0.259	0.259	strong		0.657	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
SNX32	254122	hgsc.bcm.edu	37	11	65601560	65601560	+	Silent	SNP	G	G	C	rs17854357	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65601560G>C	ENST00000308342.6	+	1	449	c.24G>C	c.(22-24)ggG>ggC	p.G8G	SNX32_ENST00000531795.1_Intron	NM_152760.2	NP_689973.2	Q86XE0	SNX32_HUMAN	sorting nexin 32	8					intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)	p.G8G(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				READ - Rectum adenocarcinoma(159;0.171)		CGGAGGTTGGGAAGGAGGGCA	0.632													G|||	369	0.0736821	0.0272	0.1196	5008	,	,		5103	0.0585		0.161	False		,,,				2504	0.0297				p.G8G		Atlas-SNP	.											SNX32,NS,carcinoma,0,1	SNX32	46	1	1	Substitution - coding silent(1)	stomach(1)	c.G24C						PASS	.	G		186,3686		7,172,1757	140.0	135.0	137.0		24	0.3	0.8	11	dbSNP_123	137	1043,6373		67,909,2732	no	coding-synonymous	SNX32	NM_152760.2		74,1081,4489	CC,CG,GG		14.0642,4.8037,10.8877		8/404	65601560	1229,10059	1936	3708	5644	SO:0001819	synonymous_variant	254122	exon1			GGTTGGGAAGGAG	AK055496	CCDS8113.2	11q13.1	2008-03-11	2008-03-11	2008-03-11	ENSG00000172803	ENSG00000172803		"""Sorting nexins"""	26423	protein-coding gene	gene with protein product			"""sorting nexin 6B"""	SNX6B		16782399	Standard	XM_005273871		Approved	FLJ30934	uc001ofr.3	Q86XE0	OTTHUMG00000128491	ENST00000308342.6:c.24G>C	11.37:g.65601560G>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_152760	Q8IW53|Q96NG4	Silent	SNP	ENST00000308342.6	37	CCDS8113.2																																																																																			G|0.893;C|0.107	0.107	strong		0.632	SNX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250295.3	NM_152760	
NBPF4	148545	hgsc.bcm.edu	37	1	108771721	108771721	+	Missense_Mutation	SNP	T	T	C	rs79996376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:108771721T>C	ENST00000415641.3	-	13	1684	c.1481A>G	c.(1480-1482)cAg>cGg	p.Q494R		NM_001143989.2	NP_001137461.1	Q96M43	NBPF4_HUMAN	neuroblastoma breakpoint family, member 4	494	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				endometrium(2)|lung(1)|skin(1)	4						CACCTCTGACTGGTGGTGGCT	0.582																																					p.Q494R		Atlas-SNP	.											.	NBPF4	4	.	0			c.A1481G						PASS	.						75.0	77.0	76.0					1																	108771721		692	1591	2283	SO:0001583	missense	148545	exon13			TCTGACTGGTGGT	AK057395	CCDS44182.1	1p13.3	2013-01-17			ENSG00000196427	ENSG00000196427		"""neuroblastoma breakpoint family"""	26550	protein-coding gene	gene with protein product		613994				16079250	Standard	NM_001143989		Approved	FLJ32833	uc009weo.2	Q96M43	OTTHUMG00000011318	ENST00000415641.3:c.1481A>G	1.37:g.108771721T>C	ENSP00000389237:p.Gln494Arg	Somatic	765	1	0.00130719		WXS	Illumina HiSeq	Phase_I	435	167	0.383908	NM_001143989	Q5T483	Missense_Mutation	SNP	ENST00000415641.3	37	CCDS44182.1	.	.	.	.	.	.	.	.	.	.	C	1.000	-0.691135	0.03303	.	.	ENSG00000196427	ENST00000415641;ENST00000428601;ENST00000370038	T	0.02158	4.42	1.55	-0.859	0.10685	.	.	.	.	.	T	0.00241	0.0007	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36212	-0.9757	9	0.06236	T	0.91	.	3.8615	0.08998	0.2811:0.5354:0.0:0.1835	.	494	Q5T483	.	R	494;523;494	ENSP00000389237:Q494R	ENSP00000359055:Q494R	Q	-	2	0	NBPF4	108573244	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.262000	0.08682	-0.739000	0.04809	-2.186000	0.00314	CAG	T|0.838;C|0.162	0.162	strong		0.582	NBPF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031255.5	NM_152488	
ZNF493	284443	hgsc.bcm.edu	37	19	21607252	21607252	+	Missense_Mutation	SNP	T	T	A	rs142288436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21607252T>A	ENST00000355504.4	+	2	1673	c.1407T>A	c.(1405-1407)gaT>gaA	p.D469E	ZNF493_ENST00000392288.2_Missense_Mutation_p.D597E|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	469					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(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	30						TTCATACTGATAAGAAACCCT	0.333													.|||	3	0.000599042	0.0	0.0	5008	,	,		19829	0.0		0.003	False		,,,				2504	0.0				p.D597E		Atlas-SNP	.											.	ZNF493	178	.	0			c.T1791A						PASS	.						33.0	33.0	33.0					19																	21607252		2200	4298	6498	SO:0001583	missense	284443	exon4			TACTGATAAGAAA	AK093823, BC006408, BC022394	CCDS12412.1, CCDS42536.1, CCDS12411.1	19p12	2013-01-08			ENSG00000196268	ENSG00000196268		"""Zinc fingers, C2H2-type"", ""-"""	23708	protein-coding gene	gene with protein product							Standard	NM_001076678		Approved	FLJ36504	uc002npw.3	Q6ZR52	OTTHUMG00000141297	ENST00000355504.4:c.1407T>A	19.37:g.21607252T>A	ENSP00000347691:p.Asp469Glu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	11	0.166667	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	1.434	-0.569466	0.03910	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.16897	2.31;2.31	1.06	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05731	0.0150	N	0.02674	-0.535	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.002	T	0.31336	-0.9947	9	0.66056	D	0.02	.	3.2801	0.06912	0.5296:0.0:0.2843:0.1862	.	469;597	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	E	597;469	ENSP00000376110:D597E;ENSP00000347691:D469E	ENSP00000347691:D469E	D	+	3	2	ZNF493	21399092	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.688000	0.01925	-3.330000	0.00186	-3.393000	0.00039	GAT	.	.	weak		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910	
KIAA1429	25962	hgsc.bcm.edu	37	8	95538468	95538468	+	Silent	SNP	T	T	C	rs2890827	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:95538468T>C	ENST00000297591.5	-	8	2079	c.2004A>G	c.(2002-2004)ccA>ccG	p.P668P	KIAA1429_ENST00000421249.2_Silent_p.P668P|KIAA1429_ENST00000437199.1_Silent_p.P668P	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	668					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)			GAACAGGGTATGGATCATCCC	0.383													C|||	1856	0.370607	0.4637	0.3156	5008	,	,		21115	0.3194		0.2545	False		,,,				2504	0.456				p.P668P		Atlas-SNP	.											.	KIAA1429	176	.	0			c.A2004G						PASS	.	C	,	1873,2533	630.9+/-395.5	429,1015,759	87.0	76.0	80.0		2004,2004	-1.3	1.0	8	dbSNP_101	80	2625,5975	687.0+/-404.2	380,1865,2055	no	coding-synonymous,coding-synonymous	KIAA1429	NM_015496.4,NM_183009.2	,	809,2880,2814	CC,CT,TT		30.5233,42.5102,34.584	,	668/1813,668/1148	95538468	4498,8508	2203	4300	6503	SO:0001819	synonymous_variant	25962	exon8			AGGGTATGGATCA	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.2004A>G	8.37:g.95538468T>C		Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	351	133	0.378917	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			T|0.651;C|0.349	0.349	strong		0.383	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
MUC16	94025	hgsc.bcm.edu	37	19	9059307	9059307	+	Missense_Mutation	SNP	C	C	T	rs12461695	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9059307C>T	ENST00000397910.4	-	3	28342	c.28139G>A	c.(28138-28140)gGt>gAt	p.G9380D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9382	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						GGTAAAGGTACCCTGCGAGGT	0.507													C|||	731	0.145966	0.0855	0.1787	5008	,	,		20436	0.2669		0.0865	False		,,,				2504	0.1411				p.G9380D		Atlas-SNP	.											MUC16_ENST00000397910,right_upper_lobe,carcinoma,-1,2	MUC16	4315	2	0			c.G28139A						PASS	.	C	ASP/GLY	381,3593		23,335,1629	140.0	139.0	140.0		28139	0.1	0.0	19	dbSNP_120	140	638,7666		25,588,3539	yes	missense	MUC16	NM_024690.2	94	48,923,5168	TT,TC,CC		7.683,9.5873,8.2994	possibly-damaging	9380/14508	9059307	1019,11259	1987	4152	6139	SO:0001583	missense	94025	exon3			AAGGTACCCTGCG	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.28139G>A	19.37:g.9059307C>T	ENSP00000381008:p.Gly9380Asp	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	243	136	0.559671	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	333	0.15247252747252749	38	0.07723577235772358	56	0.15469613259668508	169	0.29545454545454547	70	0.09234828496042216	c	4.216	0.038924	0.08148	0.095873	0.07683	ENSG00000181143	ENST00000397910	T	0.24538	1.85	1.94	0.0918	0.14469	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	.	.	.	P	0.35456	0.502	B	0.38428	0.273	T	0.41610	-0.9499	8	0.87932	D	0	.	3.6378	0.08155	0.0:0.5627:0.0:0.4373	rs12461695	9380	B5ME49	.	D	9380	ENSP00000381008:G9380D	ENSP00000381008:G9380D	G	-	2	0	MUC16	8920307	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-2.733000	0.00803	0.046000	0.15833	0.306000	0.20318	GGT	C|0.861;T|0.139	0.139	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FAM25A	643161	hgsc.bcm.edu	37	10	88782084	88782084	+	Silent	SNP	A	A	G	rs3802666	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:88782084A>G	ENST00000343959.4	+	2	106	c.87A>G	c.(85-87)gaA>gaG	p.E29E	RP11-96C23.14_ENST00000444180.3_RNA	NM_001146157.2	NP_001139629.1	B3EWG3	FM25A_HUMAN	family with sequence similarity 25, member A	29								p.E29E(1)		stomach(1)	1						ATGCCGTGGAAGAAGTGGTGA	0.622													.|||	2472	0.49361	0.5	0.3098	5008	,	,		20458	0.7173		0.4493	False		,,,				2504	0.4305				p.E29E		Atlas-SNP	.											FAM25A,NS,carcinoma,0,1	FAM25A	4	1	1	Substitution - coding silent(1)	stomach(1)	c.A87G						scavenged	.						42.0	39.0	40.0					10																	88782084		691	1591	2282	SO:0001819	synonymous_variant	643161	exon2			CGTGGAAGAAGTG		CCDS44451.1	10q23.2	2008-08-13			ENSG00000188100	ENSG00000188100			23436	protein-coding gene	gene with protein product							Standard	NM_001146157		Approved	bA96C23.5	uc010qmo.2	B3EWG3	OTTHUMG00000018664	ENST00000343959.4:c.87A>G	10.37:g.88782084A>G		Somatic	25	1	0.04		WXS	Illumina HiSeq	Phase_I	11	6	0.545455	NM_001146157	B2RV02|Q5VTM1	Silent	SNP	ENST00000343959.4	37	CCDS44451.1	902	0.413003663003663	166	0.33739837398373984	101	0.27900552486187846	367	0.6416083916083916	268	0.35356200527704484	G	6.788	0.514316	0.12944	.	.	ENSG00000188100	ENST00000343959	.	.	.	3.93	0.895	0.19247	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.35480	P	0.20192299999999996	.	.	.	.	.	.	T	0.43621	-0.9380	3	.	.	.	-16.1847	7.6603	0.28400	0.3778:0.0:0.6222:0.0	rs3802666;rs7097990;rs12784638	.	.	.	G	36	.	.	R	+	1	2	FAM25A	88772064	0.520000	0.26250	0.513000	0.27749	0.255000	0.26057	-0.446000	0.06837	-0.130000	0.11599	-0.349000	0.07799	AGA	A|0.562;G|0.438	0.438	strong		0.622	FAM25A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049182.2		
GTSE1	51512	hgsc.bcm.edu	37	22	46722531	46722531	+	Silent	SNP	C	C	T	rs9615949	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46722531C>T	ENST00000454366.1	+	9	1916	c.1704C>T	c.(1702-1704)ccC>ccT	p.P568P		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	549					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		CCTCTGAGCCCCGCAAGAACT	0.567													C|||	233	0.0465256	0.0287	0.0562	5008	,	,		17060	0.001		0.1223	False		,,,				2504	0.0327				p.P568P	GBM(153;542 1915 12487 29016 50495)	Atlas-SNP	.											.	GTSE1	100	.	0			c.C1704T						PASS	.	C		150,4256	103.4+/-141.9	2,146,2055	52.0	48.0	49.0		1704	2.4	0.8	22	dbSNP_119	49	914,7686	200.7+/-244.4	48,818,3434	no	coding-synonymous	GTSE1	NM_016426.6		50,964,5489	TT,TC,CC		10.6279,3.4044,8.1808		568/740	46722531	1064,11942	2203	4300	6503	SO:0001819	synonymous_variant	51512	exon9			TGAGCCCCGCAAG	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.1704C>T	22.37:g.46722531C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_016426	B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	37	CCDS14074.2																																																																																			C|0.928;T|0.072	0.072	strong		0.567	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
EVC2	132884	hgsc.bcm.edu	37	4	5577986	5577986	+	Silent	SNP	G	G	A	rs112554914	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:5577986G>A	ENST00000344408.5	-	18	3306	c.3253C>T	c.(3253-3255)Ctg>Ttg	p.L1085L	EVC2_ENST00000310917.2_Silent_p.L1005L|EVC2_ENST00000344938.1_Silent_p.L1085L	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	1085					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						TGTTGCTCCAGTAATGTCTGG	0.572													G|||	138	0.0275559	0.0	0.0187	5008	,	,		18039	0.0		0.0736	False		,,,				2504	0.0521				p.L1085L		Atlas-SNP	.											.	EVC2	202	.	0			c.C3253T						PASS	.	G	,	63,4343	58.1+/-94.6	0,63,2140	120.0	114.0	116.0		3013,3253	3.5	0.9	4	dbSNP_132	116	604,7996	158.9+/-212.3	26,552,3722	no	coding-synonymous,coding-synonymous	EVC2	NM_001166136.1,NM_147127.4	,	26,615,5862	AA,AG,GG		7.0233,1.4299,5.1284	,	1005/1229,1085/1309	5577986	667,12339	2203	4300	6503	SO:0001819	synonymous_variant	132884	exon18			GCTCCAGTAATGT	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.3253C>T	4.37:g.5577986G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_147127	Q86YT3|Q86YT4|Q8NG49	Silent	SNP	ENST00000344408.5	37	CCDS3382.2																																																																																			G|0.954;A|0.046	0.046	strong		0.572	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
KRT5	3852	hgsc.bcm.edu	37	12	52912906	52912906	+	Silent	SNP	G	G	T	rs641621	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52912906G>T	ENST00000252242.4	-	2	984	c.594C>A	c.(592-594)acC>acA	p.T198T		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	198	Coil 1A.|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)		GGGTCCACTTGGTGTCCAGAA	0.537													G|||	1077	0.215056	0.1089	0.2233	5008	,	,		19699	0.3393		0.2823	False		,,,				2504	0.1554				p.T198T		Atlas-SNP	.											.	KRT5	88	.	0			c.C594A						PASS	.						59.0	52.0	55.0					12																	52912906		2203	4298	6501	SO:0001819	synonymous_variant	3852	exon2			CCACTTGGTGTCC		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.594C>A	12.37:g.52912906G>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	131	37	0.282443	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	37	CCDS8830.1																																																																																			T|0.177;G|0.823	0.177	strong		0.537	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
NFATC1	4772	hgsc.bcm.edu	37	18	77211764	77211764	+	Silent	SNP	T	T	C	rs15350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:77211764T>C	ENST00000427363.2	+	6	1851	c.1851T>C	c.(1849-1851)tcT>tcC	p.S617S	NFATC1_ENST00000545796.1_Silent_p.S145S|NFATC1_ENST00000253506.5_Silent_p.S617S|NFATC1_ENST00000318065.5_Silent_p.S604S|NFATC1_ENST00000586434.1_Silent_p.S604S|NFATC1_ENST00000592223.1_Silent_p.S604S|NFATC1_ENST00000397790.2_Silent_p.S145S|NFATC1_ENST00000587635.1_Missense_Mutation_p.L589P|NFATC1_ENST00000542384.1_Silent_p.S617S|NFATC1_ENST00000591814.1_Silent_p.S617S|NFATC1_ENST00000329101.4_Silent_p.S604S			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	617					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)	TGGTCCTGTCTGGCCACAACT	0.612													C|||	1425	0.284545	0.4569	0.17	5008	,	,		18388	0.3849		0.1262	False		,,,				2504	0.1922				p.S617S	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.T1851C						PASS	.	C	,,,,	1791,2615	641.0+/-397.4	361,1069,773	104.0	99.0	101.0		1851,1812,435,1812,1851	-4.1	0.7	18	dbSNP_119	101	1334,7266	757.0+/-407.5	109,1116,3075	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	,,,,	470,2185,3848	CC,CT,TT		15.5116,40.6491,24.0274	,,,,	617/826,604/931,145/354,604/813,617/717	77211764	3125,9881	2203	4300	6503	SO:0001819	synonymous_variant	4772	exon6			CCTGTCTGGCCAC	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.1851T>C	18.37:g.77211764T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Silent	SNP	ENST00000427363.2	37																																																																																				T|0.727;C|0.273	0.273	strong		0.612	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
CARD14	79092	hgsc.bcm.edu	37	17	78178916	78178916	+	Silent	SNP	C	C	T	rs61757652	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78178916C>T	ENST00000573882.1	+	20	3017	c.2481C>T	c.(2479-2481)ccC>ccT	p.P827P	RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000576824.1_RNA|CARD14_ENST00000344227.2_Silent_p.P827P|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	827	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)			CCGCCCGGCCCCGGCCTGTGC	0.652													C|||	501	0.10004	0.0492	0.1369	5008	,	,		14544	0.1042		0.0746	False		,,,				2504	0.1646				p.P827P		Atlas-SNP	.											.	CARD14	98	.	0			c.C2481T						PASS	.	C		192,4214	114.2+/-152.2	7,178,2018	53.0	53.0	53.0		2481	-1.5	0.9	17	dbSNP_129	53	660,7940	165.8+/-217.9	26,608,3666	yes	coding-synonymous	CARD14	NM_024110.3		33,786,5684	TT,TC,CC		7.6744,4.3577,6.5508		827/1005	78178916	852,12154	2203	4300	6503	SO:0001819	synonymous_variant	79092	exon18			CCGGCCCCGGCCT	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.2481C>T	17.37:g.78178916C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	121	63	0.520661	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			C|0.928;T|0.072	0.072	strong		0.652	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
LMOD3	56203	hgsc.bcm.edu	37	3	69167851	69167851	+	Splice_Site	SNP	G	G	T	rs145387235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:69167851G>T	ENST00000420581.2	-	2	1834	c.1655C>A	c.(1654-1656)cCt>cAt	p.P552H	LMOD3_ENST00000489031.1_Splice_Site_p.P552H|LMOD3_ENST00000475434.1_Splice_Site_p.P552H	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	552	WH2.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)	13		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;7.88e-05)|Epithelial(33;0.000839)|LUSC - Lung squamous cell carcinoma(21;0.0119)|Lung(16;0.0191)|KIRC - Kidney renal clear cell carcinoma(39;0.205)|Kidney(39;0.24)		TCTACTTACAGGTTTAAGATA	0.473													G|||	37	0.00738818	0.0008	0.0187	5008	,	,		19795	0.0		0.0219	False		,,,				2504	0.001				p.P552H		Atlas-SNP	.											.	LMOD3	92	.	0			c.C1655A						PASS	.	G	HIS/PRO	18,3888		0,18,1935	63.0	62.0	63.0		1655	5.8	1.0	3	dbSNP_134	63	140,8154		2,136,4009	yes	missense-near-splice	LMOD3	NM_198271.3	77	2,154,5944	TT,TG,GG		1.688,0.4608,1.2951	probably-damaging	552/561	69167851	158,12042	1953	4147	6100	SO:0001630	splice_region_variant	56203	exon2			CTTACAGGTTTAA	AK096900	CCDS46862.1	3p14.1	2003-03-07			ENSG00000163380	ENSG00000163380			6649	protein-coding gene	gene with protein product							Standard	NM_198271		Approved		uc003dns.2	Q0VAK6	OTTHUMG00000158774	ENST00000420581.2:c.1656+1C>A	3.37:g.69167851G>T		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	239	113	0.472803	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Missense_Mutation	SNP	ENST00000420581.2	37	CCDS46862.1	21	0.009615384615384616	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	13	0.017150395778364115	G	22.1	4.238686	0.79800	0.004608	0.01688	ENSG00000163380	ENST00000420581;ENST00000489031;ENST00000475434	T;T;T	0.12361	2.69;2.69;2.69	5.84	5.84	0.93424	.	0.171431	0.56097	D	0.000032	T	0.21509	0.0518	M	0.63428	1.95	0.49582	D	0.999808	D	0.76494	0.999	D	0.65573	0.936	T	0.00293	-1.1841	10	0.62326	D	0.03	-12.4636	20.1466	0.98079	0.0:0.0:1.0:0.0	.	552	Q0VAK6	LMOD3_HUMAN	H	552	ENSP00000414670:P552H;ENSP00000417210:P552H;ENSP00000418645:P552H	ENSP00000414670:P552H	P	-	2	0	LMOD3	69250541	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.341000	0.97041	2.779000	0.95612	0.591000	0.81541	CCT	G|0.988;T|0.012	0.012	strong		0.473	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529	Missense_Mutation
CSF1R	1436	hgsc.bcm.edu	37	5	149457678	149457678	+	Silent	SNP	G	G	A	rs2228422	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149457678G>A	ENST00000286301.3	-	5	1017	c.726C>T	c.(724-726)acC>acT	p.T242T	CSF1R_ENST00000543093.1_Silent_p.T242T	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	242	Ig-like C2-type 3.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)	p.T242T(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GACTGACCTTGGTGTTGTTGT	0.572													G|||	1940	0.38738	0.2799	0.366	5008	,	,		20014	0.2113		0.5457	False		,,,				2504	0.5665				p.T242T		Atlas-SNP	.											CSF1R_ENST00000286301,NS,carcinoma,0,1	CSF1R	250	1	1	Substitution - coding silent(1)	stomach(1)	c.C726T						scavenged	.	G		1388,3018	457.5+/-351.6	220,948,1035	224.0	186.0	199.0		726	-0.9	1.0	5	dbSNP_98	199	4864,3736	618.2+/-396.8	1391,2082,827	no	coding-synonymous	CSF1R	NM_005211.3		1611,3030,1862	AA,AG,GG		43.4419,31.5025,48.0701		242/973	149457678	6252,6754	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon5			GACCTTGGTGTTG	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.726C>T	5.37:g.149457678G>A		Somatic	311	3	0.0096463		WXS	Illumina HiSeq	Phase_I	267	266	0.996255	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			G|0.561;A|0.439	0.439	strong		0.572	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
SMR3A	26952	hgsc.bcm.edu	37	4	71227877	71227877	+	Silent	SNP	G	G	A	rs62322478	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:71227877G>A	ENST00000226460.4	+	2	141	c.45G>A	c.(43-45)gcG>gcA	p.A15A		NM_012390.3	NP_036522.3	Q99954	SMR3A_HUMAN	submaxillary gland androgen regulated protein 3A	15						extracellular region (GO:0005576)		p.A15A(1)		endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(4)	15		all_hematologic(202;0.196)				CTCTTGCAGCGTGTTTCACAG	0.353													G|||	642	0.128195	0.3321	0.0807	5008	,	,		18065	0.0		0.1143	False		,,,				2504	0.0327				p.A15A		Atlas-SNP	.											SMR3A,NS,carcinoma,0,1	SMR3A	35	1	1	Substitution - coding silent(1)	ovary(1)	c.G45A						PASS	.	G		1339,3067	428.5+/-341.9	175,989,1039	210.0	188.0	196.0		45	-5.1	0.0	4	dbSNP_129	196	913,7687	201.0+/-244.6	37,839,3424	no	coding-synonymous	SMR3A	NM_012390.3		212,1828,4463	AA,AG,GG		10.6163,30.3904,17.3151		15/135	71227877	2252,10754	2203	4300	6503	SO:0001819	synonymous_variant	26952	exon2			TGCAGCGTGTTTC	D89501	CCDS34000.1	4q13.3	2009-04-17	2008-02-27	2005-02-07	ENSG00000109208	ENSG00000109208			19216	protein-coding gene	gene with protein product			"""proline rich 5 (salivary)"", ""submaxillary gland androgen regulated protein 3 homolog A (mouse)"""	PROL5		9354371, 17512016	Standard	NM_012390		Approved	PBI, PRL5	uc003hfg.1	Q99954	OTTHUMG00000160839	ENST00000226460.4:c.45G>A	4.37:g.71227877G>A		Somatic	740	0	0		WXS	Illumina HiSeq	Phase_I	723	211	0.29184	NM_012390		Silent	SNP	ENST00000226460.4	37	CCDS34000.1																																																																																			G|0.881;A|0.119	0.119	strong		0.353	SMR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362574.1	NM_012390	
GLDC	2731	hgsc.bcm.edu	37	9	6589230	6589230	+	Silent	SNP	C	C	T	rs121964976	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:6589230C>T	ENST00000321612.6	-	12	1695	c.1545G>A	c.(1543-1545)agG>agA	p.R515R		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	515			R -> S (in NKH; dbSNP:rs121964976). {ECO:0000269|PubMed:11286506}.		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)	ACGGGCTGGTCCTCTTGAACA	0.498													C|||	87	0.0173722	0.0197	0.0317	5008	,	,		15961	0.0		0.0358	False		,,,				2504	0.0031				p.R515R		Atlas-SNP	.											.	GLDC	118	.	0			c.G1545A	GRCh37	CM002029	GLDC	M	rs121964976	PASS	.	C		26,4380	31.7+/-61.6	0,26,2177	172.0	137.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1545	-2.2	0.9	9	dbSNP_133	149	264,8336	101.9+/-163.1	4,256,4040	no	coding-synonymous	GLDC	NM_000170.2		4,282,6217	TT,TC,CC		3.0698,0.5901,2.2297		515/1021	6589230	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon12			GCTGGTCCTCTTG	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.1545G>A	9.37:g.6589230C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			T|0.021;G|0.000;C|0.978	0.021	strong		0.498	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
BTBD16	118663	hgsc.bcm.edu	37	10	124094467	124094467	+	Silent	SNP	T	T	C	rs10887135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124094467T>C	ENST00000260723.4	+	14	1487	c.1236T>C	c.(1234-1236)gaT>gaC	p.D412D	BTBD16_ENST00000495370.2_3'UTR|BTBD16_ENST00000368994.2_Silent_p.D413D	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	412										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)				TCAAACATGATACTACCTCTT	0.333													T|||	458	0.0914537	0.0045	0.1988	5008	,	,		18668	0.2312		0.0308	False		,,,				2504	0.0511				p.D412D		Atlas-SNP	.											.	BTBD16	44	.	0			c.T1236C						PASS	.	T		48,4356	48.9+/-83.8	2,44,2156	114.0	116.0	116.0		1236	-4.5	0.0	10	dbSNP_120	116	249,8349	98.6+/-160.1	5,239,4055	no	coding-synonymous	BTBD16	NM_144587.2		7,283,6211	CC,CT,TT		2.896,1.0899,2.2843		412/507	124094467	297,12705	2202	4299	6501	SO:0001819	synonymous_variant	118663	exon14			ACATGATACTACC	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.1236T>C	10.37:g.124094467T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_144587	A6NM63|Q4VXL1|Q96LN0	Silent	SNP	ENST00000260723.4	37	CCDS31301.1																																																																																			T|0.943;C|0.057	0.057	strong		0.333	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
ITGA10	8515	hgsc.bcm.edu	37	1	145533175	145533175	+	Silent	SNP	T	T	C	rs11590105	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:145533175T>C	ENST00000369304.3	+	11	1445	c.1270T>C	c.(1270-1272)Ttg>Ctg	p.L424L	ITGA10_ENST00000539363.1_Silent_p.L281L|ITGA10_ENST00000538811.1_Silent_p.L293L	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	424					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)					CCCCCCTGCATTGCAGAACCA	0.582													T|||	1001	0.19988	0.062	0.3458	5008	,	,		16859	0.1617		0.3559	False		,,,				2504	0.1616				p.L424L		Atlas-SNP	.											.	ITGA10	131	.	0			c.T1270C						PASS	.	T		500,3906	230.4+/-244.6	32,436,1735	48.0	43.0	45.0		1270	-5.7	0.0	1	dbSNP_120	45	3015,5585	463.6+/-366.0	549,1917,1834	no	coding-synonymous	ITGA10	NM_003637.3		581,2353,3569	CC,CT,TT		35.0581,11.3482,27.026		424/1168	145533175	3515,9491	2203	4300	6503	SO:0001819	synonymous_variant	8515	exon11			CCTGCATTGCAGA	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.1270T>C	1.37:g.145533175T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	125	47	0.376	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Silent	SNP	ENST00000369304.3	37	CCDS918.1																																																																																			T|0.762;C|0.238	0.238	strong		0.582	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	
LDHAL6A	160287	hgsc.bcm.edu	37	11	18487305	18487305	+	Silent	SNP	C	C	G	rs17851143	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:18487305C>G	ENST00000280706.2	+	3	1163	c.366C>G	c.(364-366)ccC>ccG	p.P122P	LDHAL6A_ENST00000396213.3_Silent_p.P122P	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	122					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)			large_intestine(3)|lung(9)|urinary_tract(1)	13						TAATGATTCCCAATATTACCC	0.388													C|||	438	0.0874601	0.0545	0.1268	5008	,	,		20083	0.0615		0.1233	False		,,,				2504	0.0941				p.P122P		Atlas-SNP	.											LDHAL6A,NS,adenoma,0,1	LDHAL6A	35	1	0			c.C366G						PASS	.	C	,	317,4081	169.8+/-200.3	16,285,1898	131.0	133.0	133.0		366,366	-0.8	0.0	11	dbSNP_123	133	1153,7433	236.8+/-268.9	74,1005,3214	no	coding-synonymous,coding-synonymous	LDHAL6A	NM_001144071.1,NM_144972.4	,	90,1290,5112	GG,GC,CC		13.4288,7.2078,11.3216	,	122/333,122/333	18487305	1470,11514	2199	4293	6492	SO:0001819	synonymous_variant	160287	exon3			GATTCCCAATATT	AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.366C>G	11.37:g.18487305C>G		Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	241	114	0.473029	NM_144972	D3DQY5	Silent	SNP	ENST00000280706.2	37	CCDS7841.1																																																																																			C|0.890;G|0.110	0.110	strong		0.388	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972	
HLA-A	3105	hgsc.bcm.edu	37	6	29910562	29910562	+	Silent	SNP	A	A	C	rs281864725|rs1059418	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29910562A>C	ENST00000396634.1	+	4	443	c.102A>C	c.(100-102)acA>acC	p.T34T	HLA-A_ENST00000376806.5_Silent_p.T34T|HLA-A_ENST00000376802.2_Silent_p.T34T|HLA-A_ENST00000376809.5_Silent_p.T34T			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	34	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						ATTTCTTCACATCCGTGTCCC	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)			a|||	1002	0.20008	0.1641	0.1182	5008	,	,		13677	0.3284		0.1282	False		,,,				2504	0.2485				p.T34T		Atlas-SNP	.											.	HLA-A	89	.	0			c.A102C						PASS	.						17.0	16.0	16.0					6																	29910562		2189	4275	6464	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CTTCACATCCGTG	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.102A>C	6.37:g.29910562A>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	14	0.25	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			A|0.837;C|0.159;T|0.004	0.159	strong		0.721	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SLC12A6	9990	hgsc.bcm.edu	37	15	34544468	34544468	+	Silent	SNP	C	C	T	rs2290940	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:34544468C>T	ENST00000354181.3	-	10	1728	c.1236G>A	c.(1234-1236)tcG>tcA	p.S412S	SLC12A6_ENST00000558589.1_Silent_p.S403S|SLC12A6_ENST00000560164.1_Silent_p.S224S|SLC12A6_ENST00000451844.2_Silent_p.S224S|SLC12A6_ENST00000397707.2_Silent_p.S397S|SLC12A6_ENST00000558667.1_Silent_p.S412S|SLC12A6_ENST00000458406.2_Silent_p.S353S|SLC12A6_ENST00000397702.2_Silent_p.S353S|SLC12A6_ENST00000560611.1_Silent_p.S412S|SLC12A6_ENST00000290209.5_Silent_p.S361S			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	412					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)	AAAATTGACTCGAGTTACAGA	0.408													C|||	1036	0.206869	0.1256	0.2003	5008	,	,		19669	0.2827		0.2068	False		,,,				2504	0.2434				p.S412S		Atlas-SNP	.											.	SLC12A6	205	.	0			c.G1236A						PASS	.	C	,,,,,	550,3852	247.5+/-255.7	34,482,1685	128.0	114.0	119.0		1059,1059,1209,1191,1083,1236	-6.2	0.9	15	dbSNP_100	119	1466,7130	280.5+/-294.5	124,1218,2956	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	,,,,,	158,1700,4641	TT,TC,CC		17.0544,12.4943,15.5101	,,,,,	353/1092,353/1092,403/1142,397/1136,361/1100,412/1151	34544468	2016,10982	2201	4298	6499	SO:0001819	synonymous_variant	9990	exon9			TTGACTCGAGTTA	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.1236G>A	15.37:g.34544468C>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	162	108	0.666667	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Silent	SNP	ENST00000354181.3	37	CCDS58352.1																																																																																			C|0.821;T|0.179	0.179	strong		0.408	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
SEMA7A	8482	hgsc.bcm.edu	37	15	74706943	74706943	+	Silent	SNP	G	G	A	rs1046146	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:74706943G>A	ENST00000261918.4	-	10	1787	c.1239C>T	c.(1237-1239)gtC>gtT	p.V413V	SEMA7A_ENST00000543145.2_Silent_p.V399V|SEMA7A_ENST00000542748.1_Silent_p.V248V	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	413	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|immune response (GO:0006955)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|olfactory lobe development (GO:0021988)|osteoblast differentiation (GO:0001649)|positive regulation of axon extension (GO:0045773)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of protein phosphorylation (GO:0001934)|regulation of inflammatory response (GO:0050727)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(3)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	30						GCATGCGGTGGACGGCCACTT	0.572													G|||	922	0.184105	0.3986	0.036	5008	,	,		17268	0.1915		0.0467	False		,,,				2504	0.1329				p.V413V		Atlas-SNP	.											.	SEMA7A	58	.	0			c.C1239T						PASS	.	G	,,	1418,2976	463.0+/-353.4	231,956,1010	98.0	103.0	101.0		1197,744,1239	-6.2	0.7	15	dbSNP_86	101	392,8200	125.5+/-184.1	13,366,3917	no	coding-synonymous,coding-synonymous,coding-synonymous	SEMA7A	NM_001146029.1,NM_001146030.1,NM_003612.3	,,	244,1322,4927	AA,AG,GG		4.5624,32.2713,13.9381	,,	399/653,248/502,413/667	74706943	1810,11176	2197	4296	6493	SO:0001819	synonymous_variant	8482	exon10			GCGGTGGACGGCC	AF069493	CCDS10262.1, CCDS53958.1, CCDS53959.1	15q22.3-q23	2014-07-18	2006-02-23		ENSG00000138623	ENSG00000138623		"""Semaphorins"", ""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10741	protein-coding gene	gene with protein product	"""John Milton Hagen blood group"", ""H-Sema K1"""	607961	"""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A"", ""sema domain, immunoglobulin domain (Ig), and GPI membrane anchor, (semaphorin) 7A (JMH blood group)"""	SEMAL		9721204	Standard	NM_003612		Approved	H-Sema-L, CD108	uc002axv.3	O75326	OTTHUMG00000139000	ENST00000261918.4:c.1239C>T	15.37:g.74706943G>A		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	147	108	0.734694	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Silent	SNP	ENST00000261918.4	37	CCDS10262.1																																																																																			G|0.846;A|0.154	0.154	strong		0.572	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612	
SPECC1L	23384	hgsc.bcm.edu	37	22	24717518	24717518	+	Silent	SNP	G	G	A	rs3747113	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:24717518G>A	ENST00000314328.9	+	5	855	c.570G>A	c.(568-570)acG>acA	p.T190T	SPECC1L_ENST00000541492.1_Silent_p.T190T|SPECC1L-ADORA2A_ENST00000358654.2_Silent_p.T190T|SPECC1L_ENST00000437398.1_Silent_p.T190T|SPECC1L_ENST00000416735.1_Intron	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	190			T -> M (no effect on the stabilization of microtubules; dbSNP:rs142144652). {ECO:0000269|PubMed:21703590}.		actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)		p.T190T(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						ATCTTCTCACGCTGGCAAAAA	0.453													G|||	1037	0.207069	0.1127	0.317	5008	,	,		20502	0.2302		0.2654	False		,,,				2504	0.1728				p.T190T		Atlas-SNP	.											SPECC1L,NS,carcinoma,0,1	SPECC1L	85	1	1	Substitution - coding silent(1)	stomach(1)	c.G570A						PASS	.	G	,	603,3803	263.8+/-265.7	40,523,1640	62.0	61.0	62.0		570,570	-8.3	0.5	22	dbSNP_107	62	2172,6428	372.6+/-336.7	292,1588,2420	no	coding-synonymous,coding-synonymous	SPECC1L	NM_001145468.1,NM_015330.2	,	332,2111,4060	AA,AG,GG		25.2558,13.6859,21.3363	,	190/1118,190/1118	24717518	2775,10231	2203	4300	6503	SO:0001819	synonymous_variant	23384	exon4			TCTCACGCTGGCA	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"""cytokinesis and spindle organization A"", ""cytospin A"""	614140	"""SPECC1-like"""			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.570G>A	22.37:g.24717518G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	NM_001145468	B7Z758|F5H1H6|O15081	Silent	SNP	ENST00000314328.9	37	CCDS33619.1																																																																																			G|0.777;A|0.223	0.223	strong		0.453	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
POTEE	445582	hgsc.bcm.edu	37	2	132021684	132021684	+	Missense_Mutation	SNP	C	C	A	rs2672150		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:132021684C>A	ENST00000356920.5	+	15	2750	c.2656C>A	c.(2656-2658)Cct>Act	p.P886T	PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	886	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GCGGGAACTGCCTGACTACCT	0.592																																					p.P886T		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,-1,1	.	.	1	0			c.C2656A						scavenged	.						46.0	47.0	47.0					2																	132021684		2203	4281	6484	SO:0001583	missense	445582	exon15			GAACTGCCTGACT	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.2656C>A	2.37:g.132021684C>A	ENSP00000439189:p.Pro886Thr	Somatic	608	10	0.0164474		WXS	Illumina HiSeq	Phase_I	480	8	0.0166667	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	3.880	-0.026136	0.07589	.	.	ENSG00000188219	ENST00000356920	T	0.04360	3.64	.	.	.	.	.	.	.	.	T	0.00241	0.0007	N	0.00000	-5.39	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59606	-0.7423	8	0.02654	T	1	.	4.0636	0.09849	0.6406:0.3593:1.0E-4:0.0	.	886	Q6S8J3	POTEE_HUMAN	T	886	ENSP00000439189:P886T	ENSP00000439189:P886T	P	+	1	0	AC131180.1	131738154	1.000000	0.71417	0.081000	0.20488	0.082000	0.17680	4.531000	0.60602	-2.143000	0.00803	-2.210000	0.00300	CCT	.	.	weak		0.592	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
HOXD1	3231	hgsc.bcm.edu	37	2	177054769	177054769	+	Missense_Mutation	SNP	G	G	A	rs6710142	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:177054769G>A	ENST00000331462.4	+	2	1109	c.886G>A	c.(886-888)Gcc>Acc	p.A296T	HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000436126.1_RNA|HOXD-AS1_ENST00000413969.1_RNA|HOXD-AS1_ENST00000452365.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	296			A -> T (in dbSNP:rs6710142).		embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		TCTGGCCACGGCCATTCCTGT	0.542													G|||	937	0.187101	0.3313	0.147	5008	,	,		15751	0.0149		0.2515	False		,,,				2504	0.1319				p.A296T		Atlas-SNP	.											.	HOXD1	33	.	0			c.G886A						PASS	.	G	THR/ALA	1314,3092	441.8+/-346.5	190,934,1079	109.0	117.0	114.0		886	1.3	0.0	2	dbSNP_116	114	2020,6580	351.5+/-328.3	242,1536,2522	yes	missense	HOXD1	NM_024501.1	58	432,2470,3601	AA,AG,GG		23.4884,29.823,25.6343	benign	296/329	177054769	3334,9672	2203	4300	6503	SO:0001583	missense	3231	exon2			GCCACGGCCATTC		CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"""Homeoboxes / ANTP class : HOXL subclass"""	5132	protein-coding gene	gene with protein product		142987	"""homeo box D1"""	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.886G>A	2.37:g.177054769G>A	ENSP00000328598:p.Ala296Thr	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	163	157	0.96319	NM_024501	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	37	CCDS2271.1	394	0.1804029304029304	147	0.29878048780487804	58	0.16022099447513813	6	0.01048951048951049	183	0.24142480211081793	G	6.383	0.438828	0.12104	0.29823	0.234884	ENSG00000128645	ENST00000331462	D	0.90676	-2.71	5.66	1.3	0.21679	Homeodomain-like (1);	0.139876	0.33272	N	0.005099	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.17852	0.024;0.009	B;B	0.12156	0.005;0.007	T	0.03684	-1.1013	9	0.12766	T	0.61	.	3.1673	0.06540	0.2697:0.1163:0.4955:0.1186	rs6710142	296;296	Q96CA4;Q9GZZ0	.;HXD1_HUMAN	T	296	ENSP00000328598:A296T	ENSP00000328598:A296T	A	+	1	0	HOXD1	176763015	0.001000	0.12720	0.002000	0.10522	0.428000	0.31595	0.921000	0.28718	0.325000	0.23359	0.655000	0.94253	GCC	G|0.768;A|0.232	0.232	strong		0.542	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2		
RGR	5995	hgsc.bcm.edu	37	10	86012713	86012713	+	Silent	SNP	C	C	T	rs1042454	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:86012713C>T	ENST00000359452.4	+	4	509	c.471C>T	c.(469-471)taC>taT	p.Y157Y	RGR_ENST00000358110.5_Silent_p.Y153Y	NM_001012720.1|NM_002921.3	NP_001012738.1|NP_002912.2	P47804	RGR_HUMAN	retinal G protein coupled receptor	153					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.Y157Y(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	17						GGGGTCACTACGACTATGAGC	0.602													T|||	2520	0.503195	0.8548	0.4841	5008	,	,		16744	0.3313		0.3588	False		,,,				2504	0.3671				p.Y157Y	NSCLC(15;204 545 5889 6385 32445)	Atlas-SNP	.											RGR,NS,adenoma,0,2	RGR	42	2	1	Substitution - coding silent(1)	stomach(1)	c.C471T						scavenged	.	T	,,	3437,969	364.1+/-316.8	1366,705,132	92.0	71.0	78.0		459,459,471	2.6	1.0	10	dbSNP_86	78	3133,5467	656.7+/-401.4	552,2029,1719	no	coding-synonymous,coding-synonymous,coding-synonymous	RGR	NM_001012720.1,NM_001012722.1,NM_002921.3	,,	1918,2734,1851	TT,TC,CC		36.4302,21.9927,49.4849	,,	153/292,153/254,157/296	86012713	6570,6436	2203	4300	6503	SO:0001819	synonymous_variant	5995	exon4			TCACTACGACTAT	BC011349	CCDS7374.1, CCDS41543.1	10q23	2013-02-14			ENSG00000148604	ENSG00000148604		"""GPCR / Class A : Opsin receptors"""	9990	protein-coding gene	gene with protein product	"""RGR-opsin"""	600342				8641686	Standard	NM_002921		Approved	RP44	uc001kdd.1	P47804	OTTHUMG00000018636	ENST00000359452.4:c.471C>T	10.37:g.86012713C>T		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	61	15	0.245902	NM_002921	A6NKK7|Q96FC5	Silent	SNP	ENST00000359452.4	37	CCDS7374.1																																																																																			C|0.502;T|0.498	0.498	strong		0.602	RGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049116.1	NM_002921	
OSER1	51526	hgsc.bcm.edu	37	20	42826379	42826379	+	Splice_Site	SNP	C	C	T	rs11274	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:42826379C>T	ENST00000372970.2	-	6	372	c.192G>A	c.(190-192)ggG>ggA	p.G64G	OSER1_ENST00000255174.2_Splice_Site_p.G64G			Q9NX31	OSER1_HUMAN	oxidative stress responsive serine-rich 1	64					cellular response to hydrogen peroxide (GO:0070301)												TCCTTGTAGACCTAAAGAGGA	0.408													C|||	1916	0.382588	0.6346	0.1571	5008	,	,		22340	0.4782		0.1561	False		,,,				2504	0.3364				p.G64G		Atlas-SNP	.											.	C20orf111	28	.	0			c.G192A						PASS	.	C		2370,2036	589.2+/-387.1	648,1074,481	36.0	36.0	36.0		192	2.0	1.0	20	dbSNP_52	36	1276,7324	243.8+/-273.2	90,1096,3114	yes	coding-synonymous-near-splice	C20orf111	NM_016470.7		738,2170,3595	TT,TC,CC		14.8372,46.2097,28.0332		64/293	42826379	3646,9360	2203	4300	6503	SO:0001630	splice_region_variant	51526	exon4			TGTAGACCTAAAG	AL035447	CCDS13327.1	20q13.11	2013-05-17	2013-05-17	2013-05-17	ENSG00000132823	ENSG00000132823			16105	protein-coding gene	gene with protein product	"""peroxide-inducible transcript 1"", ""oxidative stress-responsive 1"""		"""chromosome 20 open reading frame 111"""	C20orf111		17148688	Standard	NM_016470		Approved	dJ1183I21.1, HSPC207, Perit1, Osr1		Q9NX31	OTTHUMG00000032518	ENST00000372970.2:c.192-1G>A	20.37:g.42826379C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_016470	B2RCK4|O95912|Q9NZ84|Q9P0R8	Silent	SNP	ENST00000372970.2	37	CCDS13327.1																																																																																			C|0.685;N|0.000	.	strong		0.408	OSER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079334.2	NM_016470	Silent
SNTG2	54221	hgsc.bcm.edu	37	2	1168781	1168781	+	Missense_Mutation	SNP	C	C	A	rs28505970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:1168781C>A	ENST00000308624.5	+	8	632	c.503C>A	c.(502-504)tCc>tAc	p.S168Y	SNTG2_ENST00000407292.1_Intron|SNTG2_ENST00000467759.1_3'UTR	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	168			S -> Y (in dbSNP:rs28505970).		central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)	p.S168Y(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		GCTGCAGGGTCCCCAGGGCCA	0.532													C|||	1033	0.20627	0.3608	0.098	5008	,	,		17456	0.1042		0.169	False		,,,				2504	0.2178				p.S168Y		Atlas-SNP	.											SNTG2,NS,carcinoma,0,1	SNTG2	125	1	1	Substitution - Missense(1)	stomach(1)	c.C503A						scavenged	.	C	TYR/SER	1210,2802		192,826,988	115.0	122.0	120.0		503	4.6	1.0	2	dbSNP_125	120	1260,7098		95,1070,3014	yes	missense	SNTG2	NM_018968.3	144	287,1896,4002	AA,AC,CC		15.0754,30.1595,19.9677	probably-damaging	168/540	1168781	2470,9900	2006	4179	6185	SO:0001583	missense	54221	exon8			CAGGGTCCCCAGG	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	ENST00000308624.5:c.503C>A	2.37:g.1168781C>A	ENSP00000311837:p.Ser168Tyr	Somatic	96	2	0.0208333		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_018968	Q05AH5	Missense_Mutation	SNP	ENST00000308624.5	37	CCDS46220.1	390	0.17857142857142858	173	0.3516260162601626	35	0.09668508287292818	55	0.09615384615384616	127	0.16754617414248021	C	14.49	2.550271	0.45383	0.301595	0.150754	ENSG00000172554	ENST00000308624	T	0.54866	0.55	4.58	4.58	0.56647	.	0.062085	0.64402	D	0.000003	T	0.00012	0.0000	M	0.72479	2.2	0.09310	P	1.0	D	0.76494	0.999	D	0.83275	0.996	T	0.06023	-1.0850	9	0.66056	D	0.02	.	15.1671	0.72837	0.0:1.0:0.0:0.0	rs28505970	168	Q9NY99	SNTG2_HUMAN	Y	168	ENSP00000311837:S168Y	ENSP00000311837:S168Y	S	+	2	0	SNTG2	1158781	1.000000	0.71417	0.974000	0.42286	0.065000	0.16274	4.969000	0.63735	2.067000	0.61834	0.643000	0.83706	TCC	C|0.822;A|0.178	0.178	strong		0.532	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968	
LRRC71	149499	hgsc.bcm.edu	37	1	156902222	156902222	+	Missense_Mutation	SNP	G	G	A	rs12119908	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:156902222G>A	ENST00000337428.7	+	14	1602	c.1448G>A	c.(1447-1449)cGc>cAc	p.R483H	LRRC71_ENST00000490146.1_3'UTR|ARHGEF11_ENST00000487682.1_5'Flank	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	483			R -> H (in dbSNP:rs12119908).							endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						CCAGGGAACCGCATCACAGAG	0.597													G|||	1000	0.199681	0.1936	0.1643	5008	,	,		18902	0.2907		0.174	False		,,,				2504	0.1656				p.R483H		Atlas-SNP	.											LRRC71,caecum,carcinoma,0,1	LRRC71	33	1	0			c.G1448A						scavenged	.	G	HIS/ARG	812,3466		85,642,1412	38.0	44.0	42.0		1448	2.1	1.0	1	dbSNP_120	42	1412,7094		118,1176,2959	yes	missense	LRRC71	NM_144702.2	29	203,1818,4371	AA,AG,GG		16.6,18.9808,17.3967	possibly-damaging	483/560	156902222	2224,10560	2139	4253	6392	SO:0001583	missense	149499	exon14			GGAACCGCATCAC	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1448G>A	1.37:g.156902222G>A	ENSP00000336661:p.Arg483His	Somatic	126	2	0.015873		WXS	Illumina HiSeq	Phase_I	176	171	0.971591	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	477	0.2184065934065934	96	0.1951219512195122	71	0.19613259668508287	186	0.32517482517482516	124	0.16358839050131926	G	14.54	2.567291	0.45694	0.189808	0.166	ENSG00000160838	ENST00000337428	T	0.53640	0.61	5.01	2.13	0.27403	.	0.775970	0.11438	N	0.564117	T	0.29652	0.0740	L	0.54323	1.7	0.44447	P	0.0026279999999999637	D;D	0.57571	0.976;0.98	B;P	0.48598	0.403;0.583	T	0.04650	-1.0936	9	0.35671	T	0.21	-3.6571	7.2592	0.26193	0.2849:0.0:0.7151:0.0	rs12119908;rs52826821;rs56456749;rs60342966;rs12119908	483;269	Q8N4P6;Q8N4P6-2	LRC71_HUMAN;.	H	483	ENSP00000336661:R483H	ENSP00000336661:R483H	R	+	2	0	LRRC71	155168846	0.389000	0.25205	0.989000	0.46669	0.308000	0.27856	0.171000	0.16685	0.284000	0.22305	-0.253000	0.11424	CGC	G|0.784;A|0.216	0.216	strong		0.597	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
RFWD3	55159	hgsc.bcm.edu	37	16	74664743	74664743	+	Missense_Mutation	SNP	T	T	C	rs7193541	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74664743T>C	ENST00000361070.4	-	10	1787	c.1690A>G	c.(1690-1692)Att>Gtt	p.I564V	RFWD3_ENST00000571750.1_Missense_Mutation_p.I564V	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	564			I -> V (in dbSNP:rs7193541). {ECO:0000269|Ref.3}.		DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I564V(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TATACCAGAATTGAACCATTG	0.502													T|||	1967	0.392772	0.5166	0.2896	5008	,	,		18495	0.4613		0.3936	False		,,,				2504	0.227				p.I564V		Atlas-SNP	.											RFWD3,NS,carcinoma,0,1	RFWD3	49	1	1	Substitution - Missense(1)	stomach(1)	c.A1690G						PASS	.	T	VAL/ILE	2240,2156	594.3+/-388.2	576,1088,534	118.0	94.0	102.0		1690	3.4	0.5	16	dbSNP_116	102	3637,4963	524.0+/-380.4	770,2097,1433	yes	missense	RFWD3	NM_018124.3	29	1346,3185,1967	CC,CT,TT		42.2907,49.0446,45.2216	benign	564/775	74664743	5877,7119	2198	4300	6498	SO:0001583	missense	55159	exon10			CCAGAATTGAACC	AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.1690A>G	16.37:g.74664743T>C	ENSP00000354361:p.Ile564Val	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	105	90	0.857143	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Missense_Mutation	SNP	ENST00000361070.4	37	CCDS32486.1	913	0.41804029304029305	260	0.5284552845528455	115	0.31767955801104975	245	0.42832167832167833	293	0.3865435356200528	T	9.100	1.003950	0.19199	0.509554	0.422907	ENSG00000168411	ENST00000361070	T	0.29917	1.55	5.74	3.41	0.39046	WD40/YVTN repeat-like-containing domain (1);	0.184587	0.49305	N	0.000144	T	0.00012	0.0000	N	0.11651	0.15	0.28633	P	0.9075455	B	0.13594	0.008	B	0.10450	0.005	T	0.45086	-0.9285	9	0.09843	T	0.71	-14.7735	7.6779	0.28497	0.0:0.3227:0.0:0.6773	rs7193541;rs56472058;rs58059142;rs7193541	564	Q6PCD5	RFWD3_HUMAN	V	564	ENSP00000354361:I564V	ENSP00000354361:I564V	I	-	1	0	RFWD3	73222244	0.890000	0.30428	0.485000	0.27403	0.855000	0.48748	1.552000	0.36244	0.941000	0.37499	0.533000	0.62120	ATT	T|0.562;C|0.438	0.438	strong		0.502	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
USP40	55230	hgsc.bcm.edu	37	2	234429744	234429744	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:234429744C>T	ENST00000427112.2	-	16	2250	c.2215G>A	c.(2215-2217)Gag>Aag	p.E739K	USP40_ENST00000251722.6_Missense_Mutation_p.E739K|USP40_ENST00000450966.1_Missense_Mutation_p.E751K			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	739					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)		ACCCATTTCTCTTCCTTGGTC	0.368																																					p.E751K		Atlas-SNP	.											USP40_ENST00000450966,caecum,carcinoma,+2,2	USP40	174	2	0			c.G2251A						scavenged	.						84.0	77.0	79.0					2																	234429744		1842	4083	5925	SO:0001583	missense	55230	exon16			ATTTCTCTTCCTT	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.2215G>A	2.37:g.234429744C>T	ENSP00000387898:p.Glu739Lys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	6	0.0895522	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	8.295	0.818600	0.16607	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112;ENST00000452724	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	4.75	2.88	0.33553	.	2.303910	0.01545	N	0.019397	T	0.37376	0.1001	L	0.29908	0.895	0.09310	N	1	B;B	0.28055	0.126;0.199	B;B	0.26770	0.033;0.073	T	0.22836	-1.0205	10	0.12430	T	0.62	.	9.1947	0.37220	0.0:0.8191:0.0:0.1809	.	739;751	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	K	751;739;739;34	ENSP00000415434:E751K;ENSP00000251722:E739K;ENSP00000387898:E739K;ENSP00000408853:E34K	ENSP00000251722:E739K	E	-	1	0	USP40	234094483	0.026000	0.19158	0.801000	0.32222	0.504000	0.33889	1.443000	0.35057	1.208000	0.43306	0.585000	0.79938	GAG	.	.	none		0.368	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
CCR2	729230	hgsc.bcm.edu	37	3	46399226	46399226	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46399226T>G	ENST00000400888.2	+	1	247	c.208T>G	c.(208-210)Tgc>Ggc	p.C70G	CCR2_ENST00000292301.4_Missense_Mutation_p.C70G|CCR2_ENST00000465202.1_Intron|CCR2_ENST00000445132.2_Missense_Mutation_p.C70G			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	70					blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		CTTAATAAACTGCAAAAAGCT	0.488																																					p.C70G		Atlas-SNP	.											.	CCR2	103	.	0			c.T208G						PASS	.						199.0	182.0	188.0					3																	46399226		1568	3582	5150	SO:0001583	missense	729230	exon2			ATAAACTGCAAAA		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.208T>G	3.37:g.46399226T>G	ENSP00000383681:p.Cys70Gly	Somatic	380	1	0.00263158		WXS	Illumina HiSeq	Phase_I	353	141	0.399433	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	37	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.712653	0.48517	.	.	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000421659;ENST00000400888	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	4.41	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.097576	0.46145	D	0.000305	T	0.81403	0.4815	M	0.73430	2.235	0.31410	N	0.675649	D;P	0.76494	0.999;0.851	D;P	0.71184	0.972;0.794	T	0.80899	-0.1176	10	0.25106	T	0.35	.	13.9659	0.64209	0.0:0.0:0.0:1.0	.	70;70	P41597;Q4VBL2	CCR2_HUMAN;.	G	70	ENSP00000399285:C70G;ENSP00000292301:C70G;ENSP00000396736:C70G;ENSP00000383681:C70G	ENSP00000292301:C70G	C	+	1	0	CCR2	46374230	1.000000	0.71417	0.988000	0.46212	0.949000	0.60115	1.614000	0.36911	1.774000	0.52232	0.528000	0.53228	TGC	.	.	none		0.488	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647	
DOCK3	1795	hgsc.bcm.edu	37	3	51198110	51198110	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:51198110G>A	ENST00000266037.9	+	12	1037	c.1014G>A	c.(1012-1014)aaG>aaA	p.K338K		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	338					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.K338N(1)		breast(2)|cervix(1)|endometrium(10)|kidney(4)|lung(22)|prostate(5)|urinary_tract(1)	45				BRCA - Breast invasive adenocarcinoma(193;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00449)|Kidney(197;0.00518)		AGGAAGAAAAGGATTTTGTTC	0.443																																					p.K338K		Atlas-SNP	.											DOCK3_ENST00000266037,rectum,carcinoma,0,3	DOCK3	397	3	1	Substitution - Missense(1)	large_intestine(1)	c.G1014A						scavenged	.						80.0	82.0	81.0					3																	51198110		1967	4138	6105	SO:0001819	synonymous_variant	1795	exon12			AGAAAAGGATTTT	AB002297	CCDS46835.1	3p21	2008-02-01			ENSG00000088538	ENSG00000088538			2989	protein-coding gene	gene with protein product		603123	"""dedicator of cyto-kinesis 3"""			9205841	Standard	NM_004947		Approved	KIAA0299, MOCA, PBP	uc011bds.2	Q8IZD9	OTTHUMG00000156892	ENST00000266037.9:c.1014G>A	3.37:g.51198110G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	141	2	0.0141844	NM_004947	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																			.	.	none		0.443	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947	
FAM218A	152756	hgsc.bcm.edu	37	4	165878335	165878335	+	Missense_Mutation	SNP	A	A	G	rs3733418	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	273	0	0		WXS	Illumina HiSeq	Phase_I	159	107	0.672956	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	
CDC27	996	hgsc.bcm.edu	37	17	45232075	45232075	+	Missense_Mutation	SNP	A	A	T	rs199711781		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45232075A>T	ENST00000066544.3	-	8	1013	c.920T>A	c.(919-921)gTa>gAa	p.V307E	CDC27_ENST00000531206.1_Missense_Mutation_p.V307E|CDC27_ENST00000527547.1_Missense_Mutation_p.V307E|CDC27_ENST00000446365.2_Missense_Mutation_p.V246E|CDC27_ENST00000528748.1_5'Flank	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	307					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.V307E(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						CACATCAATTACAGGAGGTGT	0.378																																					p.V307E		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	2	2	Substitution - Missense(2)	kidney(2)	c.T920A						scavenged	.						50.0	50.0	50.0					17																	45232075		2203	4300	6503	SO:0001583	missense	996	exon8			TCAATTACAGGAG	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.920T>A	17.37:g.45232075A>T	ENSP00000066544:p.Val307Glu	Somatic	91	3	0.032967		WXS	Illumina HiSeq	Phase_I	101	4	0.039604	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	15.91	2.973416	0.53614	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.69040	-0.36;-0.35;-0.04;-0.37;0.63	5.92	5.92	0.95590	.	0.302185	0.32401	N	0.006159	T	0.43299	0.1241	N	0.08118	0	0.58432	D	0.99999	P;B;B;B	0.36465	0.554;0.255;0.341;0.089	B;B;B;B	0.27608	0.081;0.075;0.076;0.034	T	0.47861	-0.9084	10	0.30078	T	0.28	-36.9477	14.323	0.66499	1.0:0.0:0.0:0.0	.	246;307;307;307	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	E	307;307;246;307;307	ENSP00000066544:V307E;ENSP00000434614:V307E;ENSP00000392802:V246E;ENSP00000437339:V307E;ENSP00000432105:V307E	ENSP00000066544:V307E	V	-	2	0	CDC27	42587074	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.746000	0.74866	2.267000	0.75376	0.477000	0.44152	GTA	A|0.999;T|0.001	0.001	weak		0.378	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
MMP17	4326	hgsc.bcm.edu	37	12	132325239	132325239	+	Missense_Mutation	SNP	G	G	A	rs6598163	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:132325239G>A	ENST00000360564.1	+	4	646	c.544G>A	c.(544-546)Gcc>Acc	p.A182T	MMP17_ENST00000535291.1_Missense_Mutation_p.A98T	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	182				A -> T (in Ref. 1; BAA82707 and 2; CAA61753). {ECO:0000305}.	positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	GGCGGGCAGCGCCGCCGACAT	0.667													g|||	2272	0.453674	0.4516	0.4424	5008	,	,		17858	0.5238		0.4583	False		,,,				2504	0.3875				p.A182T		Atlas-SNP	.											MMP17_ENST00000360564,NS,carcinoma,-2,1	MMP17	77	1	0			c.G544A						scavenged	.	A	THR/ALA	1919,2487	538.4+/-375.0	410,1099,694	90.0	78.0	82.0		544	-5.1	0.0	12	dbSNP_116	82	4217,4381	560.4+/-387.6	1047,2123,1129	yes	missense	MMP17	NM_016155.4	58	1457,3222,1823	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	49.0463,43.5542,47.1855	benign	182/604	132325239	6136,6868	2203	4299	6502	SO:0001583	missense	4326	exon4			GGCAGCGCCGCCG	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.544G>A	12.37:g.132325239G>A	ENSP00000353767:p.Ala182Thr	Somatic	30	1	0.0333333		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_016155	Q14850	Missense_Mutation	SNP	ENST00000360564.1	37	CCDS31927.1	1011	0.46291208791208793	214	0.4349593495934959	163	0.45027624309392267	277	0.48426573426573427	357	0.470976253298153	G	10.01	1.233697	0.22626	0.435542	0.490463	ENSG00000198598	ENST00000360564;ENST00000545671;ENST00000545790;ENST00000535291;ENST00000534865	T;T;T;T;T	0.20598	2.06;2.06;2.6;2.06;2.06	4.65	-5.13	0.02884	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.747497	0.12148	N	0.495209	T	0.00012	0.0000	N	0.05259	-0.085	0.80722	P	0.0	B	0.21071	0.051	B	0.18561	0.022	T	0.48364	-0.9042	9	0.54805	T	0.06	.	8.9946	0.36043	0.7137:0.0:0.1641:0.1223	rs6598163;rs17857232;rs59328534;rs6598163	182	Q9ULZ9	MMP17_HUMAN	T	182;78;98;98;23	ENSP00000353767:A182T;ENSP00000444603:A78T;ENSP00000441710:A98T;ENSP00000441106:A98T;ENSP00000442104:A23T	ENSP00000353767:A182T	A	+	1	0	MMP17	130891192	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.298000	0.08265	-0.983000	0.03511	-0.320000	0.08662	GCC	A|0.462;G|0.537;T|0.000	0.462	strong		0.667	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
SP2	6668	hgsc.bcm.edu	37	17	46002744	46002744	+	Silent	SNP	G	G	T	rs1130932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46002744G>T	ENST00000376741.4	+	6	1715	c.1578G>T	c.(1576-1578)gtG>gtT	p.V526V	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	526					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)	p.V526V(1)		endometrium(1)|large_intestine(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	13						AGAAGCACGTGTGCCACATCC	0.592													G|||	2518	0.502796	0.3805	0.4697	5008	,	,		22979	0.7708		0.4583	False		,,,				2504	0.4611				p.V526V		Atlas-SNP	.											SP2,colon,carcinoma,0,2	SP2	38	2	1	Substitution - coding silent(1)	large_intestine(1)	c.G1578T						PASS	.	G		1758,2648	521.1+/-370.4	355,1048,800	122.0	106.0	112.0		1578	5.0	1.0	17	dbSNP_86	112	3721,4879	530.3+/-381.8	807,2107,1386	no	coding-synonymous	SP2	NM_003110.5		1162,3155,2186	TT,TG,GG		43.2674,39.9001,42.1267		526/614	46002744	5479,7527	2203	4300	6503	SO:0001819	synonymous_variant	6668	exon6			GCACGTGTGCCAC		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.1578G>T	17.37:g.46002744G>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_003110	A6NK74	Silent	SNP	ENST00000376741.4	37	CCDS11521.2																																																																																			G|0.537;T|0.463	0.463	strong		0.592	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
OR7A17	26333	hgsc.bcm.edu	37	19	14992042	14992042	+	Silent	SNP	A	A	G	rs10405136	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	104	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	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	
FCGBP	8857	hgsc.bcm.edu	37	19	40368330	40368330	+	Missense_Mutation	SNP	C	C	T	rs74540349	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40368330C>T	ENST00000221347.6	-	28	13025	c.13018G>A	c.(13018-13020)Gaa>Aaa	p.E4340K		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4340						extracellular vesicular exosome (GO:0070062)		p.E4340K(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)			CGCCAGTCTTCGATGACAACC	0.642																																					p.E4340K		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	stomach(1)	c.G13018A						scavenged	.						130.0	140.0	136.0					19																	40368330		2203	4300	6503	SO:0001583	missense	8857	exon28			AGTCTTCGATGAC	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.13018G>A	19.37:g.40368330C>T	ENSP00000221347:p.Glu4340Lys	Somatic	190	2	0.0105263		WXS	Illumina HiSeq	Phase_I	170	28	0.164706	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	478	0.21886446886446886	101	0.20528455284552846	56	0.15469613259668508	196	0.34265734265734266	125	0.16490765171503957	C	6.598	0.478746	0.12521	.	.	ENSG00000090920	ENST00000221347	D	0.85955	-2.05	4.08	-8.16	0.01061	Uncharacterised domain, cysteine-rich (2);	1.549620	0.03830	N	0.268942	T	0.00012	0.0000	N	0.03084	-0.415	0.80722	P	0.0	B	0.12013	0.005	B	0.04013	0.001	T	0.03259	-1.1055	9	0.12766	T	0.61	.	2.0488	0.03566	0.1461:0.4649:0.1867:0.2022	.	4340	Q9Y6R7	FCGBP_HUMAN	K	4340	ENSP00000221347:E4340K	ENSP00000221347:E4340K	E	-	1	0	FCGBP	45060170	0.000000	0.05858	0.001000	0.08648	0.220000	0.24768	-7.283000	0.00040	-1.584000	0.01636	0.305000	0.20034	GAA	C|0.827;T|0.173	0.173	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF701	55762	hgsc.bcm.edu	37	19	53086485	53086485	+	Silent	SNP	T	T	C	rs62117247	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53086485T>C	ENST00000540331.1	+	5	1596	c.1371T>C	c.(1369-1371)ttT>ttC	p.F457F	ZNF701_ENST00000391785.3_Silent_p.F391F|ZNF701_ENST00000301093.2_Silent_p.F457F|CTD-3099C6.7_ENST00000599222.1_RNA	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	457					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)		GCAAGACCTTTGTTCAAAATT	0.383													t|||	124	0.0247604	0.0166	0.036	5008	,	,		22678	0.001		0.0636	False		,,,				2504	0.0123				p.F457F	NSCLC(89;451 1475 9611 20673 52284)	Atlas-SNP	.											.	ZNF701	44	.	0			c.T1371C						PASS	.						57.0	58.0	57.0					19																	53086485		2201	4295	6496	SO:0001819	synonymous_variant	55762	exon5			GACCTTTGTTCAA	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.1371T>C	19.37:g.53086485T>C		Somatic	520	0	0		WXS	Illumina HiSeq	Phase_I	370	125	0.337838	NM_001172655	A2RRM8|B9EGF2|F5GZM6|Q66K42	Silent	SNP	ENST00000540331.1	37	CCDS54311.1																																																																																			T|0.961;C|0.039	0.039	strong		0.383	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
AHCTF1	25909	hgsc.bcm.edu	37	1	247051714	247051714	+	Silent	SNP	A	A	G	rs144599339	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247051714A>G	ENST00000391829.2	-	18	2373	c.2250T>C	c.(2248-2250)taT>taC	p.Y750Y	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000326225.3_Silent_p.Y759Y|AHCTF1_ENST00000366508.1_Silent_p.Y785Y			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	750	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)			TAGCAGGAGGATATTTTCCTG	0.463													A|||	13	0.00259585	0.0	0.0014	5008	,	,		18465	0.0		0.006	False		,,,				2504	0.0061				p.Y759Y	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.T2277C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	134.0	125.0	128.0		2277	-1.4	1.0	1	dbSNP_134	128	54,8546	33.8+/-87.4	0,54,4246	no	coding-synonymous	AHCTF1	NM_015446.4		0,57,6446	GG,GA,AA		0.6279,0.0681,0.4383		759/2276	247051714	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	25909	exon18			AGGAGGATATTTT		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.2250T>C	1.37:g.247051714A>G		Somatic	477	1	0.00209644		WXS	Illumina HiSeq	Phase_I	565	328	0.580531	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				A|0.997;G|0.003	0.003	strong		0.463	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
WDHD1	11169	hgsc.bcm.edu	37	14	55448409	55448409	+	Missense_Mutation	SNP	G	G	C	rs61741224	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:55448409G>C	ENST00000360586.3	-	16	1977	c.1912C>G	c.(1912-1914)Cct>Gct	p.P638A	WDHD1_ENST00000359167.4_Missense_Mutation_p.P156A|WDHD1_ENST00000420358.2_Missense_Mutation_p.P515A|WDHD1_ENST00000421192.1_Missense_Mutation_p.P515A	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	638					heterochromatin maintenance (GO:0070829)|regulation of chromosome organization (GO:0033044)|RNA processing (GO:0006396)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|kidney(3)|large_intestine(9)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(2)	42						ACGTAACAAGGGGTACCTAAA	0.368													G|||	144	0.028754	0.0023	0.036	5008	,	,		15265	0.0		0.1113	False		,,,				2504	0.0041				p.P638A		Atlas-SNP	.											.	WDHD1	82	.	0			c.C1912G						PASS	.	G	ALA/PRO,ALA/PRO	81,4325	69.8+/-107.6	3,75,2125	84.0	73.0	77.0		1543,1912	5.7	1.0	14	dbSNP_129	77	837,7763	192.7+/-238.6	36,765,3499	yes	missense,missense	WDHD1	NM_001008396.2,NM_007086.3	27,27	39,840,5624	CC,CG,GG		9.7326,1.8384,7.0583	probably-damaging,probably-damaging	515/1007,638/1130	55448409	918,12088	2203	4300	6503	SO:0001583	missense	11169	exon16			AACAAGGGGTACC	AJ006266	CCDS9721.1, CCDS41955.1	14q22.2	2013-01-09			ENSG00000198554	ENSG00000198554		"""WD repeat domain containing"""	23170	protein-coding gene	gene with protein product	"""CTF4, chromosome transmission fidelity factor 4 homolog (S. cerevisiae)"""	608126				9175701, 20028748	Standard	NM_007086		Approved	AND-1, CTF4, CHTF4	uc001xbm.2	O75717	OTTHUMG00000140304	ENST00000360586.3:c.1912C>G	14.37:g.55448409G>C	ENSP00000353793:p.Pro638Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	137	80	0.583942	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	101	0.04624542124542125	0	0.0	15	0.04143646408839779	0	0.0	86	0.11345646437994723	G	24.5	4.538803	0.85917	0.018384	0.097326	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.73363	-0.34;0.28;-0.74	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.17109	0.0411	M	0.89287	3.02	0.09310	P	0.99999999845594	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.992	T	0.63093	-0.6714	9	0.35671	T	0.21	-3.4145	19.9281	0.97110	0.0:0.0:1.0:0.0	rs61741224	156;638	F8W7P7;O75717	.;WDHD1_HUMAN	A	638;156;515	ENSP00000353793:P638A;ENSP00000352085:P156A;ENSP00000391049:P515A	ENSP00000352085:P156A	P	-	1	0	WDHD1	54518159	1.000000	0.71417	0.993000	0.49108	0.815000	0.46073	7.687000	0.84139	2.708000	0.92522	0.585000	0.79938	CCT	G|0.928;C|0.072	0.072	strong		0.368	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086	
TTLL5	23093	hgsc.bcm.edu	37	14	76368544	76368544	+	Missense_Mutation	SNP	T	T	C	rs1133834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:76368544T>C	ENST00000298832.9	+	31	4005	c.3800T>C	c.(3799-3801)tTt>tCt	p.F1267S		NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1267			F -> S (in dbSNP:rs1133834). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:17116691}.		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)		CCTGCAGCCTTTGTGCCCATC	0.562													T|||	2131	0.425519	0.5832	0.366	5008	,	,		19061	0.494		0.1928	False		,,,				2504	0.4233				p.F1267S		Atlas-SNP	.											.	TTLL5	102	.	0			c.T3800C						PASS	.	T	SER/PHE	2238,2168	594.9+/-388.3	570,1098,535	85.0	77.0	80.0		3800	1.5	0.3	14	dbSNP_86	80	1537,7063	286.6+/-297.8	137,1263,2900	yes	missense	TTLL5	NM_015072.4	155	707,2361,3435	CC,CT,TT		17.8721,49.2056,29.0251	benign	1267/1282	76368544	3775,9231	2203	4300	6503	SO:0001583	missense	23093	exon31			CAGCCTTTGTGCC	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.3800T>C	14.37:g.76368544T>C	ENSP00000298832:p.Phe1267Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	110	40	0.363636	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	37	CCDS32124.1	835	0.3823260073260073	292	0.5934959349593496	125	0.3453038674033149	277	0.48426573426573427	141	0.18601583113456466	T	13.21	2.170428	0.38315	0.507944	0.178721	ENSG00000119685	ENST00000286653;ENST00000298832	T	0.02763	4.17	5.43	1.48	0.22813	.	2.780490	0.00890	N	0.002234	T	0.00012	0.0000	N	0.08118	0	0.58432	P	6.999999999979245E-6	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.38972	-0.9636	9	0.09590	T	0.72	.	1.2609	0.02001	0.1796:0.1055:0.1866:0.5283	rs1133834;rs2272583;rs3195915;rs52790173;rs61039434;rs1133834	341;1267	F8W7N3;Q6EMB2	.;TTLL5_HUMAN	S	341;1267	ENSP00000298832:F1267S	ENSP00000286653:F341S	F	+	2	0	TTLL5	75438297	0.014000	0.17966	0.310000	0.25168	0.975000	0.68041	0.410000	0.21098	0.346000	0.23899	-0.316000	0.08728	TTT	C|0.345;N|0.000	0.345	strong		0.562	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
NAPSA	9476	hgsc.bcm.edu	37	19	50865535	50865535	+	Missense_Mutation	SNP	A	A	G	rs676314	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	99	0	0		WXS	Illumina HiSeq	Phase_I	88	85	0.965909	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	
RHOBTB3	22836	hgsc.bcm.edu	37	5	95084131	95084131	+	Silent	SNP	G	G	A	rs34896	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	181	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	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	
MAST2	23139	hgsc.bcm.edu	37	1	46500613	46500613	+	Silent	SNP	T	T	C	rs17855317	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	183	0	0		WXS	Illumina HiSeq	Phase_I	122	22	0.180328	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	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15586672	15586672	+	Missense_Mutation	SNP	A	A	T	rs892145	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:15586672A>T	ENST00000340880.4	-	2	1289	c.809T>A	c.(808-810)aTg>aAg	p.M270K	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.M270K	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	270			M -> K (in dbSNP:rs892145). {ECO:0000269|PubMed:12975309}.		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.M270K(2)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						GAGGAAGGCCATGGTTAACAG	0.612													A|||	1834	0.366214	0.4077	0.3444	5008	,	,		19085	0.3631		0.3917	False		,,,				2504	0.3027				p.M270K		Atlas-SNP	.											PGLYRP2_ENST00000292609,NS,carcinoma,0,4	PGLYRP2	116	4	2	Substitution - Missense(2)	prostate(2)	c.T809A						scavenged	.	A	LYS/MET	1709,2697		339,1031,833	37.0	38.0	38.0		809	-1.1	0.9	19	dbSNP_86	38	3238,5362		641,1956,1703	yes	missense	PGLYRP2	NM_052890.3	95	980,2987,2536	TT,TA,AA		37.6512,38.788,38.0363	benign	270/577	15586672	4947,8059	2203	4300	6503	SO:0001583	missense	114770	exon2			AAGGCCATGGTTA	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.809T>A	19.37:g.15586672A>T	ENSP00000345968:p.Met270Lys	Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	815	0.3731684981684982	199	0.40447154471544716	115	0.31767955801104975	208	0.36363636363636365	293	0.3865435356200528	A	5.442	0.266646	0.10294	0.38788	0.376512	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.04194	3.69;3.68	5.31	-1.07	0.09968	.	1.255450	0.05643	N	0.583853	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B;B	0.25904	0.137;0.02	B;B	0.29598	0.104;0.013	T	0.45644	-0.9247	9	0.25751	T	0.34	-21.0741	12.7595	0.57356	0.8205:0.0:0.1795:0.0	rs892145;rs52816103;rs60008418;rs892145	270;270	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	K	270	ENSP00000345968:M270K;ENSP00000292609:M270K	ENSP00000292609:M270K	M	-	2	0	PGLYRP2	15447672	0.001000	0.12720	0.886000	0.34754	0.058000	0.15608	-0.159000	0.10056	-0.419000	0.07439	-1.447000	0.01057	ATG	A|0.632;T|0.368	0.368	strong		0.612	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
RTN2	6253	hgsc.bcm.edu	37	19	45998247	45998247	+	Silent	SNP	A	A	G	rs10401270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45998247A>G	ENST00000245923.4	-	3	331	c.96T>C	c.(94-96)tcT>tcC	p.S32S	PPM1N_ENST00000396737.2_5'Flank|PPM1N_ENST00000401705.1_Intron|RTN2_ENST00000430715.2_5'Flank|RTN2_ENST00000344680.4_Silent_p.S32S|RTN2_ENST00000590526.1_5'UTR|RTN2_ENST00000589384.1_5'UTR|PPM1N_ENST00000456399.2_5'Flank	NM_005619.4	NP_005610.1	O75298	RTN2_HUMAN	reticulon 2	32					cell death (GO:0008219)|intracellular protein transmembrane transport (GO:0065002)|regulation of glucose import (GO:0046324)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(4)|skin(1)|urinary_tract(1)	20		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00829)|Epithelial(262;0.184)|GBM - Glioblastoma multiforme(486;0.246)		CTCGAAAATCAGAGTCGTCGT	0.627													G|||	765	0.152756	0.1505	0.1326	5008	,	,		16502	0.2183		0.0984	False		,,,				2504	0.1585				p.S32S		Atlas-SNP	.											.	RTN2	45	.	0			c.T96C						PASS	.		,	638,3768	766.2+/-413.4	58,522,1623	69.0	67.0	68.0		96,96	-10.9	0.0	19	dbSNP_119	68	889,7711	777.0+/-407.7	51,787,3462	no	coding-synonymous,coding-synonymous	RTN2	NM_005619.3,NM_206900.1	,	109,1309,5085	GG,GA,AA		10.3372,14.4803,11.7407	,	32/546,32/473	45998247	1527,11479	2203	4300	6503	SO:0001819	synonymous_variant	6253	exon3			AAAATCAGAGTCG	AF038540	CCDS12665.1, CCDS12666.1, CCDS46114.1	19q13.2-q13.3	2012-03-30				ENSG00000125744			10468	protein-coding gene	gene with protein product	"""NSP-like protein 1"", ""Neuroendocrine-specific protein-like 1"""	603183	"""spastic paraplegia 12 (autosomal dominant)"""	SPG12		8812484, 9530622, 22232211	Standard	NM_005619		Approved	NSP2, NSPL1	uc002pcb.4	O75298		ENST00000245923.4:c.96T>C	19.37:g.45998247A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	59	57	0.966102	NM_206900	O60509|Q7RTM6|Q7RTN1|Q7RTN2	Silent	SNP	ENST00000245923.4	37	CCDS12665.1																																																																																			A|0.870;G|0.130	0.130	strong		0.627	RTN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459574.1	NM_005619	
CPQ	10404	hgsc.bcm.edu	37	8	97847358	97847358	+	Silent	SNP	G	G	T	rs1864384	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	223	1	0.00448431		WXS	Illumina HiSeq	Phase_I	278	274	0.985611	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	
INO80D	54891	hgsc.bcm.edu	37	2	206874307	206874307	+	Missense_Mutation	SNP	T	T	C	rs144598064	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:206874307T>C	ENST00000403263.1	-	9	2158	c.1754A>G	c.(1753-1755)cAc>cGc	p.H585R	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	585					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						TGACCGGATGTGAGAGGCCTC	0.522													T|||	7	0.00139776	0.0008	0.0014	5008	,	,		15621	0.0		0.005	False		,,,				2504	0.0				p.H585R		Atlas-SNP	.											.	INO80D	134	.	0			c.A1754G						PASS	.	T	ARG/HIS	6,3914		0,6,1954	70.0	76.0	74.0		1754	-0.7	0.1	2	dbSNP_134	74	81,8247		0,81,4083	yes	missense	INO80D	NM_017759.4	29	0,87,6037	CC,CT,TT		0.9726,0.1531,0.7103	benign	585/1028	206874307	87,12161	1960	4164	6124	SO:0001583	missense	54891	exon9			CGGATGTGAGAGG		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.1754A>G	2.37:g.206874307T>C	ENSP00000384198:p.His585Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	59	16	0.271186	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Missense_Mutation	SNP	ENST00000403263.1	37	CCDS46500.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	7.154	0.584297	0.13749	0.001531	0.009726	ENSG00000114933	ENST00000403263;ENST00000233270	T	0.30182	1.54	5.8	-0.695	0.11291	.	0.655303	0.16801	N	0.198942	T	0.10294	0.0252	N	0.22421	0.69	0.19575	N	0.999969	B	0.02656	0.0	B	0.01281	0.0	T	0.28004	-1.0057	10	0.13108	T	0.6	.	5.5793	0.17241	0.0:0.2813:0.1337:0.585	.	585	Q53TQ3-2	.	R	585	ENSP00000384198:H585R	ENSP00000233270:H585R	H	-	2	0	INO80D	206582552	1.000000	0.71417	0.149000	0.22428	0.362000	0.29581	1.785000	0.38684	-0.103000	0.12175	-0.250000	0.11733	CAC	T|0.997;C|0.003	0.003	strong		0.522	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
TMEM52B	120939	hgsc.bcm.edu	37	12	10332198	10332198	+	Missense_Mutation	SNP	G	G	T	rs140071448		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:10332198G>T	ENST00000381923.2	+	2	429	c.25G>T	c.(25-27)Gcg>Tcg	p.A9S	TMEM52B_ENST00000298530.3_Missense_Mutation_p.W3C|TMEM52B_ENST00000536952.1_Missense_Mutation_p.A9S			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	9						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TCATGTCGTGGCGGCCTCAGC	0.478													G|||	1	0.000199681	0.0	0.0	5008	,	,		17529	0.0		0.001	False		,,,				2504	0.0				p.W3C		Atlas-SNP	.											.	.	.	.	0			c.G9T						PASS	.	G	CYS/TRP	0,4406		0,0,2203	183.0	173.0	176.0		9	-5.3	0.0	12	dbSNP_134	176	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C12orf59	NM_153022.2	215	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	benign	3/164	10332198	3,13003	2203	4300	6503	SO:0001583	missense	120939	exon1			GTCGTGGCGGCCT	AY358845	CCDS8619.1, CCDS66314.1	12p13.2	2012-08-15	2012-08-15	2012-08-15	ENSG00000165685	ENSG00000165685			26438	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 59"""	C12orf59		12975309	Standard	XM_005253299		Approved	FLJ31166	uc001qxq.3	Q4KMG9	OTTHUMG00000168410	ENST00000381923.2:c.25G>T	12.37:g.10332198G>T	ENSP00000371348:p.Ala9Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_153022	Q96NA7	Missense_Mutation	SNP	ENST00000381923.2	37		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	8.571|8.571	0.879998|0.879998	0.17467|0.17467	0.0|0.0	3.49E-4|3.49E-4	ENSG00000165685|ENSG00000165685	ENST00000381923;ENST00000543484;ENST00000536952|ENST00000298530	.|.	.|.	.|.	5.3|5.3	-5.3|-5.3	0.02738|0.02738	.|.	1.353820|.	0.04491|.	N|.	0.379462|.	T|T	0.25754|0.25754	0.0627|0.0627	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.29366|0.29366	-1.0014|-1.0014	8|7	0.38643|0.87932	T|D	0.18|0	1.6513|1.6513	4.7738|4.7738	0.13169|0.13169	0.3682:0.0:0.3801:0.2518|0.3682:0.0:0.3801:0.2518	.|.	9|3	Q4KMG9|Q4KMG9-2	CL059_HUMAN|.	S|C	9|3	.|.	ENSP00000371348:A9S|ENSP00000298530:W3C	A|W	+|+	1|3	0|0	C12orf59|C12orf59	10223465|10223465	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.493000|-0.493000	0.06459|0.06459	-1.165000|-1.165000	0.02786|0.02786	-1.197000|-1.197000	0.01672|0.01672	GCG|TGG	G|1.000;T|0.000	0.000	strong		0.478	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022	
CSMD1	64478	hgsc.bcm.edu	37	8	2820043	2820043	+	Silent	SNP	G	G	T	rs4876056	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:2820043G>T	ENST00000520002.1	-	62	10131	c.9576C>A	c.(9574-9576)tcC>tcA	p.S3192S	CSMD1_ENST00000400186.3_Silent_p.S3015S|CSMD1_ENST00000602557.1_Silent_p.S3192S|CSMD1_ENST00000537824.1_Silent_p.S3191S|CSMD1_ENST00000542608.1_Silent_p.S3014S|CSMD1_ENST00000602723.1_Silent_p.S3015S			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3192	Sushi 26. {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)		AGACTCTTCTGGAGGATCCCA	0.498													T|||	638	0.127396	0.3336	0.0836	5008	,	,		16851	0.1081		0.0229	False		,,,				2504	0.0072				p.S3191S		Atlas-SNP	.											CSMD1_ENST00000318252,NS,carcinoma,-1,1	CSMD1	1469	1	0			c.C9573A						scavenged	.	T		1080,2772		146,788,992	65.0	64.0	64.0		9573	-11.2	0.0	8	dbSNP_111	64	236,8022		1,234,3894	no	coding-synonymous	CSMD1	NM_033225.5		147,1022,4886	TT,TG,GG		2.8578,28.0374,10.8671		3191/3565	2820043	1316,10794	1926	4129	6055	SO:0001819	synonymous_variant	64478	exon61			TCTTCTGGAGGAT			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.9576C>A	8.37:g.2820043G>T		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	161	52	0.322981	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		266	0.12179487179487179	169	0.3434959349593496	24	0.06629834254143646	60	0.1048951048951049	13	0.017150395778364115	T	0.437	-0.900256	0.02472	0.280374	0.028578	ENSG00000183117	ENST00000335551	.	.	.	5.6	-11.2	0.00127	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22903	P	0.99858238	.	.	.	.	.	.	T	0.24584	-1.0156	3	.	.	.	.	11.6209	0.51117	0.0:0.2273:0.1926:0.5801	rs4876056;rs4876056	.	.	.	K	2609	.	.	Q	-	1	0	CSMD1	2807450	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-2.681000	0.00837	-4.931000	0.00027	-0.256000	0.11100	CAG	G|0.871;T|0.129	0.129	strong		0.498	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
CFP	5199	hgsc.bcm.edu	37	X	47483800	47483800	+	Silent	SNP	G	G	A	rs1048118	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	65	62	0.953846	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	
NAV2	89797	hgsc.bcm.edu	37	11	19735325	19735325	+	Silent	SNP	C	C	A	rs11828836	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:19735325C>A	ENST00000396087.3	+	1	183	c.84C>A	c.(82-84)ccC>ccA	p.P28P	NAV2_ENST00000360655.4_Intron|NAV2_ENST00000396085.1_Silent_p.P28P|NAV2_ENST00000349880.4_Silent_p.P28P|RP11-359E10.1_ENST00000603468.1_lincRNA	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	28					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						TGCACGTgcccccggcccggg	0.662													C|||	112	0.0223642	0.0825	0.0043	5008	,	,		13608	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	NAV2	255	.	0			c.C84A						PASS	.	C	,,	269,4121		8,253,1934	20.0	22.0	21.0		,84,84	4.4	1.0	11	dbSNP_120	21	5,8571		0,5,4283	no	intron,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	8,258,6217	AA,AC,CC		0.0583,6.1276,2.1132	,,	,28/2430,28/2433	19735325	274,12692	2195	4288	6483	SO:0001819	synonymous_variant	89797	exon1			CGTGCCCCCGGCC	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.84C>A	11.37:g.19735325C>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	21	9	0.428571	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																																																																																			C|0.975;A|0.025	0.025	strong		0.662	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561313	32561313	+	Nonsense_Mutation	SNP	C	C	T	rs201986816	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:32561313C>T	ENST00000345122.3	+	2	1753	c.1438C>T	c.(1438-1440)Cga>Tga	p.R480*	ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000556611.1_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000432921.1_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000539826.2_Nonsense_Mutation_p.R480*|ARHGAP5_ENST00000396582.2_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	480	FF 3.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		TAGGCATCAGCGAGAAATAGT	0.383																																					p.R480X	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											.	ARHGAP5	166	.	0			c.C1438T						PASS	.						70.0	72.0	71.0					14																	32561313		2203	4298	6501	SO:0001587	stop_gained	394	exon2			CATCAGCGAGAAA	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1438C>T	14.37:g.32561313C>T	ENSP00000371897:p.Arg480*	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	126	7	0.0555556	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Nonsense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	C	39	7.554307	0.98355	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	.	.	.	6.02	5.11	0.69529	.	0.057780	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	14.0719	0.64865	0.3873:0.6127:0.0:0.0	.	.	.	.	X	480	.	ENSP00000371897:R480X	R	+	1	2	ARHGAP5	31631064	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.567000	0.45956	1.483000	0.48342	0.650000	0.86243	CGA	C|0.998;T|0.002	0.002	strong		0.383	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
ZNF492	57615	hgsc.bcm.edu	37	19	22836805	22836805	+	Missense_Mutation	SNP	G	G	A	rs200144130		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22836805G>A	ENST00000456783.2	+	3	362	c.118G>A	c.(118-120)Gct>Act	p.A40T		NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	40	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.A40T(2)		endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				TGAGATGGTAGCTGAACCCCC	0.408																																					p.A40T		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,0,4	ZNF492	129	4	2	Substitution - Missense(2)	prostate(2)	c.G118A						scavenged	.																																			SO:0001583	missense	57615	exon3			ATGGTAGCTGAAC	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.118G>A	19.37:g.22836805G>A	ENSP00000413660:p.Ala40Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	123	7	0.0569106	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	.	.	.	.	.	.	.	.	.	.	.	10.18	1.279365	0.23307	.	.	ENSG00000229676	ENST00000456783	T	0.07688	3.17	0.458	0.458	0.16670	Krueppel-associated box (1);	.	.	.	.	T	0.13372	0.0324	M	0.72576	2.205	0.09310	N	1	P	0.45011	0.848	P	0.46585	0.521	T	0.13899	-1.0492	8	0.42905	T	0.14	.	.	.	.	.	40	Q9P255	ZN492_HUMAN	T	40	ENSP00000413660:A40T	ENSP00000413660:A40T	A	+	1	0	ZNF492	22628645	0.064000	0.20934	0.002000	0.10522	0.002000	0.02628	1.318000	0.33643	0.482000	0.27582	0.484000	0.47621	GCT	.	.	weak		0.408	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
CLIP1	6249	hgsc.bcm.edu	37	12	122817580	122817580	+	Missense_Mutation	SNP	A	A	G	rs17883517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:122817580A>G	ENST00000540338.1	-	14	2862	c.2821T>C	c.(2821-2823)Tct>Cct	p.S941P	CLIP1_ENST00000361654.4_Missense_Mutation_p.S819P|CLIP1_ENST00000545889.1_Missense_Mutation_p.S516P|CLIP1_ENST00000537178.1_Missense_Mutation_p.S895P|CLIP1_ENST00000302528.7_Missense_Mutation_p.S930P|CLIP1_ENST00000358808.2_Missense_Mutation_p.S930P			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	941			S -> P (in dbSNP:rs17883517). {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)		AGCTGAGAAGAGTTATCTCCT	0.388													A|||	157	0.0313498	0.003	0.0591	5008	,	,		18646	0.001		0.1034	False		,,,				2504	0.0072				p.S941P		Atlas-SNP	.											.	CLIP1	126	.	0			c.T2821C						PASS	.	A	PRO/SER,PRO/SER	75,4331	67.0+/-104.6	1,73,2129	191.0	164.0	173.0		2788,2683	5.6	1.0	12	dbSNP_124	173	848,7748	193.0+/-238.8	37,774,3487	yes	missense,missense	CLIP1	NM_002956.2,NM_198240.1	74,74	38,847,5616	GG,GA,AA		9.8651,1.7022,7.0989	probably-damaging,probably-damaging	930/1428,895/1393	122817580	923,12079	2203	4298	6501	SO:0001583	missense	6249	exon15			GAGAAGAGTTATC		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.2821T>C	12.37:g.122817580A>G	ENSP00000439093:p.Ser941Pro	Somatic	291	1	0.00343643		WXS	Illumina HiSeq	Phase_I	241	97	0.40249	NM_001247997	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	90	0.04120879120879121	1	0.0020325203252032522	20	0.055248618784530384	1	0.0017482517482517483	68	0.08970976253298153	A	27.9	4.876504	0.91664	0.017022	0.098651	ENSG00000130779	ENST00000545889;ENST00000302528;ENST00000358808;ENST00000542885;ENST00000537178;ENST00000540338;ENST00000540304	T;T;T;T;T;T	0.78126	2.31;-1.15;-1.15;0.29;0.29;-1.0	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	M	0.72894	2.215	0.80722	D	1	D;D;D	0.71674	0.998;0.998;0.997	D;D;D	0.74348	0.983;0.97;0.961	T	0.63269	-0.6675	10	0.56958	D	0.05	-9.4204	15.837	0.78805	1.0:0.0:0.0:0.0	rs17883517;rs17883517	895;930;941	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	P	516;930;930;660;895;941;788	ENSP00000438743:S516P;ENSP00000303585:S930P;ENSP00000351665:S930P;ENSP00000445531:S895P;ENSP00000439093:S941P;ENSP00000437786:S788P	ENSP00000303585:S930P	S	-	1	0	CLIP1	121383533	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.663000	0.91134	2.140000	0.66376	0.460000	0.39030	TCT	A|0.939;G|0.061	0.061	strong		0.388	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
VN1R1	57191	hgsc.bcm.edu	37	19	57967133	57967133	+	Missense_Mutation	SNP	G	G	A	rs28649880	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57967133G>A	ENST00000321039.3	-	1	721	c.722C>T	c.(721-723)tCc>tTc	p.S241F	AC004076.9_ENST00000596831.1_Intron|AC004076.9_ENST00000415705.3_Intron	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	241			S -> F (in allele VN1R1*3; dbSNP:rs28649880). {ECO:0000269|PubMed:10973240, ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|skin(2)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)|Breast(46;0.222)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0254)|Lung(386;0.171)		GAAGACCATGGAGCCACTGGC	0.468													G|||	2073	0.413938	0.3124	0.451	5008	,	,		19142	0.5913		0.2793	False		,,,				2504	0.4806				p.S241F		Atlas-SNP	.											VN1R1,NS,adenoma,0,1	VN1R1	48	1	0			c.C722T						PASS	.	G	PHE/SER	1344,3062	450.6+/-349.4	189,966,1048	112.0	87.0	95.0		722	0.4	0.0	19	dbSNP_125	95	2453,6147	403.9+/-348.0	330,1793,2177	yes	missense	VN1R1	NM_020633.3	155	519,2759,3225	AA,AG,GG		28.5233,30.5039,29.1942	probably-damaging	241/354	57967133	3797,9209	2203	4300	6503	SO:0001583	missense	57191	exon1			ACCATGGAGCCAC	AF255342	CCDS12951.1	19q13.4	2012-08-22	2003-01-15		ENSG00000178201	ENSG00000178201		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	13548	protein-coding gene	gene with protein product		605234	"""vomeronasal olfactory receptor, (chromosome 19) subtype I, member 1"""	VNR19I1		10973240	Standard	NM_020633		Approved	V1RL1, ZVNR1, ZVNH1	uc002qos.2	Q9GZP7		ENST00000321039.3:c.722C>T	19.37:g.57967133G>A	ENSP00000322339:p.Ser241Phe	Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	239	109	0.456067	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	37	CCDS12951.1	878	0.40201465201465203	149	0.30284552845528456	135	0.3729281767955801	368	0.6433566433566433	226	0.29815303430079154	G	11.87	1.766615	0.31228	0.305039	0.285233	ENSG00000178201	ENST00000321039	T	0.08370	3.1	4.11	0.384	0.16244	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	L	0.48877	1.53	0.80722	P	0.0	P	0.45283	0.855	P	0.47573	0.55	T	0.30179	-0.9987	8	0.08599	T	0.76	.	2.0499	0.03568	0.1073:0.1653:0.4256:0.3017	rs28649880	241	Q9GZP7	VN1R1_HUMAN	F	241	ENSP00000322339:S241F	ENSP00000322339:S241F	S	-	2	0	VN1R1	62658945	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	-0.546000	0.06062	0.461000	0.27071	0.603000	0.83216	TCC	G|0.674;A|0.326	0.326	strong		0.468	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633	
RNGTT	8732	hgsc.bcm.edu	37	6	89614521	89614521	+	Silent	SNP	G	G	A	rs139029923		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:89614521G>A	ENST00000369485.4	-	6	783	c.597C>T	c.(595-597)gaC>gaT	p.D199D	RNGTT_ENST00000265607.6_Silent_p.D199D|RNGTT_ENST00000538899.1_Silent_p.D139D|RNGTT_ENST00000369475.3_Silent_p.D199D	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	199	Asp/Glu-rich.|TPase.				7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|RNA processing (GO:0006396)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|mRNA guanylyltransferase activity (GO:0004484)|polynucleotide 5'-phosphatase activity (GO:0004651)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|RNA guanylyltransferase activity (GO:0008192)|triphosphatase activity (GO:0050355)			endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	21		all_cancers(76;4.07e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;6.86e-05)		BRCA - Breast invasive adenocarcinoma(108;0.151)		CCTCATCTTCGTCTTCATCAT	0.428																																					p.D199D		Atlas-SNP	.											.	RNGTT	52	.	0			c.C597T						PASS	.	G		0,4406		0,0,2203	108.0	91.0	97.0		597	-10.6	0.9	6	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RNGTT	NM_003800.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		199/598	89614521	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8732	exon6			ATCTTCGTCTTCA	AF025654	CCDS5017.1	6q16	2011-06-09			ENSG00000111880	ENSG00000111880	2.7.7.50	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	10073	protein-coding gene	gene with protein product		603512				9828141, 9512541	Standard	NM_001286428		Approved	HCE, HCE1, hCAP	uc003pmr.2	O60942	OTTHUMG00000015190	ENST00000369485.4:c.597C>T	6.37:g.89614521G>A		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	206	103	0.5	NM_003800	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Silent	SNP	ENST00000369485.4	37	CCDS5017.1																																																																																			G|1.000;A|0.000	0.000	weak		0.428	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1		
CTIF	9811	hgsc.bcm.edu	37	18	46343666	46343666	+	Silent	SNP	C	C	T	rs3764481	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:46343666C>T	ENST00000256413.3	+	10	1741	c.1446C>T	c.(1444-1446)tgC>tgT	p.C482C	CTIF_ENST00000382998.4_Silent_p.C484C	NM_014772.2	NP_055587.1	O43310	CTIF_HUMAN	CBP80/20-dependent translation initiation factor	482	MIF4G.				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	31						CCTTCCTGTGCGAGGTCTTCG	0.642													c|||	677	0.135184	0.09	0.0951	5008	,	,		20270	0.2302		0.1173	False		,,,				2504	0.1452				p.C484C		Atlas-SNP	.											.	CTIF	102	.	0			c.C1452T						PASS	.		,	415,3991	205.2+/-227.1	8,399,1796	96.0	69.0	78.0		1452,1446	-4.2	0.9	18	dbSNP_107	78	975,7625	210.3+/-251.2	59,857,3384	no	coding-synonymous,coding-synonymous	CTIF	NM_001142397.1,NM_014772.2	,	67,1256,5180	TT,TC,CC		11.3372,9.419,10.6874	,	484/601,482/599	46343666	1390,11616	2203	4300	6503	SO:0001819	synonymous_variant	9811	exon11			CCTGTGCGAGGTC	AB007887	CCDS11935.1, CCDS45864.1	18q21.1	2011-01-20	2011-01-20	2011-01-20	ENSG00000134030	ENSG00000134030			23925	protein-coding gene	gene with protein product		613178	"""KIAA0427"""	KIAA0427		9455477, 19648179	Standard	NM_014772		Approved		uc002ldd.3	O43310	OTTHUMG00000132656	ENST00000256413.3:c.1446C>T	18.37:g.46343666C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	156	83	0.532051	NM_001142397	B3KTR8|Q8IVD5	Silent	SNP	ENST00000256413.3	37	CCDS11935.1																																																																																			C|0.881;T|0.119	0.119	strong		0.642	CTIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255907.1	NM_014772	
PTCHD4	442213	hgsc.bcm.edu	37	6	47847179	47847179	+	Silent	SNP	A	A	G	rs3799276	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:47847179A>G	ENST00000339488.4	-	3	1434	c.1401T>C	c.(1399-1401)gtT>gtC	p.V467V		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	467						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										AGAGGATGACAACAAATGGCT	0.443													G|||	3734	0.745607	0.6445	0.8516	5008	,	,		21602	0.8016		0.7475	False		,,,				2504	0.7474				p.V467V		Atlas-SNP	.											.	.	.	.	0			c.T1401C						PASS	.	G		2937,1469	473.1+/-356.6	988,961,254	110.0	100.0	104.0		1401	-11.3	0.1	6	dbSNP_107	104	6405,2195	373.7+/-337.1	2398,1609,293	no	coding-synonymous	C6orf138	NM_001013732.3		3386,2570,547	GG,GA,AA		25.5233,33.3409,28.1716		467/847	47847179	9342,3664	2203	4300	6503	SO:0001819	synonymous_variant	442213	exon3			GATGACAACAAAT		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 138"""	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.1401T>C	6.37:g.47847179A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	190	189	0.994737	NM_001013732	B0QZ29|B4DRK3|Q5T884	Silent	SNP	ENST00000339488.4	37	CCDS34473.2																																																																																			A|0.279;G|0.721	0.721	strong		0.443	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732	
LAMA2	3908	hgsc.bcm.edu	37	6	129371106	129371106	+	Silent	SNP	C	C	T	rs1140366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:129371106C>T	ENST00000421865.2	+	2	205	c.156C>T	c.(154-156)atC>atT	p.I52I		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	52	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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)		ATGCTCTTATCACGACCAATG	0.433													C|||	354	0.0706869	0.0015	0.0749	5008	,	,		17055	0.125		0.1282	False		,,,				2504	0.046				p.I52I		Atlas-SNP	.											.	LAMA2	481	.	0			c.C156T						PASS	.	C	,	104,4302	80.4+/-118.8	1,102,2100	196.0	176.0	183.0		156,156	4.6	1.0	6	dbSNP_86	183	1001,7599	216.4+/-255.5	62,877,3361	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	63,979,5461	TT,TC,CC		11.6395,2.3604,8.4961	,	52/3123,52/3119	129371106	1105,11901	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon2			TCTTATCACGACC	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.156C>T	6.37:g.129371106C>T		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	228	120	0.526316	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			C|0.907;T|0.093	0.093	strong		0.433	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
RUFY2	55680	hgsc.bcm.edu	37	10	70143826	70143826	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70143826T>C	ENST00000602465.1	-	9	904	c.804A>G	c.(802-804)aaA>aaG	p.K268K	RUFY2_ENST00000472394.2_5'UTR|RUFY2_ENST00000454950.2_Silent_p.K210K|RUFY2_ENST00000399200.2_Silent_p.K234K|RUFY2_ENST00000388768.2_Silent_p.K303K			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	317						nucleus (GO:0005634)	metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						GCTGCTGTGTTTTCATTAAAA	0.323																																					p.K303K		Atlas-SNP	.											.	RUFY2	58	.	0			c.A909G						PASS	.						146.0	131.0	136.0					10																	70143826		1832	4084	5916	SO:0001819	synonymous_variant	55680	exon9			CTGTGTTTTCATT	AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"""Zinc fingers, FYVE domain containing"""	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.804A>G	10.37:g.70143826T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	84	4	0.047619	NM_017987	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Silent	SNP	ENST00000602465.1	37																																																																																				.	.	none		0.323	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987	
CNR2	1269	hgsc.bcm.edu	37	1	24201920	24201920	+	Missense_Mutation	SNP	T	T	C	rs35761398|rs2501432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:24201920T>C	ENST00000374472.4	-	2	349	c.188A>G	c.(187-189)cAa>cGa	p.Q63R	CNR2_ENST00000536471.1_Missense_Mutation_p.Q63R	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	63			Q -> R (high incidence in Japanese depressed subjects; dbSNP:rs2501432). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18286196}.		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)	p.Q63R(1)		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)	CCGGCGGAGTTGGTGGGAGGA	0.557													C|||	3272	0.653355	0.7943	0.6383	5008	,	,		20063	0.502		0.5875	False		,,,				2504	0.6973				p.Q63R		Atlas-SNP	.											CNR2,NS,carcinoma,0,2	CNR2	78	2	1	Substitution - Missense(1)	stomach(1)	c.A188G						PASS	.	C	ARG/GLN	3208,1198		1258,692,253	61.0	71.0	68.0		188	5.1	0.9	1	dbSNP_100	68	4732,3868		1403,1926,971	yes	missense	CNR2	NM_001841.2	43	2661,2618,1224	CC,CT,TT		44.9767,27.1902,38.9513	benign	63/361	24201920	7940,5066	2203	4300	6503	SO:0001583	missense	1269	exon2			CGGAGTTGGTGGG	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.188A>G	1.37:g.24201920T>C	ENSP00000363596:p.Gln63Arg	Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	87	84	0.965517	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Missense_Mutation	SNP	ENST00000374472.4	37	CCDS245.1	1127	0.5160256410256411	298	0.6056910569105691	203	0.5607734806629834	271	0.4737762237762238	355	0.4683377308707124	C	0.013	-1.626255	0.00813	0.728098	0.550233	ENSG00000188822	ENST00000374472;ENST00000536471	T;T	0.70749	-0.51;-0.51	6.04	5.12	0.69794	GPCR, rhodopsin-like superfamily (1);	0.527042	0.20481	N	0.091487	T	0.00012	0.0000	N	0.01134	-0.995	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40608	-0.9554	9	0.11182	T	0.66	.	8.6774	0.34187	0.0:0.7287:0.0:0.2713	rs2501432	63	P34972	CNR2_HUMAN	R	63	ENSP00000363596:Q63R;ENSP00000442830:Q63R	ENSP00000363596:Q63R	Q	-	2	0	CNR2	24074507	0.286000	0.24305	0.910000	0.35882	0.091000	0.18340	1.434000	0.34958	1.585000	0.49928	-0.215000	0.12644	CAA	T|0.468;C|0.532	0.532	strong		0.557	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
DNAH14	127602	hgsc.bcm.edu	37	1	225528183	225528183	+	Missense_Mutation	SNP	C	C	A	rs377250670|rs3856145	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225528183C>A	ENST00000445597.2	+	47	7770	c.7770C>A	c.(7768-7770)gaC>gaA	p.D2590E	DNAH14_ENST00000430092.1_Missense_Mutation_p.D3393E|DNAH14_ENST00000439375.2_Missense_Mutation_p.D3393E			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2590					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						CAGAAATAGACAACCCCCATT	0.318													C|||	2653	0.529752	0.643	0.4697	5008	,	,		17622	0.5089		0.4046	False		,,,				2504	0.5695				p.D3393E		Atlas-SNP	.											.	DNAH14	300	.	0			c.C10179A						PASS	.	C	GLU/ASP	846,538		270,306,116	113.0	99.0	103.0		10179	0.7	1.0	1	dbSNP_108	103	1403,1779		323,757,511	yes	missense	DNAH14	NM_001373.1	45	593,1063,627	AA,AC,CC		44.0918,38.8728,49.2554	possibly-damaging	3393/4516	225528183	2249,2317	692	1591	2283	SO:0001583	missense	127602	exon67			AATAGACAACCCC	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.7770C>A	1.37:g.225528183C>A	ENSP00000409472:p.Asp2590Glu	Somatic	376	0	0		WXS	Illumina HiSeq	Phase_I	366	179	0.489071	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1057	0.483974358974359	305	0.6199186991869918	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	C	13.41	2.229518	0.39399	0.611272	0.440918	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.21191	2.02;2.02;2.02	5.22	0.724	0.18236	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999854566	B	0.31817	0.341	B	0.32762	0.152	T	0.33214	-0.9877	7	0.32370	T	0.25	.	1.4675	0.02408	0.2894:0.3987:0.141:0.1709	rs3856145;rs52794541;rs58846503;rs3856145	3393	Q0VDD8-4	.	E	2590;3393;3393	ENSP00000409472:D2590E;ENSP00000414402:D3393E;ENSP00000392061:D3393E	ENSP00000414402:D3393E	D	+	3	2	DNAH14	223594806	1.000000	0.71417	0.981000	0.43875	0.977000	0.68977	0.462000	0.21956	-0.062000	0.13088	0.508000	0.49915	GAC	C|0.498;A|0.500	0.500	strong		0.318	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PDE9A	5152	hgsc.bcm.edu	37	21	44180443	44180443	+	Silent	SNP	C	C	T	rs13047953	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:44180443C>T	ENST00000291539.6	+	12	963	c.903C>T	c.(901-903)tgC>tgT	p.C301C	PDE9A_ENST00000539837.1_Silent_p.C173C|PDE9A_ENST00000398225.3_Silent_p.C260C|PDE9A_ENST00000398227.3_Silent_p.C141C|PDE9A_ENST00000398229.3_Silent_p.C167C|PDE9A_ENST00000328862.6_Silent_p.C275C|PDE9A_ENST00000398224.3_Silent_p.C174C|PDE9A_ENST00000398236.3_Silent_p.C215C|PDE9A_ENST00000335440.6_Silent_p.C199C|PDE9A_ENST00000349112.3_Silent_p.C173C|PDE9A_ENST00000335512.4_Silent_p.C241C|PDE9A_ENST00000380328.2_Silent_p.C248C|PDE9A_ENST00000398234.3_Silent_p.C200C|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000398232.3_Silent_p.C234C	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	301	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)	p.C301C(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	CGCAGTTCTGCGTCCACGACA	0.607													C|||	1146	0.228834	0.0219	0.219	5008	,	,		16615	0.4127		0.4374	False		,,,				2504	0.1115				p.C301C		Atlas-SNP	.											PDE9A,NS,carcinoma,0,1	PDE9A	69	1	1	Substitution - coding silent(1)	stomach(1)	c.C903T						PASS	.	C	,,,,,,,,,,,,,,,,,,,	369,4037	186.7+/-213.5	17,335,1851	69.0	56.0	60.0		723,522,519,744,600,282,282,645,423,252,501,597,282,252,702,780,825,282,282,903	-1.1	1.0	21	dbSNP_121	60	3740,4860	531.7+/-382.0	823,2094,1383	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	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	,,,,,,,,,,,,,,,,,,,	840,2429,3234	TT,TC,CC		43.4884,8.3749,31.5931	,,,,,,,,,,,,,,,,,,,	241/534,174/467,173/466,248/541,200/493,94/387,94/387,215/508,141/434,84/377,167/460,199/492,94/387,84/377,234/527,260/553,275/568,94/387,94/387,301/594	44180443	4109,8897	2203	4300	6503	SO:0001819	synonymous_variant	5152	exon12			GTTCTGCGTCCAC	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.903C>T	21.37:g.44180443C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Silent	SNP	ENST00000291539.6	37	CCDS13690.1																																																																																			C|0.675;T|0.325	0.325	strong		0.607	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
MRGPRX2	117194	hgsc.bcm.edu	37	11	19077755	19077755	+	Silent	SNP	A	A	C	rs11024969	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:19077755A>C	ENST00000329773.2	-	2	282	c.195T>G	c.(193-195)tcT>tcG	p.S65S		NM_054030.2	NP_473371.1	Q96LB1	MRGX2_HUMAN	MAS-related GPR, member X2	65					positive regulation of cytokinesis (GO:0032467)|sensory perception of pain (GO:0019233)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide binding (GO:0042923)	p.S65S(1)		NS(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	15						GGACGTAGACAGAGAAGGCGT	0.557													A|||	566	0.113019	0.1944	0.036	5008	,	,		18324	0.1468		0.0656	False		,,,				2504	0.0716				p.S65S	GBM(198;1966 2199 4849 37227 49954)	Atlas-SNP	.											MRGPRX2,NS,carcinoma,0,1	MRGPRX2	42	1	1	Substitution - coding silent(1)	stomach(1)	c.T195G						PASS	.	A		701,3697		61,579,1559	84.0	92.0	89.0		195	-4.8	0.0	11	dbSNP_120	89	428,8158		7,414,3872	no	coding-synonymous	MRGPRX2	NM_054030.2		68,993,5431	CC,CA,AA		4.9849,15.9391,8.6953		65/331	19077755	1129,11855	2199	4293	6492	SO:0001819	synonymous_variant	117194	exon2			GTAGACAGAGAAG		CCDS7847.1	11p15.1	2013-10-10			ENSG00000183695	ENSG00000183695		"""GPCR / Class A : Orphans"""	17983	protein-coding gene	gene with protein product		607228				11551509	Standard	NM_054030		Approved	MRGX2	uc001mph.3	Q96LB1	OTTHUMG00000166098	ENST00000329773.2:c.195T>G	11.37:g.19077755A>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_054030	B5B0C7|Q4QXW4|Q4QXW7|Q4QXX0|Q4QXX2|Q4QXX3|Q4QXX4|Q4QXX6|Q4QXX7	Silent	SNP	ENST00000329773.2	37	CCDS7847.1																																																																																			A|0.900;C|0.100	0.100	strong		0.557	MRGPRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387819.1	NM_054030	
CTNNA3	29119	hgsc.bcm.edu	37	10	68535222	68535222	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:68535222T>C	ENST00000433211.2	-	8	1282	c.1108A>G	c.(1108-1110)Aca>Gca	p.T370A	CTNNA3_ENST00000373744.4_Missense_Mutation_p.T370A	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						AGGTCTCTTGTCTTCTTACAC	0.378																																					p.T370A		Atlas-SNP	.											.	CTNNA3	401	.	0			c.A1108G						PASS	.						187.0	177.0	180.0					10																	68535222		2203	4300	6503	SO:0001583	missense	29119	exon8			CTCTTGTCTTCTT	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.1108A>G	10.37:g.68535222T>C	ENSP00000389714:p.Thr370Ala	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	102	6	0.0588235	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731133	0.48939	.	.	ENSG00000183230	ENST00000433211;ENST00000373744	T;T	0.40756	1.02;1.02	6.16	5.04	0.67666	.	0.092451	0.47093	D	0.000247	T	0.48607	0.1509	M	0.82716	2.605	0.80722	D	1	B;B	0.26744	0.158;0.006	B;B	0.33196	0.159;0.012	T	0.53287	-0.8460	10	0.52906	T	0.07	-22.6925	9.8846	0.41253	0.0:0.0786:0.0:0.9214	.	370;370	Q9UI47-2;Q9UI47	.;CTNA3_HUMAN	A	370	ENSP00000389714:T370A;ENSP00000362849:T370A	ENSP00000362849:T370A	T	-	1	0	CTNNA3	68205228	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.998000	0.63927	2.367000	0.80283	0.528000	0.53228	ACA	.	.	none		0.378	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266	
OR5H6	79295	hgsc.bcm.edu	37	3	97983374	97983374	+	Silent	SNP	A	A	G	rs4857358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:97983374A>G	ENST00000383696.2	+	1	287	c.246A>G	c.(244-246)ttA>ttG	p.L82L	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TTGGGAGTTTAGCCTTTGTGG	0.408													A|||	1469	0.293331	0.3132	0.2695	5008	,	,		21749	0.4891		0.1233	False		,,,				2504	0.2566				p.L82L		Atlas-SNP	.											.	OR5H6	89	.	0			c.A246G						PASS	.	A		1375,3031		220,935,1048	200.0	208.0	205.0		246	-4.4	0.0	3	dbSNP_111	205	1031,7569		56,919,3325	no	coding-synonymous	OR5H6	NM_001005479.1		276,1854,4373	GG,GA,AA		11.9884,31.2074,18.4992		82/326	97983374	2406,10600	2203	4300	6503	SO:0001819	synonymous_variant	79295	exon1			GAGTTTAGCCTTT	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.246A>G	3.37:g.97983374A>G		Somatic	791	2	0.00252845		WXS	Illumina HiSeq	Phase_I	774	355	0.458656	NM_001005479	Q6IF88	Silent	SNP	ENST00000383696.2	37	CCDS33800.1																																																																																			A|0.785;G|0.215	0.215	strong		0.408	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2		
PCYOX1L	78991	hgsc.bcm.edu	37	5	148747902	148747902	+	Missense_Mutation	SNP	G	G	C	rs4705336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:148747902G>C	ENST00000274569.4	+	6	1232	c.1170G>C	c.(1168-1170)gaG>gaC	p.E390D	PCYOX1L_ENST00000514349.1_Missense_Mutation_p.E300D	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	390			E -> D (in dbSNP:rs4705336). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		prenylcysteine catabolic process (GO:0030328)	extracellular region (GO:0005576)|membrane (GO:0016020)	prenylcysteine oxidase activity (GO:0001735)	p.E390D(1)		breast(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCCCAGGAGGCAGCTGTTT	0.567											OREG0016912	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	427	0.0852636	0.0136	0.1499	5008	,	,		17418	0.001		0.1958	False		,,,				2504	0.1094				p.E390D	Ovarian(62;1136 1477 27277 27495)	Atlas-SNP	.											PCYOX1L,NS,carcinoma,0,1	PCYOX1L	32	1	1	Substitution - Missense(1)	stomach(1)	c.G1170C						PASS	.	G	ASP/GLU	171,4235	110.8+/-149.0	7,157,2039	92.0	98.0	96.0		1170	0.5	1.0	5	dbSNP_111	96	1635,6965	302.8+/-306.1	157,1321,2822	yes	missense	PCYOX1L	NM_024028.3	45	164,1478,4861	CC,CG,GG		19.0116,3.8811,13.8859	possibly-damaging	390/495	148747902	1806,11200	2203	4300	6503	SO:0001583	missense	78991	exon6			CCAGGAGGCAGCT		CCDS4296.1	5q33.1	2008-02-05			ENSG00000145882	ENSG00000145882			28477	protein-coding gene	gene with protein product						12477932	Standard	NM_024028		Approved	MGC3265	uc003lqk.2	Q8NBM8	OTTHUMG00000130052	ENST00000274569.4:c.1170G>C	5.37:g.148747902G>C	ENSP00000274569:p.Glu390Asp	Somatic	191	0	0	1719	WXS	Illumina HiSeq	Phase_I	193	85	0.440415	NM_024028	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Missense_Mutation	SNP	ENST00000274569.4	37	CCDS4296.1	219	0.10027472527472528	11	0.022357723577235773	55	0.15193370165745856	0	0.0	153	0.20184696569920843	G	18.72	3.684287	0.68157	0.038811	0.190116	ENSG00000145882	ENST00000274569;ENST00000514349	T;T	0.14766	2.48;2.48	5.51	0.481	0.16809	Prenylcysteine lyase (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.41824	1.3	0.18873	P	0.9999861451	D;P;P	0.76494	0.999;0.854;0.659	D;B;B	0.80764	0.994;0.376;0.305	T	0.22068	-1.0227	9	0.15066	T	0.55	-23.4901	5.324	0.15896	0.3781:0.133:0.4888:0.0	rs4705336;rs4705336	272;300;390	B3KXF9;E7EVZ5;Q8NBM8	.;.;PCYXL_HUMAN	D	390;300	ENSP00000274569:E390D;ENSP00000428512:E300D	ENSP00000274569:E390D	E	+	3	2	PCYOX1L	148728095	1.000000	0.71417	0.991000	0.47740	0.992000	0.81027	0.648000	0.24828	-0.223000	0.09943	0.561000	0.74099	GAG	G|0.877;C|0.123	0.123	strong		0.567	PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028	
FREM2	341640	hgsc.bcm.edu	37	13	39424254	39424254	+	Silent	SNP	T	T	C	rs35252750|rs9548507	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:39424254T>C	ENST00000280481.7	+	9	6675	c.6459T>C	c.(6457-6459)acT>acC	p.T2153T	FREM2_ENST00000482551.1_3'UTR	NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2153	Calx-beta 4.		T -> S (in dbSNP:rs9548506). {ECO:0000269|PubMed:17974005}.		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)		TCCATAGGACTGGGGATGTCC	0.453													C|||	460	0.091853	0.0802	0.2478	5008	,	,		19720	0.001		0.0885	False		,,,				2504	0.0941				p.T2153T		Atlas-SNP	.											.	FREM2	385	.	0			c.T6459C						PASS	.	C		4,4402		2,0,2201	122.0	110.0	114.0		6459	-2.7	0.7	13	dbSNP_119	114	22,8578		5,12,4283	no	coding-synonymous	FREM2	NM_207361.4		7,12,6484	CC,CT,TT		0.2558,0.0908,0.1999		2153/3170	39424254	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon9			TAGGACTGGGGAT	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.6459T>C	13.37:g.39424254T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			T|0.912;C|0.088	0.088	strong		0.453	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
POLM	27434	hgsc.bcm.edu	37	7	44121936	44121936	+	Silent	SNP	C	C	A	rs3218655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:44121936C>A	ENST00000242248.5	-	1	203	c.102G>T	c.(100-102)ctG>ctT	p.L34L	POLM_ENST00000395831.3_Silent_p.L34L|POLM_ENST00000335195.6_Silent_p.L34L	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	34	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						GAGGCTCGACCAGGTAGATGG	0.736								DNA polymerases (catalytic subunits)					C|||	853	0.170327	0.2163	0.1844	5008	,	,		9905	0.1111		0.1491	False		,,,				2504	0.181				p.L34L		Atlas-SNP	.											.	POLM	50	.	0			c.G102T						PASS	.	C		772,3464		79,614,1425	7.0	8.0	8.0		102	4.4	1.0	7	dbSNP_106	8	995,7359		69,857,3251	no	coding-synonymous	POLM	NM_013284.2		148,1471,4676	AA,AC,CC		11.9105,18.2247,14.0349		34/495	44121936	1767,10823	2118	4177	6295	SO:0001819	synonymous_variant	27434	exon1			CTCGACCAGGTAG	AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"""DNA polymerases"""	9185	protein-coding gene	gene with protein product	"""Pol iota"""	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.102G>T	7.37:g.44121936C>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Silent	SNP	ENST00000242248.5	37	CCDS34625.1																																																																																			C|0.841;A|0.159	0.159	strong		0.736	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284	
MAPRE1	22919	hgsc.bcm.edu	37	20	31427635	31427635	+	Silent	SNP	C	C	T	rs2070090	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:31427635C>T	ENST00000375571.5	+	5	709	c.570C>T	c.(568-570)gaC>gaT	p.D190D		NM_012325.2	NP_036457.1	Q15691	MARE1_HUMAN	microtubule-associated protein, RP/EB family, member 1	190	EB1 C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00576}.|Interaction with CDK5RAP2.|Interaction with MTUS2/TIP150.				cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of microtubule plus-end binding (GO:1903033)|protein localization to microtubule (GO:0035372)	cell projection membrane (GO:0031253)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule plus-end (GO:0035371)	microtubule plus-end binding (GO:0051010)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8						GCAACGGAGACGACGAGGCAG	0.612													C|||	1557	0.310903	0.4372	0.2161	5008	,	,		17507	0.3651		0.1461	False		,,,				2504	0.3211				p.D190D		Atlas-SNP	.											.	MAPRE1	17	.	0			c.C570T						PASS	.	C		1686,2720	513.1+/-368.2	311,1064,828	128.0	133.0	131.0		570	1.6	1.0	20	dbSNP_96	131	1437,7163	276.1+/-292.1	120,1197,2983	no	coding-synonymous	MAPRE1	NM_012325.2		431,2261,3811	TT,TC,CC		16.7093,38.266,24.012		190/269	31427635	3123,9883	2203	4300	6503	SO:0001819	synonymous_variant	22919	exon5			CGGAGACGACGAG	U24166	CCDS13208.1	20q11.1-q11.3	2013-01-17			ENSG00000101367	ENSG00000101367			6890	protein-coding gene	gene with protein product	"""adenomatous polyposis coli-binding protein EB1"""	603108				7606712, 9724749, 11470413	Standard	NM_012325		Approved	EB1	uc002wyh.3	Q15691	OTTHUMG00000032228	ENST00000375571.5:c.570C>T	20.37:g.31427635C>T		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	124	59	0.475806	NM_012325	B2R6I7|E1P5M8|Q3KQS8	Silent	SNP	ENST00000375571.5	37	CCDS13208.1																																																																																			C|0.738;T|0.261	0.261	strong		0.612	MAPRE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078647.2	NM_012325	
HSH2D	84941	hgsc.bcm.edu	37	19	16265241	16265241	+	Silent	SNP	C	C	T	rs36088948	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:16265241C>T	ENST00000253680.6	+	7	945	c.414C>T	c.(412-414)ctC>ctT	p.L138L	HSH2D_ENST00000593154.2_Silent_p.L138L|HSH2D_ENST00000397372.4_Silent_p.L49L|HSH2D_ENST00000588246.1_Silent_p.L138L			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	138					negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						ACGAGGATCTCTTCCTCTACT	0.617													C|||	324	0.0646965	0.149	0.0476	5008	,	,		18037	0.001		0.0746	False		,,,				2504	0.0184				p.L138L		Atlas-SNP	.											.	HSH2D	16	.	0			c.C414T						PASS	.	C		497,3377		25,447,1465	26.0	29.0	28.0		414	1.7	1.0	19	dbSNP_126	28	494,7612		15,464,3574	no	coding-synonymous	HSH2D	NM_032855.2		40,911,5039	TT,TC,CC		6.0943,12.8291,8.2721		138/353	16265241	991,10989	1937	4053	5990	SO:0001819	synonymous_variant	84941	exon7			GGATCTCTTCCTC	AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"""SH2 domain containing"""	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.414C>T	19.37:g.16265241C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_032855	B5ME72|Q6ZNG7	Silent	SNP	ENST00000253680.6	37																																																																																				C|0.927;T|0.073	0.073	strong		0.617	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855	
ARL13B	200894	hgsc.bcm.edu	37	3	93714763	93714763	+	Silent	SNP	C	C	T	rs146396078	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:93714763C>T	ENST00000394222.3	+	2	380	c.105C>T	c.(103-105)acC>acT	p.T35T	ARL13B_ENST00000535334.1_Intron|ARL13B_ENST00000471138.1_Silent_p.T35T|ARL13B_ENST00000539730.1_5'UTR|ARL13B_ENST00000486562.1_3'UTR|ARL13B_ENST00000303097.7_Intron	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	35					cilium assembly (GO:0042384)|dorsal/ventral pattern formation (GO:0009953)|formation of radial glial scaffolds (GO:0021943)|heart looping (GO:0001947)|interneuron migration from the subpallium to the cortex (GO:0021830)|left/right axis specification (GO:0070986)|neural tube patterning (GO:0021532)|nonmotile primary cilium assembly (GO:0035058)|small GTPase mediated signal transduction (GO:0007264)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|intracellular (GO:0005622)|primary cilium (GO:0072372)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(2)	10						CTGGTAAAACCGCAACAGCAA	0.299													C|||	29	0.00579073	0.0	0.0187	5008	,	,		16351	0.0		0.0129	False		,,,				2504	0.0031				p.T35T		Atlas-SNP	.											.	ARL13B	52	.	0			c.C105T						PASS	.	C	,,,	6,4400	11.4+/-27.6	0,6,2197	63.0	69.0	67.0		105,,,105	-8.0	0.7	3	dbSNP_134	67	106,8494	55.6+/-116.7	2,102,4196	no	coding-synonymous,intron,intron,coding-synonymous	ARL13B	NM_001174150.1,NM_001174151.1,NM_144996.3,NM_182896.2	,,,	2,108,6393	TT,TC,CC		1.2326,0.1362,0.8611	,,,	35/429,,,35/429	93714763	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	200894	exon2			TAAAACCGCAACA	AL713789	CCDS2924.1, CCDS2925.1, CCDS54615.1	3q11	2014-05-09	2005-11-18	2005-11-18	ENSG00000169379	ENSG00000169379		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	25419	protein-coding gene	gene with protein product		608922	"""ADP-ribosylation factor-like 2-like 1"""	ARL2L1		15314642, 18674751	Standard	NR_033427		Approved	DKFZp761H079, JBTS8	uc003drf.3	Q3SXY8	OTTHUMG00000159012	ENST00000394222.3:c.105C>T	3.37:g.93714763C>T		Somatic	434	0	0		WXS	Illumina HiSeq	Phase_I	382	208	0.544503	NM_182896	D3DN29|G3V1S8|Q504W8|Q8TCL5	Silent	SNP	ENST00000394222.3	37	CCDS2925.1																																																																																			C|0.990;T|0.010	0.010	strong		0.299	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896	
EIF4E	1977	hgsc.bcm.edu	37	4	99808254	99808254	+	Silent	SNP	G	G	A	rs62323192	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:99808254G>A	ENST00000450253.2	-	5	1899	c.375C>T	c.(373-375)gaC>gaT	p.D125D	EIF4E_ENST00000280892.6_Silent_p.D145D|EIF4E_ENST00000505992.1_Silent_p.D125D|EIF4E_ENST00000504432.1_Silent_p.D153D	NM_001968.3	NP_001959.1	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	125					cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of mitotic cell cycle (GO:0045931)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|mRNA cap binding complex (GO:0005845)|RISC complex (GO:0016442)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation initiation factor activity (GO:0003743)	p.D125D(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		AGCGATCGAGGTCACTTCGTC	0.383													G|||	548	0.109425	0.0144	0.1455	5008	,	,		21025	0.001		0.2734	False		,,,				2504	0.1554				p.D145D		Atlas-SNP	.											EIF4E,NS,carcinoma,0,1	EIF4E	18	1	1	Substitution - coding silent(1)	prostate(1)	c.C435T						PASS	.	G	,,	230,4176	136.1+/-172.1	7,216,1980	239.0	207.0	218.0		435,375,375	4.1	1.0	4	dbSNP_129	218	2472,6128	406.4+/-348.8	344,1784,2172	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4E	NM_001130678.1,NM_001130679.1,NM_001968.3	,,	351,2000,4152	AA,AG,GG		28.7442,5.2202,20.775	,,	145/238,125/249,125/218	99808254	2702,10304	2203	4300	6503	SO:0001819	synonymous_variant	1977	exon5			ATCGAGGTCACTT	M15353	CCDS34031.1, CCDS47109.1, CCDS54779.1	4q21-q25	2008-02-05			ENSG00000151247	ENSG00000151247			3287	protein-coding gene	gene with protein product		133440		EIF4EL1, EIF4F		9330633, 1916814	Standard	NM_001968		Approved	EIF4E1	uc011cea.1	P06730	OTTHUMG00000161090	ENST00000450253.2:c.375C>T	4.37:g.99808254G>A		Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	196	99	0.505102	NM_001130678	B7Z6V1|D6RCQ6|Q96E95	Silent	SNP	ENST00000450253.2	37	CCDS34031.1	271	0.12408424908424909	9	0.018292682926829267	54	0.14917127071823205	1	0.0017482517482517483	207	0.27308707124010556	G	10.27	1.303728	0.23736	0.052202	0.287442	ENSG00000151247	ENST00000511644	.	.	.	5.85	4.14	0.48551	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16129	-1.0413	3	.	.	.	-16.6535	9.8967	0.41322	0.2072:0.0:0.7928:0.0	rs62323192	.	.	.	S	122	.	.	P	-	1	0	EIF4E	100027277	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.700000	0.61803	0.823000	0.34589	0.557000	0.71058	CCT	G|0.819;A|0.181	0.181	strong		0.383	EIF4E-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363739.1	NM_001968	
CELSR1	9620	hgsc.bcm.edu	37	22	46760481	46760481	+	Missense_Mutation	SNP	C	C	G	rs9615351	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46760481C>G	ENST00000262738.3	-	33	8706	c.8707G>C	c.(8707-8709)Gag>Cag	p.E2903Q		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2903			E -> Q (in dbSNP:rs9615351).		anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GGGGGGTACTCTCCACGGTGA	0.687													C|||	1203	0.240216	0.5492	0.1816	5008	,	,		16369	0.005		0.2455	False		,,,				2504	0.1012				p.E2903Q		Atlas-SNP	.											CELSR1,NS,carcinoma,0,1	CELSR1	242	1	0			c.G8707C						PASS	.	C	GLN/GLU	2305,2093	560.8+/-380.6	594,1117,488	31.0	36.0	34.0		8707	-1.8	0.0	22	dbSNP_119	34	2074,6516	337.7+/-322.4	228,1618,2449	yes	missense	CELSR1	NM_014246.1	29	822,2735,2937	GG,GC,CC		24.1444,47.5898,33.7157	possibly-damaging	2903/3015	46760481	4379,8609	2199	4295	6494	SO:0001583	missense	9620	exon33			GGTACTCTCCACG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.8707G>C	22.37:g.46760481C>G	ENSP00000262738:p.Glu2903Gln	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	118	52	0.440678	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	515	0.2358058608058608	265	0.5386178861788617	73	0.20165745856353592	1	0.0017482517482517483	176	0.23218997361477572	C	11.43	1.635840	0.29068	0.524102	0.241444	ENSG00000075275	ENST00000262738	T	0.70516	-0.49	3.64	-1.76	0.08006	.	0.482328	0.14430	U	0.320053	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	P	0.39665	0.682	B	0.38428	0.273	T	0.43065	-0.9414	9	0.21540	T	0.41	.	2.3608	0.04307	0.1521:0.5191:0.1482:0.1806	rs9615351;rs60150914	2903	Q9NYQ6	CELR1_HUMAN	Q	2903	ENSP00000262738:E2903Q	ENSP00000262738:E2903Q	E	-	1	0	CELSR1	45139145	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.527000	0.22987	-0.226000	0.09899	-0.251000	0.11542	GAG	C|0.700;G|0.300	0.300	strong		0.687	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
OR13C9	286362	hgsc.bcm.edu	37	9	107379895	107379895	+	Missense_Mutation	SNP	G	G	T	rs10761054	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:107379895G>T	ENST00000259362.1	-	1	590	c.591C>A	c.(589-591)ttC>ttA	p.F197L		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	197			F -> L (in dbSNP:rs10761054).			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						CAAGCATGAGGAACTCATTGC	0.408													G|||	1140	0.227636	0.056	0.3588	5008	,	,		24048	0.381		0.2445	False		,,,				2504	0.1912				p.F197L		Atlas-SNP	.											.	OR13C9	42	.	0			c.C591A						PASS	.	G	LEU/PHE	465,3941	222.0+/-238.9	35,395,1773	126.0	106.0	113.0		591	-1.3	1.0	9	dbSNP_120	113	1977,6623	347.4+/-326.6	234,1509,2557	yes	missense	OR13C9	NM_001001956.1	22	269,1904,4330	TT,TG,GG		22.9884,10.5538,18.7759	possibly-damaging	197/319	107379895	2442,10564	2203	4300	6503	SO:0001583	missense	286362	exon1			CATGAGGAACTCA		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.591C>A	9.37:g.107379895G>T	ENSP00000259362:p.Phe197Leu	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	242	115	0.475207	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	575	0.2632783882783883	29	0.05894308943089431	125	0.3453038674033149	220	0.38461538461538464	201	0.26517150395778366	G	4.350	0.064455	0.08388	0.105538	0.229884	ENSG00000136839	ENST00000259362	T	0.00027	8.93	4.51	-1.27	0.09347	GPCR, rhodopsin-like superfamily (1);	0.378699	0.20801	N	0.085431	T	0.00012	0.0000	N	0.00099	-2.14	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.04216	-1.0968	9	0.10636	T	0.68	.	9.204	0.37278	0.6672:0.0:0.3328:0.0	rs10761054;rs10761054	197	Q8NGT0	O13C9_HUMAN	L	197	ENSP00000259362:F197L	ENSP00000259362:F197L	F	-	3	2	OR13C9	106419716	0.000000	0.05858	0.988000	0.46212	0.934000	0.57294	-2.947000	0.00680	-0.145000	0.11294	-0.148000	0.13756	TTC	G|0.786;T|0.214	0.214	strong		0.408	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
OR4N4	283694	hgsc.bcm.edu	37	15	22382704	22382704	+	Missense_Mutation	SNP	G	G	C	rs62006708	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:22382704G>C	ENST00000328795.4	+	1	323	c.232G>C	c.(232-234)Gct>Cct	p.A78P	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	78						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)		CTTCATTGTGGCTCCCAGGAT	0.498																																					p.A78P		Atlas-SNP	.											.	OR4N4	108	.	0			c.G232C						PASS	.	G	PRO/ALA	155,4251		0,155,2048	152.0	143.0	146.0		232	2.3	1.0	15	dbSNP_129	146	1405,7195		2,1401,2897	no	missense	OR4N4	NM_001005241.2	27	2,1556,4945	CC,CG,GG		16.3372,3.5179,11.9945	benign	78/317	22382704	1560,11446	2203	4300	6503	SO:0001583	missense	283694	exon1			ATTGTGGCTCCCA	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.232G>C	15.37:g.22382704G>C	ENSP00000332500:p.Ala78Pro	Somatic	509	0	0		WXS	Illumina HiSeq	Phase_I	369	35	0.0948509	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	352	0.16117216117216118	11	0.022357723577235773	45	0.12430939226519337	99	0.17307692307692307	197	0.2598944591029024	.	3.587	-0.084346	0.07097	0.035179	0.163372	ENSG00000183706	ENST00000328795	T	0.03094	4.05	3.2	2.26	0.28386	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000207	T	0.00012	0.0000	M	0.91406	3.205	0.36963	P	0.10656600000000005	B	0.12013	0.005	B	0.17433	0.018	T	0.11717	-1.0576	9	0.87932	D	0	-4.2544	8.183	0.31322	0.1273:0.0:0.8727:0.0	rs62006708	78	Q8N0Y3	OR4N4_HUMAN	P	78	ENSP00000332500:A78P	ENSP00000332500:A78P	A	+	1	0	OR4N4	19884068	0.000000	0.05858	1.000000	0.80357	0.027000	0.11550	-0.789000	0.04609	0.671000	0.31185	0.184000	0.17185	GCT	G|0.843;C|0.157	0.157	strong		0.498	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
USP31	57478	hgsc.bcm.edu	37	16	23098422	23098422	+	Missense_Mutation	SNP	A	A	G	rs13339649	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:23098422A>G	ENST00000219689.7	-	9	1612	c.1613T>C	c.(1612-1614)aTa>aCa	p.I538T		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	DUSP 1. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CCTTTCTACTATTGGGTGGCA	0.373													G|||	1212	0.242013	0.1528	0.3876	5008	,	,		17229	0.1577		0.333	False		,,,				2504	0.2526				p.I538T		Atlas-SNP	.											.	USP31	122	.	0			c.T1613C						PASS	.	G	THR/ILE	784,3610	739.3+/-411.1	61,662,1474	43.0	41.0	41.0		1613	5.2	0.3	16	dbSNP_121	41	2719,5881	672.8+/-403.0	451,1817,2032	yes	missense	USP31	NM_020718.3	89	512,2479,3506	GG,GA,AA		31.6163,17.8425,26.9586	benign	538/1353	23098422	3503,9491	2197	4300	6497	SO:0001583	missense	57478	exon9			TCTACTATTGGGT	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.1613T>C	16.37:g.23098422A>G	ENSP00000219689:p.Ile538Thr	Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	185	185	1	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	553	0.2532051282051282	79	0.16056910569105692	122	0.3370165745856354	101	0.17657342657342656	251	0.3311345646437995	G	0.103	-1.149700	0.01714	0.178425	0.316163	ENSG00000103404	ENST00000219689	T	0.05855	3.38	5.16	5.16	0.70880	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.216830	0.38605	N	0.001629	T	0.00012	0.0000	N	0.01824	-0.7	0.09310	P	0.9999999999999974	B	0.02656	0.0	B	0.01281	0.0	T	0.44097	-0.9350	9	0.06099	T	0.92	-1.3192	13.0274	0.58823	0.0773:0.0:0.9227:0.0	rs13339649;rs17796752;rs52819210;rs57007803;rs13339649	538	Q70CQ4	UBP31_HUMAN	T	538	ENSP00000219689:I538T	ENSP00000219689:I538T	I	-	2	0	USP31	23005923	1.000000	0.71417	0.349000	0.25694	0.180000	0.23129	6.345000	0.72995	1.194000	0.43101	-0.349000	0.07799	ATA	A|0.742;G|0.258	0.258	strong		0.373	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
FGD6	55785	hgsc.bcm.edu	37	12	95604290	95604290	+	Missense_Mutation	SNP	T	T	C	rs10507047	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:95604290T>C	ENST00000343958.4	-	2	993	c.770A>G	c.(769-771)cAg>cGg	p.Q257R	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Missense_Mutation_p.Q257R|FGD6_ENST00000546711.1_Missense_Mutation_p.Q257R	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	257			Q -> R (in dbSNP:rs10507047).		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)|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)	p.Q257R(1)		breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						ACTGTCATCCTGGCAAGTTTC	0.393													T|||	644	0.128594	0.0983	0.1571	5008	,	,		20012	0.2331		0.0775	False		,,,				2504	0.0941				p.Q257R		Atlas-SNP	.											FGD6,NS,carcinoma,0,2	FGD6	127	2	1	Substitution - Missense(1)	prostate(1)	c.A770G						PASS	.	T	ARG/GLN	422,3984	204.8+/-226.9	19,384,1800	73.0	73.0	73.0		770	4.8	0.2	12	dbSNP_119	73	836,7764	190.4+/-236.9	45,746,3509	yes	missense	FGD6	NM_018351.3	43	64,1130,5309	CC,CT,TT		9.7209,9.5778,9.6725	possibly-damaging	257/1431	95604290	1258,11748	2203	4300	6503	SO:0001583	missense	55785	exon2			TCATCCTGGCAAG	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.770A>G	12.37:g.95604290T>C	ENSP00000344446:p.Gln257Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	56	13	0.232143	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	307	0.14056776556776557	51	0.10365853658536585	58	0.16022099447513813	139	0.243006993006993	59	0.07783641160949868	T	5.000	0.185724	0.09495	0.095778	0.097209	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.71222	-0.45;-0.55;-0.5	5.99	4.85	0.62838	.	0.000000	0.46442	D	0.000293	T	0.00039	0.0001	M	0.62723	1.935	0.80722	P	0.0	P	0.35077	0.483	B	0.27887	0.084	T	0.07888	-1.0749	9	0.49607	T	0.09	-6.0663	7.7203	0.28729	0.0:0.0732:0.1495:0.7773	rs10507047;rs52818706;rs61586134;rs10507047	257	Q6ZV73	FGD6_HUMAN	R	257	ENSP00000344446:Q257R;ENSP00000450342:Q257R;ENSP00000449005:Q257R	ENSP00000344446:Q257R	Q	-	2	0	FGD6	94128421	0.311000	0.24536	0.174000	0.22961	0.090000	0.18270	1.955000	0.40372	1.093000	0.41377	0.533000	0.62120	CAG	T|0.842;C|0.158	0.158	strong		0.393	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
SLC22A16	85413	hgsc.bcm.edu	37	6	110760008	110760008	+	Missense_Mutation	SNP	A	A	G	rs12210538	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:110760008A>G	ENST00000368919.3	-	5	1292	c.1226T>C	c.(1225-1227)aTg>aCg	p.M409T	RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000439654.1_Missense_Mutation_p.M409T|SLC22A16_ENST00000330550.4_Missense_Mutation_p.M375T	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	409			M -> T (in dbSNP:rs12210538). {ECO:0000269|PubMed:12372408, ECO:0000269|PubMed:12384147, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15963465}.		acid secretion (GO:0046717)|amine transport (GO:0015837)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|organic cation transport (GO:0015695)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amine transmembrane transporter activity (GO:0005275)|carnitine transmembrane transporter activity (GO:0015226)|organic cation transmembrane transporter activity (GO:0015101)			breast(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	34		all_cancers(87;0.00221)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.0485)|Colorectal(196;0.101)		OV - Ovarian serous cystadenocarcinoma(136;0.0513)|Epithelial(106;0.0921)|all cancers(137;0.115)	Doxorubicin(DB00997)|L-Carnitine(DB00583)	GACCTTGTCCATGGCGATGCA	0.542													A|||	458	0.0914537	0.0121	0.1527	5008	,	,		14934	0.0		0.2445	False		,,,				2504	0.092				p.M409T		Atlas-SNP	.											.	SLC22A16	81	.	0			c.T1226C						PASS	.	A	THR/MET	225,4181	133.7+/-170.0	4,217,1982	152.0	115.0	128.0		1226	5.0	0.0	6	dbSNP_120	128	2091,6509	360.9+/-332.1	287,1517,2496	yes	missense	SLC22A16	NM_033125.2	81	291,1734,4478	GG,GA,AA		24.314,5.1067,17.8072	possibly-damaging	409/578	110760008	2316,10690	2203	4300	6503	SO:0001583	missense	85413	exon5			TTGTCCATGGCGA		CCDS5084.1	6q21	2013-05-22	2008-01-11		ENSG00000004809	ENSG00000004809		"""Solute carriers"""	20302	protein-coding gene	gene with protein product		608276	"""solute carrier family 22 (organic cation transporter), member 16"""			12372408, 12089149, 17473959	Standard	NM_033125		Approved	FLIPT2, CT2, OKB1, OAT6	uc003puf.3	Q86VW1	OTTHUMG00000016171	ENST00000368919.3:c.1226T>C	6.37:g.110760008A>G	ENSP00000357915:p.Met409Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	247	0.1130952380952381	9	0.018292682926829267	49	0.13535911602209943	0	0.0	189	0.24934036939313983	A	18.24	3.580325	0.65992	0.051067	0.24314	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949	T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81	4.98	4.98	0.66077	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.086812	0.85682	D	0.000000	T	0.76856	0.4046	M	0.70595	2.14	0.09310	P	1.0	D;P	0.53312	0.959;0.949	P;P	0.55749	0.783;0.743	T	0.80448	-0.1378	9	0.52906	T	0.07	.	14.6674	0.68918	1.0:0.0:0.0:0.0	rs12210538;rs17494155;rs12210538	409;375	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	T	409;326;375;409;239	ENSP00000357915:M409T;ENSP00000395642:M326T;ENSP00000328583:M375T;ENSP00000408799:M409T;ENSP00000409306:M239T	ENSP00000328583:M375T	M	-	2	0	SLC22A16	110866701	1.000000	0.71417	0.005000	0.12908	0.006000	0.05464	6.101000	0.71479	1.877000	0.54381	0.519000	0.50382	ATG	A|0.851;G|0.149	0.149	strong		0.542	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125	
FLG	2312	hgsc.bcm.edu	37	1	152276282	152276282	+	Missense_Mutation	SNP	C	C	G	rs55707024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152276282C>G	ENST00000368799.1	-	3	11115	c.11080G>C	c.(11080-11082)Gag>Cag	p.E3694Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3694	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.E3694Q(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGTGTGGACTCTTGGTGGCTC	0.587									Ichthyosis				C|||	911	0.181909	0.0772	0.232	5008	,	,		20697	0.3452		0.1004	False		,,,				2504	0.2035				p.E3694Q		Atlas-SNP	.											FLG,extremity,malignant_melanoma,0,1	FLG	900	1	1	Substitution - Missense(1)	skin(1)	c.G11080C						scavenged	.						50.0	56.0	54.0					1																	152276282		2202	4278	6480	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGACTCTTGGTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11080G>C	1.37:g.152276282C>G	ENSP00000357789:p.Glu3694Gln	Somatic	369	3	0.00813008		WXS	Illumina HiSeq	Phase_I	492	51	0.103659	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	8.701	0.909632	0.17833	.	.	ENSG00000143631	ENST00000368799	T	0.01787	4.64	2.52	-3.46	0.04767	.	.	.	.	.	T	0.01454	0.0047	M	0.75447	2.3	0.09310	N	1	D	0.65815	0.995	P	0.61070	0.883	T	0.34254	-0.9836	9	0.20519	T	0.43	.	0.3502	0.00348	0.1921:0.291:0.2301:0.2868	rs55707024;rs58436539	3694	P20930	FILA_HUMAN	Q	3694	ENSP00000357789:E3694Q	ENSP00000357789:E3694Q	E	-	1	0	FLG	150542906	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.189000	0.03061	-0.738000	0.04817	0.552000	0.68991	GAG	C|0.500;G|0.500	0.500	weak		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
OR2C1	4993	hgsc.bcm.edu	37	16	3406516	3406516	+	Silent	SNP	A	A	G	rs11643487	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3406516A>G	ENST00000304936.2	+	1	628	c.576A>G	c.(574-576)acA>acG	p.T192T		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	192					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						GTGGCGACACAAGTCTCAACC	0.557													G|||	1587	0.316893	0.4357	0.2882	5008	,	,		20982	0.1736		0.336	False		,,,				2504	0.3047				p.T192T		Atlas-SNP	.											.	OR2C1	38	.	0			c.A576G						PASS	.			1886,2508	629.1+/-395.2	395,1096,706	126.0	102.0	110.0		576	-9.7	0.0	16	dbSNP_120	110	2915,5685	670.0+/-402.7	485,1945,1870	no	coding-synonymous	OR2C1	NM_012368.2		880,3041,2576	GG,GA,AA		33.8953,42.9222,36.9478		192/313	3406516	4801,8193	2197	4300	6497	SO:0001819	synonymous_variant	4993	exon1			CGACACAAGTCTC	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.576A>G	16.37:g.3406516A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	105	0.981308	NM_012368	A0AVA4|Q6IF34|Q6IF55	Silent	SNP	ENST00000304936.2	37	CCDS10502.1																																																																																			A|0.659;G|0.341	0.341	strong		0.557	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3		
JRK	8629	hgsc.bcm.edu	37	8	143746701	143746701	+	RNA	SNP	A	A	G	rs3802232	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:143746701A>G	ENST00000507178.2	-	0	1109							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					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)	Acute lymphoblastic leukemia(644;2.31e-05)				ccacccaggcattcccctggg	0.567													G|||	2639	0.526957	0.7179	0.3213	5008	,	,		18708	0.5188		0.3907	False		,,,				2504	0.5634				p.N259N		Atlas-SNP	.											.	.	.	.	0			c.T777C						PASS	.	G	,	1645,1183		507,631,276	14.0	17.0	16.0		777,777	-1.2	0.0	8	dbSNP_107	16	2041,3571		395,1251,1160	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	902,1882,1436	GG,GA,AA		36.3685,41.8317,43.673	,	259/557,259/569	143746701	3686,4754	1414	2806	4220			8629	exon2			CCAGGCATTCCCC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746701A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	107	39	0.364486	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				A|0.479;G|0.521	0.521	strong		0.567	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
PATE1	160065	hgsc.bcm.edu	37	11	125617610	125617610	+	Missense_Mutation	SNP	A	A	G	rs2114084	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125617610A>G	ENST00000305738.5	+	4	152	c.140A>G	c.(139-141)cAg>cGg	p.Q47R	PATE1_ENST00000437148.2_Missense_Mutation_p.Q35R	NM_138294.2	NP_612151.1	Q8WXA2	PATE1_HUMAN	prostate and testis expressed 1	47			Q -> R (in dbSNP:rs2114084). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				large_intestine(1)|lung(5)	6						GAAATTGTTCAGTGTAGGATG	0.493													A|||	1690	0.33746	0.3797	0.2219	5008	,	,		20322	0.4375		0.2893	False		,,,				2504	0.3088				p.Q47R		Atlas-SNP	.											.	PATE1	21	.	0			c.A140G						PASS	.	A	ARG/GLN	1661,2741	505.2+/-366.1	329,1003,869	90.0	86.0	87.0		140	4.2	0.7	11	dbSNP_96	87	2480,6118	407.8+/-349.3	358,1764,2177	yes	missense	PATE1	NM_138294.2	43	687,2767,3046	GG,GA,AA		28.8439,37.7328,31.8538	possibly-damaging	47/127	125617610	4141,8859	2201	4299	6500	SO:0001583	missense	160065	exon4			TTGTTCAGTGTAG	AF462605	CCDS8464.1	11q24.2	2008-12-17				ENSG00000171053		"""PATE family"""	24664	protein-coding gene	gene with protein product	"""expressed in prostate and testis"""	606861				11880645, 15798027	Standard	NM_138294		Approved	PATE	uc001qct.3	Q8WXA2		ENST00000305738.5:c.140A>G	11.37:g.125617610A>G	ENSP00000307164:p.Gln47Arg	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	73	46	0.630137	NM_138294	Q3KNX2	Missense_Mutation	SNP	ENST00000305738.5	37	CCDS8464.1	724	0.3315018315018315	191	0.3882113821138211	96	0.26519337016574585	221	0.38636363636363635	216	0.2849604221635884	A	9.678	1.148572	0.21288	0.377328	0.288439	ENSG00000171053	ENST00000305738;ENST00000437148	T;T	0.34275	1.37;1.37	4.19	4.19	0.49359	.	0.229282	0.22480	N	0.059503	T	0.00012	0.0000	L	0.40543	1.245	0.38885	P	0.04301100000000002	D;D	0.71674	0.992;0.998	P;D	0.64776	0.876;0.929	T	0.44174	-0.9345	9	0.32370	T	0.25	0.6542	9.9222	0.41470	1.0:0.0:0.0:0.0	rs2114084;rs57813227;rs2114084	35;47	Q8WXA2-2;Q8WXA2	.;PATE1_HUMAN	R	47;35	ENSP00000307164:Q47R;ENSP00000396056:Q35R	ENSP00000307164:Q47R	Q	+	2	0	PATE1	125122820	0.341000	0.24801	0.664000	0.29753	0.188000	0.23474	1.778000	0.38614	2.115000	0.64714	0.533000	0.62120	CAG	A|0.675;G|0.325	0.325	strong		0.493	PATE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386726.2	NM_138294	
ST3GAL4	6484	hgsc.bcm.edu	37	11	126278203	126278203	+	Splice_Site	SNP	T	T	C	rs2298475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:126278203T>C	ENST00000526727.1	+	7	813	c.439T>C	c.(439-441)Ttg>Ctg	p.L147L	ST3GAL4_ENST00000227495.6_Splice_Site_p.L143L|ST3GAL4_ENST00000356132.4_Splice_Site_p.L153L|ST3GAL4_ENST00000532243.1_Splice_Site_p.L146L|ST3GAL4_ENST00000534457.1_Splice_Site_p.L142L|ST3GAL4_ENST00000392669.2_Splice_Site_p.L147L|ST3GAL4_ENST00000534083.1_Splice_Site_p.L147L|ST3GAL4_ENST00000444328.2_Splice_Site_p.L147L|ST3GAL4_ENST00000530591.1_Splice_Site_p.L143L|ST3GAL4_ENST00000449406.2_Splice_Site_p.L136L|ST3GAL4_ENST00000526756.1_3'UTR			Q11206	SIA4C_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 4	147					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cognition (GO:0050890)|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)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)|monosialoganglioside sialyltransferase activity (GO:0047288)	p.L143L(1)		endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9	all_hematologic(175;0.145)	Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0739)|all_lung(97;0.0798)|all_neural(223;0.138)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0767)		AACCCCCAGATTGAACAATGC	0.562													T|||	430	0.0858626	0.0129	0.0706	5008	,	,		18899	0.2222		0.0815	False		,,,				2504	0.0593				p.L147L		Atlas-SNP	.											ST3GAL4,NS,carcinoma,0,1	ST3GAL4	25	1	1	Substitution - coding silent(1)	stomach(1)	c.T439C						PASS	.	T		98,4304	78.3+/-116.7	1,96,2104	130.0	113.0	118.0		427	-5.7	0.3	11	dbSNP_100	118	655,7941	165.7+/-217.8	21,613,3664	yes	coding-synonymous-near-splice	ST3GAL4	NM_006278.1		22,709,5768	CC,CT,TT		7.6198,2.2263,5.7932		143/330	126278203	753,12245	2201	4298	6499	SO:0001630	splice_region_variant	6484	exon8			CCCAGATTGAACA	X74570	CCDS8474.1, CCDS58193.1, CCDS58194.1	11q23-q24	2013-03-01	2003-01-14	2005-02-07	ENSG00000110080	ENSG00000110080	2.4.99.4	"""Sialyltransferases"""	10864	protein-coding gene	gene with protein product	"""ST3Gal IV"""	104240	"""sialyltransferase 4C (beta-galactosidase alpha-2,3-sialytransferase)"""	CGS23, SIAT4, NANTA3, SIAT4C		8557707, 8288606	Standard	NM_006278		Approved	STZ, SAT3, FLJ11867	uc001qds.3	Q11206	OTTHUMG00000165830	ENST00000526727.1:c.438-1T>C	11.37:g.126278203T>C		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	269	189	0.702602	NM_001254757	A8K6B2|O60497|Q8N6A6|Q8NFG7|Q96QQ9	Silent	SNP	ENST00000526727.1	37	CCDS58193.1																																																																																			T|0.925;C|0.075	0.075	strong		0.562	ST3GAL4-003	PUTATIVE	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386470.1	NM_006278	Silent
AGPAT4	56895	hgsc.bcm.edu	37	6	161567601	161567601	+	Silent	SNP	G	G	A	rs16892215	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:161567601G>A	ENST00000320285.4	-	7	1010	c.798C>T	c.(796-798)gaC>gaT	p.D266D	AGPAT4_ENST00000457520.2_Silent_p.D104D|AGPAT4_ENST00000366911.5_3'UTR|AGPAT4_ENST00000366908.5_3'UTR	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	266					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)		ACTCGTCATCGTCTTCAGGGA	0.592													G|||	117	0.0233626	0.0802	0.0072	5008	,	,		18454	0.006		0.0	False		,,,				2504	0.0				p.D266D		Atlas-SNP	.											.	AGPAT4	50	.	0			c.C798T						PASS	.	G		263,4143	150.3+/-184.3	10,243,1950	126.0	102.0	110.0		798	-9.9	0.0	6	dbSNP_123	110	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	AGPAT4	NM_020133.2		10,245,6248	AA,AG,GG		0.0233,5.9691,2.0375		266/379	161567601	265,12741	2203	4300	6503	SO:0001819	synonymous_variant	56895	exon7			GTCATCGTCTTCA	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.798C>T	6.37:g.161567601G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_020133	B4DSF9|Q5TEF0	Silent	SNP	ENST00000320285.4	37	CCDS5280.1	47	0.02152014652014652	37	0.07520325203252033	4	0.011049723756906077	6	0.01048951048951049	0	0.0	G	0.145	-1.097373	0.01843	0.059691	2.33E-4	ENSG00000026652	ENST00000437165	.	.	.	4.95	-9.9	0.00461	.	.	.	.	.	T	0.43366	0.1244	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68112	-0.5495	4	.	.	.	-42.6356	14.5465	0.68035	0.7342:0.1664:0.0994:0.0	rs16892215;rs16892215	.	.	.	M	45	.	.	T	-	2	0	AGPAT4	161487591	0.004000	0.15560	0.014000	0.15608	0.025000	0.11179	-1.069000	0.03444	-3.051000	0.00260	-0.997000	0.02515	ACG	G|0.975;A|0.025	0.025	strong		0.592	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133	
HYOU1	10525	hgsc.bcm.edu	37	11	118925341	118925341	+	Silent	SNP	G	G	A	rs538478	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118925341G>A	ENST00000404233.3	-	7	667	c.543C>T	c.(541-543)aaC>aaT	p.N181N	HYOU1_ENST00000525859.1_Silent_p.N181N|HYOU1_ENST00000543287.1_Silent_p.N94N|HYOU1_ENST00000529972.1_Silent_p.N181N	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	181					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)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		GCTCGGCCTGGTTGAAGAAGA	0.577													G|||	2165	0.432308	0.1868	0.2954	5008	,	,		18893	0.7192		0.4821	False		,,,				2504	0.5143				p.N181N		Atlas-SNP	.											HYOU1,NS,carcinoma,-1,1	HYOU1	88	1	0			c.C543T						PASS	.	G	,	1028,3372	377.1+/-322.3	137,754,1309	69.0	63.0	65.0		543,543	2.3	1.0	11	dbSNP_83	65	3815,4775	538.2+/-383.4	857,2101,1337	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	994,2855,2646	AA,AG,GG		44.4121,23.3636,37.2825	,	181/1000,181/1000	118925341	4843,8147	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon7			GGCCTGGTTGAAG	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.543C>T	11.37:g.118925341G>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	37	CCDS8408.1																																																																																			G|0.585;A|0.415	0.415	strong		0.577	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
CACNA1C	775	hgsc.bcm.edu	37	12	2794921	2794921	+	Missense_Mutation	SNP	G	G	A	rs200231105	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:2794921G>A	ENST00000347598.4	+	46	5737	c.5737G>A	c.(5737-5739)Gaa>Aaa	p.E1913K	CACNA1C_ENST00000399597.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399637.1_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399606.1_Missense_Mutation_p.E1885K|CACNA1C_ENST00000344100.3_Missense_Mutation_p.E1906K|CACNA1C_ENST00000399617.1_Missense_Mutation_p.E1900K|CACNA1C_ENST00000399634.1_Missense_Mutation_p.E1936K|CACNA1C_ENST00000399641.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399644.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399629.1_Missense_Mutation_p.E1882K|CACNA1C_ENST00000399621.1_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399591.1_Missense_Mutation_p.E1873K|CACNA1C_ENST00000399601.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000406454.3_Missense_Mutation_p.E1936K|CACNA1C_ENST00000399638.1_Missense_Mutation_p.E1893K|CACNA1C_ENST00000327702.7_Missense_Mutation_p.E1900K|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000335762.5_Missense_Mutation_p.E1890K|CACNA1C_ENST00000402845.3_Missense_Mutation_p.E1884K|CACNA1C_ENST00000399603.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399649.1_Missense_Mutation_p.E1871K|CACNA1C_ENST00000399655.1_Missense_Mutation_p.E1865K|CACNA1C_ENST00000399595.1_Missense_Mutation_p.E1873K	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1948					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)	p.E1913K(2)|p.E1906K(2)|p.E1978K(2)|p.E1900K(2)|p.E1400K(2)		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)	CCAGGATGACGAAAATCGGCA	0.592																																					p.E1948K		Atlas-SNP	.											Q6YL47_HUMAN,NS,carcinoma,0,8	CACNA1C	1023	8	10	Substitution - Missense(10)	kidney(5)|endometrium(5)	c.G5842A						scavenged	.						47.0	48.0	48.0					12																	2794921		2013	4164	6177	SO:0001583	missense	775	exon47			GATGACGAAAATC	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.5737G>A	12.37:g.2794921G>A	ENSP00000266376:p.Glu1913Lys	Somatic	136	7	0.0514706		WXS	Illumina HiSeq	Phase_I	117	9	0.0769231	NM_199460	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	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.988512	0.53934	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39;0.39	4.26	3.35	0.38373	.	1.675690	0.03914	N	0.282339	T	0.64427	0.2597	L	0.39633	1.23	0.24214	N	0.99546	P;D;P;B;D;P;P;D;B;B;D;P;P;B;P;B;P;B;D;P;P;D;D;P;P	0.76494	0.801;0.999;0.941;0.097;0.999;0.921;0.953;0.961;0.11;0.33;0.978;0.941;0.757;0.432;0.902;0.306;0.757;0.062;0.978;0.588;0.769;0.961;0.961;0.882;0.941	B;P;B;B;D;B;B;P;B;B;P;B;B;B;B;B;B;B;P;B;B;P;P;B;B	0.78314	0.21;0.858;0.304;0.03;0.991;0.308;0.378;0.485;0.04;0.071;0.485;0.304;0.122;0.099;0.114;0.033;0.122;0.024;0.485;0.172;0.172;0.485;0.485;0.172;0.304	T	0.56056	-0.8042	10	0.07030	T	0.85	.	14.0749	0.64885	0.0:0.1521:0.8479:0.0	.	556;1906;1862;1948;1900;1884;1865;1882;1893;1865;1885;1865;1896;1913;1865;1900;1936;1873;1871;1873;1854;1884;1884;1865;1865	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	K	1890;1865;1865;1893;1865;1884;1884;1873;1865;1913;1885;1865;1906;1882;1900;1871;1884;1865;1936;1900;1936;1873;1766	ENSP00000336982:E1890K;ENSP00000382563:E1865K;ENSP00000382552:E1865K;ENSP00000382547:E1893K;ENSP00000382506:E1865K;ENSP00000382530:E1884K;ENSP00000382546:E1884K;ENSP00000382500:E1873K;ENSP00000382549:E1865K;ENSP00000266376:E1913K;ENSP00000382515:E1885K;ENSP00000382510:E1865K;ENSP00000341092:E1906K;ENSP00000382537:E1882K;ENSP00000329877:E1900K;ENSP00000382557:E1871K;ENSP00000385724:E1884K;ENSP00000382512:E1865K;ENSP00000382542:E1936K;ENSP00000382526:E1900K;ENSP00000385896:E1936K;ENSP00000382504:E1873K	ENSP00000323129:E1766K	E	+	1	0	CACNA1C	2665182	1.000000	0.71417	0.943000	0.38184	0.802000	0.45316	5.486000	0.66856	0.981000	0.38548	0.449000	0.29647	GAA	G|0.500;A|0.500	0.500	weak		0.592	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125856695	125856695	+	Silent	SNP	C	C	A	rs2305230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:125856695C>A	ENST00000393434.2	-	10	1534	c.1185G>T	c.(1183-1185)ctG>ctT	p.L395L	ALDH1L1_ENST00000273450.3_Silent_p.L405L|ALDH1L1_ENST00000472186.1_Silent_p.L395L|ALDH1L1_ENST00000393431.2_Silent_p.L395L|ALDH1L1_ENST00000452905.2_Silent_p.L294L	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	395					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)	CGTCCCCTCGCAGCTTCCTCA	0.562													C|||	1226	0.244808	0.4418	0.1945	5008	,	,		20912	0.2321		0.166	False		,,,				2504	0.1084				p.L405L		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.G1215T						PASS	.	C		1705,2701	514.7+/-368.7	331,1043,829	138.0	101.0	113.0		1185	-2.7	0.2	3	dbSNP_100	113	1424,7176	273.3+/-290.6	126,1172,3002	no	coding-synonymous	ALDH1L1	NM_012190.2		457,2215,3831	AA,AC,CC		16.5581,38.6972,24.0581		395/903	125856695	3129,9877	2203	4300	6503	SO:0001819	synonymous_variant	10840	exon10			CCCTCGCAGCTTC	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.1185G>T	3.37:g.125856695C>A		Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	254	252	0.992126	NM_001270364	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	37	CCDS3034.1																																																																																			C|0.767;A|0.233	0.233	strong		0.562	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
ZNF497	162968	hgsc.bcm.edu	37	19	58868480	58868480	+	Missense_Mutation	SNP	G	G	T	rs12609654	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:58868480G>T	ENST00000311044.3	-	3	710	c.522C>A	c.(520-522)caC>caA	p.H174Q	A1BG-AS1_ENST00000593374.1_RNA|A1BG-AS1_ENST00000600686.1_RNA|ZNF497_ENST00000425453.3_Missense_Mutation_p.H174Q|A1BG-AS1_ENST00000594950.1_RNA|A1BG-AS1_ENST00000600379.1_RNA|A1BG-AS1_ENST00000593960.1_RNA|CTD-2619J13.9_ENST00000599952.1_RNA|A1BG-AS1_ENST00000595302.1_RNA|CTD-2619J13.8_ENST00000599109.1_RNA	NM_198458.2	NP_940860.2	Q6ZNH5	ZN497_HUMAN	zinc finger protein 497	174			H -> Q (in dbSNP:rs12609654). {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(2)|lung(3)|skin(2)	7		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|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;0.168)|GBM - Glioblastoma multiforme(193;0.0278)		TGAGCTGCGAGTGCGCGCGGA	0.677													G|||	1917	0.382788	0.4856	0.3746	5008	,	,		15859	0.1825		0.4006	False		,,,				2504	0.4376				p.H174Q		Atlas-SNP	.											.	ZNF497	22	.	0			c.C522A						PASS	.	G	GLN/HIS,GLN/HIS	2210,2196	561.4+/-380.7	560,1090,553	31.0	25.0	27.0		522,522	-0.6	0.0	19	dbSNP_120	27	3902,4696	524.8+/-380.6	869,2164,1266	yes	missense,missense	ZNF497	NM_001207009.1,NM_198458.2	24,24	1429,3254,1819	TT,TG,GG		45.3826,49.8411,47.0009	benign,benign	174/499,174/499	58868480	6112,6892	2203	4299	6502	SO:0001583	missense	162968	exon2			CTGCGAGTGCGCG	AK126727	CCDS12977.1	19q13.43	2013-01-08			ENSG00000174586	ENSG00000174586		"""Zinc fingers, C2H2-type"""	23714	protein-coding gene	gene with protein product							Standard	NM_198458		Approved	FLJ44773	uc002qsi.2	Q6ZNH5		ENST00000311044.3:c.522C>A	19.37:g.58868480G>T	ENSP00000311183:p.His174Gln	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	186	96	0.516129	NM_001207009	Q05AG8|Q0VF48|Q6ZTD2|Q9UIA8	Missense_Mutation	SNP	ENST00000311044.3	37	CCDS12977.1	802	0.36721611721611724	236	0.4796747967479675	157	0.43370165745856354	108	0.1888111888111888	301	0.3970976253298153	G	13.05	2.120431	0.37436	0.501589	0.453826	ENSG00000174586	ENST00000311044;ENST00000425453;ENST00000391697	T;T	0.35605	1.3;1.3	0.62	-0.577	0.11727	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	P	0.35107	0.484	B	0.22880	0.042	T	0.46911	-0.9157	8	0.44086	T	0.13	.	5.7584	0.18186	0.2752:0.0:0.7248:0.0	rs12609654;rs58652230;rs12609654	174	Q6ZNH5	ZN497_HUMAN	Q	174;174;19	ENSP00000311183:H174Q;ENSP00000402815:H174Q	ENSP00000311183:H174Q	H	-	3	2	ZNF497	63560292	0.000000	0.05858	0.004000	0.12327	0.420000	0.31355	-1.525000	0.02231	-0.298000	0.08921	0.205000	0.17691	CAC	G|0.561;T|0.439	0.439	strong		0.677	ZNF497-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466942.2	NM_198458	
KIAA1958	158405	hgsc.bcm.edu	37	9	115421788	115421788	+	Silent	SNP	C	C	A	rs16917185	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:115421788C>A	ENST00000337530.6	+	4	1886	c.1590C>A	c.(1588-1590)atC>atA	p.I530I	KIAA1958_ENST00000536272.1_Silent_p.I558I	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	530										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						CTCGCAACATCGTCTACTTCT	0.567													C|||	533	0.10643	0.1997	0.0274	5008	,	,		20775	0.0972		0.0338	False		,,,				2504	0.1207				p.I530I		Atlas-SNP	.											.	KIAA1958	52	.	0			c.C1590A						PASS	.	C		778,3628	312.5+/-292.6	69,640,1494	62.0	53.0	56.0		1590	-0.9	1.0	9	dbSNP_123	56	229,8371	93.5+/-155.5	3,223,4074	no	coding-synonymous	KIAA1958	NM_133465.2		72,863,5568	AA,AC,CC		2.6628,17.6577,7.7426		530/717	115421788	1007,11999	2203	4300	6503	SO:0001819	synonymous_variant	158405	exon4			CAACATCGTCTAC	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.1590C>A	9.37:g.115421788C>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	151	60	0.397351	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Silent	SNP	ENST00000337530.6	37	CCDS35108.1																																																																																			C|0.916;A|0.084	0.084	strong		0.567	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465	
C22orf42	150297	hgsc.bcm.edu	37	22	32554997	32554997	+	Missense_Mutation	SNP	G	G	A	rs78036098	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:32554997G>A	ENST00000382097.3	-	1	278	c.206C>T	c.(205-207)aCg>aTg	p.T69M	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	69										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						CATCTTCGGCGTCTTCGGGAG	0.562													.|||	25	0.00499201	0.0	0.0072	5008	,	,		17976	0.001		0.0169	False		,,,				2504	0.002				p.T69M		Atlas-SNP	.											C22orf42,NS,carcinoma,-1,1	C22orf42	37	1	0			c.C206T						scavenged	.	G	MET/THR	9,4397	15.5+/-35.6	0,9,2194	177.0	173.0	174.0		206		0.0	22	dbSNP_132	174	168,8432	77.2+/-139.8	0,168,4132	yes	missense	C22orf42	NM_001010859.1	81	0,177,6326	AA,AG,GG		1.9535,0.2043,1.3609	probably-damaging	69/252	32554997	177,12829	2203	4300	6503	SO:0001583	missense	150297	exon1			TTCGGCGTCTTCG	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.206C>T	22.37:g.32554997G>A	ENSP00000371529:p.Thr69Met	Somatic	290	2	0.00689655		WXS	Illumina HiSeq	Phase_I	302	123	0.407285	NM_001010859	A4QPH5	Missense_Mutation	SNP	ENST00000382097.3	37	CCDS33639.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	G	2.354	-0.348287	0.05208	0.002043	0.019535	ENSG00000205856	ENST00000382097	T	0.23348	1.91	.	.	.	.	.	.	.	.	T	0.10508	0.0257	N	0.08118	0	0.09310	N	1	D	0.64830	0.994	P	0.62014	0.897	T	0.19160	-1.0314	7	0.20046	T	0.44	.	.	.	.	.	69	Q6IC83	CV042_HUMAN	M	69	ENSP00000371529:T69M	ENSP00000371529:T69M	T	-	2	0	C22orf42	30884997	0.002000	0.14202	0.037000	0.18230	0.041000	0.13682	-0.993000	0.03720	0.064000	0.16427	0.064000	0.15345	ACG	G|0.988;A|0.012	0.012	strong		0.562	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859	
CACTIN	58509	hgsc.bcm.edu	37	19	3611972	3611972	+	Silent	SNP	G	G	A	rs2158935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3611972G>A	ENST00000429344.2	-	10	2278	c.2226C>T	c.(2224-2226)aaC>aaT	p.N742N	CACTIN_ENST00000221899.3_Silent_p.N674N|CACTIN-AS1_ENST00000592274.1_RNA|CACTIN_ENST00000248420.5_Silent_p.N742N	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	742					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										GGAAGATGCCGTTGGCAAACT	0.637													G|||	2169	0.433107	0.3033	0.6066	5008	,	,		18889	0.3313		0.5805	False		,,,				2504	0.4387				p.N742N		Atlas-SNP	.											.	.	.	.	0			c.C2226T						PASS	.	G	,	1459,2595		245,969,813	62.0	72.0	69.0		2226,2226	-3.2	1.0	19	dbSNP_96	69	4755,3579		1343,2069,755	no	coding-synonymous,coding-synonymous	C19orf29	NM_001080543.1,NM_021231.1	,	1588,3038,1568	AA,AG,GG		42.9446,35.9891,49.8386	,	742/759,742/759	3611972	6214,6174	2027	4167	6194	SO:0001819	synonymous_variant	58509	exon10			GATGCCGTTGGCA	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"""NY REN 24 antigen"", ""functional spliceosome-associated protein c"", ""cactin homolog (Drosophila)"""		"""chromosome 19 open reading frame 29"""	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.2226C>T	19.37:g.3611972G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Silent	SNP	ENST00000429344.2	37	CCDS45920.1	1005	0.46016483516483514	155	0.3150406504065041	220	0.6077348066298343	189	0.3304195804195804	441	0.5817941952506597	G	13.87	2.366515	0.41902	0.359891	0.570554	ENSG00000226800	ENST00000447295	.	.	.	4.3	-3.21	0.05140	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999882838	.	.	.	.	.	.	T	0.43556	-0.9384	4	0.09338	T	0.73	.	6.3668	0.21459	0.6301:0.1558:0.2141:0.0	rs2158935;rs58676824;rs2158935	.	.	.	I	82	.	ENSP00000412459:V82I	V	+	1	0	C19orf29OS	3562972	0.043000	0.20138	0.988000	0.46212	0.980000	0.70556	-0.748000	0.04818	-0.334000	0.08463	0.637000	0.83480	GTT	G|0.545;A|0.455	0.455	strong		0.637	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
KRT40	125115	hgsc.bcm.edu	37	17	39135207	39135207	+	Missense_Mutation	SNP	A	A	G	rs386797018|rs150812789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39135207A>G	ENST00000398486.2	-	8	1205	c.1045T>C	c.(1045-1047)Tgt>Cgt	p.C349R	KRT40_ENST00000377755.4_Missense_Mutation_p.C349R	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	349	Coil 2.|Rod.			C -> R (in Ref. 1; CAH10353). {ECO:0000305}.		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)				TCGATCAGACACTGAATTTGG	0.582													A|||	1082	0.216054	0.0628	0.317	5008	,	,		16221	0.251		0.2425	False		,,,				2504	0.2883				p.C349R		Atlas-SNP	.											KRT40,NS,carcinoma,+2,1	KRT40	27	1	0			c.T1045C						scavenged	.	A	ARG/CYS	340,4062	169.8+/-200.3	12,316,1873	90.0	99.0	96.0		1045	3.2	1.0	17	dbSNP_134	96	1951,6639	334.5+/-321.0	205,1541,2549	yes	missense	KRT40	NM_182497.3	180	217,1857,4422	GG,GA,AA		22.7125,7.7238,17.6339	benign	349/432	39135207	2291,10701	2201	4295	6496	SO:0001583	missense	125115	exon8			TCAGACACTGAAT	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.1045T>C	17.37:g.39135207A>G	ENSP00000381500:p.Cys349Arg	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	465	0.2129120879120879	29	0.05894308943089431	111	0.30662983425414364	135	0.23601398601398602	190	0.25065963060686014	A	11.18	1.562779	0.27915	0.077238	0.227125	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.87729	-2.29;-2.29	5.56	3.25	0.37280	Filament (1);	0.000000	0.36519	N	0.002560	T	0.00012	0.0000	N	0.26092	0.79	0.22156	P	0.999322654	B	0.14012	0.009	B	0.17979	0.02	T	0.03112	-1.1071	9	0.24483	T	0.36	.	13.2354	0.59967	0.4595:0.5404:0.0:0.0	.	349	Q6A162	K1C40_HUMAN	R	349	ENSP00000366984:C349R;ENSP00000381500:C349R	ENSP00000366984:C349R	C	-	1	0	KRT40	36388733	0.000000	0.05858	0.998000	0.56505	0.967000	0.64934	-0.302000	0.08221	0.438000	0.26450	0.533000	0.62120	TGT	A|0.787;G|0.213	0.213	strong		0.582	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
TMEM63A	9725	hgsc.bcm.edu	37	1	226055595	226055595	+	Silent	SNP	G	G	A	rs2292564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:226055595G>A	ENST00000366835.3	-	7	777	c.507C>T	c.(505-507)gaC>gaT	p.D169D	TMEM63A_ENST00000537914.1_5'Flank|TMEM63A_ENST00000474478.1_5'Flank	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	169					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)	p.D169D(1)		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)					TACCCAGCAAGTCCCCTGAGA	0.547													G|||	2154	0.430112	0.5189	0.3127	5008	,	,		19546	0.5188		0.2624	False		,,,				2504	0.4744				p.D169D		Atlas-SNP	.											TMEM63A,NS,carcinoma,0,1	TMEM63A	75	1	1	Substitution - coding silent(1)	stomach(1)	c.C507T						PASS	.	G		1936,2470	549.9+/-377.9	427,1082,694	136.0	106.0	116.0		507	4.8	0.6	1	dbSNP_100	116	2486,6114	408.4+/-349.5	375,1736,2189	no	coding-synonymous	TMEM63A	NM_014698.2		802,2818,2883	AA,AG,GG		28.907,43.9401,33.9997		169/808	226055595	4422,8584	2203	4300	6503	SO:0001819	synonymous_variant	9725	exon7			CAGCAAGTCCCCT		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.507C>T	1.37:g.226055595G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			G|0.640;A|0.360	0.360	strong		0.547	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
ATXN1	6310	hgsc.bcm.edu	37	6	16327897	16327897	+	Missense_Mutation	SNP	C	C	A	rs184327938		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:16327897C>A	ENST00000244769.4	-	8	1581	c.645G>T	c.(643-645)caG>caT	p.Q215H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q215H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	215	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)	p.Q215H(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)				gctgctgctgctgctgctgct	0.667																																					p.Q215H		Atlas-SNP	.											ATXN1,NS,carcinoma,0,3	ATXN1	117	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.G645T						PASS	.						4.0	8.0	7.0					6																	16327897		1730	3633	5363	SO:0001583	missense	6310	exon7			CTGCTGCTGCTGC	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.645G>T	6.37:g.16327897C>A	ENSP00000244769:p.Gln215His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	4	0.0444444	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	161	0.07371794871794872	7	0.014227642276422764	16	0.04419889502762431	116	0.20279720279720279	22	0.029023746701846966	-	1.752	-0.489019	0.04352	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.56611	0.45;0.45	.	.	.	.	.	.	.	.	T	0.13713	0.0332	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.21245	-1.0251	5	0.59425	D	0.04	.	.	.	.	.	215	P54253	ATX1_HUMAN	H	215	ENSP00000244769:Q215H;ENSP00000416360:Q215H	ENSP00000244769:Q215H	Q	-	3	2	ATXN1	16435876	0.000000	0.05858	0.011000	0.14972	0.097000	0.18754	-0.615000	0.05597	0.107000	0.17824	0.109000	0.15622	CAG	C|0.926;A|0.074	0.074	strong		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
APOBEC1	339	hgsc.bcm.edu	37	12	7803646	7803646	+	Silent	SNP	G	G	A	rs10431309	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	138	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	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	
OR4N2	390429	hgsc.bcm.edu	37	14	20296010	20296010	+	Missense_Mutation	SNP	G	G	C	rs17114261	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	910	0	0		WXS	Illumina HiSeq	Phase_I	474	265	0.559072	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		
PPP1R36	145376	hgsc.bcm.edu	37	14	65054858	65054858	+	Silent	SNP	T	T	C	rs723594	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:65054858T>C	ENST00000298705.1	+	11	1023	c.927T>C	c.(925-927)gcT>gcC	p.A309A	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	309					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TTAAAAAAGCTATCAACATGC	0.428													C|||	213	0.0425319	0.0469	0.0461	5008	,	,		21889	0.0129		0.0845	False		,,,				2504	0.0215				p.A309A		Atlas-SNP	.											.	.	.	.	0			c.T927C						PASS	.	C		198,4208	808.1+/-415.9	4,190,2009	100.0	99.0	99.0		927	3.2	1.0	14	dbSNP_86	99	670,7930	788.6+/-407.6	30,610,3660	no	coding-synonymous	C14orf50	NM_172365.1		34,800,5669	CC,CT,TT		7.7907,4.4939,6.6738		309/423	65054858	868,12138	2203	4300	6503	SO:0001819	synonymous_variant	145376	exon11			AAAAGCTATCAAC		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.927T>C	14.37:g.65054858T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	124	39	0.314516	NM_172365	Q6NTH6	Silent	SNP	ENST00000298705.1	37	CCDS9767.1																																																																																			T|0.940;C|0.060	0.060	strong		0.428	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
MCF2L	23263	hgsc.bcm.edu	37	13	113739226	113739226	+	Silent	SNP	T	T	C	rs2281723	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:113739226T>C	ENST00000375608.3	+	20	2230	c.2172T>C	c.(2170-2172)taT>taC	p.Y724Y	MCF2L_ENST00000375597.4_Silent_p.Y692Y|MCF2L_ENST00000442652.2_Silent_p.Y724Y|MCF2L_ENST00000375601.3_Silent_p.Y698Y|MCF2L_ENST00000535094.2_Silent_p.Y694Y|MCF2L_ENST00000421756.1_Silent_p.Y698Y|MCF2L_ENST00000434480.2_Silent_p.Y700Y|MCF2L_ENST00000375604.2_Silent_p.Y751Y|MCF2L_ENST00000423482.2_Silent_p.Y692Y|MCF2L_ENST00000397030.1_Silent_p.Y727Y			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	724	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)				TCCAGATCTATGAGAAGTACT	0.582													c|||	562	0.11222	0.0764	0.0865	5008	,	,		17663	0.2649		0.0656	False		,,,				2504	0.0695				p.Y694Y		Atlas-SNP	.											.	MCF2L	182	.	0			c.T2082C						PASS	.	C	,	306,4100	797.5+/-415.4	10,286,1907	125.0	119.0	121.0		2082,2076	-3.1	1.0	13	dbSNP_100	121	607,7993	791.9+/-407.5	14,579,3707	yes	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	24,865,5614	CC,CT,TT		7.0581,6.9451,7.0198	,	694/1126,692/1124	113739226	913,12093	2203	4300	6503	SO:0001819	synonymous_variant	23263	exon19			GATCTATGAGAAG	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.2172T>C	13.37:g.113739226T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		257	0.11767399267399267	43	0.08739837398373984	32	0.08839779005524862	135	0.23601398601398602	47	0.06200527704485488	C	9.298	1.052343	0.19827	0.069451	0.070581	ENSG00000126217	ENST00000397017	.	.	.	4.64	-3.09	0.05331	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2654	0.73657	0.0:0.1181:0.0:0.8819	rs2281723;rs17692545;rs2281723	.	.	.	R	355	.	.	X	+	1	0	MCF2L	112787227	0.995000	0.38212	0.975000	0.42487	0.824000	0.46624	0.321000	0.19558	-0.859000	0.04105	-0.711000	0.03637	TGA	T|0.904;C|0.096	0.096	strong		0.582	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
ULBP3	79465	hgsc.bcm.edu	37	6	150390118	150390118	+	Missense_Mutation	SNP	C	C	T	rs113233347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:150390118C>T	ENST00000367339.2	-	1	113	c.85G>A	c.(85-87)Gcc>Acc	p.A29T	ULBP3_ENST00000438272.2_Missense_Mutation_p.A29T			Q9BZM4	N2DL3_HUMAN	UL16 binding protein 3	29					antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)|viral process (GO:0016032)	anchored component of plasma membrane (GO:0046658)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)	p.A29T(1)		central_nervous_system(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	9		Ovarian(120;0.12)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.45e-12)		AACTCACCGGCCCGCCCCGTC	0.677													C|||	338	0.067492	0.0061	0.072	5008	,	,		10072	0.0804		0.1024	False		,,,				2504	0.0982				p.A29T		Atlas-SNP	.											ULBP3,NS,carcinoma,0,1	ULBP3	22	1	1	Substitution - Missense(1)	pancreas(1)	c.G85A						PASS	.	C	THR/ALA	93,4305		4,85,2110	14.0	18.0	17.0		85	-0.6	0.0	6	dbSNP_132	17	997,7589		50,897,3346	yes	missense	ULBP3	NM_024518.1	58	54,982,5456	TT,TC,CC		11.6119,2.1146,8.3949	benign	29/245	150390118	1090,11894	2199	4293	6492	SO:0001583	missense	79465	exon1			CACCGGCCCGCCC	AF304379	CCDS5225.1	6q25	2008-04-11			ENSG00000131019	ENSG00000131019			14895	protein-coding gene	gene with protein product		605699				11239445, 11827464	Standard	NM_024518		Approved	RAET1N	uc003qns.3	Q9BZM4	OTTHUMG00000015811	ENST00000367339.2:c.85G>A	6.37:g.150390118C>T	ENSP00000356308:p.Ala29Thr	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	186	98	0.526882	NM_024518	Q5VY82|Q8IZX5|Q8TE75	Missense_Mutation	SNP	ENST00000367339.2	37	CCDS5225.1	153	0.07005494505494506	5	0.01016260162601626	30	0.08287292817679558	47	0.08216783216783216	71	0.09366754617414248	C	9.603	1.129290	0.21041	0.021146	0.116119	ENSG00000131019	ENST00000399812;ENST00000253335;ENST00000367339;ENST00000438272	T;T	0.00724	5.78;5.78	0.467	-0.6	0.11642	.	.	.	.	.	T	0.00241	0.0007	L	0.38838	1.175	0.80722	P	0.0	B;B	0.33212	0.402;0.402	B;B	0.26864	0.074;0.074	T	0.37798	-0.9690	7	0.38643	T	0.18	.	.	.	.	.	29;29	Q5VY82;Q9BZM4	.;N2DL3_HUMAN	T	29	ENSP00000356308:A29T;ENSP00000403562:A29T	ENSP00000253335:A29T	A	-	1	0	ULBP3	150431811	0.000000	0.05858	0.004000	0.12327	0.087000	0.18053	-0.305000	0.08188	-0.397000	0.07691	0.205000	0.17691	GCC	C|0.925;T|0.075	0.075	strong		0.677	ULBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042678.2		
RASA2	5922	hgsc.bcm.edu	37	3	141327474	141327474	+	Silent	SNP	G	G	A	rs295323	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:141327474G>A	ENST00000452898.1	+	21	2198	c.2163G>A	c.(2161-2163)ctG>ctA	p.L721L	RASA2_ENST00000286364.3_Silent_p.L720L|RASA2_ENST00000509118.1_3'UTR	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	721					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.L720L(1)		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						CTGTGTATCTGAACGGAAATT	0.438													A|||	2256	0.450479	0.7315	0.4625	5008	,	,		21103	0.2937		0.3797	False		,,,				2504	0.2965				p.L720L		Atlas-SNP	.											RASA2_ENST00000286364,NS,carcinoma,0,1	RASA2	169	1	1	Substitution - coding silent(1)	stomach(1)	c.G2160A						scavenged	.	A		2958,1448	467.4+/-354.8	999,960,244	123.0	124.0	124.0		2160	-10.8	0.0	3	dbSNP_79	124	3341,5259	643.9+/-400.0	601,2139,1560	no	coding-synonymous	RASA2	NM_006506.2		1600,3099,1804	AA,AG,GG		38.8488,32.8643,48.4315		720/850	141327474	6299,6707	2203	4300	6503	SO:0001819	synonymous_variant	5922	exon21			GTATCTGAACGGA	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.2163G>A	3.37:g.141327474G>A		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	227	3	0.0132159	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Silent	SNP	ENST00000452898.1	37																																																																																				G|0.523;A|0.477	0.477	strong		0.438	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	
CLCA2	9635	hgsc.bcm.edu	37	1	86909582	86909582	+	Missense_Mutation	SNP	G	G	A	rs1413426	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	124	0	0		WXS	Illumina HiSeq	Phase_I	67	13	0.19403	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	
CATSPERB	79820	hgsc.bcm.edu	37	14	92159558	92159558	+	Missense_Mutation	SNP	A	A	G	rs72629402	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:92159558A>G	ENST00000256343.3	-	9	899	c.743T>C	c.(742-744)gTt>gCt	p.V248A		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	248					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				ATTCGTTAAAACCATATCCAC	0.348													A|||	281	0.0561102	0.0113	0.0331	5008	,	,		19365	0.1409		0.0408	False		,,,				2504	0.0613				p.V248A		Atlas-SNP	.											.	CATSPERB	114	.	0			c.T743C						PASS	.	A	ALA/VAL	97,4309	79.3+/-117.8	2,93,2108	118.0	114.0	116.0		743	3.5	1.0	14	dbSNP_130	116	429,8171	131.7+/-189.4	16,397,3887	yes	missense	CATSPERB	NM_024764.2	64	18,490,5995	GG,GA,AA		4.9884,2.2015,4.0443	benign	248/1117	92159558	526,12480	2203	4300	6503	SO:0001583	missense	79820	exon9			GTTAAAACCATAT	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"""chromosome 14 open reading frame 161"", ""cation channel, sperm-associated, beta"""	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.743T>C	14.37:g.92159558A>G	ENSP00000256343:p.Val248Ala	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	155	89	0.574194	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	109	0.04990842490842491	5	0.01016260162601626	12	0.03314917127071823	69	0.12062937062937062	23	0.030343007915567283	A	14.02	2.411923	0.42817	0.022015	0.049884	ENSG00000133962	ENST00000256343	T	0.52754	0.65	5.88	3.48	0.39840	.	0.251868	0.28198	N	0.016227	T	0.00608	0.0020	L	0.55481	1.735	0.27884	N	0.939579	B	0.23249	0.082	B	0.25140	0.058	T	0.02705	-1.1121	10	0.25106	T	0.35	-24.0534	8.6627	0.34101	0.8457:0.0:0.1543:0.0	.	248	Q9H7T0	CTSRB_HUMAN	A	248	ENSP00000256343:V248A	ENSP00000256343:V248A	V	-	2	0	CATSPERB	91229311	0.999000	0.42202	1.000000	0.80357	0.697000	0.40408	3.255000	0.51484	0.464000	0.27142	0.459000	0.35465	GTT	A|0.955;G|0.045	0.045	strong		0.348	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764	
CASR	846	hgsc.bcm.edu	37	3	122003769	122003769	+	Missense_Mutation	SNP	A	A	G	rs1042636	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122003769A>G	ENST00000490131.1	+	7	3340	c.2968A>G	c.(2968-2970)Agg>Ggg	p.R990G	AC068754.1_ENST00000408547.1_RNA|CASR_ENST00000498619.1_Missense_Mutation_p.R1000G|CASR_ENST00000296154.5_Missense_Mutation_p.R990G	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	990			R -> G (associated with low serum level of calcium; dbSNP:rs1042636). {ECO:0000269|PubMed:12050233, ECO:0000269|PubMed:14985373, ECO:0000269|PubMed:15531522, ECO:0000269|PubMed:15551332, ECO:0000269|PubMed:17698911, ECO:0000269|PubMed:18756473, ECO:0000269|PubMed:7759551, ECO:0000269|Ref.5}.		anatomical structure morphogenesis (GO:0009653)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|chemosensory behavior (GO:0007635)|detection of calcium ion (GO:0005513)|G-protein coupled receptor signaling pathway (GO:0007186)|metabolic process (GO:0008152)|ossification (GO:0001503)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|phosphatidylinositol phospholipase C activity (GO:0004435)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(45)|ovary(4)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	84				GBM - Glioblastoma multiforme(114;0.226)	Cinacalcet(DB01012)	CATGGCCCACAGGAATTCTAC	0.577													A|||	1034	0.20647	0.0303	0.1988	5008	,	,		19982	0.5198		0.0736	False		,,,				2504	0.2638				p.R1000G		Atlas-SNP	.											.	CASR	190	.	0			c.A2998G	GRCh37	CM044584	CASR	M	rs1042636	PASS	.	A	GLY/ARG,GLY/ARG	189,4217	118.4+/-156.1	4,181,2018	64.0	61.0	62.0		2968,2998	3.3	1.0	3	dbSNP_86	62	629,7971	163.6+/-216.1	20,589,3691	yes	missense,missense	CASR	NM_000388.3,NM_001178065.1	125,125	24,770,5709	GG,GA,AA		7.314,4.2896,6.2894	benign,benign	990/1079,1000/1089	122003769	818,12188	2203	4300	6503	SO:0001583	missense	846	exon7			GCCCACAGGAATT	U20760	CCDS3010.1, CCDS54632.1	3q21.1	2012-08-29	2008-08-01		ENSG00000036828	ENSG00000036828		"""GPCR / Class C : Calcium-sensing receptors"""	1514	protein-coding gene	gene with protein product	"""severe neonatal hyperparathyroidism"""	601199	"""hypocalciuric hypercalcemia 1"""	HHC, HHC1		7677761	Standard	NM_000388		Approved	FHH, NSHPT, GPRC2A	uc003eew.4	P41180	OTTHUMG00000159491	ENST00000490131.1:c.2968A>G	3.37:g.122003769A>G	ENSP00000418685:p.Arg990Gly	Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	239	125	0.523013	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	37	CCDS3010.1	453	0.20741758241758243	14	0.028455284552845527	62	0.1712707182320442	315	0.5506993006993007	62	0.08179419525065963	A	10.86	1.469071	0.26335	0.042896	0.07314	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.89746	-2.56;-2.52;-2.56	5.79	3.26	0.37387	.	0.065488	0.56097	D	0.000022	T	0.00012	0.0000	L	0.27053	0.805	0.25725	P	0.9853387	B;B	0.31318	0.319;0.155	B;B	0.24155	0.051;0.051	T	0.43940	-0.9360	9	0.87932	D	0	.	11.8665	0.52496	0.7239:0.2761:0.0:0.0	rs1042636;rs3804596;rs52829576;rs59615814;rs1042636	1000;990	E7ENE0;P41180	.;CASR_HUMAN	G	990;1000;990	ENSP00000418685:R990G;ENSP00000420194:R1000G;ENSP00000296154:R990G	ENSP00000296154:R990G	R	+	1	2	CASR	123486459	1.000000	0.71417	0.996000	0.52242	0.582000	0.36321	2.918000	0.48829	1.004000	0.39156	0.459000	0.35465	AGG	A|0.871;G|0.129	0.129	strong		0.577	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388	
GLI2	2736	hgsc.bcm.edu	37	2	121742124	121742124	+	Silent	SNP	G	G	A	rs61732852	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:121742124G>A	ENST00000452319.1	+	12	1821	c.1761G>A	c.(1759-1761)acG>acA	p.T587T	GLI2_ENST00000361492.4_Silent_p.T587T|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_Silent_p.T259T					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)				ATGTGAAAACGGTCCACGGCC	0.597													G|||	22	0.00439297	0.0	0.0043	5008	,	,		19759	0.0		0.0139	False		,,,				2504	0.0051				p.T587T		Atlas-SNP	.											.	GLI2	187	.	0			c.G1761A						PASS	.	G		13,4393	19.1+/-41.9	0,13,2190	154.0	147.0	149.0		1761	-9.0	0.3	2	dbSNP_129	149	117,8483	61.7+/-123.6	0,117,4183	no	coding-synonymous	GLI2	NM_005270.4		0,130,6373	AA,AG,GG		1.3605,0.2951,0.9995		587/1587	121742124	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	2736	exon11			GAAAACGGTCCAC		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.1761G>A	2.37:g.121742124G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	180	83	0.461111	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			G|0.991;A|0.009	0.009	strong		0.597	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
DNAH14	127602	hgsc.bcm.edu	37	1	225534348	225534348	+	Missense_Mutation	SNP	G	G	A	rs7535953	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225534348G>A	ENST00000445597.2	+	49	8600	c.8600G>A	c.(8599-8601)aGa>aAa	p.R2867K	DNAH14_ENST00000430092.1_Missense_Mutation_p.R3670K|DNAH14_ENST00000439375.2_Missense_Mutation_p.R3670K			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2867					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						TCCCAGTCTAGACTTACTAGT	0.338													G|||	2650	0.529153	0.6407	0.4697	5008	,	,		17939	0.5089		0.4046	False		,,,				2504	0.5695				p.R3670K		Atlas-SNP	.											.	DNAH14	300	.	0			c.G11009A						PASS	.						48.0	44.0	45.0					1																	225534348		692	1585	2277	SO:0001583	missense	127602	exon69			AGTCTAGACTTAC	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.8600G>A	1.37:g.225534348G>A	ENSP00000409472:p.Arg2867Lys	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	236	147	0.622881	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1054	0.4826007326007326	302	0.6138211382113821	165	0.4558011049723757	281	0.49125874125874125	306	0.40369393139841686	G	1.991	-0.431729	0.04669	.	.	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.39997	1.05;1.05;1.05	4.94	-3.81	0.04294	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.40213	-0.9575	7	0.02654	T	1	.	6.7277	0.23365	0.6059:0.0:0.272:0.1221	rs7535953;rs17522510;rs52812222;rs58063527;rs7535953	3670	Q0VDD8-4	.	K	2867;3670;3670	ENSP00000409472:R2867K;ENSP00000414402:R3670K;ENSP00000392061:R3670K	ENSP00000414402:R3670K	R	+	2	0	DNAH14	223600971	0.000000	0.05858	0.000000	0.03702	0.463000	0.32649	-0.207000	0.09384	-0.823000	0.04301	-0.357000	0.07601	AGA	G|0.499;A|0.501	0.501	strong		0.338	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
SYNE2	23224	hgsc.bcm.edu	37	14	64519709	64519709	+	Missense_Mutation	SNP	A	A	T	rs34843668	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:64519709A>T	ENST00000344113.4	+	48	9290	c.9078A>T	c.(9076-9078)gaA>gaT	p.E3026D	SYNE2_ENST00000358025.3_Missense_Mutation_p.E3026D|SYNE2_ENST00000554584.1_Missense_Mutation_p.E3059D|SYNE2_ENST00000357395.3_5'UTR	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3026			E -> D (in dbSNP:rs34843668).		centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAGTATTTGAAAAAGAAAAGG	0.313													A|||	145	0.0289537	0.0053	0.0677	5008	,	,		19057	0.0546		0.0249	False		,,,				2504	0.0112				p.E3026D		Atlas-SNP	.											SYNE2,NS,carcinoma,+2,1	SYNE2	577	1	0			c.A9078T						scavenged	.	A	ASP/GLU,ASP/GLU	41,3545		0,41,1752	49.0	49.0	49.0		9078,9078	-0.5	0.4	14	dbSNP_126	49	209,7913		5,199,3857	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	45,45	5,240,5609	TT,TA,AA		2.5733,1.1433,2.1353	benign,benign	3026/6886,3026/6908	64519709	250,11458	1793	4061	5854	SO:0001583	missense	23224	exon48			ATTTGAAAAAGAA	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.9078A>T	14.37:g.64519709A>T	ENSP00000341781:p.Glu3026Asp	Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	147	57	0.387755	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	73	0.033424908424908424	1	0.0020325203252032522	23	0.06353591160220995	31	0.05419580419580419	18	0.023746701846965697	A	11.30	1.599048	0.28534	0.011433	0.025733	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57595	0.77;0.77;0.39	5.69	-0.542	0.11854	.	0.589219	0.16197	N	0.225126	T	0.03959	0.0111	N	0.24115	0.695	0.80722	D	1	P;P	0.38504	0.501;0.634	B;B	0.34242	0.086;0.178	T	0.01341	-1.1380	10	0.37606	T	0.19	.	9.1473	0.36942	0.6336:0.0:0.3664:0.0	rs34843668	3026;3026	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	D	3026;3026;3059;3059	ENSP00000350719:E3026D;ENSP00000341781:E3026D;ENSP00000452570:E3059D	ENSP00000261678:E3059D	E	+	3	2	SYNE2	63589462	0.987000	0.35691	0.372000	0.25991	0.450000	0.32258	0.955000	0.29188	-0.097000	0.12307	0.379000	0.24179	GAA	A|0.970;T|0.030	0.030	strong		0.313	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
SLC25A24	29957	hgsc.bcm.edu	37	1	108703834	108703834	+	Silent	SNP	C	C	T	rs11185293	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:108703834C>T	ENST00000565488.1	-	4	699	c.480G>A	c.(478-480)gaG>gaA	p.E160E	SLC25A24_ENST00000370041.4_Silent_p.E141E	NM_013386.4	NP_037518.3	Q6NUK1	SCMC1_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 24	160					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)		GGATAATTTCCTCAATGTCTG	0.333													C|||	172	0.034345	0.0076	0.0288	5008	,	,		16786	0.004		0.0775	False		,,,				2504	0.0613				p.E160E		Atlas-SNP	.											.	SLC25A24	65	.	0			c.G480A						PASS	.	C	,	84,4322	70.3+/-108.2	0,84,2119	105.0	104.0	104.0		480,423	3.6	1.0	1	dbSNP_120	104	765,7835	180.2+/-229.2	29,707,3564	no	coding-synonymous,coding-synonymous	SLC25A24	NM_013386.3,NM_213651.1	,	29,791,5683	TT,TC,CC		8.8953,1.9065,6.5278	,	160/478,141/459	108703834	849,12157	2203	4300	6503	SO:0001819	synonymous_variant	29957	exon4			AATTTCCTCAATG	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.480G>A	1.37:g.108703834C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	171	28	0.163743	NM_013386	B7ZAI9|Q5T331|Q5T485|Q6PJJ9|Q705K4|Q9P129	Silent	SNP	ENST00000565488.1	37	CCDS41361.1																																																																																			C|0.947;T|0.053	0.053	strong		0.333	SLC25A24-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030280.2	NM_013386	
SLC27A2	11001	hgsc.bcm.edu	37	15	50474766	50474766	+	Missense_Mutation	SNP	A	A	C	rs1648348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:50474766A>C	ENST00000267842.5	+	1	374	c.142A>C	c.(142-144)Aag>Cag	p.K48Q	SLC27A2_ENST00000380902.4_Missense_Mutation_p.K48Q	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	48			K -> Q (in dbSNP:rs1648348). {ECO:0000269|PubMed:10198260, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1, ECO:0000269|Ref.6}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)|very long-chain fatty acid catabolic process (GO:0042760)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of peroxisomal membrane (GO:0005779)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|fatty acid transporter activity (GO:0015245)|long-chain fatty acid-CoA ligase activity (GO:0004467)|phytanate-CoA ligase activity (GO:0050197)|pristanate-CoA ligase activity (GO:0070251)|receptor binding (GO:0005102)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		CAGCTACGGGAAGCGGCGGCC	0.647													A|||	3070	0.613019	0.3729	0.6326	5008	,	,		13597	0.8095		0.6501	False		,,,				2504	0.683				p.K48Q		Atlas-SNP	.											.	SLC27A2	50	.	0			c.A142C						PASS	.	A	GLN/LYS,GLN/LYS	1867,2519		393,1081,719	19.0	20.0	20.0		142,142	0.7	0.0	15	dbSNP_89	20	5703,2873		1911,1881,496	yes	missense,missense	SLC27A2	NM_001159629.1,NM_003645.3	53,53	2304,2962,1215	CC,CA,AA		33.5005,42.5673,41.5985	benign,benign	48/568,48/621	50474766	7570,5392	2193	4288	6481	SO:0001583	missense	11001	exon1			TACGGGAAGCGGC	D88308	CCDS10133.1, CCDS53943.1	15q21.2	2013-05-22			ENSG00000140284	ENSG00000140284		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10996	protein-coding gene	gene with protein product		603247		FACVL1		9730624	Standard	NM_003645		Approved	FATP2, hFACVL1, VLACS, VLCS, HsT17226, ACSVL1	uc001zxw.3	O14975	OTTHUMG00000131643	ENST00000267842.5:c.142A>C	15.37:g.50474766A>C	ENSP00000267842:p.Lys48Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	34	7	0.205882	NM_003645	A8K2J7|Q53FY6|Q6PF09	Missense_Mutation	SNP	ENST00000267842.5	37	CCDS10133.1	1413	0.646978021978022	205	0.4166666666666667	221	0.6104972375690608	471	0.8234265734265734	516	0.6807387862796834	A	1.463	-0.561990	0.03939	0.425673	0.664995	ENSG00000140284	ENST00000380902;ENST00000267842	T;T	0.60548	0.29;0.18	4.94	0.708	0.18144	.	2.094770	0.02304	N	0.071516	T	0.00012	0.0000	N	0.05280	-0.08	0.50467	P	1.2900000000004574E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.45745	-0.9240	9	0.20519	T	0.43	.	13.7473	0.62883	0.6771:0.3229:0.0:0.0	rs1648348;rs17848318;rs1648348	48;48	Q6PF09;O14975	.;S27A2_HUMAN	Q	48	ENSP00000370289:K48Q;ENSP00000267842:K48Q	ENSP00000267842:K48Q	K	+	1	0	SLC27A2	48262058	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	0.034000	0.13776	-0.049000	0.13379	-0.249000	0.11873	AAG	A|0.412;C|0.588	0.588	strong		0.647	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645	
CFAP46	54777	hgsc.bcm.edu	37	10	134748281	134748281	+	Missense_Mutation	SNP	G	G	A	rs74460040	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:134748281G>A	ENST00000368586.5	-	8	941	c.841C>T	c.(841-843)Cgc>Tgc	p.R281C	TTC40_ENST00000368585.3_Missense_Mutation_p.R281C|TTC40_ENST00000368582.2_Missense_Mutation_p.R281C	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GAGGGAAAGCGCTGGTGGTTG	0.378													G|||	134	0.0267572	0.0613	0.0346	5008	,	,		18945	0.0		0.0268	False		,,,				2504	0.002				p.R281C		Atlas-SNP	.											.	TTC40	100	.	0			c.C841T						PASS	.	G	CYS/ARG	195,4211	124.1+/-161.4	5,185,2013	98.0	93.0	95.0		841	1.0	0.0	10	dbSNP_131	95	148,8452	72.3+/-134.9	1,146,4153	yes	missense	C10orf93	NM_173572.3	180	6,331,6166	AA,AG,GG		1.7209,4.4258,2.6372	probably-damaging	281/406	134748281	343,12663	2203	4300	6503	SO:0001583	missense	54777	exon8			GAAAGCGCTGGTG																												ENST00000368586.5:c.841C>T	10.37:g.134748281G>A	ENSP00000357575:p.Arg281Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	23	0.328571	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	52	0.023809523809523808	24	0.04878048780487805	13	0.03591160220994475	0	0.0	15	0.01978891820580475	G	14.76	2.631822	0.46944	0.044258	0.017209	ENSG00000171811	ENST00000368586;ENST00000368582;ENST00000368585	T;T;T	0.55588	0.51;0.51;0.51	4.08	0.967	0.19674	.	0.829047	0.10271	N	0.694809	T	0.14700	0.0355	L	0.47716	1.5	0.09310	N	1	D	0.71674	0.998	P	0.53649	0.731	T	0.11446	-1.0587	10	0.59425	D	0.04	.	4.147	0.10220	0.1146:0.0:0.4685:0.4169	.	281	Q5SR76-1	.	C	281	ENSP00000357575:R281C;ENSP00000357571:R281C;ENSP00000357574:R281C	ENSP00000357571:R281C	R	-	1	0	C10orf93	134598271	0.007000	0.16637	0.001000	0.08648	0.208000	0.24298	0.015000	0.13355	0.385000	0.24970	0.609000	0.83330	CGC	G|0.972;A|0.028	0.028	strong		0.378	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
C15orf39	56905	hgsc.bcm.edu	37	15	75499995	75499995	+	Missense_Mutation	SNP	T	T	G	rs28509789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75499995T>G	ENST00000360639.2	+	2	1926	c.1606T>G	c.(1606-1608)Tca>Gca	p.S536A	C15orf39_ENST00000394987.4_Missense_Mutation_p.S536A|C15orf39_ENST00000567617.1_Missense_Mutation_p.S536A			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	536			S -> A (in dbSNP:rs28509789). {ECO:0000269|PubMed:15498874}.			cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						TGAGCCTGACTCAGCCCCAGC	0.617													T|||	1965	0.392372	0.4697	0.4078	5008	,	,		18530	0.3264		0.2773	False		,,,				2504	0.4632				p.S536A		Atlas-SNP	.											C15orf39,bladder,carcinoma,-1,1	C15orf39	64	1	0			c.T1606G						PASS	.	T	ALA/SER	1955,2437		448,1059,689	25.0	26.0	26.0		1606	-3.5	0.0	15	dbSNP_125	26	2337,6247		327,1683,2282	yes	missense	C15orf39	NM_015492.4	99	775,2742,2971	GG,GT,TT		27.2251,44.5128,33.0764	benign	536/1048	75499995	4292,8684	2196	4292	6488	SO:0001583	missense	56905	exon2			CCTGACTCAGCCC	AK128205	CCDS10276.1	15q23	2013-03-14	2005-10-24		ENSG00000167173	ENSG00000167173			24497	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 38~Name Same As HGNC:28782"""				Standard	NM_015492		Approved	DKFZP434H132, FLJ46337	uc002azq.4	Q6ZRI6	OTTHUMG00000142820	ENST00000360639.2:c.1606T>G	15.37:g.75499995T>G	ENSP00000353854:p.Ser536Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	82	16	0.195122	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Missense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	749	0.34294871794871795	224	0.45528455284552843	141	0.38950276243093923	189	0.3304195804195804	195	0.25725593667546176	T	3.832	-0.035507	0.07497	0.445128	0.272251	ENSG00000167173	ENST00000360639;ENST00000394987	T;T	0.80393	-1.37;-1.37	4.84	-3.54	0.04653	.	1.653880	0.03470	N	0.213444	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.31888	-0.9927	9	0.08381	T	0.77	.	0.2702	0.00230	0.2813:0.1842:0.2851:0.2495	rs28509789	536	Q6ZRI6	CO039_HUMAN	A	536	ENSP00000353854:S536A;ENSP00000378438:S536A	ENSP00000353854:S536A	S	+	1	0	C15orf39	73287048	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-0.873000	0.04214	-0.640000	0.05495	0.460000	0.39030	TCA	T|0.662;G|0.338	0.338	strong		0.617	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492	
EYS	346007	hgsc.bcm.edu	37	6	66112409	66112409	+	Silent	SNP	A	A	G	rs974110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:66112409A>G	ENST00000370621.3	-	7	1672	c.1146T>C	c.(1144-1146)aaT>aaC	p.N382N	EYS_ENST00000370618.3_Silent_p.N382N|EYS_ENST00000342421.5_Silent_p.N382N|EYS_ENST00000503581.1_Silent_p.N382N|EYS_ENST00000370616.2_Silent_p.N382N|EYS_ENST00000393380.2_Silent_p.N382N			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	382	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						TACATGTAGCATTATTCCTCA	0.299													G|||	2534	0.50599	0.5129	0.5072	5008	,	,		14830	0.4554		0.5388	False		,,,				2504	0.5143				p.N382N		Atlas-SNP	.											.	EYS	527	.	0			c.T1146C						PASS	.	G	,,	2353,2051	562.1+/-380.9	627,1099,476	61.0	61.0	61.0		1146,1146,1146	-1.5	0.0	6	dbSNP_86	61	4501,4071	554.1+/-386.4	1215,2071,1000	no	coding-synonymous,coding-synonymous,coding-synonymous	EYS	NM_001142800.1,NM_001142801.1,NM_198283.1	,,	1842,3170,1476	GG,GA,AA		47.4918,46.5713,47.1794	,,	382/3145,382/620,382/595	66112409	6854,6122	2202	4286	6488	SO:0001819	synonymous_variant	346007	exon7			TGTAGCATTATTC		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.1146T>C	6.37:g.66112409A>G		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	215	96	0.446512	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				A|0.498;G|0.502	0.502	strong		0.299	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
N4BP2	55728	hgsc.bcm.edu	37	4	40119501	40119501	+	Silent	SNP	T	T	C	rs1128372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	105	0	0		WXS	Illumina HiSeq	Phase_I	96	37	0.385417	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	
SLC2A14	144195	hgsc.bcm.edu	37	12	7966975	7966975	+	Silent	SNP	C	C	T	rs10845982		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7966975C>T	ENST00000543909.1	-	16	2259	c.1500G>A	c.(1498-1500)ggG>ggA	p.G500G	SLC2A14_ENST00000539924.1_Silent_p.G515G|SLC2A14_ENST00000431042.2_Silent_p.G477G|SLC2A14_ENST00000535295.1_Silent_p.G391G|SLC2A14_ENST00000542546.1_Silent_p.G391G|SLC2A14_ENST00000396589.2_Silent_p.G500G|SLC2A14_ENST00000542505.1_Silent_p.G141G|SLC2A14_ENST00000340749.5_Silent_p.G477G			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	500					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)		CGCCGTCCTTCCCAGATCTAT	0.557																																					p.G500G		Atlas-SNP	.											SLC2A14,NS,carcinoma,-2,1	SLC2A14	78	1	0			c.G1500A						scavenged	.						218.0	142.0	167.0					12																	7966975		2203	4299	6502	SO:0001819	synonymous_variant	144195	exon12			GTCCTTCCCAGAT	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.1500G>A	12.37:g.7966975C>T		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	157	33	0.210191	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1																																																																																			T|1.000;|0.000	1.000	weak		0.557	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274343	39274343	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39274343A>G	ENST00000391413.2	-	1	263	c.225T>C	c.(223-225)tgT>tgC	p.C75C		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	75	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			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)			AGCTGGGGCGACAGCAGCTGG	0.657																																					p.C75C		Atlas-SNP	.											KRTAP4-11,NS,malignant_melanoma,0,2	KRTAP4-11	94	2	0			c.T225C						scavenged	.																																			SO:0001819	synonymous_variant	653240	exon1			GGGGCGACAGCAG	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.225T>C	17.37:g.39274343A>G		Somatic	182	5	0.0274725		WXS	Illumina HiSeq	Phase_I	145	8	0.0551724	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	none		0.657	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
CBX2	84733	hgsc.bcm.edu	37	17	77758691	77758691	+	Silent	SNP	G	G	A	rs3751957	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:77758691G>A	ENST00000310942.4	+	5	1553	c.1449G>A	c.(1447-1449)ccG>ccA	p.P483P		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	483					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)			GACAGAACCCGTCAGTGTCCG	0.637													g|||	2119	0.423123	0.6694	0.3458	5008	,	,		16653	0.4058		0.2087	False		,,,				2504	0.3834				p.P483P		Atlas-SNP	.											CBX2,mucosal,malignant_melanoma,+2,1	CBX2	50	1	0			c.G1449A						PASS	.	A		2594,1812	634.6+/-396.2	771,1052,380	59.0	53.0	55.0		1449	-3.2	0.0	17	dbSNP_107	55	2071,6529	358.1+/-331.0	263,1545,2492	no	coding-synonymous	CBX2	NM_005189.2		1034,2597,2872	AA,AG,GG		24.0814,41.1257,35.8681		483/533	77758691	4665,8341	2203	4300	6503	SO:0001819	synonymous_variant	84733	exon5			GAACCCGTCAGTG	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.1449G>A	17.37:g.77758691G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_005189	Q0VDA5|Q9BTB1	Silent	SNP	ENST00000310942.4	37	CCDS32757.1																																																																																			G|0.630;A|0.370	0.370	strong		0.637	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
BIRC3	330	hgsc.bcm.edu	37	11	102195297	102195297	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102195297G>A	ENST00000263464.3	+	2	2807	c.57G>A	c.(55-57)acG>acA	p.T19T	BIRC3_ENST00000532808.1_Silent_p.T19T	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	19					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|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)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GCGCCAACACGTTTGAACTGA	0.413			T	MALT1	MALT																																p.T19T		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	.	BIRC3	56	.	0			c.G57A						PASS	.						144.0	129.0	134.0					11																	102195297		2203	4299	6502	SO:0001819	synonymous_variant	330	exon2			CAACACGTTTGAA	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	591	protein-coding gene	gene with protein product	"""apoptosis inhibitor 2"", ""TNFR2-TRAF signaling complex protein"", ""mammalian IAP homolog C"", ""inhibitor of apoptosis protein 1"""	601721	"""baculoviral IAP repeat-containing 3"""	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.57G>A	11.37:g.102195297G>A		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	442	95	0.214932	NM_001165	Q16628|Q9HC27|Q9UP46	Silent	SNP	ENST00000263464.3	37	CCDS8315.1																																																																																			.	.	none		0.413	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165	
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs41307110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	431	2	0.00464037		WXS	Illumina HiSeq	Phase_I	252	16	0.0634921	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		
SCN10A	6336	hgsc.bcm.edu	37	3	38753732	38753732	+	Missense_Mutation	SNP	A	A	T	rs11711062	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38753732A>T	ENST00000449082.2	-	22	4008	c.4009T>A	c.(4009-4011)Tcc>Acc	p.S1337T		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1337					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)	CTGCCAGTGGAGTTTTGAATC	0.443													A|||	6	0.00119808	0.0	0.0058	5008	,	,		22128	0.0		0.001	False		,,,				2504	0.001				p.S1337T		Atlas-SNP	.											.	SCN10A	359	.	0			c.T4009A						PASS	.	A	THR/SER	3,4403	6.2+/-15.9	0,3,2200	124.0	121.0	122.0		4009	-9.3	0.0	3	dbSNP_120	122	56,8544	35.9+/-90.5	0,56,4244	yes	missense	SCN10A	NM_006514.2	58	0,59,6444	TT,TA,AA		0.6512,0.0681,0.4536	benign	1337/1957	38753732	59,12947	2203	4300	6503	SO:0001583	missense	6336	exon22			CAGTGGAGTTTTG	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.4009T>A	3.37:g.38753732A>T	ENSP00000390600:p.Ser1337Thr	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	240	117	0.4875	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	A	5.860	0.342903	0.11069	6.81E-4	0.006512	ENSG00000185313	ENST00000449082	D	0.95588	-3.75	4.67	-9.34	0.00636	Ion transport (1);	1.035800	0.07681	N	0.937090	T	0.79885	0.4523	N	0.17082	0.46	0.09310	N	1	B	0.21688	0.059	B	0.24006	0.05	T	0.75682	-0.3233	10	0.10636	T	0.68	.	1.1596	0.01803	0.1365:0.2334:0.2164:0.4137	rs11711062;rs11711062	1337	Q9Y5Y9	SCNAA_HUMAN	T	1337	ENSP00000390600:S1337T	ENSP00000390600:S1337T	S	-	1	0	SCN10A	38728736	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-2.797000	0.00763	-1.865000	0.01147	0.454000	0.30748	TCC	A|0.996;T|0.004	0.004	strong		0.443	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
ARID4A	5926	hgsc.bcm.edu	37	14	58768333	58768333	+	Silent	SNP	C	C	T	rs45562837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	120	0	0		WXS	Illumina HiSeq	Phase_I	169	63	0.372781	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	
GBP7	388646	hgsc.bcm.edu	37	1	89599013	89599013	+	Silent	SNP	G	G	T	rs115671591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89599013G>T	ENST00000294671.2	-	10	1728	c.1590C>A	c.(1588-1590)ctC>ctA	p.L530L		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	530						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)		TCTTCTTCTTGAGTTGAGCTA	0.438													G|||	103	0.0205671	0.0068	0.0159	5008	,	,		22297	0.0119		0.0278	False		,,,				2504	0.044				p.L530L		Atlas-SNP	.											.	GBP7	57	.	0			c.C1590A						PASS	.	G		38,4366	41.6+/-74.8	0,38,2164	290.0	265.0	273.0		1590	-6.5	0.0	1	dbSNP_132	273	216,8384	90.9+/-153.0	1,214,4085	no	coding-synonymous	GBP7	NM_207398.2		1,252,6249	TT,TG,GG		2.5116,0.8629,1.9532		530/639	89599013	254,12750	2202	4300	6502	SO:0001819	synonymous_variant	388646	exon10			CTTCTTGAGTTGA	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.1590C>A	1.37:g.89599013G>T		Somatic	473	0	0		WXS	Illumina HiSeq	Phase_I	274	272	0.992701	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			G|0.979;T|0.021	0.021	strong		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
GYG1	2992	hgsc.bcm.edu	37	3	148727133	148727133	+	Silent	SNP	G	G	A	rs4938	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:148727133G>A	ENST00000345003.4	+	5	852	c.552G>A	c.(550-552)ccG>ccA	p.P184P	GYG1_ENST00000484197.1_Silent_p.P184P|GYG1_ENST00000483267.1_Intron|GYG1_ENST00000479119.1_3'UTR|GYG1_ENST00000296048.6_Silent_p.P184P	NM_004130.3	NP_004121.2	P46976	GLYG_HUMAN	glycogenin 1	184					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)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogenin glucosyltransferase activity (GO:0008466)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(3)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AACACCTGCCGTTTATTTATA	0.378													G|||	1509	0.301318	0.2844	0.3055	5008	,	,		16635	0.3284		0.335	False		,,,				2504	0.2587				p.P184P		Atlas-SNP	.											.	GYG1	29	.	0			c.G552A						PASS	.	G	,,	1211,3195	422.1+/-339.6	177,857,1169	109.0	115.0	113.0		552,552,552	0.2	1.0	3	dbSNP_52	113	2617,5983	424.5+/-354.7	399,1819,2082	no	coding-synonymous,coding-synonymous,coding-synonymous	GYG1	NM_001184720.1,NM_001184721.1,NM_004130.3	,,	576,2676,3251	AA,AG,GG		30.4302,27.4852,29.4326	,,	184/334,184/280,184/351	148727133	3828,9178	2203	4300	6503	SO:0001819	synonymous_variant	2992	exon5			CCTGCCGTTTATT	AF087942	CCDS3139.1, CCDS54654.1, CCDS54655.1	3q24-q25.1	2013-02-22	2005-11-04	2005-11-04	ENSG00000163754	ENSG00000163754	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4699	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	603942	"""glycogenin"""	GYG		8602861	Standard	NM_004130		Approved		uc003ewn.3	P46976	OTTHUMG00000159533	ENST00000345003.4:c.552G>A	3.37:g.148727133G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	91	34	0.373626	NM_004130	D3DNH0|D3DNH1|D3DNH2|Q6FHZ1|Q9UNV0	Silent	SNP	ENST00000345003.4	37	CCDS3139.1																																																																																			G|0.703;A|0.297	0.297	strong		0.378	GYG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356046.1	NM_004130	
ABCC3	8714	hgsc.bcm.edu	37	17	48761105	48761105	+	Silent	SNP	C	C	T	rs2277624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48761105C>T	ENST00000285238.8	+	27	4022	c.3942C>T	c.(3940-3942)caC>caT	p.H1314H		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1314	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|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)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	TGCATGTGCACGGTGGCGAGA	0.622													c|||	1437	0.286941	0.4032	0.268	5008	,	,		19433	0.2411		0.2227	False		,,,				2504	0.2566				p.H1314H		Atlas-SNP	.											.	ABCC3	138	.	0			c.C3942T						PASS	.			1560,2846	490.4+/-361.8	279,1002,922	128.0	120.0	123.0		3942	-11.9	0.0	17	dbSNP_100	123	1882,6718	335.6+/-321.5	206,1470,2624	no	coding-synonymous	ABCC3	NM_003786.3		485,2472,3546	TT,TC,CC		21.8837,35.4063,26.4647		1314/1528	48761105	3442,9564	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon27			TGTGCACGGTGGC	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.3942C>T	17.37:g.48761105C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			C|0.739;T|0.261	0.261	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
SP140L	93349	hgsc.bcm.edu	37	2	231226371	231226371	+	Missense_Mutation	SNP	A	A	G	rs190007801	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231226371A>G	ENST00000415673.2	+	5	568	c.482A>G	c.(481-483)gAa>gGa	p.E161G	SP140L_ENST00000444636.1_Missense_Mutation_p.E161G|SP140L_ENST00000243810.6_Missense_Mutation_p.E161G|SP140L_ENST00000458341.1_Missense_Mutation_p.E74G|SP140L_ENST00000396563.4_Missense_Mutation_p.E161G	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	161						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						GATCGAAAAGAAAGGGAAGAG	0.403													A|||	2	0.000399361	0.0015	0.0	5008	,	,		23304	0.0		0.0	False		,,,				2504	0.0				p.E161G		Atlas-SNP	.											.	SP140L	68	.	0			c.A482G						PASS	.	A	GLY/GLU	3,4039		0,3,2018	62.0	59.0	60.0		482	0.9	0.0	2		60	0,8456		0,0,4228	yes	missense	SP140L	NM_138402.4	98	0,3,6246	GG,GA,AA		0.0,0.0742,0.024	probably-damaging	161/581	231226371	3,12495	2021	4228	6249	SO:0001583	missense	93349	exon5			GAAAAGAAAGGGA	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.482A>G	2.37:g.231226371A>G	ENSP00000397911:p.Glu161Gly	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	89	4	0.0449438	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	9.805	1.181709	0.21787	7.42E-4	0.0	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563;ENST00000458341	D;T;D;D;T	0.85171	-1.82;-1.45;-1.82;-1.95;0.58	2.13	0.943	0.19531	.	.	.	.	.	D	0.84284	0.5438	L	0.44542	1.39	0.09310	N	1	D;B	0.67145	0.996;0.028	P;B	0.61722	0.893;0.007	T	0.71220	-0.4657	9	0.31617	T	0.26	.	3.9572	0.09395	0.811:0.0:0.189:0.0	.	74;161	Q9H930-3;Q9H930-4	.;.	G	161;161;161;161;74	ENSP00000395195:E161G;ENSP00000397911:E161G;ENSP00000243810:E161G;ENSP00000379811:E161G;ENSP00000395223:E74G	ENSP00000243810:E161G	E	+	2	0	SP140L	230934615	0.001000	0.12720	0.001000	0.08648	0.010000	0.07245	0.491000	0.22419	0.268000	0.21939	0.254000	0.18369	GAA	A|0.999;G|0.001	0.001	strong		0.403	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
SLC2A8	29988	hgsc.bcm.edu	37	9	130164993	130164993	+	Silent	SNP	C	C	T	rs1138739	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:130164993C>T	ENST00000373371.3	+	5	773	c.684C>T	c.(682-684)tcC>tcT	p.S228S	SLC2A8_ENST00000373352.1_Intron|SLC2A8_ENST00000373360.3_Silent_p.S228S	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	228					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						TGTGGGGCTCCGAGCAGGGCT	0.667													C|||	909	0.18151	0.0287	0.3905	5008	,	,		18586	0.1994		0.2495	False		,,,				2504	0.1513				p.S228S		Atlas-SNP	.											.	SLC2A8	27	.	0			c.C684T						PASS	.	C		247,4079		7,233,1923	13.0	13.0	13.0		684	-6.5	0.5	9	dbSNP_86	13	1703,6815		179,1345,2735	no	coding-synonymous	SLC2A8	NM_014580.3		186,1578,4658	TT,TC,CC		19.993,5.7097,15.1822		228/478	130164993	1950,10894	2163	4259	6422	SO:0001819	synonymous_variant	29988	exon5			GGGCTCCGAGCAG	AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"""Solute carriers"""	13812	protein-coding gene	gene with protein product		605245	"""solute carrier family 2 (facilitated glucose transporter) member 8"""			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.684C>T	9.37:g.130164993C>T		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_014580	Q8WUZ9|Q9NSC4	Silent	SNP	ENST00000373371.3	37	CCDS6870.1	468	0.21428571428571427	18	0.036585365853658534	119	0.3287292817679558	134	0.23426573426573427	197	0.2598944591029024	C	8.232	0.804925	0.16467	0.057097	0.19993	ENSG00000136856	ENST00000419132	.	.	.	4.85	-6.51	0.01878	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999292092	.	.	.	.	.	.	T	0.25433	-1.0132	3	.	.	.	.	9.1661	0.37052	0.1166:0.2684:0.0:0.615	rs1138739;rs3202779;rs3802365;rs17425222	.	.	.	L	138	.	.	P	+	2	0	SLC2A8	129204814	0.000000	0.05858	0.475000	0.27278	0.902000	0.53008	-6.055000	0.00083	-1.115000	0.02973	-0.471000	0.05019	CCG	C|0.827;T|0.173	0.173	strong		0.667	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595756	140595756	+	Silent	SNP	C	C	T	rs17844617	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140595756C>T	ENST00000341948.4	+	1	2248	c.2061C>T	c.(2059-2061)acC>acT	p.T687T		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	687					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)			ACTTGCTCACCGTCTACCTGG	0.687													c|||	585	0.116813	0.1233	0.1816	5008	,	,		16534	0.0397		0.159	False		,,,				2504	0.0982				p.T687T		Atlas-SNP	.											.	PCDHB13	142	.	0			c.C2061T						PASS	.	T		510,3862		33,444,1709	80.0	86.0	84.0		2061	-7.0	0.0	5	dbSNP_123	84	1400,7134		121,1158,2988	no	coding-synonymous	PCDHB13	NM_018933.2		154,1602,4697	TT,TC,CC		16.405,11.6651,14.7993		687/799	140595756	1910,10996	2186	4267	6453	SO:0001819	synonymous_variant	56123	exon1			GCTCACCGTCTAC	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.2061C>T	5.37:g.140595756C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			C|0.855;T|0.145	0.145	strong		0.687	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
STPG1	90529	hgsc.bcm.edu	37	1	24718075	24718075	+	Silent	SNP	T	T	C	rs2294520	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:24718075T>C	ENST00000374409.1	-	3	419	c.165A>G	c.(163-165)caA>caG	p.Q55Q	STPG1_ENST00000337248.4_Silent_p.Q55Q|STPG1_ENST00000003583.8_Intron|STPG1_ENST00000440416.1_Intron|STPG1_ENST00000468303.1_5'UTR	NM_001199012.1	NP_001185941.1	Q5TH74	STPG1_HUMAN	sperm-tail PG-rich repeat containing 1	55					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											ATCTCTTGGCTTGACTATTGA	0.413											OREG0013240	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1411	0.281749	0.0961	0.379	5008	,	,		18074	0.4593		0.2753	False		,,,				2504	0.2873				p.Q55Q		Atlas-SNP	.											.	.	.	.	0			c.A165G						PASS	.																																			SO:0001819	synonymous_variant	90529	exon3			CTTGGCTTGACTA	BC047705	CCDS253.1, CCDS55581.1	1p36.11	2012-10-31	2012-07-30	2012-07-30	ENSG00000001460	ENSG00000001460			28070	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 2"""	615826	"""chromosome 1 open reading frame 201"""	C1orf201		23028632	Standard	NM_001199012		Approved	FLJ33340, MAPO2	uc001bjc.3	Q5TH74	OTTHUMG00000003297	ENST00000374409.1:c.165A>G	1.37:g.24718075T>C		Somatic	77	0	0	773	WXS	Illumina HiSeq	Phase_I	48	34	0.708333	NM_001199012	Q49AP0|Q6P3R4|Q86VU9|Q8WVQ3	Silent	SNP	ENST00000374409.1	37	CCDS55581.1	642	0.29395604395604397	49	0.09959349593495935	125	0.3453038674033149	256	0.44755244755244755	212	0.2796833773087071	T	9.576	1.122403	0.20877	.	.	ENSG00000001460	ENST00000435187	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.50189	-0.8857	3	.	.	.	0.6438	11.8884	0.52615	0.0:0.0:0.0:1.0	rs2294520;rs11553729;rs59582005;rs2294520	.	.	.	R	32	.	.	K	-	2	0	C1orf201	24590662	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.953000	0.56699	2.130000	0.65690	0.533000	0.62120	AAG	T|0.728;C|0.272	0.272	strong		0.413	STPG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009172.1	NM_178122	
APPL1	26060	hgsc.bcm.edu	37	3	57269608	57269608	+	Silent	SNP	A	A	G	rs11544592	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:57269608A>G	ENST00000288266.3	+	2	216	c.69A>G	c.(67-69)ctA>ctG	p.L23L		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	23	Required for RAB5A binding.				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)		GGTCTTTACTAGGTGTATTTG	0.318													A|||	28	0.00559105	0.0	0.0086	5008	,	,		19244	0.0		0.0179	False		,,,				2504	0.0041				p.L23L		Atlas-SNP	.											.	APPL1	59	.	0			c.A69G						PASS	.	A		12,4394	17.9+/-39.9	0,12,2191	112.0	108.0	110.0		69	2.1	1.0	3	dbSNP_123	110	139,8461	69.0+/-131.5	2,135,4163	no	coding-synonymous	APPL1	NM_012096.2		2,147,6354	GG,GA,AA		1.6163,0.2724,1.161		23/710	57269608	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	26060	exon2			TTTACTAGGTGTA	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.69A>G	3.37:g.57269608A>G		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	243	121	0.497942	NM_012096	Q9P2B9	Silent	SNP	ENST00000288266.3	37	CCDS2882.1																																																																																			A|0.987;G|0.013	0.013	strong		0.318	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	
PHF2	5253	hgsc.bcm.edu	37	9	96407983	96407983	+	Silent	SNP	C	C	T	rs9695734	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:96407983C>T	ENST00000359246.4	+	4	739	c.372C>T	c.(370-372)acC>acT	p.T124T	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	124					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		ACGGCTTCACCGAGCCCATCC	0.622													C|||	530	0.105831	0.1241	0.0764	5008	,	,		20102	0.0506		0.161	False		,,,				2504	0.1022				p.T124T		Atlas-SNP	.											PHF2,NS,carcinoma,0,1	PHF2	113	1	0			c.C372T						PASS	.	C		536,3870	244.3+/-253.7	28,480,1695	81.0	75.0	77.0		372	-9.2	0.2	9	dbSNP_119	77	1498,7102	284.7+/-296.8	119,1260,2921	yes	coding-synonymous	PHF2	NM_005392.3		147,1740,4616	TT,TC,CC		17.4186,12.1652,15.6389		124/1097	96407983	2034,10972	2203	4300	6503	SO:0001819	synonymous_variant	5253	exon4			CTTCACCGAGCCC	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.372C>T	9.37:g.96407983C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			C|0.853;T|0.147	0.147	strong		0.622	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
PCDHA4	56144	hgsc.bcm.edu	37	5	140187048	140187048	+	Silent	SNP	G	G	C	rs3822349	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140187048G>C	ENST00000530339.1	+	1	276	c.276G>C	c.(274-276)cgG>cgC	p.R92R	PCDHA4_ENST00000356878.4_Silent_p.R92R|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.R92R	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	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	77	23	0.298701	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	
ZNF845	91664	hgsc.bcm.edu	37	19	53856730	53856730	+	Silent	SNP	G	G	A	rs201351032	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53856730G>A	ENST00000595091.1	+	5	3021	c.2802G>A	c.(2800-2802)aaG>aaA	p.K934K	ZNF845_ENST00000458035.1_Silent_p.K934K			Q96IR2	ZN845_HUMAN	zinc finger protein 845	934					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.K934K(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TAATTCATAAGACAATTCATA	0.368													.|||	271	0.0541134	0.0507	0.0576	5008	,	,		22260	0.0456		0.0924	False		,,,				2504	0.0256				p.K934K		Atlas-SNP	.											ZNF845,NS,carcinoma,0,5	ZNF845	101	5	3	Substitution - coding silent(3)	kidney(3)	c.G2802A						scavenged	.																																			SO:0001819	synonymous_variant	91664	exon4			TCATAAGACAATT	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.2802G>A	19.37:g.53856730G>A		Somatic	182	1	0.00549451		WXS	Illumina HiSeq	Phase_I	187	14	0.0748663	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			.	.	weak		0.368	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
BIRC3	330	hgsc.bcm.edu	37	11	102195984	102195984	+	Silent	SNP	T	T	A	rs147757750		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102195984T>A	ENST00000263464.3	+	2	3494	c.744T>A	c.(742-744)tcT>tcA	p.S248S	BIRC3_ENST00000532808.1_Silent_p.S248S	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	248					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|spermatogenesis (GO:0007283)|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)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		ACACAGTTTCTAATCTGAGCA	0.423			T	MALT1	MALT																																p.S248S		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	BIRC3,colon,carcinoma,+2,2	BIRC3	56	2	0			c.T744A						PASS	.						75.0	76.0	76.0					11																	102195984		2203	4299	6502	SO:0001819	synonymous_variant	330	exon2			AGTTTCTAATCTG	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	591	protein-coding gene	gene with protein product	"""apoptosis inhibitor 2"", ""TNFR2-TRAF signaling complex protein"", ""mammalian IAP homolog C"", ""inhibitor of apoptosis protein 1"""	601721	"""baculoviral IAP repeat-containing 3"""	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.744T>A	11.37:g.102195984T>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	106	20	0.188679	NM_001165	Q16628|Q9HC27|Q9UP46	Silent	SNP	ENST00000263464.3	37	CCDS8315.1																																																																																			T|1.000;C|0.000	.	alt		0.423	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165	
NCKIPSD	51517	hgsc.bcm.edu	37	3	48717276	48717276	+	Silent	SNP	G	G	A	rs562394435		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48717276G>A	ENST00000294129.2	-	7	1427	c.1308C>T	c.(1306-1308)aaC>aaT	p.N436N	NCKIPSD_ENST00000416649.2_Silent_p.N429N|NCKIPSD_ENST00000341520.4_Silent_p.N436N	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	436					cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ACTCGAACTCGTTTCTCTTGC	0.522													G|||	1	0.000199681	0.0	0.0	5008	,	,		24484	0.0		0.0	False		,,,				2504	0.001				p.N436N		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.C1308T						PASS	.						138.0	123.0	128.0					3																	48717276		2203	4300	6503	SO:0001819	synonymous_variant	51517	exon7			GAACTCGTTTCTC	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"""dia interacting protein"", ""diaphanous protein interacting protein"", ""SH3 protein interacting with Nck, 90 kDa"""	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.1308C>T	3.37:g.48717276G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	123	67	0.544715	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Silent	SNP	ENST00000294129.2	37	CCDS2776.1	.	.	.	.	.	.	.	.	.	.	G	5.849	0.340768	0.11069	.	.	ENSG00000213672	ENST00000415281	.	.	.	5.2	-3.89	0.04193	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2642	0.54668	0.5461:0.0:0.4539:0.0	.	.	.	.	X	172	.	.	R	-	1	2	NCKIPSD	48692280	0.845000	0.29573	0.068000	0.19968	0.913000	0.54294	-0.007000	0.12810	-1.032000	0.03304	-1.326000	0.01283	CGA	.	.	none		0.522	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553664	140553664	+	Silent	SNP	G	G	A	rs3733695|rs386692905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140553664G>A	ENST00000231137.3	+	1	1422	c.1248G>A	c.(1246-1248)gaG>gaA	p.E416E		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	416	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(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)			GGAACACTGAGTACAACATCA	0.522													G|||	758	0.151358	0.2572	0.1902	5008	,	,		20573	0.0407		0.1531	False		,,,				2504	0.093				p.E416E		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G1248A						PASS	.	G		1036,3370	383.7+/-325.0	115,806,1282	138.0	125.0	129.0		1248	0.0	1.0	5	dbSNP_107	129	1429,7171	275.0+/-291.5	126,1177,2997	no	coding-synonymous	PCDHB7	NM_018940.2		241,1983,4279	AA,AG,GG		16.6163,23.5134,18.9528		416/794	140553664	2465,10541	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			CACTGAGTACAAC	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.1248G>A	5.37:g.140553664G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	209	103	0.492823	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			G|0.819;A|0.181	0.181	strong		0.522	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
BCAM	4059	hgsc.bcm.edu	37	19	45315445	45315445	+	Missense_Mutation	SNP	G	G	A	rs28399653	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45315445G>A	ENST00000270233.6	+	3	252	c.230G>A	c.(229-231)cGc>cAc	p.R77H	BCAM_ENST00000589651.1_Missense_Mutation_p.R77H	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	77	Ig-like V-type 1.		R -> H (defines the Lu(a) antigen; dbSNP:rs28399653). {ECO:0000269|Ref.2}.		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)				GCTCGCCCCCGCCTAGCCTCG	0.692													G|||	84	0.0167732	0.0295	0.0216	5008	,	,		13249	0.0		0.0288	False		,,,				2504	0.001				p.R77H		Atlas-SNP	.											.	BCAM	53	.	0			c.G230A	GRCh37	CM973375	BCAM	M	rs28399653	PASS	.	G	HIS/ARG,HIS/ARG	124,4242		0,124,2059	11.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	230,230	-0.1	1.0	19	dbSNP_125	13	277,8273		7,263,4005	yes	missense,missense	BCAM	NM_001013257.1,NM_005581.3	29,29	7,387,6064	AA,AG,GG		3.2398,2.8401,3.1047	probably-damaging,probably-damaging	77/589,77/629	45315445	401,12515	2183	4275	6458	SO:0001583	missense	4059	exon3			GCCCCCGCCTAGC	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.230G>A	19.37:g.45315445G>A	ENSP00000270233:p.Arg77His	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	50	34	0.68	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	40	0.018315018315018316	8	0.016260162601626018	10	0.027624309392265192	0	0.0	22	0.029023746701846966	.	15.79	2.936247	0.52972	0.028401	0.032398	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.27890	1.64;1.64	3.58	-0.142	0.13448	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.06005	0.0156	L	0.29908	0.895	0.34224	D	0.675761	B	0.22346	0.068	B	0.12156	0.007	T	0.14839	-1.0458	9	0.35671	T	0.21	-11.2605	5.2337	0.15436	0.0:0.1786:0.3627:0.4587	rs28399653	77	P50895	BCAM_HUMAN	H	77	ENSP00000270233:R77H;ENSP00000375817:R77H	ENSP00000270233:R77H	R	+	2	0	BCAM	50007285	0.000000	0.05858	0.993000	0.49108	0.406000	0.30931	-1.971000	0.01503	0.232000	0.21100	0.313000	0.20887	CGC	G|0.977;A|0.023	0.023	strong		0.692	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
KIAA1244	57221	hgsc.bcm.edu	37	6	138645228	138645228	+	Silent	SNP	G	G	A	rs3734301	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:138645228G>A	ENST00000251691.4	+	31	5104	c.4938G>A	c.(4936-4938)gcG>gcA	p.A1646A		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)		TGCGAGTGGCGGCCCCGTCCT	0.642													G|||	1143	0.228235	0.6142	0.1484	5008	,	,		18962	0.1151		0.0626	False		,,,				2504	0.0501				p.A1646A		Atlas-SNP	.											KIAA1244,NS,carcinoma,+1,1	KIAA1244	236	1	0			c.G4938A						scavenged	.	G		2271,2135	557.4+/-379.7	599,1073,531	42.0	48.0	46.0		4938	-10.9	0.2	6	dbSNP_107	46	535,8065	143.6+/-199.6	18,499,3783	no	coding-synonymous	KIAA1244	NM_020340.4		617,1572,4314	AA,AG,GG		6.2209,48.4567,21.5747		1646/2178	138645228	2806,10200	2203	4300	6503	SO:0001819	synonymous_variant	57221	exon31			AGTGGCGGCCCCG	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.4938G>A	6.37:g.138645228G>A		Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																			G|0.789;A|0.211	0.211	strong		0.642	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
SEZ6L	23544	hgsc.bcm.edu	37	22	26692986	26692986	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:26692986T>C	ENST00000248933.6	+	4	1197	c.1102T>C	c.(1102-1104)Tcc>Ccc	p.S368P	SEZ6L_ENST00000529632.2_Missense_Mutation_p.S368P|SEZ6L_ENST00000403121.1_Missense_Mutation_p.S141P|SEZ6L_ENST00000343706.4_Missense_Mutation_p.S368P|SEZ6L_ENST00000360929.3_Missense_Mutation_p.S368P|SEZ6L_ENST00000402979.1_Missense_Mutation_p.S141P|SEZ6L_ENST00000404234.3_Missense_Mutation_p.S368P			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	368	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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						CAACACCATCTCCGTCTACTT	0.622																																					p.S368P		Atlas-SNP	.											SEZ6L,scalp,malignant_melanoma,-1,1	SEZ6L	174	1	0			c.T1102C						scavenged	.						61.0	51.0	54.0					22																	26692986		2203	4300	6503	SO:0001583	missense	23544	exon4			ACCATCTCCGTCT	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.1102T>C	22.37:g.26692986T>C	ENSP00000248933:p.Ser368Pro	Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	148	2	0.0135135	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.274230	0.80580	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21;0.21;0.21	5.1	5.1	0.69264	CUB (5);	0.000000	0.52532	D	0.000073	T	0.71837	0.3387	M	0.64997	1.995	0.80722	D	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	0.91635	0.998;0.998;0.999;0.999;0.998;0.999;0.998	T	0.70824	-0.4767	10	0.34782	T	0.22	.	14.0506	0.64734	0.0:0.0:0.0:1.0	.	368;368;141;368;368;368;368	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	P	368;368;368;368;368;141;141	ENSP00000384772:S368P;ENSP00000437037:S368P;ENSP00000354185:S368P;ENSP00000248933:S368P;ENSP00000342661:S368P;ENSP00000384838:S141P;ENSP00000384733:S141P	ENSP00000248933:S368P	S	+	1	0	SEZ6L	25022986	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.748000	0.68697	1.914000	0.55421	0.533000	0.62120	TCC	.	.	none		0.622	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
OSCP1	127700	hgsc.bcm.edu	37	1	36886117	36886117	+	Missense_Mutation	SNP	C	C	T	rs2275477	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:36886117C>T	ENST00000356637.5	-	9	1012	c.949G>A	c.(949-951)Gga>Aga	p.G317R	OSCP1_ENST00000433045.2_Missense_Mutation_p.G262R|OSCP1_ENST00000495222.1_Intron|OSCP1_ENST00000315643.9_Missense_Mutation_p.G317R|OSCP1_ENST00000235532.5_Missense_Mutation_p.G307R|SNORA63_ENST00000364578.1_RNA			Q8WVF1	OSCP1_HUMAN	organic solute carrier partner 1	317				G -> R (in Ref. 2; BAE16984). {ECO:0000305}.	transport (GO:0006810)	plasma membrane (GO:0005886)		p.G317R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	22						AACCGGAATCCGGGCTCAGGG	0.448											OREG0013368	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	1267	0.252995	0.32	0.1542	5008	,	,		17032	0.2599		0.2068	False		,,,				2504	0.273				p.G307R		Atlas-SNP	.											OSCP1,NS,carcinoma,0,1	OSCP1	48	1	1	Substitution - Missense(1)	stomach(1)	c.G919A						scavenged	.		ARG/GLY	1378,3028	454.4+/-350.6	210,958,1035	231.0	242.0	238.0		919	5.2	1.0	1	dbSNP_100	238	1849,6751	331.5+/-319.7	207,1435,2658	yes	missense	OSCP1	NM_145047.4	125	417,2393,3693	TT,TC,CC		21.5,31.2755,24.8116	benign	307/380	36886117	3227,9779	2203	4300	6503	SO:0001583	missense	127700	exon8			GGAATCCGGGCTC		CCDS409.1, CCDS410.1, CCDS409.2	1p34.3	2009-07-06	2009-07-06	2009-07-06	ENSG00000116885	ENSG00000116885			29971	protein-coding gene	gene with protein product	"""oxidored nitro domain containing protein"""	608854	"""chromosome 1 open reading frame 102"""	C1orf102		12477932	Standard	NM_145047		Approved	NOR1	uc001caq.3	Q8WVF1	OTTHUMG00000008139	ENST00000356637.5:c.949G>A	1.37:g.36886117C>T	ENSP00000349052:p.Gly317Arg	Somatic	140	1	0.00714286	866	WXS	Illumina HiSeq	Phase_I	97	68	0.701031	NM_145047	A6NHM5|A6NHS9|A6NIN9|Q4AEJ0|Q8N7G2|Q8TDF1	Missense_Mutation	SNP	ENST00000356637.5	37		503	0.2303113553113553	144	0.2926829268292683	62	0.1712707182320442	144	0.2517482517482518	153	0.20184696569920843	c	16.68	3.191378	0.58017	0.312755	0.215	ENSG00000116885	ENST00000235532;ENST00000356637;ENST00000433045;ENST00000315643	T;T;T;T	0.29917	1.96;1.97;1.55;1.96	6.07	5.17	0.71159	.	0.225932	0.46442	N	0.000284	T	0.00012	0.0000	L	0.57536	1.79	0.25595	P	0.9866586	B;B	0.22851	0.053;0.076	B;B	0.18871	0.023;0.01	T	0.36383	-0.9750	9	0.20046	T	0.44	.	10.6431	0.45604	0.0:0.8556:0.0:0.1444	rs2275477;rs52803946;rs57535488;rs2275477	307;317	Q8WVF1-3;Q8WVF1	.;OSCP1_HUMAN	R	307;317;262;317	ENSP00000235532:G307R;ENSP00000349052:G317R;ENSP00000390820:G262R;ENSP00000314541:G317R	ENSP00000235532:G307R	G	-	1	0	OSCP1	36658704	0.998000	0.40836	1.000000	0.80357	0.964000	0.63967	3.762000	0.55250	1.593000	0.50029	0.586000	0.80456	GGA	C|0.755;T|0.245	0.245	strong		0.448	OSCP1-010	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000389759.1	NM_145047	
KLHL33	123103	hgsc.bcm.edu	37	14	20897065	20897065	+	Silent	SNP	G	G	A	rs368179614		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20897065G>A	ENST00000344581.4	-	4	1767	c.1545C>T	c.(1543-1545)ccC>ccT	p.P515P		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	515												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)		GCTGCACAGCGGGCAGTGTCA	0.582																																					p.P515P		Atlas-SNP	.											.	KLHL33	37	.	0			c.C1545T						PASS	.	G		0,1384		0,0,692	73.0	70.0	71.0		1545	-5.4	0.0	14		71	1,3181		0,1,1590	no	coding-synonymous	KLHL33	NM_001109997.2		0,1,2282	AA,AG,GG		0.0314,0.0,0.0219		515/534	20897065	1,4565	692	1591	2283	SO:0001819	synonymous_variant	123103	exon4			CACAGCGGGCAGT		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.1545C>T	14.37:g.20897065G>A		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	302	123	0.407285	NM_001109997		Silent	SNP	ENST00000344581.4	37	CCDS53882.1																																																																																			.	.	weak		0.582	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
ACOT12	134526	hgsc.bcm.edu	37	5	80631642	80631642	+	Missense_Mutation	SNP	C	C	T	rs10371	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:80631642C>T	ENST00000307624.3	-	12	1235	c.1207G>A	c.(1207-1209)Gct>Act	p.A403T	ACOT12_ENST00000508234.1_5'UTR	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	403	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.		A -> T (in dbSNP:rs10371).		acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		AGACGATAAGCCAAATGTGCT	0.343													C|||	602	0.120208	0.1815	0.134	5008	,	,		17733	0.002		0.159	False		,,,				2504	0.1094				p.A403T		Atlas-SNP	.											.	ACOT12	57	.	0			c.G1207A						PASS	.	C	THR/ALA	849,3557	333.9+/-303.2	73,703,1427	83.0	92.0	89.0		1207	4.3	0.2	5	dbSNP_52	89	1345,7255	262.5+/-284.5	100,1145,3055	yes	missense	ACOT12	NM_130767.2	58	173,1848,4482	TT,TC,CC		15.6395,19.2692,16.8691	benign	403/556	80631642	2194,10812	2203	4300	6503	SO:0001583	missense	134526	exon12			GATAAGCCAAATG	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	24436	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 15"""	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.1207G>A	5.37:g.80631642C>T	ENSP00000303246:p.Ala403Thr	Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	204	98	0.480392	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	253	0.11584249084249085	83	0.16869918699186992	51	0.1408839779005525	2	0.0034965034965034965	117	0.15435356200527706	C	7.282	0.609265	0.14066	0.192692	0.156395	ENSG00000172497	ENST00000307624	T	0.31247	1.5	5.24	4.34	0.51931	Lipid-binding START (2);START-like domain (1);	0.256266	0.37437	N	0.002099	T	0.00039	0.0001	N	0.25890	0.77	0.27235	P	0.9592961	B	0.21071	0.051	B	0.27170	0.077	T	0.17561	-1.0365	9	0.34782	T	0.22	5.4069	11.1453	0.48426	0.0:0.9049:0.0:0.0951	rs10371;rs1132753;rs3193840;rs52811470;rs56771708;rs10371	403	Q8WYK0	ACO12_HUMAN	T	403	ENSP00000303246:A403T	ENSP00000303246:A403T	A	-	1	0	ACOT12	80667398	0.913000	0.31002	0.208000	0.23602	0.034000	0.12701	1.926000	0.40084	1.275000	0.44379	0.561000	0.74099	GCT	C|0.852;T|0.148	0.148	strong		0.343	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767	
TLN1	7094	hgsc.bcm.edu	37	9	35705759	35705759	+	Silent	SNP	G	G	A	rs11541908	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:35705759G>A	ENST00000314888.9	-	42	5954	c.5601C>T	c.(5599-5601)acC>acT	p.T1867T	TLN1_ENST00000464379.1_Intron|TLN1_ENST00000540444.1_Silent_p.T1801T	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1867	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCTCCTGAACGGTCACTGCAA	0.522													G|||	847	0.169129	0.0197	0.2305	5008	,	,		21120	0.253		0.2515	False		,,,				2504	0.1564				p.T1867T		Atlas-SNP	.											.	TLN1	185	.	0			c.C5601T						PASS	.	G		265,4141	150.3+/-184.3	14,237,1952	105.0	104.0	104.0		5601	-4.3	1.0	9	dbSNP_120	104	2295,6305	386.7+/-342.0	293,1709,2298	no	coding-synonymous	TLN1	NM_006289.3		307,1946,4250	AA,AG,GG		26.686,6.0145,19.6832		1867/2542	35705759	2560,10446	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon42			CTGAACGGTCACT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.5601C>T	9.37:g.35705759G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	39	0.619048	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			G|0.806;A|0.194	0.194	strong		0.522	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
OR4K13	390433	hgsc.bcm.edu	37	14	20502044	20502044	+	Missense_Mutation	SNP	G	G	T	rs17277025	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:20502044G>T	ENST00000315693.2	-	1	875	c.874C>A	c.(874-876)Caa>Aaa	p.Q292K	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	292			Q -> K (in dbSNP:rs17277025).			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)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TTTACCTCTTGATTTCTTAAT	0.323													G|||	438	0.0874601	0.062	0.147	5008	,	,		17248	0.0397		0.0716	False		,,,				2504	0.1452				p.Q292K		Atlas-SNP	.											.	OR4K13	68	.	0			c.C874A						PASS	.	G	LYS/GLN	234,4164		3,228,1968	17.0	19.0	18.0		874	0.5	0.0	14	dbSNP_123	18	672,7908		27,618,3645	yes	missense	OR4K13	NM_001004714.1	53	30,846,5613	TT,TG,GG		7.8322,5.3206,6.981	benign	292/305	20502044	906,12072	2199	4290	6489	SO:0001583	missense	390433	exon1			CCTCTTGATTTCT		CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"""GPCR / Class A : Olfactory receptors"""	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.874C>A	14.37:g.20502044G>T	ENSP00000319322:p.Gln292Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_001004714	Q6IF13	Missense_Mutation	SNP	ENST00000315693.2	37	CCDS32028.1	151	0.06913919413919414	27	0.054878048780487805	45	0.12430939226519337	19	0.033216783216783216	60	0.079155672823219	.	0	-2.770336	0.00081	0.053206	0.078322	ENSG00000176253	ENST00000315693	T	0.30182	1.54	3.61	0.525	0.17072	.	0.660788	0.12310	N	0.480320	T	0.00109	0.0003	N	0.01168	-0.975	0.44477	P	0.002585999999999977	B	0.06786	0.001	B	0.11329	0.006	T	0.37776	-0.9691	9	0.02654	T	1	.	7.5191	0.27618	0.0:0.1486:0.3966:0.4548	rs17277025;rs17277025	292	Q8NH42	OR4KD_HUMAN	K	292	ENSP00000319322:Q292K	ENSP00000319322:Q292K	Q	-	1	0	OR4K13	19571884	0.971000	0.33674	0.004000	0.12327	0.061000	0.15899	0.646000	0.24797	-0.097000	0.12307	0.514000	0.50259	CAA	G|0.933;T|0.067	0.067	strong		0.323	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1		
CHCHD6	84303	hgsc.bcm.edu	37	3	126451937	126451937	+	Missense_Mutation	SNP	G	G	T	rs2272487	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126451937G>T	ENST00000290913.3	+	4	376	c.283G>T	c.(283-285)Gct>Tct	p.A95S	CHCHD6_ENST00000508789.1_Missense_Mutation_p.A95S	NM_032343.2	NP_115719.1	Q9BRQ6	MIC25_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 6	95			A -> S (in dbSNP:rs2272487).		cellular response to DNA damage stimulus (GO:0006974)|cristae formation (GO:0042407)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(3)|lung(3)	8						ACAGGAGCATGCTGCTATCCA	0.547													G|||	1426	0.284744	0.2511	0.2565	5008	,	,		22414	0.3522		0.165	False		,,,				2504	0.4039				p.A95S		Atlas-SNP	.											.	CHCHD6	18	.	0			c.G283T						PASS	.	G	SER/ALA	1087,3319	393.1+/-328.7	123,841,1239	81.0	70.0	74.0		283	2.6	0.7	3	dbSNP_100	74	1409,7191	272.0+/-289.9	127,1155,3018	yes	missense	CHCHD6	NM_032343.1	99	250,1996,4257	TT,TG,GG		16.3837,24.6709,19.1911	benign	95/236	126451937	2496,10510	2203	4300	6503	SO:0001583	missense	84303	exon4			GAGCATGCTGCTA	BC006123	CCDS3041.1	3q21.3	2012-04-17			ENSG00000159685	ENSG00000159685		"""Coiled-coil-helix-coiled-coil-helix domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28184	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 23"", ""coiled-coil-helix cristae morphology 1"""	615634				17624330, 22228767	Standard	NM_032343		Approved	MGC13016, PPP1R23, CHCM1	uc003ejf.2	Q9BRQ6	OTTHUMG00000159601	ENST00000290913.3:c.283G>T	3.37:g.126451937G>T	ENSP00000290913:p.Ala95Ser	Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	229	124	0.541485	NM_032343	D6R9U0|D6RIB4|H8Y0Y7	Missense_Mutation	SNP	ENST00000290913.3	37	CCDS3041.1	507|507	0.23214285714285715|0.23214285714285715	128|128	0.2601626016260163|0.2601626016260163	96|96	0.26519337016574585|0.26519337016574585	168|168	0.2937062937062937|0.2937062937062937	115|115	0.1517150395778364|0.1517150395778364	G|G	7.333|7.333	0.619243|0.619243	0.14129|0.14129	0.246709|0.246709	0.163837|0.163837	ENSG00000159685|ENSG00000159685	ENST00000290913;ENST00000508789|ENST00000513253	T;T|.	0.50813|.	0.73;0.73|.	4.48|4.48	2.64|2.64	0.31445|0.31445	.|.	0.252628|.	0.38217|.	N|.	0.001762|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.57536|0.57536	1.79|1.79	0.34928|0.34928	P|P	0.250926|0.250926	D;P|.	0.63046|.	0.992;0.684|.	P;P|.	0.59012|.	0.85;0.553|.	T|T	0.13629|0.13629	-1.0502|-1.0502	9|4	0.38643|.	T|.	0.18|.	-4.0401|-4.0401	7.1596|7.1596	0.25657|0.25657	0.0:0.1885:0.6163:0.1952|0.0:0.1885:0.6163:0.1952	rs2272487;rs11544130;rs52805448;rs59133559;rs2272487|rs2272487;rs11544130;rs52805448;rs59133559;rs2272487	95;95|.	D6R9U0;Q9BRQ6|.	.;CHCH6_HUMAN|.	S|I	95|28	ENSP00000290913:A95S;ENSP00000422912:A95S|.	ENSP00000290913:A95S|.	A|M	+|+	1|3	0|0	CHCHD6|CHCHD6	127934627|127934627	0.983000|0.983000	0.35010|0.35010	0.656000|0.656000	0.29637|0.29637	0.053000|0.053000	0.15095|0.15095	1.839000|1.839000	0.39220|0.39220	0.496000|0.496000	0.27904|0.27904	0.591000|0.591000	0.81541|0.81541	GCT|ATG	G|0.788;T|0.212	0.212	strong		0.547	CHCHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356432.1	NM_032343	
FLG	2312	hgsc.bcm.edu	37	1	152280614	152280614	+	Missense_Mutation	SNP	C	C	G	rs3120645	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280614C>G	ENST00000368799.1	-	3	6783	c.6748G>C	c.(6748-6750)Gag>Cag	p.E2250Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2250	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGTGTCCCTCACTGTCACTG	0.592									Ichthyosis																												p.E2250Q		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,+2,1	FLG	900	1	0			c.G6748C						scavenged	.						203.0	203.0	203.0					1																	152280614		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTCCCTCACTGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6748G>C	1.37:g.152280614C>G	ENSP00000357789:p.Glu2250Gln	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	475	13	0.0273684	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	c	6.497	0.459945	0.12342	.	.	ENSG00000143631	ENST00000368799	T	0.08008	3.14	3.75	0.494	0.16884	.	.	.	.	.	T	0.01454	0.0047	N	0.13043	0.29	0.09310	N	1	P	0.43542	0.81	B	0.39503	0.301	T	0.47100	-0.9143	9	0.30078	T	0.28	.	6.151	0.20313	0.1996:0.4103:0.3901:0.0	.	2250	P20930	FILA_HUMAN	Q	2250	ENSP00000357789:E2250Q	ENSP00000357789:E2250Q	E	-	1	0	FLG	150547238	0.000000	0.05858	0.004000	0.12327	0.027000	0.11550	-0.121000	0.10643	0.707000	0.31934	-0.447000	0.05616	GAG	C|0.996;G|0.003;T|0.001	0.003	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
OR3A2	4995	hgsc.bcm.edu	37	17	3181384	3181384	+	Silent	SNP	C	C	T	rs769434	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:3181384C>T	ENST00000408891.2	-	1	884	c.846G>A	c.(844-846)ggG>ggA	p.G282G	RP11-64J4.2_ENST00000573491.1_RNA	NM_002551.3	NP_002542.3	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A, member 2	282					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)			ovary(1)	1						AAACTCCAACCCCTTTATCCT	0.468													C|||	891	0.177915	0.0144	0.3112	5008	,	,		21872	0.25		0.1561	False		,,,				2504	0.2526				p.G282G	GBM(166;478 2018 3875 5042 31983)|Esophageal Squamous(77;407 1232 1405 14297 15272)	Atlas-SNP	.											.	OR3A2	36	.	0			c.G846A						PASS	.	C		167,4131		2,163,1984	73.0	76.0	75.0		846	-2.8	1.0	17	dbSNP_86	75	1217,7339		99,1019,3160	no	coding-synonymous	OR3A2	NM_002551.3		101,1182,5144	TT,TC,CC		14.2239,3.8855,10.7671		282/322	3181384	1384,11470	2149	4278	6427	SO:0001819	synonymous_variant	4995	exon1			TCCAACCCCTTTA	U04713	CCDS42233.1	17p13.3	2012-08-09				ENSG00000221882		"""GPCR / Class A : Olfactory receptors"""	8283	protein-coding gene	gene with protein product						8921386, 10673334	Standard	NM_002551		Approved	OLFRA04, OR228, OR17-228	uc002fvg.3	P47893		ENST00000408891.2:c.846G>A	17.37:g.3181384C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_002551	Q6IFM3|Q9P1Q3	Silent	SNP	ENST00000408891.2	37	CCDS42233.1																																																																																			C|0.838;T|0.162	0.162	strong		0.468	OR3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438370.1		
CEP162	22832	hgsc.bcm.edu	37	6	84881429	84881429	+	Silent	SNP	T	T	C	rs41271603	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:84881429T>C	ENST00000403245.3	-	17	2289	c.2175A>G	c.(2173-2175)gaA>gaG	p.E725E	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Silent_p.E649E	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TATATAATCGTTCATTTTCCT	0.274													T|||	245	0.0489217	0.0121	0.0317	5008	,	,		13780	0.0258		0.0805	False		,,,				2504	0.1022				p.E725E		Atlas-SNP	.											KIAA1009,NS,carcinoma,-2,1	KIAA1009	119	1	0			c.A2175G						PASS	.	T		78,4314		1,76,2119	76.0	71.0	72.0		2175	3.0	0.9	6	dbSNP_127	72	458,8100		9,440,3830	no	coding-synonymous	KIAA1009	NM_014895.2		10,516,5949	CC,CT,TT		5.3517,1.776,4.139		725/1404	84881429	536,12414	2196	4279	6475	SO:0001819	synonymous_variant	22832	exon17			TAATCGTTCATTT																												ENST00000403245.3:c.2175A>G	6.37:g.84881429T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	144	66	0.458333	NM_014895		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																			T|0.957;C|0.043	0.043	strong		0.274	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
PCIF1	63935	hgsc.bcm.edu	37	20	44575932	44575932	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44575932T>C	ENST00000372409.3	+	16	2102	c.1738T>C	c.(1738-1740)Tcc>Ccc	p.S580P	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	580					negative regulation of phosphatase activity (GO:0010923)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	20						GGAGCCCCTGTCCTTCATCGT	0.622																																					p.S580P		Atlas-SNP	.											.	PCIF1	51	.	0			c.T1738C						PASS	.						79.0	81.0	80.0					20																	44575932		2203	4300	6503	SO:0001583	missense	63935	exon16			CCCCTGTCCTTCA	AB050014	CCDS13388.1	20q13.12	2014-06-13	2008-04-29	2008-04-29	ENSG00000100982	ENSG00000100982			16200	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 121"""		"""chromosome 20 open reading frame 67"""	C20orf67		12565871, 15121856	Standard	NM_022104		Approved	bA465L10.1, PPP1R121	uc002xqs.3	Q9H4Z3	OTTHUMG00000032635	ENST00000372409.3:c.1738T>C	20.37:g.44575932T>C	ENSP00000361486:p.Ser580Pro	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	104	6	0.0576923	NM_022104	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	37	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.371687	0.82573	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.03	5.03	0.67393	Phosphorylated CTD interacting factor 1, WW domain (1);	0.000000	0.85682	D	0.000000	D	0.84306	0.5443	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87621	0.2510	9	0.72032	D	0.01	-30.1299	14.0902	0.64984	0.0:0.0:0.0:1.0	.	580;580	B7Z5U5;Q9H4Z3	.;PCIF1_HUMAN	P	580	.	ENSP00000361486:S580P	S	+	1	0	PCIF1	44009339	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.925000	0.70062	2.114000	0.64651	0.374000	0.22700	TCC	.	.	none		0.622	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104	
DGCR2	9993	hgsc.bcm.edu	37	22	19026613	19026613	+	Missense_Mutation	SNP	A	A	G	rs2072123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:19026613A>G	ENST00000263196.7	-	10	1665	c.1418T>C	c.(1417-1419)gTg>gCg	p.V473A	DGCR2_ENST00000545799.1_3'UTR|DGCR2_ENST00000537045.1_Missense_Mutation_p.V432A	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	473			V -> A (in dbSNP:rs2072123). {ECO:0000269|PubMed:7655455}.		cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					GCTGACCTCCACAGGCTCAAA	0.642													G|||	2161	0.43151	0.5696	0.4078	5008	,	,		16113	0.3442		0.3559	False		,,,				2504	0.4294				p.V473A		Atlas-SNP	.											.	DGCR2	45	.	0			c.T1418C						PASS	.	G	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	2235,2169		580,1075,547	36.0	37.0	37.0		1295,1286,1409,1418	-4.4	0.0	22	dbSNP_96	37	3254,5346		636,1982,1682	yes	missense,missense,missense,missense	DGCR2	NM_001173533.1,NM_001173534.1,NM_001184781.1,NM_005137.2	64,64,64,64	1216,3057,2229	GG,GA,AA		37.8372,49.2507,42.2101	benign,benign,benign,benign	432/510,429/507,470/548,473/551	19026613	5489,7515	2202	4300	6502	SO:0001583	missense	9993	exon10			ACCTCCACAGGCT	D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"""integral membrane protein DGCR2"""	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.1418T>C	22.37:g.19026613A>G	ENSP00000263196:p.Val473Ala	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	183	178	0.972678	NM_005137	A6NIB5|A8K6K5|B5TY34|B7Z935	Missense_Mutation	SNP	ENST00000263196.7	37	CCDS33598.1	862	0.3946886446886447	254	0.516260162601626	145	0.4005524861878453	193	0.3374125874125874	270	0.3562005277044855	G	0.469	-0.885473	0.02511	0.507493	0.378372	ENSG00000070413	ENST00000537045;ENST00000263196	T;T	0.41400	1.0;1.0	5.61	-4.41	0.03590	.	0.768784	0.12964	N	0.424762	T	0.00012	0.0000	N	0.04043	-0.29	0.51012	P	9.300000000000974E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.35895	-0.9770	9	0.07175	T	0.84	.	2.7147	0.05184	0.4604:0.0899:0.2668:0.1829	rs2072123;rs17743390;rs56724907;rs2072123	429;473	B7Z3T5;P98153	.;IDD_HUMAN	A	432;473	ENSP00000440062:V432A;ENSP00000263196:V473A	ENSP00000263196:V473A	V	-	2	0	DGCR2	17406613	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.707000	0.05041	-1.523000	0.01767	-1.714000	0.00712	GTG	T|0.004;G|0.408	0.408	strong		0.642	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137	
IL17RE	132014	hgsc.bcm.edu	37	3	9952706	9952706	+	Silent	SNP	A	A	G	rs279572	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:9952706A>G	ENST00000383814.3	+	9	1065	c.960A>G	c.(958-960)acA>acG	p.T320T	IL17RE_ENST00000421412.1_Silent_p.T353T|IL17RE_ENST00000295980.3_Silent_p.T320T|IL17RE_ENST00000454190.2_Silent_p.T320T	NM_153480.1	NP_705613.1	Q8NFR9	I17RE_HUMAN	interleukin 17 receptor E	320					inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(11)|skin(1)	21				OV - Ovarian serous cystadenocarcinoma(96;5.34e-64)		CGAATGCCACAGCTCGAGAGT	0.617													G|||	2138	0.426917	0.6384	0.4683	5008	,	,		17881	0.0942		0.5527	False		,,,				2504	0.3252				p.T360T		Atlas-SNP	.											.	IL17RE	62	.	0			c.A1080G						PASS	.	G	,,	2733,1673	509.6+/-367.3	863,1007,333	59.0	60.0	59.0		960,960,1080	-6.6	0.3	3	dbSNP_79	59	4624,3976	552.1+/-386.1	1229,2166,905	no	coding-synonymous,coding-synonymous,coding-synonymous	IL17RE	NM_001193380.1,NM_153480.1,NM_153483.2	,,	2092,3173,1238	GG,GA,AA		46.2326,37.9709,43.4338	,,	320/534,320/668,360/708	9952706	7357,5649	2203	4300	6503	SO:0001819	synonymous_variant	132014	exon10			TGCCACAGCTCGA	AF458069	CCDS2589.1, CCDS54552.1	3p25.3	2008-02-05			ENSG00000163701	ENSG00000163701		"""Interleukins and interleukin receptors"""	18439	protein-coding gene	gene with protein product		614995					Standard	NM_153480		Approved	FLJ23658	uc003btu.3	Q8NFR9	OTTHUMG00000128649	ENST00000383814.3:c.960A>G	3.37:g.9952706A>G		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_153483	B2RB34|B2RNR1|B9EH65|Q6P532|Q8N8H7|Q8N8H8|Q8TEC2	Silent	SNP	ENST00000383814.3	37	CCDS2589.1																																																																																			A|0.492;G|0.508	0.508	strong		0.617	IL17RE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250529.1	NM_153480	
KRT32	3882	hgsc.bcm.edu	37	17	39622068	39622068	+	Missense_Mutation	SNP	G	G	T	rs2071561	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39622068G>T	ENST00000225899.3	-	3	768	c.665C>A	c.(664-666)tCc>tAc	p.S222Y	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	222	Coil 1B.|Rod.		S -> Y (in dbSNP:rs2071561).		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)				CTCCTTCAGGGACTCAACCTG	0.617													G|||	2502	0.499601	0.2413	0.5187	5008	,	,		18777	0.6369		0.4761	False		,,,				2504	0.7178				p.S222Y		Atlas-SNP	.											.	KRT32	57	.	0			c.C665A						PASS	.	G	TYR/SER	1268,3138	434.1+/-343.8	181,906,1116	82.0	70.0	74.0		665	4.1	1.0	17	dbSNP_96	74	4288,4312	576.5+/-390.4	1072,2144,1084	yes	missense	KRT32	NM_002278.3	144	1253,3050,2200	TT,TG,GG		49.8605,28.7789,42.7187	probably-damaging	222/449	39622068	5556,7450	2203	4300	6503	SO:0001583	missense	3882	exon3			TTCAGGGACTCAA	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.665C>A	17.37:g.39622068G>T	ENSP00000225899:p.Ser222Tyr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	147	59	0.401361	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	1016	0.4652014652014652	121	0.2459349593495935	205	0.5662983425414365	339	0.5926573426573427	351	0.4630606860158311	G	17.95	3.513733	0.64522	0.287789	0.498605	ENSG00000108759	ENST00000225899	D	0.90844	-2.74	5.1	4.12	0.48240	Filament (1);	0.000000	0.38720	N	0.001589	T	0.00012	0.0000	H	0.95816	3.725	0.30879	P	0.731614	D	0.58620	0.983	D	0.72338	0.977	T	0.10222	-1.0639	9	0.87932	D	0	.	9.1393	0.36894	0.0786:0.1455:0.7759:0.0	rs2071561;rs52794180;rs60448298;rs2071561	222	Q14532	K1H2_HUMAN	Y	222	ENSP00000225899:S222Y	ENSP00000225899:S222Y	S	-	2	0	KRT32	36875594	0.000000	0.05858	1.000000	0.80357	0.995000	0.86356	0.600000	0.24104	1.285000	0.44548	0.558000	0.71614	TCC	G|0.553;T|0.445	0.445	strong		0.617	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
ERI2	112479	hgsc.bcm.edu	37	16	20810067	20810067	+	Missense_Mutation	SNP	T	T	C	rs3213646	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000300005.3_Intron|ERI2_ENST00000564349.1_Missense_Mutation_p.Y259C|ERI2_ENST00000569729.1_Intron	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	109	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	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	
TTLL4	9654	hgsc.bcm.edu	37	2	219602819	219602819	+	Silent	SNP	G	G	A	rs3731876	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219602819G>A	ENST00000392102.1	+	3	760	c.420G>A	c.(418-420)ccG>ccA	p.P140P	TTLL4_ENST00000442769.1_Silent_p.P140P|TTLL4_ENST00000258398.4_Silent_p.P140P|TTLL4_ENST00000457313.1_5'UTR	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	140					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)		GTTCGAGCCCGTCAGAAAAAA	0.542													A|||	2371	0.473442	0.8585	0.4366	5008	,	,		20218	0.1409		0.4662	False		,,,				2504	0.3292				p.P140P	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.G420A						PASS	.	A		3577,829	329.9+/-301.2	1455,667,81	95.0	98.0	97.0		420	-2.1	0.0	2	dbSNP_107	97	4094,4506	592.0+/-392.9	994,2106,1200	no	coding-synonymous	TTLL4	NM_014640.4		2449,2773,1281	AA,AG,GG		47.6047,18.8153,41.0195		140/1200	219602819	7671,5335	2203	4300	6503	SO:0001819	synonymous_variant	9654	exon3			GAGCCCGTCAGAA		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.420G>A	2.37:g.219602819G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_014640	A8K6V5|Q8WW29	Silent	SNP	ENST00000392102.1	37	CCDS2422.1																																																																																			G|0.459;A|0.541	0.541	strong		0.542	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
SAR1B	51128	hgsc.bcm.edu	37	5	133945288	133945288	+	Silent	SNP	C	C	T	rs140899111	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:133945288C>T	ENST00000402673.2	-	5	599	c.321G>A	c.(319-321)agG>agA	p.R107R	SAR1B_ENST00000509937.1_Silent_p.R39R|SAR1B_ENST00000502539.1_Silent_p.R39R|SAR1B_ENST00000439578.1_Silent_p.R107R|SAR1B_ENST00000507419.1_Silent_p.R39R	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	107					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)			ACTCTAACAGCCTTTCGTGGT	0.393													C|||	4	0.000798722	0.0	0.0	5008	,	,		20631	0.0		0.004	False		,,,				2504	0.0				p.R107R		Atlas-SNP	.											.	SAR1B	19	.	0			c.G321A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	129.0	118.0	122.0		321,321	1.9	1.0	5	dbSNP_134	122	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous	SAR1B	NM_001033503.2,NM_016103.3	,	0,16,6487	TT,TC,CC		0.1744,0.0227,0.123	,	107/199,107/199	133945288	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	51128	exon6			TAACAGCCTTTCG	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.321G>A	5.37:g.133945288C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	145	56	0.386207	NM_001033503	D3DQA4|Q567T4	Silent	SNP	ENST00000402673.2	37	CCDS4177.1																																																																																			C|0.999;T|0.001	0.001	strong		0.393	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103	
CD109	135228	hgsc.bcm.edu	37	6	74497152	74497152	+	Missense_Mutation	SNP	G	G	A	rs5023688	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:74497152G>A	ENST00000287097.5	+	21	2645	c.2533G>A	c.(2533-2535)Gtc>Atc	p.V845I	CD109_ENST00000437994.2_Missense_Mutation_p.V845I|CD109_ENST00000422508.2_Missense_Mutation_p.V768I			Q6YHK3	CD109_HUMAN	CD109 molecule	845			V -> I (in dbSNP:rs5023688). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14980714, ECO:0000269|PubMed:16754747, 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						TTCTGATGCTGTCACCCAGAT	0.403													A|||	1861	0.371605	0.4644	0.4049	5008	,	,		18074	0.4087		0.339	False		,,,				2504	0.2178				p.V845I		Atlas-SNP	.											.	CD109	170	.	0			c.G2533A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	2043,2363	610.5+/-391.6	492,1059,652	94.0	92.0	93.0		2533,2302,2533	-9.1	0.0	6	dbSNP_113	93	3057,5543	660.7+/-401.8	552,1953,1795	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	29,29,29	1044,3012,2447	AA,AG,GG		35.5465,46.3686,39.2127	benign,benign,benign	845/1429,768/1369,845/1446	74497152	5100,7906	2203	4300	6503	SO:0001583	missense	135228	exon21			GATGCTGTCACCC	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.2533G>A	6.37:g.74497152G>A	ENSP00000287097:p.Val845Ile	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	878	0.40201465201465203	249	0.5060975609756098	143	0.39502762430939226	239	0.4178321678321678	247	0.3258575197889182	A	0.009	-1.810761	0.00600	0.463686	0.355465	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.30981	1.51;1.78;1.56	5.45	-9.1	0.00714	.	0.845913	0.10991	N	0.611562	T	0.04907	0.0132	N	0.25060	0.705	0.80722	P	0.0	B;B;B	0.15930	0.002;0.015;0.0	B;B;B	0.24269	0.008;0.052;0.007	T	0.28554	-1.0040	9	0.13108	T	0.6	.	11.6482	0.51273	0.525:0.1959:0.2791:0.0	rs5023688;rs52793634;rs58164751;rs5023688	768;845;845	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	I	845;768;845	ENSP00000388062:V845I;ENSP00000404475:V768I;ENSP00000287097:V845I	ENSP00000287097:V845I	V	+	1	0	CD109	74553873	0.000000	0.05858	0.001000	0.08648	0.106000	0.19336	-1.860000	0.01656	-2.465000	0.00533	-2.361000	0.00239	GTC	G|0.598;A|0.402	0.402	strong		0.403	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
OR51S1	119692	hgsc.bcm.edu	37	11	4869649	4869649	+	Missense_Mutation	SNP	G	G	A	rs12361955	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4869649G>A	ENST00000322101.2	-	1	865	c.790C>T	c.(790-792)Ctc>Ttc	p.L264F	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	264			L -> F (in dbSNP:rs12361955).			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)		AGTGCCAGGAGGATCATAGGG	0.498													G|||	1499	0.299321	0.3411	0.2608	5008	,	,		19746	0.0675		0.4046	False		,,,				2504	0.4008				p.L264F		Atlas-SNP	.											OR51S1,NS,carcinoma,+2,1	OR51S1	83	1	0			c.C790T						PASS	.	G	PHE/LEU	1535,2867	485.3+/-360.3	273,989,939	112.0	96.0	102.0		790	3.3	1.0	11	dbSNP_120	102	3700,4896	528.7+/-381.4	805,2090,1403	yes	missense	OR51S1	NM_001004758.1	22	1078,3079,2342	AA,AG,GG		43.0433,34.8705,40.2754	benign	264/324	4869649	5235,7763	2201	4298	6499	SO:0001583	missense	119692	exon1			CCAGGAGGATCAT	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.790C>T	11.37:g.4869649G>A	ENSP00000322754:p.Leu264Phe	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	621	0.28434065934065933	168	0.34146341463414637	120	0.3314917127071823	32	0.055944055944055944	301	0.3970976253298153	G	8.217	0.801715	0.16397	0.348705	0.430433	ENSG00000176922	ENST00000322101	T	0.73363	-0.74	5.25	3.29	0.37713	GPCR, rhodopsin-like superfamily (1);	0.176237	0.27469	N	0.019222	T	0.00012	0.0000	N	0.04746	-0.17	0.58432	P	1.0000000000287557E-6	B	0.10296	0.003	B	0.12156	0.007	T	0.31668	-0.9935	9	0.87932	D	0	-11.6636	8.9594	0.35838	0.0843:0.295:0.6207:0.0	rs12361955;rs58301091;rs12361955	264	Q8NGJ8	O51S1_HUMAN	F	264	ENSP00000322754:L264F	ENSP00000322754:L264F	L	-	1	0	OR51S1	4826225	0.000000	0.05858	1.000000	0.80357	0.400000	0.30750	0.704000	0.25661	1.445000	0.47624	0.655000	0.94253	CTC	G|0.658;A|0.342	0.342	strong		0.498	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
ARHGEF3	50650	hgsc.bcm.edu	37	3	56835761	56835761	+	Silent	SNP	G	G	A	rs3732508	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:56835761G>A	ENST00000296315.3	-	1	234	c.66C>T	c.(64-66)ccC>ccT	p.P22P	ARHGEF3_ENST00000495373.1_Silent_p.P22P|ARHGEF3_ENST00000338458.4_Intron|ARHGEF3_ENST00000496106.1_Intron|ARHGEF3_ENST00000498517.1_Intron	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	22					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)		CGCTGGCCGGGGGTAGCTCCA	0.652													G|||	1609	0.321286	0.0227	0.487	5008	,	,		16762	0.1944		0.5716	False		,,,				2504	0.4806				p.P22P		Atlas-SNP	.											ARHGEF3_ENST00000296315,NS,carcinoma,0,2	ARHGEF3	128	2	0			c.C66T						PASS	.	G	,	492,3902		44,404,1749	35.0	31.0	33.0		,66	4.0	1.0	3	dbSNP_107	33	4617,3949		1292,2033,958	no	intron,coding-synonymous	ARHGEF3	NM_001128615.1,NM_019555.2	,	1336,2437,2707	AA,AG,GG		46.1009,11.1971,39.4213	,	,22/527	56835761	5109,7851	2197	4283	6480	SO:0001819	synonymous_variant	50650	exon1			GGCCGGGGGTAGC	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.66C>T	3.37:g.56835761G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_019555	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Silent	SNP	ENST00000296315.3	37	CCDS2878.1																																																																																			G|0.677;A|0.323	0.323	strong		0.652	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555	
POLQ	10721	hgsc.bcm.edu	37	3	121208176	121208176	+	Missense_Mutation	SNP	T	T	C	rs3218651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:121208176T>C	ENST00000264233.5	-	16	3730	c.3602A>G	c.(3601-3603)cAt>cGt	p.H1201R		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1201					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)		TGTCTGTTCATGAGATTGCTT	0.343								DNA polymerases (catalytic subunits)					T|||	1451	0.289736	0.1203	0.2954	5008	,	,		20581	0.5496		0.1511	False		,,,				2504	0.3896				p.H1201R	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A3602G						PASS	.	T	ARG/HIS	462,3944	218.7+/-236.7	27,408,1768	203.0	208.0	206.0		3602	4.2	0.0	3	dbSNP_106	206	1261,7339	251.4+/-277.9	106,1049,3145	yes	missense	POLQ	NM_199420.3	29	133,1457,4913	CC,CT,TT		14.6628,10.4857,13.2477	benign	1201/2591	121208176	1723,11283	2203	4300	6503	SO:0001583	missense	10721	exon16			TGTTCATGAGATT	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.3602A>G	3.37:g.121208176T>C	ENSP00000264233:p.His1201Arg	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	162	97	0.598765	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	620	0.2838827838827839	69	0.1402439024390244	92	0.2541436464088398	331	0.5786713286713286	128	0.16886543535620052	T	3.626	-0.076630	0.07184	0.104857	0.146628	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.45276	0.9	5.45	4.24	0.50183	.	0.659014	0.14910	N	0.291263	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.20780	0.048;0.001	B;B	0.15870	0.014;0.0	T	0.42155	-0.9468	9	0.15499	T	0.54	.	10.3646	0.44015	0.156:0.0:0.0:0.844	rs3218651;rs52826086;rs60671312;rs3218651	1201;373	O75417;O75417-2	DPOLQ_HUMAN;.	R	824;1201;1337	ENSP00000264233:H1201R	ENSP00000264233:H1201R	H	-	2	0	POLQ	122690866	0.000000	0.05858	0.016000	0.15963	0.038000	0.13279	-0.078000	0.11375	2.289000	0.77006	0.460000	0.39030	CAT	T|0.779;C|0.221	0.221	strong		0.343	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
URB1	9875	hgsc.bcm.edu	37	21	33697576	33697576	+	Missense_Mutation	SNP	G	G	A	rs187640762	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:33697576G>A	ENST00000382751.3	-	31	5199	c.5084C>T	c.(5083-5085)tCg>tTg	p.S1695L		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1695						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						CTCCAAGTGCGAGTAGTAGGC	0.577													G|||	13	0.00259585	0.0	0.0029	5008	,	,		17029	0.0		0.006	False		,,,				2504	0.0051				p.S1695L		Atlas-SNP	.											.	URB1	176	.	0			c.C5084T						PASS	.	G	LEU/SER	0,1384		0,0,692	65.0	57.0	59.0		5084	4.2	1.0	21		59	29,3153		0,29,1562	yes	missense	URB1	NM_014825.2	145	0,29,2254	AA,AG,GG		0.9114,0.0,0.6351	probably-damaging	1695/2272	33697576	29,4537	692	1591	2283	SO:0001583	missense	9875	exon31			AAGTGCGAGTAGT	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.5084C>T	21.37:g.33697576G>A	ENSP00000372199:p.Ser1695Leu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	17.73	3.461947	0.63513	0.0	0.009114	ENSG00000142207	ENST00000382751	T	0.32753	1.44	5.15	4.2	0.49525	.	0.247939	0.42548	D	0.000682	T	0.33876	0.0878	L	0.52011	1.625	0.47094	D	0.999315	D	0.76494	0.999	P	0.61397	0.888	T	0.06862	-1.0803	10	0.10636	T	0.68	-17.8842	15.4371	0.75155	0.0:0.1391:0.8609:0.0	.	1695	O60287	NPA1P_HUMAN	L	1695	ENSP00000372199:S1695L	ENSP00000372199:S1695L	S	-	2	0	URB1	32619447	1.000000	0.71417	0.960000	0.40013	0.441000	0.31987	3.473000	0.53122	2.555000	0.86185	0.655000	0.94253	TCG	G|0.995;A|0.005	0.005	strong		0.577	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
EXOC4	60412	hgsc.bcm.edu	37	7	133749164	133749164	+	Silent	SNP	G	G	A	rs6953296	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:133749164G>A	ENST00000253861.4	+	18	2837	c.2808G>A	c.(2806-2808)caG>caA	p.Q936Q	EXOC4_ENST00000541309.1_Silent_p.Q224Q|EXOC4_ENST00000539845.1_Silent_p.Q835Q|EXOC4_ENST00000545148.1_Silent_p.Q546Q	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	936					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				ACCGCAGCCAGACTGGGGTGG	0.592													G|||	3351	0.669129	0.7065	0.7622	5008	,	,		19248	0.7609		0.6014	False		,,,				2504	0.5276				p.Q936Q		Atlas-SNP	.											.	EXOC4	118	.	0			c.G2808A						PASS	.	G		3055,1351	692.2+/-405.5	1064,927,212	59.0	54.0	56.0		2808	4.7	1.0	7	dbSNP_116	56	5128,3472	635.6+/-399.0	1548,2032,720	no	coding-synonymous	EXOC4	NM_021807.3		2612,2959,932	AA,AG,GG		40.3721,30.6627,37.0829		936/975	133749164	8183,4823	2203	4300	6503	SO:0001819	synonymous_variant	60412	exon18			CAGCCAGACTGGG	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2808G>A	7.37:g.133749164G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	59	16	0.271186	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	37	CCDS5829.1																																																																																			G|0.353;A|0.647	0.647	strong		0.592	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
HOXB5	3215	hgsc.bcm.edu	37	17	46669730	46669730	+	Silent	SNP	G	G	T	rs36049616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46669730G>T	ENST00000239151.5	-	2	929	c.651C>A	c.(649-651)cgC>cgA	p.R217R	HOXB3_ENST00000476342.1_5'Flank|HOXB3_ENST00000460160.1_5'Flank|HOXB3_ENST00000498678.1_5'Flank|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB3_ENST00000472863.1_5'Flank|HOXB-AS3_ENST00000429755.4_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000467155.2_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	217					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						GGGTCAGGTAGCGGTTGAAGT	0.612													G|||	144	0.028754	0.0734	0.0346	5008	,	,		11348	0.0		0.0179	False		,,,				2504	0.0051				p.R217R		Atlas-SNP	.											.	HOXB5	20	.	0			c.C651A						PASS	.	G		301,4105	165.8+/-197.2	13,275,1915	105.0	105.0	105.0		651	4.2	1.0	17	dbSNP_126	105	301,8299	109.4+/-169.9	6,289,4005	no	coding-synonymous	HOXB5	NM_002147.3		19,564,5920	TT,TG,GG		3.5,6.8316,4.6286		217/270	46669730	602,12404	2203	4300	6503	SO:0001819	synonymous_variant	3215	exon2			CAGGTAGCGGTTG		CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"""Homeoboxes / ANTP class : HOXL subclass"""	5116	protein-coding gene	gene with protein product		142960	"""homeo box B5"""	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.651C>A	17.37:g.46669730G>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	203	76	0.374384	NM_002147	B2RC69|P09069|Q17RP4	Silent	SNP	ENST00000239151.5	37	CCDS11530.1																																																																																			G|0.960;T|0.040	0.040	strong		0.612	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2		
MUC17	140453	hgsc.bcm.edu	37	7	100677409	100677409	+	Silent	SNP	G	G	A	rs150735476	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677409G>A	ENST00000306151.4	+	3	2776	c.2712G>A	c.(2710-2712)tcG>tcA	p.S904S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	904	59 X approximate tandem repeats.|Ser-rich.				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)					AAGCCCGTTCGTCTCCTACAA	0.527													A|||	890	0.177716	0.2292	0.0865	5008	,	,		30785	0.1954		0.0964	False		,,,				2504	0.2382				p.S904S		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.G2712A						scavenged	.	A		373,4033	760.0+/-412.9	0,373,1830	319.0	301.0	307.0		2712	-0.7	0.0	7	dbSNP_134	307	291,8309	788.8+/-407.6	0,291,4009	no	coding-synonymous	MUC17	NM_001040105.1		0,664,5839	AA,AG,GG		3.3837,8.4657,5.1053		904/4494	100677409	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CCGTTCGTCTCCT	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.2712G>A	7.37:g.100677409G>A		Somatic	131	2	0.0152672		WXS	Illumina HiSeq	Phase_I	334	78	0.233533	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.957;A|0.043	0.043	strong		0.527	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
VWA2	340706	hgsc.bcm.edu	37	10	116045993	116045993	+	Silent	SNP	G	G	A	rs566742651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:116045993G>A	ENST00000392982.3	+	11	1543	c.1293G>A	c.(1291-1293)gaG>gaA	p.E431E	VWA2_ENST00000603594.1_Silent_p.E431E			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	431	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)		AGGCGGCAGAGCGTGGCTTCG	0.662																																					p.E431E		Atlas-SNP	.											.	VWA2	64	.	0			c.G1293A						PASS	.						56.0	49.0	51.0					10																	116045993		2203	4299	6502	SO:0001819	synonymous_variant	340706	exon11			GGCAGAGCGTGGC	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.1293G>A	10.37:g.116045993G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	37																																																																																				.	.	none		0.662	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
RP1	6101	hgsc.bcm.edu	37	8	55539395	55539395	+	Missense_Mutation	SNP	A	A	T	rs2293869	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:55539395A>T	ENST00000220676.1	+	4	3101	c.2953A>T	c.(2953-2955)Aat>Tat	p.N985Y		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	985			N -> Y (associated with susceptibility to hypertriglyceridemia; dbSNP:rs2293869). {ECO:0000269|PubMed:10391212, ECO:0000269|PubMed:11095597, 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)			GACAGGAGATAATCTATGTAA	0.353													A|||	1252	0.25	0.1952	0.2522	5008	,	,		19567	0.0675		0.4264	False		,,,				2504	0.3292				p.N985Y	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A2953T	GRCh37	CM035763	RP1	M	rs2293869	PASS	.	A	TYR/ASN	944,3462	356.1+/-313.4	107,730,1366	128.0	137.0	134.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2953	1.9	0.0	8	dbSNP_100	134	3584,5016	516.2+/-378.8	719,2146,1435	yes	missense	RP1	NM_006269.1	143	826,2876,2801	TT,TA,AA		41.6744,21.4253,34.8147	possibly-damaging	985/2157	55539395	4528,8478	2203	4300	6503	SO:0001583	missense	6101	exon4			GGAGATAATCTAT	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.2953A>T	8.37:g.55539395A>T	ENSP00000220676:p.Asn985Tyr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	48	34	0.708333	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	569	0.26053113553113555	91	0.18495934959349594	108	0.2983425414364641	43	0.07517482517482517	327	0.4313984168865435	A	10.45	1.354246	0.24512	0.214253	0.416744	ENSG00000104237	ENST00000220676	T	0.56444	0.46	5.62	1.94	0.25998	.	0.392400	0.24447	N	0.038456	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	D	0.57899	0.981	P	0.57371	0.819	T	0.39210	-0.9625	9	0.87932	D	0	.	5.9509	0.19246	0.6673:0.1275:0.2052:0.0	rs2293869;rs52800054;rs2293869	985	P56715	RP1_HUMAN	Y	985	ENSP00000220676:N985Y	ENSP00000220676:N985Y	N	+	1	0	RP1	55701948	0.054000	0.20591	0.004000	0.12327	0.148000	0.21650	1.592000	0.36676	0.093000	0.17368	0.533000	0.62120	AAT	A|0.687;T|0.313	0.313	strong		0.353	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
PRDM6	93166	hgsc.bcm.edu	37	5	122425832	122425832	+	Silent	SNP	G	G	T	rs13182369	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:122425832G>T	ENST00000407847.4	+	2	537	c.123G>T	c.(121-123)gcG>gcT	p.A41A	AC106786.1_ENST00000442777.2_RNA|AC106786.1_ENST00000458103.2_RNA	NM_001136239.1	NP_001129711.1	Q9NQX0	PRDM6_HUMAN	PR domain containing 6	41					negative regulation of smooth muscle cell differentiation (GO:0051151)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.A41A(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	7						GCGGCGCCGCGGGTCTCCTGA	0.761													G|||	1111	0.221845	0.2753	0.2622	5008	,	,		8018	0.0337		0.3966	False		,,,				2504	0.135				p.A41A		Atlas-SNP	.											PRDM6,NS,NS,0,1	PRDM6	26	1	1	Substitution - coding silent(1)	NS(1)	c.G123T						PASS	.						1.0	2.0	2.0					5																	122425832		394	1099	1493	SO:0001819	synonymous_variant	93166	exon2			CGCCGCGGGTCTC	AF272898	CCDS47259.1	5q21-q23	2013-01-08			ENSG00000061455	ENSG00000061455		"""Zinc fingers, C2H2-type"""	9350	protein-coding gene	gene with protein product							Standard	NM_001136239		Approved		uc003kti.3	Q9NQX0	OTTHUMG00000150469	ENST00000407847.4:c.123G>T	5.37:g.122425832G>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_001136239	B5MCJ4|Q9NQW9	Silent	SNP	ENST00000407847.4	37	CCDS47259.1																																																																																			G|0.741;T|0.259	0.259	strong		0.761	PRDM6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318226.2	XM_049619	
MATN4	8785	hgsc.bcm.edu	37	20	43933163	43933163	+	Silent	SNP	T	T	C	rs2233094	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:43933163T>C	ENST00000372754.1	-	2	356	c.348A>G	c.(346-348)gcA>gcG	p.A116A	MATN4_ENST00000353917.5_Silent_p.A116A|MATN4_ENST00000372756.1_Silent_p.A116A|MATN4_ENST00000537548.1_Silent_p.A116A|MATN4_ENST00000372751.4_Intron|RBPJL_ENST00000372743.1_5'Flank|MATN4_ENST00000342716.4_Silent_p.A116A|MATN4_ENST00000360607.6_Silent_p.A116A|RBPJL_ENST00000343694.3_5'Flank|RBPJL_ENST00000372741.3_5'Flank			O95460	MATN4_HUMAN	matrilin 4	116	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)				CGTACTGGATTGCCAGTCCCG	0.687													T|||	2021	0.403554	0.2239	0.3444	5008	,	,		16128	0.755		0.2634	False		,,,				2504	0.4703				p.A116A		Atlas-SNP	.											MATN4,NS,carcinoma,0,1	MATN4	57	1	0			c.A348G						PASS	.	T	,,	985,3411		120,745,1333	19.0	16.0	17.0		348,348,348	-9.6	0.1	20	dbSNP_98	17	2373,6207		337,1699,2254	no	coding-synonymous,coding-synonymous,coding-synonymous	MATN4	NM_003833.3,NM_030590.2,NM_030592.2	,,	457,2444,3587	CC,CT,TT		27.6573,22.4067,25.8785	,,	116/582,116/541,116/500	43933163	3358,9618	2198	4290	6488	SO:0001819	synonymous_variant	8785	exon3			CTGGATTGCCAGT	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.348A>G	20.37:g.43933163T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	77	19	0.246753	NM_030592	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Silent	SNP	ENST00000372754.1	37																																																																																				T|0.676;C|0.324	0.324	strong		0.687	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		
MEGF6	1953	hgsc.bcm.edu	37	1	3413868	3413868	+	Missense_Mutation	SNP	C	C	G	rs4648506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:3413868C>G	ENST00000356575.4	-	27	3636	c.3410G>C	c.(3409-3411)gGc>gCc	p.G1137A	MEGF6_ENST00000294599.4_Missense_Mutation_p.G946A	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1137	EGF-like 21. {ECO:0000255|PROSITE- ProRule:PRU00076}.		G -> A (in dbSNP:rs4648506). {ECO:0000269|PubMed:9693030}.			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)		GCAGGCAGCGCCAGGCGGGCA	0.716													C|||	1222	0.24401	0.146	0.3357	5008	,	,		12528	0.1865		0.3201	False		,,,				2504	0.2924				p.G1137A	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.G3410C						PASS	.	C	ALA/GLY	547,3569		48,451,1559	8.0	13.0	11.0		3410	0.1	0.0	1	dbSNP_111	11	2204,6092		339,1526,2283	no	missense	MEGF6	NM_001409.3	60	387,1977,3842	GG,GC,CC		26.567,13.2896,22.164	possibly-damaging	1137/1542	3413868	2751,9661	2058	4148	6206	SO:0001583	missense	1953	exon27			GCAGCGCCAGGCG	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.3410G>C	1.37:g.3413868C>G	ENSP00000348982:p.Gly1137Ala	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	14	12	0.857143	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	532	0.24358974358974358	83	0.16869918699186992	101	0.27900552486187846	130	0.22727272727272727	218	0.287598944591029	C	12.32	1.903437	0.33628	0.132896	0.26567	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.71934	-0.09;-0.61	4.36	0.0897	0.14460	EGF-like, laminin (2);Epidermal growth factor-like, type 3 (1);	0.182174	0.48286	N	0.000200	T	0.00012	0.0000	M	0.91663	3.23	0.40306	P	0.021338999999999997	P;P	0.51147	0.942;0.929	P;P	0.62435	0.902;0.841	T	0.05022	-1.0911	9	0.62326	D	0.03	-7.763	6.2955	0.21083	0.0:0.6314:0.1331:0.2355	rs4648506	1137;946	O75095;O75095-2	MEGF6_HUMAN;.	A	946;1137	ENSP00000294599:G946A;ENSP00000348982:G1137A	ENSP00000294599:G946A	G	-	2	0	MEGF6	3403728	0.002000	0.14202	0.000000	0.03702	0.135000	0.20990	0.253000	0.18296	-0.064000	0.13043	0.561000	0.74099	GGC	C|0.736;G|0.264	0.264	strong		0.716	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
RRM1	6240	hgsc.bcm.edu	37	11	4141132	4141132	+	Silent	SNP	C	C	A	rs183484	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4141132C>A	ENST00000300738.5	+	9	1054	c.850C>A	c.(850-852)Cga>Aga	p.R284R	RRM1_ENST00000534285.1_Silent_p.R62R|RRM1_ENST00000423050.2_Silent_p.R187R|RRM1_ENST00000537197.1_5'UTR|RRM1_ENST00000528470.1_3'UTR	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	284					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)	CAACACAGCTCGATATGTGGA	0.403													C|||	1618	0.323083	0.0227	0.4366	5008	,	,		17753	0.378		0.5229	False		,,,				2504	0.3865				p.R284R	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.C850A						PASS	.	C		464,3938	220.0+/-237.6	25,414,1762	150.0	137.0	141.0		850	5.7	1.0	11	dbSNP_79	141	4586,4010	599.3+/-394.1	1205,2176,917	no	coding-synonymous	RRM1	NM_001033.3		1230,2590,2679	AA,AC,CC		46.6496,10.5407,38.8521		284/793	4141132	5050,7948	2201	4298	6499	SO:0001819	synonymous_variant	6240	exon9			ACAGCTCGATATG	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.850C>A	11.37:g.4141132C>A		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	155	152	0.980645	NM_001033	Q9UNN2	Silent	SNP	ENST00000300738.5	37	CCDS7750.1																																																																																			C|0.614;N|0.000	.	strong		0.403	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033	
DISP1	84976	hgsc.bcm.edu	37	1	223116472	223116472	+	Missense_Mutation	SNP	G	G	A	rs2609383|rs71583926	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:223116472G>A	ENST00000284476.6	+	2	471	c.307G>A	c.(307-309)Gag>Aag	p.E103K	DISP1_ENST00000360254.2_Missense_Mutation_p.E103K|DISP1_ENST00000495684.1_Intron	NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	103			E -> K (in dbSNP:rs2609383).		determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		GTGCCATCCCGAGGCTGGCCC	0.522													G|||	1060	0.211661	0.1566	0.1715	5008	,	,		23581	0.2907		0.1352	False		,,,				2504	0.3119				p.E103K		Atlas-SNP	.											.	DISP1	145	.	0			c.G307A						PASS	.	G	LYS/GLU	738,3668	304.1+/-288.3	59,620,1524	139.0	120.0	126.0		307	4.7	1.0	1	dbSNP_100	126	1176,7424	239.7+/-270.7	86,1004,3210	yes	missense	DISP1	NM_032890.3	56	145,1624,4734	AA,AG,GG		13.6744,16.7499,14.7163	benign	103/1525	223116472	1914,11092	2203	4300	6503	SO:0001583	missense	84976	exon4			CATCCCGAGGCTG	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.307G>A	1.37:g.223116472G>A	ENSP00000284476:p.Glu103Lys	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	207	134	0.647343	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	399	0.18269230769230768	70	0.14227642276422764	64	0.17679558011049723	156	0.2727272727272727	109	0.1437994722955145	G	9.041	0.989600	0.18966	0.167499	0.136744	ENSG00000154309	ENST00000360254;ENST00000284476	T;D	0.91577	0.92;-2.87	5.62	4.68	0.58851	.	0.682047	0.14375	N	0.323515	T	0.00039	0.0001	L	0.51422	1.61	0.42105	P	0.00864699999999996	B	0.28880	0.226	B	0.17098	0.017	T	0.43114	-0.9411	9	0.07030	T	0.85	-28.9434	15.3736	0.74587	0.0:0.2638:0.7362:0.0	rs2609383;rs3814304;rs2609383	103	Q96F81	DISP1_HUMAN	K	103	ENSP00000355848:E103K;ENSP00000284476:E103K	ENSP00000284476:E103K	E	+	1	0	DISP1	221183095	0.968000	0.33430	0.997000	0.53966	0.973000	0.67179	1.811000	0.38942	2.652000	0.90054	0.650000	0.86243	GAG	AAT|0.500;GAG|0.500	.	alt		0.522	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
GNB5	10681	hgsc.bcm.edu	37	15	52433397	52433397	+	Silent	SNP	C	C	T	rs17612637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52433397C>T	ENST00000261837.7	-	7	632	c.567G>A	c.(565-567)aaG>aaA	p.K189K	GNB5_ENST00000396335.4_Intron|GNB5_ENST00000358784.7_Silent_p.K147K|GNB5_ENST00000559348.1_5'Flank|CTD-2184D3.7_ENST00000560613.1_RNA|CTD-2184D3.7_ENST00000557898.1_RNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	189					GTP catabolic process (GO:0006184)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	chaperone binding (GO:0051087)|G-protein gamma-subunit binding (GO:0031682)|GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			large_intestine(1)|lung(1)	2				all cancers(107;0.0163)		TAGCAACAGACTTCTTTTTGG	0.473													C|||	82	0.0163738	0.0008	0.0389	5008	,	,		18151	0.0		0.0368	False		,,,				2504	0.0174				p.K189K		Atlas-SNP	.											.	GNB5	28	.	0			c.G567A						PASS	.	C	,	35,4355	39.2+/-71.8	1,33,2161	166.0	150.0	155.0		441,567	5.3	1.0	15	dbSNP_123	155	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,342,6141	TT,TC,CC		3.6921,0.7973,2.7127	,	147/354,189/396	52433397	352,12624	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon7			AACAGACTTCTTT	AF017656	CCDS10149.1, CCDS45261.1	15q21.1	2013-01-10			ENSG00000069966	ENSG00000069966		"""WD repeat domain containing"""	4401	protein-coding gene	gene with protein product		604447				9606987	Standard	NM_016194		Approved	GB5	uc031qrz.1	O14775	OTTHUMG00000131892	ENST00000261837.7:c.567G>A	15.37:g.52433397C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	94	24	0.255319	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;G|0.000;T|0.027	0.027	strong		0.473	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1		
MUC4	4585	hgsc.bcm.edu	37	3	195512531	195512531	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195512531C>T	ENST00000463781.3	-	2	6379	c.5920G>A	c.(5920-5922)Gct>Act	p.A1974T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1974T	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	353	1	0.00283286		WXS	Illumina HiSeq	Phase_I	677	23	0.0339734	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	
ADSSL1	122622	hgsc.bcm.edu	37	14	105196230	105196230	+	Start_Codon_SNP	SNP	A	A	C	rs386781068|rs80097179	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105196230A>C	ENST00000332972.5	+	1	160	c.1A>C	c.(1-3)Atg>Ctg	p.M1L	ADSSL1_ENST00000330877.2_Intron	NM_199165.1	NP_954634.1			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)		tggcgtcggcatggtggggag	0.721													a|||	1884	0.376198	0.1914	0.3646	5008	,	,		11381	0.5774		0.3241	False		,,,				2504	0.4806				p.M1L		Atlas-SNP	.											.	ADSSL1	37	.	0			c.A1C						PASS	.	A	,LEU/MET	863,3221		99,665,1278	19.0	18.0	18.0		,1	-0.3	0.0	14	dbSNP_131	18	2369,5543		361,1647,1948	no	intron,missense	ADSSL1	NM_152328.3,NM_199165.1	,15	460,2312,3226	CC,CA,AA		29.9419,21.1312,26.9423	,benign	,1/501	105196230	3232,8764	2042	3956	5998	SO:0001582	initiator_codon_variant	122622	exon1			GTCGGCATGGTGG	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		ENST00000332972.5:c.1A>C	14.37:g.105196230A>C	ENSP00000333019:p.Met1Leu	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	46	45	0.978261	NM_199165		Missense_Mutation	SNP	ENST00000332972.5	37	CCDS9991.1	784	0.358974358974359	97	0.19715447154471544	132	0.36464088397790057	317	0.5541958041958042	238	0.31398416886543534	a	2.920	-0.223509	0.06061	0.211312	0.299419	ENSG00000185100	ENST00000332972	T	0.39229	1.09	0.158	-0.317	0.12736	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	8.000000000008E-6	B	0.10296	0.003	B	0.01281	0.0	T	0.43523	-0.9386	6	0.87932	D	0	-24.6368	.	.	.	.	1	Q8N142-2	.	L	1	ENSP00000333019:M1L	ENSP00000333019:M1L	M	+	1	0	ADSSL1	104267275	0.222000	0.23652	0.018000	0.16275	0.006000	0.05464	-2.212000	0.01225	-1.178000	0.02741	-1.194000	0.01681	ATG	A|0.640;C|0.360	0.360	strong		0.721	ADSSL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410531.1		Missense_Mutation
CPVL	54504	hgsc.bcm.edu	37	7	29152416	29152416	+	Silent	SNP	G	G	A	rs2011337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:29152416G>A	ENST00000409850.1	-	7	838	c.192C>T	c.(190-192)ggC>ggT	p.G64G	CPVL_ENST00000488891.2_5'UTR|CPVL_ENST00000396276.3_Silent_p.G64G|CPVL_ENST00000265394.5_Silent_p.G64G			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	64						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						CTGGGAAAGGGCCGACCAAAC	0.438													A|||	492	0.0982428	0.2171	0.085	5008	,	,		16606	0.0337		0.0984	False		,,,				2504	0.0133				p.G64G		Atlas-SNP	.											.	CPVL	60	.	0			c.C192T						PASS	.	A	,	851,3555	745.5+/-411.7	80,691,1432	80.0	76.0	77.0		192,192	0.9	0.0	7	dbSNP_92	77	1017,7583	772.7+/-407.7	65,887,3348	no	coding-synonymous,coding-synonymous	CPVL	NM_019029.2,NM_031311.3	,	145,1578,4780	AA,AG,GG		11.8256,19.3146,14.3626	,	64/477,64/477	29152416	1868,11138	2203	4300	6503	SO:0001819	synonymous_variant	54504	exon3			GAAAGGGCCGACC	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"""carboxypeptidase WUG"", ""vitellogenic carboxypeptidase-like protein"", ""CP-Mac carboxypeptidase"""	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.192C>T	7.37:g.29152416G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	173	64	0.369942	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Silent	SNP	ENST00000409850.1	37	CCDS5419.1																																																																																			G|0.869;A|0.131	0.131	strong		0.438	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029	
LINGO1	84894	hgsc.bcm.edu	37	15	77907535	77907535	+	Silent	SNP	C	C	G	rs2271396	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:77907535C>G	ENST00000355300.6	-	2	888	c.714G>C	c.(712-714)ctG>ctC	p.L238L	LINGO1_ENST00000561030.1_Silent_p.L232L	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	238					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						TGAGTCGGTACAGCCTCTTGA	0.602													C|||	3596	0.718051	0.6846	0.6556	5008	,	,		20852	0.8016		0.6461	False		,,,				2504	0.7955				p.L238L		Atlas-SNP	.											.	LINGO1	76	.	0			c.G714C						PASS	.	C		2976,1376		1020,936,220	117.0	126.0	123.0		714	3.5	1.0	15	dbSNP_100	123	5449,3111		1721,2007,552	no	coding-synonymous	LINGO1	NM_032808.5		2741,2943,772	GG,GC,CC		36.3435,31.6176,34.7506		238/621	77907535	8425,4487	2176	4280	6456	SO:0001819	synonymous_variant	84894	exon2			TCGGTACAGCCTC	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.714G>C	15.37:g.77907535C>G		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																			C|0.298;G|0.702	0.702	strong		0.602	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
MPHOSPH8	54737	hgsc.bcm.edu	37	13	20224387	20224387	+	Silent	SNP	A	A	G	rs9578176	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:20224387A>G	ENST00000361479.5	+	5	1631	c.1563A>G	c.(1561-1563)gcA>gcG	p.A521A	MPHOSPH8_ENST00000414242.2_Silent_p.A521A	NM_017520.3	NP_059990.2	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	521					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of DNA methylation (GO:0044030)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nuclear nucleosome (GO:0000788)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	methylated histone binding (GO:0035064)			breast(2)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		TGTGCCAAGCAGATGAGAATT	0.408													A|||	534	0.106629	0.1974	0.0735	5008	,	,		17874	0.0754		0.0974	False		,,,				2504	0.0491				p.A521A		Atlas-SNP	.											.	MPHOSPH8	58	.	0			c.A1563G						PASS	.	A		783,3623	313.3+/-293.0	75,633,1495	144.0	123.0	130.0		1563	-9.1	0.0	13	dbSNP_119	130	646,7954	165.4+/-217.5	18,610,3672	no	coding-synonymous	MPHOSPH8	NM_017520.3		93,1243,5167	GG,GA,AA		7.5116,17.7712,10.9872		521/861	20224387	1429,11577	2203	4300	6503	SO:0001819	synonymous_variant	54737	exon5			CCAAGCAGATGAG	AK056785, AJ293409	CCDS9287.1	13q12.11	2013-01-10			ENSG00000196199	ENSG00000196199		"""Ankyrin repeat domain containing"""	29810	protein-coding gene	gene with protein product		611626				8885239	Standard	NM_017520		Approved	mpp8, HSMPP8	uc001umh.3	Q99549	OTTHUMG00000016498	ENST00000361479.5:c.1563A>G	13.37:g.20224387A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_017520	B7Z6F9|Q5JPE5|Q5JTQ0|Q86TK3|Q96MK4|Q9BTP1	Silent	SNP	ENST00000361479.5	37	CCDS9287.1																																																																																			A|0.886;G|0.114	0.114	strong		0.408	MPHOSPH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044028.2	NM_017520	
CPAMD8	27151	hgsc.bcm.edu	37	19	17100552	17100552	+	Silent	SNP	A	A	G	rs1973093	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17100552A>G	ENST00000443236.1	-	13	1468	c.1437T>C	c.(1435-1437)ccT>ccC	p.P479P	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	432						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						GAGCCCCCACAGGCTTCCCGT	0.607													G|||	3047	0.608427	0.8563	0.5043	5008	,	,		16498	0.629		0.5239	False		,,,				2504	0.4131				p.P479P		Atlas-SNP	.											CPAMD8,colon,carcinoma,-2,1	CPAMD8	192	1	0			c.T1437C						PASS	.	G		3096,828		1230,636,96	31.0	41.0	38.0		1437	-5.7	0.1	19	dbSNP_92	38	3989,4297		968,2053,1122	no	coding-synonymous	CPAMD8	NM_015692.2		2198,2689,1218	GG,GA,AA		48.1414,21.1009,41.9738		479/1933	17100552	7085,5125	1962	4143	6105	SO:0001819	synonymous_variant	27151	exon13			CCCCACAGGCTTC	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.1437T>C	19.37:g.17100552A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	1332	0.6098901098901099	417	0.8475609756097561	192	0.5303867403314917	347	0.6066433566433567	376	0.49604221635883905	G	0.021	-1.430601	0.01117	0.788991	0.481414	ENSG00000160111	ENST00000443236	.	.	.	2.87	-5.73	0.02398	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.23168	P	0.99818347	.	.	.	.	.	.	T	0.19289	-1.0310	3	.	.	.	.	3.5665	0.07901	0.5238:0.1882:0.1938:0.0942	rs1973093;rs59637240	.	.	.	P	490	.	.	L	-	2	0	CPAMD8	16961552	0.023000	0.18921	0.050000	0.19076	0.001000	0.01503	-1.443000	0.02405	-1.715000	0.01389	-2.582000	0.00168	CTG	A|0.428;G|0.572	0.572	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
TEDDM1	127670	hgsc.bcm.edu	37	1	182369233	182369233	+	Missense_Mutation	SNP	A	A	G	rs6674281	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:182369233A>G	ENST00000367565.1	-	1	518	c.388T>C	c.(388-390)Tat>Cat	p.Y130H		NM_172000.3	NP_741997.3	Q5T9Z0	TEDM1_HUMAN	transmembrane epididymal protein 1	130			Y -> H (in dbSNP:rs6674281).			integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(2)	7						AGCAGAGAATAAACGTGCAGC	0.512													G|||	3396	0.678115	0.761	0.6124	5008	,	,		22039	0.8294		0.5417	False		,,,				2504	0.5971				p.Y130H		Atlas-SNP	.											.	TEDDM1	32	.	0			c.T388C						PASS	.	G	HIS/TYR	3281,1125	402.8+/-332.5	1230,821,152	147.0	146.0	147.0		388	5.1	0.0	1	dbSNP_116	147	4445,4155	566.7+/-388.7	1151,2143,1006	yes	missense	TEDDM1	NM_172000.3	83	2381,2964,1158	GG,GA,AA		48.314,25.5334,40.5966	benign	130/274	182369233	7726,5280	2203	4300	6503	SO:0001583	missense	127670	exon1			GAGAATAAACGTG	AJ515384	CCDS30953.1	1q25.3	2009-09-17		2005-08-09	ENSG00000203730	ENSG00000203730			30233	protein-coding gene	gene with protein product	"""putative membrane protein HE9"", ""transmembrane protein 45C"", ""epididymal protein 9"""						Standard	NM_172000		Approved	HE9, Epdd1, TMEM45C, EDDM9	uc001gpe.3	Q5T9Z0	OTTHUMG00000037398	ENST00000367565.1:c.388T>C	1.37:g.182369233A>G	ENSP00000356536:p.Tyr130His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	190	115	0.605263	NM_172000	Q8IVJ0	Missense_Mutation	SNP	ENST00000367565.1	37	CCDS30953.1	1442	0.6602564102564102	362	0.7357723577235772	222	0.6132596685082873	461	0.8059440559440559	397	0.5237467018469657	G	0.012	-1.684426	0.00745	0.744666	0.51686	ENSG00000203730	ENST00000367565	T	0.31769	1.48	5.05	5.05	0.67936	.	0.000000	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00017	-2.845	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40136	-0.9579	9	0.02654	T	1	-45.4785	11.5331	0.50622	0.0864:0.0:0.9136:0.0	rs6674281;rs17463348;rs58719880;rs6674281	130	Q5T9Z0	TEDM1_HUMAN	H	130	ENSP00000356536:Y130H	ENSP00000356536:Y130H	Y	-	1	0	TEDDM1	180635856	0.922000	0.31269	0.020000	0.16555	0.001000	0.01503	3.052000	0.49893	1.368000	0.46115	-0.119000	0.15052	TAT	A|0.364;G|0.636	0.636	strong		0.512	TEDDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091029.1	NM_172000	
ZNF468	90333	hgsc.bcm.edu	37	19	53344118	53344118	+	Missense_Mutation	SNP	C	C	G	rs10419826	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53344118C>G	ENST00000595646.1	-	4	1549	c.1429G>C	c.(1429-1431)Ggt>Cgt	p.G477R	ZNF468_ENST00000390651.4_Missense_Mutation_p.G424R|ZNF468_ENST00000243639.4_3'UTR|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_Missense_Mutation_p.G424R			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	477			G -> R (in dbSNP:rs10419826).		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.G477R(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)		GATGTCTGACCGAAGGTCTTG	0.453													-|||	2904	0.579872	0.8041	0.6326	5008	,	,		21287	0.3254		0.4135	False		,,,				2504	0.6728				p.G477R		Atlas-SNP	.											ZNF468,NS,carcinoma,0,1	ZNF468	46	1	1	Substitution - Missense(1)	stomach(1)	c.G1429C						scavenged	.	G	ARG/GLY,ARG/GLY	3208,1198		1214,780,209	109.0	138.0	128.0		1429,1270	0.9	0.0	19	dbSNP_119	128	3625,4963		836,1953,1505	no	missense,missense	ZNF468	NM_001008801.1,NM_199132.1	125,125	2050,2733,1714	GG,GC,CC		42.2101,27.1902,47.4142	benign,benign	477/523,424/470	53344118	6833,6161	2203	4294	6497	SO:0001583	missense	90333	exon4			TCTGACCGAAGGT	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.1429G>C	19.37:g.53344118C>G	ENSP00000470381:p.Gly477Arg	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	145	52	0.358621	NM_001008801	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Missense_Mutation	SNP	ENST00000595646.1	37	CCDS33094.1	983	0.4500915750915751	320	0.6504065040650406	191	0.5276243093922652	194	0.33916083916083917	278	0.36675461741424803	-	1.040	-0.679015	0.03378	0.728098	0.422101	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651	T;T	0.07327	3.2;3.2	1.99	0.854	0.19007	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04320	-0.23	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06197	-1.0840	8	0.23891	T	0.37	.	4.2223	0.10563	0.0:0.1304:0.2093:0.6602	rs10419826;rs57381965	477	Q5VIY5	ZN468_HUMAN	R	477;424;424	ENSP00000379690:G424R;ENSP00000445669:G424R	ENSP00000243639:G477R	G	-	1	0	ZNF468	58035930	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.884000	0.01622	-0.405000	0.07599	-2.606000	0.00160	GGT	C|0.485;G|0.515	0.515	strong		0.453	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
ZNF646	9726	hgsc.bcm.edu	37	16	31091209	31091209	+	Silent	SNP	T	T	C	rs3751855	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:31091209T>C	ENST00000394979.2	+	1	3987	c.3564T>C	c.(3562-3564)acT>acC	p.T1188T	ZNF646_ENST00000300850.5_Silent_p.T1188T			O15015	ZN646_HUMAN	zinc finger protein 646	1188					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						GGCTGGAGACTGCCGAGAAGG	0.612													C|||	2402	0.479633	0.652	0.4323	5008	,	,		16321	0.1121		0.3787	False		,,,				2504	0.7628				p.T1188T		Atlas-SNP	.											.	ZNF646	133	.	0			c.T3564C						PASS	.	C		2698,1696	496.5+/-363.6	844,1010,343	29.0	37.0	35.0		3564	-10.8	0.0	16	dbSNP_107	35	3119,5477	646.4+/-400.3	571,1977,1750	no	coding-synonymous	ZNF646	NM_014699.3		1415,2987,2093	CC,CT,TT		36.2843,38.5981,44.7806		1188/1833	31091209	5817,7173	2197	4298	6495	SO:0001819	synonymous_variant	9726	exon2			GGAGACTGCCGAG	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.3564T>C	16.37:g.31091209T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																				A|0.000;C|0.415;T|0.584	0.415	strong		0.612	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
MSH3	4437	hgsc.bcm.edu	37	5	79966029	79966029	+	Silent	SNP	G	G	A	rs1805355	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79966029G>A	ENST00000265081.6	+	4	773	c.693G>A	c.(691-693)ccG>ccA	p.P231P		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	231	Interaction with EXO1.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|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)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		TCTATACGCCGCTAGAATTAC	0.378								Mismatch excision repair (MMR)					G|||	916	0.182907	0.1974	0.2651	5008	,	,		16920	0.3383		0.0537	False		,,,				2504	0.0777				p.P231P	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.G693A						PASS	.	G		797,3609	319.3+/-296.1	66,665,1472	133.0	131.0	131.0		693	-6.6	0.0	5	dbSNP_92	131	524,8076	146.6+/-202.2	14,496,3790	no	coding-synonymous	MSH3	NM_002439.3		80,1161,5262	AA,AG,GG		6.093,18.089,10.1569		231/1138	79966029	1321,11685	2203	4300	6503	SO:0001819	synonymous_variant	4437	exon4			TACGCCGCTAGAA	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.693G>A	5.37:g.79966029G>A		Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	251	129	0.513944	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																			G|0.817;A|0.183	0.183	strong		0.378	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
CACNA1H	8912	hgsc.bcm.edu	37	16	1271983	1271983	+	IGR	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1271983A>G	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Silent_p.R257R	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)	AGGCAGGGACACGAGTGTAGA	0.672																																					p.R257R		Atlas-SNP	.											TPSG1,face,carcinoma,-2,1	TPSG1	19	1	0			c.T771C						scavenged	.						29.0	39.0	35.0					16																	1271983		2195	4297	6492	SO:0001628	intergenic_variant	25823	exon6			AGGGACACGAGTG	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.1271983A>G		Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	236	3	0.0127119	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			.	.	none		0.672	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
WBP1	23559	hgsc.bcm.edu	37	2	74687781	74687781	+	Silent	SNP	G	G	A	rs61733470	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:74687781G>A	ENST00000233615.2	+	4	1057	c.783G>A	c.(781-783)ctG>ctA	p.L261L	WBP1_ENST00000409737.1_Silent_p.L258L|WBP1_ENST00000494741.1_3'UTR|MOGS_ENST00000462443.1_5'Flank|WBP1_ENST00000393972.3_Silent_p.L295L	NM_012477.3	NP_036609.1	Q96G27	WBP1_HUMAN	WW domain binding protein 1	261							WW domain binding (GO:0050699)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	8						CCATGGGGCTGTCTTCCAGTG	0.552													G|||	124	0.0247604	0.0	0.0231	5008	,	,		20306	0.0		0.0417	False		,,,				2504	0.0675				p.L261L		Atlas-SNP	.											.	WBP1	35	.	0			c.G783A						PASS	.	G		41,4363	42.3+/-75.8	0,41,2161	41.0	37.0	38.0		783	2.5	1.0	2	dbSNP_129	38	458,8140	131.7+/-189.4	15,428,3856	no	coding-synonymous	WBP1	NM_012477.3		15,469,6017	AA,AG,GG		5.3268,0.931,3.8379		261/270	74687781	499,12503	2202	4299	6501	SO:0001819	synonymous_variant	23559	exon4			GGGGCTGTCTTCC	U79457	CCDS1943.1	2p12	2012-04-20			ENSG00000239779	ENSG00000239779			12737	protein-coding gene	gene with protein product		606961				7644498	Standard	NM_012477		Approved	WBP-1	uc002slj.2	Q96G27	OTTHUMG00000129958	ENST00000233615.2:c.783G>A	2.37:g.74687781G>A		Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	255	117	0.458824	NM_012477	B2RE02|O95637	Silent	SNP	ENST00000233615.2	37	CCDS1943.1																																																																																			G|0.970;A|0.030	0.030	strong		0.552	WBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252221.2	NM_012477	
MALT1	10892	hgsc.bcm.edu	37	18	56367823	56367823	+	Splice_Site	SNP	A	A	G	rs74847855	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:56367823A>G	ENST00000348428.3	+	4	907	c.649A>G	c.(649-651)Aga>Gga	p.R217G	RP11-126O1.4_ENST00000588835.1_RNA|MALT1_ENST00000345724.3_Splice_Site_p.R217G	NM_006785.2|NM_173844.1	NP_006776.1|NP_776216.1	Q9UDY8	MALT1_HUMAN	mucosa associated lymphoid tissue lymphoma translocation gene 1	217	Ig-like C2-type 2.	Breakpoint for translocation to form BIRC2-MALT1.			activation of NF-kappaB-inducing kinase activity (GO:0007250)|B-1 B cell differentiation (GO:0001923)|defense response (GO:0006952)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|nuclear export (GO:0051168)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|protein oligomerization (GO:0051259)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of T cell receptor signaling pathway (GO:0050856)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)|protein self-association (GO:0043621)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|large_intestine(7)|lung(1)|ovary(2)|skin(1)	12						GAGCTTCCAGAGTAAGTAACG	0.358			T	BIRC3	MALT								A|||	101	0.0201677	0.0038	0.0086	5008	,	,		16547	0.0		0.0318	False		,,,				2504	0.0593				p.R217G		Atlas-SNP	.		Dom	yes		18	18q21	10892	mucosa associated lymphoid tissue lymphoma translocation gene 1		L	.	MALT1	55	.	0			c.A649G						PASS	.	A	GLY/ARG,GLY/ARG	37,4369	35.2+/-66.4	0,37,2166	60.0	54.0	56.0		649,649	-0.3	0.2	18	dbSNP_131	56	348,8252	113.1+/-173.2	12,324,3964	yes	missense-near-splice,missense-near-splice	MALT1	NM_006785.2,NM_173844.1	125,125	12,361,6130	GG,GA,AA		4.0465,0.8398,2.9602	benign,benign	217/825,217/814	56367823	385,12621	2203	4300	6503	SO:0001630	splice_region_variant	10892	exon4			TTCCAGAGTAAGT		CCDS11967.1, CCDS11968.1	18q21	2013-01-11			ENSG00000172175	ENSG00000172175		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6819	protein-coding gene	gene with protein product	"""paracaspase"""	604860		MLT		10339464, 10406266, 10523859	Standard	NM_006785		Approved		uc002lhm.1	Q9UDY8	OTTHUMG00000132761	ENST00000348428.3:c.649+1A>G	18.37:g.56367823A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_173844	Q9NTB7|Q9ULX4	Missense_Mutation	SNP	ENST00000348428.3	37	CCDS11967.1	31	0.014194139194139194	5	0.01016260162601626	4	0.011049723756906077	0	0.0	22	0.029023746701846966	A	1.142	-0.649255	0.03506	0.008398	0.040465	ENSG00000172175	ENST00000348428;ENST00000345724	T;T	0.11712	2.75;2.78	5.11	-0.311	0.12761	Immunoglobulin-like (1);	0.985312	0.08334	N	0.961859	T	0.00967	0.0032	N	0.04508	-0.205	0.27371	N	0.955684	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46373	-0.9196	10	0.15066	T	0.55	.	8.2849	0.31922	0.4325:0.0:0.5675:0.0	.	217;217	Q9UDY8-2;Q9UDY8	.;MALT1_HUMAN	G	217	ENSP00000319279:R217G;ENSP00000304161:R217G	ENSP00000304161:R217G	R	+	1	2	MALT1	54518803	0.503000	0.26115	0.185000	0.23176	0.114000	0.19823	0.657000	0.24963	-0.046000	0.13446	-0.375000	0.07067	AGA	A|0.975;G|0.025	0.025	strong		0.358	MALT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256132.2		Missense_Mutation
HIST1H3C	8352	hgsc.bcm.edu	37	6	26045737	26045737	+	Silent	SNP	C	C	G	rs3752418	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26045737C>G	ENST00000540144.1	+	1	99	c.99C>G	c.(97-99)acC>acG	p.T33T	HIST1H2BB_ENST00000357905.2_5'Flank	NM_003531.2	NP_003522.1	P68431	H31_HUMAN	histone cluster 1, H3c	33					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						CTCCGGCCACCGGTGGCGTGA	0.617													c|||	1086	0.216853	0.0734	0.2695	5008	,	,		16517	0.5149		0.0676	False		,,,				2504	0.2198				p.T33T		Atlas-SNP	.											.	HIST1H3C	34	.	0			c.C99G						PASS	.	G		400,4006	186.7+/-213.5	19,362,1822	41.0	44.0	43.0		99	-9.3	0.1	6	dbSNP_107	43	578,8020	146.3+/-201.9	15,548,3736	no	coding-synonymous	HIST1H3C	NM_003531.2		34,910,5558	GG,GC,CC		6.7225,9.0785,7.5208		33/137	26045737	978,12026	2203	4299	6502	SO:0001819	synonymous_variant	8352	exon1			GGCCACCGGTGGC	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.99C>G	6.37:g.26045737C>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_003531	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000540144.1	37	CCDS4576.1																																																																																			C|0.881;G|0.119	0.119	strong		0.617	HIST1H3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040078.1	NM_003531	
ASPRV1	151516	hgsc.bcm.edu	37	2	70188676	70188676	+	Missense_Mutation	SNP	T	T	C	rs3796097	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:70188676T>C	ENST00000320256.4	-	1	721	c.145A>G	c.(145-147)Act>Gct	p.T49A	PCBP1-AS1_ENST00000413436.1_RNA|PCBP1-AS1_ENST00000435880.2_RNA|PCBP1-AS1_ENST00000415222.1_RNA|PCBP1-AS1_ENST00000418564.1_RNA|PCBP1-AS1_ENST00000457076.1_RNA|PCBP1-AS1_ENST00000596259.1_RNA|PCBP1-AS1_ENST00000419542.1_RNA	NM_152792.2	NP_690005.2			aspartic peptidase, retroviral-like 1											endometrium(3)|large_intestine(4)|lung(6)|ovary(1)	14						CGAAGCAGAGTGGGGATGACT	0.637													C|||	3496	0.698083	0.9145	0.7421	5008	,	,		17996	0.6815		0.503	False		,,,				2504	0.592				p.T49A		Atlas-SNP	.											.	ASPRV1	41	.	0			c.A145G						PASS	.	C	ALA/THR	3733,673	283.1+/-276.9	1585,563,55	45.0	46.0	46.0		145	-4.7	0.0	2	dbSNP_107	46	4480,4120	560.7+/-387.6	1171,2138,991	yes	missense	ASPRV1	NM_152792.2	58	2756,2701,1046	CC,CT,TT		47.907,15.2746,36.8522	benign	49/344	70188676	8213,4793	2203	4300	6503	SO:0001583	missense	151516	exon1			GCAGAGTGGGGAT	AK055994	CCDS1897.1	2p13.3	2008-02-20			ENSG00000244617	ENSG00000244617			26321	protein-coding gene	gene with protein product	"""Skin ASpartic Protease"""	611765				16098038, 16565508	Standard	NM_152792		Approved	Taps, SASPase, FLJ25084	uc002sfz.4	Q53RT3	OTTHUMG00000129647	ENST00000320256.4:c.145A>G	2.37:g.70188676T>C	ENSP00000315383:p.Thr49Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_152792		Missense_Mutation	SNP	ENST00000320256.4	37	CCDS1897.1	1456	0.6666666666666666	450	0.9146341463414634	255	0.7044198895027625	370	0.6468531468531469	381	0.5026385224274407	C	2.190	-0.385484	0.04966	0.847254	0.52093	ENSG00000244617	ENST00000320256	T	0.43294	0.95	3.88	-4.7	0.03288	.	1.015840	0.07926	N	0.976770	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.23868	-1.0176	9	0.27082	T	0.32	.	11.8715	0.52523	0.0:0.5647:0.0:0.4353	rs3796097;rs13025324;rs3796097	49	Q53RT3	APRV1_HUMAN	A	49	ENSP00000315383:T49A	ENSP00000315383:T49A	T	-	1	0	ASPRV1	70042180	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.869000	0.04232	-1.206000	0.02641	-1.088000	0.02184	ACT	T|0.345;C|0.655	0.655	strong		0.637	ASPRV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334161.1	NM_152792	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389101	1389101	+	Missense_Mutation	SNP	A	A	G	rs71614971	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1389101A>G	ENST00000324803.4	+	1	3762	c.802A>G	c.(802-804)Agt>Ggt	p.S268G		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	268					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)			GCCCATGTGGAGTGCCCGCCT	0.692													A|||	1001	0.19988	0.1293	0.2795	5008	,	,		12141	0.0526		0.3529	False		,,,				2504	0.2331				p.S268G		Atlas-SNP	.											.	CRIPAK	185	.	0			c.A802G						PASS	.	A	GLY/SER	618,3788		43,532,1628	140.0	129.0	132.0		802	-1.6	0.0	4	dbSNP_130	132	3204,5392		611,1982,1705	no	missense	CRIPAK	NM_175918.3	56	654,2514,3333	GG,GA,AA		37.2732,14.0263,29.3955	benign	268/447	1389101	3822,9180	2203	4298	6501	SO:0001583	missense	285464	exon1			ATGTGGAGTGCCC	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.802A>G	4.37:g.1389101A>G	ENSP00000323978:p.Ser268Gly	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	44	43	0.977273	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	448	0.20512820512820512	61	0.12398373983739837	96	0.26519337016574585	38	0.06643356643356643	253	0.3337730870712401	-	1.677	-0.507416	0.04231	0.140263	0.372732	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.21734	1.99	0.815	-1.63	0.08345	.	.	.	.	.	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	0.47129	-0.9141	8	0.20519	T	0.43	.	2.8991	0.05700	0.2283:0.0:0.4427:0.329	.	268	Q8N1N5	CRPAK_HUMAN	G	268;210	ENSP00000323978:S268G	ENSP00000323978:S268G	S	+	1	0	CRIPAK	1379101	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.535000	0.02210	-1.564000	0.01678	-0.530000	0.04314	AGT	A|0.752;G|0.248	0.248	strong		0.692	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
THBS4	7060	hgsc.bcm.edu	37	5	79361265	79361265	+	Missense_Mutation	SNP	G	G	C	rs1866389	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79361265G>C	ENST00000350881.2	+	9	1349	c.1159G>C	c.(1159-1161)Gcg>Ccg	p.A387P	THBS4_ENST00000511733.1_Missense_Mutation_p.A296P|CTD-2201I18.1_ENST00000514042.1_RNA|CTD-2201I18.1_ENST00000503007.1_RNA	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	164	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	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		
GRIK1	2897	hgsc.bcm.edu	37	21	31062070	31062070	+	Silent	SNP	T	T	G	rs363538	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31062070T>G	ENST00000399907.1	-	3	933	c.522A>C	c.(520-522)acA>acC	p.T174T	GRIK1_ENST00000327783.4_Silent_p.T174T|GRIK1_ENST00000389124.2_Silent_p.T174T|GRIK1_ENST00000535441.1_Silent_p.T174T|GRIK1_ENST00000389125.3_Silent_p.T174T|GRIK1_ENST00000399914.1_Silent_p.T174T|GRIK1_ENST00000309434.7_Silent_p.T174T|GRIK1_ENST00000399909.1_Silent_p.T174T|GRIK1_ENST00000399913.1_Silent_p.T174T|GRIK1_ENST00000472429.1_5'UTR	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	174					adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	CATACACCACTGTCACTGTTT	0.428													G|||	1704	0.340256	0.6755	0.2925	5008	,	,		18444	0.3393		0.1163	False		,,,				2504	0.1524				p.T174T		Atlas-SNP	.											.	GRIK1	293	.	0			c.A522C						PASS	.	G	,	2527,1879	542.2+/-376.0	732,1063,408	216.0	207.0	210.0		522,522	-10.0	0.0	21	dbSNP_79	210	973,7627	774.7+/-407.7	62,849,3389	no	coding-synonymous,coding-synonymous	GRIK1	NM_000830.3,NM_175611.2	,	794,1912,3797	GG,GT,TT		11.314,42.6464,26.9107	,	174/919,174/906	31062070	3500,9506	2203	4300	6503	SO:0001819	synonymous_variant	2897	exon3			CACCACTGTCACT		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.522A>C	21.37:g.31062070T>G		Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	393	248	0.631043	NM_175611	Q13001|Q86SU9	Silent	SNP	ENST00000399907.1	37	CCDS42913.1																																																																																			T|0.690;G|0.310	0.310	strong		0.428	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1		
EDDM3B	64184	hgsc.bcm.edu	37	14	21238318	21238318	+	Silent	SNP	G	G	A	rs3827905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21238318G>A	ENST00000326783.3	+	2	107	c.9G>A	c.(7-9)tcG>tcA	p.S3S		NM_022360.4	NP_071755.1	P56851	EP3B_HUMAN	epididymal protein 3B	3						extracellular region (GO:0005576)				central_nervous_system(1)|kidney(1)|lung(3)|ovary(1)|skin(1)	7						AGATGGCATCGTCTCTAAAGA	0.483													G|||	2765	0.552117	0.1929	0.5461	5008	,	,		18089	0.7262		0.6948	False		,,,				2504	0.7157				p.S3S		Atlas-SNP	.											.	EDDM3B	23	.	0			c.G9A						PASS	.	G		1267,3139	429.3+/-342.2	181,905,1117	52.0	52.0	52.0		9	-3.1	0.0	14	dbSNP_107	52	5679,2921	670.0+/-402.7	1873,1933,494	no	coding-synonymous	EDDM3B	NM_022360.4		2054,2838,1611	AA,AG,GG		33.9651,28.7562,46.5939		3/148	21238318	6946,6060	2203	4300	6503	SO:0001819	synonymous_variant	64184	exon2			GGCATCGTCTCTA	X76386	CCDS9557.1	14q11.1	2010-03-19	2010-01-27	2010-01-27	ENSG00000181552	ENSG00000181552			19223	protein-coding gene	gene with protein product		611582	"""family with sequence similarity 12, member B (epididymal)"""	FAM12B		7514008	Standard	NM_022360		Approved	HE3-BETA	uc001vyd.3	P56851	OTTHUMG00000029583	ENST00000326783.3:c.9G>A	14.37:g.21238318G>A		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	180	105	0.583333	NM_022360	A0PK89	Silent	SNP	ENST00000326783.3	37	CCDS9557.1																																																																																			G|0.447;A|0.553	0.553	strong		0.483	EDDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073745.2		
EEA1	8411	hgsc.bcm.edu	37	12	93202801	93202801	+	Silent	SNP	C	C	T	rs7970286	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:93202801C>T	ENST00000322349.8	-	18	2595	c.2331G>A	c.(2329-2331)gaG>gaA	p.E777E		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	777					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						ACATTTCCTTCTCCATTTCAA	0.358													C|||	2346	0.46845	0.1679	0.5245	5008	,	,		13451	0.8681		0.3569	False		,,,				2504	0.5378				p.E777E		Atlas-SNP	.											.	EEA1	104	.	0			c.G2331A						PASS	.	C		921,3485	349.3+/-310.3	112,697,1394	125.0	110.0	115.0		2331	2.9	1.0	12	dbSNP_116	115	2984,5616	463.0+/-365.8	512,1960,1828	no	coding-synonymous	EEA1	NM_003566.3		624,2657,3222	TT,TC,CC		34.6977,20.9033,30.0246		777/1412	93202801	3905,9101	2203	4300	6503	SO:0001819	synonymous_variant	8411	exon18			TTCCTTCTCCATT	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.2331G>A	12.37:g.93202801C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	65	10	0.153846	NM_003566	Q14221	Silent	SNP	ENST00000322349.8	37	CCDS31874.1																																																																																			C|0.618;T|0.382	0.382	strong		0.358	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
TPO	7173	hgsc.bcm.edu	37	2	1499899	1499899	+	Silent	SNP	C	C	T	rs732608	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000329066.4_Silent_p.P715P|TPO_ENST00000382198.1_Silent_p.P542P|TPO_ENST00000497517.2_Intron|TPO_ENST00000382201.3_Silent_p.P658P|TPO_ENST00000349624.3_Silent_p.P542P|TPO_ENST00000346956.3_Silent_p.P715P	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	98	46	0.469388	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	
MYO18A	399687	hgsc.bcm.edu	37	17	27442710	27442710	+	Silent	SNP	G	G	C	rs28587908	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:27442710G>C	ENST00000527372.1	-	12	2379	c.2199C>G	c.(2197-2199)ccC>ccG	p.P733P	MYO18A_ENST00000354329.4_Silent_p.P733P|MYO18A_ENST00000533112.1_Silent_p.P733P|MYO18A_ENST00000531253.1_Silent_p.P733P	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	733	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CACTCTCCTCGGGGCCCTGGC	0.642													G|||	495	0.0988419	0.149	0.0562	5008	,	,		19160	0.0456		0.0497	False		,,,				2504	0.1667				p.P733P	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.C2199G						PASS	.	G	,	497,3575		26,445,1565	26.0	32.0	30.0		2199,2199	-10.9	0.4	17	dbSNP_125	30	355,8015		5,345,3835	no	coding-synonymous,coding-synonymous	MYO18A	NM_078471.3,NM_203318.1	,	31,790,5400	CC,CG,GG		4.2413,12.2053,6.8478	,	733/2055,733/2040	27442710	852,11590	2036	4185	6221	SO:0001819	synonymous_variant	399687	exon12			CTCCTCGGGGCCC	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2199C>G	17.37:g.27442710G>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	37	CCDS45642.1																																																																																			G|0.893;C|0.107	0.107	strong		0.642	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
CDC16	8881	hgsc.bcm.edu	37	13	115004935	115004935	+	Silent	SNP	T	T	C	rs2296970	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:115004935T>C	ENST00000356221.3	+	5	459	c.351T>C	c.(349-351)ccT>ccC	p.P117P	CDC16_ENST00000375312.3_Silent_p.P23P|CDC16_ENST00000252458.6_Silent_p.P23P|CDC16_ENST00000375310.1_Silent_p.P23P|CDC16_ENST00000375308.1_Silent_p.P23P|CDC16_ENST00000360383.3_Silent_p.P117P|CDC16_ENST00000252457.5_Silent_p.P116P			Q13042	CDC16_HUMAN	cell division cycle 16	117					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|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)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|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)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	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)			TCAAAGATCCTTCCAGCGACT	0.453													C|||	2212	0.441693	0.8366	0.3516	5008	,	,		17862	0.2024		0.3191	False		,,,				2504	0.3446				p.P117P		Atlas-SNP	.											.	CDC16	50	.	0			c.T351C						PASS	.	C	,	3269,1137	400.4+/-331.6	1229,811,163	43.0	48.0	46.0		351,351	2.6	1.0	13	dbSNP_100	46	2445,6155	694.4+/-404.7	368,1709,2223	no	coding-synonymous,coding-synonymous	CDC16	NM_001078645.1,NM_003903.3	,	1597,2520,2386	CC,CT,TT		28.4302,25.8057,43.9336	,	117/621,117/621	115004935	5714,7292	2203	4300	6503	SO:0001819	synonymous_variant	8881	exon5			AGATCCTTCCAGC	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.351T>C	13.37:g.115004935T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	62	60	0.967742	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2																																																																																			T|0.563;C|0.437	0.437	strong		0.453	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	
TTC38	55020	hgsc.bcm.edu	37	22	46682976	46682976	+	Missense_Mutation	SNP	C	C	T	rs55653327	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:46682976C>T	ENST00000381031.3	+	10	917	c.841C>T	c.(841-843)Ccc>Tcc	p.P281S	TTC38_ENST00000445282.2_Missense_Mutation_p.P223S	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	281						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						CCAGATCCTTCCCAGCCTGCA	0.662													C|||	190	0.0379393	0.003	0.0562	5008	,	,		21954	0.001		0.1133	False		,,,				2504	0.0327				p.P281S		Atlas-SNP	.											.	TTC38	40	.	0			c.C841T						PASS	.	C	SER/PRO	70,4150		1,68,2041	32.0	36.0	35.0		841	4.7	1.0	22	dbSNP_129	35	854,7630		46,762,3434	yes	missense	TTC38	NM_017931.2	74	47,830,5475	TT,TC,CC		10.066,1.6588,7.2733	benign	281/470	46682976	924,11780	2110	4242	6352	SO:0001583	missense	55020	exon10			ATCCTTCCCAGCC		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.841C>T	22.37:g.46682976C>T	ENSP00000370419:p.Pro281Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	44	28	0.636364	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	114	0.0521978021978022	0	0.0	26	0.0718232044198895	0	0.0	88	0.11609498680738786	C	17.03	3.284063	0.59867	0.016588	0.10066	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.75154	0.88;-0.91	4.7	4.7	0.59300	.	0.245457	0.39985	N	0.001218	T	0.02380	0.0073	L	0.55743	1.74	0.22066	P	0.999385888	B;B	0.32350	0.335;0.366	B;B	0.35688	0.208;0.112	T	0.47509	-0.9112	9	0.09338	T	0.73	0.3381	16.2259	0.82288	0.0:1.0:0.0:0.0	rs55653327	223;281	E7ES35;Q5R3I4	.;TTC38_HUMAN	S	281;223	ENSP00000370419:P281S;ENSP00000393960:P223S	ENSP00000370419:P281S	P	+	1	0	TTC38	45061640	1.000000	0.71417	0.992000	0.48379	0.883000	0.51084	4.894000	0.63206	2.153000	0.67306	0.563000	0.77884	CCC	C|0.941;T|0.059	0.059	strong		0.662	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
OR5T2	219464	hgsc.bcm.edu	37	11	56000600	56000600	+	Missense_Mutation	SNP	G	G	T	rs3919907	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56000600G>T	ENST00000313264.4	-	1	137	c.62C>A	c.(61-63)tCt>tAt	p.S21Y		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	21			S -> Y (in dbSNP:rs3919907).			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(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					ATGACAAAAAGAATGAACAAC	0.333													g|||	1050	0.209665	0.0265	0.2954	5008	,	,		19308	0.378		0.2286	False		,,,				2504	0.2035				p.S21Y		Atlas-SNP	.											OR5T2,NS,carcinoma,+1,1	OR5T2	107	1	0			c.C62A						PASS	.	G	TYR/SER	289,4113	156.6+/-189.7	9,271,1921	113.0	106.0	108.0		62	-0.1	0.0	11	dbSNP_108	108	1897,6695	332.9+/-320.3	219,1459,2618	yes	missense	OR5T2	NM_001004746.1	144	228,1730,4539	TT,TG,GG		22.0787,6.5652,16.8231	benign	21/360	56000600	2186,10808	2201	4296	6497	SO:0001583	missense	219464	exon1			CAAAAAGAATGAA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.62C>A	11.37:g.56000600G>T	ENSP00000323688:p.Ser21Tyr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	93	36	0.387097	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	511	0.23397435897435898	20	0.04065040650406504	119	0.3287292817679558	203	0.3548951048951049	169	0.22295514511873352	G	1.222	-0.626727	0.03610	0.065652	0.220787	ENSG00000181718	ENST00000313264	T	0.00666	5.91	0.848	-0.135	0.13477	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18863	0.031	B	0.06405	0.002	T	0.39761	-0.9598	8	0.87932	D	0	.	3.2208	0.06715	0.317:0.0:0.683:0.0	rs3919907;rs17705089;rs52830662;rs3919907	21	Q8NGG2	OR5T2_HUMAN	Y	21	ENSP00000323688:S21Y	ENSP00000323688:S21Y	S	-	2	0	OR5T2	55757176	0.540000	0.26410	0.001000	0.08648	0.065000	0.16274	-0.009000	0.12765	-0.002000	0.14469	0.271000	0.19318	TCT	G|0.810;T|0.190	0.190	strong		0.333	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
ZNF835	90485	hgsc.bcm.edu	37	19	57175121	57175121	+	Silent	SNP	G	G	A	rs115625349	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57175121G>A	ENST00000537055.2	-	2	1677	c.1446C>T	c.(1444-1446)gcC>gcT	p.A482A		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	482					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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						AGAAGCTGAAGGCCTTCCCGC	0.642													.|||	408	0.0814696	0.233	0.0346	5008	,	,		16940	0.0258		0.0099	False		,,,				2504	0.0409				p.A482A		Atlas-SNP	.											.	ZNF835	106	.	0			c.C1446T						PASS	.	G		929,3477	333.6+/-303.0	99,731,1373	123.0	137.0	133.0		1446	1.9	1.0	19	dbSNP_132	133	164,8436	76.6+/-139.3	1,162,4137	no	coding-synonymous	ZNF835	NM_001005850.2		100,893,5510	AA,AG,GG		1.907,21.0849,8.4038		482/538	57175121	1093,11913	2203	4300	6503	SO:0001819	synonymous_variant	90485	exon2			GCTGAAGGCCTTC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1446C>T	19.37:g.57175121G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	121	58	0.479339	NM_001005850	B7Z5Y0|G3V1S0	Silent	SNP	ENST00000537055.2	37	CCDS56105.1																																																																																			G|0.942;A|0.058	0.058	strong		0.642	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
TTC17	55761	hgsc.bcm.edu	37	11	43472746	43472746	+	Silent	SNP	C	C	T	rs11551137	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	51	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	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	
RCOR1	23186	hgsc.bcm.edu	37	14	103173756	103173756	+	Silent	SNP	C	C	A	rs149418829	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:103173756C>A	ENST00000570597.1	+	5	558	c.558C>A	c.(556-558)acC>acA	p.T186T	RCOR1_ENST00000262241.6_Silent_p.T189T			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	186	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interaction with HDAC1.				blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						CCAACTTTACCCCTTTCCCAG	0.363													C|||	31	0.0061901	0.0	0.0202	5008	,	,		16191	0.0		0.0129	False		,,,				2504	0.0041				p.T189T		Atlas-SNP	.											.	RCOR1	39	.	0			c.C567A						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	134.0	136.0	136.0		558	3.1	1.0	14	dbSNP_134	136	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	RCOR1	NM_015156.3		0,110,6393	AA,AC,CC		1.1163,0.3177,0.8458		186/483	103173756	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	23186	exon5			CTTTACCCCTTTC	AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"""REST corepressor"""	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.558C>A	14.37:g.103173756C>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	162	51	0.314815	NM_015156	Q15044|Q6P2I9|Q86VG5	Silent	SNP	ENST00000570597.1	37																																																																																				C|0.990;A|0.010	0.010	strong		0.363	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156	
DCAF12L2	340578	hgsc.bcm.edu	37	X	125299467	125299467	+	Missense_Mutation	SNP	G	G	T	rs10126452	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:125299467G>T	ENST00000360028.2	-	1	467	c.441C>A	c.(439-441)caC>caA	p.H147Q	DCAF12L2_ENST00000538699.1_Missense_Mutation_p.H147Q			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	147			H -> Q (in dbSNP:rs10126452).							NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						CGCAGCCCTGGTGGGCCTGGG	0.642													T|||	2113	0.559735	0.6293	0.4294	3775	,	,		11489	0.3859		0.2525	False		,,,				2504	0.3476				p.H147Q		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.C441A						PASS	.	T	GLN/HIS	2959,876		974,575,436,83,135	76.0	79.0	78.0		441	-2.2	0.0	X	dbSNP_119	78	2000,4726		221,987,571,1219,1301	no	missense	DCAF12L2	NM_001013628.2	24	1195,1562,1007,1302,1436	TT,TG,T,GG,G		29.7354,22.8422,46.9558	benign	147/464	125299467	4959,5602	2203	4299	6502	SO:0001583	missense	340578	exon1			GCCCTGGTGGGCC	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"""WD repeat domain containing"""	32950	protein-coding gene	gene with protein product			"""WD repeat domain 40C"""	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.441C>A	X.37:g.125299467G>T	ENSP00000353128:p.His147Gln	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_001013628	B2RN42	Missense_Mutation	SNP	ENST00000360028.2	37	CCDS43991.1	863	0.5201928872814949	218	0.7077922077922078	100	0.36231884057971014	146	0.35784313725490197	131	0.19969512195121952	t	0.001	-3.105942	0.00033	0.771578	0.297354	ENSG00000198354	ENST00000538699;ENST00000360028	T;T	0.25250	1.81;1.81	3.89	-2.22	0.06952	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	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	0.40459	-0.9562	8	0.02654	T	1	.	0.7994	0.01072	0.1634:0.2374:0.3197:0.2795	rs10126452;rs61089575	147	Q5VW00	DC122_HUMAN	Q	147	ENSP00000441489:H147Q;ENSP00000353128:H147Q	ENSP00000353128:H147Q	H	-	3	2	DCAF12L2	125127148	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	0.736000	0.26130	-0.650000	0.05423	-3.105000	0.00063	CAC	G|0.479;T|0.521	0.521	strong		0.642	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628	
OXR1	55074	hgsc.bcm.edu	37	8	107719336	107719336	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:107719336T>C	ENST00000442977.2	+	8	1689	c.1590T>C	c.(1588-1590)gcT>gcC	p.A530A	OXR1_ENST00000517566.2_Silent_p.A529A|OXR1_ENST00000531443.1_Silent_p.A529A|OXR1_ENST00000497705.1_Silent_p.A462A|OXR1_ENST00000445937.1_Silent_p.A529A|OXR1_ENST00000312046.6_Silent_p.A522A|OXR1_ENST00000452423.2_Silent_p.A19A	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	530					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			AAAAAGAAGCTAAGCATAAAA	0.368																																					p.A530A		Atlas-SNP	.											OXR1_ENST00000442977,NS,carcinoma,+1,3	OXR1	190	3	0			c.T1590C						scavenged	.						75.0	74.0	74.0					8																	107719336		2203	4300	6503	SO:0001819	synonymous_variant	55074	exon8			AGAAGCTAAGCAT	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.1590T>C	8.37:g.107719336T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	37	CCDS56548.1	.	.	.	.	.	.	.	.	.	.	T	7.212	0.595695	0.13875	.	.	ENSG00000164830	ENST00000519415	.	.	.	5.62	1.63	0.23807	.	.	.	.	.	T	0.52451	0.1735	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40646	-0.9552	4	.	.	.	-23.5587	5.8173	0.18500	0.0:0.2102:0.3773:0.4126	.	.	.	.	P	243	.	.	L	+	2	0	OXR1	107788512	0.003000	0.15002	0.860000	0.33809	0.830000	0.47004	-0.604000	0.05667	0.388000	0.25054	0.482000	0.46254	CTA	.	.	none		0.368	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	
SLC6A5	9152	hgsc.bcm.edu	37	11	20673867	20673867	+	Silent	SNP	G	G	A	rs2276433	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	150	0	0		WXS	Illumina HiSeq	Phase_I	174	170	0.977012	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	
MRTO4	51154	hgsc.bcm.edu	37	1	19584004	19584004	+	Silent	SNP	G	G	A	rs1042380	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19584004G>A	ENST00000330263.4	+	5	627	c.330G>A	c.(328-330)gaG>gaA	p.E110E		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	110					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8		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;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GCACAAAGGAGGAGGTGAATG	0.527													G|||	1259	0.251398	0.4932	0.183	5008	,	,		22095	0.1012		0.2266	False		,,,				2504	0.1534				p.E110E	GBM(192;2418 3032 7540 48714)	Atlas-SNP	.											.	MRTO4	17	.	0			c.G330A						PASS	.	G		2091,2315	572.9+/-383.4	505,1081,617	147.0	142.0	144.0		330	-3.3	1.0	1	dbSNP_86	144	2104,6496	363.1+/-333.0	263,1578,2459	no	coding-synonymous	MRTO4	NM_016183.3		768,2659,3076	AA,AG,GG		24.4651,47.458,32.2543		110/240	19584004	4195,8811	2203	4300	6503	SO:0001819	synonymous_variant	51154	exon5			AAAGGAGGAGGTG	AK027569	CCDS191.1	1p36.13	2008-02-05	2006-12-21	2007-01-05	ENSG00000053372	ENSG00000053372			18477	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 33"", ""MRT4, mRNA turnover 4, homolog (S. cerevisiae)"""	C1orf33			Standard	NM_016183		Approved	dJ657E11.4, MRT4	uc001bbs.3	Q9UKD2	OTTHUMG00000002496	ENST00000330263.4:c.330G>A	1.37:g.19584004G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_016183	B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	CCDS191.1																																																																																			G|0.711;A|0.289	0.289	strong		0.527	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
NLRP7	199713	hgsc.bcm.edu	37	19	55450696	55450696	+	Silent	SNP	G	G	A	rs775880	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:55450696G>A	ENST00000590030.1	-	3	1531	c.1491C>T	c.(1489-1491)atC>atT	p.I497I	NLRP7_ENST00000592784.1_Silent_p.I497I|NLRP7_ENST00000446217.1_Silent_p.I525I|NLRP7_ENST00000340844.2_Silent_p.I497I|NLRP7_ENST00000588756.1_Silent_p.I497I|NLRP7_ENST00000328092.5_Silent_p.I497I|NLRP7_ENST00000448121.2_Silent_p.I497I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	497							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		GTACGTCCCCGATGTCCCAGG	0.562													.|||	447	0.0892572	0.2368	0.0562	5008	,	,		18553	0.003		0.0706	False		,,,				2504	0.0215				p.I497I		Atlas-SNP	.											.	NLRP7	411	.	0			c.C1491T						PASS	.	A	,,	922,3484	736.7+/-410.8	100,722,1381	72.0	69.0	70.0		1491,1491,1491	-1.5	0.0	19	dbSNP_86	70	314,8286	801.4+/-407.4	3,308,3989	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	,,	103,1030,5370	AA,AG,GG		3.6512,20.926,9.5033	,,	497/1038,497/1010,497/981	55450696	1236,11770	2203	4300	6503	SO:0001819	synonymous_variant	199713	exon4			GTCCCCGATGTCC	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1491C>T	19.37:g.55450696G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	172	23	0.133721	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			G|0.908;A|0.092	0.092	strong		0.562	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
FECH	2235	hgsc.bcm.edu	37	18	55247313	55247313	+	Silent	SNP	C	C	T	rs550820935		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:55247313C>T	ENST00000262093.5	-	2	337	c.186G>A	c.(184-186)ccG>ccA	p.P62P	FECH_ENST00000382873.3_Silent_p.P62P|FECH_ENST00000585699.1_Intron	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	62			P -> R (in EPP). {ECO:0000269|PubMed:12063482}.		cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				ACCTCTTCTGCGGTTGAACTT	0.522													C|||	1	0.000199681	0.0	0.0	5008	,	,		18448	0.0		0.0	False		,,,				2504	0.001				p.P62P		Atlas-SNP	.											FECH,right_lower_lobe,carcinoma,0,2	FECH	42	2	0			c.G186A						scavenged	.						160.0	145.0	150.0					18																	55247313		2203	4300	6503	SO:0001819	synonymous_variant	2235	exon2			CTTCTGCGGTTGA	D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"""protoporphyria"""	612386	"""ferrochelatase (protoporphyria)"""			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.186G>A	18.37:g.55247313C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	192	4	0.0208333	NM_001012515	A8KA72|Q8IXN1|Q8NAN0	Silent	SNP	ENST00000262093.5	37	CCDS11964.1																																																																																			.	.	none		0.522	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1		
HLA-B	3106	hgsc.bcm.edu	37	6	31324145	31324145	+	Missense_Mutation	SNP	A	A	C	rs9266150	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:31324145A>C	ENST00000412585.2	-	3	446	c.418T>G	c.(418-420)Tac>Gac	p.Y140D		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						TCGTAGGCGTACTGGTCATGC	0.706									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.Y140D		Atlas-SNP	.											HLA-B,colon,carcinoma,+1,1	HLA-B	54	1	0			c.T418G						scavenged	.	A	ASP/TYR	318,3856		18,282,1787	26.0	21.0	22.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	418	-6.4	0.0	6	dbSNP_118	22	1185,7191		77,1031,3080	no	missense	HLA-B	NM_005514.6	160	95,1313,4867	CC,CA,AA		14.1476,7.6186,11.9761		140/363	31324145	1503,11047	2087	4188	6275	SO:0001583	missense	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	AGGCGTACTGGTC	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.418T>G	6.37:g.31324145A>C	ENSP00000399168:p.Tyr140Asp	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	116	41	0.353448	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	3.928	-0.016793	0.07681	0.076186	0.141476	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.00012	9.31;9.31	3.18	-6.36	0.01969	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	1.609830	0.05070	U	0.481455	T	0.00012	0.0000	N	0.02368	-0.58	0.80722	P	0.0	B;B	0.23377	0.084;0.01	B;B	0.26094	0.066;0.058	T	0.02138	-1.1207	9	0.10636	T	0.68	.	2.0837	0.03640	0.2816:0.3839:0.0845:0.25	rs9266150	140;140	P30480;P01889	1B42_HUMAN;1B07_HUMAN	D	140;19;19;151	ENSP00000399168:Y140D;ENSP00000405931:Y151D	ENSP00000399168:Y140D	Y	-	1	0	HLA-B	31432124	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.243000	0.01194	-2.056000	0.00898	-2.701000	0.00136	TAC	A|0.886;C|0.114	0.114	strong		0.706	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
CHRD	8646	hgsc.bcm.edu	37	3	184099378	184099378	+	Silent	SNP	C	C	A	rs35929225	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:184099378C>A	ENST00000204604.1	+	4	723	c.477C>A	c.(475-477)ggC>ggA	p.G159G	CHRD_ENST00000545352.1_5'Flank|CHRD_ENST00000482805.1_3'UTR|CHRD_ENST00000450923.1_Silent_p.G159G|CHRD_ENST00000348986.3_Silent_p.G159G|EIF2B5_ENST00000444495.1_Intron	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	159					BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGGAGCCAGGCGCTGAGGAGC	0.697													C|||	814	0.16254	0.0862	0.1988	5008	,	,		13339	0.0724		0.3131	False		,,,				2504	0.1779				p.G159G		Atlas-SNP	.											.	CHRD	149	.	0			c.C477A						PASS	.	C		509,3847		32,445,1701	10.0	15.0	13.0		477	-1.9	0.0	3	dbSNP_126	13	2737,5827		458,1821,2003	no	coding-synonymous	CHRD	NM_003741.2		490,2266,3704	AA,AC,CC		31.9594,11.685,25.1238		159/956	184099378	3246,9674	2178	4282	6460	SO:0001819	synonymous_variant	8646	exon4			GCCAGGCGCTGAG	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.477C>A	3.37:g.184099378C>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	63	50	0.793651	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	37	CCDS3266.1																																																																																			C|0.808;A|0.192	0.192	strong		0.697	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
NPAP1	23742	hgsc.bcm.edu	37	15	24921771	24921771	+	Missense_Mutation	SNP	G	G	C	rs1563102	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	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	
SIL1	64374	hgsc.bcm.edu	37	5	138456815	138456815	+	Silent	SNP	T	T	C	rs3088052	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:138456815T>C	ENST00000394817.2	-	3	292	c.153A>G	c.(151-153)acA>acG	p.T51T	SIL1_ENST00000265195.5_Silent_p.T51T|SIL1_ENST00000509534.1_Silent_p.T58T	NM_022464.4	NP_071909.1	Q9H173	SIL1_HUMAN	SIL1 nucleotide exchange factor	51	Interaction with HSPA5 and localization to the endoplasmic reticulum. {ECO:0000250}.				intracellular protein transport (GO:0006886)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTTTTCTCTCTGTTTCTTTGG	0.552									Marinesco-Sjgren syndrome				C|||	2138	0.426917	0.6861	0.4366	5008	,	,		19994	0.1815		0.4076	False		,,,				2504	0.3425				p.T51T		Atlas-SNP	.											.	SIL1	31	.	0			c.A153G						PASS	.	C	,	2983,1423	463.0+/-353.4	1006,971,226	140.0	147.0	145.0		153,153	-2.0	0.5	5	dbSNP_102	145	3705,4895	619.8+/-397.0	810,2085,1405	no	coding-synonymous,coding-synonymous	SIL1	NM_001037633.1,NM_022464.4	,	1816,3056,1631	CC,CT,TT		43.0814,32.2969,48.5776	,	51/462,51/462	138456815	6688,6318	2203	4300	6503	SO:0001819	synonymous_variant	64374	exon4	Familial Cancer Database	Marinesco-Sjogren syndrome	TCTCTCTGTTTCT	AK075177	CCDS4209.1	5q31	2013-08-21	2013-08-21		ENSG00000120725	ENSG00000120725			24624	protein-coding gene	gene with protein product		608005	"""Marinesco-Sjogren syndrome"", ""SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)"""	MSS		11101517, 12356756, 16282977	Standard	XM_006714671		Approved	BAP, ULG5	uc003ldp.3	Q9H173	OTTHUMG00000129226	ENST00000394817.2:c.153A>G	5.37:g.138456815T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	73	11	0.150685	NM_001037633	D3DQC2|Q8N2L3	Silent	SNP	ENST00000394817.2	37	CCDS4209.1																																																																																			T|0.513;C|0.487	0.487	strong		0.552	SIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251319.1	NM_022464	
ERMAP	114625	hgsc.bcm.edu	37	1	43296173	43296173	+	Silent	SNP	C	C	T	rs33950227	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43296173C>T	ENST00000372517.2	+	3	298	c.54C>T	c.(52-54)ctC>ctT	p.L18L	ERMAP_ENST00000487556.1_Intron|ERMAP_ENST00000328249.3_5'UTR|ERMAP_ENST00000372514.3_Silent_p.L18L	NM_001017922.1	NP_001017922.1	Q96PL5	ERMAP_HUMAN	erythroblast membrane-associated protein (Scianna blood group)	18						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TCATCCCTCTCGTCTTCCTCC	0.562													C|||	733	0.146366	0.0923	0.2579	5008	,	,		18309	0.0099		0.2525	False		,,,				2504	0.1718				p.L18L		Atlas-SNP	.											.	ERMAP	30	.	0			c.C54T						PASS	.	C	,	529,3877	241.8+/-252.1	31,467,1705	131.0	105.0	114.0		54,54	-5.6	0.0	1	dbSNP_126	114	2091,6509	361.8+/-332.5	250,1591,2459	no	coding-synonymous,coding-synonymous	ERMAP	NM_001017922.1,NM_018538.3	,	281,2058,4164	TT,TC,CC		24.314,12.0064,20.1445	,	18/476,18/476	43296173	2620,10386	2203	4300	6503	SO:0001819	synonymous_variant	114625	exon3			CCCTCTCGTCTTC	AF311284	CCDS475.1	1p34	2014-07-19	2006-02-23		ENSG00000164010	ENSG00000164010		"""Blood group antigens"", ""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	15743	protein-coding gene	gene with protein product		609017	"""Radin blood group"", ""Scianna blood group"", ""erythroblast membrane-associated protein"", ""erythroblast membrane-associated protein (RD and SC blood groups)"""	RD, SC		11549310	Standard	XM_005270415		Approved	BTN5	uc001cie.1	Q96PL5	OTTHUMG00000007619	ENST00000372517.2:c.54C>T	1.37:g.43296173C>T		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	96	73	0.760417	NM_001017922	D3DPW8|Q5VV53|Q6DUE0|Q7Z3X0|Q8NCV8|Q8NCW2|Q8NCW3|Q96PL6	Silent	SNP	ENST00000372517.2	37	CCDS475.1																																																																																			C|0.814;T|0.186	0.186	strong		0.562	ERMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020180.1	NM_018538	
DTD2	112487	hgsc.bcm.edu	37	14	31922515	31922515	+	Silent	SNP	G	G	A	rs61754291	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:31922515G>A	ENST00000310850.4	-	2	263	c.147C>T	c.(145-147)ttC>ttT	p.F49F	CTD-2213F21.2_ENST00000502430.2_RNA|DTD2_ENST00000356180.4_Silent_p.F49F|RP11-176H8.1_ENST00000547378.1_Silent_p.F49F	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	49					D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)										CAGCTCCCTTGAAAAAGCACA	0.403													G|||	53	0.0105831	0.0	0.0058	5008	,	,		18506	0.0		0.0278	False		,,,				2504	0.0215				p.F49F		Atlas-SNP	.											.	.	.	.	0			c.C147T						PASS	.	G		33,4373	37.6+/-69.7	0,33,2170	115.0	110.0	112.0		147	4.8	1.0	14	dbSNP_129	112	351,8249	119.2+/-178.6	15,321,3964	yes	coding-synonymous	C14orf126	NM_080664.2		15,354,6134	AA,AG,GG		4.0814,0.749,2.9525		49/169	31922515	384,12622	2203	4300	6503	SO:0001819	synonymous_variant	112487	exon2			TCCCTTGAAAAAG	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.147C>T	14.37:g.31922515G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	85	83	0.976471	NM_080664	D3DS87	Silent	SNP	ENST00000310850.4	37	CCDS9643.1																																																																																			G|0.977;A|0.023	0.023	strong		0.403	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664	
PKN1	5585	hgsc.bcm.edu	37	19	14581063	14581063	+	Silent	SNP	A	A	G	rs1042728	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	100	0	0		WXS	Illumina HiSeq	Phase_I	110	43	0.390909	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	
SASH1	23328	hgsc.bcm.edu	37	6	148841011	148841011	+	Silent	SNP	C	C	T	rs13196292	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:148841011C>T	ENST00000367467.3	+	10	1666	c.1191C>T	c.(1189-1191)ctC>ctT	p.L397L		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	397					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		AGAAGGGTCTCGGGTCCCTAA	0.567													C|||	410	0.081869	0.0862	0.0403	5008	,	,		17258	0.0903		0.0736	False		,,,				2504	0.1053				p.L397L		Atlas-SNP	.											SASH1,NS,carcinoma,0,2	SASH1	123	2	0			c.C1191T						PASS	.	C		349,4051		13,323,1864	12.0	14.0	13.0		1191	-2.3	0.4	6	dbSNP_121	13	694,7886		31,632,3627	no	coding-synonymous	SASH1	NM_015278.3		44,955,5491	TT,TC,CC		8.0886,7.9318,8.0354		397/1248	148841011	1043,11937	2200	4290	6490	SO:0001819	synonymous_variant	23328	exon10			GGGTCTCGGGTCC	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1191C>T	6.37:g.148841011C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																			C|0.926;T|0.074	0.074	strong		0.567	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
KRT1	3848	hgsc.bcm.edu	37	12	53069243	53069243	+	Missense_Mutation	SNP	T	T	C	rs77846840|rs540699806|rs267607656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53069243T>C	ENST00000252244.3	-	9	1727	c.1669A>G	c.(1669-1671)Agc>Ggc	p.S557G		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	557	Gly/Ser-rich.|Tail.				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)	p.S557_G563delSSYGSGG(3)		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						ccgtagctgctacctccggag	0.682																																					p.S557G		Atlas-SNP	.											.	KRT1	110	.	3	Deletion - In frame(3)	prostate(2)|central_nervous_system(1)	c.A1669G						PASS	.						4.0	4.0	4.0					12																	53069243		1805	3566	5371	SO:0001583	missense	3848	exon9			AGCTGCTACCTCC	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.1669A>G	12.37:g.53069243T>C	ENSP00000252244:p.Ser557Gly	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	25	8	0.32	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	t	12.77	2.037794	0.35989	.	.	ENSG00000167768	ENST00000252244	T	0.81247	-1.47	3.63	0.628	0.17681	.	.	.	.	.	T	0.54711	0.1875	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48490	-0.9031	8	0.07644	T	0.81	.	5.639	0.17552	0.0:0.6406:0.1602:0.1993	.	557	P04264	K2C1_HUMAN	G	557	ENSP00000252244:S557G	ENSP00000252244:S557G	S	-	1	0	KRT1	51355510	0.000000	0.05858	0.034000	0.17996	0.201000	0.24016	-0.192000	0.09587	-0.104000	0.12154	-1.598000	0.00824	AGC	T|0.500;C|0.500	0.500	weak		0.682	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
PLEKHG7	440107	hgsc.bcm.edu	37	12	93147901	93147901	+	Silent	SNP	C	C	T	rs74784157	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:93147901C>T	ENST00000344636.3	+	6	535	c.351C>T	c.(349-351)caC>caT	p.H117H		NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	117	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						GACGGCTCCACGTGCCAGAGC	0.512													C|||	274	0.0547125	0.0787	0.0836	5008	,	,		20165	0.0139		0.0586	False		,,,				2504	0.0399				p.H117H		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.C351T						PASS	.	C		275,4131	155.5+/-188.7	11,253,1939	104.0	93.0	96.0		351	3.2	1.0	12	dbSNP_131	96	475,8125	140.0+/-196.6	9,457,3834	no	coding-synonymous	PLEKHG7	NM_001004330.2		20,710,5773	TT,TC,CC		5.5233,6.2415,5.7666		117/380	93147901	750,12256	2203	4300	6503	SO:0001819	synonymous_variant	440107	exon6			GCTCCACGTGCCA	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"""Pleckstrin homology (PH) domain containing"""	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.351C>T	12.37:g.93147901C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	127	30	0.23622	NM_001004330	B2RNR7	Silent	SNP	ENST00000344636.3	37	CCDS31873.1																																																																																			C|0.947;T|0.053	0.053	strong		0.512	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330	
DHX37	57647	hgsc.bcm.edu	37	12	125448960	125448960	+	Silent	SNP	C	C	T	rs4076777	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:125448960C>T	ENST00000308736.2	-	15	2123	c.2025G>A	c.(2023-2025)acG>acA	p.T675T	DHX37_ENST00000544745.1_Silent_p.T462T	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	675	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						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)		GGCCGGGCTCCGTCCGTCCTG	0.632													T|||	1829	0.365216	0.2088	0.3386	5008	,	,		17000	0.6448		0.33	False		,,,				2504	0.3436				p.T675T		Atlas-SNP	.											.	DHX37	114	.	0			c.G2025A						PASS	.	T		946,3460	735.6+/-410.7	90,766,1347	69.0	68.0	68.0		2025	-3.7	0.8	12	dbSNP_108	68	2828,5772	675.3+/-403.2	461,1906,1933	no	coding-synonymous	DHX37	NM_032656.3		551,2672,3280	TT,TC,CC		32.8837,21.4707,29.0174		675/1158	125448960	3774,9232	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon15			GGGCTCCGTCCGT	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.2025G>A	12.37:g.125448960C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1	888	0.4065934065934066	111	0.22560975609756098	134	0.3701657458563536	391	0.6835664335664335	252	0.3324538258575198	T	11.92	1.782963	0.31502	0.214707	0.328837	ENSG00000150990	ENST00000543962	.	.	.	5.17	-3.66	0.04489	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999813	.	.	.	.	.	.	T	0.37820	-0.9689	4	0.87932	D	0	-36.7754	2.5483	0.04742	0.1757:0.3673:0.0949:0.3621	rs4076777;rs4316603;rs11558557	.	.	.	Q	127	.	ENSP00000443661:R127Q	R	-	2	0	DHX37	124014913	0.000000	0.05858	0.809000	0.32408	0.837000	0.47467	-2.742000	0.00798	-1.499000	0.01821	-0.521000	0.04368	CGG	C|0.671;T|0.329	0.329	strong		0.632	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
TRDMT1	1787	hgsc.bcm.edu	37	10	17243610	17243610	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:17243610C>T	ENST00000377799.3	-	1	71	c.24G>A	c.(22-24)gaG>gaA	p.E8E	TRDMT1_ENST00000457442.2_5'UTR|TRDMT1_ENST00000351358.4_Silent_p.E8E|TRDMT1_ENST00000412821.3_Silent_p.E8E|TRDMT1_ENST00000377766.5_Silent_p.E8E|TRDMT1_ENST00000358282.7_Silent_p.E8E|TRDMT1_ENST00000488990.1_Silent_p.E8E	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	8	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	CGCTGTATAGCTCCAGCACCC	0.706																																					p.E8E		Atlas-SNP	.											.	TRDMT1	46	.	0			c.G24A						PASS	.						11.0	12.0	12.0					10																	17243610		1939	3647	5586	SO:0001819	synonymous_variant	1787	exon1			GTATAGCTCCAGC	AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.24G>A	10.37:g.17243610C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	37	CCDS7114.1																																																																																			.	.	none		0.706	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138732457	138732457	+	Silent	SNP	G	G	A	rs3735008	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:138732457G>A	ENST00000242351.5	-	13	2908	c.2592C>T	c.(2590-2592)ttC>ttT	p.F864F	ZC3HAV1_ENST00000464606.1_Silent_p.F986F	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	864	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.F864L(1)		cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CACAGCTGTCGAACTGTGGAG	0.428													G|||	2122	0.423722	0.475	0.3501	5008	,	,		17669	0.3343		0.493	False		,,,				2504	0.4274				p.F864F		Atlas-SNP	.											ZC3HAV1,colon,carcinoma,0,1	ZC3HAV1	75	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2592T						scavenged	.	G		2072,2334	569.8+/-382.7	492,1088,623	153.0	149.0	150.0		2592	0.2	0.0	7	dbSNP_107	150	4310,4290	578.1+/-390.7	1107,2096,1097	yes	coding-synonymous	ZC3HAV1	NM_020119.3		1599,3184,1720	AA,AG,GG		49.8837,47.0268,49.0697		864/903	138732457	6382,6624	2203	4300	6503	SO:0001819	synonymous_variant	56829	exon13			GCTGTCGAACTGT	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2592C>T	7.37:g.138732457G>A		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	88	12	0.136364	NM_020119	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	37	CCDS5851.1																																																																																			G|0.530;A|0.470	0.470	strong		0.428	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
COL15A1	1306	hgsc.bcm.edu	37	9	101831995	101831995	+	Missense_Mutation	SNP	G	G	A	rs10519	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	141	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	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	
BPIFA2	140683	hgsc.bcm.edu	37	20	31761919	31761919	+	Missense_Mutation	SNP	A	A	G	rs17304572	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:31761919A>G	ENST00000253362.2	+	4	483	c.337A>G	c.(337-339)Aaa>Gaa	p.K113E	BPIFA2_ENST00000354932.5_Missense_Mutation_p.K113E			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	113			K -> E (in dbSNP:rs17304572).			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										CCTGGATGTCAAAGCTGAACC	0.507													A|||	36	0.0071885	0.0008	0.0447	5008	,	,		20651	0.0		0.003	False		,,,				2504	0.001				p.K113E		Atlas-SNP	.											.	.	.	.	0			c.A337G						PASS	.	A	GLU/LYS	9,4397	15.5+/-35.6	0,9,2194	190.0	130.0	150.0		337	0.5	0.0	20	dbSNP_123	150	65,8535	39.3+/-95.6	0,65,4235	yes	missense	BPIFA2	NM_080574.2	56	0,74,6429	GG,GA,AA		0.7558,0.2043,0.569	possibly-damaging	113/250	31761919	74,12932	2203	4300	6503	SO:0001583	missense	140683	exon4			GATGTCAAAGCTG	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.337A>G	20.37:g.31761919A>G	ENSP00000253362:p.Lys113Glu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	15	0.006868131868131868	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	4	0.005277044854881266	A	14.94	2.685424	0.47991	0.002043	0.007558	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.05580	3.42;3.42	4.11	0.538	0.17150	.	0.626240	0.15043	N	0.283766	T	0.02767	0.0083	L	0.50919	1.6	0.09310	N	1	P	0.41624	0.757	B	0.43728	0.429	T	0.30001	-0.9993	10	0.15952	T	0.53	-20.1787	3.5768	0.07937	0.5707:0.2098:0.2195:0.0	rs17304572;rs52835642;rs56630818;rs17304572	113	Q96DR5	BPIA2_HUMAN	E	113	ENSP00000253362:K113E;ENSP00000347012:K113E	ENSP00000253362:K113E	K	+	1	0	BPIFA2	31225580	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	0.427000	0.21379	0.060000	0.16281	0.459000	0.35465	AAA	A|0.994;G|0.006	0.006	strong		0.507	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	
CASZ1	54897	hgsc.bcm.edu	37	1	10713765	10713765	+	Silent	SNP	T	T	C	rs284294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:10713765T>C	ENST00000377022.3	-	11	2666	c.2349A>G	c.(2347-2349)tcA>tcG	p.S783S	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Silent_p.S783S	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	783					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)		CCAGGGGGATTGAGCCAGGCA	0.711													C|||	2730	0.545128	0.7194	0.4539	5008	,	,		16126	0.3095		0.5646	False		,,,				2504	0.5971				p.S783S		Atlas-SNP	.											CASZ1,colon,carcinoma,0,1	CASZ1	150	1	0			c.A2349G						PASS	.	C	,	2890,1470		976,938,266	25.0	33.0	30.0		2349,2349	3.0	0.9	1	dbSNP_79	30	4701,3873		1298,2105,884	no	coding-synonymous,coding-synonymous	CASZ1	NM_001079843.1,NM_017766.3	,	2274,3043,1150	CC,CT,TT		45.1714,33.7156,41.3097	,	783/1760,783/1167	10713765	7591,5343	2180	4287	6467	SO:0001819	synonymous_variant	54897	exon11			GGGGATTGAGCCA	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.2349A>G	1.37:g.10713765T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	19	17	0.894737	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	CCDS41246.1																																																																																			T|0.453;C|0.547	0.547	strong		0.711	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
JAK2	3717	hgsc.bcm.edu	37	9	5072551	5072551	+	Silent	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:5072551A>G	ENST00000381652.3	+	13	2195	c.1701A>G	c.(1699-1701)gtA>gtG	p.V567V	JAK2_ENST00000544510.1_Silent_p.V418V|JAK2_ENST00000539801.1_Silent_p.V567V	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	567	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|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 cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GAAGAGAAGTAGGAGACTACG	0.353		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																												p.V567V		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	JAK2,caecum,carcinoma,0,3	JAK2	35466	3	0			c.A1701G						scavenged	.						68.0	69.0	69.0					9																	5072551		2203	4300	6503	SO:0001819	synonymous_variant	3717	exon13	Familial Cancer Database		AGAAGTAGGAGAC		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.1701A>G	9.37:g.5072551A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	142	4	0.028169	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			.	.	none		0.353	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
INF2	64423	hgsc.bcm.edu	37	14	105179184	105179184	+	Missense_Mutation	SNP	G	G	A	rs142678449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105179184G>A	ENST00000392634.4	+	18	2742	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	INF2_ENST00000330634.7_Missense_Mutation_p.R877Q	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	877	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		TCGGCCTTCCGGGCACTGGAT	0.677													G|||	28	0.00559105	0.0023	0.013	5008	,	,		17221	0.0		0.0089	False		,,,				2504	0.0072				p.R877Q		Atlas-SNP	.											.	INF2	148	.	0			c.G2630A						PASS	.	G	GLN/ARG,GLN/ARG	6,4024		0,6,2009	24.0	28.0	27.0		2630,2630	-4.1	0.0	14	dbSNP_134	27	89,8255		2,85,4085	yes	missense,missense	INF2	NM_022489.3,NM_001031714.3	43,43	2,91,6094	AA,AG,GG		1.0666,0.1489,0.7677	benign,benign	877/1250,877/1241	105179184	95,12279	2015	4172	6187	SO:0001583	missense	64423	exon18			CCTTCCGGGCACT	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.2630G>A	14.37:g.105179184G>A	ENSP00000376410:p.Arg877Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	145	50	0.344828	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	37	CCDS9989.2	16	0.007326007326007326	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	6	0.0079155672823219	G	13.65	2.300727	0.40694	0.001489	0.010666	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.17213	2.29;2.29	5.06	-4.11	0.03928	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	1.264760	0.05384	N	0.537746	T	0.05731	0.0150	L	0.27053	0.805	0.09310	N	1	B;B	0.24882	0.093;0.113	B;B	0.17722	0.008;0.019	T	0.31308	-0.9948	10	0.17369	T	0.5	.	14.103	0.65070	0.6837:0.0:0.3163:0.0	.	877;877	Q27J81-2;Q27J81	.;INF2_HUMAN	Q	877	ENSP00000376406:R877Q;ENSP00000376410:R877Q	ENSP00000252527:R345Q	R	+	2	0	INF2	104250229	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.660000	0.05317	-1.495000	0.01831	0.561000	0.74099	CGG	G|0.992;A|0.008	0.008	strong		0.677	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
MANBA	4126	hgsc.bcm.edu	37	4	103557077	103557077	+	Missense_Mutation	SNP	G	G	A	rs2866413	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:103557077G>A	ENST00000226578.4	-	15	2201	c.2102C>T	c.(2101-2103)aCg>aTg	p.T701M	MANBA_ENST00000505239.1_Missense_Mutation_p.T644M	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	701			T -> M (in dbSNP:rs2866413). {ECO:0000269|PubMed:15489334}.		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)		GATATAGAACGTGTTTTCATT	0.378													G|||	2750	0.549121	0.6626	0.6542	5008	,	,		21434	0.5159		0.493	False		,,,				2504	0.4131				p.T701M		Atlas-SNP	.											MANBA,NS,adenoma,0,1	MANBA	78	1	0			c.C2102T						PASS	.	G	MET/THR	2720,1686	654.3+/-399.7	850,1020,333	100.0	96.0	97.0		2102	2.8	0.0	4	dbSNP_101	97	4413,4187	585.7+/-391.9	1120,2173,1007	yes	missense	MANBA	NM_005908.3	81	1970,3193,1340	AA,AG,GG		48.686,38.266,45.1561	benign	701/880	103557077	7133,5873	2203	4300	6503	SO:0001583	missense	4126	exon15			TAGAACGTGTTTT		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.2102C>T	4.37:g.103557077G>A	ENSP00000226578:p.Thr701Met	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	128	126	0.984375	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	1205	0.5517399267399268	311	0.6321138211382114	225	0.6215469613259669	295	0.5157342657342657	374	0.49340369393139843	G	9.422	1.083279	0.20309	0.61734	0.51314	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.58060	0.36;0.36	5.42	2.83	0.33086	.	0.610170	0.17652	N	0.166653	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B	0.21753	0.054;0.06	B;B	0.14578	0.004;0.011	T	0.42155	-0.9468	9	0.46703	T	0.11	-0.6633	8.7571	0.34652	0.8361:0.0:0.1639:0.0	rs2866413;rs3733203;rs17851324;rs52825236;rs57086295;rs2866413	644;701	E9PFW2;O00462	.;MANBA_HUMAN	M	701;644	ENSP00000226578:T701M;ENSP00000427322:T644M	ENSP00000226578:T701M	T	-	2	0	MANBA	103776125	0.002000	0.14202	0.000000	0.03702	0.017000	0.09413	1.802000	0.38853	0.344000	0.23847	-0.290000	0.09829	ACG	G|0.448;A|0.552	0.552	strong		0.378	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
DGCR14	8220	hgsc.bcm.edu	37	22	19122665	19122665	+	Silent	SNP	C	C	T	rs2240111	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	171	0	0		WXS	Illumina HiSeq	Phase_I	168	103	0.613095	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		
SLCO1C1	53919	hgsc.bcm.edu	37	12	20885931	20885931	+	Silent	SNP	A	A	G	rs16923154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:20885931A>G	ENST00000266509.2	+	10	1643	c.1275A>G	c.(1273-1275)gcA>gcG	p.A425A	SLCO1C1_ENST00000381552.1_Silent_p.A425A|SLCO1C1_ENST00000545102.1_Silent_p.A307A|SLCO1C1_ENST00000540354.1_Silent_p.A376A|SLCO1C1_ENST00000545604.1_Silent_p.A425A	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	425					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.A425A(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)	GTGGAGCTGCAAAACTCTACT	0.448													A|||	394	0.0786741	0.0522	0.0288	5008	,	,		15838	0.1855		0.0865	False		,,,				2504	0.0317				p.A425A		Atlas-SNP	.											SLCO1C1,NS,carcinoma,0,1	SLCO1C1	216	1	1	Substitution - coding silent(1)	stomach(1)	c.A1275G						PASS	.	A	,,,	239,4167	139.6+/-175.2	5,229,1969	202.0	179.0	187.0		921,1128,1275,1275	1.3	1.0	12	dbSNP_123	187	678,7922	170.3+/-221.5	31,616,3653	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	,,,	36,845,5622	GG,GA,AA		7.8837,5.4244,7.0506	,,,	307/613,376/664,425/731,425/713	20885931	917,12089	2203	4300	6503	SO:0001819	synonymous_variant	53919	exon10			AGCTGCAAAACTC	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.1275A>G	12.37:g.20885931A>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	206	114	0.553398	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Silent	SNP	ENST00000266509.2	37	CCDS8683.1																																																																																			A|0.919;G|0.081	0.081	strong		0.448	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
ZBTB1	22890	hgsc.bcm.edu	37	14	64988279	64988279	+	Silent	SNP	A	A	G	rs28626711	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:64988279A>G	ENST00000554015.1	+	4	488	c.57A>G	c.(55-57)gaA>gaG	p.E19E	ZBTB1_ENST00000358738.3_Silent_p.E19E|RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000394712.2_Silent_p.E19E			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	19					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		ACCAAAGAGAATGGGGTTTTC	0.393													A|||	812	0.162141	0.0401	0.1254	5008	,	,		19165	0.2083		0.2326	False		,,,				2504	0.2331				p.E19E		Atlas-SNP	.											.	ZBTB1	93	.	0			c.A57G						PASS	.	A	,	347,4059	179.7+/-208.2	16,315,1872	102.0	97.0	99.0		57,57	-0.4	1.0	14	dbSNP_125	99	1884,6716	336.2+/-321.7	212,1460,2628	no	coding-synonymous,coding-synonymous	ZBTB1	NM_001123329.1,NM_014950.2	,	228,1775,4500	GG,GA,AA		21.907,7.8756,17.1536	,	19/714,19/645	64988279	2231,10775	2203	4300	6503	SO:0001819	synonymous_variant	22890	exon2			AAGAGAATGGGGT	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.57A>G	14.37:g.64988279A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	161	87	0.540373	NM_014950	A8K6S8|Q86SW8	Silent	SNP	ENST00000554015.1	37	CCDS45126.1																																																																																			A|0.827;G|0.173	0.173	strong		0.393	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1		
RASAL1	8437	hgsc.bcm.edu	37	12	113565933	113565933	+	Missense_Mutation	SNP	G	G	A	rs34598602	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113565933G>A	ENST00000261729.5	-	4	488	c.173C>T	c.(172-174)aCg>aTg	p.T58M	RASAL1_ENST00000446861.3_Missense_Mutation_p.T58M|RASAL1_ENST00000546530.1_Missense_Mutation_p.T58M|RASAL1_ENST00000548055.1_Missense_Mutation_p.T58M|RASAL1_ENST00000418411.2_5'UTR			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	58	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.		T -> M (in dbSNP:rs34598602). {ECO:0000269|PubMed:15489334}.		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)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						CAGGTGCACCGTGTACTCCTC	0.617													G|||	117	0.0233626	0.0038	0.0403	5008	,	,		15576	0.0		0.0706	False		,,,				2504	0.0133				p.T58M		Atlas-SNP	.											.	RASAL1	89	.	0			c.C173T						PASS	.	G	MET/THR,MET/THR,MET/THR	70,4336	64.1+/-101.4	0,70,2133	199.0	197.0	197.0		173,173,173	5.1	0.9	12	dbSNP_126	197	535,8065	148.8+/-204.0	17,501,3782	yes	missense,missense,missense	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	81,81,81	17,571,5915	AA,AG,GG		6.2209,1.5887,4.6517	probably-damaging,probably-damaging,probably-damaging	58/807,58/777,58/805	113565933	605,12401	2203	4300	6503	SO:0001583	missense	8437	exon4			TGCACCGTGTACT	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.173C>T	12.37:g.113565933G>A	ENSP00000261729:p.Thr58Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	37	CCDS9165.1	67	0.030677655677655676	5	0.01016260162601626	12	0.03314917127071823	0	0.0	50	0.06596306068601583	G	23.2	4.393216	0.83011	0.015887	0.062209	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48	5.12	5.12	0.69794	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.31765	0.0807	L	0.60455	1.87	0.48511	D	0.999668	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.975;0.993;1.0	T	0.65965	-0.6040	10	0.52906	T	0.07	.	17.315	0.87221	0.0:0.0:1.0:0.0	rs34598602	58;58;70;58;58;58	B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;RASL1_HUMAN;.	M	58	ENSP00000450244:T58M;ENSP00000261729:T58M;ENSP00000395920:T58M;ENSP00000448510:T58M	ENSP00000261729:T58M	T	-	2	0	RASAL1	112050316	1.000000	0.71417	0.939000	0.37840	0.913000	0.54294	8.924000	0.92827	2.394000	0.81467	0.491000	0.48974	ACG	G|0.957;A|0.043	0.043	strong		0.617	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
OR8H2	390151	hgsc.bcm.edu	37	11	55873334	55873334	+	Silent	SNP	A	A	G	rs11227212	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	174	0	0		WXS	Illumina HiSeq	Phase_I	155	63	0.406452	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	
TXNDC16	57544	hgsc.bcm.edu	37	14	52923820	52923820	+	Missense_Mutation	SNP	T	T	C	rs61744423	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:52923820T>C	ENST00000281741.4	-	17	2062	c.1691A>G	c.(1690-1692)gAt>gGt	p.D564G	TXNDC16_ENST00000554399.1_Intron	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	564					cell redox homeostasis (GO:0045454)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(3)|skin(1)	21	Breast(41;0.0716)					TAGCAAAACATCTTCTTCAGA	0.289													T|||	45	0.00898562	0.0015	0.0115	5008	,	,		15466	0.0		0.0328	False		,,,				2504	0.002				p.D564G		Atlas-SNP	.											.	TXNDC16	59	.	0			c.A1691G						PASS	.	T	GLY/ASP,GLY/ASP	21,4375	28.1+/-56.4	0,21,2177	79.0	89.0	86.0		1676,1691	5.1	1.0	14	dbSNP_129	86	206,8358	87.6+/-150.0	0,206,4076	yes	missense,missense	TXNDC16	NM_001160047.1,NM_020784.2	94,94	0,227,6253	CC,CT,TT		2.4054,0.4777,1.7515	possibly-damaging,possibly-damaging	559/821,564/826	52923820	227,12733	2198	4282	6480	SO:0001583	missense	57544	exon17			AAAACATCTTCTT	AB037765	CCDS32083.1	14q22.1	2007-08-16	2007-08-16	2007-08-16		ENSG00000087301			19965	protein-coding gene	gene with protein product			"""KIAA1344"""	KIAA1344			Standard	NM_020784		Approved		uc001wzs.3	Q9P2K2		ENST00000281741.4:c.1691A>G	14.37:g.52923820T>C	ENSP00000281741:p.Asp564Gly	Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	260	149	0.573077	NM_020784	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Missense_Mutation	SNP	ENST00000281741.4	37	CCDS32083.1	34	0.015567765567765568	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	28	0.036939313984168866	T	17.67	3.447756	0.63178	0.004777	0.024054	ENSG00000087301	ENST00000281741	T	0.35048	1.33	5.05	5.05	0.67936	.	0.360200	0.31922	N	0.006853	T	0.22205	0.0535	M	0.65975	2.015	0.42835	D	0.99403	D;D	0.59357	0.984;0.985	P;P	0.62560	0.904;0.882	T	0.38714	-0.9648	10	0.56958	D	0.05	-48.734	12.4466	0.55654	0.0:0.0:0.0:1.0	.	559;564	B7ZME4;Q9P2K2	.;TXD16_HUMAN	G	564	ENSP00000281741:D564G	ENSP00000281741:D564G	D	-	2	0	TXNDC16	51993570	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.081000	0.57627	2.030000	0.59900	0.455000	0.32223	GAT	T|0.983;C|0.017	0.017	strong		0.289	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699	
LARS	51520	hgsc.bcm.edu	37	5	145508340	145508340	+	Silent	SNP	A	A	G	rs2895647	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145508340A>G	ENST00000394434.2	-	27	2941	c.2775T>C	c.(2773-2775)acT>acC	p.T925T	LARS_ENST00000274562.9_Silent_p.T898T|LARS_ENST00000510191.1_Silent_p.T871T|LARS_ENST00000545646.1_Silent_p.T879T	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	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	292	288	0.986301	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	
RP1L1	94137	hgsc.bcm.edu	37	8	10467571	10467571	+	Missense_Mutation	SNP	C	C	T	rs200175359		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	202	11	0.0544554	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		
SYN1	6853	hgsc.bcm.edu	37	X	47466361	47466361	+	Silent	SNP	A	A	G	rs1142636	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	253	2	0.00790514		WXS	Illumina HiSeq	Phase_I	95	90	0.947368	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	
FAM131C	348487	hgsc.bcm.edu	37	1	16384998	16384998	+	Silent	SNP	G	G	C	rs1807285	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:16384998G>C	ENST00000375662.4	-	7	960	c.777C>G	c.(775-777)ccC>ccG	p.P259P	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	259	Pro-rich.									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)		GGGAGCCCGGGGGGTGGGTCC	0.716													C|||	1887	0.376797	0.4032	0.2795	5008	,	,		19381	0.4315		0.336	False		,,,				2504	0.3957				p.P259P		Atlas-SNP	.											FAM131C,NS,carcinoma,-1,2	FAM131C	21	2	0			c.C777G						scavenged	.						2.0	2.0	2.0					1																	16384998		1394	3106	4500	SO:0001819	synonymous_variant	348487	exon7			GCCCGGGGGGTGG		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.777C>G	1.37:g.16384998G>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	9	4	0.444444	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.706;C|0.294	0.294	strong		0.716	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
OGFR	11054	hgsc.bcm.edu	37	20	61444693	61444693	+	Missense_Mutation	SNP	G	G	A	rs35813009	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:61444693G>A	ENST00000290291.6	+	7	1751	c.1726G>A	c.(1726-1728)Gag>Aag	p.E576K	OGFR_ENST00000370461.1_Missense_Mutation_p.E524K	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	576	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].			E -> K (in Ref. 1; AAF64406, 2 and 5; BAB15775). {ECO:0000305}.	opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CGAGCCAGCCGAGAGCCCATC	0.751													G|||	1063	0.21226	0.2927	0.2349	5008	,	,		8783	0.1677		0.2555	False		,,,				2504	0.089				p.E576K		Atlas-SNP	.											OGFR,rectum,carcinoma,0,2	OGFR	63	2	0			c.G1726A						scavenged	.						3.0	7.0	6.0					20																	61444693		1480	3390	4870	SO:0001583	missense	11054	exon7			CCAGCCGAGAGCC	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1726G>A	20.37:g.61444693G>A	ENSP00000290291:p.Glu576Lys	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	6	2	0.333333	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	491	0.22481684981684982	137	0.2784552845528455	84	0.23204419889502761	78	0.13636363636363635	192	0.2532981530343008	g	9.066	0.995706	0.19043	.	.	ENSG00000060491	ENST00000290291;ENST00000357163;ENST00000370469;ENST00000370461	T;T	0.52983	0.64;0.64	1.49	-2.99	0.05497	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.27765	0.188;0.188	B;B	0.13407	0.009;0.009	T	0.32295	-0.9912	8	0.18710	T	0.47	.	6.4368	0.21827	0.3151:0.0:0.6849:0.0	rs35813009;rs60843362	576;576	B3KMQ6;Q9NZT2	.;OGFR_HUMAN	K	576;556;411;524	ENSP00000290291:E576K;ENSP00000359491:E524K	ENSP00000290291:E576K	E	+	1	0	OGFR	60915138	0.004000	0.15560	0.000000	0.03702	0.003000	0.03518	1.586000	0.36611	-1.508000	0.01800	-1.863000	0.00559	GAG	G|0.780;A|0.220	0.220	strong		0.751	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
PSMB1	5689	hgsc.bcm.edu	37	6	170862300	170862300	+	Missense_Mutation	SNP	G	G	C	rs12717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170862300G>C	ENST00000262193.6	-	1	129	c.31C>G	c.(31-33)Cct>Gct	p.P11A	TBP_ENST00000540980.1_5'Flank|TBP_ENST00000230354.6_5'Flank|PSMB1_ENST00000462957.1_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	49	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	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	
TBXA2R	6915	hgsc.bcm.edu	37	19	3595923	3595923	+	Silent	SNP	G	G	A	rs1131882	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3595923G>A	ENST00000375190.4	-	3	1188	c.795C>T	c.(793-795)atC>atT	p.I265I	TBXA2R_ENST00000411851.3_Silent_p.I265I|TBXA2R_ENST00000589966.1_Missense_Mutation_p.R136C|TBXA2R_ENST00000587717.1_5'Flank	NM_001060.5|NM_201636.2	NP_001051.1|NP_963998.2	P21731	TA2R_HUMAN	thromboxane A2 receptor	265					blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|second-messenger-mediated signaling (GO:0019932)|thromboxane A2 signaling pathway (GO:0038193)	acrosomal vesicle (GO:0001669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|thromboxane A2 receptor activity (GO:0004961)	p.I265I(1)		kidney(1)|lung(2)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	8		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)	Ridogrel(DB01207)	CTGTCTGGGCGATGAAGACCT	0.697													G|||	1175	0.234625	0.0401	0.2795	5008	,	,		8200	0.5883		0.1471	False		,,,				2504	0.1912				p.I265I		Atlas-SNP	.											TBXA2R,NS,carcinoma,0,1	TBXA2R	31	1	1	Substitution - coding silent(1)	prostate(1)	c.C795T	GRCh37	CM022851	TBXA2R	M	rs1131882	PASS	.	G	,	226,3866		3,220,1823	11.0	12.0	12.0		795,795	-0.8	0.8	19	dbSNP_86	12	1276,7068		105,1066,3001	no	coding-synonymous,coding-synonymous	TBXA2R	NM_001060.5,NM_201636.2	,	108,1286,4824	AA,AG,GG		15.2924,5.523,12.0778	,	265/344,265/408	3595923	1502,10934	2046	4172	6218	SO:0001819	synonymous_variant	6915	exon3			CTGGGCGATGAAG		CCDS42467.1, CCDS54198.1	19p13.3	2014-09-17						"""GPCR / Class A : Prostanoid receptors"""	11608	protein-coding gene	gene with protein product		188070				1825698	Standard	NM_001060		Approved		uc021umv.1	P21731		ENST00000375190.4:c.795C>T	19.37:g.3595923G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	73	46	0.630137	NM_201636	O75228|Q6DK52|Q9UCY1|Q9UCY2	Silent	SNP	ENST00000375190.4	37	CCDS42467.1																																																																																			G|0.733;A|0.267	0.267	strong		0.697	TBXA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453081.2		
TRIML1	339976	hgsc.bcm.edu	37	4	189060900	189060900	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:189060900C>T	ENST00000332517.3	+	1	328	c.188C>T	c.(187-189)cCg>cTg	p.P63L	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	63					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.P63L(1)		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)		TTGGAGGGCCCGCATTTCCAG	0.607																																					p.P63L	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											TRIML1,NS,carcinoma,0,1	TRIML1	126	1	1	Substitution - Missense(1)	endometrium(1)	c.C188T						scavenged	.						88.0	92.0	91.0					4																	189060900		2203	4300	6503	SO:0001583	missense	339976	exon1			AGGGCCCGCATTT	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.188C>T	4.37:g.189060900C>T	ENSP00000327738:p.Pro63Leu	Somatic	254	1	0.00393701		WXS	Illumina HiSeq	Phase_I	134	2	0.0149254	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.307240	0.23821	.	.	ENSG00000184108	ENST00000332517	D	0.83419	-1.72	5.59	4.71	0.59529	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.51477	D	0.000091	T	0.75774	0.3895	M	0.62723	1.935	0.09310	N	0.999993	P	0.43750	0.816	B	0.32465	0.146	T	0.70894	-0.4748	10	0.30078	T	0.28	-14.5188	12.0642	0.53578	0.0:0.7057:0.2943:0.0	.	63	Q8N9V2	TRIML_HUMAN	L	63	ENSP00000327738:P63L	ENSP00000327738:P63L	P	+	2	0	TRIML1	189297894	0.001000	0.12720	0.028000	0.17463	0.002000	0.02628	1.472000	0.35376	2.804000	0.96469	0.655000	0.94253	CCG	.	.	none		0.607	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556	
FBN3	84467	hgsc.bcm.edu	37	19	8191401	8191401	+	Silent	SNP	G	G	A	rs3813778	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:8191401G>A	ENST00000600128.1	-	20	2919	c.2505C>T	c.(2503-2505)tgC>tgT	p.C835C	FBN3_ENST00000270509.2_Silent_p.C835C|FBN3_ENST00000601739.1_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						scavenged	.	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	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	60	33	0.55	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	
ATP2A3	489	hgsc.bcm.edu	37	17	3828702	3828702	+	Silent	SNP	T	T	C	rs887387	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:3828702T>C	ENST00000352011.3	-	22	3156	c.3102A>G	c.(3100-3102)agA>agG	p.R1034R	ATP2A3_ENST00000397039.1_Silent_p.R208R|ATP2A3_ENST00000397041.3_3'UTR|ATP2A3_ENST00000397035.3_3'UTR|ATP2A3_ENST00000397043.3_3'UTR|ATP2A3_ENST00000359983.3_3'UTR|ATP2A3_ENST00000309890.7_3'UTR			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	1034					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		GAGACTCCACTCTGTTCCCAG	0.577													T|||	1434	0.286342	0.1823	0.4424	5008	,	,		15994	0.2857		0.335	False		,,,				2504	0.2669				p.R1034R	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.A3102G						PASS	.	T	,,,,,,	978,3428	366.1+/-317.7	111,756,1336	131.0	122.0	125.0		,,,3102,,,	3.4	0.7	17	dbSNP_86	125	3267,5333	487.8+/-372.2	601,2065,1634	no	utr-3,utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	712,2821,2970	CC,CT,TT		37.9884,22.197,32.6388	,,,,,,	,,,1034/1044,,,	3828702	4245,8761	2203	4300	6503	SO:0001819	synonymous_variant	489	exon22			CTCCACTCTGTTC		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.3102A>G	17.37:g.3828702T>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	8	0.296296	NM_174955	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			T|0.680;C|0.320	0.320	strong		0.577	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
GGT1	2678	hgsc.bcm.edu	37	22	25023893	25023893	+	Missense_Mutation	SNP	G	G	A	rs201313233	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:25023893G>A	ENST00000400382.1	+	13	2038	c.1283G>A	c.(1282-1284)aGc>aAc	p.S428N	GGT1_ENST00000400383.1_Missense_Mutation_p.S428N|GGT1_ENST00000401885.1_Missense_Mutation_p.S84N|GGT1_ENST00000406383.2_Missense_Mutation_p.S428N|GGT1_ENST00000404532.1_Missense_Mutation_p.S84N|GGT1_ENST00000248923.4_Missense_Mutation_p.S428N|GGT1_ENST00000403838.1_Missense_Mutation_p.S84N|GGT1_ENST00000400380.1_Missense_Mutation_p.S428N|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404223.1_Missense_Mutation_p.S84N|GGT1_ENST00000404920.1_Missense_Mutation_p.S84N			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	428					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.S428N(8)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	AGCTCTCCCAGCATCACCAAC	0.617																																					p.S428N		Atlas-SNP	.											GGT1,scalp,carcinoma,0,10	GGT1	68	10	8	Substitution - Missense(8)	kidney(7)|skin(1)	c.G1283A						PASS	.						75.0	81.0	79.0					22																	25023893		2203	4300	6503	SO:0001583	missense	2678	exon13			CTCCCAGCATCAC	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.1283G>A	22.37:g.25023893G>A	ENSP00000383232:p.Ser428Asn	Somatic	561	1	0.00178253		WXS	Illumina HiSeq	Phase_I	719	147	0.204451	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	0.007	-1.994474	0.00435	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18	3.49	0.971	0.19698	.	0.677608	0.14536	N	0.313585	T	0.01800	0.0057	N	0.00855	-1.145	0.19300	N	0.999979	B	0.02656	0.0	B	0.06405	0.002	T	0.44757	-0.9307	10	0.08179	T	0.78	-26.6577	2.7873	0.05377	0.5605:0.0:0.2509:0.1886	.	428	P19440	GGT1_HUMAN	N	428;428;428;428;428;428;84;84;84;84;84	ENSP00000248923:S428N;ENSP00000393537:S428N;ENSP00000383232:S428N;ENSP00000383233:S428N;ENSP00000383231:S428N;ENSP00000385975:S428N;ENSP00000384381:S84N;ENSP00000385445:S84N;ENSP00000384820:S84N;ENSP00000385016:S84N;ENSP00000385001:S84N	ENSP00000248923:S428N	S	+	2	0	GGT1	23353893	0.005000	0.15991	0.993000	0.49108	0.013000	0.08279	0.113000	0.15499	0.084000	0.17077	-0.708000	0.03648	AGC	G|0.983;A|0.017	0.017	strong		0.617	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
MUC2	4583	hgsc.bcm.edu	37	11	1075920	1075920	+	Splice_Site	SNP	G	G	A	rs11825977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1075920G>A	ENST00000441003.2	+	2	373	c.346G>A	c.(346-348)Gtg>Atg	p.V116M	MUC2_ENST00000359061.5_Splice_Site_p.V116M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	116	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.		V -> M (in dbSNP:rs11825977).		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)	TAACGGGGCCGTGTGAGTGTG	0.632													A|||	578	0.115415	0.2148	0.0821	5008	,	,		17247	0.001		0.2078	False		,,,				2504	0.0276				p.V116M		Atlas-SNP	.											.	MUC2	614	.	0			c.G346A						PASS	.	A	MET/VAL	826,3184		103,620,1282	18.0	20.0	19.0		346	-7.6	0.6	11	dbSNP_120	19	1757,6545		199,1359,2593	yes	missense-near-splice	MUC2	NM_002457.2	21	302,1979,3875	AA,AG,GG		21.1636,20.5985,20.9795	possibly-damaging	116/2813	1075920	2583,9729	2005	4151	6156	SO:0001630	splice_region_variant	4583	exon2			GGGGCCGTGTGAG	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.347+1G>A	11.37:g.1075920G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	46	0.575	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		313	0.1433150183150183	102	0.2073170731707317	39	0.10773480662983426	1	0.0017482517482517483	171	0.22559366754617413	A	1.513	-0.548989	0.04024	0.205985	0.211636	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.59772	0.24;0.24	3.78	-7.56	0.01322	.	1.101460	0.07009	N	0.824818	T	0.00012	0.0000	N	0.11131	0.1	0.80722	P	0.0	B	0.31413	0.322	B	0.21708	0.036	T	0.04165	-1.0972	9	0.33141	T	0.24	.	2.0602	0.03590	0.3385:0.3431:0.2074:0.111	rs11825977;rs59632081;rs11825977	116	E7EUV1	.	M	116	ENSP00000415183:V116M;ENSP00000351956:V116M	ENSP00000351956:V116M	V	+	1	0	MUC2	1065920	0.020000	0.18652	0.582000	0.28627	0.104000	0.19210	-0.102000	0.10956	-2.618000	0.00441	-2.870000	0.00099	GTG	G|0.851;A|0.149	0.149	strong		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	Missense_Mutation
PCLO	27445	hgsc.bcm.edu	37	7	82451984	82451984	+	Missense_Mutation	SNP	T	T	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:82451984T>G	ENST00000333891.9	-	20	14955	c.14618A>C	c.(14617-14619)gAg>gCg	p.E4873A	PCLO_ENST00000423517.2_Missense_Mutation_p.E4873A|PCLO_ENST00000426442.2_5'UTR	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						ATGGGATTTCTCAATGGTGGG	0.438																																					p.E4873A		Atlas-SNP	.											.	PCLO	1506	.	0			c.A14618C						PASS	.						231.0	226.0	228.0					7																	82451984		1967	4169	6136	SO:0001583	missense	27445	exon20			GATTTCTCAATGG	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.14618A>C	7.37:g.82451984T>G	ENSP00000334319:p.Glu4873Ala	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	12	0.193548	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.635321	0.47049	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.18174	2.29;2.23	5.05	5.05	0.67936	.	.	.	.	.	T	0.30823	0.0777	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;0.997	D;D;D;D	0.87578	0.998;0.998;0.991;0.98	T	0.06826	-1.0805	9	0.87932	D	0	.	15.0845	0.72142	0.0:0.0:0.0:1.0	.	4873;4873;294;361	Q9Y6V0-5;Q9Y6V0-6;Q9Y6V0-3;Q32P40	.;.;.;.	A	4873;4873;360	ENSP00000334319:E4873A;ENSP00000388393:E4873A	ENSP00000334319:E4873A	E	-	2	0	PCLO	82289920	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.619000	0.83057	2.023000	0.59567	0.533000	0.62120	GAG	.	.	none		0.438	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
SYT15	83849	hgsc.bcm.edu	37	10	46967514	46967514	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:46967514T>C	ENST00000374321.4	-	4	629	c.563A>G	c.(562-564)tAc>tGc	p.Y188C	SYT15_ENST00000374325.3_Missense_Mutation_p.Y188C|SYT15_ENST00000503753.1_Missense_Mutation_p.Y188C|SYT15_ENST00000374323.4_Missense_Mutation_p.Y241C|RP11-38L15.3_ENST00000506914.1_RNA	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	188	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GGGCAGCAGGTAGAGCTTCAC	0.592																																					p.Y188C	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											.	SYT15	165	.	0			c.A563G						PASS	.						68.0	81.0	77.0					10																	46967514		2071	4211	6282	SO:0001583	missense	83849	exon4			AGCAGGTAGAGCT	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.563A>G	10.37:g.46967514T>C	ENSP00000363441:p.Tyr188Cys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	145	15	0.103448	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	15.71	2.913590	0.52439	.	.	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374330;ENST00000374323;ENST00000374321;ENST00000512997	T;T;T;T;T	0.09073	3.02;3.02;3.02;3.02;3.02	4.92	4.92	0.64577	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.238169	0.42964	D	0.000627	T	0.09818	0.0241	L	0.51914	1.62	0.34918	D	0.748104	B;B	0.20550	0.005;0.046	B;B	0.21708	0.013;0.036	T	0.12400	-1.0549	9	.	.	.	.	12.8277	0.57728	0.0:0.0:0.0:1.0	.	188;188	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	C	188;188;188;27;241;188;72	ENSP00000363445:Y188C;ENSP00000427607:Y188C;ENSP00000363443:Y241C;ENSP00000363441:Y188C;ENSP00000424803:Y72C	.	Y	-	2	0	SYT15	46387520	1.000000	0.71417	0.996000	0.52242	0.871000	0.50021	5.085000	0.64468	1.974000	0.57490	0.533000	0.62120	TAC	.	.	none		0.592	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
DNAH14	127602	hgsc.bcm.edu	37	1	225533931	225533931	+	Missense_Mutation	SNP	A	A	G	rs17522489	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:225533931A>G	ENST00000445597.2	+	48	8258	c.8258A>G	c.(8257-8259)cAa>cGa	p.Q2753R	DNAH14_ENST00000430092.1_Missense_Mutation_p.Q3556R|DNAH14_ENST00000439375.2_Missense_Mutation_p.Q3556R			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	2753					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						AGCAAAGAACAAGAACATAGT	0.348													A|||	698	0.139377	0.0325	0.1182	5008	,	,		17247	0.1389		0.1571	False		,,,				2504	0.2812				p.Q3556R		Atlas-SNP	.											.	DNAH14	300	.	0			c.A10667G						PASS	.	A	ARG/GLN	52,1332		1,50,641	55.0	46.0	49.0		10667	5.4	0.0	1	dbSNP_123	49	520,2662		53,414,1124	yes	missense	DNAH14	NM_001373.1	43	54,464,1765	GG,GA,AA		16.3419,3.7572,12.5274	probably-damaging	3556/4516	225533931	572,3994	692	1591	2283	SO:0001583	missense	127602	exon68			AAGAACAAGAACA	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.8258A>G	1.37:g.225533931A>G	ENSP00000409472:p.Gln2753Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	142	79	0.556338	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		267	0.12225274725274725	17	0.034552845528455285	48	0.13259668508287292	72	0.1258741258741259	130	0.17150395778364116	A	7.092	0.572263	0.13623	0.037572	0.163419	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	T;T;T	0.57107	0.42;1.51;1.51	5.45	5.45	0.79879	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	P	0.999999999524782	P	0.38677	0.642	B	0.38458	0.274	T	0.10543	-1.0625	7	0.23302	T	0.38	.	13.0181	0.58771	1.0:0.0:0.0:0.0	rs17522489;rs52821134;rs17522489	3556	Q0VDD8-4	.	R	2753;3556;3556	ENSP00000409472:Q2753R;ENSP00000414402:Q3556R;ENSP00000392061:Q3556R	ENSP00000414402:Q3556R	Q	+	2	0	DNAH14	223600554	0.000000	0.05858	0.019000	0.16419	0.680000	0.39746	0.710000	0.25748	2.055000	0.61198	0.416000	0.27883	CAA	A|0.887;G|0.113	0.113	strong		0.348	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
RHPN2	85415	hgsc.bcm.edu	37	19	33493188	33493188	+	Missense_Mutation	SNP	T	T	A	rs193179333	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:33493188T>A	ENST00000254260.3	-	9	1105	c.1070A>T	c.(1069-1071)cAc>cTc	p.H357L	RHPN2_ENST00000400226.4_Missense_Mutation_p.H206L	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	357	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.H357L(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)					AGTGAAGTAGTGGGCCAGGGC	0.647																																					p.H357L		Atlas-SNP	.											RHPN2,colon,carcinoma,0,9	RHPN2	107	9	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	c.A1070T						scavenged	.						45.0	42.0	43.0					19																	33493188		2203	4300	6503	SO:0001583	missense	85415	exon9			AAGTAGTGGGCCA	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.1070A>T	19.37:g.33493188T>A	ENSP00000254260:p.His357Leu	Somatic	154	3	0.0194805		WXS	Illumina HiSeq	Phase_I	176	19	0.107955	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.323917	0.81580	.	.	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.20598	2.06;2.06	4.61	4.61	0.57282	BRO1 domain (3);	0.045255	0.85682	D	0.000000	T	0.46619	0.1402	M	0.87269	2.87	0.80722	D	1	D	0.61080	0.989	P	0.58077	0.832	T	0.57934	-0.7725	10	0.87932	D	0	-27.93	14.3018	0.66357	0.0:0.0:0.0:1.0	.	357	Q8IUC4	RHPN2_HUMAN	L	357;87;206	ENSP00000254260:H357L;ENSP00000402244:H206L	ENSP00000254260:H357L	H	-	2	0	RHPN2	38185028	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	7.570000	0.82390	1.829000	0.53265	0.374000	0.22700	CAC	T|0.902;A|0.097	0.097	strong		0.647	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
TSSK2	23617	hgsc.bcm.edu	37	22	19119938	19119938	+	Silent	SNP	G	G	A	rs1052773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:19119938G>A	ENST00000399635.2	+	1	1618	c.1026G>A	c.(1024-1026)agG>agA	p.R342R	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	342					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)					AGACCTCCAGGGCCAAAGACC	0.632													G|||	1081	0.215855	0.2867	0.1527	5008	,	,		16419	0.1448		0.1809	False		,,,				2504	0.274				p.R342R		Atlas-SNP	.											.	TSSK2	29	.	0			c.G1026A						PASS	.	G	,	1081,3317		132,817,1250	36.0	37.0	37.0		,1026	2.2	0.2	22	dbSNP_86	37	1559,7015		173,1213,2901	no	utr-3,coding-synonymous	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,	305,2030,4151	AA,AG,GG		18.1829,24.5794,20.3515	,	,342/359	19119938	2640,10332	2199	4287	6486	SO:0001819	synonymous_variant	23617	exon1			CTCCAGGGCCAAA	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.1026G>A	22.37:g.19119938G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	NM_053006	Q8IY55	Silent	SNP	ENST00000399635.2	37	CCDS13755.1																																																																																			A|0.201;C|0.006	0.201	strong		0.632	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
MGAT1	4245	hgsc.bcm.edu	37	5	180219304	180219304	+	Missense_Mutation	SNP	C	C	T	rs7726005	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:180219304C>T	ENST00000446023.2	-	3	1418	c.668G>A	c.(667-669)cGg>cAg	p.R223Q	MGAT1_ENST00000393340.3_Missense_Mutation_p.R223Q|MGAT1_ENST00000307826.4_Missense_Mutation_p.R223Q|MGAT1_ENST00000333055.3_Missense_Mutation_p.R223Q|MGAT1_ENST00000427865.2_Missense_Mutation_p.R223Q	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	223			R -> Q (in dbSNP:rs7726005).		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|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)			ATAGGTGGCCCGAAAGTACTC	0.667													T|||	902	0.180112	0.2322	0.0764	5008	,	,		16522	0.2173		0.1014	False		,,,				2504	0.226				p.R223Q		Atlas-SNP	.											.	MGAT1	48	.	0			c.G668A						PASS	.	T	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	877,3513		96,685,1414	32.0	35.0	34.0		668,668,668,668,668	5.6	1.0	5	dbSNP_116	34	684,7900		32,620,3640	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	43,43,43,43,43	128,1305,5054	TT,TC,CC		7.9683,19.9772,12.0318	benign,benign,benign,benign,benign	223/446,223/446,223/446,223/446,223/446	180219304	1561,11413	2195	4292	6487	SO:0001583	missense	4245	exon3			GTGGCCCGAAAGT	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.668G>A	5.37:g.180219304C>T	ENSP00000404718:p.Arg223Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	347	0.15888278388278387	123	0.25	36	0.09944751381215469	110	0.19230769230769232	78	0.10290237467018469	T	5.994	0.367390	0.11352	0.199772	0.079683	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865	D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83	5.56	5.56	0.83823	.	0.067962	0.64402	N	0.000010	T	0.00039	0.0001	N	0.16166	0.38	0.42390	P	0.007476999999999956	B	0.02656	0.0	B	0.04013	0.001	T	0.05273	-1.0895	9	0.16896	T	0.51	-18.0177	10.1002	0.42499	0.0:0.0798:0.0:0.9202	rs7726005;rs59612173;rs7726005	223	P26572	MGAT1_HUMAN	Q	223;223;223;223;80;223	ENSP00000332073:R223Q;ENSP00000311888:R223Q;ENSP00000404718:R223Q;ENSP00000377010:R223Q;ENSP00000402838:R223Q	ENSP00000311888:R223Q	R	-	2	0	MGAT1	180151910	1.000000	0.71417	1.000000	0.80357	0.317000	0.28152	3.167000	0.50793	1.049000	0.40321	-0.254000	0.11334	CGG	C|0.844;T|0.156	0.156	strong		0.667	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
MYEOV	26579	hgsc.bcm.edu	37	11	69063393	69063393	+	Missense_Mutation	SNP	T	T	C	rs7103126	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:69063393T>C	ENST00000308946.3	+	3	926	c.476T>C	c.(475-477)gTg>gCg	p.V159A	MYEOV_ENST00000535407.1_Missense_Mutation_p.V101A|MYEOV_ENST00000441339.2_Missense_Mutation_p.V159A	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	159			V -> A (in dbSNP:rs7103126). {ECO:0000269|PubMed:10753852, ECO:0000269|PubMed:15489334}.							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)		TCTGCAAGGGTGGTGGGCGTT	0.612													C|||	2278	0.454872	0.8533	0.1916	5008	,	,		17638	0.4643		0.169	False		,,,				2504	0.3875				p.V159A		Atlas-SNP	.											.	MYEOV	42	.	0			c.T476C						PASS	.	C	ALA/VAL	3177,1223	422.1+/-339.6	1163,851,186	225.0	220.0	221.0		476	-1.7	0.0	11	dbSNP_116	221	1513,7075	748.0+/-407.3	122,1269,2903	yes	missense	MYEOV	NM_138768.2	64	1285,2120,3089	CC,CT,TT		17.6176,27.7955,36.1103	benign	159/314	69063393	4690,8298	2200	4294	6494	SO:0001583	missense	26579	exon3			CAAGGGTGGTGGG	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.476T>C	11.37:g.69063393T>C	ENSP00000308330:p.Val159Ala	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	261	107	0.409962	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	873	0.39972527472527475	403	0.8191056910569106	75	0.20718232044198895	271	0.4737762237762238	124	0.16358839050131926	C	1.627	-0.520073	0.04171	0.722045	0.176176	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.24151	1.87;1.87;1.87	0.867	-1.73	0.08081	.	.	.	.	.	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	0.22208	-1.0223	8	0.87932	D	0	.	5.5594	0.17135	0.0:0.4281:0.0:0.5719	rs7103126;rs17675255;rs17845310;rs17858148;rs61028296;rs7103126	159	Q96EZ4	MYEOV_HUMAN	A	159;159;101	ENSP00000412482:V159A;ENSP00000308330:V159A;ENSP00000438100:V101A	ENSP00000308330:V159A	V	+	2	0	MYEOV	68819969	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.270000	0.00262	-1.628000	0.01548	-1.554000	0.00893	GTG	T|0.606;C|0.394	0.394	strong		0.612	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
CTNS	1497	hgsc.bcm.edu	37	17	3563221	3563221	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:3563221G>A	ENST00000046640.3	+	11	1515	c.922G>A	c.(922-924)Ggg>Agg	p.G308R	CTNS_ENST00000381870.3_Missense_Mutation_p.G308R|CTNS_ENST00000441220.2_Missense_Mutation_p.G200R|CTNS_ENST00000414524.2_Missense_Mutation_p.G161R|RP11-235E17.6_ENST00000575741.1_RNA	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	308	PQ-loop 2.		G -> R (in CTNS). {ECO:0000269|PubMed:10556299, ECO:0000269|PubMed:12825071, ECO:0000269|PubMed:9792862}.|G -> V (in CTNS). {ECO:0000269|PubMed:12204010}.		adult walking behavior (GO:0007628)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|cellular amino acid metabolic process (GO:0006520)|cognition (GO:0050890)|glutathione metabolic process (GO:0006749)|grooming behavior (GO:0007625)|L-cystine transport (GO:0015811)|lens development in camera-type eye (GO:0002088)|long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	L-cystine transmembrane transporter activity (GO:0015184)			NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	GGACTTCACCGGGGGCAGCTT	0.617																																					p.G308R		Atlas-SNP	.											.	CTNS	42	.	0			c.G922A	GRCh37	CM980460	CTNS	M		PASS	.						59.0	57.0	58.0					17																	3563221		2203	4300	6503	SO:0001583	missense	1497	exon11			TTCACCGGGGGCA	AJ222967	CCDS11031.1, CCDS32530.1	17p13	2011-06-07	2011-06-07		ENSG00000040531	ENSG00000040531			2518	protein-coding gene	gene with protein product		606272	"""cystinosis, nephropathic"""			9537412, 15128704	Standard	NM_004937		Approved	CTNS-LSB, PQLC4	uc002fwa.3	O60931	OTTHUMG00000090693	ENST00000046640.3:c.922G>A	17.37:g.3563221G>A	ENSP00000046640:p.Gly308Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	174	46	0.264368	NM_001031681	D3DTJ5|Q8IZ01|Q9UNK6	Missense_Mutation	SNP	ENST00000046640.3	37	CCDS11031.1	.	.	.	.	.	.	.	.	.	.	g	35	5.491019	0.96339	.	.	ENSG00000040531	ENST00000046640;ENST00000381870;ENST00000441220;ENST00000414524	D;D;D;D	0.99507	-6.04;-6.04;-6.04;-6.04	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.99684	0.9881	H	0.94345	3.525	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	0.97688	1.0177	10	0.87932	D	0	-16.3759	18.5632	0.91108	0.0:0.0:1.0:0.0	.	200;308;308	F8W6Z1;O60931;O60931-2	.;CTNS_HUMAN;.	R	308;308;200;161	ENSP00000046640:G308R;ENSP00000371294:G308R;ENSP00000411465:G200R;ENSP00000395471:G161R	ENSP00000046640:G308R	G	+	1	0	CTNS	3509970	1.000000	0.71417	0.967000	0.41034	0.984000	0.73092	9.168000	0.94781	2.712000	0.92718	0.561000	0.74099	GGG	.	.	none		0.617	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937	
ECI1	1632	hgsc.bcm.edu	37	16	2301520	2301520	+	Silent	SNP	G	G	C	rs11541763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2301520G>C	ENST00000301729.4	-	1	95	c.48C>G	c.(46-48)cgC>cgG	p.R16R	AC009065.1_ENST00000454671.1_5'Flank|ECI1_ENST00000562238.1_Silent_p.R16R|ECI1_ENST00000570258.1_Intron	NM_001919.3	NP_001910.2	P42126	ECI1_HUMAN	enoyl-CoA delta isomerase 1	16					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|intramolecular oxidoreductase activity (GO:0016860)			endometrium(1)|large_intestine(2)|lung(6)	9						TCGCACCCGCGCGGAGCAGAA	0.736													g|||	336	0.0670927	0.0113	0.1009	5008	,	,		9052	0.0139		0.161	False		,,,				2504	0.0767				p.R16R		Atlas-SNP	.											ECI1,NS,carcinoma,0,1	ECI1	20	1	0			c.C48G						PASS	.		,	108,3680		2,104,1788	3.0	5.0	4.0		48,48	-2.7	0.0	16	dbSNP_134	4	1025,6725		61,903,2911	no	coding-synonymous,coding-synonymous	ECI1	NM_001178029.1,NM_001919.3	,	63,1007,4699	CC,CG,GG		13.2258,2.8511,9.8197	,	16/286,16/303	2301520	1133,10405	1894	3875	5769	SO:0001819	synonymous_variant	1632	exon1			ACCCGCGCGGAGC		CCDS10464.1, CCDS58410.1	16p13.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000167969	ENSG00000167969	5.3.3.8		2703	protein-coding gene	gene with protein product	"""3,2 trans-enoyl-CoA isomerase"""	600305	"""dodecenoyl-Coenzyme A delta isomerase (3,2 trans-enoyl-Coenzyme A isomerase)"", ""dodecenoyl-CoA isomerase"""	DCI		7829074	Standard	NM_001178029		Approved		uc002cpr.3	P42126	OTTHUMG00000128830	ENST00000301729.4:c.48C>G	16.37:g.2301520G>C		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	21	10	0.47619	NM_001178029	A8K512|Q13290|Q7Z2L6|Q7Z2L7|Q9BUB8|Q9BW05|Q9UDG6	Silent	SNP	ENST00000301729.4	37	CCDS10464.1																																																																																			G|0.917;C|0.083	0.083	strong		0.736	ECI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250768.1		
OR1A2	26189	hgsc.bcm.edu	37	17	3101578	3101578	+	Missense_Mutation	SNP	G	G	T	rs2241091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	224	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	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	
DACT2	168002	hgsc.bcm.edu	37	6	168708763	168708763	+	Silent	SNP	C	C	A	rs149504015	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168708763C>A	ENST00000366795.3	-	4	1762	c.1674G>T	c.(1672-1674)ggG>ggT	p.G558G	DACT2_ENST00000610183.1_Silent_p.G388G|DACT2_ENST00000607983.1_Silent_p.G150G|DACT2_ENST00000366796.3_Intron	NM_214462.3	NP_999627.2	Q5SW24	DACT2_HUMAN	dishevelled-binding antagonist of beta-catenin 2	558					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)		AACAGGAGCGCCCGGGTGCCT	0.716													C|||	25	0.00499201	0.0076	0.0029	5008	,	,		10999	0.0		0.003	False		,,,				2504	0.0102				p.G558G		Atlas-SNP	.											.	DACT2	46	.	0			c.G1674T						PASS	.	C		5,1379		0,5,687	27.0	37.0	34.0		1674	-5.1	0.3	6	dbSNP_134	34	18,3164		0,18,1573	no	coding-synonymous	DACT2	NM_214462.3		0,23,2260	AA,AC,CC		0.5657,0.3613,0.5037		558/775	168708763	23,4543	692	1591	2283	SO:0001819	synonymous_variant	168002	exon4			GGAGCGCCCGGGT	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.1674G>T	6.37:g.168708763C>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_214462	Q2NKJ2|Q569G0|Q8WYW2	Silent	SNP	ENST00000366795.3	37	CCDS47519.1																																																																																			C|0.996;A|0.004	0.004	strong		0.716	DACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043193.1		
DTX2	113878	hgsc.bcm.edu	37	7	76121509	76121509	+	Silent	SNP	C	C	T	rs148279131	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76121509C>T	ENST00000324432.5	+	6	1458	c.948C>T	c.(946-948)agC>agT	p.S316S	DTX2_ENST00000430490.2_Silent_p.S316S|DTX2_ENST00000413936.2_Silent_p.S316S|DTX2_ENST00000307569.8_Silent_p.S316S|DTX2_ENST00000446820.2_Silent_p.S316S|DTX2_ENST00000446600.1_Silent_p.S225S	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	809	3	0.00370828		WXS	Illumina HiSeq	Phase_I	697	144	0.2066	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		
OR52E6	390078	hgsc.bcm.edu	37	11	5863113	5863113	+	Silent	SNP	G	G	A	rs10742810	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5863113G>A	ENST00000329322.5	-	1	14	c.15C>T	c.(13-15)aaC>aaT	p.N5N	OR52E6_ENST00000379946.2_Silent_p.N9N|TRIM5_ENST00000380027.1_Intron	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	5						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(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACTGGGTGTCGTTAGCTATAG	0.408													A|||	1924	0.384185	0.379	0.3184	5008	,	,		20800	0.4593		0.3728	False		,,,				2504	0.3722				p.N5N		Atlas-SNP	.											OR52E6,NS,carcinoma,0,1	OR52E6	70	1	0			c.C15T						PASS	.	A		1565,2771		287,991,890	66.0	63.0	64.0		15	-0.6	0.0	11	dbSNP_120	64	2999,5575		538,1923,1826	no	coding-synonymous	OR52E6	NM_001005167.1		825,2914,2716	AA,AG,GG		34.9778,36.0932,35.3524		5/314	5863113	4564,8346	2168	4287	6455	SO:0001819	synonymous_variant	390078	exon1			GGTGTCGTTAGCT	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.15C>T	11.37:g.5863113G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	138	78	0.565217	NM_001005167	Q6IFF8	Silent	SNP	ENST00000329322.5	37	CCDS53597.1																																																																																			G|0.605;A|0.395	0.395	strong		0.408	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
CEP128	145508	hgsc.bcm.edu	37	14	81259254	81259254	+	Silent	SNP	A	A	T	rs45535733	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:81259254A>T	ENST00000555265.1	-	14	1785	c.1410T>A	c.(1408-1410)gcT>gcA	p.A470A	CEP128_ENST00000281129.3_Silent_p.A470A			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	470						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						CCTCTTTCAGAGCCTCTGACT	0.522													A|||	149	0.0297524	0.0015	0.0346	5008	,	,		18624	0.0288		0.0696	False		,,,				2504	0.0245				p.A470A		Atlas-SNP	.											.	CEP128	146	.	0			c.T1410A						PASS	.	A		46,4360	48.2+/-83.0	0,46,2157	155.0	139.0	145.0		1410	1.6	1.0	14	dbSNP_127	145	603,7997	158.6+/-212.1	18,567,3715	no	coding-synonymous	CEP128	NM_152446.3		18,613,5872	TT,TA,AA		7.0116,1.044,4.99		470/1095	81259254	649,12357	2203	4300	6503	SO:0001819	synonymous_variant	145508	exon13			TTTCAGAGCCTCT	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.1410T>A	14.37:g.81259254A>T		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	315	179	0.568254	NM_152446	B9EK52|Q86X97|Q96ML4	Silent	SNP	ENST00000555265.1	37	CCDS32130.1																																																																																			A|0.960;T|0.040	0.040	strong		0.522	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446	
IRS1	3667	hgsc.bcm.edu	37	2	227662753	227662753	+	Silent	SNP	C	C	T	rs2234931	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:227662753C>T	ENST00000305123.5	-	1	1722	c.702G>A	c.(700-702)ggG>ggA	p.G234G	IRS1_ENST00000498335.1_5'Flank|RP11-395N3.2_ENST00000607970.1_lincRNA	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	234	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cellular response to insulin stimulus (GO:0032869)|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)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		TCCAGAACTCCCCGGGCCCCG	0.622											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	265	0.0529153	0.0628	0.0317	5008	,	,		17205	0.0228		0.0855	False		,,,				2504	0.0521				p.G234G		Atlas-SNP	.											IRS1,rectum,carcinoma,-2,1	IRS1	141	1	0			c.G702A						PASS	.	C		256,4150	146.9+/-181.5	8,240,1955	82.0	91.0	88.0		702	2.9	1.0	2	dbSNP_98	88	576,8024	154.3+/-208.6	28,520,3752	no	coding-synonymous	IRS1	NM_005544.2		36,760,5707	TT,TC,CC		6.6977,5.8103,6.397		234/1243	227662753	832,12174	2203	4300	6503	SO:0001819	synonymous_variant	3667	exon1			GAACTCCCCGGGC		CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.702G>A	2.37:g.227662753C>T		Somatic	99	0	0	2321	WXS	Illumina HiSeq	Phase_I	67	47	0.701493	NM_005544		Silent	SNP	ENST00000305123.5	37	CCDS2463.1																																																																																			C|0.941;T|0.059	0.059	strong		0.622	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544	
LCP2	3937	hgsc.bcm.edu	37	5	169685163	169685163	+	Silent	SNP	C	C	T	rs315717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:169685163C>T	ENST00000046794.5	-	16	1593	c.978G>A	c.(976-978)caG>caA	p.Q326Q	LCP2_ENST00000521416.1_Silent_p.Q121Q	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	326					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		GCAAAGGTCTCTGATGCACTG	0.493													T|||	2781	0.555312	0.6762	0.5865	5008	,	,		19183	0.5675		0.4712	False		,,,				2504	0.4438				p.Q326Q		Atlas-SNP	.											.	LCP2	133	.	0			c.G978A						PASS	.	T		2494,1374		820,854,260	166.0	164.0	165.0		978	-11.4	0.0	5	dbSNP_79	165	4023,4259		962,2099,1080	yes	coding-synonymous	LCP2	NM_005565.3		1782,2953,1340	TT,TC,CC		48.5752,35.5222,46.3621		326/534	169685163	6517,5633	1934	4141	6075	SO:0001819	synonymous_variant	3937	exon16			AGGTCTCTGATGC		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.978G>A	5.37:g.169685163C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	137	134	0.978102	NM_005565	A8KA25|Q53XV4	Silent	SNP	ENST00000046794.5	37	CCDS47339.1																																																																																			C|0.429;T|0.571	0.571	strong		0.493	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
C9orf72	203228	hgsc.bcm.edu	37	9	27556780	27556780	+	Silent	SNP	G	G	A	rs10122902	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	130	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	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	
CELA1	1990	hgsc.bcm.edu	37	12	51739625	51739625	+	Missense_Mutation	SNP	C	C	T	rs74336876	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:51739625C>T	ENST00000293636.1	-	2	93	c.53G>A	c.(52-54)cGc>cAc	p.R18H		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	18					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						TCCGACTACGCGGGCATTGGT	0.592													C|||	14	0.00279553	0.0	0.0043	5008	,	,		15127	0.0		0.0089	False		,,,				2504	0.002				p.R18H		Atlas-SNP	.											.	CELA1	39	.	0			c.G53A						PASS	.	C	HIS/ARG	12,4382		0,12,2185	58.0	52.0	54.0		53	5.0	1.0	12	dbSNP_131	54	66,8516		0,66,4225	yes	missense	CELA1	NM_001971.5	29	0,78,6410	TT,TC,CC		0.7691,0.2731,0.6011	probably-damaging	18/259	51739625	78,12898	2197	4291	6488	SO:0001583	missense	1990	exon2			ACTACGCGGGCAT		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.53G>A	12.37:g.51739625C>T	ENSP00000293636:p.Arg18His	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	37	CCDS8812.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	27.9	4.875832	0.91664	0.002731	0.007691	ENSG00000139610	ENST00000293636	D	0.94966	-3.57	5.03	5.03	0.67393	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	D	0.95950	0.8681	M	0.76002	2.32	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.95423	0.8509	10	0.87932	D	0	-29.8305	17.5406	0.87846	0.0:1.0:0.0:0.0	.	18	Q9UNI1	CELA1_HUMAN	H	18	ENSP00000293636:R18H	ENSP00000293636:R18H	R	-	2	0	CELA1	50025892	0.999000	0.42202	0.998000	0.56505	0.793000	0.44817	6.004000	0.70709	2.503000	0.84419	0.563000	0.77884	CGC	C|0.995;T|0.005	0.005	strong		0.592	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
ANKRD61	100310846	hgsc.bcm.edu	37	7	6075823	6075823	+	Missense_Mutation	SNP	A	A	T	rs2302334	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	116	0	0		WXS	Illumina HiSeq	Phase_I	158	99	0.626582	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		
MUC6	4588	hgsc.bcm.edu	37	11	1017797	1017797	+	Silent	SNP	C	C	G	rs76800954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1017797C>G	ENST00000421673.2	-	31	5054	c.5004G>C	c.(5002-5004)gcG>gcC	p.A1668A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1668	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)		TCATTGTTGGCGCTGTGTGGG	0.567																																					p.A1668A		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	0			c.G5004C						scavenged	.						700.0	680.0	687.0					11																	1017797		2201	4295	6496	SO:0001819	synonymous_variant	4588	exon31			TGTTGGCGCTGTG	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.5004G>C	11.37:g.1017797C>G		Somatic	1185	72	0.0607595		WXS	Illumina HiSeq	Phase_I	1003	67	0.0667996	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			C|0.500;G|0.500	0.500	strong		0.567	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
C9orf171	389799	hgsc.bcm.edu	37	9	135374898	135374898	+	Silent	SNP	T	T	C	rs562350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:135374898T>C	ENST00000343036.2	+	4	591	c.543T>C	c.(541-543)aaT>aaC	p.N181N	C9orf171_ENST00000393216.2_Silent_p.N145N|C9orf171_ENST00000393215.3_Silent_p.N145N	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	181								p.N181N(1)		large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						GTCAGCTCAATGACATCCGCA	0.602													C|||	3397	0.678315	0.8533	0.572	5008	,	,		18275	0.8254		0.4831	False		,,,				2504	0.5665				p.N181N		Atlas-SNP	.											C9orf171,NS,carcinoma,0,2	C9orf171	53	2	1	Substitution - coding silent(1)	prostate(1)	c.T543C						scavenged	.	C		3509,897	345.4+/-308.5	1400,709,94	87.0	87.0	87.0		543	-6.7	0.6	9	dbSNP_83	87	4615,3985	553.0+/-386.2	1264,2087,949	no	coding-synonymous	C9orf171	NM_207417.1		2664,2796,1043	CC,CT,TT		46.3372,20.3586,37.5365		181/321	135374898	8124,4882	2203	4300	6503	SO:0001819	synonymous_variant	389799	exon4			GCTCAATGACATC	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.543T>C	9.37:g.135374898T>C		Somatic	117	2	0.017094		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_207417	Q147X1	Silent	SNP	ENST00000343036.2	37	CCDS6949.1																																																																																			T|0.356;C|0.644	0.644	strong		0.602	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417	
TCHH	7062	hgsc.bcm.edu	37	1	152082484	152082484	+	Missense_Mutation	SNP	G	G	T	rs377407296		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152082484G>T	ENST00000368804.1	-	2	3208	c.3209C>A	c.(3208-3210)aCg>aAg	p.T1070K		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1070	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.T1070K(4)		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)			gcgccttctcgtctcccgttc	0.597																																					p.T1070K		Atlas-SNP	.											TCHH,NS,carcinoma,0,4	TCHH	275	4	4	Substitution - Missense(4)	endometrium(3)|skin(1)	c.C3209A						scavenged	.						108.0	112.0	111.0					1																	152082484		2000	4150	6150	SO:0001583	missense	7062	exon3			CTTCTCGTCTCCC	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.3209C>A	1.37:g.152082484G>T	ENSP00000357794:p.Thr1070Lys	Somatic	153	5	0.0326797		WXS	Illumina HiSeq	Phase_I	221	4	0.0180995	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	T	5.324	0.245208	0.10077	.	.	ENSG00000159450	ENST00000368804	T	0.04317	3.65	1.72	-1.62	0.08372	.	.	.	.	.	T	0.00356	0.0011	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37502	-0.9703	9	0.06099	T	0.92	.	4.3307	0.11062	0.0:0.1458:0.429:0.4252	.	1070	Q07283	TRHY_HUMAN	K	1070	ENSP00000357794:T1070K	ENSP00000357794:T1070K	T	-	2	0	TCHH	150349108	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-3.679000	0.00395	-1.676000	0.01457	-0.539000	0.04255	ACG	.	.	none		0.597	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
ZNF676	163223	hgsc.bcm.edu	37	19	22363610	22363610	+	Silent	SNP	A	A	G	rs201622264	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22363610A>G	ENST00000397121.2	-	3	1226	c.909T>C	c.(907-909)caT>caC	p.H303H		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	303					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(49)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	67		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.114)				TCTCTCCAGTATGAATTCTCT	0.443																																					p.H303H		Atlas-SNP	.											ZNF676,rectum,carcinoma,0,2	ZNF676	146	2	0			c.T909C						scavenged	.						81.0	83.0	83.0					19																	22363610		2112	4258	6370	SO:0001819	synonymous_variant	163223	exon3			TCCAGTATGAATT	AK097798	CCDS42539.1	19p12	2013-01-08				ENSG00000196109		"""Zinc fingers, C2H2-type"""	20429	protein-coding gene	gene with protein product							Standard	NM_001001411		Approved		uc002nqs.1	Q8N7Q3		ENST00000397121.2:c.909T>C	19.37:g.22363610A>G		Somatic	43	1	0.0232558		WXS	Illumina HiSeq	Phase_I	43	11	0.255814	NM_001001411	A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																			A|0.793;G|0.207	0.207	strong		0.443	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411	
DDX50	79009	hgsc.bcm.edu	37	10	70700944	70700944	+	Silent	SNP	A	A	G	rs5030900	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70700944A>G	ENST00000373585.3	+	13	1991	c.1884A>G	c.(1882-1884)ggA>ggG	p.G628G	DDX50_ENST00000466265.1_3'UTR	NM_024045.1	NP_076950.1	Q9BQ39	DDX50_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 50	628						membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	29						TCCTGAAAGGAAATATGGTAG	0.368													A|||	3285	0.65595	0.528	0.6326	5008	,	,		17918	0.9038		0.6412	False		,,,				2504	0.6053				p.G628G		Atlas-SNP	.											.	DDX50	65	.	0			c.A1884G						PASS	.	A		2412,1994	611.9+/-391.9	661,1090,452	66.0	69.0	68.0		1884	4.6	1.0	10	dbSNP_113	68	5553,3047	657.3+/-401.5	1795,1963,542	no	coding-synonymous	DDX50	NM_024045.1		2456,3053,994	GG,GA,AA		35.4302,45.2565,38.759		628/738	70700944	7965,5041	2203	4300	6503	SO:0001819	synonymous_variant	79009	exon13			GAAAGGAAATATG	AF334103	CCDS7283.1	10q22.2	2010-09-30			ENSG00000107625	ENSG00000107625		"""DEAD-boxes"""	17906	protein-coding gene	gene with protein product		610373				11891046	Standard	NM_024045		Approved	GU2, MGC3199, GUB, RH-II/GuB	uc001jou.3	Q9BQ39	OTTHUMG00000018362	ENST00000373585.3:c.1884A>G	10.37:g.70700944A>G		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	97	71	0.731959	NM_024045	Q5VX37|Q8WV76|Q9BWI8	Silent	SNP	ENST00000373585.3	37	CCDS7283.1																																																																																			A|0.368;G|0.632	0.632	strong		0.368	DDX50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048363.1	NM_024045	
FANCA	2175	hgsc.bcm.edu	37	16	89839766	89839766	+	Missense_Mutation	SNP	G	G	C	rs17232910	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:89839766G>C	ENST00000389301.3	-	22	1957	c.1927C>G	c.(1927-1929)Ccc>Gcc	p.P643A	FANCA_ENST00000567284.2_5'UTR|FANCA_ENST00000568369.1_Missense_Mutation_p.P643A	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	643			P -> A (in dbSNP:rs17232910).		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		GCAGAGTTGGGTTCTGCCCTC	0.542			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	371	0.0740815	0.0038	0.0202	5008	,	,		17511	0.2698		0.0626	False		,,,				2504	0.0174				p.P643A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C1927G						PASS	.	G	ALA/PRO	51,4029		0,51,1989	31.0	26.0	28.0		1927	-2.4	0.0	16	dbSNP_123	28	519,7361		11,497,3432	yes	missense	FANCA	NM_000135.2	27	11,548,5421	CC,CG,GG		6.5863,1.25,4.7659	benign	643/1456	89839766	570,11390	2040	3940	5980	SO:0001583	missense	2175	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGTTGGGTTCTGC	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.1927C>G	16.37:g.89839766G>C	ENSP00000373952:p.Pro643Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	114	12	0.105263	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	190	0.08699633699633699	3	0.006097560975609756	10	0.027624309392265192	127	0.22202797202797203	50	0.06596306068601583	G	6.741	0.505585	0.12822	0.0125	0.065863	ENSG00000187741	ENST00000389301	D	0.83591	-1.74	3.82	-2.44	0.06502	.	0.752143	0.11984	N	0.510486	T	0.00039	0.0001	N	0.08118	0	0.53688	P	2.6999999999999247E-5	B;B	0.09022	0.002;0.001	B;B	0.04013	0.001;0.001	T	0.03706	-1.1011	9	0.07030	T	0.85	-10.2216	2.1006	0.03679	0.1027:0.3278:0.2668:0.3028	rs17232910	643;643	B4DRI7;O15360	.;FANCA_HUMAN	A	643	ENSP00000373952:P643A	ENSP00000373952:P643A	P	-	1	0	FANCA	88367267	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	-0.040000	0.12104	-0.163000	0.10946	-0.131000	0.14894	CCC	G|0.936;C|0.064	0.064	strong		0.542	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
PRUNE2	158471	hgsc.bcm.edu	37	9	79324408	79324408	+	Missense_Mutation	SNP	T	T	C	rs41289953	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:79324408T>C	ENST00000376718.3	-	8	2905	c.2782A>G	c.(2782-2784)Aaa>Gaa	p.K928E	PRUNE2_ENST00000428286.1_Missense_Mutation_p.K569E	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	928					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						GACCCTCCTTTCTTCATATTC	0.418													T|||	109	0.0217652	0.003	0.0447	5008	,	,		22085	0.001		0.0676	False		,,,				2504	0.0051				p.K928E		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A2782G						PASS	.	T	GLU/LYS	23,3113		0,23,1545	239.0	223.0	228.0		2782	3.2	0.5	9	dbSNP_127	228	372,6792		10,352,3220	yes	missense	PRUNE2	NM_015225.2	56	10,375,4765	CC,CT,TT		5.1926,0.7334,3.835	benign	928/3089	79324408	395,9905	1568	3582	5150	SO:0001583	missense	158471	exon8			CTCCTTTCTTCAT	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.2782A>G	9.37:g.79324408T>C	ENSP00000365908:p.Lys928Glu	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	178	86	0.483146	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	64|64	0.029304029304029304|0.029304029304029304	2|2	0.0040650406504065045|0.0040650406504065045	17|17	0.04696132596685083|0.04696132596685083	0|0	0.0|0.0	45|45	0.059366754617414245|0.059366754617414245	T|T	0.511|0.511	-0.866562|-0.866562	0.02590|0.02590	0.007334|0.007334	0.051926|0.051926	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.51817	.|0.69;0.73	5.89|5.89	3.25|3.25	0.37280|0.37280	.|.	.|0.231952	.|0.30584	.|N	.|0.009309	T|T	0.03520|0.03520	0.0101|0.0101	N|N	0.20986|0.20986	0.625|0.625	0.58432|0.58432	D|D	0.999999|0.999999	.|B	.|0.21606	.|0.058	.|B	.|0.17098	.|0.017	T|T	0.03166|0.03166	-1.1065|-1.1065	5|10	.|0.48119	.|T	.|0.1	-27.4999|-27.4999	6.1762|6.1762	0.20444|0.20444	0.0:0.204:0.134:0.662|0.0:0.204:0.134:0.662	rs41289953|rs41289953	.|928	.|Q8WUY3	.|PRUN2_HUMAN	G|E	249|928;569;927	.|ENSP00000365908:K928E;ENSP00000397425:K569E	.|ENSP00000365908:K928E	E|K	-|-	2|1	0|0	PRUNE2|PRUNE2	78514228|78514228	0.976000|0.976000	0.34144|0.34144	0.510000|0.510000	0.27712|0.27712	0.250000|0.250000	0.25880|0.25880	0.782000|0.782000	0.26788|0.26788	1.061000|1.061000	0.40601|0.40601	0.459000|0.459000	0.35465|0.35465	GAA|AAA	T|0.964;C|0.036	0.036	strong		0.418	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
TGIF1	7050	hgsc.bcm.edu	37	18	3457641	3457641	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:3457641C>T	ENST00000330513.5	+	3	1212	c.909C>T	c.(907-909)tgC>tgT	p.C303C	TGIF1_ENST00000548489.2_Silent_p.C188C|TGIF1_ENST00000343820.5_Silent_p.C174C|TGIF1_ENST00000400167.2_Silent_p.C154C|TGIF1_ENST00000405385.3_Silent_p.C154C|TGIF1_ENST00000407501.2_Silent_p.C174C|TGIF1_ENST00000472042.1_Silent_p.C154C|TGIF1_ENST00000345133.5_Silent_p.C154C|TGIF1_ENST00000551541.1_Silent_p.C154C|TGIF1_ENST00000401449.1_Silent_p.C154C	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	303					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)				CAGTGATCTGCCATACCACTG	0.522																																					p.C303C		Atlas-SNP	.											TGIF1,colon,carcinoma,0,1	TGIF1	41	1	0			c.C909T						scavenged	.						76.0	66.0	69.0					18																	3457641		2203	4300	6503	SO:0001819	synonymous_variant	7050	exon3			GATCTGCCATACC	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.909C>T	18.37:g.3457641C>T		Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	176	3	0.0170455	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	37	CCDS11834.1																																																																																			.	.	none		0.522	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
APOBEC2	10930	hgsc.bcm.edu	37	6	41029342	41029342	+	Missense_Mutation	SNP	T	T	C	rs2076472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:41029342T>C	ENST00000244669.2	+	2	451	c.407T>C	c.(406-408)aTc>aCc	p.I136T		NM_006789.3	NP_006780.1	Q9Y235	ABEC2_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2	136			I -> T (in dbSNP:rs2076472). {ECO:0000269|Ref.3}.		cytidine deamination (GO:0009972)|DNA demethylation (GO:0080111)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)		cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|prostate(2)|skin(1)	10	Ovarian(28;0.0418)|Colorectal(47;0.196)					GACCGCATTATCAAAACCCTT	0.562													T|||	888	0.177316	0.0068	0.2277	5008	,	,		20026	0.2679		0.168	False		,,,				2504	0.2883				p.I136T	Ovarian(118;1320 2185 8096 29684)	Atlas-SNP	.											.	APOBEC2	30	.	0			c.T407C						PASS	.	T	THR/ILE	178,4228	116.3+/-154.2	6,166,2031	157.0	149.0	152.0		407	1.4	0.5	6	dbSNP_96	152	1747,6853	318.4+/-313.7	181,1385,2734	yes	missense	APOBEC2	NM_006789.3	89	187,1551,4765	CC,CT,TT		20.314,4.0399,14.8009	benign	136/225	41029342	1925,11081	2203	4300	6503	SO:0001583	missense	10930	exon2			GCATTATCAAAAC	AF161698	CCDS4848.1	6p21	2008-02-05			ENSG00000124701	ENSG00000124701		"""Apolipoprotein B mRNA editing enzymes"""	605	protein-coding gene	gene with protein product		604797				10403781	Standard	NM_006789		Approved	ARCD1, ARP1	uc003opl.3	Q9Y235	OTTHUMG00000014670	ENST00000244669.2:c.407T>C	6.37:g.41029342T>C	ENSP00000244669:p.Ile136Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	158	80	0.506329	NM_006789	B2R899|Q53F28|Q5TGU5|Q5TGU6	Missense_Mutation	SNP	ENST00000244669.2	37	CCDS4848.1	364|364	0.16666666666666666|0.16666666666666666	4|4	0.008130081300813009|0.008130081300813009	81|81	0.22375690607734808|0.22375690607734808	150|150	0.26223776223776224|0.26223776223776224	129|129	0.17018469656992086|0.17018469656992086	T|T	9.339|9.339	1.062585|1.062585	0.19987|0.19987	0.040399|0.040399	0.20314|0.20314	ENSG00000124701|ENSG00000124701	ENST00000244669|ENST00000426505	T|.	0.49139|.	0.79|.	5.54|5.54	1.37|1.37	0.22104|0.22104	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);|.	0.646541|.	0.16452|.	N|.	0.213828|.	T|T	0.10294|0.10294	0.0252|0.0252	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.06405|.	0.002|.	T|T	0.11641|0.11641	-1.0579|-1.0579	9|5	0.54805|0.59425	T|D	0.06|0.04	.|.	5.8748|5.8748	0.18822|0.18822	0.0:0.2351:0.1508:0.614|0.0:0.2351:0.1508:0.614	rs2076472;rs56663139;rs2076472|rs2076472;rs56663139;rs2076472	136|.	Q9Y235|.	ABEC2_HUMAN|.	T|P	136|101	ENSP00000244669:I136T|.	ENSP00000244669:I136T|ENSP00000395214:S101P	I|S	+|+	2|1	0|0	APOBEC2|APOBEC2	41137320|41137320	0.000000|0.000000	0.05858|0.05858	0.530000|0.530000	0.27963|0.27963	0.788000|0.788000	0.44548|0.44548	0.274000|0.274000	0.18680|0.18680	0.320000|0.320000	0.23234|0.23234	-1.125000|-1.125000	0.01998|0.01998	ATC|TCA	T|0.816;C|0.184	0.184	strong		0.562	APOBEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040498.1	NM_006789	
KIAA1107	23285	hgsc.bcm.edu	37	1	92646021	92646021	+	Silent	SNP	G	G	A	rs1483022	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:92646021G>A	ENST00000370378.4	+	8	1565	c.1467G>A	c.(1465-1467)aaG>aaA	p.K489K	KIAA1107_ENST00000409154.4_Silent_p.K544K	NM_015237.2	NP_056052.2	Q9UPP5	K1107_HUMAN	KIAA1107	544										breast(4)|central_nervous_system(1)|endometrium(3)|kidney(2)|prostate(1)|skin(3)	14						ATCAGTCAAAGAAAGGTGAAA	0.358													G|||	3560	0.710863	0.6059	0.6066	5008	,	,		19115	0.9732		0.6223	False		,,,				2504	0.7474				p.K489K		Atlas-SNP	.											.	KIAA1107	60	.	0			c.G1467A						PASS	.						43.0	36.0	38.0					1																	92646021		692	1591	2283	SO:0001819	synonymous_variant	23285	exon8			GTCAAAGAAAGGT	AB029030	CCDS44172.1	1p22.1	2008-02-05			ENSG00000069712	ENSG00000069712			29192	protein-coding gene	gene with protein product						10470851	Standard	NM_015237		Approved		uc010otd.2	Q9UPP5	OTTHUMG00000010292	ENST00000370378.4:c.1467G>A	1.37:g.92646021G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	102	24	0.235294	NM_015237	O14767|Q8N3X7	Silent	SNP	ENST00000370378.4	37	CCDS44172.1																																																																																			G|0.301;A|0.699	0.699	strong		0.358	KIAA1107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028375.3	XM_034086	
ACPP	55	hgsc.bcm.edu	37	3	132075554	132075554	+	Silent	SNP	T	T	C	rs3181784	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:132075554T>C	ENST00000336375.5	+	10	1083	c.993T>C	c.(991-993)taT>taC	p.Y331Y	ACPP_ENST00000475741.1_Silent_p.Y298Y|ACPP_ENST00000351273.7_Silent_p.Y331Y	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	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	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	
UBR5	51366	hgsc.bcm.edu	37	8	103307434	103307434	+	Silent	SNP	G	G	A	rs34739767	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:103307434G>A	ENST00000520539.1	-	31	4662	c.4056C>T	c.(4054-4056)gaC>gaT	p.D1352D	UBR5_ENST00000220959.4_Silent_p.D1352D|UBR5_ENST00000521922.1_Silent_p.D1346D|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	1352					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)			ATACGTACGGGTCTTTATTCT	0.398													G|||	147	0.029353	0.003	0.1081	5008	,	,		19573	0.001		0.0318	False		,,,				2504	0.0358				p.D1352D	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.C4056T						PASS	.	G		36,4370	41.6+/-74.8	0,36,2167	72.0	70.0	71.0		4056	-0.5	1.0	8	dbSNP_126	71	340,8260	117.0+/-176.6	11,318,3971	no	coding-synonymous	UBR5	NM_015902.5		11,354,6138	AA,AG,GG		3.9535,0.8171,2.891		1352/2800	103307434	376,12630	2203	4300	6503	SO:0001819	synonymous_variant	51366	exon31			GTACGGGTCTTTA	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.4056C>T	8.37:g.103307434G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	200	47	0.235	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Silent	SNP	ENST00000520539.1	37	CCDS34933.1																																																																																			G|0.972;A|0.028	0.028	strong		0.398	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
OR51F2	119694	hgsc.bcm.edu	37	11	4842866	4842866	+	Missense_Mutation	SNP	A	A	G	rs35003053	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4842866A>G	ENST00000322110.5	+	1	316	c.251A>G	c.(250-252)gAc>gGc	p.D84G	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2	84						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(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCAGCCACAGACCTGAGCTTG	0.473													A|||	303	0.0605032	0.0371	0.1023	5008	,	,		23225	0.0		0.163	False		,,,				2504	0.0194				p.D84G		Atlas-SNP	.											OR51F2,NS,carcinoma,+1,1	OR51F2	72	1	0			c.A251G						PASS	.	A	GLY/ASP	267,4135	149.9+/-184.0	5,257,1939	187.0	178.0	181.0		251	4.4	1.0	11	dbSNP_126	181	1277,7319	255.1+/-280.1	116,1045,3137	yes	missense	OR51F2	NM_001004753.1	94	121,1302,5076	GG,GA,AA		14.8557,6.0654,11.8788	probably-damaging	84/343	4842866	1544,11454	2201	4298	6499	SO:0001583	missense	119694	exon1			CCACAGACCTGAG	BK004281	CCDS31361.1	11p15.4	2012-08-09			ENSG00000176925	ENSG00000176925		"""GPCR / Class A : Olfactory receptors"""	15197	protein-coding gene	gene with protein product							Standard	NM_001004753		Approved		uc010qyn.2	Q8NH61	OTTHUMG00000066508	ENST00000322110.5:c.251A>G	11.37:g.4842866A>G	ENSP00000323952:p.Asp84Gly	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	159	85	0.534591	NM_001004753	Q6IFI1	Missense_Mutation	SNP	ENST00000322110.5	37	CCDS31361.1	188	0.08608058608058608	17	0.034552845528455285	51	0.1408839779005525	0	0.0	120	0.158311345646438	A	18.59	3.656456	0.67586	0.060654	0.148557	ENSG00000176925	ENST00000322110	T	0.67523	-0.27	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	U	0.000666	T	0.01730	0.0055	H	0.94462	3.54	0.27477	P	0.9526828	D	0.89917	1.0	D	0.78314	0.991	T	0.55554	-0.8123	9	0.87932	D	0	.	12.924	0.58249	1.0:0.0:0.0:0.0	rs35003053;rs61744403	84	Q8NH61	O51F2_HUMAN	G	84	ENSP00000323952:D84G	ENSP00000323952:D84G	D	+	2	0	OR51F2	4799442	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.659000	0.68010	1.991000	0.58162	0.459000	0.35465	GAC	A|0.890;G|0.110	0.110	strong		0.473	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753	
CCDC30	728621	hgsc.bcm.edu	37	1	43042703	43042703	+	Silent	SNP	C	C	T	rs12049046	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43042703C>T	ENST00000340612.4	+	6	868	c.868C>T	c.(868-870)Cta>Tta	p.L290L	CCDC30_ENST00000428554.2_Silent_p.L290L|CCDC30_ENST00000390640.4_Silent_p.L79L|CCDC30_ENST00000507855.1_Silent_p.L79L|CCDC30_ENST00000342022.4_Silent_p.L290L			Q5VVM6	CCD30_HUMAN	coiled-coil domain containing 30	290						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	30						AAAGATTGAACTAAAGCATGC	0.388													C|||	1430	0.285543	0.177	0.1571	5008	,	,		19876	0.4563		0.1879	False		,,,				2504	0.4479				p.L290L		Atlas-SNP	.											.	CCDC30	78	.	0			c.C868T						PASS	.	C		808,3598	322.3+/-297.6	79,650,1474	65.0	61.0	62.0		868	3.9	1.0	1	dbSNP_120	62	1707,6893	309.3+/-309.3	176,1355,2769	no	coding-synonymous	CCDC30	NM_001080850.2		255,2005,4243	TT,TC,CC		19.8488,18.3386,19.3372		290/784	43042703	2515,10491	2203	4300	6503	SO:0001819	synonymous_variant	728621	exon7			ATTGAACTAAAGC	AY639646	CCDS30690.1	1p34.2	2009-07-09			ENSG00000186409	ENSG00000186409			26103	protein-coding gene	gene with protein product	"""prefoldin 6-like"""					16710767	Standard	NM_001080850		Approved	FLJ20972, PFD6L, LOC728621	uc009vwk.1	Q5VVM6	OTTHUMG00000007334	ENST00000340612.4:c.868C>T	1.37:g.43042703C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	86	17	0.197674	NM_001080850	Q14F06|Q5VVM5	Silent	SNP	ENST00000340612.4	37	CCDS30690.1																																																																																			C|0.778;T|0.222	0.222	strong		0.388	CCDC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019524.3	NM_025030	
DAPK1	1612	hgsc.bcm.edu	37	9	90283514	90283514	+	Silent	SNP	C	C	T	rs3750538	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:90283514C>T	ENST00000408954.3	+	19	2261	c.1926C>T	c.(1924-1926)gaC>gaT	p.D642D	DAPK1_ENST00000469640.2_Silent_p.D642D|DAPK1_ENST00000466188.1_3'UTR|DAPK1_ENST00000491893.1_Silent_p.D642D|DAPK1_ENST00000358077.5_Silent_p.D642D|DAPK1_ENST00000472284.1_Silent_p.D642D	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	642					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						TCCAACAGGACGGAAAGACGG	0.468									Chronic Lymphocytic Leukemia, Familial Clustering of				T|||	242	0.0483227	0.0303	0.0447	5008	,	,		23138	0.0873		0.0606	False		,,,				2504	0.0225				p.D642D		Atlas-SNP	.											.	DAPK1	329	.	0			c.C1926T						PASS	.	T		120,3788		2,116,1836	237.0	240.0	239.0		1926	3.6	1.0	9	dbSNP_107	239	397,7899		10,377,3761	no	coding-synonymous	DAPK1	NM_004938.2		12,493,5597	TT,TC,CC		4.7854,3.0706,4.2363		642/1431	90283514	517,11687	1954	4148	6102	SO:0001819	synonymous_variant	1612	exon19	Familial Cancer Database	Familial CLL	ACAGGACGGAAAG	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.1926C>T	9.37:g.90283514C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	45	0.592105	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			C|0.938;T|0.062	0.062	strong		0.468	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
TYW1	55253	hgsc.bcm.edu	37	7	66648199	66648199	+	Silent	SNP	G	G	A	rs55756354	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:66648199G>A	ENST00000359626.5	+	14	1949	c.1785G>A	c.(1783-1785)ggG>ggA	p.G595G		NM_018264.2	NP_060734.2	Q9NV66	TYW1_HUMAN	tRNA-yW synthesizing protein 1 homolog (S. cerevisiae)	595					tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|lyase activity (GO:0016829)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(8)|kidney(10)|large_intestine(4)|lung(13)|ovary(1)|prostate(2)|skin(3)|stomach(2)|urinary_tract(2)	46		Lung NSC(55;0.0846)|all_lung(88;0.183)				TGTCCCTGGGGAATCCTGACT	0.537																																					p.G595G		Atlas-SNP	.											.	TYW1	71	.	0			c.G1785A						PASS	.	G		1246,3160		124,998,1081	59.0	45.0	50.0		1785	0.6	0.1	7	dbSNP_129	50	1785,6805		158,1469,2668	no	coding-synonymous	TYW1	NM_018264.2		282,2467,3749	AA,AG,GG		20.78,28.2796,23.3226		595/733	66648199	3031,9965	2203	4295	6498	SO:0001819	synonymous_variant	55253	exon14			CCTGGGGAATCCT	AK001762	CCDS5538.1	7q11.21	2007-11-29	2007-11-29	2007-11-29	ENSG00000198874	ENSG00000198874			25598	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 1 homolog A (S. cerevisiae)"""	611243	"""radical S-adenosyl methionine and flavodoxin domains 1"""	RSAFD1		16162496, 17150819	Standard	NM_018264		Approved	FLJ10900, MGC23001, MGC60291, YPL207W, TYW1A	uc003tvn.4	Q9NV66	OTTHUMG00000129723	ENST00000359626.5:c.1785G>A	7.37:g.66648199G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	123	70	0.569106	NM_018264	Q6PJG8|Q75MG8|Q75MN3|Q86V12|Q8IVS7|Q9H9C4	Silent	SNP	ENST00000359626.5	37	CCDS5538.1																																																																																			.	.	weak		0.537	TYW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251932.2	NM_018264	
ZNF93	81931	hgsc.bcm.edu	37	19	20044041	20044041	+	Missense_Mutation	SNP	G	G	T	rs12151060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:20044041G>T	ENST00000343769.5	+	4	305	c.277G>T	c.(277-279)Gat>Tat	p.D93Y	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	93			D -> Y (in dbSNP:rs12151060). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|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)			endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						GAACATAAAAGATTCTTTCCA	0.328													g|||	940	0.1877	0.0809	0.17	5008	,	,		18208	0.4415		0.1531	False		,,,				2504	0.1186				p.D93Y		Atlas-SNP	.											.	ZNF93	81	.	0			c.G277T						PASS	.	G	TYR/ASP	457,3947	202.8+/-225.5	28,401,1773	56.0	59.0	58.0		277	0.9	0.3	19	dbSNP_120	58	1452,7148	271.6+/-289.6	119,1214,2967	no	missense	ZNF93	NM_031218.3	160	147,1615,4740	TT,TG,GG		16.8837,10.3769,14.6801	benign	93/621	20044041	1909,11095	2202	4300	6502	SO:0001583	missense	81931	exon4			ATAAAAGATTCTT	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"""Zinc fingers, C2H2-type"", ""-"""	13169	protein-coding gene	gene with protein product		603975	"""zinc finger protein 505"", ""zinc finger protein 93 (HTF34)"""	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.277G>T	19.37:g.20044041G>T	ENSP00000342002:p.Asp93Tyr	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	195	101	0.517949	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	37	CCDS32973.1	489	0.2239010989010989	42	0.08536585365853659	50	0.13812154696132597	269	0.47027972027972026	128	0.16886543535620052	g	13.15	2.150834	0.37923	0.103769	0.168837	ENSG00000184635	ENST00000343769;ENST00000427325;ENST00000430434	T	0.05513	3.43	0.85	0.85	0.18980	.	.	.	.	.	T	0.00012	0.0000	M	0.84326	2.69	0.44268	P	0.0028719999999999857	P	0.37573	0.6	B	0.36922	0.236	T	0.40553	-0.9557	8	0.62326	D	0.03	.	4.7959	0.13272	0.0:0.0:1.0:0.0	rs12151060;rs52830493;rs12151060	93	P35789	ZNF93_HUMAN	Y	93;93;24	ENSP00000342002:D93Y	ENSP00000342002:D93Y	D	+	1	0	ZNF93	19905041	0.000000	0.05858	0.257000	0.24404	0.256000	0.26092	-2.231000	0.01206	0.192000	0.20272	0.195000	0.17529	GAT	G|0.821;T|0.179	0.179	strong		0.328	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
PRDM2	7799	hgsc.bcm.edu	37	1	14109114	14109114	+	Silent	SNP	A	A	G	rs1203651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:14109114A>G	ENST00000235372.7	+	8	5680	c.4824A>G	c.(4822-4824)tcA>tcG	p.S1608S	PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000311066.5_Silent_p.S1608S|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000413440.1_Silent_p.S1407S|PRDM2_ENST00000343137.4_Silent_p.S1407S	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1608					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		GCAAAACATCACGGAGCCTGC	0.433													G|||	1828	0.365016	0.2322	0.5418	5008	,	,		20761	0.3988		0.328	False		,,,				2504	0.4223				p.S1608S		Atlas-SNP	.											.	PRDM2	147	.	0			c.A4824G						PASS	.	G	,,,	1163,3243	713.4+/-408.2	156,851,1196	73.0	74.0	73.0		4221,,4824,4824	0.7	0.0	1	dbSNP_87	73	3140,5460	656.3+/-401.3	533,2074,1693	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	PRDM2	NM_001007257.2,NM_001135610.1,NM_012231.4,NM_015866.4	,,,	689,2925,2889	GG,GA,AA		36.5116,26.3958,33.0847	,,,	1407/1482,,1608/1719,1608/1683	14109114	4303,8703	2203	4300	6503	SO:0001819	synonymous_variant	7799	exon8			AACATCACGGAGC	U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.4824A>G	1.37:g.14109114A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Silent	SNP	ENST00000235372.7	37	CCDS150.1																																																																																			A|0.657;G|0.343	0.343	strong		0.433	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
FRMD1	79981	hgsc.bcm.edu	37	6	168463624	168463624	+	Missense_Mutation	SNP	G	G	A	rs902393	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168463624G>A	ENST00000283309.6	-	7	884	c.820C>T	c.(820-822)Cgt>Tgt	p.R274C	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000537786.1_Missense_Mutation_p.R45C|FRMD1_ENST00000440994.2_Missense_Mutation_p.R206C	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	146	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	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	
SERPINA6	866	hgsc.bcm.edu	37	14	94772504	94772504	+	Silent	SNP	G	G	A	rs1042394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:94772504G>A	ENST00000341584.3	-	4	1082	c.936C>T	c.(934-936)ctC>ctT	p.L312L		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	312					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	GCACATCTCCGAGGTCATAGA	0.537													G|||	815	0.16274	0.1672	0.1441	5008	,	,		19990	0.0595		0.3002	False		,,,				2504	0.135				p.L312L		Atlas-SNP	.											.	SERPINA6	102	.	0			c.C936T						PASS	.	G		806,3600	322.9+/-297.8	80,646,1477	122.0	103.0	110.0		936	-2.7	0.0	14	dbSNP_86	110	2320,6280	389.2+/-342.9	359,1602,2339	no	coding-synonymous	SERPINA6	NM_001756.3		439,2248,3816	AA,AG,GG		26.9767,18.2932,24.0351		312/406	94772504	3126,9880	2203	4300	6503	SO:0001819	synonymous_variant	866	exon4			ATCTCCGAGGTCA	J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"""Serine (or cysteine) peptidase inhibitors"""	1540	protein-coding gene	gene with protein product	"""corticosteroid binding globulin"", ""transcortin"""	122500	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"""	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.936C>T	14.37:g.94772504G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	160	106	0.6625	NM_001756	A8K456|Q7Z2Q9	Silent	SNP	ENST00000341584.3	37	CCDS9924.1																																																																																			G|0.775;A|0.225	0.225	strong		0.537	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756	
POLR2D	5433	hgsc.bcm.edu	37	2	128610648	128610648	+	Silent	SNP	T	T	C	rs10210695	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:128610648T>C	ENST00000272645.4	-	2	161	c.105A>G	c.(103-105)tcA>tcG	p.S35S	POLR2D_ENST00000409955.1_Silent_p.S35S|POLR2D_ENST00000409698.1_5'UTR|POLR2D_ENST00000487079.1_Intron	NM_004805.3	NP_004796.1	O15514	RPB4_HUMAN	polymerase (RNA) II (DNA directed) polypeptide D	35					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus in response to heat stress (GO:0031990)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nucleotide-excision repair (GO:0006289)|positive regulation of translational initiation (GO:0045948)|positive regulation of viral transcription (GO:0050434)|recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO:0034402)|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)	cytoplasmic mRNA processing body (GO:0000932)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)|nucleotide binding (GO:0000166)|translation initiation factor binding (GO:0031369)			large_intestine(1)|lung(4)|urinary_tract(1)	6	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0675)		TATGAACTTCTGAATTTAGAA	0.383													T|||	619	0.123602	0.2859	0.0735	5008	,	,		20607	0.0466		0.1024	False		,,,				2504	0.0409				p.S35S		Atlas-SNP	.											.	POLR2D	13	.	0			c.A105G						PASS	.	T		1219,3187	425.7+/-340.9	172,875,1156	136.0	131.0	133.0		105	-9.8	0.9	2	dbSNP_119	133	994,7606	213.9+/-253.7	49,896,3355	no	coding-synonymous	POLR2D	NM_004805.3		221,1771,4511	CC,CT,TT		11.5581,27.6668,17.0152		35/143	128610648	2213,10793	2203	4300	6503	SO:0001819	synonymous_variant	5433	exon2			AACTTCTGAATTT	U85510	CCDS2151.1	2q21	2013-01-21			ENSG00000144231	ENSG00000144231		"""RNA polymerase subunits"""	9191	protein-coding gene	gene with protein product	"""RNA polymerase II subunit hsRBP4"""	606017				9528765	Standard	NM_004805		Approved	RBP4	uc002tpj.3	O15514	OTTHUMG00000131531	ENST00000272645.4:c.105A>G	2.37:g.128610648T>C		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	59	0.398649	NM_004805	Q52LT4	Silent	SNP	ENST00000272645.4	37	CCDS2151.1																																																																																			T|0.848;C|0.152	0.152	strong		0.383	POLR2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254388.3	NM_004805	
GDI1	2664	hgsc.bcm.edu	37	X	153667176	153667176	+	Silent	SNP	T	T	C	rs4834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:153667176T>C	ENST00000447750.2	+	3	554	c.219T>C	c.(217-219)aaT>aaC	p.N73N		NM_001493.2	NP_001484.1	P31150	GDIA_HUMAN	GDP dissociation inhibitor 1	73					negative regulation of axonogenesis (GO:0050771)|negative regulation of protein targeting to membrane (GO:0090315)|protein transport (GO:0015031)|Rab protein signal transduction (GO:0032482)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|midbody (GO:0030496)|neuron projection (GO:0043005)|protein complex (GO:0043234)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|Rab GDP-dissociation inhibitor activity (GO:0005093)			autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	16	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)					GAGACTGGAATGTTGACCTGA	0.572													C|||	1098	0.290861	0.5174	0.1686	3775	,	,		15146	0.0526		0.0845	False		,,,				2504	0.1626				p.N73N		Atlas-SNP	.											.	GDI1	36	.	0			c.T219C						PASS	.	C		2408,1427		641,745,381,246,190	179.0	184.0	182.0		219	-2.1	0.9	X	dbSNP_52	182	864,5864		40,555,229,1833,1643	no	coding-synonymous	GDI1	NM_001493.2		681,1300,610,2079,1833	CC,CT,C,TT,T		12.8419,37.2099,30.976		73/448	153667176	3272,7291	2203	4300	6503	SO:0001819	synonymous_variant	2664	exon3			CTGGAATGTTGAC	X79353	CCDS35452.1	Xq28	2008-08-01			ENSG00000203879	ENSG00000203879			4226	protein-coding gene	gene with protein product	"""mental retardation, X-linked 41"", ""mental retardation, X-linked 48"", ""rab GDP-dissociation inhibitor, alpha"""	300104		MRX48, MRX41, GDIL		7543319, 7849400	Standard	NM_001493		Approved	RABGDIA, XAP-4, OPHN2, FLJ41411	uc004fli.4	P31150	OTTHUMG00000033293	ENST00000447750.2:c.219T>C	X.37:g.153667176T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	82	78	0.951219	NM_001493	P50394|Q6FG50|Q7Z2G6|Q7Z2G9|Q7Z2H5|Q7Z2I6	Silent	SNP	ENST00000447750.2	37	CCDS35452.1																																																																																			0|0.001;C|0.314	0.314	strong		0.572	GDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081649.2	NM_001493	
TRPM5	29850	hgsc.bcm.edu	37	11	2436464	2436464	+	Missense_Mutation	SNP	C	C	T	rs34551253	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2436464C>T	ENST00000155858.6	-	9	1374	c.1366G>A	c.(1366-1368)Gcg>Acg	p.A456T	TRPM5_ENST00000452833.1_Missense_Mutation_p.A458T|TRPM5_ENST00000528453.1_Missense_Mutation_p.A456T|TRPM5_ENST00000533060.1_Missense_Mutation_p.A456T	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)		GGTGGCCCCGCGGGTGGCTCC	0.716													C|||	54	0.0107827	0.0023	0.0245	5008	,	,		13476	0.001		0.0308	False		,,,				2504	0.002				p.A456T	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1366A						PASS	.	C	THR/ALA	35,4235		1,33,2101	7.0	9.0	9.0		1366	-6.4	0.0	11	dbSNP_126	9	273,8141		6,261,3940	yes	missense	TRPM5	NM_014555.3	58	7,294,6041	TT,TC,CC		3.2446,0.8197,2.4283	benign	456/1166	2436464	308,12376	2135	4207	6342	SO:0001583	missense	29850	exon9			GCCCCGCGGGTGG	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.1366G>A	11.37:g.2436464C>T	ENSP00000155858:p.Ala456Thr	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	10	6	0.6	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	35	0.016025641025641024	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	22	0.029023746701846966	C	0.009	-1.820965	0.00595	0.008197	0.032446	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	3.19	-6.37	0.01963	.	1.134030	0.06672	N	0.766349	T	0.14227	0.0344	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.005;0.005;0.008	B;B;B	0.09377	0.002;0.001;0.004	T	0.05517	-1.0880	10	0.14252	T	0.57	0.2166	1.5474	0.02568	0.2706:0.3676:0.1989:0.1629	rs34551253	456;458;456	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	T	450;456;458;456;456;456	ENSP00000434383:A450T;ENSP00000155858:A456T;ENSP00000387965:A458T;ENSP00000434121:A456T;ENSP00000436809:A456T	ENSP00000155858:A456T	A	-	1	0	TRPM5	2393040	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.025000	0.01435	-3.859000	0.00098	-1.579000	0.00862	GCG	C|0.983;T|0.017	0.017	strong		0.716	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
DNHD1	144132	hgsc.bcm.edu	37	11	6568213	6568213	+	Missense_Mutation	SNP	T	T	C	rs58186801	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	54	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	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	
MRGPRF	116535	hgsc.bcm.edu	37	11	68773089	68773089	+	Missense_Mutation	SNP	C	C	T	rs151254404		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68773089C>T	ENST00000309099.6	-	3	1071	c.689G>A	c.(688-690)cGg>cAg	p.R230Q	MRGPRF_ENST00000441623.1_Missense_Mutation_p.R230Q|RP11-554A11.5_ENST00000562506.1_RNA	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	230						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GCGCTGGCGCCGTCGGGCCCG	0.627																																					p.R230Q		Atlas-SNP	.											.	MRGPRF	22	.	0			c.G689A						PASS	.	C	GLN/ARG,GLN/ARG	0,4368		0,0,2184	33.0	26.0	28.0		689,689	3.3	0.9	11	dbSNP_134	28	4,8528		0,4,4262	yes	missense,missense	MRGPRF	NM_001098515.1,NM_145015.4	43,43	0,4,6446	TT,TC,CC		0.0469,0.0,0.031	probably-damaging,probably-damaging	230/344,230/344	68773089	4,12896	2184	4266	6450	SO:0001583	missense	116535	exon3			TGGCGCCGTCGGG	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"""GPCR / Class A : Orphans"""	24828	protein-coding gene	gene with protein product		607233	"""G protein-coupled receptor 168"", ""G protein-coupled receptor 140"""	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.689G>A	11.37:g.68773089C>T	ENSP00000309782:p.Arg230Gln	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_001098515	B3KV43|Q8NBK8	Missense_Mutation	SNP	ENST00000309099.6	37	CCDS8188.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.103907	0.37145	0.0	4.69E-4	ENSG00000172935	ENST00000441623;ENST00000309099;ENST00000421543	T;T	0.43294	0.95;0.95	5.25	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39146	N	0.001445	T	0.27765	0.0683	L	0.54323	1.7	0.25460	N	0.987926	P	0.38827	0.649	B	0.30572	0.117	T	0.10917	-1.0609	10	0.14656	T	0.56	-24.2612	6.393	0.21597	0.0:0.7165:0.1856:0.0979	.	230	Q96AM1	MRGRF_HUMAN	Q	230;230;202	ENSP00000403660:R230Q;ENSP00000309782:R230Q	ENSP00000309782:R230Q	R	-	2	0	MRGPRF	68529665	0.064000	0.20934	0.913000	0.36048	0.963000	0.63663	0.101000	0.15251	1.215000	0.43411	0.561000	0.74099	CGG	C|1.000;T|0.000	0.000	weak		0.627	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015	
JRK	8629	hgsc.bcm.edu	37	8	143746416	143746416	+	RNA	SNP	A	A	G	rs754957	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:143746416A>G	ENST00000507178.2	-	0	1394							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					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)	Acute lymphoblastic leukemia(644;2.31e-05)				tgtagcgggcatgggggccct	0.612													G|||	2671	0.533347	0.7209	0.3213	5008	,	,		18399	0.5188		0.3917	False		,,,				2504	0.591				p.H354H		Atlas-SNP	.											.	.	.	.	0			c.T1062C						PASS	.	G	,	2462,1536		789,884,326	8.0	9.0	9.0		1062,1062	-0.7	0.0	8	dbSNP_86	9	3105,5209		657,1791,1709	yes	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	1446,2675,2035	GG,GA,AA		37.3466,38.4192,45.216	,	354/557,354/569	143746416	5567,6745	1999	4157	6156			8629	exon2			GCGGGCATGGGGG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746416A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				A|0.478;G|0.522	0.522	strong		0.612	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
CCDC159	126075	hgsc.bcm.edu	37	19	11465311	11465311	+	Silent	SNP	C	C	T	rs374274390	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11465311C>T	ENST00000588790.1	+	12	1275	c.828C>T	c.(826-828)tcC>tcT	p.S276S	DKFZP761J1410_ENST00000251473.5_5'Flank|CCDC159_ENST00000458408.1_Silent_p.S276S|DKFZP761J1410_ENST00000591608.1_5'Flank			P0C7I6	CC159_HUMAN	coiled-coil domain containing 159	391										endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	5						ACTCTGACTCCGACTGTGACC	0.647													C|||	3	0.000599042	0.0	0.0	5008	,	,		16082	0.0		0.002	False		,,,				2504	0.001				p.S276S		Atlas-SNP	.											.	CCDC159	35	.	0			c.C828T						PASS	.	C		3,4397		0,3,2197	31.0	39.0	36.0		828	-8.8	0.0	19		36	33,8555		0,33,4261	no	coding-synonymous	CCDC159	NM_001080503.2		0,36,6458	TT,TC,CC		0.3843,0.0682,0.2772		276/298	11465311	36,12952	2200	4294	6494	SO:0001819	synonymous_variant	126075	exon10			TGACTCCGACTGT	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.828C>T	19.37:g.11465311C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	124	59	0.475806	NM_001080503	B4DEG3|B4DWR8|B4E133|B7ZAM4	Silent	SNP	ENST00000588790.1	37	CCDS45976.1																																																																																			.	.	weak		0.647	CCDC159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458761.1	NM_001080503	
C1QTNF7	114905	hgsc.bcm.edu	37	4	15443951	15443951	+	Missense_Mutation	SNP	C	C	T	rs201630756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:15443951C>T	ENST00000444304.2	+	3	724	c.398C>T	c.(397-399)cCg>cTg	p.P133L	C1QTNF7_ENST00000429690.1_Missense_Mutation_p.P133L|C1QTNF7_ENST00000295297.4_Missense_Mutation_p.P140L			Q9BXJ2	C1QT7_HUMAN	C1q and tumor necrosis factor related protein 7	133	Collagen-like.				protein homooligomerization (GO:0051260)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				endometrium(5)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	16						CAAGGGGACCCGGGGCTGCCT	0.517													C|||	2	0.000399361	0.0015	0.0	5008	,	,		16969	0.0		0.0	False		,,,				2504	0.0				p.P140L		Atlas-SNP	.											C1QTNF7,NS,carcinoma,-1,1	C1QTNF7	36	1	0			c.C419T						scavenged	.	C	LEU/PRO,LEU/PRO,LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	153.0	160.0	158.0		419,398,398	4.7	1.0	4		158	0,8600		0,0,4300	no	missense,missense,missense	C1QTNF7	NM_001135170.1,NM_001135171.1,NM_031911.4	98,98,98	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign,benign,benign	140/297,133/290,133/290	15443951	2,13004	2203	4300	6503	SO:0001583	missense	114905	exon3			GGGACCCGGGGCT	AF329839	CCDS3414.1, CCDS47025.1	4p15.3	2008-08-29			ENSG00000163145	ENSG00000163145			14342	protein-coding gene	gene with protein product							Standard	NM_001135170		Approved	CTRP7	uc003gnp.3	Q9BXJ2	OTTHUMG00000097095	ENST00000444304.2:c.398C>T	4.37:g.15443951C>T	ENSP00000388914:p.Pro133Leu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	150	2	0.0133333	NM_001135170	B2RBT3|J3KPW3	Missense_Mutation	SNP	ENST00000444304.2	37	CCDS3414.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.72	2.321640	0.41096	4.54E-4	0.0	ENSG00000163145	ENST00000397700;ENST00000295297;ENST00000429690;ENST00000444304	D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.17	5.54	4.68	0.58851	.	0.279351	0.34025	N	0.004328	D	0.92004	0.7467	M	0.73598	2.24	0.58432	D	0.999997	B	0.23591	0.088	B	0.20577	0.03	D	0.88962	0.3394	10	0.20519	T	0.43	.	16.0757	0.80967	0.0:0.7747:0.2253:0.0	.	133	Q9BXJ2	C1QT7_HUMAN	L	140;140;133;133	ENSP00000380812:P140L;ENSP00000295297:P140L;ENSP00000410722:P133L;ENSP00000388914:P133L	ENSP00000295297:P140L	P	+	2	0	C1QTNF7	15053049	0.924000	0.31332	0.998000	0.56505	0.993000	0.82548	1.804000	0.38873	2.619000	0.88677	0.655000	0.94253	CCG	C|1.000;T|0.000	0.000	strong		0.517	C1QTNF7-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250891.2		
IGHMBP2	3508	hgsc.bcm.edu	37	11	68682402	68682402	+	Missense_Mutation	SNP	A	A	G	rs10896380	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68682402A>G	ENST00000255078.3	+	6	934	c.823A>G	c.(823-825)Att>Gtt	p.I275V	IGHMBP2_ENST00000539224.1_3'UTR	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	275	Leu-rich.		I -> V (in dbSNP:rs10896380). {ECO:0000269|PubMed:8349627}.		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)			CCTGGAGTCCATTCAGCAGCA	0.597													A|||	600	0.119808	0.1074	0.1888	5008	,	,		15618	0.0149		0.2674	False		,,,				2504	0.044				p.I275V		Atlas-SNP	.											IGHMBP2,NS,carcinoma,-1,2	IGHMBP2	83	2	0			c.A823G						scavenged	.	A	VAL/ILE	545,3855	246.8+/-255.3	37,471,1692	102.0	92.0	95.0		823	0.1	0.4	11	dbSNP_120	95	2127,6461	366.2+/-334.2	258,1611,2425	yes	missense	IGHMBP2	NM_002180.2	29	295,2082,4117	GG,GA,AA		24.7671,12.3864,20.5728	benign	275/994	68682402	2672,10316	2200	4294	6494	SO:0001583	missense	3508	exon6			GAGTCCATTCAGC	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.823A>G	11.37:g.68682402A>G	ENSP00000255078:p.Ile275Val	Somatic	187	2	0.0106952		WXS	Illumina HiSeq	Phase_I	152	68	0.447368	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	343	0.15705128205128205	60	0.12195121951219512	73	0.20165745856353592	11	0.019230769230769232	199	0.262532981530343	A	5.864	0.343588	0.11126	0.123864	0.247671	ENSG00000132740	ENST00000255078	T	0.81078	-1.45	3.71	0.0501	0.14292	DEAD-like helicase (1);Helicase/UvrB domain (1);ATPase, AAA+ type, core (1);	0.262406	0.37012	N	0.002293	T	0.00012	0.0000	N	0.02854	-0.475	0.09310	P	1.0	B	0.10296	0.003	B	0.15870	0.014	T	0.04915	-1.0918	9	0.02654	T	1	-23.5642	3.4248	0.07406	0.5127:0.0:0.3163:0.171	rs10896380;rs17533010;rs60474416;rs10896380	275	P38935	SMBP2_HUMAN	V	275	ENSP00000255078:I275V	ENSP00000255078:I275V	I	+	1	0	IGHMBP2	68438978	0.869000	0.29996	0.423000	0.26634	0.699000	0.40488	1.576000	0.36504	-0.090000	0.12462	0.454000	0.30748	ATT	A|0.824;G|0.176	0.176	strong		0.597	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
DNAH3	55567	hgsc.bcm.edu	37	16	21151913	21151913	+	Missense_Mutation	SNP	G	G	T	rs72780891	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:21151913G>T	ENST00000261383.3	-	5	639	c.640C>A	c.(640-642)Cag>Aag	p.Q214K	DNAH3_ENST00000575491.1_5'UTR|DNAH3_ENST00000415178.1_Missense_Mutation_p.Q214K	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	214	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)|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)		ATCTCCTGCTGTAACATGACA	0.488													G|||	856	0.170927	0.0968	0.2954	5008	,	,		22605	0.129		0.1869	False		,,,				2504	0.2096				p.Q214K		Atlas-SNP	.											DNAH3_ENST00000261383,colon,carcinoma,0,2	DNAH3	1142	2	0			c.C640A						scavenged	.	G	LYS/GLN	531,3871	240.6+/-251.3	33,465,1703	275.0	222.0	240.0		640	4.1	1.0	16	dbSNP_130	240	1751,6849	319.2+/-314.1	183,1385,2732	yes	missense	DNAH3	NM_017539.1	53	216,1850,4435	TT,TG,GG		20.3605,12.0627,17.5511	benign	214/4117	21151913	2282,10720	2201	4300	6501	SO:0001583	missense	55567	exon5			CCTGCTGTAACAT	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.640C>A	16.37:g.21151913G>T	ENSP00000261383:p.Gln214Lys	Somatic	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	217	90	0.414747	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	355	0.16254578754578755	45	0.09146341463414634	90	0.24861878453038674	65	0.11363636363636363	155	0.20448548812664907	G	8.534	0.871685	0.17322	0.120627	0.203605	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	T;T	0.20881	2.04;2.21	5.07	4.1	0.47936	.	0.771253	0.12304	N	0.480826	T	0.00012	0.0000	L	0.42245	1.32	0.40662	P	0.017862000000000045	B;B	0.26363	0.001;0.147	B;B	0.25506	0.001;0.061	T	0.35574	-0.9783	9	0.05525	T	0.97	.	3.8791	0.09071	0.0866:0.1655:0.5763:0.1716	.	214;185	Q8TD57;Q8TD57-2	DYH3_HUMAN;.	K	214;214;185	ENSP00000261383:Q214K;ENSP00000394245:Q214K	ENSP00000261383:Q214K	Q	-	1	0	DNAH3	21059414	0.540000	0.26410	1.000000	0.80357	0.906000	0.53458	0.697000	0.25556	1.318000	0.45170	0.655000	0.94253	CAG	G|0.825;T|0.175	0.175	strong		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116091629	116091629	+	Missense_Mutation	SNP	T	T	C	rs117043677	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:116091629T>C	ENST00000304129.4	-	4	277	c.248A>G	c.(247-249)aAt>aGt	p.N83S	AFAP1L2_ENST00000369271.3_Missense_Mutation_p.N83S|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.N83S			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	83					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)		GGGCTCCCCATTGGGTAGCAG	0.612													T|||	21	0.00419329	0.003	0.0043	5008	,	,		16175	0.0		0.0139	False		,,,				2504	0.0				p.N83S		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.A248G						PASS	.	T	SER/ASN,SER/ASN	8,4206		0,8,2099	48.0	34.0	39.0		248,248	5.5	1.0	10	dbSNP_132	39	58,8090		0,58,4016	yes	missense,missense	AFAP1L2	NM_001001936.1,NM_032550.2	46,46	0,66,6115	CC,CT,TT		0.7118,0.1898,0.5339	probably-damaging,probably-damaging	83/819,83/815	116091629	66,12296	2107	4074	6181	SO:0001583	missense	84632	exon4			TCCCCATTGGGTA	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.248A>G	10.37:g.116091629T>C	ENSP00000303042:p.Asn83Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	138	74	0.536232	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	37	CCDS31286.1	14	0.00641025641025641	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	10	0.013192612137203167	T	14.14	2.448016	0.43429	0.001898	0.007118	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000541919;ENST00000545353;ENST00000419268	T;T;T;T	0.31769	2.48;2.49;2.32;1.48	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.41050	0.1142	L	0.56769	1.78	0.46061	D	0.998848	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.998;0.997	D;D;D;D;P	0.87578	0.998;0.996;0.948;0.957;0.907	T	0.31696	-0.9934	10	0.30854	T	0.27	-34.4191	12.0678	0.53598	0.0:0.0:0.0:1.0	.	83;83;83;83;83	F5GZE1;B7Z2Q0;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;AF1L2_HUMAN	S	83;83;82;101;83;101	ENSP00000358276:N83S;ENSP00000303042:N83S;ENSP00000444511:N83S;ENSP00000396781:N101S	ENSP00000303042:N83S	N	-	2	0	AFAP1L2	116081619	1.000000	0.71417	0.974000	0.42286	0.228000	0.25075	5.373000	0.66162	2.103000	0.63969	0.533000	0.62120	AAT	T|0.995;C|0.005	0.005	strong		0.612	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
NPSR1	387129	hgsc.bcm.edu	37	7	34818113	34818113	+	Missense_Mutation	SNP	A	A	T	rs324981	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:34818113A>T	ENST00000360581.1	+	3	448	c.320A>T	c.(319-321)aAt>aTt	p.N107I	NPSR1_ENST00000381542.1_Intron|NPSR1_ENST00000381539.3_Missense_Mutation_p.N107I|NPSR1_ENST00000359791.1_Missense_Mutation_p.N107I|NPSR1_ENST00000531252.1_Missense_Mutation_p.N96I|NPSR1_ENST00000381553.3_Missense_Mutation_p.N107I	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	107			N -> I (in dbSNP:rs324981). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15073379, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	ACAGATATTAATTGGCGATTC	0.393													T|||	2341	0.467452	0.559	0.4092	5008	,	,		17830	0.5288		0.4622	False		,,,				2504	0.3272				p.N107I		Atlas-SNP	.											.	NPSR1	134	.	0			c.A320T	GRCh37	CM073245	NPSR1	M	rs324981	PASS	.	T	ILE/ASN,ILE/ASN	2407,1999	559.5+/-380.2	645,1117,441	110.0	98.0	102.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	320,320	5.1	0.1	7	dbSNP_79	102	3962,4638	602.0+/-394.4	920,2122,1258	yes	missense,missense	NPSR1	NM_207172.1,NM_207173.1	149,149	1565,3239,1699	TT,TA,AA		46.0698,45.37,48.9697	benign,benign	107/372,107/378	34818113	6369,6637	2203	4300	6503	SO:0001583	missense	387129	exon3			ATATTAATTGGCG	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.320A>T	7.37:g.34818113A>T	ENSP00000353788:p.Asn107Ile	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	82	0.640625	NM_207172	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	CCDS5444.1	1052	0.4816849816849817	242	0.491869918699187	162	0.44751381215469616	298	0.5209790209790209	350	0.46174142480211083	T	0.021	-1.424493	0.01126	0.5463	0.460698	ENSG00000187258	ENST00000381553;ENST00000360581;ENST00000359791;ENST00000531252;ENST00000381539	T;T;T;T;T	0.71222	1.56;1.56;1.56;-0.55;1.56	5.14	5.14	0.70334	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00427	-1.505	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	0.43376	-0.9395	9	0.02654	T	1	-10.1696	8.6008	0.33742	0.1711:0.0:0.0:0.8289	rs324981;rs56577867;rs57535228;rs324981	96;107;107;107	Q6W5P4-5;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;NPSR1_HUMAN	I	107;107;107;96;107	ENSP00000370965:N107I;ENSP00000353788:N107I;ENSP00000352839:N107I;ENSP00000433258:N96I;ENSP00000370950:N107I	ENSP00000352839:N107I	N	+	2	0	NPSR1	34784638	0.847000	0.29606	0.116000	0.21606	0.191000	0.23601	2.994000	0.49433	0.895000	0.36342	-0.364000	0.07487	AAT	A|0.515;T|0.485	0.485	strong		0.393	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
MUC17	140453	hgsc.bcm.edu	37	7	100677630	100677630	+	Missense_Mutation	SNP	C	C	T	rs78990442	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677630C>T	ENST00000306151.4	+	3	2997	c.2933C>T	c.(2932-2934)cCt>cTt	p.P978L		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	978	59 X approximate tandem repeats.|Ser-rich.				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)					ACCTCGACTCCTAGTGAAGGA	0.512													C|||	1003	0.20028	0.2678	0.0994	5008	,	,		34431	0.2282		0.1113	False		,,,				2504	0.2434				p.P978L		Atlas-SNP	.											.	MUC17	804	.	0			c.C2933T						PASS	.	C	LEU/PRO	912,3494		0,912,1291	355.0	332.0	340.0		2933	0.6	0.0	7	dbSNP_131	340	814,7786		0,814,3486	no	missense	MUC17	NM_001040105.1	98	0,1726,4777	TT,TC,CC		9.4651,20.699,13.2708	probably-damaging	978/4494	100677630	1726,11280	2203	4300	6503	SO:0001583	missense	140453	exon3			CGACTCCTAGTGA	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.2933C>T	7.37:g.100677630C>T	ENSP00000302716:p.Pro978Leu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	639	350	0.547731	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	4.251	0.045554	0.08196	0.20699	0.094651	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.632	0.632	0.17705	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.21604	N	0.999623	D	0.76494	0.999	D	0.71184	0.972	T	0.50608	-0.8808	9	0.13853	T	0.58	.	7.1889	0.25814	0.0:0.9999:0.0:1.0E-4	.	978	Q685J3	MUC17_HUMAN	L	978	ENSP00000302716:P978L	ENSP00000302716:P978L	P	+	2	0	MUC17	100464350	0.000000	0.05858	0.013000	0.15412	0.007000	0.05969	-0.008000	0.12788	0.647000	0.30713	0.134000	0.15878	CCT	C|0.935;T|0.065	0.065	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SVIL	6840	hgsc.bcm.edu	37	10	29779936	29779936	+	Silent	SNP	G	G	A	rs45519332	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:29779936G>A	ENST00000355867.4	-	22	4784	c.4032C>T	c.(4030-4032)tcC>tcT	p.S1344S	SVIL_ENST00000535393.1_Silent_p.S258S|SVIL_ENST00000375400.3_Silent_p.S918S|SVIL_ENST00000538146.1_Silent_p.S136S|SVIL_ENST00000375398.2_Silent_p.S1344S	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1344					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)				GCTCGGCCACGGAAGACGTCA	0.587													A|||	409	0.0816693	0.0976	0.1527	5008	,	,		19089	0.0347		0.0825	False		,,,				2504	0.0573				p.S1344S		Atlas-SNP	.											.	SVIL	226	.	0			c.C4032T						PASS	.	A	,	415,3991	779.2+/-414.3	10,395,1798	27.0	27.0	27.0		2754,4032	-8.2	0.0	10	dbSNP_127	27	629,7971	783.4+/-407.6	3,623,3674	no	coding-synonymous,coding-synonymous	SVIL	NM_003174.3,NM_021738.2	,	13,1018,5472	AA,AG,GG		7.314,9.419,8.0271	,	918/1789,1344/2215	29779936	1044,11962	2203	4300	6503	SO:0001819	synonymous_variant	6840	exon22			GGCCACGGAAGAC	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.4032C>T	10.37:g.29779936G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	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		0.587	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
CST1	1469	hgsc.bcm.edu	37	20	23728528	23728528	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:23728528C>T	ENST00000304749.2	-	3	421	c.351G>A	c.(349-351)ttG>ttA	p.L117L	CST1_ENST00000398402.1_Silent_p.L117L	NM_001898.2	NP_001889.2	P01037	CYTN_HUMAN	cystatin SN	117					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)	p.L117L(1)		kidney(1)|large_intestine(1)|lung(8)|ovary(1)|stomach(1)|urinary_tract(1)	13	Lung NSC(19;0.0676)|all_lung(19;0.148)					CGAAAGAGCACAACTGTTTCT	0.527																																					p.L117L		Atlas-SNP	.											CST1,NS,carcinoma,0,2	CST1	37	2	1	Substitution - coding silent(1)	lung(1)	c.G351A						scavenged	.						93.0	81.0	85.0					20																	23728528		2203	4300	6503	SO:0001819	synonymous_variant	1469	exon3			AGAGCACAACTGT	M19169	CCDS13160.1	20p11.2	2008-04-15			ENSG00000170373	ENSG00000170373			2473	protein-coding gene	gene with protein product		123855					Standard	NM_001898		Approved		uc002wtp.3	P01037	OTTHUMG00000032085	ENST00000304749.2:c.351G>A	20.37:g.23728528C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	215	6	0.027907	NM_001898	Q96LE6|Q9UCQ6	Silent	SNP	ENST00000304749.2	37	CCDS13160.1																																																																																			.	.	none		0.527	CST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078351.2	NM_001898	
ATP11B	23200	hgsc.bcm.edu	37	3	182614493	182614493	+	Silent	SNP	T	T	C	rs4859142	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:182614493T>C	ENST00000323116.5	+	26	3248	c.2988T>C	c.(2986-2988)ttT>ttC	p.F996F		NM_014616.2	NP_055431.1	Q9Y2G3	AT11B_HUMAN	ATPase, class VI, type 11B	996					aminophospholipid transport (GO:0015917)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|ion transmembrane transporter activity (GO:0015075)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|liver(2)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	41	all_cancers(143;9.04e-15)|Ovarian(172;0.0355)		all cancers(12;1.2e-42)|Epithelial(37;2.77e-36)|LUSC - Lung squamous cell carcinoma(7;7.58e-24)|Lung(8;4.66e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.35e-20)			TTTAGATGTTTGGAAACTGGA	0.323													T|||	719	0.14357	0.3472	0.1081	5008	,	,		17954	0.0417		0.0895	False		,,,				2504	0.0542				p.F996F		Atlas-SNP	.											.	ATP11B	115	.	0			c.T2988C						PASS	.	T		1361,3045	452.6+/-350.1	208,945,1050	252.0	246.0	248.0		2988	4.5	1.0	3	dbSNP_111	248	858,7740	195.2+/-240.5	39,780,3480	no	coding-synonymous	ATP11B	NM_014616.1		247,1725,4530	CC,CT,TT		9.9791,30.8897,17.064		996/1178	182614493	2219,10785	2203	4299	6502	SO:0001819	synonymous_variant	23200	exon26			GATGTTTGGAAAC	AF156548	CCDS33896.1	3q27	2010-04-20	2007-09-19		ENSG00000058063	ENSG00000058063		"""ATPases / P-type"""	13553	protein-coding gene	gene with protein product		605869	"""ATPase, Class VI, type 11B"""			10231032, 11015572	Standard	NM_014616		Approved	ATPIF, ATPIR, KIAA0956	uc003flb.3	Q9Y2G3	OTTHUMG00000158295	ENST00000323116.5:c.2988T>C	3.37:g.182614493T>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	243	98	0.403292	NM_014616	Q96FN1|Q9UKK7	Silent	SNP	ENST00000323116.5	37	CCDS33896.1	294	0.1346153846153846	156	0.3170731707317073	38	0.10497237569060773	25	0.043706293706293704	75	0.09894459102902374	T	9.681	1.149424	0.21288	0.308897	0.099791	ENSG00000058063	ENST00000498086	.	.	.	5.66	4.5	0.54988	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20207	-1.0282	3	.	.	.	.	11.301	0.49306	0.0:0.0712:0.0:0.9288	rs4859142;rs56539343;rs4859142	.	.	.	S	797	.	.	L	+	2	0	ATP11B	184097187	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.720000	0.68470	0.979000	0.38497	0.455000	0.32223	TTG	T|0.842;C|0.158	0.158	strong		0.323	ATP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350598.1	NM_014616	
CFAP46	54777	hgsc.bcm.edu	37	10	134682855	134682855	+	Silent	SNP	C	C	T	rs7908950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	64	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	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		
FAM83G	644815	hgsc.bcm.edu	37	17	18874965	18874965	+	Missense_Mutation	SNP	C	C	T	rs138715863	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:18874965C>T	ENST00000388995.6	-	6	2402	c.2179G>A	c.(2179-2181)Gtc>Atc	p.V727I	FAM83G_ENST00000345041.4_Missense_Mutation_p.V727I|SLC5A10_ENST00000395645.3_Intron|SLC5A10_ENST00000395643.2_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.V727I|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000417251.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	727					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						GAGCTCTGGACGCTGTCAGCA	0.647													C|||	6	0.00119808	0.0	0.0029	5008	,	,		15509	0.0		0.002	False		,,,				2504	0.002				p.V727I		Atlas-SNP	.											FAM83G,right_upper_lobe,carcinoma,0,1	FAM83G	51	1	0			c.G2179A						scavenged	.	C	ILE/VAL,,	12,3902		0,12,1945	43.0	51.0	49.0		2179,,	-10.0	0.0	17	dbSNP_134	49	91,8161		0,91,4035	yes	missense,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	29,,	0,103,5980	TT,TC,CC		1.1028,0.3066,0.8466	benign,,	727/824,,	18874965	103,12063	1957	4126	6083	SO:0001583	missense	644815	exon6			TCTGGACGCTGTC	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.2179G>A	17.37:g.18874965C>T	ENSP00000373647:p.Val727Ile	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	101	4	0.039604	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	3.408	-0.120880	0.06838	0.003066	0.011028	ENSG00000188522	ENST00000388995;ENST00000345041	T;T	0.10960	2.82;2.82	5.29	-10.0	0.00425	.	1.466860	0.03806	N	0.265234	T	0.03827	0.0108	L	0.34521	1.04	0.09310	N	1	B	0.25048	0.117	B	0.15052	0.012	T	0.28586	-1.0039	10	0.33141	T	0.24	-6.3304	3.3167	0.07035	0.0917:0.2544:0.1818:0.472	.	727	A6ND36	FA83G_HUMAN	I	727	ENSP00000373647:V727I;ENSP00000343279:V727I	ENSP00000343279:V727I	V	-	1	0	FAM83G	18815690	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	-2.909000	0.00699	-1.248000	0.02503	-0.221000	0.12465	GTC	C|0.995;T|0.005	0.005	strong		0.647	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
PPIG	9360	hgsc.bcm.edu	37	2	170493863	170493863	+	Missense_Mutation	SNP	A	A	G	rs8207	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:170493863A>G	ENST00000260970.3	+	14	2315	c.2095A>G	c.(2095-2097)Aat>Gat	p.N699D	PPIG_ENST00000409714.3_Missense_Mutation_p.N684D|PPIG_ENST00000448752.2_Missense_Mutation_p.N699D	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	699			N -> D (in dbSNP:rs8207). {ECO:0000269|PubMed:17525332, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:8973360, ECO:0000269|PubMed:9153302}.		protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	CAGTCAGGACAATGAATTAAA	0.353													A|||	997	0.199081	0.27	0.1542	5008	,	,		18742	0.0496		0.2545	False		,,,				2504	0.2321				p.N699D		Atlas-SNP	.											.	PPIG	100	.	0			c.A2095G	GRCh37	CM063067	PPIG	M	rs8207	PASS	.	A	ASP/ASN	1184,3222	394.2+/-329.2	165,854,1184	40.0	42.0	41.0		2095	4.6	1.0	2	dbSNP_52	41	2331,6265	378.6+/-339.0	308,1715,2275	yes	missense	PPIG	NM_004792.2	23	473,2569,3459	GG,GA,AA		27.1173,26.8724,27.0343	benign	699/755	170493863	3515,9487	2203	4298	6501	SO:0001583	missense	9360	exon14			CAGGACAATGAAT	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.2095A>G	2.37:g.170493863A>G	ENSP00000260970:p.Asn699Asp	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Missense_Mutation	SNP	ENST00000260970.3	37	CCDS2235.1	406	0.1858974358974359	135	0.27439024390243905	60	0.16574585635359115	25	0.043706293706293704	186	0.24538258575197888	A	9.312	1.055840	0.19907	0.268724	0.271173	ENSG00000138398	ENST00000260970;ENST00000409714;ENST00000448752	T;T;T	0.15372	2.43;2.43;2.43	5.73	4.58	0.56647	.	0.395778	0.25081	N	0.033292	T	0.00012	0.0000	N	0.08118	0	0.37290	P	0.09177100000000005	B;B;B	0.16166	0.016;0.016;0.016	B;B;B	0.12156	0.007;0.007;0.007	T	0.37641	-0.9697	9	0.62326	D	0.03	-14.0533	7.7959	0.29148	0.7919:0.1382:0.0699:0.0	rs8207;rs3190677;rs16841658;rs52808986;rs58499481;rs8207	684;684;699	E9PG73;Q2NKQ6;Q13427	.;.;PPIG_HUMAN	D	699;684;699	ENSP00000260970:N699D;ENSP00000386245:N684D;ENSP00000407083:N699D	ENSP00000260970:N699D	N	+	1	0	PPIG	170202109	1.000000	0.71417	0.998000	0.56505	0.716000	0.41182	2.242000	0.43106	0.998000	0.38996	-0.605000	0.04089	AAT	A|0.765;G|0.235	0.235	strong		0.353	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
ARHGEF10	9639	hgsc.bcm.edu	37	8	1877480	1877480	+	Missense_Mutation	SNP	T	T	G	rs17683288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:1877480T>G	ENST00000398564.1	+	25	3025	c.3025T>G	c.(3025-3027)Tcc>Gcc	p.S1009A	ARHGEF10_ENST00000520359.1_Missense_Mutation_p.S946A|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.S980A|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.S984A|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.S1008A			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1009					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)		CAGTCAAGGCTCCAAGAAAGT	0.433													T|||	153	0.0305511	0.0038	0.0389	5008	,	,		15810	0.001		0.0736	False		,,,				2504	0.047				p.S984A		Atlas-SNP	.											ARHGEF10_ENST00000398564,NS,carcinoma,0,2	ARHGEF10	255	2	0			c.T2950G						PASS	.	T	ALA/SER	66,4340	61.7+/-98.7	1,64,2138	87.0	87.0	87.0		2950	2.7	1.0	8	dbSNP_123	87	611,7989	159.4+/-212.7	28,555,3717	yes	missense	ARHGEF10	NM_014629.2	99	29,619,5855	GG,GT,TT		7.1047,1.498,5.2053	possibly-damaging	984/1345	1877480	677,12329	2203	4300	6503	SO:0001583	missense	9639	exon25			CAAGGCTCCAAGA	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.3025T>G	8.37:g.1877480T>G	ENSP00000381571:p.Ser1009Ala	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	266	160	0.601504	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		76	0.0347985347985348	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	57	0.07519788918205805	T	3.915	-0.019235	0.07634	0.01498	0.071047	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.05;-0.05	5.08	2.66	0.31614	.	0.308232	0.36200	N	0.002727	T	0.05731	0.0150	L	0.50919	1.6	0.09310	P	0.999999999999999	B;B	0.21688	0.059;0.01	B;B	0.22753	0.041;0.011	T	0.34428	-0.9829	9	0.07813	T	0.8	-13.8843	12.2936	0.54833	0.0:0.0:0.2956:0.7044	rs17683288;rs56496515;rs57650527;rs17683288	946;984	O15013-7;O15013-5	.;.	A	984;946;1008;1009;980;628	ENSP00000340297:S984A;ENSP00000427909:S946A;ENSP00000431012:S1008A;ENSP00000381571:S1009A;ENSP00000262112:S980A;ENSP00000427768:S628A	ENSP00000262112:S980A	S	+	1	0	ARHGEF10	1864887	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	3.497000	0.53295	0.336000	0.23639	-0.258000	0.10820	TCC	T|0.954;G|0.046	0.046	strong		0.433	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
AGXT	189	hgsc.bcm.edu	37	2	241808314	241808314	+	Missense_Mutation	SNP	C	C	T	rs34116584	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241808314C>T	ENST00000307503.3	+	1	419	c.32C>T	c.(31-33)cCc>cTc	p.P11L		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	11			P -> L (common polymorphism; reduction of specific activity in vitro; causes mistargeting when associated with R-170; dbSNP:rs34116584). {ECO:0000269|PubMed:1703535}.		cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process (GO:0042853)|L-cysteine catabolic process (GO:0019448)|oxalic acid secretion (GO:0046724)|pyruvate biosynthetic process (GO:0042866)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alanine-glyoxylate transaminase activity (GO:0008453)|amino acid binding (GO:0016597)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|receptor binding (GO:0005102)|serine-pyruvate transaminase activity (GO:0004760)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)	18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	GTGACCCCCCCCAAGGCCCTG	0.662													C|||	405	0.0808706	0.0363	0.1311	5008	,	,		14113	0.0		0.2048	False		,,,				2504	0.0613				p.P11L		Atlas-SNP	.											AGXT,NS,carcinoma,+1,1	AGXT	50	1	0			c.C32T	GRCh37	CD073566|CM910014	AGXT	D|M	rs34116584	scavenged	.	C	LEU/PRO	269,4129	144.2+/-179.2	7,255,1937	27.0	31.0	30.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	32	4.4	0.0	2	dbSNP_126	30	1749,6849	299.4+/-304.4	186,1377,2736	no	missense	AGXT	NM_000030.2	98	193,1632,4673	TT,TC,CC		20.3419,6.1164,15.5279	probably-damaging	11/393	241808314	2018,10978	2199	4299	6498	SO:0001583	missense	189	exon1			CCCCCCCCAAGGC	D13368	CCDS2543.1	2q37.3	2008-02-05	2007-04-13		ENSG00000172482	ENSG00000172482	2.6.1.44, 2.6.1.51		341	protein-coding gene	gene with protein product	"""oxalosis I"", ""primary hyperoxaluria type 1"", ""L-alanine: glyoxylate aminotransferase 1"", ""serine:pyruvate aminotransferase"", ""glycolicaciduria"""	604285		SPAT		2039493, 2045108	Standard	NM_000030		Approved	AGXT1, PH1, AGT, SPT, AGT1	uc002waa.4	P21549	OTTHUMG00000133354	ENST00000307503.3:c.32C>T	2.37:g.241808314C>T	ENSP00000302620:p.Pro11Leu	Somatic	309	3	0.00970874		WXS	Illumina HiSeq	Phase_I	305	299	0.980328	NM_000030	Q53QU6	Missense_Mutation	SNP	ENST00000307503.3	37	CCDS2543.1	236	0.10805860805860806	27	0.054878048780487805	50	0.13812154696132597	0	0.0	159	0.20976253298153033	C	15.11	2.736816	0.49045	0.061164	0.203419	ENSG00000172482	ENST00000307503	D	0.88277	-2.36	4.42	4.42	0.53409	Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.00845	0.0028	M	0.78916	2.43	0.09310	P	0.999999999521237	D	0.89917	1.0	D	0.97110	1.0	T	0.01349	-1.1378	9	0.66056	D	0.02	-18.1328	11.6352	0.51200	0.0:0.9131:0.0:0.0869	rs34116584	11	P21549	SPYA_HUMAN	L	11	ENSP00000302620:P11L	ENSP00000302620:P11L	P	+	2	0	AGXT	241456987	0.996000	0.38824	0.023000	0.16930	0.149000	0.21700	6.302000	0.72788	2.014000	0.59158	0.484000	0.47621	CCC	A|0.000;C|0.871;T|0.129	0.129	strong		0.662	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	NM_000030	
CLDN22	53842	hgsc.bcm.edu	37	4	184240981	184240981	+	Missense_Mutation	SNP	C	C	T	rs144080557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:184240981C>T	ENST00000323319.5	-	1	946	c.391G>A	c.(391-393)Gtc>Atc	p.V131I	WWC2_ENST00000403733.3_3'UTR	NM_001111319.1	NP_001104789.1	Q8N7P3	CLD22_HUMAN	claudin 22	131					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(1)	7		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.0172)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|Esophageal squamous(56;0.176)		all cancers(43;4.1e-26)|Epithelial(43;6.45e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|Colorectal(24;5.87e-06)|GBM - Glioblastoma multiforme(59;6.5e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		AGGGCTGTGACTCCCGAGGCC	0.567													c|||	30	0.00599042	0.0204	0.0014	5008	,	,		17954	0.0		0.002	False		,,,				2504	0.0				p.V131I		Atlas-SNP	.											CLDN22,NS,carcinoma,+2,1	CLDN22	20	1	0			c.G391A						scavenged	.	C	ILE/VAL,	42,3094		1,40,1527	48.0	49.0	48.0		391,	-9.4	0.0	4	dbSNP_134	48	3,7161		0,3,3579	no	missense,utr-3	CLDN22,WWC2	NM_001111319.1,NM_024949.5	29,	1,43,5106	TT,TC,CC		0.0419,1.3393,0.4369	benign,	131/221,	184240981	45,10255	1568	3582	5150	SO:0001583	missense	53842	exon1			CTGTGACTCCCGA	AK098064	CCDS43286.1	4q35.1	2010-08-05			ENSG00000177300	ENSG00000177300		"""Claudins"""	2044	protein-coding gene	gene with protein product							Standard	NM_001111319		Approved	CLDN21	uc010isa.1	Q8N7P3	OTTHUMG00000160627	ENST00000323319.5:c.391G>A	4.37:g.184240981C>T	ENSP00000318113:p.Val131Ile	Somatic	366	3	0.00819672		WXS	Illumina HiSeq	Phase_I	216	157	0.726852	NM_001111319		Missense_Mutation	SNP	ENST00000323319.5	37	CCDS43286.1	18	0.008241758241758242	12	0.024390243902439025	0	0.0	0	0.0	6	0.0079155672823219	c	0.081	-1.182846	0.01620	0.013393	4.19E-4	ENSG00000177300	ENST00000323319	D	0.88741	-2.42	6.13	-9.4	0.00616	.	0.687646	0.15048	N	0.283443	T	0.57272	0.2042	N	0.05441	-0.05	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.49943	-0.8885	10	0.15952	T	0.53	.	16.7447	0.85469	0.0:0.7209:0.0816:0.1975	.	131	Q8N7P3	CLD22_HUMAN	I	131	ENSP00000318113:V131I	ENSP00000318113:V131I	V	-	1	0	CLDN22	184477975	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-1.549000	0.02182	-1.907000	0.01087	-0.292000	0.09595	GTC	C|0.992;T|0.008	0.008	strong		0.567	CLDN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361493.1		
IGSF9B	22997	hgsc.bcm.edu	37	11	133795708	133795708	+	Missense_Mutation	SNP	C	C	T	rs202174159		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:133795708C>T	ENST00000321016.8	-	14	2190	c.1960G>A	c.(1960-1962)Gca>Aca	p.A654T	IGSF9B_ENST00000533871.2_Missense_Mutation_p.A654T			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	654	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CAGCGCTCTGCGACACGGAAC	0.592																																					p.A654T		Atlas-SNP	.											IGSF9B_ENST00000321016,NS,carcinoma,0,2	IGSF9B	290	2	0			c.G1960A						scavenged	.	C	THR/ALA	1,4181		0,1,2090	51.0	56.0	54.0		1960	5.3	0.6	11		54	2,8458		0,2,4228	yes	missense	IGSF9B	NM_014987.1	58	0,3,6318	TT,TC,CC		0.0236,0.0239,0.0237	benign	654/1350	133795708	3,12639	2091	4230	6321	SO:0001583	missense	22997	exon14			GCTCTGCGACACG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1960G>A	11.37:g.133795708C>T	ENSP00000317980:p.Ala654Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	146	2	0.0136986	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	C	18.30	3.594159	0.66219	2.39E-4	2.36E-4	ENSG00000080854	ENST00000321016;ENST00000533871;ENST00000527648	T;T;T	0.56611	0.45;0.45;0.45	5.35	5.35	0.76521	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.152969	0.30519	N	0.009451	T	0.46580	0.1400	N	0.22421	0.69	0.29679	N	0.841878	B	0.28026	0.198	B	0.34824	0.19	T	0.49643	-0.8918	10	0.45353	T	0.12	.	19.0783	0.93171	0.0:1.0:0.0:0.0	.	654	Q9UPX0	TUTLB_HUMAN	T	654;496;654	ENSP00000317980:A654T;ENSP00000436552:A496T;ENSP00000436576:A654T	ENSP00000317980:A654T	A	-	1	0	IGSF9B	133300918	0.998000	0.40836	0.644000	0.29465	0.721000	0.41392	5.833000	0.69349	2.504000	0.84457	0.655000	0.94253	GCA	.	.	weak		0.592	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
RPP21	79897	hgsc.bcm.edu	37	6	30314567	30314567	+	Missense_Mutation	SNP	C	C	A	rs974963|rs35287137	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:30314567C>A	ENST00000442966.2	+	5	458	c.445C>A	c.(445-447)Cag>Aag	p.Q149K	RPP21_ENST00000428040.2_Missense_Mutation_p.Q172K|TRIM39-RPP21_ENST00000513556.1_Missense_Mutation_p.Q410K|RPP21_ENST00000433076.2_Missense_Mutation_p.Q157K|RPP21_ENST00000436442.2_3'UTR			Q9H633	RPP21_HUMAN	ribonuclease P/MRP 21kDa subunit	149			Q -> K (in dbSNP:rs974963). {ECO:0000269|PubMed:14574404}.		response to drug (GO:0042493)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonuclease P activity (GO:0004526)			endometrium(2)|ovary(1)|prostate(1)	4						AATGCAGACTCAGGGTTCCAG	0.428													C|||	1866	0.372604	0.3018	0.4496	5008	,	,		21475	0.505		0.2435	False		,,,				2504	0.41				p.Q498K		Atlas-SNP	.											RPP21,NS,carcinoma,-1,1	.	.	1	0			c.C1492A						scavenged	.	C	LYS/GLN,LYS/GLN,,LYS/GLN	839,2183		114,611,786	159.0	163.0	162.0		1492,469,,445	3.1	0.0	6	dbSNP_86	162	1309,4109		159,991,1559	yes	missense,missense,utr-3,missense	RPP21,TRIM39-RPP21	NM_001199119.1,NM_001199120.1,NM_001199121.1,NM_024839.2	53,53,,53	273,1602,2345	AA,AC,CC		24.1602,27.7631,25.4502	,,,	498/504,157/163,,149/155	30314567	2148,6292	1511	2709	4220	SO:0001583	missense	202658	exon10			CAGACTCAGGGTT	AK026291	CCDS4679.1, CCDS56409.1, CCDS56410.1	6p21.32	2012-05-21	2007-06-26	2004-03-19	ENSG00000241370	ENSG00000241370			21300	protein-coding gene	gene with protein product		612524	"""chromosome 6 open reading frame 135"", ""ribonuclease P 21kDa subunit"""	C6orf135			Standard	NM_001199120		Approved	FLJ22638, Em:AB014085.3		Q9H633	OTTHUMG00000031220	ENST00000442966.2:c.445C>A	6.37:g.30314567C>A	ENSP00000403833:p.Gln149Lys	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_001199119	A2AAZ8|B0S834|B0S835|Q5JPL9|Q5JPM1|Q5STF8|Q5STF9|Q5STG2|Q5SU41|Q5SU42|Q86Y49|Q86Y50|Q86Y51|Q96F16	Missense_Mutation	SNP	ENST00000442966.2	37	CCDS4679.1	689	0.31547619047619047	141	0.2865853658536585	133	0.3674033149171271	256	0.44755244755244755	159	0.20976253298153033	C	9.914	1.210278	0.22289	0.277631	0.241602	ENSG00000204599;ENSG00000248167;ENSG00000241370;ENSG00000241370;ENSG00000241370	ENST00000412529;ENST00000513556;ENST00000433076;ENST00000442966;ENST00000428040	T;T;T;T	0.42131	0.98;1.52;1.52;1.52	4.94	3.1	0.35709	.	0.447252	0.19787	N	0.106087	T	0.14098	0.0341	N	0.19112	0.55	0.58432	P	1.0000000000287557E-6	B;B;B	0.10296	0.001;0.003;0.0	B;B;B	0.11329	0.006;0.004;0.0	T	0.06570	-1.0819	9	0.87932	D	0	-0.2296	11.6618	0.51352	0.0:0.6551:0.3449:0.0	rs974963;rs1060066;rs3173395;rs974963	412;149;172	F5H2V3;Q9H633;Q9H633-2	.;RPP21_HUMAN;.	K	412;410;157;149;172	ENSP00000424048:Q410K;ENSP00000409799:Q157K;ENSP00000403833:Q149K;ENSP00000394320:Q172K	ENSP00000394320:Q172K	Q	+	1	0	RPP21;TRIM39-RPP21;TRIM39	30422546	0.197000	0.23362	0.001000	0.08648	0.006000	0.05464	1.778000	0.38614	0.743000	0.32719	0.655000	0.94253	CAG	C|0.718;A|0.282	0.282	strong		0.428	RPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076451.2	NM_024839	
CKAP4	10970	hgsc.bcm.edu	37	12	106633569	106633569	+	Missense_Mutation	SNP	C	C	T	rs3088113	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	49	0	0		WXS	Illumina HiSeq	Phase_I	61	37	0.606557	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		
MOK	5891	hgsc.bcm.edu	37	14	102695693	102695693	+	Missense_Mutation	SNP	T	T	C	rs2236493	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102695693T>C	ENST00000361847.2	-	12	1424	c.1193A>G	c.(1192-1194)cAg>cGg	p.Q398R	MOK_ENST00000522874.1_Missense_Mutation_p.Q397R|MOK_ENST00000519058.1_Silent_p.A122A|MOK_ENST00000522867.1_Silent_p.A92A|MOK_ENST00000524370.1_Silent_p.A92A|MOK_ENST00000517966.1_Silent_p.A92A|MOK_ENST00000520266.1_5'UTR|MOK_ENST00000524214.1_Missense_Mutation_p.Q368R|MOK_ENST00000561150.1_Intron|MOK_ENST00000523231.1_Silent_p.A92A|MOK_ENST00000522534.1_Silent_p.A122A|MOK_ENST00000193029.6_Intron	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	398			Q -> R (in dbSNP:rs2236493). {ECO:0000269|PubMed:17344846}.		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)	p.Q398R(1)									AAGGTCCTTCTGCGGATCTGT	0.577													C|||	1499	0.299321	0.5817	0.1729	5008	,	,		16698	0.1429		0.1958	False		,,,				2504	0.2751				p.Q398R		Atlas-SNP	.											RAGE,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A1193G						PASS	.	C	ARG/GLN	2218,2188	587.6+/-386.7	582,1054,567	59.0	59.0	59.0		1193	1.7	0.0	14	dbSNP_98	59	1705,6895	738.0+/-407.0	154,1397,2749	yes	missense	MOK	NM_014226.1	43	736,2451,3316	CC,CT,TT		19.8256,49.6596,30.163	benign	398/420	102695693	3923,9083	2203	4300	6503	SO:0001583	missense	5891	exon12			TCCTTCTGCGGAT	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.1193A>G	14.37:g.102695693T>C	ENSP00000355304:p.Gln398Arg	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	37	0.316239	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	569	0.26053113553113555	278	0.5650406504065041	76	0.20994475138121546	82	0.14335664335664336	133	0.17546174142480211	C	0.030	-1.343368	0.01277	0.503404	0.198256	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	T;T;T	0.76186	-0.45;-0.51;-1.0	5.37	1.66	0.24008	.	0.461500	0.21486	N	0.073744	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.99999611406	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44128	-0.9348	9	0.06365	T	0.9	-22.8097	9.4719	0.38847	0.0:0.2379:0.0:0.7621	rs2236493;rs52809368;rs58401053;rs2236493	368;398	E7ERR8;Q9UQ07	.;MOK_HUMAN	R	397;398;368	ENSP00000429469:Q397R;ENSP00000355304:Q398R;ENSP00000428942:Q368R	ENSP00000355304:Q398R	Q	-	2	0	RAGE	101765446	1.000000	0.71417	0.027000	0.17364	0.002000	0.02628	0.935000	0.28924	-0.193000	0.10415	-1.163000	0.01768	CAG	T|0.713;C|0.287	0.287	strong		0.577	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
TGFBR3	7049	hgsc.bcm.edu	37	1	92185657	92185657	+	Silent	SNP	C	C	T	rs1805112	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:92185657C>T	ENST00000525962.1	-	8	1267	c.1206G>A	c.(1204-1206)ccG>ccA	p.P402P	TGFBR3_ENST00000212355.4_Silent_p.P402P|TGFBR3_ENST00000370399.2_Silent_p.P401P			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	402					blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|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 transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		GGAAAGGAAACGGAAGGCCTC	0.577													G|||	2034	0.40615	0.2814	0.2824	5008	,	,		18343	0.5308		0.4592	False		,,,				2504	0.4796				p.P402P		Atlas-SNP	.											TGFBR3,bladder,carcinoma,-1,1	TGFBR3	103	1	0			c.G1206A						PASS	.	G	,,	1398,3008		213,972,1018	61.0	63.0	63.0		1203,1203,1206	0.2	1.0	1	dbSNP_89	63	3566,5034		754,2058,1488	no	coding-synonymous,coding-synonymous,coding-synonymous	TGFBR3	NM_001195683.1,NM_001195684.1,NM_003243.4	,,	967,3030,2506	TT,TC,CC		41.4651,31.7295,38.167	,,	401/851,401/851,402/852	92185657	4964,8042	2203	4300	6503	SO:0001819	synonymous_variant	7049	exon9			AGGAAACGGAAGG	L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"""Proteoglycans / Cell surface : Other"""	11774	protein-coding gene	gene with protein product	"""betaglycan proteoglycan"""	600742	"""transforming growth factor, beta receptor III (betaglycan, 300kDa)"""			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.1206G>A	1.37:g.92185657C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	59	40	0.677966	NM_003243	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Silent	SNP	ENST00000525962.1	37	CCDS30770.1																																																																																			C|0.620;T|0.380	0.380	strong		0.577	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243	
PSMF1	9491	hgsc.bcm.edu	37	20	1108122	1108122	+	Silent	SNP	C	C	T	rs6514113	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:1108122C>T	ENST00000335877.6	+	3	512	c.336C>T	c.(334-336)atC>atT	p.I112I	PSMF1_ENST00000246015.4_Silent_p.I112I|PSMF1_ENST00000438768.2_Silent_p.I112I|PSMF1_ENST00000333082.3_Silent_p.I112I|PSMF1_ENST00000381898.4_Silent_p.I24I	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	112	Important for homodimerization and interaction with FBXO7.				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 endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|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)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						ATGATTATATCGATGCAGAAC	0.433													C|||	470	0.0938498	0.1657	0.0793	5008	,	,		18898	0.0546		0.1243	False		,,,				2504	0.0164				p.I112I		Atlas-SNP	.											.	PSMF1	27	.	0			c.C336T						PASS	.	C	,	740,3666	304.4+/-288.4	65,610,1528	125.0	125.0	125.0		336,336	-1.8	1.0	20	dbSNP_116	125	913,7687	202.5+/-245.8	52,809,3439	no	coding-synonymous,coding-synonymous	PSMF1	NM_006814.3,NM_178578.2	,	117,1419,4967	TT,TC,CC		10.6163,16.7953,12.7095	,	112/272,112/272	1108122	1653,11353	2203	4300	6503	SO:0001819	synonymous_variant	9491	exon3			TTATATCGATGCA	D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"""Proteasome (prosome, macropain) subunits"""	9571	protein-coding gene	gene with protein product	"""proteasome inhibitor hP131 subunit"""					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.336C>T	20.37:g.1108122C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Silent	SNP	ENST00000335877.6	37	CCDS13010.1																																																																																			C|0.885;T|0.115	0.115	strong		0.433	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518214	161518214	+	Missense_Mutation	SNP	T	T	C	rs148181339	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161518214T>C	ENST00000436743.1	-	4	470	c.316A>G	c.(316-318)Atc>Gtc	p.I106V	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000443193.1_Missense_Mutation_p.I141V|FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000367969.3_Missense_Mutation_p.I142V|FCGR3A_ENST00000540048.1_Missense_Mutation_p.I106V	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)	106				I -> V (in Ref. 3; BAD96988/BAD97015). {ECO:0000305}.	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)	AACTCACCGATATGGACTTCT	0.483																																					p.I142V		Atlas-SNP	.											FCGR3A,NS,carcinoma,+2,2	FCGR3A	38	2	0			c.A424G						PASS	.						83.0	81.0	82.0					1																	161518214		2203	4296	6499	SO:0001583	missense	2214	exon3			CACCGATATGGAC	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.316A>G	1.37:g.161518214T>C	ENSP00000416607:p.Ile106Val	Somatic	398	0	0		WXS	Illumina HiSeq	Phase_I	626	133	0.21246	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	522|522	0.23901098901098902|0.23901098901098902	75|75	0.1524390243902439|0.1524390243902439	115|115	0.31767955801104975|0.31767955801104975	185|185	0.32342657342657344|0.32342657342657344	147|147	0.19393139841688653|0.19393139841688653	T|T	6.273|6.273	0.418469|0.418469	0.11870|0.11870	.|.	.|.	ENSG00000203747|ENSG00000203747	ENST00000426740|ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336	.|T;T;T;T;T;T	.|0.03889	.|4.95;4.94;4.98;4.98;4.98;3.77	4.43|4.43	-8.86|-8.86	0.00795|0.00795	.|.	4.323350|4.323350	0.00674|0.00674	N|N	0.000659|0.000659	T|T	0.00468|0.00468	0.0015|0.0015	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.35699|0.35699	-0.9778|-0.9778	6|10	.|0.06236	.|T	.|0.91	.|.	8.7015|8.7015	0.34329|0.34329	0.0:0.1887:0.1973:0.614|0.0:0.1887:0.1973:0.614	.|.	.|106;141;106	.|P08637;E9PG94;Q9UPY7	.|FCG3A_HUMAN;.;.	M|V	122|142;141;106;106;106;105	.|ENSP00000356946:I142V;ENSP00000392047:I141V;ENSP00000416607:I106V;ENSP00000356944:I106V;ENSP00000444971:I106V;ENSP00000396567:I105V	.|ENSP00000356944:I106V	I|I	-|-	3|1	3|0	FCGR3A|FCGR3A	159784838|159784838	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-5.685000|-5.685000	0.00105|0.00105	-3.274000|-3.274000	0.00199|0.00199	-0.326000|-0.326000	0.08463|0.08463	ATA|ATC	.	.	weak		0.483	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
MUC17	140453	hgsc.bcm.edu	37	7	100678693	100678693	+	Silent	SNP	T	T	C	rs78176991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678693T>C	ENST00000306151.4	+	3	4060	c.3996T>C	c.(3994-3996)taT>taC	p.Y1332Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1332	59 X approximate tandem repeats.|Ser-rich.				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)					CCTCAACTTATAGTGAAGGAA	0.448																																					p.Y1332Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T3996C						PASS	.						241.0	232.0	235.0					7																	100678693		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAA	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.3996T>C	7.37:g.100678693T>C		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	264	39	0.147727	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.994;C|0.006	0.006	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FSIP2	401024	hgsc.bcm.edu	37	2	186671256	186671256	+	Silent	SNP	T	T	C	rs17826498	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:186671256T>C	ENST00000424728.1	+	17	17223	c.17223T>C	c.(17221-17223)aaT>aaC	p.N5741N	FSIP2_ENST00000343098.5_Silent_p.N5830N			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5741										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						CTAACAAAAATATCTCTGCCA	0.378													T|||	39	0.00778754	0.0023	0.0101	5008	,	,		17132	0.001		0.0229	False		,,,				2504	0.0051				p.N5830N		Atlas-SNP	.											.	FSIP2	251	.	0			c.T17490C						PASS	.	T		16,3594		0,16,1789	53.0	49.0	50.0		17490	0.7	0.0	2	dbSNP_123	50	242,7898		4,234,3832	no	coding-synonymous	FSIP2	NM_173651.2		4,250,5621	CC,CT,TT		2.973,0.4432,2.1957		5830/6997	186671256	258,11492	1805	4070	5875	SO:0001819	synonymous_variant	401024	exon17			CAAAAATATCTCT	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.17223T>C	2.37:g.186671256T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	37																																																																																				T|0.985;C|0.015	0.015	strong		0.378	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
NLRP12	91662	hgsc.bcm.edu	37	19	54327313	54327313	+	Missense_Mutation	SNP	C	C	A	rs34436714	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54327313C>A	ENST00000324134.6	-	1	284	c.116G>T	c.(115-117)gGa>gTa	p.G39V	NLRP12_ENST00000345770.5_Missense_Mutation_p.G39V|NLRP12_ENST00000351894.4_Missense_Mutation_p.G39V|NLRP12_ENST00000391773.1_Missense_Mutation_p.G39V|NLRP12_ENST00000391772.1_Missense_Mutation_p.G39V|NLRP12_ENST00000391775.3_Missense_Mutation_p.G39V|NLRP12_ENST00000535162.1_Missense_Mutation_p.G39V|NLRP12_ENST00000354278.3_Missense_Mutation_p.G39V	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	39	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		G -> V (in dbSNP:rs34436714).		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)		CTTGCCTTCTCCCAGCTCTGT	0.607													C|||	1280	0.255591	0.3858	0.2291	5008	,	,		16894	0.1776		0.2008	False		,,,				2504	0.2352				p.K39M		Atlas-SNP	.											.	NLRP12	236	.	0			c.A116T						PASS	.	C	VAL/GLY	1619,2787	499.3+/-364.4	299,1021,883	62.0	58.0	60.0		116	4.5	0.1	19	dbSNP_126	60	1851,6749	329.8+/-318.9	195,1461,2644	yes	missense	NLRP12	NM_144687.2	109	494,2482,3527	AA,AC,CC		21.5233,36.7453,26.68	probably-damaging	39/1062	54327313	3470,9536	2203	4300	6503	SO:0001583	missense	91662	exon1			CCTTCTCCCAGCT	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.116G>T	19.37:g.54327313C>A	ENSP00000319377:p.Gly39Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	134	50	0.373134	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	536	0.2454212454212454	213	0.4329268292682927	87	0.24033149171270718	83	0.1451048951048951	153	0.20184696569920843	C	13.08	2.130976	0.37630	0.367453	0.215233	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13;0.13	4.48	4.48	0.54585	Pyrin (2);DEATH-like (2);	0.183793	0.25991	N	0.027001	T	0.00012	0.0000	L	0.60845	1.875	0.09310	P	0.9999999899703	B;B;B;B	0.25772	0.134;0.028;0.111;0.051	B;B;B;B	0.25614	0.052;0.021;0.062;0.03	T	0.38672	-0.9650	9	0.36615	T	0.2	.	13.0212	0.58789	0.0:1.0:0.0:0.0	rs34436714;rs58032372;rs34436714	39;39;39;39	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	V	39	ENSP00000319377:G39V;ENSP00000438030:G39V;ENSP00000340473:G39V;ENSP00000346231:G39V;ENSP00000375655:G39V;ENSP00000375653:G39V;ENSP00000375652:G39V	ENSP00000319377:G39V	G	-	2	0	NLRP12	59019125	0.013000	0.17824	0.079000	0.20413	0.188000	0.23474	1.465000	0.35299	2.224000	0.72417	0.305000	0.20034	GGA	C|0.741;A|0.259	0.259	strong		0.607	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
DENND1B	163486	hgsc.bcm.edu	37	1	197480927	197480927	+	IGR	SNP	C	C	T	rs12142127	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	324	0	0		WXS	Illumina HiSeq	Phase_I	385	219	0.568831	NM_001195215		Silent	SNP		37																																																																																				C|0.754;T|0.246	0.246	strong	0	0.383								
CEP164	22897	hgsc.bcm.edu	37	11	117222691	117222691	+	Missense_Mutation	SNP	C	C	A	rs143659874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117222691C>A	ENST00000278935.3	+	5	527	c.380C>A	c.(379-381)cCc>cAc	p.P127H		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	127	Interaction with ATRIP.				cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		AGAGACCCCCCCAAAAGTTCG	0.517													C|||	9	0.00179712	0.0	0.0014	5008	,	,		16611	0.0		0.008	False		,,,				2504	0.0				p.P127H		Atlas-SNP	.											.	CEP164	121	.	0			c.C380A						PASS	.	C	HIS/PRO	3,4385		0,3,2191	21.0	23.0	22.0		380	4.9	0.1	11	dbSNP_134	22	39,8503		0,39,4232	yes	missense	CEP164	NM_014956.4	77	0,42,6423	AA,AC,CC		0.4566,0.0684,0.3248	possibly-damaging	127/1461	117222691	42,12888	2194	4271	6465	SO:0001583	missense	22897	exon4			ACCCCCCCAAAAG	AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.380C>A	11.37:g.117222691C>A	ENSP00000278935:p.Pro127His	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	49	38	0.77551	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	10.48	1.362097	0.24684	6.84E-4	0.004566	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000529538	T;T;T	0.63744	-0.05;0.32;-0.06	5.81	4.89	0.63831	.	1.313720	0.05171	N	0.499480	T	0.60945	0.2308	L	0.36672	1.1	0.09310	N	1	P;P;D;P	0.63046	0.947;0.906;0.992;0.924	B;B;P;P	0.53146	0.36;0.258;0.719;0.562	T	0.57551	-0.7792	9	.	.	.	-0.0023	14.4821	0.67590	0.0:0.6025:0.3975:0.0	.	127;81;127;127	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	H	81;127;81;81;127	ENSP00000436034:P81H;ENSP00000278935:P127H;ENSP00000435759:P81H	.	P	+	2	0	CEP164	116727901	0.001000	0.12720	0.138000	0.22173	0.013000	0.08279	1.218000	0.32467	1.422000	0.47177	0.655000	0.94253	CCC	C|0.998;A|0.002	0.002	strong		0.517	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77328990	77328990	+	Missense_Mutation	SNP	C	C	A	rs12935394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:77328990C>A	ENST00000282849.5	-	19	3254	c.2836G>T	c.(2836-2838)Gcc>Tcc	p.A946S		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	946	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		A -> S (in dbSNP:rs12935394). {ECO:0000269|PubMed:11867212}.		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						CCAGCACAGGCCTTGCTGCAT	0.478													A|||	571	0.114018	0.0053	0.183	5008	,	,		20222	0.1935		0.1262	False		,,,				2504	0.1176				p.A946S		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G2836T						PASS	.	A	SER/ALA	95,4301	816.8+/-416.3	2,91,2105	110.0	71.0	84.0		2836	3.3	0.9	16	dbSNP_121	84	1125,7475	767.1+/-407.6	71,983,3246	yes	missense	ADAMTS18	NM_199355.2	99	73,1074,5351	AA,AC,CC		13.0814,2.1611,9.3875	benign	946/1222	77328990	1220,11776	2198	4300	6498	SO:0001583	missense	170692	exon19			CACAGGCCTTGCT	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2836G>T	16.37:g.77328990C>A	ENSP00000282849:p.Ala946Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	88	0.765217	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	272	0.12454212454212454	3	0.006097560975609756	59	0.16298342541436464	111	0.19405594405594406	99	0.13060686015831136	A	0.837	-0.743407	0.03088	0.021611	0.130814	ENSG00000140873	ENST00000282849	T	0.49432	0.78	5.64	3.28	0.37604	.	0.139559	0.50627	N	0.000117	T	0.00012	0.0000	N	0.00042	-2.475	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18999	-1.0319	9	0.06757	T	0.87	.	3.9179	0.09231	0.6669:0.1343:0.0704:0.1285	rs12935394;rs52805630;rs57833891;rs12935394	946;946	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	S	946	ENSP00000282849:A946S	ENSP00000282849:A946S	A	-	1	0	ADAMTS18	75886491	0.749000	0.28305	0.943000	0.38184	0.398000	0.30690	1.489000	0.35562	0.426000	0.26116	-0.256000	0.11100	GCC	C|0.893;A|0.107	0.107	strong		0.478	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
FAM46C	54855	hgsc.bcm.edu	37	1	118166385	118166385	+	Missense_Mutation	SNP	G	G	A	rs145471785	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:118166385G>A	ENST00000369448.3	+	2	1142	c.895G>A	c.(895-897)Gaa>Aaa	p.E299K		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	299										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)		CTTCGCTGAAGAAGAGAGAAG	0.517			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			G|||	13	0.00259585	0.0	0.0029	5008	,	,		22262	0.0		0.0089	False		,,,				2504	0.002				p.E299K		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.G895A						PASS	.	G	LYS/GLU	5,4401	9.9+/-24.2	0,5,2198	123.0	116.0	118.0		895	5.7	0.9	1	dbSNP_134	118	91,8509	51.1+/-111.2	1,89,4210	yes	missense	FAM46C	NM_017709.3	56	1,94,6408	AA,AG,GG		1.0581,0.1135,0.7381	possibly-damaging	299/392	118166385	96,12910	2203	4300	6503	SO:0001583	missense	54855	exon2			GCTGAAGAAGAGA	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.895G>A	1.37:g.118166385G>A	ENSP00000358458:p.Glu299Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	53	39	0.735849	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Missense_Mutation	SNP	ENST00000369448.3	37	CCDS896.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	22.3	4.273089	0.80580	0.001135	0.010581	ENSG00000183508	ENST00000369448	T	0.22945	1.93	5.7	5.7	0.88788	Domain of unknown function DUF1693 (1);	0.079249	0.51477	D	0.000094	T	0.27454	0.0674	M	0.79693	2.465	0.80722	D	1	B	0.26902	0.163	B	0.34452	0.183	T	0.05131	-1.0904	10	0.33940	T	0.23	-11.7413	18.8168	0.92079	0.0:0.0:1.0:0.0	.	299	Q5VWP2	FA46C_HUMAN	K	299	ENSP00000358458:E299K	ENSP00000358458:E299K	E	+	1	0	FAM46C	117967908	1.000000	0.71417	0.894000	0.35097	0.979000	0.70002	5.244000	0.65400	2.686000	0.91538	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.517	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
GLO1	2739	hgsc.bcm.edu	37	6	38650588	38650588	+	Silent	SNP	T	T	A	rs1130534	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:38650588T>A	ENST00000373365.4	-	4	458	c.372A>T	c.(370-372)ggA>ggT	p.G124G	GLO1_ENST00000470973.1_5'UTR	NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	124					carbohydrate metabolic process (GO:0005975)|glutathione metabolic process (GO:0006749)|methylglyoxal metabolic process (GO:0009438)|negative regulation of apoptotic process (GO:0043066)|osteoclast differentiation (GO:0030316)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lactoylglutathione lyase activity (GO:0004462)|zinc ion binding (GO:0008270)			lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	6					Glutathione(DB00143)|Indomethacin(DB00328)	ACTTACCGAATCCTCGAGGGT	0.348													T|||	1176	0.234824	0.3525	0.1643	5008	,	,		16878	0.2312		0.1272	False		,,,				2504	0.2403				p.G124G		Atlas-SNP	.											.	GLO1	12	.	0			c.A372T						PASS	.	T		1334,3072	446.3+/-348.0	215,904,1084	142.0	119.0	127.0		372	1.9	1.0	6	dbSNP_86	127	1001,7599	215.6+/-254.9	61,879,3360	no	coding-synonymous	GLO1	NM_006708.2		276,1783,4444	AA,AT,TT		11.6395,30.2769,17.9533		124/185	38650588	2335,10671	2203	4300	6503	SO:0001819	synonymous_variant	2739	exon4			ACCGAATCCTCGA	L07837	CCDS4837.1	6p21.3-p21.1	2012-10-02			ENSG00000124767	ENSG00000124767	4.4.1.5		4323	protein-coding gene	gene with protein product	"""glyoxalase domain containing 1"""	138750				8449929, 7684374	Standard	NM_006708		Approved	GLOD1	uc003ooc.3	Q04760	OTTHUMG00000014636	ENST00000373365.4:c.372A>T	6.37:g.38650588T>A		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Silent	SNP	ENST00000373365.4	37	CCDS4837.1																																																																																			T|0.811;A|0.189	0.189	strong		0.348	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708	
MYH9	4627	hgsc.bcm.edu	37	22	36681953	36681953	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:36681953C>T	ENST00000216181.5	-	36	5338	c.5108G>A	c.(5107-5109)cGg>cAg	p.R1703Q	MYH9_ENST00000475726.1_5'UTR	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1703					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						CAGCTCATCCCGCTCCTGCTG	0.657			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.R1703Q		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	MYH9,NS,carcinoma,+1,1	MYH9	225	1	0			c.G5108A						scavenged	.						54.0	51.0	52.0					22																	36681953		2203	4300	6503	SO:0001583	missense	4627	exon36	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	TCATCCCGCTCCT		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.5108G>A	22.37:g.36681953C>T	ENSP00000216181:p.Arg1703Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	159	3	0.0188679	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.915297	0.92178	.	.	ENSG00000100345	ENST00000337818;ENST00000397231;ENST00000216181	T	0.78707	-1.2	4.96	4.96	0.65561	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.89584	0.6757	M	0.89095	3.005	0.80722	D	1	D	0.76494	0.999	D	0.69307	0.963	D	0.90916	0.4779	10	0.51188	T	0.08	.	18.2038	0.89847	0.0:1.0:0.0:0.0	.	1703	P35579	MYH9_HUMAN	Q	1125;305;1703	ENSP00000216181:R1703Q	ENSP00000216181:R1703Q	R	-	2	0	MYH9	35011899	1.000000	0.71417	1.000000	0.80357	0.454000	0.32378	7.686000	0.84128	2.294000	0.77228	0.306000	0.20318	CGG	.	.	none		0.657	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
DAAM2	23500	hgsc.bcm.edu	37	6	39851818	39851818	+	Silent	SNP	G	G	A	rs3003929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:39851818G>A	ENST00000398904.2	+	15	2108	c.1926G>A	c.(1924-1926)aaG>aaA	p.K642K	DAAM2_ENST00000274867.4_Silent_p.K642K|RP11-61I13.3_ENST00000607215.1_RNA|RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000538976.1_Silent_p.K642K			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	642	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					ATTTTGAAAAGATGTTTTCAG	0.483													A|||	3016	0.602236	0.4622	0.5504	5008	,	,		19954	0.749		0.5765	False		,,,				2504	0.7035				p.K642K		Atlas-SNP	.											.	DAAM2	101	.	0			c.G1926A						PASS	.	A	,	1900,1906		487,926,490	81.0	77.0	78.0		1926,1926	2.2	1.0	6	dbSNP_101	78	4669,3559		1309,2051,754	no	coding-synonymous,coding-synonymous	DAAM2	NM_001201427.1,NM_015345.3	,	1796,2977,1244	AA,AG,GG		43.2547,49.9212,45.413	,	642/1069,642/1068	39851818	6569,5465	1903	4114	6017	SO:0001819	synonymous_variant	23500	exon15			TGAAAAGATGTTT	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1926G>A	6.37:g.39851818G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Silent	SNP	ENST00000398904.2	37	CCDS56426.1																																																																																			G|0.407;A|0.593	0.593	strong		0.483	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
SMARCA4	6597	hgsc.bcm.edu	37	19	11170839	11170839	+	Silent	SNP	T	T	C	rs7275	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11170839T>C	ENST00000429416.3	+	35	5168	c.4887T>C	c.(4885-4887)gaT>gaC	p.D1629D	SMARCA4_ENST00000358026.2_Silent_p.D1661D|SMARCA4_ENST00000589677.1_Silent_p.D1598D|SMARCA4_ENST00000413806.3_Silent_p.D1599D|SMARCA4_ENST00000590574.1_Silent_p.D1596D|SMARCA4_ENST00000450717.3_Silent_p.D1598D|SMARCA4_ENST00000344626.4_Silent_p.D1629D|SMARCA4_ENST00000541122.2_Silent_p.D1599D|SMARCA4_ENST00000444061.3_Silent_p.D1595D	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1629					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)				TGAGTGACGATGACAGTGAGG	0.687			"""F, N, Mis"""		NSCLC								C|||	1251	0.2498	0.3094	0.1715	5008	,	,		14726	0.0724		0.2942	False		,,,				2504	0.362				p.D1661D		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	SMARCA4_ENST00000358026,caecum,carcinoma,0,2	SMARCA4	502	2	1	Unknown(1)	lung(1)	c.T4983C						PASS	.	C	,,,,,,	1060,2890		143,774,1058	26.0	31.0	29.0		4887,4797,4794,4788,4785,4983,4887	-5.1	0.0	19	dbSNP_52	29	1961,5729		253,1455,2137	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SMARCA4	NM_001128844.1,NM_001128845.1,NM_001128846.1,NM_001128847.1,NM_001128848.1,NM_001128849.1,NM_003072.3	,,,,,,	396,2229,3195	CC,CT,TT		25.5007,26.8354,25.9536	,,,,,,	1629/1648,1599/1618,1598/1617,1596/1615,1595/1614,1661/1680,1629/1648	11170839	3021,8619	1975	3845	5820	SO:0001819	synonymous_variant	6597	exon35			TGACGATGACAGT	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.4887T>C	19.37:g.11170839T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	52	50	0.961538	NM_001128849	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Silent	SNP	ENST00000429416.3	37	CCDS12253.1																																																																																			T|0.776;C|0.224	0.224	strong		0.687	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
OR10G2	26534	hgsc.bcm.edu	37	14	22102745	22102745	+	Missense_Mutation	SNP	C	C	A	rs41314525	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	253	0	0		WXS	Illumina HiSeq	Phase_I	316	200	0.632911	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		
ESYT2	57488	hgsc.bcm.edu	37	7	158528233	158528233	+	Silent	SNP	A	A	G	rs3816462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:158528233A>G	ENST00000251527.5	-	20	2612	c.2547T>C	c.(2545-2547)agT>agC	p.S849S	ESYT2_ENST00000435514.2_Silent_p.S284S	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	877	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						GGAAGCCGCCACTGTTCTTCA	0.458													G|||	1770	0.353435	0.4387	0.183	5008	,	,		18629	0.6022		0.173	False		,,,				2504	0.2883				p.S849S		Atlas-SNP	.											.	ESYT2	70	.	0			c.T2547C						PASS	.			1645,2761	504.6+/-365.9	321,1003,879	160.0	168.0	165.0		2547	-9.9	0.3	7	dbSNP_107	165	1486,7114	281.2+/-294.9	126,1234,2940	no	coding-synonymous	ESYT2	NM_020728.2		447,2237,3819	GG,GA,AA		17.2791,37.3355,24.0735		849/894	158528233	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon20			GCCGCCACTGTTC	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2547T>C	7.37:g.158528233A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	66	46	0.69697	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			A|0.703;G|0.297	0.297	strong		0.458	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
CATSPER4	378807	hgsc.bcm.edu	37	1	26527863	26527863	+	Silent	SNP	C	C	T	rs17163674	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:26527863C>T	ENST00000456354.2	+	9	1285	c.1218C>T	c.(1216-1218)cgC>cgT	p.R406R		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	406					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)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		AGGAGGTGCGCGCAATCCGCT	0.627													C|||	450	0.0898562	0.0121	0.0764	5008	,	,		17973	0.0972		0.1193	False		,,,				2504	0.1667				p.R406R		Atlas-SNP	.											.	CATSPER4	59	.	0			c.C1218T						PASS	.	C		112,4294	86.3+/-125.0	2,108,2093	67.0	62.0	64.0		1218	1.6	1.0	1	dbSNP_123	64	1165,7435	238.3+/-269.8	86,993,3221	no	coding-synonymous	CATSPER4	NM_198137.1		88,1101,5314	TT,TC,CC		13.5465,2.542,9.8185		406/473	26527863	1277,11729	2203	4300	6503	SO:0001819	synonymous_variant	378807	exon9			GGTGCGCGCAATC	BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.1218C>T	1.37:g.26527863C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	113	32	0.283186	NM_198137	A1A4W6|Q5VY71	Silent	SNP	ENST00000456354.2	37	CCDS30645.1																																																																																			C|0.906;T|0.094	0.094	strong		0.627	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	
PLEC	5339	hgsc.bcm.edu	37	8	145011204	145011204	+	Silent	SNP	A	A	G	rs6993938	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145011204A>G	ENST00000322810.4	-	5	958	c.789T>C	c.(787-789)gcT>gcC	p.A263A	PLEC_ENST00000398774.2_Silent_p.A94A|PLEC_ENST00000527096.1_Silent_p.A153A|PLEC_ENST00000357649.2_Silent_p.A130A|PLEC_ENST00000345136.3_Silent_p.A126A|PLEC_ENST00000356346.3_Silent_p.A112A|PLEC_ENST00000436759.2_Silent_p.A153A|PLEC_ENST00000354958.2_Silent_p.A104A|PLEC_ENST00000354589.3_Silent_p.A126A	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	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	205	123	0.6	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	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18656225	18656225	+	Silent	SNP	G	G	A	rs11044142	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:18656225G>A	ENST00000266497.5	+	21	2942	c.2904G>A	c.(2902-2904)caG>caA	p.Q968Q	PIK3C2G_ENST00000538779.1_Silent_p.Q1009Q|PIK3C2G_ENST00000433979.1_Silent_p.Q968Q			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	968	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|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)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				GATTGGTGCAGATGGTACCTG	0.403													G|||	804	0.160543	0.3744	0.1254	5008	,	,		16910	0.0		0.1789	False		,,,				2504	0.0429				p.Q968Q		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.G2904A						PASS	.	G		1162,2554		193,776,889	92.0	88.0	89.0		2904	3.0	1.0	12	dbSNP_120	89	1401,6805		115,1171,2817	no	coding-synonymous	PIK3C2G	NM_004570.4		308,1947,3706	AA,AG,GG		17.0729,31.2702,21.4981		968/1446	18656225	2563,9359	1858	4103	5961	SO:0001819	synonymous_variant	5288	exon22			GGTGCAGATGGTA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2904G>A	12.37:g.18656225G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			G|0.842;A|0.158	0.158	strong		0.403	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
THTPA	79178	hgsc.bcm.edu	37	14	24026046	24026046	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24026046G>A	ENST00000288014.6	+	1	816	c.80G>A	c.(79-81)gGc>gAc	p.G27D	THTPA_ENST00000554789.1_Missense_Mutation_p.G27D|RP11-66N24.4_ENST00000556354.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA|THTPA_ENST00000404535.3_Missense_Mutation_p.G27D|THTPA_ENST00000554970.1_Missense_Mutation_p.G27D|THTPA_ENST00000556015.1_Missense_Mutation_p.G27D|RP11-66N24.4_ENST00000555446.1_RNA			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	27	CYTH. {ECO:0000255|PROSITE- ProRule:PRU01044}.				dephosphorylation (GO:0016311)|generation of precursor metabolites and energy (GO:0006091)|small molecule metabolic process (GO:0044281)|thiamine diphosphate metabolic process (GO:0042357)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)|thiamin-triphosphatase activity (GO:0050333)			large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)		GAGTTGGGGGGCACCCTGGAG	0.607																																					p.G27D		Atlas-SNP	.											.	THTPA	11	.	0			c.G80A						PASS	.						53.0	43.0	46.0					14																	24026046		2203	4300	6503	SO:0001583	missense	79178	exon2			TGGGGGGCACCCT	AF432862	CCDS32053.1, CCDS58306.1, CCDS58307.1	14q11.2	2011-04-28					3.6.1.28		18987	protein-coding gene	gene with protein product		611612				11827967	Standard	NR_046051		Approved	THTPASE	uc001wkh.5	Q9BU02		ENST00000288014.6:c.80G>A	14.37:g.24026046G>A	ENSP00000288014:p.Gly27Asp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	158	93	0.588608	NM_001256321	D3DS50|G3V4J3	Missense_Mutation	SNP	ENST00000288014.6	37	CCDS32053.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799652	0.70567	.	.	ENSG00000157306	ENST00000404535;ENST00000288014;ENST00000557630;ENST00000556015;ENST00000554970;ENST00000554789	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	5.91	0.674	0.17946	CYTH domain (2);CYTH-like domain (1);	0.428933	0.25484	N	0.030357	T	0.66268	0.2772	M	0.76170	2.325	0.28533	N	0.91246	P;D	0.56746	0.928;0.977	P;P	0.60473	0.564;0.875	T	0.71155	-0.4675	10	0.62326	D	0.03	-1.7363	20.3036	0.98618	0.0:0.7093:0.2907:0.0	.	27;27	G3V4J3;Q9BU02	.;THTPA_HUMAN	D	27	ENSP00000384580:G27D;ENSP00000288014:G27D;ENSP00000452281:G27D;ENSP00000451835:G27D;ENSP00000452465:G27D;ENSP00000450459:G27D	ENSP00000288014:G27D	G	+	2	0	THTPA	23095886	0.623000	0.27094	0.764000	0.31436	0.880000	0.50808	0.727000	0.25999	-0.142000	0.11354	0.655000	0.94253	GGC	.	.	none		0.607	THTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413800.2		
CCDC110	256309	hgsc.bcm.edu	37	4	186382206	186382206	+	Silent	SNP	A	A	G	rs11132309	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:186382206A>G	ENST00000307588.3	-	5	420	c.345T>C	c.(343-345)gaT>gaC	p.D115D	CCDC110_ENST00000510617.1_Silent_p.D115D|CCDC110_ENST00000507501.1_5'UTR|CCDC110_ENST00000393540.3_Intron	NM_152775.3	NP_689988.1	Q8TBZ0	CC110_HUMAN	coiled-coil domain containing 110	115						nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(9)	30		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;7.86e-05)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|Colorectal(36;0.0381)|all_hematologic(60;0.0749)		OV - Ovarian serous cystadenocarcinoma(60;1.13e-10)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.00014)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00921)|COAD - Colon adenocarcinoma(29;0.0105)|READ - Rectum adenocarcinoma(43;0.164)		AACATACCAAATCCTTTTCAA	0.343													A|||	1924	0.384185	0.2784	0.3631	5008	,	,		15974	0.2827		0.5388	False		,,,				2504	0.4877				p.D115D		Atlas-SNP	.											.	CCDC110	78	.	0			c.T345C						PASS	.	A	,	1440,2964	458.0+/-351.8	240,960,1002	122.0	117.0	119.0		,345	4.5	1.0	4	dbSNP_120	119	4832,3764	607.4+/-395.2	1375,2082,841	no	intron,coding-synonymous	CCDC110	NM_001145411.1,NM_152775.3	,	1615,3042,1843	GG,GA,AA		43.7878,32.6975,48.2462	,	,115/834	186382206	6272,6728	2202	4298	6500	SO:0001819	synonymous_variant	256309	exon5			TACCAAATCCTTT	AB080722	CCDS3843.1, CCDS47170.1	4q35.1	2010-12-24			ENSG00000168491	ENSG00000168491			28504	protein-coding gene	gene with protein product	"""cancer/testis antigen 52"""	609488				18160854	Standard	NM_152775		Approved	KM-HN-1, MGC33607, CT52	uc003ixu.4	Q8TBZ0	OTTHUMG00000160415	ENST00000307588.3:c.345T>C	4.37:g.186382206A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	96	16	0.166667	NM_152775	Q86YI9|Q8N7W0	Silent	SNP	ENST00000307588.3	37	CCDS3843.1																																																																																			A|0.557;G|0.443	0.443	strong		0.343	CCDC110-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360519.2	NM_152775	
OCA2	4948	hgsc.bcm.edu	37	15	28230318	28230318	+	Missense_Mutation	SNP	C	C	T	rs1800407	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	88	0	0		WXS	Illumina HiSeq	Phase_I	51	11	0.215686	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	
ZNF106	64397	hgsc.bcm.edu	37	15	42720288	42720288	+	Silent	SNP	G	G	C	rs11544099	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42720288G>C	ENST00000263805.4	-	12	5183	c.4857C>G	c.(4855-4857)ctC>ctG	p.L1619L	RNU6-188P_ENST00000364207.1_RNA|ZNF106_ENST00000565380.1_Silent_p.L847L|ZNF106_ENST00000565611.1_Silent_p.L804L	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	1619					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)										TGTGGAGGCAGAGGACCCGGT	0.498													G|||	261	0.0521166	0.0431	0.0735	5008	,	,		19492	0.006		0.1173	False		,,,				2504	0.0297				p.L1619L		Atlas-SNP	.											ZFP106,NS,carcinoma,0,1	ZFP106	117	1	0			c.C4857G						PASS	.	G		258,4148	147.6+/-182.1	4,250,1949	133.0	106.0	115.0		4857	3.4	1.0	15	dbSNP_120	115	1188,7410	242.4+/-272.4	85,1018,3196	no	coding-synonymous	ZFP106	NM_022473.1		89,1268,5145	CC,CG,GG		13.8172,5.8557,11.1197		1619/1884	42720288	1446,11558	2203	4299	6502	SO:0001819	synonymous_variant	64397	exon12			GAGGCAGAGGACC	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.4857C>G	15.37:g.42720288G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Silent	SNP	ENST00000263805.4	37	CCDS32208.1																																																																																			G|0.904;C|0.096	0.096	strong		0.498	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
LIPF	8513	hgsc.bcm.edu	37	10	90438207	90438207	+	Silent	SNP	A	A	G	rs1228187	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:90438207A>G	ENST00000238983.4	+	10	1012	c.966A>G	c.(964-966)caA>caG	p.Q322Q	LIPF_ENST00000608620.1_Silent_p.Q289Q|LIPF_ENST00000355843.2_Silent_p.Q299Q|LIPF_ENST00000394375.3_Silent_p.Q332Q	NM_004190.3	NP_004181.1	P07098	LIPG_HUMAN	lipase, gastric	322					lipid catabolic process (GO:0016042)|malate metabolic process (GO:0006108)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)	lipid binding (GO:0008289)|malate dehydrogenase activity (GO:0016615)|triglyceride lipase activity (GO:0004806)			NS(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(6)	13		Colorectal(252;0.0161)		Colorectal(12;3.91e-05)|COAD - Colon adenocarcinoma(12;5.43e-05)	Orlistat(DB01083)	TCTAGTCCCAACCTCCCTACT	0.448													A|||	1144	0.228435	0.1248	0.3069	5008	,	,		19364	0.3274		0.2107	False		,,,				2504	0.229				p.Q332Q		Atlas-SNP	.											.	LIPF	62	.	0			c.A996G						PASS	.	A	,,,	618,3788	268.9+/-268.7	43,532,1628	186.0	170.0	175.0		867,996,897,966	-9.7	0.0	10	dbSNP_87	175	1777,6823	321.5+/-315.1	196,1385,2719	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LIPF	NM_001198828.1,NM_001198829.1,NM_001198830.1,NM_004190.3	,,,	239,1917,4347	GG,GA,AA		20.6628,14.0263,18.4146	,,,	289/366,332/409,299/376,322/399	90438207	2395,10611	2203	4300	6503	SO:0001819	synonymous_variant	8513	exon11			GTCCCAACCTCCC	X05997	CCDS7389.1, CCDS55718.1, CCDS55719.1, CCDS65896.1	10q23	2005-10-30			ENSG00000182333	ENSG00000182333	3.1.1.3		6622	protein-coding gene	gene with protein product		601980				3304425, 9186906	Standard	NM_004190		Approved	HGL, HLAL	uc010qmt.2	P07098	OTTHUMG00000018695	ENST00000238983.4:c.966A>G	10.37:g.90438207A>G		Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	113	73	0.646018	NM_001198829	B7Z723|F5H1P4|Q2M1P6|Q5VXI7|Q5VXI8|Q658L8	Silent	SNP	ENST00000238983.4	37	CCDS7389.1																																																																																			A|0.799;G|0.201	0.201	strong		0.448	LIPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049256.1		
MAP2K3	5606	hgsc.bcm.edu	37	17	21207844	21207844	+	Silent	SNP	C	C	T	rs2230436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:21207844C>T	ENST00000342679.4	+	8	924	c.675C>T	c.(673-675)gcC>gcT	p.A225A	MAP2K3_ENST00000361818.5_Silent_p.A196A|MAP2K3_ENST00000316920.6_Silent_p.A196A	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CGATGGATGCCGGCTGCAAGC	0.607																																					p.A225A		Atlas-SNP	.											.	MAP2K3	135	.	0			c.C675T						PASS	.						198.0	149.0	166.0					17																	21207844		2203	4300	6503	SO:0001819	synonymous_variant	5606	exon8			GGATGCCGGCTGC	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.675C>T	17.37:g.21207844C>T		Somatic	380	0	0		WXS	Illumina HiSeq	Phase_I	374	85	0.227273	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Silent	SNP	ENST00000342679.4	37	CCDS11217.1																																																																																			C|0.592;T|0.408	0.408	strong		0.607	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	
SLC30A5	64924	hgsc.bcm.edu	37	5	68419054	68419054	+	Silent	SNP	A	A	T	rs164572	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:68419054A>T	ENST00000396591.3	+	14	2410	c.1800A>T	c.(1798-1800)acA>acT	p.T600T	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	600					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		TGGCAGATACACTTGGCAGCA	0.318													A|||	2015	0.402356	0.2519	0.4107	5008	,	,		18363	0.5397		0.4225	False		,,,				2504	0.4376				p.T600T		Atlas-SNP	.											.	SLC30A5	54	.	0			c.A1800T						PASS	.	A		1157,3249	410.2+/-335.3	142,873,1188	129.0	114.0	119.0		1800	-1.5	1.0	5	dbSNP_79	119	3721,4879	533.2+/-382.4	829,2063,1408	no	coding-synonymous	SLC30A5	NM_022902.3		971,2936,2596	TT,TA,AA		43.2674,26.2596,37.5058		600/766	68419054	4878,8128	2203	4300	6503	SO:0001819	synonymous_variant	64924	exon14			AGATACACTTGGC	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"""Solute carriers"""	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.1800A>T	5.37:g.68419054A>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_022902	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Silent	SNP	ENST00000396591.3	37	CCDS3996.1																																																																																			A|0.607;T|0.393	0.393	strong		0.318	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2		
FLNB	2317	hgsc.bcm.edu	37	3	58118555	58118555	+	Missense_Mutation	SNP	G	G	A	rs12632456	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:58118555G>A	ENST00000295956.4	+	26	4576	c.4411G>A	c.(4411-4413)Gtg>Atg	p.V1471M	FLNB_ENST00000490882.1_Missense_Mutation_p.V1502M|FLNB_ENST00000419752.2_Missense_Mutation_p.V1302M|FLNB_ENST00000493452.1_Missense_Mutation_p.V1302M|FLNB_ENST00000429972.2_Missense_Mutation_p.V1471M|FLNB_ENST00000348383.5_Missense_Mutation_p.V1471M|FLNB_ENST00000357272.4_Missense_Mutation_p.V1471M|FLNB_ENST00000358537.3_Missense_Mutation_p.V1471M	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1471	Interaction with FBLP1.		V -> M (in dbSNP:rs12632456). {ECO:0000269|PubMed:11153914, ECO:0000269|PubMed:18487259, ECO:0000269|PubMed:9651345}.		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)		GCCAGTGAACGTGGTGGACAA	0.512													G|||	3046	0.608227	0.6422	0.4813	5008	,	,		23390	0.9692		0.2833	False		,,,				2504	0.6145				p.V1502M		Atlas-SNP	.											.	FLNB	430	.	0			c.G4504A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL	2573,1833	636.4+/-396.6	741,1091,371	148.0	127.0	134.0		4504,4411,4411,4411	2.8	0.7	3	dbSNP_120	134	2109,6491	363.6+/-333.2	265,1579,2456	yes	missense,missense,missense,missense	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	21,21,21,21	1006,2670,2827	AA,AG,GG		24.5233,41.6024,35.9988	benign,benign,benign,benign	1502/2634,1471/2592,1471/2579,1471/2603	58118555	4682,8324	2203	4300	6503	SO:0001583	missense	2317	exon27			GTGAACGTGGTGG	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.4411G>A	3.37:g.58118555G>A	ENSP00000295956:p.Val1471Met	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_001164317	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	37	CCDS2885.1	1232	0.5641025641025641	315	0.6402439024390244	153	0.42265193370165743	554	0.9685314685314685	210	0.2770448548812665	G	18.29	3.592206	0.66219	0.583976	0.245233	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	5.81	2.75	0.32379	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.199780	0.43110	D	0.000613	T	0.00012	0.0000	M	0.83774	2.66	0.25432	P	0.9881714	P;P;B;B;P;P	0.46395	0.877;0.588;0.382;0.057;0.807;0.807	B;B;B;B;B;B	0.43536	0.37;0.194;0.278;0.055;0.423;0.423	T	0.33828	-0.9853	9	0.49607	T	0.09	.	5.5883	0.17287	0.3207:0.1285:0.5508:0.0	rs12632456;rs52793889;rs61428936;rs12632456	1471;1502;1302;1302;1471;1471	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	M	1471;1502;1471;1471;1471;1471;1302;1302	ENSP00000295956:V1471M;ENSP00000420213:V1502M;ENSP00000351339:V1471M;ENSP00000415599:V1471M;ENSP00000232447:V1471M;ENSP00000349819:V1471M;ENSP00000418510:V1302M;ENSP00000414532:V1302M	ENSP00000295956:V1471M	V	+	1	0	FLNB	58093595	1.000000	0.71417	0.669000	0.29828	0.915000	0.54546	2.951000	0.49089	0.228000	0.21019	0.557000	0.71058	GTG	G|0.538;A|0.462	0.462	strong		0.512	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
SLC26A8	116369	hgsc.bcm.edu	37	6	35967772	35967772	+	Missense_Mutation	SNP	T	T	C	rs17713154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:35967772T>C	ENST00000490799.1	-	4	795	c.442A>G	c.(442-444)Att>Gtt	p.I148V	SLC26A8_ENST00000355574.2_Missense_Mutation_p.I148V|SLC26A8_ENST00000394602.2_Missense_Mutation_p.I148V	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						AACTCACCAATGGACATTTGA	0.393													T|||	525	0.104832	0.0885	0.1427	5008	,	,		18752	0.0506		0.1402	False		,,,				2504	0.1196				p.I148V		Atlas-SNP	.											SLC26A8,colon,carcinoma,+2,1	SLC26A8	95	1	0			c.A442G						scavenged	.	T	VAL/ILE,VAL/ILE,VAL/ILE	396,4010	196.4+/-220.7	15,366,1822	164.0	167.0	166.0		442,442,442	1.7	1.0	6	dbSNP_123	166	1145,7455	234.6+/-267.5	90,965,3245	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	29,29,29	105,1331,5067	CC,CT,TT		13.314,8.9877,11.8484	benign,benign,benign	148/971,148/971,148/866	35967772	1541,11465	2203	4300	6503	SO:0001583	missense	116369	exon4			CACCAATGGACAT	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.442A>G	6.37:g.35967772T>C	ENSP00000417638:p.Ile148Val	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	236	0.10805860805860806	36	0.07317073170731707	62	0.1712707182320442	33	0.057692307692307696	105	0.13852242744063326	T	7.036	0.561555	0.13498	0.089877	0.13314	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574	D;D;D	0.90444	-2.67;-2.67;-2.67	5.4	1.73	0.24493	.	0.168304	0.42420	N	0.000709	T	0.56411	0.1983	N	0.12853	0.265	0.31338	P	0.6840010000000001	P;B	0.38129	0.619;0.336	B;B	0.33890	0.172;0.075	T	0.59413	-0.7459	9	0.06365	T	0.9	.	6.6044	0.22718	0.0:0.2787:0.0:0.7213	rs17713154;rs52813917;rs17713154	148;148	Q96RN1;Q96RN1-2	S26A8_HUMAN;.	V	148	ENSP00000417638:I148V;ENSP00000378100:I148V;ENSP00000347778:I148V	ENSP00000347778:I148V	I	-	1	0	SLC26A8	36075750	0.990000	0.36364	1.000000	0.80357	0.996000	0.88848	0.851000	0.27751	0.443000	0.26582	0.533000	0.62120	ATT	T|0.887;C|0.113	0.113	strong		0.393	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377261	168377261	+	lincRNA	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:168377261T>C	ENST00000538528.1	-	0	358																											CTGCAGTGTGTTGGGAGGAGG	0.627																																					p.Q24Q		Atlas-SNP	.											.	.	.	.	0			c.A72G						PASS	.						9.0	10.0	10.0					6																	168377261		685	1579	2264			0	exon1			AGTGTGTTGGGAG																													6.37:g.168377261T>C		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	329	34	0.103343	NM_001129895		Silent	SNP	ENST00000538528.1	37																																																																																				.	.	none		0.627	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
GSPT1	2935	hgsc.bcm.edu	37	16	11969724	11969724	+	Silent	SNP	G	G	C	rs33657	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:11969724G>C	ENST00000563468.1	-	12	1367	c.1341C>G	c.(1339-1341)gtC>gtG	p.V447V	RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000439887.2_Silent_p.V584V|GSPT1_ENST00000434724.2_Silent_p.V585V|GSPT1_ENST00000420576.2_Silent_p.V447V			P15170	ERF3A_HUMAN	G1 to S phase transition 1	447					G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						GATCTTGTTTGACAAAACGGG	0.418													C|||	3260	0.650958	0.7761	0.5461	5008	,	,		20444	0.7917		0.4394	False		,,,				2504	0.6288				p.V585V		Atlas-SNP	.											.	GSPT1	71	.	0			c.C1755G						PASS	.	C	,,	3033,1289		1064,905,192	81.0	82.0	82.0		1752,1341,1755	2.0	1.0	16	dbSNP_76	82	3390,5176		667,2056,1560	no	coding-synonymous,coding-synonymous,coding-synonymous	GSPT1	NM_001130006.1,NM_001130007.1,NM_002094.3	,,	1731,2961,1752	CC,CG,GG		39.5751,29.8242,49.8371	,,	584/637,447/500,585/638	11969724	6423,6465	2161	4283	6444	SO:0001819	synonymous_variant	2935	exon14			TTGTTTGACAAAA	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000563468.1:c.1341C>G	16.37:g.11969724G>C		Somatic	250	1	0.004		WXS	Illumina HiSeq	Phase_I	263	137	0.520913	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	37	CCDS45414.1																																																																																			G|0.405;C|0.595	0.595	strong		0.418	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094	
ZNF229	7772	hgsc.bcm.edu	37	19	44932972	44932972	+	Missense_Mutation	SNP	C	C	T	rs1434579	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44932972C>T	ENST00000588931.1	-	6	2417	c.1984G>A	c.(1984-1986)Gga>Aga	p.G662R	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron|ZNF229_ENST00000291187.4_Missense_Mutation_p.G656R	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	662			G -> R (in dbSNP:rs1434579). {ECO:0000269|Ref.4}.		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)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				AAGCCCTTTCCGCACTCTTGG	0.493													C|||	1442	0.287939	0.0484	0.2608	5008	,	,		22657	0.3294		0.3598	False		,,,				2504	0.5143				p.G662R		Atlas-SNP	.											ZNF229,NS,carcinoma,+1,1	ZNF229	123	1	0			c.G1984A						PASS	.	C	ARG/GLY	393,3919		20,353,1783	126.0	127.0	127.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1984	3.5	0.0	19	dbSNP_88	127	2912,5640		507,1898,1871	yes	missense	ZNF229	NM_014518.2	125	527,2251,3654	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	34.0505,9.1141,25.6919	probably-damaging	662/826	44932972	3305,9559	2156	4276	6432	SO:0001583	missense	7772	exon6			CCTTTCCGCACTC	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.1984G>A	19.37:g.44932972C>T	ENSP00000466519:p.Gly662Arg	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	225	124	0.551111	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	570	0.260989010989011	20	0.04065040650406504	94	0.2596685082872928	182	0.3181818181818182	274	0.36147757255936674	C	22.8	4.337383	0.81911	0.091141	0.340505	ENSG00000167383	ENST00000291187	.	.	.	3.5	3.5	0.40072	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.81497	2.545	0.26784	P	0.969539	D	0.89917	1.0	D	0.67231	0.95	T	0.04005	-1.0985	7	0.59425	D	0.04	.	14.1802	0.65568	0.0:1.0:0.0:0.0	rs1434579;rs17347602;rs52817635;rs59210988;rs1434579	662	Q9UJW7	ZN229_HUMAN	R	662	.	ENSP00000291187:G662R	G	-	1	0	ZNF229	49624812	0.197000	0.23362	0.030000	0.17652	0.143000	0.21401	1.720000	0.38022	1.677000	0.50941	0.609000	0.83330	GGA	C|0.728;T|0.272	0.272	strong		0.493	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
RP1L1	94137	hgsc.bcm.edu	37	8	10464885	10464885	+	Silent	SNP	T	T	C	rs56382513	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:10464885T>C	ENST00000382483.3	-	4	6946	c.6723A>G	c.(6721-6723)tcA>tcG	p.S2241S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2321	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				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)		TTTCTCCTTCTGACTCTGGCT	0.597													t|||	3260	0.650958	0.475	0.6686	5008	,	,		17857	0.9792		0.5089	False		,,,				2504	0.684				p.S2241S		Atlas-SNP	.											RP1L1,NS,carcinoma,0,2	RP1L1	453	2	0			c.A6723G						scavenged	.	C		1954,1902		496,962,470	97.0	101.0	99.0		6723	-6.9	0.0	8	dbSNP_129	99	4377,3879		1167,2043,918	no	coding-synonymous	RP1L1	NM_178857.5		1663,3005,1388	CC,CT,TT		46.984,49.3257,47.7295		2241/2401	10464885	6331,5781	1928	4128	6056	SO:0001819	synonymous_variant	94137	exon4			TCCTTCTGACTCT	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.6723A>G	8.37:g.10464885T>C		Somatic	79	2	0.0253165		WXS	Illumina HiSeq	Phase_I	115	87	0.756522	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			T|0.404;C|0.596	0.596	strong		0.597	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
TULP1	7287	hgsc.bcm.edu	37	6	35477032	35477032	+	Missense_Mutation	SNP	A	A	G	rs2064317	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:35477032A>G	ENST00000229771.6	-	8	855	c.776T>C	c.(775-777)aTa>aCa	p.I259T	TULP1_ENST00000322263.4_Missense_Mutation_p.I206T	NM_003322.3	NP_003313.3	O00294	TULP1_HUMAN	tubby like protein 1	259			I -> T (in dbSNP:rs2064317). {ECO:0000269|PubMed:17962469}.		dendrite development (GO:0016358)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|phagocytosis (GO:0006909)|photoreceptor cell maintenance (GO:0045494)|phototransduction (GO:0007602)|positive regulation of phagocytosis (GO:0050766)|retina development in camera-type eye (GO:0060041)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|synapse (GO:0045202)	actin filament binding (GO:0051015)|G-protein coupled photoreceptor activity (GO:0008020)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.I259T(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	19						GCTCTTCTTTATCACCGTAGC	0.587													G|||	1973	0.39397	0.3449	0.3329	5008	,	,		19111	0.499		0.3648	False		,,,				2504	0.4254				p.I259T	GBM(55;1027 1091 11115 23439)	Atlas-SNP	.											TULP1,NS,carcinoma,0,1	TULP1	51	1	1	Substitution - Missense(1)	stomach(1)	c.T776C						PASS	.	G	THR/ILE	1564,2842	669.1+/-402.1	254,1056,893	371.0	345.0	354.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	776	3.6	0.3	6	dbSNP_94	354	3190,5410	653.8+/-401.1	609,1972,1719	yes	missense	TULP1	NM_003322.3	89	863,3028,2612	GG,GA,AA		37.093,35.497,36.5524	benign	259/543	35477032	4754,8252	2203	4300	6503	SO:0001583	missense	7287	exon8			TTCTTTATCACCG	U82468	CCDS4807.1, CCDS75436.1	6p21.3	2014-01-28			ENSG00000112041	ENSG00000112041			12423	protein-coding gene	gene with protein product		602280		RP14		9096357, 9521870	Standard	NM_003322		Approved	TUBL1, LCA15	uc003okv.4	O00294	OTTHUMG00000014575	ENST00000229771.6:c.776T>C	6.37:g.35477032A>G	ENSP00000229771:p.Ile259Thr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_003322	O43536|Q5TGM5|Q8N571	Missense_Mutation	SNP	ENST00000229771.6	37	CCDS4807.1	837	0.38324175824175827	172	0.34959349593495936	137	0.3784530386740331	256	0.44755244755244755	272	0.35883905013192613	G	0.004	-2.320881	0.00232	0.35497	0.37093	ENSG00000112041	ENST00000229771;ENST00000322263	T;T	0.79352	-1.25;-1.26	4.5	3.62	0.41486	.	0.891546	0.09851	N	0.747564	T	0.16128	0.0388	N	0.00413	-1.525	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.11966	-1.0566	9	0.02654	T	1	-11.6502	6.4263	0.21772	0.2277:0.0:0.7723:0.0	rs2064317;rs41539122;rs41539440;rs41539748;rs45630406;rs45632076;rs57520700;rs61726639;rs2064317	206;259	O00294-2;O00294	.;TULP1_HUMAN	T	259;206	ENSP00000229771:I259T;ENSP00000319414:I206T	ENSP00000229771:I259T	I	-	2	0	TULP1	35585010	0.662000	0.27439	0.260000	0.24451	0.137000	0.21094	0.696000	0.25541	0.513000	0.28278	-0.355000	0.07637	ATA	A|0.642;G|0.358	0.358	strong		0.587	TULP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040307.2		
IPO5	3843	hgsc.bcm.edu	37	13	98645253	98645253	+	Silent	SNP	A	A	G	rs626716	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:98645253A>G	ENST00000490680.1	+	7	842	c.777A>G	c.(775-777)ctA>ctG	p.L259L	IPO5_ENST00000539640.1_Silent_p.L134L|IPO5_ENST00000261574.5_Silent_p.L277L			O00410	IPO5_HUMAN	importin 5	259					cellular response to amino acid stimulus (GO:0071230)|negative regulation of catalytic activity (GO:0043086)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein import into nucleus (GO:0042307)|ribosomal protein import into nucleus (GO:0006610)|viral process (GO:0016032)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|Ran GTPase binding (GO:0008536)			breast(2)|endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	27						AAGCAACTCTACAGCTAAGTC	0.348													A|||	718	0.143371	0.1142	0.0303	5008	,	,		20955	0.3155		0.0457	False		,,,				2504	0.1861				p.L277L		Atlas-SNP	.											.	IPO5	90	.	0			c.A831G						PASS	.	A		436,3970	211.8+/-231.9	27,382,1794	116.0	110.0	112.0		831	-5.2	0.9	13	dbSNP_83	112	343,8257	117.0+/-176.6	4,335,3961	no	coding-synonymous	IPO5	NM_002271.4		31,717,5755	GG,GA,AA		3.9884,9.8956,5.9895		277/1116	98645253	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	3843	exon10			AACTCTACAGCTA	U72761	CCDS31999.1	13q32.2	2012-05-02	2008-04-15	2008-04-15	ENSG00000065150	ENSG00000065150		"""Importins"""	6402	protein-coding gene	gene with protein product		602008	"""karyopherin (importin) beta 3"", ""RAN binding protein 5"""	KPNB3, RANBP5		9114010, 9271386, 17005651	Standard	NM_002271		Approved	IMB3, MGC2068, Pse1	uc001vne.3	O00410	OTTHUMG00000017244	ENST00000490680.1:c.777A>G	13.37:g.98645253A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_002271	B4DZA0|O15257|Q5T578|Q86XC7	Silent	SNP	ENST00000490680.1	37		270	0.12362637362637363	59	0.11991869918699187	14	0.03867403314917127	163	0.28496503496503495	34	0.044854881266490766	A	10.48	1.362466	0.24684	0.098956	0.039884	ENSG00000065150	ENST00000469360	.	.	.	6.17	-5.19	0.02832	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26224	-1.0109	3	.	.	.	-25.4394	10.7192	0.46030	0.4233:0.099:0.4777:0.0	rs626716;rs2230410;rs17301628;rs626716	.	.	.	C	261	.	.	Y	+	2	0	IPO5	97443254	0.985000	0.35326	0.902000	0.35471	0.988000	0.76386	0.264000	0.18497	-0.754000	0.04715	0.533000	0.62120	TAC	A|0.901;G|0.099	0.099	strong		0.348	IPO5-006	NOVEL	alternative_5_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000354655.1	NM_002271	
FLG	2312	hgsc.bcm.edu	37	1	152283862	152283862	+	Missense_Mutation	SNP	G	G	C	rs58001094	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152283862G>C	ENST00000368799.1	-	3	3535	c.3500C>G	c.(3499-3501)gCa>gGa	p.A1167G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1167	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCCGGGTGTGCACGAATGGT	0.597									Ichthyosis				g|||	2675	0.534145	0.7806	0.4611	5008	,	,		20510	0.6577		0.1759	False		,,,				2504	0.4939				p.A1167G		Atlas-SNP	.											FLG,brain,glioma,0,1	FLG	900	1	0			c.C3500G						scavenged	.	C	GLY/ALA	2642,1764	599.0+/-389.2	734,1174,295	291.0	346.0	328.0		3500	-5.5	0.0	1	dbSNP_129	328	1392,7208	258.1+/-281.9	103,1186,3011	no	missense	FLG	NM_002016.1	60	837,2360,3306	CC,CG,GG		16.186,40.0363,31.0165	benign	1167/4062	152283862	4034,8972	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGGTGTGCACGAA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3500C>G	1.37:g.152283862G>C	ENSP00000357789:p.Ala1167Gly	Somatic	279	2	0.00716846		WXS	Illumina HiSeq	Phase_I	379	125	0.329815	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	814	0.3727106227106227	262	0.532520325203252	123	0.3397790055248619	315	0.5506993006993007	114	0.1503957783641161	g	3.006	-0.204867	0.06180	0.599637	0.16186	ENSG00000143631	ENST00000368799	T	0.03920	3.76	2.76	-5.53	0.02552	.	.	.	.	.	T	0.00271	0.0008	N	0.00049	-2.42	0.80722	P	0.0	B	0.14805	0.011	B	0.10450	0.005	T	0.48269	-0.9050	8	0.21540	T	0.41	.	10.7783	0.46363	0.0:0.1887:0.7027:0.1086	rs58001094	1167	P20930	FILA_HUMAN	G	1167	ENSP00000357789:A1167G	ENSP00000357789:A1167G	A	-	2	0	FLG	150550486	.	.	0.000000	0.03702	0.008000	0.06430	.	.	-1.865000	0.01147	-1.429000	0.01096	GCA	G|0.640;C|0.360	0.360	strong		0.597	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MDN1	23195	hgsc.bcm.edu	37	6	90397132	90397132	+	Missense_Mutation	SNP	G	G	C	rs34766278	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	89	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	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		
LIN9	286826	hgsc.bcm.edu	37	1	226474035	226474035	+	Splice_Site	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:226474035T>C	ENST00000328205.5	-	6	1116	c.571A>G	c.(571-573)Aga>Gga	p.R191G	LIN9_ENST00000481685.1_Splice_Site_p.R156G|LIN9_ENST00000366801.1_Splice_Site_p.R140G	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	175	Sufficient for interaction with RB1.				DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)				breast(3)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		TATTTTTACCTCCGTGGTTTT	0.348																																					p.R191G	Ovarian(197;1696 2974 11248 14117)	Atlas-SNP	.											.	LIN9	57	.	0			c.A571G						PASS	.						50.0	55.0	53.0					1																	226474035		2202	4298	6500	SO:0001630	splice_region_variant	286826	exon6			TTTACCTCCGTGG	AY166858	CCDS1553.1	1q42	2014-07-17	2014-07-17		ENSG00000183814	ENSG00000183814			30830	protein-coding gene	gene with protein product	"""TUDOR gene similar"", ""rb related pathway actor"""	609375	"""lin-9 homolog (C. elegans)"""			15538385, 23667535	Standard	NM_173083		Approved	TGS	uc001hqa.3	Q5TKA1	OTTHUMG00000037557	ENST00000328205.5:c.572+1A>G	1.37:g.226474035T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	99	5	0.050505	NM_173083	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	Missense_Mutation	SNP	ENST00000328205.5	37	CCDS1553.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.208799	0.58343	.	.	ENSG00000183814	ENST00000460719;ENST00000328205;ENST00000366808;ENST00000366801;ENST00000481685;ENST00000366807	.	.	.	5.85	5.85	0.93711	.	0.042455	0.85682	D	0.000000	D	0.86033	0.5836	M	0.93062	3.375	0.80722	D	1	D;P;D	0.62365	0.989;0.884;0.991	D;P;D	0.78314	0.916;0.891;0.991	D	0.89383	0.3683	9	0.87932	D	0	.	16.2265	0.82298	0.0:0.0:0.0:1.0	.	156;175;325	C9J5J4;Q5TKA1;B1ANK3	.;LIN9_HUMAN;.	G	151;191;246;140;156;325	.	ENSP00000329102:R191G	R	-	1	2	LIN9	224540658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.751000	0.62169	2.233000	0.73108	0.533000	0.62120	AGA	.	.	none		0.348	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091523.2	NM_173083	Missense_Mutation
LY75	4065	hgsc.bcm.edu	37	2	160673526	160673526	+	Missense_Mutation	SNP	A	A	G	rs2059696	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160673526A>G	ENST00000263636.4	-	30	4198	c.4171T>C	c.(4171-4173)Tat>Cat	p.Y1391H	LY75_ENST00000554112.1_Missense_Mutation_p.Y1391H|LY75_ENST00000553424.1_Missense_Mutation_p.Y1391H|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.Y1391H|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.Y1391H	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1391			Y -> H (in dbSNP:rs2059696).		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)	p.Y1391H(1)		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)		GTAGTATTATATTCTTCTTTG	0.284													A|||	1030	0.205671	0.0287	0.4827	5008	,	,		18449	0.2212		0.327	False		,,,				2504	0.1074				p.Y1391H		Atlas-SNP	.											LY75,NS,carcinoma,0,1	LY75	151	1	1	Substitution - Missense(1)	stomach(1)	c.T4171C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR	307,4099	165.4+/-196.9	9,289,1905	75.0	75.0	75.0		4171,4171,4171	2.0	1.0	2	dbSNP_94	75	2652,5948	423.7+/-354.4	411,1830,2059	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	83,83,83	420,2119,3964	GG,GA,AA		30.8372,6.9678,22.751	benign,benign,benign	1391/1874,1391/1818,1391/1723	160673526	2959,10047	2203	4300	6503	SO:0001583	missense	4065	exon30			TATTATATTCTTC	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.4171T>C	2.37:g.160673526A>G	ENSP00000263636:p.Tyr1391His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	543	0.24862637362637363	16	0.032520325203252036	156	0.430939226519337	122	0.21328671328671328	249	0.32849604221635886	A	9.660	1.143804	0.21205	0.069678	0.308372	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	5.65	1.99	0.26369	.	0.269362	0.19663	N	0.108922	T	0.00012	0.0000	L	0.27053	0.805	0.40886	P	0.015965000000000007	B;B;B	0.14438	0.003;0.003;0.01	B;B;B	0.15484	0.013;0.004;0.01	T	0.48833	-0.9000	9	0.15952	T	0.53	-6.7853	5.9111	0.19029	0.5812:0.1296:0.2892:0.0	rs2059696;rs17230537;rs2059696	1391;1391;1391	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	H	1391	ENSP00000451511:Y1391H;ENSP00000451446:Y1391H;ENSP00000263636:Y1391H;ENSP00000423463:Y1391H;ENSP00000421035:Y1391H	ENSP00000423463:Y1391H	Y	-	1	0	LY75;LY75-CD302	160381772	0.991000	0.36638	0.995000	0.50966	0.994000	0.84299	0.893000	0.28336	0.166000	0.19597	0.528000	0.53228	TAT	A|0.775;G|0.225	0.225	strong		0.284	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
XCL2	6846	hgsc.bcm.edu	37	1	168511284	168511284	+	Silent	SNP	T	T	C	rs4282797	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:168511284T>C	ENST00000367819.2	-	2	155	c.123A>G	c.(121-123)ccA>ccG	p.P41P		NM_003175.3	NP_003166.1	Q9UBD3	XCL2_HUMAN	chemokine (C motif) ligand 2	41					blood circulation (GO:0008015)|cell chemotaxis (GO:0060326)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			large_intestine(1)|lung(6)|ovary(1)	8	all_hematologic(923;0.215)					TTCTGCTAACTGGCAGTCGCT	0.478													T|||	1763	0.352037	0.2481	0.3818	5008	,	,		12214	0.6429		0.2117	False		,,,				2504	0.316				p.P41P		Atlas-SNP	.											XCL2,colon,carcinoma,-2,1	XCL2	18	1	0			c.A123G						PASS	.	T		779,3627		110,559,1534	139.0	116.0	124.0		123	-0.3	0.3	1	dbSNP_111	124	1024,7572		170,684,3444	yes	coding-synonymous	XCL2	NM_003175.3		280,1243,4978	CC,CT,TT		11.9125,17.6804,13.8671		41/115	168511284	1803,11199	2203	4298	6501	SO:0001819	synonymous_variant	6846	exon2			GCTAACTGGCAGT	BC070309	CCDS1273.1	1q24.2	2013-02-28	2002-08-22	2002-08-23	ENSG00000143185	ENSG00000143185		"""Endogenous ligands"""	10646	protein-coding gene	gene with protein product		604828	"""small inducible cytokine subfamily C, member 2"""	SCYC2		7875320	Standard	NM_003175		Approved	SCM-1b	uc001gfn.4	Q9UBD3	OTTHUMG00000034549	ENST00000367819.2:c.123A>G	1.37:g.168511284T>C		Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	307	45	0.14658	NM_003175		Silent	SNP	ENST00000367819.2	37	CCDS1273.1																																																																																			T|0.709;C|0.291	0.291	strong		0.478	XCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083613.1	NM_003175	
GDF3	9573	hgsc.bcm.edu	37	12	7842932	7842932	+	Missense_Mutation	SNP	C	C	T	rs12819884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	140	0	0		WXS	Illumina HiSeq	Phase_I	177	2	0.0112994	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		
FRMPD2	143162	hgsc.bcm.edu	37	10	49383976	49383976	+	Missense_Mutation	SNP	T	T	C	rs200957845		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:49383976T>C	ENST00000374201.3	-	23	3204	c.2902A>G	c.(2902-2904)Att>Gtt	p.I968V	FRMPD2_ENST00000463706.1_5'UTR|FRMPD2_ENST00000474573.1_5'UTR|FRMPD2_ENST00000407470.4_Missense_Mutation_p.I936V|FRMPD2_ENST00000305531.3_Missense_Mutation_p.I943V	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	968	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		CTGGTGTTAATGCCACCCTGA	0.532																																					p.I968V		Atlas-SNP	.											FRMPD2,NS,carcinoma,0,1	FRMPD2	157	1	0			c.A2902G						scavenged	.						3.0	1.0	1.0					10																	49383976		81	163	244	SO:0001583	missense	143162	exon23			TGTTAATGCCACC	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.2902A>G	10.37:g.49383976T>C	ENSP00000363317:p.Ile968Val	Somatic	303	1	0.00330033		WXS	Illumina HiSeq	Phase_I	265	46	0.173585	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	.	.	.	.	.	.	.	.	.	.	T	0.019	-1.452426	0.01080	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.26810	1.71;1.71;1.71	4.81	-0.335	0.12662	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.10723	0.0262	N	0.03891	-0.335	0.09310	N	1	B;B;B	0.18863	0.006;0.031;0.016	B;B;B	0.23419	0.016;0.046;0.024	T	0.39165	-0.9627	9	0.21540	T	0.41	.	9.0019	0.36088	0.0:0.3679:0.0:0.6321	.	943;968;936	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	V	968;943;936	ENSP00000363317:I968V;ENSP00000307079:I943V;ENSP00000384339:I936V	ENSP00000307079:I943V	I	-	1	0	FRMPD2	49053982	0.623000	0.27094	0.520000	0.27837	0.722000	0.41435	0.524000	0.22940	-0.339000	0.08401	0.528000	0.53228	ATT	T|0.500;C|0.500	0.500	weak		0.532	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
PPRC1	23082	hgsc.bcm.edu	37	10	103906612	103906612	+	Missense_Mutation	SNP	G	G	A	rs118161359	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:103906612G>A	ENST00000278070.2	+	9	3902	c.3863G>A	c.(3862-3864)cGa>cAa	p.R1288Q	PPRC1_ENST00000370012.1_Missense_Mutation_p.R255Q|PPRC1_ENST00000489648.1_Intron|PPRC1_ENST00000413464.2_Intron	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	1288					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)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		GGCCCTAGTCGAGTCCATGTG	0.597													G|||	46	0.0091853	0.003	0.0173	5008	,	,		17362	0.0		0.0268	False		,,,				2504	0.0031				p.R1288Q		Atlas-SNP	.											.	PPRC1	151	.	0			c.G3863A						PASS	.	G	GLN/ARG	21,4385	28.1+/-56.4	0,21,2182	88.0	76.0	80.0		3863	4.6	1.0	10	dbSNP_132	80	182,8418	82.6+/-145.2	1,180,4119	yes	missense	PPRC1	NM_015062.3	43	1,201,6301	AA,AG,GG		2.1163,0.4766,1.5608	benign	1288/1665	103906612	203,12803	2203	4300	6503	SO:0001583	missense	23082	exon9			CTAGTCGAGTCCA	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"""RNA binding motif (RRM) containing"""	30025	protein-coding gene	gene with protein product			"""peroxisome proliferative activated receptor, gamma, coactivator-related 1"""			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.3863G>A	10.37:g.103906612G>A	ENSP00000278070:p.Arg1288Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	48	39	0.8125	NM_015062	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	37	CCDS7529.1	30	0.013736263736263736	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	14.70	2.612675	0.46631	0.004766	0.021163	ENSG00000148840	ENST00000278070;ENST00000370012	T;T	0.28454	2.02;1.61	5.46	4.56	0.56223	.	0.232948	0.44688	D	0.000438	T	0.04588	0.0125	N	0.03608	-0.345	0.80722	D	1	P;B	0.36222	0.544;0.409	B;B	0.29077	0.098;0.028	T	0.10291	-1.0636	10	0.52906	T	0.07	.	14.438	0.67296	0.0:0.8461:0.1539:0.0	.	1168;1288	Q5VV67-2;Q5VV67	.;PPRC1_HUMAN	Q	1288;255	ENSP00000278070:R1288Q;ENSP00000359029:R255Q	ENSP00000278070:R1288Q	R	+	2	0	PPRC1	103896602	0.999000	0.42202	0.999000	0.59377	0.982000	0.71751	1.741000	0.38238	1.298000	0.44778	-0.502000	0.04539	CGA	G|0.982;A|0.018	0.018	strong		0.597	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	NM_015062	
CAMKK2	10645	hgsc.bcm.edu	37	12	121712077	121712077	+	Missense_Mutation	SNP	T	T	A	rs3817190	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:121712077T>A	ENST00000324774.5	-	2	1081	c.253A>T	c.(253-255)Acc>Tcc	p.T85S	CAMKK2_ENST00000412367.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000337174.3_Missense_Mutation_p.T85S|CAMKK2_ENST00000535524.1_5'UTR|CAMKK2_ENST00000446440.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000392473.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000402834.4_Missense_Mutation_p.T85S|CAMKK2_ENST00000404169.3_Missense_Mutation_p.T85S|CAMKK2_ENST00000538733.1_Missense_Mutation_p.T85S|CAMKK2_ENST00000392474.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000347034.2_Missense_Mutation_p.T85S	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	85			T -> S (in dbSNP:rs3817190). {ECO:0000269|PubMed:11395482, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872452}.		calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GACCCGGAGGTGTCAAGGGGG	0.692													T|||	2062	0.411741	0.6225	0.3084	5008	,	,		13569	0.2976		0.4076	False		,,,				2504	0.3221				p.T85S		Atlas-SNP	.											CAMKK2_ENST00000392473,NS,carcinoma,0,2	CAMKK2	87	2	0			c.A253T						scavenged	.	T	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	2469,1931		700,1069,431	20.0	24.0	23.0		253,253,253,253,253,253,253	-0.6	0.0	12	dbSNP_107	23	3539,5057		752,2035,1511	no	missense,missense,missense,missense,missense,missense,missense	CAMKK2	NM_006549.3,NM_153499.2,NM_153500.1,NM_172214.2,NM_172215.2,NM_172216.1,NM_172226.2	58,58,58,58,58,58,58	1452,3104,1942	AA,AT,TT		41.1703,43.8864,46.2296	benign,benign,benign,benign,benign,benign,benign	85/589,85/542,85/499,85/534,85/491,85/546,85/542	121712077	6008,6988	2200	4298	6498	SO:0001583	missense	10645	exon2			CGGAGGTGTCAAG	AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.253A>T	12.37:g.121712077T>A	ENSP00000312741:p.Thr85Ser	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Missense_Mutation	SNP	ENST00000324774.5	37	CCDS9216.1	936	0.42857142857142855	318	0.6463414634146342	121	0.3342541436464088	186	0.32517482517482516	311	0.4102902374670185	T	0.231	-1.020843	0.02061	0.561136	0.411703	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473;ENST00000543477;ENST00000544485	T;T;T;T;T;T;T;T;T;T;T	0.72167	-0.63;-0.6;-0.61;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;2.03;1.56	4.17	-0.591	0.11675	.	1.005170	0.08018	N	0.991504	T	0.00012	0.0000	N	0.03608	-0.345	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;0.0;0.001;0.0;0.0;0.0;0.001	T	0.43734	-0.9373	9	0.10902	T	0.67	-0.6485	2.7347	0.05237	0.3091:0.4379:0.152:0.101	rs3817190;rs17852337;rs3817190	85;85;85;85;85;85;85	Q96RR4-6;Q96RR4-2;Q96RR4-7;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;KKCC2_HUMAN;.	S	85;85;85;85;85;85;85;68;85;85;85;85	ENSP00000376266:T85S;ENSP00000321230:T85S;ENSP00000445944:T85S;ENSP00000336634:T85S;ENSP00000312741:T85S;ENSP00000388368:T85S;ENSP00000384600:T85S;ENSP00000388273:T85S;ENSP00000376265:T85S;ENSP00000444894:T85S;ENSP00000445400:T85S	ENSP00000312741:T85S	T	-	1	0	CAMKK2	120196460	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	-0.775000	0.04679	0.061000	0.16311	-0.464000	0.05259	ACC	T|0.543;A|0.457	0.457	strong		0.692	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
REV3L	5980	hgsc.bcm.edu	37	6	111696091	111696091	+	Missense_Mutation	SNP	T	T	C	rs458017	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:111696091T>C	ENST00000358835.3	-	14	3921	c.3467A>G	c.(3466-3468)tAt>tGt	p.Y1156C	REV3L_ENST00000435970.1_Missense_Mutation_p.Y1078C|REV3L_ENST00000368805.1_Missense_Mutation_p.Y1156C|REV3L_ENST00000368802.3_Missense_Mutation_p.Y1156C			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1156			Y -> C (in dbSNP:rs458017). {ECO:0000269|PubMed:10660610, ECO:0000269|PubMed:9925914, 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)		AGTCTTCTTATATACATTAGG	0.413								DNA polymerases (catalytic subunits)					T|||	202	0.0403355	0.0401	0.0677	5008	,	,		18281	0.001		0.0646	False		,,,				2504	0.0368				p.Y1156C		Atlas-SNP	.											.	REV3L	386	.	0			c.A3467G						PASS	.	T	CYS/TYR	210,4196	126.1+/-163.2	2,206,1995	100.0	107.0	104.0		3467	-4.5	0.0	6	dbSNP_80	104	579,8019	154.6+/-208.8	19,541,3739	yes	missense	REV3L	NM_002912.3	194	21,747,5734	CC,CT,TT		6.7341,4.7662,6.0674	benign	1156/3131	111696091	789,12215	2203	4299	6502	SO:0001583	missense	5980	exon13			TTCTTATATACAT	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.3467A>G	6.37:g.111696091T>C	ENSP00000351697:p.Tyr1156Cys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	53	0.53	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	88	0.040293040293040296	17	0.034552845528455285	24	0.06629834254143646	0	0.0	47	0.06200527704485488	T	0.028	-1.355458	0.01256	0.047662	0.067341	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01613	4.83;4.83;4.83;4.73	5.73	-4.51	0.03483	Ribonuclease H-like (1);	0.469052	0.24014	N	0.042349	T	0.00412	0.0013	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.43877	-0.9364	10	0.33940	T	0.23	.	7.2949	0.26387	0.1038:0.3682:0.0:0.528	rs458017;rs3194480;rs17539609;rs52811215;rs59783785;rs458017	1156	O60673	DPOLZ_HUMAN	C	1156;1156;1156;1078	ENSP00000357792:Y1156C;ENSP00000357795:Y1156C;ENSP00000351697:Y1156C;ENSP00000402003:Y1078C	ENSP00000351697:Y1156C	Y	-	2	0	REV3L	111802784	0.428000	0.25522	0.000000	0.03702	0.003000	0.03518	0.030000	0.13688	-0.810000	0.04375	-1.017000	0.02453	TAT	T|0.948;C|0.052	0.052	strong		0.413	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
LARS	51520	hgsc.bcm.edu	37	5	145499996	145499996	+	Missense_Mutation	SNP	C	C	T	rs10988	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145499996C>T	ENST00000394434.2	-	31	3429	c.3263G>A	c.(3262-3264)aGg>aAg	p.R1088K	RP11-118M9.3_ENST00000514002.1_RNA|LARS_ENST00000274562.9_Missense_Mutation_p.R1061K|LARS_ENST00000510191.1_Missense_Mutation_p.R1034K|LARS_ENST00000545646.1_Missense_Mutation_p.R1042K	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	165	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	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	
KRT84	3890	hgsc.bcm.edu	37	12	52778947	52778947	+	Silent	SNP	A	A	G	rs1791631	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52778947A>G	ENST00000257951.3	-	1	489	c.423T>C	c.(421-423)acT>acC	p.T141T	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	141	Head.				hair follicle development (GO:0001942)|nail development (GO:0035878)|regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of epidermis (GO:0030280)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(10)|skin(3)	27	all_hematologic(5;0.12)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTTGTTCACAGTCACAGCTG	0.547													A|||	1691	0.33766	0.6354	0.3242	5008	,	,		18746	0.1954		0.2068	False		,,,				2504	0.226				p.T141T		Atlas-SNP	.											.	KRT84	61	.	0			c.T423C						PASS	.	A		2513,1893	628.2+/-395.1	741,1031,431	173.0	176.0	175.0		423	2.8	1.0	12	dbSNP_89	175	1805,6795	324.5+/-316.5	180,1445,2675	no	coding-synonymous	KRT84	NM_033045.3		921,2476,3106	GG,GA,AA		20.9884,42.9641,33.2001		141/601	52778947	4318,8688	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon1			GTTCACAGTCACA	Y19209	CCDS8825.1	12q13	2013-06-25	2006-07-17	2006-07-17	ENSG00000161849	ENSG00000161849		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6461	protein-coding gene	gene with protein product	"""hard keratin type II 4"""	602766	"""keratin, hair, basic, 4"""	KRTHB4		2431943, 16831889	Standard	NM_033045		Approved	Hb-4	uc001sah.1	Q9NSB2	OTTHUMG00000169634	ENST00000257951.3:c.423T>C	12.37:g.52778947A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			A|0.685;G|0.315	0.315	strong		0.547	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045	
MUC4	4585	hgsc.bcm.edu	37	3	195507398	195507398	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195507398C>T	ENST00000463781.3	-	2	11512	c.11053G>A	c.(11053-11055)Gac>Aac	p.D3685N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3685N	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)		GAGGAAGTGTCCGTGACAGGA	0.592																																					p.D3685N		Atlas-SNP	.											MUC4_ENST00000463781,NS,lymphoid_neoplasm,+1,1	MUC4	1505	1	0			c.G11053A						scavenged	.						12.0	12.0	12.0					3																	195507398		561	1429	1990	SO:0001583	missense	4585	exon2			AAGTGTCCGTGAC	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.11053G>A	3.37:g.195507398C>T	ENSP00000417498:p.Asp3685Asn	Somatic	118	16	0.135593		WXS	Illumina HiSeq	Phase_I	144	61	0.423611	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	8.871	0.949360	0.18356	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.52057	1.16;0.68	0.743	-1.49	0.08718	.	.	.	.	.	T	0.18800	0.0451	N	0.08118	0	0.09310	N	1	P	0.42993	0.797	B	0.34452	0.183	T	0.14952	-1.0454	8	.	.	.	.	5.1792	0.15150	0.0:0.3745:0.6255:0.0	.	3557	E7ESK3	.	N	3685	ENSP00000417498:D3685N;ENSP00000420243:D3685N	.	D	-	1	0	MUC4	196992177	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-3.241000	0.00544	0.088000	0.17205	0.089000	0.15464	GAC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TTN	7273	hgsc.bcm.edu	37	2	179545859	179545859	+	Missense_Mutation	SNP	C	C	T	rs36051007	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R9852H|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000342175.6_Intron			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	64	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	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	
MFSD1	64747	hgsc.bcm.edu	37	3	158520011	158520011	+	Missense_Mutation	SNP	C	C	T	rs28364680	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:158520011C>T	ENST00000264266.8	+	1	132	c.70C>T	c.(70-72)Ccg>Tcg	p.P24S	MFSD1_ENST00000392813.4_Missense_Mutation_p.P73S|MFSD1_ENST00000415822.2_Missense_Mutation_p.P73S|RP11-379F4.9_ENST00000607044.1_RNA			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	24			P -> S (in dbSNP:rs28364680). {ECO:0000269|PubMed:14702039}.		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)			CAGAGGTGCCCCGGCCGCCCC	0.692													C|||	714	0.142572	0.1293	0.1282	5008	,	,		11497	0.1915		0.1501	False		,,,				2504	0.1125				p.P73S	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.C217T						PASS	.	C	SER/PRO,SER/PRO	517,3867		33,451,1708	13.0	15.0	14.0		217,217	3.2	0.0	3	dbSNP_125	14	968,7606		69,830,3388	no	missense,missense	MFSD1	NM_022736.2,NM_001167903.1	74,74	102,1281,5096	TT,TC,CC		11.2899,11.7929,11.4601	benign,benign	73/515,73/476	158520011	1485,11473	2192	4287	6479	SO:0001583	missense	64747	exon1			GGTGCCCCGGCCG	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.70C>T	3.37:g.158520011C>T	ENSP00000264266:p.Pro24Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	32	23	0.71875	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Missense_Mutation	SNP	ENST00000264266.8	37		343	0.15705128205128205	68	0.13821138211382114	52	0.143646408839779	107	0.18706293706293706	116	0.15303430079155672	C	17.11	3.306231	0.60305	0.117929	0.112899	ENSG00000118855	ENST00000415822;ENST00000392813;ENST00000264266;ENST00000361159	T;T;T	0.18502	2.27;2.21;2.33	5.04	3.15	0.36227	Major facilitator superfamily domain, general substrate transporter (1);	1.418460	0.04299	N	0.347069	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.001	T	0.34054	-0.9844	9	0.07325	T	0.83	.	4.8323	0.13447	0.1563:0.6111:0.1508:0.0818	rs28364680;rs59115350	73;24	C9JS94;Q9H3U5	.;MFSD1_HUMAN	S	73;73;24;24	ENSP00000403117:P73S;ENSP00000376560:P73S;ENSP00000264266:P24S	ENSP00000264266:P24S	P	+	1	0	MFSD1	160002705	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	-1.207000	0.03008	1.105000	0.41606	0.563000	0.77884	CCG	C|0.842;T|0.158	0.158	strong		0.692	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736	
ZGRF1	55345	hgsc.bcm.edu	37	4	113482146	113482146	+	Missense_Mutation	SNP	G	G	A	rs17605622	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:113482146G>A	ENST00000505019.1	-	19	4828	c.4703C>T	c.(4702-4704)tCg>tTg	p.S1568L		NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		1568			S -> L (in dbSNP:rs17605622).			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)		TATAGTTGGCGAAGACCTAAT	0.328													G|||	187	0.0373403	0.0083	0.0648	5008	,	,		18185	0.0		0.1183	False		,,,				2504	0.0123				p.S1568L		Atlas-SNP	.											.	C4orf21	223	.	0			c.C4703T						PASS	.	G	LEU/SER	84,4318	65.8+/-103.3	1,82,2118	66.0	61.0	63.0		4703	4.2	0.3	4	dbSNP_123	63	859,7735	184.5+/-232.4	44,771,3482	yes	missense	C4orf21	NM_018392.4	145	45,853,5600	AA,AG,GG		9.9953,1.9082,7.2561	benign	1568/2105	113482146	943,12053	2201	4297	6498	SO:0001583	missense	55345	exon19			GTTGGCGAAGACC																												ENST00000505019.1:c.4703C>T	4.37:g.113482146G>A	ENSP00000424737:p.Ser1568Leu	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	102	25	0.245098	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	4.932	0.173215	0.09391	0.019082	0.099953	ENSG00000138658	ENST00000505019	T	0.26373	1.74	5.95	4.19	0.49359	.	0.749772	0.12630	N	0.452224	T	0.00271	0.0008	M	0.65975	2.015	0.35547	P	0.19647499999999996	B;P	0.37997	0.202;0.614	B;B	0.19666	0.012;0.026	T	0.16247	-1.0409	9	0.26408	T	0.33	-0.0499	3.9261	0.09263	0.1428:0.1254:0.5945:0.1373	rs17605622;rs17605622	1568;26	G5EA02;B3KQX2	.;.	L	1568	ENSP00000424737:S1568L	ENSP00000404365:S466L	S	-	2	0	C4orf21	113701595	0.008000	0.16893	0.326000	0.25389	0.257000	0.26127	0.359000	0.20233	0.807000	0.34208	-0.145000	0.13849	TCG	G|0.939;A|0.061	0.061	strong		0.328	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
GPR162	27239	hgsc.bcm.edu	37	12	6935995	6935995	+	Missense_Mutation	SNP	G	G	A	rs138514784|rs138578985|rs58069762	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6935995G>A	ENST00000311268.3	+	5	2180	c.1393G>A	c.(1393-1395)Gag>Aag	p.E465K	GPR162_ENST00000382315.3_Missense_Mutation_p.E161K|LEPREL2_ENST00000251761.8_RNA|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000428545.2_Missense_Mutation_p.E181K|LEPREL2_ENST00000396725.2_RNA	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	465						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						GTTGGAGGACGAGGAGGACGA	0.652																																					p.E465K		Atlas-SNP	.											GPR162,bladder,carcinoma,0,1	GPR162	55	1	0			c.G1393A						scavenged	.	G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	50.0	62.0	58.0		541,1393	3.8	0.9	12	dbSNP_134	58	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	GPR162	NM_014449.1,NM_019858.1	56,56	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign,benign	181/305,465/589	6935995	4,13002	2203	4300	6503	SO:0001583	missense	27239	exon5			GAGGACGAGGAGG	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.1393G>A	12.37:g.6935995G>A	ENSP00000311528:p.Glu465Lys	Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	37	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	G	7.227	0.598598	0.13939	2.27E-4	3.49E-4	ENSG00000250510	ENST00000311268;ENST00000428545;ENST00000382315	T;T;T	0.43688	3.1;0.94;0.94	4.7	3.79	0.43588	.	.	.	.	.	T	0.21145	0.0509	N	0.08118	0	0.22389	N	0.999148	B;B	0.27679	0.133;0.185	B;B	0.18561	0.022;0.013	T	0.10776	-1.0615	9	0.36615	T	0.2	.	7.9273	0.29883	0.0:0.268:0.5194:0.2126	.	181;465	Q16538-2;Q16538	.;GP162_HUMAN	K	465;181;161	ENSP00000311528:E465K;ENSP00000399670:E181K;ENSP00000371752:E161K	ENSP00000311528:E465K	E	+	1	0	GPR162	6806256	0.985000	0.35326	0.882000	0.34594	0.215000	0.24574	2.459000	0.45023	1.299000	0.44798	0.491000	0.48974	GAG	G|1.000;A|0.000	0.000	weak		0.652	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
FCGR3A	2214	hgsc.bcm.edu	37	1	161565381	161565381	+	Intron	SNP	A	A	G	rs76277413	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:161565381A>G	ENST00000540048.1	-	2	94				RP11-25K21.6_ENST00000537821.2_RNA|FCGR2C_ENST00000473530.2_RNA|FCGR2C_ENST00000466542.2_RNA|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR2B_ENST00000367960.5_Intron|FCGR2B_ENST00000403078.3_Intron|FCGR2C_ENST00000543859.1_RNA			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						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)	CCAATTTGAGATGAGTAATCC	0.478													.|||	287	0.0573083	0.0166	0.085	5008	,	,		17686	0.001		0.1431	False		,,,				2504	0.0624				.		Atlas-SNP	.											.	FCGR2C	2	.	0			c.798+1A>G						PASS	.	G		77,4305		9,59,2123	256.0	243.0	247.0			2.1	0.6	1	dbSNP_131	247	808,7784		137,534,3625	no	splice-5	FCGR2C	NM_201563.4		146,593,5748	GG,GA,AA		9.4041,1.7572,6.8213			161565381	885,12089	2191	4296	6487	SO:0001627	intron_variant	9103	exon6			TTTGAGATGAGTA	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	ENST00000540048.1:c.61+34776T>C	1.37:g.161565381A>G		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	346	195	0.563584	NM_201563	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Splice_Site	SNP	ENST00000540048.1	37		115	0.052655677655677656	3	0.006097560975609756	22	0.06077348066298342	1	0.0017482517482517483	89	0.11741424802110818	-	7.021	0.558760	0.13436	0.017572	0.094041	ENSG00000244682	ENST00000543859	.	.	.	2.13	2.13	0.27403	.	.	.	.	.	T	0.36608	0.0973	.	.	.	0.45015	D	0.998035	.	.	.	.	.	.	T	0.21381	-1.0247	4	.	.	.	.	4.9939	0.14228	0.1795:0.0:0.8205:0.0	.	.	.	.	V	13	.	.	M	+	1	0	FCGR2C	159832005	1.000000	0.71417	0.643000	0.29450	0.003000	0.03518	2.075000	0.41538	0.470000	0.27294	-0.528000	0.04320	ATG	A|0.922;G|0.078	0.078	strong		0.478	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
JAG2	3714	hgsc.bcm.edu	37	14	105609335	105609335	+	Silent	SNP	A	A	G	rs10149229	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105609335A>G	ENST00000331782.3	-	26	3817	c.3414T>C	c.(3412-3414)atT>atC	p.I1138I	JAG2_ENST00000347004.2_Silent_p.I1100I	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	1138					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|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)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CCGGCCGCTCAATGGGGTTGC	0.726													G|||	3455	0.689896	0.8941	0.6571	5008	,	,		10693	0.5337		0.66	False		,,,				2504	0.6288				p.I1138I		Atlas-SNP	.											.	JAG2	69	.	0			c.T3414C						PASS	.	G	,	3661,665		1557,547,59	17.0	20.0	19.0		3414,3300	-1.2	1.0	14	dbSNP_119	19	5713,2733		1963,1787,473	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	3520,2334,532	GG,GA,AA		32.3585,15.3722,26.6051	,	1138/1239,1100/1201	105609335	9374,3398	2163	4223	6386	SO:0001819	synonymous_variant	3714	exon26			CCGCTCAATGGGG	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.3414T>C	14.37:g.105609335A>G		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	14	10	0.714286	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			A|0.286;G|0.714	0.714	strong		0.726	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
CATSPER1	117144	hgsc.bcm.edu	37	11	65787666	65787666	+	Silent	SNP	G	G	A	rs34769321|rs3829937	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65787666G>A	ENST00000312106.5	-	9	2207	c.2070C>T	c.(2068-2070)gcC>gcT	p.A690A		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	690					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						GGATCCGGGCGGCCCTCTGGG	0.662													G|||	814	0.16254	0.2065	0.1254	5008	,	,		15119	0.1181		0.16	False		,,,				2504	0.1779				p.A690A		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C2070T						PASS	.	G		904,3498	344.9+/-308.3	95,714,1392	43.0	45.0	44.0		2070	-9.2	0.0	11	dbSNP_107	44	1331,7261	257.5+/-281.5	102,1127,3067	no	coding-synonymous	CATSPER1	NM_053054.3		197,1841,4459	AA,AG,GG		15.4912,20.5361,17.2002		690/781	65787666	2235,10759	2201	4296	6497	SO:0001819	synonymous_variant	117144	exon9			CCGGGCGGCCCTC	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.2070C>T	11.37:g.65787666G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	131	62	0.473282	NM_053054	Q96P76	Silent	SNP	ENST00000312106.5	37	CCDS8127.1																																																																																			G|0.834;A|0.166	0.166	strong		0.662	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
IL2	3558	hgsc.bcm.edu	37	4	123377482	123377482	+	Silent	SNP	C	C	A	rs2069763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:123377482C>A	ENST00000226730.4	-	1	398	c.114G>T	c.(112-114)ctG>ctT	p.L38L		NM_000586.3	NP_000577.2	P60568	IL2_HUMAN	interleukin 2	38					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|immune response (GO:0006955)|natural killer cell activation (GO:0030101)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of heart contraction (GO:0045822)|negative regulation of inflammatory response (GO:0050728)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of T cell homeostatic proliferation (GO:0046013)|T cell differentiation (GO:0030217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|cytokine activity (GO:0005125)|glycosphingolipid binding (GO:0043208)|growth factor activity (GO:0008083)|interleukin-2 receptor binding (GO:0005134)|kinase activator activity (GO:0019209)			endometrium(2)|large_intestine(4)|lung(6)|skin(1)	13				LUSC - Lung squamous cell carcinoma(721;0.185)	Pseudoephedrine(DB00852)	GTAAATCCAGCAGTAAATGCT	0.333			T	TNFRSF17	intestinal T-cell lymphoma								C|||	1496	0.298722	0.0772	0.4366	5008	,	,		18545	0.4613		0.3449	False		,,,				2504	0.2853				p.L38L		Atlas-SNP	.		Dom	yes		4	4q26-q27	3558	interleukin 2		L	.	IL2	23	.	0			c.G114T	GRCh37	CS060537	IL2	S	rs2069763	PASS	.	C		558,3848	247.8+/-255.9	37,484,1682	115.0	107.0	110.0		114	1.4	0.0	4	dbSNP_96	110	2791,5809	439.8+/-359.3	452,1887,1961	no	coding-synonymous	IL2	NM_000586.3		489,2371,3643	AA,AC,CC		32.4535,12.6645,25.7497		38/154	123377482	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	3558	exon1			ATCCAGCAGTAAA	U25676	CCDS3726.1	4q26-q27	2011-07-14			ENSG00000109471	ENSG00000109471		"""Interleukins and interleukin receptors"""	6001	protein-coding gene	gene with protein product	"""T cell growth factor"""	147680				3260003	Standard	NM_000586		Approved	IL-2, TCGF	uc003ier.3	P60568	OTTHUMG00000133075	ENST00000226730.4:c.114G>T	4.37:g.123377482C>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_000586	P01585	Silent	SNP	ENST00000226730.4	37	CCDS3726.1																																																																																			C|0.718;A|0.282	0.282	strong		0.333	IL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256715.2		
CACNG3	10368	hgsc.bcm.edu	37	16	24373047	24373047	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:24373047C>T	ENST00000005284.3	+	4	2013	c.811C>T	c.(811-813)Ccc>Tcc	p.P271S		NM_006539.3	NP_006530.1	O60359	CCG3_HUMAN	calcium channel, voltage-dependent, gamma subunit 3	271					calcium ion transport (GO:0006816)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|prostate(4)|skin(2)	40				GBM - Glioblastoma multiforme(48;0.0809)		CTCCCGGGACCCCTCAAAGAT	0.567																																					p.P271S		Atlas-SNP	.											CACNG3,NS,carcinoma,-1,1	CACNG3	112	1	0			c.C811T						scavenged	.						105.0	113.0	110.0					16																	24373047		2197	4300	6497	SO:0001583	missense	10368	exon4			CGGGACCCCTCAA	AF131911	CCDS10620.1	16p12.1	2008-05-14			ENSG00000006116	ENSG00000006116		"""Calcium channel subunits"""	1407	protein-coding gene	gene with protein product		606403				10221464, 10493829	Standard	NM_006539		Approved		uc002dmf.3	O60359	OTTHUMG00000131651	ENST00000005284.3:c.811C>T	16.37:g.24373047C>T	ENSP00000005284:p.Pro271Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	137	2	0.0145985	NM_006539		Missense_Mutation	SNP	ENST00000005284.3	37	CCDS10620.1	.	.	.	.	.	.	.	.	.	.	c	16.93	3.259053	0.59321	.	.	ENSG00000006116	ENST00000005284	T	0.56275	0.47	4.93	4.93	0.64822	.	0.056656	0.64402	D	0.000001	T	0.50514	0.1620	L	0.53249	1.67	0.58432	D	0.999999	P	0.44986	0.847	B	0.39185	0.293	T	0.59069	-0.7523	10	0.59425	D	0.04	-23.7516	17.8078	0.88607	0.0:1.0:0.0:0.0	.	271	O60359	CCG3_HUMAN	S	271	ENSP00000005284:P271S	ENSP00000005284:P271S	P	+	1	0	CACNG3	24280548	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.228000	0.51270	2.266000	0.75297	0.645000	0.84053	CCC	.	.	none		0.567	CACNG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254548.1	NM_006539	
UBR5	51366	hgsc.bcm.edu	37	8	103307971	103307971	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:103307971C>T	ENST00000520539.1	-	29	4311	c.3705G>A	c.(3703-3705)tgG>tgA	p.W1235*	UBR5_ENST00000220959.4_Nonsense_Mutation_p.W1235*|UBR5_ENST00000521922.1_Nonsense_Mutation_p.W1229*|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	1235					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)			TACATTTCTCCCAACAATCAC	0.363																																					p.W1235X	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											UBR5,NS,carcinoma,-1,1	UBR5	285	1	0			c.G3705A						scavenged	.						106.0	98.0	101.0					8																	103307971		2203	4300	6503	SO:0001587	stop_gained	51366	exon29			TTTCTCCCAACAA	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.3705G>A	8.37:g.103307971C>T	ENSP00000429084:p.Trp1235*	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	266	3	0.0112782	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Nonsense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	48	13.903934	0.99769	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000521922	.	.	.	5.67	5.67	0.87782	.	0.061149	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.1358	0.98028	0.0:1.0:0.0:0.0	.	.	.	.	X	1235;1235;1229	.	ENSP00000220959:W1235X	W	-	3	0	UBR5	103377147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.506000	0.81665	2.833000	0.97629	0.585000	0.79938	TGG	.	.	none		0.363	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
FREM1	158326	hgsc.bcm.edu	37	9	14842557	14842557	+	Missense_Mutation	SNP	T	T	C	rs1353223	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:14842557T>C	ENST00000380880.3	-	9	2278	c.1495A>G	c.(1495-1497)Ata>Gta	p.I499V	FREM1_ENST00000380881.4_Missense_Mutation_p.I500V|FREM1_ENST00000422223.2_Missense_Mutation_p.I499V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	499			I -> V (in dbSNP:rs1353223).		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)		CCATCAAATATCCGGAAGACC	0.498													T|||	327	0.0652955	0.149	0.049	5008	,	,		20672	0.0		0.0765	False		,,,				2504	0.0194				p.I499V		Atlas-SNP	.											.	FREM1	261	.	0			c.A1495G						PASS	.	T	VAL/ILE	561,3519		41,479,1520	131.0	134.0	133.0		1495	5.6	1.0	9	dbSNP_88	133	599,7797		17,565,3616	yes	missense	FREM1	NM_144966.5	29	58,1044,5136	CC,CT,TT		7.1343,13.75,9.2979	probably-damaging	499/2180	14842557	1160,11316	2040	4198	6238	SO:0001583	missense	158326	exon10			CAAATATCCGGAA	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.1495A>G	9.37:g.14842557T>C	ENSP00000370262:p.Ile499Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	162	0.07417582417582418	88	0.17886178861788618	16	0.04419889502762431	0	0.0	58	0.07651715039577836	T	26.1	4.703239	0.88924	0.1375	0.071343	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.28454	1.61;1.61;1.61	5.63	5.63	0.86233	.	0.052976	0.85682	D	0.000000	T	0.00073	0.0002	L	0.35414	1.06	0.09310	P	0.99999626827	D	0.65815	0.995	P	0.58172	0.834	T	0.05037	-1.0910	9	0.14656	T	0.56	-17.6089	16.1485	0.81594	0.0:0.0:0.0:1.0	rs1353223;rs1353223	499	Q5H8C1	FREM1_HUMAN	V	500;499;499	ENSP00000370263:I500V;ENSP00000412940:I499V;ENSP00000370262:I499V	ENSP00000370257:I502V	I	-	1	0	FREM1	14832557	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.914000	0.69964	2.281000	0.76405	0.533000	0.62120	ATA	T|0.917;C|0.083	0.083	strong		0.498	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
TECPR1	25851	hgsc.bcm.edu	37	7	97873994	97873994	+	Silent	SNP	G	G	A	rs1874344	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:97873994G>A	ENST00000447648.2	-	5	719	c.420C>T	c.(418-420)taC>taT	p.Y140Y	TECPR1_ENST00000542604.1_Silent_p.Y61Y|TECPR1_ENST00000379795.3_Silent_p.Y140Y			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	140					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						AGTCGATGGCGTACGTCCACC	0.587													g|||	1513	0.302117	0.2126	0.3285	5008	,	,		18002	0.4534		0.2744	False		,,,				2504	0.2771				p.Y140Y		Atlas-SNP	.											TECPR1,NS,carcinoma,0,2	TECPR1	77	2	0			c.C420T						scavenged	.	A		774,3230		69,636,1297	91.0	96.0	94.0		420	-3.8	0.4	7	dbSNP_92	94	1969,6335		244,1481,2427	no	coding-synonymous	TECPR1	NM_015395.1		313,2117,3724	AA,AG,GG		23.7115,19.3307,22.2863		140/1166	97873994	2743,9565	2002	4152	6154	SO:0001819	synonymous_variant	25851	exon5			GATGGCGTACGTC		CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.420C>T	7.37:g.97873994G>A		Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			G|0.696;A|0.304	0.304	strong		0.587	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395	
HIVEP3	59269	hgsc.bcm.edu	37	1	41978959	41978959	+	Missense_Mutation	SNP	C	C	T	rs144265546		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:41978959C>T	ENST00000372583.1	-	8	6818	c.5933G>A	c.(5932-5934)cGt>cAt	p.R1978H	HIVEP3_ENST00000247584.5_Missense_Mutation_p.R1978H|HIVEP3_ENST00000372584.1_Missense_Mutation_p.R1978H|HIVEP3_ENST00000460604.1_5'UTR|HIVEP3_ENST00000429157.2_Missense_Mutation_p.R1978H	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1978					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)				TAGTGGTGGACGGCTGCCTGC	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		16700	0.001		0.0	False		,,,				2504	0.0				p.R1978H		Atlas-SNP	.											HIVEP3,NS,carcinoma,-1,1	HIVEP3	235	1	0			c.G5933A						PASS	.	C	HIS/ARG,HIS/ARG	0,4394		0,0,2197	59.0	66.0	64.0		5933,5933	0.9	0.1	1	dbSNP_134	64	1,8581		0,1,4290	no	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	29,29	0,1,6487	TT,TC,CC		0.0117,0.0,0.0077	benign,benign	1978/2406,1978/2407	41978959	1,12975	2197	4291	6488	SO:0001583	missense	59269	exon8			GGTGGACGGCTGC	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.5933G>A	1.37:g.41978959C>T	ENSP00000361664:p.Arg1978His	Somatic	398	1	0.00251256		WXS	Illumina HiSeq	Phase_I	266	194	0.729323	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	C	3.314	-0.140096	0.06669	0.0	1.17E-4	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.06849	3.27;3.25;3.25;3.27	4.9	0.906	0.19314	.	0.511179	0.16205	N	0.224759	T	0.04452	0.0122	N	0.17082	0.46	0.09310	N	1	B;B	0.15930	0.015;0.009	B;B	0.12156	0.007;0.003	T	0.43475	-0.9389	10	0.23891	T	0.37	-0.7167	5.8783	0.18842	0.0:0.5722:0.1291:0.2987	.	1978;1978	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	H	1978	ENSP00000361665:R1978H;ENSP00000361664:R1978H;ENSP00000247584:R1978H;ENSP00000410828:R1978H	ENSP00000247584:R1978H	R	-	2	0	HIVEP3	41751546	0.136000	0.22515	0.136000	0.22124	0.344000	0.29017	0.195000	0.17155	-0.021000	0.14009	-0.150000	0.13652	CGT	C|1.000;T|0.000	0.000	weak		0.612	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
KRTAP21-3	100288323	hgsc.bcm.edu	37	21	32090908	32090908	+	Missense_Mutation	SNP	C	C	T	rs2833031	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:32090908C>T	ENST00000444335.1	-	1	187	c.170G>A	c.(169-171)tGc>tAc	p.C57Y		NM_001164435.1	NP_001157907.1	Q3LHN1	KR213_HUMAN	keratin associated protein 21-3	57						intermediate filament (GO:0005882)											TGCTCAATGGCATTTCTTAGA	0.338													T|||	1388	0.277157	0.4864	0.1715	5008	,	,		19242	0.4792		0.0716	False		,,,				2504	0.0726				p.C57Y		Atlas-SNP	.											.	KRTAP21-3	5	.	0			c.G170A						PASS	.	T	TYR/CYS	595,789		130,335,227	43.0	40.0	41.0		170	2.6	0.0	21	dbSNP_100	41	149,3033		5,139,1447	yes	missense	KRTAP21-3	NM_001164435.1	194	135,474,1674	TT,TC,CC		4.6826,42.9913,16.2943		57/59	32090908	744,3822	692	1591	2283	SO:0001583	missense	100288323	exon1			CAATGGCATTTCT	AB180042	CCDS54481.1	21q22.11	2011-02-24			ENSG00000231068	ENSG00000231068		"""Keratin associated proteins"""	34216	protein-coding gene	gene with protein product							Standard	NM_001164435		Approved		uc021wii.1	Q3LHN1	OTTHUMG00000125533	ENST00000444335.1:c.170G>A	21.37:g.32090908C>T	ENSP00000404517:p.Cys57Tyr	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	209	83	0.397129	NM_001164435		Missense_Mutation	SNP	ENST00000444335.1	37	CCDS54481.1	611	0.27976190476190477	214	0.4349593495934959	57	0.1574585635359116	282	0.493006993006993	58	0.07651715039577836	T	1.342	-0.593954	0.03771	0.429913	0.046826	ENSG00000231068	ENST00000444335	.	.	.	2.64	2.64	0.31445	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.46442	-0.9191	4	0.87932	D	0	.	4.7304	0.12961	0.0:0.1484:0.0:0.8516	rs2833031;rs60581928	.	.	.	Y	57	.	ENSP00000404517:C57Y	C	-	2	0	KRTAP21-3	31012779	0.007000	0.16637	0.012000	0.15200	0.010000	0.07245	0.907000	0.28531	0.469000	0.27268	-0.268000	0.10319	TGC	C|0.760;T|0.240	0.240	strong		0.338	KRTAP21-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246864.1	XM_002343741	
YTHDC2	64848	hgsc.bcm.edu	37	5	112868693	112868693	+	Silent	SNP	C	C	A	rs6594732	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:112868693C>A	ENST00000161863.4	+	5	1006	c.793C>A	c.(793-795)Cgg>Agg	p.R265R	YTHDC2_ENST00000515883.1_Silent_p.R265R	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	265	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		CGCAGAGAGACGGGAAAGGAT	0.398													A|||	1668	0.333067	0.5802	0.4524	5008	,	,		17308	0.2093		0.2107	False		,,,				2504	0.1677				p.R265R		Atlas-SNP	.											.	YTHDC2	118	.	0			c.C793A						PASS	.	A		2362,2042	565.4+/-381.7	660,1042,500	94.0	99.0	97.0		793	4.4	1.0	5	dbSNP_116	97	1816,6784	733.0+/-406.9	187,1442,2671	no	coding-synonymous	YTHDC2	NM_022828.3		847,2484,3171	AA,AC,CC		21.1163,46.3669,32.1286		265/1431	112868693	4178,8826	2202	4300	6502	SO:0001819	synonymous_variant	64848	exon5			GAGAGACGGGAAA	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.793C>A	5.37:g.112868693C>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			C|0.678;A|0.322	0.322	strong		0.398	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
EPG5	57724	hgsc.bcm.edu	37	18	43508856	43508856	+	Missense_Mutation	SNP	C	C	G	rs3744999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:43508856C>G	ENST00000282041.5	-	13	2566	c.2532G>C	c.(2530-2532)gaG>gaC	p.E844D		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	844			E -> D (in dbSNP:rs3744999).		autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.E844D(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						GGTCAATGGTCTCTTGAACTC	0.398													C|||	361	0.0720847	0.0741	0.0245	5008	,	,		19859	0.0774		0.0378	False		,,,				2504	0.1329				p.E844D		Atlas-SNP	.											EPG5,NS,carcinoma,0,1	EPG5	199	1	1	Substitution - Missense(1)	stomach(1)	c.G2532C						PASS	.	C	ASP/GLU	264,3434		12,240,1597	107.0	99.0	102.0		2532	-2.8	1.0	18	dbSNP_107	102	280,7922		2,276,3823	yes	missense	EPG5	NM_020964.2	45	14,516,5420	GG,GC,CC		3.4138,7.139,4.5714	benign	844/2580	43508856	544,11356	1849	4101	5950	SO:0001583	missense	57724	exon13			AATGGTCTCTTGA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.2532G>C	18.37:g.43508856C>G	ENSP00000282041:p.Glu844Asp	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	129	0.059065934065934064	38	0.07723577235772358	8	0.022099447513812154	54	0.0944055944055944	29	0.03825857519788918	C	5.230	0.227927	0.09916	0.07139	0.034138	ENSG00000152223	ENST00000282041	T	0.09723	2.95	6.17	-2.81	0.05805	.	0.891536	0.09963	N	0.733186	T	0.00178	0.0005	N	0.14661	0.345	0.29489	N	0.855755	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.45264	-0.9273	10	0.09590	T	0.72	-6.0562	0.5909	0.00728	0.2525:0.1862:0.3063:0.2551	rs3744999;rs52796425;rs3744999	844;844	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	D	844	ENSP00000282041:E844D	ENSP00000282041:E844D	E	-	3	2	EPG5	41762854	0.002000	0.14202	0.954000	0.39281	0.996000	0.88848	-1.468000	0.02350	-0.550000	0.06183	-0.137000	0.14449	GAG	C|0.927;G|0.073	0.073	strong		0.398	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
HS3ST5	222537	hgsc.bcm.edu	37	6	114378722	114378722	+	Missense_Mutation	SNP	A	A	T	rs17793043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:114378722A>T	ENST00000312719.5	-	5	1928	c.740T>A	c.(739-741)aTt>aAt	p.I247N	RP3-399L15.3_ENST00000519104.1_RNA|HS3ST5_ENST00000411826.1_Missense_Mutation_p.I247N|RP3-399L15.3_ENST00000519270.1_RNA|RP3-399L15.3_ENST00000523087.1_RNA			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	247			I -> N (in dbSNP:rs17793043).		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)			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)		AAATTGCTCAATTGGAAAGTA	0.443													A|||	15	0.00299521	0.0	0.0043	5008	,	,		19731	0.0		0.0119	False		,,,				2504	0.0				p.I247N		Atlas-SNP	.											.	HS3ST5	80	.	0			c.T740A						PASS	.	A	ASN/ILE	7,4399	12.9+/-30.5	0,7,2196	192.0	185.0	187.0		740	6.1	1.0	6	dbSNP_123	187	90,8510	51.1+/-111.2	0,90,4210	yes	missense	HS3ST5	NM_153612.3	149	0,97,6406	TT,TA,AA		1.0465,0.1589,0.7458	possibly-damaging	247/347	114378722	97,12909	2203	4300	6503	SO:0001583	missense	222537	exon2			TGCTCAATTGGAA	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.740T>A	6.37:g.114378722A>T	ENSP00000427888:p.Ile247Asn	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	199	105	0.527638	NM_153612	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	37	CCDS34517.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	A	11.94	1.789740	0.31685	0.001589	0.010465	ENSG00000249853	ENST00000312719;ENST00000411826	D;D	0.81579	-1.51;-1.51	6.06	6.06	0.98353	Sulfotransferase domain (1);	0.055484	0.64402	D	0.000001	T	0.65471	0.2694	L	0.58101	1.795	0.47698	D	0.999498	B	0.32302	0.363	B	0.27796	0.083	T	0.66826	-0.5825	10	0.15499	T	0.54	.	16.6093	0.84858	1.0:0.0:0.0:0.0	rs17793043;rs17793043	247	Q8IZT8	HS3S5_HUMAN	N	247	ENSP00000427888:I247N;ENSP00000440332:I247N	ENSP00000427888:I247N	I	-	2	0	HS3ST5	114485415	1.000000	0.71417	0.992000	0.48379	0.873000	0.50193	6.369000	0.73109	2.324000	0.78689	0.533000	0.62120	ATT	A|0.994;T|0.006	0.006	strong		0.443	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612	
TRIM4	89122	hgsc.bcm.edu	37	7	99489868	99489868	+	Missense_Mutation	SNP	G	G	C	rs33998596	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99489868G>C	ENST00000355947.2	-	7	1550	c.1421C>G	c.(1420-1422)tCt>tGt	p.S474C	TRIM4_ENST00000349062.2_Missense_Mutation_p.S448C	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	474	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		S -> C (in dbSNP:rs33998596).		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)				TGAGACAGAAGAACAAGAAAA	0.517													G|||	237	0.0473243	0.0681	0.0403	5008	,	,		21310	0.002		0.0577	False		,,,				2504	0.0603				p.S474C		Atlas-SNP	.											.	TRIM4	33	.	0			c.C1421G						PASS	.	G	CYS/SER,CYS/SER	284,4122	157.4+/-190.3	15,254,1934	115.0	110.0	112.0		1421,1343	0.7	0.0	7	dbSNP_126	112	618,7982	161.4+/-214.4	18,582,3700	yes	missense,missense	TRIM4	NM_033017.3,NM_033091.2	112,112	33,836,5634	CC,CG,GG		7.186,6.4458,6.9353	possibly-damaging,possibly-damaging	474/501,448/475	99489868	902,12104	2203	4300	6503	SO:0001583	missense	89122	exon7			ACAGAAGAACAAG	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.1421C>G	7.37:g.99489868G>C	ENSP00000348216:p.Ser474Cys	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Missense_Mutation	SNP	ENST00000355947.2	37	CCDS5679.1	89	0.04075091575091575	29	0.05894308943089431	13	0.03591160220994475	2	0.0034965034965034965	45	0.059366754617414245	G	9.995	1.231779	0.22626	0.064458	0.07186	ENSG00000146833	ENST00000355947;ENST00000349062;ENST00000542799	T;T	0.70749	-0.51;-0.51	2.64	0.724	0.18236	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.08403	0.0209	L	0.36672	1.1	0.09310	N	1	B;B	0.25351	0.102;0.124	B;B	0.19391	0.015;0.025	T	0.04767	-1.0928	9	0.33141	T	0.24	.	6.5013	0.22170	0.0:0.1971:0.6012:0.2017	rs33998596	448;474	Q9C037-2;Q9C037	.;TRIM4_HUMAN	C	474;448;304	ENSP00000348216:S474C;ENSP00000275736:S448C	ENSP00000275736:S448C	S	-	2	0	TRIM4	99327804	0.000000	0.05858	0.002000	0.10522	0.411000	0.31082	0.485000	0.22324	0.181000	0.19994	0.655000	0.94253	TCT	G|0.943;C|0.057	0.057	strong		0.517	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017	
OR2C3	81472	hgsc.bcm.edu	37	1	247695427	247695427	+	Missense_Mutation	SNP	C	C	G	rs34220133	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247695427C>G	ENST00000366487.3	-	2	748	c.387G>C	c.(385-387)agG>agC	p.R129S	GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000531662.1_Intron|GCSAML_ENST00000527084.1_Intron|GCSAML_ENST00000366490.3_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000463359.1_Intron|GCSAML_ENST00000527541.1_Intron	NM_198074.4	NP_932340	Q8N628	OR2C3_HUMAN	olfactory receptor, family 2, subfamily C, member 3	129			R -> S (in dbSNP:rs34220133).			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)			AATGGAGTGGCCTGCAGATGG	0.592													C|||	346	0.0690895	0.0333	0.0504	5008	,	,		21239	0.002		0.1372	False		,,,				2504	0.1299				p.R129S		Atlas-SNP	.											OR2C3,NS,carcinoma,0,1	OR2C3	92	1	0			c.G387C						PASS	.	C	SER/ARG	219,4187	134.5+/-170.7	6,207,1990	66.0	68.0	67.0		387	2.0	0.9	1	dbSNP_126	67	1411,7189	271.1+/-289.3	117,1177,3006	yes	missense	OR2C3	NM_198074.4	110	123,1384,4996	GG,GC,CC		16.407,4.9705,12.5327	probably-damaging	129/321	247695427	1630,11376	2203	4300	6503	SO:0001583	missense	81472	exon2			GAGTGGCCTGCAG	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.387G>C	1.37:g.247695427C>G	ENSP00000355443:p.Arg129Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	146	57	0.390411	NM_198074	Q5JQS4|Q6IEZ1|Q8NGW7	Missense_Mutation	SNP	ENST00000366487.3	37	CCDS1634.2	143	0.06547619047619048	12	0.024390243902439025	25	0.06906077348066299	2	0.0034965034965034965	104	0.13720316622691292	C	17.27	3.347422	0.61183	0.049705	0.16407	ENSG00000196242	ENST00000366487	T	0.01304	5.03	3.89	2.0	0.26442	GPCR, rhodopsin-like superfamily (1);	0.430133	0.16469	U	0.213067	T	0.00012	0.0000	L	0.46157	1.445	0.42774	P	0.0061550000000000216	B	0.33694	0.421	B	0.28139	0.086	T	0.47394	-0.9121	9	0.87932	D	0	.	7.8991	0.29723	0.0:0.7916:0.0:0.2084	rs34220133	129	Q8N628	OR2C3_HUMAN	S	129	ENSP00000355443:R129S	ENSP00000355443:R129S	R	-	3	2	OR2C3	245762050	0.000000	0.05858	0.853000	0.33588	0.950000	0.60333	-2.208000	0.01229	0.418000	0.25898	0.650000	0.86243	AGG	C|0.891;G|0.109	0.109	strong		0.592	OR2C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097626.2	NM_198074	
ZNF155	7711	hgsc.bcm.edu	37	19	44496070	44496070	+	Silent	SNP	A	A	G	rs431509	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44496070A>G	ENST00000270014.2	+	4	347	c.219A>G	c.(217-219)caA>caG	p.Q73Q	ZNF155_ENST00000590615.1_Silent_p.Q73Q|ZNF155_ENST00000407951.2_Silent_p.Q84Q	NM_001260487.1|NM_198089.2	NP_001247416|NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	73	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				CAGCAACCCAAAGAGAAGGGA	0.478													A|||	2257	0.450679	0.5575	0.4942	5008	,	,		21633	0.5466		0.2893	False		,,,				2504	0.3425				p.Q84Q	NSCLC(61;554 1277 20909 42067 42312)	Atlas-SNP	.											.	ZNF155	30	.	0			c.A252G						PASS	.	A	,	2295,2111	601.2+/-389.7	607,1081,515	149.0	149.0	149.0		219,219	-2.0	0.1	19	dbSNP_80	149	2443,6157	403.2+/-347.7	355,1733,2212	no	coding-synonymous,coding-synonymous	ZNF155	NM_003445.2,NM_198089.1	,	962,2814,2727	GG,GA,AA		28.407,47.9119,36.4293	,	73/539,73/539	44496070	4738,8268	2203	4300	6503	SO:0001819	synonymous_variant	7711	exon5			AACCCAAAGAGAA	U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920		"""Zinc fingers, C2H2-type"", ""-"""	12940	protein-coding gene	gene with protein product		604086	"""zinc finger protein 155 (pHZ-96)"""			7557990	Standard	NM_001260486		Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000270014.2:c.219A>G	19.37:g.44496070A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_001260488	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	Silent	SNP	ENST00000270014.2	37	CCDS12634.1																																																																																			A|0.624;G|0.376	0.376	strong		0.478	ZNF155-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460074.1	NM_003445	
DHRS4L1	728635	hgsc.bcm.edu	37	14	24517936	24517936	+	RNA	SNP	G	G	T	rs201609317	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24517936G>T	ENST00000558293.1	+	0	584					NR_102693.1																						GCCTCAACAAGACCTTGGCCA	0.493													G|||	148	0.0295527	0.0106	0.0115	5008	,	,		24710	0.0377		0.0139	False		,,,				2504	0.0757				p.K197N		Atlas-SNP	.											.	.	.	.	0			c.G591T						PASS	.	G	ASN/LYS	5,4401	4.2+/-10.8	0,5,2198	181.0	182.0	181.0		591	3.5	1.0	14	dbSNP_134	181	5,8595	1.2+/-3.3	0,5,4295	no	missense	DHRS4L1	NM_001082488.1	94	0,10,6493	TT,TG,GG		0.0581,0.1135,0.0769	probably-damaging	197/282	24517936	10,12996	2203	4300	6503			728635	exon8			CAACAAGACCTTG																													14.37:g.24517936G>T		Somatic	1054	1	0.000948767		WXS	Illumina HiSeq	Phase_I	1915	480	0.250653	NM_001082488		Missense_Mutation	SNP	ENST00000558293.1	37		.	.	.	.	.	.	.	.	.	.	G	4.561	0.104274	0.08731	0.001135	5.81E-4	ENSG00000225766	ENST00000397065	.	.	.	4.47	3.55	0.40652	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	.	.	.	.	T	0.72439	0.3460	M	0.89287	3.02	0.38516	D	0.948595	P	0.51653	0.947	P	0.58077	0.832	T	0.80390	-0.1402	7	0.72032	D	0.01	.	7.1481	0.25595	0.201:0.0:0.799:0.0	.	197	P0CG22	DR4L1_HUMAN	N	197	.	ENSP00000380255:K197N	K	+	3	2	AL136295.1	23587776	1.000000	0.71417	1.000000	0.80357	0.074000	0.17049	1.553000	0.36255	2.311000	0.77944	0.400000	0.26472	AAG	.	.	weak		0.493	RP11-468E2.9-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417272.1		
ZSWIM2	151112	hgsc.bcm.edu	37	2	187697883	187697883	+	Missense_Mutation	SNP	A	A	G	rs10164815	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187697883A>G	ENST00000295131.2	-	7	944	c.905T>C	c.(904-906)aTt>aCt	p.I302T		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	302				I -> T (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			CTTTTCTTCAATCTCATTTTT	0.294													A|||	872	0.174121	0.4213	0.1066	5008	,	,		13175	0.0208		0.1113	False		,,,				2504	0.1104				p.I302T		Atlas-SNP	.											ZSWIM2,NS,carcinoma,-1,1	ZSWIM2	119	1	0			c.T905C						PASS	.	A	THR/ILE	1740,2658	500.1+/-364.6	342,1056,801	113.0	108.0	110.0		905	-4.1	0.1	2	dbSNP_119	110	970,7618	203.8+/-246.7	44,882,3368	yes	missense	ZSWIM2	NM_182521.2	89	386,1938,4169	GG,GA,AA		11.2948,39.5634,20.8686	benign	302/634	187697883	2710,10276	2199	4294	6493	SO:0001583	missense	151112	exon7			TCTTCAATCTCAT	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.905T>C	2.37:g.187697883A>G	ENSP00000295131:p.Ile302Thr	Somatic	312	1	0.00320513		WXS	Illumina HiSeq	Phase_I	283	128	0.452297	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	A	5.584	0.292590	0.10567	0.395634	0.112948	ENSG00000163012	ENST00000295131	T	0.22743	1.94	5.28	-4.09	0.03951	.	0.950517	0.08736	N	0.901379	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B	0.10296	0.003	B	0.09377	0.004	T	0.47598	-0.9105	9	0.02654	T	1	0.2256	0.3454	0.00340	0.2072:0.265:0.1812:0.3466	rs10164815;rs17845944;rs17858925;rs52821540;rs59170533;rs10164815	302	Q8NEG5	ZSWM2_HUMAN	T	302	ENSP00000295131:I302T	ENSP00000295131:I302T	I	-	2	0	ZSWIM2	187406128	0.035000	0.19736	0.059000	0.19551	0.932000	0.56968	-0.045000	0.12003	-0.275000	0.09219	0.477000	0.44152	ATT	A|0.809;G|0.191	0.191	strong		0.294	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
PSPH	5723	hgsc.bcm.edu	37	7	56088780	56088780	+	Silent	SNP	G	G	A	rs75497420	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:56088780G>A	ENST00000395471.3	-	4	931	c.126C>T	c.(124-126)gaC>gaT	p.D42D	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Silent_p.D42D			P78330	SERB_HUMAN	phosphoserine phosphatase	42					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CTGACACCGCGTCCTCAACGC	0.423																																					p.D42D		Atlas-SNP	.											.	PSPH	23	.	0			c.C126T						PASS	.						153.0	116.0	129.0					7																	56088780		2203	4300	6503	SO:0001819	synonymous_variant	5723	exon4			CACCGCGTCCTCA	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.126C>T	7.37:g.56088780G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	275	23	0.0836364	NM_004577	B2RCR5|Q7Z3S5	Silent	SNP	ENST00000395471.3	37	CCDS5522.1																																																																																			G|0.957;A|0.044	0.044	strong		0.423	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
PINX1	54984	hgsc.bcm.edu	37	8	10689212	10689212	+	Silent	SNP	C	C	T	rs12375394	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:10689212C>T	ENST00000314787.3	-	4	383	c.264G>A	c.(262-264)ctG>ctA	p.L88L	PINX1_ENST00000520018.2_5'Flank|SOX7_ENST00000554914.1_Silent_p.L88L|SOX7_ENST00000553390.1_Silent_p.L88L|PINX1_ENST00000519088.1_Silent_p.L88L|PINX1_ENST00000426190.2_Silent_p.L86L	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	127	0	0		WXS	Illumina HiSeq	Phase_I	171	63	0.368421	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	
MTMR14	64419	hgsc.bcm.edu	37	3	9711141	9711141	+	Missense_Mutation	SNP	T	T	A	rs189614064	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:9711141T>A	ENST00000296003.4	+	5	641	c.519T>A	c.(517-519)gaT>gaA	p.D173E	MTMR14_ENST00000353332.5_Missense_Mutation_p.D173E|MTMR14_ENST00000351233.5_Missense_Mutation_p.D173E|MTMR14_ENST00000420925.1_Intron	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	173					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(2)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	21	Medulloblastoma(99;0.227)					CCTGGGCAGATGTGGAGGACG	0.622													T|||	5	0.000998403	0.0	0.0029	5008	,	,		18559	0.001		0.002	False		,,,				2504	0.0				p.D173E		Atlas-SNP	.											.	MTMR14	43	.	0			c.T519A						PASS	.	T	GLU/ASP,GLU/ASP,GLU/ASP	1,4271		0,1,2135	174.0	193.0	187.0		519,519,519	3.1	0.3	3		187	32,8458		0,32,4213	yes	missense,missense,missense	MTMR14	NM_001077525.2,NM_001077526.2,NM_022485.4	45,45,45	0,33,6348	AA,AT,TT		0.3769,0.0234,0.2586	benign,benign,benign	173/651,173/599,173/539	9711141	33,12729	2136	4245	6381	SO:0001583	missense	64419	exon5			GGCAGATGTGGAG	BC001674	CCDS43043.1, CCDS43044.1, CCDS43045.1	3p26	2011-06-09	2006-12-18	2006-12-18	ENSG00000163719	ENSG00000163719		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	26190	protein-coding gene	gene with protein product	"""egg-derived tyrosine phosphatase homolog (Drosophila)"""	611089	"""chromosome 3 open reading frame 29"""	C3orf29		15186772	Standard	NM_022485		Approved	FLJ22405, FLJ90311, hJumpy, hEDTP	uc003brz.3	Q8NCE2	OTTHUMG00000155111	ENST00000296003.4:c.519T>A	3.37:g.9711141T>A	ENSP00000296003:p.Asp173Glu	Somatic	345	1	0.00289855		WXS	Illumina HiSeq	Phase_I	310	138	0.445161	NM_022485	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Missense_Mutation	SNP	ENST00000296003.4	37	CCDS43043.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	2	0.002638522427440633	T	10.12	1.263495	0.23136	2.34E-4	0.003769	ENSG00000163719	ENST00000353332;ENST00000296003;ENST00000351233;ENST00000419048	.	.	.	5.55	3.13	0.36017	.	0.345887	0.36665	N	0.002468	T	0.22781	0.0550	N	0.17674	0.51	0.29607	N	0.847221	B;B;B	0.20459	0.001;0.045;0.001	B;B;B	0.20384	0.003;0.029;0.001	T	0.17992	-1.0351	9	0.17832	T	0.49	-0.2856	5.6671	0.17700	0.0:0.146:0.1443:0.7097	.	173;173;173	Q8NCE2-3;Q8NCE2-2;Q8NCE2	.;.;MTMRE_HUMAN	E	173	.	ENSP00000296003:D173E	D	+	3	2	MTMR14	9686141	0.032000	0.19561	0.348000	0.25681	0.994000	0.84299	0.094000	0.15107	0.386000	0.24997	-0.323000	0.08544	GAT	T|0.998;A|0.002	0.002	strong		0.622	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48598823	48598823	+	Missense_Mutation	SNP	A	A	G	rs156631	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48598823A>G	ENST00000599921.1	-	7	964	c.607T>C	c.(607-609)Tct>Cct	p.S203P	PLA2G4C_ENST00000599111.1_Missense_Mutation_p.S213P|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.S203P|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.S203P			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	203	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		S -> P (in dbSNP:rs156631). {ECO:0000269|PubMed:10085124, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		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)		CCCAGTGCAGAGAAGCCAGCG	0.527													G|||	3151	0.629193	0.7784	0.5014	5008	,	,		19060	0.8681		0.3797	False		,,,				2504	0.5286				p.S213P		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.T637C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER	3143,1263	432.6+/-343.3	1133,877,193	117.0	134.0	128.0		637,607,607	2.2	0.8	19	dbSNP_79	128	3215,5385	652.3+/-400.9	591,2033,1676	yes	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	74,74,74	1724,2910,1869	GG,GA,AA		37.3837,28.6655,48.8851	benign,benign,benign	213/552,203/528,203/542	48598823	6358,6648	2203	4300	6503	SO:0001583	missense	8605	exon7			GTGCAGAGAAGCC	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.607T>C	19.37:g.48598823A>G	ENSP00000469473:p.Ser203Pro	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	1350	0.6181318681318682	380	0.7723577235772358	184	0.5082872928176796	503	0.8793706293706294	283	0.3733509234828496	G	0.020	-1.436880	0.01098	0.713345	0.373837	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.04119	3.7;3.7	3.31	2.22	0.28083	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.167772	0.39985	N	0.001211	T	0.00012	0.0000	N	0.00327	-1.64	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	9	0.13470	T	0.59	-6.9264	6.3932	0.21599	0.2736:0.0:0.7264:0.0	rs156631;rs3745739;rs17358791;rs56790404;rs156631	203	Q9UP65	PA24C_HUMAN	P	203	ENSP00000346228:S203P;ENSP00000400036:S203P	ENSP00000346228:S203P	S	-	1	0	PLA2G4C	53290635	0.974000	0.33945	0.765000	0.31456	0.483000	0.33249	0.859000	0.27858	0.506000	0.28125	-0.971000	0.02607	TCT	T|0.003;G|0.559	0.559	strong		0.527	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
BMP1	649	hgsc.bcm.edu	37	8	22021517	22021517	+	5'Flank	SNP	G	G	A	rs1124	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:22021517G>A	ENST00000306385.5	+	0	0				BMP1_ENST00000397814.3_5'Flank|BMP1_ENST00000397816.3_5'Flank|SFTPC_ENST00000521315.1_Missense_Mutation_p.S180N|SFTPC_ENST00000437090.2_3'UTR|BMP1_ENST00000306349.8_5'Flank|SFTPC_ENST00000524255.1_Missense_Mutation_p.S133N|BMP1_ENST00000354870.5_5'Flank|SFTPC_ENST00000318561.3_Missense_Mutation_p.S186N|SFTPC_ENST00000522109.1_3'UTR|SFTPC_ENST00000520605.1_Intron	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	279	0	0		WXS	Illumina HiSeq	Phase_I	293	290	0.989761	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	
DNAJB1	3337	hgsc.bcm.edu	37	19	14629138	14629138	+	Silent	SNP	C	C	T	rs141518218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14629138C>T	ENST00000254322.2	-	1	94	c.24G>A	c.(22-24)acG>acA	p.T8T	DNAJB1_ENST00000396969.4_Intron	NM_006145.1	NP_006136.1	P25685	DNJB1_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 1	8	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				chaperone cofactor-dependent protein refolding (GO:0070389)|chaperone mediated protein folding requiring cofactor (GO:0051085)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(1328;0.0476)		CCAGGCCCAACGTCTGGTAGT	0.711													C|||	8	0.00159744	0.0	0.0014	5008	,	,		9495	0.0		0.004	False		,,,				2504	0.0031				p.T8T		Atlas-SNP	.											.	DNAJB1	38	.	0			c.G24A						PASS	.	C		8,4394		0,8,2193	27.0	26.0	27.0		24	1.7	1.0	19	dbSNP_134	27	67,8527		0,67,4230	no	coding-synonymous	DNAJB1	NM_006145.1		0,75,6423	TT,TC,CC		0.7796,0.1817,0.5771		8/341	14629138	75,12921	2201	4297	6498	SO:0001819	synonymous_variant	3337	exon1			GCCCAACGTCTGG	D49547	CCDS12312.1, CCDS74295.1	19p13.12	2014-08-12			ENSG00000132002	ENSG00000132002		"""Heat shock proteins / DNAJ (HSP40)"""	5270	protein-coding gene	gene with protein product	"""radial spoke 16 homolog B (Chlamydomonas)"""	604572		HSPF1		8975727, 8250930	Standard	XM_006722733		Approved	Hsp40, Sis1, RSPH16B	uc002myz.1	P25685	OTTHUMG00000183289	ENST00000254322.2:c.24G>A	19.37:g.14629138C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	36	20	0.555556	NM_006145	B4DX52	Silent	SNP	ENST00000254322.2	37	CCDS12312.1																																																																																			C|0.995;T|0.005	0.005	strong		0.711	DNAJB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465987.1	NM_006145	
TOP2A	7153	hgsc.bcm.edu	37	17	38546274	38546274	+	Silent	SNP	A	A	C	rs17680289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38546274A>C	ENST00000423485.1	-	34	4568	c.4410T>G	c.(4408-4410)acT>acG	p.T1470T	Y_RNA_ENST00000410949.1_RNA	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1470					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)	AATCATCAGAAGTGGATGGCT	0.433													A|||	34	0.00678914	0.0015	0.0101	5008	,	,		17725	0.0		0.0209	False		,,,				2504	0.0041				p.T1470T		Atlas-SNP	.											.	TOP2A	124	.	0			c.T4410G						PASS	.	A		13,3797		0,13,1892	69.0	66.0	67.0		4410	0.4	0.8	17	dbSNP_123	67	163,8085		1,161,3962	no	coding-synonymous	TOP2A	NM_001067.3		1,174,5854	CC,CA,AA		1.9762,0.3412,1.4596		1470/1532	38546274	176,11882	1905	4124	6029	SO:0001819	synonymous_variant	7153	exon34			ATCAGAAGTGGAT		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.4410T>G	17.37:g.38546274A>C		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	166	87	0.524096	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			A|0.988;C|0.012	0.012	strong		0.433	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1		
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs200267449		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	283	0	0		WXS	Illumina HiSeq	Phase_I	298	34	0.114094	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	
IBTK	25998	hgsc.bcm.edu	37	6	82900811	82900811	+	Missense_Mutation	SNP	G	G	A	rs9449444	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:82900811G>A	ENST00000306270.7	-	25	4103	c.3554C>T	c.(3553-3555)gCc>gTc	p.A1185V	IBTK_ENST00000510291.1_Missense_Mutation_p.A1170V|IBTK_ENST00000503631.1_Missense_Mutation_p.A984V	NM_015525.2	NP_056340.2	Q9P2D0	IBTK_HUMAN	inhibitor of Bruton agammaglobulinemia tyrosine kinase	1185			A -> V (in dbSNP:rs9449444). {ECO:0000269|PubMed:11577348, ECO:0000269|PubMed:15489334}.		negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein tyrosine kinase activity (GO:0061099)|release of sequestered calcium ion into cytosol (GO:0051209)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine kinase inhibitor activity (GO:0030292)			central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(10)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	54		all_cancers(76;3.38e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.0037)		BRCA - Breast invasive adenocarcinoma(397;0.0901)		TGGTTTGGGGGCTTTTGAAGG	0.338													G|||	1236	0.246805	0.2519	0.3055	5008	,	,		13863	0.2014		0.2276	False		,,,				2504	0.2648				p.A1185V		Atlas-SNP	.											.	IBTK	128	.	0			c.C3554T						PASS	.	G	VAL/ALA	1064,3322		144,776,1273	103.0	94.0	97.0		3554	4.0	0.5	6	dbSNP_119	97	1772,6814		188,1396,2709	yes	missense	IBTK	NM_015525.2	64	332,2172,3982	AA,AG,GG		20.6382,24.259,21.8625	benign	1185/1354	82900811	2836,10136	2193	4293	6486	SO:0001583	missense	25998	exon25			TTGGGGGCTTTTG	AF235049	CCDS34490.1, CCDS75486.1	6q14.3	2013-01-10	2003-10-06	2003-10-08	ENSG00000005700	ENSG00000005700		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	17853	protein-coding gene	gene with protein product		606457	"""Bruton agammaglobulinemia tyrosine kinase inhibitor"""	BTKI		11577348	Standard	XM_006715453		Approved	DKFZP564B116, BTBD26	uc003pjl.1	Q9P2D0	OTTHUMG00000015102	ENST00000306270.7:c.3554C>T	6.37:g.82900811G>A	ENSP00000305721:p.Ala1185Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_015525	Q2QKU2|Q2QKU3|Q2QKU4|Q5TFD7|Q5TFD9|Q8IUQ9|Q8IUY7|Q8TAI4|Q9HBI8|Q9Y3T8	Missense_Mutation	SNP	ENST00000306270.7	37	CCDS34490.1	528	0.24175824175824176	119	0.241869918699187	109	0.3011049723756906	123	0.21503496503496503	177	0.23350923482849603	G	2.125	-0.400526	0.04865	0.24259	0.206382	ENSG00000005700	ENST00000306270;ENST00000503631;ENST00000510291	T;T;T	0.27402	1.98;1.67;1.98	5.81	4.02	0.46733	.	1.048820	0.07361	N	0.884126	T	0.06826	0.0174	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B	0.18610	0.001;0.0;0.029;0.0	B;B;B;B	0.17433	0.003;0.002;0.018;0.002	T	0.31752	-0.9932	9	0.26408	T	0.33	3.0471	8.5571	0.33487	0.1472:0.128:0.7248:0.0	rs9449444;rs17719603;rs17845821;rs17858788;rs52808118;rs61275733;rs9449444	984;1170;136;1185	E9PDR5;E7EPI0;B3KX60;Q9P2D0	.;.;.;IBTK_HUMAN	V	1185;984;1170	ENSP00000305721:A1185V;ENSP00000422762:A984V;ENSP00000426405:A1170V	ENSP00000305721:A1185V	A	-	2	0	IBTK	82957530	0.380000	0.25131	0.500000	0.27589	0.254000	0.26022	1.309000	0.33539	0.787000	0.33731	0.650000	0.86243	GCC	G|0.756;A|0.244	0.244	strong		0.338	IBTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041337.2	NM_015525	
LIPK	643414	hgsc.bcm.edu	37	10	90512306	90512306	+	Missense_Mutation	SNP	G	G	C	rs1214464	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:90512306G>C	ENST00000404190.1	+	9	993	c.993G>C	c.(991-993)atG>atC	p.M331I		NM_001080518.1	NP_001073987.1	Q5VXJ0	LIPK_HUMAN	lipase, family member K	331			M -> I (in dbSNP:rs1214464).		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	12		Colorectal(252;0.0381)		Colorectal(12;7.03e-05)|COAD - Colon adenocarcinoma(12;8.33e-05)		TTACTAAGATGGAAGTTCCAA	0.323													G|||	927	0.185104	0.0068	0.2781	5008	,	,		18940	0.2877		0.2097	False		,,,				2504	0.229				p.M331I		Atlas-SNP	.											.	LIPK	50	.	0			c.G993C						PASS	.	G	ILE/MET	181,3549		7,167,1691	39.0	36.0	37.0		993	3.7	1.0	10	dbSNP_87	37	1687,6529		201,1285,2622	yes	missense	LIPK	NM_001080518.1	10	208,1452,4313	CC,CG,GG		20.5331,4.8525,15.637	possibly-damaging	331/400	90512306	1868,10078	1865	4108	5973	SO:0001583	missense	643414	exon9			TAAGATGGAAGTT		CCDS44455.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000204021	ENSG00000204021			23444	protein-coding gene	gene with protein product		613922	"""lipase-like, ab-hydrolase domain containing 2"""	LIPL2			Standard	NM_001080518		Approved	bA186O14.2	uc010qmv.2	Q5VXJ0	OTTHUMG00000018693	ENST00000404190.1:c.993G>C	10.37:g.90512306G>C	ENSP00000383900:p.Met331Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	39	36	0.923077	NM_001080518	A7KIH8	Missense_Mutation	SNP	ENST00000404190.1	37	CCDS44455.1	404	0.184981684981685	4	0.008130081300813009	79	0.21823204419889503	168	0.2937062937062937	153	0.20184696569920843	G	14.84	2.655169	0.47467	0.048525	0.205331	ENSG00000204021	ENST00000404190	T	0.62498	0.02	5.65	3.69	0.42338	Alpha/beta hydrolase fold-1 (1);	0.373592	0.26991	N	0.021464	T	0.00012	0.0000	N	0.12920	0.275	0.30831	P	0.7366900000000001	B	0.30281	0.275	B	0.35899	0.213	T	0.11665	-1.0578	9	0.09590	T	0.72	-12.5189	10.4283	0.44391	0.0:0.1445:0.7055:0.15	rs1214464;rs56611384;rs1214464	331	Q5VXJ0	LIPK_HUMAN	I	331	ENSP00000383900:M331I	ENSP00000383900:M331I	M	+	3	0	LIPK	90502286	0.997000	0.39634	0.997000	0.53966	0.991000	0.79684	2.593000	0.46180	1.583000	0.49898	0.655000	0.94253	ATG	G|0.809;C|0.191	0.191	strong		0.323	LIPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049253.2	XM_061222	
KCNMB1	3779	hgsc.bcm.edu	37	5	169810796	169810796	+	Missense_Mutation	SNP	C	C	T	rs11739136	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:169810796C>T	ENST00000274629.4	-	3	635	c.193G>A	c.(193-195)Gag>Aag	p.E65K	KCNIP1_ENST00000518527.1_Intron|KCNMB1_ENST00000521859.1_Missense_Mutation_p.E65K|KCNIP1_ENST00000377360.4_Intron	NM_004137.3	NP_004128.1	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 1	65			E -> K (has a protective effect against diastolic hypertension; dbSNP:rs11739136). {ECO:0000269|PubMed:15057310}.		blood coagulation (GO:0007596)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to calcium ion (GO:0051592)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			endometrium(1)|large_intestine(1)|lung(7)|ovary(2)	11	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)	Miconazole(DB01110)|Procaine(DB00721)	CCCTTCAGCTCCTCCTGGTCC	0.582													C|||	474	0.0946486	0.053	0.1412	5008	,	,		20766	0.1369		0.0964	False		,,,				2504	0.0726				p.S65T		Atlas-SNP	.											.	KCNMB1	38	.	0			c.T193A	GRCh37	CM041786	KCNMB1	M	rs11739136	PASS	.	C	,LYS/GLU	266,4140	149.5+/-183.7	12,242,1949	128.0	100.0	109.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,193	3.6	1.0	5	dbSNP_120	109	870,7730	197.5+/-242.1	50,770,3480	yes	intron,missense	KCNMB1,KCNIP1	NM_001034838.1,NM_004137.2	,56	62,1012,5429	TT,TC,CC		10.1163,6.0372,8.7344	,benign	,65/192	169810796	1136,11870	2203	4300	6503	SO:0001583	missense	3779	exon3			TCAGCTCCTCCTG	AF035046	CCDS4373.1	5q34	2012-02-23			ENSG00000145936	ENSG00000145936		"""Potassium channels"""	6285	protein-coding gene	gene with protein product	"""BK channel beta subunit"""	603951				8799178, 9888999	Standard	NM_004137		Approved	hslo-beta	uc003maq.2	Q16558	OTTHUMG00000130439	ENST00000274629.4:c.193G>A	5.37:g.169810796C>T	ENSP00000274629:p.Glu65Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	NM_004137	O00707|O00708|P78475|Q53YR0|Q8TAX3|Q93005	Missense_Mutation	SNP	ENST00000274629.4	37	CCDS4373.1	212	0.09706959706959707	20	0.04065040650406504	51	0.1408839779005525	68	0.11888111888111888	73	0.09630606860158311	C	15.48	2.845846	0.51164	0.060372	0.101163	ENSG00000145936	ENST00000274629;ENST00000521859	T;T	0.10763	2.84;2.84	5.7	3.59	0.41128	.	0.102225	0.64402	D	0.000003	T	0.00073	0.0002	L	0.27053	0.805	0.34848	P	0.25866999999999996	B;B	0.21071	0.037;0.051	B;B	0.19946	0.027;0.012	T	0.35624	-0.9781	8	.	.	.	.	8.0511	0.30579	0.0:0.7393:0.1654:0.0952	rs11739136;rs52831846;rs60174556;rs11739136	65;65	Q16558-2;Q16558	.;KCMB1_HUMAN	K	65	ENSP00000274629:E65K;ENSP00000427940:E65K	.	E	-	1	0	KCNMB1	169743374	0.960000	0.32886	0.999000	0.59377	0.964000	0.63967	0.608000	0.24223	1.403000	0.46800	0.655000	0.94253	GAG	C|0.910;T|0.090	0.090	strong		0.582	KCNMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252830.3		
MAP7D1	55700	hgsc.bcm.edu	37	1	36642420	36642420	+	Silent	SNP	T	T	C	rs475591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:36642420T>C	ENST00000373151.2	+	8	1572	c.1356T>C	c.(1354-1356)tcT>tcC	p.S452S	MAP7D1_ENST00000316156.4_Silent_p.S415S|MAP7D1_ENST00000373150.4_Silent_p.S420S|MAP7D1_ENST00000373148.4_5'Flank|MAP7D1_ENST00000474796.1_3'UTR	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	452					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)				CCCGCCTCTCTGCCAGCACCG	0.642													C|||	3758	0.750399	0.8896	0.781	5008	,	,		11779	0.9137		0.5755	False		,,,				2504	0.5521				p.S452S		Atlas-SNP	.											.	MAP7D1	62	.	0			c.T1356C						PASS	.	C		3491,741		1485,521,110	10.0	18.0	16.0		1356	-10.1	0.0	1	dbSNP_83	16	4850,3516		1484,1882,817	no	coding-synonymous	MAP7D1	NM_018067.3		2969,2403,927	CC,CT,TT		42.0273,17.5095,33.7911		452/842	36642420	8341,4257	2116	4183	6299	SO:0001819	synonymous_variant	55700	exon8			CCTCTCTGCCAGC	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.1356T>C	1.37:g.36642420T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	11	8	0.727273	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1	1660	0.76007326007326	437	0.8882113821138211	270	0.7458563535911602	523	0.9143356643356644	430	0.5672823218997362	C	8.864	0.947593	0.18356	0.824905	0.579727	ENSG00000116871	ENST00000530975	.	.	.	5.04	-10.1	0.00402	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.21314	-1.0249	3	.	.	.	-15.0184	0.7178	0.00935	0.2173:0.1783:0.2234:0.381	rs475591;rs60771385	.	.	.	R	35	.	.	C	+	1	0	MAP7D1	36415007	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-7.226000	0.00041	-2.763000	0.00369	-1.032000	0.02404	TGC	T|0.240;C|0.760	0.760	strong		0.642	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
MYCBPAP	84073	hgsc.bcm.edu	37	17	48606537	48606537	+	Missense_Mutation	SNP	C	C	G	rs1133818	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48606537C>G	ENST00000323776.5	+	18	3003	c.2841C>G	c.(2839-2841)agC>agG	p.S947R	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.S910R	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)			ACACCCAGAGCCTGCACAGTG	0.542													G|||	4057	0.810104	0.9153	0.6988	5008	,	,		17926	0.8819		0.7336	False		,,,				2504	0.7515				p.S947R		Atlas-SNP	.											.	MYCBPAP	135	.	0			c.C2841G						PASS	.	G	ARG/SER	3922,484	221.7+/-238.7	1753,416,34	37.0	41.0	39.0		2841	5.3	0.6	17	dbSNP_86	39	6269,2331	387.7+/-342.3	2297,1675,328	yes	missense	MYCBPAP	NM_032133.4	110	4050,2091,362	GG,GC,CC		27.1047,10.985,21.6439	possibly-damaging	947/985	48606537	10191,2815	2203	4300	6503	SO:0001583	missense	84073	exon18			CCAGAGCCTGCAC	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.2841C>G	17.37:g.48606537C>G	ENSP00000323184:p.Ser947Arg	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	1777	0.8136446886446886	456	0.926829268292683	258	0.712707182320442	507	0.8863636363636364	556	0.7335092348284961	G	3.009	-0.204353	0.06180	0.89015	0.728953	ENSG00000136449	ENST00000323776;ENST00000436259	T;T	0.20200	2.09;2.09	5.26	5.26	0.73747	.	0.198671	0.43110	N	0.000611	T	0.00012	0.0000	N	0.00099	-2.14	0.54753	P	1.2000000000012001E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.38067	-0.9678	9	0.02654	T	1	-23.3303	13.166	0.59571	0.0:0.1604:0.8396:0.0	rs1133818;rs3178519;rs3195892;rs11559079;rs17421945;rs17642482;rs17856810;rs52811849;rs58726894;rs1133818	910	Q8TBZ2	MYBPP_HUMAN	R	947;910	ENSP00000323184:S947R;ENSP00000397209:S910R	ENSP00000323184:S947R	S	+	3	2	MYCBPAP	45961536	1.000000	0.71417	0.610000	0.28997	0.752000	0.42762	0.855000	0.27805	1.239000	0.43787	-0.120000	0.15030	AGC	C|0.198;G|0.802	0.802	strong		0.542	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
RPAP1	26015	hgsc.bcm.edu	37	15	41827757	41827757	+	Missense_Mutation	SNP	T	T	A	rs2297382	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:41827757T>A	ENST00000304330.4	-	5	610	c.494A>T	c.(493-495)aAg>aTg	p.K165M	RPAP1_ENST00000561603.1_Missense_Mutation_p.K165M|RPAP1_ENST00000568413.1_5'Flank	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	165			K -> M (in dbSNP:rs2297382).			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)		TGATGGGCCCTTGGCTTCAGC	0.522													T|||	712	0.142173	0.4017	0.0922	5008	,	,		19046	0.0149		0.0537	False		,,,				2504	0.0491				p.K165M		Atlas-SNP	.											.	RPAP1	111	.	0			c.A494T						PASS	.	T	MET/LYS	1534,2872	485.8+/-360.4	251,1032,920	88.0	89.0	89.0		494	-2.5	0.0	15	dbSNP_100	89	517,8083	145.1+/-200.9	12,493,3795	yes	missense	RPAP1	NM_015540.2	95	263,1525,4715	AA,AT,TT		6.0116,34.8162,15.7696	benign	165/1394	41827757	2051,10955	2203	4300	6503	SO:0001583	missense	26015	exon5			GGGCCCTTGGCTT	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.494A>T	15.37:g.41827757T>A	ENSP00000306123:p.Lys165Met	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	67	52	0.776119	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	279	0.12774725274725274	196	0.3983739837398374	34	0.09392265193370165	10	0.017482517482517484	39	0.051451187335092345	T	15.70	2.909962	0.52439	0.348162	0.060116	ENSG00000103932	ENST00000304330	T	0.12672	2.66	5.26	-2.47	0.06442	.	1.431580	0.03677	N	0.244940	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.31040	0.305	B	0.33295	0.161	T	0.46091	-0.9216	9	0.72032	D	0.01	-12.1361	5.4209	0.16400	0.1357:0.3919:0.0:0.4725	rs2297382;rs57017522;rs2297382	165	Q9BWH6	RPAP1_HUMAN	M	165	ENSP00000306123:K165M	ENSP00000306123:K165M	K	-	2	0	RPAP1	39615049	0.003000	0.15002	0.000000	0.03702	0.532000	0.34746	-0.115000	0.10741	-0.316000	0.08690	-0.696000	0.03686	AAG	T|0.855;A|0.145	0.145	strong		0.522	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
GALNT6	11226	hgsc.bcm.edu	37	12	51771040	51771040	+	Silent	SNP	T	T	C	rs2277379	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:51771040T>C	ENST00000543196.2	-	3	808	c.603A>G	c.(601-603)ctA>ctG	p.L201L	GALNT6_ENST00000356317.3_Silent_p.L201L|GALNT6_ENST00000603203.1_5'Flank			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	201	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	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)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GGGTGGTGTGTAGGACGCTGT	0.617													T|||	538	0.107428	0.0469	0.1585	5008	,	,		19747	0.1726		0.0497	False		,,,				2504	0.1452				p.L201L		Atlas-SNP	.											.	GALNT6	63	.	0			c.A603G						PASS	.	T		208,4198	127.4+/-164.3	7,194,2002	139.0	108.0	118.0		603	-7.9	0.5	12	dbSNP_100	118	338,8262	116.8+/-176.5	5,328,3967	no	coding-synonymous	GALNT6	NM_007210.3		12,522,5969	CC,CT,TT		3.9302,4.7208,4.1981		201/623	51771040	546,12460	2203	4300	6503	SO:0001819	synonymous_variant	11226	exon4			GGTGTGTAGGACG	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"""Glycosyltransferase family 2 domain containing"""	4128	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 6"""	605148	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"""			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.603A>G	12.37:g.51771040T>C		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	246	129	0.52439	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Silent	SNP	ENST00000543196.2	37	CCDS8813.1																																																																																			T|0.930;C|0.070	0.070	strong		0.617	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210	
MBTPS1	8720	hgsc.bcm.edu	37	16	84115393	84115393	+	Silent	SNP	G	G	A	rs12933523	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:84115393G>A	ENST00000343411.3	-	11	1902	c.1407C>T	c.(1405-1407)ctC>ctT	p.L469L	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	469	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						GATAGGCTCTGAGCAGATCGA	0.592													G|||	471	0.0940495	0.0287	0.1153	5008	,	,		14673	0.1131		0.1779	False		,,,				2504	0.0613				p.L469L		Atlas-SNP	.											.	MBTPS1	85	.	0			c.C1407T						PASS	.	G		245,4155	143.1+/-178.2	4,237,1959	100.0	94.0	96.0		1407	-3.9	0.0	16	dbSNP_121	96	1554,7046	291.7+/-300.5	130,1294,2876	no	coding-synonymous	MBTPS1	NM_003791.2		134,1531,4835	AA,AG,GG		18.0698,5.5682,13.8385		469/1053	84115393	1799,11201	2200	4300	6500	SO:0001819	synonymous_variant	8720	exon11			GGCTCTGAGCAGA	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.1407C>T	16.37:g.84115393G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	78	10	0.128205	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																			G|0.869;A|0.131	0.131	strong		0.592	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
PCDHB7	56129	hgsc.bcm.edu	37	5	140552774	140552774	+	Missense_Mutation	SNP	G	G	A	rs17286891	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140552774G>A	ENST00000231137.3	+	1	532	c.358G>A	c.(358-360)Gaa>Aaa	p.E120K		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	120	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> K (in dbSNP:rs17286891).		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)			TTTCCGTGCTGAACTATGGGT	0.448													G|||	248	0.0495208	0.003	0.121	5008	,	,		18654	0.0159		0.1044	False		,,,				2504	0.0399				p.E120K		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G358A						PASS	.	G	LYS/GLU	97,4309	77.8+/-116.1	1,95,2107	65.0	69.0	68.0		358	3.7	1.0	5	dbSNP_123	68	938,7662	204.2+/-247.0	52,834,3414	yes	missense	PCDHB7	NM_018940.2	56	53,929,5521	AA,AG,GG		10.907,2.2015,7.9579	benign	120/794	140552774	1035,11971	2203	4300	6503	SO:0001583	missense	56129	exon1			CGTGCTGAACTAT	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.358G>A	5.37:g.140552774G>A	ENSP00000231137:p.Glu120Lys	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	132	0.06043956043956044	4	0.008130081300813009	38	0.10497237569060773	10	0.017482517482517484	80	0.10554089709762533	G	14.12	2.442001	0.43326	0.022015	0.10907	ENSG00000113212	ENST00000231137	T	0.52983	0.64	4.61	3.74	0.42951	.	.	.	.	.	T	0.01489	0.0048	M	0.87456	2.885	0.51012	P	9.80000000000425E-5	B	0.18461	0.028	B	0.20955	0.032	T	0.37731	-0.9693	8	0.72032	D	0.01	.	9.1941	0.37217	0.1712:0.0:0.8288:0.0	rs17286891;rs17844447;rs56500957;rs59948906;rs17286891	120	Q9Y5E2	PCDB7_HUMAN	K	120	ENSP00000231137:E120K	ENSP00000231137:E120K	E	+	1	0	PCDHB7	140532958	0.044000	0.20184	0.983000	0.44433	0.828000	0.46876	1.888000	0.39708	1.045000	0.40225	0.655000	0.94253	GAA	G|0.934;A|0.066	0.066	strong		0.448	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
FLG	2312	hgsc.bcm.edu	37	1	152280471	152280471	+	Missense_Mutation	SNP	C	C	G	rs78179835		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152280471C>G	ENST00000368799.1	-	3	6926	c.6891G>C	c.(6889-6891)gaG>gaC	p.E2297D	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2297	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTCTGGAGCTCTCTGCAGAGT	0.547									Ichthyosis																												p.E2297D		Atlas-SNP	.											.	FLG	900	.	0			c.G6891C						PASS	.	C	ASP/GLU	403,4003		10,383,1810	272.0	285.0	281.0		6891	-4.0	0.0	1	dbSNP_131	281	921,7679		0,921,3379	no	missense	FLG	NM_002016.1	45	10,1304,5189	GG,GC,CC		10.7093,9.1466,10.1799	benign	2297/4062	152280471	1324,11682	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GGAGCTCTCTGCA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6891G>C	1.37:g.152280471C>G	ENSP00000357789:p.Glu2297Asp	Somatic	615	0	0		WXS	Illumina HiSeq	Phase_I	974	246	0.252567	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	4.465	0.086112	0.08583	0.091466	0.107093	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.00760	5.73	3.12	-3.95	0.04118	.	.	.	.	.	T	0.00109	0.0003	N	0.03209	-0.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28073	-1.0055	8	0.02654	T	1	.	8.7493	0.34605	0.1106:0.6338:0.2556:0.0	.	2297	P20930	FILA_HUMAN	D	2297;207	ENSP00000357789:E2297D	ENSP00000271820:E207D	E	-	3	2	FLG	150547095	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.925000	0.03992	-0.492000	0.06687	-1.941000	0.00496	GAG	.	.	weak		0.547	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
IRAK1BP1	134728	hgsc.bcm.edu	37	6	79577412	79577412	+	Missense_Mutation	SNP	C	C	G	rs41269339	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:79577412C>G	ENST00000369940.2	+	1	224	c.119C>G	c.(118-120)cCc>cGc	p.P40R		NM_001010844.2	NP_001010844.1	Q5VVH5	IKBP1_HUMAN	interleukin-1 receptor-associated kinase 1 binding protein 1	40	Intrinsically disordered.				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)		TTACGCCACCCCCTCTCCTCA	0.652													C|||	72	0.014377	0.0023	0.0259	5008	,	,		16173	0.0		0.0457	False		,,,				2504	0.0051				p.P40R		Atlas-SNP	.											.	IRAK1BP1	18	.	0			c.C119G						PASS	.	C	ARG/PRO	43,4363	44.6+/-78.6	0,43,2160	57.0	56.0	56.0		119	2.0	0.0	6	dbSNP_127	56	330,8270	110.4+/-170.8	10,310,3980	yes	missense	IRAK1BP1	NM_001010844.1	103	10,353,6140	GG,GC,CC		3.8372,0.9759,2.8679	benign	40/261	79577412	373,12633	2203	4300	6503	SO:0001583	missense	134728	exon1			GCCACCCCCTCTC	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.119C>G	6.37:g.79577412C>G	ENSP00000358956:p.Pro40Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_001010844		Missense_Mutation	SNP	ENST00000369940.2	37	CCDS34488.1	39	0.017857142857142856	0	0.0	9	0.024861878453038673	0	0.0	30	0.0395778364116095	C	8.257	0.810375	0.16537	0.009759	0.038372	ENSG00000146243	ENST00000369940	.	.	.	3.96	2.05	0.26809	.	0.399954	0.25408	N	0.030891	T	0.09686	0.0238	L	0.32530	0.975	0.09310	N	1	B	0.34015	0.435	B	0.30855	0.121	T	0.15954	-1.0419	8	.	.	.	-5.8883	8.9476	0.35769	0.3979:0.6021:0.0:0.0	rs41269339;rs61748613	40	Q5VVH5	IKBP1_HUMAN	R	40	.	.	P	+	2	0	IRAK1BP1	79634131	0.000000	0.05858	0.022000	0.16811	0.003000	0.03518	0.300000	0.19156	0.861000	0.35504	-0.226000	0.12346	CCC	C|0.975;G|0.025	0.025	strong		0.652	IRAK1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041296.2	XM_059729	
MAP3K10	4294	hgsc.bcm.edu	37	19	40711892	40711892	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40711892G>A	ENST00000253055.3	+	5	1551	c.1263G>A	c.(1261-1263)cgG>cgA	p.R421R	AC118344.1_ENST00000408124.1_RNA	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	421	Leucine-zipper 2.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						AGCTGCGGCGGCGGGAGCAGG	0.687																																					p.R421R		Atlas-SNP	.											MAP3K10,right_upper_lobe,carcinoma,+1,1	MAP3K10	70	1	0			c.G1263A						scavenged	.						18.0	20.0	19.0					19																	40711892		2198	4294	6492	SO:0001819	synonymous_variant	4294	exon5			GCGGCGGCGGGAG	X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6849	protein-coding gene	gene with protein product	"""MKN28 kinase"", ""mixed lineage kinase 2"", ""MKN28 derived nonreceptor_type serine/threonine kinase"""	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.1263G>A	19.37:g.40711892G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	126	2	0.015873	NM_002446	Q12761|Q14871	Silent	SNP	ENST00000253055.3	37	CCDS12549.1																																																																																			.	.	none		0.687	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446	
NFATC4	4776	hgsc.bcm.edu	37	14	24843620	24843620	+	Silent	SNP	T	T	C	rs2295298	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24843620T>C	ENST00000250373.4	+	6	1962	c.1821T>C	c.(1819-1821)acT>acC	p.T607T	NFATC4_ENST00000555167.1_Silent_p.T142T|NFATC4_ENST00000557451.1_Silent_p.T537T|NFATC4_ENST00000556279.1_Silent_p.T639T|NFATC4_ENST00000554591.1_Silent_p.T670T|NFATC4_ENST00000424781.2_Silent_p.T620T|NFATC4_ENST00000555802.1_5'UTR|NFATC4_ENST00000553879.1_Silent_p.T537T|NFATC4_ENST00000413692.2_Silent_p.T670T|NFATC4_ENST00000539237.2_Silent_p.T639T|NFATC4_ENST00000554344.1_Silent_p.T537T|NFATC4_ENST00000554966.1_Silent_p.T620T|NFATC4_ENST00000554050.1_Silent_p.T607T|NFATC4_ENST00000555393.1_5'UTR|NFATC4_ENST00000556169.1_Silent_p.T595T|NFATC4_ENST00000553708.1_Silent_p.T607T|NFATC4_ENST00000554473.1_Silent_p.T142T|NFATC4_ENST00000557767.1_5'UTR|NFATC4_ENST00000555590.1_Silent_p.T620T|NFATC4_ENST00000553469.1_Silent_p.T639T|NFATC4_ENST00000554661.1_Silent_p.T537T|NFATC4_ENST00000556759.1_Silent_p.T142T|NFATC4_ENST00000422617.3_Silent_p.T595T|NFATC4_ENST00000555453.1_Silent_p.T595T	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	607	IPT/TIG.				cellular respiration (GO:0045333)|cellular response to lithium ion (GO:0071285)|cellular response to UV (GO:0034644)|heart development (GO:0007507)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of synaptic plasticity (GO:0048167)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|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 involved in negative regulation of transcription (GO:0001078)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(7)|liver(4)|lung(12)|ovary(1)|skin(2)	34				GBM - Glioblastoma multiforme(265;0.018)		TGGTACTGACTGGCTCCAACT	0.637													T|||	1425	0.284545	0.0741	0.3876	5008	,	,		17306	0.1528		0.5885	False		,,,				2504	0.319				p.T670T		Atlas-SNP	.											.	NFATC4	115	.	0			c.T2010C						PASS	.	T	,,,,	692,3714	290.7+/-281.1	61,570,1572	79.0	61.0	67.0		2010,1821,1611,2010,1821	-1.8	1.0	14	dbSNP_100	67	5202,3398	637.7+/-399.3	1559,2084,657	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFATC4	NM_001136022.1,NM_001198965.1,NM_001198966.1,NM_001198967.1,NM_004554.4	,,,,	1620,2654,2229	CC,CT,TT		39.5116,15.7059,45.3175	,,,,	670/965,607/795,537/833,670/858,607/903	24843620	5894,7112	2203	4300	6503	SO:0001819	synonymous_variant	4776	exon7			ACTGACTGGCTCC	BC053855	CCDS9629.1, CCDS45089.1, CCDS55909.1, CCDS55910.1, CCDS55911.1, CCDS73625.1	14q11.2	2009-11-24			ENSG00000100968	ENSG00000100968		"""Nuclear factor of activated T-cells"""	7778	protein-coding gene	gene with protein product		602699				7749981	Standard	NM_004554		Approved	NFAT3	uc010tok.2	Q14934	OTTHUMG00000029351	ENST00000250373.4:c.1821T>C	14.37:g.24843620T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	191	189	0.989529	NM_001198967	B4DDG5|B4DY55|B5B2U7|B5B2U8|B5B2U9|B5B2V0|B5B2V1|B5B2V2|B5B2V3|B5B2V4|B5B2V5|B5B2V7|B5B2V8|B5B2V9|B5B2W0|B5B2W1|B5B2W2|B5B2W3|B5B2W4|B5B2W5|B5B2W6|B5B2W7|B5B2W8|B5B2W9|B5B2X0|Q7Z598|Q96H68	Silent	SNP	ENST00000250373.4	37	CCDS9629.1																																																																																			T|0.629;C|0.371	0.371	strong		0.637	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554	
TCP11L1	55346	hgsc.bcm.edu	37	11	33094059	33094059	+	Missense_Mutation	SNP	C	C	T	rs118146715	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:33094059C>T	ENST00000334274.4	+	10	1767	c.1367C>T	c.(1366-1368)tCg>tTg	p.S456L	TCP11L1_ENST00000432887.1_Missense_Mutation_p.S456L|TCP11L1_ENST00000531632.2_Missense_Mutation_p.S456L|TCP11L1_ENST00000324357.9_Missense_Mutation_p.S235L	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	456						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						TACCTTGCCTCGGGTCATCAG	0.468													C|||	35	0.00698882	0.0008	0.013	5008	,	,		21564	0.0		0.0209	False		,,,				2504	0.0041				p.S456L		Atlas-SNP	.											.	TCP11L1	40	.	0			c.C1367T						PASS	.	C	LEU/SER,LEU/SER	19,4385	25.3+/-52.1	0,19,2183	146.0	142.0	143.0		1367,1367	4.5	0.9	11	dbSNP_132	143	204,8392	89.4+/-151.6	3,198,4097	yes	missense,missense	TCP11L1	NM_001145541.1,NM_018393.3	145,145	3,217,6280	TT,TC,CC		2.3732,0.4314,1.7154	benign,benign	456/510,456/510	33094059	223,12777	2202	4298	6500	SO:0001583	missense	55346	exon10			TTGCCTCGGGTCA	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 1"""				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.1367C>T	11.37:g.33094059C>T	ENSP00000335595:p.Ser456Leu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	156	71	0.455128	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	37	CCDS7882.1	22	0.010073260073260074	0	0.0	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	8.952	0.968328	0.18659	0.004314	0.023732	ENSG00000176148	ENST00000334274;ENST00000531632;ENST00000432887;ENST00000324357	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	5.41	4.49	0.54785	.	0.251591	0.41194	D	0.000930	T	0.03651	0.0104	L	0.31476	0.935	0.53005	D	0.999963	B	0.24043	0.096	B	0.16722	0.016	T	0.09618	-1.0666	10	0.07175	T	0.84	-13.5004	15.6932	0.77473	0.0:0.8509:0.1491:0.0	.	456	Q9NUJ3	T11L1_HUMAN	L	456;456;456;235	ENSP00000335595:S456L;ENSP00000433067:S456L;ENSP00000395070:S456L;ENSP00000316279:S235L	ENSP00000316279:S235L	S	+	2	0	TCP11L1	33050635	0.993000	0.37304	0.912000	0.35992	0.958000	0.62258	3.009000	0.49552	1.243000	0.43853	0.313000	0.20887	TCG	C|0.986;T|0.014	0.014	strong		0.468	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
HLA-A	3105	hgsc.bcm.edu	37	6	29911063	29911063	+	Missense_Mutation	SNP	T	T	G	rs386698553|rs199474484|rs199474485	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29911063T>G	ENST00000396634.1	+	5	703	c.362T>G	c.(361-363)aTa>aGa	p.I121R	HLA-A_ENST00000376806.5_Missense_Mutation_p.I121R|HLA-A_ENST00000376802.2_Missense_Mutation_p.I121R|HLA-A_ENST00000376809.5_Missense_Mutation_p.I121R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	121	Alpha-2.		M -> I (in allele A*31:03 and allele A*31:04).		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						ACCATCCAGATAATGTATGGC	0.667									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|||	1562	0.311901	0.3003	0.3746	5008	,	,		10766	0.3294		0.3688	False		,,,				2504	0.2065				p.I121R		Atlas-SNP	.											.	HLA-A	89	.	0			c.T362G						PASS	.						21.0	17.0	19.0					6																	29911063		1482	2625	4107	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TCCAGATAATGTA	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.362T>G	6.37:g.29911063T>G	ENSP00000379873:p.Ile121Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	105	38	0.361905	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	655	0.2999084249084249	141	0.2865853658536585	98	0.27071823204419887	166	0.2902097902097902	250	0.32981530343007914	.	5.687	0.311295	0.10789	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00008	9.58;9.58;9.58;9.58	3.78	-7.56	0.01322	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	7739.210000	0.00447	N	0.000092	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B;B	0.18166	0.006;0.011;0.006;0.026;0.006	B;B;B;B;B	0.25291	0.011;0.047;0.011;0.059;0.011	T	0.16364	-1.0405	8	0.02654	T	1	.	1.804	0.03077	0.1442:0.2086:0.2216:0.4257	rs3180267;rs17409608;rs41543913	121;121;121;121;121	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	R	121	ENSP00000379873:I121R;ENSP00000366002:I121R;ENSP00000366005:I121R;ENSP00000365998:I121R	ENSP00000348012:I121R	I	+	2	0	HLA-A	30019042	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-3.990000	0.00318	-2.187000	0.00759	-3.159000	0.00058	ATA	G|0.303;T|0.697	0.303	strong		0.667	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
COL18A1	80781	hgsc.bcm.edu	37	21	46929467	46929467	+	Silent	SNP	G	G	A	rs1050351	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:46929467G>A	ENST00000359759.4	+	38	4713	c.4692G>A	c.(4690-4692)gcG>gcA	p.A1564A	SLC19A1_ENST00000567670.1_Intron|COL18A1_ENST00000400337.2_Silent_p.A1149A|COL18A1_ENST00000355480.5_Silent_p.A1329A|SLC19A1_ENST00000468508.1_5'Flank			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1564	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)		TGCGGCCGGCGCGACCCACAA	0.731													G|||	2522	0.503594	0.4985	0.5331	5008	,	,		9473	0.5744		0.4235	False		,,,				2504	0.499				p.A1326A		Atlas-SNP	.											.	COL18A1	129	.	0			c.G3978A						PASS	.	G	,	1341,2045		325,691,677	3.0	5.0	4.0		3987,3447	-8.6	0.0	21	dbSNP_86	4	2702,4614		621,1460,1577	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	946,2151,2254	AA,AG,GG		36.9328,39.6043,37.778	,	1329/1520,1149/1340	46929467	4043,6659	1693	3658	5351	SO:0001819	synonymous_variant	80781	exon39			GCCGGCGCGACCC		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.4692G>A	21.37:g.46929467G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	11	7	0.636364	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37		1064	0.48717948717948717	243	0.49390243902439024	168	0.46408839779005523	338	0.5909090909090909	315	0.4155672823218997	G	0.442	-0.897882	0.02472	0.396043	0.369328	ENSG00000182871	ENST00000423214	.	.	.	4.3	-8.61	0.00885	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.000000000032756E-6	.	.	.	.	.	.	T	0.25745	-1.0123	3	.	.	.	.	1.8031	0.03075	0.4365:0.2004:0.2121:0.151	rs1050351;rs3190648;rs17416842;rs58486368;rs1050351	.	.	.	H	134	.	.	R	+	2	0	COL18A1	45753895	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.970000	0.00668	-3.489000	0.00153	-1.036000	0.02392	CGC	G|0.516;A|0.484	0.484	strong		0.731	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
ITGB6	3694	hgsc.bcm.edu	37	2	160968628	160968628	+	Silent	SNP	A	A	G	rs16844790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160968628A>G	ENST00000283249.2	-	13	2301	c.2064T>C	c.(2062-2064)aaT>aaC	p.N688N	ITGB6_ENST00000409967.2_Silent_p.N581N|ITGB6_ENST00000409872.1_Silent_p.N688N|ITGB6_ENST00000428609.2_Silent_p.N646N	NM_001282353.1|NM_001282354.1|NM_001282388.1	NP_001269282.1|NP_001269283.1|NP_001269317.1	P18564	ITB6_HUMAN	integrin, beta 6	688					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						TTTTCCCCTCATTATCTGTAG	0.403													A|||	1074	0.214457	0.2247	0.4222	5008	,	,		18655	0.1796		0.1551	False		,,,				2504	0.1503				p.N688N		Atlas-SNP	.											.	ITGB6	68	.	0			c.T2064C						PASS	.	A		927,3479	355.4+/-313.0	96,735,1372	220.0	199.0	206.0		2064	-6.7	1.0	2	dbSNP_123	206	1501,7099	283.6+/-296.2	144,1213,2943	no	coding-synonymous	ITGB6	NM_000888.3		240,1948,4315	GG,GA,AA		17.4535,21.0395,18.6683		688/789	160968628	2428,10578	2203	4300	6503	SO:0001819	synonymous_variant	3694	exon13			CCCCTCATTATCT		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.2064T>C	2.37:g.160968628A>G		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	283	136	0.480565	NM_000888	B2R9W5|C9JA97|Q0VA95|Q16500|Q53RG5|Q53RR6	Silent	SNP	ENST00000283249.2	37	CCDS2212.1																																																																																			A|0.805;G|0.195	0.195	strong		0.403	ITGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255036.1	NM_000888	
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692277	31692277	+	Missense_Mutation	SNP	G	G	T	rs3804007	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31692277G>T	ENST00000360542.3	-	1	330	c.77C>A	c.(76-78)tCc>tAc	p.S26Y		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	26			S -> Y (in dbSNP:rs3804007).			intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GAGGTCGATGGAGGTGAGAGG	0.542													G|||	509	0.101637	0.2035	0.0893	5008	,	,		19648	0.0218		0.0527	False		,,,				2504	0.1053				p.S26Y		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.C77A						PASS	.	G	TYR/SER	806,3600	321.3+/-297.0	62,682,1459	66.0	68.0	67.0		77	4.9	0.0	21	dbSNP_107	67	512,8088	144.7+/-200.5	15,482,3803	yes	missense	KRTAP26-1	NM_203405.1	144	77,1164,5262	TT,TG,GG		5.9535,18.2932,10.1338	probably-damaging	26/211	31692277	1318,11688	2203	4300	6503	SO:0001583	missense	388818	exon1			TCGATGGAGGTGA	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.77C>A	21.37:g.31692277G>T	ENSP00000353742:p.Ser26Tyr	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	245	141	0.57551	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	171	0.0782967032967033	94	0.1910569105691057	28	0.07734806629834254	9	0.015734265734265736	40	0.052770448548812667	G	12.75	2.031278	0.35797	0.182932	0.059535	ENSG00000197683	ENST00000360542	T	0.05925	3.37	4.95	4.95	0.65309	.	0.351539	0.25878	N	0.027710	T	0.00039	0.0001	M	0.78456	2.415	0.80722	P	0.0	D	0.89917	1.0	D	0.79108	0.992	T	0.01053	-1.1467	9	0.66056	D	0.02	-16.96	14.402	0.67053	0.0:0.0:1.0:0.0	rs3804007;rs52829761;rs3804007	26	Q6PEX3	KR261_HUMAN	Y	26	ENSP00000353742:S26Y	ENSP00000353742:S26Y	S	-	2	0	KRTAP26-1	30614148	0.035000	0.19736	0.040000	0.18447	0.060000	0.15804	1.639000	0.37176	2.664000	0.90586	0.655000	0.94253	TCC	G|0.909;T|0.091	0.091	strong		0.542	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
MUC17	140453	hgsc.bcm.edu	37	7	100678918	100678918	+	Silent	SNP	G	G	A	rs200627718|rs71286278	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678918G>A	ENST00000306151.4	+	3	4285	c.4221G>A	c.(4219-4221)ccG>ccA	p.P1407P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1407	59 X approximate tandem repeats.|Ser-rich.				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)					GCACCACGCCGGTAGTCAGTT	0.512																																					p.P1407P		Atlas-SNP	.											MUC17,colon,carcinoma,+1,1	MUC17	804	1	0			c.G4221A						scavenged	.						272.0	277.0	276.0					7																	100678918		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACGCCGGTAGTC	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.4221G>A	7.37:g.100678918G>A		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	197	6	0.0304569	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.998;A|0.002	0.002	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CYP2S1	29785	hgsc.bcm.edu	37	19	41712275	41712275	+	Missense_Mutation	SNP	C	C	T	rs34971233	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41712275C>T	ENST00000310054.4	+	9	1613	c.1397C>T	c.(1396-1398)cCg>cTg	p.P466L	CYP2S1_ENST00000542619.1_Missense_Mutation_p.P191L	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	466			P -> L (in dbSNP:rs34971233).		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(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						CTGGAGAGCCCGTGCCCGCCG	0.612													c|||	90	0.0179712	0.025	0.0216	5008	,	,		19108	0.0		0.0239	False		,,,				2504	0.0184				p.P466L		Atlas-SNP	.											.	CYP2S1	47	.	0			c.C1397T						PASS	.	C	LEU/PRO	102,4304	80.4+/-118.8	2,98,2103	129.0	125.0	126.0		1397	3.3	0.0	19	dbSNP_126	126	197,8403	85.8+/-148.2	3,191,4106	yes	missense	CYP2S1	NM_030622.6	98	5,289,6209	TT,TC,CC		2.2907,2.315,2.2989	possibly-damaging	466/505	41712275	299,12707	2203	4300	6503	SO:0001583	missense	29785	exon9			AGAGCCCGTGCCC	AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"""Cytochrome P450s"""	15654	protein-coding gene	gene with protein product		611529	"""cytochrome P450, subfamily IIS, polypeptide 1"""			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.1397C>T	19.37:g.41712275C>T	ENSP00000308032:p.Pro466Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_030622	Q9BZ66	Missense_Mutation	SNP	ENST00000310054.4	37	CCDS12573.1	44	0.020146520146520148	15	0.03048780487804878	15	0.04143646408839779	0	0.0	14	0.018469656992084433	C	0.227	-1.023786	0.02061	0.02315	0.022907	ENSG00000167600	ENST00000301173;ENST00000310054;ENST00000542619	T;T	0.71341	-0.56;-0.56	4.35	3.31	0.37934	.	0.203095	0.42172	D	0.000750	T	0.38983	0.1061	M	0.64080	1.96	0.09310	N	0.999997	D;D	0.76494	0.972;0.999	P;P	0.59595	0.585;0.86	T	0.57165	-0.7858	10	0.02654	T	1	.	5.3402	0.15979	0.1991:0.6965:0.0:0.1043	rs34971233;rs56763907	191;466	B4DJI0;Q96SQ9	.;CP2S1_HUMAN	L	466;466;191	ENSP00000308032:P466L;ENSP00000445299:P191L	ENSP00000301173:P466L	P	+	2	0	CYP2S1	46404115	0.033000	0.19621	0.005000	0.12908	0.002000	0.02628	0.782000	0.26788	1.048000	0.40298	0.655000	0.94253	CCG	C|0.979;T|0.021	0.021	strong		0.612	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1		
GRIN2D	2906	hgsc.bcm.edu	37	19	48945044	48945044	+	Silent	SNP	C	C	T	rs144676582	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48945044C>T	ENST00000263269.3	+	11	2359	c.2271C>T	c.(2269-2271)atC>atT	p.I757I		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	757					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACGCCTTCATCTACGATGCTG	0.617													C|||	6	0.00119808	0.0	0.0058	5008	,	,		20158	0.0		0.002	False		,,,				2504	0.0				p.I757I		Atlas-SNP	.											.	GRIN2D	76	.	0			c.C2271T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	55.0	46.0	49.0		2271	2.5	1.0	19	dbSNP_134	49	29,8571	19.2+/-60.6	0,29,4271	no	coding-synonymous	GRIN2D	NM_000836.2		0,31,6472	TT,TC,CC		0.3372,0.0454,0.2384		757/1337	48945044	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	2906	exon11			CTTCATCTACGAT	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.2271C>T	19.37:g.48945044C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_000836		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
GRIN3A	116443	hgsc.bcm.edu	37	9	104449098	104449098	+	Missense_Mutation	SNP	C	C	T	rs10989591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:104449098C>T	ENST00000361820.3	-	2	1684	c.1084G>A	c.(1084-1086)Gtg>Atg	p.V362M		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	362			V -> M (in dbSNP:rs10989591). {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)	AGTTCCTCCACATTCTGGGAA	0.507													C|||	1601	0.319688	0.5295	0.2824	5008	,	,		21591	0.1081		0.326	False		,,,				2504	0.274				p.V362M		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G1084A						PASS	.	C	MET/VAL	2091,2315	575.5+/-384.0	508,1075,620	76.0	66.0	69.0		1084	5.8	1.0	9	dbSNP_120	69	2703,5897	433.1+/-357.3	412,1879,2009	yes	missense	GRIN3A	NM_133445.2	21	920,2954,2629	TT,TC,CC		31.4302,47.458,36.8599	probably-damaging	362/1116	104449098	4794,8212	2203	4300	6503	SO:0001583	missense	116443	exon2			CCTCCACATTCTG		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.1084G>A	9.37:g.104449098C>T	ENSP00000355155:p.Val362Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	655	0.2999084249084249	241	0.4898373983739837	102	0.281767955801105	66	0.11538461538461539	246	0.3245382585751979	C	21.1	4.103988	0.76983	0.47458	0.314302	ENSG00000198785	ENST00000361820	D	0.86366	-2.11	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	0.99999927067	B	0.33857	0.429	B	0.43990	0.438	T	0.14172	-1.0482	9	0.45353	T	0.12	.	20.1374	0.98035	0.0:1.0:0.0:0.0	rs10989591;rs52812520;rs59456765;rs10989591	362	Q8TCU5	NMD3A_HUMAN	M	362	ENSP00000355155:V362M	ENSP00000355155:V362M	V	-	1	0	GRIN3A	103488919	1.000000	0.71417	0.993000	0.49108	0.988000	0.76386	4.796000	0.62496	2.763000	0.94921	0.563000	0.77884	GTG	C|0.652;T|0.348	0.348	strong		0.507	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
NOP9	161424	hgsc.bcm.edu	37	14	24772967	24772967	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24772967G>A	ENST00000267425.3	+	7	1407	c.1314G>A	c.(1312-1314)cgG>cgA	p.R438R	NOP9_ENST00000396802.3_Silent_p.R438R	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	438							poly(A) RNA binding (GO:0044822)	p.R438R(1)									CCTCATCCCGGCAAGTGGCCT	0.532																																					p.R438R		Atlas-SNP	.											C14orf21,colon,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1314A						scavenged	.						77.0	73.0	74.0					14																	24772967		2203	4300	6503	SO:0001819	synonymous_variant	161424	exon7			ATCCCGGCAAGTG		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.1314G>A	14.37:g.24772967G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	237	3	0.0126582	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1	.	.	.	.	.	.	.	.	.	.	G	9.028	0.986581	0.18889	.	.	ENSG00000196943	ENST00000557362	.	.	.	5.32	3.41	0.39046	.	.	.	.	.	T	0.58623	0.2135	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55541	-0.8125	4	.	.	.	-19.0835	8.7225	0.34449	0.0824:0.4059:0.5117:0.0	.	.	.	.	D	64	.	.	G	+	2	0	C14orf21	23842807	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.331000	0.19733	1.411000	0.46957	0.655000	0.94253	GGC	.	.	none		0.532	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
CYP24A1	1591	hgsc.bcm.edu	37	20	52790027	52790027	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:52790027G>A	ENST00000216862.3	-	1	485	c.92C>T	c.(91-93)aCg>aTg	p.T31M	CYP24A1_ENST00000395954.3_5'Flank|CYP24A1_ENST00000395955.3_Missense_Mutation_p.T31M	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	31					osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	CGTGTACGCCGTAGATGTCAC	0.701																																					p.T31M		Atlas-SNP	.											.	CYP24A1	75	.	0			c.C92T						PASS	.						11.0	10.0	10.0					20																	52790027		2182	4282	6464	SO:0001583	missense	1591	exon1			TACGCCGTAGATG	U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"""Cytochrome P450s"""	2602	protein-coding gene	gene with protein product		126065	"""cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"""	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.92C>T	20.37:g.52790027G>A	ENSP00000216862:p.Thr31Met	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	NM_000782	Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	37	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	G	8.351	0.830799	0.16820	.	.	ENSG00000019186	ENST00000216862;ENST00000395955	T;T	0.71222	-0.53;-0.55	5.27	-0.451	0.12214	.	0.815815	0.11464	N	0.561406	T	0.40372	0.1114	N	0.08118	0	0.09310	N	0.999999	P;P	0.43024	0.521;0.798	B;B	0.35182	0.128;0.197	T	0.29731	-1.0002	10	0.35671	T	0.21	-0.5016	3.5654	0.07897	0.0786:0.2999:0.3524:0.2691	.	31;31	Q32ML3;Q07973	.;CP24A_HUMAN	M	31	ENSP00000216862:T31M;ENSP00000379285:T31M	ENSP00000216862:T31M	T	-	2	0	CYP24A1	52223434	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.239000	0.18023	-0.332000	0.08489	-0.309000	0.09137	ACG	.	.	none		0.701	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2		
RSPH3	83861	hgsc.bcm.edu	37	6	159398764	159398764	+	Silent	SNP	G	G	A	rs12191022	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159398764G>A	ENST00000252655.1	-	8	1678	c.1489C>T	c.(1489-1491)Ctg>Ttg	p.L497L	RSPH3_ENST00000297262.3_Silent_p.L401L|RSPH3_ENST00000367069.2_Silent_p.L355L|RSPH3_ENST00000607398.1_5'Flank|RSPH3_ENST00000449822.1_Silent_p.L259L	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	497								p.L497L(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		GAGGCCTCCAGTGACTCTGTC	0.507													G|||	993	0.198283	0.0582	0.3429	5008	,	,		15899	0.3919		0.0765	False		,,,				2504	0.2106				p.L497L		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - coding silent(1)	stomach(1)	c.C1489T						PASS	.	G		354,4052	183.6+/-211.2	10,334,1859	165.0	164.0	164.0		1489	-4.3	0.0	6	dbSNP_120	164	715,7885	174.9+/-225.1	36,643,3621	no	coding-synonymous	RSPH3	NM_031924.4		46,977,5480	AA,AG,GG		8.314,8.0345,8.2193		497/561	159398764	1069,11937	2203	4300	6503	SO:0001819	synonymous_variant	83861	exon8			CCTCCAGTGACTC	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.1489C>T	6.37:g.159398764G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	140	60	0.428571	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Silent	SNP	ENST00000252655.1	37	CCDS5260.1																																																																																			G|0.871;A|0.129	0.129	strong		0.507	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
ZNF98	148198	hgsc.bcm.edu	37	19	22574357	22574357	+	Missense_Mutation	SNP	C	C	G	rs200702907	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22574357C>G	ENST00000357774.5	-	4	1801	c.1680G>C	c.(1678-1680)aaG>aaC	p.K560N		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	560					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.K560N(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				ATTTGGAAATCTTTGCAATGT	0.323																																					p.K560N		Atlas-SNP	.											ZNF98_ENST00000357774,NS,carcinoma,0,4	ZNF98	230	4	2	Substitution - Missense(2)	prostate(2)	c.G1680C						scavenged	.						21.0	16.0	17.0					19																	22574357		1774	3947	5721	SO:0001583	missense	148198	exon4			GGAAATCTTTGCA		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1680G>C	19.37:g.22574357C>G	ENSP00000350418:p.Lys560Asn	Somatic	865	0	0		WXS	Illumina HiSeq	Phase_I	824	146	0.177184	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	0.003	-2.422641	0.00186	.	.	ENSG00000197360	ENST00000357774	T	0.07688	3.17	1.39	0.147	0.14838	.	.	.	.	.	T	0.02193	0.0068	N	0.03000	-0.44	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41858	-0.9485	9	0.05959	T	0.93	.	0.0912	0.00040	0.3312:0.2373:0.1958:0.2357	.	560	A6NK75	ZNF98_HUMAN	N	560	ENSP00000350418:K560N	ENSP00000350418:K560N	K	-	3	2	ZNF98	22366197	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-2.155000	0.01284	-0.971000	0.03564	-0.764000	0.03450	AAG	C|0.500;G|0.500	0.500	weak		0.323	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
LILRA4	23547	hgsc.bcm.edu	37	19	54848144	54848144	+	Missense_Mutation	SNP	T	T	A	rs74869671	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848144T>A	ENST00000291759.4	-	6	1279	c.1223A>T	c.(1222-1224)cAc>cTc	p.H408L	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	408	Ig-like C2-type 4.				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)		CTCACTGGGGTGAGACAGCAG	0.592													T|||	74	0.0147764	0.0333	0.0014	5008	,	,		17775	0.0		0.001	False		,,,				2504	0.0286				p.H408L		Atlas-SNP	.											.	LILRA4	91	.	0			c.A1223T						PASS	.	T	LEU/HIS	1,4405		0,1,2202	111.0	91.0	98.0		1223	-1.7	0.0	19	dbSNP_131	98	1,8599		0,1,4299	no	missense	LILRA4	NM_012276.3	99	0,2,6501	AA,AT,TT		0.0116,0.0227,0.0154	benign	408/500	54848144	2,13004	2203	4300	6503	SO:0001583	missense	23547	exon6			CTGGGGTGAGACA	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.1223A>T	19.37:g.54848144T>A	ENSP00000291759:p.His408Leu	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	179	18	0.100559	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	5.063	0.197370	0.09599	2.27E-4	1.16E-4	ENSG00000239961	ENST00000291759	T	0.00691	5.84	2.4	-1.74	0.08056	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.662820	0.00932	N	0.002721	T	0.00754	0.0025	L	0.35414	1.06	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49437	-0.8940	10	0.17832	T	0.49	.	3.0817	0.06265	0.4319:0.0:0.22:0.3481	.	408	P59901	LIRA4_HUMAN	L	408	ENSP00000291759:H408L	ENSP00000291759:H408L	H	-	2	0	LILRA4	59539956	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-2.031000	0.01427	-0.517000	0.06461	-0.714000	0.03626	CAC	T|0.995;A|0.005	0.005	strong		0.592	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
XIRP1	165904	hgsc.bcm.edu	37	3	39227495	39227495	+	Missense_Mutation	SNP	C	C	T	rs142860074	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:39227495C>T	ENST00000340369.3	-	2	3670	c.3442G>A	c.(3442-3444)Gtg>Atg	p.V1148M	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1148					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)	p.V1148M(1)		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)		AAGGTCCTCACGGGATGAGCG	0.617																																					p.V1148M		Atlas-SNP	.											XIRP1,colon,carcinoma,0,1	XIRP1	173	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3442A						PASS	.	C	,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	59.0	60.0	60.0		,3442	1.6	0.0	3	dbSNP_134	60	7,8593	5.7+/-21.5	0,7,4293	yes	intron,missense	XIRP1	NM_001198621.1,NM_194293.2	,21	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	,possibly-damaging	,1148/1844	39227495	8,12998	2203	4300	6503	SO:0001583	missense	165904	exon2			TCCTCACGGGATG	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.3442G>A	3.37:g.39227495C>T	ENSP00000343140:p.Val1148Met	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	C	5.679	0.309769	0.10733	2.27E-4	8.14E-4	ENSG00000168334	ENST00000340369	T	0.06142	3.34	4.39	1.58	0.23477	.	0.713130	0.12138	U	0.496126	T	0.05686	0.0149	L	0.43152	1.355	0.09310	N	1	B	0.28208	0.203	B	0.14578	0.011	T	0.34054	-0.9844	10	0.45353	T	0.12	.	6.8454	0.23984	0.0:0.6999:0.0:0.3001	.	1148	Q702N8	XIRP1_HUMAN	M	1148	ENSP00000343140:V1148M	ENSP00000343140:V1148M	V	-	1	0	XIRP1	39202499	0.840000	0.29493	0.025000	0.17156	0.219000	0.24729	1.440000	0.35024	0.227000	0.20999	0.561000	0.74099	GTG	C|0.999;T|0.001	0.001	strong		0.617	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
TSEN34	79042	hgsc.bcm.edu	37	19	54696027	54696027	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54696027T>C	ENST00000396383.1	+	4	859	c.548T>C	c.(547-549)cTc>cCc	p.L183P	MBOAT7_ENST00000474910.1_5'Flank|CTD-3093M3.1_ENST00000594382.1_lincRNA|TSEN34_ENST00000302937.4_Missense_Mutation_p.L183P|MBOAT7_ENST00000245615.1_5'Flank|MBOAT7_ENST00000338624.6_5'Flank|TSEN34_ENST00000396388.2_Missense_Mutation_p.L183P|MBOAT7_ENST00000391754.1_5'Flank|TSEN34_ENST00000429671.2_Missense_Mutation_p.L183P|MBOAT7_ENST00000431666.2_5'Flank			Q9BSV6	SEN34_HUMAN	TSEN34 tRNA splicing endonuclease subunit	183					mRNA processing (GO:0006397)|tRNA-type intron splice site recognition and cleavage (GO:0000379)	tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	10	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					AGATCTGCTCTCCTTGTCCAG	0.637																																					p.L183P	Esophageal Squamous(37;841 964 4869 42824)	Atlas-SNP	.											TSEN34,NS,carcinoma,-1,1	TSEN34	17	1	0			c.T548C						scavenged	.						69.0	71.0	70.0					19																	54696027		1878	4092	5970	SO:0001583	missense	79042	exon4			CTGCTCTCCTTGT	AF211970	CCDS42609.1, CCDS74446.1	19q13.4	2013-08-06	2013-08-06	2005-03-12	ENSG00000170892	ENSG00000170892		"""tRNA splicing endonuclease subunits"""	15506	protein-coding gene	gene with protein product		608754	"""leukocyte receptor cluster (LRC) member 5"", ""tRNA splicing endonuclease 34 homolog (SEN34, S. cerevisiae)"", ""tRNA splicing endonuclease 34 homolog (S. cerevisiae)"""	LENG5		10941842, 15109492	Standard	NM_024075		Approved	SEN34, SEN34L	uc002qdw.3	Q9BSV6	OTTHUMG00000066515	ENST00000396383.1:c.548T>C	19.37:g.54696027T>C	ENSP00000379667:p.Leu183Pro	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	236	4	0.0169492	NM_024075	A6NNB1|B0V3J1|Q9BVT1|Q9H6H5	Missense_Mutation	SNP	ENST00000396383.1	37	CCDS42609.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.402493	0.83230	.	.	ENSG00000170892	ENST00000455798;ENST00000456872;ENST00000302937;ENST00000429671;ENST00000396383;ENST00000396388	T;T;T;T;T;T	0.66995	-0.24;-0.16;-0.16;-0.15;-0.16;-0.16	4.56	4.56	0.56223	.	0.156002	0.51477	D	0.000082	T	0.74550	0.3731	L	0.50333	1.59	0.58432	D	0.999998	D;D	0.76494	0.999;0.997	D;P	0.66196	0.942;0.866	T	0.76979	-0.2758	10	0.72032	D	0.01	.	11.7599	0.51896	0.0:0.0:0.0:1.0	.	183;183	E7EQB3;Q9BSV6	.;SEN34_HUMAN	P	183;186;183;183;183;183	ENSP00000400743:L183P;ENSP00000408689:L186P;ENSP00000305524:L183P;ENSP00000397402:L183P;ENSP00000379667:L183P;ENSP00000379671:L183P	ENSP00000305524:L183P	L	+	2	0	TSEN34	59387839	1.000000	0.71417	0.721000	0.30653	0.973000	0.67179	5.870000	0.69620	1.842000	0.53543	0.459000	0.35465	CTC	.	.	none		0.637	TSEN34-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142200.1	NM_024075	
DENND4C	55667	hgsc.bcm.edu	37	9	19341045	19341045	+	Silent	SNP	A	A	G	rs928128	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:19341045A>G	ENST00000380432.2	+	16	2115	c.2082A>G	c.(2080-2082)gcA>gcG	p.A694A	DENND4C_ENST00000602925.1_Silent_p.A930A|DENND4C_ENST00000434457.2_Silent_p.A979A			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	204	0	0		WXS	Illumina HiSeq	Phase_I	240	119	0.495833	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	
TPO	7173	hgsc.bcm.edu	37	2	1520676	1520676	+	Missense_Mutation	SNP	T	T	C	rs1126799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:1520676T>C	ENST00000345913.4	+	15	2631	c.2540T>C	c.(2539-2541)gTg>gCg	p.V847A	TPO_ENST00000337415.3_Missense_Mutation_p.V847A|TPO_ENST00000329066.4_Missense_Mutation_p.V847A|TPO_ENST00000382198.1_Missense_Mutation_p.V674A|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000382201.3_Missense_Mutation_p.V790A|TPO_ENST00000349624.3_Missense_Mutation_p.V674A|TPO_ENST00000346956.3_Missense_Mutation_p.V803A	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	847			V -> A (in dbSNP:rs1126799). {ECO:0000269|PubMed:12454013, ECO:0000269|PubMed:3453124, ECO:0000269|PubMed:3475693, 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)	p.V847A(1)		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)	CTCCCTCGGGTGACTTGGATC	0.592													C|||	3325	0.663938	0.8283	0.6037	5008	,	,		18488	0.5833		0.5417	False		,,,				2504	0.6933				p.V847A		Atlas-SNP	.											TPO,NS,carcinoma,0,1	TPO	224	1	1	Substitution - Missense(1)	stomach(1)	c.T2540C						PASS	.	C	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	3398,1008	373.4+/-320.8	1303,792,108	68.0	71.0	70.0		2540,2540,2369,2369,2408,2021	4.6	0.1	2	dbSNP_86	70	4578,4022	555.0+/-386.6	1207,2164,929	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	64,64,64,64,64,64	2510,2956,1037	CC,CT,TT		46.7674,22.8779,38.6745	benign,benign,benign,benign,benign,benign	847/934,847/934,790/877,790/877,803/890,674/761	1520676	7976,5030	2203	4300	6503	SO:0001583	missense	7173	exon15			CTCGGGTGACTTG		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.2540T>C	2.37:g.1520676T>C	ENSP00000318820:p.Val847Ala	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	1334|1334	0.6108058608058609|0.6108058608058609	388|388	0.7886178861788617|0.7886178861788617	209|209	0.5773480662983426|0.5773480662983426	344|344	0.6013986013986014|0.6013986013986014	393|393	0.5184696569920845|0.5184696569920845	C|C	0.007|0.007	-1.960539|-1.960539	0.00465|0.00465	0.771221|0.771221	0.532326|0.532326	ENSG00000115705|ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607;ENST00000425083|ENST00000446278	T;T;T;T;T;T;T;T;T;T|.	0.68025|.	-0.13;-0.12;-0.06;0.16;-0.12;-0.07;0.16;-0.12;0.71;-0.3|.	5.52|5.52	4.6|4.6	0.57074|0.57074	.|.	1.004770|.	0.08016|.	N|.	0.991268|.	T|.	0.00012|.	0.0000|.	N|N	0.00325|0.00325	-1.645|-1.645	0.42496|0.42496	P|P	0.0070829999999999504|0.0070829999999999504	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.0;0.001;0.001;0.0|.	T|.	0.27157|.	-1.0082|.	9|.	0.02654|.	T|.	1|.	-21.4253|-21.4253	8.8585|8.8585	0.35242|0.35242	0.0:0.7477:0.1631:0.0892|0.0:0.7477:0.1631:0.0892	rs1126799;rs2276703;rs3182055;rs17723536;rs52825202;rs57954584;rs1126799|rs1126799;rs2276703;rs3182055;rs17723536;rs52825202;rs57954584;rs1126799	803;674;790;847|.	P07202-4;P07202-5;P07202-2;P07202|.	.;.;.;PERT_HUMAN|.	A|R	847;847;803;674;847;790;674;732;277;68|322	ENSP00000337263:V847A;ENSP00000318820:V847A;ENSP00000263886:V803A;ENSP00000332044:V674A;ENSP00000329869:V847A;ENSP00000371636:V790A;ENSP00000371633:V674A;ENSP00000405788:V732A;ENSP00000419461:V277A;ENSP00000389659:V68A|.	ENSP00000329869:V847A|.	V|X	+|+	2|1	0|0	TPO|TPO	1499683|1499683	0.164000|0.164000	0.22935|0.22935	0.064000|0.064000	0.19789|0.19789	0.001000|0.001000	0.01503|0.01503	0.609000|0.609000	0.24238|0.24238	1.364000|1.364000	0.46038|0.46038	-0.124000|-0.124000	0.14976|0.14976	GTG|TGA	A|0.003;C|0.612	0.612	strong		0.592	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
CLCN7	1186	hgsc.bcm.edu	37	16	1509123	1509123	+	Silent	SNP	G	G	A	rs12923538	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1509123G>A	ENST00000382745.4	-	7	1265	c.660C>T	c.(658-660)caC>caT	p.H220H	CLCN7_ENST00000262318.8_Silent_p.H196H|CLCN7_ENST00000448525.1_Silent_p.H196H	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	220					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				GCCGCACCACGTGGGGGATCT	0.662													G|||	611	0.122005	0.2352	0.1225	5008	,	,		18275	0.0099		0.1113	False		,,,				2504	0.0951				p.H220H		Atlas-SNP	.											CLCN7,colon,carcinoma,-1,1	CLCN7	53	1	0			c.C660T						scavenged	.	G	,	880,3516	332.0+/-302.3	101,678,1419	42.0	45.0	44.0		588,660	-1.5	1.0	16	dbSNP_121	44	1124,7476	228.4+/-263.5	77,970,3253	no	coding-synonymous,coding-synonymous	CLCN7	NM_001114331.1,NM_001287.4	,	178,1648,4672	AA,AG,GG		13.0698,20.0182,15.4201	,	196/782,220/806	1509123	2004,10992	2198	4300	6498	SO:0001819	synonymous_variant	1186	exon7			CACCACGTGGGGG	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.660C>T	16.37:g.1509123G>A		Somatic	242	2	0.00826446		WXS	Illumina HiSeq	Phase_I	248	142	0.572581	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			G|0.854;A|0.146	0.146	strong		0.662	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
MC1R	4157	hgsc.bcm.edu	37	16	89986608	89986608	+	Silent	SNP	A	A	G	rs2228478	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:89986608A>G	ENST00000555147.1	+	1	2322	c.942A>G	c.(940-942)acA>acG	p.T314T	TUBB3_ENST00000556922.1_Silent_p.T314T|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000554444.1_5'Flank|RP11-566K11.4_ENST00000554623.1_RNA|MC1R_ENST00000555427.1_Silent_p.T314T	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	314					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		AGGTGCTGACATGCTCCTGGT	0.592									Melanoma, Familial Clustering of				G|||	1297	0.258986	0.4871	0.0836	5008	,	,		19553	0.2927		0.0924	False		,,,				2504	0.2117				p.T314T		Atlas-SNP	.											.	MC1R	20	.	0			c.A942G						PASS	.	G		1731,2511		347,1037,737	67.0	66.0	66.0		942	0.6	0.8	16	dbSNP_98	66	914,7554		55,804,3375	no	coding-synonymous	MC1R	NM_002386.3		402,1841,4112	GG,GA,AA		10.7936,40.8062,20.8104		314/318	89986608	2645,10065	2121	4234	6355	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		GCTGACATGCTCC		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"""GPCR / Class A : Melanocortin receptors"""	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.942A>G	16.37:g.89986608A>G		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	224	33	0.147321	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			A|0.821;G|0.179	0.179	strong		0.592	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
DCAF11	80344	hgsc.bcm.edu	37	14	24587639	24587639	+	Missense_Mutation	SNP	G	G	A	rs3825584	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24587639G>A	ENST00000446197.3	+	7	1347	c.620G>A	c.(619-621)cGt>cAt	p.R207H	DCAF11_ENST00000560171.1_3'UTR|DCAF11_ENST00000559115.1_Missense_Mutation_p.R207H|DCAF11_ENST00000396936.1_Missense_Mutation_p.R107H|RP11-468E2.6_ENST00000558325.1_5'Flank|DCAF11_ENST00000396941.4_Missense_Mutation_p.R181H	NM_025230.4	NP_079506.3	Q8TEB1	DCA11_HUMAN	DDB1 and CUL4 associated factor 11	207			R -> H (in dbSNP:rs3825584). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.7}.		protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)											GGCCGTTTCCGTAAATTCAAG	0.488													g|||	1989	0.397165	0.3351	0.4625	5008	,	,		23535	0.4355		0.3032	False		,,,				2504	0.4918				p.R207H		Atlas-SNP	.											.	.	.	.	0			c.G620A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	1405,3001	461.1+/-352.8	229,947,1027	134.0	126.0	129.0		620,620,542	-5.3	0.7	14	dbSNP_107	129	2340,6260	391.3+/-343.6	326,1688,2286	yes	missense,missense,missense	DCAF11	NM_001163484.1,NM_025230.4,NM_181357.2	29,29,29	555,2635,3313	AA,AG,GG		27.2093,31.8883,28.7944	benign,benign,benign	207/547,207/547,181/521	24587639	3745,9261	2203	4300	6503	SO:0001583	missense	80344	exon7			GTTTCCGTAAATT	AF130070	CCDS9610.1, CCDS41929.1	14q11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000100897	ENSG00000100897		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	20258	protein-coding gene	gene with protein product		613317	"""WD repeat domain 23"""	WDR23			Standard	NM_025230		Approved	PRO2389, GL014	uc001wlv.3	Q8TEB1	OTTHUMG00000028793	ENST00000446197.3:c.620G>A	14.37:g.24587639G>A	ENSP00000415556:p.Arg207His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	216	138	0.638889	NM_025230	B3KQ83|D3DS56|Q5D039|Q86U00|Q86U39|Q8NDN2|Q9H2J0|Q9H3A3|Q9H5C9	Missense_Mutation	SNP	ENST00000446197.3	37	CCDS9610.1	791	0.36217948717948717	167	0.3394308943089431	162	0.44751381215469616	230	0.4020979020979021	232	0.30606860158311344	g	11.67	1.708956	0.30322	0.318883	0.272093	ENSG00000100897	ENST00000326009;ENST00000446197;ENST00000396936;ENST00000396941	T;T	0.41065	1.01;1.01	5.4	-5.29	0.02747	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.537521	0.21749	N	0.069715	T	0.00012	0.0000	N	0.02539	-0.55	0.44603	P	0.0024290000000000145	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.0	T	0.48559	-0.9025	9	0.35671	T	0.21	-0.7512	13.2261	0.59914	0.4655:0.0:0.5345:0.0	rs3825584;rs58760613;rs3825584	181;107;207;207	Q8TEB1-2;Q8TEB1-3;A8K9T2;Q8TEB1	.;.;.;DCA11_HUMAN	H	207;181;107;181	ENSP00000380142:R107H;ENSP00000380146:R181H	ENSP00000323680:R207H	R	+	2	0	DCAF11	23657479	0.716000	0.27956	0.737000	0.30932	0.986000	0.74619	0.021000	0.13489	-1.098000	0.03038	-0.290000	0.09829	CGT	G|0.685;A|0.315	0.315	strong		0.488	DCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071907.4		
GALNTL5	168391	hgsc.bcm.edu	37	7	151680175	151680175	+	Missense_Mutation	SNP	C	C	T	rs35682935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:151680175C>T	ENST00000392800.2	+	4	727	c.473C>T	c.(472-474)aCg>aTg	p.T158M	GALNTL5_ENST00000431418.2_Missense_Mutation_p.T158M	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	158	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)		TCCAGTGTCACGAACCTCACG	0.403													T|||	651	0.129992	0.0113	0.1239	5008	,	,		21285	0.1597		0.1511	False		,,,				2504	0.2423				p.T158M		Atlas-SNP	.											GALNTL5,colon,carcinoma,+1,1	GALNTL5	87	1	0			c.C473T						scavenged	.	T	MET/THR	126,4280	814.5+/-416.2	2,122,2079	157.0	142.0	147.0		473	2.2	0.0	7	dbSNP_126	147	1204,7396	763.1+/-407.6	85,1034,3181	yes	missense	GALNTL5	NM_145292.3	81	87,1156,5260	TT,TC,CC		14.0,2.8597,10.226	benign	158/444	151680175	1330,11676	2203	4300	6503	SO:0001583	missense	168391	exon4			GTGTCACGAACCT	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.473C>T	7.37:g.151680175C>T	ENSP00000376548:p.Thr158Met	Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	78	19	0.24359	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	270	0.12362637362637363	6	0.012195121951219513	46	0.1270718232044199	117	0.20454545454545456	101	0.13324538258575197	T	5.856	0.342146	0.11069	0.028597	0.14	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.61158	0.13;0.13	4.65	2.2	0.27929	Glycosyl transferase, family 2 (1);	1.380810	0.04444	N	0.371357	T	0.00039	0.0001	N	0.00738	-1.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05801	-1.0863	9	0.34782	T	0.22	.	6.4226	0.21752	0.0:0.0819:0.2984:0.6197	rs35682935;rs62480000	158	Q7Z4T8	GLTL5_HUMAN	M	158	ENSP00000392582:T158M;ENSP00000376548:T158M	ENSP00000376548:T158M	T	+	2	0	GALNTL5	151311108	0.011000	0.17503	0.000000	0.03702	0.002000	0.02628	1.946000	0.40283	0.038000	0.15604	-1.735000	0.00691	ACG	C|0.888;T|0.112	0.112	strong		0.403	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292	
CSPG4	1464	hgsc.bcm.edu	37	15	75970070	75970070	+	Missense_Mutation	SNP	C	C	T	rs8023621	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75970070C>T	ENST00000308508.5	-	9	5200	c.5108G>A	c.(5107-5109)cGc>cAc	p.R1703H	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	1703	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.		R -> H (in dbSNP:rs8023621).		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						GTGGCTGGGGCGCTGGGGACA	0.632													C|||	1317	0.262979	0.1634	0.3919	5008	,	,		18353	0.1885		0.3787	False		,,,				2504	0.2638				p.R1703H		Atlas-SNP	.											.	CSPG4	175	.	0			c.G5108A						PASS	.	C	HIS/ARG	887,3507	328.5+/-300.6	90,707,1400	82.0	84.0	83.0		5108	3.1	1.0	15	dbSNP_116	83	3435,5153	481.0+/-370.5	696,2043,1555	yes	missense	CSPG4	NM_001897.4	29	786,2750,2955	TT,TC,CC		39.9977,20.1866,33.2923	benign	1703/2323	75970070	4322,8660	2197	4294	6491	SO:0001583	missense	1464	exon9			CTGGGGCGCTGGG	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.5108G>A	15.37:g.75970070C>T	ENSP00000312506:p.Arg1703His	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	107	104	0.971963	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	573	0.2623626373626374	73	0.1483739837398374	129	0.356353591160221	80	0.13986013986013987	291	0.3839050131926121	C	15.05	2.717852	0.48622	0.201866	0.399977	ENSG00000173546	ENST00000308508	T	0.20200	2.09	4.96	3.09	0.35607	.	0.176621	0.40302	N	0.001133	T	0.00012	0.0000	L	0.38531	1.155	0.25196	P	0.99009862	B	0.09022	0.002	B	0.04013	0.001	T	0.45877	-0.9231	9	0.41790	T	0.15	.	5.5851	0.17269	0.1563:0.6778:0.0:0.1659	rs8023621;rs8023621	1703	Q6UVK1	CSPG4_HUMAN	H	1703	ENSP00000312506:R1703H	ENSP00000312506:R1703H	R	-	2	0	CSPG4	73757125	0.994000	0.37717	0.998000	0.56505	0.997000	0.91878	1.492000	0.35594	0.521000	0.28445	0.555000	0.69702	CGC	C|0.707;T|0.293	0.293	strong		0.632	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
SP2	6668	hgsc.bcm.edu	37	17	45994044	45994044	+	Silent	SNP	C	C	T	rs2228253	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45994044C>T	ENST00000376741.4	+	3	744	c.607C>T	c.(607-609)Ctg>Ttg	p.L203L	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	203					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						TGTGGTGAAGCTGACAGGTGG	0.627													T|||	2844	0.567891	0.615	0.4813	5008	,	,		17333	0.7748		0.4622	False		,,,				2504	0.4611				p.L203L		Atlas-SNP	.											.	SP2	38	.	0			c.C607T						PASS	.	T		2579,1827	534.7+/-374.0	741,1097,365	84.0	72.0	76.0		607	4.4	1.0	17	dbSNP_98	76	3754,4846	617.1+/-396.6	825,2104,1371	no	coding-synonymous	SP2	NM_003110.5		1566,3201,1736	TT,TC,CC		43.6512,41.4662,48.6929		203/614	45994044	6333,6673	2203	4300	6503	SO:0001819	synonymous_variant	6668	exon3			GTGAAGCTGACAG		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.607C>T	17.37:g.45994044C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_003110	A6NK74	Silent	SNP	ENST00000376741.4	37	CCDS11521.2																																																																																			C|0.479;T|0.521	0.521	strong		0.627	SP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316777.1	NM_003110	
HSH2D	84941	hgsc.bcm.edu	37	19	16259623	16259623	+	Silent	SNP	C	C	T	rs8103852	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:16259623C>T	ENST00000253680.6	+	4	594	c.63C>T	c.(61-63)acC>acT	p.T21T	HSH2D_ENST00000593154.2_Silent_p.T21T|HSH2D_ENST00000397372.4_Intron|HSH2D_ENST00000588246.1_Silent_p.T21T			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	21					negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						TTGTGCACACCCAGATGGGCC	0.637													C|||	617	0.123203	0.3464	0.0692	5008	,	,		14551	0.0169		0.0746	False		,,,				2504	0.0194				p.T21T		Atlas-SNP	.											.	HSH2D	16	.	0			c.C63T						PASS	.	C		1139,2703		171,797,953	50.0	58.0	56.0		63	-3.3	1.0	19	dbSNP_116	56	559,7669		19,521,3574	no	coding-synonymous	HSH2D	NM_032855.2		190,1318,4527	TT,TC,CC		6.7939,29.646,14.0679		21/353	16259623	1698,10372	1921	4114	6035	SO:0001819	synonymous_variant	84941	exon4			GCACACCCAGATG	AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"""SH2 domain containing"""	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.63C>T	19.37:g.16259623C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_032855	B5ME72|Q6ZNG7	Silent	SNP	ENST00000253680.6	37																																																																																				C|0.891;T|0.109	0.109	strong		0.637	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855	
SPAG17	200162	hgsc.bcm.edu	37	1	118624123	118624123	+	Silent	SNP	C	C	T	rs2298176	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:118624123C>T	ENST00000336338.5	-	14	1970	c.1905G>A	c.(1903-1905)ccG>ccA	p.P635P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	635						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)		GGTTGTCCCACGGTATGTTGA	0.438													T|||	633	0.126398	0.053	0.0447	5008	,	,		21696	0.2877		0.0596	False		,,,				2504	0.1861				p.P635P		Atlas-SNP	.											.	SPAG17	263	.	0			c.G1905A						PASS	.	T		258,4148	803.5+/-415.7	6,246,1951	189.0	177.0	181.0		1905	-5.0	0.9	1	dbSNP_100	181	489,8111	797.1+/-407.5	16,457,3827	no	coding-synonymous	SPAG17	NM_206996.2		22,703,5778	TT,TC,CC		5.686,5.8557,5.7435		635/2224	118624123	747,12259	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon14			GTCCCACGGTATG		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.1905G>A	1.37:g.118624123C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	87	79	0.908046	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			C|0.922;T|0.078	0.078	strong		0.438	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
COL4A3	1285	hgsc.bcm.edu	37	2	228102723	228102723	+	Missense_Mutation	SNP	G	G	C	rs13424243	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:228102723G>C	ENST00000396578.3	+	2	289	c.127G>C	c.(127-129)Ggg>Cgg	p.G43R	AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000606119.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	43	Triple-helical region.		G -> R (in dbSNP:rs13424243). {ECO:0000269|PubMed:11134255}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		CTTCTGTGACGGGGCCAAAGG	0.438													G|||	1153	0.230232	0.32	0.2637	5008	,	,		16895	0.0516		0.3539	False		,,,				2504	0.1421				p.G43R		Atlas-SNP	.											.	COL4A3	293	.	0			c.G127C						PASS	.	G	ARG/GLY	1134,2566		174,786,890	179.0	172.0	174.0		127	4.3	0.0	2	dbSNP_121	174	3032,5134		579,1874,1630	yes	missense	COL4A3	NM_000091.4	125	753,2660,2520	CC,CG,GG		37.1296,30.6486,35.1087	probably-damaging	43/1671	228102723	4166,7700	1850	4083	5933	SO:0001583	missense	1285	exon2			TGTGACGGGGCCA		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.127G>C	2.37:g.228102723G>C	ENSP00000379823:p.Gly43Arg	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	542	0.24816849816849818	141	0.2865853658536585	98	0.27071823204419887	38	0.06643356643356643	265	0.3496042216358839	G	16.02	3.004856	0.54254	0.306486	0.371296	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.97959	-4.63	5.2	4.31	0.51392	.	0.224868	0.31312	N	0.007879	T	0.00039	0.0001	H	0.96604	3.85	0.54753	P	1.2000000000012001E-5	D;D;D;D	0.89917	1.0;0.992;1.0;1.0	D;P;D;D	0.85130	0.979;0.884;0.993;0.997	T	0.00000	-1.8170	9	0.72032	D	0.01	.	9.7845	0.40668	0.0961:0.0:0.9039:0.0	rs13424243;rs52831477;rs57911954;rs13424243	43;43;43;43	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	R	43	ENSP00000379823:G43R	ENSP00000323334:G43R	G	+	1	0	COL4A3	227810967	0.254000	0.23992	0.011000	0.14972	0.089000	0.18198	1.245000	0.32790	1.315000	0.45114	0.467000	0.42956	GGG	G|0.734;C|0.266	0.266	strong		0.438	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
GSDMC	56169	hgsc.bcm.edu	37	8	130760774	130760774	+	Silent	SNP	C	C	T	rs4733559	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	181	0	0		WXS	Illumina HiSeq	Phase_I	202	112	0.554455	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		
KIAA1462	57608	hgsc.bcm.edu	37	10	30316072	30316072	+	Missense_Mutation	SNP	C	C	G	rs3739998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:30316072C>G	ENST00000375377.1	-	3	3106	c.3005G>C	c.(3004-3006)aGt>aCt	p.S1002T		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	1002			S -> T (in dbSNP:rs3739998). {ECO:0000269|PubMed:17974005}.		cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						GATTTTCGGACTTTCCTGGGG	0.557													C|||	1261	0.251797	0.0598	0.4524	5008	,	,		18976	0.1825		0.4215	False		,,,				2504	0.2658				p.S1002T		Atlas-SNP	.											.	KIAA1462	162	.	0			c.G3005C						PASS	.	C	THR/SER	454,3352		31,392,1480	115.0	108.0	110.0	http://www.ncbi.nlm.nih.gov/pubmed?term	3005	-0.7	0.0	10	dbSNP_107	110	3503,4747		740,2023,1362	yes	missense	KIAA1462	NM_020848.2	58	771,2415,2842	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	42.4606,11.9285,32.8218	possibly-damaging	1002/1360	30316072	3957,8099	1903	4125	6028	SO:0001583	missense	57608	exon3			TTCGGACTTTCCT	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.3005G>C	10.37:g.30316072C>G	ENSP00000364526:p.Ser1002Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	42	6	0.142857	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	634	0.2902930402930403	43	0.08739837398373984	153	0.42265193370165743	115	0.20104895104895104	323	0.4261213720316623	C	8.798	0.932209	0.18131	0.119285	0.424606	ENSG00000165757	ENST00000375377	T	0.12147	2.71	4.91	-0.722	0.11184	.	1.502430	0.03364	N	0.198056	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.21606	0.058	B	0.19391	0.025	T	0.47182	-0.9137	9	0.12103	T	0.63	0.5855	0.969	0.01412	0.2826:0.3586:0.1395:0.2193	rs3739998;rs17229209;rs3739998	1002	Q9P266	K1462_HUMAN	T	1002	ENSP00000364526:S1002T	ENSP00000364526:S1002T	S	-	2	0	KIAA1462	30356078	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.151000	0.16283	0.190000	0.20209	-0.253000	0.11424	AGT	C|0.706;G|0.294	0.294	strong		0.557	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
EFR3A	23167	hgsc.bcm.edu	37	8	132982824	132982824	+	Missense_Mutation	SNP	A	A	G	rs1051221	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:132982824A>G	ENST00000254624.5	+	10	1318	c.1093A>G	c.(1093-1095)Aac>Gac	p.N365D	EFR3A_ENST00000334503.4_Missense_Mutation_p.N365D|EFR3A_ENST00000519656.1_Missense_Mutation_p.N329D	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	365			N -> D (in dbSNP:rs1051221). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			AGGCAGTGTCAACTTAAATAC	0.393													A|||	2248	0.448882	0.5265	0.5	5008	,	,		17156	0.3125		0.5089	False		,,,				2504	0.3865				p.N365D		Atlas-SNP	.											.	EFR3A	96	.	0			c.A1093G						PASS	.	A	ASP/ASN	2335,2071	607.3+/-390.9	624,1087,492	113.0	112.0	112.0		1093	-1.1	0.0	8	dbSNP_86	112	4195,4405	568.1+/-389.0	1019,2157,1124	yes	missense	EFR3A	NM_015137.4	23	1643,3244,1616	GG,GA,AA		48.7791,47.0041,49.7924	benign	365/822	132982824	6530,6476	2203	4300	6503	SO:0001583	missense	23167	exon10			AGTGTCAACTTAA	D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.1093A>G	8.37:g.132982824A>G	ENSP00000254624:p.Asn365Asp	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Missense_Mutation	SNP	ENST00000254624.5	37	CCDS34942.2	1005	0.46016483516483514	266	0.540650406504065	188	0.5193370165745856	167	0.291958041958042	384	0.5065963060686016	A	7.915	0.737328	0.15574	0.529959	0.487791	ENSG00000132294	ENST00000254624;ENST00000377917;ENST00000334503;ENST00000519656	T;T;T	0.32023	1.47;1.47;1.47	5.68	-1.11	0.09840	Armadillo-like helical (1);Armadillo-type fold (1);	1.359000	0.04269	N	0.341810	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.15930	0.015	B	0.22152	0.038	T	0.48536	-0.9027	9	0.46703	T	0.11	0.3366	5.6	0.17349	0.5414:0.0:0.3371:0.1215	rs1051221;rs56516663;rs1051221	365	Q14156	EFR3A_HUMAN	D	365;365;365;329	ENSP00000254624:N365D;ENSP00000334769:N365D;ENSP00000428086:N329D	ENSP00000254624:N365D	N	+	1	0	EFR3A	133052006	0.062000	0.20869	0.001000	0.08648	0.358000	0.29455	0.548000	0.23314	-0.399000	0.07668	0.477000	0.44152	AAC	A|0.517;C|0.002	.	strong		0.393	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137	
PLSCR2	57047	hgsc.bcm.edu	37	3	146177815	146177815	+	Silent	SNP	C	C	T	rs6806535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:146177815C>T	ENST00000497985.1	-	4	535	c.96G>A	c.(94-96)caG>caA	p.Q32Q	PLSCR2_ENST00000336685.2_5'UTR	NM_001199978.1	NP_001186907.1	Q9NRY7	PLS2_HUMAN	phospholipid scramblase 2	32	Proline-rich domain (PRD). {ECO:0000250}.				phospholipid scrambling (GO:0017121)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid scramblase activity (GO:0017128)			endometrium(2)|large_intestine(5)|lung(7)|stomach(1)	15						GGTGGTCAGCCTGTTTCCCAG	0.527													C|||	2642	0.527556	0.2625	0.5865	5008	,	,		16382	0.6062		0.5636	False		,,,				2504	0.726				p.Q32Q		Atlas-SNP	.											.	PLSCR2	68	.	0			c.G96A						PASS	.																																			SO:0001819	synonymous_variant	57047	exon4			GTCAGCCTGTTTC		CCDS56284.1, CCDS3134.1, CCDS75029.1	3q24	2008-07-18			ENSG00000163746	ENSG00000163746			16494	protein-coding gene	gene with protein product		607610				10930526	Standard	NM_001199978		Approved		uc003evw.2	Q9NRY7	OTTHUMG00000159429	ENST00000497985.1:c.96G>A	3.37:g.146177815C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	NM_001199978	B4DXC3|J3KR76|Q0VAQ1|Q6NSW9|Q7Z4L7	Silent	SNP	ENST00000497985.1	37	CCDS56284.1																																																																																			C|0.496;T|0.504	0.504	strong		0.527	PLSCR2-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000355264.1	NM_020359	
SLFN13	146857	hgsc.bcm.edu	37	17	33768354	33768354	+	Missense_Mutation	SNP	C	C	T	rs3744371	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33768354C>T	ENST00000285013.6	-	6	2229	c.1954G>A	c.(1954-1956)Gaa>Aaa	p.E652K	SLFN13_ENST00000533791.1_Missense_Mutation_p.E652K|SLFN13_ENST00000542635.1_Missense_Mutation_p.E652K|SLFN13_ENST00000534689.1_Missense_Mutation_p.E334K|SLFN13_ENST00000360502.2_Missense_Mutation_p.E334K|SLFN13_ENST00000526861.1_Missense_Mutation_p.E652K	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	652			E -> K (in dbSNP:rs3744371).			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)		AGGAAAGTTTCCCGGGTCTCT	0.383													T|||	3250	0.648962	0.8684	0.4697	5008	,	,		16352	0.6508		0.5159	False		,,,				2504	0.6145				p.E652K		Atlas-SNP	.											.	SLFN13	79	.	0			c.G1954A						PASS	.	T	LYS/GLU	3243,1099		1356,531,284	55.0	70.0	65.0		1954	0.7	0.0	17	dbSNP_107	65	4264,4316		1194,1876,1220	no	missense	SLFN13	NM_144682.5	56	2550,2407,1504	TT,TC,CC		49.697,25.3109,41.9053	benign	652/898	33768354	7507,5415	2171	4290	6461	SO:0001583	missense	146857	exon6			AAGTTTCCCGGGT	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.1954G>A	17.37:g.33768354C>T	ENSP00000285013:p.Glu652Lys	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	1243	0.5691391941391941	383	0.7784552845528455	168	0.46408839779005523	359	0.6276223776223776	333	0.4393139841688654	t	0.101	-1.152030	0.01700	0.746891	0.49697	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35	3.29	0.733	0.18289	Domain of unknown function DUF2075 (1);	0.125186	0.36374	N	0.002635	T	0.00012	0.0000	N	0.00151	-1.98	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40646	-0.9552	9	0.02654	T	1	.	6.4298	0.21790	0.0:0.3655:0.0:0.6345	rs3744371;rs59618665;rs3744371	334;652	Q68D06-2;Q68D06	.;SLN13_HUMAN	K	652;334;652;652;334	ENSP00000285013:E652K;ENSP00000353692:E334K;ENSP00000434439:E652K;ENSP00000444016:E652K;ENSP00000435442:E334K	ENSP00000285013:E652K	E	-	1	0	SLFN13	30792467	0.948000	0.32251	0.009000	0.14445	0.016000	0.09150	0.960000	0.29253	-0.330000	0.08514	-1.140000	0.01884	GAA	C|0.421;T|0.579	0.579	strong		0.383	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
ZNF502	91392	hgsc.bcm.edu	37	3	44762830	44762830	+	Missense_Mutation	SNP	A	A	G	rs56084453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:44762830A>G	ENST00000296091.4	+	4	777	c.521A>G	c.(520-522)cAg>cGg	p.Q174R	ZNF502_ENST00000449836.1_Missense_Mutation_p.Q174R|ZNF502_ENST00000436624.2_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	166	0	0		WXS	Illumina HiSeq	Phase_I	161	66	0.409938	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	
ZBED5	58486	hgsc.bcm.edu	37	11	10875741	10875741	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:10875741C>T	ENST00000432999.2	-	3	1250	c.752G>A	c.(751-753)cGa>cAa	p.R251Q	ZBED5_ENST00000525350.1_Intron|ZBED5_ENST00000413761.2_Missense_Mutation_p.R251Q	NM_001143667.1|NM_021211.3	NP_001137139.1|NP_067034.2	Q49AG3	ZBED5_HUMAN	zinc finger, BED-type containing 5	251							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)	4						atccttaattcgacgtgcaac	0.373																																					p.R251Q		Atlas-SNP	.											ZBED5_ENST00000432999,NS,carcinoma,0,2	ZBED5	50	2	0			c.G752A						scavenged	.						138.0	107.0	116.0					11																	10875741		692	1591	2283	SO:0001583	missense	58486	exon3			TTAATTCGACGTG	AF205601		11p15.3	2013-05-03			ENSG00000236287	ENSG00000236287		"""Zinc fingers, BED-type"""	30803	protein-coding gene	gene with protein product		615251				10607616, 23533661	Standard	NM_021211		Approved	Buster1	uc009ygh.3	Q49AG3	OTTHUMG00000150341	ENST00000432999.2:c.752G>A	11.37:g.10875741C>T	ENSP00000398106:p.Arg251Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	134	2	0.0149254	NM_021211	B2RCC1|Q05D82|Q86WW3|Q9NT24|Q9UBJ4	Missense_Mutation	SNP	ENST00000432999.2	37		.	.	.	.	.	.	.	.	.	.	C	17.48	3.398959	0.62177	.	.	ENSG00000236287	ENST00000432999;ENST00000413761	T;T	0.13778	2.56;2.56	4.18	4.18	0.49190	.	0.000000	0.28284	N	0.015919	T	0.37046	0.0989	M	0.82132	2.575	0.27141	N	0.961648	D	0.89917	1.0	D	0.79784	0.993	T	0.09058	-1.0692	10	0.56958	D	0.05	.	12.3074	0.54910	0.0:1.0:0.0:0.0	.	251	Q49AG3	ZBED5_HUMAN	Q	251	ENSP00000398106:R251Q;ENSP00000415939:R251Q	ENSP00000415939:R251Q	R	-	2	0	ZBED5	10832317	0.999000	0.42202	0.987000	0.45799	0.999000	0.98932	1.437000	0.34991	2.620000	0.88729	0.650000	0.86243	CGA	.	.	none		0.373	ZBED5-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000317691.1	NM_021211	
DCSTAMP	81501	hgsc.bcm.edu	37	8	105361354	105361354	+	Missense_Mutation	SNP	G	G	C	rs67114147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:105361354G>C	ENST00000297581.2	+	2	623	c.574G>C	c.(574-576)Gaa>Caa	p.E192Q	DPYS_ENST00000521601.1_Intron|DCSTAMP_ENST00000517991.1_Missense_Mutation_p.E192Q	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	192					cellular response to interleukin-4 (GO:0071353)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to tumor necrosis factor (GO:0071356)|membrane fusion (GO:0061025)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of cell growth (GO:0030308)|osteoclast differentiation (GO:0030316)|osteoclast fusion (GO:0072675)|positive regulation of bone resorption (GO:0045780)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of monocyte differentiation (GO:0045657)	cell surface (GO:0009986)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)											CAGCAAAGGGGAAGTCCTGAG	0.522													G|||	583	0.116414	0.0605	0.1859	5008	,	,		18345	0.1319		0.1272	False		,,,				2504	0.1155				p.E192Q		Atlas-SNP	.											.	.	.	.	0			c.G574C						PASS	.	G	GLN/GLU	350,4056	178.3+/-207.1	18,314,1871	104.0	96.0	99.0		574	-1.9	0.0	8	dbSNP_130	99	1136,7464	231.0+/-265.1	82,972,3246	yes	missense	TM7SF4	NM_030788.2	29	100,1286,5117	CC,CG,GG		13.2093,7.9437,11.4255	benign	192/471	105361354	1486,11520	2203	4300	6503	SO:0001583	missense	81501	exon2			AAAGGGGAAGTCC	AF305068	CCDS6301.1, CCDS59111.1	8q22.3	2012-08-10	2012-03-27	2012-03-27	ENSG00000164935	ENSG00000164935			18549	protein-coding gene	gene with protein product	"""Dendritic cells (DC)-specific transmembrane protein"", ""IL-Four INDuced"""	605933	"""transmembrane 7 superfamily member 4"""	TM7SF4		11169400, 11345591	Standard	NM_030788		Approved	DC-STAMP, FIND	uc003ylx.2	Q9H295	OTTHUMG00000164890	ENST00000297581.2:c.574G>C	8.37:g.105361354G>C	ENSP00000297581:p.Glu192Gln	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	259	0.11858974358974358	34	0.06910569105691057	72	0.19889502762430938	56	0.0979020979020979	97	0.1279683377308707	G	9.109	1.006175	0.19199	0.079437	0.132093	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.33216	1.42	5.53	-1.86	0.07760	.	0.517494	0.23175	N	0.051088	T	0.00039	0.0001	L	0.34521	1.04	0.54753	P	1.2000000000012001E-5	B	0.21071	0.051	B	0.16722	0.016	T	0.33727	-0.9857	8	.	.	.	-1.1699	11.861	0.52465	0.0768:0.5286:0.3946:0.0	.	192	Q9H295	TM7S4_HUMAN	Q	192	ENSP00000297581:E192Q	.	E	+	1	0	TM7SF4	105430530	0.138000	0.22547	0.010000	0.14722	0.873000	0.50193	-0.341000	0.07811	-0.817000	0.04335	0.561000	0.74099	GAA	G|0.883;C|0.117	0.117	strong		0.522	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114256840	114256840	+	Silent	SNP	C	C	T	rs147906017	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.						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	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	246	4	0.0162602	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	
PSD3	23362	hgsc.bcm.edu	37	8	18729529	18729529	+	Missense_Mutation	SNP	C	C	G	rs78452893	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:18729529C>G	ENST00000327040.8	-	3	947	c.845G>C	c.(844-846)gGg>gCg	p.G282A	PSD3_ENST00000440756.2_Missense_Mutation_p.G282A|PSD3_ENST00000523619.1_Missense_Mutation_p.G217A	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	282					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		ATCACATCCCCCTGGGTGCTC	0.567													C|||	372	0.0742812	0.1082	0.1009	5008	,	,		17718	0.001		0.0517	False		,,,				2504	0.1084				p.G282A		Atlas-SNP	.											.	PSD3	142	.	0			c.G845C						PASS	.	C	ALA/GLY	358,3564		18,322,1621	59.0	60.0	60.0		845	1.8	0.0	8	dbSNP_132	60	462,7838		19,424,3707	yes	missense	PSD3	NM_015310.3	60	37,746,5328	GG,GC,CC		5.5663,9.128,6.7092	benign	282/1048	18729529	820,11402	1961	4150	6111	SO:0001583	missense	23362	exon3			CATCCCCCTGGGT	AF243495	CCDS34854.1, CCDS43720.1	8p21.3	2013-01-10			ENSG00000156011	ENSG00000156011		"""Pleckstrin homology (PH) domain containing"""	19093	protein-coding gene	gene with protein product		614440					Standard	NM_206909		Approved	KIAA0942, HCA67, EFA6R, DKFZp761K1423	uc003wza.3	Q9NYI0	OTTHUMG00000163711	ENST00000327040.8:c.845G>C	8.37:g.18729529C>G	ENSP00000324127:p.Gly282Ala	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	198	85	0.429293	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Missense_Mutation	SNP	ENST00000327040.8	37	CCDS43720.1	127	0.05815018315018315	56	0.11382113821138211	33	0.09116022099447514	0	0.0	38	0.05013192612137203	C	0.099	-1.154510	0.01700	0.09128	0.055663	ENSG00000156011	ENST00000327040;ENST00000440756;ENST00000523619	T;T;T	0.28895	1.59;1.59;1.59	5.81	1.83	0.25207	.	0.796549	0.10675	N	0.647010	T	0.00300	0.0009	N	0.19112	0.55	0.09310	N	1	B	0.23591	0.088	B	0.21360	0.034	T	0.29640	-1.0005	10	0.11485	T	0.65	.	3.858	0.08984	0.1651:0.5581:0.0:0.2768	.	282	E9KL50	.	A	282;282;217	ENSP00000324127:G282A;ENSP00000401704:G282A;ENSP00000430640:G217A	ENSP00000324127:G282A	G	-	2	0	PSD3	18773809	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	0.013000	0.13310	0.309000	0.22966	-1.087000	0.02190	GGG	C|0.937;G|0.063	0.063	strong		0.567	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310	
MUC6	4588	hgsc.bcm.edu	37	11	1016770	1016770	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1016770G>A	ENST00000421673.2	-	31	6081	c.6031C>T	c.(6031-6033)Cct>Tct	p.P2011S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2011	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.P2011S(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)		GTGGAGAAAGGTGGAACGTGA	0.532																																					p.P2011S		Atlas-SNP	.											MUC6_ENST00000421673,extremity,malignant_melanoma,0,1	MUC6	408	1	1	Substitution - Missense(1)	skin(1)	c.C6031T						scavenged	.																																			SO:0001583	missense	4588	exon31			AGAAAGGTGGAAC	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.6031C>T	11.37:g.1016770G>A	ENSP00000406861:p.Pro2011Ser	Somatic	1512	15	0.00992064		WXS	Illumina HiSeq	Phase_I	1260	33	0.0261905	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.638370	0.00799	.	.	ENSG00000184956	ENST00000421673	T	0.17370	2.28	2.4	-4.79	0.03200	.	.	.	.	.	T	0.06735	0.0172	N	0.21194	0.64	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39014	-0.9634	9	0.07990	T	0.79	.	1.1636	0.01810	0.3722:0.1007:0.2914:0.2356	.	2011	Q6W4X9	MUC6_HUMAN	S	2011	ENSP00000406861:P2011S	ENSP00000406861:P2011S	P	-	1	0	MUC6	1006770	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.781000	0.00773	-2.945000	0.00295	-0.671000	0.03813	CCT	.	.	none		0.532	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
PTPN21	11099	hgsc.bcm.edu	37	14	88946343	88946343	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:88946343C>T	ENST00000556564.1	-	13	1716	c.1432G>A	c.(1432-1434)Ggc>Agc	p.G478S	PTPN21_ENST00000328736.3_Missense_Mutation_p.G478S	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	478					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						TACGAGCTGCCGATGTTGAGG	0.667																																					p.G478S		Atlas-SNP	.											.	PTPN21	113	.	0			c.G1432A						PASS	.						36.0	37.0	37.0					14																	88946343		2203	4300	6503	SO:0001583	missense	11099	exon13			AGCTGCCGATGTT	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.1432G>A	14.37:g.88946343C>T	ENSP00000452414:p.Gly478Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	4	0.0816327	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.502634	0.44455	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.72051	-0.62;-0.62	5.38	4.48	0.54585	.	0.111045	0.64402	D	0.000007	T	0.50000	0.1590	L	0.27053	0.805	0.47621	D	0.999473	P	0.41214	0.742	B	0.31946	0.138	T	0.49428	-0.8941	10	0.21014	T	0.42	.	10.7907	0.46432	0.0:0.8548:0.0:0.1452	.	478	Q16825	PTN21_HUMAN	S	478	ENSP00000330276:G478S;ENSP00000452414:G478S	ENSP00000330276:G478S	G	-	1	0	PTPN21	88016096	0.997000	0.39634	0.667000	0.29798	0.960000	0.62799	3.056000	0.49923	2.528000	0.85240	0.561000	0.74099	GGC	.	.	none		0.667	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1		
PLK5	126520	hgsc.bcm.edu	37	19	1535084	1535084	+	Silent	SNP	G	G	A	rs12984316	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1535084G>A	ENST00000334770.4	+	13	1735	c.846G>A	c.(844-846)ccG>ccA	p.P282P	PLK5_ENST00000454744.2_Silent_p.P282P			Q496M5	PLK5_HUMAN	polo-like kinase 5	282	POLO box.				cellular response to growth factor stimulus (GO:0071363)|defense response to tumor cell (GO:0002357)|G2 DNA damage checkpoint (GO:0031572)|mitotic nuclear division (GO:0007067)|positive regulation of neuron projection development (GO:0010976)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|transformed cell apoptotic process (GO:0006927)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)										GTGGAGTCCCGGCCCAACTGG	0.652													g|||	2042	0.407748	0.3177	0.3732	5008	,	,		17293	0.629		0.2167	False		,,,				2504	0.5225				p.P282P		Atlas-SNP	.											PLK5,NS,carcinoma,0,1	PLK5	1	1	0			c.G846A						PASS	.																																			SO:0001819	synonymous_variant	126520	exon14			AGTCCCGGCCCAA	DQ424898	CCDS59328.1	19p13.3	2012-11-19	2011-07-14	2011-07-14	ENSG00000185988	ENSG00000185988			27001	protein-coding gene	gene with protein product			"""polo-like kinase 5 pseudogene"", ""polo-like kinase 5, pseudogene"""	PLK5P		21245385	Standard	NM_001243079		Approved	SgK384ps	uc002ltf.3	Q496M5	OTTHUMG00000180073	ENST00000334770.4:c.846G>A	19.37:g.1535084G>A		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_001243079	B3KNR4|Q1ZYM0	Silent	SNP	ENST00000334770.4	37	CCDS59328.1																																																																																			G|0.685;A|0.315	0.315	strong		0.652	PLK5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449628.1	NR_026557	
SIK1	150094	hgsc.bcm.edu	37	21	44840138	44840138	+	Silent	SNP	G	G	A	rs17004546	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:44840138G>A	ENST00000270162.6	-	8	1080	c.948C>T	c.(946-948)ggC>ggT	p.G316G		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	316	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	GCCGGTCCACGCCCAGGGTCT	0.677													G|||	210	0.0419329	0.003	0.0101	5008	,	,		16158	0.0506		0.0427	False		,,,				2504	0.1074				p.G316G		Atlas-SNP	.											.	SIK1	65	.	0			c.C948T						PASS	.	G		51,4355	50.9+/-86.3	1,49,2153	43.0	40.0	41.0		948	1.0	0.1	21	dbSNP_123	41	391,8209	125.8+/-184.4	13,365,3922	no	coding-synonymous	SIK1	NM_173354.3		14,414,6075	AA,AG,GG		4.5465,1.1575,3.3984		316/784	44840138	442,12564	2203	4300	6503	SO:0001819	synonymous_variant	150094	exon8			GTCCACGCCCAGG	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.948C>T	21.37:g.44840138G>A		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	308	176	0.571429	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Silent	SNP	ENST00000270162.6	37	CCDS33575.1																																																																																			G|0.970;A|0.030	0.030	strong		0.677	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
MUC17	140453	hgsc.bcm.edu	37	7	100682814	100682814	+	Missense_Mutation	SNP	A	A	G	rs201007776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682814A>G	ENST00000306151.4	+	3	8181	c.8117A>G	c.(8116-8118)aAt>aGt	p.N2706S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2706	59 X approximate tandem repeats.|Ser-rich.				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)					CTGTTGGCCAATTCTGAGGCT	0.493																																					p.N2706S		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	1	0			c.A8117G						scavenged	.						245.0	255.0	251.0					7																	100682814		2203	4300	6503	SO:0001583	missense	140453	exon3			TGGCCAATTCTGA	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.8117A>G	7.37:g.100682814A>G	ENSP00000302716:p.Asn2706Ser	Somatic	139	2	0.0143885		WXS	Illumina HiSeq	Phase_I	198	15	0.0757576	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.044	-1.274581	0.01410	.	.	ENSG00000169876	ENST00000306151	T	0.02015	4.5	0.37	-0.741	0.11112	.	.	.	.	.	T	0.00754	0.0025	N	0.02539	-0.55	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.43065	-0.9414	9	0.06236	T	0.91	.	0.1449	0.00087	0.2508:0.246:0.2581:0.2451	.	2706	Q685J3	MUC17_HUMAN	S	2706	ENSP00000302716:N2706S	ENSP00000302716:N2706S	N	+	2	0	MUC17	100469534	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.783000	0.04638	-2.048000	0.00907	-1.389000	0.01157	AAT	A|0.999;G|0.001	0.001	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
NAA40	79829	hgsc.bcm.edu	37	11	63713317	63713317	+	Silent	SNP	G	G	A	rs3740637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:63713317G>A	ENST00000377793.4	+	2	113	c.12G>A	c.(10-12)aaG>aaA	p.K4K	NAA40_ENST00000536939.1_3'UTR|NAA40_ENST00000456907.2_5'UTR|NAA40_ENST00000542163.1_5'UTR|NAA40_ENST00000539656.1_Silent_p.K4K	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	132	59	0.44697	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	
TAS2R41	259287	hgsc.bcm.edu	37	7	143175345	143175345	+	Missense_Mutation	SNP	C	C	T	rs10278721	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:143175345C>T	ENST00000408916.1	+	1	380	c.380C>T	c.(379-381)cCa>cTa	p.P127L	EPHA1-AS1_ENST00000429289.1_RNA	NM_176883.2	NP_795364.2	P59536	T2R41_HUMAN	taste receptor, type 2, member 41	127			P -> L (in dbSNP:rs10278721). {ECO:0000269|PubMed:12379855, ECO:0000269|PubMed:15496549}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(2)|skin(1)	18	Melanoma(164;0.15)					TGGAGGTTCCCAGGGTGGGTG	0.498													C|||	1058	0.211262	0.0227	0.2695	5008	,	,		15749	0.2956		0.2535	False		,,,				2504	0.2945				p.P127L		Atlas-SNP	.											.	TAS2R41	43	.	0			c.C380T						PASS	.	C	LEU/PRO	232,3666		9,214,1726	57.0	56.0	57.0		380	1.5	0.3	7	dbSNP_119	57	2266,6026		312,1642,2192	yes	missense	TAS2R41	NM_176883.2	98	321,1856,3918	TT,TC,CC		27.3275,5.9518,20.4922	benign	127/308	143175345	2498,9692	1949	4146	6095	SO:0001583	missense	259287	exon1			GGTTCCCAGGGTG	AF494232	CCDS43663.1	7q34	2012-08-22			ENSG00000221855	ENSG00000221855		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18883	protein-coding gene	gene with protein product		613965				12379855	Standard	NM_176883		Approved	T2R59	uc003wdc.1	P59536	OTTHUMG00000155892	ENST00000408916.1:c.380C>T	7.37:g.143175345C>T	ENSP00000386201:p.Pro127Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_176883	P59550|Q495I2|Q50KJ5|Q50KJ6|Q50KJ7|Q645W7	Missense_Mutation	SNP	ENST00000408916.1	37	CCDS43663.1	497	0.22756410256410256	19	0.03861788617886179	95	0.26243093922651933	193	0.3374125874125874	190	0.25065963060686014	C	15.91	2.973193	0.53614	0.059518	0.273275	ENSG00000221855	ENST00000408916	T	0.33654	1.4	5.7	1.47	0.22746	.	0.790114	0.10721	U	0.641758	T	0.00012	0.0000	L	0.35593	1.075	0.80722	P	0.0	B	0.33583	0.418	B	0.32393	0.145	T	0.42068	-0.9473	9	0.62326	D	0.03	.	1.6792	0.02828	0.1616:0.3844:0.2791:0.175	rs10278721;rs10278721	127	P59536	T2R41_HUMAN	L	127	ENSP00000386201:P127L	ENSP00000386201:P127L	P	+	2	0	TAS2R41	142885467	0.000000	0.05858	0.272000	0.24630	0.814000	0.46013	0.291000	0.18994	0.745000	0.32763	0.655000	0.94253	CCA	C|0.770;T|0.230	0.230	strong		0.498	TAS2R41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342149.1		
C10orf71	118461	hgsc.bcm.edu	37	10	50533463	50533463	+	Missense_Mutation	SNP	T	T	A	rs10857470	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	107	0	0		WXS	Illumina HiSeq	Phase_I	65	15	0.230769	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	
NBPF15	284565	hgsc.bcm.edu	37	1	148756664	148756664	+	Nonsense_Mutation	SNP	G	G	T	rs587742217	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:148756664G>T	ENST00000417839.1	+	16	2183	c.1993G>T	c.(1993-1995)Gga>Tga	p.G665*		NM_001102663.1	NP_001096133	Q5SXJ2	NBPFG_HUMAN		665	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4	all_hematologic(923;0.032)					GTTCCAGATGGGAGTCATATT	0.443													.|||	776	0.154952	0.1172	0.196	5008	,	,		11980	0.1181		0.2038	False		,,,				2504	0.1646				p.G665X		Atlas-SNP	.											NBPF16,NS,carcinoid-endocrine_tumour,0,1	NBPF16	7	1	0			c.G1993T						scavenged	.						7.0	7.0	7.0					1																	148756664		396	272	668	SO:0001587	stop_gained	728936	exon16			CAGATGGGAGTCA																												ENST00000417839.1:c.1993G>T	1.37:g.148756664G>T	ENSP00000395369:p.Gly665*	Somatic	196	21	0.107143		WXS	Illumina HiSeq	Phase_I	208	51	0.245192	NM_001102663	A8MPT6	Nonsense_Mutation	SNP	ENST00000417839.1	37	CCDS41384.1	.	.	.	.	.	.	.	.	.	.	g	17.60	3.430299	0.62844	.	.	ENSG00000203827	ENST00000417839;ENST00000254372	.	.	.	0.109	-0.218	0.13142	.	.	.	.	.	.	.	.	.	.	.	0.18873	N	0.999988	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	.	.	.	.	.	.	.	X	665	.	ENSP00000254372:G665X	G	+	1	0	NBPF16	147023288	1.000000	0.71417	0.005000	0.12908	0.005000	0.04900	0.720000	0.25896	-1.206000	0.02641	-1.207000	0.01640	GGA	.	.	none		0.443	NBPF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097693.1		
XDH	7498	hgsc.bcm.edu	37	2	31606682	31606682	+	Silent	SNP	A	A	G	rs145596057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:31606682A>G	ENST00000379416.3	-	10	873	c.825T>C	c.(823-825)ttT>ttC	p.F275F	XDH_ENST00000491727.1_5'UTR	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	275	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	CAATCATAGGAAACAGCATAT	0.493													A|||	2	0.000399361	0.0	0.0	5008	,	,		18724	0.0		0.002	False		,,,				2504	0.0				p.F275F	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T825C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	115.0	101.0	106.0		825	0.8	0.9	2	dbSNP_134	106	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	XDH	NM_000379.3		0,15,6488	GG,GA,AA		0.1628,0.0227,0.1153		275/1334	31606682	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	7498	exon10			CATAGGAAACAGC	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.825T>C	2.37:g.31606682A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	166	85	0.512048	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			A|0.999;G|0.001	0.001	strong		0.493	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
PAPOLB	56903	hgsc.bcm.edu	37	7	4900095	4900095	+	Silent	SNP	A	A	G	rs1553960	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:4900095A>G	ENST00000404991.1	-	1	1530	c.1344T>C	c.(1342-1344)aaT>aaC	p.N448N	RADIL_ENST00000536091.1_Intron|RADIL_ENST00000399583.3_Intron	NM_020144.4	NP_064529.4	Q9NRJ5	PAPOB_HUMAN	poly(A) polymerase beta (testis specific)	448					mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)	p.N448N(1)		kidney(1)|large_intestine(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	14		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.089)|OV - Ovarian serous cystadenocarcinoma(56;2.06e-14)		GAATTTCAGAATTATCTGGCT	0.383													G|||	2269	0.453075	0.5537	0.3559	5008	,	,		21126	0.4117		0.341	False		,,,				2504	0.544				p.N449N		Atlas-SNP	.											PAPOLB,NS,carcinoma,0,1	PAPOLB	93	1	1	Substitution - coding silent(1)	stomach(1)	c.T1347C						PASS	.	G	,	2235,2083		607,1021,531	101.0	107.0	105.0		,1347	1.5	0.6	7	dbSNP_88	105	3327,5245		628,2071,1587	yes	intron,coding-synonymous	RADIL,PAPOLB	NM_018059.4,NM_020144.4	,	1235,3092,2118	GG,GA,AA		38.8124,48.2399,43.1497	,	,449/638	4900095	5562,7328	2159	4286	6445	SO:0001819	synonymous_variant	56903	exon1			TTCAGAATTATCT	AF218840		7p22.1	2008-02-08			ENSG00000218823	ENSG00000218823	2.7.7.19		15970	protein-coding gene	gene with protein product		607436				11150526	Standard	NM_020144		Approved	PAPT	uc003snk.3	Q9NRJ5	OTTHUMG00000151759	ENST00000404991.1:c.1344T>C	7.37:g.4900095A>G		Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	399	153	0.383459	NM_020144	Q75LH1|Q8NE14	Silent	SNP	ENST00000404991.1	37																																																																																				A|0.574;G|0.426	0.426	strong		0.383	PAPOLB-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000323797.1	NM_020144	
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739865	20739865	+	Silent	SNP	G	G	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:20739865G>T	ENST00000427390.2	-	8	1975	c.1885C>A	c.(1885-1887)Cgg>Agg	p.R629R		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	629	Gln-rich.|Glu-rich.									NS(3)|endometrium(4)|kidney(1)|skin(3)	11						tcctgctcccgtatcttctcc	0.542																																					p.R629R		Atlas-SNP	.											GOLGA6L6,NS,carcinoma,+1,1	GOLGA6L6	37	1	0			c.C1885A						scavenged	.						7.0	4.0	5.0					15																	20739865		625	1376	2001	SO:0001819	synonymous_variant	727832	exon8			GCTCCCGTATCTT	AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1885C>A	15.37:g.20739865G>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_001145004	D3YTC0	Silent	SNP	ENST00000427390.2	37	CCDS45184.1																																																																																			.	.	none		0.542	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414660.3	NM_001145004	
CCDC74A	90557	hgsc.bcm.edu	37	2	132290464	132290464	+	Missense_Mutation	SNP	G	G	A	rs13660	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:132290464G>A	ENST00000295171.6	+	6	1042	c.904G>A	c.(904-906)Ggg>Agg	p.G302R	CCDC74A_ENST00000409856.3_Missense_Mutation_p.G236R|CCDC74A_ENST00000467992.2_3'UTR	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	221	0	0		WXS	Illumina HiSeq	Phase_I	195	94	0.482051	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	
PKD1	5310	hgsc.bcm.edu	37	16	2144176	2144176	+	Missense_Mutation	SNP	G	G	A	rs34197769	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2144176G>A	ENST00000262304.4	-	35	10743	c.10535C>T	c.(10534-10536)gCg>gTg	p.A3512V	PKD1_ENST00000423118.1_Missense_Mutation_p.A3511V|RP11-304L19.3_ENST00000565937.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3512			A -> V (in dbSNP:rs34197769). {ECO:0000269|PubMed:11967008, ECO:0000269|PubMed:15772804, ECO:0000269|PubMed:18837007}.		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						CCTCTGCAGCGCCAGCGTCTC	0.657													g|||	332	0.0662939	0.1203	0.0562	5008	,	,		16658	0.0		0.0934	False		,,,				2504	0.0409				p.A3512V		Atlas-SNP	.											.	PKD1	184	.	0			c.C10535T						PASS	.	G	VAL/ALA,VAL/ALA	547,3845		39,469,1688	19.0	17.0	18.0		10532,10535	-9.0	0.0	16	dbSNP_126	18	701,7889		27,647,3621	yes	missense,missense	PKD1	NM_000296.3,NM_001009944.2	64,64	66,1116,5309	AA,AG,GG		8.1607,12.4545,9.6133	benign,benign	3511/4303,3512/4304	2144176	1248,11734	2196	4295	6491	SO:0001583	missense	5310	exon35			TGCAGCGCCAGCG	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.10535C>T	16.37:g.2144176G>A	ENSP00000262304:p.Ala3512Val	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	217	120	0.552995	NM_001009944	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	150	0.06868131868131869	57	0.11585365853658537	23	0.06353591160220995	0	0.0	70	0.09234828496042216	G	4.521	0.096772	0.08681	0.124545	0.081607	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.33216	1.42;1.42	4.66	-9.01	0.00744	.	1.060420	0.07438	N	0.896761	T	0.00144	0.0004	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.28971	0.005;0.229	B;B	0.12837	0.001;0.008	T	0.21965	-1.0230	9	0.11182	T	0.66	.	9.7513	0.40477	0.24:0.0:0.5482:0.2118	rs34197769	3511;3512	P98161-3;P98161	.;PKD1_HUMAN	V	3512;3511;2846	ENSP00000262304:A3512V;ENSP00000399501:A3511V	ENSP00000262304:A3512V	A	-	2	0	PKD1	2084177	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.663000	0.25053	-2.116000	0.00830	-2.430000	0.00215	GCG	G|0.911;A|0.089	0.089	strong		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
SLC28A3	64078	hgsc.bcm.edu	37	9	86900926	86900926	+	Silent	SNP	G	G	A	rs7853758	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:86900926G>A	ENST00000376238.4	-	13	1430	c.1381C>T	c.(1381-1383)Ctg>Ttg	p.L461L	RP11-380F14.2_ENST00000419815.1_RNA|SLC28A3_ENST00000537648.1_Silent_p.L392L	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	461					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)			endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	ATAAAAGACAGCAGGGCCAGG	0.498													G|||	1015	0.202676	0.3396	0.2334	5008	,	,		18484	0.1558		0.1372	False		,,,				2504	0.1115				p.L461L	Ovarian(106;425 1539 34835 42413 43572)	Atlas-SNP	.											.	SLC28A3	72	.	0			c.C1381T						PASS	.	G	,	1284,3122	438.6+/-345.4	197,890,1116	92.0	83.0	86.0		1381,1381	-4.1	1.0	9	dbSNP_116	86	1248,7352	249.4+/-276.7	93,1062,3145	no	coding-synonymous,coding-synonymous	SLC28A3	NM_001199633.1,NM_022127.2	,	290,1952,4261	AA,AG,GG		14.5116,29.1421,19.4679	,	461/692,461/692	86900926	2532,10474	2203	4300	6503	SO:0001819	synonymous_variant	64078	exon13			AAGACAGCAGGGC	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"""Solute carriers"""	16484	protein-coding gene	gene with protein product		608269	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"""			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.1381C>T	9.37:g.86900926G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_001199633	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Silent	SNP	ENST00000376238.4	37	CCDS6670.1																																																																																			G|0.802;A|0.198	0.198	strong		0.498	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127	
PTCD1	26024	hgsc.bcm.edu	37	7	99032517	99032517	+	Missense_Mutation	SNP	G	G	A	rs34943973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99032517G>A	ENST00000292478.4	-	2	599	c.349C>T	c.(349-351)Cgg>Tgg	p.R117W	PTCD1_ENST00000485746.1_5'UTR|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.R166W|ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000555673.1_Missense_Mutation_p.R166W	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	117					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			TCATCTCTCCGTTCCCCAAAC	0.542													G|||	214	0.0427316	0.0545	0.0519	5008	,	,		19132	0.0327		0.0308	False		,,,				2504	0.0429				p.R166W		Atlas-SNP	.											.	.	.	.	0			c.C496T						PASS	.	G	TRP/ARG,TRP/ARG	210,4196	130.2+/-166.9	4,202,1997	147.0	155.0	152.0		496,349	4.8	0.3	7	dbSNP_126	152	344,8256	117.7+/-177.3	9,326,3965	yes	missense,missense	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	101,101	13,528,5962	AA,AG,GG		4.0,4.7662,4.2596	benign,benign	166/750,117/701	99032517	554,12452	2203	4300	6503	SO:0001583	missense	100526740	exon3			CTCTCCGTTCCCC	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.349C>T	7.37:g.99032517G>A	ENSP00000292478:p.Arg117Trp	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	280	120	0.428571	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	84	0.038461538461538464	19	0.03861788617886179	23	0.06353591160220995	18	0.03146853146853147	24	0.0316622691292876	G	9.519	1.107845	0.20714	0.047662	0.04	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000555673;ENST00000430982;ENST00000430029;ENST00000413834	T;T;D;D;T	0.83250	-0.16;-0.15;-1.7;-1.7;-0.15	5.86	4.8	0.61643	.	0.540484	0.20400	N	0.093068	T	0.20373	0.0490	N	0.14661	0.345	0.09310	N	1	P;P	0.45078	0.85;0.519	B;B	0.40782	0.34;0.083	T	0.42649	-0.9439	10	0.37606	T	0.19	-19.6274	6.8271	0.23889	0.0749:0.2175:0.5906:0.117	rs34943973	166;117	G3V325;O75127	.;PTCD1_HUMAN	W	117;166;117;117;166	ENSP00000292478:R117W;ENSP00000450995:R166W;ENSP00000390530:R117W;ENSP00000408059:R117W;ENSP00000400168:R166W	ENSP00000400168:R166W	R	-	1	2	ATP5J2-PTCD1;PTCD1	98870453	0.147000	0.22687	0.252000	0.24328	0.024000	0.10985	2.623000	0.46435	2.766000	0.95052	0.655000	0.94253	CGG	G|0.958;A|0.042	0.042	strong		0.542	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
TENM2	57451	hgsc.bcm.edu	37	5	167645888	167645888	+	Silent	SNP	T	T	C	rs1363560	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:167645888T>C	ENST00000518659.1	+	23	5031	c.4992T>C	c.(4990-4992)aaT>aaC	p.N1664N	TENM2_ENST00000520394.1_Silent_p.N1425N|TENM2_ENST00000403607.2_Silent_p.N1488N|TENM2_ENST00000545108.1_Silent_p.N1663N|TENM2_ENST00000519204.1_Silent_p.N1543N	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1664					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)										TGGGCACCAATGGAGGCCTCA	0.557													.|||	2052	0.409744	0.6422	0.2205	5008	,	,		20614	0.5942		0.2207	False		,,,				2504	0.2342				p.N1655N		Atlas-SNP	.											.	.	.	.	0			c.T4965C						PASS	.	T		2411,1783		709,993,395	147.0	153.0	151.0		4965	-9.2	0.0	5	dbSNP_88	151	1905,6525		229,1447,2539	no	coding-synonymous	ODZ2	NM_001122679.1		938,2440,2934	CC,CT,TT		22.5979,42.5131,34.1888		1655/2766	167645888	4316,8308	2097	4215	6312	SO:0001819	synonymous_variant	57451	exon23			CACCAATGGAGGC	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.4992T>C	5.37:g.167645888T>C		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	257	127	0.494163	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				T|0.589;C|0.411	0.411	strong		0.557	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
PLIN3	10226	hgsc.bcm.edu	37	19	4861381	4861381	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4861381T>C	ENST00000221957.4	-	2	202	c.26A>G	c.(25-27)gAt>gGt	p.D9G	PLIN3_ENST00000592528.1_Missense_Mutation_p.D9G|PLIN3_ENST00000585479.1_Missense_Mutation_p.D9G	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	9					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GGTGCTGCCATCAGCCTCTGC	0.627																																					p.D9G		Atlas-SNP	.											PLIN3,NS,carcinoma,-1,1	PLIN3	36	1	0			c.A26G						PASS	.						113.0	91.0	98.0					19																	4861381		2203	4300	6503	SO:0001583	missense	10226	exon2			CTGCCATCAGCCT	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.26A>G	19.37:g.4861381T>C	ENSP00000221957:p.Asp9Gly	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	13	0.270833	NM_001164189	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	37	CCDS12137.1	.	.	.	.	.	.	.	.	.	.	T	7.718	0.696623	0.15106	.	.	ENSG00000105355	ENST00000221957	T	0.05925	3.37	3.24	-1.14	0.09741	.	1.247070	0.05815	U	0.614699	T	0.05135	0.0137	L	0.29908	0.895	0.09310	N	1	B;B	0.15930	0.015;0.009	B;B	0.16722	0.016;0.007	T	0.45731	-0.9241	10	0.27785	T	0.31	-22.7586	5.44	0.16501	0.0:0.161:0.5605:0.2785	.	9;9	O60664-3;O60664	.;PLIN3_HUMAN	G	9	ENSP00000221957:D9G	ENSP00000221957:D9G	D	-	2	0	PLIN3	4812381	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	0.176000	0.16782	0.042000	0.15717	0.379000	0.24179	GAT	.	.	none		0.627	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817	
DIAPH3	81624	hgsc.bcm.edu	37	13	60566644	60566644	+	Missense_Mutation	SNP	T	T	C	rs36084898	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:60566644T>C	ENST00000400324.4	-	10	1308	c.1088A>G	c.(1087-1089)aAt>aGt	p.N363S	DIAPH3_ENST00000400319.1_Missense_Mutation_p.N293S|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400330.1_Missense_Mutation_p.N363S|DIAPH3_ENST00000377908.2_Missense_Mutation_p.N352S|DIAPH3_ENST00000400320.1_Missense_Mutation_p.N317S|DIAPH3_ENST00000267215.4_Missense_Mutation_p.N363S	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	363	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.		N -> S (in dbSNP:rs36084898).		actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		CATAAATTCATTTCTGATGTG	0.388													T|||	372	0.0742812	0.1074	0.121	5008	,	,		14649	0.0317		0.0557	False		,,,				2504	0.0593				p.N363S		Atlas-SNP	.											.	DIAPH3	139	.	0			c.A1088G						PASS	.	T	SER/ASN,SER/ASN	352,3414		14,324,1545	71.0	65.0	67.0		1088,299	5.8	1.0	13	dbSNP_126	67	448,7764		14,420,3672	yes	missense,missense	DIAPH3	NM_001042517.1,NM_030932.3	46,46	28,744,5217	CC,CT,TT		5.4554,9.3468,6.6789	probably-damaging,probably-damaging	363/1194,100/850	60566644	800,11178	1883	4106	5989	SO:0001583	missense	81624	exon10			AATTCATTTCTGA	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"""diaphanous (Drosophila, homolog) 3"", ""auditory neuropathy, autosomal dominant 1"", ""diaphanous homolog 3 (Drosophila)"""	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.1088A>G	13.37:g.60566644T>C	ENSP00000383178:p.Asn363Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	37	CCDS41898.1	141	0.06456043956043957	47	0.09552845528455285	36	0.09944751381215469	18	0.03146853146853147	40	0.052770448548812667	T	14.92	2.680034	0.47886	0.093468	0.054554	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	D;D;D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59;-1.59;-1.59	5.8	5.8	0.92144	GTPase-binding/formin homology 3 (1);Diaphanous FH3 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24547	0.0595	M	0.65320	2	0.43830	D	0.9964	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.992	D;D;D;D;D	0.87578	0.998;0.998;0.998;0.997;0.987	T	0.65055	-0.6261	10	0.21540	T	0.41	.	16.1372	0.81494	0.0:0.0:0.0:1.0	rs36084898	293;317;352;100;363	A8MYX0;C9JL55;C9JDG1;Q9NSV4-1;Q9NSV4	.;.;.;.;DIAP3_HUMAN	S	363;363;352;317;293;352;293;317;363;100;363	ENSP00000383178:N363S;ENSP00000383184:N363S;ENSP00000367141:N352S;ENSP00000383173:N293S;ENSP00000383174:N317S;ENSP00000267215:N363S	ENSP00000267214:N100S	N	-	2	0	DIAPH3	59464645	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.606000	0.82863	2.207000	0.71202	0.455000	0.32223	AAT	T|0.940;C|0.060	0.060	strong		0.388	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
UBR4	23352	hgsc.bcm.edu	37	1	19499560	19499560	+	Missense_Mutation	SNP	T	T	C	rs16862578	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19499560T>C	ENST00000375254.3	-	25	3346	c.3319A>G	c.(3319-3321)Acc>Gcc	p.T1107A	UBR4_ENST00000375217.2_Missense_Mutation_p.T1107A|UBR4_ENST00000375226.2_Missense_Mutation_p.T1107A|UBR4_ENST00000375267.2_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	143	0	0		WXS	Illumina HiSeq	Phase_I	76	54	0.710526	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	
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19127347	19127347	+	Missense_Mutation	SNP	C	C	T	rs11074362	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:19127347C>T	ENST00000381440.3	+	1	2094	c.1564C>T	c.(1564-1566)Ccc>Tcc	p.P522S	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	522			P -> S (in dbSNP:rs11074362).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GTGCCCCCCACCCCGGAGTCA	0.652													C|||	260	0.0519169	0.1369	0.0159	5008	,	,		15561	0.004		0.0358	False		,,,				2504	0.0286				p.P522S		Atlas-SNP	.											.	ITPRIPL2	40	.	0			c.C1564T						PASS	.	C	SER/PRO	484,3910	223.3+/-239.8	28,428,1741	55.0	57.0	56.0		1564	3.4	0.7	16	dbSNP_120	56	290,8310	106.2+/-167.1	6,278,4016	yes	missense	ITPRIPL2	NM_001034841.3	74	34,706,5757	TT,TC,CC		3.3721,11.015,5.9566	possibly-damaging	522/536	19127347	774,12220	2197	4300	6497	SO:0001583	missense	162073	exon1			CCCCCACCCCGGA		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"""inositol 1,4,5-triphosphate receptor interacting protein-like 2"""				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.1564C>T	16.37:g.19127347C>T	ENSP00000370849:p.Pro522Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	46	0.575	NM_001034841		Missense_Mutation	SNP	ENST00000381440.3	37	CCDS32395.1	95	0.043498168498168496	64	0.13008130081300814	3	0.008287292817679558	3	0.005244755244755245	25	0.032981530343007916	C	12.36	1.914419	0.33815	0.11015	0.033721	ENSG00000205730	ENST00000381440	T	0.14766	2.48	5.5	3.41	0.39046	.	0.000000	0.36555	U	0.002532	T	0.00144	0.0004	N	0.24115	0.695	0.36126	D	0.845812	D	0.56287	0.975	P	0.45712	0.491	T	0.35699	-0.9778	10	0.66056	D	0.02	-11.5233	13.222	0.59894	0.0:0.6954:0.3046:0.0	rs11074362;rs52813532;rs61562573;rs11074362	522	Q3MIP1	IPIL2_HUMAN	S	522	ENSP00000370849:P522S	ENSP00000370849:P522S	P	+	1	0	ITPRIPL2	19034848	0.112000	0.22096	0.732000	0.30844	0.937000	0.57800	0.662000	0.25038	1.302000	0.44855	0.561000	0.74099	CCC	C|0.945;T|0.055	0.055	strong		0.652	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841	
ZNF750	79755	hgsc.bcm.edu	37	17	80789628	80789628	+	Missense_Mutation	SNP	T	T	C	rs8074277	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80789628T>C	ENST00000269394.3	-	2	1536	c.703A>G	c.(703-705)Atg>Gtg	p.M235V	TBCD_ENST00000397466.2_Intron|TBCD_ENST00000539345.2_Intron|ZNF750_ENST00000572562.1_Intron|TBCD_ENST00000355528.4_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	235			M -> V (in dbSNP:rs8074277).		cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GTGGGGTGCATGTAAGGGGAA	0.567													T|||	624	0.124601	0.1263	0.3026	5008	,	,		16012	0.0833		0.1362	False		,,,				2504	0.0266				p.M235V		Atlas-SNP	.											ZNF750,NS,adenoma,0,1	ZNF750	60	1	0			c.A703G						PASS	.	T	,VAL/MET	577,3829	254.9+/-260.3	45,487,1671	53.0	56.0	55.0		,703	-11.4	0.0	17	dbSNP_116	55	1534,7066	288.1+/-298.6	135,1264,2901	yes	intron,missense	TBCD,ZNF750	NM_005993.4,NM_024702.2	,21	180,1751,4572	CC,CT,TT		17.8372,13.0958,16.231	,benign	,235/724	80789628	2111,10895	2203	4300	6503	SO:0001583	missense	79755	exon2			GGTGCATGTAAGG	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.703A>G	17.37:g.80789628T>C	ENSP00000269394:p.Met235Val	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	197	97	0.492386	NM_024702	Q9H899	Missense_Mutation	SNP	ENST00000269394.3	37	CCDS11819.1	289	0.13232600732600733	52	0.10569105691056911	78	0.2154696132596685	44	0.07692307692307693	115	0.1517150395778364	T	8.536	0.872179	0.17322	0.130958	0.178372	ENSG00000141579	ENST00000269394	T	0.13778	2.56	5.77	-11.4	0.00090	.	0.915550	0.09345	N	0.814918	T	0.00012	0.0000	N	0.16307	0.4	0.40232	P	0.022136999999999962	B	0.06786	0.001	B	0.08055	0.003	T	0.41893	-0.9483	8	.	.	.	-2.4325	13.1455	0.59459	0.0:0.1284:0.0968:0.7748	rs8074277;rs52814169;rs59556240;rs8074277	235	Q32MQ0	ZN750_HUMAN	V	235	ENSP00000269394:M235V	.	M	-	1	0	ZNF750	78382917	0.000000	0.05858	0.001000	0.08648	0.765000	0.43378	-1.308000	0.02730	-2.288000	0.00668	-0.256000	0.11100	ATG	T|0.855;C|0.145	0.145	strong		0.567	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
NWD1	284434	hgsc.bcm.edu	37	19	16860882	16860882	+	Missense_Mutation	SNP	G	G	A	rs61746179	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:16860882G>A	ENST00000552788.1	+	4	1429	c.1429G>A	c.(1429-1431)Gac>Aac	p.D477N	NWD1_ENST00000339803.6_Missense_Mutation_p.D342N|NWD1_ENST00000379808.3_Missense_Mutation_p.D477N|NWD1_ENST00000549814.1_Missense_Mutation_p.D477N|NWD1_ENST00000524140.2_Missense_Mutation_p.D477N|NWD1_ENST00000523826.1_Missense_Mutation_p.D271N			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	477	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGGGGTTTTGGACACCTTGCA	0.647													G|||	34	0.00678914	0.0008	0.0058	5008	,	,		17184	0.0		0.0268	False		,,,				2504	0.002				p.D477N		Atlas-SNP	.											.	NWD1	303	.	0			c.G1429A						PASS	.	G	ASN/ASP	20,4386	27.2+/-55.0	0,20,2183	61.0	65.0	63.0		1429	-0.6	0.0	19	dbSNP_129	63	190,8410	81.8+/-144.4	0,190,4110	yes	missense	NWD1	NM_001007525.3	23	0,210,6293	AA,AG,GG		2.2093,0.4539,1.6146	benign	477/1433	16860882	210,12796	2203	4300	6503	SO:0001583	missense	284434	exon6			GTTTTGGACACCT	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1429G>A	19.37:g.16860882G>A	ENSP00000447224:p.Asp477Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	g	5.738	0.320672	0.10845	0.004539	0.022093	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	D;D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54;-1.54	4.78	-0.559	0.11792	.	1.130240	0.06413	N	0.720955	T	0.46483	0.1395	L	0.50333	1.59	0.09310	N	1	P;P;P	0.43231	0.801;0.589;0.642	B;B;B	0.38106	0.197;0.173;0.265	T	0.51919	-0.8644	10	0.18276	T	0.48	-12.1674	3.9409	0.09326	0.3107:0.357:0.3323:0.0	rs61746179	477;477;342	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	N	342;477;477;477;271;477;342	ENSP00000428579:D477N;ENSP00000447548:D477N;ENSP00000369136:D477N;ENSP00000428955:D271N;ENSP00000447224:D477N;ENSP00000340159:D342N	ENSP00000340159:D342N	D	+	1	0	NWD1	16721882	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.050000	0.11904	0.421000	0.25980	-0.366000	0.07423	GAC	G|0.985;A|0.015	0.015	strong		0.647	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
MYBL2	4605	hgsc.bcm.edu	37	20	42343821	42343821	+	Missense_Mutation	SNP	C	C	G	rs11556379	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:42343821C>G	ENST00000217026.4	+	13	1999	c.1872C>G	c.(1870-1872)atC>atG	p.I624M	MYBL2_ENST00000396863.4_Missense_Mutation_p.I600M	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	624			I -> M (in dbSNP:rs11556379).		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			TGTCAGGTATCAAAGAAGACA	0.557													C|||	116	0.0231629	0.0045	0.013	5008	,	,		17326	0.001		0.0666	False		,,,				2504	0.0337				p.I624M		Atlas-SNP	.											.	MYBL2	82	.	0			c.C1872G	GRCh37	CM087205	MYBL2	M	rs11556379	PASS	.	C	MET/ILE	47,4359	48.2+/-83.0	0,47,2156	180.0	185.0	183.0		1872	-0.5	0.1	20	dbSNP_120	183	472,8128	138.7+/-195.5	13,446,3841	yes	missense	MYBL2	NM_002466.2	10	13,493,5997	GG,GC,CC		5.4884,1.0667,3.9905	benign	624/701	42343821	519,12487	2203	4300	6503	SO:0001583	missense	4605	exon13			AGGTATCAAAGAA		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.1872C>G	20.37:g.42343821C>G	ENSP00000217026:p.Ile624Met	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	271	127	0.468635	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	58	0.026556776556776556	3	0.006097560975609756	4	0.011049723756906077	1	0.0017482517482517483	50	0.06596306068601583	C	13.76	2.334035	0.41297	0.010667	0.054884	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.14640	2.49;2.49	4.44	-0.47	0.12131	.	5.244820	0.00166	N	0.000010	T	0.00695	0.0023	N	0.08118	0	0.09310	N	0.999996	P;B	0.38250	0.624;0.257	P;B	0.44518	0.452;0.1	T	0.10660	-1.0620	10	0.34782	T	0.22	-0.9878	4.0914	0.09972	0.162:0.5021:0.0:0.3359	rs11556379;rs52823145;rs11556379	600;624	F8W6N6;P10244	.;MYBB_HUMAN	M	600;624	ENSP00000380072:I600M;ENSP00000217026:I624M	ENSP00000217026:I624M	I	+	3	3	MYBL2	41777235	0.208000	0.23494	0.071000	0.20095	0.820000	0.46376	0.263000	0.18478	0.002000	0.14630	0.491000	0.48974	ATC	C|0.968;G|0.032	0.032	strong		0.557	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
C10orf25	220979	hgsc.bcm.edu	37	10	45496126	45496126	+	Missense_Mutation	SNP	G	G	A	rs41301609	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:45496126G>A	ENST00000298298.1	-	1	210	c.182C>T	c.(181-183)cCa>cTa	p.P61L	ZNF22_ENST00000298299.3_5'UTR|CEP164P1_ENST00000456938.2_RNA	NM_001039380.2	NP_001034469.2	Q5T742	CJ025_HUMAN	chromosome 10 open reading frame 25	61			P -> L (in dbSNP:rs41301609).			extracellular region (GO:0005576)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6						CAAAATTTGTGGAAAGTATGC	0.458													A|||	276	0.0551118	0.0749	0.013	5008	,	,		17077	0.0972		0.0427	False		,,,				2504	0.0276				p.P61L		Atlas-SNP	.											.	C10orf25	11	.	0			c.C182T						PASS	.	A	LEU/PRO	243,4163	802.0+/-415.6	7,229,1967	72.0	74.0	73.0		182	-5.2	0.0	10	dbSNP_127	73	404,8196	800.0+/-407.4	6,392,3902	yes	missense	C10orf25	NM_001039380.2	98	13,621,5869	AA,AG,GG		4.6977,5.5152,4.9746	benign	61/123	45496126	647,12359	2203	4300	6503	SO:0001583	missense	220979	exon1			ATTTGTGGAAAGT	AK055129	CCDS31187.1	10q11.21	2003-11-21			ENSG00000165511	ENSG00000165511			23509	protein-coding gene	gene with protein product							Standard	NM_001039380		Approved	FLJ30567	uc001jbv.2	Q5T742	OTTHUMG00000018066	ENST00000298298.1:c.182C>T	10.37:g.45496126G>A	ENSP00000298298:p.Pro61Leu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	60	13	0.216667	NM_001039380	A1L424|Q96NM5	Missense_Mutation	SNP	ENST00000298298.1	37	CCDS31187.1	146	0.06684981684981685	41	0.08333333333333333	6	0.016574585635359115	66	0.11538461538461539	33	0.04353562005277045	A	6.705	0.498748	0.12762	0.055152	0.046977	ENSG00000165511	ENST00000298298	T	0.39997	1.05	2.81	-5.15	0.02866	.	.	.	.	.	T	0.00271	0.0008	N	0.08118	0	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.12734	-1.0536	8	0.87932	D	0	.	9.3936	0.38388	0.1834:0.1546:0.662:0.0	rs41301609	61	Q5T742	CJ025_HUMAN	L	61	ENSP00000298298:P61L	ENSP00000298298:P61L	P	-	2	0	C10orf25	44816132	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.507000	0.06352	-1.884000	0.01119	-0.360000	0.07572	CCA	G|0.948;A|0.052	0.052	strong		0.458	C10orf25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047763.1	NM_145022	
HSPH1	10808	hgsc.bcm.edu	37	13	31729729	31729729	+	Silent	SNP	A	A	G	rs1047086	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:31729729A>G	ENST00000320027.5	-	3	572	c.228T>C	c.(226-228)aaT>aaC	p.N76N	HSPH1_ENST00000429785.2_5'UTR|HSPH1_ENST00000445273.2_Silent_p.N78N|HSPH1_ENST00000380406.5_Silent_p.N76N|HSPH1_ENST00000380405.4_Silent_p.N76N	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	76					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		TGAAGGGGTCATTGAATGCTC	0.338													A|||	1131	0.225839	0.2451	0.2723	5008	,	,		16489	0.0109		0.4642	False		,,,				2504	0.1431				p.N76N		Atlas-SNP	.											.	HSPH1	65	.	0			c.T228C						PASS	.	A		1261,3145	430.8+/-342.7	171,919,1113	118.0	116.0	117.0		228	3.3	0.9	13	dbSNP_86	117	4063,4537	557.6+/-387.1	952,2159,1189	no	coding-synonymous	HSPH1	NM_006644.2		1123,3078,2302	GG,GA,AA		47.2442,28.6201,40.935		76/859	31729729	5324,7682	2203	4300	6503	SO:0001819	synonymous_variant	10808	exon3			GGGGTCATTGAAT	AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"""Heat shock proteins / HSP70"""	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.228T>C	13.37:g.31729729A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	171	78	0.45614	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Silent	SNP	ENST00000320027.5	37	CCDS9340.1																																																																																			A|0.651;G|0.349	0.349	strong		0.338	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1		
PAX9	5083	hgsc.bcm.edu	37	14	37135752	37135752	+	Silent	SNP	C	C	T	rs12881240	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:37135752C>T	ENST00000361487.6	+	3	942	c.717C>T	c.(715-717)caC>caT	p.H239H	PAX9_ENST00000402703.2_Silent_p.H239H|PAX9_ENST00000557107.1_3'UTR|PAX9_ENST00000554201.1_Silent_p.H52H			P55771	PAX9_HUMAN	paired box 9	239					cellular response to growth factor stimulus (GO:0071363)|endoderm development (GO:0007492)|face morphogenesis (GO:0060325)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|regulation of odontogenesis (GO:0042481)	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)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(3)	12	Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)|Breast(36;0.218)		Lung(8;1.12e-09)|LUAD - Lung adenocarcinoma(9;2.16e-07)|Epithelial(34;0.00357)|all cancers(34;0.00998)|LUSC - Lung squamous cell carcinoma(13;0.0189)	GBM - Glioblastoma multiforme(112;0.0181)		CCGCCCCGCACGCGGTGAACG	0.687													C|||	802	0.160144	0.0129	0.1196	5008	,	,		13934	0.3155		0.2167	False		,,,				2504	0.1697				p.H239H		Atlas-SNP	.											PAX9,NS,carcinoma,0,1	PAX9	34	1	0			c.C717T						scavenged	.	C		209,4153		6,197,1978	20.0	14.0	16.0		717	3.5	1.0	14	dbSNP_121	16	1756,6802		203,1350,2726	no	coding-synonymous	PAX9	NM_006194.3		209,1547,4704	TT,TC,CC		20.5188,4.7914,15.209		239/342	37135752	1965,10955	2181	4279	6460	SO:0001819	synonymous_variant	5083	exon4			CCCGCACGCGGTG	AJ238381	CCDS9662.1	14q13.3	2007-07-12	2007-07-12		ENSG00000198807	ENSG00000198807		"""Paired boxes"""	8623	protein-coding gene	gene with protein product		167416	"""paired box gene 9"""			7981748	Standard	NM_006194		Approved		uc001wty.4	P55771	OTTHUMG00000140251	ENST00000361487.6:c.717C>T	14.37:g.37135752C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	221	3	0.0135747	NM_006194	Q99582|Q9UQR4	Silent	SNP	ENST00000361487.6	37	CCDS9662.1																																																																																			C|0.841;T|0.159	0.159	strong		0.687	PAX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276733.2		
VPS8	23355	hgsc.bcm.edu	37	3	184550501	184550501	+	Missense_Mutation	SNP	A	A	G	rs9830734	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:184550501A>G	ENST00000437079.3	+	4	418	c.247A>G	c.(247-249)Att>Gtt	p.I83V	VPS8_ENST00000446204.2_Missense_Mutation_p.I83V|VPS8_ENST00000287546.4_Missense_Mutation_p.I83V|VPS8_ENST00000436792.2_Missense_Mutation_p.I83V|VPS8_ENST00000424463.2_Missense_Mutation_p.I83V	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	83			I -> V (in dbSNP:rs9830734). {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)			TGAGTCTTTTATTCTTGAGGA	0.348													G|||	2774	0.553914	0.7103	0.4452	5008	,	,		18685	0.6657		0.3151	False		,,,				2504	0.5501				p.I83V		Atlas-SNP	.											.	VPS8	109	.	0			c.A247G						PASS	.	G	VAL/ILE,VAL/ILE	2431,1327		802,827,250	125.0	114.0	117.0		247,247	3.0	1.0	3	dbSNP_119	117	2377,5857		366,1645,2106	yes	missense,missense	VPS8	NM_001009921.2,NM_015303.3	29,29	1168,2472,2356	GG,GA,AA		28.8681,35.3113,40.0934	benign,benign	83/1429,83/1427	184550501	4808,7184	1879	4117	5996	SO:0001583	missense	23355	exon4			TCTTTTATTCTTG	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.247A>G	3.37:g.184550501A>G	ENSP00000397879:p.Ile83Val	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	267	122	0.456929	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	1121	0.5132783882783882	336	0.6829268292682927	171	0.4723756906077348	365	0.6381118881118881	249	0.32849604221635886	G	1.030	-0.682044	0.03353	0.646887	0.288681	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204;ENST00000422105;ENST00000424463;ENST00000441141;ENST00000445089	T;T;T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27;2.27;2.27	5.7	2.98	0.34508	.	0.257195	0.38959	N	0.001503	T	0.00012	0.0000	N	0.08118	0	0.46376	P	9.829999999999561E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.22068	-1.0227	9	0.20519	T	0.43	-3.4649	8.947	0.35764	0.358:0.0:0.642:0.0	rs9830734;rs61289304;rs9830734	83;83;83	Q8N3P4-2;C9JP71;Q8N3P4-3	.;.;.	V	83	ENSP00000287546:I83V;ENSP00000397879:I83V;ENSP00000404704:I83V;ENSP00000405483:I83V;ENSP00000415161:I83V;ENSP00000389480:I83V;ENSP00000409957:I83V;ENSP00000416150:I83V	ENSP00000287546:I83V	I	+	1	0	VPS8	186033195	1.000000	0.71417	0.995000	0.50966	0.886000	0.51366	0.871000	0.28023	0.093000	0.17368	-1.861000	0.00560	ATT	A|0.480;G|0.520	0.520	strong		0.348	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
TXNDC2	84203	hgsc.bcm.edu	37	18	9888069	9888069	+	Silent	SNP	A	A	G	rs2240905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:9888069A>G	ENST00000306084.6	+	2	1792	c.1593A>G	c.(1591-1593)gaA>gaG	p.E531E	TXNDC2_ENST00000357775.5_Silent_p.E464E|TXNDC2_ENST00000536353.2_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	531	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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						ATAAAAAAGAAGAAAAGGTGG	0.438													A|||	2778	0.554712	0.472	0.5778	5008	,	,		20063	0.8175		0.4791	False		,,,				2504	0.4571				p.E531E		Atlas-SNP	.											TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	0			c.A1593G						PASS	.	A	,	2154,2252	577.4+/-384.4	540,1074,589	43.0	44.0	44.0		1593,1392	0.3	1.0	18	dbSNP_98	44	4220,4380	568.4+/-389.0	1048,2124,1128	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	1588,3198,1717	GG,GA,AA		49.0698,48.8879,49.0082	,	531/554,464/487	9888069	6374,6632	2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			AAAAGAAGAAAAG	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.1593A>G	18.37:g.9888069A>G		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			G|0.522;N|0.000	0.522	strong		0.438	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
MUC12	10071	hgsc.bcm.edu	37	7	100635143	100635143	+	Silent	SNP	T	T	C	rs34337783	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100635143T>C	ENST00000379442.3	+	5	1728	c.1728T>C	c.(1726-1728)cgT>cgC	p.R576R	MUC12_ENST00000536621.1_Silent_p.R433R			Q9UKN1	MUC12_HUMAN	mucin 12, cell surface associated	576	28 X 19 AA approximate tandem repeats of E-E-S-X-X-X-H-X-X-P-X-X-T-X-T-X-X-X-P.|Ser-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|regulation of cell growth (GO:0001558)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)				breast(6)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)|stomach(13)	25						TCTCAGGCCGTAGTGAGGAAT	0.537													t|||	619	0.123602	0.2156	0.0922	5008	,	,		30398	0.0169		0.1352	False		,,,				2504	0.1196				p.R433R		Atlas-SNP	.											MUC12,NS,carcinoma,+2,1	MUC12	140	1	0			c.T1299C						PASS	.	T		262,1122		24,214,454	351.0	392.0	380.0		1299	0.1	0.0	7	dbSNP_126	380	454,2728		34,386,1171	no	coding-synonymous	MUC12	NM_001164462.1		58,600,1625	CC,CT,TT		14.2678,18.9306,15.6811		433/5336	100635143	716,3850	692	1591	2283	SO:0001819	synonymous_variant	10071	exon2			AGGCCGTAGTGAG	AF147790, AF147791	CCDS55139.1	7q22	2007-01-17	2006-03-14		ENSG00000205277	ENSG00000205277		"""Mucins"""	7510	protein-coding gene	gene with protein product		604609	"""mucin 11"""	MUC11		10463611	Standard	NM_001164462		Approved		uc003uxo.3	Q9UKN1	OTTHUMG00000157042	ENST00000379442.3:c.1728T>C	7.37:g.100635143T>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001164462	A6ND38|F5GWV9|Q9UKN0	Silent	SNP	ENST00000379442.3	37																																																																																				T|0.890;C|0.110	0.110	strong		0.537	MUC12-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347234.1	XM_379904	
HEATR1	55127	hgsc.bcm.edu	37	1	236767288	236767288	+	Silent	SNP	C	C	T	rs16834056	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:236767288C>T	ENST00000366582.3	-	2	222	c.108G>A	c.(106-108)gcG>gcA	p.A36A	HEATR1_ENST00000366581.2_Silent_p.A36A|HEATR1_ENST00000366579.1_Silent_p.A36A	NM_018072.5	NP_060542.4	Q9H583	HEAT1_HUMAN	HEAT repeat containing 1	36					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)			CGATTGTGGCCGCTTCCTTAG	0.473													C|||	31	0.0061901	0.0008	0.0072	5008	,	,		16862	0.0		0.0149	False		,,,				2504	0.0102				p.A36A		Atlas-SNP	.											.	HEATR1	197	.	0			c.G108A						PASS	.	C		22,4384	28.1+/-56.4	0,22,2181	67.0	66.0	66.0		108	-0.3	1.0	1	dbSNP_123	66	226,8374	93.3+/-155.3	1,224,4075	no	coding-synonymous	HEATR1	NM_018072.5		1,246,6256	TT,TC,CC		2.6279,0.4993,1.9068		36/2145	236767288	248,12758	2203	4300	6503	SO:0001819	synonymous_variant	55127	exon2			TGTGGCCGCTTCC	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.108G>A	1.37:g.236767288C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	161	54	0.335404	NM_018072	Q5T3Q8|Q6P197|Q9NW23	Silent	SNP	ENST00000366582.3	37	CCDS31066.1																																																																																			C|0.985;T|0.015	0.015	strong		0.473	HEATR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096635.1	XM_375853	
SARDH	1757	hgsc.bcm.edu	37	9	136561367	136561367	+	Silent	SNP	G	G	A	rs2502740	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136561367G>A	ENST00000371872.4	-	14	2042	c.1785C>T	c.(1783-1785)tcC>tcT	p.S595S	SARDH_ENST00000422262.2_Silent_p.S427S|SARDH_ENST00000439388.1_Silent_p.S595S|SARDH_ENST00000371868.1_Silent_p.S23S	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	595					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)		TGACATCTGCGGAGAAGAGCC	0.617																																					p.S595S		Atlas-SNP	.											SARDH,NS,carcinoma,0,1	SARDH	112	1	0			c.C1785T						PASS	.	A	,	656,3750	276.0+/-272.9	77,502,1624	61.0	56.0	58.0		1785,1785	-10.0	0.0	9	dbSNP_100	58	2932,5668	458.5+/-364.6	508,1916,1876	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	585,2418,3500	AA,AG,GG		34.093,14.8888,27.5873	,	595/919,595/919	136561367	3588,9418	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon14			ATCTGCGGAGAAG		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.1785C>T	9.37:g.136561367G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			G|0.744;A|0.256	0.256	strong		0.617	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
PYGB	5834	hgsc.bcm.edu	37	20	25255338	25255338	+	Silent	SNP	C	C	T	rs2227894	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:25255338C>T	ENST00000216962.4	+	5	749	c.639C>T	c.(637-639)ggC>ggT	p.G213G		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	213					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						CCCCCGACGGCGTGAAGTGGC	0.632													C|||	613	0.122404	0.3253	0.062	5008	,	,		18316	0.0645		0.0567	False		,,,				2504	0.0184				p.G213G		Atlas-SNP	.											PYGB,NS,carcinoma,+2,1	PYGB	84	1	0			c.C639T						PASS	.	C		1287,3119	437.2+/-344.9	185,917,1101	88.0	100.0	96.0		639	-8.1	0.0	20	dbSNP_98	96	391,8209	125.5+/-184.1	7,377,3916	no	coding-synonymous	PYGB	NM_002862.3		192,1294,5017	TT,TC,CC		4.5465,29.2102,12.9017		213/844	25255338	1678,11328	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon5			CGACGGCGTGAAG		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.639C>T	20.37:g.25255338C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			C|0.873;G|0.000;T|0.126	0.126	strong		0.632	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138732497	138732497	+	Missense_Mutation	SNP	G	G	A	rs3735007	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:138732497G>A	ENST00000242351.5	-	13	2868	c.2552C>T	c.(2551-2553)aCt>aTt	p.T851I	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.T973I	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	851	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.		T -> I (in dbSNP:rs3735007). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						ATTTCCTTCAGTAAACTTTCC	0.423													A|||	2661	0.53135	0.7141	0.3775	5008	,	,		17916	0.3611		0.5149	False		,,,				2504	0.5859				p.T851I		Atlas-SNP	.											ZC3HAV1,colon,carcinoma,+1,1	ZC3HAV1	75	1	0			c.C2552T						PASS	.	A	ILE/THR	3097,1309	442.7+/-346.8	1078,941,184	138.0	139.0	139.0		2552	-6.0	0.0	7	dbSNP_107	139	4460,4140	565.3+/-388.5	1187,2086,1027	yes	missense	ZC3HAV1	NM_020119.3	89	2265,3027,1211	AA,AG,GG		48.1395,29.7095,41.896	benign	851/903	138732497	7557,5449	2203	4300	6503	SO:0001583	missense	56829	exon13			CCTTCAGTAAACT	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2552C>T	7.37:g.138732497G>A	ENSP00000242351:p.Thr851Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	71	8	0.112676	NM_020119	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	1100	0.5036630036630036	357	0.725609756097561	151	0.4171270718232044	212	0.3706293706293706	380	0.5013192612137203	A	0.581	-0.836941	0.02692	0.702905	0.518605	ENSG00000105939	ENST00000242351;ENST00000464606	T;T	0.14391	2.51;2.51	5.23	-5.97	0.02227	Poly(ADP-ribose) polymerase, catalytic domain (2);	1.121610	0.06740	N	0.778240	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.36138	-0.9760	9	0.08599	T	0.76	.	17.2686	0.87095	0.3726:0.0:0.6274:0.0	rs3735007;rs10360867;rs17608612;rs52796775;rs3735007	851	Q7Z2W4	ZCCHV_HUMAN	I	851;973	ENSP00000242351:T851I;ENSP00000418385:T973I	ENSP00000242351:T851I	T	-	2	0	ZC3HAV1	138383037	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.368000	0.07543	-1.518000	0.01778	-1.395000	0.01148	ACT	G|0.444;N|0.000	.	strong		0.423	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
CCDC28A	25901	hgsc.bcm.edu	37	6	139094937	139094937	+	Silent	SNP	C	C	T	rs11154999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:139094937C>T	ENST00000332797.6	+	1	281	c.126C>T	c.(124-126)tcC>tcT	p.S42S		NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	42			S -> Y (in dbSNP:rs34538642).							autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		GGAGCGGGTCCCGGGATGTGA	0.637													C|||	115	0.0229633	0.0136	0.0591	5008	,	,		16196	0.001		0.0507	False		,,,				2504	0.0041				p.S42S		Atlas-SNP	.											.	CCDC28A	34	.	0			c.C126T						PASS	.	C		64,4342	59.3+/-96.0	0,64,2139	83.0	104.0	97.0		126	-4.1	0.0	6	dbSNP_120	97	348,8252	117.9+/-177.5	4,340,3956	no	coding-synonymous	CCDC28A	NM_015439.2		4,404,6095	TT,TC,CC		4.0465,1.4526,3.1678		42/275	139094937	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	25901	exon1			CGGGTCCCGGGAT	AY167571	CCDS5192.1	6q23.1-q24.1	2008-02-05	2005-09-12	2005-09-12	ENSG00000024862	ENSG00000024862			21098	protein-coding gene	gene with protein product		615353	"""chromosome 6 open reading frame 80"""	C6orf80			Standard	NM_015439		Approved	CCRL1AP, DKFZp586D0623	uc003qie.3	Q8IWP9	OTTHUMG00000015683	ENST00000332797.6:c.126C>T	6.37:g.139094937C>T		Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	176	99	0.5625	NM_015439	E1P591|Q32NC7|Q66K67|Q96E23|Q9Y430	Silent	SNP	ENST00000332797.6	37	CCDS5192.1																																																																																			C|0.970;T|0.030	0.030	strong		0.637	CCDC28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042444.1	NM_015439	
SH3TC2	79628	hgsc.bcm.edu	37	5	148408101	148408101	+	Silent	SNP	A	A	G	rs1432793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:148408101A>G	ENST00000515425.1	-	11	1295	c.1194T>C	c.(1192-1194)ggT>ggC	p.G398G	SH3TC2_ENST00000513340.1_5'UTR|SH3TC2_ENST00000538184.1_5'UTR|SH3TC2_ENST00000512049.1_Silent_p.G391G|SH3TC2_ENST00000394358.2_Silent_p.G283G	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	398					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)		p.G283G(1)|p.G398G(1)		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)			CCTCCTTGAAACCTTCAGGCT	0.607													G|||	2189	0.437101	0.6172	0.3516	5008	,	,		20639	0.2222		0.4652	False		,,,				2504	0.4468				p.G398G		Atlas-SNP	.											SH3TC2_ENST00000394358,NS,carcinoma,0,2	SH3TC2	178	2	2	Substitution - coding silent(2)	prostate(2)	c.T1194C						PASS	.	G		2469,1937	510.4+/-367.5	699,1071,433	33.0	34.0	34.0		1194	3.6	0.6	5	dbSNP_88	34	3835,4765	586.5+/-392.0	860,2115,1325	no	coding-synonymous	SH3TC2	NM_024577.3		1559,3186,1758	GG,GA,AA		44.593,43.9628,48.4699		398/1289	148408101	6304,6702	2203	4300	6503	SO:0001819	synonymous_variant	79628	exon11			CTTGAAACCTTCA	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.1194T>C	5.37:g.148408101A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Silent	SNP	ENST00000515425.1	37	CCDS4293.1																																																																																			A|0.535;G|0.465	0.465	strong		0.607	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
LHCGR	3973	hgsc.bcm.edu	37	2	48921375	48921375	+	Missense_Mutation	SNP	T	T	C	rs2293275	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:48921375T>C	ENST00000294954.7	-	10	956	c.935A>G	c.(934-936)aAt>aGt	p.N312S	LHCGR_ENST00000403273.1_Missense_Mutation_p.N312S|LHCGR_ENST00000344775.3_Missense_Mutation_p.N250S|LHCGR_ENST00000401907.1_Missense_Mutation_p.N312S|LHCGR_ENST00000405626.1_Intron|STON1-GTF2A1L_ENST00000402114.2_Intron	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	312			N -> S (in dbSNP:rs2293275). {ECO:0000269|PubMed:2244890, ECO:0000269|PubMed:7556872}.	Missing (in Ref. 3; AAA70231). {ECO:0000305}.	activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	TGTTTTGTTATTCACTTTCCT	0.323													T|||	2960	0.591054	0.2352	0.6657	5008	,	,		18928	0.9276		0.6402	False		,,,				2504	0.6217				p.N312S		Atlas-SNP	.											.	LHCGR	154	.	0			c.A935G						PASS	.	T	SER/ASN,	1307,3093	429.3+/-342.2	203,901,1096	137.0	102.0	114.0		935,	3.9	0.8	2	dbSNP_100	114	5074,3516	612.9+/-396.0	1492,2090,713	yes	missense,intron	LHCGR,STON1-GTF2A1L	NM_000233.3,NM_001198593.1	46,	1695,2991,1809	CC,CT,TT		40.9313,29.7045,49.1224	benign,	312/700,	48921375	6381,6609	2200	4295	6495	SO:0001583	missense	3973	exon10			TTGTTATTCACTT		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.935A>G	2.37:g.48921375T>C	ENSP00000294954:p.Asn312Ser	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	224	110	0.491071	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	37	CCDS1842.1	1387	0.63507326007326	125	0.2540650406504065	262	0.7237569060773481	529	0.9248251748251748	471	0.6213720316622692	T	4.051	0.007198	0.07866	0.297045	0.590687	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000403273;ENST00000401907	T;T;T;T	0.78003	-0.95;-0.77;-1.14;-0.97	5.09	3.9	0.45041	.	0.636684	0.17257	N	0.180938	T	0.00012	0.0000	N	0.17564	0.495	0.35412	P	0.20750199999999996	B	0.11235	0.004	B	0.08055	0.003	T	0.34030	-0.9845	8	.	.	.	.	9.9216	0.41468	0.0:0.0:0.3586:0.6414	rs2293275;rs17398177;rs52807977;rs60456102;rs2293275	312	P22888	LSHR_HUMAN	S	250;312;312;312	ENSP00000344301:N250S;ENSP00000294954:N312S;ENSP00000385847:N312S;ENSP00000385406:N312S	.	N	-	2	0	LHCGR	48774879	0.889000	0.30405	0.794000	0.32065	0.151000	0.21798	1.185000	0.32065	0.848000	0.35191	0.460000	0.39030	AAT	T|0.446;C|0.554	0.554	strong		0.323	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3	
ASIC2	40	hgsc.bcm.edu	37	17	31618732	31618732	+	Intron	SNP	A	A	G	rs9893935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	110	2	0.0181818		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	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	
MYO18B	84700	hgsc.bcm.edu	37	22	26164700	26164700	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:26164700C>T	ENST00000407587.2	+	4	986	c.817C>T	c.(817-819)Ccc>Tcc	p.P273S	MYO18B_ENST00000335473.7_Missense_Mutation_p.P273S|MYO18B_ENST00000536101.1_Missense_Mutation_p.P273S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	273						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						AGCCCAAGGGCCCGGCGAGGG	0.627																																					p.P273S		Atlas-SNP	.											.	MYO18B	322	.	0			c.C817T						PASS	.						16.0	20.0	19.0					22																	26164700		1895	4089	5984	SO:0001583	missense	84700	exon4			CAAGGGCCCGGCG	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.817C>T	22.37:g.26164700C>T	ENSP00000386096:p.Pro273Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	c	11.33	1.607898	0.28623	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86366	-2.09;-2.09;-2.11	3.13	-3.41	0.04839	.	0.695036	0.11932	N	0.515636	T	0.74176	0.3682	L	0.27053	0.805	0.09310	N	1	B;B;B	0.28291	0.131;0.103;0.206	B;B;B	0.25291	0.018;0.059;0.04	T	0.63278	-0.6673	10	0.66056	D	0.02	.	5.8765	0.18832	0.0:0.3595:0.3875:0.253	.	273;273;273	Q8IUG5;F5GXR6;F5GYU7	MY18B_HUMAN;.;.	S	273	ENSP00000441229:P273S;ENSP00000334563:P273S;ENSP00000386096:P273S	ENSP00000334563:P273S	P	+	1	0	MYO18B	24494700	0.000000	0.05858	0.001000	0.08648	0.367000	0.29736	-0.514000	0.06298	-0.256000	0.09473	0.306000	0.20318	CCC	.	.	none		0.627	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
PIK3R4	30849	hgsc.bcm.edu	37	3	130449222	130449222	+	Silent	SNP	A	A	G	rs2170990	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:130449222A>G	ENST00000356763.3	-	5	2072	c.1515T>C	c.(1513-1515)ctT>ctC	p.L505L		NM_014602.2	NP_055417.1	Q99570	PI3R4_HUMAN	phosphoinositide-3-kinase, regulatory subunit 4	505					innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	axoneme (GO:0005930)|cytosol (GO:0005829)|late endosome (GO:0005770)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(6)|large_intestine(16)|lung(28)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	77						TTTCCATATTAAGATTTTTTA	0.308													A|||	1154	0.230431	0.1218	0.3127	5008	,	,		15408	0.2054		0.2058	False		,,,				2504	0.3701				p.L505L		Atlas-SNP	.											.	PIK3R4	145	.	0			c.T1515C						PASS	.	A		607,3799	265.0+/-266.4	50,507,1646	72.0	77.0	75.0		1515	-0.8	1.0	3	dbSNP_96	75	1647,6947	302.8+/-306.1	168,1311,2818	no	coding-synonymous	PIK3R4	NM_014602.2		218,1818,4464	GG,GA,AA		19.1645,13.7767,17.3385		505/1359	130449222	2254,10746	2203	4297	6500	SO:0001819	synonymous_variant	30849	exon5			CATATTAAGATTT	Y08991	CCDS3067.1	3q22.1	2013-01-10	2008-02-04		ENSG00000196455	ENSG00000196455		"""WD repeat domain containing"""	8982	protein-coding gene	gene with protein product		602610				8999962	Standard	NM_014602		Approved	VPS15, p150	uc003enj.3	Q99570	OTTHUMG00000159645	ENST00000356763.3:c.1515T>C	3.37:g.130449222A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_014602	Q2TBF4	Silent	SNP	ENST00000356763.3	37	CCDS3067.1																																																																																			A|0.812;G|0.188	0.188	strong		0.308	PIK3R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356668.1	NM_014602	
UBXN6	80700	hgsc.bcm.edu	37	19	4454000	4454000	+	Silent	SNP	G	G	A	rs11909	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4454000G>A	ENST00000301281.6	-	2	298	c.174C>T	c.(172-174)gcC>gcT	p.A58A	UBXN6_ENST00000394765.3_Silent_p.A5A|CTB-50L17.9_ENST00000592034.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	58						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						GGGCTAGGGCGGCAGCGGCTG	0.682													G|||	1563	0.312101	0.2595	0.2205	5008	,	,		14553	0.2867		0.4115	False		,,,				2504	0.3722				p.A58A		Atlas-SNP	.											.	UBXN6	27	.	0			c.C174T						PASS	.	G	,	1279,3127	422.5+/-339.8	196,887,1120	67.0	83.0	78.0		15,174	-8.5	0.2	19	dbSNP_52	78	3475,5123	493.1+/-373.5	709,2057,1533	no	coding-synonymous,coding-synonymous	UBXN6	NM_001171091.1,NM_025241.2	,	905,2944,2653	AA,AG,GG		40.4164,29.0286,36.558	,	5/389,58/442	4454000	4754,8250	2203	4299	6502	SO:0001819	synonymous_variant	80700	exon2			TAGGGCGGCAGCG	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.174C>T	19.37:g.4454000G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Silent	SNP	ENST00000301281.6	37	CCDS12129.1																																																																																			G|0.653;A|0.347	0.347	strong		0.682	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
CSTL1	128817	hgsc.bcm.edu	37	20	23424613	23424613	+	Missense_Mutation	SNP	T	T	C	rs3746736	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:23424613T>C	ENST00000246020.2	+	2	282	c.262T>C	c.(262-264)Tgg>Cgg	p.W88R	CSTL1_ENST00000347397.1_Missense_Mutation_p.W88R			Q9H114	CST1L_HUMAN	cystatin-like 1	88			W -> R (in dbSNP:rs3746736). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(2)|endometrium(2)|large_intestine(3)|lung(4)|skin(2)|stomach(1)	14	Colorectal(13;0.0993)|Lung NSC(19;0.235)					GAAGATTGGCTGGACCAAATG	0.512													C|||	3280	0.654952	0.857	0.6023	5008	,	,		19368	0.7292		0.494	False		,,,				2504	0.5082				p.W88R		Atlas-SNP	.											.	CSTL1	30	.	0			c.T262C						PASS	.	C	ARG/TRP	3464,942	358.4+/-314.3	1363,738,102	145.0	121.0	129.0		262	-0.6	0.9	20	dbSNP_107	129	4335,4265	575.1+/-390.2	1110,2115,1075	yes	missense	CSTL1	NM_138283.1	101	2473,2853,1177	CC,CT,TT		49.593,21.3799,40.0354	benign	88/146	23424613	7799,5207	2203	4300	6503	SO:0001583	missense	128817	exon3			ATTGGCTGGACCA	AL096677	CCDS13153.1	20p11.21	2012-08-14			ENSG00000125823	ENSG00000125823			15958	protein-coding gene	gene with protein product						20565543	Standard	NM_138283		Approved	dJ322G13.4, CTES1	uc002wte.3	Q9H114	OTTHUMG00000032068	ENST00000246020.2:c.262T>C	20.37:g.23424613T>C	ENSP00000246020:p.Trp88Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	154	73	0.474026	NM_138283	Q17RA8|Q64FF7	Missense_Mutation	SNP	ENST00000246020.2	37	CCDS13153.1	1444	0.6611721611721612	425	0.8638211382113821	222	0.6132596685082873	434	0.7587412587412588	363	0.4788918205804749	C	0.003	-2.488228	0.00161	0.786201	0.50407	ENSG00000125823	ENST00000347397;ENST00000246020	T;T	0.10192	2.9;2.9	4.06	-0.597	0.11653	Proteinase inhibitor I25, cystatin (2);	0.000000	0.41500	N	0.000870	T	0.00012	0.0000	N	0.00020	-2.765	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.20338	-1.0278	9	0.02654	T	1	-13.8332	6.2799	0.21001	0.4857:0.4075:0.0:0.1068	rs3746736;rs17683931;rs52791027;rs58676320;rs3746736	88	Q9H114	CST1L_HUMAN	R	88	ENSP00000344907:W88R;ENSP00000246020:W88R	ENSP00000246020:W88R	W	+	1	0	CSTL1	23372613	0.062000	0.20869	0.901000	0.35422	0.035000	0.12851	-0.270000	0.08584	-0.325000	0.08577	-0.929000	0.02709	TGG	C|0.629;N|0.000	0.629	strong		0.512	CSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078328.1		
ZNF512B	57473	hgsc.bcm.edu	37	20	62591460	62591460	+	Silent	SNP	G	G	A	rs45570933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62591460G>A	ENST00000450537.1	-	17	2520	c.2460C>T	c.(2458-2460)ccC>ccT	p.P820P	ZNF512B_ENST00000217130.3_Silent_p.P820P|ZNF512B_ENST00000369888.1_Silent_p.P820P			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	820					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)					TCCTGTGTTTGGGAGGTGGGT	0.567													G|||	102	0.0203674	0.0038	0.036	5008	,	,		18765	0.0		0.0606	False		,,,				2504	0.0112				p.P820P		Atlas-SNP	.											.	ZNF512B	72	.	0			c.C2460T						PASS	.	G		65,4339	59.3+/-96.0	0,65,2137	83.0	90.0	88.0		2460	3.9	0.3	20	dbSNP_127	88	606,7994	158.6+/-212.1	23,560,3717	no	coding-synonymous	ZNF512B	NM_020713.1		23,625,5854	AA,AG,GG		7.0465,1.4759,5.16		820/893	62591460	671,12333	2202	4300	6502	SO:0001819	synonymous_variant	57473	exon17			GTGTTTGGGAGGT	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.2460C>T	20.37:g.62591460G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_020713	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			G|0.955;A|0.045	0.045	strong		0.567	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
OVCH2	341277	hgsc.bcm.edu	37	11	7727872	7727872	+	lincRNA	SNP	T	T	C	rs12289558	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	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		
ZNF302	55900	hgsc.bcm.edu	37	19	35173717	35173717	+	Missense_Mutation	SNP	T	T	A	rs199664059	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:35173717T>A	ENST00000446502.2	+	4	385	c.177T>A	c.(175-177)caT>caA	p.H59Q	ZNF302_ENST00000505365.2_Missense_Mutation_p.H15Q|ZNF302_ENST00000509528.1_Intron|ZNF302_ENST00000457781.2_Missense_Mutation_p.H15Q|ZNF302_ENST00000507959.1_Missense_Mutation_p.H15Q|ZNF302_ENST00000423823.2_Missense_Mutation_p.H15Q|ZNF302_ENST00000505242.1_Missense_Mutation_p.H15Q			Q9NR11	ZN302_HUMAN	zinc finger protein 302	15	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)			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)			ACTTCTCTCATGAAGAGTGGG	0.453																																					p.H15Q		Atlas-SNP	.											ZNF302,NS,carcinoma,0,3	ZNF302	27	3	0			c.T45A						scavenged	.						78.0	65.0	69.0					19																	35173717		1840	4067	5907	SO:0001583	missense	55900	exon3			CTCTCATGAAGAG	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.177T>A	19.37:g.35173717T>A	ENSP00000396379:p.His59Gln	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	300	87	0.29	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	37		118	0.05402930402930403	79	0.16056910569105692	6	0.016574585635359115	7	0.012237762237762238	26	0.03430079155672823	T	0.018	-1.468420	0.01053	.	.	ENSG00000089335	ENST00000502743;ENST00000506901;ENST00000457781;ENST00000505242;ENST00000505163;ENST00000423823;ENST00000507959;ENST00000446502;ENST00000505365	T;T;T;T;T;T;T;T;T	0.01304	5.03;5.03;5.03;5.03;5.03;5.03;5.03;5.03;5.03	1.39	-0.0593	0.13794	.	.	.	.	.	T	0.00012	0.0000	N	0.00121	-2.07	0.21933	N	0.999461	B;P;P	0.44195	0.024;0.761;0.828	B;B;P	0.47705	0.038;0.378;0.555	T	0.36866	-0.9730	9	0.02654	T	1	.	3.6594	0.08233	0.0:0.0:0.4123:0.5877	.	15;59;15	B4DMN2;E7EVR1;Q9NR11-2	.;.;.	Q	15;15;15;15;15;15;15;59;15	ENSP00000423460:H15Q;ENSP00000424292:H15Q;ENSP00000391067:H15Q;ENSP00000421028:H15Q;ENSP00000421696:H15Q;ENSP00000405219:H15Q;ENSP00000421201:H15Q;ENSP00000396379:H59Q;ENSP00000423235:H15Q	ENSP00000405219:H15Q	H	+	3	2	ZNF302	39865557	0.000000	0.05858	0.998000	0.56505	0.912000	0.54170	-1.662000	0.01970	0.617000	0.30160	0.260000	0.18958	CAT	T|0.954;A|0.046	0.046	strong		0.453	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
ZCCHC14	23174	hgsc.bcm.edu	37	16	87445270	87445270	+	Silent	SNP	T	T	C	rs3748399	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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						scavenged	.	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	87	2	0.0229885		WXS	Illumina HiSeq	Phase_I	61	54	0.885246	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	
FNDC3B	64778	hgsc.bcm.edu	37	3	172061988	172061988	+	Silent	SNP	C	C	T	rs200807692		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:172061988C>T	ENST00000336824.4	+	19	2289	c.2190C>T	c.(2188-2190)gtC>gtT	p.V730V	FNDC3B_ENST00000416957.1_Silent_p.V730V|FNDC3B_ENST00000415807.2_Silent_p.V730V	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	730	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		AGTGCACCGTCGGCAACCTGC	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		18074	0.001		0.0	False		,,,				2504	0.0				p.V730V		Atlas-SNP	.											.	FNDC3B	118	.	0			c.C2190T						PASS	.						183.0	166.0	172.0					3																	172061988		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon19			CACCGTCGGCAAC	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.2190C>T	3.37:g.172061988C>T		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	178	90	0.505618	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																			C|1.000;T|0.000	0.000	strong		0.567	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
ZNF845	91664	hgsc.bcm.edu	37	19	53856761	53856761	+	Missense_Mutation	SNP	T	T	C	rs528924232		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53856761T>C	ENST00000595091.1	+	5	3052	c.2833T>C	c.(2833-2835)Tgt>Cgt	p.C945R	ZNF845_ENST00000458035.1_Missense_Mutation_p.C945R			Q96IR2	ZN845_HUMAN	zinc finger protein 845	945					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.C945R(1)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						ACCTTACAAGTGTAATGAATG	0.348																																					p.C945R		Atlas-SNP	.											ZNF845,NS,carcinoma,0,1	ZNF845	101	1	1	Substitution - Missense(1)	kidney(1)	c.T2833C						PASS	.						25.0	23.0	24.0					19																	53856761		692	1590	2282	SO:0001583	missense	91664	exon4			TACAAGTGTAATG	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.2833T>C	19.37:g.53856761T>C	ENSP00000470005:p.Cys945Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	175	12	0.0685714	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	T	7.922	0.738844	0.15642	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	D	0.85258	-1.96	2.04	0.921	0.19403	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94417	0.8204	H	0.99336	4.52	0.38301	D	0.942985	D	0.89917	1.0	D	0.91635	0.999	D	0.91222	0.5007	9	0.66056	D	0.02	.	6.1858	0.20495	0.2258:0.0:0.0:0.7742	.	945	Q96IR2	ZN845_HUMAN	R	945;861	ENSP00000388311:C945R	ENSP00000412086:C861R	C	+	1	0	ZNF845	58548573	1.000000	0.71417	0.080000	0.20451	0.053000	0.15095	4.520000	0.60524	0.031000	0.15407	-0.871000	0.02989	TGT	.	.	none		0.348	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
USP35	57558	hgsc.bcm.edu	37	11	77920964	77920964	+	Missense_Mutation	SNP	C	C	T	rs118006862	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:77920964C>T	ENST00000529308.1	+	10	2324	c.2063C>T	c.(2062-2064)aCg>aTg	p.T688M	USP35_ENST00000526425.1_Missense_Mutation_p.T419M|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000441408.2_Missense_Mutation_p.T274M|USP35_ENST00000530267.1_Missense_Mutation_p.T256M	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	688	USP.				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)			gaggagagaacggagaaggaa	0.562													C|||	26	0.00519169	0.0	0.0115	5008	,	,		18342	0.0		0.0169	False		,,,				2504	0.001				p.T688M		Atlas-SNP	.											.	USP35	179	.	0			c.C2063T						PASS	.	C	MET/THR	19,4091		0,19,2036	64.0	82.0	76.0		2063	-9.8	0.0	11	dbSNP_132	76	198,8224		0,198,4013	no	missense	USP35	NM_020798.2	81	0,217,6049	TT,TC,CC		2.351,0.4623,1.7316	possibly-damaging	688/1019	77920964	217,12315	2055	4211	6266	SO:0001583	missense	57558	exon10			AGAGAACGGAGAA	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.2063C>T	11.37:g.77920964C>T	ENSP00000431876:p.Thr688Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	18	0.008241758241758242	0	0.0	5	0.013812154696132596	0	0.0	13	0.017150395778364115	C	10.48	1.361588	0.24684	0.004623	0.02351	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	T;T;T;T	0.07908	3.17;3.42;3.42;3.15	4.92	-9.84	0.00479	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	4.302940	0.01614	N	0.022689	T	0.01421	0.0046	N	0.08118	0	0.09310	N	1	P;P	0.44309	0.489;0.832	B;B	0.34138	0.164;0.176	T	0.38178	-0.9673	10	0.46703	T	0.11	2.4872	6.4557	0.21928	0.1883:0.1253:0.5478:0.1386	.	688;274	Q9P2H5;E7EWV7	UBP35_HUMAN;.	M	256;688;274;419	ENSP00000435468:T256M;ENSP00000431876:T688M;ENSP00000400825:T274M;ENSP00000434942:T419M	ENSP00000400825:T274M	T	+	2	0	USP35	77598612	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.497000	0.00969	-2.043000	0.00913	-0.499000	0.04595	ACG	C|0.991;T|0.009	0.009	strong		0.562	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
AOAH	313	hgsc.bcm.edu	37	7	36763672	36763672	+	Missense_Mutation	SNP	C	C	T	rs2228410	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:36763672C>T	ENST00000258749.5	-	1	481	c.82G>A	c.(82-84)Gat>Aat	p.D28N	AOAH_ENST00000535891.1_Missense_Mutation_p.D28N|AOAH_ENST00000431169.1_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	49	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	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	
SLAIN2	57606	hgsc.bcm.edu	37	4	48424058	48424058	+	Silent	SNP	C	C	T	rs17609614	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:48424058C>T	ENST00000264313.6	+	8	2128	c.1710C>T	c.(1708-1710)agC>agT	p.S570S	SLAIN2_ENST00000512093.1_Silent_p.S403S	NM_020846.1	NP_065897.1	Q9P270	SLAI2_HUMAN	SLAIN motif family, member 2	570					cytoplasmic microtubule organization (GO:0031122)|microtubule nucleation (GO:0007020)|positive regulation of microtubule polymerization (GO:0031116)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(1)	13						CCTATGGTAGCATGAAAGATG	0.373													C|||	151	0.0301518	0.0325	0.0591	5008	,	,		19100	0.0268		0.0229	False		,,,				2504	0.0174				p.S570S		Atlas-SNP	.											.	SLAIN2	31	.	0			c.C1710T						PASS	.	C		128,3588		2,124,1732	65.0	61.0	62.0		1710	3.7	1.0	4	dbSNP_123	62	231,7965		4,223,3871	no	coding-synonymous	SLAIN2	NM_020846.1		6,347,5603	TT,TC,CC		2.8184,3.4446,3.0138		570/582	48424058	359,11553	1858	4098	5956	SO:0001819	synonymous_variant	57606	exon8			TGGTAGCATGAAA	BC006139	CCDS47051.1	4p12	2008-02-05	2006-09-12	2006-09-12	ENSG00000109171	ENSG00000109171			29282	protein-coding gene	gene with protein product		610492	"""KIAA1458"""	KIAA1458		16546155	Standard	NM_020846		Approved	FLJ21611	uc003gya.4	Q9P270	OTTHUMG00000161701	ENST00000264313.6:c.1710C>T	4.37:g.48424058C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_020846	A8K4P1|Q8N5R3	Silent	SNP	ENST00000264313.6	37	CCDS47051.1																																																																																			C|0.968;T|0.032	0.032	strong		0.373	SLAIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365807.4	NM_020846	
SVEP1	79987	hgsc.bcm.edu	37	9	113148346	113148346	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:113148346A>G	ENST00000401783.2	-	43	10405	c.10069T>C	c.(10069-10071)Tgc>Cgc	p.C3357R	SVEP1_ENST00000374469.1_Missense_Mutation_p.C3334R|SVEP1_ENST00000297826.5_Missense_Mutation_p.C1283R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3357	Sushi 33. {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						GGAACAGGGCATGGATTTGCT	0.388																																					p.C3357R		Atlas-SNP	.											SVEP1,NS,carcinoma,+1,1	SVEP1	326	1	0			c.T10069C						scavenged	.						86.0	82.0	83.0					9																	113148346		1869	4118	5987	SO:0001583	missense	79987	exon43			CAGGGCATGGATT	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.10069T>C	9.37:g.113148346A>G	ENSP00000384917:p.Cys3357Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	105	2	0.0190476	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	A	19.95	3.921774	0.73213	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	D;D;D	0.99778	-6.73;-6.73;-6.73	5.22	5.22	0.72569	Complement control module (3);Sushi/SCR/CCP (3);	0.089147	0.85682	D	0.000000	D	0.99785	0.9910	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96953	0.9696	10	0.87932	D	0	.	15.4598	0.75346	1.0:0.0:0.0:0.0	.	3357	Q4LDE5	SVEP1_HUMAN	R	3357;3334;1283	ENSP00000384917:C3357R;ENSP00000363593:C3334R;ENSP00000297826:C1283R	ENSP00000297826:C1283R	C	-	1	0	SVEP1	112188167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.405000	0.80007	2.109000	0.64355	0.529000	0.55759	TGC	.	.	none		0.388	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DHX57	90957	hgsc.bcm.edu	37	2	39042718	39042718	+	Missense_Mutation	SNP	T	T	G	rs150735204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:39042718T>G	ENST00000295373.6	-	20	3677	c.3551A>C	c.(3550-3552)gAa>gCa	p.E1184A		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1184							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)				TTTCTCAATTTCCCTTGCTCT	0.453													T|||	11	0.00219649	0.0	0.0043	5008	,	,		19870	0.0		0.007	False		,,,				2504	0.001				p.E1184A	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											DHX57,NS,carcinoma,0,1	DHX57	127	1	0			c.A3551C						PASS	.	T	ALA/GLU	5,4401	9.9+/-24.2	0,5,2198	222.0	207.0	212.0		3551	5.3	1.0	2	dbSNP_134	212	63,8537	39.3+/-95.6	0,63,4237	yes	missense	DHX57	NM_198963.1	107	0,68,6435	GG,GT,TT		0.7326,0.1135,0.5228	benign	1184/1387	39042718	68,12938	2203	4300	6503	SO:0001583	missense	90957	exon20			TCAATTTCCCTTG	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.3551A>C	2.37:g.39042718T>G	ENSP00000295373:p.Glu1184Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	123	61	0.495935	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	11.33	1.606871	0.28623	0.001135	0.007326	ENSG00000163214	ENST00000295373	T	0.02787	4.16	5.29	5.29	0.74685	Domain of unknown function DUF1605 (1);	0.241073	0.29046	N	0.013302	T	0.01489	0.0048	N	0.11560	0.145	0.46078	D	0.99885	B;B	0.10296	0.003;0.001	B;B	0.13407	0.009;0.001	T	0.57069	-0.7874	10	0.13470	T	0.59	.	15.5408	0.76043	0.0:0.0:0.0:1.0	.	1184;576	Q6P158;Q59G60	DHX57_HUMAN;.	A	1184	ENSP00000295373:E1184A	ENSP00000295373:E1184A	E	-	2	0	DHX57	38896222	1.000000	0.71417	0.992000	0.48379	0.948000	0.59901	5.728000	0.68531	2.120000	0.65058	0.460000	0.39030	GAA	T|0.996;G|0.004	0.004	strong		0.453	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
MSH2	4436	hgsc.bcm.edu	37	2	47630528	47630528	+	Silent	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:47630528C>T	ENST00000233146.2	+	1	421	c.198C>T	c.(196-198)taC>taT	p.Y66Y	MSH2_ENST00000406134.1_Silent_p.Y66Y|MSH2_ENST00000543555.1_5'UTR	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	66					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TGATCAAGTACATGGGGCCGG	0.706			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.Y66Y		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.C198T						PASS	.						9.0	12.0	11.0					2																	47630528		2186	4271	6457	SO:0001819	synonymous_variant	4436	exon1	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	CAAGTACATGGGG	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.198C>T	2.37:g.47630528C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	111	62	0.558559	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			.	.	none		0.706	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
DPF3	8110	hgsc.bcm.edu	37	14	73137882	73137882	+	Intron	SNP	G	G	A	rs202093453		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:73137882G>A	ENST00000556509.1	-	8	871				DPF3_ENST00000541685.1_Missense_Mutation_p.R346W|DPF3_ENST00000546183.1_Missense_Mutation_p.R356W|DPF3_ENST00000557704.1_5'UTR	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3						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)		GGCGAACCCCGGCCACTGCGG	0.547													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16614	0.0		0.0	False		,,,				2504	0.0				p.R346W		Atlas-SNP	.											.	DPF3	117	.	0			c.C1036T						PASS	.	G	TRP/ARG	1,4029		0,1,2014	55.0	57.0	56.0		1036	4.8	1.0	14		56	8,8334		0,8,4163	yes	missense	DPF3	NM_012074.3	101	0,9,6177	AA,AG,GG		0.0959,0.0248,0.0727	benign	346/358	73137882	9,12363	2015	4171	6186	SO:0001627	intron_variant	8110	exon9			AACCCCGGCCACT	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.871+3065C>T	14.37:g.73137882G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	139	91	0.654676	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	37		.	.	.	.	.	.	.	.	.	.	G	17.16	3.317391	0.60524	2.48E-4	9.59E-4	ENSG00000205683	ENST00000541685;ENST00000546183	T;T	0.67523	-0.25;-0.27	5.79	4.82	0.62117	.	.	.	.	.	T	0.47619	0.1455	N	0.08118	0	0.27889	N	0.939402	D;P	0.60160	0.987;0.923	P;B	0.44561	0.453;0.237	T	0.42155	-0.9468	9	0.87932	D	0	.	7.5751	0.27931	0.0:0.117:0.3984:0.4846	.	356;346	F5H575;Q92784-2	.;.	W	346;356	ENSP00000441640:R346W;ENSP00000444662:R356W	ENSP00000381791:R401W	R	-	1	2	DPF3	72207635	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.667000	0.37471	1.366000	0.46076	0.655000	0.94253	CGG	.	.	weak		0.547	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2		
BRICD5	283870	hgsc.bcm.edu	37	16	2260567	2260567	+	Missense_Mutation	SNP	C	C	T	rs26857	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2260567C>T	ENST00000562360.1	-	2	135	c.136G>A	c.(136-138)Gtt>Att	p.V46I	RP11-304L19.8_ENST00000561544.1_lincRNA|BRICD5_ENST00000328540.3_Missense_Mutation_p.V46I|BRICD5_ENST00000566018.1_Missense_Mutation_p.V46I			Q6PL45	BRID5_HUMAN	BRICHOS domain containing 5	46			V -> I (in dbSNP:rs26857). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)		p.V46I(1)									CCAGCCACAACCCCCACAGCG	0.662													C|||	2582	0.515575	0.497	0.4841	5008	,	,		16452	0.6032		0.4702	False		,,,				2504	0.5194				p.V46I		Atlas-SNP	.											C16orf79,NS,lymphoid_neoplasm,0,1	.	.	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G136A						scavenged	.	C	ILE/VAL	2185,2205		554,1077,564	22.0	27.0	25.0		136	1.2	0.0	16	dbSNP_76	25	4030,4558		965,2100,1229	yes	missense	C16orf79	NM_182563.3	29	1519,3177,1793	TT,TC,CC		46.9259,49.7722,47.8887	benign	46/229	2260567	6215,6763	2195	4294	6489	SO:0001583	missense	283870	exon2			CCACAACCCCCAC	BC039154	CCDS10463.1	16p13.3	2012-10-10	2012-10-10	2012-10-10	ENSG00000182685	ENSG00000182685		"""BRICHOS domain containing"""	28309	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 79"""	C16orf79		12477932	Standard	NM_182563		Approved	MGC21830	uc002cpi.2	Q6PL45	OTTHUMG00000128831	ENST00000562360.1:c.136G>A	16.37:g.2260567C>T	ENSP00000455052:p.Val46Ile	Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	92	54	0.586957	NM_182563	C9J7K2|Q8IXU9	Missense_Mutation	SNP	ENST00000562360.1	37	CCDS10463.1	1127	0.5160256410256411	252	0.5121951219512195	168	0.46408839779005523	349	0.6101398601398601	358	0.47229551451187335	C	0.024	-1.388868	0.01185	0.497722	0.469259	ENSG00000182685	ENST00000328540	T	0.24151	1.87	5.48	1.17	0.20885	.	0.645519	0.15632	N	0.252357	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.11235	0.004;0.003	B;B	0.13407	0.002;0.009	T	0.43845	-0.9366	9	0.05525	T	0.97	-1.5005	4.4636	0.11678	0.0:0.5028:0.1556:0.3417	rs26857;rs1640774;rs4018449;rs12931243;rs17853879;rs59033835;rs26857	46;46	Q6PL45;Q6PL45-2	CP079_HUMAN;.	I	46	ENSP00000332389:V46I	ENSP00000332389:V46I	V	-	1	0	C16orf79	2200568	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	0.241000	0.18065	0.298000	0.22638	-0.137000	0.14449	GTT	C|0.523;T|0.477	0.477	strong		0.662	BRICD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435091.1	NM_182563	
ACSL1	2180	hgsc.bcm.edu	37	4	185687863	185687863	+	Silent	SNP	A	A	G	rs11727009	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:185687863A>G	ENST00000515030.1	-	13	1501	c.1176T>C	c.(1174-1176)ttT>ttC	p.F392F	ACSL1_ENST00000504342.1_Silent_p.F392F|ACSL1_ENST00000513317.1_Silent_p.F392F|ACSL1_ENST00000507295.1_Silent_p.F358F|ACSL1_ENST00000454703.2_Silent_p.F221F|ACSL1_ENST00000437665.3_Silent_p.F221F|ACSL1_ENST00000281455.2_Silent_p.F392F			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	392					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)	TCTTGGAGGCAAAGTCCAAGA	0.498													A|||	1076	0.214856	0.2073	0.2277	5008	,	,		20599	0.2153		0.2366	False		,,,				2504	0.1933				p.F392F		Atlas-SNP	.											.	ACSL1	77	.	0			c.T1176C						PASS	.	A		985,3421	368.6+/-318.7	112,761,1330	116.0	109.0	112.0		1176	-1.6	1.0	4	dbSNP_120	112	2018,6582	352.5+/-328.7	226,1566,2508	no	coding-synonymous	ACSL1	NM_001995.2		338,2327,3838	GG,GA,AA		23.4651,22.3559,23.0893		392/699	185687863	3003,10003	2203	4300	6503	SO:0001819	synonymous_variant	2180	exon13			GGAGGCAAAGTCC	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.1176T>C	4.37:g.185687863A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	59	46	0.779661	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Silent	SNP	ENST00000515030.1	37	CCDS3839.1																																																																																			A|0.768;G|0.232	0.232	strong		0.498	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	
SNX29	92017	hgsc.bcm.edu	37	16	12162969	12162969	+	Silent	SNP	A	A	G	rs1641843	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:12162969A>G	ENST00000566228.1	+	10	1368	c.1299A>G	c.(1297-1299)ccA>ccG	p.P433P	SNX29_ENST00000306030.3_Silent_p.P48P|SNX29_ENST00000323433.4_Silent_p.P48P	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	433						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)	p.P48P(1)		endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						ACGTTCTCCCAGATCCTGGAC	0.463													g|||	3050	0.609026	0.8116	0.5014	5008	,	,		18048	0.5258		0.4632	False		,,,				2504	0.6472				p.P433P		Atlas-SNP	.											SNX29_ENST00000306030,NS,carcinoma,0,1	SNX29	60	1	1	Substitution - coding silent(1)	stomach(1)	c.A1299G						PASS	.			2767,971		1036,695,138	89.0	97.0	95.0		144	-10.7	0.0	16	dbSNP_89	95	3365,4857		689,1987,1435	no	coding-synonymous	SNX29	NM_001080530.2		1725,2682,1573	GG,GA,AA		40.9268,25.9765,48.7291		48/429	12162969	6132,5828	1869	4111	5980	SO:0001819	synonymous_variant	92017	exon10			TCTCCCAGATCCT	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.1299A>G	16.37:g.12162969A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	120	56	0.466667	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Silent	SNP	ENST00000566228.1	37	CCDS10553.2																																																																																			A|0.468;G|0.532	0.532	strong		0.463	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
NFATC2	4773	hgsc.bcm.edu	37	20	50140627	50140627	+	Silent	SNP	G	G	C	rs3746420	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:50140627G>C	ENST00000396009.3	-	2	372	c.153C>G	c.(151-153)gtC>gtG	p.V51V	NFATC2_ENST00000610033.1_Intron|NFATC2_ENST00000609507.1_Intron|NFATC2_ENST00000371564.3_Silent_p.V51V|NFATC2_ENST00000414705.1_Silent_p.V31V|NFATC2_ENST00000609943.1_Silent_p.V31V	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	51					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	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)|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)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GTGGGCTGGCGACCTTATGTG	0.587													G|||	299	0.0597045	0.0507	0.0447	5008	,	,		13783	0.0734		0.0606	False		,,,				2504	0.0675				p.V51V		Atlas-SNP	.											.	NFATC2	112	.	0			c.C153G						PASS	.	G	,,	177,4227	106.0+/-144.5	5,167,2030	46.0	54.0	51.0		93,153,153	2.1	0.9	20	dbSNP_107	51	493,8105	137.8+/-194.7	17,459,3823	no	coding-synonymous,coding-synonymous,coding-synonymous	NFATC2	NM_001136021.1,NM_012340.3,NM_173091.2	,,	22,626,5853	CC,CG,GG		5.7339,4.0191,5.1531	,,	31/902,51/922,51/926	50140627	670,12332	2202	4299	6501	SO:0001819	synonymous_variant	4773	exon2			GCTGGCGACCTTA	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.153C>G	20.37:g.50140627G>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	77	46	0.597403	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Silent	SNP	ENST00000396009.3	37	CCDS13437.1																																																																																			G|0.939;C|0.061	0.061	strong		0.587	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12885289	12885289	+	Silent	SNP	G	G	T	rs200907281	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:12885289G>T	ENST00000535591.1	-	4	1017	c.822C>A	c.(820-822)ctC>ctA	p.L274L	RP5-845O24.8_ENST00000438401.1_lincRNA	NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	274					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)			p.L274L(3)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						GGCACTGGGAGAGATGCTTCA	0.458													.|||	1958	0.390974	0.1899	0.3501	5008	,	,		13255	0.6895		0.4553	False		,,,				2504	0.318				p.L274L		Atlas-SNP	.											PRAMEF11,NS,carcinoma,0,7	PRAMEF11	72	7	3	Substitution - coding silent(3)	kidney(2)|endometrium(1)	c.C822A						scavenged	.						67.0	40.0	49.0					1																	12885289		582	1168	1750	SO:0001819	synonymous_variant	440560	exon4			CTGGGAGAGATGC	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.822C>A	1.37:g.12885289G>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	19	3	0.157895	NM_001146344		Silent	SNP	ENST00000535591.1	37	CCDS53268.1																																																																																			T|1.000;|0.000	1.000	weak		0.458	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
ARMC5	79798	hgsc.bcm.edu	37	16	31476458	31476458	+	Intron	SNP	C	C	T	rs11150624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:31476458C>T	ENST00000563544.1	+	5	2410				ARMC5_ENST00000457010.2_Missense_Mutation_p.A705V|ARMC5_ENST00000412665.2_Intron|ARMC5_ENST00000268314.4_Intron|ARMC5_ENST00000538189.1_Intron|ARMC5_ENST00000408912.3_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	124	0	0		WXS	Illumina HiSeq	Phase_I	152	69	0.453947	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	
PALLD	23022	hgsc.bcm.edu	37	4	169819835	169819835	+	Silent	SNP	A	A	G	rs113676921	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:169819835A>G	ENST00000505667.1	+	14	2615	c.2442A>G	c.(2440-2442)acA>acG	p.T814T	PALLD_ENST00000512127.1_Silent_p.T415T|CBR4_ENST00000509108.1_Intron|PALLD_ENST00000261509.6_Silent_p.T797T|PALLD_ENST00000507735.1_Silent_p.T310T|PALLD_ENST00000335742.7_Silent_p.T639T			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1021	Interaction with ARGBP2, SPIN90, SRC and PFN1.|Interaction with EPS8. {ECO:0000250}.|Pro-rich.				cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		TAACTTTCACATGTAGAGTGG	0.423									Pancreatic Cancer, Familial Clustering of				A|||	7	0.00139776	0.0	0.0	5008	,	,		19745	0.0		0.007	False		,,,				2504	0.0				p.T814T	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.A2442G						PASS	.	A	,,,	3,4403	6.2+/-15.9	0,3,2200	103.0	98.0	100.0		2442,1245,930,2391	-7.0	0.9	4	dbSNP_132	100	48,8552	30.7+/-82.3	0,48,4252	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_001166109.1,NM_001166110.1,NM_016081.3	,,,	0,51,6452	GG,GA,AA		0.5581,0.0681,0.3921	,,,	814/1124,415/778,310/673,797/1107	169819835	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon14	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	TTTCACATGTAGA	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.2442A>G	4.37:g.169819835A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	70	47	0.671429	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			A|0.996;G|0.004	0.004	strong		0.423	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
TAS2R46	259292	hgsc.bcm.edu	37	12	11213994	11213994	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:11213994C>T	ENST00000533467.1	-	1	899	c.900G>A	c.(898-900)tgG>tgA	p.W300*	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	300					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)		CTCCTTTCACCCAGTACCTCA	0.393																																					p.W300X		Atlas-SNP	.											TAS2R46,lower_third,carcinoma,0,1	TAS2R46	43	1	0			c.G900A						scavenged	.						172.0	171.0	172.0					12																	11213994		2003	4225	6228	SO:0001587	stop_gained	259292	exon1			TTTCACCCAGTAC	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.900G>A	12.37:g.11213994C>T	ENSP00000436450:p.Trp300*	Somatic	247	3	0.0121457		WXS	Illumina HiSeq	Phase_I	286	4	0.013986	NM_176887	P59548|Q645X6	Nonsense_Mutation	SNP	ENST00000533467.1	37	CCDS53748.1	.	.	.	.	.	.	.	.	.	.	C	9.997	1.232408	0.22626	.	.	ENSG00000226761	ENST00000533467	.	.	.	2.54	-3.09	0.05331	.	.	.	.	.	.	.	.	.	.	.	0.22888	N	0.998607	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.0346	0.14428	0.4813:0.3992:0.0:0.1195	.	.	.	.	X	300	.	ENSP00000436450:W300X	W	-	3	0	TAS2R46	11105261	0.000000	0.05858	0.000000	0.03702	0.183000	0.23260	-2.223000	0.01214	-0.363000	0.08101	0.194000	0.17425	TGG	.	.	none		0.393	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887	
IDO2	169355	hgsc.bcm.edu	37	8	39872804	39872804	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:39872804T>C	ENST00000389060.4	+	10	907	c.907T>C	c.(907-909)Tcc>Ccc	p.S303P	IDO2_ENST00000502986.2_Missense_Mutation_p.S316P|IDO2_ENST00000343295.4_3'UTR			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	303					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						CATGCCTCCTTCCCATAAGGC	0.468																																					p.S316P		Atlas-SNP	.											IDO2_ENST00000502986,NS,malignant_melanoma,-1,4	IDO2	78	4	0			c.T946C						scavenged	.						89.0	83.0	85.0					8																	39872804		1991	4173	6164	SO:0001583	missense	169355	exon11			CCTCCTTCCCATA	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.907T>C	8.37:g.39872804T>C	ENSP00000426447:p.Ser303Pro	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	191	4	0.0209424	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		.	.	.	.	.	.	.	.	.	.	T	13.08	2.128953	0.37533	.	.	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.41065	1.01;1.01	5.91	4.77	0.60923	.	0.436819	0.26586	N	0.023544	T	0.19485	0.0468	N	0.05534	-0.03	0.26758	N	0.970062	B;B	0.19445	0.028;0.036	B;B	0.24541	0.018;0.054	T	0.11616	-1.0580	9	.	.	.	.	4.9099	0.13816	0.0:0.1355:0.3128:0.5517	.	316;303	F5H5G0;Q6ZQW0	.;I23O2_HUMAN	P	316;303	ENSP00000443432:S316P;ENSP00000426447:S303P	.	S	+	1	0	IDO2	39991961	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	0.430000	0.21428	2.252000	0.74401	0.533000	0.62120	TCC	.	.	none		0.468	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
LILRA4	23547	hgsc.bcm.edu	37	19	54848121	54848121	+	Missense_Mutation	SNP	C	C	T	rs141881690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848121C>T	ENST00000291759.4	-	6	1302	c.1246G>A	c.(1246-1248)Gtg>Atg	p.V416M	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	416					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)		CCTGAGACCACGAGCTCCAGG	0.597													C|||	158	0.0315495	0.0613	0.0101	5008	,	,		18423	0.0		0.0109	False		,,,				2504	0.0603				p.V416M		Atlas-SNP	.											.	LILRA4	91	.	0			c.G1246A						PASS	.						80.0	67.0	71.0					19																	54848121		2203	4300	6503	SO:0001583	missense	23547	exon6			AGACCACGAGCTC	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.1246G>A	19.37:g.54848121C>T	ENSP00000291759:p.Val416Met	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	144	13	0.0902778	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	6.736	0.504546	0.12822	.	.	ENSG00000239961	ENST00000291759	T	0.00848	5.62	2.4	-4.8	0.03190	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.277830	0.01713	N	0.027839	T	0.01489	0.0048	M	0.61703	1.905	0.09310	N	1	B	0.18166	0.026	B	0.17433	0.018	T	0.42816	-0.9429	10	0.33141	T	0.24	.	7.5849	0.27987	0.0:0.1789:0.6361:0.185	.	416	P59901	LIRA4_HUMAN	M	416	ENSP00000291759:V416M	ENSP00000291759:V416M	V	-	1	0	LILRA4	59539933	0.000000	0.05858	0.000000	0.03702	0.190000	0.23558	-4.042000	0.00307	-1.656000	0.01495	0.455000	0.32223	GTG	C|0.999;T|0.001	0.001	weak		0.597	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
LVRN	206338	hgsc.bcm.edu	37	5	115298898	115298898	+	Missense_Mutation	SNP	C	C	T	rs145336539	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:115298898C>T	ENST00000357872.4	+	1	708	c.584C>T	c.(583-585)cCc>cTc	p.P195L	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		195						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CTCAGTGAGCCCCTGAAACCT	0.622													C|||	16	0.00319489	0.0008	0.0086	5008	,	,		14129	0.0		0.008	False		,,,				2504	0.001				p.P195L		Atlas-SNP	.											.	.	.	.	0			c.C584T						PASS	.	C	LEU/PRO	3,4397		0,3,2197	21.0	22.0	22.0		584	4.6	0.9	5	dbSNP_134	22	39,8545		0,39,4253	yes	missense	AQPEP	NM_173800.4	98	0,42,6450	TT,TC,CC		0.4543,0.0682,0.3235	benign	195/991	115298898	42,12942	2200	4292	6492	SO:0001583	missense	0	exon1			GTGAGCCCCTGAA																												ENST00000357872.4:c.584C>T	5.37:g.115298898C>T	ENSP00000350541:p.Pro195Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	131	56	0.427481	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	8.710	0.911797	0.17907	6.82E-4	0.004543	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.02656	4.21	4.6	4.6	0.57074	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.383950	0.04803	N	0.433838	T	0.03305	0.0096	L	0.43554	1.36	0.80722	D	1	B	0.27013	0.166	B	0.25614	0.062	T	0.41963	-0.9479	10	0.35671	T	0.21	.	12.9406	0.58340	0.0:1.0:0.0:0.0	.	195	Q6Q4G3	AMPQ_HUMAN	L	195;184	ENSP00000350541:P195L	ENSP00000350541:P195L	P	+	2	0	AC010282.1	115326797	0.002000	0.14202	0.891000	0.34965	0.178000	0.23041	1.441000	0.35035	2.105000	0.64084	0.655000	0.94253	CCC	C|0.997;T|0.003	0.003	strong		0.622	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
EDN1	1906	hgsc.bcm.edu	37	6	12296255	12296255	+	Missense_Mutation	SNP	G	G	T	rs5370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:12296255G>T	ENST00000379375.5	+	5	861	c.594G>T	c.(592-594)aaG>aaT	p.K198N		NM_001168319.1|NM_001955.4	NP_001161791.1|NP_001946.3	P05305	EDN1_HUMAN	endothelin 1	198			K -> N (polymorphism associated with HDL cholesterol levels is some populations and in a sex-specific manner; dbSNP:rs5370). {ECO:0000269|PubMed:10334806, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17357073, ECO:0000269|PubMed:18288492, ECO:0000269|Ref.5}.		artery smooth muscle contraction (GO:0014824)|body fluid secretion (GO:0007589)|calcium-mediated signaling (GO:0019722)|cartilage development (GO:0051216)|cell growth (GO:0016049)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|dorsal/ventral pattern formation (GO:0009953)|epithelial fluid transport (GO:0042045)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose transport (GO:0015758)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|inositol phosphate-mediated signaling (GO:0048016)|leukocyte activation (GO:0045321)|maternal process involved in parturition (GO:0060137)|membrane depolarization (GO:0051899)|middle ear morphogenesis (GO:0042474)|multicellular organismal aging (GO:0010259)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of hormone secretion (GO:0046888)|negative regulation of nitric-oxide synthase biosynthetic process (GO:0051771)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell development (GO:0014032)|nitric oxide transport (GO:0030185)|patterning of blood vessels (GO:0001569)|peptide hormone secretion (GO:0030072)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phospholipase D-activating G-protein coupled receptor signaling pathway (GO:0031583)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of chemokine-mediated signaling pathway (GO:0070101)|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 endothelial cell migration (GO:0010595)|positive regulation of heart rate (GO:0010460)|positive regulation of hormone secretion (GO:0046887)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of odontogenesis (GO:0042482)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of urine volume (GO:0035810)|prostaglandin biosynthetic process (GO:0001516)|protein kinase C deactivation (GO:0042313)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|respiratory gaseous exchange (GO:0007585)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to testosterone (GO:0033574)|rhythmic excitation (GO:0043179)|sensory perception of pain (GO:0019233)|superoxide anion generation (GO:0042554)|vasoconstriction (GO:0042310)|vein smooth muscle contraction (GO:0014826)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|endothelin A receptor binding (GO:0031707)|endothelin B receptor binding (GO:0031708)|hormone activity (GO:0005179)	p.K198N(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	13	all_cancers(95;0.241)|Breast(50;0.0266)|Ovarian(93;0.12)	all_hematologic(90;0.117)				TGAAAGGCAAGCCCTCCAGAG	0.483													G|||	1239	0.247404	0.1619	0.147	5008	,	,		18203	0.2857		0.2127	False		,,,				2504	0.4305				p.K198N		Atlas-SNP	.											EDN1,NS,carcinoma,0,1	EDN1	23	1	1	Substitution - Missense(1)	stomach(1)	c.G594T	GRCh37	CM993569	EDN1	M	rs5370	scavenged	.	G	ASN/LYS,ASN/LYS	865,3541	337.0+/-304.7	98,669,1436	158.0	150.0	152.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	591,594	2.2	0.1	6	dbSNP_52	152	1817,6783	326.9+/-317.6	185,1447,2668	yes	missense,missense	EDN1	NM_001168319.1,NM_001955.4	94,94	283,2116,4104	TT,TG,GG		21.1279,19.6323,20.6213	benign,benign	197/212,198/213	12296255	2682,10324	2203	4300	6503	SO:0001583	missense	1906	exon5			AGGCAAGCCCTCC	S56805	CCDS4522.1	6p24.1	2014-03-19			ENSG00000078401	ENSG00000078401		"""Endogenous ligands"""	3176	protein-coding gene	gene with protein product		131240					Standard	NM_001168319		Approved	ET1	uc003nae.4	P05305	OTTHUMG00000014266	ENST00000379375.5:c.594G>T	6.37:g.12296255G>T	ENSP00000368683:p.Lys198Asn	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_001955	Q96DA1	Missense_Mutation	SNP	ENST00000379375.5	37	CCDS4522.1	449	0.20558608058608058	68	0.13821138211382114	63	0.17403314917127072	158	0.2762237762237762	160	0.21108179419525067	G	7.695	0.691892	0.15039	0.196323	0.211279	ENSG00000078401	ENST00000379375	D	0.84589	-1.87	5.93	2.18	0.27775	.	0.551151	0.21002	N	0.081852	T	0.60894	0.2304	L	0.38175	1.15	0.45452	P	0.001570999999999989	P;P	0.34462	0.454;0.454	B;B	0.26614	0.071;0.071	T	0.49532	-0.8930	9	0.51188	T	0.08	-14.7064	9.471	0.38842	0.276:0.0:0.724:0.0	rs5370;rs2229566;rs17845238;rs17858054;rs57072783;rs5370	198;198	Q6FH53;P05305	.;EDN1_HUMAN	N	198	ENSP00000368683:K198N	ENSP00000368683:K198N	K	+	3	2	EDN1	12404241	0.001000	0.12720	0.141000	0.22245	0.005000	0.04900	0.049000	0.14099	0.116000	0.18110	0.655000	0.94253	AAG	G|0.787;T|0.213	0.213	strong		0.483	EDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039872.1	NM_001955	
CHRNA9	55584	hgsc.bcm.edu	37	4	40337908	40337908	+	Silent	SNP	T	T	C	rs10022491	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:40337908T>C	ENST00000310169.2	+	2	268	c.129T>C	c.(127-129)tcT>tcC	p.S43S		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	43					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)	AAGATTATTCTAATGCTCTTC	0.413													C|||	3227	0.644369	0.9334	0.6427	5008	,	,		21423	0.4008		0.5338	False		,,,				2504	0.6196				p.S43S	Esophageal Squamous(115;1297 1602 22235 25158 43327)	Atlas-SNP	.											.	CHRNA9	53	.	0			c.T129C						PASS	.	C		3819,587	259.8+/-263.3	1656,507,40	170.0	159.0	163.0		129	4.0	1.0	4	dbSNP_119	163	4694,3906	546.3+/-384.9	1287,2120,893	no	coding-synonymous	CHRNA9	NM_017581.2		2943,2627,933	CC,CT,TT		45.4186,13.3227,34.5456		43/480	40337908	8513,4493	2203	4300	6503	SO:0001819	synonymous_variant	55584	exon2			TTATTCTAATGCT	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.129T>C	4.37:g.40337908T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	228	112	0.491228	NM_017581	Q14CY7|Q4W5A2|Q9NYV2	Silent	SNP	ENST00000310169.2	37	CCDS3459.1																																																																																			T|0.360;C|0.640	0.640	strong		0.413	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1		
MKI67	4288	hgsc.bcm.edu	37	10	129902281	129902281	+	Missense_Mutation	SNP	G	G	A	rs1063535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129902281G>A	ENST00000368654.3	-	13	8198	c.7823C>T	c.(7822-7824)cCc>cTc	p.P2608L	MKI67_ENST00000368653.3_Missense_Mutation_p.P2248L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2608	16 X 122 AA approximate repeats.		P -> L (in dbSNP:rs1063535).		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)				TTCTTTCCTGGGACGTGTCTT	0.483													A|||	2317	0.46266	0.4607	0.6081	5008	,	,		21089	0.378		0.5209	False		,,,				2504	0.3896				p.P2608L		Atlas-SNP	.											.	MKI67	363	.	0			c.C7823T						PASS	.	A	LEU/PRO,LEU/PRO	2021,2385	613.3+/-392.2	472,1077,654	152.0	137.0	142.0		6743,7823	-4.0	0.0	10	dbSNP_86	142	4473,4127	563.8+/-388.2	1163,2147,990	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	98,98	1635,3224,1644	AA,AG,GG		47.9884,45.8693,49.9308	benign,benign	2248/2897,2608/3257	129902281	6494,6512	2203	4300	6503	SO:0001583	missense	4288	exon13			TTCCTGGGACGTG	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.7823C>T	10.37:g.129902281G>A	ENSP00000357643:p.Pro2608Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	138	63	0.456522	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	1037	0.4748168498168498	198	0.4024390243902439	210	0.580110497237569	234	0.4090909090909091	395	0.521108179419525	A	5.806	0.333006	0.11013	0.458693	0.520116	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01414	4.92;4.92	2.27	-4.04	0.04010	.	.	.	.	.	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	0.16837	-1.0389	8	0.27082	T	0.32	.	1.3429	0.02157	0.1868:0.339:0.3053:0.1689	rs1063535;rs3204563;rs52818135;rs60716258;rs1063535	2607;2248;2608	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	2608;2248;2607	ENSP00000357643:P2608L;ENSP00000357642:P2248L	ENSP00000357642:P2248L	P	-	2	0	MKI67	129792271	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.074000	0.14662	-1.587000	0.01630	-0.360000	0.07572	CCC	G|0.522;A|0.478	0.478	strong		0.483	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
MOB3A	126308	hgsc.bcm.edu	37	19	2078176	2078176	+	Silent	SNP	C	C	T	rs35452475	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	267	267	1	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	
SLITRK5	26050	hgsc.bcm.edu	37	13	88328488	88328488	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:88328488A>G	ENST00000325089.6	+	2	1064	c.845A>G	c.(844-846)gAa>gGa	p.E282G	SLITRK5_ENST00000400028.3_Missense_Mutation_p.E41G	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	282	LRRCT 1.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					TCCAAGCAGGAACTTTGCCCA	0.542																																					p.E282G		Atlas-SNP	.											SLITRK5,NS,carcinoma,+1,2	SLITRK5	192	2	0			c.A845G						scavenged	.						79.0	81.0	80.0					13																	88328488		2203	4300	6503	SO:0001583	missense	26050	exon2			AGCAGGAACTTTG	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	ENST00000325089.6:c.845A>G	13.37:g.88328488A>G	ENSP00000366283:p.Glu282Gly	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	92	2	0.0217391	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.348684	0.61183	.	.	ENSG00000165300	ENST00000325089;ENST00000400028	T;T	0.50548	0.74;0.74	5.76	5.76	0.90799	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68933	0.3055	M	0.81682	2.555	0.58432	D	0.999996	D;D	0.76494	0.999;0.998	D;D	0.70935	0.971;0.971	T	0.71938	-0.4441	9	.	.	.	-10.5001	14.0293	0.64606	1.0:0.0:0.0:0.0	.	41;282	B4DSH5;O94991	.;SLIK5_HUMAN	G	282;41	ENSP00000366283:E282G;ENSP00000442244:E41G	.	E	+	2	0	SLITRK5	87126489	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.146000	0.77373	2.199000	0.70637	0.402000	0.26972	GAA	.	.	none		0.542	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3		
GPR20	2843	hgsc.bcm.edu	37	8	142367350	142367350	+	Missense_Mutation	SNP	C	C	T	rs201039593	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:142367350C>T	ENST00000377741.3	-	2	764	c.674G>A	c.(673-675)cGg>cAg	p.R225Q	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	225					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			CAGACCCGGCCGCGACAGTGC	0.652													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18546	0.0		0.003	False		,,,				2504	0.0				p.R225Q		Atlas-SNP	.											.	GPR20	43	.	0			c.G674A						PASS	.	C	GLN/ARG	4,4162		0,4,2079	10.0	9.0	9.0		674	3.7	0.2	8	dbSNP_134	9	52,8166		1,50,4058	yes	missense	GPR20	NM_005293.2	43	1,54,6137	TT,TC,CC		0.6328,0.096,0.4522	probably-damaging	225/359	142367350	56,12328	2083	4109	6192	SO:0001583	missense	2843	exon2			CCCGGCCGCGACA	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"""GPCR / Class A : Orphans"""	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.674G>A	8.37:g.142367350C>T	ENSP00000366970:p.Arg225Gln	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_005293	Q17R96	Missense_Mutation	SNP	ENST00000377741.3	37	CCDS34949.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.459179	0.26248	9.6E-4	0.006328	ENSG00000204882	ENST00000377741	T	0.41400	1.0	4.77	3.67	0.42095	GPCR, rhodopsin-like superfamily (1);	0.643696	0.13570	U	0.378104	T	0.29684	0.0741	L	0.35793	1.09	0.09310	N	1	D	0.55800	0.973	P	0.48166	0.569	T	0.06588	-1.0818	10	0.32370	T	0.25	-20.3414	9.5849	0.39510	0.0:0.8396:0.0:0.1604	.	225	Q99678	GPR20_HUMAN	Q	225	ENSP00000366970:R225Q	ENSP00000366970:R225Q	R	-	2	0	GPR20	142436532	0.004000	0.15560	0.175000	0.22980	0.085000	0.17905	0.829000	0.27449	2.197000	0.70478	0.462000	0.41574	CGG	.	.	weak		0.652	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293	
OAF	220323	hgsc.bcm.edu	37	11	120099791	120099791	+	Silent	SNP	C	C	T	rs2465654	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:120099791C>T	ENST00000328965.4	+	4	1275	c.762C>T	c.(760-762)ttC>ttT	p.F254F	OAF_ENST00000531220.1_Silent_p.F138F	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	254						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)		GCTACAGCTTCGACTTCTACG	0.647													C|||	810	0.161741	0.2231	0.1585	5008	,	,		14973	0.129		0.0815	False		,,,				2504	0.1973				p.F254F		Atlas-SNP	.											.	OAF	12	.	0			c.C762T						PASS	.	C		899,3507	331.2+/-301.9	91,717,1395	55.0	53.0	54.0		762	-0.5	0.8	11	dbSNP_100	54	624,7976	157.2+/-210.9	21,582,3697	no	coding-synonymous	OAF	NM_178507.2		112,1299,5092	TT,TC,CC		7.2558,20.404,11.71		254/274	120099791	1523,11483	2203	4300	6503	SO:0001819	synonymous_variant	220323	exon4			CAGCTTCGACTTC	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.762C>T	11.37:g.120099791C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	270	198	0.733333	NM_178507		Silent	SNP	ENST00000328965.4	37	CCDS8430.1																																																																																			C|0.869;T|0.131	0.131	strong		0.647	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507	
SPHK2	56848	hgsc.bcm.edu	37	19	49132634	49132634	+	Silent	SNP	G	G	A	rs3745733	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49132634G>A	ENST00000245222.4	+	7	1935	c.1569G>A	c.(1567-1569)ctG>ctA	p.L523L	SPHK2_ENST00000600537.1_Silent_p.L464L|SPHK2_ENST00000598088.1_Silent_p.L523L|SPHK2_ENST00000599029.1_Silent_p.L487L|SPHK2_ENST00000443164.1_Silent_p.L585L|SPHK2_ENST00000599748.1_Silent_p.L487L|SPHK2_ENST00000340932.3_Silent_p.L485L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	523					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TGCCTCCGCTGGGCACCCCGC	0.701													G|||	379	0.0756789	0.0272	0.0994	5008	,	,		12711	0.0714		0.1203	False		,,,				2504	0.0828				p.L523L		Atlas-SNP	.											SPHK2,NS,carcinoma,0,1	SPHK2	62	1	0			c.G1569A						PASS	.	G	,,,	176,4224		3,170,2027	20.0	23.0	22.0		1392,1569,1461,1569	-0.4	0.3	19	dbSNP_107	22	1188,7404		79,1030,3187	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	82,1200,5214	AA,AG,GG		13.8268,4.0,10.4988	,,,	464/596,523/655,487/619,523/655	49132634	1364,11628	2200	4296	6496	SO:0001819	synonymous_variant	56848	exon7			TCCGCTGGGCACC	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1569G>A	19.37:g.49132634G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.907;A|0.093	0.093	strong		0.701	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
MRGPRD	116512	hgsc.bcm.edu	37	11	68747529	68747529	+	Silent	SNP	C	C	T	rs138573323	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68747529C>T	ENST00000309106.3	-	1	926	c.927G>A	c.(925-927)ggG>ggA	p.G309G		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	309						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGGGCGTCTCCCCACCTTCCA	0.682													C|||	32	0.00638978	0.0008	0.0173	5008	,	,		14707	0.0		0.0179	False		,,,				2504	0.001				p.G309G		Atlas-SNP	.											.	MRGPRD	53	.	0			c.G927A						PASS	.	C		12,4272		0,12,2130	25.0	31.0	29.0		927	0.2	0.0	11	dbSNP_134	29	133,8199		1,131,4034	no	coding-synonymous	MRGPRD	NM_198923.2		1,143,6164	TT,TC,CC		1.5963,0.2801,1.1493		309/322	68747529	145,12471	2142	4166	6308	SO:0001819	synonymous_variant	116512	exon1			CGTCTCCCCACCT	AB083627	CCDS31625.1	11q13.3	2012-08-21			ENSG00000172938	ENSG00000172938		"""GPCR / Class A : Orphans"""	29626	protein-coding gene	gene with protein product		607231				11551509, 12909716	Standard	NM_198923		Approved	mrgD	uc010rqf.2	Q8TDS7	OTTHUMG00000167896	ENST00000309106.3:c.927G>A	11.37:g.68747529C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_198923	Q8NGK7	Silent	SNP	ENST00000309106.3	37	CCDS31625.1																																																																																			C|0.989;T|0.011	0.011	strong		0.682	MRGPRD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396874.1	NM_198923	
KIF24	347240	hgsc.bcm.edu	37	9	34256347	34256347	+	Silent	SNP	C	C	T	rs10814083	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34256347C>T	ENST00000402558.2	-	10	3282	c.3258G>A	c.(3256-3258)ggG>ggA	p.G1086G	KIF24_ENST00000345050.2_Silent_p.G952G|KIF24_ENST00000379174.3_Silent_p.G952G|KIF24_ENST00000379166.2_Silent_p.G1086G			Q5T7B8	KIF24_HUMAN	kinesin family member 24	1086					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)			CAACTGGGCCCCCTGTGCTCT	0.607													C|||	2204	0.440096	0.2685	0.4006	5008	,	,		20026	0.7351		0.3082	False		,,,				2504	0.5317				p.G1086G		Atlas-SNP	.											.	KIF24	64	.	0			c.G3258A						PASS	.	C		1226,3180	423.0+/-339.9	158,910,1135	44.0	37.0	39.0		3258	0.4	0.0	9	dbSNP_120	39	2936,5664	452.7+/-363.0	499,1938,1863	no	coding-synonymous	KIF24	NM_194313.2		657,2848,2998	TT,TC,CC		34.1395,27.8257,32.0006		1086/1369	34256347	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	347240	exon11			TGGGCCCCCTGTG	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.3258G>A	9.37:g.34256347C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Silent	SNP	ENST00000402558.2	37	CCDS6551.2	924	0.4230769230769231	142	0.2886178861788618	139	0.3839779005524862	397	0.6940559440559441	246	0.3245382585751979	C	2.713	-0.268302	0.05716	0.278257	0.341395	ENSG00000186638	ENST00000443226	.	.	.	4.81	0.37	0.16160	.	0.988720	0.08220	N	0.979213	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.40942	-0.9536	5	0.36615	T	0.2	.	6.452	0.21908	0.1277:0.6217:0.0:0.2506	rs10814083;rs58917175;rs10814083	.	.	.	R	132	.	ENSP00000414628:G132R	G	-	1	0	KIF24	34246347	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.091000	0.11146	-0.012000	0.14223	-1.119000	0.02030	GGG	C|0.626;T|0.374	0.374	strong		0.607	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
PTPRU	10076	hgsc.bcm.edu	37	1	29630455	29630455	+	Silent	SNP	C	C	T	rs2295061	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:29630455C>T	ENST00000345512.3	+	17	2724	c.2595C>T	c.(2593-2595)taC>taT	p.Y865Y	PTPRU_ENST00000356870.3_Silent_p.Y855Y|PTPRU_ENST00000373779.3_Silent_p.Y855Y|PTPRU_ENST00000323874.8_Silent_p.Y855Y|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000428026.2_Silent_p.Y855Y|PTPRU_ENST00000460170.2_Silent_p.Y855Y	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	865	Mediates interaction with CTNNB1. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GCTCCCCATACCACACGGGGC	0.662													C|||	1879	0.3752	0.3533	0.3329	5008	,	,		16610	0.6419		0.1581	False		,,,				2504	0.3834				p.Y865Y		Atlas-SNP	.											.	PTPRU	374	.	0			c.C2595T						PASS	.	C	,,,	1402,3004	440.8+/-346.1	220,962,1021	45.0	49.0	48.0		2565,2595,2565,2565	-2.5	0.7	1	dbSNP_100	48	1224,7376	240.8+/-271.4	85,1054,3161	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRU	NM_001195001.1,NM_005704.4,NM_133177.3,NM_133178.3	,,,	305,2016,4182	TT,TC,CC		14.2326,31.8202,20.1907	,,,	855/1434,865/1447,855/1441,855/1437	29630455	2626,10380	2203	4300	6503	SO:0001819	synonymous_variant	10076	exon17			CCCATACCACACG	U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9683	protein-coding gene	gene with protein product	"""pi R-PTP-Psi"""	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.2595C>T	1.37:g.29630455C>T		Somatic	360	0	0		WXS	Illumina HiSeq	Phase_I	213	61	0.286385	NM_005704	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Silent	SNP	ENST00000345512.3	37	CCDS334.1																																																																																			C|0.746;T|0.254	0.254	strong		0.662	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1		
EML5	161436	hgsc.bcm.edu	37	14	89151392	89151392	+	Silent	SNP	C	C	A	rs17204164	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:89151392C>A	ENST00000380664.5	-	20	2948	c.2949G>T	c.(2947-2949)gtG>gtT	p.V983V	EML5_ENST00000554922.1_Silent_p.V983V|EML5_ENST00000352093.5_Silent_p.V945V			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	158	0	0		WXS	Illumina HiSeq	Phase_I	200	61	0.305	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		
RADIL	55698	hgsc.bcm.edu	37	7	4874420	4874420	+	Missense_Mutation	SNP	G	G	C	rs2292498	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:4874420G>C	ENST00000399583.3	-	4	1421	c.1234C>G	c.(1234-1236)Cac>Gac	p.H412D	RADIL_ENST00000538469.1_Missense_Mutation_p.H172D|RADIL_ENST00000536091.1_Missense_Mutation_p.H412D	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	412			H -> D (in dbSNP:rs2292498). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		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)		TCCTCCAGGTGGGGCTCAAAC	0.716													G|||	1259	0.251398	0.0401	0.2853	5008	,	,		9176	0.3294		0.2873	False		,,,				2504	0.3957				p.H412D		Atlas-SNP	.											.	RADIL	110	.	0			c.C1234G						PASS	.	G	ASP/HIS	299,3725		19,261,1732	12.0	15.0	14.0		1234	2.6	0.0	7	dbSNP_100	14	2520,5808		397,1726,2041	yes	missense	RADIL	NM_018059.4	81	416,1987,3773	CC,CG,GG		30.2594,7.4304,22.8222	benign	412/1076	4874420	2819,9533	2012	4164	6176	SO:0001583	missense	55698	exon4			CCAGGTGGGGCTC	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.1234C>G	7.37:g.4874420G>C	ENSP00000382492:p.His412Asp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	116	38	0.327586	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	526	0.24084249084249085	22	0.044715447154471545	94	0.2596685082872928	195	0.3409090909090909	215	0.2836411609498681	-	0.008	-1.905182	0.00512	0.074304	0.302594	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000536091;ENST00000538469	T;T;T	0.21031	3.45;2.03;3.37	4.45	2.56	0.30785	.	1.666850	0.02995	N	0.147315	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	0.43261	-0.9402	9	0.11794	T	0.64	-5.6915	8.1854	0.31335	0.1638:0.6284:0.2079:0.0	rs2292498;rs2292498	412	Q96JH8	RADIL_HUMAN	D	412;383;146;412;172	ENSP00000382492:H412D;ENSP00000442533:H412D;ENSP00000442966:H172D	ENSP00000320946:H383D	H	-	1	0	RADIL	4840946	0.095000	0.21747	0.004000	0.12327	0.011000	0.07611	1.196000	0.32198	0.291000	0.22468	-0.218000	0.12543	CAC	G|0.754;C|0.246	0.246	strong		0.716	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
BEND3	57673	hgsc.bcm.edu	37	6	107391213	107391213	+	Silent	SNP	C	C	T	rs3814072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:107391213C>T	ENST00000369042.1	-	4	1372	c.1182G>A	c.(1180-1182)acG>acA	p.T394T	BEND3_ENST00000429433.2_Silent_p.T394T			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	394	BEN 2. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						TGAGGTCCTGCGTGTCCACCA	0.632													c|||	344	0.0686901	0.0598	0.0764	5008	,	,		18142	0.0585		0.0934	False		,,,				2504	0.0603				p.T394T		Atlas-SNP	.											.	BEND3	70	.	0			c.G1182A						PASS	.	C		322,4084	170.9+/-201.2	11,300,1892	72.0	72.0	72.0		1182	-1.3	1.0	6	dbSNP_107	72	719,7881	176.0+/-226.0	32,655,3613	no	coding-synonymous	BEND3	NM_001080450.2		43,955,5505	TT,TC,CC		8.3605,7.3082,8.004		394/829	107391213	1041,11965	2203	4300	6503	SO:0001819	synonymous_variant	57673	exon5			GTCCTGCGTGTCC	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"""BEN domain containing"""	23040	protein-coding gene	gene with protein product			"""KIAA1553"""	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.1182G>A	6.37:g.107391213C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	127	73	0.574803	NM_001080450	A2RRH2|Q9HCL9	Silent	SNP	ENST00000369042.1	37	CCDS34507.1																																																																																			C|0.925;T|0.075	0.075	strong		0.632	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
OGDHL	55753	hgsc.bcm.edu	37	10	50959965	50959965	+	Silent	SNP	C	C	T	rs7090775	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50959965C>T	ENST00000374103.4	-	6	742	c.657G>A	c.(655-657)caG>caA	p.Q219Q	OGDHL_ENST00000432695.1_Silent_p.Q10Q|OGDHL_ENST00000419399.1_Silent_p.Q162Q	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	219					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						GCCGGATCCACTGGCACTGCT	0.592													C|||	274	0.0547125	0.0877	0.0331	5008	,	,		19769	0.004		0.0219	False		,,,				2504	0.1115				p.Q219Q		Atlas-SNP	.											.	OGDHL	149	.	0			c.G657A						PASS	.	C	,,	263,4143	150.3+/-184.3	10,243,1950	193.0	187.0	189.0		486,30,657	4.7	1.0	10	dbSNP_116	189	287,8313	107.8+/-168.5	4,279,4017	no	coding-synonymous,coding-synonymous,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	14,522,5967	TT,TC,CC		3.3372,5.9691,4.2288	,,	162/954,10/802,219/1011	50959965	550,12456	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon6			GATCCACTGGCAC	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.657G>A	10.37:g.50959965C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	92	73	0.793478	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			C|0.960;T|0.040	0.040	strong		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
MTA1	9112	hgsc.bcm.edu	37	14	105930406	105930406	+	Missense_Mutation	SNP	G	G	A	rs4983413	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105930406G>A	ENST00000331320.7	+	13	1328	c.1114G>A	c.(1114-1116)Gtc>Atc	p.V372I	MTA1_ENST00000406191.1_Missense_Mutation_p.V372I|MTA1_ENST00000405646.1_Missense_Mutation_p.V355I|MTA1_ENST00000435036.2_5'UTR	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	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	240	154	0.641667	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		
OR10V1	390201	hgsc.bcm.edu	37	11	59480759	59480759	+	Missense_Mutation	SNP	C	C	T	rs141649641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:59480759C>T	ENST00000307552.2	-	1	578	c.560G>A	c.(559-561)cGc>cAc	p.R187H	STX3_ENST00000300150.7_5'Flank	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	187						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|liver(1)|lung(10)|skin(1)	16						ACAAGCCAGGCGCATGACTGC	0.483													C|||	3	0.000599042	0.0	0.0	5008	,	,		23804	0.0		0.003	False		,,,				2504	0.0				p.R187H		Atlas-SNP	.											.	OR10V1	40	.	0			c.G560A						PASS	.	C	HIS/ARG	5,4397	9.9+/-24.2	0,5,2196	104.0	89.0	94.0		560	-0.0	1.0	11	dbSNP_134	94	31,8559	21.6+/-65.8	0,31,4264	yes	missense	OR10V1	NM_001005324.1	29	0,36,6460	TT,TC,CC		0.3609,0.1136,0.2771	benign	187/310	59480759	36,12956	2201	4295	6496	SO:0001583	missense	390201	exon1			GCCAGGCGCATGA	AB065807	CCDS31565.1	11q12.1	2012-08-09			ENSG00000172289	ENSG00000172289		"""GPCR / Class A : Olfactory receptors"""	15136	protein-coding gene	gene with protein product							Standard	NM_001005324		Approved		uc001nof.1	Q8NGI7	OTTHUMG00000167406	ENST00000307552.2:c.560G>A	11.37:g.59480759C>T	ENSP00000302199:p.Arg187His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	94	52	0.553191	NM_001005324	Q6IFD9|Q96R50	Missense_Mutation	SNP	ENST00000307552.2	37	CCDS31565.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	9.722	1.159943	0.21454	0.001136	0.003609	ENSG00000172289	ENST00000307552	T	0.00137	8.68	4.47	-0.0376	0.13883	GPCR, rhodopsin-like superfamily (1);	0.258733	0.25869	N	0.027762	T	0.00109	0.0003	L	0.37800	1.135	0.24816	N	0.992619	B	0.31383	0.321	B	0.32149	0.141	T	0.28681	-1.0036	10	0.54805	T	0.06	.	5.0568	0.14537	0.142:0.5452:0.0:0.3128	.	187	Q8NGI7	O10V1_HUMAN	H	187	ENSP00000302199:R187H	ENSP00000302199:R187H	R	-	2	0	OR10V1	59237335	0.000000	0.05858	0.993000	0.49108	0.635000	0.38103	-1.103000	0.03329	-0.105000	0.12132	-0.545000	0.04230	CGC	C|0.998;T|0.002	0.002	strong		0.483	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324	
CASP12	100506742	hgsc.bcm.edu	37	11	104768098	104768098	+	Silent	SNP	T	T	C	rs555367	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:104768098T>C	ENST00000422698.2	-	2	123	c.105A>G	c.(103-105)gtA>gtG	p.V35V	CASP12_ENST00000446862.1_Silent_p.V35V|CASP12_ENST00000508062.1_Intron|CASP12_ENST00000494737.1_Silent_p.V35V|CASP12_ENST00000448103.1_Silent_p.V35V|CASP12_ENST00000447913.1_Intron|CASP12_ENST00000433738.1_Intron|CASP12_ENST00000441710.1_Silent_p.V35V|CASP12_ENST00000375726.2_Silent_p.V35V	NM_001191016.1	NP_001177945.1	Q6UXS9	CASPC_HUMAN	caspase 12 (gene/pseudogene)	35	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				endoplasmic reticulum unfolded protein response (GO:0030968)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)			breast(1)	1						CTGTATTTAATACATTATTTT	0.383													C|||	4957	0.989816	0.9629	0.9971	5008	,	,		18743	1.0		1.0	False		,,,				2504	1.0				p.V35V		Atlas-SNP	.											.	CASP12	4	.	0			c.A105G						PASS	.																																			SO:0001819	synonymous_variant	100506742	exon2			ATTTAATACATTA	AF464191		11q22.3	2011-02-14	2007-12-17	2006-02-17	ENSG00000204403	ENSG00000204403		"""Caspases"""	19004	protein-coding gene	gene with protein product		608633	"""caspase 12 pseudogene 1"", ""caspase 12"""	CASP12P1		12054529, 9038361, 16917906, 16532395	Standard	NM_001191016		Approved		uc031qdo.1	Q6UXS9	OTTHUMG00000154965	ENST00000422698.2:c.105A>G	11.37:g.104768098T>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001191016	D6RBN7	Silent	SNP	ENST00000422698.2	37	CCDS55785.1																																																																																			T|0.010;C|0.990	0.990	strong		0.383	CASP12-008	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337832.2	NM_001191016	
DHRS4	10901	hgsc.bcm.edu	37	14	24435542	24435542	+	Missense_Mutation	SNP	G	G	T	rs11556285		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24435542G>T	ENST00000313250.5	+	6	785	c.582G>T	c.(580-582)aaG>aaT	p.K194N	DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000558581.1_Missense_Mutation_p.K160N|DHRS4_ENST00000421831.1_Missense_Mutation_p.K142N|DHRS4_ENST00000397073.2_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000382761.3_Intron|DHRS4_ENST00000397074.3_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	194					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	GCCTGACCAAGACCCTGGCCA	0.502																																					p.K194N		Atlas-SNP	.											.	DHRS4	22	.	0			c.G582T						PASS	.																																			SO:0001583	missense	10901	exon6			GACCAAGACCCTG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.582G>T	14.37:g.24435542G>T	ENSP00000326219:p.Lys194Asn	Somatic	1032	1	0.000968992		WXS	Illumina HiSeq	Phase_I	1415	159	0.112367	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.739826	0.30865	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	T;T	0.46063	0.88;0.88	3.53	2.63	0.31362	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.294117	0.30639	N	0.009188	T	0.54838	0.1883	M	0.82056	2.57	0.80722	D	1	B;P	0.39862	0.326;0.692	B;P	0.52823	0.238;0.71	T	0.54609	-0.8268	10	0.72032	D	0.01	.	5.9644	0.19316	0.251:0.0:0.749:0.0	rs11556285;rs11556285	160;194	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	N	194;142	ENSP00000326219:K194N;ENSP00000404147:K142N	ENSP00000326219:K194N	K	+	3	2	DHRS4	23505382	1.000000	0.71417	0.998000	0.56505	0.689000	0.40095	1.961000	0.40432	0.599000	0.29845	0.580000	0.79431	AAG	G|0.998;T|0.002	0.002	weak		0.502	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
VEGFB	7423	hgsc.bcm.edu	37	11	64004692	64004692	+	Silent	SNP	C	C	T	rs11558381|rs12366035	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:64004692C>T	ENST00000309422.2	+	5	704	c.408C>T	c.(406-408)gaC>gaT	p.D136D	RP11-783K16.14_ENST00000534988.1_RNA|VEGFB_ENST00000426086.2_Silent_p.D136D|RP11-783K16.14_ENST00000539963.1_RNA	NM_001243733.1|NM_003377.4	NP_001230662.1|NP_003368.1	P49765	VEGFB_HUMAN	vascular endothelial growth factor B	136					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|coronary vasculature development (GO:0060976)|induction of positive chemotaxis (GO:0050930)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular wound healing (GO:0035470)|protein O-linked glycosylation (GO:0006493)|response to drug (GO:0042493)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|heparin binding (GO:0008201)|vascular endothelial growth factor receptor 1 binding (GO:0043183)	p.D136D(1)		endometrium(2)|large_intestine(2)|prostate(1)|stomach(1)	6					Aflibercept(DB08885)	TGAAGCCAGACAGGTGAGTCT	0.488													C|||	862	0.172125	0.0151	0.134	5008	,	,		14845	0.1478		0.2952	False		,,,				2504	0.3098				p.D136D		Atlas-SNP	.											VEGFB,NS,carcinoma,0,1	VEGFB	18	1	1	Substitution - coding silent(1)	stomach(1)	c.C408T						PASS	.	C		242,4160	139.6+/-175.2	7,228,1966	134.0	123.0	127.0		408	4.5	1.0	11	dbSNP_120	127	2673,5921	430.0+/-356.4	414,1845,2038	no	coding-synonymous	VEGFB	NM_003377.4		421,2073,4004	TT,TC,CC		31.1031,5.4975,22.43		136/208	64004692	2915,10081	2201	4297	6498	SO:0001819	synonymous_variant	7423	exon5			GCCAGACAGGTGA	BC008818	CCDS8062.1, CCDS58144.1	11q13	2005-09-29				ENSG00000173511			12681	protein-coding gene	gene with protein product		601398		VRF		8637916, 8919691	Standard	NM_001243733		Approved	VEGFL	uc001nyw.3	P49765		ENST00000309422.2:c.408C>T	11.37:g.64004692C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_003377	Q16528	Silent	SNP	ENST00000309422.2	37	CCDS8062.1																																																																																			C|0.792;T|0.208	0.208	strong		0.488	VEGFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396393.2	NM_003377	
FNBP1	23048	hgsc.bcm.edu	37	9	132687349	132687349	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:132687349G>A	ENST00000446176.2	-	9	1063	c.877C>T	c.(877-879)Cgc>Tgc	p.R293C	FNBP1_ENST00000478129.1_5'UTR|FNBP1_ENST00000355681.3_Missense_Mutation_p.R293C|FNBP1_ENST00000420781.1_Missense_Mutation_p.R293C	NM_015033.2	NP_055848.1	Q96RU3	FNBP1_HUMAN	formin binding protein 1	293	Interaction with microtubules. {ECO:0000250}.|Required for self-association and induction of membrane tubulation.				endocytosis (GO:0006897)	coated pit (GO:0005905)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.R293C(1)					Ovarian(14;0.000536)		GBM - Glioblastoma multiforme(294;0.0378)		GACACAGTGCGCTTCATTGGC	0.423			T	MLL	AML																																p.R293C		Atlas-SNP	.		Dom	yes		9	9q23	23048	formin binding protein 1 (FBP17)		L	FNBP1_ENST00000372416,colon,carcinoma,0,1	FNBP1	51	1	1	Substitution - Missense(1)	large_intestine(1)	c.C877T						scavenged	.						147.0	137.0	140.0					9																	132687349		1882	4120	6002	SO:0001583	missense	23048	exon9			CAGTGCGCTTCAT	AB011126	CCDS48040.1	9q34	2008-02-05			ENSG00000187239	ENSG00000187239			17069	protein-coding gene	gene with protein product		606191				9628581, 11438682	Standard	XM_005251815		Approved	FBP17, KIAA0554	uc004byw.1	Q96RU3	OTTHUMG00000020800	ENST00000446176.2:c.877C>T	9.37:g.132687349G>A	ENSP00000413625:p.Arg293Cys	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	236	4	0.0169492	NM_015033	O60301|Q3MIN8|Q5TC87|Q5TC88|Q6P658|Q7LGG2|Q9H8H8|Q9NWD1	Missense_Mutation	SNP	ENST00000446176.2	37	CCDS48040.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.752514	0.49362	.	.	ENSG00000187239	ENST00000372416;ENST00000446176;ENST00000420781;ENST00000372415;ENST00000355681	T;T;T	0.51071	0.73;0.72;0.78	5.34	5.34	0.76211	.	0.101754	0.64402	D	0.000004	T	0.68366	0.2993	M	0.76574	2.34	0.80722	D	1	P;D;P;D;D;P;D	0.89917	0.796;1.0;0.943;0.967;1.0;0.5;1.0	B;D;B;P;D;B;D	0.91635	0.139;0.999;0.225;0.584;0.999;0.066;0.972	T	0.70916	-0.4742	10	0.66056	D	0.02	-25.4201	14.8855	0.70564	0.0:0.0:0.8563:0.1437	.	293;293;293;293;254;293;293	B7ZL12;B7ZL13;B7ZL14;Q96RU3-3;Q5QP69;Q96RU3-2;Q96RU3	.;.;.;.;.;.;FNBP1_HUMAN	C	293	ENSP00000413625:R293C;ENSP00000407548:R293C;ENSP00000347907:R293C	ENSP00000347907:R293C	R	-	1	0	FNBP1	131727170	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.818000	0.55678	2.655000	0.90218	0.462000	0.41574	CGC	.	.	none		0.423	FNBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054630.2		
PCDHA4	56144	hgsc.bcm.edu	37	5	140188353	140188353	+	Silent	SNP	G	G	A	rs561061447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA4_ENST00000356878.4_Silent_p.E527E|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.E527E	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	527	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(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)			ACCACGAGGAGCTAGAGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17480	0.0		0.0755	False		,,,				2504	0.0082				p.E527E		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1581A						PASS	.						71.0	76.0	74.0					5																	140188353		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGGAGCTAGAG	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.1581G>A	5.37:g.140188353G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	65	12	0.184615	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
GPAA1	8733	hgsc.bcm.edu	37	8	145138063	145138063	+	Silent	SNP	G	G	A	rs138412600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145138063G>A	ENST00000355091.4	+	2	232	c.111G>A	c.(109-111)ttG>ttA	p.L37L	GPAA1_ENST00000361036.6_Intron	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	37					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein complex assembly (GO:0006461)|protein retention in ER lumen (GO:0006621)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	tubulin binding (GO:0015631)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(2)	19	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-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;3.38e-41)|Epithelial(56;6.02e-40)|all cancers(56;2.11e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCTGGTTCTTGGCGCTGGTTT	0.677													G|||	22	0.00439297	0.0008	0.0014	5008	,	,		12607	0.0		0.0189	False		,,,				2504	0.001				p.L37L		Atlas-SNP	.											.	GPAA1	40	.	0			c.G111A						PASS	.	G		16,4062		0,16,2023	24.0	29.0	27.0		111	4.0	1.0	8	dbSNP_134	27	153,8217		3,147,4035	no	coding-synonymous	GPAA1	NM_003801.3		3,163,6058	AA,AG,GG		1.828,0.3923,1.3576		37/622	145138063	169,12279	2039	4185	6224	SO:0001819	synonymous_variant	8733	exon2			GTTCTTGGCGCTG	AB006969	CCDS43776.1	8q24.3	2012-12-10	2012-12-10		ENSG00000197858	ENSG00000197858			4446	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	603048	"""anchor attachment protein 1 (Gaa1p, yeast) homolog"", ""GPAA1P anchor attachment protein 1 homolog (yeast)"", ""glycosylphosphatidylinositol anchor attachment protein 1 homolog (yeast)"""			9828142	Standard	NM_003801		Approved	GAA1, hGAA1	uc003zax.3	O43292	OTTHUMG00000165438	ENST00000355091.4:c.111G>A	8.37:g.145138063G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	225	76	0.337778	NM_003801	Q9NSS0|Q9UQ31	Silent	SNP	ENST00000355091.4	37	CCDS43776.1																																																																																			G|0.993;A|0.007	0.007	strong		0.677	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801	
SYNJ2	8871	hgsc.bcm.edu	37	6	158516882	158516882	+	Missense_Mutation	SNP	C	C	T	rs137935231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:158516882C>T	ENST00000355585.4	+	27	4052	c.3977C>T	c.(3976-3978)cCg>cTg	p.P1326L	SYNJ2_ENST00000367112.1_Missense_Mutation_p.P411L|SYNJ2_ENST00000367122.2_Missense_Mutation_p.P1281L	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1326	Pro-rich.				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)		CTGGAGGCGCCGCCTCTTGTG	0.657																																					p.P1326L		Atlas-SNP	.											.	SYNJ2	111	.	0			c.C3977T						PASS	.	C	LEU/PRO,LEU/PRO	5,4401	9.9+/-24.2	0,5,2198	42.0	50.0	48.0		3266,3977	2.8	0.0	6	dbSNP_134	48	23,8577	16.6+/-54.9	1,21,4278	yes	missense,missense	SYNJ2	NM_001178088.1,NM_003898.3	98,98	1,26,6476	TT,TC,CC		0.2674,0.1135,0.2153	benign,benign	1089/1260,1326/1497	158516882	28,12978	2203	4300	6503	SO:0001583	missense	8871	exon27			AGGCGCCGCCTCT	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.3977C>T	6.37:g.158516882C>T	ENSP00000347792:p.Pro1326Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.185571	0.38609	0.001135	0.002674	ENSG00000078269	ENST00000367122;ENST00000355585;ENST00000367112	D;D;T	0.93133	-3.17;-3.16;0.83	5.57	2.76	0.32466	.	0.687143	0.13870	N	0.357073	T	0.79516	0.4459	L	0.55481	1.735	0.09310	N	1	B;P	0.48998	0.066;0.918	B;B	0.35510	0.01;0.204	T	0.67898	-0.5551	10	0.25106	T	0.35	.	9.5075	0.39056	0.0:0.7068:0.0:0.2932	.	721;1326	B4DLC4;O15056	.;SYNJ2_HUMAN	L	1281;1326;411	ENSP00000356089:P1281L;ENSP00000347792:P1326L;ENSP00000356079:P411L	ENSP00000347792:P1326L	P	+	2	0	SYNJ2	158436870	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.511000	0.22739	-1.335000	0.02241	-2.210000	0.00300	CCG	C|0.997;T|0.003	0.003	strong		0.657	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2		
COBLL1	22837	hgsc.bcm.edu	37	2	165551184	165551184	+	Silent	SNP	C	C	T	rs76695941	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:165551184C>T	ENST00000392717.2	-	13	2950	c.2946G>A	c.(2944-2946)agG>agA	p.R982R	COBLL1_ENST00000194871.6_Silent_p.R1011R|COBLL1_ENST00000375458.2_Silent_p.R906R|COBLL1_ENST00000342193.4_Silent_p.R944R|COBLL1_ENST00000409184.3_Silent_p.R944R			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	982						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						GCAGCATATCCCTTTCTGCCT	0.468													C|||	47	0.00938498	0.0008	0.0043	5008	,	,		18205	0.0		0.0308	False		,,,				2504	0.0123				p.R944R		Atlas-SNP	.											COBLL1,caecum,carcinoma,-1,1	COBLL1	122	1	0			c.G2832A						scavenged	.	C		32,4374	39.2+/-71.8	1,30,2172	51.0	51.0	51.0		2832	1.8	0.0	2	dbSNP_132	51	382,8218	124.1+/-182.9	8,366,3926	no	coding-synonymous	COBLL1	NM_014900.3		9,396,6098	TT,TC,CC		4.4419,0.7263,3.1831		944/1167	165551184	414,12592	2203	4300	6503	SO:0001819	synonymous_variant	22837	exon12			CATATCCCTTTCT	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.2946G>A	2.37:g.165551184C>T		Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Silent	SNP	ENST00000392717.2	37																																																																																				C|0.970;T|0.030	0.030	strong		0.468	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
MUC4	4585	hgsc.bcm.edu	37	3	195513521	195513521	+	Missense_Mutation	SNP	C	C	G	rs111334497	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195513521C>G	ENST00000463781.3	-	2	5389	c.4930G>C	c.(4930-4932)Ggt>Cgt	p.G1644R	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G1644R	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)		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)		GTGGCGTGACCTGTGGATAAT	0.577																																					p.G1644R		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,1	MUC4	1505	1	2	Deletion - In frame(2)	stomach(2)	c.G4930C						scavenged	.						31.0	38.0	36.0					3																	195513521		690	1580	2270	SO:0001583	missense	4585	exon2			CGTGACCTGTGGA	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.4930G>C	3.37:g.195513521C>G	ENSP00000417498:p.Gly1644Arg	Somatic	833	5	0.0060024		WXS	Illumina HiSeq	Phase_I	1101	21	0.0190736	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	.	.	.	.	.	.	.	.	.	.	-	4.040	0.005027	0.07866	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.5	0.423	-0.846	0.10734	.	.	.	.	.	T	0.26955	0.0660	N	0.19112	0.55	0.09310	N	1	D	0.59357	0.985	P	0.58013	0.831	T	0.14172	-1.0482	8	.	.	.	.	4.1233	0.10116	0.651:0.3489:1.0E-4:0.0	.	1644	E7ESK3	.	R	1644	ENSP00000417498:G1644R;ENSP00000420243:G1644R	.	G	-	1	0	MUC4	196997916	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-0.948000	0.03897	-0.784000	0.04528	0.089000	0.15464	GGT	C|0.995;G|0.005	0.005	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RRM1	6240	hgsc.bcm.edu	37	11	4159457	4159457	+	Silent	SNP	A	A	G	rs9937	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4159457A>G	ENST00000300738.5	+	19	2427	c.2223A>G	c.(2221-2223)acA>acG	p.T741T	RRM1_ENST00000534285.1_Silent_p.T519T|RRM1_ENST00000423050.2_Silent_p.T644T|RRM1_ENST00000537197.1_Silent_p.T403T|RRM1-AS1_ENST00000529323.1_RNA	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	98	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	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	
VEZT	55591	hgsc.bcm.edu	37	12	95660182	95660182	+	Missense_Mutation	SNP	A	A	G	rs17855933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:95660182A>G	ENST00000436874.1	+	5	589	c.484A>G	c.(484-486)Act>Gct	p.T162A	VEZT_ENST00000356859.4_3'UTR|VEZT_ENST00000261219.6_Missense_Mutation_p.T114A	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	162			T -> A (in dbSNP:rs17855933).		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						TATGCTTCCCACTTGGTGGAT	0.418													A|||	362	0.0722843	0.084	0.0893	5008	,	,		16651	0.001		0.1074	False		,,,				2504	0.0818				p.T162A		Atlas-SNP	.											.	VEZT	106	.	0			c.A484G						PASS	.	A	ALA/THR	283,3519		10,263,1628	295.0	282.0	286.0		484	2.9	1.0	12	dbSNP_123	286	860,7408		46,768,3320	yes	missense	VEZT	NM_017599.3	58	56,1031,4948	GG,GA,AA		10.4015,7.4435,9.4698	possibly-damaging	162/780	95660182	1143,10927	1901	4134	6035	SO:0001583	missense	55591	exon5			CTTCCCACTTGGT	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.484A>G	12.37:g.95660182A>G	ENSP00000410083:p.Thr162Ala	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	195	139	0.712821	NM_017599	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Missense_Mutation	SNP	ENST00000436874.1	37	CCDS44954.1	153	0.07005494505494506	34	0.06910569105691057	35	0.09668508287292818	1	0.0017482517482517483	83	0.10949868073878628	A	3.498	-0.102452	0.06967	0.074435	0.104015	ENSG00000028203	ENST00000436874;ENST00000549002;ENST00000261219;ENST00000551472;ENST00000546445;ENST00000397792;ENST00000397796	T;T;T;T;T;T	0.45668	0.99;0.94;0.99;0.89;0.94;0.99	5.39	2.88	0.33553	.	0.295485	0.37012	N	0.002285	T	0.00356	0.0011	N	0.12182	0.205	0.35718	P	0.18310700000000002	B;B;B;B	0.09022	0.002;0.001;0.0;0.0	B;B;B;B	0.09377	0.003;0.004;0.003;0.003	T	0.05209	-1.0899	9	0.23891	T	0.37	-14.0809	4.0882	0.09957	0.497:0.0:0.1039:0.3991	rs17855933;rs17855933	162;162;114;114	C9J154;Q9HBM0;F8W8C2;F2Z3A6	.;VEZA_HUMAN;.;.	A	162;132;114;181;84;114;162	ENSP00000410083:T162A;ENSP00000449591:T132A;ENSP00000261219:T114A;ENSP00000449701:T181A;ENSP00000447151:T84A;ENSP00000380894:T114A	ENSP00000261219:T114A	T	+	1	0	VEZT	94184313	0.747000	0.28283	0.991000	0.47740	0.024000	0.10985	1.007000	0.29860	2.023000	0.59567	0.528000	0.53228	ACT	A|0.925;G|0.075	0.075	strong		0.418	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599	
CASP9	842	hgsc.bcm.edu	37	1	15844615	15844615	+	Silent	SNP	A	A	G	rs1132312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15844615A>G	ENST00000333868.5	-	2	502	c.408T>C	c.(406-408)ttT>ttC	p.F136F	CASP9_ENST00000469637.1_5'Flank|CASP9_ENST00000375890.4_Silent_p.F53F|CASP9_ENST00000348549.5_Silent_p.F136F|CASP9_ENST00000546424.1_Silent_p.F136F	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	136			F -> L (in dbSNP:rs1820204).		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|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)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)	p.F136F(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		CGACATCACCAAATCCTCCAG	0.507													G|||	2929	0.584864	0.739	0.4986	5008	,	,		18823	0.6538		0.5149	False		,,,				2504	0.4387				p.F136F		Atlas-SNP	.											CASP9,NS,carcinoma,0,1	CASP9	40	1	1	Substitution - coding silent(1)	stomach(1)	c.T408C						PASS	.	G	,	3099,1307	441.8+/-346.5	1100,899,204	113.0	101.0	105.0		408,159	-3.0	0.0	1	dbSNP_92	105	4542,4058	559.4+/-387.4	1215,2112,973	no	coding-synonymous,coding-synonymous	CASP9	NM_001229.3,NM_032996.2	,	2315,3011,1177	GG,GA,AA		47.186,29.6641,41.2502	,	136/417,53/334	15844615	7641,5365	2203	4300	6503	SO:0001819	synonymous_variant	842	exon2			ATCACCAAATCCT	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.408T>C	1.37:g.15844615A>G		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	92	88	0.956522	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Silent	SNP	ENST00000333868.5	37	CCDS158.1																																																																																			G|0.589;A|0.411	0.589	strong		0.507	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
EPS15	2060	hgsc.bcm.edu	37	1	51912760	51912760	+	Silent	SNP	T	T	G	rs34704431	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:51912760T>G	ENST00000371733.3	-	10	765	c.669A>C	c.(667-669)gcA>gcC	p.A223A	EPS15_ENST00000371730.2_Silent_p.A223A	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	223	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.|Interaction with DAB2. {ECO:0000250}.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(1)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						TAGCTTTTTCTGCAGGGGATA	0.363			T	MLL	ALL								T|||	235	0.0469249	0.0983	0.0274	5008	,	,		17178	0.0109		0.0328	False		,,,				2504	0.0429				p.A223A		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	EPS15,NS,carcinoma,-2,1	EPS15	72	1	1	Whole gene deletion(1)	central_nervous_system(1)	c.A669C						PASS	.	T		349,4057	178.3+/-207.1	14,321,1868	94.0	97.0	96.0		669	2.1	1.0	1	dbSNP_126	96	273,8327	103.1+/-164.3	4,265,4031	no	coding-synonymous	EPS15	NM_001981.2		18,586,5899	GG,GT,TT		3.1744,7.921,4.7824		223/897	51912760	622,12384	2203	4300	6503	SO:0001819	synonymous_variant	2060	exon10			TTTTTCTGCAGGG	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"""EF-hand domain containing"""	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.669A>C	1.37:g.51912760T>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	35	26	0.742857	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			T|0.955;G|0.045	0.045	strong		0.363	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
ANXA11	311	hgsc.bcm.edu	37	10	81917486	81917486	+	Missense_Mutation	SNP	T	T	C	rs1802932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:81917486T>C	ENST00000438331.1	-	16	1851	c.1369A>G	c.(1369-1371)Atc>Gtc	p.I457V	ANXA11_ENST00000535999.1_Missense_Mutation_p.I457V|ANXA11_ENST00000360615.4_Missense_Mutation_p.I457V|ANXA11_ENST00000372231.3_Missense_Mutation_p.I457V|ANXA11_ENST00000422982.3_Missense_Mutation_p.I457V|ANXA11_ENST00000265447.4_Missense_Mutation_p.I457V|ANXA11_ENST00000537102.1_Missense_Mutation_p.I424V	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	457			I -> V (in dbSNP:rs1802932).		cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			GACACCATGATGCGAATCAGG	0.597													t|||	17	0.00339457	0.0	0.0029	5008	,	,		20944	0.0		0.0139	False		,,,				2504	0.001				p.I457V		Atlas-SNP	.											.	ANXA11	32	.	0			c.A1369G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	13,4393	20.2+/-43.8	0,13,2190	127.0	110.0	116.0		1369,1369,1369	5.2	1.0	10	dbSNP_89	116	105,8495	57.5+/-118.9	1,103,4196	yes	missense,missense,missense	ANXA11	NM_001157.2,NM_145868.1,NM_145869.1	29,29,29	1,116,6386	CC,CT,TT		1.2209,0.2951,0.9073	benign,benign,benign	457/506,457/506,457/506	81917486	118,12888	2203	4300	6503	SO:0001583	missense	311	exon15			CCATGATGCGAAT	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"""Annexins"""	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.1369A>G	10.37:g.81917486T>C	ENSP00000398610:p.Ile457Val	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_145868	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	37	CCDS7364.1	15	0.006868131868131868	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	13.99	2.402389	0.42613	0.002951	0.012209	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000424188;ENST00000537102;ENST00000372219	T;T;T;T;T;T;T	0.08984	3.03;3.03;3.03;3.03;3.03;3.03;3.03	5.17	5.17	0.71159	Annexin repeat, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.03739	0.0106	L	0.28192	0.835	0.50313	D	0.999865	B;B;B	0.33345	0.284;0.409;0.409	B;B;B	0.38225	0.103;0.268;0.268	T	0.45614	-0.9249	10	0.27082	T	0.32	.	13.2804	0.60210	0.0:0.0:0.0:1.0	rs1802932;rs1802932	557;457;457	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	V	457;457;457;457;457;457;457;364;424;104	ENSP00000361305:I457V;ENSP00000404412:I457V;ENSP00000398610:I457V;ENSP00000353827:I457V;ENSP00000265447:I457V;ENSP00000441748:I457V;ENSP00000441400:I424V	ENSP00000265447:I457V	I	-	1	0	ANXA11	81907466	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.665000	0.61547	2.082000	0.62665	0.460000	0.39030	ATC	T|0.992;C|0.008	0.008	strong		0.597	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869	
C16orf96	342346	hgsc.bcm.edu	37	16	4625274	4625274	+	Missense_Mutation	SNP	A	A	G	rs1256768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4625274A>G	ENST00000444310.4	+	5	793	c.793A>G	c.(793-795)Atc>Gtc	p.I265V		NM_001145011.1	NP_001138483.1			chromosome 16 open reading frame 96											NS(1)|breast(1)|endometrium(6)|kidney(1)|skin(3)	12						TACTCGTGCCATCCAGGTCTC	0.592													A|||	726	0.144968	0.087	0.0951	5008	,	,		17680	0.131		0.163	False		,,,				2504	0.2546				p.I265V		Atlas-SNP	.											.	C16orf96	28	.	0			c.A793G						PASS	.	A	VAL/ILE	149,1235		6,137,549	47.0	46.0	46.0		793	-6.7	0.0	16	dbSNP_87	46	519,2663		44,431,1116	yes	missense	C16orf96	NM_001145011.1	29	50,568,1665	GG,GA,AA		16.3105,10.7659,14.6299	benign	265/1142	4625274	668,3898	692	1591	2283	SO:0001583	missense	342346	exon5			CGTGCCATCCAGG		CCDS53986.1	16p13.3	2012-10-10			ENSG00000205832	ENSG00000205832			40031	protein-coding gene	gene with protein product							Standard	NM_001145011		Approved		uc010uxn.2	A6NNT2	OTTHUMG00000176519	ENST00000444310.4:c.793A>G	16.37:g.4625274A>G	ENSP00000415027:p.Ile265Val	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_001145011		Missense_Mutation	SNP	ENST00000444310.4	37	CCDS53986.1	286	0.13095238095238096	56	0.11382113821138211	43	0.11878453038674033	62	0.10839160839160839	125	0.16490765171503957	A	3.473	-0.107540	0.06924	0.107659	0.163105	ENSG00000205832	ENST00000444310	.	.	.	3.33	-6.66	0.01789	.	.	.	.	.	T	0.00073	0.0002	N	0.19112	0.55	0.80722	P	0.0	B	0.12013	0.005	B	0.08055	0.003	T	0.19321	-1.0309	7	0.15952	T	0.53	.	7.8742	0.29584	0.1785:0.5159:0.3056:0.0	rs1256768;rs1256768	265	A6NNT2	CP096_HUMAN	V	265	.	ENSP00000415027:I265V	I	+	1	0	C16orf96	4565275	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-3.668000	0.00398	-2.190000	0.00757	0.379000	0.24179	ATC	A|0.856;G|0.144	0.144	strong		0.592	C16orf96-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432384.1	NM_001145011	
CCR2	729230	hgsc.bcm.edu	37	3	46399208	46399208	+	Missense_Mutation	SNP	G	G	A	rs1799864	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46399208G>A	ENST00000400888.2	+	1	229	c.190G>A	c.(190-192)Gtc>Atc	p.V64I	CCR2_ENST00000292301.4_Missense_Mutation_p.V64I|CCR2_ENST00000465202.1_Intron|CCR2_ENST00000445132.2_Missense_Mutation_p.V64I			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	64			V -> I (confers relative resistance to infection by HIV-1; delay in disease progression in African Americans but not in Caucasians; dbSNP:rs1799864). {ECO:0000269|PubMed:9252328, ECO:0000269|PubMed:9662369, ECO:0000269|Ref.4}.		blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		CATGCTGGTCGTCCTCATCTT	0.458													G|||	770	0.153754	0.1702	0.2118	5008	,	,		20792	0.2133		0.0865	False		,,,				2504	0.0982				p.V64I		Atlas-SNP	.											CCR2_ENST00000445132,colon,carcinoma,-2,2	CCR2	103	2	0			c.G190A	GRCh37	CM970245	CCR2	M	rs1799864	PASS	.	G	ILE/VAL,ILE/VAL	495,2641		33,429,1106	194.0	175.0	181.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	190,190	1.6	0.6	3	dbSNP_89	181	659,6505		35,589,2958	yes	missense,missense	CCR2	NM_001123041.2,NM_001123396.1	29,29	68,1018,4064	AA,AG,GG		9.1988,15.7844,11.2039	benign,benign	64/375,64/361	46399208	1154,9146	1568	3582	5150	SO:0001583	missense	729230	exon2			CTGGTCGTCCTCA		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.190G>A	3.37:g.46399208G>A	ENSP00000383681:p.Val64Ile	Somatic	354	1	0.00282486		WXS	Illumina HiSeq	Phase_I	310	135	0.435484	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	37	CCDS43078.1	368	0.1684981684981685	100	0.2032520325203252	70	0.19337016574585636	125	0.21853146853146854	73	0.09630606860158311	G	11.01	1.512371	0.27036	0.157844	0.091988	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000421659;ENST00000400888	T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42	4.41	1.62	0.23740	GPCR, rhodopsin-like superfamily (1);	0.439250	0.20583	N	0.089490	T	0.00039	0.0001	L	0.27975	0.815	0.58432	P	1.0000000000287557E-6	B;B	0.27679	0.079;0.185	B;B	0.31390	0.129;0.127	T	0.04900	-1.0919	9	0.34782	T	0.22	.	4.6189	0.12440	0.2407:0.0:0.6024:0.1569	rs1799864;rs17141036;rs61751656	64;64	P41597;Q4VBL2	CCR2_HUMAN;.	I	64	ENSP00000399285:V64I;ENSP00000292301:V64I;ENSP00000396736:V64I;ENSP00000383681:V64I	ENSP00000292301:V64I	V	+	1	0	CCR2	46374212	0.867000	0.29959	0.597000	0.28824	0.891000	0.51852	1.270000	0.33086	0.543000	0.28864	0.650000	0.86243	GTC	G|0.844;A|0.156	0.156	strong		0.458	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647	
PTPRO	5800	hgsc.bcm.edu	37	12	15669737	15669737	+	Silent	SNP	T	T	C	rs1050646	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:15669737T>C	ENST00000281171.4	+	9	1956	c.1626T>C	c.(1624-1626)ggT>ggC	p.G542G	PTPRO_ENST00000348962.2_Silent_p.G542G|PTPRO_ENST00000543886.1_Silent_p.G542G	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	542	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				ATCCTTTGGGTCCTACGGCCG	0.428													T|||	599	0.119609	0.0605	0.134	5008	,	,		15788	0.0843		0.1869	False		,,,				2504	0.1564				p.G542G		Atlas-SNP	.											.	PTPRO	148	.	0			c.T1626C						PASS	.	T	,	317,4089	169.4+/-200.1	11,295,1897	137.0	127.0	130.0		1626,1626	-5.4	0.7	12	dbSNP_86	130	1560,7040	292.6+/-300.9	141,1278,2881	no	coding-synonymous,coding-synonymous	PTPRO	NM_002848.3,NM_030667.2	,	152,1573,4778	CC,CT,TT		18.1395,7.1947,14.4318	,	542/1189,542/1217	15669737	1877,11129	2203	4300	6503	SO:0001819	synonymous_variant	5800	exon9			TTTGGGTCCTACG	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9678	protein-coding gene	gene with protein product	"""osteoclastic transmembrane protein-tyrosine phosphatase"""	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.1626T>C	12.37:g.15669737T>C		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Silent	SNP	ENST00000281171.4	37	CCDS8675.1																																																																																			T|0.853;C|0.147	0.147	strong		0.428	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		
NUP205	23165	hgsc.bcm.edu	37	7	135329690	135329690	+	Silent	SNP	T	T	C	rs12540688	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:135329690T>C	ENST00000285968.6	+	40	5633	c.5607T>C	c.(5605-5607)gcT>gcC	p.A1869A		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1869					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)|nuclear pore complex assembly (GO:0051292)|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)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.A1869A(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TCTCCACTGCTCAGAAATATG	0.388											OREG0018343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1258	0.251198	0.2428	0.196	5008	,	,		18544	0.253		0.1968	False		,,,				2504	0.3558				p.A1869A		Atlas-SNP	.											NUP205,NS,carcinoma,0,1	NUP205	198	1	1	Substitution - coding silent(1)	stomach(1)	c.T5607C						PASS	.	C		1068,3338		139,790,1274	159.0	144.0	149.0		5607	1.2	0.5	7	dbSNP_120	149	1612,6988		153,1306,2841	no	coding-synonymous	NUP205	NM_015135.2		292,2096,4115	CC,CT,TT		18.7442,24.2397,20.6059		1869/2013	135329690	2680,10326	2203	4300	6503	SO:0001819	synonymous_variant	23165	exon40			CACTGCTCAGAAA	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.5607T>C	7.37:g.135329690T>C		Somatic	174	0	0	1617	WXS	Illumina HiSeq	Phase_I	127	91	0.716535	NM_015135	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	CCDS34759.1																																																																																			T|0.778;C|0.222	0.222	strong		0.388	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
KIAA1456	57604	hgsc.bcm.edu	37	8	12879198	12879198	+	Missense_Mutation	SNP	A	A	T	rs34995506	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:12879198A>T	ENST00000524591.2	+	5	1499	c.1010A>T	c.(1009-1011)cAt>cTt	p.H337L	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	337			H -> L (in dbSNP:rs34995506).				methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						AATGGAGACCATCAAGGGGAA	0.433													A|||	978	0.195288	0.2436	0.1585	5008	,	,		19756	0.1885		0.1183	False		,,,				2504	0.2423				p.H337L		Atlas-SNP	.											.	KIAA1456	20	.	0			c.A1010T						PASS	.	A	LEU/HIS,LEU/HIS	829,2877		97,635,1121	71.0	70.0	70.0		632,1010	-2.3	0.0	8	dbSNP_126	70	1122,7074		80,962,3056	yes	missense,missense	KIAA1456	NM_001099677.1,NM_020844.2	99,99	177,1597,4177	TT,TA,AA		13.6896,22.3691,16.3922	benign,benign	211/329,337/455	12879198	1951,9951	1853	4098	5951	SO:0001583	missense	57604	exon5			GAGACCATCAAGG	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.1010A>T	8.37:g.12879198A>T	ENSP00000432695:p.His337Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_020844	Q96AW6	Missense_Mutation	SNP	ENST00000524591.2	37	CCDS47808.1	378	0.17307692307692307	113	0.22967479674796748	64	0.17679558011049723	112	0.1958041958041958	89	0.11741424802110818	A	4.289	0.052782	0.08291	0.223691	0.136896	ENSG00000250305	ENST00000524591;ENST00000529978	T	0.09445	2.98	4.38	-2.34	0.06704	.	2.018840	0.01919	N	0.040416	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.26400	0.148	B	0.17433	0.018	T	0.39881	-0.9592	9	0.22109	T	0.4	1.2381	0.3267	0.00312	0.3156:0.2675:0.1572:0.2598	rs34995506;rs62486881	337	Q9P272	K1456_HUMAN	L	337;250	ENSP00000432695:H337L	ENSP00000432695:H337L	H	+	2	0	AC135352.2	12923569	0.000000	0.05858	0.001000	0.08648	0.143000	0.21401	0.072000	0.14617	-0.507000	0.06549	-0.496000	0.04628	CAT	A|0.832;T|0.168	0.168	strong		0.433	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677	
OR51B6	390058	hgsc.bcm.edu	37	11	5373309	5373309	+	Missense_Mutation	SNP	C	C	A	rs386750142|rs115333544	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5373309C>A	ENST00000380219.1	+	1	572	c.572C>A	c.(571-573)aCc>aAc	p.T191N	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	191					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(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCTGACATCACCTTCAACCGT	0.433													C|||	417	0.0832668	0.1021	0.0793	5008	,	,		23860	0.0675		0.0497	False		,,,				2504	0.1115				p.T191N		Atlas-SNP	.											.	OR51B6	53	.	0			c.C572A						PASS	.						223.0	196.0	205.0					11																	5373309		2201	4297	6498	SO:0001583	missense	390058	exon1			ACATCACCTTCAA		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.572C>A	11.37:g.5373309C>A	ENSP00000369568:p.Thr191Asn	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	215	93	0.432558	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	150	0.06868131868131869	58	0.11788617886178862	32	0.08839779005524862	26	0.045454545454545456	34	0.044854881266490766	C	14.26	2.481377	0.44147	.	.	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00091	8.74	5.15	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.496162	0.17579	N	0.169198	T	0.00012	0.0000	M	0.78049	2.395	0.36857	P	0.111792	D	0.55800	0.973	D	0.64687	0.928	T	0.57124	-0.7865	9	0.62326	D	0.03	.	8.3851	0.32494	0.1543:0.7632:0.0:0.0824	.	191	Q9H340	O51B6_HUMAN	N	190;191	ENSP00000369568:T191N	ENSP00000369568:T191N	T	+	2	0	OR51B6	5329885	0.000000	0.05858	0.998000	0.56505	0.676000	0.39594	-0.838000	0.04372	1.399000	0.46721	0.557000	0.71058	ACC	C|0.937;A|0.063	0.063	strong		0.433	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
REXO1	57455	hgsc.bcm.edu	37	19	1827927	1827927	+	Silent	SNP	T	T	G	rs144940979	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1827927T>G	ENST00000170168.4	-	2	955	c.861A>C	c.(859-861)tcA>tcC	p.S287S	REXO1_ENST00000587524.1_5'UTR	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	287						nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	16		Ovarian(11;1.78e-06)|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)		CTTCTGAGTCTGAGAACCTTG	0.672													.|||	3	0.000599042	0.0	0.0	5008	,	,		13621	0.0		0.003	False		,,,				2504	0.0				p.S287S		Atlas-SNP	.											.	REXO1	55	.	0			c.A861C						PASS	.	T		0,4404		0,0,2202	41.0	44.0	43.0		861	-8.3	0.1	19	dbSNP_134	43	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	REXO1	NM_020695.3		0,14,6488	GG,GT,TT		0.1628,0.0,0.1077		287/1222	1827927	14,12990	2202	4300	6502	SO:0001819	synonymous_variant	57455	exon2			TGAGTCTGAGAAC	AB032964	CCDS32866.1	19p13.3	2014-05-28	2005-08-22	2005-08-22	ENSG00000079313	ENSG00000079313			24616	protein-coding gene	gene with protein product	"""elongin A binding protein 1"""	609614	"""transcription elongation factor B polypeptide 3 binding protein 1"""	TCEB3BP1		10574461	Standard	NM_020695		Approved	EloA-BP1, KIAA1138	uc002lua.4	Q8N1G1	OTTHUMG00000179991	ENST00000170168.4:c.861A>C	19.37:g.1827927T>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	138	71	0.514493	NM_020695	Q9ULT2	Silent	SNP	ENST00000170168.4	37	CCDS32866.1																																																																																			T|0.999;G|0.001	0.001	strong		0.672	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695	
TYROBP	7305	hgsc.bcm.edu	37	19	36398454	36398454	+	Silent	SNP	G	G	C	rs111477177	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36398454G>C	ENST00000262629.4	-	3	189	c.123C>G	c.(121-123)ggC>ggG	p.G41G	TYROBP_ENST00000544690.2_Silent_p.G30G|TYROBP_ENST00000424586.3_Silent_p.G30G|TYROBP_ENST00000585901.2_Silent_p.G41G|TYROBP_ENST00000589517.1_Silent_p.G41G	NM_003332.3|NM_198125.2	NP_003323.1|NP_937758.1	O43914	TYOBP_HUMAN	TYRO protein tyrosine kinase binding protein	41					axon guidance (GO:0007411)|cellular defense response (GO:0006968)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|regulation of immune response (GO:0050776)|regulation of osteoclast development (GO:2001204)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(4)|skin(1)	8	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)			CTGCCAGCACGCCCGGGCTCA	0.672													G|||	56	0.0111821	0.0008	0.0202	5008	,	,		16218	0.0		0.0348	False		,,,				2504	0.0061				p.G41G		Atlas-SNP	.											TYROBP,NS,carcinoma,-2,1	TYROBP	15	1	0			c.C123G						scavenged	.	G	,,,	36,4370	36.8+/-68.6	0,36,2167	36.0	38.0	37.0		90,90,123,123	-10.3	0.0	19	dbSNP_132	37	366,8234	115.9+/-175.7	8,350,3942	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TYROBP	NM_001173514.1,NM_001173515.1,NM_003332.3,NM_198125.2	,,,	8,386,6109	CC,CG,GG		4.2558,0.8171,3.0909	,,,	30/103,30/102,41/114,41/113	36398454	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	7305	exon3			CAGCACGCCCGGG	AF019563	CCDS12482.1, CCDS46058.1, CCDS54255.1, CCDS59378.1	19q13.1	2014-09-17				ENSG00000011600			12449	protein-coding gene	gene with protein product	"""killer activating receptor associated protein"", ""DNAX-activation protein 12"""	604142		PLOSL		9490415, 10888890	Standard	NM_003332		Approved	DAP12, PLO-SL, KARAP	uc002ocm.3	O43914		ENST00000262629.4:c.123C>G	19.37:g.36398454G>C		Somatic	133	2	0.0150376		WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_198125	A8K2X0|F5H389|Q6FGA5|Q9UMT3	Silent	SNP	ENST00000262629.4	37	CCDS12482.1																																																																																			A|0.000;C|0.024;G|0.976	0.024	strong		0.672	TYROBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457397.1		
USP29	57663	hgsc.bcm.edu	37	19	57642782	57642782	+	Nonsense_Mutation	SNP	C	C	A	rs9973206	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57642782C>A	ENST00000254181.4	+	4	3193	c.2739C>A	c.(2737-2739)taC>taA	p.Y913*	U3_ENST00000516874.1_RNA|USP29_ENST00000598197.1_Nonsense_Mutation_p.Y913*	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	913					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)		AGGGGGAATACGAAGGTGACT	0.478													A|||	4768	0.952077	0.9932	0.9265	5008	,	,		18674	1.0		0.837	False		,,,				2504	0.9836				p.Y913X		Atlas-SNP	.											.	USP29	186	.	0			c.C2739A						PASS	.	A	stop/TYR	4292,112		2092,108,2	67.0	76.0	73.0		2739	-0.6	0.0	19	dbSNP_119	73	7190,1410		3009,1172,119	yes	stop-gained	USP29	NM_020903.2		5101,1280,121	AA,AC,CC		16.3953,2.5431,11.7041		913/923	57642782	11482,1522	2202	4300	6502	SO:0001587	stop_gained	57663	exon4			GGAATACGAAGGT		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.2739C>A	19.37:g.57642782C>A	ENSP00000254181:p.Tyr913*	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_020903		Nonsense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	2038	0.9331501831501832	489	0.9939024390243902	335	0.925414364640884	572	1.0	642	0.8469656992084432	A	38	7.164934	0.98107	0.974569	0.836047	ENSG00000131864	ENST00000254181	.	.	.	2.3	-0.625	0.11548	.	.	.	.	.	.	.	.	.	.	.	0.44570	P	0.0024619999999999642	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	0.1149	0.00059	0.31:0.2293:0.2353:0.2255	rs9973206;rs52797075;rs56429327;rs58316037;rs9973206	.	.	.	X	913	.	ENSP00000254181:Y913X	Y	+	3	2	USP29	62334594	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.277000	0.18734	-0.616000	0.05671	-1.534000	0.00916	TAC	C|0.100;A|0.900	0.900	strong		0.478	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1		
RSPH1	89765	hgsc.bcm.edu	37	21	43913112	43913112	+	Silent	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43913112G>A	ENST00000291536.3	-	2	299	c.132C>T	c.(130-132)taC>taT	p.Y44Y	RSPH1_ENST00000398352.3_Intron	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	44					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						AGCTCCCTTCGTAGGTGTCCC	0.498																																					p.Y44Y	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											RSPH1,NS,carcinoma,0,1	RSPH1	36	1	0			c.C132T						PASS	.						262.0	232.0	242.0					21																	43913112		2203	4300	6503	SO:0001819	synonymous_variant	89765	exon2			CCCTTCGTAGGTG	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.132C>T	21.37:g.43913112G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	251	62	0.247012	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Silent	SNP	ENST00000291536.3	37	CCDS13688.1																																																																																			.	.	none		0.498	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693155	187693155	+	Missense_Mutation	SNP	A	A	T	rs10195758	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:187693155A>T	ENST00000295131.2	-	9	1497	c.1458T>A	c.(1456-1458)gaT>gaA	p.D486E		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	486				D -> E (in Ref. 4; AAH31094). {ECO:0000305}.	apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			TAATTTTATAATCATAGGTTA	0.313													T|||	872	0.174121	0.4213	0.1066	5008	,	,		18538	0.0208		0.1103	False		,,,				2504	0.1115				p.D486E		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.T1458A						PASS	.	T	GLU/ASP	1744,2660	627.9+/-395.0	343,1058,801	40.0	45.0	43.0		1458	1.6	0.7	2	dbSNP_119	43	968,7632	763.8+/-407.6	44,880,3376	yes	missense	ZSWIM2	NM_182521.2	45	387,1938,4177	TT,TA,AA		11.2558,39.6004,20.8551	benign	486/634	187693155	2712,10292	2202	4300	6502	SO:0001583	missense	151112	exon9			TTTATAATCATAG	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1458T>A	2.37:g.187693155A>T	ENSP00000295131:p.Asp486Glu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	CCDS33348.1	326	0.14926739926739926	193	0.39227642276422764	41	0.1132596685082873	10	0.017482517482517484	82	0.10817941952506596	T	0.006	-2.092970	0.00364	0.396004	0.112558	ENSG00000163012	ENST00000295131	T	0.21932	1.98	5.6	1.56	0.23342	.	0.342270	0.25377	N	0.031119	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	0.45249	-0.9274	9	0.02654	T	1	-4.9417	3.3678	0.07210	0.3418:0.2581:0.0:0.4001	rs10195758;rs17856916;rs10195758	486	Q8NEG5	ZSWM2_HUMAN	E	486	ENSP00000295131:D486E	ENSP00000295131:D486E	D	-	3	2	ZSWIM2	187401400	0.001000	0.12720	0.711000	0.30485	0.001000	0.01503	-0.697000	0.05098	0.074000	0.16767	-0.336000	0.08194	GAT	A|0.819;T|0.181	0.181	strong		0.313	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
PKD1	5310	hgsc.bcm.edu	37	16	2166542	2166542	+	Silent	SNP	G	G	A	rs367983387	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2166542G>A	ENST00000262304.4	-	8	1918	c.1710C>T	c.(1708-1710)caC>caT	p.H570H	PKD1_ENST00000423118.1_Silent_p.H570H|RP11-304L19.2_ENST00000562027.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	570					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						CCACGGGCTCGTGCGGGGCTG	0.687													g|||	17	0.00339457	0.0	0.0014	5008	,	,		12902	0.001		0.0149	False		,,,				2504	0.0				p.H570H		Atlas-SNP	.											.	PKD1	184	.	0			c.C1710T						PASS	.	G	,	3,4305		0,3,2151	7.0	8.0	8.0		1710,1710	0.9	0.0	16		8	40,8422		0,40,4191	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	0,43,6342	AA,AG,GG		0.4727,0.0696,0.3367	,	570/4303,570/4304	2166542	43,12727	2154	4231	6385	SO:0001819	synonymous_variant	5310	exon8			GGGCTCGTGCGGG	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.1710C>T	16.37:g.2166542G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.	.	weak		0.687	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
MTHFR	4524	hgsc.bcm.edu	37	1	11855269	11855269	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11855269C>T	ENST00000376592.1	-	5	1045	c.917G>A	c.(916-918)tGc>tAc	p.C306Y	MTHFR_ENST00000376585.1_Missense_Mutation_p.C347Y|MTHFR_ENST00000376590.3_Missense_Mutation_p.C306Y|MTHFR_ENST00000376583.3_Missense_Mutation_p.C347Y			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	306					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)	AAGCTCCTGGCACAGGCTCAC	0.592																																					p.C306Y		Atlas-SNP	.											.	MTHFR	65	.	0			c.G917A						PASS	.						80.0	80.0	80.0					1																	11855269		2203	4300	6503	SO:0001583	missense	4524	exon6			TCCTGGCACAGGC	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.917G>A	1.37:g.11855269C>T	ENSP00000365777:p.Cys306Tyr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	66	10	0.151515	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600241	0.87055	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	5.09	5.09	0.68999	.	0.084158	0.85682	D	0.000000	D	0.97359	0.9136	H	0.96239	3.79	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.69479	0.964;0.963	D	0.98609	1.0662	10	0.87932	D	0	.	17.8468	0.88732	0.0:1.0:0.0:0.0	.	306;347	P42898;Q5SNW6	MTHR_HUMAN;.	Y	306;347;306;347	ENSP00000365777:C306Y;ENSP00000365767:C347Y;ENSP00000365775:C306Y;ENSP00000365770:C347Y	ENSP00000365767:C347Y	C	-	2	0	MTHFR	11777856	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	7.085000	0.76875	2.517000	0.84864	0.462000	0.41574	TGC	.	.	none		0.592	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
ZNF638	27332	hgsc.bcm.edu	37	2	71577132	71577132	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:71577132C>T	ENST00000409544.1	+	2	1678	c.1048C>T	c.(1048-1050)Cgg>Tgg	p.R350W	ZNF638_ENST00000264447.4_Missense_Mutation_p.R350W|ZNF638_ENST00000355812.3_Missense_Mutation_p.R350W|ZNF638_ENST00000410075.1_3'UTR|ZNF638_ENST00000377802.2_Missense_Mutation_p.R350W	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	350					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						CCAGCAAGAGCGGATCCCACA	0.423																																					p.R350W		Atlas-SNP	.											ZNF638,rectum,carcinoma,0,4	ZNF638	179	4	0			c.C1048T						scavenged	.						127.0	126.0	126.0					2																	71577132		2203	4300	6503	SO:0001583	missense	27332	exon2			CAAGAGCGGATCC	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.1048C>T	2.37:g.71577132C>T	ENSP00000386433:p.Arg350Trp	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	159	2	0.0125786	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.925108	0.34002	.	.	ENSG00000075292	ENST00000410075;ENST00000544512;ENST00000355812;ENST00000377802;ENST00000264447;ENST00000409544	T;T;T;T;T;T	0.78003	-0.55;-1.14;0.01;-0.54;0.99;0.99	5.88	2.78	0.32641	.	0.171583	0.48767	D	0.000161	T	0.78880	0.4353	N	0.24115	0.695	0.31602	N	0.652565	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.995;0.995;0.997;0.993;0.995	T	0.80336	-0.1425	10	0.87932	D	0	-2.9758	11.5861	0.50918	0.5869:0.4131:0.0:0.0	.	456;350;350;350;350	F5H330;Q14966-4;Q14966-3;Q14966;Q14966-2	.;.;.;ZN638_HUMAN;.	W	350;456;350;350;350;350	ENSP00000386669:R350W;ENSP00000438189:R456W;ENSP00000348066:R350W;ENSP00000367033:R350W;ENSP00000264447:R350W;ENSP00000386433:R350W	ENSP00000264447:R350W	R	+	1	2	ZNF638	71430640	0.426000	0.25506	0.642000	0.29436	0.654000	0.38779	1.015000	0.29963	0.789000	0.33779	-0.181000	0.13052	CGG	.	.	none		0.423	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
ZNF99	7652	hgsc.bcm.edu	37	19	22941071	22941071	+	Missense_Mutation	SNP	T	T	C	rs144632185	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22941071T>C	ENST00000596209.1	-	4	1730	c.1640A>G	c.(1639-1641)aAc>aGc	p.N547S	ZNF99_ENST00000397104.3_Missense_Mutation_p.N456S	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	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)	p.N456S(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TGAGGAATTGTTAAAAGCTTT	0.343													T|||	449	0.0896565	0.0681	0.0879	5008	,	,		20699	0.0933		0.0934	False		,,,				2504	0.1125				p.N547S		Atlas-SNP	.											ZNF99,NS,carcinoma,0,1	ZNF99	273	1	1	Substitution - Missense(1)	stomach(1)	c.A1640G						scavenged	.	T	SER/ASN	272,3842		9,254,1794	40.0	42.0	41.0		1367	-2.6	0.0	19	dbSNP_134	41	760,7660		38,684,3488	no	missense	ZNF99	NM_001080409.2	46	47,938,5282	CC,CT,TT		9.0261,6.6116,8.2336	benign	456/912	22941071	1032,11502	2057	4210	6267	SO:0001583	missense	7652	exon4			GAATTGTTAAAAG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1640A>G	19.37:g.22941071T>C	ENSP00000472969:p.Asn547Ser	Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	189	0.08653846153846154	35	0.07113821138211382	39	0.10773480662983426	52	0.09090909090909091	63	0.08311345646437995	-	0.001	-3.452171	0.00012	0.066116	0.090261	ENSG00000213973	ENST00000397104	T	0.38077	1.16	1.29	-2.57	0.06248	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00178	0.0005	N	0.01824	-0.7	0.80722	P	0.0	B	0.15930	0.015	B	0.17722	0.019	T	0.07597	-1.0764	8	0.02654	T	1	.	2.3696	0.04327	0.15:0.2608:0.4351:0.1541	.	456	A8MXY4	ZNF99_HUMAN	S	456	ENSP00000380293:N456S	ENSP00000380293:N456S	N	-	2	0	ZNF99	22732911	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-6.223000	0.00075	-2.013000	0.00949	-0.847000	0.03039	AAC	T|0.913;C|0.087	0.087	strong		0.343	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
RNF213	57674	hgsc.bcm.edu	37	17	78261805	78261805	+	Silent	SNP	A	A	G	rs7215243	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:78261805A>G	ENST00000582970.1	+	4	596	c.453A>G	c.(451-453)ccA>ccG	p.P151P	RNF213_ENST00000319921.4_Silent_p.P151P|RNF213_ENST00000456466.1_Silent_p.P151P|RNF213_ENST00000508628.2_Silent_p.P200P	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	151					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GCCAGCCCCCAGGCACAGCCA	0.692													G|||	1481	0.295727	0.5885	0.1873	5008	,	,		12591	0.131		0.1988	False		,,,				2504	0.2464				p.P151P		Atlas-SNP	.											RNF213_ENST00000456466,NS,carcinoma,0,3	RNF213	766	3	0			c.A453G						PASS	.	G	,	2141,2209		550,1041,584	11.0	13.0	12.0		600,453	-4.2	0.0	17	dbSNP_116	12	1773,6779		200,1373,2703	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	750,2414,3287	GG,GA,AA		20.732,49.2184,30.3364	,	200/5257,151/1064	78261805	3914,8988	2175	4276	6451	SO:0001819	synonymous_variant	57674	exon4			GCCCCCAGGCACA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.453A>G	17.37:g.78261805A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			A|0.731;G|0.269	0.269	strong		0.692	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
MTRR	4552	hgsc.bcm.edu	37	5	7878192	7878192	+	Silent	SNP	T	T	C	rs161870	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:7878192T>C	ENST00000264668.2	+	5	648	c.618T>C	c.(616-618)ctT>ctC	p.L206L	MTRR_ENST00000440940.2_Silent_p.L179L|MTRR_ENST00000341013.6_3'UTR	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	206	Hinge.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|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, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GGACAGACCTTGTGAAGTCAG	0.488													T|||	1267	0.252995	0.4357	0.3516	5008	,	,		18108	0.1696		0.1352	False		,,,				2504	0.1431				p.L206L		Atlas-SNP	.											.	MTRR	74	.	0			c.T618C						PASS	.	T	,	1664,2742	507.6+/-366.7	325,1014,864	76.0	72.0	73.0		537,618	-10.9	0.0	5	dbSNP_79	73	1018,7582	218.8+/-257.1	63,892,3345	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	388,1906,4209	CC,CT,TT		11.8372,37.7667,20.6213	,	179/699,206/726	7878192	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon5			AGACCTTGTGAAG	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.618T>C	5.37:g.7878192T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1	502	0.22985347985347984	193	0.39227642276422764	111	0.30662983425414364	104	0.18181818181818182	94	0.12401055408970976	T	5.580	0.291749	0.10567	0.377667	0.118372	ENSG00000124275	ENST00000514220	.	.	.	5.47	-10.9	0.00192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.31971	-0.9924	3	.	.	.	-2.7714	2.5133	0.04662	0.1817:0.3704:0.1485:0.2994	rs161870;rs2128264;rs60733639	.	.	.	R	108	.	.	C	+	1	0	MTRR	7931192	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.799000	0.00363	-2.045000	0.00910	-0.327000	0.08410	TGT	T|0.784;C|0.216	0.216	strong		0.488	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
MDN1	23195	hgsc.bcm.edu	37	6	90499502	90499502	+	Silent	SNP	G	G	A	rs1036853	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	114	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	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		
IGF2R	3482	hgsc.bcm.edu	37	6	160468278	160468278	+	Silent	SNP	A	A	G	rs998075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160468278A>G	ENST00000356956.1	+	16	2287	c.2139A>G	c.(2137-2139)acA>acG	p.T713T		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	713					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	GAGGCGGCACACCCTATAACA	0.463													G|||	2892	0.577476	0.6384	0.4899	5008	,	,		19164	0.6925		0.4841	False		,,,				2504	0.5348				p.T713T		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2139G						PASS	.	G		2695,1711	513.7+/-368.4	840,1015,348	134.0	126.0	129.0		2139	-11.0	0.0	6	dbSNP_86	129	4025,4575	597.0+/-393.7	919,2187,1194	no	coding-synonymous	IGF2R	NM_000876.2		1759,3202,1542	GG,GA,AA		46.8023,38.8334,48.3315		713/2492	160468278	6720,6286	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon16			CGGCACACCCTAT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.2139A>G	6.37:g.160468278A>G		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	57	54	0.947368	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			A|0.458;G|0.542	0.542	strong		0.463	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
MUC17	140453	hgsc.bcm.edu	37	7	100678568	100678568	+	Missense_Mutation	SNP	A	A	T	rs75492258	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678568A>T	ENST00000306151.4	+	3	3935	c.3871A>T	c.(3871-3873)Acc>Tcc	p.T1291S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1291	59 X approximate tandem repeats.|Ser-rich.				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)					CACGCTGGTGACCAGTCCTGA	0.478																																					p.T1291S		Atlas-SNP	.											MUC17,adrenal_gland,adrenal_cortical_adenoma,0,1	MUC17	804	1	0			c.A3871T						PASS	.	G	SER/THR	962,3444		0,962,1241	269.0	257.0	261.0		3871	-0.9	0.0	7	dbSNP_131	261	807,7793		0,807,3493	no	missense	MUC17	NM_001040105.1	58	0,1769,4734	TT,TA,AA		9.3837,21.8339,13.6014	benign	1291/4494	100678568	1769,11237	2203	4300	6503	SO:0001583	missense	140453	exon3			CTGGTGACCAGTC	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.3871A>T	7.37:g.100678568A>T	ENSP00000302716:p.Thr1291Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	259	87	0.335907	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.027	-1.364480	0.01235	0.218339	0.093837	ENSG00000169876	ENST00000306151	T	0.02323	4.34	0.471	-0.942	0.10398	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.44314	-0.9336	8	0.14656	T	0.56	.	.	.	.	.	1291	Q685J3	MUC17_HUMAN	S	1291	ENSP00000302716:T1291S	ENSP00000302716:T1291S	T	+	1	0	MUC17	100465288	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.016000	0.01446	-3.635000	0.00129	-3.626000	0.00027	ACC	A|0.934;T|0.066	0.066	strong		0.478	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
LRP1B	53353	hgsc.bcm.edu	37	2	141707868	141707868	+	Silent	SNP	G	G	T	rs6748626	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:141707868G>T	ENST00000389484.3	-	20	4043	c.3072C>A	c.(3070-3072)gcC>gcA	p.A1024A		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1024	LDL-receptor class A 7. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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)		CACCATCACAGGCCCAGTGGC	0.443										TSP Lung(27;0.18)			G|||	1381	0.275759	0.4735	0.2378	5008	,	,		16069	0.249		0.1402	False		,,,				2504	0.2025				p.A1024A	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C3072A						PASS	.	G		1721,2685	517.2+/-369.4	334,1053,816	89.0	64.0	73.0		3072	0.2	1.0	2	dbSNP_116	73	1182,7418	241.0+/-271.5	85,1012,3203	yes	coding-synonymous	LRP1B	NM_018557.2		419,2065,4019	TT,TG,GG		13.7442,39.0604,22.3205		1024/4600	141707868	2903,10103	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon20			ATCACAGGCCCAG	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.3072C>A	2.37:g.141707868G>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	200	101	0.505	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.770;T|0.230	0.230	strong		0.443	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
SON	6651	hgsc.bcm.edu	37	21	34926043	34926043	+	Missense_Mutation	SNP	G	G	A	rs61743204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:34926043G>A	ENST00000356577.4	+	3	4981	c.4506G>A	c.(4504-4506)atG>atA	p.M1502I	SON_ENST00000381679.4_Missense_Mutation_p.M1502I|SON_ENST00000381692.2_Intron|SON_ENST00000290239.6_Missense_Mutation_p.M1502I|SON_ENST00000300278.4_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	61	0	0		WXS	Illumina HiSeq	Phase_I	64	21	0.328125	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	
KIAA1549	57670	hgsc.bcm.edu	37	7	138602916	138602916	+	Missense_Mutation	SNP	G	G	C	rs2718131	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:138602916G>C	ENST00000422774.1	-	2	1504	c.1456C>G	c.(1456-1458)Ccc>Gcc	p.P486A	KIAA1549_ENST00000440172.1_Missense_Mutation_p.P486A|KIAA1549_ENST00000242365.4_Missense_Mutation_p.P436A			Q9HCM3	K1549_HUMAN	KIAA1549	486				P -> A (in Ref. 3; BAB13375). {ECO:0000305}.		integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						GGTCTGGAGGGGAAAAGCGTA	0.458			O	BRAF	pilocytic astrocytoma								G|||	1054	0.210463	0.388	0.1556	5008	,	,		23406	0.0655		0.2555	False		,,,				2504	0.1125				p.P486A	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C1456G						PASS	.	G	ALA/PRO,ALA/PRO	1418,2492		265,888,802	33.0	34.0	34.0		1456,1456	4.6	1.0	7	dbSNP_100	34	1910,6392		219,1472,2460	yes	missense,missense	KIAA1549	NM_001164665.1,NM_020910.2	27,27	484,2360,3262	CC,CG,GG		23.0065,36.266,27.2519	probably-damaging,probably-damaging	486/1951,486/1935	138602916	3328,8884	1955	4151	6106	SO:0001583	missense	57670	exon2			TGGAGGGGAAAAG		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1456C>G	7.37:g.138602916G>C	ENSP00000416040:p.Pro486Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	33	32	0.969697	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	488	0.22344322344322345	199	0.40447154471544716	56	0.15469613259668508	45	0.07867132867132867	188	0.24802110817941952	G	14.07	2.424820	0.43020	0.36266	0.230065	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.60672	0.17;0.21;0.18	4.58	4.58	0.56647	.	0.000000	0.53938	D	0.000054	T	0.00012	0.0000	L	0.34521	1.04	0.22940	P	0.99853962	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	T	0.36407	-0.9749	9	0.38643	T	0.18	.	14.7063	0.69194	0.0:0.0:1.0:0.0	rs2718131;rs10362786;rs2718131	486;486	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	A	486;436;486	ENSP00000406661:P486A;ENSP00000242365:P436A;ENSP00000416040:P486A	ENSP00000242365:P436A	P	-	1	0	KIAA1549	138253456	1.000000	0.71417	0.981000	0.43875	0.021000	0.10359	4.557000	0.60782	2.388000	0.81334	0.655000	0.94253	CCC	G|0.756;C|0.244	0.244	strong		0.458	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
BTNL2	56244	hgsc.bcm.edu	37	6	32362639	32362639	+	Silent	SNP	G	G	A	rs41535850	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32362639G>A	ENST00000374993.1	-	6	1241	c.1242C>T	c.(1240-1242)caC>caT	p.H414H	BTNL2_ENST00000429232.2_3'UTR|BTNL2_ENST00000414363.1_Silent_p.H204H|BTNL2_ENST00000544175.1_Silent_p.H137H|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Silent_p.H320H|BTNL2_ENST00000540315.1_Silent_p.H204H|BTNL2_ENST00000454136.3_Silent_p.H414H	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	414						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						GGAACAGCCCGTGGCTGCCTT	0.557													g|||	821	0.163938	0.1422	0.1599	5008	,	,		21164	0.1587		0.163	False		,,,				2504	0.2025				p.H414H		Atlas-SNP	.											.	BTNL2	50	.	0			c.C1242T						PASS	.			551,3855	248.1+/-256.1	28,495,1680	210.0	203.0	205.0		1242	-9.9	0.0	6	dbSNP_127	205	1241,7359	248.3+/-276.0	92,1057,3151	no	coding-synonymous	BTNL2	NM_019602.1		120,1552,4831	AA,AG,GG		14.4302,12.5057,13.7783		414/456	32362639	1792,11214	2203	4300	6503	SO:0001819	synonymous_variant	56244	exon6			CAGCCCGTGGCTG	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.1242C>T	6.37:g.32362639G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	156	76	0.487179	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				G|0.859;A|0.141	0.141	strong		0.557	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
ZNF532	55205	hgsc.bcm.edu	37	18	56648756	56648756	+	Silent	SNP	C	C	T	rs61733373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:56648756C>T	ENST00000336078.4	+	10	4094	c.3318C>T	c.(3316-3318)caC>caT	p.H1106H	ZNF532_ENST00000591808.1_Silent_p.H1106H|ZNF532_ENST00000591230.1_Silent_p.H1106H|ZNF532_ENST00000588956.1_3'UTR|ZNF532_ENST00000589288.1_Silent_p.H1106H|ZNF532_ENST00000591083.1_Silent_p.H1106H	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1106					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						TGGAGAAGCACGTCCAGCTGA	0.473													C|||	324	0.0646965	0.0061	0.0519	5008	,	,		20176	0.0188		0.1252	False		,,,				2504	0.138				p.H1106H		Atlas-SNP	.											.	ZNF532	108	.	0			c.C3318T						PASS	.	C		105,4301	81.9+/-120.4	0,105,2098	128.0	120.0	123.0		3318	2.3	1.0	18	dbSNP_129	123	1153,7447	236.8+/-268.9	80,993,3227	no	coding-synonymous	ZNF532	NM_018181.4		80,1098,5325	TT,TC,CC		13.407,2.3831,9.6725		1106/1302	56648756	1258,11748	2203	4300	6503	SO:0001819	synonymous_variant	55205	exon10			GAAGCACGTCCAG	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.3318C>T	18.37:g.56648756C>T		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	235	111	0.47234	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Silent	SNP	ENST00000336078.4	37	CCDS11969.1																																																																																			C|0.910;T|0.090	0.090	strong		0.473	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
ERICH6	131831	hgsc.bcm.edu	37	3	150421419	150421419	+	Silent	SNP	G	G	A	rs17281287	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	106	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	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		
NPW	283869	hgsc.bcm.edu	37	16	2070200	2070200	+	Missense_Mutation	SNP	G	G	C	rs11248906	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2070200G>C	ENST00000566435.1	+	1	655	c.142G>C	c.(142-144)Gag>Cag	p.E48Q	NPW_ENST00000329610.4_Missense_Mutation_p.E100Q			Q8N729	NPW_HUMAN	neuropeptide W	100					feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				kidney(1)	1						GGAGCTGTGGGAGACGCGACG	0.756													G|||	465	0.0928514	0.0567	0.1311	5008	,	,		10039	0.0		0.2256	False		,,,				2504	0.0736				p.E100Q		Atlas-SNP	.											.	NPW	4	.	0			c.G298C						PASS	.	G	GLN/GLU	242,3078		11,220,1429	7.0	8.0	7.0		298	2.1	0.1	16	dbSNP_120	7	1359,6037		104,1151,2443	yes	missense	NPW	NM_001099456.2	29	115,1371,3872	CC,CG,GG		18.3748,7.2892,14.9403	benign	100/166	2070200	1601,9115	1660	3698	5358	SO:0001583	missense	283869	exon1			CTGTGGGAGACGC	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.142G>C	16.37:g.2070200G>C	ENSP00000456974:p.Glu48Gln	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	7	6	0.857143	NM_001099456		Missense_Mutation	SNP	ENST00000566435.1	37		243	0.11126373626373626	21	0.042682926829268296	57	0.1574585635359116	0	0.0	165	0.21767810026385223	g	10.79	1.451090	0.26074	0.072892	0.183748	ENSG00000183971	ENST00000329610	T	0.50548	0.74	3.08	2.12	0.27331	.	0.406531	0.21498	U	0.073573	T	0.00039	0.0001	N	0.17082	0.46	0.58432	P	4.000000000004E-6	D	0.63046	0.992	P	0.57620	0.824	T	0.06092	-1.0846	9	0.51188	T	0.08	.	6.1772	0.20451	0.1452:0.0:0.8548:0.0	rs11248906	100	Q8N729	NPW_HUMAN	Q	100	ENSP00000330070:E100Q	ENSP00000330070:E100Q	E	+	1	0	NPW	2010201	0.004000	0.15560	0.091000	0.20842	0.107000	0.19398	0.835000	0.27531	0.652000	0.30806	0.400000	0.26472	GAG	G|0.881;C|0.119	0.119	strong		0.756	NPW-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000434312.1	NM_001099456	
PTPN6	5777	hgsc.bcm.edu	37	12	7067226	7067226	+	Missense_Mutation	SNP	G	G	A	rs62621988		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7067226G>A	ENST00000318974.9	+	11	1595	c.1351G>A	c.(1351-1353)Gtg>Atg	p.V451M	PTPN6_ENST00000447931.2_Missense_Mutation_p.V412M|PTPN6_ENST00000399448.1_Missense_Mutation_p.V453M|PTPN6_ENST00000456013.1_Missense_Mutation_p.V451M	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	451	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						GCCCATCATCGTGCACTGCAG	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.V453M		Atlas-SNP	.											.	PTPN6	42	.	0			c.G1357A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	2,4098		0,2,2048	36.0	38.0	38.0		1351,1357,1351	5.1	1.0	12	dbSNP_129	38	12,8396		0,12,4192	yes	missense,missense,missense	PTPN6	NM_002831.5,NM_080548.4,NM_080549.3	21,21,21	0,14,6240	AA,AG,GG		0.1427,0.0488,0.1119	probably-damaging,probably-damaging,probably-damaging	451/596,453/598,451/625	7067226	14,12494	2050	4204	6254	SO:0001583	missense	5777	exon11			ATCATCGTGCACT		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.1351G>A	12.37:g.7067226G>A	ENSP00000326010:p.Val451Met	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	37	CCDS44820.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.88	3.908893	0.72868	4.88E-4	0.001427	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000318974;ENST00000456013	D;D;D;D	0.91124	-2.79;-2.79;-2.79;-2.79	5.08	5.08	0.68730	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.140227	0.48767	D	0.000171	D	0.97480	0.9175	H	0.98646	4.29	0.58432	D	0.999998	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.998;0.998;0.999	D	0.99410	1.0930	10	0.87932	D	0	.	18.4653	0.90752	0.0:0.0:1.0:0.0	rs62621988	439;412;451;451;453	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	M	453;412;451;451	ENSP00000382376:V453M;ENSP00000415979:V412M;ENSP00000326010:V451M;ENSP00000391592:V451M	ENSP00000326010:V451M	V	+	1	0	PTPN6	6937487	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.603000	0.61105	2.346000	0.79739	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.532	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831	
H6PD	9563	hgsc.bcm.edu	37	1	9323910	9323910	+	Missense_Mutation	SNP	G	G	A	rs6688832	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:9323910G>A	ENST00000377403.2	+	5	1660	c.1358G>A	c.(1357-1359)cGg>cAg	p.R453Q	H6PD_ENST00000602477.1_Missense_Mutation_p.R464Q	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	453	Glucose 1-dehydrogenase.		R -> Q (in CRD; less than 50% of activity than wild-type; dbSNP:rs6688832). {ECO:0000269|PubMed:12858176, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|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;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		AGCCCTGTGCGGGAGCGGGAC	0.597													A|||	1951	0.389577	0.4932	0.3732	5008	,	,		18364	0.4812		0.2485	False		,,,				2504	0.3119				p.R453Q		Atlas-SNP	.											.	H6PD	71	.	0			c.G1358A	GRCh37	CM031993	H6PD	M	rs6688832	PASS	.	A	GLN/ARG	2017,2389	611.7+/-391.8	456,1105,642	64.0	74.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1358	-2.1	0.1	1	dbSNP_116	71	1971,6629	723.0+/-406.4	223,1525,2552	yes	missense	H6PD	NM_004285.3	43	679,2630,3194	AA,AG,GG		22.9186,45.7785,30.6628	benign	453/792	9323910	3988,9018	2203	4300	6503	SO:0001583	missense	9563	exon5			CTGTGCGGGAGCG	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"""glucose dehyrogenase"""	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.1358G>A	1.37:g.9323910G>A	ENSP00000366620:p.Arg453Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	47	12	0.255319	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	37	CCDS101.1	795	0.364010989010989	225	0.4573170731707317	123	0.3397790055248619	260	0.45454545454545453	187	0.24670184696569922	A	0.078	-1.188930	0.01607	0.457785	0.229186	ENSG00000049239	ENST00000377403	D	0.98264	-4.83	5.53	-2.12	0.07165	.	0.705587	0.14737	N	0.301437	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.32824	-0.9892	9	0.17832	T	0.49	-13.5512	4.5195	0.11952	0.3753:0.0952:0.4337:0.0958	rs6688832;rs17286908;rs52797480;rs58250722;rs6688832	453	O95479	G6PE_HUMAN	Q	453	ENSP00000366620:R453Q	ENSP00000366620:R453Q	R	+	2	0	H6PD	9246497	0.001000	0.12720	0.054000	0.19295	0.017000	0.09413	-0.091000	0.11146	-0.530000	0.06349	-1.197000	0.01672	CGG	G|0.662;A|0.338	0.338	strong		0.597	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
CCDC146	57639	hgsc.bcm.edu	37	7	76916819	76916819	+	Silent	SNP	G	G	A	rs3763402	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76916819G>A	ENST00000285871.4	+	17	2467	c.2340G>A	c.(2338-2340)caG>caA	p.Q780Q	CCDC146_ENST00000415740.2_3'UTR|CCDC146_ENST00000431197.1_Silent_p.Q494Q	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	780										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)				TCTATGAGCAGGTCTCCAGGC	0.483													G|||	1142	0.228035	0.4115	0.1225	5008	,	,		18042	0.0923		0.173	False		,,,				2504	0.2515				p.Q780Q		Atlas-SNP	.											.	CCDC146	87	.	0			c.G2340A						PASS	.	G		1605,2801	496.7+/-363.6	299,1007,897	77.0	76.0	76.0		2340	3.4	1.0	7	dbSNP_107	76	1598,7002	296.3+/-302.9	144,1310,2846	no	coding-synonymous	CCDC146	NM_020879.2		443,2317,3743	AA,AG,GG		18.5814,36.4276,24.6271		780/956	76916819	3203,9803	2203	4300	6503	SO:0001819	synonymous_variant	57639	exon17			TGAGCAGGTCTCC	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.2340G>A	7.37:g.76916819G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	336	334	0.994048	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	37	CCDS34671.1																																																																																			G|0.769;A|0.231	0.231	strong		0.483	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
ZNF845	91664	hgsc.bcm.edu	37	19	53856776	53856776	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53856776A>G	ENST00000595091.1	+	5	3067	c.2848A>G	c.(2848-2850)Aag>Gag	p.K950E	ZNF845_ENST00000458035.1_Missense_Mutation_p.K950E			Q96IR2	ZN845_HUMAN	zinc finger protein 845	950					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						TGAATGTGGCAAGGTTTTTAA	0.343																																					p.K950E		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2848G						PASS	.						26.0	24.0	25.0					19																	53856776		692	1589	2281	SO:0001583	missense	91664	exon4			TGTGGCAAGGTTT	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.2848A>G	19.37:g.53856776A>G	ENSP00000470005:p.Lys950Glu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	156	7	0.0448718	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.999115	0.35226	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.27104	1.69	2.04	2.04	0.26737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27933	0.0688	M	0.71036	2.16	0.21802	N	0.999532	B	0.02656	0.0	B	0.06405	0.002	T	0.25984	-1.0116	9	0.62326	D	0.03	.	8.7997	0.34901	1.0:0.0:0.0:0.0	.	950	Q96IR2	ZN845_HUMAN	E	950;866	ENSP00000388311:K950E	ENSP00000412086:K866E	K	+	1	0	ZNF845	58548588	0.001000	0.12720	0.001000	0.08648	0.060000	0.15804	1.472000	0.35376	0.918000	0.36919	0.338000	0.21704	AAG	.	.	none		0.343	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
CDH24	64403	hgsc.bcm.edu	37	14	23523353	23523353	+	Silent	SNP	G	G	T	rs139832060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23523353G>T	ENST00000267383.5	-	5	1061	c.969C>A	c.(967-969)cgC>cgA	p.R323R	CDH24_ENST00000487137.2_Silent_p.R323R|CDH24_ENST00000397359.3_Silent_p.R323R|CDH24_ENST00000554034.1_Silent_p.R323R			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	323	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)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		GGCTAACCTTGCGGACAGTGA	0.547													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20441	0.0		0.0	False		,,,				2504	0.0061				p.R323R		Atlas-SNP	.											.	CDH24	129	.	0			c.C969A						PASS	.	G	,	4,4400		0,4,2198	78.0	72.0	74.0		969,969	0.3	1.0	14	dbSNP_134	74	41,8553		0,41,4256	yes	coding-synonymous,coding-synonymous	CDH24	NM_022478.3,NM_144985.3	,	0,45,6454	TT,TG,GG		0.4771,0.0908,0.3462	,	323/820,323/782	23523353	45,12953	2202	4297	6499	SO:0001819	synonymous_variant	64403	exon6			AACCTTGCGGACA	AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.969C>A	14.37:g.23523353G>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	51	34	0.666667	NM_022478	D3DS44|Q86UP1|Q9NT84	Silent	SNP	ENST00000267383.5	37	CCDS9585.1																																																																																			G|0.997;T|0.003	0.003	strong		0.547	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478	
PLAC8L1	153770	hgsc.bcm.edu	37	5	145483844	145483844	+	Missense_Mutation	SNP	A	A	T	rs12187913	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	251	2	0.00796813		WXS	Illumina HiSeq	Phase_I	223	221	0.991031	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	
OR11H12	440153	hgsc.bcm.edu	37	14	19378322	19378322	+	Missense_Mutation	SNP	G	G	A	rs201485834		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:19378322G>A	ENST00000550708.1	+	1	801	c.729G>A	c.(727-729)atG>atA	p.M243I		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGTTGGGTATGCCTTCAAGCA	0.428																																					p.M243I		Atlas-SNP	.											OR11H12,NS,malignant_melanoma,+1,1	OR11H12	58	1	0			c.G729A						scavenged	.						3.0	1.0	1.0					14																	19378322		201	443	644	SO:0001583	missense	440153	exon1			GGGTATGCCTTCA		CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"""GPCR / Class A : Olfactory receptors"""	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.729G>A	14.37:g.19378322G>A	ENSP00000449002:p.Met243Ile	Somatic	1144	1	0.000874126		WXS	Illumina HiSeq	Phase_I	1329	22	0.0165538	NM_001013354		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	g	0.944	-0.708542	0.03230	.	.	ENSG00000257115	ENST00000550708	T	0.00021	9.03	0.585	0.585	0.17428	GPCR, rhodopsin-like superfamily (1);	0.483801	0.17283	N	0.179914	T	0.00039	0.0001	N	0.02876	-0.465	0.22675	N	0.998867	B	0.13594	0.008	B	0.12837	0.008	T	0.18366	-1.0339	9	0.02654	T	1	.	3.0137	0.06052	0.3477:0.0:0.6523:0.0	.	243	B2RN74	O11HC_HUMAN	I	243	ENSP00000449002:M243I	ENSP00000449002:M243I	M	+	3	0	CR383656.1	18448322	0.000000	0.05858	0.847000	0.33407	0.095000	0.18619	-0.623000	0.05546	0.619000	0.30197	0.064000	0.15345	ATG	.	.	weak		0.428	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354	
ENPP7	339221	hgsc.bcm.edu	37	17	77707422	77707422	+	Missense_Mutation	SNP	G	G	A	rs145931726		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:77707422G>A	ENST00000328313.5	+	2	591	c.370G>A	c.(370-372)Gtg>Atg	p.V124M		NM_178543.3	NP_848638.3			ectonucleotide pyrophosphatase/phosphodiesterase 7									p.V124M(1)		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)			CAACGGCAGCGTGCCCATCTG	0.622													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19656	0.0		0.0	False		,,,				2504	0.0				p.V124M		Atlas-SNP	.											ENPP7,NS,carcinoma,0,1	ENPP7	63	1	1	Substitution - Missense(1)	kidney(1)	c.G370A						scavenged	.	G	MET/VAL	4,4402	8.1+/-20.4	0,4,2199	61.0	44.0	49.0		370	-9.6	0.0	17	dbSNP_134	49	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ENPP7	NM_178543.3	21	0,6,6497	AA,AG,GG		0.0233,0.0908,0.0461	benign	124/459	77707422	6,13000	2203	4300	6503	SO:0001583	missense	339221	exon2			GGCAGCGTGCCCA	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.370G>A	17.37:g.77707422G>A	ENSP00000332656:p.Val124Met	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	120	3	0.025	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	37	CCDS11763.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	15.61	2.885963	0.51908	9.08E-4	2.33E-4	ENSG00000182156	ENST00000328313	T	0.74632	-0.86	4.78	-9.56	0.00566	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.415210	0.22119	N	0.064366	T	0.50274	0.1606	N	0.25485	0.75	0.25781	N	0.984728	B	0.31209	0.313	B	0.32805	0.153	T	0.38866	-0.9641	10	0.39692	T	0.17	-11.4596	7.7023	0.28630	0.146:0.5996:0.1089:0.1454	.	124	Q6UWV6	ENPP7_HUMAN	M	124	ENSP00000332656:V124M	ENSP00000332656:V124M	V	+	1	0	ENPP7	75322017	0.000000	0.05858	0.017000	0.16124	0.973000	0.67179	-0.316000	0.08071	-1.934000	0.01051	0.591000	0.81541	GTG	G|1.000;A|0.000	0.000	strong		0.622	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
HGS	9146	hgsc.bcm.edu	37	17	79660570	79660570	+	Missense_Mutation	SNP	C	C	T	rs150616739		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:79660570C>T	ENST00000329138.4	+	9	835	c.700C>T	c.(700-702)Ccc>Tcc	p.P234S		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	234	Interaction with SNX1. {ECO:0000250}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CACTGAGCTGCCCCCCGAGTA	0.682																																					p.P234S		Atlas-SNP	.											.	HGS	54	.	0			c.C700T						PASS	.	C	SER/PRO	0,4406		0,0,2203	84.0	67.0	72.0		700	4.4	1.0	17	dbSNP_134	72	2,8598	2.2+/-6.3	0,2,4298	yes	missense	HGS	NM_004712.4	74	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	234/778	79660570	2,13004	2203	4300	6503	SO:0001583	missense	9146	exon9			GAGCTGCCCCCCG	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.700C>T	17.37:g.79660570C>T	ENSP00000331201:p.Pro234Ser	Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	223	117	0.524664	NM_004712	Q9NR36	Missense_Mutation	SNP	ENST00000329138.4	37	CCDS11784.1	.	.	.	.	.	.	.	.	.	.	C	32	5.166816	0.94768	0.0	2.33E-4	ENSG00000185359	ENST00000329138;ENST00000442335	T	0.42900	0.96	4.39	4.39	0.52855	.	0.184051	0.48767	D	0.000171	T	0.61223	0.2330	M	0.82323	2.585	0.80722	D	1	P	0.47545	0.897	P	0.54924	0.764	T	0.65557	-0.6139	10	0.40728	T	0.16	-24.3068	16.3019	0.82825	0.0:1.0:0.0:0.0	.	234	O14964	HGS_HUMAN	S	234	ENSP00000331201:P234S	ENSP00000331201:P234S	P	+	1	0	HGS	77270975	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.258000	0.78371	2.138000	0.66242	0.655000	0.94253	CCC	C|1.000;T|0.000	0.000	weak		0.682	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	
KRT81	3887	hgsc.bcm.edu	37	12	52681056	52681056	+	Silent	SNP	C	C	T	rs4761856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:52681056C>T	ENST00000327741.5	-	7	1145	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	KRT86_ENST00000423955.2_Intron|KRT86_ENST00000544024.1_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	359	Coil 2.|Rod.					extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|large_intestine(3)|lung(6)|prostate(1)|stomach(1)	16				BRCA - Breast invasive adenocarcinoma(357;0.189)		CACTGAGGGCCGCCTCACCCT	0.617													.|||	1921	0.383586	0.2995	0.3602	5008	,	,		18024	0.5377		0.334	False		,,,				2504	0.4059				p.A359A		Atlas-SNP	.											.	KRT81	46	.	0			c.G1077A						PASS	.	C		1321,3085		225,871,1107	28.0	30.0	29.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1077	-4.9	0.9	12	dbSNP_111	29	2681,5909		411,1859,2025	no	coding-synonymous	KRT81	NM_002281.3		636,2730,3132	TT,TC,CC		31.2107,29.9818,30.7941		359/506	52681056	4002,8994	2203	4295	6498	SO:0001819	synonymous_variant	3887	exon7			GAGGGCCGCCTCA	X81420	CCDS31805.1	12q13	2013-01-16	2006-07-17	2006-07-17	ENSG00000205426	ENSG00000205426		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6458	protein-coding gene	gene with protein product	"""hard keratin type II 1"""	602153	"""keratin, hair, basic, 1"""	KRTHB1		7556444, 16831889	Standard	NM_002281		Approved	Hb-1	uc001sab.3	Q14533	OTTHUMG00000167574	ENST00000327741.5:c.1077G>A	12.37:g.52681056C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	119	66	0.554622	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	Silent	SNP	ENST00000327741.5	37	CCDS31805.1																																																																																			C|0.673;T|0.327	0.327	strong		0.617	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281	
SEC31B	25956	hgsc.bcm.edu	37	10	102265847	102265847	+	Missense_Mutation	SNP	A	A	C	rs2295774	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102265847A>C	ENST00000370345.3	-	9	1091	c.994T>G	c.(994-996)Tct>Gct	p.S332A	SEC31B_ENST00000535773.1_Missense_Mutation_p.S175A|SEC31B_ENST00000370329.5_Missense_Mutation_p.S335A|SEC31B_ENST00000451524.1_Missense_Mutation_p.S332A	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	332			S -> A (in dbSNP:rs2295774). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CCCATCACAGAGTACAAACTG	0.542													A|||	751	0.14996	0.0719	0.1744	5008	,	,		19627	0.1319		0.1909	False		,,,				2504	0.2147				p.S332A		Atlas-SNP	.											SEC31B,colon,carcinoma,0,1	SEC31B	84	1	0			c.T994G						PASS	.	A	ALA/SER	340,4066	181.5+/-209.5	13,314,1876	158.0	156.0	157.0		994	5.9	1.0	10	dbSNP_100	157	1888,6712	335.8+/-321.6	216,1456,2628	yes	missense	SEC31B	NM_015490.3	99	229,1770,4504	CC,CA,AA		21.9535,7.7167,17.1306	probably-damaging	332/1180	102265847	2228,10778	2203	4300	6503	SO:0001583	missense	25956	exon9			TCACAGAGTACAA	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.994T>G	10.37:g.102265847A>C	ENSP00000359370:p.Ser332Ala	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	116	83	0.715517	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Missense_Mutation	SNP	ENST00000370345.3	37	CCDS7495.1	338	0.15476190476190477	19	0.03861788617886179	66	0.18232044198895028	94	0.16433566433566432	159	0.20976253298153033	A	32	5.124589	0.94429	0.077167	0.219535	ENSG00000075826	ENST00000370345;ENST00000451524;ENST00000535773;ENST00000370329	T;T;T;T	0.71817	1.47;1.47;-0.6;1.47	5.94	5.94	0.96194	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.050373	0.85682	D	0.000000	T	0.00300	0.0009	M	0.92169	3.28	0.09310	P	0.9999999837421	D;D;D;D;D	0.89917	0.999;0.999;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.999;0.979;0.994;0.979;0.987	T	0.01566	-1.1323	9	0.72032	D	0.01	-11.7028	15.579	0.76418	1.0:0.0:0.0:0.0	rs2295774;rs2295774	332;335;331;332;332	A8KAL6;B4DGE3;Q9NQW1-5;E9PKR7;Q9NQW1	.;.;.;.;SC31B_HUMAN	A	332;332;175;335	ENSP00000359370:S332A;ENSP00000391178:S332A;ENSP00000442621:S175A;ENSP00000359354:S335A	ENSP00000359354:S335A	S	-	1	0	SEC31B	102255837	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.334000	0.79224	2.279000	0.76181	0.459000	0.35465	TCT	A|0.836;C|0.164	0.164	strong		0.542	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
NIN	51199	hgsc.bcm.edu	37	14	51192659	51192659	+	Silent	SNP	G	G	A	rs1983764	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:51192659G>A	ENST00000382041.3	-	30	6394	c.6204C>T	c.(6202-6204)ccC>ccT	p.P2068P	NIN_ENST00000389868.3_Intron|NIN_ENST00000324330.9_3'UTR|RP11-248J18.3_ENST00000602615.1_RNA|NIN_ENST00000245441.5_Intron|NIN_ENST00000382043.4_Silent_p.P1355P|NIN_ENST00000530997.2_Intron	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	2068					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)					AGAGATGACCGGGTAGGCTCA	0.398			T	PDGFRB	MPD								G|||	1225	0.244609	0.0303	0.2507	5008	,	,		20594	0.2966		0.3469	False		,,,				2504	0.3712				p.P2068P		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C6204T						PASS	.	G	,,	384,4022	195.7+/-220.2	17,350,1836	233.0	203.0	213.0		4065,,6204	-4.4	0.0	14	dbSNP_92	213	3053,5547	470.4+/-367.8	530,1993,1777	no	coding-synonymous,intron,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182946.1	,,	547,2343,3613	AA,AG,GG		35.5,8.7154,26.4263	,,	1355/1378,,2068/2091	51192659	3437,9569	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon30			ATGACCGGGTAGG	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.6204C>T	14.37:g.51192659G>A		Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	337	337	1	NM_182946	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Silent	SNP	ENST00000382041.3	37	CCDS32079.1	564	0.25824175824175827	24	0.04878048780487805	86	0.23756906077348067	183	0.31993006993006995	271	0.3575197889182058	G	6.376	0.437532	0.12104	0.087154	0.355	ENSG00000100503	ENST00000389869	.	.	.	5.93	-4.4	0.03600	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44298	-0.9337	3	.	.	.	.	1.1314	0.01746	0.3536:0.2034:0.297:0.146	rs1983764;rs52794699;rs59283049;rs1983764	.	.	.	W	1559	.	.	R	-	1	2	NIN	50262409	0.000000	0.05858	0.001000	0.08648	0.213000	0.24496	-1.297000	0.02759	-1.103000	0.03019	-1.004000	0.02495	CGG	G|0.744;A|0.256	0.256	strong		0.398	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
AKAP9	10142	hgsc.bcm.edu	37	7	91660861	91660861	+	Silent	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91660861T>C	ENST00000359028.2	+	17	4542	c.4317T>C	c.(4315-4317)aaT>aaC	p.N1439N	AKAP9_ENST00000356239.3_Silent_p.N1427N|AKAP9_ENST00000358100.2_Silent_p.N1439N			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1439					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)			AGGAAACAAATATCGTTAAGT	0.284			T	BRAF	papillary thyroid																																p.N1427N		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.T4281C						PASS	.						121.0	128.0	126.0					7																	91660861		2202	4297	6499	SO:0001819	synonymous_variant	10142	exon16			AACAAATATCGTT	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.4317T>C	7.37:g.91660861T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	6	0.0659341	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				.	.	none		0.284	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
SALL4	57167	hgsc.bcm.edu	37	20	50407255	50407255	+	Silent	SNP	G	G	A	rs201329321		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:50407255G>A	ENST00000217086.4	-	2	1878	c.1767C>T	c.(1765-1767)acC>acT	p.T589T	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	589					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						GTCTCTCCCCGGTGTGGGTGC	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		19405	0.001		0.0	False		,,,				2504	0.0				p.T589T		Atlas-SNP	.											.	SALL4	168	.	0			c.C1767T						PASS	.						93.0	82.0	86.0					20																	50407255		2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			CTCCCCGGTGTGG	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.1767C>T	20.37:g.50407255G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	168	50	0.297619	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			G|1.000;A|0.000	0.000	strong		0.507	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
FLG	2312	hgsc.bcm.edu	37	1	152283236	152283236	+	Missense_Mutation	SNP	T	T	C	rs11581433	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152283236T>C	ENST00000368799.1	-	3	4161	c.4126A>G	c.(4126-4128)Aga>Gga	p.R1376G	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1376	Ser-rich.		R -> G (in dbSNP:rs11581433).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAAGCTTGTCTGTGCCCAATG	0.532									Ichthyosis				C|||	1718	0.343051	0.1218	0.4236	5008	,	,		21937	0.6062		0.171	False		,,,				2504	0.4908				p.R1376G		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.A4126G						PASS	.	C	GLY/ARG	607,3799	768.9+/-413.6	43,521,1639	411.0	383.0	392.0		4126	-4.5	0.0	1	dbSNP_120	392	1436,7160	750.9+/-407.4	123,1190,2985	no	missense	FLG	NM_002016.1	125	166,1711,4624	CC,CT,TT		16.7054,13.7767,15.713	benign	1376/4062	152283236	2043,10959	2203	4298	6501	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTTGTCTGTGCCC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4126A>G	1.37:g.152283236T>C	ENSP00000357789:p.Arg1376Gly	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	195	67	0.34359	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	588	0.2692307692307692	51	0.10365853658536585	109	0.3011049723756906	317	0.5541958041958042	111	0.14643799472295516	C	6.987	0.552125	0.13374	0.137767	0.167054	ENSG00000143631	ENST00000368799	T	0.02032	4.49	4.29	-4.46	0.03536	.	.	.	.	.	T	0.00178	0.0005	N	0.00642	-1.3	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39663	-0.9603	8	0.02654	T	1	.	8.0818	0.30750	0.0:0.1976:0.1306:0.6718	rs11581433	1376	P20930	FILA_HUMAN	G	1376	ENSP00000357789:R1376G	ENSP00000357789:R1376G	R	-	1	2	FLG	150549860	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.374000	0.01072	-0.955000	0.03636	-0.949000	0.02662	AGA	T|0.807;C|0.193	0.193	strong		0.532	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
POM121	9883	hgsc.bcm.edu	37	7	72412427	72412427	+	Missense_Mutation	SNP	G	G	A	rs201876140		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:72412427G>A	ENST00000434423.2	+	11	1895	c.1895G>A	c.(1894-1896)aGc>aAc	p.S632N	POM121_ENST00000395270.1_Missense_Mutation_p.S367N|POM121_ENST00000358357.3_Missense_Mutation_p.S367N|POM121_ENST00000257622.4_Missense_Mutation_p.S367N|POM121_ENST00000446813.1_Missense_Mutation_p.S367N			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	632	Pore side. {ECO:0000255}.				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)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.S367N(2)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				AAGACACCCAGCCTCCTACCC	0.547																																					p.S367N		Atlas-SNP	.											POM121,NS,malignant_melanoma,0,2	POM121	131	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G1100A						scavenged	.						3.0	3.0	3.0					7																	72412427		1270	2943	4213	SO:0001583	missense	9883	exon11			CACCCAGCCTCCT	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.1895G>A	7.37:g.72412427G>A	ENSP00000405562:p.Ser632Asn	Somatic	360	15	0.0416667		WXS	Illumina HiSeq	Phase_I	455	34	0.0747253	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		.	.	.	.	.	.	.	.	.	.	G	7.496	0.651738	0.14516	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.08102	3.13;3.17;3.13;3.17;3.39	2.7	2.7	0.31948	.	0.155531	0.31257	N	0.007975	T	0.09862	0.0242	L	0.58969	1.84	0.43263	D	0.995207	P;P	0.36535	0.557;0.554	B;B	0.35971	0.215;0.157	T	0.12066	-1.0562	10	0.49607	T	0.09	.	10.9555	0.47356	0.0:0.0:1.0:0.0	.	367;632	A8MXF9;Q96HA1	.;P121A_HUMAN	N	367;367;367;367;632	ENSP00000393020:S367N;ENSP00000257622:S367N;ENSP00000378687:S367N;ENSP00000351124:S367N;ENSP00000405562:S632N	ENSP00000257622:S367N	S	+	2	0	POM121	72050363	0.502000	0.26107	0.893000	0.35052	0.018000	0.09664	1.430000	0.34914	1.503000	0.48686	0.173000	0.16961	AGC	.	.	weak		0.547	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
PRSS53	339105	hgsc.bcm.edu	37	16	31096164	31096164	+	Missense_Mutation	SNP	G	G	C	rs7199949	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:31096164G>C	ENST00000280606.6	-	8	1369	c.1216C>G	c.(1216-1218)Cct>Gct	p.P406A		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	406	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						TGGTGGTCAGGATAGGGCAGG	0.692													C|||	2399	0.479034	0.652	0.4323	5008	,	,		17467	0.1121		0.3767	False		,,,				2504	0.7618				p.P406A		Atlas-SNP	.											PRSS53,NS,carcinoma,0,2	PRSS53	29	2	0			c.C1216G						scavenged	.	C	ALA/PRO	2270,1688		698,874,407	7.0	9.0	8.0		1216	-3.0	0.0	16	dbSNP_116	8	2881,5337		574,1733,1802	yes	missense	PRSS53	NM_001039503.2	27	1272,2607,2209	CC,CG,GG		35.0572,42.6478,42.3045	benign	406/554	31096164	5151,7025	1979	4109	6088	SO:0001583	missense	339105	exon8			GGTCAGGATAGGG		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"""Serine peptidases / Serine peptidases"""	34407	protein-coding gene	gene with protein product	"""polyserase 3"""	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.1216C>G	16.37:g.31096164G>C	ENSP00000280606:p.Pro406Ala	Somatic	401	4	0.00997506		WXS	Illumina HiSeq	Phase_I	337	171	0.507418	NM_001039503		Missense_Mutation	SNP	ENST00000280606.6	37	CCDS42153.1	771	0.35302197802197804	305	0.6199186991869918	140	0.3867403314917127	47	0.08216783216783216	279	0.36807387862796836	C	0.011	-1.734285	0.00687	0.573522	0.350572	ENSG00000151006	ENST00000280606	D	0.87334	-2.24	5.28	-3.03	0.05429	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.466390	0.15290	N	0.270185	T	0.00012	0.0000	N	0.02736	-0.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31336	-0.9947	9	0.02654	T	1	.	0.6908	0.00891	0.2112:0.3345:0.2057:0.2487	rs7199949;rs57732931;rs7199949	406	Q2L4Q9	PRS53_HUMAN	A	406	ENSP00000280606:P406A	ENSP00000280606:P406A	P	-	1	0	PRSS53	31003665	0.000000	0.05858	0.000000	0.03702	0.365000	0.29674	-0.533000	0.06157	-1.322000	0.02278	-0.225000	0.12378	CCT	G|0.648;C|0.352	0.352	strong		0.692	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
DCD	117159	hgsc.bcm.edu	37	12	55038536	55038536	+	Silent	SNP	G	G	A	rs139716642		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:55038536G>A	ENST00000293371.6	-	5	483	c.294C>T	c.(292-294)gcC>gcT	p.A98A	DCD_ENST00000456047.2_Missense_Mutation_p.R120C	NM_053283.2	NP_444513.1	P81605	DCD_HUMAN	dermcidin	98					defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(1001;0.0255)				CGTCATGGACGGCTCCTAGGA	0.488																																					p.A98A		Atlas-SNP	.											.	DCD	20	.	0			c.C294T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	31.0	28.0	29.0		294	-1.2	0.0	12	dbSNP_134	29	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	DCD	NM_053283.2		0,3,6499	AA,AG,GG		0.0233,0.0227,0.0231		98/111	55038536	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	117159	exon5			ATGGACGGCTCCT	AF144011	CCDS8884.1, CCDS73478.1	12q13.1	2008-08-04				ENSG00000161634			14669	protein-coding gene	gene with protein product	"""proteolysis inducing factor"", ""preproteolysin"", ""diffusible survival/evasion peptide"", ""survival promoting peptide"""	606634				11694882	Standard	XM_005268627		Approved	AIDD, PIF, DSEP, HCAP, DCD-1	uc001sgj.3	P81605	OTTHUMG00000169937	ENST00000293371.6:c.294C>T	12.37:g.55038536G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	238	120	0.504202	NM_053283	A5JHP2|A5JHP3|P58461|Q53YJ2	Silent	SNP	ENST00000293371.6	37	CCDS8884.1	.	.	.	.	.	.	.	.	.	.	G	3.323	-0.138330	0.06669	2.27E-4	2.33E-4	ENSG00000161634	ENST00000456047	.	.	.	2.5	-1.22	0.09494	.	.	.	.	.	T	0.28433	0.0703	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.29212	-1.0019	7	0.87932	D	0	.	6.2481	0.20830	0.2528:0.0:0.7472:0.0	.	120	A5JHP3	.	C	120	.	ENSP00000406773:R120C	R	-	1	0	DCD	53324803	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.482000	0.06544	-0.129000	0.11620	-0.440000	0.05779	CGT	G|1.000;A|0.000	0.000	weak		0.488	DCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406617.1	NM_053283	
ZNF404	342908	hgsc.bcm.edu	37	19	44377972	44377972	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44377972C>T	ENST00000587539.1	-	3	393	c.394G>A	c.(394-396)Gag>Aag	p.E132K	ZNF404_ENST00000324394.6_Missense_Mutation_p.E130K	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	132					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)				TCCTTACACTCATATGATTTC	0.343																																					p.E129K		Atlas-SNP	.											ZNF404,NS,carcinoma,+2,1	ZNF404	46	1	0			c.G385A						scavenged	.						106.0	125.0	119.0					19																	44377972		1867	4125	5992	SO:0001583	missense	342908	exon2			TACACTCATATGA	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.394G>A	19.37:g.44377972C>T	ENSP00000466051:p.Glu132Lys	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	240	3	0.0125	NM_001033719	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	37	CCDS59394.1	.	.	.	.	.	.	.	.	.	.	C	2.471	-0.321968	0.05386	.	.	ENSG00000176222	ENST00000324394	T	0.14144	2.53	2.99	0.784	0.18578	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05044	0.0135	N	0.11789	0.175	0.09310	N	1	P	0.35923	0.528	B	0.36335	0.222	T	0.25257	-1.0137	9	0.02654	T	1	.	2.8031	0.05420	0.2045:0.4422:0.0:0.3533	.	132	Q494X3	ZN404_HUMAN	K	130	ENSP00000319479:E130K	ENSP00000319479:E130K	E	-	1	0	ZNF404	49069812	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-2.676000	0.00840	0.133000	0.18654	0.404000	0.27445	GAG	.	.	none		0.343	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
GPD1L	23171	hgsc.bcm.edu	37	3	32181761	32181761	+	Silent	SNP	C	C	T	rs9835387	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:32181761C>T	ENST00000282541.5	+	4	609	c.408C>T	c.(406-408)gaC>gaT	p.D136D		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	136					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						TCATTTCTGACATCATCCGTG	0.512													C|||	750	0.14976	0.2965	0.1182	5008	,	,		19949	0.002		0.1362	False		,,,				2504	0.1401				p.D136D		Atlas-SNP	.											.	GPD1L	25	.	0			c.C408T						PASS	.	C		1282,3124	437.6+/-345.0	178,926,1099	178.0	178.0	178.0		408	5.5	1.0	3	dbSNP_119	178	1193,7407	241.8+/-272.0	95,1003,3202	no	coding-synonymous	GPD1L	NM_015141.3		273,1929,4301	TT,TC,CC		13.8721,29.0967,19.0297		136/352	32181761	2475,10531	2203	4300	6503	SO:0001819	synonymous_variant	23171	exon4			TTCTGACATCATC	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.408C>T	3.37:g.32181761C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	162	70	0.432099	NM_015141	A8K9U3|Q14702|Q9BRM5	Silent	SNP	ENST00000282541.5	37	CCDS33729.1																																																																																			C|0.828;T|0.172	0.172	strong		0.512	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141	
ALK	238	hgsc.bcm.edu	37	2	29473982	29473982	+	Silent	SNP	G	G	A	rs56017149		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:29473982G>A	ENST00000389048.3	-	12	3099	c.2193C>T	c.(2191-2193)acC>acT	p.T731T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	731					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)	TGTAGGTGTCGGTGGCTGGCA	0.622			"""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																												p.T731T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,colon,carcinoma,0,1	ALK	533	1	0			c.C2193T						scavenged	.						42.0	41.0	41.0					2																	29473982		2203	4300	6503	SO:0001819	synonymous_variant	238	exon12	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGTGTCGGTGGCT	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.2193C>T	2.37:g.29473982G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	98	2	0.0204082	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			.	.	weak		0.622	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
CNTLN	54875	hgsc.bcm.edu	37	9	17135322	17135322	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:17135322A>G	ENST00000380647.3	+	1	343	c.259A>G	c.(259-261)Aga>Gga	p.R87G	CNTLN_ENST00000484374.1_3'UTR|CNTLN_ENST00000425824.1_Missense_Mutation_p.R87G|CNTLN_ENST00000380641.4_Missense_Mutation_p.R87G|CNTLN_ENST00000262360.5_Missense_Mutation_p.R87G			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	87					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)		CATGGGGTCCAGACGGCTAGA	0.652																																					p.R87G		Atlas-SNP	.											.	CNTLN	128	.	0			c.A259G						PASS	.						22.0	28.0	26.0					9																	17135322		1996	4163	6159	SO:0001583	missense	54875	exon1			GGGTCCAGACGGC	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.259A>G	9.37:g.17135322A>G	ENSP00000370021:p.Arg87Gly	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	49	12	0.244898	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.135748	0.37728	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360;ENST00000380641	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	5.4	-5.91	0.02269	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.41395	-0.9511	9	0.13470	T	0.59	.	2.1611	0.03825	0.2599:0.2501:0.3609:0.1291	.	87;87;87;87	C9J1F9;Q9NXG0-2;Q9NXG0-3;B1AMC8	.;.;.;.	G	87	ENSP00000370021:R87G;ENSP00000392798:R87G;ENSP00000262360:R87G;ENSP00000370015:R87G	ENSP00000262360:R87G	R	+	1	2	CNTLN	17125322	0.756000	0.28383	0.210000	0.23637	0.766000	0.43426	-0.298000	0.08265	-1.336000	0.02238	-0.478000	0.04885	AGA	.	.	none		0.652	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	
KIF27	55582	hgsc.bcm.edu	37	9	86504005	86504005	+	Missense_Mutation	SNP	C	C	T	rs13289566	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:86504005C>T	ENST00000297814.2	-	7	2116	c.1973G>A	c.(1972-1974)gGa>gAa	p.G658E	KIF27_ENST00000376347.1_Missense_Mutation_p.G49E|KIF27_ENST00000334204.2_Missense_Mutation_p.G658E|KIF27_ENST00000413982.1_Missense_Mutation_p.G658E	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	658					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						ATACCTAGTTCCAGATTTCTC	0.328													C|||	875	0.17472	0.2451	0.1657	5008	,	,		17277	0.002		0.2336	False		,,,				2504	0.2035				p.G658E		Atlas-SNP	.											.	KIF27	103	.	0			c.G1973A						PASS	.	C	GLU/GLY	1101,3303	368.1+/-318.5	137,827,1238	52.0	51.0	51.0		1973	0.4	0.7	9	dbSNP_121	51	1869,6725	310.1+/-309.7	191,1487,2619	no	missense	KIF27	NM_017576.1	98	328,2314,3857	TT,TC,CC		21.7477,25.0,22.8497	benign	658/1402	86504005	2970,10028	2202	4297	6499	SO:0001583	missense	55582	exon7			CTAGTTCCAGATT	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.1973G>A	9.37:g.86504005C>T	ENSP00000297814:p.Gly658Glu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	346	0.15842490842490842	110	0.22357723577235772	62	0.1712707182320442	0	0.0	174	0.22955145118733508	C	7.059	0.565938	0.13560	0.25	0.217477	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204;ENST00000376347	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	4.95	0.394	0.16299	.	1.657160	0.04144	N	0.320083	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	0.04013	0.001;0.0;0.001	T	0.16571	-1.0398	9	0.02654	T	1	.	1.4027	0.02274	0.1283:0.2012:0.2611:0.4094	rs13289566;rs57559061	658;658;658	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	E	658;658;658;49	ENSP00000297814:G658E;ENSP00000401688:G658E;ENSP00000333928:G658E;ENSP00000365525:G49E	ENSP00000297814:G658E	G	-	2	0	KIF27	85693825	0.638000	0.27225	0.703000	0.30354	0.951000	0.60555	0.075000	0.14686	0.094000	0.17404	0.557000	0.71058	GGA	C|0.798;T|0.202	0.202	strong		0.328	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
MAN2A1	4124	hgsc.bcm.edu	37	5	109110591	109110591	+	Silent	SNP	G	G	A	rs61735369	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:109110591G>A	ENST00000261483.4	+	8	2351	c.1299G>A	c.(1297-1299)acG>acA	p.T433T		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	433					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		GTGAATACACGGAATGGGATT	0.373													G|||	350	0.0698882	0.1452	0.0476	5008	,	,		14544	0.0377		0.0696	False		,,,				2504	0.0174				p.T433T		Atlas-SNP	.											.	MAN2A1	136	.	0			c.G1299A						PASS	.	G		503,3901	229.4+/-244.0	26,451,1725	73.0	74.0	74.0		1299	-3.2	0.0	5	dbSNP_129	74	519,8079	145.9+/-201.5	11,497,3791	no	coding-synonymous	MAN2A1	NM_002372.2		37,948,5516	AA,AG,GG		6.0363,11.4214,7.8603		433/1145	109110591	1022,11980	2202	4299	6501	SO:0001819	synonymous_variant	4124	exon8			ATACACGGAATGG		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.1299G>A	5.37:g.109110591G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	115	61	0.530435	NM_002372	Q16767	Silent	SNP	ENST00000261483.4	37	CCDS34209.1																																																																																			G|0.920;A|0.080	0.080	strong		0.373	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
PHACTR2	9749	hgsc.bcm.edu	37	6	144081768	144081768	+	Silent	SNP	C	C	A	rs2073215	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000305766.6_Intron|PHACTR2_ENST00000367582.3_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	44	0	0		WXS	Illumina HiSeq	Phase_I	44	16	0.363636	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	
PI4KA	5297	hgsc.bcm.edu	37	22	21065645	21065645	+	Silent	SNP	A	A	G	rs444310		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:21065645A>G	ENST00000572273.1	-	51	5963	c.5733T>C	c.(5731-5733)ggT>ggC	p.G1911G	PI4KA_ENST00000255882.6_Silent_p.G1969G|PI4KA_ENST00000414196.3_Silent_p.G721G			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1911	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.G1911G(1)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-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)			GGATGATATGACCCTTCTTGT	0.587																																					p.G1969G	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	1	Substitution - coding silent(1)	stomach(1)	c.T5907C						scavenged	.	G	,	1543,2565		564,415,1075	105.0	128.0	120.0		2163,5733	1.5	1.0	22	dbSNP_80	120	936,7236		280,376,3430	no	coding-synonymous,coding-synonymous	PI4KA	NM_002650.2,NM_058004.3	,	844,791,4505	GG,GA,AA		11.4537,37.5609,20.1873	,	721/855,1911/2045	21065645	2479,9801	2054	4086	6140	SO:0001819	synonymous_variant	5297	exon51			GATATGACCCTTC	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.5733T>C	22.37:g.21065645A>G		Somatic	776	6	0.00773196		WXS	Illumina HiSeq	Phase_I	412	22	0.0533981	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				A|1.000;|0.000	.	weak		0.587	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049939	69049939	+	Missense_Mutation	SNP	G	G	T	rs4241344	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:69049939G>T	ENST00000295381.3	+	10	2084	c.1665G>T	c.(1663-1665)agG>agT	p.R555S	ARHGAP25_ENST00000467265.1_Missense_Mutation_p.R516S|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.R249S|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.R549S|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.R548S|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.R556S	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	555			R -> S (in dbSNP:rs4241344). {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						CTTTGCAGAGGATGGTCCAAG	0.448													G|||	1332	0.265974	0.1725	0.3156	5008	,	,		20655	0.4435		0.1869	False		,,,				2504	0.2556				p.R556S		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.G1668T						PASS	.	G	SER/ARG,SER/ARG,SER/ARG,SER/ARG	758,3646	286.0+/-278.5	53,652,1497	70.0	78.0	75.0		1668,1647,1548,1644	3.5	0.7	2	dbSNP_111	75	1644,6956	282.4+/-295.5	170,1304,2826	yes	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	110,110,110,110	223,1956,4323	TT,TG,GG		19.1163,17.2116,18.4712	benign,benign,benign,benign	556/647,549/640,516/607,548/639	69049939	2402,10602	2202	4300	6502	SO:0001583	missense	9938	exon10			GCAGAGGATGGTC	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.1665G>T	2.37:g.69049939G>T	ENSP00000295381:p.Arg555Ser	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		554|554	0.25366300366300365|0.25366300366300365	78|78	0.15853658536585366|0.15853658536585366	109|109	0.3011049723756906|0.3011049723756906	224|224	0.3916083916083916|0.3916083916083916	143|143	0.18865435356200527|0.18865435356200527	G|G	2.826|2.826	-0.243736|-0.243736	0.05906|0.05906	0.172116|0.172116	0.191163|0.191163	ENSG00000163219|ENSG00000163219	ENST00000497259|ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844	.|T;T;T;T;T;T	.|0.38560	.|3.05;3.05;2.8;1.13;1.13;1.13	5.42|5.42	3.55|3.55	0.40652|0.40652	.|.	.|0.731496	.|0.14039	.|N	.|0.345562	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.26403|0.26403	P|P	0.976394|0.976394	.|B;B;B;B;B	.|0.06786	.|0.001;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.04013	.|0.001;0.0;0.0;0.0;0.0	T|T	0.43925|0.43925	-0.9361|-0.9361	4|9	.|0.07030	.|T	.|0.85	.|.	1.9238|1.9238	0.03313|0.03313	0.1885:0.154:0.4993:0.1582|0.1885:0.154:0.4993:0.1582	rs4241344;rs52800040;rs60408659;rs4241344|rs4241344;rs52800040;rs60408659;rs4241344	.|516;556;549;548;555	.|E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.|.;.;.;.;RHG25_HUMAN	V|S	415|555;556;516;548;549;549;540;249	.|ENSP00000295381:R555S;ENSP00000386911:R556S;ENSP00000420583:R516S;ENSP00000386863:R548S;ENSP00000386241:R549S;ENSP00000417467:R249S	.|ENSP00000295381:R555S	G|R	+|+	2|3	0|2	ARHGAP25|ARHGAP25	68903443|68903443	0.001000|0.001000	0.12720|0.12720	0.746000|0.746000	0.31095|0.31095	0.615000|0.615000	0.37417|0.37417	0.193000|0.193000	0.17116|0.17116	0.698000|0.698000	0.31739|0.31739	0.557000|0.557000	0.71058|0.71058	GGA|AGG	G|0.789;T|0.211	0.211	strong		0.448	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
NUP93	9688	hgsc.bcm.edu	37	16	56873495	56873495	+	Silent	SNP	C	C	T	rs1138295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:56873495C>T	ENST00000308159.5	+	20	2320	c.2199C>T	c.(2197-2199)gcC>gcT	p.A733A	NUP93_ENST00000569842.1_Silent_p.A733A|NUP93_ENST00000564887.1_Silent_p.A610A|NUP93_ENST00000542526.1_Silent_p.A610A	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	733					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)|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)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GAGTGGCTGCCTTCAGAAATT	0.448													C|||	1055	0.210663	0.2126	0.2305	5008	,	,		17354	0.3075		0.1501	False		,,,				2504	0.1564				p.A733A	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.C2199T						PASS	.	C	,,	838,3558	310.0+/-291.3	85,668,1445	113.0	108.0	110.0		1830,1830,2199	5.9	1.0	16	dbSNP_86	110	1330,7270	235.6+/-268.1	107,1116,3077	no	coding-synonymous,coding-synonymous,coding-synonymous	NUP93	NM_001242795.1,NM_001242796.1,NM_014669.4	,,	192,1784,4522	TT,TC,CC		15.4651,19.0628,16.6821	,,	610/697,610/697,733/820	56873495	2168,10828	2198	4300	6498	SO:0001819	synonymous_variant	9688	exon20			GGCTGCCTTCAGA	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.2199C>T	16.37:g.56873495C>T		Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	254	201	0.791339	NM_014669	B3KPQ8|Q14705	Silent	SNP	ENST00000308159.5	37	CCDS10769.1																																																																																			C|0.811;T|0.189	0.189	strong		0.448	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669	
IFNGR1	3459	hgsc.bcm.edu	37	6	137540423	137540423	+	Silent	SNP	C	C	T	rs17181471	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:137540423C>T	ENST00000367739.4	-	1	163	c.42G>A	c.(40-42)gtG>gtA	p.V14V	IFNGR1_ENST00000478333.1_5'UTR|IFNGR1_ENST00000543628.1_5'Flank|IFNGR1_ENST00000367735.2_5'UTR	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	14					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)	CAGCCCTGCTCACACCCTGCA	0.687													C|||	22	0.00439297	0.0015	0.0086	5008	,	,		14299	0.0		0.0119	False		,,,				2504	0.002				p.V14V		Atlas-SNP	.											.	IFNGR1	46	.	0			c.G42A						PASS	.	C		10,4392	15.5+/-35.6	0,10,2191	43.0	42.0	42.0		42	3.2	0.0	6	dbSNP_123	42	58,8542	32.8+/-85.7	0,58,4242	no	coding-synonymous	IFNGR1	NM_000416.2		0,68,6433	TT,TC,CC		0.6744,0.2272,0.523		14/490	137540423	68,12934	2201	4300	6501	SO:0001819	synonymous_variant	3459	exon1			CCTGCTCACACCC		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.42G>A	6.37:g.137540423C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	131	52	0.396947	NM_000416	B4DFT7|E1P587|Q53Y96	Silent	SNP	ENST00000367739.4	37	CCDS5185.1																																																																																			C|0.995;T|0.005	0.005	strong		0.687	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1		
ERMARD	55780	hgsc.bcm.edu	37	6	170176146	170176146	+	Missense_Mutation	SNP	G	G	A	rs41265401	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170176146G>A	ENST00000366773.3	+	15	1538	c.1505G>A	c.(1504-1506)cGt>cAt	p.R502H	ERMARD_ENST00000392095.4_Missense_Mutation_p.R376H|ERMARD_ENST00000366772.2_Missense_Mutation_p.R502H|ERMARD_ENST00000418781.3_Missense_Mutation_p.R502H|ERMARD_ENST00000588451.1_Missense_Mutation_p.R366H	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	502					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											GACTTGGATCGTCTTCCTACT	0.388													G|||	393	0.0784744	0.0764	0.0562	5008	,	,		21820	0.1022		0.0785	False		,,,				2504	0.0726				p.R502H		Atlas-SNP	.											.	C6orf70	63	.	0			c.G1505A						PASS	.	G	HIS/ARG	277,4129		7,263,1933	151.0	123.0	133.0		1505	-10.5	0.0	6	dbSNP_127	133	686,7914		30,626,3644	yes	missense	C6orf70	NM_018341.1	29	37,889,5577	AA,AG,GG		7.9767,6.2869,7.4043	benign	502/679	170176146	963,12043	2203	4300	6503	SO:0001583	missense	55780	exon15			TGGATCGTCTTCC	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1505G>A	6.37:g.170176146G>A	ENSP00000355735:p.Arg502His	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	143	54	0.377622	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	176	0.08058608058608059	27	0.054878048780487805	24	0.06629834254143646	65	0.11363636363636363	60	0.079155672823219	.	3.431	-0.116188	0.06881	0.062869	0.079767	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.42900	0.96;0.96	5.27	-10.5	0.00291	.	4.533170	0.00496	N	0.000154	T	0.04634	0.0126	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	0.31888	-0.9927	9	0.40728	T	0.16	.	12.4976	0.55937	0.1824:0.2637:0.5539:0.0	rs41265401;rs61747676	502;502;502	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	H	502;502;502;376;150	ENSP00000355735:R502H;ENSP00000375945:R376H	ENSP00000355733:R150H	R	+	2	0	C6orf70	169918071	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.948000	0.03897	-3.144000	0.00232	-1.533000	0.00918	CGT	G|0.925;A|0.075	0.075	strong		0.388	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786230	75786230	+	Silent	SNP	C	C	T	rs149559986		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:75786230C>T	ENST00000478296.1	-	4	2670	c.2394G>A	c.(2392-2394)agG>agA	p.R798R	ZNF717_ENST00000422325.1_Silent_p.R848R|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000400845.3_Silent_p.R841R			Q9BY31	ZN717_HUMAN	zinc finger protein 717	838					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)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						AGAAAGTTTTCCTACATTCAT	0.393																																					p.R848R		Atlas-SNP	.											ZNF717,NS,carcinoma,0,1	ZNF717	160	1	0			c.G2544A						scavenged	.						3.0	3.0	3.0					3																	75786230		442	1082	1524	SO:0001819	synonymous_variant	100131827	exon5			AGTTTTCCTACAT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.2394G>A	3.37:g.75786230C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_001128223		Silent	SNP	ENST00000478296.1	37																																																																																				C|0.620;T|0.380	0.380	strong		0.393	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
MUC16	94025	hgsc.bcm.edu	37	19	9071916	9071916	+	Missense_Mutation	SNP	G	G	A	rs35346115	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9071916G>A	ENST00000397910.4	-	3	15733	c.15530C>T	c.(15529-15531)aCt>aTt	p.T5177I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5179	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						AATGTTTGTAGTCTCAGAGGA	0.478													G|||	49	0.00978435	0.0008	0.0216	5008	,	,		20472	0.001		0.0268	False		,,,				2504	0.0051				p.T5177I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C15530T						PASS	.	G	ILE/THR	17,3971		0,17,1977	283.0	266.0	272.0		15530	0.6	0.0	19	dbSNP_126	272	253,8085		5,243,3921	yes	missense	MUC16	NM_024690.2	89	5,260,5898	AA,AG,GG		3.0343,0.4263,2.1905	probably-damaging	5177/14508	9071916	270,12056	1994	4169	6163	SO:0001583	missense	94025	exon3			TTTGTAGTCTCAG	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.15530C>T	19.37:g.9071916G>A	ENSP00000381008:p.Thr5177Ile	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	0	0.0	6	0.016574585635359115	1	0.0017482517482517483	21	0.027704485488126648	g	2.171	-0.389853	0.04932	0.004263	0.030343	ENSG00000181143	ENST00000397910	T	0.23147	1.92	1.65	0.563	0.17296	.	.	.	.	.	T	0.11281	0.0275	L	0.55481	1.735	.	.	.	D	0.65815	0.995	P	0.51945	0.685	T	0.24621	-1.0155	8	0.87932	D	0	.	4.0586	0.09827	0.2293:0.0:0.7707:0.0	rs35346115	5177	B5ME49	.	I	5177	ENSP00000381008:T5177I	ENSP00000381008:T5177I	T	-	2	0	MUC16	8932916	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.111000	0.03303	0.269000	0.21961	0.121000	0.15741	ACT	G|0.980;A|0.020	0.020	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
BMPR2	659	hgsc.bcm.edu	37	2	203421199	203421199	+	Silent	SNP	G	G	A	rs1061157	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:203421199G>A	ENST00000374580.4	+	12	3350	c.2811G>A	c.(2809-2811)agG>agA	p.R937R	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	937					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						GAGCACAGAGGCCTAATTCTC	0.483													G|||	583	0.116414	0.0045	0.1052	5008	,	,		19640	0.1042		0.1362	False		,,,				2504	0.2679				p.R937R		Atlas-SNP	.											.	BMPR2	142	.	0			c.G2811A						PASS	.	G		108,4298	82.4+/-120.9	3,102,2098	85.0	91.0	89.0		2811	4.4	1.0	2	dbSNP_86	89	1085,7515	226.4+/-262.1	57,971,3272	no	coding-synonymous	BMPR2	NM_001204.6		60,1073,5370	AA,AG,GG		12.6163,2.4512,9.1727		937/1039	203421199	1193,11813	2203	4300	6503	SO:0001819	synonymous_variant	659	exon12			ACAGAGGCCTAAT	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.2811G>A	2.37:g.203421199G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	35	30	0.857143	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Silent	SNP	ENST00000374580.4	37	CCDS33361.1																																																																																			G|0.907;A|0.093	0.093	strong		0.483	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	
RBM6	10180	hgsc.bcm.edu	37	3	50114515	50114515	+	Silent	SNP	C	C	T	rs7061	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:50114515C>T	ENST00000266022.4	+	21	3580	c.3321C>T	c.(3319-3321)taC>taT	p.Y1107Y	RBM6_ENST00000442092.1_Silent_p.Y585Y|RBM6_ENST00000443081.1_Silent_p.Y975Y|RBM6_ENST00000421682.1_Silent_p.Y103Y|RBM6_ENST00000422955.1_Silent_p.Y585Y|RBM6_ENST00000539992.1_Silent_p.Y449Y	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	1107					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)		ACGAGACTTACCGAGATGCTG	0.458													c|||	3741	0.747005	0.7458	0.6945	5008	,	,		15235	0.879		0.5686	False		,,,				2504	0.8333				p.Y1107Y		Atlas-SNP	.											.	RBM6	85	.	0			c.C3321T						PASS	.	T	,	3176,1230	424.2+/-340.4	1145,886,172	93.0	88.0	89.0		1755,3321	3.0	1.0	3	dbSNP_52	89	4903,3697	529.7+/-381.6	1369,2165,766	no	coding-synonymous,coding-synonymous	RBM6	NM_001167582.1,NM_005777.2	,	2514,3051,938	TT,TC,CC		42.9884,27.9165,37.8825	,	585/602,1107/1124	50114515	8079,4927	2203	4300	6503	SO:0001819	synonymous_variant	10180	exon21			GACTTACCGAGAT	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.3321C>T	3.37:g.50114515C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	118	51	0.432203	NM_005777	O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	37	CCDS2809.1																																																																																			C|0.329;T|0.671	0.671	strong		0.458	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
SFXN1	94081	hgsc.bcm.edu	37	5	174936038	174936038	+	Silent	SNP	A	A	G	rs35420613	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:174936038A>G	ENST00000321442.5	+	3	422	c.168A>G	c.(166-168)caA>caG	p.Q56Q	SFXN1_ENST00000502393.1_Silent_p.Q56Q	NM_022754.5	NP_073591.2	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	56					erythrocyte differentiation (GO:0030218)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(3)	15	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TTCTTAGGCAAGGAATTGTTC	0.373													A|||	257	0.0513179	0.0045	0.0994	5008	,	,		20639	0.0228		0.0706	False		,,,				2504	0.09				p.Q56Q		Atlas-SNP	.											.	SFXN1	23	.	0			c.A168G						PASS	.	A		55,4351	48.9+/-83.8	0,55,2148	118.0	117.0	118.0		168	5.2	1.0	5	dbSNP_126	118	634,7966	154.6+/-208.8	34,566,3700	no	coding-synonymous	SFXN1	NM_022754.5		34,621,5848	GG,GA,AA		7.3721,1.2483,5.2976		56/323	174936038	689,12317	2203	4300	6503	SO:0001819	synonymous_variant	94081	exon3			TAGGCAAGGAATT	AF327346	CCDS4394.1	5q35.3	2008-02-05			ENSG00000164466	ENSG00000164466		"""Sideroflexins"""	16085	protein-coding gene	gene with protein product		615569					Standard	NM_022754		Approved	FLJ12876	uc003mda.2	Q9H9B4	OTTHUMG00000130555	ENST00000321442.5:c.168A>G	5.37:g.174936038A>G		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	151	67	0.443709	NM_022754	B3KPW3|D3DQN2|Q9HA53	Silent	SNP	ENST00000321442.5	37	CCDS4394.1																																																																																			A|0.947;G|0.053	0.053	strong		0.373	SFXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252980.2	NM_022754	
RSPH3	83861	hgsc.bcm.edu	37	6	159407446	159407446	+	Missense_Mutation	SNP	C	C	T	rs34582178	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159407446C>T	ENST00000252655.1	-	3	827	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	RSPH3_ENST00000297262.3_Intron|RP1-111C20.4_ENST00000607391.1_RNA|RSPH3_ENST00000367069.2_Missense_Mutation_p.R71Q|RSPH3_ENST00000449822.1_Intron	NM_031924.4	NP_114130.3	Q86UC2	RSPH3_HUMAN	radial spoke 3 homolog (Chlamydomonas)	213			R -> Q (in dbSNP:rs34582178).					p.R213Q(1)		endometrium(3)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|skin(1)|stomach(7)	23		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.36e-16)|BRCA - Breast invasive adenocarcinoma(81;5.92e-06)		AGAATCAGGCCGTCCGAGCTA	0.433													T|||	1064	0.21246	0.0651	0.3746	5008	,	,		17667	0.3919		0.1034	False		,,,				2504	0.2239				p.R213Q		Atlas-SNP	.											RSPH3,NS,carcinoma,0,1	RSPH3	48	1	1	Substitution - Missense(1)	stomach(1)	c.G638A						PASS	.	T	GLN/ARG	404,4002	788.9+/-415.0	12,380,1811	173.0	150.0	158.0		638	4.5	0.9	6	dbSNP_126	158	926,7674	777.0+/-407.7	61,804,3435	yes	missense	RSPH3	NM_031924.4	43	73,1184,5246	TT,TC,CC		10.7674,9.1693,10.226	benign	213/561	159407446	1330,11676	2203	4300	6503	SO:0001583	missense	83861	exon3			TCAGGCCGTCCGA	AF353618	CCDS5260.1	6q25.3	2014-05-16	2008-07-04	2007-06-26	ENSG00000130363	ENSG00000130363			21054	protein-coding gene	gene with protein product		615876	"""radial spokehead-like 2"""	RSHL2		12477932	Standard	NM_031924		Approved	dJ111C20.1, RSP3	uc003qrx.3	Q86UC2	OTTHUMG00000015924	ENST00000252655.1:c.638G>A	6.37:g.159407446C>T	ENSP00000252655:p.Arg213Gln	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	217	106	0.488479	NM_031924	Q96LQ5|Q96LX2|Q9BX75	Missense_Mutation	SNP	ENST00000252655.1	37	CCDS5260.1	469	0.21474358974358973	33	0.06707317073170732	109	0.3011049723756906	244	0.42657342657342656	83	0.10949868073878628	T	1.013	-0.687310	0.03328	0.091693	0.107674	ENSG00000130363	ENST00000367069;ENST00000252655	T;T	0.15952	2.38;2.38	5.64	4.47	0.54385	.	0.266353	0.37483	N	0.002061	T	0.00906	0.0030	N	0.00280	-1.71	0.09310	P	0.9999999999999999	B	0.06786	0.001	B	0.04013	0.001	T	0.46442	-0.9191	9	0.02654	T	1	-22.7582	9.8258	0.40910	0.0:0.1457:0.0:0.8543	rs34582178	213	Q86UC2	RSPH3_HUMAN	Q	71;213	ENSP00000356036:R71Q;ENSP00000252655:R213Q	ENSP00000252655:R213Q	R	-	2	0	RSPH3	159327434	1.000000	0.71417	0.862000	0.33874	0.024000	0.10985	2.353000	0.44089	0.981000	0.38548	-0.269000	0.10298	CGG	C|0.861;T|0.139	0.139	strong		0.433	RSPH3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031924	
IGSF10	285313	hgsc.bcm.edu	37	3	151166422	151166422	+	Silent	SNP	C	C	T	rs6798252	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151166422C>T	ENST00000282466.3	-	4	1346	c.1347G>A	c.(1345-1347)caG>caA	p.Q449Q		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	449					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)			AGTACTGGATCTGTAATGTAC	0.433													C|||	3559	0.710663	0.7057	0.7089	5008	,	,		23053	0.7401		0.7356	False		,,,				2504	0.6626				p.Q449Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.G1347A						PASS	.	C		3099,1307	696.9+/-406.1	1084,931,188	159.0	143.0	149.0		1347	0.2	1.0	3	dbSNP_116	149	6211,2389	700.9+/-405.2	2250,1711,339	no	coding-synonymous	IGSF10	NM_178822.4		3334,2642,527	TT,TC,CC		27.7791,29.6641,28.4177		449/2624	151166422	9310,3696	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon4			CTGGATCTGTAAT	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.1347G>A	3.37:g.151166422C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			C|0.276;N|0.000	.	strong		0.433	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
ADCYAP1R1	117	hgsc.bcm.edu	37	7	31104520	31104520	+	Missense_Mutation	SNP	A	A	G	rs144472289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:31104520A>G	ENST00000304166.4	+	3	414	c.125A>G	c.(124-126)aAt>aGt	p.N42S	ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.N42S|ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.N42S|ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.N42S	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	42					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						CAGAGGGCCAATGAGCTGATG	0.557													A|||	10	0.00199681	0.0	0.0014	5008	,	,		21493	0.0		0.0089	False		,,,				2504	0.0				p.N42S	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.A125G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN,SER/ASN	1,4405	2.1+/-5.4	0,1,2202	81.0	70.0	74.0		125,125,125,125	4.4	1.0	7	dbSNP_134	74	42,8556	27.4+/-76.7	0,42,4257	yes	missense,missense,missense,missense	ADCYAP1R1	NM_001118.4,NM_001199635.1,NM_001199636.1,NM_001199637.1	46,46,46,46	0,43,6459	GG,GA,AA		0.4885,0.0227,0.3307	benign,benign,benign,benign	42/469,42/497,42/496,42/448	31104520	43,12961	2203	4299	6502	SO:0001583	missense	117	exon3			GGGCCAATGAGCT		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	242	protein-coding gene	gene with protein product	"""PACAP receptor 1"""	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.125A>G	7.37:g.31104520A>G	ENSP00000306620:p.Asn42Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	139	69	0.496403	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	37	CCDS5433.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	A	13.14	2.147275	0.37923	2.27E-4	0.004885	ENSG00000078549	ENST00000304166;ENST00000409363;ENST00000431811;ENST00000396211;ENST00000409489	T;T;T;T;T	0.52057	0.68;1.16;0.98;0.68;0.68	5.58	4.36	0.52297	GPCR, family 2, extracellular hormone receptor domain (1);	0.257434	0.36066	N	0.002816	T	0.21186	0.0510	N	0.22421	0.69	0.30532	N	0.767307	B;B;B;B;B	0.11235	0.004;0.002;0.004;0.001;0.004	B;B;B;B;B	0.15052	0.012;0.007;0.007;0.0;0.004	T	0.14952	-1.0454	10	0.09590	T	0.72	.	8.9845	0.35986	0.8131:0.1869:0.0:0.0	.	42;42;42;42;42	B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586	.;.;.;.;PACR_HUMAN	S	42	ENSP00000306620:N42S;ENSP00000387335:N42S;ENSP00000400893:N42S;ENSP00000379514:N42S;ENSP00000386395:N42S	ENSP00000306620:N42S	N	+	2	0	ADCYAP1R1	31071045	0.041000	0.20044	0.992000	0.48379	0.984000	0.73092	1.464000	0.35288	2.115000	0.64714	0.460000	0.39030	AAT	A|0.997;G|0.003	0.003	strong		0.557	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118	
TOX4	9878	hgsc.bcm.edu	37	14	21960969	21960969	+	Silent	SNP	G	G	A	rs7617	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21960969G>A	ENST00000405508.1	+	8	1470	c.1194G>A	c.(1192-1194)cgG>cgA	p.R398R	TOX4_ENST00000262709.3_Silent_p.R398R|TOX4_ENST00000448790.2_Silent_p.R375R			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	191	0	0		WXS	Illumina HiSeq	Phase_I	225	223	0.991111	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	
PSG8	440533	hgsc.bcm.edu	37	19	43269705	43269705	+	Missense_Mutation	SNP	G	G	A	rs71337226|rs34129574|rs7245423	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43269705G>A	ENST00000306511.4	-	1	126	c.29C>T	c.(28-30)aCa>aTa	p.T10I	PSG8_ENST00000401467.2_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.T10I|PSG8_ENST00000406636.3_Missense_Mutation_p.T10I	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	10				TQR -> MQH (in Ref. 2; CAH18672). {ECO:0000305}.		extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				GATGCGCTGTGTGCAGGGAGG	0.592													.|||	1787	0.356829	0.7315	0.2709	5008	,	,		17015	0.0913		0.3091	False		,,,				2504	0.2342				p.T10I		Atlas-SNP	.											.	PSG8	101	.	0			c.C29T						PASS	.	A	ILE/THR,ILE/THR,ILE/THR	1734,1288		659,416,436	121.0	121.0	121.0		29,29,29	-2.7	0.0	19	dbSNP_116	121	1261,4157		251,759,1699	no	missense,missense,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	89,89,89	910,1175,2135	AA,AG,GG		23.2743,42.6208,35.4858	probably-damaging,probably-damaging,probably-damaging	10/420,10/298,10/427	43269705	2995,5445	1511	2709	4220	SO:0001583	missense	440533	exon1			CGCTGTGTGCAGG	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.29C>T	19.37:g.43269705G>A	ENSP00000305005:p.Thr10Ile	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	599	0.2742673992673993	269	0.5467479674796748	100	0.27624309392265195	40	0.06993006993006994	190	0.25065963060686014	g	5.454	0.268926	0.10349	0.573792	0.232743	ENSG00000124467	ENST00000404209;ENST00000406636;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T;T	0.25749	2.18;1.78;3.3;2.19	1.35	-2.7	0.06004	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	D;P;P	0.60160	0.987;0.848;0.918	P;P;P	0.56960	0.81;0.521;0.558	T	0.46512	-0.9186	8	0.56958	D	0.05	.	1.4681	0.02410	0.1869:0.268:0.387:0.1581	rs7245423;rs57041720	10;10;10	Q9UQ74-2;Q9UQ74;A5PKV3	.;PSG8_HUMAN;.	I	10	ENSP00000385869:T10I;ENSP00000385081:T10I;ENSP00000386090:T10I;ENSP00000305005:T10I	ENSP00000305005:T10I	T	-	2	0	PSG8	47961545	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.768000	0.04715	-2.180000	0.00766	-1.139000	0.01908	ACA	G|0.635;A|0.365	0.365	strong		0.592	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
PCDHA4	56144	hgsc.bcm.edu	37	5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G	rs142480630	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA4_ENST00000356878.4_Missense_Mutation_p.L528V|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.L528V	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	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(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)			CCACGAGGAGCTAGAGCTGCT	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17618	0.0		0.0755	False		,,,				2504	0.0082				p.L528V		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	0			c.C1582G						PASS	.						70.0	75.0	74.0					5																	140188354		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGGAGCTAGAGC	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.1582C>G	5.37:g.140188354C>G	ENSP00000435300:p.Leu528Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	64	11	0.171875	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.577307	0.28092	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.51325	0.71;0.71;0.71	4.18	2.19	0.27852	Cadherin (5);Cadherin-like (1);	0.000000	0.28952	U	0.013601	T	0.34948	0.0915	N	0.25332	0.735	0.20764	N	0.999854	P;B;B	0.43662	0.814;0.101;0.207	B;B;B	0.43508	0.422;0.421;0.214	T	0.15150	-1.0447	10	0.51188	T	0.08	.	8.8809	0.35374	0.2588:0.4914:0.2498:0.0	.	528;528;528	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	V	528	ENSP00000423470:L528V;ENSP00000349344:L528V;ENSP00000435300:L528V	ENSP00000349344:L528V	L	+	1	2	PCDHA4	140168538	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-1.847000	0.01675	0.874000	0.35823	0.580000	0.79431	CTA	C|0.999;G|0.001	0.001	weak		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
TTN	7273	hgsc.bcm.edu	37	2	179462494	179462494	+	Silent	SNP	A	A	G	rs35833641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:179462494A>G	ENST00000591111.1	-	244	52616	c.52392T>C	c.(52390-52392)caT>caC	p.H17464H	TTN_ENST00000589042.1_Silent_p.H19105H|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000342992.6_Silent_p.H16537H|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000460472.2_Silent_p.H10040H|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Silent_p.H10165H|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Silent_p.H10232H			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	177	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	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	
PKNOX2	63876	hgsc.bcm.edu	37	11	125280737	125280737	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125280737A>C	ENST00000298282.9	+	9	1052	c.781A>C	c.(781-783)Atc>Ctc	p.I261L	PKNOX2_ENST00000542175.1_Missense_Mutation_p.I197L|PKNOX2_ENST00000530517.1_3'UTR	NM_022062.2	NP_071345.2	Q96KN3	PKNX2_HUMAN	PBX/knotted 1 homeobox 2	261					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)		CACCCAAGCAATCCCCCAGGG	0.562																																					p.I261L		Atlas-SNP	.											PKNOX2,caecum,carcinoma,-1,1	PKNOX2	60	1	0			c.A781C						scavenged	.						102.0	101.0	101.0					11																	125280737		2020	4185	6205	SO:0001583	missense	63876	exon9			CAAGCAATCCCCC	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.781A>C	11.37:g.125280737A>C	ENSP00000298282:p.Ile261Leu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	195	3	0.0153846	NM_022062	B7Z5I5|F5GZ15|Q63HL6|Q86XD1	Missense_Mutation	SNP	ENST00000298282.9	37	CCDS41730.1	.	.	.	.	.	.	.	.	.	.	A	7.457	0.643961	0.14451	.	.	ENSG00000165495	ENST00000530517;ENST00000531116;ENST00000298282;ENST00000542175;ENST00000535518	D;D;D;D	0.83419	-1.71;-1.71;-1.72;-1.71	5.52	5.52	0.82312	.	0.061076	0.64402	D	0.000003	T	0.65154	0.2664	N	0.04508	-0.205	0.46416	D	0.999038	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.001	T	0.62393	-0.6864	10	0.09843	T	0.71	-16.4441	15.31	0.74023	1.0:0.0:0.0:0.0	.	197;261	F5GZ15;Q96KN3	.;PKNX2_HUMAN	L	232;232;261;197;249	ENSP00000434732:I232L;ENSP00000433971:I232L;ENSP00000298282:I261L;ENSP00000441470:I197L	ENSP00000298282:I261L	I	+	1	0	PKNOX2	124785947	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.672000	0.46850	2.091000	0.63221	0.533000	0.62120	ATC	.	.	none		0.562	PKNOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386866.3		
SFRP2	6423	hgsc.bcm.edu	37	4	154709854	154709854	+	Missense_Mutation	SNP	G	G	A	rs386680891|rs4643790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:154709854G>A	ENST00000274063.4	-	1	418	c.134C>T	c.(133-135)gCc>gTc	p.A45V		NM_003013.2	NP_003004.1	Q96HF1	SFRP2_HUMAN	secreted frizzled-related protein 2	45	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		A -> V (in dbSNP:rs4643790). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		bone morphogenesis (GO:0060349)|brain development (GO:0007420)|cardiac left ventricle morphogenesis (GO:0003214)|cell-cell signaling (GO:0007267)|cellular response to extracellular stimulus (GO:0031668)|cellular response to X-ray (GO:0071481)|chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|convergent extension involved in axis elongation (GO:0060028)|digestive tract morphogenesis (GO:0048546)|embryonic digit morphogenesis (GO:0042733)|gonad development (GO:0008406)|hematopoietic stem cell proliferation (GO:0071425)|male gonad development (GO:0008584)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell growth (GO:0030308)|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)|negative regulation of dermatome development (GO:0061185)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of gene expression (GO:0010629)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of planar cell polarity pathway involved in axis elongation (GO:2000041)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-anal tail morphogenesis (GO:0036342)|regulation of stem cell division (GO:2000035)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|sclerotome development (GO:0061056)|vasculature development (GO:0001944)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endopeptidase activator activity (GO:0061133)|fibronectin binding (GO:0001968)|integrin binding (GO:0005178)|metalloenzyme activator activity (GO:0010577)|PDZ domain binding (GO:0030165)|receptor agonist activity (GO:0048018)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(1)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	16	all_hematologic(180;0.093)	Renal(120;0.117)				CTGCAGGTTGGCAGGGATGGG	0.647													G|||	748	0.149361	0.2784	0.1066	5008	,	,		15766	0.005		0.1879	False		,,,				2504	0.1145				p.A45V		Atlas-SNP	.											SFRP2,NS,carcinoma,-1,1	SFRP2	45	1	0			c.C134T						PASS	.	G	VAL/ALA	1167,3239	379.9+/-323.5	147,873,1183	57.0	62.0	60.0		134	4.6	1.0	4	dbSNP_111	60	1580,7020	267.1+/-287.1	152,1276,2872	yes	missense	SFRP2	NM_003013.2	64	299,2149,4055	AA,AG,GG		18.3721,26.4866,21.121	possibly-damaging	45/296	154709854	2747,10259	2203	4300	6503	SO:0001583	missense	6423	exon1			AGGTTGGCAGGGA	AF017986	CCDS34082.1	4q31.3	2008-08-29			ENSG00000145423	ENSG00000145423		"""Secreted frizzled-related proteins"""	10777	protein-coding gene	gene with protein product		604157				9391078	Standard	NM_003013		Approved	SARP1, SDF-5, FRP-2	uc003inv.1	Q96HF1	OTTHUMG00000161559	ENST00000274063.4:c.134C>T	4.37:g.154709854G>A	ENSP00000274063:p.Ala45Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	82	78	0.951219	NM_003013	B3KQR2|O14778|Q9HAP5	Missense_Mutation	SNP	ENST00000274063.4	37	CCDS34082.1	340	0.15567765567765568	150	0.3048780487804878	46	0.1270718232044199	3	0.005244755244755245	141	0.18601583113456466	G	14.96	2.692402	0.48202	0.264866	0.183721	ENSG00000145423	ENST00000274063	T	0.72167	-0.63	4.63	4.63	0.57726	Frizzled domain (5);	0.049068	0.85682	D	0.000000	T	0.00012	0.0000	N	0.25201	0.72	0.09310	P	0.999999385125	B	0.15473	0.013	B	0.22152	0.038	T	0.05178	-1.0901	9	0.25751	T	0.34	.	17.8889	0.88865	0.0:0.0:1.0:0.0	rs4643790;rs17850362;rs4643790	45	Q96HF1	SFRP2_HUMAN	V	45	ENSP00000274063:A45V	ENSP00000274063:A45V	A	-	2	0	SFRP2	154929304	1.000000	0.71417	0.989000	0.46669	0.955000	0.61496	5.407000	0.66363	2.288000	0.76882	0.650000	0.86243	GCC	G|0.806;A|0.194	0.194	strong		0.647	SFRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365296.1		
CAMK2B	816	hgsc.bcm.edu	37	7	44282928	44282928	+	Silent	SNP	G	G	A	rs17172630	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:44282928G>A	ENST00000395749.2	-	8	598	c.522C>T	c.(520-522)ttC>ttT	p.F174F	CAMK2B_ENST00000395747.2_Silent_p.F174F|CAMK2B_ENST00000502837.2_Silent_p.F45F|CAMK2B_ENST00000347193.4_Silent_p.F174F|CAMK2B_ENST00000440254.2_Silent_p.F174F|CAMK2B_ENST00000353625.4_Silent_p.F174F|CAMK2B_ENST00000346990.4_Silent_p.F174F|CAMK2B_ENST00000457475.1_Silent_p.F174F|CAMK2B_ENST00000358707.3_Silent_p.F174F|CAMK2B_ENST00000258682.6_Silent_p.F174F|CAMK2B_ENST00000350811.3_Silent_p.F174F	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	174	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						GTGTGCCAGCGAAACCTAGAG	0.617													.|||	278	0.0555112	0.0023	0.0331	5008	,	,		18355	0.0675		0.0726	False		,,,				2504	0.1135				p.F174F		Atlas-SNP	.											CAMK2B,NS,carcinoma,0,1	CAMK2B	56	1	0			c.C522T						PASS	.	G	,,,,,,,	63,4343	59.3+/-96.0	0,63,2140	97.0	90.0	92.0		522,522,522,522,522,522,522,522	-0.7	0.8	7	dbSNP_123	92	707,7893	173.2+/-223.7	29,649,3622	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	,,,,,,,	29,712,5762	AA,AG,GG		8.2209,1.4299,5.9203	,,,,,,,	174/667,174/543,174/519,174/518,174/504,174/493,174/480,174/450	44282928	770,12236	2203	4300	6503	SO:0001819	synonymous_variant	816	exon8			GCCAGCGAAACCT	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.522C>T	7.37:g.44282928G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	141	41	0.29078	NM_172081	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|0.945;A|0.055	0.055	strong		0.617	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
TWF1	5756	hgsc.bcm.edu	37	12	44191625	44191625	+	Silent	SNP	G	G	A	rs12829856	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:44191625G>A	ENST00000395510.2	-	6	624	c.495C>T	c.(493-495)gaC>gaT	p.D165D	TWF1_ENST00000548315.1_Silent_p.D172D|TWF1_ENST00000552521.1_Silent_p.D67D|TWF1_ENST00000325127.4_Silent_p.D199D	NM_001242397.1|NM_002822.4	NP_001229326.1|NP_002813.3	Q12792	TWF1_HUMAN	twinfilin actin-binding protein 1	165					barbed-end actin filament capping (GO:0051016)|negative regulation of actin filament polymerization (GO:0030837)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of actin phosphorylation (GO:0043538)|sequestering of actin monomers (GO:0042989)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|ruffle membrane (GO:0032587)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|stomach(1)	14	all_cancers(12;0.00125)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.0474)		CCACACCCACGTCAGTCTGTA	0.378													G|||	491	0.0980431	0.1687	0.0677	5008	,	,		17574	0.0863		0.0964	False		,,,				2504	0.0378				p.D172D		Atlas-SNP	.											.	TWF1	37	.	0			c.C516T						PASS	.	G	,	607,3799	265.3+/-266.6	32,543,1628	99.0	95.0	96.0		516,495	-3.5	1.0	12	dbSNP_121	96	802,7798	188.0+/-235.1	26,750,3524	yes	coding-synonymous,coding-synonymous	TWF1	NM_001242397.1,NM_002822.4	,	58,1293,5152	AA,AG,GG		9.3256,13.7767,10.8335	,	172/358,165/351	44191625	1409,11597	2203	4300	6503	SO:0001819	synonymous_variant	5756	exon7			ACCCACGTCAGTC	U02680	CCDS31780.1, CCDS31780.2, CCDS55818.1	12q12	2013-04-25	2013-04-25	2006-11-13					9620	protein-coding gene	gene with protein product		610932	"""protein tyrosine kinase 9"", ""PTK9 protein tyrosine kinase 9"", ""twinfilin, actin-binding protein, homolog 1 (Drosophila)"""	PTK9		7507208	Standard	NM_002822		Approved	A6	uc001rob.3	Q12792		ENST00000395510.2:c.495C>T	12.37:g.44191625G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	19	0.351852	NM_001242397	A8K5A8|B3KXS6|B4DLX9|Q59G07|Q5U0B1|Q6FHJ1|Q6FHL6|Q6NUK9|Q86XL6|Q8TCD3	Silent	SNP	ENST00000395510.2	37	CCDS31780.2																																																																																			G|0.896;A|0.104	0.104	strong		0.378	TWF1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403956.1	NM_002822	
CRTAP	10491	hgsc.bcm.edu	37	3	33174156	33174156	+	Silent	SNP	T	T	G	rs1135127	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:33174156T>G	ENST00000320954.6	+	5	1131	c.1032T>G	c.(1030-1032)acT>acG	p.T344T	CRTAP_ENST00000449224.1_Silent_p.T301T	NM_006371.4	NP_006362.1	O75718	CRTAP_HUMAN	cartilage associated protein	344					chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation to 3-hydroxy-L-proline (GO:0018400)|protein stabilization (GO:0050821)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|macromolecular complex (GO:0032991)|proteinaceous extracellular matrix (GO:0005578)	protein complex binding (GO:0032403)	p.T344T(1)		breast(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9						ACAGGGACACTTGGGGCCTCT	0.522													T|||	1470	0.29353	0.2451	0.268	5008	,	,		18251	0.1548		0.4354	False		,,,				2504	0.3742				p.T344T		Atlas-SNP	.											CRTAP,NS,carcinoma,0,1	CRTAP	16	1	1	Substitution - coding silent(1)	stomach(1)	c.T1032G						PASS	.	T		1168,3238	411.5+/-335.8	160,848,1195	143.0	126.0	132.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1032	1.5	1.0	3	dbSNP_86	132	3831,4769	539.1+/-383.5	873,2085,1342	no	coding-synonymous	CRTAP	NM_006371.4		1033,2933,2537	GG,GT,TT		44.5465,26.5093,38.4361		344/402	33174156	4999,8007	2203	4300	6503	SO:0001819	synonymous_variant	10491	exon5			GGACACTTGGGGC	AJ006470	CCDS2657.1	3p22	2014-09-17			ENSG00000170275	ENSG00000170275			2379	protein-coding gene	gene with protein product	"""leprecan-like 3"""	605497				9217321, 10429950	Standard	NM_006371		Approved	CASP, LEPREL3	uc003cfl.4	O75718	OTTHUMG00000130746	ENST00000320954.6:c.1032T>G	3.37:g.33174156T>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	168	84	0.5	NM_006371	B2RBL6	Silent	SNP	ENST00000320954.6	37	CCDS2657.1																																																																																			T|0.645;G|0.355	0.355	strong		0.522	CRTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253246.3		
TG	7038	hgsc.bcm.edu	37	8	134108546	134108546	+	Missense_Mutation	SNP	T	T	C	rs2069569	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:134108546T>C	ENST00000220616.4	+	43	7541	c.7501T>C	c.(7501-7503)Tgg>Cgg	p.W2501R	SLA_ENST00000517648.1_Intron|SLA_ENST00000395352.3_Intron|SLA_ENST00000524345.1_Intron|SLA_ENST00000338087.5_Intron|TG_ENST00000519543.1_Missense_Mutation_p.W634R|TG_ENST00000542445.1_Missense_Mutation_p.W871R|TG_ENST00000377869.1_Missense_Mutation_p.W2444R|SLA_ENST00000518565.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2501			W -> R (in dbSNP:rs2069569). {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)				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)		GAGGTCTTTATGGGTAGAGGT	0.587													C|||	2616	0.522364	0.8275	0.5086	5008	,	,		19240	0.2302		0.5328	False		,,,				2504	0.41				p.W2501R		Atlas-SNP	.											.	TG	416	.	0			c.T7501C						PASS	.	C	,,ARG/TRP	3462,944	362.9+/-316.3	1362,738,103	158.0	154.0	156.0		,,7501	2.0	0.0	8	dbSNP_96	156	4533,4067	560.0+/-387.5	1215,2103,982	yes	intron,intron,missense	SLA,TG	NM_001045556.2,NM_001045557.2,NM_003235.4	,,101	2577,2841,1085	CC,CT,TT		47.2907,21.4253,38.5284	,,benign	,,2501/2769	134108546	7995,5011	2203	4300	6503	SO:0001583	missense	7038	exon43			TCTTTATGGGTAG	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.7501T>C	8.37:g.134108546T>C	ENSP00000220616:p.Trp2501Arg	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	192	118	0.614583	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	1131|1131	0.5178571428571429|0.5178571428571429	412|412	0.8373983739837398|0.8373983739837398	192|192	0.5303867403314917|0.5303867403314917	122|122	0.21328671328671328|0.21328671328671328	405|405	0.5343007915567283|0.5343007915567283	C|C	0.017|0.017	-1.494739|-1.494739	0.01009|0.01009	0.785747|0.785747	0.527093|0.527093	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.66280	.|-0.2;-0.2;-0.2;-0.2	5.26|5.26	2.0|2.0	0.26442|0.26442	.|Carboxylesterase, type B (1);	.|0.795765	.|0.10645	.|N	.|0.650544	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01242|0.01242	-0.935|-0.935	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	0.29882|0.29882	-0.9997|-0.9997	4|9	.|0.28530	.|T	.|0.3	.|.	5.2901|5.2901	0.15721|0.15721	0.293:0.5391:0.0:0.168|0.293:0.5391:0.0:0.168	rs56541861;rs59673778|rs56541861;rs59673778	.|634;871;2501	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	T|R	956|2444;1307;2501;871;634	.|ENSP00000367100:W2444R;ENSP00000220616:W2501R;ENSP00000441693:W871R;ENSP00000430430:W634R	.|ENSP00000220616:W2501R	M|W	+|+	2|1	0|0	TG|TG	134177728|134177728	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.018000|-0.018000	0.12568|0.12568	0.197000|0.197000	0.20387|0.20387	-0.716000|-0.716000	0.03619|0.03619	ATG|TGG	C|0.598;N|0.002	0.598	strong		0.587	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
EVC2	132884	hgsc.bcm.edu	37	4	5642274	5642274	+	Silent	SNP	T	T	C	rs13131655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:5642274T>C	ENST00000344408.5	-	10	1490	c.1437A>G	c.(1435-1437)gaA>gaG	p.E479E	EVC2_ENST00000310917.2_Silent_p.E399E|EVC2_ENST00000344938.1_Silent_p.E479E	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	211	0	0		WXS	Illumina HiSeq	Phase_I	192	74	0.385417	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	
ABI3BP	25890	hgsc.bcm.edu	37	3	100617680	100617680	+	Silent	SNP	C	C	T	rs2245370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:100617680C>T	ENST00000284322.5	-	4	517	c.408G>A	c.(406-408)tcG>tcA	p.S136S	ABI3BP_ENST00000495063.1_Silent_p.S136S|ABI3BP_ENST00000532144.1_Intron|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	109	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	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		
CDH5	1003	hgsc.bcm.edu	37	16	66432381	66432381	+	Missense_Mutation	SNP	T	T	C	rs16956504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	132	0	0		WXS	Illumina HiSeq	Phase_I	96	78	0.8125	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	
SH2D4B	387694	hgsc.bcm.edu	37	10	82363404	82363404	+	Missense_Mutation	SNP	A	A	G	rs7075840	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:82363404A>G	ENST00000470604.2	+	5	710	c.710A>G	c.(709-711)cAc>cGc	p.H237R	SH2D4B_ENST00000339284.2_Missense_Mutation_p.H238R|SH2D4B_ENST00000313455.4_Missense_Mutation_p.H189R			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						PASS	.	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	129	0	0		WXS	Illumina HiSeq	Phase_I	98	20	0.204082	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	
XIRP2	129446	hgsc.bcm.edu	37	2	168103925	168103925	+	Missense_Mutation	SNP	A	A	G	rs7607246	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168103925A>G	ENST00000409195.1	+	9	6112	c.6023A>G	c.(6022-6024)aAt>aGt	p.N2008S	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.N1786S|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.N2008S	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1833					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						TGCCATGGCAATTTAGTAGAA	0.453													A|||	865	0.172724	0.2882	0.1196	5008	,	,		18614	0.12		0.1123	False		,,,				2504	0.1708				p.N2008S		Atlas-SNP	.											.	XIRP2	914	.	0			c.A6023G						PASS	.	A	,,,SER/ASN,SER/ASN	965,2753		134,697,1028	49.0	46.0	47.0		,,,6023,5357	0.6	0.0	2	dbSNP_116	47	799,7383		42,715,3334	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,46,46	176,1412,4362	GG,GA,AA		9.7653,25.9548,14.8235	,,,benign,benign	,,,2008/3550,1786/3328	168103925	1764,10136	1859	4091	5950	SO:0001583	missense	129446	exon9			ATGGCAATTTAGT	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.6023A>G	2.37:g.168103925A>G	ENSP00000386840:p.Asn2008Ser	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	195	100	0.512821	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	353	0.16163003663003664	151	0.30691056910569103	42	0.11602209944751381	72	0.1258741258741259	88	0.11609498680738786	A	0.005	-2.172963	0.00312	0.259548	0.097653	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02280	4.36;4.36;4.37	5.31	0.559	0.17272	.	1.282890	0.04902	N	0.451569	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.001	T	0.42982	-0.9419	9	0.06365	T	0.9	-0.0303	1.6411	0.02753	0.3781:0.3315:0.1676:0.1227	rs7607246;rs57219008;rs7607246	1833;1833;1786	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	2008;2008;1786	ENSP00000386840:N2008S;ENSP00000295237:N2008S;ENSP00000387255:N1786S	ENSP00000295237:N2008S	N	+	2	0	XIRP2	167812171	0.003000	0.15002	0.000000	0.03702	0.029000	0.11900	0.881000	0.28173	0.080000	0.16959	0.528000	0.53228	AAT	A|0.837;G|0.163	0.163	strong		0.453	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167463	140167463	+	Silent	SNP	C	C	T	rs3733710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	119	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	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	
KIAA0226	9711	hgsc.bcm.edu	37	3	197408085	197408085	+	Missense_Mutation	SNP	A	A	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:197408085A>C	ENST00000296343.5	-	16	2344	c.2345T>G	c.(2344-2346)aTt>aGt	p.I782S	KIAA0226_ENST00000389665.5_Missense_Mutation_p.I807S|KIAA0226_ENST00000273582.5_Missense_Mutation_p.I737S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	782					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)		CCAGATCTTAATGAGCAGGTC	0.517																																					p.I782S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.T2345G						PASS	.						149.0	144.0	145.0					3																	197408085		2034	4226	6260	SO:0001583	missense	9711	exon16			ATCTTAATGAGCA	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.2345T>G	3.37:g.197408085A>C	ENSP00000296343:p.Ile782Ser	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	1.156|1.156|1.156	-0.645279|-0.645279|-0.645279	0.03531|0.03531|0.03531	.|.|.	.|.|.	ENSG00000145016|ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000273582;ENST00000296343;ENST00000389665|ENST00000415452	.|.|.	.|.|.	.|.|.	4.55|4.55|4.55	0.842|0.842|0.842	0.18927|0.18927|0.18927	.|.|.	.|0.449024|.	.|0.23137|.	.|N|.	.|0.051520|.	T|T|T	0.07052|0.07052|0.07052	0.0179|0.0179|0.0179	N|N|N	0.00413|0.00413|0.00413	-1.525|-1.525|-1.525	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|B;B;B|.	.|0.06786|.	.|0.001;0.0;0.001|.	.|B;B;B|.	.|0.10450|.	.|0.003;0.0;0.005|.	T|T|T	0.39035|0.39035|0.39035	-0.9633|-0.9633|-0.9633	5|9|5	.|0.07990|.	.|T|.	.|0.79|.	.|.|.	5.7617|5.7617|5.7617	0.18203|0.18203|0.18203	0.394:0.4484:0.1575:0.0|0.394:0.4484:0.1575:0.0|0.394:0.4484:0.1575:0.0	.|.|.	.|807;737;782|.	.|Q92622-3;Q92622-2;Q92622|.	.|.;.;RUBIC_HUMAN|.	Q|S|V	743|737;782;807|566	.|.|.	.|ENSP00000273582:I737S|.	H|I|L	-|-|-	3|2|1	2|0|2	KIAA0226|KIAA0226|KIAA0226	198892482|198892482|198892482	0.950000|0.950000|0.950000	0.32346|0.32346|0.32346	0.220000|0.220000|0.220000	0.23810|0.23810|0.23810	0.992000|0.992000|0.992000	0.81027|0.81027|0.81027	1.068000|1.068000|1.068000	0.30629|0.30629|0.30629	0.353000|0.353000|0.353000	0.24079|0.24079|0.24079	0.454000|0.454000|0.454000	0.30748|0.30748|0.30748	CAT|ATT|TTA	.	.	none		0.517	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
ASB6	140459	hgsc.bcm.edu	37	9	132401753	132401753	+	Silent	SNP	G	G	A	rs144137235		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:132401753G>A	ENST00000277458.4	-	3	495	c.330C>T	c.(328-330)gcC>gcT	p.A110A	ASB6_ENST00000450050.2_Silent_p.A31A|RP11-483H20.4_ENST00000455074.1_RNA|ASB6_ENST00000277459.4_Silent_p.A110A	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	110					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				NS(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	15		Ovarian(14;0.00556)				TCCGCAGGACGGCGATGTGCA	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		18818	0.0		0.001	False		,,,				2504	0.0				p.A110A		Atlas-SNP	.											.	ASB6	31	.	0			c.C330T						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	55.0	53.0	54.0		330,330,330	-7.5	0.4	9	dbSNP_134	54	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ASB6	NM_001202403.1,NM_017873.3,NM_177999.2	,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,	110/393,110/422,110/198	132401753	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	140459	exon3			CAGGACGGCGATG		CCDS6924.1, CCDS6925.1, CCDS75919.1	9q34.13	2013-01-10	2011-01-25		ENSG00000148331	ENSG00000148331		"""Ankyrin repeat domain containing"""	17181	protein-coding gene	gene with protein product		615051	"""ankyrin repeat and SOCS box-containing 6"""				Standard	NM_017873		Approved		uc004byf.2	Q9NWX5	OTTHUMG00000020787	ENST00000277458.4:c.330C>T	9.37:g.132401753G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_017873	Q5SZB7|Q9BV15	Silent	SNP	ENST00000277458.4	37	CCDS6924.1																																																																																			G|0.999;A|0.001	0.001	strong		0.607	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873	
ZFP28	140612	hgsc.bcm.edu	37	19	57066013	57066013	+	Missense_Mutation	SNP	C	C	T	rs10409531	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:57066013C>T	ENST00000301318.3	+	8	1930	c.1859C>T	c.(1858-1860)gCg>gTg	p.A620V	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	620			A -> V (in dbSNP:rs10409531).		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.A620V(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)		TTTGAATGTGCGGAGTGTGGA	0.428													C|||	2048	0.408946	0.5953	0.304	5008	,	,		20994	0.2986		0.3509	False		,,,				2504	0.4049				p.A620V	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											ZFP28,NS,carcinoma,0,1	ZFP28	99	1	1	Substitution - Missense(1)	stomach(1)	c.C1859T						scavenged	.	C	VAL/ALA	2432,1974	616.5+/-392.8	666,1100,437	97.0	107.0	103.0		1859	0.9	1.0	19	dbSNP_119	103	2867,5733	449.6+/-362.1	497,1873,1930	yes	missense	ZFP28	NM_020828.1	64	1163,2973,2367	TT,TC,CC		33.3372,44.8025,40.7427	benign	620/869	57066013	5299,7707	2203	4300	6503	SO:0001583	missense	140612	exon8			AATGTGCGGAGTG		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.1859C>T	19.37:g.57066013C>T	ENSP00000301318:p.Ala620Val	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	150	69	0.46	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	818	0.37454212454212454	284	0.5772357723577236	112	0.30939226519337015	160	0.27972027972027974	262	0.34564643799472294	C	11.19	1.566773	0.28003	0.551975	0.333372	ENSG00000196867	ENST00000301318	T	0.07688	3.17	4.23	0.896	0.19253	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.303860	0.23997	N	0.042507	T	0.00012	0.0000	N	0.17872	0.535	0.58432	P	4.000000000004E-6	B	0.29909	0.261	B	0.31614	0.133	T	0.26430	-1.0103	9	0.44086	T	0.13	.	6.5728	0.22549	0.1344:0.5349:0.3307:0.0	rs10409531;rs17305444;rs52820939;rs56805806;rs10409531	620	Q8NHY6	ZFP28_HUMAN	V	620	ENSP00000301318:A620V	ENSP00000301318:A620V	A	+	2	0	ZFP28	61757825	0.000000	0.05858	0.988000	0.46212	0.984000	0.73092	-1.939000	0.01545	0.536000	0.28733	-0.235000	0.12190	GCG	C|0.594;T|0.406	0.406	strong		0.428	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
COQ7	10229	hgsc.bcm.edu	37	16	19085298	19085298	+	Missense_Mutation	SNP	C	C	T	rs11074359	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:19085298C>T	ENST00000321998.5	+	3	374	c.308C>T	c.(307-309)aCg>aTg	p.T103M	COQ7_ENST00000569127.1_Missense_Mutation_p.T80M|COQ7_ENST00000568985.1_Missense_Mutation_p.T103M|COQ7_ENST00000544894.2_Missense_Mutation_p.T65M	NM_016138.4	NP_057222.2	Q99807	COQ7_HUMAN	coenzyme Q7 homolog, ubiquinone (yeast)	103	2 X approximate tandem repeats.		T -> M (in dbSNP:rs11074359). {ECO:0000269|PubMed:10373327, ECO:0000269|PubMed:10501970, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9020081}.		age-dependent response to oxidative stress (GO:0001306)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|in utero embryonic development (GO:0001701)|mitochondrial ATP synthesis coupled electron transport (GO:0042775)|mitochondrion morphogenesis (GO:0070584)|neural tube formation (GO:0001841)|neurogenesis (GO:0022008)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|large_intestine(1)|lung(3)|prostate(1)|skin(3)|urinary_tract(1)	10						TTGATGGTTACGTTCAGGGTC	0.448													C|||	2878	0.574681	0.2655	0.6196	5008	,	,		19214	0.8145		0.6461	False		,,,				2504	0.6401				p.T103M		Atlas-SNP	.											.	COQ7	16	.	0			c.C308T						PASS	.	C	MET/THR,MET/THR	1489,2905	475.2+/-357.2	229,1031,937	125.0	104.0	111.0		194,308	5.9	0.3	16	dbSNP_120	111	5496,3104	657.7+/-401.5	1773,1950,577	yes	missense,missense	COQ7	NM_001190983.1,NM_016138.4	81,81	2002,2981,1514	TT,TC,CC		36.093,33.8871,46.2444	possibly-damaging,possibly-damaging	65/180,103/218	19085298	6985,6009	2197	4300	6497	SO:0001583	missense	10229	exon3			TGGTTACGTTCAG	U81276	CCDS10574.1, CCDS53993.1	16p12.3	2008-05-14	2001-11-28		ENSG00000167186	ENSG00000167186			2244	protein-coding gene	gene with protein product		601683	"""coenzyme Q, 7 (rat, yeast) homolog"""			9020081, 10373325	Standard	NM_016138		Approved	CLK-1, CAT5	uc002dfr.3	Q99807	OTTHUMG00000131455	ENST00000321998.5:c.308C>T	16.37:g.19085298C>T	ENSP00000322316:p.Thr103Met	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	178	90	0.505618	NM_016138	B2RDA9|Q9BTT7|Q9H0T5|Q9UEW5|Q9UNR5	Missense_Mutation	SNP	ENST00000321998.5	37	CCDS10574.1	1329	0.6085164835164835	146	0.2967479674796748	225	0.6215469613259669	473	0.8269230769230769	485	0.6398416886543535	C	18.35	3.605641	0.66445	0.338871	0.63907	ENSG00000167186	ENST00000321998;ENST00000544894	T;T	0.43688	0.94;0.94	5.91	5.91	0.95273	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);	0.424017	0.29616	N	0.011650	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	P	0.47034	0.889	P	0.50109	0.631	T	0.13791	-1.0496	9	0.66056	D	0.02	-4.7588	19.9089	0.97019	0.0:1.0:0.0:0.0	rs11074359;rs17357840;rs60588972;rs11074359	103	Q99807	COQ7_HUMAN	M	103;65	ENSP00000322316:T103M;ENSP00000442923:T65M	ENSP00000322316:T103M	T	+	2	0	COQ7	18992799	0.228000	0.23718	0.328000	0.25416	0.913000	0.54294	3.071000	0.50041	2.793000	0.96121	0.655000	0.94253	ACG	C|0.434;T|0.566	0.566	strong		0.448	COQ7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254275.3	NM_016138	
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000457780.2_Silent_p.F193F|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000342989.5_5'Flank	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	193					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACTCCTTCTCGAAGCGGTCCA	0.602													G|||	508	0.101438	0.1664	0.0432	5008	,	,		21111	0.003		0.0746	False		,,,				2504	0.184				p.F193F		Atlas-SNP	.											.	BRD1	144	.	0			c.C579T						PASS	.	G		801,3605	322.9+/-297.8	69,663,1471	72.0	61.0	65.0		579	-5.2	1.0	22	dbSNP_120	65	702,7898	172.6+/-223.3	31,640,3629	no	coding-synonymous	BRD1	NM_014577.1		100,1303,5100	AA,AG,GG		8.1628,18.1798,11.5562		193/1059	50217387	1503,11503	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTTCTCGAAGCGG	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.579C>T	22.37:g.50217387G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			G|0.899;A|0.101	0.101	strong		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
MNDA	4332	hgsc.bcm.edu	37	1	158817521	158817521	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158817521A>G	ENST00000368141.4	+	6	1252	c.991A>G	c.(991-993)Agc>Ggc	p.S331G		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	331	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					TTTGCAGAAAAGCGTACACAA	0.368																																					p.S331G		Atlas-SNP	.											MNDA,colon,carcinoma,0,2	MNDA	147	2	0			c.A991G						PASS	.						95.0	93.0	94.0					1																	158817521		2203	4300	6503	SO:0001583	missense	4332	exon6			CAGAAAAGCGTAC	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.991A>G	1.37:g.158817521A>G	ENSP00000357123:p.Ser331Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	120	5	0.0416667	NM_002432		Missense_Mutation	SNP	ENST00000368141.4	37	CCDS1177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.768|4.768	0.142801|0.142801	0.09083|0.09083	.|.	.|.	ENSG00000163563|ENSG00000163563	ENST00000438394|ENST00000368141	T|T	0.19394|0.14766	2.15|2.48	4.15|4.15	0.259|0.259	0.15583|0.15583	.|HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	.|1.196580	.|0.06409	.|N	.|0.720183	T|T	0.02727|0.02727	0.0082|0.0082	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	0.999996|0.999996	.|B	.|0.33777	.|0.425	.|B	.|0.33121	.|0.158	T|T	0.45205|0.45205	-0.9277|-0.9277	7|10	0.72032|0.40728	D|T	0.01|0.16	0.0539|0.0539	5.0869|5.0869	0.14687|0.14687	0.4576:0.3654:0.0:0.1771|0.4576:0.3654:0.0:0.1771	.|.	.|331	.|P41218	.|MNDA_HUMAN	R|G	36|331	ENSP00000406800:K36R|ENSP00000357123:S331G	ENSP00000406800:K36R|ENSP00000357123:S331G	K|S	+|+	2|1	0|0	MNDA|MNDA	157084145|157084145	0.104000|0.104000	0.21937|0.21937	0.136000|0.136000	0.22124|0.22124	0.082000|0.082000	0.17680|0.17680	0.152000|0.152000	0.16302|0.16302	-0.064000|-0.064000	0.13043|0.13043	0.460000|0.460000	0.39030|0.39030	AAG|AGC	.	.	none		0.368	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432	
PIEZO1	9780	hgsc.bcm.edu	37	16	88789687	88789687	+	Missense_Mutation	SNP	C	C	T	rs188337046	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:88789687C>T	ENST00000301015.9	-	32	4631	c.4385G>A	c.(4384-4386)cGg>cAg	p.R1462Q	RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1462					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						CTCCTGCTGCCGCCGCCTCAG	0.706													C|||	59	0.0117812	0.0325	0.0029	5008	,	,		13050	0.0		0.0139	False		,,,				2504	0.0				p.R1462Q		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G4385A						PASS	.						18.0	26.0	24.0					16																	88789687		691	1585	2276	SO:0001583	missense	9780	exon32			TGCTGCCGCCGCC	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.4385G>A	16.37:g.88789687C>T	ENSP00000301015:p.Arg1462Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	31	27	0.870968	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	38|38	0.0173992673992674|0.0173992673992674	21|21	0.042682926829268296|0.042682926829268296	4|4	0.011049723756906077|0.011049723756906077	3|3	0.005244755244755245|0.005244755244755245	10|10	0.013192612137203167|0.013192612137203167	C|C	10.95|10.95	1.494530|1.494530	0.26774|0.26774	.|.	.|.	ENSG00000103335|ENSG00000103335	ENST00000474606|ENST00000301015	.|T	.|0.75477	.|-0.94	4.92|4.92	-1.11|-1.11	0.09840|0.09840	.|.	.|0.239959	.|0.24988	.|N	.|0.034007	T|T	0.20047|0.20047	0.0482|0.0482	N|N	0.17723|0.17723	0.515|0.515	0.80722|0.80722	D|D	1|1	.|P	.|0.44429	.|0.835	.|B	.|0.26770	.|0.073	T|T	0.23797|0.23797	-1.0178|-1.0178	5|10	.|0.33940	.|T	.|0.23	-26.7276|-26.7276	16.9282|16.9282	0.86182|0.86182	0.0:0.8303:0.0:0.1697|0.0:0.8303:0.0:0.1697	.|.	.|1462	.|Q92508	.|PIEZ1_HUMAN	S|Q	136|1462	.|ENSP00000301015:R1462Q	.|ENSP00000301015:R1462Q	G|R	-|-	1|2	0|0	FAM38A|FAM38A	87317188|87317188	0.155000|0.155000	0.22806|0.22806	0.006000|0.006000	0.13384|0.13384	0.036000|0.036000	0.12997|0.12997	0.784000|0.784000	0.26816|0.26816	-0.731000|-0.731000	0.04862|0.04862	-1.134000|-1.134000	0.01955|0.01955	GGC|CGG	C|0.983;T|0.017	0.017	strong		0.706	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
LPIN3	64900	hgsc.bcm.edu	37	20	39986549	39986549	+	Silent	SNP	G	G	A	rs41277020	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:39986549G>A	ENST00000373257.3	+	17	2158	c.2067G>A	c.(2065-2067)tcG>tcA	p.S689S		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	689	C-LIP.				fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				TGTACTGCTCGGCGCGGGCCA	0.617													G|||	6	0.00119808	0.0	0.0014	5008	,	,		18436	0.0		0.005	False		,,,				2504	0.0				p.S689S		Atlas-SNP	.											LPIN3,NS,carcinoma,+1,1	LPIN3	69	1	0			c.G2067A						PASS	.	G		5,4401	8.1+/-20.4	0,5,2198	48.0	53.0	51.0		2067	-10.7	0.0	20	dbSNP_127	51	43,8557	27.4+/-76.7	0,43,4257	no	coding-synonymous	LPIN3	NM_022896.1		0,48,6455	AA,AG,GG		0.5,0.1135,0.3691		689/852	39986549	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	64900	exon17			CTGCTCGGCGCGG	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.2067G>A	20.37:g.39986549G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	136	76	0.558824	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Silent	SNP	ENST00000373257.3	37	CCDS33469.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	7.470	0.646463	0.14451	0.001135	0.005	ENSG00000132793	ENST00000445975	.	.	.	5.37	-10.7	0.00240	.	.	.	.	.	T	0.24812	0.0602	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56220	-0.8015	4	.	.	.	-10.6211	1.2268	0.01935	0.4678:0.165:0.1306:0.2365	rs41277020;rs61739750	.	.	.	Q	179	.	.	R	+	2	0	LPIN3	39419963	0.001000	0.12720	0.011000	0.14972	0.902000	0.53008	-1.379000	0.02554	-5.039000	0.00023	-2.282000	0.00269	CGG	G|0.997;A|0.003	0.003	strong		0.617	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896	
CACUL1	143384	hgsc.bcm.edu	37	10	120489828	120489828	+	Silent	SNP	G	G	A	rs41284412	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:120489828G>A	ENST00000369151.3	-	2	945	c.462C>T	c.(460-462)gaC>gaT	p.D154D	CACUL1_ENST00000340214.4_Silent_p.D154D	NM_153810.4	NP_722517.3	Q86Y37	CACL1_HUMAN	CDK2-associated, cullin domain 1	154					G1/S transition of mitotic cell cycle (GO:0000082)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase activity (GO:0045860)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)	protein kinase binding (GO:0019901)										TGGGGATATAGTCACCAGGAC	0.348													G|||	4	0.000798722	0.0	0.0	5008	,	,		19535	0.0		0.004	False		,,,				2504	0.0				p.D154D		Atlas-SNP	.											.	.	.	.	0			c.C462T						PASS	.	G		3,3659		0,3,1828	125.0	121.0	122.0		462	5.7	1.0	10	dbSNP_127	122	41,8135		0,41,4047	no	coding-synonymous	C10orf46	NM_153810.4		0,44,5875	AA,AG,GG		0.5015,0.0819,0.3717		154/370	120489828	44,11794	1831	4088	5919	SO:0001819	synonymous_variant	143384	exon2			GATATAGTCACCA	AK097728	CCDS41570.1	10q26.13	2012-06-12	2012-06-12	2012-06-12	ENSG00000151893	ENSG00000151893			23727	protein-coding gene	gene with protein product	"""Cdk-Associated Cullin1"""		"""chromosome 10 open reading frame 46"""	C10orf46		19829063	Standard	NM_153810		Approved	FLJ40409, MGC33215, CAC1	uc001lds.1	Q86Y37	OTTHUMG00000019138	ENST00000369151.3:c.462C>T	10.37:g.120489828G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_153810	Q5XPL7|Q8IY11|Q8N7S4	Silent	SNP	ENST00000369151.3	37	CCDS41570.1																																																																																			G|0.998;A|0.002	0.002	strong		0.348	CACUL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050612.2	NM_153810	
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327909	+	Missense_Mutation	SNP	A	A	C	rs59310777	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:16327909A>C	ENST00000244769.4	-	8	1569	c.633T>G	c.(631-633)caT>caG	p.H211Q	ATXN1_ENST00000436367.1_Missense_Mutation_p.H211Q	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	211	Poly-Gln.			H -> HQ (in Ref. 1; CAA55793). {ECO:0000305}.	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.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)				gctgctgctgatgctgatgct	0.672													A|||	1334	0.266374	0.2897	0.2161	5008	,	,		12493	0.3879		0.0964	False		,,,				2504	0.32				p.H211Q		Atlas-SNP	.											ATXN1,colon,carcinoma,0,3	ATXN1	117	3	1	Deletion - In frame(1)	prostate(1)	c.T633G						PASS	.						4.0	7.0	6.0					6																	16327909		1575	3495	5070	SO:0001583	missense	6310	exon7			CTGCTGATGCTGA	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.633T>G	6.37:g.16327909A>C	ENSP00000244769:p.His211Gln	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	82	20	0.243902	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	369	0.16895604395604397	105	0.21341463414634146	59	0.16298342541436464	150	0.26223776223776224	55	0.07255936675461741	A	5.976	0.364085	0.11296	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.50813	0.73;0.73	.	.	.	.	.	.	.	.	T	0.08358	0.0208	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.31223	-0.9951	4	0.15952	T	0.53	.	.	.	.	rs59310777	211	P54253	ATX1_HUMAN	Q	211	ENSP00000244769:H211Q;ENSP00000416360:H211Q	ENSP00000244769:H211Q	H	-	3	2	ATXN1	16435888	0.694000	0.27738	0.023000	0.16930	0.066000	0.16364	1.537000	0.36083	0.000000	0.14550	0.000000	0.15137	CAT	A|0.830;C|0.170	0.170	strong		0.672	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
CYP2D6	1565	hgsc.bcm.edu	37	22	42525089	42525089	+	Missense_Mutation	SNP	G	G	C	rs78482768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:42525089G>C	ENST00000360608.5	-	3	565	c.451C>G	c.(451-453)Cag>Gag	p.Q151E	CYP2D6_ENST00000389970.3_Missense_Mutation_p.Q151E|NDUFA6-AS1_ENST00000608288.1_RNA|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Intron|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	151					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)	GTCACCCACTGCTCCAGCGAC	0.677													G|||	6	0.00119808	0.0	0.0014	5008	,	,		16419	0.0		0.005	False		,,,				2504	0.0				p.Q151E		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C451G						PASS	.	G	GLU/GLN,	5,4131		0,5,2063	19.0	23.0	22.0		451,	2.0	1.0	22	dbSNP_131	22	28,8350		1,26,4162	no	missense,intron	CYP2D6	NM_000106.4,NM_001025161.1	29,	1,31,6225	CC,CG,GG		0.3342,0.1209,0.2637	benign,	151/498,	42525089	33,12481	2068	4189	6257	SO:0001583	missense	1565	exon3			CCCACTGCTCCAG	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.451C>G	22.37:g.42525089G>C	ENSP00000353820:p.Gln151Glu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	g	0.009	-1.841892	0.00573	0.001209	0.003342	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640	T;T	0.77877	-1.13;-1.13	4.18	1.97	0.26223	.	0.756605	0.11656	N	0.542295	T	0.52008	0.1708	N	0.11341	0.13	0.22684	N	0.998852	B	0.10296	0.003	B	0.08055	0.003	T	0.38929	-0.9638	10	0.02654	T	1	.	6.6787	0.23108	0.1016:0.3458:0.5526:0.0	.	151	Q6NWU0	.	E	151;151;100	ENSP00000353820:Q151E;ENSP00000374620:Q151E	ENSP00000353820:Q151E	Q	-	1	0	CYP2D6	40855033	0.005000	0.15991	0.998000	0.56505	0.063000	0.16089	0.273000	0.18662	0.442000	0.26555	0.305000	0.20034	CAG	G|1.000;|0.000	.	weak		0.677	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
TNS4	84951	hgsc.bcm.edu	37	17	38643385	38643385	+	Silent	SNP	G	G	A	rs8071312	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38643385G>A	ENST00000254051.6	-	4	1349	c.1191C>T	c.(1189-1191)tcC>tcT	p.S397S		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	397					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)			CAGGTTGAACGGAGTTCTGGT	0.597													G|||	276	0.0551118	0.1498	0.0346	5008	,	,		17508	0.001		0.0447	False		,,,				2504	0.0082				p.S397S		Atlas-SNP	.											.	TNS4	72	.	0			c.C1191T						PASS	.	G		649,3757	279.0+/-274.6	48,553,1602	175.0	185.0	181.0		1191	-1.5	0.1	17	dbSNP_116	181	349,8251	118.1+/-177.6	8,333,3959	no	coding-synonymous	TNS4	NM_032865.5		56,886,5561	AA,AG,GG		4.0581,14.7299,7.6734		397/716	38643385	998,12008	2203	4300	6503	SO:0001819	synonymous_variant	84951	exon4			TTGAACGGAGTTC	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.1191C>T	17.37:g.38643385G>A		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	277	138	0.498195	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Silent	SNP	ENST00000254051.6	37	CCDS11368.1																																																																																			G|0.921;A|0.079	0.079	strong		0.597	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865	
CNR2	1269	hgsc.bcm.edu	37	1	24201262	24201262	+	Silent	SNP	A	A	G	rs2502993	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:24201262A>G	ENST00000374472.4	-	2	1007	c.846T>C	c.(844-846)gcT>gcC	p.A282A	CNR2_ENST00000536471.1_Silent_p.A282A	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	282					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)	p.A282A(1)		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)	TGGAGCAGAAAGCAAAGGCCT	0.572													G|||	3272	0.653355	0.7943	0.6383	5008	,	,		22050	0.502		0.5875	False		,,,				2504	0.6973				p.A282A		Atlas-SNP	.											CNR2_ENST00000374472,NS,carcinoma,-2,3	CNR2	78	3	1	Substitution - coding silent(1)	stomach(1)	c.T846C						PASS	.	G		3310,1096	395.8+/-329.8	1261,788,154	92.0	82.0	85.0		846	1.3	1.0	1	dbSNP_100	85	4934,3666	526.1+/-380.9	1402,2130,768	no	coding-synonymous	CNR2	NM_001841.2		2663,2918,922	GG,GA,AA		42.6279,24.8752,36.6139		282/361	24201262	8244,4762	2203	4300	6503	SO:0001819	synonymous_variant	1269	exon2			GCAGAAAGCAAAG	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.846T>C	1.37:g.24201262A>G		Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	96	94	0.979167	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Silent	SNP	ENST00000374472.4	37	CCDS245.1																																																																																			A|0.359;G|0.641	0.641	strong		0.572	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119964052	119964052	+	Missense_Mutation	SNP	G	G	C	rs2073618	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:119964052G>C	ENST00000297350.4	-	1	387	c.9C>G	c.(7-9)aaC>aaG	p.N3K		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	3			N -> K (in dbSNP:rs2073618). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9108485, ECO:0000269|PubMed:9492069, ECO:0000269|PubMed:9688283, ECO:0000269|Ref.6}.		apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			AGCACAGCAAGTTGTTCATTG	0.682													C|||	3339	0.666733	0.9236	0.4654	5008	,	,		12595	0.7609		0.4672	False		,,,				2504	0.5706				p.N3K		Atlas-SNP	.											TNFRSF11B_ENST00000297350,rectum,carcinoma,0,6	TNFRSF11B	87	6	0			c.C9G	GRCh37	CM045665	TNFRSF11B	M	rs2073618	PASS	.	C	LYS/ASN	3767,613		1621,525,44	17.0	18.0	18.0		9	5.3	0.8	8	dbSNP_96	18	3863,4713		867,2129,1292	yes	missense	TNFRSF11B	NM_002546.3	94	2488,2654,1336	CC,CG,GG		45.0443,13.9954,41.1084	benign	3/402	119964052	7630,5326	2190	4288	6478	SO:0001583	missense	4982	exon1			CAGCAAGTTGTTC	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"""Tumor necrosis factor receptor superfamily"""	11909	protein-coding gene	gene with protein product		602643	"""osteoprotegerin"""	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.9C>G	8.37:g.119964052G>C	ENSP00000297350:p.Asn3Lys	Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	155	98	0.632258	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	37	CCDS6326.1	1406	0.6437728937728938	436	0.8861788617886179	183	0.505524861878453	425	0.743006993006993	362	0.47757255936675463	C	7.688	0.690394	0.15039	0.860046	0.450443	ENSG00000164761	ENST00000297350	T	0.71579	-0.58	5.26	5.26	0.73747	.	0.637813	0.16792	N	0.199355	T	0.00012	0.0000	N	0.00347	-1.61	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36138	-0.9760	8	.	.	.	-1.0265	11.9629	0.53019	0.0:0.826:0.174:0.0	rs2073618;rs17751701;rs60810341;rs2073618	3	O00300	TR11B_HUMAN	K	3	ENSP00000297350:N3K	.	N	-	3	2	TNFRSF11B	120033233	0.032000	0.19561	0.781000	0.31783	0.965000	0.64279	0.645000	0.24782	1.474000	0.48178	-0.335000	0.08231	AAC	G|0.374;C|0.626	0.626	strong		0.682	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
IRX6	79190	hgsc.bcm.edu	37	16	55362625	55362625	+	Silent	SNP	C	C	T	rs199714803		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:55362625C>T	ENST00000290552.7	+	5	2067	c.735C>T	c.(733-735)agC>agT	p.S245S	RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	245					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						TTACTGCTAGCCAGGAGGCCC	0.582																																					p.S245S		Atlas-SNP	.											.	IRX6	66	.	0			c.C735T						PASS	.																																			SO:0001819	synonymous_variant	79190	exon5			TGCTAGCCAGGAG	AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"""Homeoboxes / TALE class"""	14675	protein-coding gene	gene with protein product		606196	"""iroquois homeobox protein 7"", ""iroquois homeobox protein 6"""	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.735C>T	16.37:g.55362625C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	42	36	0.857143	NM_024335	B2RN06|Q7Z2K0	Silent	SNP	ENST00000290552.7	37	CCDS32449.1																																																																																			C|0.999;T|0.001	0.001	weak		0.582	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335	
FZD6	8323	hgsc.bcm.edu	37	8	104337523	104337523	+	Nonsense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:104337523C>T	ENST00000358755.4	+	4	1506	c.1189C>T	c.(1189-1191)Cga>Tga	p.R397*	FZD6_ENST00000540287.1_Nonsense_Mutation_p.R92*|FZD6_ENST00000523739.1_Nonsense_Mutation_p.R365*|FZD6_ENST00000522566.1_Nonsense_Mutation_p.R397*	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	397					angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|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)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			AAATCATGTTCGACAAGTCAT	0.418																																					p.R397X		Atlas-SNP	.											FZD6,NS,carcinoma,-1,1	FZD6	61	1	0			c.C1189T						scavenged	.						190.0	188.0	188.0					8																	104337523		2203	4300	6503	SO:0001587	stop_gained	8323	exon4			CATGTTCGACAAG	AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"""GPCR / Class F : Frizzled receptors"""	4044	protein-coding gene	gene with protein product		603409	"""frizzled (Drosophila) homolog 6"", ""frizzled homolog 6 (Drosophila)"", ""frizzled 6, seven transmembrane spanning receptor"", ""frizzled family receptor 6"""			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.1189C>T	8.37:g.104337523C>T	ENSP00000351605:p.Arg397*	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	256	3	0.0117188	NM_003506	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Nonsense_Mutation	SNP	ENST00000358755.4	37	CCDS6298.1	.	.	.	.	.	.	.	.	.	.	C	40	8.074534	0.98640	.	.	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739;ENST00000540287;ENST00000539487	.	.	.	6.03	5.16	0.70880	.	0.059527	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4324	0.75112	0.0:0.9336:0.0:0.0664	.	.	.	.	X	397;397;365;92;342	.	ENSP00000351605:R397X	R	+	1	2	FZD6	104406699	1.000000	0.71417	0.935000	0.37517	0.983000	0.72400	4.888000	0.63164	1.567000	0.49668	0.557000	0.71058	CGA	.	.	none		0.418	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506	
BMPR1A	657	hgsc.bcm.edu	37	10	88635779	88635779	+	Missense_Mutation	SNP	C	C	A	rs11528010	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:88635779C>A	ENST00000372037.3	+	3	541	c.4C>A	c.(4-6)Cct>Act	p.P2T	BMPR1A_ENST00000480152.1_3'UTR	NM_004329.2	NP_004320.2	P36894	BMR1A_HUMAN	bone morphogenetic protein receptor, type IA	2			P -> T (in dbSNP:rs11528010). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8397373}.		BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|developmental growth (GO:0048589)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic digit morphogenesis (GO:0042733)|embryonic organ development (GO:0048568)|endocardial cushion formation (GO:0003272)|heart formation (GO:0060914)|hindlimb morphogenesis (GO:0035137)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lateral mesoderm development (GO:0048368)|lung development (GO:0030324)|mesendoderm development (GO:0048382)|mesoderm formation (GO:0001707)|Mullerian duct regression (GO:0001880)|negative regulation of neurogenesis (GO:0050768)|neural crest cell development (GO:0014032)|neural plate mediolateral regionalization (GO:0021998)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|paraxial mesoderm structural organization (GO:0048352)|pituitary gland development (GO:0021983)|positive regulation of bone mineralization (GO:0030501)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of lateral mesodermal cell fate specification (GO:0048378)|somitogenesis (GO:0001756)|stem cell maintenance (GO:0019827)|transforming growth factor beta receptor signaling pathway (GO:0007179)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|skin(1)|stomach(1)	24						TTGAACAATGCCTCAGCTATA	0.328			"""Mis, N, F"""			gastrointestinal polyps			Juvenile Polyposis;Hereditary Mixed Polyposis syndrome type 2				A|||	2503	0.4998	0.7239	0.3617	5008	,	,		19725	0.7093		0.2753	False		,,,				2504	0.3098				p.P2T	Ovarian(190;603 2086 22044 30335 47971)	Atlas-SNP	.	yes	Rec		Juvenile polyposis	10	10q22.3	657	"""bone morphogenetic protein receptor, type IA"""		E	.	BMPR1A	118	.	0			c.C4A						PASS	.	A	THR/PRO	2863,1543	485.5+/-360.3	941,981,281	197.0	195.0	196.0		4	5.3	1.0	10	dbSNP_120	196	2203,6397	709.9+/-405.7	280,1643,2377	no	missense	BMPR1A	NM_004329.2	38	1221,2624,2658	AA,AC,CC		25.6163,35.0204,38.9513	benign	2/533	88635779	5066,7940	2203	4300	6503	SO:0001583	missense	657	exon3	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HMPS2	ACAATGCCTCAGC	BC028383	CCDS7378.1	10q22.3	2014-09-17			ENSG00000107779	ENSG00000107779		"""CD molecules"""	1076	protein-coding gene	gene with protein product		601299		ACVRLK3		8397373, 9730621	Standard	NM_004329		Approved	ALK3, CD292	uc001kdy.3	P36894	OTTHUMG00000018657	ENST00000372037.3:c.4C>A	10.37:g.88635779C>A	ENSP00000361107:p.Pro2Thr	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	162	116	0.716049	NM_004329	A8K6U9|Q8NEN8	Missense_Mutation	SNP	ENST00000372037.3	37	CCDS7378.1	987	0.4519230769230769	292	0.5934959349593496	117	0.32320441988950277	391	0.6835664335664335	187	0.24670184696569922	A	1.311	-0.602108	0.03744	0.649796	0.256163	ENSG00000107779	ENST00000224764;ENST00000372037	D	0.81499	-1.5	5.3	5.3	0.74995	.	0.301588	0.34200	N	0.004161	T	0.00012	0.0000	N	0.02539	-0.55	0.54753	P	1.7000000000044757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41016	-0.9532	9	0.02654	T	1	.	11.256	0.49054	0.8467:0.1533:0.0:0.0	rs11528010	2	P36894	BMR1A_HUMAN	T	2	ENSP00000361107:P2T	ENSP00000224764:P2T	P	+	1	0	BMPR1A	88625759	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	3.768000	0.55295	0.956000	0.37904	-0.374000	0.07098	CCT	.	.	weak		0.328	BMPR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049170.3	NM_004329	
OR12D2	26529	hgsc.bcm.edu	37	6	29364615	29364615	+	Missense_Mutation	SNP	G	G	T	rs9257834	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:29364615G>T	ENST00000383555.2	+	1	200	c.139G>T	c.(139-141)Gtc>Ttc	p.V47F	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	47			V -> F (in dbSNP:rs9257834).			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(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						TCTGATGATTGTCATCTCCGA	0.463													G|||	1597	0.31889	0.1921	0.3458	5008	,	,		20479	0.3641		0.4523	False		,,,				2504	0.2873				p.V47F		Atlas-SNP	.											.	OR12D2	42	.	0			c.G139T						PASS	.	G	PHE/VAL	668,2352		75,518,917	127.0	133.0	131.0		139	3.2	0.0	6	dbSNP_118	131	2411,3007		536,1339,834	yes	missense	OR12D2	NM_013936.3	50	611,1857,1751	TT,TG,GG		44.4998,22.1192,36.4897	probably-damaging	47/308	29364615	3079,5359	1510	2709	4219	SO:0001583	missense	26529	exon1			ATGATTGTCATCT		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.139G>T	6.37:g.29364615G>T	ENSP00000373047:p.Val47Phe	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	200	198	0.99	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	788	0.3608058608058608	102	0.2073170731707317	123	0.3397790055248619	208	0.36363636363636365	355	0.4683377308707124	G	10.62	1.402237	0.25291	0.221192	0.444998	ENSG00000168787	ENST00000383555	T	0.03496	3.91	4.07	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000073	T	0.07503	0.0189	M	0.87456	2.885	0.80722	P	0.0	D	0.62365	0.991	P	0.60345	0.873	T	0.02698	-1.1122	9	0.72032	D	0.01	.	5.9657	0.19325	0.0988:0.0:0.7097:0.1915	rs9257834;rs59373671;rs9257834	47	P58182	O12D2_HUMAN	F	47	ENSP00000373047:V47F	ENSP00000373047:V47F	V	+	1	0	OR12D2	29472594	0.000000	0.05858	0.005000	0.12908	0.002000	0.02628	-0.520000	0.06252	0.897000	0.36392	0.411000	0.27672	GTC	G|0.636;T|0.364	0.364	strong		0.463	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
DOK7	285489	hgsc.bcm.edu	37	4	3494898	3494898	+	Silent	SNP	C	C	T	rs6850908	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:3494898C>T	ENST00000340083.5	+	7	1250	c.1185C>T	c.(1183-1185)taC>taT	p.Y395Y	DOK7_ENST00000389653.2_Silent_p.Y395Y|DOK7_ENST00000512714.1_3'UTR|DOK7_ENST00000507039.1_3'UTR	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	120	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	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	
CELA2B	51032	hgsc.bcm.edu	37	1	15808872	15808872	+	Missense_Mutation	SNP	G	G	A	rs3766160	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15808872G>A	ENST00000375910.3	+	4	365	c.340G>A	c.(340-342)Gac>Aac	p.D114N	CELA2B_ENST00000494280.1_3'UTR	NM_015849.2	NP_056933	P08218	CEL2B_HUMAN	chymotrypsin-like elastase family, member 2B	114	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		D -> N (in dbSNP:rs3766160). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3646943}.			extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8						CTGGAACTCCGACCAGGTCTC	0.572													G|||	1578	0.315096	0.2769	0.2896	5008	,	,		16447	0.5575		0.2376	False		,,,				2504	0.2147				p.D114N		Atlas-SNP	.											.	CELA2B	37	.	0			c.G340A						PASS	.	G	ASN/ASP	1151,3255	409.7+/-335.1	143,865,1195	117.0	114.0	115.0		340	0.5	0.1	1	dbSNP_107	115	2111,6489	363.7+/-333.3	269,1573,2458	yes	missense	CELA2B	NM_015849.2	23	412,2438,3653	AA,AG,GG		24.5465,26.1235,25.0807	benign	114/270	15808872	3262,9744	2203	4300	6503	SO:0001583	missense	51032	exon4			AACTCCGACCAGG		CCDS30605.1	1p36.21	2009-07-09			ENSG00000215704	ENSG00000215704			29995	protein-coding gene	gene with protein product	"""pancreatic elastase IIB"""	609444				3646943, 16327289	Standard	NM_015849		Approved	RP11-265F14.2, ELA2B	uc001awl.3	P08218	OTTHUMG00000002259	ENST00000375910.3:c.340G>A	1.37:g.15808872G>A	ENSP00000365075:p.Asp114Asn	Somatic	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	165	157	0.951515	NM_015849	Q14D16|Q6ISM5|Q96QV5	Missense_Mutation	SNP	ENST00000375910.3	37	CCDS30605.1	701	0.320970695970696	118	0.23983739837398374	85	0.23480662983425415	305	0.5332167832167832	193	0.2546174142480211	G	0.134	-1.110469	0.01813	0.261235	0.245465	ENSG00000215704	ENST00000375910	D	0.88818	-2.43	3.01	0.469	0.16741	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.623510	0.03801	N	0.264463	T	0.00012	0.0000	N	0.04959	-0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32981	-0.9886	9	0.02654	T	1	.	3.9956	0.09556	0.6422:0.2254:0.1324:0.0	rs3766160;rs52831934;rs61093493;rs3766160	114	P08218	CEL2B_HUMAN	N	114	ENSP00000365075:D114N	ENSP00000365075:D114N	D	+	1	0	CELA2B	15681459	0.000000	0.05858	0.073000	0.20177	0.080000	0.17528	0.067000	0.14510	-0.020000	0.14032	-0.532000	0.04303	GAC	G|0.715;A|0.285	0.285	strong		0.572	CELA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006448.1	NM_015849	
OGFOD1	55239	hgsc.bcm.edu	37	16	56485554	56485554	+	Silent	SNP	C	C	G	rs11076155	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:56485554C>G	ENST00000566157.1	+	1	153	c.30C>G	c.(28-30)ggC>ggG	p.G10G	NUDT21_ENST00000300291.5_5'Flank|OGFOD1_ENST00000568397.1_Silent_p.G10G	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	10					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)	CGGAGCCCGGCCCAGCCCGGG	0.587													C|||	265	0.0529153	0.0015	0.049	5008	,	,		15751	0.0724		0.0835	False		,,,				2504	0.0736				p.G10G		Atlas-SNP	.											.	OGFOD1	31	.	0			c.C30G						PASS	.	C		75,4321	54.9+/-90.9	0,75,2123	72.0	87.0	82.0		30	1.1	0.0	16	dbSNP_120	82	597,8003	144.0+/-200.0	18,561,3721	no	coding-synonymous	OGFOD1	NM_018233.3		18,636,5844	GG,GC,CC		6.9419,1.7061,5.1708		10/543	56485554	672,12324	2198	4300	6498	SO:0001819	synonymous_variant	55239	exon1			GCCCGGCCCAGCC	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.30C>G	16.37:g.56485554C>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	34	7	0.205882	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Silent	SNP	ENST00000566157.1	37	CCDS10761.2																																																																																			C|0.948;G|0.052	0.052	strong		0.587	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	
FAM47C	442444	hgsc.bcm.edu	37	X	37029254	37029254	+	Missense_Mutation	SNP	A	A	C	rs1995914	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:37029254A>C	ENST00000358047.3	+	1	2823	c.2771A>C	c.(2770-2772)aAt>aCt	p.N924T		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	924			N -> T (in dbSNP:rs1995914).							breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						AAAATCCAGAATGCACCAAAT	0.453													N|||	1396	0.369801	0.6445	0.2392	3775	,	,		15358	0.0982		0.0785	False		,,,				2504	0.2045				p.N924T		Atlas-SNP	.											.	FAM47C	267	.	0			c.A2771C						PASS	.	C	THR/ASN	2991,842		1003,538,447,90,124	85.0	87.0	86.0		2771	-1.7	0.0	X	dbSNP_92	86	783,5945		26,499,232,1903,1640	yes	missense	FAM47C	NM_001013736.2	65	1029,1037,679,1993,1764	CC,CA,C,AA,A		11.6379,21.9671,35.7353	benign	924/1036	37029254	3774,6787	2202	4300	6502	SO:0001583	missense	442444	exon1			TCCAGAATGCACC	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2771A>C	X.37:g.37029254A>C	ENSP00000367913:p.Asn924Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	67	65	0.970149	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	495	0.298372513562387	216	0.7058823529411765	54	0.16981132075471697	37	0.06801470588235294	43	0.05922865013774105	C	0.001	-3.759422	0.00005	0.780329	0.116379	ENSG00000198173	ENST00000358047	T	0.42131	0.98	0.829	-1.66	0.08265	.	.	.	.	.	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.45789	-0.9237	7	0.14252	T	0.57	.	.	.	.	rs1995914;rs52815039;rs59553201;rs1995914	924	Q5HY64	FA47C_HUMAN	T	924	ENSP00000367913:N924T	ENSP00000367913:N924T	N	+	2	0	FAM47C	36939175	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.842000	0.04354	-4.876000	0.00028	-4.602000	0.00004	AAT	A|0.631;C|0.369	0.369	strong		0.453	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
WSCD1	23302	hgsc.bcm.edu	37	17	6023792	6023792	+	Silent	SNP	C	C	T	rs16955477	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:6023792C>T	ENST00000574946.1	+	9	1929	c.1539C>T	c.(1537-1539)agC>agT	p.S513S	WSCD1_ENST00000539421.1_Silent_p.S513S|WSCD1_ENST00000574232.1_Silent_p.S513S|WSCD1_ENST00000317744.5_Silent_p.S513S|WSCD1_ENST00000573634.1_Silent_p.S397S			Q658N2	WSCD1_HUMAN	WSC domain containing 1	513						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						TGTCTGTGAGCGAGGAGCGGC	0.667													C|||	80	0.0159744	0.0	0.0259	5008	,	,		17440	0.002		0.0378	False		,,,				2504	0.0225				p.S513S		Atlas-SNP	.											.	WSCD1	84	.	0			c.C1539T						PASS	.	C		30,4376	36.0+/-67.5	0,30,2173	80.0	76.0	77.0		1539	-2.3	1.0	17	dbSNP_123	77	353,8247	119.2+/-178.6	6,341,3953	no	coding-synonymous	WSCD1	NM_015253.1		6,371,6126	TT,TC,CC		4.1047,0.6809,2.9448		513/576	6023792	383,12623	2203	4300	6503	SO:0001819	synonymous_variant	23302	exon9			TGTGAGCGAGGAG		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.1539C>T	17.37:g.6023792C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Silent	SNP	ENST00000574946.1	37	CCDS32538.1																																																																																			C|0.974;T|0.026	0.026	strong		0.667	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
KRT40	125115	hgsc.bcm.edu	37	17	39138692	39138692	+	Missense_Mutation	SNP	C	C	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39138692C>A	ENST00000398486.2	-	5	714	c.554G>T	c.(553-555)cGc>cTc	p.R185L	KRT40_ENST00000377755.4_Missense_Mutation_p.R185L	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	185	Coil 1B.|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)				TAACAGCTGGCGAAGGGACAG	0.517																																					p.R185L		Atlas-SNP	.											KRT40,colon,carcinoma,-1,1	KRT40	27	1	0			c.G554T						scavenged	.						80.0	79.0	79.0					17																	39138692		2011	4193	6204	SO:0001583	missense	125115	exon5			AGCTGGCGAAGGG	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.554G>T	17.37:g.39138692C>A	ENSP00000381500:p.Arg185Leu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	82	2	0.0243902	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.531212	0.64972	.	.	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.91894	-2.93;-2.93	5.18	2.1	0.27182	Filament (1);	0.000000	0.34156	N	0.004217	D	0.96682	0.8917	H	0.96208	3.785	0.33401	D	0.577308	P	0.45240	0.854	D	0.63957	0.92	D	0.97240	0.9890	10	0.87932	D	0	.	9.902	0.41353	0.0:0.7108:0.0:0.2892	.	185	Q6A162	K1C40_HUMAN	L	185	ENSP00000366984:R185L;ENSP00000381500:R185L	ENSP00000366984:R185L	R	-	2	0	KRT40	36392218	0.931000	0.31567	0.993000	0.49108	0.594000	0.36715	1.976000	0.40579	0.295000	0.22570	0.591000	0.81541	CGC	.	.	none		0.517	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
KRT77	374454	hgsc.bcm.edu	37	12	53088484	53088484	+	Missense_Mutation	SNP	C	C	T	rs10783528	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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	108	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	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	
NUDT5	11164	hgsc.bcm.edu	37	10	12209752	12209752	+	Silent	SNP	T	T	C	rs6686	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:12209752T>C	ENST00000491614.1	-	10	1004	c.609A>G	c.(607-609)gcA>gcG	p.A203A	NUDT5_ENST00000378952.3_5'UTR|SEC61A2_ENST00000495368.1_3'UTR|NUDT5_ENST00000378937.3_Silent_p.A216A|NUDT5_ENST00000537776.1_Silent_p.A203A|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	83	0	0		WXS	Illumina HiSeq	Phase_I	60	10	0.166667	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		
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1642817	1642817	+	Silent	SNP	A	A	G	rs540908783|rs374921824	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1642817A>G	ENST00000399682.1	-	1	551	c.507T>C	c.(505-507)ggT>ggC	p.G169G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				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)		ATGACCCACAACCTGAGGAGG	0.612													a|||	106	0.0211661	0.0393	0.0115	5008	,	,		14637	0.0119		0.0209	False		,,,				2504	0.0133				p.G169G		Atlas-SNP	.											KRTAP5-4,colon,carcinoma,0,3	KRTAP5-4	78	3	0			c.T507C						PASS	.						24.0	35.0	32.0					11																	1642817		692	1591	2283	SO:0001819	synonymous_variant	387267	exon1			CCCACAACCTGAG	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.507T>C	11.37:g.1642817A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	172	14	0.0813954	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.612	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
S100PBP	64766	hgsc.bcm.edu	37	1	33292189	33292189	+	Silent	SNP	C	C	T	rs41265867	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:33292189C>T	ENST00000373475.5	+	3	743	c.489C>T	c.(487-489)gaC>gaT	p.D163D	S100PBP_ENST00000373476.1_Silent_p.D163D|S100PBP_ENST00000398243.3_Silent_p.D163D|S100PBP_ENST00000356689.3_3'UTR	NM_022753.3	NP_073590.2			S100P binding protein											endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TTGATAAGGACGAGACTGATT	0.378													c|||	29	0.00579073	0.0008	0.0058	5008	,	,		22086	0.0		0.0159	False		,,,				2504	0.0082				p.D163D		Atlas-SNP	.											.	S100PBP	31	.	0			c.C489T						PASS	.	T	,	9,4397	15.5+/-35.6	0,9,2194	69.0	71.0	70.0		489,489	-8.8	0.3	1	dbSNP_127	70	67,8533	40.8+/-97.7	1,65,4234	no	coding-synonymous,coding-synonymous	S100PBP	NM_001017406.1,NM_022753.2	,	1,74,6428	TT,TC,CC		0.7791,0.2043,0.5843	,	163/342,163/409	33292189	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	64766	exon3			TAAGGACGAGACT	BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497			25768	protein-coding gene	gene with protein product	"""S100P binding protein 1"""	611889				12477932	Standard	NM_022753		Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.489C>T	1.37:g.33292189C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	26	20	0.769231	NM_001256121		Silent	SNP	ENST00000373475.5	37	CCDS30666.1																																																																																			C|0.992;T|0.008	0.008	strong		0.378	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753	
TNR	7143	hgsc.bcm.edu	37	1	175375469	175375469	+	Missense_Mutation	SNP	C	C	A	rs2239819	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:175375469C>A	ENST00000367674.2	-	3	1090	c.382G>T	c.(382-384)Gcc>Tcc	p.A128S	TNR_ENST00000263525.2_Missense_Mutation_p.A128S			Q92752	TENR_HUMAN	tenascin R	128			A -> S (in dbSNP:rs2239819).		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)					GCTGAACTGGCACATGGACAG	0.592													C|||	1438	0.287141	0.0885	0.3617	5008	,	,		21685	0.5179		0.2525	False		,,,				2504	0.3006				p.A128S		Atlas-SNP	.											TNR,NS,carcinoma,0,1	TNR	399	1	0			c.G382T						scavenged	.	C	SER/ALA	582,3824	255.8+/-260.9	47,488,1668	167.0	144.0	152.0		382	2.0	0.0	1	dbSNP_98	152	2331,6269	391.0+/-343.5	324,1683,2293	yes	missense	TNR	NM_003285.2	99	371,2171,3961	AA,AC,CC		27.1047,13.2093,22.3974	benign	128/1359	175375469	2913,10093	2203	4300	6503	SO:0001583	missense	7143	exon3			AACTGGCACATGG	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.382G>T	1.37:g.175375469C>A	ENSP00000356646:p.Ala128Ser	Somatic	301	2	0.00664452		WXS	Illumina HiSeq	Phase_I	365	225	0.616438	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	655|655	0.2999084249084249|0.2999084249084249	47|47	0.09552845528455285|0.09552845528455285	119|119	0.3287292817679558|0.3287292817679558	302|302	0.527972027972028|0.527972027972028	187|187	0.24670184696569922|0.24670184696569922	C|C	2.025|2.025	-0.423785|-0.423785	0.04734|0.04734	0.132093|0.132093	0.271047|0.271047	ENSG00000116147|ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673|ENST00000422274	T;T|T	0.34859|0.17691	1.34;1.34|2.26	5.24|5.24	2.0|2.0	0.26442|0.26442	.|.	0.180815|.	0.49916|.	N|.	0.000132|.	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;B|.	0.14438|.	0.01;0.001|.	B;B|.	0.12156|.	0.007;0.004|.	T|T	0.41161|0.41161	-0.9524|-0.9524	9|6	0.25751|0.51188	T|T	0.34|0.08	.|.	8.009|8.009	0.30342|0.30342	0.4168:0.4977:0.0:0.0854|0.4168:0.4977:0.0:0.0854	rs2239819;rs52814246;rs57824138;rs2239819|rs2239819;rs52814246;rs57824138;rs2239819	128;128|.	B4DIX8;Q92752|.	.;TENR_HUMAN|.	S|F	128|11	ENSP00000356646:A128S;ENSP00000263525:A128S|ENSP00000403413:C11F	ENSP00000263525:A128S|ENSP00000403413:C11F	A|C	-|-	1|2	0|0	TNR|TNR	173642092|173642092	1.000000|1.000000	0.71417|0.71417	0.010000|0.010000	0.14722|0.14722	0.561000|0.561000	0.35649|0.35649	3.195000|3.195000	0.51013|0.51013	0.577000|0.577000	0.29470|0.29470	0.561000|0.561000	0.74099|0.74099	GCC|TGC	C|0.755;N|0.000	.	strong		0.592	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
YIF1B	90522	hgsc.bcm.edu	37	19	38798086	38798086	+	Silent	SNP	T	T	C	rs3178327	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:38798086T>C	ENST00000339413.6	-	7	816	c.771A>G	c.(769-771)gtA>gtG	p.V257V	YIF1B_ENST00000592694.1_Silent_p.V226V|YIF1B_ENST00000337679.8_Silent_p.V254V|YIF1B_ENST00000591784.1_Silent_p.V226V|YIF1B_ENST00000591755.1_Silent_p.V254V|YIF1B_ENST00000329420.8_Silent_p.V242V|YIF1B_ENST00000587361.1_5'Flank|YIF1B_ENST00000392124.3_Silent_p.V226V|YIF1B_ENST00000592246.1_Silent_p.V191V	NM_001039672.2|NM_001039673.2	NP_001034761.1|NP_001034762.1	Q5BJH7	YIF1B_HUMAN	Yip1 interacting factor homolog B (S. cerevisiae)	257						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)	10	all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CAAAGATGGCTACGCAGCACC	0.622													C|||	1876	0.374601	0.1581	0.4712	5008	,	,		17154	0.5823		0.326	False		,,,				2504	0.4346				p.V257V		Atlas-SNP	.											YIF1B_ENST00000339413,NS,carcinoma,-2,3	YIF1B	47	3	0			c.A771G						PASS	.	C	,,,,,,	819,3587	744.1+/-411.5	72,675,1456	84.0	74.0	77.0		726,771,762,720,678,762,678	2.3	0.4	19	dbSNP_105	77	2373,6227	699.3+/-405.1	316,1741,2243	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YIF1B	NM_001039671.2,NM_001039672.2,NM_001039673.2,NM_001145461.1,NM_001145462.1,NM_001145463.1,NM_033557.3	,,,,,,	388,2416,3699	CC,CT,TT		27.593,18.5883,24.5425	,,,,,,	242/300,257/315,254/312,240/298,226/284,254/292,226/284	38798086	3192,9814	2203	4300	6503	SO:0001819	synonymous_variant	90522	exon7			GATGGCTACGCAG	AL833382	CCDS12512.1, CCDS33010.1, CCDS46066.1, CCDS46067.1	19q13.2	2008-02-05							30511	protein-coding gene	gene with protein product						12975309	Standard	NM_001039672		Approved	FinGER8	uc002ohz.2	Q5BJH7		ENST00000339413.6:c.771A>G	19.37:g.38798086T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_001039672	H7BXS8|Q5JPC2|Q8WY70|Q96C02|Q96IC4	Silent	SNP	ENST00000339413.6	37	CCDS33010.1																																																																																			T|0.699;C|0.301	0.301	strong		0.622	YIF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460511.1	NM_033557	
MYLK	4638	hgsc.bcm.edu	37	3	123419422	123419422	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:123419422T>C	ENST00000475616.1	-	15	2892	c.2893A>G	c.(2893-2895)Acc>Gcc	p.T965A	MYLK_ENST00000346322.5_Missense_Mutation_p.T896A|MYLK_ENST00000360772.3_Missense_Mutation_p.T965A|MYLK_ENST00000359169.1_Missense_Mutation_p.T965A|MYLK_ENST00000360304.3_Missense_Mutation_p.T965A|MYLK_ENST00000510775.1_5'Flank			Q15746	MYLK_HUMAN	myosin light chain kinase	965	5 X 28 AA approximate tandem repeats.				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)		GGCACGGGGGTCTTGGAAGTC	0.572																																					p.T965A		Atlas-SNP	.											.	MYLK	224	.	0			c.A2893G						PASS	.						49.0	48.0	48.0					3																	123419422		2203	4300	6503	SO:0001583	missense	4638	exon18			CGGGGGTCTTGGA	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.2893A>G	3.37:g.123419422T>C	ENSP00000418335:p.Thr965Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	5	0.0704225	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	.	.	.	.	.	.	.	.	.	.	T	6.416	0.444842	0.12164	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.64260	-0.09;-0.04;-0.09;-0.04;-0.04	5.2	2.46	0.29980	.	.	.	.	.	T	0.43344	0.1243	L	0.28556	0.865	0.80722	D	1	B;B;B;B;B;B	0.15141	0.0;0.001;0.005;0.012;0.003;0.0	B;B;B;B;B;B	0.14023	0.001;0.005;0.01;0.006;0.004;0.001	T	0.14364	-1.0475	9	0.15499	T	0.54	.	7.056	0.25099	0.0:0.1566:0.1276:0.7157	.	965;43;896;965;896;965	Q15746-6;Q15746-7;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;MYLK_HUMAN	A	965;965;965;896;965	ENSP00000354004:T965A;ENSP00000353452:T965A;ENSP00000352088:T965A;ENSP00000320622:T896A;ENSP00000418335:T965A	ENSP00000320622:T896A	T	-	1	0	MYLK	124902112	0.997000	0.39634	1.000000	0.80357	0.951000	0.60555	0.367000	0.20382	0.835000	0.34877	-0.434000	0.05882	ACC	.	.	none		0.572	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
CH25H	9023	hgsc.bcm.edu	37	10	90966546	90966546	+	Silent	SNP	C	C	T	rs4078488	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:90966546C>T	ENST00000371852.2	-	1	525	c.504G>A	c.(502-504)gcG>gcA	p.A168A		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	168					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		GCGTTGCCAGCGCGAACGAGG	0.577													C|||	1388	0.277157	0.0083	0.2579	5008	,	,		23251	0.7351		0.1332	False		,,,				2504	0.3303				p.A168A		Atlas-SNP	.											CH25H,NS,carcinoma,-1,1	CH25H	19	1	0			c.G504A						PASS	.	C		113,4293	86.8+/-125.4	5,103,2095	144.0	136.0	139.0		504	-0.9	1.0	10	dbSNP_108	139	975,7625	211.8+/-252.3	54,867,3379	no	coding-synonymous	CH25H	NM_003956.3		59,970,5474	TT,TC,CC		11.3372,2.5647,8.3654		168/273	90966546	1088,11918	2203	4300	6503	SO:0001819	synonymous_variant	9023	exon1			TGCCAGCGCGAAC	AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"""Fatty acid hydroxylase domain containing"""	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.504G>A	10.37:g.90966546C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	92	19	0.206522	NM_003956	B2RBY3	Silent	SNP	ENST00000371852.2	37	CCDS7400.1																																																																																			C|0.850;T|0.150	0.150	strong		0.577	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956	
ZMIZ2	83637	hgsc.bcm.edu	37	7	44805814	44805814	+	Missense_Mutation	SNP	C	C	T	rs145522270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:44805814C>T	ENST00000309315.4	+	17	2417	c.2294C>T	c.(2293-2295)aCg>aTg	p.T765M	ZMIZ2_ENST00000413916.1_Missense_Mutation_p.T707M|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.T739M|ZMIZ2_ENST00000441627.1_Missense_Mutation_p.T765M|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.T733M|ZMIZ2_ENST00000463931.1_3'UTR	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	765	Pro-rich.			T -> M (in Ref. 1, 6 and 8; CAB66507). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCACCCACCACGCCCAGCACC	0.637													C|||	9	0.00179712	0.0	0.0043	5008	,	,		14115	0.0		0.006	False		,,,				2504	0.0				p.T765M	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.C2294T						PASS	.	C	MET/THR,MET/THR	4,3930		0,4,1963	58.0	66.0	63.0		2294,2216	4.8	0.0	7	dbSNP_134	63	35,8221		0,35,4093	yes	missense,missense	ZMIZ2	NM_031449.3,NM_174929.2	81,81	0,39,6056	TT,TC,CC		0.4239,0.1017,0.3199	possibly-damaging,possibly-damaging	765/921,739/895	44805814	39,12151	1967	4128	6095	SO:0001583	missense	83637	exon17			CCACCACGCCCAG	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2294C>T	7.37:g.44805814C>T	ENSP00000311778:p.Thr765Met	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	48	0.578313	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	CCDS43576.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	C	16.03	3.005711	0.54254	0.001017	0.004239	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.34072	1.38;1.4;1.4;1.39;1.41	5.67	4.79	0.61399	.	0.334339	0.25166	N	0.032632	T	0.42607	0.1210	M	0.76574	2.34	0.09310	N	0.999996	D;D;D;D	0.67145	0.966;0.996;0.982;0.993	P;P;P;P	0.61397	0.608;0.888;0.775;0.78	T	0.48091	-0.9065	10	0.59425	D	0.04	-1.0546	4.509	0.11901	0.2482:0.5464:0.1286:0.0768	.	388;739;765;707	B3KR25;Q8NF64-2;Q8NF64;Q8NF64-3	.;.;ZMIZ2_HUMAN;.	M	707;765;765;733;739;768	ENSP00000409648:T707M;ENSP00000311778:T765M;ENSP00000414723:T765M;ENSP00000396601:T733M;ENSP00000265346:T739M	ENSP00000265346:T739M	T	+	2	0	ZMIZ2	44772339	0.006000	0.16342	0.038000	0.18304	0.941000	0.58515	1.778000	0.38614	1.398000	0.46701	0.561000	0.74099	ACG	C|0.994;T|0.006	0.006	strong		0.637	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449	
MARVELD3	91862	hgsc.bcm.edu	37	16	71660404	71660404	+	Missense_Mutation	SNP	G	G	A	rs61753635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:71660404G>A	ENST00000268485.3	+	1	316	c.272G>A	c.(271-273)cGg>cAg	p.R91Q	MARVELD3_ENST00000565261.1_Missense_Mutation_p.R91Q|RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000567566.1_Missense_Mutation_p.R91Q|MARVELD3_ENST00000567501.1_5'Flank|MARVELD3_ENST00000299952.4_Missense_Mutation_p.R91Q	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	91	Arg-rich.				cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				GGCCCCCGCCGGGACACACAC	0.701													G|||	958	0.191294	0.2262	0.1758	5008	,	,		12826	0.0665		0.3002	False		,,,				2504	0.1718				p.R91Q		Atlas-SNP	.											.	MARVELD3	63	.	0			c.G272A						PASS	.	G	GLN/ARG,GLN/ARG	874,3032		107,660,1186	14.0	24.0	21.0		272,272	-5.0	0.0	16	dbSNP_129	21	1976,5686		265,1446,2120	yes	missense,missense	MARVELD3	NM_052858.3,NM_001017967.2	43,43	372,2106,3306	AA,AG,GG		25.7896,22.3758,24.6369	benign,benign	91/402,91/411	71660404	2850,8718	1953	3831	5784	SO:0001583	missense	91862	exon1			CCCGCCGGGACAC	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"""MARVEL (membrane-associating) domain containing 3"""	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.272G>A	16.37:g.71660404G>A	ENSP00000268485:p.Arg91Gln	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	29	5	0.172414	NM_001017967	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	37	CCDS10904.1	462	0.21153846153846154	103	0.20934959349593496	77	0.212707182320442	43	0.07517482517482517	239	0.3153034300791557	G	14.45	2.538478	0.45176	0.223758	0.257896	ENSG00000140832	ENST00000268485;ENST00000299952	T;T	0.40225	1.04;1.04	3.96	-4.97	0.03029	.	1.273640	0.05995	N	0.646785	T	0.00012	0.0000	N	0.00926	-1.1	0.35332	P	0.214275	B;B;B	0.12630	0.002;0.002;0.006	B;B;B	0.04013	0.001;0.001;0.001	T	0.26538	-1.0100	9	0.02654	T	1	-32.2938	0.9839	0.01442	0.2747:0.2817:0.2887:0.1549	rs61753635	91;91;114	Q96A59-2;Q96A59;Q9BSH2	.;MALD3_HUMAN;.	Q	91	ENSP00000268485:R91Q;ENSP00000299952:R91Q	ENSP00000268485:R91Q	R	+	2	0	MARVELD3	70217905	0.000000	0.05858	0.028000	0.17463	0.153000	0.21895	-1.014000	0.03641	-0.568000	0.06038	-0.516000	0.04426	CGG	G|0.784;A|0.216	0.216	strong		0.701	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189402	11189402	+	Missense_Mutation	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:11189402G>A	ENST00000382435.4	+	1	1006	c.787G>A	c.(787-789)Gcc>Acc	p.A263T		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	263						integral component of membrane (GO:0016021)		p.A263T(1)									GGGGATCCTCGCCTTGGTCTC	0.627																																					p.A263T		Atlas-SNP	.											AMAC1L2,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	prostate(1)	c.G787A						scavenged	.						119.0	114.0	116.0					8																	11189402		2203	4300	6503	SO:0001583	missense	83650	exon1			ATCCTCGCCTTGG	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.787G>A	8.37:g.11189402G>A	ENSP00000371872:p.Ala263Thr	Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	350	7	0.02	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	G	7.719	0.696740	0.15106	.	.	ENSG00000177710	ENST00000382435	T	0.67171	-0.25	.	.	.	.	0.000000	0.44285	D	0.000479	T	0.49779	0.1577	L	0.51422	1.61	0.29947	N	0.820555	B	0.14012	0.009	B	0.14578	0.011	T	0.27536	-1.0071	9	0.19590	T	0.45	-2.6207	2.8509	0.05558	3.0E-4:2.0E-4:0.5024:0.497	.	263	Q96KT7	S35G5_HUMAN	T	263	ENSP00000371872:A263T	ENSP00000371872:A263T	A	+	1	0	SLC35G5	11226812	0.224000	0.23674	0.171000	0.22900	0.172000	0.22775	0.512000	0.22755	0.088000	0.17205	0.089000	0.15464	GCC	.	.	none		0.627	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
DDR1	780	hgsc.bcm.edu	37	6	30857072	30857072	+	Silent	SNP	G	G	C	rs2229933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:30857072G>C	ENST00000324771.8	+	6	830	c.282G>C	c.(280-282)ctG>ctC	p.L94L	DDR1_ENST00000376568.3_Silent_p.L94L|DDR1_ENST00000513240.1_Silent_p.L94L|DDR1_ENST00000376570.4_Silent_p.L94L|DDR1_ENST00000452441.1_Silent_p.L94L|DDR1_ENST00000376567.2_Silent_p.L94L|DDR1_ENST00000508312.1_Silent_p.L112L|DDR1_ENST00000418800.2_Silent_p.L94L|DDR1_ENST00000454612.2_Silent_p.L94L|DDR1_ENST00000376575.3_Silent_p.L94L|DDR1_ENST00000446312.1_Silent_p.L94L|DDR1_ENST00000376569.3_Silent_p.L94L|DDR1_ENST00000361741.4_5'Flank|MIR4640_ENST00000581824.1_RNA			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	94	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.			L -> V (in Ref. 2; AAA02866 and 5; AAC50917). {ECO:0000305}.	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)	TACAACGACTGCACCTGGTGG	0.667													G|||	2080	0.415335	0.2746	0.4294	5008	,	,		16904	0.6121		0.2227	False		,,,				2504	0.591				p.L112L		Atlas-SNP	.											.	DDR1	213	.	0			c.G336C						PASS	.	G	,,,,,	785,2237		104,577,830	111.0	112.0	111.0		282,282,336,282,282,282	2.3	1.0	6	dbSNP_98	111	967,4449		87,793,1828	no	coding-synonymous,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	,,,,,	191,1370,2658	CC,CG,GG		17.8545,25.9762,20.7632	,,,,,	94/509,94/768,112/895,94/877,94/914,94/920	30857072	1752,6686	1511	2708	4219	SO:0001819	synonymous_variant	780	exon4			ACGACTGCACCTG	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.282G>C	6.37:g.30857072G>C		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	184	85	0.461957	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	37	CCDS34385.1	766	0.3507326007326007	125	0.2540650406504065	144	0.39779005524861877	310	0.541958041958042	187	0.24670184696569922	G	9.040	0.989395	0.18966	0.259762	0.178545	ENSG00000204580	ENST00000424544	.	.	.	4.81	2.33	0.28932	.	.	.	.	.	T	0.13798	0.0334	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16600	-1.0397	3	.	.	.	.	2.6727	0.05071	0.3107:0.0:0.4746:0.2147	rs2229933;rs2229933	.	.	.	P	78	.	.	A	+	1	0	DDR1	30965051	0.996000	0.38824	0.995000	0.50966	0.911000	0.54048	0.384000	0.20668	0.882000	0.36016	0.305000	0.20034	GCA	G|0.733;C|0.267	0.267	strong		0.667	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
EPHA8	2046	hgsc.bcm.edu	37	1	22915753	22915753	+	Intron	SNP	T	T	C	rs606002	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:22915753T>C	ENST00000166244.3	+	5	1387				EPHA8_ENST00000538803.1_Missense_Mutation_p.S457P|EPHA8_ENST00000374644.4_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	50	0	0		WXS	Illumina HiSeq	Phase_I	38	10	0.263158	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	
XIRP2	129446	hgsc.bcm.edu	37	2	168107491	168107491	+	Missense_Mutation	SNP	A	A	G	rs3749004	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168107491A>G	ENST00000409195.1	+	9	9678	c.9589A>G	c.(9589-9591)Atc>Gtc	p.I3197V	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.I2975V|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.I3197V	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3022					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						CAAAGGGGCCATCCCATGTCC	0.473													A|||	992	0.198083	0.326	0.1326	5008	,	,		18868	0.12		0.1233	False		,,,				2504	0.229				p.I3197V		Atlas-SNP	.											.	XIRP2	914	.	0			c.A9589G						PASS	.	A	,,,VAL/ILE,VAL/ILE	1086,2824		160,766,1029	81.0	84.0	83.0		,,,9589,8923	-4.1	0.0	2	dbSNP_107	83	924,7380		56,812,3284	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,29,29	216,1578,4313	GG,GA,AA		11.1272,27.7749,16.4565	,,,benign,benign	,,,3197/3550,2975/3328	168107491	2010,10204	1955	4152	6107	SO:0001583	missense	129446	exon9			GGGGCCATCCCAT	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.9589A>G	2.37:g.168107491A>G	ENSP00000386840:p.Ile3197Val	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	176	90	0.511364	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	386	0.17673992673992675	172	0.34959349593495936	47	0.1298342541436464	72	0.1258741258741259	95	0.12532981530343007	A	0.111	-1.138744	0.01742	0.277749	0.111272	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02631	4.22;4.22;4.22	5.45	-4.1	0.03940	.	1.015070	0.07871	N	0.967851	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.002;0.004;0.003	T	0.46345	-0.9198	9	0.19590	T	0.45	-0.4673	4.6634	0.12653	0.6565:0.0998:0.146:0.0977	rs3749004;rs52810850;rs58049014;rs3749004	3022;3022;2975	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	3197;3197;2975;611	ENSP00000386840:I3197V;ENSP00000295237:I3197V;ENSP00000387255:I2975V	ENSP00000295237:I3197V	I	+	1	0	XIRP2	167815737	0.000000	0.05858	0.001000	0.08648	0.776000	0.43924	0.291000	0.18994	-0.431000	0.07307	0.377000	0.23210	ATC	A|0.817;G|0.183	0.183	strong		0.473	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
NUPR1L	389493	hgsc.bcm.edu	37	7	56183895	56183895	+	Missense_Mutation	SNP	C	C	A	rs190448728	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:56183895C>A	ENST00000329309.3	-	1	198	c.113G>T	c.(112-114)cGc>cTc	p.R38L		NM_001145712.1	NP_001139184.1	A6NF83	NUR1L_HUMAN	nuclear protein, transcriptional regulator, 1-like	38																	CGGGAAGTCGCGCAGGTAGTA	0.701													C|||	6	0.00119808	0.0008	0.0	5008	,	,		12774	0.0		0.005	False		,,,				2504	0.0				p.R38L		Atlas-SNP	.											.	.	.	.	0			c.G113T						PASS	.	C	LEU/ARG	2,1382		0,2,690	14.0	14.0	14.0		113	3.4	1.0	7		14	33,3149		0,33,1558	yes	missense	LOC389493	NM_001145712.1	102	0,35,2248	AA,AC,CC		1.0371,0.1445,0.7665	probably-damaging	38/98	56183895	35,4531	692	1591	2283	SO:0001583	missense	389493	exon1			AAGTCGCGCAGGT		CCDS59058.1	7p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000185290	ENSG00000185290			44164	protein-coding gene	gene with protein product							Standard	NM_001145712		Approved		uc003tsb.3	A6NF83	OTTHUMG00000156224	ENST00000329309.3:c.113G>T	7.37:g.56183895C>A	ENSP00000455442:p.Arg38Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	73	22	0.30137	NM_001145712		Missense_Mutation	SNP	ENST00000329309.3	37	CCDS59058.1																																																																																			A|0.001;C|0.999	0.001	strong		0.701	NUPR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343551.2	NM_001145712	
CTC1	80169	hgsc.bcm.edu	37	17	8135446	8135446	+	Silent	SNP	G	G	A	rs3027235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8135446G>A	ENST00000315684.8	-	13	2167	c.2160C>T	c.(2158-2160)acC>acT	p.T720T		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	720					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						CCTCTGGGCCGGTGGGATCTG	0.577													G|||	217	0.0433307	0.087	0.1009	5008	,	,		17092	0.0099		0.0139	False		,,,				2504	0.0082				p.T720T		Atlas-SNP	.											.	CTC1	75	.	0			c.C2160T						PASS	.	G		260,3684		9,242,1721	21.0	22.0	22.0		2160	2.3	0.0	17	dbSNP_102	22	124,8160		3,118,4021	no	coding-synonymous	CTC1	NM_025099.5		12,360,5742	AA,AG,GG		1.4969,6.5923,3.1403		720/1218	8135446	384,11844	1972	4142	6114	SO:0001819	synonymous_variant	80169	exon13			TGGGCCGGTGGGA	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.2160C>T	17.37:g.8135446G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	73	28	0.383562	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			G|0.964;A|0.036	0.036	strong		0.577	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
PI16	221476	hgsc.bcm.edu	37	6	36930814	36930814	+	Silent	SNP	T	T	C	rs41272198	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:36930814T>C	ENST00000373674.3	+	5	1024	c.696T>C	c.(694-696)acT>acC	p.T232T	PI16_ENST00000491324.1_Intron	NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	232					negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AAATGGGTACTCCTTCTTCCC	0.567													T|||	347	0.0692891	0.0174	0.1066	5008	,	,		18940	0.005		0.168	False		,,,				2504	0.0777				p.T232T		Atlas-SNP	.											.	PI16	50	.	0			c.T696C						PASS	.	T	,	199,4207	124.9+/-162.1	5,189,2009	98.0	91.0	93.0		696,696	-2.2	0.0	6	dbSNP_127	93	1275,7325	252.5+/-278.5	110,1055,3135	no	coding-synonymous,coding-synonymous	PI16	NM_001199159.1,NM_153370.2	,	115,1244,5144	CC,CT,TT		14.8256,4.5166,11.3332	,	232/464,232/464	36930814	1474,11532	2203	4300	6503	SO:0001819	synonymous_variant	221476	exon6			GGGTACTCCTTCT		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"""microseminoprotein, beta-binding protein"""		"""protease inhibitor 16"""				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.696T>C	6.37:g.36930814T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Silent	SNP	ENST00000373674.3	37	CCDS34440.1																																																																																			T|0.893;C|0.107	0.107	strong		0.567	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370	
MYEOV2	150678	hgsc.bcm.edu	37	2	241066280	241066280	+	Silent	SNP	C	C	T	rs4292120	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241066280C>T	ENST00000307266.3	-	5	458	c.459G>A	c.(457-459)gaG>gaA	p.E153E		NM_138336.1	NP_612209.1	Q8WXC6	MYOV2_HUMAN	myeloma overexpressed 2	0										breast(1)|lung(5)|pancreas(1)	7		all_epithelial(40;1.56e-11)|Breast(86;0.0002)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;3.81e-30)|all cancers(36;1.1e-27)|OV - Ovarian serous cystadenocarcinoma(60;2.74e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;8.54e-06)|Lung(119;0.00361)|LUSC - Lung squamous cell carcinoma(224;0.0153)|Colorectal(34;0.0202)|COAD - Colon adenocarcinoma(134;0.143)		ACATTAGCGCCTCCGCCCCCT	0.542													T|||	3605	0.719848	0.9705	0.6744	5008	,	,		18094	0.7252		0.5696	False		,,,				2504	0.5624				p.E153E		Atlas-SNP	.											.	MYEOV2	20	.	0			c.G459A						PASS	.	T		3975,431	209.2+/-230.0	1788,399,16	166.0	174.0	171.0		459	-0.1	0.0	2	dbSNP_111	171	4761,3839	540.2+/-383.8	1344,2073,883	no	coding-synonymous	MYEOV2	NM_138336.1		3132,2472,899	TT,TC,CC		44.6395,9.7821,32.831		153/253	241066280	8736,4270	2203	4300	6503	SO:0001819	synonymous_variant	150678	exon5			TAGCGCCTCCGCC	AF453951	CCDS2532.1, CCDS63183.1	2q37.3	2008-02-05			ENSG00000172428	ENSG00000172428			21314	protein-coding gene	gene with protein product							Standard	NM_138336		Approved		uc002vyu.1	Q8WXC6	OTTHUMG00000133352	ENST00000307266.3:c.459G>A	2.37:g.241066280C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	145	60	0.413793	NM_138336	Q8N110	Silent	SNP	ENST00000307266.3	37	CCDS2532.1																																																																																			C|0.304;T|0.696	0.696	strong		0.542	MYEOV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257182.2	NM_138336	
WDR26	80232	hgsc.bcm.edu	37	1	224599230	224599230	+	Missense_Mutation	SNP	C	C	T			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:224599230C>T	ENST00000414423.2	-	7	1250	c.1057G>A	c.(1057-1059)Gag>Aag	p.E353K	WDR26_ENST00000366852.2_3'UTR|WDR26_ENST00000295024.6_Missense_Mutation_p.E206K	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	353						cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		TTACAATGCTCCGTAAGTATC	0.348																																					p.E353K		Atlas-SNP	.											WDR26_ENST00000414423,colon,carcinoma,+2,2	WDR26	104	2	0			c.G1057A						scavenged	.						144.0	130.0	135.0					1																	224599230		2203	4300	6503	SO:0001583	missense	80232	exon7			AATGCTCCGTAAG	AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"""WD repeat domain containing"""	21208	protein-coding gene	gene with protein product	"""GID complex subunit 7 homolog (S. cerevisiae)"""						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.1057G>A	1.37:g.224599230C>T	ENSP00000408108:p.Glu353Lys	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	247	3	0.0121457	NM_025160	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Missense_Mutation	SNP	ENST00000414423.2	37	CCDS31037.2	.	.	.	.	.	.	.	.	.	.	C	36	5.723118	0.96847	.	.	ENSG00000162923	ENST00000414423;ENST00000295024	T;T	0.60797	0.16;0.16	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.59905	0.2228	L	0.51914	1.62	0.80722	D	1	B	0.31680	0.335	B	0.38880	0.284	T	0.57894	-0.7732	10	0.39692	T	0.17	.	19.3066	0.94165	0.0:1.0:0.0:0.0	.	337	Q9H7D7-2	.	K	353;206	ENSP00000408108:E353K;ENSP00000295024:E206K	ENSP00000295024:E206K	E	-	1	0	WDR26	222665853	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.772000	0.85439	2.624000	0.88883	0.563000	0.77884	GAG	.	.	none		0.348	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160	
R3HCC1	203069	hgsc.bcm.edu	37	8	23148978	23148978	+	Silent	SNP	G	G	T	rs2272760	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:23148978G>T	ENST00000411463.1	+	6	1077	c.1077G>T	c.(1075-1077)gtG>gtT	p.V359V	R3HCC1_ENST00000522012.1_3'UTR|R3HCC1_ENST00000518454.1_Silent_p.V132V|R3HCC1_ENST00000265806.6_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	133	0	0		WXS	Illumina HiSeq	Phase_I	149	102	0.684564	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	
POMGNT1	55624	hgsc.bcm.edu	37	1	46658217	46658217	+	Silent	SNP	C	C	T	rs41292143	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:46658217C>T	ENST00000371984.3	-	15	1414	c.1257G>A	c.(1255-1257)ctG>ctA	p.L419L	POMGNT1_ENST00000371986.3_Silent_p.L419L|POMGNT1_ENST00000535522.1_Silent_p.L397L|POMGNT1_ENST00000371992.1_Silent_p.L419L|POMGNT1_ENST00000396420.3_3'UTR|POMGNT1_ENST00000485714.1_5'UTR	NM_017739.3	NP_060209	Q8WZA1	PMGT1_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)	419					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)					AGATGCAGTACAGGCTGTCAT	0.522													C|||	14	0.00279553	0.0008	0.0029	5008	,	,		23221	0.0		0.0109	False		,,,				2504	0.0				p.L419L		Atlas-SNP	.											.	POMGNT1	96	.	0			c.G1257A						PASS	.	C		12,4394	19.1+/-41.9	0,12,2191	95.0	93.0	93.0		1257	-2.7	1.0	1	dbSNP_127	93	148,8452	73.2+/-135.9	1,146,4153	no	coding-synonymous	POMGNT1	NM_017739.3		1,158,6344	TT,TC,CC		1.7209,0.2724,1.2302		419/661	46658217	160,12846	2203	4300	6503	SO:0001819	synonymous_variant	55624	exon15			GCAGTACAGGCTG		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.1257G>A	1.37:g.46658217C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	92	28	0.304348	NM_017739	D3DQ16|Q5VST2|Q5VST3|Q9BV55|Q9H9L8|Q9NXF9|Q9NYF7	Silent	SNP	ENST00000371984.3	37	CCDS531.1																																																																																			C|0.991;T|0.009	0.009	strong		0.522	POMGNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020146.1	NM_017739	
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695695	45695695	+	Silent	SNP	G	G	A	rs1153849	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:45695695G>A	ENST00000305560.6	+	1	1167	c.1068G>A	c.(1066-1068)agG>agA	p.R356R	GATM_ENST00000458245.5_5'Flank|SPATA5L1_ENST00000559860.1_Silent_p.R356R	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	356						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		CGCTGCGTAGGCCCGGGAGAT	0.677													A|||	3094	0.617812	0.8676	0.5706	5008	,	,		14893	0.8145		0.2753	False		,,,				2504	0.4632				p.R356R		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.G1068A						PASS	.	A		3242,1100		1234,774,163	33.0	39.0	37.0		1068	-0.1	1.0	15	dbSNP_87	37	2239,6277		311,1617,2330	no	coding-synonymous	SPATA5L1	NM_024063.2		1545,2391,2493	AA,AG,GG		26.2917,25.3339,42.6272		356/754	45695695	5481,7377	2171	4258	6429	SO:0001819	synonymous_variant	79029	exon1			GCGTAGGCCCGGG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1068G>A	15.37:g.45695695G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	31	5	0.16129	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Silent	SNP	ENST00000305560.6	37	CCDS10123.1																																																																																			G|0.415;A|0.585	0.585	strong		0.677	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1803704T>C	ENST00000260795.2	+	6	984	c.882T>C	c.(880-882)aaT>aaC	p.N294N	FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000481110.2_Silent_p.N294N|FGFR3_ENST00000412135.2_Silent_p.N294N|FGFR3_ENST00000352904.1_Silent_p.N294N|FGFR3_ENST00000340107.4_Silent_p.N294N|FGFR3_ENST00000440486.2_Silent_p.N294N			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	294	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.N294N(5)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TGGAGGTGAATGGCAGCAAGG	0.672		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				N|||	1039	0.207468	0.3707	0.1441	5008	,	,		12849	0.0744		0.17	False		,,,				2504	0.2076				p.N294N		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	5	Substitution - coding silent(5)	upper_aerodigestive_tract(3)|skin(2)	c.T882C						scavenged	.	C	,,	1504,2902	654.3+/-399.7	251,1002,950	47.0	42.0	44.0		882,882,882	-6.8	0.9	4	dbSNP_98	44	1278,7320	749.7+/-407.4	98,1082,3119	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	349,2084,4069	CC,CT,TT		14.8639,34.1353,21.3934	,,	294/807,294/809,294/695	1803704	2782,10222	2203	4299	6502	SO:0001819	synonymous_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGTGAATGGCAGC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.882T>C	4.37:g.1803704T>C		Somatic	211	2	0.00947867		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.799;C|0.201	0.201	strong		0.672	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
SLC44A3	126969	hgsc.bcm.edu	37	1	95322903	95322903	+	Missense_Mutation	SNP	T	T	C			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:95322903T>C	ENST00000271227.6	+	10	1187	c.1085T>C	c.(1084-1086)gTt>gCt	p.V362A	SLC44A3_ENST00000527077.1_Missense_Mutation_p.V294A|SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000529450.1_Missense_Mutation_p.V330A|SLC44A3_ENST00000532427.1_Missense_Mutation_p.V282A|SLC44A3_ENST00000467909.1_Missense_Mutation_p.V314A|SLC44A3_ENST00000446120.2_Missense_Mutation_p.V326A|RP11-465K1.2_ENST00000422162.1_RNA	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	362					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)				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)	GCTGCCCAGGTTATGGAAGGC	0.443																																					p.V362A		Atlas-SNP	.											.	SLC44A3	109	.	0			c.T1085C						PASS	.						114.0	102.0	106.0					1																	95322903		2203	4300	6503	SO:0001583	missense	126969	exon10			CCCAGGTTATGGA	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.1085T>C	1.37:g.95322903T>C	ENSP00000271227:p.Val362Ala	Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	37	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	T	4.282	0.051417	0.08291	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427	T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02	4.7	3.58	0.41010	.	0.152963	0.30401	N	0.009710	T	0.07593	0.0191	L	0.59436	1.845	0.09310	N	0.999997	P;B;B;P;P	0.34462	0.454;0.05;0.007;0.454;0.454	B;B;B;B;B	0.34931	0.192;0.037;0.011;0.192;0.192	T	0.25293	-1.0136	10	0.20519	T	0.43	-12.261	8.0786	0.30731	0.0:0.1799:0.0:0.8201	.	282;326;294;330;362	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	A	326;362;294;330;314;282	ENSP00000389143:V326A;ENSP00000271227:V362A;ENSP00000433641:V294A;ENSP00000431836:V330A;ENSP00000432789:V314A;ENSP00000436661:V282A	ENSP00000271227:V362A	V	+	2	0	SLC44A3	95095491	0.928000	0.31464	0.625000	0.29200	0.926000	0.56050	1.389000	0.34453	0.851000	0.35264	0.533000	0.62120	GTT	.	.	none		0.443	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369	
PAICS	10606	hgsc.bcm.edu	37	4	57314905	57314905	+	Missense_Mutation	SNP	A	A	C	rs11549976	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:57314905A>C	ENST00000512576.1	+	5	764	c.603A>C	c.(601-603)aaA>aaC	p.K201N	PAICS_ENST00000264221.2_Missense_Mutation_p.K201N|PAICS_ENST00000514888.1_Missense_Mutation_p.K109N|PAICS_ENST00000399688.3_Missense_Mutation_p.K208N	NM_001079524.1	NP_001072992.1	P22234	PUR6_HUMAN	phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase	201	SAICAR synthetase.		K -> N (in dbSNP:rs11549976).		'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)	TAACCACCAAAGAAATTGTTC	0.368													A|||	93	0.0185703	0.0015	0.0144	5008	,	,		18801	0.0		0.0716	False		,,,				2504	0.0092				p.K208N	GBM(53;429 1144 8755 40726)	Atlas-SNP	.											.	PAICS	21	.	0			c.A624C						PASS	.	A	ASN/LYS,ASN/LYS,ASN/LYS	39,3733		0,39,1847	60.0	55.0	57.0		603,624,603	4.3	1.0	4	dbSNP_120	57	500,7720		19,462,3629	yes	missense,missense,missense	PAICS	NM_001079524.1,NM_001079525.1,NM_006452.3	94,94,94	19,501,5476	CC,CA,AA		6.0827,1.0339,4.4947	benign,benign,benign	201/426,208/433,201/426	57314905	539,11453	1886	4110	5996	SO:0001583	missense	10606	exon6			CACCAAAGAAATT	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.603A>C	4.37:g.57314905A>C	ENSP00000421096:p.Lys201Asn	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	238	120	0.504202	NM_001079525	E9PDH9|Q68CQ5	Missense_Mutation	SNP	ENST00000512576.1	37	CCDS47061.1	63	0.028846153846153848	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	57	0.07519788918205805	A	15.48	2.847040	0.51164	0.010339	0.060827	ENSG00000128050	ENST00000514888;ENST00000264221;ENST00000505164;ENST00000399688;ENST00000512576	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.53	4.35	0.52113	ATP-grasp fold, subdomain 2 (1);	0.133751	0.64402	D	0.000002	T	0.01287	0.0042	N	0.17474	0.49	0.50813	D	0.999898	B;B;B	0.17038	0.02;0.002;0.02	B;B;B	0.21360	0.034;0.007;0.034	T	0.03139	-1.1068	10	0.31617	T	0.26	-22.2505	8.4742	0.33003	0.8542:0.0:0.1458:0.0	rs11549976;rs17811673;rs11549976	201;208;201	E9PBS1;P22234-2;P22234	.;.;PUR6_HUMAN	N	109;201;201;208;201	ENSP00000424907:K109N;ENSP00000264221:K201N;ENSP00000424053:K201N;ENSP00000382595:K208N;ENSP00000421096:K201N	ENSP00000264221:K201N	K	+	3	2	PAICS	57009662	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.636000	0.46545	2.236000	0.73375	0.533000	0.62120	AAA	A|0.968;C|0.032	0.032	strong		0.368	PAICS-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363136.2	NM_006452	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744163	31744163	+	Silent	SNP	C	C	G	rs2009546	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31744163C>G	ENST00000399889.2	-	1	394	c.369G>C	c.(367-369)ggG>ggC	p.G123G		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	123						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						CACCACTGGACCCACAGCCCA	0.577													C|||	292	0.0583067	0.1036	0.0303	5008	,	,		19441	0.005		0.0398	False		,,,				2504	0.091				p.G123G		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.G369C						PASS	.	C		414,3992	202.1+/-225.0	9,396,1798	66.0	63.0	64.0		369	-9.3	0.0	21	dbSNP_92	64	359,8241	119.2+/-178.6	8,343,3949	no	coding-synonymous	KRTAP13-2	NM_181621.3		17,739,5747	GG,GC,CC		4.1744,9.3963,5.9434		123/176	31744163	773,12233	2203	4300	6503	SO:0001819	synonymous_variant	337959	exon1			ACTGGACCCACAG	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.369G>C	21.37:g.31744163C>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	219	125	0.570776	NM_181621		Silent	SNP	ENST00000399889.2	37	CCDS13589.1																																																																																			C|0.947;G|0.053	0.053	strong		0.577	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
RIN3	79890	hgsc.bcm.edu	37	14	93118668	93118668	+	Missense_Mutation	SNP	C	C	T	rs3742717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:93118668C>T	ENST00000216487.7	+	6	1433	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	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)				CCTGAGGACACGCCCCGGGAG	0.647													C|||	1465	0.292532	0.1755	0.2767	5008	,	,		13345	0.4415		0.1948	False		,,,				2504	0.409				p.T425M		Atlas-SNP	.											RIN3,rectum,carcinoma,-1,1	RIN3	81	1	0			c.C1274T						PASS	.	C	MET/THR	758,3648	305.8+/-289.2	72,614,1517	56.0	64.0	61.0		1274	-0.5	0.0	14	dbSNP_107	61	1458,7142	277.9+/-293.1	112,1234,2954	yes	missense	RIN3	NM_024832.3	81	184,1848,4471	TT,TC,CC		16.9535,17.2038,17.0383	possibly-damaging	425/986	93118668	2216,10790	2203	4300	6503	SO:0001583	missense	79890	exon6			AGGACACGCCCCG	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.1274C>T	14.37:g.93118668C>T	ENSP00000216487:p.Thr425Met	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	175	113	0.645714	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	601	0.2751831501831502	88	0.17886178861788618	98	0.27071823204419887	250	0.4370629370629371	165	0.21767810026385223	C	2.949	-0.217068	0.06101	0.172038	0.169535	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.06142	3.34	3.82	-0.538	0.11868	.	1.010830	0.07976	N	0.984748	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	1.999999999946489E-6	B;B;B;B	0.30741	0.293;0.002;0.002;0.106	B;B;B;B	0.20767	0.031;0.001;0.001;0.004	T	0.39663	-0.9603	9	0.48119	T	0.1	-7.5748	2.5115	0.04658	0.101:0.3798:0.2266:0.2926	rs3742717;rs3742717	425;471;350;425	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	M	425;349	ENSP00000216487:T425M	ENSP00000216487:T425M	T	+	2	0	RIN3	92188421	.	.	0.037000	0.18230	0.023000	0.10783	.	.	0.239000	0.21243	-0.657000	0.03884	ACG	C|0.777;T|0.223	0.223	strong		0.647	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
PCED1B	91523	hgsc.bcm.edu	37	12	47471287	47471287	+	5'Flank	SNP	G	G	A			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:47471287G>A	ENST00000546455.1	+	0	0				AMIGO2_ENST00000429635.1_Missense_Mutation_p.T500M|AMIGO2_ENST00000321382.3_Missense_Mutation_p.T500M|AMIGO2_ENST00000266581.4_Missense_Mutation_p.T500M|AMIGO2_ENST00000550413.1_Missense_Mutation_p.T500M			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										TTTCCCCCTCGTGGACTTTAG	0.468																																					p.T500M		Atlas-SNP	.											AMIGO2,NS,carcinoma,-1,1	AMIGO2	50	1	0			c.C1499T						PASS	.						70.0	66.0	67.0					12																	47471287		2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			CCCCTCGTGGACT	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.47471287G>A	Exception_encountered	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_181847	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	37	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126383	0.37533	.	.	ENSG00000139211	ENST00000266581;ENST00000550413;ENST00000429635;ENST00000321382	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.09	5.09	0.68999	.	0.380800	0.28647	N	0.014620	T	0.40839	0.1133	L	0.44542	1.39	0.25929	N	0.983015	P	0.47910	0.902	B	0.36666	0.23	T	0.47209	-0.9135	10	0.51188	T	0.08	-0.3923	18.3695	0.90402	0.0:0.0:1.0:0.0	.	500	Q86SJ2	AMGO2_HUMAN	M	500	ENSP00000266581:T500M;ENSP00000449034:T500M;ENSP00000406020:T500M;ENSP00000320848:T500M	ENSP00000266581:T500M	T	-	2	0	AMIGO2	45757554	0.970000	0.33590	0.047000	0.18901	0.988000	0.76386	4.115000	0.57865	2.745000	0.94114	0.561000	0.74099	ACG	.	.	none		0.468	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
CDH8	1006	hgsc.bcm.edu	37	16	61855012	61855012	+	Missense_Mutation	SNP	A	A	G			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:61855012A>G	ENST00000577390.1	-	6	1795	c.841T>C	c.(841-843)Tat>Cat	p.Y281H	CDH8_ENST00000577730.1_Missense_Mutation_p.Y281H|CDH8_ENST00000584337.1_Missense_Mutation_p.Y281H|CDH8_ENST00000299345.6_Missense_Mutation_p.Y281H	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	281	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)|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)	p.Y281H(1)		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)		GAGAAGTGATACAGGCCTTTA	0.418																																					p.Y281H		Atlas-SNP	.											CDH8,NS,carcinoma,0,1	CDH8	273	1	1	Substitution - Missense(1)	liver(1)	c.T841C						scavenged	.						75.0	61.0	66.0					16																	61855012		2203	4300	6503	SO:0001583	missense	1006	exon6			AGTGATACAGGCC	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.841T>C	16.37:g.61855012A>G	ENSP00000462701:p.Tyr281His	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	242	5	0.0206612	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.373269	0.82573	.	.	ENSG00000150394	ENST00000299345	T	0.01725	4.67	5.96	5.96	0.96718	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.17323	0.0416	H	0.94771	3.58	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.994	T	0.02781	-1.1111	10	0.87932	D	0	.	16.4447	0.83919	1.0:0.0:0.0:0.0	.	97;281	Q3LID3;P55286	.;CADH8_HUMAN	H	281	ENSP00000299345:Y281H	ENSP00000299345:Y281H	Y	-	1	0	CDH8	60412513	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	5.553000	0.67287	2.284000	0.76573	0.528000	0.53228	TAT	.	.	none		0.418	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
CCDC33	80125	hgsc.bcm.edu	37	15	74622533	74622533	+	Missense_Mutation	SNP	A	A	G	rs2277603	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	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_ENST00000558821.1_Missense_Mutation_p.M25V|CCDC33_ENST00000321288.5_Missense_Mutation_p.M635V	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	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	156	101	0.647436	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	
MYO3B	140469	hgsc.bcm.edu	37	2	171400449	171400449	+	Silent	SNP	T	T	C	rs56181206	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:171400449T>C	ENST00000408978.4	+	32	3827	c.3684T>C	c.(3682-3684)ccT>ccC	p.P1228P	MYO3B_ENST00000334231.6_Silent_p.P1237P|MYO3B_ENST00000409044.3_Silent_p.P1201P|MYO3B_ENST00000602629.1_3'UTR	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	1228					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						TATGCCATCCTGCTCCAGATC	0.448													T|||	46	0.0091853	0.0008	0.013	5008	,	,		19158	0.0		0.0338	False		,,,				2504	0.002				p.P1228P		Atlas-SNP	.											.	MYO3B	320	.	0			c.T3684C						PASS	.	T	,PRO/LEU,	23,3669		0,23,1823	111.0	102.0	105.0		3603,3806,3684	4.3	0.8	2	dbSNP_129	105	243,7943		4,235,3854	yes	coding-synonymous,missense,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,98,	4,258,5677	CC,CT,TT		2.9685,0.623,2.2394	,,	1201/1315,1269/1276,1228/1342	171400449	266,11612	1846	4093	5939	SO:0001819	synonymous_variant	140469	exon32			CCATCCTGCTCCA		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.3684T>C	2.37:g.171400449T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	108	56	0.518519	NM_138995	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																			T|0.981;C|0.019	0.019	strong		0.448	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
CLTCL1	8218	hgsc.bcm.edu	37	22	19175095	19175095	+	Missense_Mutation	SNP	A	A	C	rs182434700	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:19175095A>C	ENST00000263200.10	-	29	4652	c.4580T>G	c.(4579-4581)cTc>cGc	p.L1527R	CLTCL1_ENST00000427926.1_Missense_Mutation_p.L1527R|CLTCL1_ENST00000442042.2_Intron|CLTCL1_ENST00000353891.5_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1527	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					CTTCTTGCAGAGCTCCACGCT	0.572			T	?	ALCL								A|||	5	0.000998403	0.0038	0.0	5008	,	,		20542	0.0		0.0	False		,,,				2504	0.0				p.L1527R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.T4580G						PASS	.	A	ARG/LEU,	6,4150		0,6,2072	102.0	110.0	107.0		4580,	4.1	1.0	22		107	2,8418		0,2,4208	yes	missense,intron	CLTCL1	NM_007098.3,NM_001835.3	102,	0,8,6280	CC,CA,AA		0.0238,0.1444,0.0636	probably-damaging,	1527/1641,	19175095	8,12568	2078	4210	6288	SO:0001583	missense	8218	exon29			TTGCAGAGCTCCA		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.4580T>G	22.37:g.19175095A>C	ENSP00000445677:p.Leu1527Arg	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	185	90	0.486486	NM_007098	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	23.2	4.381943	0.82792	0.001444	2.38E-4	ENSG00000070371	ENST00000263200;ENST00000427926	T;T	0.29917	1.55;1.55	4.13	4.13	0.48395	.	0.000000	0.64402	D	0.000002	T	0.62392	0.2424	M	0.91038	3.17	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.72434	-0.4295	10	0.87932	D	0	-15.1854	13.2908	0.60270	1.0:0.0:0.0:0.0	.	1527	P53675	CLH2_HUMAN	R	1527	ENSP00000445677:L1527R;ENSP00000441158:L1527R	ENSP00000445677:L1527R	L	-	2	0	CLTCL1	17555095	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.286000	0.89916	1.738000	0.51689	0.533000	0.62120	CTC	A|0.999;C|0.001	0.001	strong		0.572	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
GRIN3B	116444	hgsc.bcm.edu	37	19	1003221	1003221	+	Missense_Mutation	SNP	C	C	A	rs35592366	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1003221C>A	ENST00000234389.3	+	2	538	c.519C>A	c.(517-519)gaC>gaA	p.D173E	AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	173					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)	p.D173E(1)		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)	CCTGGGAAGACGTCGGCCTGG	0.711													t|||	499	0.0996406	0.1952	0.0274	5008	,	,		12179	0.126		0.0557	False		,,,				2504	0.0399				p.D173E		Atlas-SNP	.											GRIN3B,NS,carcinoma,0,1	GRIN3B	46	1	1	Substitution - Missense(1)	prostate(1)	c.C519A						PASS	.	T	GLU/ASP	695,3611		48,599,1506	8.0	10.0	9.0		519	-0.2	0.1	19	dbSNP_126	9	433,8061		9,415,3823	yes	missense	GRIN3B	NM_138690.1	45	57,1014,5329	AA,AC,CC		5.0977,16.1403,8.8125	benign	173/1044	1003221	1128,11672	2153	4247	6400	SO:0001583	missense	116444	exon2			GGAAGACGTCGGC		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.519C>A	19.37:g.1003221C>A	ENSP00000234389:p.Asp173Glu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	207	0.09478021978021978	84	0.17073170731707318	10	0.027624309392265192	68	0.11888111888111888	45	0.059366754617414245	c	0.981	-0.697012	0.03279	0.161403	0.050977	ENSG00000116032	ENST00000234389	T	0.10382	2.88	3.27	-0.17	0.13335	.	0.415688	0.20496	U	0.091183	T	0.00012	0.0000	L	0.37630	1.12	0.58432	P	1.0000000000287557E-6	B	0.18166	0.026	B	0.13407	0.009	T	0.41520	-0.9504	9	0.18276	T	0.48	.	0.749	0.00987	0.166:0.358:0.1633:0.3126	rs35592366	173	O60391	NMD3B_HUMAN	E	173	ENSP00000234389:D173E	ENSP00000234389:D173E	D	+	3	2	GRIN3B	954221	0.001000	0.12720	0.054000	0.19295	0.017000	0.09413	-0.155000	0.10115	-0.135000	0.11495	-0.384000	0.06662	GAC	C|0.904;A|0.096	0.096	strong		0.711	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
AKAP9	10142	hgsc.bcm.edu	37	7	91712698	91712698	+	Missense_Mutation	SNP	A	A	G	rs6960867	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91712698A>G	ENST00000359028.2	+	34	8636	c.8411A>G	c.(8410-8412)aAt>aGt	p.N2804S	AKAP9_ENST00000356239.3_Missense_Mutation_p.N2792S|AKAP9_ENST00000358100.2_Missense_Mutation_p.N2804S			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2804			N -> S (in dbSNP:rs6960867).		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)			AGTAGCAGCAATCAGACTCCA	0.378			T	BRAF	papillary thyroid								A|||	1482	0.295927	0.2209	0.3458	5008	,	,		19775	0.1617		0.3837	False		,,,				2504	0.41				p.N2792S		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.A8375G						PASS	.	A	SER/ASN,SER/ASN	1180,3226	413.3+/-336.4	165,850,1188	76.0	74.0	75.0		8375,8351	-2.1	0.2	7	dbSNP_116	75	3451,5149	508.1+/-377.0	670,2111,1519	yes	missense,missense	AKAP9	NM_005751.4,NM_147185.2	46,46	835,2961,2707	GG,GA,AA		40.1279,26.7817,35.6066	benign,benign	2792/3908,2784/3900	91712698	4631,8375	2203	4300	6503	SO:0001583	missense	10142	exon33			GCAGCAATCAGAC	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.8411A>G	7.37:g.91712698A>G	ENSP00000351922:p.Asn2804Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		647	0.29624542124542125	121	0.2459349593495935	132	0.36464088397790057	100	0.17482517482517482	294	0.38786279683377306	A	7.078	0.569650	0.13560	0.267817	0.401279	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	4.8	-2.13	0.07144	.	0.961519	0.08519	N	0.933795	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B;B;B;B;B	0.17667	0.023;0.0;0.0;0.0;0.0	B;B;B;B;B	0.12156	0.007;0.002;0.001;0.002;0.002	T	0.45818	-0.9235	9	0.18276	T	0.48	.	1.523	0.02520	0.3963:0.2606:0.2292:0.114	rs6960867;rs6960867	2796;2796;2804;2792;2784	F5H3X5;Q99996-6;Q99996;Q99996-2;Q99996-3	.;.;AKAP9_HUMAN;.;.	S	2792;2804;2804;2796;638	ENSP00000348573:N2792S;ENSP00000351922:N2804S;ENSP00000350813:N2804S;ENSP00000378042:N638S	ENSP00000348573:N2792S	N	+	2	0	AKAP9	91550634	0.002000	0.14202	0.157000	0.22605	0.795000	0.44927	0.398000	0.20899	-0.542000	0.06249	0.482000	0.46254	AAT	A|0.667;G|0.333	0.333	strong		0.378	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
ELP2	55250	hgsc.bcm.edu	37	18	33718326	33718326	+	Missense_Mutation	SNP	A	A	C	rs1785934	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:33718326A>C	ENST00000358232.6	+	4	445	c.382A>C	c.(382-384)Aca>Cca	p.T128P	ELP2_ENST00000351393.6_Missense_Mutation_p.T128P|ELP2_ENST00000350494.6_Missense_Mutation_p.T128P|ELP2_ENST00000542824.1_Missense_Mutation_p.T128P|ELP2_ENST00000442325.2_Missense_Mutation_p.T128P|ELP2_ENST00000423854.2_Missense_Mutation_p.T128P	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	128			T -> P (in dbSNP:rs1785934). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						TGCATTATGTACACTGATCGT	0.443													A|||	1605	0.320487	0.382	0.3847	5008	,	,		9758	0.2024		0.3797	False		,,,				2504	0.2526				p.T128P		Atlas-SNP	.											.	ELP2	70	.	0			c.A382C						PASS	.	A	PRO/THR,PRO/THR,PRO/THR,PRO/THR,PRO/THR,PRO/THR	1614,2792	501.0+/-364.9	296,1022,885	124.0	112.0	116.0		382,382,382,382,382,382	3.5	0.4	18	dbSNP_89	116	3193,5407	483.3+/-371.1	584,2025,1691	yes	missense,missense,missense,missense,missense,missense	ELP2	NM_001242875.1,NM_001242876.1,NM_001242877.1,NM_001242878.1,NM_001242879.1,NM_018255.2	38,38,38,38,38,38	880,3047,2576	CC,CA,AA		37.1279,36.6319,36.9599	benign,benign,benign,benign,benign,benign	128/892,128/822,128/801,128/757,128/757,128/827	33718326	4807,8199	2203	4300	6503	SO:0001583	missense	55250	exon4			TTATGTACACTGA	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"""Elongator acetyltransferase complex subunits"", ""WD repeat domain containing"""	18248	protein-coding gene	gene with protein product			"""signal transducer and activator of transcription 3 interacting protein 1"", ""elongation protein 2 homolog (S. cerevisiae)"""	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.382A>C	18.37:g.33718326A>C	ENSP00000350967:p.Thr128Pro	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_001242879	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Missense_Mutation	SNP	ENST00000358232.6	37	CCDS11918.1	758	0.34706959706959706	192	0.3902439024390244	154	0.425414364640884	111	0.19405594405594406	301	0.3970976253298153	A	7.649	0.682530	0.14907	0.366319	0.371279	ENSG00000134759	ENST00000358232;ENST00000351393;ENST00000442325;ENST00000423854;ENST00000350494;ENST00000542824	T;T;T;T;T;T	0.58506	0.33;2.17;0.33;0.33;0.33;0.33	5.75	3.49	0.39957	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.377451	0.28641	N	0.014625	T	0.00012	0.0000	L	0.33093	0.98	0.51233	P	9.00000000000345E-5	B;B;B;B;B;B	0.14805	0.001;0.002;0.011;0.0;0.0;0.0	B;B;B;B;B;B	0.17979	0.012;0.02;0.015;0.0;0.0;0.001	T	0.41770	-0.9490	9	0.30078	T	0.28	-6.6852	4.8583	0.13570	0.6414:0.2526:0.106:0.0	rs1785934;rs3819176;rs17648862;rs17856949;rs52804008;rs1785934	128;128;128;128;128;128	B4DTG0;E7EP23;E9PCX0;Q6IA86-2;Q6IA86-3;Q6IA86	.;.;.;.;.;ELP2_HUMAN	P	128	ENSP00000350967:T128P;ENSP00000257191:T128P;ENSP00000414851:T128P;ENSP00000391202:T128P;ENSP00000316051:T128P;ENSP00000443800:T128P	ENSP00000316051:T128P	T	+	1	0	ELP2	31972324	0.010000	0.17322	0.424000	0.26647	0.026000	0.11368	0.654000	0.24918	1.017000	0.39495	0.455000	0.32223	ACA	A|0.654;C|0.346	0.346	strong		0.443	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255	
